PMID- 23526115 OWN - NLM STAT- Publisher DA - 20130325 IS - 1387-3806 (Print) IS - 1387-3806 (Linking) VI - 330-332 DP - 2012 Dec 15 TI - Protein structure evolution in liquid DESI as revealed by selective noncovalent adduct protein probing. PG - 220-225 AB - Previous experiments based on charge state distributions have suggested that liquid desorption electrospray ionization (DESI) is capable of preserving solution phase protein structure during transfer to the gas phase (Journal of the American Society for Mass Spectrometry 21 (2010) 1730-1736). In order to examine this possibility more carefully, we have utilized selective non-covalent adduct protein probing (SNAPP) to evaluate protein structural evolution in both liquid DESI and standard ESI under a variety of conditions. Experiments with cytochrome c (Cytc) demonstrated that methanol induced conformational shifts previously observed with ESI are also easily observed with liquid DESI. However, undesirable acid-induced unfolding becomes apparent at very high concentrations of methanol in liquid DESI due to acetic acid in the spray solvent, suggesting that there are conditions under which liquid DESI will not preserve solution phase structure. The effects of ammonium acetate buffer on liquid DESI SNAPP experiments were examined by monitoring structural changes in myoglobin. Heme retention and SNAPP distributions were both preserved better in liquid DESI than traditional ESI, suggesting superior performance for liquid DESI in buffered conditions. Finally, liquid DESI SNAPP was used to study the natively disordered proteins alpha, beta, and gamma synuclein with SNAPP. alpha-Synuclein, the main component of fibrils found in patients with Parkinson's disease, yielded a significantly different SNAPP distribution compared to beta and gamma synuclein. This difference is indicative of highly accessible protonated basic side chains, a property known to promote fibril formation in proteins. FAU - Moore, Benjamin N AU - Moore BN AD - Department of Chemistry, University of California, Riverside, CA 92521, United States. FAU - Hamdy, Omar AU - Hamdy O FAU - Julian, Ryan R AU - Julian RR LA - ENG GR - R01 GM084106/GM/NIGMS NIH HHS/United States PT - JOURNAL ARTICLE DEP - 20120818 TA - Int J Mass Spectrom JT - International journal of mass spectrometry JID - 101137096 PMC - PMC3601934 MID - NIHMS405381 OTO - NOTNLM OT - Charge residue OT - Cytochrome c OT - Ion evaporation OT - Myoglobin OT - Synuclein EDAT- 2013/03/26 06:00 MHDA- 2013/03/26 06:00 CRDT- 2013/03/26 06:00 PHST- 2012/08/18 [epublish] AID - 10.1016/j.ijms.2012.08.013 [doi] PST - ppublish SO - Int J Mass Spectrom. 2012 Dec 15;330-332:220-225. Epub 2012 Aug 18. PMID- 23828237 OWN - NLM STAT- MEDLINE DA - 20130826 DCOM- 20131114 LR - 20141113 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 34 DP - 2013 Aug 23 TI - Effects of phosphorylation on the structure and backbone dynamics of the intrinsically disordered connexin43 C-terminal domain. PG - 24857-70 LID - 10.1074/jbc.M113.454389 [doi] AB - Phosphorylation of the connexin43 C-terminal (Cx43CT) domain regulates gap junction intercellular communication. However, an understanding of the mechanisms by which phosphorylation exerts its effects is lacking. Here, we test the hypothesis that phosphorylation regulates Cx43 gap junction intercellular communication by mediating structural changes in the C-terminal domain. Circular dichroism and nuclear magnetic resonance were used to characterize the effects of phosphorylation on the secondary structure and backbone dynamics of soluble and membrane-tethered Cx43CT domains. Cx43CT phospho-mimetic isoforms, which have Asp substitutions at specific Ser/Tyr sites, revealed phosphorylation alters the alpha-helical content of the Cx43CT domain only when attached to the membrane. The changes in secondary structure are due to variations in the conformational preference and backbone flexibility of residues adjacent and distal to the site(s) of modification. In addition to the known direct effects of phosphorylation on molecular partner interactions, the data presented here suggest phosphorylation may also indirectly regulate binding affinity by altering the conformational preference of the Cx43CT domain. FAU - Grosely, Rosslyn AU - Grosely R AD - Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA. FAU - Kopanic, Jennifer L AU - Kopanic JL FAU - Nabors, Sarah AU - Nabors S FAU - Kieken, Fabien AU - Kieken F FAU - Spagnol, Gaelle AU - Spagnol G FAU - Al-Mugotir, Mona AU - Al-Mugotir M FAU - Zach, Sydney AU - Zach S FAU - Sorgen, Paul L AU - Sorgen PL LA - eng GR - GM07263/GM/NIGMS NIH HHS/United States GR - R01 GM072631/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130704 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Connexin 43) RN - 0 (GJA1 protein, human) SB - IM MH - Circular Dichroism MH - Connexin 43/*chemistry/genetics/metabolism MH - Humans MH - Phosphorylation/physiology MH - Protein Structure, Secondary MH - Protein Structure, Tertiary PMC - PMC3750180 OID - NLM: PMC3750180 OTO - NOTNLM OT - Circular Dichroism (CD) OT - Gap Junctions OT - Nuclear Magnetic Resonance OT - Phosphorylation OT - Protein Dynamics EDAT- 2013/07/06 06:00 MHDA- 2013/11/15 06:00 CRDT- 2013/07/06 06:00 PHST- 2013/07/04 [aheadofprint] AID - M113.454389 [pii] AID - 10.1074/jbc.M113.454389 [doi] PST - ppublish SO - J Biol Chem. 2013 Aug 23;288(34):24857-70. doi: 10.1074/jbc.M113.454389. Epub 2013 Jul 4. PMID- 24918971 OWN - NLM STAT- MEDLINE DA - 20140918 DCOM- 20150529 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 118 IP - 26 DP - 2014 Jul 3 TI - Dynamics and rigidity in an intrinsically disordered protein, beta-casein. PG - 7317-26 LID - 10.1021/jp503788r [doi] AB - The emergence of intrinsically disordered proteins (IDPs) as a recognized structural class has forced the community to confront a new paradigm of structure, dynamics, and mechanical properties for proteins. We present novel data on the similarities and differences in the dynamics and nanomechanical properties of IDPs and other biomacromolecules on the picosecond time scale. An IDP, beta-casein (CAS), has been studied in a calcium bound and unbound state using neutron and light scattering techniques. We show that CAS partially folds and stiffens upon calcium binding, but in the unfolded state, it is softer than folded proteins such as green fluorescence protein (GFP). We also see that some localized diffusive motions in CAS have a larger amplitude than in GFP at this time scale but are still smaller than those observed in tRNA. In spite of these differences, CAS dynamics are consistent with the classes of motions seen in folded protein on this time scale. FAU - Perticaroli, Stefania AU - Perticaroli S AD - Joint Institute for Neutron Sciences, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States. FAU - Nickels, Jonathan D AU - Nickels JD FAU - Ehlers, Georg AU - Ehlers G FAU - Mamontov, Eugene AU - Mamontov E FAU - Sokolov, Alexei P AU - Sokolov AP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140623 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Caseins) RN - 0 (Intrinsically Disordered Proteins) RN - SY7Q814VUP (Calcium) SB - IM MH - Animals MH - Calcium/chemistry/metabolism MH - Caseins/*chemistry/metabolism MH - Cattle MH - Elastic Modulus MH - Intrinsically Disordered Proteins/chemistry/metabolism MH - Light MH - Milk/metabolism MH - Neutron Diffraction MH - Protein Binding MH - Protein Denaturation MH - Protein Structure, Secondary MH - Scattering, Radiation MH - Spectroscopy, Fourier Transform Infrared MH - Temperature EDAT- 2014/06/12 06:00 MHDA- 2015/05/30 06:00 CRDT- 2014/06/12 06:00 PHST- 2014/06/23 [aheadofprint] AID - 10.1021/jp503788r [doi] PST - ppublish SO - J Phys Chem B. 2014 Jul 3;118(26):7317-26. doi: 10.1021/jp503788r. Epub 2014 Jun 23. PMID- 17605001 OWN - NLM STAT- MEDLINE DA - 20070831 DCOM- 20071109 IS - 1420-682X (Print) IS - 1420-682X (Linking) VI - 64 IP - 17 DP - 2007 Sep TI - Physiological and pathological properties of alpha-synuclein. PG - 2194-201 AB - alpha-Synuclein belongs to a small group of natively unfolded proteins that can transiently bind to lipid membranes and acquire a partial alpha-helical conformation. Under certain pathogenic conditions, alpha-synuclein aggregates to form oligomers and insoluble fibrils with increased ss-sheet configuration. Although genetic mutations and multiplications of the gene have been found in familial cases, the mechanism by which this protein aggregates in sporadic cases of Parkinson's disease, dementia with Lewy bodies and multisystem atrophy is not fully understood. Here we review the function of alpha-synuclein and recent insight into the mechanisms by which it aggregates. FAU - Tofaris, G K AU - Tofaris GK AD - Cambridge Centre for Brain Repair and Department of Clinical Neuroscience Forvie Site, Robinson Way, Cambridge CB2 2PY, United Kingdom. FAU - Spillantini, M G AU - Spillantini MG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Switzerland TA - Cell Mol Life Sci JT - Cellular and molecular life sciences : CMLS JID - 9705402 RN - 0 (alpha-Synuclein) SB - IM MH - Humans MH - Lewy Bodies/metabolism MH - Parkinson Disease/genetics/*metabolism/pathology MH - Protein Processing, Post-Translational MH - Protein Structure, Tertiary MH - alpha-Synuclein/chemistry/genetics/*physiology RF - 82 EDAT- 2007/07/03 09:00 MHDA- 2007/11/10 09:00 CRDT- 2007/07/03 09:00 AID - 10.1007/s00018-007-7217-5 [doi] PST - ppublish SO - Cell Mol Life Sci. 2007 Sep;64(17):2194-201. PMID- 23826884 OWN - NLM STAT- MEDLINE DA - 20130903 DCOM- 20131025 LR - 20141113 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 280 IP - 18 DP - 2013 Sep TI - Structural changes of CFTR R region upon phosphorylation: a plastic platform for intramolecular and intermolecular interactions. PG - 4407-16 LID - 10.1111/febs.12422 [doi] AB - Chloride channel gating and trafficking of the cystic fibrosis transmembrane conductance regulator (CFTR) are regulated by phosphorylation. Intrinsically disordered segments of the protein are responsible for phospho-regulation, particularly the regulatory (R) region that is a target for several kinases and phosphatases. The R region remains disordered following phosphorylation, with different phosphorylation states sampling various conformations. Recent studies have demonstrated the crucial role that intramolecular and intermolecular interactions of the R region play in CFTR regulation. Different partners compete for the same binding segment, with the R region containing multiple overlapping binding elements. The non-phosphorylated R region interacts with the nucleotide binding domains and inhibits channel activity by blocking heterodimerization. Phosphorylation shifts the equilibrium such that the R region is excluded from the dimer interface, facilitating gating and processing by stimulating R region interactions with other domains and proteins. The dynamic conformational sampling and transient binding of the R region to multiple partners enables complex control of CFTR channel activity and trafficking. CI - (c) 2013 The Authors. FEBS Journal published by John Wiley & Sons Ltd on behalf of FEBS. FAU - Bozoky, Zoltan AU - Bozoky Z AD - Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada. FAU - Krzeminski, Mickael AU - Krzeminski M FAU - Chong, P Andrew AU - Chong PA FAU - Forman-Kay, Julie D AU - Forman-Kay JD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20130725 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (CFTR protein, human) RN - 126880-72-6 (Cystic Fibrosis Transmembrane Conductance Regulator) SB - IM MH - Binding Sites MH - Cystic Fibrosis/genetics/*metabolism/pathology MH - Cystic Fibrosis Transmembrane Conductance Regulator/*chemistry/genetics/*metabolism MH - Humans MH - Models, Molecular MH - Phosphorylation MH - Protein Binding MH - Protein Folding MH - Protein Interaction Domains and Motifs MH - Protein Multimerization MH - *Protein Processing, Post-Translational MH - Protein Transport MH - Signal Transduction PMC - PMC4160016 OID - NLM: PMC4160016 OTO - NOTNLM OT - IDP OT - binding OT - disordered OT - hub OT - post-translational modification OT - regulation EDAT- 2013/07/06 06:00 MHDA- 2013/10/26 06:00 CRDT- 2013/07/06 06:00 PHST- 2013/04/09 [received] PHST- 2013/06/24 [revised] PHST- 2013/07/02 [accepted] PHST- 2013/07/25 [aheadofprint] AID - 10.1111/febs.12422 [doi] PST - ppublish SO - FEBS J. 2013 Sep;280(18):4407-16. doi: 10.1111/febs.12422. Epub 2013 Jul 25. PMID- 19770509 OWN - NLM STAT- MEDLINE DA - 20090922 DCOM- 20100126 LR - 20140827 IS - 1399-0047 (Electronic) IS - 0907-4449 (Linking) VI - 65 IP - Pt 10 DP - 2009 Oct TI - A new crystal form of human tear lipocalin reveals high flexibility in the loop region and induced fit in the ligand cavity. PG - 1118-25 LID - 10.1107/S0907444909031011 [doi] AB - Tear lipocalin (TLC) with the bound artificial ligand 1,4-butanediol has been crystallized in space group P2(1) with four protein molecules in the asymmetric unit and its X-ray structure has been solved at 2.6 A resolution. TLC is a member of the lipocalin family that binds ligands with diverse chemical structures, such as fatty acids, phospholipids and cholesterol as well as microbial siderophores and the antibiotic rifampin. Previous X-ray structural analysis of apo TLC crystallized in space group C2 revealed a rather large bifurcated ligand pocket and a partially disordered loop region at the entrace to the cavity. Analysis of the P2(1) crystal form uncovered major conformational changes (i) in beta-strands B, C and D, (ii) in loops 1, 2 and 4 at the open end of the beta-barrel and (iii) in the extended C-terminal segment, which is attached to the beta-barrel via a disulfide bridge. The structural comparison indicates high conformational plasticity of the loop region as well as of deeper parts of the ligand pocket, thus allowing adaptation to ligands that differ vastly in size and shape. This illustrates a mechanism for promiscuity in ligand recognition which may also be relevant for some other physiologically important members of the lipocalin protein family. FAU - Breustedt, Daniel A AU - Breustedt DA AD - Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl fur Biologische Chemie, Technische Universitat Munchen, 85350 Freising-Weihenstephan, Germany. FAU - Chatwell, Lorenz AU - Chatwell L FAU - Skerra, Arne AU - Skerra A LA - eng SI - PDB/3EYC SI - PDB/R3EYCSF PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090916 PL - England TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (Butylene Glycols) RN - 0 (LCN1 protein, human) RN - 0 (Ligands) RN - 0 (Lipocalin 1) RN - 7XOO2LE6G3 (1,4-butanediol) SB - IM MH - Butylene Glycols/chemistry/metabolism MH - *Crystallography, X-Ray MH - Humans MH - Ligands MH - Lipocalin 1/*chemistry/metabolism MH - Models, Molecular MH - Protein Binding MH - Protein Conformation PMC - PMC2756164 OID - NLM: PMC2756164 EDAT- 2009/09/23 06:00 MHDA- 2010/01/27 06:00 CRDT- 2009/09/23 06:00 PHST- 2009/05/31 [received] PHST- 2009/08/04 [accepted] PHST- 2009/09/16 [epublish] AID - S0907444909031011 [pii] AID - 10.1107/S0907444909031011 [doi] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2009 Oct;65(Pt 10):1118-25. doi: 10.1107/S0907444909031011. Epub 2009 Sep 16. PMID- 18692132 OWN - NLM STAT- MEDLINE DA - 20080923 DCOM- 20081222 LR - 20131121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1782 IP - 10 DP - 2008 Oct TI - Impact of Tyr to Ala mutations on alpha-synuclein fibrillation and structural properties. PG - 581-5 LID - 10.1016/j.bbadis.2008.07.004 [doi] AB - Substantial evidence suggests that the fibrillation of alpha-synuclein is a critical step in the development of Parkinson's disease. In vitro, alpha-synuclein forms fibrils with morphologies and a staining characteristic similar to those extracted from disease-affected brain. Monomeric alpha-synuclein is an intrinsically disordered protein, with three Tyr residues in the C-terminal region, one in the N-terminus, and lacking Trp. It is thought that interactions between the C-terminus and the central portion of the molecule may prevent or minimize aggregation/fibrillation. To test this hypothesis we examined the importance of the Tyr residues on the propensity for alpha-synuclein to fibrillate in vitro. Fibril formation of alpha-synuclein was completely inhibited, in the timescale over which measurements were made, by replacing the three C-terminal Tyr residues with Ala. In addition, substitution of Tyr133 by Ala also resulted in the absence of fibrillation, whereas the individual Y125A and Y136A mutants showed limited inhibition. Replacement of Tyr39 by Ala also resulted in substantial inhibition of fibrillation. Structural analysis showed that the Y133A mutant had a substantially different conformation, rich in alpha-helical secondary structure, as compared with the wild-type and other mutants, although the formation of any tertiary structure has not been observed as can be judged from near-UV-CD spectra. These observations suggest that the long-range intramolecular interactions between the N- and C-termini of alpha-synuclein are likely to be crucial to the fibrillation process. FAU - Ulrih, Natasa Poklar AU - Ulrih NP AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95964, USA. natasa.poklar@bf.uni-lj.si FAU - Barry, Christopher H AU - Barry CH FAU - Fink, Anthony L AU - Fink AL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080722 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Amyloid) RN - 0 (Recombinant Proteins) RN - 0 (alpha-Synuclein) RN - 42HK56048U (Tyrosine) RN - OF5P57N2ZX (Alanine) SB - IM MH - Alanine/genetics MH - *Amino Acid Substitution MH - Amyloid/chemistry/*genetics/metabolism MH - Circular Dichroism MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Kinetics MH - *Mutation, Missense MH - Parkinson Disease/genetics MH - Protein Folding MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Spectrometry, Fluorescence MH - Spectroscopy, Fourier Transform Infrared MH - Tyrosine/genetics MH - alpha-Synuclein/chemistry/*genetics/metabolism EDAT- 2008/08/12 09:00 MHDA- 2008/12/23 09:00 CRDT- 2008/08/12 09:00 PHST- 2008/05/12 [received] PHST- 2008/07/14 [revised] PHST- 2008/07/15 [accepted] PHST- 2008/07/22 [aheadofprint] AID - S0925-4439(08)00137-3 [pii] AID - 10.1016/j.bbadis.2008.07.004 [doi] PST - ppublish SO - Biochim Biophys Acta. 2008 Oct;1782(10):581-5. doi: 10.1016/j.bbadis.2008.07.004. Epub 2008 Jul 22. PMID- 12630860 OWN - NLM STAT- MEDLINE DA - 20030312 DCOM- 20030516 LR - 20080117 IS - 0002-7863 (Print) IS - 0002-7863 (Linking) VI - 125 IP - 11 DP - 2003 Mar 19 TI - Peptides derived from two dynamically disordered proteins self-assemble into amyloid-like fibrils. PG - 3200-1 AB - Short peptides derived from p14ARF and Hdm2 (14 and 15 amino acids in length, respectively), two cancer associated proteins, have been found to co-assemble into amyloid-like structures. Larger protein domains containing these peptide segments interact in cells and also undergo a disorder-to-order transition upon binding in vitro. In contrast to the association of beta-strand assemblies with amyloid diseases, the system described herein utilizes the formation of binary, extended beta-strands as a novel mechanism of biomolecular assembly. The beta-strand-containing fibrils formed from these peptides may allow the directed assembly of decorated fibrils with applications as biological nanostructures. FAU - Bothner, Brian AU - Bothner B AD - Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA. FAU - Aubin, Yves AU - Aubin Y FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng GR - CA 21765/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Amyloid) RN - 0 (Nuclear Proteins) RN - 0 (Peptide Fragments) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Tumor Suppressor Protein p14ARF) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Amino Acid Sequence MH - Amyloid/*chemistry MH - Circular Dichroism MH - Microscopy, Electron MH - Molecular Sequence Data MH - *Nuclear Proteins MH - Peptide Fragments/*chemistry MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins/*chemistry MH - Proto-Oncogene Proteins c-mdm2 MH - Spectroscopy, Fourier Transform Infrared MH - Tumor Suppressor Protein p14ARF/*chemistry EDAT- 2003/03/13 04:00 MHDA- 2003/05/17 05:00 CRDT- 2003/03/13 04:00 AID - 10.1021/ja028265w [doi] PST - ppublish SO - J Am Chem Soc. 2003 Mar 19;125(11):3200-1. PMID- 12621030 OWN - NLM STAT- MEDLINE DA - 20030505 DCOM- 20030630 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 19 DP - 2003 May 9 TI - Lipid binding inhibits alpha-synuclein fibril formation. PG - 16873-7 AB - Parkinson's disease is the second most common neurodegenerative disorder, and the cause is unknown; however, substantial evidence implicates the aggregation of alpha-synuclein as a critical factor in the etiology of the disease. alpha-Synuclein is a relatively abundant brain protein of unknown function, and the purified protein is intrinsically unfolded. The amino acid sequence has seven repeats with an apolipoprotein lipid-binding motif, which are predicted to form amphiphilic helices. We have investigated the interaction of alpha-synuclein with lipid vesicles of different sizes and properties by monitoring the effects on the conformation of the protein and the kinetics of fibrillation. The nature of the interaction of alpha-synuclein with vesicles was highly dependent on the phospholipid composition, the ratio of alpha-synuclein to phospholipid, and the size of the vesicles. The strongest interactions were between alpha-synuclein and vesicles composed of 1,2-dipalmitoyl-sn-glycero-3-phosphate/1,2-dipalmitoyl-sn-glycero-3-phosphocholin e and 1,2-dipalmitoyl-sn-glycero-3-phospho-RAC-(1-glycerol)/1,2-dipalmitoyl-sn-glycero- 3-phosphocholine and involved formation of helical structure in alpha-synuclein. A strong correlation was observed between the induction of alpha-helix in alpha-synuclein and the inhibition of fibril formation. Thus, helical, membrane-bound alpha-synuclein is unlikely to contribute to aggregation and fibrillation. Given that a significant fraction of alpha-synuclein is membrane-bound in dopaminergic neurons, this observation has significant physiological significance. FAU - Zhu, Min AU - Zhu M AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. FAU - Fink, Anthony L AU - Fink AL LA - eng GR - NS39985/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20030305 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Nerve Tissue Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Humans MH - Lipid Metabolism MH - Microscopy, Electron MH - Nerve Tissue Proteins/*chemistry/metabolism/ultrastructure MH - Parkinson Disease/etiology/metabolism MH - Protein Binding MH - Protein Folding MH - Recombinant Proteins/chemistry/metabolism MH - Synucleins MH - alpha-Synuclein EDAT- 2003/03/07 04:00 MHDA- 2003/07/02 05:00 CRDT- 2003/03/07 04:00 PHST- 2003/03/05 [aheadofprint] AID - 10.1074/jbc.M210136200 [doi] AID - M210136200 [pii] PST - ppublish SO - J Biol Chem. 2003 May 9;278(19):16873-7. Epub 2003 Mar 5. PMID- 19759002 OWN - NLM STAT- MEDLINE DA - 20091102 DCOM- 20091207 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 284 IP - 45 DP - 2009 Nov 6 TI - The molecular chaperone Hsp90 modulates intermediate steps of amyloid assembly of the Parkinson-related protein alpha-synuclein. PG - 31190-9 LID - 10.1074/jbc.M109.057240 [doi] AB - Alpha-synuclein is an intrinsically unstructured protein that binds to membranes, forms fibrils, and is involved in neurodegeneration. We used a reconstituted in vitro system to show that the molecular chaperone Hsp90 influenced alpha-synuclein vesicle binding and amyloid fibril formation, two processes that are tightly coupled to alpha-synuclein folding. Binding of Hsp90 to monomeric alpha-synuclein occurred in the low micromolar range, involving regions of alpha-synuclein that are critical for vesicle binding and amyloidogenesis. As a consequence, both processes were affected. In the absence of ATP, the accumulation of non-amyloid alpha-synuclein oligomers prevailed over fibril formation, whereas ATP favored fibril growth. This suggests that Hsp90 modulates the assembly of alpha-synuclein in an ATP-dependent manner. We propose that Hsp90 affects these folding processes by restricting conformational fluctuations of alpha-synuclein. FAU - Falsone, S Fabio AU - Falsone SF AD - Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria. fabio.falsone@uni-graz.at FAU - Kungl, Andreas J AU - Kungl AJ FAU - Rek, Angelika AU - Rek A FAU - Cappai, Roberto AU - Cappai R FAU - Zangger, Klaus AU - Zangger K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090915 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Amyloid) RN - 0 (HSP90 Heat-Shock Proteins) RN - 0 (alpha-Synuclein) RN - 8L70Q75FXE (Adenosine Triphosphate) SB - IM MH - Adenosine Triphosphate/chemistry/metabolism MH - Amyloid/*chemistry/genetics/metabolism MH - HSP90 Heat-Shock Proteins/*chemistry/genetics/metabolism MH - Humans MH - Kinetics MH - Models, Biological MH - Parkinson Disease/genetics/*metabolism MH - Protein Binding MH - Protein Folding MH - alpha-Synuclein/*chemistry/genetics/metabolism PMC - PMC2781518 OID - NLM: PMC2781518 EDAT- 2009/09/18 06:00 MHDA- 2009/12/16 06:00 CRDT- 2009/09/18 06:00 PHST- 2009/09/15 [aheadofprint] AID - M109.057240 [pii] AID - 10.1074/jbc.M109.057240 [doi] PST - ppublish SO - J Biol Chem. 2009 Nov 6;284(45):31190-9. doi: 10.1074/jbc.M109.057240. Epub 2009 Sep 15. PMID- 15213447 OWN - NLM STAT- MEDLINE DA - 20040623 DCOM- 20050131 LR - 20131121 IS - 0925-2738 (Print) IS - 0925-2738 (Linking) VI - 29 IP - 3 DP - 2004 Jul TI - 1H, 15N, 13C resonance assignments of the human protein tyrosine phosphatase PRL-1. PG - 417-8 FAU - Laurence, Jennifer S AU - Laurence JS FAU - Hallenga, Klaas AU - Hallenga K FAU - Stauffacher, Cynthia V AU - Stauffacher CV LA - eng GR - CA82673/CA/NCI NIH HHS/United States PT - Letter PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - Netherlands TA - J Biomol NMR JT - Journal of biomolecular NMR JID - 9110829 RN - 0 (Carbon Isotopes) RN - 0 (Cell Cycle Proteins) RN - 0 (Immediate-Early Proteins) RN - 0 (Membrane Proteins) RN - 0 (Neoplasm Proteins) RN - 0 (Nitrogen Isotopes) RN - 0 (Protons) RN - 7YNJ3PO35Z (Hydrogen) RN - EC 3.1.3.48 (PTP4A1 protein, human) RN - EC 3.1.3.48 (Protein Tyrosine Phosphatases) SB - IM MH - Amino Acid Motifs MH - Binding Sites MH - Carbon Isotopes MH - Cell Cycle Proteins MH - Humans MH - Hydrogen MH - Immediate-Early Proteins/*chemistry MH - Magnetic Resonance Spectroscopy/*methods MH - Membrane Proteins MH - Neoplasm Proteins MH - Nitrogen Isotopes MH - Protein Conformation MH - Protein Structure, Tertiary MH - Protein Tyrosine Phosphatases/*chemistry MH - Protons MH - Temperature EDAT- 2004/06/24 05:00 MHDA- 2005/02/03 09:00 CRDT- 2004/06/24 05:00 AID - 10.1023/B:JNMR.0000032506.16792.c6 [doi] AID - 5266114 [pii] PST - ppublish SO - J Biomol NMR. 2004 Jul;29(3):417-8. PMID- 22176582 OWN - NLM STAT- MEDLINE DA - 20120126 DCOM- 20120522 LR - 20150127 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 134 IP - 3 DP - 2012 Jan 25 TI - Long-range modulation of chain motions within the intrinsically disordered transactivation domain of tumor suppressor p53. PG - 1617-22 LID - 10.1021/ja2078619 [doi] AB - The tumor suppressor p53 is a hub protein with a multitude of binding partners, many of which target its intrinsically disordered N-terminal domain, p53-TAD. Partners, such as the N-terminal domain of MDM2, induce formation of local structure and leave the remainder of the domain apparently disordered. We investigated segmental chain motions in p53-TAD using fluorescence quenching of an extrinsic label by tryptophan in combination with fluorescence correlation spectroscopy (PET-FCS). We studied the loop closure kinetics of four consecutive segments within p53-TAD and their response to protein binding and phosphorylation. The kinetics was multiexponential, showing that the conformational ensemble of the domain deviates from random coil, in agreement with previous findings from NMR spectroscopy. Phosphorylations or binding of MDM2 changed the pattern of intrachain kinetics. Unexpectedly, we found that upon binding and phosphorylation chain motions were altered not only within the targeted segments but also in remote regions. Long-range interactions can be induced in an intrinsically disordered domain by partner proteins that induce apparently only local structure or by post-translational modification. CI - (c) 2011 American Chemical Society FAU - Lum, Jenifer K AU - Lum JK AD - Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom. FAU - Neuweiler, Hannes AU - Neuweiler H FAU - Fersht, Alan R AU - Fersht AR LA - eng GR - G0901534/Medical Research Council/United Kingdom GR - MC_EX_G0901534/Medical Research Council/United Kingdom GR - MC_UP_A024_1010/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120112 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Tumor Suppressor Protein p53) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Amino Acid Sequence MH - Humans MH - Molecular Sequence Data MH - Phosphorylation MH - Protein Binding MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-mdm2/metabolism MH - Spectrometry, Fluorescence MH - Tumor Suppressor Protein p53/*chemistry/*metabolism PMC - PMC3265989 OID - NLM: PMC3265989 EDAT- 2011/12/20 06:00 MHDA- 2012/05/23 06:00 CRDT- 2011/12/20 06:00 PHST- 2012/01/12 [aheadofprint] AID - 10.1021/ja2078619 [doi] PST - ppublish SO - J Am Chem Soc. 2012 Jan 25;134(3):1617-22. doi: 10.1021/ja2078619. Epub 2012 Jan 12. PMID- 19769346 OWN - NLM STAT- MEDLINE DA - 20091020 DCOM- 20091124 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 42 DP - 2009 Oct 27 TI - Conformational changes specific for pseudophosphorylation at serine 262 selectively impair binding of tau to microtubules. PG - 10047-55 LID - 10.1021/bi901090m [doi] AB - Aggregation of the microtubule-associated protein tau into neurofibrillary tangles is the pathological hallmark of a variety of dementias. For reasons not yet known, tau becomes excessively phosphorylated in Alzheimer's brains and as a result no longer binds properly to microtubules. Here we studied the impact of phosphorylation on the conformational and binding properties of the repeat region of tau (K18) that is necessary for microtubule assembly and forms the core of paired helical filaments. To mimic phosphorylation, we introduced four mutations of serine to glutamate residues at positions 262, 293, 324, and 356. NMR spectroscopy demonstrates that pseudophosphorylation at these sites modifies the structural properties in repeats 1 and 2, in particular for Gln265-Lys267. Gln265-Lys267 are in close proximity to Ser262, the phosphorylation site that most strongly attenuates binding to microtubules. In contrast, the pseudophosphorylation mimic of tau efficiently interacts with the polyanion heparin. Thus, phosphorylation of the repeat region of natively unfolded tau induces specific conformational changes that have a strong impact on its biological function and involvement in disease. FAU - Fischer, Daniela AU - Fischer D AD - Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany. FAU - Mukrasch, Marco D AU - Mukrasch MD FAU - Biernat, Jacek AU - Biernat J FAU - Bibow, Stefan AU - Bibow S FAU - Blackledge, Martin AU - Blackledge M FAU - Griesinger, Christian AU - Griesinger C FAU - Mandelkow, Eckhard AU - Mandelkow E FAU - Zweckstetter, Markus AU - Zweckstetter M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (tau Proteins) RN - 3KX376GY7L (Glutamic Acid) RN - 452VLY9402 (Serine) SB - IM MH - Alzheimer Disease/metabolism MH - Binding Sites MH - Circular Dichroism MH - Glutamic Acid/genetics/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Microtubules/*metabolism MH - Models, Molecular MH - Mutation MH - Phosphorylation MH - Protein Conformation MH - Serine/*genetics/metabolism MH - tau Proteins/*chemistry/*metabolism EDAT- 2009/09/23 06:00 MHDA- 2009/12/16 06:00 CRDT- 2009/09/23 06:00 AID - 10.1021/bi901090m [doi] PST - ppublish SO - Biochemistry. 2009 Oct 27;48(42):10047-55. doi: 10.1021/bi901090m. PMID- 15247907 OWN - NLM STAT- MEDLINE DA - 20040728 DCOM- 20040916 LR - 20131121 IS - 1545-9993 (Print) IS - 1545-9985 (Linking) VI - 11 IP - 8 DP - 2004 Aug TI - Structural basis for Ca(2+)-induced activation of human PAD4. PG - 777-83 AB - Peptidylarginine deiminase 4 (PAD4) is a Ca(2+)-dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. Its gene is a susceptibility locus for rheumatoid arthritis. Here we present the crystal structure of Ca(2+)-free wild-type PAD4, which shows that the polypeptide chain adopts an elongated fold in which the N-terminal domain forms two immunoglobulin-like subdomains, and the C-terminal domain forms an alpha/beta propeller structure. Five Ca(2+)-binding sites, none of which adopt an EF-hand motif, were identified in the structure of a Ca(2+)-bound inactive mutant with and without bound substrate. These structural data indicate that Ca(2+) binding induces conformational changes that generate the active site cleft. Our findings identify a novel mechanism for enzyme activation by Ca(2+) ions, and are important for understanding the mechanism of protein citrullination and for developing PAD-inhibiting drugs for the treatment of rheumatoid arthritis. FAU - Arita, Kyouhei AU - Arita K AD - Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. FAU - Hashimoto, Hiroshi AU - Hashimoto H FAU - Shimizu, Toshiyuki AU - Shimizu T FAU - Nakashima, Katsuhiko AU - Nakashima K FAU - Yamada, Michiyuki AU - Yamada M FAU - Sato, Mamoru AU - Sato M LA - eng SI - PDB/1WD8 SI - PDB/1WD9 SI - PDB/1WDA PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040711 PL - United States TA - Nat Struct Mol Biol JT - Nature structural & molecular biology JID - 101186374 RN - 0 (Ions) RN - 00BH33GNGH (Cadmium) RN - 29VT07BGDA (Citrulline) RN - 94ZLA3W45F (Arginine) RN - EC 3.- (Hydrolases) RN - EC 3.5.3.15 (peptidylarginine deiminase type IV) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Motifs MH - Arginine/chemistry MH - Binding Sites MH - Cadmium/chemistry MH - Calcium/*chemistry/metabolism MH - Catalysis MH - Citrulline/chemistry MH - Crystallography, X-Ray MH - Enzyme Activation MH - Humans MH - Hydrolases/*chemistry/metabolism MH - Hydrolysis MH - Ions MH - Models, Chemical MH - Models, Molecular MH - Mutagenesis MH - Mutation MH - Polymorphism, Single Nucleotide MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Substrate Specificity EDAT- 2004/07/13 05:00 MHDA- 2004/09/17 05:00 CRDT- 2004/07/13 05:00 PHST- 2004/03/30 [received] PHST- 2004/06/11 [accepted] PHST- 2004/07/11 [aheadofprint] AID - 10.1038/nsmb799 [doi] AID - nsmb799 [pii] PST - ppublish SO - Nat Struct Mol Biol. 2004 Aug;11(8):777-83. Epub 2004 Jul 11. PMID- 18477568 OWN - NLM STAT- MEDLINE DA - 20080714 DCOM- 20080903 LR - 20141120 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 29 DP - 2008 Jul 18 TI - Solution structure of the calponin homology (CH) domain from the smoothelin-like 1 protein: a unique apocalmodulin-binding mode and the possible role of the C-terminal type-2 CH-domain in smooth muscle relaxation. PG - 20569-78 LID - 10.1074/jbc.M800627200 [doi] AB - The SMTNL1 protein contains a single type-2 calponin homology (CH) domain at its C terminus that shares sequence identity with the smoothelin family of smooth muscle-specific proteins. In contrast to the smoothelins, SMTNL1 does not associate with F-actin in vitro, and its specific role in smooth muscle remains unclear. In addition, the biological function of the C-terminal CH-domains found in the smoothelin proteins is also poorly understood. In this work, we have therefore determined the solution structure of the CH-domain of mouse SMTNL1 (SMTNL1-CH; residues 346-459). The secondary structure and the overall fold for the C-terminal type-2 CH-domain is very similar to that of other CH-domains. However, two clusters of basic residues form a unique surface structure that is characteristic of SMTNL1-CH. Moreover, the protein has an extended C-terminal alpha-helix, which contains a calmodulin (CaM)-binding IQ-motif, that is also a distinct feature of the smoothelins. We have characterized the binding of apo-CaM to SMTNL1-CH through its IQ-motif by isothermal titration calorimetry and NMR chemical shift perturbation studies. In addition, we have used the HADDOCK protein-protein docking approach to construct a model for the complex of apo-CaM and SMTNL1-CH. The model revealed a close interaction of SMTNL1-CH with the two Ca(2+) binding loop regions of the C-terminal domain of apo-CaM; this mode of apo-CaM binding is distinct from previously reported interactions of apo-CaM with IQ-motifs. Finally, we comment on the putative role of the CH-domain in the biological function of SMTNL1. FAU - Ishida, Hiroaki AU - Ishida H AD - Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada. FAU - Borman, Meredith A AU - Borman MA FAU - Ostrander, Janina AU - Ostrander J FAU - Vogel, Hans J AU - Vogel HJ FAU - MacDonald, Justin A AU - MacDonald JA LA - eng SI - PDB/2JV9 SI - PDB/2K3S PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080512 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Calcium-Binding Proteins) RN - 0 (Calmodulin) RN - 0 (Microfilament Proteins) RN - 0 (Muscle Proteins) RN - 0 (Phosphoproteins) RN - 0 (SMTNL1 protein, mouse) RN - 0 (calponin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Calcium-Binding Proteins/*chemistry/*metabolism MH - Calmodulin/chemistry/*metabolism MH - Calorimetry MH - Chickens MH - Conserved Sequence MH - Mice MH - Microfilament Proteins/*chemistry/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Muscle Proteins/*chemistry/genetics/*metabolism MH - Muscle Relaxation MH - Muscle, Smooth/*chemistry/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphoproteins/*chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Structural Homology, Protein EDAT- 2008/05/15 09:00 MHDA- 2008/09/04 09:00 CRDT- 2008/05/15 09:00 PHST- 2008/05/12 [aheadofprint] PHST- 2008/05/30 [aheadofprint] AID - M800627200 [pii] AID - 10.1074/jbc.M800627200 [doi] PST - ppublish SO - J Biol Chem. 2008 Jul 18;283(29):20569-78. doi: 10.1074/jbc.M800627200. Epub 2008 May 12. PMID- 24507596 OWN - NLM STAT- MEDLINE DA - 20140210 DCOM- 20140925 LR - 20150204 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 106 IP - 3 DP - 2014 Feb 4 TI - Alpha-synuclein lipid-dependent membrane binding and translocation through the alpha-hemolysin channel. PG - 556-65 LID - 10.1016/j.bpj.2013.12.028 [doi] LID - S0006-3495(13)05845-1 [pii] AB - Gauging the interactions of a natively unfolded Parkinson disease-related protein, alpha-synuclein (alpha-syn) with membranes and its pathways between and within cells is important for understanding its pathogenesis. Here, to address these questions, we use a robust beta-barrel channel, alpha-hemolysin, reconstituted into planar lipid bilayers. Transient, ~95% blockage of the channel current by alpha-syn was observed when 1), alpha-syn was added from the membrane side where the shorter (stem) part of the channel is exposed; and 2), the applied potential was lower on the side of alpha-syn addition. While the on-rate of alpha-syn binding to the channel strongly increased with the applied field, the off-rate displayed a turnover behavior. Statistical analysis suggests that at voltages >50 mV, a significant fraction of the alpha-syn molecules bound to the channel undergoes subsequent translocation. The observed on-rate varied by >100 times depending on the bilayer lipid composition. Removal of the last 25 amino acids from the highly negatively charged C-terminal of alpha-syn resulted in a significant decrease in the binding rates. Taken together, these results demonstrate that beta-barrel channels may serve as sensitive probes of alpha-syn interactions with membranes as well as model systems for studies of channel-assisted protein transport. CI - Copyright (c) 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Gurnev, Philip A AU - Gurnev PA AD - Physics Department, University of Massachusetts, Amherst, Massachusetts; Section on Molecular Transport, Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland. Electronic address: gurnev@physics.umass.edu. FAU - Yap, Thai Leong AU - Yap TL AD - Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland. FAU - Pfefferkorn, Candace M AU - Pfefferkorn CM AD - Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland. FAU - Rostovtseva, Tatiana K AU - Rostovtseva TK AD - Section on Molecular Transport, Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland. FAU - Berezhkovskii, Alexander M AU - Berezhkovskii AM AD - Mathematical and Statistical Computing Laboratory, Division for Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland. FAU - Lee, Jennifer C AU - Lee JC AD - Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland. FAU - Parsegian, V Adrian AU - Parsegian VA AD - Physics Department, University of Massachusetts, Amherst, Massachusetts. FAU - Bezrukov, Sergey M AU - Bezrukov SM AD - Section on Molecular Transport, Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland. LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Hemolysin Proteins) RN - 0 (Lipid Bilayers) RN - 0 (Membrane Lipids) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Hemolysin Proteins/chemistry/*metabolism MH - Humans MH - Lipid Bilayers/*metabolism MH - Membrane Lipids/*metabolism MH - Molecular Sequence Data MH - Protein Binding MH - Protein Structure, Tertiary MH - alpha-Synuclein/chemistry/*metabolism PMC - PMC3944825 OID - NLM: PMC3944825 EDAT- 2014/02/11 06:00 MHDA- 2014/09/26 06:00 CRDT- 2014/02/11 06:00 PHST- 2013/07/25 [received] PHST- 2013/10/30 [revised] PHST- 2013/12/16 [accepted] AID - S0006-3495(13)05845-1 [pii] AID - 10.1016/j.bpj.2013.12.028 [doi] PST - ppublish SO - Biophys J. 2014 Feb 4;106(3):556-65. doi: 10.1016/j.bpj.2013.12.028. PMID- 9218780 OWN - NLM STAT- MEDLINE DA - 19970808 DCOM- 19970808 LR - 20131121 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 16 IP - 12 DP - 1997 Jun 16 TI - Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis. PG - 3373-85 AB - L-arginine:glycine amidinotransferase (AT) catalyses the committed step in creatine biosynthesis by formation of guanidinoacetic acid, the immediate precursor of creatine. We have determined the crystal structure of the recombinant human enzyme by multiple isomorphous replacement at 1.9 A resolution. A telluromethionine derivative was used in sequence assignment. The structure of AT reveals a new fold with 5-fold pseudosymmetry of circularly arranged betabeta alphabeta-modules. These enclose the active site compartment, which is accessible only through a narrow channel. The overall structure resembles a basket with handles that are formed from insertions into the betabeta alphabeta-modules. Binding of L-ornithine, a product inhibitor, reveals a marked induced-fit mechanism, with a loop at the active site entrance changing its conformation accompanied by a shift of an alpha-helix by -4 A. Binding of the arginine educt to the inactive mutant C407A shows a similar mode of binding. A reaction mechanism with a catalytic triad Cys-His-Asp is proposed on the basis of substrate and product bound states. FAU - Humm, A AU - Humm A AD - Max-Planck-Institut fur Biochemie, Martinsried, Germany. FAU - Fritsche, E AU - Fritsche E FAU - Steinbacher, S AU - Steinbacher S FAU - Huber, R AU - Huber R LA - eng SI - GENBANK/S55493 SI - GENBANK/S68805 SI - GENBANK/U07971 SI - GENBANK/X86401 SI - GENBANK/Y00549 PT - Journal Article PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Recombinant Fusion Proteins) RN - 94ZLA3W45F (Arginine) RN - E524N2IXA3 (Ornithine) RN - EC 2.1.4.- (Amidinotransferases) RN - EC 2.1.4.1 (glycine amidinotransferase) RN - MU72812GK0 (Creatine) SB - IM MH - Amidinotransferases/*chemistry/genetics/metabolism MH - Amino Acid Sequence MH - Animals MH - Arginine/*metabolism MH - Binding Sites MH - Computer Graphics MH - Creatine/*biosynthesis MH - Crystallography, X-Ray MH - Dimerization MH - Humans MH - Mitochondria/*enzymology MH - Molecular Sequence Data MH - Ornithine/metabolism MH - *Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - Recombinant Fusion Proteins/chemistry/genetics/metabolism MH - Sequence Homology, Amino Acid MH - Substrate Specificity PMC - PMC1169963 OID - NLM: PMC1169963 EDAT- 1997/06/01 MHDA- 1997/06/01 00:01 CRDT- 1997/06/01 00:00 AID - 10.1093/emboj/16.12.3373 [doi] PST - ppublish SO - EMBO J. 1997 Jun 16;16(12):3373-85. PMID- 23355471 OWN - NLM STAT- MEDLINE DA - 20130325 DCOM- 20130515 LR - 20141103 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 12 DP - 2013 Mar 22 TI - The allosteric mechanism induced by protein kinase A (PKA) phosphorylation of dematin (band 4.9). PG - 8313-20 LID - 10.1074/jbc.M112.438861 [doi] AB - Dematin (band 4.9) is an F-actin binding and bundling protein best known for its role within red blood cells, where it both stabilizes as well as attaches the spectrin/actin cytoskeleton to the erythrocytic membrane. Here, we investigate the structural consequences of phosphorylating serine 381, a covalent modification that turns off F-actin bundling activity. In contrast to the canonical doctrine, in which phosphorylation of an intrinsically disordered region/protein confers affinity for another domain/protein, we found the converse to be true of dematin: phosphorylation of the well folded C-terminal villin-type headpiece confers affinity for its intrinsically disordered N-terminal core domain. We employed analytical ultracentrifugation to demonstrate that dematin is monomeric, in contrast to the prevailing view that it is trimeric. Next, using a series of truncation mutants, we verified that dematin has two F-actin binding sites, one in the core domain and the other in the headpiece domain. Although the phosphorylation-mimicking mutant, S381E, was incapable of bundling microfilaments, it retains the ability to bind F-actin. We found that a phosphorylation-mimicking mutant, S381E, eliminated the ability to bundle, but not bind F-actin filaments. Lastly, we show that the S381E point mutant caused the headpiece domain to associate with the core domain, leading us to the mechanism for cAMP-dependent kinase control of dematin's F-actin bundling activity: when unphosphorylated, dematin's two F-actin binding domains move independent of one another permitting them to bind different F-actin filaments. Phosphorylation causes these two domains to associate, forming a compact structure, and sterically eliminating one of these F-actin binding sites. FAU - Chen, Lin AU - Chen L AD - Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118, USA. FAU - Brown, Jeffrey W AU - Brown JW FAU - Mok, Yee-Foong AU - Mok YF FAU - Hatters, Danny M AU - Hatters DM FAU - McKnight, C James AU - McKnight CJ LA - eng GR - GM62886/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130125 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Actins) RN - 0 (EPB49 protein, human) RN - 0 (Microfilament Proteins) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) SB - IM MH - Actin Cytoskeleton/chemistry MH - Actins/chemistry MH - Allosteric Regulation MH - Amino Acid Substitution MH - Cyclic AMP-Dependent Protein Kinases/*chemistry MH - Humans MH - Microfilament Proteins/*chemistry/genetics MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Phosphorylation MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - Protein Processing, Post-Translational MH - Ultracentrifugation PMC - PMC3605649 OID - NLM: PMC3605649 EDAT- 2013/01/29 06:00 MHDA- 2013/05/17 06:00 CRDT- 2013/01/29 06:00 PHST- 2013/01/25 [aheadofprint] AID - M112.438861 [pii] AID - 10.1074/jbc.M112.438861 [doi] PST - ppublish SO - J Biol Chem. 2013 Mar 22;288(12):8313-20. doi: 10.1074/jbc.M112.438861. Epub 2013 Jan 25. PMID- 21880361 OWN - NLM STAT- MEDLINE DA - 20110929 DCOM- 20120123 IS - 1878-5905 (Electronic) IS - 0142-9612 (Linking) VI - 32 IP - 34 DP - 2011 Dec TI - Splitting and self-assembling of far-red fluorescent protein with an engineered beta strand peptide: application for alpha-synuclein imaging in mammalian cells. PG - 9051-8 LID - 10.1016/j.biomaterials.2011.08.029 [doi] AB - We introduce the strategic development of self-assembling peptide/protein fragments based on the far-red fluorescent protein mPlum. The first beta strand (mPlum 1, 18 amino acids) of mPlum was engineered to spontaneously bind with the rest of the protein (mPlum 2-11, next 10 beta strands) and to form a native chromophore. The target beta strand mPlum 1 was separated from mPlum 2-11 and linked via a flexible peptide linker, resulting in fluorescently inactive circularly permuted mPlum protein (CpmPlum). In vitro evolution of this CpmPlum to a fluorescently active form and the subsequent splitting of the engineered mPlum 1 peptide afforded self-assembling mPlum fragments. Recombinantly expressed and synthetically prepared beta strand peptides were successfully assembled with the remaining mPlum protein in vitro and in cells. This developed pair of peptide/protein fragments was effectively used for peptide tag detection of alpha-synuclein in mammalian cells. Sequential expression of self-assembling mPlum fragments offered an entirely genetically encoded sensing system of naturally unfolded alpha-synuclein. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Keem, Joo Oak AU - Keem JO AD - BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon, Republic of Korea. FAU - Lee, In Hwan AU - Lee IH FAU - Kim, Sun Young AU - Kim SY FAU - Jung, Yongwon AU - Jung Y FAU - Chung, Bong Hyun AU - Chung BH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110831 PL - England TA - Biomaterials JT - Biomaterials JID - 8100316 RN - 0 (Fluorescent Dyes) RN - 0 (Luminescent Proteins) RN - 0 (Peptides) RN - 0 (Recombinant Fusion Proteins) RN - 0 (alpha-Synuclein) RN - 0 (red fluorescent protein) SB - IM MH - Amino Acid Sequence MH - Animals MH - Biosensing Techniques/*methods MH - Escherichia coli/genetics MH - Fluorescent Dyes/*chemistry MH - HeLa Cells MH - Humans MH - Luminescent Proteins/*chemistry/genetics MH - Models, Molecular MH - Molecular Sequence Data MH - Peptides/*chemistry/genetics MH - *Protein Engineering MH - Protein Structure, Secondary MH - Recombinant Fusion Proteins/chemistry/genetics MH - alpha-Synuclein/*analysis EDAT- 2011/09/02 06:00 MHDA- 2012/01/24 06:00 CRDT- 2011/09/02 06:00 PHST- 2011/08/02 [received] PHST- 2011/08/10 [accepted] PHST- 2011/08/31 [aheadofprint] AID - S0142-9612(11)00956-2 [pii] AID - 10.1016/j.biomaterials.2011.08.029 [doi] PST - ppublish SO - Biomaterials. 2011 Dec;32(34):9051-8. doi: 10.1016/j.biomaterials.2011.08.029. Epub 2011 Aug 31. PMID- 15929994 OWN - NLM STAT- MEDLINE DA - 20050602 DCOM- 20050919 LR - 20140606 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 14 IP - 6 DP - 2005 Jun TI - Human full-length Securin is a natively unfolded protein. PG - 1410-8 AB - Human Securin, also called PTTG1 (pituitary tumor transforming gene 1 product), is an estrogen-regulated proto-oncogene with multifunctional properties. We characterized human full-length Securin using a variety of biophysical techniques, such as nuclear magnetic resonance, circular dichroism, and size-exclusion chromatography. Under physiological conditions, Securin is devoid of tertiary and secondary structure except for a small amount of poly-(L-proline) type II helix and its hydrodynamic characteristics suggest it behaves as an extended polypeptide. These results suggest that Securin is unstructured in solution and so belongs to the family of natively unfolded proteins. In addition, to gain structural and quantitative insight, we investigated the binding of Securin to p53. Analytical ultracentrifugation and fluorescence anisotropy studies revealed no evidence of any direct interaction between unmodified recombinant Securin and p53 in vitro. FAU - Sanchez-Puig, Nuria AU - Sanchez-Puig N AD - Centre for Protein Engineering, Medical Research Council, Hills Road CB2 2QH, Cambridge, UK. FAU - Veprintsev, Dmitry B AU - Veprintsev DB FAU - Fersht, Alan R AU - Fersht AR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Neoplasm Proteins) RN - 0 (Securin) RN - 0 (Tumor Suppressor Protein p53) RN - 0 (pituitary tumor-transforming protein 1, human) SB - IM MH - Humans MH - Neoplasm Proteins/*chemistry/metabolism MH - Protein Binding MH - Protein Conformation MH - *Protein Folding MH - Securin MH - Tumor Suppressor Protein p53/*chemistry/metabolism PMC - PMC2253381 OID - NLM: PMC2253381 EDAT- 2005/06/03 09:00 MHDA- 2005/09/20 09:00 CRDT- 2005/06/03 09:00 AID - 14/6/1410 [pii] AID - 10.1110/ps.051368005 [doi] PST - ppublish SO - Protein Sci. 2005 Jun;14(6):1410-8. PMID- 15653326 OWN - NLM STAT- MEDLINE DA - 20050117 DCOM- 20050303 LR - 20071114 IS - 0968-0004 (Print) IS - 0968-0004 (Linking) VI - 30 IP - 1 DP - 2005 Jan TI - Substrate-induced conformational changes in glycosyltransferases. PG - 53-62 AB - Oligosaccharide chains of glycoproteins, glycolipids and glycosaminoglycans are synthesized by glycosyltransferases by the transfer of specific glycosyl moieties from activated sugar-nucleotide donors to specific acceptors. Structural studies on several of these enzymes have shown that one or two flexible loops at the substrate-binding site of the enzymes undergo a marked conformational change from an open to a closed conformation on binding the donor substrate. This conformational change, in which the loop acts as a lid covering the bound donor substrate, creates an acceptor-binding site. After the glycosyl unit is transferred from the donor to the acceptor, the saccharide product is ejected and the loop reverts to its native conformation, thereby releasing the remaining nucleotide moiety. The specificity of the sugar donor is determined by a few residues in the sugar-nucleotide-binding pocket of the enzyme that are conserved among the family members from different species. FAU - Qasba, Pradman K AU - Qasba PK AD - Structural Glycobiology Section, Laboratory of Experimental and Computational Biology, CCR, NCI-Frederick, MD 21702, USA. qsaba@helix.nih.gov FAU - Ramakrishnan, Boopathy AU - Ramakrishnan B FAU - Boeggeman, Elizabeth AU - Boeggeman E LA - eng GR - N01-CO-12400/CO/NCI NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PT - Review PL - England TA - Trends Biochem Sci JT - Trends in biochemical sciences JID - 7610674 RN - 0 (Oligosaccharides) RN - EC 2.4.- (Glycosyltransferases) SB - IM MH - Animals MH - Binding Sites MH - Glycosyltransferases/*chemistry/metabolism MH - Humans MH - *Models, Molecular MH - Oligosaccharides/*chemistry/metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Structure-Activity Relationship MH - Substrate Specificity RF - 71 EDAT- 2005/01/18 09:00 MHDA- 2005/03/04 09:00 CRDT- 2005/01/18 09:00 AID - S0968-0004(04)00295-6 [pii] AID - 10.1016/j.tibs.2004.11.005 [doi] PST - ppublish SO - Trends Biochem Sci. 2005 Jan;30(1):53-62. PMID- 20924623 OWN - NLM STAT- MEDLINE DA - 20110421 DCOM- 20110915 LR - 20131121 IS - 1438-2199 (Electronic) IS - 0939-4451 (Linking) VI - 40 IP - 5 DP - 2011 May TI - Zinc induces disorder-to-order transitions in free and membrane-associated Thellungiella salsuginea dehydrins TsDHN-1 and TsDHN-2: a solution CD and solid-state ATR-FTIR study. PG - 1485-502 LID - 10.1007/s00726-010-0759-0 [doi] AB - Dehydrins are intrinsically unstructured proteins that are expressed in plants experiencing extreme environmental conditions such as drought or low temperature. Although their role is not completely understood, it has been suggested that they stabilize proteins and membrane structures during environmental stress and also sequester metals such as zinc. Here, we investigate two dehydrins (denoted as TsDHN-1 and TsDHN-2) from Thellungiella salsuginea. This plant is a crucifer that thrives in the Canadian sub-Arctic (Yukon Territory) where it grows on saline-rich soils and experiences periods of both extreme cold and drought. We show using circular dichroism and attenuated total reflection-Fourier transform infrared spectroscopy that ordered secondary structure is induced and stabilized in these proteins, both in free and vesicle-bound form, by association with zinc. In membrane-associated form, both proteins have an increased proportion of beta-strand conformation induced by the cation, in addition to the amphipathic alpha-helices formed by their constituent K-segments. These results support the hypothesis that dehydrins stabilize plant plasma and organellar membranes in conditions of stress, and further that zinc may be an important co-factor in stabilization. Whereas dehydrins in the cytosol of a plant cell undergoing dehydration or temperature stress form bulk hydrogels and remain primarily disordered, dehydrins with specific membrane- or protein-associations will have induced ordered secondary structures. FAU - Rahman, Luna N AU - Rahman LN AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada. FAU - Bamm, Vladimir V AU - Bamm VV FAU - Voyer, Janine A M AU - Voyer JA FAU - Smith, Graham S T AU - Smith GS FAU - Chen, Lin AU - Chen L FAU - Yaish, Mahmoud W AU - Yaish MW FAU - Moffatt, Barbara A AU - Moffatt BA FAU - Dutcher, John R AU - Dutcher JR FAU - Harauz, George AU - Harauz G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101006 PL - Austria TA - Amino Acids JT - Amino acids JID - 9200312 RN - 0 (Plant Proteins) RN - 0 (Solutions) RN - 134711-03-8 (dehydrin proteins, plant) RN - J41CSQ7QDS (Zinc) SB - IM MH - Brassicaceae/*chemistry/metabolism MH - Calorimetry MH - Cell Membrane/*chemistry/*metabolism MH - Circular Dichroism MH - Plant Proteins/*chemistry/metabolism MH - Solutions MH - Spectroscopy, Fourier Transform Infrared MH - Temperature MH - Zinc/*chemistry/metabolism EDAT- 2010/10/07 06:00 MHDA- 2011/09/16 06:00 CRDT- 2010/10/07 06:00 PHST- 2010/06/14 [received] PHST- 2010/09/21 [accepted] PHST- 2010/10/06 [aheadofprint] AID - 10.1007/s00726-010-0759-0 [doi] PST - ppublish SO - Amino Acids. 2011 May;40(5):1485-502. doi: 10.1007/s00726-010-0759-0. Epub 2010 Oct 6. PMID- 9539726 OWN - NLM STAT- MEDLINE DA - 19980513 DCOM- 19980513 LR - 20140617 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 95 IP - 8 DP - 1998 Apr 14 TI - Light-activated rhodopsin induces structural binding motif in G protein alpha subunit. PG - 4270-5 AB - A large superfamily of transmembrane receptors control cellular responses to diverse extracellular signals by catalyzing activation of specific types of heterotrimeric GTP-binding proteins. How these receptors recognize and promote nucleotide exchange on G protein alpha subunits to initiate signal amplification is unknown. The three-dimensional structure of the transducin (Gt) alpha subunit C-terminal undecapeptide Gtalpha(340-350) IKENLKDCGLF was determined by transferred nuclear Overhauser effect spectroscopy while it was bound to photoexcited rhodopsin. Light activation of rhodopsin causes a dramatic shift from a disordered conformation of Gtalpha(340-350) to a binding motif with a helical turn followed by an open reverse turn centered at Gly-348, a helix-terminating C capping motif of an alphaL type. Docking of the NMR structure to the GDP-bound x-ray structure of Gt reveals that photoexcited rhodopsin promotes the formation of a continuous helix over residues 325-346 terminated by the C-terminal helical cap with a unique cluster of crucial hydrophobic side chains. A molecular mechanism by which activated receptors can control G proteins through reversible conformational changes at the receptor-G protein interface is demonstrated. FAU - Kisselev, O G AU - Kisselev OG AD - Institute for Biomedical Computing, Washington University Medical School, St. Louis, MO 63110, USA. FAU - Kao, J AU - Kao J FAU - Ponder, J W AU - Ponder JW FAU - Fann, Y C AU - Fann YC FAU - Gautam, N AU - Gautam N FAU - Marshall, G R AU - Marshall GR LA - eng GR - R01 GM106137/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Macromolecular Substances) RN - 0 (Peptide Fragments) RN - 9009-81-8 (Rhodopsin) RN - EC 3.6.1.- (GTP-Binding Proteins) RN - EC 3.6.1.- (Transducin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Calorimetry MH - Cattle MH - Computer Simulation MH - Conserved Sequence MH - GTP-Binding Proteins/*chemistry/metabolism MH - Humans MH - Kinetics MH - Light MH - Macromolecular Substances MH - Mice MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemistry MH - *Protein Conformation MH - *Protein Structure, Secondary MH - Rats MH - Rhodopsin/*chemistry/*metabolism/radiation effects MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Software MH - Transducin/*chemistry/metabolism PMC - PMC22478 OID - NLM: PMC22478 EDAT- 1998/05/16 MHDA- 1998/05/16 00:01 CRDT- 1998/05/16 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4270-5. PMID- 18155047 OWN - NLM STAT- MEDLINE DA - 20080111 DCOM- 20080214 LR - 20140916 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 375 IP - 5 DP - 2008 Feb 1 TI - Crystal structure at 2.8 A of Huntingtin-interacting protein 1 (HIP1) coiled-coil domain reveals a charged surface suitable for HIP1 protein interactor (HIPPI). PG - 1197-205 AB - Huntington's disease is a genetic neurological disorder that is triggered by the dissociation of the huntingtin protein (htt) from its obligate interaction partner Huntingtin-interacting protein 1 (HIP1). The release of the huntingtin protein permits HIP1 protein interactor (HIPPI) to bind to its recognition site on HIP1 to form a HIPPI/HIP1 complex that recruits procaspase-8 to begin the process of apoptosis. The interaction module between HIPPI and HIP1 was predicted to resemble a death-effector domain. Our 2.8-A crystal structure of the HIP1 371-481 subfragment that includes F432 and K474, which is important for HIPPI binding, is not a death-effector domain but is a partially opened coiled coil. The HIP1 371-481 model reveals a basic surface that we hypothesize to be suitable for binding HIPPI. There is an opened region next to the putative HIPPI site that is highly negatively charged. The acidic residues in this region are highly conserved in HIP1 and a related protein, HIP1R, from different organisms but are not conserved in the yeast homologue of HIP1, sla2p. We have modeled approximately 85% of the coiled-coil domain by joining our new HIP1 371-481 structure to the HIP1 482-586 model (Protein Data Bank code: 2NO2). Finally, the middle of this coiled-coil domain may be intrinsically flexible and suggests a new interaction model where HIPPI binds to a U-shaped HIP1 molecule. FAU - Niu, Qian AU - Niu Q AD - Department of Biology, Indiana University, Simon Hall 405B, 212 S. Hawthorne Drive, Bloomington, IN 47405, USA. FAU - Ybe, Joel A AU - Ybe JA LA - eng SI - PDB/2QA7 GR - R01 GM064387/GM/NIGMS NIH HHS/United States GR - R01 GM064387/GM/NIGMS NIH HHS/United States GR - R01 GM064387-04/GM/NIGMS NIH HHS/United States GR - R01 GM064387-05/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20071122 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Codon, Terminator) RN - 0 (DNA, Complementary) RN - 0 (DNA-Binding Proteins) RN - 0 (Disulfides) RN - 0 (HIP1 protein, human) RN - 0 (IFT57 protein, human) RN - 0 (Recombinant Proteins) RN - 30KYC7MIAI (Aspartic Acid) RN - EC 2.5.1.18 (Glutathione Transferase) RN - GMW67QNF9C (Leucine) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry/metabolism MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Aspartic Acid/metabolism MH - Bayes Theorem MH - Binding Sites MH - Codon, Terminator MH - Crystallography, X-Ray MH - DNA, Complementary MH - DNA-Binding Proteins/*chemistry/genetics/isolation & purification/metabolism MH - Dimerization MH - Disulfides/chemistry MH - Escherichia coli/genetics MH - Glutathione Transferase/metabolism MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Leucine/metabolism MH - Models, Chemical MH - Models, Molecular MH - Molecular Sequence Data MH - Plasmids MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Analysis, DNA MH - Surface Properties PMC - PMC2271068 MID - NIHMS39036 OID - NLM: NIHMS39036 OID - NLM: PMC2271068 EDAT- 2007/12/25 09:00 MHDA- 2008/02/15 09:00 CRDT- 2007/12/25 09:00 PHST- 2007/06/18 [received] PHST- 2007/10/17 [revised] PHST- 2007/11/14 [accepted] PHST- 2007/11/22 [aheadofprint] AID - S0022-2836(07)01508-2 [pii] AID - 10.1016/j.jmb.2007.11.036 [doi] PST - ppublish SO - J Mol Biol. 2008 Feb 1;375(5):1197-205. Epub 2007 Nov 22. PMID- 21517079 OWN - NLM STAT- MEDLINE DA - 20110511 DCOM- 20110830 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 133 IP - 19 DP - 2011 May 18 TI - Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics. PG - 7405-15 LID - 10.1021/ja1111964 [doi] AB - Histone tails are highly flexible N- or C-terminal protrusions of histone proteins which facilitate the compaction of DNA into dense superstructures known as chromatin. On a molecular scale histone tails are polyelectrolytes with high degree of conformational disorder which allows them to function as biomolecular "switches", regulating various genetic processes. Unfortunately, their intrinsically disordered nature creates obstacles for comprehensive experimental investigation of both the structural and dynamical aspects of histone tails, because of which their conformational behaviors are still not well understood. In this work we have carried out approximately 3 microsecond long all atom replica exchange molecular dynamics (REMD) simulations for each of four histone tails, H4, H3, H2B, and H2A, and probed their intrinsic conformational preferences. Our subsequent free energy landscape analysis demonstrated that most tails are not fully disordered, but show distinct conformational organization, containing specific flickering secondary structural elements. In particular, H4 forms beta-hairpins, H3 and H2B adopt alpha-helical elements, while H2A is fully disordered. We rationalized observed patterns of conformational dynamics of various histone tails using ideas from physics of polyelectrolytes and disordered systems. We also discovered an intriguing re-entrant contraction-expansion of the tails upon heating, which is caused by subtle interplay between ionic screening and chain entropy. CI - (c) 2011 American Chemical Society FAU - Potoyan, Davit A AU - Potoyan DA AD - Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA. FAU - Papoian, Garegin A AU - Papoian GA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110425 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Histones) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Computer Simulation MH - DNA/*chemistry MH - Histones/*chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Protein Structure, Secondary MH - Thermodynamics EDAT- 2011/04/27 06:00 MHDA- 2011/08/31 06:00 CRDT- 2011/04/27 06:00 PHST- 2011/04/25 [aheadofprint] AID - 10.1021/ja1111964 [doi] PST - ppublish SO - J Am Chem Soc. 2011 May 18;133(19):7405-15. doi: 10.1021/ja1111964. Epub 2011 Apr 25. PMID- 17241479 OWN - NLM STAT- MEDLINE DA - 20070202 DCOM- 20070228 LR - 20140907 IS - 1471-2202 (Electronic) IS - 1471-2202 (Linking) VI - 8 DP - 2007 TI - Amyloid-like aggregates of neuronal tau induced by formaldehyde promote apoptosis of neuronal cells. PG - 9 AB - BACKGROUND: The microtubule associated protein tau is the principle component of neurofibrillar tangles, which are a characteristic marker in the pathology of Alzheimer's disease; similar lesions are also observed after chronic alcohol abuse. Formaldehyde is a common environmental contaminant and also a metabolite of methanol. Although many studies have been done on methanol and formaldehyde intoxication, none of these address the contribution of protein misfolding to the pathological mechanism, in particular the effect of formaldehyde on protein conformation and polymerization. RESULTS: We found that unlike the typical globular protein BSA, the natively-unfolded structure of human neuronal tau was induced to misfold and aggregate in the presence of ~0.01% formaldehyde, leading to formation of amyloid-like deposits that appeared as densely staining granules by electron microscopy and atomic force microscopy, and bound the amyloid-specific dyes thioflavin T and Congo Red. The amyloid-like aggregates of tau were found to induce apoptosis in the neurotypic cell line SH-SY5Y and in rat hippocampal cells, as observed by Hoechst 33258 staining, assay of caspase-3 activity, and flow cytometry using Annexin V and Propidium Iodide staining. Further experiments showed that Congo Red specifically attenuated the caspase-3 activity induced by amyloid-like deposits of tau. CONCLUSION: The results suggest that low concentrations of formaldehyde can induce human tau protein to form neurotoxic aggregates, which could play a role in the induction of tauopathies. FAU - Nie, Chun Lai AU - Nie CL AD - State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, 15 Datun Rd, Chaoyang District, Beijing 100101, China. niecl1022@ioz.ac.cn FAU - Wang, Xing Sheng AU - Wang XS FAU - Liu, Ying AU - Liu Y FAU - Perrett, Sarah AU - Perrett S FAU - He, Rong Qiao AU - He RQ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070123 PL - England TA - BMC Neurosci JT - BMC neuroscience JID - 100966986 RN - 0 (Amyloid) RN - 0 (tau Proteins) RN - 1HG84L3525 (Formaldehyde) SB - IM MH - Amyloid/*metabolism/*ultrastructure MH - Apoptosis/*drug effects MH - Cell Line, Tumor MH - Dose-Response Relationship, Drug MH - Formaldehyde/*administration & dosage MH - Humans MH - Neuroblastoma/*metabolism/ultrastructure MH - tau Proteins/*metabolism/*ultrastructure PMC - PMC1790706 OID - NLM: PMC1790706 EDAT- 2007/01/24 09:00 MHDA- 2007/03/01 09:00 CRDT- 2007/01/24 09:00 PHST- 2006/08/15 [received] PHST- 2007/01/23 [accepted] PHST- 2007/01/23 [aheadofprint] AID - 1471-2202-8-9 [pii] AID - 10.1186/1471-2202-8-9 [doi] PST - epublish SO - BMC Neurosci. 2007 Jan 23;8:9. PMID- 24673507 OWN - NLM STAT- In-Process DA - 20140417 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 118 IP - 15 DP - 2014 Apr 17 TI - The effect of intrachain electrostatic repulsion on conformational disorder and dynamics of the Sic1 protein. PG - 4088-97 LID - 10.1021/jp500776v [doi] AB - The yeast cyclin-dependent kinase inhibitor Sic1 is a disordered protein that, upon multisite phosphorylation, forms a dynamic complex with the Cdc4 subunit of an SCF ubiquitin ligase. To understand the multisite phosphorylation dependence of the Sic1:Cdc4 interaction, which ultimately leads to a sharp cell cycle transition, the conformational properties of the disordered Sic1 N-terminal targeting region were studied using single-molecule fluorescence spectroscopy. Multiple conformational populations with different sensitivities to charge screening were identified by performing experiments in nondenaturing salts and ionic denaturants. Both the end-to-end distance and the hydrodynamic radius decrease monotonically with increasing the salt concentration, and a rollover of the chain dimensions in high denaturant conditions is observed. The data were fit to the polyelectrolyte binding-screening model, yielding parameters such as the excluded volume of the uncharged chain and the binding constant to denaturant. An overall scaling factor of approximately 1.2 was needed for fitting the data, which implies that Sic1 cannot be approximated by a random Gaussian chain. Fluorescence correlation spectroscopy reveals Sic1 structure fluctuations occurring on both fast (10-100 ns) and slow ( approximately 10 ms) time scales, with the fast phase absent in low salt solutions. The results of this study provide direct evidence that long-range intrachain electrostatic repulsions are a significant factor for the conformational landscape of Sic1, and support the role of electrostatics in determining the overall shape and hydrodynamic properties of intrinsically disordered proteins. FAU - Liu, Baoxu AU - Liu B AD - Department of Chemical and Physical Sciences, University of Toronto Mississauga , Mississauga, Ontario L5L 1C6, Canada. FAU - Chia, Darius AU - Chia D FAU - Csizmok, Veronika AU - Csizmok V FAU - Farber, Patrick AU - Farber P FAU - Forman-Kay, Julie D AU - Forman-Kay JD FAU - Gradinaru, Claudiu C AU - Gradinaru CC LA - eng GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140408 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 SB - IM EDAT- 2014/03/29 06:00 MHDA- 2014/03/29 06:00 CRDT- 2014/03/29 06:00 PHST- 2014/04/08 [aheadofprint] AID - 10.1021/jp500776v [doi] PST - ppublish SO - J Phys Chem B. 2014 Apr 17;118(15):4088-97. doi: 10.1021/jp500776v. Epub 2014 Apr 8. PMID- 17515907 OWN - NLM STAT- MEDLINE DA - 20070605 DCOM- 20080306 LR - 20131121 IS - 1545-9993 (Print) IS - 1545-9985 (Linking) VI - 14 IP - 6 DP - 2007 Jun TI - Structural basis for the transforming activity of human cancer-related signaling adaptor protein CRK. PG - 503-10 AB - CRKI (SH2-SH3) and CRKII (SH2-SH3-SH3) are splicing isoforms of the oncoprotein CRK that regulate transcription and cytoskeletal reorganization for cell growth and motility by linking tyrosine kinases to small G proteins. CRKI shows substantial transforming activity, whereas the activity of CRKII is low, and phosphorylated CRKII has no biological activity whatsoever. The molecular mechanisms underlying the distinct biological activities of the CRK proteins remain elusive. We determined the solution structures of CRKI, CRKII and phosphorylated CRKII by NMR and identified the molecular mechanism that gives rise to their activities. Results from mutational analysis using rodent 3Y1 fibroblasts were consistent with those from the structural studies. Together, these data suggest that the linker region modulates the binding of CRKII to its targets, thus regulating cell growth and motility. FAU - Kobashigawa, Yoshihiro AU - Kobashigawa Y AD - Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan. FAU - Sakai, Mieko AU - Sakai M FAU - Naito, Masato AU - Naito M FAU - Yokochi, Masashi AU - Yokochi M FAU - Kumeta, Hiroyuki AU - Kumeta H FAU - Makino, Yoshinori AU - Makino Y FAU - Ogura, Kenji AU - Ogura K FAU - Tanaka, Shinya AU - Tanaka S FAU - Inagaki, Fuyuhiko AU - Inagaki F LA - eng SI - PDB/2DVJ SI - PDB/2EYV SI - PDB/2EYW SI - PDB/2EYX SI - PDB/2EYY SI - PDB/2EYZ PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070521 PL - United States TA - Nat Struct Mol Biol JT - Nature structural & molecular biology JID - 101186374 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Protein Isoforms) RN - 0 (Proto-Oncogene Proteins c-crk) RN - G34N38R2N1 (Bromodeoxyuridine) SB - IM CIN - Nat Struct Mol Biol. 2007 Jun;14(6):465-6. PMID: 17549081 MH - Adaptor Proteins, Signal Transducing/genetics/*metabolism MH - Amino Acid Sequence MH - Animals MH - Bromodeoxyuridine MH - Cell Transformation, Neoplastic/*genetics MH - DNA Mutational Analysis MH - Humans MH - Magnetic Resonance Spectroscopy MH - *Models, Molecular MH - Molecular Sequence Data MH - Mutation/genetics MH - Protein Binding MH - Protein Isoforms/genetics/metabolism MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-crk/genetics/*metabolism MH - Signal Transduction/*physiology EDAT- 2007/05/23 09:00 MHDA- 2008/03/07 09:00 CRDT- 2007/05/23 09:00 PHST- 2006/11/19 [received] PHST- 2007/03/27 [accepted] PHST- 2007/05/21 [aheadofprint] AID - nsmb1241 [pii] AID - 10.1038/nsmb1241 [doi] PST - ppublish SO - Nat Struct Mol Biol. 2007 Jun;14(6):503-10. Epub 2007 May 21. PMID- 20174473 OWN - NLM STAT- MEDLINE DA - 20100222 DCOM- 20100930 LR - 20140827 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 5 IP - 2 DP - 2010 TI - Roles of electrostatics and conformation in protein-crystal interactions. PG - e9330 LID - 10.1371/journal.pone.0009330 [doi] AB - In vitro studies have shown that the phosphoprotein osteopontin (OPN) inhibits the nucleation and growth of hydroxyapatite (HA) and other biominerals. In vivo, OPN is believed to prevent the calcification of soft tissues. However, the nature of the interaction between OPN and HA is not understood. In the computational part of the present study, we used molecular dynamics simulations to predict the adsorption of 19 peptides, each 16 amino acids long and collectively covering the entire sequence of OPN, to the {100} face of HA. This analysis showed that there is an inverse relationship between predicted strength of adsorption and peptide isoelectric point (P<0.0001). Analysis of the OPN sequence by PONDR (Predictor of Naturally Disordered Regions) indicated that OPN sequences predicted to adsorb well to HA are highly disordered. In the experimental part of the study, we synthesized phosphorylated and non-phosphorylated peptides corresponding to OPN sequences 65-80 (pSHDHMDDDDDDDDDGD) and 220-235 (pSHEpSTEQSDAIDpSAEK). In agreement with the PONDR analysis, these were shown by circular dichroism spectroscopy to be largely disordered. A constant-composition/seeded growth assay was used to assess the HA-inhibiting potencies of the synthetic peptides. The phosphorylated versions of OPN65-80 (IC(50) = 1.93 microg/ml) and OPN220-235 (IC(50) = 1.48 microg/ml) are potent inhibitors of HA growth, as is the nonphosphorylated version of OPN65-80 (IC(50) = 2.97 microg/ml); the nonphosphorylated version of OPN220-235 has no measurable inhibitory activity. These findings suggest that the adsorption of acidic proteins to Ca2+-rich crystal faces of biominerals is governed by electrostatics and is facilitated by conformational flexibility of the polypeptide chain. FAU - Azzopardi, Paul V AU - Azzopardi PV AD - School of Dentistry and Department of Biochemistry, University of Western Ontario, London, Ontario, Canada. FAU - O'Young, Jason AU - O'Young J FAU - Lajoie, Gilles AU - Lajoie G FAU - Karttunen, Mikko AU - Karttunen M FAU - Goldberg, Harvey A AU - Goldberg HA FAU - Hunter, Graeme K AU - Hunter GK LA - eng GR - MOP-68827/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100219 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Peptides) RN - 106441-73-0 (Osteopontin) RN - 91D9GV0Z28 (Durapatite) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Computer Simulation MH - Crystallization MH - Durapatite/*chemistry MH - Kinetics MH - Models, Molecular MH - *Molecular Conformation MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Osteopontin/*chemistry MH - Peptides/chemistry MH - Protein Binding MH - *Protein Conformation MH - Protein Structure, Secondary MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Static Electricity PMC - PMC2824833 OID - NLM: PMC2824833 EDAT- 2010/02/23 06:00 MHDA- 2010/10/01 06:00 CRDT- 2010/02/23 06:00 PHST- 2009/08/26 [received] PHST- 2010/01/26 [accepted] PHST- 2010/02/19 [epublish] AID - 10.1371/journal.pone.0009330 [doi] PST - epublish SO - PLoS One. 2010 Feb 19;5(2):e9330. doi: 10.1371/journal.pone.0009330. PMID- 15855160 OWN - NLM STAT- MEDLINE DA - 20050627 DCOM- 20050816 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 26 DP - 2005 Jul 1 TI - Sites of tau important for aggregation populate {beta}-structure and bind to microtubules and polyanions. PG - 24978-86 AB - The aggregation of the microtubule-associated tau protein and formation of "neurofibrillary tangles" is one of the hallmarks of Alzheimer disease. The mechanisms underlying the structural transition of innocuous, natively unfolded tau to neurotoxic forms and the detailed mechanisms of binding to microtubules are largely unknown. Here we report the high-resolution characterization of the repeat domain of soluble tau using multidimensional NMR spectroscopy. NMR secondary chemical shifts detect residual beta-structure for 8-10 residues at the beginning of repeats R2-R4. These regions correspond to sequence motifs known to form the core of the cross-beta-structure of tau-paired helical filaments. Chemical shift perturbation studies show that polyanions, which promote paired helical filament aggregation, as well as microtubules interact with tau through positive charges near the ends of the repeats and through the beta-forming motifs at the beginning of repeats 2 and 3. The high degree of similarity between the binding of polyanions and microtubules supports the hypothesis that stable microtubules prevent paired helical filament formation by blocking the tau-polyanion interaction sites, which are crucial for paired helical filament formation. FAU - Mukrasch, Marco D AU - Mukrasch MD AD - Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany. FAU - Biernat, Jacek AU - Biernat J FAU - von Bergen, Martin AU - von Bergen M FAU - Griesinger, Christian AU - Griesinger C FAU - Mandelkow, Eckhard AU - Mandelkow E FAU - Zweckstetter, Markus AU - Zweckstetter M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050426 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Anions) RN - 0 (Polymers) RN - 0 (Protein Isoforms) RN - 0 (Tubulin) RN - 0 (polyanions) RN - 0 (tau Proteins) RN - K3Z4F929H6 (Lysine) SB - IM MH - Alzheimer Disease/metabolism MH - Amino Acid Sequence MH - Animals MH - Anions MH - Brain/metabolism MH - Crystallography, X-Ray MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - Lysine MH - Magnetic Resonance Spectroscopy MH - Microtubules/*chemistry MH - Molecular Sequence Data MH - Mutation MH - Neurofibrillary Tangles/metabolism MH - Polymers/*chemistry MH - Protein Binding MH - Protein Folding MH - Protein Isoforms MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Swine MH - Temperature MH - Tubulin/chemistry MH - tau Proteins/*chemistry EDAT- 2005/04/28 09:00 MHDA- 2005/08/17 09:00 CRDT- 2005/04/28 09:00 PHST- 2005/04/26 [aheadofprint] AID - M501565200 [pii] AID - 10.1074/jbc.M501565200 [doi] PST - ppublish SO - J Biol Chem. 2005 Jul 1;280(26):24978-86. Epub 2005 Apr 26. PMID- 22271305 OWN - NLM STAT- MEDLINE DA - 20120214 DCOM- 20120412 LR - 20131121 IS - 1573-5028 (Electronic) IS - 0167-4412 (Linking) VI - 78 IP - 4-5 DP - 2012 Mar TI - Biochemical and structural studies on native and recombinant Glycine max UreG: a detailed characterization of a plant urease accessory protein. PG - 461-75 LID - 10.1007/s11103-012-9878-1 [doi] AB - Urea is the nitrogen fertilizer most utilized in crop production worldwide. Understanding all factors involved in urea metabolism in plants is an essential step towards assessing and possibly improving the use of urea by plants. Urease, the enzyme responsible for urea hydrolysis, and its accessory proteins, necessary for nickel incorporation into the enzyme active site and concomitant activation, have been extensively characterized in bacteria. In contrast, little is known about their plant counterparts. This work reports a detailed characterization of Glycine max UreG (GmUreG), a urease accessory protein. Two forms of native GmUreG, purified from seeds, were separated by metal affinity chromatography, and their properties (GTPase activity in absence and presence of Ni(2+) or Zn(2+), secondary structure and metal content) were compared with the recombinant protein produced in Escherichia coli. The binding affinity of recombinant GmUreG (rGmUreG) for Ni(2+) and Zn(2+) was determined by isothermal titration calorimetry. rGmUreG binds Zn(2+) or Ni(2+) differently, presenting a very tight binding site for Zn(2+) (K (d) = 0.02 +/- 0.01 muM) but not for Ni(2+), thus suggesting that Zn(2+) may play a role on the plant urease assembly process, as suggested for bacteria. Size exclusion chromatography showed that Zn(2+) stabilizes a dimeric form of the rGmUreG, while NMR measurements indicate that rGmUreG belongs to the class of intrinsically disordered proteins. A homology model for the fully folded GmUreG was built and compared to bacterial UreG models, and the possible sites of interaction with other accessory proteins were investigated. FAU - Real-Guerra, Rafael AU - Real-Guerra R AD - Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Universidade Federal do Rio Grande do Sul, Av. Bento Goncalves, Porto Alegre, RS 91501-970, Brazil. rafael.guerra@ufrgs.br FAU - Staniscuaski, Fernanda AU - Staniscuaski F FAU - Zambelli, Barbara AU - Zambelli B FAU - Musiani, Francesco AU - Musiani F FAU - Ciurli, Stefano AU - Ciurli S FAU - Carlini, Celia R AU - Carlini CR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120122 PL - Netherlands TA - Plant Mol Biol JT - Plant molecular biology JID - 9106343 RN - 0 (Carrier Proteins) RN - 0 (Metals) RN - 0 (Recombinant Proteins) RN - 0 (Soybean Proteins) RN - 0 (ureG protein, Glycine max) RN - 7OV03QG267 (Nickel) RN - J41CSQ7QDS (Zinc) SB - IM MH - Amino Acid Sequence MH - Carrier Proteins/*chemistry/genetics/*metabolism MH - Circular Dichroism MH - Cloning, Molecular MH - Magnetic Resonance Spectroscopy MH - Metals/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Nickel/metabolism MH - Protein Conformation MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Soybean Proteins/*chemistry/genetics/*metabolism MH - Zinc/*metabolism EDAT- 2012/01/25 06:00 MHDA- 2012/04/13 06:00 CRDT- 2012/01/25 06:00 PHST- 2011/07/18 [received] PHST- 2012/01/03 [accepted] PHST- 2012/01/22 [aheadofprint] AID - 10.1007/s11103-012-9878-1 [doi] PST - ppublish SO - Plant Mol Biol. 2012 Mar;78(4-5):461-75. doi: 10.1007/s11103-012-9878-1. Epub 2012 Jan 22. PMID- 15644214 OWN - NLM STAT- MEDLINE DA - 20050112 DCOM- 20050215 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 345 IP - 5 DP - 2005 Feb 4 TI - The solution structure of the C-terminal domain of TonB and interaction studies with TonB box peptides. PG - 1185-97 AB - The TonB protein transduces energy from the proton gradient across the cytoplasmic membrane of Gram-negative bacteria to TonB-dependent outer membrane receptors. It is a critically important protein in iron uptake, and deletion of this protein is known to decrease virulence of bacteria in animal models. This system has been used for Trojan horse antibiotic delivery. Here, we describe the high-resolution solution structure of Escherichia coli TonB residues 103-239 (TonB-CTD). TonB-CTD is monomeric with an unstructured N terminus (103-151) and a well structured C terminus (152-239). The structure contains a four-stranded antiparallel beta-sheet packed against two alpha-helices and an extended strand in a configuration homologous to the C-terminal domain of the TolA protein. Chemical shift perturbations to the TonB-CTD (1)H-(15)N HSCQ spectrum titrated with TonB box peptides modeled from the E.coli FhuA, FepA and BtuB proteins were all equivalent, indicating that all three peptides bind to the same region of TonB. Isothermal titration calorimetry measurements demonstrate that TonB-CTD interacts with the FhuA-derived peptide with a K(D)=36(+/-7) microM. On the basis of chemical shift data, the position of Gln160, and comparison to the TolA gp3 N1 complex crystal structure, we propose that the TonB box binds to TonB-CTD along the beta3-strand. FAU - Sean Peacock, R AU - Sean Peacock R AD - Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, AB, Canada T2N 1N4. FAU - Weljie, Aalim M AU - Weljie AM FAU - Peter Howard, S AU - Peter Howard S FAU - Price, Feodor D AU - Price FD FAU - Vogel, Hans J AU - Vogel HJ LA - eng SI - PDB/1XX3 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20041215 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Escherichia coli Proteins) RN - 0 (Membrane Proteins) RN - 0 (Peptide Fragments) RN - 0 (Solutions) RN - 0 (tolA protein, E coli) RN - 0 (tonB protein, E coli) SB - IM MH - Amino Acid Sequence MH - Escherichia coli/*chemistry/genetics/metabolism MH - Escherichia coli Proteins/*chemistry/genetics/*metabolism MH - Membrane Proteins/*chemistry/genetics/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - *Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/*chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Solutions/chemistry EDAT- 2005/01/13 09:00 MHDA- 2005/02/16 09:00 CRDT- 2005/01/13 09:00 PHST- 2004/09/08 [received] PHST- 2004/11/10 [revised] PHST- 2004/11/11 [accepted] PHST- 2004/12/15 [aheadofprint] AID - S0022-2836(04)01465-2 [pii] AID - 10.1016/j.jmb.2004.11.026 [doi] PST - ppublish SO - J Mol Biol. 2005 Feb 4;345(5):1185-97. Epub 2004 Dec 15. PMID- 18541383 OWN - NLM STAT- MEDLINE DA - 20080707 DCOM- 20090629 IS - 1873-7544 (Electronic) IS - 0306-4522 (Linking) VI - 154 IP - 4 DP - 2008 Jul 17 TI - Protein array analysis of oligomerization-induced changes in alpha-synuclein protein-protein interactions points to an interference with Cdc42 effector proteins. PG - 1450-7 LID - 10.1016/j.neuroscience.2008.02.049 [doi] AB - Aggregation of alpha-synuclein may contribute to neuropathology in Parkinson's disease patients and in transgenic animal models. Natively unfolded alpha-synuclein binds to various proteins and conformational changes due to alpha-synuclein misfolding may alter physiological interactions. In the present study, we used protein arrays spotted with 5000 recombinant human proteins for a large scale interaction analysis of monomeric versus oligomeric alpha-synuclein. Monomeric alpha-synuclein bound to arrayed cAMP regulated phosphoprotein 19 and binding appears to be disrupted by alpha-synuclein oligomerization. Incubation with recombinant alpha-synuclein oligomers lead to the identification of several GTPase activating proteins and Cdc42 effector proteins as binding partners. Protein database searches revealed a Cdc42/Rac interactive binding domain in some interactors. To demonstrate in vivo relevance, we analyzed brainstem protein extracts from alpha-synuclein(A30P) transgenic mice. Pull-down assays using beads conjugated with a Cdc42/Rac interactive binding domain lead to an enrichment of endogenous alpha-synuclein oligomers. Cdc42 effector proteins were also co-immunoprecipitated with alpha-synuclein from brainstem lysates and were colocalized with alpha-synuclein aggregates in brain sections by double immunostaining. By two-dimensional gel electrophoretic analysis of synaptosomal fractions from transgenic mouse brains we detected additional isoforms of septin 6, a downstream target of Cdc42 effector proteins. Small GTPases have recently been identified in a genetic modifier screen to suppress alpha-synuclein toxicity in yeast. Our data indicate that components of small GTPase signal transduction pathways may be directly targeted by alpha-synuclein oligomers which potentially leads to signaling deficits and neurodegeneration. FAU - Schnack, C AU - Schnack C AD - Boehringer Ingelheim Pharma GmbH & Co KG, CNS Research, Biberach an der Riss, Germany. FAU - Danzer, K M AU - Danzer KM FAU - Hengerer, B AU - Hengerer B FAU - Gillardon, F AU - Gillardon F LA - eng PT - Journal Article DEP - 20080229 PL - United States TA - Neuroscience JT - Neuroscience JID - 7605074 RN - 0 (Recombinant Proteins) RN - 0 (alpha-Synuclein) RN - EC 3.6.5.2 (cdc42 GTP-Binding Protein) SB - IM MH - Animals MH - Blotting, Western MH - Brain/*metabolism/pathology MH - Electrophoresis, Gel, Two-Dimensional MH - Humans MH - Immunohistochemistry MH - Immunoprecipitation MH - Mice MH - Mice, Transgenic MH - Microscopy, Atomic Force MH - Parkinson Disease/metabolism/pathology MH - Protein Array Analysis MH - Protein Conformation MH - Protein Folding MH - Recombinant Proteins/chemistry/metabolism MH - alpha-Synuclein/*chemistry/*metabolism MH - cdc42 GTP-Binding Protein/chemistry/*metabolism EDAT- 2008/06/11 09:00 MHDA- 2009/06/30 09:00 CRDT- 2008/06/11 09:00 PHST- 2007/12/14 [received] PHST- 2008/02/15 [revised] PHST- 2008/02/19 [accepted] PHST- 2008/02/29 [aheadofprint] AID - S0306-4522(08)00306-0 [pii] AID - 10.1016/j.neuroscience.2008.02.049 [doi] PST - ppublish SO - Neuroscience. 2008 Jul 17;154(4):1450-7. doi: 10.1016/j.neuroscience.2008.02.049. Epub 2008 Feb 29. PMID- 18059284 OWN - NLM STAT- MEDLINE DA - 20110908 DCOM- 20110930 IS - 1545-9985 (Electronic) IS - 1545-9985 (Linking) VI - 14 IP - 12 DP - 2007 Dec TI - Evidence of fibril-like beta-sheet structures in a neurotoxic amyloid intermediate of Alzheimer's beta-amyloid. PG - 1157-64 AB - Diffusible subfibrillar aggregates of amyloid proteins are potent neurotoxins and primary suspects in amyloid diseases including Alzheimer's disease. Despite widespread interest, the molecular structures of the amyloid intermediates and the conformational conversions in amyloid misfolding are poorly understood. Here we present a molecular-level examination of sequence-specific secondary structures and supramolecular structures of a neurotoxic amyloid intermediate of the 40-residue beta-amyloid (Abeta) peptide involved in Alzheimer's disease. Using solid-state NMR and electron microscopy, we show that, before fibrillization, natively unstructured monomeric Abeta is subject to large conformational changes into a spherical amyloid intermediate of 15-35 nm diameter, which has predominantly parallel beta-sheet structures. Structural comparison with Abeta fibrils demonstrates that formation of this beta-sheet intermediate I(beta) largely defines conformational transitions in amyloid misfolding. Neurotoxicity assays on PC12 cells show that I(beta) shows higher toxicity than the fibril, indicating that the beta-sheet formation may trigger neurotoxicity. FAU - Chimon, Sandra AU - Chimon S AD - Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA. FAU - Shaibat, Medhat A AU - Shaibat MA FAU - Jones, Christopher R AU - Jones CR FAU - Calero, Diana C AU - Calero DC FAU - Aizezi, Buzulagu AU - Aizezi B FAU - Ishii, Yoshitaka AU - Ishii Y LA - eng GR - R01 AG028490/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Nat Struct Mol Biol JT - Nature structural & molecular biology JID - 101186374 RN - 0 (Amyloid) RN - 0 (Amyloid beta-Peptides) RN - 0 (Fluorescent Dyes) RN - 0 (Neurotoxins) RN - 0 (Peptide Fragments) RN - 0 (Thiazoles) RN - 0 (amyloid beta-protein (1-40)) RN - 2390-54-7 (thioflavin T) SB - IM MH - Amyloid/chemistry MH - Amyloid beta-Peptides/*chemistry/toxicity/ultrastructure MH - Animals MH - Fluorescent Dyes MH - Humans MH - Microscopy, Fluorescence MH - Models, Chemical MH - Neurotoxins/chemistry/toxicity MH - PC12 Cells MH - Peptide Fragments/chemistry/ultrastructure MH - Protein Folding MH - Protein Structure, Secondary MH - Rats MH - Thiazoles EDAT- 2007/12/07 09:00 MHDA- 2011/10/01 06:00 CRDT- 2007/12/07 09:00 PHST- 2006/08/11 [received] PHST- 2007/11/01 [accepted] PHST- 2007/12/02 [aheadofprint] AID - nsmb1345 [pii] AID - 10.1038/nsmb1345 [doi] PST - ppublish SO - Nat Struct Mol Biol. 2007 Dec;14(12):1157-64. PMID- 21473588 OWN - NLM STAT- MEDLINE DA - 20110509 DCOM- 20110909 IS - 1526-4602 (Electronic) IS - 1525-7797 (Linking) VI - 12 IP - 5 DP - 2011 May 9 TI - Formation of framework nacre polypeptide supramolecular assemblies that nucleate polymorphs. PG - 1883-90 LID - 10.1021/bm200231c [doi] AB - The formation of aragonite in the mollusk shell nacre layer is linked to the assembly of framework protein complexes that interact with beta-chitin polysaccharide. What is not yet understood is how framework nacre proteins control crystal growth. Recently, a 30 AA intrinsically disordered nacre protein sequence (n16N) derived from the n16 framework nacre protein was found to form aragonite, vaterite, or ACC deposits when adsorbed onto beta-chitin. Our present study now establishes that n16N assembles to form amorphous nonmineralized supramolecular complexes that nucleate calcium carbonate polymorphs in vitro. These complexes contain unfolded or disordered (54% random coil, 46% beta structures) n16N polypeptide chains that self-assemble in response to alkaline pH shift. The pH-dependent assembly process involves two stages, and it is likely that side chain salt-bridging interactions are a major driving force in n16N self-association. Intriguingly, Ca(II) ions are not required for n16N assembly but do shift the assembly process to higher pH values, and it is likely that Ca(II) plays some role in stabilizing the monomeric form of n16N. Using preassembled fibril-spheroid n16N assemblies on Si wafers or polystyrene supports, we were able to preferentially nucleate vaterite at higher incidence compared to control scenarios, and it is clear that the n16N assemblies are in contact with the nucleating crystals. We conclude that the framework nacre protein sequence n16N assembles to form supramolecular complexes whose surfaces act as nucleation sites for crystal growth. This may represent a general mineralization mechanism employed by framework nacre proteins in general. FAU - Amos, Fairland F AU - Amos FF AD - Laboratory for Chemical Physics, New York University, York, New York 10010, United States. FAU - Ponce, Christopher B AU - Ponce CB FAU - Evans, John Spencer AU - Evans JS LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110419 PL - United States TA - Biomacromolecules JT - Biomacromolecules JID - 100892849 RN - 0 (Peptides) SB - IM MH - Amino Acid Sequence MH - Microscopy, Electron, Scanning MH - Molecular Sequence Data MH - Peptides/*chemistry MH - Protein Conformation MH - X-Ray Diffraction EDAT- 2011/04/09 06:00 MHDA- 2011/09/10 06:00 CRDT- 2011/04/09 06:00 PHST- 2011/04/19 [aheadofprint] AID - 10.1021/bm200231c [doi] PST - ppublish SO - Biomacromolecules. 2011 May 9;12(5):1883-90. doi: 10.1021/bm200231c. Epub 2011 Apr 19. PMID- 20952404 OWN - NLM STAT- MEDLINE DA - 20110301 DCOM- 20110512 LR - 20141014 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 39 IP - 4 DP - 2011 Mar TI - An RNA degradosome assembly in Caulobacter crescentus. PG - 1449-59 LID - 10.1093/nar/gkq928 [doi] AB - In many bacterial species, the multi-enzyme RNA degradosome assembly makes key contributions to RNA metabolism. Powering the turnover of RNA and the processing of structural precursors, the RNA degradosome has differential activities on a spectrum of transcripts and contributes to gene regulation at a global level. Here, we report the isolation and characterization of an RNA degradosome assembly from the alpha-proteobacterium Caulobacter crescentus, which is a model organism for studying morphological development and cell-cycle progression. The principal components of the C. crescentus degradosome are the endoribonuclease RNase E, the exoribonuclease polynucleotide phosphorylase (PNPase), a DEAD-box RNA helicase and the Krebs cycle enzyme aconitase. PNPase and aconitase associate with specific segments in the C-terminal domain of RNase E that are predicted to have structural propensity. These recognition 'microdomains' punctuate structurally an extensive region that is otherwise predicted to be natively disordered. Finally, we observe that the abundance of RNase E varies through the cell cycle, with maxima at morphological differentiation and cell division. This variation may contribute to the program of gene expression during cell division. FAU - Hardwick, Steven W AU - Hardwick SW AD - Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK. FAU - Chan, Vivian S Y AU - Chan VS FAU - Broadhurst, R William AU - Broadhurst RW FAU - Luisi, Ben F AU - Luisi BF LA - eng GR - BB/E013228/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101015 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Multienzyme Complexes) RN - 0 (RNA, Ribosomal) RN - 0 (degradosome) RN - EC 2.7.7.8 (Polyribonucleotide Nucleotidyltransferase) RN - EC 3.1.- (Endoribonucleases) RN - EC 3.1.4.- (ribonuclease E) RN - EC 3.6.4.13 (RNA Helicases) RN - EC 4.2.1.3 (Aconitate Hydratase) SB - IM MH - Aconitate Hydratase/metabolism MH - Alphaproteobacteria/enzymology/isolation & purification MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Catalytic Domain MH - Caulobacter crescentus/*enzymology MH - Cell Cycle MH - Endoribonucleases/*chemistry/isolation & purification/metabolism MH - Escherichia coli/enzymology MH - Molecular Sequence Data MH - Multienzyme Complexes/*chemistry/isolation & purification/metabolism MH - Polyribonucleotide Nucleotidyltransferase/*chemistry/isolation & purification/metabolism MH - RNA Helicases/*chemistry/isolation & purification/metabolism MH - RNA Processing, Post-Transcriptional MH - RNA, Ribosomal/metabolism PMC - PMC3045602 OID - NLM: PMC3045602 EDAT- 2010/10/19 06:00 MHDA- 2011/05/13 06:00 CRDT- 2010/10/19 06:00 PHST- 2010/10/15 [aheadofprint] AID - gkq928 [pii] AID - 10.1093/nar/gkq928 [doi] PST - ppublish SO - Nucleic Acids Res. 2011 Mar;39(4):1449-59. doi: 10.1093/nar/gkq928. Epub 2010 Oct 15. PMID- 16470515 OWN - NLM STAT- MEDLINE DA - 20060831 DCOM- 20061130 IS - 0269-3879 (Print) IS - 0269-3879 (Linking) VI - 20 IP - 9 DP - 2006 Sep TI - Purification of a crystallin domain of Yersinia crystallin from inclusion bodies and its comparison to native protein from the soluble fraction. PG - 956-63 AB - It has been established that many heterologously produced proteins in E. coli accumulate as insoluble inclusion bodies. Methods for protein recovery from inclusion bodies involve solubilization using chemical denaturants such as urea and guanidine hydrochloride, followed by removal of denaturant from the solution to allow the protein to refold. In this work, we applied on-column refolding and purification to the second crystallin domain D2 of Yersinia crystallin isolated from inclusion bodies. We also purified the protein from the soluble fraction (without using any denaturant) to compare the biophysical properties and conformation, although the yield was poor. On-column refolding method allows rapid removal of denaturant and refolding at high protein concentration, which is a limitation in traditionally used methods of dialysis or dilution. We were also able to develop methods to remove the co-eluting nucleic acids during chromatography from the protein preparation. Using this protocol, we were able to rapidly refold and purify the crystallin domain using a two-step process with high yield. We used biophysical techniques to compare the conformation and calcium-binding properties of the protein isolated from the soluble fraction and inclusion bodies. CI - Copyright 2006 John Wiley & Sons, Ltd. FAU - Jobby, M K AU - Jobby MK AD - Center for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India. jobby@ccmb.res.in FAU - Sharma, Yogendra AU - Sharma Y LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biomed Chromatogr JT - Biomedical chromatography : BMC JID - 8610241 RN - 0 (Crystallins) SB - IM MH - Chromatography, DEAE-Cellulose MH - Circular Dichroism MH - Crystallins/chemistry/*isolation & purification MH - Electrophoresis, Polyacrylamide Gel MH - Inclusion Bodies/*chemistry MH - Solubility MH - Spectrometry, Fluorescence MH - Spectrophotometry, Ultraviolet MH - Yersinia/*chemistry EDAT- 2006/02/14 09:00 MHDA- 2006/12/09 09:00 CRDT- 2006/02/14 09:00 AID - 10.1002/bmc.628 [doi] PST - ppublish SO - Biomed Chromatogr. 2006 Sep;20(9):956-63. PMID- 12923182 OWN - NLM STAT- MEDLINE DA - 20031103 DCOM- 20040105 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 45 DP - 2003 Nov 7 TI - Crystal structure of human cholesterol sulfotransferase (SULT2B1b) in the presence of pregnenolone and 3'-phosphoadenosine 5'-phosphate. Rationale for specificity differences between prototypical SULT2A1 and the SULT2BG1 isoforms. PG - 44593-9 AB - The gene for human hydroxysteroid sulfotransferase (SULT2B1) encodes two peptides, SULT2B1a and SULT2B1b, that differ only at their amino termini. SULT2B1b has a predilection for cholesterol but is also capable of sulfonating pregnenolone, whereas SULT2B1a preferentially sulfonates pregnenolone and only minimally sulfonates cholesterol. We have determined the crystal structure of SULT2B1a and SULT2B1b bound to the substrate donor product 3'-phosphoadenosine 5'-phosphate at 2.9 and 2.4 A, respectively, as well as SULT2B1b in the presence of the acceptor substrate pregnenolone at 2.3 A. These structures reveal a different catalytic binding orientation for the substrate from a previously determined structure of hydroxysteroid sulfotransferase (SULT2A1) binding dehydroepiandrosterone. In addition, the amino-terminal helix comprising residues Asp19 to Lys26, which determines the specificity difference between the SULT2B1 isoforms, becomes ordered upon pregnenolone binding, covering the substrate binding pocket. FAU - Lee, Karen A AU - Lee KA AD - Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA. FAU - Fuda, Hirotoshi AU - Fuda H FAU - Lee, Young C AU - Lee YC FAU - Negishi, Masahiko AU - Negishi M FAU - Strott, Charles A AU - Strott CA FAU - Pedersen, Lars C AU - Pedersen LC LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20030814 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Isoenzymes) RN - 0 (Recombinant Fusion Proteins) RN - 1053-73-2 (adenosine 3'-phosphate-5'-phosphate) RN - 30KYC7MIAI (Aspartic Acid) RN - 459AG36T1B (Dehydroepiandrosterone) RN - 61D2G4IYVH (Adenosine Diphosphate) RN - 73R90F7MQ8 (Pregnenolone) RN - 97C5T2UQ7J (Cholesterol) RN - EC 2.8.2.- (Sulfotransferases) RN - EC 2.8.2.2 (SULT2B1 protein, human) RN - EC 2.8.2.2 (alcohol sulfotransferase) RN - K3Z4F929H6 (Lysine) SB - IM MH - Adenosine Diphosphate/*metabolism MH - Aspartic Acid MH - Binding Sites MH - Cholesterol/metabolism MH - Crystallization MH - Crystallography, X-Ray MH - Dehydroepiandrosterone/metabolism MH - Escherichia coli/genetics MH - Gene Expression MH - Humans MH - Hydrogen Bonding MH - Isoenzymes/chemistry MH - Lysine MH - Models, Molecular MH - Molecular Structure MH - Pregnenolone/*metabolism MH - Protein Structure, Secondary MH - Recombinant Fusion Proteins MH - Substrate Specificity MH - Sulfotransferases/*chemistry/genetics/metabolism MH - Transfection EDAT- 2003/08/19 05:00 MHDA- 2004/01/06 05:00 CRDT- 2003/08/19 05:00 PHST- 2003/08/14 [aheadofprint] AID - 10.1074/jbc.M308312200 [doi] AID - M308312200 [pii] PST - ppublish SO - J Biol Chem. 2003 Nov 7;278(45):44593-9. Epub 2003 Aug 14. PMID- 15368101 OWN - NLM STAT- MEDLINE DA - 20041217 DCOM- 20050404 LR - 20111117 IS - 1434-5161 (Print) IS - 1434-5161 (Linking) VI - 49 IP - 11 DP - 2004 TI - SMARCA2 and THAP11: potential candidates for polyglutamine disorders as evidenced from polymorphism and protein-folding simulation studies. PG - 596-602 AB - CAG repeat expansion is the cause of an ever-increasing list of neurodegenerative disorders, especially hereditary ataxias. However, genes responsible for 10-50% of the clinically diagnosed ataxias are still unidentified in different populations. Traditional linkage and repeat expansion-detection based methods complemented with human genome sequence and expression information can now accelerate the pace of identification of putative disease candidates. We have analyzed two CAG repeat containing loci, human SMARCA2 and THAP11, which are expressed in the brain as putative candidates for SCAs, using computational as well as polymorphism scanning approaches. Both loci exhibited features characteristic of genes associated with repeat disorders. These loci are polymorphic with respect to size and interruption pattern in the Indian population. Furthermore, computational analysis of glutamine-stretch embedded domains in the respective proteins predicted these regions to be "natively unfolded" beyond a threshold of 40 glutamines. Comparative genome analysis suggested a stabilizing influence of CAA interspersions in repeat tract in THAP11 but not in SMARCA2. Although repeat expansion could not be detected within these genes in unidentified ataxia patients reported in India, we suggest that these loci be screened in other populations, as there is a wide heterogeneity in the prevalence of these disorders in different populations. FAU - Pandey, Neeraj AU - Pandey N AD - Functional Genomics Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi University Campus, Mall Road, New Delhi, 110007, India. FAU - Mittal, Uma AU - Mittal U FAU - Srivastava, Achal K AU - Srivastava AK FAU - Mukerji, Mitali AU - Mukerji M LA - eng SI - GENBANK/AY653182 SI - GENBANK/AY653183 SI - GENBANK/AY653184 SI - GENBANK/AY653185 SI - GENBANK/AY653186 SI - GENBANK/AY653187 SI - GENBANK/AY653188 SI - GENBANK/AY653189 SI - GENBANK/AY653190 SI - GENBANK/AY653191 SI - GENBANK/AY653192 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040910 PL - Japan TA - J Hum Genet JT - Journal of human genetics JID - 9808008 RN - 0 (DNA Primers) RN - 0 (DNA-Binding Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Peptides) RN - 0 (Repressor Proteins) RN - 0 (SMARCA2 protein, human) RN - 0 (THAP11 protein, human) RN - 0 (Transcription Factors) RN - 26700-71-0 (polyglutamine) SB - IM MH - Animals MH - Base Sequence MH - Brain/*metabolism MH - Computer Simulation MH - DNA Primers MH - DNA-Binding Proteins/*genetics/metabolism MH - Humans MH - India MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*genetics/metabolism MH - Peptides/genetics MH - *Polymorphism, Genetic MH - Primates/genetics MH - Protein Folding MH - Repetitive Sequences, Nucleic Acid/genetics MH - Repressor Proteins MH - Sequence Analysis, DNA MH - Spinocerebellar Ataxias/*genetics MH - Transcription Factors/*genetics/metabolism EDAT- 2004/09/16 05:00 MHDA- 2005/04/05 09:00 CRDT- 2004/09/16 05:00 PHST- 2004/06/15 [received] PHST- 2004/07/30 [accepted] PHST- 2004/09/10 [aheadofprint] AID - 10.1007/s10038-004-0194-8 [doi] PST - ppublish SO - J Hum Genet. 2004;49(11):596-602. Epub 2004 Sep 10. PMID- 24412063 OWN - NLM STAT- MEDLINE DA - 20140210 DCOM- 20140508 LR - 20150212 IS - 1097-4164 (Electronic) IS - 1097-2765 (Linking) VI - 53 IP - 3 DP - 2014 Feb 6 TI - The intrinsically disordered Sem1 protein functions as a molecular tether during proteasome lid biogenesis. PG - 433-43 LID - 10.1016/j.molcel.2013.12.009 [doi] LID - S1097-2765(13)00899-X [pii] AB - The intrinsically disordered yeast protein Sem1 (DSS1 in mammals) participates in multiple protein complexes, including the proteasome, but its role(s) within these complexes is uncertain. We report that Sem1 enforces the ordered incorporation of subunits Rpn3 and Rpn7 into the assembling proteasome lid. Sem1 uses conserved acidic segments separated by a flexible linker to grasp Rpn3 and Rpn7. The same segments are used for protein binding in other complexes, but in the proteasome lid they are uniquely deployed for recognizing separate polypeptides. We engineered TEV protease-cleavage sites into Sem1 to show that the tethering function of Sem1 is important for the biogenesis and integrity of the Rpn3-Sem1-Rpn7 ternary complex but becomes dispensable once the ternary complex incorporates into larger lid precursors. Thus, although Sem1 is a stoichiometric component of the mature proteasome, it has a distinct, chaperone-like function specific to early stages of proteasome assembly. CI - Copyright (c) 2014 Elsevier Inc. All rights reserved. FAU - Tomko, Robert J Jr AU - Tomko RJ Jr AD - Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA. FAU - Hochstrasser, Mark AU - Hochstrasser M AD - Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA. Electronic address: mark.hochstrasser@yale.edu. LA - eng GR - GM083050/GM/NIGMS NIH HHS/United States GR - R01 GM083050/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140109 PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (RPN3 protein, S cerevisiae) RN - 0 (Rpn7 protein, S cerevisiae) RN - 0 (SEM1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Models, Biological MH - Molecular Sequence Data MH - Proteasome Endopeptidase Complex/*biosynthesis/chemistry/metabolism/physiology MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/metabolism/*physiology MH - Sequence Alignment PMC - PMC3947554 MID - NIHMS555106 OID - NLM: NIHMS555106 OID - NLM: PMC3947554 EDAT- 2014/01/15 06:00 MHDA- 2014/05/09 06:00 CRDT- 2014/01/14 06:00 PHST- 2013/10/24 [received] PHST- 2013/11/19 [revised] PHST- 2013/12/05 [accepted] PHST- 2014/01/09 [aheadofprint] AID - S1097-2765(13)00899-X [pii] AID - 10.1016/j.molcel.2013.12.009 [doi] PST - ppublish SO - Mol Cell. 2014 Feb 6;53(3):433-43. doi: 10.1016/j.molcel.2013.12.009. Epub 2014 Jan 9. PMID- 23075227 OWN - NLM STAT- MEDLINE DA - 20130909 DCOM- 20140326 LR - 20150604 IS - 1538-0254 (Electronic) IS - 0739-1102 (Linking) VI - 31 IP - 10 DP - 2013 Oct TI - An N-terminal, 830 residues intrinsically disordered region of the cytoskeleton-regulatory protein supervillin contains Myosin II- and F-actin-binding sites. PG - 1150-9 LID - 10.1080/07391102.2012.726531 [doi] AB - Supervillin, the largest member of the villin/gelsolin family, is a cytoskeleton regulating, peripheral membrane protein. Supervillin increases cell motility and promotes invasive activity in tumors. Major cytoskeletal interactors, including filamentous actin and myosin II, bind within the unique supervillin amino terminus, amino acids 1-830. The structural features of this key region of the supervillin polypeptide are unknown. Here, we utilize circular dichroism and bioinformatics sequence analysis to demonstrate that the N-terminal part of supervillin forms an extended intrinsically disordered region (IDR). Our combined data indicate that the N-terminus of human and bovine supervillin sequences (positions 1-830) represents an IDR, which is the largest IDR known to date in the villin/gelsolin family. Moreover, this result suggests a potentially novel mechanism of regulation of myosin II and F-actin via the intrinsically disordered N-terminal region of hub protein supervillin. FAU - Fedechkin, Stanislav O AU - Fedechkin SO AD - a Department of Chemistry , Western Washington University , MS-9150, 516 High Street , Bellingham , WA , 98225-9150 , USA. FAU - Brockerman, Jacob AU - Brockerman J FAU - Luna, Elizabeth J AU - Luna EJ FAU - Lobanov, Michail Yu AU - Lobanov MY FAU - Galzitskaya, Oxana V AU - Galzitskaya OV FAU - Smirnov, Serge L AU - Smirnov SL LA - eng GR - R01 GM033048/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121017 PL - England TA - J Biomol Struct Dyn JT - Journal of biomolecular structure & dynamics JID - 8404176 RN - 0 (Actins) RN - 0 (Amino Acids) RN - 0 (Microfilament Proteins) RN - 0 (villin) RN - EC 3.6.1.- (Myosin Type II) SB - IM MH - Actins/*chemistry/metabolism MH - Amino Acid Sequence MH - Amino Acids/chemistry MH - Animals MH - *Binding Sites MH - Cattle MH - Chickens MH - Humans MH - Microfilament Proteins/*chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Myosin Type II/*chemistry/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - *Protein Interaction Domains and Motifs MH - Sequence Alignment PMC - PMC4454289 MID - NIHMS690348 OID - NLM: NIHMS690348 OID - NLM: PMC4454289 EDAT- 2012/10/19 06:00 MHDA- 2014/03/29 06:00 CRDT- 2012/10/19 06:00 PHST- 2012/10/17 [aheadofprint] AID - 10.1080/07391102.2012.726531 [doi] PST - ppublish SO - J Biomol Struct Dyn. 2013 Oct;31(10):1150-9. doi: 10.1080/07391102.2012.726531. Epub 2012 Oct 17. PMID- 17892488 OWN - NLM STAT- MEDLINE DA - 20071003 DCOM- 20071212 IS - 1742-464X (Print) IS - 1742-464X (Linking) VI - 274 IP - 20 DP - 2007 Oct TI - The intracellular region of the Notch ligand Jagged-1 gains partial structure upon binding to synthetic membranes. PG - 5325-36 AB - Notch ligands are membrane-spanning proteins made of a large extracellular region, a transmembrane segment, and a approximately 100-200 residue cytoplasmic tail. The intracellular region of Jagged-1, one of the five ligands to Notch receptors in man, mediates protein-protein interactions through the C-terminal PDZ binding motif, is involved in receptor/ligand endocytosis triggered by mono-ubiquitination, and, as a consequence of regulated intramembrane proteolysis, can be released into the cytosol as a signaling fragment. The intracellular region of Jagged-1 may then exist in at least two forms: as a membrane-tethered protein located at the interface between the membrane and the cytoplasm, and as a soluble nucleocytoplasmic protein. Here, we report the characterization, in different environments, of a recombinant protein corresponding to the human Jagged-1 intracellular region (J1_tmic). In solution, J1_tmic behaves as an intrinsically disordered protein, but displays a significant helical propensity. In the presence of SDS micelles and phospholipid vesicles, used to mimick the interface between the plasma membrane and the cytosol, J1_tmic undergoes a substantial conformational change. We show that the interaction of J1_tmic with SDS micelles drives partial helix formation, as measured by circular dichroism, and that the helical content depends on pH in a reversible manner. An increase in the helical content is observed also in the presence of vesicles made of negatively charged, but not zwitterionic, phospholipids. We propose that this partial folding may have implications in the interactions of J1_tmic with its binding partners, as well as in its post-translational modifications. FAU - Popovic, Matija AU - Popovic M AD - Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Padriciano, Trieste, Italy. FAU - De Biasio, Alfredo AU - De Biasio A FAU - Pintar, Alessandro AU - Pintar A FAU - Pongor, Sandor AU - Pongor S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070924 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Calcium-Binding Proteins) RN - 0 (Intercellular Signaling Peptides and Proteins) RN - 0 (Ligands) RN - 0 (Membrane Proteins) RN - 0 (Membranes, Artificial) RN - 0 (Micelles) RN - 0 (Phospholipids) RN - 0 (Receptors, Notch) RN - 134324-36-0 (Serrate proteins) SB - IM MH - Calcium-Binding Proteins/*chemistry/isolation & purification/metabolism MH - Chromatography, Gel MH - Circular Dichroism MH - Cytoplasm/metabolism MH - Fluorescence MH - Humans MH - Intercellular Signaling Peptides and Proteins/*chemistry/isolation & purification/metabolism MH - Ligands MH - Magnetic Resonance Spectroscopy MH - Membrane Proteins/*chemistry/isolation & purification/metabolism MH - *Membranes, Artificial MH - Micelles MH - Phospholipids/*metabolism MH - Protein Folding MH - Protein Structure, Secondary MH - Receptors, Notch/*metabolism EDAT- 2007/09/26 09:00 MHDA- 2007/12/13 09:00 CRDT- 2007/09/26 09:00 PHST- 2007/09/24 [aheadofprint] AID - EJB6053 [pii] AID - 10.1111/j.1742-4658.2007.06053.x [doi] PST - ppublish SO - FEBS J. 2007 Oct;274(20):5325-36. Epub 2007 Sep 24. PMID- 24871565 OWN - NLM STAT- In-Process DA - 20140819 IS - 1520-4898 (Electronic) IS - 0001-4842 (Linking) VI - 47 IP - 8 DP - 2014 Aug 19 TI - Metal ions and intrinsically disordered proteins and peptides: from Cu/Zn amyloid-beta to general principles. PG - 2252-9 LID - 10.1021/ar400293h [doi] AB - The interaction of d-block metal ions (Cu, Zn, Fe, etc.) with intrinsically disordered proteins (IDPs) has gained interest, partly due to their proposed roles in several diseases, mainly neurodegenerative. A prominent member of IDPs is the peptide amyloid-beta (Abeta) that aggregates into metal-enriched amyloid plaques, a hallmark of Alzheimer's disease, in which Cu and Zn are bound to Abeta. IDPs are a class of proteins and peptides that lack a unique 3D structure when the protein is isolated. This disordered structure impacts their interaction with metal ions compared with structured metalloproteins. Metalloproteins either have a preorganized metal binding site or fold upon metal binding, resulting in defined 3D structure with a well-defined metal site. In contrast, for Abeta and likely most of the other IDPs, the affinity for Cu(I/II) and Zn(II) is weaker and the interaction is flexible with different coordination sites present. Coordination of Cu(I/II) with Abeta is very dynamic including fast Cu-exchange reactions (milliseconds or less) that are intrapeptidic between different sites as well as interpeptidic. This highly dynamic metal-IDP interaction has a strong impact on reactivity and potential biological role: (i) Due to the low affinity compared with classical metalloproteins, IDPs likely bind metals only at special places or under special conditions. For Abeta, this is likely in the neurons that expel Zn or Cu into the synapse and upon metal dysregulation occurring in Alzheimer's disease. (ii) Amino acid substitutions (mutations) on noncoordinating residues can change drastically the coordination sphere. (iii) Considering the Cu/Zn-Abeta aberrant interaction, therapeutic strategies can be based on removal of Cu/Zn or precluding their binding to the peptide. The latter is very difficult due to the multitude of metal-binding sites, but the fast koff facilitates removal. (iv) The high flexibility of the Cu-Abeta complex results in different conformations with different redox activity. Only some conformations are able to produce reactive oxygen species. (v) Other, more specific catalysis (like enzymes) is very unlikely for Cu/Zn-Abeta. (vi) The Cu/Zn exchange reactions with Abeta are faster than the aggregation process and can hence have a strong impact on this process. In conclusion, the coordination chemistry is fundamentally different for most of IDPs compared with the classical, structured metalloproteins or with (bio)-inorganic complexes. The dynamics is a key parameter to understand this interaction and its potential biological impact. FAU - Faller, Peter AU - Faller P AD - CNRS , LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France. FAU - Hureau, Christelle AU - Hureau C FAU - La Penna, Giovanni AU - La Penna G LA - eng PT - Journal Article DEP - 20140529 PL - United States TA - Acc Chem Res JT - Accounts of chemical research JID - 0157313 SB - IM EDAT- 2014/05/30 06:00 MHDA- 2014/05/30 06:00 CRDT- 2014/05/30 06:00 PHST- 2014/05/29 [aheadofprint] AID - 10.1021/ar400293h [doi] PST - ppublish SO - Acc Chem Res. 2014 Aug 19;47(8):2252-9. doi: 10.1021/ar400293h. Epub 2014 May 29. PMID- 15099569 OWN - NLM STAT- MEDLINE DA - 20040421 DCOM- 20050118 LR - 20131121 IS - 1047-8477 (Print) IS - 1047-8477 (Linking) VI - 146 IP - 3 DP - 2004 Jun TI - Backbone dynamic properties of the central linker region of calcium-calmodulin in 35% trifluoroethanol. PG - 272-80 AB - The backbone dynamic properties of uniformly (15)N-labeled calcium-saturated calmodulin (Ca(2+)-CaM) in 35% 2,2,2-trifluoroethanol (TFE) have been examined by (15)N NMR relaxation methods. This particular solvent was chosen in order to mimic the conditions in which CaM was crystallized, which included the presence of alcohols. Special attention was paid to the central linker region of Ca(2+)-CaM, which is a long, solvent-exposed alpha-helix in the crystal structure but is known to be partially unwound and flexible in solution. (15)N T(1), T(2), and (15)N-[(1)H] NOE values were determined for both Ca(2+)-CaM in H(2)O and Ca(2+)-CaM in 35% TFE, and the results indicated that the presence of 35% TFE did indeed induce a more ordered conformation in the central linker, with order parameters for Asp78-Glu80 of 0.29, 0.17, and 0.27 in H(2)O and 0.82, 0.66, and 0.64 in 35% TFE. However, (15)N-[(1)H] NOE values showed that these residues were still slightly more flexible than the rest of the molecule in 35% TFE (Asp78-Glu80 (15)N-[(1)H] NOE=0.46, 0.46, and 0.51). Furthermore, there is still independent motion of the two lobes of Ca(2+)-CaM in 35% TFE, with motional correlation times of approximately 10 and approximately 9 ns for the N- and C-lobes, respectively, indicating that 35% TFE was not sufficient to force Ca(2+)-CaM into a rigid dumbbell-shaped molecule as seen in the crystal structure. Additional factors that could further stabilize the structure of CaM in the crystal include pH, temperature, and crystal packing. FAU - Brokx, Richard D AU - Brokx RD AD - Structural Biology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. N.W., Calgary, Alta., Canada T2N 1N4. FAU - Scheek, Ruud M AU - Scheek RM FAU - Weljie, Aalim M AU - Weljie AM FAU - Vogel, Hans J AU - Vogel HJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - 0 (Calmodulin) RN - 0 (Nitrogen Isotopes) RN - 0 (Recombinant Proteins) RN - 059QF0KO0R (Water) RN - 75-89-8 (Trifluoroethanol) RN - SY7Q814VUP (Calcium) SB - IM MH - Calcium/*chemistry MH - Calmodulin/*chemistry MH - Kinetics MH - Motion MH - Nitrogen Isotopes MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation/drug effects MH - Protein Structure, Secondary/drug effects MH - Recombinant Proteins MH - Trifluoroethanol/pharmacology MH - Water EDAT- 2004/04/22 05:00 MHDA- 2005/01/19 09:00 CRDT- 2004/04/22 05:00 PHST- 2003/09/29 [received] PHST- 2003/12/16 [revised] AID - 10.1016/j.jsb.2003.12.007 [doi] AID - S1047847703003204 [pii] PST - ppublish SO - J Struct Biol. 2004 Jun;146(3):272-80. PMID- 21508037 OWN - NLM STAT- MEDLINE DA - 20110801 DCOM- 20111122 IS - 1756-2651 (Electronic) IS - 0021-924X (Linking) VI - 150 IP - 2 DP - 2011 Aug TI - A 68 residue N-terminal fragment of pro-atrial natriuretic peptide is a monomeric intrinsically unstructured protein. PG - 157-63 LID - 10.1093/jb/mvr046 [doi] AB - The mature pro forms of the cardiac natriuretic peptides, atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP), are proteolytically processed to their active hormone forms (28 and 32 residues, respectively) and N-terminal (NT)-pro fragments (68 and 76 residues, respectively). Far-ultraviolet circular dichroism (UV CD), 1D and 2D-homonuclear nuclear magnetic resonance (NMR), size exclusion-high performance liquid chromatography (SE-HPLC) and analytical ultracentrifuge sedimentation equilibrium (AUCSE) data are obtained for NT-proANP. CD data showed a large negative molar ellipticity for NT-proANP of -14,800 degrees cm(2)/dmol at 199-200 nm. The intensity of the 1D-(1)H NMR spectra in the amide region for NT-proANP was very low and confined to ~8-8.6 ppm. Furthermore, cross-correlation resonance peaks were absent in the corresponding 2D-(1)H NOE spectra for NT-proANP in this region. The elution peak for this fragment from a G2000SW size-exclusion column was 20.4'; myoglobin (~17 K) was also eluted at 20.4'. No higher molecular weight oligomers were evident in the AUCSE experiments for NT-proANP. Collectively, the physical data demonstrate that NT-proANP, like NT-proBNP, is primarily a disordered, monomeric protein. Lastly, we compare the predictions from two in silico metaserver disorder algorithms, MeDor and MetaPrDOS, to the experimental data. FAU - Crimmins, Dan L AU - Crimmins DL AD - Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO 63110, USA. crimmins@pathology.wustl.edu FAU - Kao, Jeffrey L-F AU - Kao JL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110420 PL - England TA - J Biochem JT - Journal of biochemistry JID - 0376600 RN - 0 (N-terminal proatrial natriuretic peptide) RN - 0 (Protein Precursors) RN - 85637-73-6 (Atrial Natriuretic Factor) SB - IM MH - Amino Acid Sequence MH - Atrial Natriuretic Factor/*chemistry MH - Chromatography, High Pressure Liquid/methods MH - Circular Dichroism/methods MH - Computer Simulation MH - Humans MH - Magnetic Resonance Spectroscopy/methods MH - Molecular Sequence Data MH - Protein Precursors/*chemistry MH - Protein Structure, Quaternary MH - Protein Structure, Secondary EDAT- 2011/04/22 06:00 MHDA- 2011/12/13 00:00 CRDT- 2011/04/22 06:00 PHST- 2011/04/20 [aheadofprint] AID - mvr046 [pii] AID - 10.1093/jb/mvr046 [doi] PST - ppublish SO - J Biochem. 2011 Aug;150(2):157-63. doi: 10.1093/jb/mvr046. Epub 2011 Apr 20. PMID- 14623186 OWN - NLM STAT- MEDLINE DA - 20031119 DCOM- 20031218 LR - 20080515 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 334 IP - 3 DP - 2003 Nov 28 TI - The solution structure of human mitochondria fission protein Fis1 reveals a novel TPR-like helix bundle. PG - 445-58 AB - Fis1 in yeast localizes to the outer mitochondrial membrane and facilitates mitochondrial fission by forming protein complexes with Dnm1 and Mdv1. Fis1 orthologs exist in higher eukaryotes, suggesting that they are functionally conserved. In the present study, we cloned the human Fis1 ortholog that was predicted in a database, and determined the protein structure using NMR spectroscopy. Following a flexible N-terminal tail, six alpha-helices connected with short loops construct a single core domain. The C-terminal tail containing a transmembrane segment appears to be disordered. In the core domain, each of two sequentially adjacent helices forms a hairpin-like conformation, resulting in a six helix assembly forming a slightly twisted slab similar to that of a tandem array of tetratrico-peptide repeat (TPR) motif folds. Within this TPR-like core domain, no significant sequence similarity to the typical TPR motif is found. The structural analogy to the TPR-containing proteins suggests that Fis1 binds to other proteins at its concave hydrophobic surface. A simple composition of Fis1 comprised of a binding domain and a transmembrane segment indicates that the protein may function as a molecular adaptor on the mitochondrial outer membrane. In HeLa cells, however, increased levels in mitochondria-associated Fis1 did not result in mitochondrial translocation of Drp1, a potential binding partner of Fis1 implicated in the regulation of mitochondrial fission, suggesting that the interaction between Drp1 and Fis1 is regulated. FAU - Suzuki, Motoshi AU - Suzuki M AD - Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA. FAU - Jeong, Seon Yong AU - Jeong SY FAU - Karbowski, Mariusz AU - Karbowski M FAU - Youle, Richard J AU - Youle RJ FAU - Tjandra, Nico AU - Tjandra N LA - eng SI - PDB/1PC2 PT - Journal Article PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Cytoskeletal Proteins) RN - 0 (FIS1 protein, human) RN - 0 (Membrane Proteins) RN - 0 (Mitochondrial Proteins) RN - 0 (Solutions) RN - 0 (Utrophin) SB - IM MH - *Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - Cytoskeletal Proteins/metabolism MH - HeLa Cells MH - Humans MH - Membrane Proteins/metabolism MH - Mitochondria/*physiology MH - Mitochondrial Proteins/*chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - *Protein Conformation MH - Protein Transport MH - Sequence Homology, Amino Acid MH - Solutions MH - Utrophin EDAT- 2003/11/19 05:00 MHDA- 2003/12/19 05:00 CRDT- 2003/11/19 05:00 AID - S002228360301221X [pii] PST - ppublish SO - J Mol Biol. 2003 Nov 28;334(3):445-58. PMID- 17971447 OWN - NLM STAT- MEDLINE DA - 20071231 DCOM- 20080617 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 1 DP - 2008 Jan 4 TI - Virulence factor of potato virus Y, genome-attached terminal protein VPg, is a highly disordered protein. PG - 213-21 AB - Potato virus Y (PVY) is a common potyvirus of agricultural importance, belonging to the picornavirus superfamily of RNA plus-stranded viruses. A covalently linked virus-encoded protein VPg required for virus infectivity is situated at the 5' end of potyvirus RNA. VPg seems to be involved in multiple interactions, both with other viral products and host proteins. VPgs of potyviruses have no known homologs, and there is no atomic structure available. To understand the molecular basis of VPg multifunctionality, we have analyzed structural features of VPg from PVY using structure prediction programs, functional assays, and biochemical and biophysical analyses. Structure predictions suggest that VPg exists in a natively unfolded conformation. In contrast with ordered proteins, PVY VPg is not denatured by elevated temperatures, has sedimentation values incompatible with a compact globular form, and shows a CD spectrum of a highly disordered protein, and HET-HETSOFAST NMR analysis suggests the presence of large unstructured regions. Although VPg has a propensity to form dimers, no functional differences were seen between the monomer and dimer. These data strongly suggest that the VPg of PVY should be classified among intrinsically disordered proteins. Intrinsic disorder lies at the basis of VPg multifunctionality, which is necessary for virus survival in the host. FAU - Grzela, Renata AU - Grzela R AD - Institut de Biologie Structurale JP Ebel, CEA/CNRS, Universite Joseph Fourier, 41 rue Jules Horowitz, F-38027 Grenoble, France. FAU - Szolajska, Ewa AU - Szolajska E FAU - Ebel, Christine AU - Ebel C FAU - Madern, Dominique AU - Madern D FAU - Favier, Adrien AU - Favier A FAU - Wojtal, Izabela AU - Wojtal I FAU - Zagorski, Wlodzimierz AU - Zagorski W FAU - Chroboczek, Jadwiga AU - Chroboczek J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20071030 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Viral Proteins) RN - 0 (Virulence Factors) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Dimerization MH - Electrophoresis, Polyacrylamide Gel MH - *Genome, Viral MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Potyvirus/genetics/*metabolism MH - Temperature MH - Viral Proteins/chemistry/genetics/*metabolism MH - Virulence Factors/chemistry/genetics/*metabolism EDAT- 2007/11/01 09:00 MHDA- 2008/06/18 09:00 CRDT- 2007/11/01 09:00 PHST- 2007/10/30 [aheadofprint] AID - M705666200 [pii] AID - 10.1074/jbc.M705666200 [doi] PST - ppublish SO - J Biol Chem. 2008 Jan 4;283(1):213-21. Epub 2007 Oct 30. PMID- 3220257 OWN - NLM STAT- MEDLINE DA - 19890321 DCOM- 19890321 LR - 20101118 IS - 0378-1119 (Print) IS - 0378-1119 (Linking) VI - 68 IP - 2 DP - 1988 Sep 7 TI - Sequence and structure of the mouse gene coding for the largest neurofilament subunit. PG - 307-14 AB - We have determined the complete nucleotide sequence of the mouse gene encoding the neurofilament NF-H protein. The C-terminal domain of NF-H is very rich in charged amino acids (aa) and contains a 3-aa sequence, Lys-Ser-Pro, that is repeated 51 times within a stretch of 368 aa. The location of this serine-rich repeat in the phosphorylated domain of NF-H indicates that it represents the major protein kinase recognition site. The nfh gene shares two common intron positions with the nfl and nfm genes, but has an additional intron that occurs at a location equivalent to one of the introns in non-neuronal intermediate filament-coding genes. This additional nfh intron may have been acquired via duplication of a primordial intermediate filament gene. FAU - Julien, J P AU - Julien JP AD - Institut du Cancer de Montreal, Centre Hospitalier Notre-Dame, Canada. FAU - Cote, F AU - Cote F FAU - Beaudet, L AU - Beaudet L FAU - Sidky, M AU - Sidky M FAU - Flavell, D AU - Flavell D FAU - Grosveld, F AU - Grosveld F FAU - Mushynski, W AU - Mushynski W LA - eng SI - GENBANK/M21497 SI - GENBANK/M23349 SI - GENBANK/M24494 SI - GENBANK/M24495 SI - GENBANK/M24496 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - Gene JT - Gene JID - 7706761 RN - 0 (Intermediate Filament Proteins) RN - 0 (Macromolecular Substances) RN - 0 (Neurofilament Proteins) RN - 108688-71-7 (neurofilament protein H) SB - IM SB - S MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Biological Evolution MH - Brain/metabolism MH - *Genes MH - Intermediate Filament Proteins/*genetics MH - Introns MH - Macromolecular Substances MH - Mice MH - Molecular Sequence Data MH - *Neurofilament Proteins MH - Restriction Mapping EDAT- 1988/09/07 MHDA- 1988/09/07 00:01 CRDT- 1988/09/07 00:00 PST - ppublish SO - Gene. 1988 Sep 7;68(2):307-14. PMID- 12644649 OWN - NLM STAT- MEDLINE DA - 20030319 DCOM- 20030617 LR - 20140611 IS - 0032-0889 (Print) IS - 0032-0889 (Linking) VI - 131 IP - 3 DP - 2003 Mar TI - Conformation of a group 2 late embryogenesis abundant protein from soybean. Evidence of poly (L-proline)-type II structure. PG - 963-75 AB - Late embryogenesis abundant (LEA) proteins are members of a large group of hydrophilic, glycine-rich proteins found in plants, algae, fungi, and bacteria known collectively as hydrophilins that are preferentially expressed in response to dehydration or hyperosmotic stress. Group 2 LEA (dehydrins or responsive to abscisic acid) proteins are postulated to stabilize macromolecules against damage by freezing, dehydration, ionic, or osmotic stress. However, the structural and physicochemical properties of group 2 LEA proteins that account for such functions remain unknown. We have analyzed the structural properties of a recombinant form of a soybean (Glycine max) group 2 LEA (rGmDHN1). Differential scanning calorimetry of purified rGmDHN1 demonstrated that the protein does not display a cooperative unfolding transition upon heating. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein is in a largely hydrated and unstructured conformation in solution. However, ultraviolet absorption and circular dichroism measurements collected at different temperatures showed that the protein exists in equilibrium between two extended conformational states: unordered and left-handed extended helical or poly (L-proline)-type II structures. It is estimated that 27% of the residues of rGmDHN1 adopt or poly (L-proline)-type II-like helical conformation at 12 degrees C. The content of extended helix gradually decreases to 15% as the temperature is increased to 80 degrees C. Studies of the conformation of the protein in solution in the presence of liposomes, trifluoroethanol, and sodium dodecyl sulfate indicated that rGmDHN1 has a very low intrinsic ability to adopt alpha-helical structure and to interact with phospholipid bilayers through amphipathic alpha-helices. The ability of the protein to remain in a highly extended conformation at low temperatures could constitute the basis of the functional role of GmDHN1 in the prevention of freezing, desiccation, ionic, or osmotic stress-related damage to macromolecular structures. FAU - Soulages, Jose L AU - Soulages JL AD - Department of Biochemistry and Molecular Biology, 355 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078-0454, USA. FAU - Kim, Kangmin AU - Kim K FAU - Arrese, Estela L AU - Arrese EL FAU - Walters, Christina AU - Walters C FAU - Cushman, John C AU - Cushman JC LA - eng GR - GM55622/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Plant Physiol JT - Plant physiology JID - 0401224 RN - 0 (Lipids) RN - 0 (Liposomes) RN - 0 (Plant Proteins) RN - 0 (Soybean Proteins) RN - 0 (late embryogenesis abundant protein, plant) RN - 134711-03-8 (dehydrin proteins, plant) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - 42HK56048U (Tyrosine) RN - 75-89-8 (Trifluoroethanol) RN - 9DLQ4CIU6V (Proline) SB - IM MH - Adaptation, Physiological/physiology MH - Amino Acid Sequence MH - Circular Dichroism MH - Gene Expression Regulation, Plant MH - Lipid Metabolism MH - Lipids/chemistry MH - Liposomes/pharmacology MH - Molecular Sequence Data MH - Plant Proteins/chemistry/*genetics/*metabolism MH - Proline/chemistry/*metabolism MH - Protein Conformation MH - Protein Structure, Secondary/drug effects MH - Sodium Dodecyl Sulfate/pharmacology MH - Soybean Proteins/chemistry/genetics/*metabolism MH - Soybeans/genetics/*metabolism MH - Spectrophotometry, Ultraviolet MH - Temperature MH - Trifluoroethanol/pharmacology MH - Tyrosine/chemistry/metabolism PMC - PMC166862 OID - NLM: PMC166862 EDAT- 2003/03/20 04:00 MHDA- 2003/06/18 05:00 CRDT- 2003/03/20 04:00 AID - 10.1104/pp.015891 [doi] PST - ppublish SO - Plant Physiol. 2003 Mar;131(3):963-75. PMID- 24115198 OWN - NLM STAT- MEDLINE DA - 20140306 DCOM- 20141118 LR - 20150422 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 82 IP - 4 DP - 2014 Apr TI - Intrinsically disordered regions in autophagy proteins. PG - 565-78 LID - 10.1002/prot.24424 [doi] AB - Autophagy is an essential eukaryotic pathway required for cellular homeostasis. Numerous key autophagy effectors and regulators have been identified, but the mechanism by which they carry out their function in autophagy is not fully understood. Our rigorous bioinformatic analysis shows that the majority of key human autophagy proteins include intrinsically disordered regions (IDRs), which are sequences lacking stable secondary and tertiary structure; suggesting that IDRs play an important, yet hitherto uninvestigated, role in autophagy. Available crystal structures corroborate the absence of structure in some of these predicted IDRs. Regions of orthologs equivalent to the IDRs predicted in the human autophagy proteins are poorly conserved, indicating that these regions may have diverse functions in different homologs. We also show that IDRs predicted in human proteins contain several regions predicted to facilitate protein-protein interactions, and delineate the network of proteins that interact with each predicted IDR-containing autophagy protein, suggesting that many of these interactions may involve IDRs. Lastly, we experimentally show that a BCL2 homology 3 domain (BH3D), within the key autophagy effector BECN1 is an IDR. This BH3D undergoes a dramatic conformational change from coil to alpha-helix upon binding to BCL2s, with the C-terminal half of this BH3D constituting a binding motif, which serves to anchor the interaction of the BH3D to BCL2s. The information presented here will help inform future in-depth investigations of the biological role and mechanism of IDRs in autophagy proteins. CI - Copyright (c) 2013 Wiley Periodicals, Inc. FAU - Mei, Yang AU - Mei Y AD - Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050. FAU - Su, Minfei AU - Su M FAU - Soni, Gaurav AU - Soni G FAU - Salem, Saeed AU - Salem S FAU - Colbert, Christopher L AU - Colbert CL FAU - Sinha, Sangita C AU - Sinha SC LA - eng GR - P20 RR015566/RR/NCRR NIH HHS/United States GR - P20-GM103442/GM/NIGMS NIH HHS/United States GR - P20-RR015566/RR/NCRR NIH HHS/United States GR - P20-RR016471/RR/NCRR NIH HHS/United States GR - P30 GM103332/GM/NIGMS NIH HHS/United States GR - P30 GM103332/GM/NIGMS NIH HHS/United States GR - R21 AI078108/AI/NIAID NIH HHS/United States GR - R21-AI078198/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20131017 PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Apoptosis Regulatory Proteins) RN - 0 (BECN1 protein, human) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Membrane Proteins) RN - 0 (Proto-Oncogene Proteins c-bcl-2) SB - IM MH - Amino Acid Sequence MH - Apoptosis Regulatory Proteins/*metabolism MH - Autophagy MH - Humans MH - Intrinsically Disordered Proteins/*metabolism MH - Membrane Proteins/*metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Interaction Domains and Motifs MH - Proto-Oncogene Proteins c-bcl-2/*metabolism MH - Sequence Alignment PMC - PMC3949125 MID - NIHMS529110 OID - NLM: NIHMS529110 OID - NLM: PMC3949125 OTO - NOTNLM OT - BCL2 OT - BECN1 OT - BH3 domain OT - autophagy OT - natively unstructured proteins OT - protein interactions OT - sequence analysis EDAT- 2013/10/12 06:00 MHDA- 2014/11/19 06:00 CRDT- 2013/10/12 06:00 PHST- 2013/05/15 [received] PHST- 2013/08/15 [revised] PHST- 2013/09/02 [accepted] PHST- 2013/10/17 [aheadofprint] AID - 10.1002/prot.24424 [doi] PST - ppublish SO - Proteins. 2014 Apr;82(4):565-78. doi: 10.1002/prot.24424. Epub 2013 Oct 17. PMID- 25116620 OWN - NLM STAT- MEDLINE DA - 20140813 DCOM- 20150413 IS - 0973-7138 (Electronic) IS - 0250-5991 (Linking) VI - 39 IP - 4 DP - 2014 Sep TI - Conserved C-terminal nascent peptide binding domain of HYPK facilitates its chaperone-like activity. PG - 659-72 AB - Human HYPK (Huntingtin Yeast-two-hybrid Protein K) is an intrinsically unstructured chaperone-like protein with no sequence homology to known chaperones. HYPK is also known to be a part of ribosome-associated protein complex and present in polysomes. The objective of the present study was to investigate the evolutionary influence on HYPK primary structure and its impact on the protein's function. Amino acid sequence analysis revealed 105 orthologs of human HYPK from plants, lower invertebrates to mammals. C-terminal part of HYPK was found to be particularly conserved and to contain nascent polypeptide-associated alpha subunit (NPAA) domain. This region experiences highest selection pressure, signifying its importance in the structural and functional evolution. NPAA domain of human HYPK has unique amino acid composition preferring glutamic acid and happens to be more stable from a conformational point of view having higher content of a-helices than the rest. Cell biology studies indicate that overexpressed C-terminal human HYPK can interact with nascent proteins, co-localizes with huntingtin, increases cell viability and decreases caspase activities in Huntington's disease (HD) cell culture model. This domain is found to be required for the chaperone-like activity of HYPK in vivo. Our study suggested that by virtue of its flexibility and nascent peptide binding activity, HYPK may play an important role in assisting protein (re)folding. FAU - Raychaudhuri, Swasti AU - Raychaudhuri S AD - Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata 700 064, India, rcswasti@ccmb.res.in. FAU - Banerjee, Rachana AU - Banerjee R FAU - Mukhopadhyay, Subhasish AU - Mukhopadhyay S FAU - Bhattacharyya, Nitai P AU - Bhattacharyya NP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - India TA - J Biosci JT - Journal of biosciences JID - 8100809 RN - 0 (Carrier Proteins) RN - 0 (DNA Primers) RN - 0 (HYPK protein, human) RN - 0 (Molecular Chaperones) RN - 0 (Tetrazolium Salts) RN - 0 (Thiazoles) RN - 0 (nascent-polypeptide-associated complex) RN - 298-93-1 (thiazolyl blue) SB - IM MH - Amino Acid Sequence MH - Carrier Proteins/*genetics/*metabolism MH - Cluster Analysis MH - Conserved Sequence/genetics MH - DNA Primers/genetics MH - Humans MH - Microscopy, Confocal MH - Models, Genetic MH - Molecular Chaperones/genetics/*metabolism MH - Molecular Sequence Data MH - *Phylogeny MH - Protein Conformation MH - Protein Structure, Tertiary/genetics MH - Sequence Analysis, Protein MH - Sequence Homology MH - Tetrazolium Salts MH - Thiazoles EDAT- 2014/08/15 06:00 MHDA- 2015/04/14 06:00 CRDT- 2014/08/14 06:00 PST - ppublish SO - J Biosci. 2014 Sep;39(4):659-72. PMID- 22315227 OWN - NLM STAT- MEDLINE DA - 20120507 DCOM- 20120730 LR - 20141019 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 19 DP - 2012 May 4 TI - alpha-Synuclein in central nervous system and from erythrocytes, mammalian cells, and Escherichia coli exists predominantly as disordered monomer. PG - 15345-64 LID - 10.1074/jbc.M111.318949 [doi] AB - Since the discovery and isolation of alpha-synuclein (alpha-syn) from human brains, it has been widely accepted that it exists as an intrinsically disordered monomeric protein. Two recent studies suggested that alpha-syn produced in Escherichia coli or isolated from mammalian cells and red blood cells exists predominantly as a tetramer that is rich in alpha-helical structure (Bartels, T., Choi, J. G., and Selkoe, D. J. (2011) Nature 477, 107-110; Wang, W., Perovic, I., Chittuluru, J., Kaganovich, A., Nguyen, L. T. T., Liao, J., Auclair, J. R., Johnson, D., Landeru, A., Simorellis, A. K., Ju, S., Cookson, M. R., Asturias, F. J., Agar, J. N., Webb, B. N., Kang, C., Ringe, D., Petsko, G. A., Pochapsky, T. C., and Hoang, Q. Q. (2011) Proc. Natl. Acad. Sci. 108, 17797-17802). However, it remains unknown whether or not this putative tetramer is the main physiological form of alpha-syn in the brain. In this study, we investigated the oligomeric state of alpha-syn in mouse, rat, and human brains. To assess the conformational and oligomeric state of native alpha-syn in complex mixtures, we generated alpha-syn standards of known quaternary structure and conformational properties and compared the behavior of endogenously expressed alpha-syn to these standards using native and denaturing gel electrophoresis techniques, size-exclusion chromatography, and an oligomer-specific ELISA. Our findings demonstrate that both human and rodent alpha-syn expressed in the central nervous system exist predominantly as an unfolded monomer. Similar results were observed when human alpha-syn was expressed in mouse and rat brains as well as mammalian cell lines (HEK293, HeLa, and SH-SY5Y). Furthermore, we show that alpha-syn expressed in E. coli and purified under denaturing or nondenaturing conditions, whether as a free protein or as a fusion construct with GST, is monomeric and adopts a disordered conformation after GST removal. These results do not rule out the possibility that alpha-syn becomes structured upon interaction with other proteins and/or biological membranes. FAU - Fauvet, Bruno AU - Fauvet B AD - Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Station 19, School of Life Sciences, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland. FAU - Mbefo, Martial K AU - Mbefo MK FAU - Fares, Mohamed-Bilal AU - Fares MB FAU - Desobry, Carole AU - Desobry C FAU - Michael, Sarah AU - Michael S FAU - Ardah, Mustafa T AU - Ardah MT FAU - Tsika, Elpida AU - Tsika E FAU - Coune, Philippe AU - Coune P FAU - Prudent, Michel AU - Prudent M FAU - Lion, Niels AU - Lion N FAU - Eliezer, David AU - Eliezer D FAU - Moore, Darren J AU - Moore DJ FAU - Schneider, Bernard AU - Schneider B FAU - Aebischer, Patrick AU - Aebischer P FAU - El-Agnaf, Omar M AU - El-Agnaf OM FAU - Masliah, Eliezer AU - Masliah E FAU - Lashuel, Hilal A AU - Lashuel HA LA - eng GR - AG019391/AG/NIA NIH HHS/United States GR - R37 AG018440/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120207 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Recombinant Proteins) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Animals MH - Brain/*metabolism MH - Cell Line, Tumor MH - Central Nervous System/metabolism MH - Chromatography, Gel MH - Enzyme-Linked Immunosorbent Assay MH - Erythrocytes/*metabolism MH - Escherichia coli/genetics MH - HEK293 Cells MH - HeLa Cells MH - Humans MH - Immunoblotting MH - Mice MH - Mice, Transgenic MH - Molecular Sequence Data MH - Mutation MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Unfolding MH - Rats MH - Rats, Sprague-Dawley MH - Recombinant Proteins/chemistry/*metabolism MH - alpha-Synuclein/chemistry/genetics/*metabolism PMC - PMC3346117 OID - NLM: PMC3346117 EDAT- 2012/02/09 06:00 MHDA- 2012/07/31 06:00 CRDT- 2012/02/09 06:00 PHST- 2012/02/07 [aheadofprint] PHST- 2012/02/07 [aheadofprint] PHST- 2012/02/07 [aheadofprint] PHST- 2012/02/08 [aheadofprint] PHST- 2012/02/09 [aheadofprint] AID - M111.318949 [pii] AID - 10.1074/jbc.M111.318949 [doi] PST - ppublish SO - J Biol Chem. 2012 May 4;287(19):15345-64. doi: 10.1074/jbc.M111.318949. Epub 2012 Feb 7. PMID- 19165719 OWN - NLM STAT- MEDLINE DA - 20090205 DCOM- 20090807 LR - 20140901 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 18 IP - 2 DP - 2009 Feb TI - Residual structure within the disordered C-terminal segment of p21(Waf1/Cip1/Sdi1) and its implications for molecular recognition. PG - 337-47 LID - 10.1002/pro.34 [doi] AB - Probably the most unusual class of proteins in nature is the intrinsically unstructured proteins (IUPs), because they are not structured yet play essential roles in protein-protein signaling. Many IUPs can bind different proteins, and in many cases, adopt different bound conformations. The p21 protein is a small IUP (164 residues) that is ubiquitous in cellular signaling, for example, cell cycle control, apoptosis, transcription, differentiation, and so forth; it binds to approximately 25 targets. How does this small, unstructured protein recognize each of these targets with high affinity? Here, we characterize residual structural elements of the C-terminal segment of p21 encompassing residues 145-164 using a combination of NMR measurements and molecular dynamics simulations. The N-terminal half of the peptide has a significant helical propensity which is recognized by calmodulin while the C-terminal half of the peptide prefers extended conformations that facilitate binding to the proliferating cell nuclear antigen (PCNA). Our results suggest that the final bound conformations of p21 (145-164) pre-exist in the free peptide even without its binding partners. While the conformational flexibility of the p21 peptide is essential for adapting to diverse binding environments, the intrinsic structural preferences of the free peptide enable promiscuous yet high affinity binding to a diverse array of molecular targets. FAU - Yoon, Mi-Kyung AU - Yoon MK AD - Department of Chemistry and National Creative Research Initiative Center, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejon, Republic of Korea. FAU - Venkatachalam, Veena AU - Venkatachalam V FAU - Huang, Austin AU - Huang A FAU - Choi, Byong-Seok AU - Choi BS FAU - Stultz, Collin M AU - Stultz CM FAU - Chou, James J AU - Chou JJ LA - eng PT - Journal Article PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (CDKN1A protein, human) RN - 0 (Calmodulin) RN - 0 (Cyclin-Dependent Kinase Inhibitor p21) RN - 0 (Peptide Fragments) RN - 0 (Proliferating Cell Nuclear Antigen) RN - SY7Q814VUP (Calcium) SB - IM MH - Algorithms MH - Binding Sites/physiology MH - Calcium/metabolism MH - Calmodulin/metabolism MH - Circular Dichroism MH - Cyclin-Dependent Kinase Inhibitor p21/*chemistry/metabolism MH - Humans MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/*chemistry/metabolism MH - Proliferating Cell Nuclear Antigen/metabolism MH - Protein Binding/physiology MH - Protein Conformation MH - Protein Folding PMC - PMC2708053 OID - NLM: PMC2708053 EDAT- 2009/01/24 09:00 MHDA- 2009/08/08 09:00 CRDT- 2009/01/24 09:00 AID - 10.1002/pro.34 [doi] PST - ppublish SO - Protein Sci. 2009 Feb;18(2):337-47. doi: 10.1002/pro.34. PMID- 19481090 OWN - NLM STAT- MEDLINE DA - 20090626 DCOM- 20090715 LR - 20140919 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 390 IP - 3 DP - 2009 Jul 17 TI - Effect of pseudorepeat rearrangement on alpha-synuclein misfolding, vesicle binding, and micelle binding. PG - 516-29 LID - 10.1016/j.jmb.2009.05.058 [doi] AB - The pathological and physiological hallmarks of the protein alpha-synuclein (aS) are its misfolding into cytotoxic aggregates and its binding to synaptic vesicles, respectively. Both events are mediated by seven 11-residue amphiphilic pseudorepeats and, most generally, involve a transition from intrinsically unstructured conformations to structured conformations. Based on aS interactions with aggregation-inhibiting small molecules, an aS variant termed shuffled alpha-synuclein (SaS), wherein the first six pseudorepeats had been rearranged, was introduced. Here, the effects of this rearrangement on misfolding, vesicle binding, and micelle binding are examined in reference to aS and beta-synuclein to study the sequence characteristics underlying these processes. Fibrillization correlates with the distinct clustering of residues with high beta-sheet propensities, while vesicle affinities depend on the mode of pseudorepeat interchange and loss. In the presence of micelles, the pseudorepeat region of SaS adopts an essentially continuous helix, whereas aS and beta-synuclein encounter a distinct helix break, indicating that a more homogeneous distribution of surfactant affinities in SaS prevented the formation of an extensive helix break in the micelle-bound state. By demonstrating the importance of the distribution of beta-sheet propensities and by revealing inhomogeneous aS surfactant affinities, the present study provides novel insights into two central themes of synuclein biology. FAU - Rao, Jampani Nageswara AU - Rao JN AD - Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, 90033, USA. FAU - Kim, Yujin E AU - Kim YE FAU - Park, Leena S AU - Park LS FAU - Ulmer, Tobias S AU - Ulmer TS LA - eng GR - HL089726/HL/NHLBI NIH HHS/United States GR - R01 HL089726/HL/NHLBI NIH HHS/United States GR - R01 HL089726-02/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20090527 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Micelles) RN - 0 (alpha-Synuclein) SB - IM MH - DNA Shuffling MH - *Micelles MH - Microscopy, Electron, Transmission MH - Models, Biological MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - *Protein Folding MH - Recombination, Genetic MH - Repetitive Sequences, Amino Acid/*genetics MH - alpha-Synuclein/*chemistry/genetics/*metabolism PMC - PMC2731582 MID - NIHMS119968 OID - NLM: NIHMS119968 OID - NLM: PMC2731582 EDAT- 2009/06/02 09:00 MHDA- 2009/07/16 09:00 CRDT- 2009/06/02 09:00 PHST- 2009/03/10 [received] PHST- 2009/05/14 [revised] PHST- 2009/05/18 [accepted] PHST- 2009/05/27 [aheadofprint] AID - S0022-2836(09)00628-7 [pii] AID - 10.1016/j.jmb.2009.05.058 [doi] PST - ppublish SO - J Mol Biol. 2009 Jul 17;390(3):516-29. doi: 10.1016/j.jmb.2009.05.058. Epub 2009 May 27. PMID- 12534279 OWN - NLM STAT- MEDLINE DA - 20030121 DCOM- 20030407 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 42 IP - 3 DP - 2003 Jan 28 TI - The N-terminal repeat domain of alpha-synuclein inhibits beta-sheet and amyloid fibril formation. PG - 672-8 AB - The conversion of alpha-synuclein into amyloid fibrils in the substantia nigra is linked to Parkinson's disease. Alpha-synuclein is natively unfolded in solution, but can be induced to form either alpha-helical or beta-sheet structure depending on its concentration and the solution conditions. The N-terminus of alpha-synuclein comprises seven 11-amino acid repeats (XKTKEGVXXXX) which can form an amphipathic alpha-helix. Why seven repeats, rather than six or eight, survived the evolutionary process is not clear. To probe this question, two sequence variants of alpha-synuclein, one with two fewer (del2) and one with two additional (plus2) repeats, were studied. As compared to wild-type alpha-synuclein, the plus2 variant disfavors the formation of beta-sheet-rich oligomers, including amyloid fibrils. In contrast, the truncated variant, del2, favors beta-sheet and fibril formation. We propose that the repeat number in WT alpha-synuclein represents an evolutionary balance between the functional conformer of alpha-synuclein (alpha-helix and/or random coil) and its pathogenic beta-sheet conformation. N-terminal truncation of alpha-synuclein may promote pathogenesis. FAU - Kessler, Jeffrey C AU - Kessler JC AD - Center for Neurologic Diseases, Brigham and Women's Hospital, and Department of Neurology, Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA. FAU - Rochet, Jean-Christophe AU - Rochet JC FAU - Lansbury, Peter T Jr AU - Lansbury PT Jr LA - eng GR - NS 38375/NS/NINDS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Nerve Tissue Proteins) RN - 0 (Peptide Fragments) RN - 0 (Propanols) RN - 0 (Protein Isoforms) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 920-66-1 (hexafluoroisopropanol) SB - IM MH - Amino Acid Sequence MH - Amyloid/*antagonists & inhibitors/*metabolism MH - Circular Dichroism MH - Cloning, Molecular MH - Humans MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*chemistry/genetics/*physiology/ultrastructure MH - Parkinson Disease/genetics/pathology MH - Peptide Fragments/*chemistry/genetics/*physiology/ultrastructure MH - Propanols/chemistry MH - Protein Folding MH - Protein Isoforms/biosynthesis/genetics/isolation & purification/ultrastructure MH - Protein Structure, Secondary/physiology MH - Protein Structure, Tertiary/genetics/physiology MH - Repetitive Sequences, Amino Acid/genetics/*physiology MH - Synucleins MH - alpha-Synuclein EDAT- 2003/01/22 04:00 MHDA- 2003/04/08 05:00 CRDT- 2003/01/22 04:00 AID - 10.1021/bi020429y [doi] PST - ppublish SO - Biochemistry. 2003 Jan 28;42(3):672-8. PMID- 9813018 OWN - NLM STAT- MEDLINE DA - 19981221 DCOM- 19981221 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 273 IP - 47 DP - 1998 Nov 20 TI - The binding of calcium to the B-repeat segment of SdrD, a cell surface protein of Staphylococcus aureus. PG - 31145-52 AB - In the Sdr family of Staphylococcus aureus cell surface proteins, three recently cloned members (Josefsson, E., McCrea, K., Ni Eidhin, D., O'Connell, D., Cox, J. A., Hook, M., and Foster, T. (1998) Microbiology, in press) display variable numbers of B-repeats, i.e. segments of 110-113 residues that probably make up one folding unit. Each B-repeat contains one conserved EF-hand motif and two acidic stretches. Equilibrium dialysis revealed that segment B1-B5 of SrdD contains 14 Ca2+-binding sites with high affinity ([Ca2+]0.5, 4 microM), whereas flow dialysis yielded 5 sites of high affinity (class I) and 10 of low affinity (class II). The discrepancy could be explained by the slow induction of high affinity in the class II sites. Kinetic experiments using fluorescent Ca2+ indicators corroborated slow binding of Ca2+ at the latter sites. Circular dichroism and Trp fluorescence showed that, whereas the Ca2+ form is well folded, the metal-free form seems strongly disorganized. The Ca2+-induced conformational changes comprise both fast and slow steps, giving thus a structural support for the induction of class II Ca2+-binding sites. The B-repeats may act as rulers or springs that modulate the distance between the interactive A region and the bacterial cell surface. FAU - Josefsson, E AU - Josefsson E AD - Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Dublin 2, Republic of Ireland. jos.cox@biochem.unie.ch FAU - O'Connell, D AU - O'Connell D FAU - Foster, T J AU - Foster TJ FAU - Durussel, I AU - Durussel I FAU - Cox, J A AU - Cox JA LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - 0 (Calcium-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SdrD protein, Staphylococcus aureus) RN - SY7Q814VUP (Calcium) SB - IM MH - *Bacterial Proteins MH - Binding Sites MH - Calcium/*metabolism MH - Calcium-Binding Proteins/chemistry/genetics/*metabolism MH - Circular Dichroism MH - Kinetics MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - *Repetitive Sequences, Amino Acid MH - Sequence Homology, Amino Acid MH - Spectrometry, Fluorescence MH - *Staphylococcus aureus MH - Thermodynamics MH - Titrimetry EDAT- 1998/11/13 MHDA- 1998/11/13 00:01 CRDT- 1998/11/13 00:00 PST - ppublish SO - J Biol Chem. 1998 Nov 20;273(47):31145-52. PMID- 16452621 OWN - NLM STAT- MEDLINE DA - 20060227 DCOM- 20060322 LR - 20140909 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 15 IP - 3 DP - 2006 Mar TI - Temperature-induced reversible conformational change in the first 100 residues of alpha-synuclein. PG - 602-8 AB - Natively disordered proteins are a growing class of anomalies to the structure-function paradigm. The natively disordered protein alpha-synuclein is the primary component of Lewy bodies, the cellular hallmark of Parkinson's disease. We noticed a dramatic difference in dilute solution 1H-15N Heteronuclear Single Quantum Coherence (HSQC) spectra of wild-type alpha-synuclein and two disease-related mutants (A30P and A53T), with spectra collected at 35 degrees C showing fewer cross-peaks than spectra acquired at 10 degrees C. Here, we show the change to be the result of a reversible conformational exchange linked to an increase in hydrodynamic radius and secondary structure as the temperature is raised. Combined with analytical ultracentrifugation data showing alpha-synuclein to be monomeric at both temperatures, we conclude that the poor quality of the 1H-15N HSQC spectra obtained at 35 degrees C is due to conformational fluctuations that occur on the proton chemical shift time scale. Using a truncated variant of alpha-synuclein, we show the conformational exchange occurs in the first 100 amino acids of the protein. Our data illustrate a key difference between globular and natively disordered proteins. The properties of globular proteins change little with solution conditions until they denature cooperatively, but the properties of natively disordered proteins can vary dramatically with solution conditions. FAU - McNulty, Brian C AU - McNulty BC AD - Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. FAU - Tripathy, Ashutosh AU - Tripathy A FAU - Young, Gregory B AU - Young GB FAU - Charlton, Lisa M AU - Charlton LM FAU - Orans, Jillian AU - Orans J FAU - Pielak, Gary J AU - Pielak GJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20060201 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Amino Acids) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acids/chemistry MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Protein Denaturation MH - Sequence Deletion MH - *Temperature MH - Ultracentrifugation MH - alpha-Synuclein/*chemistry/genetics PMC - PMC2249779 OID - NLM: PMC2249779 EDAT- 2006/02/03 09:00 MHDA- 2006/03/23 09:00 CRDT- 2006/02/03 09:00 PHST- 2006/02/01 [aheadofprint] AID - ps.051867106 [pii] AID - 10.1110/ps.051867106 [doi] PST - ppublish SO - Protein Sci. 2006 Mar;15(3):602-8. Epub 2006 Feb 1. PMID- 11380252 OWN - NLM STAT- MEDLINE DA - 20010530 DCOM- 20010816 LR - 20081121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 40 IP - 22 DP - 2001 Jun 5 TI - Expression of the Oct-1 transcription factor and characterization of its interactions with the Bob1 coactivator. PG - 6580-8 AB - The Oct-1 transcription factor regulates a variety of tissue-specific and general housekeeping genes by recruiting specialized coactivators of transcription. It acts synergistically with the B-cell-specific coactivator Bob1 (OCA-B, OBF-1) to stimulate transcription of immunoglobulin genes. To analyze Oct-1's interactions with Bob1 and other regulatory proteins, we have overexpressed and purified different functional domains of the recombinant proteins. A version of Oct-1 that encompasses the amino-terminal activation region and the POU DNA-binding domain was extensively characterized (OctDeltaC1; comprising residues 1-445). Using an in vitro transcription assay, we demonstrate that this fragment is sufficient and necessary to stimulate transcription from an immunoglobulin promoter with Bob1. It also coactivates from the herpes simplex virus ICPO promoter element in the presence of VP16. Using a range of spectroscopic and biophysical techniques, we demonstrate that the activation domains of Oct-1 and Bob1 have little globular structure and that they do not physically interact. Thus, their functional synergy is likely to arise by the co-recruitment of common factors as part of a larger regulatory assembly. We propose a hypothesis to explain why the activation domains of these and other transcription factors of metazoans have little if any intrinsic structure. FAU - Lee, L AU - Lee L AD - Department of Biochemistry, Cambridge University, 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAU - Stollar, E AU - Stollar E FAU - Chang, J AU - Chang J FAU - Grossmann, J G AU - Grossmann JG FAU - O'Brien, R AU - O'Brien R FAU - Ladbury, J AU - Ladbury J FAU - Carpenter, B AU - Carpenter B FAU - Roberts, S AU - Roberts S FAU - Luisi, B AU - Luisi B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA-Binding Proteins) RN - 0 (HCFC1 protein, human) RN - 0 (Host Cell Factor C1) RN - 0 (Octamer Transcription Factor-1) RN - 0 (Oligodeoxyribonucleotides) RN - 0 (POU2AF1 protein, human) RN - 0 (POU2F1 protein, human) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) SB - IM EIN - Biochemistry 2001 Jul 27;40(28):8430 MH - Amino Acid Sequence MH - Calorimetry MH - DNA/metabolism MH - DNA-Binding Proteins/biosynthesis/*genetics/isolation & purification/*metabolism MH - Drug Synergism MH - Genetic Vectors/metabolism MH - Host Cell Factor C1 MH - Humans MH - Molecular Sequence Data MH - Octamer Transcription Factor-1 MH - Oligodeoxyribonucleotides/metabolism MH - Peptide Fragments/biosynthesis/genetics/isolation & purification/metabolism MH - Protein Structure, Tertiary/genetics MH - Recombinant Fusion Proteins/biosynthesis/isolation & purification/metabolism MH - Scattering, Radiation MH - Trans-Activators/genetics/*metabolism MH - Transcription Factors/biosynthesis/*genetics/isolation & purification/*metabolism MH - Transcriptional Activation/genetics MH - X-Rays EDAT- 2001/06/09 10:00 MHDA- 2001/08/17 10:01 CRDT- 2001/06/09 10:00 AID - bi010095x [pii] PST - ppublish SO - Biochemistry. 2001 Jun 5;40(22):6580-8. PMID- 17426451 OWN - NLM STAT- MEDLINE DA - 20070504 DCOM- 20070807 LR - 20071004 IS - 1551-4005 (Electronic) IS - 1551-4005 (Linking) VI - 6 IP - 9 DP - 2007 May 2 TI - p27Kip1 metabolism: a fascinating labyrinth. PG - 1053-61 AB - The progression through the phases of cell division cycle is regulated by different cyclins and cyclin-dependent kinases (CDKs) complexes. Due to their key function, the activity of cyclin/CDK complexes is controlled by several mechanisms, including the inhibition by a number of proteins collectively defined CDK inhibitors or CKIs. Among the CKIs, p27Kip1 represents a protein of central activity for the control of several phenotypes, including proliferation, differentiation and malignant transformation. p27Kip1 belongs to the growing family of "natively unfolded," "intrinsically disordered" or "intrinsically unstructured" proteins. The disorder proteins present a very large number of possible conformations that, after the binding, converge to a well-defined structure with an extraordinary affinity for the target. As matter of fact, the absence of a pre-existing folding strongly facilitates p27Kip1 interaction with a number of targets. Until recently, p27Kip1 has been solely viewed as a nuclear protein with the function of modulating cyclin-CDK activity and hence, cell cycle progression. However, exhaustive studies have now demonstrated that the protein plays additional roles outside of the nucleus, including, particularly, the control of cell motility. Thus, the cellular localization is of fundamental importance in p27Kip1 function. Accordingly, at least two different mechanisms of degradation, occurring either in the nucleus or in the cytosol, have been observed. Convincing evidences have demonstrated that p27Kip1 is a phosphoprotein showing at least six to eight phosphorylatable residues. However, the precise functional roles of the phosphorylations and the identification of the kinases responsible for the post-synthetic modifications are still debated. In this brief review, we will report the Literature data that connect the post-synthetic modifications of p27Kip1 with its function, localization and metabolism. The picture that emerges demonstrates that several of the pieces of the CKI metabolism are still nebulous. FAU - Borriello, Adriana AU - Borriello A AD - Department of Biochemistry and Biophysics F. Cedrangolo, Second University of Naples, Naples, Italy. FAU - Cucciolla, Valeria AU - Cucciolla V FAU - Oliva, Adriana AU - Oliva A FAU - Zappia, Vincenzo AU - Zappia V FAU - Della Ragione, Fulvio AU - Della Ragione F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20070513 PL - United States TA - Cell Cycle JT - Cell cycle (Georgetown, Tex.) JID - 101137841 RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) SB - IM MH - Animals MH - Cell Cycle/*physiology MH - Cyclin-Dependent Kinase Inhibitor p27/*metabolism MH - Humans MH - Models, Biological MH - Signal Transduction RF - 122 EDAT- 2007/04/12 09:00 MHDA- 2007/08/08 09:00 CRDT- 2007/04/12 09:00 PHST- 2007/05/13 [aheadofprint] AID - 4142 [pii] PST - ppublish SO - Cell Cycle. 2007 May 2;6(9):1053-61. Epub 2007 May 13. PMID- 24652833 OWN - NLM STAT- MEDLINE DA - 20140602 DCOM- 20150511 IS - 1477-9137 (Electronic) IS - 0021-9533 (Linking) VI - 127 IP - Pt 11 DP - 2014 Jun 1 TI - Spd2 assists Spd1 in the modulation of ribonucleotide reductase architecture but does not regulate deoxynucleotide pools. PG - 2460-70 LID - 10.1242/jcs.139816 [doi] AB - In yeasts, small intrinsically disordered proteins (IDPs) modulate ribonucleotide reductase (RNR) activity to ensure an optimal supply of dNTPs for DNA synthesis. The Schizosaccharomyces pombe Spd1 protein can directly inhibit the large RNR subunit (R1), import the small subunit (R2) into the nucleus and induce an architectural change in the R1-R2 holocomplex. Here, we report the characterization of Spd2, a protein with sequence similarity to Spd1. We show that Spd2 is a CRL4(Cdt2)-controlled IDP that functions together with Spd1 in the DNA damage response and in modulation of RNR architecture. However, Spd2 does not regulate dNTP pools and R2 nuclear import. Furthermore, deletion of spd2 only weakly suppresses the Rad3(ATR) checkpoint dependency of CRL4(Cdt2) mutants. However, when we raised intracellular dNTP pools by inactivation of RNR feedback inhibition, deletion of spd2 could suppress the checkpoint dependency of CRL4(Cdt2) mutant cells to the same extent as deletion of spd1. Collectively, these observations suggest that Spd1 on its own regulates dNTP pools, whereas in combination with Spd2 it modulates RNR architecture and sensitizes cells to DNA damage. CI - (c) 2014. Published by The Company of Biologists Ltd. FAU - Vejrup-Hansen, Rasmus AU - Vejrup-Hansen R AD - Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N., Denmark. FAU - Fleck, Oliver AU - Fleck O AD - Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N., Denmark NWCR Institute, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK. FAU - Landvad, Katrine AU - Landvad K AD - Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N., Denmark. FAU - Fahnoe, Ulrik AU - Fahnoe U AD - Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N., Denmark. FAU - Broendum, Sebastian S AU - Broendum SS AD - Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N., Denmark. FAU - Schreurs, Ann-Sofie AU - Schreurs AS AD - Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK. FAU - Kragelund, Birthe B AU - Kragelund BB AD - Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N., Denmark. FAU - Carr, Antony M AU - Carr AM AD - Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK. FAU - Holmberg, Christian AU - Holmberg C AD - Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N., Denmark. FAU - Nielsen, Olaf AU - Nielsen O AD - Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N., Denmark onigen@bio.ku.dk. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140320 PL - England TA - J Cell Sci JT - Journal of cell science JID - 0052457 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Cdt2 protein, S pombe) RN - 0 (Cell Cycle Proteins) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Schizosaccharomyces pombe Proteins) RN - 0 (Spd1 protein, S pombe) RN - 0 (Spd2 protein, S pombe) RN - EC 1.17.4.- (Ribonucleotide Reductases) RN - EC 2.7.1.- (rad3 protein, S pombe) RN - EC 2.7.1.11 (Checkpoint Kinase 2) RN - EC 3.1.3.- (Nucleotidases) RN - EC 3.1.3.34 (deoxynucleotide 3'-phosphatase) SB - IM MH - Adaptor Proteins, Signal Transducing/metabolism MH - Allosteric Regulation/genetics MH - Amino Acid Sequence MH - Cell Cycle/genetics MH - Cell Cycle Proteins/genetics/isolation & purification/*metabolism MH - Checkpoint Kinase 2/metabolism MH - DNA Repair/genetics MH - Intrinsically Disordered Proteins/genetics/isolation & purification/*metabolism MH - Molecular Sequence Data MH - Mutation/genetics MH - Nucleotidases/metabolism MH - Protein Conformation MH - Ribonucleotide Reductases/*metabolism MH - Schizosaccharomyces/genetics/*metabolism MH - Schizosaccharomyces pombe Proteins/genetics/isolation & purification/*metabolism MH - Sequence Homology, Amino Acid OTO - NOTNLM OT - CRL4Cdt2 ubiquitin ligase OT - Cancer model OT - Genome stability OT - Intrinsically disordered proteins OT - Ribonucleotide reductase OT - S. pombe EDAT- 2014/03/22 06:00 MHDA- 2015/05/12 06:00 CRDT- 2014/03/22 06:00 PHST- 2014/03/20 [aheadofprint] AID - jcs.139816 [pii] AID - 10.1242/jcs.139816 [doi] PST - ppublish SO - J Cell Sci. 2014 Jun 1;127(Pt 11):2460-70. doi: 10.1242/jcs.139816. Epub 2014 Mar 20. PMID- 20448467 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20110106 DCOM- 20110418 LR - 20130529 IS - 1559-2324 (Electronic) IS - 1559-2316 (Linking) VI - 5 IP - 7 DP - 2010 Jul TI - PCaPs, possible regulators of PtdInsP signals on plasma membrane. PG - 848-50 LID - 10.1093/pcp/pcq003. [doi] AB - In plants, Ca(2+), phosphatidylinositol phosphates (PtdInsPs) and inositol phosphates are major components of intracellular signaling. Several kinds of proteins and enzymes, such as calmodulin (CaM), protein kinase, protein phosphatase, and the Ca(2+) channel, mediate the signaling. Two new Ca(2+)-binding proteins were identified from Arabidopsis thaliana and named PCaP1 and PCaP2 [plasma membrane (PM)-associated Ca(2+) (cation)-binding protein 1 and 2]. PCaP1 has an intrinsically disordered region in the central and C-terminal parts. The PCaP1 gene is expressed in most tissues and the PCaP2 gene is expressed predominantly in root hairs and pollen tubes. We recently demonstrated that these proteins are N-myristoylated, stably anchored in the PM, and are bound with phosphatidylinositol phosphates, especially PtdInsP2s. Here we propose a model for the switching mechanism of Ca (2+)-signaling mediated by PtdInsPs. Ca(2+) forms a complex with CaM (Ca(2+)-CaM) when there is an increase in the cytosol free Ca(2+). The binding of PCaPs with Ca(2+)-CaM causes PCaPs to release PtdInsPs. Until the release of PtdInsPs, the signaling is kept in the resting state. FAU - Kato, Mariko AU - Kato M AD - Graduate School of Bioagricultural Sciences; Nagoya University, Nagoya, Japan. FAU - Nagasaki-Takeuchi, Nahoko AU - Nagasaki-Takeuchi N FAU - Ide, Yuki AU - Ide Y FAU - Tomioka, Rie AU - Tomioka R FAU - Maeshima, Masayoshi AU - Maeshima M LA - eng PT - Comment PT - Journal Article DEP - 20100701 PL - United States TA - Plant Signal Behav JT - Plant signaling & behavior JID - 101291431 CON - Plant Cell Physiol. 2010 Mar;51(3):366-79. PMID: 20061304 PMC - PMC3014536 OID - NLM: PMC3014536 OTO - NOTNLM OT - calcium signal OT - calmodulin OT - inositol phosphate OT - intrinsically disordered protein OT - myristoylation OT - phosphatidylinositol phosphate OT - plasma membrane EDAT- 2010/05/08 06:00 MHDA- 2010/05/08 06:01 CRDT- 2010/05/08 06:00 PHST- 2010/07/01 [aheadofprint] AID - 11825 [pii] AID - 10.1093/pcp/pcq003. [doi] PST - ppublish SO - Plant Signal Behav. 2010 Jul;5(7):848-50. doi: 10.1093/pcp/pcq003.. Epub 2010 Jul 1. PMID- 19432426 OWN - NLM STAT- MEDLINE DA - 20090527 DCOM- 20090731 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 131 IP - 21 DP - 2009 Jun 3 TI - Multiple independent binding sites for small-molecule inhibitors on the oncoprotein c-Myc. PG - 7390-401 LID - 10.1021/ja900616b [doi] AB - Deregulation of the c-Myc transcription factor is involved in many types of cancer, making this oncoprotein an attractive target for drug discovery. One approach to its inhibition has been to disrupt the dimeric complex formed between its basic helix-loop-helix leucine zipper (bHLHZip) domain and a similar domain on its dimerization partner, Max. As monomers, bHLHZip proteins are intrinsically disordered (ID). Previously we showed that two c-Myc-Max inhibitors, 10058-F4 and 10074-G5, bound to distinct ID regions of the monomeric c-Myc bHLHZip domain. Here, we use circular dichroism, fluorescence polarization, and NMR to demonstrate the presence of an additional binding site located between those for 10058-F4 and 10074-G5. All seven of the originally identified Myc inhibitors are shown to bind to one of these three discrete sites within the 85-residue bHLHZip domain of c-Myc. These binding sites are composed of short contiguous stretches of amino acids that can selectively and independently bind small molecules. Inhibitor binding induces only local conformational changes, preserves the overall disorder of c-Myc, and inhibits dimerization with Max. NMR experiments further show that binding at one site on c-Myc affects neither the affinity nor the structural changes taking place upon binding to the other sites. Rather, binding can occur simultaneously and independently on the three identified sites. Our results suggest the widespread existence of peptide regions prone to small-molecule binding within ID domains. A rational and generic approach to the inhibition of protein-protein interactions involving ID proteins may therefore be possible through the targeting of ID sequence. FAU - Hammoudeh, Dalia I AU - Hammoudeh DI AD - Department of Chemistry, Georgetown University, Washington, District of Columbia 20057, USA. FAU - Follis, Ariele Viacava AU - Follis AV FAU - Prochownik, Edward V AU - Prochownik EV FAU - Metallo, Steven J AU - Metallo SJ LA - eng GR - R01-CA105033/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (10074-G5) RN - 0 (Oxadiazoles) RN - 0 (Proto-Oncogene Proteins c-myc) SB - IM MH - Binding Sites MH - Drug Discovery MH - Oxadiazoles MH - Protein Binding MH - Proto-Oncogene Proteins c-myc/*antagonists & inhibitors MH - Spectrum Analysis MH - Structure-Activity Relationship EDAT- 2009/05/13 09:00 MHDA- 2009/08/01 09:00 CRDT- 2009/05/13 09:00 AID - 10.1021/ja900616b [doi] PST - ppublish SO - J Am Chem Soc. 2009 Jun 3;131(21):7390-401. doi: 10.1021/ja900616b. PMID- 21376731 OWN - NLM STAT- MEDLINE DA - 20110412 DCOM- 20110607 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 408 IP - 3 DP - 2011 May 6 TI - Pattern recognition with a fibril-specific antibody fragment reveals the surface variability of natural amyloid fibrils. PG - 529-40 LID - 10.1016/j.jmb.2011.02.032 [doi] AB - Amyloid immunotherapy has led to the rise of antibodies, which target amyloid fibrils or structural precursors of fibrils, based on their specific conformational properties. Recently, we reported the biotechnological generation of the B10 antibody fragment, which provides conformation-specific binding to amyloid fibrils. B10 strongly interacts with fibrils from Alzheimer's beta amyloid (Abeta) peptide, while disaggregated Abeta peptide or Abeta oligomers are not explicitly recognized. B10 also enables poly-amyloid-specific binding and recognizes amyloid fibrils derived from different types of amyloidosis or different polypeptide chains. Based on our current data, however, we find that B10 does not recognize all tested amyloid fibrils and amyloid tissue deposits. It also does not specifically interact with intrinsically unfolded polypeptide chains or globular proteins even if the latter encompass high beta-sheet content or beta-solenoid domains. By contrast, B10 binds amyloid fibrils from d-amino acid or l-amino acid peptides and non-proteinaceous biopolymers with highly regular and anionic surface properties, such as heparin and DNA. These data establish that B10 binding does not depend on an amyloid-specific or protein-specific backbone structure. Instead, it involves the recognition of a highly regular and anionic surface pattern. This specificity mechanism is conserved in nature and occurs also within a group of natural amyloid receptors from the innate immune system, the pattern recognition receptors. Our data illuminate the structural diversity of naturally occurring amyloid scaffolds and enable the discrimination of distinct fibril populations in vitro and within diseased tissues. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Haupt, Christian AU - Haupt C AD - Max Planck Research Unit for Enzymology of Protein Folding, Weinbergweg 22, 06120 Halle (Saale), Germany. FAU - Bereza, Magdalena AU - Bereza M FAU - Kumar, Senthil T AU - Kumar ST FAU - Kieninger, Barbara AU - Kieninger B FAU - Morgado, Isabel AU - Morgado I FAU - Hortschansky, Peter AU - Hortschansky P FAU - Fritz, Gunter AU - Fritz G FAU - Rocken, Christoph AU - Rocken C FAU - Horn, Uwe AU - Horn U FAU - Fandrich, Marcus AU - Fandrich M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110303 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amyloid) RN - 0 (Immunoglobulin Fragments) SB - IM MH - Amyloid/*chemistry/immunology/metabolism/ultrastructure MH - Brain/pathology MH - Histocytochemistry MH - Humans MH - Immunoglobulin Fragments/metabolism MH - Microscopy, Electron, Transmission MH - Models, Molecular MH - Protein Binding EDAT- 2011/03/08 06:00 MHDA- 2011/06/08 06:00 CRDT- 2011/03/08 06:00 PHST- 2010/11/26 [received] PHST- 2011/01/24 [revised] PHST- 2011/02/13 [accepted] PHST- 2011/03/03 [aheadofprint] AID - S0022-2836(11)00189-6 [pii] AID - 10.1016/j.jmb.2011.02.032 [doi] PST - ppublish SO - J Mol Biol. 2011 May 6;408(3):529-40. doi: 10.1016/j.jmb.2011.02.032. Epub 2011 Mar 3. PMID- 9890923 OWN - NLM STAT- MEDLINE DA - 19990218 DCOM- 19990218 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 38 IP - 1 DP - 1999 Jan 5 TI - Manganese stabilizing protein of photosystem II is a thermostable, natively unfolded polypeptide. PG - 404-14 AB - The thermostability of manganese stabilizing protein of photosystem II was examined by biochemical and spectroscopic techniques. Samples of both native and recombinant spinach manganese stabilizing protein incubated at 90 degreesC and then cooled to 25 degreesC were capable of rebinding to, and of reactivating, the O2-evolution activity of photosystem II membranes from which the native protein had been removed. Far-UV circular dichroism and FT-IR spectroscopies were used to analyze the structural consequences of heating manganese stabilizing protein. The data obtained from these techniques show that heating causes a complete loss of the protein's secondary structure, and that this is a reversible, noncooperative phenomenon. Upon cooling, the secondary structures of the heat-treated proteins return to a state similar to, but not identical with, that of the native, unheated controls. Restoration of a near-native tertiary structure is confirmed both by size-exclusion chromatography and by near-UV circular dichroism. The functional and structural thermostability of manganese stabilizing protein reported here, in conjunction with additional known properties of this protein (acidic pI, high random coil and turn content, anomalous hydrodynamic behavior), identifies manganese stabilizing protein as a natively unfolded protein [Weinreb et al. (1996) Biochemistry 35, 13709-13715]. Although these proteins lack amino acid sequence identity, their functional solution conformations under physiological conditions are said to be "natively unfolded". We suggest that, as with other members of this family of proteins, the natively unfolded structure of manganese stabilizing protein facilitates the highly effective protein-protein interactions that are necessary for its assembly into photosystem II. FAU - Lydakis-Simantiris, N AU - Lydakis-Simantiris N AD - Department of Biology, Department of Chemistry, The University of Michigan, Ann Arbor 48109-1048, USA. FAU - Hutchison, R S AU - Hutchison RS FAU - Betts, S D AU - Betts SD FAU - Barry, B A AU - Barry BA FAU - Yocum, C F AU - Yocum CF LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Peptides) RN - 0 (Photosynthetic Reaction Center Complex Proteins) RN - 0 (Photosystem II Protein Complex) RN - 0 (Proteins) RN - 0 (photosystem II manganese-stabilizing protein) RN - 42Z2K6ZL8P (Manganese) RN - S88TT14065 (Oxygen) SB - IM MH - Chromatography, Gel MH - Circular Dichroism MH - Hot Temperature MH - Manganese/*chemistry/metabolism MH - Oxygen/metabolism MH - Peptides/*chemistry/metabolism MH - Photosynthetic Reaction Center Complex Proteins/*chemistry/metabolism MH - *Photosystem II Protein Complex MH - Protein Denaturation MH - *Protein Folding MH - Protein Structure, Secondary MH - Proteins/*chemistry/metabolism MH - Spectroscopy, Fourier Transform Infrared MH - Spinacia oleracea EDAT- 1999/01/16 MHDA- 1999/01/16 00:01 CRDT- 1999/01/16 00:00 AID - 10.1021/bi981847z [doi] AID - bi981847z [pii] PST - ppublish SO - Biochemistry. 1999 Jan 5;38(1):404-14. PMID- 24551051 OWN - NLM STAT- MEDLINE DA - 20140219 DCOM- 20141021 LR - 20150205 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 2 DP - 2014 TI - Targeting the intrinsically disordered structural ensemble of alpha-synuclein by small molecules as a potential therapeutic strategy for Parkinson's disease. PG - e87133 LID - 10.1371/journal.pone.0087133 [doi] AB - The misfolding of intrinsically disordered proteins such as alpha-synuclein, tau and the Abeta peptide has been associated with many highly debilitating neurodegenerative syndromes including Parkinson's and Alzheimer's diseases. Therapeutic targeting of the monomeric state of such intrinsically disordered proteins by small molecules has, however, been a major challenge because of their heterogeneous conformational properties. We show here that a combination of computational and experimental techniques has led to the identification of a drug-like phenyl-sulfonamide compound (ELN484228), that targets alpha-synuclein, a key protein in Parkinson's disease. We found that this compound has substantial biological activity in cellular models of alpha-synuclein-mediated dysfunction, including rescue of alpha-synuclein-induced disruption of vesicle trafficking and dopaminergic neuronal loss and neurite retraction most likely by reducing the amount of alpha-synuclein targeted to sites of vesicle mobilization such as the synapse in neurons or the site of bead engulfment in microglial cells. These results indicate that targeting alpha-synuclein by small molecules represents a promising approach to the development of therapeutic treatments of Parkinson's disease and related conditions. FAU - Toth, Gergely AU - Toth G AD - Department of Chemistry, University of Cambridge, Cambridge, United Kingdom ; Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - Gardai, Shyra J AU - Gardai SJ AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - Zago, Wagner AU - Zago W AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - Bertoncini, Carlos W AU - Bertoncini CW AD - Department of Chemistry, University of Cambridge, Cambridge, United Kingdom ; SEDIPFAR (Servicio De Descubrimiento, Diseno Y Desarrollo Pre-Clinico De Farmacos De La Argentina) drug discovery platform, Universidad Nacional de Rosario, Rosario, Argentina. FAU - Cremades, Nunilo AU - Cremades N AD - Department of Chemistry, University of Cambridge, Cambridge, United Kingdom. FAU - Roy, Susan L AU - Roy SL AD - Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America. FAU - Tambe, Mitali A AU - Tambe MA AD - Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America. FAU - Rochet, Jean-Christophe AU - Rochet JC AD - Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America. FAU - Galvagnion, Celine AU - Galvagnion C AD - Department of Chemistry, University of Cambridge, Cambridge, United Kingdom. FAU - Skibinski, Gaia AU - Skibinski G AD - Gladstone Institute of Neurological Disease, San Francisco, California, United States of America ; Taube-Koret Center for Neurodegenerative Disease Research, The Consortium for Frontotemporal Dementia Research, and The Hellman Family Foundation Program for Alzheimer's Disease Research, San Francisco, California, United States of America. FAU - Finkbeiner, Steven AU - Finkbeiner S AD - Gladstone Institute of Neurological Disease, San Francisco, California, United States of America ; Taube-Koret Center for Neurodegenerative Disease Research, The Consortium for Frontotemporal Dementia Research, and The Hellman Family Foundation Program for Alzheimer's Disease Research, San Francisco, California, United States of America ; Departments of Neurology and Physiology, UCSF, San Francisco, California, United States of America. FAU - Bova, Michael AU - Bova M AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - Regnstrom, Karin AU - Regnstrom K AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - Chiou, San-San AU - Chiou SS AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - Johnston, Jennifer AU - Johnston J AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - Callaway, Kari AU - Callaway K AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - Anderson, John P AU - Anderson JP AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - Jobling, Michael F AU - Jobling MF AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - Buell, Alexander K AU - Buell AK AD - Department of Chemistry, University of Cambridge, Cambridge, United Kingdom. FAU - Yednock, Ted A AU - Yednock TA AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - Knowles, Tuomas P J AU - Knowles TP AD - Department of Chemistry, University of Cambridge, Cambridge, United Kingdom. FAU - Vendruscolo, Michele AU - Vendruscolo M AD - Department of Chemistry, University of Cambridge, Cambridge, United Kingdom. FAU - Christodoulou, John AU - Christodoulou J AD - Department of Structural & Molecular Biology, University College London, London, United Kingdom. FAU - Dobson, Christopher M AU - Dobson CM AD - Department of Chemistry, University of Cambridge, Cambridge, United Kingdom. FAU - Schenk, Dale AU - Schenk D AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. FAU - McConlogue, Lisa AU - McConlogue L AD - Elan Pharmaceuticals, South San Francisco, California, United States of America. LA - eng GR - 097806/Wellcome Trust/United Kingdom GR - BB/H003843/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - MC_G1000734/Medical Research Council/United Kingdom GR - R01 NS083390/NS/NINDS NIH HHS/United States GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140214 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Small Molecule Libraries) RN - 0 (alpha-Synuclein) SB - IM EIN - PLoS One. 2014;9(5):e99274 MH - Animals MH - Binding Sites MH - Dopaminergic Neurons/drug effects/metabolism/pathology MH - Humans MH - Intrinsically Disordered Proteins/*antagonists & inhibitors/chemistry/metabolism MH - Mice MH - Models, Biological MH - Models, Molecular MH - *Molecular Targeted Therapy MH - Nerve Degeneration/metabolism/pathology MH - Parkinson Disease/*drug therapy/pathology MH - Phagocytes/drug effects/metabolism MH - Small Molecule Libraries/*pharmacology/*therapeutic use MH - Synapses/drug effects/metabolism MH - alpha-Synuclein/*antagonists & inhibitors/chemistry/metabolism PMC - PMC3925190 OID - NLM: PMC3925190 EDAT- 2014/02/20 06:00 MHDA- 2014/10/22 06:00 CRDT- 2014/02/20 06:00 PHST- 2014 [ecollection] PHST- 2013/09/24 [received] PHST- 2013/12/19 [accepted] PHST- 2014/02/14 [epublish] AID - 10.1371/journal.pone.0087133 [doi] AID - PONE-D-13-39293 [pii] PST - epublish SO - PLoS One. 2014 Feb 14;9(2):e87133. doi: 10.1371/journal.pone.0087133. eCollection 2014. PMID- 17493042 OWN - NLM STAT- MEDLINE DA - 20070511 DCOM- 20070626 IS - 1015-6305 (Print) IS - 1015-6305 (Linking) VI - 17 IP - 1 DP - 2007 Jan TI - Structural principles of tau and the paired helical filaments of Alzheimer's disease. PG - 83-90 AB - Tau, a major microtubule-associated protein in brain, forms abnormal fibers in Alzheimer's disease and several other neurodegenerative diseases. Tau is highly soluble and adopts a natively unfolded structure in solution. In the paired helical filaments of Alzheimer's disease, small segments of tau adopt a beta-conformation and interact with other tau molecules. In the filament core, the microtubule-binding repeat region of tau has a cross-beta structure, while the rest of the protein retains its largely unfolded structure and gives rise to the fuzzy coat of the filaments. FAU - Mandelkow, Eckhard AU - Mandelkow E AD - Max-Planck-Unit for Structural Molecular Biology, Hamburg, Germany. mand@mpasmb.desy.de FAU - von Bergen, Martin AU - von Bergen M FAU - Biernat, Jacek AU - Biernat J FAU - Mandelkow, Eva-Maria AU - Mandelkow EM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Switzerland TA - Brain Pathol JT - Brain pathology (Zurich, Switzerland) JID - 9216781 RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/*metabolism MH - Humans MH - Microtubules/*chemistry/metabolism MH - *Protein Folding MH - tau Proteins/*chemistry/metabolism RF - 128 EDAT- 2007/05/12 09:00 MHDA- 2007/06/27 09:00 CRDT- 2007/05/12 09:00 AID - BPA053 [pii] AID - 10.1111/j.1750-3639.2007.00053.x [doi] PST - ppublish SO - Brain Pathol. 2007 Jan;17(1):83-90. PMID- 15837201 OWN - NLM STAT- MEDLINE DA - 20050419 DCOM- 20050526 LR - 20061115 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 13 IP - 4 DP - 2005 Apr TI - Modulation of binding of DNA to the C-terminal domain of p53 by acetylation. PG - 629-36 AB - The binding of nonspecific DNA to the C-terminal negative regulatory domain (CTD) of p53 modulates its activity. The CTD is a natively unfolded region, which is subject to acetylation and phosphorylation at several residues as part of control. To measure the effect of covalent modification on binding to DNA, we synthesized a series of fluorescein-labeled CTD peptides with single and multiple acetylations at lysine residues that we had identified by NMR as making contact with DNA, and developed an analytical ultracentrifugation method to study their binding to DNA. Binding depended on ionic strength, indicating an electrostatic contribution. Monoacetylation weakened DNA binding at physiological ionic strength 2- to 3-fold, diacetylations resulted in further 2- to 3-fold decrease in the affinity, and tri- and tetraacetylations rendered DNA binding undetectable. Phosphorylation at S392 did not affect DNA binding. NMR spectroscopy showed binding to DNA did not induce significant structure into CTD, apart possibly from local helix formation. FAU - Friedler, Assaf AU - Friedler A AD - MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, United Kingdom. FAU - Veprintsev, Dmitry B AU - Veprintsev DB FAU - Freund, Stefan M V AU - Freund SM FAU - von Glos, Karoly I AU - von Glos KI FAU - Fersht, Alan R AU - Fersht AR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Tumor Suppressor Protein p53) RN - 9007-49-2 (DNA) SB - IM MH - Acetylation MH - Amino Acid Sequence MH - DNA/*metabolism MH - Molecular Sequence Data MH - Osmolar Concentration MH - Phosphorylation MH - Protein Binding MH - Spectrometry, Fluorescence MH - Tumor Suppressor Protein p53/chemistry/*metabolism EDAT- 2005/04/20 09:00 MHDA- 2005/05/27 09:00 CRDT- 2005/04/20 09:00 PHST- 2004/10/04 [received] PHST- 2004/12/15 [revised] PHST- 2005/01/26 [accepted] AID - S0969-2126(05)00083-3 [pii] AID - 10.1016/j.str.2005.01.020 [doi] PST - ppublish SO - Structure. 2005 Apr;13(4):629-36. PMID- 12358741 OWN - NLM STAT- MEDLINE DA - 20021002 DCOM- 20021028 LR - 20131121 IS - 0022-3042 (Print) IS - 0022-3042 (Linking) VI - 83 IP - 1 DP - 2002 Oct TI - Proteasomal degradation of tau protein. PG - 176-85 AB - Filamentous inclusions composed of the microtubule-associated protein tau are a defining characteristic of a large number of neurodegenerative diseases. Here we show that tau degradation in stably transfected and non-transfected SH-SY5Y cells is blocked by the irreversible proteasome inhibitor lactacystin. Further, we find that in vitro, natively unfolded tau can be directly processed by the 20S proteasome without a requirement for ubiquitylation, and that a highly reproducible pattern of degradation intermediates is readily detectable during this process. Analysis of these intermediates shows that 20S proteasomal processing of tau is bi-directional, proceeding from both N- and C-termini, and that populations of relatively stable intermediates arise probably because of less efficient digestion of the C-terminal repeat region. Our results are consistent with an in vivo role for the proteasome in tau degradation and support the existence of ubiquitin-independent pathways for the proteasomal degradation of unfolded proteins. FAU - David, Della C AU - David DC AD - Cambridge Centre for Brain Repair and Neurology Department, University of Cambridge, Cambridge, UK. FAU - Layfield, Robert AU - Layfield R FAU - Serpell, Louise AU - Serpell L FAU - Narain, Yolanda AU - Narain Y FAU - Goedert, Michel AU - Goedert M FAU - Spillantini, Maria Grazia AU - Spillantini MG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Neurochem JT - Journal of neurochemistry JID - 2985190R RN - 0 (Cysteine Proteinase Inhibitors) RN - 0 (Multienzyme Complexes) RN - 0 (Protein Isoforms) RN - 0 (Ubiquitin) RN - 0 (tau Proteins) RN - 133343-34-7 (lactacystin) RN - EC 3.4.22.- (Cysteine Endopeptidases) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) RN - WYQ7N0BPYC (Acetylcysteine) SB - IM MH - Acetylcysteine/*analogs & derivatives/pharmacology MH - Blotting, Western MH - Cysteine Endopeptidases/chemistry/*metabolism MH - Cysteine Proteinase Inhibitors/pharmacology MH - Humans MH - Multienzyme Complexes/antagonists & inhibitors/chemistry/*metabolism MH - Neuroblastoma/metabolism MH - Proteasome Endopeptidase Complex MH - Protein Folding MH - Protein Isoforms/chemistry/genetics/metabolism MH - Transfection MH - Tumor Cells, Cultured MH - Ubiquitin/metabolism MH - tau Proteins/chemistry/genetics/*metabolism EDAT- 2002/10/03 04:00 MHDA- 2002/10/29 04:00 CRDT- 2002/10/03 04:00 AID - 1137 [pii] PST - ppublish SO - J Neurochem. 2002 Oct;83(1):176-85. PMID- 19812155 OWN - NLM STAT- MEDLINE DA - 20091120 DCOM- 20091208 LR - 20140827 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 83 IP - 24 DP - 2009 Dec TI - Physical requirements and functional consequences of complex formation between the cytomegalovirus IE1 protein and human STAT2. PG - 12854-70 LID - 10.1128/JVI.01164-09 [doi] AB - Our previous work has shown that efficient evasion from type I interferon responses by human cytomegalovirus (hCMV) requires expression of the 72-kDa immediate-early 1 (IE1) protein. It has been suggested that IE1 inhibits interferon signaling through intranuclear sequestration of the signal transducer and activator of transcription 2 (STAT2) protein. Here we show that physical association and subnuclear colocalization of IE1 and STAT2 depend on short acidic and serine/proline-rich low-complexity motifs in the carboxy-terminal region of the 491-amino-acid viral polypeptide. These motifs compose an essential core (amino acids 373 to 420) and an adjacent ancillary site (amino acids 421 to 445) for STAT2 interaction that are predicted to form part of a natively unstructured domain. The presence of presumably "disordered" carboxy-terminal domains enriched in low-complexity motifs is evolutionarily highly conserved across all examined mammalian IE1 orthologs, and the murine cytomegalovirus IE1 protein appears to interact with STAT2 just like the human counterpart. A recombinant hCMV specifically mutated in the IE1 core STAT2 binding site displays hypersensitivity to alpha interferon, delayed early viral protein accumulation, and attenuated growth in fibroblasts. However, replication of this mutant virus is specifically restored by knockdown of STAT2 expression. Interestingly, complex formation with STAT2 proved to be entirely separable from disruption of nuclear domain 10 (ND10), another key activity of IE1. Finally, our results demonstrate that IE1 counteracts the antiviral interferon response and promotes viral replication by at least two distinct mechanisms, one depending on sequestration of STAT2 and the other one likely involving ND10 interaction. FAU - Krauss, Steffen AU - Krauss S AD - Institute for Medical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany. FAU - Kaps, Julia AU - Kaps J FAU - Czech, Nathalie AU - Czech N FAU - Paulus, Christina AU - Paulus C FAU - Nevels, Michael AU - Nevels M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091007 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (IE1 protein, cytomegalovirus) RN - 0 (Immediate-Early Proteins) RN - 0 (Interferon Type I) RN - 0 (STAT2 Transcription Factor) RN - 0 (STAT2 protein, human) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Cells, Cultured MH - Cytomegalovirus/drug effects/physiology MH - Humans MH - Immediate-Early Proteins/*chemistry/physiology MH - Interferon Type I/pharmacology MH - Molecular Sequence Data MH - STAT2 Transcription Factor/*chemistry/physiology MH - Virus Replication/drug effects PMC - PMC2786848 OID - NLM: PMC2786848 EDAT- 2009/10/09 06:00 MHDA- 2009/12/16 06:00 CRDT- 2009/10/09 06:00 PHST- 2009/10/07 [aheadofprint] AID - JVI.01164-09 [pii] AID - 10.1128/JVI.01164-09 [doi] PST - ppublish SO - J Virol. 2009 Dec;83(24):12854-70. doi: 10.1128/JVI.01164-09. Epub 2009 Oct 7. PMID- 17498738 OWN - NLM STAT- MEDLINE DA - 20070528 DCOM- 20070719 LR - 20081121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 369 IP - 5 DP - 2007 Jun 22 TI - Structure of calcineurin in complex with PVIVIT peptide: portrait of a low-affinity signalling interaction. PG - 1296-306 AB - The protein phosphatase calcineurin recognizes a wide assortment of substrates and controls diverse developmental and physiological pathways in eukaryotic cells. Dephosphorylation of the transcription factor NFAT and certain other calcineurin substrates depends on docking of calcineurin at a PxIxIT consensus site. We describe here the structural basis for recognition of the PxIxIT sequence by calcineurin. We demonstrate that the high-affinity peptide ligand PVIVIT adds as a beta-strand to the edge of a beta-sheet of calcineurin; that short peptide segments containing the PxIxIT consensus sequence suffice for calcineurin-substrate docking; and that sequence variations within the PxIxIT core modulate the K(d) of the interaction within the physiological range 1 microM to 1 mM. Calcineurin can adapt to a wide variety of substrates, because recognition requires only a PxIxIT sequence and because variation within the core PxIxIT sequence can fine-tune the affinity to match the physiological signalling requirements of individual substrates. FAU - Li, Huiming AU - Li H AD - The CBR Institute, for Biomedical Research, 200 Longwood Avenue, Boston, MA 02115, USA. FAU - Zhang, Lan AU - Zhang L FAU - Rao, Anjana AU - Rao A FAU - Harrison, Stephen C AU - Harrison SC FAU - Hogan, Patrick G AU - Hogan PG LA - eng SI - OMIM/2P6B GR - AI40127/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070419 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Multiprotein Complexes) RN - 0 (NFATC Transcription Factors) RN - 0 (Peptide Fragments) RN - EC 3.1.3.16 (Calcineurin) SB - IM MH - Amino Acid Motifs MH - Binding Sites MH - Calcineurin/*chemistry/*metabolism MH - Crystallography, X-Ray MH - Humans MH - Models, Molecular MH - Multiprotein Complexes MH - NFATC Transcription Factors/*chemistry/metabolism MH - Peptide Fragments/chemistry/*metabolism MH - Protein Conformation MH - Signal Transduction EDAT- 2007/05/15 09:00 MHDA- 2007/07/20 09:00 CRDT- 2007/05/15 09:00 PHST- 2007/02/10 [received] PHST- 2007/04/04 [revised] PHST- 2007/04/09 [accepted] PHST- 2007/04/19 [aheadofprint] AID - S0022-2836(07)00490-1 [pii] AID - 10.1016/j.jmb.2007.04.032 [doi] PST - ppublish SO - J Mol Biol. 2007 Jun 22;369(5):1296-306. Epub 2007 Apr 19. PMID- 21215287 OWN - NLM STAT- MEDLINE DA - 20110411 DCOM- 20110915 IS - 1638-6183 (Electronic) IS - 0300-9084 (Linking) VI - 93 IP - 5 DP - 2011 May TI - A mechanistic approach for islet amyloid polypeptide aggregation to develop anti-amyloidogenic agents for type-2 diabetes. PG - 793-805 LID - 10.1016/j.biochi.2010.12.012 [doi] AB - Type-2 diabetes mellitus (DM-2) is a conformational disease involving intrinsically disordered islet amyloid polypeptide (IAPP), in which a structural transition from physiological polypeptide to pathological deposits takes place. Different factors acquired or inherited, contribute to endoplasmic reticulum stress and/or impair mitochondrial function which leads to conformational changes in IAPP intermediates and ultimately produces oligomers of an anti-parallel crossed beta-pleated sheets that eventually accumulate as space-occupying lesions within the islets. Clusters of IAPP monomers form a pore which is linked to channel-like behavior in planar bilayers, indicating that these oligomeric IAPP pores could become incorporated into membranes and alter its barrier properties. Identification of nucleating residues and the residues responsible for this oligomeric tendency could improve understanding of structure-function relationships as well as the molecular mechanism of folding and aggregation of IAPP contributing to the onset of DM-2. A combination of biological, chemical or physical approaches is required to be extensively pursued for the development of a successful anti-amyloidogenic agent to prevent this malady. Exploring the hypothesis of pi-stacking may be a better option to control IAPP aggregation if researchers go through the mechanism of pi-pi interaction, which provides entropy driven energy and direction for self-assembly to control amyloidogenic aggregation. CI - Copyright (c) 2010 Elsevier Masson SAS. All rights reserved. FAU - Ahmad, Ejaz AU - Ahmad E AD - Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India. FAU - Ahmad, Aqeel AU - Ahmad A FAU - Singh, Saurabh AU - Singh S FAU - Arshad, Md AU - Arshad M FAU - Khan, Abdul Hameed AU - Khan AH FAU - Khan, Rizwan Hasan AU - Khan RH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20110105 PL - France TA - Biochimie JT - Biochimie JID - 1264604 RN - 0 (Islet Amyloid Polypeptide) RN - 0 (Protein Precursors) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cell Membrane/metabolism MH - Diabetes Mellitus, Type 2/pathology/*prevention & control MH - Evolution, Molecular MH - Humans MH - Islet Amyloid Polypeptide/*metabolism/secretion MH - Islets of Langerhans/metabolism/*pathology MH - Molecular Sequence Data MH - Protein Folding MH - Protein Multimerization MH - Protein Precursors/*metabolism/secretion MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary EDAT- 2011/01/11 06:00 MHDA- 2011/09/16 06:00 CRDT- 2011/01/11 06:00 PHST- 2010/10/02 [received] PHST- 2010/12/19 [accepted] PHST- 2011/01/05 [aheadofprint] AID - S0300-9084(10)00467-0 [pii] AID - 10.1016/j.biochi.2010.12.012 [doi] PST - ppublish SO - Biochimie. 2011 May;93(5):793-805. doi: 10.1016/j.biochi.2010.12.012. Epub 2011 Jan 5. PMID- 3133554 OWN - NLM STAT- MEDLINE DA - 19880729 DCOM- 19880729 LR - 20131121 IS - 0270-7306 (Print) IS - 0270-7306 (Linking) VI - 8 IP - 5 DP - 1988 May TI - Isolation, characterization, and UV-stimulated expression of two families of genes encoding polypeptides of related structure in human epidermal keratinocytes. PG - 2195-203 AB - By screening of a cDNA library made on mRNA isolated from UV-irradiated human epidermal keratinocytes for sequences whose relative concentration increases in the cytoplasm after irradiation, we have isolated 40 cDNA clones (T. Kartasova, B. J. C. Cornelissen, P. Belt, and P. van de Putte, Nucleic Acids Res. 15:5945-5962, 1987). Here we describe two distinct groups of cDNA clones which do not cross-hybridize to each other but nevertheless encode proteins of very similar primary structure. These polypeptides are small (8 to 10 kilodaltons) and exceptionally rich in proline, cysteine, and glutamine and have similar repeating elements not found elsewhere. The new proteins were designated sprI and sprII (small, proline rich). The presence of prolines and cysteines suggests that they may be either structural proteins with a strong secondary structure or metal-binding proteins such as metallothioneins. Southern blot and sequence analyses of the cDNAs indicate that at least the sprII group of clones represents a family of related genes. The nucleotide sequence of both groups seems to be conserved upon evolution. The level of mRNAs corresponding to the two groups of cDNAs is increased in the cytoplasm of human epidermal keratinocytes after both UV irradiation and treatment with 4-nitroquinoline 1-oxide or 12-O-tetradecanoylphorbol 13-acetate. FAU - Kartasova, T AU - Kartasova T AD - Laboratory of Molecular Genetics, State University of Leiden, The Netherlands. FAU - van de Putte, P AU - van de Putte P LA - eng SI - GENBANK/M19888 SI - GENBANK/M20030 SI - GENBANK/M21300 SI - GENBANK/M21301 SI - GENBANK/M21302 SI - GENBANK/M21539 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (Peptides) RN - 56-57-5 (4-Nitroquinoline-1-oxide) RN - 9007-49-2 (DNA) RN - NI40JAQ945 (Tetradecanoylphorbol Acetate) SB - IM MH - 4-Nitroquinoline-1-oxide/pharmacology MH - Amino Acid Sequence MH - Base Sequence MH - Cells, Cultured MH - DNA/genetics MH - Epidermis/cytology/drug effects/*radiation effects MH - Gene Expression Regulation/drug effects/radiation effects MH - Genes/drug effects/radiation effects MH - Humans MH - Molecular Sequence Data MH - Multigene Family/drug effects/*radiation effects MH - Peptide Biosynthesis MH - Peptides/*genetics MH - Proline-Rich Protein Domains MH - Tetradecanoylphorbol Acetate/pharmacology MH - Ultraviolet Rays PMC - PMC363401 OID - NLM: PMC363401 EDAT- 1988/05/01 MHDA- 1988/05/01 00:01 CRDT- 1988/05/01 00:00 PST - ppublish SO - Mol Cell Biol. 1988 May;8(5):2195-203. PMID- 3013692 OWN - NLM STAT- MEDLINE DA - 19860815 DCOM- 19860815 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 202 IP - 2 DP - 1986 Jul 7 TI - Expression, secretion and processing of hirudin in E. coli using the alkaline phosphatase signal sequence. PG - 373-7 AB - A DNA fragment coding for the E. coli phoA signal peptide was synthesized and inserted into the expression vector pKK223-3. A single HindIII restriction site is located just at the end of the signal sequence. A gene coding for the proteinase inhibitor hirudin, which has previously been synthesized, was inserted into this HindIII site. The hybrid protein was expressed under control of the tac-promoter and secreted into the periplasm of E. coli. From the periplasmic fraction two processed proteins were isolated. One of these was identical with desulfatohirudin and also had similar biological properties. FAU - Dodt, J AU - Dodt J FAU - Schmitz, T AU - Schmitz T FAU - Schafer, T AU - Schafer T FAU - Bergmann, C AU - Bergmann C LA - eng PT - Journal Article PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Hirudins) RN - 0 (Protein Sorting Signals) RN - EC 3.1.21.- (DNA Restriction Enzymes) RN - EC 3.1.21.- (Deoxyribonuclease HindIII) RN - EC 3.1.3.1 (Alkaline Phosphatase) RN - EC 3.4.21.5 (Thrombin) SB - IM MH - Alkaline Phosphatase/*metabolism MH - Amino Acid Sequence MH - Base Sequence MH - Chromatography, High Pressure Liquid MH - Cloning, Molecular MH - DNA Restriction Enzymes/metabolism MH - Deoxyribonuclease HindIII MH - Escherichia coli/*metabolism MH - Gene Expression Regulation MH - Hirudins/*metabolism MH - Protein Sorting Signals/*metabolism MH - Thrombin/pharmacology EDAT- 1986/07/07 MHDA- 1986/07/07 00:01 CRDT- 1986/07/07 00:00 AID - 0014-5793(86)80721-9 [pii] PST - ppublish SO - FEBS Lett. 1986 Jul 7;202(2):373-7. PMID- 20657787 OWN - NLM STAT- MEDLINE DA - 20100726 DCOM- 20101028 LR - 20140824 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 5 IP - 7 DP - 2010 TI - Structural disorder within Henipavirus nucleoprotein and phosphoprotein: from predictions to experimental assessment. PG - e11684 LID - 10.1371/journal.pone.0011684 [doi] AB - Henipaviruses are newly emerged viruses within the Paramyxoviridae family. Their negative-strand RNA genome is packaged by the nucleoprotein (N) within alpha-helical nucleocapsid that recruits the polymerase complex made of the L protein and the phosphoprotein (P). To date structural data on Henipaviruses are scarce, and their N and P proteins have never been characterized so far. Using both computational and experimental approaches we herein show that Henipaviruses N and P proteins possess large intrinsically disordered regions. By combining several disorder prediction methods, we show that the N-terminal domain of P (PNT) and the C-terminal domain of N (NTAIL) are both mostly disordered, although they contain short order-prone segments. We then report the cloning, the bacterial expression, purification and characterization of Henipavirus PNT and NTAIL domains. By combining gel filtration, dynamic light scattering, circular dichroism and nuclear magnetic resonance, we show that both NTAIL and PNT belong to the premolten globule sub-family within the class of intrinsically disordered proteins. This study is the first reported experimental characterization of Henipavirus P and N proteins. The evidence that their respective N-terminal and C-terminal domains are highly disordered under native conditions is expected to be invaluable for future structural studies by helping to delineate N and P protein domains amenable to crystallization. In addition, following previous hints establishing a relationship between structural disorder and protein interactivity, the present results suggest that Henipavirus PNT and NTAIL domains could be involved in manifold protein-protein interactions. FAU - Habchi, Johnny AU - Habchi J AD - Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS et Universites Aix-Marseille I et II, Campus de Luminy, Marseille, France. FAU - Mamelli, Laurent AU - Mamelli L FAU - Darbon, Herve AU - Darbon H FAU - Longhi, Sonia AU - Longhi S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100721 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Nucleocapsid Proteins) RN - 0 (Phosphoproteins) RN - 0 (Viral Proteins) SB - IM MH - Chromatography, Gel MH - Circular Dichroism MH - Henipavirus/genetics/*metabolism MH - Magnetic Resonance Spectroscopy MH - Nucleocapsid Proteins/*chemistry/genetics/*metabolism MH - Phosphoproteins/*chemistry/genetics/*metabolism MH - Viral Proteins/*chemistry/genetics/*metabolism PMC - PMC2908138 OID - NLM: PMC2908138 EDAT- 2010/07/27 06:00 MHDA- 2010/10/29 06:00 CRDT- 2010/07/27 06:00 PHST- 2010/05/23 [received] PHST- 2010/06/21 [accepted] PHST- 2010/07/21 [epublish] AID - 10.1371/journal.pone.0011684 [doi] PST - epublish SO - PLoS One. 2010 Jul 21;5(7):e11684. doi: 10.1371/journal.pone.0011684. PMID- 19635792 OWN - NLM STAT- MEDLINE DA - 20090914 DCOM- 20091019 LR - 20140828 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 284 IP - 38 DP - 2009 Sep 18 TI - Secretory granule to the nucleus: role of a multiply phosphorylated intrinsically unstructured domain. PG - 25723-34 LID - 10.1074/jbc.M109.035782 [doi] AB - Intrinsically unstructured domains occur in one-third of all proteins and are characterized by conformational flexibility, protease sensitivity, and the occurrence of multiple phosphorylation. They provide large interfaces for diverse protein-protein interactions. Peptidylglycine alpha-amidating monooxygenase (PAM), an enzyme essential for neuropeptide biosynthesis, is a secretory granule membrane protein. As one of the few proteins spanning the granule membrane, PAM is a candidate to relay information about the status of the granule pool and conditions in the granule lumen. Here, we show that the PAM cytosolic domain is unstructured. Mass spectroscopy and two-dimensional gel electrophoresis demonstrated phosphorylation at 10-12 sites in the cytosolic domain. Stimulation of exocytosis resulted in coupled phosphorylation and dephosphorylation of specific sites and in the endoproteolytic release of a soluble, proteasome-sensitive cytosolic domain fragment. Analysis of granule-rich tissues, such as pituitary and heart, showed that a similar fragment was generated endogenously and translocated to the nucleus. This multiply phosphorylated unstructured domain may act as a signaling molecule that relays information from secretory granules to both cytosol and nucleus. FAU - Rajagopal, Chitra AU - Rajagopal C AD - Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA. FAU - Stone, Kathryn L AU - Stone KL FAU - Francone, Victor P AU - Francone VP FAU - Mains, Richard E AU - Mains RE FAU - Eipper, Betty A AU - Eipper BA LA - eng GR - 1S10RR024617/RR/NCRR NIH HHS/United States GR - DK32949/DK/NIDDK NIH HHS/United States GR - P30 DA018343/DA/NIDA NIH HHS/United States GR - P30 DA018343/DA/NIDA NIH HHS/United States GR - R01 DK032949/DK/NIDDK NIH HHS/United States GR - UL1 RR024139/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090727 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Adaptor Proteins, Signal Transducing) RN - EC 1.- (Mixed Function Oxygenases) RN - EC 6.3.2.- (MYCBP2 protein, human) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM MH - Active Transport, Cell Nucleus/physiology MH - Adaptor Proteins, Signal Transducing/*chemistry/genetics/*metabolism MH - Cell Line MH - Cell Nucleus/*enzymology/genetics MH - Exocytosis/physiology MH - Humans MH - Mixed Function Oxygenases/*chemistry/genetics/*metabolism MH - Phosphorylation/physiology MH - Protein Structure, Tertiary/physiology MH - Secretory Vesicles/*chemistry/*enzymology/genetics MH - Ubiquitin-Protein Ligases PMC - PMC2757974 OID - NLM: PMC2757974 EDAT- 2009/07/29 09:00 MHDA- 2009/10/20 06:00 CRDT- 2009/07/29 09:00 PHST- 2009/07/27 [aheadofprint] AID - M109.035782 [pii] AID - 10.1074/jbc.M109.035782 [doi] PST - ppublish SO - J Biol Chem. 2009 Sep 18;284(38):25723-34. doi: 10.1074/jbc.M109.035782. Epub 2009 Jul 27. PMID- 22270944 OWN - NLM STAT- MEDLINE DA - 20120424 DCOM- 20121029 LR - 20131121 IS - 1432-1327 (Electronic) IS - 0949-8257 (Linking) VI - 17 IP - 4 DP - 2012 Apr TI - Calorimetric investigation of copper(II) binding to Abeta peptides: thermodynamics of coordination plasticity. PG - 531-41 LID - 10.1007/s00775-012-0874-3 [doi] AB - Metal ions have been shown to play a critical role in beta-amyloid (Abeta) neurotoxicity, thus prompting an intense investigation into the formation of metal-Abeta complexes. Isothermal titration calorimetry (ITC) has been widely used to determine binding constants (K) for a variety of metal-protein interactions, including those in metal-Abeta complexes. In this study, ITC was used to more fully quantify the thermodynamics (K, DeltaG, DeltaH, and TDeltaS) of Cu(2+) binding to Abeta16, N-acetyl-Abeta16, Abeta28, N-acetyl-Abeta28, and Abeta28 variants (H6A, H13A, H14A) at pH 7.4 and 37 degrees C. After deconvolution of competing reactions, K for Abeta16 was found to be 1.1 (+/-0.13) x 10(9) and is in strong agreement with literature values measured under similar conditions. Further, a similar K value was obtained at two additional concentrations of competing ligand, suggesting that ternary complex formation is not significant. The acetylated peptide analogs reveal a marked decrease in the overall free energy upon binding, which is the result of less favorable enthalpic and entropic contributions. Circular dichroism spectroscopy shows conformational changes that are consistent with these results. Most importantly, data for Abeta28 variants lacking a potential Cu(2+)-binding histidine residue reveal that the overall free energy of binding remains constant, which is the result of entropy/enthalpy compensation. These data provide fundamental thermodynamic evidence for coordination plasticity in Cu(2+) binding to Abeta and other intrinsically disordered peptides. CI - (c) SBIC 2012 FAU - Sacco, Cristina AU - Sacco C AD - Department of Chemistry, East Carolina University, 300 Science and Technology, Greenville, NC 27858, USA. FAU - Skowronsky, Rachel A AU - Skowronsky RA FAU - Gade, Sunitha AU - Gade S FAU - Kenney, John M AU - Kenney JM FAU - Spuches, Anne M AU - Spuches AM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120122 PL - Germany TA - J Biol Inorg Chem JT - Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry JID - 9616326 RN - 0 (Amyloid beta-Peptides) RN - 789U1901C5 (Copper) SB - IM MH - Amyloid beta-Peptides/*chemistry/metabolism MH - Binding Sites MH - Calorimetry MH - Copper/*chemistry/metabolism MH - *Thermodynamics EDAT- 2012/01/25 06:00 MHDA- 2012/10/30 06:00 CRDT- 2012/01/25 06:00 PHST- 2011/10/19 [received] PHST- 2012/01/04 [accepted] PHST- 2012/01/22 [aheadofprint] AID - 10.1007/s00775-012-0874-3 [doi] PST - ppublish SO - J Biol Inorg Chem. 2012 Apr;17(4):531-41. doi: 10.1007/s00775-012-0874-3. Epub 2012 Jan 22. PMID- 17534931 OWN - NLM STAT- MEDLINE DA - 20070730 DCOM- 20071023 LR - 20131121 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 87 IP - 1 DP - 2007 Sep TI - Conformational solution studies of the SDS micelle-bound 11-28 fragment of two Alzheimer's beta-amyloid variants (E22K and A21G) using CD, NMR, and MD techniques. PG - 23-39 AB - The beta-amyloid (Abeta) is the major peptide constituent of neuritic plaques in Alzheimer's disease (AD) and its aggregation is believed to play a central role in the pathogenesis of the disease. Naturally occurring mutations resulting in changes in the Abeta sequence (pos. 21-23) are associated with familial AD-like diseases with extensive cerebrovascular pathology. It was proved that the mutations alter the aggregation ability of Abeta and its neurotoxicity. Among five mutations at positions 21-23 there are two mutations with distinct clinical characteristics and potentially distinct pathogenic mechanism-the Italian (E22K) and the Flemish (A21G) mutations. In our studies we have examined the structures of the 11-28 fragment of the Italian and Flemish Abeta variants. The fragment was chosen because it has been shown to be the most important for amyloid fibril formation. The detailed structure of both variants Abeta(11-28) was determined using CD, 2D NMR, and molecular dynamics techniques under water-SDS micelle conditions. The NMR analysis revealed two distinct sets of proton resonances for the peptides. The studies of both peptides pointed out the existence of well-defined alpha-helical conformation in the Italian mutant, whereas the Flemish was found to be unstructured with the possibility of a bent structure in the central part of the peptide. CI - 2007 Wiley Periodicals, Inc FAU - Rodziewicz-Motowidlo, Sylwia AU - Rodziewicz-Motowidlo S AD - Faculty of Chemistry, University of Gdansk, Sobieskiego 18, 80-952 Gdansk, Poland. sylwia@chem.univ.gda.pl FAU - Juszczyk, Paulina AU - Juszczyk P FAU - Kolodziejczyk, Aleksandra S AU - Kolodziejczyk AS FAU - Sikorska, Emilia AU - Sikorska E FAU - Skwierawska, Agnieszka AU - Skwierawska A FAU - Oleszczuk, Marta AU - Oleszczuk M FAU - Grzonka, Zbigniew AU - Grzonka Z LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 RN - 0 (Amyloid beta-Peptides) RN - 0 (Micelles) RN - 0 (Peptides) RN - 368GB5141J (Sodium Dodecyl Sulfate) SB - IM MH - Alzheimer Disease MH - Amino Acid Substitution MH - Amyloid beta-Peptides/*chemistry/genetics/metabolism MH - Circular Dichroism MH - Humans MH - *Micelles MH - *Mutation, Missense MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides/*chemistry/genetics/metabolism MH - Protein Structure, Secondary/genetics MH - Sodium Dodecyl Sulfate/*chemistry EDAT- 2007/05/31 09:00 MHDA- 2007/10/24 09:00 CRDT- 2007/05/31 09:00 AID - 10.1002/bip.20768 [doi] PST - ppublish SO - Biopolymers. 2007 Sep;87(1):23-39. PMID- 18809678 OWN - NLM STAT- MEDLINE DA - 20081117 DCOM- 20090122 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 47 DP - 2008 Nov 21 TI - An unusual RNA recognition motif acts as a scaffold for multiple proteins in the pre-mRNA retention and splicing complex. PG - 32317-27 LID - 10.1074/jbc.M804977200 [doi] AB - The yeast pre-mRNA retention and splicing complex counteracts the escape of unspliced pre-mRNAs from the nucleus and activates splicing of a subset of Mer1p-dependent genes. A homologous complex is present in activated human spliceosomes. In many components of the spliceosome, RNA recognition motifs (RRMs) serve as versatile protein-RNA or protein-protein interaction platforms. Here, we show that in the retention and splicing complex, an atypical RRM of the Snu17p (small nuclear ribonucleoprotein-associated protein 17) subunit acts as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). GST pull-down experiments and size exclusion chromatography revealed that Snu17p constitutes the central platform of the complex, whereas Bud13p and Pml1p do not interact with each other. Fluorimetric structure probing showed the entire Bud13p and the N-terminal third of Pml1p to be natively disordered in isolation. Mutational analysis and tryptophan fluorescence confirmed that a conserved tryptophan-containing motif in the C terminus of Bud13p binds to the core RRM of Snu17p, whereas a different interaction surface encompassing a C-terminal extension of the Snu17p RRM is required to bind an N-terminal peptide of Pml1p. Isothermal titration calorimetry revealed 1:1 interaction stoichiometries, large negative binding entropies, and dissociation constants in the low nanomolar and micromolar ranges for the Snu17p-Bud13p and the Snu17p-Pml1p interactions, respectively. Our results demonstrate that the noncanonical Snu17p RRM concomitantly binds multiple ligand proteins via short, intrinsically unstructured peptide epitopes and thereby acts as a platform that displays functional modules of the ligands, such as a forkhead-associated domain of Pml1p and a conserved polylysine motif of Bud13p. FAU - Trowitzsch, Simon AU - Trowitzsch S AD - Zellulare Biochemie, Max-Planck-Institut fur Biophysikalische Chemie, Am Fassberg 11, D-37077 Gottingen, Germany. FAU - Weber, Gert AU - Weber G FAU - Luhrmann, Reinhard AU - Luhrmann R FAU - Wahl, Markus C AU - Wahl MC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080922 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bud13 protein, S cerevisiae) RN - 0 (Carrier Proteins) RN - 0 (IST3 protein, S cerevisiae) RN - 0 (Peptides) RN - 0 (Pml1 protein, S cerevisiae) RN - 0 (RNA Precursors) RN - 0 (Ribonucleoprotein, U2 Small Nuclear) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 25104-18-1 (Polylysine) SB - IM MH - Amino Acid Sequence MH - Animals MH - Carrier Proteins/metabolism MH - DNA Mutational Analysis MH - Humans MH - Molecular Sequence Data MH - Peptides/chemistry MH - Polylysine/metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - RNA Precursors/*metabolism MH - *RNA Splicing MH - Ribonucleoprotein, U2 Small Nuclear/metabolism MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/*metabolism MH - Sequence Homology, Amino Acid EDAT- 2008/09/24 09:00 MHDA- 2009/01/23 09:00 CRDT- 2008/09/24 09:00 PHST- 2008/09/22 [aheadofprint] AID - M804977200 [pii] AID - 10.1074/jbc.M804977200 [doi] PST - ppublish SO - J Biol Chem. 2008 Nov 21;283(47):32317-27. doi: 10.1074/jbc.M804977200. Epub 2008 Sep 22. PMID- 23557146 OWN - NLM STAT- MEDLINE DA - 20130410 DCOM- 20130808 LR - 20141116 IS - 1472-6750 (Electronic) IS - 1472-6750 (Linking) VI - 13 DP - 2013 TI - One single method to produce native and Tat-fused recombinant human alpha-synuclein in Escherichia coli. PG - 32 LID - 10.1186/1472-6750-13-32 [doi] AB - BACKGROUND: Human alpha-synuclein is a small-sized, natively unfolded protein that in fibrillar form is the primary component of Lewy bodies, the pathological hallmark of Parkinson's disease. Experimental evidence suggests that alpha-synuclein aggregation is the key event that triggers neurotoxicity although additional findings have proposed a protective role of alpha-synuclein against oxidative stress. One way to address the mechanism of this protective action is to evaluate alpha-synuclein-mediated protection by delivering this protein inside cells using a chimeric protein fused with the Tat-transduction domain of HIV Tat, named TAT-alpha-synuclein. RESULTS: A reliable protocol was designed to efficiently express and purify two different forms of human alpha-synuclein. The synthetic cDNAs encoding for the native alpha-synuclein and the fusion protein with the transduction domain of Tat protein from HIV were overexpressed in a BL21(DE3) E. coli strain as His-tagged proteins. The recombinant proteins largely localized (>/= 85%) to the periplasmic space. By using a quick purification protocol, based on recovery of periplasmic space content and metal-chelating chromatography, the recombinant alpha-synuclein protein forms could be purified in a single step to >/= 95% purity. Both alpha-synuclein recombinant proteins form fibrils and the TAT-alpha-synuclein is also cytotoxic in the micromolar concentration range. CONCLUSIONS: To further characterize the molecular mechanisms of alpha-synuclein neurotoxicity both in vitro and in vivo and to evaluate the relevance of extracellular alpha-synuclein for the pathogenesis and progression of Parkinson's disease, a suitable method to produce different high-quality forms of this pathological protein is required. Our optimized expression and purification procedure offers an easier and faster means of producing different forms (i.e., both the native and the TAT-fusion form) of soluble recombinant alpha-synuclein than previously described procedures. FAU - Caldinelli, Laura AU - Caldinelli L AD - Dipartimento di Biotecnologie e Scienze della Vita, Universita degli Studi dell'Insubria, via J.H. Dunant 3, Varese, Italy. FAU - Albani, Diego AU - Albani D FAU - Pollegioni, Loredano AU - Pollegioni L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130404 PL - England TA - BMC Biotechnol JT - BMC biotechnology JID - 101088663 RN - 0 (Recombinant Fusion Proteins) RN - 0 (SNCA protein, human) RN - 0 (alpha-Synuclein) RN - 0 (tat Gene Products, Human Immunodeficiency Virus) SB - IM MH - Chromatography, Affinity MH - Circular Dichroism MH - Cloning, Molecular MH - Escherichia coli/*metabolism MH - Humans MH - Microscopy, Confocal MH - Periplasm/metabolism MH - Recombinant Fusion Proteins/biosynthesis/chemistry/isolation & purification MH - Spectrophotometry, Ultraviolet MH - alpha-Synuclein/chemistry/genetics/*metabolism MH - tat Gene Products, Human Immunodeficiency Virus/genetics/*metabolism PMC - PMC3621789 OID - NLM: PMC3621789 EDAT- 2013/04/06 06:00 MHDA- 2013/08/09 06:00 CRDT- 2013/04/06 06:00 PHST- 2012/09/19 [received] PHST- 2013/03/25 [accepted] PHST- 2013/04/04 [aheadofprint] AID - 1472-6750-13-32 [pii] AID - 10.1186/1472-6750-13-32 [doi] PST - epublish SO - BMC Biotechnol. 2013 Apr 4;13:32. doi: 10.1186/1472-6750-13-32. PMID- 22988849 OWN - NLM STAT- MEDLINE DA - 20120919 DCOM- 20130226 LR - 20141105 IS - 1470-8752 (Electronic) IS - 0300-5127 (Linking) VI - 40 IP - 5 DP - 2012 Oct TI - Regulation of protein phosphatase 1 by intrinsically disordered proteins. PG - 969-74 AB - PP1 (protein phosphatase 1) is an essential serine/threonine phosphatase that plays a critical role in a broad range of biological processes, from muscle contraction to memory formation. PP1 achieves its biological specificity by forming holoenzymes with more than 200 known regulatory proteins. Interestingly, most of these regulatory proteins (>/= 70%) belong to the class of IDPs (intrinsically disordered proteins). Thus structural studies highlighting the interaction of these IDP regulatory proteins with PP1 are an attractive model system because it allows general parameters for a group of diverse IDPs that interact with the same binding partner to be identified, while also providing fundamental insights into PP1 biology. The present review provides a brief overview of our current understanding of IDP-PP1 interactions, including the importance of pre-formed secondary and tertiary structures for PP1 binding, as well as changes of IDP dynamics upon interacting with PP1. FAU - Choy, Meng S AU - Choy MS AD - Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA. FAU - Page, Rebecca AU - Page R FAU - Peti, Wolfgang AU - Peti W LA - eng GR - R01 GM098482/GM/NIGMS NIH HHS/United States GR - R01 NS056128/NS/NINDS NIH HHS/United States GR - R01GM098482/GM/NIGMS NIH HHS/United States GR - R01NS056128/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Biochem Soc Trans JT - Biochemical Society transactions JID - 7506897 RN - 0 (Proteins) RN - EC 3.1.3.16 (Protein Phosphatase 1) SB - IM MH - Humans MH - Protein Binding MH - Protein Conformation MH - Protein Phosphatase 1/chemistry/*metabolism MH - Proteins/chemistry/*metabolism PMC - PMC3502941 MID - NIHMS420080 OID - NLM: NIHMS420080 OID - NLM: PMC3502941 EDAT- 2012/09/20 06:00 MHDA- 2013/02/27 06:00 CRDT- 2012/09/20 06:00 AID - BST20120094 [pii] AID - 10.1042/BST20120094 [doi] PST - ppublish SO - Biochem Soc Trans. 2012 Oct;40(5):969-74. PMID- 17047358 OWN - NLM STAT- MEDLINE DA - 20061018 DCOM- 20061212 IS - 1660-2854 (Print) IS - 1660-2854 (Linking) VI - 3 IP - 4-5 DP - 2006 TI - Spectroscopic approaches to the conformation of tau protein in solution and in paired helical filaments. PG - 197-206 AB - The abnormal aggregation of the microtubule-associated protein tau into paired helical filaments is one the hallmarks of Alzheimer's disease. This aggregation is based in the partial formation of beta-structure. In contrast, the soluble protein shows a mostly random coil structure, as judged by circular dichroism, Fourier transform infrared, X-ray scattering and biochemical assays. Here, we review the basis of the natively unstructured character of tau, as well as recent studies of residual structure and long-range interactions between different domains of the protein. Analysis of the primary structure reveals a very low content of hydrophobic amino acids and a high content of charged residues, both of which tend to counteract a well-folded globular state of proteins. In the case of tau, the low overall hydrophobicity is sufficient to explain the lack of folding. This is in contrast to other proteins which also carry an excess charge at physiological pH. By tryptophan scanning mutagenesis and fluorimetry we found that most of the sequence is solvent exposed. Analysis of the hydrodynamic radii confirms a mostly random coil structure of various tau isoforms and tau domains. The proteins can be further expanded by denaturation with GdHCl which indicates some global folding. This was substantiated by a FRET-based approach where the distances between different domains of tau were determined. The combined data show that tau is mostly disordered and flexible but tends to assume a hairpin-like overall fold which may be important in the transition to a pathological aggregate. CI - Copyright 2006 S. Karger AG, Basel. FAU - von Bergen, M AU - von Bergen M AD - Max Planck Unit for Structural Molecular Biology, Hamburg, Germany. FAU - Barghorn, S AU - Barghorn S FAU - Jeganathan, S AU - Jeganathan S FAU - Mandelkow, E-M AU - Mandelkow EM FAU - Mandelkow, E AU - Mandelkow E LA - eng PT - Journal Article PT - Review PL - Switzerland TA - Neurodegener Dis JT - Neuro-degenerative diseases JID - 101189034 RN - 0 (Protein Isoforms) RN - 0 (tau Proteins) SB - IM MH - Animals MH - Humans MH - Protein Isoforms MH - Protein Structure, Secondary MH - Spectrum Analysis MH - tau Proteins/*chemistry RF - 64 EDAT- 2006/10/19 09:00 MHDA- 2006/12/13 09:00 CRDT- 2006/10/19 09:00 AID - 95257 [pii] AID - 10.1159/000095257 [doi] PST - ppublish SO - Neurodegener Dis. 2006;3(4-5):197-206. PMID- 23557784 OWN - NLM STAT- MEDLINE DA - 20131209 DCOM- 20140228 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1843 IP - 1 DP - 2014 Jan TI - Pupylation as a signal for proteasomal degradation in bacteria. PG - 103-13 LID - 10.1016/j.bbamcr.2013.03.022 [doi] LID - S0167-4889(13)00123-7 [pii] AB - Posttranslational modifications in the form of covalently attached proteins like ubiquitin (Ub), were long considered an exclusive feature of eukaryotic organisms. The discovery of pupylation, the modification of lysine residues with a prokaryotic, ubiquitin-like protein (Pup), demonstrated that certain bacteria use a tagging pathway functionally related to ubiquitination in order to target proteins for proteasomal degradation. However, functional analogies do not translate into structural or mechanistic relatedness. Bacterial Pup, unlike eukaryotic Ub, does not adopt a beta-grasp fold, but is intrinsically disordered. Furthermore, isopeptide bond formation in the pupylation process is carried out by enzymes evolutionary descendent from glutamine synthetases. While in eukaryotes, the proteasome is the main energy-dependent protein degradation machine, bacterial proteasomes exist in addition to other architecturally related degradation complexes, and their specific role along with the role of pupylation is still poorly understood. In Mycobacterium tuberculosis (Mtb), the Pup-proteasome system contributes to pathogenicity by supporting the bacterium's persistence within host macrophages. Here, we describe the mechanism and structural framework of pupylation and the targeting of pupylated proteins to the proteasome complex. Particular attention is given to the comparison of the bacterial Pup-proteasome system and the eukaryotic ubiquitin-proteasome system. Furthermore, the involvement of pupylation and proteasomal degradation in Mtb pathogenesis is discussed together with efforts to establish the Pup-proteasome system as a drug target. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf. CI - Copyright (c) 2013 Elsevier B.V. All rights reserved. FAU - Striebel, Frank AU - Striebel F AD - Max Planck Institute of Biochemistry, Department of Molecular Cell Biology, D-82152 Martinsried, Germany. FAU - Imkamp, Frank AU - Imkamp F FAU - Ozcelik, Dennis AU - Ozcelik D FAU - Weber-Ban, Eilika AU - Weber-Ban E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20130402 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Bacterial Proteins) RN - 0 (Protein Sorting Signals) RN - 0 (Ubiquitins) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Amino Acid Sequence MH - Bacteria/*metabolism MH - Bacterial Proteins/chemistry/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Proteasome Endopeptidase Complex/*metabolism MH - Protein Sorting Signals/physiology MH - *Proteolysis MH - Sequence Homology, Amino Acid MH - Ubiquitination/*physiology MH - Ubiquitins/*metabolism OTO - NOTNLM OT - Mycobacterium tuberculosis OT - Post-translational modification OT - Prokaryotic ubiquitin-like protein Pup OT - Proteasome OT - Pupylation OT - Pup-proteasome pathway EDAT- 2013/04/06 06:00 MHDA- 2014/03/01 06:00 CRDT- 2013/04/06 06:00 PHST- 2012/12/03 [received] PHST- 2013/02/21 [revised] PHST- 2013/03/12 [accepted] PHST- 2013/04/02 [aheadofprint] AID - S0167-4889(13)00123-7 [pii] AID - 10.1016/j.bbamcr.2013.03.022 [doi] PST - ppublish SO - Biochim Biophys Acta. 2014 Jan;1843(1):103-13. doi: 10.1016/j.bbamcr.2013.03.022. Epub 2013 Apr 2. PMID- 9032054 OWN - NLM STAT- MEDLINE DA - 19970319 DCOM- 19970319 LR - 20091119 IS - 0959-440X (Print) IS - 0959-440X (Linking) VI - 7 IP - 1 DP - 1997 Feb TI - Lac repressor-operator complex. PG - 76-85 AB - For many years the lac operon of Escherichia coli has been the paradigm for gene regulation. Recently, the structures of the lac repressor core bound to isopropyl-beta-D-1-thiogalactoside (IPTG), the intact apo lac repressor, the intact lac repressor complexes with IPTG and a 21-base-pair symmetric operator, and the refined headpiece of the repressor have been determined. These structures have provided a framework for understanding a wealth of biochemical and genetic information. An analysis of these structures, as well as a description of their function and a comparison to homologous proteins, is now possible. FAU - Kercher, M A AU - Kercher MA AD - Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. kercher@crystal.med.upenn.edu FAU - Lu, P AU - Lu P FAU - Lewis, M AU - Lewis M LA - eng PT - Journal Article PT - Review PL - ENGLAND TA - Curr Opin Struct Biol JT - Current opinion in structural biology JID - 9107784 RN - 0 (Bacterial Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Lac Repressors) RN - 0 (Repressor Proteins) SB - IM MH - Allosteric Regulation MH - Bacterial Proteins/*metabolism MH - Binding Sites MH - *Escherichia coli Proteins MH - *Lac Operon MH - Lac Repressors MH - Protein Binding MH - Repressor Proteins/*metabolism RF - 97 EDAT- 1997/02/01 MHDA- 1997/02/01 00:01 CRDT- 1997/02/01 00:00 AID - S0959-440X(97)80010-3 [pii] PST - ppublish SO - Curr Opin Struct Biol. 1997 Feb;7(1):76-85. PMID- 22807669 OWN - NLM STAT- MEDLINE DA - 20120718 DCOM- 20130123 LR - 20141015 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 8 IP - 7 DP - 2012 TI - Importance of electrostatic interactions in the association of intrinsically disordered histone chaperone Chz1 and histone H2A.Z-H2B. PG - e1002608 LID - 10.1371/journal.pcbi.1002608 [doi] AB - Histone chaperones facilitate assembly and disassembly of nucleosomes. Understanding the process of how histone chaperones associate and dissociate from the histones can help clarify their roles in chromosome metabolism. Some histone chaperones are intrinsically disordered proteins (IDPs). Recent studies of IDPs revealed that the recognition of the biomolecules is realized by the flexibility and dynamics, challenging the century-old structure-function paradigm. Here we investigate the binding between intrinsically disordered chaperone Chz1 and histone variant H2A.Z-H2B by developing a structure-based coarse-grained model, in which Debye-Huckel model is implemented for describing electrostatic interactions due to highly charged characteristic of Chz1 and H2A.Z-H2B. We find that major structural changes of Chz1 only occur after the rate-limiting electrostatic dominant transition state and Chz1 undergoes folding coupled binding through two parallel pathways. Interestingly, although the electrostatic interactions stabilize bound complex and facilitate the recognition at first stage, the rate for formation of the complex is not always accelerated due to slow escape of conformations with non-native electrostatic interactions at low salt concentrations. Our studies provide an ionic-strength-controlled binding/folding mechanism, leading to a cooperative mechanism of "local collapse or trapping" and "fly-casting" together and a new understanding of the roles of electrostatic interactions in IDPs' binding. FAU - Chu, Xiakun AU - Chu X AD - College of Physics, Jilin University, Changchun, Jilin, P.R. China. FAU - Wang, Yong AU - Wang Y FAU - Gan, Linfeng AU - Gan L FAU - Bai, Yawen AU - Bai Y FAU - Han, Wei AU - Han W FAU - Wang, Erkang AU - Wang E FAU - Wang, Jin AU - Wang J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120712 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (Histone Chaperones) RN - 0 (Histones) RN - 7647-14-5 (Sodium Chloride) SB - IM MH - Histone Chaperones/*chemistry/metabolism MH - Histones/*chemistry/metabolism MH - *Models, Chemical MH - Models, Molecular MH - Protein Binding MH - Protein Folding MH - Sodium Chloride/chemistry MH - Static Electricity MH - Thermodynamics PMC - PMC3395605 OID - NLM: PMC3395605 EDAT- 2012/07/19 06:00 MHDA- 2013/01/24 06:00 CRDT- 2012/07/19 06:00 PHST- 2012/02/11 [received] PHST- 2012/05/21 [accepted] PHST- 2012/07/12 [epublish] AID - 10.1371/journal.pcbi.1002608 [doi] AID - PCOMPBIOL-D-12-00243 [pii] PST - ppublish SO - PLoS Comput Biol. 2012;8(7):e1002608. doi: 10.1371/journal.pcbi.1002608. Epub 2012 Jul 12. PMID- 15035602 OWN - NLM STAT- MEDLINE DA - 20040323 DCOM- 20040721 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 12 DP - 2004 Mar 30 TI - The HPV16 E7 viral oncoprotein self-assembles into defined spherical oligomers. PG - 3310-7 AB - Despite the fact that E7 is a major transforming oncoprotein in papillomavirus, its structure and precise molecular mechanism of action remain puzzling to date. E7 proteins share sequence homology and proteasome targeting properties of tumor suppressors with adenovirus E1A and SV40 T antigen, two other paradigmatic oncoproteins from DNA tumor viruses. High-risk HPV16 E7, a nonglobular dimer with some properties of intrinsically disordered proteins, is capable of undergoing pH-dependent conformational transitions that expose hydrophobic surfaces to the solvent. We found that treatment with a chelating agent produced a protein that can readily assemble into homogeneous spherical particles with an average molecular mass of 790 kDa and a diameter of 50 nm, as determined from dynamic light scattering and electron microscopy. The protein undergoes a substantial conformational transition from coil to beta-sheet structure, with concomitant consolidation of tertiary structure as judged by circular dichroism and fluorescence. The assembly process is very slow, in agreement with a substantial energy barrier caused by structural rearrangements. The resulting particles are highly stable, cooperatively folded, and capable of binding both Congo Red and thioflavin T, reporters of repetitive beta-sheet structures similar to those found in amyloids, although no fibrillar or insoluble material was observed under our experimental conditions. FAU - Alonso, Leonardo G AU - Alonso LG AD - Instituto Leloir, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Patricias Argentinas 435, (1405) Buenos Aires, Argentina. FAU - Garcia-Alai, Maria M AU - Garcia-Alai MM FAU - Smal, Clara AU - Smal C FAU - Centeno, Juan M AU - Centeno JM FAU - Iacono, Ruben AU - Iacono R FAU - Castano, Eduardo AU - Castano E FAU - Gualfetti, Peter AU - Gualfetti P FAU - de Prat-Gay, Gonzalo AU - de Prat-Gay G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Fluorescent Dyes) RN - 0 (Oncogene Proteins, Viral) RN - 0 (Papillomavirus E7 Proteins) RN - 0 (Thiazoles) RN - 0 (oncogene protein E7, Human papillomavirus type 16) RN - 2390-54-7 (thioflavin T) RN - 3U05FHG59S (Congo Red) RN - EC 2.7.11.1 (Casein Kinase II) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - J41CSQ7QDS (Zinc) SB - IM MH - Casein Kinase II MH - Circular Dichroism MH - Congo Red/chemistry MH - Dimerization MH - Fluorescent Dyes/chemistry MH - Humans MH - Molecular Weight MH - Oncogene Proteins, Viral/*chemistry/metabolism MH - Papillomaviridae/chemistry/*physiology MH - Papillomavirus E7 Proteins MH - Phosphorylation MH - Protein Binding MH - Protein Structure, Secondary MH - Protein-Serine-Threonine Kinases/metabolism MH - Solubility MH - Thiazoles/chemistry MH - *Virus Assembly MH - Zinc/chemistry EDAT- 2004/03/24 05:00 MHDA- 2004/07/22 05:00 CRDT- 2004/03/24 05:00 AID - 10.1021/bi036037o [doi] PST - ppublish SO - Biochemistry. 2004 Mar 30;43(12):3310-7. PMID- 18809412 OWN - NLM STAT- MEDLINE DA - 20081030 DCOM- 20081117 LR - 20140912 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 384 IP - 1 DP - 2008 Dec 5 TI - Intrinsically unstructured domains of Arf and Hdm2 form bimolecular oligomeric structures in vitro and in vivo. PG - 240-54 LID - 10.1016/j.jmb.2008.09.019 [doi] AB - Arf, Hdm2, and p53 regulate the tumor-suppressor pathway that is most frequently disrupted in human cancer. In the absence of tumorigenic stress, Hdm2 actively attenuates p53-dependent cell cycle arrest and apoptosis by mediating ubiquitination-dependent degradation of p53. Mitogenic stress activates Arf, which indirectly activates p53 by binding to and nullifying the anti-p53 activities of Hdm2. Small conserved domains within Arf and Hdm2 mediate their direct interaction. Individually, these domains are intrinsically unstructured and, when combined in vitro, cofold into bimolecular oligomeric structures that resemble amyloid fibrils in some features. Detailed structural characterization of Hdm2/Arf complexes has previously been hampered by their heterogeneity and large size. Here, we report that a nine-residue fragment of the N-terminus of mouse Arf (termed "A1-mini") cofolds specifically with the Arf-binding domain of Hdm2 to form bimolecular oligomers. We characterized these unprecedented structures using analytical ultracentrifugation and NMR spectroscopy, providing insights into their structural organization. The A1-mini peptide not only binds specifically to Hdm2 in vitro but also recapitulates the nucleolar localization features of full-length Arf in cells. Furthermore, larger fragments of Arf that contain the A1-mini segment have previously been shown to activate p53 in mouse and human cells. Our studies provide the first insights into the molecular basis through which Arf nullifies the p53-inhibiting activity of Hdm2, indirectly activating the tumor-suppressor function of p53 in mammalian cells. FAU - Sivakolundu, Sivashankar G AU - Sivakolundu SG AD - Department of Structural Biology, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, TN 38105, USA. FAU - Nourse, Amanda AU - Nourse A FAU - Moshiach, Simon AU - Moshiach S FAU - Bothner, Brian AU - Bothner B FAU - Ashley, Chimere AU - Ashley C FAU - Satumba, John AU - Satumba J FAU - Lahti, Jill AU - Lahti J FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng GR - CA 82491/CA/NCI NIH HHS/United States GR - P30CA21765/CA/NCI NIH HHS/United States GR - R01 CA092035/CA/NCI NIH HHS/United States GR - R01 CA092035-01/CA/NCI NIH HHS/United States GR - R01 CA092035-02/CA/NCI NIH HHS/United States GR - R01 CA092035-02S1/CA/NCI NIH HHS/United States GR - R01 CA092035-03/CA/NCI NIH HHS/United States GR - R01 CA092035-04/CA/NCI NIH HHS/United States GR - R01 CA092035-05/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20080916 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Spin Labels) RN - 0 (Tumor Suppressor Protein p14ARF) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - 3T3 Cells MH - Amino Acid Sequence MH - Animals MH - Cell Nucleolus/metabolism MH - Conserved Sequence MH - Fibroblasts/cytology/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-mdm2/*chemistry/metabolism MH - Sequence Alignment MH - Spin Labels MH - Tumor Suppressor Protein p14ARF/*chemistry/metabolism PMC - PMC2612038 MID - NIHMS79226 OID - NLM: NIHMS79226 OID - NLM: PMC2612038 EDAT- 2008/09/24 09:00 MHDA- 2008/11/18 09:00 CRDT- 2008/09/24 09:00 PHST- 2008/04/29 [received] PHST- 2008/09/04 [revised] PHST- 2008/09/10 [accepted] PHST- 2008/09/16 [aheadofprint] AID - S0022-2836(08)01152-2 [pii] AID - 10.1016/j.jmb.2008.09.019 [doi] PST - ppublish SO - J Mol Biol. 2008 Dec 5;384(1):240-54. doi: 10.1016/j.jmb.2008.09.019. Epub 2008 Sep 16. PMID- 12824490 OWN - NLM STAT- MEDLINE DA - 20030625 DCOM- 20041102 LR - 20140611 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 12 IP - 7 DP - 2003 Jul TI - The inactivating factor of glutamine synthetase, IF7, is a "natively unfolded" protein. PG - 1443-54 AB - Glutamine synthetase (GS) is the key enzyme responsible for the primary assimilation of ammonium in all living organisms, and it catalyses the synthesis of glutamine from glutamic acid, ATP, and ammonium. One of the recently discovered mechanisms of GS regulation involves protein-protein interactions with a small 65-residue-long protein named IF7. Here, we study the structure and stability of IF7 and its binding properties to GS, by using several biophysical techniques (fluorescence, circular dichroism, Fourier transform infrared and nuclear magnetic resonance spectroscopies, and gel filtration chromatography) which provide complementary structural information. The findings show that IF7 has a small amount of residual secondary structure, but lacks a well defined tertiary structure, and is not compact. Thus, all of the studies indicate that IF7 is a "natively unfolded" protein. The binding of IF7 to GS, its natural binding partner, occurs with an apparent dissociation constant of K(D) = 0.3 +/- 0.1 microM, as measured by fluorescence. We discuss the implications for the GS regulation mechanisms of IF7 being unfolded. FAU - Muro-Pastor, M Isabel AU - Muro-Pastor MI AD - Instituto de Bioquimica Vegetal y Fotosintesis, Universidad de Sevilla-Consejo Superior de Investigaciones Cientificas, 41092 Seville, Spain. FAU - Barrera, Francisco N AU - Barrera FN FAU - Reyes, Jose C AU - Reyes JC FAU - Florencio, Francisco J AU - Florencio FJ FAU - Neira, Jose L AU - Neira JL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Bacterial Proteins) RN - 0 (IF7 protein, Synechocystis sp.) RN - EC 6.3.1.2 (Glutamate-Ammonia Ligase) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/genetics MH - Binding Sites MH - Chromatography, Gel MH - Circular Dichroism MH - Glutamate-Ammonia Ligase/antagonists & inhibitors/*chemistry MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Spectrometry, Fluorescence MH - Spectrophotometry MH - Spectroscopy, Fourier Transform Infrared MH - Temperature MH - Time Factors PMC - PMC2323932 OID - NLM: PMC2323932 EDAT- 2003/06/26 05:00 MHDA- 2004/11/04 09:00 CRDT- 2003/06/26 05:00 AID - 10.1110/ps.0303203 [doi] PST - ppublish SO - Protein Sci. 2003 Jul;12(7):1443-54. PMID- 12824491 OWN - NLM STAT- MEDLINE DA - 20030625 DCOM- 20041102 LR - 20140611 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 12 IP - 7 DP - 2003 Jul TI - Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase. PG - 1455-63 AB - Pyridoxine 5'-phosphate oxidase catalyzes the terminal step in the synthesis of pyridoxal 5'-phosphate. The cDNA for the human enzyme has been cloned and expressed in Escherichia coli. The purified human enzyme is a homodimer that exhibits a low catalytic rate constant of approximately 0.2 sec(-1) and K(m) values in the low micromolar range for both pyridoxine 5'phosphate and pyridoxamine 5'-phosphate. Pyridoxal 5'-phosphate is an effective product inhibitor. The three-dimensional fold of the human enzyme is very similar to those of the E. coli and yeast enzymes. The human and E. coli enzymes share 39% sequence identity, but the binding sites for the tightly bound FMN and substrate are highly conserved. As observed with the E. coli enzyme, the human enzyme binds one molecule of pyridoxal 5'-phosphate tightly on each subunit. FAU - Musayev, Faik N AU - Musayev FN AD - Department of Medicinal Chemistry, Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, 800 E. Leigh Street, Richmond, VA 23219, USA. FAU - Di Salvo, Martino L AU - Di Salvo ML FAU - Ko, Tzu-Ping AU - Ko TP FAU - Schirch, Verne AU - Schirch V FAU - Safo, Martin K AU - Safo MK LA - eng GR - DK 55648/DK/NIDDK NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Recombinant Proteins) RN - 5V5IOJ8338 (Pyridoxal Phosphate) RN - 7N464URE7E (Flavin Mononucleotide) RN - EC 1.4.3.5 (Pyridoxaminephosphate Oxidase) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - Escherichia coli/genetics/metabolism MH - Flavin Mononucleotide/genetics/metabolism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Pyridoxal Phosphate/metabolism MH - Pyridoxaminephosphate Oxidase/*chemistry/genetics/metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Alignment PMC - PMC2323923 OID - NLM: PMC2323923 EDAT- 2003/06/26 05:00 MHDA- 2004/11/04 09:00 CRDT- 2003/06/26 05:00 AID - 10.1110/ps.0356203 [doi] PST - ppublish SO - Protein Sci. 2003 Jul;12(7):1455-63. PMID- 24397337 OWN - NLM STAT- MEDLINE DA - 20140121 DCOM- 20140710 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 2 DP - 2014 Jan 21 TI - A four-amino acid linker between repeats in the alpha-synuclein sequence is important for fibril formation. PG - 279-81 LID - 10.1021/bi401427t [doi] AB - alpha-Synuclein is a 140-amino acid protein that can switch conformation among intrinsically disordered in solution, helical on a membrane, and beta-sheet in amyloid fibrils. Using the fluorescence of single-tryptophan mutants, we determined the immersion of different regions of the protein into lipid membranes. Our results suggest the presence of a flexible break close to residues 52-55 between two helical domains. The four-amino acid linker is not necessary for membrane binding but is important for fibril formation. A deletion mutant lacking this linker aggregates extremely slowly and slightly inhibits wild-type aggregation, possibly by blocking the growing ends of fibrils. FAU - Shvadchak, Volodymyr V AU - Shvadchak VV AD - Nanobiophysics, MESA+ Institute for Nanotechnology, and MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente , 7522 NB Enschede, The Netherlands. FAU - Subramaniam, Vinod AU - Subramaniam V LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140108 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amino Acids) RN - 0 (Amyloid) RN - 0 (alpha-Synuclein) RN - 8DUH1N11BX (Tryptophan) SB - IM MH - Amino Acid Sequence MH - Amino Acids/genetics/*metabolism MH - Amyloid/*chemistry/genetics/*metabolism MH - Fluorescence MH - Humans MH - Models, Molecular MH - Mutation MH - Protein Conformation MH - Tryptophan/genetics/metabolism MH - alpha-Synuclein/*chemistry/genetics/*metabolism EDAT- 2014/01/09 06:00 MHDA- 2014/07/11 06:00 CRDT- 2014/01/09 06:00 PHST- 2014/01/08 [aheadofprint] AID - 10.1021/bi401427t [doi] PST - ppublish SO - Biochemistry. 2014 Jan 21;53(2):279-81. doi: 10.1021/bi401427t. Epub 2014 Jan 8. PMID- 19959848 OWN - NLM STAT- MEDLINE DA - 20100301 DCOM- 20100429 LR - 20150604 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 10 DP - 2010 Mar 5 TI - The positively charged region of the myosin IIC non-helical tailpiece promotes filament assembly. PG - 7079-86 LID - 10.1074/jbc.M109.049221 [doi] AB - The motor protein, non-muscle myosin II (NMII), must undergo dynamic oligomerization into filaments to participate in cellular processes such as cell migration and cytokinesis. A small non-helical region at the tail of the long coiled-coil region (tailpiece) is a common feature of all dynamically assembling myosin II proteins. In this study, we investigated the role of the tailpiece in NMII-C self-assembly. We show that the tailpiece is natively unfolded, as seen by circular dichroism and NMR experiments, and is divided into two regions of opposite charge. The positively charged region (Tailpiece(1946-1967)) starts at residue 1946 and is extended by seven amino acids at its N terminus from the traditional coiled-coil ending proline (Tailpiece(1953-1967)). Pull-down and sedimentation assays showed that the positive Tailpiece(1946-1967) binds to assembly incompetent NMII-C fragments inducing filament assembly. The negative region, residues 1968-2000, is responsible for NMII paracrystal morphology as determined by chimeras in which the negative region was swapped between the NMII isoforms. Mixing the positive and negative peptides had no effect on the ability of the positive peptide to bind and induce filament assembly. This study provides molecular insight into the role of the structurally disordered tailpiece of NMII-C in shifting the oligomeric equilibrium of NMII-C toward filament assembly and determining its morphology. FAU - Ronen, Daniel AU - Ronen D AD - Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel. FAU - Rosenberg, Masha M AU - Rosenberg MM FAU - Shalev, Deborah E AU - Shalev DE FAU - Rosenberg, Michael AU - Rosenberg M FAU - Rotem, Shahar AU - Rotem S FAU - Friedler, Assaf AU - Friedler A FAU - Ravid, Shoshana AU - Ravid S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091203 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Peptides) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Fusion Proteins) RN - EC 3.6.1.- (Myosin Type II) SB - IM EIN - J Biol Chem. 2015 Apr 10;290(15):9362. PMID: 25862808 MH - Amino Acid Sequence MH - Animals MH - Circular Dichroism MH - *Cytoskeleton/chemistry/ultrastructure MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Myosin Type II/*chemistry/genetics/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides/chemistry/genetics/metabolism MH - Protein Folding MH - Protein Isoforms/*chemistry/genetics/*metabolism MH - *Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - Recombinant Fusion Proteins/chemistry/genetics/metabolism PMC - PMC2844157 OID - NLM: PMC2844157 EDAT- 2009/12/05 06:00 MHDA- 2010/04/30 06:00 CRDT- 2009/12/05 06:00 PHST- 2009/12/03 [aheadofprint] AID - M109.049221 [pii] AID - 10.1074/jbc.M109.049221 [doi] PST - ppublish SO - J Biol Chem. 2010 Mar 5;285(10):7079-86. doi: 10.1074/jbc.M109.049221. Epub 2009 Dec 3. PMID- 11784308 OWN - NLM STAT- MEDLINE DA - 20020110 DCOM- 20020221 LR - 20070723 IS - 0014-2956 (Print) IS - 0014-2956 (Linking) VI - 269 IP - 1 DP - 2002 Jan TI - A Raman optical activity study of rheomorphism in caseins, synucleins and tau. New insight into the structure and behaviour of natively unfolded proteins. PG - 148-56 AB - The casein milk proteins and the brain proteins alpha-synuclein and tau have been described as natively unfolded with random coil structures, which, in the case of alpha-synuclein and tau, have a propensity to form the fibrils found in a number of neurodegenerative diseases. New insight into the structures of these proteins has been provided by a Raman optical activity study, supplemented with differential scanning calorimetry, of bovine beta- and kappa-casein, recombinant human alpha-, beta- and gamma-synuclein, together with the A30P and A53T mutants of alpha-synuclein associated with familial cases of Parkinson's disease, and recombinant human tau 46 together with the tau 46 P301L mutant associated with inherited frontotemporal dementia. The Raman optical activity spectra of all these proteins are very similar, being dominated by a strong positive band centred at approximately 1318 cm(-1) that may be due to the poly(l-proline) II (PPII) helical conformation. There are no Raman optical activity bands characteristic of extended secondary structure, although some unassociated beta strand may be present. Differential scanning calorimetry revealed no thermal transitions for these proteins in the range 15-110 degrees C, suggesting that the structures are loose and noncooperative. As it is extended, flexible, lacks intrachain hydrogen bonds and is hydrated in aqueous solution, PPII helix may impart a rheomorphic (flowing shape) character to the structure of these proteins that could be essential for their native function but which may, in the case of alpha-synuclein and tau, result in a propensity for pathological fibril formation due to particular residue properties. FAU - Syme, Christopher D AU - Syme CD AD - Department of Chemistry, University of Glasgow, UK. FAU - Blanch, Ewan W AU - Blanch EW FAU - Holt, Carl AU - Holt C FAU - Jakes, Ross AU - Jakes R FAU - Goedert, Michel AU - Goedert M FAU - Hecht, Lutz AU - Hecht L FAU - Barron, Laurence D AU - Barron LD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Eur J Biochem JT - European journal of biochemistry / FEBS JID - 0107600 RN - 0 (Caseins) RN - 0 (Nerve Tissue Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 0 (gamma-Synuclein) RN - 0 (tau Proteins) SB - IM MH - Animals MH - Caseins/*chemistry MH - Cattle MH - Humans MH - Nerve Tissue Proteins/*chemistry MH - *Protein Folding MH - Protein Structure, Secondary MH - Spectrum Analysis, Raman MH - Synucleins MH - alpha-Synuclein MH - gamma-Synuclein MH - tau Proteins/*chemistry EDAT- 2002/01/11 10:00 MHDA- 2002/02/22 10:01 CRDT- 2002/01/11 10:00 AID - 2633 [pii] PST - ppublish SO - Eur J Biochem. 2002 Jan;269(1):148-56. PMID- 24956062 OWN - NLM STAT- In-Process DA - 20150219 IS - 1538-0254 (Electronic) IS - 0739-1102 (Linking) VI - 33 IP - 5 DP - 2015 TI - Cell communication using intrinsically disordered proteins: what can syndecans say? PG - 1037-50 LID - 10.1080/07391102.2014.926256 [doi] AB - Because intrinsically disordered proteins are incapable of forming unique tertiary structures in isolation, their interaction with partner structures enables them to play important roles in many different biological functions. Therefore, such proteins are usually multifunctional, and their ability to perform their major function, as well as accessory functions, depends on the characteristics of a given interaction. The present paper demonstrates, using predictions from two programs, that the transmembrane proteoglycans syndecans are natively disordered because of their diverse functions and large number of interaction partners. Syndecans perform multiple functions during development, damage repair, tumor growth, angiogenesis, and neurogenesis. By mediating the binding of a large number of extracellular ligands to their receptors, these proteoglycans trigger a cascade of reactions that subsequently regulate various cell processes: cytoskeleton formation, proliferation, differentiation, adhesion, and migration. The occurrences of 20 amino acids in syndecans 1-4 from 25 animals were compared with those in 17 animal proteomes. Gly + Ala, Thr, Glu, and Pro were observed to predominate in the syndecans, contributing to the lack of an ordered structure. In contrast, there were many fewer amino acids in syndecans that promote an ordered structure, such as Cys, Trp, Asn, and His. In addition, a region rich in Asp has been identified between two heparan sulfate-binding sites in the ectodomains, and a region rich in Lys has been identified in the conserved C1 site of the cytoplasmic domain. These particular regions play an essential role in the various functions of syndecans due to their lack of structure. FAU - Leonova, Elena I AU - Leonova EI AD - a Institute of Protein Research, Russian Academy of Sciences , Moscow Region, Pushchino 142290 , Russia. FAU - Galzitskaya, Oxana V AU - Galzitskaya OV LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140623 PL - England TA - J Biomol Struct Dyn JT - Journal of biomolecular structure & dynamics JID - 8404176 SB - IM OTO - NOTNLM OT - adhesion OT - cell matrix OT - disordered regions OT - intrinsically disordered proteins OT - library of disordered patterns OT - transmembrane proteoglycans EDAT- 2014/06/24 06:00 MHDA- 2014/06/24 06:00 CRDT- 2014/06/24 06:00 PHST- 2014/06/23 [aheadofprint] AID - 10.1080/07391102.2014.926256 [doi] PST - ppublish SO - J Biomol Struct Dyn. 2015;33(5):1037-50. doi: 10.1080/07391102.2014.926256. Epub 2014 Jun 23. PMID- 23870269 OWN - NLM STAT- MEDLINE DA - 20130722 DCOM- 20140206 LR - 20141113 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 105 IP - 2 DP - 2013 Jul 16 TI - NMR determines transient structure and dynamics in the disordered C-terminal domain of WASp interacting protein. PG - 481-93 LID - 10.1016/j.bpj.2013.05.046 [doi] LID - S0006-3495(13)00633-4 [pii] AB - WASp-interacting protein (WIP) is a 503-residue proline-rich polypeptide expressed in human T cells. The WIP C-terminal domain binds to Wiskott-Aldrich syndrome protein (WASp) and regulates its activation and degradation, and the WIP-WASp interaction has been shown to be critical for actin polymerization and implicated in the onset of WAS and X-linked thrombocytopenia. WIP is predicted to be an intrinsically disordered protein, a class of polypeptides that are of great interest because they violate the traditional structure-function paradigm. In this first (to our knowledge) study of WIP in its unbound state, we used NMR to investigate the biophysical behavior of WIP(C), a C-terminal domain fragment of WIP that includes residues 407-503 and contains the WASp-binding site. In light of the poor spectral dispersion exhibited by WIP(C) and the high occurrence (25%) of proline residues, we employed 5D-NMR(13)C-detected NMR experiments with nonuniform sampling to accomplish full resonance assignment. Secondary chemical-shift analysis, (15)N relaxation rates, and protection from solvent exchange all concurred in detecting transient structure located in motifs that span the WASp-binding site. Residues 446-456 exhibited a propensity for helical conformation, and an extended conformation followed by a short, capped helix was observed for residues 468-478. The (13)C-detected approach allows chemical-shift assignment in the WIP(C) polyproline stretches and thus sheds light on their conformation and dynamics. The effects of temperature on chemical shifts referenced to a denatured sample of the polypeptide demonstrate that heating reduces the structural character of WIP(C). Thus, we conclude that the disordered WIP(C) fragment is comprised of regions with latent structure connected by flexible loops, an architecture with implications for binding affinity and function. CI - Copyright (c) 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Haba, Noam Y AU - Haba NY AD - Department of Chemistry, Bar Ilan University, Ramat Gan, Israel. FAU - Gross, Renana AU - Gross R FAU - Novacek, Jiri AU - Novacek J FAU - Shaked, Hadassa AU - Shaked H FAU - Zidek, Lukas AU - Zidek L FAU - Barda-Saad, Mira AU - Barda-Saad M FAU - Chill, Jordan H AU - Chill JH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Cytoskeletal Proteins) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Peptides) RN - 0 (WIPF1 protein, human) RN - 25191-13-3 (polyproline) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - Cytoskeletal Proteins/*chemistry MH - Humans MH - Intracellular Signaling Peptides and Proteins/*chemistry MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Peptides/chemistry MH - Protein Structure, Tertiary PMC - PMC3714880 OID - NLM: PMC3714880 EDAT- 2013/07/23 06:00 MHDA- 2014/02/07 06:00 CRDT- 2013/07/23 06:00 PHST- 2013/01/02 [received] PHST- 2013/04/30 [revised] PHST- 2013/05/20 [accepted] AID - S0006-3495(13)00633-4 [pii] AID - 10.1016/j.bpj.2013.05.046 [doi] PST - ppublish SO - Biophys J. 2013 Jul 16;105(2):481-93. doi: 10.1016/j.bpj.2013.05.046. PMID- 12681938 OWN - NLM STAT- MEDLINE DA - 20030408 DCOM- 20031006 LR - 20051117 IS - 1359-6446 (Print) IS - 1359-6446 (Linking) VI - 8 IP - 8 DP - 2003 Apr 15 TI - Drug discovery and p53. PG - 347-55 AB - In the past two decades, the identification of commonly mutated oncogenes and tumour suppressor genes has driven an unprecedented growth in our understanding of the genetic basis of human cancer. Although oncogenes can clearly serve as classically defined drug targets whose inactivation by small molecules could place a brake on cancer cell proliferation, the restoration of mutated tumour suppressor gene activity by small molecules might appear on the surface to be unrealistic. However, there is a growing realization that many eukaryotic regulatory proteins are partially unfolded and such intrinsically disordered proteins acquire a folded structure after binding to their biological target. Molecular characterization of the p53 protein has shown that its conformational flexibility and intrinsic thermodynamic instability provide a foundation from which its conformation can be quickly post-translationally modified. FAU - Lane, David P AU - Lane DP AD - Cancer Research UK Laboratories, Department of Surgery and Molecular Oncology, University of Dundee, Dundee, Scotland DD1 9SY, UK. d.p.lane@dundee.ac.uk FAU - Hupp, Ted R AU - Hupp TR LA - eng PT - Journal Article PT - Review PL - England TA - Drug Discov Today JT - Drug discovery today JID - 9604391 RN - 0 (Antineoplastic Agents) RN - 0 (CDKN1A protein, human) RN - 0 (Cyclin-Dependent Kinase Inhibitor p21) RN - 0 (Cyclins) RN - 0 (Nuclear Proteins) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Tumor Suppressor Protein p53) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM CIN - Drug Discov Today. 2003 Jul 1;8(13):574-5. PMID: 12850330 CIN - Drug Discov Today. 2003 Jul 15;8(14):620. PMID: 12867146 MH - Allosteric Regulation MH - Antineoplastic Agents/*chemistry/therapeutic use MH - Cyclin-Dependent Kinase Inhibitor p21 MH - Cyclins/chemistry/genetics/metabolism MH - *Drug Design MH - Humans MH - Molecular Mimicry MH - Mutation MH - Neoplasms/drug therapy/genetics MH - *Nuclear Proteins MH - Protein Conformation MH - Protein Folding MH - Proto-Oncogene Proteins/chemistry/genetics/metabolism MH - Proto-Oncogene Proteins c-mdm2 MH - Transcription, Genetic MH - Tumor Suppressor Protein p53/chemistry/*genetics/*physiology RF - 71 EDAT- 2003/04/12 05:00 MHDA- 2003/10/08 05:00 CRDT- 2003/04/12 05:00 AID - S1359644603026692 [pii] PST - ppublish SO - Drug Discov Today. 2003 Apr 15;8(8):347-55. PMID- 12783876 OWN - NLM STAT- MEDLINE DA - 20030721 DCOM- 20030826 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 30 DP - 2003 Jul 25 TI - Crystal structure of the ectodomain of human FcalphaRI. PG - 27966-70 AB - Human FcalphaRI (CD89) is the receptor specific for IgA, an immunoglobulin that is abundant in mucosa and is also found in high concentrations in serum. Although FcalphaRI is an immunoglobulin Fc receptor (FcR), it differs in many ways from FcRs for other immunoglobulin classes. The genes of most FcRs are located on chromosome 1 at 1q21-23, whereas FcalphaRI is on chromosome 19, at 19q13.4, a region called the leukocyte receptor complex, because it is clustered with several leukocyte receptor families including killer cell inhibitory receptors (KIRs) and leukocyte Ig-like receptors (LIRs). The amino acid sequence of FcalphaRI shares only 20% homology with other FcRs but it has around 35% homology with its neighboring LIRs and KIRs. In this work, we analyzed the crystal structure of the ectodomain of FcalphaRI and examined structure similarities between FcalphaRI and KIR2DL1, KIR2DL2 and LIR-1. Our data show that FcalphaRI, KIRs, and LIRs share a common hydrophobic core in their interdomain interface, and FcalphaRI is evolutionally closer to LIR than KIR. FAU - Ding, Yi AU - Ding Y AD - Ministry of Education Protein Science Laboratory & Laboratory of Structural Biology, Tsinghua University, Beijing, 100084, China. FAU - Xu, Gang AU - Xu G FAU - Yang, Maojun AU - Yang M FAU - Yao, Min AU - Yao M FAU - Gao, George F AU - Gao GF FAU - Wang, Linfang AU - Wang L FAU - Zhang, Wei AU - Zhang W FAU - Rao, Zihe AU - Rao Z LA - eng SI - PDB/1UCT PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030603 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Antigens, CD) RN - 0 (Disulfides) RN - 0 (Fc(alpha) receptor) RN - 0 (Immunoglobulin A) RN - 0 (Immunoglobulin G) RN - 0 (Receptors, Cell Surface) RN - 0 (Receptors, Fc) RN - 0 (Receptors, Immunologic) SB - IM MH - Amino Acid Sequence MH - Antigens, CD/*chemistry MH - Crystallography, X-Ray MH - Disulfides/chemistry MH - Escherichia coli/metabolism MH - Humans MH - Immunoglobulin A/chemistry MH - Immunoglobulin G/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Cell Surface/chemistry MH - Receptors, Fc/*chemistry MH - Receptors, Immunologic/chemistry MH - Sequence Homology, Amino Acid EDAT- 2003/06/05 05:00 MHDA- 2003/08/27 05:00 CRDT- 2003/06/05 05:00 PHST- 2003/06/03 [aheadofprint] AID - 10.1074/jbc.C300223200 [doi] AID - C300223200 [pii] PST - ppublish SO - J Biol Chem. 2003 Jul 25;278(30):27966-70. Epub 2003 Jun 3. PMID- 15182941 OWN - NLM STAT- MEDLINE DA - 20040608 DCOM- 20040726 LR - 20081121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1672 IP - 3 DP - 2004 Jun 11 TI - Overexpression, purification and characterization of the acidic ribosomal P-proteins from Candida albicans. PG - 214-23 AB - In all eukaryotic cells, acidic ribosomal P-proteins form a lateral protuberance on the 60S ribosomal subunit-the so-called stalk-structure that plays an important role during protein synthesis. In this work, we report for the first time a full-length cloning of four genes encoding the P-proteins from Candida albicans, their expression in Escherichia coli, purification and characterization of the recombinant proteins. Considerable amino acid sequence similarity was found between the cloned proteins and other known fungal ribosomal P-proteins. On the basis of their phylogenetic relationship and amino acid similarity to their yeast counterparts, the C. albicans P-proteins were named P1A, P1B, P2A and P2B. Using three different approaches, namely: chemical cross-linking method, gel filtration and two-hybrid system, we analyzed mutual interactions among the C. albicans P-proteins. The obtained data showed all the four P-proteins able to form homo-oligomeric complexes. However, the ones found between P1B-P2A and P1A-P2B were dominant forms among the C. albicans P-proteins. Moreover, the strength of interactions between particular proteins was different in these two complexes; the strongest interactions were observed between P1B and P2A proteins, and a significantly weaker one between P1A and P2B proteins. FAU - Abramczyk, Dariusz AU - Abramczyk D AD - Department of Molecular Biology, Maria Curie-Sklodowska University, Institute of Microbiology and Biotechnology, Akademicka Street 19, 20-033 Lublin, Poland. FAU - Tchorzewski, Marek AU - Tchorzewski M FAU - Krokowski, Dawid AU - Krokowski D FAU - Boguszewska, Aleksandra AU - Boguszewska A FAU - Grankowski, Nikodem AU - Grankowski N LA - eng SI - GENBANK/AF317659 SI - GENBANK/AF317660 SI - GENBANK/AF317661 SI - GENBANK/AF317662 PT - Journal Article PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Recombinant Proteins) RN - 0 (Ribosomal Proteins) RN - EC 3.2.1.23 (beta-Galactosidase) SB - IM MH - Base Sequence MH - *Candida albicans/chemistry/genetics MH - Cloning, Molecular MH - Genes, Fungal/genetics MH - Hydrogen-Ion Concentration MH - Isoelectric Focusing MH - Molecular Sequence Data MH - Phylogeny MH - Promoter Regions, Genetic/genetics MH - Protein Binding MH - Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism MH - Ribosomal Proteins/chemistry/genetics/*isolation & purification/*metabolism MH - Sequence Alignment MH - beta-Galactosidase/analysis/genetics EDAT- 2004/06/09 05:00 MHDA- 2004/07/28 05:00 CRDT- 2004/06/09 05:00 PHST- 2003/10/21 [received] PHST- 2004/04/13 [revised] PHST- 2004/04/14 [accepted] AID - 10.1016/j.bbagen.2004.04.005 [doi] AID - S0304416504000996 [pii] PST - ppublish SO - Biochim Biophys Acta. 2004 Jun 11;1672(3):214-23. PMID- 15953616 OWN - NLM STAT- MEDLINE DA - 20050624 DCOM- 20050808 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 350 IP - 3 DP - 2005 Jul 15 TI - Structure of free MDM2 N-terminal domain reveals conformational adjustments that accompany p53-binding. PG - 587-98 AB - Critical to the inhibitory action of the oncogene product, MDM2, on the tumour suppressor, p53, is association of the N-terminal domain of MDM2 (MDM2N) with the transactivation domain of p53. The structure of MDM2N was previously solved with a p53-derived peptide, or small-molecule ligands, occupying its binding cleft, but no structure of the non-liganded MDM2N (i.e. the apo-form) has been reported. Here, we describe the solution structure and dynamics of apo-MDM2N and thus reveal the nature of the conformational changes in MDM2N that accompany binding of p53. The new structure suggests that p53 effects displacement of an N-terminal segment of apo-MDM2N that occludes access to the shallow end of the p53-binding cleft. MDM2N must also undergo an expansion upon binding, achieved through a rearrangement of its two pseudosymetrically related sub-domains resulting in outward displacements of the secondary structural elements that comprise the walls and floor of the p53-binding cleft. MDM2N becomes more rigid and stable upon binding p53. Conformational plasticity of the binding cleft of apo-MDM2N could allow the parent protein to bind specifically to several different partners, although, to date, all the known liganded structures of MDM2N are highly similar to one another. The results indicate that the more open conformation of the binding cleft of MDM2N observed in structures of complexes with small molecules and peptides is a more suitable one for ligand discovery and optimisation. FAU - Uhrinova, Stanislava AU - Uhrinova S AD - Schools of Chemistry and Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JR, UK. FAU - Uhrin, Dusan AU - Uhrin D FAU - Powers, Helen AU - Powers H FAU - Watt, Kathryn AU - Watt K FAU - Zheleva, Daniella AU - Zheleva D FAU - Fischer, Peter AU - Fischer P FAU - McInnes, Campbell AU - McInnes C FAU - Barlow, Paul N AU - Barlow PN LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Ligands) RN - 0 (Nuclear Proteins) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Tumor Suppressor Protein p53) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Animals MH - Binding Sites MH - Crystallography, X-Ray MH - Databases, Protein MH - Humans MH - Ligands MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Nuclear Proteins/*chemistry/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins/*chemistry/metabolism MH - Proto-Oncogene Proteins c-mdm2 MH - Tumor Suppressor Protein p53/metabolism MH - Xenopus EDAT- 2005/06/15 09:00 MHDA- 2005/08/09 09:00 CRDT- 2005/06/15 09:00 PHST- 2005/03/11 [received] PHST- 2005/05/04 [revised] PHST- 2005/05/05 [accepted] AID - S0022-2836(05)00529-2 [pii] AID - 10.1016/j.jmb.2005.05.010 [doi] PST - ppublish SO - J Mol Biol. 2005 Jul 15;350(3):587-98. PMID- 22902625 OWN - NLM STAT- MEDLINE DA - 20121008 DCOM- 20121231 LR - 20150630 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 41 DP - 2012 Oct 5 TI - Enhancement of NEIL1 protein-initiated oxidized DNA base excision repair by heterogeneous nuclear ribonucleoprotein U (hnRNP-U) via direct interaction. PG - 34202-11 LID - 10.1074/jbc.M112.384032 [doi] AB - Repair of oxidized base lesions in the human genome, initiated by DNA glycosylases, occurs via the base excision repair pathway using conserved repair and some non-repair proteins. However, the functions of the latter noncanonical proteins in base excision repair are unclear. Here we elucidated the role of heterogeneous nuclear ribonucleoprotein-U (hnRNP-U), identified in the immunoprecipitate of human NEIL1, a major DNA glycosylase responsible for oxidized base repair. hnRNP-U directly interacts with NEIL1 in vitro via the NEIL1 common interacting C-terminal domain, which is dispensable for its enzymatic activity. Their in-cell association increases after oxidative stress. hnRNP-U stimulates the NEIL1 in vitro base excision activity for 5-hydroxyuracil in duplex, bubble, forked, or single-stranded DNA substrate, primarily by enhancing product release. Using eluates from FLAG-NEIL1 immunoprecipitates from human cells, we observed 3-fold enhancement in complete repair activity after oxidant treatment. The lack of such enhancement in hnRNP-U-depleted cells suggests its involvement in repairing enhanced base damage after oxidative stress. The NEIL1 disordered C-terminal region binds to hnRNP-U at equimolar ratio with high affinity (K(d) = approximately 54 nm). The interacting regions in hnRNP-U, mapped to both termini, suggest their proximity in the native protein; these are also disordered, based on PONDR (Predictor of Naturally Disordered Regions) prediction and circular dichroism spectra. Finally, depletion of hnRNP-U and NEIL1 epistatically sensitized human cells at low oxidative genome damage, suggesting that the hnRNP-U protection of cells after oxidative stress is largely due to enhancement of NEIL1-mediated repair. FAU - Hegde, Muralidhar L AU - Hegde ML AD - Department of Biochemistry and Molecular Biology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555-1079, USA. FAU - Banerjee, Srijita AU - Banerjee S FAU - Hegde, Pavana M AU - Hegde PM FAU - Bellot, Larry J AU - Bellot LJ FAU - Hazra, Tapas K AU - Hazra TK FAU - Boldogh, Istvan AU - Boldogh I FAU - Mitra, Sankar AU - Mitra S LA - eng GR - ES018948/ES/NIEHS NIH HHS/United States GR - P01 AI062885/AI/NIAID NIH HHS/United States GR - P01 CA092584/CA/NCI NIH HHS/United States GR - P01 CA092584/CA/NCI NIH HHS/United States GR - P30 ES006676/ES/NIEHS NIH HHS/United States GR - R01 CA81063/CA/NCI NIH HHS/United States GR - R01 ES018948/ES/NIEHS NIH HHS/United States GR - R01 NS073976/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20120817 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Heterogeneous-Nuclear Ribonucleoprotein U) RN - EC 3.2.2.- (DNA Glycosylases) RN - EC 3.2.2.- (NEIL1 protein, human) SB - IM MH - DNA Glycosylases/genetics/*metabolism MH - DNA Repair/*physiology MH - HEK293 Cells MH - Heterogeneous-Nuclear Ribonucleoprotein U/genetics/*metabolism MH - Humans MH - Oxidation-Reduction MH - Oxidative Stress/*physiology MH - Protein Binding PMC - PMC3464528 OID - NLM: PMC3464528 EDAT- 2012/08/21 06:00 MHDA- 2013/01/01 06:00 CRDT- 2012/08/21 06:00 PHST- 2012/08/17 [aheadofprint] AID - M112.384032 [pii] AID - 10.1074/jbc.M112.384032 [doi] PST - ppublish SO - J Biol Chem. 2012 Oct 5;287(41):34202-11. doi: 10.1074/jbc.M112.384032. Epub 2012 Aug 17. PMID- 23324799 OWN - NLM STAT- MEDLINE DA - 20130204 DCOM- 20131126 IS - 1364-5528 (Electronic) IS - 0003-2654 (Linking) VI - 138 IP - 5 DP - 2013 Mar 7 TI - Characterisation of an intrinsically disordered protein complex of Swi5-Sfr1 by ion mobility mass spectrometry and small-angle X-ray scattering. PG - 1441-9 LID - 10.1039/c2an35878f [doi] AB - It is now recognized that intrinsically disordered proteins (IDPs) play important roles as hubs in intracellular networks, and their structural characterisation is of significance. However, due to their highly dynamic features, it is challenging to investigate the structures of IDPs solely by conventional methods. In the present study, we demonstrate a novel method to characterise protein complexes using electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) in combination with small-angle X-ray scattering (SAXS). This method enables structural characterisation even of proteins that have difficulties in crystallisation. With this method, we have characterised the Schizosaccharomyces pombe Swi5-Sfr1 complex, which is expected to have a long disordered region at the N-terminal portion of Sfr1. ESI-IM-MS analysis of the Swi5-Sfr1 complex revealed that its experimental collision cross-section (CCS) had a wide distribution, and the CCS values of the most dominant ions were approximately 56% of the theoretically calculated value based on the SAXS low-resolution model, suggesting a significant size reduction in the gas phase. The present study demonstrates that the newly developed method for calculation of the theoretical CCSs of the SAXS low-resolution models of proteins allows accurate evaluation of the experimental CCS values of IDPs provided by ESI-IM-MS by comparing with the low-resolution solution structures. Furthermore, it was revealed that the combination of ESI-IM-MS and SAXS is a promising method for structural characterisation of protein complexes that are unable to crystallise. FAU - Saikusa, Kazumi AU - Saikusa K AD - Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan. FAU - Kuwabara, Naoyuki AU - Kuwabara N FAU - Kokabu, Yuichi AU - Kokabu Y FAU - Inoue, Yu AU - Inoue Y FAU - Sato, Mamoru AU - Sato M FAU - Iwasaki, Hiroshi AU - Iwasaki H FAU - Shimizu, Toshiyuki AU - Shimizu T FAU - Ikeguchi, Mitsunori AU - Ikeguchi M FAU - Akashi, Satoko AU - Akashi S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Analyst JT - The Analyst JID - 0372652 RN - 0 (Cell Cycle Proteins) RN - 0 (SWI5 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Schizosaccharomyces pombe Proteins) RN - 0 (Sfr1 protein, S pombe) RN - 0 (Transcription Factors) SB - IM MH - Amino Acid Sequence MH - Cell Cycle Proteins/*chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Saccharomyces cerevisiae Proteins/*chemistry/metabolism MH - Scattering, Small Angle MH - Schizosaccharomyces/*chemistry/metabolism MH - Schizosaccharomyces pombe Proteins/*chemistry/metabolism MH - Spectrometry, Mass, Electrospray Ionization MH - Transcription Factors/*chemistry/metabolism MH - X-Ray Diffraction EDAT- 2013/01/18 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/01/18 06:00 AID - 10.1039/c2an35878f [doi] PST - ppublish SO - Analyst. 2013 Mar 7;138(5):1441-9. doi: 10.1039/c2an35878f. PMID- 20037676 OWN - NLM STAT- Publisher DA - 20110927 IS - 1349-0079 (Print) IS - 1349-0079 (Linking) VI - 50 IP - 1 DP - 2008 Jan 1 TI - Dentin Sialophophoprotein (DSPP) and Dentin. PG - 33-44 AB - The revolution in genetics disclosed the types of malformations that occur when expression of a particular gene is lost. In the case of tooth dentin, mutations in the two genes encoding type I collagen cause osteogenesis imperfecta, a bone condition that often includes dentin malformations. Besides collagen, there are a number of non-collagenous proteins in dentin. Among the genes encoding the dentin non-collagenous proteins, only mutations in DSPP (dentin sialophosphoprotein) cause inherited dental malformations. DSPP mutations cause dentinogenesis imperfecta types II and III, and dentin dysplasia type II. DSPP is the most abundant non-collagenous protein in dentin. DSPP protein is necessary for proper dentin formation, and understanding its structure and function should yield important insights into how dentin forms and biomineralization is controlled. DSPP is expressed and secreted by odontoblasts, the cells that make tooth dentin and that also maintain cell processes extending into the mineralized tissue. Following its secretion, DSPP is cleaved into smaller pieces by multiple extracellular proteases. For the last five years I have devoted myself to characterizing DSPP-derived proteins. DSPP is cleaved by proteases into three main parts : dentin sialoprotein (DSP), dentin glycoprotein (DGP), and dentin phosphoprotein (DPP). We have learned that DSP is a proteoglycan that forms covalent dimers, DGP is a phosphorylated glycoprotein, and DPP is a highly phosphorylated intrinsically disordered protein that shows extensive length polymorphisms due to the genetic heterogeneity of its coding region. FAU - Yamakoshi, Yasuo AU - Yamakoshi Y AD - Department of Biologic and Materials Sciences, University of Michigan Dental Research Lab 1210 Eisenhower Place, Ann Arbor, MI 48108, USA. LA - ENG GR - R01 DE011301/DE/NIDCR NIH HHS/United States GR - R01 DE011301-08/DE/NIDCR NIH HHS/United States GR - R01 DE015846/DE/NIDCR NIH HHS/United States GR - R01 DE015846-05/DE/NIDCR NIH HHS/United States PT - JOURNAL ARTICLE TA - J Oral Biosci JT - Journal of oral biosciences / JAOB, Japanese Association for Oral Biology JID - 101226721 PMC - PMC2797732 MID - NIHMS146985 EDAT- 2008/01/01 00:00 MHDA- 2008/01/01 00:00 CRDT- 2011/09/28 06:00 AID - 10.2330/joralbiosci.50.33 [doi] PST - ppublish SO - J Oral Biosci. 2008 Jan 1;50(1):33-44. PMID- 22096199 OWN - NLM STAT- MEDLINE DA - 20111118 DCOM- 20111129 LR - 20150510 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 334 IP - 6058 DP - 2011 Nov 18 TI - Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 A resolution. PG - 977-82 LID - 10.1126/science.1210915 [doi] AB - Gene silencing is essential for regulating cell fate in eukaryotes. Altered chromatin architectures contribute to maintaining the silenced state in a variety of species. The silent information regulator (Sir) proteins regulate mating type in Saccharomyces cerevisiae. One of these proteins, Sir3, interacts directly with the nucleosome to help generate silenced domains. We determined the crystal structure of a complex of the yeast Sir3 BAH (bromo-associated homology) domain and the nucleosome core particle at 3.0 angstrom resolution. We see multiple molecular interactions between the protein surfaces of the nucleosome and the BAH domain that explain numerous genetic mutations. These interactions are accompanied by structural rearrangements in both the nucleosome and the BAH domain. The structure explains how covalent modifications on H4K16 and H3K79 regulate formation of a silencing complex that contains the nucleosome as a central component. FAU - Armache, Karim-Jean AU - Armache KJ AD - Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA. FAU - Garlick, Joseph D AU - Garlick JD FAU - Canzio, Daniele AU - Canzio D FAU - Narlikar, Geeta J AU - Narlikar GJ FAU - Kingston, Robert E AU - Kingston RE LA - eng SI - PDB/3TU4 GR - GM043901/GM/NIGMS NIH HHS/United States GR - P41 RR012408/RR/NCRR NIH HHS/United States GR - R01 GM043901/GM/NIGMS NIH HHS/United States GR - R37 GM048405/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Histones) RN - 0 (Mutant Proteins) RN - 0 (Nucleosomes) RN - 0 (SIR3 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Silent Information Regulator Proteins, Saccharomyces cerevisiae) SB - IM MH - Acetylation MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - *Gene Silencing MH - Histones/*chemistry/metabolism MH - Hydrogen Bonding MH - Methylation MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis MH - Mutant Proteins/chemistry/metabolism MH - Nucleosomes/*chemistry/metabolism/ultrastructure MH - Physicochemical Processes MH - Protein Folding MH - *Protein Interaction Domains and Motifs MH - Protein Multimerization MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/chemistry/*genetics/metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/metabolism MH - Silent Information Regulator Proteins, Saccharomyces cerevisiae/*chemistry/genetics/metabolism MH - Static Electricity PMC - PMC4098850 MID - NIHMS343717 OID - NLM: NIHMS343717 OID - NLM: PMC4098850 EDAT- 2011/11/19 06:00 MHDA- 2011/12/13 00:00 CRDT- 2011/11/19 06:00 AID - 334/6058/977 [pii] AID - 10.1126/science.1210915 [doi] PST - ppublish SO - Science. 2011 Nov 18;334(6058):977-82. doi: 10.1126/science.1210915. PMID- 9671503 OWN - NLM STAT- MEDLINE DA - 19980805 DCOM- 19980805 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 37 IP - 29 DP - 1998 Jul 21 TI - Identification of a minimal core of the synaptic SNARE complex sufficient for reversible assembly and disassembly. PG - 10354-62 AB - Assembly of the three neuronal membrane proteins synaptobrevin, syntaxin, and SNAP-25 is thought to be one of the key steps in mediating exocytosis of synaptic vesicles. In vivo and in vitro, these proteins form a tight complex. Assembly is associated with a large increase in alpha-helical content, suggesting that major structural and conformational changes are associated with the assembly reaction. Limited proteolysis by trypsin, chymotrypsin, and proteinase K of the ternary complex formed from recombinant proteins lacking their membrane anchors revealed a SDS-resistant minimal core. The components of this core complex were purified and characterized by N-terminal sequencing and mass spectrometry. They include a slightly shortened synaptobrevin fragment, C- and N-terminal fragments of SNAP-25, and a C-terminal fragment of syntaxin that is slightly larger than the previously characterized H3 domain. Recombinant proteins corresponding to these fragments are sufficient for assembly and disassembly. In addition, each of the two SNAP-25 fragments can individually form complexes with syntaxin and synaptobrevin, suggesting that they both contribute to the assembly of the SNARE complex. Upon complex assembly, a large increase in alpha-helical content is observed along with a significantly increased melting temperature (Tm). Like the full-length complex, the minimal complex tends to form an oligomeric species; global analysis of equilibrium ultracentrifugation data suggests a monomer-trimer equilibrium exists. These conserved biophysical properties may thus be of fundamental importance in the mechanism of membrane fusion. FAU - Fasshauer, D AU - Fasshauer D AD - Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Gottingen, Germany. FAU - Eliason, W K AU - Eliason WK FAU - Brunger, A T AU - Brunger AT FAU - Jahn, R AU - Jahn R LA - eng GR - GM54160-01/GM/NIGMS NIH HHS/United States GR - NS33709-02/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Macromolecular Substances) RN - 0 (Membrane Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Qa-SNARE Proteins) RN - 0 (R-SNARE Proteins) RN - 0 (SNARE Proteins) RN - 0 (Snap25 protein, rat) RN - 0 (Synaptosomal-Associated Protein 25) RN - 0 (Vesicular Transport Proteins) RN - EC 3.4.- (Endopeptidases) SB - IM MH - Amino Acid Sequence MH - Animals MH - Circular Dichroism MH - Endopeptidases/pharmacology MH - Hydrolysis MH - Macromolecular Substances MH - Membrane Proteins/*chemistry/*metabolism MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*chemistry/*metabolism MH - Qa-SNARE Proteins MH - R-SNARE Proteins MH - Rats MH - SNARE Proteins MH - Structure-Activity Relationship MH - Synaptic Vesicles/*chemistry/metabolism MH - Synaptosomal-Associated Protein 25 MH - *Vesicular Transport Proteins EDAT- 1998/07/22 MHDA- 1998/07/22 00:01 CRDT- 1998/07/22 00:00 AID - 10.1021/bi980542h [doi] AID - bi980542h [pii] PST - ppublish SO - Biochemistry. 1998 Jul 21;37(29):10354-62. PMID- 9770451 OWN - NLM STAT- MEDLINE DA - 19981112 DCOM- 19981112 LR - 20140617 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 95 IP - 21 DP - 1998 Oct 13 TI - Structure of the Ets-1 pointed domain and mitogen-activated protein kinase phosphorylation site. PG - 12129-34 AB - The Pointed (PNT) domain and an adjacent mitogen-activated protein (MAP) kinase phosphorylation site are defined by sequence conservation among a subset of ets transcription factors and are implicated in two regulatory strategies, protein interactions and posttranslational modifications, respectively. By using NMR, we have determined the structure of a 110-residue fragment of murine Ets-1 that includes the PNT domain and MAP kinase site. The Ets-1 PNT domain forms a monomeric five-helix bundle. The architecture is distinct from that of any known DNA- or protein-binding module, including the helix-loop-helix fold proposed for the PNT domain of the ets protein TEL. The MAP kinase site is in a highly flexible region of both the unphosphorylated and phosphorylated forms of the Ets-1 fragment. Phosphorylation alters neither the structure nor monomeric state of the PNT domain. These results suggest that the Ets-1 PNT domain functions in heterotypic protein interactions and support the possibility that target recognition is coupled to structuring of the MAP kinase site. FAU - Slupsky, C M AU - Slupsky CM AD - Department of Biochemistry and Molecular Biology and Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z3. FAU - Gentile, L N AU - Gentile LN FAU - Donaldson, L W AU - Donaldson LW FAU - Mackereth, C D AU - Mackereth CD FAU - Seidel, J J AU - Seidel JJ FAU - Graves, B J AU - Graves BJ FAU - McIntosh, L P AU - McIntosh LP LA - eng SI - PDB/1BQV SI - PDB/R1BQVMR GR - CA09602/CA/NCI NIH HHS/United States GR - GM 38663/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Ets1 protein, mouse) RN - 0 (Proto-Oncogene Protein c-ets-1) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Proto-Oncogene Proteins c-ets) RN - 0 (Transcription Factors) RN - EC 2.7.11.17 (Calcium-Calmodulin-Dependent Protein Kinases) SB - IM MH - Amino Acid Sequence MH - Animals MH - Calcium-Calmodulin-Dependent Protein Kinases/*metabolism MH - Magnetic Resonance Spectroscopy MH - Mice MH - Molecular Sequence Data MH - Phosphorylation MH - Protein Conformation MH - Proto-Oncogene Protein c-ets-1 MH - Proto-Oncogene Proteins/chemistry/*metabolism MH - Proto-Oncogene Proteins c-ets MH - Sequence Homology, Amino Acid MH - Transcription Factors/chemistry/*metabolism PMC - PMC22796 OID - NLM: PMC22796 EDAT- 1998/10/15 MHDA- 1998/10/15 00:01 CRDT- 1998/10/15 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12129-34. PMID- 19010333 OWN - NLM STAT- MEDLINE DA - 20090109 DCOM- 20090203 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 385 IP - 2 DP - 2009 Jan 16 TI - Crystal structure of the Pml1p subunit of the yeast precursor mRNA retention and splicing complex. PG - 531-41 LID - 10.1016/j.jmb.2008.10.087 [doi] AB - The precursor mRNA retention and splicing (RES) complex mediates nuclear retention and enhances splicing of precursor mRNAs. The RES complex from yeast comprises three proteins, Snu17p, Bud13p and Pml1p. Snu17p acts as a central platform that concomitantly binds the Bud13p and Pml1p subunits via short peptide epitopes. As a step to decipher the molecular architecture of the RES complex, we have determined crystal structures of full-length Pml1p and N-terminally truncated Pml1p. The first 50 residues of full-length Pml1p, encompassing the Snu17p-binding region, are disordered, showing that Pml1p binds to Snu17p via an intrinsically unstructured region. The remainder of Pml1p folds as a forkhead-associated (FHA) domain, which is expanded by a number of noncanonical elements compared with known FHA domains from other proteins. An atypical N-terminal appendix runs across one beta-sheet and thereby stabilizes the domain as shown by deletion experiments. FHA domains are thought to constitute phosphopeptide-binding elements. Consistently, a sulfate ion was found at the putative phosphopeptide-binding loops of full-length Pml1p. The N-terminally truncated version of the protein lacked a similar phosphopeptide mimic but retained an almost identical structure. A long loop neighboring the putative phosphopeptide-binding site was disordered in both structures. Comparison with other FHA domain proteins suggests that this loop adopts a defined conformation upon ligand binding and thereby confers ligand specificity. Our results show that in the RES complex, an FHA domain of Pml1p is flexibly tethered via an unstructured N-terminal region to Snu17p. FAU - Trowitzsch, Simon AU - Trowitzsch S AD - Zellulare Biochemie, Max-Planck-Institut fur Biophysikalische Chemie, Am Fassberg 11, D-37077 Gottingen, Germany. FAU - Weber, Gert AU - Weber G FAU - Luhrmann, Reinhard AU - Luhrmann R FAU - Wahl, Markus C AU - Wahl MC LA - eng SI - PDB/3ELS SI - PDB/3ELV PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20081107 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Carrier Proteins) RN - 0 (Pml1 protein, S cerevisiae) RN - 0 (Protein Subunits) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Carrier Proteins/*chemistry MH - Crystallography, X-Ray MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Tertiary MH - Protein Subunits/*chemistry MH - Saccharomyces cerevisiae Proteins/*chemistry MH - Sequence Alignment MH - Sequence Deletion EDAT- 2008/11/18 09:00 MHDA- 2009/02/04 09:00 CRDT- 2008/11/18 09:00 PHST- 2008/10/15 [received] PHST- 2008/10/21 [accepted] PHST- 2008/11/07 [aheadofprint] AID - S0022-2836(08)01387-9 [pii] AID - 10.1016/j.jmb.2008.10.087 [doi] PST - ppublish SO - J Mol Biol. 2009 Jan 16;385(2):531-41. doi: 10.1016/j.jmb.2008.10.087. Epub 2008 Nov 7. PMID- 23783631 OWN - NLM STAT- MEDLINE DA - 20130620 DCOM- 20130711 LR - 20141113 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 498 IP - 7454 DP - 2013 Jun 20 TI - Modulation of allostery by protein intrinsic disorder. PG - 390-4 LID - 10.1038/nature12294 [doi] AB - Allostery is an intrinsic property of many globular proteins and enzymes that is indispensable for cellular regulatory and feedback mechanisms. Recent theoretical and empirical observations indicate that allostery is also manifest in intrinsically disordered proteins, which account for a substantial proportion of the proteome. Many intrinsically disordered proteins are promiscuous binders that interact with multiple partners and frequently function as molecular hubs in protein interaction networks. The adenovirus early region 1A (E1A) oncoprotein is a prime example of a molecular hub intrinsically disordered protein. E1A can induce marked epigenetic reprogramming of the cell within hours after infection, through interactions with a diverse set of partners that include key host regulators such as the general transcriptional coactivator CREB binding protein (CBP), its paralogue p300, and the retinoblastoma protein (pRb; also called RB1). Little is known about the allosteric effects at play in E1A-CBP-pRb interactions, or more generally in hub intrinsically disordered protein interaction networks. Here we used single-molecule fluorescence resonance energy transfer (smFRET) to study coupled binding and folding processes in the ternary E1A system. The low concentrations used in these high-sensitivity experiments proved to be essential for these studies, which are challenging owing to a combination of E1A aggregation propensity and high-affinity binding interactions. Our data revealed that E1A-CBP-pRb interactions have either positive or negative cooperativity, depending on the available E1A interaction sites. This striking cooperativity switch enables fine-tuning of the thermodynamic accessibility of the ternary versus binary E1A complexes, and may permit a context-specific tuning of associated downstream signalling outputs. Such a modulation of allosteric interactions is probably a common mechanism in molecular hub intrinsically disordered protein function. FAU - Ferreon, Allan Chris M AU - Ferreon AC AD - Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. FAU - Ferreon, Josephine C AU - Ferreon JC FAU - Wright, Peter E AU - Wright PE FAU - Deniz, Ashok A AU - Deniz AA LA - eng GR - CA96865/CA/NCI NIH HHS/United States GR - GM066833/GM/NIGMS NIH HHS/United States GR - R01 CA096865/CA/NCI NIH HHS/United States GR - R01 GM066833/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Adenovirus E1A Proteins) RN - 0 (Retinoblastoma Protein) RN - EC 2.3.1.48 (CREB-Binding Protein) RN - EC 2.3.1.48 (p300-CBP Transcription Factors) SB - IM CIN - Nature. 2013 Jun 20;498(7454):308-10. PMID: 23783624 MH - Adenovirus E1A Proteins/*chemistry/*metabolism MH - *Allosteric Regulation MH - Amino Acid Motifs MH - Animals MH - Anisotropy MH - CREB-Binding Protein/chemistry/metabolism MH - Fluorescence Resonance Energy Transfer MH - Humans MH - Mice MH - Models, Molecular MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Retinoblastoma Protein/chemistry/metabolism MH - Thermodynamics MH - p300-CBP Transcription Factors/chemistry PMC - PMC3718496 MID - NIHMS482139 OID - NLM: NIHMS482139 OID - NLM: PMC3718496 EDAT- 2013/06/21 06:00 MHDA- 2013/07/13 06:00 CRDT- 2013/06/21 06:00 PHST- 2012/11/16 [received] PHST- 2013/05/17 [accepted] AID - nature12294 [pii] AID - 10.1038/nature12294 [doi] PST - ppublish SO - Nature. 2013 Jun 20;498(7454):390-4. doi: 10.1038/nature12294. PMID- 22100452 OWN - NLM STAT- MEDLINE DA - 20120113 DCOM- 20120301 LR - 20141021 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 415 IP - 2 DP - 2012 Jan 13 TI - Structural basis for activation of calcineurin by calmodulin. PG - 307-17 LID - 10.1016/j.jmb.2011.11.008 [doi] AB - The highly conserved phosphatase calcineurin (CaN) plays vital roles in numerous processes including T-cell activation, development and function of the central nervous system, and cardiac growth. It is activated by the calcium sensor calmodulin (CaM). CaM binds to a regulatory domain (RD) within CaN, causing a conformational change that displaces an autoinhibitory domain (AID) from the active site, resulting in activation of the phosphatase. This is the same general mechanism by which CaM activates CaM-dependent protein kinases. Previously published data have hinted that the RD of CaN is intrinsically disordered. In this work, we demonstrate that the RD is unstructured and that it folds upon binding CaM, ousting the AID from the catalytic site. The RD is 95 residues long, with the AID attached to its C-terminal end and the 24-residue CaM binding region toward the N-terminal end. This is unlike the CaM-dependent protein kinases that have CaM binding sites and AIDs immediately adjacent in sequence. Our data demonstrate that not only does the CaM binding region folds but also an approximately 25- to 30-residue region between it and the AID folds, resulting in over half of the RD adopting alpha-helical structure. This appears to be the first observation of CaM inducing folding of this scale outside of its binding site on a target protein. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Rumi-Masante, Julie AU - Rumi-Masante J AD - Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky, 741 South Limestone Street, Lexington, KY 40536-0509, USA. FAU - Rusinga, Farai I AU - Rusinga FI FAU - Lester, Terrence E AU - Lester TE FAU - Dunlap, Tori B AU - Dunlap TB FAU - Williams, Todd D AU - Williams TD FAU - Dunker, A Keith AU - Dunker AK FAU - Weis, David D AU - Weis DD FAU - Creamer, Trevor P AU - Creamer TP LA - eng GR - P20 RR020171/RR/NCRR NIH HHS/United States GR - P20 RR020171/RR/NCRR NIH HHS/United States GR - P20 RR020171-06/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20111112 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Calmodulin) RN - EC 3.1.3.16 (Calcineurin) SB - IM MH - Amino Acid Sequence MH - Calcineurin/*chemistry/*metabolism MH - Calmodulin/*chemistry/*metabolism MH - Circular Dichroism MH - Humans MH - Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary PMC - PMC3258384 MID - NIHMS338645 OID - NLM: NIHMS338645 OID - NLM: PMC3258384 EDAT- 2011/11/22 06:00 MHDA- 2012/03/02 06:00 CRDT- 2011/11/22 06:00 PHST- 2011/09/29 [received] PHST- 2011/11/02 [revised] PHST- 2011/11/04 [accepted] PHST- 2011/11/12 [aheadofprint] AID - S0022-2836(11)01227-7 [pii] AID - 10.1016/j.jmb.2011.11.008 [doi] PST - ppublish SO - J Mol Biol. 2012 Jan 13;415(2):307-17. doi: 10.1016/j.jmb.2011.11.008. Epub 2011 Nov 12. PMID- 19043829 OWN - NLM STAT- MEDLINE DA - 20081126 DCOM- 20081218 LR - 20140901 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 456 IP - 7220 DP - 2008 Nov 20 TI - Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA. PG - 350-6 LID - 10.1038/nature07413 [doi] AB - Nuclear receptors are multi-domain transcription factors that bind to DNA elements from which they regulate gene expression. The peroxisome proliferator-activated receptors (PPARs) form heterodimers with the retinoid X receptor (RXR), and PPAR-gamma has been intensively studied as a drug target because of its link to insulin sensitization. Previous structural studies have focused on isolated DNA or ligand-binding segments, with no demonstration of how multiple domains cooperate to modulate receptor properties. Here we present structures of intact PPAR-gamma and RXR-alpha as a heterodimer bound to DNA, ligands and coactivator peptides. PPAR-gamma and RXR-alpha form a non-symmetric complex, allowing the ligand-binding domain (LBD) of PPAR-gamma to contact multiple domains in both proteins. Three interfaces link PPAR-gamma and RXR-alpha, including some that are DNA dependent. The PPAR-gamma LBD cooperates with both DNA-binding domains (DBDs) to enhance response-element binding. The A/B segments are highly dynamic, lacking folded substructures despite their gene-activation properties. FAU - Chandra, Vikas AU - Chandra V AD - Department of Pharmacology, and Center for Molecular Design, University of Virginia Health System, 1300 Jefferson Park Avenue, Charlottesville, Virginia 22908-0735, USA. FAU - Huang, Pengxiang AU - Huang P FAU - Hamuro, Yoshitomo AU - Hamuro Y FAU - Raghuram, Srilatha AU - Raghuram S FAU - Wang, Yongjun AU - Wang Y FAU - Burris, Thomas P AU - Burris TP FAU - Rastinejad, Fraydoon AU - Rastinejad F LA - eng SI - PDB/3DZU SI - PDB/3DZY SI - PDB/3E00 GR - R01 GM055217/GM/NIGMS NIH HHS/United States GR - R01 GM055217-11/GM/NIGMS NIH HHS/United States PT - Journal Article PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Ligands) RN - 0 (Multiprotein Complexes) RN - 0 (PPAR gamma) RN - 0 (Retinoid X Receptor alpha) RN - 9007-49-2 (DNA) SB - IM MH - Allosteric Regulation MH - Base Sequence MH - DNA/chemistry/genetics/*metabolism MH - Humans MH - Ligands MH - Models, Molecular MH - Multiprotein Complexes/*chemistry/*metabolism MH - PPAR gamma/*chemistry/*metabolism MH - Protein Binding MH - Protein Multimerization MH - Protein Structure, Tertiary MH - Response Elements/genetics MH - Retinoid X Receptor alpha/*chemistry/*metabolism PMC - PMC2743566 MID - NIHMS122709 OID - NLM: NIHMS122709 OID - NLM: PMC2743566 EDAT- 2008/12/02 09:00 MHDA- 2008/12/19 09:00 CRDT- 2008/12/02 09:00 AID - 10.1038/nature07413 [doi] PST - ppublish SO - Nature. 2008 Nov 20;456(7220):350-6. doi: 10.1038/nature07413. PMID- 22988066 OWN - NLM STAT- MEDLINE DA - 20121101 DCOM- 20130108 LR - 20141105 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 109 IP - 44 DP - 2012 Oct 30 TI - Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation. PG - 17857-62 LID - 10.1073/pnas.1201805109 [doi] AB - Intrinsically disordered proteins (IDP) are a broad class of proteins with relatively flat energy landscapes showing a high level of functional promiscuity, which are frequently regulated through posttranslational covalent modifications. Histone tails, which are the terminal segments of the histone proteins, are prominent IDPs that are implicated in a variety of signaling processes, which control chromatin organization and dynamics. Although a large body of work has been done on elucidating the roles of posttranslational modifications in functional regulation of IDPs, molecular mechanisms behind the observed behaviors are not fully understood. Using extensive atomistic molecular dynamics simulations, we found in this work that H4 tail mono-acetylation at LYS-16, which is a key covalent modification, induces a significant reorganization of the tail's conformational landscape, inducing partial ordering and enhancing the propensity for alpha-helical segments. Furthermore, our calculations of the potentials of mean force between the H4 tail and a DNA fragment indicate that contrary to the expectations based on simple electrostatic reasoning, the Lys-16 mono-acetylated H4 tail binds to DNA stronger than the unacetylated protein. Based on these results, we propose a molecular mechanism for the way Lys-16 acetylation might lead to experimentally observed disruption of compact chromatin fibers. FAU - Potoyan, Davit A AU - Potoyan DA AD - Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, Chemical Physics Program, University of Maryland, College Park, MD 20742, USA. FAU - Papoian, Garegin A AU - Papoian GA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120917 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Histones) RN - K3Z4F929H6 (Lysine) SB - IM MH - Acetylation MH - Histones/chemistry/*metabolism MH - Lysine/*metabolism MH - Molecular Dynamics Simulation MH - Protein Binding MH - Static Electricity PMC - PMC3497739 OID - NLM: PMC3497739 EDAT- 2012/09/19 06:00 MHDA- 2013/01/09 06:00 CRDT- 2012/09/19 06:00 PHST- 2012/09/17 [aheadofprint] AID - 1201805109 [pii] AID - 10.1073/pnas.1201805109 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17857-62. doi: 10.1073/pnas.1201805109. Epub 2012 Sep 17. PMID- 10985770 OWN - NLM STAT- MEDLINE DA - 20001019 DCOM- 20001019 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 39 IP - 37 DP - 2000 Sep 19 TI - Altering the reaction specificity of eukaryotic ornithine decarboxylase. PG - 11247-57 AB - Ornithine decarboxylase (ODC) catalyzes the first committed step in the biosynthesis of polyamines, and it has been identified as a drug target for the treatment of African sleeping sickness, caused by Trypanosoma brucei. ODC is a pyridoxal 5'-phosphate (PLP) dependent enzyme and an obligate homodimer. X-ray structural analysis of the complex of the T. brucei wild-type enzyme with the product putrescine reveals two structural changes that occur upon ligand binding: Lys-69 is displaced by putrescine and forms new interactions with Glu-94 and Asp-88, and the side chain of Cys-360 rotates into the active site to within 3.4 A of the imine bond. Mutation of Cys-360 to Ala or Ser reduces the k(cat) of the decarboxylation reaction by 50- and 1000-fold, respectively. However, HPLC analysis of the products demonstrates that the mutant enzymes almost exclusively catalyze a decarboxylation-dependent transamination reaction to form pyridoxamine 5-phosphate (PMP) and gamma-aminobutyraldehyde, instead of PLP and putrescine. This side reaction arises when the decarboxylated substrate intermediate is protonated at C4' of PLP instead of at the C(alpha) of substrate. For the reaction catalyzed by the wild-type enzyme, this side reaction occurs infrequently (<0.01% of the turnovers). Single turnover analysis and multiwavelength stopped-flow spectroscopic studies suggest that for the mutant ODCs protonation at C4' occurs either very rapidly or in a concerted reaction with decarboxylation and that the rate-limiting step in the steady-state reaction is Schiff base hydrolysis/product release. These studies demonstrate a role for Cys-360 in the control of the C(alpha) protonation step that catalyzes the formation of the physiological product putrescine. The results further provide insight into the mechanism by which this class of PLP-dependent enzymes controls reaction specificity. FAU - Jackson, L K AU - Jackson LK AD - Department of Pharmacology and Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390-9041, USA. FAU - Brooks, H B AU - Brooks HB FAU - Osterman, A L AU - Osterman AL FAU - Goldsmith, E J AU - Goldsmith EJ FAU - Phillips, M A AU - Phillips MA LA - eng SI - PDB/1F3T GR - F32AI09495/AI/NIAID NIH HHS/United States GR - R01AI34432/AI/NIAID NIH HHS/United States GR - T32GM07062/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 452VLY9402 (Serine) RN - EC 4.1.1.17 (Ornithine Decarboxylase) RN - K848JZ4886 (Cysteine) RN - OF5P57N2ZX (Alanine) RN - V10TVZ52E4 (Putrescine) SB - IM MH - Alanine/genetics MH - Animals MH - Binding Sites/genetics MH - Catalysis MH - Chromatography, High Pressure Liquid MH - Crystallography, X-Ray MH - Cysteine/genetics MH - Decarboxylation MH - Kinetics MH - Models, Molecular MH - *Mutagenesis, Site-Directed MH - Ornithine Decarboxylase/*chemistry/*genetics/metabolism MH - Putrescine/chemistry MH - Serine/genetics MH - Spectrometry, Fluorescence MH - Spectrophotometry, Ultraviolet MH - Substrate Specificity/genetics MH - Trypanosoma brucei brucei/enzymology/genetics EDAT- 2000/09/14 11:00 MHDA- 2000/10/21 11:01 CRDT- 2000/09/14 11:00 AID - bi001209s [pii] PST - ppublish SO - Biochemistry. 2000 Sep 19;39(37):11247-57. PMID- 18691903 OWN - NLM STAT- MEDLINE DA - 20081110 DCOM- 20090113 LR - 20131121 IS - 1044-0305 (Print) IS - 1044-0305 (Linking) VI - 19 IP - 11 DP - 2008 Nov TI - Protein-metal interactions of calmodulin and alpha-synuclein monitored by selective noncovalent adduct protein probing mass spectrometry. PG - 1663-72 LID - 10.1016/j.jasms.2008.07.006 [doi] AB - The metal binding properties of proteins are biologically significant, particularly in relationship to the molecular origins of disease and the discovery of therapeutic pharmaceutical treatments. Herein, we demonstrate that selective noncovalent adduct protein probing mass spectrometry (SNAPP-MS) is a sensitive technique to investigate the structural effects of protein-metal interactions. We utilize specific, noncovalent interactions between 18-crown-6 ether (18C6) and lysine to probe protein structure in the presence and absence of metal ions. Application of SNAPP-MS to the calmodulin-Ca2+ system demonstrates that changes in protein structure are reflected in a substantial change in the number and intensity of 18C6s, which bind to the protein as observed by MS. In this manner, SNAPP is demonstrated to be a sensitive technique for monitoring ligand-induced conformational rearrangements in proteins. In addition, SNAPP is well-suited to examine the properties of natively unfolded proteins, where structural changes are more difficult to detect by other methods. For example, alpha-synuclein is a protein associated in the pathology of Parkinson's disease, which is known to aggregate more rapidly in the presence of Al3+ and Cu2+. The 18C6 SNAPP distributions for alpha-synuclein change dramatically in the presence of 3 microM Al3+, revealing that Al3+ binding causes a significant change in the conformational dynamics of the monomeric form of this disordered protein. In contrast, binding of Cu2+ does not induce a significant shift in 18C6 binding, suggesting that noteworthy structural reorganizations at the monomeric level are minimal. These results are consistent with the idea that the metal-induced aggregation caused by Al3+ and Cu2+ proceed by independent pathways. FAU - Ly, Tony AU - Ly T AD - Department of Chemistry, University of California-Riverside, Riverside, California 92521, USA. FAU - Julian, Ryan R AU - Julian RR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080716 PL - United States TA - J Am Soc Mass Spectrom JT - Journal of the American Society for Mass Spectrometry JID - 9010412 RN - 0 (Calmodulin) RN - 0 (Crown Ethers) RN - 0 (alpha-Synuclein) RN - 63J177NC5B (18-crown-6) RN - 789U1901C5 (Copper) RN - CPD4NFA903 (Aluminum) RN - K3Z4F929H6 (Lysine) RN - SY7Q814VUP (Calcium) SB - IM MH - Aluminum/*metabolism MH - Calcium/*metabolism MH - Calmodulin/*metabolism MH - Copper/*metabolism MH - Crown Ethers/chemistry MH - Lysine/chemistry MH - Mass Spectrometry/methods MH - Protein Binding MH - alpha-Synuclein/*metabolism EDAT- 2008/08/12 09:00 MHDA- 2009/01/14 09:00 CRDT- 2008/08/12 09:00 PHST- 2008/05/12 [received] PHST- 2008/07/08 [revised] PHST- 2008/07/08 [accepted] PHST- 2008/07/16 [aheadofprint] AID - S1044-0305(08)00589-8 [pii] AID - 10.1016/j.jasms.2008.07.006 [doi] PST - ppublish SO - J Am Soc Mass Spectrom. 2008 Nov;19(11):1663-72. doi: 10.1016/j.jasms.2008.07.006. Epub 2008 Jul 16. PMID- 15784256 OWN - NLM STAT- MEDLINE DA - 20050323 DCOM- 20050503 LR - 20111117 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 347 IP - 5 DP - 2005 Apr 15 TI - Evidence for structural plasticity of heavy chain complementarity-determining region 3 in antibody-ssDNA recognition. PG - 965-78 AB - Anti-DNA antibodies play important roles in the pathogenesis of autoimmune diseases. They also represent a unique and relatively unexplored class of DNA-binding protein. Here, we present a study of conformational changes induced by DNA binding to an anti-ssDNA Fab known as DNA-1. Three crystal structures are reported: a complex of DNA-1 bound to dT3, and two structures of the ligand-free Fab. One of the ligand-free structures was determined from crystals exhibiting perfect hemihedral twinning, and the details of structure determination are provided. Unexpectedly, five residues (H97-H100A) in the apex of heavy chain complementarity-determining region 3 (HCDR3) are disordered in both ligand-free structures. Ligand binding also caused a 2-4A shift of the backbone of Tyr L92 and ordering of the L92 side-chain. In contrast, these residues are highly ordered in the Fab/dT3 complex, where Tyr H100 and Tyr H100A form intimate stacking interactions with DNA bases, and L92 forms the 5' end of the binding site. The structures suggest that HCDR3 is very flexible and adopts multiple conformations in the ligand-free state. These results are discussed in terms of induced fit and pre-existing equilibrium theories of ligand binding. Our results allow new interpretations of existing thermodynamic and mutagenesis data in terms of conformational entropy and the volume of conformational space accessible to HCDR3 in the ligand-free state. In the context of autoimmune disease, plasticity of the ligand-free antibody could provide a mechanism by which anti-DNA antibodies bind diverse host ligands, and thereby contribute to pathogenicity. FAU - Schuermann, Jonathan P AU - Schuermann JP AD - Department of Chemistry, University of Missouri-Columbia, Columbia, MO 65211, USA. FAU - Prewitt, Season P AU - Prewitt SP FAU - Davies, Christopher AU - Davies C FAU - Deutscher, Susan L AU - Deutscher SL FAU - Tanner, John J AU - Tanner JJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Antibodies, Antinuclear) RN - 0 (Complementarity Determining Regions) RN - 0 (DNA, Single-Stranded) RN - 0 (Immunoglobulin Heavy Chains) RN - 0 (Ligands) SB - IM MH - Antibodies, Antinuclear/*chemistry/*immunology/metabolism MH - *Binding Sites, Antibody MH - Complementarity Determining Regions/*chemistry/*immunology/metabolism MH - Crystallography, X-Ray MH - DNA, Single-Stranded/chemistry/*immunology/metabolism MH - Immunoglobulin Heavy Chains/chemistry/immunology/metabolism MH - Ligands MH - Models, Molecular EDAT- 2005/03/24 09:00 MHDA- 2005/05/04 09:00 CRDT- 2005/03/24 09:00 PHST- 2004/10/15 [received] PHST- 2004/12/28 [revised] PHST- 2005/02/01 [accepted] AID - S0022-2836(05)00161-0 [pii] AID - 10.1016/j.jmb.2005.02.008 [doi] PST - ppublish SO - J Mol Biol. 2005 Apr 15;347(5):965-78. PMID- 17488095 OWN - NLM STAT- MEDLINE DA - 20070529 DCOM- 20070705 LR - 20140918 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 46 IP - 22 DP - 2007 Jun 5 TI - Requirement for natively unstructured regions of mesoderm development candidate 2 in promoting low-density lipoprotein receptor-related protein 6 maturation. PG - 6570-7 AB - Proteins of the low-density lipoprotein receptor family (LRPs) are complex, multimodular type I transmembrane receptors. Productive maturation of these proteins relies on an ER-resident protein called mesoderm development candidate 2 (MESD) in mammals and Boca in Drosophila. We show here that MESD contains a central folded domain flanked by natively unstructured regions required to facilitate maturation of LRP6. Enforced expression of full-length human MESD promotes the secretion of soluble minireceptors derived from LRP6 that contain either one or two beta-propeller-EGF domain pairs. Conversely, siRNA-mediated knockdown of human MESD expression blocks secretion of native LRP6 minireceptors and dramatically reduces the level of cell-surface expression of full-length LRP6. Cell-surface expression is only rescued by simultaneous delivery of siRNA-resistant forms of mouse MESD that contain most or all of the unstructured N- and C-termini, implicating the flexible parts of MESD in its function of promoting LRP maturation. FAU - Koduri, Vidyasagar AU - Koduri V AD - Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Blacklow, Stephen C AU - Blacklow SC LA - eng GR - HL61001/HL/NHLBI NIH HHS/United States GR - R01 HL061001/HL/NHLBI NIH HHS/United States GR - R01 HL061001-06/HL/NHLBI NIH HHS/United States GR - R01 HL061001-06S1/HL/NHLBI NIH HHS/United States GR - R01 HL061001-07/HL/NHLBI NIH HHS/United States GR - R01 HL061001-08/HL/NHLBI NIH HHS/United States GR - R01 HL061001-09/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070509 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (LDL-Receptor Related Proteins) RN - 0 (LRP6 protein, human) RN - 0 (Low Density Lipoprotein Receptor-Related Protein-6) RN - 0 (Lrp6 protein, mouse) RN - 0 (MESD protein, mouse) RN - 0 (Molecular Chaperones) RN - 0 (RNA, Small Interfering) RN - 0 (Wnt Proteins) SB - IM MH - Amino Acid Motifs MH - Animals MH - Humans MH - LDL-Receptor Related Proteins/genetics/*metabolism MH - Low Density Lipoprotein Receptor-Related Protein-6 MH - Mesoderm/*metabolism MH - Mice MH - Molecular Chaperones/genetics/*metabolism MH - Protein Binding MH - *Protein Folding MH - Protein Processing, Post-Translational/genetics MH - RNA, Small Interfering/genetics/metabolism MH - Wnt Proteins/genetics/metabolism EDAT- 2007/05/10 09:00 MHDA- 2007/07/06 09:00 CRDT- 2007/05/10 09:00 PHST- 2007/05/09 [aheadofprint] AID - 10.1021/bi700049g [doi] PST - ppublish SO - Biochemistry. 2007 Jun 5;46(22):6570-7. Epub 2007 May 9. PMID- 21053335 OWN - NLM STAT- MEDLINE DA - 20110112 DCOM- 20110428 IS - 1860-7314 (Electronic) IS - 1860-6768 (Linking) VI - 6 IP - 1 DP - 2011 Jan TI - Electrospray ionization-mass spectrometry conformational analysis of isolated domains of an intrinsically disordered protein. PG - 96-100 LID - 10.1002/biot.201000253 [doi] AB - The highly dynamic and heterogeneous molecular ensembles characterizing intrinsically disordered proteins (IDP) in solution pose major challenges to the conventional methods for structural analysis. Electrospray ionization-mass spectrometry (ESI-MS) allows direct detection of distinct conformational components, effectively capturing also partially folded and short-lived states. We report the description of two complementary fragments (1-186 and 187-284) of the IDP Sic1, a cyclin-dependent protein kinase inhibitor of yeast Saccharomyces cerevisiae. Structural heterogeneity is noted in both cases, but the two fragments reveal slightly different conformational properties. The results are consistent with previously reported differences between the two protein moieties and corroborate the feasibility of IDP conformational analysis by ESI-MS. FAU - Testa, Lorenzo AU - Testa L AD - Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy. FAU - Brocca, Stefania AU - Brocca S FAU - Samalikova, Maria AU - Samalikova M FAU - Santambrogio, Carlo AU - Santambrogio C FAU - Alberghina, Lilia AU - Alberghina L FAU - Grandori, Rita AU - Grandori R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Biotechnol J JT - Biotechnology journal JID - 101265833 RN - 0 (Cyclin-Dependent Kinase Inhibitor Proteins) RN - 0 (Proteins) RN - 0 (SIC1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Cyclin-Dependent Kinase Inhibitor Proteins/chemistry MH - Protein Conformation MH - Protein Structure, Tertiary MH - Proteins/*chemistry MH - Saccharomyces cerevisiae Proteins/chemistry MH - Spectrometry, Mass, Electrospray Ionization/*methods EDAT- 2010/11/06 06:00 MHDA- 2011/04/29 06:00 CRDT- 2010/11/06 06:00 AID - 10.1002/biot.201000253 [doi] PST - ppublish SO - Biotechnol J. 2011 Jan;6(1):96-100. doi: 10.1002/biot.201000253. PMID- 9843442 OWN - NLM STAT- MEDLINE DA - 19981231 DCOM- 19981231 LR - 20071115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 37 IP - 47 DP - 1998 Nov 24 TI - Identification and characterization of the human HCG V gene product as a novel inhibitor of protein phosphatase-1. PG - 16728-34 AB - The catalytic subunit of mammalian protein phosphatase-1 (PP1) is known to bind to a number of regulatory subunits, whose functions include the targeting of the catalytic subunit to the molecular proximity of its substrate proteins. In addition, PP1 is potently inhibited by several inhibitory polypeptides that include inhibitor-1 and inhibitor-2. In this study the yeast two-hybrid system was used to screen a human cDNA library for putative PP1-binding proteins. Ten putative positive clones were identified, one of which was found to be a partial cDNA of the hemochromatosis candidate gene V (HCG V) whose function was previously unknown. The full-length protein of 126 amino acid residues was expressed in Escherichia coli as a glutathione S-transferase fusion protein and also as a nonfusion protein. The recombinant protein inhibited recombinant and rabbit muscle protein phosphatase-1 with IC50s of ca. 1 nM, but did not inhibit PP2A. The term inhibitor-3 is proposed for this novel inhibitor. It is extremely hydrophilic, is heat stable, and behaves anomalously on SDS-PAGE with an apparent molecular mass of 23 kDa and on gel filtration with a relative molecular weight of 55 000, in contrast to its calculated molecular mass of 14 kDa. These characteristics are shared by the previously described protein phosphatase-1 inhibitor-2 and inhibitor-1 proteins. FAU - Zhang, J AU - Zhang J AD - Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla 10595, USA. FAU - Zhang, L AU - Zhang L FAU - Zhao, S AU - Zhao S FAU - Lee, E Y AU - Lee EY LA - eng GR - DK18512/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Carrier Proteins) RN - 0 (Enzyme Inhibitors) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (PPP1R11 protein, human) RN - 0 (RNA-Binding Proteins) RN - 0 (protein phosphatase inhibitor-1) RN - EC 3.1.- (Endoribonucleases) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - EC 3.1.3.16 (Protein Phosphatase 1) RN - EC 3.1.3.17 (Phosphorylase Phosphatase) RN - EC 3.1.4.- (PPP1R8 protein, human) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Brain/enzymology MH - Carrier Proteins/*chemistry/genetics/metabolism MH - Cloning, Molecular MH - *Endoribonucleases MH - Enzyme Inhibitors/*chemistry/metabolism/pharmacology MH - Genetic Vectors MH - Hemochromatosis/*genetics MH - Humans MH - *Intracellular Signaling Peptides and Proteins MH - Molecular Sequence Data MH - Phosphoprotein Phosphatases MH - Phosphorylase Phosphatase/*antagonists & inhibitors/metabolism MH - Protein Phosphatase 1 MH - RNA-Binding Proteins/chemistry/genetics/metabolism MH - Rabbits MH - Saccharomyces cerevisiae/enzymology/genetics EDAT- 1998/12/08 MHDA- 1998/12/08 00:01 CRDT- 1998/12/08 00:00 AID - 10.1021/bi981169g [doi] AID - bi981169g [pii] PST - ppublish SO - Biochemistry. 1998 Nov 24;37(47):16728-34. PMID- 20164179 OWN - NLM STAT- MEDLINE DA - 20100412 DCOM- 20100506 LR - 20141120 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 16 DP - 2010 Apr 16 TI - Reaction mechanism and molecular basis for selenium/sulfur discrimination of selenocysteine lyase. PG - 12133-9 LID - 10.1074/jbc.M109.084475 [doi] AB - Selenocysteine lyase (SCL) catalyzes the pyridoxal 5'-phosphate-dependent removal of selenium from l-selenocysteine to yield l-alanine. The enzyme is proposed to function in the recycling of the micronutrient selenium from degraded selenoproteins containing selenocysteine residue as an essential component. The enzyme exhibits strict substrate specificity toward l-selenocysteine and no activity to its cognate l-cysteine. However, it remains unclear how the enzyme distinguishes between selenocysteine and cysteine. Here, we present mechanistic studies of selenocysteine lyase from rat. ESI-MS analysis of wild-type and C375A mutant SCL revealed that the catalytic reaction proceeds via the formation of an enzyme-bound selenopersulfide intermediate on the catalytically essential Cys-375 residue. UV-visible spectrum analysis and the crystal structure of SCL complexed with l-cysteine demonstrated that the enzyme reversibly forms a nonproductive adduct with l-cysteine. Cys-375 on the flexible loop directed l-selenocysteine, but not l-cysteine, to the correct position and orientation in the active site to initiate the catalytic reaction. These findings provide, for the first time, the basis for understanding how trace amounts of a selenium-containing substrate is distinguished from excessive amounts of its cognate sulfur-containing compound in a biological system. FAU - Omi, Rie AU - Omi R AD - Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan. FAU - Kurokawa, Suguru AU - Kurokawa S FAU - Mihara, Hisaaki AU - Mihara H FAU - Hayashi, Hideyuki AU - Hayashi H FAU - Goto, Masaru AU - Goto M FAU - Miyahara, Ikuko AU - Miyahara I FAU - Kurihara, Tatsuo AU - Kurihara T FAU - Hirotsu, Ken AU - Hirotsu K FAU - Esaki, Nobuyoshi AU - Esaki N LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100217 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA Primers) RN - 0 (Recombinant Proteins) RN - 70FD1KFU70 (Sulfur) RN - EC 4.- (Lyases) RN - EC 4.4.1.16 (selenocysteine lyase) RN - H6241UJ22B (Selenium) RN - K848JZ4886 (Cysteine) SB - IM MH - Amino Acid Substitution MH - Animals MH - Base Sequence MH - Catalytic Domain/genetics MH - Conserved Sequence MH - Crystallography, X-Ray MH - Cysteine/chemistry MH - DNA Primers/genetics MH - In Vitro Techniques MH - Lyases/*chemistry/genetics/*metabolism MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Protein Conformation MH - Protein Multimerization MH - Rats MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Selenium/*metabolism MH - Spectrometry, Mass, Electrospray Ionization MH - Substrate Specificity MH - Sulfur/*metabolism PMC - PMC2852952 OID - NLM: PMC2852952 EDAT- 2010/02/19 06:00 MHDA- 2010/05/07 06:00 CRDT- 2010/02/19 06:00 PHST- 2010/02/17 [aheadofprint] AID - M109.084475 [pii] AID - 10.1074/jbc.M109.084475 [doi] PST - ppublish SO - J Biol Chem. 2010 Apr 16;285(16):12133-9. doi: 10.1074/jbc.M109.084475. Epub 2010 Feb 17. PMID- 24605363 OWN - NLM STAT- MEDLINE DA - 20140313 DCOM- 20141106 LR - 20150420 IS - 1463-9084 (Electronic) IS - 1463-9076 (Linking) VI - 16 IP - 14 DP - 2014 Apr 14 TI - Predicted disorder-to-order transition mutations in IkappaBalpha disrupt function. PG - 6480-5 LID - 10.1039/c3cp54427c [doi] AB - IkappaBalpha inhibits the transcription factor, NFkappaB, by forming a very tightly bound complex in which the ankyrin repeat domain (ARD) of IkappaBalpha interacts primarily with the dimerization domain of NFkappaB. The first four ankyrin repeats (ARs) of the IkappaBalpha ARD are well-folded, but the AR5-6 region is intrinsically disordered according to amide H/D exchange and protein folding/unfolding experiments. We previously showed that mutations towards the consensus sequence for stable ankyrin repeats resulted in a "prefolded" mutant. To investigate whether the consensus mutations were solely able to order the AR5-6 region, we used a predictor of protein disordered regions PONDR VL-XT to select mutations that would alter the intrinsic disorder towards a more ordered structure (D --> O mutants). The algorithm predicted two mutations, E282W and P261F, neither of which correspond to the consensus sequence for ankyrin repeats. Amide exchange and CD were used to assess ordering. Although only the E282W was predicted to be more ordered by CD and amide exchange, stopped-flow fluorescence studies showed that both of the D --> O mutants were less efficient at dissociating NFkappaB from DNA. FAU - Dembinski, Holly AU - Dembinski H AD - Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA. ekomives@ucsd.edu. FAU - Wismer, Kevin AU - Wismer K FAU - Balasubramaniam, Deepa AU - Balasubramaniam D FAU - Gonzalez, Hector A AU - Gonzalez HA FAU - Alverdi, Vera AU - Alverdi V FAU - Iakoucheva, Lilia M AU - Iakoucheva LM FAU - Komives, Elizabeth A AU - Komives EA LA - eng GR - P01 GM071862/GM/NIGMS NIH HHS/United States GR - P01-GM071862/GM/NIGMS NIH HHS/United States GR - R01 HD065288/HD/NICHD NIH HHS/United States GR - R01 MH091350/MH/NIMH NIH HHS/United States GR - S10 OD016234/OD/NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140306 PL - England TA - Phys Chem Chem Phys JT - Physical chemistry chemical physics : PCCP JID - 100888160 RN - 0 (I-kappa B Proteins) RN - 0 (Recombinant Proteins) RN - 139874-52-5 (NF-kappaB inhibitor alpha) RN - 9007-49-2 (DNA) SB - IM MH - Algorithms MH - Amino Acid Substitution MH - Animals MH - Circular Dichroism MH - DNA/chemistry/metabolism MH - Deuterium Exchange Measurement MH - Humans MH - I-kappa B Proteins/*chemistry/genetics/metabolism MH - Kinetics MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/biosynthesis/chemistry/genetics PMC - PMC4040282 MID - NIHMS581128 OID - NLM: NIHMS581128 OID - NLM: PMC4040282 EDAT- 2014/03/08 06:00 MHDA- 2014/11/07 06:00 CRDT- 2014/03/08 06:00 PHST- 2014/03/06 [aheadofprint] PHST- 2014/03/12 [epublish] AID - 10.1039/c3cp54427c [doi] PST - ppublish SO - Phys Chem Chem Phys. 2014 Apr 14;16(14):6480-5. doi: 10.1039/c3cp54427c. Epub 2014 Mar 6. PMID- 1862343 OWN - NLM STAT- MEDLINE DA - 19910830 DCOM- 19910830 LR - 20091119 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 253 IP - 5018 DP - 1991 Jul 26 TI - Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. PG - 414-20 AB - The structure of a 20-amino acid peptide inhibitor bound to the catalytic subunit of cyclic AMP-dependent protein kinase, and its interactions with the enzyme, are described. The x-ray crystal structure of the complex is the basis of the analysis. The peptide inhibitor, derived from a naturally occurring heat-stable protein kinase inhibitor, contains an amphipathic helix that is followed by a turn and an extended conformation. The extended region occupies the cleft between the two lobes of the enzyme and contains a five-residue consensus recognition sequence common to all substrates and peptide inhibitors of the catalytic subunit. The helical portion of the peptide binds to a hydrophobic groove and conveys high affinity binding. Loops from both domains converge at the active site and contribute to a network of conserved residues at the sites of magnesium adenosine triphosphate binding and catalysis. Amino acids associated with peptide recognition, nonconserved, extend over a large surface area. FAU - Knighton, D R AU - Knighton DR AD - Department of Chemistry, University of California, San Diego, La Jolla 92093-0654. FAU - Zheng, J H AU - Zheng JH FAU - Ten Eyck, L F AU - Ten Eyck LF FAU - Xuong, N H AU - Xuong NH FAU - Taylor, S S AU - Taylor SS FAU - Sowadski, J M AU - Sowadski JM LA - eng GR - RR01644/RR/NCRR NIH HHS/United States GR - T32CA09523/CA/NCI NIH HHS/United States GR - T32DK07233/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Carrier Proteins) RN - 0 (Enzyme Inhibitors) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Macromolecular Substances) RN - 0 (protein kinase modulator) RN - EC 2.7.- (Protein Kinases) SB - IM CIN - Science. 1991 Jul 26;253(5018):383. PMID: 1862341 MH - Amino Acid Sequence MH - Carrier Proteins/*chemistry/metabolism MH - Computer Simulation MH - Enzyme Inhibitors/*chemistry MH - *Intracellular Signaling Peptides and Proteins MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Kinases/*chemistry/metabolism MH - X-Ray Diffraction EDAT- 1991/07/26 MHDA- 1991/07/26 00:01 CRDT- 1991/07/26 00:00 PST - ppublish SO - Science. 1991 Jul 26;253(5018):414-20. PMID- 21664972 OWN - NLM STAT- MEDLINE DA - 20110929 DCOM- 20120123 IS - 1096-0279 (Electronic) IS - 1046-5928 (Linking) VI - 80 IP - 1 DP - 2011 Nov TI - Expression and purification of the C-terminal fragments of TRPV5/6 channels. PG - 28-33 LID - 10.1016/j.pep.2011.05.021 [doi] AB - The transient receptor potential vanniloid 5 and 6 (TRPV5 and TRPV6) Ca(2+)-ion channels are crucial for the regulation of minute-to-minute whole body calcium homeostasis. They act as the gatekeepers of active Ca(2+) reabsorption in kidney and intestine, respectively. In spite of the great progress in the TRP channels characterization, very little is known at the atomic level about their structure and interactions with other proteins. To the major extent it is caused by difficulties in obtaining suitable samples. Here, we report expression and purification of 36 intracellular C-terminal fragments of TRPV5 and TRPV6 channels, for which no structural information is reported thus far. We demonstrate that these proteins contain intrinsically disordered regions and identify fragments suitable for biophysical characterization. By combining bioinformatic predictions and experimental results, we propose several criteria that may aid in designing a scheme for large-scale production of difficult proteins. CI - Copyright (c) 2011 Elsevier Inc. All rights reserved. FAU - Kovalevskaya, Nadezda V AU - Kovalevskaya NV AD - Department of Protein Biophysics, IMM, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands. n.kovalevskaya@science.ru.nl FAU - Schilderink, Nathalie AU - Schilderink N FAU - Vuister, Geerten W AU - Vuister GW LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110602 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (TRPV Cation Channels) RN - 0 (TRPV5 protein, human) RN - 0 (TRPV6 channel) SB - IM MH - Amino Acid Sequence MH - Animals MH - Circular Dichroism MH - *Cloning, Molecular MH - Escherichia coli/genetics MH - Gene Expression MH - Humans MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Conformation MH - Rabbits MH - Sequence Alignment MH - TRPV Cation Channels/chemistry/*genetics/*isolation & purification EDAT- 2011/06/15 06:00 MHDA- 2012/01/24 06:00 CRDT- 2011/06/14 06:00 PHST- 2011/04/13 [received] PHST- 2011/05/25 [revised] PHST- 2011/05/26 [accepted] PHST- 2011/06/02 [aheadofprint] AID - S1046-5928(11)00135-5 [pii] AID - 10.1016/j.pep.2011.05.021 [doi] PST - ppublish SO - Protein Expr Purif. 2011 Nov;80(1):28-33. doi: 10.1016/j.pep.2011.05.021. Epub 2011 Jun 2. PMID- 19076161 OWN - NLM STAT- MEDLINE DA - 20090312 DCOM- 20090528 IS - 1440-1681 (Electronic) IS - 0305-1870 (Linking) VI - 36 IP - 3 DP - 2009 Mar TI - Molecular recognition of the disordered dihydropyridine receptor II-III loop by a conserved spry domain of the type 1 ryanodine receptor. PG - 346-9 LID - 10.1111/j.1440-1681.2008.05130.x [doi] AB - 1. The dihydropyridine receptor (DHPR) II-III loop is an intrinsically unstructured region made up of alpha-helical and beta-turn secondary structure elements with the N and C termini in close spatial proximity. 2. The DHPR II-III loop interacts in vitro with a ryanodine receptor (RyR) 1 SPRY domain through alpha-helical segments located in the A and B regions. Mutations within the A and B regions in the DHPR II-III loop alter the binding affinity to the SPRY2 domain. 3. The A and C peptides derived from DHPR II-III loop show negative cooperativity in binding to the SPRY2 domain. 4. The SPRY2 domain of the RyR1 (1085-1208) forms a beta-sheet sandwich structure flanked by variable loop regions. An acidic loop region of SPRY2 (1107-1121) forms part of a negatively charged cleft that is implicated in the binding of the DHPR II-III loop. 5. The mutant E1108A located in the negatively charged loop of SPRY2 reduces the binding affinity to the DHPR II-III loop. FAU - Tae, Han-Shen AU - Tae HS AD - John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia. FAU - Norris, Nicole C AU - Norris NC FAU - Cui, Yanfang AU - Cui Y FAU - Karunasekara, Yamuna AU - Karunasekara Y FAU - Board, Philip G AU - Board PG FAU - Dulhunty, Angela F AU - Dulhunty AF FAU - Casarotto, Marco G AU - Casarotto MG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20081128 PL - Australia TA - Clin Exp Pharmacol Physiol JT - Clinical and experimental pharmacology & physiology JID - 0425076 RN - 0 (Calcium Channels, L-Type) RN - 0 (Ryanodine Receptor Calcium Release Channel) SB - IM MH - Animals MH - Calcium Channels, L-Type/*chemistry/genetics/metabolism MH - Humans MH - Models, Molecular MH - Molecular Conformation MH - Mutagenesis, Site-Directed MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - Ryanodine Receptor Calcium Release Channel/*chemistry/genetics/metabolism MH - Structural Homology, Protein RF - 29 EDAT- 2008/12/17 09:00 MHDA- 2009/05/29 09:00 CRDT- 2008/12/17 09:00 PHST- 2008/11/28 [aheadofprint] AID - CEP5130 [pii] AID - 10.1111/j.1440-1681.2008.05130.x [doi] PST - ppublish SO - Clin Exp Pharmacol Physiol. 2009 Mar;36(3):346-9. doi: 10.1111/j.1440-1681.2008.05130.x. Epub 2008 Nov 28. PMID- 17209570 OWN - NLM STAT- MEDLINE DA - 20070109 DCOM- 20070227 LR - 20141120 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 46 IP - 2 DP - 2007 Jan 16 TI - Isomers of human alpha-synuclein stabilized by disulfide bonds exhibit distinct structural and aggregative properties. PG - 602-9 AB - The discovery of three mutants in the -synuclein (alphaSyn) gene and the identification of alphaSyn as the major component of Lewy body have opened a new field for understanding the pathogenesis of Parkinson's disease (PD). AlphaSyn is a natively unfolded protein with unknown function and unspecified conformational heterogeneity. In this study, we introduce four Ser/Ala --> Cys mutations at positions 9, 42, 69, and 89 in human wild-type alphaSyn (wt-alphaSyn) and two PD-associated alphaSyn mutants, A30P-alphaSyn and A53T-alphaSyn. This allows expression of three alphaSyn mutants, wt-alphaSyn(4C), A30P-alphaSyn(4C), and A53T-Syn(4C). Subsequent oxidative folding enables each alphaSyn(4C) mutant to form three partially stabilized two-disulfide isomers, designated as alphaSyn(2SS), that are amenable to further isolation and characterization. These alphaSyn mutants exhibit the following properties. (a) A30P-alphaSyn(4C) exhibits a lower folding flexibility than wt-alphaSyn(4C) and A53T-alphaSyn(4C). (b) All three alphaSyn(4C) mutants, like wt-alphaSyn, exhibit a predominant structure of random coil. However, wt-alphaSyn(2SS) adopts an alpha-helical conformation, whereas A30P-alphaSyn(2SS) and A53T-alphaSyn(2SS) take on significant beta-sheet structure. (c) A30P-alphaSyn(2SS) shows a stronger tendency to aggregate than A53T-alphaSyn(2SS) and wt-alphaSyn(2SS). (d) Three isolated isomers of wt-alphaSyn(2SS) exhibit a propensity for forming oligomers different yet enhanced versus that for wt-alphaSyn. These data together substantiate the notion that under physiological conditions, human alphaSyn exists as diverse conformational isomers which exhibit distinct propensities for aggregation and fibril formation. FAU - Jiang, Chuantao AU - Jiang C AD - Research Center for Protein Chemistry, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases and Department of Biochemistry and Molecular Biology, The University of Texas, Houston, Texas 77030, USA. FAU - Chang, Jui-Yoa AU - Chang JY LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Multiprotein Complexes) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Fusion Proteins) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Circular Dichroism MH - Humans MH - In Vitro Techniques MH - Lewy Bodies/metabolism MH - Molecular Sequence Data MH - Multiprotein Complexes MH - Mutagenesis, Site-Directed MH - Oxidation-Reduction MH - Parkinson Disease/etiology/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Isoforms/chemistry/genetics/metabolism MH - Recombinant Fusion Proteins/chemistry/genetics/metabolism MH - alpha-Synuclein/*chemistry/genetics/metabolism EDAT- 2007/01/11 09:00 MHDA- 2007/02/28 09:00 CRDT- 2007/01/11 09:00 AID - 10.1021/bi062068i [doi] PST - ppublish SO - Biochemistry. 2007 Jan 16;46(2):602-9. PMID- 21358637 OWN - NLM STAT- MEDLINE DA - 20110322 DCOM- 20110513 LR - 20140912 IS - 1552-4469 (Electronic) IS - 1552-4450 (Linking) VI - 7 IP - 4 DP - 2011 Apr TI - Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21. PG - 214-21 LID - 10.1038/nchembio.536 [doi] AB - Traditionally, well-defined three-dimensional structure has been thought to be essential for protein function. However, myriad biological functions are performed by highly dynamic, intrinsically disordered proteins (IDPs). IDPs often fold upon binding their biological targets and frequently show 'binding diversity' by targeting multiple ligands. We sought to understand the physical basis of IDP binding diversity and report here that the cyclin-dependent kinase (Cdk) inhibitor p21(Cip1) adaptively binds to and inhibits the various Cdk-cyclin complexes that regulate eukaryotic cell division. Using results from NMR spectroscopy and biochemical and cellular assays, we show that structural adaptability of a helical subdomain within p21, termed LH, enables two other subdomains, D1 and D2, to specifically bind conserved surface features of the cyclin and Cdk subunits, respectively, within otherwise structurally distinct Cdk-cyclin complexes. Adaptive folding upon binding is likely to mediate the diverse biological functions of the thousands of IDPs present in eukaryotes. FAU - Wang, Yuefeng AU - Wang Y AD - Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. FAU - Fisher, John C AU - Fisher JC FAU - Mathew, Rose AU - Mathew R FAU - Ou, Li AU - Ou L FAU - Otieno, Steve AU - Otieno S FAU - Sublet, Jack AU - Sublet J FAU - Xiao, Limin AU - Xiao L FAU - Chen, Jianhan AU - Chen J FAU - Roussel, Martine F AU - Roussel MF FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng GR - 5R01CA082491/CA/NCI NIH HHS/United States GR - P30 CA021765/CA/NCI NIH HHS/United States GR - P30 CA021765-33/CA/NCI NIH HHS/United States GR - P30CA21765/CA/NCI NIH HHS/United States GR - R01 CA082491/CA/NCI NIH HHS/United States GR - R01 CA082491-10/CA/NCI NIH HHS/United States GR - R01CA71907/CA/NCI NIH HHS/United States GR - T35 DK007405/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110227 PL - United States TA - Nat Chem Biol JT - Nature chemical biology JID - 101231976 RN - 0 (Cyclin-Dependent Kinase Inhibitor p21) RN - 0 (Cyclins) RN - EC 2.7.11.22 (Cyclin-Dependent Kinases) SB - IM MH - Amino Acid Sequence MH - Cell Division MH - Cyclin-Dependent Kinase Inhibitor p21/chemistry/genetics/*metabolism MH - Cyclin-Dependent Kinases/antagonists & inhibitors/chemistry/genetics/*metabolism MH - Cyclins/chemistry/genetics/*metabolism MH - Eukaryota/cytology/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Binding MH - Protein Conformation MH - Sequence Homology, Amino Acid MH - Structure-Activity Relationship PMC - PMC3124363 MID - NIHMS268280 OID - NLM: NIHMS268280 OID - NLM: PMC3124363 EDAT- 2011/03/02 06:00 MHDA- 2011/05/14 06:00 CRDT- 2011/03/02 06:00 PHST- 2009/12/29 [received] PHST- 2011/01/26 [accepted] PHST- 2011/02/27 [aheadofprint] AID - nchembio.536 [pii] AID - 10.1038/nchembio.536 [doi] PST - ppublish SO - Nat Chem Biol. 2011 Apr;7(4):214-21. doi: 10.1038/nchembio.536. Epub 2011 Feb 27. PMID- 8845352 OWN - NLM STAT- MEDLINE DA - 19961022 DCOM- 19961022 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 34 IP - 50 DP - 1995 Dec 19 TI - Crystal structure of human thymidylate synthase: a structural mechanism for guiding substrates into the active site. PG - 16279-87 AB - The crystal structure of human thymidylate synthase, a target for anti-cancer drugs, is determined to 3.0 A resolution and refined to a crystallographic residual of 17.8%. The structure implicates the enzyme in a mechanism for facilitating the docking of substrates into the active site. This mechanism involves a twist of approximately 180 degrees of the active site loop, pivoted around the neighboring residues 184 and 204, and implicates ordering of external, eukaryote specific loops along with the well-characterized closure of the active site upon substrate binding. The highly conserved, but eukaryote-specific insertion of twelve residues 90-101 (h117-128), and of eight residues between 156 and 157 (h146-h153) are known to be alpha-helical in other eukaryotes, and lie close together on the outside of the protein in regions of disordered electron density in this crystal form. Two cysteines [cys 202 (h199) and 213 (h210)] are close enough to form a disulfide bond within each subunit, and a third cysteine [cys 183 (h180)] is positioned to form a disulfide bond with the active site cysteine [cys 198 (h195)] in its unliganded conformation. The amino terminal 27 residues, unique to human TS, contains 8 proline residues, is also in a region of disordered electron density, and is likely to be flexible prior to substrate binding. The drug resistance mutation, Y6H, confers a 4-fold reduction in FdUMP affinity and 8-fold reduction in kcat for the dUMP reaction. Though indirectly connected to the active site, the structure suggests a mechanism of resistance that possibly involves a change in structure. This structure offers a unique opportunity for structure-based drug design aimed at the unliganded form of the human enzyme. FAU - Schiffer, C A AU - Schiffer CA AD - Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, USA. FAU - Clifton, I J AU - Clifton IJ FAU - Davisson, V J AU - Davisson VJ FAU - Santi, D V AU - Santi DV FAU - Stroud, R M AU - Stroud RM LA - eng GR - CA14394/CA/NCI NIH HHS/United States GR - CA63081/CA/NCI NIH HHS/United States GR - R01-CA41323/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA Transposable Elements) RN - 0 (Deoxyuracil Nucleotides) RN - 365-07-1 (Thymidine Monophosphate) RN - 964-26-1 (2'-deoxyuridylic acid) RN - EC 2.1.1.45 (Thymidylate Synthase) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Conserved Sequence MH - Crystallography MH - DNA Transposable Elements MH - Deoxyuracil Nucleotides/metabolism MH - Eukaryotic Cells MH - Humans MH - Hydrogen Bonding MH - Models, Molecular MH - Molecular Sequence Data MH - *Protein Structure, Tertiary MH - Sequence Alignment MH - Structure-Activity Relationship MH - Synchrotrons MH - Thymidine Monophosphate/biosynthesis MH - Thymidylate Synthase/*chemistry/metabolism EDAT- 1995/12/19 MHDA- 1995/12/19 00:01 CRDT- 1995/12/19 00:00 PST - ppublish SO - Biochemistry. 1995 Dec 19;34(50):16279-87. PMID- 23380070 OWN - NLM STAT- MEDLINE DA - 20130409 DCOM- 20130531 LR - 20141103 IS - 1873-3468 (Electronic) IS - 0014-5793 (Linking) VI - 587 IP - 8 DP - 2013 Apr 17 TI - Islet amyloid: from fundamental biophysics to mechanisms of cytotoxicity. PG - 1106-18 LID - 10.1016/j.febslet.2013.01.046 [doi] LID - S0014-5793(13)00091-4 [pii] AB - Pancreatic islet amyloid is a characteristic feature of type 2 diabetes. The major protein component of islet amyloid is the polypeptide hormone known as islet amyloid polypeptide (IAPP, or amylin). IAPP is stored with insulin in the beta-cell secretory granules and is released in response to the stimuli that lead to insulin secretion. IAPP is normally soluble and is natively unfolded in its monomeric state, but forms islet amyloid in type 2 diabetes. Islet amyloid is not the cause of type 2 diabetes, but it leads to beta-cell dysfunction and cell death, and contributes to the failure of islet cell transplantation. The mechanism of IAPP amyloid formation is not understood and the mechanisms of cytotoxicity are not fully defined. CI - Copyright (c) 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. FAU - Cao, Ping AU - Cao P AD - Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA. FAU - Marek, Peter AU - Marek P FAU - Noor, Harris AU - Noor H FAU - Patsalo, Vadim AU - Patsalo V FAU - Tu, Ling-Hsien AU - Tu LH FAU - Wang, Hui AU - Wang H FAU - Abedini, Andisheh AU - Abedini A FAU - Raleigh, Daniel P AU - Raleigh DP LA - eng GR - F32 DK089734/DK/NIDDK NIH HHS/United States GR - F32 DK089734-02/DK/NIDDK NIH HHS/United States GR - GM078114/GM/NIGMS NIH HHS/United States GR - R01 GM078114/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review DEP - 20130201 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Amyloid) RN - 0 (Islet Amyloid Polypeptide) SB - IM MH - Amino Acid Sequence MH - Amyloid/*chemistry/genetics/metabolism MH - Biophysical Phenomena MH - Cell Survival MH - Humans MH - Islet Amyloid Polypeptide/*chemistry/genetics/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - *Protein Structure, Secondary MH - Sequence Homology, Amino Acid PMC - PMC3753196 MID - NIHMS477514 OID - NLM: NIHMS477514 OID - NLM: PMC3753196 EDAT- 2013/02/06 06:00 MHDA- 2013/06/01 06:00 CRDT- 2013/02/06 06:00 PHST- 2012/12/05 [received] PHST- 2013/01/22 [revised] PHST- 2013/01/23 [accepted] PHST- 2013/02/01 [aheadofprint] AID - S0014-5793(13)00091-4 [pii] AID - 10.1016/j.febslet.2013.01.046 [doi] PST - ppublish SO - FEBS Lett. 2013 Apr 17;587(8):1106-18. doi: 10.1016/j.febslet.2013.01.046. Epub 2013 Feb 1. PMID- 9826495 OWN - NLM STAT- MEDLINE DA - 19990125 DCOM- 19990125 LR - 20071114 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 284 IP - 3 DP - 1998 Dec 4 TI - DNA-induced conformational changes are the basis for cooperative dimerization by the DNA binding domain of the retinoid X receptor. PG - 533-9 AB - Dimerization of the DNA-binding domains of nuclear hormone receptors occurs in a manner that is highly cooperative with DNA binding. We have investigated the molecular basis for this cooperativity through an NMR study of the interaction between the monomeric DNA-binding domain (DBD) of the retinoid-X-receptor (RXR) and a single DNA half-site. Major changes were observed in the chemical shifts of the backbone resonances and in the pattern of medium-range nuclear Overhauser enhancement connectivities of the RXR upon binding to DNA, indicating that the DNA induces conformational changes in the monomer. Binding to DNA induces and stabilizes the structure in a region of the second zinc binding domain that forms the dimerization interface when RXR binds as a dimer to a direct repeat recognition element. These studies provide direct experimental evidence that DNA-induced protein conformational changes constitute the molecular basis for cooperative enhancement of dimer formation and DNA binding by the nuclear hormone receptor DBDs. In contrast to the localized folding induced in the dimerization interface, DNA binding leads to unfolding of the C-terminal helix found in the free RXR DBD. Unwinding of this helix may facilitate homodimer formation by maximizing interactions between the two DNA-bound RXR domains. CI - Copyright 1998 Academic Press FAU - Holmbeck, S M AU - Holmbeck SM AD - Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA. FAU - Dyson, H J AU - Dyson HJ FAU - Wright, P E AU - Wright PE LA - eng GR - GM 36643/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DNA-Binding Proteins) RN - 0 (Receptors, Retinoic Acid) RN - 0 (Retinoid X Receptors) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - DNA/*chemistry MH - DNA-Binding Proteins/*chemistry/metabolism MH - Dimerization MH - Molecular Sequence Data MH - Protein Conformation MH - Receptors, Retinoic Acid/*chemistry/metabolism MH - Retinoid X Receptors MH - Transcription Factors/*chemistry/metabolism EDAT- 1998/11/25 MHDA- 1998/11/25 00:01 CRDT- 1998/11/25 00:00 AID - S0022-2836(98)92207-0 [pii] AID - 10.1006/jmbi.1998.2207 [doi] PST - ppublish SO - J Mol Biol. 1998 Dec 4;284(3):533-9. PMID- 21892446 OWN - NLM STAT- MEDLINE DA - 20111202 DCOM- 20120320 LR - 20141014 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Modulation of an IDP binding mechanism and rates by helix propensity and non-native interactions: association of HIF1alpha with CBP. PG - 256-67 LID - 10.1039/c1mb05252g [doi] AB - Intrinsically disordered proteins that acquire their three dimensional structures only upon binding to their targets are very important in cellular signal regulation. While experimental studies have been made on the structures of both bound (structured) and unbound (disordered) states, less is known about the actual folding-binding transition. Coarse grained simulations using native-centric (i.e. Go) potentials have been particularly useful in addressing this problem, given the large search space for IDP binding, but have well-known deficiencies in reproducing the unfolded state structure and dynamics. Here, we investigate the interaction of HIF1alpha with CBP using a hierarchy of coarse-grained models, in each case matching the binding affinity at 300 K to the experimental value. Starting from a pure Go-like model based on the native structure of the complex we go on to consider a more realistic model of helix propensity in the HIF1alpha, and finally the effect of non-native interactions between binding partners. We find structural disorder (i.e."fuzziness") in the bound state of HIF1alpha in all models which is supported by the results of atomistic simulations. Correcting the over-stabilized helices in the unbound state gives rise to a more cooperative folding-binding transition (destabilizing partially bound intermediates). Adding non-native contacts lowers the free energy barrier for binding to an almost barrierless scenario, leading to higher binding/unbinding rates relative to the other models, in better agreement with the near diffusion-limited binding rates measured experimentally. Transition state structures for the three models are highly disordered, supporting a fly-casting mechanism for binding. FAU - De Sancho, David AU - De Sancho D AD - Cambridge University, Department of Chemistry, Cambridge, UK. FAU - Best, Robert B AU - Best RB LA - eng GR - BB/H006885/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110902 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Hypoxia-Inducible Factor 1, alpha Subunit) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - CREB-Binding Protein/*chemistry/*metabolism MH - Calibration MH - Hypoxia-Inducible Factor 1, alpha Subunit/*chemistry/*metabolism MH - Kinetics MH - Molecular Dynamics Simulation MH - Protein Binding MH - *Protein Folding MH - Protein Stability MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Temperature EDAT- 2011/09/06 06:00 MHDA- 2012/03/21 06:00 CRDT- 2011/09/06 06:00 PHST- 2011/09/02 [aheadofprint] PHST- 2011/12/01 [epublish] AID - 10.1039/c1mb05252g [doi] PST - ppublish SO - Mol Biosyst. 2012 Jan;8(1):256-67. doi: 10.1039/c1mb05252g. Epub 2011 Sep 2. PMID- 15826952 OWN - NLM STAT- MEDLINE DA - 20050606 DCOM- 20050802 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 23 DP - 2005 Jun 10 TI - Mechanism of transcription factor recruitment by acidic activators. PG - 21779-84 AB - Many transcriptional activators are intrinsically unstructured yet display unique, defined conformations when bound to target proteins. Target-induced folding provides a mechanism by which activators could form specific interactions with an array of structurally unrelated target proteins. Evidence for such a binding mechanism has been reported previously in the context of the interaction between the cancer-related c-Myc protein and the TATA-binding protein, which can be modeled as a two-step process in which a rapidly forming, low affinity complex slowly converts to a more stable form, consistent with a coupled binding and folding reaction. To test the generality of the target-induced folding model, we investigated the binding of two widely studied acidic activators, Gal4 and VP16, to a set of target proteins, including TATA-binding protein and the Swi1 and Snf5 subunits of the Swi/Snf chromatin remodeling complex. Using surface plasmon resonance, we show that these activator-target combinations also display bi-phasic kinetics suggesting two distinct steps. A fast initial binding phase that is inhibited by high ionic strength is followed by a slow phase that is favored by increased temperature. In all cases, overall affinity increases with temperature and, in most cases, with increased ionic strength. These results are consistent with a general mechanism for recruitment of transcriptional components to promoters by naturally occurring acidic activators, by which the initial contact is mediated predominantly through electrostatic interactions, whereas subsequent target-induced folding of the activator results in a stable complex. FAU - Ferreira, Monica E AU - Ferreira ME AD - Department of Life Sciences, Sodertorns Hogskola, S-141 89 Huddinge, Sweden. monica.ferreira@sh.se FAU - Hermann, Stefan AU - Hermann S FAU - Prochasson, Philippe AU - Prochasson P FAU - Workman, Jerry L AU - Workman JL FAU - Berndt, Kurt D AU - Berndt KD FAU - Wright, Anthony P H AU - Wright AP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050411 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Chromatin) RN - 0 (Chromosomal Proteins, Non-Histone) RN - 0 (DNA-Binding Proteins) RN - 0 (GAL4 protein, S cerevisiae) RN - 0 (Herpes Simplex Virus Protein Vmw65) RN - 0 (Ions) RN - 0 (Macromolecular Substances) RN - 0 (Recombinant Fusion Proteins) RN - 0 (SNF5 protein, S cerevisiae) RN - 0 (SWI1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - EC 2.5.1.18 (Glutathione Transferase) SB - IM MH - Chromatin/chemistry MH - Chromosomal Proteins, Non-Histone MH - DNA-Binding Proteins/metabolism MH - Dose-Response Relationship, Drug MH - Glutathione Transferase/metabolism MH - Herpes Simplex Virus Protein Vmw65/metabolism MH - Ions MH - Kinetics MH - Macromolecular Substances/metabolism MH - Plasmids/metabolism MH - Protein Binding MH - Protein Folding MH - Recombinant Fusion Proteins/metabolism MH - Saccharomyces cerevisiae/metabolism MH - Saccharomyces cerevisiae Proteins/metabolism MH - Surface Plasmon Resonance MH - Temperature MH - Thermodynamics MH - Time Factors MH - Trans-Activators/*metabolism MH - Transcription Factors/*metabolism EDAT- 2005/04/14 09:00 MHDA- 2005/08/03 09:00 CRDT- 2005/04/14 09:00 PHST- 2005/04/11 [aheadofprint] AID - M502627200 [pii] AID - 10.1074/jbc.M502627200 [doi] PST - ppublish SO - J Biol Chem. 2005 Jun 10;280(23):21779-84. Epub 2005 Apr 11. PMID- 16197548 OWN - NLM STAT- MEDLINE DA - 20051014 DCOM- 20060612 LR - 20140605 IS - 1472-6807 (Electronic) IS - 1472-6807 (Linking) VI - 5 DP - 2005 TI - Prediction of "hot spots" of aggregation in disease-linked polypeptides. PG - 18 AB - BACKGROUND: The polypeptides involved in amyloidogenesis may be globular proteins with a defined 3D-structure or natively unfolded proteins. The first class includes polypeptides such as beta2-microglobulin, lysozyme, transthyretin or the prion protein, whereas beta-amyloid peptide, amylin or alpha-synuclein all belong to the second class. Recent studies suggest that specific regions in the proteins act as "hot spots" driving aggregation. This should be especially relevant for natively unfolded proteins or unfolded states of globular proteins as they lack significant secondary and tertiary structure and specific intra-chain interactions that can mask these aggregation-prone regions. Prediction of such sequence stretches is important since they are potential therapeutic targets. RESULTS: In this study we exploited the experimental data obtained in an in vivo system using beta-amyloid peptide as a model to derive the individual aggregation propensities of natural amino acids. These data are used to generate aggregation profiles for different disease-related polypeptides. The approach detects the presence of "hot spots" which have been already validated experimentally in the literature and provides insights into the effect of disease-linked mutations in these polypeptides. CONCLUSION: The proposed method might become a useful tool for the future development of sequence-targeted anti-aggregation pharmaceuticals. FAU - Sanchez de Groot, Natalia AU - Sanchez de Groot N AD - Departament de Bioquimica i Biologia Molecular, Facultat de Ciencies, Universitat Autonoma de Barcelona, E-08193 Bellaterra, Spain. Natalia.Sanchezd@campus.uab.es FAU - Pallares, Irantzu AU - Pallares I FAU - Aviles, Francesc X AU - Aviles FX FAU - Vendrell, Josep AU - Vendrell J FAU - Ventura, Salvador AU - Ventura S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050930 PL - England TA - BMC Struct Biol JT - BMC structural biology JID - 101088689 RN - 0 (Amyloid beta-Peptides) RN - 0 (Insulin) RN - 0 (Peptides) RN - 0 (Prealbumin) RN - 0 (Prions) RN - 0 (Proteins) RN - 0 (alpha-Synuclein) RN - 0 (beta 2-Microglobulin) RN - EC 3.2.1.17 (Muramidase) SB - IM MH - Amyloid beta-Peptides/chemistry MH - Humans MH - Insulin/chemistry MH - Models, Molecular MH - Muramidase/chemistry MH - Mutation MH - Neurodegenerative Diseases/metabolism MH - Peptides/*chemistry MH - Prealbumin/chemistry MH - Prions/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proteins/chemistry MH - alpha-Synuclein/chemistry MH - beta 2-Microglobulin/chemistry PMC - PMC1262731 OID - NLM: PMC1262731 EDAT- 2005/10/04 09:00 MHDA- 2006/06/13 09:00 CRDT- 2005/10/04 09:00 PHST- 2005/09/28 [received] PHST- 2005/09/30 [accepted] PHST- 2005/09/30 [aheadofprint] AID - 1472-6807-5-18 [pii] AID - 10.1186/1472-6807-5-18 [doi] PST - epublish SO - BMC Struct Biol. 2005 Sep 30;5:18. PMID- 12057197 OWN - NLM STAT- MEDLINE DA - 20020611 DCOM- 20030711 LR - 20061115 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 10 IP - 6 DP - 2002 Jun TI - X-ray crystallographic studies on butyryl-ACP reveal flexibility of the structure around a putative acyl chain binding site. PG - 825-35 AB - Acyl carrier protein (ACP) is an essential cofactor in biosynthesis of fatty acids and many other reactions that require acyl transfer steps. We have determined the first crystal structures of an acylated form of ACP from E. coli, that of butyryl-ACP. Our analysis of the molecular surface of ACP reveals a plastic hydrophobic cavity in the vicinity of the phosphopantethylated Ser36 residue that is expanded and occupied by the butyryl and beta-mercaptoethylamine moieties of the acylated 4'-phosphopantetheine group in one of our crystal forms. In the other form, the cavity is contracted, and we propose that the protein has adopted the conformation after delivery of substrate into the active site of a partner enzyme. FAU - Roujeinikova, Anna AU - Roujeinikova A AD - Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, S10 2TN, Sheffield, United Kingdom. FAU - Baldock, Clair AU - Baldock C FAU - Simon, William J AU - Simon WJ FAU - Gilroy, John AU - Gilroy J FAU - Baker, Patrick J AU - Baker PJ FAU - Stuitje, Antoine R AU - Stuitje AR FAU - Rice, David W AU - Rice DW FAU - Slabas, Antoni R AU - Slabas AR FAU - Rafferty, John B AU - Rafferty JB LA - eng SI - PDB/1I0H SI - PDB/1IOI PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Acyl Carrier Protein) RN - 0 (Escherichia coli Proteins) SB - IM MH - Acyl Carrier Protein/*chemistry/metabolism MH - Binding Sites MH - Crystallography, X-Ray MH - Escherichia coli/chemistry/metabolism MH - Escherichia coli Proteins/*chemistry/metabolism MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary EDAT- 2002/06/12 10:00 MHDA- 2003/07/12 05:00 CRDT- 2002/06/12 10:00 AID - S096921260200775X [pii] PST - ppublish SO - Structure. 2002 Jun;10(6):825-35. PMID- 12057196 OWN - NLM STAT- MEDLINE DA - 20020611 DCOM- 20030711 LR - 20061115 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 10 IP - 6 DP - 2002 Jun TI - The Ig-like structure of the C-terminal domain of lamin A/C, mutated in muscular dystrophies, cardiomyopathy, and partial lipodystrophy. PG - 811-23 AB - Lamins are nuclear intermediate filaments that, together with lamin-associated proteins, maintain nuclear shape and provide a structural support for chromosomes and replicating DNA. We have determined the solution structure of the human lamin A/C C-terminal globular domain which contains specific mutations causing four different heritable diseases. This domain encompasses residues 430-545 and adopts an Ig-like fold of type s. We have also characterized by NMR and circular dichroism the structure and thermostability of three mutants, R453W and R482W/Q, corresponding to "hot spots" causing Emery-Dreifuss muscular dystrophy and Dunnigan-type lipodystrophy, respectively. Our structure determination and mutant analyses clearly show that the consequences of the mutations causing muscle-specific diseases or lipodystrophy are different at the molecular level. FAU - Krimm, Isabelle AU - Krimm I AD - Departement d'Ingenierie et d'Etudes des Proteines, CEA Saclay, 91191, Gif-sur-Yvette, France. FAU - Ostlund, Cecilia AU - Ostlund C FAU - Gilquin, Bernard AU - Gilquin B FAU - Couprie, Joel AU - Couprie J FAU - Hossenlopp, Paul AU - Hossenlopp P FAU - Mornon, Jean-Paul AU - Mornon JP FAU - Bonne, Gisele AU - Bonne G FAU - Courvalin, Jean-Claude AU - Courvalin JC FAU - Worman, Howard J AU - Worman HJ FAU - Zinn-Justin, Sophie AU - Zinn-Justin S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Immunoglobulins) RN - 0 (Lamin Type A) SB - IM MH - Amino Acid Sequence MH - Cardiomyopathies/*genetics/metabolism MH - Circular Dichroism MH - Conserved Sequence MH - Immunoglobulins/genetics MH - Lamin Type A/*genetics/metabolism MH - Lipodystrophy/*genetics/metabolism MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Muscular Dystrophies/*genetics/metabolism MH - Mutation MH - Phenotype MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Sequence Analysis, Protein EDAT- 2002/06/12 10:00 MHDA- 2003/07/12 05:00 CRDT- 2002/06/12 10:00 AID - S0969212602007773 [pii] PST - ppublish SO - Structure. 2002 Jun;10(6):811-23. PMID- 19891973 OWN - NLM STAT- MEDLINE DA - 20100128 DCOM- 20100303 LR - 20141120 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 395 IP - 3 DP - 2010 Jan 22 TI - Towards multiparametric fluorescent imaging of amyloid formation: studies of a YFP model of alpha-synuclein aggregation. PG - 627-42 LID - 10.1016/j.jmb.2009.10.066 [doi] AB - Misfolding and aggregation of proteins are characteristics of a range of increasingly prevalent neurodegenerative disorders including Alzheimer's and Parkinson's diseases. In Parkinson's disease and several closely related syndromes, the protein alpha-synuclein (AS) aggregates and forms amyloid-like deposits in specific regions of the brain. Fluorescence microscopy using fluorescent proteins, for instance the yellow fluorescent protein (YFP), is the method of choice to image molecular events such as protein aggregation in living organisms. The presence of a bulky fluorescent protein tag, however, may potentially affect significantly the properties of the protein of interest; for AS in particular, its relative small size and, as an intrinsically unfolded protein, its lack of defined secondary structure could challenge the usefulness of fluorescent-protein-based derivatives. Here, we subject a YFP fusion of AS to exhaustive studies in vitro designed to determine its potential as a means of probing amyloid formation in vivo. By employing a combination of biophysical and biochemical studies, we demonstrate that the conjugation of YFP does not significantly perturb the structure of AS in solution and find that the AS-YFP protein forms amyloid deposits in vitro that are essentially identical with those observed for wild-type AS, except that they are fluorescent. Of the several fluorescent properties of the YFP chimera that were assayed, we find that fluorescence anisotropy is a particularly useful parameter to follow the aggregation of AS-YFP, because of energy migration Forster resonance energy transfer (emFRET or homoFRET) between closely positioned YFP moieties occurring as a result of the high density of the fluorophore within the amyloid species. Fluorescence anisotropy imaging microscopy further demonstrates the ability of homoFRET to distinguish between soluble, pre-fibrillar aggregates and amyloid fibrils of AS-YFP. Our results validate the use of fluorescent protein chimeras of AS as representative models for studying protein aggregation and offer new opportunities for the investigation of amyloid aggregation in vivo using YFP-tagged proteins. CI - Copyright 2009 Elsevier Ltd. All rights reserved. FAU - van Ham, Tjakko J AU - van Ham TJ AD - Department of Genetics, University of Groningen, Groningen, The Netherlands. FAU - Esposito, Alessandro AU - Esposito A FAU - Kumita, Janet R AU - Kumita JR FAU - Hsu, Shang-Te D AU - Hsu ST FAU - Kaminski Schierle, Gabriele S AU - Kaminski Schierle GS FAU - Kaminski, Clemens F AU - Kaminski CF FAU - Dobson, Christopher M AU - Dobson CM FAU - Nollen, Ellen A A AU - Nollen EA FAU - Bertoncini, Carlos W AU - Bertoncini CW LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091103 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amyloid) RN - 0 (Bacterial Proteins) RN - 0 (Luminescent Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (alpha-Synuclein) RN - 0 (yellow fluorescent protein, Bacteria) SB - IM MH - Amyloid/*biosynthesis/*chemistry/ultrastructure MH - Bacterial Proteins/*chemistry/genetics/metabolism/ultrastructure MH - Brain/metabolism/ultrastructure MH - Fluorescence Polarization MH - Fluorescence Resonance Energy Transfer MH - Humans MH - In Vitro Techniques MH - Lewy Bodies/metabolism/ultrastructure MH - Luminescent Proteins/*chemistry/genetics/metabolism/ultrastructure MH - Microscopy, Electron, Transmission MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Multimerization MH - Recombinant Fusion Proteins/chemistry/genetics/metabolism/ultrastructure MH - alpha-Synuclein/*chemistry/genetics/metabolism/ultrastructure EDAT- 2009/11/07 06:00 MHDA- 2010/03/04 06:00 CRDT- 2009/11/07 06:00 PHST- 2009/07/17 [received] PHST- 2009/10/04 [revised] PHST- 2009/10/27 [accepted] PHST- 2009/11/03 [aheadofprint] AID - S0022-2836(09)01325-4 [pii] AID - 10.1016/j.jmb.2009.10.066 [doi] PST - ppublish SO - J Mol Biol. 2010 Jan 22;395(3):627-42. doi: 10.1016/j.jmb.2009.10.066. Epub 2009 Nov 3. PMID- 16170637 OWN - NLM STAT- MEDLINE DA - 20050919 DCOM- 20060630 LR - 20061115 IS - 0166-8595 (Print) IS - 0166-8595 (Linking) VI - 85 IP - 3 DP - 2005 Sep TI - Structure and activity of the photosystem II manganese-stabilizing protein: role of the conserved disulfide bond. PG - 359-72 AB - The 33-kDa manganese-stabilizing protein (MSP) of Photosystem II (PS II) maintains the functional stability of the Mn cluster in the enzyme's active site. This protein has been shown to possess characteristics similar to those of the intrinsically disordered, or natively unfolded proteins. Alternately it was proposed that MSP should be classified as a molten globule, based in part on the hypothesis that its lone disulfide bridge is necessary for structural stability and function in solution. A site-directed mutant MSP (C28A,C51A) that eliminates the disulfide bond reconstitutes O(2) evolution activity and binds to MSP-free PS II preparations at wild-type levels. This mutant was further characterized by incubation at 90 degrees C to determine the effect of loss of the disulfide bridge on MSP thermostability and solution structure. After heating at 90 degrees C for 20 min, C28A,C51A MSP was still able to bind to PS II preparations at molar stoichiometries similar to those of WT MSP and reconstitute O(2) evolution activity. A fraction of the protein aggregates upon heating, but after resolubilization, it regains the ability to bind to PS II and reconstitute O(2) evolution activity. Characterization of the solution structure of C28A,C51A MSP, using CD spectroscopy, UV absorption spectroscopy, and gel filtration chromatography, revealed that the mutant has a more disordered solution structure than WT MSP. The disulfide bond is therefore unnecessary for MSP function and the intrinsically disordered characteristics of MSP are not dependent on its presence. However, the disulfide bond does play a role in the solution structure of MSP in vivo, as evidenced by the lability of a C20S MSP mutation in Synechocystis 6803. FAU - Wyman, Aaron J AU - Wyman AJ AD - Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA. FAU - Yocum, Charles F AU - Yocum CF LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - Netherlands TA - Photosynth Res JT - Photosynthesis research JID - 100954728 RN - 0 (Disulfides) RN - 0 (Photosystem II Protein Complex) RN - 0 (photosystem II manganese-stabilizing protein) SB - IM MH - Amino Acid Substitution MH - Circular Dichroism MH - Disulfides/*chemistry/*metabolism MH - Mutation MH - Photosystem II Protein Complex/*chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Structure-Activity Relationship EDAT- 2005/09/20 09:00 MHDA- 2006/07/01 09:00 CRDT- 2005/09/20 09:00 PHST- 2005/02/21 [received] PHST- 2005/05/13 [accepted] AID - 10.1007/s11120-005-7385-9 [doi] PST - ppublish SO - Photosynth Res. 2005 Sep;85(3):359-72. PMID- 17623039 OWN - NLM STAT- MEDLINE DA - 20070919 DCOM- 20071107 IS - 0022-3042 (Print) IS - 0022-3042 (Linking) VI - 103 IP - 1 DP - 2007 Oct TI - Neuropathology, biochemistry, and biophysics of alpha-synuclein aggregation. PG - 17-37 AB - Aggregation of alpha-synuclein, an abundant and conserved pre-synaptic brain protein, is implicated as a critical factor in several neurodegenerative diseases. These diseases, known as synucleinopathies, include Parkinson's disease, dementia with Lewy bodies (LBs), diffuse LB disease, the LB variant of Alzheimer's disease, multiple system atrophy, and neurodegeneration with brain iron accumulation type I. Although the precise nature of in vivoalpha-synuclein function remains elusive, considerable knowledge has been accumulated about its structural properties and conformational behavior. alpha-Synuclein is a typical natively unfolded protein. It is characterized by the lack of rigid, well-defined, 3-D structure and possesses remarkable conformational plasticity. The structure of this protein depends dramatically on its environment and it accommodates a number of unrelated conformations. This paper provides an overview of the biochemistry, biophysics, and neuropathology of alpha-synuclein aggregation. FAU - Uversky, Vladimir N AU - Uversky VN AD - Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA. vuversky@iupui.edu LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20070710 PL - England TA - J Neurochem JT - Journal of neurochemistry JID - 2985190R RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Cell Death MH - Humans MH - Lewy Bodies/*metabolism/pathology MH - Neurodegenerative Diseases/*metabolism/pathology MH - Protein Conformation MH - Protein Folding MH - alpha-Synuclein/*chemistry/genetics/*metabolism RF - 313 EDAT- 2007/07/12 09:00 MHDA- 2007/11/08 09:00 CRDT- 2007/07/12 09:00 PHST- 2007/07/10 [aheadofprint] AID - JNC4764 [pii] AID - 10.1111/j.1471-4159.2007.04764.x [doi] PST - ppublish SO - J Neurochem. 2007 Oct;103(1):17-37. Epub 2007 Jul 10. PMID- 16008352 OWN - NLM STAT- MEDLINE DA - 20050712 DCOM- 20051011 LR - 20150313 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 44 IP - 28 DP - 2005 Jul 19 TI - Backbone dynamics of the olfactory marker protein as studied by 15N NMR relaxation measurements. PG - 9673-9 AB - Nuclear magnetic resonance (NMR) (15)N relaxation measurements of the olfactory marker protein (OMP) including longitudinal relaxation (T(1)), transverse relaxation (T(2)), and (15)N-{(1)H} NOE data were collected at low protein concentrations (K(CDNF), (MANF)E79-->M(CDNF) and (MANF)K88-->L(CDNF), that may account for the biological differences between the proteins. FAU - Parkash, Vimal AU - Parkash V AD - Institute of Biotechnology, University of Helsinki, Helsinki, Finland. FAU - Lindholm, Paivi AU - Lindholm P FAU - Peranen, Johan AU - Peranen J FAU - Kalkkinen, Nisse AU - Kalkkinen N FAU - Oksanen, Esko AU - Oksanen E FAU - Saarma, Mart AU - Saarma M FAU - Leppanen, Veli-Matti AU - Leppanen VM FAU - Goldman, Adrian AU - Goldman A LA - eng GR - G0500367/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090303 PL - England TA - Protein Eng Des Sel JT - Protein engineering, design & selection : PEDS JID - 101186484 RN - 0 (CDNF protein, human) RN - 0 (Disulfides) RN - 0 (MANF protein, human) RN - 0 (Nerve Growth Factors) RN - 0 (Nerve Tissue Proteins) RN - 0 (Saposins) SB - IM MH - Crystallography, X-Ray MH - Disulfides/metabolism MH - Humans MH - Lipid Metabolism MH - Nerve Growth Factors/*chemistry/genetics/metabolism MH - Nerve Tissue Proteins/*chemistry/genetics/metabolism MH - Protein Folding MH - Saposins/metabolism MH - Sequence Alignment MH - Stress, Physiological EDAT- 2009/03/05 09:00 MHDA- 2009/07/15 09:00 CRDT- 2009/03/05 09:00 PHST- 2009/03/03 [aheadofprint] AID - gzn080 [pii] AID - 10.1093/protein/gzn080 [doi] PST - ppublish SO - Protein Eng Des Sel. 2009 Apr;22(4):233-41. doi: 10.1093/protein/gzn080. Epub 2009 Mar 3. PMID- 23207295 OWN - NLM STAT- MEDLINE DA - 20130128 DCOM- 20130322 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 425 IP - 3 DP - 2013 Feb 8 TI - An intrinsically disordered domain has a dual function coupled to compartment-dependent redox control. PG - 594-608 LID - 10.1016/j.jmb.2012.11.032 [doi] LID - S0022-2836(12)00904-7 [pii] AB - The functional role of unstructured protein domains is an emerging field in the frame of intrinsically disordered proteins. The involvement of intrinsically disordered domains (IDDs) in protein targeting and biogenesis processes in mitochondria is so far not known. Here, we have characterized the structural/dynamic and functional properties of an IDD of the sulfhydryl oxidase ALR (augmenter of liver regeneration) located in the intermembrane space of mitochondria. At variance to the unfolded-to-folded structural transition of several intrinsically disordered proteins, neither substrate recognition events nor redox switch of its shuttle cysteine pair is linked to any such structural change. However, this unstructured domain performs a dual function in two cellular compartments: it acts (i) as a mitochondrial targeting signal in the cytosol and (ii) as a crucial recognition site in the disulfide relay system of intermembrane space. This domain provides an exciting new paradigm for IDDs ensuring two distinct functions that are linked to intracellular organelle targeting. CI - Copyright (c) 2012 Elsevier Ltd. All rights reserved. FAU - Banci, Lucia AU - Banci L AD - Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy. banci@cerm.unifi.it FAU - Bertini, Ivano AU - Bertini I FAU - Cefaro, Chiara AU - Cefaro C FAU - Ciofi-Baffoni, Simone AU - Ciofi-Baffoni S FAU - Gajda, Karolina AU - Gajda K FAU - Felli, Isabella C AU - Felli IC FAU - Gallo, Angelo AU - Gallo A FAU - Pavelkova, Anna AU - Pavelkova A FAU - Kallergi, Emmanouela AU - Kallergi E FAU - Andreadaki, Maria AU - Andreadaki M FAU - Katrakili, Nitsa AU - Katrakili N FAU - Pozidis, Charalambos AU - Pozidis C FAU - Tokatlidis, Kostas AU - Tokatlidis K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121201 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Mitochondrial Proteins) RN - 0 (Proteins) RN - 0 (augmenter of liver regeneration factor) SB - IM MH - Humans MH - Magnetic Resonance Spectroscopy MH - Mitochondrial Proteins/chemistry/metabolism MH - Oxidation-Reduction MH - Protein Conformation MH - Proteins/*chemistry/*metabolism MH - Saccharomyces cerevisiae/enzymology EDAT- 2012/12/05 06:00 MHDA- 2013/03/23 06:00 CRDT- 2012/12/05 06:00 PHST- 2012/09/02 [received] PHST- 2012/11/03 [revised] PHST- 2012/11/25 [accepted] PHST- 2012/12/01 [aheadofprint] AID - S0022-2836(12)00904-7 [pii] AID - 10.1016/j.jmb.2012.11.032 [doi] PST - ppublish SO - J Mol Biol. 2013 Feb 8;425(3):594-608. doi: 10.1016/j.jmb.2012.11.032. Epub 2012 Dec 1. PMID- 21354340 OWN - NLM STAT- MEDLINE DA - 20110503 DCOM- 20110719 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1814 IP - 5 DP - 2011 May TI - Binding studies of truncated variants of the Abeta peptide to the V-domain of the RAGE receptor reveal Abeta residues responsible for binding. PG - 592-609 LID - 10.1016/j.bbapap.2011.02.011 [doi] AB - Alzheimer's disease (AD) symptoms correlate with the concentration of soluble, although not necessarily monomeric forms of Abeta peptide in the brain parenchyma. The RAGE receptor has been implicated as the protein responsible for active transport of Abeta from blood circulation to the brain. In murine models of AD, inhibition of the Abeta:RAGE interaction decreases the levels of Abeta in the brain. Inhibition of the Abeta:RAGE interaction would be a promising alternative for the therapy of AD. Rational design of an Abeta:RAGE interaction blocker requires detailed knowledge of the structure of the complex. However, the binding domain of RAGE is natively unfolded in physiological conditions, which severely hampers the application of classic methods of protein structure analysis to the design of an antagonist. Here, alternative methods are used to characterize the structural properties of the RAGE-ligand binding domain and to monitor the binding of a series of truncated variants of Abeta. Using intrinsic RAGE tryptophan fluorescence and mass spectrometry of non-covalent protein-ligand complexes we have identified shorter versions of Abeta that bind to the RAGE V-domain. We have also shown in cell culture experiments that a selected shortened version of Abeta effectively inhibits full-length Abeta, RAGE-mediated, cell uptake. Thus, a truncated version of Abeta capable of blocking its receptor-mediated internalization was established, revealing the binding code and providing the lead compound in the process of drug design. CI - Copyright (c) 2011 Elsevier B.V. All rights reserved. FAU - Gospodarska, Emilia AU - Gospodarska E AD - Institute of Biochemistry and Biophysics, Pol. Acad. Sci., ul. Pawinskiego 5A, 02-106 Warszawa, Poland. FAU - Kupniewska-Kozak, Anna AU - Kupniewska-Kozak A FAU - Goch, Grazyna AU - Goch G FAU - Dadlez, Michal AU - Dadlez M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110224 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Amyloid beta-Peptides) RN - 0 (Receptors, Immunologic) RN - 0 (advanced glycosylation end-product receptor) SB - IM MH - Amyloid beta-Peptides/chemistry/*metabolism MH - Animals MH - Binding Sites MH - Cell Line MH - Circular Dichroism MH - Mass Spectrometry MH - Mice MH - Protein Binding MH - Protein Structure, Tertiary MH - Receptors, Immunologic/chemistry/*metabolism EDAT- 2011/03/01 06:00 MHDA- 2011/07/20 06:00 CRDT- 2011/03/01 06:00 PHST- 2010/08/17 [received] PHST- 2011/02/15 [revised] PHST- 2011/02/18 [accepted] PHST- 2011/02/24 [aheadofprint] AID - S1570-9639(11)00036-7 [pii] AID - 10.1016/j.bbapap.2011.02.011 [doi] PST - ppublish SO - Biochim Biophys Acta. 2011 May;1814(5):592-609. doi: 10.1016/j.bbapap.2011.02.011. Epub 2011 Feb 24. PMID- 15247283 OWN - NLM STAT- MEDLINE DA - 20040920 DCOM- 20041026 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 39 DP - 2004 Sep 24 TI - Structure and function of the membrane anchor domain of hepatitis C virus nonstructural protein 5A. PG - 40835-43 AB - Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a membrane-associated, essential component of the viral replication complex. Here, we report the three-dimensional structure of the membrane anchor domain of NS5A as determined by NMR spectroscopy. An alpha-helix extending from amino acid residue 5 to 25 was observed in the presence of different membrane mimetic media. This helix exhibited a hydrophobic, Trprich side embedded in detergent micelles, while the polar, charged side was exposed to the solvent. Thus, the NS5A membrane anchor domain forms an in-plane amphipathic alpha-helix embedded in the cytosolic leaflet of the membrane bilayer. Interestingly, mutations affecting the positioning of fully conserved residues located at the cytosolic surface of the helix impaired HCV RNA replication without interfering with the membrane association of NS5A. In conclusion, the NS5A membrane anchor domain constitutes a unique platform that is likely involved in specific interactions essential for the assembly of the HCV replication complex and that may represent a novel target for antiviral intervention. CI - Copyright 2004 American Society for Biochemistry and Molecular Biology, Inc. FAU - Penin, Francois AU - Penin F AD - Institut de Biologie et Chimie des Proteines, CNRS-UMR 5086, IFR128 BioSciences, Lyon-Gerland, Lyon F-69367, Cedex 07, France. FAU - Brass, Volker AU - Brass V FAU - Appel, Nicole AU - Appel N FAU - Ramboarina, Stephanie AU - Ramboarina S FAU - Montserret, Roland AU - Montserret R FAU - Ficheux, Damien AU - Ficheux D FAU - Blum, Hubert E AU - Blum HE FAU - Bartenschlager, Ralf AU - Bartenschlager R FAU - Moradpour, Darius AU - Moradpour D LA - eng SI - PDB/1R7C SI - PDB/1R7D SI - PDB/1R7E SI - PDB/1R7F SI - PDB/1R7G PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040707 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Antibodies, Monoclonal) RN - 0 (Lipid Bilayers) RN - 0 (Micelles) RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Peptides) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Amino Acid Sequence MH - Antibodies, Monoclonal/chemistry MH - Cell Line, Tumor MH - Cell Membrane/*metabolism MH - Cytosol/metabolism MH - Humans MH - Lipid Bilayers/chemistry MH - Magnetic Resonance Spectroscopy MH - Micelles MH - Microscopy, Confocal MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Peptides/chemistry MH - Plasmids/metabolism MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Transcription, Genetic MH - Transfection MH - Viral Nonstructural Proteins/*chemistry/metabolism EDAT- 2004/07/13 05:00 MHDA- 2004/10/27 09:00 CRDT- 2004/07/13 05:00 PHST- 2004/07/07 [aheadofprint] AID - 10.1074/jbc.M404761200 [doi] AID - M404761200 [pii] PST - ppublish SO - J Biol Chem. 2004 Sep 24;279(39):40835-43. Epub 2004 Jul 7. PMID- 20923645 OWN - NLM STAT- MEDLINE DA - 20101006 DCOM- 20110120 LR - 20140821 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 7 DP - 2010 Oct 6 TI - The N-terminus of the intrinsically disordered protein alpha-synuclein triggers membrane binding and helix folding. PG - 2116-24 LID - 10.1016/j.bpj.2010.06.035 [doi] AB - Alpha-synuclein (alphaS) is a 140-amino-acid protein that is involved in a number of neurodegenerative diseases. In Parkinson's disease, the protein is typically encountered in intracellular, high-molecular-weight aggregates. Although alphaS is abundant in the presynaptic terminals of the central nervous system, its physiological function is still unknown. There is strong evidence for the membrane affinity of the protein. One hypothesis is that lipid-induced binding and helix folding may modulate the fusion of synaptic vesicles with the presynaptic membrane and the ensuing transmitter release. Here we show that membrane recognition of the N-terminus is essential for the cooperative formation of helical domains in the protein. We used circular dichroism spectroscopy and isothermal titration calorimetry to investigate synthetic peptide fragments from different domains of the full-length alphaS protein. Site-specific truncation and partial cleavage of the full-length protein were employed to further characterize the structural motifs responsible for helix formation and lipid-protein interaction. Unilamellar vesicles of varying net charge and lipid compositions undergoing lateral phase separation or chain melting phase transitions in the vicinity of physiological temperatures served as model membranes. The results suggest that the membrane-induced helical folding of the first 25 residues may be driven simultaneously by electrostatic attraction and by a change in lipid ordering. Our findings highlight the significance of the alphaS N-terminus for folding nucleation, and provide a framework for elucidating the role of lipid-induced conformational transitions of the protein within its intracellular milieu. CI - Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Bartels, Tim AU - Bartels T AD - Department of Chemistry, University of Arizona, Tucson, AZ, USA. FAU - Ahlstrom, Logan S AU - Ahlstrom LS FAU - Leftin, Avigdor AU - Leftin A FAU - Kamp, Frits AU - Kamp F FAU - Haass, Christian AU - Haass C FAU - Brown, Michael F AU - Brown MF FAU - Beyer, Klaus AU - Beyer K LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Peptide Fragments) RN - 0 (Unilamellar Liposomes) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Calorimetry MH - Cell Membrane/*metabolism MH - Circular Dichroism MH - Humans MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/metabolism MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Secondary MH - Structure-Activity Relationship MH - Temperature MH - Unilamellar Liposomes/metabolism MH - alpha-Synuclein/*chemistry/*metabolism PMC - PMC3042581 OID - NLM: PMC3042581 EDAT- 2010/10/07 06:00 MHDA- 2011/01/21 06:00 CRDT- 2010/10/07 06:00 PHST- 2010/05/07 [received] PHST- 2010/06/15 [revised] PHST- 2010/06/16 [accepted] AID - S0006-3495(10)00778-2 [pii] AID - 10.1016/j.bpj.2010.06.035 [doi] PST - ppublish SO - Biophys J. 2010 Oct 6;99(7):2116-24. doi: 10.1016/j.bpj.2010.06.035. PMID- 25185827 OWN - NLM STAT- MEDLINE DA - 20140904 DCOM- 20150521 LR - 20150203 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 22 IP - 9 DP - 2014 Sep 2 TI - Tracing the evolution of the p53 tetramerization domain. PG - 1301-10 LID - 10.1016/j.str.2014.07.010 [doi] LID - S0969-2126(14)00240-8 [pii] AB - The tetrameric transcription factors p53, p63, and p73 evolved from a common ancestor and play key roles in tumor suppression and development. Surprisingly, p63 and p73 require a second helix in their tetramerization domain for the formation of stable tetramers that is absent in human p53, raising questions about the evolutionary processes leading to diversification. Here we determined the crystal structure of the zebrafish p53 tetramerization domain, which contains a second helix, reminiscent of p63 and p73, combined with p53-like features. Through comprehensive phylogenetic analyses, we systematically traced the evolution of vertebrate p53 family oligomerization domains back to the beginning of multicellular life. We provide evidence that their last common ancestor also had an extended p63/p73-like domain and pinpoint evolutionary events that shaped this domain during vertebrate radiation. Domain compaction and transformation of a structured into a flexible, intrinsically disordered region may have contributed to the expansion of the human p53 interactome. CI - Copyright (c) 2014 The Authors. Published by Elsevier Inc. All rights reserved. FAU - Joerger, Andreas C AU - Joerger AC AD - MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. Electronic address: acj2@mrc-lmb.cam.ac.uk. FAU - Wilcken, Rainer AU - Wilcken R AD - MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. FAU - Andreeva, Antonina AU - Andreeva A AD - MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK. LA - eng SI - PDB/4CZ5 SI - PDB/4CZ6 SI - PDB/4CZ7 SI - PDB/4D1L SI - PDB/4D1M GR - G0901534/Medical Research Council/United Kingdom GR - MC_EX_G0901534/Medical Research Council/United Kingdom GR - MC_U105192716/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Tumor Suppressor Protein p53) RN - 0 (Zebrafish Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Conserved Sequence MH - Crystallography, X-Ray MH - Evolution, Molecular MH - Humans MH - Molecular Sequence Data MH - Phylogeny MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Sequence Analysis, Protein MH - Tumor Suppressor Protein p53/*chemistry/genetics MH - Zebrafish MH - Zebrafish Proteins/*chemistry/genetics PMC - PMC4155161 OID - NLM: PMC4155161 EDAT- 2014/09/05 06:00 MHDA- 2015/05/23 06:00 CRDT- 2014/09/05 06:00 PHST- 2014/05/09 [received] PHST- 2014/07/24 [revised] PHST- 2014/07/25 [accepted] AID - S0969-2126(14)00240-8 [pii] AID - 10.1016/j.str.2014.07.010 [doi] PST - ppublish SO - Structure. 2014 Sep 2;22(9):1301-10. doi: 10.1016/j.str.2014.07.010. PMID- 21686180 OWN - NLM STAT- MEDLINE DA - 20110620 DCOM- 20150129 IS - 1422-0067 (Electronic) IS - 1422-0067 (Linking) VI - 12 IP - 5 DP - 2011 TI - Novel strategies for drug discovery based on Intrinsically Disordered Proteins (IDPs). PG - 3205-19 LID - 10.3390/ijms12053205 [doi] AB - Intrinsically disordered proteins (IDPs) are proteins that usually do not adopt well-defined native structures when isolated in solution under physiological conditions. Numerous IDPs have close relationships with human diseases such as tumor, Parkinson disease, Alzheimer disease, diabetes, and so on. These disease-associated IDPs commonly play principal roles in the disease-associated protein-protein interaction networks. Most of them in the disease datasets have more interactants and hence the size of the disease-associated IDPs interaction network is simultaneously increased. For example, the tumor suppressor protein p53 is an intrinsically disordered protein and also a hub protein in the p53 interaction network; alpha-synuclein, an intrinsically disordered protein involved in Parkinson diseases, is also a hub of the protein network. The disease-associated IDPs may provide potential targets for drugs modulating protein-protein interaction networks. Therefore, novel strategies for drug discovery based on IDPs are in the ascendant. It is dependent on the features of IDPs to develop the novel strategies. It is found out that IDPs have unique structural features such as high flexibility and random coil-like conformations which enable them to participate in both the "one to many" and "many to one" interaction. Accordingly, in order to promote novel strategies for drug discovery, it is essential that more and more features of IDPs are revealed by experimental and computing methods. FAU - Wang, Jihua AU - Wang J AD - Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou 253023, China; E-Mails: qiayilai@mail.ustc.edu.cn (Z.C.); zll2008@mail.ustc.edu.cn (L.Z.). FAU - Cao, Zanxia AU - Cao Z FAU - Zhao, Liling AU - Zhao L FAU - Li, Shuqiang AU - Li S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20110517 PL - Switzerland TA - Int J Mol Sci JT - International journal of molecular sciences JID - 101092791 RN - 0 (Intrinsically Disordered Proteins) SB - IM MH - Amino Acid Sequence MH - Drug Discovery/*methods MH - Intrinsically Disordered Proteins/*chemistry MH - Protein Interaction Maps MH - Protein Structure, Tertiary MH - Sequence Analysis, Protein PMC - PMC3116186 OID - NLM: PMC3116186 OTO - NOTNLM OT - drug-discovery OT - interaction networks OT - intrinsically disordered proteins OT - sequence characterizations OT - structural characterizations GN - NLM: Original DateCompleted: 20130704 EDAT- 2011/06/21 06:00 MHDA- 2011/06/21 06:01 CRDT- 2011/06/21 06:00 PHST- 2011/04/01 [received] PHST- 2011/04/28 [revised] PHST- 2011/05/09 [accepted] PHST- 2011/05/17 [epublish] AID - 10.3390/ijms12053205 [doi] AID - ijms-12-03205 [pii] PST - ppublish SO - Int J Mol Sci. 2011;12(5):3205-19. doi: 10.3390/ijms12053205. Epub 2011 May 17. PMID- 25096979 OWN - NLM STAT- In-Process DA - 20140901 IS - 1532-2548 (Electronic) IS - 0032-0889 (Linking) VI - 166 IP - 1 DP - 2014 Sep TI - Disordered cold regulated15 proteins protect chloroplast membranes during freezing through binding and folding, but do not stabilize chloroplast enzymes in vivo. PG - 190-201 LID - 10.1104/pp.114.245399 [doi] AB - Freezing can severely damage plants, limiting geographical distribution of natural populations and leading to major agronomical losses. Plants native to cold climates acquire increased freezing tolerance during exposure to low nonfreezing temperatures in a process termed cold acclimation. This involves many adaptative responses, including global changes in metabolite content and gene expression, and the accumulation of cold-regulated (COR) proteins, whose functions are largely unknown. Here we report that the chloroplast proteins COR15A and COR15B are necessary for full cold acclimation in Arabidopsis (Arabidopsis thaliana). They protect cell membranes, as indicated by electrolyte leakage and chlorophyll fluorescence measurements. Recombinant COR15 proteins stabilize lactate dehydrogenase during freezing in vitro. However, a transgenic approach shows that they have no influence on the stability of selected plastidic enzymes in vivo, although cold acclimation results in increased enzyme stability. This indicates that enzymes are stabilized by other mechanisms. Recombinant COR15 proteins are disordered in water, but fold into amphipathic alpha-helices at high osmolyte concentrations in the presence of membranes, a condition mimicking molecular crowding induced by dehydration during freezing. X-ray scattering experiments indicate protein-membrane interactions specifically under such crowding conditions. The COR15-membrane interactions lead to liposome stabilization during freezing. Collectively, our data demonstrate the requirement for COR15 accumulation for full cold acclimation of Arabidopsis. The function of these intrinsically disordered proteins is the stabilization of chloroplast membranes during freezing through a folding and binding mechanism, but not the stabilization of chloroplastic enzymes. This indicates a high functional specificity of these disordered plant proteins. CI - (c) 2014 American Society of Plant Biologists. All Rights Reserved. FAU - Thalhammer, Anja AU - Thalhammer A AD - Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam, Germany (A.T., R.S., D.K.H.); andCentre for Molecular and Nanoscale Physics, School of Applied Sciences, RMIT University, Melbourne 3001, Australia (G.B.). FAU - Bryant, Gary AU - Bryant G AD - Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam, Germany (A.T., R.S., D.K.H.); andCentre for Molecular and Nanoscale Physics, School of Applied Sciences, RMIT University, Melbourne 3001, Australia (G.B.). FAU - Sulpice, Ronan AU - Sulpice R AD - Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam, Germany (A.T., R.S., D.K.H.); andCentre for Molecular and Nanoscale Physics, School of Applied Sciences, RMIT University, Melbourne 3001, Australia (G.B.). FAU - Hincha, Dirk K AU - Hincha DK AD - Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam, Germany (A.T., R.S., D.K.H.); andCentre for Molecular and Nanoscale Physics, School of Applied Sciences, RMIT University, Melbourne 3001, Australia (G.B.) hincha@mpimp-golm.mpg.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140805 PL - United States TA - Plant Physiol JT - Plant physiology JID - 0401224 SB - IM PMC - PMC4149706 OID - NLM: PMC4149706 EDAT- 2014/08/07 06:00 MHDA- 2014/08/07 06:00 CRDT- 2014/08/07 06:00 PHST- 2014/08/05 [aheadofprint] AID - pp.114.245399 [pii] AID - 10.1104/pp.114.245399 [doi] PST - ppublish SO - Plant Physiol. 2014 Sep;166(1):190-201. doi: 10.1104/pp.114.245399. Epub 2014 Aug 5. PMID- 24837160 OWN - NLM STAT- MEDLINE DA - 20140618 DCOM- 20150127 IS - 1096-0279 (Electronic) IS - 1046-5928 (Linking) VI - 100 DP - 2014 Aug TI - Purification of recombinant nacre-associated mineralization protein AP7 fused with maltose-binding protein. PG - 26-32 LID - 10.1016/j.pep.2014.05.002 [doi] LID - S1046-5928(14)00095-3 [pii] AB - Formation of biominerals often involves specific proteins that modulate the process of matrix assembly, nucleation, and crystal growth. AP7 is an aragonite-associated protein of 7 kDa and is intrinsically disordered. The structural disorder of AP7 makes it very difficult to express in Escherchiacoli. In this work, we report the first successful expression and purification of recombinant AP7 using the maltose-binding protein (MBP) fusion approach. We obtain a high-yield production of recombinant MBP-AP7 protein inE. coli ( approximately 60 mg/L). We also establish an efficient protocol to remove the MBP fusion protein by Factor Xa, followed by purification using size-exclusion chromatography. Characterization of the recombinant AP7 protein has been carried out using MALDI-TOF, peptide mass fingerprinting, and circular dichroism (CD). The mass data confirm that the purified recombinant protein is AP7. The CD data suggest that the recombinant AP7 protein exists as partially disordered structure at neutral pH. The calcium carbonate precipitation assay shows that both MBP-AP7 and AP7 exhibit morphological modification on calcite crystallites. The co-precipitation of MBP-tagged AP7 derivatives and calcium carbonate generate different types of AP7 composite calcite and vaterite crystals. This system should be helpful to establish a model for understanding the structure/function relationship between the protein and inorganic mineral interaction. CI - Copyright (c) 2014 Elsevier Inc. All rights reserved. FAU - Huang, Yu-Chieh AU - Huang YC AD - Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan. FAU - Chang, Hsun-Hui AU - Chang HH AD - Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan. FAU - Mou, Yun AU - Mou Y AD - Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan. FAU - Chi, Peter AU - Chi P AD - Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan; Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan. FAU - Chan, Jerry Chun Chung AU - Chan JC AD - Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan. FAU - Luo, Shih-Chi AU - Luo SC AD - Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan. Electronic address: scluo@ntu.edu.tw. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140515 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (Maltose-Binding Proteins) RN - 0 (Nacre) RN - 0 (Recombinant Fusion Proteins) RN - H0G9379FGK (Calcium Carbonate) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Calcium Carbonate/metabolism MH - Chromatography, Affinity MH - Chromatography, Gel MH - Cloning, Molecular MH - Crystallization MH - Gastropoda/chemistry/*genetics/*metabolism MH - Genetic Vectors/genetics MH - Maltose-Binding Proteins/chemistry/*genetics/*isolation & purification/metabolism MH - Molecular Sequence Data MH - Nacre/*metabolism MH - Recombinant Fusion Proteins/chemistry/genetics/isolation & purification/metabolism OTO - NOTNLM OT - Aragonite-associated protein OT - Biomineralization OT - Calcite OT - Protein expression OT - Vaterite EDAT- 2014/05/20 06:00 MHDA- 2015/01/28 06:00 CRDT- 2014/05/20 06:00 PHST- 2014/02/23 [received] PHST- 2014/05/04 [revised] PHST- 2014/05/06 [accepted] PHST- 2014/05/15 [aheadofprint] AID - S1046-5928(14)00095-3 [pii] AID - 10.1016/j.pep.2014.05.002 [doi] PST - ppublish SO - Protein Expr Purif. 2014 Aug;100:26-32. doi: 10.1016/j.pep.2014.05.002. Epub 2014 May 15. PMID- 22987112 OWN - NLM STAT- MEDLINE DA - 20121121 DCOM- 20130830 LR - 20141105 IS - 1933-690X (Electronic) IS - 1933-6896 (Linking) VI - 6 IP - 5 DP - 2012 Nov-Dec TI - Slow spontaneous alpha-to-beta structural conversion in a non-denaturing neutral condition reveals the intrinsically disordered property of the disulfide-reduced recombinant mouse prion protein. PG - 489-97 LID - 10.4161/pri.22217 [doi] AB - In prion diseases, the normal prion protein is transformed by an unknown mechanism from a mainly alpha-helical structure to a beta-sheet-rich, disease-related isomer. In this study, we surprisingly found that a slow, spontaneous alpha-to-coil-to-beta transition could be monitored by circular dichroism spectroscopy in one full-length mouse recombinant prion mutant protein, denoted S132C/N181C, in which the endogenous cysteines C179 and C214 were replaced by Ala and S132 and N181 were replaced by Cys, during incubation in a non-denaturing neutral buffer. No denaturant was required to destabilize the native state for the conversion. The product after this structural conversion is toxic beta-oligomers with high fluorescence intensity when binding with thioflavin T. Site-directed spin-labeling ESR data suggested that the structural conversion involves the unfolding of helix 2. After examining more protein mutants, it was found that the spontaneous structural conversion is due to the disulfide-deletion (C to A mutations). The recombinant wild-type mouse prion protein could also be transformed into beta-oligomers and amyloid fibrils simply by dissolving and incubating the protein in 0.5 mM NaOAc (pH 7) and 1 mM DTT at 25 degrees C with no need of adding any denaturant to destabilize the prion protein. Our findings indicate the important role of disulfide bond reduction on the structural conversion of the recombinant prion protein, and highlight the special "intrinsically disordered" conformational character of the recombinant prion protein. FAU - Sang, Jason C AU - Sang JC AD - Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. FAU - Lee, Chung-Yu AU - Lee CY FAU - Luh, Frederick Y AU - Luh FY FAU - Huang, Ya-Wen AU - Huang YW FAU - Chiang, Yun-Wei AU - Chiang YW FAU - Chen, Rita P-Y AU - Chen RP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120917 PL - United States TA - Prion JT - Prion JID - 101472305 RN - 0 (Buffers) RN - 0 (Disulfides) RN - 0 (Peptide Fragments) RN - 0 (Prions) RN - 0 (Prnp protein, mouse) RN - 0 (Recombinant Proteins) SB - IM MH - Animals MH - Binding Sites MH - Buffers MH - Circular Dichroism MH - Disulfides/*chemistry MH - Mice MH - Peptide Fragments/chemistry MH - Prions/*chemistry/metabolism MH - Protein Conformation MH - Protein Denaturation MH - *Protein Folding MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry MH - Thermodynamics PMC - PMC3510854 OID - NLM: PMC3510854 EDAT- 2012/09/19 06:00 MHDA- 2013/08/31 06:00 CRDT- 2012/09/19 06:00 PHST- 2012/09/17 [aheadofprint] AID - 22217 [pii] AID - 10.4161/pri.22217 [doi] PST - ppublish SO - Prion. 2012 Nov-Dec;6(5):489-97. doi: 10.4161/pri.22217. Epub 2012 Sep 17. PMID- 21931162 OWN - NLM STAT- MEDLINE DA - 20111107 DCOM- 20111227 LR - 20141022 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 45 DP - 2011 Nov 11 TI - Understanding the kinetic roles of the inducer heparin and of rod-like protofibrils during amyloid fibril formation by Tau protein. PG - 38948-59 LID - 10.1074/jbc.M111.271874 [doi] AB - The aggregation of the natively disordered protein, Tau, to form lesions called neurofibrillary tangles is a characteristic feature of several neurodegenerative tauopathies. The polyanion, heparin, is commonly used as an inducer in studies of Tau aggregation in vitro, but there is surprisingly no comprehensive model describing, quantitatively, all aspects of the heparin-induced aggregation reaction. In this study, rate constants and extents of fibril formation by the four repeat domain of Tau (Tau4RD) have been reproducibly determined over a full range of heparin and protein concentrations. The kinetic role of heparin in the nucleation-dependent fibril formation reaction is shown to be limited to participation in the initial rate-limiting steps; a single heparin molecule binds two Tau4RD molecules, forming an aggregation-competent protein dimer, which then serves as a building block for further fibril growth. Importantly, the minimal kinetic model that is proposed can quantitatively account for the characteristic bell-shaped dependence of the aggregation kinetics on the stoichiometry of protein to heparin. Very importantly, this study also identifies for the first time short and thin, rod-like protofibrils that are populated transiently, early during the time course of fibril formation. The identification of these protofibrils as bona fide off-pathway species has implications for the development of therapies for tauopathies based on driving fibril formation as a means of protecting the cell from smaller, putatively toxic aggregates. FAU - Ramachandran, Gayathri AU - Ramachandran G AD - National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India. FAU - Udgaonkar, Jayant B AU - Udgaonkar JB LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110919 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Amyloid) RN - 0 (MAPT protein, human) RN - 0 (tau Proteins) RN - 9005-49-6 (Heparin) SB - IM MH - Amyloid/*chemistry/genetics/metabolism/ultrastructure MH - Heparin/*chemistry/metabolism MH - Humans MH - Kinetics MH - *Models, Chemical MH - *Protein Multimerization MH - Protein Structure, Tertiary MH - tau Proteins/*chemistry/genetics/metabolism PMC - PMC3234720 OID - NLM: PMC3234720 EDAT- 2011/09/21 06:00 MHDA- 2011/12/28 06:00 CRDT- 2011/09/21 06:00 PHST- 2011/09/19 [aheadofprint] AID - M111.271874 [pii] AID - 10.1074/jbc.M111.271874 [doi] PST - ppublish SO - J Biol Chem. 2011 Nov 11;286(45):38948-59. doi: 10.1074/jbc.M111.271874. Epub 2011 Sep 19. PMID- 15192079 OWN - NLM STAT- MEDLINE DA - 20040827 DCOM- 20050214 LR - 20111117 IS - 0888-8809 (Print) IS - 0888-8809 (Linking) VI - 18 IP - 9 DP - 2004 Sep TI - Plasticity of the ecdysone receptor DNA binding domain. PG - 2166-84 AB - Ecdysteroids coordinate molting and metamorphosis in insects via a heterodimer of two nuclear receptors, the ecdysone receptor (EcR) and the ultraspiracle (Usp) protein. Here we show how the DNA-recognition alpha-helix and the T box region of the EcR DNA-binding domain (EcRDBD) contribute to the specific interaction with the natural response element and to the stabilization of the EcRDBD molecule. The data indicate a remarkable mutational tolerance with respect to the DNA-binding function of the EcRDBD. This is particularly manifested in the heterocomplexes formed between the EcRDBD mutants and the wild-type Usp DNA-binding domain (UspDBD). Circular dichroism (CD) spectra and protein unfolding experiments indicate that, in contrast to the UspDBD, the EcRDBD is characterized by a lower alpha-helix content and a lower stability. As such, the EcRDBD appears to be an intrinsically unstructured protein-like molecule with a high degree of intramolecular plasticity. Because recently published crystal structures indicate that the ligand binding domain of the EcR is also characterized by the extreme adaptability, we suggest that plasticity of the EcR domains may be a key factor that allows a single EcR molecule to mediate diverse biological effects. FAU - Orlowski, Marek AU - Orlowski M AD - Institute of Organic Chemistry, Biochemistry and Biotechnology, Division of Biochemistry, Wroclaw University of Technology, 50-370 Wroclaw, Poland. FAU - Szyszka, Monika AU - Szyszka M FAU - Kowalska, Agnieszka AU - Kowalska A FAU - Grad, Iwona AU - Grad I FAU - Zoglowek, Anna AU - Zoglowek A FAU - Rymarczyk, Grzegorz AU - Rymarczyk G FAU - Dobryszycki, Piotr AU - Dobryszycki P FAU - Krowarsch, Daniel AU - Krowarsch D FAU - Rastinejad, Fraydoon AU - Rastinejad F FAU - Kochman, Marian AU - Kochman M FAU - Ozyhar, Andrzej AU - Ozyhar A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040610 PL - United States TA - Mol Endocrinol JT - Molecular endocrinology (Baltimore, Md.) JID - 8801431 RN - 0 (DNA-Binding Proteins) RN - 0 (Drosophila Proteins) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Receptors, Steroid) RN - 0 (Transcription Factors) RN - 0 (ecdysone receptor) RN - 0 (ultraspiracle protein, Drosophila) RN - EC 2.7.1.- (MAP-kinase-activated kinase 2) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Animals MH - DNA Mutational Analysis MH - DNA-Binding Proteins/chemistry/genetics/metabolism MH - Drosophila Proteins MH - Drosophila melanogaster/genetics/metabolism MH - Electrophoretic Mobility Shift Assay MH - Intracellular Signaling Peptides and Proteins MH - Molecular Sequence Data MH - Molting/genetics MH - Mutation/genetics MH - Promoter Regions, Genetic/genetics MH - Protein Structure, Secondary/genetics MH - Protein Structure, Tertiary/genetics MH - Protein-Serine-Threonine Kinases/genetics MH - Receptors, Steroid/*chemistry/genetics/*metabolism MH - Response Elements/*genetics MH - Transcription Factors/genetics/metabolism EDAT- 2004/06/12 05:00 MHDA- 2005/02/16 09:00 CRDT- 2004/06/12 05:00 PHST- 2004/06/10 [aheadofprint] AID - 10.1210/me.2004-0154 [doi] AID - me.2004-0154 [pii] PST - ppublish SO - Mol Endocrinol. 2004 Sep;18(9):2166-84. Epub 2004 Jun 10. PMID- 22737237 OWN - NLM STAT- MEDLINE DA - 20120627 DCOM- 20121214 LR - 20141016 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 6 DP - 2012 TI - Molecular phylogeny of OVOL genes illustrates a conserved C2H2 zinc finger domain coupled by hypervariable unstructured regions. PG - e39399 LID - 10.1371/journal.pone.0039399 [doi] AB - OVO-like proteins (OVOL) are members of the zinc finger protein family and serve as transcription factors to regulate gene expression in various differentiation processes. Recent studies have shown that OVOL genes are involved in epithelial development and differentiation in a wide variety of organisms; yet there is a lack of comprehensive studies that describe OVOL proteins from an evolutionary perspective. Using comparative genomic analysis, we traced three different OVOL genes (OVOL1-3) in vertebrates. One gene, OVOL3, was duplicated during a whole-genome-duplication event in fish, but only the copy (OVOL3b) was retained. From early-branching metazoa to humans, we found that a core domain, comprising a tetrad of C2H2 zinc fingers, is conserved. By domain comparison of the OVOL proteins, we found that they evolved in different metazoan lineages by attaching intrinsically-disordered (ID) segments of N/C-terminal extensions of 100 to 1000 amino acids to this conserved core. These ID regions originated independently across different animal lineages giving rise to different types of OVOL genes over the course of metazoan evolution. We illustrated the molecular evolution of metazoan OVOL genes over a period of 700 million years (MY). This study both extends our current understanding of the structure/function relationship of metazoan OVOL genes, and assembles a good platform for further characterization of OVOL genes from diverged organisms. FAU - Kumar, Abhishek AU - Kumar A AD - Department of Biology, University of Padua, Padova, Italy. abhishek.abhishekkumar@gmail.com FAU - Bhandari, Anita AU - Bhandari A FAU - Sinha, Rahul AU - Sinha R FAU - Sardar, Puspendu AU - Sardar P FAU - Sushma, Miss AU - Sushma M FAU - Goyal, Pankaj AU - Goyal P FAU - Goswami, Chandan AU - Goswami C FAU - Grapputo, Alessandro AU - Grapputo A LA - eng PT - Journal Article DEP - 20120621 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Carrier Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (OVOL1 protein, human) RN - 0 (Ovol2 protein, human) RN - 0 (Transcription Factors) SB - IM MH - Animals MH - Carrier Proteins/*chemistry/genetics MH - Cell Lineage MH - Conserved Sequence MH - DNA-Binding Proteins/*chemistry/genetics MH - Drosophila MH - Evolution, Molecular MH - Fishes MH - Genome MH - Genomics MH - Humans MH - Lizards MH - Mice MH - Models, Molecular MH - Opossums MH - Phylogeny MH - Protein Structure, Tertiary MH - Rats MH - Sequence Analysis, DNA MH - Transcription Factors/*chemistry/genetics MH - Turkeys MH - Xenopus MH - Zebrafish MH - *Zinc Fingers PMC - PMC3380836 OID - NLM: PMC3380836 EDAT- 2012/06/28 06:00 MHDA- 2012/12/15 06:00 CRDT- 2012/06/28 06:00 PHST- 2011/02/05 [received] PHST- 2012/05/23 [accepted] PHST- 2012/06/21 [epublish] AID - 10.1371/journal.pone.0039399 [doi] AID - PONE-D-11-02680 [pii] PST - ppublish SO - PLoS One. 2012;7(6):e39399. doi: 10.1371/journal.pone.0039399. Epub 2012 Jun 21. PMID- 19549281 OWN - NLM STAT- MEDLINE DA - 20090811 DCOM- 20090921 LR - 20140908 IS - 1471-4159 (Electronic) IS - 0022-3042 (Linking) VI - 110 IP - 4 DP - 2009 Aug TI - Inhibition of tau fibrillization by oleocanthal via reaction with the amino groups of tau. PG - 1339-51 LID - 10.1111/j.1471-4159.2009.06224.x [doi] AB - Tau is a microtubule-associated protein that promotes microtubule assembly and stability. In Alzheimer's disease and related tauopathies, tau fibrillizes and aggregates into neurofibrillary tangles. Recently, oleocanthal isolated from extra virgin olive oil was found to display non-steroidal anti-inflammatory activity similar to ibuprofen. As our unpublished data indicates an inhibitory effect of oleocanthal on amyloid beta peptide fibrillization, we reasoned that it might inhibit tau fibrillization as well. Herein, we demonstrate that oleocanthal abrogates fibrillization of tau by locking tau into the naturally unfolded state. Using PHF6 consisting of the amino acid residues VQIVYK, a hexapeptide within the third repeat of tau that is essential for fibrillization, we show that oleocanthal forms an adduct with the lysine via initial Schiff base formation. Structure and function studies demonstrate that the two aldehyde groups of oleocanthal are required for the inhibitory activity. These two aldehyde groups show certain specificity when titrated with free lysine and oleocanthal does not significantly affect the normal function of tau. These findings provide a potential scheme for the development of novel therapies for neurodegenerative tauopathies. FAU - Li, Wenkai AU - Li W AD - Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 94305, USA. FAU - Sperry, Jeffrey B AU - Sperry JB FAU - Crowe, Alex AU - Crowe A FAU - Trojanowski, John Q AU - Trojanowski JQ FAU - Smith, Amos B 3rd AU - Smith AB 3rd FAU - Lee, Virginia M-Y AU - Lee VM LA - eng GR - AG17586/AG/NIA NIH HHS/United States GR - P01 AG017586/AG/NIA NIH HHS/United States GR - P01 AG017586-01/AG/NIA NIH HHS/United States GR - P01 AG017586-10/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090615 PL - England TA - J Neurochem JT - Journal of neurochemistry JID - 2985190R RN - 0 (Aldehydes) RN - 0 (Amino Acids) RN - 0 (Anti-Inflammatory Agents) RN - 0 (Neuroprotective Agents) RN - 0 (Peptides) RN - 0 (Phenols) RN - 0 (Schiff Bases) RN - 0 (oleocanthal) RN - 0 (tau Proteins) RN - K3Z4F929H6 (Lysine) SB - IM EIN - J Neurochem. 2009 Sep;110(6):1989 MH - Aldehydes/chemistry/metabolism/*pharmacology/therapeutic use MH - Amino Acid Sequence/drug effects/physiology MH - Amino Acids/drug effects/metabolism MH - Anti-Inflammatory Agents/pharmacology/therapeutic use MH - Brain/drug effects/metabolism/pathology MH - Encephalitis/drug therapy/metabolism/physiopathology MH - Humans MH - Lysine/metabolism MH - Molecular Structure MH - Neurofibrillary Tangles/*drug effects/metabolism/pathology MH - Neurofibrils/chemistry/drug effects/metabolism MH - Neuroprotective Agents/pharmacology/therapeutic use MH - Peptides/chemistry/metabolism MH - Phenols/chemistry/*pharmacology/therapeutic use MH - Protein Folding/drug effects MH - Schiff Bases/chemistry/metabolism MH - Tauopathies/*drug therapy/metabolism/physiopathology MH - tau Proteins/chemistry/*drug effects/metabolism PMC - PMC2758489 MID - NIHMS135555 OID - NLM: NIHMS135555 OID - NLM: PMC2758489 EDAT- 2009/06/25 09:00 MHDA- 2009/09/22 06:00 CRDT- 2009/06/25 09:00 PHST- 2009/06/15 [aheadofprint] AID - JNC6224 [pii] AID - 10.1111/j.1471-4159.2009.06224.x [doi] PST - ppublish SO - J Neurochem. 2009 Aug;110(4):1339-51. doi: 10.1111/j.1471-4159.2009.06224.x. Epub 2009 Jun 15. PMID- 23811471 OWN - NLM STAT- MEDLINE DA - 20130916 DCOM- 20131107 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1834 IP - 10 DP - 2013 Oct TI - The protein-protein interaction network of the human Sirtuin family. PG - 1998-2009 LID - 10.1016/j.bbapap.2013.06.012 [doi] LID - S1570-9639(13)00243-4 [pii] AB - Protein-protein interaction networks are useful for studying human diseases and to look for possible health care through a holistic approach. Networks are playing an increasing and important role in the understanding of physiological processes such as homeostasis, signaling, spatial and temporal organizations, and pathological conditions. In this article we show the complex system of interactions determined by human Sirtuins (Sirt) largely involved in many metabolic processes as well as in different diseases. The Sirtuin family consists of seven homologous Sirt-s having structurally similar cores but different terminal segments, being rather variable in length and/or intrinsically disordered. Many studies have determined their cellular location as well as biological functions although molecular mechanisms through which they act are actually little known therefore, the aim of this work was to define, explore and understand the Sirtuin-related human interactome. As a first step, we have integrated the experimentally determined protein-protein interactions of the Sirtuin-family as well as their first and second neighbors to a Sirtuin-related sub-interactome. Our data showed that the second-neighbor network of Sirtuins encompasses 25% of the entire human interactome, and exhibits a scale-free degree distribution and interconnectedness among top degree nodes. Moreover, the Sirtuin sub interactome showed a modular structure around the core comprising mixed functions. Finally, we extracted from the Sirtuin sub-interactome subnets related to cancer, aging and post-translational modifications for information on key nodes and topological space of the subnets in the Sirt family network. CI - (c) 2013. FAU - Sharma, Ankush AU - Sharma A AD - Biochemistry, Biophysics and General Pathology Department, Second University of Naples, Naples, Italy. FAU - Costantini, Susan AU - Costantini S FAU - Colonna, Giovanni AU - Colonna G LA - eng PT - Journal Article DEP - 20130628 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - EC 3.5.1.- (Sirtuins) SB - IM MH - Acetylation MH - Aging/genetics/*metabolism MH - *Computational Biology MH - Databases, Protein MH - Humans MH - Methylation MH - Neoplasms/genetics/*metabolism MH - Phosphorylation MH - Protein Interaction Mapping MH - *Protein Interaction Maps MH - *Protein Processing, Post-Translational MH - Sirtuins/genetics/*metabolism OTO - NOTNLM OT - Aging OT - Cancer OT - Interactome OT - Network OT - Sirtuins EDAT- 2013/07/03 06:00 MHDA- 2013/11/08 06:00 CRDT- 2013/07/02 06:00 PHST- 2013/04/20 [received] PHST- 2013/05/31 [revised] PHST- 2013/06/18 [accepted] PHST- 2013/06/28 [aheadofprint] AID - S1570-9639(13)00243-4 [pii] AID - 10.1016/j.bbapap.2013.06.012 [doi] PST - ppublish SO - Biochim Biophys Acta. 2013 Oct;1834(10):1998-2009. doi: 10.1016/j.bbapap.2013.06.012. Epub 2013 Jun 28. PMID- 24086265 OWN - NLM STAT- MEDLINE DA - 20131002 DCOM- 20140718 LR - 20141112 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 9 DP - 2013 TI - Conformational dissection of a viral intrinsically disordered domain involved in cellular transformation. PG - e72760 LID - 10.1371/journal.pone.0072760 [doi] AB - Intrinsic disorder is abundant in viral genomes and provides conformational plasticity to its protein products. In order to gain insight into its structure-function relationships, we carried out a comprehensive analysis of structural propensities within the intrinsically disordered N-terminal domain from the human papillomavirus type-16 E7 oncoprotein (E7N). Two E7N segments located within the conserved CR1 and CR2 regions present transient alpha-helix structure. The helix in the CR1 region spans residues L8 to L13 and overlaps with the E2F mimic linear motif. The second helix, located within the highly acidic CR2 region, presents a pH-dependent structural transition. At neutral pH the helix spans residues P17 to N29, which include the retinoblastoma tumor suppressor LxCxE binding motif (residues 21-29), while the acidic CKII-PEST region spanning residues E33 to I38 populates polyproline type II (PII) structure. At pH 5.0, the CR2 helix propagates up to residue I38 at the expense of loss of PII due to charge neutralization of acidic residues. Using truncated forms of HPV-16 E7, we confirmed that pH-induced changes in alpha-helix content are governed by the intrinsically disordered E7N domain. Interestingly, while at both pH the region encompassing the LxCxE motif adopts alpha-helical structure, the isolated 21-29 fragment including this stretch is unable to populate an alpha-helix even at high TFE concentrations. Thus, the E7N domain can populate dynamic but discrete structural ensembles by sampling alpha-helix-coil-PII-ss-sheet structures. This high plasticity may modulate the exposure of linear binding motifs responsible for its multi-target binding properties, leading to interference with key cell signaling pathways and eventually to cellular transformation by the virus. FAU - Noval, Maria G AU - Noval MG AD - Protein Structure-Function and Engineering Laboratory, Fundacion Instituto Leloir and IIBBA- CONICET, Buenos Aires, Argentina. FAU - Gallo, Mariana AU - Gallo M FAU - Perrone, Sebastian AU - Perrone S FAU - Salvay, Andres G AU - Salvay AG FAU - Chemes, Lucia B AU - Chemes LB FAU - de Prat-Gay, Gonzalo AU - de Prat-Gay G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130927 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Oncogene Proteins, Viral) SB - IM MH - Amino Acid Sequence MH - *Cell Transformation, Neoplastic MH - Circular Dichroism MH - Hydrogen-Ion Concentration MH - Intrinsically Disordered Proteins/*chemistry MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Oncogene Proteins, Viral/*chemistry MH - Papillomaviridae/*chemistry MH - Protein Conformation MH - Spectrophotometry, Ultraviolet PMC - PMC3785498 OID - NLM: PMC3785498 EDAT- 2013/10/03 06:00 MHDA- 2014/07/19 06:00 CRDT- 2013/10/03 06:00 PHST- 2013 [ecollection] PHST- 2013/04/22 [received] PHST- 2013/07/14 [accepted] PHST- 2013/09/27 [epublish] AID - 10.1371/journal.pone.0072760 [doi] AID - PONE-D-13-16287 [pii] PST - epublish SO - PLoS One. 2013 Sep 27;8(9):e72760. doi: 10.1371/journal.pone.0072760. eCollection 2013. PMID- 19149675 OWN - NLM STAT- MEDLINE DA - 20090119 DCOM- 20090305 IS - 0929-8665 (Print) IS - 0929-8665 (Linking) VI - 16 IP - 1 DP - 2009 TI - Structure solution of misfolded conformations adopted by intrinsically disordered Alzheimer's tau protein. PG - 61-4 AB - Until now it was impossible to obtain atomic structure of intrinsically disordered protein (IDP) tau and/or its assembly in Alzheimer's paired helical filaments as neither of them could have been prepared in the form amenable to X-ray or NMR techniques. Using IDP tau property to attain regular tertiary structure after binding events during self-assembly or when complexed with its target we propose monoclonal antibodies as surrogate tau protein binding partners to form complexes and crystals for structure solution by X-ray technique. FAU - Sevcik, Jozef AU - Sevcik J AD - Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia. FAU - Skrabana, Rostislav AU - Skrabana R FAU - Kontsekova, Eva AU - Kontsekova E FAU - Novak, Michal AU - Novak M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 RN - 0 (Antibodies, Monoclonal) RN - 0 (tau Proteins) SB - IM MH - Antibodies, Monoclonal MH - *Protein Conformation MH - Protein Folding MH - tau Proteins/*chemistry/immunology EDAT- 2009/01/20 09:00 MHDA- 2009/03/06 09:00 CRDT- 2009/01/20 09:00 PST - ppublish SO - Protein Pept Lett. 2009;16(1):61-4. PMID- 11687658 OWN - NLM STAT- MEDLINE DA - 20011107 DCOM- 20011207 LR - 20140613 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 98 IP - 23 DP - 2001 Nov 6 TI - The crystal structure of human protein farnesyltransferase reveals the basis for inhibition by CaaX tetrapeptides and their mimetics. PG - 12948-53 AB - Protein farnesyltransferase (FTase) catalyzes the attachment of a farnesyl lipid group to the cysteine residue located in the C-terminal tetrapeptide of many essential signal transduction proteins, including members of the Ras superfamily. Farnesylation is essential both for normal functioning of these proteins, and for the transforming activity of oncogenic mutants. Consequently FTase is an important target for anti-cancer therapeutics. Several FTase inhibitors are currently undergoing clinical trials for cancer treatment. Here, we present the crystal structure of human FTase, as well as ternary complexes with the TKCVFM hexapeptide substrate, CVFM non-substrate tetrapeptide, and L-739,750 peptidomimetic with either farnesyl diphosphate (FPP), or a nonreactive analogue. These structures reveal the structural mechanism of FTase inhibition. Some CaaX tetrapeptide inhibitors are not farnesylated, and are more effective inhibitors than farnesylated CaaX tetrapeptides. CVFM and L-739,750 are not farnesylated, because these inhibitors bind in a conformation that is distinct from the TKCVFM hexapeptide substrate. This non-substrate binding mode is stabilized by an ion pair between the peptide N terminus and the alpha-phosphate of the FPP substrate. Conformational mapping calculations reveal the basis for the sequence specificity in the third position of the CaaX motif that determines whether a tetrapeptide is a substrate or non-substrate. The presence of beta-branched amino acids in this position prevents formation of the non-substrate conformation; all other aliphatic amino acids in this position are predicted to form the non-substrate conformation, provided their N terminus is available to bind to the FPP alpha-phosphate. These results may facilitate further development of FTase inhibitors. FAU - Long, S B AU - Long SB AD - Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA. FAU - Hancock, P J AU - Hancock PJ FAU - Kral, A M AU - Kral AM FAU - Hellinga, H W AU - Hellinga HW FAU - Beese, L S AU - Beese LS LA - eng SI - PDB/1JCQ SI - PDB/1JCR SI - PDB/1JCS GR - GM52382/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20011030 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Enzyme Inhibitors) RN - 0 (L 739750) RN - 0 (Oligopeptides) RN - 0 (Recombinant Proteins) RN - EC 2.5.- (Alkyl and Aryl Transferases) RN - EC 2.5.1.- (p21(ras) farnesyl-protein transferase) SB - IM MH - Alkyl and Aryl Transferases/antagonists & inhibitors/*chemistry MH - Amino Acid Sequence MH - Crystallography, X-Ray MH - Enzyme Inhibitors/pharmacology MH - Humans MH - Models, Molecular MH - *Molecular Mimicry MH - Oligopeptides/chemistry/*pharmacology MH - Protein Conformation MH - Recombinant Proteins/antagonists & inhibitors/chemistry PMC - PMC60805 OID - NLM: PMC60805 EDAT- 2001/11/01 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/11/01 10:00 PHST- 2001/10/30 [aheadofprint] AID - 10.1073/pnas.241407898 [doi] AID - 241407898 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2001 Nov 6;98(23):12948-53. Epub 2001 Oct 30. PMID- 9046590 OWN - NLM STAT- MEDLINE DA - 19970403 DCOM- 19970403 LR - 20130918 IS - 0032-0889 (Print) IS - 0032-0889 (Linking) VI - 113 IP - 2 DP - 1997 Feb TI - Purification, characterization, and structural analysis of a plant low-temperature-induced protein. PG - 367-76 AB - We have purified to near homogeneity a recombinant form of the protein BN28 (rBN28), expressed in response to low temperature in Brassica napus plants, and we have determined its solution structure. Antibodies raised against rBN28 were used to characterize the recombinant and native proteins. Similar to many other low-temperature-induced proteins, BN28 is extremely hydrophilic, such that it remains soluble following boiling. Immunoblot analysis of subcellular fractions indicated that BN28 was not strongly associated with cellular membranes and was localized exclusively within the soluble fraction of the cell. Contrary to predicted secondary structure that suggested significant helical content, circular dichroism analysis revealed that rBN28 existed in aqueous solution largely as a random coil. However, the helical propensity of the protein could be demonstrated in the presence of trifluoroethanol. Nuclear magnetic resonance analysis further showed that rBN28 was in fact completely unstructured (100% coil) in aqueous solution. Although it had earlier been speculated that BN28-like proteins from Arabidopsis thaliana might possess antifreeze protein activity (S. Kurkela and M. Franck [1990] Plant Mol Biol 15: 137-144), no such activity could be detected in ice recrystallization assays with rBN28. FAU - Boothe, J G AU - Boothe JG AD - Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, Canada. FAU - Sonnichsen, F D AU - Sonnichsen FD FAU - de Beus, M D AU - de Beus MD FAU - Johnson-Flanagan, A M AU - Johnson-Flanagan AM LA - eng SI - PIR/S34660 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Plant Physiol JT - Plant physiology JID - 0401224 RN - 0 (BN28 protein, Brassica napus) RN - 0 (Heat-Shock Proteins) RN - 0 (Ice) RN - 0 (Plant Proteins) RN - 0 (Recombinant Proteins) SB - IM MH - Amino Acid Sequence MH - Brassica/*chemistry/genetics MH - Circular Dichroism MH - Cloning, Molecular MH - *Cold Temperature MH - Gene Expression MH - Heat-Shock Proteins/*chemistry/genetics/immunology MH - Ice MH - Immunoblotting MH - Magnetic Resonance Spectroscopy MH - Mass Spectrometry MH - Molecular Sequence Data MH - *Plant Proteins MH - Protein Conformation MH - Recombinant Proteins/chemistry MH - Sequence Analysis, DNA MH - Sequence Homology, Amino Acid MH - Subcellular Fractions/chemistry PMC - PMC158150 OID - NLM: PMC158150 EDAT- 1997/02/01 MHDA- 1997/02/01 00:01 CRDT- 1997/02/01 00:00 AID - 113/2/367 [pii] PST - ppublish SO - Plant Physiol. 1997 Feb;113(2):367-76. PMID- 10467140 OWN - NLM STAT- MEDLINE DA - 19991014 DCOM- 19991014 LR - 20131121 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 7 IP - 8 DP - 1999 Aug 15 TI - A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase. PG - 997-1008 AB - BACKGROUND: Diol dehydratase is an enzyme that catalyzes the adenosylcobalamin (coenzyme B12) dependent conversion of 1,2-diols to the corresponding aldehydes. The reaction initiated by homolytic cleavage of the cobalt-carbon bond of the coenzyme proceeds by a radical mechanism. The enzyme is an alpha2beta2gamma2 heterooligomer and has an absolute requirement for a potassium ion for catalytic activity. The crystal structure analysis of a diol dehydratase-cyanocobalamin complex was carried out in order to help understand the mechanism of action of this enzyme. RESULTS: The three-dimensional structure of diol dehydratase in complex with cyanocobalamin was determined at 2.2 A resolution. The enzyme exists as a dimer of heterotrimers (alphabetagamma)2. The cobalamin molecule is bound between the alpha and beta subunits in the 'base-on' mode, that is, 5,6-dimethylbenzimidazole of the nucleotide moiety coordinates to the cobalt atom in the lower axial position. The alpha subunit includes a (beta/alpha)8 barrel. The substrate, 1,2-propanediol, and an essential potassium ion are deeply buried inside the barrel. The two hydroxyl groups of the substrate coordinate directly to the potassium ion. CONCLUSIONS: This is the first crystallographic indication of the 'base-on' mode of cobalamin binding. An unusually long cobalt-base bond seems to favor homolytic cleavage of the cobalt-carbon bond and therefore to favor radical enzyme catalysis. Reactive radical intermediates can be protected from side reactions by spatial isolation inside the barrel. On the basis of unique direct interactions between the potassium ion and the two hydroxyl groups of the substrate, direct participation of a potassium ion in enzyme catalysis is strongly suggested. FAU - Shibata, N AU - Shibata N AD - Department of Life Science, Himeji Institute of Technology, Hyogo, Japan. FAU - Masuda, J AU - Masuda J FAU - Tobimatsu, T AU - Tobimatsu T FAU - Toraya, T AU - Toraya T FAU - Suto, K AU - Suto K FAU - Morimoto, Y AU - Morimoto Y FAU - Yasuoka, N AU - Yasuoka N LA - eng SI - PDB/1DIO SI - PDB/1DIOS PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Cobamides) RN - 13870-90-1 (cobamamide) RN - EC 4.2.1.28 (Propanediol Dehydratase) RN - RWP5GA015D (Potassium) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Catalysis MH - Cobamides/*metabolism MH - Crystallography, X-Ray MH - Models, Molecular MH - Molecular Sequence Data MH - Potassium/*metabolism MH - Propanediol Dehydratase/chemistry/*metabolism MH - Protein Binding MH - Protein Structure, Secondary EDAT- 1999/09/01 MHDA- 1999/09/01 00:01 CRDT- 1999/09/01 00:00 AID - st7806 [pii] PST - ppublish SO - Structure. 1999 Aug 15;7(8):997-1008. PMID- 24361273 OWN - NLM STAT- MEDLINE DA - 20140210 DCOM- 20141022 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 22 IP - 2 DP - 2014 Feb 4 TI - Predictive atomic resolution descriptions of intrinsically disordered hTau40 and alpha-synuclein in solution from NMR and small angle scattering. PG - 238-49 LID - 10.1016/j.str.2013.10.020 [doi] LID - S0969-2126(13)00436-X [pii] AB - The development of molecular descriptions of intrinsically disordered proteins (IDPs) is essential for elucidating conformational transitions that characterize common neurodegenerative disorders. We use nuclear magnetic resonance, small angle scattering, and molecular ensemble approaches to characterize the IDPs Tau and alpha-synuclein. Ensemble descriptions of IDPs are highly underdetermined due to the inherently large number of degrees of conformational freedom compared with available experimental measurements. Using extensive cross-validation we show that five different types of independent experimental parameters are predicted more accurately by selected ensembles than by statistical coil descriptions. The improvement increases in regions whose local sampling deviates from statistical coil, validating the derived conformational description. Using these approaches we identify enhanced polyproline II sampling in aggregation-nucleation sites, supporting suggestions that this region of conformational space is important for aggregation. CI - Copyright (c) 2014 Elsevier Ltd. All rights reserved. FAU - Schwalbe, Martin AU - Schwalbe M AD - Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 37077 Gottingen, Germany. FAU - Ozenne, Valery AU - Ozenne V AD - University Grenoble Alpes, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CNRS, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CEA, DSV, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France. FAU - Bibow, Stefan AU - Bibow S AD - Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany. FAU - Jaremko, Mariusz AU - Jaremko M AD - Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany. FAU - Jaremko, Lukasz AU - Jaremko L AD - Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany. FAU - Gajda, Michal AU - Gajda M AD - Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany. FAU - Jensen, Malene Ringkjobing AU - Jensen MR AD - University Grenoble Alpes, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CNRS, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CEA, DSV, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France. FAU - Biernat, Jacek AU - Biernat J AD - CEASAR Research Center, 53175 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany. FAU - Becker, Stefan AU - Becker S AD - Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany. FAU - Mandelkow, Eckhard AU - Mandelkow E AD - CEASAR Research Center, 53175 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany. FAU - Zweckstetter, Markus AU - Zweckstetter M AD - Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 37077 Gottingen, Germany; Center for the Molecular Physiology of the Brain, University Medical Center, 37073 Gottingen, Germany. Electronic address: mazw@nmr.mpibpc.mpg.de. FAU - Blackledge, Martin AU - Blackledge M AD - University Grenoble Alpes, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CNRS, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CEA, DSV, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France. Electronic address: martin.blackledge@ibs.fr. LA - eng GR - 089703/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131219 PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Membrane Proteins) RN - 0 (alpha-Synuclein) RN - 0 (tau 40 protein, human) RN - 9DLQ4CIU6V (Proline) SB - IM CIN - Structure. 2014 Feb 4;22(2):177-8. PMID: 24507778 MH - Algorithms MH - Humans MH - Intrinsically Disordered Proteins/chemistry MH - Magnetic Resonance Spectroscopy/*methods MH - Membrane Proteins/*chemistry MH - Neurodegenerative Diseases/metabolism MH - Proline MH - Protein Folding MH - Protein Structure, Tertiary MH - Scattering, Radiation MH - alpha-Synuclein/*chemistry EDAT- 2013/12/24 06:00 MHDA- 2014/10/23 06:00 CRDT- 2013/12/24 06:00 PHST- 2013/09/16 [received] PHST- 2013/10/29 [revised] PHST- 2013/10/30 [accepted] PHST- 2013/12/19 [aheadofprint] AID - S0969-2126(13)00436-X [pii] AID - 10.1016/j.str.2013.10.020 [doi] PST - ppublish SO - Structure. 2014 Feb 4;22(2):238-49. doi: 10.1016/j.str.2013.10.020. Epub 2013 Dec 19. PMID- 20121219 OWN - NLM STAT- MEDLINE DA - 20100216 DCOM- 20100414 LR - 20140919 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 7 DP - 2010 Feb 23 TI - The clustering and spatial arrangement of beta-sheet sequence, but not order, govern alpha-synuclein fibrillogenesis. PG - 1533-40 LID - 10.1021/bi901753h [doi] AB - The intrinsically unstructured protein alpha-synuclein (aS) is prone to misfold into cytotoxic beta-sheet-rich oligomers and amyloid fibrils that underlie the pathogenesis of Lewy body diseases such as Parkinson's disease. An important, recognized fibrillogenesis parameter is amino acid content, whereas the influence of amino acid sequence distribution is not as well understood. The fibril core of aS encompasses five regions of high beta-sheet propensity, termed beta1-beta5. Using four aS variants with identical amino acid compositions but rearranged pseudorepeat motifs, we show that beta2-beta5 sequence clustering, but not order, is important for efficient fibrillogenesis. For molecular species progressing toward the fibrillar state, order invariably increases; i.e., the spatial arrangement of sequence elements becomes restricted. By introducing disulfide bonds in a fibril structure-based manner, we demonstrated that a successful protofibril-to-fibril conversion is dependent upon the spatial arrangement of sequence elements of high beta-sheet propensity. Moreover, a disulfide-linked aS dimer is shown to fibrillize rapidly. We propose that a conformational search underlies the emergence of a fibrillar aS nucleus that is directed by gaps in sequence between beta-sheet regions and the accessible range of spatial beta-sheet arrangements in soluble, prefibrillar oligomers. On the basis of the universal cross-beta-sheet structure of amyloid fibrils, these principles are expected to apply to a wide range of amyloidogenic proteins. FAU - Suk, Jae-Eun AU - Suk JE AD - Department of Biochemistry and Molecular Biology and Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, California 90033, USA. FAU - Lokappa, Sowmya Bekshe AU - Lokappa SB FAU - Ulmer, Tobias S AU - Ulmer TS LA - eng GR - HL089726/HL/NHLBI NIH HHS/United States GR - R01 HL089726/HL/NHLBI NIH HHS/United States GR - R01 HL089726-02/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Disulfides) RN - 0 (SNCA protein, human) RN - 0 (alpha-Synuclein) SB - IM MH - *Amino Acid Motifs/genetics MH - Amino Acid Sequence MH - Circular Dichroism MH - Disulfides/chemistry MH - Electron Spin Resonance Spectroscopy MH - Genetic Variation MH - Humans MH - Kinetics MH - Microfibrils/*chemistry/genetics/*metabolism/ultrastructure MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - *Protein Engineering MH - Protein Folding MH - Protein Structure, Secondary/genetics MH - *Repetitive Sequences, Amino Acid/genetics MH - alpha-Synuclein/*biosynthesis/*chemical synthesis/genetics/ultrastructure PMC - PMC2841006 MID - NIHMS175430 OID - NLM: NIHMS175430 OID - NLM: PMC2841006 EDAT- 2010/02/04 06:00 MHDA- 2010/04/15 06:00 CRDT- 2010/02/04 06:00 AID - 10.1021/bi901753h [doi] PST - ppublish SO - Biochemistry. 2010 Feb 23;49(7):1533-40. doi: 10.1021/bi901753h. PMID- 21498513 OWN - NLM STAT- MEDLINE DA - 20110606 DCOM- 20110805 LR - 20140820 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 23 DP - 2011 Jun 10 TI - Competing interactions stabilize pro- and anti-aggregant conformations of human Tau. PG - 20512-24 LID - 10.1074/jbc.M111.237875 [doi] AB - Aggregation of Tau into amyloid-like fibrils is a key process in neurodegenerative diseases such as Alzheimer. To understand how natively disordered Tau stabilizes conformations that favor pathological aggregation, we applied single-molecule force spectroscopy. Intramolecular interactions that fold polypeptide stretches of ~19 and ~42 amino acids in the functionally important repeat domain of full-length human Tau (hTau40) support aggregation. In contrast, the unstructured N terminus randomly folds long polypeptide stretches >100 amino acids that prevent aggregation. The pro-aggregant mutant hTau40DeltaK280 observed in frontotemporal dementia favored the folding of short polypeptide stretches and suppressed the folding of long ones. This trend was reversed in the anti-aggregant mutant hTau40DeltaK280/PP. The aggregation inducer heparin introduced strong interactions in hTau40 and hTau40DeltaK280 that stabilized aggregation-prone conformations. We show that the conformation and aggregation of Tau are regulated through a complex balance of different intra- and intermolecular interactions. FAU - Wegmann, Susanne AU - Wegmann S AD - Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland. FAU - Scholer, Jonas AU - Scholer J FAU - Bippes, Christian A AU - Bippes CA FAU - Mandelkow, Eckhard AU - Mandelkow E FAU - Muller, Daniel J AU - Muller DJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110415 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (MAPT protein, human) RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/genetics/metabolism MH - Frontotemporal Dementia/genetics/metabolism MH - Humans MH - Mutation MH - *Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - tau Proteins/*chemistry/genetics/metabolism PMC - PMC3121454 OID - NLM: PMC3121454 EDAT- 2011/04/19 06:00 MHDA- 2011/08/06 06:00 CRDT- 2011/04/19 06:00 PHST- 2011/04/15 [aheadofprint] AID - M111.237875 [pii] AID - 10.1074/jbc.M111.237875 [doi] PST - ppublish SO - J Biol Chem. 2011 Jun 10;286(23):20512-24. doi: 10.1074/jbc.M111.237875. Epub 2011 Apr 15. PMID- 22813934 OWN - NLM STAT- MEDLINE DA - 20121008 DCOM- 20130221 LR - 20131121 IS - 1095-8657 (Electronic) IS - 1047-8477 (Linking) VI - 180 IP - 1 DP - 2012 Oct TI - Contribution of hydrophobic interactions to the folding and fibrillation of histone H1 and its carboxy-terminal domain. PG - 101-9 LID - 10.1016/j.jsb.2012.07.004 [doi] LID - S1047-8477(12)00199-2 [pii] AB - Histone H1 is involved in chromatin structure and gene regulation. H1 also performs functions outside cell nuclei, which may depend on its properties as a lipid-binding protein. The H1 CTD behaves as an intrinsically disordered protein (IDP) with coupled binding and folding. Here, we used neutral detergents and anionic SDS to study the contribution of hydrophobic interactions to the folding of the CTD. In the presence of neutral detergents, the CTD folded with proportions of secondary structure motifs similar to those observed in the DNA complexes. These results identify a folding pathway for the CTD based on hydrophobic interactions, and independent of charge compensation. The CTD is phosphorylated to different extents by cyclin-dependent kinases. The general effect of phosphorylation in the presence of detergents was a decrease in the alpha-helix content and an increase in that of the beta-structure. The greatest effect was observed in the fully phosphorylated CTD (three phosphate groups) in the presence of anionic SDS (7:1, detergent/CTD molar ratio); in these conditions, the CTD became an all-beta protein, with 83% beta-structure and no alpha-helix. The CTD in all-beta conformation readily formed ribbon-like fibers. The entire H1 also formed fibers when fully phosphorylated in the CTD. Fibers were of the amyloid type, as judged by strong birefringence in the presence of Congo red and thioflavin fluorescence enhancement. Amyloid fiber formation was only observed in SDS, suggesting that it requires the joint effects of partial charge neutralization and hydrophobic interactions, together with the all-beta potential provided by full phosphorylation. CI - Copyright (c) 2012 Elsevier Inc. All rights reserved. FAU - Roque, Alicia AU - Roque A AD - Departamento de Bioquimica y Biologia Molecular, Facultad de Biociencias, Universidad Autonoma de Barcelona, 08193 Bellaterra (Cerdanyola del Valles), Barcelona, Spain. FAU - Teruel, Nuria AU - Teruel N FAU - Lopez, Rita AU - Lopez R FAU - Ponte, Inma AU - Ponte I FAU - Suau, Pedro AU - Suau P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120717 PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - 0 (Amyloid) RN - 0 (Brij 35) RN - 0 (Detergents) RN - 0 (Histones) RN - 0 (Polyethylene Glycols) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - 9002-93-1 (Octoxynol) SB - IM MH - Amyloid/chemistry MH - Animals MH - Detergents/chemistry MH - Histones/*chemistry MH - Hydrophobic and Hydrophilic Interactions MH - Mice MH - Octoxynol/chemistry MH - Phosphorylation MH - Polyethylene Glycols/chemistry MH - Protein Folding MH - *Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sodium Dodecyl Sulfate/chemistry EDAT- 2012/07/21 06:00 MHDA- 2013/02/22 06:00 CRDT- 2012/07/21 06:00 PHST- 2012/02/14 [received] PHST- 2012/05/31 [revised] PHST- 2012/07/06 [accepted] PHST- 2012/07/17 [aheadofprint] AID - S1047-8477(12)00199-2 [pii] AID - 10.1016/j.jsb.2012.07.004 [doi] PST - ppublish SO - J Struct Biol. 2012 Oct;180(1):101-9. doi: 10.1016/j.jsb.2012.07.004. Epub 2012 Jul 17. PMID- 24733915 OWN - NLM STAT- MEDLINE DA - 20140430 DCOM- 20140624 LR - 20141111 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 17 DP - 2014 Apr 29 TI - Tau mutants bind tubulin heterodimers with enhanced affinity. PG - 6311-6 LID - 10.1073/pnas.1315983111 [doi] AB - Tau is a microtubule binding protein that forms pathological aggregates in the brain in Alzheimer's disease and other tauopathies. Disease etiology is thought to arise from loss of native interactions between tau and microtubules, as well as from gain of toxicity tied to tau aggregation, although neither mechanism is well understood. Here we investigate the link between function and disease using disease-associated and disease-motivated mutants of tau. We find that mutations to highly conserved proline residues in repeats 2 and 3 of the microtubule binding domain have differential effects on tau binding to tubulin and the capacity of tau to enhance tubulin polymerization. Notably, mutations to these residues result in an increased affinity for tubulin dimers while having a negligible effect on binding to stabilized microtubules. We measure conformational changes in tau on binding to tubulin that provide a structural framework for the observed altered affinity and function. Additionally, we find that these mutations do not necessarily enhance aggregation, which could have important implications for tau therapeutic strategies that focus solely on searching for tau aggregation inhibitors. We propose a model that describes tau binding to tubulin dimers and a mechanism by which disease-relevant alterations to tau impact its function. Together, these results draw attention to the interaction between tau and free tubulin as playing an important role in mechanisms of tau pathology. FAU - Elbaum-Garfinkle, Shana AU - Elbaum-Garfinkle S AD - Departments of Molecular Biophysics and Biochemistry, Chemistry, and Physics, Yale University, New Haven, CT 06511. FAU - Cobb, Garrett AU - Cobb G FAU - Compton, Jocelyn T AU - Compton JT FAU - Li, Xiao-Han AU - Li XH FAU - Rhoades, Elizabeth AU - Rhoades E LA - eng GR - 5T32GM007223/GM/NIGMS NIH HHS/United States GR - T32GM067543/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140414 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Mutant Proteins) RN - 0 (Tubulin) RN - 0 (tau Proteins) SB - IM MH - Fluorescence Resonance Energy Transfer MH - Kinetics MH - Models, Molecular MH - Mutant Proteins/genetics/*metabolism MH - Point Mutation MH - Polymerization MH - Protein Binding MH - *Protein Multimerization MH - Protein Structure, Quaternary MH - Repetitive Sequences, Amino Acid MH - Tubulin/*chemistry/*metabolism MH - tau Proteins/chemistry/*genetics/*metabolism PMC - PMC4035965 OID - NLM: PMC4035965 OTO - NOTNLM OT - intrinsically disordered proteins OT - microtubule-associated protein OT - single molecule FRET EDAT- 2014/04/16 06:00 MHDA- 2014/06/25 06:00 CRDT- 2014/04/16 06:00 PHST- 2014/04/14 [aheadofprint] AID - 1315983111 [pii] AID - 10.1073/pnas.1315983111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6311-6. doi: 10.1073/pnas.1315983111. Epub 2014 Apr 14. PMID- 11423419 OWN - NLM STAT- MEDLINE DA - 20010625 DCOM- 20010913 LR - 20140613 IS - 0006-3495 (Print) IS - 0006-3495 (Linking) VI - 81 IP - 1 DP - 2001 Jul TI - Folding properties of functional domains of tropomodulin. PG - 345-51 AB - Tropomodulin (Tmod) stabilizes the actin-tropomyosin filament by capping the slow-growing end (P-end). The N- and C-terminal halves play distinct roles; the N-terminal half interacts with the N-terminal region of tropomyosin, whereas the C-terminal half interacts with actin. Our previous study (A. Kostyukova, K. Maeda, E. Yamauchi, I. Krieger, and Y. Maeda Y., 2000, Eur. J. Biochem. 267:6470-6475) suggested that the two halves are also structurally distinct from each other. We have now studied the folding properties of the two halves, by circular dichroism spectroscopy and by differential scanning calorimetry of the expressed chicken E-type tropomodulin and its large fragments. The results showed that the C-terminal half represents a single, independently folded unit that melts cooperatively through a two-state transition. In contrast, the N-terminal half lacks a definite tertiary structure in solution. The binding of N11, a fragment that corresponds to the first 91 amino acids of the tropomodulin, to tropomyosin substantially stabilized the tropomyosin. This may indicate that the flexible structure of the N-terminal half of tropomodulin in solution is required for binding to tropomyosin and that the N-terminal half acquires its tertiary structure upon binding to tropomyosin. FAU - Kostyukova, A S AU - Kostyukova AS AD - Laboratory for Structural Biochemistry, RIKEN Harima Institute at SPring8, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan. FAU - Tiktopulo, E I AU - Tiktopulo EI FAU - Maeda, Y AU - Maeda Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Carrier Proteins) RN - 0 (Microfilament Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Tropomodulin) SB - IM MH - Animals MH - Calorimetry, Differential Scanning MH - Carrier Proteins/*chemistry/*metabolism MH - Chickens MH - Circular Dichroism MH - *Microfilament Proteins MH - Protein Denaturation MH - *Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Temperature MH - Thermodynamics MH - Tropomodulin PMC - PMC1301516 OID - NLM: PMC1301516 EDAT- 2001/06/26 10:00 MHDA- 2001/09/14 10:01 CRDT- 2001/06/26 10:00 AID - S0006-3495(01)75704-9 [pii] AID - 10.1016/S0006-3495(01)75704-9 [doi] PST - ppublish SO - Biophys J. 2001 Jul;81(1):345-51. PMID- 17081491 OWN - NLM STAT- MEDLINE DA - 20061204 DCOM- 20070227 IS - 0003-2697 (Print) IS - 0003-2697 (Linking) VI - 359 IP - 2 DP - 2006 Dec 15 TI - Alzheimer's-disease-associated conformation of intrinsically disordered tau protein studied by intrinsically disordered protein liquid-phase competitive enzyme-linked immunosorbent assay. PG - 230-7 AB - Tau protein, the major constituent of paired helical filaments in Alzheimer's disease, belongs to the intrinsically disordered proteins (IDPs). IDPs are an emerging group in the protein kingdom characterized by the absence of a rigid three-dimensional structure. Disordered proteins usually acquire a "functional fold" upon binding to their interaction partner(s). This property of IDPs implies the need for innovative approaches to measure their binding affinity. We have mapped and measured the Alzheimer's-disease-associated epitope on intrinsically disordered tau protein with a novel two-step sandwich competitive enzyme-linked immunosorbent assay (ELISA). This approach allowed us to determine the binding affinity of disordered tau protein in liquid phase without any disturbance to the competitive equilibrium and without any need for covalent or noncovalent modification of tau protein. Furthermore, the global fitting method, used for the reconstruction of tau binding curves, significantly improved the assay readout. The proposed novel competitive ELISA allowed us to determine the changes in the standard Gibbs energy of binding, thus enabling measurement of tau protein conformation in the core of paired helical filaments. IDP competitive ELISA results showed, for the first time, that the tau protein C terminus of the Alzheimer's-disease-derived paired helical filaments core subunit adopts beta-turn type I' fold and is accessible from solution. FAU - Skrabana, Rostislav AU - Skrabana R AD - Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia. FAU - Skrabanova-Khuebachova, Michaela AU - Skrabanova-Khuebachova M FAU - Kontsek, Peter AU - Kontsek P FAU - Novak, Michal AU - Novak M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20061019 PL - United States TA - Anal Biochem JT - Analytical biochemistry JID - 0370535 RN - 0 (Antibodies, Monoclonal) RN - 0 (Epitopes) RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/metabolism MH - Animals MH - Antibodies, Monoclonal/diagnostic use MH - Binding, Competitive MH - Enzyme-Linked Immunosorbent Assay/*methods MH - Epitopes/analysis MH - Humans MH - Molecular Conformation MH - Neurofibrillary Tangles/metabolism MH - Protein Conformation MH - tau Proteins/*chemistry/*metabolism EDAT- 2006/11/04 09:00 MHDA- 2007/02/28 09:00 CRDT- 2006/11/04 09:00 PHST- 2006/08/18 [received] PHST- 2006/09/27 [revised] PHST- 2006/09/28 [accepted] PHST- 2006/10/19 [aheadofprint] AID - S0003-2697(06)00715-9 [pii] AID - 10.1016/j.ab.2006.09.031 [doi] PST - ppublish SO - Anal Biochem. 2006 Dec 15;359(2):230-7. Epub 2006 Oct 19. PMID- 21560167 OWN - NLM STAT- MEDLINE DA - 20110614 DCOM- 20110930 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 79 IP - 7 DP - 2011 Jul TI - Tat peptide-calmodulin binding studies and bioinformatics of HIV-1 protein-calmodulin interactions. PG - 2233-46 LID - 10.1002/prot.23048 [doi] AB - The human immunodeficiency virus type 1 (HIV-1) genome encodes 18 proteins and 2 peptides. Four of these proteins encode high-affinity calmodulin-binding sites for which direct interactions with calmodulin have already been described. In this study, the HIV-1 proteome is queried using an algorithm that predicts calmodulin-binding sites revealing seven new putative calmodulin-binding sites including residues 34-56 of the transactivator of transcription (Tat). Tat is a 101-residue intrinsically disordered RNA-binding protein that plays a central role in the regulation of HIV-1 replication. Interactions between a Tat peptide (residues 34-56), melittin, a well-characterized calmodulin-binding peptide, and calmodulin were examined by direct binding studies, mass spectrometry, and fluorescence. The Tat peptide binds to both calcium-saturated and apo-calmodulin with a low micromolar affinity. Conformational changes induced in the Tat peptide were determined by circular dichroism, and residues in calmodulin that interact with the peptide were identified by HSQC NMR spectroscopy. Multiple interactions between HIV-1 proteins and calmodulin, a highly promiscuous signal transduction hub protein, may be an important mechanism by which the virus controls cell physiology. CI - Copyright (c) 2011 Wiley-Liss, Inc. FAU - McQueen, Peter AU - McQueen P AD - Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2. FAU - Donald, Lynda J AU - Donald LJ FAU - Vo, Thach N AU - Vo TN FAU - Nguyen, Dung H AU - Nguyen DH FAU - Griffiths, Heather AU - Griffiths H FAU - Shojania, Shaheen AU - Shojania S FAU - Standing, Kenneth G AU - Standing KG FAU - O'Neil, Joe D AU - O'Neil JD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110510 PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Calmodulin) RN - 0 (Human Immunodeficiency Virus Proteins) RN - 0 (tat Gene Products, Human Immunodeficiency Virus) RN - 20449-79-0 (Melitten) SB - IM MH - Amino Acid Sequence MH - Calmodulin/chemistry/*metabolism MH - Circular Dichroism MH - Computational Biology MH - Human Immunodeficiency Virus Proteins/chemistry/*metabolism MH - Humans MH - Mass Spectrometry MH - Melitten MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - tat Gene Products, Human Immunodeficiency Virus/chemistry/*metabolism EDAT- 2011/05/12 06:00 MHDA- 2011/10/01 06:00 CRDT- 2011/05/12 06:00 PHST- 2010/10/29 [received] PHST- 2011/03/18 [revised] PHST- 2011/03/22 [accepted] PHST- 2011/05/10 [aheadofprint] AID - 10.1002/prot.23048 [doi] PST - ppublish SO - Proteins. 2011 Jul;79(7):2233-46. doi: 10.1002/prot.23048. Epub 2011 May 10. PMID- 21560166 OWN - NLM STAT- MEDLINE DA - 20110614 DCOM- 20110930 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 79 IP - 7 DP - 2011 Jul TI - Structural memory of natively unfolded tau protein detected by small-angle X-ray scattering. PG - 2122-31 LID - 10.1002/prot.23033 [doi] AB - Small-angle X-ray scattering (SAXS) is a universal low-resolution method to study size and shape of globular proteins in solution but recent developments facilitate the quantitative characterization of the structure and structural transitions of metastable systems like partially or completely unfolded proteins. We present here a study of temperature induced transitions in tau, a natively unfolded protein involved in Alzheimer's disease. Previous studies on full length tau and several disease-related mutants provided information about the residual structure in different domains revealing a specific role and extended conformations of the so-called repeat domains, which are considered to be responsible for the formation of amyloid-like fibrils ("paired helical filaments"). Here, we employ SAXS to investigate the temperature dependent properties of tau. Slow heating/cooling of the full length protein from 10 degrees C to 50 degrees C did not lead to detectable changes in the overall size. Surprisingly, quick heating/cooling caused tau to adopt a significantly more compact conformation, which was stable over up to 3 h and represents a structural "memory" effect. This compaction is not observed for the shorter tau constructs containing largely the repeat domains. The structural and functional implications of the observed unusual behavior of tau under nonequilibrium conditions are discussed. CI - Copyright (c) 2011 Wiley-Liss, Inc. FAU - Shkumatov, Alexander V AU - Shkumatov AV AD - European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany. FAU - Chinnathambi, Subashchandrabose AU - Chinnathambi S FAU - Mandelkow, Eckhard AU - Mandelkow E FAU - Svergun, Dmitri I AU - Svergun DI LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110510 PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Protein Isoforms) RN - 0 (tau Proteins) SB - IM MH - Circular Dichroism MH - Humans MH - Protein Conformation MH - Protein Isoforms MH - Protein Unfolding MH - *Scattering, Small Angle MH - Temperature MH - *X-Ray Diffraction MH - tau Proteins/*chemistry/metabolism EDAT- 2011/05/12 06:00 MHDA- 2011/10/01 06:00 CRDT- 2011/05/12 06:00 PHST- 2010/09/30 [received] PHST- 2011/02/04 [revised] PHST- 2011/03/13 [accepted] PHST- 2011/05/10 [aheadofprint] AID - 10.1002/prot.23033 [doi] PST - ppublish SO - Proteins. 2011 Jul;79(7):2122-31. doi: 10.1002/prot.23033. Epub 2011 May 10. PMID- 23980173 OWN - NLM STAT- MEDLINE DA - 20130911 DCOM- 20131210 LR - 20141112 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 110 IP - 37 DP - 2013 Sep 10 TI - Structure of the transition state for the binding of c-Myb and KIX highlights an unexpected order for a disordered system. PG - 14942-7 LID - 10.1073/pnas.1307337110 [doi] AB - A classical dogma of molecular biology dictates that the 3D structure of a protein is necessary for its function. However, a considerable fraction of the human proteome, although functional, does not adopt a defined folded state under physiological conditions. These intrinsically disordered proteins tend to fold upon binding to their partners with a molecular mechanism that is elusive to experimental characterization. Indeed, although many hypotheses have been put forward, the functional role (if any) of disorder in these intrinsically denatured systems is still shrouded in mystery. Here, we characterize the structure of the transition state of the binding-induced folding in the reaction between the KIX domain of the CREB-binding protein and the transactivation domain of c-Myb. The analysis, based on the characterization of a series of conservative site-directed mutants, reveals a very high content of native-like structure in the transition state and indicates that the recognition between KIX and c-Myb is geometrically precise. The implications of our results in the light of previous work on intrinsically unstructured systems are discussed. FAU - Giri, Rajanish AU - Giri R AD - Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Universita di Roma, 00185 Rome, Italy. FAU - Morrone, Angela AU - Morrone A FAU - Toto, Angelo AU - Toto A FAU - Brunori, Maurizio AU - Brunori M FAU - Gianni, Stefano AU - Gianni S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130826 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Proto-Oncogene Proteins c-myb) RN - 0 (Recombinant Proteins) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Biophysical Phenomena MH - CREB-Binding Protein/*chemistry/*metabolism MH - Humans MH - Intrinsically Disordered Proteins/chemistry/genetics/metabolism MH - Kinetics MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Protein Binding MH - Protein Folding MH - Protein Interaction Domains and Motifs MH - Proto-Oncogene Proteins c-myb/*chemistry/genetics/*metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism PMC - PMC3773806 OID - NLM: PMC3773806 OTO - NOTNLM OT - kinetics OT - mutagenesis OT - protein folding EDAT- 2013/08/28 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/08/28 06:00 PHST- 2013/08/26 [aheadofprint] AID - 1307337110 [pii] AID - 10.1073/pnas.1307337110 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):14942-7. doi: 10.1073/pnas.1307337110. Epub 2013 Aug 26. PMID- 21797254 OWN - NLM STAT- MEDLINE DA - 20110830 DCOM- 20111021 LR - 20141022 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 50 IP - 35 DP - 2011 Sep 6 TI - Homogeneous and heterogeneous tertiary structure ensembles of amyloid-beta peptides. PG - 7612-28 LID - 10.1021/bi200732x [doi] AB - The interplay of modern molecular simulation and high-quality nuclear magnetic resonance (NMR) experiments has reached a fruitful stage for quantitative characterization of structural ensembles of disordered peptides. Amyloid-beta 1-42 (Abeta42), the primary peptide associated with Alzheimer's disease, and fragments such as Abeta21-30 are both classified as intrinsically disordered peptides (IDPs). We use a variety of NMR observables to validate de novo molecular dynamics simulations in explicit water to characterize the tertiary structure ensemble of Abeta42 and Abeta21-30 from the perspective of their classification as IDPs. Unlike the Abeta21-30 fragment that conforms to expectations of an IDP that is primarily extended, we find that Abeta42 samples conformations reflecting all possible secondary structure categories and spans the range of IDP classifications from collapsed structured states to highly extended conformations, making it an IDP with a far more heterogeneous tertiary ensemble. FAU - Ball, K Aurelia AU - Ball KA AD - Graduate Group in Biophysics, University of California, Berkeley, California 94720, United States. FAU - Phillips, Aaron H AU - Phillips AH FAU - Nerenberg, Paul S AU - Nerenberg PS FAU - Fawzi, Nicolas L AU - Fawzi NL FAU - Wemmer, David E AU - Wemmer DE FAU - Head-Gordon, Teresa AU - Head-Gordon T LA - eng GR - T32 GM008295/GM/NIGMS NIH HHS/United States GR - T32 GM08295/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20110815 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (1-42)) RN - 0 (amyloid beta-protein (21-30)) SB - IM MH - Amino Acid Motifs MH - Amyloid beta-Peptides/*chemistry/classification MH - Humans MH - Molecular Dynamics Simulation MH - Peptide Fragments/*chemistry/classification MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid PMC - PMC3474852 MID - NIHMS375005 OID - NLM: NIHMS375005 OID - NLM: PMC3474852 EDAT- 2011/07/30 06:00 MHDA- 2011/10/22 06:00 CRDT- 2011/07/30 06:00 PHST- 2011/08/15 [aheadofprint] AID - 10.1021/bi200732x [doi] PST - ppublish SO - Biochemistry. 2011 Sep 6;50(35):7612-28. doi: 10.1021/bi200732x. Epub 2011 Aug 15. PMID- 11604526 OWN - NLM STAT- MEDLINE DA - 20011017 DCOM- 20020312 LR - 20140613 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 10 IP - 11 DP - 2001 Nov TI - Solvent-induced collapse of alpha-synuclein and acid-denatured cytochrome c. PG - 2195-9 AB - The effects of solution conditions on protein collapse were studied by measuring the hydrodynamic radii of two unfolded proteins, alpha-synuclein and acid-denatured ferricytochrome c, in dilute solution and in 1 M glucose. The radius of alpha-synuclein in dilute solution is less than that predicted for a highly denatured state, and adding 1 M glucose causes further collapse. Circular dichroic data show that alpha-synuclein lacks organized structure in both dilute solution and 1 M glucose. On the other hand, the radius of acid-denatured cytochrome c in dilute solution is consistent with that of a highly denatured state, and 1 M glucose induces collapse to the size and structure of native cytochrome c. Taken together, these data show that alpha-synuclein, a natively unfolded protein, is collapsed even in dilute solution, but lacks structure. FAU - Morar, A S AU - Morar AS AD - Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA. FAU - Olteanu, A AU - Olteanu A FAU - Young, G B AU - Young GB FAU - Pielak, G J AU - Pielak GJ LA - eng GR - R21 ES10774/ES/NIEHS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Cytochrome c Group) RN - 0 (Nerve Tissue Proteins) RN - 0 (Solutions) RN - 0 (Solvents) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - IY9XDZ35W2 (Glucose) SB - IM MH - Circular Dichroism MH - Cytochrome c Group/*chemistry MH - Glucose MH - Hydrogen-Ion Concentration MH - Magnetic Resonance Spectroscopy/methods MH - Nerve Tissue Proteins/*chemistry MH - Protein Denaturation MH - Protein Structure, Secondary MH - Solutions MH - Solvents/*chemistry MH - Synucleins MH - Temperature MH - alpha-Synuclein PMC - PMC2374057 OID - NLM: PMC2374057 EDAT- 2001/10/18 10:00 MHDA- 2002/03/13 10:01 CRDT- 2001/10/18 10:00 AID - 10.1110/ps.24301 [doi] PST - ppublish SO - Protein Sci. 2001 Nov;10(11):2195-9. PMID- 21641618 OWN - NLM STAT- MEDLINE DA - 20110704 DCOM- 20120514 LR - 20150325 IS - 1878-5883 (Electronic) IS - 0022-510X (Linking) VI - 307 IP - 1-2 DP - 2011 Aug 15 TI - Proteasome inhibition induces alpha-synuclein SUMOylation and aggregate formation. PG - 157-61 LID - 10.1016/j.jns.2011.04.015 [doi] AB - Parkinson's disease (PD) and Dementia with Lewy Bodies (DLB) are characterized pathologically by intraneuronal inclusions called Lewy bodies (LBs) and Lewy neurites. A major component of these inclusions is the protein alpha-synuclein, which is natively unfolded but forms oligomers and insoluble fibrillar aggregates under pathological conditions. Although alpha-synuclein is known to undergo several posttranslational modifications, the contribution of SUMOylation to alpha-synuclein aggregation and the pathogenesis of alpha-synucleinopathies have not been elucidated. Here, we provide evidence that aggregates and inclusions formed as a result of impaired proteasome activity contain SUMOylated alpha-synuclein. Additionally, SUMO1 is present in the halo of LBs colocalizing with alpha-synuclein in the brains of PD and DLB patients. Interestingly, SUMOylation does not affect the ubiquitination of alpha-synuclein. These findings suggest that proteasomal dysfunction results in the accumulation of SUMOylated alpha-synuclein and subsequently its aggregation, pointing to the contribution of this posttranslational modification to the pathogenesis of inclusion formation in alpha-synucleinopathies. CI - Copyright (c) 2011 Elsevier B.V. All rights reserved. FAU - Kim, Yong Man AU - Kim YM AD - FCB-Pharmicell, Seongnam-si, Gyeonggi-do 462-806, Republic of Korea. FAU - Jang, Won Hee AU - Jang WH FAU - Quezado, Martha M AU - Quezado MM FAU - Oh, Yohan AU - Oh Y FAU - Chung, Kwang Chul AU - Chung KC FAU - Junn, Eunsung AU - Junn E FAU - Mouradian, M Maral AU - Mouradian MM LA - eng GR - Z01 NS002826/NS/NINDS NIH HHS/United States GR - Z01 NS002826-14/Intramural NIH HHS/United States GR - Z01NS002826/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural DEP - 20110608 PL - Netherlands TA - J Neurol Sci JT - Journal of the neurological sciences JID - 0375403 RN - 0 (Macromolecular Substances) RN - 0 (Proteasome Inhibitors) RN - 0 (SUMO-1 Protein) RN - 0 (alpha-Synuclein) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Animals MH - COS Cells MH - Cercopithecus aethiops MH - Humans MH - Inclusion Bodies/enzymology/*metabolism/pathology MH - Lewy Bodies/enzymology/metabolism/pathology MH - Lewy Body Disease/enzymology/*metabolism/physiopathology MH - Macromolecular Substances/metabolism MH - Parkinson Disease/enzymology/*metabolism/physiopathology MH - Proteasome Endopeptidase Complex/physiology MH - *Proteasome Inhibitors MH - Protein Processing, Post-Translational/physiology MH - SUMO-1 Protein/*metabolism MH - Sumoylation/*physiology MH - alpha-Synuclein/*metabolism PMC - PMC3129438 MID - NIHMS293379 OID - NLM: NIHMS293379 OID - NLM: PMC3129438 EDAT- 2011/06/07 06:00 MHDA- 2012/05/15 06:00 CRDT- 2011/06/07 06:00 PHST- 2010/12/23 [received] PHST- 2011/03/12 [revised] PHST- 2011/04/21 [accepted] PHST- 2011/06/08 [aheadofprint] AID - S0022-510X(11)00218-8 [pii] AID - 10.1016/j.jns.2011.04.015 [doi] PST - ppublish SO - J Neurol Sci. 2011 Aug 15;307(1-2):157-61. doi: 10.1016/j.jns.2011.04.015. Epub 2011 Jun 8. PMID- 16006555 OWN - NLM STAT- MEDLINE DA - 20050912 DCOM- 20051020 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 37 DP - 2005 Sep 16 TI - DNA-induced secondary structure of the carboxyl-terminal domain of histone H1. PG - 32141-7 AB - We have studied the secondary structure of the carboxyl-terminal domains of linker histone H1 subtypes H1(0) (C-H1(0)) and H1t (C-H1t), free in solution and bound to DNA, by IR spectroscopy. The carboxyl-terminal domain has little structure in aqueous solution but becomes extensively folded upon interaction with DNA. The secondary structure elements present in the bound carboxyl-terminal domain include the alpha-helix, beta-structure, turns, and open loops. The structure of the bound domain shows a significant dependence on salt concentration. In low salt (10 mm NaCl), there is a residual amount of random coil, 7% in C-H1(0) and 12% in C-H1t. In physiological salt concentrations (140 mm NaCl), the carboxyl termini become fully structured. Under these conditions, C-H1(0) contained 24% alpha-helix, 25% beta-structure, 17% open loops, and 33% turns. The latter component could include a substantial proportion of the 3(10) helix. Despite their low sequence identity (approximately 30%), the representation of the different structural motifs in C-H1t was similar to that in C-H1(0). Examination of the changes in the amide I components in the 20-80 degrees C temperature interval showed that the secondary structure of the DNA-bound C-H1t is for the most part extremely stable. The H1 carboxyl-terminal domain appears to belong to the so-called disordered proteins, undergoing coupled binding and folding. FAU - Roque, Alicia AU - Roque A AD - Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias, Universidad Autonoma de Barcelona, Bellaterra, Spain. FAU - Iloro, Ibon AU - Iloro I FAU - Ponte, Imma AU - Ponte I FAU - Arrondo, Jose Luis R AU - Arrondo JL FAU - Suau, Pedro AU - Suau P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050708 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Chromatin) RN - 0 (Histones) RN - 059QF0KO0R (Water) RN - 7647-14-5 (Sodium Chloride) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Biophysical Phenomena MH - Biophysics MH - Chromatin/chemistry MH - Circular Dichroism MH - Cloning, Molecular MH - DNA/*chemistry MH - Histones/*chemistry MH - Kinetics MH - Mice MH - Molecular Sequence Data MH - *Nucleic Acid Conformation MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Sodium Chloride/pharmacology MH - Spectrophotometry MH - Temperature MH - Ultraviolet Rays MH - Water/chemistry EDAT- 2005/07/12 09:00 MHDA- 2005/10/21 09:00 CRDT- 2005/07/12 09:00 PHST- 2005/07/08 [aheadofprint] AID - M505636200 [pii] AID - 10.1074/jbc.M505636200 [doi] PST - ppublish SO - J Biol Chem. 2005 Sep 16;280(37):32141-7. Epub 2005 Jul 8. PMID- 25139280 OWN - NLM STAT- In-Data-Review DA - 20150518 IS - 1559-1182 (Electronic) IS - 0893-7648 (Linking) VI - 51 IP - 3 DP - 2015 Jun TI - alpha-Synuclein Misfolding Versus Aggregation Relevance to Parkinson's Disease: Critical Assessment and Modeling. PG - 1417-31 LID - 10.1007/s12035-014-8818-2 [doi] AB - alpha-Synuclein, an abundant and conserved presynaptic brain protein, is implicated as a critical factor in Parkinson's disease (PD). The aggregation of alpha-synuclein is believed to be a critical event in the disease process. alpha-Synuclein is characterized by a remarkable conformational plasticity, adopting different conformations depending on the environment. Therefore, it is classified as an "intrinsically disordered protein." Recently, a debate has challenged the view on the intrinsically disordered behavior of alpha-synuclein in the cell. It has been proposed that alpha-synuclein is a stable tetramer with a low propensity for aggregation; however, its destabilization leads to protein misfolding and its aggregation kinetics. In our critical analysis, we discussed about major issues: (i) why alpha-synuclein conformational behavior does not fit into the normal secondary structural characteristics of proteins, (ii) potential amino acids involved in the complexity of misfolding in alpha-synuclein that leads to aggregation, and (iii) the role of metals in misfolding and aggregation. To evaluate the above critical issues, we developed bioinformatics models related to secondary and tertiary conformations, Ramachandran plot, free energy change, intrinsic disordered prediction, solvent accessibility, and FoldIndex pattern. To the best of our knowledge, this is a novel critical assessment to understand the misfolding biology of synuclein and its relevance to Parkinson's disease. FAU - Berrocal, Ruben AU - Berrocal R AD - Centre for Neuroscience, Institute for Scientific Research and Technology Services (INDICASAT-AIP), City of Knowledge, Republic of Panama. FAU - Vasquez, Velmarini AU - Vasquez V FAU - Krs, Sambasiva Rao AU - Krs SR FAU - Gadad, Bharathi S AU - Gadad BS FAU - Ks, Rao AU - Ks R LA - eng PT - Journal Article DEP - 20140820 PL - United States TA - Mol Neurobiol JT - Molecular neurobiology JID - 8900963 SB - IM EDAT- 2014/08/21 06:00 MHDA- 2014/08/21 06:00 CRDT- 2014/08/21 06:00 PHST- 2014/04/28 [received] PHST- 2014/07/15 [accepted] PHST- 2014/08/20 [aheadofprint] AID - 10.1007/s12035-014-8818-2 [doi] PST - ppublish SO - Mol Neurobiol. 2015 Jun;51(3):1417-31. doi: 10.1007/s12035-014-8818-2. Epub 2014 Aug 20. PMID- 11017202 OWN - NLM STAT- MEDLINE DA - 20001107 DCOM- 20001107 LR - 20061115 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 7 IP - 10 DP - 2000 Oct TI - The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site. PG - 910-7 AB - Cell respiration is catalyzed by the heme-copper oxidase superfamily of enzymes, which comprises cytochrome c and ubiquinol oxidases. These membrane proteins utilize different electron donors through dissimilar access mechanisms. We report here the first structure of a ubiquinol oxidase, cytochrome bo3, from Escherichia coli. The overall structure of the enzyme is similar to those of cytochrome c oxidases; however, the membrane-spanning region of subunit I contains a cluster of polar residues exposed to the interior of the lipid bilayer that is not present in the cytochrome c oxidase. Mutagenesis studies on these residues strongly suggest that this region forms a quinone binding site. A sequence comparison of this region with known quinone binding sites in other membrane proteins shows remarkable similarities. In light of these findings we suggest specific roles for these polar residues in electron and proton transfer in ubiquinol oxidase. FAU - Abramson, J AU - Abramson J AD - Uppsala University, Department of Biochemistry, Biomedical Center Box 576, Uppsala S-75123, Sweden. FAU - Riistama, S AU - Riistama S FAU - Larsson, G AU - Larsson G FAU - Jasaitis, A AU - Jasaitis A FAU - Svensson-Ek, M AU - Svensson-Ek M FAU - Laakkonen, L AU - Laakkonen L FAU - Puustinen, A AU - Puustinen A FAU - Iwata, S AU - Iwata S FAU - Wikstrom, M AU - Wikstrom M LA - eng SI - PDB/1FFT PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 1339-63-5 (Ubiquinone) RN - EC 1.9.3.- (cytochrome o oxidase) RN - EC 1.9.3.1 (Electron Transport Complex IV) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Electron Transport Complex IV/*chemistry/genetics/metabolism MH - Escherichia coli/*enzymology MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Protein Conformation MH - Sequence Homology, Amino Acid MH - Ubiquinone/*metabolism EDAT- 2000/10/04 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/10/04 11:00 AID - 10.1038/82824 [doi] PST - ppublish SO - Nat Struct Biol. 2000 Oct;7(10):910-7. PMID- 2387396 OWN - NLM STAT- MEDLINE DA - 19900927 DCOM- 19900927 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 269 IP - 1 DP - 1990 Aug 20 TI - Cloning and sequencing of a cDNA encoding human milk beta-casein. PG - 153-6 AB - A cDNA of 1065 bp encoding the human milk beta-casein was cloned and sequenced using a synthetic oligodeoxyribonucleotide probe and a human mammary gland library. The nucleotide (nt) sequence contained an open reading frame sufficient to encode the entire amino-acid (aa) sequence of a beta-casein precursor protein consisting of 210 aa and a signal peptide of 15 aa. The nt sequence shows 45-62% homology to those of bovine, ovine, rat, and mouse beta-caseins. The highly phosphorylated site, which is responsible for the calcium-binding capacity of beta-casein, the signal peptide, and a sequence encoding for an inhibitor to the angiotensin-converting enzyme seem highly conserved among the beta-caseins with known sequences. FAU - Lonnerdal, B AU - Lonnerdal B AD - Department of Nutrition, University of California, Davis 95616. FAU - Bergstrom, S AU - Bergstrom S FAU - Andersson, Y AU - Andersson Y FAU - Hjalmarsson, K AU - Hjalmarsson K FAU - Sundqvist, A K AU - Sundqvist AK FAU - Hernell, O AU - Hernell O LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Caseins) RN - 0 (Oligonucleotide Probes) RN - 0 (Phosphoproteins) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Caseins/*genetics MH - Cloning, Molecular MH - DNA/genetics MH - Humans MH - Molecular Sequence Data MH - Oligonucleotide Probes MH - Phosphoproteins/genetics EDAT- 1990/08/20 MHDA- 1990/08/20 00:01 CRDT- 1990/08/20 00:00 PST - ppublish SO - FEBS Lett. 1990 Aug 20;269(1):153-6. PMID- 19995563 OWN - NLM STAT- MEDLINE DA - 20100127 DCOM- 20100218 IS - 1873-3468 (Electronic) IS - 0014-5793 (Linking) VI - 584 IP - 3 DP - 2010 Feb 5 TI - Natively unfolded nucleic acid binding P8 domain of SeMV polyprotein 2a affects the novel ATPase activity of the preceding P10 domain. PG - 571-6 LID - 10.1016/j.febslet.2009.12.003 [doi] AB - Open reading frame (ORF) 2a of Sesbania mosaic virus (SeMV) codes for polyprotein 2a (Membrane anchor-protease-VPg-P10-P8). The C-terminal domain of SeMV polyprotein 2a was cloned, expressed and purified in order to functionally characterize it. The protein of size 8kDa (P8) domain, like viral protein genome linked (VPg), was found to be natively unfolded and could bind to nucleic acids. Interestingly, P10-P8 but not P8 showed a novel Mg(2+) dependent ATPase activity that was inhibited in the presence of poly A. In the absence of P8, the ATPase activity of the protein of size 10kDa (P10) domain was reduced suggesting that the natively unfolded P8 domain influenced the P10 ATPase. CI - 2009 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. FAU - Nair, Smita AU - Nair S AD - Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka State, India. FAU - Savithri, H S AU - Savithri HS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091206 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Nucleic Acids) RN - 0 (Polyproteins) RN - 0 (Viral Proteins) RN - EC 3.6.1.- (Adenosine Triphosphatases) SB - IM MH - Adenosine Triphosphatases/chemistry/*metabolism MH - Circular Dichroism MH - Computational Biology MH - Mosaic Viruses/genetics/*metabolism MH - Nucleic Acids/*metabolism MH - Open Reading Frames/genetics MH - Polyproteins/chemistry/*metabolism MH - Protein Binding/genetics/physiology MH - Protein Structure, Tertiary MH - Viral Proteins/chemistry/*metabolism EDAT- 2009/12/10 06:00 MHDA- 2010/02/19 06:00 CRDT- 2009/12/10 06:00 PHST- 2009/11/03 [received] PHST- 2009/11/24 [revised] PHST- 2009/12/02 [accepted] PHST- 2009/12/06 [aheadofprint] AID - S0014-5793(09)01046-1 [pii] AID - 10.1016/j.febslet.2009.12.003 [doi] PST - ppublish SO - FEBS Lett. 2010 Feb 5;584(3):571-6. doi: 10.1016/j.febslet.2009.12.003. Epub 2009 Dec 6. PMID- 22399317 OWN - NLM STAT- MEDLINE DA - 20120308 DCOM- 20120410 IS - 0065-2598 (Print) IS - 0065-2598 (Linking) VI - 725 DP - 2012 TI - Intrinsic protein flexibility in regulation of cell proliferation: advantages for signaling and opportunities for novel therapeutics. PG - 27-49 LID - 10.1007/978-1-4614-0659-4_3 [doi] AB - It is now widely recognized that intrinsically disordered (or unstructured) proteins (IDPs, or IUPs) are found in organisms from all kingdoms of life. In eukaryotes, IDPs are highly abundant and perform a wide range of biological functions, including regulation and signaling. Despite increased interest in understanding the structural biology of IDPs, questions remain regarding the mechanisms through which disordered proteins perform their biological function(s). In other words, what are the relationships between disorder and function for IDPs? Several excellent reviews have recently been published that discuss the structural properties of IDPs.1-3 Here, we discuss two IDP systems which illustrate features of dynamic complexes. In the first section, we discuss two IDPs, p21 and p27, which regulate the mammalian cell division cycle by inhibiting cyclin-dependent kinases (Cdks). In the second section, we discuss recent results from Follis, Hammoudeh, Metallo and coworkers demonstrating that the IDP Myc can be bound and inhibited by small molecules through formation of dynamic complexes. Previous studies have shown that polypeptide segments of p21 and p27 are partially folded in isolation and fold further upon binding their biological targets. Interestingly, some portions of p27 which bind to and inhibit Cdk2/cyclin A remain flexible in the bound complex. This residual flexibility allows otherwise buried tyrosine residues within p27 to be phosphorylated by nonreceptor tyrosine kinases (NRTKs). Tyrosine phosphorylation relieves kinase inhibition, triggering Cdk2-mediated phosphorylation of a threonine residue within the flexible C-terminus of p27. This, in turn, marks p27 for ubiquitination and proteasomal degradation, unleashing full Cdk2 activity which drives cell cycle progression. p27, thus, constitutes a conduit for transmission of proliferative signals via posttranslational modifications. Importantly, activation of the p27 signaling conduit by oncogenic NRTKs contributes to tumorigenesis in some human cancers, including chronic myelogenous leukemia (CML)9 and breast cancer.10 Another IDP with important roles in human cancer is the proto-oncoprotein, Myc. Myc is a DNA binding transcription factor which critically drives cell proliferation in many cell types and is often deregulated in cancer. Myc is intrinsically disordered in isolation and folds upon binding another IDP, Max and DNA. Follis, Hammoudeh, Metallo and coworkers identified small molecules which bind disordered regions of Myc and inhibit its heterodimerization with Max. Importantly, these small molecules- through formation of dynamic complexes with Myc-have been shown to inhibit Myc function in vitro and in cellular assays, opening the door to IDP-targeted therapeutics in the future. The p21/p27 and Myc systems illustrate, from different perspectives, the role of dynamics in IDP function. Dynamic fluctuations are critical for p21/p27 signaling while the dynamic free state of Myc may represent a therapeutically approachable anticancer target. Herein we review the current state of knowledge related to these two topics in IDP research. FAU - Follis, Ariele Viacava AU - Follis AV AD - Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. FAU - Galea, Charles A AU - Galea CA FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng GR - 2R01CA082491/CA/NCI NIH HHS/United States GR - 9P30CA021765/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Adv Exp Med Biol JT - Advances in experimental medicine and biology JID - 0121103 RN - 0 (Cyclin-Dependent Kinase Inhibitor p21) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) SB - IM MH - Amino Acid Sequence MH - Animals MH - *Cell Proliferation MH - Cyclin-Dependent Kinase Inhibitor p21/*chemistry/metabolism MH - Cyclin-Dependent Kinase Inhibitor p27/*chemistry/metabolism MH - Humans MH - Molecular Sequence Data MH - Sequence Homology, Amino Acid MH - *Signal Transduction EDAT- 2012/03/09 06:00 MHDA- 2012/04/11 06:00 CRDT- 2012/03/09 06:00 AID - 10.1007/978-1-4614-0659-4_3 [doi] PST - ppublish SO - Adv Exp Med Biol. 2012;725:27-49. doi: 10.1007/978-1-4614-0659-4_3. PMID- 23313430 OWN - NLM STAT- MEDLINE DA - 20130304 DCOM- 20130430 LR - 20131121 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 425 IP - 6 DP - 2013 Mar 25 TI - Potential conformational heterogeneity of p53 bound to S100B(betabeta). PG - 999-1010 LID - 10.1016/j.jmb.2013.01.001 [doi] LID - S0022-2836(13)00004-1 [pii] AB - The negative regulatory domain (NRD) of the p53 tumor suppressor is intrinsically disordered. It contains several posttranslational modification (PTM) sites that are important for regulation of p53 activity. Calcium-dependent binding of dimeric S100B(betabeta) to p53-NRD blocks access to these PTM sites and disrupts the p53 tetramer to inhibit p53 activation. Previous nuclear magnetic resonance (NMR) structural studies have suggested that p53-NRD folds into a stable helix upon binding to S100B(betabeta). Intriguingly, despite the well-converged and stably folded nature of the NMR structure ensemble, experimentally resolved intermolecular nuclear Overhauser enhancements (NOEs) are extremely weak; most have 5- to 6-A upper bounds, and mainly involve the C-terminal segment of p53-NRD. Such a systematic lack of strong intermolecular NOEs could suggest that the p53/S100B(betabeta) interface is more dynamic than currently believed. Indeed, extensive atomistic simulations in explicit solvent (with 1.0mus total effective sampling) revealed large heterogeneity in the S100B(betabeta)-bound conformation of p53-NRD. Helix unwinding at the C-terminus allows key hydrophobic residues (Leu383 and Phe385) to make more extensive intermolecular contacts, whereas the highly helical N-terminus displays substantial flexibility in packing with S100B(betabeta). Importantly, the predicted heterogeneous ensemble as a whole is highly consistent with experimental intermolecular NOEs, although many conformational sub-states coexist and individual sub-states satisfy only subsets of the NOE restraints. Furthermore, the simulated ensemble provides similar shielding of key PTM sites to support p53 inhibition. This study not only provides new insights into the structural basis of the p53/S100B(betabeta) recognition but also highlights the importance of recognizing dynamic complexes in structural studies of intrinsically disordered protein interactions. CI - Copyright (c) 2013 Elsevier Ltd. All rights reserved. FAU - McDowell, Chester AU - McDowell C AD - Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA. FAU - Chen, Jianlin AU - Chen J FAU - Chen, Jianhan AU - Chen J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130108 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Nerve Growth Factors) RN - 0 (S100 Calcium Binding Protein beta Subunit) RN - 0 (S100 Proteins) RN - 0 (Tumor Suppressor Protein p53) RN - 47E5O17Y3R (Phenylalanine) RN - GMW67QNF9C (Leucine) SB - IM MH - Binding Sites MH - Hydrophobic and Hydrophilic Interactions MH - Leucine/genetics MH - Nerve Growth Factors/*chemistry/metabolism MH - Phenylalanine/genetics MH - Protein Structure, Secondary MH - S100 Calcium Binding Protein beta Subunit MH - S100 Proteins/*chemistry/metabolism MH - Tumor Suppressor Protein p53/*chemistry/metabolism EDAT- 2013/01/15 06:00 MHDA- 2013/05/01 06:00 CRDT- 2013/01/15 06:00 PHST- 2012/07/18 [received] PHST- 2012/12/23 [revised] PHST- 2013/01/02 [accepted] PHST- 2013/01/08 [aheadofprint] AID - S0022-2836(13)00004-1 [pii] AID - 10.1016/j.jmb.2013.01.001 [doi] PST - ppublish SO - J Mol Biol. 2013 Mar 25;425(6):999-1010. doi: 10.1016/j.jmb.2013.01.001. Epub 2013 Jan 8. PMID- 21464206 OWN - NLM STAT- MEDLINE DA - 20110512 DCOM- 20110721 LR - 20140916 IS - 1098-5549 (Electronic) IS - 0270-7306 (Linking) VI - 31 IP - 11 DP - 2011 Jun TI - Nucleosome linker DNA contacts and induces specific folding of the intrinsically disordered H1 carboxyl-terminal domain. PG - 2341-8 LID - 10.1128/MCB.05145-11 [doi] AB - Linker histones play essential roles in the chromatin structure of higher eukaryotes. While binding to the surface of nucleosomes is directed by an approximately 80-amino-acid-residue globular domain, the structure and interactions of the lysine-rich approximately 100-residue C-terminal domain (CTD), primarily responsible for the chromatin-condensing functions of linker histones, are poorly understood. By quantitatively analyzing binding of a set of H1 CTD deletion mutants to nucleosomes containing various lengths of linker DNA, we have identified interactions between distinct regions of the CTD and nucleosome linker DNA at least 21 bp from the edge of the nucleosome core. Importantly, partial CTD truncations caused increases in H1 binding affinity, suggesting that significant entropic costs are incurred upon binding due to CTD folding. van't Hoff entropy/enthalpy analysis and intramolecular fluorescent resonance energy transfer (FRET) studies indicate that the CTD undergoes substantial nucleosome-directed folding, in a manner that is distinct from that which occurs upon H1 binding to naked DNA. In addition to defining critical interactions between the H1 CTD and linker DNA, our data indicate that the H1 CTD is an intrinsically disordered domain and provide important insights into the biological function of this protein. FAU - Caterino, Tamara L AU - Caterino TL AD - Department of Biochemistry and Biophysics, Box 712, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, USA. FAU - Fang, He AU - Fang H FAU - Hayes, Jeffrey J AU - Hayes JJ LA - eng GR - GM52426/GM/NIGMS NIH HHS/United States GR - R01 GM052426/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20110404 PL - United States TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (Chromatin) RN - 0 (Histones) RN - 0 (Nucleosomes) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Chromatin/ultrastructure MH - DNA/*metabolism MH - Entropy MH - Gene Expression MH - Histones/*chemistry/*metabolism/ultrastructure MH - Nucleosomes/*metabolism MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Sequence Deletion MH - Xenopus laevis PMC - PMC3133241 OID - NLM: PMC3133241 EDAT- 2011/04/06 06:00 MHDA- 2011/07/22 06:00 CRDT- 2011/04/06 06:00 PHST- 2011/04/04 [aheadofprint] AID - MCB.05145-11 [pii] AID - 10.1128/MCB.05145-11 [doi] PST - ppublish SO - Mol Cell Biol. 2011 Jun;31(11):2341-8. doi: 10.1128/MCB.05145-11. Epub 2011 Apr 4. PMID- 19088278 OWN - NLM STAT- MEDLINE DA - 20081217 DCOM- 20090212 IS - 0022-1317 (Print) IS - 0022-1317 (Linking) VI - 90 IP - Pt 1 DP - 2009 Jan TI - Adenovirus type 5 E4 Orf3 protein targets promyelocytic leukaemia (PML) protein nuclear domains for disruption via a sequence in PML isoform II that is predicted as a protein interaction site by bioinformatic analysis. PG - 95-104 LID - 10.1099/vir.0.005512-0 [doi] AB - Human adenovirus type 5 infection causes the disruption of structures in the cell nucleus termed promyelocytic leukaemia (PML) protein nuclear domains or ND10, which contain the PML protein as a critical component. This disruption is achieved through the action of the viral E4 Orf3 protein, which forms track-like nuclear structures that associate with the PML protein. This association is mediated by a direct interaction of Orf3 with a specific PML isoform, PMLII. We show here that the Orf3 interaction properties of PMLII are conferred by a 40 aa residue segment of the unique C-terminal domain of the protein. This segment was sufficient to confer interaction on a heterologous protein. The analysis was informed by prior application of a bioinformatic tool for the prediction of potential protein interaction sites within unstructured protein sequences (predictors of naturally disordered region analysis; PONDR). This tool predicted three potential molecular recognition elements (MoRE) within the C-terminal domain of PMLII, one of which was found to form the core of the Orf3 interaction site, thus demonstrating the utility of this approach. The sequence of the mapped Orf3-binding site on PML protein was found to be relatively poorly conserved across other species; however, the overall organization of MoREs within unstructured sequence was retained, suggesting the potential for conservation of functional interactions. FAU - Leppard, Keith N AU - Leppard KN AD - Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK. Keith.Leppard@warwick.ac.uk FAU - Emmott, Edward AU - Emmott E FAU - Cortese, Marc S AU - Cortese MS FAU - Rich, Tina AU - Rich T LA - eng GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Gen Virol JT - The Journal of general virology JID - 0077340 RN - 0 (Adenovirus E4 Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Protein Isoforms) RN - 0 (Transcription Factors) RN - 0 (Tumor Suppressor Proteins) RN - 143220-95-5 (PML protein, human) SB - IM MH - Adenoviridae/*physiology MH - Adenovirus E4 Proteins/*metabolism MH - Amino Acid Sequence MH - Computational Biology/methods MH - Conserved Sequence MH - Humans MH - Molecular Sequence Data MH - Nuclear Proteins/*metabolism MH - Protein Interaction Domains and Motifs MH - *Protein Interaction Mapping MH - Protein Isoforms/genetics MH - Sequence Alignment MH - Transcription Factors/*metabolism MH - Tumor Suppressor Proteins/*metabolism EDAT- 2008/12/18 09:00 MHDA- 2009/02/13 09:00 CRDT- 2008/12/18 09:00 AID - 90/1/95 [pii] AID - 10.1099/vir.0.005512-0 [doi] PST - ppublish SO - J Gen Virol. 2009 Jan;90(Pt 1):95-104. doi: 10.1099/vir.0.005512-0. PMID- 19619473 OWN - NLM STAT- MEDLINE DA - 20090721 DCOM- 20090921 LR - 20140828 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 97 IP - 2 DP - 2009 Jul 22 TI - Molecular determinants of snurportin 1 ligand affinity and structural response upon binding. PG - 581-9 LID - 10.1016/j.bpj.2009.04.049 [doi] AB - The transport of large biomolecules such as proteins and RNA across nuclear pore complexes is a field of strong interest and research. Although the basic mechanisms are fairly well understood, the details of the underlying intermolecular interaction within these transport complexes are still unclear. The recognition dynamics and energetics of cargo binding to the transport receptor are not yet resolved. Here, the binding of dimethylated RNA-caps to snurportin 1 is studied by molecular-dynamics simulations. The simulations reveal a strong structural response of the protein upon RNA-cap release. In particular, major rearrangements occur in regions already intrinsically flexible in the holo structure. Additionally, the difference in free energy of binding to snurportin 1 between the two methylation states of the RNA-cap, responsible for the directionality of the transport is quantified. In particular, desolvation of the ligand is revealed as the key-step in binding to snurportin 1. These findings suggest that the binding of m(3)G-capped RNA is mainly driven by the enhanced water entropy gain of the solvation shell. FAU - Goette, Maik AU - Goette M AD - Theoretical and Computational Biophysics Department, Max-Planck-Institute for Biophysical Chemistry, Gottingen, Germany. FAU - Stumpe, Martin C AU - Stumpe MC FAU - Ficner, Ralf AU - Ficner R FAU - Grubmuller, Helmut AU - Grubmuller H LA - eng PT - Journal Article PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Ligands) RN - 0 (RNA Cap-Binding Proteins) RN - 0 (RNA Caps) RN - 0 (Receptors, Cytoplasmic and Nuclear) RN - 0 (SNUPN protein, human) RN - 0 (Solvents) RN - 059QF0KO0R (Water) SB - IM MH - Entropy MH - Humans MH - Ligands MH - Methylation MH - *Models, Molecular MH - Principal Component Analysis MH - Protein Binding MH - Protein Structure, Secondary MH - RNA Cap-Binding Proteins/*chemistry/*metabolism MH - RNA Caps/*metabolism MH - Receptors, Cytoplasmic and Nuclear/*chemistry/*metabolism MH - Solvents/chemistry/metabolism MH - Water/chemistry/metabolism PMC - PMC2711343 OID - NLM: PMC2711343 EDAT- 2009/07/22 09:00 MHDA- 2009/09/22 06:00 CRDT- 2009/07/22 09:00 PHST- 2008/11/03 [received] PHST- 2009/04/24 [revised] PHST- 2009/04/27 [accepted] AID - S0006-3495(09)00908-4 [pii] AID - 10.1016/j.bpj.2009.04.049 [doi] PST - ppublish SO - Biophys J. 2009 Jul 22;97(2):581-9. doi: 10.1016/j.bpj.2009.04.049. PMID- 24021023 OWN - NLM STAT- MEDLINE DA - 20140204 DCOM- 20141008 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 43 DP - 2013 Oct 30 TI - Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation. PG - 16092-101 LID - 10.1021/ja403147m [doi] AB - Amyloid fibril deposits of the intrinsically disordered hIAPP peptide are found in 95% of type II diabetes patients, and the aggregation of this peptide is suggested to induce apoptotic cell-death in insulin-producing beta-cells. Understanding the structure and dynamics of the hIAPP monomer in solution is thus important for understanding the nucleation of aggregation and the formation of oligomers. In this study, we identify the metastable conformational states of the hIAPP monomer and the dynamics of transitioning between them using Markov state models constructed from extensive molecular dynamics simulations. We show that the overall structure of the hIAPP peptide is random coil-like and lacks a dominant folded structure. Despite this fact, our model reveals a large number of reasonably well-populated metastable conformational states (or local free energy minima) having populations of a few percent or less. The time scales for transitioning between these states range from several microseconds to milliseconds. In contrast to folded proteins, there is no kinetic hub. More strikingly, a few states contain significant amounts of beta-hairpin secondary structure and extended hydrophobic surfaces that are exposed to the solvent. We propose that these states may facilitate the nucleation of hIAPP aggregation through a significant component of the conformational selection mechanism, because they may increase their populations upon aggregation by promoting hydrophobic interactions and at the same time provide a flat geometry to seed the ordered beta-strand packing of the fibrils. FAU - Qiao, Qin AU - Qiao Q AD - Bioengineering Graduate Program, Division of Biomedical Engineering, double daggerDepartment of Chemistry, section signCenter of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong. FAU - Bowman, Gregory R AU - Bowman GR FAU - Huang, Xuhui AU - Huang X LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131017 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Amyloid beta-Protein Precursor) RN - 0 (Proteins) RN - 0 (Solvents) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Amyloid beta-Protein Precursor/chemistry MH - Humans MH - Kinetics MH - Markov Chains MH - Molecular Sequence Data MH - *Protein Conformation MH - Proteins/*chemistry MH - Reproducibility of Results MH - Solvents MH - Temperature MH - Thermodynamics EDAT- 2013/09/12 06:00 MHDA- 2014/10/09 06:00 CRDT- 2013/09/12 06:00 PHST- 2013/10/17 [aheadofprint] AID - 10.1021/ja403147m [doi] PST - ppublish SO - J Am Chem Soc. 2013 Oct 30;135(43):16092-101. doi: 10.1021/ja403147m. Epub 2013 Oct 17. PMID- 17360435 OWN - NLM STAT- MEDLINE DA - 20070315 DCOM- 20070424 LR - 20140907 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 104 IP - 10 DP - 2007 Mar 6 TI - Cell-cycle-dependent phosphorylation of the nuclear pore Nup107-160 subcomplex. PG - 3811-6 AB - The nuclear pore complex (NPC) mediates macromolecular transport between the nucleus and the cytoplasm. Many NPC proteins (nucleoporins, Nups) are modified by phosphorylation. It is believed that phosphorylation regulates the breakdown of the nuclear envelope at mitosis and the disassembly of the NPC into different subcomplexes. In this study, we examined the cell-cycle-dependent phosphorylation of the Nup107-160 subcomplex, a core building block of the NPC. Using in vivo (32)P labeling in HeLa cells, we found that Nup107, Nup96, and Nup133 are phosphorylated during mitosis. To precisely map the phosphorylation sites within the complex, we used a comprehensive multiple-stage MS approach (MS, MS(2), and MS(3)), establishing that Nup160, Nup133, Nup96, and Nup107 are all targets of phosphorylation. We determined that the phosphorylation sites are clustered mainly at the N-terminal regions of these proteins, which are predicted to be natively disordered. In addition, we determined the cell-cycle dependence of the phosphorylation of these sites by using stable isotope labeling and MS(2) analysis. Measurement of the site-specific phosphorylation ratios between mitotic and G(1) cells led us to conclude that several phosphorylation events of the subcomplex are mainly mitotic. Based on these results and our finding that the entire Nup107-160 subcomplex is stable throughout the cell cycle, we propose that phosphorylation does not affect interactions within the Nup107-160 subcomplex, but regulates the association of the subcomplex with the NPC and other proteins. FAU - Glavy, Joseph S AU - Glavy JS AD - Laboratories of Mass Spectrometry and Gaseous Ion Chemistry, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. FAU - Krutchinsky, Andrew N AU - Krutchinsky AN FAU - Cristea, Ileana M AU - Cristea IM FAU - Berke, Ian C AU - Berke IC FAU - Boehmer, Thomas AU - Boehmer T FAU - Blobel, Gunter AU - Blobel G FAU - Chait, Brian T AU - Chait BT LA - eng GR - 5F32 GN 20520/PHS HHS/United States GR - RR 00862/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070228 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (NUP107 protein, human) RN - 0 (NUP160 protein, human) RN - 0 (Nuclear Pore Complex Proteins) RN - 0 (Nuclear Proteins) SB - IM MH - Amino Acid Sequence MH - *Cell Cycle MH - Cell Nucleus/metabolism MH - Cytoplasm/metabolism MH - HeLa Cells MH - Humans MH - Mass Spectrometry MH - Mitosis MH - Molecular Sequence Data MH - Nuclear Pore/*chemistry MH - Nuclear Pore Complex Proteins/chemistry/*physiology MH - Nuclear Proteins/chemistry/*physiology MH - Phosphorylation MH - Protein Binding MH - Protein Structure, Tertiary PMC - PMC1820666 OID - NLM: PMC1820666 EDAT- 2007/03/16 09:00 MHDA- 2007/04/25 09:00 CRDT- 2007/03/16 09:00 PHST- 2007/02/28 [aheadofprint] AID - 0700058104 [pii] AID - 10.1073/pnas.0700058104 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3811-6. Epub 2007 Feb 28. PMID- 18366598 OWN - NLM STAT- MEDLINE DA - 20080327 DCOM- 20080602 LR - 20140904 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 9 Suppl 1 DP - 2008 TI - Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. PG - S1 LID - 10.1186/1471-2164-9-S1-S1 [doi] AB - BACKGROUND: Proteins are involved in many interactions with other proteins leading to networks that regulate and control a wide variety of physiological processes. Some of these proteins, called hub proteins or hubs, bind to many different protein partners. Protein intrinsic disorder, via diversity arising from structural plasticity or flexibility, provide a means for hubs to associate with many partners (Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN: Flexible Nets: The roles of intrinsic disorder in protein interaction networks. FEBS J 2005, 272:5129-5148). RESULTS: Here we present a detailed examination of two divergent examples: 1) p53, which uses different disordered regions to bind to different partners and which also has several individual disordered regions that each bind to multiple partners, and 2) 14-3-3, which is a structured protein that associates with many different intrinsically disordered partners. For both examples, three-dimensional structures of multiple complexes reveal that the flexibility and plasticity of intrinsically disordered protein regions as well as induced-fit changes in the structured regions are both important for binding diversity. CONCLUSIONS: These data support the conjecture that hub proteins often utilize intrinsic disorder to bind to multiple partners and provide detailed information about induced fit in structured regions. FAU - Oldfield, Christopher J AU - Oldfield CJ AD - Center for Computational Biology and Bioinformatics, Indiana University Schools of Medicine and Informatics, 410 W, 10th Street, Indianapolis, IN 46202, USA. cjoldfie@iupui.edu FAU - Meng, Jingwei AU - Meng J FAU - Yang, Jack Y AU - Yang JY FAU - Yang, Mary Qu AU - Yang MQ FAU - Uversky, Vladimir N AU - Uversky VN FAU - Dunker, A Keith AU - Dunker AK LA - eng GR - GM071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 LM007688-01A1/LM/NLM NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 RN - 0 (14-3-3 Proteins) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - 14-3-3 Proteins/genetics/*metabolism MH - *Models, Molecular MH - *Protein Binding MH - *Protein Conformation MH - Signal Transduction/*genetics MH - Tumor Suppressor Protein p53/genetics/*metabolism PMC - PMC2386051 OID - NLM: PMC2386051 EDAT- 2008/04/17 09:00 MHDA- 2008/06/03 09:00 CRDT- 2008/04/17 09:00 PHST- 2008/03/20 [ppublish] AID - 1471-2164-9-S1-S1 [pii] AID - 10.1186/1471-2164-9-S1-S1 [doi] PST - ppublish SO - BMC Genomics. 2008;9 Suppl 1:S1. doi: 10.1186/1471-2164-9-S1-S1. PMID- 18649183 OWN - NLM STAT- MEDLINE DA - 20080723 DCOM- 20081006 LR - 20140917 IS - 1543-5180 (Electronic) IS - 1543-5180 (Linking) VI - 15 IP - 1 DP - 2008 May TI - Structural changes in the carboxyl terminus of the gap junction protein connexin 40 caused by the interaction with c-Src and zonula occludens-1. PG - 107-18 LID - 10.1080/15419060802014347 [doi] AB - c-Src can disrupt the connexin 43 (Cx43) and zonula occludens-1 (ZO-1) interaction, leading to down-regulation of gap junction intercellular communication. Previously, the authors characterized the interaction of domains from these proteins with the carboxyl terminus of Cx43 (Cx43CT) and found that binding of the c-Src SH3 domain to Cx43CT disrupted the Cx43CT/ZO-1 PDZ-2 domain complex. Because Cx43 and Cx40 form heteromeric connexons and display similar mechanisms of pH regulation, the authors addressed whether Cx40CT interacts with these domains in a similar manner as Cx43CT. Nuclear magnetic resonance (NMR) data indicate that Cx40CT is an intrinsically disordered protein. NMR titrations determined that PDZ-2 affected the last 28 Cx40CT residues and SH3 shifted numerous amino-terminal Cx40CT residues. Finally, the Cx40CT/PDZ-2 complex was unaffected by SH3 and both domains interacted simultaneously with Cx40CT. This result differs from when the same experiment was performed with Cx43CT, suggesting different mechanisms of regulation exist between connexin isoforms, even when involving the same molecular partners. FAU - Bouvier, Denis AU - Bouvier D AD - Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA. FAU - Kieken, Fabien AU - Kieken F FAU - Kellezi, Admir AU - Kellezi A FAU - Sorgen, Paul L AU - Sorgen PL LA - eng GR - GM072631/GM/NIGMS NIH HHS/United States GR - R01 GM072631/GM/NIGMS NIH HHS/United States GR - R01 GM072631-05/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Cell Commun Adhes JT - Cell communication & adhesion JID - 101096596 RN - 0 (Connexins) RN - 0 (Membrane Proteins) RN - 0 (Phosphoproteins) RN - 0 (Zonula Occludens-1 Protein) RN - 0 (connexin 40) RN - EC 2.7.10.2 (Proto-Oncogene Proteins pp60(c-src)) SB - IM MH - Amino Acid Sequence MH - Connexins/*chemistry/genetics/*metabolism MH - Magnetic Resonance Spectroscopy MH - Membrane Proteins/*metabolism MH - Molecular Sequence Data MH - Phosphoproteins/*metabolism MH - Proto-Oncogene Proteins pp60(c-src)/*metabolism MH - Tight Junctions/metabolism MH - Zonula Occludens-1 Protein PMC - PMC2917908 MID - NIHMS219062 OID - NLM: NIHMS219062 OID - NLM: PMC2917908 EDAT- 2008/07/24 09:00 MHDA- 2008/10/07 09:00 CRDT- 2008/07/24 09:00 AID - 795238999 [pii] AID - 10.1080/15419060802014347 [doi] PST - ppublish SO - Cell Commun Adhes. 2008 May;15(1):107-18. doi: 10.1080/15419060802014347. PMID- 12022860 OWN - NLM STAT- MEDLINE DA - 20020522 DCOM- 20020626 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 41 IP - 21 DP - 2002 May 28 TI - Intrinsic disorder and protein function. PG - 6573-82 FAU - Dunker, A Keith AU - Dunker AK AD - School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA. dunker@disorder.chem.wsu.edu FAU - Brown, Celeste J AU - Brown CJ FAU - Lawson, J David AU - Lawson JD FAU - Iakoucheva, Lilia M AU - Iakoucheva LM FAU - Obradovic, Zoran AU - Obradovic Z LA - eng GR - 1R01-LM-06916/LM/NLM NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Apoproteins) RN - 0 (Clusterin) RN - 0 (Cytochrome c Group) RN - 0 (Glycoproteins) RN - 0 (Molecular Chaperones) RN - 0 (Proteins) RN - 9007-43-6 (Cytochromes c) RN - EC 3.6.4.- (DNA Helicases) SB - IM MH - Apoproteins/chemistry/physiology MH - Clusterin MH - Computational Biology/methods MH - Cytochrome c Group/chemistry/physiology MH - Cytochromes c MH - DNA Helicases/chemistry/physiology MH - Glycoproteins/chemistry/physiology MH - Molecular Chaperones/chemistry/physiology MH - Molecular Structure MH - *Protein Folding MH - Proteins/*chemistry/classification/physiology MH - Structure-Activity Relationship EDAT- 2002/05/23 10:00 MHDA- 2002/06/27 10:01 CRDT- 2002/05/23 10:00 PST - ppublish SO - Biochemistry. 2002 May 28;41(21):6573-82. PMID- 22438319 OWN - NLM STAT- MEDLINE DA - 20120411 DCOM- 20121022 IS - 1439-7633 (Electronic) IS - 1439-4227 (Linking) VI - 13 IP - 6 DP - 2012 Apr 16 TI - Hunting the chameleon: structural conformations of the intrinsically disordered protein alpha-synuclein. PG - 761-8 LID - 10.1002/cbic.201200059 [doi] FAU - Drescher, Malte AU - Drescher M AD - Department of Chemistry, Konstanz Research School Chemical Biology and Zukunftskolleg, University of Konstanz, 78457 Konstanz, Germany. malte.drescher@uni-konstanz.de FAU - Huber, Martina AU - Huber M FAU - Subramaniam, Vinod AU - Subramaniam V LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20120321 PL - Germany TA - Chembiochem JT - Chembiochem : a European journal of chemical biology JID - 100937360 RN - 0 (alpha-Synuclein) SB - IM MH - Humans MH - Protein Conformation MH - alpha-Synuclein/*chemistry EDAT- 2012/03/23 06:00 MHDA- 2012/10/23 06:00 CRDT- 2012/03/23 06:00 PHST- 2012/01/23 [received] PHST- 2012/03/21 [aheadofprint] AID - 10.1002/cbic.201200059 [doi] PST - ppublish SO - Chembiochem. 2012 Apr 16;13(6):761-8. doi: 10.1002/cbic.201200059. Epub 2012 Mar 21. PMID- 20453932 OWN - NLM STAT- MEDLINE DA - 20100510 DCOM- 20100928 IS - 1208-6002 (Electronic) IS - 0829-8211 (Linking) VI - 88 IP - 2 DP - 2010 Apr TI - Structure and dynamics changes induced by 2,2,2-trifluoro-ethanol (TFE) on the N-terminal half of hepatitis C virus core protein. PG - 315-23 LID - 10.1139/o09-155 [doi] AB - The Core protein of hepatitis C virus is involved in several interactions other than the encapsidation of viral RNA. We recently proposed that this is related to the fact that the N-terminal half of this protein (C82) is an intrinsically unstructured protein (IUP) domain. IUP domains can adopt a secondary structure when they are interacting with another molecule, such as a nucleic acid or a protein. It is also possible to mimic these conditions by modifying the environment of the protein. We investigated the propensity of this protein to fold as a function of salt concentration, detergent, pH, and 2,2,2-trifluoro-ethanol (TFE); only the addition of TFE resulted in a structural change. The effect of TFE addition was studied by circular dichroism, structural, and dynamic data obtained by NMR. The data indicate that C82 can adopt an alpha-helical structure; this conformation is likely relevant to one of the functional roles of the HCV Core protein. FAU - Duvignaud, Jean-Baptiste AU - Duvignaud JB AD - PROTEO and Department of Biochemistry and Microbiology, Pavillon C-E MARCHAND, Universite Laval, 1030 avenue de Medecine, Local 3255, Quebec, QC G1V 0A6, Canada. jean-baptiste.duvignaud.1@ulaval.ca FAU - Leclerc, Denis AU - Leclerc D FAU - Gagne, Stephane M AU - Gagne SM LA - eng GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Canada TA - Biochem Cell Biol JT - Biochemistry and cell biology = Biochimie et biologie cellulaire JID - 8606068 RN - 0 (Detergents) RN - 0 (Viral Core Proteins) RN - 0 (nucleocapsid protein, Hepatitis C virus) RN - 75-89-8 (Trifluoroethanol) SB - IM MH - Detergents/pharmacology MH - Hydrogen-Ion Concentration MH - Magnetic Resonance Spectroscopy MH - Protein Conformation/drug effects MH - Trifluoroethanol/*pharmacology MH - Viral Core Proteins/*chemistry/isolation & purification EDAT- 2010/05/11 06:00 MHDA- 2010/09/30 06:00 CRDT- 2010/05/11 06:00 AID - o09-155 [pii] AID - 10.1139/o09-155 [doi] PST - ppublish SO - Biochem Cell Biol. 2010 Apr;88(2):315-23. doi: 10.1139/o09-155. PMID- 2040607 OWN - NLM STAT- MEDLINE DA - 19910710 DCOM- 19910710 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 266 IP - 17 DP - 1991 Jun 15 TI - Expression in Escherichia coli and characterization of the heat-stable inhibitor of the cAMP-dependent protein kinase. PG - 10906-11 AB - Pure heat-stable inhibitor of the cAMP-dependent protein kinase (PKI) has been isolated in high yield by using a bacterial expression vector constructed to synthesize the complete sequence of the rabbit muscle protein kinase inhibitor, plus an amino-terminal initiator methionine and glycine. Bacterially expressed PKI has an inhibitory activity identical to that of the protein isolated from rabbit skeletal muscle and, by gel filtration and gel electrophoresis, has the same physicochemical characteristics as the native physiological form of PKI. Fourier transformed infrared spectroscopy and CD establish that PKI has unusually large amounts of random coil and turn structures, with significantly smaller amounts of alpha-helix and beta structures. FAU - Thomas, J AU - Thomas J AD - Department of Physiology and Biophysics, University of Iowa, Iowa City 52242. FAU - Van Patten, S M AU - Van Patten SM FAU - Howard, P AU - Howard P FAU - Day, K H AU - Day KH FAU - Mitchell, R D AU - Mitchell RD FAU - Sosnick, T AU - Sosnick T FAU - Trewhella, J AU - Trewhella J FAU - Walsh, D A AU - Walsh DA FAU - Maurer, R A AU - Maurer RA LA - eng GR - AM21019/AM/NIADDK NIH HHS/United States GR - AM25295/AM/NIADDK NIH HHS/United States GR - HL14388/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Carrier Proteins) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Protein Kinase Inhibitors) RN - 0 (Recombinant Proteins) RN - 0 (protein kinase modulator) SB - IM MH - Animals MH - Carrier Proteins/chemistry/*genetics/isolation & purification MH - Circular Dichroism MH - Escherichia coli/*genetics MH - Genetic Vectors MH - *Intracellular Signaling Peptides and Proteins MH - Muscles/enzymology MH - Plasmids MH - Protein Conformation MH - Protein Kinase Inhibitors MH - Rabbits MH - Recombinant Proteins/chemistry/isolation & purification MH - Restriction Mapping MH - Spectrophotometry EDAT- 1991/06/15 MHDA- 1991/06/15 00:01 CRDT- 1991/06/15 00:00 PST - ppublish SO - J Biol Chem. 1991 Jun 15;266(17):10906-11. PMID- 6751823 OWN - NLM STAT- MEDLINE DA - 19821216 DCOM- 19821216 LR - 20081121 IS - 0014-2956 (Print) IS - 0014-2956 (Linking) VI - 126 IP - 2 DP - 1982 Aug TI - Optical characteristics of all individual proteins from the small subunit of Escherichia coli ribosomes. PG - 299-309 AB - The procedure of isolation and renaturation of all ribosomal proteins from the 30-S subunit of Escherichia coli ribosomes is described. Absorption spectra of these proteins in the near-ultraviolet region have been measured and molar absorption coefficients have been determined on the basis of nitrogen content. Molar absorption coefficients have been calculated for 20 proteins with a known amino acid sequence and the calculated values have been compared with the experimentally determined ones. The absorption spectra obtained allow an easy, precise and highly reproducible spectrophotometric determination of the concentration of individual ribosomal proteins. Circular dichroic spectra of 21 individual proteins from the 30-S subunit of E. coli ribosomes were measured in the range 184-310 nm. The secondary structure of the proteins studied was calculated from the spectra in the range 190-240 nm. Almost all proteins (except proteins S12, S17, S18 and S19) are characterized by a high content of secondary structure. Circular dichroic spectra in the near-ultraviolet region (240-310 nm) indicate that the side groups of aromatic amino acids are fixed in the tertiary structure of the proteins studied. Some internal characteristics (independent of the measurement conditions) of the circular dichroic spectrum in the far-ultraviolet region were proposed as a measure of the resemblance to the native state of ribosomal proteins; these characteristics may be useful for comparison of protein preparations obtained by different methods in different laboratories. FAU - Venyaminov, S Y AU - Venyaminov SY FAU - Gogia, Z V AU - Gogia ZV LA - eng PT - Journal Article PL - GERMANY, WEST TA - Eur J Biochem JT - European journal of biochemistry / FEBS JID - 0107600 RN - 0 (Amino Acids) RN - 0 (Bacterial Proteins) RN - 0 (Ribosomal Proteins) SB - IM MH - Amino Acids/analysis MH - Bacterial Proteins/*isolation & purification MH - Chemical Phenomena MH - Chemistry MH - Circular Dichroism MH - Escherichia coli/*metabolism MH - Ribosomal Proteins/*isolation & purification MH - Spectrophotometry, Ultraviolet EDAT- 1982/08/01 MHDA- 1982/08/01 00:01 CRDT- 1982/08/01 00:00 PST - ppublish SO - Eur J Biochem. 1982 Aug;126(2):299-309. PMID- 2181148 OWN - NLM STAT- MEDLINE DA - 19900510 DCOM- 19900510 LR - 20071114 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 212 IP - 2 DP - 1990 Mar 20 TI - Crystallization of the globular domain of histone H5. PG - 253-7 AB - The globular domain of histone H1/H5 binds to the nucleosome and is crucial for the formation of chromatin higher order structure. We have expressed in Escherichia coli a gene that codes for the globular domain of H5. The protein produced in E. coli is functional in nucleosome binding assays. We have obtained crystals of the protein that diffract to beyond 2.5 A (1 A = 0.1 nm) resolution. The crystals are orthorhombic with unit cell dimensions of a = 80.1 A, b = 67.5 A and c = 38.0 A. FAU - Graziano, V AU - Graziano V AD - Biology Department, Brookhaven National Laboratory, Upton, NY 11973. FAU - Gerchman, S E AU - Gerchman SE FAU - Wonacott, A J AU - Wonacott AJ FAU - Sweet, R M AU - Sweet RM FAU - Wells, J R AU - Wells JR FAU - White, S W AU - White SW FAU - Ramakrishnan, V AU - Ramakrishnan V LA - eng GR - GM 42796/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Histones) RN - 0 (Nucleosomes) SB - IM MH - Crystallization MH - Escherichia coli/*genetics MH - Gene Expression MH - *Histones/genetics/isolation & purification/metabolism MH - Nucleosomes/metabolism MH - Protein Conformation MH - X-Ray Diffraction EDAT- 1990/03/20 MHDA- 1990/03/20 00:01 CRDT- 1990/03/20 00:00 AID - 0022-2836(90)90122-3 [pii] AID - 10.1016/0022-2836(90)90122-3 [doi] PST - ppublish SO - J Mol Biol. 1990 Mar 20;212(2):253-7. PMID- 10821677 OWN - NLM STAT- MEDLINE DA - 20000621 DCOM- 20000621 LR - 20071115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 39 IP - 20 DP - 2000 May 23 TI - Human CC chemokine I-309, structural consequences of the additional disulfide bond. PG - 6053-9 AB - I-309 is a member of the CC subclass of chemokines and is one of only three human chemokines known to contain an additional, third disulfide bond. The three-dimensional solution structure of I-309 was determined by (1)H nuclear magnetic resonance spectroscopy and dynamic simulated annealing. The structure of I-309, which remains monomeric at high concentrations, was determined on the basis of 978 experimental restraints. The N-terminal region of I-309 was disordered, as has been previously observed for the CC chemokine eotaxin but not others such as MCP-1 and RANTES. This was followed in I-309 by a well-ordered region between residues 13 and 69 that consisted of a 3(10)-helix, a triple-stranded antiparallel beta-sheet, and finally a C-terminal alpha-helix. Root-mean-square deviations of 0.61 and 1.16 were observed for the backbone and heavy atoms, respectively. A comparison of I-309 to eotaxin and HCC-2 revealed a significant structural change in the C-terminal region of the protein. The alpha-helix normally present in chemokines was terminated early and was followed by a short section of extended strand. These changes were a direct result of the additional disulfide bond present in this protein. An examination of the I-309 structure will aid in an understanding of the specificity of this protein with its receptor, CCR8. FAU - Keizer, D W AU - Keizer DW AD - Protein Engineering Network Centres of Excellence (PENCE) and Department of Biochemistry, 713 Heritage Medical Research Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2S2. FAU - Crump, M P AU - Crump MP FAU - Lee, T W AU - Lee TW FAU - Slupsky, C M AU - Slupsky CM FAU - Clark-Lewis, I AU - Clark-Lewis I FAU - Sykes, B D AU - Sykes BD LA - eng SI - PDB/1ELO PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (CCL1 protein, human) RN - 0 (CCL15 protein, human) RN - 0 (Chemokine CCL1) RN - 0 (Chemokines, CC) RN - 0 (Disulfides) RN - 0 (Macrophage Inflammatory Proteins) RN - 0 (Monokines) RN - 0 (Peptide Fragments) RN - 0 (Solutions) SB - IM MH - Amino Acid Sequence MH - Chemokine CCL1 MH - Chemokines, CC/*chemistry MH - Crystallography, X-Ray MH - Dimerization MH - Disulfides/*chemistry MH - Humans MH - Macrophage Inflammatory Proteins MH - Models, Molecular MH - Molecular Sequence Data MH - *Monokines MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemistry MH - Protein Structure, Secondary MH - Solutions MH - Structure-Activity Relationship EDAT- 2000/05/23 09:00 MHDA- 2000/06/24 11:00 CRDT- 2000/05/23 09:00 AID - bi000089l [pii] PST - ppublish SO - Biochemistry. 2000 May 23;39(20):6053-9. PMID- 14534311 OWN - NLM STAT- MEDLINE DA - 20040112 DCOM- 20040212 LR - 20101118 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 3 DP - 2004 Jan 16 TI - Bcl-XL mutations suppress cellular sensitivity to antimycin A. PG - 2159-65 AB - Cells expressing high levels of the BCL-X(L) anti-apoptotic protein are preferentially killed by the mitochondrial inhibitor antimycin A (AA). Computational modeling predicts a binding site for AA in the extended hydrophobic groove on BCL-X(L), previously identified as an interface for dimerization to BAX and related proapoptotic proteins. Here, we identify BCL-X(L) hydrophobic groove mutants with normal cellular anti-apoptotic function but suppressed sensitivity to AA. The LD(50) of AA for cells expressing BCL-X(L) mutants directly correlates with the measured in vitro dissociation constants for AA binding. These results indicate that BCL-X(L) is a principal target mediating AA cytotoxicity. FAU - Manion, Michael K AU - Manion MK AD - Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. FAU - O'Neill, Jason W AU - O'Neill JW FAU - Giedt, Chris D AU - Giedt CD FAU - Kim, Kristine M AU - Kim KM FAU - Zhang, Kam Y Z AU - Zhang KY FAU - Hockenbery, David M AU - Hockenbery DM LA - eng GR - 5U01 CA 91310/CA/NCI NIH HHS/United States GR - T32 CA 80416/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20031008 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Proto-Oncogene Proteins c-bcl-2) RN - 0 (bcl-X Protein) RN - 642-15-9 (Antimycin A) SB - IM MH - Amino Acid Sequence MH - Antimycin A/*pharmacology MH - Binding Sites MH - Cell Survival/drug effects MH - Hydrophobic and Hydrophilic Interactions MH - Molecular Sequence Data MH - Point Mutation MH - Protein Folding MH - Proto-Oncogene Proteins c-bcl-2/*chemistry/physiology MH - bcl-X Protein EDAT- 2003/10/10 05:00 MHDA- 2004/02/13 05:00 CRDT- 2003/10/10 05:00 PHST- 2003/10/08 [aheadofprint] AID - 10.1074/jbc.M306021200 [doi] AID - M306021200 [pii] PST - ppublish SO - J Biol Chem. 2004 Jan 16;279(3):2159-65. Epub 2003 Oct 8. PMID- 23318954 OWN - NLM STAT- MEDLINE DA - 20130304 DCOM- 20130430 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 425 IP - 6 DP - 2013 Mar 25 TI - Fuzzy complex formation between the intrinsically disordered prothymosin alpha and the Kelch domain of Keap1 involved in the oxidative stress response. PG - 1011-27 LID - 10.1016/j.jmb.2013.01.005 [doi] LID - S0022-2836(13)00008-9 [pii] AB - Kelch-like ECH-associated protein 1 (Keap1) is an inhibitor of nuclear factor erythroid 2-related factor 2 (Nrf2), a key transcription factor for cytoprotective gene activation in the oxidative stress response. Under unstressed conditions, Keap1 interacts with Nrf2 in the cytoplasm via its Kelch domain and suppresses the transcriptional activity of Nrf2. During oxidative stress, Nrf2 is released from Keap1 and is translocated into the nucleus, where it interacts with the small Maf protein to initiate gene transcription. Prothymosin alpha (ProTalpha), an intrinsically disordered protein, also interacts with the Kelch domain of Keap1 and mediates the import of Keap1 into the nucleus to inhibit Nrf2 activity. To gain a molecular basis understanding of the oxidative stress response mechanism, we have characterized the interaction between ProTalpha and the Kelch domain of Keap1 by using nuclear magnetic resonance spectroscopy, isothermal titration calorimetry, peptide array analysis, site-directed mutagenesis, and molecular dynamic simulations. The results of nuclear magnetic resonance chemical shift mapping, amide hydrogen exchange, and spin relaxation measurements revealed that ProTalpha retains a high level of flexibility, even in the bound state with Kelch. This finding is in agreement with the observations from the molecular dynamic simulations of the ProTalpha-Kelch complex. Mutational analysis of ProTalpha, guided by peptide array data and isothermal titration calorimetry, further pinpointed that the region (38)NANEENGE(45) of ProTalpha is crucial for the interaction with the Kelch domain, while the flanking residues play relatively minor roles in the affinity of binding. CI - Copyright (c) 2013 Elsevier Ltd. All rights reserved. FAU - Khan, Halema AU - Khan H AD - Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1. FAU - Cino, Elio A AU - Cino EA FAU - Brickenden, Anne AU - Brickenden A FAU - Fan, Jingsong AU - Fan J FAU - Yang, Daiwen AU - Yang D FAU - Choy, Wing-Yiu AU - Choy WY LA - eng GR - MOP no. 74679/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130111 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (KEAP1 protein, human) RN - 0 (Protein Precursors) RN - 0 (prothymosin alpha) RN - 61512-21-8 (Thymosin) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Cell Nucleus/metabolism MH - Humans MH - Intracellular Signaling Peptides and Proteins/*chemistry/metabolism MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - *Oxidative Stress MH - Protein Interaction Domains and Motifs MH - Protein Precursors/*chemistry/metabolism MH - Protein Structure, Tertiary MH - Thymosin/*analogs & derivatives/chemistry/metabolism EDAT- 2013/01/16 06:00 MHDA- 2013/05/01 06:00 CRDT- 2013/01/16 06:00 PHST- 2012/09/14 [received] PHST- 2012/12/04 [revised] PHST- 2013/01/03 [accepted] PHST- 2013/01/11 [aheadofprint] AID - S0022-2836(13)00008-9 [pii] AID - 10.1016/j.jmb.2013.01.005 [doi] PST - ppublish SO - J Mol Biol. 2013 Mar 25;425(6):1011-27. doi: 10.1016/j.jmb.2013.01.005. Epub 2013 Jan 11. PMID- 24550393 OWN - NLM STAT- MEDLINE DA - 20140407 DCOM- 20140530 LR - 20150420 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 289 IP - 14 DP - 2014 Apr 4 TI - Conformational transitions of the cross-linking domains of elastin during self-assembly. PG - 10057-68 LID - 10.1074/jbc.M113.533893 [doi] AB - Elastin is the intrinsically disordered polymeric protein imparting the exceptional properties of extension and elastic recoil to the extracellular matrix of most vertebrates. The monomeric precursor of elastin, tropoelastin, as well as polypeptides containing smaller subsets of the tropoelastin sequence, can self-assemble through a colloidal phase separation process called coacervation. Present understanding suggests that self-assembly is promoted by association of hydrophobic domains contained within the tropoelastin sequence, whereas polymerization is achieved by covalent joining of lysine side chains within distinct alanine-rich, alpha-helical cross-linking domains. In this study, model elastin polypeptides were used to determine the structure of cross-linking domains during the assembly process and the effect of sequence alterations in these domains on assembly and structure. CD temperature melts indicated that partial alpha-helical structure in cross-linking domains at lower temperatures was absent at physiological temperature. Solid-state NMR demonstrated that beta-strand structure of the cross-linking domains dominated in the coacervate state, although alpha-helix was predominant after subsequent cross-linking of lysine side chains with genipin. Mutation of lysine residues to hydrophobic amino acids, tyrosine or alanine, leads to increased propensity for beta-structure and the formation of amyloid-like fibrils, characterized by thioflavin-T binding and transmission electron microscopy. These findings indicate that cross-linking domains are structurally labile during assembly, adapting to changes in their environment and aggregated state. Furthermore, the sequence of cross-linking domains has a dramatic effect on self-assembly properties of elastin-like polypeptides, and the presence of lysine residues in these domains may serve to prevent inappropriate ordered aggregation. FAU - Reichheld, Sean E AU - Reichheld SE AD - From the Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 and. FAU - Muiznieks, Lisa D AU - Muiznieks LD FAU - Stahl, Richard AU - Stahl R FAU - Simonetti, Karen AU - Simonetti K FAU - Sharpe, Simon AU - Sharpe S FAU - Keeley, Fred W AU - Keeley FW LA - eng GR - MOP111145/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140218 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Tropoelastin) SB - IM MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Tropoelastin/*chemistry/genetics/metabolism PMC - PMC3974977 OID - NLM: PMC3974977 OTO - NOTNLM OT - Amyloid OT - Cross-linking Domain OT - Elastin OT - Extracellular Matrix OT - Protein Self-assembly OT - Protein Structure EDAT- 2014/02/20 06:00 MHDA- 2014/05/31 06:00 CRDT- 2014/02/20 06:00 PHST- 2014/02/18 [aheadofprint] AID - M113.533893 [pii] AID - 10.1074/jbc.M113.533893 [doi] PST - ppublish SO - J Biol Chem. 2014 Apr 4;289(14):10057-68. doi: 10.1074/jbc.M113.533893. Epub 2014 Feb 18. PMID- 15157097 OWN - NLM STAT- MEDLINE DA - 20040525 DCOM- 20040816 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 21 DP - 2004 Jun 1 TI - Structural analysis of botulinum neurotoxin type E catalytic domain and its mutant Glu212-->Gln reveals the pivotal role of the Glu212 carboxylate in the catalytic pathway. PG - 6637-44 AB - The seven serotypes of botulinum neurotoxins (A-G) produced by Clostridium botulinum share significant sequence homology and structural similarity. The functions of their individual domains and the modes of action are also similar. However, the substrate specificity and the peptide bond cleavage selectivity of their catalytic domains are different. The reason for this unique specificity of botulinum neurotoxins is still baffling. If an inhibitor leading to a therapeutic drug common to all serotypes is to be developed, it is essential to understand the differences in their three-dimensional structures that empower them with this unique characteristic. Accordingly, high-resolution structures of all serotypes are required, and toward achieving this goal the crystal structure of the catalytic domain of C. botulinum neurotoxin type E has been determined to 2.1 A resolution. The crystal structure of the inactive mutant Glu212-->Gln of this protein has also been determined. While the overall conformation is unaltered in the active site, the position of the nucleophilic water changes in the mutant, thereby causing it to lose its ability to activate the catalytic reaction. The structure explains the importance of the nucleophilic water and the charge on Glu212. The structural differences responsible for the loss of activity of the mutant provide a common model for the catalytic pathway of Clostridium neurotoxins since Glu212 is conserved and has a similar role in all serotypes. This or a more nonconservative mutant (e.g., Glu212-->Ala) could provide a novel, genetically modified protein vaccine for botulinum. FAU - Agarwal, Rakhi AU - Agarwal R AD - Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA. FAU - Eswaramoorthy, Subramaniam AU - Eswaramoorthy S FAU - Kumaran, Desigan AU - Kumaran D FAU - Binz, Thomas AU - Binz T FAU - Swaminathan, Subramanyam AU - Swaminathan S LA - eng SI - PDB/1T3A SI - PDB/1T3C PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (botulinum toxin type E) RN - 0RH81L854J (Glutamine) RN - 3KX376GY7L (Glutamic Acid) RN - EC 3.4.24.69 (Botulinum Toxins) SB - IM MH - Amino Acid Sequence MH - Botulinum Toxins/*chemistry/genetics/*metabolism MH - Catalytic Domain MH - Crystallography, X-Ray MH - Glutamic Acid/genetics/metabolism MH - Glutamine/genetics/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - *Point Mutation MH - Protein Conformation MH - Sequence Homology, Amino Acid EDAT- 2004/05/26 05:00 MHDA- 2004/08/18 05:00 CRDT- 2004/05/26 05:00 AID - 10.1021/bi036278w [doi] PST - ppublish SO - Biochemistry. 2004 Jun 1;43(21):6637-44. PMID- 17105200 OWN - NLM STAT- MEDLINE DA - 20061119 DCOM- 20070124 LR - 20071203 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 46 DP - 2006 Nov 21 TI - Tubulin polymerization promoting proteins (TPPPs): members of a new family with distinct structures and functions. PG - 13818-26 AB - TPPP/p25 is a brain-specific protein, which induces tubulin polymerization and microtubule (MT) bundling and is enriched in Lewy bodies characteristic of Parkinson's disease [Tirian et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 13976-13981]. We identified two human gene sequences, CG1-38 and p25beta, which encoded homologous proteins, that we termed p20 and p18, respectively. These homologous proteins display 60% identity with tubulin polymerization promoting protein/p25 (TPPP/p25); however, the N-terminal segment of TPPP/p25 is missing. They could be clustered into three subfamilies present in mammals and other vertebrates. We cloned, isolated, and characterized the structural and functional properties of the recombinant human proteins at molecular, ultrastructural, and cellular levels using a number of tools. These data revealed that, while p20 behaved as a disorganized protein similarly to TPPP/p25, which was described as a flexible and inherently dynamic protein with a long unstructured N-terminal tail, p18 was featured in more ordered fashion. TPPP/p25 and p20 specifically attached to MTs causing MT bundling both in vitro and in vivo; p18 protein did not cross-link MTs, and it distributed homogeneously within the cytosol of the transfected HeLa cells. These data indicate that the two shorter homologues display distinct structural features that determine their associations to MTs. The properties of p20 resemble TPPP/p25. The bundling activity of these two proteins results in the stabilization of the microtubular network, which is likely related to their physiological functions. FAU - Vincze, Orsolya AU - Vincze O AD - Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, H-1113, Hungary. FAU - Tokesi, Natalia AU - Tokesi N FAU - Olah, Judit AU - Olah J FAU - Hlavanda, Emma AU - Hlavanda E FAU - Zotter, Agnes AU - Zotter A FAU - Horvath, Istvan AU - Horvath I FAU - Lehotzky, Attila AU - Lehotzky A FAU - Tirian, Laszlo AU - Tirian L FAU - Medzihradszky, Katalin F AU - Medzihradszky KF FAU - Kovacs, Janos AU - Kovacs J FAU - Orosz, Ferenc AU - Orosz F FAU - Ovadi, Judit AU - Ovadi J LA - eng GR - RR0001614/RR/NCRR NIH HHS/United States GR - RR012961/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA Primers) RN - 0 (Nerve Tissue Proteins) RN - 0 (p25 protein, human) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Circular Dichroism MH - DNA Primers MH - HeLa Cells MH - Humans MH - Hydrolysis MH - Microscopy, Electron MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*chemistry/*physiology/ultrastructure MH - Phylogeny MH - Protein Conformation MH - Sequence Homology, Amino Acid MH - Surface Plasmon Resonance EDAT- 2006/11/16 09:00 MHDA- 2007/01/25 09:00 CRDT- 2006/11/16 09:00 AID - 10.1021/bi061305e [doi] PST - ppublish SO - Biochemistry. 2006 Nov 21;45(46):13818-26. PMID- 19710023 OWN - NLM STAT- MEDLINE DA - 20091019 DCOM- 20091123 LR - 20140828 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 284 IP - 43 DP - 2009 Oct 23 TI - Structure of an arrestin2-clathrin complex reveals a novel clathrin binding domain that modulates receptor trafficking. PG - 29860-72 LID - 10.1074/jbc.M109.023366 [doi] AB - Non-visual arrestins play a pivotal role as adaptor proteins in regulating the signaling and trafficking of multiple classes of receptors. Although arrestin interaction with clathrin, AP-2, and phosphoinositides contributes to receptor trafficking, little is known about the configuration and dynamics of these interactions. Here, we identify a novel interface between arrestin2 and clathrin through x-ray diffraction analysis. The intrinsically disordered clathrin binding box of arrestin2 interacts with a groove between blades 1 and 2 in the clathrin beta-propeller domain, whereas an 8-amino acid splice loop found solely in the long isoform of arrestin2 (arrestin2L) interacts with a binding pocket formed by blades 4 and 5 in clathrin. The apposition of the two binding sites in arrestin2L suggests that they are exclusive and may function in higher order macromolecular structures. Biochemical analysis demonstrates direct binding of clathrin to the splice loop in arrestin2L, whereas functional analysis reveals that both binding domains contribute to the receptor-dependent redistribution of arrestin2L to clathrin-coated pits. Mutagenesis studies reveal that the clathrin binding motif in the splice loop is (L/I)(2)GXL. Taken together, these data provide a framework for understanding the dynamic interactions between arrestin2 and clathrin and reveal an essential role for this interaction in arrestin-mediated endocytosis. FAU - Kang, Dong Soo AU - Kang DS AD - Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA. FAU - Kern, Ronald C AU - Kern RC FAU - Puthenveedu, Manojkumar A AU - Puthenveedu MA FAU - von Zastrow, Mark AU - von Zastrow M FAU - Williams, John C AU - Williams JC FAU - Benovic, Jeffrey L AU - Benovic JL LA - eng SI - PDB/3GC3 SI - PDB/3GD1 GR - DA010711/DA/NIDA NIH HHS/United States GR - GM047417/GM/NIGMS NIH HHS/United States GR - GM068857/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090825 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Arrestin) RN - 0 (Clathrin) RN - 0 (Multiprotein Complexes) SB - IM MH - Amino Acid Motifs MH - Animals MH - Arrestin/*chemistry/genetics/metabolism MH - Cattle MH - Clathrin/*chemistry/genetics/immunology MH - Endocytosis/physiology MH - Multiprotein Complexes/*chemistry/genetics/metabolism MH - Mutagenesis MH - Protein Binding/physiology MH - Protein Structure, Quaternary/physiology MH - Protein Structure, Tertiary/physiology MH - Protein Transport/physiology MH - Structure-Activity Relationship PMC - PMC2785616 OID - NLM: PMC2785616 EDAT- 2009/08/28 09:00 MHDA- 2009/12/16 06:00 CRDT- 2009/08/28 09:00 PHST- 2009/08/25 [aheadofprint] AID - M109.023366 [pii] AID - 10.1074/jbc.M109.023366 [doi] PST - ppublish SO - J Biol Chem. 2009 Oct 23;284(43):29860-72. doi: 10.1074/jbc.M109.023366. Epub 2009 Aug 25. PMID- 16846235 OWN - NLM STAT- MEDLINE DA - 20060718 DCOM- 20060830 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 29 DP - 2006 Jul 25 TI - Intrinsically disordered structure of Bacillus pasteurii UreG as revealed by steady-state and time-resolved fluorescence spectroscopy. PG - 8918-30 AB - UreG is an essential protein for the in vivo activation of urease. In a previous study, UreG from Bacillus pasteurii was shown to behave as an intrinsically unstructured dimeric protein. Here, intrinsic and extrinsic fluorescence experiments were performed, in the absence and presence of denaturant, to provide information about the form (fully folded, molten globule, premolten globule, or random coil) that the native state of BpUreG assumes in solution. The features of the emission band of the unique tryptophan residue (W192) located on the C-terminal helix, as well as the rate of bimolecular quenching by potassium iodide, indicated that, in the native state, W192 is protected from the aqueous polar solvent, while upon addition of denaturant, a conformational change occurs that causes solvent exposure of the indole side chain. This structural change, mainly affecting the C-terminal helix, is associated with the release of static quenching, as shown by resolution of the decay-associated spectra. The exposure of protein hydrophobic sites, monitored using the fluorescent probe bis-ANS, indicated that the native dimeric state of BpUreG is disordered even though it maintains a significant amount of tertiary structure. ANS fluorescence also indicated that, upon addition of a small amount of GuHCl, a transition to a molten globule state occurs, followed by formation of a pre-molten globule state at a higher denaturant concentration. The latter form is resistant to full unfolding, as also revealed by far-UV circular dichroism spectroscopy. The hydrodynamic parameters obtained by time-resolved fluorescence anisotropy at maximal denaturant concentrations (3 M GuHCl) confirmed the existence of a disordered but stable dimeric protein core. The nature of the forces holding together the two monomers of BpUreG was investigated. Determination of free thiols in native or denaturant conditions, as well as light scattering experiments in the absence and presence of dithiothreitol as a reducing agent, under native or denaturing conditions, indicates that a disulfide bond, involving the unique conserved cysteine C68, is present under native conditions and maintained upon addition of denaturant. This covalent bond is therefore important for the stabilization of the dimer under native conditions. The intrinsically disordered structure of UreG is discussed with respect to the role of this protein as a chaperone in the urease assembly system. FAU - Neyroz, Paolo AU - Neyroz P AD - Department of Biochemistry G. Moruzzi, University of Bologna, Via San Donato 19/2, 40127 Bologna, Italy. FAU - Zambelli, Barbara AU - Zambelli B FAU - Ciurli, Stefano AU - Ciurli S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (ureG protein, Bacteria) SB - IM MH - Bacillus/chemistry MH - Bacterial Proteins/*chemistry MH - Carrier Proteins/*chemistry MH - Circular Dichroism MH - Fluorescence Polarization MH - Protein Folding MH - Protein Structure, Tertiary MH - Spectrometry, Fluorescence MH - Thermodynamics EDAT- 2006/07/19 09:00 MHDA- 2006/08/31 09:00 CRDT- 2006/07/19 09:00 AID - 10.1021/bi060227s [doi] PST - ppublish SO - Biochemistry. 2006 Jul 25;45(29):8918-30. PMID- 15735341 OWN - NLM STAT- MEDLINE DA - 20050228 DCOM- 20050901 LR - 20070724 IS - 0907-4449 (Print) IS - 0907-4449 (Linking) VI - 61 IP - Pt 3 DP - 2005 Mar TI - The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase. PG - 309-15 AB - The single-crystal X-ray structure of phosphoglycerate mutase from Mycobacterium tuberculosis has been determined at a resolution of 1.70 angstroms. The C-terminal tail of each of the subunits is flexible and disordered; however, for one of the four chains (chain A) all but five residues of the chain could be modeled. Noteworthy features of the structure include the active site and a proline-rich segment in each monomer forming a short left-handed polyprolyl helix. These segments lie on the enzyme surface and could conceivably participate in protein-protein interactions. FAU - Muller, Peter AU - Muller P AD - UCLA-DOE Institute for Genomics and Proteomics, Howard Hughes Medical Institute, Box 951570, Los Angeles, CA 90095-1570, USA. FAU - Sawaya, Michael R AU - Sawaya MR FAU - Pashkov, Inna AU - Pashkov I FAU - Chan, Sum AU - Chan S FAU - Nguyen, Chau AU - Nguyen C FAU - Wu, Yim AU - Wu Y FAU - Perry, L Jeanne AU - Perry LJ FAU - Eisenberg, David AU - Eisenberg D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050224 PL - Denmark TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (DNA Primers) RN - EC 5.4.2.1 (Phosphoglycerate Mutase) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - DNA Primers MH - Models, Molecular MH - Molecular Sequence Data MH - Mycobacterium tuberculosis/*enzymology MH - Phosphoglycerate Mutase/*chemistry MH - Protein Conformation MH - Protein Folding MH - Sequence Homology, Amino Acid EDAT- 2005/03/01 09:00 MHDA- 2005/09/02 09:00 CRDT- 2005/03/01 09:00 PHST- 2004/07/06 [received] PHST- 2004/12/15 [accepted] PHST- 2005/02/24 [epublish] AID - S0907444904033190 [pii] AID - 10.1107/S0907444904033190 [doi] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):309-15. Epub 2005 Feb 24. PMID- 19634918 OWN - NLM STAT- MEDLINE DA - 20090825 DCOM- 20090921 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 34 DP - 2009 Sep 1 TI - Molecular mechanisms underlying the flavonoid-induced inhibition of alpha-synuclein fibrillation. PG - 8206-24 LID - 10.1021/bi900506b [doi] AB - The molecular mechanism underlying the flavonoid-induced inhibition of alpha-synuclein fibrillation was thoroughly examined by various biochemical and biophysical approaches. The noncovalent binding of the inhibitory flavonoids to alpha-synuclein and the covalent modification by the flavonoid quinone led to the restriction of the conformational changes in this natively unfolded protein and to the stabilization of soluble flavonoid-modified species of alpha-synuclein (monomers and oligomers). All of these factors rather than a single one contribute to the inhibition of WT alpha-synuclein fibrillation induced by the flavonoid. The structural requirements that appear necessary to provide a flavonoid the ability to inhibit alpha-synuclein fibrillation were determined to be vicinal dihydroxyphenyl moieties, irrespective of the ring position where they are located. Flavonoids with three vicinal hydroxyl groups exhibited enhanced inhibitory effects on alpha-synuclein fibrillation. The antioxidant activities of flavonoids were generally correlated with their in vitro inhibitory effects on alpha-synuclein fibrillation. The flavonoids inhibiting alpha-synuclein fibrillation and stabilizing the protein monomeric conformation can serve as a model for the development of therapeutic drugs in combating Parkinson's disease. FAU - Meng, Xiaoyun AU - Meng X AD - Department of Chemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA. FAU - Munishkina, Larissa A AU - Munishkina LA FAU - Fink, Anthony L AU - Fink AL FAU - Uversky, Vladimir N AU - Uversky VN LA - eng GR - GM071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 LM007688-01A1/LM/NLM NIH HHS/United States GR - R01 NS39985/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cyclic N-Oxides) RN - 0 (Flavanones) RN - 0 (Flavonoids) RN - 0 (Free Radicals) RN - 0 (alpha-Synuclein) RN - 42HK56048U (Tyrosine) RN - 49QAH60606 (baicalein) RN - 7170JZ1QF3 (5,5-dimethyl-1-pyrroline-1-oxide) RN - 980-21-2 (dityrosine) RN - BBX060AN9V (Hydrogen Peroxide) RN - EC 1.11.1.6 (Catalase) SB - IM MH - Animals MH - Binding Sites MH - Catalase/pharmacology MH - Cattle MH - Cyclic N-Oxides/pharmacology MH - Flavanones/pharmacology MH - Flavonoids/metabolism/*pharmacology MH - Free Radicals/pharmacology MH - Humans MH - Hydrogen Peroxide/metabolism MH - Isoelectric Focusing MH - Mass Spectrometry MH - Mutation MH - Oxidation-Reduction MH - Protein Binding/drug effects MH - Protein Conformation/drug effects MH - Protein Stability/drug effects MH - Time Factors MH - Tyrosine/analogs & derivatives/metabolism MH - alpha-Synuclein/chemistry/genetics/*metabolism EDAT- 2009/07/29 09:00 MHDA- 2009/09/22 06:00 CRDT- 2009/07/29 09:00 AID - 10.1021/bi900506b [doi] PST - ppublish SO - Biochemistry. 2009 Sep 1;48(34):8206-24. doi: 10.1021/bi900506b. PMID- 18992225 OWN - NLM STAT- MEDLINE DA - 20081208 DCOM- 20081218 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 378 IP - 1 DP - 2009 Jan 2 TI - Structure and dynamics of the N-terminal half of hepatitis C virus core protein: an intrinsically unstructured protein. PG - 27-31 LID - 10.1016/j.bbrc.2008.10.141 [doi] AB - Hepatitis C virus core protein plays an important role in the assembly and packaging of the viral genome. We have studied the structure of the N-terminal half of the core protein (C82) which was shown to be sufficient for the formation of nucleocapsid-like particle (NLP) in vitro and in yeast. Structural bioinformatics analysis of C82 suggests that it is mostly unstructured. Circular dichroism and structural NMR data indicate that C82 lacks secondary structure. Moreover, NMR relaxation data shows that C82 is highly disordered. These results indicate that the N-terminal half of the HCV core protein belongs to the growing family of intrinsically unstructured proteins (IUP). This explains the tendency of the hepatitis C virus core protein to interact with several host proteins, a well-documented characteristic of IUPs. FAU - Duvignaud, Jean-Baptiste AU - Duvignaud JB AD - CREFSIP and Department of Biochemistry and Microbiology, Universite Laval, 1030 Avenue de la Medecine, Local 3255, Quebec, QC, Canada G1V 0A6. FAU - Savard, Christian AU - Savard C FAU - Fromentin, Remi AU - Fromentin R FAU - Majeau, Nathalie AU - Majeau N FAU - Leclerc, Denis AU - Leclerc D FAU - Gagne, Stephane M AU - Gagne SM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20081104 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Viral Core Proteins) RN - 0 (nucleocapsid protein, Hepatitis C virus) SB - IM MH - Amino Acid Sequence MH - Hepacivirus/*metabolism MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Sequence Analysis, Protein MH - Viral Core Proteins/*chemistry/ultrastructure EDAT- 2008/11/11 09:00 MHDA- 2008/12/19 09:00 CRDT- 2008/11/11 09:00 PHST- 2008/09/29 [received] PHST- 2008/10/22 [accepted] PHST- 2008/11/04 [aheadofprint] AID - S0006-291X(08)02109-8 [pii] AID - 10.1016/j.bbrc.2008.10.141 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2009 Jan 2;378(1):27-31. doi: 10.1016/j.bbrc.2008.10.141. Epub 2008 Nov 4. PMID- 20200158 OWN - NLM STAT- MEDLINE DA - 20100510 DCOM- 20100614 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 20 DP - 2010 May 14 TI - Order and disorder in the domain organization of the plasmid partition protein KorB. PG - 15440-9 LID - 10.1074/jbc.M109.096099 [doi] AB - The plasmid partition protein KorB has a dual role: it is essential for the correct segregation of the low copy number broad host range RK2 plasmid while also being an important regulator of transcription. KorB belongs to the ParB family of proteins, and partitioning in RK2 has been studied as a simplified model of bacterial chromosome segregation. Structural information on full-length ParB proteins is limited, mainly due to the inability to grow crystals suitable for diffraction studies. We show, using CD and NMR, that KorB has regions of significant intrinsic disorder and hence it adopts a multiplicity of conformations in solution. The biophysical data are consistent with bioinformatic predictions based on the amino acid sequence that the N-terminal region and also the region between the central DNA-binding domain and the C-terminal dimerization domain are intrinsically disordered. We have used small angle x-ray scattering data to determine the ensemble of solution conformations for KorB and selected deletion mutants, based on models of the known domain structures. This conformational range of KorB is likely to be biologically required for DNA partitioning and for binding to a diverse set of partner proteins. FAU - Rajasekar, Karthik AU - Rajasekar K AD - School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK. FAU - Muntaha, Sidra Tul AU - Muntaha ST FAU - Tame, Jeremy R H AU - Tame JR FAU - Kommareddy, Sireesha AU - Kommareddy S FAU - Morris, Gordon AU - Morris G FAU - Wharton, Christopher W AU - Wharton CW FAU - Thomas, Christopher M AU - Thomas CM FAU - White, Scott A AU - White SA FAU - Hyde, Eva I AU - Hyde EI FAU - Scott, David J AU - Scott DJ LA - eng GR - 067526/Z/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100303 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - 0 (KorB protein, Plasmid RK2) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry MH - Circular Dichroism MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - *Plasmids MH - Protein Conformation MH - Sequence Homology, Amino Acid PMC - PMC2865260 OID - NLM: PMC2865260 EDAT- 2010/03/05 06:00 MHDA- 2010/06/15 06:00 CRDT- 2010/03/05 06:00 PHST- 2010/03/03 [aheadofprint] AID - M109.096099 [pii] AID - 10.1074/jbc.M109.096099 [doi] PST - ppublish SO - J Biol Chem. 2010 May 14;285(20):15440-9. doi: 10.1074/jbc.M109.096099. Epub 2010 Mar 3. PMID- 23801378 OWN - NLM STAT- MEDLINE DA - 20131017 DCOM- 20140521 LR - 20141121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 81 IP - 11 DP - 2013 Nov TI - Pan1 is an intrinsically disordered protein with homotypic interactions. PG - 1944-63 LID - 10.1002/prot.24342 [doi] AB - The yeast scaffold protein Pan1 contains two EH domains at its N-terminus, a predicted coiled-coil central region, and a C-terminal proline-rich domain. Pan1 is also predicted to contain regions of intrinsic disorder, characteristic of proteins that have many binding partners. In vitro biochemical data suggest that Pan1 exists as a dimer, and we have identified amino acids 705 to 848 as critical for this homotypic interaction. Tryptophan fluorescence was used to further characterize Pan1 conformational states. Pan1 contains four endogenous tryptophans, each in a distinct region of the protein: Trp(312) and Trp(642) are each in an EH domain, Trp(957) is in the central region, and Trp(1280) is a critical residue in the Arp2/3 activation domain. To examine the local environment of each of these tryptophans, three of the four tryptophans were mutagenized to phenylalanine to create four proteins, each with only one tryptophan residue. When quenched with acrylamide, these single tryptophan mutants appeared to undergo collisional quenching exclusively and were moderately accessible to the acrylamide molecule. Quenching with iodide or cesium, however, revealed different Stern-Volmer constants due to unique electrostatic environments of the tryptophan residues. Time-resolved fluorescence anisotropy data confirmed structural and disorder predictions of Pan1. Further experimentation to fully develop a model of Pan1 conformational dynamics will assist in a deeper understanding of the mechanisms of endocytosis. CI - Copyright (c) 2013 Wiley Periodicals, Inc. FAU - Pierce, B D AU - Pierce BD AD - Department of Biology, Johns Hopkins University, Baltimore, Maryland, 21218. FAU - Toptygin, Dmitri AU - Toptygin D FAU - Wendland, Beverly AU - Wendland B LA - eng GR - GM07231/GM/NIGMS NIH HHS/United States GR - K12 GM000680/GM/NIGMS NIH HHS/United States GR - R01 GM060979/GM/NIGMS NIH HHS/United States GR - R01 GM60979/GM/NIGMS NIH HHS/United States GR - T32 GM007231/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20130819 PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Fungal Proteins) RN - 0 (Microfilament Proteins) RN - 0 (PAN1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 8DUH1N11BX (Tryptophan) SB - IM MH - Fluorescence Polarization MH - Fungal Proteins MH - Microfilament Proteins/*chemistry/*metabolism MH - Protein Binding MH - Protein Conformation MH - Saccharomyces cerevisiae Proteins/*chemistry/*metabolism MH - Tryptophan/chemistry PMC - PMC3800252 MID - NIHMS492356 OID - NLM: NIHMS492356 OID - NLM: PMC3800252 OTO - NOTNLM OT - EH domain OT - Pan1 OT - intrinsically disordered protein OT - time-resolved fluorescence anisotropy OT - tryptophan fluorescence quenching EDAT- 2013/06/27 06:00 MHDA- 2014/05/23 06:00 CRDT- 2013/06/27 06:00 PHST- 2013/02/07 [received] PHST- 2013/05/03 [revised] PHST- 2013/05/19 [accepted] PHST- 2013/08/19 [aheadofprint] AID - 10.1002/prot.24342 [doi] PST - ppublish SO - Proteins. 2013 Nov;81(11):1944-63. doi: 10.1002/prot.24342. Epub 2013 Aug 19. PMID- 10591105 OWN - NLM STAT- MEDLINE DA - 20000301 DCOM- 20000301 LR - 20061115 IS - 0887-3585 (Print) IS - 0887-3585 (Linking) VI - 37 IP - 3 DP - 1999 Nov 15 TI - Structure of the small G protein Rap2 in a non-catalytic complex with GTP. PG - 465-73 AB - We report a novel crystal form of the small G protein Rap2A in complex with GTP which has no GTPase activity in the crystal. The asymmetric unit contains two complexes which show that a conserved switch I residue, Tyr 32, contributes an extra hydrogen bond to the gamma-phosphate of GTP as compared to related structures with GTP analogs. Since GTP is not hydrolyzed in the crystal, this interaction is unlikely to contribute to the intrinsic GTPase activity. The comparison of other G protein structures to the Rap2-GTP complex suggests that an equivalent interaction is likely to exist in their GTP form, whether unbound or bound to an effector. This interaction has to be released to allow the GAP-activated GTPase, and presumably the intrinsic GTPase activity as well. We also discuss the definition of the flexible regions and their hinges in the light of this structure and the expanding database of G protein structures. We propose that the switch I and switch II undergo either partial or complete disorder-to-order transitions according to their cellular status, thus defining a complex energy landscape comprising more than two conformational states. We observe in addition that the region connecting the switch I and switch II is flexible in Rap2 and other G proteins. This region may be important for protein-protein interactions and possibly behave as a conformational lever arm, as characterized for Arf. Taken together, these observations suggest that the structural mechanisms of small G proteins are significantly driven by entropy-based free energy changes. FAU - Menetrey, J AU - Menetrey J AD - Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Gif sur Yvette, France. FAU - Cherfils, J AU - Cherfils J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Proteins JT - Proteins JID - 8700181 RN - 86-01-1 (Guanosine Triphosphate) RN - EC 3.6.1.- (GTP-Binding Proteins) RN - EC 3.6.1.- (RAP2A protein, human) RN - EC 3.6.5.2 (rap GTP-Binding Proteins) SB - IM MH - Crystallography, X-Ray MH - GTP-Binding Proteins/chemistry/metabolism MH - Guanosine Triphosphate/*chemistry MH - Models, Molecular MH - Protein Conformation MH - rap GTP-Binding Proteins/*chemistry EDAT- 1999/12/11 09:00 MHDA- 2000/03/04 09:00 CRDT- 1999/12/11 09:00 AID - 10.1002/(SICI)1097-0134(19991115)37:3<465::AID-PROT13>3.0.CO;2-O [pii] PST - ppublish SO - Proteins. 1999 Nov 15;37(3):465-73. PMID- 16302975 OWN - NLM STAT- MEDLINE DA - 20051123 DCOM- 20060117 IS - 1742-464X (Print) IS - 1742-464X (Linking) VI - 272 IP - 23 DP - 2005 Dec TI - Secondary structure assignment of mouse SOCS3 by NMR defines the domain boundaries and identifies an unstructured insertion in the SH2 domain. PG - 6120-30 AB - SOCS3 is a negative regulator of cytokine signalling that inhibits Janus kinase-signal transduction and activator of transcription (JAK-STAT) mediated signal tranduction by binding to phosphorylated tyrosine residues on intracellular subunits of various cytokine receptors, as well as possibly the JAK proteins. SOCS3 consists of a short N-terminal sequence followed by a kinase inhibitory region, an extended SH2 domain and a C-terminal suppressor of cytokine signalling (SOCS) box. SOCS3 and the related protein, cytokine-inducible SH2-containing protein, are unique among the SOCS family of proteins in containing a region of mostly low complexity sequence, between the SH2 domain and the C-terminal SOCS box. Using NMR, we assigned and determined the secondary structure of a murine SOCS3 construct. The SH2 domain, unusually, consists of 140 residues, including an unstructured insertion of 35 residues. This insertion fits the criteria for a PEST sequence and is not required for phosphotyrosine binding, as shown by isothermal titration calorimetry. Instead, we propose that the PEST sequence has a functional role unrelated to phosphotyrosine binding, possibly mediating efficient proteolytic degradation of the protein. The latter half of the kinase inhibitory region and the entire extended SH2 subdomain form a single alpha-helix. The mapping of the true SH2 domain, and the location of its C terminus more than 50 residues further downstream than predicted by sequence homology, explains a number of previously unexpected results that have shown the importance of residues close to the SOCS box for phosphotyrosine binding. FAU - Babon, Jeffrey J AU - Babon JJ AD - Walter and Eliza Hall Institute, Parkville, Victoria, Australia. babon@wehi.edu.au FAU - Yao, Shenggen AU - Yao S FAU - DeSouza, David P AU - DeSouza DP FAU - Harrison, Christopher F AU - Harrison CF FAU - Fabri, Louis J AU - Fabri LJ FAU - Liepinsh, Edvards AU - Liepinsh E FAU - Scrofani, Sergio D AU - Scrofani SD FAU - Baca, Manuel AU - Baca M FAU - Norton, Raymond S AU - Norton RS LA - eng PT - Journal Article PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Socs3 protein, mouse) RN - 0 (Suppressor of Cytokine Signaling Proteins) RN - 21820-51-9 (Phosphotyrosine) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cloning, Molecular MH - Humans MH - Mice MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphotyrosine/metabolism MH - *Protein Structure, Secondary MH - Sequence Alignment MH - Signal Transduction/physiology MH - Suppressor of Cytokine Signaling Proteins/*chemistry/metabolism MH - *src Homology Domains EDAT- 2005/11/24 09:00 MHDA- 2006/01/18 09:00 CRDT- 2005/11/24 09:00 AID - EJB5010 [pii] AID - 10.1111/j.1742-4658.2005.05010.x [doi] PST - ppublish SO - FEBS J. 2005 Dec;272(23):6120-30. PMID- 24217978 OWN - NLM STAT- MEDLINE DA - 20131217 DCOM- 20140714 LR - 20140731 IS - 1757-7012 (Electronic) IS - 1757-7004 (Linking) VI - 5 IP - 1 DP - 2014 Jan-Feb TI - YB-1 protein: functions and regulation. PG - 95-110 LID - 10.1002/wrna.1200 [doi] AB - The Y-box binding protein 1 (YB-1, YBX1) is a member of the family of DNA- and RNA-binding proteins with an evolutionarily ancient and conserved cold shock domain. It falls into a group of intrinsically disordered proteins that do not follow the classical rule 'one protein-one function' but introduce a novel principle stating that a disordered structure suggests many functions. YB-1 participates in a wide variety of DNA/RNA-dependent events, including DNA reparation, pre-mRNA transcription and splicing, mRNA packaging, and regulation of mRNA stability and translation. At the cell level, the multiple activities of YB-1 are manifested as its involvement in cell proliferation and differentiation, stress response, and malignant cell transformation. WIREs RNA 2014, 5:95-110. doi: 10.1002/wrna.1200 CONFLICT OF INTEREST: The authors have declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website. CI - (c) 2013 John Wiley & Sons, Ltd. FAU - Lyabin, Dmitry N AU - Lyabin DN AD - Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia. FAU - Eliseeva, Irina A AU - Eliseeva IA FAU - Ovchinnikov, Lev P AU - Ovchinnikov LP LA - eng PT - Journal Article PT - Review DEP - 20131111 PL - United States TA - Wiley Interdiscip Rev RNA JT - Wiley interdisciplinary reviews. RNA JID - 101536955 RN - 0 (RNA, Messenger) RN - 0 (Y-Box-Binding Protein 1) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Apoptosis MH - Cell Differentiation MH - Cell Proliferation MH - DNA/genetics/*metabolism MH - DNA Repair MH - Humans MH - Protein Biosynthesis MH - Protein Conformation MH - RNA, Messenger/genetics/*metabolism MH - Stress, Physiological MH - Transcriptional Activation MH - Y-Box-Binding Protein 1/chemistry/genetics/*metabolism EDAT- 2013/11/13 06:00 MHDA- 2014/07/16 06:00 CRDT- 2013/11/13 06:00 PHST- 2013/06/19 [received] PHST- 2013/08/23 [revised] PHST- 2013/09/27 [accepted] PHST- 2013/11/11 [aheadofprint] AID - 10.1002/wrna.1200 [doi] PST - ppublish SO - Wiley Interdiscip Rev RNA. 2014 Jan-Feb;5(1):95-110. doi: 10.1002/wrna.1200. Epub 2013 Nov 11. PMID- 15557116 OWN - NLM STAT- MEDLINE DA - 20041123 DCOM- 20050119 LR - 20140608 IS - 0021-9525 (Print) IS - 0021-9525 (Linking) VI - 167 IP - 4 DP - 2004 Nov 22 TI - Structural and functional analysis of Nup133 domains reveals modular building blocks of the nuclear pore complex. PG - 591-7 AB - Nucleocytoplasmic transport occurs through nuclear pore complexes (NPCs) whose complex architecture is generated from a set of only approximately 30 proteins, termed nucleoporins. Here, we explore the domain structure of Nup133, a nucleoporin in a conserved NPC subcomplex that is crucial for NPC biogenesis and is believed to form part of the NPC scaffold. We show that human Nup133 contains two domains: a COOH-terminal domain responsible for its interaction with its subcomplex through Nup107; and an NH2-terminal domain whose crystal structure reveals a seven-bladed beta-propeller. The surface properties and conservation of the Nup133 beta-propeller suggest it may mediate multiple interactions with other proteins. Other beta-propellers are predicted in a third of all nucleoporins. These and several other repeat-based motifs appear to be major elements of nucleoporins, indicating a level of structural repetition that may conceptually simplify the assembly and disassembly of this huge protein complex. FAU - Berke, Ian C AU - Berke IC AD - Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10021, USA. FAU - Boehmer, Thomas AU - Boehmer T FAU - Blobel, Gunter AU - Blobel G FAU - Schwartz, Thomas U AU - Schwartz TU LA - eng PT - Journal Article PL - United States TA - J Cell Biol JT - The Journal of cell biology JID - 0375356 RN - 0 (NUP133 protein, human) RN - 0 (Nuclear Pore Complex Proteins) SB - IM MH - Active Transport, Cell Nucleus/physiology MH - Amino Acid Sequence/physiology MH - Conserved Sequence/physiology MH - Crystallography, X-Ray MH - Evolution, Molecular MH - HeLa Cells MH - Humans MH - Models, Molecular MH - Nuclear Pore/*chemistry MH - Nuclear Pore Complex Proteins/*chemistry/genetics MH - Protein Structure, Tertiary/physiology MH - Sequence Homology, Amino Acid PMC - PMC2172596 OID - NLM: PMC2172596 EDAT- 2004/11/24 09:00 MHDA- 2005/01/20 09:00 CRDT- 2004/11/24 09:00 AID - jcb.200408109 [pii] AID - 10.1083/jcb.200408109 [doi] PST - ppublish SO - J Cell Biol. 2004 Nov 22;167(4):591-7. PMID- 23106082 OWN - NLM STAT- MEDLINE DA - 20121026 DCOM- 20130116 IS - 1439-7633 (Electronic) IS - 1439-4227 (Linking) VI - 12 IP - 15 DP - 2011 Oct 17 TI - High-resolution characterization of intrinsic disorder in proteins: expanding the suite of (13)C-detected NMR spectroscopy experiments to determine key observables. PG - 2347-52 AB - Order in disorder: The characterization of intrinsically disordered proteins by NMR spectroscopy is a necessity on the one hand and a continuous challenge on the other. We propose two experiments that provide diagnostic parameters to monitor the degree of unfolding of a polypeptide. The test was performed on the yeast Cox17 protein, known to gain its function through maturation from an intrinsically disordered state (see figure). FAU - Bertini, Ivano AU - Bertini I AD - CERM University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy. ivanobertini@cerm.unifi.it FAU - Felli, Isabella C AU - Felli IC FAU - Gonnelli, Leonardo AU - Gonnelli L FAU - Vasantha Kumar, M V AU - Vasantha Kumar MV FAU - Pierattelli, Roberta AU - Pierattelli R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Chembiochem JT - Chembiochem : a European journal of chemical biology JID - 100937360 RN - 0 (COX17 protein, S cerevisiae) RN - 0 (Cation Transport Proteins) RN - 0 (Disulfides) RN - 0 (Molecular Chaperones) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Cation Transport Proteins/*chemistry MH - Disulfides/chemistry MH - Models, Molecular MH - Molecular Chaperones/*chemistry MH - *Nuclear Magnetic Resonance, Biomolecular MH - Oxidation-Reduction MH - Protein Conformation MH - *Protein Unfolding MH - Saccharomyces cerevisiae/*chemistry MH - Saccharomyces cerevisiae Proteins/*chemistry EDAT- 2012/10/30 06:00 MHDA- 2013/01/17 06:00 CRDT- 2012/10/30 06:00 PST - ppublish SO - Chembiochem. 2011 Oct 17;12(15):2347-52. PMID- 19557012 OWN - NLM STAT- MEDLINE DA - 20091216 DCOM- 20100224 LR - 20120528 IS - 1476-5403 (Electronic) IS - 1350-9047 (Linking) VI - 17 IP - 1 DP - 2010 Jan TI - Ubiquitin-independent p53 proteasomal degradation. PG - 103-8 LID - 10.1038/cdd.2009.67 [doi] AB - The mechanism of p53 proteasomal degradation through polyubiquitination is well characterized. The basic assumption behind this mechanism is that p53 is inherently stable unless sensitized to degradation by polyubiquitination. However, a number of studies provide evidence for p53 to be naturally unstable. Consistent with this attribute is the fact that both p53 N- and C-termini are intrinsically unstructured. Recent findings provide evidence for p53 to be degraded by the 20S proteasome by default unless it escapes this process. A number of mechanisms were demonstrated and proposed to play a role in rescuing p53 from default degradation. These mechanisms, their biological implications, and relevance to cancer are reviewed in this article. FAU - Tsvetkov, P AU - Tsvetkov P AD - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel. FAU - Reuven, N AU - Reuven N FAU - Shaul, Y AU - Shaul Y LA - eng PT - Journal Article PT - Review PL - England TA - Cell Death Differ JT - Cell death and differentiation JID - 9437445 RN - 0 (Tumor Suppressor Protein p53) RN - 0 (Ubiquitin) RN - EC 1.6.5.2 (NAD(P)H Dehydrogenase (Quinone)) RN - EC 1.6.5.2 (NQO1 protein, human) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Humans MH - NAD(P)H Dehydrogenase (Quinone)/metabolism MH - Proteasome Endopeptidase Complex/*metabolism MH - Tumor Suppressor Protein p53/*metabolism MH - Ubiquitin/*metabolism RF - 71 EDAT- 2009/06/27 09:00 MHDA- 2010/02/25 06:00 CRDT- 2009/06/27 09:00 PHST- 2009/06/26 [aheadofprint] AID - cdd200967 [pii] AID - 10.1038/cdd.2009.67 [doi] PST - ppublish SO - Cell Death Differ. 2010 Jan;17(1):103-8. doi: 10.1038/cdd.2009.67. Epub . PMID- 2810365 OWN - NLM STAT- MEDLINE DA - 19891221 DCOM- 19891221 LR - 20081121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 209 IP - 1 DP - 1989 Sep 5 TI - Terminal regions of flagellin are disordered in solution. PG - 127-33 AB - Limited proteolysis of flagellin from Salmonella typhimurium SJW1103 by subtilisin, trypsin and thermolysin results in homologous degradation patterns. The terminal regions of flagellin are very sensitive to proteolysis. These parts are degraded into small oligopeptides at the very early stage of a mild digestion that yields a relatively stable fragment with a molecular weight of 40,000. Further proteolytic degradation results in a stable 27,000 Mr fragment. The 40,000 Mr tryptic fragment has been identified as residues 67 to 446 of the flagellin sequence, while the 27,000 Mr fragment involves the 179 to 418 segment. The NH2-terminal sequence positions for the corresponding fragments produced by subtilisin are 60 and 174 for the 40,000 Mr and 27,000 Mr fragments, respectively. The fragments lost their polymerizing ability. Structural properties of flagellin and its 40,000 Mr tryptic fragment were compared by circular dichroism spectroscopy and differential scanning calorimetry. Analysis of the calorimetric melting profiles suggests that terminal parts of flagellin have no significant internal stability and they are in extensive contact with water. However, these regions contain some secondary structure, probably alpha-helices, as revealed by comparison of the circular dichroic spectra in the far-ultraviolet region. Our results indicate that, although the terminal regions of flagellin may contain some alpha-helical secondary structure of marginal stability, they have no compact ordered tertiary structure in solution. On the contrary, the central region of the molecule involves at least two compact structural units. FAU - Vonderviszt, F AU - Vonderviszt F AD - ERATO, Molecular Dynamic Assembly Project, Tsukuba, Japan. FAU - Kanto, S AU - Kanto S FAU - Aizawa, S AU - Aizawa S FAU - Namba, K AU - Namba K LA - eng PT - Journal Article PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (Polymers) RN - 12777-81-0 (Flagellin) RN - EC 3.4.21.4 (Trypsin) SB - IM MH - Bacterial Proteins/*genetics MH - Calorimetry, Differential Scanning MH - Circular Dichroism MH - Flagellin/*genetics/metabolism MH - *Genes, Regulator MH - Models, Genetic MH - Polymers MH - Protein Conformation MH - *Terminator Regions, Genetic MH - Trypsin EDAT- 1989/09/05 MHDA- 1989/09/05 00:01 CRDT- 1989/09/05 00:00 PST - ppublish SO - J Mol Biol. 1989 Sep 5;209(1):127-33. PMID- 15035611 OWN - NLM STAT- MEDLINE DA - 20040323 DCOM- 20040721 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 12 DP - 2004 Mar 30 TI - Solution structure and backbone dynamics of the Cu(I) and apo forms of the second metal-binding domain of the Menkes protein ATP7A. PG - 3396-403 AB - The second domain of the human Menkes protein (MNK2), formed by 72 residues, has been expressed in Escherichia coli, and its structure has been determined by NMR in both the apo and copper-loaded forms. The structures, obtained with (13)C- and (15)N-labeled samples, are of high quality with backbone rmsd values of 0.51 and 0.41 A and CYANA target functions of 0.39 and 0.38 A(2), respectively. The loop involved in copper binding is part of a hydrophobic patch, which is maintained in both forms. Conformational mobility is observed in the apo form in the same loop. A comparison with metallochaperones and soluble domains of P-type ATPases allows us to relate the primary structure to the occurrence of structural rearrangements upon copper binding. FAU - Banci, Lucia AU - Banci L AD - Magnetic Resonance Center, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. FAU - Bertini, Ivano AU - Bertini I FAU - Del Conte, Rebecca AU - Del Conte R FAU - D'Onofrio, Mariapina AU - D'Onofrio M FAU - Rosato, Antonio AU - Rosato A LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Apoproteins) RN - 0 (Cation Transport Proteins) RN - 0 (Ferredoxins) RN - 0 (Metalloproteins) RN - 0 (Molecular Chaperones) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Solutions) RN - 789U1901C5 (Copper) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 3.6.3.4 (ATP7A protein, human) SB - IM MH - Adenosine Triphosphatases/*chemistry MH - Apoproteins/*chemistry MH - Cation Transport Proteins/*chemistry MH - Copper/*chemistry MH - Ferredoxins/chemistry MH - Humans MH - Menkes Kinky Hair Syndrome/enzymology MH - Metalloproteins/*chemistry MH - Molecular Chaperones/chemistry MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Peptide Fragments/*chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/*chemistry MH - Solutions MH - Thermodynamics EDAT- 2004/03/24 05:00 MHDA- 2004/07/22 05:00 CRDT- 2004/03/24 05:00 AID - 10.1021/bi036042s [doi] PST - ppublish SO - Biochemistry. 2004 Mar 30;43(12):3396-403. PMID- 16442664 OWN - NLM STAT- MEDLINE DA - 20060619 DCOM- 20060914 LR - 20071115 IS - 0171-9335 (Print) IS - 0171-9335 (Linking) VI - 85 IP - 7 DP - 2006 Jul TI - G-Protein-coupled receptor-associated A-kinase anchoring proteins: AKAP79 and AKAP250 (gravin). PG - 643-50 AB - A-kinase anchoring proteins (AKAPs) define an expanding group of scaffold proteins that display a signature binding site for the RI/RII subunit of protein kinase A. AKAPs are multivalent and a subset of these scaffold proteins also display the ability to associate with the prototypic member of G-protein-coupled receptors, the beta(2)-adrenergic receptor. Both AKAP79 (also known as AKAP5) and AKAP250 (also known as gravin or AKAP12) have been shown to associate with the beta(2)-adrenergic receptor, but each directs downstream signaling events in decidedly different manners. The primary structures, common and unique protein motifs are of interest. Both proteins display largely natively unfolded primary sequences that provide a necklace on which short, structured regions of sequence are found. Membrane association appears to involve both interactions with the lipid bilayer via docking to a G-protein-coupled receptor as well as interactions of short positively charged domains with the inner leaflet of the cell membrane. Gravin, unlike AKAP79, displays a canonical site at its N-terminus that is subject to N-myristoylation. AKAP79 appears to function in switching signaling pathways of the receptor from adenylylcyclase to activation of the mitogen-activated protein kinase cascade. Gravin, in contrast, is essential for the resensitization and recycling of the receptors following agonist-induced activation, desensitization, and internalization. Each AKAP provides a template that enables space-time continuum features to G-protein-coupled signaling pathways as well as a paradigm for explaining apparent compartmentalization of cell signaling. FAU - Wang, Hsien-Yu AU - Wang HY AD - Department of Physiology & Biophysics, Health Sciences Center, State University of New York at Stony Brook, Stony Brook, NY 11794-8661, USA. FAU - Tao, Jiangchuan AU - Tao J FAU - Shumay, Elena AU - Shumay E FAU - Malbon, Craig C AU - Malbon CC LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review DEP - 20060126 PL - Germany TA - Eur J Cell Biol JT - European journal of cell biology JID - 7906240 RN - 0 (A Kinase Anchor Proteins) RN - 0 (AKAP12 protein, human) RN - 0 (AKAP5 protein, human) RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Cell Cycle Proteins) RN - 0 (Proteins) RN - 0 (Receptors, G-Protein-Coupled) SB - IM MH - A Kinase Anchor Proteins MH - Adaptor Proteins, Signal Transducing/*physiology MH - Amino Acid Sequence MH - Cell Cycle Proteins MH - Cell Membrane/metabolism MH - Conserved Sequence MH - Humans MH - Models, Biological MH - Molecular Sequence Data MH - Protein Folding MH - Proteins/*physiology MH - Receptors, G-Protein-Coupled/*physiology MH - Signal Transduction MH - Structural Homology, Protein RF - 31 EDAT- 2006/01/31 09:00 MHDA- 2006/09/15 09:00 CRDT- 2006/01/31 09:00 PHST- 2006/01/26 [aheadofprint] AID - S0171-9335(05)00215-3 [pii] AID - 10.1016/j.ejcb.2005.12.003 [doi] PST - ppublish SO - Eur J Cell Biol. 2006 Jul;85(7):643-50. Epub 2006 Jan 26. PMID- 24785077 OWN - NLM STAT- MEDLINE DA - 20140505 DCOM- 20140707 IS - 1079-7114 (Electronic) IS - 0031-9007 (Linking) VI - 112 IP - 15 DP - 2014 Apr 18 TI - Single-molecule force spectroscopy of rapidly fluctuating, marginally stable structures in the intrinsically disordered protein alpha-synuclein. PG - 158103 AB - Intrinsically disordered proteins form transient, fluctuating structures that are difficult to observe directly. We used optical tweezers to apply force to single alpha-synuclein molecules and measure their extension, characterizing the resulting conformational transitions. Force-extension curves revealed rapid fluctuations at low force, arising from the folding of two different classes of structure that were only marginally stable. The energy landscape for these transitions was characterized via the force-dependent kinetics derived from correlation analysis of the extension trajectories. The barriers were small, only a few kBT, but the diffusion was slow, revealing a landscape that is flat but rough. FAU - Solanki, Allison AU - Solanki A AD - Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada. FAU - Neupane, Krishna AU - Neupane K AD - Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada. FAU - Woodside, Michael T AU - Woodside MT AD - Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada and National Institute for Nanotechnology, National Research Council Canada, Edmonton, Alberta T6G 2M9, Canada. LA - eng GR - NHG 91374/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140416 PL - United States TA - Phys Rev Lett JT - Physical review letters JID - 0401141 RN - 0 (alpha-Synuclein) RN - 9007-49-2 (DNA) SB - IM MH - DNA/chemistry MH - Microscopy, Atomic Force/methods MH - Models, Chemical MH - Protein Conformation MH - Protein Folding MH - Protein Stability MH - Spectrum Analysis/methods MH - Thermodynamics MH - alpha-Synuclein/*chemistry EDAT- 2014/05/03 06:00 MHDA- 2014/07/08 06:00 CRDT- 2014/05/03 06:00 PHST- 2014/04/16 [aheadofprint] PHST- 2013/11/29 [received] PST - ppublish SO - Phys Rev Lett. 2014 Apr 18;112(15):158103. Epub 2014 Apr 16. PMID- 22500761 OWN - NLM STAT- MEDLINE DA - 20120416 DCOM- 20120810 LR - 20141016 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 102 IP - 7 DP - 2012 Apr 4 TI - Solution model of the intrinsically disordered polyglutamine tract-binding protein-1. PG - 1608-16 LID - 10.1016/j.bpj.2012.02.047 [doi] AB - Polyglutamine tract-binding protein-1 (PQBP-1) is a 265-residue nuclear protein that is involved in transcriptional regulation. In addition to its role in the molecular pathology of the polyglutamine expansion diseases, mutations of the protein are associated with X-linked mental retardation. PQBP-1 binds specifically to glutamine repeat sequences and proline-rich regions, and interacts with RNA polymerase II and the spliceosomal protein U5-15kD. In this work, we obtained a biophysical characterization of this protein by employing complementary structural methods. PQBP-1 is shown to be a moderately compact but largely disordered molecule with an elongated shape, having a Stokes radius of 3.7 nm and a maximum molecular dimension of 13 nm. The protein is monomeric in solution, has residual beta-structure, and is in a premolten globule state that is unaffected by natural osmolytes. Using small-angle x-ray scattering data, we were able to generate a low-resolution, three-dimensional model of PQBP-1. CI - Copyright (c) 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Rees, Martin AU - Rees M AD - Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom. FAU - Gorba, Christian AU - Gorba C FAU - de Chiara, Cesira AU - de Chiara C FAU - Bui, Tam T T AU - Bui TT FAU - Garcia-Maya, Mitla AU - Garcia-Maya M FAU - Drake, Alex F AU - Drake AF FAU - Okazawa, Hitoshi AU - Okazawa H FAU - Pastore, Annalisa AU - Pastore A FAU - Svergun, Dmitri AU - Svergun D FAU - Chen, Yu Wai AU - Chen YW LA - eng GR - MC_U117533887/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120403 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Nuclear Proteins) RN - 0 (Solutions) SB - IM MH - *Models, Molecular MH - Nuclear Proteins/*chemistry MH - Protein Conformation MH - Scattering, Small Angle MH - Solutions MH - X-Ray Diffraction PMC - PMC3318138 OID - NLM: PMC3318138 EDAT- 2012/04/17 06:00 MHDA- 2012/08/11 06:00 CRDT- 2012/04/17 06:00 PHST- 2011/10/14 [received] PHST- 2012/01/30 [revised] PHST- 2012/02/13 [accepted] PHST- 2012/04/03 [aheadofprint] AID - S0006-3495(12)00280-9 [pii] AID - 10.1016/j.bpj.2012.02.047 [doi] PST - ppublish SO - Biophys J. 2012 Apr 4;102(7):1608-16. doi: 10.1016/j.bpj.2012.02.047. Epub 2012 Apr 3. PMID- 19170609 OWN - NLM STAT- MEDLINE DA - 20090624 DCOM- 20090717 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 6 DP - 2009 Feb 17 TI - The transcriptional repressor RYBP is a natively unfolded protein which folds upon binding to DNA. PG - 1348-60 LID - 10.1021/bi801933c [doi] AB - RYBP (Ring1A and YY1 binding protein) is a zinc finger protein with an essential role during embryonic development, which binds transcriptional factors, Polycomb products, and mediators of apoptosis, suggesting roles in, apparently, unrelated functions. To investigate mechanisms underlying its association with functionally diverse partners, we set out to study its structural properties using a number of biophysical (fluorescence, circular dichroism, Fourier transform infrared, and NMR spectroscopies) and hydrodynamic (analytical ultracentrifugation, DOSY-NMR, and gel filtration chromatography) techniques. We find RYBP to be a noncompact protein with little residual secondary structure, lacking a well-defined tertiary structure. These observations are also supported by theoretical calculations using neural networks and pairwise energy content, suggesting that RYBP is a natively unfolded protein. In addition, structural studies on its binding to the C-terminal region of the Polycomb protein Ring1B or to DNA show conformational changes in the complexed RYBP, consistent with the acquisition of a folded structure. The data provide a structural explanation for RYBP engagement in functionally unrelated pathways by means of its assembly into various macromolecular complexes as an unstructured protein with the ability to acquire a well-structured fold due to its association with different partners. FAU - Neira, Jose L AU - Neira JL AD - Instituto de Biologia Molecular y Celular, Universidad Miguel Hernandez, 03202 Elche (Alicante), Spain. jlneira@umh.es FAU - Roman-Trufero, Monica AU - Roman-Trufero M FAU - Contreras, Lellys M AU - Contreras LM FAU - Prieto, Jesus AU - Prieto J FAU - Singh, Gagandeep AU - Singh G FAU - Barrera, Francisco N AU - Barrera FN FAU - Renart, M Lourdes AU - Renart ML FAU - Vidal, Miguel AU - Vidal M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA-Binding Proteins) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Repressor Proteins) RN - 8DUH1N11BX (Tryptophan) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Computational Biology MH - DNA/*metabolism MH - DNA-Binding Proteins/metabolism MH - Fluorescence MH - Intracellular Signaling Peptides and Proteins/*chemistry/*metabolism MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Binding MH - Protein Denaturation MH - *Protein Folding MH - Protein Structure, Secondary MH - Repressor Proteins/*chemistry/*metabolism MH - *Transcription, Genetic MH - Tryptophan/metabolism EDAT- 2009/01/28 09:00 MHDA- 2009/07/18 09:00 CRDT- 2009/01/28 09:00 AID - 10.1021/bi801933c [doi] AID - 10.1021/bi801933c [pii] PST - ppublish SO - Biochemistry. 2009 Feb 17;48(6):1348-60. doi: 10.1021/bi801933c. PMID- 24252580 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20131122 DCOM- 20131122 LR - 20141011 IS - 2050-7771 (Electronic) IS - 2050-7771 (Linking) VI - 1 IP - 1 DP - 2013 TI - CETN1 is a cancer testis antigen with expression in prostate and pancreatic cancers. PG - 22 LID - 10.1186/2050-7771-1-22 [doi] AB - BACKGROUND: The Cancer Testis Antigens (CTAs) are a group of genes that are highly expressed in the normal testis and several types of cancer. Due to their restricted expression in normal adult tissues, CTAs have been attractive targets for immunotherapy and biomarker development. In this work, we discovered that Centrin 1 (CETN1) which is found in the centrosome of all eukaryotes, may be a member of this group and is highly expressed in prostate and pancreatic cancer. Three members of the centrin family of calcium binding proteins (CETN) are localized to the centrosome in all eukaryotes with CDC31 being the sole yeast homolog. CETN1 is a retrogene that probably arose from a retrotransposition of CETN2, an X-linked gene. A previous mouse study shows that CETN1 is expressed solely in the testis, while CETN2 is expressed in all organs. RESULTS: In this work, we show that CETN1 is a new member of the growing group of CTAs. Through the mining of publicly available microarray data, we discovered that human CETN1 expression but not CETN2 or CETN3 is restricted to the testis. In fact, CETN1 is actually down-regulated in testicular malignancies compared to normal testis. Using q-PCR, CETN1 expression is shown to be highly up-regulated in cancer of the prostate and in pancreatic xenografts. Unexpectedly however, CETN1 expression was virtually absent in various cell lines until they were treated with the DNA demethylation agent 5'AZA-2'Deoxycytidine (AZA) but showed no increased expression upon incubation with Histone deacetylase inhibitor Trichostatin-A (TSA) alone. Additionally, like most CTAs, CETN1 appears to be an intrinsically disordered protein which implies that it may occupy a hub position in key protein interaction networks in cancer. Neither CETN1 nor CETN2 could compensate for loss of CDC31 expression in yeast which is analogous to published data for CETN3. CONCLUSIONS: This work suggests that CETN1 is a novel CTA with expression in cancer of the prostate and pancreas. In cell lines, the expression is probably regulated by promoter methylation, while the method of regulation in normal adult tissues remains unknown. FAU - Kim, John J AU - Kim JJ AD - Department of Urology, James Buchanan Brady Urological Institute, The Johns Hopkins University, School of Medicine, Baltimore, MD, 21287, USA. smooney4@jhmi.edu. FAU - Rajagopalan, Krithika AU - Rajagopalan K FAU - Hussain, Basil AU - Hussain B FAU - Williams, Brenten H AU - Williams BH FAU - Kulkarni, Prakash AU - Kulkarni P FAU - Mooney, Steven M AU - Mooney SM LA - eng GR - P30 CA006973/CA/NCI NIH HHS/United States PT - Journal Article DEP - 20130613 PL - England TA - Biomark Res JT - Biomarker research JID - 101607860 PMC - PMC4177615 OID - NLM: PMC4177615 EDAT- 2013/11/21 06:00 MHDA- 2013/11/21 06:01 CRDT- 2013/11/21 06:00 PHST- 2013/03/24 [received] PHST- 2013/06/03 [accepted] PHST- 2013/06/13 [aheadofprint] AID - 2050-7771-1-22 [pii] AID - 10.1186/2050-7771-1-22 [doi] PST - epublish SO - Biomark Res. 2013 Jun 13;1(1):22. doi: 10.1186/2050-7771-1-22. PMID- 19636827 OWN - NLM STAT- MEDLINE DA - 20090728 DCOM- 20090917 LR - 20121115 IS - 1874-270X (Electronic) VI - 1 IP - 1 DP - 2007 Jul TI - NMR assignment of an intrinsically disordered protein under physiological conditions: the 18.5 kDa isoform of murine myelin basic protein. PG - 61-3 LID - 10.1007/s12104-007-9016-1 [doi] AB - We report the NMR assignment of 18.5 kDa recombinant murine myelin basic protein (MBP) in 100 mM KCl as a prerequisite to structural analyses of its Ca2+-dependent interaction with calmodulin. FAU - Libich, David S AU - Libich DS AD - Department of Molecular and Cellular Biology, Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada. FAU - Monette, Martine M AU - Monette MM FAU - Robertson, Valerie J AU - Robertson VJ FAU - Harauz, George AU - Harauz G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070602 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (Calmodulin) RN - 0 (Mbp protein, mouse) RN - 0 (Myelin Basic Protein) RN - 0 (Nerve Tissue Proteins) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) SB - IM MH - Animals MH - Calmodulin/metabolism MH - Mice MH - Molecular Structure MH - Molecular Weight MH - Myelin Basic Protein MH - Nerve Tissue Proteins/*chemistry/genetics/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Isoforms/chemistry/genetics MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/genetics MH - Transcription Factors/*chemistry/genetics/metabolism EDAT- 2007/07/01 00:00 MHDA- 2009/09/18 06:00 CRDT- 2009/07/29 09:00 PHST- 2007/02/15 [received] PHST- 2007/04/06 [accepted] PHST- 2007/06/02 [aheadofprint] AID - 10.1007/s12104-007-9016-1 [doi] PST - ppublish SO - Biomol NMR Assign. 2007 Jul;1(1):61-3. doi: 10.1007/s12104-007-9016-1. Epub 2007 Jun 2. PMID- 19642704 OWN - NLM STAT- MEDLINE DA - 20090825 DCOM- 20090921 LR - 20121115 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 34 DP - 2009 Sep 1 TI - Structural polymorphism and multifunctionality of myelin basic protein. PG - 8094-104 LID - 10.1021/bi901005f [doi] AB - Central nervous system myelin is a dynamic entity arising from membrane processes extended from oligodendrocytes, which form a tightly wrapped multilamellar structure around neurons enabling rapid and efficient signal propagation. The gene of oligodendrocyte lineage (golli) gives rise to a variety of developmentally regulated splice isoforms of myelin basic protein (MBP), denoted golli for early forms and classic for later ones. In mature myelin, the predominant splice isoform of classic MBP is 18.5 kDa; its central role is to maintain the structural integrity of the myelin sheath, by holding together the apposing cytoplasmic leaflets of the oligodendrocyte membrane in a tight, spiral, multilamellar arrangement. This protein's extreme physicochemical properties, net charge of +19 at neutral pH, low proportion of hydrophobic residues, alternating regions of predicted intrinsic disorder and order, induced folding upon association with membranes and other proteins, and diversification via combinatorial post-translational modifications, define not only its role as a molecular Velcro in compact myelin, but as a multifunctional hub that may also bind to a number of other proteins and small molecule ligands in myelinating oligodendrocytes. In particular, MBP may link the underlying cytoskeleton and proteins containing SH3 domains to the membrane, allowing it to transduce transmembrane signals to the cytosol. These associations are facilitated by MBP being an intrinsically disordered protein, creating a large effective protein surface, and by the formation of transient and/or induced ordered secondary structure elements for molecular recognition. These processes can be modulated by a molecular barcode of numerous post-translational modifications and interactions with proteins such as calmodulin. In the human demyelinating disease multiple sclerosis, an aberrant pattern of modifications may contribute to demyelination and confound inherent attempts at repair. The conformational dynamics of the various isoforms and modified variants of MBP and their interactions with other proteins potentially allow them to participate in events coupling extracellular signals to cytoskeletal organization during myelination or remyelination. Various biophysical and cell biological approaches are beginning to elucidate these properties of MBP and are leading to a new understanding of the role of this protein as a linker and/or hub in structural and signaling networks in oligodendrocytes and myelin. FAU - Harauz, George AU - Harauz G AD - Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1,Canada. FAU - Ladizhansky, Vladimir AU - Ladizhansky V FAU - Boggs, Joan M AU - Boggs JM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Myelin Basic Protein) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cell Membrane/metabolism MH - Humans MH - Molecular Sequence Data MH - Myelin Basic Protein/*chemistry/*metabolism MH - Oligodendroglia/cytology/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary RF - 92 EDAT- 2009/08/01 09:00 MHDA- 2009/09/22 06:00 CRDT- 2009/08/01 09:00 AID - 10.1021/bi901005f [doi] PST - ppublish SO - Biochemistry. 2009 Sep 1;48(34):8094-104. doi: 10.1021/bi901005f. PMID- 19717454 OWN - NLM STAT- MEDLINE DA - 20091006 DCOM- 20091113 LR - 20140828 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 106 IP - 37 DP - 2009 Sep 15 TI - Substrate binding site flexibility of the small heat shock protein molecular chaperones. PG - 15604-9 LID - 10.1073/pnas.0902177106 [doi] AB - Small heat shock proteins (sHSPs) serve as a first line of defense against stress-induced cell damage by binding and maintaining denaturing proteins in a folding-competent state. In contrast to the well-defined substrate binding regions of ATP-dependent chaperones, interactions between sHSPs and substrates are poorly understood. Defining substrate-binding sites of sHSPs is key to understanding their cellular functions and to harnessing their aggregation-prevention properties for controlling damage due to stress and disease. We incorporated a photoactivatable cross-linker at 32 positions throughout a well-characterized sHSP, dodecameric PsHsp18.1 from pea, and identified direct interaction sites between sHSPs and substrates. Model substrates firefly luciferase and malate dehydrogenase form strong contacts with multiple residues in the sHSP N-terminal arm, demonstrating the importance of this flexible and evolutionary variable region in substrate binding. Within the conserved alpha-crystallin domain both substrates also bind the beta-strand (beta7) where mutations in human homologs result in inherited disease. Notably, these binding sites are poorly accessible in the sHSP atomic structure, consistent with major structural rearrangements being required for substrate binding. Detectable differences in the pattern of cross-linking intensity of the two substrates and the fact that substrates make contacts throughout the sHSP indicate that there is not a discrete substrate binding surface. Our results support a model in which the intrinsically-disordered N-terminal arm can present diverse geometries of interaction sites, which is likely critical for the ability of sHSPs to protect efficiently many different substrates. FAU - Jaya, Nomalie AU - Jaya N AD - Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA. FAU - Garcia, Victor AU - Garcia V FAU - Vierling, Elizabeth AU - Vierling E LA - eng GR - R01-GM042762/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090826 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (4-benzoylphenylalanine) RN - 0 (Benzophenones) RN - 0 (Cross-Linking Reagents) RN - 0 (HSP18 protein, plant) RN - 0 (Heat-Shock Proteins) RN - 0 (Heat-Shock Proteins, Small) RN - 0 (Molecular Chaperones) RN - 0 (Plant Proteins) RN - 0 (Recombinant Proteins) RN - 47E5O17Y3R (Phenylalanine) SB - IM MH - Amino Acid Sequence MH - Animals MH - Benzophenones MH - Binding Sites MH - Cross-Linking Reagents MH - Genetic Variation MH - Heat-Shock Proteins/chemistry/genetics/metabolism MH - Heat-Shock Proteins, Small/chemistry/genetics/*metabolism MH - Humans MH - Models, Molecular MH - Molecular Chaperones/chemistry/genetics/*metabolism MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Peas/genetics/metabolism MH - Phenylalanine/analogs & derivatives MH - Plant Proteins/chemistry/genetics/metabolism MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - Recombinant Proteins/chemistry/genetics/metabolism PMC - PMC2773522 OID - NLM: PMC2773522 EDAT- 2009/09/01 06:00 MHDA- 2009/11/17 06:00 CRDT- 2009/09/01 09:00 PHST- 2009/08/26 [aheadofprint] AID - 0902177106 [pii] AID - 10.1073/pnas.0902177106 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15604-9. doi: 10.1073/pnas.0902177106. Epub 2009 Aug 26. PMID- 19878690 OWN - NLM STAT- MEDLINE DA - 20100129 DCOM- 20100412 LR - 20131121 IS - 1879-0003 (Electronic) IS - 0141-8130 (Linking) VI - 46 IP - 1 DP - 2010 Jan 1 TI - Physicochemical studies on peroxynitrite-modified H3 histone. PG - 20-6 LID - 10.1016/j.ijbiomac.2009.10.009 [doi] AB - Histones are DNA protective proteins and may adopt different structures under nitrosative stress. Peroxynitrite is a powerful oxidant and nitrating agent and has in vivo existence. In this communication, we report effect of peroxynitrite-mediated oxidation and nitration on the structure of calf thymus H3 histone. Fine details of peroxynitrite-modified H3 histone were worked out by UV, fluorescence, circular dichroism and Fourier-transformed infrared spectroscopy and polyacrylamide gel. The results revealed that peroxynitrite-mediated nitration and oxidation in H3 histone produced partially folded structure in comparison to the intrinsically disordered structure of native H3 histone. It may be concluded that the H3 histone, constituent of core histones, is highly sensitive to peroxynitrite and can adopt different structures under nitrosative stress in order to protect the packaged DNA from the deleterious insult of peroxynitrite. CI - Copyright 2009 Elsevier B.V. All rights reserved. FAU - Dixit, Kiran AU - Dixit K AD - Department of Biochemistry, Faculty of Medicine, Aligarh Muslim University (A.M.U.), Aligarh 202 002, Uttar Pradesh, India. FAU - Khan, M Asad AU - Khan MA FAU - Sharma, Y D AU - Sharma YD FAU - Moinuddin AU - Moinuddin FAU - Alam, Khursheed AU - Alam K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091028 PL - Netherlands TA - Int J Biol Macromol JT - International journal of biological macromolecules JID - 7909578 RN - 0 (Histones) RN - 14691-52-2 (Peroxynitrous Acid) RN - 42HK56048U (Tyrosine) RN - 980-21-2 (dityrosine) RN - EC 3.4.21.4 (Trypsin) SB - IM MH - Animals MH - Cattle MH - Chromatography, High Pressure Liquid MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Histones/*metabolism MH - Hydrolysis/drug effects MH - Peroxynitrous Acid/*pharmacology MH - Physicochemical Phenomena/*drug effects MH - Protein Denaturation/drug effects MH - Spectrometry, Fluorescence MH - Spectrophotometry, Ultraviolet MH - Spectroscopy, Fourier Transform Infrared MH - Temperature MH - Trypsin/pharmacology MH - Tyrosine/analogs & derivatives/metabolism EDAT- 2009/11/03 06:00 MHDA- 2010/04/13 06:00 CRDT- 2009/11/03 06:00 PHST- 2009/07/09 [received] PHST- 2009/10/12 [revised] PHST- 2009/10/16 [accepted] PHST- 2009/10/28 [aheadofprint] AID - S0141-8130(09)00232-3 [pii] AID - 10.1016/j.ijbiomac.2009.10.009 [doi] PST - ppublish SO - Int J Biol Macromol. 2010 Jan 1;46(1):20-6. doi: 10.1016/j.ijbiomac.2009.10.009. Epub 2009 Oct 28. PMID- 24442609 OWN - NLM STAT- MEDLINE DA - 20140219 DCOM- 20140408 LR - 20150311 IS - 1469-9001 (Electronic) IS - 1355-8382 (Linking) VI - 20 IP - 3 DP - 2014 Mar TI - The N-terminal extension of S12 influences small ribosomal subunit assembly in Escherichia coli. PG - 321-30 LID - 10.1261/rna.042432.113 [doi] AB - The small subunit (SSU) of the ribosome of E. coli consists of a core of ribosomal RNA (rRNA) surrounded peripherally by ribosomal proteins (r-proteins). Ten of the 15 universally conserved SSU r-proteins possess nonglobular regions called extensions. The N-terminal noncanonically structured extension of S12 traverses from the solvent to intersubunit surface of the SSU and is followed by a more C-terminal globular region that is adjacent to the decoding center of the SSU. The role of the globular region in maintaining translational fidelity is well characterized, but a role for the S12 extension in SSU structure and function is unknown. We examined the effect of stepwise truncation of the extension of S12 in SSU assembly and function in vitro and in vivo. Examination of in vitro assembly in the presence of sequential N-terminal truncated variants of S12 reveals that N-terminal deletions of greater than nine amino acids exhibit decreased tRNA-binding activity and altered 16S rRNA architecture particularly in the platform of the SSU. While wild-type S12 expressed from a plasmid can rescue a genomic deletion of the essential gene for S12, rpsl; N-terminal deletions of S12 exhibit deleterious phenotypic consequences. Partial N-terminal deletions of S12 are slow growing and cold sensitive. Strains bearing these truncations as the sole copy of S12 have increased levels of free SSUs and immature 16S rRNA as compared with the wild-type S12. These differences are hallmarks of SSU biogenesis defects, indicating that the extension of S12 plays an important role in SSU assembly. FAU - Calidas, Deepika AU - Calidas D FAU - Lyon, Hiram AU - Lyon H FAU - Culver, Gloria M AU - Culver GM LA - eng PT - Journal Article DEP - 20140117 PL - United States TA - RNA JT - RNA (New York, N.Y.) JID - 9509184 RN - 0 (Escherichia coli Proteins) RN - 0 (RNA, Ribosomal) RN - 0 (Ribosomal Proteins) SB - IM MH - Escherichia coli/genetics/growth & development/*metabolism MH - Escherichia coli Proteins/chemistry/genetics/*metabolism MH - Models, Molecular MH - Mutation/genetics MH - Protein Conformation MH - Protein Structure, Tertiary MH - RNA, Ribosomal/genetics MH - Ribosomal Proteins/chemistry/genetics/*metabolism MH - Ribosome Subunits, Small/chemistry/*physiology PMC - PMC3923127 OID - NLM: PMC3923127 OTO - NOTNLM OT - S12 OT - assembly OT - biogenesis OT - intrinsically disordered proteins OT - ribosome OT - small subunit EDAT- 2014/01/21 06:00 MHDA- 2014/04/09 06:00 CRDT- 2014/01/21 06:00 PHST- 2014/01/17 [aheadofprint] AID - rna.042432.113 [pii] AID - 10.1261/rna.042432.113 [doi] PST - ppublish SO - RNA. 2014 Mar;20(3):321-30. doi: 10.1261/rna.042432.113. Epub 2014 Jan 17. PMID- 17459940 OWN - NLM STAT- MEDLINE DA - 20070614 DCOM- 20070806 LR - 20140907 IS - 0022-538X (Print) IS - 0022-538X (Linking) VI - 81 IP - 13 DP - 2007 Jul TI - Interaction of the C-terminal domains of sendai virus N and P proteins: comparison of polymerase-nucleocapsid interactions within the paramyxovirus family. PG - 6807-16 AB - Interaction of the C-terminal domains of Sendai virus (SeV) P and N proteins is crucial for RNA synthesis by correctly positioning the polymerase complex (L+P) onto the nucleocapsid (N/RNA). To better understand this mechanism within the paramyxovirus family, we have studied the complex formed by the SeV C-terminal domains of P (PX) and N (N(TAIL)) proteins by solution nuclear magnetic resonance spectroscopy. We have characterized SeV N(TAIL), which belongs to the class of intrinsically disordered proteins, and precisely defined the binding regions within this latter domain and within PX. SeV N(TAIL) binds with residues 472 to 493, which have a helical propensity (residues 477 to 491) to the surface created by helices alpha2 and alpha3 of PX with a 1:1 stoichiometry, as was also found for measles virus (MV). The binding interface is dominated by charged residues, and the dissociation constant was determined to be 57 +/- 18 microM under conditions of the experiment (i.e., in 0.5 M NaCl). We have also shown that the extreme C terminus of SeV N(TAIL) does not interact with PX, which is in contrast to MV, where a second binding site was identified. In addition, the interaction surfaces of the MV proteins are hydrophobic and a stronger binding constant was found. This gives a good illustration of how selection pressure allowed the C-terminal domains of N and P proteins to evolve concomitantly within this family of viruses in order to lead to protein complexes having the same three-dimensional fold, and thus the same function, but with completely different binding interfaces. FAU - Houben, Klaartje AU - Houben K AD - CEA Cadarache, IBEB, LEMiRE, Saint-Paul-lez-Durance, F-13108 France. FAU - Marion, Dominique AU - Marion D FAU - Tarbouriech, Nicolas AU - Tarbouriech N FAU - Ruigrok, Rob W H AU - Ruigrok RW FAU - Blanchard, Laurence AU - Blanchard L LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070425 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (Multiprotein Complexes) RN - 0 (P protein, Sendai virus) RN - 0 (Phosphoproteins) RN - 0 (RNA, Viral) RN - 0 (Viral Proteins) RN - EC 2.7.7.6 (DNA-Directed RNA Polymerases) SB - IM MH - DNA-Directed RNA Polymerases/genetics/metabolism MH - *Evolution, Molecular MH - Multiprotein Complexes/chemistry/genetics/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Nucleocapsid/chemistry/genetics/metabolism MH - Paramyxovirinae/chemistry/genetics/metabolism MH - Phosphoproteins/*chemistry/genetics/metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA, Viral/biosynthesis/genetics MH - Sendai virus/*chemistry/genetics/metabolism MH - Structural Homology, Protein MH - Viral Proteins/*chemistry/genetics/metabolism PMC - PMC1933331 OID - NLM: PMC1933331 EDAT- 2007/04/27 09:00 MHDA- 2007/08/07 09:00 CRDT- 2007/04/27 09:00 PHST- 2007/04/25 [aheadofprint] AID - JVI.00338-07 [pii] AID - 10.1128/JVI.00338-07 [doi] PST - ppublish SO - J Virol. 2007 Jul;81(13):6807-16. Epub 2007 Apr 25. PMID- 21142030 OWN - NLM STAT- MEDLINE DA - 20110105 DCOM- 20110415 LR - 20140921 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 133 IP - 1 DP - 2011 Jan 12 TI - Structural signature of the MYPT1-PP1 interaction. PG - 73-80 LID - 10.1021/ja107810r [doi] AB - Muscle relaxation is triggered by the dephosphorylation of Ser19 in the myosin regulatory light chain. This reaction is catalyzed by the holoenzyme myosin phosphatase (MP), which includes the catalytic subunit protein phosphatase 1 (PP1) and the regulatory targeting subunit (MYPT). MYPT1 (myosin phosphatase targeting subunit 1) is responsible for both targeting the holoenzyme to subcellular compartments in the muscle and directing PP1 specificity toward myosin. To understand the molecular events leading to the MYPT1-PP1 holoenzyme formation, we used NMR spectroscopy to determine the structural and dynamic characteristics of unbound MYPT1. This allowed the conformations of MYPT1 in the free, unbound state to be directly compared to the PP1-bound state. Our results show that MYPT1(1-98) behaves like a two-domain protein in solution. The first 40 residues of MYPT1(1-98), the disordered region, are intrinsically disordered and highly dynamic, whereas residues 41-98, the folded ankyrin-repeat region, are well-structured and rigid. Furthermore, the integrated use of NMR and biophysical data enabled us to calculate an ensemble model for MYPT1(1-98). The most prominent structural feature of the MYPT1(1-98) ensemble is a 25% populated transient alpha-helix in the disordered region of MYPT1(1-98). This alpha-helix becomes fully populated when bound to PP1 and, as we show, likely plays a central role in the formation of the MYPT1-PP1 holoenzyme complex. Finally, this combined analysis shows that the structural and dynamic behaviors exhibited by MYPT1 for PP1 are distinct from those of any other previously analyzed PP1 regulatory protein. Collectively, these data enable us to present a new model of the molecular events that drive MYPT1-PP1 holoenzyme formation and demonstrate that there are structural differences in unbound PP1 regulators that have not been previously observed. Thus, this work adds significant insights to the currently limited data for molecular structures and dynamics of PP1 regulators. FAU - Pinheiro, Anderson S AU - Pinheiro AS AD - Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island 02903, USA. FAU - Marsh, Joseph A AU - Marsh JA FAU - Forman-Kay, Julie D AU - Forman-Kay JD FAU - Peti, Wolfgang AU - Peti W LA - eng GR - R01 NS056128/NS/NINDS NIH HHS/United States GR - R01 NS056128-01A2/NS/NINDS NIH HHS/United States GR - R01 NS056128-02S1/NS/NINDS NIH HHS/United States GR - R01NS056128/NS/NINDS NIH HHS/United States GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20101210 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - EC 3.1.3.16 (Protein Phosphatase 1) RN - EC 3.1.3.53 (Myosin-Light-Chain Phosphatase) SB - IM MH - Ankyrin Repeat MH - Cluster Analysis MH - Models, Molecular MH - Myosin-Light-Chain Phosphatase/*chemistry/*metabolism MH - Protein Binding MH - Protein Folding MH - Protein Phosphatase 1/*chemistry/*metabolism PMC - PMC3016445 MID - NIHMS258265 OID - NLM: NIHMS258265 OID - NLM: PMC3016445 EDAT- 2010/12/15 06:00 MHDA- 2011/04/19 06:00 CRDT- 2010/12/15 06:00 PHST- 2010/12/10 [aheadofprint] AID - 10.1021/ja107810r [doi] PST - ppublish SO - J Am Chem Soc. 2011 Jan 12;133(1):73-80. doi: 10.1021/ja107810r. Epub 2010 Dec 10. PMID- 24065419 OWN - NLM STAT- In-Process DA - 20140827 IS - 1874-270X (Electronic) VI - 8 IP - 2 DP - 2014 Oct TI - Backbone (1)H, (1)(3)C and (1)(5)N assignments of yeast Ump1, an intrinsically disordered protein that functions as a proteasome assembly chaperone. PG - 383-6 LID - 10.1007/s12104-013-9523-1 [doi] AB - Eukaryotic proteasome assembly is a highly organized process mediated by several proteasome-specific chaperones, which interact with proteasome assembly intermediates. In yeast, Ump1 and Pba1-4 have been identified as assembly chaperones that are dedicated to the formation of the proteasome 20S catalytic core complex. The crystal structures of Pba chaperones have been reported previously, but no detailed information has been provided for the structure of Ump1. Thus, to better understand the mechanisms underlying Ump1-mediated proteasome assembly, we characterized the conformation of Ump1 in solution using NMR. Backbone chemical shift data indicated that Ump1 is an intrinsically unstructured protein and largely devoid of secondary structural elements. FAU - Uekusa, Yoshinori AU - Uekusa Y AD - Graduate School and Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan. FAU - Okawa, Keisuke AU - Okawa K FAU - Yagi-Utsumi, Maho AU - Yagi-Utsumi M FAU - Serve, Olivier AU - Serve O FAU - Nakagawa, Yuki AU - Nakagawa Y FAU - Mizushima, Tsunehiro AU - Mizushima T FAU - Yagi, Hirokazu AU - Yagi H FAU - Saeki, Yasushi AU - Saeki Y FAU - Tanaka, Keiji AU - Tanaka K FAU - Kato, Koichi AU - Kato K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130925 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 SB - IM EDAT- 2013/09/26 06:00 MHDA- 2013/09/26 06:00 CRDT- 2013/09/26 06:00 PHST- 2013/05/22 [received] PHST- 2013/09/06 [accepted] PHST- 2013/09/25 [aheadofprint] AID - 10.1007/s12104-013-9523-1 [doi] PST - ppublish SO - Biomol NMR Assign. 2014 Oct;8(2):383-6. doi: 10.1007/s12104-013-9523-1. Epub 2013 Sep 25. PMID- 18457655 OWN - NLM STAT- MEDLINE DA - 20080523 DCOM- 20080703 LR - 20140911 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 371 IP - 3 DP - 2008 Jul 4 TI - The actin binding protein, fesselin, is a member of the synaptopodin family. PG - 582-6 LID - 10.1016/j.bbrc.2008.04.134 [doi] AB - Fesselin is a natively unfolded protein that is abundant in avian smooth muscle. Like many natively unfolded proteins, fesselin has multiple binding partners including actin, myosin, calmodulin and alpha-actinin. Fesselin accelerates actin polymerization and bundles actin. These and other observations suggest that fesselin is a component of the cytoskeleton. We have now cloned fesselin and have determined the cDNA derived amino acid sequence. We verified parts of the sequence by Edman analysis and by mass spectroscopy. Our results confirmed fesselin is homologous to human synaptopodin 2 and belongs to the synaptopodin family of proteins. FAU - Schroeter, Mechthild M AU - Schroeter MM AD - Department of Biochemistry & Molecular Biology, Brody School of Medicine at East Carolina University, 600 Moye Blvd, Greenville, NC 27834, USA. schroeterm@ecu.edu FAU - Beall, Brent AU - Beall B FAU - Heid, Hans W AU - Heid HW FAU - Chalovich, Joseph M AU - Chalovich JM LA - eng GR - AR035216/AR/NIAMS NIH HHS/United States GR - R01 AR035216/AR/NIAMS NIH HHS/United States GR - R01 AR035216-21/AR/NIAMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20080505 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Avian Proteins) RN - 0 (Membrane Proteins) RN - 0 (Microfilament Proteins) RN - 0 (Peptides) RN - 0 (SYNPO2 protein, human) RN - 0 (fesselin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Avian Proteins/*chemistry/*genetics MH - Humans MH - Membrane Proteins/*chemistry/*genetics MH - Microfilament Proteins/*chemistry/*genetics MH - Molecular Sequence Data MH - Peptides/chemistry/genetics MH - Sequence Alignment MH - Sequence Analysis, Protein MH - Sequence Homology, Amino Acid MH - *Turkeys PMC - PMC2453309 MID - NIHMS53360 OID - NLM: NIHMS53360 OID - NLM: PMC2453309 EDAT- 2008/05/07 09:00 MHDA- 2008/07/04 09:00 CRDT- 2008/05/07 09:00 PHST- 2008/04/04 [received] PHST- 2008/04/22 [accepted] PHST- 2008/05/05 [aheadofprint] AID - S0006-291X(08)00837-1 [pii] AID - 10.1016/j.bbrc.2008.04.134 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2008 Jul 4;371(3):582-6. doi: 10.1016/j.bbrc.2008.04.134. Epub 2008 May 5. PMID- 21592750 OWN - NLM STAT- MEDLINE DA - 20110601 DCOM- 20110920 LR - 20131121 IS - 1873-4367 (Electronic) IS - 0927-7765 (Linking) VI - 86 IP - 2 DP - 2011 Sep 1 TI - Why does the silica-binding protein "Si-tag" bind strongly to silica surfaces? Implications of conformational adaptation of the intrinsically disordered polypeptide to solid surfaces. PG - 359-63 LID - 10.1016/j.colsurfb.2011.04.020 [doi] AB - We recently reported that the bacterial 50S ribosomal protein L2 binds strongly to silica surfaces even in the presence of high salt concentrations, detergents, and denaturants such as 8 M urea. We designated L2 as Si-tag, a fusion tag for immobilizing functional proteins on silica materials. Here we discuss the remarkable properties of the Si-tag polypeptide in order to understand the mechanism underlying this binding. Experimental and theoretical studies have shown that the 60-aa N-terminal region and the 71-aa C-terminal region, both of which are rich in positively charged residues, lack a well-defined three-dimensional structure under physiological conditions. This lack of a stable tertiary structure suggests that Si-tag belongs to a family of intrinsically disordered (ID) proteins that exist as dynamic ensembles of rapidly fluctuating structures in aqueous solution. Because of its inherent flexibility, Si-tag could form a large intermolecular interface and optimize its structure for surface interactions by conformational adaptation at the binding interface. Such conformational adaptation occurring concomitantly with binding is common to many ID proteins and is called "coupled folding and binding". Through this conformational adaptation, Si-tag could optimize the interactions between its positively charged side chains and ionized surface silanol groups and between its apolar side chains and hydrophobic surface siloxane sites. The cumulative contribution of these contacts would significantly strengthen the binding of Si-tag, resulting in strong, virtually irreversible binding. Our study suggests that flexible ID proteins have tremendous potential for connecting biomolecules to inorganic materials. CI - Copyright (c) 2011 Elsevier B.V. All rights reserved. FAU - Ikeda, Takeshi AU - Ikeda T AD - Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan. ikedatakeshi@hiroshima-u.ac.jp FAU - Kuroda, Akio AU - Kuroda A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110421 PL - Netherlands TA - Colloids Surf B Biointerfaces JT - Colloids and surfaces. B, Biointerfaces JID - 9315133 RN - 0 (Bacterial Proteins) RN - 0 (Detergents) RN - 0 (Ribosomal Proteins) RN - 0 (Salts) RN - 0 (Solutions) RN - 0 (ribosomal protein L2) RN - 059QF0KO0R (Water) RN - 7631-86-9 (Silicon Dioxide) RN - 8W8T17847W (Urea) SB - IM MH - Bacterial Proteins/chemistry/*metabolism MH - Binding Sites MH - Detergents/chemistry MH - Escherichia coli/chemistry/*metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Ribosomal Proteins/chemistry/*metabolism MH - Salts/chemistry MH - Silicon Dioxide/chemistry/*metabolism MH - Solutions MH - Surface Properties MH - Urea/chemistry MH - Water EDAT- 2011/05/20 06:00 MHDA- 2011/09/21 06:00 CRDT- 2011/05/20 06:00 PHST- 2010/11/11 [received] PHST- 2011/03/15 [revised] PHST- 2011/04/12 [accepted] PHST- 2011/04/21 [aheadofprint] AID - S0927-7765(11)00227-X [pii] AID - 10.1016/j.colsurfb.2011.04.020 [doi] PST - ppublish SO - Colloids Surf B Biointerfaces. 2011 Sep 1;86(2):359-63. doi: 10.1016/j.colsurfb.2011.04.020. Epub 2011 Apr 21. PMID- 15518563 OWN - NLM STAT- MEDLINE DA - 20041102 DCOM- 20050111 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 44 DP - 2004 Nov 9 TI - Crystal structure of archaeal ribonuclease P protein aRpp29 from Archaeoglobus fulgidus. PG - 14128-38 AB - The crystal structure of ribonuclease P protein aRpp29 from the sulfate-reducing hyperthermophile Archaeoglobus fulgidus was determined at 1.7 A resolution using X-ray diffraction methods. The central feature of this archaeal protein is a sheet of six antiparallel beta-strands twisted around a conserved hydrophobic core. Residues near the N- and C-termini form helical structures that are oriented in an antiparallel manner. A comparison of conserved amino acids indicates that archaeal aRpp29 is homologous to human ribonuclease P protein Rpp29. The aRpp29 protein is structurally similar to bacterial transcription factors Hfq and NusG, as well as the Sm and Sm-like RNA-associated proteins from eukarya. The crystal structure of A. fulgidus aRpp29 differs from the previously reported solution structure, where NMR data did not detect the helices and indicated that approximately 40% of the residues are relatively flexible or disordered. Circular dichroism data indicate that the protein has less helical content than the amount observed in the crystal, suggesting that in solution the helical regions are unfolded or in equilibrium between folded and unfolded forms; this hypothesis is consistent with amide proton exchange rate data. Surface residues that are conserved from archaea to humans and are likely to interact with the ribonuclease P RNA or other protein subunits are identified in the structure. The model of the aRpp29 protein defined by this work provides an essential step toward eventually understanding the overall architecture of ribonuclease P. FAU - Sidote, David J AU - Sidote DJ AD - Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA. FAU - Heideker, Johanna AU - Heideker J FAU - Hoffman, David W AU - Hoffman DW LA - eng SI - PDB/1TS9 SI - PDB/1TSF PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Archaeal Proteins) RN - 0 (Ribonucleoproteins) RN - 0 (Solutions) RN - EC 3.1.- (Ribonucleases) RN - EC 3.1.26.5 (POP4 protein, human) RN - EC 3.1.26.5 (Ribonuclease P) SB - IM MH - Amino Acid Sequence MH - Archaeal Proteins/*chemistry MH - Archaeoglobus fulgidus/*enzymology MH - Circular Dichroism MH - Conserved Sequence MH - Crystallization MH - Crystallography, X-Ray MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Ribonuclease P/*chemistry MH - Ribonucleases/chemistry MH - Ribonucleoproteins/chemistry MH - Sequence Homology, Amino Acid MH - Solutions EDAT- 2004/11/03 09:00 MHDA- 2005/01/12 09:00 CRDT- 2004/11/03 09:00 AID - 10.1021/bi048578z [doi] PST - ppublish SO - Biochemistry. 2004 Nov 9;43(44):14128-38. PMID- 22569262 OWN - NLM STAT- MEDLINE DA - 20120509 DCOM- 20120529 LR - 20131121 IS - 1873-3468 (Electronic) IS - 0014-5793 (Linking) VI - 586 IP - 7 DP - 2012 Apr 5 TI - The bacterial-type phosphoenolpyruvate carboxylase isozyme from developing castor oil seeds is subject to in vivo regulatory phosphorylation at serine-451. PG - 1049-54 LID - 10.1016/j.febslet.2012.02.054 [doi] AB - Phosphoenolpyruvate carboxylase (PEPC) is a tightly controlled anaplerotic enzyme situated at a pivotal branch point of plant carbohydrate-metabolism. In developing castor oil seeds (COS) a novel allosterically-densensitized 910-kDa Class-2 PEPC hetero-octameric complex arises from a tight interaction between 107-kDa plant-type PEPC and 118-kDa bacterial-type PEPC (BTPC) subunits. Mass spectrometry and immunoblotting with anti-phosphoSer451 specific antibodies established that COS BTPC is in vivo phosphorylated at Ser451, a highly conserved target residue that occurs within an intrinsically disordered region. This phosphorylation was enhanced during COS development or in response to depodding. Kinetic characterization of a phosphomimetic (S451D) mutant indicated that Ser451 phosphorylation inhibits the catalytic activity of BTPC subunits within the Class-2 PEPC complex. CI - Copyright (c) 2012 Federation of European Biochemical Societies. All rights reserved. FAU - Dalziel, Katie J AU - Dalziel KJ AD - Department of Biology, Queen's University, Kingston, Ontario, Canada K7L 3N6. FAU - O'Leary, Brendan AU - O'Leary B FAU - Brikis, Carolyne AU - Brikis C FAU - Rao, Srinath K AU - Rao SK FAU - She, Yi-Min AU - She YM FAU - Cyr, Terry AU - Cyr T FAU - Plaxton, William C AU - Plaxton WC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120309 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Antibodies, Phospho-Specific) RN - 0 (Isoenzymes) RN - 0 (Mutant Proteins) RN - 0 (Plant Proteins) RN - 0 (Protein Subunits) RN - 0 (Recombinant Proteins) RN - 452VLY9402 (Serine) RN - 8001-79-4 (Castor Oil) RN - EC 4.1.1.31 (Phosphoenolpyruvate Carboxylase) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Antibodies, Phospho-Specific MH - Castor Oil/chemistry MH - Food Handling MH - Isoenzymes/chemistry/genetics/metabolism MH - Kinetics MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Mutant Proteins/chemistry/metabolism MH - Phosphoenolpyruvate Carboxylase/chemistry/genetics/*metabolism MH - Phosphorylation MH - Plant Proteins/chemistry/genetics/*metabolism MH - Protein Processing, Post-Translational MH - Protein Subunits/chemistry/genetics/metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Ricinus/*enzymology/genetics/growth & development MH - Seeds/*enzymology/growth & development MH - Sequence Alignment MH - Serine/*metabolism EDAT- 2012/05/10 06:00 MHDA- 2012/05/30 06:00 CRDT- 2012/05/10 06:00 PHST- 2011/12/23 [received] PHST- 2012/02/08 [revised] PHST- 2012/02/26 [accepted] PHST- 2012/03/09 [aheadofprint] AID - S0014-5793(12)00189-5 [pii] AID - 10.1016/j.febslet.2012.02.054 [doi] PST - ppublish SO - FEBS Lett. 2012 Apr 5;586(7):1049-54. doi: 10.1016/j.febslet.2012.02.054. Epub 2012 Mar 9. PMID- 25220806 OWN - NLM STAT- Publisher DA - 20141202 LR - 20141202 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1844 IP - 12 DP - 2014 Sep 16 TI - Molecular insights into dimerization inhibition of c-Maf transcription factor. PG - 2108-2115 LID - S1570-9639(14)00226-X [pii] LID - 10.1016/j.bbapap.2014.09.003 [doi] AB - The Maf protein family belongs to the activator protein 1 (AP-1) superfamily of transcription factors that bind specific DNA target sequences through a basic region and exploit a leucine zipper (LZ) motif for protein-protein interactions leading to homo- or hetero-dimerization. Mafs unique DNA-binding domain contains a highly conserved extended homology region (EHR) that allows to recognize longer DNA sequences than other basic leucine zipper (bZIP) transcription factors. Inspired by the fact that overexpression of Mafs is observed in about 50% of cases of multiple myeloma, a hematological malignant disorder, we undertook a peptide inhibitor approach. The LZ domain of c-Maf, one of large Mafs, was produced by solid phase peptide synthesis. We characterized its secondary structure and dimerization properties, and found that dimerization and folding events are strictly coupled. Moreover, potential peptidic c-Maf dimerization inhibitors were computationally designed and synthesized. These compounds were demonstrated by circular dichroism (CD) spectroscopy and MALDI-TOF mass spectrometry to bind to c-Maf LZ monomers, to drive folding of their partially disordered structure and to efficiently compete with dimerization, suggesting a way for interfering with the function of c-Maf and, more generally, of intrinsically disordered proteins, till now considered undruggable targets. CI - Copyright (c) 2014 Elsevier B.V. All rights reserved. FAU - Pellegrino, Sara AU - Pellegrino S AD - DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy. FAU - Ronda, Luca AU - Ronda L AD - Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy. FAU - Annoni, Chiara AU - Annoni C AD - DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy. FAU - Contini, Alessandro AU - Contini A AD - DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy. FAU - Erba, Emanuela AU - Erba E AD - DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy. FAU - Gelmi, Maria Luisa AU - Gelmi ML AD - DISFARM - Section of General and Organic Chemistry "A. Marchesini", University of Milan, Via Venezian 21, 20133 Milan, Italy. FAU - Piano, Riccardo AU - Piano R AD - Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy. FAU - Paredi, Gianluca AU - Paredi G AD - Department of Pharmacy, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; SITEIA.PARMA Interdepartmental Center, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy. FAU - Mozzarelli, Andrea AU - Mozzarelli A AD - Department of Pharmacy, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; National Institute of Biostructures and Biosystems, Viale Medaglie d'Oro 305, 00136 Rome, Italy. FAU - Bettati, Stefano AU - Bettati S AD - Department of Neurosciences, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy; National Institute of Biostructures and Biosystems, Viale Medaglie d'Oro 305, 00136 Rome, Italy. Electronic address: stefano.bettati@unipr.it. LA - ENG PT - JOURNAL ARTICLE DEP - 20140916 TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 OTO - NOTNLM OT - Dimerization inhibitor OT - Intrinsically disordered protein OT - Maf transcription factor OT - Molecular dynamics OT - Multiple myeloma OT - Solid phase peptide synthesis EDAT- 2014/09/16 06:00 MHDA- 2014/09/16 06:00 CRDT- 2014/09/16 06:00 PHST- 2014/04/22 [received] PHST- 2014/08/01 [revised] PHST- 2014/09/02 [accepted] AID - S1570-9639(14)00226-X [pii] AID - 10.1016/j.bbapap.2014.09.003 [doi] PST - aheadofprint SO - Biochim Biophys Acta. 2014 Sep 16;1844(12):2108-2115. doi: 10.1016/j.bbapap.2014.09.003. PMID- 23301700 OWN - NLM STAT- MEDLINE DA - 20130130 DCOM- 20130723 LR - 20141104 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 4 DP - 2013 Jan 30 TI - Folding and binding of an intrinsically disordered protein: fast, but not 'diffusion-limited'. PG - 1415-22 LID - 10.1021/ja309527h [doi] AB - Coupled folding and binding of intrinsically disordered proteins (IDPs) is prevalent in biology. As the first step toward understanding the mechanism of binding, it is important to know if a reaction is 'diffusion-limited' as, if this speed limit is reached, the association must proceed through an induced fit mechanism. Here, we use a model system where the 'BH3 region' of PUMA, an IDP, forms a single, contiguous alpha-helix upon binding the folded protein Mcl-1. Using stopped-flow techniques, we systematically compare the rate constant for association (k(+)) under a number of solvent conditions and temperatures. We show that our system is not 'diffusion-limited', despite having a k(+) in the often-quoted 'diffusion-limited' regime (10(5)-10(6) M(-1) s(-1) at high ionic strength) and displaying an inverse dependence on solvent viscosity. These standard tests, developed for folded protein-protein interactions, are not appropriate for reactions where one protein is disordered. FAU - Rogers, Joseph M AU - Rogers JM AD - Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. FAU - Steward, Annette AU - Steward A FAU - Clarke, Jane AU - Clarke J LA - eng GR - 095195/Wellcome Trust/United Kingdom GR - WT095195MA/Wellcome Trust/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130122 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Proteins) SB - IM MH - Binding Sites MH - Diffusion MH - Models, Molecular MH - Protein Conformation MH - Protein Folding MH - Proteins/*chemistry PMC - PMC3776562 OID - NLM: PMC3776562 EDAT- 2013/01/11 06:00 MHDA- 2013/07/24 06:00 CRDT- 2013/01/11 06:00 PHST- 2013/01/22 [aheadofprint] AID - 10.1021/ja309527h [doi] PST - ppublish SO - J Am Chem Soc. 2013 Jan 30;135(4):1415-22. doi: 10.1021/ja309527h. Epub 2013 Jan 22. PMID- 15296738 OWN - NLM STAT- MEDLINE DA - 20040806 DCOM- 20050119 LR - 20131121 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 12 IP - 8 DP - 2004 Aug TI - Structural rearrangement accompanying NAD+ synthesis within a bacterial DNA ligase crystal. PG - 1449-59 AB - DNA ligase is an enzyme important for DNA repair and replication. Eukaryotic genomes encode ligases requiring ATP as the cofactor; bacterial genomes encode NAD(+)-dependent ligase. This difference in substrate specificities and the essentiality of NAD(+)-dependent ligase for bacterial survival make NAD(+)-dependent ligase a good target for designing highly specific anti-infectives. Any such structure-guided effort would require the knowledge of the precise mechanism of NAD+ recognition by the enzyme. We report the principles of NAD+ recognition by presenting the synthesis of NAD+ from nicotinamide mononucleotide (NMN) and AMP, catalyzed by Enterococcus faecalis ligase within the crystal lattice. Unprecedented conformational change, required to reorient the two subdomains of the protein for the condensation to occur and to recognize NAD+, is captured in two structures obtained using the same protein crystal. Structural data and sequence analysis presented here confirms and extends prior functional studies of the ligase adenylation reaction. FAU - Gajiwala, Ketan S AU - Gajiwala KS AD - Quorex Pharmaceuticals, 1890 Rutherford Road, Suite 200, Carlsbad, California 92008, USA. ketang@quorex.com FAU - Pinko, Christopher AU - Pinko C LA - eng SI - PDB/1TA8 SI - PDB/1TAE PT - Journal Article PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0U46U6E8UK (NAD) RN - 1094-61-7 (Nicotinamide Mononucleotide) RN - EC 6.5.1.- (DNA Ligases) RN - EC 6.5.1.2 (DNA ligase (NAD)) SB - IM CIN - Structure. 2004 Aug;12(8):1335-6. PMID: 15296724 MH - Cloning, Molecular MH - Crystallization MH - Crystallography, X-Ray MH - DNA Ligases/*chemistry MH - Enterococcus faecalis/enzymology MH - *Models, Molecular MH - NAD/*chemistry MH - Nicotinamide Mononucleotide/*chemistry MH - Protein Structure, Tertiary EDAT- 2004/08/07 05:00 MHDA- 2005/01/20 09:00 CRDT- 2004/08/07 05:00 PHST- 2004/04/08 [received] PHST- 2004/05/14 [revised] PHST- 2004/05/17 [accepted] AID - 10.1016/j.str.2004.05.017 [doi] AID - S0969212604002357 [pii] PST - ppublish SO - Structure. 2004 Aug;12(8):1449-59. PMID- 25206938 OWN - NLM STAT- Publisher DA - 20140910 IS - 1948-7185 (Print) IS - 1948-7185 (Linking) VI - 5 IP - 17 DP - 2014 Sep 4 TI - Structural Insight into Tau Protein's Paradox of Intrinsically Disordered Behavior, Self-Acetylation Activity, and Aggregation. PG - 3026-3031 AB - Tau is an intrinsically disordered protein (IDP) implicated in Alzheimer's disease. Recently, tau proteins were discovered to be able to catalyze self-acetylation, which may promote its pathological aggregation. Understanding the paradox of tau's random-like conformations, aggregation propensity, and enzymatic activity are challenging questions. We characterized the atomic structures of two truncated tau constructs, K18 and K19, consisting of, respectively, only the four- and three-repeats of tau protein, providing structural insights into tau's paradox. Extensive 4.8 mus replica-exchange molecular dynamics simulations of the tau proteins achieved quantitative correlation with experimental Calpha chemical shifts. Our results revealed (1) dynamically ordered conformations with close lysine-cysteine distances essential for tau self-acetylation and (2) high beta-sheet content and large hydrophobic surface exposure for the two critical hexapeptides (275VQIINK280 and 306VQIVYK311), crucial for tau aggregation. Together, they illuminate tau's perplexing behavior of how its disordered state can accomplish both roles. FAU - Luo, Yin AU - Luo Y AD - State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University , Shanghai, People's Republic of China. FAU - Ma, Buyong AU - Ma B AD - Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute , Frederick, Maryland 21702, United States. FAU - Nussinov, Ruth AU - Nussinov R AD - Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute , Frederick, Maryland 21702, United States ; Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University , Tel Aviv 69978, Israel. FAU - Wei, Guanghong AU - Wei G AD - State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University , Shanghai, People's Republic of China. LA - ENG PT - JOURNAL ARTICLE DEP - 20140819 TA - J Phys Chem Lett JT - The journal of physical chemistry letters JID - 101526034 PMC - PMC4154703 EDAT- 2014/09/11 06:00 MHDA- 2014/09/11 06:00 CRDT- 2014/09/11 06:00 PMCR- 2015/08/19 00:00 PHST- 2014/07/13 [received] PHST- 2014/08/19 [accepted] PHST- 2014/08/19 [epublish] AID - 10.1021/jz501457f [doi] PST - ppublish SO - J Phys Chem Lett. 2014 Sep 4;5(17):3026-3031. Epub 2014 Aug 19. PMID- 19636953 OWN - NLM STAT- MEDLINE DA - 20090728 DCOM- 20091028 LR - 20101118 IS - 1874-270X (Electronic) VI - 3 IP - 1 DP - 2009 Jun TI - 1H, 13C, 15N backbone and side-chain resonance assignments of the Bright/ARID domain from the human histone demethylase JARID1B. PG - 85-7 LID - 10.1007/s12104-009-9147-7 [doi] AB - We report backbone and side-chain resonance assignments of the Bright/ARID domain from the human JARID1B protein. These assignments provide a basis for the detailed structural investigation of the interaction between DNA and ARID domains. FAU - Yao, Wenming AU - Yao W AD - Key Laboratory of Optical and Magnetic Resonance Spectroscopy, East China Normal University, Shanghai, 200062, China. FAU - Peng, Yu AU - Peng Y FAU - Chen, Qun AU - Chen Q FAU - Lin, Donghai AU - Lin D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090224 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (ARID3A protein, human) RN - 0 (Carbon Isotopes) RN - 0 (DNA-Binding Proteins) RN - 0 (Nitrogen Isotopes) RN - 0 (Nuclear Proteins) RN - 0 (Protein Subunits) RN - 0 (Protons) RN - 0 (Repressor Proteins) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - EC 1.14.11.- (Jumonji Domain-Containing Histone Demethylases) RN - EC 1.14.11.- (KDM5B protein, human) SB - IM MH - Amino Acid Sequence MH - Carbon Isotopes/chemistry MH - DNA-Binding Proteins MH - Humans MH - Jumonji Domain-Containing Histone Demethylases MH - Magnetic Resonance Spectroscopy/*methods MH - Molecular Sequence Data MH - Nitrogen Isotopes/chemistry MH - Nuclear Proteins/*chemistry MH - Oncogenes MH - Protein Structure, Tertiary MH - Protein Subunits MH - Protons MH - Repressor Proteins/*chemistry MH - Trans-Activators/*chemistry MH - Transcription Factors EDAT- 2009/07/29 09:00 MHDA- 2009/10/29 06:00 CRDT- 2009/07/29 09:00 PHST- 2008/11/27 [received] PHST- 2009/02/10 [accepted] PHST- 2009/02/24 [aheadofprint] AID - 10.1007/s12104-009-9147-7 [doi] PST - ppublish SO - Biomol NMR Assign. 2009 Jun;3(1):85-7. doi: 10.1007/s12104-009-9147-7. Epub 2009 Feb 24. PMID- 22267729 OWN - NLM STAT- MEDLINE DA - 20120319 DCOM- 20120612 LR - 20141019 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 12 DP - 2012 Mar 16 TI - Curcumin prevents aggregation in alpha-synuclein by increasing reconfiguration rate. PG - 9193-9 LID - 10.1074/jbc.M111.325548 [doi] AB - alpha-Synuclein is a protein that is intrinsically disordered in vitro and prone to aggregation, particularly at high temperatures. In this work, we examined the ability of curcumin, a compound found in turmeric, to prevent aggregation of the protein. We found strong binding of curcumin to alpha-synuclein in the hydrophobic non-amyloid-beta component region and complete inhibition of oligomers or fibrils. We also found that the reconfiguration rate within the unfolded protein was significantly increased at high temperatures. We conclude that alpha-synuclein is prone to aggregation because its reconfiguration rate is slow enough to expose hydrophobic residues on the same time scale that bimolecular association occurs. Curcumin rescues the protein from aggregation by increasing the reconfiguration rate into a faster regime. FAU - Ahmad, Basir AU - Ahmad B AD - Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA. FAU - Lapidus, Lisa J AU - Lapidus LJ LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120120 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (alpha-Synuclein) RN - IT942ZTH98 (Curcumin) SB - IM MH - Curcumin/*chemistry MH - Hot Temperature MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Kinetics MH - Protein Binding MH - Protein Folding MH - alpha-Synuclein/*chemistry PMC - PMC3308736 OID - NLM: PMC3308736 EDAT- 2012/01/24 06:00 MHDA- 2012/06/13 06:00 CRDT- 2012/01/24 06:00 PHST- 2012/01/20 [aheadofprint] AID - M111.325548 [pii] AID - 10.1074/jbc.M111.325548 [doi] PST - ppublish SO - J Biol Chem. 2012 Mar 16;287(12):9193-9. doi: 10.1074/jbc.M111.325548. Epub 2012 Jan 20. PMID- 20977665 OWN - NLM STAT- MEDLINE DA - 20101027 DCOM- 20101116 LR - 20121115 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 277 IP - 22 DP - 2010 Nov TI - Structure and function of human alpha-lactalbumin made lethal to tumor cells (HAMLET)-type complexes. PG - 4614-25 LID - 10.1111/j.1742-4658.2010.07890.x [doi] AB - Human alpha-lactalbumin made lethal to tumor cells (HAMLET) and equine lysozyme with oleic acid (ELOA) are complexes consisting of protein and fatty acid that exhibit cytotoxic activities, drastically differing from the activity of their respective proteinaceous compounds. Since the discovery of HAMLET in the 1990s, a wealth of information has been accumulated, illuminating the structural, functional and therapeutic properties of protein complexes with oleic acid, which is summarized in this review. In vitro, both HAMLET and ELOA are produced by using ion-exchange columns preconditioned with oleic acid. However, the complex of human alpha-lactalbumin with oleic acid with the antitumor activity of HAMLET was found to be naturally present in the acidic fraction of human milk, where it was discovered by serendipity. Structural studies have shown that alpha-lactalbumin in HAMLET and lysozyme in ELOA are partially unfolded, 'molten-globule'-like, thereby rendering the complexes dynamic and in conformational exchange. HAMLET exists in the monomeric form, whereas ELOA mostly exists as oligomers and the fatty acid stoichiometry varies, with HAMLET holding an average of approximately five oleic acid molecules, whereas ELOA contains a considerably larger number (11- 48). Potent tumoricidal activity is found in both HAMLET and ELOA, and HAMLET has also shown strong potential as an antitumor drug in different in vivo animal models and clinical studies. The gain of new, beneficial function upon partial protein unfolding and fatty acid binding is a remarkable phenomenon, and may reflect a significant generic route of functional diversification of proteins via varying their conformational states and associated ligands. CI - (c) 2010 The Authors Journal compilation (c) 2010 FEBS. FAU - Mossberg, Ann-Kristin AU - Mossberg AK AD - Department of Microbiology, Immunology and Glycobiology (MIG), Institute of Laboratory Medicine, Lund University, Lund, Sweden. Anki.Mossberg@med.lu.se FAU - Hun Mok, Kenneth AU - Hun Mok K FAU - Morozova-Roche, Ludmilla A AU - Morozova-Roche LA FAU - Svanborg, Catharina AU - Svanborg C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Chromatin) RN - 0 (Fatty Acids) RN - 0 (HAMLET complex, human) RN - 0 (Oleic Acids) RN - 0 (Proteasome Inhibitors) RN - 9013-90-5 (Lactalbumin) RN - EC 3.2.1.17 (Muramidase) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Animals MH - Apoptosis/physiology MH - Autophagy/physiology MH - Chromatin/metabolism MH - Cytoplasmic Vesicles/chemistry/metabolism MH - Fatty Acids/chemistry/metabolism MH - Humans MH - Lactalbumin/*chemistry/*metabolism/therapeutic use MH - Models, Molecular MH - Muramidase/chemistry/metabolism MH - Neoplasms/drug therapy/pathology MH - Oleic Acids/*chemistry/*metabolism/therapeutic use MH - Proteasome Endopeptidase Complex/metabolism MH - Proteasome Inhibitors MH - Protein Binding MH - *Protein Conformation MH - Protein Folding EDAT- 2010/10/28 06:00 MHDA- 2010/11/17 06:00 CRDT- 2010/10/28 06:00 AID - 10.1111/j.1742-4658.2010.07890.x [doi] PST - ppublish SO - FEBS J. 2010 Nov;277(22):4614-25. doi: 10.1111/j.1742-4658.2010.07890.x. PMID- 24058647 OWN - NLM STAT- MEDLINE DA - 20130923 DCOM- 20140930 LR - 20141112 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 9 DP - 2013 TI - Mechanistic insight into the relationship between N-terminal acetylation of alpha-synuclein and fibril formation rates by NMR and fluorescence. PG - e75018 LID - 10.1371/journal.pone.0075018 [doi] AB - Aggregation of alpha-synuclein (alphaSyn), the primary protein component in Lewy body inclusions of patients with Parkinson's disease, arises when the normally soluble intrinsically disordered protein converts to amyloid fibrils. In this work, we provide a mechanistic view of the role of N-terminal acetylation on fibrillation by first establishing a quantitative relationship between monomer secondary structural propensity and fibril assembly kinetics, and secondly by demonstrating in the N-terminal acetylated form of the early onset A53T mutation, that N-terminal transient helices formed and/or inhibited by N-terminal acetylation modulate the fibril assembly rates. Using NMR chemical shifts and fluorescence experiments, we report that secondary structural propensity in residues 5-8, 14-31, and 50-57 are highly correlated to fibril growth rate. A four-way comparison of secondary structure propensity and fibril growth rates of N-terminally acetylated A53T and WT alphaSyn with non-acetylated A53T and WT alphaSyn present novel mechanistic insight into the role of N-terminal acetylation in amyloid fibril formation. We show that N-terminal acetylation inhibits the formation of the "fibrillation promoting" transient helix at residues 14-31 resulting from the A53T mutation in the non-acetylated variant and supports the formation of the "fibrillation inhibiting" transient helix in residues 1-12 thereby resulting in slower fibrillation rates relative to the previously studied non-acetylated A53T variant. Our results highlight the critical interplay of the region-specific transient secondary structure of the N-terminal region with fibrillation, and the inhibitory role of the N-terminal acetyl group in fibril formation. FAU - Kang, Lijuan AU - Kang L AD - Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America. FAU - Janowska, Maria K AU - Janowska MK FAU - Moriarty, Gina M AU - Moriarty GM FAU - Baum, Jean AU - Baum J LA - eng GR - GM087012/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20130918 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Amyloid) RN - 0 (SNCA protein, human) RN - 0 (Snca protein, mouse) RN - 0 (alpha-Synuclein) SB - IM MH - Acetylation MH - Amino Acid Substitution MH - Amyloid/*chemistry/genetics/metabolism MH - Animals MH - Humans MH - Lewy Bodies/chemistry/genetics/metabolism MH - Mice MH - Mutation, Missense MH - Nuclear Magnetic Resonance, Biomolecular MH - Parkinson Disease/genetics/metabolism/pathology MH - Protein Structure, Secondary MH - Spectrometry, Fluorescence MH - alpha-Synuclein/*chemistry/genetics/metabolism PMC - PMC3776725 OID - NLM: PMC3776725 EDAT- 2013/09/24 06:00 MHDA- 2014/10/01 06:00 CRDT- 2013/09/24 06:00 PHST- 2013 [ecollection] PHST- 2013/05/08 [received] PHST- 2013/08/09 [accepted] PHST- 2013/09/18 [epublish] AID - 10.1371/journal.pone.0075018 [doi] AID - PONE-D-13-18874 [pii] PST - epublish SO - PLoS One. 2013 Sep 18;8(9):e75018. doi: 10.1371/journal.pone.0075018. eCollection 2013. PMID- 11183780 OWN - NLM STAT- MEDLINE DA - 20001024 DCOM- 20001031 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 302 IP - 5 DP - 2000 Oct 6 TI - Structural analysis of the transcriptional activation region on Fis: crystal structures of six Fis mutants with different activation properties. PG - 1139-51 AB - The Fis protein regulates gene expression in Escherichia coli by activating or repressing transcription of a variety of genes. Fis can activate transcription when bound to DNA upstream of the RNA-polymerase-binding site, such as in the rrnB P1 promoter, or when bound to a site overlapping the -35 RNA polymerase binding site, such as in the proP P2 promoter. It has been suggested that transcriptional activation in both promoters results from interactions between specific amino acids within a turn connecting the B and C helices (the BC turn) in Fis and the C-terminal domain of the alpha-subunit of RNA polymerase (alphaCTD of RNAP). Here, crystal structures of six Fis BC turn mutants with different transcriptional activation properties, Q68A, R71Y, R71L, G72A, G72D and Q74A, were determined at 1.9 to 2.8 A resolution. Two of these mutants, R71Y and R71L, crystallized in unit cells which are different from that of wild-type Fis, and the structure of R71L offers the most complete Fis model to date in that the extended structure of the N-terminal region is revealed. The BC turn in all of these mutant structures remains in a nearly identical gamma gamma beta-turn conformation as present in wild-type Fis. Analyses of the molecular surfaces of the transactivation region of the mutants suggest that several residues in or near the BC turn, including Gln68, Arg71, Gly72 and Gln74, form a ridge that could contact the alphaCTD of RNAP on one side. The structures and biochemical properties of the mutants suggest that Arg71 is the most critical residue for contacting RNAP within this ridge and that the glycine at position 72 helps to stabilize the structure. FAU - Cheng, Y S AU - Cheng YS AD - Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan, Republic of China. FAU - Yang, W Z AU - Yang WZ FAU - Johnson, R C AU - Johnson RC FAU - Yuan, H S AU - Yuan HS LA - eng SI - PDB/1ETK SI - PDB/1ETO SI - PDB/1ETQ SI - PDB/1ETV SI - PDB/1ETW SI - PDB/1ETX SI - PDB/1ETY GR - GM38509/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Factor For Inversion Stimulation Protein) RN - 0 (Integration Host Factors) RN - 0 (integration host factor, E coli) RN - 0RH81L854J (Glutamine) RN - 7006-34-0 (Asparagine) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Substitution/genetics MH - Asparagine/genetics/metabolism MH - Bacterial Proteins/chemistry/genetics/metabolism MH - Binding Sites MH - Carrier Proteins/*chemistry/genetics/*metabolism MH - Crystallography, X-Ray MH - DNA/chemistry/genetics/metabolism MH - DNA-Binding Proteins/chemistry/genetics/metabolism MH - Dimerization MH - Escherichia coli/*chemistry MH - *Escherichia coli Proteins MH - Factor For Inversion Stimulation Protein MH - Gene Expression Regulation, Bacterial MH - Glutamine/genetics/metabolism MH - Hydrogen Bonding MH - Integration Host Factors MH - Models, Molecular MH - Mutation/*genetics MH - Nucleic Acid Conformation MH - Protein Denaturation MH - Protein Structure, Secondary MH - Thermodynamics MH - *Transcriptional Activation EDAT- 2001/02/24 12:00 MHDA- 2001/02/28 10:01 CRDT- 2001/02/24 12:00 AID - S0022283600941238 [pii] PST - ppublish SO - J Mol Biol. 2000 Oct 6;302(5):1139-51. PMID- 11593421 OWN - NLM STAT- MEDLINE DA - 20011010 DCOM- 20011101 LR - 20131121 IS - 0950-9232 (Print) IS - 0950-9232 (Linking) VI - 20 IP - 43 DP - 2001 Sep 27 TI - High mobility group I (Y) proteins bind HIPK2, a serine-threonine kinase protein which inhibits cell growth. PG - 6132-41 AB - The HMGI proteins (HMGI, HMGY and HMGI-C) have an important role in the chromatin organization and interact with different transcriptional factors. The HMGI genes are expressed at very low levels in normal adult tissues, whereas they are very abundant during embryonic development and in several experimental and human tumours. In order to isolate proteins interacting with the HMGI(Y) proteins, a yeast two-hybrid screening was performed using the HMGI(Y) protein as bait. This analysis led to the isolation of homeodomain-interacting protein kinase-2 (HIPK2), a serine/threonine nuclear kinase. HIPK2 co-immunoprecipitates with the HMGI(Y) protein in 293T cells. The interaction between HIPK2 and HMGI(Y) occurs through the PEST domain of HIPK2 and it is direct because in vitro translated HIPK2 binds HMGI(Y). We also show that HIPK2 is able to phosphorylate the HMGI(Y) protein by an in vitro kinase assay. In order to understand a possible role of HIPK2 gene in cell growth we performed a colony assay which showed an impressive HIPK2 inhibitory effect on normal thyroid cells. Flow cytometric analysis would indicate the block of cell growth at the G2/M phase of the cell cycle. Since normal thyroid cells do not express detectable HMGI(Y) protein levels, we assume that the HIPK2 inhibitory effect is independent from the interaction with the HMGI(Y) protein. FAU - Pierantoni, G M AU - Pierantoni GM AD - Dipartimento di Biologia e Patologia Cellulare e Molecolare, c/o Centro di Endocrinologia ed Oncologia Sperimentale del CNR, Facolta di Medicina e Chirurgia, Universita degli Studi di Napoli Federico II, 80131 Naples, Italy. FAU - Fedele, M AU - Fedele M FAU - Pentimalli, F AU - Pentimalli F FAU - Benvenuto, G AU - Benvenuto G FAU - Pero, R AU - Pero R FAU - Viglietto, G AU - Viglietto G FAU - Santoro, M AU - Santoro M FAU - Chiariotti, L AU - Chiariotti L FAU - Fusco, A AU - Fusco A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Oncogene JT - Oncogene JID - 8711562 RN - 0 (Carrier Proteins) RN - 0 (DNA, Complementary) RN - 0 (High Mobility Group Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Transcription Factors) RN - 124544-67-8 (HMGA1a Protein) RN - EC 2.7.1.- (HIPK2 protein, human) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - G34N38R2N1 (Bromodeoxyuridine) SB - IM MH - Binding Sites MH - Bromodeoxyuridine/metabolism MH - Carrier Proteins/chemistry/genetics/*metabolism MH - Catalysis MH - Cell Division/drug effects MH - Cell Line MH - Cell Nucleus/enzymology MH - DNA, Complementary/metabolism MH - Flow Cytometry MH - Gene Library MH - HMGA1a Protein MH - High Mobility Group Proteins/chemistry/genetics/*metabolism MH - Humans MH - Models, Genetic MH - Phosphorylation MH - Plasmids/metabolism MH - Precipitin Tests MH - Protein Binding MH - Protein Biosynthesis MH - Protein Structure, Tertiary MH - Protein-Serine-Threonine Kinases/chemistry/genetics/*metabolism MH - Recombinant Fusion Proteins/metabolism MH - Transcription Factors/chemistry/genetics/*metabolism MH - Transfection MH - Two-Hybrid System Techniques EDAT- 2001/10/11 10:00 MHDA- 2001/11/03 10:01 CRDT- 2001/10/11 10:00 PHST- 2000/12/15 [received] PHST- 2001/05/07 [revised] PHST- 2001/05/10 [accepted] AID - 10.1038/sj.onc.1204635 [doi] PST - ppublish SO - Oncogene. 2001 Sep 27;20(43):6132-41. PMID- 1304355 OWN - NLM STAT- MEDLINE DA - 19930702 DCOM- 19930702 LR - 20100907 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 1 IP - 5 DP - 1992 May TI - Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution-state structure of the nucleocapsid protein from HIV-1. PG - 563-74 AB - All retroviral nucleocapsid (NC) proteins contain one or two copies of an invariant 3Cys-1His array (CCHC = C-X2-C-X4-H-X4-C; C = Cys, H = His, X = variable amino acid) that are essential for RNA genome packaging and infectivity and have been proposed to function as zinc-binding domains. Although the arrays are capable of binding zinc in vitro, the physiological relevance of zinc coordination has not been firmly established. We have obtained zinc-edge extended X-ray absorption fine structure (EXAFS) spectra for intact retroviruses in order to determine if virus-bound zinc, which is present in quantities nearly stoichiometric with the CCHC arrays (Bess, J.W., Jr., Powell, P.J., Issaq, H.J., Schumack, L.J., Grimes, M.K., Henderson, L.E., & Arthur, L.O., 1992, J. Virol. 66, 840-847), exists in a unique coordination environment. The viral EXAFS spectra obtained are remarkably similar to the spectrum of a model CCHC zinc finger peptide with known 3Cys-1His zinc coordination structure. This finding, combined with other biochemical results, indicates that the majority of the viral zinc is coordinated to the NC CCHC arrays in mature retroviruses. Based on these findings, we have extended our NMR studies of the HIV-1 NC protein and have determined its three-dimensional solution-state structure. The CCHC arrays of HIV-1 NC exist as independently folded, noninteracting domains on a flexible polypeptide chain, with conservatively substituted aromatic residues forming hydrophobic patches on the zinc finger surfaces. These residues are essential for RNA genome recognition, and fluorescence measurements indicate that at least one residue (Trp37) participates directly in binding to nucleic acids in vitro. The NC is only the third HIV-1 protein to be structurally characterized, and the combined EXAFS, structural, and nucleic acid-binding results provide a basis for the rational design of new NC-targeted antiviral agents and vaccines for the control of AIDS. FAU - Summers, M F AU - Summers MF AD - Department of Chemistry and Biochemistry, University of Maryland Baltimore County 21228. FAU - Henderson, L E AU - Henderson LE FAU - Chance, M R AU - Chance MR FAU - Bess, J W Jr AU - Bess JW Jr FAU - South, T L AU - South TL FAU - Blake, P R AU - Blake PR FAU - Sagi, I AU - Sagi I FAU - Perez-Alvarado, G AU - Perez-Alvarado G FAU - Sowder, R C 3rd AU - Sowder RC 3rd FAU - Hare, D R AU - Hare DR AU - et al. LA - eng GR - AI30917/AI/NIAID NIH HHS/United States GR - GM42561/GM/NIGMS NIH HHS/United States GR - N01-C0-74012/PHS HHS/United States GR - etc. PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Capsid Proteins) RN - 0 (DNA Probes) RN - 0 (Gene Products, gag) RN - 0 (NCP7 protein, Human immunodeficiency virus 1) RN - 0 (Solutions) RN - 0 (Viral Proteins) RN - 0 (gag Gene Products, Human Immunodeficiency Virus) SB - IM SB - X MH - Amino Acid Sequence MH - Base Sequence MH - *Capsid Proteins MH - DNA Probes/metabolism MH - Gene Products, gag/*chemistry MH - HIV-1/*chemistry MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Solutions MH - Spectrometry, X-Ray Emission MH - *Viral Proteins MH - *Zinc Fingers MH - gag Gene Products, Human Immunodeficiency Virus PMC - PMC2142235 OID - NLM: PMC2142235 EDAT- 1992/05/11 19:15 MHDA- 2001/03/28 10:01 CRDT- 1992/05/11 19:15 AID - 10.1002/pro.5560010502 [doi] PST - ppublish SO - Protein Sci. 1992 May;1(5):563-74. PMID- 9653036 OWN - NLM STAT- MEDLINE DA - 19980803 DCOM- 19980803 LR - 20091103 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 280 IP - 1 DP - 1998 Jul 3 TI - Refined structure of Cro repressor protein from bacteriophage lambda suggests both flexibility and plasticity. PG - 129-36 AB - The structure of the Cro repressor protein from phage lambda has been refined to a crystallographic R-value of 19.3% at 2.3 A resolution. The re fined model supports the structure as originally described in 1981 and provides a basis for comparison with the Cro-operator complex described in the accompanying paper. Changes in structure seen in different crystal forms and modifications of Cro suggest that the individual subunits are somewhat plastic in nature. In addition, the dimer of Cro suggests a high degree of flexibility, which may be important in forming the Cro-DNA complex. The structure of the Cro subunit as determined by NMR agrees reasonably well with that in the crystals (root-mean-square discrepancy of about 2 A for all atoms). There are, however, only a limited number of intersubunit distance constraints and, presumably for this reason, the different NMR models for the dimer vary substantially among themselves (discrepancies of 1.3 to 5.5 A). Because of this variation it is not possible to say whether the range of discrepancies between the X-ray and NMR Cro dimers (2.9 to 7.5 A) represent a significant difference between the X-ray and solution structures. It has previously been proposed that substitutions of Tyr26 in Cro increase thermal stability by the "reverse hydrophobic effect", i.e. by exposing 40% more hydrophobic surface to solvent in the folded form than in the unfolded state. The refined structure, however, suggests that Tyr26 is equally solvent exposed in the folded and unfolded states. The most stabilizing substitution is Tyr26-->Asp and in this case it appears that interaction with an alpha-helix dipole is at least partly responsible for the enhanced stability. CI - Copyright 1998 Academic Press. FAU - Ohlendorf, D H AU - Ohlendorf DH AD - Institute of Molecular Biology Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, OR, 97403-1229, USA. FAU - Tronrud, D E AU - Tronrud DE FAU - Matthews, B W AU - Matthews BW LA - eng GR - GM08403/GM/NIGMS NIH HHS/United States GR - GM20066/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DNA-Binding Proteins) RN - 0 (Repressor Proteins) RN - 0 (Solvents) RN - 0 (Viral Proteins) RN - 0 (Viral Regulatory and Accessory Proteins) RN - 0 (phage repressor proteins) SB - IM MH - Bacteriophage lambda/*chemistry MH - Crystallography, X-Ray MH - *DNA-Binding Proteins MH - Heating MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - *Protein Structure, Secondary MH - Repressor Proteins/*chemistry/*genetics MH - Solvents MH - Viral Proteins MH - Viral Regulatory and Accessory Proteins EDAT- 1998/07/07 MHDA- 1998/07/07 00:01 CRDT- 1998/07/07 00:00 AID - S0022-2836(98)91849-6 [pii] AID - 10.1006/jmbi.1998.1849 [doi] PST - ppublish SO - J Mol Biol. 1998 Jul 3;280(1):129-36. PMID- 8373815 OWN - NLM STAT- MEDLINE DA - 19931018 DCOM- 19931018 LR - 20131121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1202 IP - 1 DP - 1993 Sep 3 TI - Two-dimensional nuclear magnetic resonance study of the beta-casein peptide 1-25: resonance assignments and secondary structure. PG - 121-8 AB - The N-terminal 25 amino-acid residue peptide (beta-CN 1-25) obtained from a tryptic digest of bovine beta-casein was studied using two-dimensional NMR techniques. Complete sequence-specific assignment of the 1H-NMR spectrum was performed both in the presence and absence of 22 mM Ca2+. The NMR data supported earlier findings that this segment of beta-casein is highly flexible and adopts multiple conformations. The observed pattern of sequential NOEs indicated that the peptide did not contain stable folded structures. However, the structure was neither that of a fully-extended peptide nor a so-called random coil. The region Ile-12 to SerP-15 showed an enhanced population of extended structure. Furthermore, addition of Ca2+ ions induced chemical-shift changes and apparently decreased the population of conformations with extended structure in the region SerP-18 to Ile-23. FAU - Wahlgren, N M AU - Wahlgren NM AD - Department of Food Technology, University of Lund, Sweden. FAU - Leonil, J AU - Leonil J FAU - Dejmek, P AU - Dejmek P FAU - Drakenberg, T AU - Drakenberg T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Caseins) RN - 0 (Peptide Fragments) RN - EC 3.4.21.4 (Trypsin) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Calcium/pharmacology MH - Caseins/*chemistry MH - Cattle MH - Magnetic Resonance Spectroscopy/methods MH - Molecular Sequence Data MH - Peptide Fragments/*chemistry MH - Protein Conformation MH - *Protein Structure, Secondary MH - Trypsin EDAT- 1993/09/03 MHDA- 1993/09/03 00:01 CRDT- 1993/09/03 00:00 PST - ppublish SO - Biochim Biophys Acta. 1993 Sep 3;1202(1):121-8. PMID- 23821606 OWN - NLM STAT- MEDLINE DA - 20130916 DCOM- 20141231 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 22 IP - 9 DP - 2013 Sep TI - Protonation-dependent conformational variability of intrinsically disordered proteins. PG - 1196-205 LID - 10.1002/pro.2304 [doi] AB - Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity and undergo rearrangements of the time-averaged conformational ensemble on changes of environmental conditions (e.g., in ionic strength, pH, molecular crowding). In contrast to stably folded proteins, IDPs often form compact conformations at acidic pH. The biological relevance of this process was, for example, demonstrated by nuclear magnetic resonance studies of the aggregation prone (low pH) state of alpha-synuclein. In this study, we report a large-scale analysis of the pH dependence of disordered proteins using the recently developed meta-structure approach. The meta-structure analysis of a large set of IDPs revealed a significant tendency of IDPs to form alpha-helical secondary structure elements and to preferentially fold into more compact structures under acidic conditions. The predictive validity of this novel approach was demonstrated with applications to the tumor-suppressor BASP1 and the transcription factor Tcf4. CI - Copyright (c) 2013 The Protein Society. FAU - Geist, Leonhard AU - Geist L AD - Department of Computational and Structural Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria. FAU - Henen, Morkos A AU - Henen MA FAU - Haiderer, Sandra AU - Haiderer S FAU - Schwarz, Thomas C AU - Schwarz TC FAU - Kurzbach, Dennis AU - Kurzbach D FAU - Zawadzka-Kazimierczuk, Anna AU - Zawadzka-Kazimierczuk A FAU - Saxena, Saurabh AU - Saxena S FAU - Zerko, Szymon AU - Zerko S FAU - Kozminski, Wiktor AU - Kozminski W FAU - Hinderberger, Dariush AU - Hinderberger D FAU - Konrat, Robert AU - Konrat R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (BASP1 protein, human) RN - 0 (Basic Helix-Loop-Helix Leucine Zipper Transcription Factors) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Membrane Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Protons) RN - 0 (Repressor Proteins) RN - 0 (TCF4 protein, human) RN - 0 (Transcription Factors) SB - IM MH - Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/*chemistry MH - Humans MH - Hydrogen-Ion Concentration MH - Intrinsically Disordered Proteins/*chemistry MH - Membrane Proteins/*chemistry MH - Models, Molecular MH - Nerve Tissue Proteins/*chemistry MH - Osmolar Concentration MH - Protein Conformation MH - *Protons MH - Repressor Proteins/*chemistry MH - Transcription Factors/*chemistry PMC - PMC3776332 OID - NLM: PMC3776332 OTO - NOTNLM OT - EPR spectroscopy OT - biomolecular NMR OT - intrinsically disordered proteins OT - pH dependence OT - protein meta-structure OT - structural biology EDAT- 2013/07/04 06:00 MHDA- 2015/01/01 06:00 CRDT- 2013/07/04 06:00 PHST- 2013/03/21 [received] PHST- 2013/06/20 [revised] PHST- 2013/06/21 [accepted] AID - 10.1002/pro.2304 [doi] PST - ppublish SO - Protein Sci. 2013 Sep;22(9):1196-205. doi: 10.1002/pro.2304. PMID- 18284662 OWN - NLM STAT- MEDLINE DA - 20080404 DCOM- 20080616 LR - 20140904 IS - 1472-6807 (Electronic) IS - 1472-6807 (Linking) VI - 8 DP - 2008 TI - Interaction between the C-terminal region of human myelin basic protein and calmodulin: analysis of complex formation and solution structure. PG - 10 LID - 10.1186/1472-6807-8-10 [doi] AB - BACKGROUND: The myelin sheath is a multilamellar membrane structure wrapped around the axon, enabling the saltatory conduction of nerve impulses in vertebrates. Myelin basic protein, one of the most abundant myelin-specific proteins, is an intrinsically disordered protein that has been shown to bind calmodulin. In this study, we focus on a 19-mer synthetic peptide from the predicted calmodulin-binding segment near the C-terminus of human myelin basic protein. RESULTS: The interaction of native human myelin basic protein with calmodulin was confirmed by affinity chromatography. The binding of the myelin basic protein peptide to calmodulin was tested with isothermal titration calorimetry (ITC) in different temperatures, and Kd was observed to be in the low muM range, as previously observed for full-length myelin basic protein. Surface plasmon resonance showed that the peptide bound to calmodulin, and binding was accompanied by a conformational change; furthermore, gel filtration chromatography indicated a decrease in the hydrodynamic radius of calmodulin in the presence of the peptide. NMR spectroscopy was used to map the binding area to reside mainly within the hydrophobic pocket of the C-terminal lobe of calmodulin. The solution structure obtained by small-angle X-ray scattering indicates binding of the myelin basic protein peptide into the interlobal groove of calmodulin, while calmodulin remains in an extended conformation. CONCLUSION: Taken together, our results give a detailed structural insight into the interaction of calmodulin with a C-terminal segment of a major myelin protein, the myelin basic protein. The used 19-mer peptide interacts mainly with the C-terminal lobe of calmodulin, and a conformational change accompanies binding, suggesting a novel mode of calmodulin-target protein interaction. Calmodulin does not collapse and wrap around the peptide tightly; instead, it remains in an extended conformation in the solution structure. The observed affinity can be physiologically relevant, given the high abundance of both binding partners in the nervous system. FAU - Majava, Viivi AU - Majava V AD - Department of Biochemistry, University of Oulu, Oulu, Finland. viivi.majava@oulu.fi FAU - Petoukhov, Maxim V AU - Petoukhov MV FAU - Hayashi, Nobuhiro AU - Hayashi N FAU - Pirila, Paivi AU - Pirila P FAU - Svergun, Dmitri I AU - Svergun DI FAU - Kursula, Petri AU - Kursula P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080219 PL - England TA - BMC Struct Biol JT - BMC structural biology JID - 101088689 RN - 0 (Calmodulin) RN - 0 (MBP protein, human) RN - 0 (Myelin Basic Protein) RN - 0 (Nerve Tissue Proteins) RN - 0 (Transcription Factors) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Brain/metabolism MH - Calmodulin/*chemistry/genetics/*metabolism MH - Chromatography, Affinity MH - Chromatography, Gel MH - Circular Dichroism MH - Crystallography, X-Ray MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Myelin Basic Protein MH - Nerve Tissue Proteins/*chemistry/genetics/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Surface Plasmon Resonance MH - Transcription Factors/*chemistry/genetics/*metabolism PMC - PMC2288786 OID - NLM: PMC2288786 EDAT- 2008/02/21 09:00 MHDA- 2008/06/17 09:00 CRDT- 2008/02/21 09:00 PHST- 2007/06/08 [received] PHST- 2008/02/19 [accepted] PHST- 2008/02/19 [aheadofprint] AID - 1472-6807-8-10 [pii] AID - 10.1186/1472-6807-8-10 [doi] PST - epublish SO - BMC Struct Biol. 2008 Feb 19;8:10. doi: 10.1186/1472-6807-8-10. PMID- 21057194 OWN - NLM STAT- MEDLINE DA - 20110509 DCOM- 20110901 LR - 20140821 IS - 1559-2324 (Electronic) IS - 1559-2316 (Linking) VI - 5 IP - 11 DP - 2010 Nov TI - Modifications at the A-domain of the chloroplast import receptor Toc159. PG - 1513-6 LID - 10.1104/pp.110.158048 [doi] AB - Two families of GTPases, the Toc34 and Toc159 GTPase families, take on the task of preprotein recognition at the translocon at the outer membrane of chloroplasts (TOC translocon). The major Toc159 family members have highly acidic N-terminal domains (A-domains) that are non-essential and so far have escaped functional characterization. But recently, interest in the role of the A-domain has strongly increased. The new data of three independent studies provide evidence that the Toc159 A-domain I) participates in preprotein selectivity, II) has typical features of intrinsically unfolded proteins and III) is highly phosphorylated and possibly released from the rest of the protein by a proteolytic event. This hints to a complex regulation of A-domain function that is important for the maintenance of the preprotein selectivity at the TOC translocons. FAU - Agne, Birgit AU - Agne B AD - Institut fur Biochemie und Biotechnologie, Abteilung fur Pflanzenbiochemie, Martin-Luther-Universitat Halle-Wittenberg, Halle (Saale), Germany. FAU - Kessler, Felix AU - Kessler F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101101 PL - United States TA - Plant Signal Behav JT - Plant signaling & behavior JID - 101291431 RN - 0 (Arabidopsis Proteins) RN - 0 (Membrane Proteins) RN - 0 (TOC159 protein, Arabidopsis) RN - EC 3.6.1.- (GTP Phosphohydrolases) SB - IM MH - Amino Acid Sequence MH - Arabidopsis/genetics/*metabolism MH - Arabidopsis Proteins/genetics/*metabolism MH - Chloroplasts/*metabolism MH - GTP Phosphohydrolases/genetics/*metabolism MH - Gene Expression Regulation, Plant/*physiology MH - Membrane Proteins/genetics/*metabolism MH - Phosphorylation MH - Protein Structure, Tertiary MH - Protein Transport PMC - PMC3115270 OID - NLM: PMC3115270 EDAT- 2010/11/09 06:00 MHDA- 2011/09/02 06:00 CRDT- 2010/11/09 06:00 PHST- 2010/11/01 [aheadofprint] AID - 13707 [pii] AID - 10.1104/pp.110.158048 [doi] PST - ppublish SO - Plant Signal Behav. 2010 Nov;5(11):1513-6. doi: 10.1104/pp.110.158048. Epub 2010 Nov 1. PMID- 14695288 OWN - NLM STAT- MEDLINE DA - 20031225 DCOM- 20040831 LR - 20140610 IS - 0006-3495 (Print) IS - 0006-3495 (Linking) VI - 86 IP - 1 Pt 1 DP - 2004 Jan TI - Small angle x-ray scattering from lipid-bound myelin basic protein in solution. PG - 455-60 AB - The structure of myelin basic protein (MBP), purified from the myelin sheath in both lipid-free (LF-MBP) and lipid-bound (LB-MBP) forms, was investigated in solution by small angle x-ray scattering. The water-soluble LF-MBP, extracted at pH < 3.0 from defatted brain, is the classical preparation of MBP, commonly regarded as an intrinsically unfolded protein. LB-MBP is a lipoprotein-detergent complex extracted from myelin with its native lipidic environment at pH > 7.0. Under all conditions, the scattering from the two protein forms was different, indicating different molecular shapes. For the LB-MBP, well-defined scattering curves were obtained, suggesting that the protein had a unique, compact (but not globular) structure. Furthermore, these data were compatible with earlier results from molecular modeling calculations on the MBP structure which have been refined by us. In contrast, the LF-MBP data were in accordance with the expected open-coil conformation. The results represent the first direct structural information from x-ray scattering measurements on MBP in its native lipidic environment in solution. FAU - Haas, H AU - Haas H AD - Universidade de Sao Paulo-Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto, Ribeirao Preto, Brazil. FAU - Oliveira, C L P AU - Oliveira CL FAU - Torriani, I L AU - Torriani IL FAU - Polverini, E AU - Polverini E FAU - Fasano, A AU - Fasano A FAU - Carlone, G AU - Carlone G FAU - Cavatorta, P AU - Cavatorta P FAU - Riccio, P AU - Riccio P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Lipids) RN - 0 (Myelin Basic Protein) RN - 0 (Solutions) SB - IM MH - Computer Simulation MH - Lipids/analysis/*chemistry MH - *Models, Molecular MH - Myelin Basic Protein/analysis/*chemistry/classification MH - Protein Binding MH - Scattering, Radiation MH - Solutions MH - X-Ray Diffraction/*methods PMC - PMC1303811 OID - NLM: PMC1303811 EDAT- 2003/12/26 05:00 MHDA- 2004/09/01 05:00 CRDT- 2003/12/26 05:00 AID - S0006-3495(04)74122-3 [pii] AID - 10.1016/S0006-3495(04)74122-3 [doi] PST - ppublish SO - Biophys J. 2004 Jan;86(1 Pt 1):455-60. PMID- 25031324 OWN - NLM STAT- MEDLINE DA - 20140830 DCOM- 20150122 LR - 20150401 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 289 IP - 35 DP - 2014 Aug 29 TI - Expanding the proteome of an RNA virus by phosphorylation of an intrinsically disordered viral protein. PG - 24397-416 LID - 10.1074/jbc.M114.589911 [doi] AB - The human proteome contains myriad intrinsically disordered proteins. Within intrinsically disordered proteins, polyproline-II motifs are often located near sites of phosphorylation. We have used an unconventional experimental paradigm to discover that phosphorylation by protein kinase A (PKA) occurs in the intrinsically disordered domain of hepatitis C virus non-structural protein 5A (NS5A) on Thr-2332 near one of its polyproline-II motifs. Phosphorylation shifts the conformational ensemble of the NS5A intrinsically disordered domain to a state that permits detection of the polyproline motif by using (15)N-, (13)C-based multidimensional NMR spectroscopy. PKA-dependent proline resonances were lost in the presence of the Src homology 3 domain of c-Src, consistent with formation of a complex. Changing Thr-2332 to alanine in hepatitis C virus genotype 1b reduced the steady-state level of RNA by 10-fold; this change was lethal for genotype 2a. The lethal phenotype could be rescued by changing Thr-2332 to glutamic acid, a phosphomimetic substitution. Immunofluorescence and transmission electron microscopy showed that the inability to produce Thr(P)-2332-NS5A caused loss of integrity of the virus-induced membranous web/replication organelle. An even more extreme phenotype was observed in the presence of small molecule inhibitors of PKA. We conclude that the PKA-phosphorylated form of NS5A exhibits unique structure and function relative to the unphosphorylated protein. We suggest that post-translational modification of viral proteins containing intrinsic disorder may be a general mechanism to expand the viral proteome without a corresponding expansion of the genome. CI - (c) 2014 by The American Society for Biochemistry and Molecular Biology, Inc. FAU - Cordek, Daniel G AU - Cordek DG AD - From the Department of Biochemistry and Molecular Biology. FAU - Croom-Perez, Tayler J AU - Croom-Perez TJ AD - From the Department of Biochemistry and Molecular Biology. FAU - Hwang, Jungwook AU - Hwang J AD - the Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimri-ro, Seongdong-gu, Seoul, 133-791, Korea. FAU - Hargittai, Michele R S AU - Hargittai MR AD - the Department of Chemistry, Saint Francis University, Loretto, Pennsylvania 15940. FAU - Subba-Reddy, Chennareddy V AU - Subba-Reddy CV AD - the Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, and. FAU - Han, Qingxia AU - Han Q AD - From the Department of Biochemistry and Molecular Biology. FAU - Lodeiro, Maria Fernanda AU - Lodeiro MF AD - From the Department of Biochemistry and Molecular Biology. FAU - Ning, Gang AU - Ning G AD - the Huck Institutes of the Life Sciences, and. FAU - McCrory, Thomas S AU - McCrory TS AD - From the Department of Biochemistry and Molecular Biology. FAU - Arnold, Jamie J AU - Arnold JJ AD - From the Department of Biochemistry and Molecular Biology. FAU - Koc, Hasan AU - Koc H AD - the Department of Pharmaceutical Science and Research, Marshall University School of Pharmacy, Huntington, West Virginia 25755. FAU - Lindenbach, Brett D AU - Lindenbach BD AD - the Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, and. FAU - Showalter, Scott A AU - Showalter SA AD - the Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802. FAU - Cameron, Craig E AU - Cameron CE AD - From the Department of Biochemistry and Molecular Biology, cec9@psu.edu. LA - eng GR - R01GM0089001/GM/NIGMS NIH HHS/United States GR - R21 AI100590/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140716 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA Primers) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Proteome) RN - 0 (RNA, Viral) RN - 0 (Viral Proteins) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Cell Line MH - Cyclic AMP-Dependent Protein Kinases/metabolism MH - DNA Primers MH - Hepacivirus/genetics/*metabolism/physiology MH - Humans MH - Intrinsically Disordered Proteins/*metabolism MH - Molecular Sequence Data MH - Phosphorylation MH - Polymerase Chain Reaction MH - *Proteome MH - RNA, Viral/genetics MH - Tandem Mass Spectrometry MH - Viral Proteins/*metabolism MH - Virus Replication PMC - PMC4148867 OID - NLM: PMC4148867 [Available on 08/29/15] OTO - NOTNLM OT - Hepatitis C Virus (HCV) OT - Intrinsically Disordered Protein OT - NMR OT - Non-structural Protein 5A OT - Phosphorylation OT - RNA Virus OT - Viral Replication EDAT- 2014/07/18 06:00 MHDA- 2015/01/23 06:00 CRDT- 2014/07/18 06:00 PMCR- 2015/08/29 00:00 PHST- 2014/07/16 [aheadofprint] AID - M114.589911 [pii] AID - 10.1074/jbc.M114.589911 [doi] PST - ppublish SO - J Biol Chem. 2014 Aug 29;289(35):24397-416. doi: 10.1074/jbc.M114.589911. Epub 2014 Jul 16. PMID- 19520085 OWN - NLM STAT- MEDLINE DA - 20090720 DCOM- 20090811 LR - 20131121 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 391 IP - 1 DP - 2009 Aug 7 TI - Structural characterization of the natively unfolded N-terminal domain of human c-Src kinase: insights into the role of phosphorylation of the unique domain. PG - 136-48 LID - 10.1016/j.jmb.2009.06.018 [doi] AB - The N-terminal regions of the members of Src family of non-receptor protein tyrosine kinases are intrinsically unfolded and contain the maximum sequence divergence among them. In this study, we have addressed the structural characterization by nuclear magnetic resonance of this region of 84 residues that encompasses the SH4 and the unique domains (USrc) of the human c-Src. With this aim, the backbone assignment was performed using (13)C-detected experiments that overcome the spectral resolution problems and the large number of prolines that are typical for intrinsically unfolded proteins. The analysis of the residual dipolar couplings measured for the USrc indicates the presence of a low populated helical structure in the 60-75 region. No long-range contacts between remote fragments of the chain were detected with paramagnetic relaxation enhancement experiments. The structural characterization was extended to two different phosphorylation states of USrc that encompassed three different phosphorylated sites, Ser17, Thr37, and Ser75. The structural and conformational changes upon phosphorylation were monitored through chemical shift perturbations and residual dipolar couplings, indicating that modifications occur at local level and no global rearrangements were apparent. These results suggest a scenario where phosphorylation induces a global electrostatic perturbation that could be involved in the membrane unbinding of c-Src and that could be related with the localization of the enzyme. These observations suggest the unique domain of Src kinases as a source of selectivity and reinforce the relevant role of intrinsically disordered proteins in biological processes. FAU - Perez, Yolanda AU - Perez Y AD - Institute for Research in Biomedicine, Parc Cientific de Barcelona, Baldiri Reixac 10, Barcelona, Spain. FAU - Gairi, Margarida AU - Gairi M FAU - Pons, Miquel AU - Pons M FAU - Bernado, Pau AU - Bernado P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090609 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Carbon Isotopes) RN - EC 2.7.10.1 (Protein-Tyrosine Kinases) RN - EC 2.7.10.2 (CSK tyrosine-protein kinase) RN - EC 2.7.10.2 (src-Family Kinases) SB - IM MH - Carbon Isotopes/metabolism MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphorylation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein-Tyrosine Kinases/*chemistry/*metabolism MH - Staining and Labeling/methods MH - src-Family Kinases EDAT- 2009/06/13 09:00 MHDA- 2009/08/12 09:00 CRDT- 2009/06/13 09:00 PHST- 2009/04/14 [received] PHST- 2009/06/04 [revised] PHST- 2009/06/04 [accepted] PHST- 2009/06/09 [aheadofprint] AID - S0022-2836(09)00722-0 [pii] AID - 10.1016/j.jmb.2009.06.018 [doi] PST - ppublish SO - J Mol Biol. 2009 Aug 7;391(1):136-48. doi: 10.1016/j.jmb.2009.06.018. Epub 2009 Jun 9. PMID- 21978030 OWN - NLM STAT- MEDLINE DA - 20111101 DCOM- 20111220 LR - 20141022 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 50 IP - 44 DP - 2011 Nov 8 TI - Detergents stabilize the conformation of phosphodiesterase 6. PG - 9520-31 LID - 10.1021/bi2014695 [doi] AB - Membrane-bound phosphodiesterase 6 (PDE6) plays an important role in visual signal transduction by regulating cGMP levels in rod photoreceptor cells. Our understanding of PDE6 catalysis and structure suffers from inadequate characterization of the alpha and beta subunit catalytic core, interactions of the core with two intrinsically disordered, proteolysis-prone inhibitory PDEgamma (Pgamma) subunits, and binding of two types of isoprenyl-binding protein delta, called PrBP/delta, to the isoprenylated C-termini of the catalytic core. Structural studies of native PDE6 have been also been hampered by the lack of a heterologous expression system for the holoenzyme. In this work, we purified PDE6 in the presence of PrBP/delta and screened for additives and detergents that selectively suppress PDE6 basal activity while sparing that of the trypsin-activated enzyme. Some detergents removed PrBP/delta from the PDE complex, separating it from the holoenzyme after PDE6 purification. Additionally, selected detergents also significantly reduced the level of dissociation of PDE6 subunits, increasing their homogeneity and stabilizing the holoenzyme by substituting for its native membrane environment. FAU - Baker, Bo Y AU - Baker BY AD - Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States. FAU - Palczewski, Krzysztof AU - Palczewski K LA - eng GR - EY009339/EY/NEI NIH HHS/United States GR - P30 EY11373/EY/NEI NIH HHS/United States GR - R01 EY008061/EY/NEI NIH HHS/United States GR - R01 EY008061-26/EY/NEI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20111014 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Detergents) RN - 25339-99-5 (sucrose monolaurate) RN - 506T60A25R (Sorbitol) RN - 57-50-1 (Sucrose) RN - 85316-98-9 (MEGA 8) RN - EC 3.1.4.35 (Cyclic Nucleotide Phosphodiesterases, Type 6) SB - IM MH - Animals MH - Catalytic Domain/drug effects MH - Cattle MH - Cyclic Nucleotide Phosphodiesterases, Type 6/*chemistry/isolation & purification/metabolism MH - Detergents/*chemistry MH - Enzyme Stability/drug effects MH - Protein Conformation/drug effects MH - Proteolysis MH - Sorbitol/analogs & derivatives/chemistry MH - Sucrose/analogs & derivatives/chemistry PMC - PMC3215081 MID - NIHMS332162 OID - NLM: NIHMS332162 OID - NLM: PMC3215081 EDAT- 2011/10/08 06:00 MHDA- 2011/12/21 06:00 CRDT- 2011/10/08 06:00 PHST- 2011/10/14 [aheadofprint] AID - 10.1021/bi2014695 [doi] PST - ppublish SO - Biochemistry. 2011 Nov 8;50(44):9520-31. doi: 10.1021/bi2014695. Epub 2011 Oct 14. PMID- 23848194 OWN - NLM STAT- MEDLINE DA - 20130828 DCOM- 20140220 IS - 1365-2443 (Electronic) IS - 1356-9597 (Linking) VI - 18 IP - 9 DP - 2013 Sep TI - Nucleolar scaffold protein, WDR46, determines the granular compartmental localization of nucleolin and DDX21. PG - 780-97 LID - 10.1111/gtc.12077 [doi] AB - The nuclear scaffold is an insoluble nuclear structure that contributes to the inner nuclear organization. In this study, we showed that one of the nuclear scaffold proteins, WDR46, plays a role as a fundamental scaffold component of the nucleolar structure. WDR46 is a highly insoluble nucleolar protein, and its subcellular localization is dependent on neither DNA nor RNA. The N- and C-terminal regions of WDR46 are predicted to be intrinsically disordered, and both regions are critical for the nucleolar localization of WDR46 and the association with its binding partners. When WDR46 was knocked down, two of its binding partners, nucleolin and DDX21 (involved in 18S rRNA processing), were mislocalized from the granular component to the edges of the nucleoli, whereas other binding partners, NOP2 and EBP2 (involved in 28S rRNA processing), were not affected. This is because the proper recruitment of nucleolin and DDX21 to the nucleoli in daughter cells after cell division is ensured by WDR46. These findings suggest a structural role for WDR46 in organizing the 18S ribosomal RNA processing machinery. This role of WDR46 is enabled by its interaction property via intrinsically disordered regions. CI - (c) 2013 The Authors Genes to Cells (c) 2013 by the Molecular Biology Society of Japan and Wiley Publishing Asia Pty Ltd. FAU - Hirai, Yuya AU - Hirai Y AD - Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan. FAU - Louvet, Emilie AU - Louvet E FAU - Oda, Toshiyuki AU - Oda T FAU - Kumeta, Masahiro AU - Kumeta M FAU - Watanabe, Yuzo AU - Watanabe Y FAU - Horigome, Tsuneyoshi AU - Horigome T FAU - Takeyasu, Kunio AU - Takeyasu K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130715 PL - England TA - Genes Cells JT - Genes to cells : devoted to molecular & cellular mechanisms JID - 9607379 RN - 0 (Antigens, Neoplasm) RN - 0 (Carrier Proteins) RN - 0 (EBNA1BP2 protein, human) RN - 0 (Nuclear Proteins) RN - 0 (Phosphoproteins) RN - 0 (RNA, Ribosomal, 18S) RN - 0 (RNA-Binding Proteins) RN - 0 (WDR46 protein, human) RN - 0 (nucleolin) RN - EC 2.1.1.- (NOP2 protein, human) RN - EC 2.1.1.- (tRNA Methyltransferases) RN - EC 3.6.1.- (DDX21 protein, human) RN - EC 3.6.4.13 (DEAD-box RNA Helicases) SB - IM MH - Active Transport, Cell Nucleus MH - Antigens, Neoplasm/genetics/*metabolism MH - Carrier Proteins/metabolism MH - Cell Nucleolus/metabolism MH - DEAD-box RNA Helicases/*metabolism MH - HeLa Cells MH - Humans MH - Nuclear Proteins/metabolism MH - Phosphoproteins/*metabolism MH - Protein Binding MH - RNA, Ribosomal, 18S/metabolism MH - RNA-Binding Proteins/*metabolism MH - tRNA Methyltransferases/metabolism EDAT- 2013/07/16 06:00 MHDA- 2014/02/22 06:00 CRDT- 2013/07/16 06:00 PHST- 2013/03/04 [received] PHST- 2013/05/16 [accepted] PHST- 2013/07/15 [aheadofprint] AID - 10.1111/gtc.12077 [doi] PST - ppublish SO - Genes Cells. 2013 Sep;18(9):780-97. doi: 10.1111/gtc.12077. Epub 2013 Jul 15. PMID- 22560500 OWN - NLM STAT- MEDLINE DA - 20121001 DCOM- 20130308 IS - 1872-6240 (Electronic) IS - 0006-8993 (Linking) VI - 1476 DP - 2012 Oct 2 TI - From alpha-synuclein to synaptic dysfunctions: new insights into the pathophysiology of Parkinson's disease. PG - 183-202 LID - 10.1016/j.brainres.2012.04.014 [doi] LID - S0006-8993(12)00685-3 [pii] AB - Alpha-synuclein is a natively unfolded protein playing a key role in the regulation of several neuronal synaptic functions in physiological and pathological conditions. Many studies, over the past years, have shown that it is actively involved in PD pathophysiology. Alpha-synuclein is integrated in a complex network of neuronal processes through the interaction with cytosolic and synaptic proteins. Hence, it is not the sole alpha-synuclein pathology but its effects on diverse protein partners and specific cellular pathways in the membrane and/or cytosolic districts such as endoplasmic reticulum/Golgi, axonal and synaptic compartments of dopaminergic neurons, that may cause the onset of neuronal cell dysfunction and degeneration which are among the key pathological features of the PD brain. Here we summarize a series of experimental data supporting that alpha-synuclein aggregation may induce dysfunction and degeneration of synapses via these multiple mechanisms. Taken together, these data add new insights into the complex mechanisms underlying synaptic derangement in PD and other alpha-synucleinopathies. This article is part of a Special Issue entitled: Brain Integration. CI - Copyright (c) 2012 Elsevier B.V. All rights reserved. FAU - Bellucci, Arianna AU - Bellucci A AD - Division of Pharmacology, Department of Biomedical Sciences and Biotechnologies and National Institute of Neuroscience, University of Brescia, Brescia, Italy. bellucci@med.unibs.it FAU - Zaltieri, Michela AU - Zaltieri M FAU - Navarria, Laura AU - Navarria L FAU - Grigoletto, Jessica AU - Grigoletto J FAU - Missale, Cristina AU - Missale C FAU - Spano, Pierfranco AU - Spano P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20120417 PL - Netherlands TA - Brain Res JT - Brain research JID - 0045503 RN - 0 (alpha-Synuclein) SB - IM MH - Brain/*pathology MH - Humans MH - Parkinson Disease/*metabolism/*pathology MH - Synapses/*metabolism/pathology MH - alpha-Synuclein/*metabolism EDAT- 2012/05/09 06:00 MHDA- 2013/03/09 06:00 CRDT- 2012/05/08 06:00 PHST- 2012/01/04 [received] PHST- 2012/03/30 [revised] PHST- 2012/04/09 [accepted] PHST- 2012/04/17 [aheadofprint] AID - S0006-8993(12)00685-3 [pii] AID - 10.1016/j.brainres.2012.04.014 [doi] PST - ppublish SO - Brain Res. 2012 Oct 2;1476:183-202. doi: 10.1016/j.brainres.2012.04.014. Epub 2012 Apr 17. PMID- 17375930 OWN - NLM STAT- MEDLINE DA - 20070411 DCOM- 20070618 LR - 20141125 IS - 0002-7863 (Print) IS - 0002-7863 (Linking) VI - 129 IP - 15 DP - 2007 Apr 18 TI - Molecular mimicry enables competitive recruitment by a natively disordered protein. PG - 4800-7 AB - We report the crystal structure of the Escherichia coli TolB-Pal complex, a protein-protein complex involved in maintaining the integrity of the outer membrane (OM) in all Gram-negative bacteria that is parasitized by colicins (protein antibiotics) to expedite their entry into cells. Nuclease colicins competitively recruit TolB using their natively disordered regions (NDRs) to disrupt its complex with Pal, which is thought to trigger translocation of the toxin across a locally destabilized OM. The structure shows induced-fit binding of peptidoglycan-associated lipoprotein (Pal) to the beta-propeller domain of TolB causing the N-terminus of one of its alpha-helices to unwind and several residues to undergo substantial changes in conformation. The resulting interactions with TolB are known to be essential for the stability of the complex and the bacterial OM. Structural comparisons with a TolB-colicin NDR complex reveal that colicins bind at the Pal site, mimicking rearranged Pal residues while simultaneously appearing to block induced-fit changes in TolB. The study therefore explains how colicins recruit TolB in the bacterial periplasm and highlights a novel binding mechanism for a natively disordered protein. FAU - Bonsor, Daniel A AU - Bonsor DA AD - Department of Biology, University of York, Heslington, York, YO10 5YW, United Kingdom. FAU - Grishkovskaya, Irina AU - Grishkovskaya I FAU - Dodson, Eleanor J AU - Dodson EJ FAU - Kleanthous, Colin AU - Kleanthous C LA - eng GR - BB/C515520/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070322 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Amino Acids) RN - 0 (Bacterial Outer Membrane Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (ExcC protein, E. coli) RN - 0 (Lipoproteins) RN - 0 (Peptidoglycan) RN - 0 (Periplasmic Proteins) RN - 0 (tolB protein, E coli) SB - IM MH - Amino Acids/chemistry/metabolism MH - Bacterial Outer Membrane Proteins/*chemistry/genetics/*metabolism MH - Crystallography, X-Ray MH - Escherichia coli Proteins/*chemistry/genetics/*metabolism MH - Hydrogen Bonding MH - Lipoproteins/*chemistry/genetics/*metabolism MH - Models, Molecular MH - *Molecular Mimicry MH - Peptidoglycan/*chemistry/genetics/*metabolism MH - Periplasmic Proteins/*chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Denaturation MH - Protein Structure, Quaternary MH - Protein Transport MH - Thermodynamics EDAT- 2007/03/23 09:00 MHDA- 2007/06/19 09:00 CRDT- 2007/03/23 09:00 PHST- 2007/03/22 [aheadofprint] AID - 10.1021/ja070153n [doi] PST - ppublish SO - J Am Chem Soc. 2007 Apr 18;129(15):4800-7. Epub 2007 Mar 22. PMID- 16145054 OWN - NLM STAT- MEDLINE DA - 20050907 DCOM- 20050919 LR - 20140605 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 33 IP - 15 DP - 2005 TI - Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility. PG - 5006-16 AB - Escherichia coli endonuclease VIII (Nei) excises oxidized pyrimidines from DNA. It shares significant sequence homology and similar mechanism with Fpg, a bacterial 8-oxoguanine glycosylase. The structure of a covalent Nei-DNA complex has been recently determined, revealing critical amino acid residues which are important for DNA binding and catalysis. Several Fpg structures have also been reported; however, analysis of structural dynamics of Fpg/Nei family proteins has been hindered by the lack of structures of uncomplexed and DNA-bound enzymes from the same source. We report a 2.8 A resolution structure of free wild-type Nei and two structures of its inactive mutants, Nei-E2A (2.3 A) and Nei-R252A (2.05 A). All three structures are virtually identical, demonstrating that the mutations did not affect the overall conformation of the protein in its free state. The structures show a significant conformational change compared with the Nei structure in its complex with DNA, reflecting a approximately 50 degrees rotation of the two main domains of the enzyme. Such interdomain flexibility has not been reported previously for any DNA glycosylase and may present the first evidence for a global DNA-induced conformational change in this class of enzymes. Several local but functionally relevant structural changes are also evident in other parts of the enzyme. FAU - Golan, Gali AU - Golan G AD - Department of Inorganic Chemistry and the Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem Jerusalem 91904, Israel. FAU - Zharkov, Dmitry O AU - Zharkov DO FAU - Feinberg, Hadar AU - Feinberg H FAU - Fernandes, Andrea S AU - Fernandes AS FAU - Zaika, Elena I AU - Zaika EI FAU - Kycia, Jadwiga H AU - Kycia JH FAU - Grollman, Arthur P AU - Grollman AP FAU - Shoham, Gil AU - Shoham G LA - eng GR - CA17395/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050906 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Escherichia coli Proteins) RN - EC 3.1.25.1 (Deoxyribonuclease (Pyrimidine Dimer)) RN - EC 3.1.25.1 (Nei protein, E coli) RN - EC 6.5.1.- (DNA Repair Enzymes) SB - IM MH - Crystallography, X-Ray MH - DNA Repair Enzymes/*chemistry/genetics MH - Deoxyribonuclease (Pyrimidine Dimer)/*chemistry/genetics MH - Escherichia coli Proteins/*chemistry/genetics MH - *Models, Molecular MH - Mutation MH - Protein Structure, Tertiary MH - Rotation MH - Zinc Fingers PMC - PMC1199562 OID - NLM: PMC1199562 EDAT- 2005/09/08 09:00 MHDA- 2005/09/20 09:00 CRDT- 2005/09/08 09:00 PHST- 2005 [ppublish] AID - 33/15/5006 [pii] AID - 10.1093/nar/gki796 [doi] PST - epublish SO - Nucleic Acids Res. 2005 Sep 6;33(15):5006-16. Print 2005. PMID- 17660831 OWN - NLM STAT- MEDLINE DA - 20070806 DCOM- 20071002 LR - 20140904 IS - 1545-9993 (Print) IS - 1545-9985 (Linking) VI - 14 IP - 8 DP - 2007 Aug TI - CFTR regulatory region interacts with NBD1 predominantly via multiple transient helices. PG - 738-45 AB - The regulatory (R) region of the cystic fibrosis transmembrane conductance regulator (CFTR) is intrinsically disordered and must be phosphorylated at multiple sites for full CFTR channel activity, with no one specific phosphorylation site required. In addition, nucleotide binding and hydrolysis at the nucleotide-binding domains (NBDs) of CFTR are required for channel gating. We report NMR studies in the absence and presence of NBD1 that provide structural details for the isolated R region and its interaction with NBD1 at residue-level resolution. Several sites in the R region with measured fractional helical propensity mediate interactions with NBD1. Phosphorylation reduces the helicity of many R-region sites and reduces their NBD1 interactions. This evidence for a dynamic complex with NBD1 that transiently engages different sites of the R region suggests a structural explanation for the dependence of CFTR activity on multiple PKA phosphorylation sites. FAU - Baker, Jennifer M R AU - Baker JM AD - Program in Molecular Structure and Function, The Hospital for Sick Children, 555 University Ave., Toronto, Ontario M5G 1X8, Canada. FAU - Hudson, Rhea P AU - Hudson RP FAU - Kanelis, Voula AU - Kanelis V FAU - Choy, Wing-Yiu AU - Choy WY FAU - Thibodeau, Patrick H AU - Thibodeau PH FAU - Thomas, Philip J AU - Thomas PJ FAU - Forman-Kay, Julie D AU - Forman-Kay JD LA - eng GR - DK49835/DK/NIDDK NIH HHS/United States GR - R37 DK049835/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070729 PL - United States TA - Nat Struct Mol Biol JT - Nature structural & molecular biology JID - 101186374 RN - 0 (CFTR protein, human) RN - 126880-72-6 (Cystic Fibrosis Transmembrane Conductance Regulator) SB - IM MH - Binding Sites MH - Cystic Fibrosis Transmembrane Conductance Regulator/*chemistry MH - Humans MH - Hydrolysis MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphorylation MH - Protein Folding MH - Protein Structure, Tertiary PMC - PMC3943242 MID - NIHMS421347 OID - NLM: NIHMS421347 OID - NLM: PMC3943242 EDAT- 2007/07/31 09:00 MHDA- 2007/10/03 09:00 CRDT- 2007/07/31 09:00 PHST- 2007/01/30 [received] PHST- 2007/06/27 [accepted] PHST- 2007/07/29 [aheadofprint] AID - nsmb1278 [pii] AID - 10.1038/nsmb1278 [doi] PST - ppublish SO - Nat Struct Mol Biol. 2007 Aug;14(8):738-45. Epub 2007 Jul 29. PMID- 14625275 OWN - NLM STAT- MEDLINE DA - 20040202 DCOM- 20040401 LR - 20141120 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 6 DP - 2004 Feb 6 TI - Alternative splicing of Rac1 generates Rac1b, a self-activating GTPase. PG - 4743-9 AB - Rac1b was recently identified in malignant colorectal tumors as an alternative splice variant of Rac1 containing a 19-amino acid insertion next to the switch II region. The structures of Rac1b in the GDP- and the GppNHp-bound forms, determined at a resolution of 1.75 A, reveal that the insertion induces an open switch I conformation and a highly mobile switch II. As a consequence, Rac1b has an accelerated GEF-independent GDP/GTP exchange and an impaired GTP hydrolysis, which is restored partially by GTPase-activating proteins. Interestingly, Rac1b is able to bind the GTPase-binding domain of PAK but not full-length PAK in a GTP-dependent manner, suggesting that the insertion does not completely abolish effector interaction. The presented study provides insights into the structural and biochemical mechanism of a self-activating GTPase. FAU - Fiegen, Dennis AU - Fiegen D AD - Max-Planck-Institut fur molekulare Physiologie, Abteilung Strukturelle Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany. FAU - Haeusler, Lars-Christian AU - Haeusler LC FAU - Blumenstein, Lars AU - Blumenstein L FAU - Herbrand, Ulrike AU - Herbrand U FAU - Dvorsky, Radovan AU - Dvorsky R FAU - Vetter, Ingrid R AU - Vetter IR FAU - Ahmadian, Mohammad R AU - Ahmadian MR LA - eng SI - PDB/1RYF SI - PDB/1RYH PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20031118 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SLC2A4RG protein, human) RN - 0 (Transcription Factors) RN - 86-01-1 (Guanosine Triphosphate) RN - EC 3.6.5.2 (rac1 GTP-Binding Protein) SB - IM MH - Alternative Splicing MH - Binding Sites MH - Crystallography, X-Ray MH - DNA-Binding Proteins MH - Enzyme Activation MH - Guanosine Triphosphate/metabolism MH - Humans MH - Hydrolysis MH - In Vitro Techniques MH - Kinetics MH - Models, Molecular MH - Protein Conformation MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Transcription Factors/metabolism MH - rac1 GTP-Binding Protein/chemistry/*genetics/*metabolism EDAT- 2003/11/20 05:00 MHDA- 2004/04/02 05:00 CRDT- 2003/11/20 05:00 PHST- 2003/11/18 [aheadofprint] AID - 10.1074/jbc.M310281200 [doi] AID - M310281200 [pii] PST - ppublish SO - J Biol Chem. 2004 Feb 6;279(6):4743-9. Epub 2003 Nov 18. PMID- 19086270 OWN - NLM STAT- MEDLINE DA - 20081212 DCOM- 20090129 LR - 20140914 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 50 DP - 2008 Dec 16 TI - A solution NMR investigation into the early events of amelogenin nanosphere self-assembly initiated with sodium chloride or calcium chloride. PG - 13215-22 AB - Using solution-state NMR spectroscopy, new insights into the early events governing amelogenin supramolecular self-assembly have been identified using sodium chloride and calcium chloride to trigger the association. Two-dimensional 1H-15N HSQC spectra were recorded for 15N- and 13C-labeled murine amelogenin as a function of increasing NaCl and CaCl2 concentration beginning with solution conditions of 2% acetic acid at pH 3.0, where amelogenin was monomeric. Residue specific changes in molecular dynamics, manifested by the reduction in intensity and disappearance of 1H-15N HSQC cross-peaks, were observed with the addition of either salt to the protein. With increasing NaCl concentrations, residues between T21 and R31 near the N-terminus were affected first, suggesting that these residues may initiate amelogenin dimerization, the first step in nanosphere assembly. At higher NaCl concentrations, more residues near the N-terminus (Y12-I51) were affected, and with further additions of NaCl, residues near the C-terminus (L141-T171) began to show a similar change in molecular dynamics. With increasing CaCl2 concentrations, a similar stepwise change in molecular dynamics involving essentially the same set of amelogenin residues was observed. As the concentration of either salt was increased, a concomitant increase in the estimated overall rotational correlation time (tau(c)) was observed, consistent with assembly. Self-assembly into a dimer or trimer was established with dynamic light scattering studies under similar conditions that showed an increase in diameter of the smallest species from 4.1 nm in the absence of salt to 10 nm in the presence of salt. These results suggest a possible stepwise interaction mechanism, starting with the N-terminus and followed by the C-terminus, leading to amelogenin nanosphere assembly. FAU - Buchko, Garry W AU - Buchko GW AD - Pacific Northwest National Laboratory, Richland, Washington, USA. FAU - Tarasevich, Barbara J AU - Tarasevich BJ FAU - Bekhazi, Jacky AU - Bekhazi J FAU - Snead, Malcolm L AU - Snead ML FAU - Shaw, Wendy J AU - Shaw WJ LA - eng GR - DE-015347/DE/NIDCR NIH HHS/United States GR - R01 DE015347/DE/NIDCR NIH HHS/United States GR - R01 DE015347-04/DE/NIDCR NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amelogenin) RN - 0 (Solutions) RN - 7647-14-5 (Sodium Chloride) RN - M4I0D6VV5M (Calcium Chloride) SB - IM MH - Amelogenin/*chemistry/metabolism MH - Animals MH - Calcium Chloride/*chemistry MH - Light MH - Mice MH - Nanospheres/*chemistry MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - *Protein Interaction Domains and Motifs MH - Protein Processing, Post-Translational MH - Scattering, Radiation MH - Sodium Chloride/*chemistry MH - Solutions PMC - PMC2663401 MID - NIHMS92647 OID - NLM: NIHMS92647 OID - NLM: PMC2663401 EDAT- 2008/12/17 09:00 MHDA- 2009/01/30 09:00 CRDT- 2008/12/17 09:00 PST - ppublish SO - Biochemistry. 2008 Dec 16;47(50):13215-22. PMID- 15296741 OWN - NLM STAT- MEDLINE DA - 20040806 DCOM- 20050119 LR - 20061115 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 12 IP - 8 DP - 2004 Aug TI - Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1. PG - 1481-8 AB - Acylpeptide hydrolases (APH; also known as acylamino acid releasing enzyme) catalyze the removal of an N-acylated amino acid from blocked peptides. The crystal structure of an APH from the thermophilic archaeon Aeropyrum pernix K1 to 2.1 A resolution confirms it to be a member of the prolyl oligopeptidase family of serine proteases. The structure of apAPH is a symmetric homodimer with each subunit comprised of two domains. The N-terminal domain is a regular seven-bladed beta-propeller, while the C-terminal domain has a canonical alpha/beta hydrolase fold and includes the active site and a conserved Ser445-Asp524-His556 catalytic triad. The complex structure of apAPH with an organophosphorus substrate, p-nitrophenyl phosphate, has also been determined. The complex structure unambiguously maps out the substrate binding pocket and provides a basis for substrate recognition by apAPH. A conserved mechanism for protein degradation from archaea to mammals is suggested by the structural features of apAPH. FAU - Bartlam, Mark AU - Bartlam M AD - Laboratory of Structural Biology, Tsinghua University and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100084, China. FAU - Wang, Ganggang AU - Wang G FAU - Yang, Haitao AU - Yang H FAU - Gao, Renjun AU - Gao R FAU - Zhao, Xiaodong AU - Zhao X FAU - Xie, Guiqiu AU - Xie G FAU - Cao, Shuigui AU - Cao S FAU - Feng, Yan AU - Feng Y FAU - Rao, Zihe AU - Rao Z LA - eng SI - PDB/1VE6 SI - PDB/1VE7 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Amino Acids) RN - 0 (Nitrophenols) RN - 0 (Organophosphorus Compounds) RN - 0 (Peptides) RN - 330-13-2 (nitrophenylphosphate) RN - EC 3.1.- (Esterases) RN - EC 3.4.- (Peptide Hydrolases) RN - EC 3.4.19.1 (acylaminoacyl-peptidase) SB - IM MH - Aeropyrum/enzymology MH - Amino Acids/chemistry MH - Crystallography, X-Ray MH - Esterases/*chemistry MH - *Models, Molecular MH - Nitrophenols/*chemistry MH - Organophosphorus Compounds/*chemistry MH - Peptide Hydrolases/*chemistry MH - Peptides/*chemistry MH - Protein Structure, Tertiary EDAT- 2004/08/07 05:00 MHDA- 2005/01/20 09:00 CRDT- 2004/08/07 05:00 PHST- 2004/04/01 [received] PHST- 2004/05/16 [revised] PHST- 2004/05/25 [accepted] AID - 10.1016/j.str.2004.05.019 [doi] AID - S0969212604002382 [pii] PST - ppublish SO - Structure. 2004 Aug;12(8):1481-8. PMID- 18855701 OWN - NLM STAT- MEDLINE DA - 20081015 DCOM- 20081113 IS - 1389-2037 (Print) IS - 1389-2037 (Linking) VI - 9 IP - 5 DP - 2008 Oct TI - Alpha-synuclein misfolding and neurodegenerative diseases. PG - 507-40 AB - Alpha-synuclein is an abundant presynaptic brain protein, misfolding, aggregation and fibrillation of which are implicated as critical factors in several neurodegenerative diseases. The list of the well-known synucleinopathies includes such devastating disorders as Parkinson's disease, Lewy body variant of Alzheimer's disease, diffuse Lewy body disease, dementia with Lewy bodies, multiple system atrophy, and neurodegeneration with brain iron accumulation type I. The precise functions of alpha-synuclein remain elusive, but there are evidence indicating its involvement in regulation vesicular release and/or turnover and synaptic function in the central nervous system. It might play a role in neuronal plasticity responses, bind fatty acids, regulate certain enzymes, transporters, and neurotransmitter vesicles, be involved in neuronal survival and even can act as a molecular chaperone. Structurally, alpha-synuclein is an illustrative member of the rapidly growing family of natively unfolded (or intrinsically disordered) proteins and considerable knowledge has been accumulated about its structural properties and conformational behavior. The molecular mechanisms underlying misfolding, aggregation and fibrillation of alpha-synuclein and the role of various environmental and genetic factors in stimulation and inhibition of these processes are relatively well understood. Here, the main structural features of alpha-synuclein, its functions, and involvement in various human diseases are summarized providing a foundation for better understanding of the biochemistry, biophysics and neuropathology of alpha-synuclein aggregation. FAU - Uversky, Vladimir N AU - Uversky VN AD - Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA. vuversky@iupui.edu LA - eng GR - GM 071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 LM 007688-01A1/LM/NLM NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review PL - Netherlands TA - Curr Protein Pept Sci JT - Current protein & peptide science JID - 100960529 RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Animals MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Neurodegenerative Diseases/*metabolism/pathology MH - Point Mutation MH - *Protein Folding MH - Protein Processing, Post-Translational MH - alpha-Synuclein/*chemistry/genetics/*metabolism RF - 509 EDAT- 2008/10/16 09:00 MHDA- 2008/11/14 09:00 CRDT- 2008/10/16 09:00 PST - ppublish SO - Curr Protein Pept Sci. 2008 Oct;9(5):507-40. PMID- 12270711 OWN - NLM STAT- MEDLINE DA - 20020924 DCOM- 20021218 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 322 IP - 4 DP - 2002 Sep 27 TI - Structure of domain III of the blood-stage malaria vaccine candidate, Plasmodium falciparum apical membrane antigen 1 (AMA1). PG - 741-53 AB - Apical membrane antigen 1 of the malarial parasite Plasmodium falciparum (Pf AMA1) is a merozoite antigen that is considered a strong candidate for inclusion in a malaria vaccine. Antibodies reacting with disulphide bond-dependent epitopes in AMA1 block invasion of host erythrocytes by P.falciparum merozoites, and we show here that epitopes involving sites of mutations in domain III are targets of inhibitory human antibodies. The solution structure of AMA1 domain III, a 14kDa protein, has been determined using NMR spectroscopy on uniformly 15N and 13C/15N-labelled samples. The structure has a well-defined disulphide-stabilised core region separated by a disordered loop, and both the N and C-terminal regions of the molecule are unstructured. Within the disulphide-stabilised core, residues 443-447 form a turn of helix and residues 495-498 and 503-506 an anti-parallel beta-sheet with a distorted type I beta-turn centred on residues 500-501, producing a beta-hairpin-type structure. The structured region of the molecule includes all three disulphide bonds. The previously unassigned connectivities for two of these bonds could not be established with certainty from the NMR data and structure calculations, but were determined to be C490-C507 and C492-C509 from an antigenic analysis of mutated forms of this domain expressed using phage display. Naturally occurring mutations in domain III that are located far apart in the primary sequence tend to cluster in the region of the disulphide core in the three-dimensional structure of the molecule. The structure shows that nearly all the polymorphic sites have a high level of solvent accessibility, consistent with their location in epitopes recognised by protective antibodies. Even though domain III in solution contains significant regions of disorder in the structure, the disulphide-stabilised core that is structured is clearly an important element of the antigenic surface of AMA1 recognised by protective antibodies. FAU - Nair, Margie AU - Nair M AD - Biomolecular Research Institute, 343 Royal Parade, Parkville, Vic. 3052, Australia. FAU - Hinds, Mark G AU - Hinds MG FAU - Coley, Andrew M AU - Coley AM FAU - Hodder, Anthony N AU - Hodder AN FAU - Foley, Michael AU - Foley M FAU - Anders, Robin F AU - Anders RF FAU - Norton, Raymond S AU - Norton RS LA - eng SI - PDB/1HN6 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Antibodies, Protozoan) RN - 0 (Antigens, Protozoan) RN - 0 (Disulfides) RN - 0 (Malaria Vaccines) RN - 0 (Membrane Proteins) RN - 0 (Protozoan Proteins) RN - 0 (apical membrane antigen I, Plasmodium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Antibodies, Protozoan/immunology MH - Antigens, Protozoan/*chemistry/immunology MH - Disulfides MH - Humans MH - Malaria MH - Malaria Vaccines/immunology MH - Membrane Proteins/*chemistry/immunology MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Plasmodium falciparum/*immunology/pathogenicity MH - Protein Structure, Tertiary MH - Protozoan Proteins/*chemistry/immunology MH - Sequence Homology, Amino Acid EDAT- 2002/09/25 06:00 MHDA- 2002/12/19 04:00 CRDT- 2002/09/25 06:00 AID - S0022283602008069 [pii] PST - ppublish SO - J Mol Biol. 2002 Sep 27;322(4):741-53. PMID- 20298817 OWN - NLM STAT- MEDLINE DA - 20100524 DCOM- 20100722 LR - 20131121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1804 IP - 7 DP - 2010 Jul TI - Aquifex aeolicus FlgM protein exhibits a temperature-dependent disordered nature. PG - 1457-66 LID - 10.1016/j.bbapap.2010.03.002 [doi] AB - Studies on the nature and function of intrinsically disordered proteins (IDP) over the past 10 years have demonstrated the importance of IDPs in normal cellular function. Although many proteins predicted to be IDPs have been experimentally characterized on an individual basis, the conservation of disorder between homologous proteins from different organisms has not been fully studied. We now demonstrate that the FlgM protein from the thermophile Aquifex aeolicus exhibits a more ordered conformation at 20 degrees C than the previously characterized FlgM protein from Salmonella typhimurium. FlgM is an inhibitor of the RNA transcription factor sigma28, which is involved in regulation of the late-stage genes involved in flagella synthesis. Previous work has shown that the S. typhimurium FlgM protein is an intrinsically disordered protein, though the C-terminus becomes ordered when bound to sigma28 or under crowded solution conditions. In this work, we demonstrate that at 20 degrees C the A. aeolicus FlgM protein exhibits alpha-helical character in circular dichroism (CD) experiments, though the percentage of alpha-helical content decreases with increased temperature, consistent with the FlgM assuming a less folded conformation. We also show that the A. aeolicus FlgM exhibits cooperativity in chemical denaturation experiments, consistent with a globular nature. Furthermore, we use the fluorescent probe FlAsH to show that the H2 helix is ordered, even in the unbound state and that the H1 and H2 helices appear to be associated with each other in the absence of the sigma28 protein. Finally, we demonstrate that the H2 helix assumes an extended conformation at 85 degrees C. Based on our results, we propose that at 20 degrees C the A. aeolicus FlgM assumes a four-helix bundle-like conformation that becomes a more extended conformation at the A. aeolicus' physiological temperature of 85 degrees C. CI - Copyright (c) 2010 Elsevier B.V. All rights reserved. FAU - Molloy, Rhett G AU - Molloy RG AD - Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011-5698, USA. FAU - Ma, Wai Kit AU - Ma WK FAU - Allen, Andrew C AU - Allen AC FAU - Greenwood, Kevin AU - Greenwood K FAU - Bryan, Lynn AU - Bryan L FAU - Sacora, Rebecca AU - Sacora R FAU - Williams, LaBrittney AU - Williams L FAU - Gage, Matthew J AU - Gage MJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100316 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Bacterial Proteins) RN - 142462-45-1 (FlgM protein, Bacteria) RN - 8W8T17847W (Urea) SB - IM MH - Bacteria/*metabolism MH - Bacterial Proteins/chemistry/*metabolism MH - Circular Dichroism MH - Gene Expression Regulation, Bacterial MH - Microscopy, Fluorescence/methods MH - Models, Biological MH - Models, Statistical MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Salmonella typhimurium/*metabolism MH - Temperature MH - Urea/chemistry EDAT- 2010/03/20 06:00 MHDA- 2010/07/23 06:00 CRDT- 2010/03/20 06:00 PHST- 2009/11/04 [received] PHST- 2010/03/02 [revised] PHST- 2010/03/05 [accepted] PHST- 2010/03/16 [aheadofprint] AID - S1570-9639(10)00080-4 [pii] AID - 10.1016/j.bbapap.2010.03.002 [doi] PST - ppublish SO - Biochim Biophys Acta. 2010 Jul;1804(7):1457-66. doi: 10.1016/j.bbapap.2010.03.002. Epub 2010 Mar 16. PMID- 19941902 OWN - NLM STAT- MEDLINE DA - 20100311 DCOM- 20100525 IS - 1879-0984 (Electronic) IS - 0166-0934 (Linking) VI - 164 IP - 1-2 DP - 2010 Mar TI - High yield expression and purification of HIV-1 Tat1-72 for structural studies. PG - 35-42 LID - 10.1016/j.jviromet.2009.11.021 [doi] AB - The HIV-1 transactivator of transcription (Tat) is a protein essential for virus replication. Tat is an intrinsically disordered RNA-binding protein that, in cooperation with host cell factors cyclin T1 and cyclin-dependent kinase 9, regulates transcription at the level of elongation. Tat also interacts with numerous other intracellular and extracellular proteins, and is implicated in a number of pathogenic processes. The physico-chemical properties of Tat make it a particularly challenging target for structural studies: Tat contains seven Cys residues, six of which are essential for transactivation, and is highly susceptible to oxidative cross-linking and aggregation. In addition, a basic segment (residues 48-57) gives the protein a high net positive charge of +12 at pH 7, endowing it with a high affinity for anionic polymers and surfaces. In order to study the structure of Tat, both alone and in complex with partner molecules, we have developed a system for the bacterial expression and purification of 6xHistidine-tagged and isotopically enriched (in N15 and C13) recombinant HIV-1 Tat(1-72) (BH10 isolate) that yields large amounts of protein. These preparations have facilitated the assignment of 95% of the backbone NMR resonances. Analysis by mass spectrometry and NMR demonstrate that the cysteine-rich Tat protein is unambiguously reduced, monomeric, and unfolded in aqueous solution at pH 4. CI - Copyright (c) 2009 Elsevier B.V. All rights reserved. FAU - Shojania, Shaheen AU - Shojania S AD - Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada. shojania@gmail.com FAU - Henry, Gillian D AU - Henry GD FAU - Chen, Vincent C AU - Chen VC FAU - Vo, Thach N AU - Vo TN FAU - Perreault, Helene AU - Perreault H FAU - O'Neil, Joe D AU - O'Neil JD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091124 PL - Netherlands TA - J Virol Methods JT - Journal of virological methods JID - 8005839 RN - 0 (Recombinant Fusion Proteins) RN - 0 (tat Gene Products, Human Immunodeficiency Virus) RN - 0 (tat peptide (1-72), Human immunodeficiency virus 1) SB - IM MH - HIV-1/*chemistry/*genetics MH - Humans MH - Mass Spectrometry MH - Nuclear Magnetic Resonance, Biomolecular MH - Recombinant Fusion Proteins/chemistry/genetics/isolation & purification MH - tat Gene Products, Human Immunodeficiency Virus/*chemistry/genetics/*isolation & purification EDAT- 2009/11/28 06:00 MHDA- 2010/05/26 06:00 CRDT- 2009/11/28 06:00 PHST- 2009/06/23 [received] PHST- 2009/11/17 [revised] PHST- 2009/11/17 [accepted] PHST- 2009/11/24 [aheadofprint] AID - S0166-0934(09)00505-9 [pii] AID - 10.1016/j.jviromet.2009.11.021 [doi] PST - ppublish SO - J Virol Methods. 2010 Mar;164(1-2):35-42. doi: 10.1016/j.jviromet.2009.11.021. Epub 2009 Nov 24. PMID- 24100036 OWN - NLM STAT- MEDLINE DA - 20131125 DCOM- 20140204 LR - 20141125 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 47 DP - 2013 Nov 22 TI - A network of interdependent molecular interactions describes a higher order Nrd1-Nab3 complex involved in yeast transcription termination. PG - 34158-67 LID - 10.1074/jbc.M113.516765 [doi] AB - Nab3 and Nrd1 are yeast heterogeneous nuclear ribonucleoprotein (hnRNP)-like proteins that heterodimerize and bind RNA. Genetic and biochemical evidence reveals that they are integral to the termination of transcription of short non-coding RNAs by RNA polymerase II. Here we define a Nab3 mutation (nab3Delta134) that removes an essential part of the protein's C terminus but nevertheless can rescue, in trans, the phenotype resulting from a mutation in the RNA recognition motif of Nab3. This low complexity region of Nab3 appears intrinsically unstructured and can form a hydrogel in vitro. These data support a model in which multiple Nrd1-Nab3 heterodimers polymerize onto substrate RNA to effect termination, allowing complementation of one mutant Nab3 molecule by another lacking a different function. The self-association property of Nab3 adds to the previously documented interactions between these hnRNP-like proteins, RNA polymerase II, and the nascent transcript, leading to a network of nucleoprotein interactions that define a higher order Nrd1-Nab3 complex. This was underscored from the synthetic phenotypes of yeast strains with pairwise combinations of Nrd1 and Nab3 mutations known to affect their distinct biochemical activities. The mutations included a Nab3 self-association defect, a Nab3-Nrd1 heterodimerization defect, a Nrd1-polymerase II binding defect, and an Nab3-RNA recognition motif mutation. Although no single mutation was lethal, cells with any two mutations were not viable for four such pairings, and a fifth displayed a synthetic growth defect. These data strengthen the idea that a multiplicity of interactions is needed to assemble a higher order Nrd1-Nab3 complex that coats specific nascent RNAs in preparation for termination. FAU - Loya, Travis J AU - Loya TJ AD - From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322. FAU - O'Rourke, Thomas W AU - O'Rourke TW FAU - Degtyareva, Natalya AU - Degtyareva N FAU - Reines, Daniel AU - Reines D LA - eng GR - R01 GM046331/GM/NIGMS NIH HHS/United States GR - R01GM46331/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20131007 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Multiprotein Complexes) RN - 0 (NAB3 protein, S cerevisiae) RN - 0 (NRD1 protein, S cerevisiae) RN - 0 (Nuclear Proteins) RN - 0 (RNA, Fungal) RN - 0 (RNA-Binding Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 2.7.7.- (RNA Polymerase II) SB - IM MH - Amino Acid Motifs MH - Multiprotein Complexes/genetics/*metabolism MH - Mutation MH - Nuclear Proteins/genetics/*metabolism MH - Protein Multimerization/physiology MH - RNA Polymerase II/genetics/metabolism MH - RNA, Fungal/*biosynthesis/genetics MH - RNA-Binding Proteins/genetics/*metabolism MH - Saccharomyces cerevisiae/genetics/*metabolism MH - Saccharomyces cerevisiae Proteins/genetics/*metabolism MH - Transcription Termination, Genetic/*physiology PMC - PMC3837157 OID - NLM: PMC3837157 OTO - NOTNLM OT - Gene Regulation OT - Nab3 OT - Nrd1 OT - Polyglutamine OT - RNA OT - RNA Polymerase II OT - RNA-binding Protein OT - Transcription Elongation Factors OT - Transcription Termination EDAT- 2013/10/09 06:00 MHDA- 2014/02/05 06:00 CRDT- 2013/10/09 06:00 PHST- 2013/10/07 [aheadofprint] AID - M113.516765 [pii] AID - 10.1074/jbc.M113.516765 [doi] PST - ppublish SO - J Biol Chem. 2013 Nov 22;288(47):34158-67. doi: 10.1074/jbc.M113.516765. Epub 2013 Oct 7. PMID- 11959977 OWN - NLM STAT- MEDLINE DA - 20020417 DCOM- 20020614 LR - 20140613 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 99 IP - 8 DP - 2002 Apr 16 TI - Structural basis for Hif-1 alpha /CBP recognition in the cellular hypoxic response. PG - 5271-6 AB - The cellular response to low tissue oxygen concentrations is mediated by the hypoxia-inducible transcription factor HIF-1. Under hypoxic conditions, HIF-1 activates transcription of critical adaptive genes by recruitment of the general coactivators CBP/p300 through interactions with its alpha-subunit (Hif-1 alpha). Disruption of the Hif-1 alpha/p300 interaction has been linked to attenuation of tumor growth. To delineate the structural basis for this interaction, we have determined the solution structure of the complex between the carboxy-terminal activation domain (CAD) of Hif-1 alpha and the zinc-binding TAZ1 (CH1) motif of cyclic-AMP response element binding protein (CREB) binding protein (CBP). Despite the overall similarity of the TAZ1 structure to that of the TAZ2 (part of the CH3) domain of CBP, differences occur in the packing of helices that can account for differences in specificity. The unbound CAD is intrinsically disordered and remains relatively extended upon binding, wrapping almost entirely around the TAZ1 domain in a groove through much of its surface. Three short helices are formed upon binding, stabilized by intermolecular interactions. The Asn-803 side chain, which functions as a hypoxic switch, is located on the second of these helices and is buried in the molecular interface. The third helix of the Hif-1 alpha CAD docks in a deep hydrophobic groove in TAZ1, providing extensive intermolecular hydrophobic interactions that contribute to the stability of the complex. The structure of this complex provides new insights into the mechanism through which Hif-1 alpha recruits CBP/p300 in response to hypoxia. FAU - Dames, Sonja A AU - Dames SA AD - Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. FAU - Martinez-Yamout, Maria AU - Martinez-Yamout M FAU - De Guzman, Roberto N AU - De Guzman RN FAU - Dyson, H Jane AU - Dyson HJ FAU - Wright, Peter E AU - Wright PE LA - eng SI - PDB/1L8C PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Ep300 protein, mouse) RN - 0 (Hypoxia-Inducible Factor 1, alpha Subunit) RN - 0 (Nuclear Proteins) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - E0399OZS9N (Cyclic AMP) RN - EC 2.3.1.48 (E1A-Associated p300 Protein) RN - J41CSQ7QDS (Zinc) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - *Anoxia MH - Binding Sites MH - Cyclic AMP/metabolism MH - E1A-Associated p300 Protein MH - Hydrogen Bonding MH - Hypoxia-Inducible Factor 1, alpha Subunit MH - Magnetic Resonance Spectroscopy MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Proteins/*chemistry MH - Protein Binding MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Trans-Activators/*chemistry MH - Transcription Factors/*chemistry MH - Transcription, Genetic MH - Two-Hybrid System Techniques MH - Zinc/chemistry PMC - PMC122759 OID - NLM: PMC122759 EDAT- 2002/04/18 10:00 MHDA- 2002/06/18 10:01 CRDT- 2002/04/18 10:00 AID - 10.1073/pnas.082121399 [doi] AID - 99/8/5271 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5271-6. PMID- 14579366 OWN - NLM STAT- MEDLINE DA - 20031027 DCOM- 20040130 LR - 20061115 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 53 IP - 3 DP - 2003 Nov 15 TI - The intracellular domain of the Drosophila cholinesterase-like neural adhesion protein, gliotactin, is natively unfolded. PG - 758-67 AB - Drosophila gliotactin (Gli) is a 109-kDa transmembrane, cholinesterase-like adhesion molecule (CLAM), expressed in peripheral glia, that is crucial for formation of the blood-nerve barrier. The intracellular portion (Gli-cyt) was cloned and expressed in the cytosolic fraction of Escherichia coli BLR(DE3) at 45 mg/L and purified by Ni-NTA (nitrilotriacetic acid) chromatography. Although migration on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), under denaturing conditions, was unusually slow, molecular weight determination by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) confirmed that the product was consistent with its theoretical size. Gel filtration chromatography yielded an anomalously large Stokes radius, suggesting a fully unfolded conformation. Circular dichroism (CD) spectroscopy demonstrated that Gli-cyt was >50% unfolded, further suggesting a nonglobular conformation. Finally, 1D-(1)H NMR conclusively demonstrated that Gli-cyt possesses an extended unfolded structure. In addition, Gli-cyt was shown to possess charge and hydrophobic properties characteristic of natively unfolded proteins (i.e., proteins that, when purified, are intrinsically disordered under physiologic conditions in vitro). CI - Copyright 2003 Wiley-Liss, Inc. FAU - Zeev-Ben-Mordehai, Tzviya AU - Zeev-Ben-Mordehai T AD - Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel. FAU - Rydberg, Edwin H AU - Rydberg EH FAU - Solomon, Ariel AU - Solomon A FAU - Toker, Lilly AU - Toker L FAU - Auld, Vanessa J AU - Auld VJ FAU - Silman, Israel AU - Silman I FAU - Botti, Simone AU - Botti S FAU - Sussman, Joel L AU - Sussman JL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Drosophila Proteins) RN - 0 (Membrane Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (gliotactin) RN - EC 3.1.1.8 (Cholinesterases) SB - IM MH - Cell Adhesion MH - Cholinesterases/chemistry MH - Chromatography, Gel MH - Circular Dichroism MH - Cloning, Molecular MH - Drosophila Proteins/*chemistry/genetics MH - Membrane Proteins/*chemistry/genetics/isolation & purification MH - Nerve Tissue Proteins/*chemistry/genetics/isolation & purification MH - Protein Folding MH - Protein Structure, Tertiary MH - Sequence Analysis, Protein EDAT- 2003/10/28 05:00 MHDA- 2004/01/31 05:00 CRDT- 2003/10/28 05:00 AID - 10.1002/prot.10471 [doi] PST - ppublish SO - Proteins. 2003 Nov 15;53(3):758-67. PMID- 22771474 OWN - NLM STAT- MEDLINE DA - 20120924 DCOM- 20121205 LR - 20141120 IS - 1873-3468 (Electronic) IS - 0014-5793 (Linking) VI - 586 IP - 19 DP - 2012 Sep 21 TI - Methamphetamine binds to alpha-synuclein and causes a conformational change which can be detected by nanopore analysis. PG - 3222-8 LID - 10.1016/j.febslet.2012.06.040 [doi] LID - S0014-5793(12)00529-7 [pii] AB - alpha-Synuclein is an intrinsically disordered protein of 140 amino acids which is abundant in dopaminergic neurons. Misfolding and aggregation of alpha-synuclein leads to the formation of Lewy bodies inside the neurons which is the hallmark of Parkinson's disease and related dementias. Here we show by nanopore analysis that the recreational drug, methamphetamine, binds to the N-terminus of alpha-synuclein and causes a conformational change which cannot be detected by circular dichroism spectroscopy. The results suggest a mechanism for the psychoactivity of methamphetamine as well as an increased incidence of Parkinson's disease amongst users of the drug. CI - Copyright (c) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. FAU - Tavassoly, Omid AU - Tavassoly O AD - Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada. FAU - Lee, Jeremy S AU - Lee JS LA - eng PT - Journal Article DEP - 20120704 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (alpha-Synuclein) RN - 44RAL3456C (Methamphetamine) SB - IM MH - Binding Sites MH - Circular Dichroism MH - Dopaminergic Neurons/drug effects/metabolism MH - Humans MH - In Vitro Techniques MH - Lewy Bodies/drug effects/metabolism MH - Lewy Body Disease/etiology/metabolism MH - Methamphetamine/*metabolism/toxicity MH - Models, Molecular MH - Nanopores MH - Parkinson Disease/etiology/metabolism MH - Protein Binding MH - Protein Conformation/drug effects MH - Protein Folding/drug effects MH - alpha-Synuclein/*chemistry/*metabolism EDAT- 2012/07/10 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/07/10 06:00 PHST- 2012/04/05 [received] PHST- 2012/06/06 [revised] PHST- 2012/06/25 [accepted] PHST- 2012/07/04 [aheadofprint] AID - S0014-5793(12)00529-7 [pii] AID - 10.1016/j.febslet.2012.06.040 [doi] PST - ppublish SO - FEBS Lett. 2012 Sep 21;586(19):3222-8. doi: 10.1016/j.febslet.2012.06.040. Epub 2012 Jul 4. PMID- 21303342 OWN - NLM STAT- MEDLINE DA - 20110209 DCOM- 20110616 LR - 20111209 IS - 2212-3989 (Electronic) IS - 1871-5265 (Linking) VI - 11 IP - 1 DP - 2011 Feb TI - HIV-1 infected patients have antibodies recognizing folded Tat. PG - 57-63 AB - Tat is a regulatory viral protein known as transactivator of HIV-1 genes but Tat is also secreted in the blood from HIV-1 infected cells. Extra cellular Tat can cross cellular membranes to trigger apoptosis and might explain the incapacity of the cellular immunity to eliminate HIV-1 infected cells. There is a controversy regarding Tat structure with studies suggesting that Tat would be a naturally unfolded protein. Here, we show that synthetic Tat variants need to be folded to have a transactivation activity in a cellular assay but this folding is unstable regarding the buffers and/or pH used as solvent. We show also that the recognition of a Tat variant versus peptides, covering its sequence, was different. Using an indirect ELISA method with 40 sera from volunteer HIV-1 infected patients, we show that Tat was recognized by 19 human sera either exclusively (n=8) or with Tat peptides (n=11). Dot Blot showed that unfolded Tat was no longer detectable by sera of the first group (n=8) compared to folded Tat. As a conclusion, this study suggests that Tat could be a naturally folded protein in the blood of HIV infected patients. FAU - Mediouni, Sonia AU - Mediouni S AD - Equipe de Recherche Technologique 2011, Faculte de Pharmacie, 27 BD Jean Moulin, 13385 Marseille, France. FAU - Baillat, Gilbert AU - Baillat G FAU - Darque, Albert AU - Darque A FAU - Ravaux, Isabelle AU - Ravaux I FAU - Loret, Erwann AU - Loret E LA - eng PT - Journal Article PL - United Arab Emirates TA - Infect Disord Drug Targets JT - Infectious disorders drug targets JID - 101269158 RN - 0 (HIV Antibodies) RN - 0 (tat Gene Products, Human Immunodeficiency Virus) SB - IM MH - Enzyme-Linked Immunosorbent Assay MH - HIV Antibodies/biosynthesis/blood/chemistry/*immunology MH - HIV Infections/*immunology MH - *HIV-1/genetics/immunology MH - HeLa Cells MH - Humans MH - Immunoblotting MH - Protein Folding MH - tat Gene Products, Human Immunodeficiency Virus/biosynthesis/chemistry/*immunology EDAT- 2011/02/10 06:00 MHDA- 2011/06/17 06:00 CRDT- 2011/02/10 06:00 PHST- 2010/02/10 [received] PHST- 2010/07/15 [accepted] AID - BSP/ ID DT /E-Pub/-0001-11-1 [pii] PST - ppublish SO - Infect Disord Drug Targets. 2011 Feb;11(1):57-63. PMID- 18189286 OWN - NLM STAT- MEDLINE DA - 20080402 DCOM- 20080930 LR - 20131121 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 90 IP - 2 DP - 2008 TI - Using peptides to study the interaction between the p53 tetramerization domain and HIV-1 Tat. PG - 105-16 LID - 10.1002/bip.20919 [doi] AB - Peptides are valuable tools for studying protein-protein interactions, especially in cases of isolated protein domains and natively unfolded proteins. Here, we used peptides to quantitatively characterize the interaction between the natively unfolded HIV-1 Tat protein and the tetramerization domain of the cellular tumor suppressor protein p53. We used peptide mapping, fluorescence anisotropy, and NMR spectroscopy to perform a detailed structural and biophysical characterization of the interaction between the two proteins and elucidate its molecular mechanism, which have so far been studied using cell-based methods. We show that the p53 tetramerization domain, p53(326-355), binds directly to residues 1-35 and 47-57 in Tat. We have characterized the interaction between p53(326-355) and Tat(47-57) in detail. The p53 residues that are mainly involved in binding to Tat(47-57) are E343 and E349, which bind to the positively charged arginine-rich motif of Tat by a partly electrostatic mechanism. All oligomerization states of p53(326-355) bind Tat(47-57) without inhibiting p53 tetramerization, since the residues in p53(326-355) that bind Tat(47-57) face away from the tetramerization interface. We conclude that p53 is able to bind Tat as a transcriptionally active tetramer. FAU - Gabizon, Ronen AU - Gabizon R AD - Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel. FAU - Mor, Michal AU - Mor M FAU - Rosenberg, Masha M AU - Rosenberg MM FAU - Britan, Lena AU - Britan L FAU - Hayouka, Zvi AU - Hayouka Z FAU - Kotler, Moshe AU - Kotler M FAU - Shalev, Deborah E AU - Shalev DE FAU - Friedler, Assaf AU - Friedler A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 RN - 0 (Gene Products, tat) RN - 0 (Peptide Fragments) RN - 0 (Tumor Suppressor Protein p53) RN - OF5P57N2ZX (Alanine) SB - IM MH - Alanine/metabolism MH - Amino Acid Motifs MH - Enzyme-Linked Immunosorbent Assay MH - Gene Products, tat/chemical synthesis/*chemistry/*metabolism MH - HIV-1/*chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Osmolar Concentration MH - Peptide Fragments/chemical synthesis/*chemistry/*metabolism MH - Protein Binding MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Static Electricity MH - Temperature MH - Tumor Suppressor Protein p53/chemical synthesis/*chemistry/*metabolism EDAT- 2008/01/15 09:00 MHDA- 2008/10/01 09:00 CRDT- 2008/01/15 09:00 AID - 10.1002/bip.20919 [doi] PST - ppublish SO - Biopolymers. 2008;90(2):105-16. doi: 10.1002/bip.20919. PMID- 22138394 OWN - NLM STAT- MEDLINE DA - 20120116 DCOM- 20120322 LR - 20140109 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 417 IP - 1 DP - 2012 Jan 6 TI - The transiently ordered regions in intrinsically disordered ExsE are correlated with structural elements involved in chaperone binding. PG - 129-34 LID - 10.1016/j.bbrc.2011.11.070 [doi] AB - Many Gram-negative bacteria utilize a type III secretion system (T3SS) to deliver protein effectors to target host cells. Transcriptional control of T3SS gene expression is generally coupled to secretion through the release of a regulatory protein. T3SS gene expression in Pseudomonas aeruginosa is regulated by extracellular secretion of ExsE. ExsE is a small 81 residue protein that appears to lack a stable structural core as indicated by previous studies. In this study, we employed various NMR methods to characterize the structure of ExsE alone and when bound to its secretion chaperone ExsC. We found that ExsE is largely unfolded throughout the polypeptide chain, belonging to a class of proteins that are intrinsically disordered. The unfolded, extended conformation of ExsE may expedite efficient secretion through the narrow path of the T3SS secretion channel to activate gene expression in a timely manner. We also found that the structurally flexible ExsE samples through conformations with localized structurally ordered regions. Importantly, these transiently ordered elements are related to the secondary structures involved in binding ExsC based on a prior crystal structure of the ExsC-ExsE complex. These findings support the notion that preexisting structured elements facilitate binding of intrinsically disordered proteins to their targets. CI - Copyright (c) 2011 Elsevier Inc. All rights reserved. FAU - Zheng, Zhida AU - Zheng Z AD - Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA. FAU - Ma, Dejian AU - Ma D FAU - Yahr, Timothy L AU - Yahr TL FAU - Chen, Lingling AU - Chen L LA - eng GR - R01 AI055042/AI/NIAID NIH HHS/United States PT - Journal Article DEP - 20111125 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Bacterial Proteins) RN - 0 (Molecular Chaperones) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/metabolism MH - *Bacterial Secretion Systems MH - Molecular Chaperones/*chemistry/metabolism MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - Protein Unfolding MH - Pseudomonas aeruginosa/*metabolism EDAT- 2011/12/06 06:00 MHDA- 2012/03/23 06:00 CRDT- 2011/12/06 06:00 PHST- 2011/11/11 [received] PHST- 2011/11/15 [accepted] PHST- 2011/11/25 [aheadofprint] AID - S0006-291X(11)02084-5 [pii] AID - 10.1016/j.bbrc.2011.11.070 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2012 Jan 6;417(1):129-34. doi: 10.1016/j.bbrc.2011.11.070. Epub 2011 Nov 25. PMID- 19003993 OWN - NLM STAT- MEDLINE DA - 20090601 DCOM- 20090908 LR - 20131121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 75 IP - 4 DP - 2009 Jun TI - Quantitative structure activity relationship of IA3-like peptides as aspartic proteinase inhibitors. PG - 859-69 LID - 10.1002/prot.22295 [doi] AB - The IA(3) polypeptide inhibitor from Saccharomyces cerevisiae interacts potently and selectively with its target, the S. cerevisiae vacuolar aspartic proteinase (ScPr). Upon encountering the enzyme, residues 2-32 of the intrinsically unstructured IA(3) polypeptide become ordered into an almost-perfect alpha-helix. In previous IA(3) mutagenesis studies, we identified important characteristics of the enzyme inhibitor interactions and generated a large dataset of variants with K(i) values determined experimentally at pH 3.1 and 4.7. Using this information, the three-dimensional structure of each variant was modelled in silico with the correct protonation for each experimental pH value. A set of descriptors of the inhibitor/ScPr interactions was then calculated and used to establish mathematical models relating the variant sequences to their inhibitory activities at each pH. Cross-validation, external-set validation and five separate selections of the training and test samples confirmed the robustness of the equations. A major contributor to the structure-activity relationship was the free energy of binding calculated by the FoldX program. The mathematical models were challenged further (i) by in silico alanine-scanning mutagenesis of residues 2-32 in IA(3) and relating binding energy to experimentally derived inhibition constants for selected representatives of these variants; and (ii) by predicting inhibitory-potencies for two novel IA(3)-variants. The predictions of the equations for these new IA(3)-variants with ScPr matched almost precisely the kinetic data determined experimentally. The models described represent valuable tools for the future design of novel inhibitor variants active against ScPr and other aspartic proteinases. CI - Copyright 2008 Wiley-Liss, Inc. FAU - Padron-Garcia, Juan Alexander AU - Padron-Garcia JA AD - Laboratory of Theoretical and Computational Chemistry, Chemistry Faculty, Havana University, 10400, Havana, Cuba. FAU - Alonso-Tarajano, Manuel AU - Alonso-Tarajano M FAU - Alonso-Becerra, Esther AU - Alonso-Becerra E FAU - Winterburn, Tim J AU - Winterburn TJ FAU - Ruiz, Yasser AU - Ruiz Y FAU - Kay, John AU - Kay J FAU - Berry, Colin AU - Berry C LA - eng GR - 72/0014846/Biotechnology and Biological Sciences Research Council/United Kingdom GR - 72/C13544/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (PAI3 protein, S cerevisiae) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 3.4.23.- (Aspartic Acid Endopeptidases) RN - OF5P57N2ZX (Alanine) SB - IM MH - Alanine/metabolism MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Aspartic Acid Endopeptidases/*antagonists & inhibitors/*chemistry/metabolism MH - Computer Simulation MH - Escherichia coli/genetics MH - Hydrogen-Ion Concentration MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Quantitative Structure-Activity Relationship MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Reproducibility of Results MH - Saccharomyces cerevisiae/enzymology/metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism MH - Thermodynamics EDAT- 2008/11/13 09:00 MHDA- 2009/09/09 06:00 CRDT- 2008/11/13 09:00 AID - 10.1002/prot.22295 [doi] PST - ppublish SO - Proteins. 2009 Jun;75(4):859-69. doi: 10.1002/prot.22295. PMID- 25224747 OWN - NLM STAT- Publisher DA - 20141202 LR - 20141202 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1844 IP - 12 DP - 2014 Sep 16 TI - Solution conditions define morphological homogeneity of alpha-synuclein fibrils. PG - 2127-2134 LID - S1570-9639(14)00230-1 [pii] LID - 10.1016/j.bbapap.2014.09.007 [doi] AB - The intrinsically disordered human alpha-synuclein (alphaSyn) protein exhibits considerable heterogeneity in in vitro fibrillization reactions. Using atomic force microscopy (AFM) we show that depending on the solvent conditions, A140C mutant and wild-type alphaSyn can be directed to reproducibly form homogeneous populations of fibrils exhibiting regular periodicity. Results from Thioflavin-T fluorescence assays, determination of residual monomer concentrations and native polyacrylamide gel electrophoresis reveal that solvent conditions including EDTA facilitate incorporation of a larger fraction of monomers into fibrils. The fibrils formed in 10mM Tris-HCl, 10mM NaCl and 0.1mM EDTA at pH7.4 display a narrow distribution of periodicities with an average value of 102+/-6nm for the A140C mutant and 107+/-9nm for wt alphaSyn. The ability to produce a homogeneous fibril population can be instrumental in understanding the detailed structural features of fibrils and the fibril assembly process. Moreover, the availability of morphologically well-defined fibrils will enhance the potential for use of amyloids as biological nanomaterials. CI - Copyright (c) 2014 Elsevier B.V. All rights reserved. FAU - Sidhu, Arshdeep AU - Sidhu A AD - Nanobiophysics, MESA+Institute for Nanotechnology, University of Twente, Enschede, The Netherlands. FAU - Segers-Nolten, Ine AU - Segers-Nolten I AD - Nanobiophysics, MESA+Institute for Nanotechnology, University of Twente, Enschede, The Netherlands. FAU - Subramaniam, Vinod AU - Subramaniam V AD - Nanobiophysics, MESA+Institute for Nanotechnology, University of Twente, Enschede, The Netherlands; MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands; FOM Institute AMOLF, Amsterdam, The Netherlands. Electronic address: subramaniam@amolf.nl. LA - ENG PT - JOURNAL ARTICLE DEP - 20140916 TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 OTO - NOTNLM OT - Fibrillization OT - Homogeneous OT - Morphology OT - Periodicity OT - alpha-Synuclein EDAT- 2014/09/17 06:00 MHDA- 2014/09/17 06:00 CRDT- 2014/09/17 06:00 PHST- 2014/07/14 [received] PHST- 2014/09/04 [revised] PHST- 2014/09/05 [accepted] AID - S1570-9639(14)00230-1 [pii] AID - 10.1016/j.bbapap.2014.09.007 [doi] PST - aheadofprint SO - Biochim Biophys Acta. 2014 Sep 16;1844(12):2127-2134. doi: 10.1016/j.bbapap.2014.09.007. PMID- 9362499 OWN - NLM STAT- MEDLINE DA - 19980105 DCOM- 19980105 LR - 20140617 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 16 IP - 22 DP - 1997 Nov 17 TI - The transactivation region of the fis protein that controls site-specific DNA inversion contains extended mobile beta-hairpin arms. PG - 6860-73 AB - The Fis protein regulates site-specific DNA inversion catalyzed by a family of DNA invertases when bound to a cis-acting recombinational enhancer. As is often found for transactivation domains, previous crystal structures have failed to resolve the conformation of the N-terminal inversion activation region within the Fis dimer. A new crystal form of a mutant Fis protein now reveals that the activation region contains two beta-hairpin arms that protrude over 20 A from the protein core. Saturation mutagenesis identified the regulatory and structurally important amino acids. The most critical activating residues are located near the tips of the beta-arms. Disulfide cross-linking between the beta-arms demonstrated that they are highly flexible in solution and that efficient inversion activation can occur when the beta-arms are covalently linked together. The emerging picture for this regulatory motif is that contacts with the recombinase at the tip of the mobile beta-arms activate the DNA invertase in the context of an invertasome complex. FAU - Safo, M K AU - Safo MK AD - Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China. FAU - Yang, W Z AU - Yang WZ FAU - Corselli, L AU - Corselli L FAU - Cramton, S E AU - Cramton SE FAU - Yuan, H S AU - Yuan HS FAU - Johnson, R C AU - Johnson RC LA - eng SI - PDB/1F36 GR - GM 38509/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Carrier Proteins) RN - 0 (Factor For Inversion Stimulation Protein) RN - 0 (Integration Host Factors) RN - 0 (Trans-Activators) RN - EC 2.7.7.- (DNA Nucleotidyltransferases) RN - EC 2.7.7.- (Hin recombinase) RN - K848JZ4886 (Cysteine) SB - IM MH - Amino Acid Sequence MH - Carrier Proteins/*chemistry/genetics/metabolism MH - Computer Simulation MH - Crystallography, X-Ray MH - Cysteine/chemistry MH - DNA Mutational Analysis MH - DNA Nucleotidyltransferases/metabolism MH - Factor For Inversion Stimulation Protein MH - Integration Host Factors MH - Models, Molecular MH - Molecular Sequence Data MH - Oxidation-Reduction MH - *Protein Structure, Secondary MH - *Recombination, Genetic MH - Trans-Activators/*chemistry/genetics/metabolism PMC - PMC1170289 OID - NLM: PMC1170289 EDAT- 1998/01/10 MHDA- 1998/01/10 00:01 CRDT- 1998/01/10 00:00 AID - 10.1093/emboj/16.22.6860 [doi] PST - ppublish SO - EMBO J. 1997 Nov 17;16(22):6860-73. PMID- 18698566 OWN - NLM STAT- MEDLINE DA - 20080916 DCOM- 20081114 IS - 1439-7641 (Electronic) IS - 1439-4235 (Linking) VI - 9 IP - 13 DP - 2008 Sep 15 TI - Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy. PG - 1859-66 LID - 10.1002/cphc.200800210 [doi] AB - Intrinsically disordered (ID) regions of proteins are recognized to be involved in biological processes such as transcription, translation, and cellular signal transduction. Despite the important roles of ID regions, effective methods to observe these thin and flexible structures directly were not available. Herein, we use high-speed atomic force microscopy (AFM) to observe the heterodimeric FACT (facilitates chromatin transcription) protein, which is predicted to have large ID regions in each subunit. Successive AFM images of FACT on a mica surface, captured at rates of 5-17 frames per second, clearly reveal two distinct tail-like segments that protrude from the main body of FACT and fluctuate in position. Using deletion mutants of FACT, we identify these tail segments as the two major ID regions predicted from the amino acid sequences. Their mechanical properties estimated from the AFM images suggest that they have more relaxed structures than random coils. These observations demonstrate that this state-of-the-art microscopy method can be used to characterize unstructured protein segments that are difficult to visualize with other experimental techniques. FAU - Miyagi, Atsushi AU - Miyagi A AD - Department of Physics, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan. FAU - Tsunaka, Yasuo AU - Tsunaka Y FAU - Uchihashi, Takayuki AU - Uchihashi T FAU - Mayanagi, Kouta AU - Mayanagi K FAU - Hirose, Susumu AU - Hirose S FAU - Morikawa, Kosuke AU - Morikawa K FAU - Ando, Toshio AU - Ando T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Chemphyschem JT - Chemphyschem : a European journal of chemical physics and physical chemistry JID - 100954211 RN - 0 (Proteins) SB - IM MH - Gene Deletion MH - Microscopy, Atomic Force/*methods MH - Microscopy, Electron, Transmission MH - Mutation/genetics MH - Proteins/genetics/*ultrastructure MH - Time Factors EDAT- 2008/08/14 09:00 MHDA- 2008/11/15 09:00 CRDT- 2008/08/14 09:00 AID - 10.1002/cphc.200800210 [doi] PST - ppublish SO - Chemphyschem. 2008 Sep 15;9(13):1859-66. doi: 10.1002/cphc.200800210. PMID- 20399186 OWN - NLM STAT- MEDLINE DA - 20100419 DCOM- 20100727 LR - 20150325 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 18 IP - 4 DP - 2010 Mar 14 TI - Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. PG - 494-506 LID - 10.1016/j.str.2010.01.020 [doi] AB - Intrinsically disordered proteins can form highly dynamic complexes with partner proteins. One such dynamic complex involves the intrinsically disordered Sic1 with its partner Cdc4 in regulation of yeast cell cycle progression. Phosphorylation of six N-terminal Sic1 sites leads to equilibrium engagement of each phosphorylation site with the primary binding pocket in Cdc4, the substrate recognition subunit of a ubiquitin ligase. ENSEMBLE calculations using experimental nuclear magnetic resonance and small-angle X-ray scattering data reveal significant transient structure in both phosphorylation states of the isolated ensembles (Sic1 and pSic1) that modulates their electrostatic potential, suggesting a structural basis for the proposed strong contribution of electrostatics to binding. A structural model of the dynamic pSic1-Cdc4 complex demonstrates the spatial arrangements in the ubiquitin ligase complex. These results provide a physical picture of a protein that is predominantly disordered in both its free and bound states, enabling aspects of its structure/function relationship to be elucidated. CI - Copyright 2010 Elsevier Ltd. All rights reserved. FAU - Mittag, Tanja AU - Mittag T AD - Program in Molecular Structure and Function, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada. FAU - Marsh, Joseph AU - Marsh J FAU - Grishaev, Alexander AU - Grishaev A FAU - Orlicky, Stephen AU - Orlicky S FAU - Lin, Hong AU - Lin H FAU - Sicheri, Frank AU - Sicheri F FAU - Tyers, Mike AU - Tyers M FAU - Forman-Kay, Julie D AU - Forman-Kay JD LA - eng GR - Z01 DK029046-01/Intramural NIH HHS/United States GR - Wellcome Trust/United Kingdom GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (CDC4 protein, S cerevisiae) RN - 0 (Cell Cycle Proteins) RN - 0 (Cyclin-Dependent Kinase Inhibitor Proteins) RN - 0 (F-Box Proteins) RN - 0 (SIC1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 2ZD004190S (Threonine) RN - EC 6.3.2.19 (SKP Cullin F-Box Protein Ligases) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM CIN - Structure. 2010 Mar 14;18(4):416-9. PMID: 20399178 MH - Cell Cycle Proteins/genetics/*physiology MH - Crystallography, X-Ray/methods MH - Cyclin-Dependent Kinase Inhibitor Proteins/genetics/*physiology MH - F-Box Proteins/genetics/*physiology MH - Magnetic Resonance Spectroscopy MH - Molecular Conformation MH - Phosphorylation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - SKP Cullin F-Box Protein Ligases/*chemistry MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/genetics/*physiology MH - Scattering, Radiation MH - Static Electricity MH - Structure-Activity Relationship MH - Substrate Specificity MH - Threonine/chemistry MH - Ubiquitin-Protein Ligases/genetics/*physiology PMC - PMC2924144 MID - NIHMS188133 OID - NLM: NIHMS188133 OID - NLM: PMC2924144 EDAT- 2010/04/20 06:00 MHDA- 2010/07/28 06:00 CRDT- 2010/04/20 06:00 PHST- 2009/09/30 [received] PHST- 2010/01/22 [revised] PHST- 2010/01/26 [accepted] AID - S0969-2126(10)00101-2 [pii] AID - 10.1016/j.str.2010.01.020 [doi] PST - ppublish SO - Structure. 2010 Mar 14;18(4):494-506. doi: 10.1016/j.str.2010.01.020. PMID- 23908786 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20130802 DCOM- 20130805 LR - 20130812 IS - 2076-9172 (Electronic) IS - 2076-9172 (Linking) VI - 1 IP - 2 DP - 2010 Oct TI - It all starts at the ends: multifaceted involvement of C- and N-terminally modified cholinesterases in Alzheimer's disease. PG - e0014 LID - 10.5041/RMMJ.10014 [doi] AB - In Alzheimer's disease (AD), premature demise of acetylcholine-producing neurons and the consequent decline of cholinergic transmission associate with the prominent cognitive impairments of affected individuals. However, the enzymatic activities of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are altered rather late in the disease progress. This raised questions regarding the causal involvement of AChE and BChE in AD. Importantly, single nucleotide polymorphisms (SNPs), alternative splicing, and alternate promoter usage generate complex expression of combinatorial cholinesterase (ChE) variants, which called for testing the roles of specific variants in AD pathogenesis. We found accelerated amyloid fibril formation in engineered mice with enforced over-expression of the AChE-S splice variant which includes a helical C-terminus. In contrast, the AChE-R variant, which includes a naturally unfolded C-terminus, attenuated the oligomerization of amyloid fibrils and reduced amyloid plaque formation and toxicity. An extended N-terminus generated by an upstream promoter enhanced the damage caused by N-AChE-S, which in cell cultures induced caspases and GSK3 activation, tau hyperphosphorylation, and apoptosis. In the post-mortem AD brain, we found reduced levels of the neuroprotective AChE-R and increased levels of the neurotoxic N-AChE-S, suggesting bimodal contribution to AD progress. Finally, local unwinding of the alpha-helical C-terminal BChE peptide and loss of function of the pivotal tryptophan at its position 541 impair amyloid fibril attenuation by the common BChE-K variant carrying the A539T substitution, in vitro. Together, our results point to causal yet diverse involvement of the different ChEs in the early stages of AD pathogenesis. Harnessing the neuroprotective variants while reducing the levels of damaging ones may hence underlie the development of novel therapeutics. FAU - Berson, Amit AU - Berson A AD - Department of Biological Chemistry and the Edmond and Lily Safra Center of Neuroscience, The Hebrew University of Jerusalem, Jerusalem, Israel. FAU - Soreq, Hermona AU - Soreq H LA - eng PT - Journal Article DEP - 20101031 PL - Israel TA - Rambam Maimonides Med J JT - Rambam Maimonides medical journal JID - 101538065 PMC - PMC3678781 OID - NLM: PMC3678781 OTO - NOTNLM OT - Acetylcholinesterase OT - Alzheimer's disease OT - apoptosis OT - beta-amyloid OT - butyrylcholinesterase EDAT- 2010/10/01 00:00 MHDA- 2010/10/01 00:01 CRDT- 2013/08/03 06:00 PHST- 2010/10 [ppublish] PHST- 2010/10/31 [epublish] AID - 10.5041/RMMJ.10014 [doi] AID - rmmj-1-2_e0014 [pii] PST - epublish SO - Rambam Maimonides Med J. 2010 Oct 31;1(2):e0014. doi: 10.5041/RMMJ.10014. Print 2010 Oct. PMID- 9141136 OWN - NLM STAT- MEDLINE DA - 19970630 DCOM- 19970630 LR - 20061115 IS - 0887-3585 (Print) IS - 0887-3585 (Linking) VI - 27 IP - 4 DP - 1997 Apr TI - Molten globule state of equine beta-lactoglobulin. PG - 567-75 AB - The acid-unfolded state of equine beta-lactoglobulin was characterized by means of circular dichroism, nuclear magnetic resonance, analytical gel-filtration chromatography, and analytical centrifugation. The acid-unfolded state of equine beta-lactoglobulin has a substantial secondary structure as shown by the far-ultraviolet circular dichroism spectrum but lacks persistent tertiary packing of the side chains as indicated by the near-ultraviolet circular dichroism and nuclear magnetic resonance spectra. It is nearly as compact as the native conformation as shown by the gel filtration and sedimentation experiments, and it has the exposed hydrophobic surface as indicated by its tendency to aggregate. All of these characteristics indicate that the acid-unfolded state of equine beta-lactoglobulin is a molten globule state. The alpha helix content in the acid-unfolded state, which has been estimated from the circular dichroism spectrum, is larger than that in the native state, suggesting the presence of nonnative alpha helices in the molten globule state. This result suggests the generality of the intermediate with nonnative alpha helices during the folding of proteins having the beta-clam fold. FAU - Ikeguchi, M AU - Ikeguchi M AD - Department of Bioengineering, Faculty of Engineering, Soka University, Tokyo, Japan. FAU - Kato, S AU - Kato S FAU - Shimizu, A AU - Shimizu A FAU - Sugai, S AU - Sugai S LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Acids) RN - 0 (Lactoglobulins) RN - 0 (Retinol-Binding Proteins) SB - IM MH - Acids MH - Amino Acid Sequence MH - Animals MH - Chromatography, Gel MH - Circular Dichroism MH - Horses MH - Hydrogen-Ion Concentration MH - Lactoglobulins/*chemistry MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Particle Size MH - *Protein Folding MH - *Protein Structure, Secondary MH - Retinol-Binding Proteins/chemistry MH - Sequence Homology, Amino Acid MH - Species Specificity MH - Ultracentrifugation EDAT- 1997/04/01 MHDA- 2000/06/20 09:00 CRDT- 1997/04/01 00:00 AID - 10.1002/(SICI)1097-0134(199704)27:4<567::AID-PROT9>3.0.CO;2-7 [pii] PST - ppublish SO - Proteins. 1997 Apr;27(4):567-75. PMID- 9351835 OWN - NLM STAT- MEDLINE DA - 19980108 DCOM- 19980108 LR - 20140617 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 16 IP - 21 DP - 1997 Nov 3 TI - The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites. PG - 6548-58 AB - The structure of the major human apurinic/ apyrimidinic endonuclease (HAP1) has been solved at 2.2 A resolution. The enzyme consists of two symmetrically related domains of similar topology and has significant structural similarity to both bovine DNase I and its Escherichia coli homologue exonuclease III (EXOIII). A structural comparison of these enzymes reveals three loop regions specific to HAP1 and EXOIII. These loop regions apparently act in DNA abasic site (AP) recognition and cleavage since DNase I, which lacks these loops, correspondingly lacks AP site specificity. The HAP1 structure furthermore suggests a mechanism for AP site binding which involves the recognition of the deoxyribose moiety in an extrahelical conformation, rather than a 'flipped-out' base opposite the AP site. FAU - Gorman, M A AU - Gorman MA AD - Protein Structure Laboratory, Imperial Cancer Research Fund, London, UK. FAU - Morera, S AU - Morera S FAU - Rothwell, D G AU - Rothwell DG FAU - de La Fortelle, E AU - de La Fortelle E FAU - Mol, C D AU - Mol CD FAU - Tainer, J A AU - Tainer JA FAU - Hickson, I D AU - Hickson ID FAU - Freemont, P S AU - Freemont PS LA - eng GR - GM46312/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Bacterial Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 9007-49-2 (DNA) RN - EC 3.1.- (Endonucleases) RN - EC 3.1.- (Exodeoxyribonucleases) RN - EC 3.1.11.2 (exodeoxyribonuclease III) RN - EC 3.1.21.1 (Deoxyribonuclease I) RN - EC 4.2.- (Carbon-Oxygen Lyases) RN - EC 4.2.99.18 (APEX1 protein, human) RN - EC 4.2.99.18 (DNA-(Apurinic or Apyrimidinic Site) Lyase) SB - IM MH - Amino Acid Sequence MH - Animals MH - Bacterial Proteins/chemistry MH - Binding Sites MH - *Carbon-Oxygen Lyases MH - Cattle MH - Crystallography, X-Ray MH - DNA/metabolism MH - DNA Repair MH - *DNA-(Apurinic or Apyrimidinic Site) Lyase MH - Deoxyribonuclease I/chemistry MH - Endonucleases/*chemistry MH - Escherichia coli/chemistry MH - Exodeoxyribonucleases/chemistry MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Proteins/*chemistry MH - Oxidation-Reduction MH - Protein Binding MH - *Protein Conformation MH - Recombinant Fusion Proteins/chemistry MH - Sequence Alignment MH - Sequence Homology, Amino Acid PMC - PMC1170259 OID - NLM: PMC1170259 EDAT- 1997/11/14 MHDA- 1997/11/14 00:01 CRDT- 1997/11/14 00:00 AID - 10.1093/emboj/16.21.6548 [doi] PST - ppublish SO - EMBO J. 1997 Nov 3;16(21):6548-58. PMID- 9012674 OWN - NLM STAT- MEDLINE DA - 19970226 DCOM- 19970226 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 36 IP - 3 DP - 1997 Jan 21 TI - Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. PG - 586-603 AB - The reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) cycles through five detectable kinetic intermediates: holoenzyme, Michaelis complex, ternary product complex, tetrahydrofolate (THF) binary complex, and THF.NADPH complex. Isomorphous crystal structures analogous to these five intermediates and to the transition state (as represented by the methotrexate-NADPH complex) have been used to assemble a 2.1 A resolution movie depicting loop and subdomain movements during the catalytic cycle (see Supporting Information). The structures suggest that the M20 loop is predominantly closed over the reactants in the holoenzyme, Michaelis, and transition state complexes. But, during the remainder of the cycle, when nicotinamide is not bound, the loop occludes (protrudes into) the nicotinamide-ribose binding pocket. Upon changing from the closed to the occluded conformation, the central portion of the loop rearranges from beta-sheet to 3(10) helix. The change may occur by way of an irregularly structured open loop conformation, which could transiently admit a water molecule into position to protonate N5 of dihydrofolate. From the Michaelis to the transition state analogue complex, rotation between two halves of ecDHFR, the adenosine binding subdomain and loop subdomain, closes the (p-aminobenzoyl)glutamate (pABG) binding crevice by approximately 0.5 A. Resulting enhancement of contacts with the pABG moiety may stabilize puckering at C6 of the pteridine ring in the transition state. The subdomain rotation is further adjusted by cofactor-induced movements (approximately 0.5 A) of helices B and C, producing a larger pABG cleft in the THF.NADPH analogue complex than in the THF analogue complex. Such movements may explain how THF release is assisted by NADPH binding. Subdomain rotation is not observed in vertebrate DHFR structures, but an analogous loop movement (residues 59-70) appears to similarly adjust the pABG cleft width, suggesting that these movements are important for catalysis. Loop movement, also unobserved in vertebrate DHFR structures, may preferentially weaken NADP+ vs NADPH binding in ecDHFR, an evolutionary adaptation to reduce product inhibition in the NADP+ rich environment of prokaryotes. FAU - Sawaya, M R AU - Sawaya MR AD - Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0506, USA. FAU - Kraut, J AU - Kraut J LA - eng GR - CA17374/CA/NCI NIH HHS/United States GR - DK07233/DK/NIDDK NIH HHS/United States GR - HG00005/HG/NHGRI NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Tetrahydrofolates) RN - 29347-89-5 (5,6,7,8-tetrahydrofolic acid) RN - 53-59-8 (NADP) RN - EC 1.5.1.3 (Tetrahydrofolate Dehydrogenase) SB - IM MH - Crystallography, X-Ray MH - Escherichia coli MH - *Models, Molecular MH - NADP/metabolism MH - Protein Conformation MH - Tetrahydrofolate Dehydrogenase/*chemistry/metabolism MH - Tetrahydrofolates/metabolism EDAT- 1997/01/21 MHDA- 1997/01/21 00:01 CRDT- 1997/01/21 00:00 AID - 10.1021/bi962337c [doi] AID - bi962337c [pii] PST - ppublish SO - Biochemistry. 1997 Jan 21;36(3):586-603. PMID- 24205110 OWN - NLM STAT- MEDLINE DA - 20131108 DCOM- 20140918 LR - 20141112 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 10 DP - 2013 TI - Deciphering the binding between Nupr1 and MSL1 and their DNA-repairing activity. PG - e78101 LID - 10.1371/journal.pone.0078101 [doi] AB - The stress protein Nupr1 is a highly basic, multifunctional, intrinsically disordered protein (IDP). MSL1 is a histone acetyl transferase-associated protein, known to intervene in the dosage compensation complex (DCC). In this work, we show that both Nupr1 and MSL1 proteins were recruited and formed a complex into the nucleus in response to DNA-damage, which was essential for cell survival in reply to cisplatin damage. We studied the interaction of Nupr1 and MSL1, and their binding affinities to DNA by spectroscopic and biophysical methods. The MSL1 bound to Nupr1, with a moderate affinity (2.8 microM) in an entropically-driven process. MSL1 did not bind to non-damaged DNA, but it bound to chemically-damaged-DNA with a moderate affinity (1.2 microM) also in an entropically-driven process. The Nupr1 protein bound to chemically-damaged-DNA with a slightly larger affinity (0.4 microM), but in an enthalpically-driven process. Nupr1 showed different interacting regions in the formed complexes with Nupr1 or DNA; however, they were always disordered ("fuzzy"), as shown by NMR. These results underline a stochastic description of the functionality of the Nupr1 and its other interacting partners. FAU - Aguado-Llera, David AU - Aguado-Llera D AD - Instituto de Biologia Molecular y Celular, Universidad Miguel Hernandez, Elche (Alicante), Spain. FAU - Hamidi, Tewfik AU - Hamidi T FAU - Domenech, Rosa AU - Domenech R FAU - Pantoja-Uceda, David AU - Pantoja-Uceda D FAU - Gironella, Meritxell AU - Gironella M FAU - Santoro, Jorge AU - Santoro J FAU - Velazquez-Campoy, Adrian AU - Velazquez-Campoy A FAU - Neira, Jose L AU - Neira JL FAU - Iovanna, Juan L AU - Iovanna JL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131030 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Basic Helix-Loop-Helix Transcription Factors) RN - 0 (Neoplasm Proteins) RN - 0 (P8 protein, human) RN - EC 2.3.1.48 (Histone Acetyltransferases) RN - EC 2.3.1.48 (MSL1 protein, human) RN - Q20Q21Q62J (Cisplatin) SB - IM MH - Basic Helix-Loop-Helix Transcription Factors/genetics/*metabolism MH - Cell Line, Tumor MH - Cell Survival/genetics/physiology MH - Cisplatin/toxicity MH - DNA Damage/genetics/physiology MH - DNA Repair/drug effects/genetics MH - Fluorescent Antibody Technique MH - Histone Acetyltransferases/genetics/*metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Neoplasm Proteins/genetics/*metabolism MH - Protein Binding PMC - PMC3813506 OID - NLM: PMC3813506 EDAT- 2013/11/10 06:00 MHDA- 2014/09/19 06:00 CRDT- 2013/11/09 06:00 PHST- 2013 [ecollection] PHST- 2013/07/17 [received] PHST- 2013/09/06 [accepted] PHST- 2013/10/30 [epublish] AID - 10.1371/journal.pone.0078101 [doi] AID - PONE-D-13-29113 [pii] PST - epublish SO - PLoS One. 2013 Oct 30;8(10):e78101. doi: 10.1371/journal.pone.0078101. eCollection 2013. PMID- 22891813 OWN - NLM STAT- MEDLINE DA - 20120918 DCOM- 20130124 IS - 1520-5827 (Electronic) IS - 0743-7463 (Linking) VI - 28 IP - 37 DP - 2012 Sep 18 TI - Continuous thermal collapse of the intrinsically disordered protein tau is driven by its entropic flexible domain. PG - 13405-10 LID - 10.1021/la302628y [doi] AB - The tau protein belongs to the category of Intrinsically Disordered Proteins (IDP), which in their native state lack a folded structure and fluctuate between many conformations. In its physiological state, tau helps nucleating and stabilizing the microtubules' (MTs) surfaces in the axons of the neurons. Tau is mainly composed by two domains: (i) the binding domain that tightly bounds the MT surfaces and (ii) the projection domain that exerts a long-range entropic repulsive force and thus provides the proper spacing between adjacent MTs. Tau is also involved in the genesis and in the development of the Alzheimer disease when it detaches from MT surfaces and aggregates in paired helical filaments. Unfortunately, the molecular mechanisms behind these phenomena are still unclear. Temperature variation, rarely considered in biological studies, is here used to provide structural information on tau correlated to its role as an entropic spacer between adjacent MTs surfaces. In this paper, by means of small-angle X-ray scattering and molecular dynamics simulation, we demonstrate that tau undergoes a counterintuitive collapse phenomenon with increasing temperature. A detailed analysis of our results, performed by the Ensemble Optimization Method, shows that the thermal collapse is coupled to the occurrence of a transient long-range contact between a region encompassing the end of the proline-rich domain P2 and the first part of the repeats domain, and the region of the N-terminal domain entailing residues 80-150. Interestingly these two regions involved in the tau temperature collapse belong to the flexible projection domain that acts as an entropic bristle and regulates the MTs' architecture. Our results show that temperature is an important parameter that influences the dynamics of the tau projection domain, and hence its entropic behavior. FAU - Ciasca, Gabriele AU - Ciasca G AD - Physics Department, Sapienza University, 00185 Rome, Italy. FAU - Campi, Gaetano AU - Campi G FAU - Battisti, Anna AU - Battisti A FAU - Rea, Giuseppina AU - Rea G FAU - Rodio, Marina AU - Rodio M FAU - Papi, Massimiliano AU - Papi M FAU - Pernot, Petra AU - Pernot P FAU - Tenenbaum, Alexander AU - Tenenbaum A FAU - Bianconi, Antonio AU - Bianconi A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120904 PL - United States TA - Langmuir JT - Langmuir : the ACS journal of surfaces and colloids JID - 9882736 RN - 0 (tau Proteins) SB - IM MH - Adsorption MH - *Entropy MH - Humans MH - Molecular Dynamics Simulation MH - Surface Properties MH - *Temperature MH - tau Proteins/*chemistry EDAT- 2012/08/16 06:00 MHDA- 2013/01/25 06:00 CRDT- 2012/08/16 06:00 PHST- 2012/09/04 [aheadofprint] AID - 10.1021/la302628y [doi] PST - ppublish SO - Langmuir. 2012 Sep 18;28(37):13405-10. doi: 10.1021/la302628y. Epub 2012 Sep 4. PMID- 19089979 OWN - NLM STAT- MEDLINE DA - 20090601 DCOM- 20090908 LR - 20131121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 75 IP - 4 DP - 2009 Jun TI - Intrinsic structural disorder of mouse proNGF. PG - 990-1009 LID - 10.1002/prot.22311 [doi] AB - The unprocessed precursor of the Nerve Growth Factor (NGF), proNGF, has additional functions, besides its initially described role as a chaperone for NGF folding. The precursor protein endows apoptotic and/or neurotrophic properties, in contrast to the mature part. The structural and molecular basis for such distinct activities are presently unknown. Aiming to gain insights into the specific molecular interactions that govern rm-proNGF biological activities versus those of its mature counterpart, a structural study by synchrotron small angle X-ray scattering (SAXS) in solution was carried out. The different binding properties of the two proteins were investigated by surface plasmon resonance (SPR) using, as structural probes, a panel of anti-NGF antibodies and the soluble forms of TrkA and p75(NTR) receptors. SAXS measurements revealed the rm-proNGF to be dimeric and anisometric, with the propeptide domain being intrinsically unstructured. Ab initio reconstructions assuming twofold symmetry generated two types of structural models, a globular "crab-like" and an elongated shape that resulted in equally good fits of the scattering data. A novel method accounting for possible coexistence of different conformations contributing to the experimental scattering pattern, with no symmetry constraints, suggests the "crab-like" to be a more likely proNGF conformation. To exploit the potential of chemical stabilizers affecting the existing conformational protein populations, SAXS data were also collected in the presence of ammonium sulphate. An increase of the proNGF compactness was observed. SPR data pinpoints that the propeptide of proNGF may act as an intrinsically unstructured protein domain, characterized by a molecular promiscuity in the interaction/binding to multiple partners (TrkA and p75(NTR) receptors and a panel of neutralizing anti-NGF antibodies) depending on the physiological conditions of the cell. These data provide a first insight into the structural basis for the selectivity of mouse short proNGF, versus NGF, towards its binding partners. CI - Copyright 2008 Wiley-Liss, Inc. FAU - Paoletti, Francesca AU - Paoletti F AD - SISSA-ISAS, Building Q1, Area Science Park - Basovizza, S.S 14 Km 163.5, 34012 Trieste, Italy. f.paoletti@ebri.i FAU - Covaceuszach, Sonia AU - Covaceuszach S FAU - Konarev, Peter V AU - Konarev PV FAU - Gonfloni, Stefania AU - Gonfloni S FAU - Malerba, Francesca AU - Malerba F FAU - Schwarz, Elisabeth AU - Schwarz E FAU - Svergun, Dmitri I AU - Svergun DI FAU - Cattaneo, Antonino AU - Cattaneo A FAU - Lamba, Doriano AU - Lamba D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Protein Precursors) RN - 0 (Receptors, Nerve Growth Factor) RN - 0 (Recombinant Proteins) RN - 0 (TNFRSF16 protein, mouse) RN - 0 (pro-nerve growth factor, mouse) RN - 9061-61-4 (Nerve Growth Factor) RN - EC 2.7.10.1 (Receptor, trkA) RN - SU46BAM238 (Ammonium Sulfate) SB - IM MH - Amino Acid Sequence MH - Ammonium Sulfate/chemistry MH - Animals MH - Antibody Affinity MH - Computer Simulation MH - Escherichia coli/genetics MH - Humans MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Nerve Growth Factor/*chemistry/genetics/*metabolism MH - PC12 Cells MH - Phosphorylation MH - Protein Conformation MH - Protein Precursors/*chemistry/genetics/*metabolism MH - Rats MH - Receptor, trkA/chemistry/*metabolism MH - Receptors, Nerve Growth Factor/chemistry/*metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Scattering, Small Angle MH - Sequence Alignment MH - Surface Plasmon Resonance MH - X-Ray Diffraction EDAT- 2008/12/18 09:00 MHDA- 2009/09/09 06:00 CRDT- 2008/12/18 09:00 AID - 10.1002/prot.22311 [doi] PST - ppublish SO - Proteins. 2009 Jun;75(4):990-1009. doi: 10.1002/prot.22311. PMID- 22720086 OWN - NLM STAT- MEDLINE DA - 20120621 DCOM- 20121213 LR - 20141016 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 6 DP - 2012 TI - Intrinsically unstructured domain 3 of hepatitis C Virus NS5A forms a "fuzzy complex" with VAPB-MSP domain which carries ALS-causing mutations. PG - e39261 LID - 10.1371/journal.pone.0039261 [doi] AB - Hepatitis C virus (HCV) affects nearly 200 million people worldwide and is a leading factor for serious chronic liver diseases. For replicating HCV genome, the membrane-associated replication machinery needs to be formed by both HCV non-structural proteins including NS5A and human host factors. Recently NS5A has been identified to bind ER-anchored human VAP proteins and consequently this interaction may serve as a novel target for design of anti-HCV drugs. So far no biophysical characterization of this interaction has been reported. Here, we dissected the 243-residue VAPB into 4 and 447-residue NS5A into 10 fragments, followed by CD and NMR characterization of their structural properties. Subsequently, binding interactions between these fragments have been extensively assessed by NMR HSQC titration which is very powerful in detecting even very weak binding. The studies lead to three important findings: 1). a "fuzzy complex" is formed between the intrinsically-unstructured third domain (D3) of NS5A and the well-structured MSP domain of VAPB, with an average dissociation constant (Kd) of ~5 microM. 2). The binding-important residues on both NS5A-D3 and VAPB-MSP have been successfully mapped out, which provided experimental constraints for constructing the complex structure. In the complex, unstructured D3 binds to three surface pockets on one side of the MSP structure. Interestingly, two ALS-causing mutations T46I and P56S are also located on the D3-MSP interface. Moreover, NS5A-D3, FFAT-containing proteins and EphA4 appear to have overlapped binding interfaces on the MSP domain. 3). NS5A-D3 has been experimentally confirmed to competes with EphA4 in binding to the MSP domain, and T46I mutation of MSP dramatically abolishes its binding ability to D3. Our study not only provides essential foundation for further deciphering structure and function of the HCV replication machinery, but may also shed light on rationalizing a recent observation that a chronic HCV patient surprisingly developed ALS-like syndrome. FAU - Gupta, Garvita AU - Gupta G AD - Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore. FAU - Qin, Haina AU - Qin H FAU - Song, Jianxing AU - Song J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120613 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (VAPB protein, human) RN - 0 (Vesicular Transport Proteins) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Humans MH - Models, Theoretical MH - Molecular Sequence Data MH - *Mutation MH - Nuclear Magnetic Resonance, Biomolecular MH - Vesicular Transport Proteins/*chemistry/genetics MH - Viral Nonstructural Proteins/*chemistry/genetics PMC - PMC3374797 OID - NLM: PMC3374797 EDAT- 2012/06/22 06:00 MHDA- 2012/12/14 06:00 CRDT- 2012/06/22 06:00 PHST- 2012/03/22 [received] PHST- 2012/05/22 [accepted] PHST- 2012/06/13 [epublish] AID - 10.1371/journal.pone.0039261 [doi] AID - PONE-D-12-08401 [pii] PST - ppublish SO - PLoS One. 2012;7(6):e39261. doi: 10.1371/journal.pone.0039261. Epub 2012 Jun 13. PMID- 17410622 OWN - NLM STAT- MEDLINE DA - 20070430 DCOM- 20070625 LR - 20071203 IS - 1439-4227 (Print) IS - 1439-4227 (Linking) VI - 8 IP - 7 DP - 2007 May 7 TI - Structure induction of the T-cell receptor zeta-chain upon lipid binding investigated by NMR spectroscopy. PG - 820-7 AB - The conformation of the cytoplasmic part of the zeta-chain of the T-cell receptor (TCR) in its free form and bound to detergent micelles has been investigated by heteronuclear NMR spectroscopy. The zeta-chain is considered to be a mediator between the extracellular antigen and the intracellular signal-transduction cascade leading to T-cell activation. Earlier studies suggested a T-cell activation mechanism that involved a TCR-state-dependent lipid incorporation propensity of the zeta-chain accompanied by a helical folding transition. In order to support this proposed mechanism, standard protein NMR assignment and secondary-structure-elucidation techniques have been applied to the free TCR zeta-chain and to the zeta-chain bound to the detergent LMPG, which forms a micelle, in order to obtain the structural characteristics of this folding transition in a residue-resolved manner. We could assign the resonances of the free zeta-chain at 278 K, and this formed the basis for chemical-shift-perturbation studies to identify lipid binding sites. Our NMR results show that the free TCR zeta-chain is indeed intrinsically unstructured. Regions around the ITAM2 and ITAM3 sequences are involved in a highly dynamic binding of the free zeta-chain to a detergent micelle formed by the acidic lipid LMPG. FAU - Duchardt, Elke AU - Duchardt E AD - Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University Frankfurt, 60439 Frankfurt, Germany. FAU - Sigalov, Alexander B AU - Sigalov AB FAU - Aivazian, Dikran AU - Aivazian D FAU - Stern, Lawrence J AU - Stern LJ FAU - Schwalbe, Harald AU - Schwalbe H LA - eng GR - P30 AI42845-08/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - Germany TA - Chembiochem JT - Chembiochem : a European journal of chemical biology JID - 100937360 RN - 0 (Ligands) RN - 0 (Micelles) RN - 0 (Receptors, Antigen, T-Cell) SB - IM MH - Amino Acid Sequence MH - Ligands MH - Micelles MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Protein Conformation MH - Receptors, Antigen, T-Cell/*chemistry EDAT- 2007/04/06 09:00 MHDA- 2007/06/26 09:00 CRDT- 2007/04/06 09:00 AID - 10.1002/cbic.200600413 [doi] PST - ppublish SO - Chembiochem. 2007 May 7;8(7):820-7. PMID- 21533140 OWN - NLM STAT- MEDLINE DA - 20110502 DCOM- 20110830 LR - 20140820 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 4 DP - 2011 TI - Expression of measles virus nucleoprotein induces apoptosis and modulates diverse functional proteins in cultured mammalian cells. PG - e18765 LID - 10.1371/journal.pone.0018765 [doi] AB - BACKGROUND: Measles virus nucleoprotein (N) encapsidates the viral RNA, protects it from endonucleases and forms a virus specific template for transcription and replication. It is the most abundant protein during viral infection. Its C-terminal domain is intrinsically disordered imparting it the flexibility to interact with several cellular and viral partners. PRINCIPAL FINDINGS: In this study, we demonstrate that expression of N within mammalian cells resulted in morphological transitions, nuclear condensation, DNA fragmentation and activation of Caspase 3 eventuating into apoptosis. The rapid generation of intracellular reactive oxygen species (ROS) was involved in the mechanism of cell death. Addition of ascorbic acid (AA) or inhibitor of caspase-3 in the extracellular medium partially reversed N induced apoptosis. We also studied the protein profile of cells expressing N protein. MS analysis revealed the differential expression of 25 proteins out of which 11 proteins were up regulated while 14 show signs of down regulation upon N expression. 2DE results were validated by real time and semi quantitative RT-PCR analysis. CONCLUSION: These results show the pro-apoptotic effects of N indicating its possible development as an apoptogenic tool. Our 2DE results present prima facie evidence that the MV nucleoprotein interacts with or causes differential expression of a wide range of cellular factors. At this stage it is not clear as to what the adaptive response of the host cell is and what reflects a strategic modulation exerted by the virus. FAU - Bhaskar, Ashima AU - Bhaskar A AD - Applied Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India. FAU - Bala, Jyoti AU - Bala J FAU - Varshney, Akhil AU - Varshney A FAU - Yadava, Pramod AU - Yadava P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110414 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Nucleoproteins) RN - 0 (Reactive Oxygen Species) RN - 0 (Viral Proteins) RN - EC 3.4.22.- (Caspase 3) SB - IM MH - Apoptosis/*physiology MH - Caspase 3/metabolism MH - Cell Line, Tumor MH - Electrophoresis, Gel, Two-Dimensional MH - Enzyme Activation MH - Humans MH - Mass Spectrometry MH - Measles virus/*metabolism MH - Nucleoproteins/*metabolism/physiology MH - Reactive Oxygen Species/metabolism MH - Reverse Transcriptase Polymerase Chain Reaction MH - Viral Proteins/*metabolism/physiology PMC - PMC3077409 OID - NLM: PMC3077409 EDAT- 2011/05/03 06:00 MHDA- 2011/08/31 06:00 CRDT- 2011/05/03 06:00 PHST- 2010/10/01 [received] PHST- 2011/03/16 [accepted] PHST- 2011/04/14 [epublish] AID - 10.1371/journal.pone.0018765 [doi] PST - epublish SO - PLoS One. 2011 Apr 14;6(4):e18765. doi: 10.1371/journal.pone.0018765. PMID- 20460379 OWN - NLM STAT- MEDLINE DA - 20100712 DCOM- 20100806 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 29 DP - 2010 Jul 16 TI - Solution structure of human growth arrest and DNA damage 45alpha (Gadd45alpha) and its interactions with proliferating cell nuclear antigen (PCNA) and Aurora A kinase. PG - 22196-201 LID - 10.1074/jbc.M109.069344 [doi] AB - Gadd45alpha is a nuclear protein encoded by a DNA damage-inducible gene. Through its interactions with other proteins, Gadd45alpha participates in the regulation of DNA repair, cell cycle, cell proliferation, and apoptosis. The NMR structure of human Gadd45alpha has been determined and shows an alpha/beta fold with two long disordered and flexible regions at the N terminus and one of the loops. Human Gadd45alpha is predominantly monomeric in solution but exists in equilibrium with dimers and other oligomers whose population increases with protein concentration. NMR analysis shows that Aurora A interacts through its N-terminal domain with a region of human Gadd45alpha encompassing the site of dimerization, suggesting that the oligomerization of Gadd45alpha could be a regulatory mechanism to modulate its interactions with Aurora A, and possibly with other proteins too. However, Gadd45alpha appears to interact only weakly with PCNA through its flexible loop, in contrast with previous and contradictory reports. FAU - Sanchez, Ricardo AU - Sanchez R AD - Structural Biology Unit, CIC bioGUNE, Parque Tecnologico de Bizkaia, Ed. 800, Derio E-48160, Spain. FAU - Pantoja-Uceda, David AU - Pantoja-Uceda D FAU - Prieto, Jesus AU - Prieto J FAU - Diercks, Tammo AU - Diercks T FAU - Marcaida, Maria J AU - Marcaida MJ FAU - Montoya, Guillermo AU - Montoya G FAU - Campos-Olivas, Ramon AU - Campos-Olivas R FAU - Blanco, Francisco J AU - Blanco FJ LA - eng SI - PDB/2KG4 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100511 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Cell Cycle Proteins) RN - 0 (GADD45A protein, human) RN - 0 (Nuclear Proteins) RN - 0 (Proliferating Cell Nuclear Antigen) RN - 0 (Solutions) RN - EC 2.7.11.1 (Aurka protein, mouse) RN - EC 2.7.11.1 (Aurora Kinase A) RN - EC 2.7.11.1 (Aurora Kinases) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - Animals MH - Aurora Kinase A MH - Aurora Kinases MH - Cell Cycle Proteins/*chemistry/*metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Mice MH - Models, Molecular MH - Nuclear Proteins/*chemistry/*metabolism MH - Proliferating Cell Nuclear Antigen/*metabolism MH - Protein Structure, Secondary MH - Protein-Serine-Threonine Kinases/*metabolism MH - Solutions PMC - PMC2903397 OID - NLM: PMC2903397 EDAT- 2010/05/13 06:00 MHDA- 2010/08/07 06:00 CRDT- 2010/05/13 06:00 PHST- 2010/05/11 [aheadofprint] AID - M109.069344 [pii] AID - 10.1074/jbc.M109.069344 [doi] PST - ppublish SO - J Biol Chem. 2010 Jul 16;285(29):22196-201. doi: 10.1074/jbc.M109.069344. Epub 2010 May 11. PMID- 24453323 OWN - NLM STAT- MEDLINE DA - 20140123 DCOM- 20140311 LR - 20150108 IS - 1529-2401 (Electronic) IS - 0270-6474 (Linking) VI - 34 IP - 4 DP - 2014 Jan 22 TI - Functional regulation of the SLC26-family protein prestin by calcium/calmodulin. PG - 1325-32 LID - 10.1523/JNEUROSCI.4020-13.2014 [doi] AB - The solute carrier gene family 26 (SLC26) encodes membrane proteins with diverse physiological roles but with the common feature of halide involvement. Here, we present bioinformatic and biochemical evidence that SLC26 proteins have intrinsically disordered regions (IDRs) in their C-terminal domains and that these regions contain calmodulin (CaM) binding sites. The veracity of these predictions and the functional consequences of CaM binding were examined in prestin, SLC26A5, as a model for the SLC26 family and as one of the most investigated and best understood members. We found that CaM binds directly to the IDR in the C-terminal domain of prestin in a calcium-obligate manner. Using both isolated murine outer hair cells (OHCs) and a heterologous expression system, we also found that this calcium-obligate CaM binding shifts the operating point of the protein to more hyperpolarized potentials with consequent alteration of the function of the prestin. Because calcium is the main intracellular second messenger used by the efferent medial olivocochlear (MOC) pathway of the auditory system and CaM is abundant in OHCs, the CaM-prestin interaction may be involved in the MOC-mediated modulation of cochlear amplification. However, this regulatory mechanism is not likely to be restricted to cochlear OHCs, in light of both clear bioinformatic evidence and the fact that calcium and CaM are ubiquitous intracellular second messengers used by virtually all cell types. Hence, the calcium/CaM-dependent regulatory mechanism described herein is likely applicable to most, if not all, SLC26 paralogs. FAU - Keller, Jacob Pearson AU - Keller JP AD - Departments of Communication Sciences and Disorders, Molecular Biosciences, Neurobiology, and Otolaryngology-Head and Neck Surgery, and The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, Illinois 60208. FAU - Homma, Kazuaki AU - Homma K FAU - Duan, Chongwen AU - Duan C FAU - Zheng, Jing AU - Zheng J FAU - Cheatham, Mary Ann AU - Cheatham MA FAU - Dallos, Peter AU - Dallos P LA - eng GR - CA060553/CA/NCI NIH HHS/United States GR - DC00089/DC/NIDCD NIH HHS/United States GR - DC010633/DC/NIDCD NIH HHS/United States GR - R01 DC000089/DC/NIDCD NIH HHS/United States GR - R01 DC011813/DC/NIDCD NIH HHS/United States GR - RC1 DC010633/DC/NIDCD NIH HHS/United States GR - UL1 RR025741/RR/NCRR NIH HHS/United States GR - UL1 TR000150/TR/NCATS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - J Neurosci JT - The Journal of neuroscience : the official journal of the Society for Neuroscience JID - 8102140 RN - 0 (Anion Transport Proteins) RN - 0 (Calmodulin) RN - 0 (Molecular Motor Proteins) RN - 0 (Pres protein, mouse) RN - 0 (SLC26A5 protein, human) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Anion Transport Proteins/chemistry/*metabolism MH - Base Sequence MH - Binding Sites MH - Calcium/metabolism MH - Calmodulin/*metabolism MH - Female MH - Hair Cells, Auditory, Outer/metabolism MH - Humans MH - Male MH - Mice MH - Molecular Motor Proteins/chemistry/*metabolism MH - Molecular Sequence Data MH - Patch-Clamp Techniques PMC - PMC3898292 OID - NLM: PMC3898292 OTO - NOTNLM OT - SLC26 family OT - calmodulin OT - disordered region OT - mice OT - prestin EDAT- 2014/01/24 06:00 MHDA- 2014/03/13 06:00 CRDT- 2014/01/24 06:00 AID - 34/4/1325 [pii] AID - 10.1523/JNEUROSCI.4020-13.2014 [doi] PST - ppublish SO - J Neurosci. 2014 Jan 22;34(4):1325-32. doi: 10.1523/JNEUROSCI.4020-13.2014. PMID- 22730383 OWN - NLM STAT- MEDLINE DA - 20120907 DCOM- 20130116 LR - 20131121 IS - 1439-7641 (Electronic) IS - 1439-4235 (Linking) VI - 13 IP - 13 DP - 2012 Sep 17 TI - Water-in-oil micro-emulsion enhances the secondary structure of a protein by confinement. PG - 3179-84 LID - 10.1002/cphc.201200295 [doi] AB - A scheme is presented in which an organic solvent environment in combination with surfactants is used to confine a natively unfolded protein inside an inverse microemulsion droplet. This type of confinement allows a study that provides unique insight into the dynamic structure of an unfolded, flexible protein which is still solvated and thus under near-physiological conditions. In a model system, the protein osteopontin (OPN) is used. It is a highly phosphorylated glycoprotein that is expressed in a wide range of cells and tissues for which limited structural analysis exists due to the high degree of flexibility and large number of post-translational modifications. OPN is implicated in tissue functions, such as inflammation and mineralisation. It also has a key function in tumour metastasis and progression. Circular dichroism measurements show that confinement enhances the secondary structural features of the protein. Small-angle X-ray scattering and dynamic light scattering show that OPN changes from being a flexible protein in aqueous solution to adopting a less flexible and more compact structure inside the microemulsion droplets. This novel approach for confining proteins while they are still hydrated may aid in studying the structure of a wide range of natively unfolded proteins. CI - Copyright (c) 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. FAU - Shipovskov, Stepan AU - Shipovskov S AD - Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Ny Munkegade 8000 Aarhus, Denmark. stepan.shipovskov@danisco.com FAU - Oliveira, Cristiano L P AU - Oliveira CL FAU - Hoffmann, Soren Vronning AU - Hoffmann SV FAU - Schauser, Leif AU - Schauser L FAU - Sutherland, Duncan S AU - Sutherland DS FAU - Besenbacher, Flemming AU - Besenbacher F FAU - Pedersen, Jan Skov AU - Pedersen JS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120621 PL - Germany TA - Chemphyschem JT - Chemphyschem : a European journal of chemical physics and physical chemistry JID - 100954211 RN - 0 (Emulsions) RN - 0 (Oils) RN - 059QF0KO0R (Water) RN - 106441-73-0 (Osteopontin) SB - IM MH - Circular Dichroism MH - Emulsions/*chemistry MH - Models, Molecular MH - Oils/*chemistry MH - Osteopontin/*chemistry MH - Protein Structure, Secondary MH - Scattering, Small Angle MH - Water/*chemistry MH - X-Ray Diffraction EDAT- 2012/06/26 06:00 MHDA- 2013/01/17 06:00 CRDT- 2012/06/26 06:00 PHST- 2012/04/03 [received] PHST- 2012/06/21 [aheadofprint] AID - 10.1002/cphc.201200295 [doi] PST - ppublish SO - Chemphyschem. 2012 Sep 17;13(13):3179-84. doi: 10.1002/cphc.201200295. Epub 2012 Jun 21. PMID- 15752191 OWN - NLM STAT- MEDLINE DA - 20050308 DCOM- 20050714 LR - 20090112 IS - 0950-382X (Print) IS - 0950-382X (Linking) VI - 55 IP - 6 DP - 2005 Mar TI - Structural and functional studies of the enteropathogenic Escherichia coli type III needle complex protein EscJ. PG - 1658-70 AB - The type III secretion system (TTSS) is a macromolecular structure that spans the cell wall of Gram-negative bacterial pathogens, enabling delivery of virulence effector proteins directly to the membranes and cytosol of host eukaryotic cells. TTSS consists of a conserved needle complex (NC) that is composed of sets of inner and outer membranes rings connected by a periplasmic rod. Enteropathogenic Escherichia coli (EPEC) is an extracellular diarrhoeagenic pathogen that uses TTSS to induce actin polymerization and colonizes the intestinal epithelium. In EPEC, EscJ is predicted to be targeted to the periplasm, in a sec-dependent manner, and to bridge the TTSS membrane-associated rings. In this study we determined the global fold of EscJ using Nuclear Magnetic Resonance spectroscopy. We show that EscJ comprises two subdomains (D1 - amino acid residues 1-55 in the mature protein, and D2 - amino acid residues 90-170), each comprising a three-stranded beta-sheet flanked by two alpha-helices. A flexible region (residues 60-85) couples the structured regions D1 and D2. Periplasmic overexpression of EscJ(D1) and EscJ(D2) in a single escJ mutant bacterium failed to restore protein secretion activity, suggesting that the flexible linker is essential for the rod function. In contrast, periplasmic overexpression of EscJ(D1) and EscJ(D2) in the same wild-type bacterium had a dominant-negative phenotype suggesting defective assembly of the TTSS and protein translocation. FAU - Crepin, Valerie F AU - Crepin VF AD - Centres for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK. FAU - Prasannan, Sunil AU - Prasannan S FAU - Shaw, Rob K AU - Shaw RK FAU - Wilson, Rebecca K AU - Wilson RK FAU - Creasey, Elizabeth AU - Creasey E FAU - Abe, Cecilia M AU - Abe CM FAU - Knutton, Stuart AU - Knutton S FAU - Frankel, Gad AU - Frankel G FAU - Matthews, Steve AU - Matthews S LA - eng GR - JE514316/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Mol Microbiol JT - Molecular microbiology JID - 8712028 RN - 0 (Escherichia coli Proteins) RN - 0 (Macromolecular Substances) SB - IM MH - Amino Acid Sequence MH - Cell Membrane/chemistry/ultrastructure MH - Conserved Sequence MH - Escherichia coli/chemistry/metabolism/*pathogenicity MH - Escherichia coli Proteins/*chemistry/*metabolism MH - Gene Deletion MH - Genes, Bacterial MH - Genetic Complementation Test MH - Macromolecular Substances/chemistry/*metabolism MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Transport MH - Sequence Alignment MH - Sequence Deletion/genetics/physiology MH - Sequence Homology, Amino Acid EDAT- 2005/03/09 09:00 MHDA- 2005/07/15 09:00 CRDT- 2005/03/09 09:00 AID - MMI4508 [pii] AID - 10.1111/j.1365-2958.2005.04508.x [doi] PST - ppublish SO - Mol Microbiol. 2005 Mar;55(6):1658-70. PMID- 12620235 OWN - NLM STAT- MEDLINE DA - 20030306 DCOM- 20030402 LR - 20141120 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 11 IP - 2 DP - 2003 Feb TI - Structure of Rab escort protein-1 in complex with Rab geranylgeranyltransferase. PG - 483-94 AB - Posttranslational geranylgeranylation of Rab GTPases is catalyzed by Rab geranylgeranyltransferase (RabGGTase), which consists of a catalytic alpha/beta heterodimer and an accessory Rab escort protein (REP). The crystal structure of isoprenoid-bound RabGGTase complexed to REP-1 has been solved to 2.7 A resolution. The complex interface buries a surprisingly small surface area of ca. 680 A and is unexpectedly formed by helices 8, 10, and 12 of the RabGGTase alpha subunit and helices D and E of REP-1. We demonstrate that the affinity of RabGGTase for REP-1 is allosterically regulated by phosphoisoprenoid via a long-range trans-domain signal transduction event. Comparing the structure of REP-1 with the closely related RabGDI, we conclude that the specificity of the REP:RabGGTase interaction is defined by differently positioned phenylalanine residues conserved in the REP and GDI subfamilies. FAU - Pylypenko, Olena AU - Pylypenko O AD - Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany. FAU - Rak, Alexey AU - Rak A FAU - Reents, Reinhard AU - Reents R FAU - Niculae, Anca AU - Niculae A FAU - Sidorovitch, Vadim AU - Sidorovitch V FAU - Cioaca, Maria Daniela AU - Cioaca MD FAU - Bessolitsyna, Ekaterina AU - Bessolitsyna E FAU - Thoma, Nicolas H AU - Thoma NH FAU - Waldmann, Herbert AU - Waldmann H FAU - Schlichting, Ilme AU - Schlichting I FAU - Goody, Roger S AU - Goody RS FAU - Alexandrov, Kirill AU - Alexandrov K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (GDP dissociation inhibitor 1) RN - 0 (Guanine Nucleotide Dissociation Inhibitors) RN - 0 (Macromolecular Substances) RN - EC 2.5.- (Alkyl and Aryl Transferases) RN - EC 2.5.1.- (Rab geranylgeranyltransferase) RN - EC 3.6.1.- (rab GTP-Binding Proteins) RN - EC 3.6.5.2 (rab3A GTP-Binding Protein) SB - IM MH - Alkyl and Aryl Transferases/*chemistry/genetics/metabolism MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Guanine Nucleotide Dissociation Inhibitors/chemistry/genetics/metabolism MH - In Vitro Techniques MH - Lipid Metabolism MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis MH - Protein Conformation MH - Sequence Homology, Amino Acid MH - Signal Transduction MH - rab GTP-Binding Proteins/*chemistry/genetics/metabolism MH - rab3A GTP-Binding Protein/chemistry/genetics/metabolism EDAT- 2003/03/07 04:00 MHDA- 2003/04/04 05:00 CRDT- 2003/03/07 04:00 AID - S1097276503000443 [pii] PST - ppublish SO - Mol Cell. 2003 Feb;11(2):483-94. PMID- 17567567 OWN - NLM STAT- MEDLINE DA - 20071030 DCOM- 20071203 LR - 20120215 IS - 1530-6860 (Electronic) IS - 0892-6638 (Linking) VI - 21 IP - 13 DP - 2007 Nov TI - Gamma-synuclein and the progression of cancer. PG - 3419-30 AB - The synucleins are a small, soluble, highly conserved group of neuronal proteins that have been implicated in both neurodegenerative diseases and cancer. The synuclein family consists of alpha-, beta-, and gamma-synucleins (gamma-syn). They are a natively unfolded group of proteins that share sequence homologies and structural properties. So far, the biological functions of the synucleins are still unclear, but their involvement in neurodegenerative diseases and cancer may provide insights into the pathological processes that result from these two groups of debilitating diseases, and present the possibility to use them as potential targets for early diagnosis and treatment. Recently, elevated levels of gamma-syn proteins have been detected in various types of cancer, especially in advanced stages of the disease. Furthermore, studies to date indicate that overexpression of gamma-syn compromises normal mitotic checkpoint controls, resulting in multinucleation as well as faster cell growth. Gamma-syn has also been shown to promote invasion and metastasis in in vitro assays as well as in animal models. Overexpression of gamma-syn also interferes with drug-induced apoptotic responses. These observations raise questions about the involvement of gamma-syn in the process of tumorigenesis and metastasis, and efforts have already been made to use gamma-syn as a marker for assessing breast cancer progression. This review will discuss the involvement of gamma-syn in cancer progression, metastasis and its potential as a marker. FAU - Ahmad, Mushfika AU - Ahmad M AD - Department of Biochemistry, Faculty of Medicine and Health Sciences, United Arab Emirates, Al Ain, PO BOX 17666, United Arab Emirates. FAU - Attoub, Samir AU - Attoub S FAU - Singh, Maneesh N AU - Singh MN FAU - Martin, Francis L AU - Martin FL FAU - El-Agnaf, Omar M A AU - El-Agnaf OM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20070612 PL - United States TA - FASEB J JT - FASEB journal : official publication of the Federation of American Societies for Experimental Biology JID - 8804484 RN - 0 (Biological Markers) RN - 0 (gamma-Synuclein) SB - IM MH - Animals MH - Apoptosis MH - Biological Markers MH - Cell Proliferation MH - Gene Expression Regulation MH - Humans MH - Neoplasm Invasiveness MH - Neoplasm Metastasis MH - Neoplasms/genetics/*pathology/physiopathology MH - Neurodegenerative Diseases/physiopathology MH - Transcription, Genetic MH - gamma-Synuclein/genetics/*physiology RF - 144 EDAT- 2007/06/15 09:00 MHDA- 2007/12/06 09:00 CRDT- 2007/06/15 09:00 PHST- 2007/06/12 [aheadofprint] AID - fj.07-8379rev [pii] AID - 10.1096/fj.07-8379rev [doi] PST - ppublish SO - FASEB J. 2007 Nov;21(13):3419-30. Epub 2007 Jun 12. PMID- 24918957 OWN - NLM STAT- In-Process DA - 20140702 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 136 IP - 26 DP - 2014 Jul 2 TI - Metal-induced conformational changes of human metallothionein-2A: a combined theoretical and experimental study of metal-free and partially metalated intermediates. PG - 9499-508 LID - 10.1021/ja5047878 [doi] AB - Electrospray ionization ion mobility mass spectrometry (ESI IM-MS) and molecular dynamics (MD) simulations reveal new insights into metal-induced conformational changes and the mechanism for metalation of human metallothionein-2A (MT), an intrinsically disordered protein. ESI of solutions containing apoMT yields multiple charge states of apoMT; following addition of Cd(2+) to the solution, ESI yields a range of CdiMT (i = 1-7) product ions (see Chen et al. Anal. Chem. 2013, 85, 7826-33). Ion mobility arrival-time distributions (ATDs) for the CdiMT (i = 0-7) ions reveal a diverse population of ion conformations. The ion mobility data clearly show that the conformational diversity for apoMT and partially metalated ions converges toward ordered, compact conformations as the number of bound Cd(2+) ions increase. MD simulations provide additional information on conformation candidates of CdiMT (i = 0-7) that supports the convergence of distinct conformational populations upon metal binding. Integrating the IM-MS and MD data provides a global view that shows stepwise conformational transition of an ensemble as a function of metal ion bound. ApoMT is comprised of a wide range of conformational states that populate between globular-like compact and coil-rich extended conformations. During the initial stepwise metal addition (number of metal ions bound i = 1-3), the metal ions bind to different sites to yield distinct conformations, whereas for i > 4, the conformational changes appear to be domain-specific, attributed to different degrees of disorder of the beta domain; the beta domain becomes more ordered as additional metal ions are added, promoting convergences to the dumbbell-shaped conformation. FAU - Chen, Shu-Hua AU - Chen SH AD - Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States. FAU - Chen, Liuxi AU - Chen L FAU - Russell, David H AU - Russell DH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140620 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 SB - IM EDAT- 2014/06/12 06:00 MHDA- 2014/06/12 06:00 CRDT- 2014/06/12 06:00 PHST- 2014/06/20 [aheadofprint] AID - 10.1021/ja5047878 [doi] PST - ppublish SO - J Am Chem Soc. 2014 Jul 2;136(26):9499-508. doi: 10.1021/ja5047878. Epub 2014 Jun 20. PMID- 21805002 OWN - NLM STAT- MEDLINE DA - 20111202 DCOM- 20120320 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Structural disorder within paramyxovirus nucleoproteins and phosphoproteins. PG - 69-81 LID - 10.1039/c1mb05204g [doi] AB - This review focuses on the experimental data showing the abundance of structural disorder within the nucleoprotein (N) and phosphoprotein (P) from three paramyxoviruses, namely Nipah (NiV), Hendra (HeV) and measles (MeV) viruses. We provide a detailed description of the molecular mechanisms governing the disorder-to-order transition of the intrinsically disordered C-terminal domains (N(TAIL)) of their N proteins upon binding to the C-terminal X domain (XD) of the homologous P proteins. We also show that a significant flexibility persists within N(TAIL)-XD complexes, which therefore provide illustrative examples of "fuzziness". The functional implications of structural disorder are discussed in light of the ability of disordered regions to establish a complex molecular partnership, thereby leading to a variety of biological effects. Taking into account the promiscuity that typifies disordered regions, we propose that the main functional advantage of the abundance of disorder within viruses would reside in pleiotropy and genetic compaction, where a single gene would encode a single (regulatory) protein product able to establish multiple interactions via its disordered regions, and hence to exert multiple concomitant biological effects. FAU - Habchi, Johnny AU - Habchi J AD - Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS et Universites d'Aix-Marseille I et II, Marseille, France. FAU - Longhi, Sonia AU - Longhi S LA - eng GR - R01 NS031693-11A2/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20110801 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Nucleoproteins) RN - 0 (Phosphoproteins) RN - 0 (Viral Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleoproteins/*chemistry/*metabolism MH - Paramyxovirinae/*metabolism/physiology MH - Phosphoproteins/*chemistry/*metabolism MH - *Protein Folding MH - Viral Proteins/*chemistry/metabolism EDAT- 2011/08/02 06:00 MHDA- 2012/03/21 06:00 CRDT- 2011/08/02 06:00 PHST- 2011/08/01 [aheadofprint] PHST- 2011/12/01 [epublish] AID - 10.1039/c1mb05204g [doi] PST - ppublish SO - Mol Biosyst. 2012 Jan;8(1):69-81. doi: 10.1039/c1mb05204g. Epub 2011 Aug 1. PMID- 10497031 OWN - NLM STAT- MEDLINE DA - 19991028 DCOM- 19991028 LR - 20071114 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 292 IP - 3 DP - 1999 Sep 24 TI - Structural flexibility in human topoisomerase I revealed in multiple non-isomorphous crystal structures. PG - 685-96 AB - Human topoisomerase I plays a critical role in chromosomal stability by relaxing the DNA superhelical tension that arises from a variety of nuclear processes, including replication, transcription, and chromatin remodeling. Human topoisomerase I is a approximately 91 kDa enzyme composed of four major domains: a 24 kDa N-terminal domain, a56 kDa core domain, a7 kDa linker domain, and a6 kDa C-terminal domain containing the active-site Tyr723 residue. A monoclinic crystal structure of a 70 kDa N-terminally truncated form of human topoisomerase I in non-covalent complex with a 22 bp DNA duplex exhibited remarkable crystal-to-crystal non-isomorphism; shifts in cell constants of up to 9 A in the b -axis length and up to 8.5 degrees in the beta-angle were observed. Eight crystal structures of human topoisomerase I - DNA complexes from this crystal form were determined to between 2.8 and 3.25 A resolution. These structures revealed both dramatic shifts in crystal packing and functionally suggestive regions of conformational flexibility in the structure of the enzyme. Crystal packing shifts of up to 20.5 A combined with rotations of up to 11.5 degrees were observed, helping to explain the variability in cell constants. When the core subdomain III regions of the eight structures are superimposed, the "cap" (core subdomains I and II) of the molecule is observed to rotate by up to 4.6 degrees and to shift by up to 3.6 A. The linker domain shows the greatest degree of conformational flexibility, rotating and shifting by up to 2.5 degrees and 4.6 A, respectively, in five of eight structures, and becoming disordered altogether in the remaining three. These observed regions of conformational flexibility in the cap and the linker domain are consistent with the structural flexibility invoked in the "controled rotation" mechanism proposed for the relaxation of DNA superhelical tension by human topoisomerase I. CI - Copyright 1999 Academic Press. FAU - Redinbo, M R AU - Redinbo MR AD - Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA 98195, USA. FAU - Stewart, L AU - Stewart L FAU - Champoux, J J AU - Champoux JJ FAU - Hol, W G AU - Hol WG LA - eng SI - PDB/1A36 GR - 1P41 RR12408-01A1/RR/NCRR NIH HHS/United States GR - GM49156/GM/NIGMS NIH HHS/United States GR - RR-01646/RR/NCRR NIH HHS/United States GR - etc. PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Oligodeoxyribonucleotides) RN - 9007-49-2 (DNA) RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) SB - IM MH - Crystallization MH - Crystallography, X-Ray MH - DNA/*chemistry MH - DNA Topoisomerases, Type I/*chemistry MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Oligodeoxyribonucleotides/chemistry MH - Protein Conformation EDAT- 1999/09/25 MHDA- 1999/09/25 00:01 CRDT- 1999/09/25 00:00 AID - 10.1006/jmbi.1999.3065 [doi] AID - S0022-2836(99)93065-6 [pii] PST - ppublish SO - J Mol Biol. 1999 Sep 24;292(3):685-96. PMID- 8745404 OWN - NLM STAT- MEDLINE DA - 19961017 DCOM- 19961017 LR - 20130919 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 5 IP - 2 DP - 1996 Feb TI - Yeast heat shock transcription factor N-terminal activation domains are unstructured as probed by heteronuclear NMR spectroscopy. PG - 262-9 AB - The structure and dynamics of the N-terminal activation domains of the yeast heat shock transcription factors of Kluyveromyces lactis and Saccharomyces cerevisiae were probed by heteronuclear 15N[1H] correlation and 15N[1H] NOE NMR studies. Using the DNA-binding domain as a structural reference, we show that the protein backbone of the N-terminal activation domain undergoes rapid, large-amplitude motions and is therefore unstructured. Difference CD data also show that the N-terminal activation domain remains random-coil, even in the presence of DNA. Implications for a "polypeptide lasso" model of transcriptional activation are discussed. FAU - Cho, H S AU - Cho HS AD - Department of Chemistry, University of California, Berkeley 94720, USA. FAU - Liu, C W AU - Liu CW FAU - Damberger, F F AU - Damberger FF FAU - Pelton, J G AU - Pelton JG FAU - Nelson, H C AU - Nelson HC FAU - Wemmer, D E AU - Wemmer DE LA - eng GR - GM08295/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (DNA, Fungal) RN - 0 (Fungal Proteins) RN - 0 (Heat-Shock Proteins) RN - 0 (Recombinant Proteins) SB - IM MH - Base Sequence MH - Binding Sites MH - Circular Dichroism MH - DNA, Fungal/metabolism MH - Fungal Proteins/*chemistry/metabolism MH - Heat-Shock Proteins/*chemistry/metabolism MH - Kluyveromyces/*chemistry/metabolism MH - *Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Recombinant Proteins/chemistry MH - Saccharomyces cerevisiae/*chemistry/metabolism MH - Transcription, Genetic PMC - PMC2143352 OID - NLM: PMC2143352 EDAT- 1996/02/01 MHDA- 1996/02/01 00:01 CRDT- 1996/02/01 00:00 AID - 10.1002/pro.5560050210 [doi] PST - ppublish SO - Protein Sci. 1996 Feb;5(2):262-9. PMID- 20877914 OWN - NLM STAT- MEDLINE DA - 20101109 DCOM- 20110222 LR - 20140910 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 6 IP - 12 DP - 2010 Dec TI - A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins. PG - 2448-58 LID - 10.1039/c0mb00097c [doi] AB - Many pathogenic Gram-negative bacteria use a type III secretion system (T3SS) to deliver effector proteins into the host cell where they reprogram host defenses and facilitate pathogenesis. The first 20-30 N-terminal residues usually contain the 'secretion signal' that targets effector proteins for translocation, however, a consensus sequence motif has never been discerned. Recent machine-learning approaches, such as support vector machine (SVM)-based Identification and Evaluation of Virulence Effectors (SIEVE), have improved the ability to identify effector proteins from genomics sequence information. While these methods all suggest that the T3SS secretion signal has a characteristic amino acid composition bias, it is still unclear if the amino acid pattern is important and if there are any unifying structural properties that direct recognition. To address these issues a peptide corresponding to the secretion signal for Salmonella enterica serovar Typhimurium effector SseJ was synthesized (residues 1-30, SseJ) along with scrambled peptides of the same amino acid composition that produced high (SseJ-H) and low (SseJ-L) SIEVE scores. The secretion properties of these three peptides were tested using a secretion signal-CyaA fusion assay and their structural properties probed using circular dichroism, nuclear magnetic resonance, and ion mobility spectrometry-mass spectrometry. The secretion predictions from SIEVE matched signal-CyaA fusion experimental results with J774 macrophages suggesting that the SseJ secretion signal has some sequence order dependence. The structural studies showed that the SseJ, SseJ-H, and SseJ-L peptides were intrinsically disordered in aqueous solution with a small predisposition to adopt nascent helical structure only in the presence of structure stabilizing agents such as 1,1,1,3,3,3-hexafluoroisopropanol. Intrinsic disorder may be a universal feature of effector secretion signals as similar conclusions were reached following structural characterization of peptides corresponding to the N-terminal regions of the S. Typhimurium effectors SptP, SopD-2, GtgE, and the Yersinia pestis effector YopH. FAU - Buchko, Garry W AU - Buchko GW AD - Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA. garry.buchko@pnl.gov FAU - Niemann, George AU - Niemann G FAU - Baker, Erin S AU - Baker ES FAU - Belov, Mikhail E AU - Belov ME FAU - Smith, Richard D AU - Smith RD FAU - Heffron, Fred AU - Heffron F FAU - Adkins, Joshua N AU - Adkins JN FAU - McDermott, Jason E AU - McDermott JE LA - eng GR - P41 RR018522/RR/NCRR NIH HHS/United States GR - P41 RR018522-08/RR/NCRR NIH HHS/United States GR - R01 AI022933/AI/NIAID NIH HHS/United States GR - R21 CA12619-01/CA/NCI NIH HHS/United States GR - RR 18522/RR/NCRR NIH HHS/United States GR - Y1-AI-8401-01/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20100929 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Adenylate Cyclase Toxin) RN - 0 (Amino Acids) RN - 0 (Bacterial Proteins) RN - 0 (Peptides) RN - 0 (Propanols) RN - 0 (Protein Sorting Signals) RN - 75-89-8 (Trifluoroethanol) RN - 920-66-1 (hexafluoroisopropanol) RN - E0399OZS9N (Cyclic AMP) SB - IM MH - Adenylate Cyclase Toxin/metabolism MH - Algorithms MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Amino Acids/metabolism MH - Bacterial Proteins/*chemistry/*secretion MH - Biological Assay MH - Circular Dichroism MH - Computational Biology/*methods MH - Cyclic AMP/metabolism MH - Magnetic Resonance Spectroscopy MH - Mass Spectrometry MH - Molecular Sequence Data MH - Peptides/chemistry MH - Propanols/chemistry MH - *Protein Sorting Signals MH - Protein Structure, Secondary MH - Salmonella enterica/*metabolism MH - Trifluoroethanol/chemistry PMC - PMC3282560 MID - NIHMS356209 OID - NLM: NIHMS356209 OID - NLM: PMC3282560 EDAT- 2010/09/30 06:00 MHDA- 2011/02/23 06:00 CRDT- 2010/09/30 06:00 PHST- 2010/09/29 [aheadofprint] PHST- 2010/11/08 [epublish] AID - 10.1039/c0mb00097c [doi] PST - ppublish SO - Mol Biosyst. 2010 Dec;6(12):2448-58. doi: 10.1039/c0mb00097c. Epub 2010 Sep 29. PMID- 6245879 OWN - NLM STAT- MEDLINE DA - 19800722 DCOM- 19800722 LR - 20131121 IS - 0014-2956 (Print) IS - 0014-2956 (Linking) VI - 105 IP - 1 DP - 1980 Mar TI - The regulation of glycogen metabolism. Purification and properties of protein phosphatase inhibitor-2 from rabbit skeletal muscle. PG - 195-203 FAU - Foulkes, J G AU - Foulkes JG FAU - Cohen, P AU - Cohen P LA - eng PT - Journal Article PL - GERMANY, WEST TA - Eur J Biochem JT - European journal of biochemistry / FEBS JID - 0107600 RN - 0 (Enzyme Inhibitors) RN - 0 (Proteins) RN - 0 (protein phosphatase inhibitor-2) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - 9005-79-2 (Glycogen) RN - E0399OZS9N (Cyclic AMP) RN - EC 2.7.- (Protein Kinases) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) SB - IM MH - Animals MH - Chromatography, Gel MH - Cyclic AMP/pharmacology MH - Electrophoresis, Polyacrylamide Gel MH - Enzyme Inhibitors/*isolation & purification MH - Glycogen/*metabolism MH - Molecular Weight MH - Muscles/*metabolism MH - Phosphoprotein Phosphatases/antagonists & inhibitors MH - Protein Kinases/metabolism MH - *Proteins MH - Rabbits MH - Sodium Dodecyl Sulfate EDAT- 1980/03/01 MHDA- 1980/03/01 00:01 CRDT- 1980/03/01 00:00 PST - ppublish SO - Eur J Biochem. 1980 Mar;105(1):195-203. PMID- 19216110 OWN - NLM STAT- MEDLINE DA - 20090212 DCOM- 20090429 LR - 20131121 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 131 IP - 6 DP - 2009 Feb 18 TI - Intrinsically disordered p53 extreme C-terminus binds to S100B(betabeta) through "fly-casting". PG - 2088-9 AB - Intrinsically disordered proteins (IDPs) are functional proteins where a lack of stable tertiary structures is required for function. Many of the IDPs involved in cellular regulation and signaling have substantial residual structures in the unbound state and fold into stable structures upon binding to their biological partners. Specific roles of these residual structures in and the underlying mechanisms of coupled binding and folding are poorly understood. Here we use physics-based atomistic simulations to compute the multidimensional free energy surfaces of coupled folding and binding of the intrinsically disordered p53 extreme C-terminus to protein S100B(betabeta). The results show that, even though the unbound p53 peptide appears to sample several alternative folded states previously observed when in complex with various targets, it binds to S100B(betabeta) through formation of nonspecific complexes, i.e., a "fly-casting"-like process. The current work, together with previous NMR and coarse-grained modeling studies of another prototypical system, suggests that the main role of the residual structures in the unbound states of regulatory IDPs might be to provide thermodynamic control of binding through modulating the entropic cost of folding and not to enhance the binding rate by acting as initial contact sites. FAU - Chen, Jianhan AU - Chen J AD - Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Nerve Growth Factors) RN - 0 (S100 Calcium Binding Protein beta Subunit) RN - 0 (S100 Proteins) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Computer Simulation MH - Kinetics MH - Models, Molecular MH - Nerve Growth Factors/*chemistry MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - S100 Calcium Binding Protein beta Subunit MH - S100 Proteins/*chemistry MH - Surface Properties MH - Thermodynamics MH - Tumor Suppressor Protein p53/*chemistry EDAT- 2009/02/14 09:00 MHDA- 2009/04/30 09:00 CRDT- 2009/02/14 09:00 PST - ppublish SO - J Am Chem Soc. 2009 Feb 18;131(6):2088-9. PMID- 15609350 OWN - NLM STAT- MEDLINE DA - 20050224 DCOM- 20060522 LR - 20091119 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 58 IP - 3 DP - 2005 Feb 15 TI - Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: deciphering the effect of intermolecular interactions on computational structure prediction of the p27Kip1 protein bound to the cyclin A-cyclin-dependent kinase 2 complex. PG - 706-16 AB - The relationship between folding mechanism coupled to binding and structure prediction of the tertiary complexes is studied for the p27(Kip) (1) protein which has an intrinsically disordered unbound form and undergoes a functional folding transition during complex formation with the phosphorylated cyclin A-cyclin-dependent kinase 2 (Cdk2) binary complex. Hierarchy of p27(Kip1) structural loss determined in our earlier studies from temperature-induced Monte Carlo simulations and subsequent characterization of the transition state ensemble (TSE) for the folding reaction have shown that simultaneous ordering of the p27(Kip1) native intermolecular interface for the beta-hairpin and beta-strand secondary structure elements is critical for nucleating a rapid kinetic transition to the native tertiary complex. In the present study, we investigate the effect of forming specific intermolecular interactions on structure prediction of the p27(Kip1) tertiary complex. By constraining different secondary structure elements of p27(Kip1) in their native bound conformations and conducting multiple simulated annealing simulations, we analyze differences in the success rate of predicting the native structure of p27(Kip1) in the tertiary complex. In accordance with the nucleation-condensation mechanism, we have found that further stabilization of the native intermolecular interface for the beta-hairpin and beta-strand elements of p27(Kip1), that become ordered in the TSE, but are hardly populated in the unbound state, results in a consistent acquisition of the native bound structure. Conversely, the excessive stablization of the local secondary structure elements, which are rarely detected in the TSE, has a detrimental effect on convergence to the native bound structure. CI - (c) 2004 Wiley-Liss, Inc. FAU - Verkhivker, Gennady M AU - Verkhivker GM AD - Pfizer Global Research and Development, La Jolla Laboratories, San Diego, California 92121, USA. gennady.verkhivker@pfizer.com LA - eng PT - Journal Article PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Cyclin A) RN - 0 (Cyclins) RN - 0 (Microtubule-Associated Proteins) RN - 0 (Proteins) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 2) RN - EC 2.7.11.22 (Cyclin-Dependent Kinases) SB - IM MH - Cell Cycle MH - Computational Biology/*methods MH - Computer Simulation MH - Cyclin A/*chemistry MH - Cyclin-Dependent Kinase 2/*chemistry MH - Cyclin-Dependent Kinase Inhibitor p27/*chemistry MH - Cyclin-Dependent Kinases MH - Cyclins MH - Humans MH - Hydrogen Bonding MH - Kinetics MH - Microtubule-Associated Proteins MH - Models, Molecular MH - Models, Statistical MH - Molecular Conformation MH - Monte Carlo Method MH - Phosphorylation MH - Probability MH - Protein Binding MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Protein Interaction Mapping MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proteins/*chemistry MH - Proteomics/*methods MH - Temperature EDAT- 2004/12/21 09:00 MHDA- 2006/05/23 09:00 CRDT- 2004/12/21 09:00 AID - 10.1002/prot.20351 [doi] PST - ppublish SO - Proteins. 2005 Feb 15;58(3):706-16. PMID- 20071374 OWN - NLM STAT- MEDLINE DA - 20100311 DCOM- 20100517 LR - 20140827 IS - 1471-9053 (Electronic) IS - 0032-0781 (Linking) VI - 51 IP - 3 DP - 2010 Mar TI - Characterization of two soybean (Glycine max L.) LEA IV proteins by circular dichroism and Fourier transform infrared spectrometry. PG - 395-407 LID - 10.1093/pcp/pcq005 [doi] AB - Late embryogenesis-abundant (LEA) proteins, accumulating to a high level during the late stages of seed development, may play a role as osmoprotectants. However, the functions and mechanisms of LEA proteins remained to be elucidated. Five major groups of LEA proteins have been described. In the present study, we report on the characterization of two members of soybean LEA IV proteins, basic GmPM1 and acidic GmPM28, by circular dichroism and Fourier transform infrared spectroscopy. The spectra of both proteins revealed limited defined secondary structures in the fully hydrated state. Thus, the soybean LEA IV proteins are members of 'natively unfolded proteins'. GmPM1 or GmPM28 proteins showed a conformational change under hydrophobic or dry conditions. After fast or slow drying, the two proteins showed slightly increased proportions of defined secondary structures (alpha-helix and beta-sheet), from 30 to 49% and from 34 to 42% for GmPM1 and GmPm28, respectively. In the dehydrated state, GmPM1 and GmPM28 interact with non-reducing sugars to improve the transition temperature of cellular glass, with poly-l-lysine to prevent dehydration-induced aggregation and with phospholipids to maintain the liquid crystal phase over a wide temperature range. Our work suggests that soybean LEA IV proteins are functional in the dry state. They are one of the important components in cellular glasses and may stabilize desiccation-sensitive proteins and plasma membranes during dehydration. FAU - Shih, Ming-der AU - Shih MD AD - Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC. FAU - Hsieh, Tzung-Yang AU - Hsieh TY FAU - Lin, Tsai-Piao AU - Lin TP FAU - Hsing, Yue-Ie C AU - Hsing YI FAU - Hoekstra, Folkert A AU - Hoekstra FA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100112 PL - Japan TA - Plant Cell Physiol JT - Plant & cell physiology JID - 9430925 RN - 0 (Oligosaccharides) RN - 0 (Phospholipids) RN - 0 (Plant Proteins) RN - 0 (late embryogenesis abundant protein, plant) RN - 25104-18-1 (Polylysine) SB - IM MH - Circular Dichroism MH - Oligosaccharides/chemistry MH - Phospholipids/chemistry MH - Plant Proteins/*chemistry MH - Polylysine/chemistry MH - Protein Folding MH - Protein Structure, Secondary MH - Soybeans/*chemistry MH - Spectroscopy, Fourier Transform Infrared PMC - PMC2835872 OID - NLM: PMC2835872 EDAT- 2010/01/15 06:00 MHDA- 2010/05/18 06:00 CRDT- 2010/01/15 06:00 PHST- 2010/01/12 [aheadofprint] AID - pcq005 [pii] AID - 10.1093/pcp/pcq005 [doi] PST - ppublish SO - Plant Cell Physiol. 2010 Mar;51(3):395-407. doi: 10.1093/pcp/pcq005. Epub 2010 Jan 12. PMID- 10585425 OWN - NLM STAT- MEDLINE DA - 20000113 DCOM- 20000113 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 274 IP - 50 DP - 1999 Dec 10 TI - NMR structure and functional characteristics of the hydrophilic N terminus of the potassium channel beta-subunit Kvbeta1.1. PG - 35521-5 AB - Rapid N-type inactivation of voltage-dependent potassium (Kv) channels controls membrane excitability and signal propagation in central neurons and is mediated by protein domains (inactivation gates) occluding the open channel pore from the cytoplasmic side. Inactivation domains (ID) are donated either by the pore-forming alpha-subunit or certain auxiliary beta-subunits. Upon coexpression, Kvbeta1.1 was found to endow non-inactivating members of the Kv1alpha family with fast inactivation via its unique N terminus. Here we investigated structure and functional properties of the Kvbeta1.1 N terminus (amino acids 1-62, betaN-(1-62)) using NMR spectroscopy and patch clamp recordings. betaN-(1-62) showed all hallmarks of N-type inactivation: it inactivated non-inactivating Kv1.1 channels when applied to the cytoplasmic side as a synthetic peptide, and its interaction with the alpha-subunit was competed with tetraethylammonium and displayed an affinity in the lower micromolar range. In aequous and physiological salt solution, betaN-(1-62) showed no well defined three-dimensional structure, it rather existed in a fast equilibrium of multiple weakly structured states. These structural and functional properties of betaN-(1-62) closely resemble those of the "unstructured" ID from Shaker B, but differ markedly from those of the compactly folded ID of the Kv3.4 alpha-subunit. FAU - Wissmann, R AU - Wissmann R AD - Department of Physiology II, University of Tubingen, Ob dem Himmelreich 7, 72074 Tubingen, Germany. FAU - Baukrowitz, T AU - Baukrowitz T FAU - Kalbacher, H AU - Kalbacher H FAU - Kalbitzer, H R AU - Kalbitzer HR FAU - Ruppersberg, J P AU - Ruppersberg JP FAU - Pongs, O AU - Pongs O FAU - Antz, C AU - Antz C FAU - Fakler, B AU - Fakler B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Peptide Fragments) RN - 0 (Potassium Channels) RN - 0 (Potassium Channels, Voltage-Gated) RN - 0 (Recombinant Proteins) RN - 147173-20-4 (Kv1.1 Potassium Channel) RN - 66-40-0 (Tetraethylammonium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Female MH - Kv1.1 Potassium Channel MH - Membrane Potentials/drug effects/*physiology MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Oocytes/physiology MH - Peptide Fragments/chemistry/metabolism MH - Potassium Channels/*chemistry/*physiology MH - *Potassium Channels, Voltage-Gated MH - Recombinant Proteins/chemistry/metabolism MH - Tetraethylammonium/pharmacology MH - Xenopus laevis EDAT- 1999/12/10 MHDA- 1999/12/10 00:01 CRDT- 1999/12/10 00:00 PST - ppublish SO - J Biol Chem. 1999 Dec 10;274(50):35521-5. PMID- 16464864 OWN - NLM STAT- MEDLINE DA - 20060410 DCOM- 20060605 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 15 DP - 2006 Apr 14 TI - Small ubiquitin-like modifier (SUMO) modification of natively unfolded proteins tau and alpha-synuclein. PG - 9919-24 AB - Sumoylation is an important post-translational modification that provides a rapid and reversible means for controlling the activity, subcellular localization, and stability of target proteins. We have examined the covalent attachment of the small ubiquitin-like modifier (SUMO) proteins to tau and alpha-synuclein, two natively unfolded proteins that define several neurodegenerative diseases. Both brain proteins were preferentially modified by SUMO1, as compared with SUMO2 or SUMO3. Tau contains two SUMO consensus sequences, and mutational analyses identified Lys(340) as the major sumoylation site. Although both tau and alpha-synuclein are targets for proteasomal degradation, only tau sumoylation was affected by inhibitors of the proteasome pathway. Tau is a microtubule-associated protein, whose ability to bind and stabilize microtubules is negatively regulated by phosphorylation. Treatment with the phosphatase inhibitor, okadaic acid, or the microtubule depolymerizing drug, colchicine, up-regulated tau sumoylation. This suggests that SUMO modification may preferentially target a free soluble pool of the substrate. These findings revealed a new, possibly regulatory, modification of tau and alpha-synuclein that may also have implications for their pathogenic roles in neurodegenerative diseases. FAU - Dorval, Veronique AU - Dorval V AD - Department of Medical Biophysics and Centre for Research in Neurodegenerative Diseases, University of Toronto, 6 Queen's Park Crescent West, Toronto, Ontario M5S 3H2, Canada. FAU - Fraser, Paul E AU - Fraser PE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060207 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Epitopes) RN - 0 (SUMO-1 Protein) RN - 0 (SUMO1 protein, human) RN - 0 (SUMO2 protein, human) RN - 0 (SUMO3 protein, human) RN - 0 (Small Ubiquitin-Related Modifier Proteins) RN - 0 (Ubiquitin) RN - 0 (Ubiquitins) RN - 0 (alpha-Synuclein) RN - 0 (tau Proteins) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) RN - K3Z4F929H6 (Lysine) SB - IM MH - Blotting, Western MH - Cell Line MH - Epitopes/chemistry MH - Humans MH - Lysine/chemistry MH - Microtubules/metabolism MH - Neurodegenerative Diseases/metabolism MH - Phosphorylation MH - Plasmids/metabolism MH - Proteasome Endopeptidase Complex/metabolism MH - Protein Binding MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - SUMO-1 Protein MH - Small Ubiquitin-Related Modifier Proteins/chemistry/metabolism/*physiology MH - Transfection MH - Ubiquitin/chemistry MH - Ubiquitins/chemistry MH - alpha-Synuclein/*chemistry/metabolism MH - tau Proteins/*chemistry/metabolism EDAT- 2006/02/09 09:00 MHDA- 2006/06/06 09:00 CRDT- 2006/02/09 09:00 PHST- 2006/02/07 [aheadofprint] AID - M510127200 [pii] AID - 10.1074/jbc.M510127200 [doi] PST - ppublish SO - J Biol Chem. 2006 Apr 14;281(15):9919-24. Epub 2006 Feb 7. PMID- 23727127 OWN - NLM STAT- MEDLINE DA - 20131111 DCOM- 20140108 IS - 1879-1220 (Electronic) IS - 0960-0760 (Linking) VI - 138 DP - 2013 Nov TI - Multidomain sumoylation of the ecdysone receptor (EcR) from Drosophila melanogaster. PG - 162-73 LID - 10.1016/j.jsbmb.2013.05.007 [doi] LID - S0960-0760(13)00078-2 [pii] AB - The 20-hydroxyecdysone receptor (EcR) is a transcription factor belonging to the nuclear receptor superfamily. Together with the ultraspiracle nuclear receptor (Usp) it coordinates critical biological processes in insects such as development and reproduction. EcR and its ligands are used in commercially available ecdysone-inducible expression systems and are considered to be artificial gene switches with potential therapeutic applications. However, the regulation of EcR action is still unclear, especially in mammals and as far as posttranslational modifications are concerned. Up until now, there has been no study on EcR sumoylation. Using bioinformatic predictors, a Ubc9 fusion-directed sumoylation system and mutagenesis experiments, we present EcR as a new target of SUMO1 and SUMO3 modification. Our research revealed that EcR undergoes isoform-specific multisumoylation. The pattern of modification remains unchanged in the presence of the ligand and the dimerization partner. The SUMO acceptor sites are located in the DNA-binding domain and the ligand-binding domain that both exhibit structural plasticity. We also demonstrated the existence of a sumoylation site in the F region and EcRA-A/B region, both revealing characteristics of intrinsically disordered regions. The consequences of modification and the resulting impact on conformation and function may be especially crucial for the disordered sequences in these two areas. The isoform-specificity of sumoylation may explain the differences in the transcriptional activity of EcR isoforms. CI - Copyright (c) 2013 Elsevier Ltd. All rights reserved. FAU - Seliga, Justyna AU - Seliga J AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland. FAU - Bielska, Katarzyna AU - Bielska K FAU - Wieczorek, Elzbieta AU - Wieczorek E FAU - Orlowski, Marek AU - Orlowski M FAU - Niedenthal, Rainer AU - Niedenthal R FAU - Ozyhar, Andrzej AU - Ozyhar A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130529 PL - England TA - J Steroid Biochem Mol Biol JT - The Journal of steroid biochemistry and molecular biology JID - 9015483 RN - 0 (Drosophila Proteins) RN - 0 (Receptors, Steroid) RN - 0 (ecdysteroid receptor) SB - IM MH - Animals MH - Blotting, Western MH - Cell Line MH - Computational Biology MH - Drosophila Proteins/chemistry/genetics/*metabolism MH - Drosophila melanogaster MH - Humans MH - Models, Biological MH - Receptors, Steroid/chemistry/genetics/*metabolism MH - Sumoylation OTO - NOTNLM OT - 20-hydroxyecdysone OT - 20E OT - DBD OT - DNA-binding domain OT - Drosophila melanogaster OT - EcR OT - Ecdysone receptor OT - HEK293 OT - ID OT - LBD OT - MS OT - NR OT - Nuclear receptor OT - RXR OT - SUMO OT - Sumoylation OT - UFDS OT - Ubc9 fusion-directed sumoylation OT - Usp OT - ecdysone receptor OT - human embryonic kidney 293 cells OT - intrinsically disordered OT - ligand-binding domain OT - mass spectrometry OT - nuclear receptor OT - retinoid X receptor OT - small ubiquitin-like modifier OT - ultraspiracle EDAT- 2013/06/04 06:00 MHDA- 2014/01/09 06:00 CRDT- 2013/06/04 06:00 PHST- 2012/12/20 [received] PHST- 2013/05/16 [revised] PHST- 2013/05/18 [accepted] PHST- 2013/05/29 [aheadofprint] AID - S0960-0760(13)00078-2 [pii] AID - 10.1016/j.jsbmb.2013.05.007 [doi] PST - ppublish SO - J Steroid Biochem Mol Biol. 2013 Nov;138:162-73. doi: 10.1016/j.jsbmb.2013.05.007. Epub 2013 May 29. PMID- 17570761 OWN - NLM STAT- MEDLINE DA - 20070615 DCOM- 20070730 LR - 20141120 IS - 1044-5498 (Print) IS - 1044-5498 (Linking) VI - 26 IP - 6 DP - 2007 Jun TI - Genomics, evolution, and expression of TBPL2, a member of the TBP family. PG - 369-85 AB - TBPL2 is the most recently discovered and less characterized member of the TATA box binding protein (TBP) family that also comprises TBP, TATA box binding protein-like 1 (TBPL1), and Drosophila melanogaster TBP related factor (TRF). In this paper we report our in silico and in vitro data on (i) the genomics of the TBPL2 gene in Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus, Gallus gallus, Xenopus tropicalis, and Takifugu rubripes; (ii) its evolution and phylogenetic relationship with TBP, TBPL1, and TRF; (iii) the structure of the TBPL2 proteins that belong to the recently identified group of the intrinsically unstructured proteins (IUPs); and (iv) TBPL2 expression in different organs and cell types of Homo sapiens and Rattus norvegicus. Similar to TBP, both the TBPL2 gene and protein are bimodular. The 3' region of the gene encoding the DNA binding domain (DBD) was well conserved during evolution. Its high homology to vertebrate TBP suggests that TBPL2 also should bind to the TATA box and interact with the proteins binding to TBP carboxy-terminal domain, such as the TBP associated factors (TAFs). As already demonstrated for TBP, TBPL2 amino-terminal segment is intrinsically unstructured and, even though variable among vertebrates, comprises a highly conserved motif not found in any other known protein. Absence of TBPL2 from the genome of invertebrates and plants demonstrates its specific origin within the subphylum of vertebrates. Our RT-PCR analysis of human and rat RNA shows that, similar to TBP, TBPL2 is ubiquitously synthesized even though at variable levels that are at least two orders of magnitude lower. Higher expression of TBPL2 in the gonads than in other organs suggests that it could perform important functions in gametogenesis. Our genomic and expression data should contribute to clarify why TBP has a general master role within the transcription apparatus (TA), whereas both TBPL1 and TBPL2 perform tissue-specific functions. FAU - Di Pietro, Cinzia AU - Di Pietro C AD - Dipartimento di Scienze Biomediche-Unita di Biologia Genetica e BioInformatica, Universita di Catania, Catania, Italy, EU. FAU - Ragusa, Marco AU - Ragusa M FAU - Duro, Laura AU - Duro L FAU - Guglielmino, Maria Rosa AU - Guglielmino MR FAU - Barbagallo, Davide AU - Barbagallo D FAU - Carnemolla, Alisia AU - Carnemolla A FAU - Lagana, Alessandro AU - Lagana A FAU - Buffa, Pietro AU - Buffa P FAU - Angelica, Rosario AU - Angelica R FAU - Rinaldi, Antonella AU - Rinaldi A FAU - Calafato, Maria Stella AU - Calafato MS FAU - Milicia, Ionella AU - Milicia I FAU - Caserta, Cinzia AU - Caserta C FAU - Giugno, Rosalba AU - Giugno R FAU - Pulvirenti, Alfredo AU - Pulvirenti A FAU - Giunta, Veronica AU - Giunta V FAU - Rapisarda, Antonella AU - Rapisarda A FAU - Di Pietro, Valentina AU - Di Pietro V FAU - Grillo, Agata AU - Grillo A FAU - Messina, Angelo AU - Messina A FAU - Ferro, Alfredo AU - Ferro A FAU - Grzeschik, Karl Heinz AU - Grzeschik KH FAU - Purrello, Michele AU - Purrello M LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - DNA Cell Biol JT - DNA and cell biology JID - 9004522 RN - 0 (DNA Primers) RN - 0 (Nuclear Proteins) RN - 0 (TATA Box Binding Protein-Like Proteins) RN - 0 (TATA-Box Binding Protein) RN - 0 (TBPL1 protein, human) RN - 0 (TBPL2 protein, human) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - DNA Primers/genetics MH - *Evolution, Molecular MH - Gene Expression MH - Genomics MH - Humans MH - In Vitro Techniques MH - Mice MH - Molecular Sequence Data MH - Nuclear Proteins/chemistry/genetics MH - Phylogeny MH - Promoter Regions, Genetic MH - Protein Interaction Mapping MH - Rats MH - Sequence Homology, Amino Acid MH - TATA Box Binding Protein-Like Proteins/chemistry/*genetics MH - TATA-Box Binding Protein/chemistry/*genetics MH - Vertebrates/genetics EDAT- 2007/06/16 09:00 MHDA- 2007/07/31 09:00 CRDT- 2007/06/16 09:00 AID - 10.1089/dna.2006.0527 [doi] PST - ppublish SO - DNA Cell Biol. 2007 Jun;26(6):369-85. PMID- 18303844 OWN - NLM STAT- MEDLINE DA - 20080321 DCOM- 20080611 IS - 0021-8561 (Print) IS - 0021-8561 (Linking) VI - 56 IP - 6 DP - 2008 Mar 26 TI - Self-assembly of bovine beta-casein below the isoelectric pH. PG - 2192-8 LID - 10.1021/jf072630r [doi] AB - Beta-casein is an intrinsically unstructured amphiphilic protein that self-assembles into micelles at neutral pH. This paper reports that beta-casein self-organizes into micelles also under acidic conditions. The protein association behavior and micelle characteristics at pH 2.6, well below the p I, are presented. The pH was found to strongly affect the micelle shape and dimensions. Cryogenic transmission electron microscopy (cryo-TEM) experiments revealed disk-like micelles of 20-25 nm in length and approximately 3.5 nm in height in acidic conditions. An aggregation number of 6 was determined by sedimentation equilibrium under these conditions. Isothermal titration calorimetry experiments verified the association below the p I and allowed determination of the micellization enthalpy, the critical micellar concentration, and the micellization relative cooperativity (MR). Small-angle X-ray scattering results at concentrations below the critical micellization concentration (CMC) suggest that the monomeric protein is likely in a premolten globule state at low pH. Calculations of the protein charge at acidic and neutral pH reveal a similar high net charge but considerable differences in the charge distribution along the protein backbone. Overall the results show that beta-casein is amphiphilic at low pH, but the distribution of charge along the protein chain creates packing constraints that affect the micelle organization, leading at concentrations above the CMC to the formation of disk micelles. FAU - Portnaya, Irina AU - Portnaya I AD - Department of Biotechnology, Technion - Israel Institute of Technology, 32000, Israel. FAU - Ben-Shoshan, Einav AU - Ben-Shoshan E FAU - Cogan, Uri AU - Cogan U FAU - Khalfin, Rafail AU - Khalfin R FAU - Fass, Deborah AU - Fass D FAU - Ramon, Ory AU - Ramon O FAU - Danino, Dganit AU - Danino D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080228 PL - United States TA - J Agric Food Chem JT - Journal of agricultural and food chemistry JID - 0374755 RN - 0 (Caseins) RN - 0 (Micelles) SB - IM MH - Animals MH - Caseins/*chemistry MH - Cattle MH - Hydrogen-Ion Concentration MH - Isoelectric Point MH - *Micelles MH - Scattering, Radiation MH - Thermodynamics MH - X-Rays EDAT- 2008/02/29 09:00 MHDA- 2008/06/12 09:00 CRDT- 2008/02/29 09:00 PHST- 2008/02/28 [aheadofprint] AID - 10.1021/jf072630r [doi] PST - ppublish SO - J Agric Food Chem. 2008 Mar 26;56(6):2192-8. doi: 10.1021/jf072630r. Epub 2008 Feb 28. PMID- 22977176 OWN - NLM STAT- MEDLINE DA - 20121127 DCOM- 20130130 LR - 20141105 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 40 IP - 21 DP - 2012 Nov TI - SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. PG - 10628-41 LID - 10.1093/nar/gks854 [doi] AB - Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs. Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E. FAU - Davey, Norman E AU - Davey NE AD - Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Wurttemberg 69117, Germany. davey@embl.de FAU - Cowan, Joanne L AU - Cowan JL FAU - Shields, Denis C AU - Shields DC FAU - Gibson, Toby J AU - Gibson TJ FAU - Coldwell, Mark J AU - Coldwell MJ FAU - Edwards, Richard J AU - Edwards RJ LA - eng GR - BB/H006834/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BB/I006230/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120912 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Adaptor Proteins, Vesicular Transport) RN - 0 (EPN2 protein, human) RN - 0 (Eukaryotic Initiation Factor-2) RN - 0 (Eukaryotic Initiation Factor-4E) RN - 0 (F-Box Proteins) RN - 0 (Proteome) SB - IM MH - Adaptor Proteins, Vesicular Transport/chemistry MH - *Amino Acid Motifs MH - Amino Acid Sequence MH - Conserved Sequence MH - Eukaryotic Initiation Factor-2/chemistry/metabolism MH - Eukaryotic Initiation Factor-4E/metabolism MH - F-Box Proteins/chemistry MH - HeLa Cells MH - Humans MH - Molecular Sequence Data MH - Probability MH - Proteome/chemistry MH - Sequence Alignment MH - Sequence Analysis, Protein/*methods PMC - PMC3510515 OID - NLM: PMC3510515 EDAT- 2012/09/15 06:00 MHDA- 2013/01/31 06:00 CRDT- 2012/09/15 06:00 PHST- 2012/09/12 [aheadofprint] AID - gks854 [pii] AID - 10.1093/nar/gks854 [doi] PST - ppublish SO - Nucleic Acids Res. 2012 Nov;40(21):10628-41. doi: 10.1093/nar/gks854. Epub 2012 Sep 12. PMID- 21737399 OWN - NLM STAT- MEDLINE DA - 20111031 DCOM- 20120515 LR - 20131121 IS - 1756-2651 (Electronic) IS - 0021-924X (Linking) VI - 150 IP - 5 DP - 2011 Nov TI - Cu2+ triggers reversible aggregation of a disordered His-rich dehydrin MpDhn12 from Musa paradisiaca. PG - 491-9 LID - 10.1093/jb/mvr082 [doi] AB - Copper is an essential nutrient, but it is toxic in excess. Here, we cloned and characterized a His-rich low molecular weight dehydrin from Musa paradisiaca, MpDhn12. Analysis by circular dichroism (CD) spectra and a thermal stability assay showed that MpDhn12 is an intrinsically disordered protein, and immobilized-metal affinity chromatography (IMAC) analysis revealed that MpDhn12 can bind Cu(2+) both in vitro and in vivo. Interestingly, MpDhn12 aggregated under excess Cu(2+) conditions, and the aggregation was reversible and impaired by histidine modification with diethylpyrocarbonate (DEPC), while the disordered structure of another dehydrin ERD14 (as a control) was not changed. Furthermore, MpDhn12 could complement the copper-sensitive phenotype of yeast mutant Deltasod1. These results together suggested that MpDhn12 may take part in buffering copper levels through chelation and formation of aggregates in excess Cu(2+) conditions. To the best of our knowledge, it is the first report that a dehydrin interchanged between disordered and aggregated state triggered by copper. FAU - Mu, Peiqiang AU - Mu P AD - State Key Laboratory for Biocontrol and Key Laboratory of Gene Engineering of Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China. FAU - Feng, Dongru AU - Feng D FAU - Su, Jianbin AU - Su J FAU - Zhang, Yang AU - Zhang Y FAU - Dai, Jinran AU - Dai J FAU - Jin, Honglei AU - Jin H FAU - Liu, Bing AU - Liu B FAU - He, Yanming AU - He Y FAU - Qi, Kangbiao AU - Qi K FAU - Wang, Hongbin AU - Wang H FAU - Wang, Jinfa AU - Wang J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110706 PL - England TA - J Biochem JT - Journal of biochemistry JID - 0376600 RN - 0 (Plant Proteins) RN - 134711-03-8 (dehydrin proteins, plant) RN - 789U1901C5 (Copper) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Chromatography, Affinity MH - Circular Dichroism MH - Copper/*pharmacology MH - Genetic Complementation Test MH - Molecular Sequence Data MH - Musa/*chemistry MH - Plant Proteins/*chemistry/drug effects/*metabolism MH - Protein Binding MH - Sequence Alignment EDAT- 2011/07/09 06:00 MHDA- 2012/05/16 06:00 CRDT- 2011/07/09 06:00 PHST- 2011/07/06 [aheadofprint] PHST- 2011/09/06 [aheadofprint] AID - mvr082 [pii] AID - 10.1093/jb/mvr082 [doi] PST - ppublish SO - J Biochem. 2011 Nov;150(5):491-9. doi: 10.1093/jb/mvr082. Epub 2011 Jul 6. PMID- 10775411 OWN - NLM STAT- MEDLINE DA - 20000502 DCOM- 20000502 LR - 20131121 IS - 0003-9861 (Print) IS - 0003-9861 (Linking) VI - 376 IP - 2 DP - 2000 Apr 15 TI - Sweetness determinant sites of brazzein, a small, heat-stable, sweet-tasting protein. PG - 259-65 AB - Brazzein, originally isolated from the fruit of the African plant Pentadiplandra brazzeana Baillon, is the smallest, most heat-stable and pH-stable member of the set of proteins known to have intrinsic sweetness. These properties make brazzein an ideal system for investigating the chemical and structural requirements of a sweet-tasting protein. We have used the three-dimensional structure of the protein (J. E. Caldwell et al. (1998) Nat. Struct. Biol. 5, 427-431) as a guide in designing 15 synthetic genes in expression constructs aimed at delineating the sweetness determinants of brazzein. Protein was produced heterologously in Escherichia coli, isolated, and purified as described in the companion paper (Assadi-Porter, F. M., Aceti, D., Cheng, H., and Markley, J. L., this issue). Analysis by one-dimensional (1)H NMR spectroscopy indicated that all but one of these variants had folded properly under the conditions used. A taste panel compared the gustatory properties of solutions of these proteins to those of sucrose and brazzein isolated from fruit. Of the 14 mutations in the des-pGlu1-brazzein background, four exhibited almost no sweetness, six had significantly reduced sweetness, two had taste properties equivalent to des-pGlu1-brazzein (two times as sweet as the major form of brazzein isolated from fruit which contains pGlu1), and two were about twice as sweet as des-pGlu1-brazzein. Overall, the results suggest that two regions of the protein are critical for the sweetness of brazzein: a region that includes the N- and C-termini of the protein, which are located close to one another, and a region that includes the flexible loop around Arg43. CI - Copyright 2000 Academic Press. FAU - Assadi-Porter, F M AU - Assadi-Porter FM AD - Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA. FAU - Aceti, D J AU - Aceti DJ FAU - Markley, J L AU - Markley JL LA - eng GR - GM35976/GM/NIGMS NIH HHS/United States GR - RR02301/RR/NCRR NIH HHS/United States GR - RR02781/RR/NCRR NIH HHS/United States GR - etc. PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (Plant Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Solutions) RN - 0 (Sweetening Agents) RN - 0 (brazzein protein, Pentadiplandra brazzeana) RN - 57-50-1 (Sucrose) RN - 94ZLA3W45F (Arginine) SB - IM MH - Amino Acid Substitution/genetics MH - Arginine/chemistry/metabolism MH - Chromatography, High Pressure Liquid MH - Fruit/chemistry MH - *Hot Temperature MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Mutation/genetics MH - Plant Proteins/metabolism MH - Protein Conformation MH - Protein Folding MH - Recombinant Fusion Proteins/chemistry/genetics/isolation & purification/metabolism MH - Rosales/*chemistry MH - Solutions MH - Structure-Activity Relationship MH - Sucrose/chemistry/metabolism MH - Sweetening Agents/*chemistry/isolation & purification/*metabolism MH - *Taste EDAT- 2000/04/25 MHDA- 2000/04/25 00:01 CRDT- 2000/04/25 00:00 AID - 10.1006/abbi.2000.1726 [doi] AID - S0003-9861(00)91726-0 [pii] PST - ppublish SO - Arch Biochem Biophys. 2000 Apr 15;376(2):259-65. PMID- 23929272 OWN - NLM STAT- MEDLINE DA - 20130830 DCOM- 20140331 IS - 1573-5001 (Electronic) IS - 0925-2738 (Linking) VI - 57 IP - 1 DP - 2013 Sep TI - Direct correlation of consecutive C'-N groups in proteins: a method for the assignment of intrinsically disordered proteins. PG - 57-63 LID - 10.1007/s10858-013-9765-3 [doi] AB - Two novel 3D (13)C-detected experiments, hNcocaNCO and hnCOcaNCO, are proposed to facilitate the resonance assignment of intrinsically disordered proteins. The experiments correlate the (15)N and (13)C' chemical shifts of two consecutive amide moieties without involving other nuclei, thus taking advantage of the good dispersion shown by the (15)N-(13)C' correlations, even for proteins that lack a well defined tertiary structure. The new pulse sequences were successfully tested using Nupr1, an intrinsically disordered protein of 93 residues. FAU - Pantoja-Uceda, David AU - Pantoja-Uceda D AD - Instituto de Quimica Fisica Rocasolano, CSIC, Serrano 119, 28006, Madrid, Spain. FAU - Santoro, Jorge AU - Santoro J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130809 PL - Netherlands TA - J Biomol NMR JT - Journal of biomolecular NMR JID - 9110829 RN - 0 (Basic Helix-Loop-Helix Transcription Factors) RN - 0 (Carbon Isotopes) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Neoplasm Proteins) RN - 0 (Nitrogen Isotopes) RN - 0 (P8 protein, human) SB - IM MH - Basic Helix-Loop-Helix Transcription Factors/*chemistry MH - Carbon Isotopes/chemistry MH - Intrinsically Disordered Proteins/*chemistry MH - Neoplasm Proteins/*chemistry MH - Nitrogen Isotopes/chemistry MH - Nuclear Magnetic Resonance, Biomolecular/*methods EDAT- 2013/08/10 06:00 MHDA- 2014/04/01 06:00 CRDT- 2013/08/10 06:00 PHST- 2013/06/04 [received] PHST- 2013/07/24 [accepted] PHST- 2013/08/09 [aheadofprint] AID - 10.1007/s10858-013-9765-3 [doi] PST - ppublish SO - J Biomol NMR. 2013 Sep;57(1):57-63. doi: 10.1007/s10858-013-9765-3. Epub 2013 Aug 9. PMID- 24829381 OWN - NLM STAT- MEDLINE DA - 20140711 DCOM- 20150330 LR - 20150415 IS - 1939-4586 (Electronic) IS - 1059-1524 (Linking) VI - 25 IP - 14 DP - 2014 Jul 15 TI - Dynactin integrity depends upon direct binding of dynamitin to Arp1. PG - 2171-80 LID - 10.1091/mbc.E14-03-0842 [doi] AB - Dynactin is a multiprotein complex that works with cytoplasmic dynein and other motors to support a wide range of cell functions. It serves as an adaptor that binds both dynein and cargoes and enhances single-motor processivity. The dynactin subunit dynamitin (also known as p50) is believed to be integral to dynactin structure because free dynamitin displaces the dynein-binding p150(Glued) subunit from the cargo-binding Arp1 filament. We show here that the intrinsically disordered dynamitin N-terminus binds to Arp1 directly. When expressed in cells, dynamitin amino acids (AA) 1-87 causes complete release of endogenous dynamitin, p150, and p24 from dynactin, leaving behind Arp1 filaments carrying the remaining dynactin subunits (CapZ, p62, Arp11, p27, and p25). Tandem-affinity purification-tagged dynamitin AA 1-87 binds the Arp filament specifically, and binding studies with purified native Arp1 reveal that this fragment binds Arp1 directly. Neither CapZ nor the p27/p25 dimer contributes to interactions between dynamitin and the Arp filament. This work demonstrates for the first time that Arp1 can directly bind any protein besides another Arp and provides important new insight into the underpinnings of dynactin structure. CI - (c) 2014 Cheong et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution-Noncommercial-Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0). FAU - Cheong, Frances Ka Yan AU - Cheong FK AD - Department of Biology, Johns Hopkins University, Baltimore, MD 21218. FAU - Feng, Lijuan AU - Feng L AD - Department of Biology, Johns Hopkins University, Baltimore, MD 21218. FAU - Sarkeshik, Ali AU - Sarkeshik A AD - Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037. FAU - Yates, John R 3rd AU - Yates JR 3rd AD - Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA 92037. FAU - Schroer, Trina A AU - Schroer TA AD - Department of Biology, Johns Hopkins University, Baltimore, MD 21218 schroer@jhu.edu. LA - eng GR - P41 GM103533/GM/NIGMS NIH HHS/United States GR - P41 RR011823/RR/NCRR NIH HHS/United States GR - R01 GM44589/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140514 PL - United States TA - Mol Biol Cell JT - Molecular biology of the cell JID - 9201390 RN - 0 (Actins) RN - 0 (Microtubule-Associated Proteins) RN - 144198-36-7 (dynactin) SB - IM MH - Actins/*chemistry/metabolism MH - Amino Acid Sequence MH - Animals MH - COS Cells MH - Cattle MH - Cercopithecus aethiops MH - Humans MH - Microtubule-Associated Proteins/*chemistry/metabolism MH - Molecular Sequence Data MH - Protein Binding MH - Protein Interaction Domains and Motifs PMC - PMC4091830 OID - NLM: PMC4091830 EDAT- 2014/05/16 06:00 MHDA- 2015/03/31 06:00 CRDT- 2014/05/16 06:00 PHST- 2014/05/14 [aheadofprint] AID - mbc.E14-03-0842 [pii] AID - 10.1091/mbc.E14-03-0842 [doi] PST - ppublish SO - Mol Biol Cell. 2014 Jul 15;25(14):2171-80. doi: 10.1091/mbc.E14-03-0842. Epub 2014 May 14. PMID- 17262987 OWN - NLM STAT- MEDLINE DA - 20070131 DCOM- 20070315 LR - 20091111 IS - 0006-9248 (Print) IS - 0006-9248 (Linking) VI - 107 IP - 9-10 DP - 2006 TI - Intrinsically disordered tau protein in Alzheimer's tangles: a coincidence or a rule? PG - 354-8 AB - Tau protein, the major constituent of neurofibrillary tangles in Alzheimer's disease (AD) and related tauopathies, is classified as intrinsically disordered protein (IDP). IDPs in contrast to globular proteins contain high proportion of polar and charged amino acids in their sequence, which results in the absence of a well-defined three-dimensional structure of the free protein. Structural flexibility of IDPs is required to perform their important role in many cellular processes. In the course of tauopathies, highly soluble disordered tau protein acquires rigid fold and forms highly insoluble filaments. Beneficial intrinsic disorder transforms into a fatal order: is it a coincidence, or is there an underlying reason for preferential IDPs assembly? In this review we present the structural characteristics of tau protein filamentous lesions in AD and discuss the tendency of IDPs to assembly and to form amyloid deposits (Ref: 65). FAU - Skrabana, R AU - Skrabana R AD - Institute of Neuroinmmunology AD Centre, Slovak Academy of Sciences, Bratislava, Slovakia. FAU - Skrabanova, M AU - Skrabanova M FAU - Csokova, N AU - Csokova N FAU - Sevcik, J AU - Sevcik J FAU - Novak, M AU - Novak M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Slovakia TA - Bratisl Lek Listy JT - Bratislavske lekarske listy JID - 0065324 RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/*metabolism/pathology MH - Humans MH - Neurofibrillary Tangles/*metabolism MH - Tauopathies/metabolism MH - tau Proteins/chemistry/*metabolism RF - 65 EDAT- 2007/02/01 09:00 MHDA- 2007/03/16 09:00 CRDT- 2007/02/01 09:00 PST - ppublish SO - Bratisl Lek Listy. 2006;107(9-10):354-8. PMID- 23836939 OWN - NLM STAT- MEDLINE DA - 20130926 DCOM- 20131113 LR - 20141113 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 41 IP - 17 DP - 2013 Sep TI - Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion. PG - 8368-76 LID - 10.1093/nar/gkt584 [doi] AB - The p53 core domain binds to response elements (REs) that contain two continuous half-sites as a cooperative tetramer, but how p53 recognizes discontinuous REs is not well understood. Here we describe the crystal structure of the p53 core domain bound to a naturally occurring RE located at the promoter of the Bcl-2-associated X protein (BAX) gene, which contains a one base-pair insertion between the two half-sites. Surprisingly, p53 forms a tetramer on the BAX-RE that is nearly identical to what has been reported on other REs with a 0-bp spacer. Each p53 dimer of the tetramer binds in register to a half-site and maintains the same protein-DNA interactions as previously observed, and the two dimers retain all the protein-protein contacts without undergoing rotation or translation. To accommodate the additional base pair, the DNA is deformed and partially disordered around the spacer region, resulting in an apparent unwinding and compression, such that the interactions between the dimers are maintained. Furthermore, DNA deformation within the p53-bound BAX-RE is confirmed in solution by site-directed spin labeling measurements. Our results provide a structural insight into the mechanism by which p53 binds to discontinuous sites with one base-pair spacer. FAU - Chen, Yongheng AU - Chen Y AD - Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA, Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China, Department of Chemistry, Norris Comprehensive Cancer Center, Department of Physics and Astronomy and Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA. FAU - Zhang, Xiaojun AU - Zhang X FAU - Dantas Machado, Ana Carolina AU - Dantas Machado AC FAU - Ding, Yuan AU - Ding Y FAU - Chen, Zhuchu AU - Chen Z FAU - Qin, Peter Z AU - Qin PZ FAU - Rohs, Remo AU - Rohs R FAU - Chen, Lin AU - Chen L LA - eng SI - PDB/4HJE GR - GM064642/GM/NIGMS NIH HHS/United States GR - GM069557/GM/NIGMS NIH HHS/United States GR - GM077320/GM/NIGMS NIH HHS/United States GR - R01 GM064642/GM/NIGMS NIH HHS/United States GR - RR028992/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130708 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Tumor Suppressor Protein p53) RN - 0 (bcl-2-Associated X Protein) RN - 9007-49-2 (DNA) SB - IM MH - Base Pairing MH - Binding Sites MH - DNA/*chemistry MH - Models, Molecular MH - Nucleic Acid Conformation MH - *Response Elements MH - Tumor Suppressor Protein p53/*chemistry/metabolism MH - bcl-2-Associated X Protein/*genetics PMC - PMC3783167 OID - NLM: PMC3783167 EDAT- 2013/07/10 06:00 MHDA- 2013/11/14 06:00 CRDT- 2013/07/10 06:00 PHST- 2013/07/08 [aheadofprint] PHST- 2013/08/01 [aheadofprint] AID - gkt584 [pii] AID - 10.1093/nar/gkt584 [doi] PST - ppublish SO - Nucleic Acids Res. 2013 Sep;41(17):8368-76. doi: 10.1093/nar/gkt584. Epub 2013 Jul 8. PMID- 11257499 OWN - NLM STAT- MEDLINE DA - 20010321 DCOM- 20010412 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 492 IP - 3 DP - 2001 Mar 16 TI - The C-terminus of dUTPase: observation on flexibility using NMR. PG - 228-32 AB - The dynamics of the C-terminus of the dUTPases from Escherichia coli and equine infectious anaemia virus (EIAV) were studied by 1H-(15)N nuclear magnetic resonance spectroscopy. The two enzymes differ with regard to flexibility in the backbone of the 15 most C-terminal amino acid residues, some of which are conserved and essential for enzymic activity. In the bacterial enzyme, the residues closest to the C-terminus are highly flexible and display a correlation time in the nanosecond time range. No similar high flexibility could be detected for the C-terminal part of EIAV dUTPase, indicating a different time range of flexibility. FAU - Nord, J AU - Nord J AD - Department of Biochemistry, Center for Chemistry and Chemical Engineering, Lund University, Sweden. johan.nord@astrazeneca FAU - Nyman, P AU - Nyman P FAU - Larsson, G AU - Larsson G FAU - Drakenberg, T AU - Drakenberg T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Nucleotides) RN - EC 3.6.1.- (Pyrophosphatases) RN - EC 3.6.1.23 (dUTP pyrophosphatase) SB - IM MH - Escherichia coli/*enzymology MH - Infectious Anemia Virus, Equine/*enzymology MH - Magnetic Resonance Spectroscopy MH - Nucleotides/chemistry MH - Pliability MH - Protein Conformation MH - Pyrophosphatases/*chemistry/metabolism EDAT- 2001/03/21 10:00 MHDA- 2001/04/17 10:01 CRDT- 2001/03/21 10:00 AID - S0014579301022578 [pii] PST - ppublish SO - FEBS Lett. 2001 Mar 16;492(3):228-32. PMID- 17407262 OWN - NLM STAT- MEDLINE DA - 20070424 DCOM- 20070620 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 46 IP - 17 DP - 2007 May 1 TI - Fatty acids covalently bound to alpha-hemolysin of Escherichia coli are involved in the molten globule conformation: implication of disordered regions in binding promiscuity. PG - 5177-84 AB - Alpha-hemolysin (HlyA) is a pore-forming toxin secreted by pathogenic strains of Escherichia coli. The toxin is synthesized as a protoxin, ProHlyA, which is matured in the cytosol to the active form by acylation at two internal lysines, K563 and K689 (HlyA). It is widely known that the presence of fatty acids is crucial for the hemolytic and cytotoxic effects of the toxin. However, no detailed physicochemical characterization of the structural changes produced by fatty acids in the soluble protein prior to membrane binding has been carried out to date. The effects of chemical denaturants, the ANS binding parameters (Kd and n) and the sensitivity to proteases were compared between the acylated and unacylated protein forms HlyA and ProHlyA. Our results are consistent with a molten globular form of the acylated protein. Moreover, because molten globule proteins are intrinsically disordered proteins, using disorder prediction analyses, we show that HlyA contains 9 regions composed of 10-30 natively disordered amino acids. We propose that this conformation induced by covalently bound fatty acids might provide HlyA with the ability to bind to a variety of molecules during its action mechanism. FAU - Herlax, Vanesa AU - Herlax V AD - Instituto de Investigaciones Bioquimicas La Plata, Facultad de Ciencias Medicas, 60 y 120 (1900) La Plata, Argentina. FAU - Bakas, Laura AU - Bakas L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070404 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Fatty Acids) RN - 0 (Hemolysin Proteins) SB - IM MH - Escherichia coli/*metabolism MH - Fatty Acids/*metabolism MH - Hemolysin Proteins/chemistry/*metabolism MH - Hydrolysis MH - Protein Binding MH - Protein Conformation EDAT- 2007/04/05 09:00 MHDA- 2007/06/21 09:00 CRDT- 2007/04/05 09:00 PHST- 2007/04/04 [aheadofprint] AID - 10.1021/bi0618013 [doi] PST - ppublish SO - Biochemistry. 2007 May 1;46(17):5177-84. Epub 2007 Apr 4. PMID- 23780840 OWN - NLM STAT- MEDLINE DA - 20130916 DCOM- 20141231 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 22 IP - 9 DP - 2013 Sep TI - Development of a fluorescent monoclonal antibody-based assay to measure the allosteric effects of synthetic peptides on self-oligomerization of AGR2 protein. PG - 1266-78 LID - 10.1002/pro.2299 [doi] AB - Many regulatory proteins are homo-oligomeric and designing assays that measure self-assembly will provide novel approaches to study protein allostery and screen for novel small molecule modulators of protein interactions. We present an assay to begin to define the biochemical determinants that regulate dimerization of the cancer-associated oncoprotein AGR2. A two site-sandwich microtiter assay ((2S) MTA) was designed using a DyLight800-labeled monoclonal antibody that binds to an epitope in AGR2 to screen for synthetic self-peptides that might regulate dimer stability. Peptides derived from the intrinsically disordered N-terminal region of AGR2 increase in trans oligomer stability as defined using the (2S) MTA assay. A DSS-crosslinking assay that traps the AGR2 dimer through K95-K95 adducts confirmed that Delta45-AGR2 was a more stable dimer using denaturing gel electrophoresis. A titration of wt-AGR2, Delta45-AGR2 (more stable dimer), and monomeric AGR2(E60A) revealed that Delta45-AGR2 was more active in binding to Reptin than either wt-AGR2 or the AGR2(E60A) mutant. Our data have defined a functional role for the AGR2 dimer in the binding to its most well characterized interacting protein, Reptin. The ability to regulate AGR2 oligomerization in trans opens the possibility for developing small molecules that regulate its' biochemical activity as potential cancer therapeutics. The data also highlight the utility of this oligomerization assay to screen chemical libraries for ligands that could regulate AGR2 dimer stability and its' oncogenic potential. CI - (c) 2013 The Protein Society. FAU - Gray, Terry A AU - Gray TA AD - Institute of Genetics and Molecular Medicine, Cell Signaling Unit, University of Edinburgh, United Kingdom. FAU - Murray, Euan AU - Murray E FAU - Nowicki, Matthew W AU - Nowicki MW FAU - Remnant, Lucy AU - Remnant L FAU - Scherl, Alexander AU - Scherl A FAU - Muller, Petr AU - Muller P FAU - Vojtesek, Borek AU - Vojtesek B FAU - Hupp, Ted R AU - Hupp TR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130725 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Antibodies, Monoclonal) RN - 0 (Carrier Proteins) RN - 0 (Fluorescent Dyes) RN - 0 (Ligands) RN - 0 (Proteins) RN - 0 (RUVBL2 protein, human) RN - EC 3.6.4.- (DNA Helicases) RN - EC 5.3.4.1 (AGR2 protein, human) SB - IM MH - Allosteric Regulation/drug effects MH - Amino Acid Sequence MH - Antibodies, Monoclonal/*analysis/chemistry MH - Carrier Proteins/chemistry/metabolism MH - DNA Helicases/chemistry/metabolism MH - Enzyme-Linked Immunosorbent Assay MH - Fluorescence MH - Fluorescent Antibody Technique/*methods MH - Fluorescent Dyes/analysis/chemistry MH - Humans MH - Ligands MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Multimerization/*drug effects MH - Proteins/*chemistry/metabolism PMC - PMC3776338 OID - NLM: PMC3776338 OTO - NOTNLM OT - allostery OT - monoclonal antibody OT - oligomerization OT - protein interactions EDAT- 2013/06/20 06:00 MHDA- 2015/01/01 06:00 CRDT- 2013/06/20 06:00 PHST- 2013/04/02 [received] PHST- 2013/06/10 [revised] PHST- 2013/06/10 [accepted] PHST- 2013/07/25 [aheadofprint] AID - 10.1002/pro.2299 [doi] PST - ppublish SO - Protein Sci. 2013 Sep;22(9):1266-78. doi: 10.1002/pro.2299. Epub 2013 Jul 25. PMID- 22960996 OWN - NLM STAT- MEDLINE DA - 20120924 DCOM- 20130212 LR - 20150325 IS - 1573-5001 (Electronic) IS - 0925-2738 (Linking) VI - 54 IP - 2 DP - 2012 Oct TI - Deuterium isotope shifts for backbone (1)H, (1)(5)N and (1)(3)C nuclei in intrinsically disordered protein alpha-synuclein. PG - 181-91 AB - Intrinsically disordered proteins (IDPs) are abundant in nature and characterization of their potential structural propensities remains a widely pursued but challenging task. Analysis of NMR secondary chemical shifts plays an important role in such studies, but the output of such analyses depends on the accuracy of reference random coil chemical shifts. Although uniform perdeuteration of IDPs can dramatically increase spectral resolution, a feature particularly important for the poorly dispersed IDP spectra, the impact of deuterium isotope shifts on random coil values has not yet been fully characterized. Very precise (2)H isotope shift measurements for (13)C(alpha), (13)C(beta), (13)C', (15)N, and (1)H(N) have been obtained by using a mixed sample of protonated and uniformly perdeuterated alpha-synuclein, a protein with chemical shifts exceptionally close to random coil values. Decomposition of these isotope shifts into one-bond, two-bond and three-bond effects as well as intra- and sequential residue contributions shows that such an analysis, which ignores conformational dependence, is meaningful but does not fully describe the total isotope shift to within the precision of the measurements. Random coil (2)H isotope shifts provide an important starting point for analysis of such shifts in structural terms in folded proteins, where they are known to depend strongly on local geometry. FAU - Maltsev, Alexander S AU - Maltsev AS AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, MD 20892-0520, USA. FAU - Ying, Jinfa AU - Ying J FAU - Bax, Ad AU - Bax A LA - eng GR - ZIA DK029046-05/Intramural NIH HHS/United States GR - ZIA DK029047-05/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20120908 PL - Netherlands TA - J Biomol NMR JT - Journal of biomolecular NMR JID - 9110829 RN - 0 (Amino Acids) RN - 0 (Carbon Isotopes) RN - 0 (Nitrogen Isotopes) RN - 0 (alpha-Synuclein) RN - AR09D82C7G (Deuterium) SB - IM MH - Amino Acids/chemistry MH - Binding Sites MH - Carbon Isotopes MH - Deuterium MH - Nitrogen Isotopes MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Folding MH - Protein Structure, Secondary MH - alpha-Synuclein/*chemistry PMC - PMC3457063 MID - NIHMS406274 OID - NLM: NIHMS406274 OID - NLM: PMC3457063 EDAT- 2012/09/11 06:00 MHDA- 2013/02/13 06:00 CRDT- 2012/09/11 06:00 PHST- 2012/07/20 [received] PHST- 2012/08/13 [accepted] PHST- 2012/09/08 [aheadofprint] AID - 10.1007/s10858-012-9666-x [doi] PST - ppublish SO - J Biomol NMR. 2012 Oct;54(2):181-91. Epub 2012 Sep 8. PMID- 11584004 OWN - NLM STAT- MEDLINE DA - 20011203 DCOM- 20020110 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 49 DP - 2001 Dec 7 TI - DNA-induced alpha-helical structure in the NH2-terminal domain of histone H1. PG - 46429-35 AB - It is important to establish the structural properties of linker histones to understand the role they play in chromatin higher order structure and gene regulation. Here, we use CD, NMR, and IR spectroscopy to study the conformation of the amino-terminal domain of histone H1 degrees, free in solution and bound to the DNA. The NH(2)-terminal domain has little structure in aqueous solution, but it acquires a substantial amount of alpha-helical structure in the presence of trifluoroethanol (TFE). As in other H1 subtypes, the basic residues of the NH(2)-terminal domain of histone H1 degrees are clustered in its COOH-terminal half. According to the NMR results, the helical region comprises the basic cluster (Lys(11)-Lys(20)) and extends until Asp(23). The fractional helicity of this region in 90% TFE is about 50%. His(24) together with Pro(25) constitute the joint between the NH(2)-terminal helix and helix I of the globular domain. Infrared spectroscopy shows that interaction with the DNA induces an amount of alpha-helical structure equivalent to that observed in TFE. As coulombic interactions are involved in complex formation, it is highly likely in the complexes with DNA that the minimal region with alpha-helical structure is that containing the basic cluster. In chromatin, the high positive charge density of the inducible NH(2)-terminal helical element may contribute to the binding stability of the globular domain. FAU - Vila, R AU - Vila R AD - Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias, Universidad Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. FAU - Ponte, I AU - Ponte I FAU - Collado, M AU - Collado M FAU - Arrondo, J L AU - Arrondo JL FAU - Jimenez, M A AU - Jimenez MA FAU - Rico, M AU - Rico M FAU - Suau, P AU - Suau P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20011002 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Histones) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - DNA/*chemistry MH - Histones/*chemistry MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Spectrophotometry, Infrared EDAT- 2001/10/05 10:00 MHDA- 2002/01/11 10:01 CRDT- 2001/10/05 10:00 PHST- 2001/10/02 [aheadofprint] AID - 10.1074/jbc.M106952200 [doi] AID - M106952200 [pii] PST - ppublish SO - J Biol Chem. 2001 Dec 7;276(49):46429-35. Epub 2001 Oct 2. PMID- 14963040 OWN - NLM STAT- MEDLINE DA - 20040419 DCOM- 20040610 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 17 DP - 2004 Apr 23 TI - The von Hippel-Lindau tumor suppressor protein is a molten globule under native conditions: implications for its physiological activities. PG - 17190-6 AB - The von-Hippel Lindau tumor suppressor protein (pVHL) is conserved throughout evolution, as its homologues are found in organisms ranging from mammals to the Drosophila melanogaster and Anopheles gambiae insects and the Caenorhabditis elegans nematode. Although the physiological role of pVHL is not fully understood, it has been shown to interact with a large number of unrelated proteins and was suggested to play a role in protein degradation as an E3 ubiquitin ligase component in the ubiquitin pathway. To gain insight into the molecular basis of pVHL activity, we analyzed its folding and stability in solution under physiologically relevant conditions. Dynamic light-scattering and gel filtration chromatography of the purified pVHL clearly indicated that the Stokes radius of the protein is larger than what would be expected from its crystal structure. However, under these conditions, the protein shows a clear secondary structure as determined by far-UV circular dichroism. Yet, the near-UV CD experiments show an absence of a tertiary structure. Upon the addition of urea, even at very low concentrations, the protein unfolds in a non-reversible manner, leading to the formation of amorphous aggregates. Furthermore, a large increase in fluorescence (>50-fold) is observed upon the addition of pVHL into a solution containing 8-anilino-1-naphthalene sulfonic acid. We therefore conclude that, under native conditions, the non-bound pVHL has a molten globule configuration with marginal stability. Although molten globular structures can be induced in many proteins under extreme conditions, this is one of the few reported cases of such a structure under the physiological conditions of pH, ionic strength, and temperature. The significance of the pVHL structural properties is being discussed in the context of its physiological activities. FAU - Sutovsky, Hadar AU - Sutovsky H AD - Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel. FAU - Gazit, Ehud AU - Gazit E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040211 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Anilino Naphthalenesulfonates) RN - 0 (Fluorescent Dyes) RN - 0 (Ions) RN - 0 (Tumor Suppressor Proteins) RN - 0 (Ubiquitin) RN - 82-76-8 (1-anilino-8-naphthalenesulfonate) RN - 8W8T17847W (Urea) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) RN - EC 6.3.2.19 (VHL protein, human) RN - EC 6.3.2.19 (Von Hippel-Lindau Tumor Suppressor Protein) SB - IM MH - Anilino Naphthalenesulfonates/pharmacology MH - Calibration MH - Chromatography MH - Chromatography, Gel MH - Circular Dichroism MH - Escherichia coli/metabolism MH - Fluorescent Dyes/pharmacology MH - Humans MH - Hydrogen-Ion Concentration MH - Ions MH - Light MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Scattering, Radiation MH - Temperature MH - Tumor Suppressor Proteins/*chemistry/*physiology MH - Ubiquitin/chemistry MH - Ubiquitin-Protein Ligases/*chemistry/*physiology MH - Ultracentrifugation MH - Ultraviolet Rays MH - Urea/pharmacology MH - Von Hippel-Lindau Tumor Suppressor Protein EDAT- 2004/02/14 05:00 MHDA- 2004/06/21 10:00 CRDT- 2004/02/14 05:00 PHST- 2004/02/11 [aheadofprint] AID - 10.1074/jbc.M311225200 [doi] AID - M311225200 [pii] PST - ppublish SO - J Biol Chem. 2004 Apr 23;279(17):17190-6. Epub 2004 Feb 11. PMID- 11440715 OWN - NLM STAT- MEDLINE DA - 20010706 DCOM- 20010726 LR - 20111117 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 105 IP - 6 DP - 2001 Jun 15 TI - Crystal structure of glycogen synthase kinase 3 beta: structural basis for phosphate-primed substrate specificity and autoinhibition. PG - 721-32 AB - Glycogen synthase kinase 3 beta (GSK3 beta) plays a key role in insulin and Wnt signaling, phosphorylating downstream targets by default, and becoming inhibited following the extracellular signaling event. The crystal structure of human GSK3 beta shows a catalytically active conformation in the absence of activation-segment phosphorylation, with the sulphonate of a buffer molecule bridging the activation-segment and N-terminal domain in the same way as the phosphate group of the activation-segment phospho-Ser/Thr in other kinases. The location of this oxyanion binding site in the substrate binding cleft indicates direct coupling of P+4 phosphate-primed substrate binding and catalytic activation, explains the ability of GSK3 beta to processively hyperphosphorylate substrates with Ser/Thr pentad-repeats, and suggests a mechanism for autoinhibition in which the phosphorylated N terminus binds as a competitive pseudosubstrate with phospho-Ser 9 occupying the P+4 site. FAU - Dajani, R AU - Dajani R AD - Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, United Kingdom. FAU - Fraser, E AU - Fraser E FAU - Roe, S M AU - Roe SM FAU - Young, N AU - Young N FAU - Good, V AU - Good V FAU - Dale, T C AU - Dale TC FAU - Pearl, L H AU - Pearl LH LA - eng SI - PDB/1H8F PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (Insulin) RN - 17885-08-4 (Phosphoserine) RN - 21820-51-9 (Phosphotyrosine) RN - EC 2.7.11.- (Glycogen Synthase Kinases) RN - EC 2.7.11.17 (Calcium-Calmodulin-Dependent Protein Kinases) RN - EC 2.7.11.26 (Glycogen Synthase Kinase 3) SB - IM MH - Animals MH - Binding Sites MH - Calcium-Calmodulin-Dependent Protein Kinases/antagonists & inhibitors/*chemistry/genetics/metabolism MH - Catalysis MH - Crystallography, X-Ray MH - Dimerization MH - Enzyme Activation MH - Glycogen Synthase Kinase 3 MH - Glycogen Synthase Kinases MH - Humans MH - Insulin/*metabolism MH - Models, Molecular MH - Phosphorylation MH - Phosphoserine/metabolism MH - Phosphotyrosine/metabolism MH - Protein Binding MH - *Protein Conformation MH - Protein Structure, Secondary MH - Signal Transduction MH - Substrate Specificity EDAT- 2001/07/07 10:00 MHDA- 2001/07/28 10:01 CRDT- 2001/07/07 10:00 AID - S0092-8674(01)00374-9 [pii] PST - ppublish SO - Cell. 2001 Jun 15;105(6):721-32. PMID- 15628874 OWN - NLM STAT- MEDLINE DA - 20050104 DCOM- 20050304 LR - 20091119 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 44 IP - 1 DP - 2005 Jan 11 TI - Is the prion domain of soluble Ure2p unstructured? PG - 321-8 AB - The [URE3] prion is a self-propagating amyloid form of the Ure2 protein of Saccharomyces cerevisiae. Deletions in the C-terminal nitrogen regulation domain of Ure2p increase the frequency with which the N-terminal prion domain polymerizes into the prion form, suggesting that the C-terminus stabilizes the prion domain or that the structured C-terminal region sterically impairs amyloid formation. We find by in vivo two-hybrid analysis no evidence of interaction of prion domain and C-terminal domain. Furthermore, surface plasmon resonance spectrometry shows no evidence of interaction of prion domain and C-terminal domain, and cleavage at a specific site between the domains frees the two fragments. Our NMR analysis indicates that most residues of the prion domain are in fact disordered in the soluble form of Ure2p. Deleting the tether holding the C-terminal structured region to the amyloid core does not impair prion formation, arguing against steric impairment of amyloid formation. These results suggest that the N-terminal prion domain is unstructured in the soluble protein and does not have a specific interaction with the C-terminus. FAU - Pierce, Michael M AU - Pierce MM AD - Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892-0830, USA. FAU - Baxa, Ulrich AU - Baxa U FAU - Steven, Alasdair C AU - Steven AC FAU - Bax, Ad AU - Bax A FAU - Wickner, Reed B AU - Wickner RB LA - eng PT - Journal Article PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Prions) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 1.11.1.9 (Glutathione Peroxidase) RN - EC 1.11.1.9 (URE2 protein, S cerevisiae) SB - IM MH - Amino Acid Sequence MH - Escherichia coli MH - Glutathione Peroxidase MH - Magnetic Resonance Spectroscopy MH - Prions/*chemistry MH - Recombinant Proteins/chemistry MH - Restriction Mapping MH - Saccharomyces cerevisiae Proteins/*chemistry MH - Sequence Deletion MH - Solubility EDAT- 2005/01/05 09:00 MHDA- 2005/03/05 09:00 CRDT- 2005/01/05 09:00 AID - 10.1021/bi047964d [doi] PST - ppublish SO - Biochemistry. 2005 Jan 11;44(1):321-8. PMID- 18411056 OWN - NLM STAT- MEDLINE DA - 20080506 DCOM- 20080606 LR - 20140916 IS - 1096-0279 (Electronic) IS - 1046-5928 (Linking) VI - 59 IP - 2 DP - 2008 Jun TI - Purification and reconstitution of the connexin43 carboxyl terminus attached to the 4th transmembrane domain in detergent micelles. PG - 215-22 LID - 10.1016/j.pep.2008.01.023 [doi] AB - In recent years, reports have identified that many eukaryotic proteins contain disordered regions spanning greater than 30 consecutive residues in length. In particular, a number of these intrinsically disordered regions occur in the cytoplasmic segments of plasma membrane proteins. These intrinsically disordered regions play important roles in cell signaling events, as they are sites for protein-protein interactions and phosphorylation. Unfortunately, in many crystallographic studies of membrane proteins, these domains are removed because they hinder the crystallization process. Therefore, a purification procedure was developed to enable the biophysical and structural characterization of these intrinsically disordered regions while still associated with the lipid environment. The carboxyl terminal domain from the gap junction protein connexin43 attached to the 4th transmembrane domain (TM4-Cx43CT) was used as a model system (residues G178-I382). The purification was optimized for structural analysis by nuclear magnetic resonance (NMR) because this method is well suited for small membrane proteins and proteins that lack a well-structured three-dimensional fold. The TM4-Cx43CT was purified to homogeneity with a yield of approximately 6 mg/L from C41(DE3) bacterial cells, reconstituted in the anionic detergent 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-RAC-(1-glycerol)], and analyzed by circular dichroism and NMR to demonstrate that the TM4-Cx43CT was properly folded into a functional conformation by its ability to form alpha-helical structure and associate with a known binding partner, the c-Src SH3 domain, respectively. FAU - Kellezi, Admir AU - Kellezi A AD - Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA. FAU - Grosely, Rosslyn AU - Grosely R FAU - Kieken, Fabien AU - Kieken F FAU - Borgstahl, Gloria E O AU - Borgstahl GE FAU - Sorgen, Paul L AU - Sorgen PL LA - eng GR - GM072631/GM/NIGMS NIH HHS/United States GR - P30CA036727/CA/NCI NIH HHS/United States GR - R01 GM072631/GM/NIGMS NIH HHS/United States GR - R01 GM072631-02/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20080323 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (Connexin 43) RN - 0 (Detergents) RN - 0 (Micelles) SB - IM MH - Animals MH - Cell Membrane/chemistry MH - Connexin 43/biosynthesis/*chemistry/*isolation & purification MH - Detergents/chemistry MH - Micelles MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Rats PMC - PMC2446604 MID - NIHMS51939 OID - NLM: NIHMS51939 OID - NLM: PMC2446604 EDAT- 2008/04/16 09:00 MHDA- 2008/06/07 09:00 CRDT- 2008/04/16 09:00 PHST- 2007/10/11 [received] PHST- 2008/01/30 [revised] PHST- 2008/01/31 [accepted] PHST- 2008/03/23 [aheadofprint] AID - S1046-5928(08)00034-X [pii] AID - 10.1016/j.pep.2008.01.023 [doi] PST - ppublish SO - Protein Expr Purif. 2008 Jun;59(2):215-22. doi: 10.1016/j.pep.2008.01.023. Epub 2008 Mar 23. PMID- 19651438 OWN - NLM STAT- MEDLINE DA - 20090831 DCOM- 20091106 LR - 20140828 IS - 1532-1991 (Electronic) IS - 0143-4160 (Linking) VI - 46 IP - 3 DP - 2009 Sep TI - Metal-controlled interdomain cooperativity in parvalbumins. PG - 163-75 LID - 10.1016/j.ceca.2009.07.001 [doi] AB - Conformational behavior of five homologous proteins, parvalbumins (PAs) from northern pike (alpha and beta isoforms), Baltic cod, and rat (alpha and beta isoforms), was studied by scanning calorimetry, circular dichroism, and bis-ANS fluorescence. The mechanism of the temperature-induced denaturation of these proteins depends dramatically on both the peculiarities of their amino acid sequences and on their interaction with metal ions. For example, the pike alpha-PA melting can be described by two successive two-state transitions with mid-temperatures of 90 and 120 degrees C, suggesting the presence of two thermodynamic domains. The intermediate state populated at the end of the first transition was shown to bind Ca(2+) ions, and was characterized by the largely preserved secondary structure and increased solvent exposure of hydrophobic groups. Mg(2+)- and Na(+)-loaded forms of pike alpha-PA demonstrated a single two-state transition. Therefore, the mechanism of the PA thermal denaturation is controlled by metal binding. It ranged from the absence of detectable first-order transition (apo-form of pike PA), to the two-state transition (e.g., Mg(2+)- and Na(+)-loaded forms of pike alpha-PA), to the more complex mechanisms (Ca(2+)-loaded PAs) involving at least one partially folded intermediate. Analysis of isolated cavities in the protein structures revealed that the interface between the CD and EF subdomains of Ca(2+)-loaded pike alpha-PA is much more loosely packed compared with PAs manifesting single heat-sorption peak. The impairment of interactions between CD and EF subdomains may cause a loss of structural cooperativity and appearance of two separate thermodynamic domains. One more peculiar feature of pike alpha-PA is that depending on its interactions with metal ions, it can be an intrinsically disordered protein (apo-form), an ordered protein of mesophilic (Na(+)-bound state), thermophilic (Mg(2+)-form), or even of the hyperthermophilic origin (Ca(2+)-form). FAU - Permyakov, Sergei E AU - Permyakov SE AD - Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow, Russia. permyakov.s@gmail.com FAU - Bakunts, Anush G AU - Bakunts AG FAU - Permyakova, Maria E AU - Permyakova ME FAU - Denesyuk, Alexander I AU - Denesyuk AI FAU - Uversky, Vladimir N AU - Uversky VN FAU - Permyakov, Eugene A AU - Permyakov EA LA - eng GR - GM071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 GM071714-04/GM/NIGMS NIH HHS/United States GR - R01 LM007688-01A1/LM/NLM NIH HHS/United States GR - R01 LM007688-04/LM/NLM NIH HHS/United States GR - R56 LM007688-05A1/LM/NLM NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20090803 PL - Netherlands TA - Cell Calcium JT - Cell calcium JID - 8006226 RN - 0 (Metals) RN - 0 (Parvalbumins) RN - 0 (Recombinant Proteins) RN - SY7Q814VUP (Calcium) SB - IM MH - Animals MH - Calcium/metabolism MH - Calorimetry MH - Circular Dichroism MH - Metals/*metabolism MH - Parvalbumins/*chemistry/metabolism MH - Protein Binding MH - Protein Denaturation MH - Protein Structure, Tertiary MH - Rats MH - Recombinant Proteins/chemistry/metabolism MH - Spectrometry, Fluorescence MH - Thermodynamics MH - Transition Temperature PMC - PMC2754762 MID - NIHMS136437 OID - NLM: NIHMS136437 OID - NLM: PMC2754762 EDAT- 2009/08/05 09:00 MHDA- 2009/11/07 06:00 CRDT- 2009/08/05 09:00 PHST- 2009/03/13 [received] PHST- 2009/06/29 [revised] PHST- 2009/07/06 [accepted] PHST- 2009/08/03 [aheadofprint] AID - S0143-4160(09)00114-6 [pii] AID - 10.1016/j.ceca.2009.07.001 [doi] PST - ppublish SO - Cell Calcium. 2009 Sep;46(3):163-75. doi: 10.1016/j.ceca.2009.07.001. Epub 2009 Aug 3. PMID- 17202261 OWN - NLM STAT- MEDLINE DA - 20070110 DCOM- 20070216 LR - 20141120 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 104 IP - 2 DP - 2007 Jan 9 TI - Multiple aromatic side chains within a disordered structure are critical for transcription and transforming activity of EWS family oncoproteins. PG - 479-84 AB - Chromosomal translocations involving the N-terminal approximately 250 residues of the Ewings sarcoma (EWS) oncogene produce a group of EWS fusion proteins (EFPs) that cause several distinct human cancers. EFPs are potent transcriptional activators and interact with other proteins required for mRNA biogenesis, indicating that EFPs induce tumorigenesis by perturbing gene expression. Although EFPs were discovered more than a decade ago, molecular analysis has been greatly hindered by the repetitive EWS activation domain (EAD) structure, containing multiple degenerate hexapeptide repeats (consensus SYGQQS) with a conserved tyrosine residue. By exploiting total gene synthesis, we have been able to systematically mutagenize the EAD and determine the effect on transcriptional activation by EWS/ATF1 and cellular transformation by EWS/Fli1. In both assays, we find the following requirements for EAD function. First, multiple tyrosine residues are essential. Second, phenylalanine can effectively substitute for tyrosine, showing that an aromatic ring can confer EAD function in the absence of tyrosine phosphorylation. Third, there is little requirement for specific peptide sequences and, thus, overall sequence composition (and not the degenerate hexapeptide repeat) confers EAD activity. Consistent with the above findings, we also report that the EAD is intrinsically disordered. However, a sensitive computational predictor of natural protein disorder (PONDR VL3) identifies potential molecular recognition features that are tyrosine-dependent and that correlate well with EAD function. In summary we have uncovered several molecular features of the EAD that will impact future studies of the broader EFP family and molecular recognition by complex intrinsically disordered proteins. FAU - Ng, King Pan AU - Ng KP AD - Department of Biology, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, S.A.R. China. FAU - Potikyan, Gary AU - Potikyan G FAU - Savene, Rupert O V AU - Savene RO FAU - Denny, Christopher T AU - Denny CT FAU - Uversky, Vladimir N AU - Uversky VN FAU - Lee, Kevin A W AU - Lee KA LA - eng GR - 07-0922/Worldwide Cancer Research/United Kingdom GR - CA087771/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070103 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Amino Acids, Aromatic) RN - 0 (EWS-ATF1 fusion protein, human) RN - 0 (EWS-FLI fusion protein) RN - 0 (Oncogene Proteins, Fusion) RN - 0 (Proto-Oncogene Protein c-fli-1) RN - 0 (RNA-Binding Protein EWS) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) SB - IM MH - Amino Acids, Aromatic/chemistry MH - Animals MH - Cell Transformation, Neoplastic MH - Humans MH - In Vitro Techniques MH - Mice MH - Molecular Structure MH - Mutagenesis, Site-Directed MH - NIH 3T3 Cells MH - Oncogene Proteins, Fusion/chemistry/genetics/metabolism MH - Proto-Oncogene Protein c-fli-1 MH - RNA-Binding Protein EWS/*chemistry/genetics/*metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Repetitive Sequences, Amino Acid MH - Sarcoma, Ewing/genetics/metabolism MH - Transcription Factors/chemistry/genetics/metabolism MH - Transcriptional Activation PMC - PMC1766410 OID - NLM: PMC1766410 EDAT- 2007/01/05 09:00 MHDA- 2007/02/17 09:00 CRDT- 2007/01/05 09:00 PHST- 2007/01/03 [aheadofprint] AID - 0607007104 [pii] AID - 10.1073/pnas.0607007104 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):479-84. Epub 2007 Jan 3. PMID- 16081040 OWN - NLM STAT- MEDLINE DA - 20050815 DCOM- 20051014 LR - 20131121 IS - 0006-291X (Print) IS - 0006-291X (Linking) VI - 335 IP - 2 DP - 2005 Sep 23 TI - Engineered alpha-synuclein prevents wild type and familial Parkin variant fibril formation. PG - 432-6 AB - Alpha-synuclein is a major component of several pathological lesions diagnostic of specific neurodegenerative disease such as Parkinson's disease. This study focuses on the non-amyloid beta component of Alzheimer's disease amyloid, a key region for the aggregation and fibril formation of alpha-synuclein. Several mutations were introduced in an attempt to repress beta-strand formation and hydrophobic interaction-based aggregation. Although reducing the hydrophobicity drastically decreased fibril formation, the Val70Thr and Val70Pro mutations resulted in an unstable secondary structure thereby increasing non-structural aggregation, instead of fibril formation. Therefore, the stabilization of non-structural natively unfolded status is important to prevent alpha-synuclein fibril formation. Mixing the Val70Thr/Val71Thr double mutant, which has inherently low potential, with the fibril forming alpha-synucleins, WT and Ala53Thr, greatly reduced their fibril formation and aggregation. This double mutant has great potential for further therapeutic approaches. FAU - Sode, Koji AU - Sode K AD - Department of Biotechnology, Faculty of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, 184-8588 Tokyo, Koganei, Japan. sode@cc.tuat.ac.jp FAU - Usuzaka, Eri AU - Usuzaka E FAU - Kobayashi, Natsuki AU - Kobayashi N FAU - Ochiai, Sayaka AU - Ochiai S LA - eng PT - Journal Article PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Amyloid) RN - 0 (DNA, Complementary) RN - 0 (Nerve Tissue Proteins) RN - 0 (Peptides) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 9007-49-2 (DNA) RN - 9DLQ4CIU6V (Proline) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) RN - EC 6.3.2.19 (parkin protein) RN - HG18B9YRS7 (Valine) SB - IM MH - Alzheimer Disease/metabolism MH - Amino Acid Sequence MH - Amyloid/chemistry MH - Bone Marrow Cells/cytology MH - Circular Dichroism MH - DNA/chemistry MH - DNA, Complementary/metabolism MH - Gene Library MH - Humans MH - Light MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Mutation MH - Nerve Tissue Proteins/*chemistry/genetics/physiology MH - Parkinson Disease/metabolism MH - Peptides/chemistry MH - Polymerase Chain Reaction MH - Proline/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Engineering MH - Protein Structure, Secondary MH - Scattering, Radiation MH - Synucleins MH - Time Factors MH - Ubiquitin-Protein Ligases/*chemistry/genetics MH - Ultraviolet Rays MH - Valine/chemistry MH - alpha-Synuclein EDAT- 2005/08/06 09:00 MHDA- 2005/10/15 09:00 CRDT- 2005/08/06 09:00 PHST- 2005/07/15 [received] PHST- 2005/07/20 [accepted] AID - S0006-291X(05)01587-1 [pii] AID - 10.1016/j.bbrc.2005.07.100 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2005 Sep 23;335(2):432-6. PMID- 16605254 OWN - NLM STAT- MEDLINE DA - 20060411 DCOM- 20060531 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 15 DP - 2006 Apr 18 TI - Structural and functional characterization of the TgDRE multidomain protein, a DNA repair enzyme from Toxoplasma gondii. PG - 4867-74 AB - The parasite Toxoplasma gondii expresses a 55 kDa protein or TgDRE that belongs to a novel family of proteins characterized by the presence of three domains, a human splicing factor 45-like motif (SF), a glycine-rich motif (G-patch), and a RNA recognition motif (RRM). The two latter domains are mainly known as RNA-binding domains, and their presence in TgDRE, whose partial DNA repair function was demonstrated, suggests that the protein could also be involved in the RNA metabolism. In this work, we characterized the structure and function of the different domains by using single or multidomain proteins to define their putative role. The SF45-like domain has a helical conformation and is involved in the oligomerization of the protein. The G-patch domain, mainly unstructured on its own as well as in the presence of the SF upstream and RRM downstream domains, is able to bind small RNA oligonucleotides. We also report the structure determination of the RRM domain from the NMR data. It adopts a classical betaalphabetabetaalphabeta topology consisting of a four-stranded beta sheet packed against two alpha helices but does not present the key residues for the RNA interaction. In contrast, our analysis shows that the RRM of TgDRE is not only unable to bind small RNA oligonucleotides but it also shares the protein-protein interaction characteristics with two unusual RRMs of the U2AF heterodimeric splicing factor. The presence of both RNA- and protein-binding domains seems to indicate that TgDRE could also be involved in RNA metabolism. FAU - Frenal, Karine AU - Frenal K AD - Unite de Resonance Magnetique Nucleaire des Biomolecules, CNRS URA 2185, Institut Pasteur, 28 Rue du Docteur Roux, 75724 Paris Cedex 15, France. FAU - Callebaut, Isabelle AU - Callebaut I FAU - Wecker, Karine AU - Wecker K FAU - Prochnicka-Chalufour, Ada AU - Prochnicka-Chalufour A FAU - Dendouga, Najoua AU - Dendouga N FAU - Zinn-Justin, Sophie AU - Zinn-Justin S FAU - Delepierre, Muriel AU - Delepierre M FAU - Tomavo, Stanislas AU - Tomavo S FAU - Wolff, Nicolas AU - Wolff N LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Protozoan Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Regulatory Sequences, Ribonucleic Acid) RN - EC 6.5.1.- (DNA Ligases) RN - EC 6.5.1.- (DNA repair enzyme TgDRE, Toxoplasma gondii) SB - IM MH - Amino Acid Sequence MH - Animals MH - DNA Ligases/*chemistry/*metabolism MH - Enzyme Stability MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary/physiology MH - Protozoan Proteins/*chemistry/*metabolism MH - Recombinant Proteins/genetics/metabolism MH - Regulatory Sequences, Ribonucleic Acid MH - Sequence Alignment MH - Solubility MH - Structure-Activity Relationship EDAT- 2006/04/12 09:00 MHDA- 2006/06/01 09:00 CRDT- 2006/04/12 09:00 AID - 10.1021/bi051948e [doi] PST - ppublish SO - Biochemistry. 2006 Apr 18;45(15):4867-74. PMID- 8620531 OWN - NLM STAT- MEDLINE DA - 19960617 DCOM- 19960617 LR - 20061115 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 85 IP - 1 DP - 1996 Apr 5 TI - The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. PG - 125-36 AB - Telomeres, the nucleoprotein complexes at the ends of eukaryotic chromosomes, are essential for chromosome stability. In the yeast S. cerevisiae, telomeric DNA is bound in a sequence-specific manner by RAP1, a multifunctional protein also involved in transcriptional regulation. Here we report the crystal structure of the DNA-binding domain of RAP1 in complex with telomeric DNA site at 2.25 A resolution. The protein contains two similar domains that bind DNA in a tandem orientation, recognizing a tandemly repeated DNA sequence. The domains are structurally related to the homeodomain and the proto-oncogene Myb, but show novel features in their DNA-binding mode. A structured linker between the domains and a long C-terminal tail contribute to the binding specificity. This structure provides insight into the recognition of the conserved telomeric DNA sequences by a protein. FAU - Konig, P AU - Konig P AD - Medical Research Council, Laboratory of Molecular Biology, Cambridge, United Kingdom. FAU - Giraldo, R AU - Giraldo R FAU - Chapman, L AU - Chapman L FAU - Rhodes, D AU - Rhodes D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA-Binding Proteins) RN - 0 (Fungal Proteins) RN - EC 3.6.1.- (GTP-Binding Proteins) RN - EC 3.6.5.2 (rap GTP-Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Crystallography MH - DNA-Binding Proteins/chemistry/metabolism MH - Fungal Proteins/*chemistry MH - GTP-Binding Proteins/*chemistry/metabolism MH - Image Processing, Computer-Assisted MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Protein Conformation MH - Protein Structure, Tertiary MH - Telomere/*chemistry/metabolism MH - Yeasts/*chemistry/genetics/metabolism MH - rap GTP-Binding Proteins EDAT- 1996/04/05 MHDA- 1996/04/05 00:01 CRDT- 1996/04/05 00:00 AID - S0092-8674(00)81088-0 [pii] PST - ppublish SO - Cell. 1996 Apr 5;85(1):125-36. PMID- 10678179 OWN - NLM STAT- MEDLINE DA - 20000309 DCOM- 20000309 LR - 20131121 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 5 IP - 1 DP - 2000 Jan TI - The crystal structure of the nuclear receptor for vitamin D bound to its natural ligand. PG - 173-9 AB - The action of 1 alpha, 25-dihydroxyvitamin D3 is mediated by its nuclear receptor (VDR), a ligand-dependent transcription regulator. We report the 1.8 A resolution crystal structure of the complex between a VDR ligand-binding domain (LBD) construct lacking the highly variable VDR-specific insertion domain and vitamin D. The construct exhibits the same binding affinity for vitamin D and transactivation ability as the wild-type protein, showing that the N-terminal part of the LBD is essential for its structural and functional integrity while the large insertion peptide is dispensable. The structure reveals the active conformation of the bound ligand and allows understanding of the different binding properties of some synthetic analogs. FAU - Rochel, N AU - Rochel N AD - Laboratoire de Biologie Structurale, Institut de Genetique et de Biologie Moleculaire et Cellulaire CNRS/INSERM/ULP, Illkirch, France. FAU - Wurtz, J M AU - Wurtz JM FAU - Mitschler, A AU - Mitschler A FAU - Klaholz, B AU - Klaholz B FAU - Moras, D AU - Moras D LA - eng SI - PDB/1DB1 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Ligands) RN - 0 (Receptors, Calcitriol) RN - 0 (Receptors, Cytoplasmic and Nuclear) RN - 0 (Recombinant Proteins) RN - FXC9231JVH (Calcitriol) SB - IM MH - Amino Acid Sequence MH - Calcitriol/*chemistry/*metabolism MH - Crystallography, X-Ray/methods MH - Humans MH - Ligands MH - Models, Molecular MH - Molecular Conformation MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Receptors, Calcitriol/*chemistry/*metabolism MH - Receptors, Cytoplasmic and Nuclear/chemistry MH - Recombinant Proteins/chemistry/metabolism EDAT- 2000/03/11 MHDA- 2000/03/11 00:01 CRDT- 2000/03/11 00:00 AID - S1097-2765(00)80413-X [pii] PST - ppublish SO - Mol Cell. 2000 Jan;5(1):173-9. PMID- 15295116 OWN - NLM STAT- MEDLINE DA - 20040823 DCOM- 20050414 LR - 20140608 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 13 IP - 9 DP - 2004 Sep TI - The effect of an ionic detergent on the natively unfolded beta-dystroglycan ectodomain and on its interaction with alpha-dystroglycan. PG - 2437-45 AB - Dystroglycan (DG) is an adhesion complex, expressed in a wide variety of tissues, formed by an extracellular and a transmembrane subunit, alpha-DG and beta-DG, respectively, interacting noncovalently. Recently, we have shown that the recombinant ectodomain of beta-DG, beta-DG(654-750), behaves as a natively unfolded protein, as it is able to bind the C-terminal domain of alpha-DG, while not displaying a defined structural organization. We monitored the effect of a commonly used denaturing agent, the anionic detergent sodium dodecylsulphate (SDS), on beta-DG(654-750) using a number of biophysical techniques. Very low concentrations of SDS (< or =2 mM) affect both tryptophan fluorescence and circular dichroism of beta-DG, and significantly perturb the interaction with the alpha-DG subunit as shown by solid-phase binding assays and fluorescence titrations in solution. This result confirms, as recently proposed for natively unfolded proteins, that beta-DG(654-750) exists in a native state, which is crucial to fulfill its biological function. Two-dimensional NMR analysis shows that SDS does not induce any evident conformational rearrangement within the ectodomain of beta-DG. Its first 70 amino acids, which show a lower degree of mobility, interact with the detergent, but this does not change the amount of secondary structure, whereas the highly flexible and mobile C-terminal region of beta-DG(654-750) remains largely unaffected, even at a very high SDS concentration (up to 50 mM). Our data indicate that SDS can be used as a useful tool for investigating natively unfolded proteins, and confirm that the beta-DG ectodomain is an interesting model system. FAU - Bozzi, Manuela AU - Bozzi M AD - Consiglio Nazionale delle Richerche (CNR), Istituto di Chimica del Riconoscimento Molecolare, c/o Istituto di Biochimica e Biochimica Clinica, Universita Cattolica del Sacro Cuore, 00168 Rome, Italy. FAU - Di Stasio, Enrico AU - Di Stasio E FAU - Cicero, Daniel O AU - Cicero DO FAU - Giardina, Bruno AU - Giardina B FAU - Paci, Maurizio AU - Paci M FAU - Brancaccio, Andrea AU - Brancaccio A LA - eng GR - GGP030332/Telethon/Italy PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040804 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Detergents) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 146888-27-9 (Dystroglycans) RN - 368GB5141J (Sodium Dodecyl Sulfate) SB - IM MH - Amino Acid Sequence MH - Animals MH - Circular Dichroism MH - Detergents/*chemistry MH - Dystroglycans/*chemistry/*metabolism MH - Magnetic Resonance Spectroscopy MH - Mice MH - Molecular Sequence Data MH - Peptide Fragments/chemical synthesis/chemistry/metabolism MH - *Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Homology, Amino Acid MH - Sodium Dodecyl Sulfate/chemistry MH - Spectrometry, Fluorescence PMC - PMC2280000 OID - NLM: PMC2280000 EDAT- 2004/08/06 05:00 MHDA- 2005/04/15 09:00 CRDT- 2004/08/06 05:00 PHST- 2004/08/04 [aheadofprint] AID - 10.1110/ps.04762504 [doi] AID - ps.04762504 [pii] PST - ppublish SO - Protein Sci. 2004 Sep;13(9):2437-45. Epub 2004 Aug 4. PMID- 15680247 OWN - NLM STAT- MEDLINE DA - 20050131 DCOM- 20050330 LR - 20061115 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1747 IP - 1 DP - 2005 Feb 14 TI - Expression and spectroscopic characterization of a large fragment of the mu-opioid receptor. PG - 133-40 AB - We report here a procedure for the production in Escherichia coli and subsequent purification and characterization of an 80-residue fragment of the human mu-opioid receptor. The fragment ('TM2-3'), which comprises the second and third transmembrane segments as well as the first extracellular loop of the receptor, was expressed as a fusion with glutathione-S-transferase. The fusion protein, which accumulated in insoluble inclusion bodies, was solubilized with N-lauroylsarcosine, and TM2-3 was obtained by thrombin cleavage of the fusion protein followed by reversed-phase HPLC purification. CD spectroscopy of TM2-3 in lysophosphatidylcholine micelles showed that TM2-3 adopts approximately 50% alpha-helical structure in this environment, with the remainder consisting of disordered and/or beta-structure. This is consistent with the assumption of an alpha-helical structure by the two membrane-spanning regions and a nonhelical structure in the loop region of TM2-3. Fluorescence spectroscopy and fluorescence quenching experiments suggested that the extracellular loop lies near the surface of the lysophosphatidylcholine micelle. Our work shows that the study of large receptor fragments is a technically accessible approach to the study of the structural properties of the mu-opioid receptor and, possibly, other G-protein-coupled receptors as well. FAU - Kerman, Aaron AU - Kerman A AD - Department of Biochemistry, HSC 4H25, McMaster University, Hamilton, Ontario, Canada L8N 3Z5. FAU - Ananthanarayanan, Vettai S AU - Ananthanarayanan VS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20041104 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Peptide Fragments) RN - 0 (Receptors, Opioid, mu) RN - 0 (Recombinant Fusion Proteins) RN - EC 2.5.1.18 (Glutathione Transferase) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Escherichia coli/metabolism MH - Glutathione Transferase/biosynthesis/chemistry/isolation & purification MH - Humans MH - Inclusion Bodies/chemistry/metabolism MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/isolation & purification MH - Protein Structure, Secondary MH - Receptors, Opioid, mu/*biosynthesis/*chemistry/genetics MH - Recombinant Fusion Proteins/*biosynthesis/chemistry/isolation & purification EDAT- 2005/02/01 09:00 MHDA- 2005/03/31 09:00 CRDT- 2005/02/01 09:00 PHST- 2004/06/10 [received] PHST- 2004/10/13 [revised] PHST- 2004/10/13 [accepted] PHST- 2004/11/04 [aheadofprint] AID - S1570-9639(04)00291-2 [pii] AID - 10.1016/j.bbapap.2004.10.009 [doi] PST - ppublish SO - Biochim Biophys Acta. 2005 Feb 14;1747(1):133-40. Epub 2004 Nov 4. PMID- 24106084 OWN - NLM STAT- MEDLINE DA - 20140128 DCOM- 20140325 LR - 20141112 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 42 IP - 2 DP - 2014 Jan TI - Intrinsically disordered regions of nucleophosmin/B23 regulate its RNA binding activity through their inter- and intra-molecular association. PG - 1180-95 LID - 10.1093/nar/gkt897 [doi] AB - Nucleophosmin (NPM1/B23) is a nucleolar protein implicated in growth-associated functions, in which the RNA binding activity of B23 plays essential roles in ribosome biogenesis. The C-terminal globular domain (CTD) of B23 has been believed to be the RNA binding domain because the splicing variant B23.2 lacking the CTD binds considerably less efficiently to RNA. However, the recognition of target RNAs by B23 remains poorly understood. Herein, we report a novel mechanism by which B23 recognizes specific RNA targets. We observed that the nucleolar retention of B23.3 lacking the basic region of B23.1 was lower than that of B23.1 because of its low RNA binding activity. Circular dichroism measurements indicated that the basic region and adjacent acidic regions of B23 are intrinsically disordered regions (IDRs). Biochemical analyses revealed that the basic IDR alone strongly binds to RNA with low specificity. The excessive RNA binding activity of the basic IDR was restrained by intra-molecular interaction with the acidic IDR of B23. Chemical cross-linking experiments and fluorescent labeling of bipartite tetracysteine-tagged proteins suggested that the inter- and intra-molecular interactions between the two IDRs contribute to the regulation of the RNA binding activity of CTD to control the cellular localization and functions of B23. FAU - Hisaoka, Miharu AU - Hisaoka M AD - Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8575, Japan. FAU - Nagata, Kyosuke AU - Nagata K FAU - Okuwaki, Mitsuru AU - Okuwaki M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131007 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Protein Isoforms) RN - 0 (RNA-Binding Proteins) RN - 117896-08-9 (nucleophosmin) RN - 63231-63-0 (RNA) SB - IM MH - Cell Line MH - HeLa Cells MH - Humans MH - Intrinsically Disordered Proteins/chemistry/metabolism MH - Nuclear Proteins/*chemistry/metabolism MH - Phosphorylation MH - Protein Binding MH - Protein Isoforms/chemistry/metabolism MH - Protein Structure, Tertiary MH - RNA/*metabolism MH - RNA-Binding Proteins/*chemistry/metabolism PMC - PMC3902904 OID - NLM: PMC3902904 EDAT- 2013/10/10 06:00 MHDA- 2014/03/26 06:00 CRDT- 2013/10/10 06:00 PHST- 2013/10/07 [aheadofprint] AID - gkt897 [pii] AID - 10.1093/nar/gkt897 [doi] PST - ppublish SO - Nucleic Acids Res. 2014 Jan;42(2):1180-95. doi: 10.1093/nar/gkt897. Epub 2013 Oct 7. PMID- 11902841 OWN - NLM STAT- MEDLINE DA - 20020320 DCOM- 20020524 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 317 IP - 2 DP - 2002 Mar 22 TI - Crystal structure of yeast acetohydroxyacid synthase: a target for herbicidal inhibitors. PG - 249-62 AB - Acetohydroxyacid synthase (AHAS; EC 4.1.3.18) catalyzes the first step in branched-chain amino acid biosynthesis. The enzyme requires thiamin diphosphate and FAD for activity, but the latter is unexpected, because the reaction involves no oxidation or reduction. Due to its presence in plants, AHAS is a target for sulfonylurea and imidazolinone herbicides. Here, the crystal structure to 2.6 A resolution of the catalytic subunit of yeast AHAS is reported. The active site is located at the dimer interface and is near the proposed herbicide-binding site. The conformation of FAD and its position in the active site are defined. The structure of AHAS provides a starting point for the rational design of new herbicides. CI - Copyright 2002 Elsevier Science Ltd. FAU - Pang, Siew Siew AU - Pang SS AD - Centre for Protein Structure Function and Engineering, Department of Biochemistry and Molecular Biology, School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, QLD 4072, Australia. FAU - Duggleby, Ronald G AU - Duggleby RG FAU - Guddat, Luke W AU - Guddat LW LA - eng SI - PDB/1JSC PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Enzyme Inhibitors) RN - 0 (Herbicides) RN - 0 (Imidazoles) RN - 146-14-5 (Flavin-Adenine Dinucleotide) RN - 59-67-6 (Niacin) RN - 81334-34-1 (imazapyr) RN - EC 2.2.1.6 (Acetolactate Synthase) RN - I38ZP9992A (Magnesium) RN - Q57971654Y (Thiamine Pyrophosphate) SB - IM MH - Acetolactate Synthase/*chemistry/genetics/*metabolism MH - Amino Acid Sequence MH - Binding Sites MH - Catalytic Domain MH - Crystallography, X-Ray MH - Dimerization MH - Enzyme Inhibitors/chemistry/metabolism MH - Flavin-Adenine Dinucleotide/chemistry/metabolism MH - Herbicides/chemistry/*metabolism MH - Imidazoles/chemistry/*metabolism MH - Magnesium/chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Niacin/*analogs & derivatives/chemistry/*metabolism MH - Protein Conformation MH - Sequence Homology, Amino Acid MH - Thiamine Pyrophosphate/chemistry/metabolism MH - Yeasts/*enzymology EDAT- 2002/03/21 10:00 MHDA- 2002/05/25 10:01 CRDT- 2002/03/21 10:00 AID - 10.1006/jmbi.2001.5419 [doi] AID - S0022283601954191 [pii] PST - ppublish SO - J Mol Biol. 2002 Mar 22;317(2):249-62. PMID- 19395382 OWN - NLM STAT- MEDLINE DA - 20090615 DCOM- 20091020 LR - 20141120 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 284 IP - 25 DP - 2009 Jun 19 TI - Determinants of histone H4 N-terminal domain function during nucleosomal array oligomerization: roles of amino acid sequence, domain length, and charge density. PG - 16716-22 LID - 10.1074/jbc.M109.011288 [doi] AB - Mg(2+)-dependent oligomerization of nucleosomal arrays is correlated with higher order folding transitions that stabilize chromosome structure beyond the 30-nm diameter fiber. In the present studies, we have employed a novel mutagenesis-based approach to identify the macromolecular determinants that control H4 N-terminal domain (NTD) function during oligomerization. Core histones were engineered in which 1) the H2A, H2B, and H3 NTDs were swapped onto the H4 histone fold; 2) the length of the H4 NTD and the H2A NTD on the H4 histone fold, were increased; 3) the charge density of the NTDs on the H4 histone fold was increased or decreased; and 4) the H4 NTD was placed on the H2B histone fold. Model nucleosomal arrays were assembled from wild type and mutant core histone octamers, and Mg(2+)-dependent oligomerization was characterized. The results demonstrated that the H2B and H3 NTDs could replace the H4 NTD, as could the H2A NTD if it was duplicated to the length of the native H4 NTD. Arrays oligomerized at lower salt concentrations as the length of the NTD on the H4 histone fold was increased. Mutations that decreased the NTD charge density required more Mg(2+) to oligomerize, whereas mutants that increased the charge density required less salt. Finally, the H4 NTD functioned differently when attached to the H2B histone fold than the H4 histone fold. These studies have revealed new insights into the biochemical basis for H4 NTD effects on genome architecture as well as the protein chemistry that underlies the function of the intrinsically disordered H4 NTD. FAU - McBryant, Steven J AU - McBryant SJ AD - Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA. FAU - Klonoski, Joshua AU - Klonoski J FAU - Sorensen, Troy C AU - Sorensen TC FAU - Norskog, Sarah S AU - Norskog SS FAU - Williams, Sere AU - Williams S FAU - Resch, Michael G AU - Resch MG FAU - Toombs, James A 3rd AU - Toombs JA 3rd FAU - Hobdey, Sarah E AU - Hobdey SE FAU - Hansen, Jeffrey C AU - Hansen JC LA - eng GR - GM45916/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090424 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Histones) RN - 0 (Nucleosomes) RN - 0 (Recombinant Proteins) RN - 0 (Xenopus Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Histones/*chemistry/*genetics/metabolism MH - In Vitro Techniques MH - Molecular Sequence Data MH - Mutagenesis MH - Nucleosomes/*chemistry/*genetics/metabolism MH - Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Static Electricity MH - Xenopus Proteins/*chemistry/*genetics/metabolism MH - Xenopus laevis/genetics/metabolism PMC - PMC2719306 OID - NLM: PMC2719306 EDAT- 2009/04/28 09:00 MHDA- 2009/10/21 06:00 CRDT- 2009/04/28 09:00 PHST- 2009/04/24 [aheadofprint] AID - M109.011288 [pii] AID - 10.1074/jbc.M109.011288 [doi] PST - ppublish SO - J Biol Chem. 2009 Jun 19;284(25):16716-22. doi: 10.1074/jbc.M109.011288. Epub 2009 Apr 24. PMID- 23497088 OWN - NLM STAT- MEDLINE DA - 20130318 DCOM- 20130530 LR - 20141116 IS - 1471-2148 (Electronic) IS - 1471-2148 (Linking) VI - 13 DP - 2013 TI - Genealogy of an ancient protein family: the Sirtuins, a family of disordered members. PG - 60 LID - 10.1186/1471-2148-13-60 [doi] AB - BACKGROUND: Sirtuins genes are widely distributed by evolution and have been found in eubacteria, archaea and eukaryotes. While prokaryotic and archeal species usually have one or two sirtuin homologs, in humans as well as in eukaryotes we found multiple versions and in mammals this family is comprised of seven different homologous proteins being all NAD-dependent de-acylases. 3D structures of human SIRT2, SIRT3, and SIRT5 revealed the overall conformation of the conserved core domain but they were unable to give a structural information about the presence of very flexible and dynamically disordered regions, the role of which is still structurally and functionally unclear. Recently, we modeled the 3D-structure of human SIRT1, the most studied member of this family, that unexpectedly emerged as a member of the intrinsically disordered proteins with its long disordered terminal arms. Despite clear similarities in catalytic cores between the human sirtuins little is known of the general structural characteristics of these proteins. The presence of disorder in human SIRT1 and the propensity of these proteins in promoting molecular interactions make it important to understand the underlying mechanisms of molecular recognition that reasonably should involve terminal segments. The mechanism of recognition, in turn, is a prerequisite for the understanding of any functional activity. Aim of this work is to understand what structural properties are shared among members of this family in humans as well as in other organisms. RESULTS: We have studied the distribution of the structural features of N- and C-terminal segments of sirtuins in all known organisms to draw their evolutionary histories by taking into account average length of terminal segments, amino acid composition, intrinsic disorder, presence of charged stretches, presence of putative phosphorylation sites, flexibility, and GC content of genes. Finally, we have carried out a comprehensive analysis of the putative phosphorylation sites in human sirtuins confirming those sites already known experimentally for human SIRT1 and 2 as well as extending their topology to all the family to get feedback of their physiological functions and cellular localization. CONCLUSIONS: Our results highlight that the terminal segments of the majority of sirtuins possess a number of structural features and chemical and physical properties that strongly support their involvement in activities of recognition and interaction with other protein molecules. We also suggest how a multisite phosphorylation provides a possible mechanism by which flexible and intrinsically disordered segments of a sirtuin supported by the presence of positively or negatively charged stretches might enhance the strength and specificity of interaction with a particular molecular partner. FAU - Costantini, Susan AU - Costantini S AD - "Pascale Foundation" National Cancer Institute - Cancer Research Center (CROM), via Ammiraglio Bianco, 83013, Mercogliano, Italy. susan.costantini@unina2.it FAU - Sharma, Ankush AU - Sharma A FAU - Raucci, Raffaele AU - Raucci R FAU - Costantini, Maria AU - Costantini M FAU - Autiero, Ida AU - Autiero I FAU - Colonna, Giovanni AU - Colonna G LA - eng PT - Journal Article DEP - 20130305 PL - England TA - BMC Evol Biol JT - BMC evolutionary biology JID - 100966975 RN - 0 (Nuclear Export Signals) RN - 0 (Nuclear Localization Signals) RN - EC 3.5.1.- (SIRT1 protein, human) RN - EC 3.5.1.- (Sirtuin 1) RN - EC 3.5.1.- (Sirtuins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Composition MH - *Evolution, Molecular MH - Humans MH - *Multigene Family MH - Nuclear Export Signals MH - Nuclear Localization Signals MH - Phosphorylation MH - Phylogeny MH - Plants MH - Protein Structure, Secondary MH - Sequence Alignment MH - Sirtuin 1/genetics MH - Sirtuins/*genetics PMC - PMC3599600 OID - NLM: PMC3599600 EDAT- 2013/03/19 06:00 MHDA- 2013/06/01 06:00 CRDT- 2013/03/19 06:00 PHST- 2012/09/15 [received] PHST- 2013/02/25 [accepted] PHST- 2013/03/05 [aheadofprint] AID - 1471-2148-13-60 [pii] AID - 10.1186/1471-2148-13-60 [doi] PST - epublish SO - BMC Evol Biol. 2013 Mar 5;13:60. doi: 10.1186/1471-2148-13-60. PMID- 19395380 OWN - NLM STAT- MEDLINE DA - 20090608 DCOM- 20090820 LR - 20140831 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 284 IP - 24 DP - 2009 Jun 12 TI - Zinc ion-induced domain organization in metallo-beta-lactamases: a flexible "zinc arm" for rapid metal ion transfer? PG - 16419-31 LID - 10.1074/jbc.M109.001305 [doi] AB - The reversible unfolding of metallo-beta-lactamase from Chryseobacterium meningosepticum (BlaB) by guanidinium hydrochloride is best described by a three-state model including folded, intermediate, and unfolded states. The transformation of the folded apoenzyme into the intermediate state requires only very low denaturant concentrations, in contrast to the Zn2-enzyme. Similarly, circular dichroism spectra of both BlaB and metallo-beta-lactamase from Bacillus cereus 569/H/9 (BcII) display distinct differences between metal-free and Zn2-enzymes, indicating that the zinc ions affect the folding of the proteins, giving a larger alpha-helix content. To identify the regions of the protein involved in this zinc ion-induced change, a hydrogen deuterium exchange study with matrix-assisted laser desorption ionization tandem time of flight mass spectrometry on metal-free and Zn1- and Zn2-BcII was carried out. The region spanning the metal binding metallo-beta-lactamases (MBL) superfamily consensus sequence His-X-His-X-Asp motif and the loop connecting the N- and C-terminal domains of the protein undergoes a zinc ion-dependent structural change between intrinsically disordered and ordered states. The inherent flexibility even appears to allow for the formation of metal ion-bridged protein-protein complexes which may account for both electrospray ionization-mass spectroscopy results obtained upon variation of the zinc/protein ratio and stoichiometry-dependent variations of 199mHg-perturbed angular correlation of gamma-rays spectroscopic data. We suggest that this flexible "zinc arm" motif, present in all the MBL subclasses, is disordered in metal-free MBLs and may be involved in metal ion acquisition from zinc-carrying molecules different from MBL in an "activation on demand" regulation of enzyme activity. FAU - Selevsek, Nathalie AU - Selevsek N AD - Department of Biochemical Engineering, Saarland University, Saarbrucken, Germany. FAU - Rival, Sandrine AU - Rival S FAU - Tholey, Andreas AU - Tholey A FAU - Heinzle, Elmar AU - Heinzle E FAU - Heinz, Uwe AU - Heinz U FAU - Hemmingsen, Lars AU - Hemmingsen L FAU - Adolph, Hans W AU - Adolph HW LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090424 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - EC 3.5.2.- (beta-lactamase BcII) RN - EC 3.5.2.6 (BLAB3 protein, Flavobacterium meningosepticum) RN - EC 3.5.2.6 (beta-Lactamases) RN - J41CSQ7QDS (Zinc) SB - IM MH - Bacillus cereus/*enzymology MH - Bacterial Proteins/*chemistry/metabolism MH - Chryseobacterium/*enzymology MH - Circular Dichroism MH - Models, Chemical MH - Protein Folding MH - Protein Structure, Tertiary MH - Spectrometry, Mass, Electrospray Ionization MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Substrate Specificity MH - Zinc/*chemistry/metabolism MH - beta-Lactamases/*chemistry/metabolism PMC - PMC2713538 OID - NLM: PMC2713538 EDAT- 2009/04/28 09:00 MHDA- 2009/08/21 09:00 CRDT- 2009/04/28 09:00 PHST- 2009/04/24 [aheadofprint] AID - M109.001305 [pii] AID - 10.1074/jbc.M109.001305 [doi] PST - ppublish SO - J Biol Chem. 2009 Jun 12;284(24):16419-31. doi: 10.1074/jbc.M109.001305. Epub 2009 Apr 24. PMID- 19903451 OWN - NLM STAT- MEDLINE DA - 20100127 DCOM- 20100315 LR - 20131121 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 391 IP - 1 DP - 2010 Jan 1 TI - Divalent cations induce a compaction of intrinsically disordered myelin basic protein. PG - 224-9 LID - 10.1016/j.bbrc.2009.11.036 [doi] AB - Central nervous system myelin is a dynamic entity arising from membrane processes extended from oligodendrocytes, which form a tightly-wrapped multilamellar structure around neurons. In mature myelin, the predominant splice isoform of classic MBP is 18.5kDa. In solution, MBP is an extended, intrinsically disordered protein with a large effective protein surface for myriad interactions, and possesses transient and/or induced ordered secondary structure elements for molecular association or recognition. Here, we show by nanopore analysis that the divalent cations copper and zinc induce a compaction of the extended protein in vitro, suggestive of a tertiary conformation that may reflect its arrangement in myelin. CI - Copyright 2009 Elsevier Inc. All rights reserved. FAU - Baran, Christian AU - Baran C AD - Department of Biochemistry, University of Saskatchewan, Saskatoon, Sask, Canada. FAU - Smith, Graham S T AU - Smith GS FAU - Bamm, Vladimir V AU - Bamm VV FAU - Harauz, George AU - Harauz G FAU - Lee, Jeremy S AU - Lee JS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091110 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Cations, Divalent) RN - 0 (Mbp protein, mouse) RN - 0 (Myelin Basic Protein) RN - 0 (Nerve Tissue Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) RN - 789U1901C5 (Copper) RN - J41CSQ7QDS (Zinc) SB - IM MH - Animals MH - Cations, Divalent/chemistry MH - Copper/*chemistry MH - Mice MH - Myelin Basic Protein MH - Nanostructures MH - Nerve Tissue Proteins/*chemistry/genetics MH - Porosity MH - Protein Conformation MH - Protein Folding MH - Recombinant Proteins/chemistry/genetics MH - Transcription Factors/*chemistry/genetics MH - Zinc/*chemistry EDAT- 2009/11/12 06:00 MHDA- 2010/03/17 06:00 CRDT- 2009/11/12 06:00 PHST- 2009/10/29 [received] PHST- 2009/11/05 [accepted] PHST- 2009/11/10 [aheadofprint] AID - S0006-291X(09)02196-2 [pii] AID - 10.1016/j.bbrc.2009.11.036 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2010 Jan 1;391(1):224-9. doi: 10.1016/j.bbrc.2009.11.036. Epub 2009 Nov 10. PMID- 12069524 OWN - NLM STAT- MEDLINE DA - 20020618 DCOM- 20020812 LR - 20061115 IS - 0042-6822 (Print) IS - 0042-6822 (Linking) VI - 296 IP - 2 DP - 2002 May 10 TI - The N-terminal domain of the phosphoprotein of Morbilliviruses belongs to the natively unfolded class of proteins. PG - 251-62 AB - We report the bacterial expression, purification, and characterization of the N-terminal domain (PNT) of the measles virus phosphoprotein. Using nuclear magnetic resonance, circular dichroism, gel filtration, and light scattering, we show that PNT is not structured in solution. We show by two complementary computational approaches that PNT belongs to the recently described class of natively unfolded proteins, further confirming its reported similarity with acidic activation domains of cellular transcription factors. We extend these results to the N-terminal domains of other Morbillivirus phosphoproteins and to the corresponding protein W of Sendai virus, a Paramyxovirus. Unstructured proteins may undergo some degree of folding upon binding to their partners, a process termed "induced folding." Using limited proteolysis in the presence of trifluoroethanol, we identified residues 27 to 38 as a putative secondary structure element of PNT arising upon induced folding. FAU - Karlin, David AU - Karlin D AD - Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS, Universite Aix-Marseille I et II, ESIL, Campus de Luminy, Marseille Cedex 09, France. FAU - Longhi, Sonia AU - Longhi S FAU - Receveur, Veronique AU - Receveur V FAU - Canard, Bruno AU - Canard B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Virology JT - Virology JID - 0110674 RN - 0 (P protein, Sendai virus) RN - 0 (Phosphoproteins) RN - 0 (Viral Proteins) RN - 75-89-8 (Trifluoroethanol) SB - IM MH - Chromatography, Gel/methods MH - Circular Dichroism MH - Cloning, Molecular MH - Gene Expression MH - Humans MH - Measles virus/*chemistry/genetics MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Phosphoproteins/*analysis/genetics MH - *Protein Folding MH - Trifluoroethanol MH - Viral Proteins/*analysis/genetics EDAT- 2002/06/19 10:00 MHDA- 2002/08/13 10:01 CRDT- 2002/06/19 10:00 AID - 10.1006/viro.2001.1296 [doi] AID - S0042682201912966 [pii] PST - ppublish SO - Virology. 2002 May 10;296(2):251-62. PMID- 12538889 OWN - NLM STAT- MEDLINE DA - 20030122 DCOM- 20031105 LR - 20140611 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 12 IP - 2 DP - 2003 Feb TI - Stabilization of a pH-sensitive apoptosis-linked coiled coil through single point mutations. PG - 257-65 AB - The apoptosis-associated Par-4 protein has been implicated in cancers of the prostate, colon, and kidney, and in Alzheimer's and Huntington's diseases, among other neurodegenerative disorders. Previously, we have shown that a peptide from the Par-4 C-terminus, which is responsible for Par-4 self-association as well as interaction with all currently identified effector molecules, is natively unfolded at neutral pH, but forms a tightly associated coiled coil at acidic pH and low temperature. Here, we have alternately mutated the two acidic residues predicted to participate in repulsive electrostatic interactions at the coiled coil interhelical interface. Analysis of circular dichroism spectra reveals that a dramatic alteration of the folding/unfolding equilibrium of this peptide can be effected through directed-point mutagenesis, confirming that the two acidic residues are indeed key to the pH-dependent folding behavior of the Par-4 coiled coil, and further suggesting that alleviation of charge repulsion through exposure to either a low pH microenvironment or an electrostatically complementary environment may be necessary for efficient folding of the Par-4 C-terminus. FAU - Dutta, Kaushik AU - Dutta K AD - Department of Biochemistry and Biophysics, University of Rochester Medical Center, New York 14642, USA. dutta@nysbc.org FAU - Engler, Frank A AU - Engler FA FAU - Cotton, Levaughn AU - Cotton L FAU - Alexandrov, Andrei AU - Alexandrov A FAU - Bedi, Gurrinder S AU - Bedi GS FAU - Colquhoun, Jennifer AU - Colquhoun J FAU - Pascal, Steven M AU - Pascal SM LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Apoptosis Regulatory Proteins) RN - 0 (Carrier Proteins) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (prostate apoptosis response-4 protein) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution/genetics MH - *Apoptosis MH - Apoptosis Regulatory Proteins MH - Carrier Proteins/*chemistry/*genetics/metabolism MH - Circular Dichroism MH - Hydrogen-Ion Concentration MH - *Intracellular Signaling Peptides and Proteins MH - Molecular Sequence Data MH - Point Mutation/*genetics MH - Protein Folding MH - Protein Structure, Tertiary MH - Static Electricity MH - Temperature MH - Thermodynamics PMC - PMC2312421 OID - NLM: PMC2312421 EDAT- 2003/01/23 04:00 MHDA- 2003/11/06 05:00 CRDT- 2003/01/23 04:00 AID - 10.1110/ps.0223903 [doi] PST - ppublish SO - Protein Sci. 2003 Feb;12(2):257-65. PMID- 20335168 OWN - NLM STAT- MEDLINE DA - 20100517 DCOM- 20100614 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 21 DP - 2010 May 21 TI - Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin. PG - 16267-74 LID - 10.1074/jbc.M109.074526 [doi] AB - Thermostable direct hemolysin (TDH) is a major virulence factor of Vibrio parahaemolyticus that causes pandemic foodborne enterocolitis mediated by seafood. TDH exists as a tetramer in solution, and it possesses extreme hemolytic activity. Here, we present the crystal structure of the TDH tetramer at 1.5 A resolution. The TDH tetramer forms a central pore with dimensions of 23 A in diameter and approximately 50 A in depth. Pi-cation interactions between protomers comprising the tetramer were indispensable for hemolytic activity of TDH. The N-terminal region was intrinsically disordered outside of the pore. Molecular dynamic simulations suggested that water molecules permeate freely through the central and side channel pores. Electron micrographs showed that tetrameric TDH attached to liposomes, and some of the tetramer associated with liposome via one protomer. These findings imply a novel membrane attachment mechanism by a soluble tetrameric pore-forming toxin. FAU - Yanagihara, Itaru AU - Yanagihara I AD - Department of Developmental Medicine, Research Institute, Osaka Medical Center for Maternal and Child Health, Izumi City, Osaka 594-1101, Japan. itaruy@mch.pref.osaka.jp FAU - Nakahira, Kumiko AU - Nakahira K FAU - Yamane, Tsutomu AU - Yamane T FAU - Kaieda, Shuji AU - Kaieda S FAU - Mayanagi, Kouta AU - Mayanagi K FAU - Hamada, Daizo AU - Hamada D FAU - Fukui, Takashi AU - Fukui T FAU - Ohnishi, Kiyouhisa AU - Ohnishi K FAU - Kajiyama, Shin'ichiro AU - Kajiyama S FAU - Shimizu, Toshiyuki AU - Shimizu T FAU - Sato, Mamoru AU - Sato M FAU - Ikegami, Takahisa AU - Ikegami T FAU - Ikeguchi, Mitsunori AU - Ikeguchi M FAU - Honda, Takeshi AU - Honda T FAU - Hashimoto, Hiroshi AU - Hashimoto H LA - eng SI - PDB/3A57 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100324 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - 0 (Bacterial Toxins) RN - 0 (Hemolysin Proteins) RN - 0 (Liposomes) RN - 0 (Virulence Factors) RN - 135433-21-5 (thermostable direct hemolysin) SB - IM MH - Bacterial Proteins/*chemistry/metabolism MH - Bacterial Toxins/chemistry/metabolism MH - Crystallography, X-Ray MH - Hemolysin Proteins/*chemistry/metabolism MH - Liposomes/chemistry/metabolism MH - *Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Vibrio parahaemolyticus/*chemistry/metabolism MH - Virulence Factors/*chemistry/metabolism PMC - PMC2871494 OID - NLM: PMC2871494 EDAT- 2010/03/26 06:00 MHDA- 2010/06/15 06:00 CRDT- 2010/03/26 06:00 PHST- 2010/03/24 [aheadofprint] AID - M109.074526 [pii] AID - 10.1074/jbc.M109.074526 [doi] PST - ppublish SO - J Biol Chem. 2010 May 21;285(21):16267-74. doi: 10.1074/jbc.M109.074526. Epub 2010 Mar 24. PMID- 15671169 OWN - NLM STAT- MEDLINE DA - 20050202 DCOM- 20050328 LR - 20140608 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 102 IP - 5 DP - 2005 Feb 1 TI - Release of long-range tertiary interactions potentiates aggregation of natively unstructured alpha-synuclein. PG - 1430-5 AB - In idiopathic Parkinson's disease, intracytoplasmic neuronal inclusions (Lewy bodies) containing aggregates of the protein alpha-synuclein (alphaS) are deposited in the pigmented nuclei of the brainstem. The mechanisms underlying the structural transition of innocuous, presumably natively unfolded, alphaS to neurotoxic forms are largely unknown. Using paramagnetic relaxation enhancement and NMR dipolar couplings, we show that monomeric alphaS assumes conformations that are stabilized by long-range interactions and act to inhibit oligomerization and aggregation. The autoinhibitory conformations fluctuate in the range of nanoseconds to micro-seconds corresponding to the time scale of secondary structure formation during folding. Polyamine binding and/or temperature increase, conditions that induce aggregation in vitro, release this inherent tertiary structure, leading to a completely unfolded conformation that associates readily. Stabilization of the native, autoinhibitory structure of alphaS constitutes a potential strategy for reducing or inhibiting oligomerization and aggregation in Parkinson's disease. FAU - Bertoncini, Carlos W AU - Bertoncini CW AD - Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Gottingen, Germany. FAU - Jung, Young-Sang AU - Jung YS FAU - Fernandez, Claudio O AU - Fernandez CO FAU - Hoyer, Wolfgang AU - Hoyer W FAU - Griesinger, Christian AU - Griesinger C FAU - Jovin, Thomas M AU - Jovin TM FAU - Zweckstetter, Markus AU - Zweckstetter M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050125 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Macromolecular Substances) RN - 0 (Nerve Tissue Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Anisotropy MH - Binding Sites MH - Cloning, Molecular MH - Escherichia coli MH - Humans MH - Macromolecular Substances MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Nerve Tissue Proteins/*chemistry MH - Protein Conformation MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Synucleins MH - Thermodynamics MH - alpha-Synuclein PMC - PMC547830 OID - NLM: PMC547830 EDAT- 2005/01/27 09:00 MHDA- 2005/03/29 09:00 CRDT- 2005/01/27 09:00 PHST- 2005/01/25 [aheadofprint] AID - 0407146102 [pii] AID - 10.1073/pnas.0407146102 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1430-5. Epub 2005 Jan 25. PMID- 23560717 OWN - NLM STAT- MEDLINE DA - 20130430 DCOM- 20130701 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 52 IP - 17 DP - 2013 Apr 30 TI - Conformational fluctuations of UreG, an intrinsically disordered enzyme. PG - 2949-54 LID - 10.1021/bi4001744 [doi] AB - UreG proteins are small GTP binding (G) proteins that catalyze the hydrolysis of GTP necessary for the maturation of urease, a virulence factor in bacterial pathogenesis. UreG proteins are the first documented cases of intrinsically disordered enzymes. The comprehension of the dynamics of folding-unfolding events occurring in this protein could shed light on the enzymatic mechanism of UreG. Here, we used the recently developed replica exchange with solute tempering (REST2) computational methodology to explore the conformational space of UreG from Helicobacter pylori (HpUreG) and to identify its structural fluctuations. The same simulation and analysis protocol has been applied to HypB from Methanocaldococcus jannaschii (MjHypB), which is closely related to UreG in both sequence and function, even though it is not intrinsically disordered. A comparison of the two systems reveals that both HpUreG and MjHypB feature a substantial rigidity of the protein regions involved in catalysis, justifying its residual catalytic activity. On the other hand, HpUreG tends to unfold more than MjHypB in portions involved in protein-protein interactions with metallochaperones necessary for the formation of multiprotein complexes known to be involved in urease activation. FAU - Musiani, Francesco AU - Musiani F AD - Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy. FAU - Ippoliti, Emiliano AU - Ippoliti E FAU - Micheletti, Cristian AU - Micheletti C FAU - Carloni, Paolo AU - Carloni P FAU - Ciurli, Stefano AU - Ciurli S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130418 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (ureG protein, Bacteria) SB - IM MH - Bacterial Proteins/*chemistry MH - Carrier Proteins/*chemistry MH - Methanococcaceae/chemistry MH - Models, Molecular MH - Protein Conformation EDAT- 2013/04/09 06:00 MHDA- 2013/07/03 06:00 CRDT- 2013/04/09 06:00 PHST- 2013/04/18 [aheadofprint] AID - 10.1021/bi4001744 [doi] PST - ppublish SO - Biochemistry. 2013 Apr 30;52(17):2949-54. doi: 10.1021/bi4001744. Epub 2013 Apr 18. PMID- 24909411 OWN - NLM STAT- In-Process DA - 20140609 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 4 DP - 2014 TI - Transient alpha-helices in the disordered RPEL motifs of the serum response factor coactivator MKL1. PG - 5224 LID - 10.1038/srep05224 [doi] AB - The megakaryoblastic leukemia 1 (MKL1) protein functions as a transcriptional coactivator of the serum response factor. MKL1 has three RPEL motifs (RPEL1, RPEL2, and RPEL3) in its N-terminal region. MKL1 binds to monomeric G-actin through RPEL motifs, and the dissociation of MKL1 from G-actin promotes the translocation of MKL1 to the nucleus. Although structural data are available for RPEL motifs of MKL1 in complex with G-actin, the structural characteristics of RPEL motifs in the free state have been poorly defined. Here we characterized the structures of free RPEL motifs using NMR and CD spectroscopy. NMR and CD measurements showed that free RPEL motifs are largely unstructured in solution. However, NMR analysis identified transient alpha-helices in the regions where helices alpha1 and alpha2 are induced upon binding to G-actin. Proline mutagenesis showed that the transient alpha-helices are locally formed without helix-helix interactions. The helix content is higher in the order of RPEL1, RPEL2, and RPEL3. The amount of preformed structure may correlate with the binding affinity between the intrinsically disordered protein and its target molecule. FAU - Mizuguchi, Mineyuki AU - Mizuguchi M AD - Laboratory of Structural Biology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan. FAU - Fuju, Takahiro AU - Fuju T AD - Laboratory of Structural Biology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan. FAU - Obita, Takayuki AU - Obita T AD - Laboratory of Structural Biology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan. FAU - Ishikawa, Mitsuru AU - Ishikawa M AD - 1] Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan [2]. FAU - Tsuda, Masaaki AU - Tsuda M AD - Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan. FAU - Tabuchi, Akiko AU - Tabuchi A AD - Laboratory of Molecular Neurobiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140609 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM PMC - PMC4048911 OID - NLM: PMC4048911 EDAT- 2014/06/10 06:00 MHDA- 2014/06/10 06:00 CRDT- 2014/06/10 06:00 PHST- 2014/01/31 [received] PHST- 2014/05/21 [accepted] AID - srep05224 [pii] AID - 10.1038/srep05224 [doi] PST - epublish SO - Sci Rep. 2014 Jun 9;4:5224. doi: 10.1038/srep05224. PMID- 24634806 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20140317 DCOM- 20140624 LR - 20141219 IS - 2169-0693 (Print) IS - 2169-0707 (Linking) VI - 1 IP - 1 DP - 2013 Jan 1 TI - Biophysical characterization of alpha-synuclein and its controversial structure. PG - 18-39 LID - 10.4161/idp.26255 [doi] AB - alpha-synuclein, a presynaptic protein of poorly defined function, constitutes the main component of Parkinson disease-associated Lewy bodies. Extensive biophysical investigations have provided evidence that isolated alpha-synuclein is an intrinsically disordered protein (IDP) in vitro. Subsequently serving as a model IDP in numerous studies, alpha-synuclein has aided in the development of many technologies used to characterize IDPs and arguably represents the most thoroughly analyzed IDP to date. Recent reports, however, have challenged the disordered nature of alpha-synuclein inside cells and have instead proposed a physiologically relevant helical tetramer. Despite alpha-synuclein's rich biophysical history, a single coherent picture has not yet emerged concerning its in vivo structure, dynamics, and physiological role(s). We present herein a review of the biophysical discoveries, developments, and models pertinent to the characterization of alpha-synuclein's structure and analysis of the native tetramer controversy. FAU - Alderson, T Reid AU - Alderson TR AD - Biochemistry Department; University of Wisconsin-Madison; Madison, WI USA. FAU - Markley, John L AU - Markley JL AD - Biochemistry Department; University of Wisconsin-Madison; Madison, WI USA ; National Magnetic Resonance Facility at Madison; University of Wisconsin-Madison; Madison, WI USA. LA - eng GR - P41 GM103399/GM/NIGMS NIH HHS/United States GR - U01 GM094622/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Review DEP - 20130401 PL - United States TA - Intrinsically Disord Proteins JT - Intrinsically disordered proteins JID - 101615681 PMC - PMC3908606 MID - NIHMS540079 OID - NLM: NIHMS540079 OID - NLM: PMC3908606 OTO - NOTNLM OT - Parkinson disease OT - in-cell NMR OT - molecular biophysics OT - protein structure OT - synucleopathies OT - alpha-synuclein EDAT- 2013/01/01 00:00 MHDA- 2013/01/01 00:01 CRDT- 2014/03/18 06:00 PHST- 2013/08/22 [received] PHST- 2013/08/23 [accepted] PHST- 2013/04/01 [epublish] AID - 10.4161/idp.26255 [doi] AID - 2013IDP025 [pii] PST - ppublish SO - Intrinsically Disord Proteins. 2013 Jan 1;1(1):18-39. doi: 10.4161/idp.26255. Epub 2013 Apr 1. PMID- 12695505 OWN - NLM STAT- MEDLINE DA - 20030721 DCOM- 20030826 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 30 DP - 2003 Jul 25 TI - Structural basis for the specificity of bipartite nuclear localization sequence binding by importin-alpha. PG - 27981-7 AB - Importin-alpha is the nuclear import receptor that recognizes cargo proteins carrying conventional basic monopartite and bipartite nuclear localization sequences (NLSs) and facilitates their transport into the nucleus. Bipartite NLSs contain two clusters of basic residues, connected by linkers of variable lengths. To determine the structural basis of the recognition of diverse bipartite NLSs by mammalian importin-alpha, we co-crystallized a non-autoinhibited mouse receptor protein with peptides corresponding to the NLSs from human retinoblastoma protein and Xenopus laevis phosphoprotein N1N2, containing diverse sequences and lengths of the linker. We show that the basic clusters interact analogously in both NLSs, but the linker sequences adopt different conformations, whereas both make specific contacts with the receptor. The available data allow us to draw general conclusions about the specificity of NLS binding by importin-alpha and facilitate an improved definition of the consensus sequence of a conventional basic/bipartite NLS (KRX10-12KRRK) that can be used to identify novel nuclear proteins. FAU - Fontes, Marcos R M AU - Fontes MR AD - Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 41 Victoria Parade, Fitzroy, Victoria 3065, Australia. FAU - Teh, Trazel AU - Teh T FAU - Jans, David AU - Jans D FAU - Brinkworth, Ross I AU - Brinkworth RI FAU - Kobe, Bostjan AU - Kobe B LA - eng SI - PDB/1PJM SI - PDB/1PJN PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030414 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Nuclear Localization Signals) RN - 0 (Retinoblastoma Protein) RN - 0 (alpha Karyopherins) RN - 0 (karyopherin alpha 2) RN - 7YNJ3PO35Z (Hydrogen) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Cell Nucleus/*metabolism MH - Humans MH - Hydrogen/chemistry MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - *Nuclear Localization Signals MH - Peptide Biosynthesis MH - Protein Binding MH - Protein Structure, Tertiary MH - Retinoblastoma Protein/chemistry MH - Sequence Homology, Amino Acid MH - Software MH - Xenopus laevis MH - alpha Karyopherins/*chemistry/metabolism EDAT- 2003/04/16 05:00 MHDA- 2003/08/27 05:00 CRDT- 2003/04/16 05:00 PHST- 2003/04/14 [aheadofprint] AID - 10.1074/jbc.M303275200 [doi] AID - M303275200 [pii] PST - ppublish SO - J Biol Chem. 2003 Jul 25;278(30):27981-7. Epub 2003 Apr 14. PMID- 10676813 OWN - NLM STAT- MEDLINE DA - 20000224 DCOM- 20000224 LR - 20091119 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 100 IP - 3 DP - 2000 Feb 4 TI - The crystal structure of human eukaryotic release factor eRF1--mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. PG - 311-21 AB - The release factor eRF1 terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase center. The crystal structure of human eRF1 to 2.8 A resolution, combined with mutagenesis analyses of the universal GGQ motif, reveals the molecular mechanism of release factor activity. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase center. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. FAU - Song, H AU - Song H AD - Section of Structural Biology, Institute of Cancer Research, London, United Kingdom. FAU - Mugnier, P AU - Mugnier P FAU - Das, A K AU - Das AK FAU - Webb, H M AU - Webb HM FAU - Evans, D R AU - Evans DR FAU - Tuite, M F AU - Tuite MF FAU - Hemmings, B A AU - Hemmings BA FAU - Barford, D AU - Barford D LA - eng SI - PDB/1DT9 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Cell JT - Cell JID - 0413066 RN - 0 (Codon, Terminator) RN - 0 (ETF1 protein, human) RN - 0 (Peptide Termination Factors) RN - 0 (RNA, Transfer, Amino Acyl) RN - 0 (Recombinant Proteins) RN - 0 (peptide-chain-release factor 3) RN - 0 (tRNA, peptidyl-) RN - 9014-25-9 (RNA, Transfer) SB - IM MH - Amino Acid Sequence MH - *Codon, Terminator MH - Crystallography MH - Humans MH - Hydrolysis MH - Models, Molecular MH - Molecular Mimicry MH - Molecular Sequence Data MH - *Peptide Chain Termination, Translational MH - Peptide Termination Factors/*chemistry/genetics MH - RNA, Transfer/*chemistry/metabolism MH - RNA, Transfer, Amino Acyl/*chemistry/metabolism MH - Recombinant Proteins/chemistry MH - Sequence Homology, Amino Acid EDAT- 2000/02/17 09:00 MHDA- 2000/02/26 09:00 CRDT- 2000/02/17 09:00 AID - S0092-8674(00)80667-4 [pii] PST - ppublish SO - Cell. 2000 Feb 4;100(3):311-21. PMID- 16554300 OWN - NLM STAT- MEDLINE DA - 20060605 DCOM- 20060823 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 23 DP - 2006 Jun 9 TI - Control of intrinsically disordered stathmin by multisite phosphorylation. PG - 16078-83 AB - Stathmin is an intrinsically disordered protein implicated in the regulation of microtubule dynamics and in the development of cancer. The microtubule destabilizing activity of stathmin is down-regulated by phosphorylation of four serine residues, Ser16, Ser25, Ser38, and Ser63. Here we have used calorimetric and spectroscopic methods, including nuclear magnetic resonance to analyze the properties of seven stathmin phosphoisoforms to bind tubulin and inhibit microtubule formation. We found that stathmin phosphorylation results in a substantial loss in hydration entropy upon tubulin-stathmin complex formation. Remarkably, a linear correlation between the free energy change of complex formation and the microtubule inhibition activities of stathmin phosphoisoforms was observed. This finding provides a biophysical basis for understanding the mechanism by which local stathmin activity gradients important for promoting localized microtubule growth are established. We further found that phosphorylation of Ser16 and Ser63 disrupts the formation of a tubulin-interacting beta-hairpin and a helical segment, respectively, explaining the dominant role of these residues in regulating cell cycle progression. The insight into the tubulin-stathmin interaction offers a molecular basis for understanding the nature and the factors that control intrinsically disordered protein systems in general. FAU - Honnappa, Srinivas AU - Honnappa S AD - Biomolecular Research, Structural Biology, Paul Scherrer Insititut, CH-5232 Villigen PSI, Switzerland. FAU - Jahnke, Wolfgang AU - Jahnke W FAU - Seelig, Joachim AU - Seelig J FAU - Steinmetz, Michel O AU - Steinmetz MO LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060322 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Stathmin) SB - IM MH - Circular Dichroism MH - Humans MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphorylation MH - Stathmin/*metabolism MH - Thermodynamics EDAT- 2006/03/24 09:00 MHDA- 2006/08/24 09:00 CRDT- 2006/03/24 09:00 PHST- 2006/03/22 [aheadofprint] AID - M513524200 [pii] AID - 10.1074/jbc.M513524200 [doi] PST - ppublish SO - J Biol Chem. 2006 Jun 9;281(23):16078-83. Epub 2006 Mar 22. PMID- 20476778 OWN - NLM STAT- MEDLINE DA - 20100622 DCOM- 20100721 LR - 20140917 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 25 DP - 2010 Jun 29 TI - Osmolyte-induced folding of an intrinsically disordered protein: folding mechanism in the absence of ligand. PG - 5086-96 LID - 10.1021/bi100222h [doi] AB - Understanding the interconversion between thermodynamically distinguishable states present in a protein folding pathway provides not only the kinetics and energetics of protein folding but also insights into the functional roles of these states in biological systems. The protein component of the bacterial RNase P holoenzyme from Bacillus subtilis (P protein) was previously shown to be unfolded in the absence of its cognate RNA or other anionic ligands. P protein was used in this study as a model system to explore general features of intrinsically disordered protein (IDP) folding mechanisms. The use of trimethylamine N-oxide (TMAO), an osmolyte that stabilizes the unliganded folded form of the protein, enabled us to study the folding process of P protein in the absence of ligand. Transient stopped-flow kinetic traces at various final TMAO concentrations exhibited multiphasic kinetics. Equilibrium "cotitration" experiments were performed using both TMAO and urea during the titration to produce a urea-TMAO titration surface of P protein. Both kinetic and equilibrium studies show evidence of a previously undetected intermediate state in the P protein folding process. The intermediate state is significantly populated, and the folding rate constants are relatively slow compared to those of intrinsically folded proteins similar in size and topology. The experiments and analysis described serve as a useful example for mechanistic folding studies of other IDPs. FAU - Chang, Yu-Chu AU - Chang YC AD - Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, North Carolina 27710, USA. FAU - Oas, Terrence G AU - Oas TG LA - eng GR - 5R01GM061367/GM/NIGMS NIH HHS/United States GR - 5R01GM081666/GM/NIGMS NIH HHS/United States GR - R01 GM061367/GM/NIGMS NIH HHS/United States GR - R01 GM061367-04/GM/NIGMS NIH HHS/United States GR - R01 GM081666/GM/NIGMS NIH HHS/United States GR - R01 GM081666-01A2/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (Ligands) RN - 0 (Methylamines) RN - 8DUH1N11BX (Tryptophan) RN - FLD0K1SJ1A (trimethyloxamine) SB - IM MH - Bacillus subtilis/chemistry MH - Bacterial Proteins/*chemistry MH - Circular Dichroism MH - Kinetics MH - Ligands MH - Methylamines/chemistry MH - *Protein Folding MH - Spectrometry, Fluorescence MH - Thermodynamics MH - Tryptophan/chemistry PMC - PMC2937257 MID - NIHMS212292 OID - NLM: NIHMS212292 OID - NLM: PMC2937257 EDAT- 2010/05/19 06:00 MHDA- 2010/07/22 06:00 CRDT- 2010/05/19 06:00 AID - 10.1021/bi100222h [doi] PST - ppublish SO - Biochemistry. 2010 Jun 29;49(25):5086-96. doi: 10.1021/bi100222h. PMID- 20434955 OWN - NLM STAT- MEDLINE DA - 20100726 DCOM- 20111205 LR - 20140827 IS - 1873-281X (Electronic) IS - 1472-9792 (Linking) VI - 90 IP - 4 DP - 2010 Jul TI - Solution structure of Rv2377c-founding member of the MbtH-like protein family. PG - 245-51 LID - 10.1016/j.tube.2010.04.002 [doi] AB - The Mycobacterium tuberculosis protein Rv2377c (71 residues, MW=8.4kDa) has been characterized using nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. Rv2377c was the first identified member of the MbtH-like family of proteins. MbtH-like proteins have been implicated in siderophore biosynthesis, however, their precise biochemical function remain unknown. Size exclusion chromatography and NMR spectroscopy show that Rv2377c is a monomer in solution. Circular dichroism spectroscopy indicates that Rv2377c unfolds upon heating and will reversibly fold into its native conformation upon cooling. Using NMR-based methods the solution structure of Rv2377c was determined and some of the dynamic properties of the protein studied. The protein contains a three-strand, anti-parallel beta-sheet (beta3:beta1:beta2) nestled against one C-terminal alpha-helix (S44-N55). Weak or absent amide cross peaks in the (1)H-(15)N HSQC spectrum for many of the beta1 and beta2 residues suggest intermediate motion on the ms to mus time scale at the beta1:beta2 interface. Amide cross peaks in the (1)H-(15)N HSQC spectrum are absent for all but one residue at the C-terminus (W56-D71), a region that includes a highly conserved sequence WXDXR, suggesting this region is intrinsically disordered. The latter observation differs with the crystal structure of another MbtH-like protein, PA2412 from Pseudomonas aeruginosa, where a second ordered alpha-helix was observed at the extreme C-terminus. FAU - Buchko, Garry W AU - Buchko GW AD - Pacific Northwest National Laboratory, Richland, WA 99352, USA. garry.buchko@pnl.gov FAU - Kim, Chang-Yub AU - Kim CY FAU - Terwilliger, Thomas C AU - Terwilliger TC FAU - Myler, Peter J AU - Myler PJ LA - eng GR - HHSN272200700057C/PHS HHS/United States GR - HHSN272200700057C/PHS HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - Scotland TA - Tuberculosis (Edinb) JT - Tuberculosis (Edinburgh, Scotland) JID - 100971555 RN - 0 (Bacterial Proteins) RN - 0 (Siderophores) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*genetics/physiology MH - Circular Dichroism MH - Conserved Sequence MH - Magnetic Resonance Spectroscopy/methods MH - Models, Molecular MH - Molecular Sequence Data MH - Mycobacterium tuberculosis/*genetics/metabolism MH - Protein Folding MH - Protein Structure, Secondary MH - Sequence Alignment MH - Siderophores MH - Structure-Activity Relationship PMC - PMC2910232 MID - NIHMS198161 OID - NLM: NIHMS198161 OID - NLM: PMC2910232 EDAT- 2010/05/04 06:00 MHDA- 2011/12/13 00:00 CRDT- 2010/05/04 06:00 PHST- 2010/01/27 [received] PHST- 2010/04/06 [revised] PHST- 2010/04/08 [accepted] AID - S1472-9792(10)00046-6 [pii] AID - 10.1016/j.tube.2010.04.002 [doi] PST - ppublish SO - Tuberculosis (Edinb). 2010 Jul;90(4):245-51. doi: 10.1016/j.tube.2010.04.002. PMID- 21620710 OWN - NLM STAT- MEDLINE DA - 20110812 DCOM- 20111130 IS - 0968-0004 (Print) IS - 0968-0004 (Linking) VI - 36 IP - 8 DP - 2011 Aug TI - Dynamic protein-DNA recognition: beyond what can be seen. PG - 415-23 LID - 10.1016/j.tibs.2011.04.006 [doi] AB - Traditionally, specific DNA recognition is thought to rely on static contacts with the bases or phosphates. Recent results, however, indicate that residues far outside the binding context can crucially influence selectivity or binding affinity via transient, dynamic interactions with the DNA binding interface. These regions usually do not adopt a well-defined structure, even when bound to DNA, and thus form a fuzzy complex. Here, we propose the existence of a dynamic DNA readout mechanism, wherein distant segments modulate conformational preferences, flexibility or spacing of the DNA binding motifs or serve as competitive partners. Despite their low sequence similarity, these intrinsically disordered regions are often conserved at the structural level, and exploited for regulation of the transcription machinery via protein-protein interactions, post-translational modifications or alternative splicing. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Fuxreiter, Monika AU - Fuxreiter M AD - Department of Biological Chemistry, Weizmann Institute of Science, 7600 Rehovot, Israel. monika@enzim.hu FAU - Simon, Istvan AU - Simon I FAU - Bondos, Sarah AU - Bondos S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20110527 PL - England TA - Trends Biochem Sci JT - Trends in biochemical sciences JID - 7610674 RN - 0 (DNA-Binding Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Alternative Splicing/*genetics MH - DNA/chemistry/*genetics MH - DNA-Binding Proteins/genetics MH - Nucleic Acid Conformation MH - Protein Binding/genetics MH - Protein Conformation MH - Protein Interaction Domains and Motifs/*genetics MH - Protein Processing, Post-Translational/*genetics MH - Regulatory Sequences, Nucleic Acid/*genetics EDAT- 2011/05/31 06:00 MHDA- 2011/12/13 00:00 CRDT- 2011/05/31 06:00 PHST- 2011/01/08 [received] PHST- 2011/04/15 [revised] PHST- 2011/04/15 [accepted] PHST- 2011/05/27 [aheadofprint] AID - S0968-0004(11)00059-4 [pii] AID - 10.1016/j.tibs.2011.04.006 [doi] PST - ppublish SO - Trends Biochem Sci. 2011 Aug;36(8):415-23. doi: 10.1016/j.tibs.2011.04.006. Epub 2011 May 27. PMID- 24043820 OWN - NLM STAT- MEDLINE DA - 20131002 DCOM- 20131203 LR - 20141112 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 110 IP - 40 DP - 2013 Oct 1 TI - Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein. PG - E3743-52 LID - 10.1073/pnas.1308381110 [doi] AB - Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as molecular recognition elements (MoREs). They fold into ordered structures upon binding to their partner molecules. Currently, there is still a lack of in-depth understanding of how coupled binding and folding occurs in MoREs. Here, we quantified the unbound ensembles of the alpha-MoRE within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein. We developed a multiscaled approach by combining a physics-based and an atomic hybrid model to decipher the mechanism by which the alpha-MoRE interacts with the X domain of the measles virus phosphoprotein. Our multiscaled approach led to remarkable qualitative and quantitative agreements between the theoretical predictions and experimental results (e.g., chemical shifts). We found that the free alpha-MoRE rapidly interconverts between multiple discrete partially helical conformations and the unfolded state, in accordance with the experimental observations. We quantified the underlying global folding-binding landscape. This leads to a synergistic mechanism in which the recognition event proceeds via (minor) conformational selection, followed by (major) induced folding. We also provided evidence that the alpha-MoRE is a compact molten globule-like IDP and behaves as a downhill folder in the induced folding process. We further provided a theoretical explanation for the inherent connections between "downhill folding," "molten globule," and "intrinsic disorder" in IDP-related systems. Particularly, we proposed that binding and unbinding of IDPs proceed in a stepwise way through a "kinetic divide-and-conquer" strategy that confers them high specificity without high affinity. FAU - Wang, Yong AU - Wang Y AD - State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China. FAU - Chu, Xiakun AU - Chu X FAU - Longhi, Sonia AU - Longhi S FAU - Roche, Philippe AU - Roche P FAU - Han, Wei AU - Han W FAU - Wang, Erkang AU - Wang E FAU - Wang, Jin AU - Wang J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130916 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Nucleoproteins) RN - 0 (Viral Proteins) RN - 0 (nucleoprotein, Measles virus) SB - IM CIN - Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1557-8. PMID: 24639541 CIN - Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1559. PMID: 24877227 MH - Biophysics MH - Kinetics MH - Measles virus/*chemistry MH - *Models, Molecular MH - Molecular Dynamics Simulation MH - Nucleoproteins/*chemistry MH - Protein Binding MH - *Protein Conformation MH - *Protein Folding MH - Viral Proteins/*chemistry PMC - PMC3791790 OID - NLM: PMC3791790 OTO - NOTNLM OT - flexible binding OT - flexible recognition OT - free-energy surface OT - hybrid structure-based model OT - multiscale simulation EDAT- 2013/09/18 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/09/18 06:00 PHST- 2013/09/16 [aheadofprint] AID - 1308381110 [pii] AID - 10.1073/pnas.1308381110 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):E3743-52. doi: 10.1073/pnas.1308381110. Epub 2013 Sep 16. PMID- 11719810 OWN - NLM STAT- MEDLINE DA - 20011123 DCOM- 20011220 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 414 IP - 6862 DP - 2001 Nov 22 TI - Crystal structure of the tricorn protease reveals a protein disassembly line. PG - 466-70 AB - The degradation of cytosolic proteins is carried out predominantly by the proteasome, which generates peptides of 7-9 amino acids long. These products need further processing. Recently, a proteolytic system was identified in the model organism Thermoplasma acidophilum that performs this processing. The hexameric core protein of this modular system, referred to as tricorn protease, is a 720K protease that is able to assemble further into a giant icosahedral capsid, as determined by electron microscopy. Here, we present the crystal structure of the tricorn protease at 2.0 A resolution. The structure reveals a complex mosaic protein whereby five domains combine to form one of six subunits, which further assemble to form the 3-2-symmetric core protein. The structure shows how the individual domains coordinate the specific steps of substrate processing, including channelling of the substrate to, and the product from, the catalytic site. Moreover, the structure shows how accessory protein components might contribute to an even more complex protein machinery that efficiently collects the tricorn-released products. FAU - Brandstetter, H AU - Brandstetter H FAU - Kim, J S AU - Kim JS FAU - Groll, M AU - Groll M FAU - Huber, R AU - Huber R LA - eng SI - PDB/1K32 PT - Journal Article PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Archaeal Proteins) RN - EC 3.4.- (Endopeptidases) RN - EC 3.4.- (tricorn protease) SB - IM MH - Archaeal Proteins/*chemistry/genetics/metabolism MH - Binding Sites MH - Catalysis MH - Cloning, Molecular MH - Crystallography, X-Ray MH - Endopeptidases/*chemistry/genetics/metabolism MH - Escherichia coli MH - Models, Molecular MH - Protein Conformation MH - Substrate Specificity MH - Thermoplasma/*enzymology/genetics EDAT- 2001/11/24 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/11/24 10:00 AID - 10.1038/35106609 [doi] AID - 35106609 [pii] PST - ppublish SO - Nature. 2001 Nov 22;414(6862):466-70. PMID- 9236009 OWN - NLM STAT- MEDLINE DA - 19970902 DCOM- 19970902 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 36 IP - 31 DP - 1997 Aug 5 TI - The exchangeable yeast ribosomal acidic protein YP2beta shows characteristics of a partly folded state under physiological conditions. PG - 9625-35 AB - The eukaryotic acidic ribosomal P proteins, contrary to the standard r-proteins which are rapidly degraded in the cytoplasm, are found forming a large cytoplasmic pool that exchanges with the ribosome-bound proteins during translation. The native structure of the P proteins in solution is therefore an essential determinant of the protein-protein interactions that take place in the exchange process. In this work, the structure of the ribosomal acidic protein YP2beta from Saccharomyces cerevisiae has been investigated by fluorescence spectroscopy, circular dichroism (CD), nuclear magnetic resonance (NMR), and sedimentation equilibrium techniques. We have established the fact that YP2beta bears a 22% alpha-helical secondary structure and a noncompact tertiary structure under physiological conditions (pH 7.0 and 25 degrees C); the hydrophobic core of the protein appears to be solvent-exposed, and very low cooperativity is observed for heat- or urea-induced denaturation. Moreover, the 1H-NMR spectra show a small signal dispersion, and virtually all the amide protons exchange with the solvent on a very short time scale, which is characteristic of an open structure. At low pH, YP2beta maintains its secondary structure content, but there is no evidence for tertiary structure. 2,2,2-Trifluoroethanol (TFE) induces a higher amount of alpha-helical structure but also disrupts any trace of the remaining tertiary fold. These results indicate that YP2beta may have a flexible structure in the cytoplasmic pool, with some of the characteristics of a "molten globule", and also point out the physiological relevance of such flexible protein states in processes other than protein folding. FAU - Zurdo, J AU - Zurdo J AD - Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autonoma de Madrid, 28049 Madrid, Spain. FAU - Sanz, J M AU - Sanz JM FAU - Gonzalez, C AU - Gonzalez C FAU - Rico, M AU - Rico M FAU - Ballesta, J P AU - Ballesta JP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (RPP2B protein, S cerevisiae) RN - 0 (Ribosomal Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 8W8T17847W (Urea) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Hot Temperature MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Denaturation MH - Protein Folding MH - Ribosomal Proteins/*chemistry MH - Saccharomyces cerevisiae/*chemistry MH - Saccharomyces cerevisiae Proteins MH - Sequence Homology, Amino Acid MH - Spectrometry, Fluorescence MH - Urea/chemistry EDAT- 1997/08/05 MHDA- 1997/08/05 00:01 CRDT- 1997/08/05 00:00 AID - 10.1021/bi9702400 [doi] AID - bi9702400 [pii] PST - ppublish SO - Biochemistry. 1997 Aug 5;36(31):9625-35. PMID- 21237164 OWN - NLM STAT- MEDLINE DA - 20110131 DCOM- 20110317 LR - 20131121 IS - 1873-3468 (Electronic) IS - 0014-5793 (Linking) VI - 585 IP - 3 DP - 2011 Feb 4 TI - The role of the C-terminus of human alpha-synuclein: intra-disulfide bonds between the C-terminus and other regions stabilize non-fibrillar monomeric isomers. PG - 561-6 LID - 10.1016/j.febslet.2011.01.009 [doi] AB - Substantial evidence implicates that the aggregation of alpha-synuclein (alphaSyn) is a critical factor in the pathogenesis of Parkinson's disease. This study focuses on the role of alphaSyn C-terminus. We introduced two additional cysteine residues at positions 107 and 124 (A107C and A124C) to our previous construct. Five X-isomers of oxidative-folded mutation of alpha-synuclein with three disulfides were isolated and their secondary structures and aggregating features were analyzed. All isomers showed similar random coil structures as wild-type alpha-synuclein. However, these isomers did not form aggregates or fibrils, even with prolonged incubation, suggesting that the interactions between the C-terminal and N-terminal or central NAC region are important in maintaining the natively unfolded structure of alphaSyn and thus prevent alphaSyn from changing conformation, which is a critical step for fibrillation. CI - Published by Elsevier B.V. FAU - Hong, Dong-Pyo AU - Hong DP AD - Research Center for Protein Chemistry, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA. FAU - Xiong, Wei AU - Xiong W FAU - Chang, Jui-Yoa AU - Chang JY FAU - Jiang, Chuantao AU - Jiang C LA - eng GR - 00486855/PHS HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20110114 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Fluorescent Dyes) RN - 0 (Mutant Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SNCA protein, human) RN - 0 (Thiazoles) RN - 0 (alpha-Synuclein) RN - 2390-54-7 (thioflavin T) RN - 48TCX9A1VT (Cystine) RN - K848JZ4886 (Cysteine) SB - IM MH - Circular Dichroism MH - Cysteine/chemistry MH - Cystine/*chemistry MH - Fluorescent Dyes/chemistry MH - Humans MH - Isomerism MH - Kinetics MH - Mutagenesis, Site-Directed MH - Mutant Proteins/chemistry MH - Oxidation-Reduction MH - Parkinson Disease/physiopathology MH - Protein Denaturation MH - Protein Folding MH - Protein Stability MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry MH - Spectrometry, Fluorescence MH - Thiazoles/chemistry MH - alpha-Synuclein/*chemistry/genetics EDAT- 2011/01/18 06:00 MHDA- 2011/03/18 06:00 CRDT- 2011/01/18 06:00 PHST- 2010/12/17 [received] PHST- 2011/01/03 [accepted] PHST- 2011/01/14 [aheadofprint] AID - S0014-5793(11)00030-5 [pii] AID - 10.1016/j.febslet.2011.01.009 [doi] PST - ppublish SO - FEBS Lett. 2011 Feb 4;585(3):561-6. doi: 10.1016/j.febslet.2011.01.009. Epub 2011 Jan 14. PMID- 17604643 OWN - NLM STAT- MEDLINE DA - 20070730 DCOM- 20070917 IS - 1044-0305 (Print) IS - 1044-0305 (Linking) VI - 18 IP - 8 DP - 2007 Aug TI - Electrospray ionization mass spectra of acyl carrier protein are insensitive to its solution phase conformation. PG - 1525-32 AB - Electrospray ionization mass spectrometry (ESI-MS) can be used to monitor conformational changes of proteins in solution based on the charge state distribution (CSD) of the corresponding gas-phase ions, although relatively few studies of acidic proteins have been reported. Here, we have compared the CSD and solution structure of recombinant Vibrio harveyi acyl carrier protein (rACP), a small acidic protein whose secondary and tertiary structure can be manipulated by pH, fatty acylation, and site-directed mutagenesis. Circular dichroism and intrinsic fluorescence demonstrated that apo-rACP adopts a folded helical conformation in aqueous solution below pH 6 or in 50% acetonitrile/0.1% formic acid, but is unfolded at neutral and basic pH values. A rACP mutant, in which seven conserved acidic residues were replaced with their corresponding neutral amides, was folded over the entire pH range of 5 to 9. However, under the same solvent conditions, both wild type and mutant ACPs exhibited similar CSDs (6(+)-9(+) species) at all pH values. Covalent attachment of myristic acid to the phosphopantetheine prosthetic group of rACP, which is known to stabilize a folded conformation in solution, also had little influence on its CSD in either positive or negative ion modes. Overall, our results are consistent with ACP as a "natively unfolded" protein in a dynamic conformational equilibrium, which allows access to (de)protonation events during the electrospray process. FAU - Murphy, Peter W AU - Murphy PW AD - Atlantic Research Centre, Department of Pediatrics, Halifax, Nova Scotia, Canada. FAU - Rowland, Elden E AU - Rowland EE FAU - Byers, David M AU - Byers DM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070524 PL - United States TA - J Am Soc Mass Spectrom JT - Journal of the American Society for Mass Spectrometry JID - 9010412 RN - 0 (Acyl Carrier Protein) RN - 0 (Bacterial Proteins) SB - IM MH - Acyl Carrier Protein/*chemistry/genetics MH - Bacterial Proteins/*chemistry/genetics MH - Hydrogen-Ion Concentration MH - Protein Conformation MH - Spectrometry, Mass, Electrospray Ionization/*methods MH - Vibrio/*chemistry/genetics EDAT- 2007/07/03 09:00 MHDA- 2007/09/18 09:00 CRDT- 2007/07/03 09:00 PHST- 2007/01/15 [received] PHST- 2007/05/21 [revised] PHST- 2007/05/23 [accepted] PHST- 2007/05/24 [aheadofprint] AID - S1044-0305(07)00434-5 [pii] AID - 10.1016/j.jasms.2007.05.012 [doi] PST - ppublish SO - J Am Soc Mass Spectrom. 2007 Aug;18(8):1525-32. Epub 2007 May 24. PMID- 11673426 OWN - NLM STAT- MEDLINE DA - 20011023 DCOM- 20011204 LR - 20140613 IS - 0021-9193 (Print) IS - 0021-9193 (Linking) VI - 183 IP - 22 DP - 2001 Nov TI - Differential effects of replacing Escherichia coli ribosomal protein L27 with its homologue from Aquifex aeolicus. PG - 6565-72 AB - The rpmA gene, which encodes 50S ribosomal subunit protein L27, was cloned from the extreme thermophile Aquifex aeolicus, and the protein was overexpressed and purified. Comparison of the A. aeolicus protein with its homologue from Escherichia coli by circular dichroism analysis and proton nuclear magnetic resonance spectroscopy showed that it readily adopts some structure in solution that is very stable, whereas the E. coli protein is unstructured under the same conditions. A mutant of E. coli that lacks L27 was found earlier to be impaired in the assembly and function of the 50S subunit; both defects could be corrected by expression of E. coli L27 from an extrachromosomal copy of the rpmA gene. When A. aeolicus L27 was expressed in the same mutant, an increase in the growth rate occurred and the "foreign" L27 protein was incorporated into E. coli ribosomes. However, the presence of A. aeolicus L27 did not promote 50S subunit assembly. Thus, while the A. aeolicus protein can apparently replace its E. coli homologue functionally in completed ribosomes, it does not assist in the assembly of E. coli ribosomes that otherwise lack L27. Possible explanations for this paradoxical behavior are discussed. FAU - Maguire, B A AU - Maguire BA AD - Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA. FAU - Manuilov, A V AU - Manuilov AV FAU - Zimmermann, R A AU - Zimmermann RA LA - eng GR - GM22807/GM/NIGMS NIH HHS/United States GR - T32 GM08515/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - J Bacteriol JT - Journal of bacteriology JID - 2985120R RN - 0 (Bacterial Proteins) RN - 0 (Membrane Proteins) RN - 0 (Ribosomal Proteins) RN - 0 (RpmA protein, Pseudomonas aeruginosa) RN - 0 (ribosomal proteins L27) SB - IM MH - Amino Acid Sequence MH - *Bacterial Proteins MH - Circular Dichroism MH - Escherichia coli/*genetics/growth & development MH - Gram-Negative Aerobic Rods and Cocci/*genetics MH - Magnetic Resonance Spectroscopy MH - Membrane Proteins/genetics MH - Molecular Sequence Data MH - Mutation MH - Ribosomal Proteins/*genetics/isolation & purification MH - Ribosomes/chemistry MH - Sequence Alignment MH - Transformation, Bacterial PMC - PMC95487 OID - NLM: PMC95487 EDAT- 2001/10/24 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/10/24 10:00 AID - 10.1128/JB.183.22.6565-6572.2001 [doi] PST - ppublish SO - J Bacteriol. 2001 Nov;183(22):6565-72. PMID- 20368466 OWN - NLM STAT- MEDLINE DA - 20100421 DCOM- 20100527 LR - 20140915 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 107 IP - 16 DP - 2010 Apr 20 TI - Structural and functional analysis of the YAP-binding domain of human TEAD2. PG - 7293-8 LID - 10.1073/pnas.1000293107 [doi] AB - The Hippo pathway controls organ size and suppresses tumorigenesis in metazoans by blocking cell proliferation and promoting apoptosis. The TEAD1-4 proteins (which contain a DNA-binding domain but lack an activation domain) interact with YAP (which lacks a DNA-binding domain but contains an activation domain) to form functional heterodimeric transcription factors that activate proliferative and prosurvival gene expression programs. The Hippo pathway inhibits the YAP-TEAD hybrid transcription factors by phosphorylating and promoting cytoplasmic retention of YAP. Here we report the crystal structure of the YAP-binding domain (YBD) of human TEAD2. TEAD2 YBD adopts an immunoglobulin-like beta-sandwich fold with two extra helix-turn-helix inserts. NMR studies reveal that the TEAD-binding domain of YAP is natively unfolded and that TEAD binding causes localized conformational changes in YAP. In vitro binding and in vivo functional assays define an extensive conserved surface of TEAD2 YBD as the YAP-binding site. Therefore, our studies suggest that a short segment of YAP adopts an extended conformation and forms extensive contacts with a rigid surface of TEAD. Targeting a surface-exposed pocket of TEAD might be an effective strategy to disrupt the YAP-TEAD interaction and to reduce the oncogenic potential of YAP. FAU - Tian, Wei AU - Tian W AD - Departmentsof Pharmacology and Biochemistry, The University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA. FAU - Yu, Jianzhong AU - Yu J FAU - Tomchick, Diana R AU - Tomchick DR FAU - Pan, Duojia AU - Pan D FAU - Luo, Xuelian AU - Luo X LA - eng SI - PDB/3L15 GR - EY015708/EY/NEI NIH HHS/United States GR - GM085004/GM/NIGMS NIH HHS/United States GR - R01 EY015708/EY/NEI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20100405 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA-Binding Proteins) RN - 0 (TEAD2 protein, human) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Cytoplasm/metabolism MH - DNA/chemistry MH - DNA-Binding Proteins/*chemistry MH - Dimerization MH - Humans MH - Molecular Sequence Data MH - Phosphorylation MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Signal Transduction MH - Surface Properties MH - Transcription Factors/*chemistry PMC - PMC2867681 OID - NLM: PMC2867681 EDAT- 2010/04/07 06:00 MHDA- 2010/05/28 06:00 CRDT- 2010/04/07 06:00 PHST- 2010/04/05 [aheadofprint] AID - 1000293107 [pii] AID - 10.1073/pnas.1000293107 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7293-8. doi: 10.1073/pnas.1000293107. Epub 2010 Apr 5. PMID- 23566202 OWN - NLM STAT- MEDLINE DA - 20130507 DCOM- 20130705 LR - 20141116 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 52 IP - 18 DP - 2013 May 7 TI - The intrinsically disordered membrane protein selenoprotein S is a reductase in vitro. PG - 3051-61 LID - 10.1021/bi4001358 [doi] AB - Selenoprotein S (SelS or VIMP) is an intrinsically disordered membrane enzyme that provides protection against reactive oxidative species. SelS is a member of the endoplasmic reticulum-associated protein degradation pathway, but its precise enzymatic function is unknown. Because it contains the rare amino acid selenocysteine, it belongs to the family of selenoproteins, which are typically oxidoreductases. Its exact enzymatic function is key to understanding how the cell regulates the response to oxidative stress and thus influences human health and aging. To identify its enzymatic function, we have isolated the selenocysteine-containing enzyme by relying on the aggregation of forms that do not have this reactive residue. That allows us to establish that SelS is primarily a thioredoxin-dependent reductase. It is capable of reducing hydrogen peroxide but is not an efficient or broad-spectrum peroxidase. Only the selenocysteine-containing enzyme is active. In addition, the reduction potential of SelS was determined to be -234 mV using electrospray ionization mass spectrometry. This value is consistent with SelS being a partner of thioredoxin. On the basis of this information, SelS can directly combat reactive oxygen species but is also likely to participate in a signaling pathway, via a yet unidentified substrate. FAU - Liu, Jun AU - Liu J AD - Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA. FAU - Li, Fei AU - Li F FAU - Rozovsky, Sharon AU - Rozovsky S LA - eng GR - 5P30RR031160-03/RR/NCRR NIH HHS/United States GR - 8 P30 GM103519-03/GM/NIGMS NIH HHS/United States GR - P30 RR031160/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130424 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Membrane Proteins) RN - 0 (Selenoproteins) SB - IM MH - Circular Dichroism MH - Cloning, Molecular MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - Kinetics MH - Membrane Proteins/chemistry/*metabolism MH - Oxidation-Reduction MH - Plasmids MH - Selenoproteins/chemistry/*metabolism MH - Spectrometry, Mass, Electrospray Ionization PMC - PMC3675161 MID - NIHMS468064 OID - NLM: NIHMS468064 OID - NLM: PMC3675161 EDAT- 2013/04/10 06:00 MHDA- 2013/07/06 06:00 CRDT- 2013/04/10 06:00 PHST- 2013/04/24 [aheadofprint] AID - 10.1021/bi4001358 [doi] PST - ppublish SO - Biochemistry. 2013 May 7;52(18):3051-61. doi: 10.1021/bi4001358. Epub 2013 Apr 24. PMID- 24218616 OWN - NLM STAT- MEDLINE DA - 20131127 DCOM- 20140127 LR - 20141112 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 110 IP - 48 DP - 2013 Nov 26 TI - Structural and functional insights into the regulation mechanism of CK2 by IP6 and the intrinsically disordered protein Nopp140. PG - 19360-5 LID - 10.1073/pnas.1304670110 [doi] AB - Protein kinase CK2 is a ubiquitous kinase that can phosphorylate hundreds of cellular proteins and plays important roles in cell growth and development. Deregulation of CK2 is related to a variety of human cancers, and CK2 is regarded as a suppressor of apoptosis; therefore, it is a target of anticancer therapy. Nucleolar phosphoprotein 140 (Nopp140), which is an intrinsically disordered protein, interacts with CK2 and inhibits the latter's catalytic activity in vitro. Interestingly, the catalytic activity of CK2 is recovered in the presence of d-myo-inositol 1,2,3,4,5,6-hexakisphosphate (IP6). IP6 is widely distributed in animal cells, but the molecular mechanisms that govern its cellular functions in animal cells have not been completely elucidated. In this study, the crystal structure of CK2 in complex with IP6 showed that the lysine-rich cluster of CK2 plays an important role in binding to IP6. The biochemical experiments revealed that a Nopp140 fragment (residues 568-596) and IP6 competitively bind to the catalytic subunit of CK2 (CK2alpha), and phospho-Ser574 of Nopp140 significantly enhances its interaction with CK2alpha. Substitutions of K74E, K76E, and K77E in CK2alpha significantly reduced the interactions of CK2alpha with both IP6 and the Nopp140-derived peptide. Our study gives an insight into the regulation of CK2. In particular, our work suggests that CK2 activity is inhibited by Nopp140 and reactivated by IP6 by competitive binding at the substrate recognition site of CK2. FAU - Lee, Won-Kyu AU - Lee WK AD - Departments of Bio and Nano Chemistry and Integrative Biomedical Science and Engineering, Kookmin University, Seoul 136-702, Korea. FAU - Son, Sang Hyeon AU - Son SH FAU - Jin, Bong-Suk AU - Jin BS FAU - Na, Jung-Hyun AU - Na JH FAU - Kim, Soo-Youl AU - Kim SY FAU - Kim, Kook-Han AU - Kim KH FAU - Kim, Eunice Eunkyeong AU - Kim EE FAU - Yu, Yeon Gyu AU - Yu YG FAU - Lee, Hyung Ho AU - Lee HH LA - eng SI - PDB/3W8L PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131111 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Macromolecular Substances) RN - 0 (NOLC1 protein, human) RN - 0 (Nuclear Proteins) RN - 0 (Phosphoproteins) RN - 7IGF0S7R8I (Phytic Acid) RN - EC 2.7.11.1 (Casein Kinase II) SB - IM MH - Amino Acid Substitution MH - Casein Kinase II/*chemistry/*metabolism MH - Crystallization MH - Gene Expression Regulation/*physiology MH - Humans MH - Macromolecular Substances/*chemistry MH - *Models, Molecular MH - Nuclear Proteins/*chemistry/metabolism MH - Phosphoproteins/*chemistry/metabolism MH - Phytic Acid/*chemistry/metabolism MH - Protein Conformation MH - X-Ray Diffraction PMC - PMC3845154 OID - NLM: PMC3845154 OTO - NOTNLM OT - IDP OT - inositol hexakisphosphate OT - phosphorylation EDAT- 2013/11/13 06:00 MHDA- 2014/01/28 06:00 CRDT- 2013/11/13 06:00 PHST- 2013/11/11 [aheadofprint] AID - 1304670110 [pii] AID - 10.1073/pnas.1304670110 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):19360-5. doi: 10.1073/pnas.1304670110. Epub 2013 Nov 11. PMID- 19851073 OWN - NLM STAT- MEDLINE DA - 20100317 DCOM- 20100513 LR - 20131121 IS - 1423-0097 (Electronic) IS - 1018-2438 (Linking) VI - 151 IP - 4 DP - 2010 TI - Antiapoptotic seminal vesicle protein IV induces histamine release from human FcepsilonRI+ cells. PG - 318-30 LID - 10.1159/000250440 [doi] AB - BACKGROUND: Seminal vesicle protein number 4 (SV-IV) is a small, basic, multifunctional, intrinsically disordered secretory protein synthesized in large amounts by rat seminal vesicle epithelium under androgen transcriptional control. SV-IV-immunorelated proteins occur in other rat tissues and in humans. METHODS: The in vitro effect of SV-IV on human FcepsilonRI+ cells was investigated by standard immunologic, biochemical and molecular biology procedures. RESULTS: SV-IV-induced histamine release from human basophils and lung mast cells without any influence on leukotriene C(4) release and cell migration. The histamine release rate was slower compared with that induced by anti-IgE, the temperature dependence of the event being similar. SV-IV-induced histamine release was Ca2+-dependent, suggesting a physiological interaction of the protein with FcepsilonRI+ cells. SV-IV and anti-IgE acted synergistically on the histamine release. SV-IV did not induce de novo synthesis of cytokines and growth factors (transforming growth factor-beta(1), interleukin-10, interleukin-13, tumor necrosis factor-alpha, vascular endothelial growth factor A) in FcepsilonRI+ cells. CONCLUSIONS: SV-IV protein induces in human FcepsilonRI+ cells the release of histamine, a proinflammatory, antiapoptotic and immunosuppressive biogenic amine. These data: (1) are consistent with the antiapoptotic and immunosuppressive properties of SV-IV; (2) confirm a regulatory feature of SV-IV on mammal inflammatory reactivity by either inhibiting the arachidonate cascade pathway or stimulating proinflammatory cytokine release from lymphocyte/monocytes and histamine from FcepsilonRI+ cells; (3) raise the possibility of a protective role of SV-IV on implanting hemiallogenic blastocysts against maternal reactive oxygen species and immunological attacks at the uterine implantation site. CI - 2009 S. Karger AG, Basel. FAU - Prevete, Nella AU - Prevete N AD - Division of Clinical Immunology and Allergy, University of Naples Federico II, Naples, Italy. FAU - Rossi, Francesca Wanda AU - Rossi FW FAU - Triggiani, Massimo AU - Triggiani M FAU - Marone, Gianni AU - Marone G FAU - de Paulis, Amato AU - de Paulis A FAU - Metafora, Vittoria AU - Metafora V FAU - De Maria, Salvatore AU - De Maria S FAU - Carteni, Maria AU - Carteni M FAU - Ragone, Raffaele AU - Ragone R FAU - Ravagnan, Gianpietro AU - Ravagnan G FAU - Metafora, Salvatore AU - Metafora S LA - eng PT - Journal Article DEP - 20091022 PL - Switzerland TA - Int Arch Allergy Immunol JT - International archives of allergy and immunology JID - 9211652 RN - 0 (Antibodies, Anti-Idiotypic) RN - 0 (Apoptosis Regulatory Proteins) RN - 0 (FcepsilonRI alpha-chain, human) RN - 0 (Receptors, IgE) RN - 0 (Seminal Vesicle Secretory Proteins) RN - 0 (Svp4 protein, rat) RN - 0 (anti-IgE antibodies) RN - SY7Q814VUP (Calcium) SB - IM MH - Animals MH - Antibodies, Anti-Idiotypic/pharmacology MH - Apoptosis Regulatory Proteins/*pharmacology MH - Basophils/*drug effects/immunology/metabolism/pathology MH - Calcium/metabolism MH - Cell Line MH - Drug Synergism MH - Histamine Release/*drug effects/immunology MH - Humans MH - Immune Tolerance MH - Lung/pathology MH - Mast Cells/*drug effects/immunology/metabolism/pathology MH - Rats MH - Receptors, IgE/*metabolism MH - Seminal Vesicle Secretory Proteins/*pharmacology EDAT- 2009/10/24 06:00 MHDA- 2010/05/14 06:00 CRDT- 2009/10/24 06:00 PHST- 2009/03/17 [received] PHST- 2009/07/14 [accepted] PHST- 2009/10/22 [aheadofprint] AID - 000250440 [pii] AID - 10.1159/000250440 [doi] PST - ppublish SO - Int Arch Allergy Immunol. 2010;151(4):318-30. doi: 10.1159/000250440. Epub 2009 Oct 22. PMID- 9741621 OWN - NLM STAT- MEDLINE DA - 19981005 DCOM- 19981005 LR - 20131121 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 94 IP - 5 DP - 1998 Sep 4 TI - Crystal structure of a vertebrate smooth muscle myosin motor domain and its complex with the essential light chain: visualization of the pre-power stroke state. PG - 559-71 AB - The crystal structures of an expressed vertebrate smooth muscle myosin motor domain (MD) and a motor domain-essential light chain (ELC) complex (MDE), both with a transition state analog (MgADP x AIF4-) in the active site, have been determined to 2.9 A and 3.5 A resolution, respectively. The MDE structure with an ATP analog (MgADP x BeFx) was also determined to 3.6 A resolution. In all three structures, a domain of the C-terminal region, the "converter," is rotated approximately 70 degrees from that in nucleotide-free skeletal subfragment 1 (S1). We have found that the MDE-BeFx and MDE-AIF4- structures are almost identical, consistent with the fact that they both bind weakly to actin. A comparison of the lever arm positions in MDE-AIF4- and in nucleotide-free skeletal S1 shows that a potential displacement of approximately 10 nm can be achieved during the power stroke. FAU - Dominguez, R AU - Dominguez R AD - Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA. FAU - Freyzon, Y AU - Freyzon Y FAU - Trybus, K M AU - Trybus KM FAU - Cohen, C AU - Cohen C LA - eng SI - PDB/1BR1 SI - PDB/1BR2 SI - PDB/1BR4 GR - AR 17346/AR/NIAMS NIH HHS/United States GR - AR 41808/AR/NIAMS NIH HHS/United States GR - HL 38113/HL/NHLBI NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Cell JT - Cell JID - 0413066 RN - 0 (Actins) RN - 0 (Macromolecular Substances) RN - 0 (Myosin Light Chains) RN - 0 (Myosin Subfragments) RN - 61D2G4IYVH (Adenosine Diphosphate) SB - IM MH - Actins/metabolism MH - Adenosine Diphosphate/metabolism MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Chickens MH - Crystallography, X-Ray MH - Dictyostelium MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Muscle, Smooth/*chemistry/metabolism MH - Myosin Light Chains/*chemistry/metabolism MH - Myosin Subfragments/*chemistry/metabolism MH - Protein Conformation MH - *Protein Structure, Tertiary EDAT- 1998/09/19 MHDA- 1998/09/19 00:01 CRDT- 1998/09/19 00:00 AID - S0092-8674(00)81598-6 [pii] PST - ppublish SO - Cell. 1998 Sep 4;94(5):559-71. PMID- 9741622 OWN - NLM STAT- MEDLINE DA - 19981005 DCOM- 19981005 LR - 20131121 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 94 IP - 5 DP - 1998 Sep 4 TI - Solution structure of a TBP-TAF(II)230 complex: protein mimicry of the minor groove surface of the TATA box unwound by TBP. PG - 573-83 AB - General transcription factor TFIID consists of TATA box-binding protein (TBP) and TBP-associated factors (TAF(II)s), which together play a central role in both positive and negative regulation of transcription. The N-terminal region of the 230 kDa Drosophila TAF(II) (dTAF(II)230) binds directly to TBP and inhibits TBP binding to the TATA box. We report here the solution structure of the complex formed by dTAF(II)230 N-terminal region (residues 11-77) and TBP. dTAF(II)230(11-77) comprises three alpha helices and a beta hairpin, forming a core that occupies the concave DNA-binding surface of TBP. The TBP-binding surface of dTAF(II)230 markedly resembles the minor groove surface of the partially unwound TATA box in the TBP-TATA complex. This protein mimicry of the TATA element surface provides the structural basis of the mechanism by which dTAF(II)230 negatively controls the TATA box-binding activity within the TFIID complex. FAU - Liu, D AU - Liu D AD - Department of Medical Biophysics, University of Toronto, Ontario, Canada. FAU - Ishima, R AU - Ishima R FAU - Tong, K I AU - Tong KI FAU - Bagby, S AU - Bagby S FAU - Kokubo, T AU - Kokubo T FAU - Muhandiram, D R AU - Muhandiram DR FAU - Kay, L E AU - Kay LE FAU - Nakatani, Y AU - Nakatani Y FAU - Ikura, M AU - Ikura M LA - eng SI - PDB/1TBA PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA-Binding Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Solutions) RN - 0 (TATA-Binding Protein Associated Factors) RN - 0 (TATA-Box Binding Protein) RN - 0 (Transcription Factor TFIID) RN - 0 (Transcription Factors) RN - EC 2.3.1.48 (Histone Acetyltransferases) RN - EC 2.7.11.1 (TATA-binding protein associated factor 250 kDa) SB - IM CIN - Cell. 1998 Sep 4;94(5):551-3. PMID: 9741619 MH - Amino Acid Sequence MH - Animals MH - Crystallography, X-Ray MH - DNA-Binding Proteins/*chemistry/*metabolism MH - Drosophila MH - Histone Acetyltransferases MH - Humans MH - Models, Molecular MH - *Molecular Mimicry MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*chemistry/*metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Solutions MH - *TATA Box MH - *TATA-Binding Protein Associated Factors MH - TATA-Box Binding Protein MH - *Transcription Factor TFIID MH - Transcription Factors/*chemistry/*metabolism EDAT- 1998/09/19 MHDA- 1998/09/19 00:01 CRDT- 1998/09/19 00:00 AID - S0092-8674(00)81599-8 [pii] PST - ppublish SO - Cell. 1998 Sep 4;94(5):573-83. PMID- 24795046 OWN - NLM STAT- MEDLINE DA - 20140729 DCOM- 20141006 LR - 20150620 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 289 IP - 25 DP - 2014 Jun 20 TI - Cancer-relevant splicing factor CAPERalpha engages the essential splicing factor SF3b155 in a specific ternary complex. PG - 17325-37 LID - 10.1074/jbc.M114.558825 [doi] AB - U2AF homology motifs (UHMs) mediate protein-protein interactions with U2AF ligand motifs (ULMs) of pre-mRNA splicing factors. The UHM-containing alternative splicing factor CAPERalpha regulates splicing of tumor-promoting VEGF isoforms, yet the molecular target of the CAPERalpha UHM is unknown. Here we present structures of the CAPERalpha UHM bound to a representative SF3b155 ULM at 1.7 A resolution and, for comparison, in the absence of ligand at 2.2 A resolution. The prototypical UHM/ULM interactions authenticate CAPERalpha as a bona fide member of the UHM family of proteins. We identify SF3b155 as the relevant ULM-containing partner of full-length CAPERalpha in human cell extracts. Isothermal titration calorimetry comparisons of the purified CAPERalpha UHM binding known ULM-containing proteins demonstrate that high affinity interactions depend on the presence of an intact, intrinsically unstructured SF3b155 domain containing seven ULM-like motifs. The interplay among bound CAPERalpha molecules gives rise to the appearance of two high affinity sites in the SF3b155 ULM-containing domain. In conjunction with the previously identified, UHM/ULM-mediated complexes of U2AF(65) and SPF45 with SF3b155, this work demonstrates the capacity of SF3b155 to offer a platform for coordinated recruitment of UHM-containing splicing factors. CI - (c) 2014 by The American Society for Biochemistry and Molecular Biology, Inc. FAU - Loerch, Sarah AU - Loerch S AD - From the Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 and. FAU - Maucuer, Alexandre AU - Maucuer A AD - the Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605 alexandre.maucuer@inserm.fr. FAU - Manceau, Valerie AU - Manceau V AD - the Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605. FAU - Green, Michael R AU - Green MR AD - the Howard Hughes Medical Institute and Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605. FAU - Kielkopf, Clara L AU - Kielkopf CL AD - From the Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642 and clara_kielkopf@urmc.rochester.edu. LA - eng SI - PDB/4OZ0 SI - PDB/4OZ1 GR - R01 GM035490/GM/NIGMS NIH HHS/United States GR - R01 GM070503/GM/NIGMS NIH HHS/United States GR - R01 GM070503/GM/NIGMS NIH HHS/United States GR - S10 RR026501/RR/NCRR NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140502 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (HCC1 autoantigen) RN - 0 (Neoplasm Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Phosphoproteins) RN - 0 (RNA-Binding Proteins) RN - 0 (Ribonucleoprotein, U2 Small Nuclear) RN - 0 (SF3B1 protein, human) SB - IM MH - Amino Acid Motifs MH - HEK293 Cells MH - Humans MH - Neoplasm Proteins/chemistry/genetics/*metabolism MH - Nuclear Proteins/chemistry/genetics/*metabolism MH - Phosphoproteins/chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - RNA-Binding Proteins/chemistry/genetics/*metabolism MH - Ribonucleoprotein, U2 Small Nuclear/chemistry/genetics/*metabolism PMC - PMC4067167 OID - NLM: PMC4067167 OTO - NOTNLM OT - Crystal Structure OT - Gene Regulation OT - Protein Domain OT - Protein Structure and Folding OT - Protein-Protein Interaction OT - RNA Splicing EDAT- 2014/05/06 06:00 MHDA- 2014/10/07 06:00 CRDT- 2014/05/06 06:00 PHST- 2014/05/02 [aheadofprint] AID - M114.558825 [pii] AID - 10.1074/jbc.M114.558825 [doi] PST - ppublish SO - J Biol Chem. 2014 Jun 20;289(25):17325-37. doi: 10.1074/jbc.M114.558825. Epub 2014 May 2. PMID- 17105210 OWN - NLM STAT- MEDLINE DA - 20061119 DCOM- 20070124 LR - 20101118 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 46 DP - 2006 Nov 21 TI - Dissection of a human septin: definition and characterization of distinct domains within human SEPT4. PG - 13918-31 AB - The septins are a conserved family of guanosine-5'-triphosphate (GTP)-binding proteins. In mammals they are involved in a variety of cellular processes, such as cytokinesis, exocytosis, and vesicle trafficking. Specifically, SEPT4 has also been shown to be expressed in both human colorectal cancer and malignant melanoma, as well as being involved in neurodegenerative disorders. However, many of the details of the modes of action of septins in general remain unclear, and little is known of their detailed molecular architecture. Here, we define explicitly and characterize the domains of human SEPT4. Regions corresponding to the N-terminal, GTPase, and C-terminal domains as well as the latter two together were successfully expressed in Escherichia coli in soluble form and purified by affinity and size-exclusion chromatographies. The purified domains were analyzed by circular dichroism spectroscopy, fluorescence spectroscopy, dynamic light scattering, and small-angle X-ray scattering, as well as with bioinformatics tools. Of the three major domains that comprise SEPT4, the N-terminal domain contains little regular secondary structure and may be intrinsically unstructured. The central GTPase domain is a mixed alpha/beta structure, probably based on an open beta sheet. As defined here, it is catalytically active and forms stable homodimers in vitro. The C-terminal domain also forms homodimers and can be divided into two regions, the second of which is alpha-helical and consistent with a coiled-coil structure. These studies should provide a useful basis for future biophysical studies of SEPT4, including the structural basis for their involvement in diseases such as cancer and neurodegenerative disorders. FAU - Garcia, Wanius AU - Garcia W AD - Centro de Biotecnologia Molecular e Estrutural (CBME), Instituto de Fisica de Sao Carlos (IFSC), Universidade de Sao Paulo (USP), Av. Trabalhador Sao Carlense 400, centro, Box 369, Sao Carlos, SP, 13560-970, Brazil. wanius@if.sc.usp.br FAU - de Araujo, Ana Paula Ulian AU - de Araujo AP FAU - Neto, Mario de Oliveira AU - Neto Mde O FAU - Ballestero, Michel R M AU - Ballestero MR FAU - Polikarpov, Igor AU - Polikarpov I FAU - Tanaka, Manami AU - Tanaka M FAU - Tanaka, Tomoo AU - Tanaka T FAU - Garratt, Richard Charles AU - Garratt RC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cytoskeletal Proteins) RN - EC 3.6.1.- (GTP Phosphohydrolases) RN - EC 3.6.1.- (SEPT4 protein, human) RN - EC 3.6.1.- (Septins) SB - IM MH - Amino Acid Sequence MH - Chromatography, Affinity MH - Chromatography, Gel MH - Circular Dichroism MH - Cytoskeletal Proteins/chemistry/genetics/*metabolism MH - Electrophoresis, Polyacrylamide Gel MH - GTP Phosphohydrolases/chemistry/genetics/*metabolism MH - Humans MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Septins MH - Sequence Homology, Amino Acid MH - Spectrometry, Fluorescence EDAT- 2006/11/16 09:00 MHDA- 2007/01/25 09:00 CRDT- 2006/11/16 09:00 AID - 10.1021/bi061549z [doi] PST - ppublish SO - Biochemistry. 2006 Nov 21;45(46):13918-31. PMID- 19842064 OWN - NLM STAT- MEDLINE DA - 20091110 DCOM- 20100119 IS - 1874-270X (Electronic) VI - 3 IP - 2 DP - 2009 Dec TI - NMR assignments of the intrinsically disordered K2 and YSK2 dehydrins. PG - 273-5 LID - 10.1007/s12104-009-9192-2 [doi] AB - Dehydrins are proteins expressed by plants during various dehydrative stresses (drought, cold, and high salinity) to reduce cellular damage. These intrinsically disordered proteins are thought to function by binding to proteins to prevent denaturation, and to membranes to prevent leakage. Here, we report the 1H, 15N, and 13C chemical shift assignments of the K2 and YSK2 dehydrins from Vitis riparia (wild grape). Our results show that the segmental nature of dehydrins allows for the assignments of the shorter dehydrins to be used in that of the longer forms. FAU - Findlater, Emma E AU - Findlater EE AD - Department of Molecular and Cellular Biology, University of Guelph, 3455 Science Complex, Guelph, ON, Canada. FAU - Graether, Steffen P AU - Graether SP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (Plant Proteins) RN - 134711-03-8 (dehydrin proteins, plant) SB - IM MH - Nuclear Magnetic Resonance, Biomolecular MH - Plant Proteins/*chemistry MH - *Vitis EDAT- 2009/10/21 06:00 MHDA- 2010/01/20 06:00 CRDT- 2009/10/21 06:00 PHST- 2009/08/17 [received] PHST- 2009/10/08 [accepted] PHST- 2009/10/20 [aheadofprint] AID - 10.1007/s12104-009-9192-2 [doi] PST - ppublish SO - Biomol NMR Assign. 2009 Dec;3(2):273-5. doi: 10.1007/s12104-009-9192-2. PMID- 24603811 OWN - NLM STAT- MEDLINE DA - 20140307 DCOM- 20141104 LR - 20141111 IS - 1553-7374 (Electronic) IS - 1553-7366 (Linking) VI - 10 IP - 3 DP - 2014 Mar TI - The hypervariable amino-terminus of P1 protease modulates potyviral replication and host defense responses. PG - e1003985 LID - 10.1371/journal.ppat.1003985 [doi] AB - The replication of many RNA viruses involves the translation of polyproteins, whose processing by endopeptidases is a critical step for the release of functional subunits. P1 is the first protease encoded in plant potyvirus genomes; once activated by an as-yet-unknown host factor, it acts in cis on its own C-terminal end, hydrolyzing the P1-HCPro junction. Earlier research suggests that P1 cooperates with HCPro to inhibit host RNA silencing defenses. Using Plum pox virus as a model, we show that although P1 does not have a major direct role in RNA silencing suppression, it can indeed modulate HCPro function by its self-cleavage activity. To study P1 protease regulation, we used bioinformatic analysis and in vitro activity experiments to map the core C-terminal catalytic domain. We present evidence that the hypervariable region that precedes the protease domain is predicted as intrinsically disordered, and that it behaves as a negative regulator of P1 proteolytic activity in in vitro cleavage assays. In viral infections, removal of the P1 protease antagonistic regulator is associated with greater symptom severity, induction of salicylate-dependent pathogenesis-related proteins, and reduced viral loads. We suggest that fine modulation of a viral protease activity has evolved to keep viral amplification below host-detrimental levels, and thus to maintain higher long-term replicative capacity. FAU - Pasin, Fabio AU - Pasin F AD - Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain. FAU - Simon-Mateo, Carmen AU - Simon-Mateo C AD - Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain. FAU - Garcia, Juan Antonio AU - Garcia JA AD - Departamento de Genetica Molecular de Plantas, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140306 PL - United States TA - PLoS Pathog JT - PLoS pathogens JID - 101238921 RN - 0 (Viral Proteins) RN - EC 3.4.- (Peptide Hydrolases) SB - IM MH - Amino Acid Sequence MH - Blotting, Western MH - Chromatography, Liquid MH - Host-Parasite Interactions/*physiology MH - Molecular Sequence Data MH - Peptide Hydrolases/chemistry/*metabolism MH - Plant Diseases/virology MH - Potyvirus/pathogenicity/*physiology MH - Protein Structure, Tertiary/physiology MH - Reverse Transcriptase Polymerase Chain Reaction MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Tandem Mass Spectrometry MH - Tobacco/virology MH - Viral Proteins/chemistry/*metabolism MH - Virus Replication/*physiology PMC - PMC3946448 OID - NLM: PMC3946448 EDAT- 2014/03/08 06:00 MHDA- 2014/11/05 06:00 CRDT- 2014/03/08 06:00 PHST- 2014/03 [ecollection] PHST- 2013/08/10 [received] PHST- 2014/01/23 [accepted] PHST- 2014/03/06 [epublish] AID - 10.1371/journal.ppat.1003985 [doi] AID - PPATHOGENS-D-13-02085 [pii] PST - epublish SO - PLoS Pathog. 2014 Mar 6;10(3):e1003985. doi: 10.1371/journal.ppat.1003985. eCollection 2014 Mar. PMID- 19576220 OWN - NLM STAT- MEDLINE DA - 20090811 DCOM- 20090824 LR - 20140916 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 391 IP - 4 DP - 2009 Aug 28 TI - Structural reorganization of alpha-synuclein at low pH observed by NMR and REMD simulations. PG - 784-96 LID - 10.1016/j.jmb.2009.06.063 [doi] AB - alpha-Synuclein is an intrinsically disordered protein that appears in aggregated forms in the brains of patients with Parkinson's disease. The conversion from monomer to aggregate is complex, and aggregation rates are sensitive to changes in amino acid sequence and environmental conditions. It has previously been observed that alpha-synuclein aggregates faster at low pH than at neutral pH. Here, we combine NMR spectroscopy and molecular simulations to characterize alpha-synuclein conformational ensembles at both neutral and low pH in order to understand how the altered charge distribution at low pH changes the structural properties of these ensembles and leads to an increase in aggregation rate. The N-terminus, which has a small positive charge at neutral pH due to a balance of positively and negatively charged amino acid residues, is very positively charged at low pH. Conversely, the acidic C-terminus is highly negatively charged at neutral pH and becomes essentially neutral and hydrophobic at low pH. Our NMR experiments and replica exchange molecular dynamics simulations indicate that there is a significant structural reorganization within the low-pH ensemble relative to that at neutral pH in terms of long-range contacts, hydrodynamic radius, and the amount of heterogeneity within the conformational ensembles. At neutral pH, there is a very heterogeneous ensemble with transient contacts between the N-terminus and the non-amyloid beta component (NAC); however, at low pH, there is a more homogeneous ensemble that exhibits strong contacts between the NAC and the C-terminus. At both pH values, transient contacts between the N- and C-termini are observed, the NAC region shows similar exposure to solvent, and the entire protein shows similar propensities to secondary structure. Based on the comparison of the neutral- and low-pH conformational ensembles, we propose that exposure of the NAC region to solvent and the secondary-structure propensity are not factors that account for differences in propensity to aggregate in this context. Instead, the comparison of the neutral- and low-pH ensembles suggests that the change in long-range interactions between the low- and neutral-pH ensembles, the compaction of the C-terminal region at low pH, and the uneven distribution of charges across the sequence are key to faster aggregation. FAU - Wu, Kuen-Phon AU - Wu KP AD - Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. FAU - Weinstock, Daniel S AU - Weinstock DS FAU - Narayanan, Chitra AU - Narayanan C FAU - Levy, Ronald M AU - Levy RM FAU - Baum, Jean AU - Baum J LA - eng GR - 3T90DK070135/DK/NIDDK NIH HHS/United States GR - 5R90DK071502/DK/NIDDK NIH HHS/United States GR - GM 30580/GM/NIGMS NIH HHS/United States GR - GM 45302/GM/NIGMS NIH HHS/United States GR - R01 GM030580/GM/NIGMS NIH HHS/United States GR - R01 GM030580-27/GM/NIGMS NIH HHS/United States GR - R01 GM045302/GM/NIGMS NIH HHS/United States GR - R01 GM045302-16/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20090701 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (alpha-Synuclein) SB - IM MH - *Computer Simulation MH - Humans MH - *Hydrogen-Ion Concentration MH - Models, Molecular MH - Molecular Sequence Data MH - *Nuclear Magnetic Resonance, Biomolecular MH - *Protein Conformation MH - alpha-Synuclein/*chemistry/genetics/metabolism PMC - PMC2766395 MID - NIHMS134338 OID - NLM: NIHMS134338 OID - NLM: PMC2766395 EDAT- 2009/07/07 09:00 MHDA- 2009/08/25 09:00 CRDT- 2009/07/07 09:00 PHST- 2009/03/03 [received] PHST- 2009/06/04 [revised] PHST- 2009/06/25 [accepted] PHST- 2009/07/01 [aheadofprint] AID - S0022-2836(09)00795-5 [pii] AID - 10.1016/j.jmb.2009.06.063 [doi] PST - ppublish SO - J Mol Biol. 2009 Aug 28;391(4):784-96. doi: 10.1016/j.jmb.2009.06.063. Epub 2009 Jul 1. PMID- 22754618 OWN - NLM STAT- Publisher DA - 20120703 IS - 1949-100X (Electronic) IS - 1949-0992 (Linking) VI - 1 IP - 5 DP - 2011 Sep 1 TI - Structural implications of conserved aspartate residues located in tropomyosin's coiled-coil core. PG - 250-255 AB - Polar residues lying between adjacent alpha-helical chains of coiled-coils often contribute to coiled-coil curvature and flexibility, while more typical core hydrophobic residues anneal the chains together. In tropomyosins, ranging from smooth and skeletal muscle to cytoplasmic isoforms, a highly conserved Asp at residue 137 places negative charges within the tropomyosin coiled-coil core in a position which may affect the conformation needed for tropomyosin binding and regulatory movements on actin. Proteolytic susceptibility suggested that substituting a canonical Leu for the naturally occurring Asp at residue 137 increases inter-chain rigidity by stabilizing the tropomyosin coiled-coil. Using molecular dynamics, we now directly assess changes in coiled-coil curvature and flexibility caused by such mutants. Although the coiled-coil flexibility is modestly diminished near the residue 137 mutation site, as expected, a delocalized increase in flexibility along the overall coiled-coil is observed. Even though the average shape of the D137L tropomyosin is straighter than that of wild-type tropomyosin, it is still capable of binding actin due to this increase in flexibility. We conclude that the conserved, non-canonical Asp-137 destabilizes the local structure resulting in a local flexible region in the middle of tropomyosin that normally is important for tropomyosin steady-state equilibrium position on actin. FAU - Moore, Jeffrey R AU - Moore JR FAU - Li, Xiaochuan AU - Li X FAU - Nirody, Jasmine AU - Nirody J FAU - Fischer, Stefan AU - Fischer S FAU - Lehman, William AU - Lehman W LA - ENG PT - JOURNAL ARTICLE TA - Bioarchitecture JT - Bioarchitecture JID - 101518332 PMC - PMC3384579 EDAT- 2012/07/04 06:00 MHDA- 2012/07/04 06:00 CRDT- 2012/07/04 06:00 AID - 10.4161/bioa.18117 [doi] AID - 2011BIOARCHITECTURE0029 [pii] PST - ppublish SO - Bioarchitecture. 2011 Sep 1;1(5):250-255. PMID- 23357007 OWN - NLM STAT- MEDLINE DA - 20130409 DCOM- 20131218 IS - 1600-0854 (Electronic) IS - 1398-9219 (Linking) VI - 14 IP - 5 DP - 2013 May TI - Quantitative analysis of membrane protein transport across the nuclear pore complex. PG - 487-501 LID - 10.1111/tra.12048 [doi] AB - Nuclear transport of the Saccharomyces cerevisiae membrane proteins Src1/Heh1 and Heh2 across the NPC is facilitated by a long intrinsically disordered linker between the nuclear localization signal (NLS) and the transmembrane domain. The import of reporter proteins derived from Heh2 is dependent on the FG-Nups in the central channel, and the linker can position the transport factor-bound NLS in the vicinity of the FG-Nups in the central channel, while the transmembrane segment resides in the pore membrane. Here, we present a quantitative analysis of karyopherin-mediated import and passive efflux of reporter proteins derived from Heh2, including data on the mobility of the reporter proteins in different membrane compartments. We show that membrane proteins with extralumenal domains up to 174 kDa, terminal to the linker and NLS, passively leak out of the nucleus via the NPC, albeit at a slow rate. We propose that also during passive efflux, the unfolded linker facilitates the passage of extralumenal domains through the central channel of the NPC. CI - (c) 2013 John Wiley & Sons A/S. FAU - Meinema, Anne C AU - Meinema AC AD - Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. FAU - Poolman, Bert AU - Poolman B FAU - Veenhoff, Liesbeth M AU - Veenhoff LM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130221 PL - England TA - Traffic JT - Traffic (Copenhagen, Denmark) JID - 100939340 RN - 0 (Heh2 protein, S cerevisiae) RN - 0 (Karyopherins) RN - 0 (Membrane Proteins) RN - 0 (Nuclear Localization Signals) RN - 0 (Nuclear Proteins) SB - IM MH - Biological Transport MH - Cell Nucleus/metabolism MH - Diffusion MH - Genes, Reporter MH - Karyopherins/metabolism MH - Membrane Proteins/*physiology MH - Microscopy, Fluorescence MH - *Nuclear Localization Signals MH - Nuclear Pore/*metabolism MH - Nuclear Proteins/*physiology MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/*metabolism EDAT- 2013/01/30 06:00 MHDA- 2013/12/19 06:00 CRDT- 2013/01/30 06:00 PHST- 2012/03/16 [received] PHST- 2013/01/22 [revised] PHST- 2013/01/28 [accepted] PHST- 2013/02/21 [aheadofprint] AID - 10.1111/tra.12048 [doi] PST - ppublish SO - Traffic. 2013 May;14(5):487-501. doi: 10.1111/tra.12048. Epub 2013 Feb 21. PMID- 11099384 OWN - NLM STAT- MEDLINE DA - 20010102 DCOM- 20010111 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 304 IP - 4 DP - 2000 Dec 8 TI - The TolA-recognition site of colicin N. ITC, SPR and stopped-flow fluorescence define a crucial 27-residue segment. PG - 621-32 AB - Colicins translocate across the Escherichia coli outer membrane and periplasm by interacting with several receptors. After first binding to the outer membrane surface receptors via their central region, they interact with TolA or TonB proteins via their N-terminal region. Colicin N residues critical to TolA binding have been discovered, but the full extent of any colicin TolA site is unknown. We present, for the first time, a fully mapped TolA binding site for a colicin. It was determined through the use of alanine-scanning mutants, glutathione S-transferase fusion peptides and Biacore/fluorescence binding studies. The minimal TolA binding region is 27 residues and of similar size to the TolA binding region of bacteriophage g3p-D1 protein. Stopped-flow kinetic studies show that the binding to TolA follows slow association kinetics. The role of other E. coli Tol proteins in colicin translocation was also investigated. Isothermal titration microcalorimetry (ITC) and in vivo studies conclusively show that colicin N translocation does not require the presence of TolB. ITC also demonstrated colicin A interaction with TolB, and that colicin A in its native state does not interact with TolAII-III. Colicin N does not bind TolR-II. The TolA protein is shown to be unsuitable for direct immobilisation in Biacore analysis. CI - Copyright 2000 Academic Press. FAU - Gokce, I AU - Gokce I AD - Department of Chemistry Faculty of Science, Gaziomanpasa University, Tokat, Turkey. FAU - Raggett, E M AU - Raggett EM FAU - Hong, Q AU - Hong Q FAU - Virden, R AU - Virden R FAU - Cooper, A AU - Cooper A FAU - Lakey, J H AU - Lakey JH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (Colicins) RN - 0 (Escherichia coli Proteins) RN - 0 (Periplasmic Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (tolA protein, E coli) RN - 0 (tolB protein, E coli) RN - 8DUH1N11BX (Tryptophan) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution/genetics MH - Bacterial Proteins/*metabolism MH - Binding Sites MH - Calorimetry MH - Circular Dichroism MH - Colicins/*chemistry/genetics/*metabolism MH - Escherichia coli/*chemistry MH - *Escherichia coli Proteins MH - Fluorescence MH - Kinetics MH - Molecular Sequence Data MH - Mutation/genetics MH - *Periplasmic Proteins MH - Protein Binding MH - Recombinant Fusion Proteins/chemistry/metabolism MH - Sequence Alignment MH - *Surface Plasmon Resonance MH - Titrimetry MH - Tryptophan/genetics/metabolism EDAT- 2000/12/02 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/12/02 11:00 AID - 10.1006/jmbi.2000.4232 [doi] AID - S0022-2836(00)94232-3 [pii] PST - ppublish SO - J Mol Biol. 2000 Dec 8;304(4):621-32. PMID- 1909892 OWN - NLM STAT- MEDLINE DA - 19911023 DCOM- 19911023 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 30 IP - 38 DP - 1991 Sep 24 TI - Secondary structure and side-chain 1H and 13C resonance assignments of calmodulin in solution by heteronuclear multidimensional NMR spectroscopy. PG - 9216-28 AB - Heteronuclear 2D and 3D NMR experiments were carried out on recombinant Drosophila calmodulin (CaM), a protein of 148 residues and with molecular mass of 16.7 kDa, that is uniformly labeled with 15N and 13C to a level of greater than 95%. Nearly complete 1H and 13C side-chain assignments for all amino acid residues are obtained by using the 3D HCCH-COSY and HCCH-TOCSY experiments that rely on large heteronuclear one-bond scalar couplings to transfer magnetization and establish through-bond connectivities. The secondary structure of this protein in solution has been elucidated by a qualitative interpretation of nuclear Overhauser effects, hydrogen exchange data, and 3JHNH alpha coupling constants. A clear correlation between the 13C alpha chemical shift and secondary structure is found. The secondary structure in the two globular domains of Drosophila CaM in solution is essentially identical with that of the X-ray crystal structure of mammalian CaM [Babu, Y., Bugg, C. E., & Cook, W.J. (1988) J. Mol. Biol. 204, 191-204], which consists of two pairs of a "helix-loop-helix" motif in each globular domain. The existence of a short antiparallel beta-sheet between the two loops in each domain has been confirmed. The eight alpha-helix segments identified from the NMR data are located at Glu-6 to Phe-19, Thr-29 to Ser-38, Glu-45 to Glu-54, Phe-65 to Lys-77, Glu-82 to Asp-93, Ala-102 to Asn-111, Asp-118 to Glu-127, and Tyr-138 to Thr-146. Although the crystal structure has a long "central helix" from Phe-65 to Phe-92 that connects the two globular domains, NMR data indicate that residues Asp-78 to Ser-81 of this central helix adopt a nonhelical conformation with considerable flexibility. FAU - Ikura, M AU - Ikura M AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892. FAU - Spera, S AU - Spera S FAU - Barbato, G AU - Barbato G FAU - Kay, L E AU - Kay LE FAU - Krinks, M AU - Krinks M FAU - Bax, A AU - Bax A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amino Acids, Branched-Chain) RN - 0 (Amino Acids, Diamino) RN - 0 (Amino Acids, Dicarboxylic) RN - 0 (Calmodulin) RN - 0 (Recombinant Proteins) RN - 0 (Solutions) RN - 0RH81L854J (Glutamine) RN - 2ZD004190S (Threonine) RN - 452VLY9402 (Serine) RN - 7006-34-0 (Asparagine) RN - 9DLQ4CIU6V (Proline) RN - AE28F7PNPL (Methionine) RN - GMW67QNF9C (Leucine) RN - OF5P57N2ZX (Alanine) RN - SY7Q814VUP (Calcium) RN - TE7660XO1C (Glycine) SB - IM MH - Alanine/chemistry MH - Amino Acid Sequence MH - Amino Acids, Branched-Chain/chemistry MH - Amino Acids, Diamino/chemistry MH - Amino Acids, Dicarboxylic/chemistry MH - Animals MH - Asparagine/chemistry MH - Binding Sites MH - Calcium/metabolism MH - Calmodulin/*chemistry MH - Drosophila melanogaster MH - Glutamine/chemistry MH - Glycine/chemistry MH - Hydrogen Bonding MH - Leucine/chemistry MH - Magnetic Resonance Spectroscopy MH - Methionine/chemistry MH - Molecular Sequence Data MH - Molecular Structure MH - Proline/chemistry MH - Recombinant Proteins MH - Serine/chemistry MH - Solutions MH - Threonine/chemistry EDAT- 1991/09/24 MHDA- 1991/09/24 00:01 CRDT- 1991/09/24 00:00 PST - ppublish SO - Biochemistry. 1991 Sep 24;30(38):9216-28. PMID- 25139988 OWN - NLM STAT- MEDLINE DA - 20140908 DCOM- 20141112 LR - 20150421 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 35 DP - 2014 Sep 2 TI - Assembly and dynamics of the autophagy-initiating Atg1 complex. PG - 12793-8 LID - 10.1073/pnas.1407214111 [doi] AB - The autophagy-related 1 (Atg1) complex of Saccharomyces cerevisiae has a central role in the initiation of autophagy following starvation and TORC1 inactivation. The complex consists of the protein kinase Atg1, the TORC1 substrate Atg13, and the trimeric Atg17-Atg31-Atg29 scaffolding subcomplex. Autophagy is triggered when Atg1 and Atg13 assemble with the trimeric scaffold. Here we show by hydrogen-deuterium exchange coupled to mass spectrometry that the mutually interacting Atg1 early autophagy targeting/tethering domain and the Atg13 central domain are highly dynamic in isolation but together form a stable complex with approximately 100-nM affinity. The Atg1-Atg13 complex in turn binds as a unit to the Atg17-Atg31-Atg29 scaffold with approximately 10-muM affinity via Atg13. The resulting complex consists primarily of a dimer of pentamers in solution. These results lead to a model for autophagy initiation in which Atg1 and Atg13 are tightly associated with one another and assemble transiently into the pentameric Atg1 complex during starvation. FAU - Stjepanovic, Goran AU - Stjepanovic G AD - Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; and. FAU - Davies, Christopher W AU - Davies CW AD - Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; and. FAU - Stanley, Robin E AU - Stanley RE AD - Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892. FAU - Ragusa, Michael J AU - Ragusa MJ AD - Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; and Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892. FAU - Kim, Do Jin AU - Kim do J AD - Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; and. FAU - Hurley, James H AU - Hurley JH AD - Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720; and jimhurley@berkeley.edu. LA - eng GR - F32 GM112301/GM/NIGMS NIH HHS/United States GR - GM099319/GM/NIGMS NIH HHS/United States GR - GM111730/GM/NIGMS NIH HHS/United States GR - GM112301/GM/NIGMS NIH HHS/United States GR - R01 GM111730/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140819 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (ATG13 protein, S cerevisiae) RN - 0 (ATG29 protein, S cerevisiae) RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Atg17 protein, S cerevisiae) RN - 0 (Atg31 protein, S cerevisiae) RN - 0 (Carrier Proteins) RN - 0 (Multiprotein Complexes) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 2.7.- (Protein Kinases) RN - EC 2.7.1.- (ATG1 protein, S cerevisiae) SB - IM MH - Adaptor Proteins, Signal Transducing/chemistry/genetics/*metabolism MH - Amino Acid Sequence MH - Autophagy/*physiology MH - Calorimetry MH - Carrier Proteins/chemistry/genetics/metabolism MH - Crystallography, X-Ray MH - Gene Deletion MH - Molecular Sequence Data MH - Multiprotein Complexes/chemistry/*metabolism MH - Protein Binding MH - Protein Kinases/chemistry/genetics/*metabolism MH - Protein Structure, Quaternary MH - Saccharomyces cerevisiae/cytology/genetics/metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism PMC - PMC4156731 OID - NLM: PMC4156731 OTO - NOTNLM OT - analytical ultracentrifugation OT - intrinsically disordered proteins OT - isothermal titration calorimetry OT - membrane tethering OT - protein structure EDAT- 2014/08/21 06:00 MHDA- 2014/11/13 06:00 CRDT- 2014/08/21 06:00 PHST- 2014/08/19 [aheadofprint] AID - 1407214111 [pii] AID - 10.1073/pnas.1407214111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):12793-8. doi: 10.1073/pnas.1407214111. Epub 2014 Aug 19. PMID- 23851574 OWN - NLM STAT- MEDLINE DA - 20130820 DCOM- 20131105 IS - 1552-4469 (Electronic) IS - 1552-4450 (Linking) VI - 9 IP - 9 DP - 2013 Sep TI - The hepatitis B virus preS1 domain hijacks host trafficking proteins by motif mimicry. PG - 540-7 LID - 10.1038/nchembio.1294 [doi] AB - Hepatitis B virus (HBV) is an infectious, potentially lethal human pathogen. However, there are no effective therapies for chronic HBV infections. Antiviral development is hampered by the lack of high-resolution structures for essential HBV protein-protein interactions. The interaction between preS1, an HBV surface-protein domain, and its human binding partner, gamma2-adaptin, subverts the membrane-trafficking apparatus to mediate virion export. This interaction is a putative drug target. We report here atomic-resolution descriptions of the binding thermodynamics and structural biology of the interaction between preS1 and the EAR domain of gamma2-adaptin. NMR, protein engineering, X-ray crystallography and MS showed that preS1 contains multiple gamma2-EAR-binding motifs that mimic the membrane-trafficking motifs (and binding modes) of host proteins. These motifs localize together to a relatively rigid, functionally important region of preS1, an intrinsically disordered protein. The preS1-gamma2-EAR interaction was relatively weak and efficiently outcompeted by a synthetic peptide. Our data provide the structural road map for developing peptidomimetic antivirals targeting the gamma2-EAR-preS1 interaction. FAU - Jurgens, Maike C AU - Jurgens MC AD - 1] School of Medicine and Medical Science, University College Dublin, Dublin, Ireland. [2]. FAU - Voros, Judit AU - Voros J FAU - Rautureau, Gilles J P AU - Rautureau GJ FAU - Shepherd, Dale A AU - Shepherd DA FAU - Pye, Valerie E AU - Pye VE FAU - Muldoon, Jimmy AU - Muldoon J FAU - Johnson, Christopher M AU - Johnson CM FAU - Ashcroft, Alison E AU - Ashcroft AE FAU - Freund, Stefan M V AU - Freund SM FAU - Ferguson, Neil AU - Ferguson N LA - eng SI - PDB/2YMT SI - PDB/3ZHF SI - PDB/4BCX GR - BB/E012558/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - GM75915/GM/NIGMS NIH HHS/United States GR - P50GM073210/GM/NIGMS NIH HHS/United States GR - U54GM094599/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130714 PL - United States TA - Nat Chem Biol JT - Nature chemical biology JID - 101231976 RN - 0 (Adaptor Protein Complex gamma Subunits) RN - 0 (Hepatitis B Surface Antigens) RN - 0 (Protein Precursors) RN - 0 (presurface protein 1, hepatitis B surface antigen) SB - IM MH - Adaptor Protein Complex gamma Subunits/chemistry/*metabolism MH - Amino Acid Motifs MH - Hepatitis B Surface Antigens/*chemistry/*metabolism MH - Hepatitis B virus/*metabolism MH - *Molecular Mimicry MH - Protein Precursors/*chemistry/*metabolism MH - Protein Structure, Tertiary MH - Thermodynamics EDAT- 2013/07/16 06:00 MHDA- 2013/11/06 06:00 CRDT- 2013/07/16 06:00 PHST- 2013/01/25 [received] PHST- 2013/06/12 [accepted] PHST- 2013/07/14 [aheadofprint] AID - nchembio.1294 [pii] AID - 10.1038/nchembio.1294 [doi] PST - ppublish SO - Nat Chem Biol. 2013 Sep;9(9):540-7. doi: 10.1038/nchembio.1294. Epub 2013 Jul 14. PMID- 15466413 OWN - NLM STAT- MEDLINE DA - 20041213 DCOM- 20050204 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 51 DP - 2004 Dec 17 TI - Solution structure and dynamics of a prototypical chordin-like cysteine-rich repeat (von Willebrand Factor type C module) from collagen IIA. PG - 53857-66 AB - Chordin-like cysteine-rich (CR) repeats (also referred to as von Willebrand factor type C (VWC) modules) have been identified in approximately 200 extracellular matrix proteins. These repeats, named on the basis of amino acid conservation of 10 cysteine residues, have been shown to bind members of the transforming growth factor-beta (TGF-beta) superfamily and are proposed to regulate growth factor signaling. Here we describe the intramolecular disulfide bonding, solution structure, and dynamics of a prototypical chordin-like CR repeat from procollagen IIA (CR(ColIIA)), which has been previously shown to bind TGF-beta1 and bone morphogenetic protein-2. The CR(ColIIA) structure manifests a two sub-domain architecture tethered by a flexible linkage. Initial structures were calculated using RosettaNMR, a de novo prediction method, and final structure calculations were performed using CANDID within CYANA. The N-terminal region contains mainly beta-sheet and the C-terminal region is more irregular with the fold constrained by disulfide bonds. Mobility between the N- and C-terminal sub-domains on a fast timescale was confirmed using NMR relaxation measurements. We speculate that the mobility between the two sub-domains may decrease upon ligand binding. Structure and sequence comparisons have revealed an evolutionary relationship between the N-terminal sub-domain of the CR module and the fibronectin type 1 domain, suggesting that these domains share a common ancestry. Based on the previously reported mapping of fibronectin binding sites for vascular endothelial growth factor to regions containing fibronectin type 1 domains, we discuss the possibility that this structural homology might also have functional relevance. FAU - O'Leary, Joanne M AU - O'Leary JM AD - Division of Structural Biology, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. FAU - Hamilton, John M AU - Hamilton JM FAU - Deane, Charlotte M AU - Deane CM FAU - Valeyev, Najl V AU - Valeyev NV FAU - Sandell, Linda J AU - Sandell LJ FAU - Downing, A Kristina AU - Downing AK LA - eng SI - PDB/1U5M PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20041001 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (CHRDL1 protein, human) RN - 0 (CYR61 protein, human) RN - 0 (Collagen Type II) RN - 0 (Cysteine-Rich Protein 61) RN - 0 (Cytokines) RN - 0 (Disulfides) RN - 0 (Eye Proteins) RN - 0 (Fibronectins) RN - 0 (Glycoproteins) RN - 0 (Immediate-Early Proteins) RN - 0 (Intercellular Signaling Peptides and Proteins) RN - 0 (Ligands) RN - 0 (Nerve Tissue Proteins) RN - 0 (TGFB1 protein, human) RN - 0 (Transforming Growth Factor beta) RN - 0 (Transforming Growth Factor beta1) RN - 0 (Vascular Endothelial Growth Factor A) RN - 93586-27-7 (chordin) RN - K848JZ4886 (Cysteine) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Binding Sites MH - Collagen Type II/*chemistry MH - Cysteine/*chemistry MH - Cysteine-Rich Protein 61 MH - Cytokines/chemistry MH - Disulfides/chemistry MH - Evolution, Molecular MH - Extracellular Matrix/metabolism MH - Eye Proteins MH - Fibronectins/chemistry MH - Glycoproteins/*chemistry MH - Humans MH - Immediate-Early Proteins/chemistry MH - Intercellular Signaling Peptides and Proteins/*chemistry MH - Ligands MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Nerve Tissue Proteins/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proteomics MH - Sequence Homology, Amino Acid MH - Software MH - Transforming Growth Factor beta/metabolism MH - Transforming Growth Factor beta1 MH - Vascular Endothelial Growth Factor A/metabolism EDAT- 2004/10/07 09:00 MHDA- 2005/02/05 09:00 CRDT- 2004/10/07 09:00 PHST- 2004/10/01 [aheadofprint] AID - M409225200 [pii] AID - 10.1074/jbc.M409225200 [doi] PST - ppublish SO - J Biol Chem. 2004 Dec 17;279(51):53857-66. Epub 2004 Oct 1. PMID- 7663947 OWN - NLM STAT- MEDLINE DA - 19951012 DCOM- 19951012 LR - 20071114 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 3 IP - 5 DP - 1995 May 15 TI - Structure of human estrogenic 17 beta-hydroxysteroid dehydrogenase at 2.20 A resolution. PG - 503-13 AB - BACKGROUND: The principal human estrogen, 17 beta-estradiol, is a potent stimulator of certain endocrine-dependent forms of breast cancer. Because human estrogenic 17 beta-hydroxysteroid dehydrogenase (type I 17 beta-HSD) catalyzes the last step in the biosynthesis of 17 beta-estradiol from the less potent estrogen, estrone, it is an attractive target for the design of inhibitors of estrogen production and tumor growth. This human enzyme shares less than 15% sequence identity with a bacterial 3 alpha,20 beta-HSD, for which the three-dimensional structure is known. The amino acid sequence of 17 beta-HSD also differs from that of bacterial 3 alpha,20 beta-HSD by two insertions (of 11 and 14 residues) and 52 additional residues at the C terminus. RESULTS: The 2.20 A resolution structure of type I 17 beta-HSD, the first mammalian steroidogenic enzyme studied by X-ray crystallographic techniques, reveals a fold characteristic of the short-chain dehydrogenases. The active site contains a Tyr-X-X-X-Lys sequence (where X is any amino acid) and a serine residue, features that are conserved in short-chain steroid dehydrogenases. The structure also contains three alpha-helices and a helix-turn-helix motif, not observed in short-chain dehydrogenase structures reported previously. No cofactor density could be located. CONCLUSIONS: The helices present in 17 beta-HSD that were not in the two previous short-chain dehydrogenase structures are located at one end of the substrate-binding cleft away from the catalytic triad. These helices restrict access to the active site and appear to influence substrate specificity. Modeling the position of estradiol in the active site suggests that a histidine side chain may play a critical role in substrate recognition. One or more of these helices may also be involved in the reported association of the enzyme with membranes. A model for steroid and cofactor binding as well as for the estrone to estradiol transition state is proposed. The structure of the active site provides a rational basis for designing more specific inhibitors of this breast cancer associated enzyme. FAU - Ghosh, D AU - Ghosh D AD - Hauptman-Woodward Medical Research Institute, Inc., Buffalo, NY 14203, USA. FAU - Pletnev, V Z AU - Pletnev VZ FAU - Zhu, D W AU - Zhu DW FAU - Wawrzak, Z AU - Wawrzak Z FAU - Duax, W L AU - Duax WL FAU - Pangborn, W AU - Pangborn W FAU - Labrie, F AU - Labrie F FAU - Lin, S X AU - Lin SX LA - eng GR - DK26546/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Isoenzymes) RN - EC 1.1.1.62 (Estradiol Dehydrogenases) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Catalysis MH - Crystallography, X-Ray MH - Estradiol Dehydrogenases/*chemistry MH - Humans MH - Isoenzymes/*chemistry MH - *Models, Molecular MH - Molecular Sequence Data MH - Placenta/enzymology MH - *Protein Conformation MH - Substrate Specificity EDAT- 1995/05/15 MHDA- 1995/05/15 00:01 CRDT- 1995/05/15 00:00 PST - ppublish SO - Structure. 1995 May 15;3(5):503-13. PMID- 23660966 OWN - NLM STAT- MEDLINE DA - 20130802 DCOM- 20131216 IS - 1530-6860 (Electronic) IS - 0892-6638 (Linking) VI - 27 IP - 8 DP - 2013 Aug TI - Intrinsic disorder of the bacterial cell division protein ZipA: coil-to-brush conformational transition. PG - 3363-75 LID - 10.1096/fj.12-224337 [doi] AB - The full-length ZipA protein from Escherichia coli, one of the essential elements of the cell division machinery, was studied in a surface model built as adsorbed monolayers. The interplay between lateral packing and molecular conformation was probed using a combined methodology based on the scaling analysis of the surface pressure isotherms and ellipsometry measurements of the monolayer thickness. The observed behavior is compatible with the one expected for an intrinsically disordered and highly flexible protein that is preferentially structured in a random coil conformation. At low grafting densities, ZipA coils organize in a mushroom-like regime, whereas a coil-to-brush transition occurs on increasing lateral packing. The structural results suggest a functional scenario in which ZipA acts as a flexible tether anchoring bacterial proto-ring elements to the membrane during the earlier stages of division. FAU - Lopez-Montero, Ivan AU - Lopez-Montero I AD - Departamento de Quimica Fisica I, Universidad Complutense de Madrid, Ciudad Universitaria s/n, E28040 Madrid, Spain. FAU - Lopez-Navajas, Pilar AU - Lopez-Navajas P FAU - Mingorance, Jesus AU - Mingorance J FAU - Rivas, German AU - Rivas G FAU - Velez, Marisela AU - Velez M FAU - Vicente, Miguel AU - Vicente M FAU - Monroy, Francisco AU - Monroy F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130509 PL - United States TA - FASEB J JT - FASEB journal : official publication of the Federation of American Societies for Experimental Biology JID - 8804484 RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (Cell Cycle Proteins) RN - 0 (Cytoskeletal Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (FtsZ protein, Bacteria) RN - 0 (Recombinant Proteins) RN - 0 (ZipA protein, E coli) SB - IM MH - Bacterial Proteins/chemistry/genetics/metabolism MH - Carrier Proteins/*chemistry/genetics/metabolism MH - Cell Cycle Proteins/*chemistry/genetics/metabolism MH - Cell Division/genetics MH - Cell Membrane/metabolism MH - Cytoskeletal Proteins/chemistry/genetics/metabolism MH - Elasticity MH - Escherichia coli/genetics/metabolism MH - Escherichia coli Proteins/*chemistry/genetics/metabolism MH - Kinetics MH - Models, Molecular MH - Protein Binding MH - *Protein Conformation MH - Recombinant Proteins/chemistry/metabolism MH - Surface Properties MH - Thermodynamics OTO - NOTNLM OT - E. coli OT - Langmuir monolayers OT - polymer theory EDAT- 2013/05/11 06:00 MHDA- 2013/12/18 06:00 CRDT- 2013/05/11 06:00 PHST- 2013/05/09 [aheadofprint] AID - fj.12-224337 [pii] AID - 10.1096/fj.12-224337 [doi] PST - ppublish SO - FASEB J. 2013 Aug;27(8):3363-75. doi: 10.1096/fj.12-224337. Epub 2013 May 9. PMID- 11718560 OWN - NLM STAT- MEDLINE DA - 20011123 DCOM- 20011227 LR - 20071114 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 314 IP - 2 DP - 2001 Nov 23 TI - Defining the molecular basis of Arf and Hdm2 interactions. PG - 263-77 AB - Understanding the interaction of Arf and Hdm2 has recently become a central issue in cancer biology. In response to hyperproliferative signals, p14(Arf) stabilizes p53 by binding to Hdm2 and inhibits the ubiquitination and subsequent proteosome-dependent degradation of p53. The medical importance of the Arf-Hdm2-p53 regulatory system is highlighted by the finding that either p53 or p14(Arf) are lost or modified in virtually all human cancers. Isolated Arf and Hdm2 domains are dynamically disordered in solution, yet they retain the ability to interact in vitro and in cellular assays. Upon binding, domains of both Arf and Hdm2 undergo a dramatic transition from disordered conformations to extended structures comprised of beta-strands. The presence of domains from both proteins are necessary and sufficient for the formation of the highly stable extended beta structures. We have mapped sites within Arf and Hdm2 that interact at a resolution of five amino acid residues using surface plasmon resonance. Surface plasmon resonance and circular dichroism spectropolarimetry confirm the presence of multiple interaction domains within each protein. Both p14(Arf) (human) and p19(Arf) (mouse) interact with Hdm2 through two short motifs present in their N termini. The Arf interacting region of Hdm2 is also composed of two short sequences located in the central acidic domain, between residues 235-264 and 270-289. The binding-induced structural transition is also induced by short peptides, 15 amino acids in length, that contain the binding motifs. Micro-injection and live cell imaging of proteins tagged with fluorescent labels was used to confirm the in vivo function of the interaction domains. Arf and Hdm2 thus appear to interact through a novel mechanism that exerts control over the cell division cycle. The novel molecular mechanism of interaction and the limited size of the protein domains involved provide opportunities for the development of anticancer therapeutics. CI - Copyright 2001 Academic Press. FAU - Bothner, B AU - Bothner B AD - Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. FAU - Lewis, W S AU - Lewis WS FAU - DiGiammarino, E L AU - DiGiammarino EL FAU - Weber, J D AU - Weber JD FAU - Bothner, S J AU - Bothner SJ FAU - Kriwacki, R W AU - Kriwacki RW LA - eng GR - CA 21765/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Cdkn2a protein, mouse) RN - 0 (Cyclin-Dependent Kinase Inhibitor p16) RN - 0 (Nuclear Proteins) RN - 0 (Peptide Fragments) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Tumor Suppressor Protein p14ARF) RN - 0 (Tumor Suppressor Protein p53) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Mdm2 protein, mouse) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - 3T3 Cells MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Cell Nucleolus/chemistry/metabolism MH - Circular Dichroism MH - Cyclin-Dependent Kinase Inhibitor p16 MH - Gene Deletion MH - Humans MH - Magnetic Resonance Spectroscopy MH - Mice MH - Molecular Sequence Data MH - *Nuclear Proteins MH - Peptide Fragments/chemistry/metabolism MH - Protein Binding MH - Protein Interaction Mapping MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins/*chemistry/*metabolism MH - Proto-Oncogene Proteins c-mdm2 MH - Sequence Alignment MH - Surface Plasmon Resonance MH - Tumor Suppressor Protein p14ARF/*chemistry/genetics/*metabolism MH - Tumor Suppressor Protein p53/metabolism EDAT- 2001/11/24 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/11/24 10:00 AID - 10.1006/jmbi.2001.5110 [doi] AID - S0022-2836(01)95110-1 [pii] PST - ppublish SO - J Mol Biol. 2001 Nov 23;314(2):263-77. PMID- 24717772 OWN - NLM STAT- MEDLINE DA - 20140430 DCOM- 20140627 IS - 1873-3468 (Electronic) IS - 0014-5793 (Linking) VI - 588 IP - 9 DP - 2014 May 2 TI - Evidence of a conserved intrinsically disordered region in the C-terminus of the stringent response protein Rel from mycobacteria. PG - 1839-49 LID - 10.1016/j.febslet.2014.03.048 [doi] LID - S0014-5793(14)00267-1 [pii] AB - The RelA/SpoT enzyme produces (p)ppGpp that helps the bacterium survive during stress. The domains present in it are interspersed with connecting linkers whose functions have been poorly elucidated. We rationally analyzed the sequence and structural property of the regulatory C-terminal region in the Rel family of proteins and report the presence of an intrinsically disordered region between two successive domains in this region that are separated by a defined amino acid sequence length. We show that the length and secondary structure of this linker are conserved in Rel proteins, further signifying its importance in rendering flexibility for domain movement and domain-domain interaction. CI - Copyright (c) 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. FAU - Ekal, Lakhan AU - Ekal L AD - Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India. FAU - Ganesh, Bylapudi AU - Ganesh B AD - Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India. FAU - Joshi, Himanshu AU - Joshi H AD - Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India. FAU - Lama, Dilraj AU - Lama D AD - Biomolecular Modeling and Design Division, Bioinformatics Institute, A(*)STAR, Singapore 138671, Singapore. Electronic address: dilrajl@bii.a-star.edu.sg. FAU - Jain, Vikas AU - Jain V AD - Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462023, India. Electronic address: vikas@iiserb.ac.in. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140406 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Bacterial Proteins) RN - 0 (Intrinsically Disordered Proteins) RN - EC 6.- (Ligases) RN - EC 6.- (guanosine 3',5'-polyphosphate synthetases) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry MH - Circular Dichroism MH - Conserved Sequence MH - Hydrophobic and Hydrophilic Interactions MH - Intrinsically Disordered Proteins MH - Ligases/*chemistry MH - Molecular Sequence Data MH - Mycobacterium smegmatis/*enzymology MH - Phylogeny MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid OTO - NOTNLM OT - Intrinsically disordered region OT - Mycobacteria OT - RelA/SpoT OT - Stringent response OT - ppGpp EDAT- 2014/04/11 06:00 MHDA- 2014/06/28 06:00 CRDT- 2014/04/11 06:00 PHST- 2014/01/09 [received] PHST- 2014/03/22 [revised] PHST- 2014/03/24 [accepted] PHST- 2014/04/06 [aheadofprint] AID - S0014-5793(14)00267-1 [pii] AID - 10.1016/j.febslet.2014.03.048 [doi] PST - ppublish SO - FEBS Lett. 2014 May 2;588(9):1839-49. doi: 10.1016/j.febslet.2014.03.048. Epub 2014 Apr 6. PMID- 21046176 OWN - NLM STAT- MEDLINE DA - 20110914 DCOM- 20120301 LR - 20131121 IS - 1438-2199 (Electronic) IS - 0939-4451 (Linking) VI - 41 IP - 4 DP - 2011 Oct TI - Evidences of a natively unfolded state for the human topoisomerase IB N-terminal domain. PG - 945-53 LID - 10.1007/s00726-010-0794-x [doi] AB - The N-terminal domain of human topoisomerase IB has been expressed, purified and characterized by spectroscopic techniques. CD spectra as a function of concentration and pH indicate that the domain does not possess any defined secondary structure. The protein is probably in a natively unfolded state since its denaturation curve is indicative of a non-cooperative transition. Evidence of a partially folded structure comes from the fluorescence spectrum of ANS, whose intensity increases in presence of the domain. Indication of a partial structural arrangement of the domain comes also from the endogenous fluorescence of tryptophans that is centred at 350 nm in the native and shifts to 354 nm in the fully denaturated protein. Interestingly despite the poor structural degree, as also confirmed by a predictive approach, the domain efficiently binds DNA, suggesting that the absence of a defined 3D structure has a functional meaning that permits the domain to be available for the interaction with different molecular partners. FAU - Vassallo, Oscar AU - Vassallo O AD - Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133, Rome, Italy. FAU - Castelli, Silvia AU - Castelli S FAU - D'Annessa, Ilda AU - D'Annessa I FAU - della Rocca, Blasco Morozzo AU - della Rocca BM FAU - Stella, Lorenzo AU - Stella L FAU - Knudsen, Birgitta R AU - Knudsen BR FAU - Desideri, Alessandro AU - Desideri A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101103 PL - Austria TA - Amino Acids JT - Amino acids JID - 9200312 RN - 0 (8-anilino-1-naphthalenesulfonic acid) RN - 0 (Anilino Naphthalenesulfonates) RN - 0 (Recombinant Proteins) RN - 8DUH1N11BX (Tryptophan) RN - 9007-49-2 (DNA) RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) RN - EC 5.99.1.2 (TOP1 protein, human) SB - IM MH - Amino Acid Sequence MH - Anilino Naphthalenesulfonates/chemistry MH - Binding Sites MH - Circular Dichroism MH - DNA/metabolism MH - DNA Topoisomerases, Type I/*chemistry/genetics/*metabolism MH - Escherichia coli/genetics MH - Humans MH - Molecular Sequence Data MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/isolation & purification MH - Tryptophan/chemistry EDAT- 2010/11/04 06:00 MHDA- 2012/03/02 06:00 CRDT- 2010/11/04 06:00 PHST- 2010/07/20 [received] PHST- 2010/10/20 [accepted] PHST- 2010/11/03 [aheadofprint] AID - 10.1007/s00726-010-0794-x [doi] PST - ppublish SO - Amino Acids. 2011 Oct;41(4):945-53. doi: 10.1007/s00726-010-0794-x. Epub 2010 Nov 3. PMID- 22399322 OWN - NLM STAT- MEDLINE DA - 20120308 DCOM- 20120410 IS - 0065-2598 (Print) IS - 0065-2598 (Linking) VI - 725 DP - 2012 TI - The measles virus N(TAIL)-XD complex: an illustrative example of fuzziness. PG - 126-41 LID - 10.1007/978-1-4614-0659-4_8 [doi] AB - In this chapter, I focus on the biochemical and structural characterization of the complex between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N(TAIL)) and the C-terminal X domain (XD) of the viral phosphoprotein (P). I summarize the main experimental data available so far pointing out the prevalently disordered nature of N(TAIL) even after complex formation and the role of the flexible C-terminal appendage in the binding reaction. I finally discuss the possible functional role of these residual disordered regions within the complex in terms of their ability to capture other regulatory, binding partners. FAU - Longhi, Sonia AU - Longhi S AD - Architecture et Fonction des Macromolecules Biologiques, Universites d'Aix-Marseille I et II, Marseille, France. Sonia.Longhi@afmb.univ-mrs.fr LA - eng GR - R01 NS031693-11A2/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Adv Exp Med Biol JT - Advances in experimental medicine and biology JID - 0121103 RN - 0 (Nucleoproteins) RN - 0 (Phosphoproteins) RN - 0 (Viral Proteins) RN - 0 (nucleoprotein, Measles virus) SB - IM MH - Animals MH - Humans MH - Measles virus/*physiology MH - Models, Molecular MH - Nucleoproteins/*chemistry/metabolism MH - Phosphoproteins/*chemistry/metabolism MH - Protein Folding MH - Protein Structure, Tertiary MH - Viral Proteins/*chemistry/metabolism EDAT- 2012/03/09 06:00 MHDA- 2012/04/11 06:00 CRDT- 2012/03/09 06:00 AID - 10.1007/978-1-4614-0659-4_8 [doi] PST - ppublish SO - Adv Exp Med Biol. 2012;725:126-41. doi: 10.1007/978-1-4614-0659-4_8. PMID- 22399320 OWN - NLM STAT- MEDLINE DA - 20120308 DCOM- 20120410 IS - 0065-2598 (Print) IS - 0065-2598 (Linking) VI - 725 DP - 2012 TI - Roles for intrinsic disorder and fuzziness in generating context-specific function in Ultrabithorax, a Hox transcription factor. PG - 86-105 LID - 10.1007/978-1-4614-0659-4_6 [doi] AB - Surprisingly few transcription factors drive animal development relative to the number and diversity of final tissues and body structures. Therefore, most transcription factors must function in more than one tissue. In a famous example, members of the Hox transcription factor family are expressed in contiguous stripes along the anterior/posterior axis during animal development. Individual Hox transcription factors specify all tissues within their expression domain and thus must respond to cellular cues to instigate the correct tissue-specific gene regulatory cascade. We describe how, in the Drosophila Hox protein Ultrabithorax, intrinsically disordered regions implement, regulate and co-ordinate multiple functions, potentially enabling context-specific gene regulation. The large N-terminal disordered domain encodes most of the transcription activation domain and directly impacts DNA binding affinity by the Ubx homeodomain. Similarly, the C-terminal disordered domain alters DNA binding affinity and specificity, interaction with a Hox binding protein and strongly influences both transcription activation and repression. Phosphorylation of the N-terminal disordered domain and alternative splicing of the C-terminal disordered domain could allow the cell to both regulate and co-ordinate DNA binding, protein interactions and transcription regulation. For regulatory mechanisms relying on disorder to continue to be available when Ubx is bound to other proteins or DNA, fuzziness would need to be preserved in these macromolecular complexes. The intrinsically disordered domains in Hox proteins are predicted to be on the very dynamic end of the disorder spectrum, potentially allowing disorder to persist when Ubx is bound to proteins or DNA to regulate the function of these "fuzzy" complexes. Because both intrinsically disordered regions within Ubx have multiple roles, each region may implement several different regulatory mechanisms identified in fuzzy complexes. These intrinsic disorder-based regulatory mechanisms are likely to be critical for allowing Ubx to sense tissue identity and respond by implementing a context-specific gene regulatory cascade. FAU - Bondos, Sarah E AU - Bondos SE AD - Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, USA. sebondos@tamhsc.edu FAU - Hsiao, Hao-Ching AU - Hsiao HC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Adv Exp Med Biol JT - Advances in experimental medicine and biology JID - 0121103 RN - 0 (Drosophila Proteins) RN - 0 (Homeodomain Proteins) RN - 0 (Transcription Factors) RN - 0 (Ubx protein, Drosophila) SB - IM MH - Animals MH - Drosophila Proteins/*chemistry/*metabolism MH - Drosophila melanogaster/*metabolism MH - Homeodomain Proteins/*chemistry/*metabolism MH - Transcription Factors/*chemistry/*metabolism EDAT- 2012/03/09 06:00 MHDA- 2012/04/11 06:00 CRDT- 2012/03/09 06:00 AID - 10.1007/978-1-4614-0659-4_6 [doi] PST - ppublish SO - Adv Exp Med Biol. 2012;725:86-105. doi: 10.1007/978-1-4614-0659-4_6. PMID- 22399321 OWN - NLM STAT- MEDLINE DA - 20120308 DCOM- 20120410 IS - 0065-2598 (Print) IS - 0065-2598 (Linking) VI - 725 DP - 2012 TI - Molecular recognition by the EWS transcriptional activation domain. PG - 106-25 LID - 10.1007/978-1-4614-0659-4_7 [doi] AB - Interactions between Intrinsically Disordered Protein Regions (IDRs) and their targets commonly exhibit localised contacts via target-induced disorder to order transitions. Other more complex IDR target interactions have been termed "fuzzy" because the IDR does not form a well-defined induced structure. In some remarkable cases of fuzziness IDR function is apparently sequence independent and conferred by amino acid composition. Such cases have been referred to as "random fuzziness" but the molecular features involved are poorly characterised. The transcriptional activation domain (EAD) of oncogenic Ewing's Sarcoma Fusion Proteins (EFPs) is an approximately 280 residue IDR with a biased composition restricted to Ala, Gly, Gln, Pro, Ser, Thr and Tyr. Multiple aromatic side chains (exclusively from Try residues) and the particular EAD composition are crucial for molecular recognition but there appears to be no other major geometrically constrained requirement. Computational analysis of the EAD using PONDR (Molecular Kinetics, Inc. http://www.pondr. com) complements the functional data and shows, accordingly, that propensity for structural order within the EAD is conferred by Tyr residues. To conclude, molecular recognition by the EAD is extraordinarily malleable and involves multiple aromatic contacts facilitated by a flexible peptide backbone and, most likely, a limited number of weaker contributions from amenable side chains. I propose to refer to this mode of fuzzy recognition as "polyaromatic", noting that it shares some fundamental features with the "polyelectrostatic" (phosphorylation-dependent) interaction of the Sic1 Cdk inhibitor and Cdc4._I will also speculate on more detailed models for molecular recognition by the EAD and their relationship to native (non-oncogenic) EAD function. FAU - Lee, Kevin A W AU - Lee KA AD - Department of Biology, Hong Kong University of Science and Technology, Hong Kong, China. bokaw@ust.hk LA - eng PT - Journal Article PT - Review PL - United States TA - Adv Exp Med Biol JT - Advances in experimental medicine and biology JID - 0121103 RN - 0 (RNA-Binding Protein EWS) SB - IM MH - Amino Acid Sequence MH - Animals MH - Humans MH - Molecular Sequence Data MH - RNA-Binding Protein EWS/*chemistry/*genetics/*metabolism MH - Sequence Homology, Amino Acid MH - *Transcriptional Activation EDAT- 2012/03/09 06:00 MHDA- 2012/04/11 06:00 CRDT- 2012/03/09 06:00 AID - 10.1007/978-1-4614-0659-4_7 [doi] PST - ppublish SO - Adv Exp Med Biol. 2012;725:106-25. doi: 10.1007/978-1-4614-0659-4_7. PMID- 19898942 OWN - NLM STAT- MEDLINE DA - 20100121 DCOM- 20100318 LR - 20140827 IS - 1573-5001 (Electronic) IS - 0925-2738 (Linking) VI - 45 IP - 4 DP - 2009 Dec TI - Comprehensive determination of (3)J (HNHalpha) for unfolded proteins using (13)C'-resolved spin-echo difference spectroscopy. PG - 343-9 LID - 10.1007/s10858-009-9382-3 [doi] AB - An experiment is presented to determine (3)J(HNHalpha) coupling constants, with significant advantages for applications to unfolded proteins. The determination of coupling constants for the peptide chain using 1D (1)H, or 2D and 3D (1)H-(15)N correlation spectroscopy is often hampered by extensive resonance overlap when dealing with flexible, disordered proteins. In the experiment detailed here, the overlap problem is largely circumvented by recording (1)H-(13)C' correlation spectra, which demonstrate superior resolution for unfolded proteins. J-coupling constants are extracted from the peak intensities in a pair of 2D spin-echo difference experiments, affording rapid acquisition of the coupling data. In an application to the cytoplasmic domain of human neuroligin-3 (hNlg3cyt) data were obtained for 78 residues, compared to 54 coupling constants obtained from a 3D HNHA experiment. The coupling constants suggest that hNlg3cyt is intrinsically disordered, with little propensity for structure. FAU - Otten, Renee AU - Otten R AD - Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. FAU - Wood, Kathleen AU - Wood K FAU - Mulder, Frans A A AU - Mulder FA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091107 PL - Netherlands TA - J Biomol NMR JT - Journal of biomolecular NMR JID - 9110829 RN - 0 (Carbon Isotopes) RN - 0 (Cell Adhesion Molecules, Neuronal) RN - 0 (Membrane Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Proteins) RN - 0 (neuroligin 3) SB - IM MH - Carbon Isotopes MH - Cell Adhesion Molecules, Neuronal MH - Humans MH - Membrane Proteins/chemistry MH - Nerve Tissue Proteins/chemistry MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Protein Conformation MH - Proteins/*chemistry PMC - PMC2777233 EDAT- 2009/11/10 06:00 MHDA- 2010/03/20 06:00 CRDT- 2009/11/10 06:00 PHST- 2009/07/09 [received] PHST- 2009/10/01 [accepted] PHST- 2009/11/07 [aheadofprint] AID - 10.1007/s10858-009-9382-3 [doi] PST - ppublish SO - J Biomol NMR. 2009 Dec;45(4):343-9. doi: 10.1007/s10858-009-9382-3. Epub 2009 Nov 7. PMID- 18155889 OWN - NLM STAT- MEDLINE DA - 20080324 DCOM- 20080623 LR - 20131121 IS - 0927-7765 (Print) IS - 0927-7765 (Linking) VI - 63 IP - 1 DP - 2008 May 1 TI - Effect of surfactants on casein structure: a spectroscopic study. PG - 83-90 AB - Fluorescence and circular dichroism spectroscopy were used to study the effect of two surfactants having oppositely charged head groups - cationic cetyltrimethyl ammonium bromide (CTAB) and anionic sodium dodecyl sulphate (SDS) - on the structure of the intrinsically unstructured proteins alpha s-, beta- and kappa-caseins. Although globular proteins are generally known to denature on interacting with surfactants, the caseins were found to adopt more ordered conformations in presence of both SDS and CTAB. The folding induced by CTAB was more efficient than by SDS, as implied by the behaviour of fluorescence and circular dichroic spectra of the caseins in solutions containing varying concentrations of the surfactants. The differential response of the proteins to the two surfactants may lie in the fact that the negatively charged caseins experience a repulsive electrostatic interaction with the negatively charged head groups of SDS, while their interaction with the positively charged head groups of CTAB is attractive in nature. Our results are consistent with two different types of the 'necklace and bead' model for the structure of surfactant-casein complexes: while groups of SDS molecules converge tail first around exposed hydrophobic surfaces of the caseins to form micelle-like structures, the protein itself wraps around micellar aggregates of CTAB that have cationic head groups in close association with its negatively charged/polar residues. FAU - Chakraborty, Asima AU - Chakraborty A AD - Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India. FAU - Basak, Soumen AU - Basak S LA - eng PT - Journal Article DEP - 20071121 PL - Netherlands TA - Colloids Surf B Biointerfaces JT - Colloids and surfaces. B, Biointerfaces JID - 9315133 RN - 0 (Caseins) RN - 0 (Cetrimonium Compounds) RN - 0 (Pyrenes) RN - 0 (Solutions) RN - 0 (Surface-Active Agents) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - 8DUH1N11BX (Tryptophan) RN - Z7FF1XKL7A (cetrimonium) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Caseins/*chemistry MH - Cetrimonium Compounds MH - Chemistry, Physical MH - Circular Dichroism MH - Fluorescence Polarization MH - Molecular Sequence Data MH - Physicochemical Phenomena MH - Protein Conformation MH - Pyrenes/chemistry MH - Sodium Dodecyl Sulfate MH - Solutions MH - Spectrometry, Fluorescence MH - Spectrophotometry, Ultraviolet MH - Surface-Active Agents/*chemistry MH - Tryptophan/chemistry EDAT- 2007/12/25 09:00 MHDA- 2008/06/24 09:00 CRDT- 2007/12/25 09:00 PHST- 2007/09/20 [received] PHST- 2007/11/13 [accepted] PHST- 2007/11/21 [aheadofprint] AID - S0927-7765(07)00429-8 [pii] AID - 10.1016/j.colsurfb.2007.11.005 [doi] PST - ppublish SO - Colloids Surf B Biointerfaces. 2008 May 1;63(1):83-90. Epub 2007 Nov 21. PMID- 18948596 OWN - NLM STAT- MEDLINE DA - 20081029 DCOM- 20081201 LR - 20140902 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 105 IP - 43 DP - 2008 Oct 28 TI - NMR studies of a channel protein without membranes: structure and dynamics of water-solubilized KcsA. PG - 16537-42 LID - 10.1073/pnas.0805501105 [doi] AB - Structural studies of polytopic membrane proteins are often hampered by the vagaries of these proteins in membrane mimetic environments and by the difficulties in handling them with conventional techniques. Designing and creating water-soluble analogues with preserved native structures offer an attractive alternative. We report here solution NMR studies of WSK3, a water-soluble analogue of the potassium channel KcsA. The WSK3 NMR structure (PDB ID code 2K1E) resembles the KcsA crystal structures, validating the approach. By more stringent comparison criteria, however, the introduction of several charged residues aimed at improving water solubility seems to have led to the possible formations of a few salt bridges and hydrogen bonds not present in the native structure, resulting in slight differences in the structure of WSK3 relative to KcsA. NMR dynamics measurements show that WSK3 is highly flexible in the absence of a lipid environment. Reduced spectral density mapping and model-free analyses reveal dynamic characteristics consistent with an isotropically tumbling tetramer experiencing slow (nanosecond) motions with unusually low local ordering. An altered hydrogen-bond network near the selectivity filter and the pore helix, and the intrinsically dynamic nature of the selectivity filter, support the notion that this region is crucial for slow inactivation. Our results have implications not only for the design of water-soluble analogues of membrane proteins but also for our understanding of the basic determinants of intrinsic protein structure and dynamics. FAU - Ma, Dejian AU - Ma D AD - Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA. FAU - Tillman, Tommy S AU - Tillman TS FAU - Tang, Pei AU - Tang P FAU - Meirovitch, Eva AU - Meirovitch E FAU - Eckenhoff, Roderic AU - Eckenhoff R FAU - Carnini, Anna AU - Carnini A FAU - Xu, Yan AU - Xu Y LA - eng SI - PDB/2K1E GR - P01GM055876/GM/NIGMS NIH HHS/United States GR - R01GM056257/GM/NIGMS NIH HHS/United States GR - R37 GM049202/GM/NIGMS NIH HHS/United States GR - R37GM049202/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20081023 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Bacterial Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (KcsA protein, Streptomyces coelicolor) RN - 0 (Potassium Channels) RN - 0 (Potassium Channels, Voltage-Gated) RN - 0 (Solutions) RN - 059QF0KO0R (Water) SB - IM MH - Bacterial Proteins MH - Escherichia coli Proteins/*chemistry MH - Hydrogen Bonding MH - Kinetics MH - *Magnetic Resonance Spectroscopy MH - *Models, Molecular MH - Molecular Structure MH - Motion MH - Potassium Channels/*chemistry MH - Potassium Channels, Voltage-Gated MH - Solutions MH - Water PMC - PMC2572164 OID - NLM: PMC2572164 EDAT- 2008/10/25 09:00 MHDA- 2008/12/17 09:00 CRDT- 2008/10/25 09:00 PHST- 2008/10/23 [aheadofprint] AID - 0805501105 [pii] AID - 10.1073/pnas.0805501105 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16537-42. doi: 10.1073/pnas.0805501105. Epub 2008 Oct 23. PMID- 16794783 OWN - NLM STAT- MEDLINE DA - 20060908 DCOM- 20061019 LR - 20121115 IS - 1420-682X (Print) IS - 1420-682X (Linking) VI - 63 IP - 17 DP - 2006 Sep TI - Myelin basic protein: a multifunctional protein. PG - 1945-61 AB - Myelin basic protein (MBP), the second most abundant protein in central nervous system myelin, is responsible for adhesion of the cytosolic surfaces of multilayered compact myelin. A member of the 'intrinsically disordered' or conformationally adaptable protein family, it also appears to have several other functions. It can interact with a number of polyanionic proteins including actin, tubulin, Ca(2+)-calmodulin, and clathrin, and negatively charged lipids, and acquires structure on binding to them. It may act as a membrane actin-binding protein, which might allow it to participate in transmission of extracellular signals to the cytoskeleton in oligodendrocytes and tight junctions in myelin. Some size isoforms of MBP are transported into the nucleus and thus they may also bind polynucleotides. Extracellular signals received by myelin or cultured oligodendrocytes cause changes in phosphorylation of MBP, suggesting that MBP is also involved in signaling. Further study of this very abundant protein will reveal how it is utilized by the oligodendrocyte and myelin for different purposes. FAU - Boggs, J M AU - Boggs JM AD - Department of Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada. jmboggs@sickkids.ca LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Switzerland TA - Cell Mol Life Sci JT - Cellular and molecular life sciences : CMLS JID - 9705402 RN - 0 (Cytoskeletal Proteins) RN - 0 (Lipids) RN - 0 (Membrane Lipids) RN - 0 (Myelin Basic Protein) RN - 0 (Polymers) RN - 0 (Protein Isoforms) RN - 0 (polyanions) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cytoskeletal Proteins/metabolism MH - Humans MH - Lipids/chemistry MH - Membrane Lipids/chemistry/*metabolism MH - Mice MH - Models, Biological MH - Molecular Sequence Data MH - Myelin Basic Protein/genetics/*metabolism MH - Oligodendroglia/*physiology MH - Phosphorylation MH - Polymers/chemistry MH - Protein Isoforms/genetics/metabolism MH - *Protein Processing, Post-Translational RF - 204 EDAT- 2006/06/24 09:00 MHDA- 2006/10/20 09:00 CRDT- 2006/06/24 09:00 AID - 10.1007/s00018-006-6094-7 [doi] PST - ppublish SO - Cell Mol Life Sci. 2006 Sep;63(17):1945-61. PMID- 8039495 OWN - NLM STAT- MEDLINE DA - 19940819 DCOM- 19940819 LR - 20131121 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 13 IP - 13 DP - 1994 Jul 1 TI - Crystal structure of the adenovirus DNA binding protein reveals a hook-on model for cooperative DNA binding. PG - 2994-3002 AB - The adenovirus single-stranded DNA binding protein (Ad DBP) is a multifunctional protein required, amongst other things, for DNA replication and transcription control. It binds to single- and double-stranded DNA, as well as to RNA, in a sequence-independent manner. Like other single-stranded DNA binding proteins, it binds ssDNA, cooperatively. We report the crystal structure, at 2.6 A resolution, of the nucleic acid binding domain. This domain is active in DNA replication. The protein contains two zinc atoms in different, novel coordinations. The zinc atoms appear to be required for the stability of the protein fold rather than being involved in direct contacts with the DNA. The crystal structure shows that the protein contains a 17 amino acid C-terminal extension which hooks onto a second molecule, thereby forming a protein chain. Deletion of this C-terminal arm reduces cooperativity in DNA binding, suggesting a hook-on model for cooperativity. Based on this structural work and mutant studies, we propose that DBP forms a protein core around which the single-stranded DNA winds. FAU - Tucker, P A AU - Tucker PA AD - European Molecular Biology Laboratory, Heidelberg, Germany. FAU - Tsernoglou, D AU - Tsernoglou D FAU - Tucker, A D AU - Tucker AD FAU - Coenjaerts, F E AU - Coenjaerts FE FAU - Leenders, H AU - Leenders H FAU - van der Vliet, P C AU - van der Vliet PC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Adenovirus E2 Proteins) RN - 0 (DNA, Viral) RN - 0 (Recombinant Fusion Proteins) RN - J41CSQ7QDS (Zinc) SB - IM MH - Adenoviridae/*chemistry MH - Adenovirus E2 Proteins/*chemistry/genetics/metabolism MH - Amino Acid Sequence MH - Base Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - DNA, Viral/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Folding MH - Recombinant Fusion Proteins/biosynthesis/metabolism MH - Sequence Deletion MH - Zinc PMC - PMC395187 OID - NLM: PMC395187 EDAT- 1994/07/01 MHDA- 1994/07/01 00:01 CRDT- 1994/07/01 00:00 PST - ppublish SO - EMBO J. 1994 Jul 1;13(13):2994-3002. PMID- 20816082 OWN - NLM STAT- MEDLINE DA - 20100906 DCOM- 20101217 LR - 20140824 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 5 DP - 2010 Sep 8 TI - Probing structural transitions in the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by vibrational spectroscopy of cyanylated cysteines. PG - 1676-83 LID - 10.1016/j.bpj.2010.06.060 [doi] AB - Four single-cysteine variants of the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N(TAIL)) were cyanylated at cysteine and their infrared spectra in the C triple bond N stretching region were recorded both in the absence and in the presence of one of the physiological partners of N(TAIL), namely the C-terminal X domain (XD) of the viral phosphoprotein. Consistent with previous studies showing that XD triggers a disorder-to-order transition within N(TAIL), the C triple bond N stretching bands of the infrared probe were found to be significantly affected by XD, with this effect being position-dependent. When the cyanylated cysteine side chain is solvent-exposed throughout the structural transition, its changing linewidth reflects a local gain of structure. When the probe becomes partially buried due to binding, its frequency reports on the mean hydrophobicity of the microenvironment surrounding the labeled side chain of the bound form. The probe moiety is small compared to other common covalently attached spectroscopic probes, thereby minimizing possible steric hindrance/perturbation at the binding interface. These results show for the first time to our knowledge the suitability of site-specific cysteine mutagenesis followed by cyanylation and infrared spectroscopy to document structural transitions occurring within intrinsically disordered regions, with regions involved in binding and folding being identifiable at the residue level. CI - Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Bischak, Connor G AU - Bischak CG AD - Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA. FAU - Longhi, Sonia AU - Longhi S FAU - Snead, David M AU - Snead DM FAU - Costanzo, Stephanie AU - Costanzo S FAU - Terrer, Elodie AU - Terrer E FAU - Londergan, Casey H AU - Londergan CH LA - eng GR - R15-GM088749/GM/NIGMS NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Nitriles) RN - 0 (Nucleoproteins) RN - 0 (Viral Proteins) RN - K848JZ4886 (Cysteine) SB - IM MH - Binding Sites MH - Cysteine/*chemistry MH - *Measles virus MH - Models, Molecular MH - Nitriles/*chemistry MH - Nucleoproteins/*chemistry MH - Protein Structure, Tertiary MH - Spectrophotometry, Infrared/*methods MH - Substrate Specificity MH - *Vibration MH - Viral Proteins/*chemistry PMC - PMC2931715 OID - NLM: PMC2931715 EDAT- 2010/09/08 06:00 MHDA- 2010/12/18 06:00 CRDT- 2010/09/07 06:00 PHST- 2010/04/21 [received] PHST- 2010/06/23 [revised] PHST- 2010/06/28 [accepted] AID - S0006-3495(10)00804-0 [pii] AID - 10.1016/j.bpj.2010.06.060 [doi] PST - ppublish SO - Biophys J. 2010 Sep 8;99(5):1676-83. doi: 10.1016/j.bpj.2010.06.060. PMID- 11258888 OWN - NLM STAT- MEDLINE DA - 20010322 DCOM- 20010510 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 40 IP - 9 DP - 2001 Mar 6 TI - Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein. PG - 2777-89 AB - Ribonuclease P (RNase P) is the endoribonuclease responsible for the 5'-maturation of precursor tRNA transcripts. In bacteria, RNase P is composed of a catalytic RNA subunit and an associated protein subunit that enhances the substrate specificity of the holoenzyme. We have initiated a study of the biophysical properties of the protein subunit from Bacillus subtilis RNase P (P protein) toward the goal of understanding the thermodynamics of RNase P holoenzyme assembly. The P protein is predominantly unfolded in 10 mM sodium cacodylate at neutral pH based on circular dichroism and NMR studies and therefore has several characteristics typical of "intrinsically unstructured" proteins. Furthermore, the P protein folds to its native alpha/beta structure upon addition of various small molecule anions. Anion-induced folding is best attributed to the binding of these anions to the folded state of the protein, and a model is presented which describes the observed tightly coupled folding and binding phenomena. The P protein also undergoes a cooperative folding transition upon addition of the osmolyte trimethylamine N-oxide (TMAO). The equilibrium constant of folding (K(fold)) at 37 degrees C for the P protein was determined to be 0.0071 +/- 0.0005 using a two-state folding model to describe the TMAO titration data. Thus, the folding and binding equilibria observed in the anion-induced folding of the P protein can be uncoupled to determine the intrinsic binding affinities (K(a)'s) of the anionic ligands. Evidence that the osmolyte-induced and the ligand-induced folded conformations of the P protein are structurally similar is also presented. FAU - Henkels, C H AU - Henkels CH AD - Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, North Carolina 27710, USA. FAU - Kurz, J C AU - Kurz JC FAU - Fierke, C A AU - Fierke CA FAU - Oas, T G AU - Oas TG LA - eng GR - GM08487/GM/NIGMS NIH HHS/United States GR - GM45322/GM/NIGMS NIH HHS/United States GR - GM55387/GM/NIGMS NIH HHS/United States GR - R01 GM055387/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Anions) RN - 0 (Buffers) RN - 0 (Chlorides) RN - 0 (Ligands) RN - 0 (Methylamines) RN - 0 (RNA, Catalytic) RN - 0 (Ribonucleoproteins) RN - 0 (Solutions) RN - AJ2HL7EU8K (Cacodylic Acid) RN - EC 3.1.- (Endoribonucleases) RN - EC 3.1.26.5 (Ribonuclease P) RN - FLD0K1SJ1A (trimethyloxamine) SB - IM MH - Anions MH - Bacillus subtilis/*enzymology MH - Binding, Competitive MH - Buffers MH - Cacodylic Acid/chemistry/metabolism MH - Chlorides/chemistry/metabolism MH - Circular Dichroism MH - Endoribonucleases/*chemistry/*metabolism MH - Kinetics MH - Ligands MH - Methylamines/chemistry/metabolism MH - Models, Chemical MH - Nuclear Magnetic Resonance, Biomolecular MH - Osmolar Concentration MH - Protein Binding MH - *Protein Folding MH - RNA, Catalytic/*chemistry/*metabolism MH - Ribonuclease P MH - Ribonucleoproteins/*chemistry/*metabolism MH - Solutions EDAT- 2001/03/22 10:00 MHDA- 2001/05/22 10:01 CRDT- 2001/03/22 10:00 AID - bi002078y [pii] PST - ppublish SO - Biochemistry. 2001 Mar 6;40(9):2777-89. PMID- 23396917 OWN - NLM STAT- MEDLINE DA - 20130426 DCOM- 20130624 LR - 20141103 IS - 1098-5530 (Electronic) IS - 0021-9193 (Linking) VI - 195 IP - 10 DP - 2013 May TI - RNA type III secretion signals that require Hfq. PG - 2119-25 LID - 10.1128/JB.00024-13 [doi] AB - Salmonella virulence is largely mediated by two type III secretion systems (T3SS) that deliver effector proteins from the bacterium to a host cell; however, the secretion signal is poorly defined. Effector N termini are thought to contain the signal, but they lack homology, possess no identifiable motif, and adopt intrinsically disordered structures. Alternative studies suggest that RNA-encoded signals may also be recognized and that they can be located in the 5' untranslated leader sequence. We began our study by establishing the minimum sequence required for reporter translocation. Untranslated leader sequences predicted from 42 different Salmonella effector proteins were fused to the adenylate cyclase reporter (CyaA'), and each of them was tested for protein injection into J774 macrophages. RNA sequences derived from five effectors, gtgA, cigR, gogB, sseL, and steD, were sufficient for CyaA' translocation into host cells. To determine the mechanism of signal recognition, we identified proteins that bound specifically to the gtgA RNA. One of the unique proteins identified was Hfq. Hfq had no effect upon the translocation of full-length CigR and SteD, but injection of intact GtgA, GogB, and SseL was abolished in an hfq mutant, confirming the importance of Hfq. Our results demonstrated that the Salmonella pathogenicity island 2 (SPI-2) T3SS assembled into a functional apparatus independently of Hfq. Since particular effectors required Hfq for translocation, Hfq-RNA complexes may participate in signal recognition. FAU - Niemann, George S AU - Niemann GS AD - Department of Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon, USA. FAU - Brown, Roslyn N AU - Brown RN FAU - Mushamiri, Ivy T AU - Mushamiri IT FAU - Nguyen, Nhu T AU - Nguyen NT FAU - Taiwo, Rukayat AU - Taiwo R FAU - Stufkens, Afke AU - Stufkens A FAU - Smith, Richard D AU - Smith RD FAU - Adkins, Joshua N AU - Adkins JN FAU - McDermott, Jason E AU - McDermott JE FAU - Heffron, Fred AU - Heffron F LA - eng GR - 22A1-AI022933/AI/NIAID NIH HHS/United States GR - GM094623/GM/NIGMS NIH HHS/United States GR - P41 GM103493/GM/NIGMS NIH HHS/United States GR - P41 RR018522/RR/NCRR NIH HHS/United States GR - R01 AI022933/AI/NIAID NIH HHS/United States GR - RR018522/RR/NCRR NIH HHS/United States GR - U01 GM094623/GM/NIGMS NIH HHS/United States GR - Y01 AI008401/AI/NIAID NIH HHS/United States GR - Y1-AI8401-01/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130208 PL - United States TA - J Bacteriol JT - Journal of bacteriology JID - 2985120R RN - 0 (Bacterial Proteins) RN - 0 (RNA, Bacterial) SB - IM CIN - J Bacteriol. 2013 May;195(10):2117-8. PMID: 23524611 MH - Bacterial Proteins/genetics/*metabolism MH - Electrophoresis, Polyacrylamide Gel MH - Gene Expression Regulation, Bacterial/genetics/physiology MH - Genomic Islands/*genetics MH - Nucleic Acid Conformation MH - RNA, Bacterial/chemistry/genetics MH - Reverse Transcriptase Polymerase Chain Reaction MH - Salmonella typhimurium/*genetics/*metabolism PMC - PMC3650527 OID - NLM: PMC3650527 EDAT- 2013/02/12 06:00 MHDA- 2013/06/26 06:00 CRDT- 2013/02/12 06:00 PHST- 2013/02/08 [aheadofprint] AID - JB.00024-13 [pii] AID - 10.1128/JB.00024-13 [doi] PST - ppublish SO - J Bacteriol. 2013 May;195(10):2119-25. doi: 10.1128/JB.00024-13. Epub 2013 Feb 8. PMID- 23939913 OWN - NLM STAT- MEDLINE DA - 20130916 DCOM- 20140226 IS - 1521-3765 (Electronic) IS - 0947-6539 (Linking) VI - 19 IP - 37 DP - 2013 Sep 9 TI - Mapping functional interaction sites of human prune C-terminal domain by NMR spectroscopy in human cell lysates. PG - 12217-20 LID - 10.1002/chem.201302168 [doi] AB - Get well prune: The C-terminal third domain of h-prune is largely unfolded and involved in relevant protein-protein interactions, particularly with Nm23-H1 (see figure), GSK-3beta and gelsolin. This study shows that protein functions mediated by protein-protein interactions can be accurately followed in cell lysates by using fast NMR spectroscopy, which could be easily used for a very efficient NMR drug-discovery strategy. CI - Copyright (c) 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. FAU - Diana, Donatella AU - Diana D AD - Istituto di Biostrutture e Bioimmagini, CNR via Mezzocannone 16, 80134, Napoli (Italy). FAU - Smaldone, Giovanni AU - Smaldone G FAU - De Antonellis, Pasquale AU - De Antonellis P FAU - Pirone, Luciano AU - Pirone L FAU - Carotenuto, MariaNeve AU - Carotenuto M FAU - Alonzi, Alessandro AU - Alonzi A FAU - Di Gaetano, Sonia AU - Di Gaetano S FAU - Zollo, Massimo AU - Zollo M FAU - Pedone, Emilia M AU - Pedone EM FAU - Fattorusso, Roberto AU - Fattorusso R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130812 PL - Germany TA - Chemistry JT - Chemistry (Weinheim an der Bergstrasse, Germany) JID - 9513783 RN - 0 (Carrier Proteins) RN - 0 (Gelsolin) RN - 0 (NM23 Nucleoside Diphosphate Kinases) RN - 0 (PRUNE protein, human) RN - EC 2.7.11.1 (glycogen synthase kinase 3 beta) RN - EC 2.7.11.26 (Glycogen Synthase Kinase 3) SB - IM MH - Carrier Proteins/*chemistry/metabolism MH - Cell Biology MH - Drug Discovery MH - Gelsolin/chemistry MH - Glycogen Synthase Kinase 3/*chemistry/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - NM23 Nucleoside Diphosphate Kinases/*chemistry/metabolism OTO - NOTNLM OT - NMR spectroscopy OT - human cell lysates OT - intrinsically disordered proteins OT - protein-protein interactions OT - structure elucidation EDAT- 2013/08/14 06:00 MHDA- 2014/02/27 06:00 CRDT- 2013/08/14 06:00 PHST- 2013/06/06 [received] PHST- 2013/08/12 [aheadofprint] AID - 10.1002/chem.201302168 [doi] PST - ppublish SO - Chemistry. 2013 Sep 9;19(37):12217-20. doi: 10.1002/chem.201302168. Epub 2013 Aug 12. PMID- 7559631 OWN - NLM STAT- MEDLINE DA - 19951121 DCOM- 19951121 LR - 20081121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 270 IP - 42 DP - 1995 Oct 20 TI - Transactivation ability of p53 transcriptional activation domain is directly related to the binding affinity to TATA-binding protein. PG - 25014-9 AB - Tumor suppressor protein p53 is a potent transcriptional activator and regulates cell growth negatively. To characterize the transcriptional activation domain (TAD) of p53, various point mutants were constructed in the context of Gal4 DNA binding domain and tested for their transactivation ability. Our results demonstrated that the positionally conserved hydrophobic residues shared with herpes simplex virus VP16 and other transactivators are essential for transactivation. Also, the negatively charged residues and proline residues are necessary for full activity, but not essential for the activity of p53 TAD. Deletion analyses showed that p53 TAD can be divided into two subdomains, amino acids 1-40 and 43-73. An in vitro glutathione S-transferase pull-down assay establishes a linear correlation between p53 TAD-mediated transactivation in vivo and the binding activity of p53 TAD to TATA-binding protein (TBP) in vitro. Mutations that diminish the transactivation ability of Gal4-p53 TAD also impair the binding activity to TBP severely. Our results suggest that at least TBP is a direct target for p53 TAD and that the binding strength of TAD to TBP (TFIID) is an important parameter controlling activity of p53 TAD. In addition, circular dichroism spectroscopy has shown that p53 TAD peptide lacks any regular secondary structure in solution and that there is no significant difference between the spectra of the wild type TAD and that of the transactivation deficient mutant type. FAU - Chang, J AU - Chang J AD - Department of Life Science, Pohang University of Science and Technology, Republic of Korea. FAU - Kim, D H AU - Kim DH FAU - Lee, S W AU - Lee SW FAU - Choi, K Y AU - Choi KY FAU - Sung, Y C AU - Sung YC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA-Binding Proteins) RN - 0 (TATA-Box Binding Protein) RN - 0 (Transcription Factors) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Circular Dichroism MH - DNA-Binding Proteins/chemistry/*metabolism MH - Humans MH - Molecular Sequence Data MH - Mutation MH - Structure-Activity Relationship MH - *TATA Box MH - TATA-Box Binding Protein MH - Transcription Factors/chemistry/*metabolism MH - *Transcriptional Activation MH - Tumor Suppressor Protein p53/chemistry/*metabolism EDAT- 1995/10/20 MHDA- 1995/10/20 00:01 CRDT- 1995/10/20 00:00 PST - ppublish SO - J Biol Chem. 1995 Oct 20;270(42):25014-9. PMID- 8756332 OWN - NLM STAT- MEDLINE DA - 19960923 DCOM- 19960923 LR - 20091119 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 3 IP - 8 DP - 1996 Aug TI - Ras/Rap effector specificity determined by charge reversal. PG - 723-9 AB - Members of the Ras subfamily of small GTP-binding proteins have been shown to be promiscuous towards a variety of putative effector molecules such as the protein kinase c-Raf and the Ral-specific guanine nucleotide exchange factor (Ral-GEF). To address the question of specificity of interactions we have introduced the mutations E30D and K31E into Rap and show biochemically, by X-ray structure analysis and by transfection in vivo that the identical core effector region of Ras and Rap (residues 32-40) is responsible for molecular recognition, but that residues outside this region are responsible for the specificity of the interaction. The major determinant for the switch in specificity is the opposite charge of residue 31--Lys in Rap, Glu in Ras--which creates a favourable complementary interface for the Ras-Raf interaction. FAU - Nassar, N AU - Nassar N AD - Max-Planck-Institut fur molekulare Physiologie, Abteilung Strukturelle Biologie, Dortmund, Germany. FAU - Horn, G AU - Horn G FAU - Herrmann, C AU - Herrmann C FAU - Block, C AU - Block C FAU - Janknecht, R AU - Janknecht R FAU - Wittinghofer, A AU - Wittinghofer A LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Proto-Oncogene Proteins) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - EC 2.7.11.1 (Proto-Oncogene Proteins c-raf) RN - EC 3.6.1.- (GTP-Binding Proteins) RN - EC 3.6.5.2 (rap GTP-Binding Proteins) RN - EC 3.6.5.2 (ras Proteins) SB - IM CIN - Nat Struct Biol. 1996 Aug;3(8):653-5. PMID: 8756317 MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Cloning, Molecular MH - Crystallography, X-Ray MH - GTP-Binding Proteins/chemistry/genetics/*metabolism MH - Genes, Reporter MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding/genetics MH - Protein-Serine-Threonine Kinases/chemistry/genetics/*metabolism MH - Proto-Oncogene Proteins/chemistry/genetics/*metabolism MH - Proto-Oncogene Proteins c-raf MH - Rabbits MH - Structure-Activity Relationship MH - Transcriptional Activation MH - Transfection MH - rap GTP-Binding Proteins MH - ras Proteins/chemistry/genetics/*metabolism EDAT- 1996/08/01 MHDA- 1996/08/01 00:01 CRDT- 1996/08/01 00:00 PST - ppublish SO - Nat Struct Biol. 1996 Aug;3(8):723-9. PMID- 25081642 OWN - NLM STAT- In-Process DA - 20141203 IS - 1768-3254 (Electronic) IS - 0223-5234 (Linking) VI - 88 DP - 2014 Dec 17 TI - The use of nanopore analysis for discovering drugs which bind to alpha-synuclein for treatment of Parkinson's disease. PG - 42-54 LID - 10.1016/j.ejmech.2014.07.090 [doi] LID - S0223-5234(14)00705-3 [pii] AB - A major feature of Parkinson's disease is the formation of Lewy bodies in dopaminergic neurons which consist of misfolded alpha-synuclein. The binding of natural products to alpha-synuclein was evaluated by nanopore analysis and caffeine, curcumin, and nicotine all caused large conformational changes which may be related to their known neuroprotective effect in Parkinson's disease. The binding of the stereoisomers of nicotine were also studied by ITC, CD and NMR. It is proposed that (-)-nicotine causes the folding of alpha-synuclein into a loop with interaction between the N- and C-termini. For (+)-nicotine the binding is weaker and mainly involves residues in the N-terminus. Caffeine and nicotine can bind to alpha-synuclein simultaneously and may provide lead structures for the development of other compounds for the treatment of PD. CI - Crown Copyright (c) 2014. Published by Elsevier Masson SAS. All rights reserved. FAU - Tavassoly, Omid AU - Tavassoly O AD - Department of Biochemistry, 107 Wiggins Road, University of Saskatchewan, Saskatoon, Canada S7N 0W0. FAU - Kakish, Joe AU - Kakish J AD - Department of Biochemistry, 107 Wiggins Road, University of Saskatchewan, Saskatoon, Canada S7N 0W0. FAU - Nokhrin, Sergiy AU - Nokhrin S AD - Department of Biochemistry, 107 Wiggins Road, University of Saskatchewan, Saskatoon, Canada S7N 0W0. FAU - Dmitriev, Oleg AU - Dmitriev O AD - Department of Biochemistry, 107 Wiggins Road, University of Saskatchewan, Saskatoon, Canada S7N 0W0. FAU - Lee, Jeremy S AU - Lee JS AD - Department of Biochemistry, 107 Wiggins Road, University of Saskatchewan, Saskatoon, Canada S7N 0W0. Electronic address: jeremy.lee@usask.ca. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140725 PL - France TA - Eur J Med Chem JT - European journal of medicinal chemistry JID - 0420510 SB - IM OTO - NOTNLM OT - Caffeine OT - Curcumin OT - Induced folding OT - Intrinsically disordered protein OT - Nanopore analysis OT - Nicotine OT - Parkinson's disease OT - alpha-Synuclein EDAT- 2014/08/02 06:00 MHDA- 2014/08/02 06:00 CRDT- 2014/08/02 06:00 PHST- 2014/04/28 [received] PHST- 2014/07/23 [revised] PHST- 2014/07/24 [accepted] PHST- 2014/07/25 [aheadofprint] AID - S0223-5234(14)00705-3 [pii] AID - 10.1016/j.ejmech.2014.07.090 [doi] PST - ppublish SO - Eur J Med Chem. 2014 Dec 17;88:42-54. doi: 10.1016/j.ejmech.2014.07.090. Epub 2014 Jul 25. PMID- 16223749 OWN - NLM STAT- MEDLINE DA - 20060209 DCOM- 20060420 LR - 20101118 IS - 1535-9476 (Print) IS - 1535-9476 (Linking) VI - 5 IP - 2 DP - 2006 Feb TI - A novel two-dimensional electrophoresis technique for the identification of intrinsically unstructured proteins. PG - 265-73 AB - Intrinsically unstructured proteins (IUPs) lack a well defined three-dimensional structure under physiological conditions. They constitute a significant fraction of various proteomes, but only a handful of them have so far been identified. Here we report the development of a two-dimensional electrophoresis technique for their de novo recognition and characterization. This technique consists of the combination of native and 8 m urea electrophoresis of heat-treated proteins where IUPs are expected to run into the diagonal, whereas globular proteins either precipitate upon heat treatment or unfold and run off the diagonal in the second dimension. This behavior was born out by a collection of 10 known IUPs and four globular proteins. By running Escherichia coli and Saccharomyces cerevisiae extracts, several novel IUPs were also identified by mass spectrometric analysis of spots at or near the diagonal. By comparing this novel method to several other techniques, such as the PONDR(R) predictor, hydrophobicity-net charge plot, CD analysis, and gel filtration chromatography, it was shown to provide dependable global assessment of disorder even in dubious cases. Overall the reproducibility and ease of performance of this technique may promote the proteomic scale recognition and characterization of protein disorder. FAU - Csizmok, Veronika AU - Csizmok V AD - Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, Hungary. FAU - Szollosi, Edit AU - Szollosi E FAU - Friedrich, Peter AU - Friedrich P FAU - Tompa, Peter AU - Tompa P LA - eng GR - GR067595/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051013 PL - United States TA - Mol Cell Proteomics JT - Molecular & cellular proteomics : MCP JID - 101125647 RN - 0 (Escherichia coli Proteins) RN - 0 (Fungal Proteins) RN - 0 (Proteins) SB - IM MH - Electrophoresis, Gel, Two-Dimensional/*methods MH - Escherichia coli Proteins/analysis/chemistry MH - Fungal Proteins/analysis/chemistry MH - Hydrophobic and Hydrophilic Interactions MH - Mass Spectrometry MH - Proteins/*analysis/*chemistry/isolation & purification EDAT- 2005/10/15 09:00 MHDA- 2006/04/21 09:00 CRDT- 2005/10/15 09:00 PHST- 2005/10/13 [aheadofprint] AID - M500181-MCP200 [pii] AID - 10.1074/mcp.M500181-MCP200 [doi] PST - ppublish SO - Mol Cell Proteomics. 2006 Feb;5(2):265-73. Epub 2005 Oct 13. PMID- 12054823 OWN - NLM STAT- MEDLINE DA - 20020610 DCOM- 20020701 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 318 IP - 3 DP - 2002 May 3 TI - Structural dynamics of the membrane translocation domain of colicin E9 and its interaction with TolB. PG - 787-804 AB - In order for the 61 kDa colicin E9 protein toxin to enter the cytoplasm of susceptible cells and kill them by hydrolysing their DNA, the colicin must interact with the outer membrane BtuB receptor and Tol translocation pathway of target cells. The translocation function is located in the N-terminal domain of the colicin molecule. (1)H, (1)H-(1)H-(15)N and (1)H-(13)C-(15)N NMR studies of intact colicin E9, its DNase domain, minimal receptor-binding domain and two N-terminal constructs containing the translocation domain showed that the region of the translocation domain that governs the interaction of colicin E9 with TolB is largely unstructured and highly flexible. Of the expected 80 backbone NH resonances of the first 83 residues of intact colicin E9, 61 were identified, with 43 of them being assigned specifically. The absence of secondary structure for these was shown through chemical shift analyses and the lack of long-range NOEs in (1)H-(1)H-(15)N NOESY spectra (tau(m)=200 ms). The enhanced flexibility of the region of the translocation domain containing the TolB box compared to the overall tumbling rate of the protein was identified from the relatively large values of backbone and tryptophan indole (15)N spin-spin relaxation times, and from the negative (1)H-(15)N NOEs of the backbone NH resonances. Variable flexibility of the N-terminal region was revealed by the (15)N T(1)/T(2) ratios, which showed that the C-terminal end of the TolB box and the region immediately following it was motionally constrained compared to other parts of the N terminus. This, together with the observation of inter-residue NOEs involving Ile54, indicated that there was some structural ordering, resulting most probably from the interactions of side-chains. Conformational heterogeneity of parts of the translocation domain was evident from a multiplicity of signals for some of the residues. Im9 binding to colicin E9 had no effect on the chemical shifts or other NMR characteristics of the region of colicin E9 containing the TolB recognition sequence, though the interaction of TolB with intact colicin E9 bound to Im9 did affect resonances from this region. The flexibility of the translocation domain of colicin E9 may be connected with its need to recognise protein partners that assist it in crossing the outer membrane and in the translocation event itself. CI - c) 2002 Elsevier Science Ltd. FAU - Collins, Emily S AU - Collins ES AD - School of Chemical Sciences, University of East Anglia, Norwich NR4 7TJ, UK. FAU - Whittaker, Sara B-M AU - Whittaker SB FAU - Tozawa, Kaeko AU - Tozawa K FAU - MacDonald, Colin AU - MacDonald C FAU - Boetzel, Ruth AU - Boetzel R FAU - Penfold, Christopher N AU - Penfold CN FAU - Reilly, Ann AU - Reilly A FAU - Clayden, Nigel J AU - Clayden NJ FAU - Osborne, Michael J AU - Osborne MJ FAU - Hemmings, Andrew M AU - Hemmings AM FAU - Kleanthous, Colin AU - Kleanthous C FAU - James, Richard AU - James R FAU - Moore, Geoffrey R AU - Moore GR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (Colicins) RN - 0 (Escherichia coli Proteins) RN - 0 (Periplasmic Proteins) RN - 0 (colicin immunity proteins) RN - 0 (immE9 protein, E coli) RN - 0 (tolB protein, E coli) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/genetics/*metabolism MH - Biological Transport, Active MH - Colicins/*chemistry/genetics/*metabolism MH - Escherichia coli/genetics/metabolism MH - Escherichia coli Proteins/*chemistry/genetics/*metabolism MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - *Periplasmic Proteins MH - Protein Conformation MH - Protein Structure, Tertiary MH - Thermodynamics EDAT- 2002/06/11 10:00 MHDA- 2002/07/02 10:01 CRDT- 2002/06/11 10:00 AID - 10.1016/S0022-2836(02)00036-0 [doi] AID - S0022-2836(02)00036-0 [pii] PST - ppublish SO - J Mol Biol. 2002 May 3;318(3):787-804. PMID- 14717591 OWN - NLM STAT- MEDLINE DA - 20040113 DCOM- 20040525 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 2 DP - 2004 Jan 20 TI - Effect of cofactor binding and loop conformation on side chain methyl dynamics in dihydrofolate reductase. PG - 374-83 AB - Dihydrofolate reductase (DHFR) has several flexible active site loops that facilitate ligand binding and catalysis. Previous studies of backbone dynamics in several complexes of DHFR indicate that the time scale and amplitude of motion depend on the conformation of the active site loops. In this study, information on dynamics is extended to methyl-containing side chains. To understand the role of side chain dynamics in ligand binding and loop conformation, methyl deuterium relaxation rates of Escherichia coli DHFR in binary folate and ternary folate:NADP+ complexes have been measured, together with chi(1) rotamer populations for threonine, isoleucine, and valine residues, determined from measurements of 3J(CgammaCO) and 3J(CgammaN) coupling constants. The results indicate that, in addition to backbone motional restriction in the adenosine-binding site, side chain flexibility in the active site and the surrounding active site loops is diminished upon binding NADP+. Resonances for several methyls in the active site and the surrounding active site loops were severely broadened in the folate:NADP+ ternary complex, suggesting the presence of motion on the chemical shift time scale. The side chains of Ile14 and Ile94, which pack against the nicotinamide and pterin rings of the cofactor and substrate, respectively, exhibit rotamer disorder in the ternary folate:NADP+ complex. Conformational fluctuations of these side chains may play a role in transition state stabilization; the observed line broadening for Ile14 suggests motions on a microsecond/millisecond time scale. FAU - Schnell, Jason R AU - Schnell JR AD - Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. FAU - Dyson, H Jane AU - Dyson HJ FAU - Wright, Peter E AU - Wright PE LA - eng GR - GM56879/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Escherichia coli Proteins) RN - 04Y7590D77 (Isoleucine) RN - 2ZD004190S (Threonine) RN - 53-59-8 (NADP) RN - 935E97BOY8 (Folic Acid) RN - AR09D82C7G (Deuterium) RN - EC 1.5.1.3 (Tetrahydrofolate Dehydrogenase) RN - HG18B9YRS7 (Valine) SB - IM EIN - Biochemistry. 2013 Apr 2;52(13):2383 MH - Binding Sites MH - Deuterium/chemistry MH - Escherichia coli Proteins/*chemistry MH - Folic Acid/chemistry MH - Isoleucine/chemistry MH - NADP/chemistry MH - Nanotechnology MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Protein Structure, Tertiary MH - Spectrophotometry MH - Substrate Specificity MH - Tetrahydrofolate Dehydrogenase/*chemistry MH - *Thermodynamics MH - Threonine/chemistry MH - Valine/chemistry EDAT- 2004/01/14 05:00 MHDA- 2004/05/27 05:00 CRDT- 2004/01/14 05:00 AID - 10.1021/bi035464z [doi] PST - ppublish SO - Biochemistry. 2004 Jan 20;43(2):374-83. PMID- 20847048 OWN - NLM STAT- MEDLINE DA - 20101129 DCOM- 20101230 LR - 20140824 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 49 DP - 2010 Dec 3 TI - Stable alpha-synuclein oligomers strongly inhibit chaperone activity of the Hsp70 system by weak interactions with J-domain co-chaperones. PG - 38173-82 LID - 10.1074/jbc.M110.127753 [doi] AB - alpha-Synuclein aggregation and accumulation in Lewy bodies are implicated in progressive loss of dopaminergic neurons in Parkinson disease and related disorders. In neurons, the Hsp70s and their Hsp40-like J-domain co-chaperones are the only known components of chaperone network that can use ATP to convert cytotoxic protein aggregates into harmless natively refolded polypeptides. Here we developed a protocol for preparing a homogeneous population of highly stable beta-sheet enriched toroid-shaped alpha-Syn oligomers with a diameter typical of toxic pore-forming oligomers. These oligomers were partially resistant to in vitro unfolding by the bacterial Hsp70 chaperone system (DnaK, DnaJ, GrpE). Moreover, both bacterial and human Hsp70/Hsp40 unfolding/refolding activities of model chaperone substrates were strongly inhibited by the oligomers but, remarkably, not by unstructured alpha-Syn monomers even in large excess. The oligomers acted as a specific competitive inhibitor of the J-domain co-chaperones, indicating that J-domain co-chaperones may preferably bind to exposed bulky misfolded structures in misfolded proteins and, thus, complement Hsp70s that bind to extended segments. Together, our findings suggest that inhibition of the Hsp70/Hsp40 chaperone system by alpha-Syn oligomers may contribute to the disruption of protein homeostasis in dopaminergic neurons, leading to apoptosis and tissue loss in Parkinson disease and related neurodegenerative diseases. FAU - Hinault, Marie-Pierre AU - Hinault MP AD - Plant Molecular Biology Department, University of Lausanne, Biophore, 1015 Lausanne, Switzerland. FAU - Cuendet, America Farina Henriquez AU - Cuendet AF FAU - Mattoo, Rayees U H AU - Mattoo RU FAU - Mensi, Mounir AU - Mensi M FAU - Dietler, Giovanni AU - Dietler G FAU - Lashuel, Hilal A AU - Lashuel HA FAU - Goloubinoff, Pierre AU - Goloubinoff P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100916 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - 0 (HSP40 Heat-Shock Proteins) RN - 0 (HSP70 Heat-Shock Proteins) RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Apoptosis MH - Bacterial Proteins/*chemistry/metabolism MH - Cattle MH - HSP40 Heat-Shock Proteins/*chemistry/metabolism MH - HSP70 Heat-Shock Proteins/*chemistry/genetics/metabolism MH - Homeostasis MH - Humans MH - Leuconostoc/chemistry/metabolism MH - Lewy Bodies/chemistry/metabolism MH - Neurons/metabolism MH - Parkinson Disease/metabolism MH - *Protein Folding MH - *Protein Multimerization MH - Protein Structure, Tertiary MH - alpha-Synuclein/*chemistry/genetics/metabolism PMC - PMC2992251 OID - NLM: PMC2992251 EDAT- 2010/09/18 06:00 MHDA- 2010/12/31 06:00 CRDT- 2010/09/18 06:00 PHST- 2010/09/16 [aheadofprint] AID - M110.127753 [pii] AID - 10.1074/jbc.M110.127753 [doi] PST - ppublish SO - J Biol Chem. 2010 Dec 3;285(49):38173-82. doi: 10.1074/jbc.M110.127753. Epub 2010 Sep 16. PMID- 23260655 OWN - NLM STAT- MEDLINE DA - 20130114 DCOM- 20130702 LR - 20141104 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 21 IP - 1 DP - 2013 Jan 8 TI - Leukemia fusion target AF9 is an intrinsically disordered transcriptional regulator that recruits multiple partners via coupled folding and binding. PG - 176-83 LID - 10.1016/j.str.2012.11.011 [doi] LID - S0969-2126(12)00426-1 [pii] AB - Mixed lineage leukemia (MLL) fusion proteins cause oncogenic transformation of hematopoietic cells by constitutive recruitment of elongation factors to HOX promoters, resulting in overexpression of target genes. The structural basis of transactivation by MLL fusion partners remains undetermined. We show that the ANC1 homology domain (AHD) of AF9, one of the most common MLL translocation partners, is intrinsically disordered and recruits multiple transcription factors through coupled folding and binding. We determined the structure of the AF9 AHD in complex with the elongation factor AF4 and show that aliphatic residues, which are conserved in each of the AF9 binding partners, form an integral part of the hydrophobic core of the complex. Nuclear magnetic resonance relaxation measurements show that AF9 retains significant dynamic behavior which may facilitate exchange between disordered partners. We propose that AF9 functions as a signaling hub that regulates transcription through dynamic recruitment of cofactors in normal hematopoiesis and in acute leukemia. CI - Copyright (c) 2013 Elsevier Ltd. All rights reserved. FAU - Leach, Benjamin I AU - Leach BI AD - Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA. FAU - Kuntimaddi, Aravinda AU - Kuntimaddi A FAU - Schmidt, Charles R AU - Schmidt CR FAU - Cierpicki, Tomasz AU - Cierpicki T FAU - Johnson, Stephanie A AU - Johnson SA FAU - Bushweller, John H AU - Bushweller JH LA - eng SI - PDB/2LM0 GR - P30 CA044579/CA/NCI NIH HHS/United States GR - R01 CA155328/CA/NCI NIH HHS/United States GR - R01CA155328/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20121220 PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (DNA-Binding Proteins) RN - 0 (MLLT3 protein, human) RN - 0 (Nuclear Proteins) RN - 150826-18-9 (AFF1 protein, human) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - DNA-Binding Proteins/*chemistry MH - Fluorescence Polarization MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*chemistry MH - Protein Binding MH - Protein Folding MH - Protein Interaction Domains and Motifs MH - Protein Structure, Quaternary MH - Protein Structure, Secondary PMC - PMC3545106 MID - NIHMS425977 OID - NLM: NIHMS425977 OID - NLM: PMC3545106 EDAT- 2012/12/25 06:00 MHDA- 2013/07/03 06:00 CRDT- 2012/12/25 06:00 PHST- 2012/07/12 [received] PHST- 2012/10/19 [revised] PHST- 2012/11/13 [accepted] PHST- 2012/12/20 [aheadofprint] AID - S0969-2126(12)00426-1 [pii] AID - 10.1016/j.str.2012.11.011 [doi] PST - ppublish SO - Structure. 2013 Jan 8;21(1):176-83. doi: 10.1016/j.str.2012.11.011. Epub 2012 Dec 20. PMID- 20961854 OWN - NLM STAT- MEDLINE DA - 20101220 DCOM- 20110124 LR - 20140821 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 52 DP - 2010 Dec 24 TI - Molecular basis of the mixed lineage leukemia-menin interaction: implications for targeting mixed lineage leukemias. PG - 40690-8 LID - 10.1074/jbc.M110.172783 [doi] AB - Chromosomal translocations targeting the mixed lineage leukemia (MLL) gene result in MLL fusion proteins that are found in aggressive human acute leukemias. Disruption of MLL by such translocations leads to overexpression of Hox genes, resulting in a blockage of hematopoietic differentiation that ultimately leads to leukemia. Menin, which directly binds MLL, has been identified as an essential oncogenic co-factor required for the leukemogenic activity of MLL fusion proteins. Here, we characterize the molecular basis of the MLL-menin interaction. Using (13)C-detected NMR experiments, we have mapped the residues within the intrinsically unstructured fragment of MLL that are required for binding to menin. Interestingly, we found that MLL interacts with menin with a nanomolar affinity (K(d) approximately 10 nM) through two motifs, MBM1 and MBM2 (menin binding motifs 1 and 2). These motifs are located within the N-terminal 43-amino acid fragment of MLL, and the MBM1 represents a high affinity binding motif. Using alanine scanning mutagenesis of MBM1, we found that the hydrophobic residues Phe(9), Pro(10), and Pro(13) are most critical for binding. Furthermore, based on exchange-transferred nuclear Overhauser effect measurements, we established that MBM1 binds to menin in an extended conformation. In a series of competition experiments we showed that a peptide corresponding to MBM1 efficiently dissociates the menin-MLL complex. Altogether, our work establishes the molecular basis of the menin interaction with MLL and MLL fusion proteins and provides the necessary foundation for development of small molecule inhibitors targeting this interaction in leukemias with MLL translocations. FAU - Grembecka, Jolanta AU - Grembecka J AD - Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA. jolantag@umich.edu FAU - Belcher, Amalia M AU - Belcher AM FAU - Hartley, Thomas AU - Hartley T FAU - Cierpicki, Tomasz AU - Cierpicki T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101020 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (MEN1 protein, human) RN - 0 (MLL protein, human) RN - 0 (Oncogene Proteins, Fusion) RN - 0 (Proto-Oncogene Proteins) RN - 149025-06-9 (Myeloid-Lymphoid Leukemia Protein) SB - IM MH - Amino Acid Motifs MH - Amino Acid Substitution MH - Humans MH - Mutagenesis MH - Myeloid-Lymphoid Leukemia Protein/*chemistry/genetics/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Oncogene Proteins, Fusion/chemistry/genetics/metabolism MH - Protein Structure, Quaternary MH - Proto-Oncogene Proteins/*chemistry/genetics/metabolism MH - Structure-Activity Relationship PMC - PMC3003368 OID - NLM: PMC3003368 EDAT- 2010/10/22 06:00 MHDA- 2011/01/25 06:00 CRDT- 2010/10/22 06:00 PHST- 2010/10/20 [aheadofprint] AID - M110.172783 [pii] AID - 10.1074/jbc.M110.172783 [doi] PST - ppublish SO - J Biol Chem. 2010 Dec 24;285(52):40690-8. doi: 10.1074/jbc.M110.172783. Epub 2010 Oct 20. PMID- 9872404 OWN - NLM STAT- MEDLINE DA - 19990125 DCOM- 19990125 LR - 20131121 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 440 IP - 3 DP - 1998 Dec 4 TI - Random coil conformation of a Gly/Ala-rich insert in IkappaB alpha excludes structural stabilization as the mechanism for protection against proteasomal degradation. PG - 365-9 AB - Peptide segments of multiple glycine and alanine residues prevent the proteolytic degradation of ubiquitinated proteins by the proteasome. The structure of a Gly/Ala-rich insert in IkappaB alpha was probed by nuclear magnetic resonance (NMR) spectroscopy, comparing IkappaB alpha samples with and without Gly/Ala-rich insert. Narrow 1H-NMR resonances at chemical shifts indicative of random coil conformations were observed in the difference spectrum. circular dichroism (CD) measurements further confirm that the mechanism of protection against proteolytic degradation is not based on structural transition or stabilization caused by the Gly/Ala-rich segment. In addition, most of the N- and C-terminal residues outside the ankyrin repeats in wild-type IkappaB alpha were found to be flexibly disordered. FAU - Leonchiks, A AU - Leonchiks A AD - Microbiology and Tumor Biology Center (MTC), Karolinska Institute, Stockholm, Sweden. FAU - Liepinsh, E AU - Liepinsh E FAU - Barishev, M AU - Barishev M FAU - Sharipo, A AU - Sharipo A FAU - Masucci, M G AU - Masucci MG FAU - Otting, G AU - Otting G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Amino Acids) RN - 0 (DNA-Binding Proteins) RN - 0 (I-kappa B Proteins) RN - 0 (Multienzyme Complexes) RN - 0 (Peptides) RN - 139874-52-5 (NF-kappaB inhibitor alpha) RN - EC 3.4.22.- (Cysteine Endopeptidases) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) RN - OF5P57N2ZX (Alanine) RN - TE7660XO1C (Glycine) SB - IM MH - Alanine/chemistry MH - Amino Acid Sequence MH - Amino Acids/analysis MH - Cysteine Endopeptidases/*metabolism MH - DNA-Binding Proteins/*chemistry/metabolism MH - Glycine/chemistry MH - *I-kappa B Proteins MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Multienzyme Complexes/*metabolism MH - Peptides/chemistry MH - Pliability MH - Proteasome Endopeptidase Complex MH - Protein Conformation EDAT- 1999/01/01 MHDA- 1999/01/01 00:01 CRDT- 1999/01/01 00:00 AID - S0014-5793(98)01488-4 [pii] PST - ppublish SO - FEBS Lett. 1998 Dec 4;440(3):365-9. PMID- 21044603 OWN - NLM STAT- MEDLINE DA - 20101103 DCOM- 20110128 LR - 20141120 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 9 DP - 2010 Nov 3 TI - Single molecule characterization of alpha-synuclein in aggregation-prone states. PG - 3048-55 LID - 10.1016/j.bpj.2010.08.056 [doi] AB - alpha-Synuclein (alphaS) is an intrinsically disordered protein whose aggregation into ordered, fibrillar structures underlies the pathogenesis of Parkinson's disease. A full understanding of the factors that cause its conversion from soluble protein to insoluble aggregate requires characterization of the conformations of the monomer protein under conditions that favor aggregation. Here we use single molecule Forster resonance energy transfer to probe the structure of several aggregation-prone states of alphaS. Both low pH and charged molecules have been shown to accelerate the aggregation of alphaS and induce conformational changes in the protein. We find that at low pH, the C-terminus of alphaS undergoes substantial collapse, with minimal effect on the N-terminus and central region. The proximity of the N- and C-termini and the global dimensions of the protein are relatively unaffected by the C-terminal collapse. Moreover, although compact at low pH, with restricted chain motion, the structure of the C-terminus appears to be random. Low pH has a dramatically different effect on alphaS structure than the molecular aggregation inducers spermine and heparin. Binding of these molecules gives rise to only minor conformational changes in alphaS, suggesting that their mechanism of aggregation enhancement is fundamentally different from that of low pH. CI - Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Trexler, Adam J AU - Trexler AJ AD - Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA. FAU - Rhoades, Elizabeth AU - Rhoades E LA - eng GR - GM007223/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Fluorescent Dyes) RN - 0 (Recombinant Proteins) RN - 0 (alpha-Synuclein) SB - IM MH - Biophysical Phenomena MH - Fluorescence Polarization MH - Fluorescence Resonance Energy Transfer MH - Fluorescent Dyes MH - Humans MH - Hydrogen-Ion Concentration MH - In Vitro Techniques MH - Models, Molecular MH - Parkinson Disease/etiology/metabolism MH - Protein Conformation MH - Protein Multimerization MH - Recombinant Proteins/chemistry/genetics MH - alpha-Synuclein/*chemistry/genetics PMC - PMC2965999 OID - NLM: PMC2965999 EDAT- 2010/11/04 06:00 MHDA- 2011/02/01 06:00 CRDT- 2010/11/04 06:00 PHST- 2010/07/19 [received] PHST- 2010/08/23 [revised] PHST- 2010/08/27 [accepted] AID - S0006-3495(10)01052-0 [pii] AID - 10.1016/j.bpj.2010.08.056 [doi] PST - ppublish SO - Biophys J. 2010 Nov 3;99(9):3048-55. doi: 10.1016/j.bpj.2010.08.056. PMID- 23123341 OWN - NLM STAT- MEDLINE DA - 20121211 DCOM- 20130530 LR - 20141104 IS - 1873-3344 (Electronic) IS - 0162-0134 (Linking) VI - 118 DP - 2013 Jan TI - Conversion of natively unstructured alpha-synuclein to its alpha-helical conformation significantly attenuates production of reactive oxygen species. PG - 68-73 LID - 10.1016/j.jinorgbio.2012.09.001 [doi] LID - S0162-0134(12)00276-0 [pii] AB - The intracellular alpha-synuclein (alpha-syn) protein, whose conformational change and aggregation have been closely linked to the pathology of Parkingson's disease (PD), is highly populated at the presynaptic termini and remains there in the alpha-helical conformation. In this study, circular dichroism confirmed that natively unstructured alpha-syn in aqueous solution was transformed to its alpha-helical conformation upon addition of trifluoroethanol (TFE). Electrochemical and UV-visible spectroscopic experiments reveal that both Cu (I) and Cu (II) are stabilized, with the former being stabilized by about two orders of magnitude. Compared to unstructured alpha-syn (Binolfi et al., J. Am. Chem. Soc. 133 (2011) 194-196), alpha-helical alpha-syn stabilizes Cu (I) by more than three orders of magnitude. Through the measurements of H(2)O(2) and hydroxyl radicals (OH) in solutions containing different forms of Cu (II) (free and complexed by unstructured or alpha-helical alpha-syn), we demonstrate that the significantly enhanced Cu (I) binding affinity helps inhibit the production of highly toxic reactive oxygen species, especially the hydroxyl radicals. Our study provides strong evidence that, as a possible means to prevent neuronal cell damage, conversion of the natively unstructured alpha-syn to its alpha-helical conformation in vivo could significantly attenuate the copper-modulated ROS production. CI - Published by Elsevier Inc. FAU - Zhou, Binbin AU - Zhou B AD - College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China. FAU - Hao, Yuanqiang AU - Hao Y FAU - Wang, Chengshan AU - Wang C FAU - Li, Ding AU - Li D FAU - Liu, You-Nian AU - Liu YN FAU - Zhou, Feimeng AU - Zhou F LA - eng GR - SC1 NS070155/NS/NINDS NIH HHS/United States GR - SC1NS070155-01/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120908 PL - United States TA - J Inorg Biochem JT - Journal of inorganic biochemistry JID - 7905788 RN - 0 (Hydroxides) RN - 0 (Reactive Oxygen Species) RN - 0 (Solvents) RN - 0 (alpha-Synuclein) RN - 059QF0KO0R (Water) RN - 75-89-8 (Trifluoroethanol) RN - 789U1901C5 (Copper) RN - 9159UV381P (hydroxide ion) RN - BBX060AN9V (Hydrogen Peroxide) SB - IM MH - Amino Acid Sequence MH - Copper/chemistry MH - Humans MH - Hydrogen Peroxide/*chemistry MH - Hydroxides/*chemistry MH - Kinetics MH - Molecular Sequence Data MH - Protein Binding MH - Protein Stability MH - Protein Structure, Secondary MH - Reactive Oxygen Species/chemistry MH - Solvents/chemistry MH - Trifluoroethanol/chemistry MH - Water/chemistry MH - alpha-Synuclein/*chemistry PMC - PMC3518724 MID - NIHMS419226 OID - NLM: NIHMS419226 OID - NLM: PMC3518724 EDAT- 2012/11/06 06:00 MHDA- 2013/06/01 06:00 CRDT- 2012/11/06 06:00 PHST- 2012/07/14 [received] PHST- 2012/09/01 [revised] PHST- 2012/09/01 [accepted] PHST- 2012/09/08 [aheadofprint] AID - S0162-0134(12)00276-0 [pii] AID - 10.1016/j.jinorgbio.2012.09.001 [doi] PST - ppublish SO - J Inorg Biochem. 2013 Jan;118:68-73. doi: 10.1016/j.jinorgbio.2012.09.001. Epub 2012 Sep 8. PMID- 3920075 OWN - NLM STAT- MEDLINE DA - 19850508 DCOM- 19850508 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 182 IP - 2 DP - 1985 Mar 25 TI - The complete amino acid sequence of the major mammalian neurofilament protein (NF-L). PG - 475-8 AB - The first complete amino acid sequence of a neurofilament protein has been established. Porcine NF-L contains 548 residues corresponding to a molecular mass of approximately 62 kDa. This value is noticeably smaller than the 68-72 kDa estimates from gel electrophoresis. Sequence comparison among the 6 non-epithelial intermediate filament (IF) proteins of warm-blooded vertebrates shows that the three NF proteins are the most remote members. Additionally and unexpectedly they reveal among each other lower sequence identity than the three non-neuronal IF proteins GFAP, desmin, and vimentin where the last two are particularly closely related. Certain schemes of IF protein evolution are discussed. FAU - Geisler, N AU - Geisler N FAU - Plessmann, U AU - Plessmann U FAU - Weber, K AU - Weber K LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Desmin) RN - 0 (Glial Fibrillary Acidic Protein) RN - 0 (Intermediate Filament Proteins) RN - 0 (Neurofilament Proteins) RN - 0 (Peptide Fragments) RN - 0 (Vimentin) RN - 0 (neurofilament protein L) SB - IM MH - Amino Acid Sequence MH - Animals MH - Chickens MH - Cricetinae MH - Desmin MH - Glial Fibrillary Acidic Protein MH - *Intermediate Filament Proteins MH - Mice MH - Neurofilament Proteins MH - Peptide Fragments MH - Spinal Cord/analysis MH - Swine MH - Vimentin EDAT- 1985/03/25 MHDA- 1985/03/25 00:01 CRDT- 1985/03/25 00:00 AID - 0014-5793(85)80357-4 [pii] PST - ppublish SO - FEBS Lett. 1985 Mar 25;182(2):475-8. PMID- 16428606 OWN - NLM STAT- MEDLINE DA - 20060123 DCOM- 20060314 LR - 20140909 IS - 1355-8382 (Print) IS - 1355-8382 (Linking) VI - 12 IP - 2 DP - 2006 Feb TI - The bunyavirus nucleocapsid protein is an RNA chaperone: possible roles in viral RNA panhandle formation and genome replication. PG - 272-82 AB - Cellular RNA chaperones are crucial for the genesis of correctly folded functional RNAs. Using several complementary in vitro assays we find that the bunyavirus nucleocapsid protein (N) is an RNA chaperone. In the Bunyaviridae genomic RNA is in stable "panhandle" formation that arises through the hydrogen bonding of the terminal nucleotides of the RNA. The RNA chaperone function of N facilitates panhandle formation even though the termini are separated by >2 kb. RNA panhandle formation is likely driven by the exceptionally high base-pairing specificity of the terminal nucleotides as evidenced by P-num analysis. N protein can nonspecifically dissociate RNA duplexes. In addition, following panhandle formation, the RNA chaperone activity of N also appears to be involved in dissociation of the RNA panhandle and remains in association with the 5' terminus of the viral RNA following dissociation. Thus, N likely functions in the initiation of genome replication to allow efficient initiation of RNA synthesis by the viral polymerase. The RNA chaperone activity of N may be facilitated by an intrinsically disordered domain that catalyzes RNA unfolding driven by reciprocal entropy transfer. These observations highlight the essential features that are probably common to all RNA chaperones in which the role of the chaperone is to nonspecifically dissociate higher order structure and formation of functional higher order structure may often be predicted by RNA P-num value. The data also highlight features of N that are probably specifically important during replication of bunyavirus RNA. FAU - Mir, M Ayoub AU - Mir MA AD - Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA. FAU - Panganiban, Antonito T AU - Panganiban AT LA - eng GR - R21AI059330/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - RNA JT - RNA (New York, N.Y.) JID - 9509184 RN - 0 (Molecular Chaperones) RN - 0 (Nucleocapsid Proteins) RN - 0 (RNA, Viral) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Binding Sites MH - Genome, Viral MH - Molecular Chaperones/genetics/*metabolism MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Nucleocapsid Proteins/genetics/*metabolism MH - RNA, Viral/*chemistry/metabolism MH - Virus Replication PMC - PMC1370907 OID - NLM: PMC1370907 EDAT- 2006/01/24 09:00 MHDA- 2006/03/15 09:00 CRDT- 2006/01/24 09:00 AID - 12/2/272 [pii] AID - 10.1261/rna.2101906 [doi] PST - ppublish SO - RNA. 2006 Feb;12(2):272-82. PMID- 1639074 OWN - NLM STAT- MEDLINE DA - 19920828 DCOM- 19920828 LR - 20131121 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 11 IP - 8 DP - 1992 Aug TI - Determination of the structure of the nucleocapsid protein NCp7 from the human immunodeficiency virus type 1 by 1H NMR. PG - 3059-65 AB - The retroviral gag nucleocapsid protein NCp7 (72 amino acids) of HIV-1 (LAV strain), which contains two successive zinc fingers of the Cys-X2-Cys-X4-His-X4-Cys form linked by a stretch of basic residues, promotes viral RNA dimerization and encapsidation and activates annealing of the primer tRNA to the initiation site of reverse transcription. The structure of NCp7 and other shorter fragments was studied by 600 MHz 1H nuclear magnetic resonance (NMR) in aqueous solution to account for its various biological properties. Complete sequence specific 1H NMR assignments of the 13-51 residues of NCp7 encompassing the two zinc fingers was achieved by two-dimensional NMR experiments and the three-dimensional structure of (13-51)NCp7 was deduced from DIANA calculations, using nuclear Overhauser effects as constraints. The structure of the zinc complexed form of NCp7 is characterized by a kink at the Pro31 level in the basic Arg29-Ala-Pro-Arg-Lys-Lys-Gly35 RNA binding linker leading to a proximity of the Lys14-Cys18 to the Gly35-Cys39 sequences, which belong to the folded proximal and distal zinc fingers, respectively. Accordingly, the aromatic residues Phe16 and Trp37 were found to be spatially close. The Lys33 and Lys34 side-chains involved in viral RNA dimerization were solvent exposed. The N- and C-terminal sequences of NCp7 behave as flexible independent domains. The proposed structure of NCp7 might be used to rationally design new anti-viral agents aimed at inhibiting its functions. FAU - Morellet, N AU - Morellet N AD - Departement de Chimie Organique, U 266 INSERM, UA 498 CNRS, UFR des Sciences Pharmaceutiques et Biologiques, Paris, France. FAU - Jullian, N AU - Jullian N FAU - De Rocquigny, H AU - De Rocquigny H FAU - Maigret, B AU - Maigret B FAU - Darlix, J L AU - Darlix JL FAU - Roques, B P AU - Roques BP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Capsid Proteins) RN - 0 (Gene Products, gag) RN - 0 (NCP7 protein, Human immunodeficiency virus 1) RN - 0 (Peptides) RN - 0 (Viral Proteins) RN - 0 (gag Gene Products, Human Immunodeficiency Virus) RN - 7YNJ3PO35Z (Hydrogen) RN - J41CSQ7QDS (Zinc) SB - IM SB - X MH - Amino Acid Sequence MH - Binding Sites MH - *Capsid Proteins MH - Computer Graphics MH - Gene Products, gag/*chemistry/metabolism MH - HIV-1/*chemistry/metabolism MH - Hydrogen MH - Magnetic Resonance Spectroscopy/methods MH - Models, Molecular MH - Molecular Sequence Data MH - Peptides/chemical synthesis/chemistry MH - *Viral Proteins MH - Zinc/analysis/metabolism MH - *Zinc Fingers MH - gag Gene Products, Human Immunodeficiency Virus PMC - PMC556789 OID - NLM: PMC556789 EDAT- 1992/08/01 MHDA- 1992/08/01 00:01 CRDT- 1992/08/01 00:00 PST - ppublish SO - EMBO J. 1992 Aug;11(8):3059-65. PMID- 17620598 OWN - NLM STAT- MEDLINE DA - 20070726 DCOM- 20070910 LR - 20140904 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 104 IP - 30 DP - 2007 Jul 24 TI - Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex. PG - 12324-9 AB - The homotetrameric tumor suppressor p53 consists of folded core and tetramerization domains, linked and flanked by intrinsically disordered segments that impede structure analysis by x-ray crystallography and NMR. Here, we solved the quaternary structure of human p53 in solution by a combination of small-angle x-ray scattering, which defined its shape, and NMR, which identified the core domain interfaces and showed that the folded domains had the same structure in the intact protein as in fragments. We combined the solution data with electron microscopy on immobilized samples that provided medium resolution 3D maps. Ab initio and rigid body modeling of scattering data revealed an elongated cross-shaped structure with a pair of loosely coupled core domain dimers at the ends, which are accessible for binding to DNA and partner proteins. The core domains in that open conformation closed around a specific DNA response element to form a compact complex whose structure was independently determined by electron microscopy. The structure of the DNA complex is consistent with that of the complex of four separate core domains and response element fragments solved by x-ray crystallography and contacts identified by NMR. Electron microscopy on the conformationally mobile, unbound p53 selected a minor compact conformation, which resembled the closed conformation, from the ensemble of predominantly open conformations. A multipronged structural approach could be generally useful for the structural characterization of the rapidly growing number of multidomain proteins with intrinsically disordered regions. FAU - Tidow, Henning AU - Tidow H AD - Medical Research Council Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, United Kingdom. FAU - Melero, Roberto AU - Melero R FAU - Mylonas, Efstratios AU - Mylonas E FAU - Freund, Stefan M V AU - Freund SM FAU - Grossmann, J Guenter AU - Grossmann JG FAU - Carazo, Jose Maria AU - Carazo JM FAU - Svergun, Dmitri I AU - Svergun DI FAU - Valle, Mikel AU - Valle M FAU - Fersht, Alan R AU - Fersht AR LA - eng GR - MC_U105474168/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070709 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Tumor Suppressor Protein p53) RN - 9007-49-2 (DNA) SB - IM CIN - Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12231-2. PMID: 17640907 MH - DNA/*chemistry/*metabolism/ultrastructure MH - Humans MH - Microscopy, Electron MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - *Protein Structure, Quaternary MH - Spectrum Analysis MH - Tumor Suppressor Protein p53/*chemistry/genetics/*metabolism/ultrastructure PMC - PMC1941468 OID - NLM: PMC1941468 EDAT- 2007/07/11 09:00 MHDA- 2007/09/11 09:00 CRDT- 2007/07/11 09:00 PHST- 2007/07/09 [aheadofprint] AID - 0705069104 [pii] AID - 10.1073/pnas.0705069104 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12324-9. Epub 2007 Jul 9. PMID- 22153624 OWN - NLM STAT- MEDLINE DA - 20111226 DCOM- 20120910 IS - 1872-6240 (Electronic) IS - 0006-8993 (Linking) VI - 1432 DP - 2012 Jan 13 TI - alpha-Synuclein synaptic pathology and its implications in the development of novel therapeutic approaches to cure Parkinson's disease. PG - 95-113 LID - 10.1016/j.brainres.2011.11.031 [doi] AB - Parkinson's disease (PD) is characterized by a progressive loss of dopamine (DA) neurons of the nigrostriatal system and by the presence of Lewy bodies (LB), proteinaceous inclusions mainly composed of filamentous alpha-synuclein aggregates. Alpha-synuclein is a natively unfolded protein which plays a central role in the control of dopaminergic neuronal functions and which is thought to be critically implicated in PD pathophysiology. Indeed, besides the fact that alpha-synuclein is the main protein component of LB, genetic studies showed that mutations and multiplications of the alpha-synuclein gene are responsible for the onset of familial forms of PD. A large body of evidence indicates that alpha-synuclein pathology at dopaminergic synapses may underlie the onset of neuronal cell dysfunction and degeneration in the PD brain. Thus, since the available therapeutic approaches to cure this disease are still limited, we hypothesized that the analysis of the alpha-synuclein synaptic proteome/lipidome may represent a tool to identify novel potential therapeutic targets to cure this disorder. We thus performed a critical review of studies describing alpha-synuclein pathophysiology at synaptic sites in experimental models of PD and in this paper we outline the most relevant findings regarding the specific modulatory effects exerted by alpha-synuclein in the control of synaptic functions in physiological and pathological conditions. The conclusions of these studies allow to single out novel potential therapeutic targets among the alpha-synuclein synaptic partners. These targets may be considered for the development of new pharmacological and gene-based strategies to cure PD. CI - Copyright (c) 2011 Elsevier B.V. All rights reserved. FAU - Bellucci, Arianna AU - Bellucci A AD - Division of Pharmacology, Department of Biomedical Sciences and Biotechnology and National Institute of Neuroscience - Italy, School of Medicine, University of Brescia, Brescia, Italy. bellucci@med.unibs.it FAU - Navarria, Laura AU - Navarria L FAU - Zaltieri, Michela AU - Zaltieri M FAU - Missale, Cristina AU - Missale C FAU - Spano, Pierfranco AU - Spano P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20111119 PL - Netherlands TA - Brain Res JT - Brain research JID - 0045503 RN - 0 (Antiparkinson Agents) RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Antiparkinson Agents/isolation & purification/pharmacology MH - Humans MH - Nerve Degeneration/pathology/physiopathology/prevention & control MH - Parkinson Disease/*metabolism/*pathology/physiopathology MH - Synapses/*pathology/*physiology MH - alpha-Synuclein/*physiology EDAT- 2011/12/14 06:00 MHDA- 2012/09/11 06:00 CRDT- 2011/12/14 06:00 PHST- 2011/06/20 [received] PHST- 2011/11/11 [revised] PHST- 2011/11/11 [accepted] PHST- 2011/11/19 [aheadofprint] AID - S0006-8993(11)02117-2 [pii] AID - 10.1016/j.brainres.2011.11.031 [doi] PST - ppublish SO - Brain Res. 2012 Jan 13;1432:95-113. doi: 10.1016/j.brainres.2011.11.031. Epub 2011 Nov 19. PMID- 23145167 OWN - NLM STAT- MEDLINE DA - 20121112 DCOM- 20130625 LR - 20141104 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 11 DP - 2012 TI - Modeling amyloid-beta as homogeneous dodecamers and in complex with cellular prion protein. PG - e49375 LID - 10.1371/journal.pone.0049375 [doi] AB - Soluble amyloid beta (Abeta) peptide has been linked to the pathology of Alzheimer's disease. A variety of soluble oligomers have been observed to be toxic, ranging from dimers to protofibrils. No tertiary structure has been identified as a single biologically relevant form, though many models are comprised of highly ordered beta-sheets. Evidence exists for much less ordered toxic oligomers. The mechanism of toxicity remains highly debated and probably involves multiple pathways. Interaction of Abeta oligomers with the N-terminus of the cellular form of the prion protein (PrP(c)) has recently been proposed. The intrinsically disordered nature of this protein and the highly polymorphic nature of Abeta oligomers make structural resolution of the complex exceptionally challenging. In this study, molecular dynamics simulations are performed for dodecameric assemblies of Abeta comprised of monomers having a single, short antiparallel beta-hairpin at the C-terminus. The resulting models, devoid of any intermolecular hydrogen bonds, are shown to correlate well with experimental data and are found to be quite stable within the hydrophobic core, whereas the alpha-helical N-termini transform to a random coil state. This indicates that highly ordered assemblies are not required for stability and less ordered oligomers are a viable component in the population of soluble oligomers. In addition, a tentative model is proposed for the association of Abeta dimers with a double deletion mutant of the intrinsically disordered N-terminus of PrP(c). This may be useful as a conceptual working model for the binding of higher order oligomers and in the design of further experiments. FAU - Gallion, Steven L AU - Gallion SL AD - Wallingford, Connecticut, United States of America. sgallion@comcast.net LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121108 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Amyloid beta-Peptides) RN - 0 (Prions) SB - IM MH - Amyloid beta-Peptides/*chemistry/metabolism MH - Crystallography, X-Ray MH - Dimerization MH - *Models, Molecular MH - Prions/*chemistry/metabolism MH - Protein Structure, Tertiary PMC - PMC3493521 OID - NLM: PMC3493521 EDAT- 2012/11/13 06:00 MHDA- 2013/06/26 06:00 CRDT- 2012/11/13 06:00 PHST- 2012/05/08 [received] PHST- 2012/10/11 [accepted] PHST- 2012/11/08 [epublish] AID - 10.1371/journal.pone.0049375 [doi] AID - PONE-D-12-13116 [pii] PST - ppublish SO - PLoS One. 2012;7(11):e49375. doi: 10.1371/journal.pone.0049375. Epub 2012 Nov 8. PMID- 19287005 OWN - NLM STAT- MEDLINE DA - 20090511 DCOM- 20090630 LR - 20140831 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 284 IP - 20 DP - 2009 May 15 TI - Clathrin regulates the association of PIPKIgamma661 with the AP-2 adaptor beta2 appendage. PG - 13924-39 LID - 10.1074/jbc.M901017200 [doi] AB - The AP-2 clathrin adaptor differs fundamentally from the related AP-1, AP-3, and AP-4 sorting complexes because membrane deposition does not depend directly on an Arf family GTPase. Instead phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P(2)) appears to act as the principal compartmental cue for AP-2 placement at the plasma membrane as well as for the docking of numerous other important clathrin coat components at the nascent bud site. This PtdIns(4,5)P(2) dependence makes type I phosphatidylinositol 4-phosphate 5-kinases (PIPKIs) lynchpin enzymes in the assembly of clathrin-coated structures at the cell surface. PIPKIgamma is the chief 5-kinase at nerve terminals, and here we show that the 26-amino acid, alternatively spliced C terminus of PIPKIgamma661 is an intrinsically unstructured polypeptide that binds directly to the sandwich subdomain of the AP-2 beta2 subunit appendage. An aromatic side chain-based, extended interaction motif that also includes the two bulky C-terminal residues of the short PIPKIgamma635 variant is necessary for beta2 appendage engagement. The clathrin heavy chain accesses the same contact surface on the AP-2 beta2 appendage, but because of additional clathrin binding sites located within the unstructured hinge segment of the beta2 subunit, clathrin binds the beta2 chain with a higher apparent affinity than PIPKIgamma661. A clathrin-regulated interaction with AP-2 could allow PIPKIgamma661 to be strategically positioned for regional PtdIns(4,5)P(2) generation during clathrin-coated vesicle assembly at the synapse. FAU - Thieman, James R AU - Thieman JR AD - Department of Cell Biology and Physiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA. FAU - Mishra, Sanjay K AU - Mishra SK FAU - Ling, Kun AU - Ling K FAU - Doray, Balraj AU - Doray B FAU - Anderson, Richard A AU - Anderson RA FAU - Traub, Linton M AU - Traub LM LA - eng GR - R01 CA104708/CA/NCI NIH HHS/United States GR - R01 DK53249/DK/NIDDK NIH HHS/United States GR - T32 DK061296/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20090314 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Adaptor Protein Complex 2) RN - 0 (Clathrin) RN - 0 (Phosphatidylinositol 4,5-Diphosphate) RN - 0 (Protein Subunits) RN - EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)) RN - EC 2.7.1.68 (1-phosphatidylinositol-4-phosphate 5-kinase) RN - EC 3.6.5.2 (ADP-Ribosylation Factors) SB - IM MH - ADP-Ribosylation Factors/genetics/metabolism MH - Adaptor Protein Complex 2/genetics/*metabolism MH - Alternative Splicing/physiology MH - Animals MH - Clathrin/genetics/*metabolism MH - Clathrin-Coated Vesicles/genetics/*metabolism MH - Mice MH - Phosphatidylinositol 4,5-Diphosphate MH - Phosphotransferases (Alcohol Group Acceptor)/genetics/*metabolism MH - Protein Structure, Tertiary/physiology MH - Protein Subunits/genetics/metabolism MH - Rats MH - Synaptosomes/*metabolism PMC - PMC2679492 OID - NLM: PMC2679492 EDAT- 2009/03/17 09:00 MHDA- 2009/07/01 09:00 CRDT- 2009/03/17 09:00 PHST- 2009/03/14 [aheadofprint] AID - M901017200 [pii] AID - 10.1074/jbc.M901017200 [doi] PST - ppublish SO - J Biol Chem. 2009 May 15;284(20):13924-39. doi: 10.1074/jbc.M901017200. Epub 2009 Mar 14. PMID- 17666528 OWN - NLM STAT- MEDLINE DA - 20070808 DCOM- 20070920 LR - 20140904 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 104 IP - 32 DP - 2007 Aug 7 TI - Intrinsic disorder in the C-terminal domain of the Shaker voltage-activated K+ channel modulates its interaction with scaffold proteins. PG - 13022-7 AB - The interaction of membrane-embedded voltage-activated potassium channels (Kv) with intracellular scaffold proteins, such as the postsynaptic density 95 (PSD-95) protein, is mediated by the channel C-terminal segment. This interaction underlies Kv channel clustering at unique membrane sites and is important for the proper assembly and functioning of the synapse. In the current study, we address the molecular mechanism underlying Kv/PSD-95 interaction. We provide experimental evidence, based on hydrodynamic and spectroscopic analyses, indicating that the isolated C-terminal segment of the archetypical Shaker Kv channel (ShB-C) is a random coil, suggesting that ShB-C belongs to the recently defined class of intrinsically disordered proteins. We show that isolated ShB-C is still able to bind its scaffold protein partner and support protein clustering in vivo, indicating that unfoldedness is compatible with ShB-C activity. Pulldown experiments involving C-terminal chains differing in flexibility or length further demonstrate that intrinsic disorder in the C-terminal segment of the Shaker channel modulates its interaction with the PSD-95 protein. Our results thus suggest that the C-terminal domain of the Shaker Kv channel behaves as an entropic chain and support a "fishing rod" molecular mechanism for Kv channel binding to scaffold proteins. The importance of intrinsically disordered protein segments to the complex processes of synapse assembly, maintenance, and function is discussed. FAU - Magidovich, Elhanan AU - Magidovich E AD - Department of Life Sciences and Zlotowski Center for Neurosciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel. FAU - Orr, Irit AU - Orr I FAU - Fass, Deborah AU - Fass D FAU - Abdu, Uri AU - Abdu U FAU - Yifrach, Ofer AU - Yifrach O LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070731 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DLG4 protein, human) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Membrane Proteins) RN - 0 (Shaker Superfamily of Potassium Channels) SB - IM MH - Binding Sites MH - Circular Dichroism MH - Intracellular Signaling Peptides and Proteins/*chemistry MH - Membrane Proteins/*chemistry MH - Protein Structure, Tertiary MH - Shaker Superfamily of Potassium Channels/*chemistry PMC - PMC1941827 OID - NLM: PMC1941827 EDAT- 2007/08/02 09:00 MHDA- 2007/09/21 09:00 CRDT- 2007/08/02 09:00 PHST- 2007/07/31 [aheadofprint] AID - 0704059104 [pii] AID - 10.1073/pnas.0704059104 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2007 Aug 7;104(32):13022-7. Epub 2007 Jul 31. PMID- 15222016 OWN - NLM STAT- MEDLINE DA - 20040628 DCOM- 20040908 LR - 20131121 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 74 IP - 5 DP - 2004 Aug 5 TI - Structural characterization of the N-terminal mineral modification domains from the molluscan crystal-modulating biomineralization proteins, AP7 and AP24. PG - 363-76 AB - The AP7 and AP24 proteins represent a class of mineral-interaction polypeptides that are found in the aragonite-containing nacre layer of mollusk shell (H. rufescens). These proteins have been shown to preferentially interfere with calcium carbonate mineral growth in vitro. It is believed that both proteins play an important role in aragonite polymorph selection in the mollusk shell. Previously, we demonstrated the 1-30 amino acid (AA) N-terminal sequences of AP7 and AP24 represent mineral interaction/modification domains in both proteins, as evidenced by their ability to frustrate calcium carbonate crystal growth at step edge regions. In this present report, using free N-terminal, C(alpha)-amide "capped" synthetic polypeptides representing the 1-30 AA regions of AP7 (AP7-1 polypeptide) and AP24 (AP24-1 polypeptide) and NMR spectroscopy, we confirm that both N-terminal sequences possess putative Ca (II) interaction polyanionic sequence regions (2 x -DD- in AP7-1, -DDDED- in AP24-1) that are random coil-like in structure. However, with regard to the remaining sequences regions, each polypeptide features unique structural differences. AP7-1 possesses an extended beta-strand or polyproline type II-like structure within the A11-M10, S12-V13, and S28-I27 sequence regions, with the remaining sequence regions adopting a random-coil-like structure, a trait common to other polyelectrolyte mineral-associated polypeptide sequences. Conversely, AP24-1 possesses random coil-like structure within A1-S9 and Q14-N16 sequence regions, and evidence for turn-like, bend, or loop conformation within the G10-N13, Q17-N24, and M29-F30 sequence regions, similar to the structures identified within the putative elastomeric proteins Lustrin A and sea urchin spicule matrix proteins. The similarities and differences in AP7 and AP24 N-terminal domain structure are discussed with regard to joint AP7-AP24 protein modification of calcium carbonate growth. CI - Copyright 2004 Wiley Periodicals, Inc. FAU - Wustman, Brandon A AU - Wustman BA AD - Laboratory for Chemical Physics, New York University, 345 E. 24th Street, New York, NY 10010, USA. FAU - Morse, Daniel E AU - Morse DE FAU - Evans, John Spencer AU - Evans JS LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 RN - 0 (Peptides) RN - 0 (Proteins) RN - H0G9379FGK (Calcium Carbonate) SB - IM MH - Amino Acid Sequence MH - Animals MH - Calcification, Physiologic MH - Calcium Carbonate/chemistry/metabolism MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Mollusca/*chemistry MH - Peptides/chemistry/metabolism MH - Protein Binding MH - *Protein Structure, Tertiary MH - Proteins/chemistry/metabolism EDAT- 2004/06/29 05:00 MHDA- 2004/09/09 05:00 CRDT- 2004/06/29 05:00 AID - 10.1002/bip.20086 [doi] PST - ppublish SO - Biopolymers. 2004 Aug 5;74(5):363-76. PMID- 12944395 OWN - NLM STAT- MEDLINE DA - 20031103 DCOM- 20040105 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 45 DP - 2003 Nov 7 TI - Crystal structure of the measles virus phosphoprotein domain responsible for the induced folding of the C-terminal domain of the nucleoprotein. PG - 44567-73 AB - Measles virus is a negative-sense, single-stranded RNA virus belonging to the Mononegavirales order which comprises several human pathogens such as Ebola, Nipah, and Hendra viruses. The phosphoprotein of measles virus is a modular protein consisting of an intrinsically disordered N-terminal domain (Karlin, D., Longhi, S., Receveur, V., and Canard, B. (2002) Virology 296, 251-262) and of a C-terminal moiety (PCT) composed of alternating disordered and globular regions. We report the crystal structure of the extreme C-terminal domain (XD) of measles virus phosphoprotein (aa 459-507) at 1.8 A resolution. We have previously reported that the C-terminal domain of measles virus nucleoprotein, NTAIL, is intrinsically unstructured and undergoes induced folding in the presence of PCT (Longhi, S., Receveur-Brechot, V., Karlin, D., Johansson, K., Darbon, H., Bhella, D., Yeo, R., Finet, S., and Canard, B. (2003) J. Biol. Chem. 278, 18638-18648). Using far-UV circular dichroism, we show that within PCT, XD is the region responsible for the induced folding of NTAIL. The crystal structure of XD consists of three helices, arranged in an anti-parallel triple-helix bundle. The surface of XD formed between helices alpha2 and alpha3 displays a long hydrophobic cleft that might provide a complementary hydrophobic surface to embed and promote folding of the predicted alpha-helix of NTAIL. We present a tentative model of the interaction between XD and NTAIL. These results, beyond presenting the first measles virus protein structure, shed light both on the function of the phosphoprotein at the molecular level and on the process of induced folding. FAU - Johansson, Kenth AU - Johansson K AD - Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS et Universite Aix-Marseille, 13288 Marseille 09, France. FAU - Bourhis, Jean-Marie AU - Bourhis JM FAU - Campanacci, Valerie AU - Campanacci V FAU - Cambillau, Christian AU - Cambillau C FAU - Canard, Bruno AU - Canard B FAU - Longhi, Sonia AU - Longhi S LA - eng SI - PDB/1OKS SI - PDB/1OKSSF PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030827 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Nucleoproteins) RN - 0 (Peptide Fragments) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Proteins) RN - 0 (Viral Proteins) RN - 0 (nucleoprotein, Measles virus) SB - IM MH - Binding Sites MH - Circular Dichroism MH - Cloning, Molecular MH - Crystallization MH - Crystallography, X-Ray MH - Escherichia coli/genetics MH - Gene Expression MH - Light MH - Measles virus/*chemistry MH - Models, Molecular MH - Molecular Structure MH - Nucleoproteins/*chemistry/genetics MH - Peptide Fragments/*chemistry/genetics MH - Phosphoproteins/*chemistry/genetics MH - Protein Folding MH - Recombinant Proteins MH - Scattering, Radiation MH - Viral Proteins/*chemistry/genetics EDAT- 2003/08/29 05:00 MHDA- 2004/01/06 05:00 CRDT- 2003/08/29 05:00 PHST- 2003/08/27 [aheadofprint] AID - 10.1074/jbc.M308745200 [doi] AID - M308745200 [pii] PST - ppublish SO - J Biol Chem. 2003 Nov 7;278(45):44567-73. Epub 2003 Aug 27. PMID- 20303977 OWN - NLM STAT- MEDLINE DA - 20100419 DCOM- 20100430 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 398 IP - 3 DP - 2010 May 7 TI - The effects of phosphomimetic lid mutation on the thermostability of the N-terminal domain of MDM2. PG - 414-28 LID - 10.1016/j.jmb.2010.03.023 [doi] AB - The multidomain E3 ubiquitin ligase MDM2 catalyzes p53 ubiquitination by a "dual-site" docking mechanism whereby MDM2 binding to at least two distinct peptide motifs on p53 promotes ubiquitination. One protein-protein interaction occurs between the N-terminal hydrophobic pocket of MDM2 and the transactivation motif of p53, and the second interaction occurs between the acidic domain of MDM2 and a motif in the DNA-binding domain of p53. A flexible N-terminal pseudo-substrate or "lid" adjacent to the N-terminal hydrophobic pocket of MDM2 has a phosphorylation site, and there are distinct models proposed on how the phosphorylated lid could affect MDM2 function. Biochemical studies have predicted that phosphomimetic mutation will stabilize the lid on the surface of MDM2 and will "open" the hydrophobic pocket and stabilize the MDM2-p53 complex, while NMR studies proposed that phosphomimetic mutation "closes" the lid over the MDM2 pocket and inhibits MDM2-p53 complex formation. To resolve these discrepancies, we utilized a quantitative fluorescence-based dye binding assay to measure the thermal unfolding of wild-type (wt), DeltaLid, and S17D N-terminal domains of MDM2 as a function of increasing ligand concentration. Our data reveal that S17D lid mutation increases, rather than decreases, the thermostability of the N-terminal domain of MDM2 in the absence or in the presence of ligand. DeltaLid mutation, by contrast, increases MDM2 thermoinstability. This is consistent with biochemical data, using full-length MDM2, showing that the S17D mutation stabilizes the MDM2-p53 complex and increases the specific activity of the E3 ubiquitin ligase function of MDM2. These data indicate that phosphomimetic lid mutation results in an "opening," rather than a "closing," of the pocket of MDM2 and highlight the ability of small intrinsically disordered or unstructured peptide motifs to regulate the specific activity of a protein. CI - Copyright 2010 Elsevier Ltd. All rights reserved. FAU - Worrall, Erin G AU - Worrall EG AD - Institute of Genetics and Molecular Medicine, CRUK Cancer Research Center, University of Edinburgh, Edinburgh EH4 2XR, UK. FAU - Worrall, Liam AU - Worrall L FAU - Blackburn, Elizabeth AU - Blackburn E FAU - Walkinshaw, Malcolm AU - Walkinshaw M FAU - Hupp, Ted R AU - Hupp TR LA - eng GR - C483/A6354/Cancer Research UK/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100319 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Amino Acid Substitution MH - Circular Dichroism MH - Hot Temperature MH - Models, Molecular MH - *Mutation, Missense MH - Protein Stability MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-mdm2/*chemistry/*genetics EDAT- 2010/03/23 06:00 MHDA- 2010/05/01 06:00 CRDT- 2010/03/23 06:00 PHST- 2010/02/14 [received] PHST- 2010/03/11 [revised] PHST- 2010/03/11 [accepted] PHST- 2010/03/19 [aheadofprint] AID - S0022-2836(10)00276-7 [pii] AID - 10.1016/j.jmb.2010.03.023 [doi] PST - ppublish SO - J Mol Biol. 2010 May 7;398(3):414-28. doi: 10.1016/j.jmb.2010.03.023. Epub 2010 Mar 19. PMID- 22064478 OWN - NLM STAT- MEDLINE DA - 20111228 DCOM- 20120221 LR - 20141021 IS - 1098-5549 (Electronic) IS - 0270-7306 (Linking) VI - 32 IP - 2 DP - 2012 Jan TI - Regulation of estrogen receptor alpha N-terminus conformation and function by peptidyl prolyl isomerase Pin1. PG - 445-57 LID - 10.1128/MCB.06073-11 [doi] AB - Estrogen receptor alpha (ERalpha), a key driver of growth in the majority of breast cancers, contains an unstructured transactivation domain (AF1) in its N terminus that is a convergence point for growth factor and hormonal activation. This domain is controlled by phosphorylation, but how phosphorylation impacts AF1 structure and function is unclear. We found that serine 118 (S118) phosphorylation of the ERalpha AF1 region in response to estrogen (agonist), tamoxifen (antagonist), and growth factors results in recruitment of the peptidyl prolyl cis/trans isomerase Pin1. Phosphorylation of S118 is critical for Pin1 binding, and mutation of S118 to alanine prevents this association. Importantly, Pin1 isomerizes the serine118-proline119 bond from a cis to trans isomer, with a concomitant increase in AF1 transcriptional activity. Pin1 overexpression promotes ligand-independent and tamoxifen-inducible activity of ERalpha and growth of tamoxifen-resistant breast cancer cells. Pin1 expression correlates with proliferation in ERalpha-positive rat mammary tumors. These results establish phosphorylation-coupled proline isomerization as a mechanism modulating AF1 functional activity and provide insight into the role of a conformational switch in the functional regulation of the intrinsically disordered transactivation domain of ERalpha. FAU - Rajbhandari, Prashant AU - Rajbhandari P AD - Department of Oncology and UW Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA. FAU - Finn, Greg AU - Finn G FAU - Solodin, Natalia M AU - Solodin NM FAU - Singarapu, Kiran K AU - Singarapu KK FAU - Sahu, Sarata C AU - Sahu SC FAU - Markley, John L AU - Markley JL FAU - Kadunc, Kelley J AU - Kadunc KJ FAU - Ellison-Zelski, Stephanie J AU - Ellison-Zelski SJ FAU - Kariagina, Anastasia AU - Kariagina A FAU - Haslam, Sandra Z AU - Haslam SZ FAU - Lu, Kun Ping AU - Lu KP FAU - Alarid, Elaine T AU - Alarid ET LA - eng GR - CA159578/CA/NCI NIH HHS/United States GR - P30 CA014520/CA/NCI NIH HHS/United States GR - P41 GM66326/GM/NIGMS NIH HHS/United States GR - P41 RR002301/RR/NCRR NIH HHS/United States GR - P41 RR02301/RR/NCRR NIH HHS/United States GR - R01 CA159578/CA/NCI NIH HHS/United States GR - R01 GM56230/GM/NIGMS NIH HHS/United States GR - T32 GM08688/GM/NIGMS NIH HHS/United States GR - U01 ES/CA012800/CA/NCI NIH HHS/United States GR - U54 GM074901/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20111107 PL - United States TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (Antineoplastic Agents, Hormonal) RN - 0 (Estrogen Receptor alpha) RN - 0 (NIMA-interacting peptidylprolyl isomerase) RN - 094ZI81Y45 (Tamoxifen) RN - EC 5.2.1.8 (Peptidylprolyl Isomerase) SB - IM MH - Animals MH - Antineoplastic Agents, Hormonal/pharmacology MH - Breast Neoplasms/drug therapy/genetics/*metabolism MH - Cell Line, Tumor MH - Drug Resistance, Neoplasm MH - Estrogen Receptor alpha/*chemistry/genetics/*metabolism MH - Female MH - Gene Expression Regulation, Neoplastic MH - Humans MH - Peptidylprolyl Isomerase/genetics/*metabolism MH - Phosphorylation MH - Protein Binding MH - Protein Structure, Tertiary MH - Rats MH - Rats, Sprague-Dawley MH - Tamoxifen/pharmacology MH - Transcriptional Activation PMC - PMC3255769 OID - NLM: PMC3255769 EDAT- 2011/11/09 06:00 MHDA- 2012/02/22 06:00 CRDT- 2011/11/09 06:00 PHST- 2011/11/07 [aheadofprint] AID - MCB.06073-11 [pii] AID - 10.1128/MCB.06073-11 [doi] PST - ppublish SO - Mol Cell Biol. 2012 Jan;32(2):445-57. doi: 10.1128/MCB.06073-11. Epub 2011 Nov 7. PMID- 8684460 OWN - NLM STAT- MEDLINE DA - 19960820 DCOM- 19960820 LR - 20120625 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 382 IP - 6589 DP - 1996 Jul 25 TI - Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A-Cdk2 complex. PG - 325-31 AB - The crystal structure of the human p27Kip1 kinase inhibitory domain bound to the phosphorylated cyclin A-cyclin-dependent kinase 2 (Cdk2) complex has been determined at 2.3 angstrom. p27Kip1 binds the complex as an extended structure interacting with both cyclin A and Cdk2. On cyclin A, it binds in a groove formed by conserved cyclin box residues. On Cdk2, it binds and rearranges the amino-terminal lobe and also inserts into the catalytic cleft, mimicking ATP. FAU - Russo, A A AU - Russo AA AD - Cellular Biochemistry and Biophysics Program, Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York 10021, USA. FAU - Jeffrey, P D AU - Jeffrey PD FAU - Patten, A K AU - Patten AK FAU - Massague, J AU - Massague J FAU - Pavletich, N P AU - Pavletich NP LA - eng SI - PDB/UNKNOWN PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Cell Cycle Proteins) RN - 0 (Cyclins) RN - 0 (Enzyme Inhibitors) RN - 0 (Microtubule-Associated Proteins) RN - 0 (Tumor Suppressor Proteins) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - EC 2.7.11.22 (CDC2-CDC28 Kinases) RN - EC 2.7.11.22 (CDK2 protein, human) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 2) RN - EC 2.7.11.22 (Cyclin-Dependent Kinases) SB - IM CIN - Nature. 1996 Jul 25;382(6589):295-6. PMID: 8684452 MH - Amino Acid Sequence MH - Binding Sites MH - *CDC2-CDC28 Kinases MH - *Cell Cycle Proteins MH - Conserved Sequence MH - Crystallography, X-Ray MH - Cyclin-Dependent Kinase 2 MH - Cyclin-Dependent Kinase Inhibitor p27 MH - Cyclin-Dependent Kinases/antagonists & inhibitors/*chemistry/metabolism MH - Cyclins/*chemistry/metabolism MH - Enzyme Inhibitors/*chemistry/metabolism MH - Humans MH - Microtubule-Associated Proteins/*chemistry/metabolism MH - Molecular Sequence Data MH - Protein Binding MH - Protein-Serine-Threonine Kinases/antagonists & inhibitors/*chemistry/metabolism MH - *Tumor Suppressor Proteins EDAT- 1996/07/25 MHDA- 1996/07/25 00:01 CRDT- 1996/07/25 00:00 AID - 10.1038/382325a0 [doi] PST - ppublish SO - Nature. 1996 Jul 25;382(6589):325-31. PMID- 18627125 OWN - NLM STAT- MEDLINE DA - 20080716 DCOM- 20080903 LR - 20140912 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 29 DP - 2008 Jul 22 TI - Regulation of cell division by intrinsically unstructured proteins: intrinsic flexibility, modularity, and signaling conduits. PG - 7598-609 LID - 10.1021/bi8006803 [doi] AB - It is now widely recognized that intrinsically unstructured (or disordered) proteins (IUPs or IDPs) are found in organisms from all kingdoms of life. In eukaryotes, IUPs are highly abundant and perform a wide range of biological functions, including regulation and signaling. Despite an increased level of interest in understanding the structural biology of IUPs and IDPs, questions regarding the mechanisms through which disordered proteins perform their biological function(s) remain. In other words, what are the relationships between disorder and function for IUPs? There are several excellent reviews that discuss the structural properties of IUPs and IDPs since 2005 [Receveur-Brechot, V., et al. (2006) Proteins 62, 24-45; Mittag, T., and Forman-Kay, J. D. (2007) Curr. Opin. Struct. Biol. 17, 3-14; Dyson, H. J., and Wright, P. E. (2005) Nat. Rev. Mol. Cell Biol. 6, 197-208]. Here, we briefly review general concepts pertaining to IUPs and then discuss our structural, biophysical, and biochemical studies of two IUPs, p21 and p27, which regulate the mammalian cell division cycle by inhibiting cyclin-dependent kinases (Cdks). Some segments of these two proteins are partially folded in isolation, and they fold further upon binding their biological targets. Interestingly, some portions of p27 remain flexible after binding to and inhibiting the Cdk2-cyclin A complex. This residual flexibility allows otherwise buried tyrosine residues within p27 to be phosphorylated by non-receptor tyrosine kinases (NRTKs). Tyrosine phosphorylation relieves kinase inhibition, triggering Cdk2-mediated phosphorylation of a threonine residue within the flexible C-terminus of p27. This, in turn, marks p27 for ubiquitination and proteasomal degradation, unleashing full Cdk2 activity which drives cell cycle progression. p27, thus, constitutes a conduit for transmission of proliferative signals via post-translational modifications. The term "conduit" is used here to connote a means of transmission of molecular signals which, in the case of p27, correspond to tyrosine and threonine phosphorylation, ubiquitination, and, ultimately, proteolytic degradation. Transmission of these multiple signals is enabled by the inherent flexibility of p27 which persists even after tight binding to the Cdk2-cyclin A complex. Importantly, activation of the p27 signaling conduit by oncogenic NRTKs contributes to tumorigenesis in some human cancers, including chronic myelogenous leukemia (CML) [Grimmler, M., et al. (2007) Cell 128, 269-280] and breast cancer [Chu, I., et al. (2007) Cell 128, 281-294]. Other IUPs may participate in conceptually similar molecular signaling conduits, and dysregulation of these putative conduits may contribute to other human diseases. Detailed study of these IUPs, both alone and within functional complexes, is required to test these hypotheses and to more fully understand the relationships between protein disorder and biological function. FAU - Galea, Charles A AU - Galea CA AD - Department of Structural Biology, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, Tennessee 38105, USA. FAU - Wang, Yuefeng AU - Wang Y FAU - Sivakolundu, Sivashankar G AU - Sivakolundu SG FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng GR - 5P30CA021765/CA/NCI NIH HHS/United States GR - 5R01CA082491/CA/NCI NIH HHS/United States GR - R01 CA082491/CA/NCI NIH HHS/United States GR - R01 CA082491-05/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cyclin A) RN - 0 (Cyclin-Dependent Kinase Inhibitor p21) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - EC 2.7.11.22 (CDK2 protein, human) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 2) SB - IM MH - Animals MH - Cell Division/*physiology MH - Cyclin A/chemistry/metabolism MH - Cyclin-Dependent Kinase 2/chemistry/metabolism MH - Cyclin-Dependent Kinase Inhibitor p21/chemistry/*metabolism MH - Cyclin-Dependent Kinase Inhibitor p27/chemistry/*metabolism MH - Eukaryotic Cells/cytology/metabolism MH - Humans MH - Protein Binding MH - Signal Transduction/*physiology RF - 98 PMC - PMC2580775 MID - NIHMS71338 OID - NLM: NIHMS71338 OID - NLM: PMC2580775 EDAT- 2008/07/17 09:00 MHDA- 2008/09/04 09:00 CRDT- 2008/07/17 09:00 AID - 10.1021/bi8006803 [doi] PST - ppublish SO - Biochemistry. 2008 Jul 22;47(29):7598-609. doi: 10.1021/bi8006803. PMID- 21909508 OWN - NLM STAT- MEDLINE DA - 20111202 DCOM- 20120320 LR - 20140919 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Intrinsically disordered proteins as molecular shields. PG - 210-9 LID - 10.1039/c1mb05263b [doi] AB - The broad family of LEA proteins are intrinsically disordered proteins (IDPs) with several potential roles in desiccation tolerance, or anhydrobiosis, one of which is to limit desiccation-induced aggregation of cellular proteins. We show here that this activity, termed molecular shield function, is distinct from that of a classical molecular chaperone, such as HSP70 - while HSP70 reduces aggregation of citrate synthase (CS) on heating, two LEA proteins, a nematode group 3 protein, AavLEA1, and a plant group 1 protein, Em, do not; conversely, the LEA proteins reduce CS aggregation on desiccation, while HSP70 lacks this ability. There are also differences in interaction with client proteins - HSP70 can be co-immunoprecipitated with a polyglutamine-containing client, consistent with tight complex formation, whereas the LEA proteins can not, although a loose interaction is observed by Forster resonance energy transfer. In a further exploration of molecular shield function, we demonstrate that synthetic polysaccharides, like LEA proteins, are able to reduce desiccation-induced aggregation of a water-soluble proteome, consistent with a steric interference model of anti-aggregation activity. If molecular shields operate by reducing intermolecular cohesion rates, they should not protect against intramolecular protein damage. This was tested using the monomeric red fluorescent protein, mCherry, which does not undergo aggregation on drying, but the absorbance and emission spectra of its intrinsic fluorophore are dramatically reduced, indicative of intramolecular conformational changes. As expected, these changes are not prevented by AavLEA1, except for a slight protection at high molar ratios, and an AavLEA1-mCherry fusion protein is damaged to the same extent as mCherry alone. A recent hypothesis proposed that proteomes from desiccation-tolerant species contain a higher degree of disorder than intolerant examples, and that this might provide greater intrinsic stability, but a bioinformatics survey does not support this, since there are no significant differences in the degree of disorder between desiccation tolerant and intolerant species. It seems clear therefore that molecular shield function is largely an intermolecular activity implemented by specialist IDPs, distinct from molecular chaperones, but with a role in proteostasis. FAU - Chakrabortee, Sohini AU - Chakrabortee S AD - Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK. FAU - Tripathi, Rashmi AU - Tripathi R FAU - Watson, Matthew AU - Watson M FAU - Schierle, Gabriele S Kaminski AU - Schierle GS FAU - Kurniawan, Davy P AU - Kurniawan DP FAU - Kaminski, Clemens F AU - Kaminski CF FAU - Wise, Michael J AU - Wise MJ FAU - Tunnacliffe, Alan AU - Tunnacliffe A LA - eng GR - 089703/Wellcome Trust/United Kingdom GR - 233232/European Research Council/International GR - G0902243/Medical Research Council/United Kingdom GR - MC_G1000734/Medical Research Council/United Kingdom GR - Medical Research Council/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110909 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Molecular Chaperones) RN - 0 (Polysaccharides) RN - 0 (Proteins) SB - IM MH - Deinococcus/metabolism MH - Desiccation MH - Humans MH - Immunoprecipitation MH - Light MH - *Models, Molecular MH - Molecular Chaperones/chemistry/metabolism MH - Polysaccharides/chemistry MH - *Protein Folding MH - Protein Structure, Quaternary MH - Proteins/*chemistry/*metabolism MH - Scattering, Radiation EDAT- 2011/09/13 06:00 MHDA- 2012/03/21 06:00 CRDT- 2011/09/13 06:00 PHST- 2011/09/09 [aheadofprint] PHST- 2011/12/01 [epublish] AID - 10.1039/c1mb05263b [doi] PST - ppublish SO - Mol Biosyst. 2012 Jan;8(1):210-9. doi: 10.1039/c1mb05263b. Epub 2011 Sep 9. PMID- 24993791 OWN - NLM STAT- MEDLINE DA - 20140822 DCOM- 20150513 IS - 1096-0279 (Electronic) IS - 1046-5928 (Linking) VI - 101 DP - 2014 Sep TI - Rhoptry protein 6 from Toxoplasma gondii is an intrinsically disordered protein. PG - 146-51 LID - 10.1016/j.pep.2014.06.011 [doi] LID - S1046-5928(14)00155-7 [pii] AB - Rhoptry protein 6 (ROP6) from Toxoplasma gondii is a 480-amino acid protein with no homology to any reported excretory or secretory protein. Especially, unlike the many other rhoptry protein types, ROP6 does not have a kinase domain. The biochemical and biophysical properties of ROP6 are unknown. Here, we investigated its structure using an in silico analysis method and overexpression and purification using an Escherichia coli system. The protein was purified to more than 85% homogeneity using immobilized metal affinity chromatography in denaturing conditions. After purification, ROP6 showed slow migration in SDS-PAGE, including fast proteolysis. This implies that ROP6 has a high percentage of flexible regions or extended loop structures. Secondary structure prediction and prediction of intrinsically disordered regions by using various bioinformatics tools, indicated that approximately 60% of ROP6 is predicted to be intrinsically disordered or random coil regions. These observations indicate that ROP6 is an intrinsically disordered protein. CI - Copyright (c) 2014 Elsevier Inc. All rights reserved. FAU - Lee, Won-Kyu AU - Lee WK AD - Department of Chemistry, College of Natural Sciences, Kookmin University, Seoul 136-702, Republic of Korea. FAU - Ahn, Hye-Jin AU - Ahn HJ AD - Department of Parasitology and the Catholic Institute of Parasitic Diseases, College of Medicine, Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 137-701, Republic of Korea. FAU - Yu, Yeon Gyu AU - Yu YG AD - Department of Chemistry, College of Natural Sciences, Kookmin University, Seoul 136-702, Republic of Korea. FAU - Nam, Ho-Woo AU - Nam HW AD - Department of Parasitology and the Catholic Institute of Parasitic Diseases, College of Medicine, Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 137-701, Republic of Korea. Electronic address: howoo@catholic.ac.kr. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140630 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Protozoan Proteins) SB - IM MH - Amino Acid Sequence MH - Cell Line MH - Chromatography, Affinity MH - Cloning, Molecular MH - Computational Biology MH - Electrophoresis, Polyacrylamide Gel MH - Escherichia coli/genetics/metabolism MH - Humans MH - Intrinsically Disordered Proteins/biosynthesis/*genetics MH - Protein Structure, Secondary MH - Protozoan Proteins/biosynthesis/*genetics MH - Toxoplasma/*metabolism OTO - NOTNLM OT - Database OT - Expression OT - Intrinsically disordered protein OT - ROP6 OT - Rhoptry protein OT - Toxoplasma gondii EDAT- 2014/07/06 06:00 MHDA- 2015/05/15 06:00 CRDT- 2014/07/05 06:00 PHST- 2014/04/30 [received] PHST- 2014/06/10 [revised] PHST- 2014/06/20 [accepted] PHST- 2014/06/30 [aheadofprint] AID - S1046-5928(14)00155-7 [pii] AID - 10.1016/j.pep.2014.06.011 [doi] PST - ppublish SO - Protein Expr Purif. 2014 Sep;101:146-51. doi: 10.1016/j.pep.2014.06.011. Epub 2014 Jun 30. PMID- 25099811 OWN - NLM STAT- In-Process DA - 20140807 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 107 IP - 3 DP - 2014 Aug 5 TI - Multi-scale ensemble modeling of modular proteins with intrinsically disordered linker regions: application to p53. PG - 721-9 LID - 10.1016/j.bpj.2014.06.026 [doi] LID - S0006-3495(14)00666-3 [pii] AB - In eukaryotic proteins, intrinsically disordered regions (IDRs) are ubiquitous and often exist in linker regions that flank the functional domains of modular proteins, regulating their functions. For detailed structural ensemble modeling of IDRs, we propose a multiscale method for IDRs that possess significant long-range order in modular proteins and apply it to the eukaryotic transcription factor p53 as an example. First, we performed all-atom (AA) molecular dynamics (MD) simulations of the explicitly solvated p53 linker region, without experimental restraint terms, finding fractional long-range contacts within the linker. Second, we fed this AA MD ensemble into a coarse-grained (CG) model, finding an optimal set of contact potentials. The optimized CG MD simulations reproduced the contact probability map from the AA MD simulations. Finally, we performed the CG MD simulation of the tetrameric p53 fragments including the core domains, the linker, and the tetramerization domain. Using the obtained ensemble, we theoretically calculated the small angle x-ray scattering (SAXS) profile of this fragment. The obtained SAXS profile agrees well with the experiment. We also found that the long-range contacts in the p53 linker region are required to reproduce the experimental SAXS profile. The developed framework in which we calculate the long-range contact probability map from the AA MD simulation and incorporate it to the CG model can be applied to broad range of IDRs. CI - Copyright (c) 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Terakawa, Tsuyoshi AU - Terakawa T AD - Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan. FAU - Higo, Junichi AU - Higo J AD - Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan. FAU - Takada, Shoji AU - Takada S AD - Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan. Electronic address: takada@biophys.kyoto-u.ac.jp. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 SB - IM PMC - PMC4129485 OID - NLM: PMC4129485 [Available on 08/05/15] EDAT- 2014/08/08 06:00 MHDA- 2014/08/08 06:00 CRDT- 2014/08/08 06:00 PMCR- 2015/08/05 00:00 PHST- 2014/02/24 [received] PHST- 2014/05/28 [revised] PHST- 2014/06/18 [accepted] AID - S0006-3495(14)00666-3 [pii] AID - 10.1016/j.bpj.2014.06.026 [doi] PST - ppublish SO - Biophys J. 2014 Aug 5;107(3):721-9. doi: 10.1016/j.bpj.2014.06.026. PMID- 16287076 OWN - NLM STAT- MEDLINE DA - 20051219 DCOM- 20060331 LR - 20061115 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 62 IP - 1 DP - 2006 Jan 1 TI - Structure, conformational stability, and enzymatic properties of acylphosphatase from the hyperthermophile Sulfolobus solfataricus. PG - 64-79 AB - The structure of AcP from the hyperthermophilic archaeon Sulfolobus solfataricus has been determined by (1)H-NMR spectroscopy and X-ray crystallography. Solution and crystal structures (1.27 A resolution, R-factor 13.7%) were obtained on the full-length protein and on an N-truncated form lacking the first 12 residues, respectively. The overall Sso AcP fold, starting at residue 13, displays the same betaalphabetabetaalphabeta topology previously described for other members of the AcP family from mesophilic sources. The unstructured N-terminal tail may be crucial for the unusual aggregation mechanism of Sso AcP previously reported. Sso AcP catalytic activity is reduced at room temperature but rises at its working temperature to values comparable to those displayed by its mesophilic counterparts at 25-37 degrees C. Such a reduced activity can result from protein rigidity and from the active site stiffening due the presence of a salt bridge between the C-terminal carboxylate and the active site arginine. Sso AcP is characterized by a melting temperature, Tm, of 100.8 degrees C and an unfolding free energy, DeltaG(U-F)H2O, at 28 degrees C and 81 degrees C of 48.7 and 20.6 kJ mol(-1), respectively. The kinetic and structural data indicate that mesophilic and hyperthermophilic AcP's display similar enzymatic activities and conformational stabilities at their working conditions. Structural analysis of the factor responsible for Sso AcP thermostability with respect to mesophilic AcP's revealed the importance of a ion pair network stabilizing particularly the beta-sheet and the loop connecting the fourth and fifth strands, together with increased density packing, loop shortening and a higher alpha-helical propensity. CI - 2005 Wiley-Liss, Inc. FAU - Corazza, Alessandra AU - Corazza A AD - Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Udine, Italy. FAU - Rosano, Camillo AU - Rosano C FAU - Pagano, Katiuscia AU - Pagano K FAU - Alverdi, Vera AU - Alverdi V FAU - Esposito, Gennaro AU - Esposito G FAU - Capanni, Cristina AU - Capanni C FAU - Bemporad, Francesco AU - Bemporad F FAU - Plakoutsi, Georgia AU - Plakoutsi G FAU - Stefani, Massimo AU - Stefani M FAU - Chiti, Fabrizio AU - Chiti F FAU - Zuccotti, Simone AU - Zuccotti S FAU - Bolognesi, Martino AU - Bolognesi M FAU - Viglino, Paolo AU - Viglino P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Archaeal Proteins) RN - EC 3.6.- (Acid Anhydride Hydrolases) RN - EC 3.6.1.7 (acylphosphatase) SB - IM MH - Acid Anhydride Hydrolases/*chemistry/metabolism MH - Archaeal Proteins/chemistry/metabolism MH - Enzyme Stability MH - Hydrogen-Ion Concentration MH - Kinetics MH - Protein Conformation MH - Scattering, Radiation MH - Sulfolobus/*enzymology MH - Thermodynamics EDAT- 2005/11/16 09:00 MHDA- 2006/04/01 09:00 CRDT- 2005/11/16 09:00 AID - 10.1002/prot.20703 [doi] PST - ppublish SO - Proteins. 2006 Jan 1;62(1):64-79. PMID- 23783762 OWN - NLM STAT- MEDLINE DA - 20130620 DCOM- 20140623 LR - 20141113 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 3 DP - 2013 TI - Intrinsic disorder in PTEN and its interactome confers structural plasticity and functional versatility. PG - 2035 LID - 10.1038/srep02035 [doi] AB - IDPs, while structurally poor, are functionally rich by virtue of their flexibility and modularity. However, how mutations in IDPs elicit diseases, remain elusive. Herein, we have identified tumor suppressor PTEN as an intrinsically disordered protein (IDP) and elucidated the molecular principles by which its intrinsically disordered region (IDR) at the carboxyl-terminus (C-tail) executes its functions. Post-translational modifications, conserved eukaryotic linear motifs and molecular recognition features present in the C-tail IDR enhance PTEN's protein-protein interactions that are required for its myriad cellular functions. PTEN primary and secondary interactomes are also enriched in IDPs, most being cancer related, revealing that PTEN functions emanate from and are nucleated by the C-tail IDR, which form pliable network-hubs. Together, PTEN higher order functional networks operate via multiple IDP-IDP interactions facilitated by its C-tail IDR. Targeting PTEN IDR and its interaction hubs emerges as a new paradigm for treatment of PTEN related pathologies. FAU - Malaney, Prerna AU - Malaney P AD - Morsani College of Medicine, Department of Pathology and Cell Biology, University of South Florida, Tampa, FL 33612, USA FAU - Pathak, Ravi Ramesh AU - Pathak RR FAU - Xue, Bin AU - Xue B FAU - Uversky, Vladimir N AU - Uversky VN FAU - Dave, Vrushank AU - Dave V LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - EC 3.1.3.67 (PTEN Phosphohydrolase) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Gene Regulatory Networks MH - Humans MH - *Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Neoplasms/genetics/metabolism MH - PTEN Phosphohydrolase/*chemistry/genetics/*metabolism MH - Phosphorylation MH - Protein Binding MH - Protein Conformation MH - Protein Interaction Domains and Motifs MH - *Protein Interaction Maps MH - Protein Processing, Post-Translational MH - Sequence Alignment MH - Signal Transduction PMC - PMC3687229 OID - NLM: PMC3687229 EDAT- 2013/06/21 06:00 MHDA- 2014/06/24 06:00 CRDT- 2013/06/21 06:00 PHST- 2013/03/11 [received] PHST- 2013/06/03 [accepted] AID - srep02035 [pii] AID - 10.1038/srep02035 [doi] PST - ppublish SO - Sci Rep. 2013;3:2035. doi: 10.1038/srep02035. PMID- 16284250 OWN - NLM STAT- MEDLINE DA - 20051123 DCOM- 20060112 LR - 20140910 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 102 IP - 47 DP - 2005 Nov 22 TI - A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering. PG - 17002-7 AB - Natively unfolded proteins play key roles in normal and pathological biochemical processes. Despite their importance for function, this category of proteins remains beyond the reach of classical structural biology because of their inherent conformational heterogeneity. We present a description of the intrinsic conformational sampling of unfolded proteins based on residue-specific /Psi propensities from loop regions of a folded protein database and simple volume exclusion. This approach is used to propose a structural model of the 57-aa, natively disordered region of the nucleocapsid-binding domain of Sendai virus phosphoprotein. Structural ensembles obeying these simple rules of conformational sampling are used to simulate averaged residual dipolar couplings (RDCs) and small-angle x-ray scattering data. This protein is particularly informative because RDC data from the equally sized folded and unfolded domains both report on the unstructured region, allowing a quantitative analysis of the degree of order present in this part of the protein. Close agreement between experimental and simulated RDC and small-angle x-ray scattering data validates this simple model of conformational sampling, providing a precise description of local structure and dynamics and average dimensions of the ensemble of sampled structures. RDC data from two urea-unfolded systems are also closely reproduced. The demonstration that conformational behavior of unfolded proteins can be accurately predicted from the primary sequence by using a simple set of rules has important consequences for our understanding of the structure and dynamics of the unstructured state. FAU - Bernado, Pau AU - Bernado P AD - Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat a l'Energie Atomique-Centre National de la Recherche Scientifique-Universite Joseph Fourier, 41 Rue Jules Horowitz, 38027 Grenoble, France. FAU - Blanchard, Laurence AU - Blanchard L FAU - Timmins, Peter AU - Timmins P FAU - Marion, Dominique AU - Marion D FAU - Ruigrok, Rob W H AU - Ruigrok RW FAU - Blackledge, Martin AU - Blackledge M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051111 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Phosphoproteins) RN - 0 (Viral Proteins) RN - 8W8T17847W (Urea) SB - IM MH - Models, Molecular MH - Phosphoproteins/*chemistry MH - Protein Denaturation MH - Protein Structure, Tertiary MH - Scattering, Radiation MH - Sendai virus/*chemistry MH - Sequence Analysis, Protein MH - Urea MH - Viral Proteins/*chemistry MH - X-Ray Diffraction MH - X-Rays PMC - PMC1287987 OID - NLM: PMC1287987 EDAT- 2005/11/15 09:00 MHDA- 2006/01/13 09:00 CRDT- 2005/11/15 09:00 PHST- 2005/11/11 [aheadofprint] AID - 0506202102 [pii] AID - 10.1073/pnas.0506202102 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2005 Nov 22;102(47):17002-7. Epub 2005 Nov 11. PMID- 20498278 OWN - NLM STAT- MEDLINE DA - 20100712 DCOM- 20100806 LR - 20140827 IS - 1098-5549 (Electronic) IS - 0270-7306 (Linking) VI - 30 IP - 15 DP - 2010 Aug TI - c-Fos proteasomal degradation is activated by a default mechanism, and its regulation by NAD(P)H:quinone oxidoreductase 1 determines c-Fos serum response kinetics. PG - 3767-78 LID - 10.1128/MCB.00899-09 [doi] AB - The short-lived proto-oncoprotein c-Fos is a component of the activator protein 1 (AP-1) transcription factor. A large region of c-Fos is intrinsically unstructured and susceptible to a recently characterized proteasomal ubiquitin-independent degradation (UID) pathway. UID is active by a default mechanism that is inhibited by NAD(P)H:quinone oxidoreductase 1 (NQO1), a 20S proteasome gatekeeper. Here, we show that NQO1 binds and induces robust c-Fos accumulation by blocking the UID pathway. c-Jun, a partner of c-Fos, also protects c-Fos from proteasomal degradation by default. Our findings suggest that NQO1 protects monomeric c-Fos from proteasomal UID, a function that is fulfilled later by c-Jun. We show that this process regulates c-Fos homeostasis (proteostasis) in response to serum stimulation, phosphorylation, nuclear translocation, and transcription activity. In addition, we show that NQO1 is important to ensure immediate c-Fos accumulation in response to serum, since a delayed response was observed under low NQO1 expression. These data suggest that in vivo, protein unstructured regions determine the kinetics and the homeostasis of regulatory proteins. Our data provide evidence for another layer of regulation of key regulatory proteins that functions at the level of protein degradation and is designed to ensure optimal formation of functional complexes such as AP-1. FAU - Adler, Julia AU - Adler J AD - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. FAU - Reuven, Nina AU - Reuven N FAU - Kahana, Chaim AU - Kahana C FAU - Shaul, Yosef AU - Shaul Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100524 PL - United States TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (Proto-Oncogene Proteins c-fos) RN - 0 (Transcription Factor AP-1) RN - 0 (Transcription Factors) RN - 0 (Ubiquitin) RN - 0U46U6E8UK (NAD) RN - EC 1.6.5.2 (NAD(P)H Dehydrogenase (Quinone)) RN - EC 1.6.5.2 (NQO1 protein, human) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Kinetics MH - NAD/genetics/metabolism MH - NAD(P)H Dehydrogenase (Quinone)/*genetics/metabolism MH - Proteasome Endopeptidase Complex/genetics/metabolism MH - Protein Structure, Tertiary/genetics MH - Proto-Oncogene Proteins c-fos/genetics/*metabolism MH - Transcription Factor AP-1/genetics/metabolism MH - Transcription Factors/genetics/metabolism MH - Ubiquitin/genetics/*metabolism PMC - PMC2916405 OID - NLM: PMC2916405 EDAT- 2010/05/26 06:00 MHDA- 2010/08/07 06:00 CRDT- 2010/05/26 06:00 PHST- 2010/05/24 [aheadofprint] AID - MCB.00899-09 [pii] AID - 10.1128/MCB.00899-09 [doi] PST - ppublish SO - Mol Cell Biol. 2010 Aug;30(15):3767-78. doi: 10.1128/MCB.00899-09. Epub 2010 May 24. PMID- 21211726 OWN - NLM STAT- MEDLINE DA - 20110107 DCOM- 20110217 LR - 20140921 IS - 1097-4164 (Electronic) IS - 1097-2765 (Linking) VI - 41 IP - 1 DP - 2011 Jan 7 TI - Disorder targets misorder in nuclear quality control degradation: a disordered ubiquitin ligase directly recognizes its misfolded substrates. PG - 93-106 LID - 10.1016/j.molcel.2010.12.004 [doi] AB - Protein quality control (PQC) degradation systems protect the cell from the toxic accumulation of misfolded proteins. Because any protein can become misfolded, these systems must be able to distinguish abnormal proteins from normal ones, yet be capable of recognizing the wide variety of distinctly shaped misfolded proteins they are likely to encounter. How individual PQC degradation systems accomplish this remains an open question. Here we show that the yeast nuclear PQC ubiquitin ligase San1 directly recognizes its misfolded substrates via intrinsically disordered N- and C-terminal domains. These disordered domains are punctuated with small segments of order and high sequence conservation that serve as substrate-recognition sites San1 uses to target its different substrates. We propose that these substrate-recognition sites, interspersed among flexible, disordered regions, provide San1 an inherent plasticity which allows it to bind its many, differently shaped misfolded substrates. CI - Copyright A(c) 2011 Elsevier Inc. All rights reserved. FAU - Rosenbaum, Joel C AU - Rosenbaum JC AD - Department of Pharmacology, University of Washington, Seattle, WA 98195, USA. FAU - Fredrickson, Eric K AU - Fredrickson EK FAU - Oeser, Michelle L AU - Oeser ML FAU - Garrett-Engele, Carrie M AU - Garrett-Engele CM FAU - Locke, Melissa N AU - Locke MN FAU - Richardson, Lauren A AU - Richardson LA FAU - Nelson, Zara W AU - Nelson ZW FAU - Hetrick, Elizabeth D AU - Hetrick ED FAU - Milac, Thomas I AU - Milac TI FAU - Gottschling, Daniel E AU - Gottschling DE FAU - Gardner, Richard G AU - Gardner RG LA - eng GR - R01 AG031136/AG/NIA NIH HHS/United States GR - R01 AG031136-01A2/AG/NIA NIH HHS/United States GR - R01 AG031136-01A2S1/AG/NIA NIH HHS/United States GR - R01 AG031136-02/AG/NIA NIH HHS/United States GR - R01 AG031136-03/AG/NIA NIH HHS/United States GR - R01AG031136/AG/NIA NIH HHS/United States GR - R01GM043893/GM/NIGMS NIH HHS/United States GR - R21 RR025787/RR/NCRR NIH HHS/United States GR - R21 RR025787-01/RR/NCRR NIH HHS/United States GR - R21 RR025787-02/RR/NCRR NIH HHS/United States GR - R21RR025787/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 6.3.2.19 (SAN1 protein, S cerevisiae) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligase Complexes) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM CIN - Mol Cell. 2011 Jan 7;41(1):2-3. PMID: 21211716 MH - Amino Acid Sequence MH - Molecular Sequence Data MH - *Protein Folding MH - Protein Interaction Mapping MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae Proteins/chemistry/metabolism MH - Sequence Alignment MH - Substrate Specificity MH - Ubiquitin-Protein Ligase Complexes/chemistry/*physiology MH - Ubiquitin-Protein Ligases/chemistry/metabolism PMC - PMC3042722 MID - NIHMS262664 OID - NLM: NIHMS262664 OID - NLM: PMC3042722 EDAT- 2011/01/08 06:00 MHDA- 2011/02/18 06:00 CRDT- 2011/01/08 06:00 PHST- 2010/06/14 [received] PHST- 2010/09/01 [revised] PHST- 2010/10/27 [accepted] AID - S1097-2765(10)00960-3 [pii] AID - 10.1016/j.molcel.2010.12.004 [doi] PST - ppublish SO - Mol Cell. 2011 Jan 7;41(1):93-106. doi: 10.1016/j.molcel.2010.12.004. PMID- 22249765 OWN - NLM STAT- MEDLINE DA - 20120503 DCOM- 20120831 LR - 20141019 IS - 1573-6903 (Electronic) IS - 0364-3190 (Linking) VI - 37 IP - 6 DP - 2012 Jun TI - Classic 18.5- and 21.5-kDa myelin basic protein isoforms associate with cytoskeletal and SH3-domain proteins in the immortalized N19-oligodendroglial cell line stimulated by phorbol ester and IGF-1. PG - 1277-95 LID - 10.1007/s11064-011-0700-2 [doi] AB - The 18.5-kDa classic myelin basic protein (MBP) is an intrinsically disordered protein arising from the Golli (Genes of Oligodendrocyte Lineage) gene complex and is responsible for compaction of the myelin sheath in the central nervous system. This MBP splice isoform also has a plethora of post-translational modifications including phosphorylation, deimination, methylation, and deamidation, that reduce its overall net charge and alter its protein and lipid associations within oligodendrocytes (OLGs). It was originally thought that MBP was simply a structural component of myelin; however, additional investigations have demonstrated that MBP is multi-functional, having numerous protein-protein interactions with Ca(2)(+)-calmodulin, actin, tubulin, and proteins with SH3-domains, and it can tether these proteins to a lipid membrane in vitro. Here, we have examined cytoskeletal interactions of classic 18.5-kDa MBP, in vivo, using early developmental N19-OLGs transfected with fluorescently-tagged MBP, actin, tubulin, and zonula occludens 1 (ZO-1). We show that MBP redistributes to distinct 'membrane-ruffled' regions of the plasma membrane where it co-localizes with actin and tubulin, and with the SH3-domain-containing proteins cortactin and ZO-1, when stimulated with PMA, a potent activator of the protein kinase C pathway. Moreover, using phospho-specific antibody staining, we show an increase in phosphorylated Thr98 MBP (human sequence numbering) in membrane-ruffled OLGs. Previously, Thr98 phosphorylation of MBP has been shown to affect its conformation, interactions with other proteins, and tethering of other proteins to the membrane in vitro. Here, MBP and actin were also co-localized in new focal adhesion contacts induced by IGF-1 stimulation in cells grown on laminin-2. This study supports a role for classic MBP isoforms in cytoskeletal and other protein-protein interactions during membrane and cytoskeletal remodeling in OLGs. FAU - Smith, Graham S T AU - Smith GS AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada. FAU - Homchaudhuri, Lopamudra AU - Homchaudhuri L FAU - Boggs, Joan M AU - Boggs JM FAU - Harauz, George AU - Harauz G LA - eng GR - 86483/Canadian Institutes of Health Research/Canada GR - MOP 86483/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120117 PL - United States TA - Neurochem Res JT - Neurochemical research JID - 7613461 RN - 0 (Cortactin) RN - 0 (Myelin Basic Protein) RN - 0 (Protein Isoforms) RN - 0 (Tubulin) RN - 67763-96-6 (Insulin-Like Growth Factor I) RN - NI40JAQ945 (Tetradecanoylphorbol Acetate) SB - IM MH - Cell Line MH - Cell Membrane/*metabolism MH - Cortactin/metabolism MH - Focal Adhesions MH - Humans MH - Insulin-Like Growth Factor I/*pharmacology MH - Microscopy, Fluorescence MH - Myelin Basic Protein/chemistry/*metabolism MH - Oligodendroglia/drug effects/*metabolism MH - Protein Isoforms/chemistry/metabolism MH - Protein Processing, Post-Translational MH - Tetradecanoylphorbol Acetate/*pharmacology MH - Tubulin/metabolism MH - src Homology Domains PMC - PMC3527419 MID - CAMS2552 OID - NLM: CAMS2552 OID - NLM: PMC3527419 EDAT- 2012/01/18 06:00 MHDA- 2012/09/01 06:00 CRDT- 2012/01/18 06:00 PHST- 2011/09/14 [received] PHST- 2011/12/31 [accepted] PHST- 2011/11/17 [revised] PHST- 2012/01/17 [aheadofprint] AID - 10.1007/s11064-011-0700-2 [doi] PST - ppublish SO - Neurochem Res. 2012 Jun;37(6):1277-95. doi: 10.1007/s11064-011-0700-2. Epub 2012 Jan 17. PMID- 18725924 OWN - NLM STAT- MEDLINE DA - 20080826 DCOM- 20081218 LR - 20140903 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 4 IP - 8 DP - 2008 TI - The effect of a DeltaK280 mutation on the unfolded state of a microtubule-binding repeat in Tau. PG - e1000155 LID - 10.1371/journal.pcbi.1000155 [doi] AB - Tau is a natively unfolded protein that forms intracellular aggregates in the brains of patients with Alzheimer's disease. To decipher the mechanism underlying the formation of tau aggregates, we developed a novel approach for constructing models of natively unfolded proteins. The method, energy-minima mapping and weighting (EMW), samples local energy minima of subsequences within a natively unfolded protein and then constructs ensembles from these energetically favorable conformations that are consistent with a given set of experimental data. A unique feature of the method is that it does not strive to generate a single ensemble that represents the unfolded state. Instead we construct a number of candidate ensembles, each of which agrees with a given set of experimental constraints, and focus our analysis on local structural features that are present in all of the independently generated ensembles. Using EMW we generated ensembles that are consistent with chemical shift measurements obtained on tau constructs. Thirty models were constructed for the second microtubule binding repeat (MTBR2) in wild-type (WT) tau and a DeltaK280 mutant, which is found in some forms of frontotemporal dementia. By focusing on structural features that are preserved across all ensembles, we find that the aggregation-initiating sequence, PHF6*, prefers an extended conformation in both the WT and DeltaK280 sequences. In addition, we find that residue K280 can adopt a loop/turn conformation in WT MTBR2 and that deletion of this residue, which can adopt nonextended states, leads to an increase in locally extended conformations near the C-terminus of PHF6*. As an increased preference for extended states near the C-terminus of PHF6* may facilitate the propagation of beta-structure downstream from PHF6*, these results explain how a deletion at position 280 can promote the formation of tau aggregates. FAU - Huang, Austin AU - Huang A AD - Department of Electrical Engineering and Computer Science, Harvard-MIT Division of Health Sciences and Technology, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America. FAU - Stultz, Collin M AU - Stultz CM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080822 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (tau Proteins) RN - K3Z4F929H6 (Lysine) SB - IM MH - Amino Acid Motifs MH - Dimerization MH - Humans MH - Lysine/chemistry/metabolism MH - Microtubules/metabolism MH - Models, Molecular MH - *Mutation/physiology MH - Protein Binding MH - *Protein Folding MH - Protein Interaction Domains and Motifs MH - *Repetitive Sequences, Amino Acid/physiology MH - Systems Integration MH - Thermodynamics MH - tau Proteins/*chemistry/genetics/metabolism/ultrastructure PMC - PMC2494868 OID - NLM: PMC2494868 EDAT- 2008/08/30 09:00 MHDA- 2008/12/19 09:00 CRDT- 2008/08/30 09:00 PHST- 2008/04/01 [received] PHST- 2008/07/10 [accepted] AID - 10.1371/journal.pcbi.1000155 [doi] PST - epublish SO - PLoS Comput Biol. 2008 Aug 22;4(8):e1000155. doi: 10.1371/journal.pcbi.1000155. PMID- 19826005 OWN - NLM STAT- MEDLINE DA - 20091207 DCOM- 20100205 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 284 IP - 50 DP - 2009 Dec 11 TI - Low micromolar zinc accelerates the fibrillization of human tau via bridging of Cys-291 and Cys-322. PG - 34648-57 LID - 10.1074/jbc.M109.058883 [doi] AB - A hallmark of a group of neurodegenerative diseases such as Alzheimer disease is the formation of neurofibrillary tangles, which are principally composed of bundles of filaments formed by microtubule-associated protein Tau. Clarifying how natively unstructured Tau protein forms abnormal aggregates is of central importance for elucidating the etiology of these diseases. There is considerable evidence showing that zinc, as an essential element that is highly concentrated in brain, is linked to the development or progression of these diseases. Herein, by using recombinant human Tau fragment Tau(244-372) and its mutants, we have investigated the effect of zinc on the aggregation of Tau. Low micromolar concentrations of Zn(2+) dramatically accelerate fibril formation of wild-type Tau(244-372) under reducing conditions, compared with no Zn(2+). Higher concentrations of Zn(2+), however, induce wild-type Tau(244-372) to form granular aggregates in reducing conditions. Moreover, these non-fibrillar aggregates assemble into mature Tau filaments when Zn(2+) has been chelated by EDTA. Unlike wild-type Tau(244-372), low micromolar concentrations of Zn(2+) have no obvious effects on fibrillization kinetics of single mutants C291A and C322A and double mutant C291A/C322A under reducing conditions. The results from isothermal titration calorimetry show that one Zn(2+) binds to one Tau molecule via tetrahedral coordination to Cys-291 and Cys-322 as well as two histidines, with moderate, micromolar affinity. Our data demonstrate that low micromolar zinc accelerates the fibrillization of human Tau protein via bridging Cys-291 and Cys-322 in physiological reducing conditions, providing clues to understanding the relationship between zinc dyshomeostasis and the etiology of neurodegenerative diseases. FAU - Mo, Zhong-Ying AU - Mo ZY AD - State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China. FAU - Zhu, Ying-Zhu AU - Zhu YZ FAU - Zhu, Hai-Li AU - Zhu HL FAU - Fan, Jun-Bao AU - Fan JB FAU - Chen, Jie AU - Chen J FAU - Liang, Yi AU - Liang Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091013 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Disulfides) RN - 0 (MAPT protein, human) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 0 (tau Proteins) RN - J41CSQ7QDS (Zinc) RN - K848JZ4886 (Cysteine) SB - IM MH - Alzheimer Disease/metabolism/pathology MH - Cysteine/*metabolism MH - Disulfides/metabolism MH - Humans MH - Microscopy, Atomic Force MH - Molecular Sequence Data MH - *Neurofibrillary Tangles/chemistry/metabolism/pathology MH - Oxidation-Reduction MH - *Peptide Fragments/chemistry/genetics/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Thermodynamics MH - Zinc/*metabolism MH - *tau Proteins/chemistry/genetics/metabolism PMC - PMC2787327 OID - NLM: PMC2787327 EDAT- 2009/10/15 06:00 MHDA- 2010/02/06 06:00 CRDT- 2009/10/15 06:00 PHST- 2009/10/13 [aheadofprint] AID - M109.058883 [pii] AID - 10.1074/jbc.M109.058883 [doi] PST - ppublish SO - J Biol Chem. 2009 Dec 11;284(50):34648-57. doi: 10.1074/jbc.M109.058883. Epub 2009 Oct 13. PMID- 22349738 OWN - NLM STAT- MEDLINE DA - 20120409 DCOM- 20120803 IS - 1638-6183 (Electronic) IS - 0300-9084 (Linking) VI - 94 IP - 5 DP - 2012 May TI - The extreme N-terminal domain of a hordeivirus TGB1 movement protein mediates its localization to the nucleolus and interaction with fibrillarin. PG - 1180-8 LID - 10.1016/j.biochi.2012.02.005 [doi] AB - The hordeiviral movement protein encoded by the first gene of the triple gene block (TGBp1) of Poa semilatent virus (PSLV), interacts with viral genomic RNAs to form RNP particles which are considered to be a form of viral genome capable of cell-to-cell and long-distance transport in infected plants. The PSLV TGBp1 contains a C-terminal NTPase/helicase domain (HELD) and an N-terminal extension region consisting of two structurally and functionally distinct domains: an extreme N-terminal domain (NTD) and an internal domain (ID). This study demonstrates that transient expression of TGBp1 fused to GFP in Nicotiana benthamiana leaves results in faint but obvious fluorescence in the nucleolus in addition to cytosolic distribution. Mutagenesis of the basic amino acids inside the NTD clusters A (116)KSKRKKKNKK(125) and B (175)KKATKKESKKQTK(187) reveals that these clusters are indispensable for nuclear and nucleolar targeting of PSLV TGBp1 and may contain nuclear and nucleolar localization signals or their elements. The PSLV TGBp1 is able to bind to fibrillarin, the major nucleolar protein (AtFib2 from Arabidopsis thaliana) in vitro. This protein-protein interaction occurs between the glycine-arginine-rich (GAR) domain of fibrillarin and the first 82 amino acid residues of TGBp1. The interaction of TGBp1 with fibrillarin is also visualized in vivo by bimolecular fluorescence complementation (BiFC) during co-expression of TGBp1 or its deletion mutants, and fibrillarin as fusions to different halves of YFP in N. benthamiana plants. The sites responsible for nuclear/nucleolar localization and fibrillarin binding, have been located within the intrinsically disordered TGBp1 NTD. These data could suggest that specific functions of hordeivirus TGBp1 may depend on its interaction with nucleolar components. CI - Copyright (c) 2012 Elsevier Masson SAS. All rights reserved. FAU - Semashko, Maria A AU - Semashko MA AD - A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninsky Gory, Moscow, 119992, Russia. FAU - Gonzalez, Inmaculada AU - Gonzalez I FAU - Shaw, Jane AU - Shaw J FAU - Leonova, Olga G AU - Leonova OG FAU - Popenko, Vladimir I AU - Popenko VI FAU - Taliansky, Michael E AU - Taliansky ME FAU - Canto, Tomas AU - Canto T FAU - Kalinina, Natalia O AU - Kalinina NO LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120211 PL - France TA - Biochimie JT - Biochimie JID - 1264604 RN - 0 (Chromosomal Proteins, Non-Histone) RN - 0 (Plant Viral Movement Proteins) RN - 0 (fibrillarin) SB - IM MH - Blotting, Western MH - Cell Nucleolus/*metabolism/*virology MH - Chromosomal Proteins, Non-Histone/*metabolism MH - Plant Viral Movement Proteins/genetics/*metabolism MH - Protein Binding MH - RNA Viruses/*metabolism EDAT- 2012/02/22 06:00 MHDA- 2012/08/04 06:00 CRDT- 2012/02/22 06:00 PHST- 2011/12/07 [received] PHST- 2012/02/06 [accepted] PHST- 2012/02/11 [aheadofprint] AID - S0300-9084(12)00046-6 [pii] AID - 10.1016/j.biochi.2012.02.005 [doi] PST - ppublish SO - Biochimie. 2012 May;94(5):1180-8. doi: 10.1016/j.biochi.2012.02.005. Epub 2012 Feb 11. PMID- 10346815 OWN - NLM STAT- MEDLINE DA - 19990624 DCOM- 19990624 LR - 20140615 IS - 0890-9369 (Print) IS - 0890-9369 (Linking) VI - 13 IP - 10 DP - 1999 May 15 TI - Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding. PG - 1263-75 AB - Pax6, a transcription factor containing the bipartite paired DNA-binding domain, has critical roles in development of the eye, nose, pancreas, and central nervous system. The 2.5 A structure of the human Pax6 paired domain with its optimal 26-bp site reveals extensive DNA contacts from the amino-terminal subdomain, the linker region, and the carboxy-terminal subdomain. The Pax6 structure not only confirms the docking arrangement of the amino-terminal subdomain as seen in cocrystals of the Drosophila Prd Pax protein, but also reveals some interesting differences in this region and helps explain the sequence specificity of paired domain-DNA recognition. In addition, this structure gives the first detailed information about how the paired linker region and carboxy-terminal subdomain contact DNA. The extended linker makes minor groove contacts over an 8-bp region, and the carboxy-terminal helix-turn-helix unit makes base contacts in the major groove. The structure and docking arrangement of the carboxy-terminal subdomain of Pax6 is remarkably similar to that of the amino-terminal subdomain, and there is an approximate twofold symmetry axis relating the polypeptide backbones of these two helix-turn-helix units. Our structure of the Pax6 paired domain-DNA complex provides a framework for understanding paired domain-DNA interactions, for analyzing mutations that map in the linker and carboxy-terminal regions of the paired domain, and for modeling protein-protein interactions of the Pax family proteins. FAU - Xu, H E AU - Xu HE AD - Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA. FAU - Rould, M A AU - Rould MA FAU - Xu, W AU - Xu W FAU - Epstein, J A AU - Epstein JA FAU - Maas, R L AU - Maas RL FAU - Pabo, C O AU - Pabo CO LA - eng SI - PDB/6PAX GR - GM31471/GM/NIGMS NIH HHS/United States GR - R01 EY10123/EY/NEI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Genes Dev JT - Genes & development JID - 8711660 RN - 0 (DNA-Binding Proteins) RN - 0 (Eye Proteins) RN - 0 (Homeodomain Proteins) RN - 0 (PAX6 protein) RN - 0 (Paired Box Transcription Factors) RN - 0 (Repressor Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - *Crystallography, X-Ray MH - DNA/chemistry/metabolism MH - DNA-Binding Proteins/*chemistry/*physiology MH - Eye Proteins MH - Helix-Turn-Helix Motifs MH - *Homeodomain Proteins MH - Humans MH - Models, Genetic MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation, Missense MH - Nucleic Acid Conformation MH - Paired Box Transcription Factors MH - Protein Binding MH - Repressor Proteins PMC - PMC316729 OID - NLM: PMC316729 EDAT- 1999/05/27 MHDA- 1999/05/27 00:01 CRDT- 1999/05/27 00:00 PST - ppublish SO - Genes Dev. 1999 May 15;13(10):1263-75. PMID- 15049684 OWN - NLM STAT- MEDLINE DA - 20040330 DCOM- 20040729 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 13 DP - 2004 Apr 6 TI - Crystal structures of an intrinsically active cholera toxin mutant yield insight into the toxin activation mechanism. PG - 3772-82 AB - Cholera toxin (CT) is a heterohexameric bacterial protein toxin belonging to a larger family of A/B ADP-ribosylating toxins. Each of these toxins undergoes limited proteolysis and/or disulfide bond reduction to form the enzymatically active toxic fragment. Nicking and reduction render both CT and the closely related heat-labile enterotoxin from Escherichia coli (LT) unstable in solution, thus far preventing a full structural understanding of the conformational changes resulting from toxin activation. We present the first structural glimpse of an active CT in structures from three crystal forms of a single-site A-subunit CT variant, Y30S, which requires no activational modifications for full activity. We also redetermined the structure of the wild-type, proenzyme CT from two crystal forms, both of which exhibit (i) better geometry and (ii) a different A2 "tail" conformation than the previously determined structure [Zhang et al. (1995) J. Mol. Biol. 251, 563-573]. Differences between wild-type CT and active CTY30S are observed in A-subunit loop regions that had been previously implicated in activation by analysis of the structure of an LT A-subunit R7K variant [van den Akker et al. (1995) Biochemistry 34, 10996-11004]. The 25-36 activation loop is disordered in CTY30S, while the 47-56 active site loop displays varying degrees of order in the three CTY30S structures, suggesting that disorder in the activation loop predisposes the active site loop to a greater degree of flexibility than that found in unactivated wild-type CT. On the basis of these six new views of the CT holotoxin, we propose a model for how the activational modifications experienced by wild-type CT are communicated to the active site. FAU - O'Neal, Claire J AU - O'Neal CJ AD - Department of Chemistry and Biomolecular Structure Center, University of Washington, Seattle, Washington 98195, USA. FAU - Amaya, Edward I AU - Amaya EI FAU - Jobling, Michael G AU - Jobling MG FAU - Holmes, Randall K AU - Holmes RK FAU - Hol, Wim G J AU - Hol WG LA - eng SI - PDB/1S5B SI - PDB/1S5C SI - PDB/1S5D SI - PDB/1S5E SI - PDB/1S5F GR - AI-31940/AI/NIAID NIH HHS/United States GR - AI-34501/AI/NIAID NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Toxins) RN - 0 (Enterotoxins) RN - 0 (Escherichia coli Proteins) RN - 0 (Peptide Fragments) RN - 0 (Protein Subunits) RN - 0 (heat-labile enterotoxin, E coli) RN - 42HK56048U (Tyrosine) RN - 452VLY9402 (Serine) RN - 9012-63-9 (Cholera Toxin) RN - X2RN3Q8DNE (Galactose) SB - IM MH - Bacterial Toxins/chemistry MH - Binding Sites/genetics MH - Cholera Toxin/*chemistry/*genetics MH - Crystallization MH - Crystallography, X-Ray MH - Enterotoxins/chemistry MH - Escherichia coli Proteins/chemistry MH - Galactose/chemistry MH - *Mutagenesis, Site-Directed MH - Peptide Fragments/chemistry/genetics MH - Protein Binding/genetics MH - Protein Conformation MH - Protein Structure, Secondary/genetics MH - Protein Subunits/chemistry/genetics MH - Serine/genetics MH - Structure-Activity Relationship MH - Tyrosine/genetics EDAT- 2004/03/31 05:00 MHDA- 2004/07/30 05:00 CRDT- 2004/03/31 05:00 AID - 10.1021/bi0360152 [doi] PST - ppublish SO - Biochemistry. 2004 Apr 6;43(13):3772-82. PMID- 23717688 OWN - NLM STAT- MEDLINE DA - 20130529 DCOM- 20140107 LR - 20141113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 5 DP - 2013 TI - Transient oligomerization of the SARS-CoV N protein--implication for virus ribonucleoprotein packaging. PG - e65045 LID - 10.1371/journal.pone.0065045 [doi] AB - The nucleocapsid (N) phosphoprotein of the severe acute respiratory syndrome coronavirus (SARS-CoV) packages the viral genome into a helical ribonucleocapsid and plays a fundamental role during viral self-assembly. The N protein consists of two structural domains interspersed between intrinsically disordered regions and dimerizes through the C-terminal structural domain (CTD). A key activity of the protein is the ability to oligomerize during capsid formation by utilizing the dimer as a building block, but the structural and mechanistic bases of this activity are not well understood. By disulfide trapping technique we measured the amount of transient oligomers of N protein mutants with strategically located cysteine residues and showed that CTD acts as a primary transient oligomerization domain in solution. The data is consistent with the helical oligomer packing model of N protein observed in crystal. A systematic study of the oligomerization behavior revealed that altering the intermolecular electrostatic repulsion through changes in solution salt concentration or phosphorylation-mimicking mutations affects oligomerization propensity. We propose a biophysical mechanism where electrostatic repulsion acts as a switch to regulate N protein oligomerization. FAU - Chang, Chung-ke AU - Chang CK AD - Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, Republic of China. FAU - Chen, Chia-Min Michael AU - Chen CM FAU - Chiang, Ming-hui AU - Chiang MH FAU - Hsu, Yen-lan AU - Hsu YL FAU - Huang, Tai-huang AU - Huang TH LA - eng GR - Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130523 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Citrates) RN - 0 (Drug Combinations) RN - 0 (Nucleocapsid Proteins) RN - 0 (Suby's G solution) RN - 3A3U0GI71G (Magnesium Oxide) RN - 48TCX9A1VT (Cystine) RN - H0G9379FGK (Calcium Carbonate) SB - IM MH - Amino Acid Substitution MH - Calcium Carbonate MH - Citrates MH - Cystine/chemistry MH - Drug Combinations MH - Magnesium Oxide MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Nucleocapsid Proteins/*chemistry/genetics MH - Phosphorylation MH - Protein Interaction Domains and Motifs MH - Protein Multimerization MH - Protein Processing, Post-Translational MH - *SARS Virus MH - Virus Assembly PMC - PMC3662775 OID - NLM: PMC3662775 EDAT- 2013/05/30 06:00 MHDA- 2014/01/08 06:00 CRDT- 2013/05/30 06:00 PHST- 2013 [ppublish] PHST- 2012/04/20 [received] PHST- 2013/04/24 [accepted] PHST- 2013/05/23 [epublish] AID - 10.1371/journal.pone.0065045 [doi] AID - PONE-D-12-11392 [pii] PST - epublish SO - PLoS One. 2013 May 23;8(5):e65045. doi: 10.1371/journal.pone.0065045. Print 2013. PMID- 12697905 OWN - NLM STAT- MEDLINE DA - 20030430 DCOM- 20030611 LR - 20140611 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 100 IP - 9 DP - 2003 Apr 29 TI - Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding. PG - 5148-53 AB - A microscopic study of functional disorder-order folding transitions coupled to binding is performed for the p27 protein, which derives a kinetic advantage from the intrinsically disordered unbound form on binding with the phosphorylated cyclin A-cyclin-dependent kinase 2 (Cdk2) complex. Hierarchy of structural loss during p27 coupled unfolding and unbinding is simulated by using high-temperature Monte Carlo simulations initiated from the crystal structure of the tertiary complex. Subsequent determination of the transition-state ensemble and the proposed atomic picture of the folding mechanism coupled to binding provide a microscopic rationale that reconciles the initiation recruitment of p27 at the cyclin A docking site with the kinetic benefit for a disordered alpha-helix in the unbound form of p27. The emerging structural polarization in the ensemble of unfolding/unbinding trajectories and in the computationally determined transition-state ensemble is not determined by the intrinsic folding preferences of p27 but rather is attributed to the topological requirements of the native intermolecular interface to order beta-hairpin and beta-strand of p27 that could be critical for nucleating rapid folding transition coupled to binding. In agreement with the experimental data, the disorder-order folding transition for p27 is largely determined by the functional requirement to form a specific intermolecular interface that ultimately dictates the folding mechanism and overwhelms any local folding preferences for creating a stable alpha-helix in the p27 structure before overcoming the major free energy barrier. FAU - Verkhivker, Gennady M AU - Verkhivker GM AD - Pfizer Global Research and Development, La Jolla Laboratories, 10777 Science Center Drive, San Diego, CA 92121, USA. gennady.verkhivker@pfizer.com FAU - Bouzida, Djamal AU - Bouzida D FAU - Gehlhaar, Daniel K AU - Gehlhaar DK FAU - Rejto, Paul A AU - Rejto PA FAU - Freer, Stephan T AU - Freer ST FAU - Rose, Peter W AU - Rose PW LA - eng PT - Journal Article DEP - 20030415 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Proteins) SB - IM MH - Models, Molecular MH - Monte Carlo Method MH - Protein Binding MH - Protein Folding MH - Proteins/*chemistry/metabolism PMC - PMC154313 OID - NLM: PMC154313 EDAT- 2003/04/17 05:00 MHDA- 2003/06/12 05:00 CRDT- 2003/04/17 05:00 PHST- 2003/04/15 [aheadofprint] AID - 10.1073/pnas.0531373100 [doi] AID - 0531373100 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5148-53. Epub 2003 Apr 15. PMID- 22947219 OWN - NLM STAT- MEDLINE DA - 20130207 DCOM- 20130401 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 51 IP - 38 DP - 2012 Sep 25 TI - Solution nuclear magnetic resonance structure and molecular dynamics simulations of a murine 18.5 kDa myelin basic protein segment (S72-S107) in association with dodecylphosphocholine micelles. PG - 7475-87 LID - 10.1021/bi300998x [doi] AB - The 18.5 kDa myelin basic protein (MBP), the most abundant splice isoform in adult mammalian myelin, is a multifunctional, intrinsically disordered protein involved in the development and compaction of the myelin sheath in the central nervous system. A highly conserved central segment comprises a membrane-anchoring amphipathic alpha-helix followed by a proline-rich segment that represents a ligand for SH3 domain-containing proteins. Here, we have determined using solution nuclear magnetic resonance spectroscopy the structure of a 36-residue peptide fragment of MBP (murine 18.5 kDa residues S72-S107, denoted the alpha2-peptide) comprising these two structural motifs, in association with dodecylphosphocholine (DPC) micelles. The structure was calculated using CS-ROSETTA (version 1.01) because the nuclear Overhauser effect restraints were insufficient for this protein. The experimental studies were complemented by molecular dynamics simulations of a corresponding 24-residue peptide fragment (murine 18.5 kDa residues E80-G103, denoted the MD-peptide), also in association with a DPC micelle in silico. The experimental and theoretical results agreed well with one another, despite the independence of the starting structures and analyses, both showing membrane association via the amphipathic alpha-helix, and a sharp bend in the vicinity of the Pro93 residue (murine 18.5 kDa sequence numbering). Overall, the conformations elucidated here show how the SH3 ligand is presented to the cytoplasm for interaction with SH3 domain-containing proteins such as Fyn and contribute to our understanding of myelin architecture at the molecular level. FAU - Ahmed, Mumdooh A M AU - Ahmed MA AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada. FAU - De Avila, Miguel AU - De Avila M FAU - Polverini, Eugenia AU - Polverini E FAU - Bessonov, Kyrylo AU - Bessonov K FAU - Bamm, Vladimir V AU - Bamm VV FAU - Harauz, George AU - Harauz G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120914 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Micelles) RN - 0 (Myelin Basic Protein) RN - 107-73-3 (Phosphorylcholine) RN - 53949-18-1 (dodecylphosphocholine) SB - IM MH - Amino Acid Sequence MH - Animals MH - Mice MH - *Micelles MH - *Molecular Dynamics Simulation MH - Myelin Basic Protein/*chemistry MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Phosphorylcholine/*analogs & derivatives/chemistry EDAT- 2012/09/06 06:00 MHDA- 2013/04/02 06:00 CRDT- 2012/09/06 06:00 PHST- 2012/09/14 [aheadofprint] AID - 10.1021/bi300998x [doi] PST - ppublish SO - Biochemistry. 2012 Sep 25;51(38):7475-87. doi: 10.1021/bi300998x. Epub 2012 Sep 14. PMID- 11570883 OWN - NLM STAT- MEDLINE DA - 20010925 DCOM- 20011025 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 40 IP - 39 DP - 2001 Oct 2 TI - Clusterin, a binding protein with a molten globule-like region. PG - 11828-40 AB - Clusterin is a heterodimeric glycoprotein found in many tissues of the body and is the most abundant protein secreted by cultured rat Sertoli cells. The function of clusterin is unknown, but it has been associated with cellular injury, lipid transport, apoptosis, and it may be involved in the clearance of cellular debris caused by cell injury or death. Consistent with this last idea, clusterin has been shown to bind to a variety of molecules with high affinity including lipids, peptides, and proteins and the hydrophobic probe 1-anilino-8-naphthalenesulfonate (ANS). Given this variety of ligands, clusterin must have specific structural features that provide the protein with its promiscuous binding activity. Using sequence analyses, we show that clusterin likely contains three long regions of natively disordered or molten globule-like structures containing putative amphipathic alpha-helices. These disordered regions were highly sensitive to trypsin digestion, indicating a flexible nature. The effects of denaturation on the fluorescence of the clusterin-ANS complex were compared between proteins with structured binding pockets and molten globular forms of proteins. Clusterin bound ANS in a manner that was very similar to that of molten globular proteins. Furthermore, we found that, when bound to ANS, at least one cleavage site within the protease-sensitive disordered regions of clusterin was protected from trypsin digestion. In addition, we show that clusterin can function as a biological detergent that can solubilize bacteriorhodopsin. We propose that natively disordered regions with amphipathic helices form a dynamic, molten globule-like binding site and provide clusterin the ability to bind to a variety of molecules. FAU - Bailey, R W AU - Bailey RW AD - School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660,USA. FAU - Dunker, A K AU - Dunker AK FAU - Brown, C J AU - Brown CJ FAU - Garner, E C AU - Garner EC FAU - Griswold, M D AU - Griswold MD LA - eng GR - R01 HD 30692/HD/NICHD NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (CLU protein, human) RN - 0 (Clusterin) RN - 0 (Glycoproteins) RN - 0 (Molecular Chaperones) RN - 53026-44-1 (Bacteriorhodopsins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Bacteriorhodopsins/metabolism MH - Cells, Cultured MH - Circular Dichroism MH - Clusterin MH - Glycoproteins/chemistry/*metabolism MH - Humans MH - Hydrolysis MH - Male MH - Molecular Chaperones/chemistry/*metabolism MH - Molecular Sequence Data MH - Protein Binding MH - Protein Structure, Secondary MH - Rats MH - Sertoli Cells EDAT- 2001/09/26 10:00 MHDA- 2001/10/26 10:01 CRDT- 2001/09/26 10:00 AID - bi010135x [pii] PST - ppublish SO - Biochemistry. 2001 Oct 2;40(39):11828-40. PMID- 24437616 OWN - NLM STAT- MEDLINE DA - 20140418 DCOM- 20150701 IS - 1554-8937 (Electronic) IS - 1554-8929 (Linking) VI - 9 IP - 4 DP - 2014 Apr 18 TI - First site-specific incorporation of a noncanonical amino acid into the photosynthetic oxygen-evolving complex. PG - 891-6 LID - 10.1021/cb400880u [doi] AB - In photosystem II (PSII), water is oxidized at the oxygen-evolving complex. This process occurs through a light-induced cycle that produces oxygen and protons. While coupled proton and electron transfer reactions play an important role in PSII and other proteins, direct detection of internal proton transfer reactions is challenging. Here, we demonstrate that the unnatural amino acid, 7-azatryptophan (7AW), has unique, pH-sensitive vibrational frequencies, which are sensitive markers of proton transfer. The intrinsically disordered, PSII subunit, PsbO, which contains a single W residue (Trp241), was engineered to contain 7AW at position 241. Fluorescence shows that 7AW-241 is buried in a hydrophobic environment. Reconstitution of 7AW(241)PsbO to PSII had no significant impact on oxygen evolution activity or flash-dependent protein dynamics. We conclude that directed substitution of 7AW into other structural domains is likely to provide a nonperturbative spectroscopic probe, which can be used to define internal proton pathways in PsbO. FAU - Offenbacher, Adam R AU - Offenbacher AR AD - Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology , 901 Atlantic Drive NW, Atlanta, Georgia 30332, United States. FAU - Pagba, Cynthia V AU - Pagba CV FAU - Polander, Brandon C AU - Polander BC FAU - Brahmachari, Udita AU - Brahmachari U FAU - Barry, Bridgette A AU - Barry BA LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140117 PL - United States TA - ACS Chem Biol JT - ACS chemical biology JID - 101282906 RN - 0 (Amino Acids) RN - 0 (Photosystem II Protein Complex) RN - 059QF0KO0R (Water) RN - 1137-00-4 (7-azatryptophan) RN - 8DUH1N11BX (Tryptophan) RN - S88TT14065 (Oxygen) SB - IM MH - Amino Acids/*chemistry MH - Hydrogen Bonding MH - Hydrophobic and Hydrophilic Interactions MH - Molecular Structure MH - *Oxygen MH - Photosystem II Protein Complex/*chemistry MH - Spectroscopy, Fourier Transform Infrared MH - Tryptophan/*analogs & derivatives/chemistry MH - Water/chemistry EDAT- 2014/01/21 06:00 MHDA- 2015/07/02 06:00 CRDT- 2014/01/21 06:00 PHST- 2014/01/17 [aheadofprint] AID - 10.1021/cb400880u [doi] PST - ppublish SO - ACS Chem Biol. 2014 Apr 18;9(4):891-6. doi: 10.1021/cb400880u. Epub 2014 Jan 17. PMID- 22385960 OWN - NLM STAT- MEDLINE DA - 20120305 DCOM- 20120420 LR - 20150607 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 148 IP - 5 DP - 2012 Mar 2 TI - Order out of disorder: working cycle of an intrinsically unfolded chaperone. PG - 947-57 LID - 10.1016/j.cell.2012.01.045 [doi] AB - The redox-regulated chaperone Hsp33 protects organisms against oxidative stress that leads to protein unfolding. Activation of Hsp33 is triggered by the oxidative unfolding of its own redox-sensor domain, making Hsp33 a member of a recently discovered class of chaperones that require partial unfolding for full chaperone activity. Here we address the long-standing question of how chaperones recognize client proteins. We show that Hsp33 uses its own intrinsically disordered regions to discriminate between unfolded and partially structured folding intermediates. Binding to secondary structure elements in client proteins stabilizes Hsp33's intrinsically disordered regions, and this stabilization appears to mediate Hsp33's high affinity for structured folding intermediates. Return to nonstress conditions reduces Hsp33's disulfide bonds, which then significantly destabilizes the bound client proteins and in doing so converts them into less-structured, folding-competent client proteins of ATP-dependent foldases. We propose a model in which energy-independent chaperones use internal order-to-disorder transitions to control substrate binding and release. CI - Copyright A(c) 2012 Elsevier Inc. All rights reserved. FAU - Reichmann, Dana AU - Reichmann D AD - Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA. FAU - Xu, Ying AU - Xu Y FAU - Cremers, Claudia M AU - Cremers CM FAU - Ilbert, Marianne AU - Ilbert M FAU - Mittelman, Roni AU - Mittelman R FAU - Fitzgerald, Michael C AU - Fitzgerald MC FAU - Jakob, Ursula AU - Jakob U LA - eng GR - GM065318/GM/NIGMS NIH HHS/United States GR - GM084174/GM/NIGMS NIH HHS/United States GR - R01 GM065318/GM/NIGMS NIH HHS/United States GR - R01 GM065318-08/GM/NIGMS NIH HHS/United States GR - R01 GM065318-09/GM/NIGMS NIH HHS/United States GR - R01 GM084174/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (Bacterial Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (HSP33 protein, E coli) RN - 0 (HSP70 Heat-Shock Proteins) RN - 0 (Heat-Shock Proteins) RN - 0 (Peptides) RN - EC 3.6.1.- (dnaK protein, E coli) SB - IM CIN - Cell. 2012 Mar 2;148(5):843-4. PMID: 22385952 MH - Bacteria/*metabolism MH - Bacterial Proteins/*chemistry/*metabolism MH - Escherichia coli/metabolism MH - Escherichia coli Proteins/chemistry/metabolism MH - HSP70 Heat-Shock Proteins/metabolism MH - Heat-Shock Proteins/*chemistry/*metabolism MH - Models, Molecular MH - Peptides/metabolism MH - Protein Folding PMC - PMC3376891 MID - NIHMS372425 OID - NLM: NIHMS372425 OID - NLM: PMC3376891 EDAT- 2012/03/06 06:00 MHDA- 2012/04/21 06:00 CRDT- 2012/03/06 06:00 PHST- 2011/05/02 [received] PHST- 2011/10/23 [revised] PHST- 2012/01/31 [accepted] AID - S0092-8674(12)00155-9 [pii] AID - 10.1016/j.cell.2012.01.045 [doi] PST - ppublish SO - Cell. 2012 Mar 2;148(5):947-57. doi: 10.1016/j.cell.2012.01.045. PMID- 23198822 OWN - NLM STAT- MEDLINE DA - 20121203 DCOM- 20130205 LR - 20141104 IS - 1741-7007 (Electronic) IS - 1741-7007 (Linking) VI - 10 DP - 2012 TI - The pupylation pathway and its role in mycobacteria. PG - 95 LID - 10.1186/1741-7007-10-95 [doi] AB - Pupylation is a post-translational protein modification occurring in actinobacteria through which the small, intrinsically disordered protein Pup (prokaryotic ubiquitin-like protein) is conjugated to lysine residues of proteins, marking them for proteasomal degradation. Although functionally related to ubiquitination, pupylation is carried out by different enzymes that are evolutionarily linked to bacterial carboxylate-amine ligases. Here, we compare the mechanism of Pup-conjugation to target proteins with ubiquitination, describe the evolutionary emergence of pupylation and discuss the importance of this pathway for survival of Mycobacterium tuberculosis in the host. FAU - Barandun, Jonas AU - Barandun J AD - ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093 Zurich, Switzerland. FAU - Delley, Cyrille L AU - Delley CL FAU - Weber-Ban, Eilika AU - Weber-Ban E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20121130 PL - England TA - BMC Biol JT - BMC biology JID - 101190720 RN - 0 (Bacterial Proteins) RN - 0 (Pup protein, Mycobacterium tuberculosis) RN - 0 (Ubiquitins) SB - IM MH - Bacterial Proteins/genetics/*metabolism MH - Biological Evolution MH - Gene Expression Regulation, Bacterial/*physiology MH - Models, Molecular MH - Mycobacterium tuberculosis/*metabolism MH - Protein Conformation MH - Ubiquitins/genetics/*metabolism PMC - PMC3511204 OID - NLM: PMC3511204 EDAT- 2012/12/04 06:00 MHDA- 2013/02/06 06:00 CRDT- 2012/12/04 06:00 PHST- 2012/10/02 [received] PHST- 2012/11/30 [accepted] PHST- 2012/11/30 [aheadofprint] AID - 1741-7007-10-95 [pii] AID - 10.1186/1741-7007-10-95 [doi] PST - epublish SO - BMC Biol. 2012 Nov 30;10:95. doi: 10.1186/1741-7007-10-95. PMID- 20042108 OWN - NLM STAT- MEDLINE DA - 20100113 DCOM- 20100311 LR - 20140827 IS - 1471-2091 (Electronic) IS - 1471-2091 (Linking) VI - 10 DP - 2009 TI - The acidic domains of the Toc159 chloroplast preprotein receptor family are intrinsically disordered protein domains. PG - 35 LID - 10.1186/1471-2091-10-35 [doi] AB - BACKGROUND: The Toc159 family of proteins serve as receptors for chloroplast-destined preproteins. They directly bind to transit peptides, and exhibit preprotein substrate selectivity conferred by an unknown mechanism. The Toc159 receptors each include three domains: C-terminal membrane, central GTPase, and N-terminal acidic (A-) domains. Although the function(s) of the A-domain remains largely unknown, the amino acid sequences are most variable within these domains, suggesting they may contribute to the functional specificity of the receptors. RESULTS: The physicochemical properties of the A-domains are characteristic of intrinsically disordered proteins (IDPs). Using CD spectroscopy we show that the A-domains of two Arabidopsis Toc159 family members (atToc132 and atToc159) are disordered at physiological pH and temperature and undergo conformational changes at temperature and pH extremes that are characteristic of IDPs. CONCLUSIONS: Identification of the A-domains as IDPs will be important for determining their precise function(s), and suggests a role in protein-protein interactions, which may explain how these proteins serve as receptors for such a wide variety of preprotein substrates. FAU - Richardson, Lynn Gl AU - Richardson LG AD - Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada. lrichard@uoguelph.ca FAU - Jelokhani-Niaraki, Masoud AU - Jelokhani-Niaraki M FAU - Smith, Matthew D AU - Smith MD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091230 PL - England TA - BMC Biochem JT - BMC biochemistry JID - 101084098 RN - 0 (Arabidopsis Proteins) RN - 0 (Membrane Proteins) RN - 0 (Recombinant Proteins) RN - 0 (TOC159 protein, Arabidopsis) RN - 75-89-8 (Trifluoroethanol) RN - EC 3.6.1.- (GTP Phosphohydrolases) SB - IM MH - Arabidopsis/metabolism MH - Arabidopsis Proteins/*chemistry/genetics/metabolism MH - Chloroplasts/*metabolism MH - Circular Dichroism MH - GTP Phosphohydrolases/*chemistry/genetics/metabolism MH - Hydrogen-Ion Concentration MH - Membrane Proteins/*chemistry/genetics/metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Temperature MH - Trifluoroethanol/chemistry/pharmacology PMC - PMC2805684 OID - NLM: PMC2805684 EDAT- 2010/01/01 06:00 MHDA- 2010/03/12 06:00 CRDT- 2010/01/01 06:00 PHST- 2009/08/27 [received] PHST- 2009/12/30 [accepted] PHST- 2009/12/30 [aheadofprint] AID - 1471-2091-10-35 [pii] AID - 10.1186/1471-2091-10-35 [doi] PST - epublish SO - BMC Biochem. 2009 Dec 30;10:35. doi: 10.1186/1471-2091-10-35. PMID- 21979461 OWN - NLM STAT- MEDLINE DA - 20111202 DCOM- 20120320 LR - 20141022 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Understanding the structural ensembles of a highly extended disordered protein. PG - 308-19 LID - 10.1039/c1mb05243h [doi] AB - Developing a comprehensive description of the equilibrium structural ensembles for intrinsically disordered proteins (IDPs) is essential to understanding their function. The p53 transactivation domain (p53TAD) is an IDP that interacts with multiple protein partners and contains numerous phosphorylation sites. Multiple techniques were used to investigate the equilibrium structural ensemble of p53TAD in its native and chemically unfolded states. The results from these experiments show that the native state of p53TAD has dimensions similar to a classical random coil while the chemically unfolded state is more extended. To investigate the molecular properties responsible for this behavior, a novel algorithm that generates diverse and unbiased structural ensembles of IDPs was developed. This algorithm was used to generate a large pool of plausible p53TAD structures that were reweighted to identify a subset of structures with the best fit to small angle X-ray scattering data. High weight structures in the native state ensemble show features that are localized to protein binding sites and regions with high proline content. The features localized to the protein binding sites are mostly eliminated in the chemically unfolded ensemble; while, the regions with high proline content remain relatively unaffected. Data from NMR experiments support these results, showing that residues from the protein binding sites experience larger environmental changes upon unfolding by urea than regions with high proline content. This behavior is consistent with the urea-induced exposure of nonpolar and aromatic side-chains in the protein binding sites that are partially excluded from solvent in the native state ensemble. FAU - Daughdrill, Gary W AU - Daughdrill GW AD - Department of Cell Biology, Microbiology, and Molecular, University of South Florida, Tampa, FL 33612, USA. FAU - Kashtanov, Stepan AU - Kashtanov S FAU - Stancik, Amber AU - Stancik A FAU - Hill, Shannon E AU - Hill SE FAU - Helms, Gregory AU - Helms G FAU - Muschol, Martin AU - Muschol M FAU - Receveur-Brechot, Veronique AU - Receveur-Brechot V FAU - Ytreberg, F Marty AU - Ytreberg FM LA - eng GR - 5R21GM083827/GM/NIGMS NIH HHS/United States GR - P20 RR 16448/RR/NCRR NIH HHS/United States GR - P20 RR 16454-02/RR/NCRR NIH HHS/United States GR - P20 RR016448/RR/NCRR NIH HHS/United States GR - P20 RR016454/RR/NCRR NIH HHS/United States GR - R21 GM083827/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20111006 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Tumor Suppressor Protein p53) RN - 8W8T17847W (Urea) SB - IM MH - Chromatography, Gel MH - Humans MH - Hydrodynamics MH - Light MH - Models, Molecular MH - *Protein Folding MH - Protein Structure, Tertiary MH - Scattering, Small Angle MH - Tumor Suppressor Protein p53/*chemistry/*metabolism MH - Urea/metabolism MH - X-Ray Diffraction PMC - PMC3645981 MID - NIHMS465177 OID - NLM: NIHMS465177 OID - NLM: PMC3645981 EDAT- 2011/10/08 06:00 MHDA- 2012/03/21 06:00 CRDT- 2011/10/08 06:00 PHST- 2011/10/06 [aheadofprint] PHST- 2011/12/01 [epublish] AID - 10.1039/c1mb05243h [doi] PST - ppublish SO - Mol Biosyst. 2012 Jan;8(1):308-19. doi: 10.1039/c1mb05243h. Epub 2011 Oct 6. PMID- 11807946 OWN - NLM STAT- MEDLINE DA - 20020124 DCOM- 20020403 LR - 20131121 IS - 0887-3585 (Print) IS - 0887-3585 (Linking) VI - 46 IP - 2 DP - 2002 Feb 1 TI - Dynamic and structural analysis of isotropically distributed molecular ensembles. PG - 177-89 AB - An efficient new method is presented for the characterization of motional correlations derived from a set of protein structures without requiring the separation of overall and internal motion. In this method, termed isotropically distributed ensemble (IDE) analysis, each structure is represented by an ensemble of isotropically distributed replicas corresponding to the situation found in an isotropic protein solution. This leads to a covariance matrix of the cartesian atomic positions with elements proportional to the ensemble average of scalar products of the position vectors with respect to the center of mass. Diagonalization of the covariance matrix yields eigenmodes and amplitudes that describe concerted motions of atoms, including overall rotational and intramolecular dynamics. It is demonstrated that this covariance matrix naturally distinguishes between "rigid" and "mobile" parts without necessitating a priori selection of a reference structure and an atom set for the orientational alignment process. The method was applied to the analysis of a 5-ns molecular dynamics trajectory of native ubiquitin and a 40-ns trajectory of a partially folded state of ubiquitin. The results were compared with essential dynamics analysis. By taking advantage of the spherical symmetry of the IDE covariance matrix, more than a 10-fold speed up is achieved for the computation of eigenmodes and mode amplitudes. IDE analysis is particularly suitable for studying the correlated dynamics of flexible and large molecules. CI - Copyright 2001 Wiley-Liss, Inc. FAU - Prompers, Jeanine J AU - Prompers JJ AD - Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610-1477, USA. FAU - Bruschweiler, Rafael AU - Bruschweiler R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Ubiquitin) RN - OP0UW79H66 (Methane) SB - IM MH - Computer Simulation MH - Methane/chemistry MH - Motion MH - *Protein Conformation MH - Protein Folding MH - Ubiquitin/chemistry EDAT- 2002/01/25 10:00 MHDA- 2002/04/04 10:01 CRDT- 2002/01/25 10:00 AID - 10.1002/prot.10025 [pii] PST - ppublish SO - Proteins. 2002 Feb 1;46(2):177-89. PMID- 20947801 OWN - NLM STAT- MEDLINE DA - 20101103 DCOM- 20101130 LR - 20140922 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 107 IP - 44 DP - 2010 Nov 2 TI - Identification of a helical intermediate in trifluoroethanol-induced alpha-synuclein aggregation. PG - 18850-5 LID - 10.1073/pnas.1012336107 [doi] AB - Because oligomers and aggregates of the protein alpha-synuclein (alphaS) are implicated in the initiation and progression of Parkinson's disease, investigation of various alphaS aggregation pathways and intermediates aims to clarify the etiology of this common neurodegenerative disorder. Here, we report the formation of short, flexible, beta-sheet-rich fibrillar species by incubation of alphaS in the presence of intermediate (10-20% v/v) concentrations of 2,2,2-trifluoroethanol (TFE). We find that efficient production of these TFE fibrils is strongly correlated with the TFE-induced formation of a monomeric, partly helical intermediate conformation of alphaS, which exists in equilibrium with the natively disordered state at low [TFE] and with a highly alpha-helical conformation at high [TFE]. This partially helical intermediate is on-pathway to the TFE-induced formation of both the highly helical monomeric conformation and the fibrillar species. TFE-induced conformational changes in the monomer protein are similar for wild-type alphaS and the C-terminal truncation mutant alphaS1-102, indicating that TFE-induced structural transitions involve the N terminus of the protein. Moreover, the secondary structural transitions of three Parkinson's disease-associated mutants, A30P, A53T, and E46K, are nearly identical to wild-type alphaS, but oligomerization rates differ substantially among the mutants. Our results add to a growing body of evidence indicating the involvement of helical intermediates in protein aggregation processes. Given that alphaS is known to populate both highly and partially helical states upon association with membranes, these TFE-induced conformations imply relevant pathways for membrane-induced alphaS aggregation both in vitro and in vivo. FAU - Anderson, Valerie L AU - Anderson VL AD - School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA. FAU - Ramlall, Trudy F AU - Ramlall TF FAU - Rospigliosi, Carla C AU - Rospigliosi CC FAU - Webb, Watt W AU - Webb WW FAU - Eliezer, David AU - Eliezer D LA - eng GR - AG019391/AG/NIA NIH HHS/United States GR - AG025440/AG/NIA NIH HHS/United States GR - AG026650/AG/NIA NIH HHS/United States GR - R01 AG025440/AG/NIA NIH HHS/United States GR - R01 AG025440-04/AG/NIA NIH HHS/United States GR - R37 AG019391/AG/NIA NIH HHS/United States GR - R37 AG019391-10/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20101014 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (alpha-Synuclein) RN - 75-89-8 (Trifluoroethanol) SB - IM MH - Humans MH - Mutation MH - Parkinson Disease MH - Protein Structure, Secondary MH - Trifluoroethanol/*chemistry MH - alpha-Synuclein/*chemistry/genetics/metabolism PMC - PMC2973859 OID - NLM: PMC2973859 EDAT- 2010/10/16 06:00 MHDA- 2010/12/14 06:00 CRDT- 2010/10/16 06:00 PHST- 2010/10/14 [aheadofprint] AID - 1012336107 [pii] AID - 10.1073/pnas.1012336107 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18850-5. doi: 10.1073/pnas.1012336107. Epub 2010 Oct 14. PMID- 15858270 OWN - NLM STAT- MEDLINE DA - 20050428 DCOM- 20050802 LR - 20071114 IS - 0907-4449 (Print) IS - 0907-4449 (Linking) VI - 61 IP - Pt 5 DP - 2005 May TI - Structure of Escherichia coli pyridoxine 5'-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzyme. PG - 599-604 AB - Escherichia coli pyridoxine 5'-phosphate oxidase (ePNPOx) catalyzes the terminal step in the biosynthesis of pyridoxal 5'-phosphate (PLP) by the FMN oxidation of pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP), forming FMNH(2) and H(2)O(2). The crystal structure of ePNPOx is reported in a tetragonal unit cell at 2.6 A resolution. The three-dimensional fold of this structure is very similar to those of the E. coli and human enzymes that crystallized in trigonal and monoclinic unit cells. However, unlike the previous structures, the tetragonal structure shows major disorder in one of the two subunit domains that has opened up both the active site and a putative tunnel. Comparison of these structures gives an insight into the mechanistic pathway of PNPOx: from the resting enzyme with no substrate bound, to the initial binding of the substrate at the active site, to the catalytic stage and to the release of the catalytic product from the active site. FAU - Safo, Martin K AU - Safo MK AD - Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23219, USA. msafo@mail2.vcu.edu FAU - Musayev, Faik N AU - Musayev FN FAU - Schirch, Verne AU - Schirch V LA - eng GR - DK55648/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050420 PL - Denmark TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (Apoenzymes) RN - 8059-24-3 (Vitamin B 6) RN - EC 1.4.3.5 (Pyridoxaminephosphate Oxidase) SB - IM MH - Apoenzymes/chemistry MH - Binding Sites MH - Catalysis MH - Crystallization MH - Crystallography, X-Ray MH - Escherichia coli/*enzymology MH - Models, Molecular MH - Pyridoxaminephosphate Oxidase/*chemistry MH - Vitamin B 6/chemistry EDAT- 2005/04/29 09:00 MHDA- 2005/08/03 09:00 CRDT- 2005/04/29 09:00 PHST- 2004/12/21 [received] PHST- 2005/02/18 [accepted] PHST- 2005/04/20 [epublish] AID - S0907444905005512 [pii] AID - 10.1107/S0907444905005512 [doi] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2005 May;61(Pt 5):599-604. Epub 2005 Apr 20. PMID- 19858187 OWN - NLM STAT- MEDLINE DA - 20091221 DCOM- 20100108 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 284 IP - 52 DP - 2009 Dec 25 TI - A cell-penetrating peptide derived from human lactoferrin with conformation-dependent uptake efficiency. PG - 36099-108 LID - 10.1074/jbc.M109.036426 [doi] AB - The molecular events that contribute to the cellular uptake of cell-penetrating peptides (CPP) are still a matter of intense research. Here, we report on the identification and characterization of a 22-amino acid CPP derived from the human milk protein, lactoferrin. The peptide exhibits a conformation-dependent uptake efficiency that is correlated with efficient binding to heparan sulfate and lipid-induced conformational changes. The peptide contains a disulfide bridge formed by terminal cysteine residues. At concentrations exceeding 10 mum, this peptide undergoes the same rapid entry into the cytoplasm that was described previously for the arginine-rich CPPs nona-arginine and Tat. Cytoplasmic entry strictly depends on the presence of the disulfide bridge. To better understand this conformation dependence, NMR spectroscopy was performed for the free peptide, and CD measurements were performed for free and lipid-bound peptide. In solution, the peptides showed only slight differences in secondary structure, with a predominantly disordered structure both in the presence and absence of the disulfide bridge. In contrast, in complex with large unilamellar vesicles, the conformation of the oxidized and reduced forms of the peptide clearly differed. Moreover, surface plasmon resonance experiments showed that the oxidized form binds to heparan sulfate with a considerably higher affinity than the reduced form. Consistently, membrane binding and cellular uptake of the peptide were reduced when heparan sulfate chains were removed. FAU - Duchardt, Falk AU - Duchardt F AD - Interfaculty Institute for Cell Biology, University of Tubingen, Auf der Morgenstelle 15, 72076 Tubingen, Germany. FAU - Ruttekolk, Ivo R AU - Ruttekolk IR FAU - Verdurmen, Wouter P R AU - Verdurmen WP FAU - Lortat-Jacob, Hugues AU - Lortat-Jacob H FAU - Burck, Jochen AU - Burck J FAU - Hufnagel, Hansjorg AU - Hufnagel H FAU - Fischer, Rainer AU - Fischer R FAU - van den Heuvel, Maaike AU - van den Heuvel M FAU - Lowik, Dennis W P M AU - Lowik DW FAU - Vuister, Geerten W AU - Vuister GW FAU - Ulrich, Anne AU - Ulrich A FAU - de Waard, Michel AU - de Waard M FAU - Brock, Roland AU - Brock R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091026 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Disulfides) RN - 0 (Membrane Lipids) RN - 0 (Peptides) RN - 9050-30-0 (Heparitin Sulfate) RN - EC 3.4.21.- (Lactoferrin) SB - IM MH - Animals MH - Cytoplasm/metabolism MH - Disulfides/metabolism MH - Dose-Response Relationship, Drug MH - HeLa Cells MH - Heparitin Sulfate/metabolism MH - Humans MH - Lactoferrin/chemistry/*metabolism/*pharmacology MH - Membrane Lipids/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Oxidation-Reduction MH - Peptides/chemistry/*metabolism/*pharmacology MH - Protein Structure, Secondary MH - Rats MH - Structure-Activity Relationship PMC - PMC2794725 OID - NLM: PMC2794725 EDAT- 2009/10/28 06:00 MHDA- 2010/01/09 06:00 CRDT- 2009/10/28 06:00 PHST- 2009/10/26 [aheadofprint] PHST- 2009/11/25 [aheadofprint] AID - M109.036426 [pii] AID - 10.1074/jbc.M109.036426 [doi] PST - ppublish SO - J Biol Chem. 2009 Dec 25;284(52):36099-108. doi: 10.1074/jbc.M109.036426. Epub 2009 Oct 26. PMID- 19584866 OWN - NLM STAT- MEDLINE DA - 20090708 DCOM- 20090727 LR - 20150210 IS - 1546-170X (Electronic) IS - 1078-8956 (Linking) VI - 15 IP - 7 DP - 2009 Jul TI - A small molecule blocking oncogenic protein EWS-FLI1 interaction with RNA helicase A inhibits growth of Ewing's sarcoma. PG - 750-6 LID - 10.1038/nm.1983 [doi] AB - Many sarcomas and leukemias carry nonrandom chromosomal translocations encoding tumor-specific mutant fusion transcription factors that are essential to their molecular pathogenesis. Ewing's sarcoma family tumors (ESFTs) contain a characteristic t(11;22) translocation leading to expression of the oncogenic fusion protein EWS-FLI1. EWS-FLI1 is a disordered protein that precludes standard structure-based small-molecule inhibitor design. EWS-FLI1 binding to RNA helicase A (RHA) is important for its oncogenic function. We therefore used surface plasmon resonance screening to identify compounds that bind EWS-FLI1 and might block its interaction with RHA. YK-4-279, a derivative of the lead compound from the screen, blocks RHA binding to EWS-FLI1, induces apoptosis in ESFT cells and reduces the growth of ESFT orthotopic xenografts. These findings provide proof of principle that inhibiting the interaction of mutant cancer-specific transcription factors with the normal cellular binding partners required for their oncogenic activity provides a promising strategy for the development of uniquely effective, tumor-specific anticancer agents. FAU - Erkizan, Hayriye V AU - Erkizan HV AD - Georgetown University, Lombardi Comprehensive Cancer Center, Department of Oncology, Washington, DC, USA. FAU - Kong, Yali AU - Kong Y FAU - Merchant, Melinda AU - Merchant M FAU - Schlottmann, Silke AU - Schlottmann S FAU - Barber-Rotenberg, Julie S AU - Barber-Rotenberg JS FAU - Yuan, Linshan AU - Yuan L FAU - Abaan, Ogan D AU - Abaan OD FAU - Chou, Tsu-Hang AU - Chou TH FAU - Dakshanamurthy, Sivanesan AU - Dakshanamurthy S FAU - Brown, Milton L AU - Brown ML FAU - Uren, Aykut AU - Uren A FAU - Toretsky, Jeffrey A AU - Toretsky JA LA - eng GR - P01 CA47179/CA/NCI NIH HHS/United States GR - P30 CA051008/CA/NCI NIH HHS/United States GR - R01 CA088004/CA/NCI NIH HHS/United States GR - R01 CA088004-08/CA/NCI NIH HHS/United States GR - R01 CA133662/CA/NCI NIH HHS/United States GR - R01 CA133662-01A2/CA/NCI NIH HHS/United States GR - R01 CA138212/CA/NCI NIH HHS/United States GR - R01 CA138212-01/CA/NCI NIH HHS/United States GR - R01CA133662/CA/NCI NIH HHS/United States GR - R01CA138212/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20090705 PL - United States TA - Nat Med JT - Nature medicine JID - 9502015 RN - 0 (Antineoplastic Agents) RN - 0 (EWS-FLI fusion protein) RN - 0 (Indoles) RN - 0 (Neoplasm Proteins) RN - 0 (Oncogene Proteins, Fusion) RN - 0 (Proto-Oncogene Protein c-fli-1) RN - 0 (RNA-Binding Protein EWS) RN - 0 (Transcription Factors) RN - 0 (YK 4-279) RN - EC 3.4.22.- (Caspase 3) RN - EC 3.6.1.- (DHX9 protein, human) RN - EC 3.6.4.13 (DEAD-box RNA Helicases) SB - IM MH - Animals MH - Antineoplastic Agents/*pharmacology MH - COS Cells MH - Caspase 3/metabolism MH - Cells, Cultured MH - Cercopithecus aethiops MH - DEAD-box RNA Helicases/*metabolism MH - Humans MH - Indoles/*pharmacology MH - Mice MH - Neoplasm Proteins/*metabolism MH - Oncogene Proteins, Fusion/*antagonists & inhibitors MH - Proto-Oncogene Protein c-fli-1 MH - RNA-Binding Protein EWS MH - Sarcoma, Ewing/*drug therapy/pathology MH - Surface Plasmon Resonance MH - Transcription Factors/*antagonists & inhibitors MH - Xenograft Model Antitumor Assays PMC - PMC2777681 MID - NIHMS116382 OID - NLM: NIHMS116382 OID - NLM: PMC2777681 EDAT- 2009/07/09 09:00 MHDA- 2009/07/28 09:00 CRDT- 2009/07/09 09:00 PHST- 2009/03/02 [received] PHST- 2009/05/08 [accepted] PHST- 2009/07/05 [aheadofprint] AID - nm.1983 [pii] AID - 10.1038/nm.1983 [doi] PST - ppublish SO - Nat Med. 2009 Jul;15(7):750-6. doi: 10.1038/nm.1983. Epub 2009 Jul 5. PMID- 15167892 OWN - NLM STAT- MEDLINE DA - 20040616 DCOM- 20040921 LR - 20140609 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 23 IP - 12 DP - 2004 Jun 16 TI - Crystal structure of the HGF beta-chain in complex with the Sema domain of the Met receptor. PG - 2325-35 AB - The Met tyrosine kinase receptor and its ligand, hepatocyte growth factor (HGF), play important roles in normal development and in tumor growth and metastasis. HGF-dependent signaling requires proteolysis from an inactive single-chain precursor into an active alpha/beta-heterodimer. We show that the serine protease-like HGF beta-chain alone binds Met, and report its crystal structure in complex with the Sema and PSI domain of the Met receptor. The Met Sema domain folds into a seven-bladed beta-propeller, where the bottom face of blades 2 and 3 binds to the HGF beta-chain 'active site region'. Mutation of HGF residues in the area that constitutes the active site region in related serine proteases significantly impairs HGF beta binding to Met. Key binding loops in this interface undergo conformational rearrangements upon maturation and explain the necessity of proteolytic cleavage for proper HGF signaling. A crystallographic dimer interface between two HGF beta-chains brings two HGF beta:Met complexes together, suggesting a possible mechanism of Met receptor dimerization and activation by HGF. FAU - Stamos, Jennifer AU - Stamos J AD - Department of Protein Engineering, Genentech Inc., South San Francisco, CA 94080, USA. FAU - Lazarus, Robert A AU - Lazarus RA FAU - Yao, Xiaoyi AU - Yao X FAU - Kirchhofer, Daniel AU - Kirchhofer D FAU - Wiesmann, Christian AU - Wiesmann C LA - eng SI - PDB/1SHY GR - RR-01646/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20040527 PL - England TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (DNA Primers) RN - 67256-21-7 (Hepatocyte Growth Factor) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Crystallography, X-Ray MH - DNA Primers MH - Hepatocyte Growth Factor/*chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Sequence Homology, Amino Acid MH - Surface Plasmon Resonance PMC - PMC423285 OID - NLM: PMC423285 EDAT- 2004/05/29 05:00 MHDA- 2004/09/24 05:00 CRDT- 2004/05/29 05:00 PHST- 2004/02/25 [received] PHST- 2004/04/29 [accepted] PHST- 2004/05/27 [aheadofprint] AID - 10.1038/sj.emboj.7600243 [doi] AID - 7600243 [pii] PST - ppublish SO - EMBO J. 2004 Jun 16;23(12):2325-35. Epub 2004 May 27. PMID- 23462742 OWN - NLM STAT- MEDLINE DA - 20130306 DCOM- 20130822 LR - 20141116 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 3 DP - 2013 TI - Structural basis for the interaction of unstructured neuron specific substrates neuromodulin and neurogranin with Calmodulin. PG - 1392 LID - 10.1038/srep01392 [doi] AB - Neuromodulin (Nm) and neurogranin (Ng) are neuron-specific substrates of protein kinase C (PKC). Their interactions with Calmodulin (CaM) are crucial for learning and memory formation in neurons. Here, we report the structure of IQ peptides (24aa) of Nm/Ng complexed with CaM and their functional studies with full-length proteins. Nm/Ng and their respective IQ peptides are intrinsically unstructured; however, upon binding with CaM, IQ motifs adopt a helical conformation. Ser41 (Ser36) of Nm (Ng) is located in a negatively charged pocket in the apo CaM and, when phosphorylated, it will repel Nm/Ng from CaM. These observations explain the mechanism by which PKC-induced Ser phosphorylation blocks the association of Nm/Ng with CaM and interrupts several learning- and memory-associated functions. Moreover, the present study identified Arg as a key CaM interacting residue from Nm/Ng. This residue is crucial for CaM-mediated function, as evidenced by the inability of the Ng mutant (Arg-to-Ala) to potentiate synaptic transmission in CA1 hippocampal neurons. FAU - Kumar, Veerendra AU - Kumar V AD - Department of Biological Sciences, National University of Singapore, Singapore. FAU - Chichili, Vishnu Priyanka Reddy AU - Chichili VP FAU - Zhong, Ling AU - Zhong L FAU - Tang, Xuhua AU - Tang X FAU - Velazquez-Campoy, Adrian AU - Velazquez-Campoy A FAU - Sheu, Fwu-Shan AU - Sheu FS FAU - Seetharaman, J AU - Seetharaman J FAU - Gerges, Nashaat Z AU - Gerges NZ FAU - Sivaraman, J AU - Sivaraman J LA - eng SI - PDB/4E50 SI - PDB/4E53 GR - AG032320/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (Calmodulin) RN - 0 (GAP-43 Protein) RN - 132654-77-4 (Neurogranin) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Calmodulin/*metabolism MH - GAP-43 Protein/*chemistry/metabolism MH - Kinetics MH - Models, Molecular MH - Molecular Sequence Data MH - Neurogranin/*chemistry/metabolism MH - Neurons/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Unfolding MH - Rats MH - Sequence Alignment MH - Synaptic Transmission PMC - PMC3589724 OID - NLM: PMC3589724 EDAT- 2013/03/07 06:00 MHDA- 2013/08/24 06:00 CRDT- 2013/03/07 06:00 PHST- 2012/10/13 [received] PHST- 2013/02/21 [accepted] AID - srep01392 [pii] AID - 10.1038/srep01392 [doi] PST - ppublish SO - Sci Rep. 2013;3:1392. doi: 10.1038/srep01392. PMID- 15980067 OWN - NLM STAT- MEDLINE DA - 20050822 DCOM- 20051003 LR - 20091103 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 34 DP - 2005 Aug 26 TI - The YoeB toxin is a folded protein that forms a physical complex with the unfolded YefM antitoxin. Implications for a structural-based differential stability of toxin-antitoxin systems. PG - 30063-72 AB - The chromosomal YoeB-YefM toxin-antitoxin module common to numerous strains of bacteria is presumed to have a significant role in survival under stringent conditions. Recently we showed that the purified YefM antitoxin is a natively unfolded protein, as we previously reported for the Phd antitoxin in the P1 phage Doc-Phd toxin-antitoxin system. Here we report the purification and structural properties of the YoeB toxin and present physical evidence for the existence of a tight YoeB. YefM polypeptide complex in solution. YoeB and YefM proteins co-eluted as single peaks in sequential Ni-affinity FPLC and Q-Sepharose ion-exchange chromatography implying the formation of a YoeB. YefM complex. The unstable antitoxin was removed from the mixture by natural proteolysis, and the residual YoeB protein was purified using ion exchange chromatography. Fluorescence anisotropy studies of the purified YoeB and YefM proteins showed a 2:1 stoichiometry of the complex, providing direct evidence for a physical complex between the proteins. Near- and far-UV circular dichroism spectroscopy of the purified toxin revealed that, similar to the Doc toxin, YoeB is a well-folded protein. Thermal denaturation experiments confirmed the conformational stability of the YoeB toxin, which underwent reversible thermal unfolding at temperatures up to 56 degrees C. The thermodynamic features of the toxin-antitoxin complex were similar. Taken together, our results support the notion of a correlation between differential physiological and structural stability in toxin-antitoxin modules. FAU - Cherny, Izhack AU - Cherny I AD - Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel. FAU - Rockah, Liat AU - Rockah L FAU - Gazit, Ehud AU - Gazit E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050624 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Toxins) RN - 0 (Escherichia coli Proteins) RN - 0 (Peptides) RN - 0 (Toxins, Biological) RN - 0 (YefM protein, E coli) RN - 0 (YoeB protein, E coli) SB - IM MH - Anisotropy MH - Bacterial Toxins/*chemistry MH - Blotting, Western MH - Chromatography, Ion Exchange MH - Circular Dichroism MH - Cloning, Molecular MH - Dimerization MH - Dose-Response Relationship, Drug MH - Electrophoresis, Polyacrylamide Gel MH - Escherichia coli/*metabolism MH - Escherichia coli Proteins/*chemistry/*physiology MH - Hot Temperature MH - Microscopy, Fluorescence MH - Peptides/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - Spectrometry, Fluorescence MH - Spectrophotometry MH - Temperature MH - Thermodynamics MH - Time Factors MH - Toxins, Biological/*chemistry MH - Ultraviolet Rays EDAT- 2005/06/28 09:00 MHDA- 2005/10/04 09:00 CRDT- 2005/06/28 09:00 PHST- 2005/06/24 [aheadofprint] AID - M506220200 [pii] AID - 10.1074/jbc.M506220200 [doi] PST - ppublish SO - J Biol Chem. 2005 Aug 26;280(34):30063-72. Epub 2005 Jun 24. PMID- 22404138 OWN - NLM STAT- MEDLINE DA - 20120727 DCOM- 20140819 IS - 1365-313X (Electronic) IS - 0960-7412 (Linking) VI - 71 IP - 2 DP - 2012 Jul TI - Bacterial- and plant-type phosphoenolpyruvate carboxylase isozymes from developing castor oil seeds interact in vivo and associate with the surface of mitochondria. PG - 251-62 LID - 10.1111/j.1365-313X.2012.04985.x [doi] AB - Phosphoenolpyruvate carboxylase (PEPC) from developing castor oil seeds (COS) exists as two distinct oligomeric isoforms. The typical class-1 PEPC homotetramer consists of 107-kDa plant-type PEPC (PTPC) subunits, whereas the allosterically desensitized 910-kDa class-2 PEPC hetero-octamer arises from the association of class-1 PEPC with 118-kDa bacterial-type PEPC (BTPC) subunits. The in vivo interaction and subcellular location of COS BTPC and PTPC were assessed by imaging fluorescent protein (FP)-tagged PEPCs in tobacco suspension-cultured cells. The BTPC-FP mainly localized to cytoplasmic punctate/globular structures, identified as mitochondria by co-immunostaining of endogenous cytochrome oxidase. Inhibition of respiration with KCN resulted in proportional decreases and increases in mitochondrial versus cytosolic BTPC-FP, respectively. The FP-PTPC and NLS-FP-PTPC (containing an appended nuclear localization signal, NLS) localized to the cytosol and nucleus, respectively, but both co-localized with mitochondrial-associated BTPC when co-expressed with BTPC-FP. Transmission electron microscopy of immunogold-labeled developing COS revealed that BTPC and PTPC are localized at the mitochondrial (outer) envelope, as well as the cytosol. Moreover, thermolysin-sensitive BTPC and PTPC polypeptides were detected on immunoblots of purified COS mitochondria. Overall, our results demonstrate that: (i) COS BTPC and PTPC interact in vivo as a class-2 PEPC complex that associates with the surface of mitochondria, (ii) BTPC's unique and divergent intrinsically disordered region mediates its interaction with PTPC, whereas (iii) the PTPC-containing class-1 PEPC is entirely cytosolic. We hypothesize that mitochondrial-associated class-2 PEPC facilitates rapid refixation of respiratory CO(2) while sustaining a large anaplerotic flux to replenish tricarboxylic acid cycle C-skeletons withdrawn for biosynthesis. CI - (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd. FAU - Park, Joonho AU - Park J AD - Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada. FAU - Khuu, Nicholas AU - Khuu N FAU - Howard, Alexander S M AU - Howard AS FAU - Mullen, Robert T AU - Mullen RT FAU - Plaxton, William C AU - Plaxton WC LA - eng SI - GENBANK/EF634317 SI - GENBANK/EF634318 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120528 PL - England TA - Plant J JT - The Plant journal : for cell and molecular biology JID - 9207397 RN - 0 (Isoenzymes) RN - 0 (Plant Proteins) RN - 0 (Recombinant Fusion Proteins) RN - EC 4.1.1.31 (Phosphoenolpyruvate Carboxylase) SB - IM MH - Amino Acid Sequence MH - Castor Bean/cytology/*enzymology/genetics MH - Cell Culture Techniques MH - Computational Biology MH - Endosperm/cytology/enzymology/genetics MH - Gene Expression MH - Isoenzymes/genetics/metabolism MH - Mitochondria/*enzymology/genetics MH - Molecular Sequence Data MH - Phosphoenolpyruvate Carboxylase/genetics/*metabolism MH - Plant Proteins/genetics/metabolism MH - Protein Interaction Mapping MH - Protein Transport MH - Recombinant Fusion Proteins MH - Seeds/cytology/*enzymology/genetics MH - Sequence Alignment MH - Tobacco/cytology/enzymology/genetics EDAT- 2012/03/13 06:00 MHDA- 2014/08/20 06:00 CRDT- 2012/03/13 06:00 PHST- 2012/05/28 [aheadofprint] AID - 10.1111/j.1365-313X.2012.04985.x [doi] PST - ppublish SO - Plant J. 2012 Jul;71(2):251-62. doi: 10.1111/j.1365-313X.2012.04985.x. Epub 2012 May 28. PMID- 12062424 OWN - NLM STAT- MEDLINE DA - 20020613 DCOM- 20020729 LR - 20131121 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 517 IP - 1-3 DP - 2002 Apr 24 TI - Heteronuclear NMR studies of human serum apolipoprotein A-I. Part I. Secondary structure in lipid-mimetic solution. PG - 139-43 AB - The apolipoprotein A-I (apoA-I) solution structure in the presence of sodium dodecyl sulfate (SDS) was determined by combination of chemical shift index and torsion angle likelihood obtained from shift and sequence similarity methods. ApoA-I in lipid-mimetic solution is composed of alpha-helices (residues 8-32, 45-64, 67-77, 82-86, 90-97, 100-118, 122-140, 146-162, 167-205, 210-216 and 221-239), with 2-5 residue irregular segments between helical repeats, and the irregular segment 78-81 within helical repeat 2. ApoA-I is a monomer in the SDS complex and no evidence of interhelical interactions is found. Comparison of the apoA-I and apoA-I(1-186) [Okon et al., FEBS Lett. 487 (2001) 390-396] solution structures revealed that apoA-I undergoes a conformational change around Pro121. FAU - Okon, Mark AU - Okon M AD - Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada. mokon@chem.ubc.ca FAU - Frank, Philippe G AU - Frank PG FAU - Marcel, Yves L AU - Marcel YL FAU - Cushley, Robert J AU - Cushley RJ LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Apolipoprotein A-I) RN - 0 (Peptide Fragments) RN - 0 (Solutions) RN - 368GB5141J (Sodium Dodecyl Sulfate) SB - IM MH - Apolipoprotein A-I/blood/*chemistry MH - Humans MH - Magnetic Resonance Spectroscopy MH - Peptide Fragments/*chemistry MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sodium Dodecyl Sulfate/*chemistry MH - Solutions EDAT- 2002/06/14 10:00 MHDA- 2002/07/30 10:01 CRDT- 2002/06/14 10:00 AID - S0014579302026005 [pii] PST - ppublish SO - FEBS Lett. 2002 Apr 24;517(1-3):139-43. PMID- 15362858 OWN - NLM STAT- MEDLINE DA - 20040914 DCOM- 20041101 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 37 DP - 2004 Sep 21 TI - NMR solution structure of ImB2, a protein conferring immunity to antimicrobial activity of the type IIa bacteriocin, carnobacteriocin B2. PG - 11740-9 AB - Bacteriocins produced by lactic acid bacteria are potent antimicrobial compounds which are active against closely related bacteria. Producer strains are protected against the effects of their cognate bacteriocins by immunity proteins that are located on the same genetic locus and are coexpressed with the gene encoding the bacteriocin. Several structures are available for class IIa bacteriocins; however, to date, no structures are available for the corresponding immunity proteins. We report here the NMR solution structure of the 111-amino acid immunity protein for carnobacteriocin B2 (ImB2). ImB2 folds into a globular domain in aqueous solution which contains an antiparallel four-helix bundle. Extensive packing by hydrophobic side chains in adjacent helices forms the core of the protein. The C-terminus, containing a fifth helix and an extended strand, is held against the four-helix bundle by hydrophobic interactions with helices 3 and 4. Most of the charged and polar residues in the protein face the solvent. Helix 3 is well-defined to residue 55, and a stretch of nascent helix followed by an unstructured loop joins it to helix 4. No interaction is observed between ImB2 and either carnobacteriocin B2 (CbnB2) or its precursor. Protection from the action of CbnB2 is only observed when ImB2 is expressed within the cell. The loop between helices 3 and 4, and a hydrophobic pocket which it partially masks, may be important for interaction with membrane receptors responsible for sensitivity to class IIa bacteriocins. FAU - Sprules, Tara AU - Sprules T AD - Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2. FAU - Kawulka, Karen E AU - Kawulka KE FAU - Vederas, John C AU - Vederas JC LA - eng SI - PDB/1TDP PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (Bacteriocins) RN - 0 (Recombinant Fusion Proteins) RN - 155982-38-0 (bacteriocin B2 protein, Carnobacterium piscicola) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/genetics/*immunology MH - Bacteriocins/genetics/*immunology MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - Recombinant Fusion Proteins/genetics/metabolism MH - Sequence Alignment EDAT- 2004/09/15 05:00 MHDA- 2004/11/02 09:00 CRDT- 2004/09/15 05:00 AID - 10.1021/bi048854+ [doi] PST - ppublish SO - Biochemistry. 2004 Sep 21;43(37):11740-9. PMID- 18815311 OWN - NLM STAT- MEDLINE DA - 20081112 DCOM- 20081125 LR - 20140903 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 82 IP - 23 DP - 2008 Dec TI - Crystal structure and carbohydrate analysis of Nipah virus attachment glycoprotein: a template for antiviral and vaccine design. PG - 11628-36 LID - 10.1128/JVI.01344-08 [doi] AB - Two members of the paramyxovirus family, Nipah virus (NiV) and Hendra virus (HeV), are recent additions to a growing number of agents of emergent diseases which use bats as a natural host. Identification of ephrin-B2 and ephrin-B3 as cellular receptors for these viruses has enabled the development of immunotherapeutic reagents which prevent virus attachment and subsequent fusion. Here we present the structural analysis of the protein and carbohydrate components of the unbound viral attachment glycoprotein of NiV glycoprotein (NiV-G) at a 2.2-A resolution. Comparison with its ephrin-B2-bound form reveals that conformational changes within the envelope glycoprotein are required to achieve viral attachment. Structural differences are particularly pronounced in the 579-590 loop, a major component of the ephrin binding surface. In addition, the 236-245 loop is rather disordered in the unbound structure. We extend our structural characterization of NiV-G with mass spectrometric analysis of the carbohydrate moieties. We demonstrate that NiV-G is largely devoid of the oligomannose-type glycans that in viruses such as human immunodeficiency virus type 1 and Ebola virus influence viral tropism and the host immune response. Nevertheless, we find putative ligands for the endothelial cell lectin, LSECtin. Finally, by mapping structural conservation and glycosylation site positions from other members of the paramyxovirus family, we suggest the molecular surface involved in oligomerization. These results suggest possible pathways of virus-host interaction and strategies for the optimization of recombinant vaccines. FAU - Bowden, Thomas A AU - Bowden TA AD - Division of Structural Biology, University of Oxford, Henry Wellcome Building of Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN, United Kingdom. FAU - Crispin, Max AU - Crispin M FAU - Harvey, David J AU - Harvey DJ FAU - Aricescu, A Radu AU - Aricescu AR FAU - Grimes, Jonathan M AU - Grimes JM FAU - Jones, E Yvonne AU - Jones EY FAU - Stuart, David I AU - Stuart DI LA - eng GR - G0500365/Medical Research Council/United Kingdom GR - G0700232/Medical Research Council/United Kingdom GR - Cancer Research UK/United Kingdom GR - Medical Research Council/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080924 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (Antiviral Agents) RN - 0 (Carbohydrates) RN - 0 (Vaccines, Synthetic) RN - 0 (Viral Envelope Proteins) RN - 0 (Viral Vaccines) RN - 0 (attachment protein G) SB - IM MH - Antiviral Agents/*pharmacology MH - Carbohydrates/*chemistry MH - Cells, Cultured MH - Crystallization MH - Drug Design MH - Glycosylation MH - Humans MH - Nipah Virus/*chemistry/drug effects/immunology MH - Protein Conformation MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Vaccines, Synthetic/*immunology MH - Viral Envelope Proteins/*chemistry MH - Viral Vaccines/*immunology PMC - PMC2583688 OID - NLM: PMC2583688 EDAT- 2008/09/26 09:00 MHDA- 2008/12/17 09:00 CRDT- 2008/09/26 09:00 PHST- 2008/09/24 [aheadofprint] AID - JVI.01344-08 [pii] AID - 10.1128/JVI.01344-08 [doi] PST - ppublish SO - J Virol. 2008 Dec;82(23):11628-36. doi: 10.1128/JVI.01344-08. Epub 2008 Sep 24. PMID- 19819244 OWN - NLM STAT- MEDLINE DA - 20091125 DCOM- 20091221 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 394 IP - 5 DP - 2009 Dec 18 TI - Posttranslational modifications affect the interaction of S100 proteins with tumor suppressor p53. PG - 922-30 LID - 10.1016/j.jmb.2009.10.002 [doi] AB - Proteins of the S100 family bind to the intrinsically disordered transactivation domain (TAD; residues 1-57) and C-terminus (residues 293-393) of the tumor suppressor p53. Both regions provide sites that are subject to posttranslational modifications, such as phosphorylation and acetylation, that can alter the affinity for interacting proteins such as p300 and MDM2. Here, we found that S100A1, S100A2, S100A4, S100A6, and S100B bound to two subdomains of the TAD (TAD1 and TAD2). Both subdomains were mandatory for high-affinity binding to S100 proteins. Phosphorylation of Ser and Thr residues increased the affinity for the p53 TAD. Conversely, acetylation and phosphorylation of the C-terminus of p53 decreased the affinity for S100A2 and S100B. In contrast, we found that nitrosylation of S100B caused a minor increase in binding to the p53 C-terminus, whereas binding to the TAD remained unaffected. As activation of p53 is usually accompanied by phosphorylation and acetylation at several sites, our results suggest that a shift in binding from the C-terminus in favor of the N-terminus occurs upon the modification of p53. We propose that binding to the p53 TAD might be involved in the stimulation of p53 activity by S100 proteins. FAU - van Dieck, Jan AU - van Dieck J AD - MRC Laboratory of Molecular Biology and MRC Center for Protein Engineering, Hills Road, Cambridge CB2 0QH, UK. FAU - Teufel, Daniel P AU - Teufel DP FAU - Jaulent, Agnes M AU - Jaulent AM FAU - Fernandez-Fernandez, Maria R AU - Fernandez-Fernandez MR FAU - Rutherford, Trevor J AU - Rutherford TJ FAU - Wyslouch-Cieszynska, Alexandra AU - Wyslouch-Cieszynska A FAU - Fersht, Alan R AU - Fersht AR LA - eng PT - Journal Article DEP - 20091009 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (S100 Proteins) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Acetylation MH - Phosphorylation MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - *Protein Processing, Post-Translational MH - S100 Proteins/*metabolism MH - Tumor Suppressor Protein p53/*metabolism EDAT- 2009/10/13 06:00 MHDA- 2009/12/22 06:00 CRDT- 2009/10/13 06:00 PHST- 2009/08/14 [received] PHST- 2009/09/30 [revised] PHST- 2009/10/04 [accepted] PHST- 2009/10/09 [aheadofprint] AID - S0022-2836(09)01230-3 [pii] AID - 10.1016/j.jmb.2009.10.002 [doi] PST - ppublish SO - J Mol Biol. 2009 Dec 18;394(5):922-30. doi: 10.1016/j.jmb.2009.10.002. Epub 2009 Oct 9. PMID- 15959518 OWN - NLM STAT- MEDLINE DA - 20050616 DCOM- 20050628 LR - 20101118 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 435 IP - 7044 DP - 2005 Jun 16 TI - Crystal structure of thymine DNA glycosylase conjugated to SUMO-1. PG - 979-82 AB - Members of the small ubiquitin-like modifier (SUMO) family can be covalently attached to the lysine residue of a target protein through an enzymatic pathway similar to that used in ubiquitin conjugation, and are involved in various cellular events that do not rely on degradative signalling via the proteasome or lysosome. However, little is known about the molecular mechanisms of SUMO-modification-induced protein functional transfer. During DNA mismatch repair, SUMO conjugation of the uracil/thymine DNA glycosylase TDG promotes the release of TDG from the abasic (AP) site created after base excision, and coordinates its transfer to AP endonuclease 1, which catalyses the next step in the repair pathway. Here we report the crystal structure of the central region of human TDG conjugated to SUMO-1 at 2.1 A resolution. The structure reveals a helix protruding from the protein surface, which presumably interferes with the product DNA and thus promotes the dissociation of TDG from the DNA molecule. This helix is formed by covalent and non-covalent contacts between TDG and SUMO-1. The non-covalent contacts are also essential for release from the product DNA, as verified by mutagenesis. FAU - Baba, Daichi AU - Baba D AD - Graduate School of Integrated Science, Yokohama City University, Yokohama 230-0045, Japan. FAU - Maita, Nobuo AU - Maita N FAU - Jee, Jun-Goo AU - Jee JG FAU - Uchimura, Yasuhiro AU - Uchimura Y FAU - Saitoh, Hisato AU - Saitoh H FAU - Sugasawa, Kaoru AU - Sugasawa K FAU - Hanaoka, Fumio AU - Hanaoka F FAU - Tochio, Hidehito AU - Tochio H FAU - Hiroaki, Hidekazu AU - Hiroaki H FAU - Shirakawa, Masahiro AU - Shirakawa M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (SUMO-1 Protein) RN - 9007-49-2 (DNA) RN - EC 3.2.2.- (Thymine DNA Glycosylase) SB - IM MH - Catalytic Domain MH - Crystallography, X-Ray MH - DNA/genetics/metabolism MH - Humans MH - Hydrogen Bonding MH - Hydrophobic and Hydrophilic Interactions MH - Models, Molecular MH - Protein Binding MH - Response Elements/genetics MH - SUMO-1 Protein/*chemistry/*metabolism MH - Static Electricity MH - Thymine DNA Glycosylase/*chemistry/*metabolism EDAT- 2005/06/17 09:00 MHDA- 2005/06/29 09:00 CRDT- 2005/06/17 09:00 PHST- 2004/12/06 [received] PHST- 2005/04/14 [accepted] AID - nature03634 [pii] AID - 10.1038/nature03634 [doi] PST - ppublish SO - Nature. 2005 Jun 16;435(7044):979-82. PMID- 21316983 OWN - NLM STAT- MEDLINE DA - 20110603 DCOM- 20110928 LR - 20131121 IS - 1873-2682 (Electronic) IS - 1011-1344 (Linking) VI - 104 IP - 1-2 DP - 2011 Jul-Aug TI - PsbO, the manganese-stabilizing protein: analysis of the structure-function relations that provide insights into its role in photosystem II. PG - 179-90 LID - 10.1016/j.jphotobiol.2011.01.015 [doi] AB - The minireview presented here summarizes current information on the structure and function of PsbO, the photosystem II (PSII) manganese-stabilizing protein, with an emphasis on the protein's assembly into PSII, and its function in facilitating rapid turnovers of the oxygen evolving reaction. Two putative mechanisms for functional assembly of PsbO, which behaves as an intrinsically disordered polypeptide in solution, into PSII are proposed. Finally, a model is presented for the role of PsbO in relation to the function of the Mn, Ca(2+), and Cl(-) cofactors that are required for water oxidation, as well as for the action of hydroxide and small Mn reductants that inhibit the function of the active site of the oxygen-evolving complex. CI - Copyright (c) 2011 Elsevier B.V. All rights reserved. FAU - Popelkova, Hana AU - Popelkova H AD - Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA. popelka@umich.edu FAU - Yocum, Charles F AU - Yocum CF LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Review DEP - 20110121 PL - Switzerland TA - J Photochem Photobiol B JT - Journal of photochemistry and photobiology. B, Biology JID - 8804966 RN - 0 (Chlorides) RN - 0 (Coenzymes) RN - 0 (Hydroxides) RN - 0 (Photosystem II Protein Complex) RN - 0 (photosystem II manganese-stabilizing protein) RN - 42Z2K6ZL8P (Manganese) RN - SY7Q814VUP (Calcium) SB - IM MH - Calcium/chemistry/metabolism MH - Catalytic Domain MH - Chlorides/chemistry/metabolism MH - Coenzymes/chemistry/metabolism MH - Hydroxides/chemistry/metabolism MH - Manganese/chemistry/metabolism MH - Photosystem II Protein Complex/chemistry/metabolism/*physiology MH - Structure-Activity Relationship EDAT- 2011/02/15 06:00 MHDA- 2011/09/29 06:00 CRDT- 2011/02/15 06:00 PHST- 2010/10/25 [received] PHST- 2011/01/13 [revised] PHST- 2011/01/14 [accepted] PHST- 2011/01/21 [aheadofprint] AID - S1011-1344(11)00019-4 [pii] AID - 10.1016/j.jphotobiol.2011.01.015 [doi] PST - ppublish SO - J Photochem Photobiol B. 2011 Jul-Aug;104(1-2):179-90. doi: 10.1016/j.jphotobiol.2011.01.015. Epub 2011 Jan 21. PMID- 22899362 OWN - NLM STAT- MEDLINE DA - 20120817 DCOM- 20121106 LR - 20131121 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 97 IP - 11 DP - 2012 Nov TI - Toward an improved structural model of the frog-skin antimicrobial peptide esculentin-1b(1-18). PG - 873-81 LID - 10.1002/bip.22086 [doi] AB - Antimicrobial peptides (AMPs) are found in various classes of organisms as part of the innate immune system. Despite high sequence variability, they share common features such as net positive charge and an amphipathic fold when interacting with biologic membranes. Esculentin-1b is a 46-mer frog-skin peptide, which shows an outstanding antimicrobial activity. Experimental studies revealed that the N-terminal fragment encompassing the first 18 residues, Esc(1-18), is responsible for the antimicrobial activity of the whole peptide, with a negligible toxicity toward eukaryotic cells, thus representing an excellent candidate for future pharmaceutical applications. Similarly to most of the known AMPs, Esc(1-18) is expected to act by destroying/permeating the bacterial plasma-membrane but, to date, its 3D structure and the detailed mode of action remains unexplored. Before an in-depth investigation on peptide/membranes interactions could be undertaken, it is necessary to characterize peptide's folding propensity in solution, to understand what is intrinsically due to the peptide sequence, and what is actually driven by the membrane interaction. Circular dichroism and nuclear magnetic resonance spectroscopy were used to determine the structure adopted by the peptide, moving from water to increasing amounts of trifluoroethanol. The results showed that Esc(1-18) has a clear tendency to fold in a helical conformation as hydrophobicity of the environment increases, revealing an intriguing amphipathic structure. The helical folding is adopted only by the N-terminal portion of the peptide, while the rest is unstructured. The presence of a hydrophobic cluster of residues in the C-terminal portion suggests its possible membrane-anchoring role. CI - Copyright (c) 2012 Wiley Periodicals, Inc. FAU - Manzo, Giorgia AU - Manzo G AD - Department of Chemical and Geological Sciences, University of Cagliari, Italy. FAU - Sanna, Roberta AU - Sanna R FAU - Casu, Mariano AU - Casu M FAU - Mignogna, Giuseppina AU - Mignogna G FAU - Mangoni, Maria L AU - Mangoni ML FAU - Rinaldi, Andrea C AU - Rinaldi AC FAU - Scorciapino, Mariano A AU - Scorciapino MA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 RN - 0 (Amphibian Proteins) RN - 0 (Anti-Infective Agents) RN - 0 (Antimicrobial Cationic Peptides) RN - 0 (Oligopeptides) RN - 0 (Solutions) RN - 0 (esculentin protein, Rana esculenta) RN - 059QF0KO0R (Water) RN - 75-89-8 (Trifluoroethanol) SB - IM MH - Amphibian Proteins/*chemistry MH - Animals MH - Anti-Infective Agents/*analysis/chemical synthesis MH - Antimicrobial Cationic Peptides/*chemistry MH - Anura MH - Circular Dichroism MH - Hydrophobic and Hydrophilic Interactions MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Oligopeptides/*analysis/chemical synthesis MH - Protein Folding MH - Protein Structure, Secondary MH - Skin/secretion MH - Solutions MH - Static Electricity MH - Trifluoroethanol/chemistry MH - Water/chemistry EDAT- 2012/08/18 06:00 MHDA- 2012/11/07 06:00 CRDT- 2012/08/18 06:00 AID - 10.1002/bip.22086 [doi] PST - ppublish SO - Biopolymers. 2012 Nov;97(11):873-81. doi: 10.1002/bip.22086. PMID- 16949547 OWN - NLM STAT- MEDLINE DA - 20060929 DCOM- 20061127 LR - 20140918 IS - 0003-9861 (Print) IS - 0003-9861 (Linking) VI - 454 IP - 1 DP - 2006 Oct 1 TI - Studies on titin PEVK peptides and their interaction. PG - 16-25 AB - Experiments were conducted on several synthetic and expressed peptides from the PEVK region of titin, the giant muscle protein. Different secondary structure prediction methods based on amino acid sequence gave estimates ranging from over 70% alpha helical to no helix (totally disordered) for the polyE peptide corresponding to human exon 115. Circular dichroism (CD) experiments demonstrated that both the positively charged PPAK modules and the negatively charged PolyE repeats had similar spectral properties with disordered secondary structure predominating. Gel permeation chromatography showed that both PPAK and polyE peptides had 2-4 times larger Stokes radii than expected from their molecular mass. Mixtures of the oppositely charged titin peptides caused no change in apparent secondary structure as observed by circular dichroism or migration properties using native gel electrophoresis. Similarly addition of calcium did not alter the CD spectra or peptide electrophoretic mobility of the individual peptides or their mixtures. The properties of both the PPAK and polyE type peptides suggest that both had most of the characteristic properties to be classified as intrinsically disordered proteins. FAU - Duan, Yingli AU - Duan Y AD - Muscle Biology Laboratory, University of Wisconsin-Madison, Madison, WI 53706, USA. FAU - DeKeyser, Joshua G AU - DeKeyser JG FAU - Damodaran, Srinivasan AU - Damodaran S FAU - Greaser, Marion L AU - Greaser ML LA - eng GR - HL77196/HL/NHLBI NIH HHS/United States GR - R01 HL077196/HL/NHLBI NIH HHS/United States GR - RR13790/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20060815 PL - United States TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (Connectin) RN - 0 (Muscle Proteins) RN - 0 (Peptides) RN - 0 (TTN protein, human) RN - EC 2.7.- (Protein Kinases) SB - IM EIN - Arch Biochem Biophys. 2006 Dec 15;456(2):232 MH - Amino Acid Sequence MH - Binding Sites MH - Connectin MH - Humans MH - Molecular Sequence Data MH - Molecular Weight MH - Muscle Proteins/*chemistry MH - Peptides/*chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Kinases/*chemistry MH - Protein Structure, Secondary MH - Protein Structure, Tertiary PMC - PMC1635410 MID - NIHMS12762 OID - NLM: NIHMS12762 OID - NLM: PMC1635410 EDAT- 2006/09/05 09:00 MHDA- 2006/12/09 09:00 CRDT- 2006/09/05 09:00 PHST- 2006/05/04 [received] PHST- 2006/07/25 [revised] PHST- 2006/07/26 [accepted] PHST- 2006/08/15 [aheadofprint] AID - S0003-9861(06)00269-4 [pii] AID - 10.1016/j.abb.2006.07.017 [doi] PST - ppublish SO - Arch Biochem Biophys. 2006 Oct 1;454(1):16-25. Epub 2006 Aug 15. PMID- 23799450 OWN - NLM STAT- MEDLINE DA - 20130626 DCOM- 20131017 LR - 20141113 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 3 DP - 2013 TI - The transition state structure for coupled binding and folding of disordered protein domains. PG - 2076 LID - 10.1038/srep02076 [doi] AB - Intrinsically disordered proteins are abundant in the eukaryotic proteome, and they are implicated in a range of different diseases. However, there is a paucity of experimental data on molecular details of the coupled binding and folding of such proteins. Two interacting and relatively well studied disordered protein domains are the activation domain from the p160 transcriptional co-activator ACTR and the nuclear co-activator binding domain (NCBD) of CREB binding protein. We have analyzed the transition state for their coupled binding and folding by protein engineering and kinetic experiments (Phi-value analysis) and found that it involves weak native interactions between the N-terminal helices of ACTR and NCBD, but is otherwise "disordered-like". Most native hydrophobic interactions in the interface between the two domains form later, after the rate-limiting barrier for association. Linear free energy relationships suggest a cooperative formation of native interactions, reminiscent of the nucleation-condensation mechanism in protein folding. FAU - Dogan, Jakob AU - Dogan J AD - Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden. FAU - Mu, Xin AU - Mu X FAU - Engstrom, Ake AU - Engstrom A FAU - Jemth, Per AU - Jemth P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (Proteins) SB - IM MH - Kinetics MH - Models, Molecular MH - Protein Binding MH - Protein Folding MH - Proteins/*chemistry PMC - PMC3691887 OID - NLM: PMC3691887 EDAT- 2013/06/27 06:00 MHDA- 2013/10/18 06:00 CRDT- 2013/06/27 06:00 PHST- 2013/04/24 [received] PHST- 2013/06/11 [accepted] AID - srep02076 [pii] AID - 10.1038/srep02076 [doi] PST - ppublish SO - Sci Rep. 2013;3:2076. doi: 10.1038/srep02076. PMID- 2125482 OWN - NLM STAT- MEDLINE DA - 19910227 DCOM- 19910227 LR - 20071115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 29 IP - 42 DP - 1990 Oct 23 TI - Circular dichroism studies of the HIV-1 Rev protein and its specific RNA binding site. PG - 9791-5 AB - The circular dichroism (CD) spectrum of the Rev protein from HIV-1 indicates that Rev contains about 50% alpha helix and 25% beta sheet at 5 degrees C in potassium phosphate buffer, pH 3, and 300 mM KF. The spectrum is independent of protein concentration over a 20-fold range. At neutral pH, Rev is relatively insoluble but can be brought into solution by binding to its specific RNA binding site, the Rev-responsive element (RRE), at a Rev:RNA ratio of about 3:1. Nonspecific binding to tRNA does not solubilize Rev. As judged by difference CD spectra, the conformation of Rev when bound to the RRE at neutral pH is similar to the conformation of unbound Rev at pH 3, although changes in the RNA may also contribute to the difference spectrum. Indeed, some difference is observed near 260 nm, consistent with a conformational change of the RRE upon Rev binding. Rev alone at pH 3 shows irreversible aggregation as the temperature is raised, while Rev bound to the RRE at neutral pH shows a reversible transition with a Tm of 68 degrees C. FAU - Daly, T J AU - Daly TJ AD - Repligen Corporation, Cambridge, Massachusetts 02139. FAU - Rusche, J R AU - Rusche JR FAU - Maione, T E AU - Maione TE FAU - Frankel, A D AU - Frankel AD LA - eng GR - AI29135/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Carrier Proteins) RN - 0 (Gene Products, rev) RN - 0 (RNA, Messenger) RN - 0 (RNA, Viral) RN - 0 (RNA-Binding Proteins) RN - 0 (rev Gene Products, Human Immunodeficiency Virus) SB - IM SB - X MH - Amino Acid Sequence MH - Base Sequence MH - Binding Sites MH - Carrier Proteins/*metabolism MH - Circular Dichroism MH - Gene Products, rev/*metabolism MH - Genes, env MH - HIV-1/*metabolism MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Protein Conformation MH - RNA Processing, Post-Transcriptional MH - RNA, Messenger/*metabolism MH - RNA, Viral/*metabolism MH - RNA-Binding Proteins MH - rev Gene Products, Human Immunodeficiency Virus EDAT- 1990/10/23 MHDA- 1990/10/23 00:01 CRDT- 1990/10/23 00:00 PST - ppublish SO - Biochemistry. 1990 Oct 23;29(42):9791-5. PMID- 21763731 OWN - NLM STAT- MEDLINE DA - 20110829 DCOM- 20111216 IS - 1872-7492 (Electronic) IS - 0168-1702 (Linking) VI - 160 IP - 1-2 DP - 2011 Sep TI - Influenza virus hemagglutinin spike neck architectures and interaction with model enzymes evaluated by MALDI-TOF mass spectrometry and bioinformatics tools. PG - 294-304 LID - 10.1016/j.virusres.2011.07.002 [doi] AB - Interactions between model enzymes and the influenza virus hemagglutinin (HA) homotrimeric spike were addressed. We digested influenza virions (naturally occurring strains and laboratory reassortants) with bromelain or subtilisin Carlsberg and analyzed by MALDI-TOF mass spectrometry the resulting HA2 C-terminal segments. All cleavage sites, together with (minor) sites detected in undigested HAs, were situated in the linker region that connects the transmembrane domain to the ectodomain. In addition to cleavage at highly favorable amino acids, various alternative enzyme preferences were found that strongly depended on the HA subtype/type. We also evaluated the surface electrostatic potentials, binding cleft topographies and spatial dimensions of stem bromelain (homologically modeled) and subtilisin Carlsberg (X-ray resolved). The results show that the enzymes ( approximately 45A(3)) would hardly fit into the small ( approximately 18-20A) linker region of the HA-spike. However, the HA membrane proximal ectodomain region was predicted to be intrinsically disordered. We propose that its motions allow steric adjustment of the enzymes' active sites to the neck of the HA spike. The subtype/type-specific architectures in this region also influenced significantly the cleavage preferences of the enzymes. CI - Copyright (c) 2011 Elsevier B.V. All rights reserved. FAU - Serebryakova, Marina V AU - Serebryakova MV AD - Research Institute of Physical-Chemical Medicine, Federal Agency for Health Care and Social Development, Moscow, Russia. FAU - Kordyukova, Larisa V AU - Kordyukova LV FAU - Semashko, Tatiana A AU - Semashko TA FAU - Ksenofontov, Alexander L AU - Ksenofontov AL FAU - Rudneva, Irina A AU - Rudneva IA FAU - Kropotkina, Ekaterina A AU - Kropotkina EA FAU - Filippova, Irina Yu AU - Filippova IY FAU - Veit, Michael AU - Veit M FAU - Baratova, Lyudmila A AU - Baratova LA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110708 PL - Netherlands TA - Virus Res JT - Virus research JID - 8410979 RN - 0 (Hemagglutinin Glycoproteins, Influenza Virus) RN - 9001-00-7 (Bromelains) RN - EC 3.4.21.- (Subtilisins) SB - IM MH - Bromelains/chemistry/genetics/*metabolism MH - Computational Biology MH - Crystallography, X-Ray MH - Hemagglutinin Glycoproteins, Influenza Virus/chemistry/genetics/*metabolism MH - Hydrolysis MH - Models, Biological MH - Models, Molecular MH - *Protein Interaction Mapping MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Subtilisins/chemistry/genetics/*metabolism EDAT- 2011/07/19 06:00 MHDA- 2011/12/17 06:00 CRDT- 2011/07/19 06:00 PHST- 2011/05/11 [received] PHST- 2011/06/29 [revised] PHST- 2011/07/01 [accepted] PHST- 2011/07/08 [aheadofprint] AID - S0168-1702(11)00254-1 [pii] AID - 10.1016/j.virusres.2011.07.002 [doi] PST - ppublish SO - Virus Res. 2011 Sep;160(1-2):294-304. doi: 10.1016/j.virusres.2011.07.002. Epub 2011 Jul 8. PMID- 23272207 OWN - NLM STAT- MEDLINE DA - 20121228 DCOM- 20130610 LR - 20141104 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 12 DP - 2012 TI - The natively disordered loop of Bcl-2 undergoes phosphorylation-dependent conformational change and interacts with Pin1. PG - e52047 LID - 10.1371/journal.pone.0052047 [doi] AB - Bcl-2 plays a central role in the regulation of apoptosis. Structural studies of Bcl-2 revealed the presence of a flexible and natively disordered loop that bridges the Bcl-2 homology motifs, BH3 and BH4. This loop is phosphorylated on multiple sites in response to a variety of external stimuli, including the microtubule-targeting drugs, paclitaxel and colchicine. Currently, the underlying molecular mechanism of Bcl-2 phosphorylation and its biological significance remain elusive. In this study, we investigated the molecular characteristics of this anti-apoptotic protein. To this end, we generated synthetic peptides derived from the Bcl-2 loop, and multiple Bcl-2 loop truncation mutants that include the phosphorylation sites. Our results demonstrate that S87 in the flexible loop of Bcl-2 is the primary phosphorylation site for JNK and ERK2, suggesting some sequence or structural specificity for the phosphorylation by these kinases. Our NMR studies and molecular dynamics simulation studies support indicate that phosphorylation of S87 induces a conformational change in the peptide. Finally, we show that the phosphorylated peptides of the Bcl-2 loop can bind Pin1, further substantiating the phosphorylation-mediated conformation change of Bcl-2. FAU - Kang, Congbao AU - Kang C AD - Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. cbkang@etc.a-star.edu.sg FAU - Bharatham, Nagakumar AU - Bharatham N FAU - Chia, Joel AU - Chia J FAU - Mu, Yuguang AU - Mu Y FAU - Baek, Kwanghee AU - Baek K FAU - Yoon, Ho Sup AU - Yoon HS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121218 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (NIMA-interacting peptidylprolyl isomerase) RN - 0 (Peptides) RN - 0 (Proto-Oncogene Proteins c-bcl-2) RN - EC 5.2.1.8 (Peptidylprolyl Isomerase) SB - IM MH - Amino Acid Sequence MH - Humans MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Peptides/chemistry/metabolism MH - Peptidylprolyl Isomerase/*chemistry/metabolism MH - Phosphorylation MH - Protein Binding MH - Protein Conformation MH - Protein Interaction Domains and Motifs MH - Proto-Oncogene Proteins c-bcl-2/*chemistry/metabolism MH - Substrate Specificity PMC - PMC3525568 OID - NLM: PMC3525568 EDAT- 2012/12/29 06:00 MHDA- 2013/06/12 06:00 CRDT- 2012/12/29 06:00 PHST- 2012/09/12 [received] PHST- 2012/11/08 [accepted] PHST- 2012/12/18 [epublish] AID - 10.1371/journal.pone.0052047 [doi] AID - PONE-D-12-27733 [pii] PST - ppublish SO - PLoS One. 2012;7(12):e52047. doi: 10.1371/journal.pone.0052047. Epub 2012 Dec 18. PMID- 21516467 OWN - NLM STAT- MEDLINE DA - 20110905 DCOM- 20120105 IS - 1874-270X (Electronic) VI - 5 IP - 2 DP - 2011 Oct TI - 1H, 13C, and 15N resonance assignment of a 179 residue fragment of hepatitis C virus non-structural protein 5A. PG - 241-3 LID - 10.1007/s12104-011-9309-2 [doi] AB - Non-structural protein 5A (NS5A) plays an important role in the life cycle of hepatitis C virus. This proline-rich phosphoprotein is organized into three domains. Besides its role in virus replication and virus assembly, NS5A is involved in a variety of cellular regulation processes. Recent studies on domain 2 and 3 revealed that both belong to the class of intrinsically disordered proteins as they adopt a natively unfolded state. In particular, domain 2 together with its vicinal regions is responsible for NS5A's multiple interactions with other proteins necessary for virus persistence. The low chemical shift dispersion observed for instrinsically disordered proteins presents a challenge for NMR spectroscopy. Here we report sequential resonance assignment of a 179-residue fragment of NS5A, comprising the entire domain 2, using a set of sensitivity and resolution optimized 3D correlation experiments, as well as amino-acid-type editing in (1)H-(15)N correlation spectra. Our assignment reveals the presence of several segments with high propensity to form alpha-helical structure that may be of importance to the function of this protein fragment as a versatile interaction platform. FAU - Feuerstein, Sophie AU - Feuerstein S AD - Institut de Biologie Structurale, Universite Grenoble 1, 41 rue Jules Horowitz, 38027, Grenoble Cedex 1, France. FAU - Solyom, Zsofia AU - Solyom Z FAU - Aladag, Amine AU - Aladag A FAU - Hoffmann, Silke AU - Hoffmann S FAU - Willbold, Dieter AU - Willbold D FAU - Brutscher, Bernhard AU - Brutscher B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110424 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (Isotopes) RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Recombinant Proteins) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Binding Sites MH - Hepacivirus/*chemistry MH - Isotopes/chemistry MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Viral Nonstructural Proteins/*chemistry EDAT- 2011/04/26 06:00 MHDA- 2012/01/06 06:00 CRDT- 2011/04/26 06:00 PHST- 2011/02/14 [received] PHST- 2011/04/14 [accepted] PHST- 2011/04/24 [aheadofprint] AID - 10.1007/s12104-011-9309-2 [doi] PST - ppublish SO - Biomol NMR Assign. 2011 Oct;5(2):241-3. doi: 10.1007/s12104-011-9309-2. Epub 2011 Apr 24. PMID- 10497026 OWN - NLM STAT- MEDLINE DA - 19991028 DCOM- 19991028 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 292 IP - 3 DP - 1999 Sep 24 TI - Ligand-linked structural changes in the Escherichia coli biotin repressor: the significance of surface loops for binding and allostery. PG - 619-32 AB - The Escherichia coli repressor of biotin biosynthesis (BirA) is an allosteric site-specific DNA-binding protein. BirA catalyzes synthesis of biotinyl-5'-AMP from substrates biotin and ATP and the adenylate serves as the positive allosteric effector in binding of the repressor to the biotin operator sequence. Although a three-dimensional structure of the apo-repressor has been determined by X-ray crystallographic techniques, no structures of any ligand-bound forms of the repressor are yet available. Results of previously published solution studies are consistent with the occurrence of conformational changes in the protein concomitant with ligand binding. In this work the hydroxyl radical footprinting technique has been used to probe changes in reactivity of the peptide backbone of BirA that accompany ligand binding. Results of these studies indicate that binding of biotin to the protein results in protection of regions of the central domain in the vicinity of the active site and the C-terminal domain from chemical cleavage. Biotin-linked changes in reactivity constitute a subset of those linked to adenylate binding. Binding of both bio-5'-AMP and biotin operator DNA suppresses cleavage at additional sites in the amino and carboxy-terminal domains of the protein. Varying degrees of protection of the five surface loops on BirA from hydroxyl radical-mediated cleavage are observed in all complexes. These results implicate the C-terminal domain of BirA, for which no function has previously been known, in small ligand and site-specific DNA binding and highlight the significance of surface loops, some of which are disordered in the apoBirA structure, for ligand binding and transmission of allosteric information in the protein. CI - Copyright 1999 Academic Press. FAU - Streaker, E D AU - Streaker ED AD - Department of Chemistry, College of Life Sciences, University of Maryland,College Park, MD 20742-2021, USA. FAU - Beckett, D AU - Beckett D LA - eng GR - R01-GM46551/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (5'-AMP-biotin) RN - 0 (Bacterial Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Ligands) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Repressor Proteins) RN - 0 (Transcription Factors) RN - 3352-57-6 (Hydroxyl Radical) RN - 415SHH325A (Adenosine Monophosphate) RN - 6SO6U10H04 (Biotin) RN - 9007-49-2 (DNA) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) RN - EC 6.3.- (Carbon-Nitrogen Ligases) RN - EC 6.3.4.15 (birA protein, E coli) SB - IM MH - Adenosine Monophosphate/*analogs & derivatives/biosynthesis MH - Allosteric Regulation MH - Bacterial Proteins/*chemistry MH - Binding Sites MH - Biotin/*analogs & derivatives/biosynthesis/metabolism MH - Carbon-Nitrogen Ligases/*chemistry MH - Cyclic AMP-Dependent Protein Kinases/genetics MH - DNA/chemistry MH - DNA-Binding Proteins/chemistry MH - Escherichia coli/*genetics MH - *Escherichia coli Proteins MH - Gene Expression Regulation, Bacterial MH - Hydroxyl Radical/metabolism MH - Ligands MH - Models, Molecular MH - Mutation MH - Protein Binding MH - Recombinant Fusion Proteins MH - Repressor Proteins/chemistry MH - *Transcription Factors EDAT- 1999/09/25 MHDA- 1999/09/25 00:01 CRDT- 1999/09/25 00:00 AID - 10.1006/jmbi.1999.3086 [doi] AID - S0022-2836(99)93086-3 [pii] PST - ppublish SO - J Mol Biol. 1999 Sep 24;292(3):619-32. PMID- 18449534 OWN - NLM STAT- MEDLINE DA - 20080618 DCOM- 20081118 LR - 20131121 IS - 0175-7571 (Print) IS - 0175-7571 (Linking) VI - 37 IP - 6 DP - 2008 Jul TI - Solution NMR and CD spectroscopy of an intrinsically disordered, peripheral membrane protein: evaluation of aqueous and membrane-mimetic solvent conditions for studying the conformational adaptability of the 18.5 kDa isoform of myelin basic protein (MBP). PG - 1015-29 LID - 10.1007/s00249-008-0334-8 [doi] AB - The stability and secondary structure propensity of recombinant murine 18.5 kDa myelin basic protein (rmMBP, 176 residues) was assessed using circular dichroic and nuclear magnetic resonance spectroscopy (1H-15N HSQC experiments) to determine the optimal sample conditions for further NMR studies (i.e., resonance assignments and protein-protein interactions). Six solvent conditions were selected based on their ability to stabilise the protein, and their tractability to currently standard solution NMR methodology. Selected solvent conditions were further characterised as functions of concentration, temperature, and pH. The results of these trials indicated that 30% TFE-d2 in H2O (v/v), pH 6.5 at 300 K, and 100 mM KCl, pH 6.5 at 277 K were the best conditions to use for future solution NMR studies of MBP. Micelles of DPC were found to be inappropriate for backbone resonance assignments of rmMBP in this instance. FAU - Libich, David S AU - Libich DS AD - Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, N1G 2W1, Guelph, ON, Canada. FAU - Harauz, George AU - Harauz G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080501 PL - Germany TA - Eur Biophys J JT - European biophysics journal : EBJ JID - 8409413 RN - 0 (Lipid Bilayers) RN - 0 (Myelin Basic Protein) RN - 0 (Protein Isoforms) RN - 0 (Solvents) RN - 059QF0KO0R (Water) SB - IM MH - Biomimetic Materials/chemistry MH - Circular Dichroism/*methods MH - Computer Simulation MH - Lipid Bilayers/*chemistry MH - Magnetic Resonance Spectroscopy/*methods MH - *Models, Chemical MH - *Models, Molecular MH - Myelin Basic Protein/*chemistry/*ultrastructure MH - Protein Conformation MH - Protein Isoforms/chemistry MH - Solvents/chemistry MH - Water/chemistry EDAT- 2008/05/02 09:00 MHDA- 2008/11/19 09:00 CRDT- 2008/05/02 09:00 PHST- 2008/02/09 [received] PHST- 2008/04/11 [accepted] PHST- 2008/04/09 [revised] PHST- 2008/05/01 [aheadofprint] AID - 10.1007/s00249-008-0334-8 [doi] PST - ppublish SO - Eur Biophys J. 2008 Jul;37(6):1015-29. doi: 10.1007/s00249-008-0334-8. Epub 2008 May 1. PMID- 16427344 OWN - NLM STAT- MEDLINE DA - 20060918 DCOM- 20070108 IS - 1093-3263 (Print) IS - 1093-3263 (Linking) VI - 25 IP - 2 DP - 2006 Oct TI - Construction of a 3D model of CP12, a protein linker. PG - 186-95 AB - The chloroplast protein CP12 is known to play a leading role in a complex formation with the enzymes GAPDH and PRK. As a preliminary step towards the understanding of the complex formation mechanism and the exact role of this protein linker, a comparative modelling of the CP12 protein of the green alga Chlamydomonas reinhardtii was performed. Because of the very few structural information and poor template similarities, the derivation of the model consisted in an iterative trial-and-error procedure using the comparative modelling program MODELLER, the following three structure validation programs PROCHECK, PROSA, and WHATIF, and molecular mechanics energy refinement of the model using the program CHARMM. The analysis of the final model reveals a scaffold of key residues that is believed to be essential in the folding mechanism and that coincides with the residues conserved throughout the CP12 family. Our results suggest that this protein is a typical disordered protein. Finally, the various mechanisms by which the CP12 protein can self-interact or binds to other enzymes are discussed in light of its modelled structure and characteristics. FAU - Gardebien, Fabrice AU - Gardebien F AD - Laboratoire de Biochimie et Genetique Moleculaire, Universite de La Reunion, 15 Avenue Rene Cassin, 97715 Saint-Denis Messag Cedex 09, La Reunion, France. FAU - Thangudu, Rajesh R AU - Thangudu RR FAU - Gontero, Brigitte AU - Gontero B FAU - Offmann, Bernard AU - Offmann B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060119 PL - United States TA - J Mol Graph Model JT - Journal of molecular graphics & modelling JID - 9716237 RN - 0 (Algal Proteins) RN - EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases) SB - IM MH - Algal Proteins/*chemistry/genetics/metabolism MH - Amino Acid Sequence MH - Animals MH - Chlamydomonas reinhardtii/genetics/*metabolism MH - Chloroplasts/metabolism MH - Computer Simulation MH - Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Sequence Homology, Amino Acid EDAT- 2006/01/24 09:00 MHDA- 2007/01/09 09:00 CRDT- 2006/01/24 09:00 PHST- 2005/04/19 [received] PHST- 2005/11/10 [revised] PHST- 2005/12/14 [accepted] PHST- 2006/01/19 [aheadofprint] AID - S1093-3263(05)00171-3 [pii] AID - 10.1016/j.jmgm.2005.12.003 [doi] PST - ppublish SO - J Mol Graph Model. 2006 Oct;25(2):186-95. Epub 2006 Jan 19. PMID- 23884631 OWN - NLM STAT- MEDLINE DA - 20130911 DCOM- 20140310 LR - 20150522 IS - 1879-1123 (Electronic) IS - 1044-0305 (Linking) VI - 24 IP - 10 DP - 2013 Oct TI - Time window expansion for HDX analysis of an intrinsically disordered protein. PG - 1584-92 LID - 10.1007/s13361-013-0669-y [doi] AB - Application of typical HDX methods to examine intrinsically disordered proteins (IDP), proteins that are natively unstructured and highly dynamic at physiological pH, is limited because of the rapid exchange of unprotected amide hydrogens with solvent. The exchange rates of these fast exchanging amides are usually faster than the shortest time scale (10 s) employed in typical automated HDX-MS experiments. Considering the functional importance of IDPs and their association with many diseases, it is valuable to develop methods that allow the study of solution dynamics of these proteins as well as the ability to probe the interaction of IDPs with their wide range of binding partners. Here, we report the application of time window expansion to the millisecond range by altering the on-exchange pH of the HDX experiment to study a well-characterized IDP; the activation domain of the nuclear receptor coactivator, peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1alpha). This method enabled mapping the regions of PGC-1alpha that are stabilized upon binding the ligand binding domain (LBD) of the nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). We further demonstrate the method's applicability to other binding partners of the IDP PGC-1alpha and pave the way for characterizing many other biologically important ID proteins. FAU - Goswami, Devrishi AU - Goswami D AD - Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, FL, 33458, USA. FAU - Devarakonda, Srikripa AU - Devarakonda S FAU - Chalmers, Michael J AU - Chalmers MJ FAU - Pascal, Bruce D AU - Pascal BD FAU - Spiegelman, Bruce M AU - Spiegelman BM FAU - Griffin, Patrick R AU - Griffin PR LA - eng GR - GM084041/GM/NIGMS NIH HHS/United States GR - R01 GM084041/GM/NIGMS NIH HHS/United States GR - S10 RR027270/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130725 PL - United States TA - J Am Soc Mass Spectrom JT - Journal of the American Society for Mass Spectrometry JID - 9010412 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Receptors, Cytoplasmic and Nuclear) SB - IM MH - Amino Acid Sequence MH - Chromatography, High Pressure Liquid MH - Deuterium Exchange Measurement/*methods MH - Hydrogen-Ion Concentration MH - Intrinsically Disordered Proteins/*chemistry/*metabolism MH - Kinetics MH - Molecular Sequence Data MH - Protein Conformation MH - Receptors, Cytoplasmic and Nuclear/chemistry/metabolism MH - Spectrometry, Mass, Electrospray Ionization/*methods PMC - PMC3773365 MID - NIHMS509602 OID - NLM: NIHMS509602 OID - NLM: PMC3773365 EDAT- 2013/07/26 06:00 MHDA- 2014/03/13 06:00 CRDT- 2013/07/26 06:00 PHST- 2013/03/09 [received] PHST- 2013/05/08 [accepted] PHST- 2013/05/07 [revised] PHST- 2013/07/25 [aheadofprint] AID - 10.1007/s13361-013-0669-y [doi] PST - ppublish SO - J Am Soc Mass Spectrom. 2013 Oct;24(10):1584-92. doi: 10.1007/s13361-013-0669-y. Epub 2013 Jul 25. PMID- 11286553 OWN - NLM STAT- MEDLINE DA - 20010405 DCOM- 20010426 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 307 IP - 4 DP - 2001 Apr 6 TI - Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism. PG - 1023-34 AB - The major human abasic endonuclease, Ape1, is an essential DNA repair enzyme that initiates the removal of apurinic/apyrimidinic sites from DNA, excises 3' replication-blocking moieties, and modulates the DNA binding activity of several transcriptional regulators. We have determined the X-ray structure of the full-length human Ape1 enzyme in two new crystal forms, one at neutral and one at acidic pH. The new structures are generally similar to the previously determined structure of a truncated Ape1 protein, but differ in the conformation of several loop regions and in spans of residues with weak electron density. While only one active-site metal ion is present in the structure determined at low pH, the structure determined from a crystal grown at the pH optimum of Ape1 nuclease activity, pH 7.5, has two metal ions bound 5 A apart in the active site. Enzyme kinetic data indicate that at least two metal-binding sites are functionally important, since Ca(2+) exhibits complex stimulatory and inhibitory effects on the Mg(2+)-dependent catalysis of Ape1, even though Ca(2+) itself does not serve as a cofactor. In conjunction, the structural and kinetic data suggest that Ape1 catalyzes hydrolysis of the DNA backbone through a two metal ion-mediated mechanism. CI - Copyright 2001 Academic Press. FAU - Beernink, P T AU - Beernink PT AD - Molecular and Structural Biology Division, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA. FAU - Segelke, B W AU - Segelke BW FAU - Hadi, M Z AU - Hadi MZ FAU - Erzberger, J P AU - Erzberger JP FAU - Wilson, D M 3rd AU - Wilson DM 3rd FAU - Rupp, B AU - Rupp B LA - eng SI - PDB/1E9N SI - PDB/1HD7 GR - CA79056/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Cations, Divalent) RN - 0 (Coenzymes) RN - 0 (DNA-Binding Proteins) RN - 0 (Metals) RN - 9007-49-2 (DNA) RN - EC 3.1.- (Exodeoxyribonucleases) RN - EC 3.1.11.2 (exodeoxyribonuclease III) RN - I38ZP9992A (Magnesium) RN - SY7Q814VUP (Calcium) SB - IM MH - Binding Sites MH - Calcium/metabolism MH - Catalysis MH - Cations, Divalent/*metabolism MH - Coenzymes/metabolism MH - Crystallization MH - Crystallography, X-Ray MH - DNA/genetics/metabolism MH - DNA-Binding Proteins/chemistry/metabolism MH - Exodeoxyribonucleases/chemistry/*metabolism MH - Humans MH - Hydrogen-Ion Concentration MH - Hydrolysis MH - Kinetics MH - Magnesium/metabolism MH - Metals/*metabolism MH - Models, Molecular MH - Motion MH - Oxidation-Reduction MH - Protein Binding MH - Protein Structure, Tertiary MH - Structure-Activity Relationship EDAT- 2001/04/05 10:00 MHDA- 2001/05/01 10:01 CRDT- 2001/04/05 10:00 AID - 10.1006/jmbi.2001.4529 [doi] AID - S0022-2836(01)94529-2 [pii] PST - ppublish SO - J Mol Biol. 2001 Apr 6;307(4):1023-34. PMID- 14512630 OWN - NLM STAT- MEDLINE DA - 20030926 DCOM- 20031027 LR - 20111117 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 301 IP - 5641 DP - 2003 Sep 26 TI - Salmonella SipA polymerizes actin by stapling filaments with nonglobular protein arms. PG - 1918-21 AB - Like many bacterial pathogens, Salmonella spp. use a type III secretion system to inject virulence proteins into host cells. The Salmonella invasion protein A (SipA) binds host actin, enhances its polymerization near adherent extracellular bacteria, and contributes to cytoskeletal rearrangements that internalize the pathogen. By combining x-ray crystallography of SipA with electron microscopy and image analysis of SipA-actin filaments, we show that SipA functions as a "molecular staple," in which a globular domain and two nonglobular "arms" mechanically stabilize the filament by tethering actin subunits in opposing strands. Deletion analysis of the tethering arms provides strong support for this model. FAU - Lilic, Mirjana AU - Lilic M AD - Laboratory of Structural Microbiology, Rockefeller University, New York, NY 10021, USA. FAU - Galkin, Vitold E AU - Galkin VE FAU - Orlova, Albina AU - Orlova A FAU - VanLoock, Margaret S AU - VanLoock MS FAU - Egelman, Edward H AU - Egelman EH FAU - Stebbins, C Erec AU - Stebbins CE LA - eng SI - PDB/1Q5Z PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Actins) RN - 0 (Bacterial Proteins) RN - 0 (Microfilament Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SipA protein, Salmonella) RN - EC 3.4.21.62 (Subtilisin) SB - IM MH - Actin Cytoskeleton/metabolism MH - Actins/*metabolism MH - Bacterial Proteins/*chemistry/genetics/*metabolism MH - Binding Sites MH - Crystallography, X-Ray MH - Image Processing, Computer-Assisted MH - Microfilament Proteins/*chemistry/genetics/*metabolism MH - Microscopy, Electron MH - Models, Molecular MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Salmonella typhimurium/chemistry/*metabolism MH - Sequence Deletion MH - Subtilisin/metabolism EDAT- 2003/09/27 05:00 MHDA- 2003/10/28 05:00 CRDT- 2003/09/27 05:00 AID - 10.1126/science.1088433 [doi] AID - 301/5641/1918 [pii] PST - ppublish SO - Science. 2003 Sep 26;301(5641):1918-21. PMID- 22988846 OWN - NLM STAT- MEDLINE DA - 20120919 DCOM- 20130226 IS - 1470-8752 (Electronic) IS - 0300-5127 (Linking) VI - 40 IP - 5 DP - 2012 Oct TI - Bacterial in-cell NMR of human alpha-synuclein: a disordered monomer by nature? PG - 950-4 AB - The notion that human alpha-synuclein is an intrinsically disordered monomeric protein was recently challenged by a postulated alpha-helical tetramer as the physiologically relevant protein structure. The fact that this alleged conformation had evaded detection for so many years was primarily attributed to a widely used denaturation protocol to purify recombinant alpha-synuclein. In the present paper, we provide in-cell NMR evidence obtained directly in intact Escherichia coli cells that challenges a tetrameric conformation under native in vivo conditions. Although our data cannot rule out the existence of other intracellular protein states, especially in cells of higher organisms, they indicate clearly that inside E. coli alpha-synuclein is mostly monomeric and disordered. FAU - Binolfi, Andres AU - Binolfi A AD - In-cell NMR Group, Department of NMR-Assisted Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle-Strasse 10, Berlin 13125, Germany. FAU - Theillet, Francois-Xavier AU - Theillet FX FAU - Selenko, Philipp AU - Selenko P LA - eng PT - Journal Article PT - Review PL - England TA - Biochem Soc Trans JT - Biochemical Society transactions JID - 7506897 RN - 0 (alpha-Synuclein) SB - IM MH - Escherichia coli/chemistry/cytology/*metabolism MH - Humans MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - alpha-Synuclein/chemistry/*metabolism EDAT- 2012/09/20 06:00 MHDA- 2013/02/27 06:00 CRDT- 2012/09/20 06:00 AID - BST20120096 [pii] AID - 10.1042/BST20120096 [doi] PST - ppublish SO - Biochem Soc Trans. 2012 Oct;40(5):950-4. PMID- 9454599 OWN - NLM STAT- MEDLINE DA - 19980306 DCOM- 19980306 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 37 IP - 4 DP - 1998 Jan 27 TI - The C-terminal half of the anti-sigma factor FlgM contains a dynamic equilibrium solution structure favoring helical conformations. PG - 1076-82 AB - FlgM is the inhibitor of sigma 28, a transcription factor specific for the expression of bacterial flagella and chemotaxis genes. FlgM is also exported from the cytoplasm to the outside of the cell during the process of flagella filament assembly. In the absence of its targets, FlgM is a dynamic, mostly unfolded, molecule [Daughdrill, G. W., et al. (1997) Nat. Struct. Biol. 4(4), 285-291]. The NMR resonance assignments, dynamics, and average secondary structure of this mostly unfolded form of FlgM are reported here. Because of the dynamic behavior of FlgM, the deviation of C alpha chemical shifts from the random coil values was used to test for the presence of secondary structure [Wishart, D. S., and Sykes, B. D. (1994) Methods Enzymol. 239, 363-392]. This analysis shows two contiguous regions in the C-terminal half of FlgM with helical C alpha chemical shifts. These two regions, M60-G73 and A83-A90, contained less than 10 medium-range NOEs, and the 15N relaxation parameters suggest the helical structure is not rigid. However, the C alpha chemical shifts of M60-G73, A83-A90, and other residues in the C-terminal half of FlgM shift toward their canonical random coil values with the addition of a chemical denaturant. Along with the values of the order parameter, S2, this observation suggests the C-terminal half of FlgM exists in an equilibrium structural state that is nonrandom. The same analysis of the N-terminal half of FlgM suggests it more closely resembles a random coil in conditions with and without denaturant. It appears the C-terminal half of FlgM lacks sufficient intramolecular contacts to form stable secondary or tertiary structures. It is known this C-terminal region becomes rigidly held when FlgM binds sigma 28 (Daughdrill et al., 1997), and it is possible that binding stabilizes the helical structure. The potential evolutionary relationship between the inhibitory interaction of FlgM with sigma 28 and the autoinhibition observed in sigma 70 is discussed. FAU - Daughdrill, G W AU - Daughdrill GW AD - Institute of Molecular Biology, University of Oregon, Eugene 97403, USA. FAU - Hanely, L J AU - Hanely LJ FAU - Dahlquist, F W AU - Dahlquist FW LA - eng GR - AI 17808/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (FliA protein, Bacteria) RN - 0 (Nitrogen Isotopes) RN - 0 (Peptide Fragments) RN - 0 (Sigma Factor) RN - 142462-45-1 (FlgM protein, Bacteria) RN - 7YNJ3PO35Z (Hydrogen) SB - IM MH - Bacterial Proteins/*antagonists & inhibitors/*chemistry MH - Hydrogen MH - Nitrogen Isotopes MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemistry MH - Protein Denaturation MH - *Protein Structure, Secondary MH - Sigma Factor/*antagonists & inhibitors EDAT- 1998/02/10 MHDA- 1998/02/10 00:01 CRDT- 1998/02/10 00:00 AID - 10.1021/bi971952t [doi] AID - bi971952t [pii] PST - ppublish SO - Biochemistry. 1998 Jan 27;37(4):1076-82. PMID- 20603017 OWN - NLM STAT- MEDLINE DA - 20100706 DCOM- 20100802 LR - 20130218 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 142 IP - 1 DP - 2010 Jul 9 TI - Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity. PG - 101-11 LID - 10.1016/j.cell.2010.05.039 [doi] AB - Regulation of the phd/doc toxin-antitoxin operon involves the toxin Doc as co- or derepressor depending on the ratio between Phd and Doc, a phenomenon known as conditional cooperativity. The mechanism underlying this observed behavior is not understood. Here we show that monomeric Doc engages two Phd dimers on two unrelated binding sites. The binding of Doc to the intrinsically disordered C-terminal domain of Phd structures its N-terminal DNA-binding domain, illustrating allosteric coupling between highly disordered and highly unstable domains. This allosteric effect also couples Doc neutralization to the conditional regulation of transcription. In this way, higher levels of Doc tighten repression up to a point where the accumulation of toxin triggers the production of Phd to counteract its action. Our experiments provide the basis for understanding the mechanism of conditional cooperative regulation of transcription typical of toxin-antitoxin modules. This model may be applicable for the regulation of other biological systems. CI - Copyright 2010 Elsevier Inc. All rights reserved. FAU - Garcia-Pino, Abel AU - Garcia-Pino A AD - Structural Biology Brussels, Vrije Universiteit Brussels, Pleinlaan 2, B-1050 Brussels, Belgium. agarciap@vub.ac.be FAU - Balasubramanian, Sreeram AU - Balasubramanian S FAU - Wyns, Lode AU - Wyns L FAU - Gazit, Ehud AU - Gazit E FAU - De Greve, Henri AU - De Greve H FAU - Magnuson, Roy D AU - Magnuson RD FAU - Charlier, Daniel AU - Charlier D FAU - van Nuland, Nico A J AU - van Nuland NA FAU - Loris, Remy AU - Loris R LA - eng GR - 2R15GM067668-03/GM/NIGMS NIH HHS/United States GR - 2R15GM067668-04/GM/NIGMS NIH HHS/United States GR - R15 GM067668/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (Doc protein, Enterobacteria phage P1) RN - 0 (Phd protein, Enterobacteria phage P1) RN - 0 (Viral Proteins) RN - 9007-49-2 (DNA) SB - IM MH - *Allosteric Regulation MH - Allosteric Site MH - Bacteriophage P1/metabolism MH - DNA/metabolism MH - *Gene Expression Regulation MH - Hydrophobic and Hydrophilic Interactions MH - Models, Molecular MH - Operator Regions, Genetic MH - Protein Structure, Tertiary MH - Scattering, Small Angle MH - *Transcription, Genetic MH - Viral Proteins/chemistry/*metabolism MH - X-Ray Diffraction EDAT- 2010/07/07 06:00 MHDA- 2010/08/03 06:00 CRDT- 2010/07/07 06:00 PHST- 2009/10/05 [received] PHST- 2010/01/05 [revised] PHST- 2010/05/20 [accepted] AID - S0092-8674(10)00614-8 [pii] AID - 10.1016/j.cell.2010.05.039 [doi] PST - ppublish SO - Cell. 2010 Jul 9;142(1):101-11. doi: 10.1016/j.cell.2010.05.039. PMID- 1618378 OWN - NLM STAT- MEDLINE DA - 19920806 DCOM- 19920806 LR - 20071115 IS - 0234-5730 (Print) IS - 0234-5730 (Linking) VI - 37 IP - 1 DP - 1992 Jan TI - [Expression of glucocorticoid receptors and blast cell clearance in children with different variants of acute lymphoblastic leukemia]. PG - 25-8 AB - Glucocorticoid receptor (GR) levels were estimated in blast cells of 24 children with acute lymphoblastic leukemia, in different immunocytologic subvariants of the disease. No relationship was revealed between immunophenotype and GR number in blasts. It was found that the response to prednisolone therapy did not depend on the number of sites specifically bound to glucocorticoids. The response character is determined not by immunophenotype but by the initial number of blast cells in the peripheral blood (the higher blastosis, the worse response). High blastosis is probably dependent on the tumor growth rate. FAU - Torubarova, N A AU - Torubarova NA FAU - Kopyl'tsova, E A AU - Kopyl'tsova EA FAU - Koshel', I V AU - Koshel' IV FAU - Poliakova, O A AU - Poliakova OA FAU - Maiakova, S A AU - Maiakova SA LA - rus PT - English Abstract PT - Journal Article TT - Ekspressia retseptorov gliukokortikodov i klirens blastnykh kletok u detei s raznymi podvariantami ostrogo limfoblastnogo leikoza. PL - USSR TA - Gematol Transfuziol JT - Gematologiia i transfuziologiia JID - 8301796 RN - 0 (Receptors, Glucocorticoid) SB - IM MH - Adolescent MH - Blast Crisis/*metabolism/pathology MH - Child MH - Child, Preschool MH - Female MH - Humans MH - Male MH - Precursor Cell Lymphoblastic Leukemia-Lymphoma/*metabolism/pathology MH - Receptors, Glucocorticoid/*metabolism EDAT- 1992/01/01 MHDA- 1992/01/01 00:01 CRDT- 1992/01/01 00:00 PST - ppublish SO - Gematol Transfuziol. 1992 Jan;37(1):25-8. PMID- 25261014 OWN - NLM STAT- In-Process DA - 20141121 IS - 1432-1017 (Electronic) IS - 0175-7571 (Linking) VI - 43 IP - 12 DP - 2014 Dec TI - The TFE-induced transient native-like structure of the intrinsically disordered sigma(4)(7)(0) domain of Escherichia coli RNA polymerase. PG - 581-94 LID - 10.1007/s00249-014-0987-4 [doi] AB - The transient folding of domain 4 of an E. coli RNA polymerase sigma(7)(0) subunit (rECsigma(4)(7)(0)) induced by an increasing concentration of 2,2,2-trifluoroethanol (TFE) in an aqueous solution was monitored by means of CD and heteronuclear NMR spectroscopy. NMR data, collected at a 30% TFE, allowed the estimation of the population of a locally folded rECsigma(4)(7)(0) structure (CSI descriptors) and of local backbone dynamics ((15)N relaxation). The spontaneous organization of the helical regions of the initially unfolded protein into a TFE-induced 3D structure was revealed from structural constraints deduced from (15)N- to (13)C-edited NOESY spectra. In accordance with all the applied criteria, three highly populated alpha-helical regions, separated by much more flexible fragments, form a transient HLHTH motif resembling those found in PDB structures resolved for homologous proteins. All the data taken together demonstrate that TFE induces a transient native-like structure in the intrinsically disordered protein. FAU - Kaczka, Piotr AU - Kaczka P AD - Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland. FAU - Winiewska, Maria AU - Winiewska M FAU - Zhukov, Igor AU - Zhukov I FAU - Rempola, Bozenna AU - Rempola B FAU - Bolewska, Krystyna AU - Bolewska K FAU - Lozinski, Tomasz AU - Lozinski T FAU - Ejchart, Andrzej AU - Ejchart A FAU - Poznanska, Anna AU - Poznanska A FAU - Wierzchowski, Kazimierz L AU - Wierzchowski KL FAU - Poznanski, Jaroslaw AU - Poznanski J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140927 PL - Germany TA - Eur Biophys J JT - European biophysics journal : EBJ JID - 8409413 SB - IM PMC - PMC4236625 OID - NLM: PMC4236625 EDAT- 2014/09/28 06:00 MHDA- 2014/09/28 06:00 CRDT- 2014/09/28 06:00 PHST- 2014/04/25 [received] PHST- 2014/09/08 [accepted] PHST- 2014/07/31 [revised] PHST- 2014/09/27 [aheadofprint] AID - 10.1007/s00249-014-0987-4 [doi] PST - ppublish SO - Eur Biophys J. 2014 Dec;43(12):581-94. doi: 10.1007/s00249-014-0987-4. Epub 2014 Sep 27. PMID- 18167451 OWN - NLM STAT- MEDLINE DA - 20080102 DCOM- 20080325 IS - 1017-7825 (Print) IS - 1017-7825 (Linking) VI - 17 IP - 12 DP - 2007 Dec TI - Seed-dependent accelerated fibrillation of alpha-synuclein induced by periodic ultrasonication treatment. PG - 2027-32 AB - alpha-Synuclein is the major component of Lewy bodies and responsible for the amyloid deposits observed in Parkinson's disease. Ordered filamentous aggregate formation of the natively unfolded a-synuclein was investigated in vitro with the periodic ultrasonication. The ultrasonication induced the fibrillation of a-synuclein, as the random structure gradually converted into a beta-sheet structure. The resulting fibrils obtained at the stationary phase appeared heterogeneous in their size distribution, with the average length and height of 0.28 Mm+/-0.21 Mm and 5.6 nm+/-1.9 nm, respectively. After additional extensive ultrasonication in the absence of monomeric a-synuclein, the equilibrium between the fibril formation and its breakdown shifted to the disintegration of the preexisting fibrils. The resulting fragments served as nucleation centers for the subsequent seed-dependent accelerated fibrillation under a quiescent incubation condition. This self-seeding amplification process depended on the seed formation and subsequent alterations in their properties by the ultrasonication to a state that accretes the monomeric soluble protein more effectively than their reassociation of the seeds back to the original fibrils. Since many neurodegenerative disorders have been considered to be propagated via the seed-dependent amyloidosis, this study would provide a novel aspect of the significance of the seed structure and its properties leading to the accelerated amyloid formation. FAU - Kim, Hyun Jin AU - Kim HJ AD - School of Chemical and Biological Engineering, College of Engineering, Seoul National University, Seoul 151-744, Korea. FAU - Chatani, Eri AU - Chatani E FAU - Goto, Yuji AU - Goto Y FAU - Paik, Seung R AU - Paik SR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Korea (South) TA - J Microbiol Biotechnol JT - Journal of microbiology and biotechnology JID - 9431852 RN - 0 (alpha-Synuclein) SB - IM MH - Circular Dichroism MH - Kinetics MH - Lewy Bodies/chemistry/*metabolism MH - Microscopy, Atomic Force MH - Protein Folding MH - Protein Structure, Secondary MH - Ultrasonics MH - alpha-Synuclein/chemistry/*metabolism EDAT- 2008/01/03 09:00 MHDA- 2008/03/26 09:00 CRDT- 2008/01/03 09:00 AID - 7081 [pii] PST - ppublish SO - J Microbiol Biotechnol. 2007 Dec;17(12):2027-32. PMID- 12517337 OWN - NLM STAT- MEDLINE DA - 20030108 DCOM- 20031212 LR - 20131121 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 11 IP - 1 DP - 2003 Jan TI - Crystal structure of an inactive Akt2 kinase domain. PG - 21-30 AB - Akt/PKB represents a subfamily of three isoforms from the AGC serine/threonine kinase family. Amplification of Akt activity has been implicated in diseases that involve inappropriate cell survival, including a number of human malignancies. The structure of an inactive and unliganded Akt2 kinase domain reveals several features that distinguish it from other kinases. Most of the alpha helix C is disordered. The activation loop in this structure adopts a conformation that appears to sterically hinder the binding of both ATP and peptide substrate. In addition, an intramolecular disulfide bond is observed between two cysteines in the activation loop. Residues within the linker region between the N- and C-terminal lobes also contribute to the inactive conformation by partially occupying the ATP binding site. FAU - Huang, Xin AU - Huang X AD - Amgen Cambridge Research Center, One Kendall Square, Building 1000, Cambridge, MA 02139, USA. hxin@amgen.com FAU - Begley, Michael AU - Begley M FAU - Morgenstern, Kurt A AU - Morgenstern KA FAU - Gu, Yan AU - Gu Y FAU - Rose, Paul AU - Rose P FAU - Zhao, Huilin AU - Zhao H FAU - Zhu, Xiaotian AU - Zhu X LA - eng SI - PDB/1MRV SI - PDB/1MRY PT - Journal Article PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Ligands) RN - 0 (Proto-Oncogene Proteins) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 2.7.11.1 (AKT1 protein, human) RN - EC 2.7.11.1 (AKT2 protein, human) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - EC 2.7.11.1 (Proto-Oncogene Proteins c-akt) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) SB - IM MH - Adenosine Triphosphate/metabolism MH - Amino Acid Sequence MH - Binding Sites MH - Cyclic AMP-Dependent Protein Kinases/chemistry MH - Humans MH - Ligands MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - *Protein-Serine-Threonine Kinases MH - Proto-Oncogene Proteins/*chemistry/metabolism MH - Proto-Oncogene Proteins c-akt MH - Sequence Alignment EDAT- 2003/01/09 04:00 MHDA- 2003/12/13 05:00 CRDT- 2003/01/09 04:00 AID - S0969212602009371 [pii] PST - ppublish SO - Structure. 2003 Jan;11(1):21-30. PMID- 12767220 OWN - NLM STAT- MEDLINE DA - 20030527 DCOM- 20030716 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 42 IP - 21 DP - 2003 Jun 3 TI - Crystal structure of the human GGA1 GAT domain. PG - 6392-9 AB - GGAs are a family of vesicle-coating regulatory proteins that function in intracellular protein transport. A GGA molecule contains four domains, each mediating interaction with other proteins in carrying out intracellular transport. The GAT domain of GGAs has been identified as the structural entity that binds membrane-bound ARF, a molecular switch regulating vesicle-coat assembly. It also directly interacts with rabaptin5, an essential component of endosome fusion. A 2.8 A resolution crystal structure of the human GGA1 GAT domain is reported here. The GAT domain contains four helices and has an elongated shape with the longest dimension exceeding 80 A. Its longest helix is involved in two structural motifs: an N-terminal helix-loop-helix motif and a C-terminal three-helix bundle. The N-terminal motif harbors the most conservative amino acid sequence in the GGA GAT domains. Within this conserved region, a cluster of residues previously implicated in ARF binding forms a hydrophobic surface patch, which is likely to be the ARF-binding site. In addition, a structure-based mutagenesis-biochemical analysis demonstrates that the C-terminal three-helix bundle of this GAT domain is responsible for the rabaptin5 binding. These structural characteristics are consistent with a model supporting multiple functional roles for the GAT domain. FAU - Zhu, Guangyu AU - Zhu G AD - Crystallography Research Program and Protein Studies Program, Oklahoma Medical Research Foundation, 825 Northeast 13th Street, Oklahoma City, Oklahoma 73104, USA. FAU - Zhai, Peng AU - Zhai P FAU - He, Xiangyuan AU - He X FAU - Terzyan, Simon AU - Terzyan S FAU - Zhang, Rongguang AU - Zhang R FAU - Joachimiak, Andrzej AU - Joachimiak A FAU - Tang, Jordan AU - Tang J FAU - Zhang, Xuejun C AU - Zhang XC LA - eng GR - AG-18933/AG/NIA NIH HHS/United States GR - HL60626/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Adaptor Proteins, Vesicular Transport) RN - 0 (Carrier Proteins) RN - 0 (DNA, Complementary) RN - 0 (GGA adaptor proteins) RN - 0 (RABEP1 protein, human) RN - 0 (Vesicular Transport Proteins) RN - EC 3.6.5.2 (ADP-Ribosylation Factors) SB - IM MH - ADP-Ribosylation Factors/*chemistry MH - *Adaptor Proteins, Vesicular Transport MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - Carrier Proteins/*chemistry MH - Crystallography, X-Ray MH - DNA, Complementary/metabolism MH - Diffusion MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Transport MH - Sequence Homology, Amino Acid MH - Vesicular Transport Proteins/chemistry EDAT- 2003/05/28 05:00 MHDA- 2003/07/17 05:00 CRDT- 2003/05/28 05:00 AID - 10.1021/bi034334n [doi] PST - ppublish SO - Biochemistry. 2003 Jun 3;42(21):6392-9. PMID- 22575650 OWN - NLM STAT- MEDLINE DA - 20120511 DCOM- 20120720 IS - 1873-3468 (Electronic) IS - 0014-5793 (Linking) VI - 586 IP - 8 DP - 2012 Apr 24 TI - Biophysical characterization of the isolated C-terminal region of the transient receptor potential vanilloid 1. PG - 1154-9 LID - 10.1016/j.febslet.2012.03.030 [doi] AB - Transient receptor potential (TRP) proteins are sensory-related cation channels. TRPV subfamily responds to vanilloids, generating a Ca(2+) current. TRPV1, a thermal-sensitive non-selective ion channel, possesses six transmembrane helices and the intracellular N- and C-terminal domains. The latter contains the PIP(2) and calmodulin binding sites, the TRP domain and a temperature-responding flexible region. Although the function of C-TRPV1 is known, there are no experimental reports on its structural features. Here, we describe the conformational features of C-TRVP1, by using spectroscopic and biophysical approaches. Our results show that C-TRVP1 is an oligomeric protein, which shows features of natively unfolded proteins. CI - Copyright (c) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. FAU - Aguado-Llera, David AU - Aguado-Llera D AD - Instituto de Biologia Molecular y Celular, Universidad Miguel Hernandez, 03202 Elche (Alicante), Spain. FAU - Bacarizo, Julio AU - Bacarizo J FAU - Gregorio-Teruel, Lucia AU - Gregorio-Teruel L FAU - Taberner, Francisco J AU - Taberner FJ FAU - Camara-Artigas, Ana AU - Camara-Artigas A FAU - Neira, Jose L AU - Neira JL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120323 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Calmodulin) RN - 0 (TRPV Cation Channels) RN - 0 (vanilloid receptor subtype 1) SB - IM MH - Animals MH - Binding Sites MH - Biophysical Phenomena MH - Calmodulin/metabolism MH - Circular Dichroism MH - Protein Denaturation MH - Protein Structure, Tertiary MH - Protein Unfolding MH - Rats MH - TRPV Cation Channels/*chemistry/metabolism EDAT- 2012/05/12 06:00 MHDA- 2012/07/21 06:00 CRDT- 2012/05/12 06:00 PHST- 2012/03/08 [received] PHST- 2012/03/14 [revised] PHST- 2012/03/14 [accepted] PHST- 2012/03/23 [aheadofprint] AID - S0014-5793(12)00230-X [pii] AID - 10.1016/j.febslet.2012.03.030 [doi] PST - ppublish SO - FEBS Lett. 2012 Apr 24;586(8):1154-9. doi: 10.1016/j.febslet.2012.03.030. Epub 2012 Mar 23. PMID- 23500017 OWN - NLM STAT- MEDLINE DA - 20130429 DCOM- 20130805 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1830 IP - 6 DP - 2013 Jun TI - Biochemical characterization of C4 protein of Cotton leaf curl Kokhran Virus-Dabawali. PG - 3734-44 LID - 10.1016/j.bbagen.2013.02.026 [doi] LID - S0304-4165(13)00078-0 [pii] AB - BACKGROUND: Cotton leaf curl Kokhran Virus-Dabawali (CLCuKV-Dab) is a monopartite begomovirus encoding two proteins V1 and V2 in the virion sense and four proteins C1, C2, C3 and C4 in the complementary sense. The C4 protein of monopartite begomoviruses has been implicated to play a role in symptom determination and virus movement. The present work aims at the biochemical characterization of this protein. METHODS: The C4 protein of CLCuKV-Dab was purified in fusion with GST and tested for the ability to hydrolyze ATP and other phosphate containing compounds. ATPase activity was assayed by using radiolabeled gamma-[32P]-ATP and separating the product of reaction by thin layer chromatography. The hydrolysis of other compounds was monitored by the formation of a blue colored phosphomolybdate complex which was estimated by measuring the absorbance at 655nm. RESULTS: The purified GST-C4 protein exhibited metal ion dependent ATPase and inorganic pyrophosphatase activities. Deletion of a sequence resembling the catalytic motif present in phosphotyrosine phosphatases resulted in 70% reduction in both the activities. Mutational analysis suggested arginine 13 to be catalytically important for the ATPase and cysteine 8 for the pyrophosphatase activity of GST-C4. Interaction of V2 with GST-C4 resulted in an increase in both the enzymatic activities of GST-C4. CONCLUSIONS: The residues important for the enzymatic activities of GST-C4 are present in a motif different from the classical Walker motifs and the non-classical ATP binding motifs reported so far. GENERAL SIGNIFICANCE: The C4 protein of CLCuKV-Dab, a putative natively unfolded protein, exhibits enzymatic activities. CI - Copyright (c) 2013 Elsevier B.V. All rights reserved. FAU - Guha, Debojit AU - Guha D AD - Department of Biochemistry, Indian Institute of Science, Bangalore, India. FAU - Poornima Priyadarshini, C G AU - Poornima Priyadarshini CG FAU - Purakayastha, Arunima AU - Purakayastha A FAU - Thippeswamy, R AU - Thippeswamy R FAU - Lakshmikanth, M AU - Lakshmikanth M FAU - Savithri, H S AU - Savithri HS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130314 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Viral Proteins) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 3.6.1.1 (Inorganic Pyrophosphatase) SB - IM MH - Adenosine Triphosphatases/*chemistry/genetics/metabolism MH - Amino Acid Motifs MH - Begomovirus/*enzymology/genetics MH - Catalytic Domain MH - Inorganic Pyrophosphatase/*chemistry/genetics/metabolism MH - Protein Folding MH - Viral Proteins/*chemistry/genetics/metabolism EDAT- 2013/03/19 06:00 MHDA- 2013/08/06 06:00 CRDT- 2013/03/19 06:00 PHST- 2012/09/12 [received] PHST- 2013/02/10 [revised] PHST- 2013/02/27 [accepted] PHST- 2013/03/14 [aheadofprint] AID - S0304-4165(13)00078-0 [pii] AID - 10.1016/j.bbagen.2013.02.026 [doi] PST - ppublish SO - Biochim Biophys Acta. 2013 Jun;1830(6):3734-44. doi: 10.1016/j.bbagen.2013.02.026. Epub 2013 Mar 14. PMID- 20923662 OWN - NLM STAT- MEDLINE DA - 20101006 DCOM- 20110120 LR - 20140821 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 7 DP - 2010 Oct 6 TI - Role of the conformational versatility of the neurotrophin N-terminal regions in their recognition by Trk receptors. PG - 2273-8 LID - 10.1016/j.bpj.2010.07.054 [doi] AB - Neurotrophins (NTs) represent a family of proteins that play an important role in the survival, development, and function of neurons. Extensive efforts are currently being made to develop small molecules endowed with agonist or antagonist NT activity. The structurally versatile N-termini of these proteins are considered regions of interest for the design of new molecules. By combining experimental and computational approaches, we analyzed the intrinsic conformational preferences of the N-termini of two of the most important NTs: NGF (NGF-Nter) and NT4 (NT4-Nter). Circular dichroism spectra clearly indicate that both peptides show a preference for random coil states. Because this finding does not preclude the possibility that structured forms may occur in solution as minor conformational states, we performed molecular-dynamics simulations to gain insights into the structural features of populated species. In line with the circular dichroism analysis, the simulations show a preference for unstructured states for both peptides. However, the simulations also show that for NT4-Nter, and to a lesser extent for NGF-Nter, helical conformations, which are required for binding to the Trk receptor, are present in the repertoire of structures that are intrinsically accessible to these peptides. Accordingly, molecular recognition of NTs by the Trk receptor is accomplished by the general mechanism known as population shift. These findings provide a structural rationale for the observed activity of synthetic peptides based on these NT regions. They also suggest strategies for the development of biologically active peptide-based compounds. CI - Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Stanzione, Francesca AU - Stanzione F AD - Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Recerche, Naples, Italy. FAU - Esposito, Luciana AU - Esposito L FAU - Paladino, Antonella AU - Paladino A FAU - Pedone, Carlo AU - Pedone C FAU - Morelli, Giancarlo AU - Morelli G FAU - Vitagliano, Luigi AU - Vitagliano L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Nerve Growth Factors) RN - 0 (Peptides) RN - 0 (Receptors, Nerve Growth Factor) RN - 143551-63-7 (neurotrophin 4) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Hydrogen Bonding MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Nerve Growth Factors/*chemistry/*metabolism MH - Peptides/chemistry MH - Protein Conformation MH - Receptors, Nerve Growth Factor/*metabolism MH - Spectrophotometry, Ultraviolet PMC - PMC3042551 OID - NLM: PMC3042551 EDAT- 2010/10/07 06:00 MHDA- 2011/01/21 06:00 CRDT- 2010/10/07 06:00 PHST- 2010/03/02 [received] PHST- 2010/07/14 [revised] PHST- 2010/07/23 [accepted] AID - S0006-3495(10)00926-4 [pii] AID - 10.1016/j.bpj.2010.07.054 [doi] PST - ppublish SO - Biophys J. 2010 Oct 6;99(7):2273-8. doi: 10.1016/j.bpj.2010.07.054. PMID- 14674747 OWN - NLM STAT- MEDLINE DA - 20031216 DCOM- 20040423 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 42 IP - 50 DP - 2003 Dec 23 TI - Solution structure of human saposin C: pH-dependent interaction with phospholipid vesicles. PG - 14729-40 AB - Saposin C binds to membranes to activate lipid degradation in lysosomes. To get insights into saposin C's function, we have determined its three-dimensional structure by NMR and investigated its interaction with phospholipid vesicles. Saposin C adopts the saposin-fold common to other members of the family. In contrast, the electrostatic surface revealed by the NMR structure is remarkably different. We suggest that charge distribution in the protein surface can modulate membrane interaction leading to the functional diversity of this family. We find that the binding of saposin C to phospholipid vesicles is a pH-controlled reversible process. The pH dependence of this interaction is sigmoidal, with an apparent pK(a) for binding close to 5.3. The pK(a) values of many solvent-exposed Glu residues are anomalously high and close to the binding pK(a). Our NMR data are consistent with the absence of a conformational change prior to membrane binding. All this information suggests that the negatively charged electrostatic surface of saposin C needs to be partially neutralized to trigger membrane binding. We have studied the membrane-binding behavior of a mutant of saposin C designed to decrease the negative charge of the electrostatic surface. The results support our conclusion on the importance of protein surface neutralization in binding. Since saposin C is a lysosomal protein and pH gradients occur in lysosomes, we propose that lipid degradation in the lysosome could be switched on and off by saposin C's reversible binding to membranes. FAU - de Alba, Eva AU - de Alba E AD - Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 Center Drive, Bethesda, Maryland 20892, USA. dealba@helix.nih.gov FAU - Weiler, Solly AU - Weiler S FAU - Tjandra, Nico AU - Tjandra N LA - eng SI - PDB/1M12 PT - Comparative Study PT - Journal Article PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Glycoproteins) RN - 0 (Liposomes) RN - 0 (Micelles) RN - 0 (Phosphatidylcholines) RN - 0 (Phosphatidylserines) RN - 0 (Phospholipids) RN - 0 (Saposins) RN - 0 (Solutions) RN - 9002-93-1 (Octoxynol) SB - IM MH - Amino Acid Sequence MH - Crystallography, X-Ray MH - Glycoproteins/*chemistry MH - Humans MH - Hydrogen-Ion Concentration MH - Liposomes MH - Micelles MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Octoxynol MH - Phosphatidylcholines/chemistry MH - Phosphatidylserines/chemistry MH - Phospholipids/*chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Saposins MH - Solutions MH - Structure-Activity Relationship EDAT- 2003/12/17 05:00 MHDA- 2004/04/24 05:00 CRDT- 2003/12/17 05:00 AID - 10.1021/bi0301338 [doi] PST - ppublish SO - Biochemistry. 2003 Dec 23;42(50):14729-40. PMID- 19933326 OWN - NLM STAT- MEDLINE DA - 20100817 DCOM- 20100908 LR - 20150224 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 106 IP - 49 DP - 2009 Dec 8 TI - Multiple conformations of full-length p53 detected with single-molecule fluorescence resonance energy transfer. PG - 20758-63 LID - 10.1073/pnas.0909644106 [doi] AB - The tumor suppressor p53 is a member of the emerging class of proteins that have both folded and intrinsically disordered domains, which are a challenge to structural biology. Its N-terminal domain (NTD) is linked to a folded core domain, which has a disordered link to the folded tetramerization domain, which is followed by a disordered C-terminal domain. The quaternary structure of human p53 has been solved by a combination of NMR spectroscopy, electron microscopy, and small-angle X-ray scattering (SAXS), and the NTD ensemble structure has been solved by NMR and SAXS. The murine p53 is reported to have a different quaternary structure, with the N and C termini interacting. Here, we used single-molecule FRET (SM-FRET) and ensemble FRET to investigate the conformational dynamics of the NTD of p53 in isolation and in the context of tetrameric full-length p53 (flp53). Our results showed that the isolated NTD was extended in solution with a strong preference for residues 66-86 forming a polyproline II conformation. The NTD associated weakly with the DNA binding domain of p53, but not the C termini. We detected multiple conformations in flp53 that were likely to result from the interactions of NTD with the DNA binding domain of each monomeric p53. Overall, the SM-FRET results, in addition to corroborating the previous ensemble findings, enabled the identification of the existence of multiple conformations of p53, which are often averaged and neglected in conventional ensemble techniques. Our study exemplifies the usefulness of SM-FRET in exploring the dynamic landscape of multimeric proteins that contain regions of unstructured domains. FAU - Huang, Fang AU - Huang F AD - Medical Research Council Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, United Kingdom. FAU - Rajagopalan, Sridharan AU - Rajagopalan S FAU - Settanni, Giovanni AU - Settanni G FAU - Marsh, Richard J AU - Marsh RJ FAU - Armoogum, Daven A AU - Armoogum DA FAU - Nicolaou, Nick AU - Nicolaou N FAU - Bain, Angus J AU - Bain AJ FAU - Lerner, Eitan AU - Lerner E FAU - Haas, Elisha AU - Haas E FAU - Ying, Liming AU - Ying L FAU - Fersht, Alan R AU - Fersht AR LA - eng GR - JF20607/2/Biotechnology and Biological Sciences Research Council/United Kingdom GR - MC_U105474168/Medical Research Council/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091120 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Amino Acids) RN - 0 (Mutant Proteins) RN - 0 (Protein Subunits) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Amino Acids/metabolism MH - Animals MH - Diffusion MH - Fluorescence Resonance Energy Transfer/*methods MH - Humans MH - Mice MH - Models, Molecular MH - Mutant Proteins/chemistry/metabolism MH - Protein Binding MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Protein Subunits/chemistry/metabolism MH - Scattering, Small Angle MH - Time Factors MH - Tumor Suppressor Protein p53/*chemistry/*metabolism MH - X-Ray Diffraction PMC - PMC2791586 EDAT- 2009/11/26 06:00 MHDA- 2010/09/09 06:00 CRDT- 2009/11/26 06:00 PHST- 2009/11/20 [aheadofprint] AID - 0909644106 [pii] AID - 10.1073/pnas.0909644106 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2009 Dec 8;106(49):20758-63. doi: 10.1073/pnas.0909644106. Epub 2009 Nov 20. PMID- 20522010 OWN - NLM STAT- MEDLINE DA - 20100804 DCOM- 20101109 LR - 20101129 IS - 1996-3181 (Electronic) IS - 1871-5273 (Linking) VI - 9 IP - 4 DP - 2010 Aug TI - The role of phosphorylation in synucleinopathies: focus on Parkinson's disease. PG - 471-81 AB - Synuclein is a soluble, natively unfolded protein that is highly enriched in the presynaptic terminals of neurons in the central nervous system. Interest in -synuclein has increased markedly following the discovery of a relationship between its dysfunction and several neurodegenerative diseases, including Parkinson's disease. The physiological functions of -synuclein remain to be fully defined, although recent data suggest a role in regulating membrane stability and neuronal plasticity. In addition, there is increasing evidence pointing to phosphorylation as playing an important role in the oligomerization, fibrillogenesis, Lewy body formation, and neurotoxicity of -syncline in Parkinson's disease. Immunohistochemical and biochemical studies reveal that the majority of -synuclein within inclusions from patients with Parkinson's disease and other synucleinopathies is phosphorylated at Ser129. -Synuclein can be phosphorylated in vitro also at Ser87, and three C-terminal tyrosine residues (Tyr125, Tyr 133, and Tyr136). Tyrosine 125 phosphorylation diminishes during the normal aging process in both humans and flies. Notably, cortical tissue from patients with Parkinson's disease-related synucleinopathy dementia with Lewy bodies showed less phosphorylation at Tyr125. While phosphorylation at Ser87 is enhanced in synucleinopathies, it inhibits -synuclein oligomerization, and influences synuclein-membrane interactions. The possibility that -synuclein neurotoxicity in Parkinson's disease and related synucleinopathies may result from an imbalance between the detrimental, oligomer-promoting effect of Ser129 phosphorylation and a neuroprotective action of Ser87/Tyr125 phosphorylation that inhibits toxic oligomer formation merits consideration, as will be discussed in this article. FAU - Cavallarin, Nadia AU - Cavallarin N AD - Department of Veterinary Science, University of Padova, CRIBI, Italy. FAU - Vicario, Mattia AU - Vicario M FAU - Negro, Alessandro AU - Negro A LA - eng PT - Journal Article PT - Review PL - United Arab Emirates TA - CNS Neurol Disord Drug Targets JT - CNS & neurological disorders drug targets JID - 101269155 RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Animals, Genetically Modified/genetics MH - Drosophila melanogaster/genetics/metabolism MH - Humans MH - Lewy Bodies/metabolism/physiology MH - Parkinson Disease/genetics/*metabolism MH - Phosphorylation/physiology MH - Synucleins/genetics/*metabolism/physiology MH - alpha-Synuclein/genetics/metabolism/physiology EDAT- 2010/06/05 06:00 MHDA- 2010/11/10 06:00 CRDT- 2010/06/05 06:00 PHST- 2010/04/06 [received] PHST- 2010/05/14 [accepted] AID - BSP/CDTCNSND/E-Pub/00047 [pii] PST - ppublish SO - CNS Neurol Disord Drug Targets. 2010 Aug;9(4):471-81. PMID- 22304430 OWN - NLM STAT- MEDLINE DA - 20120222 DCOM- 20120410 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 51 IP - 7 DP - 2012 Feb 21 TI - Role of the helical structure of the N-terminal region of Plasmodium falciparum merozoite surface protein 2 in fibril formation and membrane interaction. PG - 1380-7 LID - 10.1021/bi201880s [doi] AB - Merozoite surface protein 2 (MSP2), an abundant glycosylphosphatidylinositol-anchored protein on the surface of Plasmodium falciparum merozoites, is a promising malaria vaccine candidate. MSP2 is intrinsically disordered and forms amyloid-like fibrils in solution under physiological conditions. The 25 N-terminal residues (MSP2(1-25)) play an important role in both fibril formation and membrane binding of the full-length protein. In this study, the fibril formation and solution structure of MSP2(1-25) in the membrane mimetic solvents sodium dodecyl sulfate (SDS), dodecylphosphocholine (DPC), and trifluoroethanol (TFE) have been investigated by transmission electronic microscopy, turbidity, thioflavin T fluorescence, circular dichroism (CD), and nuclear magnetic resonance (NMR) spectroscopy. Turbidity data showed that the aggregation of MSP2(1-25) was suppressed in the presence of membrane mimetic solvents. CD spectra indicated that helical structure in MSP2(1-25) was stabilized in SDS and DPC micelles and in high concentrations of TFE. The structure of MSP2(1-25) in 50% aqueous TFE, determined using NMR, showed that the peptide formed an amphipathic helix encompassing residues 10-24. Low concentrations of TFE favored partially folded helical conformations, as demonstrated by CD and NMR, and promoted MSP2(1-25) fibril formation. Our data suggest that partially folded helical conformations of the N-terminal region of MSP2 are on the pathway to amyloid fibril formation, while higher degrees of helical structure stabilized by high concentrations of TFE or membrane mimetics suppress self-association and thus inhibit fibril formation. The roles of the induced helical conformations in membrane interactions are also discussed. FAU - Zhang, Xuecheng AU - Zhang X AD - School of Life Sciences, Anhui University, Hefei, Anhui 230039, P R China. turenzh@ahu.edu.cn FAU - Adda, Christopher G AU - Adda CG FAU - Low, Andrew AU - Low A FAU - Zhang, Jiahai AU - Zhang J FAU - Zhang, Wen AU - Zhang W FAU - Sun, Hongbin AU - Sun H FAU - Tu, Xiaoming AU - Tu X FAU - Anders, Robin F AU - Anders RF FAU - Norton, Raymond S AU - Norton RS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120208 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Antigens, Protozoan) RN - 0 (Lipid Bilayers) RN - 0 (Micelles) RN - 0 (Protozoan Proteins) RN - 0 (Thiazoles) RN - 0 (merozoite surface protein 2, Plasmodium) RN - 2390-54-7 (thioflavin T) SB - IM MH - Amyloid/chemistry MH - Animals MH - Antigens, Protozoan/*chemistry/metabolism MH - Circular Dichroism MH - Hydrogen-Ion Concentration MH - Kinetics MH - Lipid Bilayers/chemistry MH - Magnetic Resonance Spectroscopy/methods MH - Micelles MH - Microscopy, Electron, Transmission/methods MH - Molecular Conformation MH - Plasmodium falciparum/*metabolism MH - Protein Conformation MH - Protein Structure, Tertiary MH - Protozoan Proteins/*chemistry/metabolism MH - Spectrophotometry/methods MH - Temperature MH - Thiazoles/chemistry EDAT- 2012/02/07 06:00 MHDA- 2012/04/11 06:00 CRDT- 2012/02/07 06:00 PHST- 2012/02/08 [aheadofprint] AID - 10.1021/bi201880s [doi] PST - ppublish SO - Biochemistry. 2012 Feb 21;51(7):1380-7. doi: 10.1021/bi201880s. Epub 2012 Feb 8. PMID- 20347844 OWN - NLM STAT- MEDLINE DA - 20100426 DCOM- 20100504 LR - 20140917 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 398 IP - 4 DP - 2010 May 14 TI - RCC1 uses a conformationally diverse loop region to interact with the nucleosome: a model for the RCC1-nucleosome complex. PG - 518-29 LID - 10.1016/j.jmb.2010.03.037 [doi] AB - The binding of RCC1 (regulator of chromosome condensation 1) to chromatin is critical for cellular processes such as mitosis, nucleocytoplasmic transport, and nuclear envelope formation because RCC1 recruits the small GTPase Ran (Ras-related nuclear protein) to chromatin and sets up a Ran-GTP gradient around the chromosomes. However, the molecular mechanism by which RCC1 binds to nucleosomes, the repeating unit of chromatin, is not known. We have used biochemical approaches to test structural models for how the RCC1 beta-propeller protein could bind to the nucleosome. In contrast to the prevailing model, RCC1 does not appear to use the beta-propeller face opposite to its Ran-binding face to interact with nucleosomes. Instead, we find that RCC1 uses a conformationally flexible loop region we have termed the switchback loop in addition to its N-terminal tail to bind to the nucleosome. The juxtaposition of the RCC1 switchback loop to its Ran binding surface suggests a novel mechanism for how nucleosome-bound RCC1 recruits Ran to chromatin. Furthermore, this model accounts for previously unexplained observations for how Ran can interact with the nucleosome both dependent and independent of RCC1 and how binding of the nucleosome can enhance RCC1's Ran nucleotide exchange activity. CI - (c) 2010 Elsevier Ltd. All rights reserved. FAU - England, Joseph R AU - England JR AD - Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, 108 Althouse Laboratory, The Pennsylvania State University, University Park, PA 16802-1014, USA. FAU - Huang, Jiehuan AU - Huang J FAU - Jennings, Matthew J AU - Jennings MJ FAU - Makde, Ravindra D AU - Makde RD FAU - Tan, Song AU - Tan S LA - eng GR - GM088236/GM/NIGMS NIH HHS/United States GR - R01 GM088236/GM/NIGMS NIH HHS/United States GR - R01 GM088236-01/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20100327 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Cell Cycle Proteins) RN - 0 (Guanine Nucleotide Exchange Factors) RN - 0 (Nuclear Proteins) RN - 0 (Nucleosomes) RN - 0 (RCC1 protein, human) SB - IM MH - Amino Acid Substitution/genetics MH - Cell Cycle Proteins/*metabolism MH - Guanine Nucleotide Exchange Factors/*metabolism MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Nuclear Proteins/*metabolism MH - Nucleosomes/*metabolism MH - Protein Binding MH - Protein Conformation MH - *Protein Interaction Mapping MH - Protein Structure, Tertiary PMC - PMC2895563 MID - NIHMS193271 OID - NLM: NIHMS193271 OID - NLM: PMC2895563 EDAT- 2010/03/30 06:00 MHDA- 2010/05/05 06:00 CRDT- 2010/03/30 06:00 PHST- 2009/10/26 [received] PHST- 2010/02/24 [revised] PHST- 2010/03/19 [accepted] PHST- 2010/03/27 [aheadofprint] AID - S0022-2836(10)00299-8 [pii] AID - 10.1016/j.jmb.2010.03.037 [doi] PST - ppublish SO - J Mol Biol. 2010 May 14;398(4):518-29. doi: 10.1016/j.jmb.2010.03.037. Epub 2010 Mar 27. PMID- 20826336 OWN - NLM STAT- MEDLINE DA - 20100909 DCOM- 20110118 LR - 20140921 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 18 IP - 9 DP - 2010 Sep 8 TI - Structural diversity in free and bound states of intrinsically disordered protein phosphatase 1 regulators. PG - 1094-103 LID - 10.1016/j.str.2010.05.015 [doi] AB - Complete folding is not a prerequisite for protein function, as disordered and partially folded states of proteins frequently perform essential biological functions. In order to understand their functions at the molecular level, we utilized diverse experimental measurements to calculate ensemble models of three nonhomologous, intrinsically disordered proteins: I-2, spinophilin, and DARPP-32, which bind to and regulate protein phosphatase 1 (PP1). The models demonstrate that these proteins have dissimilar propensities for secondary and tertiary structure in their unbound forms. Direct comparison of these ensemble models with recently determined PP1 complex structures suggests a significant role for transient, preformed structure in the interactions of these proteins with PP1. Finally, we generated an ensemble model of partially disordered I-2 bound to PP1 that provides insight into the relationship between flexibility and biological function in this dynamic complex. CI - Copyright (c) 2010 Elsevier Ltd. All rights reserved. FAU - Marsh, Joseph A AU - Marsh JA AD - Molecular Structure & Function, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada. FAU - Dancheck, Barbara AU - Dancheck B FAU - Ragusa, Michael J AU - Ragusa MJ FAU - Allaire, Marc AU - Allaire M FAU - Forman-Kay, Julie D AU - Forman-Kay JD FAU - Peti, Wolfgang AU - Peti W LA - eng GR - R01 NS056128/NS/NINDS NIH HHS/United States GR - R01 NS056128-02S1/NS/NINDS NIH HHS/United States GR - R01 NS056128-03/NS/NINDS NIH HHS/United States GR - R01NS056128/NS/NINDS NIH HHS/United States GR - T32 GM007601/GM/NIGMS NIH HHS/United States GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Dopamine and cAMP-Regulated Phosphoprotein 32) RN - 0 (Microfilament Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Proteins) RN - 0 (neurabin) RN - 0 (protein phosphatase inhibitor-2) RN - EC 3.1.3.16 (Protein Phosphatase 1) SB - IM CIN - Structure. 2010 Sep 8;18(9):1069-71. PMID: 20826332 MH - Dopamine and cAMP-Regulated Phosphoprotein 32/chemistry/metabolism MH - Microfilament Proteins/chemistry/metabolism MH - Models, Molecular MH - Nerve Tissue Proteins/chemistry/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Phosphatase 1/*chemistry/metabolism MH - Proteins/chemistry/metabolism MH - Structure-Activity Relationship PMC - PMC2936704 MID - NIHMS228750 OID - NLM: NIHMS228750 OID - NLM: PMC2936704 EDAT- 2010/09/10 06:00 MHDA- 2011/01/19 06:00 CRDT- 2010/09/10 06:00 PHST- 2010/03/01 [received] PHST- 2010/05/07 [revised] PHST- 2010/05/19 [accepted] AID - S0969-2126(10)00266-2 [pii] AID - 10.1016/j.str.2010.05.015 [doi] PST - ppublish SO - Structure. 2010 Sep 8;18(9):1094-103. doi: 10.1016/j.str.2010.05.015. PMID- 23875714 OWN - NLM STAT- MEDLINE DA - 20131024 DCOM- 20140522 LR - 20141113 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 117 IP - 42 DP - 2013 Oct 24 TI - Remarkably fast coupled folding and binding of the intrinsically disordered transactivation domain of cMyb to CBP KIX. PG - 13346-56 LID - 10.1021/jp404267e [doi] AB - Association rates for interactions between folded proteins have been investigated extensively, allowing the development of computational and theoretical prediction methods. Less is known about association rates for complexes where one or more partner is initially disordered, despite much speculation about how they may compare to those for folded proteins. We have attached a fluorophore to the N-terminus of the 25 amino acid cMyb peptide used previously in NMR and equilibrium studies (termed FITC-cMyb), and used this to monitor the kinetics of its interaction with the KIX protein. We have investigated the ionic strength and temperature dependence of the kinetics, and conclude that the association process is extremely fast, apparently exceeding the rates predicted by formulations applicable to interactions between pairs of folded proteins. This is despite the fact that not all collisions result in complex formation (there is an observable activation energy for the association process). We propose that this is partially a result of the disordered nature of the FITC-cMyb peptide itself. FAU - Shammas, Sarah L AU - Shammas SL AD - Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, U.K. FAU - Travis, Alexandra J AU - Travis AJ FAU - Clarke, Jane AU - Clarke J LA - eng GR - 095195/Wellcome Trust/United Kingdom GR - WT095195MA/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130815 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Membrane Proteins) RN - 0 (Pag1 protein, mouse) RN - 0 (Peptides) RN - 0 (Phosphoproteins) RN - 0 (Proto-Oncogene Proteins c-myb) RN - 0 (Recombinant Proteins) RN - I223NX31W9 (Fluorescein-5-isothiocyanate) SB - IM MH - Animals MH - Circular Dichroism MH - Fluorescein-5-isothiocyanate/chemistry MH - Kinetics MH - Membrane Proteins/chemistry/genetics/*metabolism MH - Mice MH - Osmolar Concentration MH - Peptides/chemistry/metabolism MH - Phosphoproteins/chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-myb/chemistry/*metabolism MH - Recombinant Proteins/biosynthesis/chemistry/genetics PMC - PMC3807845 OID - NLM: PMC3807845 EDAT- 2013/07/24 06:00 MHDA- 2014/05/23 06:00 CRDT- 2013/07/24 06:00 PHST- 2013/08/15 [aheadofprint] AID - 10.1021/jp404267e [doi] PST - ppublish SO - J Phys Chem B. 2013 Oct 24;117(42):13346-56. doi: 10.1021/jp404267e. Epub 2013 Aug 15. PMID- 21889463 OWN - NLM STAT- MEDLINE DA - 20110905 DCOM- 20111223 LR - 20141022 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 101 IP - 5 DP - 2011 Sep 7 TI - Structured functional domains of myelin basic protein: cross talk between actin polymerization and Ca(2+)-dependent calmodulin interaction. PG - 1248-56 LID - 10.1016/j.bpj.2011.07.035 [doi] AB - The 18.5-kDa myelin basic protein (MBP), the most abundant isoform in human adult myelin, is a multifunctional, intrinsically disordered protein that maintains compact assembly of the sheath. Solution NMR spectroscopy and a hydrophobic moment analysis of MBP's amino-acid sequence have previously revealed three regions with high propensity to form strongly amphipathic alpha-helices. These regions, located in the central, N- and C-terminal parts of the protein, have been shown to play a role in the interactions of MBP with cytoskeletal proteins, Src homology 3-domain-containing proteins, Ca(2+)-activated calmodulin (Ca(2+)-CaM), and myelin-mimetic membrane bilayers. Here, we have further characterized the structure-function relationship of these three domains. We constructed three recombinant peptides derived from the 18.5-kDa murine MBP: (A22-K56), (S72-S107), and (S133-S159) (which are denoted alpha1, alpha2, and alpha3, respectively). We used a variety of biophysical methods (circular dichroism spectroscopy, isothermal titration calorimetry, transmission electron microscopy, fluorimetry, and solution NMR spectroscopy and chemical shift index analysis) to characterize the interactions of these peptides with actin and Ca(2+)-CaM. Our results show that all three peptides can adopt alpha-helical structure inherently even in aqueous solution. Both alpha1- and alpha3-peptides showed strong binding with Ca(2+)-CaM, and both adopted an alpha-helical conformation upon interaction, but the binding of the alpha3-peptide appeared to be more dynamic. Only the alpha1-peptide exhibited actin polymerization and bundling activity, and the addition of Ca(2+)-CaM resulted in depolymerization of actin that had been polymerized by alpha1. The results of this study proved that there is an N-terminal binding domain in MBP for Ca(2+)-CaM (in addition to the primary site located in the C-terminus), and that it is sufficient for CaM-induced actin depolymerization. These three domains of MBP represent molecular recognition fragments with multiple roles in both membrane- and protein-association. CI - Copyright (c) 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Bamm, Vladimir V AU - Bamm VV AD - Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada. FAU - De Avila, Miguel AU - De Avila M FAU - Smith, Graham S T AU - Smith GS FAU - Ahmed, Mumdooh A M AU - Ahmed MA FAU - Harauz, George AU - Harauz G LA - eng GR - MOP74468/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Actins) RN - 0 (Calmodulin) RN - 0 (Myelin Basic Protein) RN - 0 (Peptide Fragments) RN - SY7Q814VUP (Calcium) SB - IM MH - Actins/*chemistry/metabolism MH - Animals MH - Calcium/*metabolism MH - Calmodulin/*metabolism MH - Mice MH - Myelin Basic Protein/*chemistry/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemistry/genetics/isolation & purification/metabolism MH - Protein Binding MH - *Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary PMC - PMC3164172 OID - NLM: PMC3164172 EDAT- 2011/09/06 06:00 MHDA- 2011/12/24 06:00 CRDT- 2011/09/06 06:00 PHST- 2011/02/02 [received] PHST- 2011/07/15 [revised] PHST- 2011/07/22 [accepted] AID - S0006-3495(11)00893-9 [pii] AID - 10.1016/j.bpj.2011.07.035 [doi] PST - ppublish SO - Biophys J. 2011 Sep 7;101(5):1248-56. doi: 10.1016/j.bpj.2011.07.035. PMID- 22582058 OWN - NLM STAT- MEDLINE DA - 20120625 DCOM- 20121126 LR - 20141016 IS - 1098-5336 (Electronic) IS - 0099-2240 (Linking) VI - 78 IP - 14 DP - 2012 Jul TI - Proteomic phenotyping of Novosphingobium nitrogenifigens reveals a robust capacity for simultaneous nitrogen fixation, polyhydroxyalkanoate production, and resistance to reactive oxygen species. PG - 4802-15 LID - 10.1128/AEM.00274-12 [doi] AB - Novosphingobium nitrogenifigens Y88(T) (Y88) is a free-living, diazotrophic Alphaproteobacterium, capable of producing 80% of its biomass as the biopolymer polyhydroxybutyrate (PHB). We explored the potential utility of this species as a polyhydroxybutyrate production strain, correlating the effects of glucose, nitrogen availability, dissolved oxygen concentration, and extracellular pH with polyhydroxybutyrate production and changes in the Y88 proteomic profile. Using two-dimensional differential in-gel electrophoresis and tandem mass spectrometry, we identified 217 unique proteins from six growth conditions. We observed reproducible, characteristic proteomic signatures for each of the physiological states we examined. We identified proteins that changed in abundance in correlation with either nitrogen fixation, dissolved oxygen concentration, or acidification of the growth medium. The proteins that correlated with nitrogen fixation were identified either as known nitrogen fixation proteins or as novel proteins that we predict play roles in aspects of nitrogen fixation based on their proteomic profiles. In contrast, the proteins involved in central carbon and polyhydroxybutyrate metabolism were constitutively abundant, consistent with the constitutive polyhydroxybutyrate production that we observed in this species. Three proteins with roles in detoxification of reactive oxygen species were identified in this obligate aerobe. The most abundant protein in all experiments was a polyhydroxyalkanoate granule-associated protein, phasin. The full-length isoform of this protein has a long, intrinsically disordered Ala/Pro/Lys-rich N-terminal segment, a feature that appears to be unique to sphingomonad phasins. The data suggest that Y88 has potential as a PHB production strain due to its aerobic tolerance and metabolic orientation toward polyhydroxybutyrate accumulation, even in low-nitrogen growth medium. FAU - Smit, Anne-Marie AU - Smit AM AD - Scion, Rotorua, New Zealand. anne-marie.smit@scionresearch.com FAU - Strabala, Timothy J AU - Strabala TJ FAU - Peng, Lifeng AU - Peng L FAU - Rawson, Pisana AU - Rawson P FAU - Lloyd-Jones, Gareth AU - Lloyd-Jones G FAU - Jordan, T William AU - Jordan TW LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120511 PL - United States TA - Appl Environ Microbiol JT - Applied and environmental microbiology JID - 7605801 RN - 0 (Bacterial Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (PHAP protein, Bacteria) RN - 0 (Polyhydroxyalkanoates) RN - 0 (Reactive Oxygen Species) SB - IM MH - Bacterial Proteins/genetics/*metabolism MH - DNA-Binding Proteins/genetics/*metabolism MH - Drug Resistance, Bacterial MH - Nitrogen Fixation/*physiology MH - Phenotype MH - Polyhydroxyalkanoates/*biosynthesis MH - Proteomics/*methods MH - Reactive Oxygen Species/*pharmacology MH - Sphingomonadaceae/classification/*drug effects/growth & development/metabolism MH - Tandem Mass Spectrometry PMC - PMC3416387 OID - NLM: PMC3416387 EDAT- 2012/05/15 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/05/15 06:00 PHST- 2012/05/11 [aheadofprint] AID - AEM.00274-12 [pii] AID - 10.1128/AEM.00274-12 [doi] PST - ppublish SO - Appl Environ Microbiol. 2012 Jul;78(14):4802-15. doi: 10.1128/AEM.00274-12. Epub 2012 May 11. PMID- 24075929 OWN - NLM STAT- MEDLINE DA - 20131125 DCOM- 20140221 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1834 IP - 12 DP - 2013 Dec TI - The structural organization of the N-terminus domain of SopB, a virulence factor of Salmonella, depends on the nature of its protein partners. PG - 2564-72 LID - 10.1016/j.bbapap.2013.09.014 [doi] LID - S1570-9639(13)00348-8 [pii] AB - The TTSS is used by Salmonella and many bacterial pathogens to inject virulence factors directly into the cytoplasm of target eukaryotic cells. Once translocated these so-called effector proteins hijack a vast array of crucial cellular functions to the benefit of the bacteria. In the bacterial cytoplasm, some effectors are stabilized and maintained in a secretion competent state by interaction with specific type III chaperones. In this work we studied the conformation of the Chaperone Binding Domain of the effector named Salmonella Outer protein B (SopB) alone and in complex with its cognate chaperone SigE by a combination of biochemical, biophysical and structural approaches. Our results show that the N-terminus part of SopB is mainly composed by alpha-helices and unfolded regions whose organization/stabilization depends on their interaction with the different partners. This suggests that the partially unfolded state of this N-terminal region, which confers the adaptability of the effector to bind very different partners during the infection cycle, allows the bacteria to modulate numerous host cells functions limiting the number of translocated effectors. CI - (c) 2013. FAU - Roblin, Pierre AU - Roblin P AD - INRA Biopolymeres, Interactions et Assemblages, Rue de la Geraudiere, 44316 Nantes, France; Synchrotron SOLEIL, L'orme des Merisiers, Saint Aubin, BP 48, 91192 Gif sur Yvette Cedex, France. Electronic address: pierre.roblin@synchrotron-soleil.fr. FAU - Lebrun, Pierre AU - Lebrun P FAU - Rucktooa, Prakash AU - Rucktooa P FAU - Dewitte, Frederique AU - Dewitte F FAU - Lens, Zoe AU - Lens Z FAU - Receveur-Brechot, Veronique AU - Receveur-Brechot V FAU - Raussens, Vincent AU - Raussens V FAU - Villeret, Vincent AU - Villeret V FAU - Bompard, Coralie AU - Bompard C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130926 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Bacterial Proteins) RN - 0 (Molecular Chaperones) RN - 0 (Sigma Factor) RN - 0 (sigE protein, Bacteria) RN - EC 3.4.- (SopB protein, Salmonella) SB - IM MH - Bacterial Proteins/*chemistry/genetics/*metabolism MH - Molecular Chaperones/*chemistry/genetics/metabolism MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Salmonella typhimurium/*chemistry/genetics/metabolism MH - Sigma Factor/genetics/*metabolism OTO - NOTNLM OT - Bacterial virulence OT - CBD OT - CD OT - Chaperone binding domain OT - DSP OT - Intrinsically disordered protein OT - R(g) OT - R(h) OT - SAXS OT - Salmonella outer protein B OT - Small angle X-ray scattering OT - SopB OT - TTSS OT - Type three secretion system OT - chaperone binding domain OT - circular dichroism OT - dithio-bis-(succinimidylpropionate) OT - hydrodynamic radius OT - radius of gyration OT - small angle X-ray scattering OT - type three secretion system EDAT- 2013/10/01 06:00 MHDA- 2014/02/22 06:00 CRDT- 2013/10/01 06:00 PHST- 2013/05/09 [received] PHST- 2013/09/03 [revised] PHST- 2013/09/18 [accepted] PHST- 2013/09/26 [aheadofprint] AID - S1570-9639(13)00348-8 [pii] AID - 10.1016/j.bbapap.2013.09.014 [doi] PST - ppublish SO - Biochim Biophys Acta. 2013 Dec;1834(12):2564-72. doi: 10.1016/j.bbapap.2013.09.014. Epub 2013 Sep 26. PMID- 17131428 OWN - NLM STAT- MEDLINE DA - 20070122 DCOM- 20070329 LR - 20121115 IS - 0360-4012 (Print) IS - 0360-4012 (Linking) VI - 85 IP - 2 DP - 2007 Feb 1 TI - Purification and spectroscopic characterization of the recombinant BG21 isoform of murine golli myelin basic protein. PG - 272-84 AB - A recombinant form of the murine Golli-myelin basic protein (MBP) isoform BG21 (rmBG21) has been expressed in E. coli, and isolated to 96% purity via metal chelation chromatography. Characteristic yields were 6-8 mg protein per liter of culture in either minimal M9 or standard Luria-Bertani media. Circular dichroism spectroscopy showed that rmBG21 had a large proportion of random coil in aqueous solution, but gained alpha-helix in the presence of monosialoganglioside G(M1) and PI(4)P, as well as in the membrane-mimetic solvent trifluoroethanol. Bioinformatics analyses of the amino acid sequence of rmBG21 predicted an N-terminal calmodulin (CaM)-binding site. It was determined by fluorescence spectroscopy and dynamic light scattering that rmBG21 and CaM interacted weakly in a 1:1 ratio in a Ca(2+)-dependent manner. Solution NMR spectra of uniformly [(13)C(15)N]-labeled protein in aqueous buffer were consistent with it being an extended protein; spectral quality was independent of temperature. Thus, like "classic" MBP and the Golli-MBP isoform J37, rmBG21 is intrinsically disordered, implying multi functionality, and that its conformation depends on its environment and bound ligands. FAU - Bamm, Vladimir V AU - Bamm VV AD - Department of Molecular and Cellular Biology, University of Guelph, Ontario, Canada. FAU - Ahmed, Mumdooh A M AU - Ahmed MA FAU - Ladizhansky, Vladimir AU - Ladizhansky V FAU - Harauz, George AU - Harauz G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Neurosci Res JT - Journal of neuroscience research JID - 7600111 RN - 0 (Mbp protein, mouse) RN - 0 (Myelin Basic Protein) RN - 0 (Nerve Tissue Proteins) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) SB - IM MH - Amino Acid Sequence MH - Animals MH - Chromatography, High Pressure Liquid MH - Electrophoresis, Polyacrylamide Gel MH - Mass Spectrometry MH - Mice MH - Molecular Sequence Data MH - Myelin Basic Protein MH - Nerve Tissue Proteins/*chemistry/genetics/*isolation & purification MH - Protein Isoforms/chemistry/genetics/isolation & purification MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/genetics/isolation & purification MH - Transcription Factors/*chemistry/genetics/*isolation & purification EDAT- 2006/11/30 09:00 MHDA- 2007/03/30 09:00 CRDT- 2006/11/30 09:00 AID - 10.1002/jnr.21129 [doi] PST - ppublish SO - J Neurosci Res. 2007 Feb 1;85(2):272-84. PMID- 22905195 OWN - NLM STAT- MEDLINE DA - 20120820 DCOM- 20130211 LR - 20141105 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 8 DP - 2012 TI - Tyrosinase degradation is prevented when EDEM1 lacks the intrinsically disordered region. PG - e42998 LID - 10.1371/journal.pone.0042998 [doi] AB - EDEM1 is a mannosidase-like protein that recruits misfolded glycoproteins from the calnexin/calreticulin folding cycle to downstream endoplasmic reticulum associated degradation (ERAD) pathway. Here, we investigate the role of EDEM1 in the processing of tyrosinase, a tumour antigen overexpressed in melanoma cells. First, we analyzed and modeled EDEM1 major domains. The homology model raised on the crystal structures of human and Saccharomyces cerevisiae ER class I alpha1,2-mannosidases reveals that the major mannosidase domain located between aminoacids 121-598 fits with high accuracy. We have further identified an N-terminal region located between aminoacids 40-119, predicted to be intrinsically disordered (ID) and susceptible to adopt multiple conformations, hence facilitating protein-protein interactions. To investigate these two domains we have constructed an EDEM1 deletion mutant lacking the ID region and a triple mutant disrupting the glycan-binding domain and analyzed their association with tyrosinase. Tyrosinase is a glycoprotein partly degraded endogenously by ERAD and the ubiquitin proteasomal system. We found that the degradation of wild type and misfolded tyrosinase was enhanced when EDEM1 was overexpressed. Glycosylated and non-glycosylated mutants co-immunoprecipitated with EDEM1 even in the absence of its intact mannosidase-like domain, but not when the ID region was deleted. In contrast, calnexin and SEL 1L associated with the deletion mutant. Our data suggest that the ID region identified in the N-terminal end of EDEM1 is involved in the binding of glycosylated and non-glycosylated misfolded proteins. Accelerating tyrosinase degradation by EDEM1 overexpression may lead to an efficient antigen presentation and enhanced elimination of melanoma cells. FAU - Marin, Marioara B AU - Marin MB AD - Department of Molecular Cell Biology, Institute of Biochemistry of Romanian Academy, Bucharest, Romania. FAU - Ghenea, Simona AU - Ghenea S FAU - Spiridon, Laurentiu N AU - Spiridon LN FAU - Chiritoiu, Gabriela N AU - Chiritoiu GN FAU - Petrescu, Andrei-Jose AU - Petrescu AJ FAU - Petrescu, Stefana-Maria AU - Petrescu SM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120808 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Antibodies) RN - 0 (EDEM1 protein, human) RN - 0 (Membrane Proteins) RN - 0 (Polysaccharides) RN - EC 1.14.18.1 (Monophenol Monooxygenase) SB - IM MH - Amino Acid Sequence MH - Antibodies/chemistry MH - Crystallography, X-Ray/methods MH - Endoplasmic Reticulum/metabolism MH - Glycosylation MH - HEK293 Cells MH - Humans MH - Melanoma/metabolism MH - Membrane Proteins/*chemistry/*physiology MH - Molecular Sequence Data MH - Monophenol Monooxygenase/genetics/*metabolism MH - Mutation MH - Polysaccharides/chemistry MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/metabolism MH - Sequence Homology, Amino Acid PMC - PMC3414498 OID - NLM: PMC3414498 EDAT- 2012/08/21 06:00 MHDA- 2013/02/12 06:00 CRDT- 2012/08/21 06:00 PHST- 2012/03/26 [received] PHST- 2012/07/16 [accepted] PHST- 2012/08/08 [epublish] AID - 10.1371/journal.pone.0042998 [doi] AID - PONE-D-12-08923 [pii] PST - ppublish SO - PLoS One. 2012;7(8):e42998. doi: 10.1371/journal.pone.0042998. Epub 2012 Aug 8. PMID- 21992216 OWN - NLM STAT- MEDLINE DA - 20111108 DCOM- 20120103 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 50 IP - 45 DP - 2011 Nov 15 TI - The inactivating factor of glutamine synthetase IF17 is an intrinsically disordered protein, which folds upon binding to its target. PG - 9767-78 LID - 10.1021/bi2009272 [doi] AB - In cyanobacteria, ammonium is incorporated into carbon skeletons by the sequential action of glutamine synthetase and glutamate synthase (GOGAT). The activity of Synechocystis sp. PCC 6803 glutamine synthetase type I (GS) is controlled by a post-transcriptional process involving protein-protein interactions with two inactivating factors: the 65-residue-long protein (IF7) and the 149-residue-long one (IF17). The sequence of the C terminus of IF17 is similar to IF7; IF7 is an intrinsically disordered protein (IDP). In this work, we study the structural propensities and affinity for GS of IF17 and a chimera protein, IF17N/IF7 (constructed by fusing the first 82 residues of IF17 with the whole IF7) by fluorescence, CD, and NMR. IF17 and IF17N/IF7 are IDPs with residual non-hydrogen-bonded structure, probably formed by alpha-helical, turn-like, and PPII conformations; several theoretical predictions support these experimental findings. IF17 seems to fold upon binding to GS, as suggested by CD thermal denaturations and steady-state far-UV spectra. The apparent affinity of IF17 for GS, as measured by fluorescence, is slightly smaller (K(D) ~1 muM) than that measured for IF7 (~0.3 muM). The K(D)s determined by CD are similar to those measured by fluorescence, but slightly larger, suggesting possible conformational rearrangements in the IFs and/or GS upon binding. Further, the results with IFN17/IF7 suggest that (i) binding of IF17 to the GS is modulated not only by its C-terminal region but also by its N-terminus and (ii) there are weakly structured (that is, "fuzzy") complexes in the ternary GS-IF system. FAU - Saelices, Lorena AU - Saelices L AD - Instituto de Bioquimica Vegetal y Fotosintesis, CSIC- Universidad de Sevilla, Seville, Spain. FAU - Galmozzi, Carla V AU - Galmozzi CV FAU - Florencio, Francisco J AU - Florencio FJ FAU - Muro-Pastor, M Isabel AU - Muro-Pastor MI FAU - Neira, Jose L AU - Neira JL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111024 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (IF17 protein, Synechocystis sp.) RN - 0 (IF7 protein, Synechocystis sp.) RN - 0 (Recombinant Proteins) RN - EC 6.3.1.2 (Glutamate-Ammonia Ligase) SB - IM MH - Bacterial Proteins/*chemistry/genetics/*metabolism MH - Circular Dichroism MH - Glutamate-Ammonia Ligase/*antagonists & inhibitors/chemistry/genetics MH - Kinetics MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Protein Denaturation MH - Protein Interaction Domains and Motifs MH - Protein Processing, Post-Translational MH - Protein Stability MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Spectrometry, Fluorescence MH - Synechocystis/genetics/*metabolism EDAT- 2011/10/14 06:00 MHDA- 2012/01/04 06:00 CRDT- 2011/10/14 06:00 PHST- 2011/10/24 [aheadofprint] AID - 10.1021/bi2009272 [doi] PST - ppublish SO - Biochemistry. 2011 Nov 15;50(45):9767-78. doi: 10.1021/bi2009272. Epub 2011 Oct 24. PMID- 20718036 OWN - NLM STAT- MEDLINE DA - 20101027 DCOM- 20110224 LR - 20141120 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 19 IP - 11 DP - 2010 Nov TI - The intermembrane space domain of Tim23 is intrinsically disordered with a distinct binding region for presequences. PG - 2045-54 LID - 10.1002/pro.482 [doi] AB - Proteins targeted to the mitochondrial matrix are translocated through the outer and the inner mitochondrial membranes by two protein complexes, the translocase of the outer membrane (TOM) and one of the translocases of the inner membrane (TIM23). The protein Tim23, the core component of TIM23, consists of an N-terminal, soluble domain in the intermembrane space (IMS) and a C-terminal domain that forms the import pore across the inner membrane. Before translocation proceeds, precursor proteins are recognized by the N-terminal domain of Tim23, Tim23N (residues 1-96). By using NMR spectroscopy, we show that Tim23N is a monomeric protein belonging to the family of intrinsically disordered proteins. Titrations of Tim23N with two presequences revealed a distinct binding region of Tim23N formed by residues 71-84. In a charge-hydropathy plot containing all soluble domains of TOM and TIM23, Tim23N was found to be the only domain with more than 40 residues in the IMS that is predicted to be intrinsically disordered, suggesting that Tim23N might function as hub in the mitochondrial import machinery protein network. FAU - de la Cruz, Laura AU - de la Cruz L AD - Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany. FAU - Bajaj, Rakhi AU - Bajaj R FAU - Becker, Stefan AU - Becker S FAU - Zweckstetter, Markus AU - Zweckstetter M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Membrane Transport Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (TIM23 protein, S cerevisiae) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Membrane Transport Proteins/*chemistry/genetics/metabolism MH - Models, Molecular MH - Molecular Sequence Annotation MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Tertiary MH - Protein Transport MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism PMC - PMC3005777 OID - NLM: PMC3005777 EDAT- 2010/08/19 06:00 MHDA- 2011/02/25 06:00 CRDT- 2010/08/19 06:00 AID - 10.1002/pro.482 [doi] PST - ppublish SO - Protein Sci. 2010 Nov;19(11):2045-54. doi: 10.1002/pro.482. PMID- 21726811 OWN - NLM STAT- MEDLINE DA - 20110705 DCOM- 20110912 LR - 20141022 IS - 1097-4164 (Electronic) IS - 1097-2765 (Linking) VI - 43 IP - 1 DP - 2011 Jul 8 TI - Opposing effects of glutamine and asparagine govern prion formation by intrinsically disordered proteins. PG - 72-84 LID - 10.1016/j.molcel.2011.05.013 [doi] AB - Sequences rich in glutamine (Q) and asparagine (N) residues often fail to fold at the monomer level. This, coupled to their unusual hydrogen-bonding abilities, provides the driving force to switch between disordered monomers and amyloids. Such transitions govern processes as diverse as human protein-folding diseases, bacterial biofilm assembly, and the inheritance of yeast prions (protein-based genetic elements). A systematic survey of prion-forming domains suggested that Q and N residues have distinct effects on amyloid formation. Here, we use cell biological, biochemical, and computational techniques to compare Q/N-rich protein variants, replacing Ns with Qs and Qs with Ns. We find that the two residues have strong and opposing effects: N richness promotes assembly of benign self-templating amyloids; Q richness promotes formation of toxic nonamyloid conformers. Molecular simulations focusing on intrinsic folding differences between Qs and Ns suggest that their different behaviors are due to the enhanced turn-forming propensity of Ns over Qs. CI - Copyright (c) 2011 Elsevier Inc. All rights reserved. FAU - Halfmann, Randal AU - Halfmann R AD - Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA. FAU - Alberti, Simon AU - Alberti S FAU - Krishnan, Rajaraman AU - Krishnan R FAU - Lyle, Nicholas AU - Lyle N FAU - O'Donnell, Charles W AU - O'Donnell CW FAU - King, Oliver D AU - King OD FAU - Berger, Bonnie AU - Berger B FAU - Pappu, Rohit V AU - Pappu RV FAU - Lindquist, Susan AU - Lindquist S LA - eng GR - GM025874/GM/NIGMS NIH HHS/United States GR - NS056114/NS/NINDS NIH HHS/United States GR - R01 GM025874/GM/NIGMS NIH HHS/United States GR - R01 GM025874-31/GM/NIGMS NIH HHS/United States GR - R01 NS056114/NS/NINDS NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Amyloid) RN - 0 (Peptide Termination Factors) RN - 0 (Prions) RN - 0 (SUP35 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0RH81L854J (Glutamine) RN - 7006-34-0 (Asparagine) SB - IM MH - Amino Acid Sequence MH - Amyloid/chemistry/metabolism MH - Asparagine/*chemistry/metabolism/physiology MH - Glutamine/*chemistry/metabolism/physiology MH - Molecular Sequence Data MH - Peptide Termination Factors/*chemistry/metabolism/physiology MH - Prions/*chemistry/metabolism/physiology MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/metabolism/physiology MH - Sequence Analysis, Protein PMC - PMC3132398 MID - NIHMS300892 OID - NLM: NIHMS300892 OID - NLM: PMC3132398 EDAT- 2011/07/06 06:00 MHDA- 2011/09/13 06:00 CRDT- 2011/07/06 06:00 PHST- 2010/11/22 [received] PHST- 2011/03/21 [revised] PHST- 2011/04/29 [accepted] AID - S1097-2765(11)00380-7 [pii] AID - 10.1016/j.molcel.2011.05.013 [doi] PST - ppublish SO - Mol Cell. 2011 Jul 8;43(1):72-84. doi: 10.1016/j.molcel.2011.05.013. PMID- 9425125 OWN - NLM STAT- MEDLINE DA - 19980220 DCOM- 19980220 LR - 20140617 IS - 0264-6021 (Print) IS - 0264-6021 (Linking) VI - 329 ( Pt 2) DP - 1998 Jan 15 TI - Structural and functional properties of the N transcriptional activation domain of thyroid transcription factor-1: similarities with the acidic activation domains. PG - 395-403 AB - The thyroid transcription factor 1 (TTF-1) is a tissue-specific transcription factor involved in the development of thyroid and lung. TTF-1 contains two transcriptional activation domains (N and C domain). The primary amino acid sequence of the N domain does not show any typical characteristic of known transcriptional activation domains. In aqueous solution the N domain exists in a random-coil conformation. The increase of the milieu hydrophobicity, by the addition of trifluoroethanol, induces a considerable gain of alpha-helical structure. Acidic transcriptional activation domains are largely unstructured in solution, but, under hydrophobic conditions, folding into alpha-helices or beta-strands can be induced. Therefore our data indicate that the inducibility of alpha-helix by hydrophobic conditions is a property not restricted to acidic domains. Co-transfections experiments indicate that the acidic domain of herpes simplex virus protein VP16 (VP16) and the TTF-1 N domain are interchangeable and that a chimaeric protein, which combines VP16 linked to the DNA-binding domain of TTF-1, undergoes the same regulatory constraints that operate for the wild-type TTF-1. In addition, we demonstrate that the TTF-1 N domain possesses two typical properties of acidic activation domains: TBP (TATA-binding protein) binding and ability to activate transcription in yeast. Accordingly, the TTF-1 N domain is able to squelch the activity of the p65 acidic domain. Altogether, these structural and functional data suggest that a non-acidic transcriptional activation domain (TTF-1 N domain) activates transcription by using molecular mechanisms similar to those used by acidic domains. TTF-1 N domain and acidic domains define a family of proteins whose common property is to activate transcription through the use of mechanisms largely conserved during evolutionary development. FAU - Tell, G AU - Tell G AD - Dipartimento di Scienze e Tecnologie Biomediche, Universita degli Studi di Udine, Via Gervasutta 48, 33100 Udine, Italy. FAU - Perrone, L AU - Perrone L FAU - Fabbro, D AU - Fabbro D FAU - Pellizzari, L AU - Pellizzari L FAU - Pucillo, C AU - Pucillo C FAU - De Felice, M AU - De Felice M FAU - Acquaviva, R AU - Acquaviva R FAU - Formisano, S AU - Formisano S FAU - Damante, G AU - Damante G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (DNA-Binding Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Recombinant Proteins) RN - 0 (TATA-Box Binding Protein) RN - 0 (Transcription Factors) RN - 0 (thyroid nuclear factor 1) SB - IM MH - Amino Acid Sequence MH - Animals MH - Circular Dichroism MH - DNA-Binding Proteins/metabolism MH - HeLa Cells MH - Humans MH - Hydrogen-Ion Concentration MH - Hydrolysis MH - Molecular Sequence Data MH - Nuclear Proteins/*chemistry/genetics/metabolism MH - Protein Binding MH - Protein Conformation MH - Rats MH - Recombinant Proteins/metabolism MH - Saccharomyces cerevisiae/genetics MH - Spectrophotometry, Ultraviolet MH - TATA-Box Binding Protein MH - Transcription Factors/*chemistry/genetics/metabolism MH - *Transcriptional Activation PMC - PMC1219057 OID - NLM: PMC1219057 EDAT- 1998/02/28 MHDA- 1998/02/28 00:01 CRDT- 1998/02/28 00:00 PST - ppublish SO - Biochem J. 1998 Jan 15;329 ( Pt 2):395-403. PMID- 18419123 OWN - NLM STAT- MEDLINE DA - 20080516 DCOM- 20080718 LR - 20140905 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 130 IP - 20 DP - 2008 May 21 TI - Differential dynamical effects of macromolecular crowding on an intrinsically disordered protein and a globular protein: implications for in-cell NMR spectroscopy. PG - 6310-1 LID - 10.1021/ja801020z [doi] AB - In-cell NMR provides a valuable means to assess how macromolecules, with concentrations up to 300 g/L in the cytoplasm, affect the structure and dynamics of proteins at atomic resolution. Here an intrinsically disordered protein, alpha-synuclein (alphaSN), and a globular protein, chymotrypsin inhibitor 2 (CI2) were examined by using in-cell NMR. High-resolution in-cell spectra of alphaSN can be obtained, but CI2 leaks from the cell and the remaining intracellular CI2 is not detectable. Even after stabilizing the cells from leakage by using alginate encapsulation, no CI2 signal is detected. From in vitro studies we conclude that this difference in detectability is the result of the differential dynamical response of disordered and ordered proteins to the changes of motion caused by the increased viscosity in cells. FAU - Li, Conggang AU - Li C AD - Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA. FAU - Charlton, Lisa M AU - Charlton LM FAU - Lakkavaram, Asha AU - Lakkavaram A FAU - Seagle, Christopher AU - Seagle C FAU - Wang, Guifang AU - Wang G FAU - Young, Gregory B AU - Young GB FAU - Macdonald, Jeffrey M AU - Macdonald JM FAU - Pielak, Gary J AU - Pielak GJ LA - eng GR - DP1 OD000783/OD/NIH HHS/United States GR - DP1 OD000783-01/OD/NIH HHS/United States GR - DP1 OD000783-02/OD/NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20080418 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Peptides) RN - 0 (Plant Proteins) RN - 0 (alpha-Synuclein) RN - 0 (chymotrypsin inhibitor 2) RN - 9003-39-8 (Povidone) SB - IM MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Peptides/*chemistry MH - Plant Proteins/*chemistry MH - Povidone/*chemistry MH - Viscosity MH - alpha-Synuclein/*chemistry PMC - PMC2435198 MID - NIHMS52633 OID - NLM: NIHMS52633 OID - NLM: PMC2435198 EDAT- 2008/04/19 09:00 MHDA- 2008/07/19 09:00 CRDT- 2008/04/19 09:00 PHST- 2008/04/18 [aheadofprint] AID - 10.1021/ja801020z [doi] PST - ppublish SO - J Am Chem Soc. 2008 May 21;130(20):6310-1. doi: 10.1021/ja801020z. Epub 2008 Apr 18. PMID- 24018100 OWN - NLM STAT- MEDLINE DA - 20131104 DCOM- 20140617 IS - 1096-0856 (Electronic) IS - 1090-7807 (Linking) VI - 236 DP - 2013 Nov TI - A new strategy for sequential assignment of intrinsically unstructured proteins based on 15N single isotope labelling. PG - 1-6 LID - 10.1016/j.jmr.2013.07.007 [doi] LID - S1090-7807(13)00176-6 [pii] AB - We describe a new efficient strategy for the sequential assignment of amide resonances of a conventional (15)N-(1)H HSQC spectrum of intrinsically unfolded proteins, based on composite NOESY-TOCSY and TOCSY-NOESY mixing times. These composite mixing times lead to a Halpha-proton mediated unidirectional transfer of amide to amide proton. We have implemented the composite mixing times in an HSQC-NOESY-HSQC manner to obtain directional connectivity between amides of neighbouring residues. We experimentally determine the optimal mixing times for both transfer schemes, and demonstrate its use in the assignment for both a fragment of the neuronal tau protein and for alpha-synuclein. CI - Copyright (c) 2013 Elsevier Inc. All rights reserved. FAU - Lopez, Juan AU - Lopez J AD - CNRS UMR 8576, Unite de Glycobiologie Structurale et Fonctionnelle, Universite des Sciences et Technologies de Lille 1, 59655 Villeneuve d'Ascq Cedex, France. FAU - Ahuja, Puneet AU - Ahuja P FAU - Gerard, Melanie AU - Gerard M FAU - Wieruszeski, Jean-Michel AU - Wieruszeski JM FAU - Lippens, Guy AU - Lippens G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130723 PL - United States TA - J Magn Reson JT - Journal of magnetic resonance (San Diego, Calif. : 1997) JID - 9707935 RN - 0 (Amides) RN - 0 (Nitrogen Isotopes) RN - 0 (Proteins) RN - 0 (Protons) RN - 0 (alpha-Synuclein) RN - 7440-44-0 (Carbon) SB - IM MH - Amides/chemistry MH - Carbon/chemistry MH - Electromagnetic Fields MH - Escherichia coli/chemistry/metabolism MH - Isotope Labeling/*methods MH - Magnetic Resonance Spectroscopy MH - Nitrogen Isotopes MH - Protein Conformation MH - Proteins/*chemistry MH - Protons MH - alpha-Synuclein/chemistry OTO - NOTNLM OT - Assignment OT - Intrinsically unstructured protein OT - NOESY OT - TOCSY EDAT- 2013/09/11 06:00 MHDA- 2014/06/18 06:00 CRDT- 2013/09/11 06:00 PHST- 2013/05/23 [received] PHST- 2013/07/08 [revised] PHST- 2013/07/09 [accepted] PHST- 2013/07/23 [aheadofprint] AID - S1090-7807(13)00176-6 [pii] AID - 10.1016/j.jmr.2013.07.007 [doi] PST - ppublish SO - J Magn Reson. 2013 Nov;236:1-6. doi: 10.1016/j.jmr.2013.07.007. Epub 2013 Jul 23. PMID- 15366930 OWN - NLM STAT- MEDLINE DA - 20040915 DCOM- 20041019 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 35 DP - 2004 Sep 7 TI - Characterization of a small metal binding protein from Nitrosomonas europaea. PG - 11206-13 AB - A small metal-binding protein (SmbP) with no known similarity to other proteins in current databases was isolated and characterized from the periplasm of Nitrosomonas europaea. The primary structure of this small (9.9 kDa) monomeric protein is characterized by a series of 10 repeats of a seven amino acid motif and an unusually high number of histidine residues. The protein was isolated from N. europaea with Cu(II) bound but was found to be capable of binding multiple equivalents of a variety of divalent and trivalent metals. The protein was overexpressed in Escherichia coli and used for the study of its metal-binding properties by UV/vis, circular dichroism (CD), and electron paramagnetic resonance (EPR) spectroscopy and equilibrium dialysis and isothermal titration calorimetry. The protein was found to bind up to six Cu(II) atoms with dissociation constants of approximately 0.1 microM for the first two metal ions and approximately 10 microM for the next four. Binding of Cu(II) resulted in spectroscopic features illustrating two distinctive geometries, as determined by EPR spectroscopy. The levels of SmbP in the periplasm were found to increase by increasing the levels of copper in the growth media. This protein is proposed to have a role in cellular copper management in the ammonia-oxidizing bacterium N. europaea. FAU - Barney, Brett M AU - Barney BM AD - Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA. FAU - LoBrutto, Russell AU - LoBrutto R FAU - Francisco, Wilson A AU - Francisco WA LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (Cations, Divalent) RN - 0 (Metalloproteins) RN - 0 (Periplasmic Binding Proteins) RN - 789U1901C5 (Copper) SB - IM MH - Amino Acid Sequence MH - *Bacterial Adhesion MH - Bacterial Proteins/*chemistry/isolation & purification/metabolism MH - Binding Sites MH - Cations, Divalent/metabolism MH - Circular Dichroism MH - Copper/chemistry/*metabolism MH - Electron Spin Resonance Spectroscopy MH - Metalloproteins/*chemistry/isolation & purification/metabolism MH - Molecular Sequence Data MH - Molecular Weight MH - Nitrosomonas europaea/*chemistry/metabolism MH - Periplasmic Binding Proteins/*chemistry/isolation & purification/metabolism MH - Protein Structure, Secondary MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization EDAT- 2004/09/16 05:00 MHDA- 2004/10/20 09:00 CRDT- 2004/09/16 05:00 AID - 10.1021/bi049318k [doi] PST - ppublish SO - Biochemistry. 2004 Sep 7;43(35):11206-13. PMID- 15890201 OWN - NLM STAT- MEDLINE DA - 20050513 DCOM- 20050621 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 349 IP - 2 DP - 2005 Jun 3 TI - Myomesin is a molecular spring with adaptable elasticity. PG - 367-79 AB - The M-band is a transverse structure in the center of the sarcomere, which is thought to stabilize the thick filament lattice. It was shown recently that the constitutive vertebrate M-band component myomesin can form antiparallel dimers, which might cross-link the neighboring thick filaments. Myomesin consists mainly of immunoglobulin-like (Ig) and fibronectin type III (Fn) domains, while several muscle types express the EH-myomesin splice isoform, generated by the inclusion of the unique EH-segment of about 100 amino acid residues (aa) in the center of the molecule. Here we use atomic force microscopy (AFM), transmission electron microscopy (TEM) and circular dichroism (CD) spectroscopy for the biophysical characterization of myomesin. The AFM identifies the "mechanical fingerprints" of the modules constituting the myomesin molecule. Stretching of homomeric polyproteins, constructed of Ig and Fn domains of human myomesin, produces a typical saw-tooth pattern in the force-extension curve. The domains readily refold after relaxation. In contrast, stretching of a heterogeneous polyprotein, containing several repeats of the My6-EH fragment reveals a long initial plateau corresponding to the sum of EH-segment contour lengths, followed by several My6 unfolding peaks. According to this, the EH-segment is characterized as an entropic chain with a persistence length of about 0.3nm. In TEM pictures, the EH-domain appears as a gap in the molecule, indicating a random coil conformation similar to the PEVK region of titin. CD spectroscopy measurements support this result, demonstrating a mostly non-folded conformation for the EH-segment. We suggest that similarly to titin, myomesin is a molecular spring, whose elasticity is modulated by alternative splicing. The Ig and Fn domains might function as reversible "shock absorbers" by sequential unfolding in the case of extremely high or long sustained stretching forces. These complex visco-elastic properties of myomesin might be crucial for the stability of the sarcomere. FAU - Schoenauer, Roman AU - Schoenauer R AD - Institute of Cell Biology, ETH Zurich-Honggerberg, CH-8093 Zurich, Switzerland. FAU - Bertoncini, Patricia AU - Bertoncini P FAU - Machaidze, Gia AU - Machaidze G FAU - Aebi, Ueli AU - Aebi U FAU - Perriard, Jean-Claude AU - Perriard JC FAU - Hegner, Martin AU - Hegner M FAU - Agarkova, Irina AU - Agarkova I LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050407 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Connectin) RN - 0 (Fibronectins) RN - 0 (Muscle Proteins) RN - 0 (Recombinant Proteins) SB - IM MH - Circular Dichroism MH - Connectin MH - Elasticity MH - Fibronectins/chemistry MH - Humans MH - Microscopy, Atomic Force MH - Microscopy, Electron, Transmission MH - Muscle Proteins/chemistry/*metabolism/ultrastructure MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism/ultrastructure EDAT- 2005/05/14 09:00 MHDA- 2005/06/23 09:00 CRDT- 2005/05/14 09:00 PHST- 2005/01/31 [received] PHST- 2005/03/11 [revised] PHST- 2005/03/21 [accepted] PHST- 2005/04/07 [aheadofprint] AID - S0022-2836(05)00345-1 [pii] AID - 10.1016/j.jmb.2005.03.055 [doi] PST - ppublish SO - J Mol Biol. 2005 Jun 3;349(2):367-79. Epub 2005 Apr 7. PMID- 24266766 OWN - NLM STAT- MEDLINE DA - 20140120 DCOM- 20140414 IS - 1470-8728 (Electronic) IS - 0264-6021 (Linking) VI - 458 IP - 1 DP - 2014 Feb 15 TI - Phosphorylation of bacterial-type phosphoenolpyruvate carboxylase by a Ca2+-dependent protein kinase suggests a link between Ca2+ signalling and anaplerotic pathway control in developing castor oil seeds. PG - 109-18 LID - 10.1042/BJ20131191 [doi] AB - The aim of the present study was to characterize the native protein kinase [BTPC (bacterial-type phosphoenolpyruvate carboxylase)-K (BTPC Ser451 kinase)] that in vivo phosphorylates Ser451 of the BTPC subunits of an unusual Class-2 PEP (phosphoenolpyruvate) carboxylase hetero-octameric complex of developing COS (castor oil seeds). COS BTPC-K was highly purified by PEG fractionation and hydrophobic size-exclusion anion-exchange and affinity chromatographies. BTPC-K phosphorylated BTPC strictly at Ser451 (Km=1.0 muM; pH optimum=7.3), a conserved target residue occurring within an intrinsically disordered region, as well as the protein histone III-S (Km=1.7 muM), but not a COS plant-type PEP carboxylase or sucrose synthase or alpha-casein. Its activity was Ca2+- (K0.5=2.7 muM) and ATP- (Km=6.6 muM) dependent, and markedly inhibited by trifluoperazine, 3-phosphoglycerate and PEP, but insensitive to calmodulin or 14-3-3 proteins. BTPC-K exhibited a native molecular mass of ~63 kDa and was soluble rather than membrane-bound. Inactivation and reactivation occurred upon BTPC-K's incubation with GSSG and then DTT respectively. Ser451 phosphorylation by BTPC-K inhibited BTPC activity by ~50% when assayed under suboptimal conditions (pH 7.3, 1 mM PEP and 10 mM L-malate). Our collective results indicate a possible link between cytosolic Ca2+ signalling and anaplerotic flux control in developing COS. FAU - Hill, Allyson T AU - Hill AT AD - *Department of Biology, Queen's University, Kingston, ON, Canada, K7L 3N6. FAU - Ying, Sheng AU - Ying S AD - *Department of Biology, Queen's University, Kingston, ON, Canada, K7L 3N6. FAU - Plaxton, William C AU - Plaxton WC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 8001-79-4 (Castor Oil) RN - EC 2.7.- (Protein Kinases) RN - EC 4.1.1.31 (Phosphoenolpyruvate Carboxylase) RN - SY7Q814VUP (Calcium) SB - IM MH - Bacteria/*enzymology MH - Calcium/*metabolism MH - *Calcium Signaling MH - Castor Oil/*metabolism MH - Phosphoenolpyruvate Carboxylase/*metabolism MH - Phosphorylation MH - Protein Kinases/*metabolism MH - Seeds/*metabolism EDAT- 2013/11/26 06:00 MHDA- 2014/04/15 06:00 CRDT- 2013/11/26 06:00 AID - BJ20131191 [pii] AID - 10.1042/BJ20131191 [doi] PST - ppublish SO - Biochem J. 2014 Feb 15;458(1):109-18. doi: 10.1042/BJ20131191. PMID- 21627111 OWN - NLM STAT- MEDLINE DA - 20110707 DCOM- 20111101 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 133 IP - 27 DP - 2011 Jul 13 TI - A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations. PG - 10448-58 LID - 10.1021/ja110338e [doi] AB - The N-terminal repressor domain of neural restrictive silencer factor (NRSF) is an intrinsically disordered protein (IDP) that binds to the paired amphipathic helix (PAH) domain of mSin3. An NMR experiment revealed that the minimal binding unit of NRSF is a 15-residue segment that adopts a helical structure upon binding to a cleft of mSin3. We computed a free-energy landscape of this system by an enhanced conformational sampling method, all-atom multicanonical molecular dynamics. The simulation started from a configuration where the NRSF segment was fully disordered and distant from mSin3 in explicit solvent. In the absence of mSin3, the disordered NRSF segment thermally fluctuated between hairpins, helices, and bent structures. In the presence of mSin3, the segment bound to mSin3 by adopting the structures involved in the isolated state, and non-native and native complexes were formed. The free-energy landscape comprised three superclusters, and free-energy barriers separated the superclusters. The native complex was located at the center of the lowest free-energy cluster. When NRSF landed in the largest supercluster, the generated non-native complex moved on the landscape to fold into the native complex, by increasing the interfacial hydrophobic contacts and the helix content. When NRSF landed in other superclusters, the non-native complex overcame the free-energy barriers between the various segment orientations in the binding cleft of mSin3. Both population-shift and induced-fit (or induced-folding) mechanisms work cooperatively in the coupled folding and binding. The diverse structural adaptability of NRSF may be related to the hub properties of the IDP. FAU - Higo, Junichi AU - Higo J AD - Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan. higo@protein.osaka-u.ac.jp FAU - Nishimura, Yoshifumi AU - Nishimura Y FAU - Nakamura, Haruki AU - Nakamura H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110616 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (RE1-silencing transcription factor) RN - 0 (Repressor Proteins) RN - 0 (Solvents) SB - IM MH - *Computer Simulation MH - *Entropy MH - *Models, Chemical MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Repressor Proteins/*chemistry MH - Solvents EDAT- 2011/06/02 06:00 MHDA- 2011/11/02 06:00 CRDT- 2011/06/02 06:00 PHST- 2011/06/16 [aheadofprint] AID - 10.1021/ja110338e [doi] PST - ppublish SO - J Am Chem Soc. 2011 Jul 13;133(27):10448-58. doi: 10.1021/ja110338e. Epub 2011 Jun 16. PMID- 23962724 OWN - NLM STAT- MEDLINE DA - 20131211 DCOM- 20140804 LR - 20150113 IS - 1460-2083 (Electronic) IS - 0964-6906 (Linking) VI - 23 IP - 1 DP - 2014 Jan 1 TI - Prion-like nuclear aggregation of TDP-43 during heat shock is regulated by HSP40/70 chaperones. PG - 157-70 LID - 10.1093/hmg/ddt408 [doi] AB - TDP-43 aggregation in the cytoplasm or nucleus is a key feature of the pathology of amyotrophic lateral sclerosis and frontotemporal dementia and is observed in numerous other neurodegenerative diseases, including Alzheimer's disease. Despite this fact, the inciting events leading to TDP-43 aggregation remain unclear. We observed that endogenous TDP-43 undergoes reversible aggregation in the nucleus after the heat shock and that this behavior is mediated by the C-terminal prion domain. Substitution of the prion domain from TIA-1 or an authentic yeast prion domain from RNQ1 into TDP-43 can completely recapitulate heat shock-induced aggregation. TDP-43 is constitutively bound to members of the Hsp40/Hsp70 family, and we found that heat shock-induced TDP-43 aggregation is mediated by the availability of these chaperones interacting with the inherently disordered C-terminal prion domain. Finally, we observed that the aggregation of TDP-43 during heat shock led to decreased binding to hnRNPA1, and a change in TDP-43 RNA-binding partners suggesting that TDP-43 aggregation alters its function in response to misfolded protein stress. These findings indicate that TDP-43 shares properties with physiologic prions from yeast, in that self-aggregation is mediated by a Q/N-rich disordered domain, is modulated by chaperone proteins and leads to altered function of the protein. Furthermore, they indicate that TDP-43 aggregation is regulated by chaperone availability, explaining the recurrent observation of TDP-43 aggregates in degenerative diseases of both the brain and muscle where protein homeostasis is disrupted. FAU - Udan-Johns, Maria AU - Udan-Johns M AD - Department of Neurology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO 63110, USA. FAU - Bengoechea, Rocio AU - Bengoechea R FAU - Bell, Shaughn AU - Bell S FAU - Shao, Jieya AU - Shao J FAU - Diamond, Marc I AU - Diamond MI FAU - True, Heather L AU - True HL FAU - Weihl, Conrad C AU - Weihl CC FAU - Baloh, Robert H AU - Baloh RH LA - eng GR - AG031867/AG/NIA NIH HHS/United States GR - AG042095/AG/NIA NIH HHS/United States GR - NS055980/NS/NINDS NIH HHS/United States GR - NS057105/NS/NINDS NIH HHS/United States GR - NS069669/NS/NINDS NIH HHS/United States GR - R01 NS069669/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130819 PL - England TA - Hum Mol Genet JT - Human molecular genetics JID - 9208958 RN - 0 (DNA-Binding Proteins) RN - 0 (HSP40 Heat-Shock Proteins) RN - 0 (HSP70 Heat-Shock Proteins) RN - 0 (Heterogeneous-Nuclear Ribonucleoprotein Group A-B) RN - 0 (Prions) RN - 0 (hnRNP A1) RN - 0 (protein TDP-43) SB - IM MH - Amino Acid Motifs MH - Animals MH - Brain/metabolism MH - COS Cells MH - Cell Nucleus/metabolism MH - Cercopithecus aethiops MH - Cytoplasm/metabolism MH - DNA-Binding Proteins/*chemistry/*metabolism MH - HEK293 Cells MH - HSP40 Heat-Shock Proteins/*physiology MH - HSP70 Heat-Shock Proteins/*physiology MH - HeLa Cells MH - Heat-Shock Response MH - Heterogeneous-Nuclear Ribonucleoprotein Group A-B/*metabolism MH - Humans MH - Muscles/metabolism MH - Prions/*chemistry/metabolism MH - Protein Folding PMC - PMC3857952 OID - NLM: PMC3857952 EDAT- 2013/08/22 06:00 MHDA- 2014/08/05 06:00 CRDT- 2013/08/22 06:00 PHST- 2013/08/19 [aheadofprint] PHST- 2013/09/04 [aheadofprint] AID - ddt408 [pii] AID - 10.1093/hmg/ddt408 [doi] PST - ppublish SO - Hum Mol Genet. 2014 Jan 1;23(1):157-70. doi: 10.1093/hmg/ddt408. Epub 2013 Aug 19. PMID- 25071818 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20140729 DCOM- 20140729 LR - 20140731 IS - 1664-8021 (Electronic) IS - 1664-8021 (Linking) VI - 5 DP - 2014 TI - Phosphorylation of unique domains of Src family kinases. PG - 181 LID - 10.3389/fgene.2014.00181 [doi] AB - Members of the Src family of kinases (SFKs) are non-receptor tyrosine kinases involved in numerous signal transduction pathways. The catalytic, SH3 and SH2 domains are attached to the membrane-anchoring SH4 domain through the intrinsically disordered "Unique" domains, which exhibit strong sequence divergence among SFK members. In the last decade, structural and biochemical studies have begun to uncover the crucial role of the Unique domain in the regulation of SFK activity. This mini-review discusses what is known about the phosphorylation events taking place on the SFK Unique domains, and their biological relevance. The modulation by phosphorylation of biologically relevant inter- and intra- molecular interactions of Src, as well as the existence of complex phosphorylation/dephosphorylation patterns observed for the Unique domain of Src, reinforces the important functional role of the Unique domain in the regulation mechanisms of the Src kinases and, in a wider context, of intrinsically disordered regions in cellular processes. FAU - Amata, Irene AU - Amata I AD - Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona Barcelona, Spain. FAU - Maffei, Mariano AU - Maffei M AD - Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona Barcelona, Spain. FAU - Pons, Miquel AU - Pons M AD - Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona Barcelona, Spain. LA - eng PT - Journal Article PT - Review DEP - 20140630 PL - Switzerland TA - Front Genet JT - Frontiers in genetics JID - 101560621 PMC - PMC4075076 OID - NLM: PMC4075076 OTO - NOTNLM OT - IDPs OT - IDRs OT - SFKs OT - Src OT - phosphorylation OT - unique domain EDAT- 2014/07/30 06:00 MHDA- 2014/07/30 06:01 CRDT- 2014/07/30 06:00 PHST- 2014 [ecollection] PHST- 2014/03/04 [received] PHST- 2014/05/29 [accepted] PHST- 2014/06/30 [epublish] AID - 10.3389/fgene.2014.00181 [doi] PST - epublish SO - Front Genet. 2014 Jun 30;5:181. doi: 10.3389/fgene.2014.00181. eCollection 2014. PMID- 23792173 OWN - NLM STAT- MEDLINE DA - 20130722 DCOM- 20140211 LR - 20150325 IS - 1872-8057 (Electronic) IS - 0303-7207 (Linking) VI - 376 IP - 1-2 DP - 2013 Aug 25 TI - Variable steroid receptor responses: Intrinsically disordered AF1 is the key. PG - 81-4 LID - 10.1016/j.mce.2013.06.007 [doi] LID - S0303-7207(13)00245-1 [pii] AB - Steroid hormones, acting through their cognate receptor proteins, see widespread clinical applications due to their ability to alter the induction or repression of numerous genes. However, steroid usage is limited by the current inability to control off-target, or non-specific, side-effects. Recent results from three separate areas of research with glucocorticoid and other steroid receptors (cofactor-induced changes in receptor structure, the ability of ligands to alter remote regions of receptor structure, and how cofactor concentration affects both ligand potency and efficacy) indicate that a key element of receptor activity is the intrinsically disordered amino-terminal domain. These results are combined to construct a novel framework within which to logically pursue various approaches that could afford increased selectivity in steroid-based therapies. CI - Published by Elsevier Ireland Ltd. FAU - Simons, S Stoney Jr AU - Simons SS Jr AD - Steroid Hormones Section, NIDDK/LERB, National Institutes of Health, Bethesda, MD, United States. stoneys@helix.nih.gov FAU - Kumar, Raj AU - Kumar R LA - eng GR - Z01 DK057800-17/Intramural NIH HHS/United States GR - ZIA DK047041-06/Intramural NIH HHS/United States GR - ZIA DK057800-21/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Review DEP - 20130617 PL - Ireland TA - Mol Cell Endocrinol JT - Molecular and cellular endocrinology JID - 7500844 RN - 0 (Hormones) RN - 0 (Ligands) RN - 0 (Receptors, Steroid) RN - 0 (Steroids) SB - IM MH - Hormones/chemistry/*metabolism/pharmacology MH - Humans MH - Ligands MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Receptors, Steroid/*chemistry/genetics/metabolism MH - Signal Transduction/drug effects MH - Steroids/chemistry/*metabolism/pharmacology MH - Transcriptional Activation/drug effects PMC - PMC3781172 MID - NIHMS501744 OID - NLM: NIHMS501744 OID - NLM: PMC3781172 OTO - NOTNLM OT - A(max) and EC(50) OT - AF1 domain as a molecular rheostat OT - Intrinsically disordered domains OT - Selective receptor modulators (SRMs) OT - Selectivity in controlling gene expression OT - Steroid receptors EDAT- 2013/06/26 06:00 MHDA- 2014/02/12 06:00 CRDT- 2013/06/25 06:00 PHST- 2013/04/25 [received] PHST- 2013/06/06 [revised] PHST- 2013/06/07 [accepted] PHST- 2013/06/17 [aheadofprint] AID - S0303-7207(13)00245-1 [pii] AID - 10.1016/j.mce.2013.06.007 [doi] PST - ppublish SO - Mol Cell Endocrinol. 2013 Aug 25;376(1-2):81-4. doi: 10.1016/j.mce.2013.06.007. Epub 2013 Jun 17. PMID- 25002472 OWN - NLM STAT- MEDLINE DA - 20140820 DCOM- 20141103 LR - 20150407 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 33 DP - 2014 Aug 19 TI - Prepaying the entropic cost for allosteric regulation in KIX. PG - 12067-72 LID - 10.1073/pnas.1405831111 [doi] AB - The kinase-inducible domain interacting (KIX) domain of the CREB binding protein (CBP) is capable of simultaneously binding two intrinsically disordered transcription factors, such as the mixed-lineage leukemia (MLL) and c-Myb peptides, at isolated interaction sites. In vitro, the affinity for binding c-Myb is approximately doubled when KIX is in complex with MLL, which suggests a positive cooperative binding mechanism, and the affinity for MLL is also slightly increased when KIX is first bound by c-Myb. Expanding the scope of recent NMR and computational studies, we explore the allosteric mechanism at a detailed molecular level that directly connects the microscopic structural dynamics to the macroscopic shift in binding affinities. To this end, we have performed molecular dynamics simulations of free KIX, KIX-c-Myb, MLL-KIX, and MLL-KIX-c-Myb using a topology-based Go-like model. Our results capture an increase in affinity for the peptide in the allosteric site when KIX is prebound by a complementary effector and both peptides follow an effector-independent folding-and-binding mechanism. More importantly, we discover that MLL binding lowers the entropic cost for c-Myb binding, and vice versa, by stabilizing the L12-G2 loop and the C-terminal region of the alpha3 helix on KIX. This work demonstrates the importance of entropy in allosteric signaling between promiscuous molecular recognition sites and can inform the rational design of small molecule stabilizers to target important regions of conformationally dynamic proteins. FAU - Law, Sean M AU - Law SM AD - Departments of Chemistry andBiophysics, and. FAU - Gagnon, Jessica K AU - Gagnon JK AD - Departments of Chemistry and. FAU - Mapp, Anna K AU - Mapp AK AD - Departments of Chemistry andLife Sciences Institute, University of Michigan, Ann Arbor, MI 48109. FAU - Brooks, Charles L 3rd AU - Brooks CL 3rd AD - Departments of Chemistry andBiophysics, and brookscl@umich.edu. LA - eng GR - GM037554/GM/NIGMS NIH HHS/United States GR - R01 GM037554/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140707 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Allosteric Regulation MH - CREB-Binding Protein/chemistry/*metabolism MH - Molecular Dynamics Simulation PMC - PMC4143015 OID - NLM: PMC4143015 OTO - NOTNLM OT - allostery OT - coupled folding and binding OT - intrinsically disordered proteins OT - kinetics OT - thermodynamics EDAT- 2014/07/09 06:00 MHDA- 2014/11/05 06:00 CRDT- 2014/07/09 06:00 PHST- 2014/07/07 [aheadofprint] AID - 1405831111 [pii] AID - 10.1073/pnas.1405831111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12067-72. doi: 10.1073/pnas.1405831111. Epub 2014 Jul 7. PMID- 9571026 OWN - NLM STAT- MEDLINE DA - 19980619 DCOM- 19980619 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 277 IP - 5 DP - 1998 Apr 17 TI - Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity. PG - 1111-28 AB - The designed G120R mutant of human growth hormone (hGH) is an antagonist and can bind only one molecule of the growth hormone receptor. We have determined the crystal structure of the 1:1 complex between this mutant and the receptor extracellular domain (hGHbp) at 2.6 A resolution, and used it to guide a detailed survey of the structural and functional basis for hormone-receptor recognition. The overall structure of the complex is very similar to the equivalent portion of the 1:2 complex, showing that formation of the active complex does not involve major conformational changes. However, a segment involved in receptor-receptor interactions in the 1:2 complex is disordered in this structure, suggesting that its productive conformation is stabilized by receptor dimerization. The hormone binding site of the receptor comprises a central hydrophobic patch dominated by Trp104 and Trp169, surrounded by a hydrophilic periphery containing several well-ordered water molecules. Previous alanine scanning showed that the hydrophobic "hot spot" confers most of the binding energy. The new structural data, coupled with binding and kinetic analysis of further mutants, indicate that the hot spot is assembled cooperatively and that many residues contribute indirectly to binding. Several hydrophobic residues serve to orient the key tryptophan residues; kinetic analysis suggests that Pro106 locks the Trp104 main-chain into a required conformation. The electrostatic contacts of Arg43 to hGH are less important than the intramolecular packing of its alkyl chain with Trp169. The true functional epitope that directly contributes binding energy may therefore comprise as few as six side-chains, participating mostly in alkyl-aromatic stacking interactions. Outside the functional epitope, multiple mutation of residues to alanine resulted in non-additive increases in affinity: up to tenfold for a hepta-alanine mutant. Contacts in the epitope periphery can therefore attenuate the affinity of the central hot spot, perhaps reflecting a role in conferring specificity to the interaction. CI - Copyright 1998 Academic Press Limited. FAU - Clackson, T AU - Clackson T AD - Department of Protein Engineering, Genentech, Inc., 460 Point San Bruno Blvd., South San Francisco, CA 94080, USA. FAU - Ultsch, M H AU - Ultsch MH FAU - Wells, J A AU - Wells JA FAU - de Vos, A M AU - de Vos AM LA - eng PT - Journal Article PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Epitopes) RN - 0 (Receptors, Somatotropin) RN - 12629-01-5 (Human Growth Hormone) RN - 8DUH1N11BX (Tryptophan) SB - IM MH - Binding Sites MH - Crystallography, X-Ray MH - Epitopes/chemistry MH - Human Growth Hormone/chemistry/*genetics MH - Humans MH - Kinetics MH - Models, Molecular MH - Mutation/genetics MH - Protein Binding/physiology MH - Protein Conformation MH - Receptors, Somatotropin/*chemistry MH - Tryptophan/chemistry EDAT- 1998/05/22 MHDA- 1998/05/22 00:01 CRDT- 1998/05/22 00:00 AID - S0022-2836(98)91669-2 [pii] AID - 10.1006/jmbi.1998.1669 [doi] PST - ppublish SO - J Mol Biol. 1998 Apr 17;277(5):1111-28. PMID- 2522624 OWN - NLM STAT- MEDLINE DA - 19890425 DCOM- 19890425 LR - 20041117 IS - 0755-4982 (Print) IS - 0755-4982 (Linking) VI - 18 IP - 7 DP - 1989 Feb 18 TI - [Biliary cysts or hepatic cysts]. PG - 322-4 FAU - Levy, V G AU - Levy VG AD - Service d'Hepato-Gastro-Enterologie A, Hopital Saint-Antoine. LA - fre PT - Journal Article TT - Kystes biliaires ou kystes hepatiques. PL - FRANCE TA - Presse Med JT - Presse medicale (Paris, France : 1983) JID - 8302490 SB - IM MH - Bile Duct Diseases/classification/*congenital MH - *Bile Ducts, Intrahepatic MH - Cysts/classification/*diagnosis/pathology MH - Dilatation, Pathologic/congenital MH - Humans MH - Liver Diseases/classification/*diagnosis/pathology EDAT- 1989/02/18 MHDA- 1989/02/18 00:01 CRDT- 1989/02/18 00:00 PST - ppublish SO - Presse Med. 1989 Feb 18;18(7):322-4. PMID- 19888685 OWN - NLM STAT- MEDLINE DA - 20091105 DCOM- 20100119 IS - 1874-270X (Electronic) VI - 3 IP - 2 DP - 2009 Dec TI - NMR assignment of the intrinsically disordered C-terminal region of Homo sapiens FCP1 in the unbound state. PG - 179-81 LID - 10.1007/s12104-009-9169-1 [doi] AB - The phosphorylation state of the RNA polymerase II C-terminal repeat domain (CTD) regulates progression through the mRNA biogenesis cycle. Termination of transcription and recycling of RNA polymerase II is promoted by an interaction between the general transcription factor IIF (TFIIF) and the TFIIF-associating CTD phosphatase (FCP1). The acidic C-terminal region of FCP1 is disordered in the free state, but adopts an alpha-helical conformation upon binding to the heavy chain of TFIIF. Here we report (1)H, (13)C, and (15)N resonance assignments for the intrinsically disordered unbound form of human C-terminal FCP1 (residues 879-961). The use of recently developed (13)C direct detected "protonless" NMR experiments allowed the nearly complete assignment of FCP1 reported here and is likely to be a generally effective strategy for the chemical shift assignment of disordered proteins. FAU - Showalter, Scott A AU - Showalter SA AD - Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA. sas76@psu.edu LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090619 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - EC 3.1.3.16 (carboxy-terminal domain phosphatase) SB - IM MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphoprotein Phosphatases/*chemistry/metabolism EDAT- 2009/11/06 06:00 MHDA- 2010/01/20 06:00 CRDT- 2009/11/06 06:00 PHST- 2009/05/18 [received] PHST- 2009/06/03 [accepted] PHST- 2009/06/19 [aheadofprint] AID - 10.1007/s12104-009-9169-1 [doi] PST - ppublish SO - Biomol NMR Assign. 2009 Dec;3(2):179-81. doi: 10.1007/s12104-009-9169-1. Epub 2009 Jun 19. PMID- 21035463 OWN - NLM STAT- MEDLINE DA - 20101221 DCOM- 20110118 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 405 IP - 1 DP - 2011 Jan 7 TI - Fab'-induced folding of antigenic N-terminal peptides from intrinsically disordered HIV-1 Tat revealed by X-ray crystallography. PG - 33-42 LID - 10.1016/j.jmb.2010.10.033 [doi] AB - Tat, the transcriptional activator protein of human immunodeficiency virus type 1 (HIV-1), is critical for viral replication and is a potential HIV-1 vaccine candidate. This intrinsically disordered protein is present in the extracellular medium and is involved in the pathogenicity of HIV through its interaction with different cellular and viral biological partners. A monoclonal antibody termed 11H6H1, which is specific for the N-terminal region of Tat, was selected for a functional and structural study of the HIV-1 Tat protein. The equilibrium dissociation constants (K(d)) of Tat and Tat fragments complexed with 11H6H1 were estimated by competitive ELISA. Tat contains a single tryptophan residue, Trp11, located in the N-terminal region. We show that the substitution of Trp11 by a phenylalanine completely abolishes the binding of 11H6H1, whereas the transactivating activity of Tat is preserved. The epitope recognized by 11H6H1 was restricted to the 9-mer peptide P(6)KLEPWKHP(14) centered on Trp11. The crystal structures of this 9-mer peptide and of an overlapping 15-mer peptide were determined in complex with Fab' 11H6H1 at 2.4 A and 2.1 A resolution, respectively. Tat is intrinsically disordered and can undergo induced folding upon association with a biological partner. Our crystallographic study reveals that the two Tat peptides, which are lodged in the U-shaped groove of the Fab' antigen-binding site, adopt a standard type I beta-turn conformation. The central Trp11 that is critical for Fab' recognition is further stabilized by pi-stacking interactions. The structural and biological consequences of this induced folding in HIV pathogenesis are discussed. CI - Copyright (c) 2010 Elsevier Ltd. All rights reserved. FAU - Serriere, Jennifer AU - Serriere J AD - Universite de Lyon, IFR128 BioSciences Gerland-Lyon Sud, 7 Passage du Vercors, France. FAU - Dugua, Jean-Marc AU - Dugua JM FAU - Bossus, Marc AU - Bossus M FAU - Verrier, Bernard AU - Verrier B FAU - Haser, Richard AU - Haser R FAU - Gouet, Patrice AU - Gouet P FAU - Guillon, Christophe AU - Guillon C LA - eng SI - PDB/3O6K SI - PDB/3O6L SI - PDB/3O6M PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20101028 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Antibodies, Monoclonal) RN - 0 (Antigens, Viral) RN - 0 (Epitopes) RN - 0 (HIV Antibodies) RN - 0 (Immunoglobulin Fab Fragments) RN - 0 (tat Gene Products, Human Immunodeficiency Virus) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution/genetics MH - Antibodies, Monoclonal/immunology/metabolism MH - Antigens, Viral/chemistry/immunology/metabolism MH - Crystallography, X-Ray MH - Enzyme-Linked Immunosorbent Assay MH - Epitope Mapping MH - Epitopes/immunology MH - HIV Antibodies/immunology/metabolism MH - HIV-1/*chemistry/*immunology MH - Immunoglobulin Fab Fragments/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Tertiary MH - tat Gene Products, Human Immunodeficiency Virus/*chemistry/immunology/*metabolism EDAT- 2010/11/03 06:00 MHDA- 2011/01/19 06:00 CRDT- 2010/11/02 06:00 PHST- 2010/09/09 [received] PHST- 2010/10/18 [revised] PHST- 2010/10/19 [accepted] PHST- 2010/10/28 [aheadofprint] AID - S0022-2836(10)01152-6 [pii] AID - 10.1016/j.jmb.2010.10.033 [doi] PST - ppublish SO - J Mol Biol. 2011 Jan 7;405(1):33-42. doi: 10.1016/j.jmb.2010.10.033. Epub 2010 Oct 28. PMID- 20184958 OWN - NLM STAT- MEDLINE DA - 20120305 DCOM- 20121108 IS - 1095-8657 (Electronic) IS - 1047-8477 (Linking) VI - 171 IP - 1 DP - 2010 Jul TI - Monoclonal antibody MN423 as a stable mold facilitates structure determination of disordered tau protein. PG - 74-81 LID - 10.1016/j.jsb.2010.02.016 [doi] AB - Flexibility of intrinsically disordered tau protein is important for performing its functions. It is believed that alteration of the flexibility is instrumental to the assembly of tau protein into paired helical filaments (PHF) in tauopathies. Tau flexibility represents the main obstacle for structure determination of its conformation in physiology and/or pathology. We have alleviated this inherited difficulty by using specific monoclonal antibodies as tau protein surrogate binding partners. In this work we compare two "antibody mold structures": (1) X-ray structure of the free form of the Alzheimer's disease PHF core-specific antibody MN423 and (2) previously solved structure of the complex of MN423 with the PHF core C-terminal tau peptide. We found that MN423 combining site is in both structures identical. As a consequence, recombinant tau assumes in the complex a fold determined by the antibody combining site. Obtained results show that MN423 functions as a molecular mold for the PHF core segment, and opens the way for structure determination of other PHF core segments providing that other conformation-specific antibodies are available. Data from in silico docking of tau peptide into antibody mold, obtained in this study, show that biochemical data and computational approaches provide results comparable to X-ray crystallography. CI - Copyright (c) 2010 Elsevier Inc. All rights reserved. FAU - Skrabana, Rostislav AU - Skrabana R AD - Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia. FAU - Dvorsky, Radovan AU - Dvorsky R FAU - Sevcik, Jozef AU - Sevcik J FAU - Novak, Michal AU - Novak M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100223 PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - 0 (Antibodies, Monoclonal) RN - 0 (Recombinant Proteins) RN - 0 (tau Proteins) SB - IM MH - Antibodies, Monoclonal/*chemistry MH - Crystallography, X-Ray MH - Models, Molecular MH - Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - tau Proteins/*chemistry EDAT- 2010/02/27 06:00 MHDA- 2012/11/09 06:00 CRDT- 2010/02/27 06:00 PHST- 2009/12/16 [received] PHST- 2010/02/18 [revised] PHST- 2010/02/19 [accepted] PHST- 2010/02/23 [aheadofprint] AID - S1047-8477(10)00063-8 [pii] AID - 10.1016/j.jsb.2010.02.016 [doi] PST - ppublish SO - J Struct Biol. 2010 Jul;171(1):74-81. doi: 10.1016/j.jsb.2010.02.016. Epub 2010 Feb 23. PMID- 21841916 OWN - NLM STAT- Publisher DA - 20110815 IS - 1543-8120 (Print) IS - 1543-8120 (Linking) VI - 8 DP - 2010 Sep 23 TI - The Cryptochrome Blue Light Receptors. PG - e0135 AB - Cryptochromes are photolyase-like blue light receptors originally discovered in Arabidopsis but later found in other plants, microbes, and animals. Arabidopsis has two cryptochromes, CRY1 and CRY2, which mediate primarily blue light inhibition of hypocotyl elongation and photoperiodic control of floral initiation, respectively. In addition, cryptochromes also regulate over a dozen other light responses, including circadian rhythms, tropic growth, stomata opening, guard cell development, root development, bacterial and viral pathogen responses, abiotic stress responses, cell cycles, programmed cell death, apical dominance, fruit and ovule development, seed dormancy, and magnetoreception. Cryptochromes have two domains, the N-terminal PHR (Photolyase-Homologous Region) domain that bind the chromophore FAD (flavin adenine dinucleotide), and the CCE (CRY C-terminal Extension) domain that appears intrinsically unstructured but critical to the function and regulation of cryptochromes. Most cryptochromes accumulate in the nucleus, and they undergo blue light-dependent phosphorylation or ubiquitination. It is hypothesized that photons excite electrons of the flavin molecule, resulting in redox reaction or circular electron shuttle and conformational changes of the photoreceptors. The photoexcited cryptochrome are phosphorylated to adopt an open conformation, which interacts with signaling partner proteins to alter gene expression at both transcriptional and posttranslational levels and consequently the metabolic and developmental programs of plants. FAU - Yu, Xuhong AU - Yu X AD - Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA. FAU - Liu, Hongtao AU - Liu H FAU - Klejnot, John AU - Klejnot J FAU - Lin, Chentao AU - Lin C LA - ENG GR - R01 GM056265/GM/NIGMS NIH HHS/United States GR - R01 GM056265-13/GM/NIGMS NIH HHS/United States GR - R01 GM056265-13S1/GM/NIGMS NIH HHS/United States GR - R01 GM056265-14/GM/NIGMS NIH HHS/United States GR - R01 GM056265-14S1/GM/NIGMS NIH HHS/United States PT - JOURNAL ARTICLE TA - Arabidopsis Book JT - The Arabidopsis book / American Society of Plant Biologists JID - 101214894 PMC - PMC3155252 MID - NIHMS312301 EDAT- 2011/08/16 06:00 MHDA- 2011/08/16 06:00 CRDT- 2011/08/16 06:00 PST - ppublish SO - Arabidopsis Book. 2010 Sep 23;8:e0135. PMID- 24898547 OWN - NLM STAT- In-Process DA - 20140703 IS - 1521-3773 (Electronic) IS - 1433-7851 (Linking) VI - 53 IP - 28 DP - 2014 Jul 7 TI - Mapping multivalency and differential affinities within large intrinsically disordered protein complexes with segmental motion analysis. PG - 7364-7 LID - 10.1002/anie.201403694 [doi] AB - Intrinsically disordered proteins (IDPs) can bind to multiple interaction partners. Numerous binding regions in the IDP that act in concert through complex cooperative effects facilitate such interactions, but complicate studying IDP complexes. To address this challenge we developed a combined fluorescence correlation and time-resolved polarization spectroscopy approach to study the binding properties of the IDP nucleoporin153 (Nup153) to nuclear transport receptors (NTRs). The detection of segmental backbone mobility of Nup153 within the unperturbed complex provided a readout of local, region-specific binding properties that are usually masked in measurements of the whole IDP. The binding affinities of functionally and structurally diverse NTRs to distinct regions of Nup153 can differ by orders of magnitudes-a result with implications for the diversity of transport routes in nucleocytoplasmic transport. CI - (c) 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. FAU - Milles, Sigrid AU - Milles S AD - Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg (Germany). FAU - Lemke, Edward A AU - Lemke EA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140604 PL - Germany TA - Angew Chem Int Ed Engl JT - Angewandte Chemie (International ed. in English) JID - 0370543 SB - IM OTO - NOTNLM OT - FG-nucleoporin OT - fluorescence OT - intrinsically disordered proteins OT - ligand binding OT - multivalency EDAT- 2014/06/06 06:00 MHDA- 2014/06/06 06:00 CRDT- 2014/06/06 06:00 PHST- 2014/03/25 [received] PHST- 2014/06/04 [aheadofprint] AID - 10.1002/anie.201403694 [doi] PST - ppublish SO - Angew Chem Int Ed Engl. 2014 Jul 7;53(28):7364-7. doi: 10.1002/anie.201403694. Epub 2014 Jun 4. PMID- 21212263 OWN - NLM STAT- MEDLINE DA - 20110330 DCOM- 20110516 LR - 20140821 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 11 DP - 2011 Mar 18 TI - The structure of lombricine kinase: implications for phosphagen kinase conformational changes. PG - 9338-50 LID - 10.1074/jbc.M110.202796 [doi] AB - Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309-317, which is disordered in substrate-free structures of homologs and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His(178). Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates. FAU - Bush, D Jeffrey AU - Bush DJ AD - Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA. FAU - Kirillova, Olga AU - Kirillova O FAU - Clark, Shawn A AU - Clark SA FAU - Davulcu, Omar AU - Davulcu O FAU - Fabiola, Felcy AU - Fabiola F FAU - Xie, Qing AU - Xie Q FAU - Somasundaram, Thayumanasamy AU - Somasundaram T FAU - Ellington, W Ross AU - Ellington WR FAU - Chapman, Michael S AU - Chapman MS LA - eng SI - PDB/3JPZ SI - PDB/3JQ3 GR - GM55837/GM/NIGMS NIH HHS/United States GR - GM77643/GM/NIGMS NIH HHS/United States GR - GM78538/GM/NIGMS NIH HHS/United States GR - RR-01646/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110106 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 61D2G4IYVH (Adenosine Diphosphate) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 2.7.3.- (Phosphotransferases (Nitrogenous Group Acceptor)) RN - EC 2.7.3.5 (lombricine kinase) SB - IM MH - Adenosine Diphosphate/chemistry/metabolism MH - Adenosine Triphosphate/chemistry/metabolism MH - Animals MH - Annelida/*enzymology MH - Catalytic Domain MH - *Computer Simulation MH - Crystallography, X-Ray MH - *Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphotransferases (Nitrogenous Group Acceptor)/*chemistry/metabolism MH - Protein Structure, Secondary PMC - PMC3058953 OID - NLM: PMC3058953 EDAT- 2011/01/08 06:00 MHDA- 2011/05/17 06:00 CRDT- 2011/01/08 06:00 PHST- 2011/01/06 [aheadofprint] AID - M110.202796 [pii] AID - 10.1074/jbc.M110.202796 [doi] PST - ppublish SO - J Biol Chem. 2011 Mar 18;286(11):9338-50. doi: 10.1074/jbc.M110.202796. Epub 2011 Jan 6. PMID- 24766768 OWN - NLM STAT- MEDLINE DA - 20140902 DCOM- 20150623 IS - 1471-499X (Electronic) IS - 1471-4914 (Linking) VI - 20 IP - 9 DP - 2014 Sep TI - MeCP2: the long trip from a chromatin protein to neurological disorders. PG - 487-98 LID - 10.1016/j.molmed.2014.03.004 [doi] LID - S1471-4914(14)00056-2 [pii] AB - Since the discovery of its fundamental involvement in Rett syndrome, methyl CpG binding protein 2 (MeCP2) has been the focus of an exhaustive biochemical and functional characterization. It is now becoming apparent that the intrinsic highly disordered nature of MeCP2, which is amenable to a plethora of post-translational modifications (PTMs), allows it to recognize a large number of protein interacting partners, including histones. MeCP2 is highly abundant in the brain and it is an important component of neuronal chromatin; nevertheless, the organization and implications of its involvement in terms of DNA methylation binding dependence and effects on transcription are still not well understood. Recent results have shown that MeCP2 plays an important role in brain development, aging, and in neurological disorders. CI - Copyright (c) 2014 Elsevier Ltd. All rights reserved. FAU - Ausio, Juan AU - Ausio J AD - Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain; Department of Biochemistry and Microbiology, University of Victoria, British Columbia, V8W 3P6, Canada. Electronic address: jausio@uvic.ca. FAU - de Paz, Alexia Martinez AU - de Paz AM AD - Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain. FAU - Esteller, Manel AU - Esteller M AD - Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Catalonia, Spain. Electronic address: mesteller@idibell.cat. LA - eng GR - MOP-130417/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20140421 PL - England TA - Trends Mol Med JT - Trends in molecular medicine JID - 100966035 RN - 0 (Chromatin) RN - 0 (Histones) RN - 0 (MECP2 protein, human) RN - 0 (Methyl-CpG-Binding Protein 2) SB - IM MH - Aging MH - Amino Acid Sequence MH - Brain/growth & development/metabolism MH - Chromatin/genetics/metabolism/ultrastructure MH - DNA Methylation MH - Histones/metabolism MH - Humans MH - Methyl-CpG-Binding Protein 2/*chemistry/*metabolism MH - Molecular Sequence Data MH - Neurodegenerative Diseases/genetics/metabolism MH - Protein Processing, Post-Translational MH - Transcription, Genetic OTO - NOTNLM OT - DNA methylation OT - MeCP2 OT - chromatin OT - intrinsically disordered proteins OT - neurological disorders EDAT- 2014/04/29 06:00 MHDA- 2015/06/24 06:00 CRDT- 2014/04/29 06:00 PHST- 2014/01/31 [received] PHST- 2014/03/12 [revised] PHST- 2014/03/14 [accepted] PHST- 2014/04/21 [aheadofprint] AID - S1471-4914(14)00056-2 [pii] AID - 10.1016/j.molmed.2014.03.004 [doi] PST - ppublish SO - Trends Mol Med. 2014 Sep;20(9):487-98. doi: 10.1016/j.molmed.2014.03.004. Epub 2014 Apr 21. PMID- 21985427 OWN - NLM STAT- MEDLINE DA - 20111110 DCOM- 20120305 LR - 20150223 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 115 IP - 45 DP - 2011 Nov 17 TI - Entropic stabilization of proteins by TMAO. PG - 13401-7 LID - 10.1021/jp207289b [doi] AB - The osmolyte trimethylamine N-oxide (TMAO) accumulates in the cell in response to osmotic stress and increases the thermodynamic stability of folded proteins. To understand the mechanism of TMAO induced stabilization of folded protein states, we systematically investigated the action of TMAO on several model dipeptides (leucine, L(2), serine, S(2), glutamine, Q(2), lysine, K(2), and glycine, G(2)) in order to elucidate the effect of residue-specific TMAO interactions on small fragments of solvent-exposed conformations of the denatured states of proteins. We find that TMAO preferentially hydrogen bonds with the exposed dipeptide backbone but generally not with nonpolar or polar side chains. However, interactions with the positively charged Lys are substantially greater than with the backbone. The dipeptide G(2) is a useful model of the pure amide backbone; interacts with TMAO by forming a hydrogen bond between the amide nitrogen and the oxygen in TMAO. In contrast, TMAO is depleted from the protein backbone in the hexapeptide G(6), which shows that the length of the polypeptide chain is relevant in aqueous TMAO solutions. These simulations lead to the hypothesis that TMAO-induced stabilization of proteins and peptides is a consequence of depletion of the solute from the protein surface provided intramolecular interactions are more favorable than those between TMAO and the backbone. To test our hypothesis, we performed additional simulations of the action of TMAO on an intrinsically disordered Abeta(16-22) (KLVFFAE) monomer. In the absence of TMAO, Abeta(16-22) is a disordered random coil. However, in aqueous TMAO solution, Abeta(16-22) monomer samples compact conformations. A transition from random coil to alpha-helical secondary structure is observed at high TMAO concentrations. The coil to alpha-helix transition is highly cooperative especially considering the small number of residues in Abeta(16-22). Our work highlights the potential similarities between the action of TMAO on long polypeptide chains and entropic stabilization of proteins in a crowded environment due to excluded volume interactions. In this sense, the chemical chaperone TMAO is a nanocrowding particle. FAU - Cho, Samuel S AU - Cho SS AD - Department of Chemistry and Biochemistry and Biophysics Program, University of Maryland, College Park, Maryland 20742, United States. FAU - Reddy, Govardhan AU - Reddy G FAU - Straub, John E AU - Straub JE FAU - Thirumalai, D AU - Thirumalai D LA - eng GR - F32 GM082076/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20111026 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Amyloid beta-Peptides) RN - 0 (Dipeptides) RN - 0 (Methylamines) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (16-22)) RN - FLD0K1SJ1A (trimethyloxamine) SB - IM MH - Amyloid beta-Peptides/*chemistry MH - Dipeptides/*chemistry MH - Hydrogen Bonding MH - Methylamines/*chemistry MH - Peptide Fragments/*chemistry MH - Protein Folding MH - Thermodynamics EDAT- 2011/10/12 06:00 MHDA- 2012/03/06 06:00 CRDT- 2011/10/12 06:00 PHST- 2011/10/26 [aheadofprint] AID - 10.1021/jp207289b [doi] PST - ppublish SO - J Phys Chem B. 2011 Nov 17;115(45):13401-7. doi: 10.1021/jp207289b. Epub 2011 Oct 26. PMID- 21524275 OWN - NLM STAT- MEDLINE DA - 20110428 DCOM- 20111121 IS - 1470-8728 (Electronic) IS - 0264-6021 (Linking) VI - 436 IP - 1 DP - 2011 May 15 TI - The remarkable diversity of plant PEPC (phosphoenolpyruvate carboxylase): recent insights into the physiological functions and post-translational controls of non-photosynthetic PEPCs. PG - 15-34 LID - 10.1042/BJ20110078 [doi] AB - PEPC [PEP (phosphoenolpyruvate) carboxylase] is a tightly controlled enzyme located at the core of plant C-metabolism that catalyses the irreversible beta-carboxylation of PEP to form oxaloacetate and Pi. The critical role of PEPC in assimilating atmospheric CO(2) during C(4) and Crassulacean acid metabolism photosynthesis has been studied extensively. PEPC also fulfils a broad spectrum of non-photosynthetic functions, particularly the anaplerotic replenishment of tricarboxylic acid cycle intermediates consumed during biosynthesis and nitrogen assimilation. An impressive array of strategies has evolved to co-ordinate in vivo PEPC activity with cellular demands for C(4)-C(6) carboxylic acids. To achieve its diverse roles and complex regulation, PEPC belongs to a small multigene family encoding several closely related PTPCs (plant-type PEPCs), along with a distantly related BTPC (bacterial-type PEPC). PTPC genes encode ~110-kDa polypeptides containing conserved serine-phosphorylation and lysine-mono-ubiquitination sites, and typically exist as homotetrameric Class-1 PEPCs. In contrast, BTPC genes encode larger ~117-kDa polypeptides owing to a unique intrinsically disordered domain that mediates BTPC's tight interaction with co-expressed PTPC subunits. This association results in the formation of unusual ~900-kDa Class-2 PEPC hetero-octameric complexes that are desensitized to allosteric effectors. BTPC is a catalytic and regulatory subunit of Class-2 PEPC that is subject to multi-site regulatory phosphorylation in vivo. The interaction between divergent PEPC polypeptides within Class-2 PEPCs adds another layer of complexity to the evolution, physiological functions and metabolic control of this essential CO(2)-fixing plant enzyme. The present review summarizes exciting developments concerning the functions, post-translational controls and subcellular location of plant PTPC and BTPC isoenzymes. FAU - O'Leary, Brendan AU - O'Leary B AD - Department of Biology, Queen's University, Kingston, ON, Canada. FAU - Park, Joonho AU - Park J FAU - Plaxton, William C AU - Plaxton WC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (Bacterial Proteins) RN - 0 (Plant Proteins) RN - EC 4.1.1.31 (Phosphoenolpyruvate Carboxylase) SB - IM MH - Amino Acid Sequence MH - Arabidopsis/enzymology/metabolism MH - Bacterial Proteins/chemistry/metabolism MH - Genetic Variation MH - Mitochondria/enzymology/metabolism MH - Models, Biological MH - Molecular Sequence Data MH - Phosphoenolpyruvate Carboxylase/*chemistry/genetics/*metabolism MH - Phylogeny MH - Plant Proteins/*chemistry/genetics/*metabolism MH - Plants/*enzymology MH - Protein Processing, Post-Translational EDAT- 2011/04/29 06:00 MHDA- 2011/12/13 00:00 CRDT- 2011/04/29 06:00 AID - BJ20110078 [pii] AID - 10.1042/BJ20110078 [doi] PST - ppublish SO - Biochem J. 2011 May 15;436(1):15-34. doi: 10.1042/BJ20110078. PMID- 21543314 OWN - NLM STAT- MEDLINE DA - 20110627 DCOM- 20110909 LR - 20140820 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 26 DP - 2011 Jul 1 TI - Lipids trigger a conformational switch that regulates signal recognition particle (SRP)-mediated protein targeting. PG - 23489-97 LID - 10.1074/jbc.M110.212340 [doi] AB - Co-translational protein targeting to the membrane is mediated by the signal recognition particle and its receptor (FtsY). Their homologous GTPase domains interact at the membrane and form a heterodimer in which both GTPases are activated. The prerequisite for protein targeting is the interaction of FtsY with phospholipids. However, the mechanism of FtsY regulation by phospholipids remained unclear. Here we show that the N terminus of FtsY (A domain) is natively unfolded in solution and define the complete membrane-targeting sequence. We show that the membrane-targeting sequence is highly dynamic in solution, independent of nucleotides and directly responds to the density of anionic phospholipids by a random coil-helix transition. This conformational switch is essential for tethering FtsY to membranes and activates the GTPase for its subsequent interaction with the signal recognition particle. Our results underline the dynamics of lipid-protein interactions and their importance in the regulation of protein targeting and translocation across biological membranes. FAU - Stjepanovic, Goran AU - Stjepanovic G AD - Biochemie Zentrum (BZH), University of Heidelberg, INF 328, 69120 Heidelberg, Germany. FAU - Kapp, Katja AU - Kapp K FAU - Bange, Gert AU - Bange G FAU - Graf, Christian AU - Graf C FAU - Parlitz, Richard AU - Parlitz R FAU - Wild, Klemens AU - Wild K FAU - Mayer, Matthias P AU - Mayer MP FAU - Sinning, Irmgard AU - Sinning I LA - eng SI - PDB/2YHS PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110503 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - 0 (FtsY protein, Bacteria) RN - 0 (Phospholipids) RN - 0 (Receptors, Cytoplasmic and Nuclear) RN - 0 (Signal Recognition Particle) RN - EC 3.6.1.- (GTP Phosphohydrolases) SB - IM MH - Bacterial Proteins/*chemistry/metabolism MH - Cell Membrane/*chemistry/metabolism MH - Escherichia coli/*enzymology MH - GTP Phosphohydrolases/*chemistry/metabolism MH - Phospholipids/*chemistry/metabolism MH - *Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Transport/physiology MH - Receptors, Cytoplasmic and Nuclear/*chemistry/metabolism MH - Signal Recognition Particle/*chemistry/metabolism PMC - PMC3123112 OID - NLM: PMC3123112 EDAT- 2011/05/06 06:00 MHDA- 2011/09/10 06:00 CRDT- 2011/05/06 06:00 PHST- 2011/05/03 [aheadofprint] AID - M110.212340 [pii] AID - 10.1074/jbc.M110.212340 [doi] PST - ppublish SO - J Biol Chem. 2011 Jul 1;286(26):23489-97. doi: 10.1074/jbc.M110.212340. Epub 2011 May 3. PMID- 18391200 OWN - NLM STAT- MEDLINE DA - 20080417 DCOM- 20080613 LR - 20140903 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 105 IP - 15 DP - 2008 Apr 15 TI - Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. PG - 5762-7 LID - 10.1073/pnas.0801353105 [doi] AB - Proteins with intrinsically disordered domains are implicated in a vast range of biological processes, especially in cell signaling and regulation. Having solved the quaternary structure of the folded domains in the tumor suppressor p53 by a multidisciplinary approach, we have now determined the average ensemble structure of the intrinsically disordered N-terminal transactivation domain (TAD) by using residual dipolar couplings (RDCs) from NMR spectroscopy and small-angle x-ray scattering (SAXS). Remarkably, not only were we able to measure RDCs of the isolated TAD, but we were also able to do so for the TAD in both the full-length tetrameric p53 protein and in its complex with a specific DNA response element. We determined the orientation of the TAD ensemble relative to the core domain, found that the TAD was stiffer in the proline-rich region (residues 64-92), which has a tendency to adopt a polyproline II (PPII) structure, and projected the TAD away from the core. We located the TAD in SAXS experiments on a complex between tetrameric p53 and four Taz2 domains that bind tightly to the TAD (residues 1-57) and acted as "reporters." The p53-Taz2 complex was an extended cross-shaped structure. The quality of the SAXS data enabled us to model the disordered termini and the folded domains in the complex with DNA. The core domains enveloped the response element in the center of the molecule, with the Taz2-bound TADs projecting outward from the core. FAU - Wells, Mark AU - Wells M AD - MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 0QH, United Kingdom. FAU - Tidow, Henning AU - Tidow H FAU - Rutherford, Trevor J AU - Rutherford TJ FAU - Markwick, Phineus AU - Markwick P FAU - Jensen, Malene Ringkjobing AU - Jensen MR FAU - Mylonas, Efstratios AU - Mylonas E FAU - Svergun, Dmitri I AU - Svergun DI FAU - Blackledge, Martin AU - Blackledge M FAU - Fersht, Alan R AU - Fersht AR LA - eng GR - MC_U105474168/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080407 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Peptide Fragments) RN - 0 (Tumor Suppressor Protein p53) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Motifs MH - DNA/chemistry MH - Humans MH - Mutation MH - Peptide Fragments MH - Protein Binding MH - Protein Structure, Tertiary MH - Response Elements MH - Scattering, Small Angle MH - *Transcriptional Activation MH - Tumor Suppressor Protein p53/*chemistry MH - X-Ray Diffraction PMC - PMC2311362 OID - NLM: PMC2311362 EDAT- 2008/04/09 09:00 MHDA- 2008/06/14 09:00 CRDT- 2008/04/09 09:00 PHST- 2008/04/07 [aheadofprint] AID - 0801353105 [pii] AID - 10.1073/pnas.0801353105 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5762-7. doi: 10.1073/pnas.0801353105. Epub 2008 Apr 7. PMID- 7891711 OWN - NLM STAT- MEDLINE DA - 19950420 DCOM- 19950420 LR - 20130922 IS - 0270-7306 (Print) IS - 0270-7306 (Linking) VI - 15 IP - 4 DP - 1995 Apr TI - Domain organization of I kappa B alpha and sites of interaction with NF-kappa B p65. PG - 2166-72 AB - The DNA-binding activity and cellular distribution of the transcription factor NF-kappa B are regulated by the inhibitor protein I kappa B alpha. I kappa B alpha belongs to a family of proteins that contain multiple repeats of a 30- to 35-amino-acid sequence that was initially recognized in the erythrocyte protein ankyrin. Partial proteolysis has been used to study the domain structure of I kappa B alpha and to determine the sites at which it interacts with NF-kappa B. The data reveal a tripartite structure for I kappa B alpha in which a central, protease-resistant domain composed of five ankyrin repeats is flanked by an unstructured N-terminal extension and a compact, highly acidic C-terminal domain that is connected to the core of the protein by a flexible linker. Functional analysis of V8 cleavage products indicates that I kappa B alpha molecules lacking the N-terminal region can interact with and inhibit the DNA-binding activity of the p65 subunit of NF-kappa B, whereas I kappa B alpha molecules which lack both the N- and C-terminal regions are incapable of doing so. Protease cleavage of the N terminus of I kappa B alpha was unaffected by the presence of the p65 subunit of NF-kappa B, whereas bound p65 blocked cleavage of the flexible linker connecting the C-terminal domain to the ankyrin repeat-containing core of the protein. This linker region is highly conserved within the human, rat, pig, and chicken homologs of I kappa B alpha, and while it has been suggested that it represents a sixth ankyrin repeat, it is also likely that this is a flexible region of the protein that interacts with NF-kappa B. FAU - Jaffray, E AU - Jaffray E AD - School of Biological and Medical Sciences, University of St. Andrews, Fife, Scotland. FAU - Wood, K M AU - Wood KM FAU - Hay, R T AU - Hay RT LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (Ankyrins) RN - 0 (DNA-Binding Proteins) RN - 0 (I-kappa B Proteins) RN - 0 (NF-kappa B) RN - 0 (Transcription Factor RelA) RN - 139874-52-5 (NF-kappaB inhibitor alpha) RN - EC 3.4.21.- (Serine Endopeptidases) RN - EC 3.4.21.1 (Chymotrypsin) RN - EC 3.4.21.19 (glutamyl endopeptidase) SB - IM MH - Ankyrins MH - Chymotrypsin/metabolism MH - DNA-Binding Proteins/*metabolism MH - *I-kappa B Proteins MH - Molecular Sequence Data MH - NF-kappa B/*antagonists & inhibitors/*metabolism MH - Protein Binding MH - Protein Conformation MH - Repetitive Sequences, Nucleic Acid MH - Serine Endopeptidases/metabolism MH - Transcription Factor RelA PMC - PMC230444 OID - NLM: PMC230444 EDAT- 1995/04/01 MHDA- 1995/04/01 00:01 CRDT- 1995/04/01 00:00 PST - ppublish SO - Mol Cell Biol. 1995 Apr;15(4):2166-72. PMID- 23561531 OWN - NLM STAT- MEDLINE DA - 20130408 DCOM- 20130925 LR - 20141116 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 104 IP - 7 DP - 2013 Apr 2 TI - Comparative studies of disordered proteins with similar sequences: application to Abeta40 and Abeta42. PG - 1546-55 LID - 10.1016/j.bpj.2013.02.023 [doi] LID - S0006-3495(13)00240-3 [pii] AB - Quantitative comparisons of intrinsically disordered proteins (IDPs) with similar sequences, such as mutant forms of the same protein, may provide insights into IDP aggregation-a process that plays a role in several neurodegenerative disorders. Here we describe an approach for modeling IDPs with similar sequences that simplifies the comparison of the ensembles by utilizing a single library of structures. The relative population weights of the structures are estimated using a Bayesian formalism, which provides measures of uncertainty in the resulting ensembles. We applied this approach to the comparison of ensembles for Abeta40 and Abeta42. Bayesian hypothesis testing finds that although both Abeta species sample beta-rich conformations in solution that may represent prefibrillar intermediates, the probability that Abeta42 samples these prefibrillar states is roughly an order of magnitude larger than the frequency in which Abeta40 samples such structures. Moreover, the structure of the soluble prefibrillar state in our ensembles is similar to the experimentally determined structure of Abeta that has been implicated as an intermediate in the aggregation pathway. Overall, our approach for comparative studies of IDPs with similar sequences provides a platform for future studies on the effect of mutations on the structure and function of disordered proteins. CI - Copyright (c) 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Fisher, Charles K AU - Fisher CK AD - Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts, USA. FAU - Ullman, Orly AU - Ullman O FAU - Stultz, Collin M AU - Stultz CM LA - eng PT - Comparative Study PT - Journal Article PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (1-40)) RN - 0 (amyloid beta-protein (1-42)) SB - IM MH - Amino Acid Sequence MH - Amyloid beta-Peptides/*chemistry MH - Models, Molecular MH - Peptide Fragments/*chemistry MH - Protein Multimerization MH - Protein Structure, Secondary MH - Protein Unfolding PMC - PMC3617440 OID - NLM: PMC3617440 EDAT- 2013/04/09 06:00 MHDA- 2013/09/26 06:00 CRDT- 2013/04/09 06:00 PHST- 2012/08/28 [received] PHST- 2013/02/03 [revised] PHST- 2013/02/08 [accepted] AID - S0006-3495(13)00240-3 [pii] AID - 10.1016/j.bpj.2013.02.023 [doi] PST - ppublish SO - Biophys J. 2013 Apr 2;104(7):1546-55. doi: 10.1016/j.bpj.2013.02.023. PMID- 9452503 OWN - NLM STAT- MEDLINE DA - 19980305 DCOM- 19980305 LR - 20101118 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 273 IP - 6 DP - 1998 Feb 6 TI - Conformation-dependent antibacterial activity of the naturally occurring human peptide LL-37. PG - 3718-24 AB - The influence of ion composition, pH, and peptide concentration on the conformation and activity of the 37-residue human antibacterial peptide LL-37 has been studied. At micromolar concentration in water, LL-37 exhibits a circular dichroism spectrum consistent with a disordered structure. The addition of 15 mM HCO3-, SO42-, or CF3CO2- causes the peptide to adopt a helical structure, with approximately equal efficiency, while 160 mM Cl- is less efficient. A cooperative transition from disordered to helical structure is observed as the peptide concentration is increased, consistent with formation of an oligomer. The extent of alpha-helicity correlates with the antibacterial activity of LL-37 against both Gram-positive and Gram-negative bacteria. Two homologous peptides, FF-33 and SK-29, containing 4 and 8 residue deletions at the N terminus, respectively, require higher concentrations of anions for helix formation and are less active than LL-37 against Escherichia coli D21. Below pH 5, the helical content of LL-37 gradually decreases, and at pH 2 it is entirely disordered. In contrast, the helical structure is retained at pH over 13. The minimal inhibitory concentration of LL-37 against E. coli is 5 microM, and at 13-25 microM the peptide is cytotoxic against several eukaryotic cells. In solutions containing the ion compositions of plasma, intracellular fluid, or interstitial fluid, LL-37 is helical, and hence it could pose a danger to human cells upon release. However, in the presence of human serum, the antibacterial and the cytotoxic activities of LL-37 are inhibited. FAU - Johansson, J AU - Johansson J AD - Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden. FAU - Gudmundsson, G H AU - Gudmundsson GH FAU - Rottenberg, M E AU - Rottenberg ME FAU - Berndt, K D AU - Berndt KD FAU - Agerberth, B AU - Agerberth B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Anions) RN - 0 (Anti-Bacterial Agents) RN - 0 (Antimicrobial Cationic Peptides) RN - 0 (Carrier Proteins) RN - 0 (Cathelicidins) RN - 0 (cathelicidin antimicrobial peptide) RN - 143108-26-3 (CAP18 lipopolysaccharide-binding protein) SB - IM MH - Animals MH - Anions MH - Anti-Bacterial Agents/chemistry/*metabolism MH - *Antimicrobial Cationic Peptides MH - Blood Bactericidal Activity MH - Carrier Proteins/chemistry/*metabolism MH - Cathelicidins MH - Escherichia coli MH - Humans MH - Hydrogen-Ion Concentration MH - Protein Structure, Secondary MH - Structure-Activity Relationship MH - Swine EDAT- 1998/03/07 MHDA- 1998/03/07 00:01 CRDT- 1998/03/07 00:00 PST - ppublish SO - J Biol Chem. 1998 Feb 6;273(6):3718-24. PMID- 17210575 OWN - NLM STAT- MEDLINE DA - 20070226 DCOM- 20070618 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 282 IP - 9 DP - 2007 Mar 2 TI - Oligomerization of the human prion protein proceeds via a molten globule intermediate. PG - 6300-7 AB - The conformational transition of the human prion protein from an alpha-helical to a beta-sheet-rich structure is believed to be the critical event in prion pathogenesis. The molecular mechanism of misfolding and the role of intermediate states during this transition remain poorly understood. To overcome the obstacle of insolubility of amyloid fibrils, we have studied a beta-sheet-rich misfolded isoform of the prion protein, the beta-oligomer, which shares some structural properties with amyloid, including partial proteinase resistance. We demonstrate here that the beta-oligomer can be studied by solution-state NMR spectroscopy and obtain insights into the misfolding mechanism via its transient monomeric precursor. It is often assumed that misfolding into beta-sheet-rich isoforms proceeds via a compatible precursor with a beta-sheet subunit structure. We show here, on the contrary, evidence for an almost natively alpha-helix-rich monomeric precursor state with molten globule characteristics, converting in vitro into the beta-oligomer. We propose a possible mechanism for the formation of the beta-oligomer, triggered by intermolecular contacts between constantly rearranging structures. It is concluded that the beta-oligomer is not preceded by precursors with beta-sheet structure but by a partially unfolded clearly distinguishable alpha-helical state. FAU - Gerber, Remo AU - Gerber R AD - Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom. remo.gerber@chem.ox.ac.uk FAU - Tahiri-Alaoui, Abdessamad AU - Tahiri-Alaoui A FAU - Hore, P J AU - Hore PJ FAU - James, William AU - James W LA - eng PT - Journal Article DEP - 20070108 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Amyloid) RN - 0 (Prions) SB - IM MH - Amyloid/chemistry MH - Dimerization MH - Humans MH - Magnetic Resonance Spectroscopy MH - Prions/*chemistry MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary EDAT- 2007/01/11 09:00 MHDA- 2007/06/19 09:00 CRDT- 2007/01/11 09:00 PHST- 2007/01/08 [aheadofprint] AID - M608926200 [pii] AID - 10.1074/jbc.M608926200 [doi] PST - ppublish SO - J Biol Chem. 2007 Mar 2;282(9):6300-7. Epub 2007 Jan 8. PMID- 14557549 OWN - NLM STAT- MEDLINE DA - 20031029 DCOM- 20040105 LR - 20140610 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 100 IP - 22 DP - 2003 Oct 28 TI - DNA-repair protein hHR23a alters its protein structure upon binding proteasomal subunit S5a. PG - 12694-9 AB - The Rad23 family of proteins, including the human homologs hHR23a and hHR23b, stimulates nucleotide excision repair and has been shown to provide a novel link between proteasome-mediated protein degradation and DNA repair. In this work, we illustrate how the proteasomal subunit S5a regulates hHR23a protein structure. By using NMR spectroscopy, we have elucidated the structure and dynamic properties of the 40-kDa hHR23a protein and show it to contain four structured domains connected by flexible linker regions. In addition, we reveal that these domains interact in an intramolecular fashion, and by using residual dipolar coupling data in combination with chemical shift perturbation analysis, we present the hHR23a structure. By itself, hHR23a adopts a closed conformation defined by the interaction of an N-terminal ubiquitin-like domain with two ubiquitin-associated domains. Interestingly, binding of the proteasomal subunit S5a disrupts the hHR23a interdomain interactions and thereby causes it to adopt an opened conformation. FAU - Walters, Kylie J AU - Walters KJ AD - Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA. walte048@umn.edu FAU - Lech, Patrycja J AU - Lech PJ FAU - Goh, Amanda M AU - Goh AM FAU - Wang, Qinghua AU - Wang Q FAU - Howley, Peter M AU - Howley PM LA - eng SI - PDB/1OQY GR - CA 097004-01A1/CA/NCI NIH HHS/United States GR - CA 64888/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20031013 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Carrier Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Multienzyme Complexes) RN - 0 (PSMD4 protein, human) RN - 0 (Protein Subunits) RN - 0 (RAD23B protein, human) RN - 156533-33-4 (RAD23A protein, human) RN - EC 3.4.22.- (Cysteine Endopeptidases) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) RN - EC 6.5.1.- (DNA Repair Enzymes) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Carrier Proteins/*chemistry/metabolism MH - Cysteine Endopeptidases/*chemistry/metabolism MH - *DNA Repair MH - DNA Repair Enzymes MH - DNA-Binding Proteins/*chemistry/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Multienzyme Complexes/*chemistry/metabolism MH - Proteasome Endopeptidase Complex MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Subunits/chemistry/metabolism PMC - PMC240680 OID - NLM: PMC240680 EDAT- 2003/10/15 05:00 MHDA- 2004/01/06 05:00 CRDT- 2003/10/15 05:00 PHST- 2003/10/13 [aheadofprint] AID - 10.1073/pnas.1634989100 [doi] AID - 1634989100 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12694-9. Epub 2003 Oct 13. PMID- 23528987 OWN - NLM STAT- MEDLINE DA - 20130401 DCOM- 20130910 LR - 20141116 IS - 1873-4200 (Electronic) IS - 0301-4622 (Linking) VI - 175-176 DP - 2013 May-Jun TI - Structural landscape of the proline-rich domain of Sos1 nucleotide exchange factor. PG - 54-62 LID - 10.1016/j.bpc.2013.02.008 [doi] LID - S0301-4622(13)00034-3 [pii] AB - Despite its key role in mediating a plethora of cellular signaling cascades pertinent to health and disease, little is known about the structural landscape of the proline-rich (PR) domain of Sos1 guanine nucleotide exchange factor. Herein, using a battery of biophysical tools, we provide evidence that the PR domain of Sos1 is structurally disordered and adopts an extended random coil-like conformation in solution. Of particular interest is the observation that while chemical denaturation of PR domain results in the formation of a significant amount of polyproline II (PPII) helices, it has little or negligible effect on its overall size as measured by its hydrodynamic radius. Our data also show that the PR domain displays a highly dynamic conformational basin in agreement with the knowledge that the intrinsically unstructured proteins rapidly interconvert between an ensemble of conformations. Collectively, our study provides new insights into the conformational equilibrium of a key signaling molecule with important consequences on its physiological function. CI - Copyright (c) 2013 Elsevier B.V. All rights reserved. FAU - McDonald, Caleb B AU - McDonald CB AD - Department of Biochemistry & Molecular Biology, Leonard Miller School of Medicine, University of Miami, Miami, FL 33136, USA. FAU - Bhat, Vikas AU - Bhat V FAU - Kurouski, Dmitry AU - Kurouski D FAU - Mikles, David C AU - Mikles DC FAU - Deegan, Brian J AU - Deegan BJ FAU - Seldeen, Kenneth L AU - Seldeen KL FAU - Lednev, Igor K AU - Lednev IK FAU - Farooq, Amjad AU - Farooq A LA - eng GR - R01 GM083897/GM/NIGMS NIH HHS/United States GR - R01-AG033719/AG/NIA NIH HHS/United States GR - R01-GM083897/GM/NIGMS NIH HHS/United States GR - T32-CA119929/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130305 PL - Netherlands TA - Biophys Chem JT - Biophysical chemistry JID - 0403171 RN - 0 (Recombinant Proteins) RN - 0 (SOS1 Protein) RN - 8W8T17847W (Urea) RN - 9DLQ4CIU6V (Proline) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Guanidine/chemistry MH - Humans MH - Light MH - Molecular Sequence Data MH - Proline/*chemistry MH - Protein Denaturation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/biosynthesis/chemistry/genetics MH - SOS1 Protein/*chemistry/genetics/metabolism MH - Scattering, Radiation MH - Urea/chemistry PMC - PMC3615079 MID - NIHMS449380 OID - NLM: NIHMS449380 OID - NLM: PMC3615079 EDAT- 2013/03/27 06:00 MHDA- 2013/09/11 06:00 CRDT- 2013/03/27 06:00 PHST- 2012/12/20 [received] PHST- 2013/02/08 [revised] PHST- 2013/02/25 [accepted] PHST- 2013/03/05 [aheadofprint] AID - S0301-4622(13)00034-3 [pii] AID - 10.1016/j.bpc.2013.02.008 [doi] PST - ppublish SO - Biophys Chem. 2013 May-Jun;175-176:54-62. doi: 10.1016/j.bpc.2013.02.008. Epub 2013 Mar 5. PMID- 24516125 OWN - NLM STAT- MEDLINE DA - 20140226 DCOM- 20140422 LR - 20141111 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 8 DP - 2014 Feb 25 TI - Lipid domains control myelin basic protein adsorption and membrane interactions between model myelin lipid bilayers. PG - E768-75 LID - 10.1073/pnas.1401165111 [doi] AB - The surface forces apparatus and atomic force microscope were used to study the effects of lipid composition and concentrations of myelin basic protein (MBP) on the structure of model lipid bilayers, as well as the interaction forces and adhesion between them. The lipid bilayers had a lipid composition characteristic of the cytoplasmic leaflets of myelin from "normal" (healthy) and "disease-like" [experimental allergic encephalomyelitis (EAE)] animals. They showed significant differences in the adsorption mechanism of MBP. MBP adsorbs on normal bilayers to form a compact film (3-4 nm) with strong intermembrane adhesion ( approximately 0.36 mJ/m(2)), in contrast to its formation of thicker (7-8 nm) swelled films with weaker intermembrane adhesion ( approximately 0.13 mJ/m(2)) on EAE bilayers. MBP preferentially adsorbs to liquid-disordered submicron domains within the lipid membranes, attributed to hydrophobic attractions. These results show a direct connection between the lipid composition of membranes and membrane-protein adsorption mechanisms that affects intermembrane spacing and adhesion and has direct implications for demyelinating diseases. FAU - Lee, Dong Woog AU - Lee DW AD - Department of Chemical Engineering, University of California, Santa Barbara, CA 93106. FAU - Banquy, Xavier AU - Banquy X FAU - Kristiansen, Kai AU - Kristiansen K FAU - Kaufman, Yair AU - Kaufman Y FAU - Boggs, Joan M AU - Boggs JM FAU - Israelachvili, Jacob N AU - Israelachvili JN LA - eng GR - MOP 86483/Canadian Institutes of Health Research/Canada GR - R01 GM076709/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140210 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Lipid Bilayers) RN - 0 (Myelin Basic Protein) SB - IM MH - Adsorption MH - Animals MH - Callithrix MH - Encephalomyelitis, Autoimmune, Experimental/*metabolism MH - Lipid Bilayers/*metabolism MH - Microscopy, Atomic Force MH - *Models, Molecular MH - Myelin Basic Protein/*metabolism MH - Myelin Sheath/*metabolism MH - Neurons/*cytology MH - Protein Structure, Tertiary MH - Sus scrofa PMC - PMC3939865 OID - NLM: PMC3939865 OTO - NOTNLM OT - biomembrane adhesion OT - intrinsically unstructured proteins OT - lipid raft OT - multiple sclerosis OT - myelin structure EDAT- 2014/02/12 06:00 MHDA- 2014/04/23 06:00 CRDT- 2014/02/12 06:00 PHST- 2014/02/10 [aheadofprint] AID - 1401165111 [pii] AID - 10.1073/pnas.1401165111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):E768-75. doi: 10.1073/pnas.1401165111. Epub 2014 Feb 10. PMID- 9054966 OWN - NLM STAT- MEDLINE DA - 19970403 DCOM- 19970403 LR - 20021101 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 266 IP - 1 DP - 1997 Feb 14 TI - Heteronuclear NMR studies of E. coli translation initiation factor IF3. Evidence that the inter-domain region is disordered in solution. PG - 15-22 AB - Initiation factor IF3 from Escherichia coli plays a critical role in the selection of the correct initiation codon. This protein is composed of two domains, connected by a lysin-rich hydrophilic linker. The conformation of native IF3 was investigated by heteronuclear NMR spectroscopy. The two domains are independent and show little or no interaction. Heteronuclear relaxation studies of a sample selectively labelled on lysine residues demonstrates that the inter-domain linker is highly flexible, exhibiting increased 15N T2 values and negative 1H[15N] nuclear Overhause effects over a length of at least eight residues. Analysis of the rotational correlation times further shows that the motions of the two domains are most likely uncorrelated. The inter-domain linker thus displays almost totally unrestricted motions. Accordingly, the amide protons in the central region are shown to be in fast exchange with water. Such a high degree of flexibility of the inter-domain linker might be required for IF3 domains to interact with distant regions of the ribosome. FAU - Moreau, M AU - Moreau M AD - Laboratoire de Synthese Organique, URA 1308 du CNRS Ecole Polytechnique, Palaiseau, France. FAU - de Cock, E AU - de Cock E FAU - Fortier, P L AU - Fortier PL FAU - Garcia, C AU - Garcia C FAU - Albaret, C AU - Albaret C FAU - Blanquet, S AU - Blanquet S FAU - Lallemand, J Y AU - Lallemand JY FAU - Dardel, F AU - Dardel F LA - eng PT - Journal Article PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (Nitrogen Isotopes) RN - 0 (Peptide Initiation Factors) RN - 0 (Prokaryotic Initiation Factor-3) RN - 0 (Solutions) SB - IM MH - Bacterial Proteins/chemistry MH - Computer Simulation MH - Escherichia coli/metabolism MH - Magnetic Resonance Spectroscopy/methods MH - Models, Structural MH - Nitrogen Isotopes MH - Peptide Initiation Factors/*chemistry/metabolism MH - Prokaryotic Initiation Factor-3 MH - *Protein Conformation MH - Ribosomes/metabolism MH - Solutions EDAT- 1997/02/14 MHDA- 1997/02/14 00:01 CRDT- 1997/02/14 00:00 AID - S0022283696907561 [pii] PST - ppublish SO - J Mol Biol. 1997 Feb 14;266(1):15-22. PMID- 10526407 OWN - NLM STAT- MEDLINE DA - 19991102 DCOM- 19991102 LR - 20061115 IS - 0925-2738 (Print) IS - 0925-2738 (Linking) VI - 14 IP - 4 DP - 1999 Aug TI - Human replication protein A: global fold of the N-terminal RPA-70 domain reveals a basic cleft and flexible C-terminal linker. PG - 321-31 AB - Human Replication Protein A (hsRPA) is required for multiple cellular processes in DNA metabolism including DNA repair, replication and recombination. It binds single-stranded DNA with high affinity and interacts specifically with multiple proteins. hsRPA forms a heterotrimeric complex composed of 70-, 32- and 14-kDa subunits (henceforth RPA70, RPA32, and RPA14). The N-terminal 168 residues of RPA70 form a structurally distinct domain that stimulates DNA polymerase alpha activity, interacts with several transcriptional activators including tumor suppressor p53, and during the cell cycle it signals escape from the DNA damage induced G2/M checkpoint. We have solved the global fold of the fragment corresponding to this domain (RPA70 delta 169) and we find residues 8-108 of the N-terminal domain are structured. The remaining C-terminal residues are unstructured and may form a flexible linker to the DNA-binding domain of RPA70. The globular region forms a five-stranded anti-parallel beta-barrel. The ends of the barrel are capped by short helices. Two loops on one side of the barrel form a large basic cleft which is a likely site for binding the acidic motifs of transcriptional activators. Many lethal or conditional lethal yeast point mutants map to this cleft, whereas no mutations with severe phenotype have been found in the linker region. FAU - Jacobs, D M AU - Jacobs DM AD - Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA. FAU - Lipton, A S AU - Lipton AS FAU - Isern, N G AU - Isern NG FAU - Daughdrill, G W AU - Daughdrill GW FAU - Lowry, D F AU - Lowry DF FAU - Gomes, X AU - Gomes X FAU - Wold, M S AU - Wold MS LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - NETHERLANDS TA - J Biomol NMR JT - Journal of biomolecular NMR JID - 9110829 RN - 0 (DNA-Binding Proteins) RN - 0 (RPA1 protein, human) RN - 0 (Replication Protein A) SB - IM MH - Amino Acid Sequence MH - *DNA Replication MH - DNA-Binding Proteins/*chemistry/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Conformation MH - *Protein Folding MH - Replication Protein A EDAT- 1999/10/20 MHDA- 1999/10/20 00:01 CRDT- 1999/10/20 00:00 PST - ppublish SO - J Biomol NMR. 1999 Aug;14(4):321-31. PMID- 23327569 OWN - NLM STAT- MEDLINE DA - 20130219 DCOM- 20131118 IS - 1520-6882 (Electronic) IS - 0003-2700 (Linking) VI - 85 IP - 4 DP - 2013 Feb 19 TI - Single-molecule studies of intrinsically disordered proteins using solid-state nanopores. PG - 2449-56 LID - 10.1021/ac3035025 [doi] AB - Partially or fully disordered proteins are instrumental for signal-transduction pathways; however, many mechanistic aspects of these proteins are not well-understood. For example, the number and nature of intermediate states along the binding pathway is still a topic of intense debate. To shed light on the conformational heterogeneity of disordered protein domains and their complexes, we performed single-molecule experiments by translocating disordered proteins through a nanopore embedded within a thin dielectric membrane. This platform allows for single-molecule statistics to be generated without the need of fluorescent labels or other modification groups. These studies were performed on two different intrinsically disordered protein domains, a binding domain from activator of thyroid hormone and retinoid receptors (ACTR) and the nuclear coactivator binding domain of CREB-binding protein (NCBD), along with their bimolecular complex. Our results demonstrate that both ACTR and NCBD populate distinct conformations upon translocation through the nanopore. The folded complex of the two disordered domains, on the other hand, translocated as one conformation. Somewhat surprisingly, we found that NCBD undergoes a charge reversal under high salt concentrations. This was verified by both translocation statistics as well as by measuring the zeta-potential. Electrostatic interactions have been previously suggested to play a key role in the association of intrinsically disordered proteins, and the observed behavior adds further complexity to their binding reactions. FAU - Japrung, Deanpen AU - Japrung D AD - Department of Chemistry, Imperial College London, South Kensington, SW7 2AZ, London, United Kingdom. FAU - Dogan, Jakob AU - Dogan J FAU - Freedman, Kevin J AU - Freedman KJ FAU - Nadzeyka, Achim AU - Nadzeyka A FAU - Bauerdick, Sven AU - Bauerdick S FAU - Albrecht, Tim AU - Albrecht T FAU - Kim, Min Jun AU - Kim MJ FAU - Jemth, Per AU - Jemth P FAU - Edel, Joshua B AU - Edel JB LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130206 PL - United States TA - Anal Chem JT - Analytical chemistry JID - 0370536 RN - 0 (Recombinant Proteins) RN - 0 (Salts) RN - 0 (Thyroid Hormones) RN - EC 2.3.1.48 (CREB-Binding Protein) RN - EC 2.3.1.48 (NCOA3 protein, human) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 3) SB - IM MH - CREB-Binding Protein/chemistry/genetics/*metabolism MH - Humans MH - *Light MH - *Nanopores MH - Nuclear Receptor Coactivator 3/chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Recombinant Proteins/biosynthesis/chemistry/genetics MH - Salts/chemistry MH - *Scattering, Radiation MH - Signal Transduction MH - Static Electricity MH - Thyroid Hormones/chemistry/*metabolism EDAT- 2013/01/19 06:00 MHDA- 2013/11/19 06:00 CRDT- 2013/01/19 06:00 PHST- 2013/02/06 [aheadofprint] AID - 10.1021/ac3035025 [doi] PST - ppublish SO - Anal Chem. 2013 Feb 19;85(4):2449-56. doi: 10.1021/ac3035025. Epub 2013 Feb 6. PMID- 12529538 OWN - NLM STAT- MEDLINE DA - 20030116 DCOM- 20030522 LR - 20140611 IS - 0032-0889 (Print) IS - 0032-0889 (Linking) VI - 131 IP - 1 DP - 2003 Jan TI - The binding of maize DHN1 to lipid vesicles. Gain of structure and lipid specificity. PG - 309-16 AB - Dehydrins (DHNs; late embryogenesis abundant D-11) are a family of plant proteins induced in response to abiotic stresses such as drought, low temperature, and salinity or during the late stages of embryogenesis. Spectral and thermal properties of these proteins in purified form suggest that they are "intrinsically unstructured." However, DHNs contain at least one copy of a consensus 15-amino acid sequence, the "K segment," which resembles a class A2 amphipathic alpha-helical, lipid-binding domain found in other proteins such as apolipoproteins and alpha-synuclein. The presence of the K segment raises the question of whether DHNs bind lipids, bilayers, or phospholipid vesicles. Here, we show that maize (Zea mays) DHN DHN1 can bind to lipid vesicles that contain acidic phospholipids. We also observe that DHN1 binds more favorably to vesicles of smaller diameter than to larger vesicles, and that the association of DHN1 with vesicles results in an apparent increase of alpha-helicity of the protein. Therefore, DHNs, and presumably somewhat similar plant stress proteins in the late embryogenesis abundant and cold-regulated classes may undergo function-related conformational changes at the water/membrane interface, perhaps related to the stabilization of vesicles or other endomembrane structures under stress conditions. FAU - Koag, Myong-Chul AU - Koag MC AD - Graduate Program in Biochemistry and Molecular Biology, University of California, Riverside, California 92521-0124, USA. FAU - Fenton, Raymond D AU - Fenton RD FAU - Wilkens, Stephan AU - Wilkens S FAU - Close, Timothy J AU - Close TJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Plant Physiol JT - Plant physiology JID - 0401224 RN - 0 (Plant Proteins) RN - 0 (late embryogenesis abundant protein, plant) RN - 134711-03-8 (dehydrin proteins, plant) RN - 7647-14-5 (Sodium Chloride) SB - IM MH - Adaptation, Physiological/drug effects/physiology MH - Circular Dichroism MH - Cold Temperature MH - Disasters MH - *Lipid Metabolism MH - Plant Proteins/chemistry/*metabolism MH - Protein Binding MH - Seeds/growth & development MH - Sodium Chloride/pharmacology MH - Transport Vesicles/*metabolism MH - Zea mays/growth & development/*metabolism PMC - PMC166810 OID - NLM: PMC166810 EDAT- 2003/01/17 04:00 MHDA- 2003/05/23 05:00 CRDT- 2003/01/17 04:00 AID - 10.1104/pp.011171 [doi] PST - ppublish SO - Plant Physiol. 2003 Jan;131(1):309-16. PMID- 24384095 OWN - NLM STAT- MEDLINE DA - 20140214 DCOM- 20150116 IS - 1567-7257 (Electronic) IS - 1567-1348 (Linking) VI - 21 DP - 2014 Jan TI - Population genetics and natural selection in the gene encoding the Duffy binding protein II in Iranian Plasmodium vivax wild isolates. PG - 424-35 LID - 10.1016/j.meegid.2013.12.012 [doi] LID - S1567-1348(13)00455-3 [pii] AB - Region II of Duffy binding protein (PvDBP-II) is one of the most promising blood-stage vaccine candidate antigens against Plasmodium vivax and having knowledge of the nature and genetic polymorphism of PvDBP-II among global P. vivax isolates is important for developing a DBP-based vaccine. By using PCR and sequencing, the present molecular population genetic approach was carried out to investigate sequence diversity and natural selection of dbp-II gene in 63 P. vivax isolates collected from unstable and low transmission malaria-endemic areas of Iran during 2008-2012. Also, phylogenetic analysis, the diversifying natural selection, and recombination across the pvdbp-II gene, including regions containing B-cell epitopes were analyzed using the DnaSP and MEGA4 programs. Twenty two single nucleotide polymorphisms (SNPs, including 20 non-synonymous and 2 synonymous) were identified in PvDBP-II, resulting in 16 different PvDBP-II haplotypes among the Iranian P. vivax isolates. High binding inhibitory B-cell epitope (H3) overlapping with intrinsically unstructured/disordered region (aa: 384-392) appeared to be highly polymorphic (D384G/E385K/ K386N/Q/R390H), and positive selective pressure acted on this region. Most of the polymorphic amino acids, which are located on the surface of the protein, are under selective pressure that implies increased recombination events and exposure to the human immune system. In summary, PvDBP-II gene displays genetic polymorphism among Iranian P. vivax isolates and it is under selective pressure. Mutations, recombination, and positive selection seem to play a role in the resulting genetic diversity, and phylogenetic analysis of DNA sequences demonstrates that Iranian isolates represent a sample of the global population. These results are useful for understanding the nature of the P. vivax population in Iran and also for development of PvDBP-II-based malaria vaccine. CI - Copyright (c) 2013 Elsevier B.V. All rights reserved. FAU - Valizadeh, Vahideh AU - Valizadeh V AD - Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Pasteur Avenue, P.O. Box 1316943551, Tehran, Iran. FAU - Zakeri, Sedigheh AU - Zakeri S AD - Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Pasteur Avenue, P.O. Box 1316943551, Tehran, Iran. Electronic address: zakeris@yahoo.com. FAU - Mehrizi, Akram Abouie AU - Mehrizi AA AD - Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Pasteur Avenue, P.O. Box 1316943551, Tehran, Iran. FAU - Djadid, Navid Dinparast AU - Djadid ND AD - Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Pasteur Avenue, P.O. Box 1316943551, Tehran, Iran. LA - eng SI - GENBANK/EU860428 SI - GENBANK/EU860430 SI - GENBANK/EU860431 SI - GENBANK/EU860432 SI - GENBANK/EU860433 SI - GENBANK/EU860434 SI - GENBANK/EU860435 SI - GENBANK/EU860436 SI - GENBANK/KF318358 SI - GENBANK/KF318359 SI - GENBANK/KF791921 SI - GENBANK/KF791922 SI - GENBANK/KF791923 SI - GENBANK/KF791924 SI - GENBANK/KF791925 SI - GENBANK/KF791926 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131230 PL - Netherlands TA - Infect Genet Evol JT - Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases JID - 101084138 RN - 0 (Antigens, Protozoan) RN - 0 (Duffy antigen binding protein, Plasmodium) RN - 0 (Epitopes, B-Lymphocyte) RN - 0 (Protozoan Proteins) RN - 0 (Receptors, Cell Surface) SB - IM MH - Adolescent MH - Adult MH - Antigens, Protozoan/chemistry/*genetics/metabolism MH - Child MH - Epitopes, B-Lymphocyte/metabolism MH - Female MH - Genetic Variation MH - Humans MH - Iran MH - Malaria, Vivax/epidemiology/*parasitology MH - Male MH - Middle Aged MH - Molecular Sequence Data MH - Phylogeny MH - Plasmodium vivax/genetics/*isolation & purification MH - Polymorphism, Single Nucleotide MH - Protozoan Proteins/chemistry/*genetics/metabolism MH - Receptors, Cell Surface/chemistry/*genetics/metabolism MH - Recombination, Genetic MH - Selection, Genetic MH - Young Adult OTO - NOTNLM OT - Duffy binding protein OT - Iran OT - Natural selection OT - Plasmodium vivax OT - Population genetics EDAT- 2014/01/05 06:00 MHDA- 2015/01/17 06:00 CRDT- 2014/01/04 06:00 PHST- 2013/11/12 [received] PHST- 2013/12/20 [revised] PHST- 2013/12/21 [accepted] PHST- 2013/12/30 [aheadofprint] AID - S1567-1348(13)00455-3 [pii] AID - 10.1016/j.meegid.2013.12.012 [doi] PST - ppublish SO - Infect Genet Evol. 2014 Jan;21:424-35. doi: 10.1016/j.meegid.2013.12.012. Epub 2013 Dec 30. PMID- 16110343 OWN - NLM STAT- MEDLINE DA - 20060605 DCOM- 20070514 LR - 20140606 IS - 1553-734X (Print) IS - 1553-734X (Linking) VI - 1 IP - 3 DP - 2005 Aug TI - Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions. PG - e26 AB - Protein interaction networks are an important part of the post-genomic effort to integrate a part-list view of the cell into system-level understanding. Using a set of 11 yeast genomes we show that combining comparative genomics and secondary structure information greatly increases consensus-based prediction of SH3 targets. Benchmarking of our method against positive and negative standards gave 83% accuracy with 26% coverage. The concept of an optimal divergence time for effective comparative genomics studies was analyzed, demonstrating that genomes of species that diverged very recently from Saccharomyces cerevisiae(S. mikatae, S. bayanus, and S. paradoxus), or a long time ago (Neurospora crassa and Schizosaccharomyces pombe), contain less information for accurate prediction of SH3 targets than species within the optimal divergence time proposed. We also show here that intrinsically disordered SH3 domain targets are more probable sites of interaction than equivalent sites within ordered regions. Our findings highlight several novel S. cerevisiae SH3 protein interactions, the value of selection of optimal divergence times in comparative genomics studies, and the importance of intrinsic disorder for protein interactions. Based on our results we propose novel roles for the S. cerevisiae proteins Abp1p in endocytosis and Hse1p in endosome protein sorting. FAU - Beltrao, Pedro AU - Beltrao P AD - EMBL Structural and Computational Biology, Heidelberg, Germany. beltrao@embl-heidelberg.de FAU - Serrano, Luis AU - Serrano L LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050812 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (Fungal Proteins) RN - 0 (Ligands) SB - IM MH - Base Sequence MH - Computational Biology MH - Conserved Sequence MH - Evolution, Molecular MH - Fungal Proteins/chemistry/*genetics/*metabolism MH - Genome, Fungal/*genetics MH - *Genomics MH - Ligands MH - Protein Binding MH - Protein Interaction Mapping/*methods MH - Protein Structure, Secondary MH - Time Factors MH - *src Homology Domains PMC - PMC1187863 OID - NLM: PMC1187863 EDAT- 2005/08/20 09:00 MHDA- 2007/05/15 09:00 CRDT- 2005/08/20 09:00 PHST- 2005/01/11 [received] PHST- 2005/07/05 [accepted] PHST- 2005/08/12 [aheadofprint] AID - 10.1371/journal.pcbi.0010026 [doi] PST - ppublish SO - PLoS Comput Biol. 2005 Aug;1(3):e26. Epub 2005 Aug 12. PMID- 19081538 OWN - NLM STAT- MEDLINE DA - 20081216 DCOM- 20090123 IS - 1937-6448 (Print) VI - 270 DP - 2008 TI - Molecular and cellular biology of synucleins. PG - 225-317 LID - 10.1016/S1937-6448(08)01406-8 [doi] AB - Synucleins are small, soluble proteins expressed primarily in neural tissues and certain tumors. The family includes three known proteins: alpha-synuclein, beta-synuclein, and gamma-synuclein. A typical structural feature of synucleins is the presence of a repetitive, degenerative AA motif KTKEGV throughout the first 87 residues and acidic stretches within the C-terminal region. Members of the synuclein family are natively unfolded proteins that are characterized by a high net charge and low hydropathy. The synuclein family recently came into the spotlight when one of its members, alpha-synuclein, was linked both genetically and neuropathologically to Parkinson's disease. It has a role in other neurodegenerative diseases, such as dementia with Lewy bodies, multiple system atrophy, neurodegeneration with brain iron accumulation type 1, and Alzheimer's disease. Interestingly, another member of the family, beta-synuclein, possesses antagonistic properties to alpha-synuclein. The third member of the family, gamma-synuclein, is implicated in different types of cancer, some neurodegenerative diseases and ocular pathology. The involvement of synuclein proteins in the etiology of common human diseases has raised exciting questions and is currently the subject of intense investigation. FAU - Surguchov, Andrei AU - Surguchov A AD - Retinal Biology Research Laboratory, VA Medical Center, Kansas City, Missouri 64128, USA. LA - eng GR - EY 02687/EY/NEI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Review PL - Netherlands TA - Int Rev Cell Mol Biol JT - International review of cell and molecular biology JID - 101475846 RN - 0 (Synucleins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Eukaryotic Cells/*physiology MH - Humans MH - Molecular Sequence Data MH - Neoplasms/*physiopathology MH - Neurodegenerative Diseases/*physiopathology MH - Synucleins/genetics/*physiology RF - 419 EDAT- 2008/12/17 09:00 MHDA- 2009/01/24 09:00 CRDT- 2008/12/17 09:00 AID - S1937-6448(08)01406-8 [pii] AID - 10.1016/S1937-6448(08)01406-8 [doi] PST - ppublish SO - Int Rev Cell Mol Biol. 2008;270:225-317. doi: 10.1016/S1937-6448(08)01406-8. PMID- 19710008 OWN - NLM STAT- MEDLINE DA - 20091116 DCOM- 20091214 LR - 20140828 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 284 IP - 47 DP - 2009 Nov 20 TI - Two lysine residues in the bacterial luciferase mobile loop stabilize reaction intermediates. PG - 32827-34 LID - 10.1074/jbc.M109.031716 [doi] AB - Bacterial luciferase catalyzes the reaction of FMNH(2), O(2), and a long chain aliphatic aldehyde, yielding FMN, carboxylic acid, and blue-green light. The most conserved contiguous region of the primary sequence corresponds to a crystallographically disordered loop adjacent to the active center (Fisher, A. J., Raushel, F. M., Baldwin, T. O., and Rayment, I. (1995) Biochemistry 34, 6581-6586; Fisher, A. J., Thompson, T. B., Thoden, J. B., Baldwin, T. O., and Rayment, I. (1996) J. Biol. Chem. 271, 21956-21968). Deletion of the mobile loop does not alter the chemistry of the reaction but decreases the total quantum yield of bioluminescence by 2 orders of magnitude (Sparks, J. M., and Baldwin, T. O. (2001) Biochemistry 40, 15436-15443). In this study, we attempt to localize the loss of activity observed in the loop deletion mutant to individual residues in the mobile loop. Using alanine mutagenesis, the effects of substitution at 15 of the 29 mobile loop residues were examined. Nine of the point mutants had reduced activity in vivo. Two mutations, K283A and K286A, resulted in a loss in quantum yield comparable with that of the loop deletion mutant. The bioluminescence emission spectrum of both mutants was normal, and both yielded the carboxylic acid chemical product at the same efficiency as the wild-type enzyme. Substitution of Lys(283) with alanine resulted in destabilization of intermediate II, whereas mutation of Lys(286) had an increase in exposure of reaction intermediates to a dynamic quencher. Based on a model of the enzyme-reduced flavin complex, the two critical lysine residues are adjacent to the quininoidal edge of the isoalloxazine. FAU - Campbell, Zachary T AU - Campbell ZT AD - Department of Biochemistry and Molecular Biophysics, University of Arizona, Biological Sciences West, Tucson, Arizona 85721-0088, USA. FAU - Baldwin, Thomas O AU - Baldwin TO LA - eng PT - Journal Article DEP - 20090826 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Carboxylic Acids) RN - 0 (Flavins) RN - EC 1.13.12.- (Luciferases) RN - K3Z4F929H6 (Lysine) RN - OF5P57N2ZX (Alanine) SB - IM MH - Alanine/chemistry MH - Amino Acid Sequence MH - Bacteria/*metabolism MH - Carboxylic Acids/chemistry MH - Escherichia coli/metabolism MH - Flavins/chemistry MH - Genetic Vectors MH - Luciferases/metabolism MH - Lysine/*chemistry MH - Molecular Sequence Data MH - Mutagenesis MH - Point Mutation MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Vibrio/metabolism PMC - PMC2781699 OID - NLM: PMC2781699 EDAT- 2009/08/28 09:00 MHDA- 2009/12/16 06:00 CRDT- 2009/08/28 09:00 PHST- 2009/08/26 [aheadofprint] AID - M109.031716 [pii] AID - 10.1074/jbc.M109.031716 [doi] PST - ppublish SO - J Biol Chem. 2009 Nov 20;284(47):32827-34. doi: 10.1074/jbc.M109.031716. Epub 2009 Aug 26. PMID- 23205890 OWN - NLM STAT- MEDLINE DA - 20130110 DCOM- 20130606 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 117 IP - 1 DP - 2013 Jan 10 TI - Structural ensemble of an intrinsically disordered polypeptide. PG - 118-24 LID - 10.1021/jp308984e [doi] AB - Intrinsically disordered proteins (IDPs), which play key roles in cell signaling and regulation, do not display specific tertiary structure when isolated in solution. Instead, they dynamically explore an ensemble of unfolded configurations, adopting more stable, ordered structures only after binding to their ligands. Whether ligands induce IDP structural changes upon binding or simply bind to pre-existing conformers that are populated within the IDP's structural ensemble is not well understood. Molecular simulations can provide information with the spatiotemporal resolution necessary to resolve these issues. Here, we report on the conformational ensemble of a 15-residue wild-type p53 fragment from the TAD domain and its mutant (TAD-P27L) obtained by replica exchange molecular dynamics simulation using an optimized (fully atomistic, explicit solvent) protein model and the experimental validation of the simulation results. We use a clustering method based on structural similarity to identify conformer states populated by the peptides in solution from the simulated ensemble. We show that p53 populates solution structures that strongly resemble the ligand (MDM2)-bound structure, but at the same time, the conformational free-energy landscape is relatively flat in the absence of the ligand. FAU - Mittal, Jeetain AU - Mittal J AD - Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States. jeetain@lehigh.edu FAU - Yoo, Tae Hyeon AU - Yoo TH FAU - Georgiou, George AU - Georgiou G FAU - Truskett, Thomas M AU - Truskett TM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20121219 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Peptides) SB - IM MH - Amino Acid Sequence MH - Biophysics MH - Circular Dichroism MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides/*chemistry MH - Protein Conformation EDAT- 2012/12/05 06:00 MHDA- 2013/06/07 06:00 CRDT- 2012/12/05 06:00 PHST- 2012/12/19 [aheadofprint] AID - 10.1021/jp308984e [doi] PST - ppublish SO - J Phys Chem B. 2013 Jan 10;117(1):118-24. doi: 10.1021/jp308984e. Epub 2012 Dec 19. PMID- 25144497 OWN - NLM STAT- MEDLINE DA - 20140918 DCOM- 20150519 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 118 IP - 37 DP - 2014 Sep 18 TI - Temperature-dependent dynamics of dry and hydrated beta-casein studied by quasielastic neutron scattering. PG - 10821-9 LID - 10.1021/jp504548w [doi] AB - beta-Casein is a component of casein micelle with amphillic nature and is recognized as a "natively disordered" protein that lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of beta-casein are explored by quasielastic neutron scattering (QENS). An upturn in the mean square displacement (MSD) of hydrated beta-casein indicates an increase of protein flexibility at a temperature of ~225 K. Another increase in MSD at ~100 K, observed in both dry and hydrated beta-casein, is ascribed to the methyl group rotations, which are not sensitive to hydration. QENS analysis in the energy domain reveals that the fraction of hydrogen atoms participating in motion in a sphere of diffusion is highly hydration dependent and increases with temperature. In the time domain analysis, a logarithmic-like decay is observed in the range of picosecond to nanosecond (beta-relaxation time) in the dynamics of hydrated beta-casein. This dynamical behavior has been observed in hydrated globular and oligomeric proteins. Our temperature-dependent QENS experiments provide evidence that lack of a secondary structure in beta-casein results in higher flexibility in its dynamics and easier reversible thermal unfolding compared to other rigid biomolecules. FAU - Dhindsa, Gurpreet K AU - Dhindsa GK AD - Department of Physics and Astronomy, Wayne State University , Detroit, Michigan 48201, United States. FAU - Tyagi, Madhusudan AU - Tyagi M FAU - Chu, Xiang-qiang AU - Chu XQ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140905 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Caseins) RN - 059QF0KO0R (Water) RN - 7YNJ3PO35Z (Hydrogen) RN - J65BV539M3 (Deuterium Oxide) SB - IM MH - Caseins/*chemistry MH - Deuterium Oxide/chemistry MH - Diffusion MH - Hydrogen/chemistry MH - *Neutron Diffraction MH - Temperature MH - Thermodynamics MH - Water/chemistry EDAT- 2014/08/22 06:00 MHDA- 2015/05/20 06:00 CRDT- 2014/08/22 06:00 PHST- 2014/09/05 [aheadofprint] AID - 10.1021/jp504548w [doi] PST - ppublish SO - J Phys Chem B. 2014 Sep 18;118(37):10821-9. doi: 10.1021/jp504548w. Epub 2014 Sep 5. PMID- 19625749 OWN - NLM STAT- MEDLINE DA - 20090930 DCOM- 20100604 IS - 1875-8908 (Electronic) IS - 1387-2877 (Linking) VI - 18 IP - 1 DP - 2009 TI - Tau aggregation followed by atomic force microscopy and surface plasmon resonance, and single molecule tau-tau interaction probed by atomic force spectroscopy. PG - 141-51 LID - 10.3233/JAD-2009-1130 [doi] AB - Intracellular neurofibrillary tangles, composed mainly of tau protein, and extracellular plaques, containing mostly amyloid-beta, are the two types of protein aggregates found upon autopsy within the brain of Alzheimer's disease patients. Polymers of tau protein can also be found in other neurodegenerative disorders known as tauopathies. Tau is a highly soluble protein, intrinsically devoid of secondary or tertiary structure, as many others proteins particularly prone to form fibrillar aggregations. The mechanism by which this unfolded molecule evolves to the well ordered helical filaments has been amply studied. In fact, it is a very slow process when followed in the absence of aggregation inducers. Herein we describe the use of surface plasmon resonance, atomic force microscopy, and atomic force spectroscopy to detect tau-tau interactions and to follow the process of aggregation in the absence of aggregation inducers. Tau-tau interactions are clearly detected, although a very long period of time is needed to observe filaments formation. Tau oligomers showing a granular appearance, however, are observed immediately as a consequence of this interaction. These granular tau oligomers slowly evolve to larger structures and eventually to filaments having a size smaller than those reported for paired helical filaments purified from Alzheimer's disease. FAU - Barrantes, Alejandro AU - Barrantes A AD - Centro de Biologia Molecular Severo Ochoa, CSIC, Madrid, Spain. FAU - Sotres, Javier AU - Sotres J FAU - Hernando-Perez, Mercedes AU - Hernando-Perez M FAU - Benitez, Maria J AU - Benitez MJ FAU - de Pablo, Pedro J AU - de Pablo PJ FAU - Baro, Arturo M AU - Baro AM FAU - Avila, Jesus AU - Avila J FAU - Jimenez, Juan S AU - Jimenez JS LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - J Alzheimers Dis JT - Journal of Alzheimer's disease : JAD JID - 9814863 RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/metabolism MH - Cell Aggregation/physiology MH - Humans MH - *Microscopy, Atomic Force/methods MH - Protein Folding MH - Protein Interaction Domains and Motifs/*physiology MH - *Surface Plasmon Resonance/methods MH - tau Proteins/chemistry/*metabolism EDAT- 2009/07/25 09:00 MHDA- 2010/06/05 06:00 CRDT- 2009/07/24 09:00 AID - V568X4152M746026 [pii] AID - 10.3233/JAD-2009-1130 [doi] PST - ppublish SO - J Alzheimers Dis. 2009;18(1):141-51. doi: 10.3233/JAD-2009-1130. PMID- 25120007 OWN - NLM STAT- In-Process DA - 20140814 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 8 DP - 2014 TI - Biophysical characterisation of calumenin as a charged F508del-CFTR folding modulator. PG - e104970 LID - 10.1371/journal.pone.0104970 [doi] AB - The cystic fibrosis transmembrane regulator (CFTR) is a cyclic-AMP dependent chloride channel expressed at the apical surface of epithelial cells lining various organs such as the respiratory tract. Defective processing and functioning of this protein caused by mutations in the CFTR gene results in loss of ionic balance, defective mucus clearance, increased proliferation of biofilms and inflammation of human airways observed in cystic fibrosis (CF) patients. The process by which CFTR folds and matures under the influence of various chaperones in the secretory pathway remains incompletely understood. Recently, calumenin, a secretory protein, belonging to the CREC family of low affinity calcium binding proteins has been identified as a putative CFTR chaperone whose biophysical properties and functions remain uncharacterized. We compared hydropathy, instability, charge, unfoldability, disorder and aggregation propensity of calumenin and other CREC family members with CFTR associated chaperones and calcium binding proteins, wild-type and mutant CFTR proteins and intrinsically disordered proteins (IDPs). We observed that calumenin, along with other CREC proteins, was significantly more charged and less folded compared to CFTR associated chaperones. Moreover like IDPs, calumenin and other CREC proteins were found to be less hydrophobic and aggregation prone. Phylogenetic analysis revealed a close link between calumenin and other CREC proteins indicating how evolution might have shaped their similar biophysical properties. Experimentally, calumenin was observed to significantly reduce F508del-CFTR aggregation in a manner similar to AavLEA1, a well-characterized IDP. Fluorescence microscopy based imaging analysis also revealed altered trafficking of calumenin in bronchial cells expressing F508del-CFTR, indicating its direct role in the pathophysiology of CF. In conclusion, calumenin is characterized as a charged protein exhibiting close similarity with IDPs and is hypothesized to regulate F508del-CFTR folding by electrostatic effects. This work provides useful insights for designing optimized synthetic structural correctors of CFTR mutant proteins in the future. FAU - Tripathi, Rashmi AU - Tripathi R AD - INSERM UMR1078, Brest, France; Universite de Bretagne Occidentale, Faculte de Medecine et des sciences de la sante, Brest, France. FAU - Benz, Nathalie AU - Benz N AD - INSERM UMR1078, Brest, France; Association Gaetan Saleun, Brest, France. FAU - Culleton, Bridget AU - Culleton B AD - Hopital Morvan, Laboratoire de Genetique Moleculaire et d'Histocompatibilite, Brest, France. FAU - Trouve, Pascal AU - Trouve P AD - INSERM UMR1078, Brest, France. FAU - Ferec, Claude AU - Ferec C AD - INSERM UMR1078, Brest, France; Universite de Bretagne Occidentale, Faculte de Medecine et des sciences de la sante, Brest, France; Hopital Morvan, Laboratoire de Genetique Moleculaire et d'Histocompatibilite, Brest, France; Etablissement Francais du Sang-Bretagne, Brest, France. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140813 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM PMC - PMC4132023 OID - NLM: PMC4132023 EDAT- 2014/08/15 06:00 MHDA- 2014/08/15 06:00 CRDT- 2014/08/15 06:00 PHST- 2014 [ecollection] PHST- 2014/03/27 [received] PHST- 2014/07/16 [accepted] PHST- 2014/08/13 [epublish] AID - 10.1371/journal.pone.0104970 [doi] AID - PONE-D-14-13343 [pii] PST - epublish SO - PLoS One. 2014 Aug 13;9(8):e104970. doi: 10.1371/journal.pone.0104970. eCollection 2014. PMID- 24048383 OWN - NLM STAT- MEDLINE DA - 20130919 DCOM- 20140421 LR - 20150606 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 4 DP - 2013 TI - Val66Met polymorphism of BDNF alters prodomain structure to induce neuronal growth cone retraction. PG - 2490 LID - 10.1038/ncomms3490 [doi] AB - A common single-nucleotide polymorphism (SNP) in the human brain-derived neurotrophic factor (BDNF) gene results in a Val66Met substitution in the BDNF prodomain region. This SNP is associated with alterations in memory and with enhanced risk to develop depression and anxiety disorders in humans. Here we show that the isolated BDNF prodomain is detected in the hippocampus and that it can be secreted from neurons in an activity-dependent manner. Using nuclear magnetic resonance spectroscopy and circular dichroism, we find that the prodomain is intrinsically disordered, and the Val66Met substitution induces structural changes. Surprisingly, application of Met66 (but not Val66) BDNF prodomain induces acute growth cone retraction and a decrease in Rac activity in hippocampal neurons. Expression of p75(NTR) and differential engagement of the Met66 prodomain to the SorCS2 receptor are required for this effect. These results identify the Met66 prodomain as a new active ligand, which modulates neuronal morphology. FAU - Anastasia, Agustin AU - Anastasia A AD - Department of Medicine, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA. FAU - Deinhardt, Katrin AU - Deinhardt K FAU - Chao, Moses V AU - Chao MV FAU - Will, Nathan E AU - Will NE FAU - Irmady, Krithi AU - Irmady K FAU - Lee, Francis S AU - Lee FS FAU - Hempstead, Barbara L AU - Hempstead BL FAU - Bracken, Clay AU - Bracken C LA - eng GR - HD23315/HD/NICHD NIH HHS/United States GR - NS030687/NS/NINDS NIH HHS/United States GR - NS052819/NS/NINDS NIH HHS/United States GR - NS064114/NS/NINDS NIH HHS/United States GR - NS21072/NS/NINDS NIH HHS/United States GR - P01 HD023315/HD/NICHD NIH HHS/United States GR - R01 AG025970/AG/NIA NIH HHS/United States GR - R01 NS021072/NS/NINDS NIH HHS/United States GR - R01 NS030687/NS/NINDS NIH HHS/United States GR - R01 NS052819/NS/NINDS NIH HHS/United States GR - R01 NS064114/NS/NINDS NIH HHS/United States GR - S10 RR023694/RR/NCRR NIH HHS/United States GR - S10-RR023694-01EWOF/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - Nat Commun JT - Nature communications JID - 101528555 RN - 0 (Brain-Derived Neurotrophic Factor) RN - 0 (NGFR protein, human) RN - 0 (Nerve Tissue Proteins) RN - 0 (Receptors, Cell Surface) RN - 0 (Receptors, Nerve Growth Factor) RN - 0 (Recombinant Proteins) RN - 0 (SORCS2 protein, human) RN - 0 (brain-derived neurotrophic factor, human) RN - EC 2.7.11.1 (Proto-Oncogene Proteins c-akt) SB - IM EIN - Nat Commun. 2014;5:3564 MH - Animals MH - Brain-Derived Neurotrophic Factor/*genetics/metabolism/secretion MH - Embryo, Mammalian MH - Escherichia coli/genetics MH - Gene Expression Regulation, Developmental MH - Growth Cones/*metabolism/pathology MH - HEK293 Cells MH - Hippocampus/growth & development/*metabolism/pathology MH - Humans MH - Magnetic Resonance Spectroscopy MH - Memory/physiology MH - Mice MH - Mice, Knockout MH - Nerve Tissue Proteins/genetics/metabolism MH - Neurogenesis/genetics MH - *Polymorphism, Single Nucleotide MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-akt/genetics/metabolism MH - Rats MH - Receptors, Cell Surface/genetics/metabolism MH - Receptors, Nerve Growth Factor/genetics/metabolism MH - Recombinant Proteins/genetics/metabolism PMC - PMC3820160 MID - NIHMS517924 OID - NLM: NIHMS517924 OID - NLM: PMC3820160 EDAT- 2013/09/21 06:00 MHDA- 2014/04/22 06:00 CRDT- 2013/09/20 06:00 PHST- 2013/04/18 [received] PHST- 2013/08/21 [accepted] AID - ncomms3490 [pii] AID - 10.1038/ncomms3490 [doi] PST - ppublish SO - Nat Commun. 2013;4:2490. doi: 10.1038/ncomms3490. PMID- 16516921 OWN - NLM STAT- MEDLINE DA - 20060327 DCOM- 20060503 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 358 IP - 1 DP - 2006 Apr 21 TI - Recognition of enolase in the Escherichia coli RNA degradosome. PG - 8-15 AB - In Escherichia coli, the glycolytic enzyme enolase is a component of the RNA degradosome, which is an RNase E mediated assembly involved in RNA processing and transcript turnover. The recruitment of enolase by the RNA degradosome has been implicated in the turnover of certain transcripts, and it is mediated by a small segment of roughly a dozen residues that lie within a natively unstructured sub-domain of RNase E. Here, we present the crystal structure of enolase in complex with its recognition site from RNase E at 1.6A resolution. A single molecule of the RNase E peptide binds asymmetrically in a conserved cleft at the interface of the enolase dimer. The recognition site is well conserved in RNase E homologues in a subfamily of the gamma-proteobacteria, including enzymes from pathogens such as Yersinia pestis, Vibrio cholera and Salmonella sp. We suggest that enolase is recruited into putative RNA degradosome machinery in these bacilli, where it plays common regulatory functions. FAU - Chandran, Vidya AU - Chandran V AD - Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAU - Luisi, Ben F AU - Luisi BF LA - eng SI - PDB/2FYM GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060221 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Multienzyme Complexes) RN - 0 (RNA, Bacterial) RN - 0 (degradosome) RN - EC 2.7.7.8 (Polyribonucleotide Nucleotidyltransferase) RN - EC 3.1.- (Endoribonucleases) RN - EC 3.1.4.- (ribonuclease E) RN - EC 3.6.4.13 (RNA Helicases) RN - EC 4.2.1.11 (Phosphopyruvate Hydratase) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - Endoribonucleases/chemistry/*metabolism MH - Escherichia coli/*cytology/*enzymology MH - Models, Molecular MH - Molecular Sequence Data MH - Multienzyme Complexes/*metabolism MH - Phosphopyruvate Hydratase/chemistry/*metabolism MH - Polyribonucleotide Nucleotidyltransferase/*metabolism MH - Protein Binding MH - RNA Helicases/*metabolism MH - RNA, Bacterial/*metabolism MH - Static Electricity EDAT- 2006/03/07 09:00 MHDA- 2006/05/04 09:00 CRDT- 2006/03/07 09:00 PHST- 2006/01/11 [received] PHST- 2006/02/05 [accepted] PHST- 2006/02/21 [aheadofprint] AID - S0022-2836(06)00181-1 [pii] AID - 10.1016/j.jmb.2006.02.012 [doi] PST - ppublish SO - J Mol Biol. 2006 Apr 21;358(1):8-15. Epub 2006 Feb 21. PMID- 19780584 OWN - NLM STAT- MEDLINE DA - 20091103 DCOM- 20091116 LR - 20150325 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 44 DP - 2009 Nov 10 TI - Interactions of the acidic domain and SRF interacting motifs with the NKX3.1 homeodomain. PG - 10601-7 LID - 10.1021/bi9013374 [doi] AB - NKX3.1 is a prostate tumor suppressor belonging to the NK-2 family of homeodomain (HD) transcription factors. NK-2 family members often possess a stretch of 10-15 residues enriched in acidic amino acids, the acidic domain (AD), in the flexible, disordered region N-terminal to the HD. Interactions between the N-terminal region of NKX3.1 and its homeodomain affect protein stability and DNA binding. CD spectroscopy measuring the thermal unfolding of NKX3.1 constructs showed a 2 degrees C intramolecular stabilization of the HD by the N-terminal region containing the acidic domain (residues 85-96). CD of mixtures of various N-terminal peptides with a construct containing just the HD showed that the acidic domain and the following region, the SRF interacting (SI) motif (residues 99-105), was necessary for this stabilization. Phosphorylation of the acidic domain is known to slow proteasomal degradation of NKX3.1 in prostate cells, and NMR spectroscopy was used to measure and map the interaction of the HD with phosphorylated and nonphosphorylated forms of the AD peptide. The interaction with the phosphorylated AD peptide was considerably stronger (K(d) = 0.5 +/- 0.2 mM), resulting in large chemical shift perturbations for residues Ser150 and Arg175 in the HD, as well as a 2 degrees C increase in the HD thermal stability compared to that of the nonphosphorylated form. NKX3.1 constructs with AD phosphorylation site threonine residues (89 and 93) mutated to glutamate were 4 degrees C more stable than HD alone. Using polymer theory, effective concentrations for interactions between domains connected by flexible linkers are predicted to be in the millimolar range, and thus, the weak intramolecular interactions observed here could conceivably modulate or compete with stronger, intermolecular interactions with the NKX3.1 HD. FAU - Ju, Jeong Ho AU - Ju JH AD - Division of Hematology/Oncology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA. FAU - Maeng, Jin-Soo AU - Maeng JS FAU - Lee, Duck-Yeon AU - Lee DY FAU - Piszczek, Grzegorz AU - Piszczek G FAU - Gelmann, Edward P AU - Gelmann EP FAU - Gruschus, James M AU - Gruschus JM LA - eng GR - ES09888/ES/NIEHS NIH HHS/United States GR - R01 ES009888/ES/NIEHS NIH HHS/United States GR - R01 ES009888-03/ES/NIEHS NIH HHS/United States GR - Z99 HL999999/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Homeodomain Proteins) RN - 0 (NKX3-1 protein, human) RN - 0 (SRF protein, human) RN - 0 (Serum Response Factor) RN - 0 (Transcription Factors) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Cell Line, Tumor MH - Circular Dichroism MH - *Genes, Tumor Suppressor MH - Homeodomain Proteins/chemistry/*metabolism MH - Humans MH - Male MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphorylation MH - Protein Binding MH - Protein Folding MH - Serum Response Factor/chemistry/*metabolism MH - Transcription Factors/chemistry/*metabolism PMC - PMC2783756 MID - NIHMS152543 OID - NLM: NIHMS152543 OID - NLM: PMC2783756 EDAT- 2009/09/29 06:00 MHDA- 2009/11/17 06:00 CRDT- 2009/09/29 06:00 AID - 10.1021/bi9013374 [doi] PST - ppublish SO - Biochemistry. 2009 Nov 10;48(44):10601-7. doi: 10.1021/bi9013374. PMID- 9545375 OWN - NLM STAT- MEDLINE DA - 19980526 DCOM- 19980526 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 277 IP - 4 DP - 1998 Apr 10 TI - ATP-independent DNA unwinding by the adenovirus single-stranded DNA binding protein requires a flexible DNA binding loop. PG - 825-38 AB - The adenovirus DNA binding protein (DBP) binds cooperatively to single-stranded (ss) DNA and stimulates both initiation and elongation of DNA replication. DBP forms protein filaments via a C-terminal arm that hooks into a neighbouring molecule. This multimerization is the driving force for ATP-independent DNA unwinding by DBP during elongation. Another conserved part of DBP forms an unstructured flexible loop that is probably directly involved in contacting DNA. By making appropriate deletion mutants that do not distort the overall DBP structure, the influence of the C-terminal arm and the flexible loop on the kinetics of ssDNA binding and on DNA replication was studied. Employing surface plasmon resonance we show that both parts of the protein are required for high affinity binding. Deletion of the C-terminal arm leads to an extremely labile DBP-ssDNA complex indicating the importance of multimerization. The flexible loop is also required for optimal stability of the DBP-ssDNA complex, providing additional evidence that this region forms part of the ssDNA-binding surface of DBP. Both deletion mutants are still able to stimulate initiation of DNA replication but are defective in supporting elongation, which may be caused by the fact that both mutants have a reduced DNA unwinding activity. Surprisingly, mixtures containing both mutants do stimulate elongation. Mixing the purified mutant proteins leads to the formation of mixed filaments that have a higher affinity for ssDNA than homogeneous mutant filaments. These results provide evidence that the C-terminal arm and the flexible loop have distinct functions in unwinding during replication. We propose the following model for ATP-independent DNA unwinding by DBP. Multimerization via the C-terminal arm is required for the formation of a protein filament that saturates the displaced strand. A high affinity of a DBP monomer for ssDNA and subsequent local destabilization of the replication fork requires the flexible loop. CI - Copyright 1998 Academic Press Limited. FAU - Dekker, J AU - Dekker J AD - Laboratory for Physiological Chemistry, Utrecht University, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands. FAU - Kanellopoulos, P N AU - Kanellopoulos PN FAU - van Oosterhout, J A AU - van Oosterhout JA FAU - Stier, G AU - Stier G FAU - Tucker, P A AU - Tucker PA FAU - van der Vliet, P C AU - van der Vliet PC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DNA Primers) RN - 0 (DNA, Single-Stranded) RN - 0 (DNA, Viral) RN - 0 (DNA-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Viral Proteins) RN - 8L70Q75FXE (Adenosine Triphosphate) SB - IM MH - Adenosine Triphosphate/metabolism MH - Adenoviridae/genetics/*metabolism MH - Animals MH - Base Sequence MH - Binding Sites MH - Biosensing Techniques MH - DNA Primers/genetics MH - DNA Replication MH - DNA, Single-Stranded/chemistry/genetics/metabolism MH - DNA, Viral/chemistry/genetics/*metabolism MH - DNA-Binding Proteins/chemistry/genetics/*metabolism MH - Nucleic Acid Conformation MH - Protein Conformation MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Sequence Deletion MH - Viral Proteins/chemistry/genetics/*metabolism EDAT- 1998/05/30 MHDA- 1998/05/30 00:01 CRDT- 1998/05/30 00:00 AID - S0022-2836(98)91652-7 [pii] AID - 10.1006/jmbi.1998.1652 [doi] PST - ppublish SO - J Mol Biol. 1998 Apr 10;277(4):825-38. PMID- 9334749 OWN - NLM STAT- MEDLINE DA - 19971113 DCOM- 19971113 LR - 20061115 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 4 IP - 10 DP - 1997 Oct TI - Structure of the collagen-binding domain from a Staphylococcus aureus adhesin. PG - 833-8 AB - The crystal structure of the recombinant 19,000 M(r) binding domain from the Staphylococcus aureus collagen adhesin has been determined at 2 A resolution. The domain fold is a jelly-roll, composed of two antiparallel beta-sheets and two short alpha-helices. Triple-helical collagen model probes were used in a systematic docking search to identify the collagen-binding site. A groove on beta-sheet I exhibited the best surface complementarity to the collagen probes. This site partially overlaps with the peptide sequence previously shown to be critical for collagen binding. Recombinant proteins containing single amino acid mutations designed to disrupt the surface of the putative binding site exhibited significantly lower affinities for collagen. Here we present a structural perspective for the mode of collagen binding by a bacterial surface protein. FAU - Symersky, J AU - Symersky J AD - Center for Macromolecular Crystallography, University of Alabama at Birmingham 35294, USA. FAU - Patti, J M AU - Patti JM FAU - Carson, M AU - Carson M FAU - House-Pompeo, K AU - House-Pompeo K FAU - Teale, M AU - Teale M FAU - Moore, D AU - Moore D FAU - Jin, L AU - Jin L FAU - Schneider, A AU - Schneider A FAU - DeLucas, L J AU - DeLucas LJ FAU - Hook, M AU - Hook M FAU - Narayana, S V AU - Narayana SV LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Adhesins, Bacterial) RN - 0 (Protein Sorting Signals) RN - 0 (Recombinant Proteins) RN - 9007-34-5 (Collagen) SB - IM MH - Adhesins, Bacterial/*chemistry/*metabolism MH - Binding Sites MH - Cloning, Molecular MH - Collagen/*metabolism MH - Crystallography, X-Ray MH - Escherichia coli MH - Models, Molecular MH - Models, Structural MH - *Protein Folding MH - Protein Sorting Signals/chemistry MH - *Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Staphylococcus aureus/metabolism EDAT- 1997/10/23 MHDA- 1997/10/23 00:01 CRDT- 1997/10/23 00:00 PST - ppublish SO - Nat Struct Biol. 1997 Oct;4(10):833-8. PMID- 18665616 OWN - NLM STAT- MEDLINE DA - 20080819 DCOM- 20080909 LR - 20140903 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 34 DP - 2008 Aug 26 TI - Guiding protein aggregation with macromolecular crowding. PG - 8993-9006 LID - 10.1021/bi8008399 [doi] AB - Macromolecular crowding is expected to have a significant effect on protein aggregation. In the present study we analyzed the effect of macromolecular crowding on fibrillation of four proteins, bovine S-carboxymethyl-alpha-lactalbumin (a disordered form of the protein with reduced three out of four disulfide bridges), human insulin, bovine core histones, and human alpha-synuclein. These proteins are structurally different, varying from natively unfolded (alpha-synuclein and core histones) to folded proteins with rigid tertiary and quaternary structures (monomeric and hexameric forms of insulin). All these proteins are known to fibrillate in diluted solutions, however their aggregation mechanisms are very divers and some of them are able to form different aggregates in addition to fibrils. We studied how macromolecular crowding guides protein between different aggregation pathways by analyzing the effect of crowding agents on the aggregation patterns under the variety of conditions favoring different aggregated end products in diluted solutions. FAU - Munishkina, Larissa A AU - Munishkina LA AD - Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA. FAU - Ahmad, Atta AU - Ahmad A FAU - Fink, Anthony L AU - Fink AL FAU - Uversky, Vladimir N AU - Uversky VN LA - eng GR - GM071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 GM071714-03/GM/NIGMS NIH HHS/United States GR - R01 LM007688-01A1/LM/NLM NIH HHS/United States GR - R01 LM007688-01A1S1/LM/NLM NIH HHS/United States GR - R01 NS039985-03/NS/NINDS NIH HHS/United States GR - R01 NS39985/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20080730 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Histones) RN - 0 (Proteins) RN - 0 (Recombinant Proteins) RN - 0 (alpha-Synuclein) RN - 9013-90-5 (Lactalbumin) SB - IM MH - Animals MH - Cattle MH - Circular Dichroism MH - Histones/chemistry/genetics/metabolism MH - Humans MH - Lactalbumin/chemistry/genetics/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Proteins/*chemistry/genetics/*metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Spectroscopy, Fourier Transform Infrared MH - alpha-Synuclein/chemistry/genetics/metabolism PMC - PMC2676887 MID - NIHMS105638 OID - NLM: NIHMS105638 OID - NLM: PMC2676887 EDAT- 2008/07/31 09:00 MHDA- 2008/09/10 09:00 CRDT- 2008/07/31 09:00 PHST- 2008/07/30 [aheadofprint] AID - 10.1021/bi8008399 [doi] PST - ppublish SO - Biochemistry. 2008 Aug 26;47(34):8993-9006. doi: 10.1021/bi8008399. Epub 2008 Jul 30. PMID- 11327838 OWN - NLM STAT- MEDLINE DA - 20010430 DCOM- 20010524 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 40 IP - 6 DP - 2001 Feb 13 TI - Stability, folding, dimerization, and assembly properties of the yeast prion Ure2p. PG - 1764-73 AB - The [URE3] factor of Saccharomyces cerevisiae propagates by a prion-like mechanism and corresponds to the loss of the function of the cellular protein Ure2. The molecular basis of the propagation of this phenotype is unknown. We recently expressed Ure2p in Escherichia coli and demonstrated that the N-terminal region of the protein is flexible and unstructured, while its C-terminal region is compactly folded. Ure2p oligomerizes in solution to form mainly dimers that assemble into fibrils [Thual et al. (1999) J. Biol. Chem. 274, 13666-13674]. To determine the role played by each domain of Ure2p in the overall properties of the protein, specifically, its stability, conformation, and capacity to assemble into fibrils, we have further analyzed the properties of Ure2p N- and C-terminal regions. We show here that Ure2p dimerizes through its C-terminal region. We also show that the N-terminal region is essential for directing the assembly of the protein into a particular pathway that yields amyloid fibrils. A full-length Ure2p variant that possesses an additional tryptophan residue in its N-terminal moiety was generated to follow conformational changes affecting this domain. Comparison of the overall conformation, folding, and unfolding properties, and the behavior upon proteolytic treatments of full-length Ure2p, Ure2pW37 variant, and Ure2p C-terminal fragment reveals that Ure2p N-terminal domain confers no additional stability to the protein. This study reveals the existence of a stable unfolding intermediate of Ure2p under conditions where the protein assembles into amyloid fibrils. Our results contradict the intramolecular interaction between the N- and C-terminal moieties of Ure2p and the single unfolding transitions reported in a number of previous studies. FAU - Thual, C AU - Thual C AD - Laboratoire d'Enzymologie et Biochimie Structurales and Centre de Genetique Moleculaire, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette Cedex, France. FAU - Bousset, L AU - Bousset L FAU - Komar, A A AU - Komar AA FAU - Walter, S AU - Walter S FAU - Buchner, J AU - Buchner J FAU - Cullin, C AU - Cullin C FAU - Melki, R AU - Melki R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Fungal Proteins) RN - 0 (Peptide Fragments) RN - 0 (Prions) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 1.11.1.9 (Glutathione Peroxidase) RN - EC 1.11.1.9 (URE2 protein, S cerevisiae) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Amyloid/metabolism MH - Circular Dichroism MH - Dimerization MH - Fungal Proteins/chemistry/genetics/*metabolism/ultrastructure MH - Glutathione Peroxidase MH - Guanidine MH - Kinetics MH - Molecular Weight MH - Peptide Fragments/chemistry/genetics/metabolism/ultrastructure MH - Prions/chemistry/genetics/*metabolism/ultrastructure MH - Protein Denaturation MH - *Protein Folding MH - Recombinant Proteins/chemistry/metabolism/ultrastructure MH - Saccharomyces cerevisiae/chemistry/genetics/*metabolism/ultrastructure MH - *Saccharomyces cerevisiae Proteins MH - Solubility MH - Spectrometry, Fluorescence EDAT- 2001/05/01 10:00 MHDA- 2001/05/26 10:01 CRDT- 2001/05/01 10:00 AID - bi001916l [pii] PST - ppublish SO - Biochemistry. 2001 Feb 13;40(6):1764-73. PMID- 21819966 OWN - NLM STAT- MEDLINE DA - 20120109 DCOM- 20120424 LR - 20150325 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1818 IP - 2 DP - 2012 Feb TI - Biophysics of alpha-synuclein membrane interactions. PG - 162-71 LID - 10.1016/j.bbamem.2011.07.032 [doi] AB - Membrane proteins participate in nearly all cellular processes; however, because of experimental limitations, their characterization lags far behind that of soluble proteins. Peripheral membrane proteins are particularly challenging to study because of their inherent propensity to adopt multiple and/or transient conformations in solution and upon membrane association. In this review, we summarize useful biophysical techniques for the study of peripheral membrane proteins and their application in the characterization of the membrane interactions of the natively unfolded and Parkinson's disease (PD) related protein, alpha-synuclein (alpha-syn). We give particular focus to studies that have led to the current understanding of membrane-bound alpha-syn structure and the elucidation of specific membrane properties that affect alpha-syn-membrane binding. Finally, we discuss biophysical evidence supporting a key role for membranes and alpha-syn in PD pathogenesis. This article is part of a Special Issue entitled: Membrane protein structure and function. CI - Copyright (c) 2011. Published by Elsevier B.V. FAU - Pfefferkorn, Candace M AU - Pfefferkorn CM AD - Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. FAU - Jiang, Zhiping AU - Jiang Z FAU - Lee, Jennifer C AU - Lee JC LA - eng GR - ZIA HL001055-04/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Review DEP - 20110728 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Biophysics/*methods MH - Cell Membrane/chemistry/genetics/*metabolism MH - Humans MH - Molecular Sequence Data MH - Parkinson Disease/*metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - alpha-Synuclein/*chemistry/genetics/*metabolism PMC - PMC3249522 MID - NIHMS319651 OID - NLM: NIHMS319651 OID - NLM: PMC3249522 EDAT- 2011/08/09 06:00 MHDA- 2012/04/25 06:00 CRDT- 2011/08/09 06:00 PHST- 2011/06/02 [received] PHST- 2011/07/20 [revised] PHST- 2011/07/21 [accepted] PHST- 2011/07/28 [aheadofprint] AID - S0005-2736(11)00237-9 [pii] AID - 10.1016/j.bbamem.2011.07.032 [doi] PST - ppublish SO - Biochim Biophys Acta. 2012 Feb;1818(2):162-71. doi: 10.1016/j.bbamem.2011.07.032. Epub 2011 Jul 28. PMID- 22021384 OWN - NLM STAT- MEDLINE DA - 20120228 DCOM- 20120423 LR - 20141021 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 40 IP - 4 DP - 2012 Feb TI - DNA and nucleosomes direct distinct folding of a linker histone H1 C-terminal domain. PG - 1475-84 LID - 10.1093/nar/gkr866 [doi] AB - We previously documented condensation of the H1 CTD consistent with adoption of a defined structure upon nucleosome binding using a bulk FRET assay, supporting proposals that the CTD behaves as an intrinsically disordered domain. In the present study, by determining the distances between two different pairs of sites in the C-terminal domain of full length H1 by FRET, we confirm that nucleosome binding directs folding of the disordered H1 C-terminal domain and provide additional distance constraints for the condensed state. In contrast to nucleosomes, FRET observed upon H1 binding to naked DNA fragments includes both intra- and inter-molecular resonance energy transfer. By eliminating inter-molecular transfer, we find that CTD condensation induced upon H1-binding naked DNA is distinct from that induced by nucleosomes. Moreover, analysis of fluorescence quenching indicates that H1 residues at either end of the CTD experience distinct environments when bound to nucleosomes, and suggest that the penultimate residue in the CTD (K195) is juxtaposed between the two linker DNA helices, proposed to form a stem structure in the H1-bound nucleosome. FAU - Fang, He AU - Fang H AD - Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14625, USA. FAU - Clark, David J AU - Clark DJ FAU - Hayes, Jeffrey J AU - Hayes JJ LA - eng GR - GM52426/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural DEP - 20111022 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Histones) RN - 0 (Nucleosomes) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - DNA/*metabolism MH - Fluorescence Resonance Energy Transfer MH - Histones/*chemistry/metabolism MH - Nucleosomes/*metabolism MH - Protein Folding MH - Protein Structure, Tertiary MH - Xenopus laevis PMC - PMC3287190 OID - NLM: PMC3287190 EDAT- 2011/10/25 06:00 MHDA- 2012/04/24 06:00 CRDT- 2011/10/25 06:00 PHST- 2011/10/22 [aheadofprint] AID - gkr866 [pii] AID - 10.1093/nar/gkr866 [doi] PST - ppublish SO - Nucleic Acids Res. 2012 Feb;40(4):1475-84. doi: 10.1093/nar/gkr866. Epub 2011 Oct 22. PMID- 21613569 OWN - NLM STAT- MEDLINE DA - 20110615 DCOM- 20110929 LR - 20141022 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 108 IP - 24 DP - 2011 Jun 14 TI - Intrinsic disorder in measles virus nucleocapsids. PG - 9839-44 LID - 10.1073/pnas.1103270108 [doi] AB - The genome of measles virus is encapsidated by multiple copies of the nucleoprotein (N), forming helical nucleocapsids of molecular mass approaching 150 Megadalton. The intrinsically disordered C-terminal domain of N (N(TAIL)) is essential for transcription and replication of the virus via interaction with the phosphoprotein P of the viral polymerase complex. The molecular recognition element (MoRE) of N(TAIL) that binds P is situated 90 amino acids from the folded RNA-binding domain (N(CORE)) of N, raising questions about the functional role of this disordered chain. Here we report the first in situ structural characterization of N(TAIL) in the context of the entire N-RNA capsid. Using nuclear magnetic resonance spectroscopy, small angle scattering, and electron microscopy, we demonstrate that N(TAIL) is highly flexible in intact nucleocapsids and that the MoRE is in transient interaction with N(CORE). We present a model in which the first 50 disordered amino acids of N(TAIL) are conformationally restricted as the chain escapes to the outside of the nucleocapsid via the interstitial space between successive N(CORE) helical turns. The model provides a structural framework for understanding the role of N(TAIL) in the initiation of viral transcription and replication, placing the flexible MoRE close to the viral RNA and, thus, positioning the polymerase complex in its functional environment. FAU - Jensen, Malene Ringkjobing AU - Jensen MR AD - Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat a l'Energie Atomique, Centre National de la Recherche Scientifique, Universite Joseph Fourier, 41 Rue Jules Horowitz, 38027 Grenoble, France. FAU - Communie, Guillaume AU - Communie G FAU - Ribeiro, Euripedes Almeida Jr AU - Ribeiro EA Jr FAU - Martinez, Nicolas AU - Martinez N FAU - Desfosses, Ambroise AU - Desfosses A FAU - Salmon, Loic AU - Salmon L FAU - Mollica, Luca AU - Mollica L FAU - Gabel, Frank AU - Gabel F FAU - Jamin, Marc AU - Jamin M FAU - Longhi, Sonia AU - Longhi S FAU - Ruigrok, Rob W H AU - Ruigrok RW FAU - Blackledge, Martin AU - Blackledge M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110525 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Nucleoproteins) RN - 0 (RNA, Viral) RN - 0 (Viral Proteins) SB - IM MH - Amino Acid Sequence MH - Binding Sites/genetics MH - Capsid/chemistry/metabolism MH - Magnetic Resonance Spectroscopy MH - Measles virus/genetics/*metabolism/ultrastructure MH - Microscopy, Electron MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleocapsid/genetics/*metabolism/ultrastructure MH - Nucleoproteins/*chemistry/genetics/metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA, Viral/chemistry/genetics/metabolism MH - Scattering, Small Angle MH - Sequence Homology, Amino Acid MH - Viral Proteins/*chemistry/genetics/metabolism PMC - PMC3116414 OID - NLM: PMC3116414 EDAT- 2011/05/27 06:00 MHDA- 2011/10/01 06:00 CRDT- 2011/05/27 06:00 PHST- 2011/05/25 [aheadofprint] AID - 1103270108 [pii] AID - 10.1073/pnas.1103270108 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):9839-44. doi: 10.1073/pnas.1103270108. Epub 2011 May 25. PMID- 23746503 OWN - NLM STAT- MEDLINE DA - 20130610 DCOM- 20140113 LR - 20141113 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 104 IP - 11 DP - 2013 Jun 4 TI - Another disordered chameleon: the Micro-Exon Gene 14 protein from Schistosomiasis. PG - 2326-8 LID - 10.1016/j.bpj.2013.04.018 [doi] LID - S0006-3495(13)00448-7 [pii] FAU - Dunker, A Keith AU - Dunker AK AD - Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA. kedunker@iupui.edu LA - eng GR - R01GM071714/GM/NIGMS NIH HHS/United States GR - R01LM007699/LM/NLM NIH HHS/United States PT - Comment PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Intrinsically Disordered Proteins) SB - IM CON - Biophys J. 2013 Jun 4;104(11):2512-20. PMID: 23746524 MH - Intrinsically Disordered Proteins/*chemistry/*metabolism MH - *Protein Folding PMC - PMC3672898 OID - NLM: PMC3672898 EDAT- 2013/06/12 06:00 MHDA- 2014/01/15 06:00 CRDT- 2013/06/11 06:00 PHST- 2013/03/12 [received] PHST- 2013/04/10 [accepted] AID - S0006-3495(13)00448-7 [pii] AID - 10.1016/j.bpj.2013.04.018 [doi] PST - ppublish SO - Biophys J. 2013 Jun 4;104(11):2326-8. doi: 10.1016/j.bpj.2013.04.018. PMID- 22349505 OWN - NLM STAT- MEDLINE DA - 20120312 DCOM- 20120507 LR - 20141019 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 419 IP - 2 DP - 2012 Mar 9 TI - The N-terminal domain of Rpn4 serves as a portable ubiquitin-independent degron and is recognized by specific 19S RP subunits. PG - 226-31 LID - 10.1016/j.bbrc.2012.01.152 [doi] AB - The number of proteasomal substrates that are degraded without prior ubiquitylation continues to grow. However, it remains poorly understood how the proteasome recognizes substrates lacking a ubiquitin (Ub) signal. Here we demonstrated that the Ub-independent degradation of Rpn4 requires the 19S regulatory particle (RP). The Ub-independent degron of Rpn4 was mapped to an N-terminal region including the first 80 residues. Inspection of its amino acid sequence revealed that the Ub-independent degron of Rpn4 consists of an intrinsically disordered domain followed by a folded segment. Using a photo-crosslinking-label transfer method, we captured three 19S RP subunits (Rpt1, Rpn2 and Rpn5) that bind the Ub-independent degron of Rpn4. This is the first time that specific 19S RP subunits have been identified interacting with a Ub-independent degron. This study provides insight into the mechanism by which Ub-independent substrates are recruited to the 26S proteasome. CI - Copyright (c) 2012 Elsevier Inc. All rights reserved. FAU - Ha, Seung-Wook AU - Ha SW AD - Barbara Ann Karmanos Cancer Institute and Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA. FAU - Ju, Donghong AU - Ju D FAU - Xie, Youming AU - Xie Y LA - eng GR - P30 CA022453/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120213 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (DNA-Binding Proteins) RN - 0 (RPN4 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Transcription Factors) RN - 0 (Ubiquitin) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - DNA-Binding Proteins/genetics/*metabolism MH - Proteasome Endopeptidase Complex/genetics/*metabolism MH - Protein Structure, Tertiary MH - *Proteolysis MH - Saccharomyces cerevisiae/genetics/*metabolism MH - Saccharomyces cerevisiae Proteins/genetics/*metabolism MH - Transcription Factors/genetics/*metabolism MH - Ubiquitin/*metabolism PMC - PMC3906847 MID - NIHMS519799 OID - NLM: NIHMS519799 OID - NLM: PMC3906847 EDAT- 2012/02/22 06:00 MHDA- 2012/05/09 06:00 CRDT- 2012/02/22 06:00 PHST- 2012/01/22 [received] PHST- 2012/01/31 [accepted] PHST- 2012/02/13 [aheadofprint] AID - S0006-291X(12)00206-9 [pii] AID - 10.1016/j.bbrc.2012.01.152 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2012 Mar 9;419(2):226-31. doi: 10.1016/j.bbrc.2012.01.152. Epub 2012 Feb 13. PMID- 20657662 OWN - NLM STAT- MEDLINE DA - 20100726 DCOM- 20101019 LR - 20140824 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 6 IP - 7 DP - 2010 TI - Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans. PG - e1000854 LID - 10.1371/journal.pcbi.1000854 [doi] AB - The proteome of the radiation- and desiccation-resistant bacterium D. radiodurans features a group of proteins that contain significant intrinsically disordered regions that are not present in non-extremophile homologues. Interestingly, this group includes a number of housekeeping and repair proteins such as DNA polymerase III, nudix hydrolase and rotamase. Here, we focus on a member of the nudix hydrolase family from D. radiodurans possessing low-complexity N- and C-terminal tails, which exhibit sequence signatures of intrinsic disorder and have unknown function. The enzyme catalyzes the hydrolysis of oxidatively damaged and mutagenic nucleotides, and it is thought to play an important role in D. radiodurans during the recovery phase after exposure to ionizing radiation or desiccation. We use molecular dynamics simulations to study the dynamics of the protein, and study its hydration free energy using the GB/SA formalism. We show that the presence of disordered tails significantly decreases the hydration free energy of the whole protein. We hypothesize that the tails increase the chances of the protein to be located in the remaining water patches in the desiccated cell, where it is protected from the desiccation effects and can function normally. We extrapolate this to other intrinsically disordered regions in proteins, and propose a novel function for them: intrinsically disordered regions increase the "surface-properties" of the folded domains they are attached to, making them on the whole more hydrophilic and potentially influencing, in this way, their localization and cellular activity. FAU - Awile, Omar AU - Awile O AD - Mediterranean Institute for Life Sciences, Split, Croatia. FAU - Krisko, Anita AU - Krisko A FAU - Sbalzarini, Ivo F AU - Sbalzarini IF FAU - Zagrovic, Bojan AU - Zagrovic B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100715 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (Bacterial Proteins) RN - 059QF0KO0R (Water) RN - EC 3.6.1.- (Pyrophosphatases) RN - EC 3.6.1.- (nudix hydrolases) SB - IM MH - Bacterial Proteins/*chemistry MH - Deinococcus/*enzymology MH - Desiccation MH - Hydrophobic and Hydrophilic Interactions MH - *Molecular Dynamics Simulation MH - Protein Conformation MH - Pyrophosphatases/*chemistry MH - Sequence Analysis, Protein MH - Surface Properties MH - Thermodynamics MH - Water/chemistry PMC - PMC2904767 OID - NLM: PMC2904767 EDAT- 2010/07/27 06:00 MHDA- 2010/10/20 06:00 CRDT- 2010/07/27 06:00 PHST- 2010/01/17 [received] PHST- 2010/06/04 [accepted] PHST- 2010/07/15 [epublish] AID - 10.1371/journal.pcbi.1000854 [doi] PST - epublish SO - PLoS Comput Biol. 2010 Jul 15;6(7):e1000854. doi: 10.1371/journal.pcbi.1000854. PMID- 11498590 OWN - NLM STAT- MEDLINE DA - 20010810 DCOM- 20010906 LR - 20131121 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 293 IP - 5532 DP - 2001 Aug 10 TI - Coordination of a transcriptional switch by HMGI(Y) acetylation. PG - 1133-6 AB - Dynamic control of interferon-beta (IFN-beta) gene expression requires the regulated assembly and disassembly of the enhanceosome, a higher-order nucleoprotein complex formed in response to virus infection. The enhanceosome activates transcription by recruiting the histone acetyltransferase proteins CREB binding protein (CBP) and p300/CBP-associated factors (PCAF)/GCN5, which, in addition to modifying histones, acetylate HMGI(Y), the architectural component required for enhanceosome assembly. We show that the accurate execution of the IFN-beta transcriptional switch depends on the ordered acetylation of the high-mobility group I protein HMGI(Y) by PCAF/GCN5 and CBP, which acetylate HMGI(Y) at distinct lysine residues on endogenous promoters. Whereas acetylation of HMGI(Y) by CBP at lysine-65 destabilizes the enhanceosome, acetylation of HMGI(Y) by PCAF/GCN5 at lysine-71 potentiates transcription by stabilizing the enhanceosome and preventing acetylation by CBP. FAU - Munshi, N AU - Munshi N AD - Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA. FAU - Agalioti, T AU - Agalioti T FAU - Lomvardas, S AU - Lomvardas S FAU - Merika, M AU - Merika M FAU - Chen, G AU - Chen G FAU - Thanos, D AU - Thanos D LA - eng GR - 1RO1GM54605/GM/NIGMS NIH HHS/United States GR - 5-T32-GM07367/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (CREBBP protein, human) RN - 0 (Cell Cycle Proteins) RN - 0 (High Mobility Group Proteins) RN - 0 (Histones) RN - 0 (Nuclear Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - 124544-67-8 (HMGA1a Protein) RN - 77238-31-4 (Interferon-beta) RN - EC 2.3.1.- (Acetyltransferases) RN - EC 2.3.1.48 (CREB-Binding Protein) RN - EC 2.3.1.48 (Histone Acetyltransferases) RN - EC 2.3.1.48 (KAT2A protein, human) RN - EC 2.3.1.48 (p300-CBP Transcription Factors) RN - EC 2.3.1.48 (p300-CBP-associated factor) RN - K3Z4F929H6 (Lysine) SB - IM CIN - Science. 2001 Aug 10;293(5532):1054-5. PMID: 11498564 MH - Acetylation MH - Acetyltransferases/metabolism MH - Amino Acid Sequence MH - CREB-Binding Protein MH - Cell Cycle Proteins MH - *Enhancer Elements, Genetic MH - *Gene Expression Regulation MH - HMGA1a Protein MH - HeLa Cells MH - High Mobility Group Proteins/chemistry/*metabolism MH - Histone Acetyltransferases MH - Histones/metabolism MH - Humans MH - Interferon-beta/*genetics MH - Lysine/metabolism MH - Molecular Sequence Data MH - Mutation MH - Nuclear Proteins/metabolism MH - Promoter Regions, Genetic MH - Protein Binding MH - Recombinant Proteins/metabolism MH - Respirovirus/physiology MH - *Saccharomyces cerevisiae Proteins MH - Trans-Activators/metabolism MH - Transcription Factors/chemistry/*metabolism MH - *Transcriptional Activation MH - Transfection MH - p300-CBP Transcription Factors EDAT- 2001/08/11 10:00 MHDA- 2001/09/08 10:01 CRDT- 2001/08/11 10:00 AID - 10.1126/science.293.5532.1133 [doi] AID - 293/5532/1133 [pii] PST - ppublish SO - Science. 2001 Aug 10;293(5532):1133-6. PMID- 15568805 OWN - NLM STAT- MEDLINE DA - 20041130 DCOM- 20050121 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 48 DP - 2004 Dec 7 TI - Solution structure and backbone dynamics of the N-terminal region of the calcium regulatory domain from soybean calcium-dependent protein kinase alpha. PG - 15131-40 AB - Ca(2+)-dependent protein kinases (CDPKs) are vital Ca(2+)-signaling proteins in plants and protists which have both a kinase domain and a self-contained calcium regulatory calmodulin-like domain (CLD). Despite being very similar to CaM (>40% identity) and sharing the same fold, recent biochemical and structural evidence suggests that the behavior of CLD is distinct from its namesake, calmodulin. In this study, NMR spectroscopy is employed to examine the structure and backbone dynamics of a 168 amino acid Ca(2+)-saturated construct of the CLD (NtH-CLD) in which almost the entire C-terminal domain is exchange broadened and not visible in the NMR spectra. Structural characterization of the N-terminal domain indicates that the first Ca(2+)-binding loop is significantly more open than in a recently reported structure of the CLD complexed with a putative intramolecular binding region (JD) in the CDPK. Backbone dynamics suggest that parts of the third helix exhibit unusually high mobility, and significant exchange, consistent with previous findings that this helix interacts with the C-terminal domain. Dynamics data also show that the "tether" region, consisting of the first 11 amino acids of CLD, is highly mobile and these residues exhibit distinctive beta-type secondary structure, which may help to position the JD and CLD. Finally, the unusual global dynamic behavior of the protein is rationalized on the basis of possible interdomain rearrangements and the highly variable environments of the C- and N-terminal domains. FAU - Weljie, Aalim M AU - Weljie AM AD - Structural Biology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4. FAU - Gagne, Stephane M AU - Gagne SM FAU - Vogel, Hans J AU - Vogel HJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Calmodulin) RN - 0 (Isoenzymes) RN - 0 (Peptide Fragments) RN - 0 (Solutions) RN - EC 2.7.- (Protein Kinases) RN - EC 2.7.1.- (calcium-dependent protein kinase) RN - SY7Q814VUP (Calcium) SB - IM MH - Calcium/*chemistry MH - Calmodulin/chemistry MH - Isoenzymes/chemistry/genetics MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/*chemistry/genetics MH - Protein Conformation MH - Protein Kinases/*chemistry/genetics MH - Protein Structure, Tertiary/genetics MH - Solutions MH - Soybeans/*enzymology/genetics MH - Structural Homology, Protein MH - *Thermodynamics EDAT- 2004/12/01 09:00 MHDA- 2005/01/22 09:00 CRDT- 2004/12/01 09:00 AID - 10.1021/bi048751r [doi] PST - ppublish SO - Biochemistry. 2004 Dec 7;43(48):15131-40. PMID- 24947816 OWN - NLM STAT- MEDLINE DA - 20140722 DCOM- 20140912 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 28 DP - 2014 Jul 22 TI - Why are the truncated cyclin Es more effective CDK2 activators than the full-length isoforms? PG - 4612-24 LID - 10.1021/bi5004052 [doi] AB - Cell cycle regulating enzymes, CDKs, become activated upon association with their regulatory proteins, cyclins. The G1 cyclin, cyclin E, is overexpressed and present in low molecular weight (LMW) isoforms in breast cancer cells and tumor tissues. In vivo and in vitro studies have shown that these LMW isoforms of cyclin E hyperactivate CDK2 and accelerate the G1-S phase of cell division. The molecular basis of CDK2 hyperactivation due to LMW cyclin E isoforms in cancer cells is, however, unknown. Here, we employ a computational approach, combining homology modeling, bioinformatics analyses, molecular dynamics (MD) simulations, and principal component analyses to unravel the key structural features of CDK2-bound full-length and LMW isoforms of cyclin E1 and correlate those features to their differential activity. Results suggest that the missing N- and C-terminal regions of the cyclin E LMW isoforms constitute the Nuclear Localization Sequence (NLS) and PEST domains and are intrinsically disordered. These regions, when present in the full-length cyclin E/CDK2 complex, weaken the cyclin-CDK interface packing due to the loss of a large number of key interface interactions. Such weakening is manifested in the decreased contact area and increased solvent accessibility at the interface and also by the absence of concerted motions between the two partner proteins in the full-length complex. More effective packing and interactions between CDK2 and LMW cyclin E isoforms, however, produce more efficient protein-protein complexes that accelerate the cell division processes in cancer cells, where these cyclin E isoforms are overexpressed. FAU - Rath, Soumya Lipsa AU - Rath SL AD - Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras , Chennai 600036, India. FAU - Senapati, Sanjib AU - Senapati S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140710 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (CCNE1 protein, human) RN - 0 (Cyclin E) RN - 0 (Multiprotein Complexes) RN - 0 (Oncogene Proteins) RN - 0 (Protein Isoforms) RN - EC 2.7.11.22 (CDK2 protein, human) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 2) SB - IM MH - Cyclin E/*chemistry/genetics/metabolism MH - Cyclin-Dependent Kinase 2/*chemistry/genetics/metabolism MH - Humans MH - *Models, Molecular MH - Multiprotein Complexes/*chemistry/genetics/metabolism MH - Oncogene Proteins/*chemistry/genetics/metabolism MH - Protein Isoforms/chemistry/genetics/metabolism EDAT- 2014/06/21 06:00 MHDA- 2014/09/13 06:00 CRDT- 2014/06/21 06:00 PHST- 2014/07/10 [aheadofprint] AID - 10.1021/bi5004052 [doi] PST - ppublish SO - Biochemistry. 2014 Jul 22;53(28):4612-24. doi: 10.1021/bi5004052. Epub 2014 Jul 10. PMID- 19555081 OWN - NLM STAT- MEDLINE DA - 20100326 DCOM- 20100624 LR - 20140916 IS - 1520-6882 (Electronic) IS - 0003-2700 (Linking) VI - 81 IP - 16 DP - 2009 Aug 15 TI - High-resolution temperature-concentration diagram of alpha-synuclein conformation obtained from a single Forster resonance energy transfer image in a microfluidic device. PG - 6929-35 LID - 10.1021/ac901008c [doi] AB - We present a microfluidic device for rapid and efficient determination of protein conformations in a range of medium conditions and temperatures. The device generates orthogonal gradients of concentration and temperature in an interrogation area that fits into the field of view of an objective lens with a numerical aperture of 0.45. A single Forster resonance energy transfer (FRET) image of the interrogation area containing a dual-labeled protein provides a 100 x 100 point map of the FRET efficiency that corresponds to a diagram of protein conformations in the coordinates of temperature and medium conditions. The device is used to explore the conformations of alpha-synuclein, an intrinsically disordered protein linked to Parkinson's and Alzheimer's diseases, in the presence of a binding partner, the lipid-mimetic sodium dodecyl sulfate (SDS). The experiment provides a diagram of conformations of alpha-synuclein with 10,000 individual data points in a range of 21-47 degrees C and 0-2.5 mM SDS. The diagram is consistent with previous reports but also reveals new conformational transitions that would be difficult to detect with conventional techniques. The microfluidic device can potentially be used to study other biomolecular and soft-matter systems. FAU - Vandelinder, Virginia AU - Vandelinder V AD - Department of Physics, University of California, San Diego, 9500 Gilman Drive, MC 0374, La Jolla, California 92093, USA. FAU - Ferreon, Allan Chris M AU - Ferreon AC FAU - Gambin, Yann AU - Gambin Y FAU - Deniz, Ashok A AU - Deniz AA FAU - Groisman, Alex AU - Groisman A LA - eng GR - GM066833/GM/NIGMS NIH HHS/United States GR - R01 GM066833/GM/NIGMS NIH HHS/United States GR - R01 GM066833-05/GM/NIGMS NIH HHS/United States GR - R01 GM066833-06A1/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Anal Chem JT - Analytical chemistry JID - 0370536 RN - 0 (alpha-Synuclein) SB - IM MH - Alzheimer Disease/metabolism MH - Fluorescence Resonance Energy Transfer MH - Humans MH - Microfluidics/*instrumentation MH - Parkinson Disease/metabolism MH - Protein Conformation MH - Temperature MH - alpha-Synuclein/*chemistry/metabolism PMC - PMC2846235 MID - NIHMS132547 OID - NLM: NIHMS132547 OID - NLM: PMC2846235 EDAT- 2009/06/27 09:00 MHDA- 2010/06/25 06:00 CRDT- 2009/06/27 09:00 AID - 10.1021/ac901008c [doi] PST - ppublish SO - Anal Chem. 2009 Aug 15;81(16):6929-35. doi: 10.1021/ac901008c. PMID- 16387655 OWN - NLM STAT- MEDLINE DA - 20060102 DCOM- 20060227 LR - 20061115 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 21 IP - 1 DP - 2006 Jan 6 TI - Structural basis for recognition and sequestration of UUU(OH) 3' temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen. PG - 75-85 AB - The nuclear phosphoprotein La was identified as an autoantigen in patients with systemic lupus erythematosus and Sjogren's syndrome. La binds to and protects the UUU(OH) 3' terminii of nascent RNA polymerase III transcripts from exonuclease digestion. We report the 1.85 angstroms crystal structure of the N-terminal domain of human La, consisting of La and RRM1 motifs, bound to r(U1-G2-C3-U4-G5-U6-U7-U8-U9OH). The U7-U8-U9OH 3' end, in a splayed-apart orientation, is sequestered within a basic and aromatic amino acid-lined cleft between the La and RRM1 motifs. The specificity-determining U8 residue bridges both motifs, in part through unprecedented targeting of the beta sheet edge, rather than the anticipated face, of the RRM1 motif. Our structural observations, supported by mutation studies of both La and RNA components, illustrate the principles behind RNA sequestration by a rheumatic disease autoantigen, whereby the UUU(OH) 3' ends of nascent RNA transcripts are protected during downstream processing and maturation events. FAU - Teplova, Marianna AU - Teplova M AD - Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA. FAU - Yuan, Yu-Ren AU - Yuan YR FAU - Phan, Anh Tuan AU - Phan AT FAU - Malinina, Lucy AU - Malinina L FAU - Ilin, Serge AU - Ilin S FAU - Teplov, Alexei AU - Teplov A FAU - Patel, Dinshaw J AU - Patel DJ LA - eng SI - PDB/1YTY SI - PDB/1ZH5 PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Autoantigens) RN - 0 (Macromolecular Substances) RN - 0 (Ribonucleoproteins) RN - 0 (SS-B antigen) RN - 63231-63-0 (RNA) RN - EC 2.7.7.- (RNA Polymerase III) SB - IM CIN - Mol Cell. 2006 Jan 20;21(2):149-52. PMID: 16427005 MH - Autoantigens/*chemistry/genetics/metabolism MH - Crystallography, X-Ray MH - Humans MH - Hydrogen Bonding MH - Macromolecular Substances MH - Models, Molecular MH - Mutation MH - Protein Binding MH - *Protein Conformation MH - *RNA/chemistry/genetics/metabolism MH - RNA Polymerase III/chemistry/*genetics/metabolism MH - Ribonucleoproteins/*chemistry/genetics/metabolism MH - *Transcription, Genetic EDAT- 2006/01/03 09:00 MHDA- 2006/02/28 09:00 CRDT- 2006/01/03 09:00 PHST- 2005/08/23 [received] PHST- 2005/09/24 [revised] PHST- 2005/10/25 [accepted] AID - S1097-2765(05)01722-3 [pii] AID - 10.1016/j.molcel.2005.10.027 [doi] PST - ppublish SO - Mol Cell. 2006 Jan 6;21(1):75-85. PMID- 10050767 OWN - NLM STAT- MEDLINE DA - 19990330 DCOM- 19990330 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 444 IP - 2-3 DP - 1999 Feb 12 TI - The structure of human parathyroid hormone-related protein(1-34) in near-physiological solution. PG - 239-44 AB - Parathyroid hormone-related protein plays a major role in the pathogenesis of humoral hypercalcemia of malignancy. Under normal physiological conditions, parathyroid hormone-related protein is produced in a wide variety of tissues and acts in an autocrine or paracrine fashion. Parathyroid hormone-related protein and parathyroid hormone bind to and activate the same G-protein-coupled receptor. Here we present the structure of the biologically active NH2-terminal domain of human parathyroid hormone-related protein(1-34) in near-physiological solution in the absence of crowding reagents as determined by two-dimensional proton magnetic resonance spectroscopy. An improved strategy for structure calculation revealed the presence of two helices, His-5-Leu-8 and Gln-16-Leu-27, connected by a flexible linker. The parathyroid hormone-related protein(1-34) structure and the structure of human parathyroid hormone(1-37) as well as human parathyroid hormone(1-34) are highly similar, except for the well defined turn, His-14-Ser-17, present in parathyroid hormone. Thus, the similarity of the binding affinities of parathyroid hormone and parathyroid hormone-related protein to their common receptor may be based on their structural similarity. FAU - Weidler, M AU - Weidler M AD - Lehrstuhl fur Biopolymere, Universitat Bayreuth, Germany. FAU - Marx, U C AU - Marx UC FAU - Seidel, G AU - Seidel G FAU - Schafer, W AU - Schafer W FAU - Hoffmann, E AU - Hoffmann E FAU - Esswein, A AU - Esswein A FAU - Rosch, P AU - Rosch P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Parathyroid Hormone) RN - 0 (Parathyroid Hormone-Related Protein) RN - 0 (Peptide Fragments) RN - 0 (Proteins) RN - 112540-82-6 (parathyroid hormone-related protein (1-34)) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Conformation MH - Molecular Sequence Data MH - Parathyroid Hormone/chemistry MH - *Parathyroid Hormone-Related Protein MH - Peptide Fragments/*chemistry MH - Protein Structure, Secondary MH - Proteins/*chemistry EDAT- 1999/03/02 MHDA- 1999/03/02 00:01 CRDT- 1999/03/02 00:00 AID - S0014-5793(98)01658-5 [pii] PST - ppublish SO - FEBS Lett. 1999 Feb 12;444(2-3):239-44. PMID- 8072525 OWN - NLM STAT- MEDLINE DA - 19940923 DCOM- 19940923 LR - 20061115 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 371 IP - 6492 DP - 1994 Sep 1 TI - Structure of influenza haemagglutinin at the pH of membrane fusion. PG - 37-43 AB - Low pH induces a conformational change in the influenza virus haemagglutinin, which then mediates fusion of the viral and host cell membranes. The three-dimensional structure of a fragment of the haemagglutinin in this conformation reveals a major refolding of the secondary and tertiary structure of the molecule. The apolar fusion peptide moves at least 100 A to one tip of the molecule. At the other end a helical segment unfolds, a subdomain relocates reversing the chain direction, and part of the structure becomes disordered. FAU - Bullough, P A AU - Bullough PA AD - Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138. FAU - Hughson, F M AU - Hughson FM FAU - Skehel, J J AU - Skehel JJ FAU - Wiley, D C AU - Wiley DC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Hemagglutinin Glycoproteins, Influenza Virus) RN - 0 (Hemagglutinins, Viral) RN - 0 (Peptide Fragments) SB - IM CIN - Nature. 1994 Sep 1;371(6492):19-20. PMID: 8072518 MH - Amino Acid Sequence MH - Computer Graphics MH - Crystallography, X-Ray MH - Hemagglutinin Glycoproteins, Influenza Virus MH - Hemagglutinins, Viral/*chemistry/ultrastructure MH - Hydrogen-Ion Concentration MH - *Membrane Fusion MH - Molecular Sequence Data MH - Mutation MH - Orthomyxoviridae/chemistry/ultrastructure MH - Peptide Fragments/chemistry MH - Protein Conformation MH - Protein Folding EDAT- 1994/09/01 MHDA- 1994/09/01 00:01 CRDT- 1994/09/01 00:00 AID - 10.1038/371037a0 [doi] PST - ppublish SO - Nature. 1994 Sep 1;371(6492):37-43. PMID- 8756321 OWN - NLM STAT- MEDLINE DA - 19960923 DCOM- 19960923 LR - 20131121 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 3 IP - 8 DP - 1996 Aug TI - Crystal structure of human estrogenic 17 beta-hydroxysteroid dehydrogenase complexed with 17 beta-estradiol. PG - 665-8 FAU - Azzi, A AU - Azzi A FAU - Rehse, P H AU - Rehse PH FAU - Zhu, D W AU - Zhu DW FAU - Campbell, R L AU - Campbell RL FAU - Labrie, F AU - Labrie F FAU - Lin, S X AU - Lin SX LA - eng PT - Letter PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 2DI9HA706A (Estrone) RN - 4TI98Z838E (Estradiol) RN - EC 1.1.- (Hydroxysteroid Dehydrogenases) RN - EC 1.1.1.209 (3(17)-hydroxysteroid dehydrogenase) SB - IM MH - Binding Sites MH - Breast Neoplasms/enzymology MH - Carcinoma/enzymology MH - Catalysis MH - Crystallography MH - Estradiol/*chemistry/metabolism MH - Estrone/metabolism MH - Female MH - Gonads/metabolism MH - Humans MH - Hydroxysteroid Dehydrogenases/*chemistry/metabolism MH - Models, Molecular MH - Protein Conformation MH - Substrate Specificity EDAT- 1996/08/01 MHDA- 1996/08/01 00:01 CRDT- 1996/08/01 00:00 PST - ppublish SO - Nat Struct Biol. 1996 Aug;3(8):665-8. PMID- 17676886 OWN - NLM STAT- MEDLINE DA - 20070907 DCOM- 20071108 LR - 20131121 IS - 1535-3893 (Print) IS - 1535-3893 (Linking) VI - 6 IP - 9 DP - 2007 Sep TI - Fesselin is a natively unfolded protein. PG - 3648-54 AB - Fesselin is a heat stable proline-rich actin binding protein. The stability, amino acid composition, and ability to bind to several proteins suggested that fesselin may be unfolded under native conditions. While the complete sequence of fesselin is unknown an analysis of a closely related protein, synaptopodin 2 from Gallus gallus, indicates that fesselin consists of a series of unstructured regions interspersed between short folded regions. To determine if fesselin is natively unfolded, we compared fesselin to a known globular protein (myosin S1) and a known unfolded protein Cad22 (the COOH terminal 22 kDa fragment of caldesmon). Fesselin, and Cad22, had larger Stokes radii than globular proteins of equivalent mass. The environments of tryptophan residues of fesselin and Cad22 were the same in the presence and absence of 6 M guanidine hydrochloride. Fesselin had a circular dichroism spectrum that was primarily random coil. Changes in pH over the range of 1.5-11.5 did not alter that spectrum. Increasing the temperature to 85 degrees C caused an increase in the degree of secondary structure. Calmodulin binding to fesselin altered the environment of the tryptophan residues so that they became less sensitive to the quencher acrylamide. These results show that fesselin is a natively unfolded protein. FAU - Khaymina, Svetlana S AU - Khaymina SS AD - Departments of Biochemistry and Molecular Biology and Physics, Brody School of Medicine at East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, USA. FAU - Kenney, John M AU - Kenney JM FAU - Schroeter, Mechthild M AU - Schroeter MM FAU - Chalovich, Joseph M AU - Chalovich JM LA - eng GR - AR35216/AR/NIAMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20070804 PL - United States TA - J Proteome Res JT - Journal of proteome research JID - 101128775 RN - 0 (Amino Acids) RN - 0 (Membrane Proteins) RN - 0 (Microfilament Proteins) RN - 0 (Myosin Subfragments) RN - 0 (fesselin) RN - 8DUH1N11BX (Tryptophan) RN - 9DLQ4CIU6V (Proline) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Amino Acids/chemistry MH - Animals MH - Chickens MH - Environment MH - Guanidine/chemistry MH - Hot Temperature MH - Hydrogen-Ion Concentration MH - Membrane Proteins/*chemistry MH - Microfilament Proteins/*chemistry MH - Myosin Subfragments/chemistry MH - Proline/chemistry MH - Protein Binding MH - Protein Denaturation MH - Protein Folding MH - Spectrometry, Fluorescence MH - Tryptophan/chemistry EDAT- 2007/08/07 09:00 MHDA- 2007/11/09 09:00 CRDT- 2007/08/07 09:00 PHST- 2007/08/04 [aheadofprint] AID - 10.1021/pr070237v [doi] PST - ppublish SO - J Proteome Res. 2007 Sep;6(9):3648-54. Epub 2007 Aug 4. PMID- 16234236 OWN - NLM STAT- MEDLINE DA - 20051226 DCOM- 20060227 LR - 20091119 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 52 DP - 2005 Dec 30 TI - Solution structure of the human immunodeficiency virus type 1 p6 protein. PG - 42515-27 AB - The human immunodeficiency virus type 1 p6 protein represents a docking site for several cellular and viral binding factors and fulfills major roles in the formation of infectious viruses. To date, however, the structure of this 52-amino acid protein, by far the smallest lentiviral protein known, either in its mature form as free p6 or as the C-terminal part of the Pr55 Gag polyprotein has not been unraveled. We have explored the high resolution structure and folding of p6 by CD and NMR spectroscopy. Under membranous solution conditions, p6 can adopt a helix-flexible helix structure; a short helix-1 (amino acids 14-18) is connected to a pronounced helix-2 (amino acids 33-44) by a flexible hinge region. Thus, p6 can be subdivided into two distinct structural and functional domains; helix-2 perfectly defines the region that binds to the virus budding factor AIP-1/ALIX, indicating that this structure is required for interaction with the endosomal sorting complex required for transport. The PTAP motif at the N terminus, comprising the primary late assembly domain, which is crucial for interaction with another cellular budding factor, Tsg101, does not exhibit secondary structure. However, the adjacent helix-1 may play an indirect role in the specific complex formation between p6 and the binding groove in Tsg101. Moreover, binding studies by NMR demonstrate that helix-2, which also comprises the LXXLF motif required for incorporation of the human immunodeficiency virus type 1 accessory protein Vpr into budding virions, specifically interacts with the Vpr binding region, indicating that under the specific solution conditions used for structure analysis, p6 adopted a functional conformation. FAU - Fossen, Torgils AU - Fossen T AD - Department of Structural Biology, Gesellschaft fur Biotechnologische Forschung, D-38124 Braunschweig, Germany. FAU - Wray, Victor AU - Wray V FAU - Bruns, Karsten AU - Bruns K FAU - Rachmat, Judhi AU - Rachmat J FAU - Henklein, Peter AU - Henklein P FAU - Tessmer, Uwe AU - Tessmer U FAU - Maczurek, Annette AU - Maczurek A FAU - Klinger, Patricia AU - Klinger P FAU - Schubert, Ulrich AU - Schubert U LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051017 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA-Binding Proteins) RN - 0 (Endosomal Sorting Complexes Required for Transport) RN - 0 (Gene Products, gag) RN - 0 (Gene Products, vpr) RN - 0 (Peptides) RN - 0 (Protons) RN - 0 (Transcription Factors) RN - 0 (Tsg101 protein) RN - 0 (gag Gene Products, Human Immunodeficiency Virus) RN - 0 (p6 gag protein, Human immunodeficiency virus 1) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Blotting, Western MH - CD4-Positive T-Lymphocytes/virology MH - Circular Dichroism MH - DNA-Binding Proteins/chemistry MH - Electrophoresis, Polyacrylamide Gel MH - Endosomal Sorting Complexes Required for Transport MH - Gene Products, gag/*chemistry/metabolism MH - Gene Products, vpr/chemistry MH - Humans MH - Immunoprecipitation MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Peptides/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protons MH - Transcription Factors/chemistry MH - gag Gene Products, Human Immunodeficiency Virus EDAT- 2005/10/20 09:00 MHDA- 2006/02/28 09:00 CRDT- 2005/10/20 09:00 PHST- 2005/10/17 [aheadofprint] AID - M507375200 [pii] AID - 10.1074/jbc.M507375200 [doi] PST - ppublish SO - J Biol Chem. 2005 Dec 30;280(52):42515-27. Epub 2005 Oct 17. PMID- 18093982 OWN - NLM STAT- MEDLINE DA - 20080317 DCOM- 20080512 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 12 DP - 2008 Mar 21 TI - A structural-dynamical characterization of human Cox17. PG - 7912-20 AB - Human Cox17 is a key mitochondrial copper chaperone responsible for supplying copper ions, through the assistance of Sco1, Sco2, and Cox11, to cytochrome c oxidase, the terminal enzyme of the mitochondrial energy transducing respiratory chain. A structural and dynamical characterization of human Cox17 in its various functional metallated and redox states is presented here. The NMR solution structure of the partially oxidized Cox17 (Cox17(2S-S)) consists of a coiled coil-helix-coiled coil-helix domain stabilized by two disulfide bonds involving Cys(25)-Cys(54) and Cys(35)-Cys(44), preceded by a flexible and completely unstructured N-terminal tail. In human Cu(I)Cox17(2S-S) the copper(I) ion is coordinated by the sulfurs of Cys(22) and Cys(23), and this is the first example of a Cys-Cys binding motif in copper proteins. Copper(I) binding as well as the formation of a third disulfide involving Cys(22) and Cys(23) cause structural and dynamical changes only restricted to the metal-binding region. Redox properties of the disulfides of human Cox17, here investigated, strongly support the current hypothesis that the unstructured fully reduced Cox17 protein is present in the cytoplasm and enters the intermembrane space (IMS) where is then oxidized by Mia40 to Cox17(2S-S), thus becoming partially structured and trapped into the IMS. Cox17(2S-S) is the functional species in the IMS, it can bind only one copper(I) ion and is then ready to enter the pathway of copper delivery to cytochrome c oxidase. The copper(I) form of Cox17(2S-S) has features specific for copper chaperones. FAU - Banci, Lucia AU - Banci L AD - Magnetic Resonance Center Centro Risonanze Magnetiche (CERM) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy. FAU - Bertini, Ivano AU - Bertini I FAU - Ciofi-Baffoni, Simone AU - Ciofi-Baffoni S FAU - Janicka, Anna AU - Janicka A FAU - Martinelli, Manuele AU - Martinelli M FAU - Kozlowski, Henryk AU - Kozlowski H FAU - Palumaa, Peep AU - Palumaa P LA - eng SI - PDB/UNKNOWN PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20071219 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (COX11 protein, human) RN - 0 (COX17 protein, human) RN - 0 (Carrier Proteins) RN - 0 (Cations, Monovalent) RN - 0 (Membrane Proteins) RN - 0 (Mitochondrial Proteins) RN - 0 (Molecular Chaperones) RN - 0 (SCO1 protein, human) RN - 0 (SCO2 protein, human) RN - 789U1901C5 (Copper) RN - EC 1.9.3.1 (Electron Transport Complex IV) SB - IM MH - Amino Acid Motifs/physiology MH - Carrier Proteins/*chemistry/genetics/metabolism MH - Cations, Monovalent/chemistry/metabolism MH - Copper/*chemistry/metabolism MH - Electron Transport Complex IV/chemistry/metabolism MH - Humans MH - Ion Transport/physiology MH - Membrane Proteins/chemistry/metabolism MH - Mitochondrial Proteins/*chemistry/genetics/metabolism MH - Molecular Chaperones/*chemistry/genetics/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Tertiary/physiology MH - Structure-Activity Relationship EDAT- 2007/12/21 09:00 MHDA- 2008/05/13 09:00 CRDT- 2007/12/21 09:00 PHST- 2007/12/19 [aheadofprint] AID - M708016200 [pii] AID - 10.1074/jbc.M708016200 [doi] PST - ppublish SO - J Biol Chem. 2008 Mar 21;283(12):7912-20. Epub 2007 Dec 19. PMID- 24028075 OWN - NLM STAT- MEDLINE DA - 20140805 DCOM- 20150511 IS - 1538-0254 (Electronic) IS - 0739-1102 (Linking) VI - 32 IP - 11 DP - 2014 TI - Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer's amyloid beta-peptide. PG - 1817-32 LID - 10.1080/07391102.2013.838518 [doi] AB - Macromolecular function arises from structure, and many diseases are associated with misfolding of proteins. Molecular simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution, but the reliability of these predictions is a function of the parameters used for the simulation. There are many biomolecular force fields available, but most are validated using stably folded structures. Here, we present the results of molecular dynamics simulations on the intrinsically disordered amyloid beta-peptide (Abeta), whose misfolding and aggregation give rise to the symptoms of Alzheimer's disease. Because of the link between secondary structure changes and pathology, being able to accurately model the structure of Abeta would greatly improve our understanding of this disease, and it may facilitate application of modeling approaches to other protein misfolding disorders. To this end, we compared five popular atomistic force fields (AMBER03, CHARMM22 + CMAP, GROMOS96 53A6, GROMOS96 54A7, and OPLS-AA) to determine which could best model the structure of Abeta. By comparing secondary structure content, NMR shifts, and radius of gyration to available experimental data, we conclude that AMBER03 and CHARMM22 + CMAP over-stabilize helical structure within Abeta, with CHARMM22 + CMAP also producing elongated Abeta structures, in conflict with experimental findings. OPLS-AA, GROMOS96 53A6, and GROMOS96 54A7 produce very similar results in terms of helical and beta-strand content, calculated NMR shifts, and radii of gyration that agree well with experimental data. FAU - Gerben, Stacey R AU - Gerben SR AD - a Department of Biochemistry , Virginia Tech , 111 Engel Hall, Blacksburg , VA , 24061 , USA . FAU - Lemkul, Justin A AU - Lemkul JA FAU - Brown, Anne M AU - Brown AM FAU - Bevan, David R AU - Bevan DR LA - eng PT - Comparative Study PT - Journal Article DEP - 20130913 PL - England TA - J Biomol Struct Dyn JT - Journal of biomolecular structure & dynamics JID - 8404176 RN - 0 (Amyloid beta-Peptides) SB - IM MH - Alzheimer Disease/*metabolism MH - Amyloid beta-Peptides/*chemistry MH - Magnetic Resonance Spectroscopy MH - Molecular Dynamics Simulation MH - Protein Structure, Secondary OTO - NOTNLM OT - force field OT - molecular dynamics OT - molecular mechanics OT - protein folding OT - simulation EDAT- 2013/09/14 06:00 MHDA- 2015/05/12 06:00 CRDT- 2013/09/14 06:00 PHST- 2013/09/13 [aheadofprint] AID - 10.1080/07391102.2013.838518 [doi] PST - ppublish SO - J Biomol Struct Dyn. 2014;32(11):1817-32. doi: 10.1080/07391102.2013.838518. Epub 2013 Sep 13. PMID- 9165070 OWN - NLM STAT- MEDLINE DA - 19970815 DCOM- 19970815 LR - 20061115 IS - 1431-6730 (Print) IS - 1431-6730 (Linking) VI - 378 IP - 3-4 DP - 1997 Mar-Apr TI - Structure and reaction mechanism of L-arginine:glycine amidinotransferase. PG - 193-7 AB - L-Arginine:glycine amidinotransferase (AT) catalyzes the committed step in creatine biosynthesis by formation of guanidinoacetic acid, the direct precursor of creatine. The X-ray structure of the human enzyme shows a novel fold with fivefold pseudosymmetry of beta beta alphabeta-modules. These modules enclose the active site compartment of the basket-like structure. The active site of AT lies at the bottom of a very narrow channel and contains a catalytic triad with the residues Cys-His-Asp. The transamidination reaction follows a ping-pong mechanism and is accompanied by large conformational changes. During catalysis the amidino group is covalently attached to the active site cysteine to give an amidino-cysteine intermediate. FAU - Humm, A AU - Humm A AD - Max-Planck-Institut fur Biochemie, Abt. Strukturforschung, Martinsried, Germany. FAU - Fritsche, E AU - Fritsche E FAU - Steinbacher, S AU - Steinbacher S LA - eng PT - Journal Article PT - Review PL - GERMANY TA - Biol Chem JT - Biological chemistry JID - 9700112 RN - EC 2.1.4.- (Amidinotransferases) RN - EC 2.1.4.1 (glycine amidinotransferase) SB - IM MH - Amidinotransferases/biosynthesis/*chemistry/*metabolism MH - Animals MH - Crystallization MH - Humans MH - Protein Structure, Tertiary RF - 43 EDAT- 1997/03/01 MHDA- 1997/03/01 00:01 CRDT- 1997/03/01 00:00 PST - ppublish SO - Biol Chem. 1997 Mar-Apr;378(3-4):193-7. PMID- 18321067 OWN - NLM STAT- MEDLINE DA - 20080325 DCOM- 20080605 LR - 20140917 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 47 IP - 13 DP - 2008 Apr 1 TI - Characterization of the neuron-specific L1-CAM cytoplasmic tail: naturally disordered in solution it exercises different binding modes for different adaptor proteins. PG - 4160-8 LID - 10.1021/bi702433q [doi] AB - L1, a highly conserved transmembrane glycoprotein member of the immunoglobulin superfamily of cell adhesion molecules, mediates many developmental processes in the nervous system. Here we present the biophysical characterization and the binding properties of the least structurally defined part of this receptor: its cytoplasmic tail (CT). We have shown by analytical ultracentrifugation and dynamic light scattering experiments that it is mostly monomeric and unstructured in aqueous solution. We have defined by nuclear magnetic resonance the molecular details of L1-CT binding to two major targets: a membrane-cytoskeletal linker (MCL), ezrin, and an endocytosis mediator, AP2. Surprisingly, in addition to the two previously identified ezrin binding motifs, the juxtamembrane and the (1176)YRSLE regions, we have discovered a third one, a part of which has been previously associated with binding to another MCL, ankyrin. For the L1 interaction with AP2 we have determined the precise interaction region surrounding the (1176)YRSLE binding site and that this overlaps with the second ezrin binding site. In addition, we have shown that the juxtamembrane region of L1-CT has some binding affinity to AP2-mu2, although the specificity of this interaction needs further investigation. These data indicate that L1-CT belongs to the class of intrinsically disordered proteins. Endogenous flexibility of L1-CT might play an important role in dynamic regulation of intracellular signaling: the ability of cytoplasmic tails to accommodate different targets has the potential to fine-tune signal transduction via cell surface receptors. FAU - Tyukhtenko, Sergiy AU - Tyukhtenko S AD - Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA. FAU - Deshmukh, Lalit AU - Deshmukh L FAU - Kumar, Vineet AU - Kumar V FAU - Lary, Jeffrey AU - Lary J FAU - Cole, James AU - Cole J FAU - Lemmon, Vance AU - Lemmon V FAU - Vinogradova, Olga AU - Vinogradova O LA - eng GR - R01 EY005285/EY/NEI NIH HHS/United States GR - R01 EY005285-23/EY/NEI NIH HHS/United States GR - R01 HD039884/HD/NICHD NIH HHS/United States GR - R01 HD039884-06/HD/NICHD NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080306 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Neural Cell Adhesion Molecule L1) RN - 0 (Solutions) SB - IM MH - Amino Acid Sequence MH - Molecular Sequence Data MH - Neural Cell Adhesion Molecule L1/*metabolism MH - Neurons/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Solutions MH - Ultracentrifugation PMC - PMC2426742 MID - NIHMS52378 OID - NLM: NIHMS52378 OID - NLM: PMC2426742 EDAT- 2008/03/07 09:00 MHDA- 2008/06/06 09:00 CRDT- 2008/03/07 09:00 PHST- 2008/03/06 [aheadofprint] AID - 10.1021/bi702433q [doi] PST - ppublish SO - Biochemistry. 2008 Apr 1;47(13):4160-8. doi: 10.1021/bi702433q. Epub 2008 Mar 6. PMID- 15005622 OWN - NLM STAT- MEDLINE DA - 20040309 DCOM- 20040712 LR - 20111117 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 10 DP - 2004 Mar 16 TI - Inhibiting aggregation of alpha-synuclein with human single chain antibody fragments. PG - 2871-8 AB - The alpha-synuclein protein has been strongly correlated with Parkinson's disease (PD) and is a major component of the hallmark Lewy body aggregates associated with PD. Two different mutations in the alpha-synuclein gene as well as increased gene dosage of wild-type alpha-synuclein all associate with early onset cases of PD; and transgenic animal models overexpressing alpha-synuclein develop PD symptoms. Alpha-synuclein, a natively unfolded protein, can adopt a number of different folded conformations including a beta-sheet form that facilitates formation of numerous aggregated morphologies, including long fibrils, spherical and linear protofibrils, and smaller aggregates or oligomers. The roles of the various morphologies of alpha-synuclein in the progression of PD are not known, and different species have been shown to be toxic. Here we show that single chain antibody fragments (scFv's) isolated from naive phage display antibody libraries can be used to control the aggregation of alpha-synuclein. We isolated an scFv with nanomolar affinity for monomeric alpha-synuclein (K(D) = 2.5 x 10(-8) M). When co-incubated with monomeric alpha-synuclein, the scFv decreased not only the rate of aggregation of alpha-synuclein, but also inhibited the formation of oligomeric and protofibrillar structures. The scFv binds the carboxyl terminal region of alpha-synuclein, suggesting that perturbation of this region can influence folding and aggregation of alpha-synuclein in vitro along with the previously identified hydrophobic core region of alpha-synuclein (residues 61-95, particularly residues 71-82). Since the scFv has been isolated from an antibody library based on human gene sequences, such scFv's can have potential therapeutic value in controlling aggregation of alpha-synuclein in vivo when expressed intracellularly as intrabodies in dopaminergic neurons. FAU - Emadi, Sharareh AU - Emadi S AD - Department of Chemical and Materials Engineering, Arizona State University, Tempe, Arizona 85287, USA. FAU - Liu, Ruitian AU - Liu R FAU - Yuan, Bin AU - Yuan B FAU - Schulz, Philip AU - Schulz P FAU - McAllister, Chad AU - McAllister C FAU - Lyubchenko, Yuri AU - Lyubchenko Y FAU - Messer, Anne AU - Messer A FAU - Sierks, Michael R AU - Sierks MR LA - eng GR - AG17984/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Fluorescent Dyes) RN - 0 (Immunoglobulin Variable Region) RN - 0 (Nerve Tissue Proteins) RN - 0 (Peptide Library) RN - 0 (Recombinant Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (Thiazoles) RN - 0 (alpha-Synuclein) RN - 2390-54-7 (thioflavin T) SB - IM MH - Amino Acid Sequence MH - Binding Sites, Antibody/genetics MH - Epitope Mapping MH - Fluorescent Dyes/metabolism MH - Humans MH - Immunoglobulin Variable Region/*chemistry/genetics/isolation & purification/ultrastructure MH - Inovirus/genetics MH - Kinetics MH - Microscopy, Atomic Force MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*antagonists & inhibitors/immunology/*metabolism/ultrastructure MH - Peptide Library MH - Protein Structure, Tertiary/genetics MH - Recombinant Proteins/biosynthesis/chemistry/isolation & purification/ultrastructure MH - Solubility MH - Synucleins MH - Thiazoles/metabolism MH - alpha-Synuclein EDAT- 2004/03/10 05:00 MHDA- 2004/07/13 05:00 CRDT- 2004/03/10 05:00 AID - 10.1021/bi036281f [doi] PST - ppublish SO - Biochemistry. 2004 Mar 16;43(10):2871-8. PMID- 9525918 OWN - NLM STAT- MEDLINE DA - 19980507 DCOM- 19980507 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 273 IP - 14 DP - 1998 Apr 3 TI - Unusual charge stabilization of NADP+ in 17beta-hydroxysteroid dehydrogenase. PG - 8145-52 AB - Type 1 17beta-hydroxysteroid dehydrogenase (17beta-HSD1), a member of the short chain dehydrogenase reductase (SDR) family, is responsible for the synthesis of 17beta-estradiol, the biologically active estrogen involved in the genesis and development of human breast cancers. Here, we report the crystal structures of the H221L 17beta-HSD1 mutant complexed to NADP+ and estradiol and the H221L mutant/NAD+ and a H221Q mutant/estradiol complexes. These structures provide a complete picture of the NADP+-enzyme interactions involving the flexible 191-199 loop (well ordered in the H221L mutant) and suggest that the hydrophobic residues Phe192-Met193 could facilitate hydride transfer. 17beta-HSD1 appears to be unique among the members of the SDR protein family in that one of the two basic residues involved in the charge compensation of the 2'-phosphate does not belong to the Rossmann-fold motif. The remarkable stabilization of the NADP+ 2'-phosphate by the enzyme also clearly establishes its preference for this cofactor relative to NAD+. Analysis of the catalytic properties of, and estradiol binding to, the two mutants suggests that the His221-steroid O3 hydrogen bond plays an important role in substrate specificity. FAU - Mazza, C AU - Mazza C AD - Laboratoire de Cristallographie et Cristallogenese des Proteines, Institut de Biologie Structurale J.-P. Ebel, CEA-CNRS, 41, avenue des Martyrs, F-38027 Grenoble cedex, France. FAU - Breton, R AU - Breton R FAU - Housset, D AU - Housset D FAU - Fontecilla-Camps, J C AU - Fontecilla-Camps JC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 53-59-8 (NADP) RN - EC 1.1.- (17-Hydroxysteroid Dehydrogenases) RN - EC 1.1.1.51 (3 (or 17)-beta-hydroxysteroid dehydrogenase) SB - IM MH - 17-Hydroxysteroid Dehydrogenases/*chemistry/genetics/metabolism MH - Amino Acid Sequence MH - Animals MH - Binding Sites/genetics MH - Cell Line MH - Humans MH - Molecular Sequence Data MH - Mutation MH - NADP/*chemistry/metabolism MH - *Protein Conformation MH - Sequence Alignment EDAT- 1998/05/09 MHDA- 1998/05/09 00:01 CRDT- 1998/05/09 00:00 PST - ppublish SO - J Biol Chem. 1998 Apr 3;273(14):8145-52. PMID- 21910444 OWN - NLM STAT- MEDLINE DA - 20111005 DCOM- 20120123 LR - 20131121 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 133 IP - 40 DP - 2011 Oct 12 TI - Structural impact of proline-directed pseudophosphorylation at AT8, AT100, and PHF1 epitopes on 441-residue tau. PG - 15842-5 LID - 10.1021/ja205836j [doi] AB - The intrinsically disordered protein tau becomes excessively phosphorylated and aggregates into neurofibrillary tangles in Alzheimer's disease. To obtain insight into the structural consequences of phosphorylation, we characterized a mutant protein of tau in which epitopes recognized by Alzheimer diagnostic antibodies were mimicked by mutation to glutamic acid [AT8 (S199E, S202E, T205E), AT100 (T212E and S214E), and PHF1 (S396E and S404E)]. A large number of distance restraints obtained from NMR paramagnetic relaxation enhancement in combination with ensemble conformer calculations demonstrate that pseudophosphorylation causes an opening of the transient folding of tau. Together with previous studies on the Parkinson-related protein alpha-synuclein, our data indicate that networks of transient long-range interactions are common properties of intrinsically disordered proteins and that their modulation is important for aggregation. FAU - Bibow, Stefan AU - Bibow S AD - Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany. FAU - Ozenne, Valery AU - Ozenne V FAU - Biernat, Jacek AU - Biernat J FAU - Blackledge, Martin AU - Blackledge M FAU - Mandelkow, Eckhard AU - Mandelkow E FAU - Zweckstetter, Markus AU - Zweckstetter M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110915 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (tau Proteins) RN - 9DLQ4CIU6V (Proline) SB - IM MH - Alzheimer Disease/genetics/metabolism MH - Humans MH - Phosphorylation MH - Point Mutation MH - Proline/*metabolism MH - Protein Folding MH - tau Proteins/chemistry/*genetics/*metabolism EDAT- 2011/09/14 06:00 MHDA- 2012/01/24 06:00 CRDT- 2011/09/14 06:00 PHST- 2011/09/15 [aheadofprint] AID - 10.1021/ja205836j [doi] PST - ppublish SO - J Am Chem Soc. 2011 Oct 12;133(40):15842-5. doi: 10.1021/ja205836j. Epub 2011 Sep 15. PMID- 19121363 OWN - NLM STAT- MEDLINE DA - 20090330 DCOM- 20090630 IS - 1638-6183 (Electronic) IS - 0300-9084 (Linking) VI - 91 IP - 4 DP - 2009 Apr TI - Characterization of the Trypanosoma cruzi ortholog of the SBDS protein reveals an intrinsically disordered extended C-terminal region showing RNA-interacting activity. PG - 475-83 LID - 10.1016/j.biochi.2008.12.001 [doi] AB - The human SBDS gene and its yeast ortholog SDO1 encode essential proteins that are involved in ribosome biosynthesis. SDO1 has been implicated in recycling of the ribosomal biogenesis factor Tif6p from pre-66S particles as well as in translation activation of 60S ribosomes. The SBDS protein is highly conserved, containing approximately 250 amino acid residues in animals, fungi and Archaea, while SBDS orthologs of plants and a group of protists contain an extended C-terminal region. In this work, we describe the characterization of the Trypanosoma cruzi SBDS ortholog (TcSBDS). TcSBDS co-fractionates with polysomes in sucrose density gradients, which is consistent with a role in ribosome biosynthesis. We show that TcSBDS contains a C-terminal extension of 200 amino acids that displays the features of intrinsically disordered proteins as determined by proteolytic, circular dichroism and NMR analyses. Interestingly, the C-terminal extension is responsible for TcSBDS-RNA interaction activity in electrophoretic mobility shift assays. This finding suggests that Trypanosomatidae and possibly also other organisms containing SBDS with extended C-terminal regions have evolved an additional function for SBDS in ribosome biogenesis. FAU - de Oliveira, Juliana Ferreira AU - de Oliveira JF AD - Center for Structural Molecular Biology, Brazilian Synchrotron Light Laboratory, LNLS, Rua Giuseppe Maximo Scolfaro 10000, PO Box 6192, CEP13083-970, Campinas SP, Brazil. FAU - Castilho, Beatriz A AU - Castilho BA FAU - Sforca, Mauricio L AU - Sforca ML FAU - Krieger, Marco Aurelio AU - Krieger MA FAU - Zeri, Ana Carolina AU - Zeri AC FAU - Guimaraes, Beatriz G AU - Guimaraes BG FAU - Zanchin, Nilson I T AU - Zanchin NI LA - eng SI - GENBANK/EU715774 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20081216 PL - France TA - Biochimie JT - Biochimie JID - 1264604 RN - 0 (Proteins) RN - 0 (Protozoan Proteins) RN - 0 (RNA-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SBDS protein, human) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Sdo1 protein, S cerevisiae) RN - 63231-63-0 (RNA) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cloning, Molecular MH - Molecular Sequence Data MH - Polyribosomes/physiology MH - Proteins/chemistry/genetics/metabolism MH - Protozoan Proteins/chemistry/genetics/*metabolism MH - RNA/*metabolism MH - RNA-Binding Proteins/chemistry/genetics/*metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Ribosomes/physiology MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism MH - Sequence Alignment MH - Trypanosoma cruzi/*metabolism EDAT- 2009/01/06 09:00 MHDA- 2009/07/01 09:00 CRDT- 2009/01/06 09:00 PHST- 2008/06/24 [received] PHST- 2008/12/05 [accepted] PHST- 2008/12/16 [aheadofprint] AID - S0300-9084(08)00324-6 [pii] AID - 10.1016/j.biochi.2008.12.001 [doi] PST - ppublish SO - Biochimie. 2009 Apr;91(4):475-83. doi: 10.1016/j.biochi.2008.12.001. Epub 2008 Dec 16. PMID- 3233216 OWN - NLM STAT- MEDLINE DA - 19890501 DCOM- 19890501 LR - 20091119 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 27 IP - 25 DP - 1988 Dec 13 TI - Variability in the amino terminus of myosin light chain 1. PG - 8953-8 AB - Three naturally occurring variants of myosin light chain 1, type I, II, and III from avian fast-twitch muscle, have been analyzed by reverse-phase HPLC peptide mapping and amino acid sequencing. Difference peptides were absent from accompanying digests of the related protein, myosin light chain 3, indicating that the heterogeneity was located in the N-terminal 50 residues unique to light chain 1. The type II variant possessed the previous published sequence for the protein [Nabeshima Y., Fujii-Kuriyama, Y., Muramatsu, M., & Ogata, K. (1984) Nature (London) 308, 333-338]. The type I variant, which migrates faster than the type II on SDS gene electrophoresis, contained a Pro----Ala substitution at residue 15, turning the Lys-Pro-(Ala)5(Pro-Ala)7 stretch in this region into Lys-Pro-(Ala)7(Pro-Ala)6. The type III variant, which migrates just faster than the type I, had an (Ala)2 deletion in the (Ala)5 run, yielding Lys-Pro-(Ala)3-(Pro-Ala)7. As indicated by the SDS gel migration rates, the type I and III variants are significantly shorter in length than the type II. The benign nature of the changes is consistent with a flexible arm function for the N-terminal region of light chain 1, with the structural changes in the variants occurring in the spacer region of the arm.(ABSTRACT TRUNCATED AT 250 WORDS) FAU - Rushbrook, J I AU - Rushbrook JI AD - State University of New York--Health Science Center, Brooklyn 11203. FAU - Wadewitz, A G AU - Wadewitz AG FAU - Elzinga, M AU - Elzinga M FAU - Yao, T T AU - Yao TT FAU - Somes, R G Jr AU - Somes RG Jr LA - eng GR - R01 AR 34307/AR/NIAMS NIH HHS/United States GR - R23 HL 27883/HL/NHLBI NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Peptide Fragments) RN - EC 3.4.21.- (Serine Endopeptidases) RN - EC 3.4.21.19 (glutamyl endopeptidase) RN - EC 3.4.21.4 (Trypsin) RN - EC 3.6.4.1 (Myosins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Chickens MH - Chromatography, High Pressure Liquid MH - Electrophoresis, Polyacrylamide Gel MH - *Genetic Variation MH - Molecular Sequence Data MH - Myosins/*genetics MH - Peptide Fragments MH - Serine Endopeptidases MH - Trypsin EDAT- 1988/12/13 MHDA- 2001/03/28 10:01 CRDT- 1988/12/13 00:00 PST - ppublish SO - Biochemistry. 1988 Dec 13;27(25):8953-8. PMID- 18484763 OWN - NLM STAT- MEDLINE DA - 20080609 DCOM- 20080821 LR - 20101118 IS - 1535-3893 (Print) IS - 1535-3893 (Linking) VI - 7 IP - 6 DP - 2008 Jun TI - Intrinsic structural disorder of DF31, a Drosophila protein of chromatin decondensation and remodeling activities. PG - 2291-9 LID - 10.1021/pr700720c [doi] AB - Protein disorder is predicted to be widespread in eukaryotic proteomes, although direct experimental evidence is rather limited so far. To fill this gap and to unveil the identity of novel intrinsically disordered proteins (IDPs), proteomic methods that combine 2D electrophoresis with mass spectrometry have been developed. Here, we applied the method developed in our laboratory [ Csizmok et al., Mol. Cell. Proteomics 2006, 5, 265- 273 ] to the proteome of Drosophila melanogaster. Protein Df31, earlier described as a histone chaperone involved in chromatin decondensation and stabilization, was among the IDPs identified. Despite some hints at the unusual structural behavior of Df31, this protein has not yet been structurally characterized. Here, we provide evidence by a variety of techniques such as CD, NMR, gel-filtration, limited proteolyzsis and bioinformatics that Df31 is intrinsically disordered along its entire length. Further, by chemical cross-linking, we provide evidence that it is a monomeric protein, and suggest that its function(s) may benefit from having an extended and highly flexible structural state. The potential functional advantages and the generality of protein disorder among chromatin organizing proteins are discussed in detail. Finally, we also would like to point out the utility of our 2DE/MS technique for discoveringor, as a matter of fact, rediscoveringIDPs even from the complicated proteome of an advanced eukaryote. FAU - Szollosi, Edit AU - Szollosi E AD - Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary. FAU - Bokor, Monika AU - Bokor M FAU - Bodor, Andrea AU - Bodor A FAU - Perczel, Andras AU - Perczel A FAU - Klement, Eva AU - Klement E FAU - Medzihradszky, Katalin F AU - Medzihradszky KF FAU - Tompa, Kalman AU - Tompa K FAU - Tompa, Peter AU - Tompa P LA - eng GR - ISRF 067595/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080517 PL - United States TA - J Proteome Res JT - Journal of proteome research JID - 101128775 RN - 0 (Chromosomal Proteins, Non-Histone) RN - 0 (Cross-Linking Reagents) RN - 0 (Df31 protein, Drosophila) RN - 0 (Drosophila Proteins) RN - 0 (chromosome decondensation factors) RN - EC 3.4.- (Peptide Hydrolases) SB - IM MH - Animals MH - Calorimetry, Differential Scanning MH - Chromatography, Gel MH - Chromosomal Proteins, Non-Histone/analysis/*chemistry MH - Circular Dichroism MH - Computational Biology MH - Cross-Linking Reagents/chemistry MH - Drosophila Proteins/analysis/*chemistry MH - Electrophoresis, Gel, Two-Dimensional/methods MH - Hot Temperature MH - Hydrophobic and Hydrophilic Interactions MH - Magnetic Resonance Spectroscopy MH - Peptide Hydrolases/chemistry MH - Protein Conformation MH - Protein Denaturation MH - Static Electricity MH - Tandem Mass Spectrometry EDAT- 2008/05/20 09:00 MHDA- 2008/08/22 09:00 CRDT- 2008/05/20 09:00 PHST- 2008/05/17 [aheadofprint] AID - 10.1021/pr700720c [doi] PST - ppublish SO - J Proteome Res. 2008 Jun;7(6):2291-9. doi: 10.1021/pr700720c. Epub 2008 May 17. PMID- 25001212 OWN - NLM STAT- In-Process DA - 20141112 IS - 1875-5305 (Electronic) IS - 0929-8665 (Linking) VI - 21 IP - 12 DP - 2014 TI - Intrinsically unstructured carboxy terminus of Bacillus lipase is essential for its function. PG - 1265-72 AB - We have identified intrinsically unstructured C-terminus of a Bacillus lipase. In an effort to understand the possible role of this C-terminus unstructured region, 10, 20 and 30 amino acids were serially deleted from C-terminal region of the lipase. The catalytic properties of wild type and resulted truncated enzymes were compared. Deletion of 10 amino acids from C-terminus region resulted in decrease in transcription of lipase, specific enzyme activity and extracellular secretion of lipase in comparison to wild type while no effect on lipase aggregation was observed. Negligible activity was observed upon deletion of 20 amino acids. The homology model of the protein demonstrated that the tertiary structure of the protein was held together by these C-terminus residues due to six critically placed hydrogen bonds. Therefore C terminus was essential for the tertiary structure and enzyme activity of lipase. Due to structural flexibility and plasticity originating from the lack of a definite-ordered 3D structure, such disordered regions might represent a major functional advantage for proteins. FAU - Khurana, Jyoti AU - Khurana J FAU - Manisha AU - Manisha FAU - Singh, Ranvir AU - Singh R FAU - Kaur, Jagdeep AU - Kaur J AD - Department of Biotechnology, Panjab University, Chandigarh-160014, India. jagsekhon@yahoo.com. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 SB - IM EDAT- 2014/07/09 06:00 MHDA- 2014/07/09 06:00 CRDT- 2014/07/09 06:00 PHST- 2013/12/03 [received] PHST- 2014/06/24 [revised] PHST- 2014/06/25 [accepted] AID - PPL-EPUB-61296 [pii] PST - ppublish SO - Protein Pept Lett. 2014;21(12):1265-72. PMID- 11546864 OWN - NLM STAT- MEDLINE DA - 20010907 DCOM- 20011004 LR - 20131121 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 293 IP - 5536 DP - 2001 Sep 7 TI - Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters. PG - 1793-800 AB - Multidrug resistance (MDR) is a serious medical problem and presents a major challenge to the treatment of disease and the development of novel therapeutics. ABC transporters that are associated with multidrug resistance (MDR-ABC transporters) translocate hydrophobic drugs and lipids from the inner to the outer leaflet of the cell membrane. To better elucidate the structural basis for the "flip-flop" mechanism of substrate movement across the lipid bilayer, we have determined the structure of the lipid flippase MsbA from Escherichia coli by x-ray crystallography to a resolution of 4.5 angstroms. MsbA is organized as a homodimer with each subunit containing six transmembrane alpha-helices and a nucleotide-binding domain. The asymmetric distribution of charged residues lining a central chamber suggests a general mechanism for the translocation of substrate by MsbA and other MDR-ABC transporters. The structure of MsbA can serve as a model for the MDR-ABC transporters that confer multidrug resistance to cancer cells and infectious microorganisms. FAU - Chang, G AU - Chang G AD - Department of Molecular Biology, MB-9, The Scripps Research Institute, La Jolla, CA 92037, USA. gchang@scripps.edu FAU - Roth, C B AU - Roth CB LA - eng SI - PDB/1JSQ GR - GM61905-01/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PT - Retracted Publication PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Bacterial Proteins) RN - 0 (Lipid A) RN - 0 (Membrane Proteins) RN - 0 (MsbA protein, Bacteria) RN - 8L70Q75FXE (Adenosine Triphosphate) SB - IM CIN - Science. 2001 Sep 7;293(5536):1782-4. PMID: 11546861 RIN - Chang G, Roth CB, Reyes CL, Pornillos O, Chen YJ, Chen AP. Science. 2006 Dec 22;314(5807):1875. PMID: 17185584 MH - *ATP-Binding Cassette Transporters MH - Adenosine Triphosphate/metabolism MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/genetics/metabolism MH - Binding Sites MH - Biological Transport MH - Crystallography, X-Ray MH - Dimerization MH - *Drug Resistance, Microbial MH - *Drug Resistance, Multiple MH - Escherichia coli/*enzymology MH - Lipid A/metabolism MH - Membrane Proteins/*chemistry/genetics/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Static Electricity MH - Structure-Activity Relationship EDAT- 2001/09/08 10:00 MHDA- 2001/10/05 10:01 CRDT- 2001/09/08 10:00 AID - 10.1126/science.293.5536.1793 [doi] AID - 293/5536/1793 [pii] PST - ppublish SO - Science. 2001 Sep 7;293(5536):1793-800. PMID- 16114886 OWN - NLM STAT- MEDLINE DA - 20050823 DCOM- 20051101 LR - 20070813 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 44 IP - 34 DP - 2005 Aug 30 TI - Clusters in an intrinsically disordered protein create a protein-binding site: the TolB-binding region of colicin E9. PG - 11496-507 AB - The 61-kDa colicin E9 protein toxin enters the cytoplasm of susceptible cells by interacting with outer membrane and periplasmic helper proteins and kills them by hydrolyzing their DNA. The membrane translocation function is located in the N-terminal domain of the colicin, with a key signal sequence being a pentapeptide region that governs the interaction with the helper protein TolB (the TolB box). Previous NMR studies [Collins et al. (2002) J. Mol. Biol. 318, 787-904; MacDonald et al. (2004), J. Biomol. NMR 30, 81-96] have shown that the N-terminal 83 residues of colicin E9, which includes the TolB box, is intrinsically disordered and contains clusters of interacting side chains. To further define the properties of this region of colicin E9, we have investigated the effects on the dynamical and TolB-binding properties of three mutations of colicin E9 that inactivate it as a toxin. The mutations were contained in a fusion protein consisting of residues 1-61 of colicin E9 connected to the N terminus of the E9 DNase by an eight-residue linking sequence. The NMR data reveals that the mutations cause major alterations to the properties of some of the clusters, consistent with some form of association between them and other more distant parts of the amino acid sequence, particularly toward the N terminus of the protein. However, (15)N T(2) measurements indicates that residues 5-13 of the fusion protein bound to the 43-kDa TolB remain as flexible as they are in the free protein. The NMR data point to considerable dynamic ordering within the intrinsically disordered translocation domain of the colicin that is important for creating the TolB-binding site. Furthermore, amino acid sequence considerations suggest that the clusters of amino acids occur because of the size and polarities of the side chains forming them influenced by the propensities of the residues within the clusters and those immediately surrounding them in sequence space to form beta turns. FAU - Tozawa, Kaeko AU - Tozawa K AD - School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom. FAU - Macdonald, Colin J AU - Macdonald CJ FAU - Penfold, Christopher N AU - Penfold CN FAU - James, Richard AU - James R FAU - Kleanthous, Colin AU - Kleanthous C FAU - Clayden, Nigel J AU - Clayden NJ FAU - Moore, Geoffrey R AU - Moore GR LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Colicins) RN - 0 (Escherichia coli Proteins) RN - 0 (Periplasmic Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (immE9 protein, E coli) RN - 0 (tolB protein, E coli) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Binding Sites MH - Colicins/*chemistry/genetics/*metabolism MH - Escherichia coli/genetics/metabolism MH - Escherichia coli Proteins/*chemistry/genetics/*metabolism MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Periplasmic Proteins/*chemistry/*metabolism MH - Recombinant Fusion Proteins/chemistry/metabolism MH - Structure-Activity Relationship EDAT- 2005/08/24 09:00 MHDA- 2005/11/03 09:00 CRDT- 2005/08/24 09:00 AID - 10.1021/bi0503596 [doi] PST - ppublish SO - Biochemistry. 2005 Aug 30;44(34):11496-507. PMID- 1409631 OWN - NLM STAT- MEDLINE DA - 19921110 DCOM- 19921110 LR - 20131121 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 89 IP - 19 DP - 1992 Oct 1 TI - Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. PG - 9257-61 AB - The three-dimensional structure of BirA, the repressor of the Escherichia coli biotin biosynthetic operon, has been determined by x-ray crystallography and refined to a crystallographic residual of 19.0% at 2.3-A resolution. BirA is a sequence-specific DNA-binding protein that also catalyzes the formation of biotinyl-5'-adenylate from biotin and ATP and transfers the biotin moiety to other proteins. The level of biotin biosynthetic enzymes in the cell is controlled by the amount of biotinyl-5'-adenylate, which is the BirA corepressor. The structure provides an example of a transcription factor that is also an enzyme. The structure of BirA is highly asymmetric and consists of three domains. The N-terminal domain is mostly alpha-helical, contains a helix-turn-helix DNA-binding motif, and is loosely connected to the remainder of the molecule. The central domain consists of a seven-stranded mixed beta-sheet with alpha-helices covering one face. The other side of the sheet is largely solvent-exposed and contains the active site. The C-terminal domain comprises a six-stranded, antiparallel beta-sheet sandwich. The location of biotin binding is consistent with mutations that affect enzymatic activity. A nearby loop has a sequence that has been associated with phosphate binding in other proteins. It is inferred that ATP binds in this region, adjacent to the biotin. It is proposed that the binding of corepressor to monomeric BirA may promote DNA binding by facilitating the formation of a multimeric BirA-corepressor-DNA complex. The structural details of this complex remain an open question, however. FAU - Wilson, K P AU - Wilson KP AD - Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene 97403. FAU - Shewchuk, L M AU - Shewchuk LM FAU - Brennan, R G AU - Brennan RG FAU - Otsuka, A J AU - Otsuka AJ FAU - Matthews, B W AU - Matthews BW LA - eng GR - GM20066/GM/NIGMS NIH HHS/United States GR - GM31757/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Bacterial Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Repressor Proteins) RN - 0 (Transcription Factors) RN - 6SO6U10H04 (Biotin) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 2.8.1.- (Sulfurtransferases) RN - EC 2.8.1.6 (biotin synthetase) RN - EC 6.3.- (Carbon-Nitrogen Ligases) RN - EC 6.3.4.15 (birA protein, E coli) SB - IM GS - birA MH - Adenosine Triphosphate/metabolism MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/metabolism MH - Binding Sites MH - Biotin/biosynthesis/metabolism MH - *Carbon-Nitrogen Ligases MH - DNA-Binding Proteins/*chemistry/metabolism MH - Escherichia coli/*enzymology/genetics MH - *Escherichia coli Proteins MH - Models, Molecular MH - *Operon MH - Protein Conformation MH - Repressor Proteins/genetics MH - Sulfurtransferases/*chemistry/metabolism MH - *Transcription Factors MH - X-Ray Diffraction PMC - PMC50105 OID - NLM: PMC50105 EDAT- 1992/10/01 MHDA- 1992/10/01 00:01 CRDT- 1992/10/01 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 1992 Oct 1;89(19):9257-61. PMID- 11917013 OWN - NLM STAT- MEDLINE DA - 20020327 DCOM- 20020503 LR - 20140612 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 30 IP - 7 DP - 2002 Apr 1 TI - Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1. PG - 1531-8 AB - The RNA-recognition motif (RRM) is a common and evolutionarily conserved RNA-binding module. Crystallographic and solution structural studies have shown that RRMs adopt a compact alpha/beta structure, in which four antiparallel beta-strands form the major RNA-binding surface. Conserved aromatic residues in the RRM are located on the surface of the beta-sheet and are important for RNA binding. To further our understanding of the structural basis of RRM-nucleic acid interaction, we carried out a high resolution analysis of UP1, the N-terminal, two-RRM domain of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), whose structure was previously solved at 1.75-1.9 A resolution. The two RRMs of hnRNP A1 are closely related but have distinct functions in regulating alternative pre-mRNA splice site selection. Our present 1.1 A resolution crystal structure reveals that two conserved solvent-exposed phenylalanines in the first RRM have alternative side chain conformations. These conformations are spatially correlated, as the individual amino acids cannot adopt each of the observed conformations independently. These phenylalanines are critical for nucleic acid binding and the observed alternative side chain conformations may serve as a mechanism for regulating nucleic acid binding by RRM-containing proteins. FAU - Vitali, Jacqueline AU - Vitali J AD - W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. FAU - Ding, Jianzhong AU - Ding J FAU - Jiang, Jianzhong AU - Jiang J FAU - Zhang, Ying AU - Zhang Y FAU - Krainer, Adrian R AU - Krainer AR FAU - Xu, Rui-Ming AU - Xu RM LA - eng SI - PDB/1L3K GR - CA13106/CA/NCI NIH HHS/United States GR - GM55874/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Amino Acids) RN - 0 (Heterogeneous-Nuclear Ribonucleoprotein Group A-B) RN - 0 (Heterogeneous-Nuclear Ribonucleoproteins) RN - 0 (RNA-Binding Proteins) RN - 0 (Ribonucleoproteins) RN - 0 (hnRNP A1) RN - 63231-63-0 (RNA) SB - IM MH - Amino Acids/chemistry/metabolism MH - Binding Sites MH - Crystallography, X-Ray MH - *Heterogeneous-Nuclear Ribonucleoprotein Group A-B MH - Heterogeneous-Nuclear Ribonucleoproteins MH - Models, Molecular MH - Nucleic Acid Conformation MH - Protein Conformation MH - RNA/*chemistry/metabolism MH - RNA-Binding Proteins/chemistry/metabolism MH - Ribonucleoproteins/*chemistry/metabolism PMC - PMC101846 OID - NLM: PMC101846 EDAT- 2002/03/28 10:00 MHDA- 2002/05/04 10:01 CRDT- 2002/03/28 10:00 PST - ppublish SO - Nucleic Acids Res. 2002 Apr 1;30(7):1531-8. PMID- 19450733 OWN - NLM STAT- MEDLINE DA - 20090519 DCOM- 20090612 LR - 20140829 IS - 1872-9428 (Electronic) IS - 0166-6851 (Linking) VI - 166 IP - 2 DP - 2009 Aug TI - Plasmodium falciparum merozoite surface protein 2 is unstructured and forms amyloid-like fibrils. PG - 159-71 LID - 10.1016/j.molbiopara.2009.03.012 [doi] AB - Several merozoite surface proteins are being assessed as potential components of a vaccine against Plasmodium falciparum, the cause of the most serious form of human malaria. One of these proteins, merozoite surface protein 2 (MSP2), is unusually hydrophilic and contains tandem sequence repeats, characteristics of intrinsically unstructured proteins. A range of physicochemical studies has confirmed that recombinant forms of MSP2 are largely unstructured. Both dimorphic types of MSP2 (3D7 and FC27) are equivalently extended in solution and form amyloid-like fibrils although with different kinetics and structural characteristics. These fibrils have a regular underlying beta-sheet structure and both fibril types stain with Congo Red, but only the FC27 fibrils stain with Thioflavin T. 3D7 MSP2 fibrils seeded the growth of fibrils from 3D7 or FC27 MSP2 monomer indicating the involvement of a conserved region of MSP2 in fibril formation. Consistent with this, digestion of fibrils with proteinase K generated resistant peptides, which included the N-terminal conserved region of MSP2. A monoclonal antibody that reacted preferentially with monomeric recombinant MSP2 did not react with the antigen in situ on the merozoite surface. Glutaraldehyde cross-linking of infected erythrocytes generated MSP2 oligomers similar to those formed by polymeric recombinant MSP2. We conclude that MSP2 oligomers containing intermolecular beta-strand interactions similar to those in amyloid fibrils may be a component of the fibrillar surface coat on P. falciparum merozoites. FAU - Adda, Christopher G AU - Adda CG AD - Department of Biochemistry, La Trobe University, Victoria 3086, Australia. FAU - Murphy, Vince J AU - Murphy VJ FAU - Sunde, Margaret AU - Sunde M FAU - Waddington, Lynne J AU - Waddington LJ FAU - Schloegel, Jesse AU - Schloegel J FAU - Talbo, Gert H AU - Talbo GH FAU - Vingas, Kleo AU - Vingas K FAU - Kienzle, Vivian AU - Kienzle V FAU - Masciantonio, Rosella AU - Masciantonio R FAU - Howlett, Geoffrey J AU - Howlett GJ FAU - Hodder, Anthony N AU - Hodder AN FAU - Foley, Michael AU - Foley M FAU - Anders, Robin F AU - Anders RF LA - eng GR - R01 AI059229-01A1/AI/NIAID NIH HHS/United States GR - R01AI59229/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090409 PL - Netherlands TA - Mol Biochem Parasitol JT - Molecular and biochemical parasitology JID - 8006324 RN - 0 (Amyloid) RN - 0 (Antigens, Protozoan) RN - 0 (Protozoan Proteins) RN - 0 (merozoite surface protein 2, Plasmodium) SB - IM MH - Amino Acid Sequence MH - Amyloid/*chemistry/genetics/immunology MH - Animals MH - Antigens, Protozoan/*chemistry/genetics/immunology MH - Humans MH - Malaria, Falciparum/immunology/*parasitology MH - Molecular Sequence Data MH - Plasmodium falciparum/*chemistry/genetics/immunology MH - Protozoan Proteins/*chemistry/genetics/immunology PMC - PMC2713819 MID - NIHMS108821 OID - NLM: NIHMS108821 OID - NLM: PMC2713819 EDAT- 2009/05/20 09:00 MHDA- 2009/06/13 09:00 CRDT- 2009/05/20 09:00 PHST- 2008/10/02 [received] PHST- 2009/03/30 [revised] PHST- 2009/03/30 [accepted] PHST- 2009/04/09 [aheadofprint] AID - S0166-6851(09)00114-5 [pii] AID - 10.1016/j.molbiopara.2009.03.012 [doi] PST - ppublish SO - Mol Biochem Parasitol. 2009 Aug;166(2):159-71. doi: 10.1016/j.molbiopara.2009.03.012. Epub 2009 Apr 9. PMID- 15774032 OWN - NLM STAT- MEDLINE DA - 20050318 DCOM- 20060331 LR - 20140608 IS - 1465-6914 (Electronic) IS - 1465-6906 (Linking) VI - 6 IP - 3 DP - 2005 TI - Flexible peptides and cytoplasmic gels. PG - 106 AB - Recent progress in predicting protein structures has revealed a surprising abundance of proteins that are significantly unfolded under physiological conditions. Unstructured, flexible polypeptides are likely to be functionally important and may cause local cytoplasmic regions to become gel-like. FAU - Bray, Dennis AU - Bray D AD - Department of Anatomy, University of Cambridge, Cambridge CB2 3DY, UK. db10009@cam.ac.uk LA - eng PT - Journal Article DEP - 20050228 PL - England TA - Genome Biol JT - Genome biology JID - 100960660 RN - 0 (Peptides) RN - 0 (Polymers) RN - 0 (Proteins) SB - IM MH - Cell Membrane/physiology MH - Cytoplasm/*chemistry MH - Models, Biological MH - Peptides/*chemistry MH - Pliability MH - Polymers/chemistry MH - Protein Folding MH - Proteins/*chemistry PMC - PMC1088933 OID - NLM: PMC1088933 EDAT- 2005/03/19 09:00 MHDA- 2006/04/01 09:00 CRDT- 2005/03/19 09:00 PHST- 2005/02/28 [aheadofprint] AID - gb-2005-6-3-106 [pii] AID - 10.1186/gb-2005-6-3-106 [doi] PST - ppublish SO - Genome Biol. 2005;6(3):106. Epub 2005 Feb 28. PMID- 22153507 OWN - NLM STAT- MEDLINE DA - 20111214 DCOM- 20120412 LR - 20131121 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 19 IP - 12 DP - 2011 Dec 7 TI - Structure basis for the regulation of glyceraldehyde-3-phosphate dehydrogenase activity via the intrinsically disordered protein CP12. PG - 1846-54 LID - 10.1016/j.str.2011.08.016 [doi] AB - The reversible formation of a glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-CP12-phosphoribulokinase (PRK) supramolecular complex, identified in oxygenic photosynthetic organisms, provides light-dependent Calvin cycle regulation in a coordinated manner. An intrinsically disordered protein (IDP) CP12 acts as a linker to sequentially bind GAPDH and PRK to downregulate both enzymes. Here, we report the crystal structures of the ternary GAPDH-CP12-NAD and binary GAPDH-NAD complexes from Synechococcus elongates. The GAPDH-CP12 complex structure reveals that the oxidized CP12 becomes partially structured upon GAPDH binding. The C-terminus of CP12 is inserted into the active-site region of GAPDH, resulting in competitive inhibition of GAPDH. This study also provides insight into how the GAPDH-CP12 complex is dissociated by a high NADP(H)/NAD(H) ratio. An unexpected increase in negative charge potential that emerged upon CP12 binding highlights the biological function of CP12 in the sequential assembly of the supramolecular complex. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Matsumura, Hiroyoshi AU - Matsumura H AD - Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. matsumura@chem.eng.osaka-u.ac.jp FAU - Kai, Akihiro AU - Kai A FAU - Maeda, Takayuki AU - Maeda T FAU - Tamoi, Masahiro AU - Tamoi M FAU - Satoh, Atsuko AU - Satoh A FAU - Tamura, Haruka AU - Tamura H FAU - Hirose, Mika AU - Hirose M FAU - Ogawa, Taketo AU - Ogawa T FAU - Kizu, Natsuko AU - Kizu N FAU - Wadano, Akira AU - Wadano A FAU - Inoue, Tsuyoshi AU - Inoue T FAU - Shigeoka, Shigeru AU - Shigeoka S LA - eng SI - PDB/3B1J SI - PDB/3B1K SI - PDB/3B20 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Bacterial Proteins) RN - 0 (Multiprotein Complexes) RN - 0U46U6E8UK (NAD) RN - EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases) SB - IM CIN - Structure. 2011 Dec 7;19(12):1728-9. PMID: 22153493 MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/metabolism MH - Binding Sites MH - Crystallography, X-Ray MH - Glyceraldehyde-3-Phosphate Dehydrogenases/*chemistry/metabolism MH - Molecular Sequence Data MH - Multiprotein Complexes/chemistry/metabolism MH - NAD/chemistry/metabolism MH - Synechococcus/enzymology/metabolism EDAT- 2011/12/14 06:00 MHDA- 2012/04/13 06:00 CRDT- 2011/12/14 06:00 PHST- 2011/07/17 [received] PHST- 2011/08/14 [revised] PHST- 2011/08/23 [accepted] AID - S0969-2126(11)00330-3 [pii] AID - 10.1016/j.str.2011.08.016 [doi] PST - ppublish SO - Structure. 2011 Dec 7;19(12):1846-54. doi: 10.1016/j.str.2011.08.016. PMID- 15660128 OWN - NLM STAT- MEDLINE DA - 20050210 DCOM- 20050328 LR - 20141120 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 24 IP - 3 DP - 2005 Feb 9 TI - Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1. PG - 439-51 AB - E1 enzymes facilitate conjugation of ubiquitin and ubiquitin-like proteins through adenylation, thioester transfer within E1, and thioester transfer from E1 to E2 conjugating proteins. Structures of human heterodimeric Sae1/Sae2-Mg.ATP and Sae1/Sae2-SUMO-1-Mg.ATP complexes were determined at 2.2 and 2.75 A resolution, respectively. Despite the presence of Mg.ATP, the Sae1/Sae2-SUMO-1-Mg.ATP structure reveals a substrate complex insomuch as the SUMO C-terminus remains unmodified within the adenylation site and 35 A from the catalytic cysteine, suggesting that additional changes within the adenylation site may be required to facilitate chemistry prior to adenylation and thioester transfer. A mechanism for E2 recruitment to E1 is suggested by biochemical and genetic data, each of which supports a direct role for the E1 C-terminal ubiquitin-like domain for E2 recruitment during conjugation. FAU - Lois, Luisa Maria AU - Lois LM AD - Structural Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA. FAU - Lima, Christopher D AU - Lima CD LA - eng GR - GM65872/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050120 PL - England TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Multiprotein Complexes) RN - 0 (NEDD8 protein, human) RN - 0 (Recombinant Proteins) RN - 0 (SUMO-1 Protein) RN - 0 (Ubiquitins) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 6.3.2.19 (SAE1 protein, human) RN - EC 6.3.2.19 (UBA2 protein, human) RN - EC 6.3.2.19 (Ubiquitin-Activating Enzymes) SB - IM MH - Adenosine Triphosphate/chemistry/metabolism MH - Amino Acid Sequence MH - Catalytic Domain MH - Crystallography, X-Ray MH - Dimerization MH - Enzyme Activation MH - Humans MH - In Vitro Techniques MH - Models, Molecular MH - Molecular Sequence Data MH - Multiprotein Complexes MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism MH - SUMO-1 Protein/*chemistry/genetics/metabolism MH - Sequence Homology, Amino Acid MH - Ubiquitin-Activating Enzymes/*chemistry/genetics/metabolism MH - Ubiquitins/metabolism PMC - PMC548657 OID - NLM: PMC548657 EDAT- 2005/01/22 09:00 MHDA- 2005/03/29 09:00 CRDT- 2005/01/22 09:00 PHST- 2004/10/20 [received] PHST- 2004/12/21 [accepted] PHST- 2005/01/20 [aheadofprint] AID - 7600552 [pii] AID - 10.1038/sj.emboj.7600552 [doi] PST - ppublish SO - EMBO J. 2005 Feb 9;24(3):439-51. Epub 2005 Jan 20. PMID- 9735293 OWN - NLM STAT- MEDLINE DA - 19981014 DCOM- 19981014 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 282 IP - 2 DP - 1998 Sep 18 TI - Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases. PG - 359-68 AB - Human immunodeficiency virus (HIV) integrase is the enzyme responsible for insertion of a DNA copy of the viral genome into host DNA, an essential step in the replication cycle of HIV. HIV-1 integrase comprises three functional and structural domains: an N-terminal zinc-binding domain, a catalytic core domain and a C-terminal DNA-binding domain. The catalytic core domain with the F185H mutation has been crystallized without sodium cacodylate in a new crystal form, free and complexed with the catalytic metal Mg2+. The structures have been determined and refined to about 2.2 A. Unlike the previously reported structures, the three active-site carboxylate residues (D,D-35-E motif) are well ordered and both aspartate residues delineate a proper metal-binding site. Comparison of the active binding site of this domain with that of other members from the polynucleotidyl transferases superfamily shows a high level of similarity, providing a confident template for the design of antiviral agents. CI - Copyright 1998 Academic Press. FAU - Maignan, S AU - Maignan S AD - Rhone-Poulenc Rorer, 13, Quai J. Guesde, Vitry/Seine, F-94403, France. FAU - Guilloteau, J P AU - Guilloteau JP FAU - Zhou-Liu, Q AU - Zhou-Liu Q FAU - Clement-Mella, C AU - Clement-Mella C FAU - Mikol, V AU - Mikol V LA - eng PT - Journal Article PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - AJ2HL7EU8K (Cacodylic Acid) RN - EC 2.7.7.- (HIV Integrase) RN - I38ZP9992A (Magnesium) SB - IM SB - X MH - Binding Sites MH - Cacodylic Acid/metabolism MH - Catalysis MH - Crystallography, X-Ray MH - HIV Integrase/*chemistry/metabolism MH - Magnesium/*chemistry/metabolism MH - Models, Chemical MH - Molecular Structure MH - *Protein Structure, Tertiary EDAT- 1998/09/15 MHDA- 1998/09/15 00:01 CRDT- 1998/09/15 00:00 AID - S0022-2836(98)92002-2 [pii] AID - 10.1006/jmbi.1998.2002 [doi] PST - ppublish SO - J Mol Biol. 1998 Sep 18;282(2):359-68. PMID- 21898648 OWN - NLM STAT- MEDLINE DA - 20111114 DCOM- 20120229 LR - 20141022 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 20 IP - 12 DP - 2011 Dec TI - The interplay between transient alpha-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts. PG - 2023-34 LID - 10.1002/pro.726 [doi] AB - The peptide backbones of disordered proteins are routinely characterized by NMR with respect to transient structure and dynamics. Little experimental information is, however, available about the side chain conformations and how structure in the backbone affects the side chains. Methyl chemical shifts can in principle report the conformations of aliphatic side chains in disordered proteins and in order to examine this two model systems were chosen: the acid denatured state of acyl-CoA binding protein (ACBP) and the intrinsically disordered activation domain of the activator for thyroid hormone and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the gamma-gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation of gamma-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow a quantitative analysis of the ensemble of chi(2)-angles of especially leucine residues in disordered proteins. The changes in the rotamer distributions upon denaturation correlate to the changes upon helix induction by the co-solvent trifluoroethanol, suggesting that the side chain conformers are directly or indirectly related to formation of transient alpha-helices. CI - Copyright (c) 2011 The Protein Society. FAU - Kjaergaard, Magnus AU - Kjaergaard M AD - Department of Biology, University of Copenhagen, Kobenhavn N, Denmark. FAU - Iesmantavicius, Vytautas AU - Iesmantavicius V FAU - Poulsen, Flemming M AU - Poulsen FM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Diazepam Binding Inhibitor) RN - 0 (Proteins) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 3) SB - IM MH - Animals MH - Cattle MH - Diazepam Binding Inhibitor/chemistry MH - Hydrophobic and Hydrophilic Interactions MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Nuclear Receptor Coactivator 3/chemistry MH - Protein Denaturation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - *Protein Unfolding MH - Proteins/*chemistry PMC - PMC3302646 OID - NLM: PMC3302646 EDAT- 2011/09/08 06:00 MHDA- 2012/03/01 06:00 CRDT- 2011/09/08 06:00 AID - 10.1002/pro.726 [doi] PST - ppublish SO - Protein Sci. 2011 Dec;20(12):2023-34. doi: 10.1002/pro.726. PMID- 21156135 OWN - NLM STAT- MEDLINE DA - 20101215 DCOM- 20110328 LR - 20140821 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 12 DP - 2010 Dec 15 TI - Functional role of ribosomal signatures. PG - 3930-40 LID - 10.1016/j.bpj.2010.09.062 [doi] AB - Although structure and sequence signatures in ribosomal RNA and proteins are defining characteristics of the three domains of life and instrumental in constructing the modern phylogeny, little is known about their functional roles in the ribosome. In this work, the largest coevolving RNA/protein signatures in the bacterial 30S ribosome are investigated both experimentally and computationally through all-atom molecular-dynamics simulations. The complex includes the N-terminal fragment of the ribosomal protein S4, which is a primary binding protein that initiates 30S small subunit assembly from the 5' domain, and helix 16 (h16), which is part of the five-way junction in 16S rRNA. Our results show that the S4 N-terminus signature is intrinsically disordered in solution, whereas h16 is relatively stable by itself. The dynamic disordered property of the protein is exploited to couple the folding and binding process to the five-way junction, and the results provide insight into the mechanism for the early and fast binding of S4 in the assembly of the ribosomal small subunit. CI - Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Chen, Ke AU - Chen K AD - Center for Biophysics and Computational Biology, Department of Chemistry, University of Illinois, Urbana, Illinois, USA. FAU - Eargle, John AU - Eargle J FAU - Sarkar, Krishnarjun AU - Sarkar K FAU - Gruebele, Martin AU - Gruebele M FAU - Luthey-Schulten, Zaida AU - Luthey-Schulten Z LA - eng GR - P41-RR005969/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (RNA, Ribosomal, 16S) RN - 0 (Ribosomal Proteins) RN - 0 (ribosomal protein S4) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Computer Simulation MH - Escherichia coli/*metabolism MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Pliability MH - Protein Binding MH - Protein Stability MH - Protein Structure, Secondary MH - Protein Unfolding MH - RNA, Ribosomal, 16S/chemistry/genetics/metabolism MH - Ribosomal Proteins/chemistry/metabolism MH - Ribosomes/*metabolism MH - Temperature PMC - PMC3000519 OID - NLM: PMC3000519 EDAT- 2010/12/16 06:00 MHDA- 2011/03/29 06:00 CRDT- 2010/12/16 06:00 PHST- 2010/06/23 [received] PHST- 2010/08/20 [revised] PHST- 2010/09/14 [accepted] AID - S0006-3495(10)01213-0 [pii] AID - 10.1016/j.bpj.2010.09.062 [doi] PST - ppublish SO - Biophys J. 2010 Dec 15;99(12):3930-40. doi: 10.1016/j.bpj.2010.09.062. PMID- 15996101 OWN - NLM STAT- MEDLINE DA - 20050705 DCOM- 20050915 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 44 IP - 27 DP - 2005 Jul 12 TI - The modular structure of SIP facilitates its role in stabilizing multiprotein assemblies. PG - 9462-71 AB - Siah-interacting protein (SIP) was identified as a novel adaptor that physically links the E3 ubiquitin ligase activity of Siah-1 with Skp1 and Ebi F-Box protein in the degradation of beta-catenin, a transcriptional activator of TCF/LEF genes. In this study, we have used solution NMR spectroscopy to characterize the domain structure of SIP, which includes a novel helical hairpin domain at the N-terminus flexibly linked to a CS domain and an unstructured carboxy terminal SGS domain. These studies have been complemented by mapping the sites of functionally important protein-protein interactions involving Siah-1 and Skp1 to individual domains of SIP. NMR-based chemical shift perturbation assays show that Siah-1 interacts with the flexible linker between SIP N and CS domains. This site for interaction in the linker does not perturb residues in the structured region at the N-terminus but does appear to restrict the rotational freedom of the SIP CS domain in the context of the full-length protein. In contrast, Skp1 engages the SIP CS domain exclusively through weak interactions that are not coupled to the other domains. The principal role of the modular structure of SIP appears to be in bringing these two proteins into physical proximity and orchestrating the orientation required for polyubiquitination of beta-catenin in the intact SCF-type complex. FAU - Bhattacharya, Shibani AU - Bhattacharya S AD - Department of Biochemistry, Center for Structural Biology, 5140 BIOSCI/MRBIII, Vanderbilt University, Nashville, Tennessee 37232-8725, USA. FAU - Lee, Young-Tae AU - Lee YT FAU - Michowski, Wojciech AU - Michowski W FAU - Jastrzebska, Beata AU - Jastrzebska B FAU - Filipek, Anna AU - Filipek A FAU - Kuznicki, Jacek AU - Kuznicki J FAU - Chazin, Walter J AU - Chazin WJ LA - eng SI - PDB/1YSM GR - P30CA68485/CA/NCI NIH HHS/United States GR - P30ES00267/ES/NIEHS NIH HHS/United States GR - R01 GM62112/GM/NIGMS NIH HHS/United States GR - R03 TW00136005/TW/FIC NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cacybp protein, mouse) RN - 0 (Calcium-Binding Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Peptide Fragments) RN - 0 (S-Phase Kinase-Associated Proteins) RN - EC 6.3.2.19 (SKP Cullin F-Box Protein Ligases) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) RN - EC 6.3.2.19 (seven in absentia proteins) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Calcium-Binding Proteins/*chemistry/metabolism/*physiology MH - Crystallography, X-Ray MH - Dimerization MH - Mice MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/metabolism MH - Peptide Fragments/chemistry/metabolism/physiology MH - Protein Interaction Mapping MH - Protein Processing, Post-Translational/*physiology MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - S-Phase Kinase-Associated Proteins/metabolism MH - SKP Cullin F-Box Protein Ligases/metabolism MH - Ubiquitin-Protein Ligases/metabolism EDAT- 2005/07/06 09:00 MHDA- 2005/09/16 09:00 CRDT- 2005/07/06 09:00 AID - 10.1021/bi0502689 [doi] PST - ppublish SO - Biochemistry. 2005 Jul 12;44(27):9462-71. PMID- 25039985 OWN - NLM STAT- MEDLINE DA - 20140904 DCOM- 20141104 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 281 IP - 17 DP - 2014 Sep TI - The intrinsically disordered structural platform of the plant defence hub protein RPM1-interacting protein 4 provides insights into its mode of action in the host-pathogen interface and evolution of the nitrate-induced domain protein family. PG - 3955-79 LID - 10.1111/febs.12937 [doi] AB - Arabidopsis thaliana (At) RPM1-interacting protein 4 (RIN4), targeted by many defence-suppressing bacterial type III effectors and monitored by several resistance proteins, regulates plant immune responses to pathogen-associated molecular patterns and type III effectors. Little is known about the overall protein structure of AtRIN4, especially in its unbound form, and the relevance of structure to its diverse biological functions. AtRIN4 contains two nitrate-induced (NOI) domains and is a member of the NOI family. Using experimental and bioinformatic approaches, we demonstrate that the unbound AtRIN4 is intrinsically disordered under physiological conditions. The intrinsically disordered polypeptide chain of AtRIN4 is interspersed with molecular recognition features (MoRFs) and anchor-identified long-binding regions, potentially allowing it to undergo disorder-to-order transitions upon binding to partner(s). A poly-l-proline II structure, often responsible for protein recognition, is also identified in AtRIN4. By performing bioinformatics analyses on RIN4 homologues from different plant species and the NOI proteins from Arabidopsis, we infer the conservation of intrinsic disorder, MoRFs and long-binding regions of AtRIN4 in other plant species and the NOI family. Intrinsic disorder and MoRFs could provide RIN4 proteins with the binding promiscuity and plasticity required to act as hubs in a pivotal position within plant defence signalling cascades. CI - (c) 2014 FEBS. FAU - Sun, Xiaolin AU - Sun X AD - The New Zealand Institute of Plant & Food Research (PFR), Palmerston North, New Zealand. FAU - Greenwood, David R AU - Greenwood DR FAU - Templeton, Matthew D AU - Templeton MD FAU - Libich, David S AU - Libich DS FAU - McGhie, Tony K AU - McGhie TK FAU - Xue, Bin AU - Xue B FAU - Yoon, Minsoo AU - Yoon M FAU - Cui, Wei AU - Cui W FAU - Kirk, Christopher A AU - Kirk CA FAU - Jones, William T AU - Jones WT FAU - Uversky, Vladimir N AU - Uversky VN FAU - Rikkerink, Erik H A AU - Rikkerink EH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140808 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Arabidopsis Proteins) RN - 0 (Carrier Proteins) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Plant Proteins) RN - 0 (RIN4 protein, Arabidopsis) RN - 75-89-8 (Trifluoroethanol) RN - EC 3.4.21.4 (Trypsin) SB - IM MH - Amino Acid Sequence MH - Arabidopsis Proteins/*chemistry/metabolism MH - Carrier Proteins/*chemistry/metabolism MH - Circular Dichroism MH - Host-Pathogen Interactions/*drug effects MH - Hydrophobic and Hydrophilic Interactions MH - Intrinsically Disordered Proteins/*chemistry MH - Plant Proteins/chemistry MH - Plants/metabolism MH - Protein Folding/drug effects MH - Protein Structure, Secondary/drug effects MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Temperature MH - Trifluoroethanol/pharmacology MH - Trypsin/metabolism OTO - NOTNLM OT - RIN4 OT - binding-induced folding OT - intrinsic disorder OT - molecular recognition features (MoRFs) OT - plant-microbe interaction EDAT- 2014/07/22 06:00 MHDA- 2014/11/05 06:00 CRDT- 2014/07/22 06:00 PHST- 2014/02/14 [received] PHST- 2014/07/01 [revised] PHST- 2014/07/15 [accepted] PHST- 2014/08/08 [aheadofprint] AID - 10.1111/febs.12937 [doi] PST - ppublish SO - FEBS J. 2014 Sep;281(17):3955-79. doi: 10.1111/febs.12937. Epub 2014 Aug 8. PMID- 8805523 OWN - NLM STAT- MEDLINE DA - 19970325 DCOM- 19970325 LR - 20071114 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 4 IP - 2 DP - 1996 Feb 15 TI - The structure of simian virus 40 refined at 3.1 A resolution. PG - 165-82 AB - BACKGROUND: The structure of simian virus 40 (SV40), previously determined at 3.8 degree resolution, shows how its pentameric VP1 assembly units are tied together by extended C-terminal arms. In order to define more precisely the possible assembly mechanisms, we have refined the structure at 3.1 degree resolution. RESULTS: New data from a high-intensity synchrotron source have been used for phase extension by electron-density averaging and refinement, exploiting only the strict 5-fold non-crystallographic symmetry for the real-space averaging steps. The accurate model enables us to study important structural features of the virus particle in detail. The remarkably invariant core of the VP1 pentamer bears the docking sites for the C-terminal arms from other pentamers. These contacts are the principal way in which pentameric assembly units are linked together in the capsid. Only at the interface between five-coordinated and six-coordinated pentamers do the pentamer cores appear to interact strongly. There are two cation-binding sites per VP1 monomer, seen in a soaking experiment with gadolinium nitrate. These sites are quite close to each other at the interfaces between pentamers. CONCLUSION: We propose that the contact between five-coordinated and six-coordinated pentamers may help to generate a six-pentamer nucleus, with which further pentamers can assemble to generate the complete particle. Calcium ions probably stabilize the structure of the assembled particle, rather than direct its assembly. FAU - Stehle, T AU - Stehle T AD - Howard Hughes Medical Institute and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. FAU - Gamblin, S J AU - Gamblin SJ FAU - Yan, Y AU - Yan Y FAU - Harrison, S C AU - Harrison SC LA - eng GR - CA13202/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Biopolymers) RN - 0 (Capsid Proteins) RN - 0 (VP1 protein, polyomavirus) SB - IM MH - Amino Acid Sequence MH - Biopolymers MH - Capsid/*chemistry MH - *Capsid Proteins MH - Electrons MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Simian virus 40/*chemistry MH - Temperature EDAT- 1996/02/15 MHDA- 1996/02/15 00:01 CRDT- 1996/02/15 00:00 PST - ppublish SO - Structure. 1996 Feb 15;4(2):165-82. PMID- 20974845 OWN - NLM STAT- MEDLINE DA - 20110110 DCOM- 20110302 LR - 20140821 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 2 DP - 2011 Jan 14 TI - Light chain-dependent self-association of dynein intermediate chain. PG - 1556-66 LID - 10.1074/jbc.M110.171686 [doi] AB - Dynein light chains are bivalent dimers that bind two copies of dynein intermediate chain IC to form a cargo attachment subcomplex. The interaction of light chain LC8 with the natively disordered N-terminal domain of IC induces helix formation at distant IC sites in or near a region predicted to form a coiled-coil. This fostered the hypothesis that LC8 binding promotes IC self-association to form a coiled-coil or other interchain helical structure. However, recent studies show that the predicted coiled-coil sequence partially overlaps the light chain LC7 recognition sequence on IC, raising questions about the apparently contradictory effects of LC8 and LC7. Here, we use NMR and fluorescence quenching to localize IC self-association to residues within the predicted coiled-coil that also correspond to helix 1 of the LC7 recognition sequence. LC8 binding promotes IC self-association of helix 1 from each of two IC chains, whereas LC7 binding reverses self-association by incorporating the same residues into two symmetrical, but distant, helices of the LC7-IC complex. Isothermal titration experiments confirm the distinction of LC8 enhancement of IC self-association and LC7 binding effects. When all three light chains are bound, IC self-association is shifted to another region. Such flexibility in association modes may function in maintaining a stable and versatile light chain-intermediate chain assembly under changing cellular conditions. FAU - Nyarko, Afua AU - Nyarko A AD - Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA. FAU - Barbar, Elisar AU - Barbar E LA - eng GR - 00210/PHS HHS/United States GR - GM 084276/GM/NIGMS NIH HHS/United States GR - R01 GM084276/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20101025 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Carrier Proteins) RN - 0 (Drosophila Proteins) RN - 0 (ctp protein, Drosophila) RN - 0 (roadblock protein, Drosophila) RN - EC 3.6.4.2 (Dyneins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Carrier Proteins/*chemistry/genetics/metabolism MH - Dimerization MH - Drosophila Proteins/*chemistry/genetics/metabolism MH - Drosophila melanogaster/genetics/*metabolism MH - Dyneins/*chemistry/genetics/metabolism MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Thermodynamics PMC - PMC3020764 OID - NLM: PMC3020764 EDAT- 2010/10/27 06:00 MHDA- 2011/03/03 06:00 CRDT- 2010/10/27 06:00 PHST- 2010/10/25 [aheadofprint] AID - M110.171686 [pii] AID - 10.1074/jbc.M110.171686 [doi] PST - ppublish SO - J Biol Chem. 2011 Jan 14;286(2):1556-66. doi: 10.1074/jbc.M110.171686. Epub 2010 Oct 25. PMID- 19383694 OWN - NLM STAT- MEDLINE DA - 20090602 DCOM- 20090722 IS - 1350-0872 (Print) IS - 1350-0872 (Linking) VI - 155 IP - Pt 6 DP - 2009 Jun TI - Cloning of feather-degrading minor extracellular protease from Bacillus cereus DCUW: dissection of the structural domains. PG - 2049-57 LID - 10.1099/mic.0.027573-0 [doi] AB - Bacterial extracellular proteases play an important role in cell survival and cell-cell communication. A high-molecular-mass minor extracellular protease (Vpr) from a feather-degrading bacterium, Bacillus cereus DCUW, has been reported by our laboratory. In the present study, we cloned and expressed Vpr in Escherichia coli. Complete nucleotide sequencing of this gene predicted that the protease is a member of the serine protease family, and smart domain analysis revealed that the protease consists of an N-terminal signal sequence for secretion, a subtilisin_N sequence that is a signature for N-terminal processing, a catalytic S_8 peptidase domain, and finally a long C-terminal protease-associated (PA) region containing nine intrinsically disordered subdomains. Four truncated constructs of the Vpr protease were cloned and expressed in E. coli. We found that the catalytic domain (amino acid residues 172-583) is sufficient for protease activity. Maturation of the Vpr protease needed both N-terminal and C-terminal processing. We have demonstrated that the oligomerization property is associated with the C-terminal protease-associated domain and also shown that the substrate-binding specificity to raw feather resides in this domain. FAU - Ghosh, Abhrajyoti AU - Ghosh A AD - Department of Biochemistry, University of Calcutta, India. FAU - Chakrabarti, Krishanu AU - Chakrabarti K FAU - Chattopadhyay, Dhrubajyoti AU - Chattopadhyay D LA - eng SI - GENBANK/EU626488 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090421 PL - England TA - Microbiology JT - Microbiology (Reading, England) JID - 9430468 RN - 0 (Protein Sorting Signals) RN - 0 (RNA, Bacterial) RN - 0 (Recombinant Fusion Proteins) RN - EC 3.4.21.- (Serine Endopeptidases) SB - IM MH - Animals MH - Bacillus cereus/*enzymology MH - Cloning, Molecular MH - Enzyme Activation MH - Feathers/*metabolism MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Protein Sorting Signals MH - Protein Structure, Tertiary/physiology MH - RNA, Bacterial/isolation & purification MH - Rabbits MH - Recombinant Fusion Proteins/biosynthesis MH - Sequence Analysis, DNA MH - Serine Endopeptidases/chemistry/genetics/*metabolism EDAT- 2009/04/23 09:00 MHDA- 2009/07/23 09:00 CRDT- 2009/04/23 09:00 PHST- 2009/04/21 [aheadofprint] AID - mic.0.027573-0 [pii] AID - 10.1099/mic.0.027573-0 [doi] PST - ppublish SO - Microbiology. 2009 Jun;155(Pt 6):2049-57. doi: 10.1099/mic.0.027573-0. Epub 2009 Apr 21. PMID- 12490543 OWN - NLM STAT- MEDLINE DA - 20030129 DCOM- 20030228 LR - 20131121 IS - 1530-6860 (Electronic) IS - 0892-6638 (Linking) VI - 17 IP - 2 DP - 2003 Feb TI - Pseudo-symmetry of C19 steroids, alternative binding orientations, and multispecificity in human estrogenic 17beta-hydroxysteroid dehydrogenase. PG - 274-6 AB - Steroids are implicated in many physiological processes, such as reproduction, aging, metabolism, and cancer. To understand the molecular basis for steroid recognition and discrimination, we studied the human estrogenic 17beta-hydroxysteroid dehydrogenase (17beta-HSD1) responsible for the last step in the bioactivation of all estrogens. Here we report the first observation of the conversion of dihydrotestosterone (DHT) into 3beta,17beta-androstanediol (3beta-diol) by 17beta-HSD1, an estrogenic enzyme studied for more than half a century. Kinetic observations demonstrate that both the 3beta-reduction of DHT into 3beta-diol (kcat = 0.040 s(-1)1; Km = 32 +/- 9 microM) and the 17beta-oxidation of DHT into androstandione (A-dione) (kcat = 0.19 s(-1); Km = 26 +/-6 microM) are catalyzed by 17beta-HSD1 via alternative binding orientation of the steroid. The reduction of DHT was also observed in intact cells by using HEK-293 cells stably transformed with 17beta-HSD1. The high-resolution structure of a 17beta-HSD1-C19-steroid (testosterone) complex solved at 1.54 A demonstrates that the steroid is reversibly oriented in the active site, which strongly supports the existence of alternative binding mode. Such a phenomenon can be explained by the pseudo-symmetric structure of C19-steroids. Our results confirm the role of the Leu149 residue in C18/C19-steroid discrimination and suggest a possible mechanism of 17beta-HSD1 in the modulation of DHT levels in tissues, such as the breast, where both the enzyme and DHT are present. FAU - Gangloff, Anne AU - Gangloff A AD - Oncology and Molecular Endocrinology Research Center, CHUL Research Center and Laval University, Quebec, Canada, G1V 4G2. FAU - Shi, Rong AU - Shi R FAU - Nahoum, Virginie AU - Nahoum V FAU - Lin, Sheng-Xiang AU - Lin SX LA - eng PT - Journal Article DEP - 20021217 PL - United States TA - FASEB J JT - FASEB journal : official publication of the Federation of American Societies for Experimental Biology JID - 8804484 RN - 0 (Carbon Radioisotopes) RN - 08J2K08A3Y (Dihydrotestosterone) RN - 3XMK78S47O (Testosterone) RN - EC 1.1.- (17-Hydroxysteroid Dehydrogenases) RN - EC 1.1.1.51 (3 (or 17)-beta-hydroxysteroid dehydrogenase) SB - IM MH - 17-Hydroxysteroid Dehydrogenases/chemistry/genetics/*metabolism MH - Binding Sites MH - Carbon Radioisotopes MH - Cell Line MH - Dihydrotestosterone/chemistry/*metabolism MH - Humans MH - Models, Molecular MH - Oxidation-Reduction MH - Protein Binding MH - Testosterone/chemistry/metabolism EDAT- 2002/12/20 04:00 MHDA- 2003/03/01 04:00 CRDT- 2002/12/20 04:00 PHST- 2002/12/17 [aheadofprint] AID - 10.1096/fj.02-0397fje [doi] AID - 02-0397fje [pii] PST - ppublish SO - FASEB J. 2003 Feb;17(2):274-6. Epub 2002 Dec 17. PMID- 24130866 OWN - NLM STAT- MEDLINE DA - 20131016 DCOM- 20140611 LR - 20141112 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 10 DP - 2013 TI - Large extent of disorder in Adenomatous Polyposis Coli offers a strategy to guard Wnt signalling against point mutations. PG - e77257 LID - 10.1371/journal.pone.0077257 [doi] AB - Mutations in the central region of the signalling hub Adenomatous Polyposis Coli (APC) cause colorectal tumourigenesis. The structure of this region remained unknown. Here, we characterise the Mutation Cluster Region in APC (APC-MCR) as intrinsically disordered and propose a model how this structural feature may contribute to regulation of Wnt signalling by phosphorylation. APC-MCR was susceptible to proteolysis, lacked alpha-helical secondary structure and did not display thermal unfolding transition. It displayed an extended conformation in size exclusion chromatography and was accessible for phosphorylation by CK1epsilon in vitro. The length of disordered regions in APC increases with species complexity, from C. elegans to H. sapiens. We speculate that the large disordered region harbouring phosphorylation sites could be a successful strategy to stabilise tight regulation of Wnt signalling against single missense mutations. FAU - Minde, David P AU - Minde DP AD - Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands. FAU - Radli, Martina AU - Radli M FAU - Forneris, Federico AU - Forneris F FAU - Maurice, Madelon M AU - Maurice MM FAU - Rudiger, Stefan G D AU - Rudiger SG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131009 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Adenomatous Polyposis Coli Protein) RN - 0 (Wnt Proteins) SB - IM MH - Adenomatous Polyposis Coli/*genetics/metabolism MH - Adenomatous Polyposis Coli Protein/chemistry/*genetics/metabolism MH - Animals MH - Hot Temperature MH - Humans MH - Mutation MH - Phosphorylation MH - *Point Mutation MH - Protein Structure, Secondary MH - Protein Unfolding MH - Proteolysis MH - Signal Transduction MH - Wnt Proteins/genetics/*metabolism PMC - PMC3793970 OID - NLM: PMC3793970 EDAT- 2013/10/17 06:00 MHDA- 2014/06/12 06:00 CRDT- 2013/10/17 06:00 PHST- 2013 [ecollection] PHST- 2013/04/25 [received] PHST- 2013/09/02 [accepted] PHST- 2013/10/09 [epublish] AID - 10.1371/journal.pone.0077257 [doi] AID - PONE-D-13-17370 [pii] PST - epublish SO - PLoS One. 2013 Oct 9;8(10):e77257. doi: 10.1371/journal.pone.0077257. eCollection 2013. PMID- 23542007 OWN - NLM STAT- MEDLINE DA - 20130617 DCOM- 20130822 LR - 20150214 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 425 IP - 13 DP - 2013 Jul 10 TI - The disordered C-terminal domain of human DNA glycosylase NEIL1 contributes to its stability via intramolecular interactions. PG - 2359-71 LID - 10.1016/j.jmb.2013.03.030 [doi] LID - S0022-2836(13)00193-9 [pii] AB - NEIL1 [Nei (endonuclease VIII)-like protein 1], one of the five mammalian DNA glycosylases that excise oxidized DNA base lesions in the human genome to initiate base excision repair, contains an intrinsically disordered C-terminal domain (CTD; ~100 residues), not conserved in its Escherichia coli prototype Nei. Although dispensable for NEIL1's lesion excision and AP lyase activities, this segment is required for efficient in vivo enzymatic activity and may provide an interaction interface for many of NEIL1's interactions with other base excision repair proteins. Here, we show that the CTD interacts with the folded domain in native NEIL1 containing 389 residues. The CTD is poised for local folding in an ordered structure that is induced in the purified fragment by osmolytes. Furthermore, deletion of the disordered tail lacking both Tyr and Trp residues causes a red shift in NEIL1's intrinsic Trp-specific fluorescence, indicating a more solvent-exposed environment for the Trp residues in the truncated protein, which also exhibits reduced stability compared to the native enzyme. These observations are consistent with stabilization of the native NEIL1 structure via intramolecular, mostly electrostatic, interactions that were disrupted by mutating a positively charged (Lys-rich) cluster of residues (amino acids 355-360) near the C-terminus. Small-angle X-ray scattering (SAXS) analysis confirms the flexibility and dynamic nature of NEIL1's CTD, a feature that may be critical to providing specificity for NEIL1's multiple, functional interactions. CI - Copyright (c) 2013 Elsevier Ltd. All rights reserved. FAU - Hegde, Muralidhar L AU - Hegde ML AD - Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA. FAU - Tsutakawa, Susan E AU - Tsutakawa SE FAU - Hegde, Pavana M AU - Hegde PM FAU - Holthauzen, Luis Marcelo F AU - Holthauzen LM FAU - Li, Jing AU - Li J FAU - Oezguen, Numan AU - Oezguen N FAU - Hilser, Vincent J AU - Hilser VJ FAU - Tainer, John A AU - Tainer JA FAU - Mitra, Sankar AU - Mitra S LA - eng GR - CA158910/CA/NCI NIH HHS/United States GR - P01 CA092584/CA/NCI NIH HHS/United States GR - P01 CA92854/CA/NCI NIH HHS/United States GR - P30 ES006676/ES/NIEHS NIH HHS/United States GR - R01 CA081063/CA/NCI NIH HHS/United States GR - R01 CA158910/CA/NCI NIH HHS/United States GR - R01 CA81063/CA/NCI NIH HHS/United States GR - R01 GM 63747/GM/NIGMS NIH HHS/United States GR - R01 GM046312/GM/NIGMS NIH HHS/United States GR - R01 GM046312/GM/NIGMS NIH HHS/United States GR - R01 GM063747/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130327 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - EC 3.2.2.- (DNA Glycosylases) RN - EC 3.2.2.- (NEIL1 protein, human) SB - IM MH - DNA Glycosylases/*chemistry/*metabolism MH - DNA Mutational Analysis MH - Enzyme Stability MH - Models, Molecular MH - Protein Binding MH - Protein Conformation MH - *Protein Folding MH - Protein Interaction Mapping MH - *Protein Stability MH - Protein Structure, Tertiary MH - Scattering, Small Angle PMC - PMC3779128 MID - NIHMS461717 OID - NLM: NIHMS461717 OID - NLM: PMC3779128 EDAT- 2013/04/02 06:00 MHDA- 2013/08/24 06:00 CRDT- 2013/04/02 06:00 PHST- 2012/11/15 [received] PHST- 2013/03/09 [revised] PHST- 2013/03/13 [accepted] PHST- 2013/03/27 [aheadofprint] AID - S0022-2836(13)00193-9 [pii] AID - 10.1016/j.jmb.2013.03.030 [doi] PST - ppublish SO - J Mol Biol. 2013 Jul 10;425(13):2359-71. doi: 10.1016/j.jmb.2013.03.030. Epub 2013 Mar 27. PMID- 9878427 OWN - NLM STAT- MEDLINE DA - 19990311 DCOM- 19990311 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 285 IP - 2 DP - 1999 Jan 15 TI - The glutamine-rich domain of the Drosophila GAGA factor is necessary for amyloid fibre formation in vitro, but not for chromatin remodelling. PG - 527-44 AB - The Drosophila GAGA factor binds specifically to the sequence GAGAG, and synergises with nucleosome remodelling factor to remodel chromatin in vitro. It consists of an N-terminal domain (POZ/BTB) which mediates protein-protein interactions, a central region which contains the DNA-binding domain, and a C-terminal glutamine-rich region. It is shown that the glutamine-rich region is responsible for the formation of fibres in vitro which, on the basis of their tinctorial properties and CD spectra, may be classified as amyloid fibres. A large structural change, probably resulting in beta-sheet structure, is observed upon fibre formation. Mutants containing the central region, either alone or together with the glutamine-rich region, are largely lacking in secondary structure but they bind specifically to the cognate DNA and are able to remodel chromatin in vitro. Consequently, neither the N-terminal domain nor the C-terminal glutamine-rich regions of the GAGA factor are necessary for chromatin remodelling in vitro. CI - Copyright 1999 Academic Press. FAU - Agianian, B AU - Agianian B AD - Structural Biology Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1 D-69117, Heidelgberg, Germany. FAU - Leonard, K AU - Leonard K FAU - Bonte, E AU - Bonte E FAU - Van der Zandt, H AU - Van der Zandt H FAU - Becker, P B AU - Becker PB FAU - Tucker, P A AU - Tucker PA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amyloid) RN - 0 (Chromatin) RN - 0 (DNA-Binding Proteins) RN - 0 (Drosophila Proteins) RN - 0 (Fluorescent Dyes) RN - 0 (Homeodomain Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Thiazoles) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - 0 (Trl protein, Drosophila) RN - 0RH81L854J (Glutamine) RN - 2390-54-7 (thioflavin T) RN - 3U05FHG59S (Congo Red) SB - IM MH - Amyloid/chemistry/*physiology MH - Animals MH - Binding Sites MH - Birefringence MH - Chromatin/*physiology MH - Congo Red MH - DNA-Binding Proteins/genetics/*physiology MH - *Drosophila Proteins MH - Drosophila melanogaster MH - Fluorescent Dyes MH - Glutamine/genetics/*physiology MH - Homeodomain Proteins/genetics/*physiology MH - Mutagenesis MH - Protein Structure, Secondary MH - Recombinant Fusion Proteins/genetics MH - Structure-Activity Relationship MH - Thiazoles MH - Trans-Activators/chemistry MH - Transcription Factors/genetics/*physiology EDAT- 1999/01/08 MHDA- 1999/01/08 00:01 CRDT- 1999/01/08 00:00 AID - S0022-2836(98)92355-5 [pii] AID - 10.1006/jmbi.1998.2355 [doi] PST - ppublish SO - J Mol Biol. 1999 Jan 15;285(2):527-44. PMID- 18310078 OWN - NLM STAT- MEDLINE DA - 20080421 DCOM- 20080619 LR - 20141206 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 17 DP - 2008 Apr 25 TI - Deletion of the protein kinase A/protein kinase G target SMTNL1 promotes an exercise-adapted phenotype in vascular smooth muscle. PG - 11850-9 LID - 10.1074/jbc.M708628200 [doi] AB - In vivo protein kinases A and G (PKA and PKG) coordinately phosphorylate a broad range of substrates to mediate their various physiological effects. The functions of many of these substrates have yet to be defined genetically. Herein we show a role for smoothelin-like protein 1 (SMTNL1), a novel in vivo target of PKG/PKA, in mediating vascular adaptations to exercise. Aortas from smtnl1(-/-) mice exhibited strikingly enhanced vasorelaxation before exercise, similar in extent to that achieved after endurance training of wild-type littermates. Additionally, contractile responses to alpha-adrenergic agonists were greatly attenuated. Immunological studies showed SMTNL1 is expressed in smooth muscle and type 2a striated muscle fibers. Consistent with a role in adaptations to exercise, smtnl1(-/-) mice also exhibited increased type 2a fibers before training and better performance after forced endurance training compared smtnl1(+/+) mice. Furthermore, exercise was found to reduce expression of SMTNL1, particularly in female mice. In both muscle types, SMTNL1 is phosphorylated at Ser-301 in response to adrenergic signals. In vitro SMTNL1 suppresses myosin phosphatase activity through a substrate-directed effect, which is relieved by Ser-301 phosphorylation. Our findings suggest roles for SMTNL1 in cGMP/cAMP-mediated adaptations to exercise through mechanisms involving direct modulation of contractile activity. FAU - Wooldridge, Anne A AU - Wooldridge AA AD - Department of Pharmacology, Medicine, Duke University, Medical Center, Durham, North Carolina 27710, USA. FAU - Fortner, Christopher N AU - Fortner CN FAU - Lontay, Beata AU - Lontay B FAU - Akimoto, Takayuki AU - Akimoto T FAU - Neppl, Ronald L AU - Neppl RL FAU - Facemire, Carie AU - Facemire C FAU - Datto, Michael B AU - Datto MB FAU - Kwon, Ashley AU - Kwon A FAU - McCook, Everett AU - McCook E FAU - Li, Ping AU - Li P FAU - Wang, Shiliang AU - Wang S FAU - Thresher, Randy J AU - Thresher RJ FAU - Miller, Sara E AU - Miller SE FAU - Perriard, Jean-Claude AU - Perriard JC FAU - Gavin, Timothy P AU - Gavin TP FAU - Hickner, Robert C AU - Hickner RC FAU - Coffman, Thomas M AU - Coffman TM FAU - Somlyo, Avril V AU - Somlyo AV FAU - Yan, Zhen AU - Yan Z FAU - Haystead, Timothy A J AU - Haystead TA LA - eng GR - 5 R01 HL078795-04/HL/NHLBI NIH HHS/United States GR - DK065954-02/DK/NIDDK NIH HHS/United States GR - R01 AR050429/AR/NIAMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20080229 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Muscle Proteins) RN - 0 (Phosphoproteins) RN - 0 (SMTNL1 protein, mouse) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) RN - EC 2.7.11.12 (Cyclic GMP-Dependent Protein Kinases) RN - EC 3.6.4.1 (Myosins) SB - IM MH - Animals MH - Cyclic AMP-Dependent Protein Kinases/*metabolism MH - Cyclic GMP-Dependent Protein Kinases/*metabolism MH - Female MH - Gene Deletion MH - Humans MH - Mice MH - Models, Biological MH - Muscle Fibers, Skeletal/metabolism MH - Muscle Proteins/*biosynthesis/genetics/*physiology MH - Muscle, Smooth, Vascular/*metabolism MH - Myosins/metabolism MH - Phenotype MH - Phosphoproteins/*genetics/physiology MH - Phosphorylation MH - Physical Conditioning, Animal PMC - PMC2431077 OID - NLM: PMC2431077 EDAT- 2008/03/04 09:00 MHDA- 2008/06/20 09:00 CRDT- 2008/03/04 09:00 PHST- 2008/02/29 [aheadofprint] AID - M708628200 [pii] AID - 10.1074/jbc.M708628200 [doi] PST - ppublish SO - J Biol Chem. 2008 Apr 25;283(17):11850-9. doi: 10.1074/jbc.M708628200. Epub 2008 Feb 29. PMID- 21416544 OWN - NLM STAT- MEDLINE DA - 20110414 DCOM- 20110804 LR - 20140821 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 20 IP - 5 DP - 2011 May TI - Monitoring the conformational changes of an intrinsically disordered peptide using a quartz crystal microbalance. PG - 925-30 LID - 10.1002/pro.625 [doi] AB - Intrinsically disordered peptides (IDPs) have recently garnered much interest because of their role in biological processes such as molecular recognition and their ability to undergo stimulus-responsive conformational changes. The block V repeat-in-toxin motif of the Bordetella pertussis adenylate cyclase is an example of an IDP that undergoes a transition from a disordered state to an ordered beta roll conformation in the presence of calcium ions. In solution, a C-terminal capping domain is necessary for this transition to occur. To further explore the conformational behavior and folding requirements of this IDP, we have cysteine modified three previously characterized constructs, allowing for attachment to the gold surface of a quartz crystal microbalance (QCM). We demonstrate that, while immobilized, the C-terminally capped peptide exhibits similar calcium-binding properties to what have been observed in solution. In addition, immobilization on the solid surface appears to enable calcium-responsiveness in the uncapped peptides, in contrast to the behavior observed in solution. This work demonstrates the power of QCM as a tool to study the conformational changes of IDPs immobilized on surfaces and has implications for a range of potential applications where IDPs may be engineered and used including protein purification, biosensors, and other bionanotechnology applications. CI - Copyright (c) 2011 The Protein Society. FAU - Shur, Oren AU - Shur O AD - Department of Chemical Engineering, Columbia University, New York, New York, USA. FAU - Wu, Jun AU - Wu J FAU - Cropek, Donald M AU - Cropek DM FAU - Banta, Scott AU - Banta S LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110408 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Bacterial Proteins) RN - 0 (Peptides) RN - EC 4.6.1.1 (Adenylate Cyclase) SB - IM MH - Adenylate Cyclase/chemistry MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Bacterial Proteins/chemistry MH - Bordetella pertussis/enzymology MH - Circular Dichroism MH - Peptides/*chemistry MH - *Protein Conformation MH - *Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - Quartz Crystal Microbalance Techniques/*methods MH - Reproducibility of Results PMC - PMC3125875 OID - NLM: PMC3125875 EDAT- 2011/03/19 06:00 MHDA- 2011/08/05 06:00 CRDT- 2011/03/19 06:00 PHST- 2011/01/04 [received] PHST- 2011/03/04 [revised] PHST- 2011/03/07 [accepted] PHST- 2011/04/08 [aheadofprint] AID - 10.1002/pro.625 [doi] PST - ppublish SO - Protein Sci. 2011 May;20(5):925-30. doi: 10.1002/pro.625. Epub 2011 Apr 8. PMID- 19218568 OWN - NLM STAT- MEDLINE DA - 20090414 DCOM- 20090616 IS - 1741-0134 (Electronic) IS - 1741-0126 (Linking) VI - 22 IP - 5 DP - 2009 May TI - The C-terminal domain of the HIV-1 Vif protein is natively unfolded in its unbound state. PG - 281-7 LID - 10.1093/protein/gzp004 [doi] AB - The human immunodeficiency virus type-1 (HIV-1) Vif protein neutralizes the cellular defense mechanism against the virus. The C-terminal domain of Vif (CTD, residues 141-192) mediates many of its interactions. Full-length Vif is difficult to purify in large amounts, hence the only available structure of Vif is of residues 140-155 within the ElonginBC complex. Other structural information, derived from modeling and indirect experiments, indicates that the Vif CTD may be unstructured. Here, we chemically synthesized the Vif CTD using pseudo-proline-building blocks, studied its solution structure in the unbound state using biophysical techniques and found that it is unstructured under physiological conditions. The circular dichroism (CD) spectrum of Vif CTD showed a pattern of random coil with residual helical structure. The (15)N-HSQC nuclear magnetic resonance (NMR) spectrum was characteristic of natively unfolded peptides. Vif CTD eluted from an analytical gel filtration column earlier than expected, indicating an extended conformation. Disorder predictions found the CTD to be unstructured, in agreement with our experimental results. CD experiments showed that Vif CTD underwent a conformational change upon interacting with membrane-mimicking DPC micelles, but not upon binding to a peptide derived from its binding region in ElonginC. Our results provide direct evidence for the unfolded structure of the free Vif CTD and indicate that it may gain structure upon binding its natural ligands. FAU - Reingewertz, Tali H AU - Reingewertz TH AD - Institute of Chemistry, Hebrew University of Jerusalem, Safra Campus, Givat Ram, 91904 Jerusalem, Israel. FAU - Benyamini, Hadar AU - Benyamini H FAU - Lebendiker, Mario AU - Lebendiker M FAU - Shalev, Deborah E AU - Shalev DE FAU - Friedler, Assaf AU - Friedler A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090213 PL - England TA - Protein Eng Des Sel JT - Protein engineering, design & selection : PEDS JID - 101186484 RN - 0 (vif Gene Products, Human Immunodeficiency Virus) RN - 0 (vif protein, Human immunodeficiency virus 1) SB - IM MH - Biophysics MH - Circular Dichroism MH - HIV-1/*genetics MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - *Protein Folding MH - Protein Structure, Tertiary/*genetics MH - vif Gene Products, Human Immunodeficiency Virus/*genetics EDAT- 2009/02/17 09:00 MHDA- 2009/06/17 09:00 CRDT- 2009/02/17 09:00 PHST- 2009/02/13 [aheadofprint] AID - gzp004 [pii] AID - 10.1093/protein/gzp004 [doi] PST - ppublish SO - Protein Eng Des Sel. 2009 May;22(5):281-7. doi: 10.1093/protein/gzp004. Epub 2009 Feb 13. PMID- 12956606 OWN - NLM STAT- MEDLINE DA - 20030905 DCOM- 20040616 LR - 20061115 IS - 0739-1102 (Print) IS - 0739-1102 (Linking) VI - 21 IP - 2 DP - 2003 Oct TI - A protein-chameleon: conformational plasticity of alpha-synuclein, a disordered protein involved in neurodegenerative disorders. PG - 211-34 AB - Under the physiological conditions in vitro, alpha-synuclein, a conservative presynaptic protein, the aggregation and fibrillation of which is assumed to be involved into the pathogenesis of Parkinson's disease and several other neurodegenerative disorders, known as synucleinopathies, is characterized by the lack of rigid well-defined structure; i.e., it belongs to the class of intrinsically unstructured proteins. Intriguingly, alpha-synuclein is characterized by a remarkable conformational plasticity, adopting a series of different conformations depending on the environment. For example, this protein may either stay substantially unfolded, or adopt an amyloidogenic partially folded conformation, or fold into alpha-helical or beta-structural species, both monomeric and oligomeric. Furthermore, it might form several morphologically different types of aggregates, including oligomers (spheres or doughnuts), amorphous aggregates, and or amyloid-like fibrils. The peculiarities of this astonishing conformational behavior are analyzed to shed light on structural plasticity of this protein-chameleon. FAU - Uversky, Vladimir N AU - Uversky VN AD - Institute for Biological Instrumentation, Russian Academy of Sciences Pushchino, Moscow Region, Russia. uversky@hydrogen.ucsc.edu LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - J Biomol Struct Dyn JT - Journal of biomolecular structure & dynamics JID - 8404176 RN - 0 (Alcohols) RN - 0 (Metals) RN - 0 (Nerve Tissue Proteins) RN - 0 (Pesticides) RN - 0 (Polymers) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Alcohols/chemistry MH - Animals MH - Humans MH - Hydrogen-Ion Concentration MH - Metals/chemistry MH - Models, Molecular MH - Nerve Tissue Proteins/*chemistry/*metabolism/ultrastructure MH - Neurodegenerative Diseases/*metabolism MH - Parkinson Disease/metabolism MH - Pesticides/chemistry MH - Polymers/chemistry MH - *Protein Conformation MH - Protein Folding MH - Synucleins MH - alpha-Synuclein RF - 204 EDAT- 2003/09/06 05:00 MHDA- 2004/06/17 05:00 CRDT- 2003/09/06 05:00 AID - d=3013&c=4118&p=11847&do=detail [pii] AID - 10.1080/07391102.2003.10506918 [doi] PST - ppublish SO - J Biomol Struct Dyn. 2003 Oct;21(2):211-34. PMID- 16893186 OWN - NLM STAT- MEDLINE DA - 20060808 DCOM- 20060913 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 32 DP - 2006 Aug 15 TI - B-myc: N-terminal recognition of myc binding proteins. PG - 9857-65 AB - B-Myc is an endogenous, N-terminal homologue of transcription factor c-Myc that lacks the C-terminal DNA binding and protein dimerization domain of c-Myc. Clinical mutations in the c-Myc N-terminal region, and the subsequent misregulation of Myc, are implicated in the development of numerous human cancers. Myc functions to both activate and repress transcription by associating with multiple binding partners. We investigated the structural and dynamical properties of B-Myc, free or associated with the transactivation inhibitor, MM-1, and the activator, TBP, using NMR spectroscopy. B-Myc has no persistent tertiary structure, yet regions corresponding to Myc homology boxes 1 and 2 (MBI and MBII, respectively) have molten globule-like characteristics. B-Myc binds to MM-1 in a specific manner without becoming highly structured. The local regions of B-Myc involved in binding differ for MM-1 and TBP, and regions not identified by mutagenesis are found to be involved in MM-1 binding. The results provide new insights into Myc N-terminal protein-protein interactions. We propose a model for Myc regulation through differential involvement of MBI and MBII in the binding of Myc interacting proteins. FAU - Burton, Robert A AU - Burton RA AD - Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907-2091, USA. FAU - Mattila, Sampo AU - Mattila S FAU - Taparowsky, Elizabeth J AU - Taparowsky EJ FAU - Post, Carol Beth AU - Post CB LA - eng GR - CA23568/CA/NCI NIH HHS/United States GR - GM008296/GM/NIGMS NIH HHS/United States GR - GM39478/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bmyc protein, mouse) RN - 0 (Proto-Oncogene Proteins c-myc) SB - IM MH - Amino Acid Sequence MH - Animals MH - Circular Dichroism MH - Humans MH - Mice MH - Models, Biological MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Transport MH - Proto-Oncogene Proteins c-myc/chemistry/*metabolism MH - Sequence Alignment EDAT- 2006/08/09 09:00 MHDA- 2006/09/14 09:00 CRDT- 2006/08/09 09:00 AID - 10.1021/bi060379n [doi] PST - ppublish SO - Biochemistry. 2006 Aug 15;45(32):9857-65. PMID- 25195896 OWN - NLM STAT- MEDLINE DA - 20140908 DCOM- 20150520 IS - 2053-230X (Electronic) VI - 70 IP - Pt 9 DP - 2014 Sep TI - Cloning, expression, purification, crystallization and preliminary crystallographic analysis of the C-terminal domain of Par-4 (PAWR). PG - 1224-7 LID - 10.1107/S2053230X14014691 [doi] AB - Prostate apoptosis response-4 protein is an intrinsically disordered pro-apoptotic protein with tumour suppressor function. Par-4 is known for its selective induction of apoptosis in cancer cells only and its ability to interact with various apoptotic proteins via its C-terminus. Par-4, with its unique function and various interacting partners, has gained importance as a potential target for cancer therapy. The C-terminus of the rat homologue of Par-4 was crystallized and a 3.7 A resolution X-ray diffraction data set was collected. Preliminary data analysis shows the space group to be P41212. The unit-cell parameters are a = b = 115.351, c = 123.663 A, alpha = beta = gamma = 90 degrees . FAU - Tiruttani Subhramanyam, Udaya Kumar AU - Tiruttani Subhramanyam UK AD - Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany. FAU - Kubicek, Jan AU - Kubicek J AD - Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany. FAU - Eidhoff, Ulf B AU - Eidhoff UB AD - Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany. FAU - Labahn, Joerg AU - Labahn J AD - Centre for Structural Systems Biology (CSSB), DESY, Notkestrasse 85, 22607 Hamburg, Germany. LA - eng PT - Journal Article DEP - 20140827 PL - United States TA - Acta Crystallogr F Struct Biol Commun JT - Acta crystallographica. Section F, Structural biology communications JID - 101620319 RN - 0 (Apoptosis Regulatory Proteins) RN - 0 (prostate apoptosis response-4 protein) SB - IM MH - Apoptosis Regulatory Proteins/*chemistry/genetics/isolation & purification MH - Cloning, Molecular MH - Crystallization MH - Crystallography, X-Ray OTO - NOTNLM OT - Par-4 OT - coiled coil OT - leucine zipper EDAT- 2014/09/10 06:00 MHDA- 2015/05/21 06:00 CRDT- 2014/09/09 06:00 PHST- 2014/05/21 [received] PHST- 2014/06/21 [accepted] PHST- 2014/08/27 [epublish] AID - S2053230X14014691 [pii] AID - 10.1107/S2053230X14014691 [doi] PST - ppublish SO - Acta Crystallogr F Struct Biol Commun. 2014 Sep;70(Pt 9):1224-7. doi: 10.1107/S2053230X14014691. Epub 2014 Aug 27. PMID- 16280326 OWN - NLM STAT- MEDLINE DA - 20060117 DCOM- 20060317 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 3 DP - 2006 Jan 20 TI - Glutamic acid-rich proteins of rod photoreceptors are natively unfolded. PG - 1449-60 AB - The outer segment of vertebrate photoreceptors is a specialized compartment that hosts all the signaling components required for visual transduction. Specific to rod photoreceptors is an unusual set of three glutamic acid-rich proteins (GARPs) as follows: two soluble forms, GARP1 and GARP2, and the N-terminal cytoplasmic domain (GARP' part) of the B1 subunit of the cyclic GMP-gated channel. GARPs have been shown to interact with proteins at the rim of the disc membrane. Here we characterized native GARP1 and GARP2 purified from bovine rod photoreceptors. Amino acid sequence analysis of GARPs revealed structural features typical of "natively unfolded" proteins. By using biophysical techniques, including size-exclusion chromatography, dynamic light scattering, NMR spectroscopy, and circular dichroism, we showed that GARPs indeed exhibit a large degree of intrinsic disorder. Analytical ultracentrifugation and chemical cross-linking showed that GARPs exist in a monomer/multimer equilibrium. The results suggested that the function of GARP proteins is linked to their structural disorder. They may provide flexible spacers or linkers tethering the cyclic GMP-gated channel in the plasma membrane to peripherin at the disc rim to produce a stack of rings of these protein complexes along the long axis of the outer segment. GARP proteins could then provide the environment needed for protein interactions in the rim region of discs. FAU - Batra-Safferling, Renu AU - Batra-Safferling R AD - Institut fur Biologische Informationsverarbeitung 1, Forschungszentrum Julich, Germany. FAU - Abarca-Heidemann, Karin AU - Abarca-Heidemann K FAU - Korschen, Heinz Gerd AU - Korschen HG FAU - Tziatzios, Christos AU - Tziatzios C FAU - Stoldt, Matthias AU - Stoldt M FAU - Budyak, Ivan AU - Budyak I FAU - Willbold, Dieter AU - Willbold D FAU - Schwalbe, Harald AU - Schwalbe H FAU - Klein-Seetharaman, Judith AU - Klein-Seetharaman J FAU - Kaupp, U Benjamin AU - Kaupp UB LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051109 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (CNGB1 protein, Bos taurus) RN - 0 (Cyclic Nucleotide-Gated Cation Channels) RN - 0 (Nerve Tissue Proteins) RN - 0 (Peptide Fragments) RN - 0 (Protein Subunits) RN - 3KX376GY7L (Glutamic Acid) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cattle MH - Cyclic Nucleotide-Gated Cation Channels MH - *Glutamic Acid MH - Kinetics MH - Light MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*chemistry/*metabolism MH - Peptide Fragments/chemistry/metabolism MH - Protein Denaturation MH - Protein Folding MH - Protein Subunits/chemistry/metabolism MH - Retinal Rod Photoreceptor Cells/*metabolism MH - Scattering, Radiation MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization EDAT- 2005/11/11 09:00 MHDA- 2006/03/18 09:00 CRDT- 2005/11/11 09:00 PHST- 2005/11/09 [aheadofprint] AID - M505012200 [pii] AID - 10.1074/jbc.M505012200 [doi] PST - ppublish SO - J Biol Chem. 2006 Jan 20;281(3):1449-60. Epub 2005 Nov 9. PMID- 24646893 OWN - NLM STAT- MEDLINE DA - 20140320 DCOM- 20141223 LR - 20150609 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 3 DP - 2014 TI - High-throughput screening reveals alsterpaullone, 2-cyanoethyl as a potent p27Kip1 transcriptional inhibitor. PG - e91173 LID - 10.1371/journal.pone.0091173 [doi] AB - p27Kip1 is a cell cycle inhibitor that prevents cyclin dependent kinase (CDK)/cyclin complexes from phosphorylating their targets. p27Kip1 is a known tumor suppressor, as the germline loss of p27Kip1 results in sporadic pituitary formation in aged rodents, and its presence in human cancers is indicative of a poor prognosis. In addition to its role in cancer, loss of p27Kip1 results in regenerative phenotypes in some tissues and maintenance of stem cell pluripotency, suggesting that p27Kip1 inhibitors could be beneficial for tissue regeneration. Because p27Kip1 is an intrinsically disordered protein, identifying direct inhibitors of the p27Kip1 protein is difficult. Therefore, we pursued a high-throughput screening strategy to identify novel p27Kip1 transcriptional inhibitors. We utilized a luciferase reporter plasmid driven by the p27Kip1 promoter to transiently transfect HeLa cells and used cyclohexamide as a positive control for non-specific inhibition. We screened a "bioactive" library consisting of 8,904 (4,359 unique) compounds, of which 830 are Food and Drug Administration (FDA) approved. From this screen, we successfully identified 111 primary hits with inhibitory effect against the promoter of p27Kip1. These hits were further refined using a battery of secondary screens. Here we report four novel p27Kip1 transcriptional inhibitors, and further demonstrate that our most potent hit compound (IC50 = 200 nM) Alsterpaullone 2-cyanoethyl, inhibits p27Kip1 transcription by preventing FoxO3a from binding to the p27Kip1 promoter. This screen represents one of the first attempts to identify inhibitors of p27Kip1 and may prove useful for future tissue regeneration studies. FAU - Walters, Brandon J AU - Walters BJ AD - Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America. FAU - Lin, Wenwei AU - Lin W AD - Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America. FAU - Diao, Shiyong AU - Diao S AD - Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America. FAU - Brimble, Mark AU - Brimble M AD - Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America; University of Bath, Bath, United Kingdom. FAU - Iconaru, Luigi I AU - Iconaru LI AD - Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America. FAU - Dearman, Jennifer AU - Dearman J AD - Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America. FAU - Goktug, Asli AU - Goktug A AD - Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America. FAU - Chen, Taosheng AU - Chen T AD - Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America. FAU - Zuo, Jian AU - Zuo J AD - Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America. LA - eng GR - CA21765/CA/NCI NIH HHS/United States GR - DC06471/DC/NIDCD NIH HHS/United States GR - GM086415/GM/NIGMS NIH HHS/United States GR - P30 CA021765/CA/NCI NIH HHS/United States GR - R01 GM086415/GM/NIGMS NIH HHS/United States GR - R21 DC013879/DC/NIDCD NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140319 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Benzazepines) RN - 0 (FOXO3 protein, human) RN - 0 (Forkhead Transcription Factors) RN - 0 (Indoles) RN - 0 (Small Molecule Libraries) RN - 0 (Tumor Suppressor Proteins) RN - 0 (alsterpaullone) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - EC 1.13.12.- (Luciferases) SB - IM MH - Benzazepines/chemistry/*pharmacology MH - Cyclin-Dependent Kinase Inhibitor p27/*antagonists & inhibitors/genetics/metabolism MH - Forkhead Transcription Factors/antagonists & inhibitors/genetics/metabolism MH - *Gene Expression Regulation, Neoplastic MH - Genes, Reporter MH - HeLa Cells MH - High-Throughput Screening Assays MH - Humans MH - Indoles/chemistry/*pharmacology MH - Luciferases/antagonists & inhibitors/genetics/metabolism MH - Promoter Regions, Genetic MH - Small Molecule Libraries/chemistry/*pharmacology MH - Transcription, Genetic/*drug effects MH - Tumor Suppressor Proteins/*antagonists & inhibitors/genetics/metabolism PMC - PMC3960108 OID - NLM: PMC3960108 EDAT- 2014/03/22 06:00 MHDA- 2014/12/24 06:00 CRDT- 2014/03/21 06:00 PHST- 2014 [ecollection] PHST- 2013/11/20 [received] PHST- 2014/02/09 [accepted] PHST- 2014/03/19 [epublish] AID - 10.1371/journal.pone.0091173 [doi] AID - PONE-D-13-48939 [pii] PST - epublish SO - PLoS One. 2014 Mar 19;9(3):e91173. doi: 10.1371/journal.pone.0091173. eCollection 2014. PMID- 24253305 OWN - NLM STAT- MEDLINE DA - 20140228 DCOM- 20140507 LR - 20141112 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 42 IP - 4 DP - 2014 Feb TI - Molecular recognition by the KIX domain and its role in gene regulation. PG - 2112-25 LID - 10.1093/nar/gkt1147 [doi] AB - The kinase-inducible domain interacting (KIX) domain is a highly conserved independently folding three-helix bundle that serves as a docking site for transcription factors, whereupon promoter activation and target specificity are achieved during gene regulation. This docking event is a harbinger of an intricate multi-protein assembly at the transcriptional apparatus and is regulated in a highly precise manner in view of the critical role it plays in multiple cellular processes. KIX domains have been characterized in transcriptional coactivators such as p300/CREB-binding protein and mediator of RNA polymerase II transcription subunit 15, and even recQ protein-like 5 helicases in various organisms. Their targets are often intrinsically disordered regions within the transactivation domains of transcription factors that attain stable secondary structure only upon complexation with KIX. In this article, we review the KIX domain in terms of its sequence and structure and present the various implications of its ability to act as a transcriptional switch, the mechanistic basis of molecular recognition by KIX, its binding specificity, target promiscuity, combinatorial potential and unique mode of regulation via allostery. We also discuss the possible roles of KIX domains in plants and hope that this review will accelerate scientific interest in KIX and pave the way for novel avenues of research on this critical domain. FAU - Thakur, Jitendra K AU - Thakur JK AD - National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India. FAU - Yadav, Archana AU - Yadav A FAU - Yadav, Gitanjali AU - Yadav G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20131118 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Cyclic AMP Response Element-Binding Protein) RN - 0 (Mediator Complex) RN - 0 (RECQL5 protein, human) RN - EC 2.3.1.48 (CREB-Binding Protein) RN - EC 3.6.4.12 (RecQ Helicases) SB - IM MH - Allosteric Regulation MH - Amino Acid Sequence MH - Animals MH - CREB-Binding Protein/chemistry MH - Cyclic AMP Response Element-Binding Protein/chemistry MH - *Gene Expression Regulation MH - Humans MH - Mediator Complex/chemistry MH - Mice MH - Molecular Sequence Data MH - *Protein Structure, Tertiary MH - RecQ Helicases/chemistry MH - *Transcription, Genetic PMC - PMC3936767 OID - NLM: PMC3936767 EDAT- 2013/11/21 06:00 MHDA- 2014/05/08 06:00 CRDT- 2013/11/21 06:00 PHST- 2013/11/18 [aheadofprint] AID - gkt1147 [pii] AID - 10.1093/nar/gkt1147 [doi] PST - ppublish SO - Nucleic Acids Res. 2014 Feb;42(4):2112-25. doi: 10.1093/nar/gkt1147. Epub 2013 Nov 18. PMID- 21858098 OWN - NLM STAT- MEDLINE DA - 20110822 DCOM- 20120215 LR - 20141022 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 8 DP - 2011 TI - Effects of clinically relevant MPL mutations in the transmembrane domain revealed at the atomic level through computational modeling. PG - e23396 LID - 10.1371/journal.pone.0023396 [doi] AB - BACKGROUND: Mutations in the thrombopoietin receptor (MPL) may activate relevant pathways and lead to chronic myeloproliferative neoplasms (MPNs). The mechanisms of MPL activation remain elusive because of a lack of experimental structures. Modern computational biology techniques were utilized to explore the mechanisms of MPL protein activation due to various mutations. RESULTS: Transmembrane (TM) domain predictions, homology modeling, ab initio protein structure prediction, and molecular dynamics (MD) simulations were used to build structural dynamic models of wild-type and four clinically observed mutants of MPL. The simulation results suggest that S505 and W515 are important in keeping the TM domain in its correct position within the membrane. Mutations at either of these two positions cause movement of the TM domain, altering the conformation of the nearby intracellular domain in unexpected ways, and may cause the unwanted constitutive activation of MPL's kinase partner, JAK2. CONCLUSIONS: Our findings represent the first full-scale molecular dynamics simulations of the wild-type and clinically observed mutants of the MPL protein, a critical element of the MPL-JAK2-STAT signaling pathway. In contrast to usual explanations for the activation mechanism that are based on the relative translational movement between rigid domains of MPL, our results suggest that mutations within the TM region could result in conformational changes including tilt and rotation (azimuthal) angles along the membrane axis. Such changes may significantly alter the conformation of the adjacent and intrinsically flexible intracellular domain. Hence, caution should be exercised when interpreting experimental evidence based on rigid models of cytokine receptors or similar systems. FAU - Lee, Tai-Sung AU - Lee TS AD - BioMaPS Institute, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America. cancersimulation@gmail.com FAU - Kantarjian, Hagop AU - Kantarjian H FAU - Ma, Wanlong AU - Ma W FAU - Yeh, Chen-Hsiung AU - Yeh CH FAU - Giles, Francis AU - Giles F FAU - Albitar, Maher AU - Albitar M LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110817 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (PIAS4 protein, human) RN - 0 (Protein Inhibitors of Activated STAT) RN - 0 (Receptors, Thrombopoietin) RN - 0 (STAT Transcription Factors) RN - 143641-95-6 (MPL protein, human) RN - EC 2.7.10.2 (Janus Kinase 2) SB - IM MH - Amino Acid Substitution MH - Computational Biology/methods MH - Humans MH - Janus Kinase 2/chemistry/metabolism MH - Models, Biological MH - *Models, Molecular MH - Molecular Conformation MH - Molecular Dynamics Simulation MH - *Mutation MH - Myeloproliferative Disorders/genetics/metabolism/pathology MH - Protein Inhibitors of Activated STAT MH - *Protein Structure, Tertiary MH - Receptors, Thrombopoietin/*chemistry/*genetics/metabolism MH - STAT Transcription Factors/chemistry/metabolism MH - Signal Transduction PMC - PMC3157383 OID - NLM: PMC3157383 EDAT- 2011/08/23 06:00 MHDA- 2012/02/16 06:00 CRDT- 2011/08/23 06:00 PHST- 2011/05/25 [received] PHST- 2011/07/14 [accepted] PHST- 2011/08/17 [epublish] AID - 10.1371/journal.pone.0023396 [doi] AID - PONE-D-11-09464 [pii] PST - ppublish SO - PLoS One. 2011;6(8):e23396. doi: 10.1371/journal.pone.0023396. Epub 2011 Aug 17. PMID- 24734879 OWN - NLM STAT- MEDLINE DA - 20140514 DCOM- 20150514 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 136 IP - 19 DP - 2014 May 14 TI - Transient electrostatic interactions dominate the conformational equilibrium sampled by multidomain splicing factor U2AF65: a combined NMR and SAXS study. PG - 7068-76 LID - 10.1021/ja502030n [doi] AB - Multidomain proteins containing intrinsically disordered linkers exhibit large-scale dynamic modes that play key roles in a multitude of molecular recognition and signaling processes. Here, we determine the conformational space sampled by the multidomain splicing factor U2AF65 using complementary nuclear magnetic resonance spectroscopy and small-angle scattering data. Available degrees of conformational freedom are initially stochastically sampled and experimental data then used to delineate the potential energy landscape in terms of statistical probability. The spatial distribution of U2AF65 conformations is found to be highly anisotropic, comprising significantly populated interdomain contacts that appear to be electrostatic in origin. This hypothesis is supported by the reduction of signature PREs reporting on expected interfaces with increasing salt concentration. The described spatial distribution reveals the complete spectrum of the unbound forms of U2AF65 that coexist with the small percentage of a preformed RNA-bound domain arrangement required for polypyrimidine-tract recognition by conformational selection. More generally, the proposed approach to describing conformational equilibria of multidomain proteins can be further combined with other experimental data that are sensitive to domain dynamics. FAU - Huang, Jie-rong AU - Huang JR AD - University Grenoble Alpes, double daggerCNRS, and section signCEA, Protein Dynamics and Flexibility, Institut de Biologie Structurale , 38000 Grenoble, France. FAU - Warner, Lisa R AU - Warner LR FAU - Sanchez, Carolina AU - Sanchez C FAU - Gabel, Frank AU - Gabel F FAU - Madl, Tobias AU - Madl T FAU - Mackereth, Cameron D AU - Mackereth CD FAU - Sattler, Michael AU - Sattler M FAU - Blackledge, Martin AU - Blackledge M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140429 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Nuclear Proteins) RN - 0 (Ribonucleoproteins) RN - 0 (splicing factor U2AF) RN - 63231-63-0 (RNA) SB - IM MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*chemistry/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - RNA/metabolism MH - Ribonucleoproteins/*chemistry/metabolism MH - Scattering, Small Angle MH - Static Electricity MH - X-Ray Diffraction EDAT- 2014/04/17 06:00 MHDA- 2015/05/15 06:00 CRDT- 2014/04/17 06:00 PHST- 2014/04/29 [aheadofprint] AID - 10.1021/ja502030n [doi] PST - ppublish SO - J Am Chem Soc. 2014 May 14;136(19):7068-76. doi: 10.1021/ja502030n. Epub 2014 Apr 29. PMID- 24056937 OWN - NLM STAT- MEDLINE DA - 20131002 DCOM- 20140508 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 9 IP - 11 DP - 2013 Nov TI - Dynamics of the intrinsically disordered protein CP12 in its association with GAPDH in the green alga Chlamydomonas reinhardtii: a fuzzy complex. PG - 2869-76 LID - 10.1039/c3mb70190e [doi] AB - CP12 is a widespread regulatory protein of oxygenic photosynthetic organisms that contributes to the regulation of the Calvin cycle by forming a supra-molecular complex with at least two enzymes: glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK). CP12 shares some similarities with intrinsically disordered proteins (IDPs) depending on its redox state. In this study, site-directed spin labeling (SDSL) combined with EPR spectroscopy was used to probe the dynamic behavior of CP12 from Chlamydomonas reinhardtii upon binding to GAPDH, the first step towards ternary complex formation. The two N-terminal cysteine residues were labeled using the classical approach while the tyrosine located at the C-terminal end of CP12 was modified following an original procedure. The results show that the label grafted at the C-terminal extremity is in the vicinity of the interaction site whereas the N-terminal region remains fully disordered upon binding to GAPDH. In conclusion, GAPDH-CP12 is a fuzzy complex, in which the N-terminal region of CP12 keeps a conformational freedom in the bound form. This fuzziness could be one of the keys to facilitate binding of PRK to CP12-GAPDH and to form the ternary supra-molecular complex. FAU - Mileo, Elisabetta AU - Mileo E AD - Aix-Marseille Universite, CNRS, BIP UMR 7281, 31 chemin J. Aiguier, 13402 Marseille Cedex 20, France. belle@imm.cnrs.fr bmeunier@imm.cnrs.fr. FAU - Lorenzi, Magali AU - Lorenzi M FAU - Erales, Jenny AU - Erales J FAU - Lignon, Sabrina AU - Lignon S FAU - Puppo, Carine AU - Puppo C FAU - Le Breton, Nolwenn AU - Le Breton N FAU - Etienne, Emilien AU - Etienne E FAU - Marque, Sylvain R A AU - Marque SR FAU - Guigliarelli, Bruno AU - Guigliarelli B FAU - Gontero, Brigitte AU - Gontero B FAU - Belle, Valerie AU - Belle V LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Plant Proteins) RN - EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases) SB - IM MH - Chlamydomonas reinhardtii/*metabolism MH - Glyceraldehyde-3-Phosphate Dehydrogenases/chemistry/*metabolism MH - Kinetics MH - Models, Molecular MH - Photosynthesis MH - Plant Proteins/chemistry/*metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Interaction Domains and Motifs MH - Substrate Specificity EDAT- 2013/09/24 06:00 MHDA- 2014/05/09 06:00 CRDT- 2013/09/24 06:00 PHST- 2013/09/11 [aheadofprint] PHST- 2013/10/01 [epublish] AID - 10.1039/c3mb70190e [doi] PST - ppublish SO - Mol Biosyst. 2013 Nov;9(11):2869-76. doi: 10.1039/c3mb70190e. PMID- 14715270 OWN - NLM STAT- MEDLINE DA - 20040112 DCOM- 20040419 LR - 20061115 IS - 0006-291X (Print) IS - 0006-291X (Linking) VI - 314 IP - 1 DP - 2004 Jan 30 TI - Biophysical characterization of Gir2, a highly acidic protein of Saccharomyces cerevisiae with anomalous electrophoretic behavior. PG - 229-34 AB - Gir2 is an uncharacterized protein of Saccharomyces cerevisiae, containing a RWD/GI domain. In this work, we report the biophysical characterization of Gir2. His-tagged Gir2, expressed and purified from Escherichia coli, showed an abnormally slow migration on SDS-PAGE. The yeast expressed protein behaves similarly. Using mass spectrometry and peptide mass fingerprinting we demonstrated that the protein has the expected molecular mass (34kDa). EDC modification of carboxylate groups reverted the anomalous migration on SDS-PAGE. Size exclusion chromatography showed that Gir2 has a Stokes radius larger than expected. Gir2 is thermostable and lacks extensive structure, as determined by CD analysis. Based on these findings, we suggest that Gir2 is a representative of the growing group of "natively unfolded" proteins. FAU - Alves, Viviane S AU - Alves VS AD - Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, SP, Brazil. FAU - Pimenta, Daniel C AU - Pimenta DC FAU - Sattlegger, Evelyn AU - Sattlegger E FAU - Castilho, Beatriz A AU - Castilho BA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Fungal Proteins) RN - 0 (Gir2 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Amino Acid Sequence MH - Electrophoresis/*methods MH - Fungal Proteins/*chemistry MH - Hydrogen-Ion Concentration MH - Molecular Sequence Data MH - Molecular Weight MH - Peptide Mapping/methods MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/*chemistry MH - Saccharomyces cerevisiae Proteins/*chemistry MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization EDAT- 2004/01/13 05:00 MHDA- 2004/04/20 05:00 CRDT- 2004/01/13 05:00 AID - S0006291X03026949 [pii] PST - ppublish SO - Biochem Biophys Res Commun. 2004 Jan 30;314(1):229-34. PMID- 23134341 OWN - NLM STAT- MEDLINE DA - 20130110 DCOM- 20130307 LR - 20131121 IS - 1470-8728 (Electronic) IS - 0264-6021 (Linking) VI - 449 IP - 3 DP - 2013 Feb 1 TI - DNA-binding regulates site-specific ubiquitination of IRF-1. PG - 707-17 LID - 10.1042/BJ20121076 [doi] AB - Understanding the determinants for site-specific ubiquitination by E3 ligase components of the ubiquitin machinery is proving to be a challenge. In the present study we investigate the role of an E3 ligase docking site (Mf2 domain) in an intrinsically disordered domain of IRF-1 [IFN (interferon) regulatory factor-1], a short-lived IFNgamma-regulated transcription factor, in ubiquitination of the protein. Ubiquitin modification of full-length IRF-1 by E3 ligases such as CHIP [C-terminus of the Hsc (heat-shock cognate) 70-interacting protein] and MDM2 (murine double minute 2), which dock to the Mf2 domain, was specific for lysine residues found predominantly in loop structures that extend from the DNA-binding domain, whereas no modification was detected in the more conformationally flexible C-terminal half of the protein. The E3 docking site was not available when IRF-1 was in its DNA-bound conformation and cognate DNA-binding sequences strongly suppressed ubiquitination, highlighting a strict relationship between ligase binding and site-specific modification at residues in the DNA-binding domain. Hyperubiquitination of a non-DNA-binding mutant supports a mechanism where an active DNA-bound pool of IRF-1 is protected from polyubiquitination and degradation. FAU - Landre, Vivien AU - Landre V AD - Cell Signalling Unit, Edinburgh Cancer Research Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XR, UK. FAU - Pion, Emmanuelle AU - Pion E FAU - Narayan, Vikram AU - Narayan V FAU - Xirodimas, Dimitris P AU - Xirodimas DP FAU - Ball, Kathryn L AU - Ball KL LA - eng GR - C377/ A6355/Cancer Research UK/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (IRF1 protein, human) RN - 0 (Interferon Regulatory Factor-1) RN - 0 (Mutant Proteins) RN - 0 (Recombinant Proteins) RN - 9007-49-2 (DNA) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) RN - EC 6.3.2.19 (STUB1 protein, human) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) RN - K3Z4F929H6 (Lysine) SB - IM MH - Amino Acid Sequence MH - Binding Sites/genetics MH - Cell Line MH - DNA/*metabolism MH - Humans MH - Interferon Regulatory Factor-1/*chemistry/genetics/*metabolism MH - Lysine/chemistry MH - Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Mutant Proteins/chemistry/genetics/metabolism MH - Protein Conformation MH - Protein Interaction Domains and Motifs MH - Proto-Oncogene Proteins c-mdm2/metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Ubiquitin-Protein Ligases/metabolism MH - Ubiquitination EDAT- 2012/11/09 06:00 MHDA- 2013/03/08 06:00 CRDT- 2012/11/09 06:00 AID - BJ20121076 [pii] AID - 10.1042/BJ20121076 [doi] PST - ppublish SO - Biochem J. 2013 Feb 1;449(3):707-17. doi: 10.1042/BJ20121076. PMID- 21134384 OWN - NLM STAT- MEDLINE DA - 20110131 DCOM- 20110321 LR - 20150325 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 406 IP - 2 DP - 2011 Feb 18 TI - HIV-1 Gag extension: conformational changes require simultaneous interaction with membrane and nucleic acid. PG - 205-14 LID - 10.1016/j.jmb.2010.11.051 [doi] AB - The retroviral Gag polyprotein mediates viral assembly. The Gag protein has been shown to interact with other Gag proteins, with the viral RNA, and with the cell membrane during the assembly process. Intrinsically disordered regions linking ordered domains make characterization of the protein structure difficult. Through small-angle scattering and molecular modeling, we have previously shown that monomeric human immunodeficiency virus type 1 (HIV-1) Gag protein in solution adopts compact conformations. However, cryo-electron microscopic analysis of immature virions shows that in these particles, HIV-1 Gag protein molecules are rod shaped. These differing results imply that large changes in Gag conformation are possible and may be required for viral formation. By recapitulating key interactions in the assembly process and characterizing the Gag protein using neutron scattering, we have identified interactions capable of reversibly extending the Gag protein. In addition, we demonstrate advanced applications of neutron reflectivity in resolving Gag conformations on a membrane. Several kinds of evidence show that basic residues found on the distal N- and C-terminal domains enable both ends of Gag to bind to either membranes or nucleic acid. These results, together with other published observations, suggest that simultaneous interactions of an HIV-1 Gag molecule with all three components (protein, nucleic acid, and membrane) are required for full extension of the protein. CI - Published by Elsevier Ltd. FAU - Datta, Siddhartha A K AU - Datta SA AD - HIV Drug Resistance Program, National Cancer Institute, PO Box B, Building 535, Fredrick, MD 21702-1201, USA. FAU - Heinrich, Frank AU - Heinrich F FAU - Raghunandan, Sindhu AU - Raghunandan S FAU - Krueger, Susan AU - Krueger S FAU - Curtis, Joseph E AU - Curtis JE FAU - Rein, Alan AU - Rein A FAU - Nanda, Hirsh AU - Nanda H LA - eng GR - ZIA BC010511-08/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20101204 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DNA, Viral) RN - 0 (RNA, Viral) RN - 0 (gag Gene Products, Human Immunodeficiency Virus) SB - IM MH - Cell Membrane/chemistry/*metabolism MH - DNA, Viral/chemistry/*metabolism MH - HIV-1/*metabolism MH - Humans MH - Neutrons MH - Protein Binding MH - Protein Conformation MH - RNA, Viral/chemistry/*metabolism MH - Virus Assembly MH - gag Gene Products, Human Immunodeficiency Virus/chemistry/*metabolism PMC - PMC3046808 MID - NIHMS265107 OID - NLM: NIHMS265107 OID - NLM: PMC3046808 EDAT- 2010/12/08 06:00 MHDA- 2011/03/22 06:00 CRDT- 2010/12/08 06:00 PHST- 2010/09/27 [received] PHST- 2010/11/24 [revised] PHST- 2010/11/25 [accepted] PHST- 2010/12/04 [aheadofprint] AID - S0022-2836(10)01281-7 [pii] AID - 10.1016/j.jmb.2010.11.051 [doi] PST - ppublish SO - J Mol Biol. 2011 Feb 18;406(2):205-14. doi: 10.1016/j.jmb.2010.11.051. Epub 2010 Dec 4. PMID- 19635593 OWN - NLM STAT- MEDLINE DA - 20090923 DCOM- 20091214 LR - 20131121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1794 IP - 11 DP - 2009 Nov TI - The rod-shaped conformation of Starmaker. PG - 1616-24 LID - 10.1016/j.bbapap.2009.07.010 [doi] AB - Fish otoliths are calcium carbonate biominerals responsible for gravity sensing and the perception of sound. The otoliths formation is controlled by Starmaker (Stm), a protein which belongs to a class of intrinsically disordered proteins. Here, we utilized analytical ultracentrifugation along with Ferguson's analysis of the electrophoretic data to demonstrate that Stm exists in solution as a monomer. The Stm frictional ratio has an unusually high value ranging from 2.6 to 3.1 depending on the method used to analyse the data obtained from analytical ultracentrifugation or gel filtration experiments. These unusually high values of frictional ratio indicate that monomeric Stm has a significantly extended rod-shaped conformation. Calcium ions, which are putative ligands of Stm, induce compaction of the extended conformation of Stm. In particular, increasing the calcium ion concentration from 1 mM to 50 mM lowered the Stokes radius by about 9.5 A. Gel filtration experiments done under denaturing conditions showed only small changes in the dimensions of Stm, which suggests the presence of residual ordered structures. These structures were estimated to be 23% of the Stm structure by detailed analysis of the data obtained by differential scanning microcalorimetry. The elongation of Stm polypeptide chain may facilitate its simultaneous interaction with other components of the composed calcium carbonate crystals which build up otoliths. FAU - Kaplon, Tomasz M AU - Kaplon TM AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland. FAU - Michnik, Anna AU - Michnik A FAU - Drzazga, Zofia AU - Drzazga Z FAU - Richter, Klaus AU - Richter K FAU - Kochman, Marian AU - Kochman M FAU - Ozyhar, Andrzej AU - Ozyhar A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090725 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Zebrafish Proteins) RN - 0 (starmaker protein, zebrafish) RN - SY7Q814VUP (Calcium) SB - IM MH - Animals MH - Calcium/pharmacology MH - Chromatography, Gel MH - Molecular Weight MH - Otolithic Membrane/metabolism MH - Protein Conformation/drug effects MH - Protein Denaturation MH - Ultracentrifugation MH - Zebrafish Proteins/*chemistry EDAT- 2009/07/29 09:00 MHDA- 2009/12/16 06:00 CRDT- 2009/07/29 09:00 PHST- 2009/04/28 [received] PHST- 2009/07/14 [revised] PHST- 2009/07/16 [accepted] PHST- 2009/07/25 [aheadofprint] AID - S1570-9639(09)00176-9 [pii] AID - 10.1016/j.bbapap.2009.07.010 [doi] PST - ppublish SO - Biochim Biophys Acta. 2009 Nov;1794(11):1616-24. doi: 10.1016/j.bbapap.2009.07.010. Epub 2009 Jul 25. PMID- 21348834 OWN - NLM STAT- MEDLINE DA - 20110511 DCOM- 20110829 LR - 20120131 IS - 1875-5550 (Electronic) IS - 1389-2037 (Linking) VI - 12 IP - 3 DP - 2011 May TI - Structures behind the amyloid aggregation of alpha-synuclein: an NMR based approach. PG - 188-204 AB - The misfolding of proteins into a toxic conformation is proposed to be at the molecular foundation of a number of neurodegenerative disorders including Alzheimer's and Parkinson's diseases. Evidence that alpha-synuclein amyloidogenesis plays a causative role in the development of Parkinson's disease is furnished by a variety of genetic, neuropathological and biochemical studies. There is a major interest in understanding the structural and toxicity features of the various species populated along the aggregation pathway of this protein. The development of multidimensional nuclear magnetic resonance (NMR) spectroscopy in liquid and solid state over the last decade has significantly increased the scope of molecules that are amenable for structural studies. The aim of this review is to provide a picture of how NMR tools were used in concert to decipher the structural and dynamic properties of the intrinsically disordered protein alpha-synuclein in its native, oligomeric, fibril and membrane-bound states. Understanding the structural and molecular basis behind the aggregation pathway of alpha-synuclein is key to advance in the design of a therapeutic strategy. FAU - Orcellet, Maria L AU - Orcellet ML AD - Instituto de Biologia Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Cientificas y Tecnicas, Universidad Nacional de Rosario, Argentina. FAU - Fernandez, Claudio O AU - Fernandez CO LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Netherlands TA - Curr Protein Pept Sci JT - Current protein & peptide science JID - 100960529 RN - 0 (Amyloid) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - *Amyloid/chemistry MH - Humans MH - *Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Parkinson Disease/physiopathology MH - Protein Folding MH - Proteostasis Deficiencies/physiopathology MH - Sequence Alignment MH - alpha-Synuclein/*chemistry EDAT- 2011/02/26 06:00 MHDA- 2011/08/30 06:00 CRDT- 2011/02/26 06:00 PHST- 2011/01/10 [received] PHST- 2011/02/20 [accepted] AID - CPPS-113 [pii] PST - ppublish SO - Curr Protein Pept Sci. 2011 May;12(3):188-204. PMID- 21355573 OWN - NLM STAT- MEDLINE DA - 20110330 DCOM- 20110713 LR - 20131121 IS - 1520-5827 (Electronic) IS - 0743-7463 (Linking) VI - 27 IP - 7 DP - 2011 Apr 5 TI - Molecular dynamics simulations of the interactions of kinin peptides with an anionic POPG bilayer. PG - 3713-22 LID - 10.1021/la104046z [doi] AB - We have performed molecular dynamics simulations of peptide hormone bradykinin (BK) and its fragment des-Arg9-BK in the presence of an anionic lipid bilayer, with an aim toward delineating the mechanism of action related to their bioactivity. Starting from the initial aqueous environment, both of the peptides are quickly adsorbed and stabilized on the cell surface. Whereas BK exhibits a stronger interaction with the membrane and prefers to stay on the interface, des-Arg9-BK, with the loss of C-terminal Arg, penetrates further. The heterogeneous lipid-water interface induces beta-turn-like structure in the otherwise inherently flexible peptides. In the membrane-bound state, we observed C-terminal beta-turn formation in BK, whereas for des-Arg9-BK, with the deletion of Arg9, turn formation occurred in the middle of the peptide. The basic Arg residues anchor the peptide to the bilayer by strong electrostatic interactions with charged lipid headgroups. Simulations with different starting orientations of the peptides with respect to the bilayer surface lead to the same observations, namely, the relative positioning of the peptides on the membrane surface, deeper penetration of the des-Arg9-BK, and the formation of turn structures. The lipid headgroups adjacent to the bound peptides become substantially tilted, causing bilayer thinning near the peptide contact region and increase the degree of disorder in nearby lipids. Again, because of hydrogen bonding with the peptide, the neighboring lipid's polar heads exhibit considerably reduced flexibility. Corroborating findings from earlier experiments, our results provide important information about how the lipid environment promotes peptide orientation/conformation and how the peptide adapts to the environment. FAU - Manna, Moutusi AU - Manna M AD - Department of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata-700 009, India. FAU - Mukhopadhyay, Chaitali AU - Mukhopadhyay C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110228 PL - United States TA - Langmuir JT - Langmuir : the ACS journal of surfaces and colloids JID - 9882736 RN - 0 (Anions) RN - 0 (Kinins) RN - 0 (Lipid Bilayers) RN - 0 (Peptides) RN - 0 (Phosphatidylglycerols) RN - 059QF0KO0R (Water) RN - 81490-05-3 (1-palmitoyl-2-oleoylglycero-3-phosphoglycerol) SB - IM MH - Anions/*chemistry MH - Kinins/*chemistry MH - Lipid Bilayers/*chemistry MH - *Molecular Dynamics Simulation MH - Peptides/*chemistry MH - Phosphatidylglycerols/*chemistry MH - Water/chemistry EDAT- 2011/03/02 06:00 MHDA- 2011/07/14 06:00 CRDT- 2011/03/02 06:00 PHST- 2011/02/28 [aheadofprint] AID - 10.1021/la104046z [doi] PST - ppublish SO - Langmuir. 2011 Apr 5;27(7):3713-22. doi: 10.1021/la104046z. Epub 2011 Feb 28. PMID- 24055379 OWN - NLM STAT- MEDLINE DA - 20131223 DCOM- 20140224 LR - 20140527 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 426 IP - 1 DP - 2014 Jan 9 TI - Mechanism of assembly of the non-covalent spectrin tetramerization domain from intrinsically disordered partners. PG - 21-35 LID - 10.1016/j.jmb.2013.08.027 [doi] LID - S0022-2836(13)00582-2 [pii] AB - Interdomain interactions of spectrin are critical for maintenance of the erythrocyte cytoskeleton. In particular, "head-to-head" dimerization occurs when the intrinsically disordered C-terminal tail of beta-spectrin binds the N-terminal tail of alpha-spectrin, folding to form the "spectrin tetramer domain". This non-covalent three-helix bundle domain is homologous in structure and sequence to previously studied spectrin domains. We find that this tetramer domain is surprisingly kinetically stable. Using a protein engineering Phi-value analysis to probe the mechanism of formation of this tetramer domain, we infer that the domain folds by the docking of the intrinsically disordered beta-spectrin tail onto the more structured alpha-spectrin tail. CI - (c) 2013. Published by Elsevier Ltd. All rights reserved. FAU - Hill, Stephanie A AU - Hill SA AD - University of Cambridge Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK; Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. FAU - Kwa, Lee Gyan AU - Kwa LG AD - University of Cambridge Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK. FAU - Shammas, Sarah L AU - Shammas SL AD - University of Cambridge Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK. FAU - Lee, Jennifer C AU - Lee JC AD - Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. FAU - Clarke, Jane AU - Clarke J AD - University of Cambridge Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK. Electronic address: jc162@cam.ac.uk. LA - eng GR - 095195/Wellcome Trust/United Kingdom GR - WT095195/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't DEP - 20130917 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 12634-43-4 (Spectrin) SB - IM CIN - J Mol Biol. 2014 Jan 9;426(1):7-10. PMID: 24112938 MH - Kinetics MH - *Protein Folding MH - Protein Interaction Domains and Motifs MH - *Protein Multimerization MH - Protein Stability MH - Spectrin/*chemistry/*metabolism OTO - NOTNLM OT - GdmCl OT - IDP OT - ITC OT - NIH OT - National Institutes of Health OT - guanidinium chloride OT - intrinsically disordered protein OT - isothermal titration calorimetry OT - natively unfolded protein OT - protein engineering OT - protein folding OT - Phi-value analysis EDAT- 2013/09/24 06:00 MHDA- 2014/02/25 06:00 CRDT- 2013/09/24 06:00 PHST- 2013/06/11 [received] PHST- 2013/07/24 [revised] PHST- 2013/08/20 [accepted] PHST- 2013/09/17 [aheadofprint] AID - S0022-2836(13)00582-2 [pii] AID - 10.1016/j.jmb.2013.08.027 [doi] PST - ppublish SO - J Mol Biol. 2014 Jan 9;426(1):21-35. doi: 10.1016/j.jmb.2013.08.027. Epub 2013 Sep 17. PMID- 17045239 OWN - NLM STAT- MEDLINE DA - 20061023 DCOM- 20061218 LR - 20150127 IS - 0006-291X (Print) IS - 0006-291X (Linking) VI - 350 IP - 4 DP - 2006 Dec 1 TI - Structural studies of human Naked2: a biologically active intrinsically unstructured protein. PG - 911-5 AB - Naked1 and 2 are two mammalian orthologs of Naked Cuticle, a canonical Wnt signaling antagonist in Drosophila. Naked2, but not Naked1, interacts with transforming growth factor-alpha (TGFalpha) and escorts TGFalpha-containing vesicles to the basolateral membrane of polarized epithelial cells. Full-length Naked2 is poorly soluble. Since most functional domains, including the Dishevelled binding region, EF-hand, vesicle recognition, and membrane targeting motifs, reside in the N-terminal half of the protein, we expressed and purified the first 217 residues of human Naked2 and performed a functional analysis of this fragment. Its circular dichroism (CD) and nuclear magnetic resonance (NMR) spectra showed no evidence of secondary and/or tertiary structure. The fragment did not bind calcium or zinc. These results indicate that the N-terminal half of Naked2 behaves as an intrinsically unstructured protein. FAU - Hu, Tianhui AU - Hu T AD - Department of Medicine and Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA. FAU - Krezel, Andrzej M AU - Krezel AM FAU - Li, Cunxi AU - Li C FAU - Coffey, Robert J AU - Coffey RJ LA - eng GR - 5R01CA046413/CA/NCI NIH HHS/United States GR - 5T32HL007751/HL/NHLBI NIH HHS/United States GR - P50 CA095103/CA/NCI NIH HHS/United States GR - P50CA095103/CA/NCI NIH HHS/United States GR - R01 CA046413/CA/NCI NIH HHS/United States GR - T32 HL007751/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20061002 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Carrier Proteins) RN - 0 (NKD2 protein, human) RN - 0 (Wnt Proteins) SB - IM MH - Amino Acid Sequence MH - Carrier Proteins/*chemistry/*ultrastructure MH - Humans MH - Molecular Conformation MH - Protein Conformation MH - Solubility MH - Wnt Proteins/*chemistry PMC - PMC1661664 MID - NIHMS13607 OID - NLM: NIHMS13607 OID - NLM: PMC1661664 EDAT- 2006/10/19 09:00 MHDA- 2006/12/19 09:00 CRDT- 2006/10/19 09:00 PHST- 2006/09/15 [received] PHST- 2006/09/22 [accepted] PHST- 2006/10/02 [aheadofprint] AID - S0006-291X(06)02166-8 [pii] AID - 10.1016/j.bbrc.2006.09.121 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2006 Dec 1;350(4):911-5. Epub 2006 Oct 2. PMID- 22044151 OWN - NLM STAT- MEDLINE DA - 20120329 DCOM- 20120724 IS - 1875-5550 (Electronic) IS - 1389-2037 (Linking) VI - 13 IP - 1 DP - 2012 Feb TI - HSF transcription factor family, heat shock response, and protein intrinsic disorder. PG - 86-103 AB - Intrinsically disordered proteins are highly abundant in all kingdoms of life, and several protein functional classes, such as transcription factors, transcriptional regulators, hub and scaffold proteins, signaling proteins, and chaperones are especially enriched in intrinsic disorder. One of the unique cellular reactions to protein damaging stress is the so-called heat shock response that results in the upregulation of heat shock proteins including molecular chaperones. This molecular protective mechanism is conserved from prokaryotes to eukaryotes and allows an organism to respond to various proteotoxic stressors, such as heat shock, oxidative stress, exposure to heavy metals, and drugs. The heat shock response- related proteins can be expressed during normal conditions (e.g., during the cell growth and development) or can be induced by various pathological conditions, such as infection, inflammation, and protein conformation diseases. The initiation of the heat shock response is manifested by the activation of the heat shock transcription factors HSF 1, part of a family of related HSF transcription factors. This review analyzes the abundance and functional roles of intrinsic disorder in various heat shock transcription factors and clearly shows that the heat shock response requires HSF flexibility to be more efficient. CI - (c) 2012 Bentham Science Publishers FAU - Westerheide, Sandy D AU - Westerheide SD AD - Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL 33612, USA. FAU - Raynes, Rachel AU - Raynes R FAU - Powell, Chase AU - Powell C FAU - Xue, Bin AU - Xue B FAU - Uversky, Vladimir N AU - Uversky VN LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Netherlands TA - Curr Protein Pept Sci JT - Current protein & peptide science JID - 100960529 RN - 0 (DNA-Binding Proteins) RN - 0 (Heat-Shock Proteins) RN - 0 (Transcription Factors) RN - 0 (heat shock transcription factor) SB - IM MH - Alternative Splicing MH - Animals MH - DNA-Binding Proteins/chemistry/genetics/*metabolism MH - Heat-Shock Proteins/chemistry/genetics/metabolism MH - Heat-Shock Response/*physiology MH - Humans MH - Protein Binding MH - Protein Conformation MH - Protein Interaction Domains and Motifs MH - RNA Processing, Post-Transcriptional MH - Transcription Factors/chemistry/genetics/*metabolism MH - Transcription, Genetic EDAT- 2011/11/03 06:00 MHDA- 2012/07/25 06:00 CRDT- 2011/11/03 06:00 PHST- 2010/12/20 [received] PHST- 2011/08/04 [revised] PHST- 2011/08/04 [accepted] AID - BSP/CPPS/E-Pub/167 [pii] PST - ppublish SO - Curr Protein Pept Sci. 2012 Feb;13(1):86-103. PMID- 16139844 OWN - NLM STAT- MEDLINE DA - 20050913 DCOM- 20051025 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 352 IP - 4 DP - 2005 Sep 30 TI - Crystal structure at high resolution of ferric-pyochelin and its membrane receptor FptA from Pseudomonas aeruginosa. PG - 893-904 AB - Pyochelin is a siderophore and virulence factor common to Burkholderia cepacia and several Pseudomonas strains. We describe at 2.0 A resolution the crystal structure of the pyochelin outer membrane receptor FptA bound to the iron-pyochelin isolated from Pseudomonas aeruginosa. One pyochelin molecule bound to iron is found in the protein structure, providing the first three-dimensional structure at the atomic level of this siderophore. The pyochelin molecule provides a tetra-dentate coordination of iron, while the remaining bi-dentate coordination is ensured by another molecule not specifically recognized by the protein. The overall structure of the pyochelin receptor is typical of the TonB-dependent transporter superfamily, which uses the proton motive force from the cytoplasmic membrane through the TonB-ExbB-ExbD energy transducing complex to transport ferric ions across the bacterial outer membrane: a transmembrane 22 beta-stranded barrel occluded by a N-terminal domain that contains a mixed four-stranded beta-sheet. The N-terminal TonB box is disordered in two crystal forms, and loop L8 is found to point towards the iron-pyochelin complex, suggesting that the receptor is in a transport-competent conformation. FAU - Cobessi, David AU - Cobessi D AD - Departement Recepteurs et Proteines Membranaires, UMR7100 CNRS, Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sebastien Brant, 67412 Illkirch, France. cobessi@esbs.u.strasbg.fr FAU - Celia, Herve AU - Celia H FAU - Pattus, Franc AU - Pattus F LA - eng SI - PDB/1XKW PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Outer Membrane Proteins) RN - 0 (FPTA protein, Pseudomonas) RN - 0 (Iron Chelating Agents) RN - 0 (Phenols) RN - 0 (Receptors, Cell Surface) RN - 0 (Siderophores) RN - 0 (Thiazoles) RN - 69772-54-9 (pyochelin) RN - E1UOL152H7 (Iron) SB - IM MH - Amino Acid Sequence MH - Animals MH - Bacterial Outer Membrane Proteins/*chemistry/metabolism MH - Binding Sites MH - Crystallography, X-Ray MH - Iron/*chemistry/metabolism MH - Iron Chelating Agents/*chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Molecular Structure MH - Phenols/*chemistry/metabolism MH - Protein Binding MH - *Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Pseudomonas aeruginosa/*metabolism MH - Receptors, Cell Surface/*chemistry/metabolism MH - Siderophores/*chemistry/metabolism MH - Thiazoles/*chemistry/metabolism EDAT- 2005/09/06 09:00 MHDA- 2005/10/26 09:00 CRDT- 2005/09/06 09:00 PHST- 2005/06/10 [received] PHST- 2005/08/03 [revised] PHST- 2005/08/07 [accepted] AID - S0022-2836(05)00904-6 [pii] AID - 10.1016/j.jmb.2005.08.004 [doi] PST - ppublish SO - J Mol Biol. 2005 Sep 30;352(4):893-904. PMID- 18216271 OWN - NLM STAT- MEDLINE DA - 20080130 DCOM- 20080225 LR - 20140916 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 105 IP - 4 DP - 2008 Jan 29 TI - Regulation of Escherichia coli SOS mutagenesis by dimeric intrinsically disordered umuD gene products. PG - 1152-7 LID - 10.1073/pnas.0706067105 [doi] AB - Products of the umuD gene in Escherichia coli play key roles in coordinating the switch from accurate DNA repair to mutagenic translesion DNA synthesis (TLS) during the SOS response to DNA damage. Homodimeric UmuD(2) is up-regulated 10-fold immediately after damage, after which slow autocleavage removes the N-terminal 24 amino acids of each UmuD. The remaining fragment, UmuD'(2), is required for mutagenic TLS. The small proteins UmuD(2) and UmuD'(2) make a large number of specific protein-protein contacts, including three of the five known E. coli DNA polymerases, parts of the replication machinery, and RecA recombinase. We show that, despite forming stable homodimers, UmuD(2) and UmuD'(2) have circular dichroism (CD) spectra with almost no alpha-helix or beta-sheet signal at physiological concentrations in vitro. High protein concentrations, osmolytic crowding agents, and specific interactions with a partner protein can produce CD spectra that resemble the expected beta-sheet signature. A lack of secondary structure in vitro is characteristic of intrinsically disordered proteins (IDPs), many of which act as regulators. A stable homodimer that lacks significant secondary structure is unusual but not unprecedented. Furthermore, previous single-cysteine cross-linking studies of UmuD(2) and UmuD'(2) show that they have a nonrandom structure at physiologically relevant concentrations in vitro. Our results offer insights into structural characteristics of relatively poorly understood IDPs and provide a model for how the umuD gene products can regulate diverse aspects of the bacterial SOS response. FAU - Simon, S M AU - Simon SM AD - Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. FAU - Sousa, F J R AU - Sousa FJ FAU - Mohana-Borges, R AU - Mohana-Borges R FAU - Walker, G C AU - Walker GC LA - eng GR - CA21615-27/CA/NCI NIH HHS/United States GR - GM68762/GM/NIGMS NIH HHS/United States GR - P30 ES002109/ES/NIEHS NIH HHS/United States GR - P30 ES002109/ES/NIEHS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20080123 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Cross-Linking Reagents) RN - 0 (Escherichia coli Proteins) RN - 0 (Isoenzymes) RN - EC 2.7.7.7 (DNA-Directed DNA Polymerase) RN - EC 2.7.7.7 (UmuD protein, E coli) RN - EC 3.4.21.1 (Chymotrypsin) RN - K848JZ4886 (Cysteine) SB - IM MH - Chymotrypsin/chemistry MH - Circular Dichroism MH - Cross-Linking Reagents/chemistry MH - Cysteine/chemistry/genetics MH - DNA-Directed DNA Polymerase/*chemistry/genetics/metabolism/*physiology MH - Dimerization MH - Escherichia coli/*enzymology/*genetics MH - Escherichia coli Proteins/*chemistry/genetics/metabolism/*physiology MH - Hydrolysis MH - Isoenzymes/chemistry/genetics/metabolism/physiology MH - Models, Biological MH - *Mutagenesis MH - Protein Folding MH - Protein Structure, Secondary/genetics MH - Protein Structure, Tertiary/genetics MH - SOS Response (Genetics)/*genetics PMC - PMC2234107 OID - NLM: PMC2234107 EDAT- 2008/01/25 09:00 MHDA- 2008/02/26 09:00 CRDT- 2008/01/25 09:00 PHST- 2008/01/23 [aheadofprint] AID - 0706067105 [pii] AID - 10.1073/pnas.0706067105 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1152-7. doi: 10.1073/pnas.0706067105. Epub 2008 Jan 23. PMID- 19856323 OWN - NLM STAT- MEDLINE DA - 20091222 DCOM- 20100302 LR - 20121115 IS - 1099-1352 (Electronic) IS - 0952-3499 (Linking) VI - 23 IP - 1 DP - 2010 Jan-Feb TI - Probing the interaction between recombinant human myelin basic protein and caseins using surface plasmon resonance and diffusing wave spectroscopy. PG - 84-92 LID - 10.1002/jmr.991 [doi] AB - An intrinsically unstructured human myelin basic protein (hMBP) was expressed in the milk of transgenic cows (TGmilk) and found exclusively associated with the casein micellar phase. The interaction between the recombinant protein and milk caseins was investigated using surface plasmon resonance (SPR). An anti-human myelin basic protein antibody was covalently immobilized to the surface of the sensor chip. Subsequently the interaction between the recombinant protein (captured by this antibody) and caseins was studied in comparison to that noted with its human counterpart. Results showed a calcium-mediated interaction between the recombinant protein and caseins. The order of magnitude of this interaction was in agreement with the number of phosphorylated residues carried by each type of casein (alpha(s)- > beta- > kappa-casein). This selective interaction was not noted between the human protein and milk caseins indicating that the recombinant protein was phosphorylated to a higher extent than the human protein. The obtained results indicated that the co-expression of the recombinant protein and caseins by the mammary gland along with the recombinant protein's ability to form calcium bridges played a key role in the association of the recombinant human myelin basic protein (rhMBP) with the casein micelles of milk. Despite this association between the recombinant protein and milk caseins, light scattering investigations using diffusing wave spectroscopy (DWS) showed no significant differences between the milks of the transgenic and the non-transgenic control cows, with respect to both the average micelle size and surface charges. This was attributed to the low expression levels of the recombinant protein in milk. CI - (c) 2009 John Wiley & Sons, Ltd. FAU - Al-Ghobashy, Medhat A AU - Al-Ghobashy MA AD - Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand. FAU - Cucheval, Aurelie AU - Cucheval A FAU - Williams, Martin A K AU - Williams MA FAU - Laible, Gotz AU - Laible G FAU - Harding, David R K AU - Harding DR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Recognit JT - Journal of molecular recognition : JMR JID - 9004580 RN - 0 (Caseins) RN - 0 (MBP protein, human) RN - 0 (Micelles) RN - 0 (Myelin Basic Protein) RN - 0 (Nerve Tissue Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) SB - IM MH - Animals MH - Animals, Genetically Modified/metabolism MH - Caseins/*chemistry/metabolism MH - Cattle MH - Humans MH - Kinetics MH - Micelles MH - Myelin Basic Protein MH - Nerve Tissue Proteins/*chemistry/genetics/metabolism MH - Protein Structure, Tertiary MH - Recombinant Proteins/*chemistry/metabolism MH - Spectrum Analysis/methods MH - Surface Plasmon Resonance MH - Transcription Factors/*chemistry/genetics/metabolism EDAT- 2009/10/27 06:00 MHDA- 2010/03/03 06:00 CRDT- 2009/10/27 06:00 AID - 10.1002/jmr.991 [doi] PST - ppublish SO - J Mol Recognit. 2010 Jan-Feb;23(1):84-92. doi: 10.1002/jmr.991. PMID- 18946767 OWN - NLM STAT- MEDLINE DA - 20081023 DCOM- 20090707 LR - 20121115 IS - 1532-4281 (Electronic) IS - 1079-9893 (Linking) VI - 28 IP - 5 DP - 2008 TI - Osmolyte-induced folding of an intrinsically disordered activation function subdomain of glucocorticoid receptor. PG - 465-74 LID - 10.1080/10799890802412385 [doi] AB - Intrinsically disordered (ID) regions are disproportionately higher in cell-signaling proteins, suggesting an important role in their regulatory capacity. Activation domains of many transcription factors exist in ID conformation(s). It has been suggested that large flexible regions in ID activation domains have an advantage over proteins with ordered conformations such that ID regions/domains can make more efficient interactions with their target partners. The major activation function-1 (AF1) region, located in the N-terminal domain of several steroid receptors, including the glucocorticoid receptor (GR) possess ID sequences. Recently, we reported that osmolytes fold AF1 into functionally active conformation. Most of known AF1:coregulatory proteins interactions take place in a core subdomain (AF1(C)) that is indispensible for AF1-mediated GR activity. However, it is not known whether osmolytes can induce functionally folded conformation in AF1(C). In this study we have found that a naturally occurring osmolyte, trimethylamine-N-oxide, can cooperatively fold AF1(C) into a compact structure. FAU - Kumar, Raj AU - Kumar R AD - Division of Gastroenterology, Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas 77555-0655, USA. rakumar@utmb.edu LA - eng GR - 5R01DK058829-07/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - J Recept Signal Transduct Res JT - Journal of receptor and signal transduction research JID - 9509432 RN - 0 (Methylamines) RN - 0 (Oxidants) RN - 0 (Receptors, Glucocorticoid) RN - FLD0K1SJ1A (trimethyloxamine) SB - IM MH - Humans MH - Methylamines/*pharmacology MH - Oxidants/*pharmacology MH - Protein Folding MH - Protein Structure, Tertiary/drug effects MH - Receptors, Glucocorticoid/*agonists/chemistry/drug effects/*metabolism EDAT- 2008/10/24 09:00 MHDA- 2009/07/08 09:00 CRDT- 2008/10/24 09:00 AID - 904706098 [pii] AID - 10.1080/10799890802412385 [doi] PST - ppublish SO - J Recept Signal Transduct Res. 2008;28(5):465-74. doi: 10.1080/10799890802412385 . PMID- 20385607 OWN - NLM STAT- MEDLINE DA - 20100812 DCOM- 20101214 IS - 1741-0134 (Electronic) IS - 1741-0126 (Linking) VI - 23 IP - 7 DP - 2010 Jul TI - Structural characterisation of the natively unfolded enterocin EJ97. PG - 507-18 LID - 10.1093/protein/gzq020 [doi] AB - Bacteriocins belong to the wide variety of antimicrobial ribosomal peptides synthesised by bacteria. Enterococci are Gram-positive, catalase-negative bacteria that produce lactic acid as the major end product of glucose fermentation. Many enterococcal strains produce bacteriocins, named enterocins. We describe in this work, the structural characterisation of the 44 residues-long enterocin EJ97, produced by Enterococcus faecalis EJ97. To this end, we have used a combined theoretical and experimental approach. First, we have characterised experimentally the conformational properties of EJ97 in solution under different conditions by using a number of spectroscopic techniques, namely fluorescence, CD, FTIR and NMR. Then, we have used several bioinformatic tools as an aid to complement the experimental information about the conformational properties of EJ97. We have shown that EJ97 is monomeric in aqueous solution and that it appears to be chiefly unfolded, save some flickering helical- or turn-like structures, probably stabilised by hydrophobic clustering. Accordingly, EJ97 does not show a cooperative sigmoidal transition when heated or upon addition of GdmCl. These conformational features are essentially pH-independent, as shown by NMR assignments at pHs 5.9 and 7.0. The computational results were puzzling, since some algorithms revealed the natively unfolded character of EJ97 (FoldIndex, the mean scaled hydropathy), whereas some others suggested the presence of ordered structure in its central region (PONDR, RONN and IUPRED). A future challenge is to produce much more experimental results to aid the development of accurate software tools for predicting disorder in proteins. FAU - Neira, Jose L AU - Neira JL AD - Instituto de Biologia Molecular y Celular, Edificio Torregaitan, 50009 Zaragoza, Spain. jlneira@umh.es FAU - Contreras, Lellys M AU - Contreras LM FAU - de los Panos, Olga Ruiz AU - de los Panos OR FAU - Sanchez-Hidalgo, Marina AU - Sanchez-Hidalgo M FAU - Martinez-Bueno, Manuel AU - Martinez-Bueno M FAU - Maqueda, Mercedes AU - Maqueda M FAU - Rico, Manuel AU - Rico M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100412 PL - England TA - Protein Eng Des Sel JT - Protein engineering, design & selection : PEDS JID - 101186484 RN - 0 (Bacteriocins) RN - 0 (enterocin EJ97, Enterococcus faecalis) SB - IM MH - Amino Acid Sequence MH - Bacteriocins/*chemistry/metabolism MH - Circular Dichroism MH - Computational Biology MH - Computer Simulation MH - Hydrogen-Ion Concentration MH - Models, Molecular MH - Molecular Sequence Annotation MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Spectrometry, Fluorescence MH - Spectroscopy, Fourier Transform Infrared EDAT- 2010/04/14 06:00 MHDA- 2010/12/16 06:00 CRDT- 2010/04/14 06:00 PHST- 2010/04/12 [aheadofprint] AID - gzq020 [pii] AID - 10.1093/protein/gzq020 [doi] PST - ppublish SO - Protein Eng Des Sel. 2010 Jul;23(7):507-18. doi: 10.1093/protein/gzq020. Epub 2010 Apr 12. PMID- 21247890 OWN - NLM STAT- MEDLINE DA - 20110314 DCOM- 20110516 LR - 20140821 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 11 DP - 2011 Mar 18 TI - Binding of Efb from Staphylococcus aureus to fibrinogen blocks neutrophil adherence. PG - 9865-74 LID - 10.1074/jbc.M110.199687 [doi] AB - In addition to its pivotal role in hemostasis, fibrinogen (Fg) and provisional fibrin matrices play important roles in inflammation and regulate innate immune responses by interacting with leukocytes. Efb (the extracellular fibrinogen-binding protein) is a secreted Staphylococcus aureus protein that engages host Fg and complement C3. However, the molecular details underlying the Efb-Fg interaction and the biological relevance of this interaction have not been determined. In the present study, we characterize the interaction of Efb with Fg. We demonstrate that the Fg binding activity is located within the intrinsically disordered N-terminal half of Efb (Efb-N) and that the D fragment of Fg is the region that mediates Efb-N binding. More detailed studies of the Efb-N-Fg interactions using ELISA and surface plasmon resonance analyses revealed that Efb-N exhibits a much higher affinity for Fg than typically observed with Fg-binding MSCRAMMs (microbial surface components recognizing adhesive matrix molecules), and data obtained from ELISA analyses using truncated Efb-N constructs demonstrate that Efb-N contains two binding sites located within residues 30-67 and 68-98, respectively. Efb-N inhibits neutrophil adhesion to immobilized Fg by binding to Fg and blocking the interaction of the protein with the leukocyte integrin receptor, alpha(M)beta(2). A motif in the Fg gamma chain previously shown to be central to the alpha(M)beta(2) interaction was shown to be functionally distinguishable from the Efb-N binding site, suggesting that the Fg-Efb interaction indirectly impedes Fg engagement by alpha(M)beta(2). Taken together, these studies provide insights into how Efb interacts with Fg and suggest that Efb may support bacterial virulence at least in part by impeding Fg-driven leukocyte adhesion events. FAU - Ko, Ya-Ping AU - Ko YP AD - Center for Infectious and Inflammatory Disease, Institute of Bioscience and Technology, Texas A&M Health Science Center, Houston, Texas 77030, USA. FAU - Liang, Xiaowen AU - Liang X FAU - Smith, C Wayne AU - Smith CW FAU - Degen, Jay L AU - Degen JL FAU - Hook, Magnus AU - Hook M LA - eng GR - AI20624/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20110119 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Adhesins, Bacterial) RN - 0 (Bacterial Proteins) RN - 0 (Efb protein, Staphylococcus aureus) RN - 0 (MSCRAMM proteins, Staphylococcus) RN - 9001-32-5 (Fibrinogen) SB - IM MH - Adhesins, Bacterial/chemistry/metabolism MH - Amino Acid Motifs MH - Bacterial Proteins/chemistry/*metabolism MH - Binding Sites MH - Cell Adhesion MH - Fibrinogen/chemistry/*metabolism MH - HEK293 Cells MH - Humans MH - Neutrophils/chemistry/*metabolism MH - Protein Binding MH - Staphylococcus aureus/chemistry/*metabolism/pathogenicity PMC - PMC3059020 OID - NLM: PMC3059020 EDAT- 2011/01/21 06:00 MHDA- 2011/05/17 06:00 CRDT- 2011/01/21 06:00 PHST- 2011/01/19 [aheadofprint] AID - M110.199687 [pii] AID - 10.1074/jbc.M110.199687 [doi] PST - ppublish SO - J Biol Chem. 2011 Mar 18;286(11):9865-74. doi: 10.1074/jbc.M110.199687. Epub 2011 Jan 19. PMID- 8608129 OWN - NLM STAT- MEDLINE DA - 19960528 DCOM- 19960528 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 35 IP - 9 DP - 1996 Mar 5 TI - Membrane structure of protein kinase C and calmodulin binding domain of myristoylated alanine rich C kinase substrate determined by site-directed spin labeling. PG - 2917-25 AB - Cysteine-substituted peptides based on the membrane, calmodulin, and protein kinase C binding domain of the myristoylated alanine rich C kinase substrate (MARCKS) were synthesized and derivatized with a sulfhydryl reactive proxyl nitroxide. These spin-labeled peptides were used in combination with continuous wave power saturation electron paramagnetic resonance (EPR) spectroscopy to determine the position and structure of the peptide on membranes containing phosphatidylserine. These peptides bind at the membrane interface, with nitroxide side chains in the central and C-terminal regions lying several angstroms below the level of the head group. In contrast, the N-terminus of the peptide is extended out of the membrane interface so that the two N-terminal residues are positioned on the aqueous side of the head group. When bound to the membrane, the N-terminal segment of this peptide is sensitive to the membrane surface charge density. Higher charge densities decrease the amplitude of side chain motions at the N-terminus and bring this end of the peptide closer to the membrane interface. When the location of successive residues along the bilayer normal is compared, no helical trend is seen, and no evidence for aggregation of the peptide is found. The EPR spectra of double spin-labeled peptides also show no evidence for a helical structure. Thus, these basic peptides are in an extended configuration at the membrane interface with hydrophobic side chains oriented inward toward the membrane hydrocarbon. FAU - Qin, Z AU - Qin Z AD - Department of Chemistry and Biophysics Program at the University of Virginia, Charlottesville, 22901, USA. FAU - Cafiso, D S AU - Cafiso DS LA - eng GR - GM 47525/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Liposomes) RN - 0 (Membrane Proteins) RN - 0 (Myristic Acids) RN - 0 (Peptide Fragments) RN - 0 (Phosphatidylcholines) RN - 0 (Phosphatidylserines) RN - 0 (Proteins) RN - 0 (Spin Labels) RN - 0I3V7S25AW (Myristic Acid) RN - 125267-21-2 (myristoylated alanine-rich C kinase substrate) RN - EC 2.7.11.13 (Protein Kinase C) RN - OF5P57N2ZX (Alanine) SB - IM MH - *Alanine MH - Amino Acid Sequence MH - Binding Sites MH - Electron Spin Resonance Spectroscopy MH - *Intracellular Signaling Peptides and Proteins MH - Liposomes MH - *Membrane Proteins MH - Models, Molecular MH - Molecular Sequence Data MH - Myristic Acid MH - Myristic Acids/metabolism MH - Peptide Fragments/chemical synthesis/chemistry/metabolism MH - Phosphatidylcholines MH - Phosphatidylserines MH - Protein Conformation MH - Protein Kinase C/*chemistry/*metabolism MH - Proteins/*chemistry/*metabolism MH - Spin Labels MH - Substrate Specificity EDAT- 1996/03/05 MHDA- 1996/03/05 00:01 CRDT- 1996/03/05 00:00 AID - 10.1021/bi9521452 [doi] AID - bi9521452 [pii] PST - ppublish SO - Biochemistry. 1996 Mar 5;35(9):2917-25. PMID- 19860484 OWN - NLM STAT- MEDLINE DA - 20091125 DCOM- 20091217 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 47 DP - 2009 Dec 1 TI - A FRET-based method for probing the conformational behavior of an intrinsically disordered repeat domain from Bordetella pertussis adenylate cyclase. PG - 11273-82 LID - 10.1021/bi901447j [doi] AB - A better understanding of the conformational changes exhibited by intrinsically disordered proteins is necessary as we continue to unravel their myriad biological functions. In repeats in toxin (RTX) domains, calcium binding triggers the natively unstructured domain to adopt a beta roll structure. Here we present an in vitro Forster resonance energy transfer (FRET)-based method for the investigation of the conformational behavior of an RTX domain from the Bordetella pertussis adenylate cyclase consisting of nine repeat units. Equilibrium and stopped-flow FRET between fluorescent proteins, attached to the termini of the domain, were measured in an analysis of the end-to-end distance changes in the RTX domain. The method was complemented with circular dichroism spectroscopy, tryptophan fluorescence, and bis-ANS dye binding. High ionic strength was observed to decrease the calcium affinity of the RTX domain. A truncation and single amino acid mutations yielded insights into the structural determinants of beta roll formation. Mutating the conserved Asp residue in one of the nine repeats significantly reduced the affinity of the domains for calcium ions. Removal of the sequences flanking the repeat domain prevented folding, but replacing them with fluorescent proteins restored the conformational behavior, suggesting an entropic stabilization. The FRET-based method is a useful technique that complements other low-resolution techniques for investigating the dynamic conformational behavior of the RTX domain and other intrinsically disordered protein domains. FAU - Szilvay, Geza R AU - Szilvay GR AD - Department of Chemical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, USA. FAU - Blenner, Mark A AU - Blenner MA FAU - Shur, Oren AU - Shur O FAU - Cropek, Donald M AU - Cropek DM FAU - Banta, Scott AU - Banta S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amino Acids) RN - 0 (Cations, Divalent) RN - EC 4.6.1.1 (Adenylate Cyclase) RN - SY7Q814VUP (Calcium) SB - IM MH - Adenylate Cyclase/*chemistry/genetics/metabolism MH - Amino Acids/chemistry/genetics/metabolism MH - Binding Sites MH - Bordetella pertussis/*enzymology MH - Calcium/chemistry/metabolism MH - Cations, Divalent MH - Circular Dichroism MH - Fluorescence Resonance Energy Transfer/*methods MH - Osmolar Concentration MH - Protein Structure, Tertiary EDAT- 2009/10/29 06:00 MHDA- 2009/12/18 06:00 CRDT- 2009/10/29 06:00 AID - 10.1021/bi901447j [doi] PST - ppublish SO - Biochemistry. 2009 Dec 1;48(47):11273-82. doi: 10.1021/bi901447j. PMID- 10625652 OWN - NLM STAT- MEDLINE DA - 20000218 DCOM- 20000218 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 275 IP - 2 DP - 2000 Jan 14 TI - Dehydroepiandrosterone and dihydrotestosterone recognition by human estrogenic 17beta-hydroxysteroid dehydrogenase. C-18/c-19 steroid discrimination and enzyme-induced strain. PG - 1105-11 AB - Steroid hormones share a very similar structure, but they behave distinctly. We present structures of human estrogenic 17beta-hydroxysteroid dehydrogenase (17beta-HSD1) complexes with dehydroepiandrosterone (DHEA) and dihydrotestosterone (DHT), providing the first pictures to date of DHEA and DHT bound to a protein. Comparisons of these structures with that of the enzyme complexed with the most potent estrogen, estradiol, revealed the structural basis and general model for sex hormone recognition and discrimination. Although the binding cavity is almost entirely composed of hydrophobic residues that can make only nonspecific interactions, the arrangement of residues is highly complementary to that of the estrogenic substrate. Relatively small changes in the shape of the steroid hormone can significantly affect the binding affinity and specificity. The K(m) of estrone is more than 1000-fold lower than that of DHEA and the K(m) of estradiol is about 10 times lower than that of DHT. The structures suggest that Leu-149 is the primary contributor to the discrimination of C-19 steroids and estrogens by 17beta-HSD1. The critical role of Leu-149 has been well confirmed by site-directed mutagenesis experiments, as the Leu-149 --> Val variant showed a significantly decreased K(m) for C-19 steroids while losing discrimination between estrogens and C-19 steroids. The electron density of DHEA also revealed a distortion of its 17-ketone toward a beta-oriented form, which approaches the transition-state conformation for DHEA reduction. FAU - Han, Q AU - Han Q AD - Medical Research Council Group in Molecular Endocrinology, CHUL Research Center and Laval University, Ste-Foy, Quebec G1V 4G2, Canada. FAU - Campbell, R L AU - Campbell RL FAU - Gangloff, A AU - Gangloff A FAU - Huang, Y W AU - Huang YW FAU - Lin, S X AU - Lin SX LA - eng SI - PDB/1DHT SI - PDB/3DHE PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Recombinant Proteins) RN - 08J2K08A3Y (Dihydrotestosterone) RN - 459AG36T1B (Dehydroepiandrosterone) RN - 4TI98Z838E (Estradiol) RN - EC 1.1.- (17-Hydroxysteroid Dehydrogenases) RN - EC 1.1.1.51 (3 (or 17)-beta-hydroxysteroid dehydrogenase) SB - IM MH - 17-Hydroxysteroid Dehydrogenases/*chemistry/*metabolism MH - Amino Acid Sequence MH - Conserved Sequence MH - Crystallography, X-Ray MH - Dehydroepiandrosterone/chemistry/*metabolism MH - Dihydrotestosterone/chemistry/*metabolism MH - Estradiol/chemistry/*metabolism MH - Humans MH - Models, Molecular MH - Molecular Conformation MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Protein Conformation MH - Recombinant Proteins/chemistry/metabolism MH - Substrate Specificity EDAT- 2000/01/08 09:00 MHDA- 2000/02/26 09:00 CRDT- 2000/01/08 09:00 PST - ppublish SO - J Biol Chem. 2000 Jan 14;275(2):1105-11. PMID- 22458631 OWN - NLM STAT- MEDLINE DA - 20120615 DCOM- 20121105 LR - 20141016 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 116 IP - 23 DP - 2012 Jun 14 TI - Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Go simulations. PG - 6819-31 LID - 10.1021/jp212614b [doi] AB - Assembly of the bacterial ribosomal small subunit (SSU) begins with the folding of the five-way junction upon interaction with the primary binding protein S4. This complex contains the largest contiguous molecular signature, which is a conserved feature in all bacterial 16S rRNAs. In a previous study, we used all-atom molecular dynamics simulations to demonstrate that the co-evolving signature in the N-terminus of S4 is intrinsically disordered and capable of accelerating the binding process through a fly casting mechanism. In this paper, comparisons between the all-atom MD simulations and FRET experiments identify multiple metastable conformations of the naked five-way junction without the presence of S4. Furthermore, we capture the simultaneous folding and binding of the five-way junction and r-protein S4 by use of a structure-based Go potential implemented within the framework of the all-atom molecular dynamics CHARMM force field. Different folding pathways are observed for the refolding of the five-way junction upon partial binding of S4. Our simulations illustrate the complex nature of RNA folding in the presence of a protein binding partner and provide insight into the role of population shift and the induced fit mechanisms in the protein:RNA folding and binding process. FAU - Chen, Ke AU - Chen K AD - Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. FAU - Eargle, John AU - Eargle J FAU - Lai, Jonathan AU - Lai J FAU - Kim, Hajin AU - Kim H FAU - Abeysirigunawardena, Sanjaya AU - Abeysirigunawardena S FAU - Mayerle, Megan AU - Mayerle M FAU - Woodson, Sarah AU - Woodson S FAU - Ha, Taekjip AU - Ha T FAU - Luthey-Schulten, Zaida AU - Luthey-Schulten Z LA - eng GR - GM-065367/GM/NIGMS NIH HHS/United States GR - R01 GM060819/GM/NIGMS NIH HHS/United States GR - R01 GM065367/GM/NIGMS NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120525 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Protein Subunits) RN - 0 (RNA, Ribosomal, 16S) SB - IM MH - Fluorescence Resonance Energy Transfer MH - *Molecular Dynamics Simulation MH - Protein Conformation MH - Protein Folding MH - Protein Subunits/*chemistry MH - RNA, Ribosomal, 16S/*chemistry PMC - PMC3422213 MID - NIHMS380963 OID - NLM: NIHMS380963 OID - NLM: PMC3422213 EDAT- 2012/03/31 06:00 MHDA- 2012/11/06 06:00 CRDT- 2012/03/31 06:00 PHST- 2012/05/25 [aheadofprint] AID - 10.1021/jp212614b [doi] PST - ppublish SO - J Phys Chem B. 2012 Jun 14;116(23):6819-31. doi: 10.1021/jp212614b. Epub 2012 May 25. PMID- 1515108 OWN - NLM STAT- MEDLINE DA - 19921006 DCOM- 19921006 LR - 20071114 IS - 0108-7681 (Print) IS - 0108-7681 (Linking) VI - 48 ( Pt 2) DP - 1992 Apr 1 TI - Structure determination of turkey egg-white lysozyme using Laue diffraction data. PG - 200-7 AB - The three-dimensional structure of turkey egg-white lysozyme (TEWL) has been solved and refined at 2.5 A resolution using X-ray data collected by the Laue method. This is the first protein structure determination undertaken using Laue diffraction data. A re-examination of the existing structure of TEWL was necessary when attempts to refine an atomic model based on the C alpha positions in the Protein Data Bank (entry 1LZ2) failed. The correct orientation and position of the turkey lysozyme molecules within the crystallographic unit cell were determined by molecular replacement using a refined model of the homologous hen egg-white lysozyme crystal structure. After modification of the model to reflect the differences in amino-acid sequence between the chicken and turkey enzymes, the structure was subjected to crystallographic refinement using the simulated-annealing refinement technique and conventional least-squares refinement. This yielded a final residual of R = 20.7%. This crystal form is of potential interest for time-resolved crystallographic studies since the amino-acid residues involved in catalysis (Asp52 and Glu35) are accessible to solvent and not blocked by crystal contacts. FAU - Howell, P L AU - Howell PL AD - Chemistry Department, Massachusetts Institute of Technology, Cambridge 02139. FAU - Almo, S C AU - Almo SC FAU - Parsons, M R AU - Parsons MR FAU - Hajdu, J AU - Hajdu J FAU - Petsko, G A AU - Petsko GA LA - eng GR - GM26788/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - DENMARK TA - Acta Crystallogr B JT - Acta crystallographica. Section B, Structural science JID - 8403252 RN - EC 3.2.1.17 (Muramidase) SB - IM MH - Animals MH - Female MH - Models, Molecular MH - Muramidase/*chemistry MH - Ovum MH - Protein Conformation MH - Turkeys MH - X-Ray Diffraction/methods EDAT- 1992/04/01 MHDA- 1992/04/01 00:01 CRDT- 1992/04/01 00:00 PST - ppublish SO - Acta Crystallogr B. 1992 Apr 1;48 ( Pt 2):200-7. PMID- 16542678 OWN - NLM STAT- MEDLINE DA - 20060424 DCOM- 20060523 LR - 20131002 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 358 IP - 3 DP - 2006 May 5 TI - Elucidating quantitative stability/flexibility relationships within thioredoxin and its fragments using a distance constraint model. PG - 882-904 AB - Numerous quantitative stability/flexibility relationships, within Escherichia coli thioredoxin (Trx) and its fragments are determined using a minimal distance constraint model (DCM). A one-dimensional free energy landscape as a function of global flexibility reveals Trx to fold in a low-barrier two-state process, with a voluminous transition state. Near the folding transition temperature, the native free energy basin is markedly skewed to allow partial unfolded forms. Under native conditions the skewed shape is lost, and the protein forms a compact structure with some flexibility. Predictions on ten Trx fragments are generally consistent with experimental observations that they are disordered, and that complementary fragments reconstitute. A hierarchical unfolding pathway is uncovered using an exhaustive computational procedure of breaking interfacial cross-linking hydrogen bonds that span over a series of fragment dissociations. The unfolding pathway leads to a stable core structure (residues 22-90), predicted to act as a kinetic trap. Direct connection between degree of rigidity within molecular structure and non-additivity of free energy is demonstrated using a thermodynamic cycle involving fragments and their hierarchical unfolding pathway. Additionally, the model provides insight about molecular cooperativity within Trx in its native state, and about intermediate states populating the folding/unfolding pathways. Native state cooperativity correlation plots highlight several flexibly correlated regions, giving insight into the catalytic mechanism that facilitates access to the active site disulfide bond. Residual native cooperativity correlations are present in the core substructure, suggesting that Trx can function when it is partly unfolded. This natively disordered kinetic trap, interpreted as a molten globule, has a wide temperature range of metastability, and it is identified as the "slow intermediate state" observed in kinetic experiments. These computational results are found to be in overall agreement with a large array of experimental data. FAU - Jacobs, Donald J AU - Jacobs DJ AD - Department of Physics and Optical Science, University of North Carolina, Charlotte, 9201 University City Blvd, Charlotte, NC 28227, USA. djacobs1@email.uncc.edu FAU - Livesay, Dennis R AU - Livesay DR FAU - Hules, Jeremy AU - Hules J FAU - Tasayco, Maria Luisa AU - Tasayco ML LA - eng GR - S06 GM048680/GM/NIGMS NIH HHS/United States GR - S06 GM48680-0952/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20060224 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Peptide Fragments) RN - 52500-60-4 (Thioredoxins) SB - IM MH - Computer Simulation MH - Escherichia coli/chemistry/metabolism MH - *Models, Biological MH - Models, Molecular MH - Peptide Fragments/*chemistry/*metabolism MH - Pliability MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - Temperature MH - Thermodynamics MH - Thioredoxins/*chemistry/*metabolism EDAT- 2006/03/18 09:00 MHDA- 2006/05/24 09:00 CRDT- 2006/03/18 09:00 PHST- 2005/10/31 [received] PHST- 2006/01/17 [revised] PHST- 2006/02/07 [accepted] PHST- 2006/02/24 [aheadofprint] AID - S0022-2836(06)00184-7 [pii] AID - 10.1016/j.jmb.2006.02.015 [doi] PST - ppublish SO - J Mol Biol. 2006 May 5;358(3):882-904. Epub 2006 Feb 24. PMID- 23139418 OWN - NLM STAT- MEDLINE DA - 20121224 DCOM- 20130226 LR - 20141120 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 52 DP - 2012 Dec 21 TI - The stability of the small nucleolar ribonucleoprotein (snoRNP) assembly protein Pih1 in Saccharomyces cerevisiae is modulated by its C terminus. PG - 43205-14 LID - 10.1074/jbc.M112.408849 [doi] AB - Pih1 is an unstable protein and a subunit of the R2TP complex that, in yeast Saccharomyces cerevisiae, also contains the helicases Rvb1, Rvb2, and the Hsp90 cofactor Tah1. Pih1 and the R2TP complex are required for the box C/D small nucleolar ribonucleoprotein (snoRNP) assembly and ribosomal RNA processing. Purified Pih1 tends to aggregate in vitro. Molecular chaperone Hsp90 and its cochaperone Tah1 are required for the stability of Pih1 in vivo. We had shown earlier that the C terminus of Pih1 destabilizes the protein and that the C terminus of Tah1 binds to the Pih1 C terminus to form a stable complex. Here, we analyzed the secondary structure of the Pih1 C terminus and identified two intrinsically disordered regions and five hydrophobic clusters. Site-directed mutagenesis indicated that one predicted intrinsically disordered region IDR2 is involved in Tah1 binding, and that the C terminus of Pih1 contains multiple destabilization or degron elements. Additionally, the Pih1 N-terminal domain, Pih1(1-230), was found to be able to complement the physiological role of full-length Pih1 at 37 degrees C. Pih1(1-230) as well as a shorter Pih1 N-terminal fragment Pih1(1-195) is able to bind Rvb1/Rvb2 heterocomplex. However, the sequence between the two disordered regions in Pih1 significantly enhances the Pih1 N-terminal domain binding to Rvb1/Rvb2. Based on these data, a model of protein-protein interactions within the R2TP complex is proposed. FAU - Paci, Alexandr AU - Paci A AD - Department of Biological Sciences, University of Toronto, Toronto, Ontario M1C 1A4, Canada. FAU - Liu, Xiao Hu AU - Liu XH FAU - Huang, Hao AU - Huang H FAU - Lim, Abelyn AU - Lim A FAU - Houry, Walid A AU - Houry WA FAU - Zhao, Rongmin AU - Zhao R LA - eng GR - MOP-93778/Canadian Institutes of Health Research/Canada GR - TGF-53910/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121108 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Nuclear Proteins) RN - 0 (PIH1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Transcription Factors) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 3.6.1.- (RVB1 protein, S cerevisiae) RN - EC 3.6.1.- (RVB2 protein, S cerevisiae) RN - EC 3.6.4.- (DNA Helicases) SB - IM MH - Adenosine Triphosphatases/chemistry/genetics/metabolism MH - DNA Helicases/chemistry/genetics/metabolism MH - *Models, Molecular MH - Mutagenesis, Site-Directed MH - Nuclear Proteins/*chemistry/genetics/metabolism MH - Protein Binding MH - Protein Stability MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/*chemistry/genetics/metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism MH - Transcription Factors/chemistry/genetics/metabolism PMC - PMC3527908 OID - NLM: PMC3527908 EDAT- 2012/11/10 06:00 MHDA- 2013/02/27 06:00 CRDT- 2012/11/10 06:00 PHST- 2012/11/08 [aheadofprint] AID - M112.408849 [pii] AID - 10.1074/jbc.M112.408849 [doi] PST - ppublish SO - J Biol Chem. 2012 Dec 21;287(52):43205-14. doi: 10.1074/jbc.M112.408849. Epub 2012 Nov 8. PMID- 18834853 OWN - NLM STAT- MEDLINE DA - 20081030 DCOM- 20081204 IS - 1096-0309 (Electronic) IS - 0003-2697 (Linking) VI - 383 IP - 2 DP - 2008 Dec 15 TI - Preserving free thiols of intrinsically disordered tau protein without the use of a reducing agent. PG - 343-5 LID - 10.1016/j.ab.2008.09.022 [doi] AB - Intrinsically disordered proteins (IDPs) represent key mediators in many physiological as well as pathological processes. Solution-exposed cysteines of IDPs are highly reactive and therefore reducing agents are frequently included during their preparation to prevent formation of nonnative disulfides. However, reductants can potentially interfere with subsequent assays performed on the purified IDPs. Herein we report a method for purification of IDP tau in an atmosphere of inert argon, which eliminates the need for reducing agents. We have used this method for preparing several IDP tau isoforms and found it useful in the investigation of monomeric tau toxicity in rat cerebral neurons. FAU - Krajciova, Gabriela AU - Krajciova G AD - Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia. FAU - Skrabana, Rostislav AU - Skrabana R FAU - Filipcik, Peter AU - Filipcik P FAU - Novak, Michal AU - Novak M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080920 PL - United States TA - Anal Biochem JT - Analytical biochemistry JID - 0370535 RN - 0 (Protein Isoforms) RN - 0 (Reducing Agents) RN - 0 (Sulfhydryl Compounds) RN - 0 (tau Proteins) SB - IM MH - Animals MH - Brain/cytology MH - Dimerization MH - Humans MH - Neurons/drug effects MH - Protein Isoforms/chemistry/metabolism/toxicity MH - Protein Structure, Quaternary MH - Rats MH - Reducing Agents MH - Sulfhydryl Compounds/*metabolism MH - tau Proteins/*chemistry/*metabolism/toxicity EDAT- 2008/10/07 09:00 MHDA- 2008/12/17 09:00 CRDT- 2008/10/07 09:00 PHST- 2008/08/12 [received] PHST- 2008/09/12 [revised] PHST- 2008/09/12 [accepted] PHST- 2008/09/20 [aheadofprint] AID - S0003-2697(08)00630-1 [pii] AID - 10.1016/j.ab.2008.09.022 [doi] PST - ppublish SO - Anal Biochem. 2008 Dec 15;383(2):343-5. doi: 10.1016/j.ab.2008.09.022. Epub 2008 Sep 20. PMID- 23822324 OWN - NLM STAT- MEDLINE DA - 20130704 DCOM- 20140213 IS - 1089-7690 (Electronic) IS - 0021-9606 (Linking) VI - 139 IP - 1 DP - 2013 Jul 7 TI - Identification of slow molecular order parameters for Markov model construction. PG - 015102 LID - 10.1063/1.4811489 [doi] AB - A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes via (i) identification of the structural changes involved in these processes and (ii) estimation of the rates or timescales at which these slow processes occur. Most of the approaches to this task, including Markov models, master-equation models, and kinetic network models, start by discretizing the high-dimensional state space and then characterize relaxation processes in terms of the eigenvectors and eigenvalues of a discrete transition matrix. The practical success of such an approach depends very much on the ability to finely discretize the slow order parameters. How can this task be achieved in a high-dimensional configuration space without relying on subjective guesses of the slow order parameters? In this paper, we use the variational principle of conformation dynamics to derive an optimal way of identifying the "slow subspace" of a large set of prior order parameters - either generic internal coordinates or a user-defined set of parameters. Using a variational formulation of conformational dynamics, it is shown that an existing method-the time-lagged independent component analysis-provides the optional solution to this problem. In addition, optimal indicators-order parameters indicating the progress of the slow transitions and thus may serve as reaction coordinates-are readily identified. We demonstrate that the slow subspace is well suited to construct accurate kinetic models of two sets of molecular dynamics simulations, the 6-residue fluorescent peptide MR121-GSGSW and the 30-residue intrinsically disordered peptide kinase inducible domain (KID). The identified optimal indicators reveal the structural changes associated with the slow processes of the molecular system under analysis. FAU - Perez-Hernandez, Guillermo AU - Perez-Hernandez G AD - Department of Mathematics and Computer Science, Freie Universitat Berlin, Berlin, Germany. FAU - Paul, Fabian AU - Paul F FAU - Giorgino, Toni AU - Giorgino T FAU - De Fabritiis, Gianni AU - De Fabritiis G FAU - Noe, Frank AU - Noe F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Chem Phys JT - The Journal of chemical physics JID - 0375360 RN - EC 2.7.- (Phosphotransferases) SB - IM MH - Algorithms MH - Kinetics MH - *Markov Chains MH - *Molecular Conformation MH - *Molecular Dynamics Simulation MH - Phosphotransferases/*chemistry MH - Protein Structure, Tertiary MH - Temperature EDAT- 2013/07/05 06:00 MHDA- 2014/02/14 06:00 CRDT- 2013/07/05 06:00 AID - 10.1063/1.4811489 [doi] PST - ppublish SO - J Chem Phys. 2013 Jul 7;139(1):015102. doi: 10.1063/1.4811489. PMID- 24956595 OWN - NLM STAT- MEDLINE DA - 20140901 DCOM- 20150511 IS - 1769-714X (Electronic) IS - 1286-4579 (Linking) VI - 16 IP - 8 DP - 2014 Aug TI - Virological characterization of HIV-2 vpx gene mutants in various cell systems. PG - 695-701 LID - 10.1016/j.micinf.2014.06.004 [doi] LID - S1286-4579(14)00074-4 [pii] AB - Requirement of intrinsically disordered protein Vpx for HIV-2 replication is cell-type dependent. To define Vpx-dependent conditions, replication ability of HIV-2 vpx mutants was analyzed in various cell lines that differ in cellular type, differentiation state and/or expression level of anti-HIV-1 SAMHD1 degraded by Vpx. Induction of Vpx-sensitive anti-HIV-2 state was not always associated with SAMHD1 expression. Compared with our previous data in lymphocytic cells, growth-defectiveness of the vpx mutants in differentiated THP-1 cells, a newly established multi-cycle infection system, was considerably different. Taken together, our results suggest that Vpx plays cell-type dependent role through its undetermined structure and/or function. CI - Copyright (c) 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved. FAU - Nomaguchi, Masako AU - Nomaguchi M AD - Department of Microbiology, Institute of Health Biosciences, The University of Tokushima Graduate School, 3-18-15 Kuramoto, Tokushima 770-8503, Japan. FAU - Doi, Naoya AU - Doi N AD - Department of Microbiology, Institute of Health Biosciences, The University of Tokushima Graduate School, 3-18-15 Kuramoto, Tokushima 770-8503, Japan; Japanese Foundation for AIDS Prevention, Chiyoda-ku, Tokyo 101-0061, Japan. FAU - Adachi, Akio AU - Adachi A AD - Department of Microbiology, Institute of Health Biosciences, The University of Tokushima Graduate School, 3-18-15 Kuramoto, Tokushima 770-8503, Japan. Electronic address: adachi@basic.med.tokushima-u.ac.jp. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140621 PL - France TA - Microbes Infect JT - Microbes and infection / Institut Pasteur JID - 100883508 RN - 0 (Mutant Proteins) RN - 0 (VPX protein, Human immunodeficiency virus 2) RN - 0 (Viral Regulatory and Accessory Proteins) RN - EC 3.6.5.2 (Monomeric GTP-Binding Proteins) SB - IM MH - Animals MH - Cell Line MH - HIV-2/genetics/immunology/*physiology MH - Host-Pathogen Interactions MH - Humans MH - Macaca fascicularis MH - Monomeric GTP-Binding Proteins/metabolism MH - Mutant Proteins/genetics/metabolism MH - Viral Regulatory and Accessory Proteins/*genetics/*metabolism MH - *Virus Replication OTO - NOTNLM OT - HIV-2 OT - Natural target cells OT - SIVmac OT - Target protein OT - Vpx EDAT- 2014/06/24 06:00 MHDA- 2015/05/12 06:00 CRDT- 2014/06/24 06:00 PHST- 2014/04/02 [received] PHST- 2014/06/13 [revised] PHST- 2014/06/13 [accepted] PHST- 2014/06/21 [aheadofprint] AID - S1286-4579(14)00074-4 [pii] AID - 10.1016/j.micinf.2014.06.004 [doi] PST - ppublish SO - Microbes Infect. 2014 Aug;16(8):695-701. doi: 10.1016/j.micinf.2014.06.004. Epub 2014 Jun 21. id: 200967043 Error occurred: The following PMID is not available: 200967043 PMID- 24956930 OWN - NLM STAT- MEDLINE DA - 20140702 DCOM- 20150420 IS - 1756-0500 (Electronic) IS - 1756-0500 (Linking) VI - 7 DP - 2014 TI - Interaction of myelin basic protein with cytoskeletal and signaling proteins in cultured primary oligodendrocytes and N19 oligodendroglial cells. PG - 387 LID - 10.1186/1756-0500-7-387 [doi] AB - BACKGROUND: The classic myelin basic protein (MBP) isoforms are intrinsically-disordered proteins of 14-21.5 kDa in size arising from the Golli (Gene in the Oligodendrocyte Lineage) gene complex, and are responsible for formation of the multilayered myelin sheath in the central nervous system. The predominant membrane-associated isoform of MBP is not simply a structural component of compact myelin but is highly post-translationally modified and multi-functional, having interactions with numerous proteins such as Ca2+-calmodulin, and with actin, tubulin, and proteins with SH3-domains, which it can tether to a lipid membrane in vitro. It co-localizes with such proteins in primary oligodendrocytes (OLGs) and in early developmental N19-OLGs transfected with fluorescently-tagged MBP. RESULTS: To provide further evidence for MBP associations with these proteins in vivo, we show here that MBP isoforms are co-immunoprecipitated from detergent extracts of primary OLGs together with actin, tubulin, zonula occludens 1 (ZO-1), cortactin, and Fyn kinase. We also carry out live-cell imaging of N19-OLGs co-transfected with fluorescent MBP and actin, and show that when actin filaments re-assemble after recovery from cytochalasin D treatment, MBP and actin are rapidly enriched and co-localized at certain sites at the plasma membrane and in newly-formed membrane ruffles. The MBP and actin distributions change similarly with time, suggesting a specific and dynamic association. CONCLUSIONS: These results provide more direct evidence for association of the predominant 18.5-kDa MBP isoform with these proteins in primary OLGs and in live cells than previously could be inferred from co-localization observations. This study supports further a role for classic MBP isoforms in protein-protein interactions during membrane and cytoskeletal extension and remodeling in OLGs. FAU - Boggs, Joan M AU - Boggs JM AD - Molecular Structure and Function Program, Research Institute, Hospital for Sick Children, 686 Bay St, Toronto, ON M5G 0A4, Canada. jmboggs@sickkids.ca. FAU - Homchaudhuri, Lopamudra AU - Homchaudhuri L FAU - Ranagaraj, Godha AU - Ranagaraj G FAU - Liu, Yuanfang AU - Liu Y FAU - Smith, Graham S T AU - Smith GS FAU - Harauz, George AU - Harauz G LA - eng GR - MOP 86483/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140624 PL - England TA - BMC Res Notes JT - BMC research notes JID - 101462768 RN - 0 (Actins) RN - 0 (Cortactin) RN - 0 (Cytoskeletal Proteins) RN - 0 (Luminescent Proteins) RN - 0 (Myelin Basic Protein) RN - 0 (Nucleic Acid Synthesis Inhibitors) RN - 0 (Protein Isoforms) RN - 0 (Tubulin) RN - 0 (Zonula Occludens-1 Protein) RN - 22144-77-0 (Cytochalasin D) RN - EC 2.7.10.2 (Fyn protein, mouse) RN - EC 2.7.10.2 (Proto-Oncogene Proteins c-fyn) SB - IM MH - Actin Cytoskeleton/drug effects/metabolism MH - Actins/genetics/metabolism MH - Animals MH - Blotting, Western MH - Cell Line MH - Cell Membrane/drug effects/metabolism MH - Cells, Cultured MH - Cortactin/genetics/metabolism MH - Cytochalasin D/pharmacology MH - Cytoskeletal Proteins/genetics/*metabolism MH - Luminescent Proteins/genetics/metabolism MH - Mice MH - Microscopy, Fluorescence MH - Myelin Basic Protein/genetics/*metabolism MH - Nucleic Acid Synthesis Inhibitors/pharmacology MH - Oligodendroglia/cytology/*metabolism MH - Protein Binding MH - Protein Isoforms/genetics/metabolism MH - Proto-Oncogene Proteins c-fyn/genetics/metabolism MH - Rats, Wistar MH - Tubulin/genetics/metabolism MH - Zonula Occludens-1 Protein/genetics/metabolism PMC - PMC4078013 OID - NLM: PMC4078013 EDAT- 2014/06/25 06:00 MHDA- 2015/04/22 06:00 CRDT- 2014/06/25 06:00 PHST- 2014/01/16 [received] PHST- 2014/06/18 [accepted] PHST- 2014/06/24 [aheadofprint] AID - 1756-0500-7-387 [pii] AID - 10.1186/1756-0500-7-387 [doi] PST - epublish SO - BMC Res Notes. 2014 Jun 24;7:387. doi: 10.1186/1756-0500-7-387. PMID- 23679641 OWN - NLM STAT- MEDLINE DA - 20130517 DCOM- 20130802 IS - 1079-7114 (Electronic) IS - 0031-9007 (Linking) VI - 110 IP - 16 DP - 2013 Apr 19 TI - Nucleation process of a fibril precursor in the C-terminal segment of amyloid-beta. PG - 168103 AB - By extended atomistic simulations in explicit solvent and bias-exchange metadynamics, we study the aggregation process of 18 chains of the C-terminal segment of amyloid-beta, an intrinsically disordered protein involved in Alzheimer's disease and prone to form fibrils. Starting from a disordered aggregate, we are able to observe the formation of an ordered nucleus rich in beta sheets. The rate limiting step in the nucleation pathway involves crossing a barrier of approximately 40 kcal/mol and is associated with the formation of a very specific interdigitation of the side chains belonging to different sheets. This structural pattern is different from the one observed experimentally in a microcrystal of the same system, indicating that the structure of a "nascent" fibril may differ from the one of an "extended" fibril. FAU - Baftizadeh, Fahimeh AU - Baftizadeh F AD - SISSA, via Bonomea 265, I-34136 Trieste, Italy. FAU - Pietrucci, Fabio AU - Pietrucci F FAU - Biarnes, Xevi AU - Biarnes X FAU - Laio, Alessandro AU - Laio A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130417 PL - United States TA - Phys Rev Lett JT - Physical review letters JID - 0401141 RN - 0 (Amyloid) RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptide Fragments) SB - IM MH - Amyloid/*chemistry/*metabolism MH - Amyloid beta-Peptides/*chemistry/*metabolism MH - Crystallography, X-Ray MH - Molecular Dynamics Simulation MH - Peptide Fragments/chemistry MH - Protein Structure, Secondary MH - Thermodynamics EDAT- 2013/05/18 06:00 MHDA- 2013/08/03 06:00 CRDT- 2013/05/18 06:00 PHST- 2012/12/04 [received] PHST- 2013/04/17 [aheadofprint] PST - ppublish SO - Phys Rev Lett. 2013 Apr 19;110(16):168103. Epub 2013 Apr 17. PMID- 20643086 OWN - NLM STAT- MEDLINE DA - 20100720 DCOM- 20101027 LR - 20140824 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 2 DP - 2010 Jul 21 TI - Proline-rich salivary proteins have extended conformations. PG - 656-65 LID - 10.1016/j.bpj.2010.04.050 [doi] AB - Three basic proline-rich salivary proteins have been produced through the recombinant route. IB5 is a small basic proline-rich protein that is involved in the binding of plant tannins in the oral cavity. II-1 is a larger protein with a closely related backbone; it is glycosylated, and it is also able to bind plant tannins. II-1 ng has the same polypeptidic backbone as II-1, but it is not glycosylated. Small angle x-ray scattering experiments on dilute solutions of these proteins confirm that they are intrinsically disordered. IB5 and II-1 ng can be described through a chain model including a persistence length and cross section. The measured radii of gyration (Rg=27.9 and 41.0+/-1 A respectively) and largest distances (rmax=110 and 155+/-10 A respectively) show that their average conformations are rather extended. The length of the statistical segment (twice the persistence length) is b=30 A, which is larger than the usual value (18 A-20 A) for unstructured polypeptide chains. These characteristics are presumably related to the presence of polyproline helices within the polypeptidic backbones. For both proteins, the radius of gyration of the chain cross-section is Rc=2.7+/-0.2A. The glycosylated protein II-1 has similar conformations but the presence of large polyoside sidegroups yields the structure of a branched macromolecule with the same hydrophobic backbone and hydrophilic branches. It is proposed that the unusually extended conformations of these proteins in solution facilitate the capture of plant tannins in the oral cavity. CI - Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Boze, Helene AU - Boze H AD - INRA, Montpellier SupAgro, UMR 1083 Sciences pour l'OEnologie, F-34060 Montpellier, France. FAU - Marlin, Therese AU - Marlin T FAU - Durand, Dominique AU - Durand D FAU - Perez, Javier AU - Perez J FAU - Vernhet, Aude AU - Vernhet A FAU - Canon, Francis AU - Canon F FAU - Sarni-Manchado, Pascale AU - Sarni-Manchado P FAU - Cheynier, Veronique AU - Cheynier V FAU - Cabane, Bernard AU - Cabane B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Recombinant Proteins) RN - 0 (Salivary Proline-Rich Proteins) SB - IM MH - Amino Acid Sequence MH - Computational Biology MH - Electrophoresis, Polyacrylamide Gel MH - Glycosylation MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Recombinant Proteins/chemistry MH - Salivary Proline-Rich Proteins/*chemistry MH - Scattering, Small Angle MH - X-Ray Diffraction PMC - PMC2905104 OID - NLM: PMC2905104 EDAT- 2010/07/21 06:00 MHDA- 2010/10/28 06:00 CRDT- 2010/07/21 06:00 PHST- 2010/01/28 [received] PHST- 2010/04/17 [revised] PHST- 2010/04/21 [accepted] AID - S0006-3495(10)00548-5 [pii] AID - 10.1016/j.bpj.2010.04.050 [doi] PST - ppublish SO - Biophys J. 2010 Jul 21;99(2):656-65. doi: 10.1016/j.bpj.2010.04.050. PMID- 24805353 OWN - NLM STAT- MEDLINE DA - 20140508 DCOM- 20150616 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 5 DP - 2014 TI - Calponin-like Chd64 is partly disordered. PG - e96809 LID - 10.1371/journal.pone.0096809 [doi] AB - 20-hydroxyecdysone (20E) and juvenile hormone (JH) signaling pathways interact to regulate insect development. Recently, two proteins, a calponin-like Chd64 and immunophilin FKBP39 have been found to play a pivotal role in the cross-talk between 20E and JH, although the molecular basis of interaction remains unknown. The aim of this work was to identify the structural features that would provide understanding of the role of Chd64 in multiple and dynamic complex that cross-links the signaling pathways. Here, we demonstrate the results of in silico and in vitro analyses of the structural organization of Chd64 from Drosophila melanogaster and its homologue from Tribolium castaneum. Computational analysis predicted the existence of disordered regions on the termini of both proteins, while the central region appeared to be globular, probably corresponding to the calponin homology (CH) domain. In vitro analyses of the hydrodynamic properties of the proteins from analytical size-exclusion chromatography and analytical ultracentrifugation revealed that DmChd64 and TcChd64 had an asymmetrical, elongated shape, which was further confirmed by small angle X-ray scattering (SAXS). The Kratky plot indicated disorderness in both Chd64 proteins, which could possibly be on the protein termini and which would give rise to specific hydrodynamic properties. Disordered tails are often involved in diverse interactions. Therefore, it is highly possible that there are intrinsically disordered regions (IDRs) on both termini of the Chd64 proteins that serve as platforms for multiple interaction with various partners and constitute the foundation for their regulatory function. FAU - Kozlowska, Malgorzata AU - Kozlowska M AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland. FAU - Tarczewska, Aneta AU - Tarczewska A AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland. FAU - Jakob, Michal AU - Jakob M AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland. FAU - Szpotkowski, Kamil AU - Szpotkowski K AD - Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland. FAU - Wojtas, Magdalena AU - Wojtas M AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland. FAU - Rymarczyk, Grzegorz AU - Rymarczyk G AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland. FAU - Ozyhar, Andrzej AU - Ozyhar A AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140507 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Calcium-Binding Proteins) RN - 0 (Chd64 protein, Drosophila) RN - 0 (DNA-Binding Proteins) RN - 0 (Drosophila Proteins) RN - 0 (Juvenile Hormones) RN - 0 (Microfilament Proteins) RN - 0 (calponin) RN - 5289-74-7 (Ecdysterone) SB - IM MH - Animals MH - Calcium-Binding Proteins/*chemistry/genetics MH - Circular Dichroism MH - DNA-Binding Proteins/*chemistry MH - Drosophila Proteins/*chemistry MH - Drosophila melanogaster/chemistry MH - Ecdysterone/*chemistry/metabolism MH - Juvenile Hormones/*chemistry/metabolism MH - Microfilament Proteins/*chemistry/genetics MH - *Protein Conformation MH - Protein Structure, Tertiary MH - Scattering, Small Angle MH - Sequence Analysis, Protein MH - Tribolium/chemistry MH - X-Ray Diffraction PMC - PMC4013081 OID - NLM: PMC4013081 EDAT- 2014/05/09 06:00 MHDA- 2015/06/17 06:00 CRDT- 2014/05/09 06:00 PHST- 2014 [ecollection] PHST- 2014/01/14 [received] PHST- 2014/04/11 [accepted] PHST- 2014/05/07 [epublish] AID - 10.1371/journal.pone.0096809 [doi] AID - PONE-D-14-01896 [pii] PST - epublish SO - PLoS One. 2014 May 7;9(5):e96809. doi: 10.1371/journal.pone.0096809. eCollection 2014. PMID- 23883288 OWN - NLM STAT- MEDLINE DA - 20130821 DCOM- 20140806 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 33 DP - 2013 Aug 21 TI - Precision vs flexibility in GPCR signaling. PG - 12305-12 LID - 10.1021/ja405133k [doi] AB - The G protein coupled receptor (GPCR) rhodopsin activates the heterotrimeric G protein transducin (Gt) to transmit the light signal into retinal rod cells. The rhodopsin activity is virtually zero in the dark and jumps by more than one billion fold after photon capture. Such perfect switching implies both high fidelity and speed of rhodopsin/Gt coupling. We employed Fourier transform infrared (FTIR) spectroscopy and supporting all-atom molecular dynamics (MD) simulations to study the conformational diversity of rhodopsin in membrane environment and extend the static picture provided by the available crystal structures. The FTIR results show how the equilibria of inactive and active protein states of the receptor (so-called metarhodopsin states) are regulated by the highly conserved E(D)RY and Yx7K(R) motives. The MD data identify an intrinsically unstructured cytoplasmic loop region connecting transmembrane helices 5 and 6 (CL3) and show how each protein state is split into conformational substates. The C-termini of the Gtgamma- and Gtalpha-subunits (GalphaCT and GgammaCT), prepared as synthetic peptides, are likely to bind sequentially and at different sites of the active receptor. The peptides have different effects on the receptor conformation. While GgammaCT stabilizes the active states but preserves CL3 flexibility, GalphaCT selectively stabilizes a single conformational substate with largely helical CL3, as it is found in crystal structures. Based on these results we propose a mechanism for the fast and precise signal transfer from rhodopsin to Gt, which assumes a stepwise and mutual reduction of their conformational space. The mechanism relies on conserved amino acids and may therefore underlie GPCR/G protein coupling in general. FAU - Elgeti, Matthias AU - Elgeti M AD - Institut fur Medizinische Physik und Biophysik (CC2), Charite-Universitatsmedizin Berlin, Chariteplatz 1, 10117 Berlin, Germany. matthias.elgeti@charite.de FAU - Rose, Alexander S AU - Rose AS FAU - Bartl, Franz J AU - Bartl FJ FAU - Hildebrand, Peter W AU - Hildebrand PW FAU - Hofmann, Klaus-Peter AU - Hofmann KP FAU - Heck, Martin AU - Heck M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130809 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Peptide Fragments) RN - 9009-81-8 (Rhodopsin) RN - EC 3.6.1.- (Transducin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Cattle MH - Molecular Dynamics Simulation MH - Mutagenesis, Site-Directed MH - Mutation MH - Peptide Fragments/chemistry/metabolism/pharmacology MH - Protein Conformation MH - Rhodopsin/agonists/chemistry/genetics/*metabolism MH - *Signal Transduction MH - Spectroscopy, Fourier Transform Infrared MH - Transducin/chemistry EDAT- 2013/07/26 06:00 MHDA- 2014/08/07 06:00 CRDT- 2013/07/26 06:00 PHST- 2013/08/09 [aheadofprint] AID - 10.1021/ja405133k [doi] PST - ppublish SO - J Am Chem Soc. 2013 Aug 21;135(33):12305-12. doi: 10.1021/ja405133k. Epub 2013 Aug 9. PMID- 20516199 OWN - NLM STAT- MEDLINE DA - 20100602 DCOM- 20100608 LR - 20140827 IS - 1549-5477 (Electronic) IS - 0890-9369 (Linking) VI - 24 IP - 11 DP - 2010 Jun 1 TI - Regulation of ribonucleotide reductase by Spd1 involves multiple mechanisms. PG - 1145-59 LID - 10.1101/gad.561910 [doi] AB - The correct levels of deoxyribonucleotide triphosphates and their relative abundance are important to maintain genomic integrity. Ribonucleotide reductase (RNR) regulation is complex and multifaceted. RNR is regulated allosterically by two nucleotide-binding sites, by transcriptional control, and by small inhibitory proteins that associate with the R1 catalytic subunit. In addition, the subcellular localization of the R2 subunit is regulated through the cell cycle and in response to DNA damage. We show that the fission yeast small RNR inhibitor Spd1 is intrinsically disordered and regulates R2 nuclear import, as predicted by its relationship to Saccharomyces cerevisiae Dif1. We demonstrate that Spd1 can interact with both R1 and R2, and show that the major restraint of RNR in vivo by Spd1 is unrelated to R2 subcellular localization. Finally, we identify a new behavior for RNR complexes that potentially provides yet another mechanism to regulate dNTP synthesis via modulation of RNR complex architecture. FAU - Nestoras, Konstantinos AU - Nestoras K AD - Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN19RQ, United Kingdom. FAU - Mohammed, Asma Hadi AU - Mohammed AH FAU - Schreurs, Ann-Sofie AU - Schreurs AS FAU - Fleck, Oliver AU - Fleck O FAU - Watson, Adam T AU - Watson AT FAU - Poitelea, Marius AU - Poitelea M FAU - O'Shea, Charlotte AU - O'Shea C FAU - Chahwan, Charly AU - Chahwan C FAU - Holmberg, Christian AU - Holmberg C FAU - Kragelund, Birthe B AU - Kragelund BB FAU - Nielsen, Olaf AU - Nielsen O FAU - Osborne, Mark AU - Osborne M FAU - Carr, Antony M AU - Carr AM FAU - Liu, Cong AU - Liu C LA - eng GR - 10722/Cancer Research UK/United Kingdom GR - G0600233/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Genes Dev JT - Genes & development JID - 8711660 RN - 0 (Cell Cycle Proteins) RN - 0 (Protein Subunits) RN - 0 (Schizosaccharomyces pombe Proteins) RN - 0 (Spd1 protein, S pombe) RN - 0 (cdc22 protein, S pombe) RN - EC 1.17.4.- (Ribonucleotide Reductases) RN - EC 1.17.4.1 (SUC22 protein, S pombe) RN - OF5P57N2ZX (Alanine) SB - IM MH - Active Transport, Cell Nucleus/physiology MH - Alanine/metabolism MH - Cell Cycle Proteins/genetics/*metabolism MH - *Gene Expression Regulation, Fungal MH - Mutagenesis MH - Protein Subunits/metabolism MH - Ribonucleotide Reductases/*metabolism MH - Schizosaccharomyces/genetics/*metabolism MH - Schizosaccharomyces pombe Proteins/genetics/*metabolism PMC - PMC2878652 OID - NLM: PMC2878652 EDAT- 2010/06/03 06:00 MHDA- 2010/06/09 06:00 CRDT- 2010/06/03 06:00 AID - 24/11/1145 [pii] AID - 10.1101/gad.561910 [doi] PST - ppublish SO - Genes Dev. 2010 Jun 1;24(11):1145-59. doi: 10.1101/gad.561910. PMID- 23516402 OWN - NLM STAT- MEDLINE DA - 20130321 DCOM- 20130912 LR - 20141116 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 3 DP - 2013 TI - Actinidia DRM1--an intrinsically disordered protein whose mRNA expression is inversely correlated with spring budbreak in kiwifruit. PG - e57354 LID - 10.1371/journal.pone.0057354 [doi] AB - Intrinsically disordered proteins (IDPs) are a relatively recently defined class of proteins which, under native conditions, lack a unique tertiary structure whilst maintaining essential biological functions. Functional classification of IDPs have implicated such proteins as being involved in various physiological processes including transcription and translation regulation, signal transduction and protein modification. Actinidia DRM1 (Ade DORMANCY ASSOCIATED GENE 1), represents a robust dormancy marker whose mRNA transcript expression exhibits a strong inverse correlation with the onset of growth following periods of physiological dormancy. Bioinformatic analyses suggest that DRM1 is plant specific and highly conserved at both the nucleotide and protein levels. It is predicted to be an intrinsically disordered protein with two distinct highly conserved domains. Several Actinidia DRM1 homologues, which align into two distinct Actinidia-specific families, Type I and Type II, have been identified. No candidates for the Arabidopsis DRM1-Homologue (AtDRM2) an additional family member, has been identified in Actinidia. FAU - Wood, Marion AU - Wood M AD - Genomics Research, The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand. marion.wood@plantandfood.co.nz FAU - Rae, Georgina M AU - Rae GM FAU - Wu, Rong-Mei AU - Wu RM FAU - Walton, Eric F AU - Walton EF FAU - Xue, Bin AU - Xue B FAU - Hellens, Roger P AU - Hellens RP FAU - Uversky, Vladimir N AU - Uversky VN LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130313 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Plant Proteins) RN - 0 (RNA, Messenger) SB - IM MH - Actinidia/classification/*genetics/*metabolism MH - Amino Acid Sequence MH - Computational Biology/methods MH - *Fruit MH - Gene Expression Regulation, Plant MH - *Genetic Association Studies MH - Molecular Sequence Data MH - Phylogeny MH - Plant Proteins/chemistry/*genetics/metabolism MH - Protein Structure, Secondary MH - *RNA, Messenger MH - Seasons MH - Sequence Alignment PMC - PMC3596386 OID - NLM: PMC3596386 EDAT- 2013/03/22 06:00 MHDA- 2013/09/13 06:00 CRDT- 2013/03/22 06:00 PHST- 2012/10/28 [received] PHST- 2013/01/21 [accepted] PHST- 2013/03/13 [epublish] AID - 10.1371/journal.pone.0057354 [doi] AID - PONE-D-12-33226 [pii] PST - ppublish SO - PLoS One. 2013;8(3):e57354. doi: 10.1371/journal.pone.0057354. Epub 2013 Mar 13. PMID- 23978162 OWN - NLM STAT- MEDLINE DA - 20140204 DCOM- 20141104 LR - 20141112 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 117 IP - 39 DP - 2013 Oct 3 TI - Insight into alpha-synuclein plasticity and misfolding from differential micelle binding. PG - 11448-59 LID - 10.1021/jp402589x [doi] AB - Misfolded species of the 140-residue protein alpha-synuclein (alphaS) are implicated in the demise of dopaminergic neurons, resulting in fatal neurodegeneration. The intrinsically unstructured protein binds curved synaptic vesicle membranes in helical conformations but misfolds into amyloid fibrils via beta-sheet interactions. Breaks in helical alphaS conformation may offer a pathway to transition from helical to sheet conformation. Here, we explore the evolution of broken alphaS helix conformations formed in complex with SDS and SLAS micelles by molecular dynamics simulations. The population distribution of experimentally observed alphaS conformations is related to the spatial concentration of intrinsic micelle shape perturbations. For the success of micelle-induced alphaS folding, we posit the length of the first helical segment formed, which controls micelle ellipticity, to be a key determinant. The degree of micelle curvature relates to the arrangement and segmental motions of helical secondary structure elements. A criterion for assessing the reproduction of such intermediate time scale protein dynamics is introduced by comparing the sampling of experimental and simulated spin label distributions. Finally, at the sites of breaks in the elongated, marginally stable alphaS helix, vulnerability to forming a transient, intramolecular beta-sheet is identified. Upon subsequent intermolecular beta-sheet pairing, pathological alphaS amyloid formation from initial helical conformation is thus achievable. FAU - Mazumder, Parichita AU - Mazumder P AD - Department of Biochemistry & Molecular Biology, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , 1501 San Pablo Street, Los Angeles, California 90033, United States. FAU - Suk, Jae-Eun AU - Suk JE FAU - Ulmer, Tobias S AU - Ulmer TS LA - eng GR - HL089726/HL/NHLBI NIH HHS/United States GR - R01 HL089726/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130912 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Micelles) RN - 0 (Spin Labels) RN - 0 (alpha-Synuclein) RN - 368GB5141J (Sodium Dodecyl Sulfate) SB - IM MH - Diffusion MH - *Micelles MH - Molecular Dynamics Simulation MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Sodium Dodecyl Sulfate/chemistry MH - Spin Labels MH - Time Factors MH - alpha-Synuclein/*chemistry PMC - PMC3946565 MID - NIHMS522435 OID - NLM: NIHMS522435 OID - NLM: PMC3946565 EDAT- 2013/08/28 06:00 MHDA- 2014/11/05 06:00 CRDT- 2013/08/28 06:00 PHST- 2013/09/12 [aheadofprint] AID - 10.1021/jp402589x [doi] PST - ppublish SO - J Phys Chem B. 2013 Oct 3;117(39):11448-59. doi: 10.1021/jp402589x. Epub 2013 Sep 12. PMID- 22915553 OWN - NLM STAT- MEDLINE DA - 20121018 DCOM- 20130304 LR - 20141105 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 21 IP - 11 DP - 2012 Nov TI - Three intrinsically unstructured mussel adhesive proteins, mfp-1, mfp-2, and mfp-3: analysis by circular dichroism. PG - 1689-95 LID - 10.1002/pro.2147 [doi] AB - Mussel foot proteins (mfps) mediate fouling by the byssal holdfast and have been extensively investigated as models for versatile polymer-mediated underwater adhesion and coatings. However, insights into the structural properties of mfps have lagged far behind the nanomechanical advances, owing in part to the inability of these proteins to crystallize as well as their limited solubility. Here, solution secondary structures of mfp-1, mfp-2, and mfp-3, localized in the mussel byssal cuticle, adhesive plaque, and plaque-substratum interface, respectively, were investigated using circular dichroism. All three have significant extended coil solution structure, but two, mfp-1 and mfp-2, appear to have punctuated regions of structure separated by unstructured domains. Apart from its punctuated distribution, the structure in mfp-1 resembles other structural proteins such as collagen and plant cell-wall proteins with prominent polyproline II helical structure. As in collagen, PP II structure of mfp-1 is incrementally disrupted by increasing the temperature and by raising pH. However, no recognizable change in mfp-1's PP II structure was evident with the addition with Ca(2)(+) and Fe(3)(+). In contrast, mfp-2 exhibits Ca(2)(+)- and disulfide-stabilized epidermal growth factor-like domains separated by unstructured sequence. Mfp-2 showed calcium-binding ability. Bound calcium in mfp-2 was not removed by chelation at pH 5.5, but it was released upon reduction of disulfide bonds. Mfp-3, in contrast, appears to consist largely of unstructured extended coils. CI - Copyright (c) 2012 The Protein Society. FAU - Hwang, Dong Soo AU - Hwang DS AD - POSTECH Ocean Science and Technology Institute and School of Environmental Science and Engineering, Pohang University of Science and Technology, Hyoja-Dong, Nam-Gu, Pohang, Gyeongbuk 790-784, Korea. dshwang@postech.ac.kr FAU - Waite, J Herbert AU - Waite JH LA - eng PT - Journal Article DEP - 20120925 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Disulfides) RN - 0 (Proteins) RN - 0 (adhesive protein, mussel) RN - E1UOL152H7 (Iron) RN - SY7Q814VUP (Calcium) SB - IM MH - Animals MH - Calcium MH - Circular Dichroism MH - Disulfides MH - Hydrogen-Ion Concentration MH - Iron MH - Mytilus/*chemistry MH - Protein Conformation MH - Protein Stability MH - Proteins/*chemistry MH - Temperature PMC - PMC3527705 OID - NLM: PMC3527705 EDAT- 2012/08/24 06:00 MHDA- 2013/03/05 06:00 CRDT- 2012/08/24 06:00 PHST- 2012/07/09 [received] PHST- 2012/08/15 [revised] PHST- 2012/08/16 [accepted] PHST- 2012/09/25 [aheadofprint] AID - 10.1002/pro.2147 [doi] PST - ppublish SO - Protein Sci. 2012 Nov;21(11):1689-95. doi: 10.1002/pro.2147. Epub 2012 Sep 25. PMID- 22915551 OWN - NLM STAT- MEDLINE DA - 20121018 DCOM- 20130304 LR - 20141105 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 21 IP - 11 DP - 2012 Nov TI - Thermal unfolding of the N-terminal region of p53 monitored by circular dichroism spectroscopy. PG - 1682-8 LID - 10.1002/pro.2146 [doi] AB - It has been estimated that 30% of eukaryotic protein and 70% of transcription factors are intrinsically disordered (ID). The biochemical significance of proteins that lack stable tertiary structure, however, is not clearly understood, largely owing to an inability to assign well-defined structures to specific biological tasks. In an attempt to investigate the structural character of ID protein, we have measured the circular dichroism spectrum of the N-terminal region of p53 over a range of temperatures and solution conditions. p53 is a well-studied transcription factor that has a proline-rich N-terminal ID region containing two activation domains. High proline content is a property commonly associated with ID, and thus p53 may be a good model system for investigating the biochemical importance of ID. The spectra presented here suggest that the N-terminal region of p53 may adopt an ordered structure under physiological conditions and that this structure can be thermally unfolded in an apparent two-state manner. The midpoint temperature for this thermal unfolding of the N-terminal region of p53 was at the near-physiological temperature of 39 degrees C, suggesting the possibility of a physiological role for the observed structural equilibrium. CI - Copyright (c) 2012 The Protein Society. FAU - Schaub, Leasha J AU - Schaub LJ AD - Department of Chemistry and Biochemistry, Texas State University-San Marcos, San Marcos, Texas 78666, USA. FAU - Campbell, James C AU - Campbell JC FAU - Whitten, Steven T AU - Whitten ST LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120925 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Recombinant Proteins) RN - 0 (TP53 protein, human) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Circular Dichroism MH - Escherichia coli/genetics MH - Humans MH - Protein Stability MH - Protein Unfolding MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Temperature MH - Tumor Suppressor Protein p53/*chemistry/genetics/metabolism PMC - PMC3527704 OID - NLM: PMC3527704 EDAT- 2012/08/24 06:00 MHDA- 2013/03/05 06:00 CRDT- 2012/08/24 06:00 PHST- 2012/07/16 [received] PHST- 2012/08/14 [revised] PHST- 2012/08/20 [accepted] PHST- 2012/09/25 [aheadofprint] AID - 10.1002/pro.2146 [doi] PST - ppublish SO - Protein Sci. 2012 Nov;21(11):1682-8. doi: 10.1002/pro.2146. Epub 2012 Sep 25. PMID- 19647513 OWN - NLM STAT- MEDLINE DA - 20090803 DCOM- 20090821 IS - 1097-4164 (Electronic) IS - 1097-2765 (Linking) VI - 35 IP - 2 DP - 2009 Jul 31 TI - Rejuvenation of CcdB-poisoned gyrase by an intrinsically disordered protein domain. PG - 154-63 LID - 10.1016/j.molcel.2009.05.025 [doi] AB - Toxin-antitoxin modules are small regulatory circuits that ensure survival of bacterial populations under challenging environmental conditions. The ccd toxin-antitoxin module on the F plasmid codes for the toxin CcdB and its antitoxin CcdA. CcdB poisons gyrase while CcdA actively dissociates CcdB:gyrase complexes in a process called rejuvenation. The CcdA:CcdB ratio modulates autorepression of the ccd operon. The mechanisms behind both rejuvenation and regulation of expression are poorly understood. We show that CcdA binds consecutively to two partially overlapping sites on CcdB, which differ in affinity by six orders of magnitude. The first, picomolar affinity interaction triggers a conformational change in CcdB that initiates the dissociation of CcdB:gyrase complexes by an allosteric segmental binding mechanism. The second, micromolar affinity binding event regulates expression of the ccd operon. Both functions of CcdA, rejuvenation and autoregulation, are mechanistically intertwined and depend crucially on the intrinsically disordered nature of the CcdA C-terminal domain. FAU - De Jonge, Natalie AU - De Jonge N AD - Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. FAU - Garcia-Pino, Abel AU - Garcia-Pino A FAU - Buts, Lieven AU - Buts L FAU - Haesaerts, Sarah AU - Haesaerts S FAU - Charlier, Daniel AU - Charlier D FAU - Zangger, Klaus AU - Zangger K FAU - Wyns, Lode AU - Wyns L FAU - De Greve, Henri AU - De Greve H FAU - Loris, Remy AU - Loris R LA - eng SI - PDB/3G7Z SI - PDB/3HPW PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Bacterial Proteins) RN - 0 (Bacterial Toxins) RN - 0 (CcdA protein, Bacteria) RN - 0 (CcdB protein, Plasmid F) RN - 0 (Escherichia coli Proteins) SB - IM MH - Bacterial Proteins/chemistry/genetics/*metabolism/*physiology MH - Bacterial Toxins/genetics/*metabolism MH - Binding Sites MH - Crystallography, X-Ray MH - Dimerization MH - Escherichia coli/genetics/*metabolism MH - Escherichia coli Proteins/chemistry/genetics/*physiology MH - Gene Expression Regulation, Bacterial MH - Homeostasis MH - Models, Molecular MH - Operon MH - Protein Structure, Tertiary EDAT- 2009/08/04 09:00 MHDA- 2009/08/22 09:00 CRDT- 2009/08/04 09:00 PHST- 2008/11/06 [received] PHST- 2009/04/14 [revised] PHST- 2009/05/21 [accepted] AID - S1097-2765(09)00386-4 [pii] AID - 10.1016/j.molcel.2009.05.025 [doi] PST - ppublish SO - Mol Cell. 2009 Jul 31;35(2):154-63. doi: 10.1016/j.molcel.2009.05.025. PMID- 20096704 OWN - NLM STAT- MEDLINE DA - 20100308 DCOM- 20100325 LR - 20131121 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 397 IP - 2 DP - 2010 Mar 26 TI - Characterization of the regions involved in the calcium-induced folding of the intrinsically disordered RTX motifs from the bordetella pertussis adenylate cyclase toxin. PG - 534-49 LID - 10.1016/j.jmb.2010.01.031 [doi] AB - Repeat in toxin (RTX) motifs are nonapeptide sequences found among numerous virulence factors of Gram-negative bacteria. In the presence of calcium, these RTX motifs are able to fold into an idiosyncratic structure called the parallel beta-roll. The adenylate cyclase toxin (CyaA) produced by Bordetella pertussis, the causative agent of whooping cough, is one of the best-characterized RTX cytolysins. CyaA contains a C-terminal receptor domain (RD) that mediates toxin binding to the eukaryotic cell receptor. The receptor-binding domain is composed of about forty RTX motifs organized in five successive blocks (I to V). The RTX blocks are separated by non-RTX flanking regions of variable lengths. It has been shown that block V with its N- and C-terminal flanking regions constitutes an autonomous subdomain required for the toxicity of CyaA. Here, we investigated the calcium-induced biophysical changes of this subdomain to identify the respective contributions of the flanking regions to the folding process of the RTX motifs. We showed that the RTX polypeptides, in the absence of calcium, exhibited the hallmarks of intrinsically disordered proteins and that the C-terminal flanking region was critical for the calcium-dependent folding of the RTX polypeptides, while the N-terminal flanking region was not involved. Furthermore, the secondary and tertiary structures were acquired concomitantly upon cooperative binding of several calcium ions. This suggests that the RTX polypeptide folding is a two-state reaction, from a calcium-free unfolded state to a folded and compact conformation, in which the calcium-bound RTX motifs adopt a beta-roll structure. The relevance of these results to the toxin physiology, in particular to its secretion, is discussed. FAU - Sotomayor Perez, Ana-Cristina AU - Sotomayor Perez AC AD - Unite de Biochimie des Interactions Macromoleculaires, Departement de Biologie Structurale et Chimie, CNRS URA 2185, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France. FAU - Karst, Johanna C AU - Karst JC FAU - Davi, Marilyne AU - Davi M FAU - Guijarro, J Inaki AU - Guijarro JI FAU - Ladant, Daniel AU - Ladant D FAU - Chenal, Alexandre AU - Chenal A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100122 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Adenylate Cyclase Toxin) RN - SY7Q814VUP (Calcium) SB - IM MH - Adenylate Cyclase Toxin/*chemistry/*metabolism MH - Amino Acid Motifs MH - Bordetella pertussis/chemistry/*enzymology MH - Calcium/*metabolism MH - Circular Dichroism MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Repetitive Sequences, Amino Acid MH - Spectrum Analysis EDAT- 2010/01/26 06:00 MHDA- 2010/03/26 06:00 CRDT- 2010/01/26 06:00 PHST- 2009/09/11 [received] PHST- 2009/12/22 [revised] PHST- 2010/01/12 [accepted] PHST- 2010/01/22 [aheadofprint] AID - S0022-2836(10)00077-X [pii] AID - 10.1016/j.jmb.2010.01.031 [doi] PST - ppublish SO - J Mol Biol. 2010 Mar 26;397(2):534-49. doi: 10.1016/j.jmb.2010.01.031. Epub 2010 Jan 22. PMID- 14654695 OWN - NLM STAT- MEDLINE DA - 20031205 DCOM- 20040114 LR - 20140610 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 31 IP - 24 DP - 2003 Dec 15 TI - The linker histone homolog Hho1p from Saccharomyces cerevisiae represents a winged helix-turn-helix fold as determined by NMR spectroscopy. PG - 7199-207 AB - Hho1p is assumed to serve as a linker histone in Saccharomyces cerevisiae and, notably, it possesses two putative globular domains, designated HD1 (residues 41-118) and HD2 (residues 171-252), that are homologous to histone H5 from chicken erythrocytes. We have determined the three-dimensional structure of globular domain HD1 with high precision by heteronuclear magnetic resonance spectroscopy. The structure had a winged helix-turn-helix motif composed of an alphabetaalphaalphabetabeta fold and closely resembled the structure of the globular domain of histone H5. Interestingly, the second globular domain, HD2, in Hho1p was unstructured under physiological conditions. Gel mobility assay demonstrated that Hho1p preferentially binds to supercoiled DNA over linearized DNA. Furthermore, NMR analysis of the complex of a deletion mutant protein (residues 1-118) of Hho1p with a linear DNA duplex revealed that four regions within the globular domain HD1 are involved in the DNA binding. The above results suggested that Hho1p possesses properties similar to those of linker histones in higher eukaryotes in terms of the structure and binding preference towards supercoiled DNA. FAU - Ono, Katsuki AU - Ono K AD - School of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan. FAU - Kusano, Osamu AU - Kusano O FAU - Shimotakahara, Sakurako AU - Shimotakahara S FAU - Shimizu, Mitsuhiro AU - Shimizu M FAU - Yamazaki, Toshimasa AU - Yamazaki T FAU - Shindo, Heisaburo AU - Shindo H LA - eng SI - PDB/1UHM PT - Journal Article PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (DNA, Superhelical) RN - 0 (HHO1 protein, S cerevisiae) RN - 0 (Histones) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - DNA, Superhelical/chemistry/metabolism MH - *Helix-Turn-Helix Motifs MH - Histones/*chemistry/genetics/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - *Nuclear Magnetic Resonance, Biomolecular MH - Pliability MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/*chemistry MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism MH - Sequence Deletion/genetics PMC - PMC291871 OID - NLM: PMC291871 EDAT- 2003/12/05 05:00 MHDA- 2004/01/15 05:00 CRDT- 2003/12/05 05:00 PST - ppublish SO - Nucleic Acids Res. 2003 Dec 15;31(24):7199-207. PMID- 18771286 OWN - NLM STAT- MEDLINE DA - 20080924 DCOM- 20081201 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 39 DP - 2008 Sep 30 TI - Domain conformation of tau protein studied by solution small-angle X-ray scattering. PG - 10345-53 LID - 10.1021/bi800900d [doi] AB - Tau is one of the two main proteins involved in the pathology of Alzheimer's disease via formation of beta-sheet rich intracellular aggregates named paired helical filaments (PHFs). Given that tau is a natively unfolded protein with no folded core (even upon binding to physiological partners such as microtubules), its structural analysis by high-resolution techniques has been difficult. In this study, employing solution small-angle X-ray scattering from the full length isoforms and from a variety of deletion and point mutants the conformation of tau in solution is structurally characterized. A recently developed ensemble optimization method was employed to generate pools of random models and to select ensembles of coexisting conformations, which fitted simultaneously the scattering data from the full length protein and deletion mutants. The analysis of the structural properties of these selected ensembles allowed us to extract information about residual structure in different domains of the native protein. The short deletion mutants containing the repeat domain (considered the core constituent of the PHFs) are significantly more extended than random coils, suggesting an extended conformation of the repeat domain. The longer tau constructs are comparable in size with the random coils, pointing to long-range contacts between the N- and C-termini compensating for the extension of the repeat domain. Moreover, most of the aggregation-promoting mutants did not show major differences in structure from their wild-type counterparts, indicating that their increased pathological effect is triggered only after an aggregation core has been formed. FAU - Mylonas, Efstratios AU - Mylonas E AD - European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany. FAU - Hascher, Antje AU - Hascher A FAU - Bernado, Pau AU - Bernado P FAU - Blackledge, Martin AU - Blackledge M FAU - Mandelkow, Eckhard AU - Mandelkow E FAU - Svergun, Dmitri I AU - Svergun DI LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080905 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (MAPT protein, human) RN - 0 (Protein Isoforms) RN - 0 (Solutions) RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/pathology MH - Humans MH - Models, Molecular MH - Protein Conformation MH - Protein Folding MH - Protein Isoforms/chemistry MH - Solutions MH - X-Ray Diffraction MH - tau Proteins/*chemistry/genetics EDAT- 2008/09/06 09:00 MHDA- 2008/12/17 09:00 CRDT- 2008/09/06 09:00 PHST- 2008/09/05 [aheadofprint] AID - 10.1021/bi800900d [doi] PST - ppublish SO - Biochemistry. 2008 Sep 30;47(39):10345-53. doi: 10.1021/bi800900d. Epub 2008 Sep 5. PMID- 19919104 OWN - NLM STAT- MEDLINE DA - 20091216 DCOM- 20100217 LR - 20140917 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 50 DP - 2009 Dec 22 TI - Dss1 regulates interaction of Brh2 with DNA. PG - 11929-38 LID - 10.1021/bi901775j [doi] AB - Brh2, the BRCA2 homologue in Ustilago maydis, plays a crucial role in homologous recombination by controlling Rad51. In turn, Brh2 is governed by Dss1, an intrinsically disordered protein that forms a tight complex with the C-terminal region of Brh2. This region of the protein associating with Dss1 is highly conserved in sequence and by comparison with mammalian BRCA2 corresponds to a part of the DNA binding domain with characteristic OB folds. The N-terminal region of Brh2 harbors a less-defined but powerful DNA binding site, the activity of which is revealed upon deletion of the C-terminal region. Full-length Brh2 complexed with Dss1 binds DNA slowly, while the N-terminal fragment binds quickly. The DNA binding activity of full-length Brh2 appears to correlate with dissociation of Dss1. Addition of Dss1 to the heterotypic Brh2-Dss1 complex attenuates DNA binding activity, but not by direct competition for the N-terminal DNA binding site. Conversely, the Brh2-Dss1 complex dissociates more quickly when DNA is present. These findings suggest a model in which binding of Brh2 to DNA is subject to allosteric regulation by Dss1. FAU - Zhou, Qingwen AU - Zhou Q AD - Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA. FAU - Mazloum, Nayef AU - Mazloum N FAU - Mao, Ninghui AU - Mao N FAU - Kojic, Milorad AU - Kojic M FAU - Holloman, William K AU - Holloman WK LA - eng GR - GM42482/GM/NIGMS NIH HHS/United States GR - GM79859/GM/NIGMS NIH HHS/United States GR - R01 GM042482/GM/NIGMS NIH HHS/United States GR - R01 GM042482-18/GM/NIGMS NIH HHS/United States GR - R01 GM042482-19/GM/NIGMS NIH HHS/United States GR - R01 GM079859/GM/NIGMS NIH HHS/United States GR - R01 GM079859-02/GM/NIGMS NIH HHS/United States GR - R01 GM079859-03/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (BRCA2 Protein) RN - 0 (BRCA2 protein, mouse) RN - 0 (DNA, Fungal) RN - 0 (DNA-Binding Proteins) RN - 0 (Fungal Proteins) RN - 0 (Peptide Fragments) RN - EC 2.7.7.- (Rad51 Recombinase) SB - IM MH - BRCA2 Protein/chemistry MH - DNA Damage/genetics MH - DNA Repair/genetics MH - DNA, Fungal/genetics/*metabolism MH - DNA-Binding Proteins/genetics/*metabolism MH - Fungal Proteins/*chemistry/genetics MH - Peptide Fragments/genetics/metabolism MH - Rad51 Recombinase/genetics/metabolism MH - Recombination, Genetic MH - Ustilago/*genetics PMC - PMC2795026 MID - NIHMS161429 OID - NLM: NIHMS161429 OID - NLM: PMC2795026 EDAT- 2009/11/19 06:00 MHDA- 2010/02/18 06:00 CRDT- 2009/11/19 06:00 AID - 10.1021/bi901775j [doi] PST - ppublish SO - Biochemistry. 2009 Dec 22;48(50):11929-38. doi: 10.1021/bi901775j. PMID- 21961597 OWN - NLM STAT- MEDLINE DA - 20111003 DCOM- 20120118 LR - 20141022 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 101 IP - 7 DP - 2011 Oct 5 TI - Single molecule study of the intrinsically disordered FG-repeat nucleoporin 153. PG - 1710-9 LID - 10.1016/j.bpj.2011.08.025 [doi] AB - Nucleoporins (Nups), which are intrinsically disordered, form a selectivity filter inside the nuclear pore complex, taking a central role in the vital nucleocytoplasmic transport mechanism. These Nups display a complex and nonrandom amino-acid architecture of phenylalanine glycine (FG)-repeat clusters and intra-FG linkers. How such heterogeneous sequence composition relates to function and could give rise to a transport mechanism is still unclear. Here we describe a combined chemical biology and single-molecule fluorescence approach to study the large human Nup153 FG-domain. In order to obtain insights into the properties of this domain beyond the average behavior, we probed the end-to-end distance (R(E)) of several approximately 50-residues long FG-repeat clusters in the context of the whole protein domain. Despite the sequence heterogeneity of these FG-clusters, we detected a reoccurring and consistent compaction from a relaxed coil behavior under denaturing conditions (R(E)/R(E,RC) = 0.99 +/- 0.15 with R(E,RC) corresponding to ideal relaxed coil behavior) to a collapsed state under native conditions (R(E)/R(E,RC) = 0.79 +/- 0.09). We then analyzed the properties of this protein on the supramolecular level, and determined that this human FG-domain was in fact able to form a hydrogel with physiological permeability barrier properties. CI - Copyright (c) 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Milles, Sigrid AU - Milles S AD - European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany. FAU - Lemke, Edward A AU - Lemke EA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (NUP153 protein, human) RN - 0 (Nuclear Pore Complex Proteins) RN - 0 (Peptide Fragments) SB - IM MH - Active Transport, Cell Nucleus MH - Cell Nucleus/metabolism MH - Humans MH - Nuclear Pore Complex Proteins/*chemistry/metabolism MH - Peptide Fragments/chemistry/metabolism MH - Porosity MH - Protein Denaturation MH - Protein Structure, Tertiary MH - *Repetitive Sequences, Amino Acid MH - Spectrometry, Fluorescence/*methods PMC - PMC3183753 OID - NLM: PMC3183753 EDAT- 2011/10/04 06:00 MHDA- 2012/01/19 06:00 CRDT- 2011/10/04 06:00 PHST- 2011/06/17 [received] PHST- 2011/07/27 [revised] PHST- 2011/08/11 [accepted] AID - S0006-3495(11)00971-4 [pii] AID - 10.1016/j.bpj.2011.08.025 [doi] PST - ppublish SO - Biophys J. 2011 Oct 5;101(7):1710-9. doi: 10.1016/j.bpj.2011.08.025. PMID- 15784254 OWN - NLM STAT- MEDLINE DA - 20050323 DCOM- 20050503 LR - 20071114 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 347 IP - 5 DP - 2005 Apr 15 TI - Domain study of bacteriophage p22 coat protein and characterization of the capsid lattice transformation by hydrogen/deuterium exchange. PG - 935-48 AB - Viral capsids are dynamic structures which undergo a series of structural transformations to form infectious viruses. The dsDNA bacteriophage P22 is used as a model system to study the assembly and maturation of icosahedral dsDNA viruses. The P22 procapsid, which is the viral capsid precursor, is assembled from coat protein with the aid of scaffolding protein. Upon DNA packaging, the capsid lattice expands and becomes a stable virion. Limited proteolysis and biochemical experiments indicated that the coat protein consists of two domains connected by a flexible loop. To investigate the properties and roles of the sub-domains, we have cloned them and initiated structure and function studies. The N-terminal domain, which is made up of 190 amino acid residues, is largely unstructured in solution, while the C-terminal domain, which consists of 239 amino acid residues, forms a stable non-covalent dimer. The N-terminal domain adopts additional structure in the context of the C-terminal domain which might form a platform on which the N-terminal domain can fold. The local dynamics of the coat protein in both procapsids and mature capsids was monitored by hydrogen/deuterium exchange combined with mass spectrometry. The exchange rate for C-terminal domain peptides was similar in both forms. However, the N-terminal domain was more flexible in the empty procapsid shells than in the mature capsids. The flexibility of the N-terminal domain observed in the solution persisted into the procapsid form, but was lost upon maturation. The loop region connecting the two domains exchanged rapidly in the empty procapsid shells, but more slowly in the mature capsids. The global stabilization of the N-terminal domain and the flexibility encoded in the loop region may be a key component of the maturation process. FAU - Kang, Sebyung AU - Kang S AD - Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA. FAU - Prevelige, Peter E Jr AU - Prevelige PE Jr LA - eng GR - GM47980/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Capsid Proteins) RN - 0 (Peptide Fragments) RN - 0 (Solutions) SB - IM MH - Amino Acid Sequence MH - Bacteriophage P22/*chemistry MH - Capsid/*chemistry/*metabolism MH - Capsid Proteins/*chemistry/*metabolism MH - Cell Transformation, Viral MH - Circular Dichroism MH - Deuterium Exchange Measurement MH - Dimerization MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/metabolism MH - Protein Structure, Tertiary MH - Solutions MH - Spectrometry, Fluorescence EDAT- 2005/03/24 09:00 MHDA- 2005/05/04 09:00 CRDT- 2005/03/24 09:00 PHST- 2005/01/04 [received] PHST- 2005/02/04 [revised] PHST- 2005/02/04 [accepted] AID - S0022-2836(05)00173-7 [pii] AID - 10.1016/j.jmb.2005.02.021 [doi] PST - ppublish SO - J Mol Biol. 2005 Apr 15;347(5):935-48. PMID- 17359979 OWN - NLM STAT- MEDLINE DA - 20070327 DCOM- 20070606 LR - 20140219 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 581 IP - 7 DP - 2007 Apr 3 TI - Empirical rules for rationalising visible circular dichroism of Cu2+ and Ni2+ histidine complexes: applications to the prion protein. PG - 1430-4 AB - A natively unfolded region of the prion protein, PrP(90-126) binds Cu(2+) ions and is vital for prion propagation. Pentapeptides, acyl-GGGTH(92-96) and acyl-TNMKH(107-111), represent the minimum motif for this Cu(2+) binding region. EPR and (1)H NMR suggests that the coordination geometry for the two binding sites is very similar. However, the visible CD spectra of the two sites are very different, producing almost mirror image spectra. We have used a series of analogues of the pentapeptides containing His(96) and His(111) to rationalise these differences in the visible CD spectra. Using simple histidine-containing tri-peptides we have formulated a set of empirical rules that can predict the appearance of Cu(2+) visible CD spectra involving histidine and amide main-chain coordination. FAU - Klewpatinond, Mark AU - Klewpatinond M AD - School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK. FAU - Viles, John H AU - Viles JH LA - eng GR - MC_U117533887/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070306 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Oligopeptides) RN - 0 (Prions) RN - 4QD397987E (Histidine) RN - 789U1901C5 (Copper) RN - 7OV03QG267 (Nickel) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Circular Dichroism/*standards MH - Copper/*analysis MH - Electron Spin Resonance Spectroscopy MH - Histidine/*analysis MH - Nickel/*analysis MH - Nuclear Magnetic Resonance, Biomolecular MH - Oligopeptides/chemistry MH - Prions/*chemistry MH - Protein Folding EDAT- 2007/03/16 09:00 MHDA- 2007/06/07 09:00 CRDT- 2007/03/16 09:00 PHST- 2007/02/07 [received] PHST- 2007/02/27 [revised] PHST- 2007/02/27 [accepted] PHST- 2007/03/06 [aheadofprint] AID - S0014-5793(07)00240-2 [pii] AID - 10.1016/j.febslet.2007.02.068 [doi] PST - ppublish SO - FEBS Lett. 2007 Apr 3;581(7):1430-4. Epub 2007 Mar 6. PMID- 21961598 OWN - NLM STAT- MEDLINE DA - 20111003 DCOM- 20120118 LR - 20141022 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 101 IP - 7 DP - 2011 Oct 5 TI - Chain collapse of an amyloidogenic intrinsically disordered protein. PG - 1720-9 LID - 10.1016/j.bpj.2011.08.024 [doi] AB - Natively unfolded or intrinsically disordered proteins (IDPs) are under intense scrutiny due to their involvement in both normal biological functions and abnormal protein misfolding disorders. Polypeptide chain collapse of amyloidogenic IDPs is believed to play a key role in protein misfolding, oligomerization, and aggregation leading to amyloid fibril formation, which is implicated in a number of human diseases. In this work, we used bovine kappa-casein, which serves as an archetypal model protein for amyloidogenic IDPs. Using a variety of biophysical tools involving both prediction and spectroscopic techniques, we first established that monomeric kappa-casein adopts a collapsed premolten-globule-like conformational ensemble under physiological conditions. Our time-resolved fluorescence and light-scattering data indicate a change in the mean hydrodynamic radius from approximately 4.6 nm to approximately 1.9 nm upon chain collapse. We then took the advantage of two cysteines separated by 77 amino-acid residues and covalently labeled them using thiol-reactive pyrene maleimide. This dual-labeled protein demonstrated a strong excimer formation upon renaturation from urea- and acid-denatured states under both equilibrium and kinetic conditions, providing compelling evidence of polypeptide chain collapse under physiological conditions. The implication of the IDP chain collapse in protein aggregation and amyloid formation is also discussed. CI - Copyright (c) 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Jain, Neha AU - Jain N AD - Indian Institute of Science Education and Research Mohali, Knowledge City, Mohali, India. FAU - Bhattacharya, Mily AU - Bhattacharya M FAU - Mukhopadhyay, Samrat AU - Mukhopadhyay S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Amyloidogenic Proteins) RN - 0 (Caseins) RN - 0 (Peptides) RN - 0 (Pyrenes) RN - 9E0T7WFW93 (pyrene) SB - IM MH - Amino Acid Sequence MH - Amyloidogenic Proteins/*chemistry/metabolism MH - Animals MH - Caseins/*chemistry/metabolism MH - Cattle MH - Computational Biology MH - Fluorescence Polarization MH - Fluorescence Resonance Energy Transfer MH - Kinetics MH - Light MH - Molecular Sequence Data MH - Peptides/chemistry/metabolism MH - Protein Multimerization MH - Pyrenes/chemistry MH - Scattering, Radiation PMC - PMC3183800 OID - NLM: PMC3183800 EDAT- 2011/10/04 06:00 MHDA- 2012/01/19 06:00 CRDT- 2011/10/04 06:00 PHST- 2011/06/30 [received] PHST- 2011/08/15 [revised] PHST- 2011/08/17 [accepted] AID - S0006-3495(11)00970-2 [pii] AID - 10.1016/j.bpj.2011.08.024 [doi] PST - ppublish SO - Biophys J. 2011 Oct 5;101(7):1720-9. doi: 10.1016/j.bpj.2011.08.024. PMID- 8043577 OWN - NLM STAT- MEDLINE DA - 19940901 DCOM- 19940901 LR - 20051117 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 33 IP - 30 DP - 1994 Aug 2 TI - Solution conformation of an atrial natriuretic peptide variant selective for the type A receptor. PG - 8897-904 AB - Two-dimensional NMR spectroscopy has been used to characterize the solution conformation of an atrial natriuretic peptide (ANP) variant which is selective for the human natriuretic peptide receptor A (NPR-A) relative to receptor C (NPR-C). The ANP mutant, containing six substitutions, has reduced flexibility in aqueous solution relative to wild-type ANP and allows the observation of sufficient NOE connectivities for structure determination by distance geometry and restrained molecular dynamics calculations. The solution conformation is reasonably well defined, having an average backbone atom rms deviation from the average coordinates of approximately 1.1 A for residues 7-27. The structure is consistent with available functional data and shows a spatial separation between known receptor binding determinants and residues found to be outside the hormone-receptor interface. FAU - Fairbrother, W J AU - Fairbrother WJ AD - Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080-4990. FAU - McDowell, R S AU - McDowell RS FAU - Cunningham, B C AU - Cunningham BC LA - eng PT - Journal Article PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Solutions) RN - 85637-73-6 (Atrial Natriuretic Factor) RN - EC 4.6.1.2 (Receptors, Atrial Natriuretic Factor) SB - IM MH - Amino Acid Sequence MH - Atrial Natriuretic Factor/*chemistry/metabolism MH - Humans MH - Molecular Sequence Data MH - Protein Conformation MH - Receptors, Atrial Natriuretic Factor/*metabolism MH - Sequence Alignment MH - Solutions EDAT- 1994/08/02 MHDA- 1994/08/02 00:01 CRDT- 1994/08/02 00:00 PST - ppublish SO - Biochemistry. 1994 Aug 2;33(30):8897-904. PMID- 15491138 OWN - NLM STAT- MEDLINE DA - 20041019 DCOM- 20041202 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 42 DP - 2004 Oct 26 TI - Structural studies on a protein-binding zinc-finger domain of Eos reveal both similarities and differences to classical zinc fingers. PG - 13318-27 AB - The oligomerization domain that is present at the C terminus of Ikaros-family proteins and the protein Trps-1 is important for the proper regulation of developmental processes such as hematopoiesis. Remarkably, this domain is predicted to contain two classical zinc fingers (ZnFs), domains normally associated with the recognition of nucleic acids. The preference for protein binding by these predicted ZnFs is not well-understood. We have used a range of methods to gain insight into the structure of this domain. Circular dichroism, UV-vis, and NMR experiments carried out on the C-terminal domain of Eos (EosC) revealed that the two putative ZnFs (C1 and C2) are separable, i.e., capable of folding independently in the presence of Zn(II). We next determined the structure of EosC2 using NMR spectroscopy, revealing that, although the overall fold of EosC2 is similar to other classical ZnFs, a number of differences exist. For example, the conformation of the C terminus of EosC2 appears to be flexible and may result in a major rearrangement of the zinc ligands. Finally, alanine-scanning mutagenesis was used to identify the residues that are involved in the homo- and hetero-oligomerization of Eos, and these results are discussed in the context of the structure of EosC. These studies provide the first structural insights into how EosC mediates protein-protein interactions and contributes to our understanding of why it does not exhibit high-affinity DNA binding. FAU - Westman, Belinda J AU - Westman BJ AD - School of Molecular and Microbial Biosciences, University of Sydney, Sydney, New South Wales 2006, Australia. FAU - Perdomo, Jose AU - Perdomo J FAU - Matthews, Jacqueline M AU - Matthews JM FAU - Crossley, Merlin AU - Crossley M FAU - Mackay, Joel P AU - Mackay JP LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Carrier Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (IKZF1 protein, human) RN - 0 (IKZF5 protein, human) RN - 0 (Nerve Tissue Proteins) RN - 0 (Peptide Fragments) RN - 0 (Protein Isoforms) RN - 0 (Transcription Factors) RN - 0 (Xenopus Proteins) RN - 0 (Zfpn1a1 protein, mouse) RN - 0 (Zfpn1a4 protein, mouse) RN - 148971-36-2 (Ikaros Transcription Factor) RN - J41CSQ7QDS (Zinc) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites/genetics MH - Carrier Proteins/*chemistry/genetics MH - DNA-Binding Proteins/*chemistry/genetics MH - Humans MH - Ikaros Transcription Factor MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Nerve Tissue Proteins/*chemistry/genetics MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/*chemistry/genetics MH - Protein Binding/genetics MH - Protein Conformation MH - Protein Folding MH - Protein Isoforms/chemistry/genetics MH - Protein Structure, Tertiary/genetics MH - Static Electricity MH - Structural Homology, Protein MH - Transcription Factors/*chemistry/genetics MH - Xenopus Proteins/chemistry/genetics MH - Zinc/chemistry MH - *Zinc Fingers/genetics EDAT- 2004/10/20 09:00 MHDA- 2004/12/16 09:00 CRDT- 2004/10/20 09:00 AID - 10.1021/bi049506a [doi] PST - ppublish SO - Biochemistry. 2004 Oct 26;43(42):13318-27. PMID- 20598937 OWN - NLM STAT- MEDLINE DA - 20100809 DCOM- 20101202 LR - 20140913 IS - 1879-0402 (Electronic) IS - 1367-5931 (Linking) VI - 14 IP - 4 DP - 2010 Aug TI - Intrinsically disordered proteins are potential drug targets. PG - 481-8 LID - 10.1016/j.cbpa.2010.06.169 [doi] AB - Intrinsically disordered (ID) proteins that lack stable secondary and tertiary structure in substantial regions (or throughout) are prevalent in eukaryotes. They exist as ensembles of rapidly fluctuating structures and many undergo coupled folding and binding reactions. Because ID proteins are overrepresented in major disease pathways they are desirable targets for inhibition; however, the feasibility of targeting proteins without defined structures was unclear. Recently, small molecules have been found that bind to the disordered regions of c-Myc, Abeta, EWS-Fli1, and various peptides. As with structured targets, initial hits were further optimized to increase specificity and affinity. Given the number and biological importance of ID proteins, the ability to inhibit their interactions opens tremendous potential in chemical biology and drug discovery. CI - 2010 Elsevier Ltd. All rights reserved. FAU - Metallo, Steven J AU - Metallo SJ AD - Department of Chemistry, Georgetown University, 37th & O Streets, NW, Washington, DC 20057, United States. sjm24@georgetown.edu LA - eng GR - 1R01CA140624/CA/NCI NIH HHS/United States GR - R01 CA140624/CA/NCI NIH HHS/United States GR - R01 CA140624-01/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review DEP - 20100702 PL - England TA - Curr Opin Chem Biol JT - Current opinion in chemical biology JID - 9811312 RN - 0 (Pharmaceutical Preparations) RN - 0 (Proteins) SB - IM MH - Drug Delivery Systems MH - Molecular Structure MH - Pharmaceutical Preparations/administration & dosage/chemistry/metabolism MH - Protein Binding MH - Proteins/*chemistry MH - Structure-Activity Relationship PMC - PMC2918680 MID - NIHMS214355 OID - NLM: NIHMS214355 OID - NLM: PMC2918680 EDAT- 2010/07/06 06:00 MHDA- 2010/12/14 06:00 CRDT- 2010/07/06 06:00 PHST- 2010/05/11 [received] PHST- 2010/06/03 [revised] PHST- 2010/06/08 [accepted] PHST- 2010/07/02 [aheadofprint] AID - S1367-5931(10)00074-8 [pii] AID - 10.1016/j.cbpa.2010.06.169 [doi] PST - ppublish SO - Curr Opin Chem Biol. 2010 Aug;14(4):481-8. doi: 10.1016/j.cbpa.2010.06.169. Epub 2010 Jul 2. PMID- 20005203 OWN - NLM STAT- MEDLINE DA - 20100127 DCOM- 20100315 LR - 20140917 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 391 IP - 1 DP - 2010 Jan 1 TI - Biophysical characterization reveals structural disorder in the developmental transcriptional regulator LBH. PG - 1104-9 LID - 10.1016/j.bbrc.2009.12.032 [doi] AB - Limb-bud and heart (LBH) is a key transcriptional regulator in vertebrates with pivotal roles in embryonic development and human disease. Herein, using a diverse array of biophysical techniques, we report the first structural characterization of LBH pertinent to its biological function. Our data reveal that LBH is structurally disordered with no discernable secondary or tertiary structure and exudes rod-like properties in solution. Consistent with these observations, we also demonstrate that LBH is conformationally flexible and thus may be capable of adapting distinct conformations under specific physiological contexts. We propose that LBH is a member of the intrinsically disordered protein (IDP) family, and that conformational plasticity may play a significant role in modulating LBH-dependent transcriptional processes. CI - Copyright 2009 Elsevier Inc. All rights reserved. FAU - Al-Ali, Hassan AU - Al-Ali H AD - Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA. FAU - Rieger, Megan E AU - Rieger ME FAU - Seldeen, Kenneth L AU - Seldeen KL FAU - Harris, Thomas K AU - Harris TK FAU - Farooq, Amjad AU - Farooq A FAU - Briegel, Karoline J AU - Briegel KJ LA - eng GR - R01 GM069868-05/GM/NIGMS NIH HHS/United States GR - R01 GM083897/GM/NIGMS NIH HHS/United States GR - R01 GM083897-02/GM/NIGMS NIH HHS/United States GR - R01-GM083897/GM/NIGMS NIH HHS/United States GR - R01-GM69868/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20091211 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Lbh protein, mouse) RN - 0 (Nuclear Proteins) RN - 0 (Recombinant Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Biophysical Processes MH - Escherichia coli/metabolism MH - Humans MH - Mice MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*chemistry/genetics MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Rats MH - Recombinant Proteins/chemistry/genetics PMC - PMC2827303 MID - NIHMS167678 OID - NLM: NIHMS167678 OID - NLM: PMC2827303 EDAT- 2009/12/17 06:00 MHDA- 2010/03/17 06:00 CRDT- 2009/12/17 06:00 PHST- 2009/12/01 [received] PHST- 2009/12/08 [accepted] PHST- 2009/12/11 [aheadofprint] AID - S0006-291X(09)02405-X [pii] AID - 10.1016/j.bbrc.2009.12.032 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2010 Jan 1;391(1):1104-9. doi: 10.1016/j.bbrc.2009.12.032. Epub 2009 Dec 11. PMID- 23877929 OWN - NLM STAT- MEDLINE DA - 20130828 DCOM- 20140521 IS - 1573-5001 (Electronic) IS - 0925-2738 (Linking) VI - 56 IP - 4 DP - 2013 Aug TI - Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c. PG - 291-301 LID - 10.1007/s10858-013-9761-7 [doi] AB - Microtubule-associated proteins (MAPs) are abundantly present in axons and dendrites, and have been shown to play crucial role during the neuronal morphogenesis. The period of main dendritic outgrowth and synaptogenesis coincides with high expression levels of one of MAPs, the MAP2c, in rats. The MAP2c is a 49.2 kDa intrinsically disordered protein. To achieve an atomic resolution characterization of such a large protein, we have developed a protocol based on the acquisition of two five-dimensional (13)C-directly detected NMR experiments. Our previously published 5D CACONCACO experiment (Novacek et al. in J Biomol NMR 50(1):1-11, 2011) provides the sequential assignment of the backbone resonances, which is not interrupted by the presence of the proline residues in the amino acid sequence. A novel 5D HC(CC-TOCSY)CACON experiment facilitates the assignment of the aliphatic side chain resonances. To streamline the data analysis, we have developed a semi-automated procedure for signal assignments. The obtained data provides the first atomic resolution insight into the conformational state of MAP2c and constitutes a model for further functional studies of MAPs. FAU - Novacek, Jiri AU - Novacek J AD - Faculty of Science, NCBR, and CEITEC, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic. FAU - Janda, Lubomir AU - Janda L FAU - Dopitova, Radka AU - Dopitova R FAU - Zidek, Lukas AU - Zidek L FAU - Sklenar, Vladimir AU - Sklenar V LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130723 PL - Netherlands TA - J Biomol NMR JT - Journal of biomolecular NMR JID - 9110829 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Microtubule-Associated Proteins) RN - TE7660XO1C (Glycine) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Animals MH - Glycine MH - Intrinsically Disordered Proteins/*chemistry/*metabolism MH - Microtubule-Associated Proteins/*chemistry/*metabolism MH - Molecular Sequence Data MH - Molecular Weight MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Rats EDAT- 2013/07/24 06:00 MHDA- 2014/05/23 06:00 CRDT- 2013/07/24 06:00 PHST- 2013/04/08 [received] PHST- 2013/07/07 [accepted] PHST- 2013/07/23 [aheadofprint] AID - 10.1007/s10858-013-9761-7 [doi] PST - ppublish SO - J Biomol NMR. 2013 Aug;56(4):291-301. doi: 10.1007/s10858-013-9761-7. Epub 2013 Jul 23. PMID- 16977336 OWN - NLM STAT- MEDLINE DA - 20061003 DCOM- 20061222 LR - 20140908 IS - 1469-221X (Print) IS - 1469-221X (Linking) VI - 7 IP - 10 DP - 2006 Oct TI - Coexistence of two protein folding states in the crystal structure of ribosomal protein L20. PG - 1013-8 AB - The recent finding of intrinsically unstructured proteins defies the classical structure-function paradigm. However, owing to their flexibility, intrinsically unstructured proteins generally escape detailed structural investigations. Consequently little is known about the extent of conformational disorder and its role in biological functions. Here, we present the X-ray structure of the unbound ribosomal protein L20, the long basic amino-terminal extension of which has been previously interpreted as fully disordered in the absence of RNA. This study provides the first detailed picture of two protein folding states trapped together in a crystal and indicates that unfolding occurs in discrete regions of the whole protein, corresponding mainly to RNA-binding residues. The electrostatic destabilization of the long alpha-helix and a structural communication between the two L20 domains are reminiscent of those observed in calmodulin. The detailed comparison of the two conformations observed in the crystal provides new insights into the role of unfolded extensions in ribosomal assembly. FAU - Timsit, Youri AU - Timsit Y AD - Laboratoire de Cristallographie UPR9080, Institut de Biologie Physico-Chimique CNRS, 13, rue Pierre et Marie Curie, Paris 75005, France. timsit@ibpc.fr FAU - Allemand, Frederic AU - Allemand F FAU - Chiaruttini, Claude AU - Chiaruttini C FAU - Springer, Mathias AU - Springer M LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060915 PL - England TA - EMBO Rep JT - EMBO reports JID - 100963049 RN - 0 (Bacterial Proteins) RN - 0 (L20 ribosomal protein, bacteria) RN - 0 (RNA, Ribosomal, 23S) RN - 0 (RNA-Binding Proteins) RN - 0 (Ribosomal Proteins) SB - IM MH - Bacterial Proteins/*chemistry MH - Crystallography, X-Ray/*methods MH - Data Collection/methods/statistics & numerical data MH - Deinococcus/chemistry MH - Escherichia coli/chemistry MH - Models, Biological MH - Models, Molecular MH - Optical Rotatory Dispersion/methods MH - Protein Binding MH - Protein Conformation MH - *Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA, Ribosomal, 23S/metabolism MH - RNA-Binding Proteins/chemistry MH - Ribosomal Proteins/*chemistry PMC - PMC1618378 OID - NLM: PMC1618378 EDAT- 2006/09/16 09:00 MHDA- 2006/12/23 09:00 CRDT- 2006/09/16 09:00 PHST- 2006/05/02 [received] PHST- 2006/08/03 [revised] PHST- 2006/08/03 [accepted] PHST- 2006/09/15 [aheadofprint] AID - 7400803 [pii] AID - 10.1038/sj.embor.7400803 [doi] PST - ppublish SO - EMBO Rep. 2006 Oct;7(10):1013-8. Epub 2006 Sep 15. PMID- 21713006 OWN - NLM STAT- MEDLINE DA - 20110629 DCOM- 20111121 LR - 20141022 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 6 DP - 2011 TI - Identification of a highly antigenic linear B cell epitope within Plasmodium vivax apical membrane antigen 1 (AMA-1). PG - e21289 LID - 10.1371/journal.pone.0021289 [doi] AB - Apical membrane antigen 1 (AMA-1) is considered to be a major candidate antigen for a malaria vaccine. Previous immunoepidemiological studies of naturally acquired immunity to Plasmodium vivax AMA-1 (PvAMA-1) have shown a higher prevalence of specific antibodies to domain II (DII) of AMA-1. In the present study, we confirmed that specific antibody responses from naturally infected individuals were highly reactive to both full-length AMA-1 and DII. Also, we demonstrated a strong association between AMA-1 and DII IgG and IgG subclass responses. We analyzed the primary sequence of PvAMA-1 for B cell linear epitopes co-occurring with intrinsically unstructured/disordered regions (IURs). The B cell epitope comprising the amino acid sequence 290-307 of PvAMA-1 (SASDQPTQYEEEMTDYQK), with the highest prediction scores, was identified in domain II and further selected for chemical synthesis and immunological testing. The antigenicity of the synthetic peptide was identified by serological analysis using sera from P. vivax-infected individuals who were knowingly reactive to the PvAMA-1 ectodomain only, domain II only, or reactive to both antigens. Although the synthetic peptide was recognized by all serum samples specific to domain II, serum with reactivity only to the full-length protein presented 58.3% positivity. Moreover, IgG reactivity against PvAMA-1 and domain II after depletion of specific synthetic peptide antibodies was reduced by 18% and 33% (P = 0.0001 for both), respectively. These results suggest that the linear epitope SASDQPTQYEEEMTDYQK is highly antigenic during natural human infections and is an important antigenic region of the domain II of PvAMA-1, suggesting its possible future use in pre-clinical studies. FAU - Bueno, Lilian Lacerda AU - Bueno LL AD - Departamento de Parasitologia, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil. FAU - Lobo, Francisco Pereira AU - Lobo FP FAU - Morais, Cristiane Guimaraes AU - Morais CG FAU - Mourao, Luiza Carvalho AU - Mourao LC FAU - de Avila, Ricardo Andrez Machado AU - de Avila RA FAU - Soares, Irene Silva AU - Soares IS FAU - Fontes, Cor Jesus AU - Fontes CJ FAU - Lacerda, Marcus Vinicius AU - Lacerda MV FAU - Chavez Olortegui, Carlos AU - Chavez Olortegui C FAU - Bartholomeu, Daniella Castanheira AU - Bartholomeu DC FAU - Fujiwara, Ricardo Toshio AU - Fujiwara RT FAU - Braga, Erika Martins AU - Braga EM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110621 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Antibodies, Protozoan) RN - 0 (Antigens, Protozoan) RN - 0 (Epitopes, B-Lymphocyte) RN - 0 (Membrane Proteins) RN - 0 (Peptides) RN - 0 (Protozoan Proteins) RN - 0 (apical membrane antigen I, Plasmodium) SB - IM MH - Adolescent MH - Adult MH - Aged MH - Amino Acid Sequence MH - Animals MH - Antibodies, Protozoan/blood/genetics/immunology MH - Antigens, Protozoan/genetics/*immunology MH - Epitopes, B-Lymphocyte/*immunology MH - Humans MH - Malaria, Vivax/blood/immunology/microbiology MH - Membrane Proteins/genetics/*immunology MH - Middle Aged MH - Molecular Sequence Data MH - Peptides/genetics/immunology MH - Plasmodium vivax/cytology/*immunology MH - Protozoan Proteins/genetics/*immunology MH - Young Adult PMC - PMC3119695 OID - NLM: PMC3119695 EDAT- 2011/06/30 06:00 MHDA- 2011/12/13 00:00 CRDT- 2011/06/30 06:00 PHST- 2010/12/21 [received] PHST- 2011/05/25 [accepted] PHST- 2011/06/21 [epublish] AID - 10.1371/journal.pone.0021289 [doi] AID - PONE-D-11-00265 [pii] PST - ppublish SO - PLoS One. 2011;6(6):e21289. doi: 10.1371/journal.pone.0021289. Epub 2011 Jun 21. PMID- 14534297 OWN - NLM STAT- MEDLINE DA - 20040105 DCOM- 20040210 LR - 20051117 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 2 DP - 2004 Jan 9 TI - Crystal structure of a superstable mutant of human p53 core domain. Insights into the mechanism of rescuing oncogenic mutations. PG - 1291-6 AB - Most of the cancer-associated mutations in the tumor suppressor p53 map to its DNA-binding core domain. Many of them inactivate p53 by decreasing its thermodynamic stability. We have previously designed the superstable quadruple mutant M133L/V203A/N239Y/N268D containing the second-site suppressor mutations N239Y and N268D, which specifically restore activity and stability in several oncogenic mutants. Here we present the x-ray structure of this quadruple mutant at 1.9 A resolution, which was solved in a new crystal form in the absence of DNA. This structure reveals that the four point mutations cause only small local structural changes, whereas the overall structure of the central beta-sandwich and the DNA-binding surface is conserved. The suppressor mutation N268D results in an altered hydrogen bond pattern connecting strands S1 and S10, thus bridging the two sheets of the beta-sandwich scaffold in an energetically more favorable way. The second suppressor mutation N239Y, which is located in close proximity to the DNA-binding surface in loop L3, seems to reduce the plasticity of the structure in large parts of loop L3 as indicated by decreased crystallographic temperature factors. The same is observed for residues in the vicinity of the N268D substitution. This increase in rigidity provides the structural basis for the increase in thermostability and an understanding how N268D and N239Y rescue some of the common cancer mutants. FAU - Joerger, Andreas C AU - Joerger AC AD - Cambridge Centre for Protein Engineering, MRC Centre, Hills Road, Cambridge CB2 2QH, UK. FAU - Allen, Mark D AU - Allen MD FAU - Fersht, Alan R AU - Fersht AR LA - eng PT - Journal Article DEP - 20031008 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Tumor Suppressor Protein p53) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Crystallography, X-Ray MH - DNA/metabolism MH - *Genes, p53 MH - Humans MH - Hydrogen Bonding MH - Models, Molecular MH - Molecular Sequence Data MH - *Mutation MH - Neoplasms/genetics MH - Point Mutation MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Tumor Suppressor Protein p53/*chemistry EDAT- 2003/10/10 05:00 MHDA- 2004/02/11 05:00 CRDT- 2003/10/10 05:00 PHST- 2003/10/08 [aheadofprint] AID - 10.1074/jbc.M309732200 [doi] AID - M309732200 [pii] PST - ppublish SO - J Biol Chem. 2004 Jan 9;279(2):1291-6. Epub 2003 Oct 8. PMID- 24192038 OWN - NLM STAT- MEDLINE DA - 20131106 DCOM- 20150306 IS - 2050-084X (Electronic) IS - 2050-084X (Linking) VI - 2 DP - 2013 TI - Intrinsic disorder within an AKAP-protein kinase A complex guides local substrate phosphorylation. PG - e01319 LID - 10.7554/eLife.01319 [doi] LID - e01319 [pii] AB - Anchoring proteins sequester kinases with their substrates to locally disseminate intracellular signals and avert indiscriminate transmission of these responses throughout the cell. Mechanistic understanding of this process is hampered by limited structural information on these macromolecular complexes. A-kinase anchoring proteins (AKAPs) spatially constrain phosphorylation by cAMP-dependent protein kinases (PKA). Electron microscopy and three-dimensional reconstructions of type-II PKA-AKAP18gamma complexes reveal hetero-pentameric assemblies that adopt a range of flexible tripartite configurations. Intrinsically disordered regions within each PKA regulatory subunit impart the molecular plasticity that affords an approximately 16 nanometer radius of motion to the associated catalytic subunits. Manipulating flexibility within the PKA holoenzyme augmented basal and cAMP responsive phosphorylation of AKAP-associated substrates. Cell-based analyses suggest that the catalytic subunit remains within type-II PKA-AKAP18gamma complexes upon cAMP elevation. We propose that the dynamic movement of kinase sub-structures, in concert with the static AKAP-regulatory subunit interface, generates a solid-state signaling microenvironment for substrate phosphorylation. DOI: http://dx.doi.org/10.7554/eLife.01319.001. FAU - Smith, F Donelson AU - Smith FD AD - Department of Pharmacology, Howard Hughes Medical Institute, University of Washington, Seattle, United States. FAU - Reichow, Steve L AU - Reichow SL FAU - Esseltine, Jessica L AU - Esseltine JL FAU - Shi, Dan AU - Shi D FAU - Langeberg, Lorene K AU - Langeberg LK FAU - Scott, John D AU - Scott JD FAU - Gonen, Tamir AU - Gonen T LA - eng GR - GM48231/GM/NIGMS NIH HHS/United States GR - HL088366/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20131105 PL - United States TA - Elife JT - eLife JID - 101579614 RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) SB - IM MH - Chromatography, Gel MH - Cyclic AMP-Dependent Protein Kinases/*metabolism MH - Microscopy, Electron MH - Phosphorylation MH - Substrate Specificity PMC - PMC3814001 OID - NLM: PMC3814001 OTO - NOTNLM OT - A-kinase anchoring protein (AKAP) OT - cAMP signaling OT - cAMP-dependent kinase (PKA) OT - electron microscopy OT - intrinsic disorder OT - single particle reconstruction GN - NLM: Original DateCompleted: 20131106 EDAT- 2013/11/07 06:00 MHDA- 2013/11/07 06:01 CRDT- 2013/11/07 06:00 AID - 2/0/e01319 [pii] AID - 10.7554/eLife.01319 [doi] PST - epublish SO - Elife. 2013 Nov 5;2:e01319. doi: 10.7554/eLife.01319. PMID- 15628855 OWN - NLM STAT- MEDLINE DA - 20050104 DCOM- 20050304 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 44 IP - 1 DP - 2005 Jan 11 TI - Role for the alpha-helix in aberrant protein aggregation. PG - 149-56 AB - Is the alpha-helix structure capable of triggering the formation of aberrant protein aggregates? To answer this question, we investigate the in vitro aggregation of tau protein in the presence of the helix-inducing agent TFE. Tau is a natively unfolded protein that binds to microtubules and forms aggregates in Alzheimer's disease. We find that full-length tau has residual alpha-helix structure, which is further enhanced by three mutations involved in genetic neurological disorders. TFE concentrations matching an alpha-helical content of 40% in full-length tau and the triple mutant induce the formation of aggregates that are morphologically and structurally heterogeneous. A simple dilution experiment reveals that heterogeneity results from the competition between alpha-helical fibrillar aggregates and more classical amyloid-like aggregates. The alpha-helical aggregates are more resilient to dilution and have the spectroscopic features of alpha-helical coiled coils. We propose a general mechanism by which intrinsically stable alpha-helices can associate into aggregates with only coarse coiled-coil symmetry. In tau, high intrinsic alpha-helix stability and coarse coiled-coil symmetry could be byproducts of its biological function. FAU - Kunjithapatham, Rani AU - Kunjithapatham R AD - Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, USA. FAU - Oliva, Fabiana Y AU - Oliva FY FAU - Doshi, Urmi AU - Doshi U FAU - Perez, Mar AU - Perez M FAU - Avila, Jesus AU - Avila J FAU - Munoz, Victor AU - Munoz V LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Proteins) RN - 0 (tau Proteins) RN - 9002-84-0 (Polytetrafluoroethylene) SB - IM MH - Binding Sites MH - Circular Dichroism MH - Humans MH - Microscopy, Atomic Force MH - Polytetrafluoroethylene MH - Protein Conformation MH - Protein Denaturation MH - Protein Structure, Secondary MH - Proteins/*chemistry MH - Spectrophotometry, Infrared MH - Spectrophotometry, Ultraviolet MH - Spectroscopy, Fourier Transform Infrared MH - tau Proteins/chemistry/metabolism/ultrastructure EDAT- 2005/01/05 09:00 MHDA- 2005/03/05 09:00 CRDT- 2005/01/05 09:00 AID - 10.1021/bi048564t [doi] PST - ppublish SO - Biochemistry. 2005 Jan 11;44(1):149-56. PMID- 19538146 OWN - NLM STAT- MEDLINE DA - 20091028 DCOM- 20100111 LR - 20140910 IS - 1875-5550 (Electronic) IS - 1389-2037 (Linking) VI - 10 IP - 5 DP - 2009 Oct TI - Biophysics of Parkinson's disease: structure and aggregation of alpha-synuclein. PG - 483-99 AB - Parkinson's disease (PD) is a slowly progressive movement disorder that results from the loss of dopaminergic neurons in the substantia nigra, a small area of cells in the mid-brain. PD is a multifactorial disorder with unknown etiology, in which both genetic and environmental factors play important roles. Substantial evidence links alpha-synuclein, a small highly conserved presynaptic protein with unknown function, to both familial and sporadic PD. Rare familial cases of PD are associated with missense point mutations in alpha-synuclein, or with the hyper-expression of the wild type protein due to its gene duplication/triplication. Furthermore, alpha-synuclein was identified as the major component of amyloid fibrils found in Lewy body and Lewy neurites, the characteristic proteinaceous deposits that are the diagnostic hallmarks of PD. alpha-Synuclein is abundant in various regions of the brain and has two closely related homologs, beta-synuclein and gamma-synuclein. When isolated in solution, the protein is intrinsically disordered, but in the presence of lipid surfaces alpha-synuclein adopts a highly helical structure that is believed to mediate its normal function(s). A number of different conformational states of alpha-synuclein have been observed. Besides the membrane-bound form, other critical conformations include a partially-folded state that is a key intermediate in aggregation and fibrillation, various oligomeric species, and fibrillar and amorphous aggregates. A number of intrinsic and extrinsic factors that either accelerate or inhibit the rate of alpha-synuclein aggregation and fibrillation in vitro are known. There is a strong correlation between the conformation of alpha-synuclein (induced by various factors) and its rate of fibrillation. The aggregation process appears to be branched, with one pathway leading to fibrils and another to oligomeric intermediates that may ultimately form amorphous deposits. The molecular basis of Parkinson's disease appears to be tightly coupled to the aggregation of alpha-synuclein and the factors that affect its conformation. This review focuses on the contributions of Prof. Anthony L. Fink to the field and presents some recent developments in this exciting area. FAU - Uversky, Vladimir N AU - Uversky VN AD - Institite for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. vuversky@iupui.edu FAU - Eliezer, David AU - Eliezer D LA - eng GR - R01 AG019391/AG/NIA NIH HHS/United States GR - R01 AG019391/AG/NIA NIH HHS/United States GR - R01 AG019391-09/AG/NIA NIH HHS/United States GR - R01 AG025440/AG/NIA NIH HHS/United States GR - R01 AG025440/AG/NIA NIH HHS/United States GR - R01 AG025440-04/AG/NIA NIH HHS/United States GR - R01 GM071714/GM/NIGMS NIH HHS/United States GR - R01 LM007688/LM/NLM NIH HHS/United States GR - R37 AG019391/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review PL - Netherlands TA - Curr Protein Pept Sci JT - Current protein & peptide science JID - 100960529 RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Biophysics/*methods MH - Dementia/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Biological MH - Parkinson Disease/*metabolism/*pathology MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - alpha-Synuclein/chemistry/*physiology RF - 254 PMC - PMC3786709 MID - NIHMS355830 OID - NLM: NIHMS355830 OID - NLM: PMC3786709 EDAT- 2009/06/23 09:00 MHDA- 2010/01/12 06:00 CRDT- 2009/06/23 09:00 PHST- 2009/01/20 [received] PHST- 2009/02/05 [accepted] AID - CPPS-11 [pii] PST - ppublish SO - Curr Protein Pept Sci. 2009 Oct;10(5):483-99. PMID- 20480043 OWN - NLM STAT- MEDLINE DA - 20100518 DCOM- 20141013 IS - 1422-0067 (Electronic) IS - 1422-0067 (Linking) VI - 11 IP - 4 DP - 2010 TI - Intrinsically disordered proteins in bcl-2 regulated apoptosis. PG - 1808-24 LID - 10.3390/ijms11041808 [doi] AB - Intrinsic cell death is mediated by interaction between pro-apoptotic and pro-survival proteins of the B-cell lymphoma-2 (Bcl-2) family. Members of this family are either intrinsically disordered or contain intrinsically disordered regions/domains that are critical to their function. Alternate splicing and post-translational modifications can determine the extent of these disordered regions and are critical for regulating Bcl-2 proteins. Conformational plasticity and structural transitions characterize the interactions within the Bcl-2 family, with conserved sequence motifs on both binding partners required for their molecular recognition. FAU - Rautureau, Gilles J P AU - Rautureau GJ AD - Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. FAU - Day, Catherine L AU - Day CL FAU - Hinds, Mark G AU - Hinds MG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20100416 PL - Switzerland TA - Int J Mol Sci JT - International journal of molecular sciences JID - 101092791 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Proto-Oncogene Proteins c-bcl-2) SB - IM MH - Alternative Splicing MH - *Apoptosis MH - Humans MH - Intrinsically Disordered Proteins/chemistry/*metabolism MH - Protein Processing, Post-Translational MH - Proto-Oncogene Proteins c-bcl-2/chemistry/*metabolism PMC - PMC2871139 OID - NLM: PMC2871139 OTO - NOTNLM OT - BH3-only OT - Bcl-2 OT - apoptosis OT - intrinsically disordered protein OT - protein structure GN - NLM: Original DateCompleted: 20100702 EDAT- 2010/05/19 06:00 MHDA- 2010/05/19 06:01 CRDT- 2010/05/19 06:00 PHST- 2010/03/01 [received] PHST- 2010/03/23 [revised] PHST- 2010/04/14 [accepted] PHST- 2010/04/16 [epublish] AID - 10.3390/ijms11041808 [doi] PST - epublish SO - Int J Mol Sci. 2010 Apr 16;11(4):1808-24. doi: 10.3390/ijms11041808. PMID- 11595744 OWN - NLM STAT- MEDLINE DA - 20011203 DCOM- 20020110 LR - 20141120 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 49 DP - 2001 Dec 7 TI - The N-terminal regions of estrogen receptor alpha and beta are unstructured in vitro and show different TBP binding properties. PG - 45939-44 AB - The N-terminal regions of the estrogen receptor alpha (ER alpha-N) and beta (ER beta-N) were expressed and purified to homogeneity. Using NMR and circular dichroism spectroscopy, we conclude that both ER alpha-N and ER beta-N are unstructured in solution. The TATA box-binding protein (TBP) has been shown previously to interact with ER alpha-N in vitro and to potentiate ER-activated transcription. We used surface plasmon resonance and circular dichroism spectroscopy to confirm and further characterize the ER-N-TBP interaction. Our results show that the intrinsically unstructured ER alpha-N interacts with TBP, and suggest that structural changes are induced in ER alpha-N upon TBP interaction. Conformational changes upon target factor interaction have not previously been demonstrated for any N-terminal region of nuclear receptors. In addition, no binding of ER beta-N to TBP was detected. This difference in TBP binding could imply differential recruitment of target proteins by ER alpha-N and ER beta-N. The affinity of the ER alpha-N-TBP interaction was determined to be in the micromolar range (K(D) = 10(-6) to 10(-5) m). Our results support models of TBP as a target protein for the N-terminal activation domain of ER alpha. Further, our results suggest that target proteins can induce and/or stabilize ordered structure in N-terminal regions of nuclear receptors upon interaction. FAU - Warnmark, A AU - Warnmark A AD - Department of Biosciences, Novum, Karolinska Institutet, Huddinge SE-141 57, Sweden. anette.warnmark@cbt.ki.se FAU - Wikstrom, A AU - Wikstrom A FAU - Wright, A P AU - Wright AP FAU - Gustafsson, J A AU - Gustafsson JA FAU - Hard, T AU - Hard T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20011010 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA Primers) RN - 0 (DNA-Binding Proteins) RN - 0 (Estrogen Receptor alpha) RN - 0 (Estrogen Receptor beta) RN - 0 (Receptors, Estrogen) RN - 0 (TATA-Box Binding Protein) RN - 0 (Transcription Factors) SB - IM MH - Base Sequence MH - Cell Line, Transformed MH - Circular Dichroism MH - DNA Primers MH - DNA-Binding Proteins/*metabolism MH - Electrophoresis, Polyacrylamide Gel MH - Estrogen Receptor alpha MH - Estrogen Receptor beta MH - In Vitro Techniques MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Receptors, Estrogen/chemistry/*metabolism MH - Surface Plasmon Resonance MH - TATA-Box Binding Protein MH - Transcription Factors/*metabolism EDAT- 2001/10/12 10:00 MHDA- 2002/01/11 10:01 CRDT- 2001/10/12 10:00 PHST- 2001/10/10 [aheadofprint] AID - 10.1074/jbc.M107875200 [doi] AID - M107875200 [pii] PST - ppublish SO - J Biol Chem. 2001 Dec 7;276(49):45939-44. Epub 2001 Oct 10. PMID- 24720254 OWN - NLM STAT- MEDLINE DA - 20140429 DCOM- 20140820 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 16 DP - 2014 Apr 29 TI - A nacre protein, n16.3, self-assembles to form protein oligomers that dimensionally limit and organize mineral deposits. PG - 2739-48 LID - 10.1021/bi401721z [doi] AB - The mollusk shell is a complex biological material that integrates mineral phases with organic macromolecular components such as proteins. The role of proteins in the formation of the nacre layer (aragonite mineral phase) is poorly understood, particularly with regard to the organization of mineral deposits within the protein extracellular matrix and the identification of which proteins are responsible for this task. We report new experiments that provide insight into the role of the framework nacre protein, n16.3 (Pinctada fucata), as an organizer or assembler of calcium carbonate mineral clusters. Using a combination of biophysical techniques, we find that recombinant n16.3 (r-n16.3) oligomerizes to form amorphous protein films and particles that possess regions of disorder and mobility. These supramolecular assemblies possess an intrinsically disordered C-terminal region (T64-W98) and reorganize in the presence of Ca(2+) ions to form clustered protein oligomers. This Ca(2+)-induced reorganization leads to alterations in the molecular environments of Trp residues, the majority of which reside in putative aggregation-prone cross-beta strand regions. Potentiometric Ca(2+) titrations reveal that r-n16.3 does not significantly affect the formation of prenucleation clusters in solution, and this suggests a role for this protein in postnucleation mineralization events. This is verified in subsequent in vitro mineralization assays in which r-n16.3 demonstrates its ability to form gel-like protein phases that organize and cluster nanometer-sized single-crystal calcite relative to protein-deficient controls. We conclude that the n16 nacre framework proteome creates a protein gel matrix that organizes and dimensionally limits mineral deposits. This process is highly relevant to the formation of ordered, nanometer-sized nacre tablets in the mollusk shell. FAU - Perovic, Iva AU - Perovic I AD - Laboratory for Chemical Physics, Division of Basic Sciences and Craniofacial Biology, New York University , 345 East 24th Street, New York, New York 10010, United States. FAU - Chang, Eric P AU - Chang EP FAU - Lui, Michael AU - Lui M FAU - Rao, Ashit AU - Rao A FAU - Colfen, Helmut AU - Colfen H FAU - Evans, John Spencer AU - Evans JS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140418 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Nacre) RN - 0 (Proteins) RN - 8DUH1N11BX (Tryptophan) RN - H0G9379FGK (Calcium Carbonate) RN - SY7Q814VUP (Calcium) SB - IM MH - Animals MH - Calcium/chemistry/metabolism MH - Calcium Carbonate/chemistry/*metabolism MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Microscopy, Atomic Force MH - Nacre/*chemistry MH - Pinctada/*chemistry MH - Protein Structure, Tertiary MH - Proteins/*chemistry/genetics/*metabolism MH - Spectrometry, Fluorescence MH - Tryptophan/chemistry EDAT- 2014/04/12 06:00 MHDA- 2014/08/21 06:00 CRDT- 2014/04/12 06:00 PHST- 2014/04/18 [aheadofprint] AID - 10.1021/bi401721z [doi] PST - ppublish SO - Biochemistry. 2014 Apr 29;53(16):2739-48. doi: 10.1021/bi401721z. Epub 2014 Apr 18. PMID- 15339921 OWN - NLM STAT- MEDLINE DA - 20041115 DCOM- 20050111 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 47 DP - 2004 Nov 19 TI - The NS5A protein of hepatitis C virus is a zinc metalloprotein. PG - 48576-87 AB - The NS5A protein of hepatitis C virus is believed to be an integral part of the viral replicase. Despite extensive investigation, the role of this protein remains elusive. Only limited biochemical characterization of NS5A has been performed, with most research to date involving the myriad of host proteins and signaling cascades that interact with NS5A. The need for better characterization of NS5A is paramount for elucidating the role of this protein in the virus life cycle. Examination of NS5A using bioinformatics tools suggested the protein consisted of three domains and contained an unconventional zinc binding motif within the N-terminal domain. We have developed a method to produce NS5A and performed limited proteolysis to confirm the domain organization model. The zinc content of purified NS5A and the N-terminal domain of NS5A was determined, and each of these proteins was found to coordinate one zinc atom per protein. The predicted zinc binding motif consists of four cysteine residues, conserved among the Hepacivirus and Pestivirus genera, fitting the formula of CX17CXCX20C. Mutation of any of the four cysteine components of this motif reduced NS5A zinc coordination and led to a lethal phenotype for HCV RNA replication, whereas mutation of other potential metal coordination residues in the N-terminal domain of NS5A, but outside the zinc binding motif, had little effect on zinc binding and, aside from one exception, were tolerated for replication. Collectively, these results indicate that NS5A is a zinc metalloprotein and that zinc coordination is likely required for NS5A function in the hepatitis C replicase. FAU - Tellinghuisen, Timothy L AU - Tellinghuisen TL AD - Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, New York 10021, USA. FAU - Marcotrigiano, Joseph AU - Marcotrigiano J FAU - Gorbalenya, Alexander E AU - Gorbalenya AE FAU - Rice, Charles M AU - Rice CM LA - eng GR - 5 F32 AI51820-03/AI/NIAID NIH HHS/United States GR - 5 R01 CA57973-12/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20040831 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Metalloproteins) RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Viral Nonstructural Proteins) RN - 63231-63-0 (RNA) RN - EC 3.4.21.4 (Trypsin) RN - J41CSQ7QDS (Zinc) RN - K848JZ4886 (Cysteine) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - Cell Line, Tumor MH - Cloning, Molecular MH - Computational Biology MH - Cysteine/chemistry MH - Electroporation MH - Humans MH - Metalloproteins/*chemistry MH - Molecular Sequence Data MH - Mutagenesis MH - Mutation MH - Phenotype MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA/metabolism MH - Sequence Homology, Amino Acid MH - Signal Transduction MH - Spectrophotometry, Atomic MH - Transcription, Genetic MH - Trypsin/pharmacology MH - Viral Nonstructural Proteins/*chemistry/metabolism MH - Zinc/*chemistry EDAT- 2004/09/02 05:00 MHDA- 2005/01/12 09:00 CRDT- 2004/09/02 05:00 PHST- 2004/08/31 [aheadofprint] AID - 10.1074/jbc.M407787200 [doi] AID - M407787200 [pii] PST - ppublish SO - J Biol Chem. 2004 Nov 19;279(47):48576-87. Epub 2004 Aug 31. PMID- 20556825 OWN - NLM STAT- MEDLINE DA - 20100728 DCOM- 20101126 LR - 20140824 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 19 IP - 8 DP - 2010 Aug TI - Temperature-dependent structural changes in intrinsically disordered proteins: formation of alpha-helices or loss of polyproline II? PG - 1555-64 LID - 10.1002/pro.435 [doi] AB - Structural characterization of intrinsically disordered proteins (IDPs) is mandatory for deciphering their potential unique physical and biological properties. A large number of circular dichroism (CD) studies have demonstrated that a structural change takes place in IDPs with increasing temperature, which most likely reflects formation of transient alpha-helices or loss of polyproline II (PPII) content. Using three IDPs, ACTR, NHE1, and Spd1, we show that the temperature-induced structural change is common among IDPs and is accompanied by a contraction of the conformational ensemble. This phenomenon was explored at residue resolution by multidimensional NMR spectroscopy. Intrinsic chemical shift referencing allowed us to identify regions of transiently formed helices and their temperature-dependent changes in helicity. All helical regions were found to lose rather than gain helical structures with increasing temperature, and accordingly these were not responsible for the change in the CD spectra. In contrast, the nonhelical regions exhibited a general temperature-dependent structural change that was independent of long-range interactions. The temperature-dependent CD spectroscopic signature of IDPs that has been amply documented can be rationalized to represent redistribution of the statistical coil involving a general loss of PPII conformations. FAU - Kjaergaard, Magnus AU - Kjaergaard M AD - Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N DK-2200, Denmark. FAU - Norholm, Ann-Beth AU - Norholm AB FAU - Hendus-Altenburger, Ruth AU - Hendus-Altenburger R FAU - Pedersen, Stine F AU - Pedersen SF FAU - Poulsen, Flemming M AU - Poulsen FM FAU - Kragelund, Birthe B AU - Kragelund BB LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Cation Transport Proteins) RN - 0 (Fungal Proteins) RN - 0 (Peptides) RN - 0 (SLC9A1 protein, human) RN - 0 (Sodium-Hydrogen Antiporter) RN - 25191-13-3 (polyproline) SB - IM MH - Cation Transport Proteins/chemistry/genetics MH - Circular Dichroism MH - Fungal Proteins/chemistry/genetics MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides/*chemistry MH - *Protein Structure, Secondary MH - Scattering, Small Angle MH - Sodium-Hydrogen Antiporter/chemistry/genetics MH - *Temperature PMC - PMC2923508 OID - NLM: PMC2923508 EDAT- 2010/06/18 06:00 MHDA- 2010/12/14 06:00 CRDT- 2010/06/18 06:00 AID - 10.1002/pro.435 [doi] PST - ppublish SO - Protein Sci. 2010 Aug;19(8):1555-64. doi: 10.1002/pro.435. PMID- 23880650 OWN - NLM STAT- MEDLINE DA - 20131021 DCOM- 20131217 IS - 1095-8673 (Electronic) IS - 0022-4804 (Linking) VI - 185 IP - 1 DP - 2013 Nov TI - TC-1 (c8orf4) enhances aggressive biologic behavior in lung cancer through the Wnt/beta-catenin pathway. PG - 255-63 LID - 10.1016/j.jss.2013.05.075 [doi] LID - S0022-4804(13)00558-1 [pii] AB - BACKGROUND: The thyroid cancer-1 (TC-1) or c8orf4 gene encodes a 106-residue naturally disordered protein that has been found to be associated with thyroid, gastric, and breast cancer. A recent study has indicated that the protein functions as a positive regulator in the Wnt/beta-catenin signaling pathway in human breast cancer. However, no research has been done in the area of lung cancer. Therefore, the goal of the present study was to confirm the relationship among TC-1, lung cancer, and the Wnt/beta-catenin signaling pathway. MATERIALS AND METHODS: The expression of TC-1 was immunohistochemically examined in 147 patients with non-small-cell lung cancer. TC-1-overexpressed and silenced A549 cells were infected using lentivirus and MTT cell proliferation analysis, and Matrigel invasion assays and scratch-wound assays were performed to confirm the biologic behavioral changes in different A549 cell subsets. The Wnt/beta-catenin signaling pathway, key gene beta-catenin, target genes of vascular endothelial growth factor, cyclin D1, matrix metalloproteinase-7, c-myc, and survivin were tested at the mRNA and protein level. RESULTS: TC-1 was detected in 97 of the 147 non-small-cell lung cancer primary tumor specimens, and its expression correlated with the TNM stage and regional lymph node metastasis (P < 0.01). In vitro experiments demonstrated that TC-1 expression affected both proliferation and invasion in the A549 cell line. Furthermore, expression of TC-1 protein affected the Wnt/beta-catenin signaling pathway's downstream genes, such as vascular endothelial growth factor and matrix metalloproteinase-7, at the mRNA and protein level. CONCLUSIONS: TC-1 expression is associated with aggressive biologic behavior in lung cancer and might coordinate with the Wnt/beta-catenin pathway as a positive upstream regulator that induces these behaviors. CI - Copyright (c) 2013 Elsevier Inc. All rights reserved. FAU - Su, Kai AU - Su K AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China. FAU - Huang, Lijun AU - Huang L FAU - Li, Wenhai AU - Li W FAU - Yan, Xiaolong AU - Yan X FAU - Li, Xiaofei AU - Li X FAU - Zhang, Zhipei AU - Zhang Z FAU - Jin, Faguang AU - Jin F FAU - Lei, Jie AU - Lei J FAU - Ba, Guangzhen AU - Ba G FAU - Liu, Boya AU - Liu B FAU - Wang, Xiaoping AU - Wang X FAU - Wang, Yunjie AU - Wang Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130611 PL - United States TA - J Surg Res JT - The Journal of surgical research JID - 0376340 RN - 0 (C8orf4 protein, human) RN - 0 (CTNNB1 protein, human) RN - 0 (Neoplasm Proteins) RN - 0 (RNA, Small Interfering) RN - 0 (beta Catenin) SB - IM MH - *Adenocarcinoma/genetics/metabolism/secondary MH - Biopsy MH - Carcinoma, Non-Small-Cell Lung/genetics/metabolism/secondary MH - Cell Line, Tumor MH - Cell Movement/genetics MH - Disease Progression MH - Female MH - Gene Expression Regulation, Neoplastic MH - Humans MH - *Lung Neoplasms/genetics/metabolism/pathology MH - Lymphatic Metastasis/genetics/pathology MH - Male MH - Middle Aged MH - Neoplasm Invasiveness/pathology MH - Neoplasm Proteins/*genetics/*metabolism MH - RNA, Small Interfering/genetics MH - Wnt Signaling Pathway/*physiology MH - beta Catenin/*metabolism OTO - NOTNLM OT - Cancer metastasis OT - Lung cancer OT - TC-1 OT - Wnt/beta-catenin EDAT- 2013/07/25 06:00 MHDA- 2013/12/18 06:00 CRDT- 2013/07/25 06:00 PHST- 2013/01/16 [received] PHST- 2013/05/06 [revised] PHST- 2013/05/16 [accepted] PHST- 2013/06/11 [aheadofprint] AID - S0022-4804(13)00558-1 [pii] AID - 10.1016/j.jss.2013.05.075 [doi] PST - ppublish SO - J Surg Res. 2013 Nov;185(1):255-63. doi: 10.1016/j.jss.2013.05.075. Epub 2013 Jun 11. PMID- 15892946 OWN - NLM STAT- MEDLINE DA - 20050516 DCOM- 20051004 LR - 20130405 IS - 0003-9969 (Print) IS - 0003-9969 (Linking) VI - 50 IP - 7 DP - 2005 Jul TI - A review of protein structure and gene organisation for proteins associated with mineralised tissue and calcium phosphate stabilisation encoded on human chromosome 4. PG - 599-609 AB - Several proteins associated with mineralised tissue (teeth and bone) or involved in calcium phosphate stabilisation in the body fluids, milk and saliva have been mapped to the q arm of human chromosome 4. These include the dentine/bone proteins dentine sialophosphoprotein (DSPP), dentine matrix protein 1 (DMP1), bone sialoprotein (BSP), matrix extracellular phosphoglycoprotein, osteopontin (OPN), enamelin, ameloblastin, milk caseins, salivary statherin, and proline-rich proteins. The proposed function of those that are multiphosphorylated is: (i) the stabilisation of calcium phosphate in solution (e.g. casein, statherin) preventing spontaneous precipitation and seeded-crystal growth or (ii) promoting biomineralisation (e.g. the phosphophoryn domain of DSPP), where the protein described as a template macromolecule, is proposed to act as a nucleator/promoter of crystal growth. The genes of these proteins have been subjected to conserved chromosomal synteny during mammalian evolution. The multiphosphorylated proteins statherin, caseins, phosphophoryn, BSP and OPN have been characterised as intrinsically disordered. The codon usage patterns for the amino acid serine reveal a bias for AGC and AGT codons within the human genes dspp, dmp1 and bsp, mouse dspp and dmp1 but not significantly for statherin or caseins. This pattern was also observed in the gene encoding hen phosvitin that also contains stretches of multiphosphorylated serines and in the dmp1 gene sequences of mammalian, reptilian and avian classes. In conclusion, these intrinsically disordered multiphosphorylated proteins are the translation products of genes displaying examples of codon usage bias, internal repeats and conserved chromosomal synteny within the mammalian class. FAU - Huq, N Laila AU - Huq NL AD - Cooperative Research Centre for Oral Health Science, School of Dental Science, The University of Melbourne, 711 Elizabeth Street, Melbourne, Vic. 3010, Australia. FAU - Cross, Keith J AU - Cross KJ FAU - Ung, Men AU - Ung M FAU - Reynolds, Eric C AU - Reynolds EC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Arch Oral Biol JT - Archives of oral biology JID - 0116711 RN - 0 (Calcium Phosphates) RN - 0 (Proteins) RN - 97Z1WI3NDX (calcium phosphate) SB - D SB - IM MH - Animals MH - Bone and Bones/metabolism MH - Calcification, Physiologic/*genetics/physiology MH - Calcium Phosphates/*metabolism MH - Chromosomes, Human, Pair 4/*physiology MH - Evolution, Molecular MH - Humans MH - Proteins/*genetics/physiology RF - 65 EDAT- 2005/05/17 09:00 MHDA- 2005/10/05 09:00 CRDT- 2005/05/17 09:00 PHST- 2004/09/06 [received] PHST- 2004/12/23 [accepted] AID - S0003-9969(05)00008-7 [pii] AID - 10.1016/j.archoralbio.2004.12.009 [doi] PST - ppublish SO - Arch Oral Biol. 2005 Jul;50(7):599-609. PMID- 21628581 OWN - NLM STAT- MEDLINE DA - 20110622 DCOM- 20110929 LR - 20150511 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 108 IP - 25 DP - 2011 Jun 21 TI - Visualization of the nanospring dynamics of the IkappaBalpha ankyrin repeat domain in real time. PG - 10178-83 LID - 10.1073/pnas.1102226108 [doi] AB - IkappaBalpha is a crucial regulator of NFkappaB transcription. NFkappaB-mediated gene activation is robust because levels of free IkappaBalpha are kept extremely low by rapid, ubiquitin-independent degradation of newly synthesized IkappaBalpha. IkappaBalpha has a weakly folded ankyrin repeat 5-6 (AR5-6) region that is critical in establishing its short intracellular half-life. The AR5-6 region of IkappaBalpha folds upon binding to NFkappaB. The NFkappaB-bound IkappaBalpha has a long half-life and requires ubiquitin-targeted degradation. We present single molecule FRET evidence that the native state of IkappaBalpha transiently populates an intrinsically disordered state characterized by a more extended structure and fluctuations on the millisecond time scale. Binding to NFkappaB or introduction of stabilizing mutations in AR 6 suppressed the fluctuations, whereas higher temperature or small amounts of urea increased them. The results reveal that intrinsically disordered protein regions transition between collapsed and extended conformations under native conditions. FAU - Lamboy, Jorge A AU - Lamboy JA AD - Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92092-0378, USA. FAU - Kim, Hajin AU - Kim H FAU - Lee, Kyung Suk AU - Lee KS FAU - Ha, Taekjip AU - Ha T FAU - Komives, Elizabeth A AU - Komives EA LA - eng GR - P01-GM071862/GM/NIGMS NIH HHS/United States GR - R21 RR025341/RR/NCRR NIH HHS/United States GR - R21 RR025341/RR/NCRR NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110531 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (I-kappa B Proteins) RN - 0 (NF-kappa B) RN - 139874-52-5 (NF-kappaB inhibitor alpha) SB - IM MH - *Ankyrin Repeat MH - Fluorescence Resonance Energy Transfer MH - I-kappa B Proteins/*chemistry/genetics/metabolism MH - Models, Molecular MH - NF-kappa B/chemistry/metabolism MH - Nanostructures/*chemistry MH - Protein Binding MH - Protein Structure, Tertiary MH - Time Factors PMC - PMC3121830 OID - NLM: PMC3121830 EDAT- 2011/06/02 06:00 MHDA- 2011/10/01 06:00 CRDT- 2011/06/02 06:00 PHST- 2011/05/31 [aheadofprint] AID - 1102226108 [pii] AID - 10.1073/pnas.1102226108 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10178-83. doi: 10.1073/pnas.1102226108. Epub 2011 May 31. PMID- 23841450 OWN - NLM STAT- MEDLINE DA - 20131210 DCOM- 20131231 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 52 IP - 31 DP - 2013 Aug 6 TI - N-terminal disordered domain of Saccharomyces cerevisiae Hop1 protein is dispensable for DNA binding, bridging, and synapsis of double-stranded DNA molecules but is necessary for spore formation. PG - 5265-79 LID - 10.1021/bi4005528 [doi] AB - The cytological architecture of the synaptonemal complex (SC), a meiosis-specific proteinaceous structure, is evolutionarily conserved among eukaryotes. However, little is known about the biochemical properties of SC components or the mechanisms underlying their roles in meiotic chromosome synapsis and recombination. Functional analysis of Saccharomyces cerevisiae Hop1, a key structural component of SC, has begun to reveal important insights into its function in interhomolog recombination. Previously, we showed that Hop1 is a structure-specific DNA-binding protein, exhibits higher binding affinity for the Holliday junction, and induces structural distortion at the core of the junction. Furthermore, Hop1 promotes DNA condensation and intra- and intermolecular synapsis between duplex DNA molecules. Here, we show that Hop1 possesses a modular domain organization, consisting of an intrinsically disordered N-terminal domain and a protease-resistant C-terminal domain (Hop1CTD). Furthermore, we found that Hop1CTD exhibits strong homotypic as well as heterotypic protein-protein interactions, and its biochemical activities were similar to those of the full-length Hop1 protein. However, Hop1CTD failed to complement the meiotic recombination defects of the Deltahop1 strain, indicating that both N- and C-terminal domains of Hop1 are essential for meiosis and spore formation. Altogether, our findings reveal novel insights into the structure-function relationships of Hop1 and help to further our understanding of its role in meiotic chromosome synapsis and recombination. FAU - Khan, Krishnendu AU - Khan K AD - Department of Biochemistry, and double daggerDepartment of Microbiology and Cell Biology, Indian Institute of Science , Bangalore 560012, India. FAU - Madhavan, T P Vipin AU - Madhavan TP FAU - Kshirsagar, Rucha AU - Kshirsagar R FAU - Boosi, Kannan N AU - Boosi KN FAU - Sadhale, Parag AU - Sadhale P FAU - Muniyappa, K AU - Muniyappa K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130722 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA, Fungal) RN - 0 (DNA-Binding Proteins) RN - 0 (HOP1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Motifs MH - *Chromosome Pairing MH - DNA/chemistry/*genetics/metabolism MH - DNA, Fungal/chemistry/genetics/metabolism MH - DNA-Binding Proteins/*chemistry/genetics/*metabolism MH - Nucleic Acid Conformation MH - Saccharomyces cerevisiae/chemistry/genetics/growth & development/*metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism MH - Spores, Fungal/chemistry/genetics/*growth & development/metabolism EDAT- 2013/07/12 06:00 MHDA- 2014/01/01 06:00 CRDT- 2013/07/12 06:00 PHST- 2013/07/22 [aheadofprint] AID - 10.1021/bi4005528 [doi] PST - ppublish SO - Biochemistry. 2013 Aug 6;52(31):5265-79. doi: 10.1021/bi4005528. Epub 2013 Jul 22. PMID- 18976814 OWN - NLM STAT- MEDLINE DA - 20081201 DCOM- 20090909 LR - 20131121 IS - 1873-3344 (Electronic) IS - 0162-0134 (Linking) VI - 103 IP - 1 DP - 2009 Jan TI - Dopamine complexes of iron in the etiology and pathogenesis of Parkinson's disease. PG - 87-93 LID - 10.1016/j.jinorgbio.2008.09.007 [doi] AB - Parkinson's disease (PD) is the second most common neurodegenerative disease after Alzheimers. The main pathological hallmark of Parkinson's is the deterioration and death of neurons that produce the neurotransmitter dopamine. Much of the neuronal damage takes place in the substantia nigra, a small region of the midbrain that contains the cell bodies of neurons that produce dopamine. The deterioration and death of dopaminergic neurons are directly associated with misfolding and aggregation of proteins, principally alpha-synuclein, that are natively unfolded. Present also in the substantia nigra is an unusually high concentration of vestigial iron. Protein misfolding in non-genetic (sporadic) cases of PD has been associated with reactive oxygen species formed as products of O(2) reduction by the combination of dopamine and iron. Combinations of Fe(3+), dopamine hydrochloride (DA(H+)Cl), and various ancillary ligands have been studied as a function of pH in aqueous solution to determine the optimum pH for complex formation. With ancillary ligands (L(4)) derived from nitrilotriacetic acid and ethylenediamine diacetic acid spectral changes are consistent with the formation of L(4)Fe(DA(H+)) species that reach a maximum concentration at pH 7.2. With edta as the ancillary ligand, spectral features at pH 7 resemble those of Fe(3+)-catecholate complexes that contain catecholate ligands bonded through a single oxygen. This demonstrates the ability of the dopamine catechol functionality to penetrate the coordination sphere of even exceptionally stable iron chelates. FAU - Arreguin, Shelly AU - Arreguin S AD - Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA. FAU - Nelson, Paul AU - Nelson P FAU - Padway, Shelby AU - Padway S FAU - Shirazi, Matthew AU - Shirazi M FAU - Pierpont, Cortlandt AU - Pierpont C LA - eng PT - Journal Article DEP - 20080926 PL - United States TA - J Inorg Biochem JT - Journal of inorganic biochemistry JID - 7905788 RN - 0 (Iron Chelating Agents) RN - 0 (alpha-Synuclein) RN - 789U1901C5 (Copper) RN - E1UOL152H7 (Iron) RN - VTD58H1Z2X (Dopamine) SB - IM MH - Copper/*metabolism MH - Dopamine/*metabolism MH - Humans MH - Iron/*metabolism MH - Iron Chelating Agents/*metabolism MH - Neurons/metabolism MH - Parkinson Disease/etiology/*metabolism MH - alpha-Synuclein/metabolism EDAT- 2008/11/04 09:00 MHDA- 2009/09/10 06:00 CRDT- 2008/11/04 09:00 PHST- 2008/05/14 [received] PHST- 2008/09/16 [revised] PHST- 2008/09/18 [accepted] PHST- 2008/09/26 [aheadofprint] AID - S0162-0134(08)00222-5 [pii] AID - 10.1016/j.jinorgbio.2008.09.007 [doi] PST - ppublish SO - J Inorg Biochem. 2009 Jan;103(1):87-93. doi: 10.1016/j.jinorgbio.2008.09.007. Epub 2008 Sep 26. PMID- 11685242 OWN - NLM STAT- MEDLINE DA - 20011030 DCOM- 20011204 LR - 20091119 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 8 IP - 11 DP - 2001 Nov TI - The role of conformational flexibility in prion propagation and maintenance for Sup35p. PG - 958-62 AB - The [PSI(+)] factor of Saccharomyces cerevisiae is a protein-based genetic element (prion) comprised of a heritable altered conformation of the cytosolic translation termination factor Sup35p. In vitro, the prion-determining region (NM) of Sup35p undergoes conformational conversion from a highly flexible soluble state to structured amyloid fibers, with a rate that is greatly accelerated by preformed NM fiber nuclei. Nucleated conformational conversion is the molecular basis of the genetic inheritance of [PSI(+)] and provides a new model for studying amyloidogenesis. Here we investigate the importance of structure and structural flexibility in soluble NM. Elevated temperatures, chemical chaperones and certain mutations in NM increase or change its structural content and inhibit or enhance nucleated conformational conversion. We propose that the structural flexibility of NM is particularly suited to allowing heritable protein-based changes in cellular behavior. FAU - Scheibel, T AU - Scheibel T AD - Howard Hughes Medical Institute and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA. FAU - Lindquist, S L AU - Lindquist SL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Fungal Proteins) RN - 0 (Molecular Chaperones) RN - 0 (Oligopeptides) RN - 0 (Peptide Termination Factors) RN - 0 (Prions) RN - 0 (SUP35 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - *Amyloidosis/genetics MH - Fungal Proteins/*chemistry/genetics/*metabolism MH - Molecular Chaperones/genetics MH - Mutation/genetics MH - Oligopeptides/chemistry/genetics/metabolism MH - Osmolar Concentration MH - Peptide Termination Factors MH - Pliability MH - Prions/*chemistry/genetics/*metabolism MH - Protein Biosynthesis MH - Protein Denaturation MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Repetitive Sequences, Amino Acid/genetics MH - *Saccharomyces cerevisiae/chemistry/genetics/metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism MH - Solubility MH - Temperature EDAT- 2001/10/31 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/10/31 10:00 AID - 10.1038/nsb1101-958 [doi] AID - nsb1101-958 [pii] PST - ppublish SO - Nat Struct Biol. 2001 Nov;8(11):958-62. PMID- 23271955 OWN - NLM STAT- MEDLINE DA - 20121228 DCOM- 20130521 LR - 20141104 IS - 1545-7885 (Electronic) IS - 1544-9173 (Linking) VI - 10 IP - 12 DP - 2012 TI - Order-disorder transitions govern kinetic cooperativity and allostery of monomeric human glucokinase. PG - e1001452 LID - 10.1371/journal.pbio.1001452 [doi] AB - Glucokinase (GCK) catalyzes the rate-limiting step of glucose catabolism in the pancreas, where it functions as the body's principal glucose sensor. GCK dysfunction leads to several potentially fatal diseases including maturity-onset diabetes of the young type II (MODY-II) and persistent hypoglycemic hyperinsulinemia of infancy (PHHI). GCK maintains glucose homeostasis by displaying a sigmoidal kinetic response to increasing blood glucose levels. This positive cooperativity is unique because the enzyme functions exclusively as a monomer and possesses only a single glucose binding site. Despite nearly a half century of research, the mechanistic basis for GCK's homotropic allostery remains unresolved. Here we explain GCK cooperativity in terms of large-scale, glucose-mediated disorder-order transitions using 17 isotopically labeled isoleucine methyl groups and three tryptophan side chains as sensitive nuclear magnetic resonance (NMR) probes. We find that the small domain of unliganded GCK is intrinsically disordered and samples a broad conformational ensemble. We also demonstrate that small-molecule diabetes therapeutic agents and hyperinsulinemia-associated GCK mutations share a strikingly similar activation mechanism, characterized by a population shift toward a more narrow, well-ordered ensemble resembling the glucose-bound conformation. Our results support a model in which GCK generates its cooperative kinetic response at low glucose concentrations by using a millisecond disorder-order cycle of the small domain as a "time-delay loop," which is bypassed at high glucose concentrations, providing a unique mechanism to allosterically regulate the activity of human GCK under physiological conditions. FAU - Larion, Mioara AU - Larion M AD - Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America. FAU - Salinas, Roberto Kopke AU - Salinas RK FAU - Bruschweiler-Li, Lei AU - Bruschweiler-Li L FAU - Miller, Brian G AU - Miller BG FAU - Bruschweiler, Rafael AU - Bruschweiler R LA - eng GR - 1R01DK081358/DK/NIDDK NIH HHS/United States GR - R01 DK081358/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20121218 PL - United States TA - PLoS Biol JT - PLoS biology JID - 101183755 RN - 04Y7590D77 (Isoleucine) RN - EC 2.7.1.2 (Glucokinase) RN - IY9XDZ35W2 (Glucose) SB - IM MH - Allosteric Regulation MH - Amino Acid Substitution/genetics MH - Catalytic Domain MH - Congenital Hyperinsulinism/drug therapy/enzymology/genetics MH - Enzyme Activation MH - Enzyme Stability MH - Glucokinase/*chemistry/*metabolism MH - Glucose/metabolism MH - Humans MH - Isoleucine/chemistry MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Models, Biological MH - Models, Molecular MH - Protein Structure, Secondary MH - Protein Structure, Tertiary PMC - PMC3525530 OID - NLM: PMC3525530 EDAT- 2012/12/29 06:00 MHDA- 2013/05/23 06:00 CRDT- 2012/12/29 06:00 PHST- 2012/06/19 [received] PHST- 2012/11/07 [accepted] PHST- 2012/12/18 [epublish] AID - 10.1371/journal.pbio.1001452 [doi] AID - PBIOLOGY-D-12-02417 [pii] PST - ppublish SO - PLoS Biol. 2012;10(12):e1001452. doi: 10.1371/journal.pbio.1001452. Epub 2012 Dec 18. PMID- 10860732 OWN - NLM STAT- MEDLINE DA - 20000707 DCOM- 20000707 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 299 IP - 1 DP - 2000 May 26 TI - Four crystal structures of the 60 kDa flavoprotein monomer of the sulfite reductase indicate a disordered flavodoxin-like module. PG - 199-212 AB - Escherichia coli NADPH-sulfite reductase (SiR) is a 780 kDa multimeric hemoflavoprotein composed of eight alpha-subunits (SiR-FP) and four beta-subunits (SiR-HP) that catalyses the six electron reduction of sulfite to sulfide. Each beta-subunit contains a Fe4S4 cluster and a siroheme, and each alpha-subunit binds one FAD and one FMN as prosthetic groups. The FAD gets electrons from NADPH, and the FMN transfers the electrons to the metal centers of the beta-subunit for sulfite reduction. We report here the 1.94 A X-ray structure of SiR-FP60, a recombinant monomeric fragment of SiR-FP that binds both FAD and FMN and retains the catalytic properties of the native protein. The structure can be divided into three domains. The carboxy-terminal part of the enzyme is composed of an antiparallel beta-barrel which binds the FAD, and a variant of the classical pyridine dinucleotide binding fold which binds NADPH. These two domains form the canonic FNR-like module, typical of the ferredoxin NADP+ reductase family. By analogy with the structure of the cytochrome P450 reductase, the third domain, composed of seven alpha-helices, is supposed to connect the FNR-like module to the N-terminal flavodoxine-like module. In four different crystal forms, the FMN-binding module is absent from electron density maps, although mass spectroscopy, amino acid sequencing and activity experiments carried out on dissolved crystals indicate that a functional module is present in the protein. Our results clearly indicate that the interaction between the FNR-like and the FMN-like modules displays lower affinity than in the case of cytochrome P450 reductase. The flexibility of the FMN-binding domain may be related, as observed in the case of cytochrome bc1, to a domain reorganisation in the course of electron transfer. Thus, a movement of the FMN-binding domain relative to the rest of the enzyme may be a requirement for its optimal positioning relative to both the FNR-like module and the beta-subunit. FAU - Gruez, A AU - Gruez A AD - Laboratoire de Cristallographie et Cristallogenese des Proteines Institut de Biologie Structurale J.P. Ebel, CEA-CNRS, Grenoble, France. FAU - Pignol, D AU - Pignol D FAU - Zeghouf, M AU - Zeghouf M FAU - Coves, J AU - Coves J FAU - Fontecave, M AU - Fontecave M FAU - Ferrer, J L AU - Ferrer JL FAU - Fontecilla-Camps, J C AU - Fontecilla-Camps JC LA - eng SI - PDB/1DDG SI - PDB/1DDI PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Flavodoxin) RN - 0 (Peptide Fragments) RN - 146-14-5 (Flavin-Adenine Dinucleotide) RN - 53-59-8 (NADP) RN - 7N464URE7E (Flavin Mononucleotide) RN - EC 1.6.- (NADH, NADPH Oxidoreductases) RN - EC 1.6.2.4 (NADPH-Ferrihemoprotein Reductase) RN - EC 1.8.- (Oxidoreductases Acting on Sulfur Group Donors) RN - EC 1.8.1.2 (Sulfite Reductase (NADPH)) RN - EC 1.8.1.2 (sulfite reductase (NADPH), E coli) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Catalysis MH - Crystallization MH - Crystallography, X-Ray MH - Escherichia coli/*enzymology MH - Flavin Mononucleotide/metabolism MH - Flavin-Adenine Dinucleotide/metabolism MH - Flavodoxin/*chemistry/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Molecular Weight MH - Motion MH - NADH, NADPH Oxidoreductases/chemistry/metabolism MH - NADP/metabolism MH - NADPH-Ferrihemoprotein Reductase MH - Oxidoreductases Acting on Sulfur Group Donors/*chemistry/*metabolism MH - Peptide Fragments/chemistry/metabolism MH - Pliability MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Static Electricity MH - Sulfite Reductase (NADPH) EDAT- 2000/06/22 10:00 MHDA- 2000/07/15 11:00 CRDT- 2000/06/22 10:00 AID - 10.1006/jmbi.2000.3748 [doi] AID - S0022-2836(00)93748-3 [pii] PST - ppublish SO - J Mol Biol. 2000 May 26;299(1):199-212. PMID- 7642559 OWN - NLM STAT- MEDLINE DA - 19950918 DCOM- 19950918 LR - 20041117 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 270 IP - 32 DP - 1995 Aug 11 TI - Adducin: a physical model with implications for function in assembly of spectrin-actin complexes. PG - 18990-6 AB - Adducin binds to spectrin-actin complexes, promotes association of spectrin with actin, and is subject to regulation by calmodulin as well as protein kinases A and C. Adducin is a heteromer comprised of homologous alpha and beta-subunits with an NH2-terminal protease-resistant head domain, connected by a neck region to a COOH-terminal hydrophilic, protease-sensitive region. This study provides evidence that adducin in solution is a mixture of heterodimers and tetramers. CD spectroscopy of COOH-terminal domains of alpha- and beta-adducin bacterial recombinants provides direct evidence for an unstructured random coil configuration. Cross-linking, proteolysis, and blot-binding experiments suggest a model for the adducin tetramer in which four head domains contact one another to form a globular core with extended interacting alpha- and beta-adducin tails. The site for binding to spectrin-actin complexes on adducin was identified as the COOH-terminal tail of both the alpha- and beta-adducin subunits. The capacity of native adducin to recruit spectrin to actin filaments is similar to that of adducin tail domains. Thus, adducin tail domains alone are sufficient to interact with F-actin and a single spectrin and to recruit additional spectrin molecules to the ternary complex. FAU - Hughes, C A AU - Hughes CA AD - Howard Hughes Medical Institute, Duke University Medical Center, Durham, North Carolina 27710, USA. FAU - Bennett, V AU - Bennett V LA - eng PT - Journal Article PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Actins) RN - 0 (Blood Proteins) RN - 0 (Calmodulin-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 0 (adducin) RN - 12634-43-4 (Spectrin) SB - IM MH - Actins/*chemistry MH - Animals MH - Blood Proteins/*chemistry MH - Calmodulin-Binding Proteins/*chemistry MH - Humans MH - Models, Structural MH - Rabbits MH - Recombinant Proteins/chemistry MH - Spectrin/*chemistry EDAT- 1995/08/11 MHDA- 1995/08/11 00:01 CRDT- 1995/08/11 00:00 PST - ppublish SO - J Biol Chem. 1995 Aug 11;270(32):18990-6. PMID- 24311597 OWN - NLM STAT- MEDLINE DA - 20131206 DCOM- 20140709 LR - 20141112 IS - 1399-0047 (Electronic) IS - 0907-4449 (Linking) VI - 69 IP - Pt 12 DP - 2013 Dec TI - Structural basis of SUFU-GLI interaction in human Hedgehog signalling regulation. PG - 2563-79 LID - 10.1107/S0907444913028473 [doi] AB - Hedgehog signalling plays a fundamental role in the control of metazoan development, cell proliferation and differentiation, as highlighted by the fact that its deregulation is associated with the development of many human tumours. SUFU is an essential intracellular negative regulator of mammalian Hedgehog signalling and acts by binding and modulating the activity of GLI transcription factors. Despite its central importance, little is known about SUFU regulation and the nature of SUFU-GLI interaction. Here, the crystal and small-angle X-ray scattering structures of full-length human SUFU and its complex with the key SYGHL motif conserved in all GLIs are reported. It is demonstrated that GLI binding is associated with major conformational changes in SUFU, including an intrinsically disordered loop that is also crucial for pathway activation. These findings reveal the structure of the SUFU-GLI interface and suggest a mechanism for an essential regulatory step in Hedgehog signalling, offering possibilities for the development of novel pathway modulators and therapeutics. FAU - Cherry, Amy L AU - Cherry AL AD - Department of Biosciences and Nutrition and Center for Biosciences, Karolinska Institutet, Novum, Halsovagen 7, SE-141 83 Huddinge, Sweden. FAU - Finta, Csaba AU - Finta C FAU - Karlstrom, Mikael AU - Karlstrom M FAU - Jin, Qianren AU - Jin Q FAU - Schwend, Thomas AU - Schwend T FAU - Astorga-Wells, Juan AU - Astorga-Wells J FAU - Zubarev, Roman A AU - Zubarev RA FAU - Del Campo, Mark AU - Del Campo M FAU - Criswell, Angela R AU - Criswell AR FAU - de Sanctis, Daniele AU - de Sanctis D FAU - Jovine, Luca AU - Jovine L FAU - Toftgard, Rune AU - Toftgard R LA - eng SI - PDB/4BL8 SI - PDB/4BL9 SI - PDB/4BLA SI - PDB/4BLB SI - PDB/4BLD PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131119 PL - United States TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (GLI1 protein, human) RN - 0 (Repressor Proteins) RN - 0 (SUFU protein, human) RN - 0 (Transcription Factors) SB - IM MH - Amino Acid Sequence MH - Animals MH - Crystallography, X-Ray MH - Hedgehogs/*metabolism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Interaction Maps MH - Repressor Proteins/*chemistry/*metabolism MH - Signal Transduction MH - Transcription Factors/*chemistry/*metabolism PMC - PMC3852661 OID - NLM: PMC3852661 OTO - NOTNLM OT - GLI OT - Hedgehog signalling regulation OT - SUFU EDAT- 2013/12/07 06:00 MHDA- 2014/07/10 06:00 CRDT- 2013/12/07 06:00 PHST- 2013/08/27 [received] PHST- 2013/10/16 [accepted] PHST- 2013/11/19 [epublish] AID - S0907444913028473 [pii] AID - 10.1107/S0907444913028473 [doi] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2013 Dec;69(Pt 12):2563-79. doi: 10.1107/S0907444913028473. Epub 2013 Nov 19. PMID- 23946424 OWN - NLM STAT- MEDLINE DA - 20130828 DCOM- 20131122 LR - 20141113 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 110 IP - 35 DP - 2013 Aug 27 TI - Signaling through dynamic linkers as revealed by PKA. PG - 14231-6 LID - 10.1073/pnas.1312644110 [doi] AB - Protein kinase A (PKA) is a prototype of multidomain signaling proteins functioning as allosteric conformational switches. Allosteric transitions have been the subject of extensive structural and dynamic investigations focusing mainly on folded domains. However, the current understanding of the allosteric role of partially unstructured linkers flanking globular domains is limited. Here, we show that a dynamic linker in the regulatory subunit (R) of PKA serves not only as a passive covalent thread, but also as an active allosteric element that controls activation of the kinase subunit (C) by tuning the inhibitory preequilibrium of a minimally populated intermediate (apo R). Apo R samples both C-binding competent (inactive) and incompetent (active) conformations within a nearly degenerate free-energy landscape and such degeneracy maximally amplifies the response to weak ( approximately 2RT), but conformation-selective interactions elicited by the linker. Specifically, the R linker that in the R:C complex docks in the active site of C in apo R preferentially interacts with the C-binding incompetent state of the adjacent cAMP-binding domain (CBD). These unanticipated findings imply that the formation of the intermolecular R:C inhibitory interface occurs at the expense of destabilizing the intramolecular linker/CBD interactions in R. A direct implication of this model, which was not predictable solely based on protein structure, is that the disruption of a linker/CBD salt bridge in the R:C complex unexpectedly leads to increased affinity of R for C. The linker includes therefore sites of R:C complex frustration and frustration-relieving mutations enhance the kinase inhibitory potency of R without compromising its specificity. FAU - Akimoto, Madoka AU - Akimoto M AD - Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada L8S 4M1. FAU - Selvaratnam, Rajeevan AU - Selvaratnam R FAU - McNicholl, E Tyler AU - McNicholl ET FAU - Verma, Geeta AU - Verma G FAU - Taylor, Susan S AU - Taylor SS FAU - Melacini, Giuseppe AU - Melacini G LA - eng GR - Howard Hughes Medical Institute/United States GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130814 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Cyclic AMP-Dependent Protein Kinase RIalpha Subunit) RN - E0399OZS9N (Cyclic AMP) SB - IM MH - Allosteric Regulation MH - Cyclic AMP/metabolism MH - Cyclic AMP-Dependent Protein Kinase RIalpha Subunit/chemistry/*metabolism MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - *Signal Transduction PMC - PMC3761587 OID - NLM: PMC3761587 OTO - NOTNLM OT - NMR OT - allostery OT - cAMP OT - dynamics OT - intrinsically disordered proteins EDAT- 2013/08/16 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/08/16 06:00 PHST- 2013/08/14 [aheadofprint] AID - 1312644110 [pii] AID - 10.1073/pnas.1312644110 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14231-6. doi: 10.1073/pnas.1312644110. Epub 2013 Aug 14. PMID- 18762866 OWN - NLM STAT- MEDLINE DA - 20080909 DCOM- 20090306 IS - 0925-2738 (Print) IS - 0925-2738 (Linking) VI - 42 IP - 1 DP - 2008 Sep TI - A simple method for amino acid selective isotope labeling of recombinant proteins in E. coli. PG - 59-67 LID - 10.1007/s10858-008-9264-0 [doi] AB - A simple and user-friendly method of labeling protein selectively with amino acids in vivo is introduced. This technique does not require the use of transaminase-deficient or auxotrophic strains. By manipulating the product feedback inhibitory loops of the E. coli amino acid metabolic pathways and, if necessary, by using enzyme inhibitors, proteins were labeled efficiently in vivo even with amino acid types that are central to the metabolic pathways, such as glutamine. The sequential backbone resonance assignment of the Neh2 domain of Nrf2 transcriptional factor, an intrinsically disordered protein with high spectral degeneracy, was achieved using this labeling method. FAU - Tong, Kit I AU - Tong KI AD - Center for Tsukuba Advanced Research Alliance, Graduate School of Comprehensive Human Sciences, JST-ERATO Environmental Response Project, University of Tsukuba, Tsukuba, 305-8577, Japan. FAU - Yamamoto, Masayuki AU - Yamamoto M FAU - Tanaka, Toshiyuki AU - Tanaka T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080902 PL - Netherlands TA - J Biomol NMR JT - Journal of biomolecular NMR JID - 9110829 RN - 0 (Amino Acids) RN - 0 (Recombinant Proteins) SB - IM MH - Amino Acid Sequence MH - Amino Acids/*analysis/*chemistry MH - Escherichia coli/chemistry/genetics/metabolism MH - Isotope Labeling/*methods MH - Nuclear Magnetic Resonance, Biomolecular MH - Recombinant Proteins/analysis/chemistry/genetics/metabolism EDAT- 2008/09/03 09:00 MHDA- 2009/03/07 09:00 CRDT- 2008/09/03 09:00 PHST- 2008/02/26 [received] PHST- 2008/08/06 [accepted] PHST- 2008/09/02 [aheadofprint] AID - 10.1007/s10858-008-9264-0 [doi] PST - ppublish SO - J Biomol NMR. 2008 Sep;42(1):59-67. doi: 10.1007/s10858-008-9264-0. Epub 2008 Sep 2. PMID- 19914198 OWN - NLM STAT- MEDLINE DA - 20100127 DCOM- 20100218 LR - 20131121 IS - 1096-0384 (Electronic) IS - 0003-9861 (Linking) VI - 494 IP - 1 DP - 2010 Feb 1 TI - Tyr74 is essential for the formation, stability and function of Plasmodium falciparum triosephosphate isomerase dimer. PG - 46-57 LID - 10.1016/j.abb.2009.11.009 [doi] AB - Plasmodium falciparum triosephosphate isomerase (PfTIM) is known to be functional only as a homodimer. Although many studies have shown that the interface Cys13 plays a major role in the stability of the dimer, a few reports have demonstrated that structurally conserved Tyr74 may be essential for the stability of PfTIM dimer. To understand the role of Tyr74, we have performed molecular dynamics (MD) simulations of monomeric and dimeric PfTIM mutated to glycine and cysteine at position 74. Simulations of the monomer revealed that mutant Tyr74Gly does not produce changes in folding and stability of the monomer. Interestingly, comparison of the flexibility of Tyr74 in the monomer and dimer revealed that this residue possesses an intrinsic restricted mobility, indicating that Tyr74 is an anchor residue required for homodimerization. Tyr74 also appears to play an important role in binding by facilitating the disorder-to-order transitions of loops 1 and 3, which allows Cys13 to form favorable interactions with loop 3 and Lys12 to be locked in a favorable position for catalysis. High-temperature MD simulations of the wild-type and Tyr74Gly PfTIM dimers showed that the aromatic moiety of Tyr74 is necessary to preserve the geometry and native contacts between loops 1 and 3 at the interface of the dimer. Disulfide cross-linking between mutant Tyr74Cys and Cys13 further revealed that Tyr74 stabilizes the geometry of loop 1 (which contains the catalytic residue Lys12) and the interactions between loops 1 and 3 via aromatic-aromatic interactions with residues Phe69, Tyr101, and Phe102. Principal component analysis showed that Tyr74 is also necessary to preserve the collective motions in the dimer that contribute to the catalytic efficiency of PfTIM dimer. We conclude that Tyr74 not only plays a role in the stability of the dimer, but also participates in the dimerization process and collective motions via coupled disorder-to-order transitions of intrinsically disordered regions, necessary for efficiency in the catalytic function of PfTIM. CI - Copyright (c) 2009 Elsevier Inc. All rights reserved. FAU - Espinoza-Fonseca, L Michel AU - Espinoza-Fonseca LM AD - Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA. mef@ddt.biochem.umn.edu FAU - Wong-Ramirez, Carlos AU - Wong-Ramirez C FAU - Trujillo-Ferrara, Jose G AU - Trujillo-Ferrara JG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091113 PL - United States TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 42HK56048U (Tyrosine) RN - EC 5.3.1.1 (Triose-Phosphate Isomerase) SB - IM MH - Animals MH - Crystallography, X-Ray MH - Dimerization MH - Enzyme Stability MH - Models, Molecular MH - Molecular Dynamics Simulation MH - Plasmodium falciparum/*enzymology MH - Protein Conformation MH - Triose-Phosphate Isomerase/chemistry/*metabolism MH - Tyrosine/*metabolism EDAT- 2009/11/17 06:00 MHDA- 2010/02/19 06:00 CRDT- 2009/11/17 06:00 PHST- 2009/09/16 [received] PHST- 2009/11/09 [revised] PHST- 2009/11/09 [accepted] PHST- 2009/11/13 [aheadofprint] AID - S0003-9861(09)00369-5 [pii] AID - 10.1016/j.abb.2009.11.009 [doi] PST - ppublish SO - Arch Biochem Biophys. 2010 Feb 1;494(1):46-57. doi: 10.1016/j.abb.2009.11.009. Epub 2009 Nov 13. PMID- 19710012 OWN - NLM STAT- MEDLINE DA - 20091012 DCOM- 20091124 LR - 20140828 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 284 IP - 42 DP - 2009 Oct 16 TI - Inhibition of Schistosoma mansoni thioredoxin-glutathione reductase by auranofin: structural and kinetic aspects. PG - 28977-85 LID - 10.1074/jbc.M109.020701 [doi] AB - Schistosomiasis is a parasitic disease affecting over 200 million people currently treated with one drug, praziquantel. A possible drug target is the seleno-protein thioredoxin-glutathione reductase (TGR), a key enzyme in the pathway of the parasite for detoxification of reactive oxygen species. The enzyme is a unique fusion of a glutaredoxin domain with a thioredoxin reductase domain, which contains a selenocysteine (Sec) as the penultimate amino acid. Auranofin (AF), a gold-containing compound already in clinical use as an anti-arthritic drug, has been shown to inhibit TGR and to substantially reduce worm burden in mice. Using x-ray crystallography we solved (at 2.5 A resolution) the structure of wild type TGR incubated with AF. The electron density maps show that the actual inhibitor is gold, released from AF. Gold is bound at three different sites not directly involving the C-terminal Sec residue; however, because the C terminus in the electron density maps is disordered, we cannot exclude the possibility that gold may also bind to Sec. To investigate the possible role of Sec in the inactivation kinetics, we tested the effect of AF on a model enzyme of the same superfamily, i.e. the naturally Sec-lacking glutathione reductase, and on truncated TGR. We demonstrate that the role of selenium in the onset of inhibition by AF is catalytic and can be mimicked by an external source of selenium (benzeneselenol). Therefore, we propose that Sec mediates the transfer of gold from its ligands in AF to the redox-active Cys couples of TGR. FAU - Angelucci, Francesco AU - Angelucci F AD - Department of Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, P. Le Aldo Moro 5, 00185 Rome, Italy. FAU - Sayed, Ahmed A AU - Sayed AA FAU - Williams, David L AU - Williams DL FAU - Boumis, Giovanna AU - Boumis G FAU - Brunori, Maurizio AU - Brunori M FAU - Dimastrogiovanni, Daniela AU - Dimastrogiovanni D FAU - Miele, Adriana E AU - Miele AE FAU - Pauly, Frida AU - Pauly F FAU - Bellelli, Andrea AU - Bellelli A LA - eng SI - PDB/3H4K GR - AI065622/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090826 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Antirheumatic Agents) RN - 0 (Helminth Proteins) RN - 0 (Multienzyme Complexes) RN - 3H04W2810V (Auranofin) RN - EC 1.6.- (NADH, NADPH Oxidoreductases) RN - EC 1.6.4.- (thioredoxin glutathione reductase) RN - H6241UJ22B (Selenium) RN - K848JZ4886 (Cysteine) SB - IM MH - Animals MH - Antirheumatic Agents/*chemistry/pharmacology MH - Auranofin/*chemistry/pharmacology MH - Catalysis MH - Crystallography, X-Ray/methods MH - Cysteine/chemistry MH - Dose-Response Relationship, Drug MH - *Gene Expression Regulation MH - Helminth Proteins/*chemistry MH - Kinetics MH - Models, Molecular MH - Multienzyme Complexes/antagonists & inhibitors/*chemistry MH - NADH, NADPH Oxidoreductases/antagonists & inhibitors/*chemistry MH - Oxidation-Reduction MH - Protein Structure, Tertiary MH - Schistosoma mansoni/*metabolism MH - Selenium/chemistry PMC - PMC2781444 OID - NLM: PMC2781444 EDAT- 2009/08/28 09:00 MHDA- 2009/12/16 06:00 CRDT- 2009/08/28 09:00 PHST- 2009/08/26 [aheadofprint] AID - M109.020701 [pii] AID - 10.1074/jbc.M109.020701 [doi] PST - ppublish SO - J Biol Chem. 2009 Oct 16;284(42):28977-85. doi: 10.1074/jbc.M109.020701. Epub 2009 Aug 26. PMID- 565710 OWN - NLM STAT- MEDLINE DA - 19780724 DCOM- 19780724 LR - 20070723 IS - 0014-2956 (Print) IS - 0014-2956 (Linking) VI - 84 IP - 1 DP - 1978 Mar TI - Studies on the conformational properties of the high-mobility-group chromosomal protein HMG 17 and its interaction with DNA. PG - 173-7 AB - The conformation of the non-histone chromatin protein, HMG 17, has been studied using circular dichroism, infrared and nuclear magnetic resonance spectroscopies, and by small-angle scattering. The results show that in free solution this protein has little or no secondary or tertiary structure in contrast to the other high-mobility-group proteins, HMG 1 and 2, which exhibit highly ordered structures. Protein HMG 17 binds to calf thymus DNA in an ionic-dependent manner, precipitating the DNA at high protein/DNA ratio. The nuclear magnetic resonance data suggest that the principle DNA-binding segment of HMG 17 is that between about residues 15 and 40. FAU - Abercrombie, B D AU - Abercrombie BD FAU - Kneale, G G AU - Kneale GG FAU - Crane-Robinson, C AU - Crane-Robinson C FAU - Bradbury, E M AU - Bradbury EM FAU - Goodwin, G H AU - Goodwin GH FAU - Walker, J M AU - Walker JM FAU - Johns, E W AU - Johns EW LA - eng PT - Journal Article PL - GERMANY, WEST TA - Eur J Biochem JT - European journal of biochemistry / FEBS JID - 0107600 RN - 0 (Chromosomal Proteins, Non-Histone) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Cattle MH - *Chromosomal Proteins, Non-Histone MH - Circular Dichroism MH - *DNA MH - Magnetic Resonance Spectroscopy MH - Protein Binding MH - Protein Conformation EDAT- 1978/03/01 MHDA- 1978/03/01 00:01 CRDT- 1978/03/01 00:00 PST - ppublish SO - Eur J Biochem. 1978 Mar;84(1):173-7. PMID- 11823864 OWN - NLM STAT- MEDLINE DA - 20020201 DCOM- 20020312 LR - 20061115 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 415 IP - 6871 DP - 2002 Jan 31 TI - Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators. PG - 549-53 AB - Nuclear hormone receptors are ligand-activated transcription factors that regulate the expression of genes that are essential for development, reproduction and homeostasis. The hormone response is mediated through recruitment of p160 receptor coactivators and the general transcriptional coactivator CBP/p300, which function synergistically to activate transcription. These coactivators exhibit intrinsic histone acetyltransferase activity, function in the remodelling of chromatin, and facilitate the recruitment of RNA polymerase II and the basal transcription machinery. The activities of the p160 coactivators are dependent on CBP. Both coactivators are essential for proper cell-cycle control, differentiation and apoptosis, and are implicated in cancer and other diseases. To elucidate the molecular basis of assembling the multiprotein activation complex, we undertook a structural and thermodynamic analysis of the interaction domains of CBP and the activator for thyroid hormone and retinoid receptors. Here we show that although the isolated domains are intrinsically disordered, they combine with high affinity to form a cooperatively folded helical heterodimer. Our study uncovers a unique mechanism, called 'synergistic folding', through which p160 coactivators recruit CBP/p300 to allow transmission of the hormonal signal to the transcriptional machinery. FAU - Demarest, Stephen J AU - Demarest SJ AD - Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. FAU - Martinez-Yamout, Maria AU - Martinez-Yamout M FAU - Chung, John AU - Chung J FAU - Chen, Hongwu AU - Chen H FAU - Xu, Wei AU - Xu W FAU - Dyson, H Jane AU - Dyson HJ FAU - Evans, Ronald M AU - Evans RM FAU - Wright, Peter E AU - Wright PE LA - eng SI - PDB/1KBH PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Carrier Proteins) RN - 0 (Cyclic AMP Response Element-Binding Protein) RN - 0 (Ep300 protein, mouse) RN - 0 (Mybbp1a protein, mouse) RN - 0 (Nuclear Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Trans-Activators) RN - EC 2.3.1.48 (E1A-Associated p300 Protein) SB - IM MH - Amino Acid Sequence MH - Animals MH - Carrier Proteins/chemistry/genetics/*metabolism MH - Cell Nucleus/metabolism MH - Cyclic AMP Response Element-Binding Protein/metabolism MH - E1A-Associated p300 Protein MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Proteins/chemistry/genetics/*metabolism MH - *Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Trans-Activators/chemistry/genetics/*metabolism EDAT- 2002/02/02 10:00 MHDA- 2002/03/13 10:01 CRDT- 2002/02/02 10:00 AID - 10.1038/415549a [doi] AID - 415549a [pii] PST - ppublish SO - Nature. 2002 Jan 31;415(6871):549-53. PMID- 19053469 OWN - NLM STAT- MEDLINE DA - 20081216 DCOM- 20090206 LR - 20131121 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 130 IP - 50 DP - 2008 Dec 17 TI - Structural and dynamic characterization of intrinsically disordered human securin by NMR spectroscopy. PG - 16873-9 LID - 10.1021/ja805510b [doi] AB - Understanding the molecular action of securin, the inhibitor of separase in mitosis, is of immense theoretical and biomedical importance. The residue-level structural description of an intrinsically disordered protein of this length (202 amino acids, containing 24 prolines), however, represents a particular challenge. Here we combined (1)H-detected and (13)C-detected protonless NMR experiments to achieve full assignment of securin's backbone amide resonances. Chemical shifts, (15)N relaxation rates (R(1), R(2), (1)H-(15)N NOEs), (1)H exchange rates with the solvent (CLEANEX-PM), and (1)H-(15)N residual dipolar couplings were determined along the entire length of the protein. This analysis showed that securin is not entirely disordered, but segregates into a largely disordered N-terminal half and a C-terminal half with transient segmental order, within which the segment D(150)-F(159) has a significant helical tendency and segments E(113)-S(127) and W(174)-L(178) also show a significant deviation from random-coil behavior. These results, in combination with bioinformatic and biochemical data on the securin/separase interaction, shed light on the inhibitory action of securin on separase. FAU - Csizmok, Veronika AU - Csizmok V AD - Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Karolina ut 29, H-1113, Hungary. FAU - Felli, Isabella C AU - Felli IC FAU - Tompa, Peter AU - Tompa P FAU - Banci, Lucia AU - Banci L FAU - Bertini, Ivano AU - Bertini I LA - eng GR - ISRF 067595/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Cell Cycle Proteins) RN - 0 (Neoplasm Proteins) RN - 0 (Securin) RN - 0 (pituitary tumor-transforming protein 1, human) RN - EC 3.4.- (Endopeptidases) RN - EC 3.4.22.49 (ESPL1 protein, human) RN - EC 3.4.22.49 (Separase) SB - IM MH - Algorithms MH - Cell Cycle Proteins/metabolism MH - Endopeptidases/metabolism MH - Humans MH - Neoplasm Proteins/*chemistry/genetics/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Securin MH - Separase EDAT- 2008/12/05 09:00 MHDA- 2009/02/07 09:00 CRDT- 2008/12/05 09:00 AID - 10.1021/ja805510b [doi] AID - 10.1021/ja805510b [pii] PST - ppublish SO - J Am Chem Soc. 2008 Dec 17;130(50):16873-9. doi: 10.1021/ja805510b. PMID- 20337445 OWN - NLM STAT- MEDLINE DA - 20100414 DCOM- 20100708 LR - 20121115 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 132 IP - 15 DP - 2010 Apr 21 TI - In situ misfolding of human islet amyloid polypeptide at interfaces probed by vibrational sum frequency generation. PG - 5405-12 LID - 10.1021/ja909546b [doi] AB - Kinetic analysis of conformational changes of proteins at interfaces is crucial for understanding many biological processes at membrane surfaces. In this study, we demonstrate that surface-selective sum frequency generation (SFG) spectroscopy can be used to investigate kinetics of conformational changes of proteins at interfaces. We focus on an intrinsically disordered protein, human islet amyloid polypeptide (hIAPP) that is known to misfold into the beta-sheet structure upon interaction with membranes. Using the ssp polarization setting (s-polarized SFG, s-polarized visible, and p-polarized infrared), we observe changes in the amide I spectra of hIAPP at the air/water interface after addition of dipalmitoylphosphoglycerol (DPPG) that correspond to the lipid-induced changes in secondary structures. We also used the chiral-sensitive psp polarization setting to obtain amide I spectra and observed a gradual buildup of the chiral structures that display the vibrational characteristics of parallel beta-sheets. We speculate that the second-order chiral-optical response at the antisymmetric stretch frequency of parallel beta-sheet at 1622 cm(-1) could be a highly characteristic optical property of the beta-sheet aggregates not only for hIAPP, but possibly also for other amyloid proteins. Analyzing the achiral and chiral amide I spectra, we conclude that DPPG induces the misfolding of hIAPP from alpha-helical and random-coil structures to the parallel beta-sheet structure at the air/water interface. We propose that SFG could complement existing techniques in obtaining kinetic and structural information for probing structures and functions of proteins at interfaces. FAU - Fu, Li AU - Fu L AD - Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, USA. FAU - Ma, Gang AU - Ma G FAU - Yan, Elsa C Y AU - Yan EC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Amyloid) RN - 0 (Islet Amyloid Polypeptide) RN - 0 (Phosphatidylglycerols) RN - VA9U6BR3SB (1,2-dipalmitoylphosphatidylglycerol) SB - IM MH - Amyloid/*chemistry/drug effects MH - Humans MH - Islet Amyloid Polypeptide MH - Kinetics MH - Phosphatidylglycerols/pharmacology MH - Protein Conformation MH - Protein Folding MH - Spectrum Analysis/methods EDAT- 2010/03/27 06:00 MHDA- 2010/07/09 06:00 CRDT- 2010/03/27 06:00 AID - 10.1021/ja909546b [doi] PST - ppublish SO - J Am Chem Soc. 2010 Apr 21;132(15):5405-12. doi: 10.1021/ja909546b. PMID- 12586824 OWN - NLM STAT- MEDLINE DA - 20030421 DCOM- 20030716 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 17 DP - 2003 Apr 25 TI - A broken alpha -helix in folded alpha -Synuclein. PG - 15313-8 AB - alpha-Synuclein is a small cytosolic protein of presynaptic nerve terminals composed of seven 11-residue repeats and a hydrophilic tail. alpha-Synuclein misfolding and dysfunction may contribute to the pathogenesis of Parkinson's disease and neurodegenerative dementias, but its normal folding and function are unknown. In solution, alpha-synuclein is natively unstructured but assumes an alpha-helical conformation upon binding to phospholipid membranes. We now show that this conformation of alpha-synuclein consists of two alpha-helical regions that are interrupted by a short break. The structural organization of the alpha-helices of alpha-synuclein was not anticipated by sequence analyses and may be important for its pathogenic role. FAU - Chandra, Sreeganga AU - Chandra S AD - Center for Basic Neuroscience, Department of Molecular Genetics, and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9111, USA. Sreeganga.Chandra@UTSouthwestern.edu FAU - Chen, Xiaocheng AU - Chen X FAU - Rizo, Josep AU - Rizo J FAU - Jahn, Reinhard AU - Jahn R FAU - Sudhof, Thomas C AU - Sudhof TC LA - eng GR - 1-R01-NS40057/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20030213 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Detergents) RN - 0 (Liposomes) RN - 0 (Nerve Tissue Proteins) RN - 0 (Phospholipids) RN - 0 (Phosphoproteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Detergents/metabolism/pharmacology MH - Humans MH - Liposomes/chemistry/metabolism/pharmacology MH - Magnetic Resonance Spectroscopy MH - Nerve Tissue Proteins/*chemistry/metabolism MH - Parkinsonian Disorders/etiology MH - Peptide Mapping MH - Phospholipids/metabolism/*pharmacology MH - Phosphoproteins/chemistry/metabolism MH - *Protein Folding MH - Protein Structure, Secondary/drug effects MH - Synucleins MH - alpha-Synuclein EDAT- 2003/02/15 04:00 MHDA- 2003/07/17 05:00 CRDT- 2003/02/15 04:00 PHST- 2003/02/13 [aheadofprint] AID - 10.1074/jbc.M213128200 [doi] AID - M213128200 [pii] PST - ppublish SO - J Biol Chem. 2003 Apr 25;278(17):15313-8. Epub 2003 Feb 13. PMID- 10704311 OWN - NLM STAT- MEDLINE DA - 20000410 DCOM- 20000410 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 297 IP - 1 DP - 2000 Mar 17 TI - Conformation of the RNA polymerase II C-terminal domain: circular dichroism of long and short fragments. PG - 119-33 AB - The C-terminal domain (CTD) of the largest subunit of RNA polymerase II consists of tandemly repeated copies of a heptapeptide with the Y(1)S(2)P(3)T(4)S(5)P(6)S(7) consensus sequence. This repeat contains two overlapping SPXX motifs that can adopt a beta-turn conformation. In addition, each CTD repeat contains the PXXP sequence characteristic of the left-handed helix of polyproline II (P(II)) found in SH3 domain ligands and the PXY sequence that is the target for WW domains. We have studied CTD fragments using circular dichroism (CD) to characterize the conformation of the CTD in water and in the hydrogen bond-promoting solvent trifluoroethanol (TFE). In water, an eight-repeat fragment is predominantly unordered, but at 32 degrees C has P(II) and beta-turn contents estimated to be about 15 % and less than 10 %, respectively. In 90 % TFE, the beta-turn fraction is estimated to be about 75 %, the remainder being unordered and P(II) conformations. The Tyr side-chains are ordered to a significant extent in 90 % TFE. Replacement of the fully conserved Pro residues by alpha-aminoisobutyric acid leads to a large increase in beta-turn. Replacement of Ser2 by Ala does not substantially alter the CTD conformation in water or TFE. Ser5 replacement by Ala increases the P(II) content in water and affects the conformation in TFE-rich solutions. Phosphorylation of Ser2 and Ser5 has little effect in water, but Ser2 affects the conformation in TFE-rich solution in much the same way as Ser5-->Ala substitution. The CD of the full-length murine CTD in water is similar to that of the eight-repeat fragment, indicating little difference in conformation with increasing chain length beyond eight repeats. The roles of P(II) and beta-turn in the interaction of CTD with its target proteins (mediator and RNA-processing components) are discussed. The most likely interactions are between P(II) and WW or SH3 domains, or with some unknown P(II)-binding motif. CI - Copyright 2000 Academic Press. FAU - Bienkiewicz, E A AU - Bienkiewicz EA AD - Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA. FAU - Moon Woody, A AU - Moon Woody A FAU - Woody, R W AU - Woody RW LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Aminoisobutyric Acids) RN - 0 (Peptide Fragments) RN - 0 (Solvents) RN - 059QF0KO0R (Water) RN - 1E7ZW41IQU (2-aminoisobutyric acid) RN - 42HK56048U (Tyrosine) RN - 452VLY9402 (Serine) RN - 75-89-8 (Trifluoroethanol) RN - 9DLQ4CIU6V (Proline) RN - EC 2.7.7.- (RNA Polymerase II) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Aminoisobutyric Acids/metabolism MH - Animals MH - Binding Sites MH - Circular Dichroism MH - Conserved Sequence MH - Hydrogen Bonding MH - Mice MH - Molecular Weight MH - Peptide Fragments/*chemistry/*metabolism MH - Phosphorylation MH - Proline/metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA Polymerase II/*chemistry/*metabolism MH - Repetitive Sequences, Amino Acid MH - Serine/metabolism MH - Solvents MH - Temperature MH - Trifluoroethanol/metabolism MH - Tyrosine/metabolism MH - Water/metabolism EDAT- 2000/03/08 09:00 MHDA- 2000/04/15 09:00 CRDT- 2000/03/08 09:00 AID - 10.1006/jmbi.2000.3545 [doi] AID - S0022283600935459 [pii] PST - ppublish SO - J Mol Biol. 2000 Mar 17;297(1):119-33. PMID- 22882870 OWN - NLM STAT- MEDLINE DA - 20121001 DCOM- 20130214 LR - 20141105 IS - 1471-2229 (Electronic) IS - 1471-2229 (Linking) VI - 12 DP - 2012 TI - Identification of the dehydrin gene family from grapevine species and analysis of their responsiveness to various forms of abiotic and biotic stress. PG - 140 AB - BACKGROUND: Dehydrins (DHNs) protect plant cells from desiccation damage during environmental stress, and also participate in host resistance to various pathogens. In this study, we aimed to identify and characterize the DHN gene families from Vitis vinifera and wild V. yeshanensis, which is tolerant to both drought and cold, and moderately resistant to powdery mildew. RESULTS: Four DHN genes were identified in both V. vinifera and V. yeshanensis, which shared a high sequence identity between the two species but little homology between the genes themselves. These genes were designated DHN1, DHN2, DHN3 and DHN4. All four of the DHN proteins were highly hydrophilic and were predicted to be intrinsically disordered, but they differed in their isoelectric points, kinase selectivities and number of functional motifs. Also, the expression profiles of each gene differed appreciably from one another. Grapevine DHN1 was not expressed in vegetative tissues under normal growth conditions, but was induced by drought, cold, heat, embryogenesis, as well as the application of abscisic acid (ABA), salicylic acid (SA), and methyl jasmonate (MeJA). It was expressed earlier in V. yeshanensis under drought conditions than in V. vinifera, and also exhibited a second round of up-regulation in V. yeshanensis following inoculation with Erysiphe necator, which was not apparent in V. vinifera. Like DHN1, DHN2 was induced by cold, heat, embryogenesis and ABA; however, it exhibited no responsiveness to drought, E. necator infection, SA or MeJA, and was also expressed constitutively in vegetative tissues under normal growth conditions. Conversely, DHN3 was only expressed during seed development at extremely low levels, and DHN4 was expressed specifically during late embryogenesis. Neither DHN3 nor DHN4 exhibited responsiveness to any of the treatments carried out in this study. Interestingly, the presence of particular cis-elements within the promoter regions of each gene was positively correlated with their expression profiles. CONCLUSIONS: The grapevine DHN family comprises four divergent members. While it is likely that their functions overlap to some extent, it seems that DHN1 provides the main stress-responsive function. In addition, our results suggest a close relationship between expression patterns, physicochemical properties, and cis-regulatory elements in the promoter regions of the DHN genes. FAU - Yang, Yazhou AU - Yang Y AD - College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China. FAU - He, Mingyang AU - He M FAU - Zhu, Ziguo AU - Zhu Z FAU - Li, Shuxiu AU - Li S FAU - Xu, Yan AU - Xu Y FAU - Zhang, Chaohong AU - Zhang C FAU - Singer, Stacy D AU - Singer SD FAU - Wang, Yuejin AU - Wang Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120810 PL - England TA - BMC Plant Biol JT - BMC plant biology JID - 100967807 RN - 0 (Acetates) RN - 0 (Cyclopentanes) RN - 0 (Oxylipins) RN - 0 (Plant Proteins) RN - 1211-29-6 (methyl jasmonate) RN - 134711-03-8 (dehydrin proteins, plant) RN - 72S9A8J5GW (Abscisic Acid) RN - O414PZ4LPZ (Salicylic Acid) SB - IM MH - Abscisic Acid/pharmacology MH - Acetates/pharmacology MH - Amino Acid Sequence MH - Ascomycota/pathogenicity MH - Chromosomes, Plant/genetics MH - Cold Temperature MH - Cyclopentanes/pharmacology MH - Droughts MH - *Gene Expression Regulation, Plant MH - *Genes, Plant MH - Molecular Sequence Data MH - Oxylipins/pharmacology MH - Phylogeny MH - Plant Diseases/microbiology MH - Plant Proteins/genetics/*metabolism MH - Promoter Regions, Genetic MH - Regulatory Sequences, Nucleic Acid MH - Salicylic Acid/pharmacology MH - Seeds/drug effects/genetics MH - Sequence Alignment MH - *Stress, Physiological MH - Transcriptome MH - Vitis/drug effects/*genetics/microbiology PMC - PMC3460772 OID - NLM: PMC3460772 EDAT- 2012/08/14 06:00 MHDA- 2013/02/15 06:00 CRDT- 2012/08/14 06:00 PHST- 2012/02/28 [received] PHST- 2012/08/02 [accepted] PHST- 2012/08/10 [aheadofprint] AID - 1471-2229-12-140 [pii] AID - 10.1186/1471-2229-12-140 [doi] PST - epublish SO - BMC Plant Biol. 2012 Aug 10;12:140. PMID- 24559112 OWN - NLM STAT- MEDLINE DA - 20140318 DCOM- 20140615 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 10 DP - 2014 Mar 18 TI - Cysteine-rich positions outside the structural zinc motif of human papillomavirus E7 provide conformational modulation and suggest functional redox roles. PG - 1680-96 LID - 10.1021/bi401562e [doi] AB - The E7 protein from high-risk human papillomavirus is essential for cell transformation in cervical, oropharyngeal, and other HPV-related cancers, mainly through the inactivation of the retinoblastoma (Rb) tumor suppressor. Its high cysteine content (~7%) and the observation that HPV-transformed cells are under oxidative stress prompted us to investigate the redox properties of the HPV16 E7 protein under biologically compatible oxidative conditions. The seven cysteines in HPV16 E7 remain reduced in conditions resembling the basal reduced state of a cell. However, under oxidative stress, a stable disulfide bridge forms between cysteines 59 and 68. Residue 59 has a protective effect on the other cysteines, and its mutation leads to an overall increase in the oxidation propensity of E7, including cysteine 24 central to the Rb binding motif. Gluthationylation of Cys 24 abolishes Rb binding, which is reversibly recovered upon reduction. Cysteines 59 and 68 are located 18.6 A apart, and the formation of the disulfide bridge leads to a large structural rearrangement while retaining strong Zn association. These conformational and covalent changes are fully reversible upon restoration of the reductive environment. In addition, this is the first evidence of an interaction between the N-terminal intrinsically disordered and the C-terminal globular domains, known to be highly and separately conserved among human papillomaviruses. The significant conservation of such noncanonical cysteines in HPV E7 proteins leads us to propose a functional redox activity. Such an activity adds to the previously discovered chaperone activity of E7 and supports the picture of a moonlighting pathological role of this paradigmatic viral oncoprotein. FAU - Chemes, Lucia B AU - Chemes LB AD - Protein Structure-Function and Engineering Laboratory, Fundacion Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina. FAU - Camporeale, Gabriela AU - Camporeale G FAU - Sanchez, Ignacio E AU - Sanchez IE FAU - de Prat-Gay, Gonzalo AU - de Prat-Gay G FAU - Alonso, Leonardo G AU - Alonso LG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140306 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Papillomavirus E7 Proteins) RN - 0 (oncogene protein E7, Human papillomavirus type 16) RN - K848JZ4886 (Cysteine) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Cysteine/*chemistry/genetics/metabolism MH - Human papillomavirus 16/chemistry/genetics/*metabolism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Oxidative Stress MH - Papillomavirus E7 Proteins/chemistry/genetics/*metabolism MH - Papillomavirus Infections/*metabolism/virology MH - Sequence Alignment MH - Zinc Fingers EDAT- 2014/02/25 06:00 MHDA- 2014/06/16 06:00 CRDT- 2014/02/25 06:00 PHST- 2014/03/06 [aheadofprint] AID - 10.1021/bi401562e [doi] PST - ppublish SO - Biochemistry. 2014 Mar 18;53(10):1680-96. doi: 10.1021/bi401562e. Epub 2014 Mar 6. PMID- 24817693 OWN - NLM STAT- MEDLINE DA - 20140610 DCOM- 20140902 LR - 20150104 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 21 DP - 2014 May 27 TI - Solution conditions determine the relative importance of nucleation and growth processes in alpha-synuclein aggregation. PG - 7671-6 LID - 10.1073/pnas.1315346111 [doi] AB - The formation of amyloid fibrils by the intrinsically disordered protein alpha-synuclein is a hallmark of Parkinson disease. To characterize the microscopic steps in the mechanism of aggregation of this protein we have used in vitro aggregation assays in the presence of preformed seed fibrils to determine the molecular rate constant of fibril elongation under a range of different conditions. We show that alpha-synuclein amyloid fibrils grow by monomer and not oligomer addition and are subject to higher-order assembly processes that decrease their capacity to grow. We also find that at neutral pH under quiescent conditions homogeneous primary nucleation and secondary processes, such as fragmentation and surface-assisted nucleation, which can lead to proliferation of the total number of aggregates, are undetectable. At pH values below 6, however, the rate of secondary nucleation increases dramatically, leading to a completely different balance between the nucleation and growth of aggregates. Thus, at mildly acidic pH values, such as those, for example, that are present in some intracellular locations, including endosomes and lysosomes, multiplication of aggregates is much faster than at normal physiological pH values, largely as a consequence of much more rapid secondary nucleation. These findings provide new insights into possible mechanisms of alpha-synuclein aggregation and aggregate spreading in the context of Parkinson disease. FAU - Buell, Alexander K AU - Buell AK AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; and. FAU - Galvagnion, Celine AU - Galvagnion C AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; and. FAU - Gaspar, Ricardo AU - Gaspar R AD - Departments of Physical Chemistry and. FAU - Sparr, Emma AU - Sparr E AD - Departments of Physical Chemistry and. FAU - Vendruscolo, Michele AU - Vendruscolo M AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; and. FAU - Knowles, Tuomas P J AU - Knowles TP AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; and. FAU - Linse, Sara AU - Linse S AD - Biochemistry and Structural Biology, Lund University, SE221 00 Lund, Sweden. FAU - Dobson, Christopher M AU - Dobson CM AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; and cmd44@cam.ac.uk. LA - eng GR - BB/H003843/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140509 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Amyloid) RN - 0 (alpha-Synuclein) SB - IM MH - Amyloid/*biosynthesis MH - Humans MH - Hydrogen-Ion Concentration MH - Kinetics MH - Microscopy, Atomic Force MH - Parkinson Disease/*metabolism MH - Static Electricity MH - alpha-Synuclein/*metabolism PMC - PMC4040554 OID - NLM: PMC4040554 OTO - NOTNLM OT - electrostatic interactions OT - kinetic analysis OT - neurodegenerative disease OT - prion-like behavior OT - seeding EDAT- 2014/05/13 06:00 MHDA- 2014/09/03 06:00 CRDT- 2014/05/13 06:00 PHST- 2014/05/09 [aheadofprint] AID - 1315346111 [pii] AID - 10.1073/pnas.1315346111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 May 27;111(21):7671-6. doi: 10.1073/pnas.1315346111. Epub 2014 May 9. PMID- 9712872 OWN - NLM STAT- MEDLINE DA - 19980924 DCOM- 19980924 LR - 20071115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 273 IP - 35 DP - 1998 Aug 28 TI - Solution structure of eotaxin, a chemokine that selectively recruits eosinophils in allergic inflammation. PG - 22471-9 AB - The solution structure of the CCR3-specific chemokine, eotaxin, has been determined by NMR spectroscopy. The quaternary structure of eotaxin was investigated by ultracentrifugation and NMR, and it was found to be in equilibrium between monomer and dimer under a wide range of conditions. At pH 3.0.CO;2-D [pii] AID - 10.1002/(SICI)1097-0134(199607)25:3<267::AID-PROT1>3.0.CO;2-D [doi] PST - ppublish SO - Proteins. 1996 Jul;25(3):267-85. PMID- 22421432 OWN - NLM STAT- MEDLINE DA - 20120404 DCOM- 20120521 LR - 20141019 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 109 IP - 14 DP - 2012 Apr 3 TI - Direct observation of multiple misfolding pathways in a single prion protein molecule. PG - 5283-8 LID - 10.1073/pnas.1107736109 [doi] AB - Protein misfolding is a ubiquitous phenomenon associated with a wide range of diseases. Single-molecule approaches offer a powerful tool for deciphering the mechanisms of misfolding by measuring the conformational fluctuations of a protein with high sensitivity. We applied single-molecule force spectroscopy to observe directly the misfolding of the prion protein PrP, a protein notable for having an infectious misfolded state that is able to propagate by recruiting natively folded PrP. By measuring folding trajectories of single PrP molecules held under tension in a high-resolution optical trap, we found that the native folding pathway involves only two states, without evidence for partially folded intermediates that have been proposed to mediate misfolding. Instead, frequent but fleeting transitions were observed into off-pathway intermediates. Three different misfolding pathways were detected, all starting from the unfolded state. Remarkably, the misfolding rate was even higher than the rate for native folding. A mutant PrP with higher aggregation propensity showed increased occupancy of some of the misfolded states, suggesting these states may act as intermediates during aggregation. These measurements of individual misfolding trajectories demonstrate the power of single-molecule approaches for characterizing misfolding directly by mapping out nonnative folding pathways. FAU - Yu, Hao AU - Yu H AD - Department of Physics, University of Alberta, Edmonton AB, T6G 2G7 Canada. FAU - Liu, Xia AU - Liu X FAU - Neupane, Krishna AU - Neupane K FAU - Gupta, Amar Nath AU - Gupta AN FAU - Brigley, Angela M AU - Brigley AM FAU - Solanki, Allison AU - Solanki A FAU - Sosova, Iveta AU - Sosova I FAU - Woodside, Michael T AU - Woodside MT LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120315 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Prions) SB - IM MH - Prions/*metabolism MH - Protein Folding MH - Spectrum Analysis/methods PMC - PMC3325692 OID - NLM: PMC3325692 EDAT- 2012/03/17 06:00 MHDA- 2012/05/23 06:00 CRDT- 2012/03/17 06:00 PHST- 2012/03/15 [aheadofprint] AID - 1107736109 [pii] AID - 10.1073/pnas.1107736109 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5283-8. doi: 10.1073/pnas.1107736109. Epub 2012 Mar 15. PMID- 25260075 OWN - NLM STAT- MEDLINE DA - 20140927 DCOM- 20150610 LR - 20150501 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 9 DP - 2014 TI - General amyloid inhibitors? A critical examination of the inhibition of IAPP amyloid formation by inositol stereoisomers. PG - e104023 LID - 10.1371/journal.pone.0104023 [doi] AB - Islet amyloid polypeptide (IAPP or amylin) forms amyloid deposits in the islets of Langerhans; a process that is believed to contribute to the progression of type 2 diabetes and to the failure of islet transplants. An emerging theme in amyloid research is the hypothesis that the toxic species produced during amyloid formation by different polypeptides share common features and exert their effects by common mechanisms. If correct, this suggests that inhibitors of amyloid formation by one polypeptide might be effective against other amyloidogenic sequences. IAPP and Abeta, the peptide responsible for amyloid formation in Alzheimer's disease, are particularly interesting in this regard as they are both natively unfolded in their monomeric states and share some common characteristics. Comparatively little effort has been expended on the design of IAPP amyloid inhibitors, thus it is natural to inquire if Abeta inhibitors are effective against IAPP, especially since no IAPP inhibitors have been clinically approved. A range of compounds inhibit Abeta amyloid formation, including various stereoisomers of inositol. Myo-, scyllo-, and epi-inositol have been shown to induce conformational changes in Abeta and prevent Abeta amyloid fibril formation by stabilizing non-fibrillar beta-sheet structures. We investigate the ability of inositol stereoisomers to inhibit amyloid formation by IAPP. The compounds do not induce a conformational change in IAPP and are ineffective inhibitors of IAPP amyloid formation, although some do lead to modest apparent changes in IAPP amyloid fibril morphology. Thus not all classes of Abeta inhibitors are effective against IAPP. This work provides a basis of comparison to work on polyphenol based inhibitors of IAPP amyloid formation and helps provide clues as to the features which render them effective. The study also helps provide information for further efforts in rational inhibitor design. FAU - Wang, Hui AU - Wang H AD - Department of Chemistry, Stony Brook University, Stony Brook, New York, United States of America. FAU - Raleigh, Daniel P AU - Raleigh DP AD - Department of Chemistry, Stony Brook University, Stony Brook, New York, United States of America; Graduate Program in Biochemistry and Structural Biology, Graduate Program in Biophysics, Stony Brook University, Stony Brook, New York, United States of America. LA - eng GR - GM078114/GM/NIGMS NIH HHS/United States GR - R01 GM078114/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140926 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Amyloid) RN - 0 (Islet Amyloid Polypeptide) RN - 4L6452S749 (Inositol) SB - IM MH - Alzheimer Disease/metabolism MH - Amino Acid Sequence MH - Amyloid/chemistry/*metabolism MH - Diabetes Mellitus, Type 2/metabolism MH - Inositol/chemistry/*pharmacology MH - Islet Amyloid Polypeptide/chemistry/genetics/*metabolism MH - Molecular Sequence Data MH - Molecular Structure MH - *Protein Aggregation, Pathological MH - Protein Conformation/drug effects MH - Stereoisomerism PMC - PMC4178012 OID - NLM: PMC4178012 EDAT- 2014/09/27 06:00 MHDA- 2015/06/11 06:00 CRDT- 2014/09/27 06:00 PHST- 2014 [ecollection] PHST- 2014/04/01 [received] PHST- 2014/07/09 [accepted] PHST- 2014/09/26 [epublish] AID - 10.1371/journal.pone.0104023 [doi] AID - PONE-D-14-14660 [pii] PST - epublish SO - PLoS One. 2014 Sep 26;9(9):e104023. doi: 10.1371/journal.pone.0104023. eCollection 2014. PMID- 18061582 OWN - NLM STAT- MEDLINE DA - 20071217 DCOM- 20080305 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 581 IP - 30 DP - 2007 Dec 22 TI - X-ray structure of the PHF core C-terminus: insight into the folding of the intrinsically disordered protein tau in Alzheimer's disease. PG - 5872-8 AB - The major constituent of Alzheimer's disease paired helical filaments (PHF) core is intrinsically disordered protein (IDP) tau. In spite of a considerable effort, insoluble character of PHF together with inherent physical properties of IDP tau have precluded so far reconstruction of PHF 3D structure by X-ray crystallography or NMR spectroscopy. Here we present first crystallographic study of PHF core C-terminus. Using monoclonal antibody MN423 specific to the tertiary structure of the PHF core, the in vivo PHF structure was imprinted into recombinant core PHF tau. Crystallization of the complex led to determination of the structure of the core PHF tau protein fragment 386TDHGAE391 at 1.65A resolution. Structural analysis suggests important role of the core PHF C-terminus for PHF assembly. It is reasonable to expect that this approach will help to reveal the structural principles underlying the tau protein assembly into PHF and possibly will facilitate rationale drug design for inhibition of Alzheimer neurofibrillary changes. FAU - Sevcik, Jozef AU - Sevcik J AD - Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, 845 10 Bratislava, Slovakia. FAU - Skrabana, Rostislav AU - Skrabana R FAU - Dvorsky, Radovan AU - Dvorsky R FAU - Csokova, Natalia AU - Csokova N FAU - Iqbal, Khalid AU - Iqbal K FAU - Novak, Michal AU - Novak M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20071203 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Antibodies, Monoclonal) RN - 0 (Antigen-Antibody Complex) RN - 0 (Immunoglobulin Fab Fragments) RN - 0 (Immunoglobulin Heavy Chains) RN - 0 (Immunoglobulin Light Chains) RN - 0 (Ligands) RN - 0 (Peptides) RN - 0 (Recombinant Proteins) RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/*metabolism MH - Amino Acid Sequence MH - Antibodies, Monoclonal MH - Antigen-Antibody Complex MH - Crystallography, X-Ray MH - Hydrogen Bonding MH - Immunoglobulin Fab Fragments/chemistry MH - Immunoglobulin Heavy Chains/chemistry MH - Immunoglobulin Light Chains/chemistry MH - Ligands MH - Models, Molecular MH - Molecular Sequence Data MH - Neurofibrillary Tangles/*chemistry MH - Peptides/chemistry MH - Protein Binding MH - Protein Conformation MH - *Protein Folding MH - Recombinant Proteins/chemistry MH - tau Proteins/*chemistry/*metabolism EDAT- 2007/12/07 09:00 MHDA- 2008/03/06 09:00 CRDT- 2007/12/07 09:00 PHST- 2007/10/03 [received] PHST- 2007/11/15 [revised] PHST- 2007/11/19 [accepted] PHST- 2007/12/03 [aheadofprint] AID - S0014-5793(07)01221-5 [pii] AID - 10.1016/j.febslet.2007.11.067 [doi] PST - ppublish SO - FEBS Lett. 2007 Dec 22;581(30):5872-8. Epub 2007 Dec 3. PMID- 23775688 OWN - NLM STAT- MEDLINE DA - 20130618 DCOM- 20131114 LR - 20131121 IS - 0065-2598 (Print) IS - 0065-2598 (Linking) VI - 991 DP - 2013 TI - The driving force of alpha-synuclein insertion and amyloid channel formation in the plasma membrane of neural cells: key role of ganglioside- and cholesterol-binding domains. PG - 15-26 LID - 10.1007/978-94-007-6331-9_2 [doi] AB - Alpha-synuclein is an amyloidogenic protein expressed in brain and involved in Parkinson's disease. It is an intrinsically disordered protein that folds into an alpha-helix rich structure upon binding to membrane lipids. Helical alpha-synuclein can penetrate the membrane and form oligomeric ion channels, thereby eliciting important perturbations of calcium fluxes. The study of alpha-synuclein/lipid interactions had shed some light on the molecular mechanisms controlling the targeting and functional insertion of alpha-synuclein in neural membranes. The protein first interacts with a cell surface glycosphingolipid (ganglioside GM3 in astrocytes or GM1 in neurons). This induces the folding of an alpha-helical domain containing a tilted peptide (67-78) that displays a high affinity for cholesterol. The driving force of the insertion process is the formation of a transient OH-Pi hydrogen bond between the ganglioside and the aromatic ring of the alpha-synuclein residue Tyr-39. The higher polarity of Tyr-39 vs. the lipid bilayer forces the protein to cross the membrane, allowing the tilted peptide to reach cholesterol. The tilted geometry of the cholesterol/alpha-synuclein complex facilitates the formation of an oligomeric channel. Interestingly, this functional cooperation between glycosphingolipids and cholesterol presents a striking analogy with virus fusion mechanisms. FAU - Fantini, Jacques AU - Fantini J AD - Faculte des Sciences Saint-Jerome, Aix Marseille University, Marseille, France. jacques.fantini@univ-amu.fr FAU - Yahi, Nouara AU - Yahi N LA - eng PT - Journal Article PT - Review PL - United States TA - Adv Exp Med Biol JT - Advances in experimental medicine and biology JID - 0121103 RN - 0 (Amyloid) RN - 0 (G(M3) Ganglioside) RN - 0 (Ion Channels) RN - 0 (alpha-Synuclein) RN - 97C5T2UQ7J (Cholesterol) SB - IM MH - Amyloid/*chemistry MH - Animals MH - Binding Sites MH - Cell Membrane/metabolism MH - Cholesterol/*chemistry MH - G(M3) Ganglioside/*chemistry MH - Humans MH - Ion Channels/*chemistry MH - Neurons/*metabolism MH - alpha-Synuclein/*chemistry/physiology EDAT- 2013/06/19 06:00 MHDA- 2013/11/15 06:00 CRDT- 2013/06/19 06:00 AID - 10.1007/978-94-007-6331-9_2 [doi] PST - ppublish SO - Adv Exp Med Biol. 2013;991:15-26. doi: 10.1007/978-94-007-6331-9_2. PMID- 21677644 OWN - NLM STAT- MEDLINE DA - 20110707 DCOM- 20110819 LR - 20141022 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 475 IP - 7354 DP - 2011 Jul 7 TI - Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. PG - 96-100 LID - 10.1038/nature10154 [doi] AB - Many globular and natively disordered proteins can convert into amyloid fibrils. These fibrils are associated with numerous pathologies as well as with normal cellular functions, and frequently form during protein denaturation. Inhibitors of pathological amyloid fibril formation could be useful in the development of therapeutics, provided that the inhibitors were specific enough to avoid interfering with normal processes. Here we show that computer-aided, structure-based design can yield highly specific peptide inhibitors of amyloid formation. Using known atomic structures of segments of amyloid fibrils as templates, we have designed and characterized an all-D-amino-acid inhibitor of the fibril formation of the tau protein associated with Alzheimer's disease, and a non-natural L-amino-acid inhibitor of an amyloid fibril that enhances sexual transmission of human immunodeficiency virus. Our results indicate that peptides from structure-based designs can disrupt the fibril formation of full-length proteins, including those, such as tau protein, that lack fully ordered native structures. Because the inhibiting peptides have been designed on structures of dual-beta-sheet 'steric zippers', the successful inhibition of amyloid fibril formation strengthens the hypothesis that amyloid spines contain steric zippers. CI - (c)2011 Macmillan Publishers Limited. All rights reserved FAU - Sievers, Stuart A AU - Sievers SA AD - Department of Biological Chemistry, Howard Hughes Medical Institute, UCLA, Box 951970, Los Angeles, California 90095-1570, USA. FAU - Karanicolas, John AU - Karanicolas J FAU - Chang, Howard W AU - Chang HW FAU - Zhao, Anni AU - Zhao A FAU - Jiang, Lin AU - Jiang L FAU - Zirafi, Onofrio AU - Zirafi O FAU - Stevens, Jason T AU - Stevens JT FAU - Munch, Jan AU - Munch J FAU - Baker, David AU - Baker D FAU - Eisenberg, David AU - Eisenberg D LA - eng SI - OMIM/3PPD GR - P50 AG016570/AG/NIA NIH HHS/United States GR - R01 AG029430/AG/NIA NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110615 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Amino Acids) RN - 0 (Amyloid) RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptides) RN - 0 (tau Proteins) RN - 25104-18-1 (Polylysine) SB - IM MH - Amino Acid Sequence MH - Amino Acids/*chemistry/*pharmacology MH - Amyloid/*antagonists & inhibitors/*chemistry/metabolism MH - Amyloid beta-Peptides/antagonists & inhibitors/chemistry/metabolism MH - Computer-Aided Design MH - *Drug Design MH - HIV Infections/virology MH - Hydrogen Bonding MH - Kinetics MH - Models, Molecular MH - Peptides/*chemistry/*pharmacology MH - Polylysine/pharmacology MH - Protein Conformation MH - tau Proteins/antagonists & inhibitors PMC - PMC4073670 MID - NIHMS591364 OID - NLM: NIHMS591364 OID - NLM: PMC4073670 EDAT- 2011/06/17 06:00 MHDA- 2011/08/20 06:00 CRDT- 2011/06/17 06:00 PHST- 2010/12/06 [received] PHST- 2011/04/21 [accepted] PHST- 2011/06/15 [aheadofprint] AID - nature10154 [pii] AID - 10.1038/nature10154 [doi] PST - epublish SO - Nature. 2011 Jun 15;475(7354):96-100. doi: 10.1038/nature10154. PMID- 24127580 OWN - NLM STAT- MEDLINE DA - 20131030 DCOM- 20140108 LR - 20141112 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 110 IP - 44 DP - 2013 Oct 29 TI - MDMX contains an autoinhibitory sequence element. PG - 17814-9 LID - 10.1073/pnas.1317398110 [doi] AB - MDM2 and MDMX are homologous proteins that bind to p53 and regulate its activity. Both contain three folded domains and ~70% intrinsically disordered regions. Previous detailed structural and biophysical studies have concentrated on the isolated folded domains. The N-terminal domains of both exhibit high affinity for the disordered N-terminal of p53 (p53TAD) and inhibit its transactivation function. Here, we have studied full-length MDMX and found a ~100-fold weaker affinity for p53TAD than does its isolated N-terminal domain. We found from NMR spectroscopy and binding studies that MDMX (but not MDM2) contains a conserved, disordered self-inhibitory element that competes intramolecularly for binding with p53TAD. This motif, which we call the WWW element, is centered around residues Trp200 and Trp201. Deletion or mutation of the element increased binding affinity of MDMX to that of the isolated N-terminal domain level. The self-inhibition of MDMX implies a regulatory, allosteric mechanism of its activity. MDMX rests in a latent state in which its binding activity with p53TAD is masked by autoinhibition. Activation of MDMX would require binding to a regulatory protein. The inhibitory function of the WWW element may explain the oncogenic effects of an alternative splicing variant of MDMX that does not contain the WWW element and is found in some aggressive cancers. FAU - Bista, Michal AU - Bista M AD - Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom. FAU - Petrovich, Miriana AU - Petrovich M FAU - Fersht, Alan R AU - Fersht AR LA - eng GR - G0901534/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131014 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (MDM4 protein, human) RN - 0 (Nuclear Proteins) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Calorimetry MH - Chromatography, Gel MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*genetics MH - Oncogenes/*genetics MH - Protein Binding MH - Proto-Oncogene Proteins/*genetics MH - Regulatory Elements, Transcriptional/*genetics MH - Tumor Suppressor Protein p53/*antagonists & inhibitors/genetics MH - Ubiquitination MH - Ultracentrifugation PMC - PMC3816421 OID - NLM: PMC3816421 OTO - NOTNLM OT - HDMX OT - IDP OT - MDM4 OT - MDMX-S OT - TROSY EDAT- 2013/10/16 06:00 MHDA- 2014/01/09 06:00 CRDT- 2013/10/16 06:00 PHST- 2013/10/14 [aheadofprint] AID - 1317398110 [pii] AID - 10.1073/pnas.1317398110 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17814-9. doi: 10.1073/pnas.1317398110. Epub 2013 Oct 14. PMID- 23791195 OWN - NLM STAT- MEDLINE DA - 20130624 DCOM- 20130830 LR - 20141113 IS - 1097-4199 (Electronic) IS - 0896-6273 (Linking) VI - 78 IP - 6 DP - 2013 Jun 19 TI - mSYD1A, a mammalian synapse-defective-1 protein, regulates synaptogenic signaling and vesicle docking. PG - 1012-23 LID - 10.1016/j.neuron.2013.05.010 [doi] LID - S0896-6273(13)00403-0 [pii] AB - Structure and function of presynaptic terminals are critical for the transmission and processing of neuronal signals. Trans-synaptic signaling systems instruct the differentiation and function of presynaptic release sites, but their downstream mediators are only beginning to be understood. Here, we identify the intracellular mSYD1A (mouse Synapse-Defective-1A) as a regulator of presynaptic function in mice. mSYD1A forms a complex with presynaptic receptor tyrosine phosphatases and controls tethering of synaptic vesicles at synapses. mSYD1A function relies on an intrinsically disordered domain that interacts with multiple structurally unrelated binding partners, including the active zone protein liprin-alpha2 and nsec1/munc18-1. In mSYD1A knockout mice, synapses assemble in normal numbers but there is a significant reduction in synaptic vesicle docking at the active zone and an impairment of synaptic transmission. Thus, mSYD1A is a regulator of presynaptic release sites at central synapses. CI - Copyright (c) 2013 Elsevier Inc. All rights reserved. FAU - Wentzel, Corinna AU - Wentzel C AD - Biozentrum, University of Basel, 4056 Basel, Switzerland. FAU - Sommer, Julia E AU - Sommer JE FAU - Nair, Ramya AU - Nair R FAU - Stiefvater, Adeline AU - Stiefvater A FAU - Sibarita, Jean-Baptiste AU - Sibarita JB FAU - Scheiffele, Peter AU - Scheiffele P LA - eng GR - R01 DA020844/DA/NIDA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Neuron JT - Neuron JID - 8809320 RN - 0 (Nerve Tissue Proteins) RN - 0 (synapse-defective-1A protein, mouse) RN - EC 3.6.5.2 (rho GTP-Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Animals, Newborn MH - COS Cells MH - Cells, Cultured MH - Cercopithecus aethiops MH - HEK293 Cells MH - Humans MH - Mice MH - Mice, Knockout MH - Molecular Sequence Data MH - Nerve Tissue Proteins/physiology MH - Organ Culture Techniques MH - Presynaptic Terminals/*metabolism MH - Protein Binding/physiology MH - Signal Transduction/*physiology MH - Synapses/genetics/*metabolism MH - Synaptic Vesicles/genetics/*metabolism MH - rho GTP-Binding Proteins/*physiology PMC - PMC3719036 MID - NIHMS483036 OID - NLM: NIHMS483036 OID - NLM: PMC3719036 EDAT- 2013/06/26 06:00 MHDA- 2013/08/31 06:00 CRDT- 2013/06/25 06:00 PHST- 2013/05/13 [accepted] AID - S0896-6273(13)00403-0 [pii] AID - 10.1016/j.neuron.2013.05.010 [doi] PST - ppublish SO - Neuron. 2013 Jun 19;78(6):1012-23. doi: 10.1016/j.neuron.2013.05.010. PMID- 9312017 OWN - NLM STAT- MEDLINE DA - 19971114 DCOM- 19971114 LR - 20140617 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 16 IP - 18 DP - 1997 Sep 15 TI - Crystal structures of the small G protein Rap2A in complex with its substrate GTP, with GDP and with GTPgammaS. PG - 5582-91 AB - The small G protein Rap2A has been crystallized in complex with GDP, GTP and GTPgammaS. The Rap2A-GTP complex is the first structure of a small G protein with its natural ligand GTP. It shows that the hydroxyl group of Tyr32 forms a hydrogen bond with the gamma-phosphate of GTP and with Gly13. This interaction does not exist in the Rap2A-GTPgammaS complex. Tyr32 is conserved in many small G proteins, which probably also form this hydrogen bond with GTP. In addition, Tyr32 is structurally equivalent to a conserved arginine that binds GTP in trimeric G proteins. The actual participation of Tyr32 in GTP hydrolysis is not yet clear, but several possible roles are discussed. The conformational changes between the GDP and GTP complexes are located essentially in the switch I and II regions as described for the related oncoprotein H-Ras. However, the mobile segments vary in length and in the amplitude of movement. This suggests that even though similar regions might be involved in the GDP-GTP cycle of small G proteins, the details of the changes will be different for each G protein and will ensure the specificity of its interaction with a given set of cellular proteins. FAU - Cherfils, J AU - Cherfils J AD - Laboratoire d'Enzymologie et de Biochimie Structurales, UPR 9063-CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France. FAU - Menetrey, J AU - Menetrey J FAU - Le Bras, G AU - Le Bras G FAU - Janoueix-Lerosey, I AU - Janoueix-Lerosey I FAU - de Gunzburg, J AU - de Gunzburg J FAU - Garel, J R AU - Garel JR FAU - Auzat, I AU - Auzat I LA - eng SI - PDB/UNKNOWN PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Macromolecular Substances) RN - 0 (Recombinant Proteins) RN - 146-91-8 (Guanosine Diphosphate) RN - 37589-80-3 (Guanosine 5'-O-(3-Thiotriphosphate)) RN - 86-01-1 (Guanosine Triphosphate) RN - EC 3.6.1.- (GTP-Binding Proteins) RN - EC 3.6.5.2 (rap GTP-Binding Proteins) RN - EC 3.6.5.2 (ras Proteins) SB - IM MH - Amino Acid Sequence MH - Conserved Sequence MH - Crystallography, X-Ray MH - Escherichia coli MH - GTP-Binding Proteins/biosynthesis/*chemistry/*metabolism MH - Guanosine 5'-O-(3-Thiotriphosphate)/*metabolism MH - Guanosine Diphosphate/*metabolism MH - Guanosine Triphosphate/*metabolism MH - Hydrogen Bonding MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - *Protein Conformation MH - Protein Structure, Secondary MH - Recombinant Proteins/biosynthesis/chemistry/metabolism MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - rap GTP-Binding Proteins MH - ras Proteins/chemistry PMC - PMC1170190 OID - NLM: PMC1170190 EDAT- 1997/10/06 MHDA- 1997/10/06 00:01 CRDT- 1997/10/06 00:00 AID - 10.1093/emboj/16.18.5582 [doi] PST - ppublish SO - EMBO J. 1997 Sep 15;16(18):5582-91. PMID- 20499903 OWN - NLM STAT- MEDLINE DA - 20100616 DCOM- 20100915 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 132 IP - 24 DP - 2010 Jun 23 TI - NMR characterization of long-range order in intrinsically disordered proteins. PG - 8407-18 LID - 10.1021/ja101645g [doi] AB - Intrinsically disordered proteins (IDPs) are predicted to represent a significant fraction of the human genome, and the development of meaningful molecular descriptions of these proteins remains a key challenge for contemporary structural biology. In order to describe the conformational behavior of IDPs, a molecular representation of the disordered state based on diverse sources of structural data that often exhibit complex and very different averaging behavior is required. In this study, we propose a combination of paramagnetic relaxation enhancements (PREs) and residual dipolar couplings (RDCs) to define both long-range and local structural features of IDPs in solution. We demonstrate that ASTEROIDS, an ensemble selection algorithm, faithfully reproduces intramolecular contacts, even in the presence of highly diffuse, ill-defined target interactions. We also show that explicit modeling of spin-label mobility significantly improves the reproduction of experimental PRE data, even in the case of highly disordered proteins. Prediction of the effects of transient long-range contacts on RDC profiles reveals that weak intramolecular interactions can induce a severe distortion of the profiles that compromises the description of local conformational sampling if it is not correctly taken into account. We have developed a solution to this problem that involves efficiently combining RDC and PRE data to simultaneously determine long-range and local structure in highly flexible proteins. This combined analysis is shown to be essential for the accurate interpretation of experimental data from alpha-synuclein, an important IDP involved in human neurodegenerative disease, confirming the presence of long-range order between distant regions in the protein. FAU - Salmon, Loic AU - Salmon L AD - Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, CEA; CNRS; UJF UMR 5075, 41 Rue Jules Horowitz, Grenoble 38027, France. FAU - Nodet, Gabrielle AU - Nodet G FAU - Ozenne, Valery AU - Ozenne V FAU - Yin, Guowei AU - Yin G FAU - Jensen, Malene Ringkjobing AU - Jensen MR FAU - Zweckstetter, Markus AU - Zweckstetter M FAU - Blackledge, Martin AU - Blackledge M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Solutions) RN - 0 (alpha-Synuclein) SB - IM MH - Biophysical Processes MH - Magnetics MH - Models, Molecular MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Reproducibility of Results MH - Solutions MH - alpha-Synuclein/*chemistry EDAT- 2010/05/27 06:00 MHDA- 2010/09/16 06:00 CRDT- 2010/05/27 06:00 AID - 10.1021/ja101645g [doi] PST - ppublish SO - J Am Chem Soc. 2010 Jun 23;132(24):8407-18. doi: 10.1021/ja101645g. PMID- 23649393 OWN - NLM STAT- MEDLINE DA - 20130507 DCOM- 20140409 IS - 1347-5231 (Electronic) IS - 0031-6903 (Linking) VI - 133 IP - 5 DP - 2013 TI - [Structural study of polyglutamine tract-binding protein 1]. PG - 519-26 AB - Polyglutamine tract-binding protein 1 (PQBP1) is a nuclear protein that regulates transcription and pre-mRNA splicing. In addition, the mutations in the PQBP1 gene are known to cause hereditary mental retardation. This review summarizes current knowledge about the solution structure of PQBP1. PQBP1 is an intrinsically disordered protein: its polar-rich domain and C-terminal domain are disordered under physiological conditions. PQBP1 binds to its target molecule U5-15kD via a continuous 23-residue segment of the C-terminal domain. The function of PQBP1 in the pre-mRNA splicing is also discussed. FAU - Mizuguchi, Mineyuki AU - Mizuguchi M AD - Faculty of Pharmaceutical Sciences, University of Toyama. mineyuki@pha.u-toyama.ac.jp FAU - Okazawa, Hitoshi AU - Okazawa H LA - jpn PT - English Abstract PT - Journal Article PT - Review PL - Japan TA - Yakugaku Zasshi JT - Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan JID - 0413613 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Oligopeptides) RN - 0 (RNA Precursors) RN - 0 (Ribonucleoprotein, U5 Small Nuclear) RN - 0 (TXNL4A protein, human) RN - 0 (polyglutamine-binding protein 1) SB - IM MH - Amino Acid Sequence MH - Animals MH - Humans MH - Intellectual Disability/*genetics MH - Intrinsically Disordered Proteins MH - Molecular Sequence Data MH - Mutation MH - Oligopeptides/*chemistry/*genetics/metabolism/physiology MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - RNA Precursors/genetics MH - RNA Splicing/genetics MH - Ribonucleoprotein, U5 Small Nuclear/metabolism MH - Transcription, Genetic EDAT- 2013/05/08 06:00 MHDA- 2014/04/10 06:00 CRDT- 2013/05/08 06:00 AID - DN/JST.JSTAGE/yakushi/13-00001-2 [pii] PST - ppublish SO - Yakugaku Zasshi. 2013;133(5):519-26. PMID- 20058326 OWN - NLM STAT- MEDLINE DA - 20100902 DCOM- 20101216 LR - 20110405 IS - 1099-1352 (Electronic) IS - 0952-3499 (Linking) VI - 23 IP - 5 DP - 2010 Sep-Oct TI - Solution structure of the C-terminal X domain of the measles virus phosphoprotein and interaction with the intrinsically disordered C-terminal domain of the nucleoprotein. PG - 435-47 LID - 10.1002/jmr.1010 [doi] AB - In this report, the solution structure of the nucleocapsid-binding domain of the measles virus phosphoprotein (XD, aa 459-507) is described. A dynamic description of the interaction between XD and the disordered C-terminal domain of the nucleocapsid protein, (N(TAIL), aa 401-525), is also presented. XD is an all alpha protein consisting of a three-helix bundle with an up-down-up arrangement of the helices. The solution structure of XD is very similar to the crystal structures of both the free and bound form of XD. One exception is the presence of a highly dynamic loop encompassing XD residues 489-491, which is involved in the embedding of the alpha-helical XD-binding region of N(TAIL). Secondary chemical shift values for full-length N(TAIL) were used to define the precise boundaries of a transient helical segment that coincides with the XD-binding domain, thus shedding light on the pre-recognition state of N(TAIL). Titration experiments with unlabeled XD showed that the transient alpha-helical conformation of N(TAIL) is stabilized upon binding. Lineshape analysis of NMR resonances revealed that residues 483-506 of N(TAIL) are in intermediate exchange with XD, while the 475-482 and 507-525 regions are in fast exchange. The N(TAIL) resonance behavior in the titration experiments is consistent with a complex binding model with more than two states. FAU - Gely, Stephane AU - Gely S AD - Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 6098, CNRS, France and Universites d'Aix-Marseille I and II, 163 Avenue de Luminy, 13288 Marseille Cedex 09, France. FAU - Lowry, David F AU - Lowry DF FAU - Bernard, Cedric AU - Bernard C FAU - Jensen, Malene R AU - Jensen MR FAU - Blackledge, Martin AU - Blackledge M FAU - Costanzo, Stephanie AU - Costanzo S FAU - Bourhis, Jean-Marie AU - Bourhis JM FAU - Darbon, Herve AU - Darbon H FAU - Daughdrill, Gary AU - Daughdrill G FAU - Longhi, Sonia AU - Longhi S LA - eng GR - R01 NS031693-11A2/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - J Mol Recognit JT - Journal of molecular recognition : JMR JID - 9004580 RN - 0 (Nucleoproteins) RN - 0 (Phosphoproteins) RN - 0 (Solutions) SB - IM MH - Crystallography, X-Ray MH - Measles virus/*chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleoproteins/*chemistry/metabolism MH - Phosphoproteins/*chemistry/metabolism MH - *Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - Solutions EDAT- 2010/01/09 06:00 MHDA- 2010/12/17 06:00 CRDT- 2010/01/09 06:00 AID - 10.1002/jmr.1010 [doi] PST - ppublish SO - J Mol Recognit. 2010 Sep-Oct;23(5):435-47. doi: 10.1002/jmr.1010. PMID- 8538787 OWN - NLM STAT- MEDLINE DA - 19960208 DCOM- 19960208 LR - 20131121 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 379 IP - 6562 DP - 1996 Jan 18 TI - Structure and mechanism of DNA topoisomerase II. PG - 225-32 AB - The crystal structure of a large fragment of yeast type II DNA topoisomerase reveals a heart-shaped dimeric protein with a large central hole. It provides a molecular model of the enzyme as an ATP-modulated clamp with two sets of jaws at opposite ends, connected by multiple joints. An enzyme with bound DNA can admit a second DNA duplex through one set of jaws, transport it through the cleaved first duplex, and expel it through the other set of jaws. FAU - Berger, J M AU - Berger JM AD - Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA. FAU - Gamblin, S J AU - Gamblin SJ FAU - Harrison, S C AU - Harrison SC FAU - Wang, J C AU - Wang JC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Peptide Fragments) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - 9007-49-2 (DNA) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 5.99.1.3 (DNA Gyrase) RN - EC 5.99.1.3 (DNA Topoisomerases, Type II) SB - IM EIN - Nature 1996 Mar 14;380(6570):179 MH - Adenosine Triphosphatases/chemistry/metabolism MH - Adenosine Triphosphate/metabolism MH - Amino Acid Sequence MH - Crystallography, X-Ray MH - DNA/metabolism MH - DNA Gyrase MH - DNA Topoisomerases, Type II/*chemistry/metabolism MH - Escherichia coli/enzymology MH - Models, Molecular MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/metabolism MH - Protein Binding MH - Protein Conformation MH - Saccharomyces cerevisiae/enzymology EDAT- 1996/01/18 MHDA- 1996/01/18 00:01 CRDT- 1996/01/18 00:00 AID - 10.1038/379225a0 [doi] PST - ppublish SO - Nature. 1996 Jan 18;379(6562):225-32. PMID- 21378313 OWN - NLM STAT- MEDLINE DA - 20110307 DCOM- 20110613 LR - 20140220 IS - 1477-9137 (Electronic) IS - 0021-9533 (Linking) VI - 124 IP - Pt 6 DP - 2011 Mar 15 TI - BIM(EL), an intrinsically disordered protein, is degraded by 20S proteasomes in the absence of poly-ubiquitylation. PG - 969-77 LID - 10.1242/jcs.058438 [doi] AB - BIM-extra long (BIM(EL)), a pro-apoptotic BH3-only protein and part of the BCL-2 family, is degraded by the proteasome following activation of the ERK1/2 signalling pathway. Although studies have demonstrated poly-ubiquitylation of BIM(EL) in cells, the nature of the ubiquitin chain linkage has not been defined. Using ubiquitin-binding domains (UBDs) specific for defined ubiquitin chain linkages, we show that BIM(EL) undergoes K48-linked poly-ubiquitylation at either of two lysine residues. Surprisingly, BIM(EL)DeltaKK, which lacks both lysine residues, was not poly-ubiquitylated but still underwent ERK1/2-driven, proteasome-dependent turnover. BIM has been proposed to be an intrinsically disordered protein (IDP) and some IDPs can be degraded by uncapped 20S proteasomes in the absence of poly-ubiquitylation. We show that BIM(EL) is degraded by isolated 20S proteasomes but that this is prevented when BIM(EL) is bound to its pro-survival target protein MCL-1. Furthermore, knockdown of the proteasome cap component Rpn2 does not prevent BIM(EL) turnover in cells, and inhibition of the E3 ubiquitin ligase beta-TrCP, which catalyses poly-Ub of BIM(EL), causes Cdc25A accumulation but does not inhibit BIM(EL) turnover. These results provide new insights into the regulation of BIM(EL) by defining a novel ubiquitin-independent pathway for the proteasome-dependent destruction of this highly toxic protein. FAU - Wiggins, Ceri M AU - Wiggins CM AD - Laboratory of Molecular Signalling, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK. FAU - Tsvetkov, Peter AU - Tsvetkov P FAU - Johnson, Mark AU - Johnson M FAU - Joyce, Claire L AU - Joyce CL FAU - Lamb, Christopher A AU - Lamb CA FAU - Bryant, Nia J AU - Bryant NJ FAU - Komander, David AU - Komander D FAU - Shaul, Yosef AU - Shaul Y FAU - Cook, Simon J AU - Cook SJ LA - eng GR - BB/E02162X/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - MC_U105192732/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Cell Sci JT - Journal of cell science JID - 0052457 RN - 0 (Apoptosis Regulatory Proteins) RN - 0 (Bcl-2-like protein 11) RN - 0 (Membrane Proteins) RN - 0 (Proto-Oncogene Proteins) RN - EC 2.7.11.24 (Mitogen-Activated Protein Kinase 1) RN - EC 2.7.11.24 (Mitogen-Activated Protein Kinase 3) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Animals MH - Apoptosis Regulatory Proteins/genetics/*metabolism MH - Cell Line MH - Membrane Proteins/genetics/*metabolism MH - Mice MH - Mice, Knockout MH - Mitogen-Activated Protein Kinase 1/genetics/metabolism MH - Mitogen-Activated Protein Kinase 3/genetics/metabolism MH - Proteasome Endopeptidase Complex/genetics/*metabolism MH - Proto-Oncogene Proteins/genetics/*metabolism MH - Ubiquitination EDAT- 2011/03/08 06:00 MHDA- 2011/06/15 06:00 CRDT- 2011/03/08 06:00 AID - 124/6/969 [pii] AID - 10.1242/jcs.058438 [doi] PST - ppublish SO - J Cell Sci. 2011 Mar 15;124(Pt 6):969-77. doi: 10.1242/jcs.058438. PMID- 24457896 OWN - NLM STAT- In-Process DA - 20140124 IS - 2041-1723 (Electronic) IS - 2041-1723 (Linking) VI - 5 DP - 2014 TI - Two potential therapeutic antibodies bind to a peptide segment of membrane-bound IgE in different conformations. PG - 3139 LID - 10.1038/ncomms4139 [doi] AB - IgE mediates hypersensitivity reactions responsible for most allergic diseases, which affect 20-40% of the population in developed countries. A 52-residue domain of membrane-bound IgE (mIgE) called CepsilonmX is currently a target for developing therapeutic antibodies; however, its structure is unknown. Here we show that two antibodies with therapeutic potential in IgE-mediated allergic diseases, which can cause cytolytic effects on mIgE-expressing B lymphocytes and downregulate IgE production, target different conformations of an intrinsically disordered region (IDR) in the extracellular CepsilonmX domain. We provide an important example of antibodies targeting an extracellular IDR of a receptor on the surface of intended target cells. We also provide fundamental structural characteristics unique to human mIgE, which may stimulate further studies to investigate whether other monoclonal antibodies (mAbs) targeting intrinsically disordered peptide segments or vaccine-like products targeting IDRs of a membrane protein can be developed. FAU - Chu, Hsing-Mao AU - Chu HM AD - The Genomics Research Center, Academia Sinica, Taipei 115, Taiwan. FAU - Wright, Jon AU - Wright J AD - 1] The Genomics Research Center, Academia Sinica, Taipei 115, Taiwan [2] Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan. FAU - Chan, Yueh-Hsuan AU - Chan YH AD - Fountain Biopharma Inc. Taipei, Taipei 115, Taiwan. FAU - Lin, Chien-Jen AU - Lin CJ AD - The Genomics Research Center, Academia Sinica, Taipei 115, Taiwan. FAU - Chang, Tse Wen AU - Chang TW AD - The Genomics Research Center, Academia Sinica, Taipei 115, Taiwan. FAU - Lim, Carmay AU - Lim C AD - 1] Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan [2] Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan. LA - eng SI - PDB/4LKX PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Nat Commun JT - Nature communications JID - 101528555 SB - IM EDAT- 2014/01/25 06:00 MHDA- 2014/01/25 06:00 CRDT- 2014/01/25 06:00 PHST- 2013/08/09 [received] PHST- 2013/12/17 [accepted] AID - ncomms4139 [pii] AID - 10.1038/ncomms4139 [doi] PST - ppublish SO - Nat Commun. 2014;5:3139. doi: 10.1038/ncomms4139. PMID- 18215165 OWN - NLM STAT- MEDLINE DA - 20080131 DCOM- 20080617 IS - 1742-464X (Print) IS - 1742-464X (Linking) VI - 275 IP - 4 DP - 2008 Feb TI - Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle. PG - 763-74 LID - 10.1111/j.1742-4658.2007.06242.x [doi] AB - The potent immunomodulatory, anti-inflammatory and procoagulant properties of protein no. 4 secreted from the rat seminal vesicle epithelium (SV-IV) have previously been found to be modulated by a supramolecular monomer-trimer equilibrium. More structural details that integrate experimental data into a predictive framework have recently been reported. Unfortunately, homology modelling and fold-recognition strategies were not successful in creating a theoretical model of the structural organization of SV-IV. It was inferred that the global structure of SV-IV is not similar to that of any protein of known three-dimensional structure. Reversing the classical approach to the sequence-structure-function paradigm, in this paper we report novel information obtained by comparing the physicochemical parameters of SV-IV with two datasets composed of intrinsically unfolded and ideally globular proteins. In addition, we analyse the SV-IV sequence by several publicly available disorder-oriented predictors. Overall, disorder predictions and a re-examination of existing experimental data strongly suggest that SV-IV needs large plasticity to efficiently interact with the different targets that characterize its multifaceted biological function, and should therefore be better classified as an intrinsically disordered protein. FAU - Vilasi, Silvia AU - Vilasi S AD - Dipartimento di Biochimica e Biofisica, Naples, Italy. FAU - Ragone, Raffaele AU - Ragone R LA - eng PT - Journal Article DEP - 20080122 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Androgens) RN - 0 (Seminal Vesicle Secretory Proteins) RN - 0 (Svp4 protein, rat) SB - IM MH - Amino Acid Sequence MH - Androgens/*metabolism MH - Animals MH - Computational Biology MH - Databases, Protein MH - Male MH - Molecular Sequence Data MH - Rats MH - Seminal Vesicle Secretory Proteins/*chemistry/genetics/*metabolism MH - Sequence Analysis, Protein EDAT- 2008/01/25 09:00 MHDA- 2008/06/18 09:00 CRDT- 2008/01/25 09:00 PHST- 2008/01/22 [aheadofprint] AID - EJB6242 [pii] AID - 10.1111/j.1742-4658.2007.06242.x [doi] PST - ppublish SO - FEBS J. 2008 Feb;275(4):763-74. doi: 10.1111/j.1742-4658.2007.06242.x. Epub 2008 Jan 22. PMID- 21525002 OWN - NLM STAT- MEDLINE DA - 20110620 DCOM- 20110830 LR - 20140820 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 25 DP - 2011 Jun 24 TI - Cyclization of the intrinsically disordered alpha1S dihydropyridine receptor II-III loop enhances secondary structure and in vitro function. PG - 22589-99 LID - 10.1074/jbc.M110.205476 [doi] AB - A key component of excitation contraction (EC) coupling in skeletal muscle is the cytoplasmic linker (II-III loop) between the second and third transmembrane repeats of the alpha(1S) subunit of the dihydropyridine receptor (DHPR). The II-III loop has been previously examined in vitro using a linear II-III loop with unrestrained N- and C-terminal ends. To better reproduce the loop structure in its native environment (tethered to the DHPR transmembrane domains), we have joined the N and C termini using intein-mediated technology. Circular dichroism and NMR spectroscopy revealed a structural shift in the cyclized loop toward a protein with increased alpha-helical and beta-strand structure in a region of the loop implicated in its in vitro function and also in a critical region for EC coupling. The affinity of binding of the II-III loop binding to the SPRY2 domain of the skeletal ryanodine receptor (RyR1) increased 4-fold, and its ability to activate RyR1 channels in lipid bilayers was enhanced 3-fold by cyclization. These functional changes were predicted consequences of the structural enhancement. We suggest that tethering the N and C termini stabilized secondary structural elements in the DHPR II-III loop and may reflect structural and dynamic characteristics of the loop that are inherent in EC coupling. FAU - Tae, Han-Shen AU - Tae HS AD - John Curtin School of Medical Research, Australian National University, PO Box 334, Canberra, Australian Capital Territory 2601, Australia. FAU - Cui, Yanfang AU - Cui Y FAU - Karunasekara, Yamuna AU - Karunasekara Y FAU - Board, Philip G AU - Board PG FAU - Dulhunty, Angela F AU - Dulhunty AF FAU - Casarotto, Marco G AU - Casarotto MG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110427 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Calcium Channels, L-Type) RN - 0 (Lipid Bilayers) RN - 0 (Protein Subunits) RN - 0 (Ryanodine Receptor Calcium Release Channel) RN - EC 3.6.4.12 (DnaB Helicases) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Calcium Channels, L-Type/*chemistry/genetics/*metabolism MH - Cyclization MH - DnaB Helicases/chemistry/metabolism MH - Inteins/genetics MH - Ion Channel Gating MH - Lipid Bilayers/metabolism MH - Molecular Sequence Data MH - Muscle Contraction/genetics MH - Muscle, Skeletal/metabolism/physiology MH - Protein Engineering/*methods MH - Protein Splicing MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Subunits/chemistry/genetics/metabolism MH - Rabbits MH - Ryanodine Receptor Calcium Release Channel/metabolism MH - Substrate Specificity MH - Synechocystis/enzymology PMC - PMC3121403 OID - NLM: PMC3121403 EDAT- 2011/04/29 06:00 MHDA- 2011/08/31 06:00 CRDT- 2011/04/29 06:00 PHST- 2011/04/27 [aheadofprint] AID - M110.205476 [pii] AID - 10.1074/jbc.M110.205476 [doi] PST - ppublish SO - J Biol Chem. 2011 Jun 24;286(25):22589-99. doi: 10.1074/jbc.M110.205476. Epub 2011 Apr 27. PMID- 20448140 OWN - NLM STAT- MEDLINE DA - 20100902 DCOM- 20100921 LR - 20141120 IS - 1530-6860 (Electronic) IS - 0892-6638 (Linking) VI - 24 IP - 9 DP - 2010 Sep TI - A new amyloidosis caused by fibrillar aggregates of mutated corneodesmosin. PG - 3416-26 LID - 10.1096/fj.10-155622 [doi] AB - Heterozygous nonsense mutations in the CDSN gene encoding corneodesmosin (CDSN), an adhesive protein expressed in cornified epithelia and hair follicles, cause hypotrichosis simplex of the scalp (HSS), a nonsyndromic form of alopecia. Truncated mutants of CDSN ((mut)CDSN), which bear the N-terminal adhesive Gly/Ser-rich domain (GS domain) of the protein, abnormally accumulate as amorphous deposits at the periphery of hair follicles and in the papillary dermis of the patient skin. Here, we present evidence that the (mut)CDSN deposits display an affinity for amyloidophilic dyes, namely Congo red and thioflavin T. We also detected the serum amyloid protein component in the dermis of HSS patients. We demonstrated that recombinant forms of (mut)CDSN and of the GS domain assemble in vitro into ring-shaped oligomeric structures and fibrils. The amyloid-like nature of the fibrils was demonstrated by dye binding and Fourier transform infrared spectrometry measurements. We showed that the ring-shaped oligomers of (mut)CDSN, but not the fibrillar forms, are toxic to cultured keratinocytes. Finally, online algorithms predicted the GS domain to be a particularly disordered region of CDSN in agreement with circular dichroism measurements. This identifies HSS as a human amyloidosis related to the aggregation of natively unfolded (mut)CDSN polypeptides into amyloid fibrils. FAU - Caubet, Cecile AU - Caubet C AD - UMR5165 Centre National de la Recherche Scientifique - University of Toulouse III, Toulouse, France. FAU - Bousset, Luc AU - Bousset L FAU - Clemmensen, Ole AU - Clemmensen O FAU - Sourigues, Yannick AU - Sourigues Y FAU - Bygum, Anette AU - Bygum A FAU - Chavanas, Stephane AU - Chavanas S FAU - Coudane, Fanny AU - Coudane F FAU - Hsu, Chiung-Yueh AU - Hsu CY FAU - Betz, Regina C AU - Betz RC FAU - Melki, Ronald AU - Melki R FAU - Simon, Michel AU - Simon M FAU - Serre, Guy AU - Serre G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100506 PL - United States TA - FASEB J JT - FASEB journal : official publication of the Federation of American Societies for Experimental Biology JID - 8804484 RN - 0 (CDSN protein, human) RN - 0 (Glycoproteins) SB - IM MH - Aged MH - Amyloidosis/genetics/*metabolism MH - Cells, Cultured MH - Circular Dichroism MH - Glycoproteins/genetics/*metabolism/*ultrastructure MH - Humans MH - Hypotrichosis/metabolism/pathology MH - In Vitro Techniques MH - Male MH - Microscopy, Electron, Transmission MH - Microscopy, Immunoelectron MH - Mutation MH - Protein Folding MH - Scalp/metabolism/pathology MH - Spectroscopy, Fourier Transform Infrared MH - X-Ray Diffraction EDAT- 2010/05/08 06:00 MHDA- 2010/09/23 06:00 CRDT- 2010/05/08 06:00 PHST- 2010/05/06 [aheadofprint] AID - fj.10-155622 [pii] AID - 10.1096/fj.10-155622 [doi] PST - ppublish SO - FASEB J. 2010 Sep;24(9):3416-26. doi: 10.1096/fj.10-155622. Epub 2010 May 6. PMID- 10339411 OWN - NLM STAT- MEDLINE DA - 19990715 DCOM- 19990715 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 289 IP - 1 DP - 1999 May 28 TI - Structure of the anchor-domain of myristoylated and non-myristoylated HIV-1 Nef protein. PG - 123-38 AB - Negative factor (Nef) is a regulatory myristoylated protein of human immunodeficiency virus (HIV) that has a two-domain structure consisting of an anchor domain and a core domain separated by a specific cleavage site of the HIV proteases. For structural analysis, the HIV-1 Nef anchor domain (residues 2-57) was synthesized with a myristoylated and non-myristoylated N terminus. The structures of the two peptides were studied by1H NMR spectroscopy and a structural model was obtained by restrained molecular dynamic simulations. The non-myristoylated peptide does not have a unique, compactly folded structure but occurs in a relatively extended conformation. The only rather well-defined canonical secondary structure element is a short two-turn alpha-helix (H2) between Arg35 and Gly41. A tendency for another helical secondary structure element (H1) can be observed for the arginine-rich region (Arg17 to Arg22). Myristoylation of the N-terminal glycine residue leads to stabilization of both helices, H1 and H2. The first helix in the arginine-rich region is stabilized by the myristoylation and now contains residues Pro14 to Arg22. The second helix appears to be better defined and to contain more residues (Ala33 to Gly41) than in the absence of myristoylation. In addition, the hydrophobic N-terminal myristic acid residue interacts closely with the side-chain of Trp5 and thereby forms a loop with Gly2, Gly3 and Lys4 in the kink region. This interaction could possibly be disturbed by phosphorylation of a nearby serine residue, and modifiy the characteristic membrane interactions of the HIV-1 Nef anchor domain. CI - Copyright 1999 Academic Press. FAU - Geyer, M AU - Geyer M AD - Abteilung Biophysik, Max-Planck-Institut fur medizinische Forschung, Heidelberg, D-69120, Germany. FAU - Munte, C E AU - Munte CE FAU - Schorr, J AU - Schorr J FAU - Kellner, R AU - Kellner R FAU - Kalbitzer, H R AU - Kalbitzer HR LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Gene Products, nef) RN - 0 (Peptide Fragments) RN - 0 (nef Gene Products, Human Immunodeficiency Virus) RN - 0I3V7S25AW (Myristic Acid) SB - IM SB - X MH - Amino Acid Sequence MH - Computer Graphics MH - Conserved Sequence MH - Gene Products, nef/*chemistry/*metabolism MH - *HIV-1 MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Myristic Acid/*analysis/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemical synthesis/chemistry MH - Protein Conformation MH - Protein Structure, Secondary MH - Sequence Alignment MH - Solubility MH - nef Gene Products, Human Immunodeficiency Virus EDAT- 1999/05/26 MHDA- 1999/05/26 00:01 CRDT- 1999/05/26 00:00 AID - 10.1006/jmbi.1999.2740 [doi] AID - S0022-2836(99)92740-7 [pii] PST - ppublish SO - J Mol Biol. 1999 May 28;289(1):123-38. PMID- 22590549 OWN - NLM STAT- MEDLINE DA - 20120516 DCOM- 20120919 LR - 20141016 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 5 DP - 2012 TI - Ordered self-assembly mechanism of a spherical oncoprotein oligomer triggered by zinc removal and stabilized by an intrinsically disordered domain. PG - e36457 LID - 10.1371/journal.pone.0036457 [doi] AB - BACKGROUND: Self-assembly is a common theme in proteins of unrelated sequences or functions. The human papillomavirus E7 oncoprotein is an extended dimer with an intrinsically disordered domain, that can form large spherical oligomers. These are the major species in the cytosol of HPV transformed and cancerous cells. E7 binds to a large number of targets, some of which lead to cell transformation. Thus, the assembly process not only is of biological relevance, but represents a model system to investigate a widely distributed mechanism. METHODOLOGY/PRINCIPAL FINDINGS: Using various techniques, we monitored changes in secondary, tertiary and quaternary structure in a time course manner. By applying a robust kinetic model developed by Zlotnik, we determined the slow formation of a monomeric "Z-nucleus" after zinc removal, followed by an elongation phase consisting of sequential second-order events whereby one monomer is added at a time. This elongation process takes place at a strikingly slow overall average rate of one monomer added every 28 seconds at 20 microM protein concentration, strongly suggesting either a rearrangement of the growing complex after binding of each monomer or the existence of a "conformation editing" mechanism through which the monomer binds and releases until the appropriate conformation is adopted. The oligomerization determinant lies within its small 5 kDa C-terminal globular domain and, remarkably, the E7 N-terminal intrinsically disordered domain stabilizes the oligomer, preventing an insoluble amyloid route. CONCLUSION: We described a controlled ordered mechanism with features in common with soluble amyloid precursors, chaperones, and other spherical oligomers, thus sharing determining factors for symmetry, size and shape. In addition, such a controlled and discrete polymerization reaction provides a valuable tool for nanotechnological applications. Finally, its increased immunogenicity related to its supramolecular structure is the basis for the development of a promising therapeutic vaccine candidate for treating HPV cancerous lesions. FAU - Smal, Clara AU - Smal C AD - Fundacion Instituto Leloir and Instituto de Investigaciones Bioquimicas-Conicet, Buenos Aires, Argentina. FAU - Alonso, Leonardo G AU - Alonso LG FAU - Wetzler, Diana E AU - Wetzler DE FAU - Heer, Angeles AU - Heer A FAU - de Prat Gay, Gonzalo AU - de Prat Gay G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120509 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Papillomavirus E7 Proteins) RN - 0 (oncogene protein E7, Human papillomavirus type 16) RN - J41CSQ7QDS (Zinc) SB - IM MH - Human papillomavirus 16/*chemistry/genetics/metabolism MH - Humans MH - Papillomavirus E7 Proteins/*chemistry/genetics/metabolism MH - *Protein Multimerization MH - Protein Stability MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Zinc/*chemistry/metabolism PMC - PMC3348928 OID - NLM: PMC3348928 EDAT- 2012/05/17 06:00 MHDA- 2012/09/20 06:00 CRDT- 2012/05/17 06:00 PHST- 2012/01/17 [received] PHST- 2012/04/06 [accepted] PHST- 2012/05/09 [epublish] AID - 10.1371/journal.pone.0036457 [doi] AID - PONE-D-12-01768 [pii] PST - ppublish SO - PLoS One. 2012;7(5):e36457. doi: 10.1371/journal.pone.0036457. Epub 2012 May 9. PMID- 25210774 OWN - NLM STAT- MEDLINE DA - 20140912 DCOM- 20150525 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 9 DP - 2014 TI - Cross dimerization of amyloid-beta and alphasynuclein proteins in aqueous environment: a molecular dynamics simulations study. PG - e106883 LID - 10.1371/journal.pone.0106883 [doi] AB - Self-assembly of the intrinsically unstructured proteins, amyloid beta (Abeta) and alpha synclein (alphaSyn), are associated with Alzheimer's Disease, and Parkinson's and Lewy Body Diseases, respectively. Importantly, pathological overlaps between these neurodegenerative diseases, and the possibilities of interactions between Abeta and alphaSyn in biological milieu emerge from several recent clinical reports and in vitro studies. Nevertheless, there are very few molecular level studies that have probed the nature of spontaneous interactions between these two sequentially dissimilar proteins and key characteristics of the resulting cross complexes. In this study, we have used atomistic molecular dynamics simulations to probe the possibility of cross dimerization between alphaSyn1-95 and Abeta1-42, and thereby gain insights into their plausible early assembly pathways in aqueous environment. Our analyses indicate a strong probability of association between the two sequences, with inter-protein attractive electrostatic interactions playing dominant roles. Principal component analysis revealed significant heterogeneity in the strength and nature of the associations in the key interaction modes. In most, the interactions of repeating Lys residues, mainly in the imperfect repeats 'KTKEGV' present in alphaSyn1-95 were found to be essential for cross interactions and formation of inter-protein salt bridges. Additionally, a hydrophobicity driven interaction mode devoid of salt bridges, where the non-amyloid component (NAC) region of alphaSyn1-95 came in contact with the hydrophobic core of Abeta1-42 was observed. The existence of such hetero complexes, and therefore hetero assembly pathways may lead to polymorphic aggregates with variations in pathological attributes. Our results provide a perspective on development of therapeutic strategies for preventing pathogenic interactions between these proteins. FAU - Jose, Jaya C AU - Jose JC AD - Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India. FAU - Chatterjee, Prathit AU - Chatterjee P AD - Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India. FAU - Sengupta, Neelanjana AU - Sengupta N AD - Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140911 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Amyloid beta-Peptides) RN - 0 (alpha-Synuclein) RN - 059QF0KO0R (Water) SB - IM MH - Alzheimer Disease/*genetics/metabolism/pathology MH - Amyloid beta-Peptides/*chemistry/genetics/metabolism MH - Dimerization MH - Entropy MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - *Molecular Dynamics Simulation MH - Principal Component Analysis MH - Protein Interaction Maps MH - Water/chemistry MH - alpha-Synuclein/*chemistry/genetics/metabolism PMC - PMC4161357 OID - NLM: PMC4161357 EDAT- 2014/09/12 06:00 MHDA- 2015/05/26 06:00 CRDT- 2014/09/12 06:00 PHST- 2014 [ecollection] PHST- 2014/04/08 [received] PHST- 2014/08/07 [accepted] PHST- 2014/09/11 [epublish] AID - 10.1371/journal.pone.0106883 [doi] AID - PONE-D-14-15688 [pii] PST - epublish SO - PLoS One. 2014 Sep 11;9(9):e106883. doi: 10.1371/journal.pone.0106883. eCollection 2014. PMID- 23583776 OWN - NLM STAT- MEDLINE DA - 20130729 DCOM- 20131001 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 425 IP - 16 DP - 2013 Aug 23 TI - Solid-state (1)(3)C NMR reveals annealing of raft-like membranes containing cholesterol by the intrinsically disordered protein alpha-Synuclein. PG - 2973-87 LID - 10.1016/j.jmb.2013.04.002 [doi] LID - S0022-2836(13)00231-3 [pii] AB - Misfolding and aggregation of the intrinsically disordered protein alpha-Synuclein (alphaS) in Lewy body plaques are characteristic markers of late-stage Parkinson's disease. It is well established that membrane binding is initiated at the N-terminus of the protein and affects biasing of conformational ensembles of alphaS. However, little is understood about the effect of alphaS on the membrane lipid bilayer. One hypothesis is that intrinsically disordered alphaS alters the structural properties of the membrane, thereby stabilizing the bilayer against fusion. Here, we used two-dimensional (13)C separated local-field NMR to study interaction of the wild-type alpha-Synuclein (wt-alphaS) or its N-terminal (1-25) amino acid sequence (N-alphaS) with a cholesterol-enriched ternary membrane system. This lipid bilayer mimics cellular raft-like domains in the brain that are proposed to be involved in neuronal membrane fusion. The two-dimensional dipolar-recoupling pulse sequence DROSS (dipolar recoupling on-axis with scaling and shape preservation) was implemented to measure isotropic (13)C chemical shifts and (13)C-(1)H residual dipolar couplings under magic-angle spinning. Site-specific changes in NMR chemical shifts and segmental order parameters indicate that both wt-alphaS and N-alphaS bind to the membrane interface and change lipid packing within raft-like membranes. Mean-torque modeling of (13)C-(1)H NMR order parameters shows that alphaS induces a remarkable thinning of the bilayer ( approximately 6A), accompanied by an increase in phospholipid cross-sectional area ( approximately 10A(2)). This perturbation is characterized as membrane annealing and entails structural remodeling of the raft-like liquid-ordered phase. We propose this process is implicated in regulation of synaptic membrane fusion that may be altered by aggregation of alphaS in Parkinson's disease. CI - Copyright (c) 2013 Elsevier Ltd. All rights reserved. FAU - Leftin, Avigdor AU - Leftin A AD - Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA. FAU - Job, Constantin AU - Job C FAU - Beyer, Klaus AU - Beyer K FAU - Brown, Michael F AU - Brown MF LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130411 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Carbon Isotopes) RN - 0 (alpha-Synuclein) SB - IM MH - Carbon Isotopes/metabolism MH - Magnetic Resonance Spectroscopy MH - Membrane Microdomains/*chemistry/*metabolism MH - Models, Molecular MH - Protein Binding MH - Protein Conformation MH - Staining and Labeling MH - alpha-Synuclein/*chemistry/*metabolism OTO - NOTNLM OT - 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine OT - 2D OT - Chol OT - DROSS OT - ESYM OT - INEPT OT - MAS OT - N-terminal alpha-Synuclein (1-25) OT - N-alphaS OT - POPC OT - Parkinson's disease OT - RDC OT - SLF OT - cholesterol OT - dipolar recoupling on-axis with scaling and shape preservation OT - egg yolk sphingomyelin OT - insensitive nuclei enhanced by polarization transfer OT - magic-angle spinning OT - membrane lipid raft OT - residual dipolar coupling OT - segmental order parameter OT - separated local-field OT - two-dimensional OT - wild-type alpha-Synuclein OT - wt-alphaS OT - alpha-Synuclein OT - alphaS EDAT- 2013/04/16 06:00 MHDA- 2013/10/18 06:00 CRDT- 2013/04/16 06:00 PHST- 2012/12/23 [received] PHST- 2013/03/14 [revised] PHST- 2013/04/02 [accepted] PHST- 2013/04/11 [aheadofprint] AID - S0022-2836(13)00231-3 [pii] AID - 10.1016/j.jmb.2013.04.002 [doi] PST - ppublish SO - J Mol Biol. 2013 Aug 23;425(16):2973-87. doi: 10.1016/j.jmb.2013.04.002. Epub 2013 Apr 11. PMID- 11713476 OWN - NLM STAT- MEDLINE DA - 20011127 DCOM- 20020102 LR - 20101118 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 8 IP - 12 DP - 2001 Dec TI - Structure of a human Tcf4-beta-catenin complex. PG - 1053-7 AB - The multifunctional protein beta-catenin is important for cell adhesion, because it binds cadherins, and the Wnt signal transduction pathway, where it interacts with the Adenomatous polyposis coli (APC) protein and TCF/Lef family transcription factors. Mutations in APC or in beta-catenin are estimated to trigger formation of over 90% of all colon cancers. In colonic epithelia, these mutations produce elevated levels of Tcf4-beta-catenin, which stimulates a transcriptional response that initiates polyp formation and eventually malignant growth. Thus, disruption of the Tcf4-beta-catenin interaction may be an attractive goal for therapeutic intervention. Here we describe the crystal structure of a human Tcf4-beta-catenin complex and compare it with recent structures of beta-catenin in complex with Xenopus Tcf3 (XTcf3) and mammalian E-cadherin. The structure reveals anticipated similarities with the closely related XTcf3 complex but unexpectedly lacks one component observed in the XTcf3 structure. FAU - Poy, F AU - Poy F AD - Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA. FAU - Lepourcelet, M AU - Lepourcelet M FAU - Shivdasani, R A AU - Shivdasani RA FAU - Eck, M J AU - Eck MJ LA - eng SI - PDB/1JPW PT - Comparative Study PT - Journal Article PL - United States TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (CTNNB1 protein, human) RN - 0 (Cadherins) RN - 0 (Cytoskeletal Proteins) RN - 0 (HMGB Proteins) RN - 0 (TCF Transcription Factors) RN - 0 (TCF7L1 protein, human) RN - 0 (TCF7L2 protein, human) RN - 0 (Trans-Activators) RN - 0 (Transcription Factor 7-Like 1 Protein) RN - 0 (Transcription Factor 7-Like 2 Protein) RN - 0 (Transcription Factors) RN - 0 (Xenopus Proteins) RN - 0 (beta Catenin) RN - 0 (tcf7l2 protein, Xenopus) SB - IM MH - Animals MH - Binding Sites MH - Cadherins/chemistry/metabolism MH - Cell Line MH - Crystallography, X-Ray MH - Cytoskeletal Proteins/antagonists & inhibitors/*chemistry/*metabolism MH - Drug Design MH - Genes, Reporter/genetics MH - *HMGB Proteins MH - Humans MH - Hydrogen Bonding MH - Models, Molecular MH - Protein Binding MH - Protein Conformation MH - Repetitive Sequences, Amino Acid MH - Static Electricity MH - TCF Transcription Factors MH - *Trans-Activators MH - Transcription Factor 7-Like 1 Protein MH - Transcription Factor 7-Like 2 Protein MH - Transcription Factors/antagonists & inhibitors/*chemistry/genetics/*metabolism MH - Transfection MH - Xenopus Proteins/chemistry/metabolism MH - beta Catenin EDAT- 2001/11/20 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/11/20 10:00 AID - 10.1038/nsb720 [doi] AID - nsb720 [pii] PST - ppublish SO - Nat Struct Biol. 2001 Dec;8(12):1053-7. PMID- 16223878 OWN - NLM STAT- MEDLINE DA - 20051026 DCOM- 20051212 LR - 20140605 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 102 IP - 43 DP - 2005 Oct 25 TI - Structure and properties of alpha-synuclein and other amyloids determined at the amino acid level. PG - 15477-82 AB - The structure of alpha-synuclein (alpha-syn) amyloid was studied by hydrogen-deuterium exchange by using a fragment separation-MS analysis. The conditions used made it possible to distinguish the exchange of unprotected and protected amide hydrogens and to define the order/disorder boundaries at close to amino acid resolution. The soluble alpha-syn monomer exchanges its amide hydrogens with water hydrogens at random coil rates, consistent with its natively unstructured condition. In assembled amyloid, long N-terminal and C-terminal segments remain unprotected (residues 1- approximately 38 and 102-140), although the N-terminal segment shows some heterogeneity. A continuous middle segment (residues approximately 39-101) is strongly protected by systematically H-bonded cross-beta structure. This segment is much too long to fit the amyloid ribbon width, but non-H-bonded amides expected for direction-changing loops are not apparent. These results and other known constraints specify that alpha-syn amyloid adopts a chain fold like that suggested before for amyloid-beta [Petkova et al. (2002) Proc. Natl. Acad Sci. USA 99, 16742-16747] but with a short, H-bonded interlamina turn. More generally, we suggest that the prevalence of accidental amyloid formation derives mainly from the exceptional ability of the main chain in a structurally relaxed beta-conformation to adapt to and energy-minimize side-chain mismatching. Seeding specificity, strain variability, and species barriers then arise because newly added parallel in-register chains must faithfully reproduce the same set of adaptations. FAU - Del Mar, Charyl AU - Del Mar C AD - The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA. FAU - Greenbaum, Eric A AU - Greenbaum EA FAU - Mayne, Leland AU - Mayne L FAU - Englander, S Walter AU - Englander SW FAU - Woods, Virgil L Jr AU - Woods VL Jr LA - eng GR - CA 099835/CA/NCI NIH HHS/United States GR - CA 118595/CA/NCI NIH HHS/United States GR - GM 031847/GM/NIGMS NIH HHS/United States GR - GM 074150/GM/NIGMS NIH HHS/United States GR - GM 205001/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20051013 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Amyloid) RN - 0 (alpha-Synuclein) SB - IM MH - Amyloid/*chemistry MH - Circular Dichroism MH - Hydrogen Bonding MH - Mass Spectrometry MH - alpha-Synuclein/*chemistry PMC - PMC1266128 OID - NLM: PMC1266128 EDAT- 2005/10/15 09:00 MHDA- 2005/12/15 09:00 CRDT- 2005/10/15 09:00 PHST- 2005/10/13 [aheadofprint] AID - 0507405102 [pii] AID - 10.1073/pnas.0507405102 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15477-82. Epub 2005 Oct 13. PMID- 15096050 OWN - NLM STAT- MEDLINE DA - 20040420 DCOM- 20040817 LR - 20140909 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 16 DP - 2004 Apr 27 TI - Effects of Parkinson's disease-linked mutations on the structure of lipid-associated alpha-synuclein. PG - 4810-8 AB - Alpha-synuclein (alphaS) is a lipid-binding synaptic protein of unknown function that is found in an aggregated amyloid fibril form in the intraneuronal Lewy body deposits that are a defining characteristic of Parkinson's disease (PD). Although intrinsically unstructured when free in solution, alphaS adopts a highly helical conformation in association with lipid membranes or membrane mimetic detergent micelles. Two mutations in the alphaS gene have been linked to early onset autosomal dominant hereditary forms of PD, and have been shown to affect the aggregation kinetics of the protein in vitro. We have used high-resolution NMR spectroscopy, circular dichroism, and limited proteolysis to investigate the effects of these PD-linked mutations on the helical structure adopted by alphaS in the lipid or detergent micelle-bound form. We show that neither the A53T nor the A30P mutation has a significant effect on the structure of the folded protein, although the A30P mutation may cause a minor perturbation in the helical structure around the site of the mutation. The A30P, but not the A53T, mutation also appears to decrease the affinity of the protein for lipid surfaces, possibly by perturbing the nascent helical structure of the free protein. The potential implications of these results for the role of alphaS in PD are discussed. FAU - Bussell, Robert Jr AU - Bussell R Jr AD - Department of Physiology, Biophysics and Molecular Medicine, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10021, USA. FAU - Eliezer, David AU - Eliezer D LA - eng GR - AG19391/AG/NIA NIH HHS/United States GR - R01 AG019391/AG/NIA NIH HHS/United States GR - R01 AG019391-04/AG/NIA NIH HHS/United States GR - R37 AG019391/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (1-palmitoyl-2-oleoyl-glycero-3-phosphatidic acid) RN - 0 (Liposomes) RN - 0 (Micelles) RN - 0 (Nerve Tissue Proteins) RN - 0 (Phosphatidic Acids) RN - 0 (Phosphatidylcholines) RN - 0 (Recombinant Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 2ZD004190S (Threonine) RN - 9DLQ4CIU6V (Proline) RN - OF5P57N2ZX (Alanine) RN - TE895536Y5 (1-palmitoyl-2-oleoylphosphatidylcholine) SB - IM MH - Alanine/genetics MH - Humans MH - *Lipid Metabolism MH - Liposomes MH - Micelles MH - *Mutation, Missense MH - Nerve Tissue Proteins/chemistry/*genetics/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Parkinson Disease/*genetics MH - Phosphatidic Acids/metabolism MH - Phosphatidylcholines/metabolism MH - Proline/genetics MH - Protein Binding/genetics MH - Protein Structure, Secondary/genetics MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Synucleins MH - Threonine/genetics MH - alpha-Synuclein EDAT- 2004/04/21 05:00 MHDA- 2004/08/18 05:00 CRDT- 2004/04/21 05:00 AID - 10.1021/bi036135+ [doi] PST - ppublish SO - Biochemistry. 2004 Apr 27;43(16):4810-8. PMID- 15096055 OWN - NLM STAT- MEDLINE DA - 20040420 DCOM- 20040817 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 16 DP - 2004 Apr 27 TI - The bZIP region of the plant transcription factor opaque-2 forms stable homodimers in solution and retains its helical structure upon subunit dissociation. PG - 4862-8 AB - Opaque-2 (O2) is a plant bZIP transcription factor that regulates the expression of alpha and beta prolamines, the main storage proteins in seeds of cereals such as maize and Coix. One of the main processes modulating O2 activity is the heterodimerization with other bZIP transcription factors, but the primary mechanism underlying the partner choice is still unknown. In this paper, we have characterized the bZIP domain of O2 by nuclear magnetic resonance (NMR), circular dichroism (CD), and size-exclusion chromatography. Results obtained from CD measurements suggested that the native O2bZIP has about 40 of its 49 leucine-zipper residues in helical structure, while the DNA-binding domain is completely unstructured. Diffusion-ordered NMR spectroscopy and size-exclusion chromatography showed that O2 forms homodimers in solution. Thermal denaturation experiments indicate that O2 reversibly undergoes dissociation and unfolding in a process that is fully dependent on the protein concentration. Subunit dissociation of O2bZIP dimers, upon dilution of the protein, led to partially folded monomers that retained approximately 80% of the native CD ellipticity at 222 nm. We believe that the existence of partially folded monomers could decrease the entropic penalty for helix formation involved in the DNA binding and in the subunit association of O2bZIP. Stabilization of partially folded monomers may also play a significant role in the dimerization of O2 with other bZIP transcription factors and, consequently, can be important for the regulation of the biological functions of O2 in plants. FAU - Moreau, Vitor Hugo AU - Moreau VH AD - Centro Nacional de Ressonancia Magnetica Nuclear de Macromoleculas, Departamento Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. vitorhm@bioqmed.ufrj.br FAU - da Silva, Alba C AU - da Silva AC FAU - Siloto, Rodrigo M P AU - Siloto RM FAU - Valente, Ana Paula AU - Valente AP FAU - Leite, Adilson AU - Leite A FAU - Almeida, Fabio C L AU - Almeida FC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Basic-Leucine Zipper Transcription Factors) RN - 0 (DNA-Binding Proteins) RN - 0 (G-Box Binding Factors) RN - 0 (Nuclear Proteins) RN - 0 (OHP1 protein, Zea mays) RN - 0 (Plant Proteins) RN - 0 (Protein Subunits) RN - 0 (Solutions) RN - 0 (Transcription Factors) RN - 0 (opaque-2 protein, Zea mays) SB - IM MH - Amino Acid Sequence MH - Basic-Leucine Zipper Transcription Factors MH - Coix/chemistry MH - DNA-Binding Proteins/chemistry/*metabolism MH - Dimerization MH - G-Box Binding Factors MH - Isoelectric Point MH - *Leucine Zippers MH - Molecular Sequence Data MH - Nuclear Proteins/*metabolism MH - Plant Proteins/chemistry/*metabolism MH - Protein Denaturation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Subunits/chemistry/*metabolism MH - Solutions MH - Thermodynamics MH - Transcription Factors/chemistry/*metabolism EDAT- 2004/04/21 05:00 MHDA- 2004/08/18 05:00 CRDT- 2004/04/21 05:00 AID - 10.1021/bi035905e [doi] PST - ppublish SO - Biochemistry. 2004 Apr 27;43(16):4862-8. PMID- 9264546 OWN - NLM STAT- MEDLINE DA - 19970908 DCOM- 19970908 LR - 20131121 IS - 0003-9861 (Print) IS - 0003-9861 (Linking) VI - 344 IP - 2 DP - 1997 Aug 15 TI - Aluminum-induced structural alterations of the precursor of the non-A beta component of Alzheimer's disease amyloid. PG - 325-34 AB - The precursor of the non-A beta component of Alzheimer's disease amyloid (NACP) is a presynaptic protein whose function has been suspected to be tightly involved in neuronal biogenesis including synaptic regulations. NACP was suggested to seed the neuritic plaque formation in the presence of A beta during the development of Alzheimer's disease (AD). Recombinant NACP purified through heat treatment, DEAE-Sephacel anion-exchange, Sephacryl S-200 size-exclusion, and S-Sepharose cation-exchange chromatography steps appeared as a single band on SDS-PAGE with Mr of 19 kDa. Its N-terminal amino acid sequence clearly confirmed that the protein was NACP. Interestingly, however, the protein was split into a doublet on a nondenaturing (ND)-PAGE with equal intensities. The doublet was located slightly above a 45-kDa marker protein on a 12.5% ND-PAGE. In addition, the size of NACP was more carefully estimated as 53 kDa with high-performance gel-permeation chromatography using a TSK G3000sw size-exclusion column. Recently, Lansbury and his colleagues (Biochemistry 35, 13709-13715) have reported that NACP exists as an elongated "natively unfolded" structure which would make the protein more actively involved in protein-protein interactions and Kim (Mol. Cells 7, 78-83) has also shown that the natively unfolded protein is extremely sensitive to proteases. Here, we report that the structure of NACP could be altered by certain environmental factors. Aluminum, a suspected risk factor for AD, converged the doublet of NACP into a singlet with slightly lower mobility on ND-PAGE. Spectroscopic analysis employing uv absorption, intrinsic fluorescence, and circular dichroism indicated that NACP experienced the structural alterations in the presence of aluminum such as the secondary structure transition to generate about 33% alpha-helix. This altered structure of NACP became resistant to proteases such as trypsin, alpha-chymotrypsin, and calpain. Therefore, it is suggested that aluminum, which influences two pathologically critical processes in AD such as the protein turnover and the protein aggregation via the structural modifications, could participate in the disease. FAU - Paik, S R AU - Paik SR AD - Department of Biochemistry, College of Medicine, Inha University, Nam-Ku, Inchon, Korea. srpaik@dragon.inha.ac.kr FAU - Lee, J H AU - Lee JH FAU - Kim, D H AU - Kim DH FAU - Chang, C S AU - Chang CS FAU - Kim, J AU - Kim J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (Amyloid) RN - 0 (Nerve Tissue Proteins) RN - 0 (Protein Precursors) RN - 0 (Recombinant Proteins) RN - 0 (Synucleins) RN - CPD4NFA903 (Aluminum) RN - EC 3.4.21.1 (Chymotrypsin) RN - EC 3.4.21.4 (Trypsin) RN - EC 3.4.22.- (Calpain) SB - IM MH - Aluminum/*pharmacology MH - Alzheimer Disease/*metabolism MH - Amino Acid Sequence MH - Amyloid/*chemistry/genetics/metabolism MH - Calpain/metabolism MH - Chymotrypsin/metabolism MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - Molecular Sequence Data MH - Molecular Weight MH - *Nerve Tissue Proteins MH - Neurofibrillary Tangles/metabolism MH - Protein Conformation/*drug effects MH - Protein Precursors/*chemistry/genetics/metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Analysis MH - Spectrometry, Fluorescence MH - Spectrophotometry MH - Synucleins MH - Trypsin/metabolism EDAT- 1997/08/15 MHDA- 1997/08/15 00:01 CRDT- 1997/08/15 00:00 AID - S0003-9861(97)90207-1 [pii] AID - 10.1006/abbi.1997.0207 [doi] PST - ppublish SO - Arch Biochem Biophys. 1997 Aug 15;344(2):325-34. PMID- 21487502 OWN - NLM STAT- Publisher DA - 20110413 IS - 1938-2030 (Print) IS - 1938-2030 (Linking) VI - 1 IP - 4 DP - 2010 Oct TI - Unusual biophysics of immune signaling-related intrinsically disordered proteins. PG - 271-281 AB - Intrinsically disordered (ID) regions, the regions that lack a well-defined three-dimensional structure under physiological conditions, are preferentially located in the cytoplasmic segments of plasma membrane proteins, many of which are known to be involved in cell signaling. This is in line with our studies that demonstrated that cytoplasmic domains of signaling subunits of immune receptors, including those of zeta, CD3epsilon, CD3delta and CD3gamma chains of T cell receptor, Igalpha and Igbeta chains of B cell receptor as well as the Fc receptor gamma chain represent a novel class of ID proteins (IDPs). The domains all have one or more copies of an immunoreceptor tyrosine-based activation motif, tyrosine residues of which are phosphorylated upon receptor engagement in an early and obligatory event in the signaling cascade. Our studies of these IDPs revealed several unusual biophysical phenomena, including (1) the specific dimerization of disordered protein molecules, (2) the fast and slow dimerization equilibrium, depending on the protein, (3) no disorder-to-order transition and the lack of significant chemical shift and peak intensity changes upon dimerization or interaction with a well-folded partner protein and (4) the dual mode of binding to model membranes (with and without folding), depending on the lipid bilayer stability. Here, I highlight several of these studies that not only facilitate a rethinking process of the fundamental paradigms in protein biophysics but also open new perspectives on the molecular mechanisms involved in receptor signaling. FAU - Sigalov, Alexander B AU - Sigalov AB AD - SignaBlok Inc.; Shrewsbury, MA USA. LA - ENG PT - JOURNAL ARTICLE TA - Self Nonself JT - Self/nonself JID - 101495364 PMC - PMC3062382 EDAT- 2011/04/14 06:00 MHDA- 2011/04/14 06:00 CRDT- 2011/04/14 06:00 PHST- 2010/08/25 [received] PHST- 2010/09/15 [revised] PHST- 2010/09/15 [accepted] AID - 10.4161/self.1.4.13641 [doi] PST - ppublish SO - Self Nonself. 2010 Oct;1(4):271-281. PMID- 24098099 OWN - NLM STAT- MEDLINE DA - 20131007 DCOM- 20140506 LR - 20141112 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 9 IP - 10 DP - 2013 TI - Ligand clouds around protein clouds: a scenario of ligand binding with intrinsically disordered proteins. PG - e1003249 LID - 10.1371/journal.pcbi.1003249 [doi] AB - Intrinsically disordered proteins (IDPs) were found to be widely associated with human diseases and may serve as potential drug design targets. However, drug design targeting IDPs is still in the very early stages. Progress in drug design is usually achieved using experimental screening; however, the structural disorder of IDPs makes it difficult to characterize their interaction with ligands using experiments alone. To better understand the structure of IDPs and their interactions with small molecule ligands, we performed extensive simulations on the c-Myc(3)(7)(0)(-)(4)(0)(9) peptide and its binding to a reported small molecule inhibitor, ligand 10074-A4. We found that the conformational space of the apo c-Myc(3)(7)(0)(-)(4)(0)(9) peptide was rather dispersed and that the conformations of the peptide were stabilized mainly by charge interactions and hydrogen bonds. Under the binding of the ligand, c-Myc(3)(7)(0)(-)(4)(0)(9) remained disordered. The ligand was found to bind to c-Myc(3)(7)(0)(-)(4)(0)(9) at different sites along the chain and behaved like a 'ligand cloud'. In contrast to ligand binding to more rigid target proteins that usually results in a dominant bound structure, ligand binding to IDPs may better be described as ligand clouds around protein clouds. Nevertheless, the binding of the ligand and a non-ligand to the c-Myc(3)(7)(0)(-)(4)(0)(9) target could be clearly distinguished. The present study provides insights that will help improve rational drug design that targets IDPs. FAU - Jin, Fan AU - Jin F AD - BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing, China ; Center for Quantitative Biology, Peking University, Beijing, China. FAU - Yu, Chen AU - Yu C FAU - Lai, Luhua AU - Lai L FAU - Liu, Zhirong AU - Liu Z LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131003 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Ligands) RN - 0 (MYC protein, human) RN - 0 (Proto-Oncogene Proteins c-myc) SB - IM MH - Computational Biology MH - Drug Design MH - Intrinsically Disordered Proteins/*chemistry/*metabolism MH - *Ligands MH - Molecular Dynamics Simulation MH - Protein Binding MH - Protein Conformation MH - Proto-Oncogene Proteins c-myc/antagonists & inhibitors/chemistry/metabolism MH - Thermodynamics PMC - PMC3789766 OID - NLM: PMC3789766 EDAT- 2013/10/08 06:00 MHDA- 2014/05/07 06:00 CRDT- 2013/10/08 06:00 PHST- 2013/10 [ecollection] PHST- 2013/04/03 [received] PHST- 2013/08/15 [accepted] PHST- 2013/10/03 [epublish] AID - 10.1371/journal.pcbi.1003249 [doi] AID - PCOMPBIOL-D-13-00558 [pii] PST - ppublish SO - PLoS Comput Biol. 2013;9(10):e1003249. doi: 10.1371/journal.pcbi.1003249. Epub 2013 Oct 3. PMID- 23607785 OWN - NLM STAT- MEDLINE DA - 20130919 DCOM- 20131125 LR - 20141116 IS - 1948-7193 (Electronic) IS - 1948-7193 (Linking) VI - 4 IP - 7 DP - 2013 Jul 17 TI - Structures and free energy landscapes of the A53T mutant-type alpha-synuclein protein and impact of A53T mutation on the structures of the wild-type alpha-synuclein protein with dynamics. PG - 1101-13 LID - 10.1021/cn400041j [doi] AB - The A53T genetic missense mutation of the wild-type alpha-synuclein (alphaS) protein was initially identified in Greek and Italian families with familial Parkinson's disease. Detailed understanding of the structures and the changes induced in the wild-type alphaS structure by the A53T mutation, as well as establishing the direct relationships between the rapid conformational changes and free energy landscapes of these intrinsically disordered fibrillogenic proteins, helps to enhance our fundamental knowledge and to gain insights into the pathogenic mechanism of Parkinson's disease. We employed extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations to determine the secondary and tertiary structural properties as well as the conformational free energy surfaces of the wild-type and A53T mutant-type alphaS proteins in an aqueous solution medium using both implicit and explicit water models. The confined aqueous volume effect in the simulations of disordered proteins using an explicit model for water is addressed for a model disordered protein. We also assessed the stabilities of the residual secondary structure component interconversions in alphaS based on free energy calculations at the atomic level with dynamics using our recently developed theoretical strategy. To the best of our knowledge, this study presents the first detailed comparison of the structural properties linked directly to the conformational free energy landscapes of the monomeric wild-type and A53T mutant-type alpha-synuclein proteins in an aqueous solution environment. Results demonstrate that the beta-sheet structure is significantly more altered than the helical structure upon A53T mutation of the monomeric wild-type alphaS protein in aqueous solution. The beta-sheet content close to the mutation site in the N-terminal region is more abundant while the non-amyloid-beta component (NAC) and C-terminal regions show a decrease in beta-sheet abundance upon A53T mutation. Obtained results utilizing our new theoretical strategy show that the residual secondary structure conversion stabilities resulting in alpha-helix formation are not significantly affected by the mutation. Interestingly, the residual secondary structure conversion stabilities show that secondary structure conversions resulting in beta-sheet formation are influenced by the A53T mutation and the most stable residual transition yielding beta-sheet occurs directly from the coil structure. Long-range interactions detected between the NAC region and the N- or C-terminal regions of the wild-type alphaS disappear upon A53T mutation. The A53T mutant-type alphaS structures are thermodynamically more stable than those of the wild-type alphaS protein structures in aqueous solution. Overall, the higher propensity of the A53T mutant-type alphaS protein to aggregate in comparison to the wild-type alphaS protein is related to the increased beta-sheet formation and lack of strong intramolecular long-range interactions in the N-terminal region in comparison to its wild-type form. The specific residual secondary structure component stabilities reported herein provide information helpful for designing and synthesizing small organic molecules that can block the beta-sheet forming residues, which are reactive toward aggregation. FAU - Coskuner, Orkid AU - Coskuner O AD - Department of Chemistry and double daggerNeurosciences Institute, University of Texas at San Antonio, One UTSA Circle, TX 78249, USA. orkid.coskuner@utsa.edu FAU - Wise-Scira, Olivia AU - Wise-Scira O LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130517 PL - United States TA - ACS Chem Neurosci JT - ACS chemical neuroscience JID - 101525337 RN - 0 (DNA-Binding Proteins) RN - 0 (Mutant Proteins) RN - 0 (SNCA protein, human) RN - 0 (alpha-Synuclein) RN - EC 1.1.- (Alcohol Oxidoreductases) RN - EC 1.1.1.- (C-terminal binding protein) SB - IM MH - Alcohol Oxidoreductases/physiology MH - DNA-Binding Proteins/physiology MH - Entropy MH - Humans MH - Molecular Dynamics Simulation MH - Mutant Proteins/*genetics/ultrastructure MH - Mutation, Missense MH - Parkinson Disease/*genetics MH - Protein Structure, Secondary/genetics/physiology MH - Protein Structure, Tertiary/physiology MH - alpha-Synuclein/*genetics/physiology/ultrastructure PMC - PMC3715894 OID - NLM: PMC3715894 EDAT- 2013/04/24 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/04/24 06:00 PHST- 2013/05/17 [aheadofprint] AID - 10.1021/cn400041j [doi] PST - ppublish SO - ACS Chem Neurosci. 2013 Jul 17;4(7):1101-13. doi: 10.1021/cn400041j. Epub 2013 May 17. PMID- 22820921 OWN - NLM STAT- MEDLINE DA - 20120821 DCOM- 20130327 LR - 20141105 IS - 0219-1032 (Electronic) IS - 1016-8478 (Linking) VI - 34 IP - 2 DP - 2012 Aug TI - Structural characterization of an intrinsically unfolded mini-HBX protein from hepatitis B virus. PG - 165-9 LID - 10.1007/s10059-012-0060-z [doi] AB - The hepatitis B virus x protein (HBX) is expressed in HBV-infected liver cells and can interact with a wide range of cellular proteins. In order to understand such promiscuous behavior of HBX we expressed a truncated mini-HBX protein (named Tr-HBX) (residues 18-142) with 5 Cys --> Ser mutations and characterized its structural features using circular dichroism (CD) spectropolarimetry, NMR spectroscopy as well as bioinformatics tools for predicting disorder in intrinsically unstructured proteins (IUPs). The secondary structural content of Tr-HBX from CD data suggests that Tr-HBX is only partially folded. The protein disorder prediction by IUPred reveals that the unstructured region encompasses its N-terminal ~30 residues of Tr-HBX. A two-dimensional (1)H-(15)N HSQC NMR spectrum exhibits fewer number of resonances than expected, suggesting that Tr-HBX is a hybrid type IUP where its folded C-terminal half coexists with a disordered N-terminal region. Many IUPs are known to be capable of having promiscuous interactions with a multitude of target proteins. Therefore the intrinsically disordered nature of Tr-HBX revealed in this study provides a partial structural basis for the promiscuous structure-function behavior of HBX. FAU - Lee, Si-Hyung AU - Lee SH AD - Biomedical Translational Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea. FAU - Cha, Eun-Ji AU - Cha EJ FAU - Lim, Ji-Eun AU - Lim JE FAU - Kwon, Soon-Hwan AU - Kwon SH FAU - Kim, Do-Hyoung AU - Kim DH FAU - Cho, Hyeseong AU - Cho H FAU - Han, Kyou-Hoon AU - Han KH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120720 PL - Korea (South) TA - Mol Cells JT - Molecules and cells JID - 9610936 RN - 0 (Trans-Activators) RN - 0 (hepatitis B virus X protein) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism/methods MH - Hepatitis B virus/genetics/*metabolism MH - Mutagenesis, Site-Directed MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Protein Unfolding MH - Trans-Activators/*chemistry/genetics/isolation & purification/*metabolism PMC - PMC3887815 OID - NLM: PMC3887815 EDAT- 2012/07/24 06:00 MHDA- 2013/03/28 06:00 CRDT- 2012/07/24 06:00 PHST- 2012/02/23 [received] PHST- 2012/05/25 [accepted] PHST- 2012/05/24 [revised] PHST- 2012/07/20 [aheadofprint] AID - 10.1007/s10059-012-0060-z [doi] PST - ppublish SO - Mol Cells. 2012 Aug;34(2):165-9. doi: 10.1007/s10059-012-0060-z. Epub 2012 Jul 20. PMID- 22866172 OWN - NLM STAT- Publisher DA - 20120806 IS - 1877-9468 (Print) IS - 1877-9468 (Linking) VI - 2 IP - 1 DP - 2012 Jan TI - Folding of Intrinsically Disordered Protein Phosphatase 1 Regulatory Proteins. PG - 107-114 AB - Intrinsically disordered but biologically active proteins, commonly referred to as IDPs, are readily identified in many biological systems and play critical roles in multiple protein regulatory processes. While disordered in their unbound states, IDPs often, but not always, fold upon binding with their protein interaction partners. Here, we discuss how a class of IDPs directs the targeting, specificity and activity of Protein Phosphatase 1 (PP1). PP1 is major ser/thr phosphatase that plays a critical role in a broad range of biological processes, from muscle contraction to memory formation. In the cell, PP1 is regulated through its interaction with more than 200 regulatory proteins, the majority of which are IDPs. Critically, these PP1:regulatory protein holoenzyme complexes confer specificity to PP1 and are thus the functional forms of the PP1 enzyme in vivo. Furthermore, we discuss the distinct modes of interaction utilized by IDPs to complex with their protein binding partners. We subsequently show, by integrating multiple biophysical tools, that the majority of IDPs that regulate PP1, prefer a conformational selection model. FAU - Peti, Wolfgang AU - Peti W AD - Department of Molecular Pharmacology, Physiology and Biotechnology & Department of Chemistry, Brown University, Providence, RI 02912, USA. FAU - Nairn, Angus C AU - Nairn AC FAU - Page, Rebecca AU - Page R LA - ENG GR - R01 GM098482/GM/NIGMS NIH HHS/United States GR - R01 NS056128/NS/NINDS NIH HHS/United States PT - JOURNAL ARTICLE TA - Curr Phys Chem JT - Current physical chemistry JID - 101574540 PMC - PMC3409662 MID - NIHMS387960 EDAT- 2012/08/07 06:00 MHDA- 2012/08/07 06:00 CRDT- 2012/08/07 06:00 PST - ppublish SO - Curr Phys Chem. 2012 Jan;2(1):107-114. PMID- 18508761 OWN - NLM STAT- MEDLINE DA - 20080721 DCOM- 20080908 LR - 20140903 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 30 DP - 2008 Jul 25 TI - Multiple intrinsically disordered sequences alter DNA binding by the homeodomain of the Drosophila hox protein ultrabithorax. PG - 20874-87 LID - 10.1074/jbc.M800375200 [doi] AB - During animal development, distinct tissues, organs, and appendages are specified through differential gene transcription by Hox transcription factors. However, the conserved Hox homeodomains bind DNA with high affinity yet low specificity. We have therefore explored the structure of the Drosophila melanogaster Hox protein Ultrabithorax and the impact of its nonhomeodomain regions on DNA binding properties. Computational and experimental approaches identified several conserved, intrinsically disordered regions outside the homeodomain of Ultrabithorax that impact DNA binding by the homeodomain. Full-length Ultrabithorax bound to target DNA 2.5-fold weaker than its isolated homeodomain. Using N-terminal and C-terminal deletion mutants, we demonstrate that the YPWM region and the disordered microexons (termed the I1 region) inhibit DNA binding approximately 2-fold, whereas the disordered I2 region inhibits homeodomain-DNA interaction a further approximately 40-fold. Binding is restored almost to homeodomain affinity by the mostly disordered N-terminal 174 amino acids (R region) in a length-dependent manner. Both the I2 and R regions contain portions of the activation domain, functionally linking DNA binding and transcription regulation. Given that (i) the I1 region and a portion of the R region alter homeodomain-DNA binding as a function of pH and (ii) an internal deletion within I1 increases Ultrabithorax-DNA affinity, I1 must directly impact homeodomain-DNA interaction energetics. However, I2 appears to indirectly affect DNA binding in a manner countered by the N terminus. The amino acid sequences of I2 and much of the I1 and R regions vary significantly among Ultrabithorax orthologues, potentially diversifying Hox-DNA interactions. FAU - Liu, Ying AU - Liu Y AD - Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA. FAU - Matthews, Kathleen S AU - Matthews KS FAU - Bondos, Sarah E AU - Bondos SE LA - eng GR - GM 22441/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20080527 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Drosophila Proteins) RN - 0 (Homeodomain Proteins) RN - 0 (Transcription Factors) RN - 0 (Ubx protein, Drosophila) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Animals MH - DNA/*chemistry MH - Drosophila Proteins/*metabolism MH - Drosophila melanogaster MH - Gene Deletion MH - Homeodomain Proteins/*metabolism MH - Hydrogen-Ion Concentration MH - Models, Biological MH - Molecular Sequence Data MH - Mutation MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Transcription Factors/*metabolism MH - Transcription, Genetic MH - Transcriptional Activation PMC - PMC2475714 OID - NLM: PMC2475714 EDAT- 2008/05/30 09:00 MHDA- 2008/09/09 09:00 CRDT- 2008/05/30 09:00 PHST- 2008/05/27 [aheadofprint] AID - M800375200 [pii] AID - 10.1074/jbc.M800375200 [doi] PST - ppublish SO - J Biol Chem. 2008 Jul 25;283(30):20874-87. doi: 10.1074/jbc.M800375200. Epub 2008 May 27. PMID- 16368689 OWN - NLM STAT- MEDLINE DA - 20060227 DCOM- 20060523 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 9 DP - 2006 Mar 3 TI - Isoform specificity of ankyrin-B: a site in the divergent C-terminal domain is required for intramolecular association. PG - 5741-9 AB - Ankyrins contain significant amino acid identity and are co-expressed in many cell types yet maintain unique functions in vivo. Recent studies have identified the highly divergent C-terminal domain in ankyrin-B as the key domain for driving ankyrin-B-specific functions in cardiomyocytes. Here we identify an intramolecular interaction between the C-terminal domain and the membrane-binding domain of ankyrin-B using pure proteins in solution and the yeast two-hybrid assay. Through extensive deletion and alanine-scanning mutagenesis we have mapped key residues for interaction in both domains. Amino acids (1597)EED(1599) located in the ankyrin-B C-terminal domain and amino acids Arg(37)/Arg(40) located in ANK repeat 1 are necessary for inter-domain interactions in yeast two-hybrid assays. Furthermore, conversion of amino acids EED(1597) to AAA(1597) leads to a loss of function in the localization of inositol 1,4,5-trisphosphate receptors in ankyrin-B mutant cardiomyocytes. Physical properties of the ankyrin-B C-terminal domain determined by circular dichroism spectroscopy and hydrodynamic parameters reveal it is unstructured and highly extended in solution. Similar structural studies performed on full-length 220-kDa ankyrin-B harboring alanine substitutions, (1597)AAA(1599), reveal a more extended conformation compared with wild-type ankyrin-B. Taken together these results suggest a model of an extended and unstructured C-terminal domain folding back to bind and potentially regulate the membrane-binding domain of ankyrin-B. FAU - Abdi, Khadar M AU - Abdi KM AD - Howard Hughes Medical Institute, and Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA. FAU - Mohler, Peter J AU - Mohler PJ FAU - Davis, Jonathan Q AU - Davis JQ FAU - Bennett, Vann AU - Bennett V LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051219 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Ankyrins) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Fusion Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Ankyrins/chemistry/genetics/*metabolism MH - Binding Sites MH - Humans MH - Mice MH - Molecular Sequence Data MH - Mutagenesis MH - Myocytes, Cardiac/cytology/metabolism MH - *Protein Conformation MH - Protein Isoforms/chemistry/genetics/*metabolism MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/genetics/metabolism MH - Sequence Alignment MH - Two-Hybrid System Techniques EDAT- 2005/12/22 09:00 MHDA- 2006/05/24 09:00 CRDT- 2005/12/22 09:00 PHST- 2005/12/19 [aheadofprint] AID - M506697200 [pii] AID - 10.1074/jbc.M506697200 [doi] PST - ppublish SO - J Biol Chem. 2006 Mar 3;281(9):5741-9. Epub 2005 Dec 19. PMID- 16889404 OWN - NLM STAT- MEDLINE DA - 20060807 DCOM- 20070205 LR - 20071203 IS - 1535-3893 (Print) IS - 1535-3893 (Linking) VI - 5 IP - 8 DP - 2006 Aug TI - Protein intrinsic disorder and human papillomaviruses: increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs. PG - 1829-42 AB - It is recognized now that many functional proteins or their long segments are devoid of stable secondary and/or tertiary structure and exist instead as very dynamic ensembles of conformations. They are known by different names including natively unfolded, intrinsically disordered, intrinsically unstructured, rheomorphic, pliable, and different combinations thereof. Many important functions and activities have been associated with these intrinsically disordered proteins (IDPs), including molecular recognition, signaling, and regulation. It is also believed that disorder of these proteins allows function to be readily modified through phosphorylation, acetylation, ubiquitination, hydroxylation, and proteolysis. Bioinformatics analysis revealed that IDPs comprise a large fraction of different proteomes. Furthermore, it is established that the intrinsic disorder is relatively abundant among cancer-related and other disease-related proteins and IDPs play a number of key roles in oncogenesis. There are more than 100 different types of human papillomaviruses (HPVs), which are the causative agents of benign papillomas/warts, and cofactors in the development of carcinomas of the genital tract, head and neck, and epidermis. With respect to their association with cancer, HPVs are grouped into two classes, known as low (e.g., HPV-6 and HPV-11) and high-risk (e.g., HPV-16 and HPV-18) types. The entire proteome of HPV includes six nonstructural proteins [E1, E2, E4, E5, E6, and E7 (the latter two are known to function as oncoproteins in the high-risk HPVs)] and two structural proteins (L1 and L2). To understand whether intrinsic disorder plays a role in the oncogenic potential of different HPV types, we have performed a detailed bioinformatics analysis of proteomes of high-risk and low-risk HPVs with the major focus on E6 and E7 oncoproteins. The results of this analysis are consistent with the conclusion that high-risk HPVs are characterized by the increased amount of intrinsic disorder in transforming proteins E6 and E7. FAU - Uversky, Vladimir N AU - Uversky VN AD - Department of Biochemistry and Molecular Biology, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, 46202, USA. vuversky@iupui.edu FAU - Roman, Ann AU - Roman A FAU - Oldfield, Christopher J AU - Oldfield CJ FAU - Dunker, A Keith AU - Dunker AK LA - eng GR - 1 R01 LM007688-0A1/LM/NLM NIH HHS/United States GR - AI49294/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - J Proteome Res JT - Journal of proteome research JID - 101128775 RN - 0 (Oncogene Proteins, Viral) RN - 0 (Papillomavirus E7 Proteins) RN - 0 (Proteome) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Animals MH - Computational Biology MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Neoplasms/virology MH - Oncogene Proteins, Viral/*chemistry/genetics/metabolism MH - Papillomaviridae/chemistry/genetics/*metabolism/pathogenicity MH - Papillomavirus E7 Proteins/*chemistry/genetics/metabolism MH - Papillomavirus Infections/metabolism MH - *Protein Conformation MH - *Proteome/analysis MH - Risk Factors EDAT- 2006/08/08 09:00 MHDA- 2007/02/06 09:00 CRDT- 2006/08/08 09:00 AID - 10.1021/pr0602388 [doi] PST - ppublish SO - J Proteome Res. 2006 Aug;5(8):1829-42. PMID- 9132005 OWN - NLM STAT- MEDLINE DA - 19970429 DCOM- 19970429 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 36 IP - 12 DP - 1997 Mar 25 TI - Physical studies of conformational plasticity in a recombinant prion protein. PG - 3543-53 AB - PrP(Sc) is known to be the major, if not the only, component of the infectious prion. Limited proteolysis of PrP(Sc) produces an N-terminally truncated polypeptide of about 142 residues, designated PrP 27-30. Recently, a recombinant protein (rPrP) of 142 residues corresponding to the Syrian hamster PrP 27-30 was expressed in Escherichia coli and purified (Mehlhorn et al., 1996). rPrP has been refolded into both alpha-helical and beta-sheet structures as well as various intermediates in aqueous buffers. The beta-sheet state and two pH-dependent alpha-helical states were characterized by CD and NMR. The alpha-helical conformation occurred only after the formation of an intramolecular disulfide bond, whereas the beta-sheet form was accessible either with or without the disulfide. Of the different alpha-helical forms studied, only those refolded in the pH range 5-8 were substantially soluble at physiological pH, exhibiting similar conformations and monomeric analytical sedimentation profiles throughout the above pH range. Furthermore, refolded alpha-rPrP showed NMR chemical shift dispersion typical of proteins with native conformations, although 2D NMR indicated large segments of conformational flexibility. It displayed a cooperative thermal denaturation transition; at elevated temperatures, it converted rapidly and irreversibly to the thermodynamically more stable beta-sheet form. Unfolding of alpha-rPrP by GdnHCl revealed a two-phase transition with a relatively stable folding intermediate at 2 M GdnHCl. The deltaG values were estimated to be 1.9 +/- 0.4 kcal/mol for the first phase and 6.5 +/- 1.2 kcal/mol for the second, consistent with a folding core surrounded by significant segments of flexible conformation. By NMR, alpha-rPrP(acid) isolated at pH 2 without refolding exhibited heterogeneous line widths, consistent with an acid-denatured molten globular state. We conclude that to the extent that rPrP constitutes a relevant folding domain of PrP(C), the various conformations exhibited by rPrP suggest that the PrP sequence may be intrinsically plastic in its conformations; indeed, portions of PrP(C) may possess a relatively open conformation which makes it susceptible to conversion into PrP(Sc) under appropriate conditions. FAU - Zhang, H AU - Zhang H AD - Department of Neurology, University of California, San Francisco 94143, USA. FAU - Stockel, J AU - Stockel J FAU - Mehlhorn, I AU - Mehlhorn I FAU - Groth, D AU - Groth D FAU - Baldwin, M A AU - Baldwin MA FAU - Prusiner, S B AU - Prusiner SB FAU - James, T L AU - James TL FAU - Cohen, F E AU - Cohen FE LA - eng GR - AG02132/AG/NIA NIH HHS/United States GR - AG08967/AG/NIA NIH HHS/United States GR - NS14069/NS/NINDS NIH HHS/United States GR - etc. PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Prions) RN - 0 (Recombinant Proteins) SB - IM MH - Animals MH - Chromatography, High Pressure Liquid MH - Circular Dichroism MH - Cricetinae MH - Magnetic Resonance Spectroscopy MH - Mass Spectrometry MH - Mesocricetus MH - Pliability MH - Prions/*chemistry MH - Protein Conformation MH - Recombinant Proteins/*chemistry MH - Spectroscopy, Fourier Transform Infrared MH - Ultracentrifugation EDAT- 1997/03/25 MHDA- 1997/03/25 00:01 CRDT- 1997/03/25 00:00 AID - 10.1021/bi961965r [doi] AID - bi961965r [pii] PST - ppublish SO - Biochemistry. 1997 Mar 25;36(12):3543-53. PMID- 12062405 OWN - NLM STAT- MEDLINE DA - 20020613 DCOM- 20020729 LR - 20101118 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 517 IP - 1-3 DP - 2002 Apr 24 TI - Amyloid fibrils from the mammalian protein prothymosin alpha. PG - 37-40 AB - Mammalian prothymosin alpha, a small (12 kDa) and extremely acidic protein (pI 3.5), is a member of the growing family of 'natively' unfolded proteins. We demonstrate that at low pH ( approximately 3) and high concentrations, prothymosin alpha is capable of forming regular elongated fibrils with flat ribbon structure 4-5 nm in height and 12-13 nm in width as judged from scanning force and electron microscopy. These aggregates induced a characteristic spectral shift of thioflavin T fluorescence and their circular dichroism spectra were indicative of significant beta-sheet content, suggesting formation of classical amyloid. Our findings indicate that natively unfolded proteins may have a general propensity to form amyloid fibrils under conditions inducing partially folded conformations. FAU - Pavlov, Nikolai A AU - Pavlov NA AD - Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany. FAU - Cherny, Dmitry I AU - Cherny DI FAU - Heim, Gudrun AU - Heim G FAU - Jovin, Thomas M AU - Jovin TM FAU - Subramaniam, Vinod AU - Subramaniam V LA - eng PT - Journal Article PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Amyloid beta-Peptides) RN - 0 (Fluorescent Dyes) RN - 0 (Protein Precursors) RN - 0 (Thiazoles) RN - 0 (prothymosin alpha) RN - 2390-54-7 (thioflavin T) RN - 61512-21-8 (Thymosin) SB - IM MH - Amyloid beta-Peptides/*chemistry MH - Circular Dichroism MH - Fluorescent Dyes/analysis MH - Humans MH - Hydrogen-Ion Concentration MH - Kinetics MH - Microscopy, Atomic Force MH - Microscopy, Electron MH - Protein Folding MH - Protein Precursors/*chemistry/isolation & purification MH - Protein Structure, Secondary MH - Spectrometry, Fluorescence MH - Thiazoles/*analysis MH - Thymosin/*analogs & derivatives/*chemistry/isolation & purification EDAT- 2002/06/14 10:00 MHDA- 2002/07/30 10:01 CRDT- 2002/06/14 10:00 AID - S0014579302025723 [pii] PST - ppublish SO - FEBS Lett. 2002 Apr 24;517(1-3):37-40. PMID- 8876186 OWN - NLM STAT- MEDLINE DA - 19961204 DCOM- 19961204 LR - 20130918 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 93 IP - 21 DP - 1996 Oct 15 TI - Interplay of structure and disorder in cochaperonin mobile loops. PG - 11622-7 AB - Protein-protein interactions typically are characterized by highly specific interfaces that mediate binding with precisely tuned affinities. Binding of the Escherichia coli cochaperonin GroES to chaperonin GroEL is mediated, at least in part, by a mobile polypeptide loop in GroES that becomes immobilized in the GroEL/GroES/nucleotide complex. The bacteriophage T4 cochaperonin Gp31 possesses a similar highly flexible polypeptide loop in a region of the protein that shows low, but significant, amino acid similarity with GroES and other cochaperonins. When bound to GroEL, a synthetic peptide representing the mobile loop of either GroES or Gp31 adopts a characteristic bulged hairpin conformation as determined by transferred nuclear Overhauser effects in NMR spectra. Thermodynamic considerations suggest that flexible disorder in the cochaperonin mobile loops moderates their affinity for GroEL to facilitate cycles of chaperonin-mediated protein folding. FAU - Landry, S J AU - Landry SJ AD - Department of Biochemistry, Tulane University School of Medicine, New Orleans, LA 70112-2699, USA. FAU - Taher, A AU - Taher A FAU - Georgopoulos, C AU - Georgopoulos C FAU - van der Vies, S M AU - van der Vies SM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Chaperonin 10) RN - 0 (Chaperonin 60) RN - 0 (Peptide Fragments) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Calorimetry MH - Chaperonin 10/*chemistry/*metabolism MH - Chaperonin 60/*chemistry/*metabolism MH - Entropy MH - Escherichia coli/*metabolism MH - Hydrogen Bonding MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/isolation & purification MH - Peptide Mapping MH - *Protein Structure, Secondary MH - Thermodynamics PMC - PMC38108 OID - NLM: PMC38108 EDAT- 1996/10/15 MHDA- 1996/10/15 00:01 CRDT- 1996/10/15 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11622-7. PMID- 11891239 OWN - NLM STAT- MEDLINE DA - 20020313 DCOM- 20020618 LR - 20140613 IS - 0032-0889 (Print) IS - 0032-0889 (Linking) VI - 128 IP - 3 DP - 2002 Mar TI - Temperature-induced extended helix/random coil transitions in a group 1 late embryogenesis-abundant protein from soybean. PG - 822-32 AB - Group 1 late embryogenesis-abundant (LEA) proteins are a subset of hydrophilins that are postulated to play important roles in protecting plant macromolecules from damage during freezing, desiccation, or osmotic stress. To better understand the putative functional roles of group 1 LEA proteins, we analyzed the structure of a group 1 LEA protein from soybean (Glycine max). Differential scanning calorimetry of the purified, recombinant protein demonstrated that the protein assumed a largely unstructured state in solution. In the presence of trifluoroethanol (50% [w/v]), the protein acquired a 30% alpha-helical content, indicating that the polypeptide is highly restricted to adopt alpha-helical structures. In the presence of sodium dodecyl sulfate (1% [w/v]), 8% of the polypeptide chain adopted an alpha-helical structure. However, incubation with phospholipids showed no effect on the protein structure. Ultraviolet absorption and circular dichroism spectroscopy revealed that the protein existed in equilibrium between two conformational states. Ultraviolet absorption spectroscopy studies also showed that the protein became more hydrated upon heating. Furthermore, circular dichroism spectral measurements indicated that a minimum of 14% of amino acid residues existed in a solvent-exposed, left-handed extended helical or poly (L-proline)-type (PII) conformation at 20 degrees C with the remainder of the protein being unstructured. The content of PII-like structure increased as temperature was lowered. We hypothesize that by favoring the adoption of PII structure, instead of the formation of alpha-helical or beta-sheet structures, group 1 LEA proteins retain a high content of surface area available for interaction with the solvent. This feature could constitute the basis of a potential role of LEA proteins in preventing freezing, desiccation, or osmotic stress damage. FAU - Soulages, Jose L AU - Soulages JL AD - Department of Biochemistry and Molecular Biology, 355 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma 74078-0454, USA. FAU - Kim, Kangmin AU - Kim K FAU - Walters, Christina AU - Walters C FAU - Cushman, John C AU - Cushman JC LA - eng GR - GM 55622/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Plant Physiol JT - Plant physiology JID - 0401224 RN - 0 (Liposomes) RN - 0 (Phospholipids) RN - 0 (Plant Proteins) RN - 0 (Recombinant Proteins) RN - 0 (late embryogenesis abundant protein, plant) RN - 059QF0KO0R (Water) RN - 75-89-8 (Trifluoroethanol) SB - IM MH - Circular Dichroism MH - Cloning, Molecular MH - Escherichia coli/genetics MH - Gene Expression MH - Liposomes/pharmacology MH - Osmotic Pressure MH - Phospholipids/pharmacology MH - Plant Proteins/chemistry/genetics/*metabolism MH - Protein Structure, Secondary/drug effects MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Soybeans/genetics/*metabolism MH - Spectrophotometry, Ultraviolet MH - Temperature MH - Trifluoroethanol/pharmacology MH - Water/metabolism PMC - PMC152196 OID - NLM: PMC152196 EDAT- 2002/03/14 10:00 MHDA- 2002/06/19 10:01 CRDT- 2002/03/14 10:00 AID - 10.1104/pp.010521 [doi] PST - ppublish SO - Plant Physiol. 2002 Mar;128(3):822-32. PMID- 12582818 OWN - NLM STAT- MEDLINE DA - 20030212 DCOM- 20031016 LR - 20131121 IS - 0175-7571 (Print) IS - 0175-7571 (Linking) VI - 31 IP - 8 DP - 2003 Feb TI - Are there temperature-dependent structural transitions in the "intrinsically unstructured" protein prothymosin alpha? PG - 586-94 AB - Prothymosin alpha, a typical member of the class of the so-called "intrinsically unstructured" proteins, adopts a random-chain conformation under physiological environmental conditions. An apparent formation of ordered secondary structure and a moderate compaction are observed upon the change from neutral to acid pH at room temperature. We have addressed the question of whether there are temperature-dependent changes of the conformational state of prothymosin alpha at low pH using circular dichroism spectroscopy and static and dynamic light scattering. In contrast to previous investigations, we did not observe a heat-induced conformational transition. For comparison, we have also carried out the same experimental procedures with acid-unfolded phosphoglycerate kinase from yeast. In this case we observed a weak compaction and a slight apparent increase in ordered secondary structure with increasing temperature, probably caused by the higher average hydrophobicity as compared to prothymosin alpha. In the absence of a clear structural transition, we deduce the observed effects result mainly from a progressive redistribution in the population of phi-psi angles of the polypeptide backbone when the temperature is increased. Furthermore, the paper should demonstrate the difficulties in distinguishing between such a progressive change amongst a continuum of states within the ensemble of unfolded conformations from the formation of authentic stable secondary structures in highly unfolded proteins. This problem is not solved presently and convincing evidence can only be supplied by the combination of various experimental techniques. FAU - Gast, Klaus AU - Gast K AD - Max-Delbruck-Centrum fur Molekulare Medizin Berlin-Buch, Robert-Rossle Strasse 10, 13125 Berlin, Germany. gast@mdc-berlin.de FAU - Zirwer, Dietrich AU - Zirwer D FAU - Damaschun, Gregor AU - Damaschun G LA - eng PT - Journal Article DEP - 20021003 PL - Germany TA - Eur Biophys J JT - European biophysics journal : EBJ JID - 8409413 RN - 0 (Protein Precursors) RN - 0 (prothymosin alpha) RN - 61512-21-8 (Thymosin) RN - QTT17582CB (Hydrochloric Acid) SB - IM MH - Circular Dichroism/methods MH - Crystallography/*methods MH - *Hot Temperature MH - Hydrochloric Acid/chemistry MH - Protein Conformation MH - Protein Denaturation/radiation effects MH - Protein Precursors/*chemistry/radiation effects MH - Protein Structure, Secondary/radiation effects MH - Spectrophotometry, Ultraviolet/methods MH - Temperature MH - Thymosin/*analogs & derivatives/*chemistry/radiation effects EDAT- 2003/02/13 04:00 MHDA- 2003/10/17 05:00 CRDT- 2003/02/13 04:00 PHST- 2002/06/06 [received] PHST- 2002/08/20 [accepted] PHST- 2002/10/03 [aheadofprint] AID - 10.1007/s00249-002-0254-y [doi] PST - ppublish SO - Eur Biophys J. 2003 Feb;31(8):586-94. Epub 2002 Oct 3. PMID- 10601302 OWN - NLM STAT- MEDLINE DA - 20000113 DCOM- 20000113 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 274 IP - 52 DP - 1999 Dec 24 TI - A mixture of alpha-helical and 3(10)-helical conformations for involucrin in the human epidermal corneocyte envelope provides a scaffold for the attachment of both lipids and proteins. PG - 37340-4 AB - Involucrin plays an important role in the lipid and protein compound envelopes of mammalian epidermal corneocytes. In the present study, model peptides containing the consensus repeating units PEQQEGQLEL and LEQQEGQLEH, found in the central region of human involucrin, were studied by circular dichroism spectroscopy, molecular modeling, and energy minimization. These peptides have intrinsic alpha-helix-forming properties as indicated by their circular dichroic spectra obtained in the presence of 2,2,2-trifluoroethanol. Peptide (LEQQEGQLEH)(3) had an alpha-helix content of 100% in 100% 2, 2,2-trifluoroethanol at 0 degrees C. The energy-minimized alpha-helix showed that only 50% of the glutamate side chains may be available for the attachment of lipids. However, when a 3(10)-helix was assumed for the GQL or GQLE residues in LEQQEGQLEH, all of the glutamate side chains were arrayed on one face of the helix, and all of the glutamine side chains were arrayed on the opposite face. A similar result was obtained when the nonhelical part of PEQQEGQLEL was assumed to contain a beta-turn III, which is equivalent to a short portion of 3(10)-helix. The results of this study suggest that when the central segment of human involucrin is predominantly alpha-helical, accompanied by short 3(10)-helical segments, the protein can function as a scaffold for the attachment of both lipids and proteins. FAU - Lazo, N D AU - Lazo ND AD - Department of Dermatology, University of Iowa, Iowa City, Iowa 52242, USA. noellazo@uiowa.edu FAU - Downing, D T AU - Downing DT LA - eng GR - AR 32374/AR/NIAMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Protein Precursors) RN - 0 (Proteins) RN - 60108-77-2 (involucrin) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - *Lipid Metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Precursors/*chemistry/physiology MH - *Protein Structure, Secondary MH - Proteins/*metabolism MH - Structure-Activity Relationship EDAT- 1999/12/22 MHDA- 1999/12/22 00:01 CRDT- 1999/12/22 00:00 PST - ppublish SO - J Biol Chem. 1999 Dec 24;274(52):37340-4. PMID- 23185649 OWN - NLM STAT- Publisher DA - 20121127 IS - 1948-7185 (Print) IS - 1948-7185 (Linking) VI - 3 IP - 18 DP - 2012 Sep 20 TI - Disordered Protein Diffusion under Crowded Conditions. PG - 2703-2706 AB - Intrinsically disordered proteins are important in signaling, regulation, and translocation. Understanding their diffusion under physiologically relevant conditions will yield insight into their functions. We used NMR to quantify the translational diffusion of a globular and a disordered protein in dilute solution and under crowded conditions. In dilute solution, the globular protein chymotrypsin inhibitor 2 (CI2, 7.4 kDa) diffuses faster than the disordered protein alpha-synuclein (14 kDa). Surprisingly, the opposite occurs under crowded conditions; alpha-synuclein diffuses faster than CI2, even though alpha-synuclein is larger than CI2. These data show that shape is a key parameter determining protein diffusion under crowded conditions, adding to the properties known to be affected by macromolecular crowding. The results also offer a clue about why many signaling proteins are disordered. FAU - Wang, Yaqiang AU - Wang Y AD - Chemistry, University of North Carolina, Chapel Hill, NC 27599. FAU - Benton, Laura A AU - Benton LA FAU - Singh, Vishavpreet AU - Singh V FAU - Pielak, Gary J AU - Pielak GJ LA - ENG GR - DP1 OD000783/OD/NIH HHS/United States PT - JOURNAL ARTICLE DEP - 20120906 TA - J Phys Chem Lett JT - The journal of physical chemistry letters JID - 101526034 PMC - PMC3505085 MID - NIHMS407197 EDAT- 2012/11/28 06:00 MHDA- 2012/11/28 06:00 CRDT- 2012/11/28 06:00 PHST- 2012/09/06 [epublish] AID - 10.1021/jz3010915 [doi] PST - ppublish SO - J Phys Chem Lett. 2012 Sep 20;3(18):2703-2706. Epub 2012 Sep 6. PMID- 23858448 OWN - NLM STAT- MEDLINE DA - 20130731 DCOM- 20131126 LR - 20141113 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 110 IP - 31 DP - 2013 Jul 30 TI - Atg29 phosphorylation regulates coordination of the Atg17-Atg31-Atg29 complex with the Atg11 scaffold during autophagy initiation. PG - E2875-84 LID - 10.1073/pnas.1300064110 [doi] AB - Macroautophagy (hereafter autophagy) functions in the nonselective clearance of cytoplasm. This process participates in many aspects of cell physiology, and is conserved in all eukaryotes. Autophagy begins with the organization of the phagophore assembly site (PAS), where most of the AuTophaGy-related (Atg) proteins are at least transiently localized. Autophagy occurs at a basal level and can be induced by various types of stress; the process must be tightly regulated because insufficient or excessive autophagy can be deleterious. A complex composed of Atg17-Atg31-Atg29 is vital for PAS organization and autophagy induction, implying a significant role in autophagy regulation. In this study, we demonstrate that Atg29 is a phosphorylated protein and that this modification is critical to its function; alanine substitution at the phosphorylation sites blocks its interaction with the scaffold protein Atg11 and its ability to facilitate assembly of the PAS. Atg29 has the characteristics of an intrinsically disordered protein, suggesting that it undergoes dynamic conformational changes on interaction with a binding partner(s). Finally, single-particle electron microscopy analysis of the Atg17-Atg31-Atg29 complex reveals an elongated structure with Atg29 located at the opposing ends. FAU - Mao, Kai AU - Mao K AD - Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA. FAU - Chew, Leon H AU - Chew LH FAU - Inoue-Aono, Yuko AU - Inoue-Aono Y FAU - Cheong, Heesun AU - Cheong H FAU - Nair, Usha AU - Nair U FAU - Popelka, Hana AU - Popelka H FAU - Yip, Calvin K AU - Yip CK FAU - Klionsky, Daniel J AU - Klionsky DJ LA - eng GR - GM053396/GM/NIGMS NIH HHS/United States GR - R01 GM053396/GM/NIGMS NIH HHS/United States GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130715 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (ATG29 protein, S cerevisiae) RN - 0 (Atg11 protein, S cerevisiae) RN - 0 (Atg17 protein, S cerevisiae) RN - 0 (Atg31 protein, S cerevisiae) RN - 0 (Carrier Proteins) RN - 0 (Multiprotein Complexes) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Vesicular Transport Proteins) SB - IM MH - Autophagy/*physiology MH - Carrier Proteins/genetics/*metabolism MH - Multiprotein Complexes/genetics/*metabolism/ultrastructure MH - Phosphorylation/physiology MH - Saccharomyces cerevisiae/genetics/*metabolism/ultrastructure MH - Saccharomyces cerevisiae Proteins/genetics/*metabolism MH - Vesicular Transport Proteins/genetics/*metabolism PMC - PMC3732952 OID - NLM: PMC3732952 OTO - NOTNLM OT - lysosome OT - organelle biogenesis OT - vacuole OT - yeast EDAT- 2013/07/17 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/07/17 06:00 PHST- 2013/07/15 [aheadofprint] AID - 1300064110 [pii] AID - 10.1073/pnas.1300064110 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2013 Jul 30;110(31):E2875-84. doi: 10.1073/pnas.1300064110. Epub 2013 Jul 15. PMID- 23223634 OWN - NLM STAT- MEDLINE DA - 20130128 DCOM- 20130402 LR - 20141104 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 4 DP - 2013 Jan 25 TI - Multiple recognition motifs in nucleoporin Nup159 provide a stable and rigid Nup159-Dyn2 assembly. PG - 2614-22 LID - 10.1074/jbc.M112.432831 [doi] AB - Dyn2 is the yeast ortholog of the molecular hub LC8, which binds disordered proteins and promotes their self-association and higher order assembly. Dyn2 is proposed to dimerize and stabilize the Nup82-Nsp1-Nup159 complex of the nuclear pore assembly through its interaction with nucleoporin Nup159. Nup159 has six LC8 recognition motifs separated by short linkers. NMR experiments reported here show that the Dyn2 binding domain of Nup159 is intrinsically disordered and that binding of one equivalent of Dyn2 dimer aligns two Nup159 chains along the full Dyn2 binding domain to form a bivalent scaffold that promotes binding of other Dyn2 dimers. Isothermal titration calorimetry of Dyn2 binding to Nup constructs of increasing lengths determine that the third LC8 recognition motifs does not bind Dyn2. A new approach to identifying active LC8 recognition motifs based on NMR-detected beta-sheet propensities is presented. Isothermal titration calorimetry experiments also show that, due to unfavorable entropy changes, a Nup-Dyn2 complex with three Dyn2 dimers is more stable than the wild-type complex with five Dyn2 dimers. The calorimetric results argue that, from a thermodynamics perspective, only three Dyn2 dimers are needed for optimal stability and suggest that the evolutionary adaptation of multiple tandem LC8 recognition motifs imparts to the complex other properties such as rigidity and a kink in the rod-like structure. These findings extend the repertoire of functions of intrinsically disordered protein to fine-tuning and versatile assembly of higher order macromolecular complexes. FAU - Nyarko, Afua AU - Nyarko A AD - Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA. FAU - Song, Yujuan AU - Song Y FAU - Novacek, Jiri AU - Novacek J FAU - Zidek, Lukas AU - Zidek L FAU - Barbar, Elisar AU - Barbar E LA - eng GR - GM 084276/GM/NIGMS NIH HHS/United States GR - NIEHS 00210/PHS HHS/United States GR - R01 GM084276/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20121208 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (NUP159 protein, S cerevisiae) RN - 0 (Nuclear Pore Complex Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 3.6.4.2 (Dyneins) RN - EC 3.6.4.2 (SLC1 protein, S cerevisiae) SB - IM MH - Amino Acid Motifs MH - Binding Sites MH - Calorimetry/methods MH - Cloning, Molecular MH - Dimerization MH - Dyneins/*chemistry MH - Kinetics MH - Magnetic Resonance Spectroscopy/methods MH - Nuclear Pore Complex Proteins/*chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry MH - Thermodynamics PMC - PMC3554928 OID - NLM: PMC3554928 EDAT- 2012/12/12 06:00 MHDA- 2013/04/03 06:00 CRDT- 2012/12/11 06:00 PHST- 2012/12/08 [aheadofprint] AID - M112.432831 [pii] AID - 10.1074/jbc.M112.432831 [doi] PST - ppublish SO - J Biol Chem. 2013 Jan 25;288(4):2614-22. doi: 10.1074/jbc.M112.432831. Epub 2012 Dec 8. PMID- 21481779 OWN - NLM STAT- MEDLINE DA - 20110412 DCOM- 20110804 LR - 20141113 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 19 IP - 4 DP - 2011 Apr 13 TI - Beyond the random coil: stochastic conformational switching in intrinsically disordered proteins. PG - 566-76 LID - 10.1016/j.str.2011.01.011 [doi] AB - Intrinsically disordered proteins (IDPs) participate in critical cellular functions that exploit the flexibility and rapid conformational fluctuations of their native state. Limited information about the native state of IDPs can be gained by the averaging over many heterogeneous molecules that is unavoidable in ensemble approaches. We used single molecule fluorescence to characterize native state conformational dynamics in five synaptic proteins confirmed to be disordered by other techniques. For three of the proteins, SNAP-25, synaptobrevin and complexin, their conformational dynamics could be described with a simple semiflexible polymer model. Surprisingly, two proteins, neuroligin and the NMDAR-2B glutamate receptor, were observed to stochastically switch among distinct conformational states despite the fact that they appeared intrinsically disordered by other measures. The hop-like intramolecular diffusion found in these proteins is suggested to define a class of functionality previously unrecognized for IDPs. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Choi, Ucheor B AU - Choi UB AD - Department of Physics, North Carolina State University, Raleigh, NC 27695, USA. FAU - McCann, James J AU - McCann JJ FAU - Weninger, Keith R AU - Weninger KR FAU - Bowen, Mark E AU - Bowen ME LA - eng GR - GM076039/GM/NIGMS NIH HHS/United States GR - MH081923/MH/NIMH NIH HHS/United States GR - R01 MH081923/MH/NIMH NIH HHS/United States GR - R01 MH081923-03/MH/NIMH NIH HHS/United States GR - T32 GM007518/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Adaptor Proteins, Vesicular Transport) RN - 0 (Cell Adhesion Molecules, Neuronal) RN - 0 (NR2B NMDA receptor) RN - 0 (Nerve Tissue Proteins) RN - 0 (Proteins) RN - 0 (R-SNARE Proteins) RN - 0 (Receptors, N-Methyl-D-Aspartate) RN - 0 (Snap25 protein, rat) RN - 0 (Synaptosomal-Associated Protein 25) RN - 0 (complexin I) RN - 0 (neuroligin 1) SB - IM MH - Adaptor Proteins, Vesicular Transport/chemistry MH - Animals MH - Cell Adhesion Molecules, Neuronal/chemistry MH - Fluorescence Resonance Energy Transfer/methods MH - Molecular Dynamics Simulation MH - Nerve Tissue Proteins/chemistry MH - *Protein Conformation MH - *Protein Denaturation MH - *Protein Folding MH - Proteins/*chemistry MH - R-SNARE Proteins/chemistry MH - Rats MH - Receptors, N-Methyl-D-Aspartate/chemistry MH - Reproducibility of Results MH - Synaptosomal-Associated Protein 25/chemistry PMC - PMC3075556 MID - NIHMS273308 OID - NLM: NIHMS273308 OID - NLM: PMC3075556 EDAT- 2011/04/13 06:00 MHDA- 2011/08/05 06:00 CRDT- 2011/04/13 06:00 PHST- 2010/10/04 [received] PHST- 2011/01/21 [revised] PHST- 2011/01/26 [accepted] AID - S0969-2126(11)00061-X [pii] AID - 10.1016/j.str.2011.01.011 [doi] PST - ppublish SO - Structure. 2011 Apr 13;19(4):566-76. doi: 10.1016/j.str.2011.01.011. PMID- 11248694 OWN - NLM STAT- MEDLINE DA - 20010315 DCOM- 20010503 LR - 20091119 IS - 0014-2956 (Print) IS - 0014-2956 (Linking) VI - 268 IP - 6 DP - 2001 Mar TI - Structural and functional properties of Escherichia coli-derived nucleoplasmin. A comparative study of recombinant and natural proteins. PG - 1739-48 AB - Fourier transform infrared spectroscopy, circular dichroism and prediction techniques have been used to investigate the conformational properties of nucleoplasmin isolated from oocytes and eggs of Xenopus. laevis and overexpressed in Escherichia coli. A simple and fast method allows purification of recombinant nucleoplasmin free of truncated and/or aggregated forms, and therefore provides a suitable sample to carry out the structural and functional comparison between these proteins. The secondary structure of the three proteins estimated from both spectroscopic techniques was very similar, and was found to be 31--33% loops, 27--34% beta structure, 22--26% turns and 9-14% alpha helix. Prediction studies, in good agreement with experimental data, also suggest that beta structure is the major regular conformation, and that loops and turns are the most abundant conformational features within the secondary structure of nucleoplasmin. Furthermore, the spectroscopic characterization of a truncated version of the protein, lacking 80 residues at the C-terminus, and the prediction data indicate that the secondary structure elements of the protein are segregated into two regions. The N-terminal fragment (comprising residues 1--120) which holds all the putative beta strands, and the solvent-exposed C-terminal region, that is suggested to be enriched in turn and loop structures. The phosphate/protein monomer molar ratios, obtained from chemical analysis and mass spectrometry, are 0, 3 and 7--10 for recombinant, oocyte and egg nucleoplasmin, respectively. Phosphorylation does not significantly affect the secondary structure of the protein, but clearly modulates its ability to decondense sperm nuclei and to remove basic proteins from DNA. FAU - Hierro, A AU - Hierro A AD - Unidad de Biofisica (CSIC-UPV/EHU), Universidad del Pais Vasco, Aptdo. 644, 48080 Bilbao, Spain. FAU - Arizmendi, J M AU - Arizmendi JM FAU - De Las Rivas, J AU - De Las Rivas J FAU - Urbaneja, M A AU - Urbaneja MA FAU - Prado, A AU - Prado A FAU - Muga, A AU - Muga A LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Eur J Biochem JT - European journal of biochemistry / FEBS JID - 0107600 RN - 0 (Chromatin) RN - 0 (Nuclear Proteins) RN - 0 (Nucleoplasmins) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Chromatin/metabolism MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Escherichia coli/*chemistry MH - Molecular Sequence Data MH - Nuclear Proteins/*chemistry/isolation & purification/*metabolism MH - Nucleoplasmins MH - Phosphoproteins/*chemistry/isolation & purification/*metabolism MH - Phosphorylation MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/isolation & purification/metabolism MH - Sequence Homology, Amino Acid MH - Spectroscopy, Fourier Transform Infrared MH - Xenopus laevis EDAT- 2001/03/15 10:00 MHDA- 2001/05/05 10:01 CRDT- 2001/03/15 10:00 AID - ejb2043 [pii] PST - ppublish SO - Eur J Biochem. 2001 Mar;268(6):1739-48. PMID- 20007319 OWN - NLM STAT- MEDLINE DA - 20100208 DCOM- 20100511 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 7 DP - 2010 Feb 12 TI - A large intrinsically disordered region in SKIP and its disorder-order transition induced by PPIL1 binding revealed by NMR. PG - 4951-63 LID - 10.1074/jbc.M109.087528 [doi] AB - Intrinsically disordered proteins or protein regions play an important role in fundamental biological processes. During spliceosome activation, a large structural rearrangement occurs. The Prp19 complex and related factors are involved in the catalytic activation of the spliceosome. Recent mass spectrometric analyses have shown that Ski interaction protein (SKIP) and peptidylprolyl isomerase-like protein 1 (PPIL1) are Prp19-related factors that constitute the spliceosome B, B*, and C complexes. Here, we report that a highly flexible region of SKIP (SKIPN, residues 59-129) is intrinsically disordered. Upon binding to PPIL1, SKIPN undergoes a disorder-order transition. A highly conserved fragment of SKIP (residues 59-79) called the PPIL1-binding fragment (PBF) was sufficient to bind PPIL1. The structure of PBF.PPIL1 complex, solved by NMR, shows that PBF exhibits an ordered structure and interacts with PPIL1 through electrostatic and hydrophobic interactions. Three subfragments in the PBF (residues 59-67, 68-73, and 74-79) show hook-like backbone structure, and interactions between these subfragments are necessary for PBF.PPIL1 complex formation. PPIL1 is a cyclophilin family protein. It is recruited by SKIP into the spliceosome by a region other than the peptidylprolyl isomerase active site. This enables the active site of PPIL1 to remain open in the complex and still function as a peptidylprolyl cis/trans-isomerase or molecular chaperon to facilitate the folding of other proteins in the spliceosomes. The large disordered region in SKIP provides an interaction platform. Its disorder-order transition, induced by PPIL1 binding, may adapt the requirement for a large structural rearrangement occurred in the activation of spliceosome. FAU - Wang, Xingsheng AU - Wang X AD - Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China. FAU - Zhang, Shaojie AU - Zhang S FAU - Zhang, Jiahai AU - Zhang J FAU - Huang, Xiaojuan AU - Huang X FAU - Xu, Chao AU - Xu C FAU - Wang, Weiwei AU - Wang W FAU - Liu, Zhijun AU - Liu Z FAU - Wu, Jihui AU - Wu J FAU - Shi, Yunyu AU - Shi Y LA - eng SI - PDB/2K7NM PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091209 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (SKIP protein, human) RN - EC 5.2.1.8 (PPIL1 protein, human) RN - EC 5.2.1.8 (Peptidylprolyl Isomerase) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry/genetics/*metabolism MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - *Magnetic Resonance Spectroscopy MH - Peptidylprolyl Isomerase/*chemistry/genetics/*metabolism MH - Protein Binding/genetics/physiology MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Surface Plasmon Resonance PMC - PMC2836099 OID - NLM: PMC2836099 EDAT- 2009/12/17 06:00 MHDA- 2010/05/12 06:00 CRDT- 2009/12/17 06:00 PHST- 2009/12/09 [aheadofprint] AID - M109.087528 [pii] AID - 10.1074/jbc.M109.087528 [doi] PST - ppublish SO - J Biol Chem. 2010 Feb 12;285(7):4951-63. doi: 10.1074/jbc.M109.087528. Epub 2009 Dec 9. PMID- 10676968 OWN - NLM STAT- MEDLINE DA - 20000229 DCOM- 20000229 LR - 20061115 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 403 IP - 6769 DP - 2000 Feb 3 TI - Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins. PG - 567-71 AB - Interferon-gamma is an immunomodulatory substance that induces the expression of many genes to orchestrate a cellular response and establish the antiviral state of the cell. Among the most abundant antiviral proteins induced by interferon-gamma are guanylate-binding proteins such as GBP1 and GBP2. These are large GTP-binding proteins of relative molecular mass 67,000 with a high-turnover GTPase activity and an antiviral effect. Here we have determined the crystal structure of full-length human GBP1 to 1.8 A resolution. The amino-terminal 278 residues constitute a modified G domain with a number of insertions compared to the canonical Ras structure, and the carboxy-terminal part is an extended helical domain with unique features. From the structure and biochemical experiments reported here, GBP1 appears to belong to the group of large GTP-binding proteins that includes Mx and dynamin, the common property of which is the ability to undergo oligomerization with a high concentration-dependent GTPase activity. FAU - Prakash, B AU - Prakash B AD - Max-Planck-Institut fur Molekulare Physiologie, Dortmund, Germany. FAU - Praefcke, G J AU - Praefcke GJ FAU - Renault, L AU - Renault L FAU - Wittinghofer, A AU - Wittinghofer A FAU - Herrmann, C AU - Herrmann C LA - eng SI - PDB/1DG3 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (DNA-Binding Proteins) RN - 0 (GBP1 protein, human) RN - 0 (Recombinant Proteins) RN - EC 3.6.1.- (GTP Phosphohydrolases) RN - EC 3.6.1.- (GTP-Binding Proteins) RN - EC 3.6.5.5 (Dynamins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Crystallography, X-Ray MH - DNA-Binding Proteins/*chemistry/genetics MH - Dynamins MH - Escherichia coli MH - GTP Phosphohydrolases/chemistry MH - GTP-Binding Proteins/*chemistry/genetics MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Recombinant Proteins/chemistry MH - Sequence Homology, Amino Acid EDAT- 2000/02/17 09:00 MHDA- 2000/03/04 09:00 CRDT- 2000/02/17 09:00 AID - 10.1038/35000617 [doi] PST - ppublish SO - Nature. 2000 Feb 3;403(6769):567-71. PMID- 18973346 OWN - NLM STAT- MEDLINE DA - 20090220 DCOM- 20090316 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 47 DP - 2008 Nov 25 TI - Membrane-induced folding of the cAMP-regulated phosphoprotein endosulfine-alpha. PG - 12357-64 LID - 10.1021/bi801450t [doi] AB - Endosulfine-alpha (ENSA) is a 121-residue cAMP-regulated phosphoprotein, originally identified as an endogenous regulator of ATP-sensitive potassium channels. ENSA has been implicated in the regulation of insulin secretion, and expression of ENSA is decreased in brains of both Alzheimer's disease (AD) and Down's syndrome patients. We recently described membrane-dependent interactions between ENSA and the Parkinson's disease associated protein alpha-synuclein. Here we characterize the conformational change in ENSA that occurs upon binding to membranes. Secondary chemical shift analysis demonstrates formation of four helices in the lipid-bound state that are not present in the absence of lipid. The helical structure is maintained in several different lipid mimetics (sodium dodecyl sulfate, dodecyl phosphocholine, lyso 1-palmitoyl phosphatidylglycerol, and phospholipid vesicles). Introduction of a mutation (S109E) to mimic PKA phosphorylation of ENSA leads to a perturbation of the fourth helix and disrupts the interaction with alpha-synuclein. These data establish ENSA as an intrinsically unstructured protein that adopts a stable structure upon membrane binding, properties it shares with its binding partner alpha-synuclein. FAU - Boettcher, John M AU - Boettcher JM AD - Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA. FAU - Hartman, Kevin L AU - Hartman KL FAU - Ladror, Daniel T AU - Ladror DT FAU - Qi, Zhi AU - Qi Z FAU - Woods, Wendy S AU - Woods WS FAU - George, Julia M AU - George JM FAU - Rienstra, Chad M AU - Rienstra CM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Glycolipids) RN - 0 (Inositol Phosphates) RN - 0 (LPPG glycoinositolphosphoceramide) RN - 0 (Micelles) RN - 0 (Peptides) RN - 0 (Phospholipids) RN - 0 (Phosphoproteins) RN - 0 (alpha-Synuclein) RN - 0 (endosulfine) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) SB - IM MH - Biomimetic Materials/metabolism/pharmacology MH - Cell Membrane/*metabolism MH - Chromatography, Gel MH - Circular Dichroism MH - Cyclic AMP-Dependent Protein Kinases/metabolism MH - Glycolipids/metabolism/pharmacology MH - Inositol Phosphates/metabolism/pharmacology MH - Magnetic Resonance Spectroscopy MH - Micelles MH - Peptides/*chemistry/*metabolism MH - Phospholipids/metabolism/pharmacology MH - Phosphoproteins/*chemistry/*metabolism MH - Phosphorylation MH - Protein Binding/drug effects MH - *Protein Folding MH - Protein Structure, Secondary/drug effects MH - Sodium Dodecyl Sulfate/metabolism/pharmacology MH - alpha-Synuclein/metabolism EDAT- 2008/11/01 09:00 MHDA- 2009/03/17 09:00 CRDT- 2008/11/01 09:00 AID - 10.1021/bi801450t [doi] PST - ppublish SO - Biochemistry. 2008 Nov 25;47(47):12357-64. doi: 10.1021/bi801450t. PMID- 12151412 OWN - NLM STAT- MEDLINE DA - 20020923 DCOM- 20021113 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 277 IP - 39 DP - 2002 Sep 27 TI - pH-dependent intramolecular binding and structure involving Cx43 cytoplasmic domains. PG - 36706-14 AB - pH-induced closure of connexin43 (Cx43) channels involves interaction of the Cx43 carboxyl-terminal (Cx43CT) with a separate "receptor" domain. The receptor location and structure and whether the interaction is directly intramolecular are unknown. Here we show resonant mirror technology, enzyme-linked sorbent assays, and nuclear magnetic resonance (NMR) experiments demonstrating pH-dependent binding of Cx43CT to region 119-144 of Cx43 (Cx43L2), which we propose is the receptor. NMR showed that acidification induced alpha-helical order in Cx43L2, whereas only a minor modification in Cx43CT structure was detected. These data provide the first demonstration of chemically induced structural order and binding between cytoplasmic connexin domains. FAU - Duffy, Heather S AU - Duffy HS AD - Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA. FAU - Sorgen, Paul L AU - Sorgen PL FAU - Girvin, Mark E AU - Girvin ME FAU - O'Donnell, Phyllis AU - O'Donnell P FAU - Coombs, Wanda AU - Coombs W FAU - Taffet, Steven M AU - Taffet SM FAU - Delmar, Mario AU - Delmar M FAU - Spray, David C AU - Spray DC LA - eng GR - NS07098/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20020731 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Connexin 43) RN - 0 (Peptides) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Recombinant Proteins) RN - 4QD397987E (Histidine) RN - EC 2.5.1.18 (Glutathione Transferase) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cloning, Molecular MH - Connexin 43/*chemistry/*metabolism MH - Cytoplasm/metabolism MH - Diffusion MH - Dose-Response Relationship, Drug MH - Enzyme-Linked Immunosorbent Assay MH - Glutathione Transferase/metabolism MH - Histidine/chemistry MH - Hydrogen Bonding MH - Hydrogen-Ion Concentration MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Peptide Biosynthesis MH - Peptides/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - Rats MH - Recombinant Fusion Proteins/metabolism MH - Recombinant Proteins/metabolism MH - Time Factors EDAT- 2002/08/02 10:00 MHDA- 2002/11/26 04:00 CRDT- 2002/08/02 10:00 PHST- 2002/07/31 [aheadofprint] AID - 10.1074/jbc.M207016200 [doi] AID - M207016200 [pii] PST - ppublish SO - J Biol Chem. 2002 Sep 27;277(39):36706-14. Epub 2002 Jul 31. PMID- 15643843 OWN - NLM STAT- MEDLINE DA - 20050112 DCOM- 20050303 LR - 20080117 IS - 0002-7863 (Print) IS - 0002-7863 (Linking) VI - 127 IP - 2 DP - 2005 Jan 19 TI - Mapping long-range interactions in alpha-synuclein using spin-label NMR and ensemble molecular dynamics simulations. PG - 476-7 AB - The intrinsically disordered protein alpha-synuclein plays a key role in the pathogenesis of Parkinson's disease (PD). We show here that the native state of alpha-synuclein consists of a broad distribution of conformers with an ensemble-averaged hydrodynamic radius significantly smaller than that expected for a random coil structure. This partial condensation is driven by interactions between the highly charged C-terminus and a large hydrophobic central region of the protein sequence. We suggest that this structure could inhibit the formation of alpha-synuclein aggregates, which are thought to be the cytotoxic species responsible for neurodegeneration in PD. FAU - Dedmon, Matthew M AU - Dedmon MM AD - Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. FAU - Lindorff-Larsen, Kresten AU - Lindorff-Larsen K FAU - Christodoulou, John AU - Christodoulou J FAU - Vendruscolo, Michele AU - Vendruscolo M FAU - Dobson, Christopher M AU - Dobson CM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Ligands) RN - 0 (Nerve Tissue Proteins) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Computer Simulation MH - Ligands MH - Models, Molecular MH - Nerve Tissue Proteins/*chemistry/metabolism MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Protein Conformation MH - Synucleins MH - alpha-Synuclein EDAT- 2005/01/13 09:00 MHDA- 2005/03/04 09:00 CRDT- 2005/01/13 09:00 AID - 10.1021/ja044834j [doi] PST - ppublish SO - J Am Chem Soc. 2005 Jan 19;127(2):476-7. PMID- 18650809 OWN - NLM STAT- MEDLINE DA - 20080822 DCOM- 20080905 LR - 20140916 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 454 IP - 7207 DP - 2008 Aug 21 TI - Structural mechanism of WASP activation by the enterohaemorrhagic E. coli effector EspF(U). PG - 1009-13 LID - 10.1038/nature07160 [doi] AB - During infection, enterohaemorrhagic Escherichia coli (EHEC) takes over the actin cytoskeleton of eukaryotic cells by injecting the EspF(U) protein into the host cytoplasm. EspF(U) controls actin by activating members of the Wiskott-Aldrich syndrome protein (WASP) family. Here we show that EspF(U) binds to the autoinhibitory GTPase binding domain (GBD) in WASP proteins and displaces it from the activity-bearing VCA domain (for verprolin homology, central hydrophobic and acidic regions). This interaction potently activates WASP and neural (N)-WASP in vitro and induces localized actin assembly in cells. In the solution structure of the GBD-EspF(U) complex, EspF(U) forms an amphipathic helix that binds the GBD, mimicking interactions of the VCA domain in autoinhibited WASP. Thus, EspF(U) activates WASP by competing directly for the VCA binding site on the GBD. This mechanism is distinct from that used by the eukaryotic activators Cdc42 and SH2 domains, which globally destabilize the GBD fold to release the VCA. Such diversity of mechanism in WASP proteins is distinct from other multimodular systems, and may result from the intrinsically unstructured nature of the isolated GBD and VCA elements. The structural incompatibility of the GBD complexes with EspF(U) and Cdc42/SH2, plus high-affinity EspF(U) binding, enable EHEC to hijack the eukaryotic cytoskeletal machinery effectively. FAU - Cheng, Hui-Chun AU - Cheng HC AD - Department of Biochemistry and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. FAU - Skehan, Brian M AU - Skehan BM FAU - Campellone, Kenneth G AU - Campellone KG FAU - Leong, John M AU - Leong JM FAU - Rosen, Michael K AU - Rosen MK LA - eng SI - PDB/2K42 GR - R01 AI046454/AI/NIAID NIH HHS/United States GR - R01 AI046454-09/AI/NIAID NIH HHS/United States GR - R01 GM056322/GM/NIGMS NIH HHS/United States GR - R01 GM056322-12A1/GM/NIGMS NIH HHS/United States GR - R01-AI46454/AI/NIAID NIH HHS/United States GR - R01-GM56322/GM/NIGMS NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20080723 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Actins) RN - 0 (Carrier Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (EspFU protein, E coli) RN - 0 (Wiskott-Aldrich Syndrome Protein) RN - 0 (Wiskott-Aldrich Syndrome Protein, Neuronal) SB - IM MH - Actins/metabolism MH - Amino Acid Sequence MH - Animals MH - Carrier Proteins/chemistry/*metabolism MH - Cells, Cultured MH - Enterohemorrhagic Escherichia coli/chemistry/genetics/*metabolism MH - Escherichia coli Proteins/chemistry/*metabolism MH - Fibroblasts/cytology MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Tertiary MH - Wiskott-Aldrich Syndrome Protein/chemistry/*metabolism MH - Wiskott-Aldrich Syndrome Protein, Neuronal/chemistry/metabolism PMC - PMC2719906 MID - NIHMS78477 OID - NLM: NIHMS78477 OID - NLM: PMC2719906 EDAT- 2008/07/25 09:00 MHDA- 2008/09/06 09:00 CRDT- 2008/07/25 09:00 PHST- 2007/12/24 [received] PHST- 2008/06/10 [accepted] PHST- 2008/07/23 [aheadofprint] AID - nature07160 [pii] AID - 10.1038/nature07160 [doi] PST - ppublish SO - Nature. 2008 Aug 21;454(7207):1009-13. doi: 10.1038/nature07160. Epub 2008 Jul 23. PMID- 23803659 OWN - NLM STAT- In-Process DA - 20130627 IS - 1422-0067 (Electronic) IS - 1422-0067 (Linking) VI - 14 IP - 7 DP - 2013 TI - NS3 protease from hepatitis C virus: biophysical studies on an intrinsically disordered protein domain. PG - 13282-306 LID - 10.3390/ijms140713282 [doi] AB - The nonstructural protein 3 (NS3) from the hepatitis C virus (HCV) is responsible for processing the non-structural region of the viral precursor polyprotein in infected hepatic cells. NS3 protease activity, located at the N-terminal domain, is a zinc-dependent serine protease. A zinc ion, required for the hydrolytic activity, has been considered as a structural metal ion essential for the structural integrity of the protein. In addition, NS3 interacts with another cofactor, NS4A, an accessory viral protein that induces a conformational change enhancing the hydrolytic activity. Biophysical studies on the isolated protease domain, whose behavior is similar to that of the full-length protein (e.g., catalytic activity, allosteric mechanism and susceptibility to inhibitors), suggest that a considerable global conformational change in the protein is coupled to zinc binding. Zinc binding to NS3 protease can be considered as a folding event, an extreme case of induced-fit binding. Therefore, NS3 protease is an intrinsically (partially) disordered protein with a complex conformational landscape due to its inherent plasticity and to the interaction with its different effectors. Here we summarize the results from a detailed biophysical characterization of this enzyme and present new experimental data. FAU - Vega, Sonia AU - Vega S AD - Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit BIFI-IQFR (CSIC), University of Zaragoza, Zaragoza 50018, Spain. oabifra@unizar.es. FAU - Neira, Jose L AU - Neira JL FAU - Marcuello, Carlos AU - Marcuello C FAU - Lostao, Anabel AU - Lostao A FAU - Abian, Olga AU - Abian O FAU - Velazquez-Campoy, Adrian AU - Velazquez-Campoy A LA - eng PT - Journal Article DEP - 20130626 PL - Switzerland TA - Int J Mol Sci JT - International journal of molecular sciences JID - 101092791 SB - IM PMC - PMC3742187 OID - NLM: PMC3742187 GN - NLM: Original DateCompleted: 20130628 EDAT- 2013/06/28 06:00 MHDA- 2013/06/28 06:01 CRDT- 2013/06/28 06:00 PHST- 2013/04/22 [received] PHST- 2013/06/04 [revised] PHST- 2013/06/13 [accepted] AID - ijms140713282 [pii] AID - 10.3390/ijms140713282 [doi] PST - epublish SO - Int J Mol Sci. 2013 Jun 26;14(7):13282-306. doi: 10.3390/ijms140713282. PMID- 9007989 OWN - NLM STAT- MEDLINE DA - 19970410 DCOM- 19970410 LR - 20130918 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 6 IP - 1 DP - 1997 Jan TI - Conformational analysis of peptides corresponding to all the secondary structure elements of protein L B1 domain: secondary structure propensities are not conserved in proteins with the same fold. PG - 162-74 AB - The solution conformation of three peptides corresponding to the two beta-hairpins and the alpha-helix of the protein L B1 domain have been analyzed by circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMR). In aqueous solution, the three peptides show low populations of native and non-native locally folded structures, but no well-defined hairpin or helix structures are formed. In 30% aqueous trifluoroethanol (TFE), the peptide corresponding to the alpha-helix adopts a high populated helical conformation three residues longer than in the protein. The hairpin peptides aggregate in TFE, and no significant conformational change occurs in the NMR observable fraction of molecules. These results indicate that the helical peptide has a significant intrinsic tendency to adopt its native structure and that the hairpin sequences seem to be selected as non-helical. This suggests that these sequences favor the structure finally attained in the protein, but the contribution of the local interactions alone is not enough to drive the formation of a detectable population of native secondary structures. This pattern of secondary structure tendencies is different to those observed in two structurally related proteins: ubiquitin and the protein G B1 domain. The only common feature is a certain propensity of the helical segments to form the native structure. These results indicate that for a protein to fold, there is no need for large native-like secondary structure propensities, although a minimum tendency to avoid non-native structures and to favor native ones could be required. FAU - Ramirez-Alvarado, M AU - Ramirez-Alvarado M AD - European Molecular Biology Laboratory, Heidelberg, Germany. FAU - Serrano, L AU - Serrano L FAU - Blanco, F J AU - Blanco FJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Bacterial Proteins) RN - 0 (Ig L-binding protein, Peptostreptococcus) RN - 0 (Peptide Fragments) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry MH - Circular Dichroism MH - Conserved Sequence MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Peptide Fragments/chemistry MH - Protein Folding MH - Protein Structure, Secondary MH - Spectrophotometry, Ultraviolet PMC - PMC2143513 OID - NLM: PMC2143513 EDAT- 1997/01/01 MHDA- 1997/01/01 00:01 CRDT- 1997/01/01 00:00 AID - 10.1002/pro.5560060119 [doi] PST - ppublish SO - Protein Sci. 1997 Jan;6(1):162-74. PMID- 19114306 OWN - NLM STAT- MEDLINE DA - 20090127 DCOM- 20100706 IS - 1464-3405 (Electronic) IS - 0960-894X (Linking) VI - 19 IP - 3 DP - 2009 Feb 1 TI - Small-molecule perturbation of competing interactions between c-Myc and Max. PG - 807-10 LID - 10.1016/j.bmcl.2008.12.025 [doi] AB - The oncogenic transcription factor c-Myc undergoes coupled binding and folding of its basic-helix-loop-helix-leucine zipper domain (bHLHZip) upon heterodimerization with its partner protein Max. The latter exists in two isoforms: p21, which homodimerizes poorly, and p22, which homodimerizes well. We show that the effect of 10058-F4 (a small-molecule that binds disordered c-Myc monomers and disrupts the c-Myc-Max complex) on both c-Myc-Max heterodimerization and DNA binding is dependent on the nature of the Max isoform. In the presence of p22 Max the effective inhibitor concentration is lower than in the presence of p21 Max, as the p22 Max homodimer formation affects the thermodynamics by competing against the c-Myc-Max heterodimerization event. FAU - Follis, Ariele Viacava AU - Follis AV AD - Department of Chemistry, Georgetown University, 37th & O Streets, NW, Reiss Science Center, Washington, DC 20057, USA. FAU - Hammoudeh, Dalia I AU - Hammoudeh DI FAU - Daab, Andrew T AU - Daab AT FAU - Metallo, Steven J AU - Metallo SJ LA - eng PT - Journal Article DEP - 20081210 PL - England TA - Bioorg Med Chem Lett JT - Bioorganic & medicinal chemistry letters JID - 9107377 RN - 0 (Basic-Leucine Zipper Transcription Factors) RN - 0 (Myc associated factor X) RN - 0 (Protein Isoforms) RN - 0 (Proto-Oncogene Proteins c-myc) RN - 9007-49-2 (DNA) SB - IM MH - Basic-Leucine Zipper Transcription Factors/*chemistry MH - Binding Sites MH - Chemistry, Pharmaceutical/methods MH - DNA/chemistry MH - Dimerization MH - Drug Design MH - Humans MH - Kinetics MH - Models, Biological MH - Protein Binding/*drug effects MH - Protein Isoforms MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-myc/*chemistry MH - Thermodynamics EDAT- 2008/12/31 09:00 MHDA- 2010/07/07 06:00 CRDT- 2008/12/31 09:00 PHST- 2008/11/18 [received] PHST- 2008/12/02 [revised] PHST- 2008/12/03 [accepted] PHST- 2008/12/10 [aheadofprint] AID - S0960-894X(08)01511-4 [pii] AID - 10.1016/j.bmcl.2008.12.025 [doi] PST - ppublish SO - Bioorg Med Chem Lett. 2009 Feb 1;19(3):807-10. doi: 10.1016/j.bmcl.2008.12.025. Epub 2008 Dec 10. PMID- 19490121 OWN - NLM STAT- MEDLINE DA - 20090922 DCOM- 20091013 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 276 IP - 14 DP - 2009 Jul TI - Intrinsic disorder and coiled-coil formation in prostate apoptosis response factor 4. PG - 3710-28 LID - 10.1111/j.1742-4658.2009.07087.x [doi] AB - Prostate apoptosis response factor-4 (Par-4) is an ubiquitously expressed pro-apoptotic and tumour suppressive protein that can both activate cell-death mechanisms and inhibit pro-survival factors. Par-4 contains a highly conserved coiled-coil region that serves as the primary recognition domain for a large number of binding partners. Par-4 is also tightly regulated by the aforementioned binding partners and by post-translational modifications. Biophysical data obtained in the present study indicate that Par-4 primarily comprises an intrinsically disordered protein. Bioinformatic analysis of the highly conserved Par-4 reveals low sequence complexity and enrichment in polar and charged amino acids. The high proteolytic susceptibility and an increased hydrodynamic radius are consistent with a largely extended structure in solution. Spectroscopic measurements using CD and NMR also reveal characteristic features of intrinsic disorder. Under physiological conditions, the data obtained show that Par-4 self-associates via the C-terminal domain, forming a coiled-coil. Interruption of self-association by urea also resulted in loss of secondary structure. These results are consistent with the stabilization of the coiled-coil motif through an intramolecular association. FAU - Libich, David S AU - Libich DS AD - Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand. d.s.libich@massey.ac.nz FAU - Schwalbe, Martin AU - Schwalbe M FAU - Kate, Sachin AU - Kate S FAU - Venugopal, Hariprasad AU - Venugopal H FAU - Claridge, Jolyon K AU - Claridge JK FAU - Edwards, Patrick J B AU - Edwards PJ FAU - Dutta, Kaushik AU - Dutta K FAU - Pascal, Steven M AU - Pascal SM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090528 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Receptors, Thrombin) RN - 0 (protease-activated receptor 4) SB - IM MH - Amino Acid Sequence MH - Animals MH - Circular Dichroism MH - Conserved Sequence MH - Humans MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Rats MH - Receptors, Thrombin/*chemistry/genetics MH - Sequence Alignment EDAT- 2009/06/06 09:00 MHDA- 2009/10/14 06:00 CRDT- 2009/06/04 09:00 PHST- 2009/05/28 [aheadofprint] AID - EJB7087 [pii] AID - 10.1111/j.1742-4658.2009.07087.x [doi] PST - ppublish SO - FEBS J. 2009 Jul;276(14):3710-28. doi: 10.1111/j.1742-4658.2009.07087.x. Epub 2009 May 28. PMID- 23908350 OWN - NLM STAT- MEDLINE DA - 20130923 DCOM- 20131126 LR - 20141113 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 38 DP - 2013 Sep 20 TI - Double-membraned liposomes sculpted by poliovirus 3AB protein. PG - 27287-98 LID - 10.1074/jbc.M113.498899 [doi] AB - Infection with many positive-strand RNA viruses dramatically remodels cellular membranes, resulting in the accumulation of double-membraned vesicles that resemble cellular autophagosomes. In this study, a single protein encoded by poliovirus, 3AB, is shown to be sufficient to induce the formation of double-membraned liposomes via the invagination of single-membraned liposomes. Poliovirus 3AB is a 109-amino acid protein with a natively unstructured N-terminal domain. HeLa cells transduced with 3AB protein displayed intracellular membrane disruption; specifically, the formation of cytoplasmic invaginations. The ability of a single viral protein to produce structures of similar topology to cellular autophagosomes should facilitate the understanding of both cellular and viral mechanisms for membrane remodeling. FAU - Wang, Jing AU - Wang J AD - From the Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118 and. FAU - Ptacek, Jennifer B AU - Ptacek JB FAU - Kirkegaard, Karla AU - Kirkegaard K FAU - Bullitt, Esther AU - Bullitt E LA - eng GR - GM102474/GM/NIGMS NIH HHS/United States GR - R01 GM102474/GM/NIGMS NIH HHS/United States GR - S10 RR025434/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130801 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (3AB protein, poliovirus) RN - 0 (Liposomes) RN - 0 (Membrane Proteins) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Cell Membrane/*chemistry/genetics/metabolism MH - HeLa Cells MH - Humans MH - Liposomes/*chemistry/metabolism MH - Membrane Proteins/*chemistry/genetics/metabolism MH - *Poliovirus MH - Protein Structure, Tertiary MH - Viral Nonstructural Proteins/*chemistry/genetics/metabolism PMC - PMC3779724 OID - NLM: PMC3779724 OTO - NOTNLM OT - Lipoprotein OT - Liposomes OT - Membrane Bilayer OT - Membrane Biophysics OT - Membrane Reconstitution OT - Positive-strand RNA Viruses OT - Viral Protein OT - Viral Replication EDAT- 2013/08/03 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/08/03 06:00 PHST- 2013/08/01 [aheadofprint] AID - M113.498899 [pii] AID - 10.1074/jbc.M113.498899 [doi] PST - ppublish SO - J Biol Chem. 2013 Sep 20;288(38):27287-98. doi: 10.1074/jbc.M113.498899. Epub 2013 Aug 1. PMID- 21055425 OWN - NLM STAT- MEDLINE DA - 20101220 DCOM- 20110404 LR - 20140911 IS - 1872-9428 (Electronic) IS - 0166-6851 (Linking) VI - 175 IP - 2 DP - 2011 Feb TI - Regions of intrinsic disorder help identify a novel nuclear localization signal in Toxoplasma gondii histone acetyltransferase TgGCN5-B. PG - 192-5 LID - 10.1016/j.molbiopara.2010.10.009 [doi] AB - We have previously shown that protozoan parasites, such as Toxoplasma gondii, contain a high prevalence of intrinsically disordered regions in their predicted proteins. Here, we determine that both TgGCN5-family histone acetyltransferases (HATs) contain unusually high levels of intrinsic disorder. A previously identified basic-rich nuclear localization signal (NLS) in the N-terminus of TgGCN5-A is located within such a region of predicted disorder, but this NLS is not conserved in TgGCN5-B. We therefore analyzed the intrinsically disordered regions of TgGCN5-B for basic-rich sequences that could be indicative of a functional NLS, and this led to the identification of a novel NLS for TgGCN5-B, RPAENKKRGR. The functionality of the GCN5-B NLS was validated experimentally and has predictive value. These studies demonstrate that basic-rich sequences within regions predicted to be intrinsically disordered constitute criteria for a candidate NLS. CI - Copyright (c) 2010 Elsevier B.V. All rights reserved. FAU - Dixon, Stacy E AU - Dixon SE AD - Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. FAU - Bhatti, Micah M AU - Bhatti MM FAU - Uversky, Vladimir N AU - Uversky VN FAU - Dunker, A Keith AU - Dunker AK FAU - Sullivan, William J Jr AU - Sullivan WJ Jr LA - eng GR - AI077502/AI/NIAID NIH HHS/United States GR - R01 AI077502/AI/NIAID NIH HHS/United States GR - R01 AI077502-07/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20101103 PL - Netherlands TA - Mol Biochem Parasitol JT - Molecular and biochemical parasitology JID - 8006324 RN - 0 (GCN5 protein, Toxoplasma gondii) RN - 0 (Nuclear Localization Signals) RN - 0 (Protozoan Proteins) RN - EC 2.3.1.48 (Histone Acetyltransferases) SB - IM MH - Computational Biology/methods MH - Histone Acetyltransferases/*chemistry/genetics/*metabolism MH - Microscopy, Confocal MH - Microscopy, Fluorescence MH - *Nuclear Localization Signals MH - Protozoan Proteins/*chemistry/genetics/*metabolism MH - Toxoplasma/chemistry/*enzymology/genetics/metabolism PMC - PMC3005016 MID - NIHMS251304 OID - NLM: NIHMS251304 OID - NLM: PMC3005016 EDAT- 2010/11/09 06:00 MHDA- 2011/04/05 06:00 CRDT- 2010/11/09 06:00 PHST- 2010/07/22 [received] PHST- 2010/10/18 [revised] PHST- 2010/10/22 [accepted] PHST- 2010/11/03 [aheadofprint] AID - S0166-6851(10)00275-6 [pii] AID - 10.1016/j.molbiopara.2010.10.009 [doi] PST - ppublish SO - Mol Biochem Parasitol. 2011 Feb;175(2):192-5. doi: 10.1016/j.molbiopara.2010.10.009. Epub 2010 Nov 3. PMID- 11812782 OWN - NLM STAT- MEDLINE DA - 20020401 DCOM- 20020513 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 277 IP - 14 DP - 2002 Apr 5 TI - Biophysical properties of the synucleins and their propensities to fibrillate: inhibition of alpha-synuclein assembly by beta- and gamma-synucleins. PG - 11970-8 AB - The pathological hallmark of Parkinson's disease is the presence of intracellular inclusions, Lewy bodies, and Lewy neurites, in the dopaminergic neurons of the substantia nigra and several other brain regions. Filamentous alpha-synuclein is the major component of these deposits and its aggregation is believed to play an important role in Parkinson's disease and several other neurodegenerative diseases. Two homologous proteins, beta- and gamma-synucleins, are also abundant in the brain. The synucleins are natively unfolded proteins. beta-Synuclein, which lacks 11 central hydrophobic residues compared with its homologs, exhibited the properties of a random coil, whereas alpha- and gamma-synucleins were slightly more compact and structured. gamma-Synuclein, unlike its homologs, formed a soluble oligomer at relatively low concentrations, which appears to be an off-fibrillation pathway species. Here we show that, although they have similar biophysical properties to alpha-synuclein, beta- And gamma-synucleins inhibit alpha-synuclein fibril formation. Complete inhibition of alpha-synuclein fibrillation was observed at 4:1 molar excess of beta- and gamma-synucleins. No significant incorporation of beta-synuclein into the fibrils was detected. The lack of fibrils formed by beta-synuclein is most readily explained by the absence of a stretch of hydrophobic residues from the middle region of the protein. A model for the inhibition is proposed. FAU - Uversky, Vladimir N AU - Uversky VN AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. enzyme@cats.ucsc.edu FAU - Li, Jie AU - Li J FAU - Souillac, Pierre AU - Souillac P FAU - Millett, Ian S AU - Millett IS FAU - Doniach, Sebastian AU - Doniach S FAU - Jakes, Ross AU - Jakes R FAU - Goedert, Michel AU - Goedert M FAU - Fink, Anthony L AU - Fink AL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20020125 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Nerve Tissue Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SNCA protein, human) RN - 0 (SNCB protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 0 (beta-Synuclein) RN - 0 (gamma-Synuclein) SB - IM MH - Amino Acid Sequence MH - Brain/metabolism MH - Chromatography, Gel MH - Circular Dichroism MH - Humans MH - Hydrogen-Ion Concentration MH - Kinetics MH - Microscopy, Electron MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*chemistry/*metabolism MH - Protein Binding MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/metabolism MH - Scattering, Radiation MH - Sequence Homology, Amino Acid MH - Spectrometry, Fluorescence MH - Spectroscopy, Fourier Transform Infrared MH - Synucleins MH - Time Factors MH - Ultraviolet Rays MH - X-Rays MH - alpha-Synuclein MH - beta-Synuclein MH - gamma-Synuclein EDAT- 2002/01/29 10:00 MHDA- 2002/05/15 10:01 CRDT- 2002/01/29 10:00 PHST- 2002/01/25 [aheadofprint] AID - 10.1074/jbc.M109541200 [doi] AID - M109541200 [pii] PST - ppublish SO - J Biol Chem. 2002 Apr 5;277(14):11970-8. Epub 2002 Jan 25. PMID- 12679333 OWN - NLM STAT- MEDLINE DA - 20030609 DCOM- 20030722 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 24 DP - 2003 Jun 13 TI - Concerted folding and binding of a flexible colicin domain to its periplasmic receptor TolA. PG - 21860-8 AB - Compared with folded structures, natively unfolded protein domains are over-represented in protein-protein and protein-DNA interactions. Such domains are common features of all colicins and are required for their translocation across the outer membrane of the target Escherichia coli cell. All of these domains bind to at least one periplasmic protein of the Tol or Ton family. Similar domains are found in Ton-dependent outer membrane transporters, indicating they may interact in a related manner. In this article we have studied binding of the colicin N translocation domain to its periplasmic receptor TolA, by fluorescence resonance energy transfer (FRET) using fluorescent probes attached to engineered cysteine residues and NMR techniques. The domain exhibits a random coil circular dichroism spectrum. However, FRET revealed that guanidinium hydrochloride denaturation caused increases in all measured intramolecular distances showing that, although natively unfolded, the domain is not extended. Furthermore NMR reported a compact hydrodynamic radius of 18 A. Nevertheless the FRET-derived distances changed upon binding to TolA indicating a significant structural rearrangement. Using 1H-15N NMR we show that, when bound, the peptide switches from a disordered state to an ordered state. The kinetics of binding and the associated structural change were measured by stopped-flow methods, and both events appear to occur simultaneously. The data therefore suggest that this molecular recognition involves the concerted binding and folding of a flexible but collapsed state. FAU - Anderluh, Gregor AU - Anderluh G AD - Department of Biology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia. FAU - Hong, Qi AU - Hong Q FAU - Boetzel, Ruth AU - Boetzel R FAU - MacDonald, Colin AU - MacDonald C FAU - Moore, Geoffrey R AU - Moore GR FAU - Virden, Richard AU - Virden R FAU - Lakey, Jeremy H AU - Lakey JH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030404 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Colicins) RN - 0 (Escherichia coli Proteins) RN - 0 (tolA protein, E coli) RN - 059QF0KO0R (Water) RN - 8DUH1N11BX (Tryptophan) RN - JU58VJ6Y3B (Guanidine) RN - K848JZ4886 (Cysteine) SB - IM MH - Amino Acid Sequence MH - Anisotropy MH - Circular Dichroism MH - Colicins/*chemistry MH - Cysteine/chemistry MH - Escherichia coli/metabolism MH - Escherichia coli Proteins/*chemistry/metabolism MH - Fluorescence Resonance Energy Transfer MH - Guanidine/chemistry MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Spectrometry, Fluorescence MH - Surface Plasmon Resonance MH - Time Factors MH - Tryptophan/chemistry MH - Water/chemistry EDAT- 2003/04/08 05:00 MHDA- 2003/07/23 05:00 CRDT- 2003/04/08 05:00 PHST- 2003/04/04 [aheadofprint] AID - 10.1074/jbc.M300411200 [doi] AID - M300411200 [pii] PST - ppublish SO - J Biol Chem. 2003 Jun 13;278(24):21860-8. Epub 2003 Apr 4. PMID- 20169168 OWN - NLM STAT- MEDLINE DA - 20100219 DCOM- 20100930 LR - 20140827 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 5 IP - 2 DP - 2010 TI - Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration. PG - e9222 LID - 10.1371/journal.pone.0009222 [doi] AB - Mycobacterium tuberculosis (Mtb), a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC), an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA). The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants) prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of approximately 3.5 A in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP) domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In-depth analyses of the sequence and the structure also provide answers to the reported lower affinities of Mtb-BirA toward ATP and biotin substrates. This dehydrated crystal structure not only provides key leads to the understanding of the structure/function relationships in the protein in the absence of any ligand-bound structure, but also demonstrates the merit of dehydration of crystals as an inimitable technique to have a glance at proteins in action. FAU - Gupta, Vibha AU - Gupta V AD - Department of Biochemistry, University of Delhi, New Delhi, India. FAU - Gupta, Rakesh K AU - Gupta RK FAU - Khare, Garima AU - Khare G FAU - Salunke, Dinakar M AU - Salunke DM FAU - Surolia, Avadhesha AU - Surolia A FAU - Tyagi, Anil K AU - Tyagi AK LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100215 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Bacterial Proteins) RN - 0 (Ligands) RN - 059QF0KO0R (Water) RN - 6SO6U10H04 (Biotin) RN - EC 6.3.- (Carbon-Nitrogen Ligases) RN - EC 6.3.4.15 (biotin-(acetyl-CoA carboxylase)synthetase) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/genetics/metabolism MH - Binding Sites/genetics MH - Biotin/*chemistry/metabolism MH - Carbon-Nitrogen Ligases/*chemistry/genetics/metabolism MH - Crystallization MH - Ligands MH - Models, Molecular MH - Molecular Sequence Data MH - Mycobacterium tuberculosis/metabolism MH - Protein Binding MH - *Protein Conformation MH - Protein Multimerization MH - Protein Structure, Tertiary MH - Substrate Specificity MH - Water/chemistry MH - X-Ray Diffraction PMC - PMC2821413 OID - NLM: PMC2821413 EDAT- 2010/02/20 06:00 MHDA- 2010/10/01 06:00 CRDT- 2010/02/20 06:00 PHST- 2009/12/11 [received] PHST- 2010/01/23 [accepted] PHST- 2010/02/15 [epublish] AID - 10.1371/journal.pone.0009222 [doi] PST - epublish SO - PLoS One. 2010 Feb 15;5(2):e9222. doi: 10.1371/journal.pone.0009222. PMID- 10978144 OWN - NLM STAT- MEDLINE DA - 20000928 DCOM- 20000928 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 39 IP - 35 DP - 2000 Sep 5 TI - Inhibition of fibrillization and accumulation of prefibrillar oligomers in mixtures of human and mouse alpha-synuclein. PG - 10619-26 AB - Parkinson's disease (PD) is a neurodegenerative disorder attributed to the loss of dopaminergic neurons from the substantia nigra. Some surviving neurons are characterized by cytoplasmic Lewy bodies, which contain fibrillar alpha-synuclein. Two mutants of human alpha-synuclein (A53T and A30P) have been linked to early-onset, familial PD. Oligomeric forms of these mutants accumulate more rapidly and/or persist for longer periods of time than oligomeric, human wild-type alpha-synuclein (WT), suggesting a link between oligomerization and cell death. The amino acid sequences of the mouse protein and WT differ at seven positions. Mouse alpha-synuclein, like A53T, contains a threonine residue at position 53. We have assessed the conformational properties and fibrillogenicity of the murine protein. Like WT and the two PD mutants, mouse alpha-synuclein adopts a "natively unfolded" or disordered structure. However, at elevated concentrations, the mouse protein forms amyloid fibrils more rapidly than WT, A53T, or A30P. The fibrillization of mouse alpha-synuclein is slowed by WT and A53T. Inhibition of fibrillization leads to the accumulation of nonfibrillar, potentially toxic oligomers. The results are relevant to the interpretation of the phenotypes of transgenic animal models of PD and suggest a novel approach for testing the cause and effect relationship between fibrillization and neurodegeneration. FAU - Rochet, J C AU - Rochet JC AD - Morris K. Udall Parkinson's Disease Research Center of Excellence, Center for Neurologic Diseases, Brigham and Women's Hospital, and Department of Neurology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA. FAU - Conway, K A AU - Conway KA FAU - Lansbury, P T Jr AU - Lansbury PT Jr LA - eng GR - AG08470/AG/NIA NIH HHS/United States GR - AG14366/AG/NIA NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Nerve Tissue Proteins) RN - 0 (Protein Precursors) RN - 0 (SNCA protein, human) RN - 0 (Snca protein, mouse) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 2ZD004190S (Threonine) RN - OF5P57N2ZX (Alanine) SB - IM MH - Alanine/genetics MH - Amyloid/chemistry/metabolism MH - Animals MH - Chromatography, Gel MH - Humans MH - Mice MH - Microscopy, Atomic Force MH - Mutagenesis, Site-Directed MH - Nerve Tissue Proteins/*antagonists & inhibitors/genetics/*metabolism/ultrastructure MH - Parkinson Disease/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Precursors/*antagonists & inhibitors/genetics/*metabolism/ultrastructure MH - Spectroscopy, Fourier Transform Infrared MH - Synucleins MH - Threonine/genetics MH - alpha-Synuclein EDAT- 2000/09/09 11:00 MHDA- 2000/09/30 11:01 CRDT- 2000/09/09 11:00 AID - bi001315u [pii] PST - ppublish SO - Biochemistry. 2000 Sep 5;39(35):10619-26. PMID- 15265035 OWN - NLM STAT- MEDLINE DA - 20040721 DCOM- 20041102 LR - 20070723 IS - 0014-2956 (Print) IS - 0014-2956 (Linking) VI - 271 IP - 15 DP - 2004 Aug TI - Structural and functional analysis of ataxin-2 and ataxin-3. PG - 3155-70 AB - Spinocerebellar ataxia types 2 (SCA2) and 3 (SCA3) are autosomal-dominantly inherited, neurodegenerative diseases caused by CAG repeat expansions in the coding regions of the genes encoding ataxin-2 and ataxin-3, respectively. To provide a rationale for further functional experiments, we explored the protein architectures of ataxin-2 and ataxin-3. Using structure-based multiple sequence alignments of homologous proteins, we investigated domains, sequence motifs, and interaction partners. Our analyses focused on presumably functional amino acids and the construction of tertiary structure models of the RNA-binding Lsm domain of ataxin-2 and the deubiquitinating Josephin domain of ataxin-3. We also speculate about distant evolutionary relationships of ubiquitin-binding UIM, GAT, UBA and CUE domains and helical ANTH and UBX domain extensions. FAU - Albrecht, Mario AU - Albrecht M AD - Max-Planck-Institute for Informatics, Saarbrucken, Germany. mario.albrecht@mpi-sb.mpg.de FAU - Golatta, Michael AU - Golatta M FAU - Wullner, Ullrich AU - Wullner U FAU - Lengauer, Thomas AU - Lengauer T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Eur J Biochem JT - European journal of biochemistry / FEBS JID - 0107600 RN - 0 (Nerve Tissue Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Peptides) RN - 0 (Proteins) RN - 0 (Repressor Proteins) RN - 0 (SCA2 protein) RN - 0 (Ubiquitin) RN - 26700-71-0 (polyglutamine) RN - 63231-63-0 (RNA) RN - EC 3.4.22.- (ATXN3 protein, human) SB - IM MH - Amino Acid Sequence MH - Animals MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*chemistry/*metabolism MH - Nuclear Proteins MH - Peptides/chemistry/metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Proteins/*chemistry/*metabolism MH - RNA/metabolism MH - Repressor Proteins MH - Sequence Alignment MH - Structure-Activity Relationship MH - Ubiquitin/metabolism EDAT- 2004/07/22 05:00 MHDA- 2004/11/04 09:00 CRDT- 2004/07/22 05:00 AID - 10.1111/j.1432-1033.2004.04245.x [doi] AID - EJB4245 [pii] PST - ppublish SO - Eur J Biochem. 2004 Aug;271(15):3155-70. PMID- 20616042 OWN - NLM STAT- MEDLINE DA - 20100714 DCOM- 20100819 LR - 20140824 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 107 IP - 28 DP - 2010 Jul 13 TI - Conformational selection in the molten globule state of the nuclear coactivator binding domain of CBP. PG - 12535-40 LID - 10.1073/pnas.1001693107 [doi] AB - Native molten globules are the most folded kind of intrinsically disordered proteins. Little is known about the mechanism by which native molten globules bind to their cognate ligands to form fully folded complexes. The nuclear coactivator binding domain (NCBD) of CREB binding protein is particularly interesting in this respect as structural studies of its complexes have shown that NCBD folds into two remarkably different states depending on the ligand being ACTR or IRF-3. The ligand-free state of NCBD was characterized in order to understand the mechanism of folding upon ligand binding. Biophysical studies show that despite the molten globule nature of the domain, it contains a small cooperatively folded core. By NMR spectroscopy, we have demonstrated that the folded core of NCBD has a well ordered conformer with specific side chain packing. This conformer resembles the structure of the NCBD in complex with the protein ligand, ACTR, suggesting that ACTR binds to prefolded NCBD molecules from the ensemble of interconverting structures. FAU - Kjaergaard, Magnus AU - Kjaergaard M AD - Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Kobenhavn N, Denmark. FAU - Teilum, Kaare AU - Teilum K FAU - Poulsen, Flemming M AU - Poulsen FM LA - eng SI - PDB/2KKJ PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100624 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (CREBBP protein, human) RN - 0 (Ligands) RN - 0 (Proteins) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Animals MH - CREB-Binding Protein/metabolism MH - Ligands MH - Magnetic Resonance Spectroscopy MH - Mice MH - Molecular Conformation MH - Proteins/*metabolism PMC - PMC2906600 OID - NLM: PMC2906600 EDAT- 2010/07/10 06:00 MHDA- 2010/08/20 06:00 CRDT- 2010/07/10 06:00 PHST- 2010/06/24 [aheadofprint] AID - 1001693107 [pii] AID - 10.1073/pnas.1001693107 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2010 Jul 13;107(28):12535-40. doi: 10.1073/pnas.1001693107. Epub 2010 Jun 24. PMID- 24449148 OWN - NLM STAT- MEDLINE DA - 20140204 DCOM- 20140929 IS - 1521-3773 (Electronic) IS - 1433-7851 (Linking) VI - 53 IP - 6 DP - 2014 Feb 3 TI - Helical propensity in an intrinsically disordered protein accelerates ligand binding. PG - 1548-51 LID - 10.1002/anie.201307712 [doi] AB - Many intrinsically disordered proteins fold upon binding to other macromolecules. The secondary structure present in the well-ordered complex is often formed transiently in the unbound state. The consequence of such transient structure for the binding process is, however, not clear. The activation domain of the activator for thyroid hormone and retinoid receptors (ACTR) is intrinsically disordered and folds upon binding to the nuclear coactivator binding domain (NCBD) of the CREB binding protein. A number of mutants was designed that selectively perturbs the amount of secondary structure in unbound ACTR without interfering with the intermolecular interactions between ACTR and NCBD. Using NMR spectroscopy and fluorescence-monitored stopped-flow kinetic measurements we show that the secondary structure content in helix 1 of ACTR indeed influences the binding kinetics. The results thus support the notion of preformed secondary structure as an important determinant for molecular recognition in intrinsically disordered proteins. CI - Copyright (c) 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. FAU - Iesmantavicius, Vytautas AU - Iesmantavicius V AD - Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Kobenhavn N (Denmark). FAU - Dogan, Jakob AU - Dogan J FAU - Jemth, Per AU - Jemth P FAU - Teilum, Kaare AU - Teilum K FAU - Kjaergaard, Magnus AU - Kjaergaard M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140121 PL - Germany TA - Angew Chem Int Ed Engl JT - Angewandte Chemie (International ed. in English) JID - 0370543 RN - 0 (CREB1 protein, human) RN - 0 (Cyclic AMP Response Element-Binding Protein) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Ligands) RN - EC 2.3.1.48 (NCOA3 protein, human) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 3) SB - IM MH - Cyclic AMP Response Element-Binding Protein/chemistry/genetics/metabolism MH - Humans MH - Intrinsically Disordered Proteins/chemistry/*metabolism MH - Kinetics MH - *Ligands MH - Mutation MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Receptor Coactivator 3/chemistry/genetics/metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary OTO - NOTNLM OT - NMR spectroscopy OT - conformational selection OT - ligand binding OT - proteins OT - secondary structure EDAT- 2014/01/23 06:00 MHDA- 2014/09/30 06:00 CRDT- 2014/01/23 06:00 PHST- 2013/09/02 [received] PHST- 2013/10/28 [revised] PHST- 2014/01/21 [aheadofprint] AID - 10.1002/anie.201307712 [doi] PST - ppublish SO - Angew Chem Int Ed Engl. 2014 Feb 3;53(6):1548-51. doi: 10.1002/anie.201307712. Epub 2014 Jan 21. PMID- 7577957 OWN - NLM STAT- MEDLINE DA - 19951214 DCOM- 19951214 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 34 IP - 41 DP - 1995 Oct 17 TI - Solution structure of bovine neutrophil beta-defensin-12: the peptide fold of the beta-defensins is identical to that of the classical defensins. PG - 13663-71 AB - The solution structure is reported for bovine neutrophil beta-defensin-12 (BNBD-12), a member of the beta-defensin family of antimicrobial peptides. Structural constraints in the form of proton-proton distances, dihedral angles, and hydrogen bond constraints were derived from two-dimensional, homonuclear magnetic resonance spectroscopy experiments. The three-dimensional structure of BNBD-12 was calculated using distance geometry and restrained molecular dynamics. An ensemble of structures with low NOE constraint violation energies revealed a precisely defined triple-stranded, antiparallel beta-sheet as the structural core of the peptide. The N-terminal beta-strand and three locally well-defined tight turns form a hydrophobic face. Conserved isoleucine and glycine residues form a beta-bulge structure which initiates a beta-hairpin secondary structure motif composed of the second and C-terminal beta-strands. The beta-hairpin contains numerous charged residues and forms the cationic face of BNBD-12. The N-terminal residues were found to be disordered, due to an absence of tertiary NOEs. The triple-stranded beta-sheet, the beta-bulge preceding the hairpin, and the cationic/hydrophobic amphiphilic character are definitive features of all defensin structures determined to date. Further, we predict that the tracheal antimicrobial peptide (TAP) and the recently described gallinacins will have tertiary structures similar to that of BNBD-12. FAU - Zimmermann, G R AU - Zimmermann GR AD - Department of Chemistry and Biochemistry, University of Colorado at Boulder 80309-0215, USA. FAU - Legault, P AU - Legault P FAU - Selsted, M E AU - Selsted ME FAU - Pardi, A AU - Pardi A LA - eng GR - AI 01051/AI/NIAID NIH HHS/United States GR - AI 22931/AI/NIAID NIH HHS/United States GR - AI 27026/AI/NIAID NIH HHS/United States GR - etc. PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Blood Proteins) RN - 0 (Defensins) RN - 0 (Solutions) RN - 0 (beta-Defensins) RN - 0 (bovine neutrophil beta-defensin 12) SB - IM MH - Amino Acid Sequence MH - Animals MH - Blood Proteins/*chemistry/isolation & purification/metabolism MH - Cattle MH - Defensins MH - Female MH - Hydrogen Bonding MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Neutrophils/*physiology MH - *Protein Folding MH - *Protein Structure, Secondary MH - Sequence Homology, Amino Acid MH - Solutions MH - Structure-Activity Relationship MH - *beta-Defensins EDAT- 1995/10/17 MHDA- 1995/10/17 00:01 CRDT- 1995/10/17 00:00 PST - ppublish SO - Biochemistry. 1995 Oct 17;34(41):13663-71. PMID- 21336827 OWN - NLM STAT- MEDLINE DA - 20110905 DCOM- 20120105 IS - 1874-270X (Electronic) VI - 5 IP - 2 DP - 2011 Oct TI - Full backbone assignment and dynamics of the intrinsically disordered dehydrin ERD14. PG - 189-93 LID - 10.1007/s12104-011-9297-2 [doi] AB - Dehydrins are a class of stress proteins that belong to the family of Late Embryogenesis Abundant (LEA) proteins in plants, so named because they are highly expressed in late stages of seed formation. In somatic cells, their expression is very low under normal conditions, but increases critically upon dehydration elicited by water stress, high salinity or cold. Dehydrins are thought to be intrinsically disordered proteins, which represents a challenge in understanding their structure-function relationship. Herein we present the backbone (1)H, (15)N and (13)C NMR assignment of the 185 amino acid long ERD14 (Early Response to Dehydration 14), which is a K(3)S-type, typical dehydrin of A. thaliana. Secondary chemical shifts as well as NMR relaxation data show that ERD14 is fully disordered under near native conditions, with short regions of somewhat restricted motion and 5-25% helical propensity. These results suggest that ERD14 may have partially preformed elements for functional interaction with its partner(s) and set the stage for further detailed structural and functional studies of ERD14 both in vitro and in vivo. FAU - Szalaine Agoston, Bianka AU - Szalaine Agoston B AD - Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Karolina ut 29., 1113, Budapest, Hungary. FAU - Kovacs, Denes AU - Kovacs D FAU - Tompa, Peter AU - Tompa P FAU - Perczel, Andras AU - Perczel A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110219 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (Arabidopsis Proteins) RN - 0 (ERD14 protein, Arabidopsis) RN - 0 (Isotopes) RN - 0 (Molecular Chaperones) RN - 0 (Plant Proteins) RN - 134711-03-8 (dehydrin proteins, plant) SB - IM MH - Arabidopsis/chemistry MH - Arabidopsis Proteins/*chemistry MH - Isotopes/chemistry MH - Molecular Chaperones MH - *Nuclear Magnetic Resonance, Biomolecular MH - Plant Proteins EDAT- 2011/02/22 06:00 MHDA- 2012/01/06 06:00 CRDT- 2011/02/22 06:00 PHST- 2010/11/15 [received] PHST- 2011/01/27 [accepted] PHST- 2011/02/19 [aheadofprint] AID - 10.1007/s12104-011-9297-2 [doi] PST - ppublish SO - Biomol NMR Assign. 2011 Oct;5(2):189-93. doi: 10.1007/s12104-011-9297-2. Epub 2011 Feb 19. PMID- 24590112 OWN - NLM STAT- MEDLINE DA - 20140326 DCOM- 20140527 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1844 IP - 4 DP - 2014 Apr TI - Structural characterization of a neuroblast-specific phosphorylated region of MARCKS. PG - 837-49 LID - 10.1016/j.bbapap.2014.02.016 [doi] LID - S1570-9639(14)00043-0 [pii] AB - MARCKS (Myristoylated Alanine-Rich C Kinase substrate) is a natively unfolded protein that interacts with actin, Ca(2+)-Calmodulin, and some plasma membrane lipids. Such interactions occur at a highly conserved region that is specifically phosphorylated by PKC: the Effector Domain. There are two other conserved domains, MH1 (including a myristoylation site) and MH2, also located in the amino terminal region and whose structure and putative protein binding capabilities are currently unknown. MH2 sequence contains a serine that we described as being phosphorylated only in differentiating neurons (S25 in chick). Here, Circular Dichroism (CD) and Nuclear Magnetic Resonance (NMR) spectroscopy were used to characterize the phosphorylated and unphosphorylated forms of a peptide with the MARCKS sequence surrounding S25. The peptide phosphorylated at this residue is recognized by monoclonal antibody 3C3 (mAb 3C3). CD and NMR data indicated that S25 phosphorylation does not cause extensive modifications in the peptide structure. However, the sharper lines, the absence of multiple spin systems and relaxation dispersion data observed for the phosphorylated peptide suggested a more ordered structure. Surface Plasmon Resonance was employed to compare the binding properties of mAb 3C3 to MARCKS protein and peptide. SPR showed that mAb 3C3 binds to the whole protein and the peptide with a similar affinity, albeit different kinetics. The slightly ordered structure of the phosphorylated peptide might be at the origin of its ability to interact with mAb 3C3 antibody, but this binding did not noticeably modify the peptide structure. CI - Copyright (c) 2014 Elsevier B.V. All rights reserved. FAU - Tinoco, Luzineide W AU - Tinoco LW AD - Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Cidade Universitaria, CCS, Bloco H, Rio de Janeiro 21941-902, RJ, Brazil. Electronic address: lwtinoco@nppn.ufrj.br. FAU - Fraga, Jully L AU - Fraga JL AD - Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Cidade Universitaria, CCS, Bloco H, Rio de Janeiro 21941-902, RJ, Brazil. Electronic address: jully.lfraga@gmail.com. FAU - Anobom, Cristiane D AU - Anobom CD AD - Departamento de Bioquimica, Instituto de Quimica, Universidade Federal do Rio de Janeiro, Cidade Universitaria, CT, Bloco A, Rio de Janeiro 21941-909, RJ, Brazil. Electronic address: anobom@iq.ufrj.br. FAU - Zolessi, Flavio R AU - Zolessi FR AD - Laboratorio de Cultivo de Tejidos, Seccion Biologia Celular, DBCM, Facultad de Ciencias, Universidad de la Republica, Igua 4225, 11400 Montevideo, Uruguay. Electronic address: fzolessi@fcien.edu.uy. FAU - Obal, Gonzalo AU - Obal G AD - Unidad de Biofisica de Proteinas, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay. Electronic address: gobal@pasteur.edu.uy. FAU - Toledo, Andrea AU - Toledo A AD - Laboratorio de Cultivo de Tejidos, Seccion Biologia Celular, DBCM, Facultad de Ciencias, Universidad de la Republica, Igua 4225, 11400 Montevideo, Uruguay. Electronic address: atoledo@fcien.edu.uy. FAU - Pritsch, Otto AU - Pritsch O AD - Unidad de Biofisica de Proteinas, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay. Electronic address: pritsch@pasteur.edu.uy. FAU - Arruti, Cristina AU - Arruti C AD - Laboratorio de Cultivo de Tejidos, Seccion Biologia Celular, DBCM, Facultad de Ciencias, Universidad de la Republica, Igua 4225, 11400 Montevideo, Uruguay. Electronic address: arruti@fcien.edu.uy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140228 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Antibodies, Monoclonal) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Membrane Proteins) RN - 0 (Peptides) RN - 0 (Phosphoproteins) RN - 125267-21-2 (myristoylated alanine-rich C kinase substrate) RN - EC 2.7.11.13 (Protein Kinase C) SB - IM MH - Amino Acid Sequence MH - Animals MH - Antibodies, Monoclonal/immunology MH - Brain Chemistry MH - Chick Embryo MH - Circular Dichroism MH - Intracellular Signaling Peptides and Proteins/*chemistry/immunology/metabolism MH - Membrane Proteins/*chemistry/immunology/metabolism MH - Mice MH - Molecular Sequence Data MH - Peptides/chemical synthesis/*chemistry/metabolism MH - Phosphoproteins/*chemistry/isolation & purification/metabolism MH - Phosphorylation MH - Protein Interaction Domains and Motifs MH - Protein Kinase C/chemistry/metabolism MH - Protein Structure, Secondary MH - Surface Plasmon Resonance OTO - NOTNLM OT - Antibody binding OT - Circular Dichroism OT - MARCKS OT - Nuclear Magnetic Resonance OT - Serine phosphorylation OT - Surface Plasmon Resonance EDAT- 2014/03/05 06:00 MHDA- 2014/05/28 06:00 CRDT- 2014/03/05 06:00 PHST- 2013/10/18 [received] PHST- 2014/02/07 [revised] PHST- 2014/02/20 [accepted] PHST- 2014/02/28 [aheadofprint] AID - S1570-9639(14)00043-0 [pii] AID - 10.1016/j.bbapap.2014.02.016 [doi] PST - ppublish SO - Biochim Biophys Acta. 2014 Apr;1844(4):837-49. doi: 10.1016/j.bbapap.2014.02.016. Epub 2014 Feb 28. PMID- 20018841 OWN - NLM STAT- MEDLINE DA - 20100215 DCOM- 20100311 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 8 DP - 2010 Feb 19 TI - The C terminus of the Alb3 membrane insertase recruits cpSRP43 to the thylakoid membrane. PG - 5954-62 LID - 10.1074/jbc.M109.084996 [doi] AB - The YidC/Oxa1/Alb3 family of membrane proteins controls the insertion and assembly of membrane proteins in bacteria, mitochondria, and chloroplasts. Here we describe the molecular mechanisms underlying the interaction of Alb3 with the chloroplast signal recognition particle (cpSRP). The Alb3 C-terminal domain (A3CT) is intrinsically disordered and recruits cpSRP to the thylakoid membrane by a coupled binding and folding mechanism. Two conserved, positively charged motifs reminiscent of chromodomain interaction motifs in histone tails are identified in A3CT that are essential for the Alb3-cpSRP43 interaction. They are absent in the C-terminal domain of Alb4, which therefore does not interact with cpSRP43. Chromodomain 2 in cpSRP43 appears as a central binding platform that can interact simultaneously with A3CT and cpSRP54. The observed negative cooperativity of the two binding events provides the first insights into cargo release at the thylakoid membrane. Taken together, our data show how Alb3 participates in cpSRP-dependent membrane targeting, and our data provide a molecular explanation why Alb4 cannot compensate for the loss of Alb3. Oxa1 and YidC utilize their positively charged, C-terminal domains for ribosome interaction in co-translational targeting. Alb3 is adapted for the chloroplast-specific Alb3-cpSRP43 interaction in post-translational targeting by extending the spectrum of chromodomain interactions. FAU - Falk, Sebastian AU - Falk S AD - Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany. FAU - Ravaud, Stephanie AU - Ravaud S FAU - Koch, Joachim AU - Koch J FAU - Sinning, Irmgard AU - Sinning I LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091217 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (ALBINO 3 protein, Arabidopsis) RN - 0 (Alb4 protein, Arabidopsis) RN - 0 (Arabidopsis Proteins) RN - 0 (Chloroplast Proteins) RN - 0 (Mitochondrial Proteins) RN - 0 (Nuclear Proteins) RN - 0 (OXA1 protein) RN - 0 (Signal Recognition Particle) RN - EC 1.9.3.1 (Electron Transport Complex IV) SB - IM MH - Arabidopsis/genetics/*metabolism MH - Arabidopsis Proteins/genetics/*metabolism MH - Chloroplast Proteins MH - Electron Transport Complex IV/genetics/metabolism MH - Mitochondrial Proteins/genetics/metabolism MH - Nuclear Proteins/genetics/metabolism MH - Protein Binding/physiology MH - *Protein Folding MH - Protein Structure, Tertiary/physiology MH - Protein Transport/physiology MH - Signal Recognition Particle/genetics/*metabolism MH - Thylakoids/genetics/*metabolism PMC - PMC2820820 OID - NLM: PMC2820820 EDAT- 2009/12/19 06:00 MHDA- 2010/03/12 06:00 CRDT- 2009/12/19 06:00 PHST- 2009/12/17 [aheadofprint] AID - M109.084996 [pii] AID - 10.1074/jbc.M109.084996 [doi] PST - ppublish SO - J Biol Chem. 2010 Feb 19;285(8):5954-62. doi: 10.1074/jbc.M109.084996. Epub 2009 Dec 17. PMID- 24037535 OWN - NLM STAT- In-Data-Review DA - 20140117 LR - 20150113 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 102 IP - 1 DP - 2014 Jan TI - NMR based solvent exchange experiments to understand the conformational preference of intrinsically disordered proteins using FG-nucleoporin peptide as a model. PG - 69-77 LID - 10.1002/bip.22402 [doi] AB - The conformational preference of a peptide with three phenylalanine-glycine (FG) repeats from the intrinsically disordered domain of nucleoporin 159 (nup159) from the yeast nucleopore complex is studied. Conformational states of this FG-peptide in dimethyl sulfoxide (DMSO), a non-native solvent, are first studied. A solvent exchange scheme is designed and performed to understand how the conformational preferences of the peptide are altered as the solvent shifts from DMSO to water. An ensemble of structures of a 19-residue peptide is determined based on (13) Calpha, (1) Halpha, and (1) HN chemical shifts and with inter-proton distances. An experimental model is then presented where chemical shifts and amide-proton temperature dependence is probed at changing DMSO to water ratios. These co-solvent experiments provide evidence of a conformational change as the fraction of water increases by the stark change in the behavior of amide protons under varied temperature. This investigation provides a NMR based experimental method in the field of intrinsically disordered proteins to realize conformational transitions from a non-native set of structures (in DMSO) to a native set of disordered conformers (in water). (c) 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 69-77, 2014. CI - Copyright (c) 2013 Wiley Periodicals, Inc. FAU - Heisel, Kurt A AU - Heisel KA AD - Department of Chemistry, California State University, Fresno, CA, 93740. FAU - Krishnan, V V AU - Krishnan VV LA - eng GR - P20 CA138025/CA/NCI NIH HHS/United States GR - P20 MD002732/MD/NIMHD NIH HHS/United States PT - Journal Article PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 SB - IM PMC - PMC4020917 MID - NIHMS573554 OID - NLM: NIHMS573554 OID - NLM: PMC4020917 OTO - NOTNLM OT - intrinsically disordered protein OT - nuclear magnetic resonance OT - nucleoporins OT - solvent perturbation EDAT- 2013/09/17 06:00 MHDA- 2013/09/17 06:00 CRDT- 2013/09/17 06:00 PHST- 2013/05/30 [received] PHST- 2013/08/16 [revised] PHST- 2013/08/22 [accepted] AID - 10.1002/bip.22402 [doi] PST - ppublish SO - Biopolymers. 2014 Jan;102(1):69-77. doi: 10.1002/bip.22402. PMID- 23339032 OWN - NLM STAT- MEDLINE DA - 20140317 DCOM- 20141112 IS - 1874-270X (Electronic) VI - 8 IP - 1 DP - 2014 Apr TI - Backbone and partial side chain assignment of the microtubule binding domain of the MAP1B light chain. PG - 123-7 LID - 10.1007/s12104-013-9466-6 [doi] AB - Microtubule-associated protein 1B (MAP1B) is a classical high molecular mass microtubule-associated protein expressed at high levels in the brain. It confers specific properties to neuronal microtubules and is essential for neuronal differentiation, brain development and synapse maturation. Misexpression of the protein contributes to the development of brain disorders in humans. However, despite numerous reports demonstrating the importance of MAP1B in regulation of the neuronal cytoskeleton during neurite extension and axon guidance, its mechanism of action is still elusive. Here we focus on the intrinsically disordered microtubule binding domain of the light chain of MAP1B. In order to obtain more detailed structural information about this domain we assigned NMR chemical shifts of backbone and aliphatic side chain atoms. FAU - Orban-Nemeth, Zsuzsanna AU - Orban-Nemeth Z AD - Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 1, 1030, Vienna, Austria. FAU - Henen, Morkos A AU - Henen MA FAU - Geist, Leonhard AU - Geist L FAU - Zerko, Szymon AU - Zerko S FAU - Saxena, Saurabh AU - Saxena S FAU - Stanek, Jan AU - Stanek J FAU - Kozminski, Wiktor AU - Kozminski W FAU - Propst, Friedrich AU - Propst F FAU - Konrat, Robert AU - Konrat R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130122 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (Microtubule-Associated Proteins) RN - 0 (microtubule-associated protein 1B) SB - IM MH - Amino Acid Sequence MH - Animals MH - Microtubule-Associated Proteins/*chemistry/*metabolism MH - Microtubules/*metabolism MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Rats PMC - PMC3955483 OID - NLM: PMC3955483 EDAT- 2013/01/23 06:00 MHDA- 2014/11/13 06:00 CRDT- 2013/01/23 06:00 PHST- 2012/11/21 [received] PHST- 2013/01/12 [accepted] PHST- 2013/01/22 [aheadofprint] AID - 10.1007/s12104-013-9466-6 [doi] PST - ppublish SO - Biomol NMR Assign. 2014 Apr;8(1):123-7. doi: 10.1007/s12104-013-9466-6. Epub 2013 Jan 22. PMID- 24038467 OWN - NLM STAT- MEDLINE DA - 20131209 DCOM- 20140213 LR - 20150510 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 41 IP - 22 DP - 2013 Dec TI - A transient alpha-helical molecular recognition element in the disordered N-terminus of the Sgs1 helicase is critical for chromosome stability and binding of Top3/Rmi1. PG - 10215-27 LID - 10.1093/nar/gkt817 [doi] AB - The RecQ-like DNA helicase family is essential for the maintenance of genome stability in all organisms. Sgs1, a member of this family in Saccharomyces cerevisiae, regulates early and late steps of double-strand break repair by homologous recombination. Using nuclear magnetic resonance spectroscopy, we show that the N-terminal 125 residues of Sgs1 are disordered and contain a transient alpha-helix that extends from residue 25 to 38. Based on the residue-specific knowledge of transient secondary structure, we designed proline mutations to disrupt this alpha-helix and observed hypersensitivity to DNA damaging agents and increased frequency of genome rearrangements. In vitro binding assays show that the defects of the proline mutants are the result of impaired binding of Top3 and Rmi1 to Sgs1. Extending mutagenesis N-terminally revealed a second functionally critical region that spans residues 9-17. Depending on the position of the proline substitution in the helix functional impairment of Sgs1 function varied, gradually increasing from the C- to the N-terminus. The multiscale approach we used to interrogate structure/function relationships in the long disordered N-terminal segment of Sgs1 allowed us to precisely define a functionally critical region and should be generally applicable to other disordered proteins. FAU - Kennedy, Jessica A AU - Kennedy JA AD - Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA, Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL 33612, USA and Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA. FAU - Daughdrill, Gary W AU - Daughdrill GW FAU - Schmidt, Kristina H AU - Schmidt KH LA - eng GR - R01 GM081425/GM/NIGMS NIH HHS/United States GR - R01GM081425/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130914 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (DNA-Binding Proteins) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Rmi1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (TOP3 protein, S cerevisiae) RN - 9DLQ4CIU6V (Proline) RN - EC 3.6.1.- (SGS1 protein, S cerevisiae) RN - EC 3.6.4.12 (RecQ Helicases) SB - IM MH - *Chromosomal Instability MH - DNA-Binding Proteins/*metabolism MH - Intrinsically Disordered Proteins/chemistry MH - Mutagenesis MH - Proline/genetics MH - Protein Structure, Secondary MH - RecQ Helicases/*chemistry/metabolism MH - Saccharomyces cerevisiae/genetics MH - Saccharomyces cerevisiae Proteins/*chemistry/*metabolism PMC - PMC3905885 OID - NLM: PMC3905885 EDAT- 2013/09/17 06:00 MHDA- 2014/02/14 06:00 CRDT- 2013/09/17 06:00 PHST- 2013/09/14 [aheadofprint] AID - gkt817 [pii] AID - 10.1093/nar/gkt817 [doi] PST - ppublish SO - Nucleic Acids Res. 2013 Dec;41(22):10215-27. doi: 10.1093/nar/gkt817. Epub 2013 Sep 14. PMID- 17279794 OWN - NLM STAT- MEDLINE DA - 20070223 DCOM- 20070509 LR - 20140916 IS - 1520-6106 (Print) IS - 1520-5207 (Linking) VI - 111 IP - 8 DP - 2007 Mar 1 TI - Alpha-synuclein tertiary contact dynamics. PG - 2107-12 AB - Tertiary contact formation rates in alpha-synuclein, an intrinsically disordered polypeptide implicated in Parkinson's disease, have been determined from measurements of diffusion-limited electron-transfer kinetics between triplet-excited tryptophan:3-nitrotyrosine pairs separated by 10, 12, 55, and 90 residues. Calculations based on a Markovian lattice model developed to describe intrachain diffusion dynamics for a disordered polypeptide give contact quenching rates for various loop sizes ranging from 6 to 48 that are in reasonable agreement with experimentally determined values for small loops (10-20 residues). Contrary to expectations, measured contact rates in alpha-synuclein do not continue to decrease as the loop size increases (>/=35 residues), and substantial deviations from calculated rates are found for the pairs W4-Y94, Y39-W94, and W4-Y136. The contact rates for these large loops indicate much shorter average donor-acceptor separations than expected for a random polymer. FAU - Lee, Jennifer C AU - Lee JC AD - Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, Maryland 20892, USA. FAU - Lai, Bert T AU - Lai BT FAU - Kozak, John J AU - Kozak JJ FAU - Gray, Harry B AU - Gray HB FAU - Winkler, Jay R AU - Winkler JR LA - eng GR - DK19038/DK/NIDDK NIH HHS/United States GR - GM068461/GM/NIGMS NIH HHS/United States GR - R01 GM068461/GM/NIGMS NIH HHS/United States GR - R01 GM068461-05/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070206 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (alpha-Synuclein) RN - 3604-79-3 (3-nitrotyrosine) RN - 42HK56048U (Tyrosine) RN - 8DUH1N11BX (Tryptophan) SB - IM MH - Amino Acid Sequence MH - Electron Transport MH - Molecular Sequence Data MH - Protein Conformation MH - Tryptophan/*chemistry MH - Tyrosine/*analogs & derivatives/chemistry MH - alpha-Synuclein/*chemistry PMC - PMC2519050 MID - NIHMS61888 OID - NLM: NIHMS61888 OID - NLM: PMC2519050 EDAT- 2007/02/07 09:00 MHDA- 2007/05/10 09:00 CRDT- 2007/02/07 09:00 PHST- 2007/02/06 [aheadofprint] AID - 10.1021/jp068604y [doi] PST - ppublish SO - J Phys Chem B. 2007 Mar 1;111(8):2107-12. Epub 2007 Feb 6. PMID- 14622405 OWN - NLM STAT- MEDLINE DA - 20031119 DCOM- 20040429 LR - 20061115 IS - 0950-382X (Print) IS - 0950-382X (Linking) VI - 50 IP - 4 DP - 2003 Nov TI - ParG, a protein required for active partition of bacterial plasmids, has a dimeric ribbon-helix-helix structure. PG - 1141-53 AB - The ParG protein (8.6 kDa) is an essential component of the DNA partition complex of multidrug resistance plasmid TP228. ParG is a dimer in solution, interacts with DNA sequences upstream of the parFG genes and also with the ParF partition protein both in the absence and presence of target DNA. Here, the solution nuclear magnetic resonance structure of ParG is reported. The ParG dimer is composed of a folded domain formed by two closely intertwined C-terminal parts (residues 33-76), and two highly mobile tails consisting of N-terminal regions (residues 1-32). The folded part of ParG has the ribbon-helix-helix (RHH) architecture similar to that of the Arc/MetJ superfamily of DNA-binding transcriptional repressors, although the primary sequence similarity is very low. ParG interacts with DNA predominantly via its folded domain; this interaction is coupled with ParG oligomerization. The dimeric RHH structure of ParG suggests that it binds to DNA by inserting the double-stranded beta-sheet into the major groove of DNA, in a manner similar to transcriptional repressors from the Arc/MetJ superfamily, and that ParG can function as a transcriptional repressor itself. A new classification of proteins belonging to the Arc/MetJ superfamily and ParG homologues is proposed, based on the location of a conserved positively charged residue at either the beginning or at the end of the beta-strand which forms part of the DNA recognition motif. FAU - Golovanov, Alexander P AU - Golovanov AP AD - Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology (UMIST), PO Box 88, Manchester M60 1QD, UK. FAU - Barilla, Daniela AU - Barilla D FAU - Golovanova, Marina AU - Golovanova M FAU - Hayes, Finbarr AU - Hayes F FAU - Lian, Lu-Yun AU - Lian LY LA - eng SI - PDB/1P94 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Mol Microbiol JT - Molecular microbiology JID - 8712028 RN - 0 (Bacterial Proteins) RN - 0 (DNA, Bacterial) RN - 0 (DNA-Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/genetics/metabolism MH - DNA, Bacterial/metabolism MH - DNA-Binding Proteins/*chemistry/genetics/metabolism MH - Dimerization MH - Genes, Bacterial MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Plasmids/genetics/*metabolism MH - *Protein Structure, Quaternary MH - *Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Alignment EDAT- 2003/11/19 05:00 MHDA- 2004/04/30 05:00 CRDT- 2003/11/19 05:00 AID - 3750 [pii] PST - ppublish SO - Mol Microbiol. 2003 Nov;50(4):1141-53. PMID- 21044600 OWN - NLM STAT- MEDLINE DA - 20101103 DCOM- 20110128 LR - 20141120 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 9 DP - 2010 Nov 3 TI - Copper uptake induces self-assembly of 18.5 kDa myelin basic protein (MBP). PG - 3020-8 LID - 10.1016/j.bpj.2010.08.022 [doi] AB - Myelin basic protein (MBP) is predominantly found in the membranes of the myelin sheath of the central nervous system and is involved in important protein-protein and protein-lipid interactions in vivo and in vitro. Furthermore, divalent transition metal ions, especially Zn(2+) and Cu(2+), seem to directly affect the MBP-mediated formation and stabilization of the myelin sheath of the central nervous system. MBP belongs to the realm of intrinsically disordered proteins, and only fragmentary information is available regarding its partial structure(s) or supramolecular arrangements. Here, using standard continuous wave and modern pulse electron paramagnetic resonance methods, as well as dynamic light scattering, we demonstrate the uptake and specific coordination of two Cu(2+) atoms or one Zn(2+) atom per MBP molecule in solution. In the presence of phosphates, further addition of divalent metal ions above a characteristic threshold of four Cu(2+) atoms or two Zn(2+) atoms per MBP molecule leads to the formation of large MBP aggregates within the protein solution. In vivo, MBP-MBP interactions may thus be mediated by divalent cations. CI - Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Bund, Timo AU - Bund T AD - Max Planck Institute for Polymer Research, Mainz, Germany. FAU - Boggs, Joan M AU - Boggs JM FAU - Harauz, George AU - Harauz G FAU - Hellmann, Nadja AU - Hellmann N FAU - Hinderberger, Dariush AU - Hinderberger D LA - eng GR - MOP 86483/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Myelin Basic Protein) RN - 0 (Solutions) RN - 789U1901C5 (Copper) RN - J41CSQ7QDS (Zinc) SB - IM MH - Animals MH - Biophysical Phenomena MH - Cattle MH - Copper/*chemistry/*metabolism MH - Electron Spin Resonance Spectroscopy MH - In Vitro Techniques MH - Ion Transport MH - Light MH - Models, Molecular MH - Myelin Basic Protein/*chemistry/*metabolism MH - Particle Size MH - Protein Multimerization MH - Scattering, Radiation MH - Solutions MH - Zinc/metabolism PMC - PMC2965959 OID - NLM: PMC2965959 EDAT- 2010/11/04 06:00 MHDA- 2011/02/01 06:00 CRDT- 2010/11/04 06:00 PHST- 2010/06/01 [received] PHST- 2010/07/23 [revised] PHST- 2010/08/02 [accepted] AID - S0006-3495(10)00991-4 [pii] AID - 10.1016/j.bpj.2010.08.022 [doi] PST - ppublish SO - Biophys J. 2010 Nov 3;99(9):3020-8. doi: 10.1016/j.bpj.2010.08.022. PMID- 20056465 OWN - NLM STAT- MEDLINE DA - 20100201 DCOM- 20100514 IS - 1873-4243 (Electronic) IS - 1093-3263 (Linking) VI - 28 IP - 6 DP - 2010 Feb 26 TI - The solution structures of the cucumber mosaic virus and tomato aspermy virus coat proteins explored with molecular dynamics simulations. PG - 569-76 LID - 10.1016/j.jmgm.2009.12.002 [doi] AB - The three-dimensional structures of two cucumovirus coat proteins (CP), namely Cucumber mosaic virus (CMV) and Tomato aspermy virus (TAV), were explored by molecular dynamics (MD) simulations. The N-terminal domain and the C-terminal tail of the CPs proved to be intrinsically unstructured protein regions in aqueous solution. The N-terminal alpha-helix had a partially unrolled conformation. The thermal factor analysis of the CP loop regions demonstrated that the CMV CP had more flexible loop regions than the TAV CP. The principal component analysis (PCA) of the MD trajectories showed that the first three eigenvectors represented the three main conformational motions in the CPs. The first motion components with the highest variance contribution described an opening movement between the hinge and the N-terminal domain of both CPs. The second eigenvector showed a closing motion, while the third eigenvector represented crosswise conformational fluctuations. These new findings, together with previous results, suggest that the hinge region of CPs plays a central role in the recognition and binding of viral RNA. CI - Copyright 2009 Elsevier Inc. All rights reserved. FAU - Gellert, Akos AU - Gellert A AD - Agricultural Research Institute of the Hungarian Academy of Sciences, Department of Applied Genomics, H-2462 Martonvasar, Brunszvik u. 2. Hungary. gellerta@mail.mgki.hu FAU - Balazs, Ervin AU - Balazs E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091221 PL - United States TA - J Mol Graph Model JT - Journal of molecular graphics & modelling JID - 9716237 RN - 0 (Capsid Proteins) RN - 0 (Solutions) SB - IM MH - Amino Acid Sequence MH - Capsid Proteins/*chemistry MH - Cluster Analysis MH - Crystallography, X-Ray MH - Cucumovirus/*chemistry MH - *Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Plant Viruses/*chemistry MH - Principal Component Analysis MH - Protein Structure, Secondary MH - Sequence Alignment MH - Solutions EDAT- 2010/01/09 06:00 MHDA- 2010/05/15 06:00 CRDT- 2010/01/09 06:00 PHST- 2009/10/05 [received] PHST- 2009/12/01 [revised] PHST- 2009/12/08 [accepted] PHST- 2009/12/21 [aheadofprint] AID - S1093-3263(09)00180-6 [pii] AID - 10.1016/j.jmgm.2009.12.002 [doi] PST - ppublish SO - J Mol Graph Model. 2010 Feb 26;28(6):569-76. doi: 10.1016/j.jmgm.2009.12.002. Epub 2009 Dec 21. PMID- 21044602 OWN - NLM STAT- MEDLINE DA - 20101103 DCOM- 20110128 LR - 20141120 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 9 DP - 2010 Nov 3 TI - Evidence that alphaC region is origin of low modulus, high extensibility, and strain stiffening in fibrin fibers. PG - 3038-47 LID - 10.1016/j.bpj.2010.08.060 [doi] AB - Fibrin fibers form the structural scaffold of blood clots and perform the mechanical task of stemming blood flow. Several decades of investigation of fibrin fiber networks using macroscopic techniques have revealed remarkable mechanical properties. More recently, the microscopic origins of fibrin's mechanics have been probed through direct measurements on single fibrin fibers and individual fibrinogen molecules. Using a nanomanipulation system, we investigated the mechanical properties of individual fibrin fibers. The fibers were stretched with the atomic force microscope, and stress-versus-strain data was collected for fibers formed with and without ligation by the activated transglutaminase factor XIII (FXIIIa). We observed that ligation with FXIIIa nearly doubled the stiffness of the fibers. The stress-versus-strain behavior indicates that fibrin fibers exhibit properties similar to other elastomeric biopolymers. We propose a mechanical model that fits our observed force extension data, is consistent with the results of the ligation data, and suggests that the large observed extensibility in fibrin fibers is mediated by the natively unfolded regions of the molecule. Although some models attribute fibrin's force-versus-extension behavior to unfolding of structured regions within the monomer, our analysis argues that these models are inconsistent with the measured extensibility and elastic modulus. CI - Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Houser, John R AU - Houser JR AD - Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. FAU - Hudson, Nathan E AU - Hudson NE FAU - Ping, Lifang AU - Ping L FAU - O'Brien, E Timothy 3rd AU - O'Brien ET 3rd FAU - Superfine, Richard AU - Superfine R FAU - Lord, Susan T AU - Lord ST FAU - Falvo, Michael R AU - Falvo MR LA - eng GR - HL31048/HL/NHLBI NIH HHS/United States GR - P41-EB002025/EB/NIBIB NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Elastomers) RN - 0 (Recombinant Proteins) RN - 9001-31-4 (Fibrin) RN - EC 2.3.2.13 (Factor XIIIa) SB - IM MH - Biomechanical Phenomena MH - Biophysical Phenomena MH - Blood Coagulation/physiology MH - Elastic Modulus MH - Elastomers/chemistry MH - Factor XIIIa/chemistry/physiology MH - Fibrin/*chemistry/*physiology MH - Humans MH - In Vitro Techniques MH - Microscopy, Atomic Force MH - Models, Biological MH - *Models, Molecular MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Stress, Mechanical MH - Tensile Strength MH - Unfolded Protein Response PMC - PMC2965937 OID - NLM: PMC2965937 EDAT- 2010/11/04 06:00 MHDA- 2011/02/01 06:00 CRDT- 2010/11/04 06:00 PHST- 2010/05/27 [received] PHST- 2010/08/04 [revised] PHST- 2010/08/23 [accepted] AID - S0006-3495(10)01056-8 [pii] AID - 10.1016/j.bpj.2010.08.060 [doi] PST - ppublish SO - Biophys J. 2010 Nov 3;99(9):3038-47. doi: 10.1016/j.bpj.2010.08.060. PMID- 16753179 OWN - NLM STAT- MEDLINE DA - 20060703 DCOM- 20060814 LR - 20071114 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 360 IP - 1 DP - 2006 Jun 30 TI - The third 20 amino acid repeat is the tightest binding site of APC for beta-catenin. PG - 133-44 AB - Adenomatous polyposis coli (APC) plays a critical role in the Wnt signaling pathway by tightly regulating beta-catenin turnover and localization. The central region of APC is responsible for APC-beta-catenin interactions through its seven 20 amino acid (20aa) repeats and three 15 amino acid (15aa) repeats. Using isothermal titration calorimetry, we have determined the binding affinities of beta-catenin with an APC 15aa repeat fragment and each of the seven 20aa repeats in both phosphorylated and unphosphorylated states. Despite sequence homology, different beta-catenin binding repeats of APC have dramatically different binding affinities with beta-catenin and thus may play different biological roles. The third 20aa repeat is by far the tightest binding site for beta-catenin among all the repeats. The fact that most APC mutations associated with colon cancers have lost the third 20aa repeat underlines the importance of APC-beta-catenin interaction in Wnt signaling and human diseases. For every 20aa repeat, phosphorylation dramatically increases its binding affinity for beta-catenin, suggesting phosphorylation has a critical regulatory role in APC function. In addition, our CD and NMR studies demonstrate that the central region of APC is unstructured in the absence of beta-catenin and Axin, and suggest that beta-catenin may interact with each of the APC 15aa and 20aa repeats independently. FAU - Liu, Jing AU - Liu J AD - Department of Biological Structure, University of Washington, Seattle, WA 98195, USA. FAU - Xing, Yi AU - Xing Y FAU - Hinds, Thomas R AU - Hinds TR FAU - Zheng, Jie AU - Zheng J FAU - Xu, Wenqing AU - Xu W LA - eng GR - CA90351/CA/NCI NIH HHS/United States GR - GM61739/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20060515 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (beta Catenin) SB - IM MH - Adenomatous Polyposis Coli/*metabolism MH - Amino Acid Sequence MH - Binding Sites MH - DNA Mutational Analysis MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Phosphorylation MH - Protein Binding MH - Signal Transduction MH - Thermodynamics MH - beta Catenin/*chemistry/metabolism EDAT- 2006/06/07 09:00 MHDA- 2006/08/15 09:00 CRDT- 2006/06/07 09:00 PHST- 2006/01/05 [received] PHST- 2006/04/13 [revised] PHST- 2006/04/27 [accepted] PHST- 2006/05/15 [aheadofprint] AID - S0022-2836(06)00557-2 [pii] AID - 10.1016/j.jmb.2006.04.064 [doi] PST - ppublish SO - J Mol Biol. 2006 Jun 30;360(1):133-44. Epub 2006 May 15. PMID- 20876941 OWN - NLM STAT- MEDLINE DA - 20101008 DCOM- 20110111 LR - 20140824 IS - 1945-4589 (Electronic) IS - 1945-4589 (Linking) VI - 2 IP - 9 DP - 2010 Sep TI - Unfolded p53 in the pathogenesis of Alzheimer's disease: is HIPK2 the link? PG - 545-54 AB - p53 transcriptional activity depends mainly on posttranslational modifications and protein/protein interaction. Another important mechanism that controls p53 function is its conformational stability since p53 is an intrinsically unstable protein. An altered conformational state of p53, independent from point mutations, has been reported in tissues from patients with Alzheimer's disease (AD), leading to an impaired and dysfunctional response to stressors. Recent evidence shows that one of the activators that induces p53 posttranslational modification and wild-type conformational stability is homeodomain interacting protein kinase 2 (HIPK2). Hence, conditions that induce HIPK2 deregulation would result in a dysfunctional response to stressors by affecting p53 activity. Discovering the mechanisms of HIPK2 activation/inhibition and the ways to manipulate HIPK2 activity are an interesting option to affect several biological pathways, including those underlying AD. Soluble beta-amyloid peptides have recently been involved in HIPK2 degradation, in turn regulating the p53 conformational state and vulnerability to a noxious stimulus, before triggering the amyloidogenic cascade. Here we discuss about these findings and the potential relevance of HIPK2 as a target for AD and highlight the existence of a novel amyloid-based mechanism in AD potentially leading to the survival of injured dysfunctional cells. FAU - Stanga, Serena AU - Stanga S AD - Department of Experimental and Applied Pharmacology, Centre of Excellence in Applied Biology, University of Pavia, Italy. FAU - Lanni, Cristina AU - Lanni C FAU - Govoni, Stefano AU - Govoni S FAU - Uberti, Daniela AU - Uberti D FAU - D'Orazi, Gabriella AU - D'Orazi G FAU - Racchi, Marco AU - Racchi M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Aging (Albany NY) JT - Aging JID - 101508617 RN - 0 (Amyloid beta-Peptides) RN - 0 (Carrier Proteins) RN - 0 (Tumor Suppressor Protein p53) RN - EC 2.7.1.- (HIPK2 protein, human) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - Aging/physiology MH - Alzheimer Disease/*etiology/physiopathology MH - Amyloid beta-Peptides/physiology MH - Carrier Proteins/*physiology MH - Humans MH - Neurodegenerative Diseases/physiopathology MH - Protein Folding MH - Protein-Serine-Threonine Kinases/*physiology MH - Tumor Suppressor Protein p53/*physiology PMC - PMC2984604 OID - NLM: PMC2984604 EDAT- 2010/09/30 06:00 MHDA- 2011/01/12 06:00 CRDT- 2010/09/30 06:00 AID - 100205 [pii] PST - ppublish SO - Aging (Albany NY). 2010 Sep;2(9):545-54. PMID- 10388840 OWN - NLM STAT- MEDLINE DA - 19990824 DCOM- 19990824 LR - 20061115 IS - 0269-2139 (Print) IS - 0269-2139 (Linking) VI - 12 IP - 6 DP - 1999 Jun TI - Crystal structure of human serum albumin at 2.5 A resolution. PG - 439-46 AB - A new triclinic crystal form of human serum albumin (HSA), derived either from pool plasma (pHSA) or from a Pichia pastoris expression system (rHSA), was obtained from polyethylene glycol 4000 solution. Three-dimensional structures of pHSA and rHSA were determined at 2.5 A resolution from the new triclinic crystal form by molecular replacement, using atomic coordinates derived from a multiple isomorphous replacement work with a known tetragonal crystal form. The structures of pHSA and rHSA are virtually identical, with an r.m. s. deviation of 0.24 A for all Calpha atoms. The two HSA molecules involved in the asymmetric unit are related by a strict local twofold symmetry such that the Calpha atoms of the two molecules can be superimposed with an r.m.s. deviation of 0.28 A in pHSA. Cys34 is the only cysteine with a free sulfhydryl group which does not participate in a disulfide linkage with any external ligand. Domains II and III both have a pocket formed mostly of hydrophobic and positively charged residues and in which a very wide range of compounds may be accommodated. Three tentative binding sites for long-chain fatty acids, each with different surroundings, are located at the surface of each domain. FAU - Sugio, S AU - Sugio S AD - Osaka Laboratories, Yoshitomi Pharmaceutical Industries Ltd,2-25-1, Shodai-Ohtani, Hirakata, Osaka 573-1153, Japan. FAU - Kashima, A AU - Kashima A FAU - Mochizuki, S AU - Mochizuki S FAU - Noda, M AU - Noda M FAU - Kobayashi, K AU - Kobayashi K LA - eng PT - Comparative Study PT - Journal Article PL - ENGLAND TA - Protein Eng JT - Protein engineering JID - 8801484 RN - 0 (Disulfides) RN - 0 (Recombinant Proteins) RN - 0 (Serum Albumin) RN - 0 (Sulfhydryl Compounds) SB - IM MH - Binding Sites MH - Crystallization MH - Crystallography, X-Ray MH - Disulfides/chemistry MH - Humans MH - Models, Molecular MH - Pichia/metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Serum Albumin/*chemistry/metabolism MH - Sulfhydryl Compounds/chemistry EDAT- 1999/07/02 MHDA- 1999/07/02 00:01 CRDT- 1999/07/02 00:00 PST - ppublish SO - Protein Eng. 1999 Jun;12(6):439-46. PMID- 21425832 OWN - NLM STAT- MEDLINE DA - 20110426 DCOM- 20110628 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 50 IP - 17 DP - 2011 May 3 TI - The intracellular distal tail of the Na+/H+ exchanger NHE1 is intrinsically disordered: implications for NHE1 trafficking. PG - 3469-80 LID - 10.1021/bi1019989 [doi] AB - Intrinsic disorder is important for protein regulation, yet its role in regulation of ion transport proteins is essentially uninvestigated. The ubiquitous plasma membrane carrier protein Na(+)/H(+) Exchanger isoform 1 (NHE1) plays pivotal roles in cellular pH and volume homeostasis, and its dysfunction is implicated in several clinically important diseases. This study shows, for the first time for any carrier protein, that the distal part of the C-terminal intracellular tail (the cdt, residues V686-Q815) from human (h) NHE1 is intrinsically disordered. Further, we experimentally demonstrated the presence of a similar region of intrinsic disorder (ID) in NHE1 from the teleost fish Pleuronectes americanus (paNHE1), and bioinformatic analysis suggested ID to be conserved in the NHE1 family. The sequential variation in structure propensity as determined by NMR, but not the amplitude, was largely conserved between the h- and paNHE1cdt. This suggests that both proteins contain molecular recognition features (MoRFs), i.e., local, transiently formed structures within an ID region. The functional relevance of the most conserved MoRF was investigated by introducing a point mutation that significantly disrupted the putative binding feature. When this mutant NHE1 was expressed in full length NHE1 in AP1 cells, it exhibited impaired trafficking to the plasma membrane. This study demonstrated that the distal regulatory domain of NHE1 is intrinsically disordered yet contains conserved regions of transient structure. We suggest that normal NHE1 function depends on a protein recognition element within the ID region that may be linked to NHE1 trafficking via an acidic ER export motif. FAU - Norholm, Ann-Beth AU - Norholm AB AD - Cell and Developmental Biology, Department of Biology, University of Copenhagen, Denmark. FAU - Hendus-Altenburger, Ruth AU - Hendus-Altenburger R FAU - Bjerre, Gabriel AU - Bjerre G FAU - Kjaergaard, Magnus AU - Kjaergaard M FAU - Pedersen, Stine F AU - Pedersen SF FAU - Kragelund, Birthe B AU - Kragelund BB LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110408 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cation Transport Proteins) RN - 0 (Fish Proteins) RN - 0 (SLC9A1 protein, human) RN - 0 (Sodium-Hydrogen Antiporter) SB - IM MH - Amino Acid Motifs MH - Animals MH - Cation Transport Proteins/*chemistry/genetics/metabolism MH - Cell Line MH - Cell Membrane/metabolism MH - Computational Biology MH - Conserved Sequence MH - Fish Proteins/chemistry MH - Flounder MH - Glycosylation MH - Humans MH - Molecular Sequence Data MH - Mutation MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Protein Transport MH - Scattering, Small Angle MH - Sequence Alignment MH - Sodium-Hydrogen Antiporter/*chemistry/genetics/metabolism MH - Species Specificity MH - X-Ray Diffraction EDAT- 2011/03/24 06:00 MHDA- 2011/06/29 06:00 CRDT- 2011/03/24 06:00 PHST- 2011/04/08 [aheadofprint] AID - 10.1021/bi1019989 [doi] PST - ppublish SO - Biochemistry. 2011 May 3;50(17):3469-80. doi: 10.1021/bi1019989. Epub 2011 Apr 8. PMID- 19364499 OWN - NLM STAT- MEDLINE DA - 20090512 DCOM- 20090605 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 383 IP - 4 DP - 2009 Jun 12 TI - NMR studies reveal a novel mode for hFADD to bind with the unstructured hRTN3 which initiates the ER-stress activated apoptosis. PG - 433-9 LID - 10.1016/j.bbrc.2009.04.024 [doi] AB - RTN3 can recruit Fas-associated death domain (FADD), thus initiating the ER-stress activated apoptosis. It also interacts with the beta-secretase and its aggregation is critically associated with Alzheimer's disease. Here, we first investigated the solution conformation of hRTN3, subsequently characterized its binding with hFADD. The results reveal: (1) both hRTN3 N- and C-termini are intrinsically unstructured. Nevertheless, the C-terminus contains two short helix-populated regions. (2) The unstructured hRTN3 C-terminus can bind to hFADD as shown by ITC. Further NMR investigation successfully identified the binding involved hRTN3 residues. (3) Although upon hRTN3-binding, the perturbed hFADD residues were distributed over the whole sequence, the majority of the significantly perturbed are over its death effector domain, very different from the previously observed binding mode for FADD. This study also implies a possible linkage between Alzheimer's disease and ER-stress activated apoptosis. FAU - Liu, Jingxian AU - Liu J AD - Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore. FAU - Zhu, Wanlong AU - Zhu W FAU - Qin, Haina AU - Qin H FAU - Song, Jianxing AU - Song J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090411 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Carrier Proteins) RN - 0 (Fas-Associated Death Domain Protein) RN - 0 (Membrane Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (RTN3 protein, human) SB - IM MH - Alzheimer Disease/metabolism/pathology MH - Amino Acid Sequence MH - Apoptosis MH - Carrier Proteins/chemistry/genetics/*metabolism MH - Endoplasmic Reticulum/*metabolism MH - Fas-Associated Death Domain Protein/chemistry/genetics/*metabolism MH - Humans MH - Membrane Proteins/chemistry/genetics/*metabolism MH - Molecular Sequence Data MH - Mutation MH - Nerve Tissue Proteins/chemistry/genetics/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding/genetics EDAT- 2009/04/15 09:00 MHDA- 2009/06/09 09:00 CRDT- 2009/04/15 09:00 PHST- 2009/03/24 [received] PHST- 2009/04/08 [accepted] PHST- 2009/04/11 [aheadofprint] AID - S0006-291X(09)00706-2 [pii] AID - 10.1016/j.bbrc.2009.04.024 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2009 Jun 12;383(4):433-9. doi: 10.1016/j.bbrc.2009.04.024. Epub 2009 Apr 11. PMID- 23995840 OWN - NLM STAT- MEDLINE DA - 20131021 DCOM- 20131231 LR - 20150522 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 42 DP - 2013 Oct 18 TI - Regulation of the structurally dynamic N-terminal domain of progesterone receptor by protein-induced folding. PG - 30285-99 LID - 10.1074/jbc.M113.491787 [doi] AB - The N-terminal domain (NTD) of steroid receptors harbors a transcriptional activation function (AF1) that is composed of an intrinsically disordered polypeptide. We examined the interaction of the TATA-binding protein (TBP) with the NTD of the progesterone receptor (PR) and its ability to regulate AF1 activity through coupled folding and binding. As assessed by solution phase biophysical methods, the isolated NTD of PR contains a large content of random coil, and it is capable of adopting secondary alpha-helical structure and more stable tertiary folding either in the presence of the natural osmolyte trimethylamine-N-oxide or through a direct interaction with TBP. Hydrogen-deuterium exchange coupled with mass spectrometry confirmed the highly dynamic intrinsically disordered property of the NTD within the context of full-length PR. Deletion mapping and point mutagenesis defined a region of the NTD (amino acids 350-428) required for structural folding in response to TBP interaction. Overexpression of TBP in cells enhanced transcriptional activity mediated by the PR NTD, and deletion mutations showed that a region (amino acids 327-428), similar to that required for TBP-induced folding, was required for functional response. TBP also increased steroid receptor co-activator 1 (SRC-1) interaction with the PR NTD and cooperated with SRC-1 to stimulate NTD-dependent transcriptional activity. These data suggest that TBP can mediate structural reorganization of the NTD to facilitate the binding of co-activators required for maximal transcriptional activation. FAU - Kumar, Raj AU - Kumar R AD - From the Departments of Molecular and Cellular Biology and. FAU - Moure, Carmen M AU - Moure CM FAU - Khan, Shagufta H AU - Khan SH FAU - Callaway, Celetta AU - Callaway C FAU - Grimm, Sandra L AU - Grimm SL FAU - Goswami, Devrishi AU - Goswami D FAU - Griffin, Patrick R AU - Griffin PR FAU - Edwards, Dean P AU - Edwards DP LA - eng GR - GM084041/GM/NIGMS NIH HHS/United States GR - P30 NCI-CA125123/CA/NCI NIH HHS/United States GR - R01 GM084041/GM/NIGMS NIH HHS/United States GR - R01CA046938/CA/NCI NIH HHS/United States GR - S10 RR027270/RR/NCRR NIH HHS/United States GR - U54 MH084512/MH/NIMH NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20130830 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Receptors, Progesterone) RN - 0 (TATA-Box Binding Protein) RN - 0 (TBP protein, human) RN - EC 2.3.1.48 (NCOA1 protein, human) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 1) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cell Line MH - Humans MH - Nuclear Receptor Coactivator 1/chemistry/genetics/*metabolism MH - Point Mutation MH - *Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Progesterone/chemistry/genetics/*metabolism MH - Sequence Deletion MH - TATA-Box Binding Protein/chemistry/genetics/*metabolism MH - Transcriptional Activation/*physiology PMC - PMC3798494 OID - NLM: PMC3798494 OTO - NOTNLM OT - Hydrogen Deuterium Exchange Mass OT - Intrinsically Disordered Proteins OT - Mass Spectrometry (MS) OT - N-terminal Transcription Activation domain AF1 OT - Progesterone OT - Progesterone Receptor OT - Protein Folding OT - Steroid Hormone Receptor OT - TATA-binding Protein EDAT- 2013/09/03 06:00 MHDA- 2014/01/01 06:00 CRDT- 2013/09/03 06:00 PHST- 2013/08/30 [aheadofprint] AID - M113.491787 [pii] AID - 10.1074/jbc.M113.491787 [doi] PST - ppublish SO - J Biol Chem. 2013 Oct 18;288(42):30285-99. doi: 10.1074/jbc.M113.491787. Epub 2013 Aug 30. PMID- 21884706 OWN - NLM STAT- MEDLINE DA - 20111014 DCOM- 20111207 LR - 20141120 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 413 IP - 2 DP - 2011 Oct 21 TI - Analyses of the functional regions of DEAD-box RNA "helicases" with deletion and chimera constructs tested in vivo and in vitro. PG - 451-72 LID - 10.1016/j.jmb.2011.08.032 [doi] AB - The DEAD-box family of putative RNA helicases is composed of ubiquitous proteins that are found in nearly all organisms and that are involved in virtually all processes involving RNA. They are characterized by two tandemly linked, RecA-like domains that contain 11 conserved motifs and highly variable amino- and carboxy-terminal flanking sequences. For this reason, they are often considered to be modular multi-domain proteins. We tested this by making extensive BLASTs and sequence alignments to elucidate the minimal functional unit in nature. We then used this information to construct chimeras and deletions of six essential yeast proteins that were assayed in vivo. We purified many of the different constructs and characterized their biochemical properties in vitro. We found that sequence elements can only be switched between closely related proteins and that the carboxy-terminal sequences are important for high ATPase and strand displacement activities and for high RNA binding affinity. The amino-terminal elements were often toxic when overexpressed in vivo, and they may play regulatory roles. Both the amino and the carboxyl regions have a high frequency of sequences that are predicted to be intrinsically disordered, indicating that the flanking regions do not form distinct modular domains but probably assume an ordered structure with ligand binding. Finally, the minimal functional unit of the DEAD-box core starts two amino acids before the isolated phenylalanine of the Q motif and extends to about 35 residues beyond motif VI. These experiments provide evidence for how a highly conserved structural domain can be adapted to different cellular needs. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Banroques, Josette AU - Banroques J AD - Institut de Biologie Physico-chimique, CNRS UPR9073, Paris 75005, France. FAU - Cordin, Olivier AU - Cordin O FAU - Doere, Monique AU - Doere M FAU - Linder, Patrick AU - Linder P FAU - Tanner, N Kyle AU - Tanner NK LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110823 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DNA Primers) RN - 0 (Mutant Chimeric Proteins) RN - 0 (RNA, Fungal) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 3.6.4.13 (DEAD-box RNA Helicases) SB - IM MH - Adenosine Triphosphatases/metabolism MH - Adenosine Triphosphate/metabolism MH - Amino Acid Motifs MH - Conserved Sequence MH - DEAD-box RNA Helicases/*chemistry/genetics/metabolism MH - DNA Primers/chemistry/genetics MH - In Vitro Techniques MH - Mutant Chimeric Proteins/genetics/*metabolism MH - Mutation/genetics MH - Protein Structure, Tertiary MH - RNA, Fungal/genetics MH - Saccharomyces cerevisiae/*genetics/*growth & development/metabolism MH - *Sequence Deletion EDAT- 2011/09/03 06:00 MHDA- 2011/12/13 00:00 CRDT- 2011/09/03 06:00 PHST- 2011/06/22 [received] PHST- 2011/08/11 [revised] PHST- 2011/08/16 [accepted] PHST- 2011/08/23 [aheadofprint] AID - S0022-2836(11)00930-2 [pii] AID - 10.1016/j.jmb.2011.08.032 [doi] PST - ppublish SO - J Mol Biol. 2011 Oct 21;413(2):451-72. doi: 10.1016/j.jmb.2011.08.032. Epub 2011 Aug 23. PMID- 24373767 OWN - NLM STAT- MEDLINE DA - 20140210 DCOM- 20141022 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 22 IP - 2 DP - 2014 Feb 4 TI - NleH defines a new family of bacterial effector kinases. PG - 250-9 LID - 10.1016/j.str.2013.11.006 [doi] LID - S0969-2126(13)00456-5 [pii] AB - Upon host cell infection, pathogenic Escherichia coli hijacks host cellular processes with the help of 20-60 secreted effector proteins that subvert cellular processes to create an environment conducive to bacterial survival. The NleH effector kinases manipulate the NF-kappaB pathway and prevent apoptosis. They show low sequence similarity to human regulatory kinases and contain two domains, the N-terminal, likely intrinsically unfolded, and a C-terminal kinase-like domain. We show that these effectors autophosphorylate on sites located predominantly in the N-terminal segment. The kinase domain displays a minimal kinase fold, but lacks an activation loop and the GHI subdomain. Nevertheless, all catalytically important residues are conserved. ATP binding proceeds with minimal structural rearrangements. The NleH structure is the first for the bacterial effector kinases family. NleHs and their homologous effector kinases form a new kinase family within the cluster of eukaryotic-like kinases that includes also Rio, Bud32, and KdoK families. CI - Copyright (c) 2014 Elsevier Ltd. All rights reserved. FAU - Grishin, Andrey M AU - Grishin AM AD - Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada. Electronic address: andrey.grishin@usask.ca. FAU - Cherney, Maia AU - Cherney M AD - Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada. FAU - Anderson, Deborah H AU - Anderson DH AD - Cancer Research, Saskatchewan Cancer Agency, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada. FAU - Phanse, Sadhna AU - Phanse S AD - Department of Biochemistry, Research and Innovation Centre, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada. FAU - Babu, Mohan AU - Babu M AD - Department of Biochemistry, Research and Innovation Centre, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada. FAU - Cygler, Miroslaw AU - Cygler M AD - Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada; Department of Biochemistry, McGill University, 3655 Promenade Sir Willam Osler, Montreal, QC H3G 1Y6, Canada. Electronic address: miroslaw.cygler@usask.ca. LA - eng GR - MOP-48370/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131226 PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Escherichia coli Proteins) RN - 0 (NF-kappa B) RN - 0 (NleH protein, E coli) RN - 0 (Recombinant Proteins) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 2.7.- (Phosphotransferases) SB - IM MH - Adenosine Triphosphate/chemistry MH - Amino Acid Sequence MH - Apoptosis MH - Catalysis MH - Escherichia coli/enzymology MH - Escherichia coli Proteins/*chemistry MH - Mass Spectrometry MH - Molecular Sequence Data MH - NF-kappa B/chemistry MH - Phosphorylation MH - Phosphotransferases/*chemistry MH - Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Sequence Homology, Amino Acid EDAT- 2014/01/01 06:00 MHDA- 2014/10/23 06:00 CRDT- 2013/12/31 06:00 PHST- 2013/09/14 [received] PHST- 2013/11/04 [revised] PHST- 2013/11/11 [accepted] PHST- 2013/12/26 [aheadofprint] AID - S0969-2126(13)00456-5 [pii] AID - 10.1016/j.str.2013.11.006 [doi] PST - ppublish SO - Structure. 2014 Feb 4;22(2):250-9. doi: 10.1016/j.str.2013.11.006. Epub 2013 Dec 26. PMID- 11807546 OWN - NLM STAT- MEDLINE DA - 20020124 DCOM- 20020315 LR - 20091119 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 415 IP - 6870 DP - 2002 Jan 24 TI - Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin. PG - 396-402 AB - Oedema factor, a calmodulin-activated adenylyl cyclase, is important in the pathogenesis of anthrax. Here we report the X-ray structures of oedema factor with and without bound calmodulin. Oedema factor shares no significant structural homology with mammalian adenylyl cyclases or other proteins. In the active site, 3'-deoxy-ATP and a single metal ion are well positioned for catalysis with histidine 351 as the catalytic base. This mechanism differs from the mechanism of two-metal-ion catalysis proposed for mammalian adenylyl cyclases. Four discrete regions of oedema factor form a surface that recognizes an extended conformation of calmodulin, which is very different from the collapsed conformation observed in other structures of calmodulin bound to effector peptides. On calmodulin binding, an oedema factor helical domain of relative molecular mass 15,000 undergoes a 15 A translation and a 30 degrees rotation away from the oedema factor catalytic core, which stabilizes a disordered loop and leads to enzyme activation. These allosteric changes provide the first molecular details of how calmodulin modulates one of its targets. FAU - Drum, Chester L AU - Drum CL AD - Ben-May Institute for Cancer Research, The University of Chicago, 924 East 57th Street, Chicago, Illinois 60637, USA. FAU - Yan, Shui-Zhong AU - Yan SZ FAU - Bard, Joel AU - Bard J FAU - Shen, Yue-Quan AU - Shen YQ FAU - Lu, Dan AU - Lu D FAU - Soelaiman, Sandriyana AU - Soelaiman S FAU - Grabarek, Zenon AU - Grabarek Z FAU - Bohm, Andrew AU - Bohm A FAU - Tang, Wei-Jen AU - Tang WJ LA - eng SI - PDB/1K8T SI - PDB/1K90 SI - PDB/1K93 PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Antigens, Bacterial) RN - 0 (Bacterial Toxins) RN - 0 (Calmodulin) RN - 0 (Exotoxins) RN - 0 (Macromolecular Substances) RN - 0 (anthrax toxin) RN - EC 4.6.1.1 (Adenylate Cyclase) SB - IM CIN - Nature. 2002 Jan 24;415(6870):373-4. PMID: 11807530 MH - Adenylate Cyclase/*chemistry/metabolism MH - Amino Acid Sequence MH - Animals MH - Antigens, Bacterial MH - Bacillus anthracis/*enzymology MH - Bacterial Toxins MH - Calmodulin/*chemistry/pharmacology MH - Catalytic Domain MH - Crystallography, X-Ray MH - Enzyme Activation MH - Exotoxins/*chemistry/metabolism MH - Humans MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Conformation MH - Structure-Activity Relationship EDAT- 2002/01/25 10:00 MHDA- 2002/03/16 10:01 CRDT- 2002/01/25 10:00 AID - 10.1038/415396a [doi] AID - 415396a [pii] PST - ppublish SO - Nature. 2002 Jan 24;415(6870):396-402. PMID- 14580193 OWN - NLM STAT- MEDLINE DA - 20031028 DCOM- 20031210 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 42 IP - 43 DP - 2003 Nov 4 TI - KIX-mediated assembly of the CBP-CREB-HTLV-1 tax coactivator-activator complex. PG - 12481-7 AB - The HTLV-1 transcriptional activator Tax is required for viral replication and pathogenesis. In concert with human CREB, Tax recruits the human transcriptional coactivator and histone acetyltransferase p300/CBP to the HTLV-1 promoter. Here we investigate the structural features of the interaction between Tax and the KIX domain of p300/CBP. Circular dichroism spectroscopy, nuclear magnetic resonance chemical shift perturbation mapping, and sedimentation equilibrium analysis show that KIX binds a Tax subdomain corresponding to residues 59-98 of Tax (called Tax(59-98)). Circular dichroism spectroscopy suggests that Tax(59-98) is intrinsically disordered (natively unfolded) in isolation and adopts an ordered conformation upon binding KIX. The interaction is disrupted by a single amino acid variation of Tax(59-98) in which leucine 68 is substituted with proline. Chemical shift perturbation mapping reveals that the Tax-binding surface of KIX is distinct from that utilized by CREB, and corresponds to the site of KIX that interacts with the human transcription factors c-Jun and mixed lineage leukemia protein (MLL). Sedimentation equilibrium analysis shows that Tax and the phosphorylated KID domain of CREB can simultaneously bind KIX to form a ternary 1:1:1 complex. The results provide a molecular description of the concerted recruitment of p300/CBP via the KIX domain by Tax and phosphorylated CREB during Tax-mediated gene expression. FAU - Vendel, Andrew C AU - Vendel AC AD - Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA. FAU - McBryant, Steven J AU - McBryant SJ FAU - Lumb, Kevin J AU - Lumb KJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cyclic AMP Response Element-Binding Protein) RN - 0 (Gene Products, tax) RN - 0 (Nuclear Proteins) RN - 0 (Trans-Activators) SB - IM MH - Circular Dichroism MH - Cyclic AMP Response Element-Binding Protein/*metabolism MH - Gene Products, tax/*metabolism MH - Humans MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*metabolism MH - Trans-Activators/*metabolism EDAT- 2003/10/29 05:00 MHDA- 2003/12/12 05:00 CRDT- 2003/10/29 05:00 AID - 10.1021/bi0353023 [doi] PST - ppublish SO - Biochemistry. 2003 Nov 4;42(43):12481-7. PMID- 15615633 OWN - NLM STAT- MEDLINE DA - 20041223 DCOM- 20050203 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1739 IP - 2-3 DP - 2005 Jan 3 TI - Potential structure/function relationships of predicted secondary structural elements of tau. PG - 140-9 AB - The microtubule-associated protein tau is believed to be a natively unfolded molecule with virtually no secondary structure. However, this protein self-associates into filamentous forms in various neurodegenerative diseases. Since these filamentous forms show a remarkable degree of higher order due to their regular widths and periodicity, it is widely speculated that tau does contain secondary structures that come together to form tertiary and quaternary structures in the filamentous form. The purpose of this review is to use the primary sequence of tau along with predictive methods in an effort to identify potential secondary structural elements that could be involved in its normal and pathological functions. Although there are few predicted structural elements in the tau molecule, these analyses should lead to a better understanding of the structure/function relationships that regulate the behavior of tau. FAU - Gamblin, T Chris AU - Gamblin TC AD - Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave. Lawrence, KS 66045, USA. gamblin@ku.edu LA - eng PT - Journal Article PT - Review PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (tau Proteins) SB - IM MH - Amino Acid Sequence MH - Humans MH - Microtubules/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Structure-Activity Relationship MH - tau Proteins/*chemistry/*physiology RF - 53 EDAT- 2004/12/24 09:00 MHDA- 2005/02/04 09:00 CRDT- 2004/12/24 09:00 PHST- 2004/05/28 [received] PHST- 2004/08/30 [accepted] AID - S0925-4439(04)00160-7 [pii] AID - 10.1016/j.bbadis.2004.08.013 [doi] PST - ppublish SO - Biochim Biophys Acta. 2005 Jan 3;1739(2-3):140-9. PMID- 19747489 OWN - NLM STAT- MEDLINE DA - 20091027 DCOM- 20091110 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 394 IP - 1 DP - 2009 Nov 20 TI - Mutations that alter RcdA surface residues decouple protein localization and CtrA proteolysis in Caulobacter crescentus. PG - 46-60 LID - 10.1016/j.jmb.2009.08.076 [doi] AB - Periodic activation and deactivation of the essential transcriptional regulator CtrA is necessary to drive cell cycle progression in Caulobacter crescentus. At the onset of DNA replication (the G1-S cell cycle transition), CtrA and the AAA+ protease ClpXP colocalize at one cell pole along with three accessory proteins, RcdA, CpdR, and PopA, and CtrA is rapidly degraded. RcdA is required for polar sequestration and regulated proteolysis of CtrA in vivo, but it does not stimulate CtrA degradation by ClpXP in vitro; thus, the function of RcdA is unknown. We determined the 2.9-A-resolution crystal structure of RcdA and generated structure-guided mutations in rcdA. We assayed the ability of each RcdA variant to support CtrA proteolysis and polar protein localization in Caulobacter. Deletion of an intrinsically disordered peptide at the C-terminus of RcdA prevents efficient CtrA degradation and blocks the transient localization of RcdA and CtrA at the cell pole. Surprisingly, substitutions in two groups of highly conserved, charged surface residues disrupt polar RcdA or CtrA localization but do not affect CtrA proteolysis. This is the first report showing that localization of RcdA can be decoupled from its effects on CtrA degradation. In addition, we used epistasis experiments to show that RcdA is still required for regulated CtrA proteolysis when all SsrA-tagged proteins, abundant substrates of ClpXP, are absent from the cell. Our results argue that RcdA stimulates CtrA proteolysis neither by localizing CtrA at the cell pole nor by preventing competition from SsrA-tagged substrates. FAU - Taylor, James A AU - Taylor JA AD - Department of Plant and Microbial Biology, 251 Koshland Hall, University of California, Berkeley, Berkeley, CA 94720-3102, USA. FAU - Wilbur, Jeremy D AU - Wilbur JD FAU - Smith, Stephen C AU - Smith SC FAU - Ryan, Kathleen R AU - Ryan KR LA - eng SI - PDB/3CTW PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20090908 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amino Acids) RN - 0 (Bacterial Proteins) RN - 0 (CtrA protein, Caulobacter) RN - 0 (DNA-Binding Proteins) RN - 0 (Mutant Proteins) RN - 0 (Transcription Factors) SB - IM MH - Amino Acids/*genetics MH - Bacterial Proteins/*chemistry/*metabolism MH - Caulobacter crescentus/cytology/*metabolism MH - Cell Polarity MH - Crystallography, X-Ray MH - DNA-Binding Proteins/*metabolism MH - G1 Phase MH - Half-Life MH - Mutant Proteins/chemistry/metabolism MH - Mutation/*genetics MH - Protein Binding MH - Protein Multimerization MH - *Protein Processing, Post-Translational MH - Protein Structure, Secondary MH - Protein Transport MH - S Phase MH - Sequence Deletion MH - Structure-Activity Relationship MH - Surface Properties MH - Transcription Factors/*metabolism EDAT- 2009/09/15 06:00 MHDA- 2009/11/11 06:00 CRDT- 2009/09/15 06:00 PHST- 2009/05/13 [received] PHST- 2009/08/24 [revised] PHST- 2009/08/27 [accepted] PHST- 2009/09/08 [aheadofprint] AID - S0022-2836(09)01082-1 [pii] AID - 10.1016/j.jmb.2009.08.076 [doi] PST - ppublish SO - J Mol Biol. 2009 Nov 20;394(1):46-60. doi: 10.1016/j.jmb.2009.08.076. Epub 2009 Sep 8. PMID- 14645906 OWN - NLM STAT- MEDLINE DA - 20031203 DCOM- 20040120 LR - 20061115 IS - 0022-1317 (Print) IS - 0022-1317 (Linking) VI - 84 IP - Pt 12 DP - 2003 Dec TI - Structural disorder and modular organization in Paramyxovirinae N and P. PG - 3239-52 AB - The existence and extent of disorder within the replicative complex (N, P and the polymerase, L) of Paramyxovirinae were investigated, drawing on the discovery that the N-terminal moiety of the phosphoprotein (P) and the C-terminal moiety of the nucleoprotein (N) of measles virus are intrinsically unstructured. We show that intrinsic disorder is a widespread property within Paramyxovirinae N and P, using a combination of different computational approaches relying on different physico-chemical concepts. Notably, experimental support that has often gone unnoticed for most of the predictions has been found in the literature. Identification of disordered regions allows the unveiling of a common organization in all Paramyxovirinae P, which are composed of six modules defined on the basis of structure or sequence conservation. The possible functional significance of intrinsic disorder is discussed in the light of experimental data, which show that unstructured regions of P and N are involved in numerous interactions with several protein and protein-RNA partners. This study provides a contribution to the rather poorly investigated field of intrinsically disordered proteins and helps in targeting protein domains for structural studies. FAU - Karlin, David AU - Karlin D AD - Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS et Universite Aix-Marseille I et II, ESIL, Campus de Luminy, 13288 Marseille Cedex 09, France. FAU - Ferron, Francois AU - Ferron F FAU - Canard, Bruno AU - Canard B FAU - Longhi, Sonia AU - Longhi S LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Gen Virol JT - The Journal of general virology JID - 0077340 RN - 0 (DNA-Binding Proteins) RN - 0 (Drosophila Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Nucleoproteins) RN - 0 (Phosphoproteins) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Transcription Factors) RN - 0 (Viral Proteins) RN - 0 (pnt protein, Drosophila) SB - IM MH - Amino Acid Sequence MH - DNA-Binding Proteins MH - Drosophila Proteins MH - Molecular Sequence Data MH - Morbillivirus/chemistry MH - Nerve Tissue Proteins MH - Nucleoproteins/*chemistry/genetics MH - Paramyxovirinae/*chemistry/genetics MH - Phosphoproteins/*chemistry MH - Protein Structure, Secondary MH - Proto-Oncogene Proteins/chemistry MH - Rubulavirus/chemistry MH - Sequence Alignment MH - Transcription Factors MH - Viral Proteins/*chemistry/genetics EDAT- 2003/12/04 05:00 MHDA- 2004/01/21 05:00 CRDT- 2003/12/04 05:00 PST - ppublish SO - J Gen Virol. 2003 Dec;84(Pt 12):3239-52. PMID- 23289531 OWN - NLM STAT- MEDLINE DA - 20130130 DCOM- 20130723 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 4 DP - 2013 Jan 30 TI - Energetic basis of uncoupling folding from binding for an intrinsically disordered protein. PG - 1288-94 LID - 10.1021/ja305081b [doi] AB - Intrinsically disordered proteins (IDPs) are proteins that lack a unique three-dimensional structure in their native state. Many have, however, been found to fold into a defined structure when interacting with specific binding partners. The energetic implications of such behavior have been widely discussed, yet experimental thermodynamic data is scarce. We present here a thorough thermodynamic and structural study of the binding of an IDP (antitoxin CcdA) to its molecular target (gyrase poison CcdB). We show that the binding-coupled folding of CcdA is driven by a combination of specific intramolecular interactions that favor the final folded structure and a less specific set of intermolecular contacts that provide a desolvation entropy boost. The folded structure of the bound IDP appears to be defined largely by its own amino acid sequence, with the binding partner functioning more as a facilitator than a mold to conform to. On the other hand, specific intermolecular interactions do increase the binding affinity up to the picomolar range. Overall, this study shows how an IDP can achieve very strong and structurally well-defined binding and it provides significant insight into the molecular forces that enable such binding properties. FAU - Drobnak, Igor AU - Drobnak I AD - Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Askerceva 5, 1000 Ljubljana, Slovenia. FAU - De Jonge, Natalie AU - De Jonge N FAU - Haesaerts, Sarah AU - Haesaerts S FAU - Vesnaver, Gorazd AU - Vesnaver G FAU - Loris, Remy AU - Loris R FAU - Lah, Jurij AU - Lah J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130116 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Proteins) SB - IM MH - Binding Sites MH - Models, Molecular MH - Protein Conformation MH - Protein Folding MH - Proteins/*chemistry MH - *Thermodynamics EDAT- 2013/01/08 06:00 MHDA- 2013/07/24 06:00 CRDT- 2013/01/08 06:00 PHST- 2013/01/16 [aheadofprint] AID - 10.1021/ja305081b [doi] PST - ppublish SO - J Am Chem Soc. 2013 Jan 30;135(4):1288-94. doi: 10.1021/ja305081b. Epub 2013 Jan 16. PMID- 21672523 OWN - NLM STAT- MEDLINE DA - 20110711 DCOM- 20110916 LR - 20131121 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 410 IP - 3 DP - 2011 Jul 8 TI - The disordered C-terminus of the RNA polymerase II phosphatase FCP1 is partially helical in the unbound state. PG - 461-5 LID - 10.1016/j.bbrc.2011.05.160 [doi] AB - Intrinsically disordered proteins (IDPs) lack unique 3D structures under native conditions and yet retain critical functions. Recycling of RNA Polymerase II after transcription is promoted by an interaction between the winged helix domain of RAP74, a component of the general transcription factor IIF (TFIIF), and the C-terminus of the TFIIF-associating CTD phosphatase (FCP1). Sixteen residues from the C-terminus of FCP1 form an alpha-helix in the complex, but the protein is otherwise agreed in the literature to be intrinsically disordered. Here we show through CD and recently developed carbon-detected NMR that, although FCP1 is intrinsically disordered, the above 16 residues composing the RAP74 binding surface form nascent alpha-helical structure in the unbound state. We further show retention of general FCP1 disorder and the nascent helical content in HeLa extract, establishing cellular relevance. The conformational bias observed leads to a mechanistic proposal for FCP1's transition from a disordered ensemble to an ordered conformation upon binding. CI - Copyright (c) 2011 Elsevier Inc. All rights reserved. FAU - Lawrence, Chad W AU - Lawrence CW AD - Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802, USA. cwl137@psu.edu FAU - Bonny, Alain AU - Bonny A FAU - Showalter, Scott A AU - Showalter SA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110606 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Cell Extracts) RN - 0 (Nuclear Proteins) RN - 0 (Transcription Factors, TFII) RN - 0 (transcription factor TFIIF) RN - 8W8T17847W (Urea) RN - EC 3.1.3.16 (CTDSP2 protein, human) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - K3R6ZDH4DU (Dextrans) SB - IM MH - Cell Extracts/chemistry MH - Circular Dichroism MH - Dextrans/chemistry MH - HeLa Cells MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*chemistry MH - Phosphoprotein Phosphatases/*chemistry MH - Protein Binding MH - Protein Structure, Secondary MH - Transcription Factors, TFII/chemistry MH - Urea/chemistry EDAT- 2011/06/16 06:00 MHDA- 2011/09/17 06:00 CRDT- 2011/06/16 06:00 PHST- 2011/05/20 [received] PHST- 2011/05/31 [accepted] PHST- 2011/06/06 [aheadofprint] AID - S0006-291X(11)00944-2 [pii] AID - 10.1016/j.bbrc.2011.05.160 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2011 Jul 8;410(3):461-5. doi: 10.1016/j.bbrc.2011.05.160. Epub 2011 Jun 6. PMID- 10329170 OWN - NLM STAT- MEDLINE DA - 19990609 DCOM- 19990609 LR - 20140219 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 288 IP - 4 DP - 1999 May 14 TI - Crystal structure of the two N-terminal domains of g3p from filamentous phage fd at 1.9 A: evidence for conformational lability. PG - 649-57 AB - Infection of Escherichia coli by filamentous bacteriophages is mediated by the minor phage coat protein g3p and involves two distinct cellular receptors, the F' pilus and the periplasmic protein TolA. Recently we have shown that the two receptors are contacted in a sequential manner, such that binding of TolA by the N-terminal domain g3p-D1 is conditional on a primary interaction of the second g3p domain D2 with the F' pilus. In order to better understand this process, we have solved the crystal structure of the g3p-D1D2 fragment (residues 2-217) from filamentous phage fd to 1.9 A resolution and compared it to the recently published structure of the same fragment from the related Ff phage M13. While the structure of individual domains D1 and D2 of the two phages are very similar (rms<0.7 A), there is comparatively poor agreement for the overall D1D2 structure (rms>1.2 A). This is due to an apparent movement of domain D2 with respect to D1, which results in a widening of the inter-domain groove compared to the structure of the homologous M13 protein. The movement of D2 can be described as a rigid-body rotation around a hinge located at the end of a short anti-parallel beta-sheet connecting domains D1 and D2. Structural flexibility of at least parts of the D1D2 structure was also suggested by studying the thermal unfolding of g3p: the TolA binding site on D1, while fully blocked by D2 at 37 degrees C, becomes accessible after incubation at temperatures as low as 45 degrees C. Our results support a model for the early steps of phage infection whereby exposure of the coreceptor binding site on D1 is facilitated by a conformational change in the D1D2 structure, which in vivo is induced by binding to the F' pilus on the host cell and which can be mimicked in vitro by thermal unfolding. CI - Copyright 1999 Academic Press. FAU - Holliger, P AU - Holliger P AD - MRC Centre for Protein Engineering, Cambridge CB2 2QH, UK. ph1@mrc-lmb.cam.ac.uk FAU - Riechmann, L AU - Riechmann L FAU - Williams, R L AU - Williams RL LA - eng SI - PDB/2G3P GR - MC_U105184308/Medical Research Council/United Kingdom PT - Journal Article PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Capsid Proteins) RN - 0 (DNA Primers) RN - 0 (DNA-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Viral Fusion Proteins) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Capsid Proteins MH - Crystallography, X-Ray MH - DNA Primers MH - DNA-Binding Proteins/*chemistry MH - Inovirus/*chemistry MH - Molecular Sequence Data MH - Protein Conformation MH - Recombinant Proteins/chemistry MH - Viral Fusion Proteins/*chemistry EDAT- 1999/05/18 MHDA- 1999/05/18 00:01 CRDT- 1999/05/18 00:00 AID - S0022-2836(99)92720-1 [pii] AID - 10.1006/jmbi.1999.2720 [doi] PST - ppublish SO - J Mol Biol. 1999 May 14;288(4):649-57. PMID- 8202136 OWN - NLM STAT- MEDLINE DA - 19940705 DCOM- 19940705 LR - 20131121 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 369 IP - 6480 DP - 1994 Jun 9 TI - Crystal structure of human chorionic gonadotropin. PG - 455-61 AB - The three-dimensional structure of human chorionic gonadotropin shows that each of its two different subunits has a similar topology, with three disulphide bonds forming a cystine knot. This same folding motif is found in some protein growth factors. The heterodimer is stabilized by a segment of the beta-subunit which wraps around the alpha-subunit and is covalently linked like a seat belt by the disulphide Cys 26-Cys 110. This extraordinary feature appears to be essential not only for the association of these heterodimers but also for receptor binding by the glycoprotein hormones. FAU - Lapthorn, A J AU - Lapthorn AJ AD - Department of Chemistry, University of Glasgow, UK. FAU - Harris, D C AU - Harris DC FAU - Littlejohn, A AU - Littlejohn A FAU - Lustbader, J W AU - Lustbader JW FAU - Canfield, R E AU - Canfield RE FAU - Machin, K J AU - Machin KJ FAU - Morgan, F J AU - Morgan FJ FAU - Isaacs, N W AU - Isaacs NW LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Chorionic Gonadotropin) RN - 0 (Disulfides) RN - 0 (Glycoproteins) RN - 0 (Growth Substances) RN - 0 (Hormones) RN - 0 (Receptors, LH) RN - 48TCX9A1VT (Cystine) SB - IM CIN - Nature. 1994 Jun 9;369(6480):438-9. PMID: 8202130 MH - Amino Acid Sequence MH - Carbohydrate Conformation MH - Chorionic Gonadotropin/*chemistry/metabolism MH - Computer Graphics MH - Crystallography, X-Ray MH - Cystine/chemistry MH - Disulfides/chemistry MH - Glycoproteins/chemistry MH - Growth Substances/chemistry MH - Hormones/chemistry MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Folding MH - Receptors, LH/metabolism EDAT- 1994/06/09 MHDA- 1994/06/09 00:01 CRDT- 1994/06/09 00:00 AID - 10.1038/369455a0 [doi] PST - ppublish SO - Nature. 1994 Jun 9;369(6480):455-61. PMID- 18028445 OWN - NLM STAT- MEDLINE DA - 20080104 DCOM- 20080403 LR - 20140921 IS - 1742-464X (Print) IS - 1742-464X (Linking) VI - 275 IP - 1 DP - 2008 Jan TI - Structure-function analysis of the filamentous actin binding domain of the neuronal scaffolding protein spinophilin. PG - 59-68 AB - Spinophilin, a neuronal scaffolding protein, is essential for synaptic transmission, and functions to target protein phosphatase-1 to distinct subcellular locations in dendritic spines. It is vital for the regulation of dendritic spine formation and motility, and functions by regulating glutamatergic receptors and binding to filamentous actin. To investigate its role in regulating actin cytoskeletal structure, we initiated structural studies of the actin binding domain of spinophilin. We demonstrate that the spinophilin actin binding domain is intrinsically unstructured, and that, with increasing C-terminal length, the domain shows augmented secondary structure content. Further characterization confirmed the previously known crosslinking activity and uncovered a novel filamentous actin pointed-end capping activity. Both of these functions seem to be fully contained within residues 1-154 of spinophilin. FAU - Schuler, Herwig AU - Schuler H AD - Max Delbruck Center for Molecular Medicine, Berlin-Buch, Germany. herwig.schueler@med.uni-heidelberg.de FAU - Peti, Wolfgang AU - Peti W LA - eng GR - R01 NS056128/NS/NINDS NIH HHS/United States GR - R01 NS056128-01A2/NS/NINDS NIH HHS/United States GR - R01 NS056128-02/NS/NINDS NIH HHS/United States GR - R01NS056128/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20071120 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Microfilament Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (neurabin) SB - IM MH - Animals MH - Circular Dichroism MH - Cloning, Molecular MH - Microfilament Proteins/*chemistry/*metabolism MH - Nerve Tissue Proteins/*chemistry/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Rats MH - Structure-Activity Relationship PMC - PMC2927859 MID - NIHMS228921 OID - NLM: NIHMS228921 OID - NLM: PMC2927859 EDAT- 2007/11/22 09:00 MHDA- 2008/04/04 09:00 CRDT- 2007/11/22 09:00 PHST- 2007/11/20 [aheadofprint] AID - EJB6171 [pii] AID - 10.1111/j.1742-4658.2007.06171.x [doi] PST - ppublish SO - FEBS J. 2008 Jan;275(1):59-68. Epub 2007 Nov 20. PMID- 21196244 OWN - NLM STAT- MEDLINE DA - 20110103 DCOM- 20110421 LR - 20130729 IS - 1093-4715 (Electronic) IS - 1093-4715 (Linking) VI - 16 DP - 2011 TI - Biological properties of the PrP-like Shadoo protein. PG - 1505-16 AB - The SPRN gene encodes the Shadoo glycoprotein (Sho), a central nervous system-expressed member of the prion protein superfamily. Sho has similarity to two features within PrPC's natively unstructured N-terminus, a hydrophobic domain and tandem repeats with positively charged residues. Indeed, scrutiny of Sho's biochemical properties in uninfected cells has revealed overlaps with the properties of PrPC, these including shared protein binding partners. SPRN is conserved in mammals, as is the prion gene PRNP, but in sheep SPRN and PRNP are both marked by polymorphic variation, suggestive of a shared selection pressure within these scrapie disease-prone livestock animals. In rodent models of prion disease there are reduced levels of Sho in infected tissues, defining a form of cross-regulation between full-length Sho holoprotein and PrPSc. In human prion disease an SPRN signal peptide polymorphism is associated with risk for sporadic Creutzfeldt-Jakob Disease (CJD), while two patients with early-onset variant CJD carried putatively inactive SPRN alleles. Further investigation of Sho as a novel tracer or modifier for the accumulation of pathologic forms of PrP may prove advantageous. FAU - Daude, Nathalie AU - Daude N AD - Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, Canada. FAU - Westaway, David AU - Westaway D LA - eng GR - MOP36377/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20110101 PL - United States TA - Front Biosci (Landmark Ed) JT - Frontiers in bioscience (Landmark edition) JID - 101612996 RN - 0 (GPI-Linked Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (PrPC Proteins) RN - 0 (Prions) RN - 0 (SPRN protein, human) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cattle MH - Down-Regulation MH - GPI-Linked Proteins/biosynthesis/genetics/physiology MH - Humans MH - Mice MH - Nerve Tissue Proteins/biosynthesis/genetics/*physiology MH - PrPC Proteins/biosynthesis MH - Prion Diseases/genetics MH - Prions/*genetics MH - Scrapie/etiology MH - Sheep MH - Sheep Diseases/etiology MH - Tissue Distribution EDAT- 2011/01/05 06:00 MHDA- 2011/04/22 06:00 CRDT- 2011/01/04 06:00 AID - 3801 [pii] PST - epublish SO - Front Biosci (Landmark Ed). 2011 Jan 1;16:1505-16. PMID- 9927655 OWN - NLM STAT- MEDLINE DA - 19990305 DCOM- 19990305 LR - 20140617 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 96 IP - 3 DP - 1999 Feb 2 TI - Structure of the ternary complex of human 17beta-hydroxysteroid dehydrogenase type 1 with 3-hydroxyestra-1,3,5,7-tetraen-17-one (equilin) and NADP+. PG - 840-5 AB - Excess 17beta-estradiol (E2), the most potent of human estrogens, is known to act as a stimulus for the growth of breast tumors. Human estrogenic 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1), which catalyzes the reduction of inactive estrone (E1) to the active 17beta-estradiol in breast tissues, is a key enzyme responsible for elevated levels of E2 in breast tumor tissues. We present here the structure of the ternary complex of 17beta-HSD1 with the cofactor NADP+ and 3-hydroxyestra-1,3,5,7-tetraen-17-one (equilin), an equine estrogen used in estrogen replacement therapy. The ternary complex has been crystallized with a homodimer, the active form of the enzyme, in the asymmetric unit. Structural and kinetic data presented here show that the 17beta-HSD1-catalyzed reduction of E1 to E2 in vitro is specifically inhibited by equilin. The crystal structure determined at 3.0-A resolution reveals that the equilin molecule is bound at the active site in a mode similar to the binding of substrate. The orientation of the 17-keto group with respect to the nicotinamide ring of NADP+ and catalytic residues Tyr-155 and Ser-142 is different from that of E2 in the 17beta-HSD1-E2 complex. The ligand and substrate-entry loop densities are well defined in one subunit. The substrate-entry loop adopts a closed conformation in this subunit. The result demonstrates that binding of equilin at the active site of 17beta-HSD1 is the basis for inhibition of E1-to-E2 reduction by this equine estrogen in vitro. One possible outcome of estrogen replacement therapy in vivo could be reduction of E2 levels in breast tissues and hence the reduced risk of estrogen-dependent breast cancer. FAU - Sawicki, M W AU - Sawicki MW AD - Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA. FAU - Erman, M AU - Erman M FAU - Puranen, T AU - Puranen T FAU - Vihko, P AU - Vihko P FAU - Ghosh, D AU - Ghosh D LA - eng SI - PDB/1EQU GR - DK26546/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Macromolecular Substances) RN - 0 (Recombinant Proteins) RN - 08O86EX0J4 (Equilin) RN - 53-59-8 (NADP) RN - EC 1.1.1.62 (Estradiol Dehydrogenases) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Crystallography, X-Ray MH - Dimerization MH - Equilin/chemistry/*metabolism MH - Estradiol Dehydrogenases/*chemistry/*metabolism MH - Humans MH - Least-Squares Analysis MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - NADP/chemistry/*metabolism MH - *Protein Conformation MH - *Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Spodoptera MH - Transfection PMC - PMC15312 OID - NLM: PMC15312 EDAT- 1999/02/03 MHDA- 1999/02/03 00:01 CRDT- 1999/02/03 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 1999 Feb 2;96(3):840-5. PMID- 24086133 OWN - NLM STAT- MEDLINE DA - 20131002 DCOM- 20140428 LR - 20141112 IS - 1553-7374 (Electronic) IS - 1553-7366 (Linking) VI - 9 IP - 9 DP - 2013 TI - Atomic resolution description of the interaction between the nucleoprotein and phosphoprotein of Hendra virus. PG - e1003631 LID - 10.1371/journal.ppat.1003631 [doi] AB - Hendra virus (HeV) is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The HeV genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid. Recruitment of the viral polymerase onto the nucleocapsid template relies on the interaction between the C-terminal domain, N(TAIL), of N and the C-terminal X domain, XD, of the polymerase co-factor phosphoprotein (P). Here, we provide an atomic resolution description of the intrinsically disordered N(TAIL) domain in its isolated state and in intact nucleocapsids using nuclear magnetic resonance (NMR) spectroscopy. Using electron microscopy, we show that HeV nucleocapsids form herringbone-like structures typical of paramyxoviruses. We also report the crystal structure of XD of P that consists of a three-helix bundle. We study the interaction between N(TAIL) and XD using NMR titration experiments and provide a detailed mapping of the reciprocal binding sites. We show that the interaction is accompanied by alpha-helical folding of the molecular recognition element of N(TAIL) upon binding to a hydrophobic patch on the surface of XD. Finally, using solution NMR, we investigate the interaction between intact nucleocapsids and XD. Our results indicate that monomeric XD binds to N(TAIL) without triggering an additional unwinding of the nucleocapsid template. The present results provide a structural description at the atomic level of the protein-protein interactions required for transcription and replication of HeV, and the first direct observation of the interaction between the X domain of P and intact nucleocapsids in Paramyxoviridae. FAU - Communie, Guillaume AU - Communie G AD - Universite Grenoble Alpes, Institut de Biologie Structurale (IBS), Grenoble, France ; CEA, DSV, IBS, Grenoble, France ; CNRS, IBS, Grenoble, France ; Universite Grenoble Alpes, UVHCI, Grenoble, France ; CNRS, UVHCI, Grenoble, France ; Unit for Virus Host Cell Interactions, Universite Grenoble Alpes-EMBL-CNRS, Grenoble, France. FAU - Habchi, Johnny AU - Habchi J FAU - Yabukarski, Filip AU - Yabukarski F FAU - Blocquel, David AU - Blocquel D FAU - Schneider, Robert AU - Schneider R FAU - Tarbouriech, Nicolas AU - Tarbouriech N FAU - Papageorgiou, Nicolas AU - Papageorgiou N FAU - Ruigrok, Rob W H AU - Ruigrok RW FAU - Jamin, Marc AU - Jamin M FAU - Jensen, Malene Ringkjobing AU - Jensen MR FAU - Longhi, Sonia AU - Longhi S FAU - Blackledge, Martin AU - Blackledge M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130926 PL - United States TA - PLoS Pathog JT - PLoS pathogens JID - 101238921 RN - 0 (Nucleocapsid Proteins) RN - 0 (Phosphoproteins) SB - IM MH - Crystallography, X-Ray MH - Hendra Virus/*chemistry/genetics/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Microscopy, Electron, Transmission MH - Nucleocapsid Proteins/*chemistry/genetics/metabolism MH - Phosphoproteins/*chemistry/genetics/metabolism MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary PMC - PMC3784471 OID - NLM: PMC3784471 EDAT- 2013/10/03 06:00 MHDA- 2014/04/29 06:00 CRDT- 2013/10/03 06:00 PHST- 2013/09 [ecollection] PHST- 2013/04/18 [received] PHST- 2013/08/01 [accepted] PHST- 2013/09/26 [epublish] AID - 10.1371/journal.ppat.1003631 [doi] AID - PPATHOGENS-D-13-01021 [pii] PST - ppublish SO - PLoS Pathog. 2013;9(9):e1003631. doi: 10.1371/journal.ppat.1003631. Epub 2013 Sep 26. PMID- 8142349 OWN - NLM STAT- MEDLINE DA - 19940502 DCOM- 19940502 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 33 IP - 12 DP - 1994 Mar 29 TI - Solution structure and dynamics of ras p21.GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy. PG - 3515-31 AB - A high-resolution solution structure of the GDP form of a truncated version of the ras p21 protein (residues 1-166) has been determined using NMR spectroscopy. Ras p21 is the product of the human ras protooncogene and a member of a ubiquitous eukaryotic gene family which is highly conserved in evolution. A virtually complete assignment (13C, 15N, and 1H), including stereospecific assignments of 54 C beta methylene protons and 10 C gamma methyl protons of valine residues, was obtained by analysis of three- and four-dimensional (3D and 4D) heteronuclear NMR spectra using a newly developed 3D/4D version of the ANSIG software. A total of 40 converged structures were computed from 3369 experimental restraints consisting of 3,167 nuclear Overhauser effect (NOE) derived distances, 14 phi and 54 chi 1 torsion angle restraints, 109 hydrogen bond distance restraints, and an additional 25 restraints derived from literature data defining interactions between the GDP ligand, the magnesium ion, and the protein. The structure in the region of residues 58-66 (loop L4), and to a lesser degree residues 30-38 (loop L2), is ill-defined. Analysis of the dynamics of the backbone 15N nuclei in the protein showed that residues within the regions 58-66, 107-109, and, to a lesser degree, 30-38 are dynamically mobile on the nanosecond time scale. The root mean square (rms) deviations between the 40 solution structures and the mean atomic coordinates are 0.78 A for the backbone heavy atoms and 1.29 A for all non-hydrogen atoms if all residues (1-166) are included in the analysis. If residues 30-38 and residues 58-66 are excluded from the analysis, the rms deviations are reduced to 0.55 and 1.00 A, respectively. The structure was compared to the most highly refined X-ray crystal structure of ras p21.GDP (1-189) [Milburn, M. V., Tong, L., de Vos, A. M., Brunger, A. T., Yamaizumi, Z., Nishimura, S., & Kim, S.-H. (1990) Science 24, 939-945]. The structures are very similar except in the regions found to be mobile by NMR spectroscopy. In addition, the second alpha-helix (helix-2) has a slightly different orientation. The rms deviation between the average of the solution structures and the X-ray crystal structure is 0.94 A for the backbone heavy atoms if residues 31-37 and residues 59-73 are excluded from the analysis. FAU - Kraulis, P J AU - Kraulis PJ AD - Department of Biochemistry, University of Cambridge, U.K. FAU - Domaille, P J AU - Domaille PJ FAU - Campbell-Burk, S L AU - Campbell-Burk SL FAU - Van Aken, T AU - Van Aken T FAU - Laue, E D AU - Laue ED LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Solutions) RN - 146-91-8 (Guanosine Diphosphate) RN - 86-01-1 (Guanosine Triphosphate) RN - 9DLQ4CIU6V (Proline) RN - AE28F7PNPL (Methionine) RN - EC 3.6.5.2 (Proto-Oncogene Proteins p21(ras)) RN - I38ZP9992A (Magnesium) RN - TE7660XO1C (Glycine) SB - IM MH - Chemistry, Physical MH - Crystallography, X-Ray MH - Glycine/chemistry MH - Guanosine Diphosphate/*metabolism MH - Guanosine Triphosphate/metabolism MH - Hydrogen Bonding MH - Magnesium/metabolism MH - *Magnetic Resonance Spectroscopy MH - Methionine/chemistry MH - Models, Molecular MH - Molecular Structure MH - Physicochemical Phenomena MH - Proline/chemistry MH - Proto-Oncogene Proteins p21(ras)/*chemistry/metabolism MH - Software MH - *Solutions EDAT- 1994/03/29 MHDA- 1994/03/29 00:01 CRDT- 1994/03/29 00:00 PST - ppublish SO - Biochemistry. 1994 Mar 29;33(12):3515-31. PMID- 24030713 OWN - NLM STAT- MEDLINE DA - 20131209 DCOM- 20140213 LR - 20141112 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 41 IP - 22 DP - 2013 Dec TI - Dissecting the oligonucleotide binding properties of a disordered chaperone protein using surface plasmon resonance. PG - 10414-25 LID - 10.1093/nar/gkt792 [doi] AB - We have used surface plasmon resonance to investigate the nucleic acid binding properties of the core protein of hepatitis C virus, a disordered protein believed to chaperone the genomic RNA. It was previously shown that a peptide (peptide E) corresponding to the association of two basic clusters of core enhances the annealing and the dimerization of nucleic acid fragments derived from a stem loop (SL2) in the 3' untranslated region of the hepatitis C virus genome. However, strong aggregation of nucleic acids by core or peptide E in the excess of the latter precluded the characterization of their binding parameters up to now. By careful design of surface plasmon resonance experiments, we obtained accurate binding parameters for the interaction of peptide E with SL2-derived oligonucleotides of different lengths and sequences, in form of stem-loop, duplex or strand. Peptide E was found to bind in a salt dependent manner to all oligonucleotides assayed. Affinity data identify at least two binding modes, of which one is independent of sequence/structure, and the other is specific to the SL2 stem-loop fold. Stoichiometry data support a multi-motif binding model allowing formation of higher-order complexes. We propose that the modular binding mode demonstrated for structured RNA-binding proteins also applies to this disordered chaperone and is relevant to its activity. FAU - Baltzinger, Mireille AU - Baltzinger M AD - Biotechnologie et signalisation cellulaire, Universite de Strasbourg, CNRS, BP10413, 67412 Illkirch, France and Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculte de Pharmacie, Universite de Strasbourg, 67401, Illkirch, France. FAU - Sharma, Kamal Kant AU - Sharma KK FAU - Mely, Yves AU - Mely Y FAU - Altschuh, Daniele AU - Altschuh D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130911 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Oligodeoxyribonucleotides) RN - 0 (Oligoribonucleotides) RN - 0 (Peptides) RN - 0 (RNA-Binding Proteins) RN - 0 (Viral Core Proteins) RN - 0 (nucleocapsid protein, Hepatitis C virus) SB - IM MH - Intrinsically Disordered Proteins/chemistry/*metabolism MH - Oligodeoxyribonucleotides/metabolism MH - Oligoribonucleotides/chemistry/*metabolism MH - Peptides/chemistry/metabolism MH - Protein Binding MH - RNA-Binding Proteins/chemistry/*metabolism MH - Surface Plasmon Resonance MH - Viral Core Proteins/chemistry/*metabolism PMC - PMC3905882 OID - NLM: PMC3905882 EDAT- 2013/09/14 06:00 MHDA- 2014/02/14 06:00 CRDT- 2013/09/14 06:00 PHST- 2013/09/11 [aheadofprint] AID - gkt792 [pii] AID - 10.1093/nar/gkt792 [doi] PST - ppublish SO - Nucleic Acids Res. 2013 Dec;41(22):10414-25. doi: 10.1093/nar/gkt792. Epub 2013 Sep 11. PMID- 19075750 OWN - NLM STAT- MEDLINE DA - 20081216 DCOM- 20090824 LR - 20140916 IS - 1389-2037 (Print) IS - 1389-2037 (Linking) VI - 9 IP - 6 DP - 2008 Dec TI - The retinal cGMP phosphodiesterase gamma-subunit - a chameleon. PG - 611-25 AB - Intrinsically disordered proteins (IDPs) represent an emerging class of proteins (or domains) that are characterized by a lack of ordered secondary and tertiary structure. This group of proteins has recently attracted tremendous interest primarily because of a unique feature: they can bind to different targets due to their structural plasticity, and thus fulfill diverse functions. The inhibitory gamma-subunit (PDEgamma) of retinal PDE6 is an intriguing IDP, of which unique protein properties are being uncovered. PDEgamma critically regulates the turn on as well as the turn off of visual signaling through alternate interactions with the PDE6 catalytic core, transducin, and the regulator of G protein signaling RGS9-1. The intrinsic disorder of PDEgamma does not compromise, but rather, optimizes its functionality. PDEgamma "curls up" when free in solution but "stretches out" when binding with the PDE6 catalytic core. Conformational changes of PDEgamma also likely occur in its C-terminal PDE6-binding region upon interacting with transducin during PDE6 activation. Growing evidence shows that PDEgamma is also a player in non-phototransduction pathways, suggesting additional protein targets. Thus, PDEgamma is highly likely to be adaptive in its structure and function, hence a "chameleon". FAU - Guo, Lian-Wang AU - Guo LW AD - Department of Pharmacology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA. lianwangguo@wisc.edu FAU - Ruoho, Arnold E AU - Ruoho AE LA - eng GR - GM033138/GM/NIGMS NIH HHS/United States GR - R01 GM033138/GM/NIGMS NIH HHS/United States GR - R01 GM033138-32/GM/NIGMS NIH HHS/United States GR - R01 GM033138-33/GM/NIGMS NIH HHS/United States GR - R01 GM033138-34/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review PL - Netherlands TA - Curr Protein Pept Sci JT - Current protein & peptide science JID - 100960529 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Membrane Proteins) RN - 0 (RGS9BP protein, human) RN - EC 3.1.4.35 (Cyclic Nucleotide Phosphodiesterases, Type 6) RN - EC 3.6.1.- (Transducin) SB - IM MH - Adaptor Proteins, Signal Transducing MH - Animals MH - Cyclic Nucleotide Phosphodiesterases, Type 6/*chemistry/*metabolism MH - Enzyme Activation MH - Eye Diseases/*enzymology MH - Humans MH - Membrane Proteins/metabolism MH - Transducin/metabolism RF - 220 PMC - PMC3219533 MID - NIHMS324701 OID - NLM: NIHMS324701 OID - NLM: PMC3219533 EDAT- 2008/12/17 09:00 MHDA- 2009/08/25 09:00 CRDT- 2008/12/17 09:00 PST - ppublish SO - Curr Protein Pept Sci. 2008 Dec;9(6):611-25. PMID- 16908029 OWN - NLM STAT- MEDLINE DA - 20060828 DCOM- 20061107 LR - 20140909 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 362 IP - 2 DP - 2006 Sep 15 TI - Folding of the repeat domain of tau upon binding to lipid surfaces. PG - 312-26 AB - The microtubule-associated protein tau is impacted in neurodegeneration and dementia through its deposition in the form of paired helical filaments in Alzheimer's disease neurofibrillary tangles and through mutations linking it to the autosomal dominant disorder frontotemporal dementia with Parkinsonism. When isolated in solution tau is intrinsically unstructured and does not fold, while the conformation of the protein in the microtubule-bound state remains uncharacterized. Here we show that the repeat region of tau, which has been reported both to mediate tau microtubule interactions and to constitute the proteolysis-resistant core of disease-associated tau aggregates, associates with lipid micelles and vesicles and folds into an ordered structure upon doing so. In addition to providing the first structural insights into a folded state of tau, our results support a role for lipid membranes in mediating tau function and tau pathology. FAU - Barre, Patrick AU - Barre P AD - Department of Biochemistry and Program in Structural Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA. FAU - Eliezer, David AU - Eliezer D LA - eng GR - AG025440/AG/NIA NIH HHS/United States GR - GM66354/GM/NIGMS NIH HHS/United States GR - R01 AG019391/AG/NIA NIH HHS/United States GR - R01 AG019391-06/AG/NIA NIH HHS/United States GR - R01 AG025440/AG/NIA NIH HHS/United States GR - R01 AG025440-01A1/AG/NIA NIH HHS/United States GR - R37 AG019391/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20060715 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Lipids) RN - 0 (Peptide Fragments) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Fusion Proteins) RN - 0 (tau Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Circular Dichroism MH - Humans MH - Lipids/*chemistry MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/*chemistry/genetics/metabolism MH - Protein Binding MH - *Protein Conformation MH - *Protein Folding MH - Protein Isoforms/chemistry/genetics/metabolism MH - Recombinant Fusion Proteins/chemistry/genetics/metabolism MH - Surface Properties MH - tau Proteins/*chemistry/genetics/metabolism EDAT- 2006/08/16 09:00 MHDA- 2006/11/09 09:00 CRDT- 2006/08/16 09:00 PHST- 2006/05/15 [received] PHST- 2006/07/11 [revised] PHST- 2006/07/11 [accepted] PHST- 2006/07/15 [aheadofprint] AID - S0022-2836(06)00870-9 [pii] AID - 10.1016/j.jmb.2006.07.018 [doi] PST - ppublish SO - J Mol Biol. 2006 Sep 15;362(2):312-26. Epub 2006 Jul 15. PMID- 24634216 OWN - NLM STAT- MEDLINE DA - 20140814 DCOM- 20141217 LR - 20150518 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 289 IP - 20 DP - 2014 May 16 TI - Structural and biophysical characterization of murine rif1 C terminus reveals high specificity for DNA cruciform structures. PG - 13903-11 LID - 10.1074/jbc.M114.557843 [doi] AB - Mammalian Rif1 is a key regulator of DNA replication timing, double-stranded DNA break repair, and replication fork restart. Dissecting the molecular functions of Rif1 is essential to understand how it regulates such diverse processes. However, Rif1 is a large protein that lacks well defined functional domains and is predicted to be largely intrinsically disordered; these features have hampered recombinant expression of Rif1 and subsequent functional characterization. Here we applied ESPRIT (expression of soluble proteins by random incremental truncation), an in vitro evolution-like approach, to identify high yielding soluble fragments encompassing conserved regions I and II (CRI and CRII) at the C-terminal region of murine Rif1. NMR analysis showed CRI to be intrinsically disordered, whereas CRII is partially folded. CRII binds cruciform DNA with high selectivity and micromolar affinity and thus represents a functional DNA binding domain. Mutational analysis revealed an alpha-helical region of CRII to be important for cruciform DNA binding and identified critical residues. Thus, we present the first structural study of the mammalian Rif1, identifying a domain that directly links its function to DNA binding. The high specificity of Rif1 for cruciform structures is significant given the role of this key protein in regulating origin firing and DNA repair. CI - (c) 2014 by The American Society for Biochemistry and Molecular Biology, Inc. FAU - Sukackaite, Rasa AU - Sukackaite R AD - From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France, the European Molecular Biology Laboratory, Monterotondo Outstation, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy. FAU - Jensen, Malene Ringkjobing AU - Jensen MR AD - the University of Grenoble Alpes, Institut de Biologie Structurale (IBS), 6 rue Jules Horowitz, F-38027 Grenoble, France, CEA, DSV, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, CNRS, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, and. FAU - Mas, Philippe J AU - Mas PJ AD - From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France. FAU - Blackledge, Martin AU - Blackledge M AD - the University of Grenoble Alpes, Institut de Biologie Structurale (IBS), 6 rue Jules Horowitz, F-38027 Grenoble, France, CEA, DSV, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, CNRS, IBS, 6 rue Jules Horowitz, F-38027 Grenoble, France, and. FAU - Buonomo, Sara B AU - Buonomo SB AD - the European Molecular Biology Laboratory, Monterotondo Outstation, Adriano Buzzati-Traverso Campus, Via Ramarini 32, 00015 Monterotondo, Italy sara.buonomo@embl.it. FAU - Hart, Darren J AU - Hart DJ AD - From the European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 France, the Unit for Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 France, hart@embl.fr. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140314 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA, Cruciform) RN - 0 (Peptide Fragments) RN - 0 (Rif1 protein, mouse) RN - 0 (Telomere-Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - *Biophysical Processes MH - DNA, Cruciform/genetics/*metabolism MH - Mice MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/metabolism MH - Solubility MH - Substrate Specificity MH - Telomere-Binding Proteins/*chemistry/*metabolism PMC - PMC4022862 OID - NLM: PMC4022862 OTO - NOTNLM OT - Cell Cycle OT - DNA Replication OT - Directed Evolution OT - Intrinsically Disordered Proteins OT - NMR EDAT- 2014/03/19 06:00 MHDA- 2014/12/18 06:00 CRDT- 2014/03/18 06:00 PHST- 2014/03/14 [aheadofprint] AID - M114.557843 [pii] AID - 10.1074/jbc.M114.557843 [doi] PST - ppublish SO - J Biol Chem. 2014 May 16;289(20):13903-11. doi: 10.1074/jbc.M114.557843. Epub 2014 Mar 14. PMID- 24009497 OWN - NLM STAT- MEDLINE DA - 20130906 DCOM- 20140227 LR - 20141112 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 9 IP - 8 DP - 2013 TI - Structural similarities and differences between amyloidogenic and non-amyloidogenic islet amyloid polypeptide (IAPP) sequences and implications for the dual physiological and pathological activities of these peptides. PG - e1003211 LID - 10.1371/journal.pcbi.1003211 [doi] AB - IAPP, a 37 amino-acid peptide hormone belonging to the calcitonin family, is an intrinsically disordered protein that is coexpressed and cosecreted along with insulin by pancreatic islet beta-cells in response to meals. IAPP plays a physiological role in glucose regulation; however, in certain species, IAPP can aggregate and this process is linked to beta-cell death and Type II Diabetes. Using replica exchange molecular dynamics with extensive sampling (16 replicas per sequence and 600 ns per replica), we investigate the structure of the monomeric state of two species of aggregating peptides (human and cat IAPP) and two species of non-aggregating peptides (pig and rat IAPP). Our simulations reveal that the pig and rat conformations are very similar, and consist of helix-coil and helix-hairpin conformations. The aggregating sequences, on the other hand, populate the same helix-coil and helix-hairpin conformations as the non-aggregating sequence, but, in addition, populate a hairpin structure. Our exhaustive simulations, coupled with available peptide-activity data, leads us to a structure-activity relationship (SAR) in which we propose that the functional role of IAPP is carried out by the helix-coil conformation, a structure common to both aggregating and non-aggregating species. The pathological role of this peptide may have multiple origins, including the interaction of the helical elements with membranes. Nonetheless, our simulations suggest that the hairpin structure, only observed in the aggregating species, might be linked to the pathological role of this peptide, either as a direct precursor to amyloid fibrils, or as part of a cylindrin type of toxic oligomer. We further propose that the helix-hairpin fold is also a possible aggregation prone conformation that would lead normally non-aggregating variants of IAPP to form fibrils under conditions where an external perturbation is applied. The SAR relationship is used to suggest the rational design of therapeutics for treating diabetes. FAU - Wu, Chun AU - Wu C AD - Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California, United States of America. FAU - Shea, Joan-Emma AU - Shea JE LA - eng GR - AG027818/AG/NIA NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130829 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (Islet Amyloid Polypeptide) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cats MH - Humans MH - Islet Amyloid Polypeptide/*chemistry/genetics/metabolism/*physiology MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Folding MH - Rats MH - Sequence Alignment MH - Swine PMC - PMC3757079 OID - NLM: PMC3757079 EDAT- 2013/09/07 06:00 MHDA- 2014/02/28 06:00 CRDT- 2013/09/07 06:00 PHST- 2013/08 [ecollection] PHST- 2013/04/19 [received] PHST- 2013/07/20 [accepted] PHST- 2013/08/29 [epublish] AID - 10.1371/journal.pcbi.1003211 [doi] AID - PCOMPBIOL-D-13-00670 [pii] PST - ppublish SO - PLoS Comput Biol. 2013;9(8):e1003211. doi: 10.1371/journal.pcbi.1003211. Epub 2013 Aug 29. PMID- 25212215 OWN - NLM STAT- MEDLINE DA - 20141022 DCOM- 20150623 IS - 1741-0134 (Electronic) IS - 1741-0126 (Linking) VI - 27 IP - 11 DP - 2014 Nov TI - The disordered region of Arabidopsis VIP1 binds the Agrobacterium VirE2 protein outside its DNA-binding site. PG - 439-46 LID - 10.1093/protein/gzu036 [doi] AB - Agrobacterium is a pathogen that genetically transforms plants. The bacterial VirE2 protein envelopes the T-DNA of Agrobacterium and protects it from degradation. Within the transfected cells, VirE2 interacts with the plant VIP1 leading to nuclear transport of the T-DNA complex. Active VirE2 is an oligomer with a tendency to aggregate, hampering its studies at the molecular level. In addition, no structural or quantitative information is available regarding VIP1 or its interactions. The lack of information is mainly because both VIP1 and VirE2 are difficult to express and purify. Here, we present the development of efficient protocols that resulted in pure and stable His-tagged VIP1 and VirE2. Circular dichroism spectroscopy and computational predictions indicated that VIP1 is mostly intrinsically disordered. This may explain the variety of protein-protein interactions it participates in. Size exclusion chromatography revealed that VirE2 exists in a two-state equilibrium between a monomer and an oligomeric form. Using the purified proteins, we performed peptide array screening and revealed the binding sites on both proteins. VirE2 binds the disordered regions of VIP1, while the site in VirE2 that binds VIP1 is different from the VirE2 DNA-binding site. Peptides derived from these sites may be used as lead compounds that block Agrobacterium infection of plants. CI - (c) The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. FAU - Maes, Michal AU - Maes M AD - Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel. FAU - Amit, Einav AU - Amit E AD - Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel. FAU - Danieli, Tsafi AU - Danieli T AD - Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel. FAU - Lebendiker, Mario AU - Lebendiker M AD - Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel. FAU - Loyter, Abraham AU - Loyter A AD - Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel. FAU - Friedler, Assaf AU - Friedler A AD - Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel assaf.friedler@mail.huji.ac.il. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140911 PL - England TA - Protein Eng Des Sel JT - Protein engineering, design & selection : PEDS JID - 101186484 RN - 0 (Arabidopsis Proteins) RN - 0 (Bacterial Proteins) RN - 0 (DNA, Plant) RN - 0 (DNA-Binding Proteins) RN - 0 (Ion Channels) RN - 0 (Recombinant Proteins) RN - 0 (VIP1 protein, Arabidopsis) RN - 0 (virE2 protein, Agrobacterium) SB - IM MH - Arabidopsis Proteins/*chemistry/genetics/*metabolism MH - Bacterial Proteins/*chemistry/genetics/*metabolism MH - Binding Sites MH - DNA, Plant/chemistry/*metabolism MH - DNA-Binding Proteins/*chemistry/genetics/*metabolism MH - Escherichia coli/genetics/metabolism MH - Ion Channels/*chemistry/genetics/*metabolism MH - Protein Binding MH - Recombinant Proteins/chemistry/genetics/metabolism OTO - NOTNLM OT - Agrobacterium OT - VIP1 OT - VirE2 OT - peptide arrays OT - protein expression and purification EDAT- 2014/09/13 06:00 MHDA- 2015/06/24 06:00 CRDT- 2014/09/13 06:00 PHST- 2014/09/11 [aheadofprint] AID - gzu036 [pii] AID - 10.1093/protein/gzu036 [doi] PST - ppublish SO - Protein Eng Des Sel. 2014 Nov;27(11):439-46. doi: 10.1093/protein/gzu036. Epub 2014 Sep 11. PMID- 17513864 OWN - NLM STAT- MEDLINE DA - 20070716 DCOM- 20070917 LR - 20150214 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 282 IP - 29 DP - 2007 Jul 20 TI - Identification of a minimal myosin Va binding site within an intrinsically unstructured domain of melanophilin. PG - 21518-28 AB - Myosin V is a molecular motor that transports a variety of cellular cargo, including organelles, vesicles, and messenger RNA. The proper peripheral distribution of melanosomes, a dense pigment-containing organelle, is dependent on actin and the activity of myosin Va. The recruitment of myosin Va to the melanosome and proper transport of the melanosome requires melanophilin, which directly binds to myosin Va and is tethered to the melanosome membrane via Rab27a. Here we use highly purified proteins to demonstrate that the globular tail domain of myosin Va binds directly to an intrinsically unstructured domain of melanophilin. The myosin Va binding domain of melanophilin lacks stable secondary structure, and (1)H NMR measurements indicate that the protein is unfolded. This domain is extremely sensitive to mild proteolysis and has a hydrodynamic radius that is consistent with a random coil-like polypeptide. We show that myosin Va binding does not induce the global folding of melanophilin. Truncations of melanophilin were utilized to define a short peptide sequence (26 residues) within melanophilin that is critical for myosin Va binding. We demonstrate that a peptide corresponding to these residues binds directly to the globular tail domain with the same affinity as melanophilin. We discuss the possible implications of protein intrinsic disorder in recruitment and maintenance of myosin Va on melanosome membranes. FAU - Geething, Nathan C AU - Geething NC AD - Department of Biochemistry, Stanford University, Stanford, California 94041, USA. FAU - Spudich, James A AU - Spudich JA LA - eng GR - P01 AR42895/AR/NIAMS NIH HHS/United States GR - R01 GM033289/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20070519 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Carrier Proteins) RN - 0 (Mlph protein, mouse) RN - 0 (Myo5a protein, mouse) RN - 0 (Recombinant Proteins) RN - EC 3.6.1.- (Myosin Type V) RN - EC 3.6.1.- (rab GTP-Binding Proteins) RN - EC 3.6.1.-. (Rab27a protein, mouse) RN - EC 3.6.4.1 (Myosin Heavy Chains) SB - IM MH - Adaptor Proteins, Signal Transducing MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Carrier Proteins/chemistry MH - Magnetic Resonance Spectroscopy MH - Melanosomes/metabolism MH - Mice MH - Molecular Sequence Data MH - Myosin Heavy Chains/*chemistry MH - Myosin Type V/*chemistry MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Sequence Homology, Amino Acid MH - rab GTP-Binding Proteins/chemistry EDAT- 2007/05/22 09:00 MHDA- 2007/09/18 09:00 CRDT- 2007/05/22 09:00 PHST- 2007/05/19 [aheadofprint] AID - M701932200 [pii] AID - 10.1074/jbc.M701932200 [doi] PST - ppublish SO - J Biol Chem. 2007 Jul 20;282(29):21518-28. Epub 2007 May 19. PMID- 9753329 OWN - NLM STAT- MEDLINE DA - 19981013 DCOM- 19981013 LR - 20071114 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 94 IP - 6 DP - 1998 Sep 18 TI - Structure of type IIbeta phosphatidylinositol phosphate kinase: a protein kinase fold flattened for interfacial phosphorylation. PG - 829-39 AB - Phosphoinositide kinases play central roles in signal transduction by phosphorylating the inositol ring at specific positions. The structure of one such enzyme, type IIbeta phosphatidylinositol phosphate kinase, reveals a protein kinase ATP-binding core and demonstrates that all phosphoinositide kinases belong to one superfamily. The enzyme is a disc-shaped homodimer with a 33 x 48 A basic flat face that suggests an electrostatic mechanism for plasma membrane targeting. Conserved basic residues form a putative phosphatidylinositol phosphate specificity site. The substrate-binding site is open on one side, consistent with dual specificity for phosphatidylinositol 3- and 5-phosphates. A modeled complex with membrane-bound substrate and ATP shows how a phosphoinositide kinase can phosphorylate its substrate in situ at the membrane interface. FAU - Rao, V D AU - Rao VD AD - Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0580, USA. FAU - Misra, S AU - Misra S FAU - Boronenkov, I V AU - Boronenkov IV FAU - Anderson, R A AU - Anderson RA FAU - Hurley, J H AU - Hurley JH LA - eng SI - PDB/1BOL GR - GM51968/GM/NIGMS NIH HHS/United States GR - GM57549/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Cell JT - Cell JID - 0413066 RN - 0 (Bacterial Proteins) RN - EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)) RN - EC 2.7.1.68 (1-phosphatidylinositol-4-phosphate 5-kinase) SB - IM MH - Bacterial Proteins/chemistry/genetics/metabolism MH - Crystallography MH - Dimerization MH - Escherichia coli MH - Molecular Sequence Data MH - Phosphorylation MH - Phosphotransferases (Alcohol Group Acceptor)/*chemistry/genetics/*metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Signal Transduction/*physiology MH - Subcellular Fractions/enzymology MH - Substrate Specificity EDAT- 1998/09/30 MHDA- 1998/09/30 00:01 CRDT- 1998/09/30 00:00 AID - S0092-8674(00)81741-9 [pii] PST - ppublish SO - Cell. 1998 Sep 18;94(6):829-39. PMID- 23272104 OWN - NLM STAT- MEDLINE DA - 20121228 DCOM- 20130626 LR - 20141104 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 12 DP - 2012 TI - Identification of HYPK-interacting proteins reveals involvement of HYPK in regulating cell growth, cell cycle, unfolded protein response and cell death. PG - e51415 LID - 10.1371/journal.pone.0051415 [doi] AB - Huntingtin Yeast Two-Hybrid Protein K (HYPK) is an intrinsically unstructured huntingtin (HTT)-interacting protein with chaperone-like activity. To obtain more information about the function(s) of the protein, we identified 27 novel interacting partners of HYPK by pull-down assay coupled with mass spectrometry and, further, 9 proteins were identified by co-localization and co-immunoprecipitation (co-IP) assays. In neuronal cells, (EEF1A1 and HSPA1A), (HTT and LMNB2) and (TP53 and RELA) were identified in complex with HYPK in different experiments. Various Gene Ontology (GO) terms for biological processes, like protein folding (GO: 0006457), response to unfolded protein (GO: 0006986), cell cycle arrest (GO: 0007050), anti-apoptosis (GO: 0006916) and regulation of transcription (GO: 0006355) were significantly enriched with the HYPK-interacting proteins. Cell growth and the ability to refold heat-denatured reporter luciferase were decreased, but cytotoxicity was increased in neuronal cells where HYPK was knocked-down using HYPK antisense DNA construct. The proportion of cells in different phases of cell cycle was also altered in cells with reduced levels of HYPK. These results show that HYPK is involved in several biological processes, possibly through interaction with its partners. FAU - Choudhury, Kamalika Roy AU - Choudhury KR AD - Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India. FAU - Raychaudhuri, Swasti AU - Raychaudhuri S FAU - Bhattacharyya, Nitai P AU - Bhattacharyya NP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121210 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Carrier Proteins) RN - 0 (HTT protein, human) RN - 0 (HYPK protein, human) RN - 0 (HYPK protein, mouse) RN - 0 (Nerve Tissue Proteins) RN - 0 (Serotonin Plasma Membrane Transport Proteins) RN - 0 (Slc6a4 protein, mouse) SB - IM MH - Animals MH - Brain/metabolism MH - Carrier Proteins/genetics/*metabolism MH - Cell Cycle MH - Cell Death MH - Cell Proliferation MH - Cell Survival MH - Computational Biology/methods MH - Electrophoresis, Polyacrylamide Gel MH - Flow Cytometry/methods MH - Humans MH - Immunohistochemistry/methods MH - Mass Spectrometry/methods MH - Mice MH - Models, Biological MH - Nerve Tissue Proteins/metabolism MH - Neurons/metabolism MH - Protein Binding MH - Protein Folding MH - Serotonin Plasma Membrane Transport Proteins/*metabolism MH - Two-Hybrid System Techniques MH - Unfolded Protein Response PMC - PMC3525516 OID - NLM: PMC3525516 EDAT- 2012/12/29 06:00 MHDA- 2013/06/28 06:00 CRDT- 2012/12/29 06:00 PHST- 2012/04/13 [received] PHST- 2012/11/01 [accepted] PHST- 2012/12/10 [epublish] AID - 10.1371/journal.pone.0051415 [doi] AID - PONE-D-12-10439 [pii] PST - ppublish SO - PLoS One. 2012;7(12):e51415. doi: 10.1371/journal.pone.0051415. Epub 2012 Dec 10. PMID- 20947504 OWN - NLM STAT- MEDLINE DA - 20110103 DCOM- 20110131 LR - 20140821 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 1 DP - 2011 Jan 7 TI - Docking-dependent ubiquitination of the interferon regulatory factor-1 tumor suppressor protein by the ubiquitin ligase CHIP. PG - 607-19 LID - 10.1074/jbc.M110.153122 [doi] AB - Characteristically for a regulatory protein, the IRF-1 tumor suppressor turns over rapidly with a half-life of between 20-40 min. This allows IRF-1 to reach new steady state protein levels swiftly in response to changing environmental conditions. Whereas CHIP (C terminus of Hsc70-interacting protein), appears to chaperone IRF-1 in unstressed cells, formation of a stable IRF-1.CHIP complex is seen under specific stress conditions. Complex formation, in heat- or heavy metal-treated cells, is accompanied by a decrease in IRF-1 steady state levels and an increase in IRF-1 ubiquitination. CHIP binds directly to an intrinsically disordered domain in the central region of IRF-1 (residues 106-140), and this site is sufficient to form a stable complex with CHIP in cells and to compete in trans with full-length IRF-1, leading to a reduction in its ubiquitination. The study reveals a complex relationship between CHIP and IRF-1 and highlights the role that direct binding or "docking" of CHIP to its substrate(s) can play in its mechanism of action as an E3 ligase. FAU - Narayan, Vikram AU - Narayan V AD - CRUK Interferon and Cell Signalling Group, Cell Signalling Unit, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH4 2XR, United Kingdom. FAU - Pion, Emmanuelle AU - Pion E FAU - Landre, Vivien AU - Landre V FAU - Muller, Petr AU - Muller P FAU - Ball, Kathryn L AU - Ball KL LA - eng GR - C377/A6355/Cancer Research UK/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101014 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (HSP70 Heat-Shock Proteins) RN - 0 (Interferon Regulatory Factor-1) RN - 0 (Metals, Heavy) RN - 0 (Peptide Fragments) RN - 0 (Tumor Suppressor Proteins) RN - EC 6.3.2.19 (STUB1 protein, human) RN - EC 6.3.2.19 (UBE2D1 protein, human) RN - EC 6.3.2.19 (UBE2E1 protein, human) RN - EC 6.3.2.19 (Ubiquitin-Conjugating Enzymes) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Cell Line, Tumor MH - HSP70 Heat-Shock Proteins/metabolism MH - Heat-Shock Response MH - Humans MH - Interferon Regulatory Factor-1/chemistry/*metabolism MH - Metals, Heavy/toxicity MH - Molecular Sequence Data MH - Peptide Fragments/metabolism MH - Protein Binding/drug effects MH - Protein Structure, Tertiary MH - Tumor Suppressor Proteins/chemistry/*metabolism MH - Ubiquitin-Conjugating Enzymes/metabolism MH - Ubiquitin-Protein Ligases/*metabolism MH - *Ubiquitination/drug effects PMC - PMC3013021 OID - NLM: PMC3013021 EDAT- 2010/10/16 06:00 MHDA- 2011/02/01 06:00 CRDT- 2010/10/16 06:00 PHST- 2010/10/14 [aheadofprint] AID - M110.153122 [pii] AID - 10.1074/jbc.M110.153122 [doi] PST - ppublish SO - J Biol Chem. 2011 Jan 7;286(1):607-19. doi: 10.1074/jbc.M110.153122. Epub 2010 Oct 14. PMID- 19236004 OWN - NLM STAT- MEDLINE DA - 20090310 DCOM- 20091217 LR - 20140914 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 10 DP - 2009 Mar 17 TI - The tooth enamel protein, porcine amelogenin, is an intrinsically disordered protein with an extended molecular configuration in the monomeric form. PG - 2272-81 LID - 10.1021/bi802175a [doi] AB - Amelogenins make up a class of proteins associated with the formation of mineralized enamel in vertebrates, possess highly conserved N- and C-terminal sequence regions, and represent an interesting model protein system for understanding biomineralization and protein assembly. Using bioinformatics, we report here the identification of molecular traits that classify 12 amelogenin proteins as members of the intrinsically disordered or unstructured protein family (IDPs), a group of proteins that normally exist as unfolded species but are capable of transformation to a folded state as part of their overall function. Using biophysical techniques (CD and NMR), we follow up on our bioinformatics studies and confirm that one of the amelogenins, recombinant porcine rP172, exists in an extended, unfolded state in the monomeric form. This protein exhibits evidence of conformational exchange between two states, and this exchange may be mediated by Pro residues in the sequence. Although the protein is globally unfolded, we detect the presence of local residual secondary structure [alpha-helix, extended beta-strand, turn/loop, and polyproline type II (PPII)] that may serve several functional roles within the enamel matrix. The extended, labile conformation of rP172 amelogenin is compatible with the known functions of amelogenin in enamel biomineralization, i.e., self-assembly, associations with other enamel matrix proteins and with calcium phosphate biominerals, and interaction with cell receptors. It is likely that the labile structure of this protein facilitates interactions of amelogenin with other macromolecules or with minerals for achievement of internal protein stabilization. FAU - Delak, Katya AU - Delak K AD - Laboratory for Chemical Physics, New York University, 345 East 24th Street, Room 1007, New York, New York 10010, USA. FAU - Harcup, Craig AU - Harcup C FAU - Lakshminarayanan, Rajamani AU - Lakshminarayanan R FAU - Sun, Zhi AU - Sun Z FAU - Fan, Yuwwei AU - Fan Y FAU - Moradian-Oldak, Janet AU - Moradian-Oldak J FAU - Evans, John Spencer AU - Evans JS LA - eng GR - DE-013414/DE/NIDCR NIH HHS/United States GR - P41 GM66354/GM/NIGMS NIH HHS/United States GR - P41 RR001614/RR/NCRR NIH HHS/United States GR - P41 RR001614-266394/RR/NCRR NIH HHS/United States GR - R01 DE013414/DE/NIDCR NIH HHS/United States GR - R01 DE013414-06/DE/NIDCR NIH HHS/United States GR - R01 DE015644/DE/NIDCR NIH HHS/United States GR - R01 DE015644-04/DE/NIDCR NIH HHS/United States GR - R01 DE020099/DE/NIDCR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amelogenin) RN - 0 (Recombinant Proteins) RN - 059QF0KO0R (Water) SB - IM MH - Amelogenin/*chemistry/genetics MH - Animals MH - Circular Dichroism MH - Hydrogen-Ion Concentration MH - Hydrophobic and Hydrophilic Interactions MH - Light MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Phase Transition MH - Protein Conformation MH - Protein Stability MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/genetics MH - Scattering, Radiation MH - Sequence Analysis, Protein MH - Solubility MH - Static Electricity MH - Swine MH - Water/chemistry PMC - PMC2748245 MID - NIHMS91056 OID - NLM: NIHMS91056 OID - NLM: PMC2748245 EDAT- 2009/02/25 09:00 MHDA- 2009/12/18 06:00 CRDT- 2009/02/25 09:00 AID - 10.1021/bi802175a [doi] PST - ppublish SO - Biochemistry. 2009 Mar 17;48(10):2272-81. doi: 10.1021/bi802175a. PMID- 21216290 OWN - NLM STAT- MEDLINE DA - 20110222 DCOM- 20110606 LR - 20131121 IS - 1096-0279 (Electronic) IS - 1046-5928 (Linking) VI - 77 IP - 1 DP - 2011 May TI - Heterologous expression of Translocated promoter region protein, Tpr, identified as a transcription factor from Rattus norvegicus. PG - 112-7 LID - 10.1016/j.pep.2011.01.001 [doi] AB - Our earlier studies have demonstrated that the 35 kDa isoform of Translocated promoter region protein (Tpr) of Rattus norvegicus was able to augment c-jun transcription efficiently. Identification of direct targets that may in part downregulate c-jun transcription might prove to be an ideal target to curtail the proliferation of normal cells under pathophysiological conditions. In order to evaluate its potential as a pharmaceutical target, the protein must be produced and purified in sufficiently high yields. In the present study, we report the high level expression of Tpr protein of R. norvegicus employing heterologous host, Escherichia coli, to permit its structural characterization in great detail. We here demonstrate that the Tpr protein was expressed in soluble form and approximately 90 mg/L of the purified protein at the shake flask level could be achieved to near homogeneity using single step-metal chelate affinity chromatography. The amino acid sequence of the protein was confirmed by mass spectroscopic analysis. The highly unstable and disordered Tpr protein was imparted structural and functional stability by the addition of glycerol and it has been shown that the natively unfolded Tpr protein retains DNA binding ability under these conditions only. Thus, the present study emphasizes the significance of an efficient prokaryotic system, which results in a high level soluble expression of a DNA binding protein of eukaryotic origin. Thus, the present strategy employed for purification of the R. norvegicus Tpr protein bypasses the need for the tedious expression strategies associated with the eukaryotic expression systems. CI - Copyright (c) 2011 Elsevier Inc. All rights reserved. FAU - Agarwal, Shivani AU - Agarwal S AD - Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110 067, India. FAU - Yadav, Sunita Kumari AU - Yadav SK FAU - Dixit, Aparna AU - Dixit A LA - eng PT - Journal Article DEP - 20110107 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (DNA-Binding Proteins) RN - 0 (His-His-His-His-His-His) RN - 0 (Oligopeptides) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Transcription Factors) RN - 4QD397987E (Histidine) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cloning, Molecular MH - DNA/metabolism MH - DNA-Binding Proteins/*biosynthesis/chemistry/genetics MH - Electrophoresis, Polyacrylamide Gel MH - Escherichia coli/genetics/metabolism MH - Histidine/genetics/metabolism MH - Mice MH - Mice, Inbred BALB C MH - Molecular Sequence Data MH - Oligopeptides/genetics/metabolism MH - Promoter Regions, Genetic MH - Rats MH - Recombinant Fusion Proteins/biosynthesis/chemistry/genetics MH - Solubility MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Transcription Factors/*biosynthesis/chemistry/genetics EDAT- 2011/01/11 06:00 MHDA- 2011/06/07 06:00 CRDT- 2011/01/11 06:00 PHST- 2010/11/21 [received] PHST- 2010/12/31 [revised] PHST- 2011/01/03 [accepted] PHST- 2011/01/07 [aheadofprint] AID - S1046-5928(11)00002-7 [pii] AID - 10.1016/j.pep.2011.01.001 [doi] PST - ppublish SO - Protein Expr Purif. 2011 May;77(1):112-7. doi: 10.1016/j.pep.2011.01.001. Epub 2011 Jan 7. PMID- 11152691 OWN - NLM STAT- MEDLINE DA - 20010403 DCOM- 20010524 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 14 DP - 2001 Apr 6 TI - Evidence for a partially folded intermediate in alpha-synuclein fibril formation. PG - 10737-44 AB - Intracellular proteinaceous aggregates (Lewy bodies and Lewy neurites) of alpha-synuclein are hallmarks of neurodegenerative diseases such as Parkinson's disease, dementia with Lewy bodies, and multiple systemic atrophy. However, the molecular mechanisms underlying alpha-synuclein aggregation into such filamentous inclusions remain unknown. An intriguing aspect of this problem is that alpha-synuclein is a natively unfolded protein, with little or no ordered structure under physiological conditions. This raises the question of how an essentially disordered protein is transformed into highly organized fibrils. In the search for an answer to this question, we have investigated the effects of pH and temperature on the structural properties and fibrillation kinetics of human recombinant alpha-synuclein. Either a decrease in pH or an increase in temperature transformed alpha-synuclein into a partially folded conformation. The presence of this intermediate is strongly correlated with the enhanced formation of alpha-synuclein fibrils. We propose a model for the fibrillation of alpha-synuclein in which the first step is the conformational transformation of the natively unfolded protein into the aggregation-competent partially folded intermediate. FAU - Uversky, V N AU - Uversky VN AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. FAU - Li, J AU - Li J FAU - Fink, A L AU - Fink AL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20010110 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Nerve Tissue Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Humans MH - Nerve Tissue Proteins/*chemistry MH - *Protein Folding MH - Recombinant Proteins/chemistry MH - Synucleins MH - alpha-Synuclein EDAT- 2001/01/22 19:15 MHDA- 2001/06/02 10:01 CRDT- 2001/01/22 19:15 PHST- 2001/01/10 [aheadofprint] AID - 10.1074/jbc.M010907200 [doi] AID - M010907200 [pii] PST - ppublish SO - J Biol Chem. 2001 Apr 6;276(14):10737-44. Epub 2001 Jan 10. PMID- 23052212 OWN - NLM STAT- MEDLINE DA - 20130211 DCOM- 20130404 IS - 1420-9071 (Electronic) IS - 1420-682X (Linking) VI - 70 IP - 5 DP - 2013 Mar TI - A SAXS-based ensemble model of the native and phosphorylated regulatory domain of the CFTR. PG - 923-33 LID - 10.1007/s00018-012-1172-5 [doi] AB - The cystic fibrosis transmembrane conductance regulator (CFTR), the defective protein in cystic fibrosis, is an anion channel activated by protein kinase A phosphorylation. The regulatory domain (RD) of CFTR has multiple phosphorylation sites, and is responsible for channel activation. This domain is intrinsically disordered, rendering the structural analysis a difficult task, as high-resolution techniques are barely applicable. In this work, we obtained a biophysical characterization of the native and phosphorylated RD in solution by employing complementary structural methods. The native RD has a gyration radius of 3.25 nm, and a maximum molecular dimension of 11.4 nm, larger than expected for a globular protein of the same molecular mass. Phosphorylation causes compaction of the structure, yielding a significant reduction of the gyration radius, to 2.92 nm, and on the maximum molecular dimension to 10.2 nm. Using an ensemble optimization method, we were able to generate a low-resolution, three-dimensional model of the native and the phosphorylated RD based on small-angle X-ray scattering data. We have obtained the first experiment-based model of the CFTR regulatory domain, which will be useful to understand the molecular mechanisms of normal and pathological CFTR functioning. FAU - Marasini, Carlotta AU - Marasini C AD - Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Via De Marini, 6, 16149, Genoa, Italy. FAU - Galeno, Lauretta AU - Galeno L FAU - Moran, Oscar AU - Moran O LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121004 PL - Switzerland TA - Cell Mol Life Sci JT - Cellular and molecular life sciences : CMLS JID - 9705402 RN - 0 (Recombinant Proteins) RN - 126880-72-6 (Cystic Fibrosis Transmembrane Conductance Regulator) SB - IM MH - Cystic Fibrosis/metabolism MH - Cystic Fibrosis Transmembrane Conductance Regulator/*chemistry/*metabolism MH - Humans MH - Models, Molecular MH - Phosphorylation MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Scattering, Small Angle MH - X-Ray Diffraction EDAT- 2012/10/12 06:00 MHDA- 2013/04/05 06:00 CRDT- 2012/10/12 06:00 PHST- 2012/06/15 [received] PHST- 2012/09/17 [accepted] PHST- 2012/08/24 [revised] PHST- 2012/10/04 [aheadofprint] AID - 10.1007/s00018-012-1172-5 [doi] PST - ppublish SO - Cell Mol Life Sci. 2013 Mar;70(5):923-33. doi: 10.1007/s00018-012-1172-5. Epub 2012 Oct 4. PMID- 21490720 OWN - NLM STAT- MEDLINE DA - 20110414 DCOM- 20110829 LR - 20140820 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 7 IP - 4 DP - 2011 Apr TI - Multi-scaled explorations of binding-induced folding of intrinsically disordered protein inhibitor IA3 to its target enzyme. PG - e1001118 LID - 10.1371/journal.pcbi.1001118 [doi] AB - Biomolecular function is realized by recognition, and increasing evidence shows that recognition is determined not only by structure but also by flexibility and dynamics. We explored a biomolecular recognition process that involves a major conformational change - protein folding. In particular, we explore the binding-induced folding of IA3, an intrinsically disordered protein that blocks the active site cleft of the yeast aspartic proteinase saccharopepsin (YPrA) by folding its own N-terminal residues into an amphipathic alpha helix. We developed a multi-scaled approach that explores the underlying mechanism by combining structure-based molecular dynamics simulations at the residue level with a stochastic path method at the atomic level. Both the free energy profile and the associated kinetic paths reveal a common scheme whereby IA3 binds to its target enzyme prior to folding itself into a helix. This theoretical result is consistent with recent time-resolved experiments. Furthermore, exploration of the detailed trajectories reveals the important roles of non-native interactions in the initial binding that occurs prior to IA3 folding. In contrast to the common view that non-native interactions contribute only to the roughness of landscapes and impede binding, the non-native interactions here facilitate binding by reducing significantly the entropic search space in the landscape. The information gained from multi-scaled simulations of the folding of this intrinsically disordered protein in the presence of its binding target may prove useful in the design of novel inhibitors of aspartic proteinases. FAU - Wang, Jin AU - Wang J AD - State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, People's Republic of China. jin.wang.1@stonybrook.edu FAU - Wang, Yong AU - Wang Y FAU - Chu, Xiakun AU - Chu X FAU - Hagen, Stephen J AU - Hagen SJ FAU - Han, Wei AU - Han W FAU - Wang, Erkang AU - Wang E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110407 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (PAI3 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 3.4.- (Aspartic Acid Proteases) RN - EC 3.4.23.1 (Pepsin A) SB - IM MH - Algorithms MH - Aspartic Acid Proteases/chemistry MH - Computational Biology/methods MH - Computer Simulation MH - Kinetics MH - Pepsin A/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry MH - Stochastic Processes MH - Surface Properties MH - Temperature MH - Thermodynamics PMC - PMC3072359 OID - NLM: PMC3072359 EDAT- 2011/04/15 06:00 MHDA- 2011/08/30 06:00 CRDT- 2011/04/15 06:00 PHST- 2010/08/17 [received] PHST- 2011/03/07 [accepted] PHST- 2011/04/07 [epublish] AID - 10.1371/journal.pcbi.1001118 [doi] PST - ppublish SO - PLoS Comput Biol. 2011 Apr;7(4):e1001118. doi: 10.1371/journal.pcbi.1001118. Epub 2011 Apr 7. PMID- 14594809 OWN - NLM STAT- MEDLINE DA - 20040119 DCOM- 20040423 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 4 DP - 2004 Jan 23 TI - Interaction of the TAZ1 domain of the CREB-binding protein with the activation domain of CITED2: regulation by competition between intrinsically unstructured ligands for non-identical binding sites. PG - 3042-9 AB - The TAZ1 domain of the homologous transcriptional coactivators CREB-binding protein (CBP) and p300 forms a complex with CITED2 (CBP/p300-interacting transactivator with ED-rich tail), inhibiting the activity of the hypoxia inducible factor (HIF-1alpha) and thereby attenuating the cellular response to low tissue oxygen concentration. We report the NMR structure of the CBP TAZ1 domain bound to the activation domain of CIT-ED2. The structure of TAZ1, consisting of four alpha-helices (alpha(1)-alpha(4)) stabilized by three zinc atoms, is very similar in the CITED2 and HIF-1alpha complexes. The activation domain of CITED2 is unstructured when free and folds upon binding, forming a helix (termed alpha(A)) and an extended structure that wraps around TAZ1. The CITED2 alpha(A) helix packs in the TAZ1 alpha(1)/alpha(4) interface, a site that forms weak interactions with the poorly defined aminoterminal alpha-helix of HIF-1alpha. CITED2 and HIF-1alpha both contain a four residue motif, LP(E/Q)L, which binds in the TAZ1 alpha(1)/alpha(2)/alpha(3) junction in each complex. The carboxyl-terminal region of CITED2 forms an extended structure with hydrophobic contacts in the TAZ1 alpha(1)/alpha(3) interface in the site occupied by the HIF-1alpha alpha(B) helix. CITED2 does not bind at all to the TAZ1 site occupied by the HIF-1alpha carboxyl-terminal helix. The HIF-1alpha and CITED2 domains utilize partly overlapping surfaces of TAZ1 to achieve high affinity binding and to compete effectively with each other for interaction with CBP/p300; CITED2 and HIF-1alpha use these binding sites differently to maintain similar binding affinities in order to displace each other in a feedback loop during the hypoxic response. FAU - De Guzman, Roberto N AU - De Guzman RN AD - Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA. FAU - Martinez-Yamout, Maria A AU - Martinez-Yamout MA FAU - Dyson, H Jane AU - Dyson HJ FAU - Wright, Peter E AU - Wright PE LA - eng SI - PDB/1R8U GR - CA96865/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20031031 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (CITED2 protein, human) RN - 0 (CREBBP protein, human) RN - 0 (Cited2 protein, mouse) RN - 0 (Crebbp protein, mouse) RN - 0 (DNA-Binding Proteins) RN - 0 (HIF1A protein, human) RN - 0 (Hif1a protein, mouse) RN - 0 (Hypoxia-Inducible Factor 1) RN - 0 (Hypoxia-Inducible Factor 1, alpha Subunit) RN - 0 (Ligands) RN - 0 (Nuclear Proteins) RN - 0 (Repressor Proteins) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - CREB-Binding Protein MH - DNA-Binding Proteins/chemistry/*metabolism MH - Humans MH - Hypoxia-Inducible Factor 1 MH - Hypoxia-Inducible Factor 1, alpha Subunit MH - Ligands MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Proteins/chemistry/*metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - Repressor Proteins/chemistry/*metabolism MH - Sequence Alignment MH - Trans-Activators/chemistry/*metabolism MH - *Transcription Factors EDAT- 2003/11/05 05:00 MHDA- 2004/04/24 05:00 CRDT- 2003/11/05 05:00 PHST- 2003/10/31 [aheadofprint] AID - 10.1074/jbc.M310348200 [doi] AID - M310348200 [pii] PST - ppublish SO - J Biol Chem. 2004 Jan 23;279(4):3042-9. Epub 2003 Oct 31. PMID- 22073178 OWN - NLM STAT- MEDLINE DA - 20111110 DCOM- 20120326 LR - 20141021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 11 DP - 2011 TI - Characterization of intrinsically disordered prostate associated gene (PAGE5) at single residue resolution by NMR spectroscopy. PG - e26633 LID - 10.1371/journal.pone.0026633 [doi] AB - BACKGROUND: The Cancer-Testis antigens (CTA) are proteins expressed in human germ line and certain cancer cells. CTAs form a large gene family, representing 10% of X-chromosomal genes. They have high potential for cancer-specific immunotherapy. However, their biological functions are currently unknown. Prostate associated genes (PAGE) are characterized as CTAs. PAGE5 is one of six proteins belonging to this protein family, also called CT16. METHODOLOGY/PRINCIPAL FINDINGS: In this study we show, using bioinformatics, chromatographic and solution state NMR spectroscopic methods, that PAGE5 is an intrinsically disordered protein (IDP). CONCLUSION/SIGNIFICANCE: The study stands out as the first time structural characterization of the PAGE family protein and introduces how solution state NMR spectroscopy can be effectively utilized for identification of molecular recognition regions (MoRF) in IDPs, known often as transiently populated secondary structures. FAU - Hellman, Maarit AU - Hellman M AD - Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland. FAU - Tossavainen, Helena AU - Tossavainen H FAU - Rappu, Pekka AU - Rappu P FAU - Heino, Jyrki AU - Heino J FAU - Permi, Perttu AU - Permi P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111102 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Melanoma-Specific Antigens) RN - 0 (melanoma-derived CT16 cancer testis antigen, human) SB - IM MH - Amino Acid Sequence MH - Chromatography, Gel MH - Humans MH - Melanoma-Specific Antigens/*chemistry MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Protein Structure, Secondary MH - Sequence Homology, Amino Acid PMC - PMC3206799 OID - NLM: PMC3206799 EDAT- 2011/11/11 06:00 MHDA- 2012/03/27 06:00 CRDT- 2011/11/11 06:00 PHST- 2011/07/08 [received] PHST- 2011/09/29 [accepted] PHST- 2011/11/02 [epublish] AID - 10.1371/journal.pone.0026633 [doi] AID - PONE-D-11-12971 [pii] PST - ppublish SO - PLoS One. 2011;6(11):e26633. doi: 10.1371/journal.pone.0026633. Epub 2011 Nov 2. PMID- 8706682 OWN - NLM STAT- MEDLINE DA - 19960906 DCOM- 19960906 LR - 20070723 IS - 0014-2956 (Print) IS - 0014-2956 (Linking) VI - 238 IP - 3 DP - 1996 Jun 15 TI - The role of a beta barrel loop 4 extension in modulating the physical and functional properties of long-chain 2-hydroxy-acid oxidase isozymes. PG - 790-8 AB - Peroxisomal long-chain 2-hydroxy-acid oxidase, an FMN-dependent enzyme, catalyzes the oxidation of a variety of L-2-hydroxy acids into keto acids at the expense of oxygen. We recently reported the cloning and sequencing of its CDNA and the existence of a weakly expressed isozyme [Belmouden, A., Le, K. H. D., Lederer, F. & Garchon, H. J. (1993) Eur. J. Biochem. 214, 17-251. This isozyme, beta 2 differs from the major one in having a three-residue insertion, -VRK-, in loop 4 of the beta 8 alpha 8 barrel. In the crystal structures of homologous flavocytochrome beta 2, and glycolate oxidase, the corresponding region of loop 4 is disordered. We now report on the constitutive high-level expression of isozymes beta 1, and beta 2 in Escherichia coli under control of the lambda pL promoter, and on the influence of the E. coli genetic background and the growth medium on the expression level. We describe the properties of isozyme beta 2 and compare them with those of pure isoform beta 1. The visible spectra of the purified enzymes differ in the position of the near-ultraviolet band of the prosthetic group. pH titration studies indicate that the FMN ionizes at N3 at a lower pH than free flavin and that there is a small pKa difference between the isozymes. To our knowledge, the only other known case of a lowered pKa for the protein-bound flavin is that of glycolate oxidase. In the CD spectra of the FMN region, a marked difference between isozymes in the 270-300-nm region appears to be related to the pKa difference for the N3-H bond. Kinetic parameters for a number of substrates and inhibitors are indistinguishable within the limits of experimental error, with the exception of values for kcat for mandelate (the most active substrate), Km for hydroxyhippurate (a new substrate), Ki for cinnamate and oxalate, and Kd for sulfite. The differences are no larger than twofold. The foregoing comparison between isozymes beta 1 and beta 2 shows that the naturally engineered insertion in loop 4 exerts some influence on the flavin spectral properties and the active-site reactivity. Since the corresponding loop 4 regions in the three-dimensional structures of flavocytochrome 2 and glycolate oxidase are 1.5-2.0 nm removed from the flavin, it would appear either that loop 4 has a very different conformation in hydroxy-acid oxidase, or that it may interact with the active site due to mobility. FAU - Belmouden, A AU - Belmouden A AD - URA 1461, Centre National de la Recherche Scientifique and Universite Paris V. Hopital Necker, Paris, France. FAU - Lederer, F AU - Lederer F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - GERMANY TA - Eur J Biochem JT - European journal of biochemistry / FEBS JID - 0107600 RN - 0 (Enzyme Inhibitors) RN - 0 (Flavins) RN - 0 (Isoenzymes) RN - 0 (Recombinant Proteins) RN - EC 1.1.- (Alcohol Oxidoreductases) RN - EC 1.1.3.15 (L-2-hydroxyacid oxidase) SB - IM MH - Absorption MH - Alcohol Oxidoreductases/antagonists & inhibitors/*chemistry/*physiology MH - Base Sequence MH - Enzyme Inhibitors/metabolism/pharmacology MH - Escherichia coli/genetics/growth & development MH - Flavins/chemistry MH - Isoenzymes/antagonists & inhibitors/chemistry/physiology MH - Kinetics MH - Models, Molecular MH - Molecular Sequence Data MH - Plasmids/genetics MH - Protein Conformation MH - Recombinant Proteins/chemistry/genetics MH - Spectrum Analysis MH - Structure-Activity Relationship EDAT- 1996/06/15 MHDA- 1996/06/15 00:01 CRDT- 1996/06/15 00:00 PST - ppublish SO - Eur J Biochem. 1996 Jun 15;238(3):790-8. PMID- 12906822 OWN - NLM STAT- MEDLINE DA - 20030808 DCOM- 20040414 LR - 20061115 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 11 IP - 8 DP - 2003 Aug TI - Coupling of folding and binding in the PTB domain of the signaling protein Shc. PG - 905-13 AB - The notion that certain proteins lack intrinsic globular structure under physiological conditions and that the attainment of fully folded structure only occurs upon the binding of target molecules has been recently gaining popularity. We report here the solution structure of the PTB domain of the signaling protein Shc in the free form. Comparison of this structure with that of the complex form, obtained previously with a phosphopeptide ligand, reveals that the Shc PTB domain is structurally disordered in the free form, particularly around the regions constituting the peptide binding pocket. The binding of the ligand appears to reorganize this pocket through local folding events triggering a conformational switch between the free and the complex forms. FAU - Farooq, Amjad AU - Farooq A AD - Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, New York, NY 10029, USA. amjad.farooq@mssm.edu FAU - Zeng, Lei AU - Zeng L FAU - Yan, Kelley S AU - Yan KS FAU - Ravichandran, Kodi S AU - Ravichandran KS FAU - Zhou, Ming-Ming AU - Zhou MM LA - eng SI - PDB/1N3H SI - PDB/1OY2 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Carrier Proteins) RN - 0 (Ligands) RN - 0 (Protein Isoforms) RN - 0 (Proteins) RN - 21820-51-9 (Phosphotyrosine) SB - IM MH - Alternative Splicing MH - Amino Acid Sequence MH - Binding Sites MH - Carrier Proteins/metabolism MH - Hydrogen Bonding MH - Ligands MH - Magnetic Resonance Spectroscopy MH - Models, Chemical MH - Models, Molecular MH - Phosphotyrosine/*metabolism MH - *Protein Binding MH - Protein Conformation MH - *Protein Folding MH - Protein Isoforms/chemistry MH - Protein Structure, Tertiary MH - Proteins/*chemistry/*metabolism MH - *Signal Transduction MH - Spectrum Analysis, Raman MH - *src Homology Domains EDAT- 2003/08/09 05:00 MHDA- 2004/04/15 05:00 CRDT- 2003/08/09 05:00 AID - S0969212603001345 [pii] PST - ppublish SO - Structure. 2003 Aug;11(8):905-13. PMID- 22947085 OWN - NLM STAT- MEDLINE DA - 20130207 DCOM- 20130401 LR - 20150423 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 51 IP - 38 DP - 2012 Sep 25 TI - The neuroendocrine protein 7B2 is intrinsically disordered. PG - 7456-64 LID - 10.1021/bi300871k [doi] AB - The small neuroendocrine protein 7B2 has been shown to be required for the productive maturation of proprotein convertase 2 (proPC2) to an active enzyme form; this action is accomplished via its ability to block aggregation of proPC2 into nonactivatable forms. Recent data show that 7B2 can also act as a postfolding chaperone to block the aggregation of a number of other proteins, for example, alpha-synuclein. To gain insight into the mechanism of action of 7B2 in blocking protein aggregation, we performed structural studies of this protein using gel filtration chromatography, intrinsic tryptophan fluorescence, 1-anilino-8-naphthalenesulfonate (ANS) binding, circular dichroism (CD), and nuclear magnetic resonance (NMR) spectroscopy. Gel filtration studies indicated that 7B2 exists as an extended monomer, eluting at a molecular mass higher than that expected for a globular protein of similar size. However, chemical cross-linking showed that 7B2 exhibits concentration-dependent oligomerization. CD experiments showed that both full-length 27 kDa 7B2 and the C-terminally truncated 21 kDa form lack appreciable secondary structure, although the longer protein exhibited more structural content than the latter, as demonstrated by intrinsic and ANS fluorescence studies. NMR spectra confirmed the lack of structure in native 7B2, but a disorder-to-order transition was observed upon incubation with one of its client proteins, alpha-synuclein. We conclude that 7B2 is a natively disordered protein whose function as an antiaggregant chaperone is likely facilitated by its lack of appreciable secondary structure and tendency to form oligomers. FAU - Dasgupta, Indrani AU - Dasgupta I AD - Department of Anatomy and Neurobiology, School of Medicine, University of Maryland-Baltimore, Baltimore, MD 21201, USA. FAU - Sanglas, Laura AU - Sanglas L FAU - Enghild, Jan J AU - Enghild JJ FAU - Lindberg, Iris AU - Lindberg I LA - eng GR - DK49703/DK/NIDDK NIH HHS/United States GR - R01 DK049703/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120914 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Neuroendocrine Secretory Protein 7B2) RN - 0 (SCG5 protein, human) SB - IM MH - Chromatography, Gel MH - Circular Dichroism MH - Humans MH - Neuroendocrine Secretory Protein 7B2/*chemistry/isolation & purification MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Spectrometry, Fluorescence MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization PMC - PMC3457758 OID - NLM: PMC3457758 EDAT- 2012/09/06 06:00 MHDA- 2013/04/02 06:00 CRDT- 2012/09/06 06:00 PHST- 2012/09/14 [aheadofprint] AID - 10.1021/bi300871k [doi] PST - ppublish SO - Biochemistry. 2012 Sep 25;51(38):7456-64. doi: 10.1021/bi300871k. Epub 2012 Sep 14. PMID- 17211892 OWN - NLM STAT- MEDLINE DA - 20070402 DCOM- 20070511 LR - 20091119 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 67 IP - 1 DP - 2007 Apr 1 TI - Modelling of the ABL and ARG proteins predicts two functionally critical regions that are natively unfolded. PG - 1-11 AB - The ABL and ARG tyrosine kinases regulate many pivotal cellular processes and are implicated in the pathogenesis of several forms of leukemia. We have modelled the previously uncharacterized core domain (SH3-SH2-tyrosine kinase) and C-terminal actin-binding domain of ARG. We have also investigated the structural arrangement of the ABL and ARG Cap region and of the long multifunctional region located downstream of the tyrosine kinase domain. We report that the ARG core domain is homologous to the corresponding ABL region, therefore suggesting that ARG catalytic activity is likely regulated by the same SH3-SH2 clamp described for ABL. We also report that the Cap of both ABL and ARG is natively unfolded. Hence, biological events determining the folding of the Cap are critical to allow its interaction with the tyrosine kinase C-lobe. Furthermore, our results show that, with the exception of the C-terminal actin-binding domain, the entire region encoded by the ABL and ARG last exon is natively unfolded. Phosphorylation events or protein-protein interactions regulating the folding of this region will therefore modulate the activity of its numerous functional domains. Finally, our analyses show that the C-terminal actin-binding domain of ARG displays a four-helix bundle structure similar to the one reported for the corresponding ABL region. Our findings imply that many biological activities attributed to ABL, ARG, and their oncogenic counterparts are regulated by natively unfolded regions. CI - (c) 2007 Wiley-Liss, Inc. FAU - Buffa, Pietro AU - Buffa P AD - Department of Biomedical Sciences, Section of General Pathology, University of Catania, Catania, Italy. FAU - Manzella, Livia AU - Manzella L FAU - Consoli, Maria Letizia AU - Consoli ML FAU - Messina, Angelo AU - Messina A FAU - Vigneri, Paolo AU - Vigneri P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (DNA-Binding Proteins) RN - EC 2.7.1.- (ARG tyrosine kinase) RN - EC 2.7.10.1 (Protein-Tyrosine Kinases) RN - EC 2.7.10.2 (Proto-Oncogene Proteins c-abl) SB - IM MH - Amino Acid Sequence MH - Cell Movement/physiology MH - DNA-Binding Proteins/metabolism MH - Exons MH - Models, Molecular MH - Molecular Sequence Data MH - Phosphorylation MH - Protein Folding MH - *Protein Structure, Tertiary MH - Protein-Tyrosine Kinases/*chemistry/metabolism MH - Proto-Oncogene Proteins c-abl/*chemistry/metabolism MH - Sequence Alignment MH - src Homology Domains/physiology EDAT- 2007/01/11 09:00 MHDA- 2007/05/12 09:00 CRDT- 2007/01/11 09:00 AID - 10.1002/prot.21161 [doi] PST - ppublish SO - Proteins. 2007 Apr 1;67(1):1-11. PMID- 20953180 OWN - NLM STAT- MEDLINE DA - 20101122 DCOM- 20110111 LR - 20140919 IS - 1545-9985 (Electronic) IS - 1545-9985 (Linking) VI - 17 IP - 11 DP - 2010 Nov TI - Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation. PG - 1352-7 LID - 10.1038/nsmb.1918 [doi] AB - Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an alpha-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis. FAU - Wang, Tao AU - Wang T AD - Biology Department, Brookhaven National Laboratory, Upton, New York, USA. FAU - Darwin, K Heran AU - Darwin KH FAU - Li, Huilin AU - Li H LA - eng SI - PDB/3M91 SI - PDB/3M9B SI - PDB/3M9D SI - PDB/3M9H GR - AI070285/AI/NIAID NIH HHS/United States GR - HL092774/HL/NHLBI NIH HHS/United States GR - P30 EB009998/EB/NIBIB NIH HHS/United States GR - R01 AI070285/AI/NIAID NIH HHS/United States GR - R01 AI070285-05/AI/NIAID NIH HHS/United States GR - R01 HL092774/HL/NHLBI NIH HHS/United States GR - R01 HL092774-05/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20101017 PL - United States TA - Nat Struct Mol Biol JT - Nature structural & molecular biology JID - 101186374 RN - 0 (Bacterial Proteins) RN - 0 (Pup protein, Mycobacterium tuberculosis) RN - 0 (Ubiquitins) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 3.6.1.3 (Mpa protein, Mycobacterium tuberculosis) SB - IM MH - Adenosine Triphosphatases/chemistry/metabolism/*physiology MH - Bacterial Proteins/chemistry/*metabolism MH - Crystallography, X-Ray MH - Hydrogen Bonding MH - Models, Molecular MH - Mycobacterium/*metabolism MH - Protein Folding MH - Protein Interaction Mapping MH - Ubiquitins/chemistry/*metabolism PMC - PMC2988878 MID - NIHMS232421 OID - NLM: NIHMS232421 OID - NLM: PMC2988878 EDAT- 2010/10/19 06:00 MHDA- 2011/01/12 06:00 CRDT- 2010/10/19 06:00 PHST- 2010/05/19 [received] PHST- 2010/08/27 [accepted] PHST- 2010/10/17 [aheadofprint] AID - nsmb.1918 [pii] AID - 10.1038/nsmb.1918 [doi] PST - ppublish SO - Nat Struct Mol Biol. 2010 Nov;17(11):1352-7. doi: 10.1038/nsmb.1918. Epub 2010 Oct 17. PMID- 8710867 OWN - NLM STAT- MEDLINE DA - 19960912 DCOM- 19960912 LR - 20131121 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 93 IP - 16 DP - 1996 Aug 6 TI - The solution structure of the Raf-1 cysteine-rich domain: a novel ras and phospholipid binding site. PG - 8312-7 AB - The Raf-1 protein kinase is the best-characterized downstream effector of activated Ras. Interaction with Ras leads to Raf-1 activation and results in transduction of cell growth and differentiation signals. The details of Raf-1 activation are unclear, but our characterization of a second Ras-binding site in the cysteine-rich domain (CRD) and the involvement of both Ras-binding sites in effective Raf-1-mediated transformation provides insight into the molecular aspects and consequences of Ras-Raf interactions. The Raf-1 CRD is a member of an emerging family of domains, many of which are found within signal transducing proteins. Several contain binding sites for diacylglycerol (or phorbol esters) and phosphatidylserine and are believed to play a role in membrane translocation and enzyme activation. The CRD from Raf-1 does not bind diacylglycerol but interacts with Ras and phosphatidylserine. To investigate the ligand-binding specificities associated with CRDs, we have determined the solution structure of the Raf-1 CRD using heteronuclear multidimensional NMR. We show that there are differences between this structure and the structures of two related domains from protein kinase C (PKC). The differences are confined to regions of the CRDs involved in binding phorbol ester in the PKC domains. Since phosphatidylserine is a common ligand, we expect its binding site to be located in regions where the structures of the Raf-1 and PKC domains are similar. The structure of the Raf-1 CRD represents an example of this family of domains that does not bind diacylglycerol and provides a framework for investigating its interactions with other molecules. FAU - Mott, H R AU - Mott HR AD - Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill 27599, USA. FAU - Carpenter, J W AU - Carpenter JW FAU - Zhong, S AU - Zhong S FAU - Ghosh, S AU - Ghosh S FAU - Bell, R M AU - Bell RM FAU - Campbell, S L AU - Campbell SL LA - eng GR - R01 CA70308-1/CA/NCI NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Phospholipids) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Solutions) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - EC 2.7.11.1 (Proto-Oncogene Proteins c-raf) RN - EC 2.7.11.13 (Protein Kinase C) RN - K848JZ4886 (Cysteine) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Cysteine/chemistry MH - Hydrogen Bonding MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Phospholipids/metabolism MH - Protein Binding MH - Protein Kinase C/chemistry MH - Protein Structure, Secondary MH - Protein-Serine-Threonine Kinases/*chemistry MH - Proto-Oncogene Proteins/*chemistry MH - Proto-Oncogene Proteins c-raf MH - Recombinant Proteins MH - Sequence Alignment MH - Solutions PMC - PMC38667 OID - NLM: PMC38667 EDAT- 1996/08/06 MHDA- 1996/08/06 00:01 CRDT- 1996/08/06 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 1996 Aug 6;93(16):8312-7. PMID- 22468560 OWN - NLM STAT- MEDLINE DA - 20120614 DCOM- 20120912 LR - 20131121 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 134 IP - 16 DP - 2012 Apr 25 TI - Disorder-to-order transition of an intrinsically disordered region of sortase revealed by multiscale enhanced sampling. PG - 7094-101 LID - 10.1021/ja3008402 [doi] AB - Molecular functions of intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs), such as molecular recognition and cellular signaling, are ascribed to dynamic changes in the conformational space in response to binding of target molecules. Sortase, a transpeptitase in Gram-positive bacteria, has an IDR in a loop which undergoes a disordered-to-ordered transition (called "disordered loop"), accompanying a tilt of another loop ("dynamic loop"), upon binding of a signal peptide and a calcium ion. In this study, all-atom conformational ensembles of sortase were calculated for the four different binding states (with/without the peptide and with/without a calcium ion) by the multiscale enhanced sampling (MSES) simulation to examine how the binding of the peptide and/or calcium influences the conformational ensemble. The MSES is a multiscale and multicopy simulation method that allows an enhanced sampling of the all-atom model of large proteins including explicit solvent. A 100 ns MSES simulation of the ligand-free sortase using 20 replicas (in total 2 mus) demonstrated large flexibility in both the disordered and dynamic loops; however, their distributions were not random but had a clear preference which populates the N-terminal part of the disordered loop near the bound form. The MSES simulations of the three binding states clarified the allosteric mechanism of sortase: the N- and C-terminal parts of the disordered loop undergo a disorder-to-order transition independently of each other upon binding of the peptide and a calcium ion, respectively; however, upon binding of both ligands, the two parts work cooperatively to stabilize the bound peptide. FAU - Moritsugu, Kei AU - Moritsugu K AD - Research Program for Computational Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. moritsuguk@riken.jp FAU - Terada, Tohru AU - Terada T FAU - Kidera, Akinori AU - Kidera A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120411 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Ligands) RN - 0 (Peptides) RN - EC 2.3.2.12 (Peptidyl Transferases) RN - SY7Q814VUP (Calcium) SB - IM MH - Calcium/chemistry/metabolism MH - Ligands MH - Models, Molecular MH - Peptides/chemistry/metabolism MH - Peptidyl Transferases/*chemistry/metabolism MH - Protein Conformation EDAT- 2012/04/04 06:00 MHDA- 2012/09/13 06:00 CRDT- 2012/04/04 06:00 PHST- 2012/04/11 [aheadofprint] AID - 10.1021/ja3008402 [doi] PST - ppublish SO - J Am Chem Soc. 2012 Apr 25;134(16):7094-101. doi: 10.1021/ja3008402. Epub 2012 Apr 11. PMID- 9384558 OWN - NLM STAT- MEDLINE DA - 19980227 DCOM- 19980227 LR - 20071114 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 5 IP - 11 DP - 1997 Nov 15 TI - The role of DNA in the mechanism of NFkappaB dimer formation: crystal structures of the dimerization domains of the p50 and p65 subunits. PG - 1427-36 AB - BACKGROUND: Members of the rel/NFkappaB family of transcription factors play a vital role in the regulation of rapid cellular responses, such as those required to fight infection or react to cellular stress. Members of this family of proteins form homo- and heterodimers with differing affinities for dimerization. They share a structural motif known as the rel homology region (RHR), the C-terminal one third of which mediates protein dimerization. Crystal structures of the rel/NFkappaB family members p50 and p65 in their DNA-bound homodimeric form have been solved. These structures showed that the residues from the dimerization domains of both p50 and p65 participate in DNA binding and that the DNA-protein and protein dimerization surfaces form one continuous overlapping interface. We desired to investigate the contribution of DNA to NFkappaB dimerization and to identify the mechanism for the selective association of rel/NFkappaB family peptides into transcriptionally active dimers. RESULTS: We report here the crystal structures of the dimerization domains of murine p50 and p65 at 2.2 A and 2.0 A resolution, respectively. A comparison of these two structures suggests that conservative amino acid changes at three positions are responsible for the differences in their dimer interfaces. The presence of the target DNA does not change the dimer interface of either protein in any significant manner. CONCLUSIONS: These two structures suggest that the rel/NFkappaB family of transcription factors use only a few conservative changes in their amino acid sequences to form a host of dimers with varying affinities for dimerization. Amino acids at positions corresponding to 254, 267, and 307 of murine p50, function as primary determinants for the observed differences in dimerization affinity. The DNA-contacting charged amino acid sidechains from the dimerization domains are held in a similar conformation in both the DNA-bound and free states, therefore, no major structural rearrangement is required to bring these residues into contact with the DNA. FAU - Huang, D B AU - Huang DB AD - Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0359, USA. FAU - Huxford, T AU - Huxford T FAU - Chen, Y Q AU - Chen YQ FAU - Ghosh, G AU - Ghosh G LA - eng SI - PDB/1BFS SI - PDB/1BFT GR - 5 T32 CA09523-13/CA/NCI NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (NF-kappa B) RN - 0 (NF-kappa B p50 Subunit) RN - 0 (Transcription Factor RelA) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Crystallography, X-Ray MH - DNA/chemistry/*metabolism MH - Dimerization MH - Models, Molecular MH - Molecular Sequence Data MH - NF-kappa B/*chemistry/metabolism MH - NF-kappa B p50 Subunit MH - Protein Conformation MH - Transcription Factor RelA EDAT- 1998/03/07 MHDA- 1998/03/07 00:01 CRDT- 1998/03/07 00:00 PST - ppublish SO - Structure. 1997 Nov 15;5(11):1427-36. PMID- 21841800 OWN - NLM STAT- MEDLINE DA - 20110902 DCOM- 20110908 LR - 20141022 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 477 IP - 7362 DP - 2011 Sep 1 TI - alpha-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation. PG - 107-10 LID - 10.1038/nature10324 [doi] AB - Parkinson's disease is the second most common neurodegenerative disorder. Growing evidence indicates a causative role of misfolded forms of the protein alpha-synuclein in the pathogenesis of Parkinson's disease. Intraneuronal aggregates of alpha-synuclein occur in Lewy bodies and Lewy neurites, the cytopathological hallmarks of Parkinson's disease and related disorders called synucleinopathies. alpha-Synuclein has long been defined as a 'natively unfolded' monomer of about 14 kDa (ref. 6) that is believed to acquire alpha-helical secondary structure only upon binding to lipid vesicles. This concept derives from the widespread use of recombinant bacterial expression protocols for in vitro studies, and of overexpression, sample heating and/or denaturing gels for cell culture and tissue studies. In contrast, we report that endogenous alpha-synuclein isolated and analysed under non-denaturing conditions from neuronal and non-neuronal cell lines, brain tissue and living human cells occurs in large part as a folded tetramer of about 58 kDa. Several methods, including analytical ultracentrifugation, scanning transmission electron microscopy and in vitro cell crosslinking confirmed the occurrence of the tetramer. Native, cell-derived alpha-synuclein showed alpha-helical structure without lipid addition and had much greater lipid-binding capacity than the recombinant alpha-synuclein studied heretofore. Whereas recombinantly expressed monomers readily aggregated into amyloid-like fibrils in vitro, native human tetramers underwent little or no amyloid-like aggregation. On the basis of these findings, we propose that destabilization of the helically folded tetramer precedes alpha-synuclein misfolding and aggregation in Parkinson's disease and other human synucleinopathies, and that small molecules that stabilize the physiological tetramer could reduce alpha-synuclein pathogenicity. FAU - Bartels, Tim AU - Bartels T AD - Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Choi, Joanna G AU - Choi JG FAU - Selkoe, Dennis J AU - Selkoe DJ LA - eng GR - NS038375/NS/NINDS NIH HHS/United States GR - NS051318/NS/NINDS NIH HHS/United States GR - R01 NS051318/NS/NINDS NIH HHS/United States GR - R01 NS051318-02/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20110814 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Recombinant Proteins) RN - 0 (alpha-Synuclein) SB - IM CIN - Mov Disord. 2011 Nov;26(13):2324. PMID: 22319787 CIN - Nat Rev Neurosci. 2011 Oct;12(10):550. PMID: 21886184 CIN - Nature. 2013 Jun 13;498(7453):E4-6; discussion E6-7. PMID: 23765500 MH - Animals MH - Blotting, Western MH - COS Cells MH - Cell Line, Tumor MH - Cercopithecus aethiops MH - Erythrocytes/chemistry MH - Escherichia coli/genetics MH - HEK293 Cells MH - HeLa Cells MH - Humans MH - Lipid Metabolism MH - Mice MH - Protein Folding MH - Recombinant Proteins/chemistry/metabolism MH - Time Factors MH - alpha-Synuclein/*chemistry/genetics/*metabolism PMC - PMC3166366 MID - NIHMS313099 OID - NLM: NIHMS313099 OID - NLM: PMC3166366 EDAT- 2011/08/16 06:00 MHDA- 2011/09/09 06:00 CRDT- 2011/08/16 06:00 PHST- 2010/11/15 [received] PHST- 2011/06/20 [accepted] PHST- 2011/08/14 [aheadofprint] AID - nature10324 [pii] AID - 10.1038/nature10324 [doi] PST - epublish SO - Nature. 2011 Aug 14;477(7362):107-10. doi: 10.1038/nature10324. PMID- 22383402 OWN - NLM STAT- MEDLINE DA - 20120309 DCOM- 20120716 LR - 20150210 IS - 1949-2553 (Electronic) IS - 1949-2553 (Linking) VI - 3 IP - 2 DP - 2012 Feb TI - Single enantiomer of YK-4-279 demonstrates specificity in targeting the oncogene EWS-FLI1. PG - 172-82 AB - Oncogenic fusion proteins, such as EWS-FLI1, are excellent therapeutic targets as they are only located within the tumor. However, there are currently no agents targeted toward transcription factors, which are often considered to be 'undruggable.' A considerable body of evidence is accruing that refutes this claim based upon the intrinsic disorder of transcription factors. Our previous studies show that RNA Helicase A (RHA) enhances the oncogenesis of EWS-FLI1, a putative intrinsically disordered protein. Interruption of this protein-protein complex by small molecule inhibitors validates this interaction as a unique therapeutic target. Single enantiomer activity from a chiral compound has been recognized as strong evidence for specificity in a small molecule-protein interaction. Our compound, YK-4-279, has a chiral center and can be separated into two enantiomers by chiral HPLC. We show that there is a significant difference in activity between the two enantiomers. (S)-YK-4-279 is able to disrupt binding between EWS-FLI1 and RHA in an immunoprecipitation assay and blocks the transcriptional activity of EWS-FLI1, while (R)-YK-4-279 cannot. Enantiospecific effects are also established in cytotoxicity assays and caspase assays, where up to a log-fold difference is seen between (S)-YK-4-279 and the racemic YK-4-279. Our findings indicate that only one enantiomer of our small molecule is able to specifically target a protein-protein interaction. This work is significant for its identification of a single enantiomer effect upon a protein interaction suggesting that small molecule targeting of intrinsically disordered proteins can be specific. Furthermore, proving YK-4-279 has only one functional enantiomer will be helpful in moving this compound towards clinical trials. FAU - Barber-Rotenberg, Julie S AU - Barber-Rotenberg JS AD - Department of Oncology, Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, USA. FAU - Selvanathan, Saravana P AU - Selvanathan SP FAU - Kong, Yali AU - Kong Y FAU - Erkizan, Hayriye V AU - Erkizan HV FAU - Snyder, Tara M AU - Snyder TM FAU - Hong, S Peter AU - Hong SP FAU - Kobs, Christina L AU - Kobs CL FAU - South, Natalie L AU - South NL FAU - Summer, Steven AU - Summer S FAU - Monroe, Philip J AU - Monroe PJ FAU - Chruszcz, Maksymilian AU - Chruszcz M FAU - Dobrev, Veselin AU - Dobrev V FAU - Tosso, Perrer N AU - Tosso PN FAU - Scher, Lauren J AU - Scher LJ FAU - Minor, Wladek AU - Minor W FAU - Brown, Milton L AU - Brown ML FAU - Metallo, Steven J AU - Metallo SJ FAU - Uren, Aykut AU - Uren A FAU - Toretsky, Jeffrey A AU - Toretsky JA LA - eng GR - R01 CA133662/CA/NCI NIH HHS/United States GR - R01 CA138212/CA/NCI NIH HHS/United States GR - R01CA133662/CA/NCI NIH HHS/United States GR - R01CA138212/CA/NCI NIH HHS/United States GR - RC4 CA156509/CA/NCI NIH HHS/United States GR - RC4CA156509/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Oncotarget JT - Oncotarget JID - 101532965 RN - 0 (EWS-FLI fusion protein) RN - 0 (Indoles) RN - 0 (Oncogene Proteins, Fusion) RN - 0 (Proto-Oncogene Protein c-fli-1) RN - 0 (RNA-Binding Protein EWS) RN - 0 (Transcription Factors) RN - 0 (YK 4-279) RN - EC 3.4.22.- (Caspase 3) SB - IM MH - Animals MH - Caspase 3/metabolism MH - Cell Line, Tumor MH - Cell Proliferation MH - Humans MH - Indoles/*pharmacology MH - Oncogene Proteins, Fusion/*antagonists & inhibitors MH - Proto-Oncogene Protein c-fli-1/*antagonists & inhibitors MH - RNA-Binding Protein EWS/*antagonists & inhibitors MH - Rats MH - Rats, Sprague-Dawley MH - Sarcoma, Ewing/*drug therapy MH - Stereoisomerism MH - Transcription Factors/metabolism MH - Transcriptional Activation MH - Transplantation, Heterologous PMC - PMC3326647 OID - NLM: PMC3326647 EDAT- 2012/03/03 06:00 MHDA- 2012/07/17 06:00 CRDT- 2012/03/03 06:00 AID - 454 [pii] PST - ppublish SO - Oncotarget. 2012 Feb;3(2):172-82. PMID- 16171389 OWN - NLM STAT- MEDLINE DA - 20050920 DCOM- 20051128 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 44 IP - 38 DP - 2005 Sep 27 TI - Structural and thermodynamical characterization of the complete p21 gene product of Max. PG - 12746-58 AB - The b-HLH-LZ family of transcription factors contains numerous proteins including the Myc and Mad families of proteins. Max heterodimerizes with other members to bind the E-Box DNA sequence in target gene promoters. Max is the only protein in this network that recognizes and binds E-Box DNA sequences as a homodimer in vitro and represses transcription of Myc target genes in vivo. Key information such as the structure of p21 Max, the complete gene product, and its KD in the absence of DNA are still unknown. Here, we report the characterization of the secondary and quaternary structures, the dimerization and DNA binding of p21 Max and a thermodynamically stable mutant. The helical content of p21 Max indicates that its N-terminal and C-terminal regions are unstructured in the absence of DNA. NMR experiments further support the location of folded and unfolded domains. We also show that p21 Max has an apparent KD (37 degrees C) of 7 x 10(-6), a value 10-100 times smaller than the b-HLH-LZ itself. We demonstrate that electrostatic repulsions are responsible for the higher KD of the b-HLH-LZ. Finally, we show that a p21 Max double mutant forms a very stable dimer with a KD (37 degrees C) of 3 x 10(-10) and that the protein/DNA complex depicts a higher temperature of denaturation than p21 Max/DNA complex. Our results indicate that Max could homodimerize, bind DNA, and repress transcription in vivo and that its mutant could be more efficient at repressing the expression of c-Myc target genes. FAU - Naud, Jean-Francois AU - Naud JF AD - Departement de pharmacologie, Faculte de medecine, Universite de Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4. FAU - McDuff, Francois-Olivier AU - McDuff FO FAU - Sauve, Simon AU - Sauve S FAU - Montagne, Martin AU - Montagne M FAU - Webb, Bradley A AU - Webb BA FAU - Smith, Steven P AU - Smith SP FAU - Chabot, Benoit AU - Chabot B FAU - Lavigne, Pierre AU - Lavigne P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Basic-Leucine Zipper Transcription Factors) RN - 0 (Myc associated factor X) SB - IM MH - Amino Acid Sequence MH - Basic-Leucine Zipper Transcription Factors/*chemistry/genetics MH - Circular Dichroism MH - Dimerization MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - *Thermodynamics MH - Ultracentrifugation EDAT- 2005/09/21 09:00 MHDA- 2005/12/13 09:00 CRDT- 2005/09/21 09:00 AID - 10.1021/bi0500729 [doi] PST - ppublish SO - Biochemistry. 2005 Sep 27;44(38):12746-58. PMID- 20450479 OWN - NLM STAT- MEDLINE DA - 20100726 DCOM- 20101019 LR - 20110331 IS - 1875-5305 (Electronic) IS - 0929-8665 (Linking) VI - 17 IP - 8 DP - 2010 Aug TI - Intrinsic disorder and function of the HIV-1 Tat protein. PG - 999-1011 AB - The type 1 Human Immunodeficiency Virus transcriptional regulator Tat is a small RNA-binding protein essential for viral gene expression and replication. The protein binds to a large number of proteins within infected cells and non-infected cells, and has been demonstrated to impact a wide variety of cellular activities. Early circular dichroism studies showed a lack of regular secondary structure in the protein whereas proton NMR studies suggested several different conformations. Multinuclear NMR structure and dynamics analysis indicates that the reduced protein is intrinsically disordered with a predominantly extended conformation at pH 4. Multiple resonances for several atoms suggest the existence of multiple local conformers in rapid equilibrium. An X-ray diffraction structure of equine Tat, in a complex with its cognate RNA and cyclin T1, supports this conclusion. Intrinsic disorder explains the protein's capacity to interact with multiple partners and effect multiple biological functions; the large buried surface in the X-ray diffraction structure illustrates how a disordered protein can have a high affinity and high specificity for its partners and how disordered Tat assembles a protein complex to enhance transcription elongation. FAU - Shojania, Shaheen AU - Shojania S AD - Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada. joneil@cc.umanitoba.ca. FAU - O'Neil, Joe D AU - O'Neil JD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 RN - 0 (Gene Products, tat) RN - 0 (Trans-Activators) SB - IM MH - Gene Products, tat/*chemistry MH - HIV-1/*chemistry/genetics MH - Humans MH - Protein Conformation MH - Trans-Activators MH - Transcription, Genetic EDAT- 2010/05/11 06:00 MHDA- 2010/10/20 06:00 CRDT- 2010/05/11 06:00 PHST- 2009/12/01 [received] PHST- 2010/04/08 [accepted] AID - BSP/ PPL/ E pub/0162 [pii] PST - ppublish SO - Protein Pept Lett. 2010 Aug;17(8):999-1011. PMID- 8128220 OWN - NLM STAT- MEDLINE DA - 19940413 DCOM- 19940413 LR - 20131121 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 263 IP - 5152 DP - 1994 Mar 11 TI - The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). PG - 1404-10 AB - The crystal structure of Thermus thermophilus seryl-transfer RNA synthetase, a class 2 aminoacyl-tRNA synthetase, complexed with a single tRNA(Ser) molecule was solved at 2.9 A resolution. The structure revealed how insertion of conserved base G20b from the D loop into the core of the tRNA determines the orientation of the long variable arm, which is a characteristic feature of most serine specific tRNAs. On tRNA binding, the antiparallel coiled-coil domain of one subunit of the synthetase makes contacts with the variable arm and T psi C loop of the tRNA and directs the acceptor stem of the tRNA into the active site of the other subunit. Specificity depends principally on recognition of the shape of tRNA(Ser) through backbone contacts and secondarily on sequence specific interactions. FAU - Biou, V AU - Biou V AD - European Molecular Biology Laboratory, Grenoble Outstation, France. FAU - Yaremchuk, A AU - Yaremchuk A FAU - Tukalo, M AU - Tukalo M FAU - Cusack, S AU - Cusack S LA - eng SI - SWISSPROT/P07284 SI - SWISSPROT/P09156 SI - SWISSPROT/P26638 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (RNA, Transfer, Amino Acyl) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 6.1.1.11 (Serine-tRNA Ligase) SB - IM MH - Adenosine Triphosphate/metabolism MH - Amino Acid Sequence MH - Base Composition MH - Base Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Protein Conformation MH - Protein Structure, Secondary MH - RNA, Transfer, Amino Acyl/*chemistry/metabolism MH - Serine-tRNA Ligase/*chemistry/metabolism MH - Substrate Specificity MH - Thermus thermophilus/*enzymology EDAT- 1994/03/11 MHDA- 1994/03/11 00:01 CRDT- 1994/03/11 00:00 PST - ppublish SO - Science. 1994 Mar 11;263(5152):1404-10. PMID- 21112299 OWN - NLM STAT- MEDLINE DA - 20101129 DCOM- 20110307 LR - 20140821 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 11 DP - 2010 Dec 1 TI - Calcium-induced folding and stabilization of the intrinsically disordered RTX domain of the CyaA toxin. PG - 3744-53 LID - 10.1016/j.bpj.2010.10.016 [doi] AB - The adenylate cyclase toxin (CyaA) is one of the major virulence factors of Bordetella pertussis, the causative agent of whooping cough. Its C-terminal region, the receptor-binding domain (RD), contains approximately 40 calcium-binding Repeat in ToXin (RTX) motifs, which are characteristic of many virulence factors of pathogenic bacteria. We previously showed that RD is intrinsically disordered in the absence of calcium and acquires its functional three-dimensional structure upon calcium binding. To gain further insight into the physicochemical properties of RD, we characterized its calcium-induced conformational and stability changes by combining spectroscopic approaches. We show that RD, in the absence of calcium, adopts premolten globule conformations, due in part to the strong internal electrostatic repulsions between the negative charges of the aspartate-rich polypeptide sequence. Accordingly, sodium is able to screen these electrostatic repulsions, allowing a partial compaction of the polypeptide, whereas calcium triggers a strong compaction as well as the acquisition of secondary and tertiary structures in a highly cooperative manner. The differential sensitivity of the calcium-loaded state to guanidinium- and urea-induced denaturations provides further evidence that electrostatic interactions play a critical role in the folding and stability of RD. These results provide new insights into the folding/function relationship of the RTX motifs. CI - Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Chenal, Alexandre AU - Chenal A AD - Unite de Biochimie des Interactions Macromoleculaires, Institut Pasteur, Centre National de la Recherche Scientifique URA 2185, Paris, France. alexandre.chenal@pasteur.fr FAU - Karst, Johanna C AU - Karst JC FAU - Sotomayor Perez, Ana Cristina AU - Sotomayor Perez AC FAU - Wozniak, Anna Katarzyna AU - Wozniak AK FAU - Baron, Bruno AU - Baron B FAU - England, Patrick AU - England P FAU - Ladant, Daniel AU - Ladant D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Adenylate Cyclase Toxin) RN - 7647-14-5 (Sodium Chloride) RN - 8DUH1N11BX (Tryptophan) RN - 8W8T17847W (Urea) RN - JU58VJ6Y3B (Guanidine) RN - SY7Q814VUP (Calcium) SB - IM MH - Adenylate Cyclase Toxin/*chemistry/*metabolism MH - Bordetella pertussis/*metabolism MH - Calcium/*pharmacology MH - Circular Dichroism MH - Fluorescence MH - Guanidine/pharmacology MH - Models, Molecular MH - Protein Folding/*drug effects MH - Protein Stability/drug effects MH - Protein Structure, Tertiary MH - Sodium Chloride/pharmacology MH - Spectroscopy, Fourier Transform Infrared MH - Tryptophan/metabolism MH - Urea/pharmacology PMC - PMC2998614 OID - NLM: PMC2998614 EDAT- 2010/11/30 06:00 MHDA- 2011/03/08 06:00 CRDT- 2010/11/30 06:00 PHST- 2010/06/17 [received] PHST- 2010/10/06 [revised] PHST- 2010/10/08 [accepted] AID - S0006-3495(10)01266-X [pii] AID - 10.1016/j.bpj.2010.10.016 [doi] PST - ppublish SO - Biophys J. 2010 Dec 1;99(11):3744-53. doi: 10.1016/j.bpj.2010.10.016. PMID- 11719352 OWN - NLM STAT- MEDLINE DA - 20011123 DCOM- 20011220 LR - 20071114 IS - 0006-4971 (Print) IS - 0006-4971 (Linking) VI - 98 IP - 12 DP - 2001 Dec 1 TI - Functional consequences of naturally occurring mutations in human uroporphyrinogen decarboxylase. PG - 3179-85 AB - Functional consequences of 12 mutations-10 missense, 1 splicing defect, and 1 frameshift mutation-were characterized in the uroporphyrinogen decarboxylase (URO-D) gene found in Utah pedigrees with familial porphyria cutanea tarda (F-PCT). All but one mutation altered a restriction site in the URO-D gene, permitting identification of affected relatives using a combination of polymerase chain reaction and restriction enzyme digestion. In a bacterial expression system, 3 of the missense mutants were found in inclusion bodies, but 7 were expressed as soluble proteins. Enzymatic activity of soluble, recombinant mutant URO-D genes ranged from 29% to 94% of normal. URO-D mRNA levels in Epstein-Barr-virus transformed cells derived from patients were normal (with the exception of the frameshift mutation) even though protein levels were lower than normal, suggesting that missense mutations generally cause unstable URO-Ds in vivo. The crystal structures of 3 mutant URO-Ds were solved, and the structural consequences of the mutations were defined. All missense mutations reported here and by others were mapped to the crystal structure of URO-D, and structural effects were predicted. These studies define structural and functional consequences of URO-D mutations occurring in patients with F-PCT. FAU - Phillips, J D AU - Phillips JD AD - Department of Medicine, University of Utah School of Medicine, Salt Lake City 84132, USA. FAU - Parker, T L AU - Parker TL FAU - Schubert, H L AU - Schubert HL FAU - Whitby, F G AU - Whitby FG FAU - Hill, C P AU - Hill CP FAU - Kushner, J P AU - Kushner JP LA - eng GR - MO-1 RR00064/RR/NCRR NIH HHS/United States GR - P-30 CA42014/CA/NCI NIH HHS/United States GR - R0-1 GM56775/GM/NIGMS NIH HHS/United States GR - R37 DK20503/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Blood JT - Blood JID - 7603509 RN - 0 (RNA, Messenger) RN - 0 (Recombinant Proteins) RN - EC 4.1.1.37 (Uroporphyrinogen Decarboxylase) SB - AIM SB - IM MH - Cell Line, Transformed MH - Crystallization MH - Frameshift Mutation MH - Gene Expression MH - Herpesvirus 4, Human MH - Humans MH - Lymphocytes/chemistry MH - Models, Molecular MH - Molecular Structure MH - *Mutation MH - Mutation, Missense MH - Pedigree MH - Polymerase Chain Reaction MH - Porphyria Cutanea Tarda/*genetics MH - RNA Splicing MH - RNA, Messenger/analysis MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Analysis, DNA MH - Uroporphyrinogen Decarboxylase/chemistry/*genetics/metabolism MH - Utah EDAT- 2001/11/24 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/11/24 10:00 PST - ppublish SO - Blood. 2001 Dec 1;98(12):3179-85. PMID- 12198488 OWN - NLM STAT- MEDLINE DA - 20020828 DCOM- 20020918 LR - 20061115 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 9 IP - 9 DP - 2002 Sep TI - The structural basis for specificity in human ABO(H) blood group biosynthesis. PG - 685-90 AB - The human ABO(H) blood group antigens are produced by specific glycosyltransferase enzymes. An N-acetylgalactosaminyltransferase (GTA) uses a UDP-GalNAc donor to convert the H-antigen acceptor to the A antigen, whereas a galactosyltransferase (GTB) uses a UDP-galactose donor to convert the H-antigen acceptor to the B antigen. GTA and GTB differ only in the identity of four critical amino acid residues. Crystal structures at 1.8-1.32 A resolution of the GTA and GTB enzymes both free and in complex with disaccharide H-antigen acceptor and UDP reveal the basis for donor and acceptor specificity and show that only two of the critical amino acid residues are positioned to contact donor or acceptor substrates. Given the need for stringent stereo- and regioselectivity in this biosynthesis, these structures further demonstrate that the ability of the two enzymes to distinguish between the A and B donors is largely determined by a single amino acid residue. FAU - Patenaude, Sonia I AU - Patenaude SI AD - Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, K1H 8M5 Canada. FAU - Seto, Nina O L AU - Seto NO FAU - Borisova, Svetlana N AU - Borisova SN FAU - Szpacenko, Adam AU - Szpacenko A FAU - Marcus, Sandra L AU - Marcus SL FAU - Palcic, Monica M AU - Palcic MM FAU - Evans, Stephen V AU - Evans SV LA - eng SI - PDB/1LZ0 SI - PDB/1LZ7 SI - PDB/1LZI SI - PDB/1LZJ PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (ABO Blood-Group System) RN - 58-98-0 (Uridine Diphosphate) RN - EC 2.4.1.- (Galactosyltransferases) RN - EC 2.4.1.- (N-Acetylgalactosaminyltransferases) RN - EC 2.4.1.- (UDPgalactosamine-galactose acetylgalactosaminyltransferase) RN - EC 2.4.1.37 (blood-group-substance alpha-D-galactosyltransferase) SB - IM MH - *ABO Blood-Group System MH - Crystallography, X-Ray MH - Galactosyltransferases/biosynthesis/*chemistry/metabolism MH - Humans MH - Models, Molecular MH - N-Acetylgalactosaminyltransferases/biosynthesis/*chemistry/metabolism MH - Protein Conformation MH - Substrate Specificity MH - Uridine Diphosphate/metabolism EDAT- 2002/08/29 10:00 MHDA- 2002/09/19 10:01 CRDT- 2002/08/29 10:00 AID - 10.1038/nsb832 [doi] AID - nsb832 [pii] PST - ppublish SO - Nat Struct Biol. 2002 Sep;9(9):685-90. PMID- 23062340 OWN - NLM STAT- MEDLINE DA - 20121015 DCOM- 20130228 LR - 20141105 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 103 IP - 7 DP - 2012 Oct 3 TI - Conformational dynamics of titin PEVK explored with FRET spectroscopy. PG - 1480-9 LID - 10.1016/j.bpj.2012.08.042 [doi] LID - S0006-3495(12)00968-X [pii] AB - The proline-, glutamate-, valine-, and lysine-rich (PEVK) domain of the giant muscle protein titin is thought to be an intrinsically unstructured random-coil segment. Various observations suggest, however, that the domain may not be completely devoid of internal interactions and structural features. To test the validity of random polymer models for PEVK, we determined the mean end-to-end distances of an 11- and a 21-residue synthetic PEVK peptide, calculated from the efficiency of the fluorescence resonance energy transfer (FRET) between an N-terminal intrinsic tryptophan donor and a synthetically added C-terminal IAEDANS acceptor obtained in steady-state and time-resolved experiments. We find that the contour-length scaling of mean end-to-end distance deviates from predictions of a purely statistical polymer chain. Furthermore, the addition of guanidine hydrochloride decreased, whereas the addition of salt increased the FRET efficiency, pointing at the disruption of structure-stabilizing interactions. Increasing temperature between 10 and 50 degrees C increased the normalized FRET efficiency in both peptides but with different trajectories, indicating that their elasticity and conformational stability are different. Simulations suggest that whereas the short PEVK peptide displays an overall random structure, the long PEVK peptide retains residual, loose helical configurations. Transitions in the local structure and dynamics of the PEVK domain may play a role in the modulation of passive muscle mechanics. CI - Copyright (c) 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Huber, Tamas AU - Huber T AD - Department of Biophysics and Radiation Biology and MTA-SE Molecular Biophysics Research Group, Semmelweis University, Budapest, Hungary. FAU - Grama, Laszlo AU - Grama L FAU - Hetenyi, Csaba AU - Hetenyi C FAU - Schay, Gusztav AU - Schay G FAU - Fulop, Livia AU - Fulop L FAU - Penke, Botond AU - Penke B FAU - Kellermayer, Miklos S Z AU - Kellermayer MS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121002 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Connectin) RN - 0 (Muscle Proteins) RN - EC 2.7.- (Protein Kinases) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Amino Acid Sequence MH - Connectin MH - *Fluorescence Resonance Energy Transfer MH - Guanidine/pharmacology MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Muscle Proteins/*chemistry MH - Osmolar Concentration MH - Protein Denaturation/drug effects MH - Protein Kinases/*chemistry MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Temperature PMC - PMC3471467 OID - NLM: PMC3471467 EDAT- 2012/10/16 06:00 MHDA- 2013/03/01 06:00 CRDT- 2012/10/16 06:00 PHST- 2012/04/30 [received] PHST- 2012/08/03 [revised] PHST- 2012/08/09 [accepted] PHST- 2012/10/02 [aheadofprint] AID - S0006-3495(12)00968-X [pii] AID - 10.1016/j.bpj.2012.08.042 [doi] PST - ppublish SO - Biophys J. 2012 Oct 3;103(7):1480-9. doi: 10.1016/j.bpj.2012.08.042. Epub 2012 Oct 2. PMID- 9336833 OWN - NLM STAT- MEDLINE DA - 19980220 DCOM- 19980220 LR - 20140617 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 6 IP - 10 DP - 1997 Oct TI - The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue. PG - 2097-106 AB - Thymidine kinase from Herpes simplex virus type 1 (TK) was crystallized in an N-terminally truncated but fully active form. The structures of TK complexed with ADP at the ATP-site and deoxythymidine-5'-monophosphate (dTMP), deoxythymidine (dT), or idoxuridine-5'-phosphate (5-iodo-dUMP) at the substrate-site were refined to 2.75 A, 2.8 A, and 3.0 A resolution, respectively. TK catalyzes the phosphorylation of dT resulting in an ester, and the phosphorylation of dTMP giving rise to an anhydride. The presented TK structures indicate that there are only small differences between these two modes of action. Glu83 serves as a general base in the ester reaction. Arg163 parks at an internal aspartate during ester formation and binds the alpha-phosphate of dTMP during anhydride formation. The bound deoxythymidine leaves a 35 A3 cavity at position 5 of the base and two sequestered water molecules at position 2. Cavity and water molecules reduce the substrate specificity to such an extent that TK can phosphorylate various substrate analogues useful in pharmaceutical applications. TK is structurally homologous to the well-known nucleoside monophosphate kinases but contains large additional peptide segments. FAU - Wild, K AU - Wild K AD - Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Freiburg im Breisgau, Germany. FAU - Bohner, T AU - Bohner T FAU - Folkers, G AU - Folkers G FAU - Schulz, G E AU - Schulz GE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Deoxyuracil Nucleotides) RN - 0 (Recombinant Proteins) RN - 1763-02-6 (iododeoxyuridylate) RN - 365-07-1 (Thymidine Monophosphate) RN - 61D2G4IYVH (Adenosine Diphosphate) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 2.7.1.21 (Thymidine Kinase) RN - VC2W18DGKR (Thymidine) SB - IM MH - Adenosine Diphosphate/metabolism MH - Adenosine Triphosphate/metabolism MH - Amino Acid Sequence MH - Binding Sites MH - Crystallization MH - Crystallography, X-Ray MH - Deoxyuracil Nucleotides/metabolism MH - Dimerization MH - Herpesvirus 1, Human/*enzymology MH - Models, Molecular MH - Molecular Sequence Data MH - Phosphorylation MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Homology MH - Thymidine/metabolism MH - Thymidine Kinase/*chemistry/*metabolism MH - Thymidine Monophosphate/metabolism PMC - PMC2143568 OID - NLM: PMC2143568 EDAT- 1997/10/23 MHDA- 1997/10/23 00:01 CRDT- 1997/10/23 00:00 AID - 10.1002/pro.5560061005 [doi] PST - ppublish SO - Protein Sci. 1997 Oct;6(10):2097-106. PMID- 10191146 OWN - NLM STAT- MEDLINE DA - 19990513 DCOM- 19990513 LR - 20101118 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 287 IP - 4 DP - 1999 Apr 9 TI - Conformational transitions of islet amyloid polypeptide (IAPP) in amyloid formation in vitro. PG - 781-96 AB - Amyloid aggregates have been recognized to be a pathological hallmark of several fatal diseases, including Alzheimer's disease, the prion-related diseases, and type II diabetes. Pancreatic amyloidosis is characterized by the deposition of amyloid consisting of islet amyloid polypeptide (IAPP). We followed the steps preceding IAPP insolubilization and amyloid formation in vitro using a variety of biochemical methods, including a filtration assay, far and near-UV circular dichroism (CD) spectropolarimetry, 1-anilino-8-naphthalenesulfonic acid (ANS) binding, and atomic force (AFM) and electron (EM) microscopy. IAPP insolubilization and amyloid formation followed kinetics that were consistent with the nucleation-dependent polymerization mechanism. Nucleation of IAPP amyloid formation with traces of preformed fibrils induced a rapid conformational transition into beta-sheets that subsequently aggregated into insoluble amyloid fibrils. Transition proceeded via a molten globule-like conformeric state with large contents of secondary structure, fluctuating tertiary and quaternary aromatic interactions, and strongly solvent-exposed hydrophobic patches. In the temperature denaturation pathway at 5 microM peptide, we found that this state was mostly populated at about 45 degrees C, and either aggregated rapidly into amyloid by prolonged exposure to this temperature, or melted into denaturated but still structured IAPP, when heated further to 65 degrees C. The state at 45 degrees C was also found to be populated at 4.25 M GdnHCl at 25 degrees C during GdnHCl-induced equilibrium denaturation, and was stable in solution for several hours before aggregating into amyloid fibrils. Our studies suggested that this amyloidogenic state was a self-associated form of an aggregation-prone, partially folded state of IAPP. We propose that this partially folded population and its self-associated forms are in a concentration-dependent equilibrium with a non-amyloidogenic IAPP conformer and may act as early, soluble precursors of beta-sheet and amyloid formation. Our findings on the molecular mechanism of IAPP amyloid formation in vitro should assist in gaining insight into the pathogenesis and inhibition of pancreatic amyloidosis and other amyloid-related diseases. CI - Copyright 1999 Academic Press. FAU - Kayed, R AU - Kayed R AD - University of Tubingen, Tubingen, D-72076, Germany. FAU - Bernhagen, J AU - Bernhagen J FAU - Greenfield, N AU - Greenfield N FAU - Sweimeh, K AU - Sweimeh K FAU - Brunner, H AU - Brunner H FAU - Voelter, W AU - Voelter W FAU - Kapurniotu, A AU - Kapurniotu A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amyloid) RN - 0 (Anilino Naphthalenesulfonates) RN - 0 (Islet Amyloid Polypeptide) RN - 82-76-8 (1-anilino-8-naphthalenesulfonate) SB - IM MH - Amyloid/*biosynthesis/*chemistry/metabolism MH - Anilino Naphthalenesulfonates/metabolism MH - Circular Dichroism MH - Filtration MH - Hot Temperature MH - Humans MH - Islet Amyloid Polypeptide MH - Kinetics MH - Microscopy, Atomic Force MH - Microscopy, Electron MH - Protein Binding MH - Protein Conformation MH - Protein Denaturation MH - Spectrophotometry, Ultraviolet EDAT- 1999/04/07 MHDA- 1999/04/07 00:01 CRDT- 1999/04/07 00:00 AID - S0022-2836(99)92646-3 [pii] AID - 10.1006/jmbi.1999.2646 [doi] PST - ppublish SO - J Mol Biol. 1999 Apr 9;287(4):781-96. PMID- 18191449 OWN - NLM STAT- MEDLINE DA - 20080307 DCOM- 20080609 LR - 20091119 IS - 0143-4179 (Print) IS - 0143-4179 (Linking) VI - 42 IP - 2 DP - 2008 Apr TI - Insights into the interaction of sortilin with proneurotrophins: a computational approach. PG - 205-14 LID - 10.1016/j.npep.2007.11.004 [doi] AB - Sortilin is a member of the recently discovered family of type-1 transmembrane Vps10p-domain receptors, which are expressed in several tissues, including brain and spinal chord. It has been recently demonstrated that the interaction between sortilin and the N-terminal portion of the precursor forms of the nerve growth factor (pro-NGF) and the brain-derived neurotrophic factor (pro-BDNF) represents a key event in the process that controls neurotrophins-mediated cell survival and death in developing neuronal tissue and post-traumatic neuronal apoptosis. Moreover, it is known that the cleavage of the N-terminal propeptide of sortilin is required for full functional activity of the receptor. The propeptide, indeed, hinders ligands from accessing the binding site of sortilin. However, to date, the molecular mechanism underlying the interaction between sortilin and pro-NGF/pro-BDNF remains unknown. By means of computational approaches, we suggest that the N-terminal Vps10p domain of sortilin, which is responsible for the interaction with the neurotrophins, adopts a beta-propeller fold, and that the N-terminal regions of sortilin, pro-NGF and pro-BDNF are mainly intrinsically disordered regions (IDRs). The following mechanism is therefore proposed: the Vps10p-domain of sortilin is a beta-propeller able to bind its own IDR and the IDRs of neurotrophins. The excision of its N-terminal disordered peptide allows the interaction with the intrinsically disordered N-terminus of pro-BDNF and pro-NGF, possibly through a disorder-to-order transition behaviour. FAU - Paiardini, Alessandro AU - Paiardini A AD - Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Universita di Roma La Sapienza, Piazzale Aldo Moro 5, Via degli Apuli 9, 00185 Rome, Italy. alessandro.paiardini@uniroma1.it FAU - Caputo, Viviana AU - Caputo V LA - eng PT - Journal Article DEP - 20080108 PL - Scotland TA - Neuropeptides JT - Neuropeptides JID - 8103156 RN - 0 (Adaptor Proteins, Vesicular Transport) RN - 0 (Brain-Derived Neurotrophic Factor) RN - 0 (Ligands) RN - 0 (Membrane Glycoproteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Protein Precursors) RN - 0 (pro-nerve growth factor, human) RN - 0 (sortilin) RN - 9061-61-4 (Nerve Growth Factor) SB - IM MH - Adaptor Proteins, Vesicular Transport MH - Amino Acid Sequence MH - Binding Sites/physiology MH - Brain/*metabolism MH - Brain-Derived Neurotrophic Factor/chemistry/*metabolism MH - Computational Biology MH - *Databases, Protein MH - Humans MH - Ligands MH - Membrane Glycoproteins/chemistry/*metabolism MH - Molecular Sequence Data MH - Nerve Growth Factor/chemistry/*metabolism MH - Nerve Tissue Proteins/chemistry/*metabolism MH - Protein Binding/physiology MH - Protein Precursors/chemistry/*metabolism MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary EDAT- 2008/01/15 09:00 MHDA- 2008/06/10 09:00 CRDT- 2008/01/15 09:00 PHST- 2007/07/24 [received] PHST- 2007/10/29 [revised] PHST- 2007/11/22 [accepted] PHST- 2008/01/08 [aheadofprint] AID - S0143-4179(07)00115-1 [pii] AID - 10.1016/j.npep.2007.11.004 [doi] PST - ppublish SO - Neuropeptides. 2008 Apr;42(2):205-14. doi: 10.1016/j.npep.2007.11.004. Epub 2008 Jan 8. PMID- 17766372 OWN - NLM STAT- MEDLINE DA - 20070925 DCOM- 20071105 LR - 20140904 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 16 IP - 10 DP - 2007 Oct TI - Pre-structured motifs in the natively unstructured preS1 surface antigen of hepatitis B virus. PG - 2108-17 AB - The preS1 surface antigen of hepatitis B virus (HBV) is known to play an important role in the initial attachment of HBV to hepatocytes. We have characterized structural features of the full-length preS1 using heteronuclear NMR methods and discovered that this 119-residue protein is inherently unstructured without a unique tertiary structure under a nondenaturing condition. Yet, combination of various NMR parameters shows that the preS1 contains "pre-structured" domains broadly covering its functional domains. The most prominent domain is formed by residues 27-45 and overlaps with the putative hepatocyte-binding domain (HBD) encompassing residues 21-47, within which two well-defined pre-structured motifs, formed by Pro(32)-Ala(36) and Pro(41)-Phe(45) are found. Additional, somewhat less prominent, pre-structured motifs are also formed by residues 11-18, 22-25, 37-40, and 46-50. Overall results suggest that the preS1 is a natively unstructured protein (NUP) whose N-terminal 50 residues, populated with multiple pre-structured motifs, contribute critically to hepatocyte binding. FAU - Chi, Seung-Wook AU - Chi SW AD - Molecular Cancer Research Center, Division of Molecular Therapeutics, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea. FAU - Kim, Do-Hyoung AU - Kim DH FAU - Lee, Si-Hyung AU - Lee SH FAU - Chang, Iksoo AU - Chang I FAU - Han, Kyou-Hoon AU - Han KH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070831 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Hepatitis B Surface Antigens) RN - 0 (Protein Precursors) RN - 0 (presurface protein 1, hepatitis B surface antigen) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Hepatitis B Surface Antigens/*chemistry MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Precursors/*chemistry PMC - PMC2204132 OID - NLM: PMC2204132 EDAT- 2007/09/04 09:00 MHDA- 2007/11/06 09:00 CRDT- 2007/09/04 09:00 PHST- 2007/08/31 [aheadofprint] AID - ps.072983507 [pii] AID - 10.1110/ps.072983507 [doi] PST - ppublish SO - Protein Sci. 2007 Oct;16(10):2108-17. Epub 2007 Aug 31. PMID- 16361428 OWN - NLM STAT- MEDLINE DA - 20051219 DCOM- 20060316 LR - 20061115 IS - 0022-1317 (Print) IS - 0022-1317 (Linking) VI - 87 IP - Pt 1 DP - 2006 Jan TI - Structural analysis of the human respiratory syncytial virus phosphoprotein: characterization of an alpha-helical domain involved in oligomerization. PG - 159-69 AB - Human respiratory syncytial virus (HRSV) phosphoprotein (P), an essential cofactor of the viral polymerase, is much shorter (241 aa) than and has no sequence similarity to P of other paramyxoviruses. Nevertheless, bioinformatic analysis of HRSV P sequence revealed a modular organization, reminiscent of other paramyxovirus Ps, with a central structured domain (aa 100-200), flanked by two intrinsically disordered regions (1-99 and 201-241). To test the predicted structure experimentally, HRSV P was purified from cell extracts infected with recombinant vaccinia virus or HRSV. The estimated molecular mass of P by gel filtration (approximately 500 kDa) greatly exceeded the theoretical mass of a homotetramer, proposed as the oligomeric form of native P. Nevertheless, the profile of cross-linked products obtained with purified P resembled that reported by others with P purified from bacteria or mammalian cells. Thus, the shape of HRSV P probably influences its elution from the gel filtration column, as reported for other paramyxovirus Ps. Digestion of purified HRSV P with different proteases identified a trypsin-resistant fragment (X) that reacted with a previously characterized monoclonal antibody (021/2P). N-terminal sequencing and mass spectrometry analysis placed the X fragment boundaries (Glu-104 and Arg-163) within the predicted structured domain of P. Cross-linking and circular dichroism analyses indicated that fragment X was oligomeric, with a high alpha-helical content, properties resembling those of the multimerization domain of Sendai and rinderpest virus P. These results denote structural features shared by HRSV and other paramyxovirus Ps and should assist in elucidation of the HRSV P structure. FAU - Llorente, Maria T AU - Llorente MT AD - Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain. FAU - Garcia-Barreno, Blanca AU - Garcia-Barreno B FAU - Calero, Miguel AU - Calero M FAU - Camafeita, Emilio AU - Camafeita E FAU - Lopez, Juan A AU - Lopez JA FAU - Longhi, Sonia AU - Longhi S FAU - Ferron, Francois AU - Ferron F FAU - Varela, Paloma F AU - Varela PF FAU - Melero, Jose A AU - Melero JA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Gen Virol JT - The Journal of general virology JID - 0077340 RN - 0 (Phosphoproteins) RN - EC 3.4.21.4 (Trypsin) SB - IM MH - Cell Line MH - Computational Biology MH - Humans MH - Phosphoproteins/*chemistry/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Respiratory Syncytial Virus, Human/*chemistry MH - Structure-Activity Relationship MH - Trypsin/metabolism EDAT- 2005/12/20 09:00 MHDA- 2006/03/17 09:00 CRDT- 2005/12/20 09:00 AID - 87/1/159 [pii] AID - 10.1099/vir.0.81430-0 [doi] PST - ppublish SO - J Gen Virol. 2006 Jan;87(Pt 1):159-69. PMID- 8639521 OWN - NLM STAT- MEDLINE DA - 19960715 DCOM- 19960715 LR - 20091119 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 35 IP - 18 DP - 1996 May 7 TI - Structure and dynamics of a CheY-binding domain of the chemotaxis kinase CheA determined by nuclear magnetic resonance spectroscopy. PG - 5633-40 AB - The Escherichia coli histidine autokinase CheA plays an important role in coupling signals received from membrane-bound receptors to changes in the swimming behavior of the cells in order to respond appropriately to environmental signals. Here we describe the structure of the 14 kDa fragment of the chemotaxis kinase CheA, residues 124--257, which binds to the downstream targets of phosphorylation, the response regulators CheY and CheB. This protein fragment contains the CheY-binding domain flanked on each side by regions that correspond to domain linkers in the intact protein. The structure of the domain was determined from 1429 restraints derived from heteronuclear multidimensional NMR experiments. Hybrid distance geometry--dynamical simulated annealing methods were used to calculate a family of structures that satisfy the experimental distance restraints and torsion angle restraints. The root mean square deviation of the 69 ordered residues in the domain is 0.52 A for the backbone heavy atoms and 0.99 A for all heavy atoms. The residues that have been implicated as important for CheY binding form a face consisting of several partially buried hydrophobic residues, framed by charged residues. The dynamic properties of this protein fragment were measured and analyzed using both isotropic and anisotropic models of molecular motion. The linker regions are very flexible and disordered, as evidenced by the very dynamics properties as compared to the CheY-binding domain. The CheY-binding domain of CheA is structurally similar to the histidine-containing phosphocarrier, HPr, which is a protein involved in the phosphoenolpyruvate:sugar phosphotransferase (PTS) pathway. This structural similarity suggests a possible evolutionary relationship of the PTS and chemotaxis pathways. FAU - McEvoy, M M AU - McEvoy MM AD - Institute of Molecular Biology, University of Oregon, Eugene 97403, USA. FAU - Muhandiram, D R AU - Muhandiram DR FAU - Kay, L E AU - Kay LE FAU - Dahlquist, F W AU - Dahlquist FW LA - eng GR - GM33677/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (Membrane Proteins) RN - 0 (Peptide Fragments) RN - 0 (methyl-accepting chemotaxis proteins) RN - EC 2.7.- (Protein Kinases) RN - EC 2.7.1.- (Phosphoenolpyruvate Sugar Phosphotransferase System) RN - EC 2.7.1.- (phosphocarrier protein HPr) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/genetics/metabolism MH - Binding Sites MH - Chemotaxis MH - Escherichia coli/enzymology/genetics MH - Evolution, Molecular MH - Magnetic Resonance Spectroscopy MH - Membrane Proteins/*chemistry/genetics/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Molecular Structure MH - Peptide Fragments/chemistry/genetics/metabolism MH - Phosphoenolpyruvate Sugar Phosphotransferase System/chemistry MH - Protein Kinases/*chemistry/genetics/metabolism MH - Thermodynamics EDAT- 1996/05/07 MHDA- 1996/05/07 00:01 CRDT- 1996/05/07 00:00 AID - 10.1021/bi952707h [doi] AID - bi952707h [pii] PST - ppublish SO - Biochemistry. 1996 May 7;35(18):5633-40. PMID- 22443319 OWN - NLM STAT- MEDLINE DA - 20120425 DCOM- 20120810 LR - 20131121 IS - 1520-5118 (Electronic) IS - 0021-8561 (Linking) VI - 60 IP - 16 DP - 2012 Apr 25 TI - Methionine oxidation enhances kappa-casein amyloid fibril formation. PG - 4144-55 LID - 10.1021/jf205168t [doi] AB - The effects of protein oxidation, for example of methionine residues, are linked to many diseases, including those of protein misfolding, such as Alzheimer's disease. Protein misfolding diseases are characterized by the accumulation of insoluble proteinaceous aggregates comprised mainly of amyloid fibrils. Amyloid-containing bodies known as corpora amylacea (CA) are also found in mammary secretory tissue, where their presence slows milk flow. The major milk protein kappa-casein readily forms amyloid fibrils under physiological conditions. Milk exists in an extracellular oxidizing environment. Accordingly, the two methionine residues in kappa-casein (Met(95) and Met(106)) were selectively oxidized and the effects on the fibril-forming propensity, cellular toxicity, chaperone ability, and structure of kappa-casein were determined. Oxidation resulted in an increase in the rate of fibril formation and a greater level of cellular toxicity. beta-Casein, which inhibits kappa-casein fibril formation in vitro, was less effective at suppressing fibril formation of oxidized kappa-casein. The ability of kappa-casein to prevent the amorphous aggregation of target proteins was slightly enhanced upon methionine oxidation, which may arise from the protein's greater exposed surface hydrophobicity. No significant changes to kappa-casein's intrinsically disordered structure occurred upon oxidation. The enhanced rate of fibril formation of oxidized kappa-casein, coupled with the reduced chaperone ability of beta-casein to prevent this aggregation, may affect casein-casein interaction within the casein micelle and thereby promote kappa-casein aggregation and contribute to the formation of CA. FAU - Koudelka, Tomas AU - Koudelka T AD - School of Chemistry & Physics, University of Adelaide, Adelaide, South Australia 5005, Australia. FAU - Dehle, Francis C AU - Dehle FC FAU - Musgrave, Ian F AU - Musgrave IF FAU - Hoffmann, Peter AU - Hoffmann P FAU - Carver, John A AU - Carver JA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120411 PL - United States TA - J Agric Food Chem JT - Journal of agricultural and food chemistry JID - 0374755 RN - 0 (Amyloid) RN - 0 (Caseins) RN - AE28F7PNPL (Methionine) SB - IM MH - Amyloid/*chemistry/metabolism MH - Animals MH - Caseins/*chemistry/metabolism MH - Cattle MH - Methionine/*chemistry/metabolism MH - Oxidation-Reduction MH - PC12 Cells MH - Rats EDAT- 2012/03/27 06:00 MHDA- 2012/08/11 06:00 CRDT- 2012/03/27 06:00 PHST- 2012/04/11 [aheadofprint] AID - 10.1021/jf205168t [doi] PST - ppublish SO - J Agric Food Chem. 2012 Apr 25;60(16):4144-55. doi: 10.1021/jf205168t. Epub 2012 Apr 11. PMID- 15797734 OWN - NLM STAT- MEDLINE DA - 20050330 DCOM- 20050802 LR - 20150612 IS - 1047-8477 (Print) IS - 1047-8477 (Linking) VI - 150 IP - 1 DP - 2005 Apr TI - Prepore to pore transition of a cholesterol-dependent cytolysin visualized by electron microscopy. PG - 100-8 AB - Perfringolysin O (PFO), a soluble toxin secreted by the pathogenic Clostridium perfringens, forms large homo-oligomeric pore complexes comprising up to 50 PFO molecules in cholesterol-containing membranes. In this study, electron microscopy (EM) and single-particle image analysis were used to reconstruct two-dimensional (2D) projection maps from images of oligomeric PFO prepore and pore complexes formed on cholesterol-rich lipid layers. The projection maps are characterized by an outer and an inner ring of density peaks. The outer rings of the prepore and pore complexes are very similar; however, the protein densities that make up the inner ring of the pore complex are more intense and discretely resolved than they are for the prepore complex. The change in inner-ring protein density is consistent with a mechanism in which the monomers within the prepore complex make a transition from a partially disordered state to a more ordered transmembrane beta-barrel in the pore complex. Finally, the orientation of the monomers within the oligomeric complexes was determined by visualization of streptavidin (SA) molecules bound to biotinylated cysteine-substituted residues predicted to face either the inner or outer surface of the oligomeric pore complex. This study provides an unprecedented view of the conversion of the PFO prepore to pore complex. FAU - Dang, Thanh X AU - Dang TX AD - Department of Cell Biology, The Scripps Research Institute, 10550 N.Torrey Pines Rd, La Jolla, CA 92037, USA. FAU - Hotze, Eileen M AU - Hotze EM FAU - Rouiller, Isabelle AU - Rouiller I FAU - Tweten, Rodney K AU - Tweten RK FAU - Wilson-Kubalek, Elizabeth M AU - Wilson-Kubalek EM LA - eng GR - 61938-01/PHS HHS/United States GR - AI037657/AI/NIAID NIH HHS/United States GR - R01 AI037657/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - 0 (Bacterial Toxins) RN - 0 (Hemolysin Proteins) RN - 71329-60-7 (Clostridium perfringens theta-toxin) RN - 97C5T2UQ7J (Cholesterol) SB - IM MH - Bacterial Toxins/*chemistry MH - Cholesterol/chemistry MH - Clostridium perfringens/metabolism MH - Hemolysin Proteins MH - Microscopy, Electron MH - Molecular Structure EDAT- 2005/03/31 09:00 MHDA- 2005/08/03 09:00 CRDT- 2005/03/31 09:00 PHST- 2004/11/19 [received] PHST- 2005/01/24 [revised] AID - S1047-8477(05)00044-4 [pii] AID - 10.1016/j.jsb.2005.02.003 [doi] PST - ppublish SO - J Struct Biol. 2005 Apr;150(1):100-8. PMID- 9439992 OWN - NLM STAT- MEDLINE DA - 19980302 DCOM- 19980302 LR - 20081121 IS - 0739-1102 (Print) IS - 0739-1102 (Linking) VI - 15 IP - 3 DP - 1997 Dec TI - Molecular dynamics simulation in solvent of the estrogen receptor protein DNA binding domain in complex with a non-consensus estrogen response element DNA sequence. PG - 407-30 AB - We investigated protein/DNA interactions, using molecular dynamics simulations computed between a 10 Angstom water layer model of the estrogen receptor (ER) protein DNA binding domain (DBD) amino acids and DNA of a non-consensus estrogen response element (ERE) consisting of 29 nucleotide base pairs. This ERE nucleotide sequence occurs naturally upstream of the Xenopus laevis Vitelligenin A1 gene. The ER DBD is encoded by three exons. Namely, exons 2 and 3 which encode the two zinc binding motifs and a sequence of exon 4 which encodes a predicted alpha helix. We generated a computer model of the ER DBD using atomic coordinates derived from the average of 30 nuclear magnetic resonance (NMR) spectroscopy coordinate sets. Amino acids on the carboxyl end of the ER DBD were disordered in both X-ray crystallography and NMR determinations and no coordinates were reported. This disordered region includes 10 amino acids of a predicted alpha helix encoded in exon 4 at the exon 3/4 splice junction. These amino acids are known to be important in DNA binding and are also believed to function as a nuclear translocation signal sequence for the ER protein. We generated a computer model of the predicted alpha helix consisting of the 10 amino acids encoded in exon 4 and attached this helix to the carboxyl end of the ER DBD at the exon 3/4 splice junction site. We docked the ER DBD model within the DNA major groove halfsites of the 29 base pair non-consensus ERE and flanking nucleotides. We constructed a solvated model with the ER DBD/ERE complex surrounded by a ten Angstrom water layer and conducted molecular dynamics simulations. Hydrogen bonding interactions were monitored. In addition, van der Waals and electrostatic interaction energies were calculated. Amino acids of the ER DBD DNA recognition helix formed both direct and water mediated hydrogen bonds at cognate codon-anticodon nucleotide base and backbone sites within the ERE DNA right major groove halfsite. Amino acids of the ER DBD exon 4 encoded predicted alpha helix formed direct and water mediated H-bonds with base and backbone sites of their cognate codon-anticodon nucleotides within the minor grooves flanking the ERE DNA major groove halfsites. These interactions together induced bending of the DNA into the protein. FAU - Harris, L F AU - Harris LF AD - David F. Hickok Memorial Cancer Research Laboratory, Abbott Northwestern Hospital, Minneapolis, MN 55407, USA. Mg90601@sk.msc.edu FAU - Sullivan, M R AU - Sullivan MR FAU - Popken-Harris, P D AU - Popken-Harris PD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biomol Struct Dyn JT - Journal of biomolecular structure & dynamics JID - 8404176 RN - 0 (DNA-Binding Proteins) RN - 0 (Estrogens) RN - 0 (Receptors, Estrogen) RN - 0 (Solvents) SB - IM MH - Animals MH - Base Sequence MH - Binding Sites MH - *Computer Simulation MH - Consensus Sequence MH - Conserved Sequence MH - DNA-Binding Proteins/chemistry/genetics/*metabolism MH - Estrogens/*genetics MH - Humans MH - Hydrogen Bonding MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Receptors, Estrogen/chemistry/genetics/*metabolism MH - Solvents MH - Static Electricity MH - Xenopus laevis EDAT- 1998/01/24 MHDA- 1998/01/24 00:01 CRDT- 1998/01/24 00:00 AID - 10.1080/07391102.1997.10508956 [doi] PST - ppublish SO - J Biomol Struct Dyn. 1997 Dec;15(3):407-30. PMID- 17880107 OWN - NLM STAT- MEDLINE DA - 20071009 DCOM- 20080116 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 46 IP - 41 DP - 2007 Oct 16 TI - Domain 2 of nonstructural protein 5A (NS5A) of hepatitis C virus is natively unfolded. PG - 11550-8 AB - Nonstructural protein 5A protein (NS5A) of hepatitis C virus (HCV) plays an important role in the regulation of viral replication, interferon resistance, and apoptosis. HCV NS5A comprises three domains. Recently the structure of domain 1 has been determined, revealing a structural scaffold with a novel zinc-binding motif and a disulfide bond. At present, the structures of domains 2 and 3 remain undefined. Domain 2 of HCV NS5A (NS5A-D2) is important for functions of NS5A and involved in molecular interactions with its own NS5B and PKR, a cellular interferon-inducible serine/threonine specific protein kinase. In this study we performed structural analysis of domain 2 by multinuclear nuclear magnetic resonance (NMR) spectroscopy. The analysis of the backbone 1H, 13C, and 15N resonances, 3JHNalpha coupling constants ,and 3D NOE data indicates that NS5A-D2 lacks secondary structural elements and reveals characteristics of unfolded proteins. NMR relaxation parameters confirmed the lack of rigid structure in the domain. The absence of an ordered conformation and the observation of a highly dynamic behavior of NS5A-D2 may provide an underlying molecular basis on its physiological function to allow NS5A-D2 to interact with a variety of biological partners. FAU - Liang, Yu AU - Liang Y AD - Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637511, Singapore. FAU - Ye, Hong AU - Ye H FAU - Kang, Cong Bao AU - Kang CB FAU - Yoon, Ho Sup AU - Yoon HS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070919 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Amino Acid Sequence MH - Apoptosis MH - Hepacivirus/*chemistry/physiology MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Peptide Fragments/chemistry MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Recombinant Proteins/chemistry/metabolism MH - Viral Nonstructural Proteins/*chemistry/genetics/metabolism MH - Virus Replication EDAT- 2007/09/21 09:00 MHDA- 2008/01/17 09:00 CRDT- 2007/09/21 09:00 PHST- 2007/09/19 [aheadofprint] AID - 10.1021/bi700776e [doi] PST - ppublish SO - Biochemistry. 2007 Oct 16;46(41):11550-8. Epub 2007 Sep 19. PMID- 21189124 OWN - NLM STAT- Publisher DA - 20101229 IS - 2212-3989 (Electronic) IS - 1871-5265 (Linking) DP - 2010 Dec 28 TI - HIV-1 Infected Patients Have Antibodies Recognizing Folded Tat. AB - Tat is a regulatory viral protein known as transactivator of HIV-1 genes but Tat is also secreted in the blood from HIV-1 infected cells. Extra cellular Tat can cross cellular membranes to trigger apoptosis and might explain the incapacity of the cellular immunity to eliminate HIV-1 infected cells. There is a controversy regarding Tat structure with studies suggesting that Tat would be a naturally unfolded protein. Here, we show that synthetic Tat variants need to be folded to have a transactivation activity in a cellular assay but this folding is unstable regarding the buffers and/or pH used as solvent. We show also that the recognition of a Tat variant versus peptides, covering its sequence, was different. Using an indirect ELISA method with 40 HIV-1 infected patients sera in ELISA test, we show Tat was recognized by 19 human sera either exclusively (n=8) or with Tat peptides (n=11). Dot Blot showed that unfolded Tat was no longer detectable by sera of the first group (n=8) compared to folded Tat. As a conclusion, this study suggests that Tat could be a naturally folded protein in the blood of HIV infected patients. FAU - Mediouni, Sonia AU - Mediouni S AD - Equipe de Recherche Technologique 2011, Faculte de Pharmacie, 27 BD Jean Moulin, 13385 Marseille, France. Erwann.loret@univmed.fr. FAU - Baillat, Gilbert AU - Baillat G FAU - Darque, Albert AU - Darque A FAU - Ravaux, Isabelle AU - Ravaux I FAU - Loret, Erwann AU - Loret E LA - ENG PT - JOURNAL ARTICLE DEP - 20101228 TA - Infect Disord Drug Targets JT - Infectious disorders drug targets JID - 101269158 EDAT- 2010/12/30 06:00 MHDA- 2010/12/30 06:00 CRDT- 2010/12/30 06:00 PHST- 2010/02/10 [received] PHST- 2010/07/15 [accepted] AID - BSP/ ID DT /E-Pub/-0001-11-1 [pii] PST - aheadofprint SO - Infect Disord Drug Targets. 2010 Dec 28. PMID- 16817888 OWN - NLM STAT- MEDLINE DA - 20060704 DCOM- 20060925 LR - 20061115 IS - 1742-464X (Print) IS - 1742-464X (Linking) VI - 273 IP - 12 DP - 2006 Jun TI - Structure-activity relationships of fowlicidin-1, a cathelicidin antimicrobial peptide in chicken. PG - 2581-93 AB - Cationic antimicrobial peptides are naturally occurring antibiotics that are actively being explored as a new class of anti-infective agents. We recently identified three cathelicidin antimicrobial peptides from chicken, which have potent and broad-spectrum antibacterial activities in vitro (Xiao Y, Cai Y, Bommineni YR, Fernando SC, Prakash O, Gilliland SE & Zhang G (2006) J Biol Chem281, 2858-2867). Here we report that fowlicidin-1 mainly adopts an alpha-helical conformation with a slight kink induced by glycine close to the center, in addition to a short flexible unstructured region near the N terminus. To gain further insight into the structural requirements for function, a series of truncation and substitution mutants of fowlicidin-1 were synthesized and tested separately for their antibacterial, cytolytic and lipopolysaccharide (LPS)-binding activities. The short C-terminal helical segment after the kink, consisting of a stretch of eight amino acids (residues 16-23), was shown to be critically involved in all three functions, suggesting that this region may be required for the peptide to interact with LPS and lipid membranes and to permeabilize both prokaryotic and eukaryotic cells. We also identified a second segment, comprising three amino acids (residues 5-7) in the N-terminal flexible region, that participates in LPS binding and cytotoxicity but is less important in bacterial killing. The fowlicidin-1 analog, with deletion of the second N-terminal segment (residues 5-7), was found to retain substantial antibacterial potency with a significant reduction in cytotoxicity. Such a peptide analog may have considerable potential for development as an anti-infective agent. FAU - Xiao, Yanjing AU - Xiao Y AD - Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA. FAU - Dai, Huaien AU - Dai H FAU - Bommineni, Yugendar R AU - Bommineni YR FAU - Soulages, Jose L AU - Soulages JL FAU - Gong, Yu-Xi AU - Gong YX FAU - Prakash, Om AU - Prakash O FAU - Zhang, Guolong AU - Zhang G LA - eng SI - PDB/2AMN PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Anti-Bacterial Agents) RN - 0 (Antimicrobial Cationic Peptides) RN - 0 (Lipopolysaccharides) RN - 143108-26-3 (CAP18 lipopolysaccharide-binding protein) SB - IM MH - Animals MH - Anti-Bacterial Agents/*chemistry/metabolism/*pharmacology MH - Antimicrobial Cationic Peptides/*chemistry/metabolism/*pharmacology MH - Binding Sites MH - Cells, Cultured MH - Chickens/metabolism MH - Dogs MH - Gram-Negative Bacteria/drug effects MH - Gram-Positive Bacteria/drug effects MH - Humans MH - Lipopolysaccharides/metabolism MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Structure-Activity Relationship EDAT- 2006/07/05 09:00 MHDA- 2006/09/26 09:00 CRDT- 2006/07/05 09:00 AID - EJB5261 [pii] AID - 10.1111/j.1742-4658.2006.05261.x [doi] PST - ppublish SO - FEBS J. 2006 Jun;273(12):2581-93. PMID- 20806220 OWN - NLM STAT- MEDLINE DA - 20101109 DCOM- 20110215 LR - 20140824 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 78 IP - 16 DP - 2010 Dec TI - Order within disorder: aggrecan chondroitin sulphate-attachment region provides new structural insights into protein sequences classified as disordered. PG - 3317-27 LID - 10.1002/prot.22839 [doi] AB - Structural investigation of proteins containing large stretches of sequences without predicted secondary structure is the focus of much increased attention. Here, we have produced an unglycosylated 30 kDa peptide from the chondroitin sulphate (CS)-attachment region of human aggrecan (CS-peptide), which was predicted to be intrinsically disordered and compared its structure with the adjacent aggrecan G3 domain. Biophysical analyses, including analytical ultracentrifugation, light scattering, and circular dichroism showed that the CS-peptide had an elongated and stiffened conformation in contrast to the globular G3 domain. The results suggested that it contained significant secondary structure, which was sensitive to urea, and we propose that the CS-peptide forms an elongated wormlike molecule based on a dynamic range of energetically equivalent secondary structures stabilized by hydrogen bonds. The dimensions of the structure predicted from small-angle X-ray scattering analysis were compatible with EM images of fully glycosylated aggrecan and a partly glycosylated aggrecan CS2-G3 construct. The semiordered structure identified in CS-peptide was not predicted by common structural algorithms and identified a potentially distinct class of semiordered structure within sequences currently identified as disordered. Sequence comparisons suggested some evidence for comparable structures in proteins encoded by other genes (PRG4, MUC5B, and CBP). The function of these semiordered sequences may serve to spatially position attached folded modules and/or to present polypeptides for modification, such as glycosylation, and to provide templates for the multiple pleiotropic interactions proposed for disordered proteins. CI - Copyright (c) 2010 Wiley-Liss, Inc. FAU - Jowitt, Thomas A AU - Jowitt TA AD - Wellcome Trust Centre for Cell Matrix Research, University of Manchester, Manchester, M13 9PT, United Kingdom. t.jowitt@manchester.ac.uk FAU - Murdoch, Alan D AU - Murdoch AD FAU - Baldock, Clair AU - Baldock C FAU - Berry, Richard AU - Berry R FAU - Day, Joanna M AU - Day JM FAU - Hardingham, Timothy E AU - Hardingham TE LA - eng GR - 01325/05/Biotechnology and Biological Sciences Research Council/United Kingdom GR - 077100/Z/05/A/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Aggrecans) RN - 0 (Peptides) RN - 8W8T17847W (Urea) RN - 9007-28-7 (Chondroitin Sulfates) SB - IM MH - Aggrecans/*chemistry/*metabolism/ultrastructure MH - Amino Acid Sequence MH - Binding Sites MH - Chondroitin Sulfates/*chemistry/*metabolism MH - Computational Biology MH - Humans MH - Hydrodynamics MH - Molecular Sequence Data MH - Peptides/chemistry MH - Protein Denaturation/drug effects MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Scattering, Small Angle MH - Structural Homology, Protein MH - Urea/pharmacology MH - X-Ray Diffraction PMC - PMC3546398 OID - NLM: PMC3546398 EDAT- 2010/09/02 06:00 MHDA- 2011/02/16 06:00 CRDT- 2010/09/01 06:00 AID - 10.1002/prot.22839 [doi] PST - ppublish SO - Proteins. 2010 Dec;78(16):3317-27. doi: 10.1002/prot.22839. PMID- 21715330 OWN - NLM STAT- MEDLINE DA - 20110822 DCOM- 20111018 LR - 20141022 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 34 DP - 2011 Aug 26 TI - Incomplete folding upon binding mediates Cdk4/cyclin D complex activation by tyrosine phosphorylation of inhibitor p27 protein. PG - 30142-51 LID - 10.1074/jbc.M111.244095 [doi] AB - p27(Kip1) (p27), an intrinsically disordered protein, regulates the various Cdk/cyclin complexes that control cell cycle progression. The kinase inhibitory domain of p27 contains a cyclin-binding subdomain (D1), a Cdk-binding subdomain (D2), and a linker helix subdomain that connects D1 and D2. Here, we report that, despite extensive sequence conservation between Cdk4/cyclin D1 (hereafter Cdk4/cyclin D) and Cdk2/cyclin A, the thermodynamic details describing how the individual p27 subdomains contribute to equally high affinity binding to these two Cdk/cyclin complexes are strikingly different. Differences in enthalpy/entropy compensation revealed that the D2 subdomain of p27 folds incompletely when binding Cdk4/cyclin D versus Cdk2/cyclin A. Incomplete binding-induced folding exposes tyrosine 88 of p27 for phosphorylation by the nonreceptor tyrosine kinase Abl. Importantly, tyrosine phosphorylation (of p27) relieves Cdk inhibition by p27, enabling cell cycle entry. Furthermore, the interaction between a conserved hydrophobic patch on cyclin D and subdomain D1 is much weaker than that with cyclin A; consequently, a construct containing subdomains D1 and LH (p27-D1LH) does not inhibit substrate binding to Cdk4/cyclin D as it does to Cdk2/cyclin A. Our results provide a mechanism by which Cdk4 (within the p27/Cdk4/cyclin D complex) is poised to be activated by extrinsic mitogenic signals that impinge upon p27 at the earliest stage of cell division. More broadly, our results further illustrate the regulatory versatility of intrinsically disordered proteins. FAU - Ou, Li AU - Ou L AD - Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA. FAU - Ferreira, Antonio M AU - Ferreira AM FAU - Otieno, Steve AU - Otieno S FAU - Xiao, Limin AU - Xiao L FAU - Bashford, Donald AU - Bashford D FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng GR - 2P30CA021765/CA/NCI NIH HHS/United States GR - R01 CA082491/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20110629 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (CDKN1B protein, human) RN - 0 (Cyclin D) RN - 0 (Multiprotein Complexes) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - EC 2.7.10.2 (Proto-Oncogene Proteins c-abl) RN - EC 2.7.11.22 (CDK4 protein, human) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 4) SB - IM MH - Cyclin D/*chemistry/genetics/metabolism MH - Cyclin-Dependent Kinase 4/*chemistry/genetics/metabolism MH - Cyclin-Dependent Kinase Inhibitor p27/*chemistry/genetics/metabolism MH - Entropy MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Multiprotein Complexes/*chemistry/genetics/metabolism MH - Phosphorylation/physiology MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-abl/chemistry/genetics/metabolism PMC - PMC3191053 OID - NLM: PMC3191053 EDAT- 2011/07/01 06:00 MHDA- 2011/10/19 06:00 CRDT- 2011/07/01 06:00 PHST- 2011/06/29 [aheadofprint] AID - M111.244095 [pii] AID - 10.1074/jbc.M111.244095 [doi] PST - ppublish SO - J Biol Chem. 2011 Aug 26;286(34):30142-51. doi: 10.1074/jbc.M111.244095. Epub 2011 Jun 29. PMID- 22955885 OWN - NLM STAT- MEDLINE DA - 20120928 DCOM- 20121205 LR - 20141105 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 109 IP - 39 DP - 2012 Sep 25 TI - Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity. PG - 15781-6 AB - Like animals and plants, multicellular fungi possess cell-to-cell channels (septal pores) that allow intercellular communication and transport. Here, using a combination of MS of Woronin body-associated proteins and a bioinformatics approach that identifies related proteins based on composition and character, we identify 17 septal pore-associated (SPA) proteins that localize to the septal pore in rings and pore-centered foci. SPA proteins are not homologous at the primary sequence level but share overall physical properties with intrinsically disordered proteins. Some SPA proteins form aggregates at the septal pore, and in vitro assembly assays suggest aggregation through a nonamyloidal mechanism involving mainly alpha-helical and disordered structures. SPA loss-of-function phenotypes include excessive septation, septal pore degeneration, and uncontrolled Woronin body activation. Together, our data identify the septal pore as a complex subcellular compartment and focal point for the assembly of unstructured proteins controlling diverse aspects of intercellular connectivity. FAU - Lai, Julian AU - Lai J AD - Temasek Life Sciences Laboratory, National University of Singapore, Singapore. FAU - Koh, Chuan Hock AU - Koh CH FAU - Tjota, Monika AU - Tjota M FAU - Pieuchot, Laurent AU - Pieuchot L FAU - Raman, Vignesh AU - Raman V FAU - Chandrababu, Karthik Balakrishna AU - Chandrababu KB FAU - Yang, Daiwen AU - Yang D FAU - Wong, Limsoon AU - Wong L FAU - Jedd, Gregory AU - Jedd G LA - eng GR - P01 GM068087/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120906 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Fungal Proteins) RN - 0 (Multiprotein Complexes) SB - IM MH - Cell Membrane/genetics/*metabolism MH - Fungal Proteins/genetics/*metabolism MH - Multiprotein Complexes/genetics/*metabolism MH - Neurospora crassa/genetics/*metabolism/ultrastructure MH - Protein Structure, Secondary PMC - PMC3465371 OID - NLM: PMC3465371 EDAT- 2012/09/08 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/09/08 06:00 PHST- 2012/09/06 [aheadofprint] AID - 1207467109 [pii] AID - 10.1073/pnas.1207467109 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):15781-6. Epub 2012 Sep 6. PMID- 12649428 OWN - NLM STAT- MEDLINE DA - 20030321 DCOM- 20031023 LR - 20140611 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 12 IP - 4 DP - 2003 Apr TI - Polycation-induced oligomerization and accelerated fibrillation of human alpha-synuclein in vitro. PG - 702-7 AB - The aggregation and fibrillation of alpha-synuclein has been implicated as a causative factor in Parkinson's disease and several other neurodegenerative disorders known as synucleinopathies. The effect of different factors on the process of fibril formation has been intensively studied in vitro. We show here that alpha-synuclein interacts with different unstructured polycations (spermine, polylysine, polyarginine, and polyethyleneimine) to form specific complexes. In addition, the polycations catalyze alpha-synuclein oligomerization. The formation of alpha-synuclein-polycation complexes was not accompanied by significant structural changes in alpha-synuclein. However, alpha-synuclein fibrillation was dramatically accelerated in the presence of polycations. The magnitude of the accelerating effect depended on the nature of the polymer, its length, and concentration. The results illustrate the potential critical role of electrostatic interactions in protein aggregation, and the potential role of naturally occurring polycations in modulating alpha-synuclein aggregation. FAU - Goers, John AU - Goers J AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. FAU - Uversky, Vladimir N AU - Uversky VN FAU - Fink, Anthony L AU - Fink AL LA - eng GR - NS39985/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Nerve Tissue Proteins) RN - 0 (Polyamines) RN - 0 (Polymers) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 0 (polycations) SB - IM MH - Circular Dichroism MH - Humans MH - Microscopy, Electron MH - Nerve Tissue Proteins/*metabolism/ultrastructure MH - Polyamines/*metabolism MH - Polymers/*metabolism MH - Synucleins MH - alpha-Synuclein PMC - PMC2323845 OID - NLM: PMC2323845 EDAT- 2003/03/22 04:00 MHDA- 2003/10/24 05:00 CRDT- 2003/03/22 04:00 AID - 10.1110/ps.0230903 [doi] PST - ppublish SO - Protein Sci. 2003 Apr;12(4):702-7. PMID- 11575936 OWN - NLM STAT- MEDLINE DA - 20010928 DCOM- 20011025 LR - 20091119 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 312 IP - 4 DP - 2001 Sep 28 TI - Solution NMR structure and folding dynamics of the N terminus of a rat non-muscle alpha-tropomyosin in an engineered chimeric protein. PG - 833-47 AB - Tropomyosin is an alpha-helical coiled-coil protein that aligns head-to-tail along the length of the actin filament and regulates its function. The solution structure of the functionally important N terminus of a short 247-residue non-muscle tropomyosin was determined in an engineered chimeric protein, GlyTM1bZip, consisting of the first 19 residues of rat short alpha-tropomyosin and the last 18 residues of the GCN4 leucine zipper. A gene encoding GlyTM1bZip was synthesized, cloned and expressed in Escherichia coli. Triple resonance NMR spectra were analyzed with the program AutoAssign to assign its backbone resonances. Multidimensional nuclear Overhauser effect spectra, X-filtered spectra and (3)J(H(N)-H(alpha)) scalar coupling were analyzed using AutoStructure. This is the first application of this new program to determine the three-dimensional structure of a symmetric homodimer and a structure not previously reported. Residues 7-35 in GlyTM1bZip form a coiled coil, but neither end is helical. Heteronuclear (15)N-(1)H nuclear Overhauser effect data showed that the non-helical N-terminal residues are flexible. The (13)C' chemical shifts of the coiled-coil backbone carbonyl groups in GlyTM1bZip showed a previously unreported periodicity, where resonances arising from residues at the coiled-coil interface in a and d positions of the heptad repeat were displaced relatively upfield and those arising from residues in c positions were displaced relatively downfield. Heteronuclear single quantum coherence spectra, collected as a function of temperature, showed that cross-peaks arising from the alpha-helical backbone and side-chains at the coiled-coil interface broadened or shifted with T(M) values approximately 20 degrees C lower than the loss of alpha-helix measured by circular dichroism, suggesting the presence of a folding intermediate. The side-chain of Ile14, a residue essential for binding interactions, exhibited multiple conformations. The conformational flexibility of the N termini of short tropomyosins may be important for their binding specificity. CI - Copyright 2001 Academic Press. FAU - Greenfield, N J AU - Greenfield NJ AD - Department of Neuroscience and Cell Biology, UMDNJ-Robert Wood Johnson Medical School, Piscataway, NJ 08854-5635, USA. greenfie@rwja.umdnj.edu FAU - Huang, Y J AU - Huang YJ FAU - Palm, T AU - Palm T FAU - Swapna, G V AU - Swapna GV FAU - Monleon, D AU - Monleon D FAU - Montelione, G T AU - Montelione GT FAU - Hitchcock-DeGregori, S E AU - Hitchcock-DeGregori SE LA - eng SI - PDB/1IHQ GR - GM-36326/GM/NIGMS NIH HHS/United States GR - HL-35726/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DNA-Binding Proteins) RN - 0 (Fungal Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Solutions) RN - 0 (Tropomyosin) RN - EC 2.7.- (Protein Kinases) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Circular Dichroism MH - *DNA-Binding Proteins MH - Exons/genetics MH - Fungal Proteins/chemistry/genetics/metabolism MH - Leucine Zippers MH - Models, Molecular MH - Molecular Sequence Data MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Denaturation MH - *Protein Engineering MH - *Protein Folding MH - Protein Kinases/chemistry/genetics/metabolism MH - Protein Structure, Secondary MH - Rats MH - Recombinant Fusion Proteins/chemistry/metabolism MH - *Saccharomyces cerevisiae Proteins MH - Sequence Alignment MH - Solutions MH - Temperature MH - Tropomyosin/*chemistry/genetics/*metabolism EDAT- 2001/09/29 10:00 MHDA- 2001/10/26 10:01 CRDT- 2001/09/29 10:00 AID - 10.1006/jmbi.2001.4982 [doi] AID - S0022-2836(01)94982-4 [pii] PST - ppublish SO - J Mol Biol. 2001 Sep 28;312(4):833-47. PMID- 24303310 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20131204 DCOM- 20131204 LR - 20141007 IS - 2153-4063 (Electronic) VI - 2013 DP - 2013 TI - Order-disorder interface characterization reveals critical factors for disease and drug targets. PG - 101 AB - Signal transduction pathways are of critical importance in disease and regulation of cellular functions. Proteins that do not fold to a state of stable tertiary structure, known as intrinsically disordered proteins, are highly represented in signaling pathways and protein interaction networks. Important examples of disordered signaling proteins include p53 and BRCA1, and approximately 40% of Eukaryotic proteins are estimated to have significant disordered regions. Certain regions within these disordered proteins, however, can take on an ordered structure upon binding to a partner. The nature of the resulting protein-protein interactions has not yet been established. Here we categorize and identify interactions between binding segments of disordered proteins and their ordered partners using a Bayesian network framework, constructed on a test set of 964 proteins mined for Molecular Recognition Feature (MoRF) characteristics from the PDB. This framework, more specifically Bayesian network learning, enables us to investigate the underlying biological processes involved, including the sequential and structural determinants of these interactions. After the construction of the training set (80% of data), features were successively eliminated to determine relative significances. The Bayesian network model was validated on the test set with excellent accuracy(>90% AUC). Examining features underlying the model provides a plethora of new and potentially useful biological information. The results also lend themselves to a strategy for rational drug design whereby disordered regions can be targeted with a high degree of specificity and small molecule peptide mimetics of their binding regions can be utilized as drugs. FAU - Kallenbach, Jonah AU - Kallenbach J AD - Center for Biomedical Informatics, Harvard Medical School [Boston, MA 02115]. FAU - Hsu, Wei-Lun AU - Hsu WL FAU - Dunker, A Keith AU - Dunker AK FAU - Alterovitz, Gil AU - Alterovitz G LA - eng PT - Journal Article DEP - 20130318 PL - United States TA - AMIA Jt Summits Transl Sci Proc JT - AMIA Joint Summits on Translational Science proceedings AMIA Summit on Translational Science JID - 101539486 EDAT- 2013/12/05 06:00 MHDA- 2013/12/05 06:01 CRDT- 2013/12/05 06:00 PHST- 2013 [ecollection] PHST- 2013/03/18 [epublish] PST - epublish SO - AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:101. eCollection 2013. PMID- 22317784 OWN - NLM STAT- MEDLINE DA - 20120618 DCOM- 20121023 IS - 1873-2550 (Electronic) IS - 0304-4017 (Linking) VI - 187 IP - 3-4 DP - 2012 Jul 6 TI - BQP35 is a novel member of the intrinsically unstructured protein (IUP) family which is a potential antigen for the sero-diagnosis of Babesia sp. BQ1 (Lintan) infection. PG - 421-30 LID - 10.1016/j.vetpar.2012.01.021 [doi] AB - A new gene of Babesia sp. BQ1 (Lintan) (BQP35) was cloned by screening a merozoite cDNA expression library with infected sheep serum and using rapid amplification of cDNA ends (RACE). The nucleotide sequence of the cDNA was 1140bp with an open reading frame (ORF) of 936bp encoding a 35-kDa predicted polypeptide with 311 amino acid residues. Comparison of BQP35 cDNA and genomic DNA sequences showed that BQP35 does not possess an intron. Recombinant BQP35 (rBQP35), expressed in a prokaryotic expression system, showed abnormally slow migration on SDS-PAGE. Gel shifting, amino acid sequence and in silico disorder region prediction indicated that BQP35 protein has characteristics of intrinsically unstructured proteins (IUPs). This is the first description of such proteins in the Babesia genus. BQP35 induced antibodies production as early as one week after Babesia sp. BQ1 (Lintan) infection in sheep. No cross-reaction was observed with sera from sheep infected with other ovine piroplasms dominant in China, except with Babesia sp. Tianzhu. The interest of BQP35 as a diagnostic antigen is discussed. CI - Copyright (c) 2012 Elsevier B.V. All rights reserved. FAU - Guan, Guiquan AU - Guan G AD - State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Xujiaping 1, Lanzhou, Gansu 730046, PR China. FAU - Moreau, Emmanuelle AU - Moreau E FAU - Liu, Junlong AU - Liu J FAU - Ma, Miling AU - Ma M FAU - Rogniaux, Helene AU - Rogniaux H FAU - Liu, Aihong AU - Liu A FAU - Niu, Qingli AU - Niu Q FAU - Li, Youquan AU - Li Y FAU - Ren, Qiaoyun AU - Ren Q FAU - Luo, Jianxun AU - Luo J FAU - Chauvin, Alain AU - Chauvin A FAU - Yin, Hong AU - Yin H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120121 PL - Netherlands TA - Vet Parasitol JT - Veterinary parasitology JID - 7602745 RN - 0 (Antigens, Protozoan) RN - 0 (Protozoan Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Antigens, Protozoan/chemistry/genetics/*metabolism MH - Babesia/classification/*metabolism MH - Babesiosis/diagnosis/*parasitology MH - Base Sequence MH - Electrophoresis, Polyacrylamide Gel MH - Enzyme-Linked Immunosorbent Assay/veterinary MH - Gene Expression Regulation MH - Gene Library MH - Molecular Sequence Data MH - Protozoan Proteins MH - Reproducibility of Results MH - Sensitivity and Specificity MH - Serologic Tests/veterinary MH - Sheep MH - Sheep Diseases/diagnosis/*parasitology EDAT- 2012/02/10 06:00 MHDA- 2012/10/24 06:00 CRDT- 2012/02/10 06:00 PHST- 2011/04/27 [received] PHST- 2012/01/04 [revised] PHST- 2012/01/13 [accepted] PHST- 2012/01/21 [aheadofprint] AID - S0304-4017(12)00040-4 [pii] AID - 10.1016/j.vetpar.2012.01.021 [doi] PST - ppublish SO - Vet Parasitol. 2012 Jul 6;187(3-4):421-30. doi: 10.1016/j.vetpar.2012.01.021. Epub 2012 Jan 21. PMID- 20516128 OWN - NLM STAT- MEDLINE DA - 20100602 DCOM- 20100908 LR - 20140827 IS - 1943-0264 (Electronic) VI - 2 IP - 6 DP - 2010 Jun TI - The tumor suppressor p53: from structures to drug discovery. PG - a000919 LID - 10.1101/cshperspect.a000919 [doi] AB - Even 30 years after its discovery, the tumor suppressor protein p53 is still somewhat of an enigma. p53's intimate and multifaceted role in the cell cycle is mirrored in its equally complex structural biology that is being unraveled only slowly. Here, we discuss key structural aspects of p53 function and its inactivation by oncogenic mutations. Concerted action of folded and intrinsically disordered domains of the highly dynamic p53 protein provides binding promiscuity and specificity, allowing p53 to process a myriad of cellular signals to maintain the integrity of the human genome. Importantly, progress in elucidating the structural biology of p53 and its partner proteins has opened various avenues for structure-guided rescue of p53 function in tumors. These emerging anticancer strategies include targeting mutant-specific lesions on the surface of destabilized cancer mutants with small molecules and selective inhibition of p53's degradative pathways. FAU - Joerger, Andreas C AU - Joerger AC AD - MRC Centre for Protein Engineering, Hills Road, Cambridge, United Kingdom. acj2@mrc-lmb.cam.ac.uk FAU - Fersht, Alan R AU - Fersht AR LA - eng PT - Journal Article PT - Review DEP - 20100210 PL - United States TA - Cold Spring Harb Perspect Biol JT - Cold Spring Harbor perspectives in biology JID - 101513680 RN - 0 (Antineoplastic Agents) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Antineoplastic Agents/*pharmacology MH - Drug Delivery Systems MH - *Drug Discovery MH - Gene Expression Regulation/*physiology MH - Humans MH - Tumor Suppressor Protein p53/genetics/*metabolism RF - 98 PMC - PMC2869527 OID - NLM: PMC2869527 EDAT- 2010/06/03 06:00 MHDA- 2010/09/09 06:00 CRDT- 2010/06/03 06:00 PHST- 2010/02/10 [aheadofprint] AID - cshperspect.a000919 [pii] AID - 10.1101/cshperspect.a000919 [doi] PST - ppublish SO - Cold Spring Harb Perspect Biol. 2010 Jun;2(6):a000919. doi: 10.1101/cshperspect.a000919. Epub 2010 Feb 10. PMID- 23314729 OWN - NLM STAT- MEDLINE DA - 20130402 DCOM- 20130916 LR - 20141104 IS - 1573-5001 (Electronic) IS - 0925-2738 (Linking) VI - 55 IP - 3 DP - 2013 Mar TI - Fast hydrogen exchange affects (1)(5)N relaxation measurements in intrinsically disordered proteins. PG - 249-56 LID - 10.1007/s10858-013-9706-1 [doi] AB - Unprotected amide protons can undergo fast hydrogen exchange (HX) with protons from the solvent. Generally, NMR experiments using the out-and-back coherence transfer with amide proton detection are affected by fast HX and result in reduced signal intensity. When one of these experiments, (1)H-(15)N HSQC, is used to measure the (15)N transverse relaxation rate (R2), the measured R2 rate is convoluted with the HX rate (kHX) and has higher apparent R2 values. Since the (15)N R2 measurement is important for analyzing protein backbone dynamics, the HX effect on the R2 measurement is investigated and described here by multi-exponential signal decay. We demonstrate these effects by performing (15)N R 2 (CPMG) experiments on alpha-synuclein, an intrinsically disordered protein, in which the amide protons are exposed to solvent. We show that the HX effect on R 2 (CPMG) can be extracted by the derived equation. In conclusion, the HX effect may be pulse sequence specific and results from various sources including the J coupling evolution, the change of steady state water proton magnetization, and the D2O content in the sample. To avoid the HX effect on the analysis of relaxation data of unprotected amides, it is suggested that NMR experimental conditions insensitive to the HX should be considered or that intrinsic R 2 (CPMG) values be obtained by methods described herein. FAU - Kim, Seho AU - Kim S AD - Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. FAU - Wu, Kuen-Phon AU - Wu KP FAU - Baum, Jean AU - Baum J LA - eng GR - 5R90DK071502/DK/NIDDK NIH HHS/United States GR - GM087012/GM/NIGMS NIH HHS/United States GR - GM45302/GM/NIGMS NIH HHS/United States GR - R01 GM045302/GM/NIGMS NIH HHS/United States GR - R01 GM087012/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130112 PL - Netherlands TA - J Biomol NMR JT - Journal of biomolecular NMR JID - 9110829 RN - 0 (Nitrogen Isotopes) RN - 0 (Proteins) RN - 7YNJ3PO35Z (Hydrogen) SB - IM MH - Hydrogen/*chemistry MH - Hydrogen-Ion Concentration MH - Nitrogen Isotopes/*chemistry MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Proteins/*chemistry PMC - PMC3615062 MID - NIHMS435336 OID - NLM: NIHMS435336 OID - NLM: PMC3615062 EDAT- 2013/01/15 06:00 MHDA- 2013/09/17 06:00 CRDT- 2013/01/15 06:00 PHST- 2012/04/08 [received] PHST- 2013/01/05 [accepted] PHST- 2013/01/12 [aheadofprint] AID - 10.1007/s10858-013-9706-1 [doi] PST - ppublish SO - J Biomol NMR. 2013 Mar;55(3):249-56. doi: 10.1007/s10858-013-9706-1. Epub 2013 Jan 12. PMID- 22665783 OWN - NLM STAT- MEDLINE DA - 20120620 DCOM- 20120910 LR - 20141218 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 109 IP - 25 DP - 2012 Jun 19 TI - Capturing directed molecular motion in the nuclear pore complex of live cells. PG - 9863-8 LID - 10.1073/pnas.1200486109 [doi] AB - Nuclear pore complexes (NPCs) are gateways for nucleocytoplasmic exchange. Intrinsically disordered nucleoporins (Nups) form a selective filter inside the NPC, taking a central role in the vital nucleocytoplasmic transport mechanism. How such intricate meshwork relates to function and gives rise to a transport mechanism is still unclear. Here we set out to tackle this issue in intact cells by an established combination of fluorescence correlation spectroscopy and real-time tracking of the center of mass of single NPCs. We find the dynamics of nucleoporin Nup153 to be regulated so as to produce rapid, discrete exchange between two separate positions within the NPC. A similar behavior is also observed for both karyopherinbeta1 transport-receptor and cargoes destined to nuclear import. Thus, we argue that directed Nup-mediated molecular motion may represent an intrinsic feature of the overall selective gating through intact NPCs. FAU - Cardarelli, Francesco AU - Cardarelli F AD - Center for Nanotechnology Innovation at National Enterprise for nanoScience and nanoTechnology, Istituto Italiano di Tecnologia, 56127 Pisa, Italy. FAU - Lanzano, Luca AU - Lanzano L FAU - Gratton, Enrico AU - Gratton E LA - eng GR - 5P41RR003155/RR/NCRR NIH HHS/United States GR - 5P50 GM076516/GM/NIGMS NIH HHS/United States GR - 8P41GM103540/GM/NIGMS NIH HHS/United States GR - P30 CA062203/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20120604 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Nuclear Pore Complex Proteins) RN - 147336-22-9 (Green Fluorescent Proteins) SB - IM MH - Animals MH - CHO Cells MH - Cricetinae MH - Cricetulus MH - Green Fluorescent Proteins/metabolism MH - Nuclear Pore/*metabolism MH - Nuclear Pore Complex Proteins/metabolism MH - Protein Transport MH - Spectrometry, Fluorescence PMC - PMC3382504 OID - NLM: PMC3382504 EDAT- 2012/06/06 06:00 MHDA- 2012/09/11 06:00 CRDT- 2012/06/06 06:00 PHST- 2012/06/04 [aheadofprint] AID - 1200486109 [pii] AID - 10.1073/pnas.1200486109 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2012 Jun 19;109(25):9863-8. doi: 10.1073/pnas.1200486109. Epub 2012 Jun 4. PMID- 22203819 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20111228 DCOM- 20121002 LR - 20130813 IS - 1664-302X (Electronic) IS - 1664-302X (Linking) VI - 2 DP - 2011 TI - The Structure of the Hantavirus Zinc Finger Domain is Conserved and Represents the Only Natively Folded Region of the Gn Cytoplasmic Tail. PG - 251 LID - 10.3389/fmicb.2011.00251 [doi] AB - Hantaviruses, of the family Bunyaviridae, are present throughout the world and cause a variety of infections ranging from the asymptomatic to mild and severe hemorrhagic fevers. Hantaviruses are enveloped anti-sense RNA viruses that contain three genomic segments that encode for a nucleocapsid protein, two membrane glycoproteins (Gn and Gc), and an RNA polymerase. Recently, the pathogenicity of hantaviruses has been mapped to the carboxyl end of the 150 residue Gn cytoplasmic tail. The Gn tail has also been shown to play a role in binding the ribonucleoprotein (RNP), a step critical for virus assembly. In this study, we use NMR spectroscopy to compare the structure of a Gn tail zinc finger domain of both a pathogenic (Andes) and a non-pathogenic (Prospect Hill) hantavirus. We demonstrate that despite a stark difference in the virulence of both of these viruses, the structure of the Gn core zinc finger domain is largely conserved in both strains. We also use NMR backbone relaxation studies to demonstrate that the regions of the Andes virus Gn tail immediately outside the zinc finger domain, sites known to bind the RNP, are disordered and flexible, thus intimating that the zinc finger domain is the only structured region of the Gn tail. These structural observations provide further insight into the role of the Gn tail during viral assembly as well as its role in pathogenesis. FAU - Estrada, D Fernando AU - Estrada DF AD - Department of Molecular Biosciences, University of Kansas Lawrence, KS, USA. FAU - Conner, Michael AU - Conner M FAU - Jeor, Stephen C AU - Jeor SC FAU - Guzman, Roberto N De AU - Guzman RN LA - eng PT - Journal Article DEP - 20111221 PL - Switzerland TA - Front Microbiol JT - Frontiers in microbiology JID - 101548977 PMC - PMC3243910 OID - NLM: PMC3243910 OTO - NOTNLM OT - Prospect Hill virus OT - andes virus OT - glycoprotein OT - hantavirus OT - zinc finger EDAT- 2011/12/29 06:00 MHDA- 2011/12/29 06:01 CRDT- 2011/12/29 06:00 PHST- 2011/11/09 [received] PHST- 2011/11/27 [accepted] PHST- 2011/12/21 [epublish] AID - 10.3389/fmicb.2011.00251 [doi] PST - epublish SO - Front Microbiol. 2011 Dec 21;2:251. doi: 10.3389/fmicb.2011.00251. eCollection 2011. PMID- 12668765 OWN - NLM STAT- MEDLINE DA - 20030416 DCOM- 20030617 LR - 20141120 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 100 IP - 8 DP - 2003 Apr 15 TI - Structure of the GAT domain of human GGA1: a syntaxin amino-terminal domain fold in an endosomal trafficking adaptor. PG - 4451-6 AB - The Golgi-associated, gamma-adaptin homologous, ADP-ribosylation factor (ARF)-interacting proteins (GGAs) are adaptors that sort receptors from the trans-Golgi network into the endosomallysosomal pathway. The GGAs and TOM1 (GAT) domains of the GGAs are responsible for their ARF-dependent localization. The 2.4-A crystal structure of the GAT domain of human GGA1 reveals a three-helix bundle, with a long N-terminal helical extension that is not conserved in GAT domains that do not bind ARF. The ARF binding site is located in the N-terminal extension and is separate from the core three-helix bundle. An unanticipated structural similarity to the N-terminal domain of syntaxin 1a was discovered, comprising the entire three-helix bundle. A conserved binding site on helices 2 and 3 of the GAT domain three-helix bundle is predicted to interact with coiled-coil-containing proteins. We propose that the GAT domain is descended from the same ancestor as the syntaxin 1a N-terminal domain, and that both protein families share a common function in binding coiled-coil domain proteins. FAU - Suer, Silke AU - Suer S AD - Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA. FAU - Misra, Saurav AU - Misra S FAU - Saidi, Layla F AU - Saidi LF FAU - Hurley, James H AU - Hurley JH LA - eng SI - PDB/1NWM PT - Journal Article DEP - 20030331 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Adaptor Proteins, Vesicular Transport) RN - 0 (Antigens, Surface) RN - 0 (Carrier Proteins) RN - 0 (GGA adaptor proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Recombinant Proteins) RN - 0 (STX1A protein, human) RN - 0 (Syntaxin 1) RN - EC 3.6.5.2 (ADP-Ribosylation Factor 1) RN - EC 3.6.5.2 (ADP-Ribosylation Factors) SB - IM MH - ADP-Ribosylation Factor 1/metabolism MH - ADP-Ribosylation Factors/*chemistry/genetics/metabolism MH - *Adaptor Proteins, Vesicular Transport MH - Amino Acid Sequence MH - Antigens, Surface/chemistry/genetics MH - Binding Sites MH - Carrier Proteins/*chemistry/genetics/metabolism MH - Crystallography, X-Ray MH - Endosomes/metabolism MH - Humans MH - In Vitro Techniques MH - Models, Molecular MH - Molecular Sequence Data MH - Molecular Structure MH - Nerve Tissue Proteins/chemistry/genetics MH - Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Sequence Homology, Amino Acid MH - Static Electricity MH - Syntaxin 1 PMC - PMC404691 OID - NLM: PMC404691 EDAT- 2003/04/02 05:00 MHDA- 2003/06/18 05:00 CRDT- 2003/04/02 05:00 PHST- 2003/03/31 [aheadofprint] AID - 10.1073/pnas.0831133100 [doi] AID - 0831133100 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4451-6. Epub 2003 Mar 31. PMID- 18398853 OWN - NLM STAT- MEDLINE DA - 20080623 DCOM- 20090128 LR - 20131121 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 90 IP - 4 DP - 2008 TI - Structural propensities in the heme binding region of apocytochrome b5. I. Free peptides. PG - 544-55 LID - 10.1002/bip.20996 [doi] AB - The water-soluble domain of rat microsomal cytochrome b5 is a small globular hemoprotein. Under native conditions, the apoprotein consists of a well-folded hydrophobic core and a 42-residue loop, which is substantially disordered in solution. Association with the heme cofactor causes the loop to organize into a second well-folded hydrophobic core encompassing four short helices, H2-H5. Of these, H3 and H4 are recognized as intrinsically disordered by algorithms that analyze primary structures for folding propensities. Three peptides, spanning H2-H5, H2-H3, and H4-H5, were designed, synthesized, and characterized to identify local structural preferences in the isolated loop. In addition, two replacements (D60R and N57P, which are known to stabilize holocytochrome b5) were introduced individually in the H4-H5 peptide. Helical content measured by nuclear magnetic resonance and far-UV circular dichroism spectroscopy in solutions of 2,2,2-trifluoroethanol revealed that H4 possessed a lower propensity to form the holoprotein structure than H3. Both replacements in H4 resulted in measurable changes in observed overall helical propensities. It was concluded that the prediction of intrinsic disorder was reliable. Furthermore, the stability of the holoprotein did not correlate simply with helical propensities in the disordered regions. CI - Copyright (c) 2008 Wiley Periodicals, Inc. FAU - Davis, Ronald B Jr AU - Davis RB Jr AD - Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA. FAU - Lecomte, Juliette T J AU - Lecomte JT LA - eng GR - GM-54217/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 RN - 0 (Peptides) RN - 0 (Solutions) RN - 42VZT0U6YR (Heme) RN - 4QD397987E (Histidine) RN - 75-89-8 (Trifluoroethanol) RN - 9035-39-6 (Cytochromes b5) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Circular Dichroism MH - Cytochromes b5/*chemistry MH - Heme/*metabolism MH - Histidine MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Peptides/*chemistry MH - Protein Structure, Secondary MH - Rats MH - Solubility MH - Solutions MH - Trifluoroethanol EDAT- 2008/04/10 09:00 MHDA- 2009/01/29 09:00 CRDT- 2008/04/10 09:00 AID - 10.1002/bip.20996 [doi] PST - ppublish SO - Biopolymers. 2008;90(4):544-55. doi: 10.1002/bip.20996. PMID- 16384580 OWN - NLM STAT- MEDLINE DA - 20060130 DCOM- 20061108 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 356 IP - 3 DP - 2006 Feb 24 TI - Structure of a putative lipoate protein ligase from Thermoplasma acidophilum and the mechanism of target selection for post-translational modification. PG - 625-37 AB - Lipoyl-lysine swinging arms are crucial to the reactions catalysed by the 2-oxo acid dehydrogenase multienzyme complexes. A gene encoding a putative lipoate protein ligase (LplA) of Thermoplasma acidophilum was cloned and expressed in Escherichia coli. The recombinant protein, a monomer of molecular mass 29 kDa, was catalytically inactive. Crystal structures in the absence and presence of bound lipoic acid were solved at 2.1 A resolution. The protein was found to fall into the alpha/beta class and to be structurally homologous to the catalytic domains of class II aminoacyl-tRNA synthases and biotin protein ligase, BirA. Lipoic acid in LplA was bound in the same position as biotin in BirA. The structure of the T.acidophilum LplA and limited proteolysis of E.coli LplA together highlighted some key features of the post-translational modification. A loop comprising residues 71-79 in the T.acidophilum ligase is proposed as interacting with the dithiolane ring of lipoic acid and discriminating against the entry of biotin. A second loop comprising residues 179-193 was disordered in the T.acidophilum structure; tryptic cleavage of the corresponding loop in the E.coli LplA under non-denaturing conditions rendered the enzyme catalytically inactive, emphasizing its importance. The putative LplA of T.acidophilum lacks a C-terminal domain found in its counterparts in E.coli (Gram-negative) or Streptococcus pneumoniae (Gram-positive). A gene encoding a protein that appears to have structural homology to the additional domain in the E.coli and S.pneumoniae enzymes was detected alongside the structural gene encoding the putative LplA in the T.acidophilum genome. It is likely that this protein is required to confer activity on the LplA as currently purified, one protein perhaps catalysing the formation of the obligatory lipoyl-AMP intermediate, and the other transferring the lipoyl group from it to the specific lysine residue in the target protein. FAU - McManus, Edward AU - McManus E AD - Department of Biochemistry, University of Cambridge, Old Addenbrooke's Site, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAU - Luisi, Ben F AU - Luisi BF FAU - Perham, Richard N AU - Perham RN LA - eng SI - PDB/2C7I SI - PDB/2C8M GR - Wellcome Trust/United Kingdom PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051205 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Archaeal Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Repressor Proteins) RN - 0 (Transcription Factors) RN - 6SO6U10H04 (Biotin) RN - 73Y7P0K73Y (Thioctic Acid) RN - EC 3.4.21.4 (Trypsin) RN - EC 6.3.- (Carbon-Nitrogen Ligases) RN - EC 6.3.2.- (Peptide Synthases) RN - EC 6.3.2.- (lipoate-protein ligase) RN - EC 6.3.4.15 (birA protein, E coli) SB - IM MH - Amino Acid Sequence MH - Archaeal Proteins/*chemistry/genetics MH - Biotin/metabolism MH - Carbon-Nitrogen Ligases/chemistry MH - Crystallography, X-Ray MH - Escherichia coli/enzymology MH - Escherichia coli Proteins/chemistry MH - Molecular Sequence Data MH - Peptide Synthases/*chemistry/genetics MH - Protein Binding MH - *Protein Processing, Post-Translational MH - Protein Structure, Tertiary MH - Repressor Proteins/chemistry MH - Substrate Specificity MH - Thermoplasma/*enzymology/genetics MH - Thioctic Acid/metabolism MH - Transcription Factors/chemistry MH - Trypsin/chemistry EDAT- 2005/12/31 09:00 MHDA- 2006/11/10 09:00 CRDT- 2005/12/31 09:00 PHST- 2005/08/16 [received] PHST- 2005/11/03 [revised] PHST- 2005/11/15 [accepted] PHST- 2005/12/05 [aheadofprint] AID - S0022-2836(05)01453-1 [pii] AID - 10.1016/j.jmb.2005.11.057 [doi] PST - ppublish SO - J Mol Biol. 2006 Feb 24;356(3):625-37. Epub 2005 Dec 5. PMID- 15050829 OWN - NLM STAT- MEDLINE DA - 20040330 DCOM- 20040511 LR - 20141125 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 338 IP - 1 DP - 2004 Apr 16 TI - Two homologous domains of similar structure but different stability in the yeast linker histone, Hho1p. PG - 139-48 AB - The Saccharomyces cerevisiae homologue of the linker histone H1, Hho1p, has two domains that are similar in sequence to the globular domain of H1 (and variants such as H5). It is an open question whether both domains are functional and whether they play similar structural roles. Preliminary structural studies showed that the two isolated domains, GI and GII, differ significantly in stability. In 10 mM sodium phosphate (pH 7), the GI domain, like the globular domains of H1 and H5, GH1 and GH5, was stably folded, whereas GII was largely unstructured. However, at high concentrations of large tetrahedral anions (phosphate, sulphate, perchlorate), which might mimic the charge-screening effects of DNA phosphate groups, GII was folded. In view of the potential significance of these observations in relation to the role of Hho1p, we have now determined the structures of its GI and GII domains by NMR spectroscopy under conditions in which GII (like GI) is folded. The backbone r.m.s.d. over the ordered residues is 0.43 A for GI and 0.97 A for GII. Both structures show the "winged-helix" fold typical of GH1 and GH5 and are very similar to each other, with an r.m.s.d. over the structured regions of 1.3 A, although there are distinct differences. The potential for GII to adopt a structure similar to that of GI when Hho1p is bound to chromatin in vivo suggests that both globular domains might be functional. Whether Hho1p performs a structural role by bridging two nucleosomes remains to be determined. FAU - Ali, Tariq AU - Ali T AD - Cambridge Centre for Molecular Recognition and Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAU - Coles, Patrick AU - Coles P FAU - Stevens, Timothy J AU - Stevens TJ FAU - Stott, Katherine AU - Stott K FAU - Thomas, Jean O AU - Thomas JO LA - eng SI - PDB/1USS SI - PDB/1UST GR - B19489/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Anions) RN - 0 (DNA, Fungal) RN - 0 (HHO1 protein, S cerevisiae) RN - 0 (Histones) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Amino Acid Sequence MH - Anions/metabolism MH - Conserved Sequence MH - DNA, Fungal/*chemistry/*metabolism MH - Histones/*chemistry/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - *Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Saccharomyces cerevisiae/*chemistry MH - Saccharomyces cerevisiae Proteins/*chemistry/*metabolism MH - Sequence Homology, Amino Acid EDAT- 2004/03/31 05:00 MHDA- 2004/05/12 05:00 CRDT- 2004/03/31 05:00 PHST- 2003/12/05 [received] PHST- 2004/02/10 [revised] PHST- 2004/02/13 [accepted] AID - 10.1016/j.jmb.2004.02.046 [doi] AID - S0022283604002232 [pii] PST - ppublish SO - J Mol Biol. 2004 Apr 16;338(1):139-48. PMID- 21091436 OWN - NLM STAT- MEDLINE DA - 20110128 DCOM- 20110315 LR - 20110906 IS - 1470-8728 (Electronic) IS - 0264-6021 (Linking) VI - 434 IP - 1 DP - 2011 Feb 15 TI - Flexibility of the Ure2 prion domain is important for amyloid fibril formation. PG - 143-51 LID - 10.1042/BJ20101895 [doi] AB - Ure2, the protein determinant of the Saccharomyces cerevisiae prion [URE3], has a natively disordered N-terminal domain that is important for prion formation in vivo and amyloid formation in vitro; the globular C-domain has a glutathione transferase-like fold. In the present study, we swapped the position of the N- and C-terminal regions, with or without an intervening peptide linker, to create the Ure2 variants CLN-Ure2 and CN-Ure2 respectively. The native structural content and stability of the variants were the same as wild-type Ure2, as indicated by enzymatic activity, far-UV CD analysis and equilibrium denaturation. CLN-Ure2 was able to form amyloid-like fibrils, but with a significantly longer lag time than wild-type Ure2; and the two proteins were unable to cross-seed. Under the same conditions, CN-Ure2 showed limited ability to form fibrils, but this was improved after addition of 0.03 M guanidinium chloride. As for wild-type Ure2, allosteric enzyme activity was observed in fibrils of CLN-Ure2 and CN-Ure2, consistent with retention of the native-like dimeric structure of the C-domains within the fibrils. Proteolytically digested fibrils of CLN-Ure2 and CN-Ure2 showed the same residual fibril core morphology as wild-type Ure2. The results suggest that the position of the prion domain affects the ability of Ure2 to form fibrils primarily due to effects on its flexibility. FAU - Yu, Yong AU - Yu Y AD - National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, China. FAU - Wang, Hai-Yan AU - Wang HY FAU - Bai, Ming AU - Bai M FAU - Perrett, Sarah AU - Perrett S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (Amyloid) RN - 0 (Prions) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 1.11.1.9 (Glutathione Peroxidase) RN - EC 1.11.1.9 (URE2 protein, S cerevisiae) SB - IM MH - Amyloid/*metabolism MH - Gene Expression Regulation, Fungal/physiology MH - Glutathione Peroxidase/*genetics/*metabolism MH - Kinetics MH - Mutation MH - Prions/genetics/*metabolism MH - Protein Folding MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/*genetics/*metabolism EDAT- 2010/11/26 06:00 MHDA- 2011/03/16 06:00 CRDT- 2010/11/25 06:00 AID - BJ20101895 [pii] AID - 10.1042/BJ20101895 [doi] PST - ppublish SO - Biochem J. 2011 Feb 15;434(1):143-51. doi: 10.1042/BJ20101895. PMID- 15489503 OWN - NLM STAT- MEDLINE DA - 20041231 DCOM- 20050721 LR - 20071115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 1 DP - 2005 Jan 7 TI - The 1.8-A crystal structure of human tear lipocalin reveals an extended branched cavity with capacity for multiple ligands. PG - 484-93 AB - In contrast with earlier assumptions, which classified human tear lipocalin (Tlc) as an outlier member of the lipocalin protein family, the 1.8-A resolution crystal structure of the recombinant apoprotein confirms the typical eight-stranded antiparallel beta-barrel architecture with an alpha-helix attached to it. The fold of Tlc most closely resembles the bovine dander allergen Bos d 2, a well characterized prototypic lipocalin, but also reveals similarity with beta-lactoglobulin. However, compared with other lipocalin structures Tlc exhibits an extremely wide ligand pocket, whose entrance is formed by four partially disordered loops. The cavity deeply extends into the beta-barrel structure, where it ends in two distinct lobes. This unusual structural feature explains the known promiscuity of Tlc for various ligands, with chemical structures ranging from lipids and retinoids to the macrocyclic antibiotic rifampin and even to microbial siderophores. Notably, earlier findings of biological activity as a thiol protease inhibitor have no correspondence in the three-dimensional structure of Tlc, rather it appears that its proteolytic fragments could be responsible for this phenomenon. Hence, the present structural analysis sheds new light on the ligand binding activity of this functionally obscure but abundant human lipocalin. FAU - Breustedt, Daniel A AU - Breustedt DA AD - Lehrstuhl fur Biologische Chemie, Technische Universitat Munchen, D-85350 Freising-Weihenstephan, Germany. FAU - Korndorfer, Ingo P AU - Korndorfer IP FAU - Redl, Bernhard AU - Redl B FAU - Skerra, Arne AU - Skerra A LA - eng SI - PDB/1XK1 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20041015 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Carrier Proteins) RN - 0 (LCN1 protein, human) RN - 0 (Ligands) RN - 0 (Lipocalin 1) RN - 0 (Macromolecular Substances) RN - 0 (Protease Inhibitors) RN - 0 (Recombinant Proteins) SB - IM MH - Amino Acid Sequence MH - Carrier Proteins/*chemistry/metabolism MH - Humans MH - Ligands MH - Lipocalin 1 MH - Macromolecular Substances/chemistry MH - *Models, Molecular MH - Molecular Sequence Data MH - Protease Inhibitors/chemistry MH - Protein Binding MH - Protein Conformation MH - Recombinant Proteins/chemistry/metabolism MH - Structure-Activity Relationship EDAT- 2004/10/19 09:00 MHDA- 2005/07/22 09:00 CRDT- 2004/10/19 09:00 PHST- 2004/10/15 [aheadofprint] AID - M410466200 [pii] AID - 10.1074/jbc.M410466200 [doi] PST - ppublish SO - J Biol Chem. 2005 Jan 7;280(1):484-93. Epub 2004 Oct 15. PMID- 17034249 OWN - NLM STAT- MEDLINE DA - 20061012 DCOM- 20070817 LR - 20131121 IS - 1520-6106 (Print) IS - 1520-5207 (Linking) VI - 110 IP - 41 DP - 2006 Oct 19 TI - Assessing induced folding of an intrinsically disordered protein by site-directed spin-labeling electron paramagnetic resonance spectroscopy. PG - 20596-608 AB - We used site-directed spin-labeling electron paramagnetic resonance (EPR) spectroscopy to study the induced folding of the intrinsically disordered C-terminal domain of measles virus nucleoprotein (N(TAIL)). Four single-site N(TAIL) mutants (S407C, S488C, L496C, and V517C), located in three conserved regions, were prepared and labeled with a nitroxide paramagnetic probe. We could monitor the gain of rigidity that N(TAIL) undergoes in the presence of either the secondary structure stabilizer 2,2,2-trifluoroethanol (TFE) or one of its physiological partners, namely, the C-terminal domain (XD) of the viral phosphoprotein. The mobility of the spin label grafted at positions 488, 496, and 517 was significantly reduced upon addition of XD, contrary to that of the spin label bound to position 407, which was unaffected. Furthermore, the EPR spectra of spin-labeled S488C and L496C bound to XD in the presence of 30% sucrose are indicative of the formation of an alpha-helix in the proximity of the spin labels. Such an alpha-helix had been already identified by previous biochemical and structural studies. Using TFE we unveiled a previously undetected structural propensity within the N-terminal region of N(TAIL) and showed that its C-terminal region "resists" gaining structure even at high TFE concentrations. Finally, we for the first time showed the reversibility of the induced folding process that N(TAIL) undergoes in the presence of XD. These results highlight the suitability of site-directed spin-labeling EPR spectroscopy to identify protein regions involved in binding and folding events, while providing insights at the residue level. FAU - Morin, Benjamin AU - Morin B AD - Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS et Universites Aix-Marseille I et II, Campus de Luminy, 163 Avenue de Luminy, Case 932, 13288 Marseille Cedex 09, France. FAU - Bourhis, Jean-Marie AU - Bourhis JM FAU - Belle, Valerie AU - Belle V FAU - Woudstra, Mireille AU - Woudstra M FAU - Carriere, Frederic AU - Carriere F FAU - Guigliarelli, Bruno AU - Guigliarelli B FAU - Fournel, Andre AU - Fournel A FAU - Longhi, Sonia AU - Longhi S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Phosphoproteins) RN - 0 (Proteins) RN - 0 (Spin Labels) RN - 31C4KY9ESH (Nitric Oxide) SB - IM MH - Biophysics/*methods MH - Chemistry, Physical/*methods MH - Electron Spin Resonance Spectroscopy MH - Escherichia coli/metabolism MH - Magnetics MH - Molecular Conformation MH - Mutation MH - Nitric Oxide/chemistry MH - Phosphoproteins/chemistry MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proteins/*chemistry MH - Spin Labels EDAT- 2006/10/13 09:00 MHDA- 2007/08/19 09:00 CRDT- 2006/10/13 09:00 AID - 10.1021/jp063708u [doi] PST - ppublish SO - J Phys Chem B. 2006 Oct 19;110(41):20596-608. PMID- 22282160 OWN - NLM STAT- MEDLINE DA - 20120306 DCOM- 20120629 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 4 DP - 2012 Apr TI - Inter-domain movements in polyketide synthases: a molecular dynamics study. PG - 1157-71 LID - 10.1039/c2mb05425f [doi] AB - Insights into the structure and dynamics of modular polyketide synthases (PKS) are essential for understanding the mechanistic details of the biosynthesis of a large number of pharmaceutically important secondary metabolites. The crystal structures of the KS-AT di-domain from erythromycin synthase have revealed the relative orientation of various catalytic domains in a minimal PKS module. However, the relatively large distance between catalytic centers of KS and AT domains in the static structure has posed certain intriguing questions regarding mechanistic details of substrate transfer during polyketide biosynthesis. In order to investigate the role of inter-domain movements in substrate channeling, we have carried out a series of explicit solvent MD simulations for time periods ranging from 10 to 15 ns on the KS-AT di-domain and its sub-fragments. Analyses of these MD trajectories have revealed that both the catalytic domains and the structured inter-domain linker region remain close to their starting structures. Inter-domain movements at KS-linker and linker-AT interfaces occur around hinge regions which connect the structured linker region to the catalytic domains. The KS-linker interface was found to be more flexible compared to the linker-AT interface. However, inter-domain movements observed during the timescale of our simulations do not significantly reduce the distance between catalytic centers of KS and AT domains for facilitating substrate channeling. Based on these studies and prediction of intrinsic disorder we propose that the intrinsically unstructured linker stretch preceding the ACP domain might be facilitating movement of ACP domains to various catalytic centers. FAU - Anand, Swadha AU - Anand S AD - National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India. FAU - Mohanty, Debasisa AU - Mohanty D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120127 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 79956-01-7 (Polyketide Synthases) SB - IM MH - Amino Acid Sequence MH - Catalytic Domain MH - *Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Polyketide Synthases/*metabolism MH - Protein Structure, Tertiary MH - Substrate Specificity EDAT- 2012/01/28 06:00 MHDA- 2012/06/30 06:00 CRDT- 2012/01/28 06:00 PHST- 2012/01/27 [aheadofprint] PHST- 2012/04/01 [epublish] AID - 10.1039/c2mb05425f [doi] PST - ppublish SO - Mol Biosyst. 2012 Apr;8(4):1157-71. doi: 10.1039/c2mb05425f. Epub 2012 Jan 27. PMID- 23684953 OWN - NLM STAT- MEDLINE DA - 20130717 DCOM- 20130926 LR - 20150122 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1833 IP - 10 DP - 2013 Oct TI - N-terminally truncated forms of human cathepsin F accumulate in aggresome-like inclusions. PG - 2254-66 LID - 10.1016/j.bbamcr.2013.05.007 [doi] LID - S0167-4889(13)00187-0 [pii] AB - The contribution of individual cysteine cathepsins as positive mediators of programmed cell death is dependent on several factors, such as the type of stimuli, intensity and duration of the stimulus, and cell type involved. Of the eleven human cysteine cathepsins, cathepsin F is the only cathepsin that exhibits an extended N-terminal proregion, which contains a cystatin-like domain. We predicted that the wild-type human cathepsin F contains three natively disordered regions within the enzyme's propeptide and various amino acid stretches with high fibrillation propensity. Wild-type human cathepsin F and its N-terminally truncated forms, Ala(20)-Asp(484) (Delta(19)CatF), Pro(126)-Asp(484) (Delta(125)CatF), and Met(147)-Asp(484) (Delta(146)CatF) were cloned into the pcDNA3 vector and overexpressed in HEK 293T cells. Wild-type human cathepsin F displayed a clear vesicular labeling and colocalized with the LAMP2 protein, a lysosomal marker. However, all three N-terminally truncated forms of human cathepsin F were recovered as insoluble proteins, suggesting that the deletion of at least the signal peptides (Delta(19)CatF), results in protein aggregation. Noteworthy, they concentrated large perinuclear-juxtanuclear aggregates that accumulated within aggresome-like inclusions. These inclusions showed p62-positive immunoreactivity and were colocalized with the autophagy marker LC3B, but not with the LAMP2 protein. In addition, an approximately 2-3 fold increase in DEVDase activity was not sufficient to induce apoptotic cell death. These results suggested the clearance of the N-terminally truncated forms of human cathepsin F via the autophagy pathway, underlying its protective and prosurvival mechanisms. CI - Copyright (c) 2013 The Authors. Published by Elsevier B.V. All rights reserved. FAU - Jeric, Barbara AU - Jeric B AD - Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Ljubljana, Slovenia. FAU - Dolenc, Iztok AU - Dolenc I FAU - Mihelic, Marko AU - Mihelic M FAU - Klaric, Martina AU - Klaric M FAU - Zavasnik-Bergant, Tina AU - Zavasnik-Bergant T FAU - Guncar, Gregor AU - Guncar G FAU - Turk, Boris AU - Turk B FAU - Turk, Vito AU - Turk V FAU - Stoka, Veronika AU - Stoka V LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130514 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (LAMP2 protein, human) RN - 0 (Lysosomal-Associated Membrane Protein 2) RN - 0 (Lysosome-Associated Membrane Glycoproteins) RN - 0 (MAP1LC3B protein, human) RN - 0 (Microtubule-Associated Proteins) RN - 0 (SQSTM1 protein, human) RN - EC 3.4.22.- (Caspases) RN - EC 3.4.22.41 (Cathepsin F) SB - IM MH - Adaptor Proteins, Signal Transducing/*metabolism MH - Amino Acid Sequence MH - Apoptosis MH - Autophagy MH - Blotting, Western MH - Caspases/*metabolism MH - Cathepsin F/genetics/*metabolism MH - Cells, Cultured MH - Enzyme Activation MH - Fluorescent Antibody Technique MH - Glycosylation MH - Humans MH - Immunoenzyme Techniques MH - Lysosomal-Associated Membrane Protein 2 MH - Lysosome-Associated Membrane Glycoproteins/*metabolism MH - Microtubule-Associated Proteins/*metabolism MH - Molecular Sequence Data MH - Plasmids MH - Protein Multimerization MH - Subcellular Fractions OTO - NOTNLM OT - Aggregation-prone OT - Aggresome OT - Aggresome-like inclusion OT - Autophagy OT - Caspase activation OT - Cathepsin F OT - HRP OT - Mw OT - horseradish peroxidase OT - molecular weight OT - truncated form of human cathepsin F (Ala(20)-Asp(484)) OT - truncated form of human cathepsin F (Met(147)-Asp(484)) OT - truncated form of human cathepsin F (Pro(126)-Asp(484)) OT - wild-type cathepsin F OT - wtCatF OT - Delta(125)CatF OT - Delta(146)CatF OT - Delta(19)CatF EDAT- 2013/05/21 06:00 MHDA- 2013/09/27 06:00 CRDT- 2013/05/21 06:00 PHST- 2012/11/19 [received] PHST- 2013/05/06 [revised] PHST- 2013/05/07 [accepted] PHST- 2013/05/14 [aheadofprint] AID - S0167-4889(13)00187-0 [pii] AID - 10.1016/j.bbamcr.2013.05.007 [doi] PST - ppublish SO - Biochim Biophys Acta. 2013 Oct;1833(10):2254-66. doi: 10.1016/j.bbamcr.2013.05.007. Epub 2013 May 14. PMID- 19636917 OWN - NLM STAT- MEDLINE DA - 20090728 DCOM- 20090826 LR - 20110406 IS - 1874-270X (Electronic) VI - 2 IP - 1 DP - 2008 Jun TI - Backbone assignment of osteopontin, a cytokine and cell attachment protein implicated in tumorigenesis. PG - 29-31 LID - 10.1007/s12104-007-9076-2 [doi] AB - OPN is an RGD-containing protein overexpressed in cells transformed by v-myc and v-mil(raf) oncogenes. Here we report the resonance assignment of recombinant quail OPN and provide NMR evidence that quail OPN is an intrinsically unstructured protein in solution. FAU - Schedlbauer, Andreas AU - Schedlbauer A AD - Department of Biomolecular Structural Chemistry, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria. FAU - Ozdowy, Przemyslaw AU - Ozdowy P FAU - Kontaxis, Georg AU - Kontaxis G FAU - Hartl, Markus AU - Hartl M FAU - Bister, Klaus AU - Bister K FAU - Konrat, Robert AU - Konrat R LA - eng GR - P 17041-B12/Austrian Science Fund FWF/Austria GR - P 18148-B12/Austrian Science Fund FWF/Austria PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080118 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (Carbon Isotopes) RN - 0 (Cell Adhesion Molecules) RN - 0 (Cytokines) RN - 0 (Nitrogen Isotopes) RN - 0 (Protons) RN - 106441-73-0 (Osteopontin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Carbon Isotopes/chemistry MH - Cell Adhesion Molecules/*chemistry MH - Cytokines/*chemistry MH - Magnetic Resonance Spectroscopy/*methods MH - Molecular Sequence Data MH - Molecular Weight MH - Neoplasms/metabolism MH - Nitrogen Isotopes/chemistry MH - Osteopontin/*chemistry MH - Protons MH - Quail/*metabolism EDAT- 2009/07/29 09:00 MHDA- 2009/08/27 09:00 CRDT- 2009/07/29 09:00 PHST- 2007/11/14 [received] PHST- 2007/12/11 [accepted] PHST- 2008/01/18 [aheadofprint] AID - 10.1007/s12104-007-9076-2 [doi] PST - ppublish SO - Biomol NMR Assign. 2008 Jun;2(1):29-31. doi: 10.1007/s12104-007-9076-2. Epub 2008 Jan 18. PMID- 21317293 OWN - NLM STAT- MEDLINE DA - 20110411 DCOM- 20110628 LR - 20140821 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 15 DP - 2011 Apr 15 TI - Characterization of the interactions between the nucleoprotein and the phosphoprotein of Henipavirus. PG - 13583-602 LID - 10.1074/jbc.M111.219857 [doi] AB - The Henipavirus genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that recruits the polymerase complex via the phosphoprotein (P). In a previous study, we reported that in henipaviruses, the N-terminal domain of the phosphoprotein and the C-terminal domain of the nucleoprotein (N(TAIL)) are both intrinsically disordered. Here we show that Henipavirus N(TAIL) domains are also disordered in the context of full-length nucleoproteins. We also report the cloning, purification, and characterization of the C-terminal X domains (P(XD)) of Henipavirus phosphoproteins. Using isothermal titration calorimetry, we show that N(TAIL) and P(XD) form a 1:1 stoichiometric complex that is stable under NaCl concentrations as high as 1 M and has a K(D) in the muM range. Using far-UV circular dichroism and nuclear magnetic resonance, we show that P(XD) triggers an increase in the alpha-helical content of N(TAIL). Using fluorescence spectroscopy, we show that P(XD) has no impact on the chemical environment of a Trp residue introduced at position 527 of the Henipavirus N(TAIL) domain, thus arguing for the lack of stable contacts between the C termini of N(TAIL) and P(XD). Finally, we present a tentative structural model of the N(TAIL)-P(XD) interaction in which a short, order-prone region of N(TAIL) (alpha-MoRE; amino acids 473-493) adopts an alpha-helical conformation and is embedded between helices alpha2 and alpha3 of P(XD), leading to a relatively small interface dominated by hydrophobic contacts. The present results provide the first detailed experimental characterization of the N-P interaction in henipaviruses and designate the N(TAIL)-P(XD) interaction as a valuable target for rational antiviral approaches. FAU - Habchi, Johnny AU - Habchi J AD - Laboratoire d' Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France. FAU - Blangy, Stephanie AU - Blangy S FAU - Mamelli, Laurent AU - Mamelli L FAU - Jensen, Malene Ringkjobing AU - Jensen MR FAU - Blackledge, Martin AU - Blackledge M FAU - Darbon, Herve AU - Darbon H FAU - Oglesbee, Michael AU - Oglesbee M FAU - Shu, Yaoling AU - Shu Y FAU - Longhi, Sonia AU - Longhi S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110211 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Nucleoproteins) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Proteins) RN - 0 (Viral Proteins) SB - IM MH - Henipavirus/*chemistry/genetics MH - *Models, Molecular MH - Nucleoproteins/*chemistry/genetics MH - Phosphoproteins/*chemistry/genetics MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics MH - Viral Proteins/*chemistry/genetics PMC - PMC3075704 OID - NLM: PMC3075704 EDAT- 2011/02/15 06:00 MHDA- 2011/06/29 06:00 CRDT- 2011/02/15 06:00 PHST- 2011/02/11 [aheadofprint] AID - M111.219857 [pii] AID - 10.1074/jbc.M111.219857 [doi] PST - ppublish SO - J Biol Chem. 2011 Apr 15;286(15):13583-602. doi: 10.1074/jbc.M111.219857. Epub 2011 Feb 11. PMID- 11434766 OWN - NLM STAT- MEDLINE DA - 20010703 DCOM- 20010927 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 40 IP - 27 DP - 2001 Jul 10 TI - Solution structure of the squash trypsin inhibitor MCoTI-II. A new family for cyclic knottins. PG - 7973-83 AB - The "knottin" fold is a stable cysteine-rich scaffold, in which one disulfide crosses the macrocycle made by two other disulfides and the connecting backbone segments. This scaffold is found in several protein families with no evolutionary relationships. In the past few years, several homologous peptides from the Rubiaceae and Violaceae families were shown to define a new structural family based on macrocyclic knottin fold. We recently isolated from Momordica cochinchinensis seeds the first known macrocyclic squash trypsin inhibitors. These compounds are the first members of a new family of cyclic knottins. In this paper, we present NMR structural studies of one of them, MCoTI-II, and of a beta-Asp rearranged form, MCoTI-IIb. Both compounds display similar and well-defined conformations. These cyclic squash inhibitors share a similar conformation with noncyclic squash inhibitors such as CPTI-II, and it is postulated that the main effect of the cyclization is a reduced sensitivity to exo-proteases. On the contrary, clear differences were detected with the three-dimensional structures of other known cyclic knottins, i.e., kalata B1 or circulin A. The two-disulfide cystine-stabilized beta-sheet motif [Heitz et al. (1999) Biochemistry 38, 10615-10625] is conserved in the two families, whereas in the C-to-N linker, one disulfide bridge and one loop are differently located. The molecular surface of MCoTI-II is almost entirely charged in contrast to circulin A that displays a well-marked amphiphilic character. These differences might explain why the isolated macrocyclic squash inhibitors from M. cochinchinensis display no significant antibacterial activity, whereas circulins and kalata B1 do. FAU - Heitz, A AU - Heitz A AD - Centre de Biochimie Structurale, UMR5048 CNRS-Universite Montpellier I, UMR554 INSERM-Universite Montpellier I, Faculte de pharmacie, 15 avenue Charles Flahault, 34060 Montpellier, France. FAU - Hernandez, J F AU - Hernandez JF FAU - Gagnon, J AU - Gagnon J FAU - Hong, T T AU - Hong TT FAU - Pham, T T AU - Pham TT FAU - Nguyen, T M AU - Nguyen TM FAU - Le-Nguyen, D AU - Le-Nguyen D FAU - Chiche, L AU - Chiche L LA - eng SI - PDB/1HA9 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cyclotides) RN - 0 (Isoenzymes) RN - 0 (Peptides, Cyclic) RN - 0 (Solutions) RN - 0 (trypsin inhibitor MCoTI-II) RN - 30KYC7MIAI (Aspartic Acid) SB - IM MH - Amino Acid Sequence MH - Aspartic Acid/chemistry/metabolism MH - Crystallography, X-Ray MH - Cucurbitaceae/*enzymology MH - *Cyclotides MH - Isoenzymes/metabolism MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides, Cyclic/*chemistry/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Sequence Homology, Amino Acid MH - Solutions MH - Static Electricity EDAT- 2001/07/04 10:00 MHDA- 2001/09/28 10:01 CRDT- 2001/07/04 10:00 AID - bi0106639 [pii] PST - ppublish SO - Biochemistry. 2001 Jul 10;40(27):7973-83. PMID- 22683332 OWN - NLM STAT- MEDLINE DA - 20120709 DCOM- 20120920 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 423 IP - 3 DP - 2012 Jul 6 TI - Thermodynamic study of the native and phosphorylated regulatory domain of the CFTR. PG - 549-52 LID - 10.1016/j.bbrc.2012.05.165 [doi] AB - The regulatory domain (RD) of the cystic fibrosis transmembrane conductance regulator (CFTR), the defective protein in cystic fibrosis, is the region of the channel that regulates the CFTR activity with multiple phosphorylation sites. This domain is an intrinsically disordered protein, characterized by lack of stable or unique tertiary structure. The disordered character of a protein is directly correlated with its function. The flexibility of RD may be important for its regulatory role: the continuous conformational change may be necessary for the progressive phosphorylation, and thus activation, of the channel. However, the lack of a defined and stable structure results in a considerable limitation when trying to in build a unique molecular model for the RD. Moreover, several evidences indicate significant structural differences between the native, non-phosphorylated state, and the multiple phosphorylated state of the protein. The aim of our work is to provide data to describe the conformations and the thermodynamic properties in these two functional states of RD. We have done the circular dichroism (CD) spectra in samples with a different degree of phosphorylation, from the non-phosphorylated state to a bona fide completely phosphorylated state. Analysis of CD spectra showed that the random coil and beta-sheets secondary structure decreased with the polypeptide phosphorylation, at expenses of an increase of alpha-helix. This observation lead to interpret phosphorylation as a mechanism favoring a more structured state. We also studied the thermal denaturation curves of the protein in the two conditions, monitoring the changes of the mean residue ellipticity measured at 222 nm as a function of temperature, between 20 and 95 degrees C. The thermodynamic analysis of the denaturation curves shows that phosphorylation of the protein induces a state of lower stability of R domain, characterized by a lower transition temperature, and by a smaller Gibbs free energy difference between the native and the unfolded states. CI - Copyright (c) 2012 Elsevier Inc. All rights reserved. FAU - Marasini, Carlotta AU - Marasini C AD - Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via De Marini 6, 16149 Genova, Italy. marasini@ge.ibf.cnr.it FAU - Galeno, Lauretta AU - Galeno L FAU - Moran, Oscar AU - Moran O LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120607 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 126880-72-6 (Cystic Fibrosis Transmembrane Conductance Regulator) SB - IM MH - Cystic Fibrosis Transmembrane Conductance Regulator/*chemistry MH - Humans MH - Phosphorylation MH - Protein Denaturation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - *Thermodynamics EDAT- 2012/06/12 06:00 MHDA- 2012/09/21 06:00 CRDT- 2012/06/12 06:00 PHST- 2012/05/24 [received] PHST- 2012/05/31 [accepted] PHST- 2012/06/07 [aheadofprint] AID - S0006-291X(12)01073-X [pii] AID - 10.1016/j.bbrc.2012.05.165 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2012 Jul 6;423(3):549-52. doi: 10.1016/j.bbrc.2012.05.165. Epub 2012 Jun 7. PMID- 22836948 OWN - NLM STAT- MEDLINE DA - 20130902 DCOM- 20140318 IS - 1874-270X (Electronic) VI - 7 IP - 2 DP - 2013 Oct TI - Backbone (1)H, (1)(3)C and (1)(5)N resonance assignments of an intrinsically unstructured betagamma-crystallin from Hahella chejuensis. PG - 221-4 LID - 10.1007/s12104-012-9414-x [doi] AB - The sequence specific backbone (1)H, (13)C and (15)N resonance assignments of an intrinsically unstructured betagamma-crystallin from Hahella chejuensis are reported. The secondary structure chracterization of the unstructured protein reveals that large fraction of residues exhibits beta-strand propensity, as in the case of the Ca(2+)-bound structured protein. FAU - Ramanujam, Venkatraman AU - Ramanujam V AD - Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India. FAU - Patel, Sunita AU - Patel S FAU - Srivastava, Atul K AU - Srivastava AK FAU - Sharma, Yogendra AU - Sharma Y FAU - Chary, Kandala V R AU - Chary KV LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120727 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (Apoproteins) RN - 0 (Bacterial Proteins) RN - 0 (Carbon Isotopes) RN - 0 (Crystallins) RN - 0 (Nitrogen Isotopes) RN - 0 (Protons) SB - IM MH - Amino Acid Sequence MH - Apoproteins/chemistry MH - Bacterial Proteins/*chemistry MH - Carbon Isotopes MH - Crystallins/*chemistry MH - Gammaproteobacteria/*metabolism MH - Nitrogen Isotopes MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - *Protons EDAT- 2012/07/28 06:00 MHDA- 2014/03/19 06:00 CRDT- 2012/07/28 06:00 PHST- 2012/05/08 [received] PHST- 2012/07/16 [accepted] PHST- 2012/07/27 [aheadofprint] AID - 10.1007/s12104-012-9414-x [doi] PST - ppublish SO - Biomol NMR Assign. 2013 Oct;7(2):221-4. doi: 10.1007/s12104-012-9414-x. Epub 2012 Jul 27. PMID- 18327957 OWN - NLM STAT- MEDLINE DA - 20080326 DCOM- 20080505 IS - 0743-7463 (Print) IS - 0743-7463 (Linking) VI - 24 IP - 7 DP - 2008 Apr 1 TI - Effect of temperature on self-assembly of bovine beta-casein above and below isoelectric pH. Structural analysis by cryogenic-transmission electron microscopy and small-angle X-ray scattering. PG - 3020-9 LID - 10.1021/la702802a [doi] AB - beta-Casein is one of the main proteins in milk, recently classified as an intrinsically unstructured protein. At neutral pH, it is composed of a highly polar N-terminus domain and a hydrophobic C-terminus tail. This amphiphilic block-copolymer-like structure leads to self-organization of the protein monomers into defined micelles. Recently, it has been shown that at room temperature, beta-casein also self-organizes into micelles in an acidic environment, but the effect of temperature on the micelles' formation and properties at the low pH regime were not explored. In the present study, we used two complementary techniques, cryogenic-transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering (SAXS), to characterize at high-resolution the micelles' shape, dimensions, and aggregation numbers and to determine how these properties are affected by temperature between 1 and 40 degrees C. Two different regimes were studied: highly acidic pH where the protein is cationic, and neutral pH, where it is anionic. We found that flat disk-like micelles with low aggregation numbers formed at low temperature in the two pH regimes. Close to neutral pH increase in temperature involves a transition in the micelles' shape and dimensions from flat disks to bulky, almost spheroidal micelles, coupled with a sharp increase in the micelles' aggregation number. In contrast, no effects on the micelles' morphology or aggregation number were detected in the acidic environment within the entire temperature range studied. The self-organization into disk micelles and the lack of effect of temperature in the acidic environment are linked to the unstructured character of the protein and to the charge distribution map. The latter indicates that below the isoelectric pH (pI), beta-casein loses the distinct separation of hydrophobic and hydrophilic domains, thereby suggesting that it may no longer be considered as a classical head-tail block-copolymer amphiphile as in neutral pH. FAU - Moitzi, Christian AU - Moitzi C AD - Institute of Chemistry and Physical Chemistry, University of Graz, Graz A-8010, Austria. FAU - Portnaya, Irina AU - Portnaya I FAU - Glatter, Otto AU - Glatter O FAU - Ramon, Ory AU - Ramon O FAU - Danino, Dganit AU - Danino D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080308 PL - United States TA - Langmuir JT - Langmuir : the ACS journal of surfaces and colloids JID - 9882736 RN - 0 (Caseins) SB - IM MH - Animals MH - Caseins/*chemistry MH - Cattle MH - Cryoelectron Microscopy MH - Hydrogen-Ion Concentration MH - Microscopy, Electron, Transmission MH - Protein Conformation MH - *Temperature MH - X-Ray Diffraction EDAT- 2008/03/11 09:00 MHDA- 2008/05/06 09:00 CRDT- 2008/03/11 09:00 PHST- 2008/03/08 [aheadofprint] AID - 10.1021/la702802a [doi] PST - ppublish SO - Langmuir. 2008 Apr 1;24(7):3020-9. doi: 10.1021/la702802a. Epub 2008 Mar 8. PMID- 8638105 OWN - NLM STAT- MEDLINE DA - 19960710 DCOM- 19960710 LR - 20091119 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 271 IP - 5253 DP - 1996 Mar 1 TI - Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. PG - 1247-54 AB - The lac operon of Escherichia coli is the paradigm for gene regulation. Its key component is the lac repressor, a product of the lacI gene. The three-dimensional structures of the intact lac repressor, the lac repressor bound to the gratuitous inducer isopropyl-beta-D-1-thiogalactoside (IPTG) and the lac repressor complexed with a 21-base pair symmetric operator DNA have been determined. These three structures show the conformation of the molecule in both the induced and repressed states and provide a framework for understanding a wealth of biochemical and genetic information. The DNA sequence of the lac operon has three lac repressor recognition sites in a stretch of 500 base pairs. The crystallographic structure of the complex with DNA suggests that the tetrameric repressor functions synergistically with catabolite gene activator protein (CAP) and participates in the quaternary formation of repression loops in which one tetrameric repressor interacts simultaneously with two sites on the genomic DNA. FAU - Lewis, M AU - Lewis M AD - Johnson Research Foundation, University of Pennsylvania, Philadelphia 19104, USA. FAU - Chang, G AU - Chang G FAU - Horton, N C AU - Horton NC FAU - Kercher, M A AU - Kercher MA FAU - Pace, H C AU - Pace HC FAU - Schumacher, M A AU - Schumacher MA FAU - Brennan, R G AU - Brennan RG FAU - Lu, P AU - Lu P LA - eng SI - PDB/1LBG SI - PDB/1LBH SI - PDB/1LBI GR - 2-T32-GM082745/GM/NIGMS NIH HHS/United States GR - GM44617/GM/NIGMS NIH HHS/United States GR - P41-RR06017/RR/NCRR NIH HHS/United States GR - etc. PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Bacterial Proteins) RN - 0 (Cyclic AMP Receptor Protein) RN - 0 (DNA, Bacterial) RN - 0 (Escherichia coli Proteins) RN - 0 (Lac Repressors) RN - 0 (Repressor Proteins) RN - 367-93-1 (Isopropyl Thiogalactoside) SB - IM CIN - Science. 1996 Dec 13;274(5294):1930-1; author reply 1931-2. PMID: 8984648 CIN - Science. 1996 Mar 1;271(5253):1245-6. PMID: 8638104 CIN - Science. 1996 Dec 13;274(5294):1929-30; author reply 1931-2. PMID: 8984647 MH - Allosteric Regulation MH - Bacterial Proteins/*chemistry/genetics/metabolism MH - Base Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - Cyclic AMP Receptor Protein/metabolism MH - DNA, Bacterial/chemistry/*metabolism MH - *Escherichia coli Proteins MH - Hydrogen Bonding MH - Isopropyl Thiogalactoside/*metabolism MH - *Lac Operon MH - Lac Repressors MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Operator Regions, Genetic MH - Point Mutation MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Repressor Proteins/*chemistry/genetics/metabolism EDAT- 1996/03/01 MHDA- 1996/03/01 00:01 CRDT- 1996/03/01 00:00 PST - ppublish SO - Science. 1996 Mar 1;271(5253):1247-54. PMID- 19037309 OWN - NLM STAT- MEDLINE DA - 20081127 DCOM- 20081229 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 456 IP - 7221 DP - 2008 Nov 27 TI - Gibberellin-induced DELLA recognition by the gibberellin receptor GID1. PG - 459-63 LID - 10.1038/nature07519 [doi] AB - Gibberellins control a range of growth and developmental processes in higher plants and have been widely used in the agricultural industry. By binding to a nuclear receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), gibberellins regulate gene expression by promoting degradation of the transcriptional regulator DELLA proteins, including GIBBERELLIN INSENSITIVE (GAI). The precise manner in which GID1 discriminates and becomes activated by bioactive gibberellins for specific binding to DELLA proteins remains unclear. Here we present the crystal structure of a ternary complex of Arabidopsis thaliana GID1A, a bioactive gibberellin and the amino-terminal DELLA domain of GAI. In this complex, GID1A occludes gibberellin in a deep binding pocket covered by its N-terminal helical switch region, which in turn interacts with the DELLA domain containing DELLA, VHYNP and LExLE motifs. Our results establish a structural model of a plant hormone receptor that is distinct from the mechanism of the hormone perception and effector recognition of the known auxin receptors. FAU - Murase, Kohji AU - Murase K AD - Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. FAU - Hirano, Yoshinori AU - Hirano Y FAU - Sun, Tai-ping AU - Sun TP FAU - Hakoshima, Toshio AU - Hakoshima T LA - eng SI - PDB/2ZSH SI - PDB/2ZSI PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Arabidopsis Proteins) RN - 0 (GAI protein, Arabidopsis) RN - 0 (GID1a protein, Arabidopsis) RN - 0 (Gibberellins) RN - 0 (Plant Growth Regulators) RN - 0 (Receptors, Cell Surface) SB - IM CIN - Nature. 2008 Nov 27;456(7221):455-6. PMID: 19037306 MH - Amino Acid Motifs MH - Arabidopsis/*chemistry/metabolism MH - Arabidopsis Proteins/*chemistry/genetics/*metabolism MH - Circular Dichroism MH - Crystallography, X-Ray MH - Gibberellins/metabolism/*pharmacology MH - Models, Biological MH - Models, Molecular MH - Plant Growth Regulators/metabolism/*pharmacology MH - Protein Binding MH - Protein Structure, Tertiary/drug effects MH - Receptors, Cell Surface/*chemistry/genetics/*metabolism MH - Substrate Specificity EDAT- 2008/11/28 09:00 MHDA- 2008/12/30 09:00 CRDT- 2008/11/28 09:00 PHST- 2008/08/27 [received] PHST- 2008/10/02 [accepted] AID - nature07519 [pii] AID - 10.1038/nature07519 [doi] PST - ppublish SO - Nature. 2008 Nov 27;456(7221):459-63. doi: 10.1038/nature07519. PMID- 19864490 OWN - NLM STAT- MEDLINE DA - 20091223 DCOM- 20100316 LR - 20140916 IS - 1460-2083 (Electronic) IS - 0964-6906 (Linking) VI - 19 IP - 2 DP - 2010 Jan 15 TI - Consortin, a trans-Golgi network cargo receptor for the plasma membrane targeting and recycling of connexins. PG - 262-75 LID - 10.1093/hmg/ddp490 [doi] AB - Targeting of numerous transmembrane proteins to the cell surface is thought to depend on their recognition by cargo receptors that interact with the adaptor machinery for anterograde traffic at the distal end of the Golgi complex. We report here on consortin, a novel integral membrane protein that is predicted to be intrinsically disordered, i.e. that contains large segments whose native state is unstructured. We identified consortin as a binding partner of connexins, the building blocks of gap junctions. Consortin is located at the trans-Golgi network (TGN), in tubulovesicular transport organelles, and at the plasma membrane. It directly interacts with the TGN clathrin adaptors GGA1 and GGA2, and disruption of this interaction by expression of a consortin mutant lacking the acidic cluster-dileucine (DXXLL) GGA interaction motif causes an intracellular accumulation of several connexins. RNA interference-mediated silencing of consortin expression in HeLa cells blocks the cell surface targeting of these connexins, which accumulate intracellularly, whereas partial depletion and redistribution of the consortin pool slows down the intracellular degradation of gap junction plaques. Altogether, our results show that, by studying connexin trafficking, we have identified the first TGN cargo receptor for the targeting of transmembrane proteins to the plasma membrane. The identification of consortin provides in addition a potential target for therapies aimed at diseases in which connexin traffic is altered, including cardiac ischemia, peripheral neuropathies, cataracts and hearing impairment. Sequence accession numbers. GenBank: Human CNST cDNA, NM_152609; mouse Cnst cDNA, NM_146105. FAU - del Castillo, Francisco J AU - del Castillo FJ AD - Unite de Genetique et Physiologie de l'Audition, Institut Pasteur, Paris, France. FAU - Cohen-Salmon, Martine AU - Cohen-Salmon M FAU - Charollais, Anne AU - Charollais A FAU - Caille, Dorothee AU - Caille D FAU - Lampe, Paul D AU - Lampe PD FAU - Chavrier, Philippe AU - Chavrier P FAU - Meda, Paolo AU - Meda P FAU - Petit, Christine AU - Petit C LA - eng SI - RefSeq/NM_146105 SI - RefSeq/NM_152609 GR - GM55632/GM/NIGMS NIH HHS/United States GR - R01 GM055632/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20091028 PL - England TA - Hum Mol Genet JT - Human molecular genetics JID - 9208958 RN - 0 (Adaptor Proteins, Vesicular Transport) RN - 0 (CNST protein, human) RN - 0 (Carrier Proteins) RN - 0 (Connexins) RN - 0 (GGA adaptor proteins) RN - 0 (GGA2 protein, human) RN - 0 (Membrane Proteins) RN - 0 (consortin protein, mouse) SB - IM MH - Adaptor Proteins, Vesicular Transport/genetics/metabolism MH - Animals MH - Carrier Proteins/genetics/*metabolism MH - Cell Membrane/genetics/*metabolism MH - Connexins/genetics/*metabolism MH - HeLa Cells MH - Humans MH - Membrane Proteins/genetics/*metabolism MH - Mice MH - Protein Binding MH - Protein Transport MH - trans-Golgi Network/genetics/*metabolism PMC - PMC2796891 OID - NLM: PMC2796891 EDAT- 2009/10/30 06:00 MHDA- 2010/03/17 06:00 CRDT- 2009/10/30 06:00 PHST- 2009/10/28 [aheadofprint] PHST- 2009/11/11 [aheadofprint] AID - ddp490 [pii] AID - 10.1093/hmg/ddp490 [doi] PST - ppublish SO - Hum Mol Genet. 2010 Jan 15;19(2):262-75. doi: 10.1093/hmg/ddp490. Epub 2009 Oct 28. PMID- 7958432 OWN - NLM STAT- MEDLINE DA - 19941129 DCOM- 19941129 LR - 20061115 IS - 0012-1606 (Print) IS - 0012-1606 (Linking) VI - 165 IP - 2 DP - 1994 Oct TI - A Drosophila homolog of cadherin associated with armadillo and essential for embryonic cell-cell adhesion. PG - 716-26 AB - We have identified a Drosophila homolog of vertebrate classic cadherins. A monoclonal antibody to Drosophila alpha-catenin (D alpha-catenin) copurifies a 150-kDa glycoprotein (gp150) along with the alpha-catenin. To further characterize this protein, we generated monoclonal antibodies to gp150 and isolated its cDNAs using the antibodies. Predicted sequences of the encoded product revealed that it is a transmembrane protein with similarity to vertebrate classic cadherins, and so we designated this molecule DE-cadherin. The extracellular domain has six cadherin-specific repeats, although the first repeat seems to be cleaved off upon maturation, and the cytoplasmic domain shows significant identity to that of vertebrate classic cadherins. DE-cadherin is distinguishable from its vertebrate counterparts by a large insertion with local sequence similarity to Fat, laminin A chain, Slit, and neurexin I at the proximal region of the extracellular domain. Despite such differences, DE-cadherin is functionally similar to vertebrate classic cadherins. For example, it is associated with alpha-catenin and beta-catenin (Armadillo), and protected from trypsin digestion only in the presence of Ca2+, as is the case for many of classic cadherins. Transfection of S2 cells with the DE-cadherin cDNA enhances their Ca(2+)-dependent cell aggregation. Antibodies to this molecule inhibited aggregation of not only the transfectants but also early embryonic cells. DE-cadherin is concentrated at the apical poles of epithelial cell-cell junctions. All these results suggest that DE-cadherin is a homolog of vertebrate classic cadherins and that the vertebrate and invertebrate share common mechanisms for regulation of cell-cell adhesion. FAU - Oda, H AU - Oda H AD - Department of Biophysics, Faculty of Science, Kyoto University, Japan. FAU - Uemura, T AU - Uemura T FAU - Harada, Y AU - Harada Y FAU - Iwai, Y AU - Iwai Y FAU - Takeichi, M AU - Takeichi M LA - eng SI - GENBANK/D28749 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Dev Biol JT - Developmental biology JID - 0372762 RN - 0 (Armadillo Domain Proteins) RN - 0 (Cadherins) RN - 0 (DNA, Complementary) RN - 0 (Drosophila Proteins) RN - 0 (Glycoproteins) RN - 0 (Proteins) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - 0 (armadillo protein, Drosophila) SB - IM GS - arm MH - Amino Acid Sequence MH - Animals MH - Armadillo Domain Proteins MH - Cadherins/*chemistry MH - Cell Adhesion MH - Cell Aggregation MH - Cloning, Molecular MH - DNA, Complementary/genetics MH - *Drosophila Proteins MH - Drosophila melanogaster/*chemistry/embryology MH - Glycoproteins/chemistry/genetics MH - Molecular Sequence Data MH - Multigene Family MH - Proteins/metabolism MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - *Trans-Activators MH - Transcription Factors EDAT- 1994/10/01 MHDA- 1994/10/01 00:01 CRDT- 1994/10/01 00:00 AID - S0012-1606(84)71287-5 [pii] AID - 10.1006/dbio.1994.1287 [doi] PST - ppublish SO - Dev Biol. 1994 Oct;165(2):716-26. PMID- 18824006 OWN - NLM STAT- MEDLINE DA - 20081110 DCOM- 20081210 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 384 IP - 3 DP - 2008 Dec 19 TI - Biochemical and structural characterization of an intramolecular interaction in FOXO3a and its binding with p53. PG - 590-603 LID - 10.1016/j.jmb.2008.09.025 [doi] AB - FOXO3a, a forkhead transcription factor and member of the forkhead box class O (FOXO) subfamily, has been shown to promote the translocation of p53 to the cytoplasm, thereby inducing the mitochondria-associated apoptotic pathway. However, the binding sites that mediate this interaction between FOXO3a and p53 have not been identified. Here, we show that two regions within FOXO3a, the forkhead (FH) DNA binding domain and a conserved C-terminal transactivation domain (CR3), interact with the DNA binding domain of p53, with affinities in the low millimolar range and low micromolar range, respectively. Our data further suggest that within the FOXO3a molecule, the FH and CR3 domains engage in an intramolecular interaction with low micromolar affinity. Moreover, we used NMR to determine the solution structure of the FH domain. This enabled us to map the binding site for the CR3, which overlaps with the DNA binding site. We demonstrate that an intrinsically disordered linker between the FH and CR3 domains is required for full p53 binding activity. We also show that p53 disrupts the intramolecular interaction between FH and CR3. These results provide evidence for interplay of the FH and CR3 domains in association with p53. FAU - Wang, Feng AU - Wang F AD - Division of Signaling Biology, Ontario Cancer Institute, Toronto, Ontario, Canada M5G 2M9. FAU - Marshall, Christopher B AU - Marshall CB FAU - Yamamoto, Kazuo AU - Yamamoto K FAU - Li, Guang-Yao AU - Li GY FAU - Plevin, Michael J AU - Plevin MJ FAU - You, Han AU - You H FAU - Mak, Tak W AU - Mak TW FAU - Ikura, Mitsuhiko AU - Ikura M LA - eng SI - PDB/2K86 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080918 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (FOXO3 protein, human) RN - 0 (Forkhead Transcription Factors) RN - 0 (TP53 protein, human) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Amino Acid Sequence MH - Apoptosis MH - Binding Sites MH - Circular Dichroism MH - Forkhead Transcription Factors/*metabolism MH - Humans MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Transcriptional Activation MH - Tumor Suppressor Protein p53/*metabolism EDAT- 2008/10/01 09:00 MHDA- 2008/12/17 09:00 CRDT- 2008/10/01 09:00 PHST- 2008/06/09 [received] PHST- 2008/08/23 [revised] PHST- 2008/09/02 [accepted] PHST- 2008/09/18 [aheadofprint] AID - S0022-2836(08)01149-2 [pii] AID - 10.1016/j.jmb.2008.09.025 [doi] PST - ppublish SO - J Mol Biol. 2008 Dec 19;384(3):590-603. doi: 10.1016/j.jmb.2008.09.025. Epub 2008 Sep 18. PMID- 17371874 OWN - NLM STAT- MEDLINE DA - 20070514 DCOM- 20070718 LR - 20071203 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 282 IP - 20 DP - 2007 May 18 TI - Intrinsic disorder and autonomous domain function in the multifunctional nuclear protein, MeCP2. PG - 15057-64 AB - To probe the tertiary structure and domain organization of native methyl CpG-binding protein 2 (MeCP2), the recombinant human e2 isoform was purified to homogeneity and characterized by analytical ultracentrifugation, CD, and protease digestion. The location of intrinsic disorder in the MeCP2 sequence was predicted using the FoldIndex algorithm. MeCP2 was found to be monomeric in low and high salt and over a nearly 1000-fold concentration range. CD indicated that the MeCP2 monomer was nearly 60% unstructured under conditions where it could preferentially recognize CpG dinucleotides and condense chromatin. Protease digestion experiments demonstrate that MeCP2 is composed of at least six structurally distinct domains, two of which correspond to the well characterized methyl DNA binding domain and transcriptional repression domain. These domains collectively are organized into a tertiary structure with coil-like hydrodynamic properties, reflecting the extensive disorder in the MeCP2 sequence. When expressed as individual fragments, the methyl DNA binding domain and transcriptional repression domain both could function as nonspecific DNA binding domains. The unusual structural features of MeCP2 provide a basis for understanding MeCP2 multifunctionality in vitro and in vivo. These studies also establish an experimental paradigm for characterizing the tertiary structures of other highly disordered proteins. FAU - Adams, Valerie H AU - Adams VH AD - Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA. FAU - McBryant, Steven J AU - McBryant SJ FAU - Wade, Paul A AU - Wade PA FAU - Woodcock, Christopher L AU - Woodcock CL FAU - Hansen, Jeffrey C AU - Hansen JC LA - eng GR - GM45916/GM/NIGMS NIH HHS/United States GR - GM66834/GM/NIGMS NIH HHS/United States GR - GM70897/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't DEP - 20070319 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (CPG-oligonucleotide) RN - 0 (MECP2 protein, human) RN - 0 (Methyl-CpG-Binding Protein 2) RN - 0 (Oligodeoxyribonucleotides) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Proteins) SB - IM MH - *Algorithms MH - Circular Dichroism MH - Humans MH - Methyl-CpG-Binding Protein 2/*chemistry/genetics/metabolism MH - Oligodeoxyribonucleotides/*chemistry MH - Protein Binding/physiology MH - Protein Isoforms/chemistry/genetics/metabolism MH - Protein Structure, Tertiary/physiology MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Structure-Activity Relationship MH - Ultracentrifugation EDAT- 2007/03/21 09:00 MHDA- 2007/07/19 09:00 CRDT- 2007/03/21 09:00 PHST- 2007/03/19 [aheadofprint] AID - M700855200 [pii] AID - 10.1074/jbc.M700855200 [doi] PST - ppublish SO - J Biol Chem. 2007 May 18;282(20):15057-64. Epub 2007 Mar 19. PMID- 25245670 OWN - NLM STAT- In-Process DA - 20141203 IS - 1875-5550 (Electronic) IS - 1389-2037 (Linking) VI - 15 IP - 8 DP - 2014 TI - Structural heterogeneity and multifunctionality of lactoferrin. PG - 778-97 AB - Lactoferrin or lactotransferrin is a multifunctional glycoprotein found in blood circulation, mucosal surfaces, neutrophils, and in various secretory fluids, such as milk, bile, tears, nasal secretion, pancreatic juice, and saliva. The lactoferrin content in milk varies between different mammalian species and, within one species, between lactation periods. Although lactoferrin is known to be involved with immunoprotection, its functions are not limited to the regulation of innate immunity, but extend to iron transfer to cells, control of the level of free iron in blood and external secretions, interaction with DNA, RNA, heparin, and polysaccharides, and pronounced antimicrobial and antiviral activities. This multifunctionality is determined by the fact that lactoferrin belongs to the class of hybrid proteins possessing both ordered domains and functionally important intrinsically disordered regions. Structurally, lactoferrin is a globular glycoprotein with a molecular mass of about 80 kDa consisting of two homologous domains known as N-terminal and C-terminal lobes. These lobes are unevenly glycosylated (with the C-lobe typically containing more N-linked glycosylation sites). Each lobe can bind a single ferric ion concomitantly with one bicarbonate anion. Lactoferrin and its lobes have a wide spectrum of antimicrobial and antiviral activities, with the antimicrobial and antiviral potentials dependent on the type of microbes and viruses. Often, the N-lobe possesses the majority of antimicrobial activities. In addition, lactoferrin and its lobes possess clear anti-cancer, wound healing, anti-inflammatory, and immunomodulation activities. FAU - Albar, Abdulgader H AU - Albar AH FAU - Almehdar, Hussein A AU - Almehdar HA FAU - Uversky, Vladimir N AU - Uversky VN FAU - Redwan, Elrashdy M AU - Redwan EM AD - Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, PO Box 80203, Jeddah 21589, Saudi Arabia. redwan1961@yahoo.com. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - Curr Protein Pept Sci JT - Current protein & peptide science JID - 100960529 SB - IM EDAT- 2014/09/24 06:00 MHDA- 2014/09/24 06:00 CRDT- 2014/09/24 06:00 PHST- 2014/06/26 [received] PHST- 2014/09/17 [revised] PHST- 2014/09/17 [accepted] AID - CPPS-EPUB-62433 [pii] PST - ppublish SO - Curr Protein Pept Sci. 2014;15(8):778-97. PMID- 17586564 OWN - NLM STAT- MEDLINE DA - 20070924 DCOM- 20071211 LR - 20140904 IS - 0006-3495 (Print) IS - 0006-3495 (Linking) VI - 93 IP - 8 DP - 2007 Oct 15 TI - Intrinsic dynamics of the partly unstructured PX domain from the Sendai virus RNA polymerase cofactor P. PG - 2830-44 AB - Despite their evident importance for function, dynamics of intrinsically unstructured proteins are poorly understood. Sendai virus phosphoprotein, cofactor of the RNA polymerase, contains a partly unstructured protein domain. The phosphoprotein X domain (PX) is responsible for binding the polymerase to the nucleocapsid assembling the viral RNA. For RNA synthesis, the interplay of the dynamics of the unstructured and structured PX subdomains is thought to drive progression of the RNA polymerase along the nucleocapsid. Here we present a detailed study of the dynamics of PX using hydrogen/deuterium exchange and different NMR relaxation measurements. In the unstructured subdomain, large amplitude fast motions were found to be fine-tuned by the presence of residues with short side chains. In the structured subdomain, where fast motions of both backbone and side chains are fairly restricted, the first helix undergoes slow conformational exchange corresponding to a local unfolding event. The other two helices, which represent the nucleocapsid binding site, were found to be more stable and to reorient with respect to each other, as probed by slow conformational exchange identified for residues on the third helix. The study illustrates the intrinsically differential dynamics of this partly unstructured protein and proposes the relation between these dynamics and its function. FAU - Houben, Klaartje AU - Houben K AD - Institut de Biologie Structurale Jean-Pierre Ebel, CNRS, CEA, UJF, UMR-5075, 38027 Grenoble cedex 1, France. FAU - Blanchard, Laurence AU - Blanchard L FAU - Blackledge, Martin AU - Blackledge M FAU - Marion, Dominique AU - Marion D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070622 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - EC 2.7.7.6 (DNA-Directed RNA Polymerases) SB - IM MH - Computer Simulation MH - DNA-Directed RNA Polymerases/*chemistry/*ultrastructure MH - Deuterium Exchange Measurement MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - *Models, Chemical MH - *Models, Molecular MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - Sendai virus/*enzymology PMC - PMC1989709 OID - NLM: PMC1989709 EDAT- 2007/06/26 09:00 MHDA- 2007/12/12 09:00 CRDT- 2007/06/26 09:00 PHST- 2007/06/22 [aheadofprint] AID - biophysj.107.108829 [pii] AID - 10.1529/biophysj.107.108829 [doi] PST - ppublish SO - Biophys J. 2007 Oct 15;93(8):2830-44. Epub 2007 Jun 22. PMID- 22174264 OWN - NLM STAT- MEDLINE DA - 20111216 DCOM- 20131210 IS - 2335-6936 (Print) DP - 2012 TI - Quasi-anharmonic analysis reveals intermediate states in the nuclear co-activator receptor binding domain ensemble. PG - 70-81 AB - The molten globule nuclear receptor co-activator binding domain (NCBD) of CREB binding protein (CBP) selectively recruits transcription co-activators (TCAs) during the formation of the transcription preinitiation complex. NCBD:TCA interactions have been implicated in several cancers, however, the mechanisms of NCBD:TCA recognition remain uncharacterized. NCBD:TCA intermolecular recognition has challenged traditional investigation as both NCBD and several of its corresponding TCAs are intrinsically disordered. Using 40mus of explicit solvent molecular dynamics simulations, we relate the conformational diversity of ligand-free NCBD to its bound configurations. We introduce two novel techniques to quantify the conformational heterogeneity of ligand-free NCBD, dihedral quasi-anharmonic analysis (dQAA) and hierarchical graph-based diffusive clustering. With this integrated approach we find that three of four ligand-bound states are natively accessible to the ligand-free NCBD simulations with root-mean squared deviation (RMSD) less than 2A These conformations are accessible via diverse pathways while a rate-limiting barrier must be crossed in order to access the fourth bound state. FAU - Burger, Virginia M AU - Burger VM AD - Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania, USA. FAU - Ramanathan, Arvind AU - Ramanathan A FAU - Savol, Andrej J AU - Savol AJ FAU - Stanley, Christopher B AU - Stanley CB FAU - Agarwal, Pratul K AU - Agarwal PK FAU - Chennubhotla, Chakra S AU - Chennubhotla CS LA - eng PT - Journal Article PL - Singapore TA - Pac Symp Biocomput JT - Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing JID - 9711271 RN - 0 (CREBBP protein, human) RN - 0 (Ligands) RN - 0 (Nuclear Receptor Coactivators) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Binding Sites MH - CREB-Binding Protein/*chemistry/metabolism MH - Computational Biology MH - Crystallography, X-Ray MH - Humans MH - Ligands MH - Models, Molecular MH - Molecular Dynamics Simulation MH - Neutron Diffraction MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Receptor Coactivators/*chemistry/metabolism MH - Protein Conformation MH - Protein Structure, Tertiary MH - Scattering, Small Angle EDAT- 2011/12/17 06:00 MHDA- 2013/12/16 06:00 CRDT- 2011/12/17 06:00 AID - 9789814366496_0008 [pii] PST - ppublish SO - Pac Symp Biocomput. 2012:70-81. PMID- 20170198 OWN - NLM STAT- MEDLINE DA - 20100323 DCOM- 20100423 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 12 DP - 2010 Mar 30 TI - Substrate specificity determinants of the methanogen homoaconitase enzyme: structure and function of the small subunit. PG - 2687-96 LID - 10.1021/bi901766z [doi] AB - The aconitase family of hydro-lyase enzymes includes three classes of proteins that catalyze the isomerization of alpha-hydroxy acids to beta-hydroxy acids. Besides aconitase, isopropylmalate isomerase (IPMI) proteins specifically catalyze the isomerization of alpha,beta-dicarboxylates with hydrophobic gamma-chain groups, and homoaconitase (HACN) proteins catalyze the isomerization of tricarboxylates with variable chain length gamma-carboxylate groups. These enzymes' stereospecific hydro-lyase activities make them attractive catalysts to produce diastereomers from unsaturated precursors. However, sequence similarity and convergent evolution among these proteins lead to widespread misannotation and uncertainty about gene function. To find the substrate specificity determinants of homologous IPMI and HACN proteins from Methanocaldococcus jannaschii, the small-subunit HACN protein (MJ1271) was crystallized for X-ray diffraction. The structural model showed characteristic residues in a flexible loop region between alpha2 and alpha3 that distinguish HACN from IPMI and aconitase proteins. Site-directed mutagenesis of MJ1271 produced loop-region variant proteins that were reconstituted with wild-type MJ1003 large-subunit protein. The heteromers formed promiscuous hydro-lyases with reduced activity but broader substrate specificity. Both R26K and R26V variants formed relatively efficient IPMI enzymes, while the T27A variant had uniformly lower specificity constants for both IPMI and HACN substrates. The R26V T27Y variant resembles the MJ1277 IPMI small subunit in its flexible loop sequence but demonstrated the broad substrate specificity of the R26V variant. These mutations may reverse the evolution of HACN activity from an ancestral IPMI gene, demonstrating the evolutionary potential for promiscuity in hydro-lyase enzymes. Understanding these specificity determinants enables the functional reannotation of paralogous HACN and IPMI genes in numerous genome sequences. These structural and kinetic results will help to engineer new stereospecific hydro-lyase enzymes for chemoenzymatic syntheses. FAU - Jeyakanthan, Jeyaraman AU - Jeyakanthan J AD - Life Science Group, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinch 30076, Taiwan. FAU - Drevland, Randy M AU - Drevland RM FAU - Gayathri, Dasara Raju AU - Gayathri DR FAU - Velmurugan, Devadasan AU - Velmurugan D FAU - Shinkai, Akeo AU - Shinkai A FAU - Kuramitsu, Seiki AU - Kuramitsu S FAU - Yokoyama, Shigeyuki AU - Yokoyama S FAU - Graham, David E AU - Graham DE LA - eng SI - PDB/2PKP PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Archaeal Proteins) RN - 0 (Protein Subunits) RN - EC 4.2.1.- (Hydro-Lyases) RN - EC 4.2.1.3 (Aconitate Hydratase) RN - EC 4.2.1.33 (isopropylmalate isomerase) RN - EC 4.2.1.36 (homoaconitate hydratase) RN - EC 5.- (Isomerases) SB - IM MH - Aconitate Hydratase/chemistry MH - Amino Acid Substitution MH - Archaeal Proteins/chemistry MH - Base Sequence MH - Binding Sites/*genetics MH - Catalysis MH - Euryarchaeota/enzymology/metabolism MH - Evolution, Molecular MH - Hydro-Lyases/*chemistry/genetics MH - Isomerases/chemistry MH - Kinetics MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed/*methods MH - Protein Conformation MH - Protein Subunits MH - Sequence Alignment MH - Structure-Activity Relationship MH - Substrate Specificity/*genetics EDAT- 2010/02/23 06:00 MHDA- 2010/04/24 06:00 CRDT- 2010/02/23 06:00 AID - 10.1021/bi901766z [doi] PST - ppublish SO - Biochemistry. 2010 Mar 30;49(12):2687-96. doi: 10.1021/bi901766z. PMID- 16503666 OWN - NLM STAT- MEDLINE DA - 20060228 DCOM- 20060428 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 9 DP - 2006 Mar 7 TI - Mutagenesis of basic residues R151 and R161 in manganese-stabilizing protein of photosystem II causes inefficient binding of chloride to the oxygen-evolving complex. PG - 3107-15 AB - Manganese-stabilizing protein of photosystem II, an intrinsically disordered polypeptide, contains a high ratio of charged to hydrophobic amino acid residues. Arg151 and Arg161 are conserved in all known MSP sequences. To examine the role of these basic residues in MSP structure and function, three mutants of spinach MSP, R151G, R151D, and R161G, were produced. Here, we present evidence that replacement of Arg151 or Arg161 yields proteins that have lower PSII binding affinity, and are functionally deficient even though about 2 mol of mutant MSP/mol PSII can be rebound to MSP depleted PSII membranes. R161G reconstitutes O(2) evolution activity to 40% of the control, while R151G and R151D reconstitute only 20% of the control activity. Spectroscopic and biochemical techniques fail to detect significant changes in solution structure. More extensive O(2) evolution assays revealed that the Mn cluster is stable in samples reconstituted with each mutated MSP, and that all three Arg mutants have the same ability to retain Ca(2+) as the wild-type protein. Activity assays exploring the effect of these mutations on retention of Cl(-), however, showed that the R151G, R151D, and R161G MSPs are defective in Cl(-) binding to the OEC. The mutants have Cl(-) K(M) values that are about four (R161G) or six times (R151G and R151D) higher than the value for the wild-type protein. The results reported here suggest that conserved positive charges on the manganese-stabilizing protein play a role in proper functional assembly of the protein into PSII, and, consequently, in retention of Cl(-) by the O(2)-evolving complex. FAU - Popelkova, Hana AU - Popelkova H AD - Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109-1048, USA. FAU - Betts, Scott D AU - Betts SD FAU - Lydakis-Symantiris, Nikos AU - Lydakis-Symantiris N FAU - Im, Michael M AU - Im MM FAU - Swenson, Ellen AU - Swenson E FAU - Yocum, Charles F AU - Yocum CF LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Algal Proteins) RN - 0 (Chlorides) RN - 0 (Photosystem II Protein Complex) RN - 0 (Plant Proteins) RN - 0 (Recombinant Proteins) RN - 0 (oxygen-evolving enhancer protein 1, plant) RN - 42Z2K6ZL8P (Manganese) RN - 94ZLA3W45F (Arginine) RN - SY7Q814VUP (Calcium) SB - IM MH - Algal Proteins/genetics MH - Arginine/genetics/metabolism MH - Calcium/metabolism MH - Chlorides/*metabolism MH - Circular Dichroism MH - Manganese/metabolism MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Mutation MH - Photosystem II Protein Complex/*genetics/*metabolism MH - Plant Proteins/genetics MH - Protein Binding MH - Protein Folding MH - Recombinant Proteins/genetics/metabolism MH - Spinacia oleracea/metabolism EDAT- 2006/03/01 09:00 MHDA- 2006/04/29 09:00 CRDT- 2006/03/01 09:00 AID - 10.1021/bi0523759 [doi] PST - ppublish SO - Biochemistry. 2006 Mar 7;45(9):3107-15. PMID- 16519533 OWN - NLM STAT- MEDLINE DA - 20060307 DCOM- 20060503 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 10 DP - 2006 Mar 14 TI - Association of alpha-synuclein and mutants with lipid membranes: spin-label ESR and polarized IR. PG - 3386-95 AB - Alpha-synuclein is a presynaptic protein, the A53T and A30P mutants of which are linked independently to early-onset familial Parkinson's disease. The association of wild-type alpha-synuclein with lipid membranes was characterized previously by electron spin resonance (ESR) spectroscopy with spin-labeled lipids [Ramakrishnan, M., Jensen, P. H., and Marsh, D. (2003) Biochemistry 42, 12919-12926]. Here, we study the interaction of the A53T and A30P alpha-synuclein mutants and a truncated form that lacks the acidic C-terminal domain with phosphatidylglycerol bilayer membranes, using anionic phospholipid spin labels. The strength of the interaction with phosphatidylglycerol membranes lies in the order: wild type approximately truncated > A53T > A30P > fibrils approximately 0, and only the truncated form interacts with phosphatidylcholine membranes. The selectivity of the interaction of the mutant alpha-synucleins with different spin-labeled lipid species is reduced considerably, relative to the wild-type protein, whereas that of the truncated protein is increased. Polarized infrared (IR) spectroscopy is used to study the interactions of the wild-type and truncated proteins with aligned lipid membranes and additionally to characterize the fibrillar form. Wild-type alpha-synuclein is natively unfolded in solution and acquires secondary structure upon binding to membranes containing phosphatidylglycerol. Up to 30-40% of the amide I band intensity of the membrane-bound wild-type and truncated proteins is attributable to beta-sheet structure, at the surface densities used for IR spectroscopy. The remainder is alpha-helix and residual unordered structure. Fibrillar alpha-synuclein contains 62% antiparallel beta-sheet and is oriented on the substrate surface but does not interact with deposited lipid membranes. The beta-sheet secondary-structural elements of the wild-type and truncated proteins are partially oriented on the surface of membranes with which they interact. FAU - Ramakrishnan, Muthu AU - Ramakrishnan M AD - Max-Planck-Institut fur biophysikalische Chemie, Abt. Spektroskopie, 37070 Gottingen, Germany. FAU - Jensen, Poul H AU - Jensen PH FAU - Marsh, Derek AU - Marsh D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Lipid Bilayers) RN - 0 (Lipids) RN - 0 (Phosphatidylcholines) RN - 0 (Phosphatidylglycerols) RN - 0 (Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Spin Labels) RN - 0 (alpha-Synuclein) SB - IM MH - Circular Dichroism MH - Electron Spin Resonance Spectroscopy/*methods MH - Humans MH - Lipid Bilayers/*chemistry/metabolism MH - Lipids/chemistry MH - Membranes/*chemistry/metabolism MH - Phosphatidylcholines/chemistry MH - Phosphatidylglycerols MH - Protein Binding MH - Protein Conformation MH - Proteins/chemistry/metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Spectrophotometry, Infrared/*methods MH - Spin Labels MH - Titrimetry MH - alpha-Synuclein/*chemistry/genetics/metabolism EDAT- 2006/03/08 09:00 MHDA- 2006/05/04 09:00 CRDT- 2006/03/08 09:00 AID - 10.1021/bi052344d [doi] PST - ppublish SO - Biochemistry. 2006 Mar 14;45(10):3386-95. PMID- 24925644 OWN - NLM STAT- MEDLINE DA - 20140822 DCOM- 20150513 IS - 1096-0279 (Electronic) IS - 1046-5928 (Linking) VI - 101 DP - 2014 Sep TI - Over-expression in E. coli and purification of functional full-length murine small C-terminal domain phosphatase (SCP1, or Golli-interacting protein). PG - 106-14 LID - 10.1016/j.pep.2014.05.013 [doi] LID - S1046-5928(14)00136-3 [pii] AB - During myelination in the central nervous system, proteins arising from the gene in the oligodendrocyte lineage (golli) participate in diverse events in signal transduction and gene regulation. One of the interacting partners of the Golli-isoform BG21 was discovered by yeast-2-hybrid means and was denoted the Golli-interacting-protein (GIP). In subsequent in vitro studies of recombinant murine GIP, it was not possible to produce a full-length version of recombinant murine rmGIP in functional form under native conditions, primarily because of solubility issues, necessitating the study of a hexahistidine-tagged, truncated form DeltaN-rmGIP. This protein is an acidic phosphatase belonging to the family of RNA-polymerase-2, small-subunit, C-terminal phosphatases (SCP1), and studies of the human ortholog hSCP1 have also been performed on truncated forms. Here, a new SUMO-expression and purification protocol has been developed for the preparation of a functional, full-length mSCP1/GIP (our nomenclature henceforth), with no additional purification tags. Both full-length mSCP1/GIP and the truncated murine form (now denoted DeltaN-rmSCP1/GIP) had similar melting temperatures, indicating that the integrity of the catalytic core per se was minimally affected by the N-terminus. Characterization of mSCP1/GIP activity with the artificial substrate p-NPP (p-nitrophenylphosphate) yielded kinetic parameters comparable to those of DeltaN-rmSCP1/GIP and the truncated human ortholog DeltaN-hSCP1. Similarly, mSCP1/GIP dephosphorylated a more natural CTD-peptide substrate (but not protein kinase C-phosphorylated BG21) with comparable kinetics to DeltaN-hSCP1. The successful production of an active, full-length mSCP1/GIP will enable future evaluation of the functional role of its N-terminus in protein-protein interactions (e.g., BG21) that regulate its phosphatase activity. CI - Copyright (c) 2014 Elsevier Inc. All rights reserved. FAU - Jaramillo-Tatis, Sergio AU - Jaramillo-Tatis S AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada. FAU - Bamm, Vladimir V AU - Bamm VV AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada. FAU - Vassall, Kenrick A AU - Vassall KA AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada. FAU - Harauz, George AU - Harauz G AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada. Electronic address: gharauz@uoguelph.ca. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140609 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (4-nitrophenylphosphocholine) RN - 0 (Myelin Basic Protein) RN - 0 (Nerve Tissue Proteins) RN - 0 (Nitrobenzenes) RN - 0 (Nuclear Proteins) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Proteins) RN - 0 (golli-interacting protein, mouse) RN - 107-73-3 (Phosphorylcholine) SB - IM MH - Animals MH - Central Nervous System/metabolism MH - Chromatography, Affinity MH - Escherichia coli/genetics/*metabolism MH - Gene Expression MH - Gene Expression Regulation MH - Mice MH - Myelin Basic Protein/biosynthesis/*genetics/metabolism MH - Nerve Tissue Proteins/biosynthesis/*genetics/metabolism MH - Nitrobenzenes/metabolism MH - Nuclear Proteins/biosynthesis/*genetics/metabolism MH - Phosphorylation MH - Phosphorylcholine/analogs & derivatives/metabolism MH - Protein Isoforms/genetics MH - Recombinant Proteins/*genetics/metabolism MH - Signal Transduction/genetics OTO - NOTNLM OT - Golli (gene in the oligodendrocyte lineage) OT - Golli-interacting protein OT - Intrinsically-disordered protein OT - Myelin basic protein OT - Myelination OT - Oligodendrocyte OT - Phosphorylation OT - Small C-terminal domain phosphatase EDAT- 2014/06/14 06:00 MHDA- 2015/05/15 06:00 CRDT- 2014/06/14 06:00 PHST- 2014/04/15 [received] PHST- 2014/05/26 [revised] PHST- 2014/05/31 [accepted] PHST- 2014/06/09 [aheadofprint] AID - S1046-5928(14)00136-3 [pii] AID - 10.1016/j.pep.2014.05.013 [doi] PST - ppublish SO - Protein Expr Purif. 2014 Sep;101:106-14. doi: 10.1016/j.pep.2014.05.013. Epub 2014 Jun 9. PMID- 23567152 OWN - NLM STAT- MEDLINE DA - 20130617 DCOM- 20140219 IS - 1347-4421 (Electronic) IS - 1347-4421 (Linking) VI - 116 IP - 2 DP - 2013 Aug TI - Nuclear magnetic resonance approaches for characterizing interactions between the bacterial chaperonin GroEL and unstructured proteins. PG - 160-4 LID - 10.1016/j.jbiosc.2013.02.012 [doi] LID - S1389-1723(13)00054-6 [pii] AB - GroEL-protein interactions were characterized by stable isotope-assisted nuclear magnetic resonance (NMR) spectroscopy using chemically denatured bovine rhodanese and an intrinsically disordered protein, alpha-synuclein, as model ligands. NMR data indicated that proteins tethered to GroEL remain largely unfolded and highly mobile, enabling identification of the interaction hot spots displayed on intrinsically disordered proteins. CI - Copyright (c) 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved. FAU - Nishida, Noritaka AU - Nishida N AD - Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. FAU - Yagi-Utsumi, Maho AU - Yagi-Utsumi M FAU - Motojima, Fumihiro AU - Motojima F FAU - Yoshida, Masasuke AU - Yoshida M FAU - Shimada, Ichio AU - Shimada I FAU - Kato, Koichi AU - Kato K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130406 PL - Japan TA - J Biosci Bioeng JT - Journal of bioscience and bioengineering JID - 100888800 RN - 0 (Chaperonin 60) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (alpha-Synuclein) RN - EC 2.8.1.1 (Thiosulfate Sulfurtransferase) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Cattle MH - Chaperonin 60/chemistry/*metabolism MH - Intrinsically Disordered Proteins/*chemistry/metabolism MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Thiosulfate Sulfurtransferase/chemistry/metabolism MH - alpha-Synuclein/chemistry/metabolism EDAT- 2013/04/10 06:00 MHDA- 2014/02/20 06:00 CRDT- 2013/04/10 06:00 PHST- 2012/12/27 [received] PHST- 2013/02/05 [revised] PHST- 2013/02/19 [accepted] PHST- 2013/04/06 [aheadofprint] AID - S1389-1723(13)00054-6 [pii] AID - 10.1016/j.jbiosc.2013.02.012 [doi] PST - ppublish SO - J Biosci Bioeng. 2013 Aug;116(2):160-4. doi: 10.1016/j.jbiosc.2013.02.012. Epub 2013 Apr 6. PMID- 2146682 OWN - NLM STAT- MEDLINE DA - 19901204 DCOM- 19901204 LR - 20131002 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 87 IP - 20 DP - 1990 Oct TI - Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex. PG - 8165-9 AB - The structure of a complex of bacteriophage lambda Cro protein with a 17-base-pair operator has been determined at 3.9-A resolution. Isomorphous derivatives obtained by the synthesis of site-specific iodinated DNA oligomers were of critical importance in solving the structure. The crystal structure contains three independent Cro-operator complexes that have very similar, although not necessarily identical, conformations. In the complex, the protein dimer undergoes a large conformational change relative to the crystal structure of the free protein. One monomer rotates by about 40 degrees relative to the other, this being accomplished primarily by a twisting of the two beta-sheet strands that connect one monomer with the other. In the complex, the DNA is bent by about 40 degrees into the shape of a boomerang but maintains essentially Watson-Crick B-form. In contrast to other known protein-DNA complexes, the DNA is not stacked end-to-end. The structure confirms the general features of the model previously proposed for the interaction of Cro with DNA. FAU - Brennan, R G AU - Brennan RG AD - Department of Physics, University of Oregon, Eugene 97403. FAU - Roderick, S L AU - Roderick SL FAU - Takeda, Y AU - Takeda Y FAU - Matthews, B W AU - Matthews BW LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA-Binding Proteins) RN - 0 (Repressor Proteins) RN - 0 (Transcription Factors) RN - 0 (Viral Proteins) RN - 0 (Viral Regulatory and Accessory Proteins) RN - 0 (phage repressor proteins) SB - IM MH - Amino Acid Sequence MH - Bacteriophage lambda/genetics/*metabolism MH - *DNA-Binding Proteins MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - *Operon MH - Protein Binding MH - Protein Conformation MH - Repressor Proteins/*metabolism MH - Transcription Factors/metabolism MH - Viral Proteins MH - Viral Regulatory and Accessory Proteins MH - X-Ray Diffraction PMC - PMC54913 OID - NLM: PMC54913 EDAT- 1990/10/01 MHDA- 1990/10/01 00:01 CRDT- 1990/10/01 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 1990 Oct;87(20):8165-9. PMID- 10837469 OWN - NLM STAT- MEDLINE DA - 20001003 DCOM- 20001003 LR - 20071115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 275 IP - 35 DP - 2000 Sep 1 TI - Crystal structure of human parathyroid hormone 1-34 at 0.9-A resolution. PG - 27238-44 AB - The N-terminal fragment 1-34 of parathyroid hormone (PTH), administered intermittently, results in increased bone formation in patients with osteoporosis. PTH and a related molecule, parathyroid hormone-related peptide (PTHrP), act on cells via a common PTH/PTHrP receptor. To define more precisely the ligand-receptor interactions, we have crystallized human PTH (hPTH)-(1-34) and determined the structure to 0.9-A resolution. hPTH-(1-34) crystallizes as a slightly bent, long helical dimer. Analysis reveals that the extended helical conformation of hPTH-(1-34) is the likely bioactive conformation. We have developed molecular models for the interaction of hPTH-(1-34) and hPTHrP-(1-34) with the PTH/PTHrP receptor. A receptor binding pocket for the N terminus of hPTH-(1-34) and a hydrophobic interface with the receptor for the C terminus of hPTH-(1-34) are proposed. FAU - Jin, L AU - Jin L AD - Lilly Research Laboratories, Eli Lilly & Company, Indianapolis, Indiana 46285, USA. FAU - Briggs, S L AU - Briggs SL FAU - Chandrasekhar, S AU - Chandrasekhar S FAU - Chirgadze, N Y AU - Chirgadze NY FAU - Clawson, D K AU - Clawson DK FAU - Schevitz, R W AU - Schevitz RW FAU - Smiley, D L AU - Smiley DL FAU - Tashjian, A H AU - Tashjian AH FAU - Zhang, F AU - Zhang F LA - eng SI - PDB/1ET1 SI - PDB/1ET2 SI - PDB/1ET3 PT - Journal Article PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Parathyroid Hormone) RN - 0 (Peptide Fragments) RN - 0 (Receptors, Parathyroid Hormone) SB - IM MH - Amino Acid Sequence MH - Animals MH - Crystallography, X-Ray MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Parathyroid Hormone/*chemistry/metabolism MH - Peptide Fragments/*chemistry/metabolism MH - Protein Binding MH - Protein Conformation MH - Receptors, Parathyroid Hormone/metabolism MH - Sequence Homology, Amino Acid EDAT- 2000/06/06 09:00 MHDA- 2000/10/07 11:01 CRDT- 2000/06/06 09:00 AID - 10.1074/jbc.M001134200 [doi] AID - M001134200 [pii] PST - ppublish SO - J Biol Chem. 2000 Sep 1;275(35):27238-44. PMID- 21278419 OWN - NLM STAT- MEDLINE DA - 20110530 DCOM- 20110809 LR - 20150630 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 39 IP - 10 DP - 2011 May TI - Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes. PG - 4122-35 LID - 10.1093/nar/gkr005 [doi] AB - MeCP2 is a highly abundant chromatin architectural protein with key roles in post-natal brain development in humans. Mutations in MeCP2 are associated with Rett syndrome, the main cause of mental retardation in girls. Structural information on the intrinsically disordered MeCP2 protein is restricted to the methyl-CpG binding domain; however, at least four regions capable of DNA and chromatin binding are distributed over its entire length. Here we use small angle X-ray scattering (SAXS) and other solution-state approaches to investigate the interaction of MeCP2 and a truncated, disease-causing version of MeCP2 with nucleosomes. We demonstrate that MeCP2 forms defined complexes with nucleosomes, in which all four histones are present. MeCP2 retains an extended conformation when binding nucleosomes without extra-nucleosomal DNA. In contrast, nucleosomes with extra-nucleosomal DNA engage additional DNA binding sites in MeCP2, resulting in a rather compact higher-order complex. We present ab initio envelope reconstructions of nucleosomes and their complexes with MeCP2 from SAXS data. SAXS studies also revealed unexpected sequence-dependent conformational variability in the nucleosomes themselves. FAU - Yang, Chenghua AU - Yang C AD - Department of Biochemistry and Molecular Biology and Howard Hughes Medical Institute, Colorado State University, Fort Collins, CO 80523-1870, USA. FAU - van der Woerd, Mark J AU - van der Woerd MJ FAU - Muthurajan, Uma M AU - Muthurajan UM FAU - Hansen, Jeffrey C AU - Hansen JC FAU - Luger, Karolin AU - Luger K LA - eng GR - CA92584/CA/NCI NIH HHS/United States GR - P01 CA092584/CA/NCI NIH HHS/United States GR - R01 GM061909/GM/NIGMS NIH HHS/United States GR - R01 GM066834/GM/NIGMS NIH HHS/United States GR - R01 GM066834-09/GM/NIGMS NIH HHS/United States GR - R01 GM096192/GM/NIGMS NIH HHS/United States GR - R01GM061909/GM/NIGMS NIH HHS/United States GR - R01GM066834/GM/NIGMS NIH HHS/United States GR - R01GM096192/GM/NIGMS NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110129 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (MECP2 protein, human) RN - 0 (Methyl-CpG-Binding Protein 2) RN - 0 (Nucleosomes) RN - 9007-49-2 (DNA) SB - IM MH - Binding Sites MH - DNA/chemistry MH - Humans MH - Methyl-CpG-Binding Protein 2/*chemistry/metabolism MH - Models, Molecular MH - Nucleic Acid Conformation MH - Nucleosomes/*chemistry/metabolism MH - Scattering, Small Angle MH - X-Ray Diffraction PMC - PMC3105411 OID - NLM: PMC3105411 EDAT- 2011/02/01 06:00 MHDA- 2011/08/10 06:00 CRDT- 2011/02/01 06:00 PHST- 2011/01/29 [aheadofprint] AID - gkr005 [pii] AID - 10.1093/nar/gkr005 [doi] PST - ppublish SO - Nucleic Acids Res. 2011 May;39(10):4122-35. doi: 10.1093/nar/gkr005. Epub 2011 Jan 29. PMID- 19278259 OWN - NLM STAT- MEDLINE DA - 20090408 DCOM- 20090624 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 131 IP - 14 DP - 2009 Apr 15 TI - Atomistic details of the disordered states of KID and pKID. Implications in coupled binding and folding. PG - 5214-23 LID - 10.1021/ja808999m [doi] AB - Intrinsically disordered proteins (IDPs) are a newly recognized class of functional proteins for which a lack of stable tertiary fold is required for function. Because of the heterogeneous and dynamical nature, molecular modeling is necessary to provide the missing details of disordered states of IDP that are crucial for understanding their functions. In particular, generalized Born (GB) implicit solvent, combined with replica exchange (REX), might offer an optimal balance between accuracy and efficiency for modeling IDPs. We carried out extensive REX simulations in an optimized GB force field to characterize the disordered states of a regulatory IDP, KID domain of transcription factor CREB, and its phosphorylated form, pKID. The results revealed that both KID and pKID, though highly disordered on the tertiary level, are compact and mainly occupy a small number of helical substates. Interestingly, although phosphorylation of KID Ser133 leads only to marginal changes in average helicities on the ensemble level, underlying conformational substates differ significantly. In particular, pSer133 appears to restrict the accessible conformational space of the loop region and thus reduces the entropic cost of KID folding upon binding to the KIX domain of CREB-binding protein. Such an expanded role of phosphorylation in the KID:KIX recognition was not previously recognized because of a lack of substantial conformational changes on the ensemble level and inaccessibility of the structural details from experiments. The results also suggest that an implicit solvent-based modeling framework, despite various existing limitations, might be feasible for accurate atomistic simulation of small IDPs in general. FAU - Ganguly, Debabani AU - Ganguly D AD - Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506, USA. FAU - Chen, Jianhan AU - Chen J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Cyclic AMP Response Element-Binding Protein) RN - 0 (Phosphates) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Amino Acid Sequence MH - CREB-Binding Protein/chemistry/metabolism MH - Computer Simulation MH - Cyclic AMP Response Element-Binding Protein/*chemistry/genetics/metabolism MH - Entropy MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Phosphates/chemistry MH - Phosphorylation MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary EDAT- 2009/03/13 09:00 MHDA- 2009/06/25 09:00 CRDT- 2009/03/13 09:00 AID - 10.1021/ja808999m [doi] PST - ppublish SO - J Am Chem Soc. 2009 Apr 15;131(14):5214-23. doi: 10.1021/ja808999m. PMID- 24150971 OWN - NLM STAT- MEDLINE DA - 20140306 DCOM- 20141118 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 82 IP - 4 DP - 2014 Apr TI - Temperature effects on the hydrodynamic radius of the intrinsically disordered N-terminal region of the p53 protein. PG - 668-78 LID - 10.1002/prot.24449 [doi] AB - Intrinsically disordered proteins (IDPs) are often characterized in terms of the hydrodynamic radius, Rh . The Rh of IDPs are known to depend on fractional proline content and net charge, where increased numbers of proline residues and increased net charge cause larger Rh . Though sequence and charge effects on the Rh of IDPs have been studied, the temperature sensitivity has been noted only briefly. Reported here are Rh measurements in the temperature range of 5-75 degrees C for the intrinsically disordered N-terminal region of the p53 protein, p53(1-93). Of note, the Rh of this protein fragment was highly sensitive to temperature, decreasing from 35 A at 5 degrees C to 26 A at 75 degrees C. Computer generated simulations of conformationally dynamic and disordered polypeptide chains were performed to provide a hypothesis for the heat-induced compaction of p53(1-93) structure, which was opposite to the heat-induced increase in Rh observed for a model folded protein. The simulations demonstrated that heat caused Rh to trend toward statistical coil values for both proteins, indicating that the effects of heat on p53(1-93) structure could be interpreted as thermal denaturation. The simulation data also predicted that proline content contributed minimally to the native Rh of p53(1-93), which was confirmed by measuring Rh for a substitution variant that had all 22 proline residues changed for glycine. CI - Copyright (c) 2013 Wiley Periodicals, Inc. FAU - Langridge, Timothy D AU - Langridge TD AD - Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, 78666. FAU - Tarver, Micheal J AU - Tarver MJ FAU - Whitten, Steven T AU - Whitten ST LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131122 PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Tumor Suppressor Protein p53) RN - 9DLQ4CIU6V (Proline) RN - TE7660XO1C (Glycine) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Circular Dichroism MH - Computer Simulation MH - Electrophoresis, Polyacrylamide Gel MH - Glycine/chemistry MH - Hydrodynamics MH - Hydrophobic and Hydrophilic Interactions MH - Intrinsically Disordered Proteins/*chemistry/ultrastructure MH - Models, Molecular MH - Proline/chemistry MH - *Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Temperature MH - Tumor Suppressor Protein p53/*chemistry/*ultrastructure OTO - NOTNLM OT - acidic activation domain OT - heat OT - hydrodynamic radius OT - intrinsically disordered protein OT - net charge OT - polyproline EDAT- 2013/10/24 06:00 MHDA- 2014/11/19 06:00 CRDT- 2013/10/24 06:00 PHST- 2013/08/13 [received] PHST- 2013/09/20 [revised] PHST- 2013/10/10 [accepted] PHST- 2013/11/22 [aheadofprint] AID - 10.1002/prot.24449 [doi] PST - ppublish SO - Proteins. 2014 Apr;82(4):668-78. doi: 10.1002/prot.24449. Epub 2013 Nov 22. PMID- 21507961 OWN - NLM STAT- MEDLINE DA - 20110613 DCOM- 20110830 LR - 20140820 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 24 DP - 2011 Jun 17 TI - Covalent structural changes in unfolded GroES that lead to amyloid fibril formation detected by NMR: insight into intrinsically disordered proteins. PG - 21796-805 LID - 10.1074/jbc.M111.228445 [doi] AB - Co-chaperonin GroES from Escherichia coli works with chaperonin GroEL to mediate the folding reactions of various proteins. However, under specific conditions, i.e. the completely disordered state in guanidine hydrochloride, this molecular chaperone forms amyloid fibrils similar to those observed in various neurodegenerative diseases. Thus, this is a good model system to understand the amyloid fibril formation mechanism of intrinsically disordered proteins. Here, we identified a critical intermediate of GroES in the early stages of this fibril formation using NMR and mass spectroscopy measurements. A covalent rearrangement of the polypeptide bond at Asn(45)-Gly(46) and/or Asn(51)-Gly(52) that eventually yield beta-aspartic acids via deamidation of asparagine was observed to precede fibril formation. Mutation of these asparagines to alanines resulted in delayed nucleus formation. Our results indicate that peptide bond rearrangement at Asn-Gly enhances the formation of GroES amyloid fibrils. The finding provides a novel insight into the structural process of amyloid fibril formation from a disordered state, which may be applicable to intrinsically disordered proteins in general. FAU - Iwasa, Hisanori AU - Iwasa H AD - Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan. FAU - Meshitsuka, Shunsuke AU - Meshitsuka S FAU - Hongo, Kunihiro AU - Hongo K FAU - Mizobata, Tomohiro AU - Mizobata T FAU - Kawata, Yasushi AU - Kawata Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110420 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Amyloid) RN - 0 (Chaperonin 10) RN - 0 (Peptides) RN - 30KYC7MIAI (Aspartic Acid) RN - 7006-34-0 (Asparagine) RN - JU58VJ6Y3B (Guanidine) RN - OF5P57N2ZX (Alanine) SB - IM MH - Alanine/chemistry MH - Amino Acid Sequence MH - Amyloid/*chemistry MH - Asparagine/chemistry MH - Aspartic Acid/chemistry MH - Chaperonin 10/*metabolism MH - Escherichia coli/metabolism MH - Guanidine/chemistry MH - Magnetic Resonance Spectroscopy/methods MH - Mass Spectrometry/methods MH - Molecular Sequence Data MH - Mutation MH - Peptides/chemistry MH - Protein Binding MH - Protein Conformation PMC - PMC3122234 OID - NLM: PMC3122234 EDAT- 2011/04/22 06:00 MHDA- 2011/08/31 06:00 CRDT- 2011/04/22 06:00 PHST- 2011/04/20 [aheadofprint] AID - M111.228445 [pii] AID - 10.1074/jbc.M111.228445 [doi] PST - ppublish SO - J Biol Chem. 2011 Jun 17;286(24):21796-805. doi: 10.1074/jbc.M111.228445. Epub 2011 Apr 20. PMID- 12370410 OWN - NLM STAT- MEDLINE DA - 20021016 DCOM- 20021204 LR - 20140611 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 99 IP - 21 DP - 2002 Oct 15 TI - Structure of the single-strand annealing domain of human RAD52 protein. PG - 13492-7 AB - In eukaryotic cells, RAD52 protein plays a central role in genetic recombination and DNA repair by (i) promoting the annealing of complementary single-stranded DNA and (ii) stimulation of the RAD51 recombinase. The single-strand annealing domain resides in the N-terminal region of the protein and is highly conserved, whereas the nonconserved RAD51-interaction domain is located in the C-terminal region. An N-terminal fragment of human RAD52 (residues 1-209) has been purified to homogeneity and, similar to the full-size protein (residues 1-418), shown to promote single-strand annealing in vitro. We have determined the crystal structure of this single-strand annealing domain at 2.7 A. The structure reveals an undecameric (11) subunit ring with extensive subunit contacts. A large, positively charged groove runs along the surface of the ring, readily suggesting a mechanism by which RAD52 presents the single strand for reannealing with complementary single-stranded DNA. FAU - Singleton, Martin R AU - Singleton MR AD - Cancer Research U.K., London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, UK. FAU - Wentzell, Lois M AU - Wentzell LM FAU - Liu, Yilun AU - Liu Y FAU - West, Stephen C AU - West SC FAU - Wigley, Dale B AU - Wigley DB LA - eng SI - PDB/1H21 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20021007 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA, Single-Stranded) RN - 0 (DNA-Binding Proteins) RN - 0 (Peptide Fragments) RN - 0 (Protein Subunits) RN - 0 (RAD52 protein, human) RN - 0 (Rad52 DNA Repair and Recombination Protein) RN - 0 (Recombinant Proteins) SB - IM MH - Binding Sites MH - Crystallography, X-Ray MH - DNA Repair MH - DNA, Single-Stranded/metabolism MH - DNA-Binding Proteins/*chemistry/genetics/metabolism MH - Humans MH - Models, Molecular MH - Molecular Structure MH - Peptide Fragments/chemistry/genetics MH - Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Protein Subunits MH - Rad52 DNA Repair and Recombination Protein MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Static Electricity PMC - PMC129701 OID - NLM: PMC129701 EDAT- 2002/10/09 04:00 MHDA- 2002/12/05 04:00 CRDT- 2002/10/09 04:00 PHST- 2002/10/07 [aheadofprint] AID - 10.1073/pnas.212449899 [doi] AID - 212449899 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13492-7. Epub 2002 Oct 7. PMID- 19399222 OWN - NLM STAT- MEDLINE DA - 20090428 DCOM- 20140415 LR - 20140829 IS - 1422-0067 (Electronic) IS - 1422-0067 (Linking) VI - 10 IP - 3 DP - 2009 Mar TI - The role of disordered ribosomal protein extensions in the early steps of eubacterial 50 S ribosomal subunit assembly. PG - 817-34 LID - 10.3390/ijms10030817 [doi] AB - Although during the past decade research has shown the functional importance of disorder in proteins, many of the structural and dynamics properties of intrinsically unstructured proteins (IUPs) remain to be elucidated. This review is focused on the role of the extensions of the ribosomal proteins in the early steps of the assembly of the eubacterial 50 S subunit. The recent crystallographic structures of the ribosomal particles have revealed the picture of a complex assembly pathway that condenses the rRNA and the ribosomal proteins into active ribosomes. However, little is know about the molecular mechanisms of this process. It is thought that the long basic r-protein extensions that penetrate deeply into the subunit cores play a key role through disorder-order transitions and/or co-folding mechanisms. A current view is that such structural transitions may facilitate the proper rRNA folding. In this paper, the structures of the proteins L3, L4, L13, L20, L22 and L24 that have been experimentally found to be essential for the first steps of ribosome assembly have been compared. On the basis of their structural and dynamics properties, three categories of extensions have been identified. Each of them seems to play a distinct function. Among them, only the coil-helix transition that occurs in a phylogenetically conserved cluster of basic residues of the L20 extension appears to be strictly required for the large subunit assembly in eubacteria. The role of alpha helix-coil transitions in 23 S RNA folding is discussed in the light of the calcium binding protein calmodulin that shares many structural and dynamics properties with L20. FAU - Timsit, Youri AU - Timsit Y AD - Institut de Biologie Physico-Chimique CNRS, Paris, France. FAU - Acosta, Zahir AU - Acosta Z FAU - Allemand, Frederic AU - Allemand F FAU - Chiaruttini, Claude AU - Chiaruttini C FAU - Springer, Mathias AU - Springer M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20090302 PL - Switzerland TA - Int J Mol Sci JT - International journal of molecular sciences JID - 101092791 RN - 0 (Ribosomal Proteins) SB - IM MH - Eubacterium/*metabolism MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Ribosomal Proteins/chemistry/*metabolism MH - Ribosome Subunits, Large, Bacterial/chemistry/*metabolism MH - Static Electricity PMC - PMC2672003 OID - NLM: PMC2672003 OTO - NOTNLM OT - Flexibility OT - calmodulin OT - electrostatic OT - helix unwinding OT - helix-coil OT - linker OT - structural transitions OT - unfolding GN - NLM: Original DateCompleted: 20100624 EDAT- 2009/04/29 09:00 MHDA- 2009/04/29 09:01 CRDT- 2009/04/29 09:00 PHST- 2009/02/05 [received] PHST- 2009/02/23 [revised] PHST- 2009/02/24 [accepted] PHST- 2009/03/02 [epublish] AID - 10.3390/ijms10030817 [doi] PST - ppublish SO - Int J Mol Sci. 2009 Mar;10(3):817-34. doi: 10.3390/ijms10030817. Epub 2009 Mar 2. PMID- 20436290 OWN - NLM STAT- MEDLINE DA - 20101215 DCOM- 20110503 IS - 1551-4005 (Electronic) IS - 1551-4005 (Linking) VI - 9 IP - 10 DP - 2010 May 15 TI - The molecular dynamics of MDM2. PG - 1878-81 AB - The pro-oncogenic signals of a vast number of anti-cancer drug targets are mediated by protein-protein interactions. This has made such targets less attractive to classic drug discovery programmes. New paradigms in the protein science field have revealed, however, that many protein-protein complexes are stabilized by an interaction between an intrinsically disordered peptide motif and a highly structured globular domain. This type of protein-protein interaction embodied by the MDM2-p53 complex can form a drugable interface. Extensive research has already uncovered the structure of the MDM2-bound p53 peptide to create p53 mimetics like Nutlin, but there has been less emphasis on understanding the dynamic nature of MDM2 itself. The work summarized by Joseph et al. forms a comprehensive and innovative roadmap using molecular dynamics simulations that provide solutions for understanding the flexible nature of a peptide-protein interface. This includes concepts on the plasticity of the peptide-binding groove and induced-fit mechanisms that explain the diversity of linear peptide motifs accommodated by globular domains. The success of molecular dynamics should inspire us to build further the structural biology of full-length MDM2 and other challenging oncoproteins for developing rules on how to develop small molecules that allosterically regulate multi-protein complexes. FAU - Nicholson, Judith AU - Nicholson J FAU - Hupp, Ted R AU - Hupp TR LA - eng PT - Editorial DEP - 20100515 PL - United States TA - Cell Cycle JT - Cell cycle (Georgetown, Tex.) JID - 101137841 RN - 0 (Tumor Suppressor Protein p53) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Animals MH - Humans MH - Models, Biological MH - Models, Molecular MH - Protein Binding MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-mdm2/chemistry/genetics/*metabolism MH - Tumor Suppressor Protein p53/genetics/metabolism EDAT- 2010/05/04 06:00 MHDA- 2011/05/04 06:00 CRDT- 2010/05/04 06:00 PHST- 2010/05/15 [aheadofprint] AID - 11597 [pii] PST - ppublish SO - Cell Cycle. 2010 May 15;9(10):1878-81. Epub 2010 May 15. PMID- 16214166 OWN - NLM STAT- MEDLINE DA - 20051024 DCOM- 20051221 LR - 20091119 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 353 IP - 5 DP - 2005 Nov 11 TI - Disordered p27Kip1 exhibits intrinsic structure resembling the Cdk2/cyclin A-bound conformation. PG - 1118-28 AB - p27Kip1 (p27) influences cell division by regulating nuclear cyclin-dependent kinases. Before binding, p27 is at least partially disordered and folds upon binding its Cdk/cyclin targets. 30-40% of human proteins, including p27, are predicted to contain disordered segments, and have been termed intrinsically unstructured proteins (IUPs). Unfortunately, the inherent dynamics of IUPs hamper detailed analysis of their structure/function relationships. Here, we describe the use of molecular dynamics (MD) computations and solution NMR spectroscopy to reveal that several segments of the p27 kinase inhibitory domain (p27-KID), in addition to the previously characterized helical segment, exist as highly populated, intrinsically folded structural units (IFSUs). Several IFSUs resemble structural features of bound p27-KID, while another exhibits alternative conformations. Interestingly, the highly conserved, specificity determining segment of p27 is shown to be highly disordered. Elucidation of IFSUs within p27-KID allows consideration of their influences on the thermodynamics and kinetics of Cdk/cyclin binding. The degree to which IFSUs are populated within p27-KID is surprising and suggests that other putative IUPs contain IFSUs that may be studied using similar techniques. FAU - Sivakolundu, Sivashankar G AU - Sivakolundu SG AD - Department of Structural Biology, St. Jude Children's Research Hospital, 332 North Lauderdale St., Memphis, TN 38105, USA. FAU - Bashford, Donald AU - Bashford D FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng GR - CA21765/CA/NCI NIH HHS/United States GR - CA82491/CA/NCI NIH HHS/United States GR - GM57513/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20050920 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Cyclin A) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 2) SB - IM MH - Computer Simulation MH - Cyclin A/*chemistry MH - Cyclin-Dependent Kinase 2/*chemistry MH - Cyclin-Dependent Kinase Inhibitor p27/*chemistry MH - Humans MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - Protein Folding EDAT- 2005/10/11 09:00 MHDA- 2005/12/22 09:00 CRDT- 2005/10/11 09:00 PHST- 2005/07/06 [received] PHST- 2005/08/25 [revised] PHST- 2005/08/29 [accepted] PHST- 2005/09/20 [aheadofprint] AID - S0022-2836(05)01054-5 [pii] AID - 10.1016/j.jmb.2005.08.074 [doi] PST - ppublish SO - J Mol Biol. 2005 Nov 11;353(5):1118-28. Epub 2005 Sep 20. PMID- 1324168 OWN - NLM STAT- MEDLINE DA - 19920922 DCOM- 19920922 LR - 20131121 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 11 IP - 9 DP - 1992 Sep TI - Restoration of a lost metal-binding site: construction of two different copper sites into a subunit of the E. coli cytochrome o quinol oxidase complex. PG - 3209-17 AB - The cupredoxin fold, a Greek key beta-barrel, is a common structural motif in a family of small blue copper proteins and a subdomain in many multicopper oxidases. Here we show that a cupredoxin domain is present in subunit II of cytochrome c and quinol oxidase complexes. In the former complex this subunit is thought to bind a copper centre called CuA which is missing from the latter complex. We have expressed the C-terminal fragment of the membrane-bound CyoA subunit of the Escherichia coli cytochrome o quinol oxidase as a water-soluble protein. Two mutants have been designed into the CyoA fragment. The optical spectrum shows that one mutant is similar to blue copper proteins. The second mutant has an optical spectrum and redox potential like the purple copper site in nitrous oxide reductase (N2OR). This site is closely related to CuA, which is the copper centre typical of cytochrome c oxidase. The electron paramagnetic resonance (EPR) spectra of both this mutant and the entire cytochrome o complex, into which the CuA site has been introduced, are similar to the EPR spectra of the native CuA site in cytochrome oxidase. These results give the first experimental evidence that CuA is bound to the subunit II of cytochrome c oxidase and open a new way to study this peculiar copper site. FAU - van der Oost, J AU - van der Oost J AD - European Molecular Biology Laboratory, Heidelberg, Germany. FAU - Lappalainen, P AU - Lappalainen P FAU - Musacchio, A AU - Musacchio A FAU - Warne, A AU - Warne A FAU - Lemieux, L AU - Lemieux L FAU - Rumbley, J AU - Rumbley J FAU - Gennis, R B AU - Gennis RB FAU - Aasa, R AU - Aasa R FAU - Pascher, T AU - Pascher T FAU - Malmstrom, B G AU - Malmstrom BG AU - et al. LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Cytochrome b Group) RN - 0 (Cytochromes) RN - 0 (Escherichia coli Proteins) RN - 0 (Macromolecular Substances) RN - 0 (Peptide Fragments) RN - 0 (cupredoxin) RN - 12284-43-4 (Azurin) RN - 789U1901C5 (Copper) RN - 9035-48-7 (cytochrome bo, E coli) RN - EC 1.- (Oxidoreductases) RN - EC 1.- (duroquinol oxidase) RN - EC 1.9.3.1 (Electron Transport Complex IV) SB - IM GS - CyoA MH - Amino Acid Sequence MH - Azurin/analogs & derivatives/genetics/metabolism MH - Base Sequence MH - Binding Sites MH - Copper/*metabolism MH - *Cytochrome b Group MH - Cytochromes/genetics/*metabolism MH - Electron Spin Resonance Spectroscopy MH - Electron Transport Complex IV/*metabolism MH - Escherichia coli/*enzymology MH - *Escherichia coli Proteins MH - Genetic Engineering MH - Macromolecular Substances MH - Molecular Sequence Data MH - Mutagenesis MH - Oxidoreductases/genetics/*metabolism MH - Peptide Fragments/biosynthesis/genetics MH - Protein Conformation MH - Sequence Homology, Nucleic Acid MH - Spectrophotometry PMC - PMC556854 OID - NLM: PMC556854 EDAT- 1992/09/01 MHDA- 1992/09/01 00:01 CRDT- 1992/09/01 00:00 PST - ppublish SO - EMBO J. 1992 Sep;11(9):3209-17. PMID- 16631104 OWN - NLM STAT- MEDLINE DA - 20060626 DCOM- 20060816 LR - 20071115 IS - 0003-9861 (Print) IS - 0003-9861 (Linking) VI - 451 IP - 1 DP - 2006 Jul 1 TI - CG15031/PPYR1 is an intrinsically unstructured protein that interacts with protein phosphatase Y. PG - 59-67 AB - Protein phosphatase Y (PPY) is a Drosophila testis-specific enzyme of unknown function. In a yeast two-hybrid screen we identified CG15031/PPYR1 as a PPY interacting protein. The specificity of the protein-protein interaction was proven by directed two-hybrid tests. The complex formation between PPY and PPYR1 was confirmed under in vitro and in vivo conditions by plasmon resonance spectroscopy, co-immunoprecipitation, and pull down experiments. Recombinant PPYR1 expressed in Escherichia coli is a heatstable, protease sensitive, intrinsically unstructured RNA-binding protein that migrates anomalously in SDS-polyacrylamide gel electrophoresis. It can be phosphorylated by cAMP-dependent protein kinase in vitro. PPYR1 moderately inhibits PPY activity, the inhibitory potential of the protein is slightly increased by phosphorylation. We suggest that PPYR1 may function as a scaffolding protein that targets PPY to RNA and other protein partners in Drosophila melanogaster. FAU - Kokai, Endre AU - Kokai E AD - Department of Medical Chemistry, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, H-4032 Debrecen, Egyetem ter 1, Hungary. FAU - Tantos, Agnes AU - Tantos A FAU - Vissi, Emese AU - Vissi E FAU - Szoor, Balazs AU - Szoor B FAU - Tompa, Peter AU - Tompa P FAU - Gausz, Janos AU - Gausz J FAU - Alphey, Luke AU - Alphey L FAU - Friedrich, Peter AU - Friedrich P FAU - Dombradi, Viktor AU - Dombradi V LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060405 PL - United States TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (CG15031 protein, Drosophila) RN - 0 (Drosophila Proteins) RN - 0 (RNA-Binding Proteins) RN - 0 (Receptors, Neuropeptide Y) RN - 0 (Recombinant Proteins) RN - 0 (neuropeptide Y4 receptor) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) RN - EC 3.1.3.- (PpY-55A protein, Drosophila) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) SB - IM MH - Animals MH - Base Sequence MH - Binding Sites MH - Cyclic AMP-Dependent Protein Kinases/metabolism MH - Drosophila Proteins/genetics/*metabolism MH - Drosophila melanogaster MH - Electrophoresis, Polyacrylamide Gel MH - Escherichia coli/genetics MH - Phosphoprotein Phosphatases/genetics/*metabolism MH - Phosphorylation MH - RNA-Binding Proteins/metabolism MH - Receptors, Neuropeptide Y/genetics/*metabolism MH - Recombinant Proteins/genetics/metabolism MH - Surface Plasmon Resonance EDAT- 2006/04/25 09:00 MHDA- 2006/08/17 09:00 CRDT- 2006/04/25 09:00 PHST- 2006/02/17 [received] PHST- 2006/03/21 [revised] PHST- 2006/03/22 [accepted] PHST- 2006/04/05 [aheadofprint] AID - S0003-9861(06)00116-0 [pii] AID - 10.1016/j.abb.2006.03.020 [doi] PST - ppublish SO - Arch Biochem Biophys. 2006 Jul 1;451(1):59-67. Epub 2006 Apr 5. PMID- 16214169 OWN - NLM STAT- MEDLINE DA - 20051115 DCOM- 20060110 LR - 20071115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 354 IP - 2 DP - 2005 Nov 25 TI - Crystal structure of an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1. PG - 317-29 AB - Peroxiredoxins (Prxs) are thiol-dependent peroxidases that catalyze the detoxification of various peroxide substrates such as H2O2, peroxinitrite, and hydroperoxides, and control some signal transduction in eukaryotic cells. Prxs are found in all cellular organisms and represent an enormous superfamily. Recent genome sequencing projects and biochemical studies have identified a novel subfamily, the archaeal Prxs. Their primary sequences are similar to those of the 1-Cys Prxs, which use only one cysteine residue in catalysis, while their catalytic properties resemble those of the typical 2-Cys Prxs, which utilize two cysteine residues from adjacent monomers within a dimer in catalysis. We present here the X-ray crystal structure of an archaeal Prx from the aerobic hyperthermophilic crenarchaeon, Aeropyrum pernix K1, determined at 2.3 A resolution (Rwork of 17.8% and Rfree of 23.0%). The overall subunit arrangement of the A.pernix archaeal Prx is a toroid-shaped pentamer of homodimers, or an (alpha2)5 decamer, as observed in the previously reported crystal structures of decameric Prxs. The basic folding topology and the peroxidatic active site structure are essentially the same as those of the 1-Cys Prx, hORF6, except that the C-terminal extension of the A.pernix archaeal Prx forms a unique helix with its flanking loops. The thiol group of the peroxidatic cysteine C50 is overoxidized to sulfonic acid. Notably, the resolving cysteine C213 forms the intra-monomer disulfide bond with the third cysteine, C207, which should be a unique structural characteristic in the many archaeal Prxs that retain two conserved cysteine residues in the C-terminal region. The conformational flexibility near the intra-monomer disulfide linkage might be necessary for the dramatic structural rearrangements that occur in the catalytic cycle. FAU - Mizohata, Eiichi AU - Mizohata E AD - RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan. FAU - Sakai, Hiroaki AU - Sakai H FAU - Fusatomi, Emiko AU - Fusatomi E FAU - Terada, Takaho AU - Terada T FAU - Murayama, Kazutaka AU - Murayama K FAU - Shirouzu, Mikako AU - Shirouzu M FAU - Yokoyama, Shigeyuki AU - Yokoyama S LA - eng SI - PDB/2CV4 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050922 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - EC 1.11.1.- (Peroxidases) RN - EC 1.11.1.15 (Peroxiredoxins) SB - IM MH - Aeropyrum/classification/*enzymology MH - Amino Acid Sequence MH - Archaea/*chemistry MH - Binding Sites MH - Catalysis MH - Cloning, Molecular MH - Crystallization MH - Crystallography, X-Ray MH - Kinetics MH - Models, Molecular MH - Molecular Sequence Data MH - Peroxidases/*chemistry/*metabolism MH - Peroxiredoxins MH - Protein Conformation MH - Sequence Homology, Amino Acid MH - Substrate Specificity EDAT- 2005/10/11 09:00 MHDA- 2006/01/13 09:00 CRDT- 2005/10/11 09:00 PHST- 2005/06/02 [received] PHST- 2005/08/31 [revised] PHST- 2005/09/06 [accepted] PHST- 2005/09/22 [aheadofprint] AID - S0022-2836(05)01059-4 [pii] AID - 10.1016/j.jmb.2005.09.006 [doi] PST - ppublish SO - J Mol Biol. 2005 Nov 25;354(2):317-29. Epub 2005 Sep 22. PMID- 2402636 OWN - NLM STAT- MEDLINE DA - 19901026 DCOM- 19901026 LR - 20070319 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 249 IP - 4975 DP - 1990 Sep 21 TI - Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. PG - 1425-8 AB - Triosephosphate isomerase (TIM) is used as a model system for the study of how a localized conformational change in a protein structure is produced and related to enzyme reactivity. An 11-residue loop region moves more than 7 angstroms and closes over the active site when substrate binds. The loop acts like a "lid" in that it moves rigidly and is attached by two hinges to the remainder of the protein. The nature of the motion appears to be built into the loop by conserved residues; the hinge regions, in contrast, are not conserved. Results of molecular dynamics calculations confirm the structural analysis and suggest a possible ligand-induced mechanism for loop closure. FAU - Joseph, D AU - Joseph D AD - Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139. FAU - Petsko, G A AU - Petsko GA FAU - Karplus, M AU - Karplus M LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - EC 5.1.3.- (Carbohydrate Epimerases) RN - EC 5.3.1.1 (Triose-Phosphate Isomerase) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Carbohydrate Epimerases/*metabolism MH - Hydrogen Bonding MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - *Protein Conformation MH - Software MH - Triose-Phosphate Isomerase/*metabolism EDAT- 1990/09/21 MHDA- 1990/09/21 00:01 CRDT- 1990/09/21 00:00 PST - ppublish SO - Science. 1990 Sep 21;249(4975):1425-8. PMID- 20490633 OWN - NLM STAT- MEDLINE DA - 20101216 DCOM- 20110328 LR - 20120730 IS - 1573-4994 (Electronic) IS - 1053-0509 (Linking) VI - 20 IP - 6 DP - 2010 Nov TI - Studies of interaction between cyanine dye T-284 and fibrillar alpha-synuclein. PG - 1267-74 LID - 10.1007/s10895-010-0678-1 [doi] AB - A key feature of Parkinson's disease is the formation and accumulation of amyloid fibrils of the natively unfolded protein alpha-synuclein (ASN) inside neurons. Recently we have proposed novel sensitive monomethinecyanine dye T-284 as fluorescent probe for quantitative detection of ASN amyloid fibrils. In this study the T-284 dye complex with ASN fibril was characterized by means of fluorescence anisotropy, atomic force microscopy and time-resolved fluorescence techniques to give further insights into the mode of dye interaction with amyloid fibrils. The fluorescence anisotropy of T-284 was shown to noticeably increase upon addition of aggregated proteins indicating on stable dye/amyloid fibril complex formation. AFM imaging of fibrillar wild-type ASN revealed differences in heights between ASN fibrils alone and in presence of the T-284 dye (6.37 +/- 1.0 nm and 8.0 +/- 1.1 nm respectively), that is believed to be caused by embedding of T-284 dye molecules in the "binding channel" running along the fibril. Fluorescence decay analysis of the T-284 in complexes with fibrillar ASN variants revealed the fluorescence lifetime values for T-284/fibril complexes to be an order of magnitude higher as compared to the free dye. Also, the fluorescence decay of free T-284 was bi-exponential, while dye bound to protein yields tri-exponential decay. We suppose that in complexes with fibrillar ASN variants T-284 dye might exist in different "populations" due to interaction with fibrils in different conformers and ways. The exact binding mode of T-284 with ASN fibrils needs further studies. Studied parameters of dye/amyloid fibril complexes are important for the characterization and screening of newly-developed amyloid-sensitive dyes. FAU - Volkova, Kateryna D AU - Volkova KD AD - Department of Combinatorial Chemistry, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, 150 Zabolotnogo St., 03143, Kyiv, Ukraine. FAU - Kovalska, Vladyslava B AU - Kovalska VB FAU - Yu Losytskyy, Mykhaylo AU - Yu Losytskyy M FAU - Veldhuis, Gertjan AU - Veldhuis G FAU - Segers-Nolten, G M J AU - Segers-Nolten GM FAU - Tolmachev, Olexiy I AU - Tolmachev OI FAU - Subramaniam, Vinod AU - Subramaniam V FAU - Yarmoluk, Sergiy M AU - Yarmoluk SM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100519 PL - Netherlands TA - J Fluoresc JT - Journal of fluorescence JID - 9201341 RN - 0 (Carbocyanines) RN - 0 (Fluorescent Dyes) RN - 0 (T-284 dye) RN - 0 (alpha-Synuclein) SB - IM MH - Carbocyanines/*chemistry MH - Fluorescence Polarization MH - Fluorescent Dyes/*chemistry MH - Microscopy, Atomic Force MH - Molecular Structure MH - alpha-Synuclein/*chemistry EDAT- 2010/05/22 06:00 MHDA- 2011/03/29 06:00 CRDT- 2010/05/22 06:00 PHST- 2010/02/15 [received] PHST- 2010/05/05 [accepted] PHST- 2010/05/19 [aheadofprint] AID - 10.1007/s10895-010-0678-1 [doi] PST - ppublish SO - J Fluoresc. 2010 Nov;20(6):1267-74. doi: 10.1007/s10895-010-0678-1. Epub 2010 May 19. PMID- 15692043 OWN - NLM STAT- MEDLINE DA - 20050204 DCOM- 20050216 LR - 20131121 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 307 IP - 5710 DP - 2005 Feb 4 TI - Crystal structure of a complex between the catalytic and regulatory (RIalpha) subunits of PKA. PG - 690-6 AB - The 2.0-angstrom structure of the cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) catalytic subunit bound to a deletion mutant of a regulatory subunit (RIalpha) defines a previously unidentified extended interface. The complex provides a molecular mechanism for inhibition of PKA and suggests how cAMP binding leads to activation. The interface defines the large lobe of the catalytic subunit as a stable scaffold where Tyr247 in the G helix and Trp196 in the phosphorylated activation loop serve as anchor points for binding RIalpha. These residues compete with cAMP for the phosphate binding cassette in RIalpha. In contrast to the catalytic subunit, RIalpha undergoes major conformational changes when the complex is compared with cAMP-bound RIalpha. The inhibitor sequence docks to the active site, whereas the linker, also disordered in free RIalpha, folds across the extended interface. The beta barrel of cAMP binding domain A, which is the docking site for cAMP, remains largely intact in the complex, whereas the helical subdomain undergoes major reorganization. FAU - Kim, Choel AU - Kim C AD - Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA. FAU - Xuong, Nguyen-Huu AU - Xuong NH FAU - Taylor, Susan S AU - Taylor SS LA - eng SI - PDB/1U7E GR - DK07233/DK/NIDDK NIH HHS/United States GR - GM19301/GM/NIGMS NIH HHS/United States GR - GM34921/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Cyclic AMP-Dependent Protein Kinase RIalpha Subunit) RN - 42HK56048U (Tyrosine) RN - 8DUH1N11BX (Tryptophan) RN - E0399OZS9N (Cyclic AMP) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) SB - IM MH - Binding Sites MH - *Catalytic Domain MH - Crystallization MH - Crystallography, X-Ray MH - Cyclic AMP/metabolism MH - Cyclic AMP-Dependent Protein Kinase RIalpha Subunit MH - Cyclic AMP-Dependent Protein Kinases/antagonists & inhibitors/*chemistry/*metabolism MH - Enzyme Activation MH - Hydrogen Bonding MH - Hydrophobic and Hydrophilic Interactions MH - Models, Molecular MH - Phosphorylation MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Tryptophan/chemistry MH - Tyrosine/chemistry EDAT- 2005/02/05 09:00 MHDA- 2005/02/17 09:00 CRDT- 2005/02/05 09:00 AID - 307/5710/690 [pii] AID - 10.1126/science.1104607 [doi] PST - ppublish SO - Science. 2005 Feb 4;307(5710):690-6. PMID- 25435324 OWN - NLM STAT- In-Process DA - 20150123 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 22 IP - 12 DP - 2014 Dec 2 TI - Structural mechanism of nuclear transport mediated by importin beta and flexible amphiphilic proteins. PG - 1699-710 AB - Karyopherin beta family proteins mediate the nuclear/cytoplasmic transport of various proteins through the nuclear pore complex (NPC), although they are substantially larger than the size limit of the NPC.To elucidate the molecular mechanism underlying this paradoxical function, we focused on the unique structures called HEAT repeats, which consist of repetitive amphiphilic alpha helices. An in vitro transport assay and FRAP analyses demonstrated that not only karyopherin beta family proteins but also other proteins with HEAT repeats could pass through the NPC by themselves, and serve as transport mediators for their binding partners. Biochemical and spectroscopic analyses and molecular dynamics simulations of purified HEAT-rich proteins revealed that they interact with hydrophobic groups, including phenyl and alkyl groups, and undergo reversible conformational changes in tertiary structures, but not in secondary structures. These results show that conformational changes in the flexible amphiphilic motifs play a critical role in translocation through the NPC. FAU - Yoshimura, Shige H AU - Yoshimura SH FAU - Kumeta, Masahiro AU - Kumeta M FAU - Takeyasu, Kunio AU - Takeyasu K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 SB - IM CIN - Structure. 2014 Dec 2;22(12):1693-4. PMID: 25470426 EDAT- 2014/12/02 06:00 MHDA- 2014/12/02 06:00 CRDT- 2014/12/02 06:00 PHST- 2014/05/26 [received] PHST- 2014/10/03 [revised] PHST- 2014/10/04 [accepted] AID - S0969-2126(14)00336-0 [pii] AID - 10.1016/j.str.2014.10.009 [doi] PST - ppublish SO - Structure. 2014 Dec 2;22(12):1699-710. PMID- 10913306 OWN - NLM STAT- MEDLINE DA - 20000824 DCOM- 20000824 LR - 20081121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 39 IP - 30 DP - 2000 Aug 1 TI - Structural differences between Saccharomyces cerevisiae ribosomal stalk proteins P1 and P2 support their functional diversity. PG - 8935-43 AB - The eukaryotic acidic P1 and P2 proteins modulate the activity of the ribosomal stalk but playing distinct roles. The aim of this work was to analyze the structural features that are behind their different function. A structural characterization of Saccharomyces cerevisaie P1 alpha and P2 beta proteins was performed by circular dichroism, nuclear magnetic resonance, fluorescence spectroscopy, thermal denaturation, and protease sensitivity. The results confirm the low structure present in both proteins but reveal clear differences between them. P1 alpha shows a virtually unordered secondary structure with a residual helical content that disappears below 30 degrees C and a clear tendency to acquire secondary structure at low pH and in the presence of trifluoroethanol. In agreement with this higher disorder P1 alpha has a fully solvent-accessible tryptophan residue and, in contrast to P2 beta, is highly sensitive to protease degradation. An interaction between both proteins was observed, which induces an increase in the global secondary structure content of both proteins. Moreover, mixing of both proteins causes a shift of the P1 alpha tryptophan 40 signal, pointing to an involvement of this region in the interaction. This evidence directly proves an interaction between P1 alpha and P2 beta before ribosome binding and suggests a functional complementation between them. On a whole, the results provide structural support for the different functional roles played by the proteins of the two groups showing, at the same time, that relatively small structural differences between the two stalk acidic protein types can result in significant functional changes. FAU - Zurdo, J AU - Zurdo J AD - Centro de Biologia Molecular Severo Ochoa (CSIC and UAM), Canto Blanco, 28049 Madrid, Spain. FAU - Gonzalez, C AU - Gonzalez C FAU - Sanz, J M AU - Sanz JM FAU - Rico, M AU - Rico M FAU - Remacha, M AU - Remacha M FAU - Ballesta, J P AU - Ballesta JP LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Fungal Proteins) RN - 0 (Phosphoproteins) RN - 0 (Ribosomal Proteins) RN - 0 (phosphoprotein P2, ribosomal) RN - 0 (ribosomal phosphoprotein P1) RN - EC 3.4.21.64 (Endopeptidase K) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Endopeptidase K/metabolism MH - Fungal Proteins/*chemistry/metabolism/physiology MH - Hot Temperature MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphoproteins/*chemistry/metabolism/physiology MH - Protein Denaturation MH - Protein Structure, Secondary MH - Ribosomal Proteins/*chemistry/metabolism/physiology MH - Saccharomyces cerevisiae/metabolism/*physiology MH - Sequence Homology, Amino Acid MH - Spectrometry, Fluorescence MH - Structure-Activity Relationship EDAT- 2000/07/29 11:00 MHDA- 2000/08/29 11:01 CRDT- 2000/07/29 11:00 AID - bi000363b [pii] PST - ppublish SO - Biochemistry. 2000 Aug 1;39(30):8935-43. PMID- 6487597 OWN - NLM STAT- MEDLINE DA - 19841212 DCOM- 19841212 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 23 IP - 18 DP - 1984 Aug 28 TI - Amino acid sequence of the regulatory subunit of bovine type I adenosine cyclic 3',5'-phosphate dependent protein kinase. PG - 4193-9 AB - The complete amino acid sequence of the regulatory subunit of type I cAMP-dependent protein kinase from bovine skeletal muscle is presented. The S-carboxymethylated protein was cleaved with cyanogen bromide to provide a complete set of nonoverlapping fragments. These fragments were overlapped and aligned by using peptides generated by proteolytic cleavage. The protein contains 379 amino acid residues corresponding to a molecular weight of 42 804. As in the type II regulatory subunit of cAMP-dependent protein kinase, a pattern of internal gene duplication is observed, which is consistent with two cAMP-binding domains. The two types of regulatory subunit from type I and type II kinase display similarities in domain substructure and in amino acid sequence, which provide a molecular basis for new insight into their regulatory roles. Detailed analyses of the homology of the regulatory subunits of type I and type II cAMP-dependent protein kinase and of similar relationships to cGMP-dependent protein kinase and Escherichia coli catabolite gene activator protein are presented in accompanying reports from this laboratory [Takio, K., Smith, S. B., Krebs, E. G., Walsh, K., & Titani, K. (1984) Biochemistry (second paper of three in this issue); Takio, K., Wade, R. D., Smith, S. B., Krebs, E. G., Walsh, K. A., & Titani, K. (1984) Biochemistry (third paper of three in this issue)]. FAU - Titani, K AU - Titani K FAU - Sasagawa, T AU - Sasagawa T FAU - Ericsson, L H AU - Ericsson LH FAU - Kumar, S AU - Kumar S FAU - Smith, S B AU - Smith SB FAU - Krebs, E G AU - Krebs EG FAU - Walsh, K A AU - Walsh KA LA - eng GR - GM 15731/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Carbon Radioisotopes) RN - 0 (Macromolecular Substances) RN - 0 (Peptide Fragments) RN - EC 2.7.- (Protein Kinases) RN - EC 3.4.21.4 (Trypsin) RN - OS382OHJ8P (Cyanogen Bromide) SB - IM MH - Amino Acid Sequence MH - Animals MH - Carbon Radioisotopes/diagnostic use MH - Cattle MH - Cyanogen Bromide MH - Macromolecular Substances MH - Muscles/enzymology MH - Peptide Fragments/analysis MH - *Protein Kinases MH - Trypsin EDAT- 1984/08/28 MHDA- 1984/08/28 00:01 CRDT- 1984/08/28 00:00 PST - ppublish SO - Biochemistry. 1984 Aug 28;23(18):4193-9. PMID- 25312846 OWN - NLM STAT- MEDLINE DA - 20141118 DCOM- 20150126 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 45 DP - 2014 Nov 18 TI - DYNLL2 dynein light chain binds to an extended linear motif of myosin 5a tail that has structural plasticity. PG - 7107-22 LID - 10.1021/bi500574z [doi] AB - LC8 dynein light chains (DYNLL) are conserved homodimeric eukaryotic hub proteins that participate in diverse cellular processes. Among the binding partners of DYNLL2, myosin 5a (myo5a) is a motor protein involved in cargo transport. Here we provide a profound characterization of the DYNLL2 binding motif of myo5a in free and DYNLL2-bound form by using nuclear magnetic resonance spectroscopy, X-ray crystallography, and molecular dynamics simulations. In the free form, the DYNLL2 binding region, located in an intrinsically disordered domain of the myo5a tail, has a nascent helical character. The motif becomes structured and folds into a beta-strand upon binding to DYNLL2. Despite differences of the myo5a sequence from the consensus binding motif, one peptide is accommodated in each of the parallel DYNLL2 binding grooves, as for all other known partners. Interestingly, while the core motif shows a similar interaction pattern in the binding groove as seen in other complexes, the flanking residues make several additional contacts, thereby lengthening the binding motif. The N-terminal extension folds back and partially blocks the free edge of the beta-sheet formed by the binding motif itself. The C-terminal extension contacts the dimer interface and interacts with symmetry-related residues of the second myo5a peptide. The involvement of flanking residues of the core binding site of myo5a could modify the quaternary structure of the full-length myo5a and affect its biological functions. Our results deepen the knowledge of the diverse partner recognition of DYNLL proteins and provide an example of a Janus-faced linear motif. FAU - Bodor, Andrea AU - Bodor A AD - Laboratory of Structural Chemistry and Biology, Institute of Chemistry, and double daggerDepartment of Biochemistry, Eotvos Lorand University , Budapest, 1117 Hungary. FAU - Radnai, Laszlo AU - Radnai L FAU - Hetenyi, Csaba AU - Hetenyi C FAU - Rapali, Peter AU - Rapali P FAU - Lang, Andras AU - Lang A FAU - Kover, Katalin E AU - Kover KE FAU - Perczel, Andras AU - Perczel A FAU - Wahlgren, Weixiao Y AU - Wahlgren WY FAU - Katona, Gergely AU - Katona G FAU - Nyitray, Laszlo AU - Nyitray L LA - eng SI - PDB/4D07 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141105 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - EC 3.6.4.1 (Myosins) RN - EC 3.6.4.2 (Cytoplasmic Dyneins) RN - EC 3.6.4.2 (DYNLL2 protein, human) SB - IM MH - Amino Acid Motifs/physiology MH - Amino Acid Sequence MH - Crystallography, X-Ray MH - Cytoplasmic Dyneins/*chemistry/genetics/*metabolism MH - Humans MH - Molecular Sequence Data MH - Myosins/*chemistry/genetics/*metabolism MH - Protein Binding/physiology MH - Protein Structure, Secondary MH - Protein Structure, Tertiary EDAT- 2014/10/15 06:00 MHDA- 2015/01/27 06:00 CRDT- 2014/10/15 06:00 PHST- 2014/11/05 [aheadofprint] AID - 10.1021/bi500574z [doi] PST - ppublish SO - Biochemistry. 2014 Nov 18;53(45):7107-22. doi: 10.1021/bi500574z. Epub 2014 Nov 5. PMID- 20436279 OWN - NLM STAT- MEDLINE DA - 20101027 DCOM- 20110209 IS - 1555-8584 (Electronic) IS - 1547-6286 (Linking) VI - 7 IP - 3 DP - 2010 May-Jun TI - From protein interaction profile to functional assignment: the human protein Ki-1/57 is associated with pre-mRNA splicing events. PG - 268-71 AB - The mapping of protein-protein interactions of a determined organism is considered fundamental to assign protein function in the post-genomic era. As part of this effort, screenings for pairwise interactions by yeast two-hybrid system have been used popularly to reveal protein interaction networks in different biological systems. Through the identification of protein interaction partners we have successfully obtained interesting functional clues for Ki-1/57, a human protein with no previous functional annotation, in the context of RNA metabolism. We briefly discuss the way we approached protein-protein interaction data to conduct and interpret further molecular biological and cellular studies as well as structural analyses on this protein. Our data suggest that Ki-1/57 belongs to the family of intrinsically unstructured proteins and that the structural flexibility may be crucial for its capacity to interact with many different proteins. A large fraction of these proteins are involved in pre-mRNA splicing control. Finally, Ki-1/57 is localized to several subnuclear domains, all of which have been described to splicing and other RNA processing events. FAU - Bressan, Gustavo Costa AU - Bressan GC AD - Centro Nacional de Pesquisa em Energia e Materiais, Campinas, Sao Paulo, Brasil. FAU - Kobarg, Jorg AU - Kobarg J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100509 PL - United States TA - RNA Biol JT - RNA biology JID - 101235328 RN - 0 (HABP4 protein, human) RN - 0 (Myogenic Regulatory Factors) RN - 0 (Proteins) RN - 0 (RNA Precursors) SB - IM MH - Animals MH - Computational Biology/methods MH - Gene Regulatory Networks MH - Humans MH - Metabolome/physiology MH - Models, Biological MH - Myogenic Regulatory Factors/genetics/metabolism/*physiology MH - Protein Binding/physiology MH - Protein Interaction Mapping/methods MH - Proteins/*metabolism/*physiology MH - RNA Precursors/*metabolism MH - RNA Splicing/genetics/*physiology MH - Structure-Activity Relationship EDAT- 2010/05/04 06:00 MHDA- 2011/02/10 06:00 CRDT- 2010/05/04 06:00 PHST- 2010/05/09 [aheadofprint] AID - 11489 [pii] PST - ppublish SO - RNA Biol. 2010 May-Jun;7(3):268-71. Epub 2010 May 9. PMID- 7498455 OWN - NLM STAT- MEDLINE DA - 19960117 DCOM- 19960117 LR - 20131121 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 375 IP - 1-2 DP - 1995 Nov 13 TI - NMR identification of calcineurin B residues affected by binding of a calcineurin A peptide. PG - 108-12 AB - Triple resonance 3D NMR methods have been used to study the interaction between calcineurin B and a peptide fragment of calcineurin A for which it has high affinity (KD approximately 4 x 10(-7) M). Although calcineurin B aggregates at NMR concentrations of approximately 1 mM, in the presence of a target peptide fragment of calcineurin A it becomes monomeric and yields NMR spectra that are very similar to those reported previously for calcineurin B solubilized by the zwitterionic detergent CHAPS. Changes in chemical shifts between CHAPS- and peptide-solubilized calcineurin B are small which is indicative of no differences in secondary structure. Residues most affected by binding to target peptide are found primarily on the hydrophobic faces of the four helices, present in each of the two globular domains in calcineurin B, and in the loops connecting helices II and III, IV and V, and possibly in the C-terminal 12 residues, which also exhibit a change in mobility. FAU - Anglister, J AU - Anglister J AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA. FAU - Ren, H AU - Ren H FAU - Klee, C B AU - Klee CB FAU - Bax, A AU - Bax A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Calcium-Binding Proteins) RN - 0 (Calmodulin-Binding Proteins) RN - 0 (Cholic Acids) RN - 0 (Detergents) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 75621-03-3 (3-((3-cholamidopropyl)dimethylammonium)-1-propanesulfonate) RN - EC 3.1.3.16 (Calcineurin) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Calcineurin MH - Calcium/metabolism MH - Calcium-Binding Proteins/*chemistry/*metabolism MH - Calmodulin-Binding Proteins/chemistry/*metabolism MH - Cholic Acids MH - Detergents MH - Kinetics MH - Magnetic Resonance Spectroscopy/methods MH - Molecular Sequence Data MH - Peptide Fragments/chemical synthesis/chemistry/*metabolism MH - Phosphoprotein Phosphatases/chemistry/*metabolism MH - *Protein Conformation MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Solubility EDAT- 1995/11/13 MHDA- 1995/11/13 00:01 CRDT- 1995/11/13 00:00 AID - 0014-5793(95)01192-H [pii] PST - ppublish SO - FEBS Lett. 1995 Nov 13;375(1-2):108-12. PMID- 7766599 OWN - NLM STAT- MEDLINE DA - 19950703 DCOM- 19950703 LR - 20091119 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 34 IP - 21 DP - 1995 May 30 TI - Solution structure of the Ras-binding domain of c-Raf-1 and identification of its Ras interaction surface. PG - 6911-8 AB - The structure of the Ras-binding domain of human c-Raf-1 (residues 55-132) has been determined in solution by nuclear magnetic resonance (NMR) spectroscopy. Following complete assignment of the backbone and side-chain 1H, 15N, and 13C resonances, the structure was calculated using the program CHARMM. Over 1300 NOE-derived constraints were applied, resulting in a detailed structure. The fold of Raf55-132 consists of a five-stranded beta-sheet, a 12-residue alpha-helix, and an additional one-turn helix. It is similar to those of ubiquitin and the IgG-binding domain of protein G, although the three proteins share very little sequence identity. The surface of Raf55-132 that interacts with Ras has been identified by monitoring perturbation of line widths and chemical shifts of 15N-labeled Raf55-132 resonances during titration with unlabeled Ras-GMPPNP. The Ras-binding site is contained within a spatially contiguous patch comprised of the N-terminal beta-hairpin and the C-terminal end of the alpha-helix. FAU - Emerson, S D AU - Emerson SD AD - Roche Research Center, Hoffmann-La Roche Inc., Nutley, New Jersey 07110, USA. FAU - Madison, V S AU - Madison VS FAU - Palermo, R E AU - Palermo RE FAU - Waugh, D S AU - Waugh DS FAU - Scheffler, J E AU - Scheffler JE FAU - Tsao, K L AU - Tsao KL FAU - Kiefer, S E AU - Kiefer SE FAU - Liu, S P AU - Liu SP FAU - Fry, D C AU - Fry DC LA - eng PT - Journal Article PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Proto-Oncogene Proteins) RN - 0 (Solutions) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - EC 2.7.11.1 (Proto-Oncogene Proteins c-raf) RN - EC 3.6.5.2 (ras Proteins) SB - IM MH - Binding Sites MH - Humans MH - Magnetic Resonance Spectroscopy MH - Protein Conformation MH - Protein-Serine-Threonine Kinases/chemistry/*metabolism MH - Proto-Oncogene Proteins/chemistry/*metabolism MH - Proto-Oncogene Proteins c-raf MH - Solutions MH - ras Proteins/*metabolism EDAT- 1995/05/30 MHDA- 1995/05/30 00:01 CRDT- 1995/05/30 00:00 PST - ppublish SO - Biochemistry. 1995 May 30;34(21):6911-8. PMID- 17636256 OWN - NLM STAT- MEDLINE DA - 20070924 DCOM- 20071108 LR - 20071115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 282 IP - 39 DP - 2007 Sep 28 TI - Structural basis for regulation of protein phosphatase 1 by inhibitor-2. PG - 28874-83 AB - The functional specificity of type 1 protein phosphatases (PP1) depends on the associated regulatory/targeting and inhibitory subunits. To gain insights into the mechanism of PP1 regulation by inhibitor-2, an ancient and intrinsically disordered regulator, we solved the crystal structure of the complex to 2.5A resolution. Our studies show that, when complexed with PP1c, I-2 acquires three regions of order: site 1, residues 12-17, binds adjacent to a region recognized by many PP1 regulators; site 2, amino acids 44-56, interacts along the RVXF binding groove through an unsuspected sequence, KSQKW; and site 3, residues 130-169, forms alpha-helical regions that lie across the substrate-binding cleft. Specifically, residues 148-151 interact at the catalytic center, displacing essential metal ions, accounting for both rapid inhibition and slower inactivation of PP1c. Thus, our structure provides novel insights into the mechanism of PP1 inhibition and subsequent reactivation, has broad implications for the physiological regulation of PP1, and highlights common inhibitory interactions among phosphoprotein phosphatase family members. FAU - Hurley, Thomas D AU - Hurley TD AD - Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA. thurley@iupui.edu FAU - Yang, Jie AU - Yang J FAU - Zhang, Lili AU - Zhang L FAU - Goodwin, Kristie D AU - Goodwin KD FAU - Zou, Qin AU - Zou Q FAU - Cortese, Marc AU - Cortese M FAU - Dunker, A Keith AU - Dunker AK FAU - DePaoli-Roach, Anna A AU - DePaoli-Roach AA LA - eng GR - LM007688-04/LM/NLM NIH HHS/United States GR - R01-DK036569/DK/NIDDK NIH HHS/United States GR - R01-DK063285/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20070718 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Proteins) RN - 0 (protein phosphatase inhibitor-2) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - EC 3.1.3.16 (Ppp1cc protein, mouse) RN - EC 3.1.3.16 (Ppp1cc protein, rat) RN - EC 3.1.3.16 (Protein Phosphatase 1) SB - IM MH - Animals MH - Binding Sites MH - Crystallography, X-Ray MH - Enzyme Activation MH - Mice MH - Phosphoprotein Phosphatases/antagonists & inhibitors/*chemistry/metabolism MH - Protein Binding MH - Protein Phosphatase 1 MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Proteins/genetics/*metabolism MH - Rats EDAT- 2007/07/20 09:00 MHDA- 2007/11/09 09:00 CRDT- 2007/07/20 09:00 PHST- 2007/07/18 [aheadofprint] AID - M703472200 [pii] AID - 10.1074/jbc.M703472200 [doi] PST - ppublish SO - J Biol Chem. 2007 Sep 28;282(39):28874-83. Epub 2007 Jul 18. PMID- 24333369 OWN - NLM STAT- MEDLINE DA - 20140218 DCOM- 20141008 IS - 1096-0279 (Electronic) IS - 1046-5928 (Linking) VI - 95 DP - 2014 Mar TI - Production and characterization of a retinoic acid receptor RARgamma construction encompassing the DNA binding domain and the disordered N-terminal proline rich domain. PG - 113-20 LID - 10.1016/j.pep.2013.12.001 [doi] LID - S1046-5928(13)00263-5 [pii] AB - Gene activation by retinoic acid nuclear receptors (RAR) is regulated by a number of molecular events such as ligand binding, interaction with cognate DNA sequences and co-regulatory proteins, and phosphorylation. Among the several phosphorylation sites that are involved in the non-genomic regulatory pathways of the RAR, two are located in a proline rich domain (PRD) within the N-terminal domain (NTD) of the receptor. This region is predicted to be intrinsically disordered, complicating its production and purification. We present here an approach enabling the high yield production of RAR fragments encompassing the PRD and the DNA binding domain (DBD). We found that expression levels were dependent on where the position of the N-terminal boundary of the fragment was placed within the RAR sequence. The purification protocol involves the use of maltose binding protein as a solubilising tag and extensive centrifugation steps at critical points of the purification process. This protocol is suitable to express (15)N, (13)C labeled proteins enabling nuclear magnetic resonance studies. The resulting proteins were characterized by biophysical methods including Small Angle X-ray Scattering and NMR. These studies showed that PRD extension of RARgamma is disordered in solution, a state that is compatible with modifications such as phosphorylation. CI - Copyright (c) 2013 Elsevier Inc. All rights reserved. FAU - Martinez-Zapien, Denise AU - Martinez-Zapien D AD - Institut de Genetique et de Biologie Moleculaire et Cellulaire, Universite de Strasbourg/CNRS UMR 7104/INSERM U964, 1 rue Laurent Fries, 67404 Illkirch, France. FAU - Delsuc, Marc-Andre AU - Delsuc MA AD - Institut de Genetique et de Biologie Moleculaire et Cellulaire, Universite de Strasbourg/CNRS UMR 7104/INSERM U964, 1 rue Laurent Fries, 67404 Illkirch, France. FAU - Trave, Gilles AU - Trave G AD - Equipe Oncoproteines, Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sebastien Brandt, BP10413, 67412 Illkirch Cedex, France. FAU - Lutzing, Regis AU - Lutzing R AD - Institut de Genetique et de Biologie Moleculaire et Cellulaire, Universite de Strasbourg/CNRS UMR 7104/INSERM U964, 1 rue Laurent Fries, 67404 Illkirch, France. FAU - Rochette-Egly, Cecile AU - Rochette-Egly C AD - Institut de Genetique et de Biologie Moleculaire et Cellulaire, Universite de Strasbourg/CNRS UMR 7104/INSERM U964, 1 rue Laurent Fries, 67404 Illkirch, France. FAU - Kieffer, Bruno AU - Kieffer B AD - Institut de Genetique et de Biologie Moleculaire et Cellulaire, Universite de Strasbourg/CNRS UMR 7104/INSERM U964, 1 rue Laurent Fries, 67404 Illkirch, France. Electronic address: kieffer@igbmc.fr. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131213 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Receptors, Retinoic Acid) RN - 0 (Recombinant Proteins) RN - 0 (retinoic acid receptor gamma) RN - 9007-49-2 (DNA) RN - 9DLQ4CIU6V (Proline) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - DNA/chemistry/metabolism MH - Electrophoresis, Polyacrylamide Gel MH - Escherichia coli/genetics MH - Humans MH - Intrinsically Disordered Proteins/chemistry/genetics/metabolism MH - Mice MH - Molecular Sequence Data MH - Proline MH - Protein Structure, Tertiary MH - Receptors, Retinoic Acid/*chemistry/genetics/*metabolism MH - Recombinant Proteins/*chemistry/genetics/*metabolism MH - Sequence Alignment OTO - NOTNLM OT - Intrinsically disordered proteins OT - Proline rich domain OT - Retinoic acid receptor EDAT- 2013/12/18 06:00 MHDA- 2014/10/09 06:00 CRDT- 2013/12/17 06:00 PHST- 2013/10/23 [received] PHST- 2013/11/27 [revised] PHST- 2013/12/03 [accepted] PHST- 2013/12/13 [aheadofprint] AID - S1046-5928(13)00263-5 [pii] AID - 10.1016/j.pep.2013.12.001 [doi] PST - ppublish SO - Protein Expr Purif. 2014 Mar;95:113-20. doi: 10.1016/j.pep.2013.12.001. Epub 2013 Dec 13. PMID- 17855524 OWN - NLM STAT- MEDLINE DA - 20071029 DCOM- 20071212 LR - 20140904 IS - 0022-538X (Print) IS - 0022-538X (Linking) VI - 81 IP - 22 DP - 2007 Nov TI - Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS. PG - 12406-17 AB - Aminoacyl-tRNA synthetases are pivotal in determining how the genetic code is translated in amino acids and in providing the substrate for protein synthesis. As such, they fulfill a key role in a process universally conserved in all cellular organisms from their most complex to their most reduced parasitic forms. In contrast, even complex viruses were not found to encode much translation machinery, with the exception of isolated components such as tRNAs. In this context, the discovery of four aminoacyl-tRNA synthetases encoded in the genome of mimivirus together with a full set of translation initiation, elongation, and termination factors appeared to blur what was once a clear frontier between the cellular and viral world. Functional studies of two mimivirus tRNA synthetases confirmed the MetRS specificity for methionine and the TyrRS specificity for tyrosine and conformity with the identity rules for tRNA(Tyr) for archea/eukarya. The atomic structure of the mimivirus tyrosyl-tRNA synthetase in complex with tyrosinol exhibits the typical fold and active-site organization of archaeal-type TyrRS. However, the viral enzyme presents a unique dimeric conformation and significant differences in its anticodon binding site. The present work suggests that mimivirus aminoacyl-tRNA synthetases function as regular translation enzymes in infected amoebas. Their phylogenetic classification does not suggest that they have been acquired recently by horizontal gene transfer from a cellular host but rather militates in favor of an intricate evolutionary relationship between large DNA viruses and ancestral eukaryotes. FAU - Abergel, Chantal AU - Abergel C AD - Structural and Genomic Information Laboratory, CNRS-UPR2589, IBSM-IFR88, 163 Avenue de Luminy, Case 934, 13288, Marseille Cedex 9, France. Chantal.Abergel@igs.cnrs-mrs.fr FAU - Rudinger-Thirion, Joelle AU - Rudinger-Thirion J FAU - Giege, Richard AU - Giege R FAU - Claverie, Jean-Michel AU - Claverie JM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070912 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (Anticodon) RN - 0 (RNA, Transfer, Met) RN - 0 (RNA, Transfer, Tyr) RN - 0 (Viral Proteins) RN - EC 6.1.1.1 (Tyrosine-tRNA Ligase) RN - EC 6.1.1.10 (Methionine-tRNA Ligase) SB - IM MH - Acanthamoeba/*virology MH - Animals MH - Anticodon/chemistry/metabolism MH - Crystallography, X-Ray MH - DNA Viruses/*enzymology MH - Methionine-tRNA Ligase/*chemistry/classification/genetics MH - Phylogeny MH - Protein Structure, Secondary MH - RNA, Transfer, Met/chemistry/metabolism MH - RNA, Transfer, Tyr/chemistry/metabolism MH - Tyrosine-tRNA Ligase/*chemistry/classification/genetics MH - Viral Proteins/*chemistry/classification/genetics PMC - PMC2169003 OID - NLM: PMC2169003 EDAT- 2007/09/15 09:00 MHDA- 2007/12/13 09:00 CRDT- 2007/09/15 09:00 PHST- 2007/09/12 [aheadofprint] AID - JVI.01107-07 [pii] AID - 10.1128/JVI.01107-07 [doi] PST - ppublish SO - J Virol. 2007 Nov;81(22):12406-17. Epub 2007 Sep 12. PMID- 24146948 OWN - NLM STAT- MEDLINE DA - 20131022 DCOM- 20140805 LR - 20141112 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 10 DP - 2013 TI - The transcriptional repressor domain of Gli3 is intrinsically disordered. PG - e76972 LID - 10.1371/journal.pone.0076972 [doi] AB - The transcription factor Gli3 is acting mainly as a transcriptional repressor in the Sonic hedgehog signal transduction pathway. Gli3 contains a repressor domain in its N-terminus from residue G106 to E236. In this study we have characterized the intracellular structure of the Gli3 repressor domain using a combined bioinformatics and experimental approach. According to our findings the Gli3 repressor domain while being intrinsically disordered contains predicted anchor sites for partner interactions. The obvious interaction partners to test were Ski and DNA; however, with both of these the structure of Gli3 repressor domain remained disordered. To locate residues important for the repressor function we mutated several residues within the Gli3 repressor domain. Two of these, H141A and H157N, targeting predicted helical regions, significantly decreased transcriptional repression and thus identify important functional parts of the domain. FAU - Tsanev, Robert AU - Tsanev R AD - Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia. FAU - Vanatalu, Kalju AU - Vanatalu K FAU - Jarvet, Juri AU - Jarvet J FAU - Tanner, Risto AU - Tanner R FAU - Laur, Kristi AU - Laur K FAU - Tiigimagi, Piret AU - Tiigimagi P FAU - Kragelund, Birthe B AU - Kragelund BB FAU - Osterlund, Torben AU - Osterlund T FAU - Kogerman, Priit AU - Kogerman P LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131017 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA-Binding Proteins) RN - 0 (GLI3 protein, human) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Kruppel-Like Transcription Factors) RN - 0 (Nerve Tissue Proteins) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Repressor Proteins) RN - 126648-96-2 (SKI protein, human) SB - IM MH - Amino Acid Sequence MH - Cell Line MH - DNA-Binding Proteins/metabolism MH - Humans MH - Intrinsically Disordered Proteins/chemistry/genetics/*metabolism MH - Kruppel-Like Transcription Factors/chemistry/genetics/*metabolism MH - Mutation MH - Nerve Tissue Proteins/chemistry/genetics/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - *Protein Interaction Domains and Motifs MH - Proto-Oncogene Proteins/metabolism MH - Recombinant Fusion Proteins MH - Repressor Proteins/chemistry/genetics/*metabolism PMC - PMC3798401 OID - NLM: PMC3798401 EDAT- 2013/10/23 06:00 MHDA- 2014/08/06 06:00 CRDT- 2013/10/23 06:00 PHST- 2013 [ecollection] PHST- 2013/06/18 [received] PHST- 2013/08/26 [accepted] PHST- 2013/10/17 [epublish] AID - 10.1371/journal.pone.0076972 [doi] AID - PONE-D-13-25394 [pii] PST - epublish SO - PLoS One. 2013 Oct 17;8(10):e76972. doi: 10.1371/journal.pone.0076972. eCollection 2013. PMID- 22155633 OWN - NLM STAT- MEDLINE DA - 20120117 DCOM- 20120410 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1820 IP - 2 DP - 2012 Feb TI - Inhibiting effect of alpha(s1)-casein on Abeta(1-40) fibrillogenesis. PG - 124-32 LID - 10.1016/j.bbagen.2011.11.010 [doi] AB - BACKGROUND: alpha(s1)-Casein is one of the four types of caseins, the largest protein component of bovine milk. The lack of a compact folded conformation and the capability to form micelles suggest a relationship of alpha(s1)-casein with the class of the intrinsically disordered (or natively unfolded) proteins. These proteins are known to exert a stabilizing activity on biomolecules through specific interaction with hydrophobic surfaces. In the present work we focused on the effect of alpha(s1)-casein on the fibrillogenesis of 1-40 beta-amyloid peptide, involved in Alzheimer's disease. METHODS: The aggregation kinetics of beta-peptide in presence and absence of alpha(s1)-casein was followed under shear at 37 degrees C by recording the Thioflavine fluorescence, usually taken as an indicator of fibers formation. Measurements of Static and Dynamic Light Scattering, Circular Dichroism, and AFM imaging were done to reveal the details of alpha(s1)-casein-Abeta(1-40) interaction. RESULTS AND DISCUSSIONS: alpha(s1)-Casein addition sizably increases the lag-time of the nucleation phase and slows down the entire fibrillization process. alpha(s1)-Casein sequesters the amyloid peptide on its surface thus exerting a chaperone-like activity by means a colloidal inhibition mechanism. GENERAL SIGNIFICANCE: Insights on the working mechanism of natural chaperones in preventing or controlling the amyloid aggregation. CI - Copyright (c) 2011 Elsevier B.V. All rights reserved. FAU - Carrotta, R AU - Carrotta R AD - Inst. of Biophysics, National Research Council, Via U. La Malfa 153, I-90146, Palermo, Italy. FAU - Canale, C AU - Canale C FAU - Diaspro, A AU - Diaspro A FAU - Trapani, A AU - Trapani A FAU - Biagio, P L San AU - Biagio PL FAU - Bulone, D AU - Bulone D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111201 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Amyloid) RN - 0 (Amyloid beta-Peptides) RN - 0 (Caseins) RN - 0 (Peptide Fragments) RN - 0 (Thiazoles) RN - 0 (amyloid beta-protein (1-40)) RN - 2390-54-7 (thioflavin T) SB - IM MH - Amyloid/*drug effects MH - Amyloid beta-Peptides/*antagonists & inhibitors/metabolism MH - Caseins/*pharmacology MH - Circular Dichroism MH - Hydrodynamics MH - Light MH - Microscopy, Atomic Force MH - Particle Size MH - Peptide Fragments/*antagonists & inhibitors/metabolism MH - Protein Structure, Quaternary MH - Scattering, Radiation MH - Spectrometry, Fluorescence MH - Thiazoles/metabolism MH - Time Factors EDAT- 2011/12/14 06:00 MHDA- 2012/04/11 06:00 CRDT- 2011/12/14 06:00 PHST- 2011/08/01 [received] PHST- 2011/11/17 [revised] PHST- 2011/11/18 [accepted] PHST- 2011/12/01 [aheadofprint] AID - S0304-4165(11)00287-X [pii] AID - 10.1016/j.bbagen.2011.11.010 [doi] PST - ppublish SO - Biochim Biophys Acta. 2012 Feb;1820(2):124-32. doi: 10.1016/j.bbagen.2011.11.010. Epub 2011 Dec 1. PMID- 24845231 OWN - NLM STAT- MEDLINE DA - 20140618 DCOM- 20140807 LR - 20150113 IS - 1552-4469 (Electronic) IS - 1552-4450 (Linking) VI - 10 IP - 7 DP - 2014 Jul TI - Targeting the disordered C terminus of PTP1B with an allosteric inhibitor. PG - 558-66 LID - 10.1038/nchembio.1528 [doi] AB - PTP1B, a validated therapeutic target for diabetes and obesity, has a critical positive role in HER2 signaling in breast tumorigenesis. Efforts to develop therapeutic inhibitors of PTP1B have been frustrated by the chemical properties of the active site. We define a new mechanism of allosteric inhibition that targets the C-terminal, noncatalytic segment of PTP1B. We present what is to our knowledge the first ensemble structure of PTP1B containing this intrinsically disordered segment, within which we identified a binding site for the small-molecule inhibitor MSI-1436. We demonstrate binding to a second site close to the catalytic domain, with cooperative effects between the two sites locking PTP1B in an inactive state. MSI-1436 antagonized HER2 signaling, inhibited tumorigenesis in xenografts and abrogated metastasis in the NDL2 mouse model of breast cancer, validating inhibition of PTP1B as a therapeutic strategy in breast cancer. This new approach to inhibition of PTP1B emphasizes the potential of disordered segments of proteins as specific binding sites for therapeutic small molecules. FAU - Krishnan, Navasona AU - Krishnan N AD - Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. FAU - Koveal, Dorothy AU - Koveal D AD - Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA. FAU - Miller, Daniel H AU - Miller DH AD - 1] Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, USA. [2] Department of Chemistry, Brown University, Providence, Rhode Island, USA. FAU - Xue, Bin AU - Xue B AD - 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2]. FAU - Akshinthala, Sai Dipikaa AU - Akshinthala SD AD - Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. FAU - Kragelj, Jaka AU - Kragelj J AD - Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, Grenoble, France. FAU - Jensen, Malene Ringkjobing AU - Jensen MR AD - Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, Grenoble, France. FAU - Gauss, Carla-Maria AU - Gauss CM AD - Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. FAU - Page, Rebecca AU - Page R AD - Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA. FAU - Blackledge, Martin AU - Blackledge M AD - Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, CEA, CNRS, Grenoble, France. FAU - Muthuswamy, Senthil K AU - Muthuswamy SK AD - 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] Department of Medical Biophysics, Ontario Cancer Institute, Campbell Family Institute for Breast Cancer Research, University of Toronto, Toronto, Canada. FAU - Peti, Wolfgang AU - Peti W AD - 1] Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, USA. [2] Department of Chemistry, Brown University, Providence, Rhode Island, USA. FAU - Tonks, Nicholas K AU - Tonks NK AD - Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. LA - eng GR - CA45508/CA/NCI NIH HHS/United States GR - CA53840/CA/NCI NIH HHS/United States GR - GM098482/GM/NIGMS NIH HHS/United States GR - GM100910/GM/NIGMS NIH HHS/United States GR - GM55989/GM/NIGMS NIH HHS/United States GR - R01 GM098482/GM/NIGMS NIH HHS/United States GR - R01 GM100910/GM/NIGMS NIH HHS/United States GR - S10-RR017269/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140520 PL - United States TA - Nat Chem Biol JT - Nature chemical biology JID - 101231976 RN - 0 (3-N-1(spermine)-7, 24-dihydroxy-5-cholestane 24-sulfate) RN - 0 (Antineoplastic Agents) RN - 0 (Cholestanes) RN - 2FZ7Y3VOQX (Spermine) RN - EC 2.7.10.1 (ERBB2 protein, human) RN - EC 2.7.10.1 (Receptor, ErbB-2) RN - EC 3.1.3.48 (PTPN1 protein, human) RN - EC 3.1.3.48 (Protein Tyrosine Phosphatase, Non-Receptor Type 1) SB - IM MH - Allosteric Regulation/drug effects MH - Allosteric Site/*drug effects MH - Animals MH - Antineoplastic Agents/chemistry/*pharmacology MH - Breast Neoplasms/drug therapy/enzymology/genetics/pathology MH - Catalytic Domain MH - Cholestanes/chemistry/*pharmacology MH - Female MH - *Gene Expression Regulation, Neoplastic MH - Humans MH - Kinetics MH - Mammary Neoplasms, Experimental/*drug therapy/enzymology/genetics/pathology MH - Mice MH - Models, Molecular MH - Molecular Targeted Therapy MH - Protein Binding/drug effects MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Tyrosine Phosphatase, Non-Receptor Type 1/*antagonists & inhibitors/genetics/metabolism MH - Receptor, ErbB-2/genetics/metabolism MH - Signal Transduction MH - Spermine/*analogs & derivatives/chemistry/pharmacology PMC - PMC4062594 MID - NIHMS587115 OID - NLM: NIHMS587115 OID - NLM: PMC4062594 EDAT- 2014/05/23 06:00 MHDA- 2014/08/08 06:00 CRDT- 2014/05/22 06:00 PHST- 2013/12/11 [received] PHST- 2014/04/16 [accepted] PHST- 2014/05/20 [aheadofprint] AID - nchembio.1528 [pii] AID - 10.1038/nchembio.1528 [doi] PST - ppublish SO - Nat Chem Biol. 2014 Jul;10(7):558-66. doi: 10.1038/nchembio.1528. Epub 2014 May 20. PMID- 22147495 OWN - NLM STAT- MEDLINE DA - 20120206 DCOM- 20120723 LR - 20131121 IS - 1616-5195 (Electronic) IS - 1616-5187 (Linking) VI - 12 IP - 2 DP - 2012 Feb TI - Natively unfolded state for engineering nanoscale fibrillar arrays. PG - 195-201 LID - 10.1002/mabi.201100295 [doi] AB - A generic rationale for the fabrication of high aspect ratio fibrillar nanoscale arrays is described. The design emulates an intermittence effect observed for beta-structured alpha-synunclein fibrils, reported herein, in a structurally unrelated alpha-helical fiber. The generated nanoarrays are composed of periodic nanosized segments separated at uniform distances of unfolded regions. These regions can be targeted for conformational binding and refolding with metal nanoparticle-peptide conjugates for the conversion of fibrillar arrays into nanoparticle arrays. The introduced concept opens new strategies for engineering novel nanoscale materials and devices. CI - Copyright (c) 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. FAU - Ryadnov, Maxim G AU - Ryadnov MG AD - National Physical Laboratory, Teddington, Middlesex, UK. max.ryadnov@npl.co.uk FAU - Cherny, Dmitry I AU - Cherny DI LA - eng GR - 088113/Z/08/Z/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111206 PL - Germany TA - Macromol Biosci JT - Macromolecular bioscience JID - 101135941 RN - 0 (Peptides) RN - 0 (alpha-Synuclein) RN - 3M4G523W1G (Silver) RN - 7440-57-5 (Gold) SB - IM MH - Amino Acid Sequence MH - Bioengineering/*methods MH - Chromatography, High Pressure Liquid MH - Circular Dichroism MH - Gold/chemistry MH - Metal Nanoparticles/*chemistry MH - Microscopy, Electron MH - Molecular Sequence Data MH - Nanotechnology/*methods MH - Peptides/*chemical synthesis MH - Protein Array Analysis MH - Protein Folding MH - Protein Structure, Secondary MH - Silver/chemistry MH - Solid-Phase Synthesis Techniques MH - alpha-Synuclein/*chemistry EDAT- 2011/12/08 06:00 MHDA- 2012/07/24 06:00 CRDT- 2011/12/08 06:00 PHST- 2011/07/25 [received] PHST- 2011/12/06 [aheadofprint] AID - 10.1002/mabi.201100295 [doi] PST - ppublish SO - Macromol Biosci. 2012 Feb;12(2):195-201. doi: 10.1002/mabi.201100295. Epub 2011 Dec 6. PMID- 18440022 OWN - NLM STAT- MEDLINE DA - 20080509 DCOM- 20080606 LR - 20150518 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 379 IP - 1 DP - 2008 May 23 TI - Solution conformation, backbone dynamics and lipid interactions of the intrinsically unstructured malaria surface protein MSP2. PG - 105-21 LID - 10.1016/j.jmb.2008.03.039 [doi] AB - Merozoite surface protein 2 (MSP2), one of the most abundant proteins on the surface of the merozoite stage of Plasmodium falciparum, is a potential component of a malaria vaccine, having shown some efficacy in a clinical trial in Papua New Guinea. MSP2 is a GPI-anchored protein consisting of conserved N- and C-terminal domains and a variable central region. Previous studies have shown that it is an intrinsically unstructured protein with a high propensity for fibril formation, in which the conserved N-terminal domain has a key role. Secondary structure predictions suggest that MSP2 contains long stretches of random coil with very little alpha-helix or beta-strand. Circular dichroism spectroscopy confirms this prediction under physiological conditions (pH 7.4) and in more acidic solutions (pH 6.2 and 3.4). Pulsed field gradient NMR diffusion measurements showed that MSP2 under physiological conditions has a large effective hydrodynamic radius consistent with an intrinsic pre-molten globule state, as defined by Uversky. This was supported by sedimentation velocity studies in the analytical ultracentrifuge. NMR resonance assignments have been obtained for FC27 MSP2, allowing the residual secondary structure and backbone dynamics to be defined. There is some motional restriction in the conserved C-terminal region in the vicinity of an intramolecular disulfide bond. Two other regions show motional restrictions, both of which display helical structure propensities. One of these helical regions is within the conserved N-terminal domain, which adopts essentially the same conformation in full-length MSP2 as in corresponding peptide fragments. We see no evidence of long-range interactions in the full-length protein. MSP2 associates with lipid micelles, but predominantly through the N-terminal region rather than the C terminus, which is GPI-anchored to the membrane in the parasite. FAU - Zhang, Xuecheng AU - Zhang X AD - The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3050, Australia. FAU - Perugini, Matthew A AU - Perugini MA FAU - Yao, Shenggen AU - Yao S FAU - Adda, Christopher G AU - Adda CG FAU - Murphy, Vincent J AU - Murphy VJ FAU - Low, Andrew AU - Low A FAU - Anders, Robin F AU - Anders RF FAU - Norton, Raymond S AU - Norton RS LA - eng GR - R01 AI059229-01A1/AI/NIAID NIH HHS/United States GR - R01AI059229/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20080328 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Antigens, Protozoan) RN - 0 (Disulfides) RN - 0 (Lipids) RN - 0 (Micelles) RN - 0 (Peptides) RN - 0 (Protozoan Proteins) RN - 0 (Solutions) RN - 0 (merozoite surface protein 2, Plasmodium) RN - 107-73-3 (Phosphorylcholine) RN - 53949-18-1 (dodecylphosphocholine) SB - IM MH - Amino Acid Sequence MH - Animals MH - Antigens, Protozoan/*chemistry/genetics MH - Circular Dichroism MH - Disulfides/chemistry MH - Lipids/*chemistry MH - Micelles MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Oxidation-Reduction MH - Peptides/chemistry/genetics MH - Phosphorylcholine/analogs & derivatives MH - *Plasmodium falciparum MH - Protein Structure, Secondary MH - Protozoan Proteins/*chemistry/genetics MH - Sequence Analysis, Protein MH - Solutions MH - Ultracentrifugation PMC - PMC4432223 MID - NIHMS51493 OID - NLM: NIHMS51493 OID - NLM: PMC4432223 EDAT- 2008/04/29 09:00 MHDA- 2008/06/07 09:00 CRDT- 2008/04/29 09:00 PHST- 2007/12/17 [received] PHST- 2008/03/17 [revised] PHST- 2008/03/19 [accepted] PHST- 2008/03/28 [aheadofprint] AID - S0022-2836(08)00359-8 [pii] AID - 10.1016/j.jmb.2008.03.039 [doi] PST - ppublish SO - J Mol Biol. 2008 May 23;379(1):105-21. doi: 10.1016/j.jmb.2008.03.039. Epub 2008 Mar 28. PMID- 10756036 OWN - NLM STAT- MEDLINE DA - 20000518 DCOM- 20000518 LR - 20140615 IS - 0022-538X (Print) IS - 0022-538X (Linking) VI - 74 IP - 9 DP - 2000 May TI - The phage infection process: a functional role for the distal linker region of bacteriophage protein 3. PG - 4229-35 AB - The filamentous bacteriophage infects Escherichia coli by interaction with the F pilus and the TolQRA complex. The virus-encoded protein initiating this process is the gene 3 protein (g3p). The g3p molecule can be divided into three different domains separated by two glycine-rich linker regions. Though there has been extensive evaluation of the importance of the diverse domains of g3p, no proper function has so far been assigned to these linker regions. Through the design of mutated variants of g3p that were displayed on the surface of bacteriophage, we were able to elucidate a possible role for the distal glycine-rich linker region. A phage that displayed a g3p comprised of only the N1 domain, the first linker region, and the C-terminal domain was able to infect cells at almost the same frequency as the wild-type phage. This infection was proven to be dependent on the motif between amino acid residues 68 and 86 (i.e., the first glycine-rich linker region of g3p) and on F-pilus expression. FAU - Nilsson, N AU - Nilsson N AD - Department of Immunotechnology, Lund University, S-220 07 Lund, Sweden. FAU - Malmborg, A C AU - Malmborg AC FAU - Borrebaeck, C A AU - Borrebaeck CA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (Capsid Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Viral Fusion Proteins) RN - M4I0D6VV5M (Calcium Chloride) RN - TE7660XO1C (Glycine) SB - IM MH - Binding Sites MH - Calcium Chloride/pharmacology MH - Capsid Proteins MH - Coliphages/drug effects/*physiology MH - DNA-Binding Proteins/*metabolism MH - Escherichia coli/*virology MH - Glycine/metabolism MH - Pili, Sex/metabolism MH - Viral Fusion Proteins/*metabolism PMC - PMC111938 OID - NLM: PMC111938 EDAT- 2001/02/07 11:00 MHDA- 2001/02/07 11:01 CRDT- 2001/02/07 11:00 PST - ppublish SO - J Virol. 2000 May;74(9):4229-35. PMID- 16186124 OWN - NLM STAT- MEDLINE DA - 20051205 DCOM- 20060306 LR - 20150224 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 49 DP - 2005 Dec 9 TI - Structure of human phytanoyl-CoA 2-hydroxylase identifies molecular mechanisms of Refsum disease. PG - 41101-10 AB - Refsum disease (RD), a neurological syndrome characterized by adult onset retinitis pigmentosa, anosmia, sensory neuropathy, and phytanic acidaemia, is caused by elevated levels of phytanic acid. Many cases of RD are associated with mutations in phytanoyl-CoA 2-hydroxylase (PAHX), an Fe(II) and 2-oxoglutarate (2OG)-dependent oxygenase that catalyzes the initial alpha-oxidation step in the degradation of phytenic acid in peroxisomes. We describe the x-ray crystallographic structure of PAHX to 2.5 A resolution complexed with Fe(II) and 2OG and predict the molecular consequences of mutations causing RD. Like other 2OG oxygenases, PAHX possesses a double-stranded beta-helix core, which supports three iron binding ligands (His(175), Asp(177), and His(264)); the 2-oxoacid group of 2OG binds to the Fe(II) in a bidentate manner. The manner in which PAHX binds to Fe(II) and 2OG together with the presence of a cysteine residue (Cys(191)) 6.7 A from the Fe(II) and two further histidine residues (His(155) and His(281)) at its active site distinguishes it from that of the other human 2OG oxygenase for which structures are available, factor inhibiting hypoxia-inducible factor. Of the 15 PAHX residues observed to be mutated in RD patients, 11 cluster in two distinct groups around the Fe(II) (Pro(173), His(175), Gln(176), Asp(177), and His(220)) and 2OG binding sites (Trp(193), Glu(197), Ile(199), Gly(204), Asn(269), and Arg(275)). PAHX may be the first of a new subfamily of coenzyme A-binding 2OG oxygenases. FAU - McDonough, Michael A AU - McDonough MA AD - Oxford Centre for Molecular Sciences and Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom. FAU - Kavanagh, Kathryn L AU - Kavanagh KL FAU - Butler, Danica AU - Butler D FAU - Searls, Timothy AU - Searls T FAU - Oppermann, Udo AU - Oppermann U FAU - Schofield, Christopher J AU - Schofield CJ LA - eng SI - OMIM/266500 SI - PDB/2A1X GR - B18672/Biotechnology and Biological Sciences Research Council/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050925 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Ferrous Compounds) RN - 0 (Ketoglutaric Acids) RN - 0 (Recombinant Proteins) RN - 14721-66-5 (Phytanic Acid) RN - 30KYC7MIAI (Aspartic Acid) RN - 328-50-7 (alpha-ketoglutaric acid) RN - 3653-46-1 (phytenic acid) RN - 4QD397987E (Histidine) RN - EC 1.- (Mixed Function Oxygenases) RN - EC 1.14.- (PHYH protein, human) RN - K848JZ4886 (Cysteine) RN - SAA04E81UX (Coenzyme A) SB - IM MH - Aspartic Acid/metabolism MH - Binding Sites/genetics MH - Coenzyme A/metabolism MH - Crystallization MH - Crystallography, X-Ray MH - Cysteine/metabolism MH - Escherichia coli/genetics MH - Ferrous Compounds/metabolism MH - Histidine/metabolism MH - Humans MH - Ketoglutaric Acids/metabolism MH - Mixed Function Oxygenases/*chemistry/*genetics MH - Models, Molecular MH - Mutation MH - Peroxisomes/enzymology MH - Phytanic Acid/analogs & derivatives/metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Recombinant Proteins MH - Refsum Disease/drug therapy/*enzymology MH - Structure-Activity Relationship MH - Transfection EDAT- 2005/09/28 09:00 MHDA- 2006/03/07 09:00 CRDT- 2005/09/28 09:00 PHST- 2005/09/25 [aheadofprint] AID - M507528200 [pii] AID - 10.1074/jbc.M507528200 [doi] PST - ppublish SO - J Biol Chem. 2005 Dec 9;280(49):41101-10. Epub 2005 Sep 25. PMID- 25246635 OWN - NLM STAT- MEDLINE DA - 20141030 DCOM- 20150112 LR - 20150601 IS - 1098-5549 (Electronic) IS - 0270-7306 (Linking) VI - 34 IP - 23 DP - 2014 Dec 1 TI - Rapid proteasomal degradation of posttranscriptional regulators of the TIS11/tristetraprolin family is induced by an intrinsically unstructured region independently of ubiquitination. PG - 4315-28 LID - 10.1128/MCB.00643-14 [doi] AB - The TIS11/tristetraprolin (TTP) CCCH tandem zinc finger proteins are major effectors in the destabilization of mRNAs bearing AU-rich elements (ARE) in their 3' untranslated regions. In this report, we demonstrate that the Drosophila melanogaster dTIS11 protein is short-lived due to its rapid ubiquitin-independent degradation by the proteasome. Our data indicate that this mechanism is tightly associated with the intrinsically unstructured, disordered N- and C-terminal domains of the protein. Furthermore, we show that TTP, the mammalian TIS11/TTP protein prototype, shares the same three-dimensional characteristics and is degraded by the same proteolytic pathway as dTIS11, thereby indicating that this mechanism has been conserved across evolution. Finally, we observed a phosphorylation-dependent inhibition of dTIS11 and TTP degradation by the proteasome in vitro, raising the possibility that such modifications directly affect proteasomal recognition for these proteins. As a group, RNA-binding proteins (RNA-BPs) have been described as enriched in intrinsically disordered regions, thus raising the possibility that the mechanism that we uncovered for TIS11/TTP turnover is widespread among other RNA-BPs. CI - Copyright (c) 2014, American Society for Microbiology. All Rights Reserved. FAU - Ngoc, Long Vo AU - Ngoc LV AD - Laboratoire de Biologie Moleculaire du Gene, IBMM, Faculte des Sciences, Universite Libre de Bruxelles, Gosselies, Belgium. FAU - Wauquier, Corinne AU - Wauquier C AD - Laboratoire de Biologie Moleculaire du Gene, IBMM, Faculte des Sciences, Universite Libre de Bruxelles, Gosselies, Belgium. FAU - Soin, Romuald AU - Soin R AD - Laboratoire de Biologie Moleculaire du Gene, IBMM, Faculte des Sciences, Universite Libre de Bruxelles, Gosselies, Belgium. FAU - Bousbata, Sabrina AU - Bousbata S AD - Laboratoire de Microbiologie et Biologie Structurale, IBMM, Faculte des Sciences, Universite Libre de Bruxelles, Gosselies, Belgium. FAU - Twyffels, Laure AU - Twyffels L AD - Laboratoire de Biologie Moleculaire du Gene, IBMM, Faculte des Sciences, Universite Libre de Bruxelles, Gosselies, Belgium Center for Microscopy and Molecular Imaging, Universite Libre de Bruxelles, Gosselies, Belgium. FAU - Kruys, Veronique AU - Kruys V AD - Laboratoire de Biologie Moleculaire du Gene, IBMM, Faculte des Sciences, Universite Libre de Bruxelles, Gosselies, Belgium Center for Microscopy and Molecular Imaging, Universite Libre de Bruxelles, Gosselies, Belgium. FAU - Gueydan, Cyril AU - Gueydan C AUID- ORCID: http://orcid.org/0000-0003-3097-7667 AD - Laboratoire de Biologie Moleculaire du Gene, IBMM, Faculte des Sciences, Universite Libre de Bruxelles, Gosselies, Belgium cgueydan@ulb.ac.be. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140922 PL - United States TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (3' Untranslated Regions) RN - 0 (Drosophila Proteins) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (RNA, Small Interfering) RN - 0 (RNA-Binding Proteins) RN - 0 (Tis11 protein, Drosophila) RN - 0 (Tristetraprolin) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - 3' Untranslated Regions/genetics MH - AU Rich Elements MH - Animals MH - Cell Line MH - Drosophila Proteins/*metabolism MH - Drosophila melanogaster/genetics/*metabolism MH - Gene Expression Regulation MH - HEK293 Cells MH - Humans MH - Intrinsically Disordered Proteins/*metabolism MH - Mice MH - Proteasome Endopeptidase Complex/*metabolism MH - RNA Interference MH - RNA Processing, Post-Transcriptional/genetics MH - RNA Stability/genetics MH - RNA, Small Interfering MH - RNA-Binding Proteins/*metabolism MH - Tristetraprolin/metabolism MH - *Ubiquitination PMC - PMC4248748 OID - NLM: PMC4248748 EDAT- 2014/09/24 06:00 MHDA- 2015/01/13 06:00 CRDT- 2014/09/24 06:00 PHST- 2014/09/22 [aheadofprint] AID - MCB.00643-14 [pii] AID - 10.1128/MCB.00643-14 [doi] PST - ppublish SO - Mol Cell Biol. 2014 Dec 1;34(23):4315-28. doi: 10.1128/MCB.00643-14. Epub 2014 Sep 22. PMID- 23744817 OWN - NLM STAT- MEDLINE DA - 20130930 DCOM- 20140423 IS - 1439-7633 (Electronic) IS - 1439-4227 (Linking) VI - 14 IP - 14 DP - 2013 Sep 23 TI - Multi-phosphorylation of the intrinsically disordered unique domain of c-Src studied by in-cell and real-time NMR spectroscopy. PG - 1820-7 LID - 10.1002/cbic.201300139 [doi] AB - Intrinsically disordered regions (IDRs) are preferred sites for post-translational modifications essential for regulating protein function. The enhanced local mobility of IDRs facilitates their observation by NMR spectroscopy in vivo. Phosphorylation events can occur at multiple sites and respond dynamically to changes in kinase-phosphatase networks. Here we used real-time NMR spectroscopy to study the effect of kinases and phosphatases present in Xenopus oocytes and egg extracts on the phosphorylation state of the "unique domain" of c-Src. We followed the phosphorylation of S17 in oocytes, and of S17, S69, and S75 in egg extracts by NMR spectroscopy, MS, and western blotting. Addition of specific kinase inhibitors showed that S75 and S69 are phosphorylated by CDKs (cyclin-dependent kinases) differently from Cdk1. Moreover, although PKA (cAMP-dependent protein kinase) can phosphorylate S17 in vitro, this was not the major S17 kinase in egg extracts. Changes in PKA activity affected the phosphorylation levels of CDK-dependent sites, thus suggesting indirect effects of kinase-phosphatase networks. This study provides a proof-of-concept of the use of real-time in vivo NMR spectroscopy to characterize kinase/phosphatase effects on intrinsically disordered regulatory domains. CI - Copyright (c) 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. FAU - Amata, Irene AU - Amata I AD - Biomolecular NMR Laboratory, Department of Organic Chemistry, University of Barcelona, Baldiri Reixac, 10-12, 08028 Barcelona (Spain); Signaling and Cell Cycle Laboratory, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona (Spain). FAU - Maffei, Mariano AU - Maffei M FAU - Igea, Ana AU - Igea A FAU - Gay, Marina AU - Gay M FAU - Vilaseca, Marta AU - Vilaseca M FAU - Nebreda, Angel R AU - Nebreda AR FAU - Pons, Miquel AU - Pons M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130606 PL - Germany TA - Chembiochem JT - Chembiochem : a European journal of chemical biology JID - 100937360 RN - 0 (Nitrogen Isotopes) RN - EC 2.7.10.2 (CSK tyrosine-protein kinase) RN - EC 2.7.10.2 (src-Family Kinases) SB - IM MH - Amino Acid Sequence MH - Animals MH - Molecular Sequence Data MH - Nitrogen Isotopes MH - *Nuclear Magnetic Resonance, Biomolecular MH - Oocytes/metabolism MH - Phosphorylation MH - Protein Processing, Post-Translational MH - Xenopus/growth & development/metabolism MH - src-Family Kinases/*chemistry/genetics/metabolism OTO - NOTNLM OT - NMR spectroscopy OT - c-Src OT - intrinsically disordered proteins OT - mass spectrometry OT - phosphoproteins EDAT- 2013/06/08 06:00 MHDA- 2014/04/24 06:00 CRDT- 2013/06/08 06:00 PHST- 2013/03/09 [received] PHST- 2013/06/06 [aheadofprint] AID - 10.1002/cbic.201300139 [doi] PST - ppublish SO - Chembiochem. 2013 Sep 23;14(14):1820-7. doi: 10.1002/cbic.201300139. Epub 2013 Jun 6. PMID- 15117963 OWN - NLM STAT- MEDLINE DA - 20040719 DCOM- 20040921 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 30 DP - 2004 Jul 23 TI - Crystal structures of Staphylococcus aureus sortase A and its substrate complex. PG - 31383-9 AB - The cell wall envelope of staphylococci and other Gram-positive pathogens is coated with surface proteins that interact with human host tissues. Surface proteins of Staphylococcus aureus are covalently linked to the cell wall envelope by a mechanism requiring C-terminal sorting signals with an LPXTG motif. Sortase (SrtA) cleaves surface proteins between the threonine (T) and the glycine (G) of the LPXTG motif and catalyzes the formation of an amide bond between threonine at the C-terminal end of polypeptides and cell wall cross-bridges. The active site architecture and catalytic mechanism of sortase A has hitherto not been revealed. Here we present the crystal structures of native SrtA, of an active site mutant of SrtA, and of the mutant SrtA complexed with its substrate LPETG peptide and describe the substrate binding pocket of the enzyme. Highly conserved proline (P) and threonine (T) residues of the LPXTG motif are held in position by hydrophobic contacts, whereas the glutamic acid residue (E) at the X position points out into the solvent. The scissile T-G peptide bond is positioned between the active site Cys(184) and Arg(197) residues and at a greater distance from the imidazolium side chain of His(120). All three residues, His(120), Cys(184), and Arg(197), are conserved in sortase enzymes from Gram-positive bacteria. Comparison of the active sites of S. aureus sortase A and sortase B provides insight into substrate specificity and suggests a universal sortase-catalyzed mechanism of bacterial surface protein anchoring in Gram-positive bacteria. FAU - Zong, Yinong AU - Zong Y AD - Center for Biophysical Sciences and Engineering, School of Optometry, University of Alabama, Birmingham, Alabama 35294, USA. FAU - Bice, Todd W AU - Bice TW FAU - Ton-That, Hung AU - Ton-That H FAU - Schneewind, Olaf AU - Schneewind O FAU - Narayana, Sthanam V L AU - Narayana SV LA - eng GR - AI38897/AI/NIAID NIH HHS/United States GR - AI52765/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20040426 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - 0 (Isoenzymes) RN - EC 2.3.2.- (Aminoacyltransferases) RN - EC 2.3.2.- (sortase A) RN - EC 3.4.22.- (Cysteine Endopeptidases) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Aminoacyltransferases/*chemistry/genetics/metabolism MH - Bacterial Proteins MH - Catalytic Domain/genetics MH - Conserved Sequence MH - Crystallography, X-Ray MH - Cysteine Endopeptidases MH - Isoenzymes/chemistry/genetics/metabolism MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Protein Conformation MH - Staphylococcus aureus/*enzymology/genetics MH - Substrate Specificity EDAT- 2004/05/01 05:00 MHDA- 2004/09/24 05:00 CRDT- 2004/05/01 05:00 PHST- 2004/04/26 [aheadofprint] AID - 10.1074/jbc.M401374200 [doi] AID - M401374200 [pii] PST - ppublish SO - J Biol Chem. 2004 Jul 23;279(30):31383-9. Epub 2004 Apr 26. PMID- 19306883 OWN - NLM STAT- MEDLINE DA - 20090504 DCOM- 20090602 LR - 20141125 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 388 IP - 4 DP - 2009 May 15 TI - A common interaction for the entry of colicin N and filamentous phage into Escherichia coli. PG - 880-93 LID - 10.1016/j.jmb.2009.03.035 [doi] AB - Colicin N is a pore-forming bacteriocin that enters target Escherichia coli cells with the assistance of TolA, a protein in the periplasm of the target cell. The N-terminal domain of the colicin that carries the TolA-binding epitope, the translocation domain (T-domain), is intrinsically disordered. From (1)H-(13)C-(15)N NMR studies of isotopically labeled T-domain interacting with unlabeled TolAIII (the C-terminal domain of TolA), we have identified the TolA-binding epitope and have shown that the extent of its disorder is reduced on binding TolA, although it does not fold into a globular structure with defined secondary structure elements. Residues upstream and downstream of the 27-residue TolA-binding epitope remain disordered in the TolA-bound T-domain as they are in the free T-domain. Filamentous phage also exploits TolAIII to enter target cells, with TolAIII retaining its main secondary structure elements and global fold. In contrast to this, binding of the disordered T-domain of colicin A causes dramatic conformational changes in TolAIII marked by increased flexibility and lack of a rigid tertiary structure consistent with at least partial unfolding of TolAIII, suggesting that bacteriocins and bacteriophages parasitize E. coli using different modes of interaction with TolAIII. We have found that the colicin N T-domain-TolAIII interaction is strikingly similar to the previously described g3p-TolAIII interaction. The fact that both colicin N and filamentous phage exploit TolAIII in a similar manner, with one being a bacterial intrinsically disordered protein and the other being a viral structurally well-ordered protein, suggests that these represent a good example of convergent evolution at the molecular level. FAU - Hecht, Oliver AU - Hecht O AD - Center for Molecular and Structural Biochemistry, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich, UK. FAU - Ridley, Helen AU - Ridley H FAU - Lakey, Jeremy H AU - Lakey JH FAU - Moore, Geoffrey R AU - Moore GR LA - eng GR - 40422/Wellcome Trust/United Kingdom GR - 55979/Wellcome Trust/United Kingdom GR - 56232/Wellcome Trust/United Kingdom GR - 66850/Wellcome Trust/United Kingdom GR - BB/C507396/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090320 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Colicins) RN - 0 (Epitopes) RN - 0 (Escherichia coli Proteins) RN - 0 (tolA protein, E coli) SB - IM MH - Amino Acid Sequence MH - *Colicins/chemistry/metabolism MH - Epitopes/chemistry MH - Escherichia coli/*metabolism MH - *Escherichia coli Proteins/chemistry/metabolism MH - Inovirus/chemistry/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - Protein Folding EDAT- 2009/03/25 09:00 MHDA- 2009/06/03 09:00 CRDT- 2009/03/25 09:00 PHST- 2008/12/22 [received] PHST- 2009/03/06 [revised] PHST- 2009/03/06 [accepted] PHST- 2009/03/20 [aheadofprint] AID - S0022-2836(09)00278-2 [pii] AID - 10.1016/j.jmb.2009.03.035 [doi] PST - ppublish SO - J Mol Biol. 2009 May 15;388(4):880-93. doi: 10.1016/j.jmb.2009.03.035. Epub 2009 Mar 20. PMID- 20116397 OWN - NLM STAT- MEDLINE DA - 20100308 DCOM- 20100608 LR - 20121115 IS - 1879-0003 (Electronic) IS - 0141-8130 (Linking) VI - 46 IP - 3 DP - 2010 Apr 1 TI - Structure changes of natively disordered Humanin in the presence of lipid. PG - 375-9 LID - 10.1016/j.ijbiomac.2010.01.012 [doi] AB - While neuroprotective activities of Humanin peptides have been clearly demonstrated, the functional mechanism has not been fully understood. Humanin and a majority of Humanin analogs showed a disordered structure at low peptide concentrations and aggregation at higher concentrations in aqueous solution at pH 7.0. Here we have examined the structure in lipid environments, i.e., in the presence of liposome by circular dichroism. Humanin underwent a large structure change into a typical beta-sheet structure at neutral pH in the presence liposome made of a negatively charged 1,2-dioleoyl-sn-glycero-3-phosphoglycerol (DOPG), but not an electrically neutral 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC). As Humanin possesses a positive charge at neutral pH, the observed structure changes with DOPG suggest electrostatic binding of the peptide with the lipid. No effect of NaCl on the Humanin structure was observed in neutral solution and in the presence of DOPC liposome. Increasing temperature resulted in changes in the structure due to aggregation. On the other hand, the effects of temperature on the Humanin structure showed that it has a relatively stable structure in the presence of DOPG liposome independent of the presence of NaCl. CI - Copyright 2010 Elsevier B.V. All rights reserved. FAU - Hirano, Atsushi AU - Hirano A AD - Institute of Applied Physics, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan. FAU - Shiraki, Kentaro AU - Shiraki K FAU - Niikura, Takako AU - Niikura T FAU - Arakawa, Tsutomu AU - Arakawa T FAU - Kita, Yoshiko AU - Kita Y LA - eng PT - Journal Article DEP - 20100129 PL - Netherlands TA - Int J Biol Macromol JT - International journal of biological macromolecules JID - 7909578 RN - 0 (Buffers) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Phosphatidylcholines) RN - 0 (Phosphatidylglycerols) RN - 0 (Solutions) RN - 0 (humanin) RN - 66322-31-4 (1,2-dioleoyl-sn-glycero-3-phosphoglycerol) RN - H026DM5V6U (1,2-oleoylphosphatidylcholine) SB - IM MH - Amino Acid Sequence MH - Buffers MH - Circular Dichroism MH - Intracellular Signaling Peptides and Proteins/*chemistry MH - Molecular Sequence Data MH - Phosphatidylcholines/*pharmacology MH - Phosphatidylglycerols/*pharmacology MH - Protein Structure, Quaternary MH - Solutions MH - Temperature MH - Time Factors EDAT- 2010/02/02 06:00 MHDA- 2010/06/09 06:00 CRDT- 2010/02/02 06:00 PHST- 2009/12/27 [received] PHST- 2010/01/13 [revised] PHST- 2010/01/14 [accepted] PHST- 2010/01/29 [aheadofprint] AID - S0141-8130(10)00022-X [pii] AID - 10.1016/j.ijbiomac.2010.01.012 [doi] PST - ppublish SO - Int J Biol Macromol. 2010 Apr 1;46(3):375-9. doi: 10.1016/j.ijbiomac.2010.01.012. Epub 2010 Jan 29. PMID- 24552879 OWN - NLM STAT- MEDLINE DA - 20140730 DCOM- 20150221 LR - 20150521 IS - 1933-690X (Electronic) IS - 1933-6896 (Linking) VI - 8 IP - 1 DP - 2014 Jan-Feb TI - In vitro aggregation assays for the characterization of alpha-synuclein prion-like properties. PG - 19-32 AB - Aggregation of alpha-synuclein plays a crucial role in the pathogenesis of synucleinopathies, a group of neurodegenerative diseases including Parkinson disease (PD), dementia with Lewy bodies (DLB), diffuse Lewy body disease (DLBD) and multiple system atrophy (MSA). The common feature of these diseases is a pathological deposition of protein aggregates, known as Lewy bodies (LBs) in the central nervous system. The major component of these aggregates is alpha-synuclein, a natively unfolded protein, which may undergo dramatic structural changes resulting in the formation of beta-sheet rich assemblies. In vitro studies have shown that recombinant alpha-synuclein protein may polymerize into amyloidogenic fibrils resembling those found in LBs. These aggregates may be uptaken and propagated between cells in a prion-like manner. Here we present the mechanisms and kinetics of alpha-synuclein aggregation in vitro, as well as crucial factors affecting this process. We also describe how PD-linked alpha-synuclein mutations and some exogenous factors modulate in vitro aggregation. Furthermore, we present a current knowledge on the mechanisms by which extracellular aggregates may be internalized and propagated between cells, as well as the mechanisms of their toxicity. FAU - Narkiewicz, Joanna AU - Narkiewicz J FAU - Giachin, Gabriele AU - Giachin G FAU - Legname, Giuseppe AU - Legname G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Prion JT - Prion JID - 101472305 RN - 0 (Prions) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - In Vitro Techniques MH - Kinetics MH - Molecular Sequence Data MH - *Prions MH - alpha-Synuclein/chemistry/*metabolism/toxicity PMC - PMC4116381 OID - NLM: PMC4116381 EDAT- 2014/02/21 06:00 MHDA- 2015/02/24 06:00 CRDT- 2014/02/21 06:00 AID - 28125 [pii] PST - ppublish SO - Prion. 2014 Jan-Feb;8(1):19-32. PMID- 15465825 OWN - NLM STAT- MEDLINE DA - 20041213 DCOM- 20050204 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 51 DP - 2004 Dec 17 TI - Yeast cox17 solution structure and Copper(I) binding. PG - 53584-92 AB - Cox17 is a 69-residue cysteine-rich, copper-binding protein that has been implicated in the delivery of copper to the Cu(A) and Cu(B) centers of cytochrome c oxidase via the copper-binding proteins Sco1 and Cox11, respectively. According to isothermal titration calorimetry experiments, fully reduced Cox17 binds one Cu(I) ion with a K(a) of (6.15 +/- 5.83) x 10(6) M(-1). The solution structures of both apo and Cu(I)-loaded Cox17 reveal two alpha helices preceded by an extensive, unstructured N-terminal region. This region is reminiscent of intrinsically unfolded proteins. The two structures are very similar overall with residues in the copper-binding region becoming more ordered in Cu(I)-loaded Cox17. Based on the NMR data, the Cu(I) ion has been modeled as two-coordinate with ligation by conserved residues Cys(23) and Cys(26). This site is similar to those observed for the Atx1 family of copper chaperones and is consistent with reported mutagenesis studies. A number of conserved, positively charged residues may interact with complementary surfaces on Sco1 and Cox11, facilitating docking and copper transfer. Taken together, these data suggest that Cox17 is not only well suited to a copper chaperone function but is specifically designed to interact with two different target proteins. FAU - Abajian, Carnie AU - Abajian C AD - Department of Biochemistry, Northwestern University, Evanston, IL 60208, USA. FAU - Yatsunyk, Liliya A AU - Yatsunyk LA FAU - Ramirez, Benjamin E AU - Ramirez BE FAU - Rosenzweig, Amy C AU - Rosenzweig AC LA - eng SI - PDB/1U96 SI - PDB/1U97 GR - GM58518/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20041001 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (COX11 protein, S cerevisiae) RN - 0 (COX17 protein, S cerevisiae) RN - 0 (Cation Transport Proteins) RN - 0 (Fungal Proteins) RN - 0 (Membrane Proteins) RN - 0 (Mitochondrial Proteins) RN - 0 (Molecular Chaperones) RN - 0 (SCO1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 789U1901C5 (Copper) RN - EC 1.9.3.1 (Electron Transport Complex IV) RN - K848JZ4886 (Cysteine) SB - IM MH - Binding Sites MH - Calorimetry MH - Cation Transport Proteins/metabolism/*physiology MH - Cloning, Molecular MH - Copper/*chemistry MH - Cysteine/chemistry MH - Electron Transport Complex IV/metabolism MH - Fungal Proteins/*chemistry MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Membrane Proteins/metabolism MH - Mitochondrial Proteins MH - Models, Molecular MH - Molecular Chaperones/chemistry MH - Oxidation-Reduction MH - Protein Binding MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae Proteins/metabolism/*physiology EDAT- 2004/10/07 09:00 MHDA- 2005/02/05 09:00 CRDT- 2004/10/07 09:00 PHST- 2004/10/01 [aheadofprint] AID - M408099200 [pii] AID - 10.1074/jbc.M408099200 [doi] PST - ppublish SO - J Biol Chem. 2004 Dec 17;279(51):53584-92. Epub 2004 Oct 1. PMID- 21454565 OWN - NLM STAT- MEDLINE DA - 20110509 DCOM- 20110712 LR - 20140820 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 19 DP - 2011 May 13 TI - Calcium-induced folding of intrinsically disordered repeat-in-toxin (RTX) motifs via changes of protein charges and oligomerization states. PG - 16997-7004 LID - 10.1074/jbc.M110.210393 [doi] AB - Ligand-induced disorder-to-order transition plays a key role in the biological functions of many proteins that contain intrinsically disordered regions. This trait is exhibited by so-called RTX (repeat-in-toxin) motifs found in many virulence factors secreted by numerous gram-negative pathogenic bacteria: RTX proteins are natively disordered in the absence of calcium but fold upon calcium binding. The adenylate cyclase toxin (CyaA) produced by Bordetella pertussis, the causative agent of whooping cough, contains approximately 40 RTX motifs organized in five successive blocks separated by non-RTX flanking regions. This RTX domain mediates toxin binding to its eukaryotic cell receptor. We previously showed that the last block of the RTX domain, block V, which is critical for CyaA toxicity, exhibits the hallmarks of intrinsically disordered proteins in the absence of calcium. Moreover, the C-terminal flanking region of CyaA block V is required for its calcium-induced folding. Here, we describe a comprehensive analysis of the hydrodynamic and electrophoretic properties of several block V RTX polypeptides that differ in the presence and/or length of the flanking regions. Our results indicate that the length of the C-terminal flanking region not only controls the calcium-induced folding but also the calcium-induced multimerization of the RTX polypeptides. Moreover, we showed that calcium binding is accompanied by a strong reduction of the net charge of the RTX polypeptides. These data indicate that the disorder-to-order transition in RTX proteins is controlled by a calcium-induced change of the polypeptide charges and stabilized by multimerization. FAU - Sotomayor-Perez, Ana Cristina AU - Sotomayor-Perez AC AD - Institut Pasteur, CNRS URA 2185, Unite de Biochimie des Interactions Macromoleculaires, Departement de Biologie Structurale et Chimie, 75724 Paris Cedex 15, France. FAU - Ladant, Daniel AU - Ladant D FAU - Chenal, Alexandre AU - Chenal A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110315 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Calcium-Binding Proteins) RN - 0 (Peptides) RN - 0 (Proteins) RN - 8DUH1N11BX (Tryptophan) RN - EC 4.6.1.1 (Adenylate Cyclase) RN - SY7Q814VUP (Calcium) SB - IM MH - Adenylate Cyclase/chemistry MH - Amino Acid Motifs MH - Anisotropy MH - Biophysics/methods MH - Bordetella pertussis/metabolism MH - Calcium/*chemistry MH - Calcium-Binding Proteins/chemistry MH - Peptides/chemistry MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Proteins/*chemistry MH - Spectrophotometry/methods MH - Tryptophan/chemistry MH - Ultracentrifugation PMC - PMC3089544 OID - NLM: PMC3089544 EDAT- 2011/04/02 06:00 MHDA- 2011/07/13 06:00 CRDT- 2011/04/02 06:00 PHST- 2011/03/15 [aheadofprint] AID - M110.210393 [pii] AID - 10.1074/jbc.M110.210393 [doi] PST - ppublish SO - J Biol Chem. 2011 May 13;286(19):16997-7004. doi: 10.1074/jbc.M110.210393. Epub 2011 Mar 15. PMID- 19647750 OWN - NLM STAT- MEDLINE DA - 20091005 DCOM- 20091020 LR - 20140828 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 393 IP - 2 DP - 2009 Oct 23 TI - Helix stabilization precedes aqueous and bilayer-catalyzed fiber formation in islet amyloid polypeptide. PG - 383-96 LID - 10.1016/j.jmb.2009.07.077 [doi] AB - Islet amyloid polypeptide (IAPP) is an unstructured polypeptide hormone that is cosecreted with insulin. In patients with type 2 diabetes, IAPP undergoes a transition from its natively disordered state to a highly ordered, all-beta-strand amyloid fiber. Although predominantly disordered, IAPP transiently samples alpha-helical structure in solution. IAPP adopts a fully helical structure when bound to membrane surfaces in a process associated with catalysis of amyloid formation. Here, we use spectroscopic techniques to study the structure of full-length, monomeric IAPP under amyloidogenic conditions. We observe that the residues with helical propensity in solution (1-22) also form the membrane-associated helix. Additionally, reduction of the N-terminal disulfide bond (Cys2-Cys7) decreases the extent of helix formed throughout this region. Through manipulation of sample conditions to increase or decrease the amount of helix, we show that the degree of helix formed affects the rate of amyloid assembly. Formation of helical structure is directly correlated with enhanced amyloid formation both on the membrane surface and in solution. These observations support suggested mechanisms in which parallel helix associations bring together regions of the peptide that could nucleate beta-strand structure. Remarkably, stabilization of non-amyloid structure appears to be a key intermediate in assembly of IAPP amyloid. FAU - Williamson, Jessica A AU - Williamson JA AD - Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA. FAU - Loria, J Patrick AU - Loria JP FAU - Miranker, Andrew D AU - Miranker AD LA - eng GR - DK54899/DK/NIDDK NIH HHS/United States GR - R01 DK054899/DK/NIDDK NIH HHS/United States GR - T32 GM008283/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090730 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amyloid) RN - 0 (Islet Amyloid Polypeptide) RN - 0 (Lipid Bilayers) RN - 0 (Liposomes) RN - 0 (Recombinant Proteins) SB - IM MH - Amyloid/*chemistry/genetics/*metabolism MH - Animals MH - Circular Dichroism MH - Humans MH - Islet Amyloid Polypeptide MH - Lipid Bilayers/chemistry MH - Liposomes/chemistry MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Protein Binding MH - Protein Folding MH - Protein Structure, Secondary MH - Rats MH - Recombinant Proteins/chemistry/genetics/metabolism PMC - PMC3343364 MID - NIHMS144805 OID - NLM: NIHMS144805 OID - NLM: PMC3343364 EDAT- 2009/08/04 09:00 MHDA- 2009/10/21 06:00 CRDT- 2009/08/04 09:00 PHST- 2009/04/15 [received] PHST- 2009/07/12 [revised] PHST- 2009/07/27 [accepted] PHST- 2009/07/30 [aheadofprint] AID - S0022-2836(09)00967-X [pii] AID - 10.1016/j.jmb.2009.07.077 [doi] PST - ppublish SO - J Mol Biol. 2009 Oct 23;393(2):383-96. doi: 10.1016/j.jmb.2009.07.077. Epub 2009 Jul 30. PMID- 14656435 OWN - NLM STAT- MEDLINE DA - 20031205 DCOM- 20040810 LR - 20081121 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 11 IP - 12 DP - 2003 Dec TI - The crystal structures of EDA-A1 and EDA-A2: splice variants with distinct receptor specificity. PG - 1513-20 AB - EDA is a tumor necrosis factor family member involved in ectodermal development. Splice variants EDA-A1 and EDA-A2 differ only by the presence of Glu 308 and Val 309 in the expected receptor binding region of EDA-A1 but not EDA-A2. This two amino acid difference functions as a switch controlling receptor specificity. EDA-A1 binds only to EDAR, while EDA-A2 is specific for XEDAR. In order to understand the structural basis of this switch, we determined the X-ray crystal structures of the TNF domain of both EDA-A1 and EDA-A2 at 2.3 A and 2.2 A, respectively. While the backbone conformation around the splice difference is similar in both isoforms, the conformation of the following loop, the surface charge, and the shape of the expected receptor binding site differ significantly. FAU - Hymowitz, Sarah G AU - Hymowitz SG AD - Department of Protein Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. hymowitz@gene.com FAU - Compaan, Deanne M AU - Compaan DM FAU - Yan, Minhong AU - Yan M FAU - Wallweber, Heidi J A AU - Wallweber HJ FAU - Dixit, Vishva M AU - Dixit VM FAU - Starovasnik, Melissa A AU - Starovasnik MA FAU - de Vos, Abraham M AU - de Vos AM LA - eng SI - PDB/1RJ7 SI - PDB/1RJ8 PT - Journal Article PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (EDA protein, human) RN - 0 (Ectodysplasins) RN - 0 (Ligands) RN - 0 (Membrane Proteins) RN - 0 (Protein Isoforms) SB - IM MH - *Alternative Splicing MH - Binding Sites MH - Crystallography, X-Ray MH - Ectodysplasins MH - Escherichia coli/metabolism MH - Humans MH - Ligands MH - Membrane Proteins/*chemistry/genetics MH - Models, Biological MH - Models, Molecular MH - Mutation MH - Protein Binding MH - Protein Conformation MH - Protein Isoforms MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Static Electricity EDAT- 2003/12/06 05:00 MHDA- 2004/08/11 05:00 CRDT- 2003/12/06 05:00 AID - S0969212603002685 [pii] PST - ppublish SO - Structure. 2003 Dec;11(12):1513-20. PMID- 7849597 OWN - NLM STAT- MEDLINE DA - 19950313 DCOM- 19950313 LR - 20130922 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 3 IP - 10 DP - 1994 Oct TI - Solution structure of the DNA-binding domain of the heat shock transcription factor determined by multidimensional heteronuclear magnetic resonance spectroscopy. PG - 1806-21 AB - The solution structure of the 92-residue DNA-binding domain of the heat shock transcription factor from Kluyveromyces lactis has been determined using multidimensional NMR methods. Three-dimensional (3D) triple resonance, 1H-13C-13C-1H total correlation spectroscopy, and 15N-separated total correlation spectroscopy-heteronuclear multiple quantum correlation experiments were used along with various 2D spectra to make nearly complete assignments for the backbone and side-chain 1H, 15N, and 13C resonances. Five-hundred eighty-three NOE constraints identified in 3D 13C- and 15N-separated NOE spectroscopy (NOESY)-heteronuclear multiple quantum correlation spectra and a 4-dimensional 13C/13C-edited NOESY spectrum, along with 35 phi, 9 chi 1, and 30 hydrogen bond constraints, were used to calculate 30 structures by hybrid distance geometry/stimulated annealing protocol, of which 24 were used for structural comparison. The calculations revealed that a 3-helix bundle packs against a small 4-stranded antiparallel beta-sheet. The backbone RMS deviation (RMSD) for the family of structures was 1.03 +/- 0.19 A with respect to the average structure. The topology is analogous to that of the C-terminal domain of the catabolite gene activator protein and appears to be in the helix-turn-helix family of DNA-binding proteins. The overall fold determined by the NMR data is consistent with recent crystallographic work on this domain (Harrison CJ, Bohm AA, Nelson HCM, 1994, Science 263:224) as evidenced by RMSD between backbone atoms in the NMR and X-ray structures of 1.77 +/- 0.20 A. Several differences were identified some of which may be due to protein-protein interactions in the crystal. FAU - Damberger, F F AU - Damberger FF AD - Biophysics Graduate Group, University of California, Berkeley 94720. FAU - Pelton, J G AU - Pelton JG FAU - Harrison, C J AU - Harrison CJ FAU - Nelson, H C AU - Nelson HC FAU - Wemmer, D E AU - Wemmer DE LA - eng GR - GM 44086/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (DNA-Binding Proteins) RN - 0 (HSF1 protein, S cerevisiae) RN - 0 (Heat-Shock Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Solutions) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - DNA/*metabolism MH - DNA-Binding Proteins/*chemistry MH - Escherichia coli MH - *Heat-Shock Proteins MH - Hydrogen Bonding MH - Kluyveromyces/*chemistry MH - *Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Molecular Structure MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - *Saccharomyces cerevisiae Proteins MH - Solutions MH - Transcription Factors/*chemistry PMC - PMC2142621 OID - NLM: PMC2142621 EDAT- 1994/10/01 MHDA- 1994/10/01 00:01 CRDT- 1994/10/01 00:00 AID - 10.1002/pro.5560031020 [doi] PST - ppublish SO - Protein Sci. 1994 Oct;3(10):1806-21. PMID- 12372316 OWN - NLM STAT- MEDLINE DA - 20021009 DCOM- 20030314 LR - 20131121 IS - 1047-8477 (Print) IS - 1047-8477 (Linking) VI - 139 IP - 1 DP - 2002 Jul TI - Effects of the osmolyte trimethylamine-N-oxide on conformation, self-association, and two-dimensional crystallization of myelin basic protein. PG - 13-26 AB - The osmolyte trimethylamine-N-oxide (TMAO) is a naturally in vivo occurring "chemical chaperone" that has been shown to stabilise the folding of numerous proteins. Myelin basic protein (MBP) is a molecule that has not yet been suitably crystallized either in three dimensions for X-ray crystallography or in two dimensions for electron crystallography. Here, we describe lipid monolayer crystallization experiments of two species of recombinant murine MBP in the presence of TMAO. One protein was unmodified, whereas the other contained six Arg/Lys-->Gln substitutions to mimic the effects of deimination (i.e., the enzymatic modification of Arg to citrulline), which reduces the net positive charge. Planar arrays of both proteins were formed on binary lipid monolayers containing a nickel-chelating lipid and a phosphoinositide. In the presence of TMAO, the diffraction spots of these arrays became sharper and more distinct than in its absence, indicating some improvement of crystallinity. The osmolyte also induced the formation of epitaxial growth of protein arrays, especially with the mutant protein. However, none of these assemblies was sufficiently ordered to extract high-resolution structural information. Circular dichroic spectroscopy showed that MBP gained no increase in ordered secondary structure in the presence of TMAO in bulk solution, whereas it did in the presence of lipids. Dynamic light-scattering experiments confirmed that the MBP preparations were monomodal under the optimal crystallization conditions determined by electron microscopy trials. The salt and osmolyte concentrations used were shown to result in a largely unassociated population of MBP. The amino acid composition of MBP overwhelmingly favours a disordered state, and a neural-network-based scheme predicted large segments that would be unlikely to adopt a regular conformation. Thus, this protein has an inherently disordered nature, which mitigates strongly against its crystallization for high-resolution structure determination. FAU - Hill, Christopher M AU - Hill CM AD - Department of Molecular Biology and Genetics, University of Guelph, 50 Stone Road East, Guelph, Ont., Canada N1G 2W1. FAU - Bates, Ian R AU - Bates IR FAU - White, Gisele F AU - White GF FAU - Hallett, F Ross AU - Hallett FR FAU - Harauz, G AU - Harauz G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - 0 (Methylamines) RN - 0 (Myelin Basic Protein) RN - 0 (Oxidants) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Proteins) RN - 0RH81L854J (Glutamine) RN - 7647-14-5 (Sodium Chloride) RN - 94ZLA3W45F (Arginine) RN - FLD0K1SJ1A (trimethyloxamine) RN - K3Z4F929H6 (Lysine) SB - IM MH - Amino Acid Sequence MH - Animals MH - Arginine/chemistry MH - Circular Dichroism MH - Crystallization MH - Dose-Response Relationship, Drug MH - Electrophoresis, Polyacrylamide Gel MH - Glutamine/chemistry MH - Light MH - Lipid Metabolism MH - Lysine/chemistry MH - Methylamines/*pharmacology MH - Mice MH - Microscopy, Electron MH - Molecular Sequence Data MH - Mutation MH - Myelin Basic Protein/*chemistry/metabolism MH - Oxidants/*pharmacology MH - Protein Binding MH - Protein Conformation MH - Protein Isoforms MH - Recombinant Proteins/chemistry/metabolism MH - Scattering, Radiation MH - Sequence Homology, Amino Acid MH - Sodium Chloride/pharmacology EDAT- 2002/10/10 04:00 MHDA- 2003/03/15 04:00 CRDT- 2002/10/10 04:00 AID - S1047847702005130 [pii] PST - ppublish SO - J Struct Biol. 2002 Jul;139(1):13-26. PMID- 15238634 OWN - NLM STAT- MEDLINE DA - 20040726 DCOM- 20050216 LR - 20140609 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 13 IP - 8 DP - 2004 Aug TI - A mobile loop order-disorder transition modulates the speed of chaperonin cycling. PG - 2139-48 AB - Molecular machines order and disorder polypeptides as they form and dissolve large intermolecular interfaces, but the biological significance of coupled ordering and binding has been established in few, if any, macromolecular systems. The ordering and binding of GroES co-chaperonin mobile loops accompany an ATP-dependent conformational change in the GroEL chaperonin that promotes client protein folding. Following ATP hydrolysis, disordering of the mobile loops accompanies co-chaperonin dissociation, reversal of the GroEL conformational change, and release of the client protein. "High-affinity" GroEL mutants were identified by their compatibility with "low-affinity" co-chaperonin mutants and incompatibility with high-affinity co-chaperonin mutants. Analysis of binding kinetics using the intrinsic fluorescence of tryptophan-containing co-chaperonin variants revealed that excessive affinity causes the chaperonin to stall in a conformation that forms in the presence of ATP. Destabilizing the beta-hairpins formed by the mobile loops restores the normal rate of dissociation. Thus, the free energy of mobile-loop ordering and disordering acts like the inertia of an engine's flywheel by modulating the speed of chaperonin conformational changes. FAU - Shewmaker, Frank AU - Shewmaker F AD - Department of Biochemistry, Tulane University Health Sciences Center, New Orleans, Louisiana 70112, USA. FAU - Kerner, Michael J AU - Kerner MJ FAU - Hayer-Hartl, Manajit AU - Hayer-Hartl M FAU - Klein, Gracjana AU - Klein G FAU - Georgopoulos, Costa AU - Georgopoulos C FAU - Landry, Samuel J AU - Landry SJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20040706 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Chaperonin 10) RN - 0 (Chaperonin 60) RN - 0 (Escherichia coli Proteins) RN - 8L70Q75FXE (Adenosine Triphosphate) SB - IM MH - Adenosine Triphosphate/chemistry MH - Amino Acid Substitution/*genetics MH - Chaperonin 10/*chemistry/genetics MH - Chaperonin 60/*chemistry/genetics MH - Escherichia coli/*enzymology MH - Escherichia coli Proteins/*chemistry/genetics MH - Nuclear Magnetic Resonance, Biomolecular MH - Point Mutation/*genetics MH - Protein Structure, Secondary MH - Substrate Cycling/genetics MH - Surface Plasmon Resonance PMC - PMC2279813 OID - NLM: PMC2279813 EDAT- 2004/07/09 05:00 MHDA- 2005/02/17 09:00 CRDT- 2004/07/09 05:00 PHST- 2004/07/06 [aheadofprint] AID - 10.1110/ps.04773204 [doi] AID - ps.04773204 [pii] PST - ppublish SO - Protein Sci. 2004 Aug;13(8):2139-48. Epub 2004 Jul 6. PMID- 20958083 OWN - NLM STAT- MEDLINE DA - 20101124 DCOM- 20110303 LR - 20131121 IS - 1936-086X (Electronic) IS - 1936-0851 (Linking) VI - 4 IP - 11 DP - 2010 Nov 23 TI - Oriented immobilization of prion protein demonstrated via precise interfacial nanostructure measurements. PG - 6607-16 LID - 10.1021/nn101872w [doi] AB - Nanopatterning of biomolecules on functionalized surfaces offers an excellent route for ultrasensitive protein immobilization, for interaction measurements, and for the fabrication of devices such as protein nanoarrays. An improved understanding of the physics and chemistry underlying the device properties and the recognition process is necessary for performance optimization. This is especially important for the recognition and immobilization of intrinsically disordered proteins (IDPs), like the prion protein (PrP), a partial IDP, whose folding and stability may be influenced by local environment and confinement. Atomic force microscopy allows for both highly controllable nanolithography and for sensitive and accurate direct detection, via precise topographic measurements on ultraflat surfaces, of protein interactions in a liquid environment, thus different environmental parameters affecting the biorecognition phenomenon can be investigated in situ. Using nanografting, a tip-induced lithographic technique, and an affinity immobilization strategy based on two different histidine tagged antibodies, with high nM affinity for two different regions of PrP, we successfully demonstrated the immobilization of recombinant mouse PrP onto nanostructured surfaces, in two different orientations. Clear discrimination of the two molecular orientations was shown by differential height (i.e., topographic) measurements, allowing for the estimation of binding parameters and the full characterization of the nanoscale biorecognition process. Our work opens the way to several high sensitivity diagnostic applications and, by controlling PrP orientation, allows for the investigation of unconventional interactions with partially folded proteins, and may serve as a platform for protein misfolding and refolding studies on PrP and other thermodynamically unstable, fibril forming, proteins. FAU - Sanavio, Barbara AU - Sanavio B AD - SISSA/ELETTRA NanoInnovation Laboratory, Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy. FAU - Scaini, Denis AU - Scaini D FAU - Grunwald, Christian AU - Grunwald C FAU - Legname, Giuseppe AU - Legname G FAU - Scoles, Giacinto AU - Scoles G FAU - Casalis, Loredana AU - Casalis L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101019 PL - United States TA - ACS Nano JT - ACS nano JID - 101313589 RN - 0 (Alkanes) RN - 0 (Antibodies) RN - 0 (Immobilized Proteins) RN - 0 (Polyethylene Glycols) RN - 0 (Prions) RN - 0 (Sulfhydryl Compounds) RN - 3P5SU53360 (triethylene glycol) RN - 7440-57-5 (Gold) RN - KA90006V9D (Nitrilotriacetic Acid) SB - IM MH - Alkanes/chemistry MH - Animals MH - Antibodies/immunology MH - Gold/chemistry MH - Immobilized Proteins/*chemistry/immunology MH - Mice MH - Models, Molecular MH - Nanostructures/*chemistry MH - Nanotechnology/*methods MH - Nitrilotriacetic Acid/chemistry MH - Polyethylene Glycols/chemistry MH - Prions/*chemistry/immunology MH - Protein Conformation MH - Sulfhydryl Compounds/chemistry MH - Surface Properties EDAT- 2010/10/21 06:00 MHDA- 2011/03/04 06:00 CRDT- 2010/10/21 06:00 PHST- 2010/10/19 [aheadofprint] AID - 10.1021/nn101872w [doi] PST - ppublish SO - ACS Nano. 2010 Nov 23;4(11):6607-16. doi: 10.1021/nn101872w. Epub 2010 Oct 19. PMID- 16571022 OWN - NLM STAT- MEDLINE DA - 20060330 DCOM- 20070731 LR - 20131121 IS - 1520-6106 (Print) IS - 1520-5207 (Linking) VI - 110 IP - 13 DP - 2006 Apr 6 TI - Alpha-synuclein structures probed by 5-fluorotryptophan fluorescence and 19F NMR spectroscopy. PG - 7058-61 AB - Alpha-synuclein, the main protein component of fibrillar deposits found in Parkinson's disease, is intrinsically disordered in vitro. Site-specific information on the protein conformation has been obtained by biosynthetic incorporation of an unnatural amino acid, 5-fluorotryptophan (5FW), into the recombinant protein. Using fluorescence and 19F NMR spectroscopy, we have characterized three proteins with 5FW at positions 4, 39, and 94. Steady-state emission spectra (maxima at 353 nm; quantum yields approximately 0.2) indicate that all three indole side chains are exposed to the aqueous medium. Virtually identical single-exponential excited-state decays (tau approximately 3.4 ns) were observed in all three cases. Single 19F NMR resonances were measured for W4, W39, and W94 at -49.0 +/- 0.1 ppm. Our analysis of the spectroscopic data suggests that the protein conformations are very similar in the regions near the three sites. FAU - Winkler, Gates R AU - Winkler GR AD - Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA. FAU - Harkins, Seth B AU - Harkins SB FAU - Lee, Jennifer C AU - Lee JC FAU - Gray, Harry B AU - Gray HB LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Isotopes) RN - 0 (alpha-Synuclein) RN - 284SYP0193 (Fluorine) RN - 343-91-9 (5-fluorotryptophan) RN - 8DUH1N11BX (Tryptophan) SB - IM MH - Fluorescence MH - Fluorine/chemistry MH - Isotopes MH - Magnetic Resonance Spectroscopy MH - Tryptophan/*analogs & derivatives/chemistry MH - alpha-Synuclein/*chemistry EDAT- 2006/03/31 09:00 MHDA- 2007/08/01 09:00 CRDT- 2006/03/31 09:00 AID - 10.1021/jp060043n [doi] PST - ppublish SO - J Phys Chem B. 2006 Apr 6;110(13):7058-61. PMID- 20463021 OWN - NLM STAT- MEDLINE DA - 20100726 DCOM- 20100914 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 31 DP - 2010 Jul 30 TI - The multifunctional protein in peroxisomal beta-oxidation: structure and substrate specificity of the Arabidopsis thaliana protein MFP2. PG - 24066-77 LID - 10.1074/jbc.M110.106005 [doi] AB - Plant fatty acids can be completely degraded within the peroxisomes. Fatty acid degradation plays a role in several plant processes including plant hormone synthesis and seed germination. Two multifunctional peroxisomal isozymes, MFP2 and AIM1, both with 2-trans-enoyl-CoA hydratase and l-3-hydroxyacyl-CoA dehydrogenase activities, function in mouse ear cress (Arabidopsis thaliana) peroxisomal beta-oxidation, where fatty acids are degraded by the sequential removal of two carbon units. A deficiency in either of the two isozymes gives rise to a different phenotype; the biochemical and molecular background for these differences is not known. Structure determination of Arabidopsis MFP2 revealed that plant peroxisomal MFPs can be grouped into two families, as defined by a specific pattern of amino acid residues in the flexible loop of the acyl-binding pocket of the 2-trans-enoyl-CoA hydratase domain. This could explain the differences in substrate preferences and specific biological functions of the two isozymes. The in vitro substrate preference profiles illustrate that the Arabidopsis AIM1 hydratase has a preference for short chain acyl-CoAs compared with the Arabidopsis MFP2 hydratase. Remarkably, neither of the two was able to catabolize enoyl-CoA substrates longer than 14 carbon atoms efficiently, suggesting the existence of an uncharacterized long chain enoyl-CoA hydratase in Arabidopsis peroxisomes. FAU - Arent, Susan AU - Arent S AD - Protein Chemistry Group, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark. FAU - Christensen, Caspar E AU - Christensen CE FAU - Pye, Valerie E AU - Pye VE FAU - Norgaard, Allan AU - Norgaard A FAU - Henriksen, Anette AU - Henriksen A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100512 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Arabidopsis Proteins) RN - 0 (Fatty Acids) RN - 0 (MFP2 protein, Arabidopsis) RN - 0 (Protein Isoforms) RN - S88TT14065 (Oxygen) SB - IM MH - Arabidopsis/*enzymology MH - Arabidopsis Proteins/*chemistry/metabolism MH - Crystallography, X-Ray/methods MH - Fatty Acids/chemistry MH - *Gene Expression Regulation, Plant MH - Models, Biological MH - Oxidation-Reduction MH - Oxygen/*chemistry MH - Peroxisomes/*chemistry MH - Phenotype MH - Protein Binding MH - Protein Conformation MH - Protein Isoforms MH - Protein Structure, Tertiary MH - Substrate Specificity PMC - PMC2911295 OID - NLM: PMC2911295 EDAT- 2010/05/14 06:00 MHDA- 2010/09/16 06:00 CRDT- 2010/05/14 06:00 PHST- 2010/05/12 [aheadofprint] AID - M110.106005 [pii] AID - 10.1074/jbc.M110.106005 [doi] PST - ppublish SO - J Biol Chem. 2010 Jul 30;285(31):24066-77. doi: 10.1074/jbc.M110.106005. Epub 2010 May 12. PMID- 10891278 OWN - NLM STAT- MEDLINE DA - 20000815 DCOM- 20000815 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 300 IP - 4 DP - 2000 Jul 21 TI - The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution. PG - 917-33 AB - Using a new expression construct, rhamnose isomerase from Escherichia coli was purified and crystallized. The crystal structure was solved by multiple isomorphous replacement and refined to a crystallographic residual of 17.4 % at 1.6 A resolution. Rhamnose isomerase is a tight tetramer of four (beta/alpha)(8)-barrels. A comparison with other known structures reveals that rhamnose isomerase is most similar to xylose isomerase. Alignment of the sequences of the two enzymes based on their structures reveals a hitherto undetected sequence identity of 13 %, suggesting that the two enzymes evolved from a common precursor. The structure and arrangement of the (beta/alpha)(8)-barrels of rhamnose isomerase are very similar to xylose isomerase. Each enzyme does, however, have additional alpha-helical domains, which are involved in tetramer association, and largely differ in structure. The structures of complexes of rhamnose isomerase with the inhibitor l-rhamnitol and the natural substrate l-rhamnose were determined and suggest that an extended loop, which is disordered in the native enzyme, becomes ordered on substrate binding, and may exclude bulk solvent during catalysis. Unlike xylose isomerase, this loop does not extend across a subunit interface but contributes to the active site of its own subunit. It illustrates how an interconversion between inter and intra-subunit complementation can occur during evolution. In the crystal structure (although not necessarily in vivo) rhamnose isomerase appears to bind Zn(2+) at a "structural" site. In the presence of substrate the enzyme also binds Mn(2+) at a nearby "catalytic" site. An array of hydrophobic residues, not present in xylose isomerase, is likely to be responsible for the recognition of l-rhamnose as a substrate. The available structural data suggest that a metal-mediated hydride-shift mechanism, which is generally favored for xylose isomerase, is also feasible for rhamnose isomerase. CI - Copyright 2000 Academic Press. FAU - Korndorfer, I P AU - Korndorfer IP AD - Institute of Molecular Biology Howard Hughes Medical Institute and Department of Physics, 1229 University of Oregon, Eugene, OR, 97403-1229, USA. FAU - Fessner, W D AU - Fessner WD FAU - Matthews, B W AU - Matthews BW LA - eng SI - PDB/1D8W SI - PDB/1DE5 SI - PDB/1DE6 GR - GM20066/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Enzyme Inhibitors) RN - 3OWL53L36A (Mannitol) RN - 42Z2K6ZL8P (Manganese) RN - 59-85-8 (p-Chloromercuribenzoic Acid) RN - EC 5.3.1.- (Aldose-Ketose Isomerases) RN - EC 5.3.1.14 (L-rhamnose isomerase) RN - EC 5.3.1.5 (xylose isomerase) RN - J41CSQ7QDS (Zinc) RN - QN34XC755A (Rhamnose) SB - IM SB - S MH - Aldose-Ketose Isomerases/antagonists & inhibitors/*chemistry/genetics/metabolism MH - Amino Acid Sequence MH - Binding Sites MH - Catalysis/drug effects MH - Crystallography, X-Ray MH - Enzyme Inhibitors/metabolism/pharmacology MH - Escherichia coli/*enzymology MH - *Evolution, Molecular MH - Genetic Complementation Test MH - Isomerism MH - Manganese/metabolism MH - Mannitol/analogs & derivatives/metabolism/pharmacology MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Rhamnose/metabolism MH - Sequence Alignment MH - Zinc/metabolism MH - p-Chloromercuribenzoic Acid/metabolism/pharmacology EDAT- 2000/07/13 11:00 MHDA- 2000/08/19 11:00 CRDT- 2000/07/13 11:00 AID - 10.1006/jmbi.2000.3896 [doi] AID - S0022-2836(00)93896-8 [pii] PST - ppublish SO - J Mol Biol. 2000 Jul 21;300(4):917-33. PMID- 10367903 OWN - NLM STAT- MEDLINE DA - 19990617 DCOM- 19990617 LR - 20071114 IS - 1074-7613 (Print) IS - 1074-7613 (Linking) VI - 10 IP - 5 DP - 1999 May TI - Crystal structure of the MHC class I homolog MIC-A, a gammadelta T cell ligand. PG - 577-84 AB - The major histocompatibility complex (MHC) class I homolog MIC-A functions as a stress-inducible antigen that is recognized by a subset of gammadelta T cells independent of beta2-microglobulin and bound peptides. Its crystal structure reveals a dramatically altered MHC class I fold, both in detail and overall domain organization. The only remnant of a peptide-binding groove is a small cavity formed as the result of disordering a large section of one of the groove-defining helices. Loss of beta2-microglobulin binding is due to a restructuring of the interaction interfaces. Structural mapping of sequence variation suggests potential receptor binding sites on the underside of the platform on the side opposite of the surface recognized by alphabeta T cell receptors on MHC class I-peptide complexes. FAU - Li, P AU - Li P AD - Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. FAU - Willie, S T AU - Willie ST FAU - Bauer, S AU - Bauer S FAU - Morris, D L AU - Morris DL FAU - Spies, T AU - Spies T FAU - Strong, R K AU - Strong RK LA - eng SI - PDB/1B3J GR - AI30581/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Immunity JT - Immunity JID - 9432918 RN - 0 (Histocompatibility Antigens Class I) RN - 0 (beta 2-Microglobulin) SB - IM MH - Crystallography, X-Ray MH - Histocompatibility Antigens Class I/*chemistry MH - Humans MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Structure, Tertiary MH - beta 2-Microglobulin/metabolism EDAT- 1999/06/15 MHDA- 1999/06/15 00:01 CRDT- 1999/06/15 00:00 AID - S1074-7613(00)80057-6 [pii] PST - ppublish SO - Immunity. 1999 May;10(5):577-84. PMID- 7703231 OWN - NLM STAT- MEDLINE DA - 19950510 DCOM- 19950510 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 34 IP - 13 DP - 1995 Apr 4 TI - Secretion and circular dichroism analysis of the C-terminal signal peptides of HlyA and LktA. PG - 4193-201 AB - The secretion of the 107 kDa hemolysin A (HlyA) from Escherichia coli is mediated by membrane proteins hemolysin B (HlyB) and hemolysin D (HlyD). The signal for transport has been mapped to the C-terminal 60 amino acids of the HylA molecule. We have shown previously that the C-terminal 70 amino acids of leukotoxin (LktA) from Pasteurella hemolytica can substitute functionally for the HlyA signal sequence. This 70 amino acid peptide contains little primary sequence similarity to the HlyA signal sequence, and we have hypothesized that these signal sequences assume a similar higher-order structure which is recognized by the HlyB/D transporter. In the present study, we have expressed and purified small peptides containing the C-terminal 61 amino acids of HlyA and the C-terminal 70 amino acids of LktA. We show that these signal peptides are sufficient for secretion from E. coli in a HlyB/D dependent manner. Circular dichroism analyses show that both molecules exhibit common biophysical properties. In aqueous solution, they appear to be mainly unstructured, but in a membrane mimetic environment they assume a helical secondary structure. The conformational change observed for both peptides going from an aqueous to a membrane mimetic environment may be an important feature of these signal sequences necessary for their recognition and transport. FAU - Zhang, F AU - Zhang F AD - Division of Molecular and Structural Biology, Ontario Cancer Institute, Canada. FAU - Yin, Y AU - Yin Y FAU - Arrowsmith, C H AU - Arrowsmith CH FAU - Ling, V AU - Ling V LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Exotoxins) RN - 0 (Hemolysin Proteins) RN - 0 (Hlya protein, E coli) RN - 0 (Protein Sorting Signals) RN - 0 (Recombinant Fusion Proteins) RN - 0 (leukotoxin) RN - EC 2.5.1.18 (Glutathione Transferase) SB - IM MH - Bacterial Proteins/*chemistry/genetics MH - Base Sequence MH - Circular Dichroism MH - Escherichia coli/*metabolism MH - *Escherichia coli Proteins MH - Exotoxins/*chemistry/genetics/secretion MH - Glutathione Transferase/genetics MH - Hemolysin Proteins/*chemistry/genetics MH - Magnetic Resonance Spectroscopy MH - Mannheimia haemolytica/*metabolism MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Sorting Signals/*chemistry/genetics MH - Protein Structure, Secondary MH - Recombinant Fusion Proteins/chemistry/metabolism EDAT- 1995/04/04 MHDA- 1995/04/04 00:01 CRDT- 1995/04/04 00:00 PST - ppublish SO - Biochemistry. 1995 Apr 4;34(13):4193-201. PMID- 20109190 OWN - NLM STAT- MEDLINE DA - 20100309 DCOM- 20100506 LR - 20140827 IS - 1471-2091 (Electronic) IS - 1471-2091 (Linking) VI - 11 DP - 2010 TI - NMR characterisation of the minimal interacting regions of centrosomal proteins 4.1R and NuMA1: effect of phosphorylation. PG - 7 LID - 10.1186/1471-2091-11-7 [doi] AB - BACKGROUND: Some functions of 4.1R in non-erythroid cells are directly related with its distinct sub-cellular localisation during cell cycle phases. During mitosis, 4.1R is implicated in cell cycle progression and spindle pole formation, and co-localizes with NuMA1. However, during interphase 4.1R is located in the nucleus and only partially co-localizes with NuMA1. RESULTS: We have characterized by NMR the structural features of the C-terminal domain of 4.1R and those of the minimal region (the last 64 residues) involved in the interaction with NuMA1. This subdomain behaves as an intrinsically unfolded protein containing a central region with helical tendency. The specific residues implicated in the interaction with NuMA1 have been mapped by NMR titrations and involve the N-terminal and central helical regions. The segment of NuMA1 that interacts with 4.1R is phosphorylated during mitosis. Interestingly, NMR data indicates that the phosphorylation of NuMA1 interacting peptide provokes a change in the interaction mechanism. In this case, the recognition occurs through the central helical region as well as through the C-terminal region of the subdomain meanwhile the N-terminal region do not interact. CONCLUSIONS: These changes in the interaction derived from the phosphorylation state of NuMA1 suggest that phosphorylation can act as subtle mechanism of temporal and spatial regulation of the complex 4.1R-NuMA1 and therefore of the processes where both proteins play a role. FAU - Trevino, Miguel A AU - Trevino MA AD - Departamento de Espectroscopia y Estructura Molecular, Instituto de Quimica Fisica Rocasolano, Consejo Superior de Investigaciones Cientificas, Serrano 119, 28006 Madrid, Spain. mbruix@iqfr.csic.es FAU - Rodriguez-Rodriguez, Mar AU - Rodriguez-Rodriguez M FAU - Correas, Isabel AU - Correas I FAU - Marcilla, Miguel AU - Marcilla M FAU - Albar, Juan P AU - Albar JP FAU - Rico, Manuel AU - Rico M FAU - Jimenez, M Angeles AU - Jimenez MA FAU - Bruix, Marta AU - Bruix M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100128 PL - England TA - BMC Biochem JT - BMC biochemistry JID - 101084098 RN - 0 (Antigens, Nuclear) RN - 0 (Cytoskeletal Proteins) RN - 0 (Membrane Proteins) RN - 0 (NUMA1 protein, human) RN - 0 (Nuclear Matrix-Associated Proteins) RN - 0 (erythrocyte membrane band 4.1 protein) SB - IM MH - Amino Acid Sequence MH - Antigens, Nuclear/*chemistry MH - Cytoskeletal Proteins/*chemistry MH - Humans MH - Magnetic Resonance Spectroscopy MH - Membrane Proteins/*chemistry MH - Molecular Sequence Data MH - Nuclear Matrix-Associated Proteins/*chemistry MH - Phosphorylation MH - Protein Interaction Domains and Motifs PMC - PMC2834593 OID - NLM: PMC2834593 EDAT- 2010/01/30 06:00 MHDA- 2010/05/07 06:00 CRDT- 2010/01/30 06:00 PHST- 2010/01/19 [received] PHST- 2010/01/28 [accepted] PHST- 2010/01/28 [aheadofprint] AID - 1471-2091-11-7 [pii] AID - 10.1186/1471-2091-11-7 [doi] PST - epublish SO - BMC Biochem. 2010 Jan 28;11:7. doi: 10.1186/1471-2091-11-7. PMID- 18060858 OWN - NLM STAT- MEDLINE DA - 20071225 DCOM- 20080205 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 366 IP - 1 DP - 2008 Feb 1 TI - Neurofilament protein aggregation in a cell line model system. PG - 73-9 AB - Protein aggregates are associated with many diseases and even aggregates of proteins that have no role in disease are inherently toxic to both neuronal and non-neuronal cells. We have developed a model system to explore the mechanism of protein aggregation using a mouse muscle cell line expressing chimeric neurofilament (NF) proteins, a constituent of the protein aggregates in ALS, Lewy body dementia, and Charcot-Marie-Tooth disease. Formation of protein aggregates in these cells leads to reduced cell viability and activated caspases. Aggregates contained both chimeric NF proteins and ubiquitin by immunolocalization and were predominately cytosolic when proteins were expressed at low levels or for shorter periods of time but were present in the nucleus when expression levels increased. This system represents a flexible, new tool to decipher the molecular mechanism of protein aggregation and the contributions of aggregation to cell toxicity. FAU - Hull, Elizabeth AU - Hull E AD - Biomedical Sciences Program, Midwestern University, 19555 N. 59th Avenue, Glendale, AZ 85308, USA. FAU - Spoja, Christoffer AU - Spoja C FAU - Cordova, Matt AU - Cordova M FAU - Cohlberg, Jeffrey A AU - Cohlberg JA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20071203 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Neurofilament Proteins) SB - IM MH - Animals MH - Apoptosis/physiology MH - Cell Line MH - Dimerization MH - Mice MH - Muscle Cells/*cytology/*physiology MH - Neurofilament Proteins/*chemistry/genetics/*metabolism MH - Protein Engineering/*methods EDAT- 2007/12/07 09:00 MHDA- 2008/02/06 09:00 CRDT- 2007/12/07 09:00 PHST- 2007/11/15 [received] PHST- 2007/11/15 [accepted] PHST- 2007/12/03 [aheadofprint] AID - S0006-291X(07)02494-1 [pii] AID - 10.1016/j.bbrc.2007.11.105 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2008 Feb 1;366(1):73-9. Epub 2007 Dec 3. PMID- 12741823 OWN - NLM STAT- MEDLINE DA - 20030513 DCOM- 20030620 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 42 IP - 19 DP - 2003 May 20 TI - New insight into the solution structures of wheat gluten proteins from Raman optical activity. PG - 5665-73 AB - Vibrational Raman optical activity (ROA) spectra of the wheat proteins alpha-gliadin (A-gliadin), omega-gliadin, and a 30 kDa peptide called T-A-1 from the high molecular weight glutenin subunit (HMW-GS) Dx5 were measured to obtain new information about their solution structures. The spectral data show that, under the conditions investigated, A-gliadin contains a considerable amount of hydrated alpha-helix, most of which probably lies within a relatively structured C-terminal domain. Smaller quantities of beta-structure and poly(l-proline) II (PPII) helix were also identified. Addition of methanol was found to increase the alpha-helix content at the expense of some of the beta and PPII structure. In comparison, omega-gliadin and the T-A-1 peptide were found to consist of large amounts of well-defined PPII structure with some turns but no alpha-helix. The results for the T-A-1 peptide are in agreement with a model in which HMW-GS are extended but not highly rigid. Application of a pattern recognition technique, based on principal component analysis (PCA), to the ROA spectra reinforces these conclusions. FAU - Blanch, Ewan W AU - Blanch EW AD - Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom. E.Blanch@umist.ac.uk FAU - Kasarda, Donald D AU - Kasarda DD FAU - Hecht, Lutz AU - Hecht L FAU - Nielsen, Kurt AU - Nielsen K FAU - Barron, Laurence D AU - Barron LD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Solutions) RN - 8002-80-0 (Glutens) RN - 9007-90-3 (Gliadin) RN - 9061-41-0 (glutenin) RN - Y4S76JWI15 (Methanol) SB - IM MH - Amino Acid Sequence MH - Gliadin/*chemistry/genetics MH - Glutens/*analogs & derivatives/*chemistry/genetics MH - Methanol MH - Molecular Sequence Data MH - Molecular Structure MH - Molecular Weight MH - Principal Component Analysis MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Solutions MH - Spectrum Analysis, Raman MH - Triticum/chemistry/genetics EDAT- 2003/05/14 05:00 MHDA- 2003/06/21 05:00 CRDT- 2003/05/14 05:00 AID - 10.1021/bi027059y [doi] PST - ppublish SO - Biochemistry. 2003 May 20;42(19):5665-73. PMID- 24506136 OWN - NLM STAT- MEDLINE DA - 20140318 DCOM- 20140615 LR - 20150212 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 10 DP - 2014 Mar 18 TI - Glycosylation of Skp1 affects its conformation and promotes binding to a model f-box protein. PG - 1657-69 LID - 10.1021/bi401707y [doi] AB - In the social amoeba Dictyostelium, Skp1 is hydroxylated on proline 143 and further modified by three cytosolic glycosyltransferases to yield an O-linked pentasaccharide that contributes to O2 regulation of development. Skp1 is an adapter in the Skp1/cullin1/F-box protein family of E3 ubiquitin ligases that targets specific proteins for polyubiquitination and subsequent proteasomal degradation. To investigate the biochemical consequences of glycosylation, untagged full-length Skp1 and several of its posttranslationally modified isoforms were expressed and purified to near homogeneity using recombinant and in vitro strategies. Interaction studies with the soluble mammalian F-box protein Fbs1/Fbg1/OCP1 revealed preferential binding to the glycosylated isoforms of Skp1. This difference correlated with the increased alpha-helical and decreased beta-sheet content of glycosylated Skp1s based on circular dichroism and increased folding order based on small-angle X-ray scattering. A comparison of the molecular envelopes of fully glycosylated Skp1 and the apoprotein indicated that both isoforms exist as an antiparallel dimer that is more compact and extended in the glycosylated state. Analytical gel filtration and chemical cross-linking studies showed a growing tendency of less modified isoforms to dimerize. Considering that regions of free Skp1 are intrinsically disordered and Skp1 can adopt distinct folds when bound to F-box proteins, we propose that glycosylation, which occurs adjacent to the F-box binding site, influences the spectrum of energetically similar conformations that vary inversely in their propensity to dock with Fbs1 or another Skp1. Glycosylation may thus influence Skp1 function by modulating F-box protein binding in cells. FAU - Sheikh, M Osman AU - Sheikh MO AD - Department of Biochemistry and Molecular Biology and double daggerOklahoma Center for Medical Glycobiology, University of Oklahoma Health Sciences Center , Oklahoma City, Oklahoma 73104, United States. FAU - Schafer, Christopher M AU - Schafer CM FAU - Powell, John T AU - Powell JT FAU - Rodgers, Karla K AU - Rodgers KK FAU - Mooers, Blaine H M AU - Mooers BH FAU - West, Christopher M AU - West CM LA - eng GR - P20 GM103504/GM/NIGMS NIH HHS/United States GR - P20 GM103640/GM/NIGMS NIH HHS/United States GR - P41 GM103393/GM/NIGMS NIH HHS/United States GR - P41 RR001209/RR/NCRR NIH HHS/United States GR - R01 AI088011/AI/NIAID NIH HHS/United States GR - R01 AI088011/AI/NIAID NIH HHS/United States GR - R01 GM037539/GM/NIGMS NIH HHS/United States GR - R01 GM037539/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140303 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (F-Box Proteins) RN - 0 (Protozoan Proteins) RN - EC 6.3.2.19 (SKP Cullin F-Box Protein Ligases) SB - IM MH - Dictyostelium/chemistry/*enzymology/genetics MH - F-Box Proteins/chemistry/genetics/*metabolism MH - Glycosylation MH - Protein Binding MH - Protein Structure, Secondary MH - Protozoan Proteins/*chemistry/genetics/*metabolism MH - SKP Cullin F-Box Protein Ligases/*chemistry/genetics/*metabolism PMC - PMC3985704 OID - NLM: PMC3985704 EDAT- 2014/02/11 06:00 MHDA- 2014/06/16 06:00 CRDT- 2014/02/11 06:00 PHST- 2014/03/03 [aheadofprint] AID - 10.1021/bi401707y [doi] PST - ppublish SO - Biochemistry. 2014 Mar 18;53(10):1657-69. doi: 10.1021/bi401707y. Epub 2014 Mar 3. PMID- 21988473 OWN - NLM STAT- MEDLINE DA - 20111117 DCOM- 20120327 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 115 IP - 46 DP - 2011 Nov 24 TI - Atomistic simulations reveal structural disorder in the RAP74-FCP1 complex. PG - 13731-9 LID - 10.1021/jp208008m [doi] AB - We report atomically detailed molecular dynamics simulations characterizing the interaction of the RAP74 winged helix domain with the intrinsically disordered C-terminal of FCP1. The RAP74-FCP1 complex promotes the essential dephosphorylation of RNA polymerase II prior to initiation of transcription. Although disordered in solution, the C-terminal of FCP1 forms an amphipathic helix when bound to RAP74. Our simulations demonstrate that this interaction also reorganizes and stabilizes RAP74. These simulations illuminate the significance of hydrophobic contacts for stabilizing disordered protein complexes, provide new insight into the mechanism of protein binding by winged helix domains, and also reveal "dynamic fuzziness" in the complex as FCP1 retains significant flexibility after binding. In conjunction with our recent NMR experiments identifying residual structure in unbound FCP1, these simulations suggest that FCP1 loses relatively little conformational entropy upon binding and that the associated coupled folding-binding transition may be less sharp than expected. CI - (c) 2011 American Chemical Society FAU - Wostenberg, Christopher AU - Wostenberg C AD - Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, USA. FAU - Kumar, Sushant AU - Kumar S FAU - Noid, William G AU - Noid WG FAU - Showalter, Scott A AU - Showalter SA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20111027 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Transcription Factors, TFII) RN - 0 (transcription factor TFIIF) RN - EC 2.7.7.- (RNA Polymerase II) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - EC 3.1.3.16 (carboxy-terminal domain phosphatase) SB - IM MH - Binding Sites MH - Entropy MH - Molecular Dynamics Simulation MH - Phosphoprotein Phosphatases/chemistry/*metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA Polymerase II/metabolism MH - Transcription Factors, TFII/chemistry/*metabolism EDAT- 2011/10/13 06:00 MHDA- 2012/03/28 06:00 CRDT- 2011/10/13 06:00 PHST- 2011/10/27 [aheadofprint] AID - 10.1021/jp208008m [doi] PST - ppublish SO - J Phys Chem B. 2011 Nov 24;115(46):13731-9. doi: 10.1021/jp208008m. Epub 2011 Oct 27. PMID- 19519451 OWN - NLM STAT- MEDLINE DA - 20090612 DCOM- 20090902 LR - 20121115 IS - 1389-2037 (Print) IS - 1389-2037 (Linking) VI - 10 IP - 3 DP - 2009 Jun TI - The classic basic protein of myelin--conserved structural motifs and the dynamic molecular barcode involved in membrane adhesion and protein-protein interactions. PG - 196-215 AB - The myelin basic protein (MBP) family comprises a variety of developmentally-regulated members arising from different transcription start sites, differential splicing, and post-translational modifications. The "classic" isoforms of MBP include the 18.5 kDa form, which predominates in adult human myelin and facilitates compaction of the mature myelin sheath in the central nervous system, thereby maintaining its structural integrity. In addition to membrane-association, the 18.5 kDa and all other classic isoforms are able to interact with a multitude of proteins, including Ca(2+)-calmodulin, actin, tubulin, and SH3-domain containing proteins, and thus may be signalling linkers during myelin development and remodelling. All proteins in this family are intrinsically disordered, creating a large effective surface to facilitate multiple protein associations, and are post-translationally modified to various degrees by methylation, phosphorylation, and deimination. We have used spectroscopic (fluorescence, CD, EPR, and NMR) approaches to study MBP's conformational adaptability. A highly-conserved central domain presents an amphipathic alpha-helix in association with a phospholipid membrane, and contains a threonyl residue that is phosphorylated by MAP-kinases. In multiple sclerosis, this segment represents a primary immunodominant epitope. This helical structure is adjacent to a proline-rich region that presents a classic SH3-ligand, comprises a second MAP-kinase phosphorylation site, and forms a polyproline type II helix. This domain of the protein is thus essential to proper positioning of a protein-interaction motif, with the local conformation and accessibility being modulated by MAP-kinases. In addition, the C-terminus of 18.5 kDa MBP has been identified by NMR spectroscopy as a Ca(2+)-calmodulin-binding site, and is of note for having a high density of post-translational modifications (protein kinase C phosphorylation, and deimination). For the most part, any classic protein isoform functions as an entropic spring that interacts in its entirety with membranes and cytoskeletal proteins, but the central and C-terminal motifs may represent molecular switches. FAU - Harauz, George AU - Harauz G AD - Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada. N1G 2W1. gharauz@uoguelph.ca FAU - Libich, David S AU - Libich DS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Netherlands TA - Curr Protein Pept Sci JT - Current protein & peptide science JID - 100960529 RN - 0 (Myelin Basic Protein) SB - IM MH - Adhesiveness MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Cell Membrane/*metabolism MH - *Conserved Sequence MH - Humans MH - Molecular Sequence Data MH - Myelin Basic Protein/*chemistry/*metabolism MH - Protein Binding RF - 200 EDAT- 2009/06/13 09:00 MHDA- 2009/09/03 06:00 CRDT- 2009/06/13 09:00 PST - ppublish SO - Curr Protein Pept Sci. 2009 Jun;10(3):196-215. PMID- 9169453 OWN - NLM STAT- MEDLINE DA - 19970626 DCOM- 19970626 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 272 IP - 23 DP - 1997 Jun 6 TI - DNA bending is essential for the site-specific recognition of DNA response elements by the DNA binding domain of the tumor suppressor protein p53. PG - 14842-9 AB - We have used circular permutation assays to determine the extent and location of the DNA bend induced by the DNA binding domain of human wild type p53 (p53DBD) upon binding to several naturally occurring DNA response elements. We have found that p53DBD binding induces axial bending in all of the response elements investigated. In particular, response elements having a d(CATG) sequence at the junction of two consensus pentamers in each half-site favor highly bent complexes (bending angle is approximately 50 degrees ), whereas response elements having d(CTTG) bases at this position are less bent (bending angles from approximately 37 to approximately 25 degrees ). Quantitative electrophoretic mobility shift assays of different complexes show a direct correlation between the DNA bending angle and the binding affinity of the p53DBD with the response elements, i.e. the greater the stability of the complex, the more the DNA is bent by p53DBD binding. The study provides evidence that the energetics of DNA bending, as determined by the presence or absence of flexible sites in the response elements, may contribute significantly to the overall binding affinity of the p53DBD for different sequences. The results therefore suggest that both the structure and the stability of the p53-DNA complex may vary with different response elements. This variability may be correlated with variability in p53 function. FAU - Nagaich, A K AU - Nagaich AK AD - Department of Biochemistry/330, University of Nevada Reno, Reno, Nevada 89557-0014, USA. FAU - Appella, E AU - Appella E FAU - Harrington, R E AU - Harrington RE LA - eng GR - CA70274/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (CDKN1A protein, human) RN - 0 (Cyclin-Dependent Kinase Inhibitor p21) RN - 0 (Cyclins) RN - 0 (DNA-Binding Proteins) RN - 0 (Oligodeoxyribonucleotides) RN - 0 (Recombinant Proteins) RN - 0 (Tumor Suppressor Protein p53) RN - 9007-49-2 (DNA) RN - EC 3.1.21.- (DNA Restriction Enzymes) SB - IM MH - Base Sequence MH - Binding Sites MH - Cloning, Molecular MH - Consensus Sequence MH - Cyclin-Dependent Kinase Inhibitor p21 MH - Cyclins/chemistry/metabolism MH - DNA/*chemistry/metabolism MH - DNA Restriction Enzymes MH - DNA-Binding Proteins/*chemistry MH - Humans MH - Molecular Sequence Data MH - *Nucleic Acid Conformation MH - Oligodeoxyribonucleotides/chemical synthesis/*chemistry MH - Recombinant Proteins/chemistry/metabolism MH - Thermodynamics MH - Tumor Suppressor Protein p53/*chemistry/metabolism EDAT- 1997/06/06 MHDA- 1997/06/06 00:01 CRDT- 1997/06/06 00:00 PST - ppublish SO - J Biol Chem. 1997 Jun 6;272(23):14842-9. PMID- 10563800 OWN - NLM STAT- MEDLINE DA - 19991220 DCOM- 19991220 LR - 20141120 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 38 IP - 46 DP - 1999 Nov 16 TI - X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine. PG - 15174-84 AB - Ornithine decarboxylase (ODC) is a pyridoxal 5'-phosphate (PLP) dependent homodimeric enzyme. It is a recognized drug target against African sleeping sickness, caused by Trypanosoma brucei. One of the currently used drugs, alpha-difluoromethylornithine (DFMO), is a suicide inhibitor of ODC. The structure of the T. brucei ODC (TbODC) mutant K69A bound to DFMO has been determined by X-ray crystallography to 2.0 A resolution. The protein crystallizes in the space group P2(1) (a = 66.8 A, b = 154.5 A, c = 77.1 A, beta = 90.58 degrees ), with two dimers per asymmetric unit. The initial phasing was done by molecular replacement with the mouse ODC structure. The structure of wild-type uncomplexed TbODC was also determined to 2.9 A resolution by molecular replacement using the TbODC DFMO-bound structure as the search model. The N-terminal domain of ODC is a beta/alpha-barrel, and the C-terminal domain of ODC is a modified Greek key beta-barrel. In comparison to structurally related alanine racemase, the two domains are rotated 27 degrees relative to each other. In addition, two of the beta-strands in the C-terminal domain have exchanged positions in order to maintain the location of essential active site residues in the context of the domain rotation. In ODC, the contacts in the dimer interface are formed primarily by the C-terminal domains, which interact through six aromatic rings that form stacking interactions across the domain boundary. The PLP binding site is formed by the C-termini of beta-strands and loops in the beta/alpha-barrel. In the native structure Lys69 forms a Schiff base with PLP. In both structures, the phosphate of PLP is bound between the seventh and eighth strands forming interactions with Arg277 and a Gly loop (residues 235-237). The pyridine nitrogen of PLP interacts with Glu274. DFMO forms a Schiff base with PLP and is covalently attached to Cys360. It is bound at the dimer interface and the delta-carbon amino group of DFMO is positioned between Asp361 of one subunit and Asp332 of the other. In comparison to the wild-type uncomplexed structure, Cys-360 has rotated 145 degrees toward the active site in the DFMO-bound structure. No domain, subunit rotations, or other significant structural changes are observed upon ligand binding. The structure offers insight into the enzyme mechanism by providing details of the enzyme/inhibitor binding site and allows for a detailed comparison between the enzymes from the host and parasite which will aid in selective inhibitor design. FAU - Grishin, N V AU - Grishin NV AD - Department of Pharmacology, The University of Texas Southwestern Medical Center at Dallas 75235, USA. FAU - Osterman, A L AU - Osterman AL FAU - Brooks, H B AU - Brooks HB FAU - Phillips, M A AU - Phillips MA FAU - Goldsmith, E J AU - Goldsmith EJ LA - eng SI - PDB/1QU4 SI - PDB/2TOD GR - F32 AI09495/AI/NIAID NIH HHS/United States GR - R01 AI34432/AI/NIAID NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Enzyme Inhibitors) RN - 0 (Ornithine Decarboxylase Inhibitors) RN - 0 (Recombinant Fusion Proteins) RN - 5V5IOJ8338 (Pyridoxal Phosphate) RN - EC 4.1.1.17 (Ornithine Decarboxylase) RN - ZQN1G5V6SR (Eflornithine) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Crystallography, X-Ray MH - Dimerization MH - Eflornithine/*chemistry/metabolism MH - Enzyme Inhibitors/*chemistry MH - Mice MH - Molecular Sequence Data MH - Ornithine Decarboxylase/*chemistry/genetics/metabolism MH - *Ornithine Decarboxylase Inhibitors MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Pyridoxal Phosphate/metabolism MH - Recombinant Fusion Proteins/antagonists & inhibitors/chemistry/metabolism MH - Substrate Specificity MH - Trypanosoma brucei brucei/*enzymology EDAT- 1999/11/24 MHDA- 1999/11/24 00:01 CRDT- 1999/11/24 00:00 AID - bi9915115 [pii] PST - ppublish SO - Biochemistry. 1999 Nov 16;38(46):15174-84. PMID- 20817927 OWN - NLM STAT- MEDLINE DA - 20110110 DCOM- 20110209 LR - 20140824 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 39 IP - 1 DP - 2011 Jan TI - Characterization of SMG-9, an essential component of the nonsense-mediated mRNA decay SMG1C complex. PG - 347-58 LID - 10.1093/nar/gkq749 [doi] AB - SMG-9 is part of a protein kinase complex, SMG1C, which consists of the SMG-1 kinase, SMG-8 and SMG-9. SMG1C mediated phosphorylation of Upf1 triggers nonsense-mediated mRNA decay (NMD), a eukaryotic surveillance pathway that detects and targets for degradation mRNAs harboring premature translation termination codons. Here, we have characterized SMG-9, showing that it comprises an N-terminal 180 residue intrinsically disordered region (IDR) followed by a well-folded C-terminal domain. Both domains are required for SMG-1 binding and the integrity of the SMG1C complex, whereas the C-terminus is sufficient to interact with SMG-8. In addition, we have found that SMG-9 assembles in vivo into SMG-9:SMG-9 and, most likely, SMG-8:SMG-9 complexes that are not constituents of SMG1C. SMG-9 self-association is driven by interactions between the C-terminal domains and surprisingly, some SMG-9 oligomers are completely devoid of SMG-1 and SMG-8. We propose that SMG-9 has biological functions beyond SMG1C, as part of distinct SMG-9-containing complexes. Some of these complexes may function as intermediates potentially regulating SMG1C assembly, tuning the activity of SMG-1 with the NMD machinery. The structural malleability of IDRs could facilitate the transit of SMG-9 through several macromolecular complexes. FAU - Fernandez, Israel S AU - Fernandez IS AD - Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain. FAU - Yamashita, Akio AU - Yamashita A FAU - Arias-Palomo, Ernesto AU - Arias-Palomo E FAU - Bamba, Yumi AU - Bamba Y FAU - Bartolome, Ruben A AU - Bartolome RA FAU - Canales, M Angeles AU - Canales MA FAU - Teixido, Joaquin AU - Teixido J FAU - Ohno, Shigeo AU - Ohno S FAU - Llorca, Oscar AU - Llorca O LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100903 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Codon, Nonsense) RN - 0 (Protein Subunits) RN - 0 (RNA, Messenger) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - Codon, Nonsense MH - HeLa Cells MH - Humans MH - Protein Multimerization MH - Protein Structure, Tertiary MH - Protein Subunits/*chemistry/metabolism MH - Protein-Serine-Threonine Kinases/*metabolism MH - RNA Stability MH - RNA, Messenger/metabolism PMC - PMC3017601 OID - NLM: PMC3017601 EDAT- 2010/09/08 06:00 MHDA- 2011/02/10 06:00 CRDT- 2010/09/07 06:00 PHST- 2010/09/03 [aheadofprint] AID - gkq749 [pii] AID - 10.1093/nar/gkq749 [doi] PST - ppublish SO - Nucleic Acids Res. 2011 Jan;39(1):347-58. doi: 10.1093/nar/gkq749. Epub 2010 Sep 3. PMID- 19241372 OWN - NLM STAT- MEDLINE DA - 20090304 DCOM- 20090814 LR - 20140901 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 18 IP - 3 DP - 2009 Mar TI - Dematin exhibits a natively unfolded core domain and an independently folded headpiece domain. PG - 629-36 LID - 10.1002/pro.59 [doi] AB - Dematin is an actin-binding protein originally identified in the junctional complex of the erythrocyte plasma membrane, and is present in many nonerythroid cells. Dematin headpiece knockout mice display a spherical red cell phenotype and develop a compensated anemia. Dematin has two domains: a 315-residue, proline-rich "core" domain and a 68-residue carboxyl-terminal villin-type "headpiece" domain. Expression of full-length dematin in E. coli as a GST recombinant protein results in truncation within a proline, glutamic acid, serine, threonine rich region (PEST). Therefore, we designed a mutant construct that replaces the PEST sequence. The modified dematin has high actin binding activity as determined by actin sedimentation assays. Negative stain electron microscopy demonstrates that the modified dematin also exhibits actin bundling activity like that of native dematin. Circular dichroism (CD) and NMR spectral analysis, however, show little secondary structure in the modified dematin. The lack of secondary structure is also observed in native dematin purified from human red blood cells. (15)N-HSQC NMR spectra of modified dematin indicate that the headpiece domain is fully folded whereas the core region is primarily unfolded. Our finding suggests that the core is natively unfolded and may serve as a scaffold to organize the components of the junctional complex. FAU - Chen, Lin AU - Chen L AD - Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118, USA. FAU - Jiang, Zhenghui G AU - Jiang ZG FAU - Khan, Anwar A AU - Khan AA FAU - Chishti, Athar H AU - Chishti AH FAU - McKnight, C James AU - McKnight CJ LA - eng GR - GM62886/GM/NIGMS NIH HHS/United States GR - HL051445/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Actins) RN - 0 (Blood Proteins) RN - 0 (EPB49 protein, human) RN - 0 (Microfilament Proteins) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Proteins) SB - IM MH - Actin Cytoskeleton/metabolism MH - Actins/metabolism MH - Amino Acid Sequence MH - Blood Proteins/*chemistry/genetics/metabolism MH - Escherichia coli/genetics MH - Humans MH - Microfilament Proteins MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphoproteins/*chemistry/genetics/metabolism MH - *Protein Folding MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Surface Plasmon Resonance PMC - PMC2760368 OID - NLM: PMC2760368 EDAT- 2009/02/26 09:00 MHDA- 2009/08/15 09:00 CRDT- 2009/02/26 09:00 AID - 10.1002/pro.59 [doi] PST - ppublish SO - Protein Sci. 2009 Mar;18(3):629-36. doi: 10.1002/pro.59. PMID- 4093242 OWN - NLM STAT- MEDLINE DA - 19860402 DCOM- 19860402 LR - 20081121 IS - 0367-8377 (Print) IS - 0367-8377 (Linking) VI - 26 IP - 6 DP - 1985 Dec TI - Circular dichroism and fluorescence spectroscopic analyses of a proline-rich glycoprotein from human parotid saliva. PG - 621-9 AB - A proline-rich glycoprotein (PRG) was isolated from human parotid saliva and examined by circular dichroism and fluorescence spectroscopy. Addition of guanidine hydrochloride to PRG labeled with an extrinsic dansyl probe had no effect on the fluorescence spectra's 511 nm lambda-max location. Thermodynamic calculations supported the contention that PRG has no significant tertiary structure. Circular dichroism results for PRG were simulated by computer and a secondary structure composed of 70% random coil and 30% beta-form conformation was predicted. Circular dichroism of PRG failed to detect either poly-L-proline type I or II structures. Deglycosylation of PRG had no measurable effect on the circular dichroism spectrum, indicating that the carbohydrate side chains had little influence on PRG secondary structure. Based upon mathematical calculations, beta-turns were predicted around three glycosylated Asn residues of PRG. These collective data suggest that PRG is composed of a disordered polypeptide chain with at least three of the N-linked Asn residues participating in some type of beta-turn. FAU - Loomis, R E AU - Loomis RE FAU - Bergey, E J AU - Bergey EJ FAU - Levine, M J AU - Levine MJ FAU - Tabak, L A AU - Tabak LA LA - eng GR - DEO4518/DE/NIDCR NIH HHS/United States GR - DEO4971/DE/NIDCR NIH HHS/United States GR - DEO5893/DE/NIDCR NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - DENMARK TA - Int J Pept Protein Res JT - International journal of peptide and protein research JID - 0330420 RN - 0 (Amino Acids) RN - 0 (Dansyl Compounds) RN - 0 (Peptides) SB - IM MH - Adult MH - Amino Acids/analysis MH - Circular Dichroism MH - Dansyl Compounds/analysis MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - Male MH - Parotid Gland/secretion MH - Peptides/*analysis MH - Proline-Rich Protein Domains MH - Protein Conformation MH - Saliva/*analysis MH - Spectrometry, Fluorescence EDAT- 1985/12/01 MHDA- 1985/12/01 00:01 CRDT- 1985/12/01 00:00 PST - ppublish SO - Int J Pept Protein Res. 1985 Dec;26(6):621-9. PMID- 23457638 OWN - NLM STAT- MEDLINE DA - 20130304 DCOM- 20130828 LR - 20141116 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 2 DP - 2013 TI - A new family of intrinsically disordered proteins: structural characterization of the major phasin PhaF from Pseudomonas putida KT2440. PG - e56904 LID - 10.1371/journal.pone.0056904 [doi] AB - Phasins are intracellular polyhydroxyalkanoat4e (PHA)-associated proteins involved in the stabilization of these bacterial carbon storage granules. Despite its importance in PHA metabolism and regulation, only few reports have focused so far on the structure of these proteins. In this work we have investigated the structure and stability of the PhaF phasin from Pseudomonas putida KT2440, a protein that is involved in PHA granule stabilization and distribution to daughter cells upon cell division. A structural, three-dimensional model of the protein was built from homology modeling procedures and consensus secondary structure predictions. The model predicts that PhaF is an elongated protein, with a long, amphipathic N-terminal helix with PHA binding capacity, followed by a short leucine zipper involved in protein oligomerization and a superhelical C-terminal domain wrapped around the chromosomal DNA. Hydrodynamic, spectroscopical and thermodynamic experiments validated the model and confirmed both that free PhaF is a tetramer in solution and that most part of the protein is intrinsically disordered in the absence of its ligands. The results lay a molecular basis for the explanation of the biological role of PhaF and, along with an exhaustive analysis of phasin sequence databases, suggest that intrinsic disorder and oligomerization through coiled-coils may be a widespread mechanism among these proteins. FAU - Maestro, Beatriz AU - Maestro B AD - Instituto de Biologia Molecular y Celular, Universidad Miguel Hernandez, Elche, Spain. FAU - Galan, Beatriz AU - Galan B FAU - Alfonso, Carlos AU - Alfonso C FAU - Rivas, German AU - Rivas G FAU - Prieto, Maria A AU - Prieto MA FAU - Sanz, Jesus M AU - Sanz JM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130215 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Bacterial Proteins) RN - 0 (DNA, Bacterial) RN - 0 (Polyhydroxyalkanoates) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/*metabolism MH - DNA, Bacterial/metabolism MH - Hydrogen-Ion Concentration MH - Models, Molecular MH - Molecular Sequence Data MH - Polyhydroxyalkanoates/metabolism MH - Protein Binding MH - Protein Stability MH - Protein Structure, Tertiary MH - Protein Unfolding/drug effects MH - *Pseudomonas putida MH - Temperature PMC - PMC3574117 OID - NLM: PMC3574117 EDAT- 2013/03/05 06:00 MHDA- 2013/08/29 06:00 CRDT- 2013/03/05 06:00 PHST- 2012/11/04 [received] PHST- 2013/01/15 [accepted] PHST- 2013/02/15 [epublish] AID - 10.1371/journal.pone.0056904 [doi] AID - PONE-D-12-34308 [pii] PST - ppublish SO - PLoS One. 2013;8(2):e56904. doi: 10.1371/journal.pone.0056904. Epub 2013 Feb 15. PMID- 21840989 OWN - NLM STAT- MEDLINE DA - 20111031 DCOM- 20120109 LR - 20150114 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 44 DP - 2011 Nov 4 TI - Structural and functional analysis of the tandem beta-zipper interaction of a Streptococcal protein with human fibronectin. PG - 38311-20 LID - 10.1074/jbc.M111.276592 [doi] AB - Bacterial fibronectin-binding proteins (FnBPs) contain a large intrinsically disordered region (IDR) that mediates adhesion of bacteria to host tissues, and invasion of host cells, through binding to fibronectin (Fn). These FnBP IDRs consist of Fn-binding repeats (FnBRs) that form a highly extended tandem beta-zipper interaction on binding to the N-terminal domain of Fn. Several FnBR residues are highly conserved across bacterial species, and here we investigate their contribution to the interaction. Mutation of these residues to alanine in SfbI-5 (a disordered FnBR from the human pathogen Streptococcus pyogenes) reduced binding, but for each residue the change in free energy of binding was <2 kcal/mol. The structure of an SfbI-5 peptide in complex with the second and third F1 modules from Fn confirms that the conserved FnBR residues play equivalent functional roles across bacterial species. Thus, in SfbI-5, the binding energy for the tandem beta-zipper interaction with Fn is distributed across the interface rather than concentrated in a small number of "hot spot" residues that are frequently observed in the interactions of folded proteins. We propose that this might be a common feature of the interactions of IDRs and is likely to pose a challenge for the development of small molecule inhibitors of FnBP-mediated adhesion to and invasion of host cells. FAU - Norris, Nicole C AU - Norris NC AD - Department of Biology, University of York, York, YO10 5DD, United Kingdom. FAU - Bingham, Richard J AU - Bingham RJ FAU - Harris, Gemma AU - Harris G FAU - Speakman, Adrian AU - Speakman A FAU - Jones, Richard P O AU - Jones RP FAU - Leech, Andrew AU - Leech A FAU - Turkenburg, Johan P AU - Turkenburg JP FAU - Potts, Jennifer R AU - Potts JR LA - eng SI - PDB/3ZRZ GR - BB/D010608/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - D010608/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - FS/07/034/22969/British Heart Foundation/United Kingdom GR - PG/09/079/28008/British Heart Foundation/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110812 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Adhesins, Bacterial) RN - 0 (Fibronectins) RN - 0 (fibronectin-binding proteins, bacterial) SB - IM MH - Adhesins, Bacterial/*chemistry/metabolism MH - Calorimetry MH - Crystallography, X-Ray/methods MH - Fibronectins/*chemistry MH - Humans MH - Kinetics MH - Magnetic Resonance Spectroscopy/methods MH - Markov Chains MH - Molecular Conformation MH - Mutagenesis, Site-Directed MH - Mutation MH - Protein Binding MH - Protein Conformation MH - Streptococcus pyogenes/*metabolism MH - Surface Plasmon Resonance MH - Thermodynamics PMC - PMC3207447 OID - NLM: PMC3207447 EDAT- 2011/08/16 06:00 MHDA- 2012/01/10 06:00 CRDT- 2011/08/16 06:00 PHST- 2011/08/12 [aheadofprint] AID - M111.276592 [pii] AID - 10.1074/jbc.M111.276592 [doi] PST - ppublish SO - J Biol Chem. 2011 Nov 4;286(44):38311-20. doi: 10.1074/jbc.M111.276592. Epub 2011 Aug 12. PMID- 10924115 OWN - NLM STAT- MEDLINE DA - 20000907 DCOM- 20000907 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 39 IP - 31 DP - 2000 Aug 8 TI - A closer look at the active site of gamma-class carbonic anhydrases: high-resolution crystallographic studies of the carbonic anhydrase from Methanosarcina thermophila. PG - 9222-31 AB - The prototype of the gamma-class of carbonic anhydrase has been characterized from the methanogenic archaeon Methanosarcina thermophila. Previously reported kinetic studies of the gamma-class carbonic anhydrase are consistent with this enzyme having a reaction mechanism similar to that of the mammalian alpha-class carbonic anhydrase. However, the overall folds of these two enzymes are dissimilar, and apart from the zinc-coordinating histidines, the active site residues bear little resemblance to one another. The crystal structures of zinc-containing and cobalt-substituted gamma-class carbonic anhydrases from M. thermophila are reported here between 1.46 and 1.95 A resolution in the unbound form and cocrystallized with either SO(4)(2)(-) or HCO(3)(-). Relative to the tetrahedral coordination geometry seen at the active site in the alpha-class of carbonic anhydrases, the active site of the gamma-class enzyme contains additional metal-bound water ligands, so the overall coordination geometry is trigonal bipyramidal for the zinc-containing enzyme and octahedral for the cobalt-substituted enzyme. Ligands bound to the active site all make contacts with the side chain of Glu 62 in manners that suggest the side chain is likely protonated. In the uncomplexed zinc-containing enzyme, the side chains of Glu 62 and Glu 84 appear to share a proton; additionally, Glu 84 exhibits multiple conformations. This suggests that Glu 84 may act as a proton shuttle, which is an important aspect of the reaction mechanism of alpha-class carbonic anhydrases. A hydrophobic pocket on the surface of the enzyme may participate in the trapping of CO(2) at the active site. On the basis of the coordination geometry at the active site, ligand binding modes, the behavior of the side chains of Glu 62 and Glu 84, and analogies to the well-characterized alpha-class of carbonic anhydrases, a more-defined reaction mechanism is proposed for the gamma-class of carbonic anhydrases. FAU - Iverson, T M AU - Iverson TM AD - Graduate Option in Biochemistry, California Institute of Technology, Pasadena 91125, USA. FAU - Alber, B E AU - Alber BE FAU - Kisker, C AU - Kisker C FAU - Ferry, J G AU - Ferry JG FAU - Rees, D C AU - Rees DC LA - eng SI - PDB/1QQ0 SI - PDB/1QRE SI - PDB/1QRF SI - PDB/1QRG SI - PDB/1QRL SI - PDB/1QRM GR - GM07737/GM/NIGMS NIH HHS/United States GR - GM44661/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Archaeal Proteins) RN - 0 (Bicarbonates) RN - 0 (Ligands) RN - 0 (Macromolecular Substances) RN - 0 (Recombinant Proteins) RN - 0 (Sulfates) RN - 3G0H8C9362 (Cobalt) RN - EC 4.2.1.1 (Carbonic Anhydrases) RN - J41CSQ7QDS (Zinc) SB - IM MH - Archaeal Proteins/chemistry/classification/genetics MH - Bicarbonates/chemistry MH - Binding Sites/genetics MH - Carbonic Anhydrases/*chemistry/classification/genetics MH - Cobalt/chemistry MH - Computer Simulation MH - Crystallization MH - Crystallography, X-Ray MH - Escherichia coli/enzymology/genetics MH - Ligands MH - Macromolecular Substances MH - Methanosarcina/*enzymology/genetics MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Folding MH - Recombinant Proteins/chemistry MH - Sulfates/chemistry MH - Zinc/chemistry EDAT- 2000/08/05 11:00 MHDA- 2000/09/09 11:01 CRDT- 2000/08/05 11:00 AID - bi000204s [pii] PST - ppublish SO - Biochemistry. 2000 Aug 8;39(31):9222-31. PMID- 22573613 OWN - NLM STAT- MEDLINE DA - 20120615 DCOM- 20121009 LR - 20141016 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 21 IP - 7 DP - 2012 Jul TI - N-terminal acetylation of alpha-synuclein induces increased transient helical propensity and decreased aggregation rates in the intrinsically disordered monomer. PG - 911-7 LID - 10.1002/pro.2088 [doi] AB - The conformational properties of soluble alpha-synuclein, the primary protein found in patients with Parkinson's disease, are thought to play a key role in the structural transition to amyloid fibrils. In this work, we report that recombinant 100% N-terminal acetylated alpha-synuclein purified under mild physiological conditions presents as a primarily monomeric protein, and that the N-terminal acetyl group affects the transient secondary structure and fibril assembly rates of the protein. Residue-specific NMR chemical shift analysis indicates substantial increase in transient helical propensity in the first 9 N-terminal residues, as well as smaller long-range changes in residues 28-31, 43-46, and 50-66: regions in which the three familial mutations currently known to be causative of early onset disease are found. In addition, we show that the N-terminal acetylated protein forms fibrils that are morphologically similar to those formed from nonacetylated alpha-synuclein, but that their growth rates are slower. Our results highlight that N-terminal acetylation does not form significant numbers of dimers, tetramers, or higher molecular weight species, but does alter the conformational distributions of monomeric alpha-synuclein species in regions known to be important in metal binding, in association with membranes, and in regions known to affect fibril formation rates. CI - Copyright (c) 2012 The Protein Society. FAU - Kang, Lijuan AU - Kang L AD - Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA. FAU - Moriarty, Gina M AU - Moriarty GM FAU - Woods, Lucy A AU - Woods LA FAU - Ashcroft, Alison E AU - Ashcroft AE FAU - Radford, Sheena E AU - Radford SE FAU - Baum, Jean AU - Baum J LA - eng GR - BB/526502/1BB/E012558/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BB/E012558/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - GM087012/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120611 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Amyloid) RN - 0 (alpha-Synuclein) SB - IM MH - Acetylation MH - Amyloid/*chemistry/metabolism/ultrastructure MH - Humans MH - Mass Spectrometry MH - Nuclear Magnetic Resonance, Biomolecular MH - Parkinson Disease/*metabolism MH - Protein Multimerization MH - Protein Structure, Secondary MH - alpha-Synuclein/*chemistry/metabolism/ultrastructure PMC - PMC3403430 OID - NLM: PMC3403430 EDAT- 2012/05/11 06:00 MHDA- 2012/10/10 06:00 CRDT- 2012/05/11 06:00 PHST- 2012/04/23 [received] PHST- 2012/04/27 [accepted] PHST- 2012/06/11 [aheadofprint] AID - 10.1002/pro.2088 [doi] PST - ppublish SO - Protein Sci. 2012 Jul;21(7):911-7. doi: 10.1002/pro.2088. Epub 2012 Jun 11. PMID- 22009045 OWN - NLM STAT- MEDLINE DA - 20111202 DCOM- 20120320 LR - 20131121 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Kinetic measurements give new insights into lipid membrane permeabilization by alpha-synuclein oligomers. PG - 338-45 LID - 10.1039/c1mb05293d [doi] AB - Interactions of oligomeric aggregates of the intrinsically disordered protein alpha-synuclein with lipid membranes appear to play an important role in the development of Parkinson's disease. The permeabilization of cellular membranes by oligomers has been proposed to result in neuronal death. The detailed mechanisms by which alpha-synuclein oligomers permeabilize lipid bilayers remain unknown. Two different mechanisms are conceivable. Oligomers may either insert into membranes forming pores through which small molecules can cross the membrane or their interaction with the membrane may disorder the lipid packing, giving rise to membrane defects. Here we show, using kinetic leakage measurements, that alpha-synuclein oligomer induced impairment of membrane integrity is not limited to the formation of permanent membrane spanning pores. Fast membrane permeabilization could be observed in a fraction of the large unilamellar vesicles. We have also observed, for the first time, that alpha-synuclein oligomers cause an enhanced lipid flip-flop. In neuronal cells, most of the alpha-synuclein is not expected to be present in an oligomeric form, but as monomers. In our in vitro experiments, we find that membrane bound monomeric alpha-synuclein can only delay the onset of oligomer-induced membrane permeabilization, implying that alpha-synuclein monomers cannot counteract oligomer toxicity. FAU - Stockl, Martin AU - Stockl M AD - Nanobiophysics, MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands. m.t.stockl@utwente.nl FAU - Claessens, Mireille M A E AU - Claessens MM FAU - Subramaniam, Vinod AU - Subramaniam V LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111018 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (1-acyl-2-(12-((7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)dodecanoyl)phosphatidylch oline) RN - 0 (Membrane Lipids) RN - 0 (Phosphatidylcholines) RN - 0 (Unilamellar Liposomes) RN - 0 (alpha-Synuclein) RN - 14844-07-6 (Dithionite) RN - EQF2794IRE (4-Chloro-7-nitrobenzofurazan) SB - IM MH - 4-Chloro-7-nitrobenzofurazan/analogs & derivatives MH - Dithionite MH - Humans MH - Kinetics MH - Membrane Lipids/*metabolism MH - Permeability MH - Phosphatidylcholines MH - Protein Structure, Quaternary MH - Unilamellar Liposomes/*metabolism MH - alpha-Synuclein/*chemistry/*metabolism EDAT- 2011/10/20 06:00 MHDA- 2012/03/21 06:00 CRDT- 2011/10/20 06:00 PHST- 2011/10/18 [aheadofprint] PHST- 2011/12/01 [epublish] AID - 10.1039/c1mb05293d [doi] PST - ppublish SO - Mol Biosyst. 2012 Jan;8(1):338-45. doi: 10.1039/c1mb05293d. Epub 2011 Oct 18. PMID- 11101311 OWN - NLM STAT- MEDLINE DA - 20010105 DCOM- 20010105 LR - 20081121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 39 IP - 48 DP - 2000 Dec 5 TI - Probing the three-dimensional structure of human calreticulin. PG - 14950-9 AB - Calreticulin (CRT) is an abundant soluble protein of the endoplasmic reticulum lumen that functions as a molecular chaperone for nascent glycoproteins. We have probed the three-dimensional structure of human CRT using a series of biochemical and biophysical approaches in an effort to understand the molecular basis of its chaperone function. Sedimentation analysis and chemical cross-linking experiments showed that CRT is monodisperse and monomeric in solution with a molecular mass (MW) of 46 +/- 1 kDa. This MW value together with a sedimentation coefficient, s(o)(20,w), of 2.71 S yielded a frictional ratio, f/f(0), of 1.65. Assuming CRT to be a prolate ellipsoid, we calculated an apparent length of 29.8 nm and diameter of 2.44 nm consistent with an asymmetric elongated molecule. These hydrodynamic dimensions account for the apparent anomalous elution position of CRT on gel filtration columns. Far-UV circular dichroism experiments showed that CRT has a cooperative thermal denaturation transition with a midpoint temperature of 42.5 degrees C suggesting a marginally stable structure. Proteolysis experiments showed that the highly acidic segment at the C-terminus of CRT is most susceptible to digest, consistent with the absence of a well-defined polypeptide backbone structure in this region of the protein. Temperature-dependent proteolysis with thermolysin revealed a stable core region within the N- and P-domains. A stable fragment encompassing most of the P-domain was also identified in the thermolytic mixture. Collectively, our results suggest that CRT is likely to be a flexible molecule in solution which may be important for its chaperone function. FAU - Bouvier, M AU - Bouvier M AD - School of Pharmacy, University of Connecticut, Storrs, Connecticut 06269, USA. bouvier@uconnvm.uconn.edu FAU - Stafford, W F AU - Stafford WF LA - eng GR - AI45070/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Calcium-Binding Proteins) RN - 0 (Calreticulin) RN - 0 (Cross-Linking Reagents) RN - 0 (Molecular Chaperones) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 0 (Ribonucleoproteins) RN - 0 (Solutions) RN - EC 3.4.24.27 (Thermolysin) SB - IM MH - Calcium-Binding Proteins/*chemistry MH - Calreticulin MH - Chromatography, Gel MH - Circular Dichroism MH - Cross-Linking Reagents MH - Hot Temperature MH - Humans MH - Molecular Chaperones/*chemistry MH - Peptide Fragments/metabolism MH - Pliability MH - Protein Denaturation MH - Recombinant Proteins/chemistry MH - Ribonucleoproteins/*chemistry MH - Solutions MH - Thermolysin/metabolism MH - Ultracentrifugation EDAT- 2000/12/02 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/12/02 11:00 AID - bi0019545 [pii] PST - ppublish SO - Biochemistry. 2000 Dec 5;39(48):14950-9. PMID- 15501918 OWN - NLM STAT- MEDLINE DA - 20041103 DCOM- 20041206 LR - 20141120 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 101 IP - 44 DP - 2004 Nov 2 TI - Crystal structure of the dimeric protein core of decorin, the archetypal small leucine-rich repeat proteoglycan. PG - 15633-8 AB - Decorin is a ubiquitous extracellular matrix proteoglycan with a variety of important biological functions that are mediated by its interactions with extracellular matrix proteins, cytokines, and cell surface receptors. Decorin is the prototype of the family of small leucine-rich repeat proteoglycans and proteins (SLRPs), characterized by a protein core composed of leucine-rich repeats (LRRs), flanked by two cysteine-rich regions. We report here the crystal structure of the dimeric protein core of decorin, the best characterized member of the SLRP family. Each monomer adopts the curved solenoid fold characteristic of LRR domains, with a parallel beta-sheet on the inside interwoven with loops containing short segments of beta-strands, 3(10) helices, and polyproline II helices on the outside. Two main features are unique to this structure. First, decorin dimerizes through the concave surfaces of the LRR domains, which have been implicated previously in protein-ligand interactions. The amount of surface buried in this dimer rivals the buried surfaces of some of the highest-affinity macromolecular complexes reported to date. Second, the C-terminal region adopts an unusual capping motif that involves a laterally extended LRR and a disulfide bond. This motif seems to be unique to SLRPs and has not been observed in any other LRR protein structure to date. Possible implications of these features for decorin ligand binding and SLRP function are discussed. FAU - Scott, Paul G AU - Scott PG AD - Department of Biochemistry and Alberta Synchrotron Institute, University of Alberta, Edmonton, Alberta, Canada T6G 2H7. FAU - McEwan, Paul A AU - McEwan PA FAU - Dodd, Carole M AU - Dodd CM FAU - Bergmann, Ernst M AU - Bergmann EM FAU - Bishop, Paul N AU - Bishop PN FAU - Bella, Jordi AU - Bella J LA - eng SI - PDB/1XEC SI - PDB/1XKU SI - PDB/2XCD PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20041022 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DCN protein, human) RN - 0 (Decorin) RN - 0 (Extracellular Matrix Proteins) RN - 0 (Ligands) RN - 0 (Proteoglycans) RN - 0 (Recombinant Proteins) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Cattle MH - Crystallography, X-Ray MH - Decorin MH - Dimerization MH - Extracellular Matrix Proteins MH - Humans MH - In Vitro Techniques MH - Ligands MH - Molecular Sequence Data MH - Protein Structure, Quaternary MH - Proteoglycans/*chemistry/genetics/metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Repetitive Sequences, Amino Acid MH - Sequence Homology, Amino Acid MH - Static Electricity PMC - PMC524833 OID - NLM: PMC524833 EDAT- 2004/10/27 09:00 MHDA- 2004/12/16 09:00 CRDT- 2004/10/27 09:00 PHST- 2004/10/22 [aheadofprint] AID - 0402976101 [pii] AID - 10.1073/pnas.0402976101 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15633-8. Epub 2004 Oct 22. PMID- 20627399 OWN - NLM STAT- MEDLINE DA - 20100719 DCOM- 20101029 IS - 1873-4200 (Electronic) IS - 0301-4622 (Linking) VI - 151 IP - 1-2 DP - 2010 Sep TI - Characterizing the denatured state of human prion 121-230. PG - 86-90 LID - 10.1016/j.bpc.2010.05.002 [doi] AB - Misfolding and aggregation of the prion protein (PrP) are responsible for the development of fatal transmissible neurodegenerative diseases. PrP undergoes structural conversion from a natively folded state into a misfolded state, resulting in insoluble amyloid fibrils. Partial unfolding has been recognized as an essential step in fibrillation. The strong correlation of unfolding and fibrillation emphasizes the importance of denatured states. To gain insight into possible aggregation-prone denatured states, we characterized the denatured state of human prion (huPrP) 121-230 near extended conformation by self-guided Langevin dynamics simulations. Our results revealed that denatured huPrP is partially folded with alpha-helical structure. CI - 2010 Elsevier B.V. All rights reserved. FAU - Lee, Cheng-I AU - Lee CI AD - Department of Life Science, National Chung Cheng University, Ming-Hsiung, Chia-Yi, Taiwan, ROC. biocil@ccu.edu.tw FAU - Chang, Nai-yuan AU - Chang NY LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100515 PL - Netherlands TA - Biophys Chem JT - Biophysical chemistry JID - 0403171 RN - 0 (Amyloid) RN - 0 (Prions) SB - IM MH - Amyloid/chemistry MH - Cluster Analysis MH - Humans MH - Molecular Dynamics Simulation MH - Prions/*chemistry MH - Protein Denaturation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary EDAT- 2010/07/16 06:00 MHDA- 2010/10/30 06:00 CRDT- 2010/07/15 06:00 PHST- 2010/03/17 [received] PHST- 2010/05/06 [revised] PHST- 2010/05/08 [accepted] PHST- 2010/05/15 [aheadofprint] AID - S0301-4622(10)00133-X [pii] AID - 10.1016/j.bpc.2010.05.002 [doi] PST - ppublish SO - Biophys Chem. 2010 Sep;151(1-2):86-90. doi: 10.1016/j.bpc.2010.05.002. Epub 2010 May 15. PMID- 25062251 OWN - NLM STAT- MEDLINE DA - 20140726 DCOM- 20150416 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 7 DP - 2014 TI - Association between the intrinsically disordered protein PEX19 and PEX3. PG - e103101 LID - 10.1371/journal.pone.0103101 [doi] AB - In peroxisomes, peroxins (PEXs) 3 and 19 are the principal protein components of the machinery required for early peroxisomal biogenesis. For further insight into the interaction of PEX3 and PEX19, we used hydrogen exchange mass spectrometry to monitor conformational changes during complex formation between PEX3 and PEX19 in vitro. Our data showed that PEX19 remained highly flexible during interaction with PEX3. However, we could detect three changes, one each in the N-and C-terminus along with a small stretch in the middle of PEX19 (F64-L74) which became shielded from hydrogen exchange when interacting with PEX3. PEX3 became more protected from hydrogen exchange in the binding groove for PEX19 with only small changes elsewhere. Most likely the N-terminus of PEX19 initiates the binding to PEX3, and then subtle conformational changes in PEX3 affect the surface of the PEX3 molecule. PEX19 in turn, is stabilized by folding of a short helix and its C-terminal folding core permitting PEX19 to bind to PEX3 with higher affinity than just the N-terminal interaction allows. Thus within the cell, PEX3 is stabilized by PEX19 preventing PEX3 aggregation. FAU - Hattula, Katarina AU - Hattula K AD - Institute of Biotechnology, University of Helsinki, Helsinki, Finland. FAU - Hirschberg, Daniel AU - Hirschberg D AD - Institute of Biotechnology, University of Helsinki, Helsinki, Finland. FAU - Kalkkinen, Nisse AU - Kalkkinen N AD - Institute of Biotechnology, University of Helsinki, Helsinki, Finland. FAU - Butcher, Sarah J AU - Butcher SJ AD - Institute of Biotechnology, University of Helsinki, Helsinki, Finland. FAU - Ora, Ari AU - Ora A AD - Institute of Biotechnology, University of Helsinki, Helsinki, Finland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140725 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Lipoproteins) RN - 0 (Membrane Proteins) RN - 0 (Multiprotein Complexes) RN - 0 (Pex3 protein, human) RN - 157153-79-2 (PEX19 protein, human) SB - IM MH - Amino Acid Sequence MH - Humans MH - Lipoproteins/biosynthesis/*chemistry/ultrastructure MH - Membrane Proteins/biosynthesis/*chemistry/ultrastructure MH - Multiprotein Complexes/chemistry/ultrastructure MH - Peroxisomes/*chemistry/genetics MH - Protein Conformation MH - Protein Folding MH - Protein Interaction Maps/*genetics PMC - PMC4111287 OID - NLM: PMC4111287 EDAT- 2014/07/26 06:00 MHDA- 2015/04/17 06:00 CRDT- 2014/07/26 06:00 PHST- 2014 [ecollection] PHST- 2014/04/07 [received] PHST- 2014/06/24 [accepted] PHST- 2014/07/25 [epublish] AID - 10.1371/journal.pone.0103101 [doi] AID - PONE-D-14-15539 [pii] PST - epublish SO - PLoS One. 2014 Jul 25;9(7):e103101. doi: 10.1371/journal.pone.0103101. eCollection 2014. PMID- 12620094 OWN - NLM STAT- MEDLINE DA - 20030521 DCOM- 20030722 LR - 20140611 IS - 0264-6021 (Print) IS - 0264-6021 (Linking) VI - 372 IP - Pt 2 DP - 2003 Jun 1 TI - The random-coil 'C' fragment of the dihydropyridine receptor II-III loop can activate or inhibit native skeletal ryanodine receptors. PG - 305-16 AB - The actions of peptide C, corresponding to (724)Glu-Pro(760) of the II-III loop of the skeletal dihydropyridine receptor, on ryanodine receptor (RyR) channels incorporated into lipid bilayers with the native sarcoplasmic reticulum membrane show that the peptide is a high-affinity activator of native skeletal RyRs at cytoplasmic concentrations of 100 nM-10 microM. In addition, we found that peptide C inhibits RyRs in a voltage-independent manner when added for longer times or at higher concentrations (up to 150 microM). Peptide C had a random-coil structure indicating that it briefly assumes a variety of structures, some of which might activate and others which might inhibit RyRs. The results suggest that RyR activation and inhibition by peptide C arise from independent stochastic processes. A rate constant of 7.5 x 10(5) s(-1).M(-1) was obtained for activation and a lower estimate for the rate constant for inhibition of 5.9 x 10(3) s(-1).M(-1). The combined actions of peptide C and peptide A (II-III loop sequence (671)Thr-Leu(690)) showed that peptide C prevented activation but not blockage of RyRs by peptide A. We suggest that the effects of peptide C indicate functional interactions between a part of the dihydropyridine receptor and the RyR. These interactions could reflect either dynamic changes that occur during excitation-contraction coupling or interactions between the proteins at rest. FAU - Haarmann, Claudia S AU - Haarmann CS AD - Muscle Research Group, John Curtin School of Medical Research, Australian National University, P.O. Box 334, Canberra, ACT 2601, Australia. FAU - Green, Daniel AU - Green D FAU - Casarotto, Marco G AU - Casarotto MG FAU - Laver, Derek R AU - Laver DR FAU - Dulhunty, Angela F AU - Dulhunty AF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (Calcium Channels, L-Type) RN - 0 (Lipid Bilayers) RN - 0 (Peptides) RN - 0 (Ryanodine Receptor Calcium Release Channel) RN - 0 (polypeptide C) RN - 8L70Q75FXE (Adenosine Triphosphate) SB - IM MH - Adenosine Triphosphate/pharmacology MH - Animals MH - Calcium Channels, L-Type/*metabolism MH - Cell Membrane/physiology MH - Circular Dichroism MH - Lipid Bilayers/*metabolism MH - Magnetic Resonance Spectroscopy MH - Membrane Potentials/physiology MH - Muscle, Skeletal/*drug effects/metabolism MH - Peptides/*pharmacology MH - Rabbits MH - Ryanodine Receptor Calcium Release Channel/*metabolism MH - Sarcoplasmic Reticulum/physiology PMC - PMC1223419 OID - NLM: PMC1223419 EDAT- 2003/03/07 04:00 MHDA- 2003/07/23 05:00 CRDT- 2003/03/07 04:00 PHST- 2003/03/06 [accepted] PHST- 2003/02/13 [revised] PHST- 2002/11/12 [received] AID - 10.1042/BJ20021763 [doi] AID - BJ20021763 [pii] PST - ppublish SO - Biochem J. 2003 Jun 1;372(Pt 2):305-16. PMID- 17029844 OWN - NLM STAT- MEDLINE DA - 20070515 DCOM- 20070716 IS - 1047-8477 (Print) IS - 1047-8477 (Linking) VI - 158 IP - 2 DP - 2007 May TI - Structure and thermodynamics of the tubulin-stathmin interaction. PG - 137-47 AB - Oncoprotein 18/stathmin (stathmin) is a phosphorylation-controlled key regulator of microtubule dynamics. In recent years, substantial efforts were undertaken to characterize the complex formed between tubulin and the intrinsically disordered stathmin molecule. Here, I summarize and illustrate the current structural and thermodynamic studies on the tubulin-stathmin interaction. Based on these and on functional information I formulate an updated molecular mechanism on how tubulin-binding by stathmin regulates microtubule dynamics. FAU - Steinmetz, Michel O AU - Steinmetz MO AD - Biomolecular Research, Structural Biology, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland. michel.steinmetz@psi.ch LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20060823 PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - 0 (Stathmin) RN - 0 (Tubulin) SB - IM MH - Amino Acid Sequence MH - Humans MH - Molecular Sequence Data MH - Phosphorylation MH - Protein Structure, Secondary MH - Stathmin/*chemistry/*ultrastructure MH - Thermodynamics MH - Tubulin/*chemistry/*ultrastructure RF - 51 EDAT- 2006/10/13 09:00 MHDA- 2007/07/17 09:00 CRDT- 2006/10/13 09:00 PHST- 2006/05/12 [received] PHST- 2006/07/10 [accepted] PHST- 2006/08/23 [aheadofprint] AID - S1047-8477(06)00243-7 [pii] AID - 10.1016/j.jsb.2006.07.018 [doi] PST - ppublish SO - J Struct Biol. 2007 May;158(2):137-47. Epub 2006 Aug 23. PMID- 15542602 OWN - NLM STAT- MEDLINE DA - 20050207 DCOM- 20050405 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 6 DP - 2005 Feb 11 TI - UreG, a chaperone in the urease assembly process, is an intrinsically unstructured GTPase that specifically binds Zn2+. PG - 4684-95 AB - Bacillus pasteurii UreG, a chaperone involved in the urease active site assembly, was overexpressed in Escherichia coli BL21(DE3) and purified to homogeneity. The identity of the recombinant protein was confirmed by SDS-PAGE, protein sequencing, and mass spectrometry. A combination of size exclusion chromatography and multiangle and dynamic laser light scattering established that BpUreG is present in solution as a dimer. Analysis of circular dichroism spectra indicated that the protein contains large portions of helices (15%) and strands (29%), whereas NMR spectroscopy indicated the presence of conformational fluxionality of the protein backbone in solution. BpUreG catalyzes the hydrolysis of GTP with a kcat=0.04 min(-1), confirming a role for this class of proteins in coupling energy requirements and nickel incorporation into the urease active site. BpUreG binds two Zn2+ ions per dimer, with a KD=42 +/- 3 microm, and has a 10-fold lower affinity for Ni2+. A structural model for BpUreG was calculated by using threading algorithms. The protein, in the fully folded state, features the typical structural architecture of GTPases, with an open beta-barrel surrounded by alpha-helices and a P-loop at the N terminus. The protein dynamic behavior observed in solution is critically discussed relative to the structural model, using algorithms for disorder predictions. The results suggest that UreG proteins belong to the class of intrinsically unstructured proteins that need the interaction with cofactors or other protein partners to perform their function. It is also proposed that metal ions such as Zn2+ could have important structural roles in the urease activation process. FAU - Zambelli, Barbara AU - Zambelli B AD - Laboratory of Bioinorganic Chemistry, Department of Agro-Environmental Science and Technology, University of Bologna, I-40127 Bologna, Italy. FAU - Stola, Massimiliano AU - Stola M FAU - Musiani, Francesco AU - Musiani F FAU - De Vriendt, Kris AU - De Vriendt K FAU - Samyn, Bart AU - Samyn B FAU - Devreese, Bart AU - Devreese B FAU - Van Beeumen, Jozef AU - Van Beeumen J FAU - Turano, Paola AU - Turano P FAU - Dikiy, Alexander AU - Dikiy A FAU - Bryant, Donald A AU - Bryant DA FAU - Ciurli, Stefano AU - Ciurli S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20041112 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (Ions) RN - 0 (Metals) RN - 0 (Recombinant Proteins) RN - 0 (ureG protein, Bacteria) RN - 7OV03QG267 (Nickel) RN - EC 3.5.1.5 (Urease) RN - EC 3.6.1.- (GTP Phosphohydrolases) RN - J41CSQ7QDS (Zinc) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Bacillus/enzymology MH - Bacterial Proteins/chemistry/*physiology MH - Binding Sites MH - Carrier Proteins/chemistry/*physiology MH - Circular Dichroism MH - Cloning, Molecular MH - Dimerization MH - Electrophoresis, Polyacrylamide Gel MH - Enzyme Activation MH - Escherichia coli/metabolism MH - GTP Phosphohydrolases/*metabolism MH - Hydrolysis MH - Ions MH - Kinetics MH - Lasers MH - Light MH - Magnetic Resonance Spectroscopy MH - Mass Spectrometry MH - Metals/chemistry MH - Models, Chemical MH - Models, Molecular MH - Molecular Sequence Data MH - Nickel/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Scattering, Radiation MH - Sequence Homology, Amino Acid MH - Static Electricity MH - Urease/metabolism MH - Zinc/*chemistry EDAT- 2004/11/16 09:00 MHDA- 2005/04/06 09:00 CRDT- 2004/11/16 09:00 PHST- 2004/11/12 [aheadofprint] AID - M408483200 [pii] AID - 10.1074/jbc.M408483200 [doi] PST - ppublish SO - J Biol Chem. 2005 Feb 11;280(6):4684-95. Epub 2004 Nov 12. PMID- 18779323 OWN - NLM STAT- MEDLINE DA - 20081103 DCOM- 20081223 LR - 20140903 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 45 DP - 2008 Nov 7 TI - An unusual intrinsically disordered protein from the model legume Lotus japonicus stabilizes proteins in vitro. PG - 31142-52 LID - 10.1074/jbc.M805024200 [doi] AB - Intrinsic structural disorder is a prevalent feature of proteins with chaperone activity. Using a complementary set of techniques, we have structurally characterized LjIDP1 (intrinsically disordered protein 1) from the model legume Lotus japonicus, and our results provide the first structural characterization of a member of the Lea5 protein family (PF03242). Contrary to in silico predictions, we show that LjIDP1 is intrinsically disordered and probably exists as an ensemble of conformations with limited residual beta-sheet, turn/loop, and polyproline II secondary structure. Furthermore, we show that LjIDP1 has an inherent propensity to undergo a large conformational shift, adopting a largely alpha-helical structure when it is dehydrated and in the presence of different detergents and alcohols. This is consistent with an overrepresentation of order-promoting residues in LjIDP1 compared with the average of intrinsically disordered proteins. In line with functioning as a chaperone, we show that LjIDP1 effectively prevents inactivation of two model enzymes under conditions that promote protein misfolding and aggregation. The LjIdp1 gene is expressed in all L. japonicus tissues tested. A higher expression level was found in the root tip proximal zone, in roots inoculated with compatible endosymbiotic M. loti, and in functional nitrogen-fixing root nodules. We suggest that the ability of LjIDP1 to prevent protein misfolding and aggregation may play a significant role in tissues, such as symbiotic root nodules, which are characterized by high metabolic activity. FAU - Haaning, Svend AU - Haaning S AD - Department of Molecular Biology, University of Aarhus, 8000 Aarhus, Denmark. FAU - Radutoiu, Simona AU - Radutoiu S FAU - Hoffmann, Soren V AU - Hoffmann SV FAU - Dittmer, Jens AU - Dittmer J FAU - Giehm, Lise AU - Giehm L FAU - Otzen, Daniel E AU - Otzen DE FAU - Stougaard, Jens AU - Stougaard J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080908 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Molecular Chaperones) RN - 0 (Plant Proteins) RN - 0 (late embryogenesis abundant protein, plant) SB - IM MH - Genetic Complementation Test/methods MH - Lotus/genetics/*metabolism MH - *Models, Biological MH - Molecular Chaperones/genetics/*metabolism MH - Plant Proteins/genetics/metabolism MH - *Protein Folding MH - Protein Structure, Secondary MH - Root Nodules, Plant/genetics/*metabolism PMC - PMC2662180 OID - NLM: PMC2662180 EDAT- 2008/09/10 09:00 MHDA- 2008/12/24 09:00 CRDT- 2008/09/10 09:00 PHST- 2008/09/08 [aheadofprint] AID - M805024200 [pii] AID - 10.1074/jbc.M805024200 [doi] PST - ppublish SO - J Biol Chem. 2008 Nov 7;283(45):31142-52. doi: 10.1074/jbc.M805024200. Epub 2008 Sep 8. PMID- 23071750 OWN - NLM STAT- MEDLINE DA - 20121016 DCOM- 20130404 LR - 20141105 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 10 DP - 2012 TI - Probing the role of nascent helicity in p27 function as a cell cycle regulator. PG - e47177 LID - 10.1371/journal.pone.0047177 [doi] AB - p27 regulates the activity of Cdk complexes which are the principal governors of phase transitions during cell division. Members of the p27 family of proteins, which also includes p21 and p57, are called the Cip/Kip cyclin-dependent kinase regulators (CKRs). Interestingly, the Cip/Kip CKRs play critical roles in cell cycle regulation by being intrinsically unstructured, a characteristic contrary to the classical structure-function paradigm. They exhibit nascent helicity which has been localized to a segment referred to as sub-domain LH. The nascent helicity of this sub-domain is conserved and we hypothesize that it is an important determinant of their functional properties. To test this hypothesis, we successfully designed and prepared p27 variants in which domain LH was either more or less helical with respect to the wild-type protein. Thermal denaturation experiments showed that the ternary complexes of the p27 variants bound to Cdk2/Cyclin A were less stable compared to the wild-type complex. Isothermal titration calorimetry experiments showed a decrease in the enthalpy of binding for all the mutants with respect to p27. The free energies of binding varied within a much narrower range. In vitro Cdk2 inhibition assays showed that the p27 variants exhibited disparate inhibitory potencies. Furthermore, when over-expressed in NIH 3T3 mouse fibroblast cells, the less helical p27 variants were less effective in causing cell cycle arrest relative to the wild-type p27. Our results indicate that the nascent helicity of sub-domain LH plays a key role mediating the biological function of p27. FAU - Otieno, Steve AU - Otieno S AD - Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA. FAU - Kriwacki, Richard AU - Kriwacki R LA - eng GR - P30CA21765/CA/NCI NIH HHS/United States GR - R01CA082491/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20121012 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Cyclin A) RN - 0 (Cyclin-Dependent Kinase Inhibitor p21) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Cyclin A/chemistry/metabolism MH - Cyclin-Dependent Kinase Inhibitor p21/chemistry/metabolism MH - Cyclin-Dependent Kinase Inhibitor p27/*chemistry/physiology MH - Humans MH - Mice MH - Molecular Sequence Data MH - NIH 3T3 Cells MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Structure-Activity Relationship MH - Thermodynamics PMC - PMC3470550 OID - NLM: PMC3470550 EDAT- 2012/10/17 06:00 MHDA- 2013/04/05 06:00 CRDT- 2012/10/17 06:00 PHST- 2012/07/24 [received] PHST- 2012/09/10 [accepted] PHST- 2012/10/12 [epublish] AID - 10.1371/journal.pone.0047177 [doi] AID - PONE-D-12-22195 [pii] PST - ppublish SO - PLoS One. 2012;7(10):e47177. doi: 10.1371/journal.pone.0047177. Epub 2012 Oct 12. PMID- 22721951 OWN - NLM STAT- MEDLINE DA - 20120903 DCOM- 20121119 LR - 20141016 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 422 IP - 5 DP - 2012 Oct 5 TI - Electrostatically accelerated coupled binding and folding of intrinsically disordered proteins. PG - 674-84 LID - 10.1016/j.jmb.2012.06.019 [doi] AB - Intrinsically disordered proteins (IDPs) are now recognized to be prevalent in biology, and many potential functional benefits have been discussed. However, the frequent requirement of peptide folding in specific interactions of IDPs could impose a kinetic bottleneck, which could be overcome only by efficient folding upon encounter. Intriguingly, existing kinetic data suggest that specific binding of IDPs is generally no slower than that of globular proteins. Here, we exploited the cell cycle regulator p27(Kip1) (p27) as a model system to understand how IDPs might achieve efficient folding upon encounter for facile recognition. Combining experiments and coarse-grained modeling, we demonstrate that long-range electrostatic interactions between enriched charges on p27 and near its binding site on cyclin A not only enhance the encounter rate (i.e., electrostatic steering) but also promote folding-competent topologies in the encounter complexes, allowing rapid subsequent formation of short-range native interactions en route to the specific complex. In contrast, nonspecific hydrophobic interactions, while hardly affecting the encounter rate, can significantly reduce the efficiency of folding upon encounter and lead to slower binding kinetics. Further analysis of charge distributions in a set of known IDP complexes reveals that, although IDP binding sites tend to be more hydrophobic compared to the rest of the target surface, their vicinities are frequently enriched with charges to complement those on IDPs. This observation suggests that electrostatically accelerated encounter and induced folding might represent a prevalent mechanism for promoting facile IDP recognition. CI - Copyright (c) 2012 Elsevier Ltd. All rights reserved. FAU - Ganguly, Debabani AU - Ganguly D AD - Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA. FAU - Otieno, Steve AU - Otieno S FAU - Waddell, Brett AU - Waddell B FAU - Iconaru, Luigi AU - Iconaru L FAU - Kriwacki, Richard W AU - Kriwacki RW FAU - Chen, Jianhan AU - Chen J LA - eng GR - 5R01-CA082491/CA/NCI NIH HHS/United States GR - P30-CA21765/CA/NCI NIH HHS/United States GR - R01 CA082491/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120619 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Cyclin A) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) SB - IM MH - Amino Acid Sequence MH - Cyclin A/metabolism MH - Cyclin-Dependent Kinase Inhibitor p27/*chemistry/*metabolism MH - Kinetics MH - Models, Molecular MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Protein Binding MH - Protein Conformation MH - *Protein Folding MH - *Static Electricity PMC - PMC3432731 MID - NIHMS388170 OID - NLM: NIHMS388170 OID - NLM: PMC3432731 EDAT- 2012/06/23 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/06/23 06:00 PHST- 2012/03/23 [received] PHST- 2012/06/08 [revised] PHST- 2012/06/11 [accepted] PHST- 2012/06/19 [aheadofprint] AID - S0022-2836(12)00492-5 [pii] AID - 10.1016/j.jmb.2012.06.019 [doi] PST - ppublish SO - J Mol Biol. 2012 Oct 5;422(5):674-84. doi: 10.1016/j.jmb.2012.06.019. Epub 2012 Jun 19. PMID- 11054294 OWN - NLM STAT- MEDLINE DA - 20001128 DCOM- 20001207 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 303 IP - 4 DP - 2000 Nov 3 TI - Structure of a mutant EF-G reveals domain III and possibly the fusidic acid binding site. PG - 593-603 AB - The crystal structure of Thermus thermophilus elongation factor G (EF-G) carrying the point mutation His573Ala was determined at a resolution of 2.8 A. The mutant has a more closed structure than that previously reported for wild-type EF-G. This is obtained by a 10 degrees rigid rotation of domains III, IV and V with regard to domains I and II. This rotation results in a displacement of the tip of domain IV by approximately 9 A. The structure of domain III is now fully visible and reveals the double split beta-alpha-beta motif also observed for EF-G domain V and for several ribosomal proteins. A large number of fusidic acid resistant mutations found in domain III have now been possible to locate. Possible locations for the effector loop and a possible binding site for fusidic acid are discussed in relation to some of the fusidic acid resistant mutations. CI - Copyright 2000 Academic Press. FAU - Laurberg, M AU - Laurberg M AD - Department of Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, Lund, SE-221 00, Sweden. FAU - Kristensen, O AU - Kristensen O FAU - Martemyanov, K AU - Martemyanov K FAU - Gudkov, A T AU - Gudkov AT FAU - Nagaev, I AU - Nagaev I FAU - Hughes, D AU - Hughes D FAU - Liljas, A AU - Liljas A LA - eng SI - PDB/1FNM PT - Journal Article PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Peptide Elongation Factor G) RN - 146-91-8 (Guanosine Diphosphate) RN - 59XE10C19C (Fusidic Acid) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Amino Acid Substitution/*genetics MH - Binding Sites MH - Conserved Sequence MH - Crystallography, X-Ray MH - Drug Resistance, Microbial MH - Fusidic Acid/metabolism MH - Guanosine Diphosphate/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Peptide Elongation Factor G/*chemistry/genetics/*metabolism MH - Point Mutation/*genetics MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Thermus thermophilus/*chemistry/genetics EDAT- 2000/10/31 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/10/31 11:00 AID - 10.1006/jmbi.2000.4168 [doi] AID - S0022-2836(00)94168-8 [pii] PST - ppublish SO - J Mol Biol. 2000 Nov 3;303(4):593-603. PMID- 10050037 OWN - NLM STAT- MEDLINE DA - 19990625 DCOM- 19990625 LR - 20071219 IS - 0021-924X (Print) IS - 0021-924X (Linking) VI - 125 IP - 3 DP - 1999 Mar TI - Resonance assignments, solution structure, and backbone dynamics of the DNA- and RPA-binding domain of human repair factor XPA. PG - 495-506 AB - XPA is involved in the damage recognition step of nucleotide excision repair (NER). XPA binds to other repair factors, and acts as a key element in NER complex formation. The central domain of human repair factor XPA (residues Met98 to Phe219) is responsible for the preferential binding to damaged DNA and to replication protein A (RPA). The domain consists of a zinc-containing subdomain with a compact globular structure and a C-terminal subdomain with a positively charged cleft in a novel alpha/beta structure. The resonance assignments and backbone dynamics of the central domain of human XPA were studied by multidimensional heteronuclear NMR methods. 15N relaxation data were obtained at two static magnetic fields, and analyzed by means of the model-free formalism under the assumption of isotropic or anisotropic rotational diffusion. In addition, exchange contributions were estimated by analysis of the spectral density function at zero frequency. The results show that the domain exhibits a rotational diffusion anisotropy (Dparallel/Dperpendicular) of 1.38, and that most of the flexible regions exist on the DNA binding surface in the cleft in the C-terminal subdomain. This flexibility may be involved in the interactions of XPA with various kinds of damaged DNA. FAU - Ikegami, T AU - Ikegami T AD - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0101, Japan. FAU - Kuraoka, I AU - Kuraoka I FAU - Saijo, M AU - Saijo M FAU - Kodo, N AU - Kodo N FAU - Kyogoku, Y AU - Kyogoku Y FAU - Morikawa, K AU - Morikawa K FAU - Tanaka, K AU - Tanaka K FAU - Shirakawa, M AU - Shirakawa M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - JAPAN TA - J Biochem JT - Journal of biochemistry JID - 0376600 RN - 0 (DNA-Binding Proteins) RN - 0 (RPA1 protein, human) RN - 0 (Replication Protein A) RN - 0 (XPA protein, human) RN - 0 (Xeroderma Pigmentosum Group A Protein) RN - 9007-49-2 (DNA) SB - IM MH - Binding Sites MH - DNA/*metabolism MH - DNA Repair MH - DNA-Binding Proteins/*chemistry/genetics/*metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Protein Binding MH - Protein Conformation MH - Replication Protein A MH - Xeroderma Pigmentosum MH - Xeroderma Pigmentosum Group A Protein MH - Zinc Fingers EDAT- 1999/03/02 MHDA- 1999/03/02 00:01 CRDT- 1999/03/02 00:00 PST - ppublish SO - J Biochem. 1999 Mar;125(3):495-506. PMID- 12146968 OWN - NLM STAT- MEDLINE DA - 20020730 DCOM- 20020905 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 41 IP - 31 DP - 2002 Aug 6 TI - N-terminal truncations of manganese stabilizing protein identify two amino acid sequences required for binding of the eukaryotic protein to photosystem II and reveal the absence of one binding-related sequence in cyanobacteria. PG - 10038-45 AB - Manganese stabilizing protein (MSP) is an intrinsically disordered extrinsic subunit of photosystem II that regulates the stability and kinetic performance of the tetranuclear manganese cluster that oxidizes water to oxygen. An earlier study showed that deletion of the (1)E-(3)G domain of MSP caused no loss of activity reconstitution, whereas deletion of the (4)K-(10)E domain reduced binding of the protein from 2 to 1 mol of MSP/mol of photosystem II and lowered activity reconstitution to about 50% of the control value [Popelkova et al. (2002) Biochemistry 41, 2702-2711]. In this work we present evidence that deletion of 13 or 14 amino acid residues from the MSP N-terminus (mutants DeltaS13M and DeltaK14M) does not interfere either with functional binding of one copy of MSP to photosystem II or with reconstitution of oxygen evolution activity to 50% of the control level. Both of these mutants exhibit nonspecific binding to photosystem II at higher protein concentrations. Truncation of the MSP sequence by 18 amino acids (mutant DeltaE18M), however, causes a loss of protein binding and activity reconstitution. This result demonstrates that the N-terminal domain (15)T-(18)E is required for binding of at least one copy of MSP to photosystem II. Analyses of CD spectra reveal changes in the structure of DeltaE18M (loss of beta-sheet, gain of unordered structure). Use of the information gained from these experiments in analyses of N-terminal sequences of MSP from a number of species indicates that higher plants and algae possess two recognition domains that are required for MSP binding to PSII, whereas cyanobacteria lack the first N-terminal domain found in eukaryotes. This may explain the absence of a second copy of MSP in the crystal structure of PSII from Synechococcus elongatus [Zouni et al. (2001) Nature 409, 739-743]. FAU - Popelkova, Hana AU - Popelkova H AD - Department of Molecular, Cellular, and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109-1048, USA. FAU - Im, Michael M AU - Im MM FAU - Yocum, Charles F AU - Yocum CF LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA Primers) RN - 0 (Photosynthetic Reaction Center Complex Proteins) RN - 0 (Photosystem II Protein Complex) RN - 0 (Proteins) RN - 0 (photosystem II manganese-stabilizing protein) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Cyanobacteria/*metabolism MH - DNA Primers MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Photosynthetic Reaction Center Complex Proteins/*metabolism MH - *Photosystem II Protein Complex MH - Protein Binding MH - Protein Conformation MH - Proteins/chemistry/genetics/*metabolism MH - Sequence Homology, Amino Acid EDAT- 2002/07/31 10:00 MHDA- 2002/09/06 10:01 CRDT- 2002/07/31 10:00 AID - bi020228u [pii] PST - ppublish SO - Biochemistry. 2002 Aug 6;41(31):10038-45. PMID- 9707123 OWN - NLM STAT- MEDLINE DA - 19980824 DCOM- 19980824 LR - 20061115 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 394 IP - 6693 DP - 1998 Aug 6 TI - Crystal structure of a small heat-shock protein. PG - 595-9 AB - The principal heat-shock proteins that have chaperone activity (that is, they protect newly made proteins from misfolding) belong to five conserved classes: HSP100, HSP90, HSP70, HSP60 and the small heat-shock proteins (sHSPs). The sHSPs can form large multimeric structures and have a wide range of cellular functions, including endowing cells with thermotolerance in vivo and being able to act as molecular chaperones in vitro; sHSPs do this by forming stable complexes with folding intermediates of their protein substrates. However, there is little information available about these structures or the mechanism by which substrates are protected from thermal denaturation by sHSPs. Here we report the crystal structure of a small heat-shock protein from Methanococcus jannaschii, a hyperthermophilic archaeon. The monomeric folding unit is a composite beta-sandwich in which one of the beta-strands comes from a neighbouring molecule. Twenty-four monomers form a hollow spherical complex of octahedral symmetry, with eight trigonal and six square 'windows'. The sphere has an outer diameter of 120 A and an inner diameter of 65 A. FAU - Kim, K K AU - Kim KK AD - Physical Biosciences Division of the Lawrence Berkeley National Laboratory and the Department of Chemistry, University of California at Berkeley, 94720-5230, USA. FAU - Kim, R AU - Kim R FAU - Kim, S H AU - Kim SH LA - eng SI - PDB/1SHS SI - PDB/R1SHSSF PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Archaeal Proteins) RN - 0 (HSP16.5 protein, Methanococcus jannaschii) RN - 0 (Heat-Shock Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Archaeal Proteins/chemistry MH - Crystallography, X-Ray MH - Heat-Shock Proteins/*chemistry MH - Methanococcus/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Sequence Homology, Amino Acid EDAT- 1998/08/26 02:15 MHDA- 2001/03/23 10:01 CRDT- 1998/08/26 02:15 AID - 10.1038/29106 [doi] PST - ppublish SO - Nature. 1998 Aug 6;394(6693):595-9. PMID- 19244328 OWN - NLM STAT- MEDLINE DA - 20090410 DCOM- 20090506 LR - 20140901 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 83 IP - 9 DP - 2009 May TI - Crystal structure of a novel dimeric form of NS5A domain I protein from hepatitis C virus. PG - 4395-403 LID - 10.1128/JVI.02352-08 [doi] AB - A new protein expression vector design utilizing an N-terminal six-histidine tag and tobacco etch virus protease cleavage site upstream of the hepatitis C virus NS5A sequence has resulted in a more straightforward purification method and improved yields of purified NS5A domain I protein. High-resolution diffracting crystals of NS5A domain I (amino acids 33 to 202) [NS5A(33-202)] were obtained by using detergent additive crystallization screens, leading to the structure of a homodimer which is organized differently from that published previously (T. L. Tellinghuisen, J. Marcotrigiano, and C. M. Rice, Nature 435:374-379, 2005) yet is consistent with a membrane association model for NS5A. The monomer-monomer interface of NS5A(33-202) features an extensive buried surface area involving the most-highly conserved face of each monomer. The two alternate structural forms of domain I now available may be indicative of the multiple roles emerging for NS5A in viral RNA replication and viral particle assembly. FAU - Love, Robert A AU - Love RA AD - Structural Biology Group, Pfizer Global Research and Development, La Jolla Laboratories, San Diego, California 92121, USA. robert.love@pfizer.com FAU - Brodsky, Oleg AU - Brodsky O FAU - Hickey, Michael J AU - Hickey MJ FAU - Wells, Peter A AU - Wells PA FAU - Cronin, Ciaran N AU - Cronin CN LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090225 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Recombinant Proteins) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Crystallography, X-Ray MH - Hepacivirus/*chemistry/genetics/*metabolism MH - Models, Molecular MH - *Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Static Electricity MH - Structural Homology, Protein MH - Viral Nonstructural Proteins/*chemistry/genetics/*metabolism PMC - PMC2668466 OID - NLM: PMC2668466 EDAT- 2009/02/27 09:00 MHDA- 2009/05/07 09:00 CRDT- 2009/02/27 09:00 PHST- 2009/02/25 [aheadofprint] AID - JVI.02352-08 [pii] AID - 10.1128/JVI.02352-08 [doi] PST - ppublish SO - J Virol. 2009 May;83(9):4395-403. doi: 10.1128/JVI.02352-08. Epub 2009 Feb 25. PMID- 6480588 OWN - NLM STAT- MEDLINE DA - 19841114 DCOM- 19841114 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 259 IP - 19 DP - 1984 Oct 10 TI - Characterization of skeletal muscle calsequestrin by 1H NMR spectroscopy. PG - 11876-81 AB - Calsequestrin (Mr = 44,000) is a calcium-binding (KD congruent to 1 mM, congruent to 50 sites/molecule) protein found in the lumen of the sarcoplasmic reticulum of skeletal muscle. The 1H NMR spectrum of calsequestrin in the calcium-free form is presented and is characteristic of a protein largely in the random coil configuration. A number of peaks in the aromatic region have been assigned based on their chemical shifts and sensitivity to pH. The interaction of this protein with Ca2+ and K+ was studied by 1H NMR. Potassium ion binding to calsequestrin caused broadening and concomitant loss of intensity in both the aromatic and aliphatic regions of the spectrum. Calcium ion binding caused similar effects but at much lower metal ion concentrations. It was found that the binding of Ca2+ to calsequestrin was cooperative (Hill coefficient n = 2.9 +/- 0.2) with a dissociation constant of 0.25 +/- 0.06 mM in the absence of K+. In contrast, K+ showed binding to a single class of independent sites (KD = 0.20 +/- 0.04 M). Calcium binding was also studied by circular dichroism at protein concentrations similar to the NMR experiments. The binding profile and cooperativity (n = 2.0 +/- 0.1, KD = 0.19 +/- 0.04 mM) were in agreement with the 1H NMR results. Circular dichroism studies performed at low protein concentrations to reduce the possible effect of calcium binding on the concentration of free calcium gave similar values of n = 2.42 +/- 0.14 and KD = 0.21 +/- 0.005 mM. This cooperativity was also observed in the presence of 100 mM KCl although the affinity for calcium has been significantly reduced (n = 1.65 +/- 0.09, KD = 0.87 +/- 0.036 mM). In view of the large number of calcium binding sites in calsequestrin, these small Hill coefficients show that calcium binding to calsequestrin is only mildly cooperative. FAU - Aaron, B M AU - Aaron BM FAU - Oikawa, K AU - Oikawa K FAU - Reithmeier, R A AU - Reithmeier RA FAU - Sykes, B D AU - Sykes BD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Calsequestrin) RN - 0 (Muscle Proteins) RN - 660YQ98I10 (Potassium Chloride) RN - M4I0D6VV5M (Calcium Chloride) SB - IM MH - Animals MH - Calcium Chloride MH - *Calsequestrin MH - Circular Dichroism MH - Hydrogen-Ion Concentration MH - Magnetic Resonance Spectroscopy MH - *Muscle Proteins MH - Muscles/*analysis MH - Potassium Chloride MH - Rabbits EDAT- 1984/10/10 MHDA- 1984/10/10 00:01 CRDT- 1984/10/10 00:00 PST - ppublish SO - J Biol Chem. 1984 Oct 10;259(19):11876-81. PMID- 24236406 OWN - NLM STAT- MEDLINE DA - 20131211 DCOM- 20140723 LR - 20141112 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 49 DP - 2013 Dec 11 TI - Naturally split inteins assemble through a "capture and collapse" mechanism. PG - 18673-81 LID - 10.1021/ja4104364 [doi] AB - Split inteins are a class of naturally occurring proteins that carry out protein splicing in trans. The chemical mechanism of protein trans-splicing is well-understood and has been exploited to develop several powerful protein engineering technologies. Split intein chemistry is preceded by efficient molecular recognition between two protomers that become intertwined in their bound state. It is currently unclear how this unique topology is achieved upon fragment association. Using biophysical techniques in conjunction with protein engineering methods, including segmental isotopic labeling, we show that one split intein fragment is partly folded, while the other is completely disordered. These polypeptides capture each other through their disordered regions and form an ordered intermediate with native-like structure at their interface. This intermediate then collapses into the canonical intein fold. This mechanism provides insight into the evolutionary constraints on split intein assembly and should enhance the development of split intein-based technologies. FAU - Shah, Neel H AU - Shah NH AD - Department of Chemistry, Princeton University , Frick Laboratory, Princeton, New Jersey 08544, United States. FAU - Eryilmaz, Ertan AU - Eryilmaz E FAU - Cowburn, David AU - Cowburn D FAU - Muir, Tom W AU - Muir TW LA - eng GR - GM086868/GM/NIGMS NIH HHS/United States GR - P41-GM066354/GM/NIGMS NIH HHS/United States GR - R37 GM086868/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20131123 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 SB - IM MH - *Inteins MH - Models, Molecular MH - Protein Conformation MH - Static Electricity PMC - PMC3865799 OID - NLM: PMC3865799 EDAT- 2013/11/19 06:00 MHDA- 2014/07/24 06:00 CRDT- 2013/11/19 06:00 PHST- 2013/11/23 [aheadofprint] AID - 10.1021/ja4104364 [doi] PST - ppublish SO - J Am Chem Soc. 2013 Dec 11;135(49):18673-81. doi: 10.1021/ja4104364. Epub 2013 Nov 23. PMID- 23189168 OWN - NLM STAT- MEDLINE DA - 20121128 DCOM- 20130516 LR - 20141104 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 11 DP - 2012 TI - Effects of molecular crowding on the dynamics of intrinsically disordered proteins. PG - e49876 LID - 10.1371/journal.pone.0049876 [doi] AB - Inside cells, the concentration of macromolecules can reach up to 400 g/L. In such crowded environments, proteins are expected to behave differently than in vitro. It has been shown that the stability and the folding rate of a globular protein can be altered by the excluded volume effect produced by a high density of macromolecules. However, macromolecular crowding effects on intrinsically disordered proteins (IDPs) are less explored. These proteins can be extremely dynamic and potentially sample a wide ensemble of conformations under non-denaturing conditions. The dynamic properties of IDPs are intimately related to the timescale of conformational exchange within the ensemble, which govern target recognition and how these proteins function. In this work, we investigated the macromolecular crowding effects on the dynamics of several IDPs by measuring the NMR spin relaxation parameters of three disordered proteins (ProTalpha, TC1, and alpha-synuclein) with different extents of residual structures. To aid the interpretation of experimental results, we also performed an MD simulation of ProTalpha. Based on the MD analysis, a simple model to correlate the observed changes in relaxation rates to the alteration in protein motions under crowding conditions was proposed. Our results show that 1) IDPs remain at least partially disordered despite the presence of high concentration of other macromolecules, 2) the crowded environment has differential effects on the conformational propensity of distinct regions of an IDP, which may lead to selective stabilization of certain target-binding motifs, and 3) the segmental motions of IDPs on the nanosecond timescale are retained under crowded conditions. These findings strongly suggest that IDPs function as dynamic structural ensembles in cellular environments. FAU - Cino, Elio A AU - Cino EA AD - Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada. FAU - Karttunen, Mikko AU - Karttunen M FAU - Choy, Wing-Yiu AU - Choy WY LA - eng GR - MOP 74679/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121126 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Proteins) SB - IM MH - Humans MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Folding MH - Protein Structure, Secondary MH - Proteins/*chemistry/metabolism PMC - PMC3506533 OID - NLM: PMC3506533 EDAT- 2012/11/29 06:00 MHDA- 2013/05/17 06:00 CRDT- 2012/11/29 06:00 PHST- 2012/07/19 [received] PHST- 2012/10/15 [accepted] PHST- 2012/11/26 [epublish] AID - 10.1371/journal.pone.0049876 [doi] AID - PONE-D-12-21815 [pii] PST - ppublish SO - PLoS One. 2012;7(11):e49876. doi: 10.1371/journal.pone.0049876. Epub 2012 Nov 26. PMID- 15883183 OWN - NLM STAT- MEDLINE DA - 20050602 DCOM- 20050919 LR - 20140606 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 14 IP - 6 DP - 2005 Jun TI - p25alpha is flexible but natively folded and binds tubulin with oligomeric stoichiometry. PG - 1396-409 AB - p25alpha is a 219-residue protein which stimulates aberrant tubulin polymerization and is implicated in a variety of other functions. The protein has unusual secondary structure involving significant amounts of random coil, and binding to microtubules is accompanied by a large structural change, suggesting a high degree of plasticity. p25alpha has been proposed to be natively unfolded, so that folding is coupled to interaction with its physiological partners. Here we show that recombinant human p25alpha is folded under physiological conditions, since it has a well structured and solvent-sequestered aromatic environment and considerable chemical shift dispersion of amide and aliphatic protons. With increasing urea concentrations, p25alpha undergoes clear spectral changes suggesting significant loss of structure. p25alpha unfolds cooperatively in urea according to a simple two-state transition with a stability in water of approximately 5 kcal/mol. The protein behaves as a monomer and refolds with a transient on-pathway folding intermediate. However, high sensitivity to proteolytic attack and abnormal gel filtration migration behavior suggests a relatively extended structure, possibly organized in distinct domains. A deletion mutant of p25alpha lacking residues 3-43 also unfolds cooperatively and with similar stability, suggesting that the N-terminal region is largely unstructured. Both proteins undergo significant loss of structure when bound to monomeric tubulin. The stoichiometry of binding is estimated to be 3-4 molecules of tubulin per p25alpha and is not significantly affected by the deletion of residues 3-43. In conclusion, we dismiss the proposal that p25alpha is natively unfolded, although the protein is relatively flexible. This flexibility may be linked to its tubulin-binding properties. FAU - Otzen, Daniel E AU - Otzen DE AD - Dept. of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark. dao@bio.aau.dk. FAU - Lundvig, Ditte M S AU - Lundvig DM FAU - Wimmer, Reinhard AU - Wimmer R FAU - Nielsen, Lotte H AU - Nielsen LH FAU - Pedersen, Jakob R AU - Pedersen JR FAU - Jensen, Poul H AU - Jensen PH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050509 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Nerve Tissue Proteins) RN - 0 (Tubulin) RN - 0 (p25 protein, human) SB - IM MH - Humans MH - Microtubules/chemistry/metabolism MH - Nerve Tissue Proteins/chemistry/metabolism MH - Protein Binding MH - *Protein Folding MH - Tubulin/*chemistry/metabolism PMC - PMC2253386 OID - NLM: PMC2253386 EDAT- 2005/05/11 09:00 MHDA- 2005/09/20 09:00 CRDT- 2005/05/11 09:00 PHST- 2005/05/09 [aheadofprint] AID - ps.041285605 [pii] AID - 10.1110/ps.041285605 [doi] PST - ppublish SO - Protein Sci. 2005 Jun;14(6):1396-409. Epub 2005 May 9. PMID- 16228284 OWN - NLM STAT- MEDLINE DA - 20060126 DCOM- 20060925 LR - 20061115 IS - 1021-7770 (Print) IS - 1021-7770 (Linking) VI - 13 IP - 1 DP - 2006 Jan TI - Modular organization of SARS coronavirus nucleocapsid protein. PG - 59-72 AB - The SARS-CoV nucleocapsid (N) protein is a major antigen in severe acute respiratory syndrome. It binds to the viral RNA genome and forms the ribonucleoprotein core. The SARS-CoV N protein has also been suggested to be involved in other important functions in the viral life cycle. Here we show that the N protein consists of two non-interacting structural domains, the N-terminal RNA-binding domain (RBD) (residues 45-181) and the C-terminal dimerization domain (residues 248-365) (DD), surrounded by flexible linkers. The C-terminal domain exists exclusively as a dimer in solution. The flexible linkers are intrinsically disordered and represent potential interaction sites with other protein and protein-RNA partners. Bioinformatics reveal that other coronavirus N proteins could share the same modular organization. This study provides information on the domain structure partition of SARS-CoV N protein and insights into the differing roles of structured and disordered regions in coronavirus nucleocapsid proteins. FAU - Chang, Chung-ke AU - Chang CK AD - Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, Taiwan, ROC. FAU - Sue, Shih-Che AU - Sue SC FAU - Yu, Tsan-hung AU - Yu TH FAU - Hsieh, Chiu-Min AU - Hsieh CM FAU - Tsai, Cheng-Kun AU - Tsai CK FAU - Chiang, Yen-Chieh AU - Chiang YC FAU - Lee, Shin-jye AU - Lee SJ FAU - Hsiao, Hsin-hao AU - Hsiao HH FAU - Wu, Wen-Jin AU - Wu WJ FAU - Chang, Wei-Lun AU - Chang WL FAU - Lin, Chun-Hung AU - Lin CH FAU - Huang, Tai-huang AU - Huang TH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051014 PL - Netherlands TA - J Biomed Sci JT - Journal of biomedical science JID - 9421567 RN - 0 (Antigens, Viral) RN - 0 (Nucleocapsid Proteins) RN - 0 (Peptide Fragments) RN - 0 (nucleocapsid protein, Coronavirus) SB - IM MH - Amino Acid Sequence MH - Animals MH - Antigens, Viral/*chemistry/genetics MH - Humans MH - Molecular Sequence Data MH - Nucleocapsid Proteins/*chemistry/genetics MH - Peptide Fragments/chemistry/genetics MH - *Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Sequence Homology, Amino Acid EDAT- 2005/10/18 09:00 MHDA- 2006/09/26 09:00 CRDT- 2005/10/18 09:00 PHST- 2005/06/23 [received] PHST- 2005/09/12 [accepted] PHST- 2005/10/14 [aheadofprint] AID - 10.1007/s11373-005-9035-9 [doi] PST - ppublish SO - J Biomed Sci. 2006 Jan;13(1):59-72. Epub 2005 Oct 14. PMID- 2122519 OWN - NLM STAT- MEDLINE DA - 19901206 DCOM- 19901206 LR - 20071114 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 250 IP - 4980 DP - 1990 Oct 26 TI - Biophysical and molecular mechanisms of Shaker potassium channel inactivation. PG - 533-8 AB - The potassium channels encoded by the Drosophila Shaker gene activate and inactivate rapidly when the membrane potential becomes more positive. Site-directed mutagenesis and single-channel patch-clamp recording were used to explore the molecular transitions that underlie inactivation in Shaker potassium channels expressed in Xenopus oocytes. A region near the amino terminus with an important role in inactivation has now been identified. The results suggest a model where this region forms a cytoplasmic domain that interacts with the open channel to cause inactivation. FAU - Hoshi, T AU - Hoshi T AD - Department of Molecular and Cellular Physiology, Stanford University, School of Medicine, CA 94305. FAU - Zagotta, W N AU - Zagotta WN FAU - Aldrich, R W AU - Aldrich RW LA - eng GR - NS07158/NS/NINDS NIH HHS/United States GR - NS23294/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Potassium Channels) RN - 9007-49-2 (DNA) RN - EC 3.4.21.4 (Trypsin) SB - IM CIN - Science. 1990 Oct 26;250(4980):506-7. PMID: 1700473 GS - Shaker MH - Amino Acid Sequence MH - Animals MH - DNA/genetics MH - Drosophila melanogaster/*genetics MH - Electric Conductivity MH - Ion Channel Gating/drug effects/*physiology MH - Kinetics MH - Membrane Potentials/physiology MH - Molecular Sequence Data MH - Mutagenesis MH - Mutagenesis, Site-Directed MH - Oocytes/metabolism MH - Potassium Channels/genetics/*physiology MH - RNA Splicing MH - Structure-Activity Relationship MH - Trypsin/pharmacology MH - Xenopus EDAT- 1990/10/26 MHDA- 1990/10/26 00:01 CRDT- 1990/10/26 00:00 PST - ppublish SO - Science. 1990 Oct 26;250(4980):533-8. PMID- 24086122 OWN - NLM STAT- MEDLINE DA - 20131002 DCOM- 20140421 LR - 20141112 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 9 IP - 9 DP - 2013 TI - Polycation-pi interactions are a driving force for molecular recognition by an intrinsically disordered oncoprotein family. PG - e1003239 LID - 10.1371/journal.pcbi.1003239 [doi] AB - Molecular recognition by intrinsically disordered proteins (IDPs) commonly involves specific localized contacts and target-induced disorder to order transitions. However, some IDPs remain disordered in the bound state, a phenomenon coined "fuzziness", often characterized by IDP polyvalency, sequence-insensitivity and a dynamic ensemble of disordered bound-state conformations. Besides the above general features, specific biophysical models for fuzzy interactions are mostly lacking. The transcriptional activation domain of the Ewing's Sarcoma oncoprotein family (EAD) is an IDP that exhibits many features of fuzziness, with multiple EAD aromatic side chains driving molecular recognition. Considering the prevalent role of cation-pi interactions at various protein-protein interfaces, we hypothesized that EAD-target binding involves polycation- pi contacts between a disordered EAD and basic residues on the target. Herein we evaluated the polycation-pi hypothesis via functional and theoretical interrogation of EAD variants. The experimental effects of a range of EAD sequence variations, including aromatic number, aromatic density and charge perturbations, all support the cation-pi model. Moreover, the activity trends observed are well captured by a coarse-grained EAD chain model and a corresponding analytical model based on interaction between EAD aromatics and surface cations of a generic globular target. EAD-target binding, in the context of pathological Ewing's Sarcoma oncoproteins, is thus seen to be driven by a balance between EAD conformational entropy and favorable EAD-target cation-pi contacts. Such a highly versatile mode of molecular recognition offers a general conceptual framework for promiscuous target recognition by polyvalent IDPs. FAU - Song, Jianhui AU - Song J AD - Departments of Biochemistry, Molecular Genetics, and Physics, University of Toronto, Toronto, Ontario, Canada. FAU - Ng, Sheung Chun AU - Ng SC FAU - Tompa, Peter AU - Tompa P FAU - Lee, Kevin A W AU - Lee KA FAU - Chan, Hue Sun AU - Chan HS LA - eng GR - MOP-84281/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130926 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Oncogene Proteins) RN - 0 (Polyamines) RN - 0 (polycations) SB - IM MH - Intrinsically Disordered Proteins/*chemistry MH - Models, Chemical MH - Oncogene Proteins/*chemistry MH - Polyamines/*chemistry MH - Sarcoma, Ewing/chemistry PMC - PMC3784488 OID - NLM: PMC3784488 EDAT- 2013/10/03 06:00 MHDA- 2014/04/22 06:00 CRDT- 2013/10/03 06:00 PHST- 2013/09 [ecollection] PHST- 2013/06/27 [received] PHST- 2013/08/12 [accepted] PHST- 2013/09/26 [epublish] AID - 10.1371/journal.pcbi.1003239 [doi] AID - PCOMPBIOL-D-13-01151 [pii] PST - ppublish SO - PLoS Comput Biol. 2013;9(9):e1003239. doi: 10.1371/journal.pcbi.1003239. Epub 2013 Sep 26. PMID- 22662273 OWN - NLM STAT- MEDLINE DA - 20120604 DCOM- 20121213 LR - 20141016 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 5 DP - 2012 TI - Effect of spermidine on misfolding and interactions of alpha-synuclein. PG - e38099 LID - 10.1371/journal.pone.0038099 [doi] AB - Alpha-synuclein (alpha-Syn) is a 140 aa presynaptic protein which belongs to a group of natively unfolded proteins that are unstructured in aqueous solutions. The aggregation rate of alpha-Syn is accelerated in the presence of physiological levels of cellular polyamines. Here we applied single molecule AFM force spectroscopy to characterize the effect of spermidine on the very first stages of alpha-Syn aggregation--misfolding and assembly into dimers. Two alpha-Syn variants, the wild-type (WT) protein and A30P, were studied. The two protein molecules were covalently immobilized at the C-terminus, one at the AFM tip and the other on the substrate, and intermolecular interactions between the two molecules were measured by multiple approach-retraction cycles. At conditions close to physiological ones at which alpha-Syn misfolding is a rare event, the addition of spermidine leads to a dramatic increase in the propensity of the WT and mutant proteins to misfold. Importantly, misfolding is characterized by a set of conformations, and A30P changes the misfolding pattern as well as the strength of the intermolecular interactions. Together with the fact that spermidine facilitates late stages of alpha-Syn aggregation, our data demonstrate that spermidine promotes the very early stages of protein aggregation including alpha-Syn misfolding and dimerization. This finding suggests that increased levels of spermidine and potentially other polyamines can initiate the disease-related process of alpha-Syn. FAU - Krasnoslobodtsev, Alexey V AU - Krasnoslobodtsev AV AD - Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, United States of America. FAU - Peng, Jie AU - Peng J FAU - Asiago, Josephat M AU - Asiago JM FAU - Hindupur, Jagadish AU - Hindupur J FAU - Rochet, Jean-Christophe AU - Rochet JC FAU - Lyubchenko, Yuri L AU - Lyubchenko YL LA - eng GR - 1 R01 GM096039-01A1/GM/NIGMS NIH HHS/United States GR - 1P01GM091743-01A1/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120525 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (alpha-Synuclein) RN - U87FK77H25 (Spermidine) SB - IM MH - Humans MH - Microscopy, Atomic Force MH - Protein Folding/drug effects MH - Protein Multimerization/drug effects MH - Spermidine/*pharmacology MH - alpha-Synuclein/*chemistry/metabolism PMC - PMC3360652 OID - NLM: PMC3360652 EDAT- 2012/06/05 06:00 MHDA- 2012/12/14 06:00 CRDT- 2012/06/05 06:00 PHST- 2012/02/20 [received] PHST- 2012/05/03 [accepted] PHST- 2012/05/25 [epublish] AID - 10.1371/journal.pone.0038099 [doi] AID - PONE-D-12-06187 [pii] PST - ppublish SO - PLoS One. 2012;7(5):e38099. doi: 10.1371/journal.pone.0038099. Epub 2012 May 25. PMID- 17585875 OWN - NLM STAT- MEDLINE DA - 20070703 DCOM- 20070905 IS - 0006-291X (Print) IS - 0006-291X (Linking) VI - 360 IP - 1 DP - 2007 Aug 17 TI - Nogo-B receptor possesses an intrinsically unstructured ectodomain and a partially folded cytoplasmic domain. PG - 128-34 AB - RTN4/Nogo proteins containing three isoforms have been implicated in a large and diverse spectrum of biological functions. By contrast, only two functional receptors were known for them, namely NgR binding the 66-residue ectodomain shared by all three Nogos and NgBR specifically binding Nogo-B. The 297-residue NgBR was recently identified to be essential for stimulating chemotaxis and morphogenesis of endothelial cells but its structural property still remains completely unknown. In the present study, we expressed and subsequently conducted bioinformatics, CD and NMR characterization of NgBR and its two dissected domains. Very surprisingly, our results indicate that the NgBR ectodomain is intrinsically unstructured without both secondary and tertiary structures while the cytoplasmic domain is only partially folded with secondary structures but without a tight tertiary packing. Therefore, NgBR is a very rare example showing that the entire ectodomain of a transmembrane receptor could be predominantly disordered and the results presented here may bear important implications in understanding NgBR functions in the future. FAU - Li, Minfen AU - Li M AD - Department of Biological Sciences, Faculty of Science, Yong Loo Lin School of Medicine and National University of Singapore, 10 Kent Ridge Crescent, 119260, Singapore. FAU - Song, Jianxing AU - Song J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070613 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Nogo-B receptor, mouse) RN - 0 (Receptors, Cell Surface) SB - IM MH - Amino Acid Sequence MH - Animals MH - Mice MH - Molecular Sequence Data MH - NIH 3T3 Cells MH - Protein Folding MH - Protein Structure, Tertiary MH - Receptors, Cell Surface/*chemistry/*metabolism/ultrastructure EDAT- 2007/06/26 09:00 MHDA- 2007/09/06 09:00 CRDT- 2007/06/26 09:00 PHST- 2007/05/26 [received] PHST- 2007/06/05 [accepted] PHST- 2007/06/13 [aheadofprint] AID - S0006-291X(07)01233-8 [pii] AID - 10.1016/j.bbrc.2007.06.031 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2007 Aug 17;360(1):128-34. Epub 2007 Jun 13. PMID- 8243650 OWN - NLM STAT- MEDLINE DA - 19931230 DCOM- 19931230 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 334 IP - 3 DP - 1993 Nov 22 TI - Nature of the pH-induced conformational changes and exposure of the C-terminal region of chromogranin A. PG - 373-7 AB - Chromogranin A is known to undergo pH induced conformational changes, and the difference in conformation is supposed to be responsible for the difference in Ca2+ binding property. To gain insight regarding the overall structure and the nature of pH-induced conformational changes of chromogranin A, limited trypsin digestions were carried out at pH 5.5 and pH 7.5. The resulting fragments were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the amino acid sequences of the tryptic fragments were determined. From these analyses it was shown that the chromogranin A structure consists of an N-terminal compact core region and a rather loosely organized C-terminal region and that the change of pH from 7.5 to 5.5 loosened the overall structure of chromogranin A, exposing the C-terminal region. Since the conserved C-terminal region (residues 407-431) was shown to exist in monomer-dimer and monomer-tetramer equilibria at pH 7.5 and 5.5, respectively, the conformational changes of the region at pH 7.5 and 5.5 were studied by circular dichroism spectroscopy using a synthetic peptide representing the conserved C-terminal region. When the pH was changed from 7.5 to 5.5, the coil structure of the C-terminal peptide decreased with an accompanying increase of alpha-helicity. FAU - Yoo, S H AU - Yoo SH AD - Laboratory of Cellular Biology, National Institute of Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892. FAU - Ferretti, J A AU - Ferretti JA LA - eng PT - Journal Article PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Chromogranin A) RN - 0 (Chromogranins) RN - EC 3.4.21.4 (Trypsin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cattle MH - Chromogranin A MH - Chromogranins/*chemistry MH - Circular Dichroism MH - Hydrogen-Ion Concentration MH - Molecular Sequence Data MH - Protein Conformation MH - Trypsin EDAT- 1993/11/22 MHDA- 1993/11/22 00:01 CRDT- 1993/11/22 00:00 AID - 0014-5793(93)80715-7 [pii] PST - ppublish SO - FEBS Lett. 1993 Nov 22;334(3):373-7. PMID- 24947516 OWN - NLM STAT- MEDLINE DA - 20140802 DCOM- 20141215 LR - 20150401 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 289 IP - 31 DP - 2014 Aug 1 TI - Multiple interactions of the intrinsically disordered region between the helicase and nuclease domains of the archaeal Hef protein. PG - 21627-39 LID - 10.1074/jbc.M114.554998 [doi] AB - Hef is an archaeal protein that probably functions mainly in stalled replication fork repair. The presence of an unstructured region was predicted between the two distinct domains of the Hef protein. We analyzed the interdomain region of Thermococcus kodakarensis Hef and demonstrated its disordered structure by CD, NMR, and high speed atomic force microscopy (AFM). To investigate the functions of this intrinsically disordered region (IDR), we screened for proteins interacting with the IDR of Hef by a yeast two-hybrid method, and 10 candidate proteins were obtained. We found that PCNA1 and a RecJ-like protein specifically bind to the IDR in vitro. These results suggested that the Hef protein interacts with several different proteins that work together in the pathways downstream from stalled replication fork repair by converting the IDR structure depending on the partner protein. CI - (c) 2014 by The American Society for Biochemistry and Molecular Biology, Inc. FAU - Ishino, Sonoko AU - Ishino S AD - From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, and Faculty of Agriculture, Kyushu University, Fukuoka 812-8581. FAU - Yamagami, Takeshi AU - Yamagami T AD - From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, and Faculty of Agriculture, Kyushu University, Fukuoka 812-8581. FAU - Kitamura, Makoto AU - Kitamura M AD - From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, and Faculty of Agriculture, Kyushu University, Fukuoka 812-8581. FAU - Kodera, Noriyuki AU - Kodera N AD - the Bio-AFM Frontier Research Center and Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa 920-1192, and. FAU - Mori, Tetsuya AU - Mori T AD - the Bio-AFM Frontier Research Center and Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa 920-1192, and. FAU - Sugiyama, Shyogo AU - Sugiyama S AD - the Bio-AFM Frontier Research Center and Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa 920-1192, and. FAU - Ando, Toshio AU - Ando T AD - the Bio-AFM Frontier Research Center and Department of Physics, College of Science and Engineering, Kanazawa University, Kanazawa 920-1192, and. FAU - Goda, Natsuko AU - Goda N AD - the Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan. FAU - Tenno, Takeshi AU - Tenno T AD - the Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan. FAU - Hiroaki, Hidekazu AU - Hiroaki H AD - the Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya 464-8601, Japan. FAU - Ishino, Yoshizumi AU - Ishino Y AD - From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, and Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, ishino@agr.kyushu-u.ac.jp. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140619 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Archaeal Proteins) RN - 0 (DNA Primers) RN - 0 (Intrinsically Disordered Proteins) RN - EC 3.1.- (Endonucleases) RN - EC 3.6.4.- (DNA Helicases) SB - IM MH - Archaeal Proteins/*metabolism MH - Base Sequence MH - Circular Dichroism MH - DNA Helicases/*metabolism MH - DNA Primers MH - DNA Repair MH - Endonucleases/*metabolism MH - Intrinsically Disordered Proteins/*metabolism MH - Microscopy, Atomic Force MH - Nuclear Magnetic Resonance, Biomolecular MH - Polymerase Chain Reaction MH - Protein Binding MH - Thermococcus/*metabolism MH - Two-Hybrid System Techniques PMC - PMC4118122 OID - NLM: PMC4118122 [Available on 08/01/15] OTO - NOTNLM OT - Archaea OT - DNA Repair OT - DNA Replication OT - Extremophiles OT - Fancni Anemia OT - Intrinsically Disordered Protein OT - Protein-Protein Interaction OT - Stalled Replication Fork EDAT- 2014/06/21 06:00 MHDA- 2014/12/17 06:00 CRDT- 2014/06/21 06:00 PMCR- 2015/08/01 00:00 PHST- 2014/06/19 [aheadofprint] AID - M114.554998 [pii] AID - 10.1074/jbc.M114.554998 [doi] PST - ppublish SO - J Biol Chem. 2014 Aug 1;289(31):21627-39. doi: 10.1074/jbc.M114.554998. Epub 2014 Jun 19. PMID- 8142351 OWN - NLM STAT- MEDLINE DA - 19940502 DCOM- 19940502 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 33 IP - 12 DP - 1994 Mar 29 TI - 1H, 13C, 15N nuclear magnetic resonance backbone assignments and secondary structure of human calcineurin B. PG - 3540-7 AB - The calmodulin- and calcium-stimulated protein phosphatase calcineurin, PP2B, consists of two subunits: calcineurin B, which binds Ca2+, and calcineurin A, which contains the catalytic site and a calmodulin binding site. Heteronuclear 3D and 4D NMR experiments were carried out on a recombinant human calcineurin B which is a 170-residue protein of molecular mass 19.3 kDa, uniformly labeled with 15N and 13C. The nondenaturing detergent CHAPS was used to obtain a monomeric form of calcineurin B. Three-dimensional triple resonance experiments yielded complete sequential assignment of the backbone nuclei (1H, 13C, and 15N). This assignment was verified by a 4D HN(COCA)NH experiment carried out with 50% randomly deuteriated and uniformly 15N- and 13C-enriched calcineurin B. The secondary structure of calcineurin B has been determined on the basis of the 13C alpha and 13C beta secondary chemical shifts, J(HNH alpha) couplings, and NOE connectivities obtained from 3D 15N-separated and 4D 13C/15N-separated NOESY spectra. Calcineurin B has eight helices distributed in four EF-hand, helix-loop-helix [Kretsinger, R. H. (1980) CRC Crit. Rev. Biochem. 8, 119-174] calcium binding domains. The secondary structure of calcineurin B is highly homologous to that of calmodulin. In comparison to calmodulin, helices B and C are shorter while helix G is considerably longer. As was observed for calmodulin in solution, calcineurin B does not have a single long central helix; rather, helices D and E are separated by a six-residue sequence in a flexible nonhelical conformation. FAU - Anglister, J AU - Anglister J AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892. FAU - Grzesiek, S AU - Grzesiek S FAU - Wang, A C AU - Wang AC FAU - Ren, H AU - Ren H FAU - Klee, C B AU - Klee CB FAU - Bax, A AU - Bax A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Calmodulin-Binding Proteins) RN - 0 (Cholic Acids) RN - 0 (Macromolecular Substances) RN - 75621-03-3 (3-((3-cholamidopropyl)dimethylammonium)-1-propanesulfonate) RN - 7YNJ3PO35Z (Hydrogen) RN - AR09D82C7G (Deuterium) RN - EC 3.1.3.16 (Calcineurin) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Binding Sites MH - Calcineurin MH - Calcium/metabolism MH - Calmodulin-Binding Proteins/*chemistry MH - Cholic Acids MH - Deuterium MH - Humans MH - Hydrogen MH - Macromolecular Substances MH - *Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Phosphoprotein Phosphatases/*chemistry MH - Protein Structure, Secondary EDAT- 1994/03/29 MHDA- 1994/03/29 00:01 CRDT- 1994/03/29 00:00 PST - ppublish SO - Biochemistry. 1994 Mar 29;33(12):3540-7. PMID- 18004752 OWN - NLM STAT- MEDLINE DA - 20080429 DCOM- 20080815 LR - 20131121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 71 IP - 3 DP - 2008 May 15 TI - Intrinsically disordered protein from a pathogenic mesophile Mycobacterium tuberculosis adopts structured conformation at high temperature. PG - 1123-33 AB - Compared to eukaryotes, the occurrence of "intrinsically disordered" or "natively unfolded" proteins in prokaryotes has not been explored extensively. Here, we report the occurrence of an intrinsically disordered protein from the mesophilic human pathogen Mycobacterium tuberculosis. The Histidine-tagged recombinant Rv3221c biotin-binding protein is intrinsically disordered at ambient and physiological growth temperatures as revealed by circular dichroism and Fourier transform infrared (FTIR) spectroscopic studies. However, an increase in temperature induces a transition from disordered to structured state with a folding temperature of approximately 53 degrees C. Addition of a structure inducing solvent trifluoroethanol (TFE) causes the protein to fold at lower temperatures suggesting that TFE fosters hydrophobic interactions, which drives protein folding. Differential Scanning Calorimetry studies revealed that folding is endothermic and the transition from a disordered to structured state is continuous (higher-order), implying existence of intermediates during folding process. Secondary structure analysis revealed that the protein has propensity to form beta-sheets. This is in conformity with FTIR spectrum that showed an absorption peak at wave number of 1636 cm(-1), indicative of disordered beta-sheet conformation in the native state. These data suggest that although Rv3221c may be disordered under ambient or optimal growth temperature conditions, it has the potential to fold into ordered structure at high temperature driven by increased hydrophobic interactions. In contrast to the generally known behavior of other intrinsically disordered proteins folding at high temperature, Rv3221c does not appear to oligomerize or aggregate as revealed through numerous experiments including Congo red binding, Thioflavin T-binding, turbidity measurements, and examining molar ellipticity as a function of protein concentration. The amino acid composition of Rv3221c reveals that it has 24% charged and 54.9% hydrophobic amino acid residues. In this respect, this protein, although belonging to the class of intrinsically disordered proteins, has distinct features. The intrinsically disordered state and the biotin-binding feature of this protein suggest that it may participate in many biochemical processes requiring biotin as a cofactor and adopt suitable conformations upon binding other folded targets. CI - 2007 Wiley-Liss, Inc. FAU - Kumar, Niti AU - Kumar N AD - Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India. FAU - Shukla, Swati AU - Shukla S FAU - Kumar, Sanjiv AU - Kumar S FAU - Suryawanshi, Anju AU - Suryawanshi A FAU - Chaudhry, Uma AU - Chaudhry U FAU - Ramachandran, Srinivasan AU - Ramachandran S FAU - Maiti, Souvik AU - Maiti S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Bacterial Proteins) RN - 4QD397987E (Histidine) RN - 6SO6U10H04 (Biotin) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/genetics/metabolism/*physiology MH - Biotin/chemistry/metabolism MH - Body Temperature MH - Histidine/chemistry MH - *Hot Temperature MH - Molecular Sequence Data MH - Mycobacterium tuberculosis/*chemistry/genetics/pathogenicity/*physiology MH - Protein Binding/genetics MH - Protein Conformation MH - Protein Folding EDAT- 2007/11/16 09:00 MHDA- 2008/08/16 09:00 CRDT- 2007/11/16 09:00 AID - 10.1002/prot.21798 [doi] PST - ppublish SO - Proteins. 2008 May 15;71(3):1123-33. PMID- 18456828 OWN - NLM STAT- MEDLINE DA - 20080728 DCOM- 20080828 LR - 20140903 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 95 IP - 4 DP - 2008 Aug TI - Biophysical characterization of the unstructured cytoplasmic domain of the human neuronal adhesion protein neuroligin 3. PG - 1928-44 LID - 10.1529/biophysj.107.126995 [doi] AB - Cholinesterase-like adhesion molecules (CLAMs) are a family of neuronal cell adhesion molecules with important roles in synaptogenesis, and in maintaining structural and functional integrity of the nervous system. Our earlier study on the cytoplasmic domain of one of these CLAMs, the Drosophila protein, gliotactin, showed that it is intrinsically unstructured in vitro. Bioinformatic analysis suggested that the cytoplasmic domains of other CLAMs are also intrinsically unstructured, even though they bear no sequence homology to each other or to any known protein. In this study, we overexpress and purify the cytoplasmic domain of human neuroligin 3, notwithstanding its high sensitivity to the Escherichia coli endogenous proteases that cause its rapid degradation. Using bioinformatic analysis, sensitivity to proteases, size exclusion chromatography, fluorescence correlation spectroscopy, analytical ultracentrifugation, small angle x-ray scattering, circular dichroism, electron spin resonance, and nuclear magnetic resonance, we show that the cytoplasmic domain of human neuroligin 3 is intrinsically unstructured. However, several of these techniques indicate that it is not fully extended, but becomes significantly more extended under denaturing conditions. FAU - Paz, Aviv AU - Paz A AD - Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel. FAU - Zeev-Ben-Mordehai, Tzviya AU - Zeev-Ben-Mordehai T FAU - Lundqvist, Martin AU - Lundqvist M FAU - Sherman, Eilon AU - Sherman E FAU - Mylonas, Efstratios AU - Mylonas E FAU - Weiner, Lev AU - Weiner L FAU - Haran, Gilad AU - Haran G FAU - Svergun, Dmitri I AU - Svergun DI FAU - Mulder, Frans A A AU - Mulder FA FAU - Sussman, Joel L AU - Sussman JL FAU - Silman, Israel AU - Silman I LA - eng GR - AS1324/Autism Speaks/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080502 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Cell Adhesion Molecules) RN - 0 (Cell Adhesion Molecules, Neuronal) RN - 0 (Membrane Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (neuroligin 3) SB - IM MH - Biophysics/methods MH - Cell Adhesion Molecules/*chemistry MH - Cell Adhesion Molecules, Neuronal MH - Computer Simulation MH - Cytoplasm/*chemistry MH - Humans MH - Membrane Proteins/*chemistry/*ultrastructure MH - *Models, Chemical MH - *Models, Molecular MH - Nerve Tissue Proteins/*chemistry/*ultrastructure MH - Protein Conformation MH - Protein Structure, Tertiary PMC - PMC2483779 OID - NLM: PMC2483779 EDAT- 2008/05/06 09:00 MHDA- 2008/08/30 09:00 CRDT- 2008/05/06 09:00 PHST- 2008/05/02 [aheadofprint] AID - S0006-3495(08)70151-6 [pii] AID - 10.1529/biophysj.107.126995 [doi] PST - ppublish SO - Biophys J. 2008 Aug;95(4):1928-44. doi: 10.1529/biophysj.107.126995. Epub 2008 May 2. PMID- 20665010 OWN - NLM STAT- MEDLINE DA - 20100915 DCOM- 20110118 LR - 20131121 IS - 1618-2650 (Electronic) VI - 398 IP - 2 DP - 2010 Sep TI - Ability of a salivary intrinsically unstructured protein to bind different tannin targets revealed by mass spectrometry. PG - 815-22 LID - 10.1007/s00216-010-3997-9 [doi] AB - Astringency is thought to result from the interaction between salivary proline-rich proteins (PRP) that belong to the intrinsically unstructured protein group (IUP), and tannins, which are phenolic compounds. IUPs have the ability to bind several and/or different targets. At the same time, tannins have different chemical features reported to contribute to the sensation of astringency. The ability of both electrospray ionization mass spectrometry and tandem mass spectrometry to investigate the noncovalent interaction occurring between a human salivary PRP, IB5, and a model tannin, epigallocatechin 3-O-gallate (EgCG), has been reported. Herein, we extend this method to study the effect of tannin chemical features on their interaction with IB5. We used five model tannins, epigallocatechin (EgC), epicatechin 3-O-gallate (ECG), epigallocatechin 3-O-gallate (EgCG), procyanidin dimer B2 and B2 3'-O-gallate, which cover the main tannin chemical features: presence of a gallate moiety (galloylation), the degree of polymerization, and the degree of B ring hydroxylation. We show the ability of IB5 to bind these tannins. We report differences in stoichiometries and in stability of the IB5*1 tannin complexes. These results demonstrate the main role of hydroxyl groups in these interactions and show the involvement of hydrogen bonds. Finally, these results are in line with sensory analysis, by Vidal et al. (J Sci Food Agric 83:564-573, 2003) pointing out that the chain length and the level of galloylation are the main factors affecting astringency perception. FAU - Canon, Francis AU - Canon F AD - INRA, UMR 1083 Sciences Pour l'Oenologie, 2, place Viala, F-34060, Montpellier, France. FAU - Giuliani, Alexandre AU - Giuliani A FAU - Pate, Franck AU - Pate F FAU - Sarni-Manchado, Pascale AU - Sarni-Manchado P LA - eng PT - Journal Article DEP - 20100728 PL - Germany TA - Anal Bioanal Chem JT - Analytical and bioanalytical chemistry JID - 101134327 RN - 0 (Salivary Proline-Rich Proteins) RN - 0 (Tannins) RN - 8R1V1STN48 (Catechin) RN - BQM438CTEL (epigallocatechin gallate) SB - IM MH - Catechin/*analogs & derivatives/chemistry/metabolism MH - Humans MH - Molecular Structure MH - Protein Binding MH - Salivary Proline-Rich Proteins/*metabolism MH - Spectrometry, Mass, Electrospray Ionization/*methods MH - Tandem Mass Spectrometry/*methods MH - Tannins/chemistry/*metabolism EDAT- 2010/07/29 06:00 MHDA- 2011/01/19 06:00 CRDT- 2010/07/29 06:00 PHST- 2010/04/23 [received] PHST- 2010/07/01 [accepted] PHST- 2010/06/28 [revised] PHST- 2010/07/28 [aheadofprint] AID - 10.1007/s00216-010-3997-9 [doi] PST - ppublish SO - Anal Bioanal Chem. 2010 Sep;398(2):815-22. doi: 10.1007/s00216-010-3997-9. Epub 2010 Jul 28. PMID- 23133622 OWN - NLM STAT- MEDLINE DA - 20121107 DCOM- 20130507 LR - 20150210 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 11 DP - 2012 TI - An intrinsically disordered region of the acetyltransferase p300 with similarity to prion-like domains plays a role in aggregation. PG - e48243 LID - 10.1371/journal.pone.0048243 [doi] AB - Several human diseases including neurodegenerative disorders and cancer are associated with abnormal accumulation and aggregation of misfolded proteins. Proteins with high tendency to aggregate include the p53 gene product, TAU and alpha synuclein. The potential toxicity of aberrantly folded proteins is limited via their transport into intracellular sub-compartments, the aggresomes, where misfolded proteins are stored or cleared via autophagy. We have identified a region of the acetyltransferase p300 that is highly disordered and displays similarities with prion-like domains. We show that this region is encoded as an alternative spliced variant independently of the acetyltransferase domain, and provides an interaction interface for various misfolded proteins, promoting their aggregation. p300 enhances aggregation of TAU and of p53 and is a component of cellular aggregates in both tissue culture cells and in alpha-synuclein positive Lewy bodies of patients affected by Parkinson disease. Down-regulation of p300 impairs aggresome formation and enhances cytotoxicity induced by misfolded protein stress. These data unravel a novel activity of p300, offer new insights into the function of disordered domains and implicate p300 in pathological aggregation that occurs in neurodegeneration and cancer. FAU - Kirilyuk, Alexander AU - Kirilyuk A AD - Lombardi Comprehensive Cancer Center, Department of Oncology, Georgetown University, Washington, District of Columbia, United States of America. FAU - Shimoji, Mika AU - Shimoji M FAU - Catania, Jason AU - Catania J FAU - Sahu, Geetaram AU - Sahu G FAU - Pattabiraman, Nagarajan AU - Pattabiraman N FAU - Giordano, Antonio AU - Giordano A FAU - Albanese, Christopher AU - Albanese C FAU - Mocchetti, Italo AU - Mocchetti I FAU - Toretsky, Jeffrey A AU - Toretsky JA FAU - Uversky, Vladimir N AU - Uversky VN FAU - Avantaggiati, Maria Laura AU - Avantaggiati ML LA - eng GR - R01 CA083979/CA/NCI NIH HHS/United States GR - R01 CA102746/CA/NCI NIH HHS/United States GR - R01CA030716/CA/NCI NIH HHS/United States GR - R01CA102746/CA/NCI NIH HHS/United States GR - T32 CA009686/CA/NCI NIH HHS/United States GR - UL1 TR000101/TR/NCATS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20121101 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Prions) RN - 0 (alpha-Synuclein) RN - EC 2.3.1.48 (p300-CBP Transcription Factors) RN - EC 2.3.1.48 (p300-CBP-associated factor) SB - IM MH - Alternative Splicing MH - Amino Acid Sequence MH - Animals MH - Autophagy MH - COS Cells MH - Cercopithecus aethiops MH - Down-Regulation MH - Humans MH - Lewy Bodies/metabolism MH - Molecular Sequence Data MH - Neoplasms/metabolism MH - Neurodegenerative Diseases/metabolism MH - Oxidative Stress MH - Parkinson Disease/metabolism MH - Prions/chemistry MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - alpha-Synuclein/metabolism MH - p300-CBP Transcription Factors/*chemistry/physiology PMC - PMC3486812 OID - NLM: PMC3486812 EDAT- 2012/11/08 06:00 MHDA- 2013/05/08 06:00 CRDT- 2012/11/08 06:00 PHST- 2012/02/22 [received] PHST- 2012/09/24 [accepted] PHST- 2012/11/01 [epublish] AID - 10.1371/journal.pone.0048243 [doi] AID - PONE-D-12-05467 [pii] PST - ppublish SO - PLoS One. 2012;7(11):e48243. doi: 10.1371/journal.pone.0048243. Epub 2012 Nov 1. PMID- 16604168 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20060410 DCOM- 20060511 LR - 20100915 IS - 1550-7629 (Electronic) IS - 1550-7629 (Linking) VI - 4 DP - 2006 TI - The cell-specific activity of the estrogen receptor alpha may be fine-tuned by phosphorylation-induced structural gymnastics. PG - e005 AB - The estrogen receptor alpha (ERalpha) regulates the transcription of target genes by recruiting coregulator proteins through several domains including the two activation functions AF1 and AF2. The contribution of the N-terminally located AF1 activity is particularly important in differentiated cells, and for ERalpha to integrate inputs from other signaling pathways. However, how the phosphorylation of key residues influences AF1 activity has long remained mysterious, in part because the naturally disordered AF1 domain has resisted a structural characterization. The recent discovery of two coregulators that are specific for a phosphorylated form of AF1 suggests that phosphorylation, possibly in conjunction with the subsequent binding of these coregulators, may enforce a stable structure. The binding of the "pioneer" coregulators might facilitate the subsequent recruitment of yet other coregulators. Different AF1 folds may be enabled by the combinatorial action of posttranslational modifications and coregulator binding thereby fine-tuning ERalpha activities in a cell- and promoter-specific fashion. FAU - Gburcik, Valentina AU - Gburcik V AD - Department of Cell Biology, University of Geneva, Geneva, Switzerland. FAU - Picard, Didier AU - Picard D LA - eng PT - Journal Article DEP - 20060208 PL - United States TA - Nucl Recept Signal JT - Nuclear receptor signaling JID - 101237902 PMC - PMC1402211 OID - NLM: PMC1402211 EDAT- 2006/04/11 09:00 MHDA- 2006/04/11 09:01 CRDT- 2006/04/11 09:00 PHST- 2005/11/10 [received] PHST- 2006/01/30 [accepted] PHST- 2006/02/08 [aheadofprint] AID - 10.1621/nrs.04005 [doi] PST - ppublish SO - Nucl Recept Signal. 2006;4:e005. Epub 2006 Feb 8. PMID- 24739176 OWN - NLM STAT- MEDLINE DA - 20140417 DCOM- 20141204 LR - 20150419 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 106 IP - 8 DP - 2014 Apr 15 TI - Conformational recognition of an intrinsically disordered protein. PG - 1771-9 LID - 10.1016/j.bpj.2014.03.004 [doi] LID - S0006-3495(14)00271-9 [pii] AB - There is a growing interest in understanding the properties of intrinsically disordered proteins (IDPs); however, the characterization of these states remains an open challenge. IDPs appear to have functional roles that diverge from those of folded proteins and revolve around their ability to act as hubs for protein-protein interactions. To gain a better understanding of the modes of binding of IDPs, we combined statistical mechanics, calorimetry, and NMR spectroscopy to investigate the recognition and binding of a fragment from the disordered protein Gab2 by the growth factor receptor-bound protein 2 (Grb2), a key interaction for normal cell signaling and cancer development. Structural ensemble refinement by NMR chemical shifts, thermodynamics measurements, and analysis of point mutations indicated that the population of preexisting bound conformations in the free-state ensemble of Gab2 is an essential determinant for recognition and binding by Grb2. A key role was found for transient polyproline II (PPII) structures and extended conformations. Our findings are likely to have very general implications for the biological behavior of IDPs in light of the evidence that a large fraction of these proteins possess a specific propensity to form PPII and to adopt conformations that are more extended than the typical random-coil states. CI - Copyright (c) 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Krieger, James M AU - Krieger JM AD - Department of Life Sciences, Imperial College London, London, UK. FAU - Fusco, Giuliana AU - Fusco G AD - Department of Chemistry, University of Cambridge, Cambridge, UK. FAU - Lewitzky, Marc AU - Lewitzky M AD - Department of Oncology, University of Oxford, Oxford, UK; Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany. FAU - Simister, Philip C AU - Simister PC AD - Department of Oncology, University of Oxford, Oxford, UK. FAU - Marchant, Jan AU - Marchant J AD - Department of Life Sciences, Imperial College London, London, UK. FAU - Camilloni, Carlo AU - Camilloni C AD - Department of Chemistry, University of Cambridge, Cambridge, UK. FAU - Feller, Stephan M AU - Feller SM AD - Department of Oncology, University of Oxford, Oxford, UK; Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany. FAU - De Simone, Alfonso AU - De Simone A AD - Department of Life Sciences, Imperial College London, London, UK. Electronic address: adesimon@imperial.ac.uk. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (GRB2 Adaptor Protein) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Mutant Proteins) RN - 0 (Peptides) SB - IM CIN - Biophys J. 2014 Oct 21;107(8):1999-2000. PMID: 25418182 CIN - Biophys J. 2014 Apr 15;106(8):1557-8. PMID: 24739154 CIN - Biophys J. 2014 Oct 21;107(8):1997-8. PMID: 25418181 MH - Adaptor Proteins, Signal Transducing/*chemistry/metabolism MH - Amino Acid Sequence MH - GRB2 Adaptor Protein/chemistry/metabolism MH - Intrinsically Disordered Proteins/*chemistry/metabolism MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Mutant Proteins/chemistry/metabolism MH - Peptides/chemistry/metabolism MH - Point Mutation MH - Protein Binding MH - src Homology Domains PMC - PMC4008819 OID - NLM: PMC4008819 EDAT- 2014/04/18 06:00 MHDA- 2014/12/15 06:00 CRDT- 2014/04/18 06:00 PHST- 2014/01/16 [received] PHST- 2014/03/02 [revised] PHST- 2014/03/06 [accepted] AID - S0006-3495(14)00271-9 [pii] AID - 10.1016/j.bpj.2014.03.004 [doi] PST - ppublish SO - Biophys J. 2014 Apr 15;106(8):1771-9. doi: 10.1016/j.bpj.2014.03.004. PMID- 24739174 OWN - NLM STAT- MEDLINE DA - 20140417 DCOM- 20141204 LR - 20150419 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 106 IP - 8 DP - 2014 Apr 15 TI - Karyopherin-centric control of nuclear pores based on molecular occupancy and kinetic analysis of multivalent binding with FG nucleoporins. PG - 1751-62 LID - 10.1016/j.bpj.2014.02.021 [doi] LID - S0006-3495(14)00227-6 [pii] AB - Intrinsically disordered Phe-Gly nucleoporins (FG Nups) within nuclear pore complexes exert multivalent interactions with transport receptors (Karyopherins (Kaps)) that orchestrate nucleocytoplasmic transport. Current FG-centric views reason that selective Kap translocation is promoted by alterations in the barrier-like FG Nup conformations. However, the strong binding of Kaps with the FG Nups due to avidity contradicts rapid Kap translocation in vivo. Here, using surface plasmon resonance, we innovate a means to correlate in situ mechanistic (molecular occupancy and conformational changes) with equilibrium (binding affinity) and kinetic (multivalent binding kinetics) aspects of Karyopherinbeta1 (Kapbeta1) binding to four different FG Nups. A general feature of the FxFG domains of Nup214, Nup62, and Nup153 is their capacity to extend and accommodate large numbers of Kapbeta1 molecules at physiological Kapbeta1 concentrations. A notable exception is the GLFG domain of Nup98, which forms a partially penetrable cohesive layer. Interestingly, we find that a slowly exchanging Kapbeta1 phase forms an integral constituent within the FG Nups that coexists with a fast phase, which dominates transport kinetics due to limited binding with the pre-occupied FG Nups at physiological Kapbeta1 concentrations. Altogether, our data reveal an emergent Kap-centric barrier mechanism that may underlie mechanistic and kinetic control in the nuclear pore complex. CI - Copyright (c) 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Kapinos, Larisa E AU - Kapinos LE AD - Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland. FAU - Schoch, Rafael L AU - Schoch RL AD - Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland. FAU - Wagner, Raphael S AU - Wagner RS AD - Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland. FAU - Schleicher, Kai D AU - Schleicher KD AD - Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland. FAU - Lim, Roderick Y H AU - Lim RY AD - Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland. Electronic address: roderick.lim@unibas.ch. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (KPNB1 protein, human) RN - 0 (Nuclear Pore Complex Proteins) RN - 0 (beta Karyopherins) RN - 69-91-0 (2-phenylglycine) RN - TE7660XO1C (Glycine) SB - IM MH - Animals MH - Glycine/*analogs & derivatives/metabolism MH - Humans MH - Kinetics MH - Models, Molecular MH - Nuclear Pore/*metabolism MH - Nuclear Pore Complex Proteins/*chemistry/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Surface Plasmon Resonance MH - Xenopus laevis MH - beta Karyopherins/*metabolism PMC - PMC4008817 OID - NLM: PMC4008817 EDAT- 2014/04/18 06:00 MHDA- 2014/12/15 06:00 CRDT- 2014/04/18 06:00 PHST- 2013/12/03 [received] PHST- 2014/02/07 [revised] PHST- 2014/02/12 [accepted] AID - S0006-3495(14)00227-6 [pii] AID - 10.1016/j.bpj.2014.02.021 [doi] PST - ppublish SO - Biophys J. 2014 Apr 15;106(8):1751-62. doi: 10.1016/j.bpj.2014.02.021. PMID- 23672584 OWN - NLM STAT- MEDLINE DA - 20130621 DCOM- 20140106 LR - 20141116 IS - 1365-2958 (Electronic) IS - 0950-382X (Linking) VI - 89 IP - 1 DP - 2013 Jul TI - The unstructured domain of colicin N kills Escherichia coli. PG - 84-95 LID - 10.1111/mmi.12260 [doi] AB - Bacteria often produce toxins which kill competing bacteria. Colicins, produced by and toxic to Escherichia coli bacteria are three-domain proteins so efficient that one molecule can kill a cell. The C-terminal domain carries the lethal activity and the central domain is required for surface receptor binding. The N-terminal domain, required for translocation across the outer membrane, is always intrinsically unstructured. It has always been assumed therefore that the C-terminal cytotoxic domain is required for the bactericidal activity. Here we report the unexpected finding that in isolation, the 90-residue unstructured N-terminal domain of colicin N is cytotoxic. Furthermore it causes ion leakage from cells but, unlike known antimicrobial peptides (AMPs) with this property, shows no membrane binding behaviour. Finally, its activity remains strictly dependent upon the same receptor proteins (OmpF and TolA) used by full-length colicin N. This mechanism of rapid membrane disruption, via receptor mediated binding of a soluble peptide, may reveal a new target for the development of highly specific antibacterials. CI - (c) 2013 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd. FAU - Johnson, Christopher L AU - Johnson CL AD - Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle- upon-Tyne, NE2 4HH, UK. FAU - Ridley, Helen AU - Ridley H FAU - Pengelly, Robert J AU - Pengelly RJ FAU - Salleh, Mohd Zulkifli AU - Salleh MZ FAU - Lakey, Jeremy H AU - Lakey JH LA - eng GR - 080342/Wellcome Trust/United Kingdom GR - 093581/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130605 PL - England TA - Mol Microbiol JT - Molecular microbiology JID - 8712028 RN - 0 (Colicins) RN - 0 (Escherichia coli Proteins) RN - 0 (OmpF protein) RN - 0 (Porins) RN - 0 (tolA protein, E coli) SB - IM MH - Cell Membrane/drug effects MH - Colicins/*toxicity MH - DNA Mutational Analysis MH - Escherichia coli/*drug effects/physiology MH - Escherichia coli Proteins/metabolism MH - Microbial Viability/*drug effects MH - Porins/metabolism MH - Protein Structure, Tertiary PMC - PMC3739937 OID - NLM: PMC3739937 EDAT- 2013/05/16 06:00 MHDA- 2014/01/07 06:00 CRDT- 2013/05/16 06:00 PHST- 2013/05/10 [accepted] PHST- 2013/06/05 [aheadofprint] AID - 10.1111/mmi.12260 [doi] PST - ppublish SO - Mol Microbiol. 2013 Jul;89(1):84-95. doi: 10.1111/mmi.12260. Epub 2013 Jun 5. PMID- 21501657 OWN - NLM STAT- MEDLINE DA - 20111128 DCOM- 20120319 IS - 1872-8057 (Electronic) IS - 0303-7207 (Linking) VI - 348 IP - 2 DP - 2012 Jan 30 TI - Folding of the glucocorticoid receptor N-terminal transactivation function: dynamics and regulation. PG - 450-6 LID - 10.1016/j.mce.2011.03.024 [doi] AB - The glucocorticoid receptor (GR) mediates biological effects of glucocorticoids at the level of gene regulation, and plays important roles in many aspects of physiology. In recent years, it has become quite evident that GR behaves very dynamically, controlled by its reversible interactions with a variety of coregulatory proteins at various DNA and non-DNA sites. The N-terminal activation function domain (AF1) of the GR exists in an intrinsically disordered (ID) state, which promotes molecular recognition by providing surfaces capable of binding specific target molecules. Several studies suggest that when in action, the GR AF1 gains structure. Thus, it is hypothesized that the GR AF1 domain may be structured in vivo, at least when directly involved in transcriptional activation. Our recent work supports this conclusion. We propose that by allowing AF1 to rapidly and reversibly adopt various configurations through structural arrangements, AF1 can create protein surfaces that are readily available for selective binding to coregulatory proteins, resulting in GR-mediated transcriptional regulation of target genes. CI - Copyright (c) 2011 Elsevier Ireland Ltd. All rights reserved. FAU - Kumar, R AU - Kumar R AD - Department of Basic Sciences, The Commonwealth Medical College, Scranton, PA-18510, USA. rkumar@tcmedc.org FAU - Thompson, E B AU - Thompson EB LA - eng GR - R01DK058829/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review DEP - 20110408 PL - Ireland TA - Mol Cell Endocrinol JT - Molecular and cellular endocrinology JID - 7500844 RN - 0 (Receptors, Glucocorticoid) SB - IM MH - Allosteric Regulation MH - Animals MH - Humans MH - Models, Molecular MH - Phosphorylation MH - Promoter Regions, Genetic MH - Protein Binding MH - Protein Folding MH - Protein Stability MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Glucocorticoid/*chemistry/metabolism MH - Surface Properties MH - *Transcriptional Activation EDAT- 2011/04/20 06:00 MHDA- 2012/03/20 06:00 CRDT- 2011/04/20 06:00 PHST- 2010/12/14 [received] PHST- 2011/03/14 [revised] PHST- 2011/03/31 [accepted] PHST- 2011/04/08 [aheadofprint] AID - S0303-7207(11)00197-3 [pii] AID - 10.1016/j.mce.2011.03.024 [doi] PST - ppublish SO - Mol Cell Endocrinol. 2012 Jan 30;348(2):450-6. doi: 10.1016/j.mce.2011.03.024. Epub 2011 Apr 8. PMID- 10048921 OWN - NLM STAT- MEDLINE DA - 19990225 DCOM- 19990225 LR - 20061115 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 6 IP - 2 DP - 1999 Feb TI - Folding intermediates of SNARE complex assembly. PG - 117-23 AB - SNARE (soluble NSF attachment protein receptor) proteins assemble into a stable complex essential for vesicle-membrane fusion. To further understand SNARE function we have used solution nuclear magnetic resonance (NMR) spectroscopy to characterize three assembly states of a yeast SNARE complex: first, the 'closed' conformation of Sso1; second, the binary complex of Sso1 and Sec9; and third, the ternary complex of Sso1, Sec9 and Snc1. Sec9 and Snc1 are unstructured in isolation. Sso1 likely consists of a four helix bundle formed by part of the C-terminal Hcore domain and the N-terminal H(A)H(B)H(C) domain, and this bundle is flanked on both sides by large flexible regions. Sso1 switches to an 'open' state when its Hcore domain binds Sec9. Conformational switching of the Hcore domain, via H(A)H(B)H(C), may provide a key regulatory mechanism in SNARE assembly. Formation of binary and ternary complexes induces additional alpha-helical structure in previously unstructured regions. Our data suggest a directed assembly process beginning distal to the membrane surfaces and proceeding toward them, bringing membranes into close proximity and possibly leading to membrane fusion. FAU - Fiebig, K M AU - Fiebig KM AD - The Howard Hughes Medical Institute, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA. FAU - Rice, L M AU - Rice LM FAU - Pollock, E AU - Pollock E FAU - Brunger, A T AU - Brunger AT LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Fungal Proteins) RN - 0 (Membrane Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Qa-SNARE Proteins) RN - 0 (Qc-SNARE Proteins) RN - 0 (SEC9 protein, S cerevisiae) RN - 0 (SNARE Proteins) RN - 0 (SSO1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Vesicular Transport Proteins) SB - IM MH - Circular Dichroism MH - Fungal Proteins/chemistry MH - Magnetic Resonance Spectroscopy MH - Membrane Proteins/*chemistry MH - Nerve Tissue Proteins/*chemistry MH - Protein Conformation MH - *Protein Folding MH - Qa-SNARE Proteins MH - Qc-SNARE Proteins MH - SNARE Proteins MH - Saccharomyces cerevisiae/chemistry MH - *Saccharomyces cerevisiae Proteins MH - *Vesicular Transport Proteins EDAT- 1999/02/27 03:15 MHDA- 2001/03/23 10:01 CRDT- 1999/02/27 03:15 AID - 10.1038/5803 [doi] PST - ppublish SO - Nat Struct Biol. 1999 Feb;6(2):117-23. PMID- 21853134 OWN - NLM STAT- MEDLINE DA - 20110819 DCOM- 20111219 LR - 20141022 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 8 DP - 2011 TI - Sequencing of DISC1 pathway genes reveals increased burden of rare missense variants in schizophrenia patients from a northern Swedish population. PG - e23450 LID - 10.1371/journal.pone.0023450 [doi] AB - In recent years, DISC1 has emerged as one of the most credible and best supported candidate genes for schizophrenia and related neuropsychiatric disorders. Furthermore, increasing evidence--both genetic and functional--indicates that many of its protein interaction partners are also involved in the development of these diseases. In this study, we applied a pooled sample 454 sequencing strategy, to explore the contribution of genetic variation in DISC1 and 10 of its interaction partners (ATF5, Grb2, FEZ1, LIS-1, PDE4B, NDE1, NDEL1, TRAF3IP1, YWHAE, and ZNF365) to schizophrenia susceptibility in an isolated northern Swedish population. Mutation burden analysis of the identified variants in a population of 486 SZ patients and 514 control individuals, revealed that non-synonymous rare variants with a MAF<0.01 were significantly more present in patients compared to controls (8.64% versus 4.7%, P = 0.018), providing further evidence for the involvement of DISC1 and some of its interaction partners in psychiatric disorders. This increased burden of rare missense variants was even more striking in a subgroup of early onset patients (12.9% versus 4.7%, P = 0.0004), highlighting the importance of studying subgroups of patients and identifying endophenotypes. Upon investigation of the potential functional effects associated with the identified missense variants, we found that approximately 90% of these variants reside in intrinsically disordered protein regions. The observed increase in mutation burden in patients provides further support for the role of the DISC1 pathway in schizophrenia. Furthermore, this study presents the first evidence supporting the involvement of mutations within intrinsically disordered protein regions in the pathogenesis of psychiatric disorders. As many important biological functions depend directly on the disordered state, alteration of this disorder in key pathways may represent an intriguing new disease mechanism for schizophrenia and related neuropsychiatric diseases. Further research into this unexplored domain will be required to elucidate the role of the identified variants in schizophrenia etiology. FAU - Moens, Lotte N AU - Moens LN AD - Applied Molecular Genomics Group, Department of Molecular Genetics, Flanders Institute for Biotechnology (VIB), Flanders, Belgium. FAU - De Rijk, Peter AU - De Rijk P FAU - Reumers, Joke AU - Reumers J FAU - Van den Bossche, Maarten J A AU - Van den Bossche MJ FAU - Glassee, Wim AU - Glassee W FAU - De Zutter, Sonia AU - De Zutter S FAU - Lenaerts, An-Sofie AU - Lenaerts AS FAU - Nordin, Annelie AU - Nordin A FAU - Nilsson, Lars-Goran AU - Nilsson LG FAU - Medina Castello, Ignacio AU - Medina Castello I FAU - Norrback, Karl-Fredrik AU - Norrback KF FAU - Goossens, Dirk AU - Goossens D FAU - Van Steen, Kristel AU - Van Steen K FAU - Adolfsson, Rolf AU - Adolfsson R FAU - Del-Favero, Jurgen AU - Del-Favero J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110811 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DISC1 protein, human) RN - 0 (Nerve Tissue Proteins) SB - IM MH - Adult MH - Age of Onset MH - Case-Control Studies MH - Computational Biology MH - DNA Mutational Analysis MH - Frameshift Mutation/genetics MH - Gene Frequency/genetics MH - *Genetic Predisposition to Disease MH - Genetics, Population MH - Humans MH - Middle Aged MH - Mutation, Missense/*genetics MH - Nerve Tissue Proteins/*genetics MH - Reproducibility of Results MH - Schizophrenia/epidemiology/*genetics MH - Sequence Analysis, DNA/*methods MH - Signal Transduction/*genetics MH - Sweden/epidemiology MH - Young Adult PMC - PMC3154939 OID - NLM: PMC3154939 EDAT- 2011/08/20 06:00 MHDA- 2011/12/20 06:00 CRDT- 2011/08/20 06:00 PHST- 2011/03/17 [received] PHST- 2011/07/18 [accepted] PHST- 2011/08/11 [epublish] AID - 10.1371/journal.pone.0023450 [doi] AID - PONE-D-11-05196 [pii] PST - ppublish SO - PLoS One. 2011;6(8):e23450. doi: 10.1371/journal.pone.0023450. Epub 2011 Aug 11. PMID- 21949740 OWN - NLM STAT- MEDLINE DA - 20110928 DCOM- 20120130 LR - 20141022 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 9 DP - 2011 TI - Mechanism of the interaction between the intrinsically disordered C-terminus of the pro-apoptotic ARTS protein and the Bir3 domain of XIAP. PG - e24655 LID - 10.1371/journal.pone.0024655 [doi] AB - ARTS (Sept4_i2) is a mitochondrial pro-apoptotic protein that functions as a tumor suppressor. Its expression is significantly reduced in leukemia and lymphoma patients. ARTS binds and inhibits XIAP (X-linked Inhibitor of Apoptosis protein) by interacting with its Bir3 domain. ARTS promotes degradation of XIAP through the proteasome pathway. By doing so, ARTS removes XIAP inhibition of caspases and enables apoptosis to proceed. ARTS contains 27 unique residues in its C-terminal domain (CTD, residues 248-274) which are important for XIAP binding. Here we characterized the molecular details of this interaction. Biophysical and computational methods were used to show that the ARTS CTD is intrinsically disordered under physiological conditions. Direct binding of ARTS CTD to Bir3 was demonstrated using NMR and fluorescence spectroscopy. The Bir3 interacting region in ARTS CTD was mapped to ARTS residues 266-274, which are the nine C-terminal residues in the protein. Alanine scan of ARTS 266-274 showed the importance of several residues for Bir3 binding, with His268 and Cys273 contributing the most. Adding a reducing agent prevented binding to Bir3. A dimer of ARTS 266-274 formed by oxidation of the Cys residues into a disulfide bond bound with similar affinity and was probably required for the interaction with Bir3. The detailed analysis of the ARTS - Bir3 interaction provides the basis for setting it as a target for anti cancer drug design: It will enable the development of compounds that mimic ARTS CTD, remove IAPs inhibition of caspases, and thereby induce apoptosis. FAU - Reingewertz, Tali H AU - Reingewertz TH AD - Institute of Chemistry, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, Israel. FAU - Shalev, Deborah E AU - Shalev DE FAU - Sukenik, Shahar AU - Sukenik S FAU - Blatt, Ofrah AU - Blatt O FAU - Rotem-Bamberger, Shahar AU - Rotem-Bamberger S FAU - Lebendiker, Mario AU - Lebendiker M FAU - Larisch, Sarit AU - Larisch S FAU - Friedler, Assaf AU - Friedler A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110920 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Peptides) RN - 0 (X-Linked Inhibitor of Apoptosis Protein) RN - EC 3.6.1.- (Septins) RN - OF5P57N2ZX (Alanine) SB - IM MH - Alanine/metabolism MH - Amino Acid Sequence MH - Apoptosis MH - Circular Dichroism MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Peptides/chemistry/metabolism MH - Protein Binding MH - Protein Interaction Mapping MH - Protein Multimerization MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Septins/*chemistry/*metabolism MH - Structure-Activity Relationship MH - X-Linked Inhibitor of Apoptosis Protein/*chemistry/*metabolism PMC - PMC3176765 OID - NLM: PMC3176765 EDAT- 2011/09/29 06:00 MHDA- 2012/01/31 06:00 CRDT- 2011/09/28 06:00 PHST- 2011/07/12 [received] PHST- 2011/08/15 [accepted] PHST- 2011/09/20 [epublish] AID - 10.1371/journal.pone.0024655 [doi] AID - PONE-D-11-13266 [pii] PST - ppublish SO - PLoS One. 2011;6(9):e24655. doi: 10.1371/journal.pone.0024655. Epub 2011 Sep 20. PMID- 16421638 OWN - NLM STAT- MEDLINE DA - 20060420 DCOM- 20060630 LR - 20061115 IS - 0304-8608 (Print) IS - 0304-8608 (Linking) VI - 151 IP - 5 DP - 2006 May TI - Vanilla mosaic virus isolates from French Polynesia and the Cook Islands are Dasheen mosaic virus strains that exclusively infect vanilla. PG - 905-19 AB - Sequence was determined for the coat protein (CP) gene and 3' non-translated region (3'NTR) of two vanilla mosaic virus (VanMV) isolates from Vanilla tahitensis, respectively from the Cook Islands (VanMV-CI) and French Polynesia (VanMV-FP). Both viruses displayed distinctive features in the N-terminal region of their CPs; for VanMV-CI, a 16-amino-acid deletion including the aphid transmission-related DAG motif, and for VanMV-FP, a stretch of GTN repeats that putatively belongs to the class of natively unfolded proteins. VanMV-FP CP also has a novel DVG motif in place of the DAG motif, and an uncommon Q//V protease cleavage site. The sequences were compared to a range of Dasheen mosaic virus (DsMV) strains and to potyviruses infecting orchids. Identity was low to DsMV strains across the entire CP coding region and across the 3'NTR, but high across the CP core and the CI-6K2-NIa region. In accordance with current ICTV criteria for species demarcation within the family Potyviridae, VanMV-CI and VanMV-FP are strains of DsMV that exclusively infect vanilla. FAU - Farreyrol, K AU - Farreyrol K AD - School of Biological Sciences, The University of Auckland, Auckland, New Zealand. k.farreyrol@auckland.ac.nz FAU - Pearson, M N AU - Pearson MN FAU - Grisoni, M AU - Grisoni M FAU - Cohen, D AU - Cohen D FAU - Beck, D AU - Beck D LA - eng SI - GENBANK/AJ616719 SI - GENBANK/AJ616720 SI - GENBANK/AJ616721 SI - GENBANK/AJ616722 PT - Comparative Study PT - Journal Article DEP - 20060119 PL - Austria TA - Arch Virol JT - Archives of virology JID - 7506870 RN - 0 (3' Untranslated Regions) RN - 0 (Capsid Proteins) SB - IM MH - 3' Untranslated Regions/genetics MH - Amino Acid Motifs/genetics MH - Amino Acid Sequence MH - Capsid Proteins/genetics MH - Molecular Sequence Data MH - Phylogeny MH - Plant Diseases/*virology MH - Polymorphism, Genetic MH - Polynesia MH - Potyvirus/*classification/*genetics/isolation & purification MH - Sequence Alignment MH - Sequence Analysis, DNA MH - Sequence Deletion MH - Sequence Homology MH - Vanilla/*virology EDAT- 2006/01/20 09:00 MHDA- 2006/07/01 09:00 CRDT- 2006/01/20 09:00 PHST- 2005/05/09 [received] PHST- 2005/10/14 [accepted] PHST- 2006/01/19 [aheadofprint] AID - 10.1007/s00705-005-0680-0 [doi] PST - ppublish SO - Arch Virol. 2006 May;151(5):905-19. Epub 2006 Jan 19. PMID- 10647180 OWN - NLM STAT- MEDLINE DA - 20000203 DCOM- 20000203 LR - 20061115 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 7 IP - 12 DP - 1999 Dec 15 TI - Crystal structure of a transcriptionally active Smad4 fragment. PG - 1493-503 AB - BACKGROUND: Smad4 functions as a common mediator of transforming growth factor beta (TGF-beta) signaling by forming complexes with the phosphorylated state of pathway-restricted SMAD proteins that act in specific signaling pathways to activate transcription. SMAD proteins comprise two domains, the MH1 and MH2 domain, separated by a linker region. The transcriptional activity and synergistic effect of Smad4 require a stretch of proline-rich sequence, the SMAD-activation domain (SAD), located N-terminal of the MH2 domain. To understand how the SAD contributes to Smad4 function, the crystal structure of a fragment including the SAD and MH2 domain (S4AF) was determined. RESULTS: The structure of the S4AF trimer reveals novel features important for Smad4 function. A Smad4-specific sequence insertion within the MH2 domain interacts with the C-terminal tail to form a structural extension from the core. This extension (the TOWER) contains a solvent-accessible glutamine-rich helix. The SAD reinforces the TOWER and the structural core through interactions; two residues involved in these interactions are targets of tumorigenic mutation. The solvent-accessible proline residues of the SAD are located on the same face as the glutamine-rich helix of the TOWER, forming a potential transcription activation surface. A tandem sulfate-ion-binding site was identified within the subunit interface, which may interact with the phosphorylated C-terminal sequence of pathway-restricted SMAD proteins. CONCLUSIONS: The structure suggests that the SAD provides transcriptional capability by reinforcing the structural core and coordinating with the TOWER to present the proline-rich and glutamine-rich surfaces for interaction with transcription partners. The sulfate-ion-binding sites are potential 'receptors' for the phosphorylated sequence of pathway-restricted SMAD proteins in forming a heteromeric complex. The structure thus provides a new model that can be tested using biochemical and cellular approaches. FAU - Qin, B AU - Qin B AD - Department of Pharmacology and Molecular Toxicology, University of Massachusetts Medical School, Worcester 01655, USA. FAU - Lam, S S AU - Lam SS FAU - Lin, K AU - Lin K LA - eng SI - PDB/1DD1 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (DNA-Binding Proteins) RN - 0 (Macromolecular Substances) RN - 0 (Madh4 protein, rat) RN - 0 (Peptide Fragments) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Proteins) RN - 0 (SMAD4 protein, human) RN - 0 (Smad4 Protein) RN - 0 (Smad4 protein, mouse) RN - 0 (Trans-Activators) SB - IM MH - Amino Acid Sequence MH - Animals MH - Crystallography, X-Ray MH - DNA-Binding Proteins/*chemistry/*metabolism MH - Humans MH - Macromolecular Substances MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Peptide Fragments/*chemistry/*metabolism MH - Protein Isoforms/chemistry/metabolism MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Rats MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Signal Transduction MH - Smad4 Protein MH - Software MH - Trans-Activators/*chemistry/*metabolism EDAT- 2000/01/27 MHDA- 2000/01/27 00:01 CRDT- 2000/01/27 00:00 PST - ppublish SO - Structure. 1999 Dec 15;7(12):1493-503. PMID- 18812399 OWN - NLM STAT- MEDLINE DA - 20081014 DCOM- 20081124 LR - 20140903 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 36 IP - 18 DP - 2008 Oct TI - 14-3-3 activation of DNA binding of p53 by enhancing its association into tetramers. PG - 5983-91 LID - 10.1093/nar/gkn598 [doi] AB - Activation of the tumour suppressor p53 on DNA damage involves post-translational modification by phosphorylation and acetylation. Phosphorylation of certain residues is critical for p53 stabilization and plays an important role in DNA-binding activity. The 14-3-3 family of proteins activates the DNA-binding affinity of p53 upon stress by binding to a site in its intrinsically disordered C-terminal domain containing a phosphorylated serine at 378. We have screened various p53 C-terminal phosphorylated peptides for binding to two different isoforms of 14-3-3, epsilon and gamma. We found that phosphorylation at either S366 or T387 caused even tighter binding to 14-3-3. We made by semi-synthesis a tetrameric construct comprised of the tetramerization plus C-terminal domains of p53 that was phosphorylated on S366, S378 and T387. It bound 10 times tighter than did the monomeric counterpart to dimeric 14-3-3. We showed indirectly from binding curves and directly from fluorescence-detection analytical ultracentrifugation that 14-3-3 enhanced the binding of sequence-specific DNA to p53 by causing p53 dimers to form tetramers at lower concentrations. If the in vitro data extrapolate to in vivo, then it is an attractive hypothesis that p53 activity may be subject to control by accessory proteins lowering its tetramer-dimer dissociation constant from its normal value of 120-150 nM. FAU - Rajagopalan, Sridharan AU - Rajagopalan S AD - MRC Laboratory of Molecular Biology and MRC Centre for Protein Engineering, Hills Road, Cambridge, CB2 0QH, UK. FAU - Jaulent, Agnes M AU - Jaulent AM FAU - Wells, Mark AU - Wells M FAU - Veprintsev, Dmitry B AU - Veprintsev DB FAU - Fersht, Alan R AU - Fersht AR LA - eng GR - MC_U105474168/Medical Research Council/United Kingdom GR - Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080923 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (14-3-3 Proteins) RN - 0 (Peptides) RN - 0 (Phosphopeptides) RN - 0 (Tumor Suppressor Protein p53) RN - 9007-49-2 (DNA) SB - IM MH - 14-3-3 Proteins/*chemistry/metabolism MH - Base Sequence MH - Binding Sites MH - DNA/*chemistry/metabolism MH - Fluorescence Polarization MH - Peptides/metabolism MH - Phosphopeptides/metabolism MH - Phosphorylation MH - Protein Binding MH - Protein Structure, Tertiary MH - Tumor Suppressor Protein p53/*chemistry/metabolism PMC - PMC2566891 OID - NLM: PMC2566891 EDAT- 2008/09/25 09:00 MHDA- 2008/12/17 09:00 CRDT- 2008/09/25 09:00 PHST- 2008/09/23 [aheadofprint] AID - gkn598 [pii] AID - 10.1093/nar/gkn598 [doi] PST - ppublish SO - Nucleic Acids Res. 2008 Oct;36(18):5983-91. doi: 10.1093/nar/gkn598. Epub 2008 Sep 23. PMID- 18452657 OWN - NLM STAT- MEDLINE DA - 20080502 DCOM- 20080710 LR - 20131121 IS - 1976-6696 (Print) IS - 1976-6696 (Linking) VI - 41 IP - 4 DP - 2008 Apr 30 TI - Isolation of a novel dehydrin gene from Codonopsis lanceolata and analysis of its response to abiotic stresses. PG - 338-43 AB - Dehydrins (DHNs) compose a family of intrinsically unstructured proteins that have high water solubility and accumulate during late seed development at low temperature or in water-deficit conditions. They are believed to play a protective role in freezing and drought-tolerance in plants. A full-length cDNA encoding DHN (designated as ClDhn) was isolated from an oriental medicinal plant Codonopsis lanceolata, which has been used widely in Asia for its anticancer and anti-inflammatory properties. The full-length cDNA of ClDhn was 813 bp and contained a 477 bp open reading frame (ORF) encoding a polypeptide of 159 amino acids. Deduced ClDhn protein had high similarities with other plant DHNs. RT-PCR analysis showed that different abiotic stresses such as salt, wounding, chilling and light, triggered a significant induction of ClDhn at different time points within 4-48 hrs post-treatment. This study revealed that ClDhn assisted C. lanceolata in becoming resistant to dehydration. FAU - Pulla, Rama Krishna AU - Pulla RK AD - Korean Ginseng Center and Ginseng Genetic Resource Bank, Kyung Hee University, Seocheon-dong, Kiheung-gu Yongin, Kyunggi-do, South Korea. FAU - Kim, Yu-Jin AU - Kim YJ FAU - Kim, Myung Kyum AU - Kim MK FAU - Senthil, Kalai Selvi AU - Senthil KS FAU - In, Jun-Gyo AU - In JG FAU - Yang, Deok-Chun AU - Yang DC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Korea (South) TA - BMB Rep JT - BMB reports JID - 101465334 RN - 0 (DNA, Complementary) RN - 0 (Plant Proteins) RN - 134711-03-8 (dehydrin proteins, plant) RN - 72S9A8J5GW (Abscisic Acid) RN - 7647-14-5 (Sodium Chloride) SB - IM MH - Abscisic Acid/pharmacology MH - Amino Acid Sequence MH - Base Sequence MH - Cloning, Molecular MH - Codonopsis/*genetics MH - Cold Temperature MH - DNA, Complementary/isolation & purification MH - Dehydration/*genetics MH - Gene Expression Regulation, Plant/drug effects MH - Molecular Sequence Data MH - Phylogeny MH - Plant Proteins/*genetics/isolation & purification/metabolism MH - Sequence Homology, Amino Acid MH - Sodium Chloride/pharmacology EDAT- 2008/05/03 09:00 MHDA- 2008/07/11 09:00 CRDT- 2008/05/03 09:00 PST - ppublish SO - BMB Rep. 2008 Apr 30;41(4):338-43. PMID- 21245151 OWN - NLM STAT- MEDLINE DA - 20110418 DCOM- 20110628 LR - 20140821 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 16 DP - 2011 Apr 22 TI - A multiprotein binding interface in an intrinsically disordered region of the tumor suppressor protein interferon regulatory factor-1. PG - 14291-303 LID - 10.1074/jbc.M110.204602 [doi] AB - The interferon-regulated transcription factor and tumor suppressor protein IRF-1 is predicted to be largely disordered outside of the DNA-binding domain. One of the advantages of intrinsically disordered protein domains is thought to be their ability to take part in multiple, specific but low affinity protein interactions; however, relatively few IRF-1-interacting proteins have been described. The recent identification of a functional binding interface for the E3-ubiquitin ligase CHIP within the major disordered domain of IRF-1 led us to ask whether this region might be employed more widely by regulators of IRF-1 function. Here we describe the use of peptide aptamer-based affinity chromatography coupled with mass spectrometry to define a multiprotein binding interface on IRF-1 (Mf2 domain; amino acids 106-140) and to identify Mf2-binding proteins from A375 cells. Based on their function as known transcriptional regulators, a selection of the Mf2 domain-binding proteins (NPM1, TRIM28, and YB-1) have been validated using in vitro and cell-based assays. Interestingly, although NPM1, TRIM28, and YB-1 all bind to the Mf2 domain, they have differing amino acid specificities, demonstrating the degree of combinatorial diversity and specificity available through linear interaction motifs. FAU - Narayan, Vikram AU - Narayan V AD - CRUK Interferon and Cell Signalling Group, Cell Signalling Unit, Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh EH4 2XR, United Kingdom. FAU - Halada, Petr AU - Halada P FAU - Hernychova, Lenka AU - Hernychova L FAU - Chong, Yuh Ping AU - Chong YP FAU - Zakova, Jitka AU - Zakova J FAU - Hupp, Ted R AU - Hupp TR FAU - Vojtesek, Borivoj AU - Vojtesek B FAU - Ball, Kathryn L AU - Ball KL LA - eng GR - C377/A6355/Cancer Research UK/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110118 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA-Binding Proteins) RN - 0 (Interferon Regulatory Factor-1) RN - 0 (Nuclear Proteins) RN - 0 (Peptides) RN - 0 (Repressor Proteins) RN - 0 (TRIM28 protein, human) RN - 0 (Y-Box-Binding Protein 1) RN - 0 (YBX1 protein, human) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Cell Line, Tumor MH - Chromatography, Affinity/methods MH - DNA-Binding Proteins/chemistry MH - *Gene Expression Regulation MH - Humans MH - Interferon Regulatory Factor-1/*metabolism MH - Molecular Sequence Data MH - Nuclear Proteins/chemistry MH - Peptides/chemistry MH - Protein Binding MH - Protein Interaction Mapping MH - Repressor Proteins/chemistry MH - Sequence Homology, Amino Acid MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Ubiquitin-Protein Ligases/*metabolism MH - Y-Box-Binding Protein 1 PMC - PMC3077630 OID - NLM: PMC3077630 EDAT- 2011/01/20 06:00 MHDA- 2011/06/29 06:00 CRDT- 2011/01/20 06:00 PHST- 2011/01/18 [aheadofprint] AID - M110.204602 [pii] AID - 10.1074/jbc.M110.204602 [doi] PST - ppublish SO - J Biol Chem. 2011 Apr 22;286(16):14291-303. doi: 10.1074/jbc.M110.204602. Epub 2011 Jan 18. PMID- 16162499 OWN - NLM STAT- MEDLINE DA - 20051115 DCOM- 20060110 LR - 20111117 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 46 DP - 2005 Nov 18 TI - Amyloid fibril formation of alpha-synuclein is accelerated by preformed amyloid seeds of other proteins: implications for the mechanism of transmissible conformational diseases. PG - 38609-16 AB - Alpha-synuclein is one of the causative proteins of familial Parkinson disease, which is characterized by neuronal inclusions named Lewy bodies. Lewy bodies include not only alpha-synuclein but also aggregates of other proteins. This fact raises a question as to whether the formation of alpha-synuclein amyloid fibrils in Lewy bodies may occur via interaction with fibrils derived from different proteins. To probe this hypothesis, we investigated in vitro fibril formation of human alpha-synuclein in the presence of preformed fibril seeds of various different proteins. We used three proteins, Escherichia coli chaperonin GroES, hen lysozyme, and bovine insulin, all of which have been shown to form amyloid fibrils. Very surprisingly, the formation of alpha-synuclein amyloid fibril was accelerated markedly in the presence of preformed seeds of GroES, lysozyme, and insulin fibrils. The structural characteristics of the natively unfolded state of alpha-synuclein may allow binding to various protein particles, which in turn triggers the formation (extension) of alpha-synuclein amyloid fibrils. This finding is very important for understanding the molecular mechanism of Parkinson disease and also provides interesting implications into the mechanism of transmissible conformational diseases. FAU - Yagi, Hisashi AU - Yagi H AD - Department of Biotechnology, Faculty of Engineering, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Koyama-Minami, Tottori 680-8552, Japan. FAU - Kusaka, Eiko AU - Kusaka E FAU - Hongo, Kunihiro AU - Hongo K FAU - Mizobata, Tomohiro AU - Mizobata T FAU - Kawata, Yasushi AU - Kawata Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050914 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Amyloid) RN - 0 (Chaperonin 10) RN - 0 (Insulin) RN - 0 (Molecular Chaperones) RN - 0 (Peptides) RN - 0 (Thiazoles) RN - 0 (alpha-Synuclein) RN - 2390-54-7 (thioflavin T) RN - EC 3.2.1.- (hen egg lysozyme) RN - EC 3.2.1.17 (Muramidase) SB - IM MH - Amyloid/*chemistry MH - Animals MH - Biochemistry/methods MH - Cattle MH - Chaperonin 10/chemistry MH - Chickens MH - Circular Dichroism MH - Escherichia coli/metabolism MH - Humans MH - Insulin/chemistry/metabolism MH - Lewy Bodies/metabolism MH - Microscopy, Atomic Force MH - Microscopy, Electron, Transmission MH - Microscopy, Fluorescence MH - Models, Biological MH - Molecular Chaperones/chemistry MH - Muramidase/chemistry MH - Parkinson Disease/metabolism MH - Peptides/chemistry MH - Protein Binding MH - Protein Conformation MH - Scattering, Radiation MH - Thiazoles/chemistry MH - X-Rays MH - alpha-Synuclein/*chemistry/metabolism EDAT- 2005/09/16 09:00 MHDA- 2006/01/13 09:00 CRDT- 2005/09/16 09:00 PHST- 2005/09/14 [aheadofprint] AID - M508623200 [pii] AID - 10.1074/jbc.M508623200 [doi] PST - ppublish SO - J Biol Chem. 2005 Nov 18;280(46):38609-16. Epub 2005 Sep 14. PMID- 22457068 OWN - NLM STAT- MEDLINE DA - 20120723 DCOM- 20121022 LR - 20141016 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 40 IP - 13 DP - 2012 Jul TI - Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding. PG - 6353-66 AB - The crucial role of Myc as an oncoprotein and as a key regulator of cell growth makes it essential to understand the molecular basis of Myc function. The N-terminal region of c-Myc coordinates a wealth of protein interactions involved in transformation, differentiation and apoptosis. We have characterized in detail the intrinsically disordered properties of Myc-1-88, where hierarchical phosphorylation of S62 and T58 regulates activation and destruction of the Myc protein. By nuclear magnetic resonance (NMR) chemical shift analysis, relaxation measurements and NOE analysis, we show that although Myc occupies a very heterogeneous conformational space, we find transiently structured regions in residues 22-33 and in the Myc homology box I (MBI; residues 45-65); both these regions are conserved in other members of the Myc family. Binding of Bin1 to Myc-1-88 as assayed by NMR and surface plasmon resonance (SPR) revealed primary binding to the S62 region in a dynamically disordered and multivalent complex, accompanied by population shifts leading to altered intramolecular conformational dynamics. These findings expand the increasingly recognized concept of intrinsically disordered regions mediating transient interactions to Myc, a key transcriptional regulator of major medical importance, and have important implications for further understanding its multifaceted role in gene regulation. FAU - Andresen, Cecilia AU - Andresen C AD - Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linkoping University, SE-58183 Linkoping, Sweden. FAU - Helander, Sara AU - Helander S FAU - Lemak, Alexander AU - Lemak A FAU - Fares, Christophe AU - Fares C FAU - Csizmok, Veronika AU - Csizmok V FAU - Carlsson, Jonas AU - Carlsson J FAU - Penn, Linda Z AU - Penn LZ FAU - Forman-Kay, Julie D AU - Forman-Kay JD FAU - Arrowsmith, Cheryl H AU - Arrowsmith CH FAU - Lundstrom, Patrik AU - Lundstrom P FAU - Sunnerhagen, Maria AU - Sunnerhagen M LA - eng GR - U54 GM094597/GM/NIGMS NIH HHS/United States GR - U54 GM094597/GM/NIGMS NIH HHS/United States GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120328 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (MYC protein, human) RN - 0 (Proto-Oncogene Proteins c-myc) RN - 0 (Trans-Activators) RN - 0 (Tumor Suppressor Proteins) SB - IM MH - Binding Sites MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-myc/*chemistry/metabolism MH - Trans-Activators/*chemistry/metabolism MH - Tumor Suppressor Proteins/*chemistry/metabolism MH - src Homology Domains PMC - PMC3401448 OID - NLM: PMC3401448 EDAT- 2012/03/30 06:00 MHDA- 2012/10/23 06:00 CRDT- 2012/03/30 06:00 PHST- 2012/03/28 [aheadofprint] AID - gks263 [pii] AID - 10.1093/nar/gks263 [doi] PST - ppublish SO - Nucleic Acids Res. 2012 Jul;40(13):6353-66. Epub 2012 Mar 28. PMID- 14724277 OWN - NLM STAT- MEDLINE DA - 20040329 DCOM- 20040511 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 14 DP - 2004 Apr 2 TI - Aggregation of the Acylphosphatase from Sulfolobus solfataricus: the folded and partially unfolded states can both be precursors for amyloid formation. PG - 14111-9 AB - Protein aggregation is associated with a number of human pathologies including Alzheimer's and Creutzfeldt-Jakob diseases and the systemic amyloidoses. In this study, we used the acylphosphatase from the hyperthermophilic Archaea Sulfolobus solfataricus (Sso AcP) to investigate the mechanism of aggregation under conditions in which the protein maintains a folded structure. In the presence of 15-25% (v/v) trifluoroethanol, Sso AcP was found to form aggregates able to bind specific dyes such as thioflavine T, Congo red, and 1-anilino-8-naphthalenesulfonic acid. The presence of aggregates was confirmed by circular dichroism and dynamic light scattering. Electron microscopy revealed the presence of small aggregates generally referred to as amyloid protofibrils. The monomeric form adopted by Sso AcP prior to aggregation under these conditions retained enzymatic activity; in addition, folding was remarkably faster than unfolding. These observations indicate that Sso AcP adopts a folded, although possibly distorted, conformation prior to aggregation. Most important, aggregation appeared to be 100-fold faster than unfolding under these conditions. Although aggregation of Sso AcP was faster at higher trifluoroethanol concentrations, in which the protein adopted a partially unfolded conformation, these findings suggest that the early events of amyloid fibril formation may involve an aggregation process consisting of the assembly of protein molecules in their folded state. This conclusion has a biological relevance as globular proteins normally spend most of their lifetime in folded structures. FAU - Plakoutsi, Georgia AU - Plakoutsi G AD - Dipartimento di Scienze Biochimiche, Universita di Firenze, Viale Morgagni 50, 50134 Firenze, Italy. FAU - Taddei, Niccolo AU - Taddei N FAU - Stefani, Massimo AU - Stefani M FAU - Chiti, Fabrizio AU - Chiti F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040114 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Archaeal Proteins) RN - 0 (Coloring Agents) RN - EC 3.6.- (Acid Anhydride Hydrolases) RN - EC 3.6.1.7 (acylphosphatase) SB - IM MH - Acid Anhydride Hydrolases/*chemistry/genetics/*metabolism MH - Amino Acid Sequence MH - Archaeal Proteins/*chemistry/genetics/*metabolism MH - Circular Dichroism MH - Cloning, Molecular MH - Coloring Agents MH - Energy Transfer MH - Microscopy, Electron MH - Molecular Sequence Data MH - Protein Folding MH - Sulfolobus/*enzymology/genetics EDAT- 2004/01/16 05:00 MHDA- 2004/05/12 05:00 CRDT- 2004/01/16 05:00 PHST- 2004/01/14 [aheadofprint] AID - 10.1074/jbc.M312961200 [doi] AID - M312961200 [pii] PST - ppublish SO - J Biol Chem. 2004 Apr 2;279(14):14111-9. Epub 2004 Jan 14. PMID- 21297620 OWN - NLM STAT- MEDLINE DA - 20110301 DCOM- 20110413 LR - 20140921 IS - 1548-7105 (Electronic) IS - 1548-7091 (Linking) VI - 8 IP - 3 DP - 2011 Mar TI - Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing. PG - 239-41 LID - 10.1038/nmeth.1568 [doi] AB - We combined rapid microfluidic mixing with single-molecule fluorescence resonance energy transfer to study the folding kinetics of the intrinsically disordered human protein alpha-synuclein. The time-resolution of 0.2 ms revealed initial collapse of the unfolded protein induced by binding with lipid mimics and subsequent rapid formation of transient structures in the encounter complex. The method also enabled analysis of rapid dissociation and unfolding of weakly bound complexes triggered by massive dilution. FAU - Gambin, Yann AU - Gambin Y AD - Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA. y.gambin@imb.uq.edu FAU - VanDelinder, Virginia AU - VanDelinder V FAU - Ferreon, Allan Chris M AU - Ferreon AC FAU - Lemke, Edward A AU - Lemke EA FAU - Groisman, Alex AU - Groisman A FAU - Deniz, Ashok A AU - Deniz AA LA - eng GR - R01 GM066833/GM/NIGMS NIH HHS/United States GR - R01 GM066833/GM/NIGMS NIH HHS/United States GR - R01 GM066833-06A1/GM/NIGMS NIH HHS/United States GR - R01 GM066833-07/GM/NIGMS NIH HHS/United States GR - R21 AG033382/AG/NIA NIH HHS/United States GR - R21 AG033382/AG/NIA NIH HHS/United States GR - R21 AG033382-02/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110206 PL - United States TA - Nat Methods JT - Nature methods JID - 101215604 RN - 0 (alpha-Synuclein) SB - IM CIN - Nat Methods. 2011 Mar;8(3):213-5. PMID: 21358623 MH - Fluorescence Resonance Energy Transfer/*methods MH - Humans MH - Kinetics MH - Microfluidic Analytical Techniques/*methods MH - Protein Binding MH - Protein Folding MH - alpha-Synuclein/*chemistry PMC - PMC3071799 MID - NIHMS264963 OID - NLM: NIHMS264963 OID - NLM: PMC3071799 EDAT- 2011/02/08 06:00 MHDA- 2011/04/14 06:00 CRDT- 2011/02/08 06:00 PHST- 2010/09/09 [received] PHST- 2010/01/14 [accepted] PHST- 2011/02/06 [aheadofprint] AID - nmeth.1568 [pii] AID - 10.1038/nmeth.1568 [doi] PST - ppublish SO - Nat Methods. 2011 Mar;8(3):239-41. doi: 10.1038/nmeth.1568. Epub 2011 Feb 6. PMID- 10380229 OWN - NLM STAT- MEDLINE DA - 19990810 DCOM- 19990810 LR - 20130220 IS - 2335-6936 (Print) DP - 1999 TI - The hydrophilic, protease-sensitive terminal domains of eucaryotic DNA topoisomerases have essential intracellular functions. PG - 578-89 AB - The amino-terminus of eucaryotic DNA topoisomerase I and the carboxy-terminus of eucaryotic DNA topoisomerase II contain sequences that are enriched in charged amino acid residues, hyper-sensitive to protease digestion, not required for the in vitro topoisomerase activities, able to tolerate insertion and deletion mutations, and thus may have a disordered structure. In an interesting contrast to the catalytically essential core domain, the sequences in these terminal hydrophilic domains are not conserved among the topoisomerases from different species. However, many lines of evidence, including those presented here, demonstrate that the topoisomerase tail domains have critical intracellular functions. The biological functions of the amino-terminus of topoisomerase I include the nuclear import and targeting to the transcriptionally active loci. The carboxy-terminus of topoisomerase II also contains the sequences necessary for nuclear localization and possibly sequences necessary for other critical functions. FAU - Shaiu, W L AU - Shaiu WL AD - Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA. FAU - Hu, T AU - Hu T FAU - Hsieh, T S AU - Hsieh TS LA - eng GR - GM29006/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - SINGAPORE TA - Pac Symp Biocomput JT - Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing JID - 9711271 RN - 0 (Peptide Fragments) RN - 0 (Recombinant Fusion Proteins) RN - EC 2.7.7.- (RNA Polymerase II) RN - EC 3.4.- (Endopeptidases) RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) RN - EC 5.99.1.3 (DNA Topoisomerases, Type II) SB - IM MH - Animals MH - Arabidopsis/enzymology MH - Catalytic Domain MH - DNA Topoisomerases, Type I/*chemistry/metabolism MH - DNA Topoisomerases, Type II/*chemistry/metabolism MH - Drosophila melanogaster/enzymology MH - Endopeptidases MH - Humans MH - Oocytes/enzymology MH - Peptide Fragments/chemistry/metabolism MH - RNA Polymerase II/metabolism MH - Recombinant Fusion Proteins/chemistry/metabolism MH - Saccharomyces cerevisiae/enzymology MH - Transcription, Genetic MH - Xenopus EDAT- 1999/06/25 MHDA- 1999/06/25 00:01 CRDT- 1999/06/25 00:00 PST - ppublish SO - Pac Symp Biocomput. 1999:578-89. PMID- 18773978 OWN - NLM STAT- MEDLINE DA - 20081028 DCOM- 20090109 LR - 20131121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1784 IP - 11 DP - 2008 Nov TI - Tryptophan fluorescence reveals induced folding of Vibrio harveyi acyl carrier protein upon interaction with partner enzymes. PG - 1835-43 LID - 10.1016/j.bbapap.2008.07.017 [doi] AB - We have introduced tryptophan as a local fluorescent probe to monitor the conformation of Vibrio harveyi acyl carrier protein (ACP), a small flexible protein that is unfolded at neutral pH but must undergo reversible conformational change during the synthesis and delivery of bacterial fatty acids. Consistent with known 3D structures of ACP, steady-state fluorescence and quenching experiments indicated that Trp at positions 46, 50, and 72 are buried in the hydrophobic core upon Mg(2+)-induced ACP folding, whereas residues 25 and 45 remain in a hydrophilic environment on the protein surface. Attachment of fatty acids to the phosphopantetheine prosthetic group progressively stabilized the folded conformation of all Trp-substituted ACPs, but longer chains (14:0) were less effective than medium chains (8:0) in shielding Trp from acrylamide quenching in the L46W protein. Interaction with ACP-dependent enzymes LpxA and holo-ACP synthase also caused folding of L46W; fluorescence quenching indicated proximity of Trp-45 in helix II of ACP in LpxA binding. Our results suggest that divalent cations and fatty acylation produce differing environments in the ACP core and also reveal enzyme partner-induced folding of ACP, a key feature of "natively unfolded" proteins. FAU - Gong, Huansheng AU - Gong H AD - Atlantic Research Centre, Department of Pediatrics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada. FAU - Murphy, Peter W AU - Murphy PW FAU - Langille, Gavin M AU - Langille GM FAU - Minielly, Sarah J AU - Minielly SJ FAU - Murphy, Anne AU - Murphy A FAU - McMaster, Christopher R AU - McMaster CR FAU - Byers, David M AU - Byers DM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080816 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Acyl Carrier Protein) RN - 0 (Enzymes) RN - 8DUH1N11BX (Tryptophan) RN - EC 2.3.- (Acyltransferases) RN - I38ZP9992A (Magnesium) SB - IM MH - Acyl Carrier Protein/*chemistry/isolation & purification/*metabolism MH - Acylation MH - Acyltransferases/metabolism MH - Circular Dichroism MH - Enzymes/*metabolism MH - Fluorescence MH - Magnesium/pharmacology MH - Models, Molecular MH - Protein Binding MH - Protein Conformation MH - *Protein Folding MH - Tryptophan/*chemistry/drug effects MH - Vibrio/chemistry/*metabolism EDAT- 2008/09/09 09:00 MHDA- 2009/01/10 09:00 CRDT- 2008/09/09 09:00 PHST- 2008/04/18 [received] PHST- 2008/06/30 [revised] PHST- 2008/07/29 [accepted] PHST- 2008/08/16 [aheadofprint] AID - S1570-9639(08)00242-2 [pii] AID - 10.1016/j.bbapap.2008.07.017 [doi] PST - ppublish SO - Biochim Biophys Acta. 2008 Nov;1784(11):1835-43. doi: 10.1016/j.bbapap.2008.07.017. Epub 2008 Aug 16. PMID- 8245034 OWN - NLM STAT- MEDLINE DA - 19940104 DCOM- 19940104 LR - 20101118 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 268 IP - 34 DP - 1993 Dec 5 TI - Structural and functional characterization of the HPV16 E7 protein expressed in bacteria. PG - 26018-25 AB - The E7 gene of the human papillomaviruses (HPV) encodes a 98-amino acid, multifunctional nuclear phosphoprotein with functional and structural similarities to adenovirus E1A and the papovavirus T antigens. E7 is a viral oncoprotein, which will cooperate with an activated ras oncogene to transform primary rodent cells, and can cooperate with the HPV E6 protein for the efficient immortalization of primary human keratinocytes. Due to the compelling epidemiological and experimental association between HPV infection and cervical cancer, we have undertaken a detailed study of the structure of the HPV16 E7 protein. The E7 protein was expressed in Escherichia coli as a native, unfused polypeptide, and soluble protein was purified by conventional chromatographic techniques. The purified protein was assessed for various biochemical and biophysical properties. Purified E7 binds the retinoblastoma protein avidly and specifically, and it can dissociate the E2F transcription factor when assayed in vitro. Circular dichroism spectroscopy indicated that E7 reversibly binds Zn2+ and Cd2+, resulting in a substantial increase in the alpha-helical content of the metal-bound E7 consistent with the stabilization of a hydrophobic core in the COOH terminus of the protein. FAU - Pahel, G AU - Pahel G AD - Wellcome Research Laboratories, Burroughs Wellcome Co., Research Triangle Park, North Carolina 27709. FAU - Aulabaugh, A AU - Aulabaugh A FAU - Short, S A AU - Short SA FAU - Barnes, J A AU - Barnes JA FAU - Painter, G R AU - Painter GR FAU - Ray, P AU - Ray P FAU - Phelps, W C AU - Phelps WC LA - eng PT - Comparative Study PT - Journal Article PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA Primers) RN - 0 (Oncogene Proteins, Viral) RN - 0 (Papillomavirus E7 Proteins) RN - 0 (Peptides) RN - 0 (Recombinant Proteins) RN - 0 (Retinoblastoma Protein) RN - 0 (oncogene protein E7, Human papillomavirus type 16) SB - IM GS - E7 MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Binding, Competitive MH - Chromatography, DEAE-Cellulose MH - Chromatography, Gel MH - Cloning, Molecular MH - DNA Primers MH - Escherichia coli MH - Female MH - Genes, Viral MH - Kinetics MH - Molecular Sequence Data MH - Oncogene Proteins, Viral/*chemistry/isolation & purification/*metabolism MH - Papillomaviridae/*metabolism MH - Papillomavirus E7 Proteins MH - Papillomavirus Infections/complications MH - Peptides/chemical synthesis/pharmacology MH - Protein Binding MH - *Protein Structure, Secondary MH - Recombinant Proteins/chemistry/isolation & purification/metabolism MH - Retinoblastoma Protein/*metabolism MH - Sequence Homology, Amino Acid MH - Tumor Virus Infections/complications MH - Uterine Cervical Neoplasms/microbiology MH - Vero Cells EDAT- 1993/12/05 MHDA- 1993/12/05 00:01 CRDT- 1993/12/05 00:00 PST - ppublish SO - J Biol Chem. 1993 Dec 5;268(34):26018-25. PMID- 19341745 OWN - NLM STAT- MEDLINE DA - 20090504 DCOM- 20090522 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 388 IP - 5 DP - 2009 May 22 TI - Modular organization of rabies virus phosphoprotein. PG - 978-96 LID - 10.1016/j.jmb.2009.03.061 [doi] AB - A phosphoprotein (P) is found in all viruses of the Mononegavirales order. These proteins form homo-oligomers, fulfil similar roles in the replication cycles of the various viruses, but differ in their length and oligomerization state. Sequence alignments reveal no sequence similarity among proteins from viruses belonging to the same family. Sequence analysis and experimental data show that phosphoproteins from viruses of the Paramyxoviridae contain structured domains alternating with intrinsically disordered regions. Here, we used predictions of disorder of secondary structure, and an analysis of sequence conservation to predict the domain organization of the phosphoprotein from Sendai virus, vesicular stomatitis virus (VSV) and rabies virus (RV P). We devised a new procedure for combining the results from multiple prediction methods and locating the boundaries between disordered regions and structured domains. To validate the proposed modular organization predicted for RV P and to confirm that the putative structured domains correspond to autonomous folding units, we used two-hybrid and biochemical approaches to characterize the properties of several fragments of RV P. We found that both central and C-terminal domains can fold in isolation, that the central domain is the oligomerization domain, and that the C-terminal domain binds to nucleocapsids. Our results suggest a conserved organization of P proteins in the Rhabdoviridae family in concatenated functional domains resembling that of the P proteins in the Paramyxoviridae family. FAU - Gerard, Francine C A AU - Gerard FC AD - UJF-EMBL-CNRS UMI 3265 - Unit of Virus Host Cell Interactions, Grenoble, France. FAU - Ribeiro, Euripedes de Almeida Jr AU - Ribeiro Ede A Jr FAU - Leyrat, Cedric AU - Leyrat C FAU - Ivanov, Ivan AU - Ivanov I FAU - Blondel, Danielle AU - Blondel D FAU - Longhi, Sonia AU - Longhi S FAU - Ruigrok, Rob W H AU - Ruigrok RW FAU - Jamin, Marc AU - Jamin M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090331 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (P phosphoprotein, Rabies virus) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Proteins) RN - 0 (Viral Structural Proteins) SB - IM MH - Amino Acid Sequence MH - Molecular Sequence Data MH - Phosphoproteins/*chemistry/genetics/metabolism MH - *Protein Conformation MH - Protein Folding MH - Rabies virus/*chemistry MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Sequence Analysis, Protein MH - Two-Hybrid System Techniques MH - Viral Structural Proteins/*chemistry/genetics/metabolism EDAT- 2009/04/04 09:00 MHDA- 2009/05/23 09:00 CRDT- 2009/04/04 09:00 PHST- 2008/11/12 [received] PHST- 2009/03/23 [revised] PHST- 2009/03/25 [accepted] PHST- 2009/03/31 [aheadofprint] AID - S0022-2836(09)00368-4 [pii] AID - 10.1016/j.jmb.2009.03.061 [doi] PST - ppublish SO - J Mol Biol. 2009 May 22;388(5):978-96. doi: 10.1016/j.jmb.2009.03.061. Epub 2009 Mar 31. PMID- 25298002 OWN - NLM STAT- In-Data-Review DA - 20141124 LR - 20150501 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 103 IP - 2 DP - 2015 Feb TI - Interactions of amelogenin with phospholipids. PG - 96-108 LID - 10.1002/bip.22573 [doi] AB - Amelogenin protein has the potential to interact with other enamel matrix proteins, mineral, and cell surfaces. We investigated the interactions of recombinant amelogenin rP172 with small unilamellar vesicles as model membranes, toward the goal of understanding the mechanisms of amelogenin-cell interactions during amelogenesis. Dynamic light scattering (DLS), fluorescence spectroscopy, circular dichroism (CD), and nuclear magnetic resonance (NMR) were used. In the presence of phospholipid vesicles, a blue shift in the Trp fluorescence emission maxima of rP172 was observed ( approximately 334 nm) and the Trp residues of rP172 were inaccessible to the aqueous quencher acrylamide. DLS studies indicated complexation of rP172 and phospholipids, although the possibility of fusion of phospholipids following amelogenin addition cannot be ruled out. NMR and CD studies revealed a disorder-order transition of rP172 in a model membrane environment. Strong fluorescence resonance energy transfer from Trp in rP172 to DNS-bound-phospholipid was observed, and fluorescence polarization studies indicated that rP172 interacted with the hydrophobic core region of model membranes. Our data suggest that amelogenin has ability to interact with phospholipids and that such interactions may play key roles in enamel biomineralization as well as reported amelogenin signaling activities. (c) 2014 Wiley Periodicals, Inc. Biopolymers 103: 96-108, 2015. CI - (c) 2014 Wiley Periodicals, Inc. FAU - Bekshe Lokappa, Sowmya AU - Bekshe Lokappa S AD - Center for Craniofacial Molecular Biology, Division of Biomedical Sciences, University of Southern California, Herman Ostrow School of Dentistry of USC, Los Angeles, CA, 90033. FAU - Balakrishna Chandrababu, Karthik AU - Balakrishna Chandrababu K FAU - Dutta, Kaushik AU - Dutta K FAU - Perovic, Iva AU - Perovic I FAU - Spencer Evans, John AU - Spencer Evans J FAU - Moradian-Oldak, Janet AU - Moradian-Oldak J LA - eng GR - P41 GM103481/GM/NIGMS NIH HHS/United States GR - R01 DE013414/DE/NIDCR NIH HHS/United States GR - R01 DE020099/DE/NIDCR NIH HHS/United States PT - Journal Article PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 SB - IM PMC - PMC4415992 MID - NIHMS634854 OID - NLM: NIHMS634854 [Available on 02/01/16] OID - NLM: PMC4415992 [Available on 02/01/16] OTO - NOTNLM OT - amelogenin OT - cell membrane OT - enamel OT - intrinsically disordered protein OT - lipid vesicles EDAT- 2014/10/10 06:00 MHDA- 2014/10/10 06:00 CRDT- 2014/10/10 06:00 PMCR- 2016/02/01 00:00 PHST- 2014/06/03 [received] PHST- 2014/08/29 [revised] PHST- 2014/10/02 [accepted] AID - 10.1002/bip.22573 [doi] PST - ppublish SO - Biopolymers. 2015 Feb;103(2):96-108. doi: 10.1002/bip.22573. PMID- 23317817 OWN - NLM STAT- MEDLINE DA - 20130115 DCOM- 20130916 IS - 1937-6448 (Print) VI - 301 DP - 2013 TI - New insights into desiccation-associated gene regulation by Lilium longiflorum ASR during pollen maturation and in transgenic Arabidopsis. PG - 37-94 LID - 10.1016/B978-0-12-407704-1.00002-6 [doi] LID - B978-0-12-407704-1.00002-6 [pii] AB - LLA23, a member of the abscisic acid-, stress-, and ripening-induced (ASR) protein family, was previously isolated from lily (Lilium longiflorum) pollen. The lily ASR is induced through desiccation-associated ABA signaling transduction in the pollen. ASRs are highly hydrophilic and intrinsically unstructured proteins with molecular masses generally less than 18 kDa. LLA23 is abundant in the cytoplasm and nuclei of both vegetative and generative cells of pollen grains. The protein in the nucleus and in the cytoplasm is partly regulated by dehydration. A dual role is proposed for LLA23, as a regulator and a protective molecule, upon exposure to water deficits. This chapter reviews the current state of literature on Asr genes, protein structure, function, and their responses to various stresses. In a study, a genome-wide microarray was used to monitor the expression of LLA23-regulated genes, focusing on the relationship between ASR-, glucose-, and drought-inducible genes, and outlined the difference and cross talk of gene expression among these signaling networks. A strong association was observed in the expression of stress-responsive genes and found 25 genes that respond to all three treatments. Highly inducible genes were also found in each specific stress treatment. Promoter sequence analysis of LLA23-inducible genes enabled us not only to identify possible known cis-acting elements in the promoter regions but also to expect the existence of novel cis-acting elements involved in ASR-responsive gene expression. ASR can be used to improve crops and economically important plants against various environmental stresses. CI - Copyright (c) 2013 Elsevier Inc. All rights reserved. FAU - Wang, Co-Shine AU - Wang CS AD - Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan. cswang2@nchu.edu.tw FAU - Hsu, Ssu-Wei AU - Hsu SW FAU - Hsu, Yi-Feng AU - Hsu YF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Netherlands TA - Int Rev Cell Mol Biol JT - International review of cell and molecular biology JID - 101475846 RN - 0 (Plant Proteins) SB - IM MH - Arabidopsis/*genetics/physiology MH - *Desiccation MH - *Gene Expression Regulation, Plant MH - Lilium/*genetics MH - Plant Proteins/chemistry/genetics/*metabolism MH - Plants, Genetically Modified MH - Pollen/*genetics/*growth & development EDAT- 2013/01/16 06:00 MHDA- 2013/09/17 06:00 CRDT- 2013/01/16 06:00 AID - B978-0-12-407704-1.00002-6 [pii] AID - 10.1016/B978-0-12-407704-1.00002-6 [doi] PST - ppublish SO - Int Rev Cell Mol Biol. 2013;301:37-94. doi: 10.1016/B978-0-12-407704-1.00002-6. PMID- 10543947 OWN - NLM STAT- MEDLINE DA - 19991119 DCOM- 19991119 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 293 IP - 3 DP - 1999 Oct 29 TI - Crystal structure of human catecholamine sulfotransferase. PG - 521-30 AB - Sulfonation, like phosphorylation, can modify the activity of a variety of biological molecules. The sulfotransferase enzymes sulfonate neurotransmitters, drugs, steroid hormones, dietary carcinogens and proteins. SULT1A3 specifically sulfonates catecholamines such as dopamine, adrenaline and noradrenaline. The crystal structure of SULT1A3 with a sulfate bound at the active site, has been determined at 2.4 A resolution. Although the core alpha/beta fold is like that of estrogen and heparan sulfotransferases, major differences occur in and around the active site. Most notably, several regions surrounding the active site, including a section of 40 residues, are disordered in SULT1A3. Regions that are topologically equivalent to the disordered parts of SULT1A3 are involved in substrate and cofactor binding in estrogen and heparan sulfotransferase. Flexibility in these regions suggests that ligand binding elicits a disorder-order transition in and around the active site of sulfotransferases and might contribute to the broad substrate specificity of these enzymes. CI - Copyright 1999 Academic Press. FAU - Bidwell, L M AU - Bidwell LM AD - Department of Physiology, University of Queensland, Brisbane, Queensland, 4072, Australia. FAU - McManus, M E AU - McManus ME FAU - Gaedigk, A AU - Gaedigk A FAU - Kakuta, Y AU - Kakuta Y FAU - Negishi, M AU - Negishi M FAU - Pedersen, L AU - Pedersen L FAU - Martin, J L AU - Martin JL LA - eng SI - PDB/1CJM PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Catecholamines) RN - 0 (Recombinant Proteins) RN - 0 (Sulfates) RN - EC 2.8.2.1 (Arylsulfotransferase) SB - IM MH - Amino Acid Sequence MH - Animals MH - Arylsulfotransferase/*chemistry/genetics/metabolism MH - Binding Sites MH - Catalytic Domain MH - Catecholamines/*metabolism MH - Conserved Sequence MH - Crystallization MH - Crystallography, X-Ray MH - Humans MH - Hydrogen Bonding MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Substrate Specificity MH - Sulfates/chemistry/metabolism EDAT- 1999/11/02 MHDA- 1999/11/02 00:01 CRDT- 1999/11/02 00:00 AID - 10.1006/jmbi.1999.3153 [doi] AID - S0022-2836(99)93153-4 [pii] PST - ppublish SO - J Mol Biol. 1999 Oct 29;293(3):521-30. PMID- 24976112 OWN - NLM STAT- MEDLINE DA - 20140812 DCOM- 20150419 LR - 20141215 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 23 IP - 9 DP - 2014 Sep TI - A maximum entropy approach to the study of residue-specific backbone angle distributions in alpha-synuclein, an intrinsically disordered protein. PG - 1275-90 LID - 10.1002/pro.2511 [doi] AB - alpha-Synuclein is an intrinsically disordered protein of 140 residues that switches to an alpha-helical conformation upon binding phospholipid membranes. We characterize its residue-specific backbone structure in free solution with a novel maximum entropy procedure that integrates an extensive set of NMR data. These data include intraresidue and sequential H(N) - H(alpha) and H(N) - H(N) NOEs, values for (3) JHNHalpha, (1) JHalphaCalpha, (2) JCalphaN, and (1) JCalphaN, as well as chemical shifts of (15)N, (13)C(alpha), and (13)C' nuclei, which are sensitive to backbone torsion angles. Distributions of these torsion angles were identified that yield best agreement to the experimental data, while using an entropy term to minimize the deviation from statistical distributions seen in a large protein coil library. Results indicate that although at the individual residue level considerable deviations from the coil library distribution are seen, on average the fitted distributions agree fairly well with this library, yielding a moderate population (20-30%) of the PPII region and a somewhat higher population of the potentially aggregation-prone beta region (20-40%) than seen in the database. A generally lower population of the alphaR region (10-20%) is found. Analysis of (1)H - (1)H NOE data required consideration of the considerable backbone diffusion anisotropy of a disordered protein. CI - Published 2014. This article is a U.S. Government work and is in the public domain in the USA. FAU - Mantsyzov, Alexey B AU - Mantsyzov AB AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892. FAU - Maltsev, Alexander S AU - Maltsev AS FAU - Ying, Jinfa AU - Ying J FAU - Shen, Yang AU - Shen Y FAU - Hummer, Gerhard AU - Hummer G FAU - Bax, Ad AU - Bax A LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140722 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (alpha-Synuclein) SB - IM MH - *Entropy MH - Molecular Dynamics Simulation MH - Nuclear Magnetic Resonance, Biomolecular MH - alpha-Synuclein/*chemistry PMC - PMC4243998 OID - NLM: PMC4243998 [Available on 09/01/15] OTO - NOTNLM OT - Karplus curve OT - diffusion anisotropy OT - intrinsically disordered proteins OT - random coil OT - short-range NOE EDAT- 2014/07/01 06:00 MHDA- 2015/04/22 06:00 CRDT- 2014/07/01 06:00 PMCR- 2015/09/01 00:00 PHST- 2014/04/23 [received] PHST- 2014/06/16 [accepted] PHST- 2014/07/22 [aheadofprint] AID - 10.1002/pro.2511 [doi] PST - ppublish SO - Protein Sci. 2014 Sep;23(9):1275-90. doi: 10.1002/pro.2511. Epub 2014 Jul 22. PMID- 24465598 OWN - NLM STAT- MEDLINE DA - 20140127 DCOM- 20141027 LR - 20141111 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 1 DP - 2014 TI - Transcription regulation of HYPK by Heat Shock Factor 1. PG - e85552 LID - 10.1371/journal.pone.0085552 [doi] AB - HYPK (Huntingtin Yeast Partner K) was originally identified by yeast two-hybrid assay as an interactor of Huntingtin, the protein mutated in Huntington's disease. HYPK was characterized earlier as an intrinsically unstructured protein having chaperone-like activity in vitro and in vivo. HYPK has the ability of reducing rate of aggregate formation and subsequent toxicity caused by mutant Huntingtin. Further investigation revealed that HYPK is involved in diverse cellular processes and required for normal functioning of cells. In this study we observed that hyperthermia increases HYPK expression in human and mouse cells in culture. Expression of exogenous Heat Shock Factor 1 (HSF1), upon heat treatment could induce HYPK expression, whereas HSF1 knockdown reduced endogenous as well as heat-induced HYPK expression. Putative HSF1-binding site present in the promoter of human HYPK gene was identified and validated by reporter assay. Chromatin immunoprecipitation revealed in vivo interaction of HSF1 and RNA polymerase II with HYPK promoter sequence. Additionally, acetylation of histone H4, a known epigenetic marker of inducible HSF1 binding, was observed in response to heat shock in HYPK gene promoter. Overexpression of HYPK inhibited cells from lethal heat-induced death whereas knockdown of HYPK made the cells susceptible to lethal heat shock-induced death. Apart from elevated temperature, HYPK was also upregulated by hypoxia and proteasome inhibition, two other forms of cellular stress. We concluded that chaperone-like protein HYPK is induced by cellular stress and under transcriptional regulation of HSF1. FAU - Das, Srijit AU - Das S AD - Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India. FAU - Bhattacharyya, Nitai Pada AU - Bhattacharyya NP AD - Crystallography & Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140121 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Carrier Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (HYPK protein, human) RN - 0 (Histones) RN - 0 (Proteasome Inhibitors) RN - 0 (Transcription Factors) RN - 0 (heat shock transcription factor) RN - EC 1.13.12.- (Luciferases) RN - EC 2.7.7.- (RNA Polymerase II) SB - IM MH - Acetylation MH - Animals MH - Binding Sites MH - Carrier Proteins/*genetics/metabolism MH - Cell Hypoxia MH - Cell Line, Tumor MH - DNA-Binding Proteins/*genetics/metabolism MH - *Gene Expression Regulation MH - Genes, Reporter MH - Histones/genetics/metabolism MH - Hot Temperature MH - Humans MH - Luciferases/genetics/metabolism MH - Mice MH - Promoter Regions, Genetic MH - Proteasome Inhibitors/pharmacology MH - Protein Binding MH - RNA Polymerase II/genetics/metabolism MH - Signal Transduction MH - Stress, Physiological/*genetics MH - Transcription Factors/*genetics/metabolism MH - Transcription, Genetic PMC - PMC3897489 OID - NLM: PMC3897489 EDAT- 2014/01/28 06:00 MHDA- 2014/10/28 06:00 CRDT- 2014/01/28 06:00 PHST- 2014 [ecollection] PHST- 2013/09/17 [received] PHST- 2013/12/04 [accepted] PHST- 2014/01/21 [epublish] AID - 10.1371/journal.pone.0085552 [doi] AID - PONE-D-13-38218 [pii] PST - epublish SO - PLoS One. 2014 Jan 21;9(1):e85552. doi: 10.1371/journal.pone.0085552. eCollection 2014. PMID- 14500891 OWN - NLM STAT- MEDLINE DA - 20030922 DCOM- 20040519 LR - 20140610 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 12 IP - 10 DP - 2003 Oct TI - Binding-induced folding transitions in calpastatin subdomains A and C. PG - 2327-36 AB - Calpastatin, the endogenous inhibitor of calpain, is an intrinsically unstructured protein proposed to undergo folding transitions upon binding to the enzyme. As this feature has never been experimentally tested, we have set out to characterize the conformation of two peptides corresponding to its conserved subdomains, A and C, known to interact with calpain in a Ca(2+)-dependent manner. The peptides are disordered in water but show a high propensity for alpha-helical conformation in the presence of trifluoroethanol. The conformational transition is sensitive to Ca(2+), and is clearly seen upon binding of the peptides to the enzyme. Secondary-structure prediction of all calpastatin sequences shows that the helix-forming potential within these regions is a conserved feature of the inhibitor. Furthermore, quantitative data on the binding strength of calpastatin fragments reveal that binding of the inhibitor is accompanied by a large decrease in its configurational entropy. Taken together, these observations point to significant binding-induced local folding transitions in calpastatin, in a way that ensures highly specific, yet reversible, action of the inhibitor. FAU - Mucsi, Zoltan AU - Mucsi Z AD - Department of Organic Chemistry, Eotvos Lorand University, H-1117 Budapest, Hungary. FAU - Hudecz, Ferenc AU - Hudecz F FAU - Hollosi, Miklos AU - Hollosi M FAU - Tompa, Peter AU - Tompa P FAU - Friedrich, Peter AU - Friedrich P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Calcium-Binding Proteins) RN - 0 (Peptides) RN - 0 (Recombinant Proteins) RN - 059QF0KO0R (Water) RN - 75-89-8 (Trifluoroethanol) RN - 79079-11-1 (calpastatin) RN - EC 3.4.22.- (Calpain) RN - SY7Q814VUP (Calcium) SB - IM MH - Animals MH - Binding Sites MH - Calcium/chemistry MH - Calcium-Binding Proteins/*chemistry/genetics/metabolism MH - Calpain/chemistry MH - Cattle MH - Circular Dichroism MH - Computational Biology MH - Databases, Protein MH - Entropy MH - Humans MH - Mice MH - Peptides/chemical synthesis/chemistry MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Secondary MH - Rabbits MH - Rats MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Alignment MH - Trifluoroethanol/chemistry MH - Water/chemistry PMC - PMC2366912 OID - NLM: PMC2366912 EDAT- 2003/09/23 05:00 MHDA- 2004/05/20 05:00 CRDT- 2003/09/23 05:00 AID - 10.1110/ps.03138803 [doi] PST - ppublish SO - Protein Sci. 2003 Oct;12(10):2327-36. PMID- 15292204 OWN - NLM STAT- MEDLINE DA - 20040927 DCOM- 20041115 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 40 DP - 2004 Oct 1 TI - BBK32, a fibronectin binding MSCRAMM from Borrelia burgdorferi, contains a disordered region that undergoes a conformational change on ligand binding. PG - 41706-14 AB - BBK32 is a fibronectin-binding lipoprotein on Borrelia burgdorferi, the causative agent of Lyme disease. Analysis using secondary structure prediction programs suggested that BBK32 is composed of two domains, an N-terminal segment lacking well defined secondary structure and a C-terminal segment composed largely of alpha-helices. Analysis of purified recombinant forms of the two domains by circular dichroism spectroscopy, gel permeation chromatography, and intrinsic viscosity determination were consistent with an N-terminal-extended, unstructured segment and a C-terminal globular domain in BBK32. Solid phase binding experiments suggest that the unstructured N-terminal domain binds fibronectin. Analysis of changes in circular dichroism spectra of the N-terminal segment of BBK32 upon binding of the N-terminal domain of fibronectin revealed an increase in beta-sheet content in the complex. Hence, BBK32, which belongs to a different family of proteins and shows no overall sequence similarity with the fibronectin binding MSCRAMMs (microbial surface components recognizing adhesive matrix molecules) of Gram-positive bacteria, binds fibronectin by a mechanism that is reminiscent of the "tandem beta-zipper" previously demonstrated for the fibronectin binding of streptococcal adhesins. FAU - Kim, Jung Hwa AU - Kim JH AD - Center for Extracellular Matrix Biology, Albert B. Alkek Institute of Biosciences and Technology, Texas A and M University System Health Science Center, Houston, Texas 77030, USA. FAU - Singvall, Jenny AU - Singvall J FAU - Schwarz-Linek, Ulrich AU - Schwarz-Linek U FAU - Johnson, Barbara J B AU - Johnson BJ FAU - Potts, Jennifer R AU - Potts JR FAU - Hook, Magnus AU - Hook M LA - eng GR - AI20624/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20040729 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Adhesins, Bacterial) RN - 0 (Bacterial Proteins) RN - 0 (Fibronectins) RN - 0 (Ligands) RN - 0 (p35 antigen, Borrelia) SB - IM MH - Adhesins, Bacterial/metabolism MH - Amino Acid Motifs MH - Bacterial Proteins/*chemistry/*metabolism MH - Borrelia burgdorferi Group/*chemistry MH - Fibronectins/*metabolism MH - Ligands MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary EDAT- 2004/08/05 05:00 MHDA- 2004/11/16 09:00 CRDT- 2004/08/05 05:00 PHST- 2004/07/29 [aheadofprint] AID - 10.1074/jbc.M401691200 [doi] AID - M401691200 [pii] PST - ppublish SO - J Biol Chem. 2004 Oct 1;279(40):41706-14. Epub 2004 Jul 29. PMID- 15713488 OWN - NLM STAT- MEDLINE DA - 20050216 DCOM- 20050329 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 346 IP - 5 DP - 2005 Mar 11 TI - Solution structure of human saposin C in a detergent environment. PG - 1381-92 AB - Saposin C is a lysosomal, membrane-binding protein that acts as an activator for the hydrolysis of glucosylceramide by the enzyme glucocerebrosidase. We used high-resolution NMR to determine the three-dimensional solution structure of saposin C in the presence of the detergent sodium dodecyl sulfate (SDS). This structure provides the first representation of membrane bound saposin C at the atomic level. In the presence of SDS, the protein adopts an open conformation with an exposed hydrophobic pocket. In contrast, the previously reported NMR structure of saposin C in the absence of SDS is compact and contains a hydrophobic core that is not exposed to the solvent. NMR data indicate that the SDS molecules interact with the hydrophobic pocket. The structure of saposin C in the presence of SDS is very similar to a monomer in the saposin B homodimer structure. Their comparison reveals possible similarity in the type of protein/lipid interaction as well as structural components differentiating their quaternary structures and functional specificity. FAU - Hawkins, Cheryl A AU - Hawkins CA AD - Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 Center Drive, Bethesda, MD 20892, USA. FAU - de Alba, Eva AU - de Alba E FAU - Tjandra, Nico AU - Tjandra N LA - eng SI - PDB/1SN6 PT - Journal Article DEP - 20050120 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Saposins) RN - 0 (Solutions) RN - 368GB5141J (Sodium Dodecyl Sulfate) SB - IM MH - Crystallography, X-Ray MH - Humans MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - *Protein Conformation MH - Saposins/*chemistry/metabolism MH - Sodium Dodecyl Sulfate/*chemistry/metabolism MH - Solutions EDAT- 2005/02/17 09:00 MHDA- 2005/03/30 09:00 CRDT- 2005/02/17 09:00 PHST- 2004/06/15 [received] PHST- 2004/11/04 [revised] PHST- 2004/12/20 [accepted] PHST- 2005/01/20 [aheadofprint] AID - S0022-2836(04)01615-8 [pii] AID - 10.1016/j.jmb.2004.12.045 [doi] PST - ppublish SO - J Mol Biol. 2005 Mar 11;346(5):1381-92. Epub 2005 Jan 20. PMID- 15024385 OWN - NLM STAT- MEDLINE DA - 20040329 DCOM- 20040519 LR - 20120625 IS - 1545-9993 (Print) IS - 1545-9985 (Linking) VI - 11 IP - 4 DP - 2004 Apr TI - p27 binds cyclin-CDK complexes through a sequential mechanism involving binding-induced protein folding. PG - 358-64 AB - p27 controls cell proliferation by binding and regulating nuclear cyclin-dependent kinases (CDKs). In addition, p27 interacts with other nuclear and cytoplasmic targets and has diverse biological functions. We seek to understand how the structural and dynamic properties of p27 mediate its several functions. We show that, despite showing disorder before binding its targets, p27 has nascent secondary structure that may have a function in molecular recognition. Binding to Cdk2-cyclin A is accompanied by p27 folding, and kinetic data suggest a sequential mechanism that is initiated by binding to cyclin A. p27 regulates CDK-cyclin complexes involved directly in cell cycle control and does not interact with other closely related CDKs. We show that p27-cyclin interactions are an important determinant of this specificity and propose that the homologous cell cycle regulators p21 and p57 function by a similar sequential, folding-on-binding mechanism. FAU - Lacy, Eilyn R AU - Lacy ER AD - Department of Structural Biology, St. Jude Children's Research Hospital, 332, North Lauderdale Street, Memphis, Tennessee 38105, USA. FAU - Filippov, Igor AU - Filippov I FAU - Lewis, William S AU - Lewis WS FAU - Otieno, Steve AU - Otieno S FAU - Xiao, Limin AU - Xiao L FAU - Weiss, Sonja AU - Weiss S FAU - Hengst, Ludger AU - Hengst L FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng SI - PDB/1JSU GR - P30 CA21765/CA/NCI NIH HHS/United States GR - R01 CA82491/CA/NCI NIH HHS/United States GR - S10 RR014675/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20040314 PL - United States TA - Nat Struct Mol Biol JT - Nature structural & molecular biology JID - 101186374 RN - 0 (Cyclins) RN - 0 (Microfilament Proteins) RN - 0 (Muscle Proteins) RN - 0 (Solutions) RN - 0 (Tagln protein, mouse) RN - EC 2.7.11.22 (CDC2-CDC28 Kinases) RN - EC 2.7.11.22 (CDK2 protein, human) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 2) SB - IM MH - Amino Acid Sequence MH - CDC2-CDC28 Kinases/chemistry/*metabolism MH - Conserved Sequence MH - Cyclin-Dependent Kinase 2 MH - Cyclins/*chemistry/metabolism MH - Humans MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Microfilament Proteins/*chemistry/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - *Muscle Proteins MH - Protein Conformation MH - Protein Folding MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Solutions MH - Thermodynamics EDAT- 2004/03/17 05:00 MHDA- 2004/05/20 05:00 CRDT- 2004/03/17 05:00 PHST- 2003/10/09 [received] PHST- 2004/02/18 [accepted] PHST- 2004/03/14 [aheadofprint] AID - 10.1038/nsmb746 [doi] AID - nsmb746 [pii] PST - ppublish SO - Nat Struct Mol Biol. 2004 Apr;11(4):358-64. Epub 2004 Mar 14. PMID- 24192542 OWN - NLM STAT- MEDLINE DA - 20140207 DCOM- 20140923 IS - 1660-2862 (Electronic) IS - 1660-2854 (Linking) VI - 13 IP - 2-3 DP - 2014 TI - Defining the native state of alpha-synuclein. PG - 114-7 LID - 10.1159/000355516 [doi] AB - Misfolding and pathogenic aggregation of alpha-synuclein (alphaSyn) is a hallmark of familial and sporadic Parkinson's disease, but the physiological state of the protein in cells remains unsettled. We have further examined our hypothesis that endogenous alphaSyn can occur in normal cells as a metastable, helically folded tetramer, not solely as the unfolded monomer long thought to be its native form. At this meeting, we reviewed our recent approaches for trapping alphaSyn in intact cells via in vivo crosslinking, a 5-step purification of alphaSyn from normal human brain, and the generation of new monoclonal antibodies to alphaSyn that enable general and oligomer-selective ELISAs. Crosslinking in intact living cells confirmed that alphaSyn occurs in the cytosol of neurons and non-neural cells in substantial part as metastable tetramers and related oligomers, plus varying amounts of free monomers. The non-pathogenic homolog, beta-synuclein, forms closely similar oligomeric assemblies, suggesting that the oligomers we observe for alphaSyn are also physiological. In contrast to other normal oligomeric proteins (e.g., DJ-1), alphaSyn tetramers dissociate rapidly to monomers upon conventional cell lysis but are retained partially as tetramers if cells are lysed at high protein concentrations ('molecular crowding'). Thus, alphaSyn exists natively as helical tetramers that are in dynamic equilibrium with unfolded monomers. The tetramers appear relatively resistant to aggregation, in contrast to monomers, which may give rise to fibrillar inclusions. FAU - Selkoe, Dennis AU - Selkoe D AD - Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass., USA. FAU - Dettmer, Ulf AU - Dettmer U FAU - Luth, Eric AU - Luth E FAU - Kim, Nora AU - Kim N FAU - Newman, Andrew AU - Newman A FAU - Bartels, Tim AU - Bartels T LA - eng PT - Journal Article PT - Review DEP - 20131030 PL - Switzerland TA - Neurodegener Dis JT - Neuro-degenerative diseases JID - 101189034 RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Brain/metabolism/pathology MH - Humans MH - Parkinson Disease/metabolism/pathology MH - alpha-Synuclein/*chemistry/*isolation & purification EDAT- 2013/11/07 06:00 MHDA- 2014/09/24 06:00 CRDT- 2013/11/07 06:00 PHST- 2013/05/06 [received] PHST- 2013/09/06 [accepted] PHST- 2013/10/30 [aheadofprint] AID - 000355516 [pii] AID - 10.1159/000355516 [doi] PST - ppublish SO - Neurodegener Dis. 2014;13(2-3):114-7. doi: 10.1159/000355516. Epub 2013 Oct 30. PMID- 22995936 OWN - NLM STAT- MEDLINE DA - 20121112 DCOM- 20130722 LR - 20140220 IS - 1878-3279 (Electronic) IS - 0171-2985 (Linking) VI - 217 IP - 12 DP - 2012 Dec TI - KAP1/TRIM28: an inhibitor of IRF5 function in inflammatory macrophages. PG - 1315-24 LID - 10.1016/j.imbio.2012.07.026 [doi] LID - S0171-2985(12)00190-8 [pii] AB - IRF5 plays a key role in the induction of pro-inflammatory cytokines, contributing to the plasticity and polarisation of macrophages to an M1 phenotype and initiation of a potent T(H)1-T(H)17 response. To better understand the means of IRF5 transcriptional action, we conducted a screen for IRF5-interacting partners by affinity purification coupled to mass spectrometry and identified KAP1/TRIM28 as a novel protein-protein interaction partner of IRF5. KAP1 acts as a transcriptional co-repressor, chiefly via recruitment of complexes involved in chromatin silencing, such as histone deacetylases and methyltransferases. We mapped the N-terminus of IRF5, encompassing its DNA-binding domain together with a highly intrinsically disordered region, as crucial for the IRF5-KAP1 interaction interface, and demonstrated that IRF5 can also form complexes with the methyltransferase SETDB1. Knockdown of KAP1 (TRIM28) gene expression in human M1 macrophages potentiated IRF5-mediated expression of TNF and other M1 macrophage markers. This effect may be linked to methyltransferase activity of SETDB1, such as trimethylation of lysine 9 of histone 3 (H3K9me3), deposition of which was decreased at the human TNF locus upon KAP1 knockdown. Our study furthers an understanding of the complex molecular interactions between the TRIM and IRF protein families, and highlights a role of the inhibitory properties of KAP1 in association with IRF5-mediated gene expression. CI - Copyright (c) 2012 Elsevier GmbH. All rights reserved. FAU - Eames, H L AU - Eames HL AD - Kennedy Institute of Rheumatology, Imperial College, 65 Aspenlea Road, London W6 8LH, United Kingdom. h.eames09@imperial.ac.uk FAU - Saliba, D G AU - Saliba DG FAU - Krausgruber, T AU - Krausgruber T FAU - Lanfrancotti, A AU - Lanfrancotti A FAU - Ryzhakov, G AU - Ryzhakov G FAU - Udalova, I A AU - Udalova IA LA - eng GR - MR/J001899/1/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120811 PL - Netherlands TA - Immunobiology JT - Immunobiology JID - 8002742 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Chromatin) RN - 0 (Co-Repressor Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (IRF5 protein, human) RN - 0 (Interferon Regulatory Factors) RN - 0 (Irf5 protein, mouse) RN - 0 (Membrane Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Repressor Proteins) RN - 0 (TNF protein, human) RN - 0 (TRIM protein, human) RN - 0 (TRIM28 protein, human) RN - 0 (Trim28 protein, mouse) RN - 0 (Tumor Necrosis Factor-alpha) RN - EC 2.1.1.- (Protein Methyltransferases) RN - EC 2.1.1.- (SETDB1 protein, human) RN - EC 3.5.1.98 (Histone Deacetylases) SB - IM MH - Adaptor Proteins, Signal Transducing/genetics/metabolism MH - Animals MH - Cells, Cultured MH - Chromatin/genetics/metabolism MH - Co-Repressor Proteins/genetics/metabolism MH - DNA-Binding Proteins/genetics/metabolism MH - Gene Silencing MH - HEK293 Cells MH - Histone Deacetylases/genetics/metabolism MH - Humans MH - Inflammation/genetics/metabolism/*pathology MH - Interferon Regulatory Factors/*antagonists & inhibitors/genetics/*metabolism MH - Macrophages/*metabolism/pathology MH - Membrane Proteins/genetics/metabolism MH - Mice MH - Nuclear Proteins/genetics/*metabolism MH - Protein Interaction Domains and Motifs MH - Protein Methyltransferases/genetics/metabolism MH - Repressor Proteins/genetics/*metabolism MH - Transcription, Genetic MH - Tumor Necrosis Factor-alpha/genetics/metabolism EDAT- 2012/09/22 06:00 MHDA- 2013/07/23 06:00 CRDT- 2012/09/22 06:00 PHST- 2012/04/24 [received] PHST- 2012/07/20 [revised] PHST- 2012/07/27 [accepted] PHST- 2012/08/11 [aheadofprint] AID - S0171-2985(12)00190-8 [pii] AID - 10.1016/j.imbio.2012.07.026 [doi] PST - ppublish SO - Immunobiology. 2012 Dec;217(12):1315-24. doi: 10.1016/j.imbio.2012.07.026. Epub 2012 Aug 11. PMID- 21463585 OWN - NLM STAT- MEDLINE DA - 20110405 DCOM- 20110712 LR - 20140820 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 100 IP - 7 DP - 2011 Apr 6 TI - The calponin regulatory region is intrinsically unstructured: novel insight into actin-calponin and calmodulin-calponin interfaces using NMR spectroscopy. PG - 1718-28 LID - 10.1016/j.bpj.2011.01.040 [doi] AB - Calponin is an actin- and calmodulin-binding protein believed to regulate the function of actin. Low-resolution studies based on proteolysis established that the recombinant calponin fragment 131-228 contained actin and calmodulin recognition sites but failed to precisely identify the actin-binding determinants. In this study, we used NMR spectroscopy to investigate the structure of this functionally important region of calponin and map its interaction with actin and calmodulin at amino-acid resolution. Our data indicates that the free calponin peptide is largely unstructured in solution, although four short amino-acid stretches corresponding to residues 140-146, 159-165, 189-195, and 199-205 display the propensity to form alpha-helices. The presence of four sequential transient helices probably provides the conformational malleability needed for the promiscuous nature of this region of calponin. We identified all amino acids involved in actin binding and demonstrated for the first time, to our knowledge, that the N-terminal flanking region of Lys(137)-Tyr(144) is an integral part of the actin-binding site. We have also delineated the second actin-binding site to amino acids Thr(180)-Asp(190). Ca(2+)-calmodulin binding extends beyond the previously identified minimal sequence of 153-163 and includes most amino acids within the stretch 143-165. In addition, we found that calmodulin induces chemical shift perturbations of amino acids 188-190 demonstrating for the first time, to our knowledge, an effect of Ca(2+)-calmodulin on this region. The spatial relationship of the actin and calmodulin contacts as well as the transient alpha-helical structures within the regulatory region of calponin provides a structural framework for understanding the Ca(2+)-dependent regulation of the actin-calponin interaction by calmodulin. CI - Copyright (c) 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Pfuhl, Mark AU - Pfuhl M AD - Department of Biochemistry, University of Leicester, Leicester, United Kingdom. FAU - Al-Sarayreh, Sameeh AU - Al-Sarayreh S FAU - El-Mezgueldi, Mohammed AU - El-Mezgueldi M LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Actins) RN - 0 (Amino Acids) RN - 0 (Calcium-Binding Proteins) RN - 0 (Calmodulin) RN - 0 (Microfilament Proteins) RN - 0 (calponin) SB - IM MH - Actins/*metabolism MH - Amino Acid Sequence MH - Amino Acids/metabolism MH - Animals MH - Binding Sites MH - Calcium-Binding Proteins/*chemistry/*metabolism MH - Calmodulin/*metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Mice MH - Microfilament Proteins/*chemistry/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Rabbits MH - Structure-Activity Relationship MH - Temperature MH - Titrimetry PMC - PMC3072660 OID - NLM: PMC3072660 EDAT- 2011/04/06 06:00 MHDA- 2011/07/13 06:00 CRDT- 2011/04/06 06:00 PHST- 2010/07/27 [received] PHST- 2010/12/30 [revised] PHST- 2011/01/03 [accepted] AID - S0006-3495(11)00123-8 [pii] AID - 10.1016/j.bpj.2011.01.040 [doi] PST - ppublish SO - Biophys J. 2011 Apr 6;100(7):1718-28. doi: 10.1016/j.bpj.2011.01.040. PMID- 19106096 OWN - NLM STAT- MEDLINE DA - 20090316 DCOM- 20090514 LR - 20140901 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 284 IP - 12 DP - 2009 Mar 20 TI - PEP-19, an intrinsically disordered regulator of calmodulin signaling. PG - 7455-64 LID - 10.1074/jbc.M808067200 [doi] AB - PEP-19 is a small calmodulin (CaM)-binding protein that greatly increases the rates of association and dissociation of Ca(2+) from the C-domain of CaM, an effect that is mediated by an acidic/IQ sequence in PEP-19. We show here using NMR that PEP-19 is an intrinsically disordered protein, but with residual structure localized to its acidic/IQ motif. We also show that the k(on) and k(off) rates for binding PEP-19 to apo-CaM are at least 50-fold slower than for binding to Ca(2+)-CaM. These data indicate that intrinsic disorder confers plasticity that allows PEP-19 to bind to either apo- or Ca(2+)-CaM via different structural modes, and that complex formation may be facilitated by conformational selection of residual structure in the acidic/IQ sequence. FAU - Kleerekoper, Quinn K AU - Kleerekoper QK AD - Department of Biochemistry and Molecular Biology and the Structural Biology Center, University of Texas, Houston Medical School, Houston, Texas 77030, USA. FAU - Putkey, John A AU - Putkey JA LA - eng GR - GM069611/GM/NIGMS NIH HHS/United States GR - NS038310/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20081223 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Calmodulin) RN - 0 (Nerve Tissue Proteins) RN - 106494-08-0 (PCP4 protein, human) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Motifs/physiology MH - Animals MH - Calcium/chemistry/metabolism MH - Calmodulin/*chemistry/metabolism MH - Humans MH - Nerve Tissue Proteins/*chemistry/metabolism MH - Protein Binding/physiology MH - Protein Structure, Tertiary/physiology MH - Signal Transduction/*physiology PMC - PMC2658041 OID - NLM: PMC2658041 EDAT- 2008/12/25 09:00 MHDA- 2009/05/15 09:00 CRDT- 2008/12/25 09:00 PHST- 2008/12/23 [aheadofprint] AID - M808067200 [pii] AID - 10.1074/jbc.M808067200 [doi] PST - ppublish SO - J Biol Chem. 2009 Mar 20;284(12):7455-64. doi: 10.1074/jbc.M808067200. Epub 2008 Dec 23. PMID- 18710925 OWN - NLM STAT- MEDLINE DA - 20080826 DCOM- 20080916 LR - 20140903 IS - 1540-8140 (Electronic) IS - 0021-9525 (Linking) VI - 182 IP - 4 DP - 2008 Aug 25 TI - Structural basis for distinctive recognition of fibrinogen gammaC peptide by the platelet integrin alphaIIbbeta3. PG - 791-800 LID - 10.1083/jcb.200801146 [doi] AB - Hemostasis and thrombosis (blood clotting) involve fibrinogen binding to integrin alpha(IIb)beta(3) on platelets, resulting in platelet aggregation. alpha(v)beta(3) binds fibrinogen via an Arg-Asp-Gly (RGD) motif in fibrinogen's alpha subunit. alpha(IIb)beta(3) also binds to fibrinogen; however, it does so via an unstructured RGD-lacking C-terminal region of the gamma subunit (gammaC peptide). These distinct modes of fibrinogen binding enable alpha(IIb)beta(3) and alpha(v)beta(3) to function cooperatively in hemostasis. In this study, crystal structures reveal the integrin alpha(IIb)beta(3)-gammaC peptide interface, and, for comparison, integrin alpha(IIb)beta(3) bound to a lamprey gammaC primordial RGD motif. Compared with RGD, the GAKQAGDV motif in gammaC adopts a different backbone configuration and binds over a more extended region. The integrin metal ion-dependent adhesion site (MIDAS) Mg(2+) ion binds the gammaC Asp side chain. The adjacent to MIDAS (ADMIDAS) Ca(2+) ion binds the gammaC C terminus, revealing a contribution for ADMIDAS in ligand binding. Structural data from this natively disordered gammaC peptide enhances our understanding of the involvement of gammaC peptide and integrin alpha(IIb)beta(3) in hemostasis and thrombosis. FAU - Springer, Timothy A AU - Springer TA AD - Department of Pathology, Immune Disease Institute, Harvard Medical School, Boston, MA 02115, USA. FAU - Zhu, Jianghai AU - Zhu J FAU - Xiao, Tsan AU - Xiao T LA - eng GR - HL48675/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20080818 PL - United States TA - J Cell Biol JT - The Journal of cell biology JID - 0375356 RN - 0 (Oligopeptides) RN - 0 (Peptides) RN - 0 (Peptides, Cyclic) RN - 0 (Platelet Glycoprotein GPIIb-IIIa Complex) RN - 0 (Protein Subunits) RN - 9001-32-5 (Fibrinogen) RN - 99896-85-2 (arginyl-glycyl-aspartic acid) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Blood Platelets/*metabolism MH - Fibrinogen/*chemistry/*metabolism MH - Lampreys MH - Models, Molecular MH - Molecular Sequence Data MH - Oligopeptides/metabolism MH - Peptides/*chemistry/*metabolism MH - Peptides, Cyclic/metabolism MH - Platelet Glycoprotein GPIIb-IIIa Complex/chemistry/*metabolism MH - Protein Subunits/chemistry/metabolism MH - Structure-Activity Relationship MH - X-Ray Diffraction PMC - PMC2518716 OID - NLM: PMC2518716 EDAT- 2008/08/20 09:00 MHDA- 2008/09/17 09:00 CRDT- 2008/08/20 09:00 PHST- 2008/08/18 [aheadofprint] AID - jcb.200801146 [pii] AID - 10.1083/jcb.200801146 [doi] PST - ppublish SO - J Cell Biol. 2008 Aug 25;182(4):791-800. doi: 10.1083/jcb.200801146. Epub 2008 Aug 18. PMID- 22004751 OWN - NLM STAT- MEDLINE DA - 20111018 DCOM- 20120202 LR - 20141021 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 101 IP - 8 DP - 2011 Oct 19 TI - Mechanical unfolding of cardiac myosin binding protein-C by atomic force microscopy. PG - 1968-77 LID - 10.1016/j.bpj.2011.08.030 [doi] AB - Cardiac myosin-binding protein-C (cMyBP-C) is a thick-filament-associated protein that performs regulatory and structural roles within cardiac sarcomeres. It is a member of the immunoglobulin (Ig) superfamily of proteins consisting of eight Ig- and three fibronectin (FNIII)-like domains, along with a unique regulatory sequence referred to as the M-domain, whose structure is unknown. Domains near the C-terminus of cMyBP-C bind tightly to myosin and mediate the association of cMyBP-C with thick (myosin-containing) filaments, whereas N-terminal domains, including the regulatory M-domain, bind reversibly to myosin S2 and/or actin. The ability of MyBP-C to bind to both myosin and actin raises the possibility that cMyBP-C cross-links myosin molecules within the thick filament and/or cross-links myosin and thin (actin-containing) filaments together. In either scenario, cMyBP-C could be under mechanical strain. However, the physical properties of cMyBP-C and its behavior under load are completely unknown. Here, we investigated the mechanical properties of recombinant baculovirus-expressed cMyBP-C using atomic force microscopy to assess the stability of individual cMyBP-C molecules in response to stretch. Force-extension curves showed the presence of long extensible segment(s) that became stretched before the unfolding of individual Ig and FNIII domains, which were evident as sawtooth peaks in force spectra. The forces required to unfold the Ig/FNIII domains at a stretch rate of 500 nm/s increased monotonically from approximately 30 to approximately 150 pN, suggesting a mechanical hierarchy among the different Ig/FNIII domains. Additional experiments using smaller recombinant proteins showed that the regulatory M-domain lacks significant secondary or tertiary structure and is likely an intrinsically disordered region of cMyBP-C. Together, these data indicate that cMyBP-C exhibits complex mechanical behavior under load and contains multiple domains with distinct mechanical properties. CI - Copyright (c) 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Karsai, Arpad AU - Karsai A AD - University of California-Davis, Davis, California, USA. FAU - Kellermayer, Miklos S Z AU - Kellermayer MS FAU - Harris, Samantha P AU - Harris SP LA - eng GR - R01 HL080367/HL/NHLBI NIH HHS/United States GR - R01 HL080367/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Carrier Proteins) RN - 0 (Fibronectins) RN - 0 (Immunoglobulins) RN - 0 (myosin-binding protein C) SB - IM MH - Animals MH - Biomechanical Phenomena MH - Carrier Proteins/*chemistry MH - Disease MH - Fibronectins/chemistry MH - Immunoglobulins/chemistry MH - Kinetics MH - *Mechanical Processes MH - Mice MH - *Microscopy, Atomic Force MH - Muscle Contraction MH - Protein Stability MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - *Protein Unfolding PMC - PMC3192966 OID - NLM: PMC3192966 EDAT- 2011/10/19 06:00 MHDA- 2012/02/03 06:00 CRDT- 2011/10/19 06:00 PHST- 2011/06/17 [received] PHST- 2011/08/12 [revised] PHST- 2011/08/19 [accepted] AID - S0006-3495(11)01003-4 [pii] AID - 10.1016/j.bpj.2011.08.030 [doi] PST - ppublish SO - Biophys J. 2011 Oct 19;101(8):1968-77. doi: 10.1016/j.bpj.2011.08.030. PMID- 17722063 OWN - NLM STAT- MEDLINE DA - 20080115 DCOM- 20080513 IS - 1097-4547 (Electronic) IS - 0360-4012 (Linking) VI - 86 IP - 2 DP - 2008 Feb 1 TI - Structure, properties, and functions of the human small heat-shock protein HSP22 (HspB8, H11, E2IG1): a critical review. PG - 264-9 AB - The recently described human HSP22 belongs to the superfamily of small heat-shock proteins containing a conservative alpha-crystallin domain. HSP22 seems to be involved in regulation of cell proliferation, cardiac hypertrophy, apoptosis, and carcinogenesis, and expression of point mutants of HSP22 correlates with development of different neuromuscular diseases. Therefore, an investigation of the structure and properties of HSP22 is desirable for understanding its multiple functions. HSP22 seems to belong to the group of so-called intrinsically disordered proteins and possesses a highly flexible structure. HSP22 tends to form small-molecular-mass oligomers and interacts with biological membranes and many different proteins, among them glycolytic enzymes and different protein kinases. HSP22 possesses chaperonelike activity and prevents aggregation of denatured proteins both in vitro and in vivo. Depending on the cell type and its expression, HSP22 might have either pro- or anti-apoptotic effects. Chaperonelike activity seems to be important for antiapoptotic effects, whereas interaction with and regulation of certain protein kinases might be important for the proapoptotic effects of HSP22. Expression of K141N or K141E mutants of HSP22 correlates with development of distal hereditary motor neuropathy and/or Charcot-Marie-Tooth disease. These mutations destabilize the structure of HSP22, affect its interaction with other small heat-shock proteins, and decrease its chaperonelike activity. HSP22 decreases or prevents aggregation of Huntingtin fragments and amyloid-beta peptide 1-40 of the Dutch type. Thus, HSP22 seems to play an important role in the nervous system, and further investigations are needed to understand the molecular mechanisms of its functioning. CI - (c) 2007 Wiley-Liss, Inc. FAU - Shemetov, Anton A AU - Shemetov AA AD - Department of Biochemistry, School of Biology, Moscow State University, Moscow, Russia. FAU - Seit-Nebi, Alim S AU - Seit-Nebi AS FAU - Gusev, Nikolai B AU - Gusev NB LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - J Neurosci Res JT - Journal of neuroscience research JID - 7600111 RN - 0 (Heat-Shock Proteins) RN - EC 2.7.1.- (HSPB8 protein, human) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - Heat-Shock Proteins/*chemistry/*physiology MH - Humans MH - Protein-Serine-Threonine Kinases/*chemistry/*physiology MH - Structure-Activity Relationship RF - 54 EDAT- 2007/08/28 09:00 MHDA- 2008/05/14 09:00 CRDT- 2007/08/28 09:00 AID - 10.1002/jnr.21441 [doi] PST - ppublish SO - J Neurosci Res. 2008 Feb 1;86(2):264-9. PMID- 2537470 OWN - NLM STAT- MEDLINE DA - 19890406 DCOM- 19890406 LR - 20101118 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 337 IP - 6209 DP - 1989 Feb 23 TI - The three-dimensional structure of foot-and-mouth disease virus at 2.9 A resolution. PG - 709-16 AB - The structure of foot-and-mouth disease virus has been determined at close to atomic resolution by X-ray diffraction without experimental phase information. The virus shows similarities with other picornaviruses but also several unique features. The canyon or pit found in other picornaviruses is absent; this has important implications for cell attachment. The most immunogenic portion of the capsid, which acts as a potent peptide vaccine, forms a disordered protrusion on the virus surface. FAU - Acharya, R AU - Acharya R AD - Laboratory of Molecular Biophysics, Oxford, UK. FAU - Fry, E AU - Fry E FAU - Stuart, D AU - Stuart D FAU - Fox, G AU - Fox G FAU - Rowlands, D AU - Rowlands D FAU - Brown, F AU - Brown F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Viral Proteins) RN - 0 (Viral Vaccines) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Aphthovirus/*ultrastructure MH - Biological Evolution MH - Capsid/immunology/ultrastructure MH - Computer Simulation MH - Molecular Sequence Data MH - Picornaviridae/ultrastructure MH - Viral Proteins/analysis MH - Viral Vaccines MH - X-Ray Diffraction EDAT- 1989/02/23 MHDA- 1989/02/23 00:01 CRDT- 1989/02/23 00:00 AID - 10.1038/337709a0 [doi] PST - ppublish SO - Nature. 1989 Feb 23;337(6209):709-16. PMID- 20828147 OWN - NLM STAT- MEDLINE DA - 20101026 DCOM- 20101130 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 43 DP - 2010 Nov 2 TI - The conformation and the aggregation kinetics of alpha-synuclein depend on the proline residues in its C-terminal region. PG - 9345-52 LID - 10.1021/bi1010927 [doi] AB - The neuronal protein alpha-synuclein (alpha-syn) plays a central role in Parkinson's disease (PD). The pathological features of PD are the loss of dopaminergic neurons in the substantia nigra pars compacta and the presence of Lewy bodies. The C-terminal domain of alpha-syn is characterized by the presence of 15 acidic amino acids and all five proline residues of the protein (P108, P117, P120, P128, and P138). The aggregation of this natively unfolded protein is accelerated in vitro by FK506 binding proteins (FKBPs) showing peptidyl-prolyl cis-trans isomerase activity. These proteins catalyze the cis-trans conformational change of the X-Pro peptide bond, often a rate-limiting step in protein folding. The acceleration of the folding of alpha-syn by FKBPs may accelerate disease-associated aggregation. To further elucidate the role of the proline residues in the conformation and aggregation of alpha-syn, we constructed several mutants of alpha-syn in which one or more proline residues are mutated to alanine via site-directed mutagenesis. For this purpose, we produced and purified His-WT alpha-syn, a recombinant alpha-syn with a polyhistidine tag (six His residues) and a linker, and a number of Pro-to-Ala mutants. The aggregation kinetics of these mutants and His-WT alpha-syn were studied by turbidity, thioflavin T fluorescence, and CD measurements. We can conclude that mutation of the proline residues to alanine accelerates the aggregation kinetics of alpha-syn while all proline mutants formed fibrils similar to His-WT alpha-syn, as visualized via transmission electron microscopy. We also demonstrate that the accelerating effect of hFKBP12 is abolished via removal of the proline residues from the C-terminus. Finally, we show that the mutant of His alpha-syn with all five proline residues mutated to alanine is more structured (more alpha-helix) than His-WT alpha-syn, indicating the role of the Pro residues as potential helix breakers in the inhibitory conformation of the C-terminus. FAU - Meuvis, Jessika AU - Meuvis J AD - Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, Celestijnenlaan 200G, Leuven, Belgium. FAU - Gerard, Melanie AU - Gerard M FAU - Desender, Linda AU - Desender L FAU - Baekelandt, Veerle AU - Baekelandt V FAU - Engelborghs, Yves AU - Engelborghs Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (alpha-Synuclein) RN - 9DLQ4CIU6V (Proline) RN - EC 5.2.1.- (Tacrolimus Binding Protein 1A) SB - IM MH - Humans MH - Kinetics MH - Mutagenesis, Site-Directed MH - Proline/*chemistry MH - Protein Conformation MH - *Protein Multimerization MH - Tacrolimus Binding Protein 1A/pharmacology MH - alpha-Synuclein/*chemistry/genetics EDAT- 2010/09/11 06:00 MHDA- 2010/12/14 06:00 CRDT- 2010/09/11 06:00 AID - 10.1021/bi1010927 [doi] PST - ppublish SO - Biochemistry. 2010 Nov 2;49(43):9345-52. doi: 10.1021/bi1010927. PMID- 15663936 OWN - NLM STAT- MEDLINE DA - 20050124 DCOM- 20050311 LR - 20081121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 346 IP - 1 DP - 2005 Feb 11 TI - N and C-terminal sub-regions in the c-Myc transactivation region and their joint role in creating versatility in folding and binding. PG - 175-89 AB - The proto-oncogene c-myc governs the expression of a number of genes targeting cell growth and apoptosis, and its expression levels are distorted in many cancer forms. The current investigation presents an analysis by proteolysis, circular dichroism, fluorescence and Biacore of the folding and ligand-binding properties of the N-terminal transactivation domain (TAD) in the c-Myc protein. A c-Myc sub-region comprising residues 1-167 (Myc1-167) has been investigated that includes the unstructured c-Myc transactivation domain (TAD, residues 1-143) together with a C-terminal segment, which appears to promote increased folding. Myc1-167 is partly helical, binds both to the target proteins Myc modulator-1 (MM-1) and TATA box-binding protein (TBP), and displays the characteristics of a molten globule. Limited proteolysis divides Myc1-167 in two halves, by cleaving in a predicted linker region between two hotspot mutation regions: Myc box I (MBI) and Myc box II (MBII). The N-terminal half (Myc1-88) is unfolded and does not alone bind to target proteins, whereas the C-terminal half (Myc92-167) has a partly helical fold and specifically binds both MM-1 and TBP. Although this might suggest a bipartite organization in the c-Myc TAD, none of the N and C-terminal fragments bind target protein with as high affinity as the entire Myc1-167, or display molten globule properties. Furthermore, merely linking the MBI with the C-terminal region, in Myc38-167, is not sufficient to achieve binding and folding properties as in Myc1-167. Thus, the entire N and C-terminal regions of c-Myc TAD act in concert to achieve high specificity and affinity to two structurally and functionally orthogonal target proteins, TBP and MM-1, possibly through a mechanism involving molten globule formation. This hints towards understanding how binding of a range of targets can be accomplished to a single transactivation domain. FAU - Fladvad, Malin AU - Fladvad M AD - Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden. FAU - Zhou, Kaisong AU - Zhou K FAU - Moshref, Ahmad AU - Moshref A FAU - Pursglove, Sharon AU - Pursglove S FAU - Safsten, Par AU - Safsten P FAU - Sunnerhagen, Maria AU - Sunnerhagen M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20041210 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (MYC protein, human) RN - 0 (Proto-Oncogene Proteins c-myc) SB - IM MH - Amino Acid Sequence MH - Animals MH - Circular Dichroism MH - Cloning, Molecular MH - Humans MH - Molecular Sequence Data MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-myc/*chemistry/genetics/*metabolism MH - Sequence Alignment MH - Spectrometry, Fluorescence MH - *Transcriptional Activation EDAT- 2005/01/25 09:00 MHDA- 2005/03/12 09:00 CRDT- 2005/01/25 09:00 PHST- 2004/10/01 [received] PHST- 2004/11/12 [revised] PHST- 2004/11/12 [accepted] PHST- 2004/12/10 [aheadofprint] AID - S0022-2836(04)01468-8 [pii] AID - 10.1016/j.jmb.2004.11.029 [doi] PST - ppublish SO - J Mol Biol. 2005 Feb 11;346(1):175-89. Epub 2004 Dec 10. PMID- 16332393 OWN - NLM STAT- MEDLINE DA - 20060102 DCOM- 20060417 LR - 20061115 IS - 0162-0134 (Print) IS - 0162-0134 (Linking) VI - 100 IP - 1 DP - 2006 Jan TI - Comparative analysis of polyphenol oxidase from plant and fungal species. PG - 108-23 AB - Polyphenol oxidase from plants and fungi is a metalloenzyme containing a type-3 copper center and is homologous to oxygen-carrying hemocyanin of molluscs. Molluscan hemocyanin consists of two domains, an N-terminal domain containing the copper center and a smaller C-terminal domain, connected by an alpha-helical linker. It is presumed that the same is true of polyphenol oxidase from plants and fungi although the structure of a polyphenol oxidase containing the C-terminal domain has not been determined. We show that a number of important structural features are conserved in the N-terminal domains of polyphenol oxidases from various plants and fungi, including a tyrosine motif which can be considered a landmark indicating the beginning of the linker region connecting the N- and C-terminal domains. Our sequence alignments and secondary structure predictions indicate that the C-terminal domains of polyphenol oxidases are likely to be similar in tertiary structure to that of hemocyanin. Detailed bioinformatics analyses of the linker regions predict that this section of the polypeptide chain is intrinsically disordered (lacking fixed tertiary structure) and contains a site of proteolytic processing as well as a potential phosphorylation site. FAU - Marusek, Carrie M AU - Marusek CM AD - Indiana University School of Medicine-Terre Haute, 135 Holmstedt Hall, Terre Haute, IN 47809, United States. FAU - Trobaugh, Nicole M AU - Trobaugh NM FAU - Flurkey, William H AU - Flurkey WH FAU - Inlow, Jennifer K AU - Inlow JK LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051205 PL - United States TA - J Inorg Biochem JT - Journal of inorganic biochemistry JID - 7905788 RN - 9013-72-3 (Hemocyanin) RN - EC 1.10.3.1 (Catechol Oxidase) SB - IM MH - Amino Acid Sequence MH - Catechol Oxidase/*chemistry/genetics MH - Computational Biology/methods MH - Conserved Sequence MH - Fungi/chemistry/*enzymology/genetics MH - Glycosylation MH - Hemocyanin/chemistry MH - Molecular Sequence Data MH - Phosphorylation MH - Plants/chemistry/*enzymology/genetics MH - Protein Structure, Tertiary MH - Sequence Alignment EDAT- 2005/12/08 09:00 MHDA- 2006/04/18 09:00 CRDT- 2005/12/08 09:00 PHST- 2005/08/05 [received] PHST- 2005/09/29 [revised] PHST- 2005/10/16 [accepted] PHST- 2005/12/05 [aheadofprint] AID - S0162-0134(05)00305-3 [pii] AID - 10.1016/j.jinorgbio.2005.10.008 [doi] PST - ppublish SO - J Inorg Biochem. 2006 Jan;100(1):108-23. Epub 2005 Dec 5. PMID- 17088319 OWN - NLM STAT- MEDLINE DA - 20061129 DCOM- 20070313 LR - 20140907 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 15 IP - 12 DP - 2006 Dec TI - Sensitivity of secondary structure propensities to sequence differences between alpha- and gamma-synuclein: implications for fibrillation. PG - 2795-804 AB - The synucleins are a family of intrinsically disordered proteins involved in various human diseases. alpha-Synuclein has been extensively characterized due to its role in Parkinson's disease where it forms intracellular aggregates, while gamma-synuclein is overexpressed in a majority of late-stage breast cancers. Despite fairly strong sequence similarity between the amyloid-forming regions of alpha- and gamma-synuclein, gamma-synuclein has only a weak propensity to form amyloid fibrils. We hypothesize that the different fibrillation tendencies of alpha- and gamma-synuclein may be related to differences in structural propensities. Here we have measured chemical shifts for gamma-synuclein and compared them to previously published shifts for alpha-synuclein. In order to facilitate direct comparison, we have implemented a simple new technique for re-referencing chemical shifts that we have found to be highly effective for both disordered and folded proteins. In addition, we have developed a new method that combines different chemical shifts into a single residue-specific secondary structure propensity (SSP) score. We observe significant differences between alpha- and gamma-synuclein secondary structure propensities. Most interestingly, gamma-synuclein has an increased alpha-helical propensity in the amyloid-forming region that is critical for alpha-synuclein fibrillation, suggesting that increased structural stability in this region may protect against gamma-synuclein aggregation. This comparison of residue-specific secondary structure propensities between intrinsically disordered homologs highlights the sensitivity of transient structure to sequence changes, which we suggest may have been exploited as an evolutionary mechanism for fast modulation of protein structure and, hence, function. FAU - Marsh, Joseph A AU - Marsh JA AD - Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada. FAU - Singh, Vinay K AU - Singh VK FAU - Jia, Zongchao AU - Jia Z FAU - Forman-Kay, Julie D AU - Forman-Kay JD LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20061106 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Amyloid) RN - 0 (alpha-Synuclein) RN - 0 (gamma-Synuclein) SB - IM MH - Amino Acid Sequence MH - Amyloid/*biosynthesis MH - Animals MH - Evolution, Molecular MH - Humans MH - Magnetic Resonance Imaging/methods MH - Mice MH - Models, Theoretical MH - Molecular Sequence Data MH - Protein Folding MH - Protein Structure, Secondary MH - Sequence Homology, Amino Acid MH - alpha-Synuclein/*chemistry MH - gamma-Synuclein/*chemistry PMC - PMC2242444 OID - NLM: PMC2242444 EDAT- 2006/11/08 09:00 MHDA- 2007/03/14 09:00 CRDT- 2006/11/08 09:00 PHST- 2006/11/06 [aheadofprint] AID - ps.062465306 [pii] AID - 10.1110/ps.062465306 [doi] PST - ppublish SO - Protein Sci. 2006 Dec;15(12):2795-804. Epub 2006 Nov 6. PMID- 20169373 OWN - NLM STAT- MEDLINE DA - 20100723 DCOM- 20101028 LR - 20131121 IS - 1438-2199 (Electronic) IS - 0939-4451 (Linking) VI - 39 IP - 3 DP - 2010 Aug TI - The interaction of zinc with membrane-associated 18.5 kDa myelin basic protein: an attenuated total reflectance-Fourier transform infrared spectroscopic study. PG - 739-50 LID - 10.1007/s00726-010-0513-7 [doi] AB - Myelin basic protein (MBP) is an essential structural protein required for tight compaction of the myelin sheath of the central nervous system, and belongs to the family of intrinsically disordered proteins. It contains a high proportion of polar and charged amino acids, and has an adaptive conformation depending on its environment and binding surfaces (membranes) or partners (other proteins or small ligands including divalent cations). Zinc is an important stabilizing component of myelin and its concentration is substantially higher than that of any other trace element in the brain. In this study, we investigate the effect of zinc on different variants of 18.5 kDa MBP, including new recombinant forms lacking hexahistidine tags which would interfere with the binding of the cation. Isothermal titration calorimetry showed the dissociation constant to be in the micromolar range for all variants. Circular dichroism spectroscopy showed that there was minimal effect of zinc on the secondary structure on MBP in aqueous solution. When MBP was reconstituted with myelin-mimetic membranes, attenuated total reflectance-Fourier transform infrared spectroscopy revealed that there was a rearrangement of secondary structure components upon addition of zinc that was subtly different for each variant, indicative of a synergistic protein-membrane-cation interaction. FAU - Smith, Graham S T AU - Smith GS AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada. FAU - Chen, Lin AU - Chen L FAU - Bamm, Vladimir V AU - Bamm VV FAU - Dutcher, John R AU - Dutcher JR FAU - Harauz, George AU - Harauz G LA - eng GR - MOP #74468/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100219 PL - Austria TA - Amino Acids JT - Amino acids JID - 9200312 RN - 0 (Myelin Basic Protein) RN - J41CSQ7QDS (Zinc) SB - IM MH - Animals MH - Cell Membrane/chemistry/*metabolism MH - Kinetics MH - Mice MH - Molecular Sequence Data MH - Molecular Weight MH - Myelin Basic Protein/*chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Spectroscopy, Fourier Transform Infrared MH - Zinc/*metabolism EDAT- 2010/02/20 06:00 MHDA- 2010/10/29 06:00 CRDT- 2010/02/20 06:00 PHST- 2009/11/23 [received] PHST- 2010/02/03 [accepted] PHST- 2010/02/19 [aheadofprint] AID - 10.1007/s00726-010-0513-7 [doi] PST - ppublish SO - Amino Acids. 2010 Aug;39(3):739-50. doi: 10.1007/s00726-010-0513-7. Epub 2010 Feb 19. PMID- 21182262 OWN - NLM STAT- MEDLINE DA - 20110201 DCOM- 20110414 LR - 20140821 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 50 IP - 5 DP - 2011 Feb 8 TI - Structural characterization of partially disordered human Chibby: insights into its function in the Wnt-signaling pathway. PG - 715-26 LID - 10.1021/bi101236z [doi] AB - The Wnt/beta-catenin signaling pathway is critical to embryonic development as well as adult tissue regeneration. Dysregulation of this pathway can lead to a variety of human diseases, in particular cancers. Chibby (Cby), a small and highly conserved protein, plays an antagonistic role in Wnt signaling by inhibiting the binding of beta-catenin to Tcf/Lef family proteins, a protein interaction that is essential for the transcriptional activation of Wnt target genes. Cby is also involved in regulating intracellular distribution of beta-catenin. Phosphorylated Cby forms a ternary complex with 14-3-3 protein and beta-catenin, facilitating the export of beta-catenin from the nucleus. On the other hand, the antagonistic function of Cby is inhibited upon binding to thyroid cancer-1 (TC-1). To dissect the structure-function relationship of Cby, we have used NMR spectroscopy, ESI-MS, CD, and DLS to extensively characterize the structure of human Cby. Our results show that the 126-residue Cby is partially disordered under nondenaturing conditions. While the N-terminal portion of the protein is predominantly unstructured in solution, the C-terminal half of Cby adopts a coiled-coil structure through self-association. Initial data for the binding studies of Cby to 14-3-3zeta (one of the isoforms in the 14-3-3 family) and TC-1 via these two distinct structural modules have also been obtained. It is noteworthy that in a recent large-scale analysis of the intrinsically disordered proteome of mouse, a substantial number of disordered proteins are predicted to have coiled-coil motif presence in their sequences. The combination of these two molecular recognition features could facilitate disordered Cby in assembling protein complexes via different modes of interaction. FAU - Mokhtarzada, Sulayman AU - Mokhtarzada S AD - Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1. FAU - Yu, Corey AU - Yu C FAU - Brickenden, Anne AU - Brickenden A FAU - Choy, Wing-Yiu AU - Choy WY LA - eng GR - MOP no. 74679/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110114 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (CBY1 protein, human) RN - 0 (Carrier Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Wnt Proteins) SB - IM MH - Amino Acid Sequence MH - Carrier Proteins/*chemistry/genetics/*metabolism MH - Humans MH - Molecular Conformation MH - Molecular Sequence Data MH - Nuclear Proteins/*chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - *Signal Transduction MH - Wnt Proteins/genetics/*metabolism PMC - PMC3031990 OID - NLM: PMC3031990 EDAT- 2010/12/25 06:00 MHDA- 2011/04/16 06:00 CRDT- 2010/12/25 06:00 PHST- 2011/01/14 [aheadofprint] AID - 10.1021/bi101236z [doi] PST - ppublish SO - Biochemistry. 2011 Feb 8;50(5):715-26. doi: 10.1021/bi101236z. Epub 2011 Jan 14. PMID- 20589454 OWN - NLM STAT- MEDLINE DA - 20101217 DCOM- 20110329 IS - 1559-0305 (Electronic) IS - 1073-6085 (Linking) VI - 47 IP - 1 DP - 2011 Jan TI - Defining structural domains of an intrinsically disordered protein: Sic1, the cyclin-dependent kinase inhibitor of Saccharomyces cerevisiae. PG - 34-42 LID - 10.1007/s12033-010-9309-y [doi] AB - The cyclin-dependent kinase inhibitor Sic1 is an intrinsically disordered protein (IDP) involved in cell-cycle regulation in the yeast Saccharomyces cerevisiae. Notwithstanding many studies on its biological function, structural characterization has been attempted only recently, fostering the development of production and purification protocols suitable to yield large amounts of this weakly expressed protein. In this study, we describe the identification of protein domains by the heterologous expression, purification, and characterization of Sic1-derived fragment. Four C-terminal fragments (Sic1(C-ter)) were produced based on functional studies and limited-proteolysis results. The N-terminal fragment (Sic1(1-186)) was complementary to the most stable C-terminal fragments (Sic1(Delta186)). Both Sic1(1-186) and Sic1(C-ter) fragments were, in general, less susceptible to spontaneous proteolysis than the full-length protein. The boundaries of the C-terminal fragments turned out to be crucial for integrity of the recombinant proteins and required two rounds of design and production. Sic1 fragments were purified by a simple procedure, based on their resistance to heat treatment, at the amount and purity required for structural characterization. Circular dichroism (CD) measurements and nuclear magnetic resonance (NMR) spectra of N- and C-terminal fragments confirm their disordered nature but reveal minor structural differences that may reflect their distinct functional roles. FAU - Brocca, Stefania AU - Brocca S AD - Department of Biotechnology and Biosciences, Universita di Milano-Bicocca, P.zza della Scienza 2, 20126, Milan, Italy. stefania.brocca@unimib.it FAU - Testa, Lorenzo AU - Testa L FAU - Samalikova, Maria AU - Samalikova M FAU - Grandori, Rita AU - Grandori R FAU - Lotti, Marina AU - Lotti M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biotechnol JT - Molecular biotechnology JID - 9423533 RN - 0 (Cyclin-Dependent Kinase Inhibitor Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SIC1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Circular Dichroism MH - Cyclin-Dependent Kinase Inhibitor Proteins/*chemistry/isolation & purification MH - Escherichia coli/genetics MH - Gene Expression Regulation, Fungal MH - Magnetic Resonance Spectroscopy MH - Phosphorylation MH - Plasmids MH - *Protein Structure, Secondary MH - Recombinant Proteins/chemistry/isolation & purification MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/isolation & purification EDAT- 2010/07/01 06:00 MHDA- 2011/03/30 06:00 CRDT- 2010/07/01 06:00 AID - 10.1007/s12033-010-9309-y [doi] PST - ppublish SO - Mol Biotechnol. 2011 Jan;47(1):34-42. doi: 10.1007/s12033-010-9309-y. PMID- 17174309 OWN - NLM STAT- MEDLINE DA - 20061226 DCOM- 20070227 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 581 IP - 1 DP - 2007 Jan 9 TI - Identification of the WW domain-interaction sites in the unstructured N-terminal domain of EBV LMP 2A. PG - 65-70 AB - Epstein-Barr virus latency is maintained by the latent membrane protein (LMP) 2A, which mimics the B-cell receptor (BCR) and perturbs BCR signaling. The cytoplasmic N-terminal domain of LMP2A is composed of 119 amino acids. The N-terminal domain of LMP2A (LMP2A NTD) contains two PY motifs (PPPPY) that interact with the WW domains of Nedd4 family ubiquitin-protein ligases. Based on our analysis of NMR data, we found that the LMP2A NTD adopts an overall random-coil structure in its native state. However, the region between residues 60 and 90 was relatively ordered, and seemed to form the hydrophobic core of the LMP2A NTD. This region resides between two PY motifs and is important for WW domain binding. Mapping of the residues involved in the interaction between the LMP2A NTD and WW domains was achieved by chemical shift perturbation, by the addition of WW2 and WW3 peptides. Interestingly, the binding of the WW domains mainly occurred in the hydrophobic core of the LMP2A NTD. In addition, we detected a difference in the binding modes of the two PY motifs against the two WW peptides. The binding of the WW3 peptide caused the resonances of five residues (Tyr(60), Glu(61), Asp(62), Trp(65), and Gly(66)) just behind the N-terminal PY motif of the LMP2A NTD to disappear. A similar result was obtained with WW2 binding. However, near the C-terminal PY motif, the chemical shift perturbation caused by WW2 binding was different from that due to WW3 binding, indicating that the residues near the PY motifs are involved in selective binding of WW domains. The present work represents the first structural study of the LMP2A NTD and provides fundamental structural information about its interaction with ubiquitin-protein ligase. FAU - Seo, Min-Duk AU - Seo MD AD - National Research Laboratory, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, San 56-1, Shillim-Dong, Kwanak-Gu, Seoul, Republic of Korea. FAU - Park, Sung Jean AU - Park SJ FAU - Kim, Hyun-Jung AU - Kim HJ FAU - Lee, Bong Jin AU - Lee BJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20061211 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (EBV-associated membrane antigen, Epstein-Barr virus) RN - 0 (Peptides) RN - 0 (Receptors, Antigen, B-Cell) RN - 0 (Viral Matrix Proteins) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) RN - EC 6.3.2.19 (WWP2 protein, human) SB - IM MH - Amino Acid Motifs/physiology MH - Herpesvirus 4, Human/chemistry/*physiology MH - Humans MH - Molecular Mimicry/physiology MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Peptides/chemistry/*metabolism MH - Protein Structure, Tertiary/physiology MH - Receptors, Antigen, B-Cell/metabolism MH - Signal Transduction/physiology MH - Structure-Activity Relationship MH - Ubiquitin-Protein Ligases/chemistry/*metabolism MH - Viral Matrix Proteins/chemistry/*metabolism MH - Virus Latency/*physiology EDAT- 2006/12/19 09:00 MHDA- 2007/02/28 09:00 CRDT- 2006/12/19 09:00 PHST- 2006/04/11 [received] PHST- 2006/11/06 [revised] PHST- 2006/11/30 [accepted] PHST- 2006/12/11 [aheadofprint] AID - S0014-5793(06)01428-1 [pii] AID - 10.1016/j.febslet.2006.11.078 [doi] PST - ppublish SO - FEBS Lett. 2007 Jan 9;581(1):65-70. Epub 2006 Dec 11. PMID- 21147767 OWN - NLM STAT- MEDLINE DA - 20110221 DCOM- 20110414 LR - 20140821 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 8 DP - 2011 Feb 25 TI - The structure and interactions of SpoIISA and SpoIISB, a toxin-antitoxin system in Bacillus subtilis. PG - 6808-19 LID - 10.1074/jbc.M110.172429 [doi] AB - Spore formation in Bacillus subtilis begins with an asymmetric cell division, following which differential gene expression is established by alternative compartment-specific RNA polymerase sigma factors. The spoIISAB operon of B. subtilis was identified as a locus whose mutation leads to increased activity of the first sporulation-specific sigma factor, sigma(F). Inappropriate spoIISA expression causes lysis of vegetatively growing B. subtilis cells and Escherichia coli cells when expressed heterologously, effects that are countered by co-expression of spoIISB, identifying SpoIISA-SpoIISB as a toxin-antitoxin system. SpoIISA has three putative membrane-spanning segments and a cytoplasmic domain. Here, the crystal structure of a cytoplasmic fragment of SpoIISA (CSpoIISA) in complex with SpoIISB has been determined by selenomethionine-multiwavelength anomalous dispersion phasing to 2.5 A spacing, revealing a CSpoIISA(2).SpoIISB(2) heterotetramer. CSpoIISA has a single domain alpha/beta structure resembling a GAF domain with an extended alpha-helix at its N terminus. The two CSpoIISA protomers form extensive interactions through an intermolecular four-helix bundle. Each SpoIISB chain is highly extended and lacking tertiary structure. The SpoIISB chains wrap around the CSpoIISA dimer, forming extensive interactions with both CSpoIISA protomers. CD spectroscopy experiments indicate that SpoIISB is a natively disordered protein that adopts structure only in the presence of CSpoIISA, whereas surface plasmon resonance experiments revealed that the CSpoIISA.SpoIISB complex is stable with a dissociation constant in the nanomolar range. The results are interpreted in relation to sequence conservation and mutational data, and possible mechanisms of cell killing by SpoIISA are discussed. FAU - Florek, Patrik AU - Florek P AD - Institute of Molecular Biology, Slovak Academy of Sciences, 845 51 Bratislava 45, Slovakia. FAU - Levdikov, Vladimir M AU - Levdikov VM FAU - Blagova, Elena AU - Blagova E FAU - Lebedev, Andrey A AU - Lebedev AA FAU - Skrabana, Rostislav AU - Skrabana R FAU - Resetarova, Stanislava AU - Resetarova S FAU - Pavelcikova, Pamela AU - Pavelcikova P FAU - Barak, Imrich AU - Barak I FAU - Wilkinson, Anthony J AU - Wilkinson AJ LA - eng SI - PDB/3O6Q GR - 082829/Z/07/Z/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101207 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Sigma Factor) RN - 0 (Transcription Factors) RN - 0 (sporulation-specific sigma factors) SB - IM MH - Bacillus subtilis/*chemistry/genetics/metabolism MH - Crystallography, X-Ray MH - Escherichia coli/chemistry/genetics/metabolism MH - Operon/physiology MH - Protein Stability MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Sigma Factor/chemistry/genetics/metabolism MH - Structure-Activity Relationship MH - Transcription Factors/*chemistry/genetics/metabolism PMC - PMC3057836 OID - NLM: PMC3057836 EDAT- 2010/12/15 06:00 MHDA- 2011/04/16 06:00 CRDT- 2010/12/15 06:00 PHST- 2010/12/07 [aheadofprint] AID - M110.172429 [pii] AID - 10.1074/jbc.M110.172429 [doi] PST - ppublish SO - J Biol Chem. 2011 Feb 25;286(8):6808-19. doi: 10.1074/jbc.M110.172429. Epub 2010 Dec 7. PMID- 7559428 OWN - NLM STAT- MEDLINE DA - 19951106 DCOM- 19951106 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 270 IP - 39 DP - 1995 Sep 29 TI - Interleukin 4-inducible phosphorylation of HMG-I(Y) is inhibited by rapamycin. PG - 22924-32 AB - The non-histone chromosomal protein HMG-I(Y) participates in repression of transcription directed by a promoter which confers interleukin 4 (IL-4)-inducible activation in transfected B cell lines. Metabolic labeling, phosphoamino acid analyses, and in vitro phosphorylation studies demonstrate that IL-4 induces serine phosphorylation of HMG-I(Y) in B lymphocytes. Phosphopeptide mapping shows that the predominant site of phosphorylation contains a casein kinase II consensus motif. The immunosuppressive agent rapamycin has been shown preferentially to inhibit IgE production by IL-4-treated human B cells. It is shown here that rapamycin inhibits both activation of the human germ line epsilon promoter by IL-4 and IL-4-inducible phosphorylation of HMG-I(Y). These findings demonstrate a rapamycin-sensitive pathway that transduces signals from the IL-4 receptor to nuclear factors that regulate inducible transcription. The affinity of normal nuclear HMG-I(Y) for DNA is increased by dephosphorylation in vitro, whereas in vitro kinase reactions using casein kinase II decrease recombinant HMG-I(Y) binding to DNA. These data further suggest a novel mechanism in which phosphorylation triggered by IL-4 or other cytokines could regulate the effects of HMG-I(Y) on gene transcription. FAU - Wang, D Z AU - Wang DZ AD - Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-2363, USA. FAU - Ray, P AU - Ray P FAU - Boothby, M AU - Boothby M LA - eng GR - GM42550/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA-Binding Proteins) RN - 0 (High Mobility Group Proteins) RN - 0 (Immunosuppressive Agents) RN - 0 (Oligodeoxyribonucleotides) RN - 0 (Peptide Fragments) RN - 0 (Phosphates) RN - 0 (Phosphopeptides) RN - 0 (Polyenes) RN - 0 (Recombinant Proteins) RN - 124544-67-8 (HMGA1a Protein) RN - 207137-56-2 (Interleukin-4) RN - EC 2.7.11.1 (Casein Kinase II) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - EC 3.4.21.4 (Trypsin) RN - W36ZG6FT64 (Sirolimus) SB - IM MH - Amino Acid Sequence MH - Animals MH - B-Lymphocytes MH - Base Sequence MH - Casein Kinase II MH - Cell Line MH - Cell Nucleus/metabolism MH - Consensus Sequence MH - DNA-Binding Proteins/*metabolism MH - HMGA1a Protein MH - High Mobility Group Proteins/chemistry/isolation & purification/*metabolism MH - Humans MH - Immunosuppressive Agents/*pharmacology MH - Interleukin-4/antagonists & inhibitors/*pharmacology MH - Mice MH - Molecular Sequence Data MH - Oligodeoxyribonucleotides MH - Peptide Fragments/chemistry/isolation & purification MH - Peptide Mapping MH - Phosphates/metabolism MH - Phosphopeptides/chemistry/isolation & purification MH - Phosphorylation MH - Polyenes/*pharmacology MH - Promoter Regions, Genetic MH - Protein-Serine-Threonine Kinases/chemistry/metabolism MH - Recombinant Proteins/chemistry/isolation & purification/metabolism MH - Sequence Homology, Amino Acid MH - Signal Transduction/drug effects MH - Sirolimus MH - Transfection MH - Trypsin EDAT- 1995/09/29 MHDA- 1995/09/29 00:01 CRDT- 1995/09/29 00:00 PST - ppublish SO - J Biol Chem. 1995 Sep 29;270(39):22924-32. PMID- 20124700 OWN - NLM STAT- MEDLINE DA - 20100203 DCOM- 20100301 LR - 20131121 IS - 1399-0047 (Electronic) IS - 0907-4449 (Linking) VI - 66 IP - Pt 2 DP - 2010 Feb TI - Studies on a Tyr residue critical for the binding of coenzyme and substrate in mouse 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21): structure of the Y224D mutant enzyme. PG - 198-204 LID - 10.1107/S0907444909051464 [doi] AB - Mouse 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21) is the only aldo-keto reductase that catalyzes the stereospecific reduction of 3- and 17-ketosteroids to the corresponding 3(17)alpha-hydroxysteroids. The Y224D mutation of AKR1C21 reduced the K(m) value for NADP(H) by up to 80-fold and completely reversed the 17alpha stereospecificity of the enzyme. The crystal structure of the Y224D mutant at 2.3 A resolution revealed that the mutation resulted in a change in the conformation of the flexible loop B, including the V-shaped groove, which is a unique feature of the active-site architecture of wild-type AKR1C21 and is formed by the side chains of Tyr224 and Trp227. Furthermore, mutations (Y224F and Q222N) of residues involved in forming the safety belt for binding of the coenzyme showed similar alterations in kinetic constants for 3alpha-hydroxy/3-ketosteroids and 17-hydroxy/ketosteroids compared with the wild type. FAU - Dhagat, Urmi AU - Dhagat U AD - Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia. FAU - Endo, Satoshi AU - Endo S FAU - Mamiya, Hiroaki AU - Mamiya H FAU - Hara, Akira AU - Hara A FAU - El-Kabbani, Ossama AU - El-Kabbani O LA - eng PT - Journal Article DEP - 20100122 PL - England TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (Apoenzymes) RN - 0 (Holoenzymes) RN - 42HK56048U (Tyrosine) RN - 53-59-8 (NADP) RN - EC 1.1.- (Hydroxysteroid Dehydrogenases) RN - EC 1.1.1.209 (3(17)-hydroxysteroid dehydrogenase) SB - IM MH - Animals MH - Apoenzymes/chemistry/genetics/metabolism MH - Crystallography, X-Ray MH - Holoenzymes/chemistry/genetics/metabolism MH - Hydroxysteroid Dehydrogenases/*chemistry/genetics/metabolism MH - Mice MH - Models, Molecular MH - *Mutation MH - NADP/*chemistry/metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Substrate Specificity MH - Tyrosine/chemistry/genetics/metabolism EDAT- 2010/02/04 06:00 MHDA- 2010/03/02 06:00 CRDT- 2010/02/04 06:00 PHST- 2009/05/25 [received] PHST- 2009/11/29 [accepted] PHST- 2010/01/22 [epublish] AID - S0907444909051464 [pii] AID - 10.1107/S0907444909051464 [doi] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):198-204. doi: 10.1107/S0907444909051464. Epub 2010 Jan 22. PMID- 19075586 OWN - NLM STAT- MEDLINE DA - 20081216 DCOM- 20090116 LR - 20101118 IS - 1567-2050 (Print) IS - 1567-2050 (Linking) VI - 5 IP - 6 DP - 2008 Dec TI - Tau oligomerization: a role for tau aggregation intermediates linked to neurodegeneration. PG - 591-8 AB - Intracellular accumulation of filamentous tau proteins is a defining feature of neurodegenerative diseases, including Alzheimer's disease, progressive supranuclear palsy, corticobasal degeneration, Pick's disease, and frontotemporal dementia with Parkinsonism linked to chromosome 17, all known collectively as tauopathies. Tau protein is a member of microtubule (MT)-associated proteins. Tau is a highly soluble and natively unfolded protein dominated by a random coil structure in solution. It is believed that aberrant modifications of tau, including phosphorylation, truncation, and conformational changes, induce filamentous aggregation. However, the mechanism underlying the conversion of tau protein from a soluble state to one of insoluble aggregates still remains elusive. The importance of tau aggregation intermediates (e.g. tau dimer, tau multimer, and granular tau oligomer) in disease pathogenesis was suggested by recent studies. Here, we review the latest developments in tracking the structural changes of tau protein and discuss the utility improving our understanding of tau aggregation pathway leading to human tauopathies. FAU - Sahara, N AU - Sahara N AD - Laboratory for Alzheimer's Disease, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan. saharanaruhiko@brain.riken.jp FAU - Maeda, S AU - Maeda S FAU - Takashima, A AU - Takashima A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United Arab Emirates TA - Curr Alzheimer Res JT - Current Alzheimer research JID - 101208441 RN - 0 (Amyloid beta-Peptides) RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/pathology/psychology MH - Amyloid beta-Peptides/metabolism MH - Animals MH - Humans MH - Microscopy, Atomic Force MH - Neurodegenerative Diseases/*metabolism/pathology MH - Phosphorylation MH - Protein Conformation MH - tau Proteins/*metabolism RF - 72 EDAT- 2008/12/17 09:00 MHDA- 2009/01/17 09:00 CRDT- 2008/12/17 09:00 PST - ppublish SO - Curr Alzheimer Res. 2008 Dec;5(6):591-8. PMID- 22937102 OWN - NLM STAT- MEDLINE DA - 20120831 DCOM- 20130212 LR - 20141105 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 8 DP - 2012 TI - A skeletal muscle ryanodine receptor interaction domain in triadin. PG - e43817 LID - 10.1371/journal.pone.0043817 [doi] AB - Excitation-contraction coupling in skeletal muscle depends, in part, on a functional interaction between the ligand-gated ryanodine receptor (RyR1) and integral membrane protein Trisk 95, localized to the sarcoplasmic reticulum membrane. Various domains on Trisk 95 can associate with RyR1, yet the domain responsible for regulating RyR1 activity has remained elusive. We explored the hypothesis that a luminal Trisk 95 KEKE motif (residues 200-232), known to promote RyR1 binding, may also form the RyR1 activation domain. Peptides corresponding to Trisk 95 residues 200-232 or 200-231 bound to RyR1 and increased the single channel activity of RyR1 by 1.49 +/- 0.11-fold and 1.8 +/- 0.15-fold respectively, when added to its luminal side. A similar increase in [(3)H]ryanodine binding, which reflects open probability of the channels, was also observed. This RyR1 activation is similar to activation induced by full length Trisk 95. Circular dichroism showed that both peptides were intrinsically disordered, suggesting a defined secondary structure is not necessary to mediate RyR1 activation. These data for the first time demonstrate that Trisk 95's 200-231 region is responsible for RyR1 activation. Furthermore, it shows that no secondary structure is required to achieve this activation, the Trisk 95 residues themselves are critical for the Trisk 95-RyR1 interaction. FAU - Wium, Elize AU - Wium E AD - John Curtin School of Medical Research, Australian Capital Territory, Australia. FAU - Dulhunty, Angela F AU - Dulhunty AF FAU - Beard, Nicole A AU - Beard NA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120824 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Carrier Proteins) RN - 0 (Muscle Proteins) RN - 0 (Ryanodine Receptor Calcium Release Channel) RN - 0 (triadin) RN - 15662-33-6 (Ryanodine) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Carrier Proteins/*metabolism MH - Excitation Contraction Coupling/*physiology MH - Molecular Sequence Data MH - Muscle Proteins/*metabolism MH - Muscle, Skeletal/*metabolism MH - Rabbits MH - Ryanodine/metabolism MH - Ryanodine Receptor Calcium Release Channel/*metabolism MH - Sarcoplasmic Reticulum/metabolism PMC - PMC3427183 OID - NLM: PMC3427183 EDAT- 2012/09/01 06:00 MHDA- 2013/02/13 06:00 CRDT- 2012/09/01 06:00 PHST- 2012/05/09 [received] PHST- 2012/07/26 [accepted] PHST- 2012/08/24 [epublish] AID - 10.1371/journal.pone.0043817 [doi] AID - PONE-D-12-13263 [pii] PST - ppublish SO - PLoS One. 2012;7(8):e43817. doi: 10.1371/journal.pone.0043817. Epub 2012 Aug 24. PMID- 23398174 OWN - NLM STAT- MEDLINE DA - 20130227 DCOM- 20130812 LR - 20141103 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 8 DP - 2013 Feb 27 TI - Site-specific interaction between alpha-synuclein and membranes probed by NMR-observed methionine oxidation rates. PG - 2943-6 LID - 10.1021/ja312415q [doi] AB - alpha-Synuclein (alphaS) is an intrinsically disordered protein that is water-soluble but also can bind negatively charged lipid membranes while adopting an alpha-helical conformation. Membrane affinity is increased by post-translational N-terminal acetylation, a common modification in all eukaryotic cells. In the presence of lipid vesicles containing a small fraction of peroxidized lipids, the N-terminal Met residues in alphaS (Met1 and Met5) rapidly oxidize while reducing the toxic lipid hydroperoxide to a nonreactive lipid hydroxide, whereas C-terminal Met residues remain unaffected. Met oxidation can be probed conveniently and quantitatively by NMR spectroscopy. The results show that oxidation of Met1 reduces the rate of oxidation of Met5 and vice versa as a result of decreased membrane affinity of the partially oxidized protein. The effect of Met oxidation on the alphaS-membrane affinity extends over large distances, as in the V49M mutant, oxidation of Met1 and Met5 strongly impacts the oxidation rate of Met49 and vice versa. When not bound to membrane, oxidized Met1 and Met5 of alphaS are excellent substrates for methionine sulfoxide reductase (Msr), thereby providing an efficient vehicle for water-soluble Msr enzymes to protect the membrane against oxidative damage. FAU - Maltsev, Alexander S AU - Maltsev AS AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA. FAU - Chen, Jue AU - Chen J FAU - Levine, Rodney L AU - Levine RL FAU - Bax, Ad AU - Bax A LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20130214 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (alpha-Synuclein) RN - AE28F7PNPL (Methionine) SB - IM MH - Magnetic Resonance Spectroscopy/*methods MH - Methionine/*chemistry MH - Oxidation-Reduction MH - alpha-Synuclein/*chemistry PMC - PMC3585462 OID - NLM: PMC3585462 EDAT- 2013/02/13 06:00 MHDA- 2013/08/13 06:00 CRDT- 2013/02/13 06:00 PHST- 2013/02/14 [aheadofprint] AID - 10.1021/ja312415q [doi] PST - ppublish SO - J Am Chem Soc. 2013 Feb 27;135(8):2943-6. doi: 10.1021/ja312415q. Epub 2013 Feb 14. PMID- 3430618 OWN - NLM STAT- MEDLINE DA - 19880323 DCOM- 19880323 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 198 IP - 3 DP - 1987 Dec 5 TI - Molecular dynamics simulations of "loop closing" in the enzyme triose phosphate isomerase. PG - 533-46 AB - We present molecular dynamics simulations on the active site region of dimeric triose phosphate isomerase (TIM) using the co-ordinates of native chicken muscle TIM as a starting point and performing simulations with no substrate, with dihydroxyacetone phosphate (DHAP), the natural substrate, and with dihydroxyacetone sulfate (DHAS), a substrate analog. Whereas most of the protein moves less than 1 A during the simulation, some residues in the active site loop move more than 8 A during the 10.5 picoseconds of dynamics for each of the simulations. Most interestingly, the nature of the loop motion depends on the substrate, with the largest motion found in the presence of DHAP, and only in the presence of DHAP does the loop move to "close off" the active site pocket. The final structure found for the DHAP-chicken TIM complex is qualitatively similar to that described by Alber et al. for DHAP-yeast TIM. Simulations on the monomeric protein gives insight into why the molecule is active only as a dimer. FAU - Brown, F K AU - Brown FK AD - Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143. FAU - Kollman, P A AU - Kollman PA LA - eng GR - GM-29072/GM/NIGMS NIH HHS/United States GR - RR-02441/RR/NCRR NIH HHS/United States GR - RR-1081/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Pyrones) RN - 1364PS73AF (Acetone) RN - 2KAG279R6R (dehydroacetic acid) RN - 57-04-5 (Dihydroxyacetone Phosphate) RN - EC 5.1.3.- (Carbohydrate Epimerases) RN - EC 5.3.1.1 (Triose-Phosphate Isomerase) SB - IM MH - Acetone/analogs & derivatives/metabolism MH - Animals MH - Binding Sites MH - *Carbohydrate Epimerases/metabolism MH - *Computer Simulation MH - Dihydroxyacetone Phosphate/metabolism MH - Models, Molecular MH - Protein Conformation MH - *Pyrones MH - *Triose-Phosphate Isomerase/metabolism EDAT- 1987/12/05 MHDA- 1987/12/05 00:01 CRDT- 1987/12/05 00:00 AID - 0022-2836(87)90298-1 [pii] PST - ppublish SO - J Mol Biol. 1987 Dec 5;198(3):533-46. PMID- 11413144 OWN - NLM STAT- MEDLINE DA - 20010813 DCOM- 20010906 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 33 DP - 2001 Aug 17 TI - Induction of secondary structure in a COOH-terminal peptide of histone H1 by interaction with the DNA: an infrared spectroscopy study. PG - 30898-903 AB - We have studied the conformation of the peptide Ac-EPKRSVAFKKTKKEVKKVATPKK (CH-1), free in solution and bound to the DNA, by Fourier-transform infrared spectroscopy. The peptide belongs to the COOH-terminal domain of histone H1(0) (residues 99-121) and is adjacent to the central globular domain of the protein. In aqueous (D(2)O) solution the amide I' is dominated by component bands at 1643 cm(-1) and 1662 cm(-1), which have been assigned to random coil conformations and turns, respectively. In accordance with previous NMR results, the latter component has been interpreted as arising in turn-like conformations in rapid equilibrium with unfolded states. The peptide becomes fully structured either in 90% trifluoroethanol (TFE) solution or upon interaction with the DNA. In these conditions, the contributions of turn (1662 cm(-1)) and random coil components virtually disappear. In TFE, the spectrum is dominated by the alpha-helical component (1654 cm(-1)). The band at 1662 cm(-1) shifts to 1670 cm(-1), and has been assigned to the COOH-terminal TPKK motif in a more stable turn conformation. A band at 1637 cm(-1), also present in TFE, has been assigned to 3(10) helical structure. The amide I' band of the complexes with the DNA retains the components that were attributed to 3(10) helix and the TPKK turn. In the complexes with the DNA, the alpha-helical component observed in TFE splits into two components at 1657 cm(-1) and 1647 cm(-1). Both components are inside the spectral region of alpha-helical structures. Our results support the presence of inducible helical and turn elements, both sharing the character of DNA-binding motifs. FAU - Vila, R AU - Vila R AD - Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias, Universidad Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. FAU - Ponte, I AU - Ponte I FAU - Collado, M AU - Collado M FAU - Arrondo, J L AU - Arrondo JL FAU - Suau, P AU - Suau P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20010618 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Histones) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - DNA/*chemistry MH - Histones/*chemistry MH - Molecular Sequence Data MH - *Protein Structure, Secondary MH - Spectrophotometry, Infrared EDAT- 2001/06/20 10:00 MHDA- 2001/09/08 10:01 CRDT- 2001/06/20 10:00 PHST- 2001/06/18 [aheadofprint] AID - 10.1074/jbc.M104189200 [doi] AID - M104189200 [pii] PST - ppublish SO - J Biol Chem. 2001 Aug 17;276(33):30898-903. Epub 2001 Jun 18. PMID- 12357034 OWN - NLM STAT- MEDLINE DA - 20021016 DCOM- 20021204 LR - 20141120 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 99 IP - 21 DP - 2002 Oct 15 TI - Crystal structure of human calcineurin complexed with cyclosporin A and human cyclophilin. PG - 13522-6 AB - Calcineurin (Cn), a Ca(2+)/calmodulin-dependent Ser/Thr protein phosphatase, is an important participant in signaling pathways that activate T cells. It is the target of the immunosuppressive drugs cyclosporin A (CsA) and FK506. These drugs bind proteins known as cyclophilin (Cyp) and FK506-binding protein, respectively, and the drug-protein complexes in turn inhibit Cn. We report the crystal structure of a Cyp/CsA/Cn ternary complex, determined to a resolution of 3.1 A. Residues 3-9 of CsA, particularly N-methyl leucines 4 and 6, and Trp-121 of Cyp form a composite surface for interaction with Cn. The hydrophobic interface buries two hydrogen bonds. The structure accounts clearly for the effects of mutations in Cn on CsA-resistance and for the way modifications of CsA alter immunosuppressive activity. FAU - Jin, Lei AU - Jin L AD - Department of Molecular and Cellular Biology, and Howard Hughes Medical Institute, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA. FAU - Harrison, Stephen C AU - Harrison SC LA - eng SI - PDB/1MF8 PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20020930 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Calcineurin Inhibitors) RN - 0 (Immunosuppressive Agents) RN - 0 (Macromolecular Substances) RN - 0 (Recombinant Proteins) RN - 83HN0GTJ6D (Cyclosporine) RN - EC 3.1.3.16 (Calcineurin) RN - EC 5.2.1.- (Cyclophilins) RN - EC 5.2.1.- (Tacrolimus Binding Proteins) RN - WM0HAQ4WNM (Tacrolimus) SB - IM MH - Binding Sites MH - Calcineurin/*chemistry/genetics MH - Calcineurin Inhibitors MH - Crystallography, X-Ray MH - Cyclophilins/*chemistry MH - Cyclosporine/*chemistry/pharmacology MH - Humans MH - Immunosuppressive Agents/*chemistry/pharmacology MH - In Vitro Techniques MH - Macromolecular Substances MH - Models, Molecular MH - Mutation MH - Protein Conformation MH - Recombinant Proteins/antagonists & inhibitors/chemistry/genetics MH - Static Electricity MH - Structure-Activity Relationship MH - Tacrolimus/chemistry MH - Tacrolimus Binding Proteins/chemistry PMC - PMC129706 OID - NLM: PMC129706 EDAT- 2002/10/03 04:00 MHDA- 2002/12/05 04:00 CRDT- 2002/10/03 04:00 PHST- 2002/09/30 [aheadofprint] AID - 10.1073/pnas.212504399 [doi] AID - 212504399 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13522-6. Epub 2002 Sep 30. PMID- 23227221 OWN - NLM STAT- MEDLINE DA - 20121211 DCOM- 20130521 LR - 20141104 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 12 DP - 2012 TI - Identification of regions involved in substrate binding and dimer stabilization within the central domains of yeast Hsp40 Sis1. PG - e50927 LID - 10.1371/journal.pone.0050927 [doi] AB - Protein folding, refolding and degradation are essential for cellular life and are regulated by protein homeostatic processes such those that involve the molecular chaperone DnaK/Hsp70 and its co-chaperone DnaJ. Hsp70 action is initiated when proteins from the DnaJ family bind an unfolded protein for delivery purposes. In eukaryotes, the DnaJ family can be divided into two main groups, Type I and Type II, represented by yeast cytosolic Ydj1 and Sis1, respectively. Although sharing some unique features both members of the DnaJ family, Ydj1 and Sis1 are structurally and functionally distinct as deemed by previous studies, including the observation that their central domains carry the structural and functional information even in switched chimeras. In this study, we combined several biophysical tools for evaluating the stability of Sis1 and mutants that had the central domains (named Gly/Met rich domain and C-terminal Domain I) deleted or switched to those of Ydj1 to gain insight into the role of these regions in the structure and function of Sis1. The mutants retained some functions similar to full length wild-type Sis1, however they were defective in others. We found that: 1) Sis1 unfolds in at least two steps as follows: folded dimer to partially folded monomer and then to an unfolded monomer. 2) The Gly/Met rich domain had intrinsically disordered characteristics and its deletion had no effect on the conformational stability of the protein. 3) The deletion of the C-terminal Domain I perturbed the stability of the dimer. 4) Exchanging the central domains perturbed the conformational stability of the protein. Altogether, our results suggest the existence of two similar subdomains in the C-terminal domain of DnaJ that could be important for stabilizing each other in order to maintain a folded substrate-binding site as well as the dimeric state of the protein. FAU - Borges, Julio C AU - Borges JC AD - Institute of Chemistry of Sao Carlos, University of Sao Paulo, Sao Carlos, Sao Paulo, Brazil. FAU - Seraphim, Thiago V AU - Seraphim TV FAU - Mokry, David Z AU - Mokry DZ FAU - Almeida, Fabio C L AU - Almeida FC FAU - Cyr, Douglas M AU - Cyr DM FAU - Ramos, Carlos H I AU - Ramos CH LA - eng GR - R01 GM056981/GM/NIGMS NIH HHS/United States GR - R01 GM067785/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121205 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (HSP40 Heat-Shock Proteins) RN - 0 (Mutant Proteins) RN - 0 (SIS1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 139874-78-5 (YDJ1 protein, S cerevisiae) RN - 8W8T17847W (Urea) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Calorimetry, Differential Scanning MH - Circular Dichroism MH - HSP40 Heat-Shock Proteins/*chemistry/*metabolism MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Mutant Proteins/chemistry/metabolism MH - *Protein Multimerization MH - Protein Stability MH - Protein Structure, Tertiary MH - Protein Unfolding/drug effects MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/*metabolism MH - Spectrometry, Fluorescence MH - Substrate Specificity/drug effects MH - Temperature MH - Urea/pharmacology PMC - PMC3515540 OID - NLM: PMC3515540 EDAT- 2012/12/12 06:00 MHDA- 2013/05/23 06:00 CRDT- 2012/12/11 06:00 PHST- 2012/07/04 [received] PHST- 2012/10/26 [accepted] PHST- 2012/12/05 [epublish] AID - 10.1371/journal.pone.0050927 [doi] AID - PONE-D-12-19383 [pii] PST - ppublish SO - PLoS One. 2012;7(12):e50927. doi: 10.1371/journal.pone.0050927. Epub 2012 Dec 5. PMID- 25001481 OWN - NLM STAT- MEDLINE DA - 20140725 DCOM- 20150602 IS - 1745-7270 (Electronic) IS - 1672-9145 (Linking) VI - 46 IP - 8 DP - 2014 Aug TI - Cloning and characterization of the shell matrix protein Shematrin in scallop Chlamys farreri. PG - 709-19 LID - 10.1093/abbs/gmu054 [doi] AB - The Shematrin family is unique to the organic matrices of pearl oyster shells, containing repetitive, low-complexity domains designated as XGnX (where X is a hydrophobic amino acid). Current studies suggested that Shematrins are framework proteins in the prismatic layer of Pinctada fucata; however, the exact function of Shematrin during shell formation is unclear. In this study, we cloned and characterized Shematrin, a protein highly homologous to Shematrin-2, from the mantle tissue of scallop (Chlamys farreri). Semi-quantitative reverse transcript polymerase chain reaction analysis showed that Shematrin is exclusively expressed in the mantle. Knocking down the expression of Shematrin in adult scallops via double-stranded RNA injection led to an abnormal folia surface. After the shell was notched, the expression level of Shematrin remarkably increased and then gradually decreased, suggesting that Shematrin is critically involved in the shell repair progress. Injection of Shematrin double-stranded RNA reduced the speed of shell regeneration and caused abnormal surface morphology of the regenerated shell. The RNA interference and shell notching experiments indicated that Shematrin plays a key role in the folia formation of C. farreri. Structure prediction showed that Shematrin may be an intrinsically disordered protein, with high flexibility and elasticity of the molecular conformation, which facilitate binding multiple protein partners. Based on the structure features, we hypothesized that Shematrin may participate in framework organization via binding with several specific acidic proteins, functioning as a molecular hub in the protein interaction networks. CI - (c) The Author 2014. Published by ABBS Editorial Office in association with Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. FAU - Lin, Ya AU - Lin Y AD - Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China. FAU - Jia, Ganchu AU - Jia G AD - Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China. FAU - Xu, Guangrui AU - Xu G AD - Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China. FAU - Su, Jingtan AU - Su J AD - Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China. FAU - Xie, Liping AU - Xie L AD - Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China Protein Science Laboratory of the Ministry of Education, Tsinghua University, Beijing 100084, China lpxie@mail.tsinghua.edu.cn. FAU - Hu, Xiaoli AU - Hu X AD - Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China. FAU - Zhang, Rongqing AU - Zhang R AD - Institute of Marine Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, China Protein Science Laboratory of the Ministry of Education, Tsinghua University, Beijing 100084, China. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140707 PL - China TA - Acta Biochim Biophys Sin (Shanghai) JT - Acta biochimica et biophysica Sinica JID - 101206716 RN - 0 (DNA Primers) RN - 0 (Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Cloning, Molecular MH - DNA Primers MH - Microscopy, Electron, Scanning MH - Molecular Sequence Data MH - Pectinidae MH - Polymerase Chain Reaction MH - Proteins/chemistry/*genetics MH - RNA Interference MH - Spectroscopy, Fourier Transform Infrared OTO - NOTNLM OT - Chlamys farreri OT - Shematrin OT - folia OT - framework OT - shell EDAT- 2014/07/09 06:00 MHDA- 2015/06/03 06:00 CRDT- 2014/07/09 06:00 PHST- 2014/07/07 [aheadofprint] AID - gmu054 [pii] AID - 10.1093/abbs/gmu054 [doi] PST - ppublish SO - Acta Biochim Biophys Sin (Shanghai). 2014 Aug;46(8):709-19. doi: 10.1093/abbs/gmu054. Epub 2014 Jul 7. PMID- 11425308 OWN - NLM STAT- MEDLINE DA - 20010626 DCOM- 20010920 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 40 IP - 26 DP - 2001 Jul 3 TI - Vesicle permeabilization by protofibrillar alpha-synuclein: implications for the pathogenesis and treatment of Parkinson's disease. PG - 7812-9 AB - Fibrillar alpha-synuclein is a component of the Lewy body, the characteristic neuronal inclusion of the Parkinson's disease (PD) brain. Both alpha-synuclein mutations linked to autosomal dominant early-onset forms of PD promote the in vitro conversion of the natively unfolded protein into ordered prefibrillar oligomers, suggesting that these protofibrils, rather than the fibril itself, may induce cell death. We report here that protofibrils differ markedly from fibrils with respect to their interactions with synthetic membranes. Protofibrillar alpha-synuclein, in contrast to the monomeric and the fibrillar forms, binds synthetic vesicles very tightly via a beta-sheet-rich structure and transiently permeabilizes these vesicles. The destruction of vesicular membranes by protofibrillar alpha-synuclein was directly observed by atomic force microscopy. The possibility that the toxicity of alpha-synuclein fibrillization may derive from an oligomeric intermediate, rather than the fibril, has implications regarding the design of therapeutics for PD. FAU - Volles, M J AU - Volles MJ AD - Center for Neurologic Diseases, Brigham and Women's Hospital, and Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Lee, S J AU - Lee SJ FAU - Rochet, J C AU - Rochet JC FAU - Shtilerman, M D AU - Shtilerman MD FAU - Ding, T T AU - Ding TT FAU - Kessler, J C AU - Kessler JC FAU - Lansbury, P T Jr AU - Lansbury PT Jr LA - eng GR - AG08470/AG/NIA NIH HHS/United States GR - AG14366/AG/NIA NIH HHS/United States GR - NS38375/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cytotoxins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Phosphatidic Acids) RN - 0 (Phosphatidylcholines) RN - 0 (Phosphatidylglycerols) RN - 0 (Phospholipids) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Adsorption MH - Cytotoxins/metabolism MH - Humans MH - Lewy Bodies/metabolism MH - Nerve Tissue Proteins/chemistry/isolation & purification/*metabolism/toxicity MH - Parkinson Disease/*etiology/*metabolism/therapy MH - Permeability MH - Phosphatidic Acids/metabolism MH - Phosphatidylcholines/metabolism MH - Phosphatidylglycerols/metabolism MH - Phospholipids/*metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Synucleins MH - Time Factors MH - alpha-Synuclein EDAT- 2001/06/27 10:00 MHDA- 2001/09/21 10:01 CRDT- 2001/06/27 10:00 AID - bi0102398 [pii] PST - ppublish SO - Biochemistry. 2001 Jul 3;40(26):7812-9. PMID- 11425309 OWN - NLM STAT- MEDLINE DA - 20010626 DCOM- 20010920 LR - 20071115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 40 IP - 26 DP - 2001 Jul 3 TI - NMR solution structure and backbone dynamics of the CC chemokine eotaxin-3. PG - 7820-31 AB - Eotaxin-3 is one of three related chemokines that specifically activate chemokine receptor CCR3. We report the 3D structure and backbone dynamics of eotaxin-3 determined by NMR spectroscopy. Eotaxin-3 is monomeric under the conditions in this study and consists of an unstructured N-terminus before the first two conserved cysteine residues, an irregularly structured N-loop following the second conserved cysteine, a single turn of 3(10)-helix, a three-stranded antiparallel beta-sheet, an alpha-helix, and an unstructured C-terminal tail. As in other chemokines, the alpha-helix packs against one face of the beta-sheet. The average backbone and heavy atom rmsd values of the 20 structures (residues 9-65) are 0.44 and 1.01 A, respectively. A comparison between the structures of eotaxin-3 and related chemokines suggests that the electrostatic potential in the vicinity of a surface groove and the structure of the beta2-beta3 turn may be important for maintaining receptor specificity. The backbone dynamics of eotaxin-3 were determined from 15N NMR relaxation data using the extended model free dynamics formalism. Large amplitude motions on the picosecond to nanosecond time scale were observed in both termini and in some residues in the N-loop, the beta1-beta2 turn, and the beta3 strand; the location of these residues suggests a possible role for dynamics in receptor binding and activation. In contrast to eotaxin, eotaxin-3 exhibits no substantial mobility on the microsecond to millisecond time scale. FAU - Ye, J AU - Ye J AD - Department of Chemistry, Indiana University, Bloomington, Indiana 47405-0001, USA. FAU - Mayer, K L AU - Mayer KL FAU - Mayer, M R AU - Mayer MR FAU - Stone, M J AU - Stone MJ LA - eng SI - PDB/1G2S SI - PDB/1G2T GR - GM 55055/GM/NIGMS NIH HHS/United States GR - S10 RR11841/RR/NCRR NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (CCL26 protein, human) RN - 0 (CCR3 protein, human) RN - 0 (Chemokines, CC) RN - 0 (Receptors, CCR3) RN - 0 (Receptors, Chemokine) RN - 0 (Recombinant Proteins) RN - 0 (Solutions) SB - IM MH - Amino Acid Sequence MH - Binding, Competitive MH - Chemokines, CC/biosynthesis/*chemistry/metabolism MH - Molecular Sequence Data MH - *Nuclear Magnetic Resonance, Biomolecular/methods MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Radioligand Assay MH - Receptors, CCR3 MH - Receptors, Chemokine/metabolism MH - Recombinant Proteins/biosynthesis/chemistry/metabolism MH - Sequence Homology, Amino Acid MH - Solutions MH - Thermodynamics EDAT- 2001/06/27 10:00 MHDA- 2001/09/21 10:01 CRDT- 2001/06/27 10:00 AID - bi010252s [pii] PST - ppublish SO - Biochemistry. 2001 Jul 3;40(26):7820-31. PMID- 11717490 OWN - NLM STAT- MEDLINE DA - 20011121 DCOM- 20020123 LR - 20131121 IS - 0907-4449 (Print) IS - 0907-4449 (Linking) VI - 57 IP - Pt 12 DP - 2001 Dec TI - The first structure of pectate lyase belonging to polysaccharide lyase family 3. PG - 1786-92 AB - The crystal structure of a highly alkaline low molecular weight pectate lyase (Pel-15) was determined at 1.5 A resolution by the multiple isomorphous replacement (MIR) method. This is the first pectate lyase structure from polysaccharide lyase family 3. The overall structure is a simple eight-turn right-handed parallel beta-helix domain with one long loop protruding from one side of the beta-helix. The low molecular weight of Pel-15 derives from the lack of N- and C-terminal extensions that are found in many beta-helix proteins. Although the structure has one calcium ion at pH 6.7, raising the pH to 9.5 results in the binding of an additional calcium ion. The common calcium ion found in both the pH 6.5 and 9.5 structures seems to stabilize both the beta-helix structure and the long protruding loop. The additional calcium ion found in the pH 9.5 structure alone may neutralize the acidic substrate. The region around the additional calcium ion is thought to bind to the substrate, as this region is rich in charged amino-acid residues which are required in catalysis. FAU - Akita, M AU - Akita M AD - Department of Biotechnology and Biomaterial Chemistry, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan. h991401d@mbox.media.nagoya-u.ac.jp FAU - Suzuki, A AU - Suzuki A FAU - Kobayashi, T AU - Kobayashi T FAU - Ito, S AU - Ito S FAU - Yamane, T AU - Yamane T LA - eng SI - PDB/1EE6 PT - Comparative Study PT - Journal Article DEP - 20011121 PL - Denmark TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (Isoenzymes) RN - EC 4.2.2.- (Polysaccharide-Lyases) RN - EC 4.2.2.2 (pectate lyase) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Calcium/metabolism MH - Crystallization MH - Crystallography, X-Ray MH - Data Collection MH - Hydrogen-Ion Concentration MH - Isoenzymes/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Molecular Weight MH - Polysaccharide-Lyases/*chemistry/isolation & purification MH - Protein Conformation EDAT- 2001/11/22 10:00 MHDA- 2002/01/24 10:01 CRDT- 2001/11/22 10:00 PHST- 2001/02/21 [received] PHST- 2001/09/03 [accepted] PHST- 2001/11/21 [epublish] AID - S0907444901014482 [pii] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2001 Dec;57(Pt 12):1786-92. Epub 2001 Nov 21. PMID- 16092089 OWN - NLM STAT- MEDLINE DA - 20050815 DCOM- 20051213 LR - 20141120 IS - 0885-3185 (Print) IS - 0885-3185 (Linking) VI - 20 Suppl 12 DP - 2005 Aug TI - Alpha-synuclein dysfunction in Lewy body diseases. PG - S37-44 AB - alpha-Synuclein belongs to a small group of natively unfolded proteins that can transiently bind to lipid membranes and acquire a partial alpha-helical conformation. Its relevance to Parkinson's disease (PD) is based on mutations found in familial cases of the disease and its presence in filaments of Lewy bodies (LB) and Lewy neurites (LN) in sporadic cases where it is packed in a beta-sheet configuration. This structural plasticity of alpha-synuclein has raised the possibility that neurodegeneration may be a consequence of abnormal protein folding. The extent to which abnormal folding and aggregation of neuronal proteins is directly toxic to the cell, an inert biochemical marker of an underlying harmful metabolic defect, or a protective reaction remains to be seen. We review the function of alpha-synuclein and recent studies that have shed light on the mechanisms by which it aggregates. CI - Copyright 2005 Movement Disorder Society. FAU - Tofaris, George K AU - Tofaris GK AD - Cambridge Centre for Brain Repair, University of Cambridge, UK. FAU - Spillantini, Maria Grazia AU - Spillantini MG LA - eng PT - Journal Article PL - United States TA - Mov Disord JT - Movement disorders : official journal of the Movement Disorder Society JID - 8610688 RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Chromosomes, Human, Pair 6/genetics MH - Cytoskeleton/metabolism MH - Drosophila MH - Humans MH - In Vitro Techniques MH - Lewy Body Disease/*genetics/metabolism/*physiopathology MH - Mice MH - Parkinson Disease/genetics/physiopathology MH - Phenotype MH - Phosphorylation MH - Point Mutation/*genetics MH - alpha-Synuclein/*genetics/metabolism EDAT- 2005/08/11 09:00 MHDA- 2005/12/15 09:00 CRDT- 2005/08/11 09:00 AID - 10.1002/mds.20538 [doi] PST - ppublish SO - Mov Disord. 2005 Aug;20 Suppl 12:S37-44. PMID- 19156821 OWN - NLM STAT- MEDLINE DA - 20090727 DCOM- 20100223 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 76 IP - 2 DP - 2009 Aug 1 TI - Isoform-specific variation in the intrinsic disorder of the ecdysteroid receptor N-terminal domain. PG - 291-308 LID - 10.1002/prot.22342 [doi] AB - The Drosophila melanogaster ecdysteroid receptor (EcR) is a member of the nuclear hormone receptor superfamily. EcR controls animal development and metamorphosis by activating or repressing the transcription of target genes. There are three EcR isoforms, EcRA, EcRB1, and EcRB2 that exhibit diverse spatial and temporal distributions within various tissues and reveal essential functional differences. These differences can be attributed to the isoform-specific N-terminal domains (NTDs), which differ in length and primary structure. To lay a foundation for understanding of the molecular mechanism underlying functional diversity of the isoforms, we have carried out a comprehensive biochemical and biophysical analysis of purified hexahistidine-tagged EcRA and EcRB1 NTDs (EcRA-NTD and EcRB1-NTD). The results, along with in silico examinations of the primary structures indicate that the EcR NTDs exhibit properties of premolten globule-like intrinsically disordered proteins. Furthermore, we demonstrate for the first time that NTDs of isoforms of a particular nuclear hormone receptor exhibit distinct structural properties. In silico analysis revealed that the EcRA-NTD sequence has a bigger tendency for disorder than the EcRB1-NTD sequence. Accordingly, the circular dichroism experiments demonstrated that EcRA-NTD has lower regular secondary structure content than EcRB1-NTD and the size-exclusion chromatography showed that EcRA-NTD is less compact than EcRB1-NTD. Furthermore, the limited proteolysis analysis revealed that the C-terminal region common to both NTDs is more susceptible to the enzymatic cleavage in EcRA-NTD than in EcRB1-NTD. We postulate that unique conformational states of EcRA-NTD and EcRB1-NTD might act as the starting points for the functional diversity of EcRA and EcRB1 isoforms. CI - 2008 Wiley-Liss, Inc. FAU - Nocula-Lugowska, Malgorzata AU - Nocula-Lugowska M AD - Department of Biochemistry, Wroclaw University of Technology, Poland. FAU - Rymarczyk, Grzegorz AU - Rymarczyk G FAU - Lisowski, Marek AU - Lisowski M FAU - Ozyhar, Andrzej AU - Ozyhar A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Drosophila Proteins) RN - 0 (Protein Isoforms) RN - 0 (Receptors, Steroid) RN - 0 (ecdysteroid receptor) SB - IM MH - Animals MH - Circular Dichroism MH - Drosophila Proteins/*chemistry/genetics/isolation & purification/metabolism MH - Drosophila melanogaster/metabolism MH - Protein Conformation MH - Protein Isoforms/chemistry/genetics/metabolism MH - Protein Structure, Tertiary MH - Receptors, Steroid/*chemistry/genetics/isolation & purification/metabolism EDAT- 2009/01/22 09:00 MHDA- 2010/02/24 06:00 CRDT- 2009/01/22 09:00 AID - 10.1002/prot.22342 [doi] PST - ppublish SO - Proteins. 2009 Aug 1;76(2):291-308. doi: 10.1002/prot.22342. PMID- 23063534 OWN - NLM STAT- MEDLINE DA - 20121226 DCOM- 20130318 LR - 20131121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1834 IP - 1 DP - 2013 Jan TI - Different pressure-temperature behavior of the structured and unstructured regions of titin. PG - 112-8 LID - 10.1016/j.bbapap.2012.10.001 [doi] LID - S1570-9639(12)00220-8 [pii] AB - Contrary to the classical view, according to which all proteins adopt a specific folded conformation necessary for their function, intrinsically unstructured proteins (IUPs) display random-coil-like conformation under physiological conditions. We compared the structured and unstructured domains from titin, a giant protein responsible for striated-muscle elasticity. A 171-residue-long fragment (polyE) of the disordered PEVK domain, and an Ig domain (I27) with ordered structure were investigated. FTIR (Fourier transform infrared) and fluorescence spectroscopy combined with a diamond anvil cell were used for investigation of the secondary structures under wide range of pressure and temperature. PolyE preserves its disordered characteristics across the entire range of investigated pressure (0-16kbar), temperature (0-100 degrees C), pD (3-10.5) and different solvent conditions. The detailed temperature-pressure phase diagram of titin I27 was determined. At 30 degrees C, increasing pressure unfolds titin I27 in one step at 10.5kbar. Increasing temperature at atmospheric pressure results in two transitions. At 50 degrees C the secondary structure is loosened and the protein transforms into a molten-globule state. At 65 degrees C the protein completely unfolds. Unfolding is followed by aggregation at ambient pressure. Moderate pressures (>2kbar), however, can prevent the protein from aggregation. Our experiments in wide range of physical parameters revealed four different structures for I27, while the unstructured character of the PEVK fragment is insensitive to these parameters. CI - Copyright (c) 2012 Elsevier B.V. All rights reserved. FAU - Somkuti, Judit AU - Somkuti J AD - Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Tuzolto utca 37-47, Budapest, Hungary. FAU - Martonfalvi, Zsolt AU - Martonfalvi Z FAU - Kellermayer, Miklos S Z AU - Kellermayer MS FAU - Smeller, Laszlo AU - Smeller L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121010 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Connectin) RN - 0 (Muscle Proteins) RN - 0 (TTN protein, human) RN - EC 2.7.- (Protein Kinases) SB - IM MH - Connectin MH - *Hot Temperature MH - Humans MH - Muscle Proteins/*chemistry/genetics MH - *Pressure MH - Protein Kinases/*chemistry/genetics MH - Protein Structure, Secondary MH - Protein Structure, Tertiary EDAT- 2012/10/16 06:00 MHDA- 2013/03/19 06:00 CRDT- 2012/10/16 06:00 PHST- 2012/06/29 [received] PHST- 2012/10/01 [revised] PHST- 2012/10/03 [accepted] PHST- 2012/10/10 [aheadofprint] AID - S1570-9639(12)00220-8 [pii] AID - 10.1016/j.bbapap.2012.10.001 [doi] PST - ppublish SO - Biochim Biophys Acta. 2013 Jan;1834(1):112-8. doi: 10.1016/j.bbapap.2012.10.001. Epub 2012 Oct 10. PMID- 11799399 OWN - NLM STAT- MEDLINE DA - 20020128 DCOM- 20020221 LR - 20041117 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 9 IP - 2 DP - 2002 Feb TI - The solution structure and interactions of CheW from Thermotoga maritima. PG - 121-5 AB - Using protein from the hyperthermophile Thermotoga maritima, we have determined the solution structure of CheW, an essential component in the formation of the bacterial chemotaxis signaling complex. The overall fold is similar to the regulatory domain of the chemotaxis kinase CheA. In addition, interactions of CheW with CheA were monitored by nuclear magnetic resonance (NMR) techniques. The chemical shift perturbation data show the probable contacts that CheW makes with CheA. In combination with previous genetic data, the structure also suggests a possible binding site for the chemotaxis receptor. These results provide a structural basis for a model in which CheW acts as a molecular bridge between CheA and the cytoplasmic tails of the receptor. FAU - Griswold, Ian J AU - Griswold IJ AD - Institute of Molecular Biology, Department of Chemistry, University of Oregon Eugene, Oregon 97403, USA. FAU - Zhou, Hongjun AU - Zhou H FAU - Matison, Mikenzie AU - Matison M FAU - Swanson, Ronald V AU - Swanson RV FAU - McIntosh, Lawrence P AU - McIntosh LP FAU - Simon, Melvin I AU - Simon MI FAU - Dahlquist, Frederick W AU - Dahlquist FW LA - eng SI - PDB/1K0S PT - Journal Article PL - United States TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Bacterial Proteins) RN - 0 (Membrane Proteins) RN - 0 (Receptors, Cell Surface) RN - 0 (Solutions) RN - 0 (methyl-accepting chemotaxis proteins) RN - 107217-07-2 (CheW protein, Bacteria) SB - IM MH - Bacterial Proteins/*chemistry/*metabolism MH - Binding Sites MH - Chemotaxis MH - Membrane Proteins/chemistry/*metabolism MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Cell Surface/metabolism MH - Solutions MH - Structure-Activity Relationship MH - Thermotoga maritima/*chemistry EDAT- 2002/01/19 10:00 MHDA- 2002/02/22 10:01 CRDT- 2002/01/19 10:00 AID - 10.1038/nsb753 [doi] AID - nsb753 [pii] PST - ppublish SO - Nat Struct Biol. 2002 Feb;9(2):121-5. PMID- 15478127 OWN - NLM STAT- MEDLINE DA - 20041025 DCOM- 20050624 LR - 20061115 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 76 IP - 5 DP - 2004 TI - Cyclization of pyrrhocoricin retains structural elements crucial for the antimicrobial activity of the native peptide. PG - 446-58 AB - Pyrrhocoricin is a naturally occurring antimicrobial peptide from the European fire bug Pyrrhocoris apterus. It has submicromolar activity against a range of Gram-negative bacterial strains and has created recent interest as a lead for the development of novel antibiotic compounds. In this study, we have used NMR spectroscopy to determine the solution structures of pyrrhocoricin and a synthetic macrocyclic derivative that has improved in vivo pharmaceutical properties. Native pyrrhocoricin is largely disordered in solution, but there is evidence of a subpopulation with ordered turn regions over residues 2-5, 4-7, and 16-19. The macrocyclic derivative incorporates a nine amino acid linker joining the N- and C-termini, which does not adversely affect the antimicrobial potency but leads to a broader spectrum of activity. The NMR data suggest that the turn conformations in the cyclic derivative are similar to those in the native form, thus implicating them in the biological function. CI - (c) 2004 Wiley Periodicals, Inc. FAU - Rosengren, K Johan AU - Rosengren KJ AD - Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia. FAU - Goransson, Ulf AU - Goransson U FAU - Otvos, Laszlo Jr AU - Otvos L Jr FAU - Craik, David J AU - Craik DJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 RN - 0 (Amino Acids) RN - 0 (Antimicrobial Cationic Peptides) RN - 0 (Insect Proteins) RN - 0 (Peptides, Cyclic) RN - 156548-23-1 (pyrrhocoricin protein, Pyrrhocoris apterus) SB - IM MH - Amino Acids/genetics/metabolism MH - Animals MH - Antimicrobial Cationic Peptides/*chemistry/genetics/metabolism/pharmacology MH - Bacteria/*drug effects MH - Insect Proteins/*chemistry/genetics/metabolism/pharmacology MH - Insects MH - Magnetic Resonance Spectroscopy MH - Peptides, Cyclic/*chemistry/genetics/metabolism/pharmacology EDAT- 2004/10/13 09:00 MHDA- 2005/06/25 09:00 CRDT- 2004/10/13 09:00 AID - 10.1002/bip.20159 [doi] PST - ppublish SO - Biopolymers. 2004;76(5):446-58. PMID- 22887965 OWN - NLM STAT- MEDLINE DA - 20120921 DCOM- 20130221 LR - 20141105 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 21 IP - 10 DP - 2012 Oct TI - Interaction between the C-terminal domains of measles virus nucleoprotein and phosphoprotein: a tight complex implying one binding site. PG - 1577-85 LID - 10.1002/pro.2138 [doi] AB - The intrinsically disordered C-terminal domain (N(TAIL) ) of the measles virus (MeV) nucleoprotein undergoes alpha-helical folding upon binding to the C-terminal X domain (XD) of the phosphoprotein. The N(TAIL) region involved in binding coupled to folding has been mapped to a conserved region (Box2) encompassing residues 489-506. In the previous studies published in this journal, we obtained experimental evidence supporting a K(D) for the N(TAIL) -XD binding reaction in the nM range and also showed that an additional N(TAIL) region (Box3, aa 517-525) plays a role in binding to XD. In striking contrast with these data, studies published in this journal by Kingston and coworkers pointed out a much less stable complex (K(D) in the muM range) and supported lack of involvement of Box3 in complex formation. The objective of this study was to critically re-evaluate the role of Box3 in N(TAIL) -XD binding. Since our previous studies relied on N(TAIL) -truncated forms possessing an irrelevant Flag sequence appended at their C-terminus, we, herein, generated an N(TAIL) devoid of Box3 and any additional C-terminal residues, as well as a form encompassing only residues 482-525. We then used isothermal titration calorimetry to characterize the binding reactions between XD and these N(TAIL) forms. Results effectively argue for the presence of a single XD-binding site located within Box2, in agreement with the results by Kingston et al., while providing clear experimental support for a high-affinity complex. Altogether, the present data provide mechanistic insights into the replicative machinery of MeV and clarify a hitherto highly debated point. CI - Copyright (c) 2012 The Protein Society. FAU - Blocquel, David AU - Blocquel D AD - CNRS, Aix-Marseille Universite, Architecture et Fonction des Macromolecules Biologiques (AFMB) UMR 7257, 13288 Marseille, France. FAU - Habchi, Johnny AU - Habchi J FAU - Costanzo, Stephanie AU - Costanzo S FAU - Doizy, Anthony AU - Doizy A FAU - Oglesbee, Michael AU - Oglesbee M FAU - Longhi, Sonia AU - Longhi S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120917 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Nucleoproteins) RN - 0 (P protein, Sendai virus) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Proteins) RN - 0 (Viral Proteins) RN - 0 (nucleoprotein, Measles virus) SB - IM MH - Calorimetry MH - Crystallography MH - Models, Molecular MH - Nucleoproteins/*chemistry/*metabolism MH - Phosphoproteins/*chemistry/*metabolism MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Thermodynamics MH - Viral Proteins/*chemistry/*metabolism PMC - PMC3526999 OID - NLM: PMC3526999 EDAT- 2012/08/14 06:00 MHDA- 2013/02/22 06:00 CRDT- 2012/08/14 06:00 PHST- 2012/05/15 [received] PHST- 2012/06/27 [revised] PHST- 2012/07/17 [accepted] PHST- 2012/09/17 [aheadofprint] AID - 10.1002/pro.2138 [doi] PST - ppublish SO - Protein Sci. 2012 Oct;21(10):1577-85. doi: 10.1002/pro.2138. Epub 2012 Sep 17. PMID- 20224939 OWN - NLM STAT- MEDLINE DA - 20100318 DCOM- 20100826 LR - 20101118 IS - 1573-5079 (Electronic) IS - 0166-8595 (Linking) VI - 103 IP - 3 DP - 2010 Mar TI - Comparative sequence analysis of CP12, a small protein involved in the formation of a Calvin cycle complex in photosynthetic organisms. PG - 183-94 LID - 10.1007/s11120-010-9542-z [doi] AB - CP12, a small intrinsically unstructured protein, plays an important role in the regulation of the Calvin cycle by forming a complex with phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). An extensive search in databases revealed 129 protein sequences from, higher plants, mosses and liverworts, different groups of eukaryotic algae and cyanobacteria. CP12 was identified throughout the Plantae, apart from in the Prasinophyceae. Within the Chromalveolata, two putative CP12 proteins have been found in the genomes of the diatom Thalassiosira pseudonana and the haptophyte Emiliania huxleyi, but specific searches in further chromalveolate genomes or EST datasets did not reveal any CP12 sequences in other Prymnesiophyceae, Dinophyceae or Pelagophyceae. A species from the Euglenophyceae within the Excavata also appeared to lack CP12. Phylogenetic analysis showed a clear separation into a number of higher taxonomic clades and among different forms of CP12 in higher plants. Cyanobacteria, Chlorophyceae, Rhodophyta and Glaucophyceae, Bryophyta, and the CP12-3 forms in higher plants all form separate clades. The degree of disorder of CP12 was higher in higher plants than in the eukaryotic algae and cyanobacteria apart from the green algal class Mesostigmatophyceae, which is ancestral to the streptophytes. This suggests that CP12 has evolved to become more flexible and possibly take on more general roles. Different features of the CP12 sequences in the different taxonomic groups and their potential functions and interactions in the Calvin cycle are discussed. FAU - Groben, Rene AU - Groben R AD - Centre for Hydrology and Ecology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK. FAU - Kaloudas, Dimitrios AU - Kaloudas D FAU - Raines, Christine A AU - Raines CA FAU - Offmann, Bernard AU - Offmann B FAU - Maberly, Stephen C AU - Maberly SC FAU - Gontero, Brigitte AU - Gontero B LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100312 PL - Netherlands TA - Photosynth Res JT - Photosynthesis research JID - 100954728 RN - 0 (Algal Proteins) RN - 0 (Plant Proteins) SB - IM MH - Algal Proteins/chemistry MH - Amino Acid Sequence MH - Eukaryota/genetics MH - Expressed Sequence Tags MH - Genome/genetics MH - Molecular Sequence Data MH - *Photosynthesis MH - Phylogeny MH - Plant Proteins/*chemistry MH - Plants/*metabolism MH - *Sequence Analysis, Protein MH - Sequence Homology, Amino Acid EDAT- 2010/03/13 06:00 MHDA- 2010/08/27 06:00 CRDT- 2010/03/13 06:00 PHST- 2009/10/09 [received] PHST- 2010/02/28 [accepted] PHST- 2010/03/12 [aheadofprint] AID - 10.1007/s11120-010-9542-z [doi] PST - ppublish SO - Photosynth Res. 2010 Mar;103(3):183-94. doi: 10.1007/s11120-010-9542-z. Epub 2010 Mar 12. PMID- 19763886 OWN - NLM STAT- MEDLINE DA - 20091110 DCOM- 20100119 IS - 1874-270X (Electronic) VI - 3 IP - 2 DP - 2009 Dec TI - (1)H, (13)C and (15)N assignments of a camelid nanobody directed against human alpha-synuclein. PG - 231-3 LID - 10.1007/s12104-009-9182-4 [doi] AB - Nanobodies are single chain antibodies that are uniquely produced in Camelidae, e.g. camels and llamas. They have the desirable features of small sizes (Mw < 14 kDa) and high affinities against antigens (Kd approximately nM), making them ideal as structural probes for biomedically relevant motifs both in vitro and in vivo. We have previously shown that nanobody binding to amyloidogenic human lysozyme variants can effectively inhibit their aggregation, the process that is at the origin of systemic amyloid disease. Here we report the NMR assignments of a new nanobody, termed NbSyn2, which recognises the C-terminus of the intrinsically disordered protein, human alpha-synuclein (aS), whose aberrant self-association is implicated in Parkinson's disease. FAU - Vuchelen, Anneleen AU - Vuchelen A AD - Department of Chemistry, University of Cambridge, Cambridge, UK. FAU - O'Day, Elizabeth AU - O'Day E FAU - De Genst, Erwin AU - De Genst E FAU - Pardon, Els AU - Pardon E FAU - Wyns, Lode AU - Wyns L FAU - Dumoulin, Mireille AU - Dumoulin M FAU - Dobson, Christopher M AU - Dobson CM FAU - Christodoulou, John AU - Christodoulou J FAU - Hsu, Shang-Te Danny AU - Hsu ST LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (Single-Chain Antibodies) RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Camelids, New World MH - Camels MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Single-Chain Antibodies/*chemistry/*immunology MH - alpha-Synuclein/*immunology EDAT- 2009/09/19 06:00 MHDA- 2010/01/20 06:00 CRDT- 2009/09/19 06:00 PHST- 2009/07/01 [received] PHST- 2009/09/05 [accepted] PHST- 2009/09/18 [aheadofprint] AID - 10.1007/s12104-009-9182-4 [doi] PST - ppublish SO - Biomol NMR Assign. 2009 Dec;3(2):231-3. doi: 10.1007/s12104-009-9182-4. PMID- 2121770 OWN - NLM STAT- MEDLINE DA - 19901210 DCOM- 19901210 LR - 20061115 IS - 0021-972X (Print) IS - 0021-972X (Linking) VI - 71 IP - 5 DP - 1990 Nov TI - Highly vectorial secretion of inhibin by primate Sertoli cells in vitro. PG - 1235-8 AB - Having recently demonstrated highly vectorial and FSH-stimulated inhibin secretion by immature rat Sertoli cells in vitro, we wished to determine if vectorial secretion of inhibin was also characteristic of primate Sertoli cells. By adapting techniques for isolation of Sertoli cells from testes of the immature rat and cynomolgus monkey. Sertoli cells were isolated from immature baboon testes. Sertoli cells were then plated onto matrix-impregnated porous filters and cultured in twin chamber assemblies in fully defined, supplemented HEPES-buffered Eagles medium. Inhibin was measured in conditioned culture media by an heterologous RIA validated for primate inhibins. Throughout 28 days of culture immunoreactive inhibin was readily detectable in the upper chambers whereas inhibin was undetectable or just detectable in the lower chambers. The median ratio of upper to lower chamber inhibin content was 15.3 under basal conditions rising to 41 under FSH stimulation. Inhibin secretion into the upper chamber was increased 2.5 +/- 0.4 times by stimulation with ovine FSH (100 ng/ml). We conclude that immature Sertoli cells from a nonhuman primate demonstrate FSH-responsive and highly vectorial secretion of inhibin almost exclusively into the upper chamber. These data suggest that during maturation mammalian Sertoli cells secrete inhibin vectorially mainly from the apical surface of the cell towards the seminiferous tubular lumen. The predominance of inhibin secretion into the seminiferous tubule during testicular maturation suggests that inhibin may have an important paracrine or autocrine role in the developmental biology of spermiogenesis. FAU - Handelsman, D J AU - Handelsman DJ AD - Department of Obstetrics and Gynecology, University of Sydney, Australia. FAU - Spaliviero, J A AU - Spaliviero JA FAU - Phippard, A F AU - Phippard AF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Clin Endocrinol Metab JT - The Journal of clinical endocrinology and metabolism JID - 0375362 RN - 57285-09-3 (Inhibins) RN - 9002-68-0 (Follicle Stimulating Hormone) SB - AIM SB - IM MH - Animals MH - Cells, Cultured MH - Follicle Stimulating Hormone/pharmacology MH - Haplorhini MH - Inhibins/analysis/*metabolism MH - Male MH - Papio MH - Rats MH - Sertoli Cells/drug effects/*metabolism MH - Testis/metabolism EDAT- 1990/11/01 MHDA- 1990/11/01 00:01 CRDT- 1990/11/01 00:00 AID - 10.1210/jcem-71-5-1235 [doi] PST - ppublish SO - J Clin Endocrinol Metab. 1990 Nov;71(5):1235-8. PMID- 24131107 OWN - NLM STAT- MEDLINE DA - 20131113 DCOM- 20140617 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 45 DP - 2013 Nov 13 TI - Ion mobility spectrometry reveals the mechanism of amyloid formation of Abeta(25-35) and its modulation by inhibitors at the molecular level: epigallocatechin gallate and scyllo-inositol. PG - 16926-37 LID - 10.1021/ja406197f [doi] AB - Amyloid cascades leading to peptide beta-sheet fibrils and plaques are central to many important diseases. Recently, intermediate assemblies of these cascades were identified as the toxic agents that interact with the cellular machinery. The relationship between the transformation from natively unstructured assembly to the beta-sheet oligomers to disease is important in understanding disease onset and the development of therapeutic agents. Research on this early oligomeric region has largely been unsuccessful since traditional techniques measure only ensemble average oligomer properties. Here, ion mobility methods are utilized to deduce the modulation of peptide self-assembly pathways in the amyloid-beta protein fragment Abeta(25-35) by two amyloid inhibitors (epigallocatechin gallate and scyllo-inositol) that are currently in clinical trials for Alzheimer's Disease. We provide evidence that suppression of beta-extended oligomers from the onset of the conversion into beta-oligomer conformations is essential for effective attenuation of beta-structured amyloid oligomeric species often associated with oligomer toxicity. Furthermore, we demonstrate the ease with which ion mobility spectrometry-mass spectrometry can guide the development of therapeutic agents and drug evaluation by providing molecular level insight into the amyloid formation process and its modulation by small molecule assembly modulators. FAU - Bleiholder, Christian AU - Bleiholder C AD - Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States. FAU - Do, Thanh D AU - Do TD FAU - Wu, Chun AU - Wu C FAU - Economou, Nicholas J AU - Economou NJ FAU - Bernstein, Summer S AU - Bernstein SS FAU - Buratto, Steven K AU - Buratto SK FAU - Shea, Joan-Emma AU - Shea JE FAU - Bowers, Michael T AU - Bowers MT LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20131101 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (25-35)) RN - 488-59-5 (scyllitol) RN - 4L6452S749 (Inositol) RN - 8R1V1STN48 (Catechin) RN - BQM438CTEL (epigallocatechin gallate) SB - IM MH - Alzheimer Disease/drug therapy/metabolism MH - Amyloid beta-Peptides/*antagonists & inhibitors/*metabolism MH - Catechin/*analogs & derivatives/pharmacology MH - Humans MH - Inositol/*pharmacology MH - Mass Spectrometry MH - Models, Molecular MH - Peptide Fragments/*antagonists & inhibitors/*metabolism MH - Protein Multimerization/drug effects MH - Protein Structure, Secondary/drug effects EDAT- 2013/10/18 06:00 MHDA- 2014/06/18 06:00 CRDT- 2013/10/18 06:00 PHST- 2013/11/01 [aheadofprint] AID - 10.1021/ja406197f [doi] PST - ppublish SO - J Am Chem Soc. 2013 Nov 13;135(45):16926-37. doi: 10.1021/ja406197f. Epub 2013 Nov 1. PMID- 15901248 OWN - NLM STAT- MEDLINE DA - 20050519 DCOM- 20051024 LR - 20140606 IS - 1470-8728 (Electronic) IS - 0264-6021 (Linking) VI - 388 IP - Pt 2 DP - 2005 Jun 1 TI - Grb10 and Grb14: enigmatic regulators of insulin action--and more? PG - 393-406 AB - The Grb proteins (growth factor receptor-bound proteins) Grb7, Grb10 and Grb14 constitute a family of structurally related multidomain adapters with diverse cellular functions. Grb10 and Grb14, in particular, have been implicated in the regulation of insulin receptor signalling, whereas Grb7 appears predominantly to be involved in focal adhesion kinase-mediated cell migration. However, at least in vitro, these adapters can bind to a variety of growth factor receptors. The highest identity within the Grb7/10/14 family occurs in the C-terminal SH2 (Src homology 2) domain, which mediates binding to activated receptors. A second well-conserved binding domain, BPS [between the PH (pleckstrin homology) and SH2 domains], can act to enhance binding to the IR (insulin receptor). Consistent with a putative adapter function, some non-receptor-binding partners, including protein kinases, have also been identified. Grb10 and Grb14 are widely, but not uniformly, expressed in mammalian tissues, and there are various isoforms of Grb10. Binding of Grb10 or Grb14 to autophosphorylated IR in vitro inhibits tyrosine kinase activity towards other substrates, but studies on cultured cell lines have been conflicting as to whether Grb10 plays a positive or negative role in insulin signalling. Recent gene knockouts in mice have established that Grb10 and Grb14 act as inhibitors of intracellular signalling pathways regulating growth and metabolism, although the phenotypes of the two knockouts are distinct. Ablation of Grb14 enhances insulin action in liver and skeletal muscle and improves whole-body tolerance, with little effect on embryonic growth. Ablation of Grb10 results in disproportionate overgrowth of the embryo and placenta involving unidentified pathways, and also impacts on hepatic glycogen synthesis, and probably on glucose homoeostasis. This review discusses the extent to which previous studies in vitro can account for the observed phenotype of knockout animals, and considers evidence that aberrant function of Grb10 or Grb14 may contribute to disorders of growth and metabolism in humans. FAU - Holt, Lowenna J AU - Holt LJ AD - University of Cambridge, Department of Clinical Biochemistry, Addenbrooke's Hospital, Cambridge CB2 2QR, UK. l.holt@garvan.org.au FAU - Siddle, Kenneth AU - Siddle K LA - eng PT - Journal Article PT - Review PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (Grb14 protein, mouse) RN - 0 (Insulin) RN - 0 (Protein Isoforms) RN - 0 (Proteins) RN - 151441-47-3 (GRB10 Adaptor Protein) SB - IM MH - Amino Acid Motifs MH - Animals MH - GRB10 Adaptor Protein MH - Gene Expression Regulation MH - Genetic Predisposition to Disease MH - Humans MH - Insulin/*physiology MH - Protein Conformation MH - Protein Isoforms MH - Protein Structure, Tertiary MH - Proteins/*chemistry/*physiology MH - Structure-Activity Relationship RF - 125 PMC - PMC1138946 OID - NLM: PMC1138946 EDAT- 2005/05/20 09:00 MHDA- 2005/10/26 09:00 CRDT- 2005/05/20 09:00 AID - BJ20050216 [pii] AID - 10.1042/BJ20050216 [doi] PST - ppublish SO - Biochem J. 2005 Jun 1;388(Pt 2):393-406. PMID- 18078811 OWN - NLM STAT- MEDLINE DA - 20080102 DCOM- 20080205 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 366 IP - 2 DP - 2008 Feb 8 TI - A novel nucleolar transcriptional activator ApLLP for long-term memory formation is intrinsically unstructured but functionally active. PG - 585-91 AB - A novel Aplysia nucleolar protein ApLLP has been recently characterized to be a transcriptional activator that binds to the cAMP-response element (CRE) and thus induces ApC/EBP expression required for establishing long-term memory. So far, no structural information is available for both ApLLP and its homologs. Here, we expressed the entire ApLLP and its two dissected fragments, followed by structural and binding studies using CD and NMR spectroscopy. The study leads to two interesting findings: (1) all three ApLLP proteins are highly disordered, owning no predominant secondary and tertiary structures; (2) ApLLP is capable of binding the CRE DNA element but this induces no significant change in its secondary and tertiary structures. Intriguingly, it appears that the DNA-binding residues are mainly located on the C-half of the ApLLP molecule. Taken together, our results define ApLLP as an intrinsically unstructured protein and may bear important implications in understanding the molecular mechanism underlying ApLLP functions. FAU - Liu, Jingxian AU - Liu J AD - Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore. FAU - Song, Jianxing AU - Song J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20071217 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Nuclear Proteins) RN - 0 (Trans-Activators) SB - IM MH - Amino Acid Sequence MH - Memory/*physiology MH - Molecular Sequence Data MH - Nuclear Proteins/*chemistry/*ultrastructure MH - Protein Conformation MH - Structure-Activity Relationship MH - Trans-Activators/*chemistry/*ultrastructure EDAT- 2007/12/15 09:00 MHDA- 2008/02/06 09:00 CRDT- 2007/12/15 09:00 PHST- 2007/11/24 [received] PHST- 2007/12/04 [accepted] PHST- 2007/12/17 [aheadofprint] AID - S0006-291X(07)02639-3 [pii] AID - 10.1016/j.bbrc.2007.12.022 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2008 Feb 8;366(2):585-91. Epub 2007 Dec 17. PMID- 20687482 OWN - NLM STAT- MEDLINE DA - 20100806 DCOM- 20100820 IS - 0065-2598 (Print) IS - 0065-2598 (Linking) VI - 677 DP - 2010 TI - Interfacial interactions of pore-forming colicins. PG - 81-90 AB - Colicins are water soluble toxins secreted by E. coli cells to kill other E. coli and related species. To do this they need to cross the outer membrane, periplasm and inner membrane. Pore forming colicins, as their name suggests form a voltage dependent pore in the inner membrane. This chapter deals with the interfaces, both lipid and protein, that the colicins experience as they make the short but complex journey that brings them to the point of pore formation. The succession of molecular interactions with lipid and protein receptors causes a series of conformational changes which allow these large > 40 kDa proteins to outwit the normally tight defensive shield of the target cell. This is done by combining general physico-chemical interfacial interactions, such as the use of amphipathic helical peptides, with precisely targeted protein-protein interactions involving both rigid and natively disordered protein domains. FAU - Ridley, Helen AU - Ridley H AD - Institute for Cell and Molecular Biosciences, University of Newcastle upon Tyne, Newcastle upon Tyne, UK. FAU - Johnson, Christopher L AU - Johnson CL FAU - Lakey, Jeremy H AU - Lakey JH LA - eng PT - Journal Article PT - Review PL - United States TA - Adv Exp Med Biol JT - Advances in experimental medicine and biology JID - 0121103 RN - 0 (Colicins) RN - 0 (Membrane Lipids) RN - 0 (Pore Forming Cytotoxic Proteins) SB - IM MH - Cell Membrane/*chemistry/metabolism MH - Colicins/*chemistry/metabolism MH - Escherichia coli/*chemistry/metabolism MH - Membrane Lipids/*chemistry/metabolism MH - Periplasm/chemistry/metabolism MH - Pore Forming Cytotoxic Proteins/*chemistry/metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Transport RF - 67 EDAT- 2010/08/07 06:00 MHDA- 2010/08/21 06:00 CRDT- 2010/08/07 06:00 PST - ppublish SO - Adv Exp Med Biol. 2010;677:81-90. PMID- 15222745 OWN - NLM STAT- MEDLINE DA - 20040629 DCOM- 20040903 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 26 DP - 2004 Jul 6 TI - NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system. PG - 8322-32 AB - Mercury resistant bacteria have developed a system of two enzymes (MerA and MerB), which allows them to efficiently detoxify both ionic and organomercurial compounds. The organomercurial lyase (MerB) catalyzes the protonolysis of the carbon-mercury bond resulting in the formation of ionic mercury and a reduced hydrocarbon. The ionic mercury [Hg(II)] is subsequently reduced to the less reactive elemental mercury [Hg(0)] by a specific mercuric reductase (MerA). To better understand MerB's unique enzymatic activity, we used nuclear magnetic resonance (NMR) spectroscopy to determine the structure of the free enzyme. MerB is characterized by a novel protein fold consisting of three noninteracting antiparallel beta-sheets surrounded by six alpha-helices. By comparing the NMR data of free MerB and the MerB/Hg/DTT complex, we identified a set of residues that likely define a Hg/DTT binding site. These residues cluster around two cysteines (C(96) and C(159)) that are crucial to MerB's catalytic activity. A detailed analysis of the structure revealed the presence of an extensive hydrophobic groove adjacent to this Hg/DTT binding site. This extensive hydrophobic groove has the potential to interact with the hydrocarbon moiety of a wide variety of substrates and may explain the broad substrate specificity of MerB. FAU - Di Lello, Paola AU - Di Lello P AD - Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia 30602, USA. FAU - Benison, Gregory C AU - Benison GC FAU - Valafar, Homayoun AU - Valafar H FAU - Pitts, Keith E AU - Pitts KE FAU - Summers, Anne O AU - Summers AO FAU - Legault, Pascale AU - Legault P FAU - Omichinski, James G AU - Omichinski JG LA - eng SI - PDB/1S6L PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (Hydrocarbons) RN - 0 (Ions) RN - 0 (Organomercury Compounds) RN - 7440-44-0 (Carbon) RN - EC 4.- (Lyases) RN - EC 4.99.1.2 (MerB protein, Bacteria) RN - FXS1BY2PGL (Mercury) RN - K848JZ4886 (Cysteine) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry MH - Binding Sites MH - Carbon/chemistry MH - Catalysis MH - Cysteine/chemistry MH - Drug Resistance MH - Hydrocarbons MH - Hydrogen-Ion Concentration MH - Ions MH - Lyases/*chemistry MH - Magnetic Resonance Spectroscopy/methods MH - Mercury/chemistry/*pharmacology MH - Models, Molecular MH - Molecular Sequence Data MH - Organomercury Compounds/chemistry MH - Plasmids/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Substrate Specificity MH - Temperature EDAT- 2004/06/30 05:00 MHDA- 2004/09/04 05:00 CRDT- 2004/06/30 05:00 AID - 10.1021/bi049669z [doi] PST - ppublish SO - Biochemistry. 2004 Jul 6;43(26):8322-32. PMID- 15004032 OWN - NLM STAT- MEDLINE DA - 20040517 DCOM- 20040630 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 21 DP - 2004 May 21 TI - A natively unfolded toxin domain uses its receptor as a folding template. PG - 22002-9 AB - Natively unfolded proteins range from molten globules to disordered coils. They are abundant in eukaryotic genomes and commonly involved in molecular interactions. The essential N-terminal translocation domains of colicin toxins from Escherichia coli are disordered bacterial proteins that bind at least one protein of the Tol or Ton family. The colicin N translocation domain (ColN-(1-90)), which binds to the C-terminal domain of TolA (TolA-(296-421)), shows a disordered far-UV CD spectrum, no near-UV CD signal, and non-cooperative thermal unfolding. As expected, TolA-(296-421) displays both secondary structure in far-UV CD and tertiary structure in near-UV CD. Furthermore it shows a cooperative unfolding transition at 65 degrees C. CD spectra of the 1:1 complex show both increased secondary structure and colicin N-specific near-UV CD signals. A new cooperative thermal transition at 35 degrees C is followed by the unchanged unfolding behavior of TolA-(296-421). Fluorescence and surface plasmon resonance confirm that the new unfolding transition accompanies dissociation of ColN-(1-90). Hence upon binding the disordered structure of ColN-(1-90) converts to a cooperatively folded domain without altering the TolA-(296-421) structure. FAU - Anderluh, Gregor AU - Anderluh G AD - School of Cell and Molecular Biosciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom. FAU - Gokce, Isa AU - Gokce I FAU - Lakey, Jeremy H AU - Lakey JH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040305 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Colicins) SB - IM MH - Chromatography, Gel MH - Circular Dichroism MH - Colicins/*chemistry MH - Escherichia coli/metabolism MH - Kinetics MH - Microscopy, Fluorescence MH - Protein Binding MH - Protein Denaturation MH - *Protein Folding MH - Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - Surface Plasmon Resonance MH - Temperature MH - Ultraviolet Rays EDAT- 2004/03/09 05:00 MHDA- 2004/07/01 05:00 CRDT- 2004/03/09 05:00 PHST- 2004/03/05 [aheadofprint] AID - 10.1074/jbc.M313603200 [doi] AID - M313603200 [pii] PST - ppublish SO - J Biol Chem. 2004 May 21;279(21):22002-9. Epub 2004 Mar 5. PMID- 23026051 OWN - NLM STAT- MEDLINE DA - 20121119 DCOM- 20130326 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 428 IP - 2 DP - 2012 Nov 16 TI - A folding-after-binding mechanism describes the recognition between the transactivation domain of c-Myb and the KIX domain of the CREB-binding protein. PG - 205-9 LID - 10.1016/j.bbrc.2012.09.112 [doi] LID - S0006-291X(12)01871-2 [pii] AB - A large body of evidence suggests that a considerable fraction of the human proteome may be at least in part intrinsically unstructured. While disordered, intrinsically unstructured proteins are nevertheless functional and mediate many interactions. Despite their significant role in regulation, however, little is known about the molecular mechanism whereby intrinsically unstructured proteins exert their function. This basic problem is critical to establish the role, if any, of disorder in cellular systems. Here we present kinetic experiments supporting a mechanism of binding-induced-folding when the KIX domain of the CREB-binding protein binds the transactivation domain of c-Myb, an intrinsically unstructured domain. The high-resolution structure of this physiologically important complex was previously determined by NMR spectroscopy. Our data reveal that c-Myb recognizes KIX by first forming a weak encounter complex in a disordered conformation, which is subsequently locked-in by a folding step, i.e. binding precedes folding. On the basis of the pH dependence of the observed combination and dissociation rate constants we propose a plausible mechanism for complex formation. The implications of our results in the light of previous work on intrinsically unstructured systems are discussed. CI - Copyright (c) 2012 Elsevier Inc. All rights reserved. FAU - Gianni, Stefano AU - Gianni S AD - Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Universita di Roma, Piazzale A. Moro 5, 00185 Rome, Italy. stefano.gianni@uniroma1.it FAU - Morrone, Angela AU - Morrone A FAU - Giri, Rajanish AU - Giri R FAU - Brunori, Maurizio AU - Brunori M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120928 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Proto-Oncogene Proteins c-myb) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Binding Sites MH - CREB-Binding Protein/*chemistry/genetics MH - Humans MH - Hydrogen-Ion Concentration MH - Kinetics MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-myb/*chemistry MH - Transcriptional Activation EDAT- 2012/10/03 06:00 MHDA- 2013/03/27 06:00 CRDT- 2012/10/03 06:00 PHST- 2012/09/14 [received] PHST- 2012/09/20 [accepted] PHST- 2012/09/28 [aheadofprint] AID - S0006-291X(12)01871-2 [pii] AID - 10.1016/j.bbrc.2012.09.112 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2012 Nov 16;428(2):205-9. doi: 10.1016/j.bbrc.2012.09.112. Epub 2012 Sep 28. PMID- 24066973 OWN - NLM STAT- MEDLINE DA - 20140117 DCOM- 20140903 LR - 20141112 IS - 1573-4935 (Electronic) IS - 0144-8463 (Linking) VI - 33 IP - 5 DP - 2013 TI - The interplay between lipids and dopamine on alpha-synuclein oligomerization and membrane binding. LID - 10.1042/BSR20130092 [doi] LID - e00074 [pii] AB - The deposition of alpha-syn (alpha-synuclein) as amyloid fibrils and the selective loss of DA (dopamine) containing neurons in the substantia nigra are two key features of PD (Parkinson's disease). alpha-syn is a natively unfolded protein and adopts an alpha-helical conformation upon binding to lipid membrane. Oligomeric species of alpha-syn have been proposed to be the pathogenic species associated with PD because they can bind lipid membranes and disrupt membrane integrity. DA is readily oxidized to generate reactive intermediates and ROS (reactive oxygen species) and in the presence of DA, alpha-syn form of SDS-resistant soluble oligomers. It is postulated that the formation of the alpha-syn:DA oligomers involves the cross-linking of DA-melanin with alpha-syn, via covalent linkage, hydrogen and hydrophobic interactions. We investigate the effect of lipids on DA-induced alpha-syn oligomerization and studied the ability of alpha-syn:DA oligomers to interact with lipids vesicles. Our results show that the interaction of alpha-syn with lipids inhibits the formation of DA-induced alpha-syn oligomers. Moreover, the alpha-syn:DA oligomer cannot interact with lipid vesicles or cause membrane permeability. Thus, the formation of alpha-syn:DA oligomers may alter the actions of alpha-syn which require membrane association, leading to disruption of its normal cellular function. FAU - Pham, Chi L L AU - Pham CL FAU - Cappai, Roberto AU - Cappai R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131022 PL - United States TA - Biosci Rep JT - Bioscience reports JID - 8102797 RN - 0 (Fluoresceins) RN - 0 (Fluorescent Dyes) RN - 0 (Liposomes) RN - 0 (Phospholipids) RN - 0 (Surface-Active Agents) RN - 0 (alpha-Synuclein) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - V0YM2B16TS (fluorexon) RN - VTD58H1Z2X (Dopamine) SB - IM MH - Cell Membrane MH - Cell Membrane Permeability MH - Dopamine/*chemistry MH - Fluoresceins/chemistry MH - Fluorescent Dyes/chemistry MH - Humans MH - Liposomes/chemistry MH - Phospholipids/*chemistry MH - Protein Binding MH - Protein Multimerization MH - Sodium Dodecyl Sulfate/chemistry MH - Surface-Active Agents/chemistry MH - alpha-Synuclein/*chemistry PMC - PMC3804888 OID - NLM: PMC3804888 EDAT- 2013/09/27 06:00 MHDA- 2014/09/04 06:00 CRDT- 2013/09/27 06:00 AID - BSR20130092 [pii] AID - 10.1042/BSR20130092 [doi] PST - epublish SO - Biosci Rep. 2013 Oct 22;33(5). pii: e00074. doi: 10.1042/BSR20130092. PMID- 21056617 OWN - NLM STAT- MEDLINE DA - 20110207 DCOM- 20110506 IS - 1873-5118 (Electronic) IS - 0301-0082 (Linking) VI - 93 IP - 1 DP - 2011 Jan TI - Hsp90 regulates tau pathology through co-chaperone complexes in Alzheimer's disease. PG - 99-110 LID - 10.1016/j.pneurobio.2010.10.006 [doi] AB - Alzheimer's disease is a tauopathy which involves the deposition of microtubule-associated tau proteins into neurofibrillary tangles. Post-translational modifications, in particular site-specific phosphorylations, affect the conformation of tau protein which is an intrinsically disordered protein. These structural changes significantly increase the affinity of tau protein for certain molecular chaperones. Hsp90 is a major cellular chaperone which assembles large complexes with a variety of co-chaperones. The main function of Hsp90 complexes is to maintain protein quality control and assist in protein degradation via proteasomal and autophagic-lysosomal pathways. Tau protein is a client protein for these Hsp90 complexes. If the tau protein is in an abnormal or modified form, then it can trigger the recruitment of CHIP protein, a co-chaperone with E3 activity, to the complex which induces the ubiquitination of tau protein and activates its downstream degradation processes. Large immunophilins, FKBP51 and FKBP52 are also co-chaperones of Hsp90-tau complexes. These proteins contain peptidylprolyl cis/trans isomerase activity which catalyzes phosphorylation-dependent rotation in pSer/Thr-Pro peptide bond. The proline switch in the tau conformation triggers dephosphorylation of Ser/Thr residues phosphorylated, e.g. by two well-known tau kinases Cdk5 and GSK-3beta. Binding of PP5 protein phosphatase to Hsp90 complex, can also dephosphorylate tau protein. Subsequently, dephosphorylated tau protein can be shuttled back to the microtubules. It seems that high-affinity binding of abnormal tau to Hsp90 complexes may have some counteracting effects on the aggregation process, since Hsp90 inhibitors can ameliorate the aggregation process in several neurodegenerative diseases. We will review the role of Hsp90 chaperone network in the regulation of tau biology and pathology in Alzheimer's disease. CI - Copyright (c) 2010 Elsevier Ltd. All rights reserved. FAU - Salminen, Antero AU - Salminen A AD - Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland. antero.salminen@uef.fi FAU - Ojala, Johanna AU - Ojala J FAU - Kaarniranta, Kai AU - Kaarniranta K FAU - Hiltunen, Mikko AU - Hiltunen M FAU - Soininen, Hilkka AU - Soininen H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20101105 PL - England TA - Prog Neurobiol JT - Progress in neurobiology JID - 0370121 RN - 0 (HSP90 Heat-Shock Proteins) RN - 0 (Molecular Chaperones) RN - 0 (tau Proteins) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Alzheimer Disease/*metabolism/*pathology MH - HSP90 Heat-Shock Proteins/*metabolism MH - Humans MH - Molecular Chaperones/*metabolism MH - Neurofibrillary Tangles/metabolism/*pathology MH - Proteasome Endopeptidase Complex/metabolism MH - Tauopathies/metabolism/pathology MH - tau Proteins/*metabolism EDAT- 2010/11/09 06:00 MHDA- 2011/05/07 06:00 CRDT- 2010/11/09 06:00 PHST- 2010/08/20 [received] PHST- 2010/10/19 [revised] PHST- 2010/10/28 [accepted] PHST- 2010/11/05 [aheadofprint] AID - S0301-0082(10)00185-1 [pii] AID - 10.1016/j.pneurobio.2010.10.006 [doi] PST - ppublish SO - Prog Neurobiol. 2011 Jan;93(1):99-110. doi: 10.1016/j.pneurobio.2010.10.006. Epub 2010 Nov 5. PMID- 12672694 OWN - NLM STAT- MEDLINE DA - 20030421 DCOM- 20030515 LR - 20140611 IS - 0890-9369 (Print) IS - 0890-9369 (Linking) VI - 17 IP - 8 DP - 2003 Apr 15 TI - XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators. PG - 977-90 AB - In Caenorhabditis elegans, an X chromosome-counting mechanism specifies sexual fate. Specific genes termed X-signal elements, which are present on the X chromosome, act in a concerted dose-dependent fashion to regulate levels of the developmental switch gene xol-1. In turn, xol-1 levels determine sexual fate and the activation state of the dosage compensation mechanism. The crystal structure of the XOL-1 protein at 1.55 A resolution unexpectedly reveals that xol-1 encodes a GHMP kinase family member, despite sequence identity of 10% or less. Because GHMP kinases, thus far, have only been characterized as small molecule kinases involved in metabolic pathways, for example, amino acid and cholesterol synthesis, XOL-1 is the first member that controls nonmetabolic processes. Biochemical investigations demonstrated that XOL-1 does not bind ATP under standard conditions, suggesting that XOL-1 acts by a mechanism distinct from that of other GHMP kinases. In addition, we have cloned a XOL-1 ortholog from Caenorhabditis briggsae, a related nematode that diverged from C. elegans approximately 50-100 million years ago. These findings demonstrate an unanticipated role for GHMP kinase family members as mediators of sexual differentiation and dosage compensation and, possibly, other aspects of differentiation and development. FAU - Luz, John Gately AU - Luz JG AD - Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA. FAU - Hassig, Christian A AU - Hassig CA FAU - Pickle, Catherine AU - Pickle C FAU - Godzik, Adam AU - Godzik A FAU - Meyer, Barbara J AU - Meyer BJ FAU - Wilson, Ian A AU - Wilson IA LA - eng SI - PDB/1MG7 GR - GM30702/GM/NIGMS NIH HHS/United States GR - GM38273/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20030402 PL - United States TA - Genes Dev JT - Genes & development JID - 8711660 RN - 0 (Caenorhabditis elegans Proteins) RN - 0 (Helminth Proteins) RN - 161477-65-2 (XOL-1 protein, C elegans) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)) RN - EC 2.7.1.36 (mevalonate kinase) RN - EC 2.7.1.39 (homoserine kinase) RN - EC 2.7.4.- (Phosphotransferases (Phosphate Group Acceptor)) RN - EC 2.7.4.2 (phosphomevalonate kinase) RN - EC 3.6.1.- (Adenosine Triphosphatases) SB - IM MH - Adenosine Triphosphatases/metabolism MH - Adenosine Triphosphate/metabolism MH - Amino Acid Sequence MH - Animals MH - Caenorhabditis/*genetics/growth & development/metabolism MH - Caenorhabditis elegans/*genetics/growth & development MH - *Caenorhabditis elegans Proteins MH - Cloning, Molecular MH - Crystallization MH - Crystallography, X-Ray MH - Disorders of Sex Development/genetics MH - *Dosage Compensation, Genetic MH - Helminth Proteins/*chemistry/*physiology MH - Molecular Sequence Data MH - Phosphotransferases (Alcohol Group Acceptor)/chemistry MH - Phosphotransferases (Phosphate Group Acceptor)/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - *Sex Determination Processes MH - Signal Transduction MH - Spectrometry, Fluorescence MH - *X Chromosome PMC - PMC196039 OID - NLM: PMC196039 EDAT- 2003/04/04 05:00 MHDA- 2003/05/16 05:00 CRDT- 2003/04/04 05:00 PHST- 2003/04/02 [aheadofprint] AID - 10.1101/gad.1082303 [doi] AID - U-10823R [pii] PST - ppublish SO - Genes Dev. 2003 Apr 15;17(8):977-90. Epub 2003 Apr 2. PMID- 22811526 OWN - NLM STAT- MEDLINE DA - 20120827 DCOM- 20121121 LR - 20141015 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 86 IP - 18 DP - 2012 Sep TI - Evolution of the hepatitis E virus polyproline region: order from disorder. PG - 10186-93 LID - 10.1128/JVI.01374-12 [doi] AB - The hepatitis E virus (HEV) polyproline region (PPR) is an intrinsically unstructured region (IDR). This relaxed structure allows IDRs, which are implicated in the regulation of transcription and translation, to bind multiple ligands. Originally the nucleotide variability seen in the HEV PPR was assumed to be due to high rates of insertion and deletion. This study shows that the mutation rate is about the same in the PPR as in the rest of the nonstructural polyprotein. The difference between the PPR and the rest of the polyprotein is due to the higher tolerance of the PPR for substitutions at the first and second codon positions. With this higher promiscuity there is a shift in nucleotide occupation of these codons leading to translation of more cytosine residues: a shift that leads to more proline, alanine, serine, and threonine being encoded rather than histidine, phenylalanine, tryptophan, and tyrosine. This pattern of amino acid usage is typical of proline-rich IDRs. Increased usage of cytosine also leads to >22% of all amino acids in the PPR being prolines. Alignments of PPR sequences from HEV strains representing all genotypes indicate that all zoonotic isolates share an ancestor, and the carboxyl half of the PPR is more tolerant of mutations than the amino half. The evolution of HEV PPR, in contrast with that of the rest of the nonstructural polyprotein, is molded by pressures that lead toward increased proline usage with a corresponding decrease in the usage of aromatic amino acids, favoring formation of IDR structures. FAU - Purdy, Michael A AU - Purdy MA AD - Centers for Disease Control and Prevention, Office of Infectious Diseases, National Center for HIV/Hepatitis/STD/TB Prevention, Division of Viral Hepatitis, MS-A33, Atlanta, Georgia, USA. mup3@cdc.gov LA - eng PT - Journal Article DEP - 20120718 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (Codon) RN - 0 (Peptides) RN - 0 (RNA, Viral) RN - 0 (Viral Nonstructural Proteins) RN - 25191-13-3 (polyproline) SB - IM MH - Animals MH - Base Sequence MH - Codon/genetics MH - *Evolution, Molecular MH - Genetic Variation MH - Hepatitis E virus/chemistry/classification/*genetics MH - Humans MH - INDEL Mutation MH - Molecular Sequence Data MH - Mutation MH - Peptides/chemistry/*genetics MH - RNA, Viral/genetics MH - Rabbits MH - Sequence Homology, Nucleic Acid MH - Viral Nonstructural Proteins/chemistry/*genetics PMC - PMC3446631 OID - NLM: PMC3446631 EDAT- 2012/07/20 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/07/20 06:00 PHST- 2012/07/18 [aheadofprint] AID - JVI.01374-12 [pii] AID - 10.1128/JVI.01374-12 [doi] PST - ppublish SO - J Virol. 2012 Sep;86(18):10186-93. doi: 10.1128/JVI.01374-12. Epub 2012 Jul 18. PMID- 24591642 OWN - NLM STAT- MEDLINE DA - 20140407 DCOM- 20140529 LR - 20141111 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 11 DP - 2014 Mar 18 TI - Understanding the antagonism of retinoblastoma protein dephosphorylation by PNUTS provides insights into the PP1 regulatory code. PG - 4097-102 LID - 10.1073/pnas.1317395111 [doi] AB - The serine/threonine protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets by associating with nearly 200 regulatory proteins to form highly specific holoenzymes. However, how these proteins direct PP1 specificity and the ability to predict how these PP1 interacting proteins bind PP1 from sequence alone is still missing. PP1 nuclear targeting subunit (PNUTS) is a PP1 targeting protein that, with PP1, plays a central role in the nucleus, where it regulates chromatin decondensation, RNA processing, and the phosphorylation state of fundamental cell cycle proteins, including the retinoblastoma protein (Rb), p53, and MDM2. The molecular function of PNUTS in these processes is completely unknown. Here, we show that PNUTS, which is intrinsically disordered in its free form, interacts strongly with PP1 in a highly extended manner. Unexpectedly, PNUTS blocks one of PP1's substrate binding grooves while leaving the active site accessible. This interaction site, which we have named the arginine site, allowed us to define unique PP1 binding motifs, which advances our ability to predict how more than a quarter of the known PP1 regulators bind PP1. Additionally, the structure shows how PNUTS inhibits the PP1-mediated dephosphorylation of critical substrates, especially Rb, by blocking their binding sites on PP1, insights that are providing strategies for selectively enhancing Rb activity. FAU - Choy, Meng S AU - Choy MS AD - Departments of Molecular Pharmacology, Physiology, and Biotechnology, Molecular Biology, Cell Biology, and Biochemistry, and Chemistry, Brown University, Providence, RI 02912. FAU - Hieke, Martina AU - Hieke M FAU - Kumar, Ganesan Senthil AU - Kumar GS FAU - Lewis, Greyson R AU - Lewis GR FAU - Gonzalez-DeWhitt, Kristofer R AU - Gonzalez-DeWhitt KR FAU - Kessler, Rene P AU - Kessler RP FAU - Stein, Benjamin J AU - Stein BJ FAU - Hessenberger, Manuel AU - Hessenberger M FAU - Nairn, Angus C AU - Nairn AC FAU - Peti, Wolfgang AU - Peti W FAU - Page, Rebecca AU - Page R LA - eng SI - PDB/4MOV SI - PDB/4MOY SI - PDB/4MP0 GR - P41GM103473/GM/NIGMS NIH HHS/United States GR - P41RR012408/RR/NCRR NIH HHS/United States GR - R01 GM098482/GM/NIGMS NIH HHS/United States GR - R01GM098482/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140303 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (DNA-Binding Proteins) RN - 0 (Nuclear Proteins) RN - 0 (PPP1R10 protein, human) RN - 0 (RNA-Binding Proteins) RN - 0 (Retinoblastoma Protein) RN - EC 3.1.3.16 (Protein Phosphatase 1) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Amino Acid Sequence MH - Calorimetry MH - Chromatin Assembly and Disassembly/physiology MH - Cloning, Molecular MH - Computational Biology MH - Crystallization MH - DNA-Binding Proteins/chemistry/genetics/*metabolism MH - Gene Expression Regulation, Enzymologic/*genetics MH - Humans MH - Magnetic Resonance Spectroscopy MH - *Models, Molecular MH - Molecular Sequence Data MH - Nuclear Proteins/chemistry/genetics/*metabolism MH - Phosphorylation MH - *Protein Conformation MH - Protein Interaction Domains and Motifs/genetics MH - Protein Phosphatase 1/chemistry/genetics/*metabolism MH - Proto-Oncogene Proteins c-mdm2/metabolism MH - RNA-Binding Proteins/chemistry/genetics/*metabolism MH - Retinoblastoma Protein/*metabolism MH - Sequence Alignment MH - Substrate Specificity PMC - PMC3964120 OID - NLM: PMC3964120 OTO - NOTNLM OT - X-ray crystal structure OT - enzyme regulation OT - enzyme specificity OT - nuclear magnetic resonance OT - nuclear phosphatases EDAT- 2014/03/05 06:00 MHDA- 2014/05/30 06:00 CRDT- 2014/03/05 06:00 PHST- 2014/03/03 [aheadofprint] AID - 1317395111 [pii] AID - 10.1073/pnas.1317395111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4097-102. doi: 10.1073/pnas.1317395111. Epub 2014 Mar 3. PMID- 21887699 OWN - NLM STAT- MEDLINE DA - 20111117 DCOM- 20120313 LR - 20141022 IS - 1097-4547 (Electronic) IS - 0360-4012 (Linking) VI - 90 IP - 1 DP - 2012 Jan TI - Proline substitutions and threonine pseudophosphorylation of the SH3 ligand of 18.5-kDa myelin basic protein decrease its affinity for the Fyn-SH3 domain and alter process development and protein localization in oligodendrocytes. PG - 28-47 LID - 10.1002/jnr.22733 [doi] AB - The developmentally regulated myelin basic proteins (MBPs), which arise from the golli (gene of oligodendrocyte lineage) complex, are highly positively charged, intrinsically disordered, multifunctional proteins having several alternatively spliced isoforms and posttranslational modifications, and they play key roles in myelin compaction. The classic 18.5-kDa MBP isoform has a proline-rich region comprising amino acids 92-99 (murine sequence -T(92)PRTPPPS(99)-) that contains a minimal SH3 ligand domain. We have previously shown that 18.5-kDa MBP binds to several SH3 domains, including that of Fyn, a member of the Src family of tyrosine kinases involved in a number of signaling pathways during CNS development. To determine the physiological role of this binding as well as the role of phosphorylation of Thr92 and Thr95, in the current study we have produced several MBP variants specifically targeting phosphorylation sites and key structural regions of MBP's SH3 ligand domain. Using isothermal titration calorimetry, we have demonstrated that, compared with the wild-type protein, these variants have lower affinity for the SH3 domain of Fyn. Moreover, overexpression of N-terminal-tagged GFP versions in immortalized oligodendroglial N19 and N20.1 cell cultures results in aberrant elongation of membrane processes and increased branching complexity and inhibits the ability of MBP to decrease Ca(2+) influx. Phosphorylation of Thr92 can also cause MBP to traffic to the nucleus, where it may participate in additional protein-protein interactions. Coexpression of MBP with a constitutively active form of Fyn kinase resulted in membrane process elaboration, a phenomenon that was abolished by point amino acid substitutions in MBP's SH3 ligand domain. These results suggest that MBP's SH3 ligand domain plays a key role in intracellular protein interactions in vivo and may be required for proper membrane elaboration of developing oligodendrocytes and, further, that phosphorylation of Thr92 and Thr95 can regulate this function. CI - Copyright (c) 2011 Wiley Periodicals, Inc. FAU - Smith, Graham S T AU - Smith GS AD - Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada. FAU - De Avila, Miguel AU - De Avila M FAU - Paez, Pablo M AU - Paez PM FAU - Spreuer, Vilma AU - Spreuer V FAU - Wills, Melanie K B AU - Wills MK FAU - Jones, Nina AU - Jones N FAU - Boggs, Joan M AU - Boggs JM FAU - Harauz, George AU - Harauz G LA - eng GR - 86483/Canadian Institutes of Health Research/Canada GR - MOP 86483/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110901 PL - United States TA - J Neurosci Res JT - Journal of neuroscience research JID - 7600111 RN - 0 (Calcium Channels) RN - 0 (Myelin Basic Protein) RN - 147336-22-9 (Green Fluorescent Proteins) RN - 2ZD004190S (Threonine) RN - 9DLQ4CIU6V (Proline) RN - EC 2.7.10.2 (FYN protein, human) RN - EC 2.7.10.2 (Proto-Oncogene Proteins c-fyn) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Analysis of Variance MH - Animals MH - Calcium/metabolism MH - Calcium Channels/genetics/metabolism MH - Calcium Signaling/genetics MH - Calorimetry MH - Cell Line, Transformed MH - Cell Size MH - Green Fluorescent Proteins/genetics MH - Mice MH - *Myelin Basic Protein/chemistry/genetics/metabolism MH - Oligodendroglia/*metabolism MH - Proline/*genetics MH - Protein Binding/genetics MH - Protein Biosynthesis/genetics MH - Protein Processing, Post-Translational/genetics MH - Proto-Oncogene Proteins c-fyn/genetics/*metabolism MH - Threonine/*genetics MH - Transfection MH - src Homology Domains/*physiology PMC - PMC3527418 MID - CAMS2549 OID - NLM: CAMS2549 OID - NLM: PMC3527418 EDAT- 2011/09/03 06:00 MHDA- 2012/03/14 06:00 CRDT- 2011/09/03 06:00 PHST- 2011/04/27 [received] PHST- 2011/06/02 [revised] PHST- 2011/06/06 [accepted] PHST- 2011/09/01 [aheadofprint] AID - 10.1002/jnr.22733 [doi] PST - ppublish SO - J Neurosci Res. 2012 Jan;90(1):28-47. doi: 10.1002/jnr.22733. Epub 2011 Sep 1. PMID- 19439573 OWN - NLM STAT- MEDLINE DA - 20090703 DCOM- 20090914 LR - 20140829 IS - 0032-0889 (Print) IS - 0032-0889 (Linking) VI - 150 IP - 3 DP - 2009 Jul TI - The K-segment of maize DHN1 mediates binding to anionic phospholipid vesicles and concomitant structural changes. PG - 1503-14 LID - 10.1104/pp.109.136697 [doi] AB - Dehydrins (DHNs; late embryogenesis abundant D11 family) are a family of intrinsically unstructured plant proteins that accumulate in the late stages of seed development and in vegetative tissues subjected to water deficit, salinity, low temperature, or abscisic acid treatment. We demonstrated previously that maize (Zea mays) DHNs bind preferentially to anionic phospholipid vesicles; this binding is accompanied by an increase in alpha-helicity of the protein, and adoption of alpha-helicity can be induced by sodium dodecyl sulfate. All DHNs contain at least one "K-segment," a lysine-rich 15-amino acid consensus sequence. The K-segment is predicted to form a class A2 amphipathic alpha-helix, a structural element known to interact with membranes and proteins. Here, three K-segment deletion proteins of maize DHN1 were produced. Lipid vesicle-binding assays revealed that the K-segment is required for binding to anionic phospholipid vesicles, and adoption of alpha-helicity of the K-segment accounts for most of the conformational change of DHNs upon binding to anionic phospholipid vesicles or sodium dodecyl sulfate. The adoption of structure may help stabilize cellular components, including membranes, under stress conditions. FAU - Koag, Myong-Chul AU - Koag MC AD - Graduate Program in Biochemistry and Molecular Biology, University of California, Riverside, California 92521-0124, USA. FAU - Wilkens, Stephan AU - Wilkens S FAU - Fenton, Raymond D AU - Fenton RD FAU - Resnik, Josh AU - Resnik J FAU - Vo, Evanly AU - Vo E FAU - Close, Timothy J AU - Close TJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20090513 PL - United States TA - Plant Physiol JT - Plant physiology JID - 0401224 RN - 0 (Liposomes) RN - 0 (Phospholipids) RN - 0 (Plant Proteins) RN - 134711-03-8 (dehydrin proteins, plant) RN - 368GB5141J (Sodium Dodecyl Sulfate) SB - IM MH - Amino Acid Sequence MH - Consensus Sequence MH - Cytoplasmic Vesicles/*metabolism MH - Escherichia coli/genetics MH - Liposomes/metabolism MH - Molecular Sequence Data MH - Phospholipids/*metabolism MH - Plant Proteins/*chemistry/genetics/physiology MH - Protein Structure, Tertiary MH - Seeds/growth & development/metabolism MH - Sodium Dodecyl Sulfate/pharmacology MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Zea mays/*metabolism/ultrastructure PMC - PMC2705017 OID - NLM: PMC2705017 EDAT- 2009/05/15 09:00 MHDA- 2009/09/15 06:00 CRDT- 2009/05/15 09:00 PHST- 2009/05/13 [aheadofprint] AID - pp.109.136697 [pii] AID - 10.1104/pp.109.136697 [doi] PST - ppublish SO - Plant Physiol. 2009 Jul;150(3):1503-14. doi: 10.1104/pp.109.136697. Epub 2009 May 13. PMID- 19021565 OWN - NLM STAT- MEDLINE DA - 20081121 DCOM- 20090203 LR - 20141125 IS - 1470-8752 (Electronic) IS - 0300-5127 (Linking) VI - 36 IP - Pt 6 DP - 2008 Dec TI - Colicins exploit native disorder to gain cell entry: a hitchhiker's guide to translocation. PG - 1409-13 LID - 10.1042/BST0361409 [doi] AB - The translocation of protein toxins into a cell relies on a myriad of protein-protein interactions. One such group of toxins are enzymatic E colicins, protein antibiotics produced by Escherichia coli in times of stress. These proteins subvert ordinary nutrient uptake mechanisms to enter the cell and unleash nuclease activity. We, and others, have previously shown that uptake of ColE9 (colicin E9) is dependent on engagement of the OM (outer membrane) receptors BtuB and OmpF as well as recruitment of the periplasmic protein TolB, forming a large supramolecular complex. Intriguingly, colicins bind TolB using a natively disordered region to mimic the interaction of TolB with Pal (peptidoglycan-associated lipoprotein). This is thought to trigger OM instability and prime the system for translocation. Here, we review key interactions in the assembly of this 'colicin translocon' and discuss the key role disorder plays in achieving uptake. FAU - Bonsor, Daniel A AU - Bonsor DA AD - Department of Biology Area 10, University of York, Heslington, York, UK. FAU - Meenan, Nicola A AU - Meenan NA FAU - Kleanthous, Colin AU - Kleanthous C LA - eng GR - BB/E011306/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Review PL - England TA - Biochem Soc Trans JT - Biochemical Society transactions JID - 7506897 RN - 0 (Colicins) SB - IM MH - Cell Membrane/*metabolism MH - Colicins/chemistry/*metabolism MH - Molecular Mimicry MH - Periplasm/metabolism MH - Protein Binding MH - Protein Transport RF - 40 EDAT- 2008/11/22 09:00 MHDA- 2009/02/04 09:00 CRDT- 2008/11/22 09:00 AID - BST0361409 [pii] AID - 10.1042/BST0361409 [doi] PST - ppublish SO - Biochem Soc Trans. 2008 Dec;36(Pt 6):1409-13. doi: 10.1042/BST0361409. PMID- 23865482 OWN - NLM STAT- MEDLINE DA - 20130820 DCOM- 20131126 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 52 IP - 33 DP - 2013 Aug 20 TI - A pearl protein self-assembles to form protein complexes that amplify mineralization. PG - 5696-703 LID - 10.1021/bi400808j [doi] AB - The formation of the nacre pearl in marine invertebrates represents an on-demand production of mineralization in response to an irritant or parasite threat to the mantle organ. In the Japanese pearl oyster (Pinctada fucata), this process is mediated by a 12-member protein family known as PFMG (Pinctada fucata mantle gene). One of these proteins, PFGM1, has been implicated in modulating calcium carbonate crystal growth and has been reported to possess an EF-hand-like domain. In this report, we establish that the recombinant PFMG1 (rPFMG1) is an intrinsically disordered "imitator" EF-hand protein that increases the number of calcium carbonate mineral crystals that form relative to control scenarios and does not induce aragonite formation. This protein possesses a modified pseudo-EF-hand sequence at the C-terminal end which exhibits low homology (30-40%) to the pseudo-EF-hand mitochondrial SCaMCs buffering/solute transport proteins. This low sequence homology is the result of the inclusion of disorder-promoting amino acids and short amyloid-like aggregation-prone cross-beta-strand sequences within the putative PFMG1 pseudo-EF-hand sequence region. Similar to other nacre proteins, rPFMG1 oligomerizes to form amorphous, heterogeneously sized protein oligomers and films in vitro, and this process is enhanced by Ca(2+), which promotes the formation of aggregation-prone extended beta-strand structure within rPFMG1. From these results, we conclude that PFMG1 forms supramolecular assemblies that play an important role in amplifying the nucleation process that is crucial for coating or neutralizing invasive threats to the mantle organ. FAU - Perovic, Iva AU - Perovic I AD - Laboratory for Chemical Physics, Division of Basic Sciences and Craniofacial Biology, New York University, 345 E. 24th Street, NY 10010, USA. FAU - Mandal, Trinanjana AU - Mandal T FAU - Evans, John Spencer AU - Evans JS LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130801 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Nacre) RN - 0 (Proteins) RN - 0 (Recombinant Proteins) RN - H0G9379FGK (Calcium Carbonate) SB - IM MH - Animals MH - *Calcification, Physiologic MH - Calcium Carbonate/chemistry/*metabolism MH - Circular Dichroism MH - Hydrogen-Ion Concentration MH - Microscopy, Atomic Force MH - Microscopy, Electron, Scanning MH - Nacre/chemistry/metabolism MH - Pinctada/genetics/*metabolism/ultrastructure MH - Protein Multimerization MH - Proteins/chemistry/genetics/*metabolism MH - Recombinant Proteins/chemistry/metabolism/ultrastructure MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - X-Ray Diffraction EDAT- 2013/07/20 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/07/20 06:00 PHST- 2013/08/01 [aheadofprint] AID - 10.1021/bi400808j [doi] PST - ppublish SO - Biochemistry. 2013 Aug 20;52(33):5696-703. doi: 10.1021/bi400808j. Epub 2013 Aug 1. PMID- 23002146 OWN - NLM STAT- MEDLINE DA - 20121127 DCOM- 20130130 LR - 20141105 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 40 IP - 21 DP - 2012 Nov TI - Rbg1-Tma46 dimer structure reveals new functional domains and their role in polysome recruitment. PG - 11100-14 LID - 10.1093/nar/gks867 [doi] AB - Developmentally Regulated GTP-binding (DRG) proteins are highly conserved GTPases that associate with DRG Family Regulatory Proteins (DFRP). The resulting complexes have recently been shown to participate in eukaryotic translation. The structure of the Rbg1 GTPase, a yeast DRG protein, in complex with the C-terminal region of its DFRP partner, Tma46, was solved by X-ray diffraction. These data reveal that DRG proteins are multimodular factors with three additional domains, helix-turn-helix (HTH), S5D2L and TGS, packing against the GTPase platform. Surprisingly, the S5D2L domain is inserted in the middle of the GTPase sequence. In contrast, the region of Tma46 interacting with Rbg1 adopts an extended conformation typical of intrinsically unstructured proteins and contacts the GTPase and TGS domains. Functional analyses demonstrate that the various domains of Rbg1, as well as Tma46, modulate the GTPase activity of Rbg1 and contribute to the function of these proteins in vivo. Dissecting the role of the different domains revealed that the Rbg1 TGS domain is essential for the recruitment of this factor in polysomes, supporting further the implication of these conserved factors in translation. FAU - Francis, Sandrea M AU - Francis SM AD - Instituto de Biomedicina de Valencia (IBV-CSIC), Calle Jaime Roig, 11, Valencia E-46010, Spain. FAU - Gas, Maria-Eugenia AU - Gas ME FAU - Daugeron, Marie-Claire AU - Daugeron MC FAU - Bravo, Jeronimo AU - Bravo J FAU - Seraphin, Bertrand AU - Seraphin B LA - eng SI - PDB/4A9A PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120923 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Fungal Proteins) RN - 149371-72-2 (developmentally regulated GTP-binding protein) RN - 86-01-1 (Guanosine Triphosphate) RN - EC 3.6.1.- (GTP-Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Dimerization MH - Fungal Proteins/*chemistry/genetics/metabolism MH - GTP-Binding Proteins/*chemistry/metabolism MH - Gene Deletion MH - Guanosine Triphosphate/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Polyribosomes/*metabolism MH - Protein Structure, Tertiary MH - Static Electricity PMC - PMC3510508 OID - NLM: PMC3510508 EDAT- 2012/09/25 06:00 MHDA- 2013/01/31 06:00 CRDT- 2012/09/25 06:00 PHST- 2012/09/23 [aheadofprint] AID - gks867 [pii] AID - 10.1093/nar/gks867 [doi] PST - ppublish SO - Nucleic Acids Res. 2012 Nov;40(21):11100-14. doi: 10.1093/nar/gks867. Epub 2012 Sep 23. PMID- 20304108 OWN - NLM STAT- MEDLINE DA - 20100907 DCOM- 20101018 LR - 20140914 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1804 IP - 9 DP - 2010 Sep TI - A solution NMR investigation into the murine amelogenin splice-variant LRAP (Leucine-Rich Amelogenin Protein). PG - 1768-74 LID - 10.1016/j.bbapap.2010.03.006 [doi] AB - Amelogenins are the dominant proteins present in ameloblasts during the early stages of enamel biomineralization, making up >90% of the matrix protein. Along with the full-length protein there are several splice-variant isoforms of amelogenin present including LRAP (Leucine-Rich Amelogenin Protein), a protein that consists of the first 33 and the last 26 residues of full-length amelogenin. Using solution-state NMR spectroscopy we have assigned the (1)H-(15)N HSQC spectrum of murine LRAP (rp(H)LRAP) in 2% acetic acid at pH 3.0 by making extensive use of previous chemical shift assignments for full-length murine amelogenin (rp(H)M180). This correlation was possible because LRAP, like the full-length protein, is intrinsically disordered under these solution conditions. The major difference between the (1)H-(15)N HSQC spectra of rp(H)M180 and rp(H)LRAP was an additional set of amide resonances for each of the seven non-proline residues between S12 and Y12 near the N-terminus of rp(H)LRAP indicating that the N-terminal region of LRAP exists in two different conformations. Analysis of the proline carbon chemical shifts suggests that the molecular basis for the two states is not a cis-trans isomerization of one or more of the proline residues in the N-terminal region. Starting from 2% acetic acid, where rp(H)LRAP was monomeric in solution, NaCl addition effected residue specific changes in molecular dynamics manifested by the reduction in intensity and disappearance of (1)H-(15)N HSQC cross peaks. As observed for the full-length protein, these perturbations may signal early events governing supramolecular self-assembly of rp(H)LRAP into nanospheres. However, the different patterns of (1)H-(15)N HSQC cross peak perturbation between rp(H)LRAP and rp(H)M180 in high salt suggest that the termini may behave differently in their respective nanospheres, and perhaps, these differences contribute to the cell signaling properties attributable to LRAP but not to the full-length protein. CI - Copyright (c) 2010 Elsevier B.V. All rights reserved. FAU - Buchko, Garry W AU - Buchko GW AD - Biological Science Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. FAU - Tarasevich, Barbara J AU - Tarasevich BJ FAU - Roberts, Jacky AU - Roberts J FAU - Snead, Malcolm L AU - Snead ML FAU - Shaw, Wendy J AU - Shaw WJ LA - eng GR - DE-015347/DE/NIDCR NIH HHS/United States GR - DE06988/DE/NIDCR NIH HHS/United States GR - R01 DE015347/DE/NIDCR NIH HHS/United States GR - R01 DE015347-06/DE/NIDCR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20100319 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Amelogenin) RN - 0 (Amides) RN - 0 (Dental Enamel Proteins) RN - 0 (leucine-rich amelogenin peptide) RN - 7647-14-5 (Sodium Chloride) SB - IM MH - *Alternative Splicing MH - Amelogenin/*chemistry/genetics/metabolism MH - Amides/chemistry/metabolism MH - Animals MH - Dental Enamel Proteins/*chemistry/genetics MH - *Magnetic Resonance Spectroscopy MH - Mice MH - Sodium Chloride/pharmacology PMC - PMC2910175 MID - NIHMS190915 OID - NLM: NIHMS190915 OID - NLM: PMC2910175 EDAT- 2010/03/23 06:00 MHDA- 2010/10/19 06:00 CRDT- 2010/03/23 06:00 PHST- 2009/12/03 [received] PHST- 2010/03/09 [revised] PHST- 2010/03/12 [accepted] PHST- 2010/03/19 [aheadofprint] AID - S1570-9639(10)00084-1 [pii] AID - 10.1016/j.bbapap.2010.03.006 [doi] PST - ppublish SO - Biochim Biophys Acta. 2010 Sep;1804(9):1768-74. doi: 10.1016/j.bbapap.2010.03.006. Epub 2010 Mar 19. PMID- 19894758 OWN - NLM STAT- MEDLINE DA - 20091201 DCOM- 20091221 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 48 DP - 2009 Dec 8 TI - Thermodynamic aspects of coupled binding and folding of an intrinsically disordered protein: a computational alanine scanning study. PG - 11332-4 LID - 10.1021/bi901705z [doi] AB - We have performed computational alanine scanning to gain insight into thermodynamic aspects of coupled folding and binding of the phosphorylated kinase-inducible activation domain (pKID) of CREB, and intrinsically disorder protein (IDP), to KIX. Residues of pKID directly involved in nativelike interactions at the interface were found to steeply lower their contribution to the free energy of binding. The results suggest that, with a steep lowering of the free energy of binding, it is ensured that pKID has full control of binding specificity, is not trapped in a non-native conformational state, has full plasticity for folding, and forms a thermodynamically stable complex with KIX without compromising binding kinetics. FAU - Espinoza-Fonseca, L Michel AU - Espinoza-Fonseca LM AD - Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA. mef@ddt.biochem.umn.edu LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cyclic AMP Response Element-Binding Protein) RN - EC 2.7.- (Phosphotransferases) RN - OF5P57N2ZX (Alanine) SB - IM MH - Alanine/*metabolism MH - Algorithms MH - Binding Sites MH - Computational Biology MH - Cyclic AMP Response Element-Binding Protein/*chemistry/*metabolism MH - Enzyme Activation MH - Kinetics MH - Phosphotransferases/chemistry/metabolism MH - Protein Conformation MH - *Protein Folding MH - *Thermodynamics EDAT- 2009/11/10 06:00 MHDA- 2009/12/22 06:00 CRDT- 2009/11/10 06:00 AID - 10.1021/bi901705z [doi] PST - ppublish SO - Biochemistry. 2009 Dec 8;48(48):11332-4. doi: 10.1021/bi901705z. PMID- 21539793 OWN - NLM STAT- MEDLINE DA - 20110504 DCOM- 20110817 LR - 20140820 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 100 IP - 9 DP - 2011 May 4 TI - Compaction properties of an intrinsically disordered protein: Sic1 and its kinase-inhibitor domain. PG - 2243-52 LID - 10.1016/j.bpj.2011.02.055 [doi] AB - IDPs in their unbound state can transiently acquire secondary and tertiary structure. Describing such intrinsic structure is important to understand the transition between free and bound state, leading to supramolecular complexes with physiological interactors. IDP structure is highly dynamic and, therefore, difficult to study by conventional techniques. This work focuses on conformational analysis of the KID fragment of the Sic1 protein, an IDP with a key regulatory role in the cell-cycle of Saccharomyces cerevisiae. FT-IR spectroscopy, ESI-MS, and IM measurements are used to capture dynamic and short-lived conformational states, probing both secondary and tertiary protein structure. The results indicate that the isolated Sic1 KID retains dynamic helical structure and populates collapsed states of different compactness. A metastable, highly compact species is detected. Comparison between the fragment and the full-length protein suggests that chain length is crucial to the stabilization of compact states of this IDP. The two proteins are compared by a length-independent compaction index. CI - Copyright (c) 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Brocca, Stefania AU - Brocca S AD - Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy. FAU - Testa, Lorenzo AU - Testa L FAU - Sobott, Frank AU - Sobott F FAU - Samalikova, Maria AU - Samalikova M FAU - Natalello, Antonino AU - Natalello A FAU - Papaleo, Elena AU - Papaleo E FAU - Lotti, Marina AU - Lotti M FAU - De Gioia, Luca AU - De Gioia L FAU - Doglia, Silvia Maria AU - Doglia SM FAU - Alberghina, Lilia AU - Alberghina L FAU - Grandori, Rita AU - Grandori R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Cyclin-Dependent Kinase Inhibitor Proteins) RN - 0 (Protein Kinase Inhibitors) RN - 0 (SIC1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Amino Acid Sequence MH - Chromatography, Gel MH - Cyclin-Dependent Kinase Inhibitor Proteins/*chemistry/*metabolism MH - Hydrodynamics MH - Molecular Sequence Data MH - Protein Kinase Inhibitors/*chemistry/*metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Unfolding MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/*metabolism MH - Sequence Analysis, Protein MH - Spectrometry, Mass, Electrospray Ionization MH - Spectroscopy, Fourier Transform Infrared PMC - PMC3149264 OID - NLM: PMC3149264 EDAT- 2011/05/05 06:00 MHDA- 2011/08/19 06:00 CRDT- 2011/05/05 06:00 PHST- 2010/07/12 [received] PHST- 2011/02/04 [revised] PHST- 2011/02/22 [accepted] AID - S0006-3495(11)00308-0 [pii] AID - 10.1016/j.bpj.2011.02.055 [doi] PST - ppublish SO - Biophys J. 2011 May 4;100(9):2243-52. doi: 10.1016/j.bpj.2011.02.055. PMID- 24224051 OWN - NLM STAT- MEDLINE DA - 20131113 DCOM- 20140620 LR - 20141112 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 11 DP - 2013 TI - Solution and crystallographic structures of the central region of the phosphoprotein from human metapneumovirus. PG - e80371 LID - 10.1371/journal.pone.0080371 [doi] AB - Human metapneumovirus (HMPV) of the family Paramyxoviridae is a major cause of respiratory illness worldwide. Phosphoproteins (P) from Paramyxoviridae are essential co-factors of the viral RNA polymerase that form tetramers and possess long intrinsically disordered regions (IDRs). We located the central region of HMPV P (P(ced)) which is involved in tetramerization using disorder analysis and modeled its 3D structure ab initio using Rosetta fold-and-dock. We characterized the solution-structure of P(ced) using small angle X-ray scattering (SAXS) and carried out direct fitting to the scattering data to filter out incorrect models. Molecular dynamics simulations (MDS) and ensemble optimization were employed to select correct models and capture the dynamic character of P(ced). Our analysis revealed that oligomerization involves a compact central core located between residues 169-194 (P(core)), that is surrounded by flexible regions with alpha-helical propensity. We crystallized this fragment and solved its structure at 3.1 A resolution by molecular replacement, using the folded core from our SAXS-validated ab initio model. The RMSD between modeled and experimental tetramers is as low as 0.9 A, demonstrating the accuracy of the approach. A comparison of the structure of HMPV P to existing mononegavirales P(ced) structures suggests that P(ced) evolved under weak selective pressure. Finally, we discuss the advantages of using SAXS in combination with ab initio modeling and MDS to solve the structure of small, homo-oligomeric protein complexes. FAU - Leyrat, Cedric AU - Leyrat C AD - Division of Structural Biology, University of Oxford, Oxford, United Kingdom. FAU - Renner, Max AU - Renner M FAU - Harlos, Karl AU - Harlos K FAU - Grimes, Jonathan M AU - Grimes JM LA - eng SI - PDB/4BXT GR - 075491/Z/04/Wellcome Trust/United Kingdom GR - 090532/Wellcome Trust/United Kingdom GR - 090532/Z/09/Z/Wellcome Trust/United Kingdom GR - 099667/Z/12/Z/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131104 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Phosphoproteins) RN - 0 (Viral Proteins) SB - IM MH - Humans MH - Metapneumovirus/*metabolism MH - Phosphoproteins/*chemistry MH - Scattering, Small Angle MH - Viral Proteins/*chemistry MH - X-Ray Diffraction PMC - PMC3817118 OID - NLM: PMC3817118 EDAT- 2013/11/14 06:00 MHDA- 2014/06/21 06:00 CRDT- 2013/11/14 06:00 PHST- 2013 [ecollection] PHST- 2013/07/23 [received] PHST- 2013/10/09 [accepted] PHST- 2013/11/04 [epublish] AID - 10.1371/journal.pone.0080371 [doi] AID - PONE-D-13-30386 [pii] PST - epublish SO - PLoS One. 2013 Nov 4;8(11):e80371. doi: 10.1371/journal.pone.0080371. eCollection 2013. PMID- 15897454 OWN - NLM STAT- MEDLINE DA - 20050525 DCOM- 20050804 LR - 20140606 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 102 IP - 21 DP - 2005 May 24 TI - A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal. PG - 7541-6 AB - Little is known about prokaryotic homologs of Cu,Zn superoxide dismutase (SOD), an enzyme highly conserved among eukaryotic species. In 138 Archaea and Bacteria genomes, 57 of these putative homologs were found, 11 of which lack at least one of the metal ligands. Both the solution and the crystal structures of the SOD-like protein from Bacillus subtilis, lacking two Cu ligands and found to be enzymatically inactive, were determined. In solution, the protein is monomeric. The available nuclear Overhauser effects, together with chemical-shift index values, allowed us to define and to recognize the typical Cu,Zn SOD Greek beta-barrel but with largely unstructured loops (which, therefore, sample a wide range of conformations). On the contrary, in the crystal structure (obtained in the presence of slight excess of Zn), the protein is well structured and organized in covalent dimers held by a symmetric bridge consisting of a Zn ion bound to an Asp-His dyad in a tetrahedral geometry. Couples of dimers held by hydrophobic interactions and H bonds are further organized in long chains. The order/disorder transition is discussed in terms of metal binding and physical state. FAU - Banci, Lucia AU - Banci L AD - Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto, Florence, Italy. FAU - Bertini, Ivano AU - Bertini I FAU - Calderone, Vito AU - Calderone V FAU - Cramaro, Fiorenza AU - Cramaro F FAU - Del Conte, Rebecca AU - Del Conte R FAU - Fantoni, Adele AU - Fantoni A FAU - Mangani, Stefano AU - Mangani S FAU - Quattrone, Alessandro AU - Quattrone A FAU - Viezzoli, Maria Silvia AU - Viezzoli MS LA - eng SI - PDB/1S4I SI - PDB/1U3N PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050516 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Ligands) RN - EC 1.15.1.1 (Superoxide Dismutase) SB - IM MH - Amino Acid Sequence MH - Bacillus subtilis/genetics/*metabolism MH - Computational Biology MH - Crystallography, X-Ray MH - Dimerization MH - *Genome, Archaeal MH - *Genome, Bacterial MH - Genomics MH - Ligands MH - Magnetic Resonance Spectroscopy MH - *Models, Molecular MH - Molecular Sequence Data MH - Phylogeny MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Superoxide Dismutase/genetics/metabolism/*ultrastructure PMC - PMC1140445 OID - NLM: PMC1140445 EDAT- 2005/05/18 09:00 MHDA- 2005/08/05 09:00 CRDT- 2005/05/18 09:00 PHST- 2005/05/16 [aheadofprint] AID - 0502450102 [pii] AID - 10.1073/pnas.0502450102 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2005 May 24;102(21):7541-6. Epub 2005 May 16. PMID- 1606151 OWN - NLM STAT- MEDLINE DA - 19920721 DCOM- 19920721 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 31 IP - 23 DP - 1992 Jun 16 TI - Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible. PG - 5269-78 AB - The backbone dynamics of Ca(2+)-saturated recombinant Drosophila calmodulin has been studied by 15N longitudinal and transverse relaxation experiments, combined with 15N(1H) NOE measurements. Results indicate a high degree of mobility near the middle of the central helix of calmodulin, from residue K77 through S81, with order parameters (S2) in the 0.5-0.6 range. The anisotropy observed in the motion of the two globular calmodulin domains is much smaller than expected on the basis of hydrodynamic calculations for a rigid dumbbell type structure. This indicates that, for the purposes of 15N relaxation, the tumbling of the N-terminal (L4-K77) and C-terminal (E82-S147) lobes of calmodulin is effectively independent. A slightly shorter motional correlation time (tau c approximately 6.3 ns) is obtained for the C-terminal domain compared to the N-terminal domain (tau c approximately 7.1 ns), in agreement with the smaller size of the C-terminal domain. A high degree of mobility, with order parameters of approximately 0.5, is also observed in the loop that connects the first with the second EF-hand type calcium binding domain and in the loop connecting the third and fourth calcium binding domain. FAU - Barbato, G AU - Barbato G AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892. FAU - Ikura, M AU - Ikura M FAU - Kay, L E AU - Kay LE FAU - Pastor, R W AU - Pastor RW FAU - Bax, A AU - Bax A LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Calmodulin) RN - 0 (Recombinant Proteins) SB - IM MH - Animals MH - Calmodulin/*chemistry/ultrastructure MH - Drosophila melanogaster MH - Magnetic Resonance Spectroscopy MH - Motion MH - Protein Conformation MH - Recombinant Proteins MH - Rotation EDAT- 1992/06/16 MHDA- 1992/06/16 00:01 CRDT- 1992/06/16 00:00 PST - ppublish SO - Biochemistry. 1992 Jun 16;31(23):5269-78. PMID- 11846551 OWN - NLM STAT- MEDLINE DA - 20020215 DCOM- 20020227 LR - 20141120 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 314 IP - 3 DP - 2001 Nov 30 TI - Homology between O-linked GlcNAc transferases and proteins of the glycogen phosphorylase superfamily. PG - 365-74 AB - The O-linked GlcNAc transferases (OGTs) are a recently characterized group of largely eukaryotic enzymes that add a single beta-N-acetylglucosamine moiety to specific serine or threonine hydroxyls. In humans, this process may be part of a sugar regulation mechanism or cellular signaling pathway that is involved in many important diseases, such as diabetes, cancer, and neurodegeneration. However, no structural information about the human OGT exists, except for the identification of tetratricopeptide repeats (TPR) at the N terminus. The locations of substrate binding sites are unknown and the structural basis for this enzyme's function is not clear. Here, remote homology is reported between the OGTs and a large group of diverse sugar processing enzymes, including proteins with known structure such as glycogen phosphorylase, UDP-GlcNAc 2-epimerase, and the glycosyl transferase MurG. This relationship, in conjunction with amino acid similarity spanning the entire length of the sequence, implies that the fold of the human OGT consists of two Rossmann-like domains C-terminal to the TPR region. A conserved motif in the second Rossmann domain points to the UDP-GlcNAc donor binding site. This conclusion is supported by a combination of statistically significant PSI-BLAST hits, consensus secondary structure predictions, and a fold recognition hit to MurG. Additionally, iterative PSI-BLAST database searches reveal that proteins homologous to the OGTs form a large and diverse superfamily that is termed GPGTF (glycogen phosphorylase/glycosyl transferase). Up to one-third of the 51 functional families in the CAZY database, a glycosyl transferase classification scheme based on catalytic residue and sequence homology considerations, can be unified through this common predicted fold. GPGTF homologs constitute a substantial fraction of known proteins: 0.4% of all non-redundant sequences and about 1% of proteins in the Escherichia coli genome are found to belong to the GPGTF superfamily. CI - Copyright 2001 Academic Press. FAU - Wrabl, J O AU - Wrabl JO AD - Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas TX 75390-9050, USA. FAU - Grishin, N V AU - Grishin NV LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Outer Membrane Proteins) RN - 0 (Bacterial Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 2.4.1.- (Glycogen Phosphorylase) RN - EC 2.4.1.- (N-Acetylglucosaminyltransferases) RN - EC 2.4.1.227 (UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecapreno l N-acetylglucosamine transferase) RN - EC 5.1.3.- (Carbohydrate Epimerases) RN - EC 5.1.3.14 (UDP acetylglucosamine-2-epimerase) RN - EC 5.1.3.14 (wecB protein, E coli) SB - IM MH - Amino Acid Sequence MH - *Bacterial Outer Membrane Proteins MH - Bacterial Proteins/chemistry/metabolism MH - Binding Sites MH - Carbohydrate Epimerases/chemistry/metabolism MH - Computational Biology MH - Conserved Sequence MH - Databases, Protein MH - *Escherichia coli Proteins MH - Glycogen Phosphorylase/*chemistry/metabolism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Multigene Family MH - N-Acetylglucosaminyltransferases/*chemistry/metabolism MH - Protein Conformation MH - Protein Folding MH - Saccharomyces cerevisiae Proteins/chemistry/metabolism MH - Sequence Alignment MH - *Sequence Homology, Amino Acid EDAT- 2002/02/16 10:00 MHDA- 2002/03/19 10:01 CRDT- 2002/02/16 10:00 AID - 10.1006/jmbi.2001.5151 [doi] AID - S0022-2836(01)95151-4 [pii] PST - ppublish SO - J Mol Biol. 2001 Nov 30;314(3):365-74. PMID- 18421143 OWN - NLM STAT- MEDLINE DA - 20080418 DCOM- 20080731 LR - 20140903 IS - 0909-0495 (Print) IS - 0909-0495 (Linking) VI - 15 IP - Pt 3 DP - 2008 May TI - Solution structures of RseA and its complex with RseB. PG - 219-22 LID - 10.1107/S0909049507066319 [doi] AB - The bacterial envelope stress response, which is responsible for sensing stress signals in the envelope and for turning on the sigma(E)-dependent transcription, is modulated by the binding of RseB to RseA. In this study, the solution structures of RseA and its complex with RseB were analyzed using circular dichroism and small-angle X-ray scattering. The periplasmic domain of RseA is unstructured and flexible when it is not bound to RseB. However, upon the formation of the stable complex with RseB, RseA induces conformational changes in RseB and, at the same time, RseA becomes more structured. Furthermore, it appears that some other undefined region of RseA, as well as the previously identified minimum region (amino acid 169-186), is also involved in RseB binding. It is thought that these conformational changes are relevant to the proteolytic cleavage of RseA and the modulation of envelope stress response. FAU - Jin, Kyeong Sik AU - Jin KS AD - Department of Chemistry, National Research Laboratory for Polymer Synthesis and Physics, Pohang Accelerator Laboratory, Center for Integrated Molecular Systems, Polymer Research Institute, Pohang 790-784, Republic of Korea. FAU - Kim, Dong Young AU - Kim DY FAU - Rho, Yecheol AU - Rho Y FAU - Le, Van Binh AU - Le VB FAU - Kwon, Eunju AU - Kwon E FAU - Kim, Kyeong Kyu AU - Kim KK FAU - Ree, Moonhor AU - Ree M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080418 PL - Denmark TA - J Synchrotron Radiat JT - Journal of synchrotron radiation JID - 9888878 RN - 0 (Escherichia coli Proteins) RN - 0 (Membrane Proteins) RN - 0 (RseA protein, E coli) RN - 0 (RseB protein, E coli) RN - 0 (Transcription Factors) SB - IM MH - Circular Dichroism MH - Escherichia coli Proteins/*chemistry/metabolism MH - Hydrolysis MH - Membrane Proteins/*chemistry/metabolism MH - Protein Conformation MH - Scattering, Radiation MH - Transcription Factors/*chemistry/metabolism PMC - PMC2394797 OID - NLM: PMC2394797 EDAT- 2008/04/19 09:00 MHDA- 2008/08/01 09:00 CRDT- 2008/04/19 09:00 PHST- 2007/08/01 [received] PHST- 2007/12/10 [accepted] PHST- 2008/04/18 [epublish] AID - S0909049507066319 [pii] AID - 10.1107/S0909049507066319 [doi] PST - ppublish SO - J Synchrotron Radiat. 2008 May;15(Pt 3):219-22. doi: 10.1107/S0909049507066319. Epub 2008 Apr 18. PMID- 2204805 OWN - NLM STAT- MEDLINE DA - 19901018 DCOM- 19901018 LR - 20131002 IS - 0270-7306 (Print) IS - 0270-7306 (Linking) VI - 10 IP - 10 DP - 1990 Oct TI - Mutations that define the optimal half-site for binding yeast GCN4 activator protein and identify an ATF/CREB-like repressor that recognizes similar DNA sites. PG - 5077-86 AB - The yeast GCN4 transcriptional activator protein binds as a dimer to a dyad-symmetric sequence, indicative of a protein-DNA complex in which two protein monomers interact with adjacent half-sites. However, the optimal GCN4 recognition site, ATGA(C/G)TCAT, is inherently asymmetric because it contains an odd number of base pairs and because mutation of the central C.G base pair strongly reduces specific DNA binding. From this asymmetry, we suggested previously that GCN4 interacts with nonequivalent and possibly overlapping half-sites (ATGAC and ATGAG) that have different affinities. Here, we examine the nature of GCN4 half-sites by creating symmetrical derivatives of the optimal GCN4 binding sequence that delete or insert a single base pair at the center of the site. In vitro, GCN4 bound efficiently to the sequence ATGACGTCAT, whereas it failed to bind to ATGAGCTCAT or ATGATCAT. These observations strongly suggest that (i) GCN4 specifically recognizes the central base pair, (ii) the optimal half-site for GCN4 binding is ATGAC, not ATGAG, and (iii) GCN4 is a surprisingly flexible protein that can accommodate the insertion of a single base pair in the center of its compact binding site. The ATGACGTCAT sequence strongly resembles sites bound by the yeast and mammalian ATF/CREB family of proteins, suggesting that GCN4 and the ATF/CREB proteins recognize similar half-sites but have different spacing requirements. Unexpectedly, in the context of the his3 promoter, the ATGACGTCAT derivative reduced transcription below the basal level in a GCN4-independent manner, presumably reflecting DNA binding by a distinct ATF/CREB-like repressor protein. In other promoter contexts, however, the same site acted as a weak upstream activating sequence. FAU - Sellers, J W AU - Sellers JW AD - Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115. FAU - Vincent, A C AU - Vincent AC FAU - Struhl, K AU - Struhl K LA - eng GR - GM 30186/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (DNA-Binding Proteins) RN - 0 (Fungal Proteins) RN - 0 (Oligonucleotides) RN - 0 (RNA, Messenger) RN - 0 (Repressor Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Transcription Factors) RN - EC 2.7.- (Protein Kinases) SB - IM MH - Base Sequence MH - DNA-Binding Proteins/physiology MH - Fungal Proteins/*genetics MH - Molecular Sequence Data MH - Mutation MH - Oligonucleotides MH - *Protein Kinases MH - RNA, Messenger/genetics MH - *Regulatory Sequences, Nucleic Acid MH - Repressor Proteins/metabolism MH - Saccharomyces cerevisiae/*genetics MH - *Saccharomyces cerevisiae Proteins MH - Structure-Activity Relationship MH - Transcription Factors/*genetics MH - Transcription, Genetic PMC - PMC361174 OID - NLM: PMC361174 EDAT- 1990/10/01 MHDA- 1990/10/01 00:01 CRDT- 1990/10/01 00:00 PST - ppublish SO - Mol Cell Biol. 1990 Oct;10(10):5077-86. PMID- 14592974 OWN - NLM STAT- MEDLINE DA - 20031031 DCOM- 20031216 LR - 20140610 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 22 IP - 21 DP - 2003 Nov 3 TI - The crystal structure of the human polo-like kinase-1 polo box domain and its phospho-peptide complex. PG - 5757-68 AB - Human polo-like kinase Plk1 localizes to the centrosomes, kinetochores and central spindle structures during mitosis. It plays an essential role in promoting mitosis and cytokinesis through phosphorylation of a number of different substrates. Kinase activity is regulated by a conserved C-terminal domain, termed the polo box domain (PBD), which acts both as an autoinhibitory domain and as a subcellular localization domain. We have determined the crystal structure of Plk1 PBD (residues 367-603) to 2.2 A resolution and the structure of a phospho-peptide-PBD (residues 345-603) complex to 2.3 A resolution. The two polo boxes of the PBD exhibit identical folds based on a six-stranded beta-sheet and an alpha-helix, despite only 12% sequence identity. The phospho-peptide binds at a site between the two polo boxes. It makes a short antiparallel beta-sheet connection and critical contacts to residues Trp414, Leu490, His538 and Lys540. Most of these residues had been shown to be important for biological activity through mutational studies. The results provide an explanation for phospho-peptide recognition and create the basis for new functional studies. FAU - Cheng, Kin-Yip AU - Cheng KY AD - Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. FAU - Lowe, Edward D AU - Lowe ED FAU - Sinclair, John AU - Sinclair J FAU - Nigg, Erich A AU - Nigg EA FAU - Johnson, Louise N AU - Johnson LN LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Cell Cycle Proteins) RN - 0 (Macromolecular Substances) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Recombinant Proteins) RN - EC 2.7.- (Protein Kinases) RN - EC 2.7.1.- (PLK4 protein, human) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - EC 2.7.11.1 (polo-like kinase 1) SB - IM MH - Amino Acid Sequence MH - Cell Cycle Proteins MH - Crystallography, X-Ray MH - Humans MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Folding MH - Protein Kinases/*chemistry/genetics MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein-Serine-Threonine Kinases/chemistry/genetics MH - Proto-Oncogene Proteins MH - Recombinant Proteins/chemistry/genetics MH - Sequence Homology, Amino Acid MH - Static Electricity PMC - PMC275415 OID - NLM: PMC275415 EDAT- 2003/11/01 05:00 MHDA- 2003/12/17 05:00 CRDT- 2003/11/01 05:00 AID - 10.1093/emboj/cdg558 [doi] PST - ppublish SO - EMBO J. 2003 Nov 3;22(21):5757-68. PMID- 7510518 OWN - NLM STAT- MEDLINE DA - 19940418 DCOM- 19940418 LR - 20081121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 33 IP - 10 DP - 1994 Mar 15 TI - Helix-loop-helix motif in HIV-1 Rev. PG - 2988-96 AB - Circular dichroism (CD) spectra of C-terminal deletion mutants of the HIV-1 Rev protein, Rev M9 delta 14 (missing aa 68-112) and Rev M11 delta 14 (lacking aa 92-112), indicated that Rev contains 46-49 residues in alpha-helical conformation within the N-terminal 71 or 95 amino acids of the 116 residue protein. Complexation with a 40-nucleotide fragment of the Rev responsive element, RRE, (G39 to C78), containing the minimal element for Rev binding, induced an A to B form structural transition in the RRE fragment, whereas the percentage of alpha-helical conformation in the protein stays constant on substrate binding. When complexed to the RNA, neither mutant protein showed structural changes upon raising the temperature to 40 degrees C, as determined by the lack of decrease of the signal intensity at 222 nm, indicative for alpha-helical conformation. In contrast, Rev M9 delta 14, which is shorter than Rev M11 delta 14 by 24 amino acids, in the absence of RNA, lost about 60% of the spectral minima at 222 nm at the same temperature. The Rev M11 delta 14 mutant, in the absence of RNA, showed a decrease of 20% in spectral intensity upon heating to 40 degrees C. Free and RNA-bound mutant proteins showed reversible transitions upon heating to 80 degrees C and subsequent cooling down to 10 degrees C overnight. The Rev peptide Cys 75-93, spanning the Rev transactivation domain, showed secondary structure in 40% and 60% hexafluoropropanol (HFP) solutions.(ABSTRACT TRUNCATED AT 250 WORDS) FAU - Auer, M AU - Auer M AD - Sandoz Research Institute, Vienna, Austria. FAU - Gremlich, H U AU - Gremlich HU FAU - Seifert, J M AU - Seifert JM FAU - Daly, T J AU - Daly TJ FAU - Parslow, T G AU - Parslow TG FAU - Casari, G AU - Casari G FAU - Gstach, H AU - Gstach H LA - eng PT - Journal Article PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Gene Products, rev) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 0 (rev Gene Products, Human Immunodeficiency Virus) RN - 63231-63-0 (RNA) SB - IM SB - X MH - Amino Acid Sequence MH - Base Sequence MH - Circular Dichroism MH - Gene Products, rev/biosynthesis/*chemistry/metabolism MH - HIV-1/*metabolism MH - *Helix-Loop-Helix Motifs MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Peptide Fragments/chemical synthesis/chemistry MH - Protein Conformation MH - RNA/*chemistry/metabolism MH - Recombinant Proteins/biosynthesis/chemistry/metabolism MH - Sequence Deletion MH - Transcriptional Activation MH - rev Gene Products, Human Immunodeficiency Virus EDAT- 1994/03/15 MHDA- 1994/03/15 00:01 CRDT- 1994/03/15 00:00 PST - ppublish SO - Biochemistry. 1994 Mar 15;33(10):2988-96. PMID- 24622397 OWN - NLM STAT- In-Process DA - 20140909 LR - 20150601 IS - 1559-2308 (Electronic) IS - 1559-2294 (Linking) VI - 9 IP - 6 DP - 2014 Jun TI - dBigH1, a second histone H1 in Drosophila, and the consequences for histone fold nomenclature. PG - 791-7 LID - 10.4161/epi.28427 [doi] AB - Recently, Perez-Montero and colleagues (Developmental cell, 26: 578-590, 2013) described the occurrence of a new histone H1 variant (dBigH1) in Drosophila. The presence of unusual acidic amino acid patches at the N-terminal end of dBigH1 is in contrast to the arginine patches that exist at the N- and C-terminal domains of other histone H1-related proteins found in the sperm of some organisms. This departure from the strictly lysine-rich composition of the somatic histone H1 raises a question about the true definition of its protein members. Their minimal essential requirements appear to be the presence of a lysine- and alanine-rich, intrinsically disordered C-terminal domain, with a highly helicogenic potential upon binding to the linker DNA regions of chromatin. In metazoans, specific targeting of these regions is further achieved by a linker histone fold domain (LHFD), distinctively different from the characteristic core histone fold domain (CHFD) of the nucleosome core histones. FAU - Gonzalez-Romero, Rodrigo AU - Gonzalez-Romero R AD - Department of Biochemistry and Microbiology; University of Victoria; Victoria, BC, Canada. FAU - Ausio, Juan AU - Ausio J AD - Department of Biochemistry and Microbiology; University of Victoria; Victoria, BC, Canada. LA - eng GR - MOP-97878/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20140312 PL - United States TA - Epigenetics JT - Epigenetics : official journal of the DNA Methylation Society JID - 101265293 SB - IM PMC - PMC4065175 OID - NLM: PMC4065175 OTO - NOTNLM OT - chromatin OT - histone OT - histone-fold OT - linker DNA OT - nucleosome EDAT- 2014/03/14 06:00 MHDA- 2014/03/14 06:00 CRDT- 2014/03/14 06:00 PHST- 2014/03/12 [aheadofprint] AID - 28427 [pii] AID - 10.4161/epi.28427 [doi] PST - ppublish SO - Epigenetics. 2014 Jun;9(6):791-7. doi: 10.4161/epi.28427. Epub 2014 Mar 12. PMID- 11080143 OWN - NLM STAT- MEDLINE DA - 20001215 DCOM- 20010104 LR - 20140615 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 19 IP - 22 DP - 2000 Nov 15 TI - Crystal structure of the Xrcc4 DNA repair protein and implications for end joining. PG - 5962-70 AB - XRCC4 is essential for carrying out non-homologous DNA end joining (NHEJ) in all eukaryotes and, in particular, V(D)J recombination in vertebrates. Xrcc4 protein forms a complex with DNA ligase IV that rejoins two DNA ends in the last step of V(D)J recombination and NHEJ to repair double strand breaks. XRCC4-defective cells are extremely sensitive to ionizing radiation, and disruption of the XRCC4 gene results in embryonic lethality in mice. Here we report the crystal structure of a functional fragment of Xrcc4 at 2.7 A resolution. Xrcc4 protein forms a strikingly elongated dumb-bell-like tetramer. Each of the N-terminal globular head domains consists of a beta-sandwich and a potentially DNA-binding helix- turn-helix motif. The C-terminal stalk comprising a single alpha-helix >120 A in length is partly incorporated into a four-helix bundle in the Xrcc4 tetramer and partly involved in interacting with ligase IV. The Xrcc4 structure suggests a possible mode of coupling ligase IV association with DNA binding for effective ligation of DNA ends. FAU - Junop, M S AU - Junop MS AD - Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. FAU - Modesti, M AU - Modesti M FAU - Guarne, A AU - Guarne A FAU - Ghirlando, R AU - Ghirlando R FAU - Gellert, M AU - Gellert M FAU - Yang, W AU - Yang W LA - eng PT - Comparative Study PT - Journal Article PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Bacterial Proteins) RN - 0 (Cell Cycle Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Macromolecular Substances) RN - 0 (SMC protein, Bacteria) RN - 0 (XRCC4 protein, human) RN - 9007-49-2 (DNA) RN - EC 6.5.1.- (DNA Ligases) RN - EC 6.5.1.1 (DNA ligase (ATP)) SB - IM MH - Amino Acid Sequence MH - Animals MH - Bacterial Proteins/chemistry MH - Binding Sites MH - Cell Cycle Proteins/chemistry MH - Crystallization MH - Crystallography, X-Ray MH - DNA/chemistry/metabolism MH - DNA Ligases/chemistry/metabolism MH - *DNA Repair MH - DNA-Binding Proteins/*chemistry/genetics/*metabolism MH - Dimerization MH - Humans MH - Macromolecular Substances MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Quaternary MH - Saccharomyces cerevisiae/genetics MH - Sequence Homology, Amino Acid PMC - PMC305814 OID - NLM: PMC305814 EDAT- 2000/11/18 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/11/18 11:00 AID - 10.1093/emboj/19.22.5962 [doi] PST - ppublish SO - EMBO J. 2000 Nov 15;19(22):5962-70. PMID- 15640140 OWN - NLM STAT- MEDLINE DA - 20050314 DCOM- 20050425 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 11 DP - 2005 Mar 18 TI - MARCKS is a natively unfolded protein with an inaccessible actin-binding site: evidence for long-range intramolecular interactions. PG - 9946-56 AB - Myristoylated alanine-rich C kinase substrate (MARCKS) is an unfolded protein that contains well characterized actin-binding sites within the phosphorylation site domain (PSD), yet paradoxically, we now find that intact MARCKS does not bind to actin. Intact MARCKS also does not bind as well to calmodulin as does the PSD alone. Myristoylation at the N terminus alters how calmodulin binds to MARCKS, implying that, despite its unfolded state, the distant N terminus influences binding events at the PSD. We show that the free PSD binds with site specificity to MARCKS, suggesting that long-range intramolecular interactions within MARCKS are also possible. Because of the unusual primary sequence of MARCKS with an overall isoelectric point of 4.2 yet a very basic PSD (overall charge of +13), we speculated that ionic interactions between oppositely charged domains of MARCKS were responsible for long-range interactions within MARCKS that sterically influence binding events at the PSD and that explain the observed differences between properties of the PSD and MARCKS. Consistent with this hypothesis, chemical modifications of MARCKS that neutralize negatively charged residues outside of the PSD allow the PSD to bind to actin and increase the affinity of MARCKS for calmodulin. Similarly, both myristoylation of MARCKS and cleavage of MARCKS by calpain are shown to increase the availability of the PSD so as to activate its actin-binding activity. Because abundant evidence supports the conclusion that MARCKS is an important protein in regulating actin dynamics, our data imply that post-translational modifications of MARCKS are necessary and sufficient to regulate actin-binding activity. FAU - Tapp, Hazel AU - Tapp H AD - Department of Medicine, University of Florida College of Medicine, Gainesville, Florida 32610, USA. FAU - Al-Naggar, Iman M AU - Al-Naggar IM FAU - Yarmola, Elena G AU - Yarmola EG FAU - Harrison, Alexis AU - Harrison A FAU - Shaw, Gerry AU - Shaw G FAU - Edison, Arthur S AU - Edison AS FAU - Bubb, Michael R AU - Bubb MR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20050106 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Actins) RN - 0 (Calmodulin) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Ions) RN - 0 (Membrane Proteins) RN - 0 (Myristic Acids) RN - 0 (Recombinant Proteins) RN - 125267-21-2 (myristoylated alanine-rich C kinase substrate) RN - 9007-49-2 (DNA) RN - EC 3.4.22.- (Calpain) SB - IM MH - Actins/chemistry MH - Animals MH - Anisotropy MH - Binding Sites MH - Calmodulin/chemistry MH - Calpain/chemistry/pharmacology MH - DNA/chemistry MH - Dose-Response Relationship, Drug MH - Escherichia coli/metabolism MH - Intracellular Signaling Peptides and Proteins/*chemistry MH - Ions MH - Membrane Proteins/*chemistry MH - Mice MH - Muscle, Skeletal/metabolism MH - Myristic Acids/metabolism MH - Protein Binding MH - Protein Denaturation MH - Protein Folding MH - Protein Processing, Post-Translational MH - Protein Structure, Tertiary MH - Rabbits MH - Recombinant Proteins/chemistry MH - Spectrometry, Fluorescence MH - Time Factors EDAT- 2005/01/11 09:00 MHDA- 2005/04/26 09:00 CRDT- 2005/01/11 09:00 PHST- 2005/01/06 [aheadofprint] AID - M414614200 [pii] AID - 10.1074/jbc.M414614200 [doi] PST - ppublish SO - J Biol Chem. 2005 Mar 18;280(11):9946-56. Epub 2005 Jan 6. PMID- 19675186 OWN - NLM STAT- MEDLINE DA - 20091111 DCOM- 20091201 IS - 1465-2099 (Electronic) IS - 0022-1317 (Linking) VI - 90 IP - Pt 12 DP - 2009 Dec TI - Domain organization of the N-terminal portion of hordeivirus movement protein TGBp1. PG - 3022-32 LID - 10.1099/vir.0.013862-0 [doi] AB - Three 'triple gene block' proteins known as TGBp1, TGBp2 and TGBp3 are required for cell-to-cell movement of plant viruses belonging to a number of genera including Hordeivirus. Hordeiviral TGBp1 interacts with viral genomic RNAs to form ribonucleoprotein (RNP) complexes competent for translocation between cells through plasmodesmata and over long distances via the phloem. Binding of hordeivirus TGBp1 to RNA involves two protein regions, the C-terminal NTPase/helicase domain and the N-terminal extension region. This study demonstrated that the extension region of hordeivirus TGBp1 consists of two structurally and functionally distinct domains called the N-terminal domain (NTD) and the internal domain (ID). In agreement with secondary structure predictions, analysis of circular dichroism spectra of the isolated NTD and ID demonstrated that the NTD represents a natively unfolded protein domain, whereas the ID has a pronounced secondary structure. Both the NTD and ID were able to bind ssRNA non-specifically. However, whilst the NTD interacted with ssRNA non-cooperatively, the ID bound ssRNA in a cooperative manner. Additionally, both domains bound dsRNA. The NTD and ID formed low-molecular-mass oligomers, whereas the ID also gave rise to high-molecular-mass complexes. The isolated ID was able to interact with both the NTD and the C-terminal NTPase/helicase domain in solution. These data demonstrate that the hordeivirus TGBp1 has three RNA-binding domains and that interaction between these structural units can provide a basis for remodelling of viral RNP complexes at different steps of cell-to-cell and long-distance transport of virus infection. FAU - Makarov, Valentin V AU - Makarov VV AD - A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia. FAU - Rybakova, Ekaterina N AU - Rybakova EN FAU - Efimov, Alexander V AU - Efimov AV FAU - Dobrov, Eugene N AU - Dobrov EN FAU - Serebryakova, Marina V AU - Serebryakova MV FAU - Solovyev, Andrey G AU - Solovyev AG FAU - Yaminsky, Igor V AU - Yaminsky IV FAU - Taliansky, Michael E AU - Taliansky ME FAU - Morozov, Sergey Yu AU - Morozov SY FAU - Kalinina, Natalia O AU - Kalinina NO LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090812 PL - England TA - J Gen Virol JT - The Journal of general virology JID - 0077340 RN - 0 (Plant Viral Movement Proteins) RN - 0 (RNA, Viral) RN - 0 (Ribonucleoproteins) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Escherichia coli/genetics/metabolism MH - Mass Spectrometry MH - Mutation MH - Plant Viral Movement Proteins/*chemistry/genetics/metabolism MH - *Plant Viruses/genetics/metabolism/physiology MH - Protein Structure, Tertiary MH - *RNA Viruses/genetics/metabolism/physiology MH - RNA, Viral/genetics/metabolism MH - Recombination, Genetic MH - Ribonucleoproteins/genetics/metabolism MH - Ultracentrifugation EDAT- 2009/08/14 09:00 MHDA- 2009/12/16 06:00 CRDT- 2009/08/14 09:00 PHST- 2009/08/12 [aheadofprint] AID - vir.0.013862-0 [pii] AID - 10.1099/vir.0.013862-0 [doi] PST - ppublish SO - J Gen Virol. 2009 Dec;90(Pt 12):3022-32. doi: 10.1099/vir.0.013862-0. Epub 2009 Aug 12. PMID- 12196540 OWN - NLM STAT- MEDLINE DA - 20021126 DCOM- 20030108 LR - 20130603 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 277 IP - 48 DP - 2002 Nov 29 TI - Structure of the epidermal growth factor receptor kinase domain alone and in complex with a 4-anilinoquinazoline inhibitor. PG - 46265-72 AB - The crystal structure of the kinase domain from the epidermal growth factor receptor (EGFRK) including forty amino acids from the carboxyl-terminal tail has been determined to 2.6-A resolution, both with and without an EGFRK-specific inhibitor currently in Phase III clinical trials as an anti-cancer agent, erlotinib (OSI-774, CP-358,774, Tarceva(TM)). The EGFR family members are distinguished from all other known receptor tyrosine kinases in possessing constitutive kinase activity without a phosphorylation event within their kinase domains. Despite its lack of phosphorylation, we find that the EGFRK activation loop adopts a conformation similar to that of the phosphorylated active form of the kinase domain from the insulin receptor. Surprisingly, key residues of a putative dimerization motif lying between the EGFRK domain and carboxyl-terminal substrate docking sites are found in close contact with the kinase domain. Significant intermolecular contacts involving the carboxyl-terminal tail are discussed with respect to receptor oligomerization. FAU - Stamos, Jennifer AU - Stamos J AD - Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA. FAU - Sliwkowski, Mark X AU - Sliwkowski MX FAU - Eigenbrot, Charles AU - Eigenbrot C LA - eng SI - PDB/1M14 SI - PDB/1M17 PT - Journal Article DEP - 20020823 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Enzyme Inhibitors) RN - 0 (Quinazolines) RN - EC 2.7.10.1 (Receptor, Epidermal Growth Factor) RN - J4T82NDH7E (erlotinib) SB - IM MH - Amino Acid Motifs MH - Animals MH - Catalytic Domain MH - Cell Line MH - Crystallography MH - Enzyme Activation MH - Enzyme Inhibitors/*chemistry/pharmacology MH - Models, Molecular MH - Molecular Structure MH - Quinazolines/*chemistry/pharmacology MH - Receptor, Epidermal Growth Factor/antagonists & inhibitors/*chemistry MH - Spodoptera EDAT- 2002/08/28 10:00 MHDA- 2003/01/09 04:00 CRDT- 2002/08/28 10:00 PHST- 2002/08/23 [aheadofprint] AID - 10.1074/jbc.M207135200 [doi] AID - M207135200 [pii] PST - ppublish SO - J Biol Chem. 2002 Nov 29;277(48):46265-72. Epub 2002 Aug 23. PMID- 15465854 OWN - NLM STAT- MEDLINE DA - 20041201 DCOM- 20050426 LR - 20140608 IS - 0006-3495 (Print) IS - 0006-3495 (Linking) VI - 87 IP - 6 DP - 2004 Dec TI - SAXS study of the PIR domain from the Grb14 molecular adaptor: a natively unfolded protein with a transient structure primer? PG - 4056-64 AB - Grb14 belongs to the Grb7 family of adapters and was identified as a negative regulator of insulin signal transduction. Between the PH (pleckstrin homology) and SH2 (Src homology 2) domains is a new binding domain implicated in the interaction with receptor tyrosine kinases called PIR (phosphorylated insulin receptor interaction region). Both PIR and SH2 domains interact with the insulin receptor, but their relative role varies considering the member of the Grb7 family and the tyrosine kinase receptor. In the case of Grb14, PIR is the main binding domain and is sufficient to inhibit the insulin receptor kinase activity. We have proposed, on the basis of NMR measurements, that PIR lacks ordered structure and presents a high flexibility, although remaining fully active. To complement this first study, we have used small-angle x-ray scattering in solution together with a modeling approach representing the PIR domain as a chain of pseudo residues. Circular dichroism experiments were also performed in the presence of variable amounts of trifluoroethanol. These observations, together with an ensemble of sequence analyses and previous NMR results, all support the view of PIR as essentially unstructured but with a potentially structured short stretch encompassing residues 399-407. This stretch, which may be only structured transiently in the isolated molecule, could play a major role in Grb14 PIR binding to a biological partner by undergoing a structural transition. FAU - Moncoq, K AU - Moncoq K AD - Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Faculte de Pharmacie, Universite Paris 5, 75270 Paris Cedex 06, France. FAU - Broutin, I AU - Broutin I FAU - Craescu, C T AU - Craescu CT FAU - Vachette, P AU - Vachette P FAU - Ducruix, A AU - Ducruix A FAU - Durand, D AU - Durand D LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20041001 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Grb14 protein, rat) RN - 0 (Proteins) RN - EC 2.7.10.1 (Receptor, Insulin) SB - IM MH - Amino Acid Sequence MH - Computer Simulation MH - *Models, Chemical MH - *Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proteins/*analysis/*chemistry MH - Receptor, Insulin/*chemistry MH - Sequence Analysis, Protein/*methods MH - Structure-Activity Relationship MH - X-Ray Diffraction/*methods PMC - PMC1304914 OID - NLM: PMC1304914 EDAT- 2004/10/07 09:00 MHDA- 2005/04/27 09:00 CRDT- 2004/10/07 09:00 PHST- 2004/10/01 [aheadofprint] AID - S0006-3495(04)73869-2 [pii] AID - 10.1529/biophysj.104.048645 [doi] PST - ppublish SO - Biophys J. 2004 Dec;87(6):4056-64. Epub 2004 Oct 1. PMID- 7506692 OWN - NLM STAT- MEDLINE DA - 19940217 DCOM- 19940217 LR - 20071114 IS - 0378-1119 (Print) IS - 0378-1119 (Linking) VI - 137 IP - 1 DP - 1993 Dec 27 TI - Isolation and characterization of nucleic acid-binding antibody fragments from autoimmune mice-derived bacteriophage display libraries. PG - 77-83 AB - The display of antibody fragments (Fab) on the surface of filamentous bacteriophage and selection of phage that bind to a particular antigen has enabled the isolation of Fab with numerous specificities, including haptens, proteins and viral particles. We have examined the possibility of isolating nucleic acid-binding Fab by constructing a combinatorial library of phage displaying Fab derived from autoimmune (MRL/lpr) mice. Autoimmune mice were chosen because they contain antibodies (Ab) reactive against nuclear components, including DNA, RNA and protein complexes. The library was panned against single-stranded (ss) calf thymus (CT) DNA and the selected Fabs were analyzed further. Characterization of the nucleic acid-binding phage led to the identification of two kinds of Fab with quite different properties. One Fab bound with high affinity a variety of ssDNA molecules, as well as several model RNA substrates. This Fab has been affinity purified to greater than 95% and competition studies revealed a marked preference for binding to poly(dT). The second Fab showed a reduced binding to RNA ligands and a restricted number of ssDNA molecules. Analysis of the deduced amino acid (aa) sequences of the Fab variable (V) regions revealed that the heavy (H) chain V region from the strong nucleic acid-binding Fab was derived from a VH gene that is used recurrently in autoantibodies. This VH domain was most similar to an anti-ssDNA autoimmune monoclonal antibody (mAb) suggesting that antigen-binding specificities present in an autoimmune repertoire may be directly accessed by this approach.(ABSTRACT TRUNCATED AT 250 WORDS) FAU - Calcutt, M J AU - Calcutt MJ AD - Department of Biochemistry, University of Missouri, Columbia 65212. FAU - Kremer, M T AU - Kremer MT FAU - Giblin, M F AU - Giblin MF FAU - Quinn, T P AU - Quinn TP FAU - Deutscher, S L AU - Deutscher SL LA - eng SI - GENBANK/L11593 SI - GENBANK/L11594 SI - GENBANK/L24529 SI - GENBANK/U00927 SI - GENBANK/U00929 SI - GENBANK/U00940 SI - GENBANK/U00941 SI - GENBANK/X69763 SI - GENBANK/Z15047 SI - GENBANK/Z15048 GR - 5R29 GM47979/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - NETHERLANDS TA - Gene JT - Gene JID - 7706761 RN - 0 (Antibodies, Antinuclear) RN - 0 (DNA-Binding Proteins) RN - 0 (Immunoglobulin Fab Fragments) RN - 0 (Recombinant Fusion Proteins) RN - 63231-63-0 (RNA) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Animals MH - Antibodies, Antinuclear/metabolism MH - Antibody Specificity MH - Autoimmunity MH - DNA/*metabolism MH - DNA-Binding Proteins MH - Immunoglobulin Fab Fragments/*isolation & purification MH - *Inovirus MH - Mice MH - Molecular Sequence Data MH - RNA/*metabolism MH - Recombinant Fusion Proteins EDAT- 1993/12/27 MHDA- 1993/12/27 00:01 CRDT- 1993/12/27 00:00 AID - 0378-1119(93)90254-Z [pii] PST - ppublish SO - Gene. 1993 Dec 27;137(1):77-83. PMID- 22448726 OWN - NLM STAT- MEDLINE DA - 20120410 DCOM- 20120615 LR - 20141016 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 51 IP - 14 DP - 2012 Apr 10 TI - Influence of the carboxy terminus of serum amyloid A on protein oligomerization, misfolding, and fibril formation. PG - 3092-9 LID - 10.1021/bi201903s [doi] AB - The fibrillar deposition of serum amyloid A (SAA) has been linked to the disease amyloid A (AA) amyloidosis. We have used the SAA isoform, SAA2.2, from the CE/J mouse strain, as a model system to explore the inherent structural and biophysical properties of SAA. Despite its nonpathogenic nature in vivo, SAA2.2 spontaneously forms fibrils in vitro, suggesting that SAA proteins are inherently amyloidogenic. However, whereas the importance of the amino terminus of SAA for fibril formation has been well documented, the influence of the proline-rich and presumably disordered carboxy terminus remains poorly understood. To clarify the inherent role of the carboxy terminus in the oligomerization and fibrillation of SAA, we truncated the proline-rich final 13 residues of SAA2.2. We found that unlike full-length SAA2.2, the carboxy-terminal truncated SAA2.2 (SAA2.2DeltaC) did not oligomerize to a hexamer or octamer, but formed a high molecular weight soluble aggregate. Moreover, SAA2.2DeltaC also exhibited a pronounced decrease in the rate of fibril formation. Intriguingly, when equimolar amounts of denatured SAA2.2 and SAA2.2DeltaC were mixed and allowed to refold together, the mixture formed an octamer and exhibited rapid fibrillation kinetics, similar to those for full-length SAA2.2. These results suggest that the carboxy terminus of SAA, which is highly conserved among SAA sequences in all vertebrates, might play important structural roles, including modulating the folding, oligomerization, misfolding, and fibrillation of SAA. CI - (c) 2012 American Chemical Society FAU - Patke, Sanket AU - Patke S AD - Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA. FAU - Maheshwari, Ronak AU - Maheshwari R FAU - Litt, Jeffrey AU - Litt J FAU - Srinivasan, Saipraveen AU - Srinivasan S FAU - Aguilera, J Javier AU - Aguilera JJ FAU - Colon, Wilfredo AU - Colon W FAU - Kane, Ravi S AU - Kane RS LA - eng GR - R01 AG028158/AG/NIA NIH HHS/United States GR - R01 AG028158/AG/NIA NIH HHS/United States GR - R01 AG028158-05/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120326 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Protein Isoforms) RN - 0 (Saa2 protein, mouse) RN - 0 (Serum Amyloid A Protein) SB - IM MH - Amyloid/*chemistry/metabolism MH - Animals MH - Kinetics MH - Mice MH - Microscopy, Atomic Force MH - Molecular Weight MH - *Protein Folding MH - Protein Isoforms/chemistry/genetics/metabolism MH - Serum Amyloid A Protein/*chemistry/genetics/metabolism PMC - PMC3332083 MID - NIHMS366701 OID - NLM: NIHMS366701 OID - NLM: PMC3332083 EDAT- 2012/03/28 06:00 MHDA- 2012/06/16 06:00 CRDT- 2012/03/28 06:00 PHST- 2012/03/26 [aheadofprint] AID - 10.1021/bi201903s [doi] PST - ppublish SO - Biochemistry. 2012 Apr 10;51(14):3092-9. doi: 10.1021/bi201903s. Epub 2012 Mar 26. PMID- 10655612 OWN - NLM STAT- MEDLINE DA - 20000303 DCOM- 20000303 LR - 20131121 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 7 IP - 2 DP - 2000 Feb TI - The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix. PG - 113-7 AB - Aspartic proteinase A from yeast is specifically and potently inhibited by a small protein called IA3 from Saccharomyces cerevisiae. Although this inhibitor consists of 68 residues, we show that the inhibitory activity resides within the N-terminal half of the molecule. Structures solved at 2.2 and 1.8 A, respectively, for complexes of proteinase A with full-length IA3 and with a truncated form consisting only of residues 2-34, reveal an unprecedented mode of inhibitor-enzyme interactions. Neither form of the free inhibitor has detectable intrinsic secondary structure in solution. However, upon contact with the enzyme, residues 2-32 become ordered and adopt a near-perfect alpha-helical conformation. Thus, the proteinase acts as a folding template, stabilizing the helical conformation in the inhibitor, which results in the potent and specific blockage of the proteolytic activity. FAU - Li, M AU - Li M AD - Macromolecular Crystallography Laboratory, Program in Structural Biology, National Cancer Institute-FCRDC, Frederick, Maryland 21702, USA. FAU - Phylip, L H AU - Phylip LH FAU - Lees, W E AU - Lees WE FAU - Winther, J R AU - Winther JR FAU - Dunn, B M AU - Dunn BM FAU - Wlodawer, A AU - Wlodawer A FAU - Kay, J AU - Kay J FAU - Gustchina, A AU - Gustchina A LA - eng SI - PDB/1DP5 SI - PDB/1DPJ PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Fungal Proteins) RN - 0 (PAI3 protein, S cerevisiae) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - AE28F7PNPL (Methionine) RN - EC 3.4.21.4 (Trypsin) RN - EC 3.4.23 (aspartic proteinase A) RN - EC 3.4.23. (PEP4 protein, S cerevisiae) RN - EC 3.4.23.- (Aspartic Acid Endopeptidases) SB - IM MH - Amino Acid Sequence MH - Aspartic Acid Endopeptidases/*antagonists & inhibitors/*chemistry/metabolism MH - Circular Dichroism MH - Crystallography, X-Ray MH - Fungal Proteins/*antagonists & inhibitors/*chemistry/genetics/metabolism MH - Hydrogen-Ion Concentration MH - Methionine MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Protein Conformation MH - Protein Folding MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Saccharomyces cerevisiae/*enzymology MH - *Saccharomyces cerevisiae Proteins MH - Trypsin/metabolism EDAT- 2000/02/03 09:00 MHDA- 2000/03/11 09:00 CRDT- 2000/02/03 09:00 AID - 10.1038/72378 [doi] PST - ppublish SO - Nat Struct Biol. 2000 Feb;7(2):113-7. PMID- 24981796 OWN - NLM STAT- MEDLINE DA - 20140728 DCOM- 20140912 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1844 IP - 9 DP - 2014 Sep TI - Self-recognition behavior of a helix-loop-helix domain by a fragment scan. PG - 1675-83 LID - 10.1016/j.bbapap.2014.06.015 [doi] LID - S1570-9639(14)00164-2 [pii] AB - The inhibitors of DNA binding Id1-4 are helix-loop-helix (HLH) proteins that exert their biological function by interacting with members of the basic-HLH (bHLH) transcription-factor family. The HLH domains of the Id and bHLH proteins allow both self- and hetero-association. Due to their abnormal expression in cancer cells, the Id proteins are potential protein targets for cancer treatment. Suitable Id-protein inactivators should promote self-association and/or prevent hetero-association. In this work we evaluated the ability of the Id-protein HLH domain to recognize itself in form of short sequences extracted from the helical and loop regions. We performed a peptide scan of the Id1 HLH domain 64-106 based on three-residue overlapping octapeptides. Interaction of each octapeptide with the natively folded Id1 HLH domain was investigated by CD and fluorescence spectroscopy. The results from both techniques showed that the helix-based but not the loop-based octapeptides interacted with the Id1 HLH domain in the low-micromolar range. In contrast, a nitrotyrosine-containing analog of the Id1 HLH region, which was unable to reproduce the native-like conformation, quenched only the 2-amino-benzoyl-(Abz)-labeled loop-based octapeptides. This opposite self-recognition pattern suggests that the short helix-based and loop-based sequences should be able to distinguish different folding states of the Id1 HLH domain. This feature may be biologically relevant, as the Id proteins are predicted to behave as intrinsically disordered proteins, being in equilibrium between rapidly exchanging monomeric conformations and structurally better-defined homo-/heterodimers displaying the parallel four-helix bundle. CI - Copyright (c) 2014 Elsevier B.V. All rights reserved. FAU - Beisswenger, Michael AU - Beisswenger M AD - Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitatsstrasse 150, 44801 Bochum, Germany. FAU - Cabrele, Chiara AU - Cabrele C AD - Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitatsstrasse 150, 44801 Bochum, Germany; Department of Molecular Biology, Division of Chemistry and Bioanalytics, Paris-Lodron University Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria. Electronic address: chiara.cabrele@sbg.ac.at. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140627 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Inhibitor of Differentiation Protein 1) RN - 0 (Ligands) RN - 0 (Oligopeptides) RN - 0 (ortho-Aminobenzoates) RN - 3604-79-3 (3-nitrotyrosine) RN - 42HK56048U (Tyrosine) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - *Helix-Loop-Helix Motifs MH - High-Throughput Screening Assays MH - Humans MH - Inhibitor of Differentiation Protein 1/*antagonists & inhibitors/chemistry MH - Kinetics MH - Ligands MH - Molecular Sequence Data MH - Oligopeptides/chemical synthesis/*chemistry MH - Protein Binding MH - Protein Structure, Tertiary MH - Spectrometry, Fluorescence MH - Staining and Labeling MH - Tyrosine/analogs & derivatives/chemistry MH - ortho-Aminobenzoates/chemistry OTO - NOTNLM OT - Circular dichroism OT - Helix-loop-helix OT - Id proteins OT - Protein-ligand interaction EDAT- 2014/07/02 06:00 MHDA- 2014/09/13 06:00 CRDT- 2014/07/02 06:00 PHST- 2014/03/04 [received] PHST- 2014/06/09 [revised] PHST- 2014/06/17 [accepted] PHST- 2014/06/27 [aheadofprint] AID - S1570-9639(14)00164-2 [pii] AID - 10.1016/j.bbapap.2014.06.015 [doi] PST - ppublish SO - Biochim Biophys Acta. 2014 Sep;1844(9):1675-83. doi: 10.1016/j.bbapap.2014.06.015. Epub 2014 Jun 27. PMID- 11036070 OWN - NLM STAT- MEDLINE DA - 20010523 DCOM- 20010621 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 5 DP - 2001 Feb 2 TI - The crystal structure of the fab fragment of the monoclonal antibody MAK33. Implications for folding and interaction with the chaperone bip. PG - 3287-94 AB - The Fab fragment of the murine monoclonal antibody, MAK33, directed against human creatine kinase of the muscle-type, was crystallized and the three-dimensional structure was determined to 2.9 A. The antigen-binding surface of MAK33 shows a convex overall shape typical for immunoglobulins binding large antigens. The structure allows us to analyze the environment of cis-prolyl-peptide bonds whose isomerization is of key importance in the folding process. These residues seem to be involved with not only domain stability but also seem to play a role in the association of heavy and light chains, reinforcing the importance of beta-strand recognition in antibody assembly. The structure also allows the localization of segments of primary sequence postulated to represent binding sites for the ER-specific chaperone BiP within the context of the entire Fab fragment. These sequences are found primarily in beta-strands that are necessary for interactions between the individual domains. FAU - Augustine, J G AU - Augustine JG AD - Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - de La Calle, A AU - de La Calle A FAU - Knarr, G AU - Knarr G FAU - Buchner, J AU - Buchner J FAU - Frederick, C A AU - Frederick CA LA - eng SI - PDB/1FH5 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20001017 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Antibodies, Monoclonal) RN - 0 (Carrier Proteins) RN - 0 (Heat-Shock Proteins) RN - 0 (Immunoglobulin Fab Fragments) RN - 0 (Molecular Chaperones) RN - 0 (Peptide Fragments) RN - 0 (molecular chaperone GRP78) RN - EC 2.7.3.2 (Creatine Kinase) SB - IM MH - Animals MH - Antibodies, Monoclonal/*chemistry/immunology MH - Binding Sites MH - Carrier Proteins/*metabolism MH - Creatine Kinase/immunology MH - Crystallography, X-Ray MH - *Heat-Shock Proteins MH - Humans MH - Immunoglobulin Fab Fragments/*chemistry/immunology MH - Mice MH - Molecular Chaperones/*metabolism MH - Peptide Fragments/metabolism MH - Protein Conformation EDAT- 2000/10/19 MHDA- 2001/06/22 10:01 CRDT- 2000/10/19 00:00 PHST- 2000/10/17 [aheadofprint] AID - 10.1074/jbc.M005221200 [doi] AID - M005221200 [pii] PST - ppublish SO - J Biol Chem. 2001 Feb 2;276(5):3287-94. Epub 2000 Oct 17. PMID- 9564029 OWN - NLM STAT- MEDLINE DA - 19980618 DCOM- 19980618 LR - 20140617 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 17 IP - 9 DP - 1998 May 1 TI - Crystal structure of human uroporphyrinogen decarboxylase. PG - 2463-71 AB - Uroporphyrinogen decarboxylase (URO-D) catalyzes the fifth step in the heme biosynthetic pathway, converting uroporphyrinogen to coproporphyrinogen by decarboxylating the four acetate side chains of the substrate. This activity is essential in all organisms, and subnormal activity of URO-D leads to the most common form of porphyria in humans, porphyria cutanea tarda (PCT). We have determined the crystal structure of recombinant human URO-D at 1.60 A resolution. The 40.8 kDa protein is comprised of a single domain containing a (beta/alpha)8-barrel with a deep active site cleft formed by loops at the C-terminal ends of the barrel strands. Many conserved residues cluster at this cleft, including the invariant side chains of Arg37, Arg41 and His339, which probably function in substrate binding, and Asp86, Tyr164 and Ser219, which may function in either binding or catalysis. URO-D is a dimer in solution (Kd = 0.1 microM), and this dimer also appears to be formed in the crystal. Assembly of the dimer juxtaposes the active site clefts of the monomers, suggesting a functionally important interaction between the catalytic centers. FAU - Whitby, F G AU - Whitby FG AD - Department of Biochemistry, University of Utah School of Medicine, 50 N.Medical Drive, Salt Lake City, UT 84132, USA. FAU - Phillips, J D AU - Phillips JD FAU - Kushner, J P AU - Kushner JP FAU - Hill, C P AU - Hill CP LA - eng GR - MO1RR00064/RR/NCRR NIH HHS/United States GR - R01DK20503/DK/NIDDK NIH HHS/United States GR - R01GM856775/GM/NIGMS NIH HHS/United States GR - etc. PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Recombinant Proteins) RN - EC 4.1.1.37 (Uroporphyrinogen Decarboxylase) SB - IM MH - Amino Acid Sequence MH - Animals MH - Bacteria/enzymology MH - Binding Sites MH - Catalysis MH - Crystallography, X-Ray MH - Dimerization MH - Humans MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Molecular Weight MH - Plants/enzymology MH - *Protein Structure, Secondary MH - Rats MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Uroporphyrinogen Decarboxylase/*chemistry/metabolism PMC - PMC1170588 OID - NLM: PMC1170588 EDAT- 1998/06/20 MHDA- 1998/06/20 00:01 CRDT- 1998/06/20 00:00 AID - 10.1093/emboj/17.9.2463 [doi] PST - ppublish SO - EMBO J. 1998 May 1;17(9):2463-71. PMID- 16246365 OWN - NLM STAT- MEDLINE DA - 20051121 DCOM- 20051228 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 354 IP - 3 DP - 2005 Dec 2 TI - Structure, dynamics, and membrane topology of stannin: a mediator of neuronal cell apoptosis induced by trimethyltin chloride. PG - 652-65 AB - Organotin compounds or alkyltins are ubiquitous environmental toxins that have been implicated in cellular death. Unlike other xenobiotic compounds, such as organomercurials and organoleads, alkyltins activate apoptotic cascades at low concentrations. Trimethyltin (TMT) chloride is amongst the most toxic organotin compounds, and is known to selectively inflict injury to specific regions of the brain. Stannin (SNN), an 88-residue mitochondrial membrane protein, has been identified as the specific marker for neuronal cell apoptosis induced by TMT intoxication. This high specificity of TMT makes SNN an ideal model system for understanding the mechanism of organotin neurotoxicity at a molecular level. Here, we report the three-dimensional structure and dynamics of SNN in detergent micelles, and its topological orientation in lipid bilayers as determined by solution and solid-state NMR spectroscopy. We found that SNN is a monotopic membrane protein composed of three domains: a single transmembrane helix (residues 10-33) that transverses the lipid bilayer at approximately a 20 degrees angle with respect to the membrane normal; a 28 residue unstructured linker, which includes a conserved CXC metal-binding motif and a putative 14-3-3zeta binding domain; and a distorted cytoplasmic helix (residues 61-79) that is partially absorbed into the plane of the lipid bilayer with a tilt angle of approximately 80 degrees from the membrane normal. The structure and architecture of SNN within the lipid environment provides insight about how this protein transmits toxic insults caused by TMT across the membrane. FAU - Buck-Koehntop, Bethany A AU - Buck-Koehntop BA AD - Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA. FAU - Mascioni, Alessandro AU - Mascioni A FAU - Buffy, Jarrod J AU - Buffy JJ FAU - Veglia, Gianluigi AU - Veglia G LA - eng SI - PDB/1ZZA GR - GM-08700/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20050930 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amides) RN - 0 (Micelles) RN - 0 (Neuropeptides) RN - 0 (Trimethyltin Compounds) RN - 289-78-1 (stannin) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - 9E3BCA3684 (trimethyltin chloride) SB - IM MH - Amides/chemistry MH - Apoptosis/*drug effects MH - Cell Membrane/chemistry/*metabolism MH - Magnetic Resonance Spectroscopy MH - Micelles MH - Neurons/*cytology/*drug effects/metabolism MH - Neuropeptides/*chemistry/*metabolism MH - Sodium Dodecyl Sulfate MH - Trimethyltin Compounds/*pharmacology EDAT- 2005/10/26 09:00 MHDA- 2005/12/29 09:00 CRDT- 2005/10/26 09:00 PHST- 2005/06/14 [received] PHST- 2005/09/12 [revised] PHST- 2005/09/13 [accepted] PHST- 2005/09/30 [aheadofprint] AID - S0022-2836(05)01104-6 [pii] AID - 10.1016/j.jmb.2005.09.038 [doi] PST - ppublish SO - J Mol Biol. 2005 Dec 2;354(3):652-65. Epub 2005 Sep 30. PMID- 18953106 OWN - NLM STAT- MEDLINE DA - 20081027 DCOM- 20081216 IS - 1387-2877 (Print) IS - 1387-2877 (Linking) VI - 15 IP - 2 DP - 2008 Oct TI - Chaperone-like antibodies targeting misfolded tau protein: new vistas in the immunotherapy of neurodegenerative foldopathies. PG - 169-79 AB - Neurodegenerative foldopathies are characterized by aberrant folding of proteins leading to the intracellular and extracellular accumulation of insoluble misfolded proteins. One of the most prominent protein folding disorders is Alzheimer's disease (AD). In AD, there were identified two major driving forces behind neurodegeneration, misfolded proteins tau and amyloid-beta. Tau belongs to a family of intrinsically disordered proteins that are characterized by the absence of a rigid three-dimensional structure in their natural environment. However, in disease condition, tau truncation and hyperphosphorylation could lead to tau transformation from intrinsically disordered protein into highly ordered soluble and insoluble misfolded structures. Increased understanding of the molecular mechanism underlying pathological transformation of tau protein has opened up the possibility of targeting misfolded tau for therapeutic purposes. Pharmacological research has identified several therapeutic approaches targeting directly or indirectly tau cascade. Novel promising field of AD treatment represent monoclonal antibodies with chaperon like activities that will be able to neutralize the toxic gain of function of misfolded tau and thus increase its degradation. We suggest that chaperon like antibodies targeting disease modified tau may hold promise for the successful treatment of AD and related foldopathies. FAU - Zilka, Norbert AU - Zilka N AD - Institute of Neuroimmunology, Slovak Academy of Sciences, AD Centre, Bratislava, Slovak Republic. FAU - Kontsekova, Eva AU - Kontsekova E FAU - Novak, Michal AU - Novak M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Netherlands TA - J Alzheimers Dis JT - Journal of Alzheimer's disease : JAD JID - 9814863 RN - 0 (Antibodies) RN - 0 (Molecular Chaperones) RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/therapy MH - Animals MH - Antibodies/*immunology/*therapeutic use MH - Humans MH - *Immunotherapy MH - Molecular Chaperones/*immunology MH - Neurodegenerative Diseases/*therapy MH - Protein Folding MH - tau Proteins/*antagonists & inhibitors/genetics/*immunology RF - 100 EDAT- 2008/10/28 09:00 MHDA- 2008/12/17 09:00 CRDT- 2008/10/28 09:00 PST - ppublish SO - J Alzheimers Dis. 2008 Oct;15(2):169-79. PMID- 19467292 OWN - NLM STAT- MEDLINE DA - 20090706 DCOM- 20091013 IS - 1638-6183 (Electronic) IS - 0300-9084 (Linking) VI - 91 IP - 8 DP - 2009 Aug TI - SECIS-binding protein 2, a key player in selenoprotein synthesis, is an intrinsically disordered protein. PG - 1003-9 LID - 10.1016/j.biochi.2009.05.004 [doi] AB - Selenocysteine (Sec) is co-translationally incorporated into selenoproteins at a reprogrammed UGA codon. In mammals, this requires a dedicated machinery comprising a stem-loop structure in the 3' UTR RNA (the SECIS element) and the specific SECIS Binding Protein 2. In this report, disorder-prediction methods and several biophysical techniques showed that ca. 70% of the SBP2 sequence is disordered, whereas the RNA binding domain appears to be folded and functional. These results are consistent with a recent report on the role of the Hsp90 chaperone for the folding of SBP2 and other functionally unrelated proteins bearing an RNA binding domain homologous to SBP2. FAU - Olieric, Vincent AU - Olieric V AD - Architecture et Reactivite de l'ARN, Universite de Strasbourg, CNRS, IBMC, France. FAU - Wolff, Philippe AU - Wolff P FAU - Takeuchi, Akiko AU - Takeuchi A FAU - Bec, Guillaume AU - Bec G FAU - Birck, Catherine AU - Birck C FAU - Vitorino, Marc AU - Vitorino M FAU - Kieffer, Bruno AU - Kieffer B FAU - Beniaminov, Artemy AU - Beniaminov A FAU - Cavigiolio, Giorgio AU - Cavigiolio G FAU - Theil, Elizabeth AU - Theil E FAU - Allmang, Christine AU - Allmang C FAU - Krol, Alain AU - Krol A FAU - Dumas, Philippe AU - Dumas P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090523 PL - France TA - Biochimie JT - Biochimie JID - 1264604 RN - 0 (RNA-Binding Proteins) RN - 0 (Secisbp2 protein, rat) RN - 0 (Selenoproteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Humans MH - Molecular Sequence Data MH - Protein Denaturation MH - RNA-Binding Proteins/*chemistry/*metabolism MH - Rats MH - Selenoproteins/*biosynthesis MH - Sequence Analysis, DNA EDAT- 2009/05/27 09:00 MHDA- 2009/10/14 06:00 CRDT- 2009/05/27 09:00 PHST- 2009/04/02 [received] PHST- 2009/05/12 [accepted] PHST- 2009/05/23 [aheadofprint] AID - S0300-9084(09)00146-1 [pii] AID - 10.1016/j.biochi.2009.05.004 [doi] PST - ppublish SO - Biochimie. 2009 Aug;91(8):1003-9. doi: 10.1016/j.biochi.2009.05.004. Epub 2009 May 23. PMID- 21878629 OWN - NLM STAT- MEDLINE DA - 20111107 DCOM- 20111227 LR - 20141022 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 45 DP - 2011 Nov 11 TI - Outer membrane targeting of secretin PulD protein relies on disordered domain recognition by a dedicated chaperone. PG - 38833-43 LID - 10.1074/jbc.M111.279851 [doi] AB - Interaction of bacterial outer membrane secretin PulD with its dedicated lipoprotein chaperone PulS relies on a disorder-to-order transition of the chaperone binding (S) domain near the PulD C terminus. PulS interacts with purified S domain to form a 1:1 complex. Circular dichroism, one-dimensional NMR, and hydrodynamic measurements indicate that the S domain is elongated and intrinsically disordered but gains secondary structure upon binding to PulS. Limited proteolysis and mass spectrometry identified the 28 C-terminal residues of the S domain as a minimal binding site with low nanomolar affinity for PulS in vitro that is sufficient for outer membrane targeting of PulD in vivo. The region upstream of this binding site is not required for targeting or multimerization and does not interact with PulS, but it is required for secretin function in type II secretion. Although other secretin chaperones differ substantially from PulS in sequence and secondary structure, they have all adopted at least superficially similar mechanisms of interaction with their cognate secretins, suggesting that intrinsically disordered regions facilitate rapid interaction between secretins and their chaperones. FAU - Nickerson, Nicholas N AU - Nickerson NN AD - Institut Pasteur, Molecular Genetics Unit, Microbiology Department, rue du Dr. Roux, 75015 Paris, France. FAU - Tosi, Tommaso AU - Tosi T FAU - Dessen, Andrea AU - Dessen A FAU - Baron, Bruno AU - Baron B FAU - Raynal, Bertrand AU - Raynal B FAU - England, Patrick AU - England P FAU - Pugsley, Anthony P AU - Pugsley AP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110830 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Outer Membrane Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Lipoproteins) RN - 0 (Molecular Chaperones) RN - 0 (PulD protein, E coli) RN - 0 (PulS protein, E coli) SB - IM MH - Bacterial Outer Membrane Proteins/*chemistry/genetics/metabolism MH - Bacterial Secretion Systems/physiology MH - Escherichia coli/*chemistry/genetics/metabolism MH - Escherichia coli Proteins/*chemistry/genetics/metabolism MH - Lipoproteins/chemistry/genetics/metabolism MH - Molecular Chaperones/*chemistry/genetics/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary PMC - PMC3234708 OID - NLM: PMC3234708 EDAT- 2011/09/01 06:00 MHDA- 2011/12/28 06:00 CRDT- 2011/09/01 06:00 PHST- 2011/08/30 [aheadofprint] AID - M111.279851 [pii] AID - 10.1074/jbc.M111.279851 [doi] PST - ppublish SO - J Biol Chem. 2011 Nov 11;286(45):38833-43. doi: 10.1074/jbc.M111.279851. Epub 2011 Aug 30. PMID- 12872120 OWN - NLM STAT- MEDLINE DA - 20030730 DCOM- 20030904 LR - 20081015 IS - 1529-2908 (Print) IS - 1529-2908 (Linking) VI - 4 IP - 8 DP - 2003 Aug TI - Binding of the Drosophila cytokine Spatzle to Toll is direct and establishes signaling. PG - 794-800 AB - The extracellular protein Spatzle is required for activation of the Toll signaling pathway in the embryonic development and innate immune defense of Drosophila. Spatzle is synthesized as a pro-protein and is processed to a functional form by a serine protease. We show here that the mature form of Spatzle triggers a Toll-dependent immune response after injection into the hemolymph of flies. Spatzle specifically bound to Drosophila cells and to Cos-7 cells expressing Toll. Furthermore, in vitro experiments showed that the mature form of Spatzle bound to the Toll ectodomain with high affinity and with a stoichiometry of one Spatzle dimer to two receptors. The Spatzle pro-protein was inactive in all these assays, indicating that the pro-domain sequence, which is natively unstructured, acts to prevent interaction of the cytokine and its receptor Toll. These results show that, in contrast to the human Toll-like receptors, Drosophila Toll requires only an endogenous protein ligand for activation and signaling. FAU - Weber, Alexander N R AU - Weber AN AD - Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom. FAU - Tauszig-Delamasure, Servane AU - Tauszig-Delamasure S FAU - Hoffmann, Jules A AU - Hoffmann JA FAU - Lelievre, Eric AU - Lelievre E FAU - Gascan, Hugues AU - Gascan H FAU - Ray, Keith P AU - Ray KP FAU - Morse, Mary A AU - Morse MA FAU - Imler, Jean-Luc AU - Imler JL FAU - Gay, Nicholas J AU - Gay NJ LA - eng GR - 5P01AI44220-02/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20030720 PL - United States TA - Nat Immunol JT - Nature immunology JID - 100941354 RN - 0 (Drosophila Proteins) RN - 0 (Insect Proteins) RN - 0 (Receptors, Cell Surface) RN - 0 (Tl protein, Drosophila) RN - 0 (Toll-Like Receptors) RN - 0 (spatzle protein, Drosophila) SB - IM CIN - Nat Immunol. 2003 Aug;4(8):723-4. PMID: 12888789 MH - Animals MH - Drosophila/chemistry/immunology/*metabolism MH - Drosophila Proteins/chemistry/*metabolism MH - Insect Proteins/chemistry/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Receptors, Cell Surface/chemistry/*metabolism MH - Signal Transduction/*physiology MH - Toll-Like Receptors EDAT- 2003/07/23 05:00 MHDA- 2003/09/05 05:00 CRDT- 2003/07/23 05:00 PHST- 2003/07/20 [aheadofprint] PHST- 2003/03/31 [received] PHST- 2003/06/23 [accepted] AID - 10.1038/ni955 [doi] AID - ni955 [pii] PST - ppublish SO - Nat Immunol. 2003 Aug;4(8):794-800. Epub 2003 Jul 20. PMID- 9472037 OWN - NLM STAT- MEDLINE DA - 19980316 DCOM- 19980316 LR - 20140617 IS - 0021-9525 (Print) IS - 0021-9525 (Linking) VI - 140 IP - 4 DP - 1998 Feb 23 TI - Titin extensibility in situ: entropic elasticity of permanently folded and permanently unfolded molecular segments. PG - 853-9 AB - Titin (also known as connectin) is a giant protein that spans half of the striated muscle sarcomere. In the I-band titin extends as the sarcomere is stretched, developing what is known as passive force. The I-band region of titin contains tandem Ig segments (consisting of serially linked immunoglobulin-like domains) with the unique PEVK segment in between (Labeit, S., and B. Kolmerer. 1995. Science. 270:293-296). Although the tandem Ig and PEVK segments have been proposed to behave as stiff and compliant springs, respectively, precise experimental testing of the hypothesis is still needed. Here, sequence-specific antibodies were used to mark the ends of the tandem Ig and PEVK segments. By following the extension of the segments as a function of sarcomere length (SL), their respective contributions to titin's elastic behavior were established. In slack sarcomeres (approximately 2.0 micron) the tandem Ig and PEVK segments were contracted. Upon stretching sarcomeres from approximately 2.0 to 2.7 micron, the "contracted" tandem Ig segments straightened while their individual Ig domains remained folded. When sarcomeres were stretched beyond approximately 2.7 micron, the tandem Ig segments did not further extend, instead PEVK extension was now dominant. Modeling tandem Ig and PEVK segments as entropic springs with different bending rigidities (Kellermayer, M., S. Smith, H. Granzier, and C. Bustamante. 1997. Science. 276:1112-1116) indicated that in the physiological SL range (a) the Ig-like domains of the tandem Ig segments remain folded and (b) the PEVK segment behaves as a permanently unfolded polypeptide. Our model provides a molecular basis for the sequential extension of titin's different segments. Initially, the tandem Ig segments extend at low forces due to their high bending rigidity. Subsequently, extension of the PEVK segment occurs only upon reaching sufficiently high external forces due to its low bending rigidity. The serial linking of tandem Ig and PEVK segments with different bending rigidities provides a unique passive force-SL relation that is not achievable with a single elastic segment. FAU - Trombitas, K AU - Trombitas K AD - Department of Veterinary and Comparative Anatomy, Pharmacology, and Physiology, Washington State University, Pullman, Washington 99164-6520, USA. FAU - Greaser, M AU - Greaser M FAU - Labeit, S AU - Labeit S FAU - Jin, J P AU - Jin JP FAU - Kellermayer, M AU - Kellermayer M FAU - Helmes, M AU - Helmes M FAU - Granzier, H AU - Granzier H LA - eng GR - AR-42652/AR/NIAMS NIH HHS/United States GR - HL-47053/HL/NHLBI NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Cell Biol JT - The Journal of cell biology JID - 0375356 RN - 0 (Connectin) RN - 0 (Immunoglobulins) RN - 0 (Muscle Proteins) RN - 0 (TTN protein, human) RN - EC 2.7.- (Protein Kinases) SB - IM MH - Chemistry, Physical MH - Computer Simulation MH - Connectin MH - Elasticity MH - Entropy MH - Humans MH - Immunoglobulins/chemistry MH - Microscopy, Immunoelectron MH - Muscle Fibers, Skeletal/ultrastructure MH - Muscle Proteins/*chemistry/ultrastructure MH - Muscle, Skeletal/cytology MH - Physicochemical Phenomena MH - Protein Conformation MH - Protein Folding MH - Protein Kinases/*chemistry/ultrastructure MH - Repetitive Sequences, Nucleic Acid MH - Sarcomeres/chemistry PMC - PMC2141751 OID - NLM: PMC2141751 EDAT- 1998/03/21 MHDA- 1998/03/21 00:01 CRDT- 1998/03/21 00:00 PST - ppublish SO - J Cell Biol. 1998 Feb 23;140(4):853-9. PMID- 10724160 OWN - NLM STAT- MEDLINE DA - 20000407 DCOM- 20000407 LR - 20061115 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 404 IP - 6774 DP - 2000 Mar 9 TI - Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein. PG - 151-8 AB - The Rho-family GTPase, Cdc42, can regulate the actin cytoskeleton through activation of Wiskott-Aldrich syndrome protein (WASP) family members. Activation relieves an autoinhibitory contact between the GTPase-binding domain and the carboxy-terminal region of WASP proteins. Here we report the autoinhibited structure of the GTPase-binding domain of WASP, which can be induced by the C-terminal region or by organic co-solvents. In the autoinhibited complex, intramolecular interactions with the GTPase-binding domain occlude residues of the C terminus that regulate the Arp2/3 actin-nucleating complex. Binding of Cdc42 to the GTPase-binding domain causes a dramatic conformational change, resulting in disruption of the hydrophobic core and release of the C terminus, enabling its interaction with the actin regulatory machinery. These data show that 'intrinsically unstructured' peptides such as the GTPase-binding domain of WASP can be induced into distinct structural and functional states depending on context. FAU - Kim, A S AU - Kim AS AD - Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA. FAU - Kakalis, L T AU - Kakalis LT FAU - Abdul-Manan, N AU - Abdul-Manan N FAU - Liu, G A AU - Liu GA FAU - Rosen, M K AU - Rosen MK LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Fungal Proteins) RN - 0 (Microfilament Proteins) RN - 0 (Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (VRP1 protein, S cerevisiae) RN - 0 (WAS protein, human) RN - 0 (Wiskott-Aldrich Syndrome Protein) RN - EC 3.6.5.2 (cdc42 GTP-Binding Protein) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Circular Dichroism MH - Cloning, Molecular MH - Fungal Proteins/chemistry MH - Humans MH - Magnetic Resonance Spectroscopy MH - Microfilament Proteins/chemistry MH - Molecular Sequence Data MH - Mutation MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Proteins/antagonists & inhibitors/chemistry/genetics/*metabolism MH - *Saccharomyces cerevisiae Proteins MH - Signal Transduction MH - Thermodynamics MH - *Wiskott-Aldrich Syndrome/genetics/metabolism MH - Wiskott-Aldrich Syndrome Protein MH - cdc42 GTP-Binding Protein/metabolism EDAT- 2000/03/21 09:00 MHDA- 2001/03/23 10:01 CRDT- 2000/03/21 09:00 AID - 10.1038/35004513 [doi] PST - ppublish SO - Nature. 2000 Mar 9;404(6774):151-8. PMID- 23624714 OWN - NLM STAT- MEDLINE DA - 20130527 DCOM- 20131231 LR - 20141116 IS - 1532-298X (Electronic) IS - 1040-4651 (Linking) VI - 25 IP - 4 DP - 2013 Apr TI - BINDING PROTEIN is a master regulator of the endoplasmic reticulum stress sensor/transducer bZIP28 in Arabidopsis. PG - 1416-29 LID - 10.1105/tpc.113.110684 [doi] AB - BINDING PROTEIN (BiP) is a major chaperone in the endoplasmic reticulum (ER) lumen, and this study shows that BiP binds to the C-terminal tail of the stress sensor/transducer bZIP28, a membrane-associated transcription factor, retaining it in the ER under unstressed conditions. In response to ER stress, BiP dissociates from bZIP28, allowing it to be mobilized from the ER to the Golgi where it is proteolytically processed and released to enter the nucleus. Under unstressed conditions, BiP binds to bZIP28 as it binds to other client proteins, through its substrate binding domain. BiP dissociates from bZIP28 even when bZIP28's exit from the ER or its release from the Golgi is blocked. Both BiP1 and BiP3 bind bZIP28, and overexpression of either BiP detains bZIP28 in the ER under stress conditions. A C-terminally truncated mutant of bZIP28 eliminating most of the lumenal domain does not bind BiP and is not retained in the ER under unstressed conditions. BiP binding sites in the C-terminal tail of bZIP28 were identified in a phage display system. BiP was found to bind to intrinsically disordered regions on bZIP28's lumen-facing tail. Thus, the dissociation of BiP from the C-terminal tail of bZIP28 is a major switch that activates one arm of the unfolded protein response signaling pathway in plants. FAU - Srivastava, Renu AU - Srivastava R AD - Plant Sciences Institute, Iowa State University, Ames, Iowa 50011, USA. FAU - Deng, Yan AU - Deng Y FAU - Shah, Shweta AU - Shah S FAU - Rao, Aragula Gururaj AU - Rao AG FAU - Howell, Stephen H AU - Howell SH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130426 PL - United States TA - Plant Cell JT - The Plant cell JID - 9208688 RN - 0 (Arabidopsis Proteins) RN - 0 (Basic-Leucine Zipper Transcription Factors) RN - 0 (BiP1 protein, Arabidopsis) RN - 0 (BiP2 protein, Arabidopsis) RN - 0 (BiP3 protein, Arabidopsis) RN - 0 (Carrier Proteins) RN - 0 (Luminescent Proteins) RN - 0 (Molecular Chaperones) RN - 0 (Protein Isoforms) RN - 0 (bZIP28 protein, Arabidopsis) RN - 139568-85-7 (BIP protein, Arabidopsis) SB - IM MH - Amino Acid Sequence MH - Arabidopsis/genetics/*metabolism MH - Arabidopsis Proteins/genetics/*metabolism MH - Basic-Leucine Zipper Transcription Factors/genetics/*metabolism MH - Carrier Proteins/genetics/*metabolism MH - Endoplasmic Reticulum/metabolism MH - *Endoplasmic Reticulum Stress MH - Golgi Apparatus/metabolism MH - Immunoblotting MH - Luminescent Proteins/genetics/metabolism MH - Microscopy, Confocal MH - Molecular Chaperones/genetics/metabolism MH - Molecular Sequence Data MH - Mutation MH - Plants, Genetically Modified MH - Protein Binding MH - Protein Isoforms/genetics/metabolism MH - Protein Transport MH - Sequence Homology, Amino Acid PMC - PMC3663277 OID - NLM: PMC3663277 EDAT- 2013/04/30 06:00 MHDA- 2014/01/01 06:00 CRDT- 2013/04/30 06:00 PHST- 2013/04/26 [aheadofprint] AID - tpc.113.110684 [pii] AID - 10.1105/tpc.113.110684 [doi] PST - ppublish SO - Plant Cell. 2013 Apr;25(4):1416-29. doi: 10.1105/tpc.113.110684. Epub 2013 Apr 26. PMID- 15047759 OWN - NLM STAT- MEDLINE DA - 20040527 DCOM- 20040831 LR - 20131121 IS - 0022-0957 (Print) IS - 0022-0957 (Linking) VI - 55 IP - 400 DP - 2004 May TI - Emergence of new regulatory mechanisms in the Benson-Calvin pathway via protein-protein interactions: a glyceraldehyde-3-phosphate dehydrogenase/CP12/phosphoribulokinase complex. PG - 1245-54 AB - Protein-protein interactions are involved in many metabolic pathways. This review will focus on the role of such associations in CO2 assimilation (Benson-Calvin cycle) and especially on the involvement of a GAPDH/CP12/PRK complex which has been identified in many photosynthetic organisms and may have an important role in the regulation of CO2 assimilation. The emergence of new kinetic and regulatory properties as a consequence of protein-protein interactions will be addressed as well as some of the questions raised by the existence of these supramolecular complexes such as composition, function, and assembly pathways. The presence and role of small intrinsically unstructured proteins like the 8.5 kDa protein CP12, involved in the regulation and/or assembly of these complexes will be discussed. CI - Copyright 2004 Society for Experimental Biology FAU - Graciet, Emmanuelle AU - Graciet E AD - Laboratoire d'ingenierie des proteines et controle metabolique, Departement Biologie des genomes, Institut Jacques Monod, UMR 7592 CNRS, Universites Paris VI-VII, 2 place Jussieu, F-75251 Paris cedex 05, France. FAU - Lebreton, Sandrine AU - Lebreton S FAU - Gontero, Brigitte AU - Gontero B LA - eng PT - Journal Article PT - Review DEP - 20040326 PL - England TA - J Exp Bot JT - Journal of experimental botany JID - 9882906 RN - 0 (Plant Proteins) RN - 142M471B3J (Carbon Dioxide) RN - EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases) RN - EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)) RN - EC 2.7.1.19 (phosphoribulokinase) RN - EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase) SB - IM MH - Animals MH - Carbon Dioxide/*metabolism MH - Chlamydomonas reinhardtii/metabolism MH - Glyceraldehyde-3-Phosphate Dehydrogenases/*metabolism MH - Kinetics MH - Models, Molecular MH - Oxidation-Reduction MH - Phosphotransferases (Alcohol Group Acceptor)/*metabolism MH - Photosynthesis MH - Plant Proteins/*metabolism MH - Plants/metabolism MH - Protein Interaction Mapping MH - Ribulose-Bisphosphate Carboxylase/metabolism RF - 81 EDAT- 2004/03/30 05:00 MHDA- 2004/09/01 05:00 CRDT- 2004/03/30 05:00 PHST- 2004/03/26 [aheadofprint] AID - 10.1093/jxb/erh107 [doi] AID - erh107 [pii] PST - ppublish SO - J Exp Bot. 2004 May;55(400):1245-54. Epub 2004 Mar 26. PMID- 24713697 OWN - NLM STAT- MEDLINE DA - 20140729 DCOM- 20141028 LR - 20150523 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 289 IP - 21 DP - 2014 May 23 TI - Neurogranin alters the structure and calcium binding properties of calmodulin. PG - 14644-55 LID - 10.1074/jbc.M114.560656 [doi] AB - Neurogranin (Ng) is a member of the IQ motif class of calmodulin (CaM)-binding proteins, and interactions with CaM are its only known biological function. In this report we demonstrate that the binding affinity of Ng for CaM is weakened by Ca(2+) but to a lesser extent (2-3-fold) than that previously suggested from qualitative observations. We also show that Ng induced a >10-fold decrease in the affinity of Ca(2+) binding to the C-terminal domain of CaM with an associated increase in the Ca(2+) dissociation rate. We also discovered a modest, but potentially important, increase in the cooperativity in Ca(2+) binding to the C-lobe of CaM in the presence of Ng, thus sharpening the threshold for the C-domain to become Ca(2+)-saturated. Domain mapping using synthetic peptides indicated that the IQ motif of Ng is a poor mimetic of the intact protein and that the acidic sequence just N-terminal to the IQ motif plays an important role in reproducing Ng-mediated decreases in the Ca(2+) binding affinity of CaM. Using NMR, full-length Ng was shown to make contacts largely with residues in the C-domain of CaM, although contacts were also detected in residues in the N-terminal domain. Together, our results can be consolidated into a model where Ng contacts residues in the N- and C-lobes of both apo- and Ca(2+)-bound CaM and that although Ca(2+) binding weakens Ng interactions with CaM, the most dramatic biochemical effect is the impact of Ng on Ca(2+) binding to the C-terminal lobe of CaM. CI - (c) 2014 by The American Society for Biochemistry and Molecular Biology, Inc. FAU - Hoffman, Laurel AU - Hoffman L AD - From the Departments of Neurobiology and Anatomy and. FAU - Chandrasekar, Anuja AU - Chandrasekar A AD - From the Departments of Neurobiology and Anatomy and. FAU - Wang, Xu AU - Wang X AD - Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, Texas 77030. FAU - Putkey, John A AU - Putkey JA AD - Biochemistry and Molecular Biology, University of Texas Medical School at Houston, Houston, Texas 77030. FAU - Waxham, M Neal AU - Waxham MN AD - From the Departments of Neurobiology and Anatomy and m.n.waxham@uth.tmc.edu. LA - eng GR - GM097553/GM/NIGMS NIH HHS/United States GR - GM104290/GM/NIGMS NIH HHS/United States GR - R01 GM104290/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140408 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Calmodulin) RN - 132654-77-4 (Neurogranin) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Motifs/genetics MH - Amino Acid Sequence MH - Binding Sites/genetics MH - Binding, Competitive MH - Blotting, Western MH - Calcium/chemistry/*metabolism MH - Calmodulin/chemistry/*metabolism MH - Calorimetry/methods MH - Humans MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Neurogranin/chemistry/genetics/*metabolism MH - Protein Binding PMC - PMC4031520 OID - NLM: PMC4031520 OTO - NOTNLM OT - Calcium OT - Calmodulin OT - Cell Signaling OT - Intrinsically Disordered Proteins OT - Isothermal Titration Calorimetry OT - Kinetics OT - Nuclear Magnetic Resonance OT - Protein Structure OT - Protein-Protein Interactions OT - Signal Transduction EDAT- 2014/04/10 06:00 MHDA- 2014/10/29 06:00 CRDT- 2014/04/10 06:00 PHST- 2014/04/08 [aheadofprint] AID - M114.560656 [pii] AID - 10.1074/jbc.M114.560656 [doi] PST - ppublish SO - J Biol Chem. 2014 May 23;289(21):14644-55. doi: 10.1074/jbc.M114.560656. Epub 2014 Apr 8. PMID- 24098788 OWN - NLM STAT- MEDLINE DA - 20131007 DCOM- 20140616 LR - 20141112 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 9 DP - 2013 TI - 2mit, an intronic gene of Drosophila melanogaster timeless2, is involved in behavioral plasticity. PG - e76351 LID - 10.1371/journal.pone.0076351 [doi] AB - BACKGROUND: Intronic genes represent ~6% of the total gene complement in Drosophila melanogaster and ~85% of them encode for proteins. We recently characterized the D. melanogaster timeless2 (tim2) gene, showing its active involvement in chromosomal stability and light synchronization of the adult circadian clock. The protein coding gene named 2mit maps on the 11(th) tim2 intron in the opposite transcriptional orientation. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the molecular and functional characterization of 2mit. The 2mit gene is expressed throughout Drosophila development, localizing mainly in the nervous system during embryogenesis and mostly in the mushroom bodies and ellipsoid body of the central complex in the adult brain. In silico analyses revealed that 2mit encodes a putative leucine-Rich Repeat transmembrane receptor with intrinsically disordered regions, harboring several fully conserved functional interaction motifs in the cytosolic side. Using insertional mutations, tissue-specific over-expression, and down-regulation approaches, it was found that 2mit is implicated in adult short-term memory, assessed by a courtship conditioning assay. In D. melanogaster, tim2 and 2mit do not seem to be functionally related. Bioinformatic analyses identified 2MIT orthologs in 21 Drosophilidae, 4 Lepidoptera and in Apis mellifera. In addition, the tim2-2mit host-nested gene organization was shown to be present in A. mellifera and maintained among Drosophila species. Within the Drosophilidae 2mit-hosting tim2 intron, in silico approaches detected a neuronal specific transcriptional binding site which might have contributed to preserve the specific host-nested gene association across Drosophila species. CONCLUSIONS/SIGNIFICANCE: Taken together, these results indicate that 2mit, a gene mainly expressed in the nervous system, has a role in the behavioral plasticity of the adult Drosophila. The presence of a putative 2mit regulatory enhancer within the 2mit-hosting tim2 intron could be considered an evolutionary constraint potentially involved in maintaining the tim2-2mit host-nested chromosomal architecture during the evolution of Drosophila species. FAU - Baggio, Francesca AU - Baggio F AD - Dipartimento di Biologia, Universita degli Studi di Padova Padova, Italy. FAU - Bozzato, Andrea AU - Bozzato A FAU - Benna, Clara AU - Benna C FAU - Leonardi, Emanuela AU - Leonardi E FAU - Romoli, Ottavia AU - Romoli O FAU - Cognolato, Moira AU - Cognolato M FAU - Tosatto, Silvio C E AU - Tosatto SC FAU - Costa, Rodolfo AU - Costa R FAU - Sandrelli, Federica AU - Sandrelli F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130930 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (2mit protein, Drosophila) RN - 0 (Drosophila Proteins) RN - 0 (Receptors, Cell Surface) RN - 0 (timeless2 protein, Drosophila) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Circadian Rhythm/*genetics/physiology MH - Cluster Analysis MH - Computational Biology MH - Drosophila Proteins/*genetics/metabolism MH - Drosophila melanogaster/*genetics MH - *Evolution, Molecular MH - Gene Components MH - Gene Expression Regulation, Developmental/*genetics MH - Introns/*genetics MH - Memory/physiology MH - Models, Molecular MH - Molecular Sequence Data MH - Nervous System/metabolism MH - Phylogeny MH - Receptors, Cell Surface/*genetics/metabolism MH - Sequence Analysis, DNA MH - Sexual Behavior, Animal/*physiology PMC - PMC3786989 OID - NLM: PMC3786989 EDAT- 2013/10/08 06:00 MHDA- 2014/06/17 06:00 CRDT- 2013/10/08 06:00 PHST- 2013 [ecollection] PHST- 2012/09/28 [received] PHST- 2013/08/27 [accepted] PHST- 2013/09/30 [epublish] AID - 10.1371/journal.pone.0076351 [doi] AID - PONE-D-12-29783 [pii] PST - epublish SO - PLoS One. 2013 Sep 30;8(9):e76351. doi: 10.1371/journal.pone.0076351. eCollection 2013. PMID- 6319628 OWN - NLM STAT- MEDLINE DA - 19840315 DCOM- 19840315 LR - 20131121 IS - 0270-6474 (Print) IS - 0270-6474 (Linking) VI - 4 IP - 1 DP - 1984 Jan TI - DARPP-32, a dopamine- and adenosine 3':5'-monophosphate-regulated phosphoprotein enriched in dopamine-innervated brain regions. II. Purification and characterization of the phosphoprotein from bovine caudate nucleus. PG - 99-110 AB - DARPP-32 is a neuronal phosphoprotein of Mr = 32,000, originally identified in rat brain (Walaas, S.I., D.W. Aswad, and P. Greengard (1983) Nature 301: 69-72). This protein has now been identified in bovine caudate nucleus cytosol and purified 435-fold to apparent homogeneity as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purification procedure involved acid extraction at pH 2, CM-cellulose chromatography, DEAE-cellulose chromatography, hydroxylapatite chromatography, and gel filtration on Ultrogel AcA 44. The purified catalytic subunit of cAMP-dependent protein kinase catalyzed the incorporation of 0.96 mol of phosphate/mol of purified DARPP-32. Phosphorylation occurred exclusively on threonine. The isoelectric point of dephospho-DARPP-32 was 4.7, and that of phospho-DARPP-32 was 4.6. The amino acid composition showed a high content of glutamate/glutamine and proline, and a low content of hydrophobic amino acids. DARPP-32 was found to have a Stokes radius of 34 A and a sedimentation coefficient of 2.05 S, indicating that it exists as an elongated monomer. FAU - Hemmings, H C Jr AU - Hemmings HC Jr FAU - Nairn, A C AU - Nairn AC FAU - Aswad, D W AU - Aswad DW FAU - Greengard, P AU - Greengard P LA - eng GR - GM-02044/GM/NIGMS NIH HHS/United States GR - MH-17387/MH/NIMH NIH HHS/United States GR - NS-08440/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Neurosci JT - The Journal of neuroscience : the official journal of the Society for Neuroscience JID - 8102140 RN - 0 (Amino Acids) RN - 0 (Dopamine and cAMP-Regulated Phosphoprotein 32) RN - 0 (Nerve Tissue Proteins) RN - 0 (Phosphoproteins) RN - E0399OZS9N (Cyclic AMP) RN - VTD58H1Z2X (Dopamine) SB - IM MH - Amino Acids/analysis MH - Animals MH - Cattle MH - Caudate Nucleus/drug effects/*metabolism MH - Cyclic AMP/*physiology MH - Dopamine/*physiology MH - Dopamine and cAMP-Regulated Phosphoprotein 32 MH - Electrophoresis, Polyacrylamide Gel MH - Isoelectric Focusing MH - Molecular Weight MH - Nerve Tissue Proteins/*isolation & purification/metabolism MH - Phosphoproteins/*isolation & purification/metabolism MH - Phosphorylation MH - Protein Conformation EDAT- 1984/01/01 MHDA- 2001/03/28 10:01 CRDT- 1984/01/01 00:00 PST - ppublish SO - J Neurosci. 1984 Jan;4(1):99-110. PMID- 24374342 OWN - NLM STAT- MEDLINE DA - 20140127 DCOM- 20140327 IS - 1873-3468 (Electronic) IS - 0014-5793 (Linking) VI - 588 IP - 3 DP - 2014 Jan 31 TI - The N-terminus of alpha-synuclein is essential for both monomeric and oligomeric interactions with membranes. PG - 497-502 LID - 10.1016/j.febslet.2013.12.015 [doi] LID - S0014-5793(13)00923-X [pii] AB - The intrinsically disordered protein alpha-synuclein (alphaSN) is linked to Parkinson's Disease and forms both oligomeric species and amyloid fibrils. The N-terminal part of monomeric alphaSN interacts strongly with membranes and alphaSN cytotoxicity has been attributed to oligomers' ability to interact with and perturb membranes. We show that membrane folding of monomeric wt alphaSN and N-terminally truncated variants correlates with membrane permeabilization. Further, the first 11 N-terminal residues are crucial for monomers' and oligomers' interactions with and permeabilization of membranes. We attribute oligomer permeabilization both to cooperative electrostatic interactions through the N-terminus and interactions mediated by hydrophobic regions in the oligomer. CI - Copyright (c) 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. FAU - Lorenzen, Nikolai AU - Lorenzen N AD - Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark. FAU - Lemminger, Lasse AU - Lemminger L AD - Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark. FAU - Pedersen, Jannik Nedergaard AU - Pedersen JN AD - Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark. FAU - Nielsen, Soren Bang AU - Nielsen SB AD - Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark. FAU - Otzen, Daniel Erik AU - Otzen DE AD - Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark. Electronic address: dao@inano.au.dk. LA - eng PT - Journal Article DEP - 20131225 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Amyloid) RN - 0 (alpha-Synuclein) SB - IM MH - Amyloid/*chemistry/metabolism/ultrastructure MH - Cell Membrane Permeability/genetics MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Membranes/chemistry/ultrastructure MH - Parkinson Disease/etiology/*metabolism/pathology MH - Protein Multimerization MH - Protein Structure, Quaternary MH - Static Electricity MH - alpha-Synuclein/*chemistry/metabolism OTO - NOTNLM OT - 1-anilinonaphthalene-8-sulfonate OT - A4F OT - ANS OT - CD OT - DLS OT - Membrane folding OT - Membrane interaction OT - Oligomer OT - PD OT - Parkinson's Disease OT - Permeabilization OT - SDS OT - SEC OT - ThT OT - Toxicity OT - asymmetrical flow field-flow fractionation OT - circular dichroism OT - dynamic light scattering OT - size exclusion chromatography OT - sodium dodecyl sulfate OT - thioflavin T OT - alpha-synuclein OT - alphaSN EDAT- 2014/01/01 06:00 MHDA- 2014/03/29 06:00 CRDT- 2013/12/31 06:00 PHST- 2013/10/22 [received] PHST- 2013/12/04 [revised] PHST- 2013/12/13 [accepted] PHST- 2013/12/25 [aheadofprint] AID - S0014-5793(13)00923-X [pii] AID - 10.1016/j.febslet.2013.12.015 [doi] PST - ppublish SO - FEBS Lett. 2014 Jan 31;588(3):497-502. doi: 10.1016/j.febslet.2013.12.015. Epub 2013 Dec 25. PMID- 15107424 OWN - NLM STAT- MEDLINE DA - 20040712 DCOM- 20040817 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 29 DP - 2004 Jul 16 TI - An androgen receptor NH2-terminal conserved motif interacts with the COOH terminus of the Hsp70-interacting protein (CHIP). PG - 30643-53 AB - The NH2-terminal sequence of steroid receptors is highly variable between different receptors and in the same receptor from different species. In this study, a primary sequence homology comparison identified a 14-amino acid NH2-terminal motif of the human androgen receptor (AR) that is common to AR from all species reported, including the lower vertebrates. The evolutionarily conserved motif is unique to AR, with the exception of a partial sequence in the glucocorticoid receptor of higher species. The presence of the conserved motif in AR and the glucocorticoid receptor and its absence in other steroid receptors suggests convergent evolution. The function of the AR NH2-terminal conserved motif was suggested from a yeast two-hybrid screen that identified the COOH terminus of the Hsp70-interacting protein (CHIP) as a binding partner. We found that CHIP functions as a negative regulator of AR transcriptional activity by promoting AR degradation. In support of this, two mutations in the AR NH2-terminal conserved motif previously identified in the transgenic adenocarcinoma of mouse prostate model reduced the interaction between CHIP and AR. Our results suggest that the AR NH2-terminal domain contains an evolutionarily conserved motif that functions to limit AR transcriptional activity. Moreover, we demonstrate that the combination of comparative sequence alignment and yeast two-hybrid screening using short conserved peptides as bait provides an effective strategy to probe the structure-function relationships of steroid receptor NH2-terminal domains and other intrinsically unstructured transcriptional regulatory proteins. FAU - He, Bin AU - He B AD - Laboratories for Reproductive Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA. FAU - Bai, Suxia AU - Bai S FAU - Hnat, Andrew T AU - Hnat AT FAU - Kalman, Rebecca I AU - Kalman RI FAU - Minges, John T AU - Minges JT FAU - Patterson, Cam AU - Patterson C FAU - Wilson, Elizabeth M AU - Wilson EM LA - eng GR - HD16910/HD/NICHD NIH HHS/United States GR - P01-CA77739/CA/NCI NIH HHS/United States GR - R30TW001234/TW/FIC NIH HHS/United States GR - U54-HD35041/HD/NICHD NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20040423 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (HSP90 Heat-Shock Proteins) RN - 0 (Receptors, Androgen) RN - EC 2.5.1.18 (Glutathione Transferase) RN - EC 6.3.2.19 (STUB1 protein, human) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - COS Cells MH - Cell Line, Tumor MH - Cytoplasm/metabolism MH - Evolution, Molecular MH - Glutathione Transferase/metabolism MH - HSP90 Heat-Shock Proteins/chemistry MH - HeLa Cells MH - Humans MH - Immunoblotting MH - Immunohistochemistry MH - Male MH - Mice MH - Microscopy, Fluorescence MH - Models, Biological MH - Molecular Sequence Data MH - Mutation MH - Plasmids/metabolism MH - Prostate/metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Receptors, Androgen/*chemistry MH - Sequence Homology, Amino Acid MH - Structure-Activity Relationship MH - Transcription, Genetic MH - Transfection MH - Transgenes MH - Two-Hybrid System Techniques MH - Ubiquitin-Protein Ligases/*chemistry EDAT- 2004/04/27 05:00 MHDA- 2004/08/18 05:00 CRDT- 2004/04/27 05:00 PHST- 2004/04/23 [aheadofprint] AID - 10.1074/jbc.M403117200 [doi] AID - M403117200 [pii] PST - ppublish SO - J Biol Chem. 2004 Jul 16;279(29):30643-53. Epub 2004 Apr 23. PMID- 15902263 OWN - NLM STAT- MEDLINE DA - 20050519 DCOM- 20050607 LR - 20140911 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 435 IP - 7040 DP - 2005 May 19 TI - Structure of the zinc-binding domain of an essential component of the hepatitis C virus replicase. PG - 374-9 AB - Hepatitis C virus (HCV) is a human pathogen affecting nearly 3% of the world's population. Chronic infections can lead to cirrhosis and liver cancer. The RNA replication machine of HCV is a multi-subunit membrane-associated complex. The non-structural protein NS5A is an active component of HCV replicase, as well as a pivotal regulator of replication and a modulator of cellular processes ranging from innate immunity to dysregulated cell growth. NS5A is a large phosphoprotein (56-58 kDa) with an amphipathic alpha-helix at its amino terminus that promotes membrane association. After this helix region, NS5A is organized into three domains. The N-terminal domain (domain I) coordinates a single zinc atom per protein molecule. Mutations disrupting either the membrane anchor or zinc binding of NS5A are lethal for RNA replication. However, probing the role of NS5A in replication has been hampered by a lack of structural information about this multifunctional protein. Here we report the structure of NS5A domain I at 2.5-A resolution, which contains a novel fold, a new zinc-coordination motif and a disulphide bond. We use molecular surface analysis to suggest the location of protein-, RNA- and membrane-interaction sites. FAU - Tellinghuisen, Timothy L AU - Tellinghuisen TL AD - Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, 1230 York Avenue Box 64, New York, New York 10021, USA. FAU - Marcotrigiano, Joseph AU - Marcotrigiano J FAU - Rice, Charles M AU - Rice CM LA - eng SI - PDB/1ZH1 GR - R01 CA057973/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Disulfides) RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Viral Nonstructural Proteins) RN - EC 2.7.7.48 (RNA Replicase) RN - J41CSQ7QDS (Zinc) SB - IM MH - Amino Acid Motifs MH - Binding Sites MH - Crystallography, X-Ray MH - Dimerization MH - Disulfides/chemistry/metabolism MH - Hepacivirus/*enzymology/genetics MH - Models, Molecular MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - RNA Replicase/*chemistry/metabolism MH - Viral Nonstructural Proteins/*chemistry/genetics/*metabolism MH - Zinc/*metabolism PMC - PMC1440517 MID - NIHMS4378 OID - NLM: NIHMS4378 OID - NLM: PMC1440517 EDAT- 2005/05/20 09:00 MHDA- 2005/06/09 09:00 CRDT- 2005/05/20 09:00 PHST- 2005/01/24 [received] PHST- 2005/04/01 [accepted] AID - nature03580 [pii] AID - 10.1038/nature03580 [doi] PST - ppublish SO - Nature. 2005 May 19;435(7040):374-9. PMID- 15327958 OWN - NLM STAT- MEDLINE DA - 20040825 DCOM- 20041007 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 342 IP - 2 DP - 2004 Sep 10 TI - Solution structure of subunit F(6) from the peripheral stalk region of ATP synthase from bovine heart mitochondria. PG - 593-603 AB - The ATP synthase enzyme structure includes two stalk assemblies, the central stalk and the peripheral stalk. Catalysis involves rotation of the central stalk assembly together with the membrane-embedded ring of c-subunits driven by the trans-membrane proton-motive force, while the alpha and beta-subunits of F(1) are prevented from co-rotating by their attachment to the peripheral stalk. In the absence of structures of either the intact peripheral stalk or larger complexes containing it, we are studying its individual components and their interactions to build up an overall picture of its structure. Here, we describe an NMR structural characterisation of F(6), which is a 76-residue protein located in the peripheral stalk of the bovine ATP synthase and is essential for coupling between the proton-motive force and catalysis. Isolated F(6) has a highly flexible structure comprising two helices packed together through a loose hydrophobic core and connected by an unstructured linker. Analysis of chemical shifts, (15)N relaxation and RDC measurements confirm that the F(6) structure is flexible on a wide range of timescales ranging from nanoseconds to seconds. The relationship between this structure for isolated F(6) and its role in the intact peripheral stalk is discussed. FAU - Carbajo, Rodrigo J AU - Carbajo RJ AD - MRC Dunn Human Nutrition Unit, Hills Road, Cambridge CB2 2XY, UK. FAU - Silvester, Jocelyn A AU - Silvester JA FAU - Runswick, Michael J AU - Runswick MJ FAU - Walker, John E AU - Walker JE FAU - Neuhaus, David AU - Neuhaus D LA - eng SI - PDB/1VZS PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - EC 3.6.1.- (ATP synthase subunit 6) RN - EC 3.6.3.- (Mitochondrial Proton-Translocating ATPases) SB - IM MH - Animals MH - Cattle MH - Magnetic Resonance Spectroscopy MH - Mitochondria/*chemistry/enzymology MH - Mitochondrial Proton-Translocating ATPases/*chemistry MH - Myocardium/*chemistry/enzymology MH - Protein Structure, Tertiary EDAT- 2004/08/26 05:00 MHDA- 2004/10/08 09:00 CRDT- 2004/08/26 05:00 PHST- 2004/06/04 [received] PHST- 2004/07/12 [revised] PHST- 2004/07/12 [accepted] AID - 10.1016/j.jmb.2004.07.013 [doi] AID - S0022-2836(04)00823-X [pii] PST - ppublish SO - J Mol Biol. 2004 Sep 10;342(2):593-603. PMID- 22821534 OWN - NLM STAT- MEDLINE DA - 20120723 DCOM- 20121123 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 896 DP - 2012 TI - The effect of counter ions on the conformation of intrinsically disordered proteins studied by size-exclusion chromatography. PG - 319-30 LID - 10.1007/978-1-4614-3704-8_21 [doi] AB - Counter ions are able to change the conformation of intrinsically disordered proteins (IDPs) to a more compact structure via the reduction of electrostatic repulsion. When the extended IDP conformation is transformed into a more ordered one, the value of the Stokes radius should decrease. Size-exclusion chromatography is a simple method for the determination of the Stokes radius, which describes the hydrodynamic properties of protein molecules. In our paper size-exclusion chromatography experiments of Starmaker (a highly acidic IDP), in the presence of various counter ions, are presented as an example of a simple experimental method, which provides valuable information about subtle counter ions-induced conformational changes in IDP. FAU - Wojtas, Magdalena AU - Wojtas M AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland. FAU - Kaplon, Tomasz M AU - Kaplon TM FAU - Dobryszycki, Piotr AU - Dobryszycki P FAU - Ozyhar, Andrzej AU - Ozyhar A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (Ions) RN - 0 (Zebrafish Proteins) RN - 0 (starmaker protein, zebrafish) SB - IM MH - Calibration MH - Chromatography, Gel/*methods MH - Hydrodynamics MH - Ions/pharmacology MH - Protein Conformation/drug effects MH - Zebrafish Proteins/*chemistry EDAT- 2012/07/24 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/07/24 06:00 AID - 10.1007/978-1-4614-3704-8_21 [doi] PST - ppublish SO - Methods Mol Biol. 2012;896:319-30. doi: 10.1007/978-1-4614-3704-8_21. PMID- 23876315 OWN - NLM STAT- MEDLINE DA - 20130816 DCOM- 20131104 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 438 IP - 1 DP - 2013 Aug 16 TI - NMR binding and crystal structure reveal that intrinsically-unstructured regulatory domain auto-inhibits PAK4 by a mechanism different from that of PAK1. PG - 169-74 LID - 10.1016/j.bbrc.2013.07.047 [doi] LID - S0006-291X(13)01198-4 [pii] AB - Six human PAK members are classified into groups I (PAKs 1-3) and II (PAK4-6). Previously, only group I PAKs were thought to be auto-inhibited but very recently PAK4, the prototype of group II PAKs, has also been shown to be auto-inhibited by its N-terminal regulatory domain. However, the complete auto-inhibitory domain (AID) sequence remains undefined and the mechanism underlying its auto-inhibition is largely elusive. Here, the N-terminal regulatory domain of PAK4 sufficient for auto-inhibiting and binding Cdc42/Rac was characterized to be intrinsically unstructured, but nevertheless we identified the entire AID sequence by NMR. Strikingly, an AID peptide was derived by deleting the binding-unnecessary residues, which has a Kd of 320 nM to the PAK4 catalytic domain. Consequently, the PAK4 crystal structure complexed with the entire AID has been determined, which reveals that the complete kinase cleft is occupied by 20 AID residuescomposed of an N-terminal alpha-helix and a previously-identified pseudosubstrate motif, thus achieving auto-inhibition. Our study reveals that PAK4 is auto-inhibited by a novel mechanism which is completely different from that for PAK1, thus bearing critical implications for design of inhibitors specific for group II PAKs. CI - Copyright (c) 2013 Elsevier Inc. All rights reserved. FAU - Wang, Wei AU - Wang W AD - Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore. FAU - Lim, Liangzhong AU - Lim L FAU - Baskaran, Yohendran AU - Baskaran Y FAU - Manser, Ed AU - Manser E FAU - Song, Jianxing AU - Song J LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130720 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Enzyme Inhibitors) RN - 0 (Protein Kinase Inhibitors) RN - EC 2.7.1.11 (PAK4 protein, human) RN - EC 2.7.11.1 (p21-Activated Kinases) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography/methods MH - Enzyme Inhibitors MH - Magnetic Resonance Spectroscopy/methods MH - Molecular Sequence Data MH - Protein Binding MH - Protein Conformation MH - Protein Kinase Inhibitors/*chemistry MH - p21-Activated Kinases/*chemistry/*ultrastructure OTO - NOTNLM OT - Auto-inhibition OT - Intrinsically unstructured protein (IUP) OT - Isothermal titration calorimetry (ITC) OT - NMR spectroscopy OT - X-ray crystallography OT - p21-activated kinases (PAKs) EDAT- 2013/07/24 06:00 MHDA- 2013/11/05 06:00 CRDT- 2013/07/24 06:00 PHST- 2013/07/11 [received] PHST- 2013/07/12 [accepted] PHST- 2013/07/20 [aheadofprint] AID - S0006-291X(13)01198-4 [pii] AID - 10.1016/j.bbrc.2013.07.047 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2013 Aug 16;438(1):169-74. doi: 10.1016/j.bbrc.2013.07.047. Epub 2013 Jul 20. PMID- 23110718 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20130108 DCOM- 20130109 LR - 20130314 IS - 1478-811X (Electronic) IS - 1478-811X (Linking) VI - 10 IP - 1 DP - 2012 TI - What's in a loop? PG - 31 LID - 10.1186/1478-811X-10-31 [doi] AB - DNAs and proteins are major classes of biomolecules that differ in many aspects. However, a considerable number of their members also share a common architectural feature that enables the assembly of multi-protein complexes and thereby permits the effective processing of signals: loop structures of substantial sizes. Here we briefly review a few representative examples and suggest a functional classification of different types of loop structures. In proteins, these loops occur in protein regions classified as intrinsically disordered. Studying such loops, their binders and their interactions with other loops should reveal much about cellular information computation and signaling network architectures. It is also expected to provide critical information for synthetic biologists and bioengineers. FAU - Feller, Stephan M AU - Feller SM AD - Biological Systems Architecture Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK. stephan.feller@imm.ox.ac.uk. FAU - Lewitzky, Marc AU - Lewitzky M LA - eng PT - Editorial DEP - 20121030 PL - England TA - Cell Commun Signal JT - Cell communication and signaling : CCS JID - 101170464 PMC - PMC3538565 OID - NLM: PMC3538565 EDAT- 2012/11/01 06:00 MHDA- 2012/11/01 06:01 CRDT- 2012/11/01 06:00 PHST- 2012/07/27 [received] PHST- 2012/09/24 [accepted] PHST- 2012/10/30 [aheadofprint] AID - 1478-811X-10-31 [pii] AID - 10.1186/1478-811X-10-31 [doi] PST - epublish SO - Cell Commun Signal. 2012 Oct 30;10(1):31. doi: 10.1186/1478-811X-10-31. PMID- 22760321 OWN - NLM STAT- MEDLINE DA - 20120704 DCOM- 20121024 LR - 20150325 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 895 DP - 2012 TI - 5-fluoro-D,L-tryptophan as a dual NMR and fluorescent probe of alpha-synuclein. PG - 197-209 LID - 10.1007/978-1-61779-927-3_14 [doi] AB - Analysis of conventional proton nuclear magnetic resonance (NMR) experiments on intrinsically disordered proteins (IDPs) is challenging because of the highly flexible and multiple rapidly exchanging conformations typifying this class of proteins. One method to circumvent some of these difficulties is to incorporate nonnative fluorine ((19)F) nuclei at specific sites within the polypeptide. (19)F NMR is particularly suitable for characterization of unfolded structures because (19)F chemical shifts are highly sensitive to local environments and conformations. Furthermore, the incorporation of fluorine analogs of fluorescent amino acids such as 5-fluoro-D: ,L: -tryptophan (5FW) allows for complementary studies of protein microenvironment via fluorescence spectroscopy. Herein, we describe methods to produce, purify, characterize, and perform steady-state fluorescence and 1D NMR experiments on 5FW analogs of the IDP alpha-synuclein. FAU - Pfefferkorn, Candace M AU - Pfefferkorn CM AD - Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA. FAU - Lee, Jennifer C AU - Lee JC LA - eng GR - ZIA HL001055-06/Intramural NIH HHS/United States PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (Fluorescent Dyes) RN - 0 (alpha-Synuclein) RN - 343-91-9 (5-fluorotryptophan) RN - 8DUH1N11BX (Tryptophan) SB - IM MH - Chromatography, Ion Exchange MH - Electrophoresis, Polyacrylamide Gel MH - Escherichia coli MH - Fluorescent Dyes/*chemistry MH - Humans MH - Isotope Labeling MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Spectrometry, Mass, Electrospray Ionization MH - Tryptophan/*analogs & derivatives/chemistry MH - alpha-Synuclein/biosynthesis/*chemistry/isolation & purification PMC - PMC3515851 MID - NIHMS424233 OID - NLM: NIHMS424233 OID - NLM: PMC3515851 EDAT- 2012/07/05 06:00 MHDA- 2012/10/25 06:00 CRDT- 2012/07/05 06:00 AID - 10.1007/978-1-61779-927-3_14 [doi] PST - ppublish SO - Methods Mol Biol. 2012;895:197-209. doi: 10.1007/978-1-61779-927-3_14. PMID- 2406906 OWN - NLM STAT- MEDLINE DA - 19900326 DCOM- 19900326 LR - 20071114 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 247 IP - 4945 DP - 1990 Feb 23 TI - Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins. PG - 939-45 AB - Ras proteins participate as a molecular switch in the early steps of the signal transduction pathway that is associated with cell growth and differentiation. When the protein is in its GTP complexed form it is active in signal transduction, whereas it is inactive in its GDP complexed form. A comparison of eight three-dimensional structures of ras proteins in four different crystal lattices, five with a nonhydrolyzable GTP analog and three with GDP, reveals that the "on" and "off" states of the switch are distinguished by conformational differences that span a length of more than 40 A, and are induced by the gamma-phosphate. The most significant differences are localized in two regions: residues 30 to 38 (the switch I region) in the second loop and residues 60 to 76 (the switch II region) consisting of the fourth loop and the short alpha-helix that follows the loop. Both regions are highly exposed and form a continuous strip on the molecular surface most likely to be the recognition sites for the effector and receptor molecule(or molecules). The conformational differences also provide a structural basis for understanding the biological and biochemical changes of the proteins due to oncogenic mutations, autophosphorylation, and GTP hydrolysis, and for understanding the interactions with other proteins. FAU - Milburn, M V AU - Milburn MV AD - Department of Chemistry, University of California, Berkeley. FAU - Tong, L AU - Tong L FAU - deVos, A M AU - deVos AM FAU - Brunger, A AU - Brunger A FAU - Yamaizumi, Z AU - Yamaizumi Z FAU - Nishimura, S AU - Nishimura S FAU - Kim, S H AU - Kim SH LA - eng GR - CA45593/CA/NCI NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Proto-Oncogene Proteins) RN - 146-91-8 (Guanosine Diphosphate) RN - 86-01-1 (Guanosine Triphosphate) RN - EC 3.6.5.2 (HRAS protein, human) RN - EC 3.6.5.2 (Proto-Oncogene Proteins p21(ras)) SB - IM MH - Binding Sites MH - Crystallization MH - Crystallography MH - Guanosine Diphosphate/metabolism MH - Guanosine Triphosphate/metabolism MH - Humans MH - Models, Molecular MH - Molecular Structure MH - Protein Conformation MH - Proto-Oncogene Proteins/*metabolism MH - Proto-Oncogene Proteins p21(ras) MH - *Signal Transduction MH - Structure-Activity Relationship EDAT- 1990/02/23 MHDA- 1990/02/23 00:01 CRDT- 1990/02/23 00:00 PST - ppublish SO - Science. 1990 Feb 23;247(4945):939-45. PMID- 25200810 OWN - NLM STAT- In-Process DA - 20141122 IS - 1432-1327 (Electronic) IS - 0949-8257 (Linking) VI - 19 IP - 8 DP - 2014 Dec TI - The conformational response to Zn(II) and Ni(II) binding of Sporosarcina pasteurii UreG, an intrinsically disordered GTPase. PG - 1341-54 LID - 10.1007/s00775-014-1191-9 [doi] AB - Urease is an essential Ni(II) enzyme involved in the nitrogen metabolism of bacteria, plants and fungi. Ni(II) delivery into the enzyme active site requires the presence of four accessory proteins, named UreD, UreF, UreG and UreE, acting through a complex protein network regulated by metal binding and GTP hydrolysis. The GTPase activity is catalyzed by UreG, which couples this function to a non-enzymatic role as a molecular chaperone. This moonlighting activity is reflected in a flexible fold that makes UreG the first discovered intrinsically disordered enzyme. UreG binds Ni(II) and Zn(II),which in turn modulate the interactions with other urease chaperones. The aim of this study is to understand the structural implications of metal binding to Sporosarcina pasteurii UreG (SpUreG). A combination of light scattering, calorimetry, mass spectrometry, and NMR spectroscopy revealed that SpUreG exists in monomer-dimer equilibrium (K(d)= 45 microM), sampling three distinct folding populations with different degrees of compactness. Binding of Zn(II) ions, occurring in two distinct sites (K(d1) = 3 nM, K(d2) = 0.53 microM), shifts the protein conformational landscape toward the more compact population, while maintaining the overall protein structural plasticity. Differently, binding of Ni(II) ions occurs in three binding sites (K(d1(= 14 microM; K(d2) = 270 microM; K(d3)= 160 microM), with much weaker influence on the protein conformational equilibrium. These distinct conformational responses of SpUreG to Ni(II) and Zn(II) binding suggest that selective metal binding modulates protein plasticity, possibly having an impact on the protein-protein interactions and the enzymatic activity of UreG. FAU - D'Urzo, Annalisa AU - D'Urzo A AD - Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy. FAU - Santambrogio, Carlo AU - Santambrogio C FAU - Grandori, Rita AU - Grandori R FAU - Ciurli, Stefano AU - Ciurli S FAU - Zambelli, Barbara AU - Zambelli B LA - eng PT - Journal Article DEP - 20140909 PL - Germany TA - J Biol Inorg Chem JT - Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry JID - 9616326 SB - IM EDAT- 2014/09/10 06:00 MHDA- 2014/09/10 06:00 CRDT- 2014/09/10 06:00 PHST- 2014/07/09 [received] PHST- 2014/08/25 [accepted] PHST- 2014/09/09 [aheadofprint] AID - 10.1007/s00775-014-1191-9 [doi] PST - ppublish SO - J Biol Inorg Chem. 2014 Dec;19(8):1341-54. doi: 10.1007/s00775-014-1191-9. Epub 2014 Sep 9. PMID- 17102635 OWN - NLM STAT- MEDLINE DA - 20070702 DCOM- 20070711 LR - 20131121 IS - 1551-4005 (Electronic) IS - 1551-4005 (Linking) VI - 5 IP - 21 DP - 2006 Nov 1 TI - Phospho-dependent protein recognition motifs contained in C/EBP family of transcription factors: in silico studies. PG - 2501-8 AB - CCAAT/enhancer-binding proteins (C/EBPs) are transcriptional regulators implicated in cell proliferation, differentiation, survival, and tumorigenesis. Their biological activities require interactions with several protein partners. This report presents insights from in silico analysis aimed at identifying phosphorylation-dependent protein recognition motifs in C/EBPs. (1) All C/EBP variants contain intrinsically disordered Ser/Thr- and Pro-rich segments with potential docking sites for WW and Polo-box domains of prolyl isomerase Pin1 and Polo-like kinases (Plks), respectively. (2) Consensus phosphorylation sequences for Plks are located in a highly conserved region of transactivation domains, suggesting that Plks might modulate transcriptional activities of C/EBPs in a cell cycle-dependent manner. (3) Phosphorylation at these positions, as well as at conserved Ser in the extended basic region, would create phosphoserine-containing motifs (pSXXF/Y/I/L), which could be recognized by BRCT repeats containing proteins such as the PAX-transactivation-domain-interacting protein (PTIP), and the breast cancer-associated protein (BRCA1). Proteins containing BRCT domains serve as scaffolds, mediating protein-protein interactions and formation of functional multiprotein complexes involved in DNA repair and cell cycle control. These findings add a new perspective to studies aimed at elucidation of molecular mechanisms underlying the diverse functions of C/EBPs. FAU - Miller, Maria AU - Miller M AD - Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Maryland 21702-1201, USA. millerm@ncifcrf.gov LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20060920 PL - United States TA - Cell Cycle JT - Cell cycle (Georgetown, Tex.) JID - 101137841 RN - 0 (CCAAT-Enhancer-Binding Proteins) RN - 0 (NIMA-interacting peptidylprolyl isomerase) RN - 0 (Transcription Factors) RN - 452VLY9402 (Serine) RN - EC 5.2.1.8 (Peptidylprolyl Isomerase) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - CCAAT-Enhancer-Binding Proteins/metabolism/*physiology MH - Cell Line, Tumor MH - Gene Expression Regulation, Neoplastic MH - Humans MH - Models, Biological MH - Molecular Sequence Data MH - Peptidylprolyl Isomerase/metabolism MH - Phosphorylation MH - Protein Folding MH - Sequence Homology, Amino Acid MH - Serine/chemistry MH - Transcription Factors/*metabolism EDAT- 2006/11/15 09:00 MHDA- 2007/07/12 09:00 CRDT- 2006/11/15 09:00 PHST- 2006/09/20 [aheadofprint] AID - 3421 [pii] PST - ppublish SO - Cell Cycle. 2006 Nov 1;5(21):2501-8. Epub 2006 Sep 20. PMID- 24031640 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20130913 DCOM- 20130913 LR - 20130918 IS - 1517-8382 (Print) IS - 1517-8382 (Linking) VI - 42 IP - 1 DP - 2011 Jan TI - Structural analysis of human respiratory syncytial virus p protein: identification of intrinsically disordered domains. PG - 340-5 LID - 10.1590/S1517-83822011000100043 [doi] AB - Human Respiratory Syncytial Virus P protein plus the viral RNA, N and L viral proteins, constitute the viral replication complex. In this report we describe that HRSV P protein has putative intrinsically disordered domains predicted by in silico methods. These two domains, located at the amino and caboxi terminus, were identified by mass spectrometry analysis of peptides obtained from degradation fragments observed in purified P protein expressed in bacteria. The degradation is not occurring at the central oligomerization domain, since we also demonstrate that the purified fragments are able to oligomerize, similarly to the protein expressed in cells infected by HRSV. Disordered domains can play a role in protein interaction, and the present data contribute to the comprehension of HRSV P protein interactions in the viral replication complex. FAU - Simabuco, Fernando M AU - Simabuco FM AD - Departamento de Microbiologia, Instituto de Ciencias Biomedicas, Universidade de Sao Paulo , Sao Paulo, SP , Brasil . FAU - Asara, John M AU - Asara JM FAU - Guerrero, Manuel C AU - Guerrero MC FAU - Libermann, Towia A AU - Libermann TA FAU - Zerbini, Luiz F AU - Zerbini LF FAU - Ventura, Armando M AU - Ventura AM LA - eng PT - Journal Article PL - Brazil TA - Braz J Microbiol JT - Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] JID - 101095924 PMC - PMC3768923 OID - NLM: PMC3768923 OTO - NOTNLM OT - Human respiratory syncytial virus OT - P protein OT - intrinsically disordered domains OT - oligomerization EDAT- 2011/01/01 00:00 MHDA- 2011/01/01 00:01 CRDT- 2013/09/14 06:00 PHST- 2010/02/23 [received] PHST- 2010/05/12 [revised] PHST- 2010/06/21 [accepted] AID - 10.1590/S1517-83822011000100043 [doi] AID - S1517-83822011000100043 [pii] PST - ppublish SO - Braz J Microbiol. 2011 Jan;42(1):340-5. doi: 10.1590/S1517-83822011000100043. PMID- 24010662 OWN - NLM STAT- MEDLINE DA - 20130909 DCOM- 20140415 LR - 20141112 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 105 IP - 5 DP - 2013 Sep 3 TI - Identification of fibril-like tertiary contacts in soluble monomeric alpha-synuclein. PG - 1192-8 LID - 10.1016/j.bpj.2013.07.044 [doi] LID - S0006-3495(13)00866-7 [pii] AB - Structural conversion of the presynaptic, intrinsically disordered protein alpha-synuclein into amyloid fibrils underlies neurotoxicity in Parkinson's disease. The detailed mechanism by which this conversion occurs is largely unknown. Here, we identify a discrete pattern of transient tertiary interactions in monomeric alpha-synuclein involving amino acid residues that are, in the fibrillar state, part of beta-strands. Importantly, this pattern of pairwise interactions does not correspond to that found in the amyloid state. A redistribution of this network of fibril-like contacts must precede aggregation into the amyloid structure. CI - Copyright (c) 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Esteban-Martin, Santiago AU - Esteban-Martin S AD - Joint BSC-IRB Research Programme in Computational Biology, Barcelona Supercomputing Center BSC, Barcelona, Spain. FAU - Silvestre-Ryan, Jordi AU - Silvestre-Ryan J FAU - Bertoncini, Carlos W AU - Bertoncini CW FAU - Salvatella, Xavier AU - Salvatella X LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - *Protein Multimerization MH - Protein Structure, Secondary MH - Solubility MH - alpha-Synuclein/*chemistry/metabolism PMC - PMC3762368 OID - NLM: PMC3762368 EDAT- 2013/09/10 06:00 MHDA- 2014/04/16 06:00 CRDT- 2013/09/10 06:00 PHST- 2013/03/22 [received] PHST- 2013/07/16 [revised] PHST- 2013/07/25 [accepted] AID - S0006-3495(13)00866-7 [pii] AID - 10.1016/j.bpj.2013.07.044 [doi] PST - ppublish SO - Biophys J. 2013 Sep 3;105(5):1192-8. doi: 10.1016/j.bpj.2013.07.044. PMID- 2567183 OWN - NLM STAT- MEDLINE DA - 19890727 DCOM- 19890727 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 28 IP - 6 DP - 1989 Mar 21 TI - Solution structure of recombinant hirudin and the Lys-47----Glu mutant: a nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing study. PG - 2601-17 AB - The solution structure of recombinant wild-type hirudin and of the putative active site mutant Lys-47----Glu has been investigated by nuclear magnetic resonance (NMR) spectroscopy at 600 MHz. The 1H NMR spectra of the two hirudin variants are assigned in a sequential manner with a combination of two-dimensional NMR techniques. Some assignments made in our previous paper [Sukumaran, D. K., Clore, G. M., Preuss, A., Zarbock, J., & Gronenborn, A. M. (1987) Biochemistry 26, 333-338] were found to be incorrect and are now corrected. Analysis of the NOE data indicates that hirudin consists of an N-terminal compact domain (residues 1-49) held together by three disulfide linkages and a disordered C-terminal tail (residues 50-65) which does not fold back on the rest of the protein. This last observation corrects conclusions drawn by us previously on hirudin extracted from its natural source, the leech Hirudo medicinalis. The improved sensitivity of the 600-MHz spectrometer relative to that of our old 500-MHz spectrometer, the availability of two variants with slightly different chemical shifts, and the additional information arising from stereospecific assignments of methylene beta-protons and methyl protons of valine have permitted the determination of the solution structure of hirudin with much greater precision than before. Structure calculations on the N-terminal domain using the hybrid distance geometry-dynamical simulated annealing method were based on 685 and 661 approximate interproton distance restraints derived from nuclear Overhauser enhancement (NOE) data for the wild-type and mutant hirudin, respectively, together with 16 distance restraints for 8 backbone hydrogen bonds identified on the basis of NOE and amide NH exchange data and 26 phi backbone and 18 chi 1 side-chain torsion angle restraints derived from NOE and three-bond coupling constant data. A total of 32 structures were computed for both the wild-type and mutant hirudin. The structure of residues 2-30 and 37-48 which form the core of the N-terminal domain is well determined in both cases with an average atomic rms difference between the individual structures and the respective mean structures of approximately 0.7 A for the backbone atoms and approximately 1 A for all atoms. As found previously, the orientation of the exposed finger of antiparallel beta-sheet (residues 31-36) with respect to the core could not be determined on the basis of the present data due to the absence of any long-range NOEs between the exposed finger and the core.(ABSTRACT TRUNCATED AT 250 WORDS) FAU - Folkers, P J AU - Folkers PJ AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892. FAU - Clore, G M AU - Clore GM FAU - Driscoll, P C AU - Driscoll PC FAU - Dodt, J AU - Dodt J FAU - Kohler, S AU - Kohler S FAU - Gronenborn, A M AU - Gronenborn AM LA - eng SI - PDB/UNKNOWN PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Glutamates) RN - 0 (Hirudins) RN - 0 (Recombinant Proteins) RN - 3KX376GY7L (Glutamic Acid) RN - K3Z4F929H6 (Lysine) SB - IM MH - Amino Acid Sequence MH - Escherichia coli/genetics MH - Genes MH - Genes, Synthetic MH - *Glutamates MH - Glutamic Acid MH - *Hirudins MH - *Lysine MH - Magnetic Resonance Spectroscopy/methods MH - Models, Molecular MH - Molecular Sequence Data MH - *Mutation MH - Protein Conformation MH - *Recombinant Proteins EDAT- 1989/03/21 MHDA- 1989/03/21 00:01 CRDT- 1989/03/21 00:00 PST - ppublish SO - Biochemistry. 1989 Mar 21;28(6):2601-17. PMID- 17893145 OWN - NLM STAT- MEDLINE DA - 20071120 DCOM- 20080123 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 282 IP - 47 DP - 2007 Nov 23 TI - Conformation-specific binding of alpha-synuclein to novel protein partners detected by phage display and NMR spectroscopy. PG - 34555-67 AB - Alpha-synuclein (AS) is an intrinsically unstructured protein in aqueous solution but is capable of forming beta-sheet-rich fibrils that accumulate as intracytoplasmic inclusions in Parkinson disease and certain other neurological disorders. However, AS binding to phospholipid membranes leads to a distinct change in protein conformation, stabilizing an extended amphipathic alpha-helical domain reminiscent of the exchangeable apolipoproteins. To better understand the significance of this conformational change, we devised a novel bacteriophage display screen to identify protein binding partners of helical AS and have identified 20 proteins with roles in diverse cellular processes related to membrane trafficking, ion channel modulation, redox metabolism, and gene regulation. To verify that the screen identifies proteins with specificity for helical AS, we further characterized one of these candidates, endosulfine alpha (ENSA), a small cAMP-regulated phosphoprotein implicated in the regulation of insulin secretion but also expressed abundantly in the brain. We used solution NMR to probe the interaction between ENSA and AS on the surface of SDS micelles. Chemical shift perturbation mapping experiments indicate that ENSA interacts specifically with residues in the N-terminal helical domain of AS in the presence of SDS but not in aqueous buffer lacking SDS. The ENSA-related protein ARPP-19 (cAMP-regulated phosphoprotein 19) also displays specific interactions with helical AS. These results confirm that the helical N terminus of AS can mediate specific interactions with other proteins and suggest that membrane binding may regulate the physiological activity of AS in vivo. FAU - Woods, Wendy S AU - Woods WS AD - Department of Molecular and Integrative Physiology, University of Illinois, 407 S. Goodwin Avenue, Urbana, IL 61801, USA. FAU - Boettcher, John M AU - Boettcher JM FAU - Zhou, Donghua H AU - Zhou DH FAU - Kloepper, Kathryn D AU - Kloepper KD FAU - Hartman, Kevin L AU - Hartman KL FAU - Ladror, Daniel T AU - Ladror DT FAU - Qi, Zhi AU - Qi Z FAU - Rienstra, Chad M AU - Rienstra CM FAU - George, Julia M AU - George JM LA - eng GR - R01 AG 13762/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070924 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Nerve Tissue Proteins) RN - 0 (Peptide Library) RN - 0 (Peptides) RN - 0 (Phospholipids) RN - 0 (Phosphoproteins) RN - 0 (SNCA protein, human) RN - 0 (alpha-Synuclein) RN - 0 (cyclic AMP-regulated phosphoprotein 19) RN - 0 (endosulfine) SB - IM MH - Cell Membrane/genetics/metabolism MH - Humans MH - Intranuclear Inclusion Bodies/chemistry/genetics/metabolism MH - Nerve Tissue Proteins/chemistry/*genetics/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Parkinson Disease/genetics/metabolism MH - *Peptide Library MH - Peptides/chemistry/*genetics MH - Phospholipids/genetics/metabolism MH - Phosphoproteins/chemistry/*genetics/metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - alpha-Synuclein/chemistry/*genetics/metabolism EDAT- 2007/09/26 09:00 MHDA- 2008/01/24 09:00 CRDT- 2007/09/26 09:00 PHST- 2007/09/24 [aheadofprint] AID - M705283200 [pii] AID - 10.1074/jbc.M705283200 [doi] PST - ppublish SO - J Biol Chem. 2007 Nov 23;282(47):34555-67. Epub 2007 Sep 24. PMID- 15322276 OWN - NLM STAT- MEDLINE DA - 20040901 DCOM- 20041116 LR - 20140608 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 101 IP - 35 DP - 2004 Aug 31 TI - An enzymatic molten globule: efficient coupling of folding and catalysis. PG - 12860-4 AB - A highly active, monomeric chorismate mutase, obtained by topological redesign of a dimeric helical bundle enzyme from Methanococcus jannaschii, was investigated by NMR and various other biochemical techniques, including H/D exchange. Although structural disorder is generally considered to be incompatible with efficient catalysis, the monomer, unlike its natural counterpart, unexpectedly possesses all of the characteristics of a molten globule. Global conformational ordering, observed upon binding of a transition state analog, indicates that folding can be coupled to catalysis with minimal energetic penalty. These results support the suggestion that many modern enzymes might have evolved from molten globule precursors. Insofar as their structural plasticity confers relaxed substrate specificity and/or catalytic promiscuity, molten globules may also be attractive starting points for the evolution of new catalysts in the laboratory. CI - Copyright 2004 The National Academy of Sciencs of the USA FAU - Vamvaca, Katherina AU - Vamvaca K AD - Laboratory of Organic Chemistry, Swiss Federal Institute of Technology, ETH-Honggerberg, CH-8093 Zurich, Switzerland. FAU - Vogeli, Beat AU - Vogeli B FAU - Kast, Peter AU - Kast P FAU - Pervushin, Konstantin AU - Pervushin K FAU - Hilvert, Donald AU - Hilvert D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040820 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - EC 5.4.99.5 (Chorismate Mutase) SB - IM MH - Chorismate Mutase/*chemistry/metabolism MH - Circular Dichroism MH - Magnetic Resonance Spectroscopy MH - Methanococcus/*chemistry/metabolism MH - Protein Engineering MH - *Protein Folding MH - Protein Structure, Tertiary MH - Spectrophotometry MH - Temperature PMC - PMC516485 OID - NLM: PMC516485 EDAT- 2004/08/24 05:00 MHDA- 2004/11/17 09:00 CRDT- 2004/08/24 05:00 PHST- 2004/08/20 [aheadofprint] AID - 10.1073/pnas.0404109101 [doi] AID - 0404109101 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12860-4. Epub 2004 Aug 20. PMID- 24145447 OWN - NLM STAT- MEDLINE DA - 20131106 DCOM- 20131231 LR - 20141112 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 110 IP - 45 DP - 2013 Nov 5 TI - Charge-dependent secretion of an intrinsically disordered protein via the autotransporter pathway. PG - E4246-55 LID - 10.1073/pnas.1310345110 [doi] AB - Autotransporters are a large class of virulence proteins produced by Gram-negative bacteria. They contain an N-terminal extracellular ("passenger") domain that folds into a beta-helical structure and a C-terminal beta-barrel ("beta") domain that anchors the protein to the outer membrane. Because the periplasm lacks ATP, the source of energy that drives passenger domain secretion is unknown. The prevailing model postulates that vectorial folding of the beta-helix in the extracellular space facilitates unidirectional secretion of the passenger domain. In this study we used a chimeric protein composed of the 675-residue receptor-binding domain (RD) of the Bordetella pertussis adenylate cyclase toxin CyaA fused to the C terminus of the Escherichia coli O157:H7 autotransporter EspP to test this hypothesis. The RD is a highly acidic, repetitive polypeptide that is intrinsically disordered in the absence of calcium. Surprisingly, we found that the RD moiety was efficiently secreted when it remained in an unfolded conformation. Furthermore, we found that neutralizing or reversing the charge of acidic amino acid clusters stalled translocation in the vicinity of the altered residues. These results challenge the vectorial folding model and, together with the finding that naturally occurring passenger domains are predominantly acidic, provide evidence that a net negative charge plays a significant role in driving the translocation reaction. FAU - Kang'ethe, Wanyoike AU - Kang'ethe W AD - Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892. FAU - Bernstein, Harris D AU - Bernstein HD LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20131021 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Adenylate Cyclase Toxin) RN - 0 (Escherichia coli Proteins) RN - 0 (Membrane Transport Proteins) RN - 0 (Oligonucleotides) RN - EC 3.4.21.- (EspP protein, E coli) RN - EC 3.4.21.- (Serine Endopeptidases) SB - IM MH - Adenylate Cyclase Toxin/*metabolism MH - Bacterial Secretion Systems/*physiology MH - Bordetella pertussis/*enzymology/genetics MH - Computational Biology MH - Escherichia coli O157 MH - Escherichia coli Proteins/*metabolism MH - Kinetics MH - Membrane Transport Proteins/chemistry/*metabolism MH - Oligonucleotides/genetics MH - Plasmids/genetics MH - *Protein Conformation MH - *Protein Folding MH - Serine Endopeptidases/*metabolism PMC - PMC3831499 OID - NLM: PMC3831499 OTO - NOTNLM OT - bacterial pathogenesis OT - membrane protein assembly OT - type Va secretion EDAT- 2013/10/23 06:00 MHDA- 2014/01/01 06:00 CRDT- 2013/10/23 06:00 PHST- 2013/10/21 [aheadofprint] AID - 1310345110 [pii] AID - 10.1073/pnas.1310345110 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2013 Nov 5;110(45):E4246-55. doi: 10.1073/pnas.1310345110. Epub 2013 Oct 21. PMID- 18033802 OWN - NLM STAT- MEDLINE DA - 20080213 DCOM- 20080304 LR - 20140904 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 36 IP - 3 DP - 2008 Feb TI - RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae. PG - 712-25 AB - RNA chaperone proteins are essential partners of RNA in living organisms and viruses. They are thought to assist in the correct folding and structural rearrangements of RNA molecules by resolving misfolded RNA species in an ATP-independent manner. RNA chaperoning is probably an entropy-driven process, mediated by the coupled binding and folding of intrinsically disordered protein regions and the kinetically trapped RNA. Previously, we have shown that the core protein of hepatitis C virus (HCV) is a potent RNA chaperone that can drive profound structural modifications of HCV RNA in vitro. We now examined the RNA chaperone activity and the disordered nature of core proteins from different Flaviviridae genera, namely that of HCV, GBV-B (GB virus B), WNV (West Nile virus) and BVDV (bovine viral diarrhoea virus). Despite low-sequence similarities, all four proteins demonstrated general nucleic acid annealing and RNA chaperone activities. Furthermore, heat resistance of core proteins, as well as far-UV circular dichroism spectroscopy suggested that a well-defined 3D protein structure is not necessary for core-induced RNA structural rearrangements. These data provide evidence that RNA chaperoning-possibly mediated by intrinsically disordered protein segments-is conserved in Flaviviridae core proteins. Thus, besides nucleocapsid formation, core proteins may function in RNA structural rearrangements taking place during virus replication. FAU - Ivanyi-Nagy, Roland AU - Ivanyi-Nagy R AD - LaboRetro INSERM #758, Ecole Normale Superieure de Lyon, IFR 128 Biosciences Lyon-Gerland, 69364 Lyon Cedex 07, France. FAU - Lavergne, Jean-Pierre AU - Lavergne JP FAU - Gabus, Caroline AU - Gabus C FAU - Ficheux, Damien AU - Ficheux D FAU - Darlix, Jean-Luc AU - Darlix JL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20071122 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Molecular Chaperones) RN - 0 (RNA, Catalytic) RN - 0 (RNA-Binding Proteins) RN - 0 (Viral Core Proteins) RN - 0 (hammerhead ribozyme) RN - 63231-63-0 (RNA) RN - 9007-49-2 (DNA) SB - IM MH - Circular Dichroism MH - DNA/chemistry MH - *Flaviviridae MH - Molecular Chaperones/*chemistry/metabolism MH - Protein Denaturation MH - Protein Structure, Secondary MH - RNA/*chemistry MH - RNA, Catalytic/metabolism MH - RNA-Binding Proteins/chemistry MH - Viral Core Proteins/*chemistry/metabolism PMC - PMC2241907 OID - NLM: PMC2241907 EDAT- 2007/11/24 09:00 MHDA- 2008/03/05 09:00 CRDT- 2007/11/24 09:00 PHST- 2007/11/22 [aheadofprint] AID - gkm1051 [pii] AID - 10.1093/nar/gkm1051 [doi] PST - ppublish SO - Nucleic Acids Res. 2008 Feb;36(3):712-25. Epub 2007 Nov 22. PMID- 19232355 OWN - NLM STAT- MEDLINE DA - 20090330 DCOM- 20090416 LR - 20140910 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 387 IP - 4 DP - 2009 Apr 10 TI - Analysis of PKR structure by small-angle scattering. PG - 910-20 LID - 10.1016/j.jmb.2009.02.019 [doi] AB - Protein kinase R (PKR) is a key component of the interferon antiviral defense pathway. Upon binding double-stranded RNA, PKR undergoes autophosphorylation reactions that activate the kinase. PKR contains an N-terminal double-stranded RNA binding domain, which consists of two tandem double-stranded RNA binding motifs, and a C-terminal kinase domain. We have used small-angle X-ray scattering and small-angle neutron scattering to define the conformation of latent PKR in solution. Guinier analysis indicates a radius of gyration of about 35 A. The p(r) distance distribution function exhibits a peak near 30 A, with a broad shoulder extending to longer distances. Good fits to the scattering data require models that incorporate multiple compact and extended conformations of the two interdomain linker regions. Thus, PKR belongs to the growing family of proteins that contain intrinsically unstructured regions. We propose that the flexible linkers may allow PKR to productively dimerize upon interaction with RNA activators that have diverse structures. FAU - VanOudenhove, Jennifer AU - VanOudenhove J AD - Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA. FAU - Anderson, Eric AU - Anderson E FAU - Krueger, Susan AU - Krueger S FAU - Cole, James L AU - Cole JL LA - eng GR - AI-53615/AI/NIAID NIH HHS/United States GR - R01 AI053615/AI/NIAID NIH HHS/United States GR - R01 AI053615-05/AI/NIAID NIH HHS/United States GR - RR-08630/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20090214 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (RNA, Double-Stranded) RN - EC 2.7.11.1 (eIF-2 Kinase) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Dimerization MH - Humans MH - Immunity, Innate MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - RNA, Double-Stranded/metabolism MH - Scattering, Small Angle MH - Sequence Homology, Amino Acid MH - X-Ray Diffraction MH - eIF-2 Kinase/*chemistry/genetics/immunology/metabolism PMC - PMC2663012 MID - NIHMS96403 OID - NLM: NIHMS96403 OID - NLM: PMC2663012 EDAT- 2009/02/24 09:00 MHDA- 2009/04/17 09:00 CRDT- 2009/02/24 09:00 PHST- 2009/01/06 [received] PHST- 2009/02/05 [revised] PHST- 2009/02/10 [accepted] PHST- 2009/02/14 [aheadofprint] AID - S0022-2836(09)00175-2 [pii] AID - 10.1016/j.jmb.2009.02.019 [doi] PST - ppublish SO - J Mol Biol. 2009 Apr 10;387(4):910-20. doi: 10.1016/j.jmb.2009.02.019. Epub 2009 Feb 14. PMID- 22632137 OWN - NLM STAT- MEDLINE DA - 20120903 DCOM- 20121106 LR - 20131121 IS - 1349-7006 (Electronic) IS - 1347-9032 (Linking) VI - 103 IP - 9 DP - 2012 Sep TI - Molecular biology of chronic myeloid leukemia. PG - 1601-10 LID - 10.1111/j.1349-7006.2012.02346.x [doi] AB - Detailed information on the crystal structure of the pharmacologically targeted domains of the BCR-ABL molecule and on its intracellular signaling, which are potentially involved in growth, anti-apoptosis, metabolism and stemness, has made the study of chronic myeloid leukemia the most successful field in tumor biology. However, we now face the issue of drug resistance due to deregulation in the quality control of both DNA and protein. BCR-ABL is basically a misfolded protein with intrinsically disordered regions, which not only produces endoplasmic reticulum stress followed by unfolded protein response in some settings, but also conformational plasticity that may affect the structure of the whole molecule. The intercellular signaling derived from the leukemic cell microenvironment may influence the intracellular responses that take place in a manner both dependent on and independent of BCR-ABL tyrosine kinase activity. CI - (c) 2012 Japanese Cancer Association. FAU - Maru, Yoshiro AU - Maru Y AD - Department of Pharmacology, Tokyo Women's Medical University, Japan. ymaru@research.twmu.ac.jp LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20120711 PL - England TA - Cancer Sci JT - Cancer science JID - 101168776 RN - EC 2.7.10.2 (Fusion Proteins, bcr-abl) SB - IM MH - Animals MH - Fusion Proteins, bcr-abl/chemistry/genetics/*metabolism MH - Humans MH - Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics/*metabolism MH - Mutation MH - Neoplastic Stem Cells/metabolism MH - Phenotype MH - Protein Conformation MH - Protein Processing, Post-Translational MH - Signal Transduction MH - Tumor Microenvironment EDAT- 2012/05/29 06:00 MHDA- 2012/11/07 06:00 CRDT- 2012/05/29 06:00 PHST- 2012/03/07 [received] PHST- 2012/05/21 [revised] PHST- 2012/05/23 [accepted] PHST- 2012/07/11 [aheadofprint] AID - 10.1111/j.1349-7006.2012.02346.x [doi] PST - ppublish SO - Cancer Sci. 2012 Sep;103(9):1601-10. doi: 10.1111/j.1349-7006.2012.02346.x. Epub 2012 Jul 11. PMID- 23515417 OWN - NLM STAT- MEDLINE DA - 20130523 DCOM- 20131209 LR - 20141116 IS - 1463-9084 (Electronic) IS - 1463-9076 (Linking) VI - 15 IP - 23 DP - 2013 Jun 21 TI - Initiation of assembly of tau(273-284) and its DeltaK280 mutant: an experimental and computational study. PG - 8916-28 LID - 10.1039/c3cp00063j [doi] AB - The microtubule associated protein tau is essential for the development and maintenance of the nervous system. Tau dysfunction is associated with a class of diseases called tauopathies, in which tau is found in an aggregated form. This paper focuses on a small aggregating fragment of tau, (273)GKVQIINKKLDL(284), encompassing the (PHF6*) region that plays a central role in tau aggregation. Using a combination of simulations and experiments, we probe the self-assembly of this peptide, with an emphasis on characterizing the early steps of aggregation. Ion-mobility mass spectrometry experiments provide a size distribution of early oligomers, TEM studies provide a time course of aggregation, and enhanced sampling molecular dynamics simulations provide atomistically detailed structural information about this intrinsically disordered peptide. Our studies indicate that a point mutation, as well the addition of heparin, lead to a shift in the conformations populated by the earliest oligomers, affecting the kinetics of subsequent fibril formation as well as the morphology of the resulting aggregates. In particular, a mutant associated with a K280 deletion (a mutation that causes a heritable form of neurodegeneration/dementia in the context of full length tau) is seen to aggregate more readily than its wild-type counterpart. Simulations and experiment reveal that the DeltaK280 mutant peptide adopts extended conformations to a greater extent than the wild-type peptide, facilitating aggregation through the pre-structuring of the peptide into a fibril-competent structure. FAU - Larini, Luca AU - Larini L AD - Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA. FAU - Gessel, Megan Murray AU - Gessel MM FAU - LaPointe, Nichole E AU - LaPointe NE FAU - Do, Thanh D AU - Do TD FAU - Bowers, Michael T AU - Bowers MT FAU - Feinstein, Stuart C AU - Feinstein SC FAU - Shea, Joan-Emma AU - Shea JE LA - eng GR - NS-35010/NS/NINDS NIH HHS/United States GR - R01 NS035010/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130320 PL - England TA - Phys Chem Chem Phys JT - Physical chemistry chemical physics : PCCP JID - 100888160 RN - 0 (tau Proteins) RN - 9005-49-6 (Heparin) SB - IM MH - Amino Acid Sequence MH - Heparin/metabolism MH - Humans MH - Molecular Dynamics Simulation MH - Point Mutation MH - Protein Conformation MH - Protein Multimerization MH - *Sequence Deletion MH - Tauopathies/*genetics/*metabolism MH - tau Proteins/chemistry/*genetics/*metabolism/ultrastructure PMC - PMC3663921 MID - NIHMS458037 OID - NLM: NIHMS458037 OID - NLM: PMC3663921 EDAT- 2013/03/22 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/03/22 06:00 PHST- 2013/03/20 [aheadofprint] PHST- 2013/05/22 [epublish] AID - 10.1039/c3cp00063j [doi] PST - ppublish SO - Phys Chem Chem Phys. 2013 Jun 21;15(23):8916-28. doi: 10.1039/c3cp00063j. Epub 2013 Mar 20. PMID- 16641491 OWN - NLM STAT- MEDLINE DA - 20060427 DCOM- 20060922 LR - 20140909 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 15 IP - 5 DP - 2006 May TI - Structure of the Sir3 protein bromo adjacent homology (BAH) domain from S. cerevisiae at 1.95 A resolution. PG - 1182-6 AB - Sir3p is a silent-information-regulator (SIR) protein required for the assembly of a transcriptionally "silent" chromatin structure at telomeres and the cryptic HM mating-type loci in Saccharomyces cerevisiae. Sir3p contains a putative "bromo adjacent homology" (BAH) domain at its N terminus that shares strong sequence similarity with the BAH domain of a subunit of the origin recognition complex (ORC), Orc1p. The Orc1p-BAH domain forms a well-defined complex with the ORC interaction region (OIR) of another Sir protein, Sir1p, which targets formation of silent chromatin to the HM-loci. Interestingly, despite sequence similarity of the Sir3p and Orc1p BAH domains and Sir3p's established importance in silencing, Sir3p does not bind the Sir1p-OIR. Here we report the 1.95 A resolution crystal structure of the Sir3p-BAH domain. The structure reveals two key features that can account for Sir3p-BAH domain's inability to interact with Sir1p. First, several Orc1p-BAH domain residues known to directly contact Sir1p are altered in the Sir3p-BAH domain. Second, a critical OIR-binding pocket present on the surface of the Orc1p-BAH domain is "filled" in the Sir3p-BAH domain structure, potentially making it inaccessible to Sir1p. These findings imply that the Sir3p-BAH domain structure has evolved for functions distinct from those of the Orc1p-BAH domain. FAU - Hou, Zhonggang AU - Hou Z AD - Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706-1532, USA. FAU - Danzer, John R AU - Danzer JR FAU - Fox, Catherine A AU - Fox CA FAU - Keck, James L AU - Keck JL LA - eng SI - PDB/2FL7 GR - GM056890/GM/NIGMS NIH HHS/United States GR - GM072392/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Silent Information Regulator Proteins, Saccharomyces cerevisiae) SB - IM MH - Amino Acid Sequence MH - Gene Expression Regulation, Fungal MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Silent Information Regulator Proteins, Saccharomyces cerevisiae/*chemistry MH - Structure-Activity Relationship PMC - PMC2242508 OID - NLM: PMC2242508 EDAT- 2006/04/28 09:00 MHDA- 2006/09/23 09:00 CRDT- 2006/04/28 09:00 AID - 15/5/1182 [pii] AID - 10.1110/ps.052061006 [doi] PST - ppublish SO - Protein Sci. 2006 May;15(5):1182-6. PMID- 21191186 OWN - NLM STAT- MEDLINE DA - 20110120 DCOM- 20111115 IS - 1551-4005 (Electronic) IS - 1551-4005 (Linking) VI - 10 IP - 1 DP - 2011 Jan 1 TI - Chemical states of the N-terminal "lid" of MDM2 regulate p53 binding: simulations reveal complexities of modulation. PG - 82-9 AB - Phosphorylation of S17 in the N-terminal "lid" of MDM2 (residues 1-24) is proposed to regulate the binding of p53. The lid is composed of an intrinsically disordered peptide motif that is not resolved in the crystal structure of the MDM2 N-terminal domain. Molecular dynamics simulations of MDM2 provide novel insight into how the lid undergoes complex dynamics depending on its phosphorylation state that have not been revealed by NMR analyses. The difference in charges between the phosphate and the phosphomimetic 'Asp' and the change in shape from tetrahedral to planar are manifested in differences in strengths and durations of interactions that appear to modulate access of the binding site to ligands and peptides differentially. These findings unveil the complexities that underlie protein-protein interactions and reconcile some differences between the biochemical and NMR data suggesting that lid mutation or deletion can change the specific activity of MDM2 and provide concepts for future approaches to evaluate the effects of S17 modification on p53 binding. FAU - Dastidar, Shubhra Ghosh AU - Dastidar SG AD - Bioinformatics Institute (A-STAR), Singapore. sgducd@gmail.com FAU - Raghunathan, Devanathan AU - Raghunathan D FAU - Nicholson, Judith AU - Nicholson J FAU - Hupp, Ted R AU - Hupp TR FAU - Lane, David P AU - Lane DP FAU - Verma, Chandra S AU - Verma CS LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110101 PL - United States TA - Cell Cycle JT - Cell cycle (Georgetown, Tex.) JID - 101137841 RN - 0 (Tumor Suppressor Protein p53) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Amino Acid Motifs MH - *Computer Simulation MH - Humans MH - *Molecular Dynamics Simulation MH - Phosphorylation MH - Protein Binding/physiology MH - Protein Conformation MH - Proto-Oncogene Proteins c-mdm2/*chemistry/*physiology MH - Tumor Suppressor Protein p53/*metabolism EDAT- 2010/12/31 06:00 MHDA- 2011/11/16 06:00 CRDT- 2010/12/31 06:00 PHST- 2011/01/01 [aheadofprint] AID - 14345 [pii] PST - ppublish SO - Cell Cycle. 2011 Jan 1;10(1):82-9. Epub 2011 Jan 1. PMID- 10926528 OWN - NLM STAT- MEDLINE DA - 20000816 DCOM- 20000816 LR - 20131121 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 289 IP - 5480 DP - 2000 Aug 4 TI - Crystal structure of rhodopsin: A G protein-coupled receptor. PG - 739-45 AB - Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) respond to a variety of different external stimuli and activate G proteins. GPCRs share many structural features, including a bundle of seven transmembrane alpha helices connected by six loops of varying lengths. We determined the structure of rhodopsin from diffraction data extending to 2.8 angstroms resolution. The highly organized structure in the extracellular region, including a conserved disulfide bridge, forms a basis for the arrangement of the seven-helix transmembrane motif. The ground-state chromophore, 11-cis-retinal, holds the transmembrane region of the protein in the inactive conformation. Interactions of the chromophore with a cluster of key residues determine the wavelength of the maximum absorption. Changes in these interactions among rhodopsins facilitate color discrimination. Identification of a set of residues that mediate interactions between the transmembrane helices and the cytoplasmic surface, where G-protein activation occurs, also suggests a possible structural change upon photoactivation. FAU - Palczewski, K AU - Palczewski K AD - Department of Ophthalmology, University of Washington, Seattle, WA 98195, USA. palczews@u.washington.edu FAU - Kumasaka, T AU - Kumasaka T FAU - Hori, T AU - Hori T FAU - Behnke, C A AU - Behnke CA FAU - Motoshima, H AU - Motoshima H FAU - Fox, B A AU - Fox BA FAU - Le Trong, I AU - Le Trong I FAU - Teller, D C AU - Teller DC FAU - Okada, T AU - Okada T FAU - Stenkamp, R E AU - Stenkamp RE FAU - Yamamoto, M AU - Yamamoto M FAU - Miyano, M AU - Miyano M LA - eng SI - PDB/1F88 GR - EY09339/EY/NEI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Receptors, Cell Surface) RN - 0 (Schiff Bases) RN - 9009-81-8 (Rhodopsin) RN - EC 3.6.5.1 (Heterotrimeric GTP-Binding Proteins) RN - RR725D715M (Retinaldehyde) SB - IM SB - S CIN - Science. 2000 Aug 4;289(5480):733-4. PMID: 10950717 MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Cattle MH - Cell Membrane/chemistry MH - Crystallography, X-Ray MH - Heterotrimeric GTP-Binding Proteins/*metabolism MH - Hydrogen Bonding MH - Light MH - Molecular Sequence Data MH - Receptors, Cell Surface/*chemistry/metabolism MH - Retinaldehyde/chemistry/metabolism MH - Rhodopsin/*chemistry/metabolism MH - Schiff Bases MH - Stereoisomerism MH - Vision, Ocular EDAT- 2000/08/05 11:00 MHDA- 2000/08/19 11:00 CRDT- 2000/08/05 11:00 AID - 8725 [pii] PST - ppublish SO - Science. 2000 Aug 4;289(5480):739-45. PMID- 17522259 OWN - NLM STAT- MEDLINE DA - 20070606 DCOM- 20080122 LR - 20140904 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 104 IP - 23 DP - 2007 Jun 5 TI - Polyelectrostatic interactions of disordered ligands suggest a physical basis for ultrasensitivity. PG - 9650-5 AB - Regulation of biological processes often involves phosphorylation of intrinsically disordered protein regions, thereby modulating protein interactions. Initiation of DNA replication in yeast requires elimination of the cyclin-dependent kinase inhibitor Sic1 via the SCF(Cdc4) ubiquitin ligase. Intriguingly, the substrate adapter subunit Cdc4 binds to Sic1 only after phosphorylation of a minimum of any six of the nine cyclin-dependent kinase sites on Sic1. To investigate the physical basis of this ultrasensitive interaction, we consider a mean-field statistical mechanical model for the electrostatic interactions between a single receptor site and a conformationally disordered polyvalent ligand. The formulation treats phosphorylation sites as negative contributions to the total charge of the ligand and addresses its interplay with the strength of the favorable ligand-receptor contact. Our model predicts a threshold number of phosphorylation sites for receptor-ligand binding, suggesting that ultrasensitivity in the Sic1-Cdc4 system may be driven at least in part by cumulative electrostatic interactions. This hypothesis is supported by experimental affinities of Cdc4 for Sic1 fragments with different total charges. Thus, polyelectrostatic interactions may provide a simple yet powerful framework for understanding the modulation of protein interactions by multiple phosphorylation sites in disordered protein regions. FAU - Borg, Mikael AU - Borg M AD - Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada M5S 1A8. FAU - Mittag, Tanja AU - Mittag T FAU - Pawson, Tony AU - Pawson T FAU - Tyers, Mike AU - Tyers M FAU - Forman-Kay, Julie D AU - Forman-Kay JD FAU - Chan, Hue Sun AU - Chan HS LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070523 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (CDC4 protein, S cerevisiae) RN - 0 (Cell Cycle Proteins) RN - 0 (Cyclin-Dependent Kinase Inhibitor Proteins) RN - 0 (F-Box Proteins) RN - 0 (Ligands) RN - 0 (SIC1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM MH - Cell Cycle Proteins/chemistry/*metabolism MH - Cyclin-Dependent Kinase Inhibitor Proteins MH - DNA Replication/*physiology MH - F-Box Proteins MH - Ligands MH - *Models, Biological MH - Phosphorylation MH - Protein Binding MH - Protein Interaction Domains and Motifs/*physiology MH - Saccharomyces cerevisiae Proteins/chemistry/*metabolism MH - Static Electricity MH - Ubiquitin-Protein Ligases/chemistry/*metabolism MH - Yeasts PMC - PMC1887549 OID - NLM: PMC1887549 EDAT- 2007/05/25 09:00 MHDA- 2008/01/23 09:00 CRDT- 2007/05/25 09:00 PHST- 2007/05/23 [aheadofprint] AID - 0702580104 [pii] AID - 10.1073/pnas.0702580104 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9650-5. Epub 2007 May 23. PMID- 23484883 OWN - NLM STAT- MEDLINE DA - 20130411 DCOM- 20130923 LR - 20131121 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 117 IP - 14 DP - 2013 Apr 11 TI - Effects of confinement on the structure and dynamics of an intrinsically disordered peptide: a molecular-dynamics study. PG - 3707-19 LID - 10.1021/jp310623x [doi] AB - In vivo, proteins and peptides are exposed to radically different environments than those in bulk. Because of the abundance of other cellular components, proteins perform their function in crowded and confined spaces. Confinement has been shown to alter the structure, dynamics, and folding of proteins that possess a native fold. Little is known, however, of the effects of confinement on biologically important intrinsically disordered proteins or peptides (IDP). Here, we use extensive molecular dynamics simulations to investigate the effects of confinement in an IDP, the Abeta21-30, a central folding nucleus of the full length amyloid beta-protein. In this study, we report results derived from 107 mus of molecular dynamics simulations that subjected the Abeta21-30 to two types of confinement: hydrophilic and hydrophobic pores. Results show that turn structures are enhanced as a function of decreasing pore size (increasing confinement) over other structures, including coils, beta-hairpins, and bridges. However, the percentage occurrence of the dominant hydrogen bond between amino acids Asp23 and Ser26 shown to stabilize the turn in bulk simulations does not increase as a function of confinement signifying a disconnect between structure and internal hydrogen bonding. Differences in structure and dynamics of the decapeptide due to hydrophilic and hydrophobic confinement are more apparent at the extreme confinement conditions, where a reduction of the available phase space in hydrophilic confinement is explained in terms of interactions between the decapeptide and a layer of water at the interface between the decapeptide and the surface of the pore, and a smaller size of the decapeptide in the hydrophobic pores is rationalized in terms of peptide-surface interactions. FAU - Rao, J Srinivasa AU - Rao JS AD - Department of Physics, 3141 Chestnut Street, Drexel University, Philadelphia, Pennsylvania 19104, USA. FAU - Cruz, Luis AU - Cruz L LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130328 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (21-30)) RN - 059QF0KO0R (Water) SB - IM MH - Amyloid beta-Peptides/*chemistry MH - Hydrogen Bonding MH - Hydrophobic and Hydrophilic Interactions MH - *Molecular Dynamics Simulation MH - Peptide Fragments/*chemistry MH - Porosity MH - Protein Structure, Secondary MH - Surface Properties MH - Thermodynamics MH - Water/*chemistry EDAT- 2013/03/15 06:00 MHDA- 2013/09/24 06:00 CRDT- 2013/03/15 06:00 PHST- 2013/03/28 [aheadofprint] AID - 10.1021/jp310623x [doi] PST - ppublish SO - J Phys Chem B. 2013 Apr 11;117(14):3707-19. doi: 10.1021/jp310623x. Epub 2013 Mar 28. PMID- 19553340 OWN - NLM STAT- MEDLINE DA - 20090811 DCOM- 20090831 LR - 20140828 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 83 IP - 17 DP - 2009 Sep TI - Identification of unusual E6 and E7 proteins within avian papillomaviruses: cellular localization, biophysical characterization, and phylogenetic analysis. PG - 8759-70 LID - 10.1128/JVI.01777-08 [doi] AB - Papillomaviruses (PVs) are a large family of small DNA viruses infecting mammals, reptiles, and birds. PV infection induces cell proliferation that may lead to the formation of orogenital or skin tumors. PV-induced cell proliferation has been related mainly to the expression of two small oncoproteins, E6 and E7. In mammalian PVs, E6 contains two 70-residue zinc-binding repeats, whereas E7 consists of a natively unfolded N-terminal region followed by a zinc-binding domain which folds as an obligate homodimer. Here, we show that both the novel francolin bird PV Francolinus leucoscepus PV type 1 (FlPV-1) and the chaffinch bird PV Fringilla coelebs PV contain unusual E6 and E7 proteins. The avian E7 proteins contain an extended unfolded N terminus and a zinc-binding domain of reduced size, whereas the avian E6 proteins consist of a single zinc-binding domain. A comparable single-domain E6 protein may have existed in a common ancestor of mammalian and avian PVs. Mammalian E6 C-terminal domains are phylogenetically related to those of single-domain avian E6, whereas mammalian E6 N-terminal domains seem to have emerged by duplication and subsequently diverged from the original ancestral domain. In avian and mammalian cells, both FlPV-1 E6 and FlPV-1 E7 were evenly expressed in the cytoplasm and the nucleus. Finally, samples of full-length FlPV-1 E6 and the FlPV-1 E7 C-terminal zinc-binding domain were prepared for biophysical analysis. Both constructs were highly soluble and well folded, according to nuclear magnetic resonance spectroscopy measurements. FAU - Van Doorslaer, Koenraad AU - Van Doorslaer K AD - Laboratory of Clinical Virology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium. FAU - Sidi, Abdellahi Ould M'hamed Ould AU - Sidi AO FAU - Zanier, Katia AU - Zanier K FAU - Rybin, Vladimir AU - Rybin V FAU - Deryckere, Francois AU - Deryckere F FAU - Rector, Annabel AU - Rector A FAU - Burk, Robert D AU - Burk RD FAU - Lienau, E Kurt AU - Lienau EK FAU - van Ranst, Marc AU - van Ranst M FAU - Trave, Gilles AU - Trave G LA - eng SI - GENBANK/EU188799 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090624 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (DNA, Viral) RN - 0 (Oncogene Proteins, Viral) SB - IM MH - Amino Acid Sequence MH - Animals MH - Bird Diseases/*virology MH - Birds MH - Cell Nucleus/chemistry MH - Cluster Analysis MH - Cytoplasm/chemistry MH - DNA, Viral/chemistry/genetics MH - Evolution, Molecular MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Oncogene Proteins, Viral/analysis/*chemistry/*genetics MH - Papillomaviridae/*genetics/isolation & purification MH - Papillomavirus Infections/*veterinary MH - Phylogeny MH - Protein Folding MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Sequence Analysis, DNA MH - Sequence Homology PMC - PMC2738182 OID - NLM: PMC2738182 EDAT- 2009/06/26 09:00 MHDA- 2009/09/01 06:00 CRDT- 2009/06/26 09:00 PHST- 2009/06/24 [aheadofprint] AID - JVI.01777-08 [pii] AID - 10.1128/JVI.01777-08 [doi] PST - ppublish SO - J Virol. 2009 Sep;83(17):8759-70. doi: 10.1128/JVI.01777-08. Epub 2009 Jun 24. PMID- 16420483 OWN - NLM STAT- MEDLINE DA - 20060119 DCOM- 20060328 LR - 20131121 IS - 1742-464X (Print) IS - 1742-464X (Linking) VI - 273 IP - 3 DP - 2006 Feb TI - Solution NMR structure of an immunodominant epitope of myelin basic protein. Conformational dependence on environment of an intrinsically unstructured protein. PG - 601-14 AB - Using solution NMR spectroscopy, three-dimensional structures have been obtained for an 18-residue synthetic polypeptide fragment of 18.5 kDa myelin basic protein (MBP, human residues Q81-T98) under three conditions emulating the protein's natural environment in the myelin membrane to varying degrees: (a) an aqueous solution (100 mM KCl pH 6.5), (b) a mixture of trifluoroethanol (TFE-d2) and water (30 : 70% v/v), and (c) a dispersion of 100 mM dodecylphosphocholine (DPC-d38, 1 : 100 protein/lipid molar ratio) micelles. This polypeptide sequence is highly conserved in MBP from mammals, amphibians, and birds, and comprises a major immunodominant epitope (human residues N83-T92) in the autoimmune disease multiple sclerosis. In the polypeptide fragment, this epitope forms a stable, amphipathic, alpha helix under organic and membrane-mimetic conditions, but has only a partially helical conformation in aqueous solution. These results are consistent with recent molecular dynamics simulations that showed this segment to have a propensity to form a transient alpha helix in aqueous solution, and with electron paramagnetic resonance (EPR) experiments that suggested a alpha-helical structure when bound to a membrane [I. R. Bates, J. B. Feix, J. M. Boggs & G. Harauz (2004) J Biol Chem, 279, 5757-5764]. The high sensitivity of the epitope structure to its environment is characteristic of intrinsically unstructured proteins, like MBP, and reflects its association with diverse ligands such as lipids and other proteins. FAU - Fares, Christophe AU - Fares C AD - Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, Canada. FAU - Libich, David S AU - Libich DS FAU - Harauz, George AU - Harauz G LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Immunodominant Epitopes) RN - 0 (Micelles) RN - 0 (Myelin Basic Protein) RN - 0 (Peptides) RN - 0 (Solutions) RN - 059QF0KO0R (Water) RN - 107-73-3 (Phosphorylcholine) RN - 53949-18-1 (dodecylphosphocholine) RN - 75-89-8 (Trifluoroethanol) SB - IM MH - Animals MH - Crystallography, X-Ray MH - Humans MH - Immunodominant Epitopes/*chemistry/immunology MH - Magnetic Resonance Spectroscopy/*methods MH - Micelles MH - Models, Molecular MH - Myelin Basic Protein/*chemistry/immunology MH - Peptides/chemical synthesis/chemistry MH - Phosphorylcholine/analogs & derivatives/chemistry MH - Protein Conformation MH - Protein Structure, Secondary MH - Sensitivity and Specificity MH - Solutions/chemistry MH - Trifluoroethanol/chemistry MH - Water/chemistry EDAT- 2006/01/20 09:00 MHDA- 2006/03/29 09:00 CRDT- 2006/01/20 09:00 AID - EJB5093 [pii] AID - 10.1111/j.1742-4658.2005.05093.x [doi] PST - ppublish SO - FEBS J. 2006 Feb;273(3):601-14. PMID- 14499615 OWN - NLM STAT- MEDLINE DA - 20030922 DCOM- 20031201 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 332 IP - 5 DP - 2003 Oct 3 TI - The N-terminal domain of p53 is natively unfolded. PG - 1131-41 AB - p53 is one of the key molecules regulating cell proliferation, apoptosis and tumor suppression by integrating a wide variety of signals. The structural basis for this function is still poorly understood. p53 appears to exercise its function as a modular protein in which different functions are associated with distinct domains. Presumably, p53 contains both folded and partially structured parts. Here, we have investigated the structure of the isolated N-terminal part of p53 (amino acid residues 1-93) using biophysical techniques. We demonstrate that this domain is devoid of tertiary structure and largely missing secondary structure elements. It exhibits a large hydrodynamic radius, typical for unfolded proteins. These findings suggest strongly that the entire N-terminal part of p53 is natively unfolded under physiological conditions. Furthermore, the binding affinity to its functional antagonist Mdm2 was investigated. A comparison of the binding of human Mdm2 to the N-terminal part of p53 and full-length p53 suggests that unfolded and folded parts of p53 function synergistically. FAU - Dawson, Roger AU - Dawson R AD - Institut fur Organische Chemie und Biochemie, Technische Universitat Munchen, Garching D-85747, Germany. FAU - Muller, Lin AU - Muller L FAU - Dehner, Alexander AU - Dehner A FAU - Klein, Christian AU - Klein C FAU - Kessler, Horst AU - Kessler H FAU - Buchner, Johannes AU - Buchner J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Nuclear Proteins) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Tumor Suppressor Protein p53) RN - 059QF0KO0R (Water) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Apoptosis MH - Biophysical Phenomena MH - Biophysics MH - Cell Division MH - Chromatography, Gel MH - Circular Dichroism MH - Humans MH - Magnetic Resonance Spectroscopy MH - *Nuclear Proteins MH - Plasmids/metabolism MH - Protein Binding MH - Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins/chemistry MH - Proto-Oncogene Proteins c-mdm2 MH - Spectrometry, Fluorescence MH - Tumor Suppressor Protein p53/*chemistry MH - Ultracentrifugation MH - Water/chemistry EDAT- 2003/09/23 05:00 MHDA- 2003/12/03 05:00 CRDT- 2003/09/23 05:00 AID - S0022283603010246 [pii] PST - ppublish SO - J Mol Biol. 2003 Oct 3;332(5):1131-41. PMID- 23927048 OWN - NLM STAT- MEDLINE DA - 20130919 DCOM- 20131122 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 280 IP - 19 DP - 2013 Oct TI - alpha-Synuclein as an intrinsically disordered monomer--fact or artefact? PG - 4915-27 LID - 10.1111/febs.12471 [doi] AB - Fibrillization of the protein alpha-synuclein (alpha-syn) is a hallmark of Parkinson's disease and other alpha-synucleinopathies. The well-established idea that alpha-syn is a natively disordered monomer prone to forming fibrils was recently challenged by data showing that the protein mostly exists in vitro and in vivo as helically folded tetramers that are resistant to fibrillization. These apparently conflicting findings may be reconciled by the idea that alpha-syn exists as a disordered monomer in equilibrium with variable amounts of dynamic oligomeric species. In this context, varying the approaches used for protein purification, such as the method used to lyse cells or the inclusion of denaturing agents, could dramatically perturb this equilibrium and hence alter the relative abundance of the disordered monomer. In the present study, we investigated how the current methods for alpha-syn purification affect the structure and oligomeric state of the protein, and we discuss the main pitfalls associated with the production of recombinant alpha-syn in Escherichia coli. We demonstrate that alpha-syn was expressed in E. coli as a disordered monomer independent of both the cell lysis method and the use of heating/acidification for protein purification. In addition, we provide convincing evidence that the disordered monomer exists in equilibrium with a dynamic dimer, which is not an artefact of the cross-linking protocol as previously suggested. Unlike the helically folded tetramer, alpha-syn dimer is prone to fibrillate and thus it may be an interesting target for anti-fibrillogenic molecules. CI - (c) 2013 FEBS. FAU - Coelho-Cerqueira, Eduardo AU - Coelho-Cerqueira E AD - Department of Physical Chemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Brazil. FAU - Carmo-Goncalves, Phelippe AU - Carmo-Goncalves P FAU - Pinheiro, Anderson Sa AU - Pinheiro AS FAU - Cortines, Juliana AU - Cortines J FAU - Follmer, Cristian AU - Follmer C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130902 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (alpha-Synuclein) SB - IM MH - Circular Dichroism MH - Escherichia coli/genetics/*metabolism MH - Magnetic Resonance Spectroscopy MH - Protein Multimerization MH - alpha-Synuclein/*chemistry/*metabolism OTO - NOTNLM OT - Escherichia coli OT - dimer OT - disordered monomer OT - purification OT - alpha-synuclein EDAT- 2013/08/10 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/08/10 06:00 PHST- 2013/05/28 [received] PHST- 2013/07/12 [revised] PHST- 2013/07/31 [accepted] PHST- 2013/09/02 [aheadofprint] AID - 10.1111/febs.12471 [doi] PST - ppublish SO - FEBS J. 2013 Oct;280(19):4915-27. doi: 10.1111/febs.12471. Epub 2013 Sep 2. PMID- 16423825 OWN - NLM STAT- MEDLINE DA - 20060327 DCOM- 20060523 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 13 DP - 2006 Mar 31 TI - HIV-1 Tat is a natively unfolded protein: the solution conformation and dynamics of reduced HIV-1 Tat-(1-72) by NMR spectroscopy. PG - 8347-56 AB - Tat (transactivator of transcription) is a small RNA-binding protein that plays a central role in the regulation of human immunodeficiency virus type 1 replication and in approaches to treating latently infected cells. Its interactions with a wide variety of both intracellular and extracellular molecules is well documented. A molecular understanding of the multitude of Tat activities requires a determination of its structure and interactions with cellular and viral partners. To increase the dispersion of NMR signals and permit dynamics analysis by multinuclear NMR spectroscopy, we have prepared uniformly 15N- and 15N/13C-labeled Tat-(1-72) protein. The cysteine-rich protein is unambiguously reduced at pH 4.1, and NMR chemical shifts and coupling constants suggest that it exists in a random coil conformation. Line broadening and multiple peaks in the Cys-rich and core regions suggest that transient folding occurs in two of the five sequence domains. NMR relaxation parameters were measured and analyzed by spectral density and Lipari-Szabo approaches, both confirming the lack of structure throughout the length of the molecule. The absence of a fixed conformation and the observation of fast dynamics are consistent with the ability of Tat protein to interact with a wide variety of proteins and nucleic acid and support the concept of a natively unfolded protein. FAU - Shojania, Shaheen AU - Shojania S AD - Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada. FAU - O'Neil, Joe D AU - O'Neil JD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060119 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Enzyme Inhibitors) RN - 0 (Gene Products, tat) RN - 0 (Peptide Fragments) RN - 0 (Solutions) RN - 0 (tat Gene Products, Human Immunodeficiency Virus) RN - 4QD397987E (Histidine) RN - 968JJ8C9DV (Sodium Azide) RN - K848JZ4886 (Cysteine) SB - IM MH - *Computer Simulation MH - Cysteine/chemistry MH - Enzyme Inhibitors/pharmacology MH - Freeze Drying MH - Gene Products, tat/*chemistry/genetics MH - HIV-1/*chemistry/genetics MH - Histidine/chemistry MH - Humans MH - Hydrogen-Ion Concentration MH - *Nuclear Magnetic Resonance, Biomolecular MH - Oxidation-Reduction MH - Peptide Fragments/chemistry/genetics MH - Protein Conformation MH - *Protein Folding MH - Protein Structure, Tertiary MH - Sodium Azide/pharmacology MH - Solutions MH - Temperature MH - tat Gene Products, Human Immunodeficiency Virus EDAT- 2006/01/21 09:00 MHDA- 2006/05/24 09:00 CRDT- 2006/01/21 09:00 PHST- 2006/01/19 [aheadofprint] AID - M510748200 [pii] AID - 10.1074/jbc.M510748200 [doi] PST - ppublish SO - J Biol Chem. 2006 Mar 31;281(13):8347-56. Epub 2006 Jan 19. PMID- 22828513 OWN - NLM STAT- MEDLINE DA - 20120827 DCOM- 20121218 LR - 20131121 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 425 IP - 2 DP - 2012 Aug 24 TI - Biophysical studies with AICD-47 reveal unique binding behavior characteristic of an unfolded domain. PG - 201-6 LID - 10.1016/j.bbrc.2012.07.067 [doi] AB - APP intracellular C-terminal domain (AICD-47), generated upon gamma-secretase cleavage of amyloid precursor's protein (APP), bears the signature of a classical intrinsically unstructured domain (IUD). Comparing the recent crystal structures of AICD-47 peptides bound to its different adaptors such as protein-tyrosine-binding domain-2 (PTB2) of Fe65 and Src homology 2 (SH2) domain of growth factor receptor binding protein 2 (Grb2), the "conformational switching" of AICD-47 becomes evident. In order to understand different binding processes undertaken by this flexible molecule, upon recognizing different interfaces resulting in different 3D conformations, spectroscopic and calorimetric studies have been done. CD spectroscopy has revealed an overall random coil like structure in different pHs while TFE (2'-2'-2'-trifluoro ethanol) and HFIP (Hexa fluoro isopropanol) induced alpha-helicity to a certain extent. Binding of Tyr phosphorylated AICD-47 ((P)AICD-47) to Grb2-SH2 domain was carried out by a favorable enthalpic change (DeltaH=-197.5+/-6.2 kcal mole(-1) at 25 degrees C) and an unfavorable entropic contribution (DeltaS=-631 cal mol(-1) deg(-1) at 25 degrees C). Alternative conformation of AICD-47 in different biological contexts is another remarkable feature of IUDs which presumably has definitive roles in regulating Alzheimer's disease phenotype. CI - Copyright (c) 2012 Elsevier Inc. All rights reserved. FAU - Das, Samir AU - Das S AD - Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700 064, WB, India. FAU - Ghosh, Saptaparni AU - Ghosh S FAU - Dasgupta, Dipak AU - Dasgupta D FAU - Sen, Udayaditya AU - Sen U FAU - Mukhopadhyay, Debashis AU - Mukhopadhyay D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120722 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Amyloid beta-Protein Precursor) RN - 0 (GRB2 Adaptor Protein) RN - 0 (Peptide Fragments) RN - 42HK56048U (Tyrosine) SB - IM MH - Amyloid beta-Protein Precursor/*chemistry/*metabolism MH - Crystallography, X-Ray MH - Endosomes/*metabolism MH - GRB2 Adaptor Protein/chemistry MH - Humans MH - Peptide Fragments/chemistry/metabolism MH - Phosphorylation MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Transport MH - Tyrosine/chemistry MH - src Homology Domains EDAT- 2012/07/26 06:00 MHDA- 2012/12/19 06:00 CRDT- 2012/07/26 06:00 PHST- 2012/07/04 [received] PHST- 2012/07/16 [accepted] PHST- 2012/07/22 [aheadofprint] AID - S0006-291X(12)01363-0 [pii] AID - 10.1016/j.bbrc.2012.07.067 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2012 Aug 24;425(2):201-6. doi: 10.1016/j.bbrc.2012.07.067. Epub 2012 Jul 22. PMID- 24022511 OWN - NLM STAT- MEDLINE DA - 20140423 DCOM- 20150416 IS - 1364-548X (Electronic) IS - 1359-7345 (Linking) VI - 50 IP - 40 DP - 2014 May 25 TI - The STIL protein contains intrinsically disordered regions that mediate its protein-protein interactions. PG - 5245-7 LID - 10.1039/c3cc45096a [doi] AB - The STIL protein participates in mitosis and malignant transformation by regulating centrosomal duplication. Using biophysical methods we studied the structure and interactions of STIL. We revealed that its central domain is intrinsically disordered and mediates protein-protein interactions of STIL. The intrinsic disorder may provide STIL with the conformational flexibility required for its multitude binding. FAU - Amartely, Hadar AU - Amartely H AD - Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel. assaf.friedler@mail.huji.ac.il. FAU - David, Ahuvit AU - David A FAU - Lebendiker, Mario AU - Lebendiker M FAU - Benyamini, Hadar AU - Benyamini H FAU - Izraeli, Shai AU - Izraeli S FAU - Friedler, Assaf AU - Friedler A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130911 PL - England TA - Chem Commun (Camb) JT - Chemical communications (Cambridge, England) JID - 9610838 RN - 0 (CHFR protein, human) RN - 0 (Cell Cycle Proteins) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Neoplasm Proteins) RN - 0 (Peptide Fragments) RN - 0 (STIL protein, human) SB - IM MH - Cell Cycle Proteins/*chemistry/*metabolism MH - Circular Dichroism MH - Fluorescence Polarization MH - Humans MH - Intracellular Signaling Peptides and Proteins/*chemistry/*metabolism MH - Neoplasm Proteins/*chemistry/*metabolism MH - Peptide Fragments/*chemistry/*metabolism MH - Protein Conformation MH - Protein Interaction Domains and Motifs EDAT- 2013/09/12 06:00 MHDA- 2015/04/17 06:00 CRDT- 2013/09/12 06:00 PHST- 2013/09/11 [aheadofprint] PHST- 2014/04/22 [epublish] AID - 10.1039/c3cc45096a [doi] PST - ppublish SO - Chem Commun (Camb). 2014 May 25;50(40):5245-7. doi: 10.1039/c3cc45096a. Epub 2013 Sep 11. PMID- 19605348 OWN - NLM STAT- MEDLINE DA - 20090831 DCOM- 20091005 LR - 20140828 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 284 IP - 36 DP - 2009 Sep 4 TI - Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements. PG - 24610-21 LID - 10.1074/jbc.M109.001958 [doi] AB - FACT is a heterodimer of SPT16 and SSRP1, which each contain several conserved regions in the primary structure. The interaction of FACT with nucleosomes induces chromatin remodeling through the combinatorial action of its distinct functional protein regions. However, there is little mechanistic insight into how these regions cooperatively contribute to FACT functions, particularly regarding the recognition of nucleosomal DNA. Here, we report the identification of novel phosphorylation sites of Drosophila melanogaster FACT (dFACT) expressed in Sf9 cells. These sites are densely concentrated in the acidic intrinsically disordered (ID) region of the SSRP1 subunit and control nucleosomal DNA binding by dFACT. This region and the adjacent segment of the HMG domain form weak electrostatic intramolecular interactions, which is reinforced by the phosphorylation, thereby blocking DNA binding competitively. Importantly, this control mechanism appears to support rapid chromatin transactions during early embryogenesis through the dephosphorylation of some sites in the maternally transmitted dSSRP1. FAU - Tsunaka, Yasuo AU - Tsunaka Y AD - Takara-Bio Endowed Laboratory, Institute for Protein Research, Osaka University, Suita, Osaka 565-0874, Japan. FAU - Toga, Junko AU - Toga J FAU - Yamaguchi, Hiroto AU - Yamaguchi H FAU - Tate, Shin-ichi AU - Tate S FAU - Hirose, Susumu AU - Hirose S FAU - Morikawa, Kosuke AU - Morikawa K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090715 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Carrier Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Drosophila Proteins) RN - 0 (FACT protein, Drosophila) RN - 0 (High Mobility Group Proteins) RN - 0 (Nucleosomes) RN - 0 (SSRP protein, Drosophila) RN - 0 (Transcriptional Elongation Factors) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Carrier Proteins/genetics/*metabolism MH - Chromatin Assembly and Disassembly/*physiology MH - DNA/genetics/*metabolism MH - DNA-Binding Proteins/genetics/*metabolism MH - Drosophila Proteins/genetics/*metabolism MH - Drosophila melanogaster MH - Embryo, Nonmammalian/metabolism MH - Embryonic Development/physiology MH - High Mobility Group Proteins/genetics/*metabolism MH - Nucleosomes/genetics/*metabolism MH - Phosphorylation/physiology MH - Protein Structure, Tertiary/physiology MH - Transcriptional Elongation Factors/genetics/*metabolism PMC - PMC2782050 OID - NLM: PMC2782050 EDAT- 2009/07/17 09:00 MHDA- 2009/10/06 06:00 CRDT- 2009/07/17 09:00 PHST- 2009/07/15 [aheadofprint] AID - M109.001958 [pii] AID - 10.1074/jbc.M109.001958 [doi] PST - ppublish SO - J Biol Chem. 2009 Sep 4;284(36):24610-21. doi: 10.1074/jbc.M109.001958. Epub 2009 Jul 15. PMID- 9687368 OWN - NLM STAT- MEDLINE DA - 19981022 DCOM- 19981022 LR - 20090929 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 6 IP - 7 DP - 1998 Jul 15 TI - Crystal structure of a colicin N fragment suggests a model for toxicity. PG - 863-74 AB - BACKGROUND: Pore-forming colicins are water-soluble bacteriocins capable of binding to and translocating through the Escherichia coli cell envelope. They then undergo a transition to a transmembrane ion channel in the cytoplasmic membrane leading to bacterial death. Colicin N is the smallest pore-forming colicin known to date (40 kDa instead of the more usual 60 kDa) and the crystal structure of its membrane receptor, the porin OmpF, is already known. Structural knowledge of colicin N is therefore important for a molecular understanding of colicin toxicity and is relevant to toxic mechanisms in general. RESULTS: The crystal structure of colicin N reveals a novel receptor-binding domain containing a six-stranded antiparallel beta sheet wrapped around the 63 A long N-terminal alpha helix of the pore-forming domain. The pore-forming domain adopts a ten alpha-helix bundle that has been observed previously in the pore-forming domains of colicin A, la and E1. The translocation domain, however, does not appear to adopt any regular structure. Models for receptor binding and translocation through the outer membrane are proposed based on the structure and biochemical data. CONCLUSIONS: The colicin N-ompF system is now the structurally best-defined translocation pathway. Knowledge of the colicin N structure, coupled with the structure of its receptor, OmpF, and previously published biochemical data, limits the numerous possibilities of translocation and leads to a model in which the translocation domain inserts itself through the porin pore, the receptor-binding domain stays outside and the pore-forming domain translocates along the outer wall of the trimeric porin channel. FAU - Vetter, I R AU - Vetter IR AD - European Molecular Biology Laboratory, Heidelberg, Germany. ingrid.vetter@mpi-dortmund.mpg.de FAU - Parker, M W AU - Parker MW FAU - Tucker, A D AU - Tucker AD FAU - Lakey, J H AU - Lakey JH FAU - Pattus, F AU - Pattus F FAU - Tsernoglou, D AU - Tsernoglou D LA - eng SI - PDB/1A87 GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Colicins) RN - 0 (OmpF protein) RN - 0 (Peptide Fragments) RN - 0 (Porins) SB - IM MH - Binding Sites MH - Colicins/*chemistry/metabolism/*toxicity MH - Crystallography, X-Ray MH - Models, Molecular MH - Peptide Fragments/chemistry MH - Porins/metabolism MH - Protein Conformation EDAT- 1998/08/04 MHDA- 1998/08/04 00:01 CRDT- 1998/08/04 00:00 PST - ppublish SO - Structure. 1998 Jul 15;6(7):863-74. PMID- 21518955 OWN - NLM STAT- MEDLINE DA - 20110610 DCOM- 20110823 LR - 20140820 IS - 1098-5549 (Electronic) IS - 0270-7306 (Linking) VI - 31 IP - 13 DP - 2011 Jul TI - Distinct properties of human HMGN5 reveal a rapidly evolving but functionally conserved nucleosome binding protein. PG - 2742-55 LID - 10.1128/MCB.05216-11 [doi] AB - The HMGN family is a family of nucleosome-binding architectural proteins that affect the structure and function of chromatin in vertebrates. We report that the HMGN5 variant, encoded by a gene located on chromosome X, is a rapidly evolving protein with an acidic C-terminal domain that differs among vertebrate species. We found that the intranuclear organization and nucleosome interactions of human HMGN5 are distinct from those of mouse HMGN5 and that the C-terminal region of the protein is the main determinant of the chromatin interaction properties. Despite their apparent differences, both mouse and human HMGN5 proteins interact with histone H1, reduce its chromatin residence time, and can induce large-scale chromatin decompaction in living cells. Analysis of HMGN5 mutants suggests that distinct domains in HMGN5 affect specific steps in the interaction of H1 with chromatin. Elevated levels of either human or mouse HMGN5 affect the transcription of numerous genes, most in a variant-specific manner. Our study identifies HMGN5 as a rapidly evolving vertebrate nuclear protein with species-specific properties. HMGN5 has a highly disordered structure, binds dynamically to nucleosome core particles, modulates the binding of H1 to chromatin, reduces the compaction of the chromatin fiber, and affects transcription. FAU - Malicet, Cedric AU - Malicet C AD - Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. FAU - Rochman, Mark AU - Rochman M FAU - Postnikov, Yuri AU - Postnikov Y FAU - Bustin, Michael AU - Bustin M LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20110425 PL - United States TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (Chromatin) RN - 0 (HMGN Proteins) RN - 0 (HMGN5 protein, human) RN - 0 (Histones) RN - 0 (RNA, Small Interfering) RN - 0 (Trans-Activators) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cell Line MH - Chromatin/metabolism MH - Chromosomes, Human, X/genetics MH - *Conserved Sequence MH - Gene Expression MH - Gene Expression Profiling MH - HMGN Proteins/genetics/*metabolism MH - Histones/metabolism MH - Humans MH - Mice MH - Molecular Sequence Data MH - Protein Structure, Tertiary/genetics MH - RNA, Small Interfering/genetics MH - Trans-Activators/genetics/*metabolism PMC - PMC3133374 OID - NLM: PMC3133374 EDAT- 2011/04/27 06:00 MHDA- 2011/08/24 06:00 CRDT- 2011/04/27 06:00 PHST- 2011/04/25 [aheadofprint] AID - MCB.05216-11 [pii] AID - 10.1128/MCB.05216-11 [doi] PST - ppublish SO - Mol Cell Biol. 2011 Jul;31(13):2742-55. doi: 10.1128/MCB.05216-11. Epub 2011 Apr 25. PMID- 15379538 OWN - NLM STAT- MEDLINE DA - 20040921 DCOM- 20041109 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 38 DP - 2004 Sep 28 TI - NMR structure of the flavin domain from soluble methane monooxygenase reductase from Methylococcus capsulatus (Bath). PG - 11983-91 AB - Soluble methane monooxygenase (sMMO) catalyzes the hydroxylation of methane by dioxygen to methanol, the first step in carbon assimilation by methanotrophs. This multicomponent system transfers electrons from NADH through a reductase component to the non-heme diiron center in the hydroxylase where O(2) is activated. The reductase component comprises three distinct domains, a [2Fe-2S] ferredoxin domain along with FAD- and NADH-binding domains. We report the solution structure of the reduced 27.6 kDa FAD- and NADH-binding domains (MMOR-FAD) of the reductase from Methylococcus capsulatus (Bath). The FAD-binding domain consists of a six-stranded antiparallel beta-barrel and one alpha-helix, with the first 10 N-terminal residues unstructured. In the interface between the two domains, the FAD cofactor is tightly bound in an unprecedented extended conformation. The NADH-binding domain consists of a five-stranded parallel beta-sheet with four alpha-helices packing closely around this sheet. MMOR-FAD is structurally homologous to other FAD-containing oxidoreductases, and we expect similar structures for the FAD/NADH-binding domains of reductases that occur in other multicomponent monooxygenases. FAU - Chatwood, Lisa L AU - Chatwood LL AD - Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA. FAU - Muller, Jens AU - Muller J FAU - Gross, John D AU - Gross JD FAU - Wagner, Gerhard AU - Wagner G FAU - Lippard, Stephen J AU - Lippard SJ LA - eng SI - PDB/1TVC GR - GM32134/GM/NIGMS NIH HHS/United States GR - GM47467/GM/NIGMS NIH HHS/United States GR - RR00995/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Flavins) RN - 0U46U6E8UK (NAD) RN - 146-14-5 (Flavin-Adenine Dinucleotide) RN - EC 1.- (Oxidoreductases) RN - EC 1.13.- (Oxygenases) RN - EC 1.14.13.25 (methane monooxygenase) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Flavin-Adenine Dinucleotide/chemistry/metabolism MH - Flavins/*chemistry/*metabolism MH - Methylococcus capsulatus/*enzymology MH - Models, Molecular MH - Molecular Sequence Data MH - NAD/chemistry/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Oxidoreductases/*chemistry/*metabolism MH - Oxygenases/*chemistry/*metabolism MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Solubility EDAT- 2004/09/24 05:00 MHDA- 2004/11/13 09:00 CRDT- 2004/09/24 05:00 AID - 10.1021/bi049066n [doi] PST - ppublish SO - Biochemistry. 2004 Sep 28;43(38):11983-91. PMID- 25031352 OWN - NLM STAT- MEDLINE DA - 20140909 DCOM- 20141111 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 88 IP - 19 DP - 2014 Oct TI - Structural insights into the human metapneumovirus glycoprotein ectodomain. PG - 11611-6 LID - 10.1128/JVI.01726-14 [doi] AB - Human metapneumovirus is a major cause of respiratory tract infections worldwide. Previous reports have shown that the viral attachment glycoprotein (G) modulates innate and adaptive immune responses, leading to incomplete immunity and promoting reinfection. Using bioinformatics analyses, static light scattering, and small-angle X-ray scattering, we show that the extracellular region of G behaves as a heavily glycosylated, intrinsically disordered polymer. We discuss potential implications of these findings for the modulation of immune responses by G. CI - Copyright (c) 2014 Leyrat et al. FAU - Leyrat, Cedric AU - Leyrat C AD - Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom. FAU - Paesen, Guido C AU - Paesen GC AD - Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom. FAU - Charleston, James AU - Charleston J AD - Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom. FAU - Renner, Max AU - Renner M AD - Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom. FAU - Grimes, Jonathan M AU - Grimes JM AD - Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom Diamond Light Source Ltd., Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, United Kingdom jonathan@strubi.ox.ac.uk. LA - eng SI - PDB/3FXI SI - PDB/4DAG GR - 090532/Z/09/Z/Wellcome Trust/United Kingdom GR - 099667/Z/12/Z/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140716 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (G glycoprotein, human metapneumovirus) RN - 0 (Glycoproteins) RN - 0 (Viral Proteins) SB - IM MH - Glycoproteins/*chemistry/immunology/metabolism MH - Glycosylation MH - Humans MH - Immunity, Innate MH - Metapneumovirus/*chemistry/immunology/metabolism MH - Models, Molecular MH - Protein Structure, Tertiary MH - Viral Proteins/*chemistry/immunology/metabolism PMC - PMC4178817 OID - NLM: PMC4178817 EDAT- 2014/07/18 06:00 MHDA- 2014/11/12 06:00 CRDT- 2014/07/18 06:00 PHST- 2014/07/16 [aheadofprint] AID - JVI.01726-14 [pii] AID - 10.1128/JVI.01726-14 [doi] PST - ppublish SO - J Virol. 2014 Oct;88(19):11611-6. doi: 10.1128/JVI.01726-14. Epub 2014 Jul 16. PMID- 15536081 OWN - NLM STAT- MEDLINE DA - 20050111 DCOM- 20050225 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 2 DP - 2005 Jan 14 TI - Calcium-binding crystallins from Yersinia pestis. Characterization of two single betagamma-crystallin domains of a putative exported protein. PG - 1209-16 AB - Betagamma-crystallin is a superfamily with diverse members from vertebrate lens to microbes. However, not many members have been identified and studied. Here, we report the identification of a putative exported protein from Yersinia pestis as a member of the betagamma-crystallin superfamily. Even though calcium has been known to play an important role in the physiology and virulence of the Yersinia genus, calcium-binding proteins have not yet been identified. We have studied the calcium-binding properties of two of the three crystallin domains present in this putative exported protein designated "Yersinia crystallin." These two domains (D1 and D2) have unique AA and BB types of arrangement of their Greek key motifs unlike the domains of other members of the betagamma-crystallin superfamily, which are either AB or BA types. These domains bind two calcium ions with low and high affinity-binding sites. We showed their calcium-binding properties using various probes for calcium and the effect of calcium on their secondary and tertiary structures. Although both domains bind calcium, D1 underwent drastic changes in secondary and tertiary structure and hydrodynamic volume upon calcium binding. Domain D1, which is intrinsically unstructured in the apo form, requires calcium for the typical betagamma-crystallin fold. Calcium exerted an extrinsic stabilization effect on domain D1 but not on D2, which is also largely unstructured. We suggest that this protein might be involved in calcium-dependent processes, such as stress response or physiology in the Yersinia genus, similar to its microbial relatives and mammalian lens crystallins. FAU - Jobby, Maroor K AU - Jobby MK AD - Center for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India. FAU - Sharma, Yogendra AU - Sharma Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20041109 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - 0 (Crystallins) RN - 0 (Peptide Fragments) RN - 06SSF7P179 (Terbium) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Bacterial Proteins/chemistry/genetics/isolation & purification/metabolism MH - Binding Sites MH - Calcium/*metabolism/pharmacology MH - Circular Dichroism MH - Cloning, Molecular MH - Crystallins/*chemistry/genetics/*metabolism MH - Fluorescence MH - Models, Molecular MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/genetics/isolation & purification/metabolism MH - Protein Structure, Tertiary/drug effects MH - Protein Transport MH - Sequence Analysis, DNA MH - Terbium/metabolism MH - Thermodynamics MH - Yersinia pestis/*chemistry/genetics EDAT- 2004/11/13 09:00 MHDA- 2005/02/26 09:00 CRDT- 2004/11/13 09:00 PHST- 2004/11/09 [aheadofprint] AID - M409253200 [pii] AID - 10.1074/jbc.M409253200 [doi] PST - ppublish SO - J Biol Chem. 2005 Jan 14;280(2):1209-16. Epub 2004 Nov 9. PMID- 21088782 OWN - NLM STAT- MEDLINE DA - 20110110 DCOM- 20110429 IS - 1463-9084 (Electronic) IS - 1463-9076 (Linking) VI - 13 IP - 4 DP - 2011 Jan 28 TI - Conformational selection or induced fit for Brinker and DNA recognition. PG - 1407-12 LID - 10.1039/c0cp00701c [doi] AB - Brinker is the key target protein of the Drosophila Decapentaplegic morphogen signalling pathway. Brinker is widely expressed and can bind with DNA. NMR spectra suggest that apo-Brinker is intrinsically unstructured and undergoes a folding transition upon DNA-binding. However, the coupled mechanism of binding and folding is poorly understood. Here, we performed molecular dynamics (MD) simulations for both bound and apo-Brinker to study the mechanism. Room-temperature MD simulations suggest that Brinker becomes more rigid and stable upon DNA-binding. Kinetic analysis of high-temperature MD simulations shows that both bound and apo-Brinker unfold via a two-state process. The time scale of tertiary unfolding is significantly different between bound and apo-Brinker. The predicted Phi-values suggest that there are more residues with native-like transition state ensembles (TSEs) for bound Brinker than for apo-Brinker. The average RMSD differences between bound and apo-Brinker and Kolmogorov-Smirnov (KS) test analysis illustrate that Brinker folding upon DNA-binding might obey induced-fit mechanism based on MD simulations. These methods can be used for the research of other biomolecular folding upon ligand-binding. FAU - Qin, Fang AU - Qin F AD - College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China. FAU - Jiang, Yaobin AU - Jiang Y FAU - Chen, Yue AU - Chen Y FAU - Wu, Maoying AU - Wu M FAU - Yan, Guanwen AU - Yan G FAU - Ye, Wenjun AU - Ye W FAU - Li, Yixue AU - Li Y FAU - Zhang, Jian AU - Zhang J FAU - Chen, Hai-Feng AU - Chen HF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101118 PL - England TA - Phys Chem Chem Phys JT - Physical chemistry chemical physics : PCCP JID - 100888160 RN - 0 (Apoproteins) RN - 0 (Drosophila Proteins) RN - 0 (Repressor Proteins) RN - 0 (Solvents) RN - 0 (brinker protein, Drosophila) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Apoproteins/chemistry/metabolism MH - DNA/chemistry/*metabolism MH - Drosophila Proteins/*chemistry/*metabolism MH - Drosophila melanogaster MH - Kinetics MH - *Molecular Dynamics Simulation MH - Nucleic Acid Conformation MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Unfolding MH - Repressor Proteins/*chemistry/*metabolism MH - Solvents/chemistry MH - Substrate Specificity EDAT- 2010/11/20 06:00 MHDA- 2011/04/30 06:00 CRDT- 2010/11/20 06:00 PHST- 2010/11/18 [aheadofprint] PHST- 2011/01/10 [epublish] AID - 10.1039/c0cp00701c [doi] PST - ppublish SO - Phys Chem Chem Phys. 2011 Jan 28;13(4):1407-12. doi: 10.1039/c0cp00701c. Epub 2010 Nov 18. PMID- 9298899 OWN - NLM STAT- MEDLINE DA - 19971016 DCOM- 19971016 LR - 20141120 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 90 IP - 5 DP - 1997 Sep 5 TI - Three-dimensional structure of the armadillo repeat region of beta-catenin. PG - 871-82 AB - Beta-catenin is essential for cadherin-based cell adhesion and Wnt/Wingless growth factor signaling. In these roles, it binds to cadherins, Tcf-family transcription factors, and the tumor suppressor gene product Adenomatous Polyposis Coli (APC). A core region of beta-catenin, composed of 12 copies of a 42 amino acid sequence motif known as an armadillo repeat, mediates these interactions. The three-dimensional structure of a protease-resistant fragment of beta-catenin containing the armadillo repeat region has been determined. The 12 repeats form a superhelix of helices that features a long, positively charged groove. Although unrelated in sequence, the beta-catenin binding regions of cadherins, Tcfs, and APC are acidic and are proposed to interact with this groove. FAU - Huber, A H AU - Huber AH AD - Department of Structural Biology, Stanford University School of Medicine, California 94305, USA. FAU - Nelson, W J AU - Nelson WJ FAU - Weis, W I AU - Weis WI LA - eng SI - PDB/2BCT SI - PDB/3BCT PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Cell JT - Cell JID - 0413066 RN - 0 (Armadillo Domain Proteins) RN - 0 (CTNNB1 protein, mouse) RN - 0 (Cadherins) RN - 0 (Cytoskeletal Proteins) RN - 0 (Drosophila Proteins) RN - 0 (Insect Proteins) RN - 0 (Trans-Activators) RN - 0 (beta Catenin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Armadillo Domain Proteins MH - Binding Sites MH - Cadherins/chemistry/genetics/metabolism MH - Cytoskeletal Proteins/*chemistry/*genetics/metabolism MH - *Drosophila Proteins MH - Insect Proteins/chemistry MH - Mice MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - *Repetitive Sequences, Nucleic Acid MH - *Trans-Activators MH - beta Catenin EDAT- 1997/09/23 MHDA- 1997/09/23 00:01 CRDT- 1997/09/23 00:00 AID - S0092-8674(00)80352-9 [pii] PST - ppublish SO - Cell. 1997 Sep 5;90(5):871-82. PMID- 16228381 OWN - NLM STAT- Publisher DA - 20051017 IS - 1573-5079 (Electronic) IS - 0166-8595 (Linking) VI - 77 IP - 1 DP - 2003 TI - Amino acid sequences and solution structures of manganese stabilizing protein that affect reconstitution of Photosystem II activity. PG - 21-34 AB - This minireview presents a summary of information available on the secondary and tertiary structure of manganese stabilizing protein (MSP) in solution, and on the identity of amino acid residues that affect binding and functional assembly of this protein into Photosystem II. New data on the secondary structure of C-terminal mutants and 90 degrees C-heated manganese stabilizing protein, along with earlier data on the secondary structure of N-terminal mutants and the tertiary structure of all modified MSP species, allow for an evaluation of models for spinach MSP secondary and tertiary structure. This summary of previous and new information better documents the natively unfolded behavior of the protein in solution. A two-step mechanism for binding of manganese stabilizing protein to Photosystem II is discussed and possible solution three-dimensional conformations of the wild-type protein and some of its unfolded mutants, are proposed. FAU - Popelkova, Hana AU - Popelkova H AD - Department of Molecular, Cellular, and Developmental Biology, USA. FAU - Wyman, Aaron AU - Wyman A FAU - Yocum, Charles AU - Yocum C LA - eng PT - Journal Article PL - Netherlands TA - Photosynth Res JT - Photosynthesis research JID - 100954728 EDAT- 2005/10/18 09:00 MHDA- 2005/10/18 09:00 CRDT- 2005/10/18 09:00 AID - 10.1023/A:1024970926655 [doi] PST - ppublish SO - Photosynth Res. 2003;77(1):21-34. PMID- 21559969 OWN - NLM STAT- MEDLINE DA - 20110811 DCOM- 20111121 IS - 1432-203X (Electronic) IS - 0721-7714 (Linking) VI - 30 IP - 9 DP - 2011 Sep TI - PELPK1 (At5g09530) contains a unique pentapeptide repeat and is a positive regulator of germination in Arabidopsis thaliana. PG - 1735-45 LID - 10.1007/s00299-011-1081-3 [doi] AB - Arabidopsis gene At5g09530 has been previously annotated as a cell wall protein of either the hydroxyproline-rich glycoprotein (HRGP), extensin-like, or proline-rich protein families (e.g. PRP10). However, At5g09530 shows important differences between its amino acid sequence and these other proteins. At5g09530 lacks any motifs typical of major groups of cell wall proteins, but contains 36 repeats of a unique pentapeptide (Pro-Glu-Leu|Ile|Val-Pro-Lys), which we have named the PELPK motif. This motif is repeated in only one other Arabidopsis protein (At5g09520), but proteins containing repeated PELPK motifs are found in many other angiosperms. At5g09530 is predicted to encode an intrinsically disordered protein. We characterized the phenotype of transgenic Arabidopsis with either reduced (RNAi) or increased constitutive (35S promoter) transcript expression of At5g09530. RNAi lines exhibited significantly slower germination and root growth, while overexpression lines had accelerated germination and root growth compared to wild type. Similarly, when grown on soil, RNAi lines had delayed growth and flowering, while overexpression lines had accelerated growth and flowering as compared to wild type. Based on amino acid composition, the presence of a distinct repeated pentapeptide motif and predicted intrinsically disordered structure, we conclude that At5g09530 is not an HRGP, PRP, or extensin-like protein. Because At5g09530 is a distinct and conserved protein, we propose to name it PELPK1, and to name its presumptive inparalog (At5g09520) PELPK2. PELPK1 is necessary for normal rates of germination and growth, while overexpression of PELPK1 is sufficient to accelerate germination and growth. FAU - Rashid, Abdur AU - Rashid A AD - Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada. FAU - Deyholos, Michael K AU - Deyholos MK LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110511 PL - Germany TA - Plant Cell Rep JT - Plant cell reports JID - 9880970 RN - 0 (Arabidopsis Proteins) RN - 0 (Soil) SB - IM MH - Amino Acid Sequence MH - Arabidopsis/*genetics/growth & development/metabolism MH - Arabidopsis Proteins/genetics/*metabolism MH - Flowers/growth & development MH - Gene Expression Regulation, Developmental MH - Gene Expression Regulation, Plant MH - *Genes, Plant MH - Genetic Vectors MH - *Germination MH - Molecular Sequence Data MH - Phenotype MH - Plant Roots/genetics/*growth & development/metabolism MH - Plants, Genetically Modified/genetics/growth & development/metabolism MH - RNA Interference MH - Soil MH - Transformation, Genetic EDAT- 2011/05/12 06:00 MHDA- 2011/12/13 00:00 CRDT- 2011/05/12 06:00 PHST- 2011/03/19 [received] PHST- 2011/04/27 [accepted] PHST- 2011/04/27 [revised] PHST- 2011/05/11 [aheadofprint] AID - 10.1007/s00299-011-1081-3 [doi] PST - ppublish SO - Plant Cell Rep. 2011 Sep;30(9):1735-45. doi: 10.1007/s00299-011-1081-3. Epub 2011 May 11. PMID- 21330354 OWN - NLM STAT- MEDLINE DA - 20110614 DCOM- 20110823 LR - 20150224 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 39 IP - 11 DP - 2011 Jun TI - Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq. PG - 4900-15 LID - 10.1093/nar/gkq1346 [doi] AB - The hexameric Escherichia coli RNA chaperone Hfq (Hfq(Ec)) is involved in riboregulation of target mRNAs by small trans-encoded RNAs. Hfq proteins of different bacteria comprise an evolutionarily conserved core, whereas the C-terminus is variable in length. Although the structure of the conserved core has been elucidated for several Hfq proteins, no structural information has yet been obtained for the C-terminus. Using bioinformatics, nuclear magnetic resonance spectroscopy, synchrotron radiation circular dichroism (SRCD) spectroscopy and small angle X-ray scattering we provide for the first time insights into the conformation and dynamic properties of the C-terminal extension of Hfq(Ec). These studies indicate that the C-termini are flexible and extend laterally away from the hexameric core, displaying in this way features typical of intrinsically disordered proteins that facilitate intermolecular interactions. We identified a minimal, intrinsically disordered region of the C-terminus supporting the interactions with longer RNA fragments. This minimal region together with rest of the C-terminal extension provides a flexible moiety capable of tethering long and structurally diverse RNA molecules. Furthermore, SRCD spectroscopy supported the hypothesis that RNA fragments exceeding a certain length interact with the C-termini of Hfq(Ec). FAU - Beich-Frandsen, Mads AU - Beich-Frandsen M AD - Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria. FAU - Vecerek, Branislav AU - Vecerek B FAU - Konarev, Petr V AU - Konarev PV FAU - Sjoblom, Bjorn AU - Sjoblom B FAU - Kloiber, Karin AU - Kloiber K FAU - Hammerle, Hermann AU - Hammerle H FAU - Rajkowitsch, Lukas AU - Rajkowitsch L FAU - Miles, Andrew J AU - Miles AJ FAU - Kontaxis, Georg AU - Kontaxis G FAU - Wallace, B A AU - Wallace BA FAU - Svergun, Dimitri I AU - Svergun DI FAU - Konrat, Robert AU - Konrat R FAU - Blasi, Udo AU - Blasi U FAU - Djinovic-Carugo, Kristina AU - Djinovic-Carugo K LA - eng GR - BB/H01070X/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110217 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Escherichia coli Proteins) RN - 0 (Hfq protein, E coli) RN - 0 (Host Factor 1 Protein) RN - 63231-63-0 (RNA) SB - IM MH - Circular Dichroism MH - Computational Biology MH - Escherichia coli Proteins/*chemistry/genetics MH - Host Factor 1 Protein/*chemistry/genetics MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - RNA/chemistry MH - Sequence Deletion PMC - PMC3113564 OID - NLM: PMC3113564 EDAT- 2011/02/19 06:00 MHDA- 2011/08/24 06:00 CRDT- 2011/02/19 06:00 PHST- 2011/02/17 [aheadofprint] AID - gkq1346 [pii] AID - 10.1093/nar/gkq1346 [doi] PST - ppublish SO - Nucleic Acids Res. 2011 Jun;39(11):4900-15. doi: 10.1093/nar/gkq1346. Epub 2011 Feb 17. PMID- 20889975 OWN - NLM STAT- MEDLINE DA - 20101206 DCOM- 20110110 LR - 20140824 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 50 DP - 2010 Dec 10 TI - Low temperature dynamic mapping reveals unexpected order and disorder in troponin. PG - 38978-86 LID - 10.1074/jbc.M110.181305 [doi] AB - Troponin is a pivotal regulatory protein that binds Ca(2+) reversibly to act as the muscle contraction on-off switch. To understand troponin function, the dynamic behavior of the Ca(2+)-saturated cardiac troponin core domain was mapped in detail at 10 degrees C, using H/D exchange-mass spectrometry. The low temperature conditions of the present study greatly enhanced the dynamic map compared with previous work. Approximately 70% of assessable peptide bond hydrogens were protected from exchange sufficiently for dynamic measurement. This allowed the first characterization by this method of many regions of regulatory importance. Most of the TnI COOH terminus was protected from H/D exchange, implying an intrinsically folded structure. This region is critical to the troponin inhibitory function and has been implicated in thin filament activation. Other new findings include unprotected behavior, suggesting high mobility, for the residues linking the two domains of TnC, as well as for the inhibitory peptide residues preceding the TnI switch helix. These data indicate that, in solution, the regulatory subdomain of cardiac troponin is mobile relative to the remainder of troponin. Relatively dynamic properties were observed for the interacting TnI switch helix and TnC NH(2)-domain, contrasting with stable, highly protected properties for the interacting TnI helix 1 and TnC COOH-domain. Overall, exchange protection via protein folding was relatively weak or for a majority of peptide bond hydrogens. Several regions of TnT and TnI were unfolded even at low temperature, suggesting intrinsic disorder. Finally, change in temperature prominently altered local folding stability, suggesting that troponin is an unusually mobile protein under physiological conditions. FAU - Kowlessur, Devanand AU - Kowlessur D AD - Department of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, USA. FAU - Tobacman, Larry S AU - Tobacman LS LA - eng GR - HL038834/HL/NHLBI NIH HHS/United States GR - HL063774/HL/NHLBI NIH HHS/United States GR - R01 HL038834/HL/NHLBI NIH HHS/United States GR - R01 HL063774/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20101002 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Actins) RN - 0 (Peptides) RN - 0 (Troponin C) RN - 0 (Troponin I) RN - 0 (Troponin T) RN - SY7Q814VUP (Calcium) SB - IM MH - Actins/chemistry MH - Calcium/chemistry MH - Humans MH - Kinetics MH - Models, Biological MH - Molecular Conformation MH - Peptides/chemistry MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Spectroscopy, Fourier Transform Infrared MH - Temperature MH - Troponin C/*chemistry MH - Troponin I/*chemistry MH - Troponin T/*chemistry PMC - PMC2998147 OID - NLM: PMC2998147 EDAT- 2010/10/05 06:00 MHDA- 2011/01/11 06:00 CRDT- 2010/10/05 06:00 PHST- 2010/10/02 [aheadofprint] AID - M110.181305 [pii] AID - 10.1074/jbc.M110.181305 [doi] PST - ppublish SO - J Biol Chem. 2010 Dec 10;285(50):38978-86. doi: 10.1074/jbc.M110.181305. Epub 2010 Oct 2. PMID- 24725464 OWN - NLM STAT- MEDLINE DA - 20140619 DCOM- 20140815 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 281 IP - 12 DP - 2014 Jun TI - Cu(II) and dopamine bind to alpha-synuclein and cause large conformational changes. PG - 2738-53 LID - 10.1111/febs.12817 [doi] AB - alpha-Synuclein (AS) is an intrinsically disordered protein that can misfold and aggregate to form Lewy bodies in dopaminergic neurons, a classic hallmark of Parkinson's disease. The binding of Cu(II) and dopamine to AS was evaluated by nanopore analysis with alpha-hemolysin. In the absence of Cu(II), wild-type AS (1 muM) readily translocated through the pore with a blockade current of--85 pA, but mostly bumping events were observed in the presence of 25 muM Cu(II). A binding site in the N-terminus was confirmed, because Cu(II) had no effect on the event profile of a peptide consisting of the C-terminal 96-140 residues. In the presence of dopamine (25 muM), the translocation events at--85 pA shifted to--80 pA, which also represents translocation events, because the event time decreases with increasing voltage. Events at--80 pA were also observed for the mutant A30P AS in the presence of dopamine. Event profiles for an N-terminal 1-60-residue peptide and a C-terminal 96-140-residue peptide were both altered in the presence of 25 muM dopamine. In contrast, dopamine had little effect on the CD spectrum of AS, and a single binding site with a Ka of 3.5 x 10(3) m(-1) was estimated by isothermal titration calorimetry. Thus, dopamine can interact with both the N-terminus and the C-terminus. Two-dimensional NMR spectroscopy of AS in the presence of dopamine showed that there were significant changes in the spectra in all regions of the protein. According to these findings, a model is presented in which dopamine induces folding between the N-terminus and C-terminus of AS. Partially folding conformations such as this may represent important intermediates in the misfolding of AS that leads to fibrillization. CI - (c) 2014 FEBS. FAU - Tavassoly, Omid AU - Tavassoly O AD - Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada. FAU - Nokhrin, Sergiy AU - Nokhrin S FAU - Dmitriev, Oleg Y AU - Dmitriev OY FAU - Lee, Jeremy S AU - Lee JS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140507 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (alpha-Synuclein) RN - 789U1901C5 (Copper) RN - VTD58H1Z2X (Dopamine) SB - IM MH - Binding Sites MH - Calorimetry MH - Copper/*metabolism MH - Dopamine/*metabolism MH - Protein Conformation MH - Protein Transport MH - alpha-Synuclein/chemistry/*metabolism OTO - NOTNLM OT - Parkinson's disease OT - dopamine OT - intrinsically disordered protein OT - nanopore analysis OT - alpha-synuclein EDAT- 2014/04/15 06:00 MHDA- 2014/08/16 06:00 CRDT- 2014/04/15 06:00 PHST- 2013/10/31 [received] PHST- 2014/04/04 [revised] PHST- 2014/04/09 [accepted] PHST- 2014/05/07 [aheadofprint] AID - 10.1111/febs.12817 [doi] PST - ppublish SO - FEBS J. 2014 Jun;281(12):2738-53. doi: 10.1111/febs.12817. Epub 2014 May 7. PMID- 22940584 OWN - NLM STAT- MEDLINE DA - 20121015 DCOM- 20130322 LR - 20141105 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 20 IP - 10 DP - 2012 Oct 10 TI - The molecular basis for substrate specificity of the nuclear NIPP1:PP1 holoenzyme. PG - 1746-56 LID - 10.1016/j.str.2012.08.003 [doi] LID - S0969-2126(12)00284-5 [pii] AB - Regulation of protein phosphatase 1 (PP1) is controlled by a diverse array of regulatory proteins. However, how these proteins direct PP1 specificity is not well understood. More than one-third of the nuclear pool of PP1 forms a holoenzyme with the nuclear inhibitor of PP1, NIPP1, to regulate chromatin remodeling, among other essential biological functions. Here, we show that the PP1-binding domain of NIPP1 is an intrinsically disordered protein, which binds PP1 in an unexpected manner. NIPP1 forms an alpha helix that engages PP1 at a unique interaction site, using polar rather than hydrophobic contacts. Importantly, the structure also reveals a shared PP1 interaction site outside of the RVxF motif, the PhiPhi motif. Finally, we show that NIPP1:PP1 substrate selectivity is determined by altered electrostatics and enhanced substrate localization. Together, our results provide the molecular basis by which NIPP1 directs PP1 substrate specificity in the nucleus. CI - Copyright (c) 2012 Elsevier Ltd. All rights reserved. FAU - O'Connell, Nichole AU - O'Connell N AD - Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02912, USA. FAU - Nichols, Scott R AU - Nichols SR FAU - Heroes, Ewald AU - Heroes E FAU - Beullens, Monique AU - Beullens M FAU - Bollen, Mathieu AU - Bollen M FAU - Peti, Wolfgang AU - Peti W FAU - Page, Rebecca AU - Page R LA - eng SI - PDB/3V4Y GR - R01 GM098482/GM/NIGMS NIH HHS/United States GR - R01 NS056128/NS/NINDS NIH HHS/United States GR - R01GM098482/GM/NIGMS NIH HHS/United States GR - R01NS056128/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120830 PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (RNA-Binding Proteins) RN - EC 2.4.1.- (Glycogen Phosphorylase) RN - EC 3.1.- (Endoribonucleases) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - EC 3.1.3.16 (Protein Phosphatase 1) RN - EC 3.1.4.- (PPP1R8 protein, human) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Catalytic Domain MH - Crystallography, X-Ray MH - Endoribonucleases/*chemistry MH - Glycogen Phosphorylase/chemistry MH - Humans MH - Hydrogen Bonding MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphoprotein Phosphatases/*chemistry MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - Protein Phosphatase 1/*chemistry MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - RNA-Binding Proteins/*chemistry MH - Substrate Specificity PMC - PMC3472097 MID - NIHMS401481 OID - NLM: NIHMS401481 OID - NLM: PMC3472097 EDAT- 2012/09/04 06:00 MHDA- 2013/03/23 06:00 CRDT- 2012/09/04 06:00 PHST- 2012/06/13 [received] PHST- 2012/08/06 [revised] PHST- 2012/08/07 [accepted] PHST- 2012/08/30 [aheadofprint] AID - S0969-2126(12)00284-5 [pii] AID - 10.1016/j.str.2012.08.003 [doi] PST - ppublish SO - Structure. 2012 Oct 10;20(10):1746-56. doi: 10.1016/j.str.2012.08.003. Epub 2012 Aug 30. PMID- 25284680 OWN - NLM STAT- MEDLINE DA - 20141021 DCOM- 20141231 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 41 DP - 2014 Oct 21 TI - Resonance Raman spectroscopic measurements delineate the structural changes that occur during tau fibril formation. PG - 6550-65 LID - 10.1021/bi500528x [doi] AB - The aggregation of the microtubule-associated protein, tau, into amyloid fibrils is a hallmark of neurodegenerative diseases such as the tauopathies and Alzheimer's disease. Since monomeric tau is an intrinsically disordered protein and the polymeric fibrils possess an ordered cross-beta core, the aggregation process is known to involve substantial conformational conversion besides growth. The aggregation mechanism of tau in the presence of inducers such as heparin, deciphered using probes such as thioflavin T/S fluorescence, light scattering, and electron microscopy assays, has been shown to conform to ligand-induced nucleation-dependent polymerization. These probes do not, however, distinguish between the processes of conformational conversion and fibril growth. In this study, UV resonance Raman spectroscopy is employed to look directly at signatures of changes in secondary structure and side-chain packing during fibril formation by the four repeat functional domain of tau in the presence of the inducer heparin, at pH 7 and at 37 degrees C. Changes in the positions and intensities of the amide Raman bands are shown to occur in two distinct stages during the fibril formation process. The first stage of UVRR spectral changes corresponds to the transformation of monomer into early fibrillar aggregates. The second stage corresponds to the transformation of these early fibrillar aggregates into the final, ordered, mature fibrils and during this stage; the processes of conformational conversion and the consolidation of the fibril core occur simultaneously. Delineation of these secondary structural changes accompanying the formation of tau fibrils holds significance for the understanding of generic and tau-specific principles of amyloid assembly. FAU - Ramachandran, Gayathri AU - Ramachandran G AD - National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India. FAU - Milan-Garces, Erix A AU - Milan-Garces EA FAU - Udgaonkar, Jayant B AU - Udgaonkar JB FAU - Puranik, Mrinalini AU - Puranik M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141006 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Fluorescent Dyes) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (MAPT protein, human) RN - 0 (Recombinant Proteins) RN - 0 (Thiazoles) RN - 0 (tau Proteins) RN - 2390-54-7 (thioflavin T) RN - 9005-49-6 (Heparin) SB - IM MH - Amyloid/*chemistry/genetics/metabolism/ultrastructure MH - Fluorescent Dyes MH - Heparin/chemistry/metabolism MH - Humans MH - Intrinsically Disordered Proteins/*chemistry/genetics/metabolism/ultrastructure MH - Kinetics MH - Microscopy, Atomic Force MH - *Models, Molecular MH - Protein Aggregation, Pathological MH - Protein Conformation MH - Protein Interaction Domains and Motifs MH - Protein Stability MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Repetitive Sequences, Amino Acid MH - Spectrometry, Fluorescence MH - Spectrophotometry, Ultraviolet MH - Spectrum Analysis, Raman MH - Thiazoles/chemistry MH - tau Proteins/*chemistry/genetics/metabolism/ultrastructure EDAT- 2014/10/07 06:00 MHDA- 2015/01/01 06:00 CRDT- 2014/10/07 06:00 PHST- 2014/10/06 [aheadofprint] AID - 10.1021/bi500528x [doi] PST - ppublish SO - Biochemistry. 2014 Oct 21;53(41):6550-65. doi: 10.1021/bi500528x. Epub 2014 Oct 6. PMID- 15235593 OWN - NLM STAT- MEDLINE DA - 20040728 DCOM- 20040916 LR - 20071114 IS - 1545-9993 (Print) IS - 1545-9985 (Linking) VI - 11 IP - 8 DP - 2004 Aug TI - Chemical inhibition of N-WASP by stabilization of a native autoinhibited conformation. PG - 747-55 AB - Current drug discovery efforts focus primarily on proteins with defined enzymatic or small molecule binding sites. Autoregulatory domains represent attractive alternative targets for small molecule inhibitors because they also occur in noncatalytic proteins and because allosteric inhibitors may avoid specificity problems inherent in active site-directed inhibitors. We report here the identification of wiskostatin, a chemical inhibitor of the neural Wiskott-Aldrich syndrome protein (N-WASP). Wiskostatin interacts with a cleft in the regulatory GTPase-binding domain (GBD) of WASP in the solution structure of the complex. Wiskostatin induces folding of the isolated, unstructured GBD into its autoinhibited conformation, suggesting that wiskostatin functions by stabilizing N-WASP in its autoinhibited state. The use of small molecules to bias conformational equilibria represents a potentially general strategy for chemical inhibition of autoinhibited proteins, even in cases where such sites have not been naturally evolved in a target. FAU - Peterson, Jeffrey R AU - Peterson JR AD - Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA. FAU - Bickford, Lincoln C AU - Bickford LC FAU - Morgan, David AU - Morgan D FAU - Kim, Annette S AU - Kim AS FAU - Ouerfelli, Ouathek AU - Ouerfelli O FAU - Kirschner, Marc W AU - Kirschner MW FAU - Rosen, Michael K AU - Rosen MK LA - eng SI - PDB/1T84 GR - GM07739/GM/NIGMS NIH HHS/United States GR - GM197000/GM/NIGMS NIH HHS/United States GR - GM56322/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20040704 PL - United States TA - Nat Struct Mol Biol JT - Nature structural & molecular biology JID - 101186374 RN - 0 (Carbazoles) RN - 0 (Nerve Tissue Proteins) RN - 0 (Propanolamines) RN - 0 (Wiskott-Aldrich Syndrome Protein, Neuronal) RN - 0 (wiskostatin) SB - IM MH - Allosteric Site MH - Animals MH - Binding Sites MH - Carbazoles/chemistry/*pharmacology MH - Catalysis MH - Cytoplasm/metabolism MH - Dose-Response Relationship, Drug MH - Drug Design MH - Magnetic Resonance Spectroscopy MH - Models, Chemical MH - Models, Molecular MH - Nerve Tissue Proteins/chemistry/*physiology MH - Propanolamines/chemistry/*pharmacology MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Signal Transduction MH - Structure-Activity Relationship MH - Time Factors MH - Wiskott-Aldrich Syndrome Protein, Neuronal MH - Xenopus laevis/metabolism EDAT- 2004/07/06 05:00 MHDA- 2004/09/17 05:00 CRDT- 2004/07/06 05:00 PHST- 2004/03/05 [received] PHST- 2004/05/24 [accepted] PHST- 2004/07/04 [aheadofprint] AID - 10.1038/nsmb796 [doi] AID - nsmb796 [pii] PST - ppublish SO - Nat Struct Mol Biol. 2004 Aug;11(8):747-55. Epub 2004 Jul 4. PMID- 10496225 OWN - NLM STAT- MEDLINE DA - 19991005 DCOM- 19991005 LR - 20140615 IS - 1355-8382 (Print) IS - 1355-8382 (Linking) VI - 5 IP - 9 DP - 1999 Sep TI - Dissecting FMR1, the protein responsible for fragile X syndrome, in its structural and functional domains. PG - 1248-58 AB - FMR1 is an RNA-binding protein that is either absent or mutated in patients affected by the fragile X syndrome, the most common inherited cause of mental retardation in humans. Sequence analysis of the FMR1 protein has suggested that RNA binding is related to the presence of two K-homologous (KH) modules and an RGG box. However, no attempt has been so far made to map the RNA-binding sites along the protein sequence and to identify possible differential RNA-sequence specificity. In the present article, we describe work done to dissect FMR1 into regions with structurally and functionally distinct properties. A semirational approach was followed to identify four regions: an N-terminal stretch of 200 amino acids, the two KH regions, and a C-terminal stretch. Each region was produced as a recombinant protein, purified, and probed for its state of folding by spectroscopical techniques. Circular dichroism and NMR spectra of the N-terminus show formation of secondary structure with a strong tendency to aggregate. Of the two homologous KH motifs, only the first one is folded whereas the second remains unfolded even when it is extended both N- and C-terminally. The C-terminus is, as expected from its amino acid composition, nonglobular. Binding assays were then performed using the 4-nt homopolymers. Our results show that only the first KH domain but not the second binds to RNA, and provide the first direct evidence for RNA binding of both the N-terminal and the C-terminal regions. RNA binding for the N-terminus could not be predicted from sequence analysis because no known RNA-binding motif is identifiable in this region. Different sequence specificity was observed for the fragments: both the N-terminus of the protein and KH1 bind preferentially to poly-(rG). The C-terminal region, which contains the RGG box, is nonspecific, as it recognizes the bases with comparable affinity. We therefore conclude that FMR1 is a protein with multiple sites of interaction with RNA: sequence specificity is most likely achieved by the whole block that comprises the first approximately 400 residues, whereas the C-terminus provides a nonspecific binding surface. FAU - Adinolfi, S AU - Adinolfi S AD - The National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom. FAU - Bagni, C AU - Bagni C FAU - Musco, G AU - Musco G FAU - Gibson, T AU - Gibson T FAU - Mazzarella, L AU - Mazzarella L FAU - Pastore, A AU - Pastore A LA - eng GR - MC_U117584256/Medical Research Council/United Kingdom PT - Journal Article PL - UNITED STATES TA - RNA JT - RNA (New York, N.Y.) JID - 9509184 RN - 0 (FMR1 protein, human) RN - 0 (Nerve Tissue Proteins) RN - 0 (RNA-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 139135-51-6 (Fragile X Mental Retardation Protein) RN - 63231-63-0 (RNA) SB - IM MH - Amino Acid Sequence MH - Blotting, Western MH - Circular Dichroism MH - Fragile X Mental Retardation Protein MH - Fragile X Syndrome/*genetics MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Genetic MH - Molecular Sequence Data MH - Mutagenesis MH - Nerve Tissue Proteins/*chemistry/*genetics MH - Protein Binding MH - Protein Folding MH - RNA/*metabolism MH - *RNA-Binding Proteins MH - Recombinant Proteins/metabolism MH - Sequence Homology, Amino Acid MH - Structure-Activity Relationship PMC - PMC1369847 OID - NLM: PMC1369847 EDAT- 1999/09/25 MHDA- 1999/09/25 00:01 CRDT- 1999/09/25 00:00 PST - ppublish SO - RNA. 1999 Sep;5(9):1248-58. PMID- 15476391 OWN - NLM STAT- MEDLINE DA - 20041012 DCOM- 20041109 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 41 DP - 2004 Oct 19 TI - Overexpression, purification, and characterization of ProQ, a posttranslational regulator for osmoregulatory transporter ProP of Escherichia coli. PG - 12979-89 AB - ProP is an osmosensor and osmoregulatory transporter in Escherichia coli. Osmotic activation of ProP is attenuated 5-fold in the absence of soluble protein ProQ, but proQ lesions do not influence proP transcription or ProP levels. The mechanism by which ProQ amplifies ProP activity is unknown. Putative proQ orthologues are found in Gram-negative bacteria (only), but none have known functions. ProQ was overexpressed to low and high levels with and without a C-terminal histidine tag (His(6)). Plasmid-encoded ProQ or ProQ-His(6) complemented in-frame chromosomal deletion DeltaproQ676, restoring ProP activity. After overexpression, both proteins were poorly soluble unless cells were lysed in media of high salinity. ProQ copurified with DNA binding proteins of similar size (HU and a histone-like protein) by ion exchange and exclusion chromatographies, whereas ProQ-His(6) could be purified to homogeneity by nickel chelate affinity chromatography. Sequence-based analysis and modeling suggest that ProQ includes distinct N- and C-terminal domains linked by an unstructured sequence. The N-terminal domain can be modeled on the crystal structure of alpha-helical RNA binding protein FinO, whereas the C-terminal domain can be modeled on an SH3-like domain (beta-structure). Both ProQ and ProQ-His(6) appeared to be monomeric, though the higher Stokes radius of ProQ-His(6) may reflect altered domain interactions. The measured secondary structure content of ProQ (circular dichroism (CD) spectroscopy) contrasted with sequence-based prediction but was as expected if the spectrum of the C-terminal domain is analogous to those reported for SH3 domains. The CD spectrum of ProQ was pH- but not NaCl-sensitive. FAU - Smith, Michelle N AU - Smith MN AD - Department of Microbiology, and Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, University of Guelph, Guelph, ON N1G 2W1, Canada. FAU - Crane, Rebecca A AU - Crane RA FAU - Keates, Robert A B AU - Keates RA FAU - Wood, Janet M AU - Wood JM LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Carrier Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Membrane Transport Proteins) RN - 0 (ProP protein, E coli) RN - 0 (ProQ protein, E coli) RN - 0 (Recombinant Proteins) RN - 0 (Symporters) RN - 4QD397987E (Histidine) SB - IM MH - Amino Acid Sequence MH - Carrier Proteins/biosynthesis/*chemistry/*genetics/isolation & purification MH - Dimerization MH - Escherichia coli Proteins/biosynthesis/*chemistry/*genetics/isolation & purification/*metabolism MH - Gene Deletion MH - Genetic Complementation Test MH - Histidine/genetics MH - *Membrane Transport Proteins MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Osmolar Concentration MH - Plasmids MH - *Protein Processing, Post-Translational MH - Protein Structure, Secondary MH - Recombinant Proteins/biosynthesis/chemistry/isolation & purification MH - Spectrophotometry, Ultraviolet MH - Structure-Activity Relationship MH - Symporters/*metabolism EDAT- 2004/10/13 09:00 MHDA- 2004/11/13 09:00 CRDT- 2004/10/13 09:00 AID - 10.1021/bi048561g [doi] PST - ppublish SO - Biochemistry. 2004 Oct 19;43(41):12979-89. PMID- 15476390 OWN - NLM STAT- MEDLINE DA - 20041012 DCOM- 20041109 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 41 DP - 2004 Oct 19 TI - Transient aggregation and stable dimerization induced by introducing an Alzheimer sequence into a water-soluble protein. PG - 12964-78 AB - Transient contacts between denatured polypeptide chains are likely to play an important part in the initial stages of protein aggregation and fibrillation. To analyze the nature of such contacts, we have carried out a protein engineering study of the 102-residue protein U1A, which aggregates transiently in the wild-type form during refolding from the guanidinium chloride-denatured state. We have prepared a series of mutants with increased aggregation tendencies by increasing the homology between two beta-strands of U1A and the Alzheimer peptide (beta-AP). These mutants undergo transient aggregation during refolding, as measured by concentration dependence, double-jump experiments, and binding of ANS, a probe for exposed hydrophobic patches on protein surfaces. The propensity to aggregate increases with increasing homology to beta-AP. Further, the degree of transient ANS binding correlates reasonably well with the structural parameters recently shown to play a role in the fibrillation of natively unfolded proteins. Two mutants highly prone to transient aggregation, U1A-J and U1A-G, were also studied by NMR. Secondary structural elements of the U1A-J construct (with lower beta-AP homology) are very similar to those observed in U1A-wt. In contrast, the high-homology construct U1A-G exhibits local unfolding of the C-terminal helix, which packs against the beta-sheet in the wild-type protein. U1A-G is mainly dimeric according to (15)N spin relaxation data, and the dimer interface most likely involves the beta-sheet. Our data suggest that the transient aggregate relies on specific intermolecular interactions mediated by structurally flexible regions and that contacts may be formed in different beta-strand registers. FAU - Otzen, Daniel E AU - Otzen DE AD - Department of Life Science, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark. dao@bio.aau.dk FAU - Miron, Simona AU - Miron S FAU - Akke, Mikael AU - Akke M FAU - Oliveberg, Mikael AU - Oliveberg M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid beta-Peptides) RN - 0 (Anilino Naphthalenesulfonates) RN - 0 (Peptide Fragments) RN - 0 (RNA-Binding Proteins) RN - 0 (Ribonucleoprotein, U1 Small Nuclear) RN - 0 (U1A protein) RN - 059QF0KO0R (Water) RN - 82-76-8 (1-anilino-8-naphthalenesulfonate) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Alzheimer Disease/metabolism MH - Amino Acid Sequence MH - Amyloid beta-Peptides/*chemistry/genetics/metabolism MH - Anilino Naphthalenesulfonates/metabolism MH - Dimerization MH - Guanidine/chemistry MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Peptide Fragments/*chemistry/genetics/metabolism MH - Protein Binding/genetics MH - Protein Denaturation/genetics MH - Protein Folding MH - Protein Structure, Tertiary/genetics MH - RNA-Binding Proteins/*chemistry/genetics/metabolism MH - Ribonucleoprotein, U1 Small Nuclear/*chemistry/genetics/metabolism MH - Sequence Homology, Amino Acid MH - Solubility MH - *Water EDAT- 2004/10/13 09:00 MHDA- 2004/11/13 09:00 CRDT- 2004/10/13 09:00 AID - 10.1021/bi048509k [doi] PST - ppublish SO - Biochemistry. 2004 Oct 19;43(41):12964-78. PMID- 24014766 OWN - NLM STAT- MEDLINE DA - 20131028 DCOM- 20140623 LR - 20150401 IS - 1535-9786 (Electronic) IS - 1535-9786 (Linking) VI - 12 IP - 11 DP - 2013 Nov TI - Structural and functional characterization of the N terminus of Schizosaccharomyces pombe Cwf10. PG - 1472-89 LID - 10.1128/EC.00140-13 [doi] AB - The spliceosome is a dynamic macromolecular machine that catalyzes the removal of introns from pre-mRNA, yielding mature message. Schizosaccharomyces pombe Cwf10 (homolog of Saccharomyces cerevisiae Snu114 and human U5-116K), an integral member of the U5 snRNP, is a GTPase that has multiple roles within the splicing cycle. Cwf10/Snu114 family members are highly homologous to eukaryotic translation elongation factor EF2, and they contain a conserved N-terminal extension (NTE) to the EF2-like portion, predicted to be an intrinsically unfolded domain. Using S. pombe as a model system, we show that the NTE is not essential, but cells lacking this domain are defective in pre-mRNA splicing. Genetic interactions between cwf10-DeltaNTE and other pre-mRNA splicing mutants are consistent with a role for the NTE in spliceosome activation and second-step catalysis. Characterization of Cwf10-NTE by various biophysical techniques shows that in solution the NTE contains regions of both structure and disorder. The first 23 highly conserved amino acids of the NTE are essential for its role in splicing but when overexpressed are not sufficient to restore pre-mRNA splicing to wild-type levels in cwf10-DeltaNTE cells. When the entire NTE is overexpressed in the cwf10-DeltaNTE background, it can complement the truncated Cwf10 protein in trans, and it immunoprecipitates a complex similar in composition to the late-stage U5.U2/U6 spliceosome. These data show that the structurally flexible NTE is capable of independently incorporating into the spliceosome and improving splicing function, possibly indicating a role for the NTE in stabilizing conformational rearrangements during a splice cycle. FAU - Livesay, S Brent AU - Livesay SB AD - Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA. FAU - Collier, Scott E AU - Collier SE FAU - Bitton, Danny A AU - Bitton DA FAU - Bahler, Jurg AU - Bahler J FAU - Ohi, Melanie D AU - Ohi MD LA - eng GR - 095598/Wellcome Trust/United Kingdom GR - DP2OD004483/OD/NIH HHS/United States GR - P30 CA68485/CA/NCI NIH HHS/United States GR - T32 CA009582/CA/NCI NIH HHS/United States GR - T32 GM008320/GM/NIGMS NIH HHS/United States GR - T32 GM08320/GM/NIGMS NIH HHS/United States GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130906 PL - United States TA - Eukaryot Cell JT - Eukaryotic cell JID - 101130731 RN - 0 (Ribonucleoprotein, U5 Small Nuclear) RN - 0 (Schizosaccharomyces pombe Proteins) RN - EC 3.6.1.- (Cwf10 protein, S pombe) RN - EC 3.6.1.- (GTP Phosphohydrolases) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - GTP Phosphohydrolases/genetics/*metabolism MH - Molecular Sequence Data MH - Mutation MH - Protein Binding MH - Protein Structure, Tertiary MH - RNA Splicing MH - Ribonucleoprotein, U5 Small Nuclear/chemistry/genetics/*metabolism MH - Schizosaccharomyces/chemistry/*enzymology/genetics MH - Schizosaccharomyces pombe Proteins/chemistry/genetics/*metabolism MH - Spliceosomes/metabolism PMC - PMC3837936 OID - NLM: PMC3837936 EDAT- 2013/09/10 06:00 MHDA- 2014/06/24 06:00 CRDT- 2013/09/10 06:00 PHST- 2013/09/06 [aheadofprint] AID - EC.00140-13 [pii] AID - 10.1128/EC.00140-13 [doi] PST - ppublish SO - Eukaryot Cell. 2013 Nov;12(11):1472-89. doi: 10.1128/EC.00140-13. Epub 2013 Sep 6. PMID- 22507829 OWN - NLM STAT- MEDLINE DA - 20120528 DCOM- 20120921 IS - 1095-8657 (Electronic) IS - 1047-8477 (Linking) VI - 178 IP - 3 DP - 2012 Jun TI - C-Terminal acidic domain of ubiquitin-conjugating enzymes: a multi-functional conserved intrinsically disordered domain in family 3 of E2 enzymes. PG - 245-59 LID - 10.1016/j.jsb.2012.04.003 [doi] AB - E2 ubiquitin-conjugating enzymes are key elements of the ubiquitin (Ub) pathway, since they influence processivity and topology of the Ub chain assembly and, as a consequence, the fate of the target substrates. E2s are multi-domain proteins, with accessory N-terminal or C-terminal domains that can contribute to the specificity for the cognate Ub-like molecules, or even the E3. In this context, the thorough structural characterization of E2 accessory domains is mandatory, in particular when they are associated to specific functions. We here provide, by computational and comparative studies, the first evidence of an acidic domain (AD) conserved in the E2 sub-family 3R. It is an intrinsically disordered domain, in which elements for Ub or E3 recognition are maintained. This conserved acidic domain (AD) shows propensity for alpha-helix structures (185-192 and 204-218) in the proximity of the sites for interaction with the Ub or the cognate E3. Moreover, our results also suggest that AD can explore conformations with tertiary contacts mainly driven by aromatic and hydrophobic interactions, in absence of its interaction partners. The globular states are likely to be regulated by multiple phosphorylation events, which can trigger conformational changes toward more extended conformations, as judged by MD simulations of the phospho-variants. The extended conformations, in turn, promote the accessibility of the interaction sites for Ub and the E3. We also trace a parallel between this new and natively unfolded structural motif for Ub-recognition and the natively folded ubiquitin associated domain (UBA) typical of family 1 of E2 enzymes, which includes Ubc1. In fact, according to our calculations, Ubc1 maps at the interface between the space of the natively unfolded and folded proteins, as well as it shares common features with the acidic domain of family 3 members. CI - Copyright (c) 2012 Elsevier Inc. All rights reserved. FAU - Arrigoni, Alberto AU - Arrigoni A AD - Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy. FAU - Grillo, Barbara AU - Grillo B FAU - Vitriolo, Alessandro AU - Vitriolo A FAU - De Gioia, Luca AU - De Gioia L FAU - Papaleo, Elena AU - Papaleo E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120413 PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - 0 (Ubiquitin) RN - EC 6.3.2.19 (Ubiquitin-Conjugating Enzymes) SB - IM MH - Amino Acid Sequence MH - Humans MH - Molecular Sequence Data MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Ubiquitin/metabolism MH - Ubiquitin-Conjugating Enzymes/*chemistry/genetics/*metabolism EDAT- 2012/04/18 06:00 MHDA- 2012/09/22 06:00 CRDT- 2012/04/18 06:00 PHST- 2011/10/22 [received] PHST- 2012/04/01 [revised] PHST- 2012/04/03 [accepted] PHST- 2012/04/13 [aheadofprint] AID - S1047-8477(12)00106-2 [pii] AID - 10.1016/j.jsb.2012.04.003 [doi] PST - ppublish SO - J Struct Biol. 2012 Jun;178(3):245-59. doi: 10.1016/j.jsb.2012.04.003. Epub 2012 Apr 13. PMID- 16823031 OWN - NLM STAT- MEDLINE DA - 20060731 DCOM- 20060925 LR - 20141120 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 15 IP - 8 DP - 2006 Aug TI - Hydrogen/deuterium-exchange (H/D-Ex) of PPARgamma LBD in the presence of various modulators. PG - 1883-92 AB - A nuclear receptor, peroxisome proliferator-activated receptor gamma (PPARgamma), is a ligand-dependent transcription factor involved in glucose homeostasis and adipocyte differentiation. PPARgamma is the molecular target of various natural and synthetic molecules, including anti-diabetic agents such as rosiglitazone. Amide hydrogen/deuterium-exchange (H/D-Ex), coupled with proteolysis and mass spectrometry, was applied to study the dynamics of the PPARgamma ligand binding domain (LBD) with or without molecules that modulate PPARgamma activity. The H/D-Ex patterns of ligand-free PPARgamma LBD show that the ligand binding pocket of LBD is significantly more dynamic than the rest of the LBD. Presumably, the binding pocket is intrinsically disordered in order to accommodate different ligands. The presence of two full agonists (rosiglitazone and GW1929), a partial agonist (nTZDpa), and a covalent antagonist (GW9662), changed the dynamics/conformation of PPARgamma LBD and slowed the H/D exchange rate in various regions of the protein. The full agonists slowed the H/D exchange more globally and to a greater extent than the partial agonist or the antagonist, indicating that the full agonist stabilizes the PPARgamma LBD more than the partial agonist or the antagonist. One interesting observation is that the two full agonists significantly stabilized helix 12 while the partial agonist and the antagonist did not perturb the H/D exchange of this region. The results showed that the change in protein dynamics induced by ligand binding may be an important factor for the activation of genes and that H/D-Ex is a useful method for analyzing the biological activity of drug leads. FAU - Hamuro, Yoshitomo AU - Hamuro Y AD - ExSAR Corp., Monmouth Junction, New Jersey 08852, USA. yhamuro@exsar.com FAU - Coales, Stephen J AU - Coales SJ FAU - Morrow, Jeffrey A AU - Morrow JA FAU - Molnar, Kathleen S AU - Molnar KS FAU - Tuske, Steven J AU - Tuske SJ FAU - Southern, Mark R AU - Southern MR FAU - Griffin, Patrick R AU - Griffin PR LA - eng PT - Journal Article DEP - 20060705 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (2-chloro-5-nitrobenzanilide) RN - 0 (5-chloro-1-(4-chlorobenzyl)-3-(phenylthio)indole-2-carboxylic acid) RN - 0 (Amides) RN - 0 (Anilides) RN - 0 (Benzophenones) RN - 0 (GW 1929) RN - 0 (Indoles) RN - 0 (Ligands) RN - 0 (PPAR gamma) RN - 0 (Peptide Fragments) RN - 0 (Sulfides) RN - 0 (Thiazolidinediones) RN - 05V02F2KDG (rosiglitazone) RN - 42HK56048U (Tyrosine) RN - EC 3.4.23.1 (Pepsin A) SB - IM MH - Amides/chemistry MH - Amino Acid Sequence MH - Anilides/pharmacology MH - Benzophenones/pharmacology MH - Binding Sites MH - *Deuterium Exchange Measurement MH - Indoles/pharmacology MH - Ligands MH - Mass Spectrometry MH - Models, Molecular MH - PPAR gamma/agonists/antagonists & inhibitors/*chemistry MH - Pepsin A/metabolism MH - Peptide Fragments/metabolism MH - Protein Conformation/drug effects MH - Protein Structure, Tertiary/*drug effects MH - Sulfides/pharmacology MH - Thiazolidinediones/pharmacology MH - Tyrosine/analogs & derivatives/pharmacology PMC - PMC2242592 OID - NLM: PMC2242592 EDAT- 2006/07/11 09:00 MHDA- 2006/09/26 09:00 CRDT- 2006/07/11 09:00 PHST- 2006/07/05 [aheadofprint] AID - ps.062103006 [pii] AID - 10.1110/ps.062103006 [doi] PST - ppublish SO - Protein Sci. 2006 Aug;15(8):1883-92. Epub 2006 Jul 5. PMID- 18537269 OWN - NLM STAT- MEDLINE DA - 20080625 DCOM- 20080721 LR - 20140916 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 26 DP - 2008 Jul 1 TI - Structure of yeast poly(A) polymerase in complex with a peptide from Fip1, an intrinsically disordered protein. PG - 6859-69 LID - 10.1021/bi800204k [doi] AB - In yeast, the mRNA processing enzyme poly(A) polymerase is tethered to the much larger 3'-end processing complex via Fip1, a 36 kDa protein of unknown structure. We report the 2.6 A crystal structure of yeast poly(A) polymerase in complex with a peptide containing residues 80-105 of Fip1. The Fip1 peptide binds to the outside surface of the C-terminal domain of the polymerase. On the basis of this structure, we designed a mutant of the polymerase (V498Y, C485R) that is lethal to yeast. The mutant is unable to bind Fip1 but retains full polymerase activity. Fip1 is found in all eukaryotes and serves to connect poly(A) polymerase to pre-mRNA processing complexes in yeast, plants, and mammals. However, the Fip1 sequence is highly divergent, and residues on both Pap1 and Fip1 at the observed interaction surface are poorly conserved. Herein we demonstrate using analytical ultracentrifugation, circular dichroism, proteolytic studies, and other techniques that, in the absence of Pap1, Fip1 is largely, if not completely, unfolded. We speculate that flexibility may be important for Fip1's function as a molecular scaffold. FAU - Meinke, Gretchen AU - Meinke G AD - Department of Biochemistry, Tufts University, 136 Harrison Avenue, Boston, Massachusetts 02111, USA. FAU - Ezeokonkwo, Chukwudi AU - Ezeokonkwo C FAU - Balbo, Paul AU - Balbo P FAU - Stafford, Walter AU - Stafford W FAU - Moore, Claire AU - Moore C FAU - Bohm, Andrew AU - Bohm A LA - eng SI - PDB/1FA0 SI - PDB/201P SI - PDB/2HHP SI - PDB/2Q66 SI - PDB/3C66 GR - GM041752/GM/NIGMS NIH HHS/United States GR - GM065972/GM/NIGMS NIH HHS/United States GR - P30 EB009998/EB/NIBIB NIH HHS/United States GR - R01 GM065972/GM/NIGMS NIH HHS/United States GR - R01 GM065972-05/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20080607 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (FIP1 protein, S cerevisiae) RN - 0 (Peptides) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (mRNA Cleavage and Polyadenylation Factors) RN - EC 2.7.7.19 (Polynucleotide Adenylyltransferase) SB - IM MH - Amino Acid Sequence MH - Biophysical Phenomena MH - Biophysics MH - Conserved Sequence MH - Crystallography, X-Ray MH - Humans MH - Kinetics MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation/genetics MH - Peptides/*chemistry/*metabolism MH - Polynucleotide Adenylyltransferase/*chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Quaternary MH - Saccharomyces cerevisiae/*enzymology/genetics MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism MH - Sequence Alignment MH - mRNA Cleavage and Polyadenylation Factors/*chemistry/genetics/*metabolism PMC - PMC2615413 MID - NIHMS77858 OID - NLM: NIHMS77858 OID - NLM: PMC2615413 EDAT- 2008/06/10 09:00 MHDA- 2008/07/22 09:00 CRDT- 2008/06/10 09:00 PHST- 2008/06/07 [aheadofprint] AID - 10.1021/bi800204k [doi] PST - ppublish SO - Biochemistry. 2008 Jul 1;47(26):6859-69. doi: 10.1021/bi800204k. Epub 2008 Jun 7. PMID- 18537264 OWN - NLM STAT- MEDLINE DA - 20080625 DCOM- 20080721 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 26 DP - 2008 Jul 1 TI - Local structural preferences of calpastatin, the intrinsically unstructured protein inhibitor of calpain. PG - 6936-45 LID - 10.1021/bi800201a [doi] AB - Calpain, the calcium-activated intracellular cysteine protease, is under the tight control of its intrinsically unstructured inhibitor, calpastatin. Understanding how potent inhibition by calpastatin can be reconciled with its unstructured nature provides deeper insight into calpain function and a more general understanding of how proteins devoid of a well-defined structure carry out their function. To this end, we performed a full NMR assignment of hCSD1 to characterize it in its solution state. Secondary chemical shift values and NMR relaxation data, R 1, R 2, and hetero-NOE, as well as spectral density function analysis have shown that conserved regions of calpastatin, subdomains A and C, which are responsible for calcium-dependent anchoring of the inhibitor to the enzyme, preferentially sample partially helical backbone conformations of a reduced flexibility. Moreover, the linker regions between subdomains are more flexible with no structural preference. The primary determinant of calpain inhibition, subdomain B, also has a non-fully random conformational preference, resembling a beta-turn structure also ascertained by prior studies of a 27-residue peptide encompassing the inhibitory region. This local structural preference is also confirmed by a deviation in chemical shift values between full-length calpastatin domain 1 and a truncated construct cut in the middle of subdomain B. At the C-terminal end of the molecule, a nascent helical region was found, which in contrast to the overall structural properties of the molecule may indicate a previously unknown functional region. Overall, these observations provide further evidence that supports previous suggestions that intrinsically unstructured proteins use preformed structural elements in efficient partner recognition. FAU - Kiss, Robert AU - Kiss R AD - Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eotvos Lorand University, Budapest, Hungary. FAU - Kovacs, Denes AU - Kovacs D FAU - Tompa, Peter AU - Tompa P FAU - Perczel, Andras AU - Perczel A LA - eng GR - 067595/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080607 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Calcium-Binding Proteins) RN - 0 (Enzyme Inhibitors) RN - 79079-11-1 (calpastatin) RN - EC 3.4.22.- (Calpain) SB - IM MH - Amino Acid Sequence MH - Calcium-Binding Proteins/*chemistry/genetics/*metabolism/pharmacology MH - Calpain/*antagonists & inhibitors/metabolism MH - Crystallography, X-Ray MH - Enzyme Inhibitors/*chemistry/*metabolism/pharmacology MH - Humans MH - Hydrogen-Ion Concentration MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Temperature EDAT- 2008/06/10 09:00 MHDA- 2008/07/22 09:00 CRDT- 2008/06/10 09:00 PHST- 2008/06/07 [aheadofprint] AID - 10.1021/bi800201a [doi] PST - ppublish SO - Biochemistry. 2008 Jul 1;47(26):6936-45. doi: 10.1021/bi800201a. Epub 2008 Jun 7. PMID- 16118206 OWN - NLM STAT- MEDLINE DA - 20051017 DCOM- 20051213 LR - 20140921 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 42 DP - 2005 Oct 21 TI - Rational design of p53, an intrinsically unstructured protein, for the fabrication of novel molecular sensors. PG - 35641-6 AB - The dominant paradigm of protein engineering is structure-based site-directed mutagenesis. This rational approach is generally more effective for the engineering of local properties, such as substrate specificity, than global ones such as allostery. Previous workers have modified normally unregulated reporter enzymes, including beta-galactosidase, alkaline phosphatase, and beta-lactamase, so that the engineered versions are activated (up to 4-fold) by monoclonal antibodies. A reporter that could easily be "reprogrammed" for the facile detection of novel effectors (binding or modifying activities) would be useful in high throughput screens for directed evolution or drug discovery. Here we describe a straightforward and general solution to this potentially difficult design problem. The transcription factor p53 is normally regulated by a variety of post-translational modifications. The insertion of peptides into intrinsically unstructured domains of p53 generated variants that were activated up to 100-fold by novel effectors (proteases or antibodies). An engineered p53 was incorporated into an existing high throughput screen for the detection of human immunodeficiency virus protease, an arbitrarily chosen novel effector. These results suggest that the molecular recognition properties of intrinsically unstructured proteins are relatively easy to engineer and that the absence of crystal structures should not deter the rational engineering of this class of proteins. FAU - Geddie, Melissa L AU - Geddie ML AD - Department of Biochemistry, Center for Fundamental and Applied Molecular Evolution, Emory University School of Medicine, Atlanta, Georgia 30322, USA. FAU - O'Loughlin, Taryn L AU - O'Loughlin TL FAU - Woods, Kristen K AU - Woods KK FAU - Matsumura, Ichiro AU - Matsumura I LA - eng GR - 1 R21AI054602-01/AI/NIAID NIH HHS/United States GR - R21 AI054602/AI/NIAID NIH HHS/United States GR - R21 AI054602-02/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050823 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Antibodies, Monoclonal) RN - 0 (Peptides) RN - 0 (Tumor Suppressor Protein p53) RN - EC 3.1.3.1 (Alkaline Phosphatase) RN - EC 3.2.1.23 (beta-Galactosidase) RN - EC 3.4.23.- (HIV Protease) RN - EC 3.5.2.6 (beta-Lactamases) SB - IM MH - Alkaline Phosphatase/metabolism MH - Antibodies, Monoclonal/chemistry MH - Bacillus anthracis/metabolism MH - Cell Membrane/metabolism MH - Crystallography, X-Ray MH - Escherichia coli/metabolism MH - Genes, Reporter MH - Genetic Variation MH - Genetic Vectors MH - HIV/metabolism MH - HIV Protease/metabolism MH - Humans MH - Models, Genetic MH - Mutagenesis, Site-Directed MH - Mutation MH - Peptides/chemistry MH - Protein Engineering/*methods MH - RNA Processing, Post-Transcriptional MH - Substrate Specificity MH - Time Factors MH - Tumor Suppressor Protein p53/metabolism/*physiology MH - beta-Galactosidase/metabolism MH - beta-Lactamases/metabolism PMC - PMC2045634 MID - NIHMS31537 OID - NLM: NIHMS31537 OID - NLM: PMC2045634 EDAT- 2005/08/25 09:00 MHDA- 2005/12/15 09:00 CRDT- 2005/08/25 09:00 PHST- 2005/08/23 [aheadofprint] AID - M508149200 [pii] AID - 10.1074/jbc.M508149200 [doi] PST - ppublish SO - J Biol Chem. 2005 Oct 21;280(42):35641-6. Epub 2005 Aug 23. PMID- 16823039 OWN - NLM STAT- MEDLINE DA - 20060731 DCOM- 20060925 LR - 20140909 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 15 IP - 8 DP - 2006 Aug TI - Crystal structures of saposins A and C. PG - 1849-57 AB - Saposins A and C are sphingolipid activator proteins required for the lysosomal breakdown of galactosylceramide and glucosylceramide, respectively. The saposins interact with lipids, leading to an enhanced accessibility of the lipid headgroups to their cognate hydrolases. We have determined the crystal structures of human saposins A and C to 2.0 Angstroms and 2.4 Angstroms, respectively, and both reveal the compact, monomeric saposin fold. We confirmed that these two proteins were monomeric in solution at pH 7.0 by analytical centrifugation. However, at pH 4.8, in the presence of the detergent C(8)E(5), saposin A assembled into dimers, while saposin C formed trimers. Saposin B was dimeric under all conditions tested. The self-association of the saposins is likely to be relevant to how these small proteins interact with lipids, membranes, and hydrolase enzymes. FAU - Ahn, Victoria E AU - Ahn VE AD - Department of Medical Biophysics, University of Toronto, Canada. FAU - Leyko, Paul AU - Leyko P FAU - Alattia, Jean-Rene AU - Alattia JR FAU - Chen, Lu AU - Chen L FAU - Prive, Gilbert G AU - Prive GG LA - eng SI - PDB/2DOB SI - PDB/2GTG PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060705 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Detergents) RN - 0 (Ethers) RN - 0 (Polyethylene Glycols) RN - 0 (Saposins) RN - 0 (pentaethylene glycol n-octyl ether) SB - IM MH - Amino Acid Sequence MH - Crystallization MH - Crystallography, X-Ray MH - Detergents MH - Dimerization MH - Ethers MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Polyethylene Glycols MH - Protein Structure, Quaternary MH - Saposins/*chemistry MH - Sequence Alignment MH - Ultracentrifugation PMC - PMC2242594 OID - NLM: PMC2242594 EDAT- 2006/07/11 09:00 MHDA- 2006/09/26 09:00 CRDT- 2006/07/11 09:00 PHST- 2006/07/05 [aheadofprint] AID - ps.062256606 [pii] AID - 10.1110/ps.062256606 [doi] PST - ppublish SO - Protein Sci. 2006 Aug;15(8):1849-57. Epub 2006 Jul 5. PMID- 20346955 OWN - NLM STAT- MEDLINE DA - 20100507 DCOM- 20100518 LR - 20150325 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 398 IP - 5 DP - 2010 May 21 TI - Extensive and modular intrinsically disordered segments in C. elegans TTN-1 and implications in filament binding, elasticity and oblique striation. PG - 672-89 LID - 10.1016/j.jmb.2010.03.032 [doi] AB - TTN-1, a titin like protein in Caenorhabditis elegans, is encoded by a single gene and consists of multiple Ig and fibronectin 3 domains, a protein kinase domain and several regions containing tandem short repeat sequences. We have characterized TTN-1's sarcomere distribution, protein interaction with key myofibrillar proteins as well as the conformation malleability of representative motifs of five classes of short repeats. We report that two antibodies developed to portions of TTN-1 detect an approximately 2-MDa polypeptide on Western blots. In addition, by immunofluorescence staining, both of these antibodies localize to the I-band and may extend into the outer edge of the A-band in the obliquely striated muscle of the nematode. Six different 300-residue segments of TTN-1 were shown to variously interact with actin and/or myosin in vitro. Conformations of synthetic peptides of representative copies of each of the five classes of repeats--39-mer PEVT, 51-mer CEEEI, 42-mer AAPLE, 32-mer BLUE and 30-mer DispRep--were investigated by circular dichroism at different temperatures, ionic strengths and solvent polarities. The PEVT, CEEEI, DispRep and AAPLE peptides display a combination of a polyproline II helix and an unordered structure in aqueous solution and convert in trifluoroethanol to alpha-helix (PEVT, CEEEI, DispRep) and beta-turn (AAPLE) structures, respectively. The octads in BLUE motifs form unstable alpha-helix-like structures coils in aqueous solution and negligible heptad-based, alpha-helical coiled-coils. The alpha-helical structure, as modeled by threading and molecular dynamics simulations, tends to form helical bundles and crosses based on its 8-4-2-2 hydrophobic helical patterns and charge arrays on its surface. Our finding indicates that APPLE, PEVT, CEEEI and DispRep regions are all intrinsically disordered and highly reminiscent of the conformational malleability and elasticity of vertebrate titin PEVK segments. The proposed presence of long, modular and unstable alpha-helical oligomerization domains in the BLUE region of TTN-1 could bundle TTN-1 and stabilize oblique striation of the sarcomere. CI - (c) 2010 Elsevier B.V. All rights reserved. FAU - Forbes, Jeffrey G AU - Forbes JG AD - Muscle Proteomics and Nanotechnology Section, Laboratory of Muscle Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA. FAU - Flaherty, Denise B AU - Flaherty DB FAU - Ma, Kan AU - Ma K FAU - Qadota, Hiroshi AU - Qadota H FAU - Benian, Guy M AU - Benian GM FAU - Wang, Kuan AU - Wang K LA - eng GR - AR051466/AR/NIAMS NIH HHS/United States GR - R01 AR051466-01/AR/NIAMS NIH HHS/United States GR - R01 AR051466-02/AR/NIAMS NIH HHS/United States GR - R01 AR051466-03/AR/NIAMS NIH HHS/United States GR - R01 AR051466-04/AR/NIAMS NIH HHS/United States GR - R01 AR051466-05/AR/NIAMS NIH HHS/United States GR - Z01 AR041118-10/Intramural NIH HHS/United States GR - Z01 AR041118-11/Intramural NIH HHS/United States GR - Z99 AR999999/Intramural NIH HHS/United States GR - ZIA AR041118-12/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural DEP - 20100325 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Antibodies) RN - 0 (Connectin) RN - 0 (Muscle Proteins) RN - EC 2.7.- (Protein Kinases) SB - IM MH - Amino Acid Sequence MH - Animals MH - Antibodies/immunology MH - Caenorhabditis elegans/*chemistry/*physiology MH - Circular Dichroism MH - Connectin MH - Elasticity MH - Microscopy, Fluorescence MH - Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Muscle Proteins/*chemistry/*metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Kinases/*chemistry/*metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Staining and Labeling/methods MH - Temperature PMC - PMC2908218 MID - NIHMS192545 OID - NLM: NIHMS192545 OID - NLM: PMC2908218 EDAT- 2010/03/30 06:00 MHDA- 2010/05/19 06:00 CRDT- 2010/03/30 06:00 PHST- 2010/01/25 [received] PHST- 2010/03/17 [revised] PHST- 2010/03/17 [accepted] PHST- 2010/03/25 [aheadofprint] AID - S0022-2836(10)00294-9 [pii] AID - 10.1016/j.jmb.2010.03.032 [doi] PST - ppublish SO - J Mol Biol. 2010 May 21;398(5):672-89. doi: 10.1016/j.jmb.2010.03.032. Epub 2010 Mar 25. PMID- 18615714 OWN - NLM STAT- MEDLINE DA - 20081217 DCOM- 20090130 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 74 IP - 1 DP - 2009 Jan TI - Human FEZ1 has characteristics of a natively unfolded protein and dimerizes in solution. PG - 104-21 LID - 10.1002/prot.22135 [doi] AB - The fasciculation and elongation protein Zeta 1 (FEZ1) is the mammalian orthologue of the Caenorhabditis elegans protein UNC-76, which is necessary for axon growth. Human FEZ1 interacts with Protein Kinase C (PKC) and several regulatory proteins involved in functions ranging from microtubule associated transport to transcriptional regulation. Theoretical prediction, circular dichroism, fluorescence spectroscopy, and limited proteolysis of recombinant FEZ1 suggest that it contains disordered regions, especially in its N-terminal region, and that it may belong to the group of natively unfolded proteins. Small angle X-ray scattering experiments indicated a mainly disordered conformation, proved that FEZ1 is a dimer of elongated shape and provided overall dimensional parameters for the protein. In vitro pull down experiments confirmed these results and demonstrated that dimerization involves the N-terminus. Ab-initio 3D low resolution models of the full-length conformation of the dimeric constructs 6xHis-FEZ1(1-392) and 6xHis-FEZ1(1-227) were obtained. Furthermore, we performed in vitro phosphorylation assays of FEZ1 with PKC. The phosphorylation occurred mainly in its C-terminal region, and does not cause any significant conformational changes, but nonetheless inhibited its interaction with the FEZ1 interacting domain of the protein CLASP2 in vitro. The C terminus of FEZ1 has been reported to bind to several interacting proteins. This suggests that FEZ1 binding and transport function of interacting proteins may be subject to regulation by phosphorylation. CI - (c) 2008 Wiley-Liss, Inc. FAU - Lanza, Daniel C F AU - Lanza DC AD - Laboratorio Nacional de Luz Sincrotron, Campinas, SP, Brasil. FAU - Silva, Julio C AU - Silva JC FAU - Assmann, Eliana M AU - Assmann EM FAU - Quaresma, Alexandre J C AU - Quaresma AJ FAU - Bressan, Gustavo C AU - Bressan GC FAU - Torriani, Iris L AU - Torriani IL FAU - Kobarg, Jorg AU - Kobarg J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (CLASP2 protein, human) RN - 0 (FEZ1 protein, human) RN - 0 (Microtubule-Associated Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 0 (protein kinase C (19-31)) RN - EC 2.7.11.13 (Protein Kinase C) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry/*metabolism MH - Circular Dichroism MH - Humans MH - Microtubule-Associated Proteins/metabolism MH - Nerve Tissue Proteins/*chemistry/*metabolism MH - Peptide Fragments/metabolism MH - Phosphorylation MH - Protein Folding MH - Protein Kinase C/metabolism MH - Protein Multimerization MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Scattering, Small Angle MH - X-Ray Diffraction EDAT- 2008/07/11 09:00 MHDA- 2009/01/31 09:00 CRDT- 2008/07/11 09:00 AID - 10.1002/prot.22135 [doi] PST - ppublish SO - Proteins. 2009 Jan;74(1):104-21. doi: 10.1002/prot.22135. PMID- 21541066 OWN - NLM STAT- MEDLINE DA - 20110504 DCOM- 20150122 IS - 1422-0067 (Electronic) IS - 1422-0067 (Linking) VI - 12 IP - 2 DP - 2011 TI - Anchoring intrinsically disordered proteins to multiple targets: lessons from N-terminus of the p53 protein. PG - 1410-30 LID - 10.3390/ijms12021410 [doi] AB - Anchor residues, which are deeply buried upon binding, play an important role in protein-protein interactions by providing recognition specificity and facilitating the binding kinetics. Up to now, studies on anchor residues have been focused mainly on ordered proteins. In this study, we investigated anchor residues in intrinsically disordered proteins (IDPs) which are flexible in the free state. We identified the anchor residues of the N-terminus of the p53 protein (Glu17-Asn29, abbreviated as p53N) which are involved in binding with two different targets (MDM2 and Taz2), and analyzed their side chain conformations in the unbound states. The anchor residues in the unbound p53N were found to frequently sample conformations similar to those observed in the bound complexes (i.e., Phe19, Trp23, and Leu26 in the p53N-MDM2 complex, and Leu22 in the p53N-Taz2 complex). We argue that the bound-like conformations of the anchor residues in the unbound state are important for controlling the specific interactions between IDPs and their targets. Further, we propose a mechanism to account for the binding promiscuity of IDPs in terms of anchor residues and molecular recognition features (MoRFs). FAU - Huang, Yongqi AU - Huang Y AD - State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China. FAU - Liu, Zhirong AU - Liu Z LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110223 PL - Switzerland TA - Int J Mol Sci JT - International journal of molecular sciences JID - 101092791 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Transcription Factors) RN - 0 (Tumor Suppressor Protein p53) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Humans MH - Intrinsically Disordered Proteins/*chemistry/metabolism MH - Molecular Docking Simulation MH - *Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Protein Binding MH - Proto-Oncogene Proteins c-mdm2/chemistry/metabolism MH - Transcription Factors/chemistry/metabolism MH - Tumor Suppressor Protein p53/*chemistry/metabolism PMC - PMC3083713 OID - NLM: PMC3083713 OTO - NOTNLM OT - MDM2 OT - Taz2 OT - anchor residue OT - binding promiscuity OT - intrinsically disordered proteins OT - molecular recognition features OT - p53 GN - NLM: Original DateCompleted: 20110714 EDAT- 2011/05/05 06:00 MHDA- 2011/05/05 06:01 CRDT- 2011/05/05 06:00 PHST- 2011/01/25 [received] PHST- 2011/02/10 [revised] PHST- 2011/02/16 [accepted] PHST- 2011/02/23 [epublish] AID - 10.3390/ijms12021410 [doi] PST - epublish SO - Int J Mol Sci. 2011 Feb 23;12(2):1410-30. doi: 10.3390/ijms12021410. PMID- 11606569 OWN - NLM STAT- MEDLINE DA - 20011217 DCOM- 20020131 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 51 DP - 2001 Dec 21 TI - Mutations of tau protein in frontotemporal dementia promote aggregation of paired helical filaments by enhancing local beta-structure. PG - 48165-74 AB - The microtubule-associated protein tau is a natively unfolded protein in solution, yet it is able to polymerize into the ordered paired helical filaments (PHF) of Alzheimer's disease. In the splice isoforms lacking exon 10, this process is facilitated by the formation of beta-structure around the hexapeptide motif PHF6 ((306)VQIVYK(311)) encoded by exon 11. We have investigated the structural requirements for PHF polymerization in the context of adult tau isoforms containing four repeats (including exon 10). In addition to the PHF6 motif there exists a related PHF6* motif ((275)VQIINK(280)) in the repeat encoded by the alternatively spliced exon 10. We show that this PHF6* motif also promotes aggregation by the formation of beta-structure and that there is a cross-talk between the two hexapeptide motifs during PHF aggregation. We also show that two of the tau mutations found in hereditary frontotemporal dementias, DeltaK280 and P301L, have a much stronger tendency for PHF aggregation which correlates with their high propensity for beta-structure around the hexapeptide motifs. FAU - von Bergen, M AU - von Bergen M AD - Max-Planck-Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany. FAU - Barghorn, S AU - Barghorn S FAU - Li, L AU - Li L FAU - Marx, A AU - Marx A FAU - Biernat, J AU - Biernat J FAU - Mandelkow, E M AU - Mandelkow EM FAU - Mandelkow, E AU - Mandelkow E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20011017 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Biopolymers) RN - 0 (Oligopeptides) RN - 0 (tau Proteins) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Biopolymers MH - Dementia/*metabolism/pathology MH - Microscopy, Electron MH - Molecular Sequence Data MH - *Mutation MH - Oligopeptides/chemistry MH - Protein Conformation MH - Spectroscopy, Fourier Transform Infrared MH - tau Proteins/chemistry/*genetics/ultrastructure EDAT- 2001/10/19 10:00 MHDA- 2002/02/01 10:01 CRDT- 2001/10/19 10:00 PHST- 2001/10/17 [aheadofprint] AID - 10.1074/jbc.M105196200 [doi] AID - M105196200 [pii] PST - ppublish SO - J Biol Chem. 2001 Dec 21;276(51):48165-74. Epub 2001 Oct 17. PMID- 17434535 OWN - NLM STAT- MEDLINE DA - 20070508 DCOM- 20070801 LR - 20140916 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 369 IP - 2 DP - 2007 Jun 1 TI - A threefold RNA-protein interface in the signal recognition particle gates native complex assembly. PG - 512-24 AB - Intermediate states play well-established roles in the folding and misfolding reactions of individual RNA and protein molecules. In contrast, the roles of transient structural intermediates in multi-component ribonucleoprotein (RNP) assembly processes and their potential for misassembly are largely unexplored. The SRP19 protein is unstructured but forms a compact core domain and two extended RNA-binding loops upon binding the signal recognition particle (SRP) RNA. The SRP54 protein subsequently binds to the fully assembled SRP19-RNA complex to form an intimate threefold interface with both SRP19 and the RNA and without significantly altering the structure of SRP19. We show, however, that the presence of SRP54 during SRP19-RNA assembly dramatically alters the folding energy landscape to create a non-native folding pathway that leads to an aberrant SRP19-RNA conformation. The misassembled complex arises from the surprising ability of SRP54 to bind rapidly to an SRP19-RNA assembly intermediate and to interfere with subsequent folding of one of the RNA binding loops at the three-way protein-RNA interface. An incorrect temporal order of assembly thus readily yields a non-native three-component ribonucleoprotein particle. We propose there may exist a general requirement to regulate the order of interaction in multi-component RNP assembly reactions by spatial or temporal compartmentalization of individual constituents in the cell. FAU - Maity, Tuhin Subhra AU - Maity TS AD - Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290, USA. FAU - Weeks, Kevin M AU - Weeks KM LA - eng GR - GM065491/GM/NIGMS NIH HHS/United States GR - R01 GM065491/GM/NIGMS NIH HHS/United States GR - R01 GM065491-01A1/GM/NIGMS NIH HHS/United States GR - R01 GM065491-02/GM/NIGMS NIH HHS/United States GR - R01 GM065491-03/GM/NIGMS NIH HHS/United States GR - R01 GM065491-04/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20070320 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Fluorescent Dyes) RN - 0 (Macromolecular Substances) RN - 0 (Ribonucleoproteins) RN - 0 (SRP19 protein, human) RN - 0 (SRP54 protein, human) RN - 0 (Signal Recognition Particle) RN - 63231-63-0 (RNA) SB - IM MH - Base Sequence MH - Fluorescence Resonance Energy Transfer MH - Fluorescent Dyes/metabolism MH - Humans MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Protein Folding MH - Protein Structure, Quaternary MH - RNA/*chemistry/metabolism MH - Ribonucleoproteins/*chemistry/metabolism MH - Signal Recognition Particle/*chemistry/*genetics/metabolism PMC - PMC1940241 MID - NIHMS23932 OID - NLM: NIHMS23932 OID - NLM: PMC1940241 EDAT- 2007/04/17 09:00 MHDA- 2007/08/02 09:00 CRDT- 2007/04/17 09:00 PHST- 2006/12/07 [received] PHST- 2007/03/09 [revised] PHST- 2007/03/10 [accepted] PHST- 2007/03/20 [aheadofprint] AID - S0022-2836(07)00373-7 [pii] AID - 10.1016/j.jmb.2007.03.032 [doi] PST - ppublish SO - J Mol Biol. 2007 Jun 1;369(2):512-24. Epub 2007 Mar 20. PMID- 10543959 OWN - NLM STAT- MEDLINE DA - 19991119 DCOM- 19991119 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 293 IP - 3 DP - 1999 Oct 29 TI - An unstructured C-terminal region of the Hsp90 co-chaperone p23 is important for its chaperone function. PG - 685-91 AB - p23 is a co-chaperone of the heat shock protein Hsp90. p23 binds to Hsp90 in its ATP-bound state and, on its own, interacts specifically with non-native proteins. In our attempt to correlate these functions to specific regions of p23 we have identified an unstructured region in p23 that maps to the C-terminal part of the protein sequence. This unstructured region is dispensible for interaction of p23 with Hsp90, since truncated p23 can still form complexes with Hsp90. In contrast, however, truncation of the C-terminal 30 amino acid residues of p23 affects the ability of p23 to bind non-native proteins and to prevent their non-specific aggregation. The isolated C-terminal region itself is not able to act as a chaperone nor is it possible to complement truncated p23 by addition of this peptide. These results imply that the binding site for Hsp90 is contained in the folded domain of p23 and that for efficient interaction of p23 with non-native proteins both the folded domain and the C-terminal unstructured region are required. CI - Copyright 1999 Academic Press. FAU - Weikl, T AU - Weikl T AD - Technische Universitat Munchen, Garching, 83747, Germany. FAU - Abelmann, K AU - Abelmann K FAU - Buchner, J AU - Buchner J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (HSP90 Heat-Shock Proteins) RN - 0 (Molecular Chaperones) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 2.3.3.1 (Citrate (si)-Synthase) RN - EC 3.4.21.64 (Endopeptidase K) SB - IM MH - Adenosine Triphosphate/metabolism MH - Binding Sites MH - Circular Dichroism MH - Citrate (si)-Synthase/chemistry/metabolism MH - Endopeptidase K/metabolism MH - HSP90 Heat-Shock Proteins/*metabolism MH - Humans MH - Molecular Chaperones/*chemistry/genetics/isolation & purification/*metabolism MH - Molecular Weight MH - Peptide Fragments/chemistry/genetics/isolation & purification/metabolism MH - Protein Binding MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism MH - Sequence Deletion/genetics MH - Structure-Activity Relationship EDAT- 1999/11/02 MHDA- 1999/11/02 00:01 CRDT- 1999/11/02 00:00 AID - 10.1006/jmbi.1999.3172 [doi] AID - S0022-2836(99)93172-8 [pii] PST - ppublish SO - J Mol Biol. 1999 Oct 29;293(3):685-91. PMID- 23817832 OWN - NLM STAT- MEDLINE DA - 20130809 DCOM- 20140226 LR - 20141113 IS - 1879-1123 (Electronic) IS - 1044-0305 (Linking) VI - 24 IP - 9 DP - 2013 Sep TI - Binding of Dopamine to Alpha-Synuclein is Mediated by Specific Conformational States. PG - 1346-54 LID - 10.1007/s13361-013-0676-z [doi] AB - Parkinson's disease is the second most common neurodegenerative disorder, in which both alpha-synuclein (alpha-syn) and dopamine (DA) have a critical role. alpha-Syn is known to be natively unstructured in equilibrium with subpopulations of more compact structures. It is these compact structures that are thought to be linked to amyloid formation. In the presence of DA, alpha-syn yields a diverse range of SDS-resistant, non-amyloid oligomers, however the precursor state conformation has not been established. Here, three DA molecules have been observed to bind per alpha-syn monomer by electrospray-ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS). Each of these DA molecules binds exclusively to the extended conformation of alpha-syn, and binding is not observed in the compact state of the protein. Measurements of collisional cross sectional areas show that the incremental uptake of DA pushes the protein towards a highly extended population, becoming fully populated upon the binding of three DA ligands. Tyrosine (Tyr) as a closely related structural analog, exhibited limited binding to the protein as compared with DA, with a maximum of two ligands being observed. Those Tyr ligands that do bind were observed as adducts to the extended conformation akin to DA. These findings suggest DA is able to modulate alpha-syn self-assembly by inducing the population of a highly extended state. FAU - Illes-Toth, Eva AU - Illes-Toth E AD - Biomedical Research Centre, Sheffield Hallam University, Sheffield, United Kingdom. FAU - Dalton, Caroline F AU - Dalton CF FAU - Smith, David P AU - Smith DP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130702 PL - United States TA - J Am Soc Mass Spectrom JT - Journal of the American Society for Mass Spectrometry JID - 9010412 RN - 0 (alpha-Synuclein) RN - VTD58H1Z2X (Dopamine) SB - IM MH - Animals MH - Dopamine/*metabolism MH - Humans MH - Parkinson Disease/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Spectrometry, Mass, Electrospray Ionization MH - alpha-Synuclein/chemistry/*metabolism PMC - PMC3738842 OID - NLM: PMC3738842 EDAT- 2013/07/03 06:00 MHDA- 2014/02/27 06:00 CRDT- 2013/07/03 06:00 PHST- 2013/02/21 [received] PHST- 2013/05/09 [accepted] PHST- 2013/05/08 [revised] PHST- 2013/07/02 [aheadofprint] AID - 10.1007/s13361-013-0676-z [doi] PST - ppublish SO - J Am Soc Mass Spectrom. 2013 Sep;24(9):1346-54. doi: 10.1007/s13361-013-0676-z. Epub 2013 Jul 2. PMID- 16597837 OWN - NLM STAT- MEDLINE DA - 20060427 DCOM- 20060922 LR - 20140909 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 15 IP - 5 DP - 2006 May TI - The C-terminal domain of the transcriptional corepressor CtBP is intrinsically unstructured. PG - 1042-50 AB - C-terminal binding proteins (CtBPs) are moonlighting proteins involved in nuclear transcriptional corepression and in Golgi membrane tubule fission. Structural information on CtBPs is available for their substrate-binding domain, responsible for transcriptional repressor recognition/binding, and for the nucleotide-binding domain, involved in NAD(H)-binding and dimerization. On the contrary, little is known about the structure of CtBP C-terminal region ( approximately 90 residues), hosting sites for post-translational modifications. In the present communication we apply a combined approach based on bioinformatics, nuclear magnetic resonance, circular dichroism spectroscopy, and small-angle X-ray scattering, and we show that the CtBP C-terminal region is intrinsically unstructured in the full-length CtBP and in constructs lacking the substrate- and/or the nucleotide-binding domains. The flexible nature of this protein region, and its structural transitions, may be instrumental for CtBP recognition and binding to diverse molecular partners. FAU - Nardini, Marco AU - Nardini M AD - Department of Biomolecular Sciences and Biotechnology, and CNR-INFM, University of Milano, I-20131 Milano, Italy. FAU - Svergun, Dmitri AU - Svergun D FAU - Konarev, Peter V AU - Konarev PV FAU - Spano, Stefania AU - Spano S FAU - Fasano, Mauro AU - Fasano M FAU - Bracco, Chiara AU - Bracco C FAU - Pesce, Alessandra AU - Pesce A FAU - Donadini, Alessandra AU - Donadini A FAU - Cericola, Claudia AU - Cericola C FAU - Secundo, Francesco AU - Secundo F FAU - Luini, Alberto AU - Luini A FAU - Corda, Daniela AU - Corda D FAU - Bolognesi, Martino AU - Bolognesi M LA - eng GR - GGP04235/Telethon/Italy PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060405 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (DNA-Binding Proteins) RN - 0 (Phosphoproteins) RN - 0 (Repressor Proteins) RN - 0 (Transcription Factors) RN - EC 1.1.- (Alcohol Oxidoreductases) RN - EC 1.1.1.- (C-terminal binding protein) SB - IM MH - Alcohol Oxidoreductases MH - Amino Acid Sequence MH - Binding Sites MH - Circular Dichroism MH - DNA-Binding Proteins MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Phosphoproteins MH - Protein Folding MH - Repressor Proteins/*chemistry MH - Transcription Factors/*chemistry MH - *Transcription, Genetic PMC - PMC2242513 OID - NLM: PMC2242513 EDAT- 2006/04/07 09:00 MHDA- 2006/09/23 09:00 CRDT- 2006/04/07 09:00 PHST- 2006/04/05 [aheadofprint] AID - ps.062115406 [pii] AID - 10.1110/ps.062115406 [doi] PST - ppublish SO - Protein Sci. 2006 May;15(5):1042-50. Epub 2006 Apr 5. PMID- 17976647 OWN - NLM STAT- MEDLINE DA - 20071112 DCOM- 20080306 LR - 20140916 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 374 IP - 4 DP - 2007 Dec 7 TI - Structure of the full-length human RPA14/32 complex gives insights into the mechanism of DNA binding and complex formation. PG - 865-76 AB - Replication protein A (RPA) is the ubiquitous, eukaryotic single-stranded DNA (ssDNA) binding protein and is essential for DNA replication, recombination, and repair. Here, crystal structures of the soluble RPA heterodimer, composed of the RPA14 and RPA32 subunits, have been determined for the full-length protein in multiple crystal forms. In all crystals, the electron density for the N-terminal (residues 1-42) and C-terminal (residues 175-270) regions of RPA32 is weak and of poor quality indicating that these regions are disordered and/or assume multiple positions in the crystals. Hence, the RPA32 N terminus, that is hyperphosphorylated in a cell-cycle-dependent manner and in response to DNA damaging agents, appears to be inherently disordered in the unphosphorylated state. The C-terminal, winged helix-loop-helix, protein-protein interaction domain adopts several conformations perhaps to facilitate its interaction with various proteins. Although the ordered regions of RPA14/32 resemble the previously solved protease-resistant core crystal structure, the quaternary structures between the heterodimers are quite different. Thus, the four-helix bundle quaternary assembly noted in the original core structure is unlikely to be related to the quaternary structure of the intact heterotrimer. An organic ligand binding site between subunits RPA14 and RPA32 was identified to bind dioxane. Comparison of the ssDNA binding surfaces of RPA70 with RPA14/32 showed that the lower affinity of RPA14/32 can be attributed to a shallower binding crevice with reduced positive electrostatic charge. FAU - Deng, Xiaoyi AU - Deng X AD - The Eppley Institute for Research in Cancer and Allied Diseases, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA. FAU - Habel, Jeff E AU - Habel JE FAU - Kabaleeswaran, Venkataramen AU - Kabaleeswaran V FAU - Snell, Edward H AU - Snell EH FAU - Wold, Marc S AU - Wold MS FAU - Borgstahl, Gloria E O AU - Borgstahl GE LA - eng SI - PDB/2PI2 SI - PDB/2PQA SI - PDB/2Z6K GR - GM044721/GM/NIGMS NIH HHS/United States GR - R01 GM044721/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20071002 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DNA, Single-Stranded) RN - 0 (Dioxanes) RN - 0 (Protein Subunits) RN - 0 (Replication Protein A) RN - J8A3S10O7S (1,4-dioxane) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - DNA, Single-Stranded/*chemistry MH - Dioxanes/chemistry MH - Humans MH - *Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Structure, Quaternary MH - Protein Subunits/*chemistry MH - Replication Protein A/*chemistry EDAT- 2007/11/03 09:00 MHDA- 2008/03/07 09:00 CRDT- 2007/11/03 09:00 PHST- 2007/05/19 [received] PHST- 2007/09/22 [revised] PHST- 2007/09/26 [accepted] PHST- 2007/10/02 [aheadofprint] AID - S0022-2836(07)01286-7 [pii] AID - 10.1016/j.jmb.2007.09.074 [doi] PST - ppublish SO - J Mol Biol. 2007 Dec 7;374(4):865-76. Epub 2007 Oct 2. PMID- 16254343 OWN - NLM STAT- MEDLINE DA - 20051028 DCOM- 20060127 LR - 20140910 IS - 0022-538X (Print) IS - 0022-538X (Linking) VI - 79 IP - 22 DP - 2005 Nov TI - Crystal structure of enteric adenovirus serotype 41 short fiber head. PG - 14088-94 AB - Human enteric adenoviruses of species F contain two fibers in the same virion, a long fiber which binds to coxsackievirus and adenovirus receptor (CAR) and a short fiber of unknown function. We have determined the high-resolution crystal structure of the short fiber head of human adenovirus serotype 41 (Ad41). The short fiber head has the characteristic fold of other known fiber heads but has three unusual features. First, it has much shorter loops between the beta-strands. Second, one of the usually well-ordered beta-strands on the distal face of the fiber head is highly disordered and this same region is sensitive to digestion with pepsin, an enzyme occurring naturally in the intestinal tract, the physiological environment of Ad41. Third, the AB loop has a deletion giving it a distinct conformation incompatible with CAR binding. FAU - Seiradake, Elena AU - Seiradake E AD - EMBL Grenoble Outstation, France. FAU - Cusack, Stephen AU - Cusack S LA - eng SI - GENBANK/X17016 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (DNA Primers) RN - 0 (Viral Proteins) SB - IM MH - Adenoviruses, Human/classification/genetics/*ultrastructure MH - Amino Acid Sequence MH - Base Sequence MH - Conserved Sequence MH - DNA Primers MH - Escherichia coli/genetics MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Serotyping MH - Viral Proteins/chemistry PMC - PMC1280240 OID - NLM: PMC1280240 EDAT- 2005/10/29 09:00 MHDA- 2006/01/28 09:00 CRDT- 2005/10/29 09:00 AID - 79/22/14088 [pii] AID - 10.1128/JVI.79.22.14088-14094.2005 [doi] PST - ppublish SO - J Virol. 2005 Nov;79(22):14088-94. PMID- 10541551 OWN - NLM STAT- MEDLINE DA - 19991115 DCOM- 19991115 LR - 20140615 IS - 0890-9369 (Print) IS - 0890-9369 (Linking) VI - 13 IP - 20 DP - 1999 Oct 15 TI - Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface. PG - 2650-7 AB - We have determined the crystal structure, at 3.2 A, of a ternary complex containing an OCA-B peptide, the Oct-1 POU domain, and an octamer DNA site. The OCA-B peptide binds in the major groove near the center of the octamer site, and its polypeptide backbone forms a pair of hydrogen bonds with the adenine base at position 5 of the octamer DNA. Numerous protein-protein contacts between the OCA-B peptide and the POU domain are also involved in the ternary complex. In particular, the hydrophobic surface from a short alpha-helix of OCA-B helps to stabilize the complex by binding to a hydrophobic pocket on the POU-specific domain. The structure of this ternary complex is consistent with previous biochemical studies and shows how peptide-DNA and peptide-protein contacts from OCA-B provide structural and functional specificity in the regulation of immunoglobulin transcription. FAU - Chasman, D AU - Chasman D AD - Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. FAU - Cepek, K AU - Cepek K FAU - Sharp, P A AU - Sharp PA FAU - Pabo, C O AU - Pabo CO LA - eng GR - GM31471/GM/NIGMS NIH HHS/United States GR - P01-CA42063/CA/NCI NIH HHS/United States GR - P30-CA14051/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Genes Dev JT - Genes & development JID - 8711660 RN - 0 (DNA-Binding Proteins) RN - 0 (HCFC1 protein, human) RN - 0 (Host Cell Factor C1) RN - 0 (Macromolecular Substances) RN - 0 (Octamer Transcription Factor-1) RN - 0 (POU2AF1 protein, human) RN - 0 (POU2F1 protein, human) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Binding Sites/genetics MH - Crystallography, X-Ray MH - DNA/*chemistry/genetics/metabolism MH - DNA-Binding Proteins/*genetics MH - Host Cell Factor C1 MH - Humans MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Octamer Transcription Factor-1 MH - Peptide Fragments/chemistry/genetics/metabolism MH - Protein Conformation MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Static Electricity MH - Trans-Activators/*chemistry/genetics/metabolism MH - Transcription Factors/*genetics PMC - PMC317104 OID - NLM: PMC317104 EDAT- 1999/10/29 MHDA- 1999/10/29 00:01 CRDT- 1999/10/29 00:00 PST - ppublish SO - Genes Dev. 1999 Oct 15;13(20):2650-7. PMID- 20828133 OWN - NLM STAT- MEDLINE DA - 20101026 DCOM- 20101130 LR - 20140824 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 43 DP - 2010 Nov 2 TI - Dynamic regulation of fibrinogen: integrin alphaIIbbeta3 binding. PG - 9217-25 LID - 10.1021/bi1009858 [doi] AB - This study demonstrates that two orthogonal events regulate integrin alphaIIbbeta3's interactions with fibrinogen, its primary physiological ligand: (1) conformational changes at the alphaIIb-beta3 interface and (2) flexibility in the carboxy terminus of fibrinogen's gamma-module. The first postulate was tested by capturing alphaIIbbeta3 on a biosensor and measuring binding by surface plasmon resonance. Binding of fibrinogen to eptifibatide-primed alphaIIbbeta3 was characterized by a k(on) of ~2 x 10(4) L mol(-1) s(-1) and a k(off) of ~8 x 10(-5) s(-1) at 37 degrees C. In contrast, even at 150 nM fibrinogen, no binding was detected with resting alphaIIbbeta3. Eptifibatide competitively inhibited fibrinogen's interactions with primed alphaIIbbeta3 (K(i) ~0.4 nM), while a synthetic gamma-module peptide (HHLGGAKQAGDV) was only weakly inhibitory (K(i) > 10 muM). The second postulate was tested by measuring alphaIIbbeta3's interactions with recombinant fibrinogen, both normal (rFgn) and a deletion mutant lacking the gamma-chain AGDV sites (rFgn gammaDelta408-411). Normal rFgn bound rapidly, tightly, and specifically to primed alphaIIbbeta3; no interaction was detected with rFgn gammaDelta408-411. Equilibrium and transition-state thermodynamic data indicated that binding of fibrinogen to primed alphaIIbbeta3, while enthalpy-favorable, must overcome an entropy-dominated activation energy barrier. The hypothesis that fibrinogen binding is enthalpy-driven fits with structural data showing that its gamma-C peptide and eptifibatide exhibit comparable electrostatic contacts with alphaIIbbeta3's ectodomain. The concept that fibrinogen's alphaIIbbeta3 targeting sequence is intrinsically disordered may explain the entropy penalty that limits its binding rate. In the hemostatic milieu, platelet-platelet interactions may be localized to vascular injury sites because integrins must be activated before they can bind their most abundant ligand. FAU - Hantgan, Roy R AU - Hantgan RR AD - Department of Biochemistry, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157-1016, USA. rhantgan@wfubmc.edu FAU - Stahle, Mary C AU - Stahle MC FAU - Lord, Susan T AU - Lord ST LA - eng GR - HL031048-22/HL/NHLBI NIH HHS/United States GR - R01 HL031048-23/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Hemostatics) RN - 0 (Peptides) RN - 0 (Platelet Glycoprotein GPIIb-IIIa Complex) RN - 0 (eptifibatide) RN - 9001-32-5 (Fibrinogen) SB - IM MH - Entropy MH - Fibrinogen/*chemistry/metabolism MH - Hemostatics MH - Humans MH - Peptides/pharmacology MH - Platelet Glycoprotein GPIIb-IIIa Complex/*chemistry/metabolism MH - Protein Binding MH - Protein Conformation MH - Surface Plasmon Resonance MH - Thermodynamics PMC - PMC3210020 MID - NIHMS332503 OID - NLM: NIHMS332503 OID - NLM: PMC3210020 EDAT- 2010/09/11 06:00 MHDA- 2010/12/14 06:00 CRDT- 2010/09/11 06:00 AID - 10.1021/bi1009858 [doi] PST - ppublish SO - Biochemistry. 2010 Nov 2;49(43):9217-25. doi: 10.1021/bi1009858. PMID- 19643037 OWN - NLM STAT- MEDLINE DA - 20090731 DCOM- 20090902 IS - 1976-6696 (Print) IS - 1976-6696 (Linking) VI - 42 IP - 7 DP - 2009 Jul 31 TI - Multiple hTAF(II)31-binding motifs in the intrinsically unfolded transcriptional activation domain of VP16. PG - 411-7 AB - Transcriptional activation domain (TAD) in virion protein 16 (VP16) of herpes simplex virus does not have any globular structure, yet exhibits a potent transcriptional activity. In order to probe the structural basis for the transcriptional activity of VP16 TAD, we have used NMR spectroscopy to investigate its detailed structural features. Results show that an unbound VP16 TAD is not merely "unstructured" but contains four short motifs (residues 424-433, 442-446, 465-467 and 472-479) with transient structural order. Pre-structured motifs in other intrinsically unfolded proteins (IUPs) were shown to be critically involved in target protein binding. The 472-479 motif was previously shown to bind to hTAF(II)31, whereas the hTAF(II)31-binding ability of other motifs found in this study has not been addressed. The VP16 TAD represents another IUP whose prestructured motifs mediate promiscuous binding to various target proteins. FAU - Kim, Do-Hyoung AU - Kim DH AD - Bioinformatics Research Center, KRIBB, Daejeon 305-806, Korea. FAU - Lee, Si-Hyung AU - Lee SH FAU - Nam, Ki Hoon AU - Nam KH FAU - Chi, Seung-Wook AU - Chi SW FAU - Chang, Iksoo AU - Chang I FAU - Han, Kyou-Hoon AU - Han KH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Korea (South) TA - BMB Rep JT - BMB reports JID - 101465334 RN - 0 (Herpes Simplex Virus Protein Vmw65) RN - 0 (Recombinant Proteins) RN - 0 (TAF9 protein, human) RN - 0 (TATA-Binding Protein Associated Factors) RN - 0 (Transcription Factor TFIID) SB - IM MH - Amino Acid Motifs MH - Binding Sites MH - Herpes Simplex Virus Protein Vmw65/*chemistry/*metabolism/physiology MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - *Protein Folding MH - Protein Structure, Tertiary/physiology MH - Recombinant Proteins/chemistry/metabolism MH - TATA-Binding Protein Associated Factors/*metabolism MH - Transcription Factor TFIID/*metabolism MH - Transcriptional Activation/physiology EDAT- 2009/08/01 09:00 MHDA- 2009/09/03 06:00 CRDT- 2009/08/01 09:00 PST - ppublish SO - BMB Rep. 2009 Jul 31;42(7):411-7. PMID- 20677831 OWN - NLM STAT- MEDLINE DA - 20100803 DCOM- 20100907 LR - 20140824 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 31 DP - 2010 Aug 10 TI - Solution structure and membrane binding of the toxin fst of the par addiction module. PG - 6567-75 LID - 10.1021/bi1005128 [doi] AB - The par toxin-antitoxin system is required for the stable inheritance of the plasmid pAD1 in its native host Enterococcus faecalis. It codes for the toxin Fst and a small antisense RNA which inhibits translation of toxin mRNA, and it is the only known antisense regulated toxin-antitoxin system in Gram-positive bacteria. This study presents the structure of the par toxin Fst, the first atomic resolution structure of a component of an antisense regulated toxin-antitoxin system. The mode of membrane binding was determined by relaxation enhancements in a paramagnetic environment and molecular dynamics simulation. Fst forms a membrane-binding alpha-helix in the N-terminal part and contains an intrinsically disordered region near the C-terminus. It binds in a transmembrane orientation with the C-terminus likely pointing toward the cytosol. Membrane-bound, alpha-helical peptides are frequently found in higher organisms as components of the innate immune system. Despite similarities to these antimicrobial peptides, Fst shows neither hemolytic nor antimicrobial activity when applied externally to a series of bacteria, fungal cells, and erythrocytes. Moreover, its charge distribution, orientation in the membrane, and structure distinguish it from antimicrobial peptides. FAU - Gobl, Christoph AU - Gobl C AD - Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria. FAU - Kosol, Simone AU - Kosol S FAU - Stockner, Thomas AU - Stockner T FAU - Ruckert, Hanna M AU - Ruckert HM FAU - Zangger, Klaus AU - Zangger K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Antitoxins) RN - 0 (Bacterial Toxins) RN - 0 (RNA, Antisense) RN - 0 (Solutions) RN - 0 (fst toxin, Enterococcus faecalis) SB - IM MH - Antitoxins MH - Bacterial Toxins/*chemistry/genetics/pharmacokinetics MH - Cell Membrane/*metabolism MH - Electron Spin Resonance Spectroscopy MH - Molecular Dynamics Simulation MH - Protein Binding MH - Protein Conformation MH - RNA, Antisense/chemistry MH - Solutions PMC - PMC2914490 OID - NLM: PMC2914490 EDAT- 2010/08/04 06:00 MHDA- 2010/09/08 06:00 CRDT- 2010/08/04 06:00 AID - 10.1021/bi1005128 [doi] PST - ppublish SO - Biochemistry. 2010 Aug 10;49(31):6567-75. doi: 10.1021/bi1005128. PMID- 18502763 OWN - NLM STAT- MEDLINE DA - 20080721 DCOM- 20080908 LR - 20140910 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 30 DP - 2008 Jul 25 TI - The type III secretion chaperone SycE promotes a localized disorder-to-order transition in the natively unfolded effector YopE. PG - 20857-63 LID - 10.1074/jbc.M802339200 [doi] AB - Many virulence-related, bacterial effector proteins are translocated directly into the cytosol of host cells by the type III secretion (TTS) system. Translocation of most TTS effectors requires binding by specific chaperones in the bacterial cytosol, although how chaperones promote translocation is unclear. To provide insight into the action of such chaperones, we studied the consequences of binding by the Yersinia chaperone SycE to the effector YopE by NMR. These studies examined the intact form of the effector, whereas prior studies have been limited to well ordered fragments. We found that YopE had the characteristics of a natively unfolded protein, with its N-terminal 100 residues, including its chaperone-binding (Cb) region, flexible and disordered in the absence of SycE. SycE binding caused a pronounced disorder-to-order transition in the Cb region of YopE. The effect of SycE was strictly localized to the Cb region, with other portions of YopE being unperturbed. These results provide stringent limits on models of chaperone action and are consistent with the chaperone promoting formation of a three-dimensional targeting signal in the Cb region of the effector. The target of this putative signal is unknown but appears to be a bacterial component other than the TTS ATPase YscN. FAU - Rodgers, Loren AU - Rodgers L AD - Section of Molecular Biology, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. FAU - Gamez, Alicia AU - Gamez A FAU - Riek, Roland AU - Riek R FAU - Ghosh, Partho AU - Ghosh P LA - eng GR - R01 AI 061452/AI/NIAID NIH HHS/United States GR - R01 AI061452/AI/NIAID NIH HHS/United States GR - T32 GM 007240/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20080523 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Outer Membrane Proteins) RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (Molecular Chaperones) RN - 0 (SycE protein, Yersinia) RN - 0 (Trans-Activators) RN - 0 (yopE protein, Yersinia) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 3.6.1.- (YscN protein, Yersinia) SB - IM MH - Adenosine Triphosphatases/*metabolism MH - Bacterial Outer Membrane Proteins/*chemistry MH - Bacterial Proteins/*metabolism MH - Biological Transport MH - Biotinylation MH - Carrier Proteins/*metabolism MH - Crystallography, X-Ray MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Chaperones/metabolism MH - Molecular Conformation MH - Protein Binding MH - Protein Conformation MH - Protein Denaturation MH - Protein Structure, Tertiary MH - Trans-Activators/*metabolism MH - Yersinia/*metabolism PMC - PMC2475703 OID - NLM: PMC2475703 EDAT- 2008/05/27 09:00 MHDA- 2008/09/09 09:00 CRDT- 2008/05/27 09:00 PHST- 2008/05/23 [aheadofprint] AID - M802339200 [pii] AID - 10.1074/jbc.M802339200 [doi] PST - ppublish SO - J Biol Chem. 2008 Jul 25;283(30):20857-63. doi: 10.1074/jbc.M802339200. Epub 2008 May 23. PMID- 12860121 OWN - NLM STAT- MEDLINE DA - 20030715 DCOM- 20030825 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 330 IP - 5 DP - 2003 Jul 25 TI - Mutual induced fit binding of Xenopus ribosomal protein L5 to 5S rRNA. PG - 979-92 AB - A library of random mutations in Xenopus ribosomal protein L5 was generated by error-prone PCR and used to delineate the binding domain for 5S rRNA. All but one of the amino acid substitutions that affected binding affinity are clustered in the central region of the protein. Several of the mutations are conservative substitutions of non-polar amino acid residues that are unlikely to form energetically significant contacts to the RNA. Thermal denaturation, monitored by circular dichroism (CD), indicates that L5 is not fully structured and association with 5S rRNA increases the t(m) of the protein by 16 degrees C. L5 induces changes in the CD spectrum of 5S rRNA, establishing that the complex forms by a mutual induced fit mechanism. Deuterium exchange reveals that a considerable amount of L5 is unstructured in the absence of 5S rRNA. The fluorescence emission of W266 provides evidence for structural changes in the C-terminal region of L5 upon binding to 5S rRNA; whereas, protection experiments demonstrate that the N terminus remains highly sensitive to protease digestion in the complex. Analysis of the amino acid sequence of L5 by the program PONDR predicts that the N and C-terminal regions of L5 are intrinsically disordered, but that the central region, which contains three essential tyrosine residues and other residues important for binding to 5S rRNA, is likely to be structured. Initial interaction of the protein with 5S rRNA likely occurs through this region, followed by induced folding of the C-terminal region. The persistent disorder in the N-terminal domain is possibly exploited for interactions between the L5-5S rRNA complex and other proteins. FAU - DiNitto, Jonathan P AU - DiNitto JP AD - Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. FAU - Huber, Paul W AU - Huber PW LA - eng GR - GM 38200/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (RNA, Ribosomal, 5S) RN - 0 (Ribosomal Proteins) RN - 0 (ribosomal protein L5) RN - 20R035KLCI (Acrylamide) RN - EC 3.4.- (Endopeptidases) SB - IM MH - Acrylamide/pharmacology MH - Animals MH - Base Sequence MH - Circular Dichroism MH - Dose-Response Relationship, Drug MH - Endopeptidases/metabolism MH - Molecular Sequence Data MH - Mutagenesis MH - Mutagenesis, Site-Directed MH - Mutation MH - Nucleic Acid Conformation MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - RNA, Ribosomal, 5S/*chemistry MH - Ribosomal Proteins/*chemistry MH - Spectrometry, Fluorescence MH - Temperature MH - Xenopus EDAT- 2003/07/16 05:00 MHDA- 2003/08/26 05:00 CRDT- 2003/07/16 05:00 AID - S0022283603006855 [pii] PST - ppublish SO - J Mol Biol. 2003 Jul 25;330(5):979-92. PMID- 21767525 OWN - NLM STAT- MEDLINE DA - 20110808 DCOM- 20110929 LR - 20141120 IS - 1096-0384 (Electronic) IS - 0003-9861 (Linking) VI - 513 IP - 1 DP - 2011 Sep 1 TI - Biochemical characterization of small heat shock protein HspB8 (Hsp22)-Bag3 interaction. PG - 1-9 LID - 10.1016/j.abb.2011.06.014 [doi] AB - Interaction of human Bag3 with small heat shock proteins HspB6, HspB8 and its K141E mutant was analyzed by different biochemical methods. The data of size-exclusion chromatography indicate that the wild type HspB8 forms tight complexes with Bag3. K141E mutant of HspB8 and especially HspB6 weaker interact with Bag3. The data of chemical crosslinking and analytical ultracentrifugation indicate that in vitro the stoichiometry of complexes formed by HspB8 and Bag3 is variable and is dependent on concentration of protein partners. Interaction of Bag3 and HspB8 is accompanied by increase of thermal stability measured by intrinsic tryptophan fluorescence and increased resistance to limited chymotrypsinolysis. The data of size-exclusion chromatography, analytical ultracentrifugation and limited proteolysis indicate that Bag3 belongs to the group of intrinsically disordered proteins. It is supposed that having unordered structure Bag3 might weakly interact with different small heat shock proteins which recognize unfolded proteins and this interaction is especially strong with intrinsically disordered HspB8. The complexes formed by Bag3 and HspB8 might have variable stoichiometry and can participate in different processes including clearing of the cell from improperly folded proteins. CI - Copyright (c) 2011 Elsevier Inc. All rights reserved. FAU - Shemetov, Anton A AU - Shemetov AA AD - Department of Biochemistry, School of Biology, Moscow State University, Russian Federation. FAU - Gusev, Nikolai B AU - Gusev NB LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110713 PL - United States TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Apoptosis Regulatory Proteins) RN - 0 (BAG3 protein, human) RN - 0 (Heat-Shock Proteins) RN - 0 (Multiprotein Complexes) RN - 0 (Recombinant Proteins) RN - EC 2.7.1.- (HSPB8 protein, human) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry/genetics/metabolism MH - Amino Acid Substitution MH - Apoptosis Regulatory Proteins MH - Heat-Shock Proteins/*chemistry/genetics/metabolism MH - Humans MH - Multiprotein Complexes/*chemistry/genetics/metabolism MH - Mutation, Missense MH - Protein Folding MH - Protein Stability MH - Protein-Serine-Threonine Kinases/*chemistry/genetics/metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism EDAT- 2011/07/20 06:00 MHDA- 2011/10/01 06:00 CRDT- 2011/07/20 06:00 PHST- 2011/05/25 [received] PHST- 2011/06/25 [revised] PHST- 2011/06/30 [accepted] PHST- 2011/07/13 [aheadofprint] AID - S0003-9861(11)00249-9 [pii] AID - 10.1016/j.abb.2011.06.014 [doi] PST - ppublish SO - Arch Biochem Biophys. 2011 Sep 1;513(1):1-9. doi: 10.1016/j.abb.2011.06.014. Epub 2011 Jul 13. PMID- 18948383 OWN - NLM STAT- MEDLINE DA - 20090130 DCOM- 20090216 LR - 20120215 IS - 1530-6860 (Electronic) IS - 0892-6638 (Linking) VI - 23 IP - 2 DP - 2009 Feb TI - Structural insights on physiological functions and pathological effects of alpha-synuclein. PG - 329-40 LID - 10.1096/fj.08-119784 [doi] AB - Alpha-synuclein is an intrinsically unfolded protein that can adopt a partially helical structure when it interacts with different lipid membranes. Its pathological relevance is linked to its involvement in several neurodegenerative disorders including Parkinson's disease, Alzheimer's disease, and dementia with Lewy bodies. Typical of such ailments is the presence of alpha-synuclein aggregates in a beta-structure that can be soluble or precipitate. This review focuses on the structural knowledge acquired in recent years on the various conformations accessible to alpha-synuclein and to its pathologically relevant mutants. Furthermore, the role of the different variables of the chemical environments that govern the equilibria among the accessible conformations is also reviewed. The hypotheses that rationalize the relevance of the individual structural features and conformations for the physiological function of the protein or for its purported pathological role are described and compared. FAU - Bisaglia, Marco AU - Bisaglia M AD - Department of Biology, University of Padova, Via U. Bassi 58B, 35121, Padova, Italy. FAU - Mammi, Stefano AU - Mammi S FAU - Bubacco, Luigi AU - Bubacco L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20081023 PL - United States TA - FASEB J JT - FASEB journal : official publication of the Federation of American Societies for Experimental Biology JID - 8804484 RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Brain Diseases/*metabolism/*physiopathology MH - Cell Membrane/metabolism MH - Humans MH - Protein Conformation MH - Protein Multimerization MH - alpha-Synuclein/*chemistry/genetics/*metabolism/ultrastructure RF - 126 EDAT- 2008/10/25 09:00 MHDA- 2009/02/17 09:00 CRDT- 2008/10/25 09:00 PHST- 2008/10/23 [aheadofprint] AID - fj.08-119784 [pii] AID - 10.1096/fj.08-119784 [doi] PST - ppublish SO - FASEB J. 2009 Feb;23(2):329-40. doi: 10.1096/fj.08-119784. Epub 2008 Oct 23. PMID- 17876814 OWN - NLM STAT- MEDLINE DA - 20080227 DCOM- 20080331 LR - 20101118 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 70 IP - 4 DP - 2008 Mar TI - Computational analysis of folding and mutation properties of C5 domain of myosin binding protein C. PG - 1313-22 AB - Thermal folding molecular dynamics simulations of the domain C5 of Myosin binding protein C were performed using a native-centric model to study the role of three mutations related to Familial Hypertrophic Cardiomyopathy. Mutation of Asn755 causes the largest shift of the folding temperature, and the residue is located in the CFGA' beta-sheet featuring the highest phi-values. The mutation thus appears to reduce the thermodynamic stability in agreement with experimental data. The mutations on Arg654 and Arg668, conversely, cause little change in the folding temperature and they reside in the low phi-value BDE beta-sheet, so that their pathological role cannot be related to impairment of the folding process but possibly to the binding with target molecules. As the typical signature of Domain C5 is the presence of a longer and destibilizing CD-loop with respect to the other Ig-like domains, we completed the work with a bioinformatic analysis of this loop showing a high density of negative charge and low hydrophobicity. This indicates the CD-loop as a natively unfolded sequence with a likely coupling between folding and ligand binding. CI - 2007 Wiley-Liss, Inc. FAU - Guardiani, Carlo AU - Guardiani C AD - Centro Interdipartimentale per lo Studio delle Dinamiche Complesse Sezione INFN di Firenze, Italy. FAU - Cecconi, Fabio AU - Cecconi F FAU - Livi, Roberto AU - Livi R LA - eng PT - Journal Article PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Carrier Proteins) RN - 0 (myosin-binding protein C) SB - IM MH - Carrier Proteins/*chemistry/genetics MH - *Computational Biology MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - *Mutation MH - *Protein Folding MH - Protein Structure, Tertiary MH - Static Electricity EDAT- 2007/09/19 09:00 MHDA- 2008/04/01 09:00 CRDT- 2007/09/19 09:00 AID - 10.1002/prot.21621 [doi] PST - ppublish SO - Proteins. 2008 Mar;70(4):1313-22. PMID- 9714161 OWN - NLM STAT- MEDLINE DA - 19981020 DCOM- 19981020 LR - 20001218 IS - 0887-3585 (Print) IS - 0887-3585 (Linking) VI - 32 IP - 2 DP - 1998 Aug 1 TI - Functional protein domains from the thermally driven motion of polypeptide chains: a proposal. PG - 223-8 AB - It is proposed that the thermally driven motion of certain polypeptide chains, including those that are part of an otherwise stable folded protein, produces time-averaged three-dimensional domains that confer unique functions to a protein. These domains may be controlled by collapsing the polypeptide into an enthalpically favored structure, or extending it into an entropically dominated form. In the extended form, these domains occupy a relatively large space, which may be used to regulate protein-protein interactions and confer mechanical properties to proteins. This "entropic bristle" model makes several predictions about the structure and properties of these domains, and the predictions are used to reevaluate a range of biophysical studies on proteins. The outcome of the analysis suggests that the entropic bristle can be used to explain a wide range of disparate and apparently unrelated experimental observations. FAU - Hoh, J H AU - Hoh JH AD - Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. jan.hoh@jhu.edu LA - eng PT - Journal Article PL - UNITED STATES TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Peptides) SB - IM MH - Allosteric Regulation MH - Binding Sites MH - Crystallization MH - Entropy MH - Enzyme Activation MH - Glycosylation MH - Hydrogen-Ion Concentration MH - Kinetics MH - Models, Chemical MH - Molecular Weight MH - Peptides/*chemistry MH - Phosphorylation MH - *Protein Conformation MH - *Protein Folding MH - Stochastic Processes MH - Structure-Activity Relationship MH - Temperature EDAT- 1998/08/26 02:24 MHDA- 2000/06/20 09:00 CRDT- 1998/08/26 02:24 AID - 10.1002/(SICI)1097-0134(19980801)32:2<223::AID-PROT8>3.0.CO;2-L [pii] PST - ppublish SO - Proteins. 1998 Aug 1;32(2):223-8. PMID- 15751956 OWN - NLM STAT- MEDLINE DA - 20050308 DCOM- 20050607 LR - 20091119 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 44 IP - 10 DP - 2005 Mar 15 TI - Role of structural plasticity in signal transduction by the cryptochrome blue-light photoreceptor. PG - 3795-805 AB - Cryptochromes are blue-light photoreceptors that regulate a variety of responses such as growth and circadian rhythms in organisms ranging from bacteria to humans. Cryptochromes share a high level of sequence identity with the light-activated DNA repair enzyme photolyase. Photolyase uses energy from blue light to repair UV-induced photoproducts in DNA through cyclic electron transfer between the catalytic flavin adenine dinucleotide cofactor and the damaged DNA. Cryptochromes lack DNA repair activity, and their mechanism of signal transduction is not known. It is hypothesized that a light-dependent signaling state in cryptochromes is created as a result of an intramolecular redox reaction, resulting in conformational rearrangement and effector binding. Plant and animal cryptochromes possess 30-250 amino acid carboxy-terminal extensions beyond the photolyase-homology region that have been shown to mediate phototransduction. We analyzed the structures of C-terminal domains from an animal and a plant cryptochrome by computational, biophysical, and biochemical methods and found these domains to be intrinsically unstructured. We show that the photolyase-homology region interacts with the C-terminal domain, inducing stable tertiary structure in the C-terminal domain. Importantly, we demonstrate a light-dependent conformational change in the C-terminal domain of Arabidopsis Cry1. Collectively, these findings provide the first biochemical evidence for the proposed conformational rearrangement of cryptochromes upon light exposure. FAU - Partch, Carrie L AU - Partch CL AD - Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA. FAU - Clarkson, Michael W AU - Clarkson MW FAU - Ozgur, Sezgin AU - Ozgur S FAU - Lee, Andrew L AU - Lee AL FAU - Sancar, Aziz AU - Sancar A LA - eng GR - GM066009/GM/NIGMS NIH HHS/United States GR - GM31082/GM/NIGMS NIH HHS/United States GR - MH070151-01/MH/NIMH NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Arabidopsis Proteins) RN - 0 (CRY1 protein, human) RN - 0 (Cryptochromes) RN - 0 (Drosophila Proteins) RN - 0 (Flavoproteins) RN - 0 (Peptide Fragments) RN - EC 3.4.21.4 (Trypsin) RN - EC 4.1.99.3 (Deoxyribodipyrimidine Photo-Lyase) SB - IM MH - Amino Acid Sequence MH - Animals MH - Arabidopsis Proteins/*chemistry/metabolism/*physiology MH - Circular Dichroism MH - Computational Biology/methods MH - Cryptochromes MH - Deoxyribodipyrimidine Photo-Lyase/chemistry/metabolism/physiology MH - Drosophila Proteins/chemistry/metabolism/physiology MH - Flavoproteins/*chemistry/metabolism/*physiology MH - Humans MH - Hydrolysis MH - *Light MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemistry/metabolism/physiology MH - Photoreceptor Cells, Vertebrate/chemistry/metabolism/physiology MH - Protein Interaction Mapping MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Signal Transduction/*physiology MH - Structural Homology, Protein MH - Structure-Activity Relationship MH - Trypsin/chemistry EDAT- 2005/03/09 09:00 MHDA- 2005/06/09 09:00 CRDT- 2005/03/09 09:00 AID - 10.1021/bi047545g [doi] PST - ppublish SO - Biochemistry. 2005 Mar 15;44(10):3795-805. PMID- 16461914 OWN - NLM STAT- MEDLINE DA - 20060215 DCOM- 20060407 LR - 20140909 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 103 IP - 7 DP - 2006 Feb 14 TI - Core domain interactions in full-length p53 in solution. PG - 2115-9 AB - The tumor suppressor p53 consists of four 393-residue chains, each of which has two natively unfolded (N- and C-terminal) and two folded (core and tetramerization) domains. Their structural organization is poorly characterized as the protein tends to aggregate, has defied crystallization, and is at the limits of NMR studies. We first stabilized the protein by mutation to make it more suitable for extended study and then acquired NMR spectra on full-length protein and various combinations of shorter domain constructs. The NMR spectrum (15N,1H transverse relaxation optimized spectroscopy) of full-length p53 was close to that expected from the sum of the spectra of isolated individual domains. However, patterns of changes in chemical shifts revealed unexpected interactions between the core domains. We used the NMR data as constraints in docking algorithms and found a previously uncharacterized self-complementary surface for the association of core domains into dimers within the tetrameric complex. Binding to DNA requires about a 70 degrees rotation to break those subunit interactions and form the known protein:protein interface in the p53-DNA complex. We verified the interactions by the effects of mutation on DNA binding. Spectroscopic, biophysical, and mutational data conspired to give a picture of the p53 tetramer as a dimer of loosely tethered core dimers of appropriate symmetry to be poised to bind target DNA. FAU - Veprintsev, Dmitry B AU - Veprintsev DB AD - Medical Research Council Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom. FAU - Freund, Stefan M V AU - Freund SM FAU - Andreeva, Antonina AU - Andreeva A FAU - Rutledge, Stacey E AU - Rutledge SE FAU - Tidow, Henning AU - Tidow H FAU - Canadillas, Jose Manuel Perez AU - Canadillas JM FAU - Blair, Caroline M AU - Blair CM FAU - Fersht, Alan R AU - Fersht AR LA - eng GR - MC_U105474168/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060206 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Solutions) RN - 0 (Tumor Suppressor Protein p53) RN - 9007-49-2 (DNA) SB - IM MH - Crystallography MH - DNA/chemistry MH - Dimerization MH - Humans MH - Mutagenesis MH - Protein Structure, Tertiary MH - Solutions/chemistry MH - Tumor Suppressor Protein p53/*chemistry/genetics PMC - PMC1413758 OID - NLM: PMC1413758 EDAT- 2006/02/08 09:00 MHDA- 2006/04/08 09:00 CRDT- 2006/02/08 09:00 PHST- 2006/02/06 [aheadofprint] AID - 0511130103 [pii] AID - 10.1073/pnas.0511130103 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2006 Feb 14;103(7):2115-9. Epub 2006 Feb 6. PMID- 19303059 OWN - NLM STAT- MEDLINE DA - 20090505 DCOM- 20090720 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1794 IP - 6 DP - 2009 Jun TI - Polyglutamine tract binding protein-1 is an intrinsically unstructured protein. PG - 936-43 LID - 10.1016/j.bbapap.2009.03.001 [doi] AB - Polyglutamine tract binding protein-1 (PQBP-1) is a nuclear protein that interacts with disease proteins containing expanded polyglutamine repeats. PQBP-1 also interacts with RNA polymerase II and a spliceosomal protein U5-15kD. In the present study, we demonstrate that PQBP-1 is composed of a large unstructured region and a small folded core. Intriguingly, the large unstructured region encompasses two functional domains: a polar amino acid rich domain and a C-terminal domain. These findings suggest that PQBP-1 belongs to the family of intrinsically unstructured/disordered proteins. Furthermore, the binding of the target molecule U5-15kD induces only minor conformational changes into PQBP-1. Our results suggest that PQBP-1 includes high content of unstructured regions in the C-terminal domain, in spite of the binding of U5-15kD. FAU - Takahashi, Masaki AU - Takahashi M AD - Faculty of Pharmaceutical Sciences, University of Toyama, 2630, Sugitani, Toyama 930-0194, Japan. FAU - Mizuguchi, Mineyuki AU - Mizuguchi M FAU - Shinoda, Hiroyuki AU - Shinoda H FAU - Aizawa, Tomoyasu AU - Aizawa T FAU - Demura, Makoto AU - Demura M FAU - Okazawa, Hitoshi AU - Okazawa H FAU - Kawano, Keiichi AU - Kawano K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090317 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Carrier Proteins) RN - 0 (Nuclear Proteins) RN - 0 (PQBP1 protein, human) SB - IM MH - Carrier Proteins/*chemistry/genetics/isolation & purification MH - Chromatography, Gel MH - Circular Dichroism MH - Hydrolysis MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*chemistry/genetics/isolation & purification MH - Surface Plasmon Resonance EDAT- 2009/03/24 09:00 MHDA- 2009/07/21 09:00 CRDT- 2009/03/24 09:00 PHST- 2008/09/30 [received] PHST- 2009/02/27 [revised] PHST- 2009/03/03 [accepted] PHST- 2009/03/17 [aheadofprint] AID - S1570-9639(09)00053-3 [pii] AID - 10.1016/j.bbapap.2009.03.001 [doi] PST - ppublish SO - Biochim Biophys Acta. 2009 Jun;1794(6):936-43. doi: 10.1016/j.bbapap.2009.03.001. Epub 2009 Mar 17. PMID- 11526233 OWN - NLM STAT- MEDLINE DA - 20010829 DCOM- 20011004 LR - 20140613 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 98 IP - 18 DP - 2001 Aug 28 TI - Structure of the yeast ribonucleotide reductase Y2Y4 heterodimer. PG - 10073-8 AB - The R2 subunits of class I ribonucleotide reductases (RNRs) house a diferric-tyrosyl radical (Y*) cofactor essential for DNA synthesis. In yeast, there are two R2 proteins, Y2 and Y4. Although both Y2 and Y4 are homologous to R2s from other organisms, Y4 lacks three conserved iron-binding residues, and its exact function is unclear. Y4 is required for assembly of the diferric-Y* cofactor in Y2, and the two proteins can form both homodimeric and heterodimeric complexes. The Y2Y4 heterodimer was crystallized from a mixture of the two proteins, and its structure was determined to 2.8 A resolution. Both Y2 and Y4 are completely alpha helical and resemble the mouse and Escherichia coli R2s in overall fold. Three alpha helices not observed in the mouse R2 structure are present at the Y2 N terminus, and one extra N-terminal helix is observed in Y4. In addition, one of the eight principal helices in both Y2 and Y4, alphaD, is shifted significantly from its position in mouse R2. The heterodimer interface is similar to the mouse R2 homodimer interface in size and interacting residues, but loop regions at the interface edges differ. A single metal ion, assigned as Zn(II), occupies the Fe2 position in the Y2 active site. Treatment of the crystals with Fe(II) results in difference electron density consistent with formation of a diiron center. No metal-binding site is observed in Y4. Instead, the residues in the active site region form a hydrogen-bonding network involving an arginine, two glutamic acids, and a water molecule. FAU - Voegtli, W C AU - Voegtli WC AD - Department of Biochemistry, Northwestern University, Evanston, IL 60208, USA. FAU - Ge, J AU - Ge J FAU - Perlstein, D L AU - Perlstein DL FAU - Stubbe, J AU - Stubbe J FAU - Rosenzweig, A C AU - Rosenzweig AC LA - eng SI - PDB/1JK0 GR - GM08382/GM/NIGMS NIH HHS/United States GR - GM29595/GM/NIGMS NIH HHS/United States GR - GM58518/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Protein Subunits) RN - EC 1.17.4.- (Ribonucleotide Reductases) SB - IM MH - Amino Acid Sequence MH - Animals MH - Catalytic Domain MH - Crystallography, X-Ray MH - Dimerization MH - Escherichia coli/enzymology/genetics MH - Hydrogen Bonding MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Subunits MH - Ribonucleotide Reductases/*chemistry/genetics/metabolism MH - Saccharomyces cerevisiae/*enzymology/genetics MH - Sequence Homology, Amino Acid MH - Static Electricity PMC - PMC56917 OID - NLM: PMC56917 EDAT- 2001/08/30 10:00 MHDA- 2001/10/05 10:01 CRDT- 2001/08/30 10:00 AID - 10.1073/pnas.181336398 [doi] AID - 98/18/10073 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10073-8. PMID- 8610010 OWN - NLM STAT- MEDLINE DA - 19960530 DCOM- 19960530 LR - 20061115 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 381 IP - 6578 DP - 1996 May 9 TI - Crystal structure of a yeast TFIIA/TBP/DNA complex. PG - 127-51 AB - The X-ray crystal structure of the transcription factor IIA (TFIIA) in complex with the TATA-box-binding protein (TBP) and TATA-element DNA is presented at 2.5 A resolution. TFIIA is composed of a beta-barrel and a four-helix bundle motif that together have a boot-like appearance. The beta-barrel extends the TBP beta-sheet and bridges over the DNA major groove immediately upstream of the TATA box. The four-helix bundle contributes substantially to the surface of the complex available for interaction with additional transcription factors. FAU - Tan, S AU - Tan S AD - Institut fur Molekularbiologie und Biophysik, ETH-Honggerberg, Zurich, Switzerland. FAU - Hunziker, Y AU - Hunziker Y FAU - Sargent, D F AU - Sargent DF FAU - Richmond, T J AU - Richmond TJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (CYC1 protein, S cerevisiae) RN - 0 (Cytochrome c Group) RN - 0 (DNA, Fungal) RN - 0 (DNA-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (TATA-Box Binding Protein) RN - 0 (Transcription Factor TFIIA) RN - 0 (Transcription Factors) RN - 9007-43-6 (Cytochromes c) SB - IM CIN - Nature. 1996 May 9;381(6578):112-3. PMID: 8610004 MH - Amino Acid Sequence MH - Base Sequence MH - Crystallography, X-Ray MH - Cytochrome c Group/genetics MH - *Cytochromes c MH - DNA, Fungal/*chemistry MH - DNA-Binding Proteins/*chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Protein Conformation MH - Recombinant Proteins/chemistry MH - Saccharomyces cerevisiae/chemistry/genetics MH - *Saccharomyces cerevisiae Proteins MH - TATA Box MH - TATA-Box Binding Protein MH - Transcription Factor TFIIA MH - Transcription Factors/*chemistry MH - Transcription, Genetic EDAT- 1996/05/09 MHDA- 1996/05/09 00:01 CRDT- 1996/05/09 00:00 AID - 10.1038/381127a0 [doi] PST - ppublish SO - Nature. 1996 May 9;381(6578):127-51. PMID- 9680221 OWN - NLM STAT- MEDLINE DA - 19981020 DCOM- 19981020 LR - 20131121 IS - 0950-382X (Print) IS - 0950-382X (Linking) VI - 28 IP - 6 DP - 1998 Jun TI - Discovery of critical Tol A-binding residues in the bactericidal toxin colicin N: a biophysical approach. PG - 1335-43 AB - Colicins translocate across the Escherichia coli outer membrane and periplasm by interacting with several receptors. After first binding to outer membrane surface receptors via their central region, they interact with TolA or TonB proteins via their N-terminal regions. Finally, the toxic C-terminal region is inserted into or across the cytoplasmic membrane. We have measured the binding of colicin N to TolA by isothermal titration microcalorimetry (ITC) and tryptophan fluorescence. The isolated N-terminal domain exhibits a higher affinity for TolA (Kd = 1 microM) than does the whole colicin (18 microM), and similar behaviour has been observed when the N-terminal domain of the g3p protein of the bacteriophage fd, which also binds TolA, is examined in isolation and in situ. This may indicate a similar mechanism in which a cryptic TolA binding site is revealed after primary receptor binding. The isolated colicin N N-terminal domain appears to be unstructured in circular dichroism and fluorescence studies. We have used mutagenesis and ITC to characterize the TolA binding site and have shown it to be of a different sequence and much further from the N-terminus than previously thought. FAU - Raggett, E M AU - Raggett EM AD - Department of Biochemistry and Genetics, The Medical School, University of Newcastle Upon Tyne, UK. FAU - Bainbridge, G AU - Bainbridge G FAU - Evans, L J AU - Evans LJ FAU - Cooper, A AU - Cooper A FAU - Lakey, J H AU - Lakey JH LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Mol Microbiol JT - Molecular microbiology JID - 8712028 RN - 0 (Bacterial Proteins) RN - 0 (Colicins) RN - 0 (Escherichia coli Proteins) RN - 0 (OmpF protein) RN - 0 (Porins) RN - 0 (tolA protein, E coli) RN - 8DUH1N11BX (Tryptophan) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*metabolism MH - Binding Sites MH - Biophysical Phenomena MH - Biophysics MH - Calorimetry MH - Circular Dichroism MH - Colicins/chemistry/genetics/*metabolism MH - Escherichia coli/*metabolism MH - *Escherichia coli Proteins MH - Fluorescence MH - Molecular Sequence Data MH - Mutagenesis MH - Porins/metabolism MH - Thermodynamics MH - Tryptophan/analysis EDAT- 1998/07/29 MHDA- 1998/07/29 00:01 CRDT- 1998/07/29 00:00 PST - ppublish SO - Mol Microbiol. 1998 Jun;28(6):1335-43. PMID- 23609977 OWN - NLM STAT- MEDLINE DA - 20130911 DCOM- 20140320 LR - 20141116 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 81 IP - 10 DP - 2013 Oct TI - Impact of the K24N mutation on the transactivation domain of p53 and its binding to murine double-minute clone 2. PG - 1738-47 LID - 10.1002/prot.24310 [doi] AB - The level of the p53 transcription factor is negatively regulated by the E3 ubiquitin ligase murine double-minute clone 2 (MDM2). The interaction between p53 and MDM2 is essential for the maintenance of genomic integrity for most eukaryotes. Previous structural studies revealed that MDM2 binds to p53 transactivation domain (p53TAD) from residues 17 to 29. The K24N mutation of p53TAD changes a lysine at position 24 to an asparagine. This mutation occurs naturally in the bovine family and is also found in a rare form of human gestational cancer called choriocarcinoma. In this study, we have investigated how the K24N mutation affects the affinity, structure, and dynamics of p53TAD binding to MDM2. Nuclear magnetic resonance studies of p53TAD show that the K24N mutant is more flexible and has less transient helical secondary structure than the wild type. Isothermal titration calorimetry measurements demonstrate that these changes in structure and dynamics do not significantly change the binding affinity for p53TAD-MDM2. Finally, free-energy perturbation and standard molecular dynamic simulations suggest the negligible affinity change is due to a compensating interaction energy between the K24N mutant and the MDM2 when it is bound. Overall, the data suggest that the K24N-MDM2 complex is able to, at least partly, compensate for an increase in the conformational entropy in unbound K24N with an increase in the bound-state electrostatic interaction energy. CI - Copyright (c) 2013 Wiley Periodicals, Inc. FAU - Zhan, Yingqian Ada AU - Zhan YA AD - Department of Physics, University of Idaho, Moscow, Idaho. FAU - Wu, Hongwei AU - Wu H FAU - Powell, Anne T AU - Powell AT FAU - Daughdrill, Gary W AU - Daughdrill GW FAU - Ytreberg, F Marty AU - Ytreberg FM LA - eng GR - R21 GM083827/GM/NIGMS NIH HHS/United States GR - R21GM83827/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130722 PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Tumor Suppressor Protein p53) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Amino Acid Sequence MH - Calorimetry MH - Humans MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Mutation/genetics/physiology MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - *Proto-Oncogene Proteins c-mdm2/chemistry/metabolism MH - *Tumor Suppressor Protein p53/chemistry/genetics/metabolism PMC - PMC4160123 MID - NIHMS623857 OID - NLM: NIHMS623857 OID - NLM: PMC4160123 OTO - NOTNLM OT - binding mechanism OT - intrinsically disordered protein OT - isothermal titration calorimetry OT - molecular dynamics OT - nuclear magnetic resonance spectroscopy EDAT- 2013/04/24 06:00 MHDA- 2014/03/22 06:00 CRDT- 2013/04/24 06:00 PHST- 2012/09/13 [received] PHST- 2013/04/02 [revised] PHST- 2013/04/08 [accepted] PHST- 2013/07/22 [aheadofprint] AID - 10.1002/prot.24310 [doi] PST - ppublish SO - Proteins. 2013 Oct;81(10):1738-47. doi: 10.1002/prot.24310. Epub 2013 Jul 22. PMID- 19523119 OWN - NLM STAT- MEDLINE DA - 20090922 DCOM- 20091013 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 276 IP - 14 DP - 2009 Jul TI - High levels of structural disorder in scaffold proteins as exemplified by a novel neuronal protein, CASK-interactive protein1. PG - 3744-56 LID - 10.1111/j.1742-4658.2009.07090.x [doi] AB - CASK-interactive protein1 is a newly recognized post-synaptic density protein in mammalian neurons. Although its N-terminal region contains several well-known functional domains, its entire C-terminal proline-rich region of 800 amino acids lacks detectable sequence homology to any previously characterized protein. We used multiple techniques for the structural characterization of this region and its three fragments. By bioinformatics predictions, CD spectroscopy, wide-line and 1H-NMR spectroscopy, limited proteolysis and gel filtration chromatography, we provided evidence that the entire proline-rich region of CASK-interactive protein1 is intrinsically disordered. We also showed that the proline-rich region is biochemically functional, as it interacts with the adaptor protein Abl-interactor-2. To extend the finding of a high level of disorder in this scaffold protein, we collected 74 scaffold proteins (also including proteins denoted as anchor and docking), and predicted their disorder by three different algorithms. We found that a very high fraction (53.6; on average) of the residues fall into local disorder and their ordered domains are connected by linker regions which are mostly disordered (64.5 on average). Because of this high frequency of disorder, the usual design of scaffold proteins of short globular domains (86 amino acids on average) connected by longer linker regions (140 amino acids on average) and the noted binding functions of these regions in both CASK-interactive protein1 and the other proteins studied, we suggest that structurally disordered regions prevail and play key recognition roles in scaffold proteins. FAU - Balazs, Annamaria AU - Balazs A AD - Department of Medical Chemistry, Semmelweis University Medical School, Budapest, Hungary. FAU - Csizmok, Veronika AU - Csizmok V FAU - Buday, Laszlo AU - Buday L FAU - Rakacs, Marianna AU - Rakacs M FAU - Kiss, Robert AU - Kiss R FAU - Bokor, Monika AU - Bokor M FAU - Udupa, Roopesh AU - Udupa R FAU - Tompa, Kalman AU - Tompa K FAU - Tompa, Peter AU - Tompa P LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090611 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Caskin1 protein, rat) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry/genetics/metabolism MH - Amino Acid Motifs MH - Animals MH - COS Cells MH - Cercopithecus aethiops MH - Circular Dichroism MH - Magnetic Resonance Spectroscopy MH - Neurons/metabolism MH - Protein Binding MH - Rats EDAT- 2009/06/16 09:00 MHDA- 2009/10/14 06:00 CRDT- 2009/06/16 09:00 PHST- 2009/06/11 [aheadofprint] AID - EJB7090 [pii] AID - 10.1111/j.1742-4658.2009.07090.x [doi] PST - ppublish SO - FEBS J. 2009 Jul;276(14):3744-56. doi: 10.1111/j.1742-4658.2009.07090.x. Epub 2009 Jun 11. PMID- 19012413 OWN - NLM STAT- MEDLINE DA - 20090220 DCOM- 20090323 LR - 20140922 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 49 DP - 2008 Dec 9 TI - The intrinsically disordered cytoplasmic domain of the T cell receptor zeta chain binds to the nef protein of simian immunodeficiency virus without a disorder-to-order transition. PG - 12942-4 LID - 10.1021/bi801602p [doi] AB - Intrinsically disordered proteins are thought to undergo coupled binding and folding upon interaction with their folded partners. In this study, we investigate whether binding of the intrinsically disordered T cell receptor zeta cytoplasmic tail to the well-folded simian immunodeficiency virus Nef core domain is accompanied by a disorder-to-order transition. We show that zeta forms a 1:1 complex with Nef and remains unfolded in the complex. Thus, our findings oppose the generally accepted view of the behavior of intrinsically disordered proteins and provide new evidence of the existence of specific interactions for unfolded protein molecules. FAU - Sigalov, Alexander B AU - Sigalov AB AD - Department of Pathology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, USA. Alexander.Sigalov@umassmed.edu FAU - Kim, Walter M AU - Kim WM FAU - Saline, Maria AU - Saline M FAU - Stern, Lawrence J AU - Stern LJ LA - eng SI - PDB/1AVV GR - P30 AI042845/AI/NIAID NIH HHS/United States GR - P30 AI42845/AI/NIAID NIH HHS/United States GR - R21 AI074616/AI/NIAID NIH HHS/United States GR - R21 AI074616-01A1/AI/NIAID NIH HHS/United States GR - R21-AI074616/AI/NIAID NIH HHS/United States GR - R25 GM062467/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Gene Products, nef) RN - 0 (Receptors, Antigen, T-Cell) RN - 0 (antigen T cell receptor, zeta chain) SB - IM MH - Binding Sites MH - Cytoplasm/metabolism MH - Dimerization MH - Electrophoresis, Polyacrylamide Gel MH - Gene Products, nef/chemistry/*metabolism MH - Protein Folding MH - Protein Structure, Tertiary MH - Receptors, Antigen, T-Cell/*chemistry/*metabolism MH - Simian immunodeficiency virus/*chemistry PMC - PMC3226742 MID - NIHMS337503 OID - NLM: NIHMS337503 OID - NLM: PMC3226742 EDAT- 2008/11/18 09:00 MHDA- 2009/03/24 09:00 CRDT- 2008/11/18 09:00 AID - 10.1021/bi801602p [doi] PST - ppublish SO - Biochemistry. 2008 Dec 9;47(49):12942-4. doi: 10.1021/bi801602p. PMID- 15504034 OWN - NLM STAT- MEDLINE DA - 20041026 DCOM- 20041130 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 43 DP - 2004 Nov 2 TI - Three-dimensional structure of the R115E mutant of T4-bacteriophage 2'-deoxycytidylate deaminase. PG - 13715-23 AB - 2'-Deoxycytidylate deaminase (dCD) converts deoxycytidine 5'-monophosphate (dCMP) to deoxyuridine 5'-monophosphate and is a major supplier of the substrate for thymidylate synthase, an important enzyme in DNA synthesis and a major target for cancer chemotherapy. Wild-type dCD is allosterically regulated by the end products of its metabolic pathway, deoxycytidine 5'-triphosphate and deoxythymidine 5'-triphosphate, which act as an activator and an inhibitor, respectively. The first crystal structure of a dCD, in the form of the R115E mutant of the T4-bacteriophage enzyme complexed with the active site inhibitor pyrimidin-2-one deoxyribotide, has been determined at 2.2 A resolution. This mutant of dCD is active, even in the absence of the allosteric regulators. The molecular topology of dCD is related to that of cytidine deaminase (CDA) but with modifications for formation of the binding site for the phosphate group of dCMP. The enzyme has a zinc ion-based mechanism that is similar to that of CDA. A second zinc ion that is present in bacteriophage dCD, but absent in mammalian dCD and CDA, is important for the structural integrity of the enzyme and for the binding of the phosphate group of the substrate or inhibitor. Although the R115E mutant of dCD is a dimer in solution, it crystallizes as a hexamer, mimicking the natural state of the wild-type enzyme. Residues 112 and 115, which are known to be important for the binding of the allosteric regulators, are found in a pocket that is at the intersubunit interfaces in the hexamer but distant from the substrate-binding site. The substrate-binding site is composed of residues from a single protein molecule and is sequestered in a deep groove. This groove is located at the outer surface of the hexamer but ends at the subunit interface that also includes residue 115. It is proposed that the absence of subunit interactions at this interface in the dimeric R115E mutant renders the substrate-binding site accessible. In contrast, for the wild-type enzyme, binding of dCTP induces an allosteric effect that affects the subunit interactions and results in an increase in the accessibility of the binding site. FAU - Almog, Rami AU - Almog R AD - Wadsworth Center, New York State Department of Health, Albany, New York 12201-0509, USA. FAU - Maley, Frank AU - Maley F FAU - Maley, Gladys F AU - Maley GF FAU - Maccoll, Robert AU - Maccoll R FAU - Van Roey, Patrick AU - Van Roey P LA - eng SI - PDB/1TEO PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Protein Subunits) RN - 0 (Pyrimidine Nucleosides) RN - 0 (Viral Proteins) RN - 3690-10-6 (pyrimidin-2-one beta-ribofuranoside) RN - 3KX376GY7L (Glutamic Acid) RN - 5CSZ8459RP (Cytidine) RN - 94ZLA3W45F (Arginine) RN - EC 3.5.4.- (Nucleoside Deaminases) RN - EC 3.5.4.12 (DCMP Deaminase) RN - EC 3.5.4.14 (deoxycytidine deaminase) RN - EC 3.5.4.5 (Cytidine Deaminase) RN - J41CSQ7QDS (Zinc) SB - IM MH - Allosteric Regulation/genetics MH - Amino Acid Substitution/*genetics MH - Arginine/genetics MH - Bacteriophage T4/*chemistry/*genetics MH - Binding Sites/genetics MH - Crystallization MH - Crystallography, X-Ray MH - Cytidine/analogs & derivatives MH - Cytidine Deaminase/chemistry MH - DCMP Deaminase/antagonists & inhibitors/*chemistry/*genetics MH - Glutamic Acid/genetics MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Nucleoside Deaminases/chemistry MH - Protein Structure, Quaternary/genetics MH - Protein Subunits/chemistry/genetics MH - Pyrimidine Nucleosides/chemistry MH - Substrate Specificity/genetics MH - Viral Proteins/antagonists & inhibitors/chemistry/genetics MH - Zinc/chemistry EDAT- 2004/10/27 09:00 MHDA- 2004/12/16 09:00 CRDT- 2004/10/27 09:00 AID - 10.1021/bi048928h [doi] PST - ppublish SO - Biochemistry. 2004 Nov 2;43(43):13715-23. PMID- 18417251 OWN - NLM STAT- MEDLINE DA - 20080818 DCOM- 20081112 LR - 20140219 IS - 0171-9335 (Print) IS - 0171-9335 (Linking) VI - 87 IP - 8-9 DP - 2008 Sep TI - Identification of the insulin-responsive tyrosine phosphorylation sites on IRSp53. PG - 699-708 LID - 10.1016/j.ejcb.2008.02.010 [doi] AB - The 53-kDa insulin receptor substrate protein (IRSp53) is part of a regulatory network that organises the actin cytoskeleton in response to stimulation by small GTPases, promoting formation of actin-rich cell protrusions such as filopodia and lamellipodia. It had been established earlier that IRSp53 is tyrosine phosphorylated in response to stimulation of the insulin and insulin-related growth factor receptors, but the consequences of tyrosine phosphorylation for IRSp53 function are unknown. Here, we have used a variety of IRSp53 truncation and point mutants to identify insulin-responsive tyrosine phosphorylation sites on IRSp53. We have found that the C-terminal half of IRSp53 (residues 251-521) undergoes tyrosine phosphorylation in response to insulin stimulation of the insulin beta receptor or epidermal growth factor stimulation via the epidermal growth factor receptor, and that the key residue for insulin receptor-mediated phosphorylation is tyrosine 310, located in a region between the N-terminal IRSp53/MIM homology domain (IMD, residue 1-250) and the central SH3 domain (residues 374-438) that is predicted to be natively unstructured. Mutation of tyrosine 310 to phenylalanine or glutamic acid abrogates the phosphorylation in response to insulin stimulation, but not in response to stimulation of the epidermal growth factor receptor. The N-terminal IMD, which mediates dimerisation of IRSp53, is required for efficient tyrosine phosphorylation downstream of either the insulin or epidermal growth factor receptor stimulation, yet does not appear to include a tyrosine-phosphorylated site itself. Thus, we have identified tyrosine 310 as a primary site of tyrosine phosphorylation in response to insulin signalling and we have shown that although IRSp53 is tyrosine phosphorylated in response to epidermal growth factor receptor signalling, tyrosine 310 is not crucial. Furthermore, the tyrosine phosphorylation status does not appear to affect the cell morphology and production of filopod-like structures upon expression of IRSp53. FAU - Heung, Man-Yeung AU - Heung MY AD - School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK. FAU - Visegrady, Balazs AU - Visegrady B FAU - Futterer, Klaus AU - Futterer K FAU - Machesky, Laura M AU - Machesky LM LA - eng GR - G117/569/Medical Research Council/United Kingdom GR - Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080415 PL - Germany TA - Eur J Cell Biol JT - European journal of cell biology JID - 7906240 RN - 0 (Actins) RN - 0 (BAIAP2 protein, human) RN - 0 (Nerve Tissue Proteins) RN - 42HK56048U (Tyrosine) RN - EC 2.7.10.1 (Receptor, Epidermal Growth Factor) RN - EC 2.7.10.1 (Receptor, Insulin) SB - IM MH - Actins/metabolism MH - Animals MH - Binding Sites MH - COS Cells MH - Cercopithecus aethiops MH - Nerve Tissue Proteins/chemistry/*metabolism MH - Phosphorylation MH - Protein Structure, Tertiary MH - Pseudopodia/metabolism MH - Receptor, Epidermal Growth Factor/metabolism MH - Receptor, Insulin/metabolism MH - Signal Transduction MH - Transfection MH - Tyrosine/*metabolism EDAT- 2008/04/18 09:00 MHDA- 2008/11/13 09:00 CRDT- 2008/04/18 09:00 PHST- 2008/01/25 [received] PHST- 2008/02/15 [revised] PHST- 2008/02/19 [accepted] PHST- 2008/04/15 [aheadofprint] AID - S0171-9335(08)00049-6 [pii] AID - 10.1016/j.ejcb.2008.02.010 [doi] PST - ppublish SO - Eur J Cell Biol. 2008 Sep;87(8-9):699-708. doi: 10.1016/j.ejcb.2008.02.010. Epub 2008 Apr 15. PMID- 15492000 OWN - NLM STAT- MEDLINE DA - 20041221 DCOM- 20050314 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 52 DP - 2004 Dec 24 TI - Structural changes in the carboxyl terminus of the gap junction protein connexin43 indicates signaling between binding domains for c-Src and zonula occludens-1. PG - 54695-701 AB - Regulation of cell-cell communication by the gap junction protein connexin43 can be modulated by a variety of connexin-associating proteins. In particular, c-Src can disrupt the connexin43 (Cx43)-zonula occludens-1 (ZO-1) interaction, leading to down-regulation of gap junction intercellular communication. The binding sites for ZO-1 and c-Src correspond to widely separated Cx43 domains (approximately 100 residues apart); however, little is known about the structural modifications that may allow information to be transferred over this distance. Here, we have characterized the structure of the connexin43 carboxyl-terminal domain (Cx43CT) to assess its ability to interact with domains from ZO-1 and c-Src. NMR data indicate that the Cx43CT exists primarily as an elongated random coil, with two regions of alpha-helical structure. NMR titration experiments determined that the ZO-1 PDZ-2 domain affected the last 19 Cx43CT residues, a region larger than that reported to be required for Cx43CT-ZO-1 binding. The c-Src SH3 domain affected Cx43CT residues Lys-264-Lys-287, Ser-306-Glu-316, His-331-Phe-337, Leu-356-Val-359, and Ala-367-Ser-372. Only region Lys-264-Lys-287 contains the residues previously reported to act as an SH3 binding domain. The specificity of these interactions was verified by peptide competition experiments. Finally, we demonstrated that the SH3 domain could partially displace the Cx43CT-PDZ-2 complex. These studies represent the first structural characterization of a connexin domain when integrated in a multimolecular complex. Furthermore, we demonstrate that the structural characteristics of a disordered Cx43CT are advantageous for signaling between different binding partners that may be important in describing the mechanism of channel closure or internalization in response to pathophysiological stimuli. FAU - Sorgen, Paul L AU - Sorgen PL AD - Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA. psorgen@unmc.edu FAU - Duffy, Heather S AU - Duffy HS FAU - Sahoo, Prangya AU - Sahoo P FAU - Coombs, Wanda AU - Coombs W FAU - Delmar, Mario AU - Delmar M FAU - Spray, David C AU - Spray DC LA - eng SI - PDB/1R5S GR - GM57691/GM/NIGMS NIH HHS/United States GR - HL39707/HL/NHLBI NIH HHS/United States GR - MH65495/MH/NIMH NIH HHS/United States GR - NS41282/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20041018 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Connexin 43) RN - 0 (Membrane Proteins) RN - 0 (Peptide Fragments) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Sulfhydryl Compounds) RN - 0 (Zonula Occludens-1 Protein) RN - EC 2.5.1.18 (Glutathione Transferase) RN - EC 2.7.10.1 (Protein-Tyrosine Kinases) RN - EC 2.7.10.2 (CSK tyrosine-protein kinase) RN - EC 2.7.10.2 (src-Family Kinases) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Binding, Competitive MH - Connexin 43/*chemistry/genetics/*metabolism MH - Glutathione Transferase/genetics MH - Hydrogen Bonding MH - Hydrogen-Ion Concentration MH - Magnetic Resonance Spectroscopy MH - Membrane Proteins/chemistry/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Molecular Structure MH - Peptide Fragments/chemistry/metabolism MH - Phosphoproteins/chemistry/*metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Protein-Tyrosine Kinases/chemistry/*metabolism MH - Recombinant Fusion Proteins MH - *Signal Transduction MH - Structure-Activity Relationship MH - Sulfhydryl Compounds/metabolism MH - Zonula Occludens-1 Protein MH - src-Family Kinases EDAT- 2004/10/20 09:00 MHDA- 2005/03/15 09:00 CRDT- 2004/10/20 09:00 PHST- 2004/10/18 [aheadofprint] AID - M409552200 [pii] AID - 10.1074/jbc.M409552200 [doi] PST - ppublish SO - J Biol Chem. 2004 Dec 24;279(52):54695-701. Epub 2004 Oct 18. PMID- 11746698 OWN - NLM STAT- MEDLINE DA - 20011217 DCOM- 20020305 LR - 20091119 IS - 0887-3585 (Print) IS - 0887-3585 (Linking) VI - 46 IP - 1 DP - 2002 Jan 1 TI - Intrinsic structural disorder and sequence features of the cell cycle inhibitor p57Kip2. PG - 1-7 AB - The cell cycle inhibitor p57Kip2 induces cell cycle arrest by inhibiting the activity of cyclin-dependent kinases. p57, although active as a cyclin A-CDK2 inhibitor, is largely unfolded or intrinsically disordered as shown by circular dichroism and fluorescence spectra characteristic of an unfolded protein and a hydrodynamic radius consistent with an unfolded structure. In addition, the N-terminal domain of p57 is both functionally independent as a cyclin A-CDK2 inhibitor and unstructured, as demonstrated by circular dichroism and fluorescence spectra indicative of unfolded proteins, a lack of 1H chemical shift dispersion and a hydrodynamic radius consistent with a highly unfolded structure. The amino acid compositions of full-length p57 and the excised QT domain of p57 exhibit significant deviations from the average composition of globular proteins that are consistent with the observed intrinsic disorder. However, the amino acid composition of the CDK inhibition domain of p57 does not exhibit such a striking deviation from the average values observed for proteins, implying that a general low level of hydrophobicity, rather than depletion or enrichment in specific amino acids, contributes to the intrinsic disorder of the excised p57 CDK inhibition domain. CI - Copyright 2001 Wiley-Liss, Inc. FAU - Adkins, Joshua N AU - Adkins JN AD - Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA. FAU - Lumb, Kevin J AU - Lumb KJ LA - eng GR - GM55156/GM/NIGMS NIH HHS/United States GR - RR11847/RR/NCRR NIH HHS/United States GR - RR11981/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (CDKN1C protein, human) RN - 0 (Cyclin-Dependent Kinase Inhibitor p57) RN - 0 (Enzyme Inhibitors) RN - 0 (Nuclear Proteins) RN - EC 2.7.11.22 (Cyclin-Dependent Kinases) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - *Cell Cycle MH - Circular Dichroism MH - Cloning, Molecular MH - Cyclin-Dependent Kinase Inhibitor p57 MH - Cyclin-Dependent Kinases/antagonists & inhibitors MH - Enzyme Inhibitors/chemistry MH - Escherichia coli MH - Humans MH - Molecular Sequence Data MH - Nuclear Proteins/*chemistry/metabolism MH - Phosphorylation MH - Protein Folding MH - Protein Structure, Tertiary EDAT- 2001/12/18 10:00 MHDA- 2002/03/07 10:01 CRDT- 2001/12/18 10:00 AID - 10.1002/prot.10018 [pii] PST - ppublish SO - Proteins. 2002 Jan 1;46(1):1-7. PMID- 9089808 OWN - NLM STAT- MEDLINE DA - 19970603 DCOM- 19970603 LR - 20081121 IS - 0269-2139 (Print) IS - 0269-2139 (Linking) VI - 10 IP - 2 DP - 1997 Feb TI - Circular dichroism analysis of the interaction between the alpha and beta subunits in a killer toxin produced by a halotolerant yeast, Pichia farinosa. PG - 99-101 AB - SMK toxin is a killer toxin produced by a halotolerant yeast, Pichia farinosa. It is a heterodimer consisting of alpha (63 aa) and beta (77 aa) subunits, between which no disulfide bond exists. The two subunits interact tightly with each other below pH 5. However, the subunits dissociate under neutral conditions, resulting in the aggregation of the alpha subunit and the concomitant loss of killer activity. CD spectral measurements showed that the secondary structure of the SMK toxin changes drastically in the pH range 5.1-5.5 and that after the dissociation of the subunits, the soluble beta subunit alone cannot take any secondary structure. It was also shown that the concentration of NaCl does not affect the secondary structure of the SMK toxin. FAU - Suzuki, C AU - Suzuki C AD - National Food Research Institute, Tsukuba-shi, Ibaraki. FAU - Kashiwagi, T AU - Kashiwagi T FAU - Tsuchiya, F AU - Tsuchiya F FAU - Kunishima, N AU - Kunishima N FAU - Morikawa, K AU - Morikawa K FAU - Nikkuni, S AU - Nikkuni S FAU - Arata, Y AU - Arata Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Protein Eng JT - Protein engineering JID - 8801484 RN - 0 (Killer Factors, Yeast) RN - 0 (Mycotoxins) SB - IM MH - Binding Sites MH - Circular Dichroism MH - Hydrogen-Ion Concentration MH - Killer Factors, Yeast MH - Models, Molecular MH - Molecular Structure MH - Mycotoxins/*chemistry MH - Pichia/*chemistry MH - Protein Conformation MH - Protein Engineering MH - Protein Structure, Secondary EDAT- 1997/02/01 MHDA- 1997/02/01 00:01 CRDT- 1997/02/01 00:00 PST - ppublish SO - Protein Eng. 1997 Feb;10(2):99-101. PMID- 8218200 OWN - NLM STAT- MEDLINE DA - 19931126 DCOM- 19931126 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 32 IP - 42 DP - 1993 Oct 26 TI - Metal ion binding to dog osteocalcin studied by 1H NMR spectroscopy. PG - 11352-62 AB - One-dimensional 1H NMR was employed to study the effects of Ca2+ and Lu3+ binding on the apo and calcium-saturated forms of dog bone Gla protein (BGP, osteocalcin). Titration of apo dog BGP with Ca2+ in 20 mM NaCl showed spectral perturbations consistent with the binding of 5 mol equiv of calcium in the NMR slow-exchange limit. The first 2 Ca2+ equiv induced significant conformational changes in the apoprotein, binding cooperatively with a Kd1 approximately 5.0 x 10(-4) M and a Hill coefficient H = 2.3 in 20 mM NaCl. The last 3 equiv bound with a slightly weaker affinity and did not induce significant structural changes. Neither the affinity nor the stoichiometry of calcium binding was significantly altered at 150 mM NaCl. The addition of only 1 Lu3+ equiv to apo dog osteocalcin was sufficient to induce the same spectral perturbations as 2 Ca2+ ions. The addition of 2 Lu3+ equiv to calcium-saturated osteocalcin had little effect on its 1H NMR spectrum, and BGP aggregated at [Lu3+]o/[BGP]o ratios greater than 2 in either the presence or absence of calcium. The spectrum of calcium-saturated osteocalcin was invariant at < or = 55 degrees C (< or = 50 degrees C in 150 mM NaCl), after which the proton resonances shifted to frequencies more characteristic of apo BGP. Saturation with calcium somewhat stabilized the apo dog osteocalcin protein against conformational changes induced at pH extremes; apo BGP was stable at 6.0 < or = pH < or = 10, and calcium-saturated BGP was stable at 5.8 < or = pH < or = 10. Both our NMR and gel filtration data indicate that calcium-saturated osteocalcin exists as a dimer at both high and low protein concentrations. A conformational change in dog osteocalcin was thus induced by the cooperative association of Ca2+ to two high-affinity sites on the protein and stabilized by the association of 3 additional Ca2+ equiv. The results of our temperature and calcium binding studies were consistent with an estimated Kd1 approximately 5.0 x 10(-4) M for the two high-affinity sites. Lutetium induced the same structural changes in osteocalcin as calcium, but the two high-affinity Ca2+ binding sites did not have equal affinities for Lu3+. The BGP:Ca2+ complex was unstable at the low pH conditions induced by osteoclasts during bone resorption, yet the osteocalcin protein retained a BGP:Ca(2+)-like conformation at low pH. However, unlike the calcium-saturated form of the protein, osteocalcin was monomeric at low pH. FAU - Isbell, D T AU - Isbell DT AD - Department of Biochemistry, University of Kentucky, Lexington 40536-0084. FAU - Du, S AU - Du S FAU - Schroering, A G AU - Schroering AG FAU - Colombo, G AU - Colombo G FAU - Shelling, J G AU - Shelling JG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Apoproteins) RN - 0 (Macromolecular Substances) RN - 104982-03-8 (Osteocalcin) RN - 7YNJ3PO35Z (Hydrogen) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Apoproteins/chemistry/metabolism MH - Binding Sites MH - Calcium/*metabolism MH - Dogs MH - Hydrogen MH - Hydrogen-Ion Concentration MH - Kinetics MH - Macromolecular Substances MH - Magnetic Resonance Spectroscopy/methods MH - Molecular Sequence Data MH - Osteocalcin/*chemistry/isolation & purification/*metabolism MH - Thermodynamics EDAT- 1993/10/26 MHDA- 1993/10/26 00:01 CRDT- 1993/10/26 00:00 PST - ppublish SO - Biochemistry. 1993 Oct 26;32(42):11352-62. PMID- 24941347 OWN - NLM STAT- In-Process DA - 20140619 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 6 DP - 2014 TI - TC-1 overexpression promotes cell proliferation in human non-small cell lung cancer that can be inhibited by PD173074. PG - e100075 LID - 10.1371/journal.pone.0100075 [doi] AB - Thyroid cancer-1 (TC-1), a natively disordered protein, is widely expressed in vertebrates and overexpressed in many kinds of tumors. However, its exact role and regulation mechanism in human non-small cell lung cancer (NSCLC) are still unclear. In the present study, we found that TC-1 is highly expressed in NSCLC and that its aberrant expression is strongly associated with NSCLC cell proliferation. Exogenous TC-1 overexpression promotes cell proliferation, accelerates the cell G1-to-S-phase transition, and reduces apoptosis in NSCLC. The knockdown of TC-1, however, inhibits NSCLC cell proliferation, cycle transition, and apoptosis resistance. Furthermore, we also demonstrated that PD173074, which functions as an inhibitor of the TC-1 in NSCLC, decreases the expression of TC-1 and inhibits TC-1 overexpression mediated cell proliferation in vitro and in vivo. Nevertheless, the inhibition function of PD173074 on NSCLC cell proliferation was eliminated in cells with TC-1 knockdown. These results suggest that PD173074 plays a significant role in TC-1 overexpression mediated NSCLC cell proliferation and may be a potential intervention target for the prevention of cell proliferation in NSCLC. FAU - Lei, Jie AU - Lei J AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China. FAU - Li, Wenhai AU - Li W AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China. FAU - Yang, Ye AU - Yang Y AD - Department of thoracic surgery, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, China. FAU - Lu, Qiang AU - Lu Q AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China. FAU - Zhang, Na AU - Zhang N AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China. FAU - Bai, Guangzhen AU - Bai G AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China. FAU - Zhong, Daixing AU - Zhong D AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China. FAU - Su, Kai AU - Su K AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China. FAU - Liu, Boya AU - Liu B AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China. FAU - Li, Xiaofei AU - Li X AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China. FAU - Wang, Yunjie AU - Wang Y AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China. FAU - Wang, Xiaoping AU - Wang X AD - Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China. LA - eng PT - Journal Article DEP - 20140618 PL - United States TA - PLoS One JT - PloS one JID - 101285081 SB - IM PMC - PMC4062440 OID - NLM: PMC4062440 EDAT- 2014/06/19 06:00 MHDA- 2014/06/19 06:00 CRDT- 2014/06/19 06:00 PHST- 2014 [ecollection] PHST- 2014/01/20 [received] PHST- 2014/05/21 [accepted] PHST- 2014/06/18 [epublish] AID - 10.1371/journal.pone.0100075 [doi] AID - PONE-D-14-02946 [pii] PST - epublish SO - PLoS One. 2014 Jun 18;9(6):e100075. doi: 10.1371/journal.pone.0100075. eCollection 2014. PMID- 24810542 OWN - NLM STAT- MEDLINE DA - 20140811 DCOM- 20150417 IS - 1569-1802 (Electronic) IS - 0945-053X (Linking) VI - 36 DP - 2014 Jun TI - The hinge region of type VII collagen is intrinsically disordered. PG - 77-83 LID - 10.1016/j.matbio.2014.04.006 [doi] LID - S0945-053X(14)00065-1 [pii] AB - Type VII collagen (Col7) is important for skin integrity. As a major component of the anchoring fibrils, Col7 is essential for linking different skin layers together. The central collagenous domain of Col7 contains several interruptions of the collagen triple helix. The longest interruption is 39 amino acids long and referred to as the hinge region. The hinge region is highly conserved between species. This region was predicted to adopt a coiled coil structure and to serve as the trimerization domain of Col7. To gain insight into the potential function of the hinge region we investigated a heterologous expressed peptide by CD and NMR spectroscopy. CD spectroscopy implies that the hinge region is intrinsically disordered. Resonance assignment was performed and allowed secondary structure analysis based on the chemical shift values. Seven amino acids in the N-terminal moiety show residual alpha-helical conformation. Subsequent investigation of temperature dependency of amide chemical shifts indicated participation in hydrogen bonding of amino acid residues in the C-terminal moiety of the hinge region. Therefore, the hinge region does not form a coiled coil structure under the employed experimental conditions. The intrinsic disorder of the hinge region might be desired for flexibility to serve as a "hinge" or the hinge region is an important interaction site as typically observed for intrinsically disordered proteins. CI - Copyright (c) 2014. Published by Elsevier B.V. FAU - Richer, Barbara Christine AU - Richer BC AD - Institute of Chemistry, University of Lubeck, 23538 Lubeck, Germany. FAU - Seeger, Karsten AU - Seeger K AD - Institute of Chemistry, University of Lubeck, 23538 Lubeck, Germany. Electronic address: karsten.seeger@chemie.uni-luebeck.de. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140505 PL - Netherlands TA - Matrix Biol JT - Matrix biology : journal of the International Society for Matrix Biology JID - 9432592 RN - 0 (Collagen Type VII) SB - IM MH - *Amino Acid Sequence MH - Animals MH - Binding Sites MH - Circular Dichroism MH - Collagen Type VII/*chemistry/genetics MH - Humans MH - Hydrogen Bonding MH - Magnetic Resonance Spectroscopy MH - Phylogeny MH - Polymorphism, Single Nucleotide MH - Protein Conformation MH - *Protein Structure, Secondary OTO - NOTNLM OT - Extracellular matrix OT - Hinge OT - Intrinsically disordered protein OT - NMR OT - Type VII collagen EDAT- 2014/05/09 06:00 MHDA- 2015/04/18 06:00 CRDT- 2014/05/10 06:00 PHST- 2014/02/14 [received] PHST- 2014/04/23 [revised] PHST- 2014/04/25 [accepted] PHST- 2014/05/05 [aheadofprint] AID - S0945-053X(14)00065-1 [pii] AID - 10.1016/j.matbio.2014.04.006 [doi] PST - ppublish SO - Matrix Biol. 2014 Jun;36:77-83. doi: 10.1016/j.matbio.2014.04.006. Epub 2014 May 5. PMID- 25227946 OWN - NLM STAT- MEDLINE DA - 20141014 DCOM- 20150219 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 40 DP - 2014 Oct 14 TI - The conformational ensemble of the beta-casein phosphopeptide reveals two independent intrinsically disordered segments. PG - 6402-8 LID - 10.1021/bi500107u [doi] AB - The beta-casein phosphopeptide 1-25 (betaCPP) is involved in calcium binding, cellular transduction, and dental remineralization. Though the net charge of 13e suggests an intrinsically disordered peptide, it has been shown to possibly maintain partial structure. To investigate the nature and extent of its conformational disorder, 100 independent molecular dynamics simulations (cumulative time of 30 mus) were conducted in explicit water with 0.1 M sodium chloride. betaCPP adopted an ensemble of conformations (Rg = 8.61 +/- 0.06 A) stabilized primarily by ionic interactions and less so by hydrogen bonding (HB). Intramolecular contact maps showed a lack of interaction between the peptide's head (RELEELNVPGEIVESigma) and tail (SigmaSigmaSigmaEESITR) segments, suggesting their conformational independence. While many backbone HB interactions were observed between the amino acids in each segment, there was no persistent secondary structure evident. Our findings provide a framework for further investigation of betaCPP's conformation and mechanism of action upon binding to calcium phosphate. FAU - Naqvi, Muhammad Ali AU - Naqvi MA AD - Department of Chemistry and Biology, Ryerson University , Toronto, Ontario M5B 2K3, Canada. FAU - Rauscher, Sarah AU - Rauscher S FAU - Pomes, Regis AU - Pomes R FAU - Rousseau, Derick AU - Rousseau D LA - eng GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141002 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Caseins) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Phosphopeptides) SB - IM MH - Amino Acid Sequence MH - Caseins/*chemistry MH - Intrinsically Disordered Proteins/chemistry MH - *Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Phosphopeptides/chemistry MH - Protein Structure, Secondary EDAT- 2014/09/18 06:00 MHDA- 2015/02/20 06:00 CRDT- 2014/09/18 06:00 PHST- 2014/10/02 [aheadofprint] AID - 10.1021/bi500107u [doi] PST - ppublish SO - Biochemistry. 2014 Oct 14;53(40):6402-8. doi: 10.1021/bi500107u. Epub 2014 Oct 2. PMID- 24810540 OWN - NLM STAT- MEDLINE DA - 20140721 DCOM- 20150420 LR - 20150506 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 23 IP - 8 DP - 2014 Aug TI - The high-molecular-weight kininogen domain 5 is an intrinsically unstructured protein and its interaction with ferritin is metal mediated. PG - 1013-22 LID - 10.1002/pro.2486 [doi] AB - High-molecular-weight kininogen domain 5 (HK5) is an angiogenic modulator that is capable of inhibiting endothelial cell proliferation, migration, adhesion, and tube formation. Ferritin can bind to a histidine-glycine-lysine-rich region within HK5 and block its antiangiogenic effects. However, the molecular intricacies of this interaction are not well understood. Analysis of the structure of HK5 using circular dichroism and nuclear magnetic resonance [(1) H, (15) N]-heteronuclear single quantum coherence determined that HK5 is an intrinsically unstructured protein, consistent with secondary structure predictions. Equilibrium binding studies using fluorescence anisotropy were used to study the interaction between ferritin and HK5. The interaction between the two proteins is mediated by metal ions such as Co(2+) , Cd(2+) , and Fe(2+) . This metal-mediated interaction works independently of the loaded ferrihydrite core of ferritin and is demonstrated to be a surface interaction. Ferritin H and L bind to HK5 with similar affinity in the presence of metals. The ferritin interaction with HK5 is the first biological function shown to occur on the surface of ferritin using its surface-bound metals. CI - (c) 2014 The Protein Society. FAU - Huhn, Annissa J AU - Huhn AJ AD - Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina; Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina. FAU - Parsonage, Derek AU - Parsonage D FAU - Horita, David A AU - Horita DA FAU - Torti, Frank M AU - Torti FM FAU - Torti, Suzy V AU - Torti SV FAU - Hollis, Thomas AU - Hollis T LA - eng SI - PDB/2FFX SI - PDB/2FHA GR - CA171101/CA/NCI NIH HHS/United States GR - DK071892/DK/NIDDK NIH HHS/United States GR - P30 CA012197/CA/NCI NIH HHS/United States GR - R01 CA171101/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140522 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Kininogen, High-Molecular-Weight) RN - 0 (Metals, Heavy) RN - 9007-73-2 (Ferritins) SB - IM MH - Ferritins/*chemistry/metabolism MH - Humans MH - Intrinsically Disordered Proteins/*chemistry/isolation & purification/metabolism MH - Kininogen, High-Molecular-Weight/*chemistry/isolation & purification/metabolism MH - Metals, Heavy/*chemistry/metabolism MH - Models, Molecular PMC - PMC4116651 OID - NLM: PMC4116651 [Available on 08/01/15] OTO - NOTNLM OT - angiogenesis OT - ferritin OT - intrinsically unstructured protein OT - kininogen OT - metal ions OT - protein interaction EDAT- 2014/05/09 06:00 MHDA- 2015/04/22 06:00 CRDT- 2014/05/10 06:00 PMCR- 2015/08/01 00:00 PHST- 2014/01/15 [received] PHST- 2014/05/06 [revised] PHST- 2014/05/06 [accepted] PHST- 2014/05/22 [aheadofprint] AID - 10.1002/pro.2486 [doi] PST - ppublish SO - Protein Sci. 2014 Aug;23(8):1013-22. doi: 10.1002/pro.2486. Epub 2014 May 22. PMID- 8218209 OWN - NLM STAT- MEDLINE DA - 19931126 DCOM- 19931126 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 32 IP - 42 DP - 1993 Oct 26 TI - Identification and biochemical characterization of the ligand binding domain of the collagen adhesin from Staphylococcus aureus. PG - 11428-35 AB - We have recently shown that the expression of a collagen adhesin is both necessary and sufficient to mediate the attachment of Staphylococcus aureus to cartilage, a complex collagen-containing substrate [Switalski, L. M., Patti, J. M., Butcher, W., Gristina, A. G., Speziale, P., & Hook, M. (1993) Mol. Microbiol. 7, 99-107]. We now report on the localization of the ligand binding site within the 135-kDa S. aureus collagen adhesin. Using deletion mutagenesis in combination with Western ligand blot and direct binding assays, the collagen binding domain (CBD) was localized to a 168 amino acid long segment [CBD(151-318)] within the N-terminal portion of the adhesin. Using biospecific interaction analysis, pepsin-digested bovine type II collagen was found to contain eight binding sites for CBD(151-318); two binding sites were of "high" affinity (Kd = 3 microM) and six sites were of low affinity (Kd = 30 microM). Short truncations in the terminal flanking regions of CBD(151-318) resulted in two CBDs (180-318 and 151-297) that lacked collagen binding activity. Analysis by circular dichroism of the recombinant CBDs in the far UV revealed similar secondary structures, predominantly beta-sheet, whereas the near-UV spectra indicated dramatic changes in the degree of intermolecular packing (tertiary structure). The deduced amino acid sequence of the ligand binding domain of the collagen adhesin is presented. FAU - Patti, J M AU - Patti JM AD - Institute of Biosciences and Technology, Texas A & M University, Houston 77030. FAU - Boles, J O AU - Boles JO FAU - Hook, M AU - Hook M LA - eng GR - HL-47313/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Adhesins, Bacterial) RN - 0 (DNA Primers) RN - 0 (Recombinant Proteins) RN - 0 (adhesin, Staphylococcus aureus) RN - 9007-34-5 (Collagen) SB - IM GS - cna MH - *Adhesins, Bacterial MH - Amino Acid Sequence MH - Animals MH - *Bacterial Adhesion MH - Base Sequence MH - Binding Sites MH - Cattle MH - Chickens MH - Circular Dichroism MH - Collagen/*metabolism MH - DNA Primers MH - Genes, Bacterial MH - Kinetics MH - Molecular Sequence Data MH - Polymerase Chain Reaction MH - Protein Conformation MH - Recombinant Proteins/chemistry/isolation & purification/metabolism MH - Restriction Mapping MH - Staphylococcus aureus/*metabolism EDAT- 1993/10/26 MHDA- 1993/10/26 00:01 CRDT- 1993/10/26 00:00 PST - ppublish SO - Biochemistry. 1993 Oct 26;32(42):11428-35. PMID- 25034251 OWN - NLM STAT- MEDLINE DA - 20140730 DCOM- 20141031 LR - 20150224 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 30 DP - 2014 Jul 29 TI - Structural effects of PrP polymorphisms on intra- and interspecies prion transmission. PG - 11169-74 LID - 10.1073/pnas.1404739111 [doi] AB - Understanding the molecular parameters governing prion propagation is crucial for controlling these lethal, proteinaceous, and infectious neurodegenerative diseases. To explore the effects of prion protein (PrP) sequence and structural variations on intra- and interspecies transmission, we integrated studies in deer, a species naturally susceptible to chronic wasting disease (CWD), a burgeoning, contagious epidemic of uncertain origin and zoonotic potential, with structural and transgenic (Tg) mouse modeling and cell-free prion amplification. CWD properties were faithfully maintained in deer following passage through Tg mice expressing cognate PrP, and the influences of naturally occurring PrP polymorphisms on CWD susceptibility were accurately reproduced in Tg mice or cell-free systems. Although Tg mice also recapitulated susceptibility of deer to sheep prions, polymorphisms that provided protection against CWD had distinct and varied influences. Whereas substitutions at residues 95 and 96 in the unstructured region affected CWD propagation, their protective effects were overridden during replication of sheep prions in Tg mice and, in the case of residue 96, deer. The inhibitory effects on sheep prions of glutamate at residue 226 in elk PrP, compared with glutamine in deer PrP, and the protective effects of the phenylalanine for serine substitution at the adjacent residue 225, coincided with structural rearrangements in the globular domain affecting interaction between alpha-helix 3 and the loop between beta2 and alpha-helix 2. These structure-function analyses are consistent with previous structural investigations and confirm a role for plasticity of this tertiary structural epitope in the control of PrP conversion and strain propagation. FAU - Angers, Rachel AU - Angers R AD - Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY 40506; FAU - Christiansen, Jeffrey AU - Christiansen J AD - Prion Research Center and Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523; FAU - Nalls, Amy V AU - Nalls AV AD - Prion Research Center and Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523; FAU - Kang, Hae-Eun AU - Kang HE AD - Prion Research Center and Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523; FAU - Hunter, Nora AU - Hunter N AD - The Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom; and. FAU - Hoover, Edward AU - Hoover E AD - Prion Research Center and Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523; FAU - Mathiason, Candace K AU - Mathiason CK AD - Prion Research Center and Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523; FAU - Sheetz, Michael AU - Sheetz M AD - Center for Computational Sciences, University of Kentucky, Lexington, KY 40506. FAU - Telling, Glenn C AU - Telling GC AD - Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY 40506;Prion Research Center and Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523; glenn.telling@colostate.edu. LA - eng GR - BBS/E/D/20251967/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BBS/E/D/20251968/Biotechnology and Biological Sciences Research Council/United Kingdom GR - P01 AI077774/AI/NIAID NIH HHS/United States GR - R01 NS040334/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140717 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (PrPSc Proteins) SB - IM MH - Amino Acid Substitution MH - Animals MH - Deer MH - Mice MH - Mice, Transgenic MH - Mutation, Missense MH - *Polymorphism, Genetic MH - PrPSc Proteins/*genetics/metabolism MH - Protein Structure, Secondary MH - Sheep MH - Sheep Diseases/genetics/metabolism MH - Wasting Disease, Chronic/genetics/metabolism PMC - PMC4121815 OID - NLM: PMC4121815 OTO - NOTNLM OT - prion replication OT - protective polymorphisms OT - protein structure OT - structural plasticity EDAT- 2014/07/19 06:00 MHDA- 2014/11/02 06:00 CRDT- 2014/07/19 06:00 PHST- 2014/07/17 [aheadofprint] AID - 1404739111 [pii] AID - 10.1073/pnas.1404739111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):11169-74. doi: 10.1073/pnas.1404739111. Epub 2014 Jul 17. PMID- 19281819 OWN - NLM STAT- MEDLINE DA - 20090407 DCOM- 20090519 LR - 20131121 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 388 IP - 1 DP - 2009 Apr 24 TI - Solution and crystal structures of mRNA exporter Dbp5p and its interaction with nucleotides. PG - 1-10 LID - 10.1016/j.jmb.2009.03.004 [doi] AB - DEAD-box protein 5 (Dbp5p) plays very important roles in RNA metabolism from transcription, to translation, to RNA decay. It is an RNA helicase and functions as an essential RNA export factor from nucleus. Here, we report the solution NMR structures of the N- and C-terminal domains (NTD and CTD, respectively) of Dbp5p from Saccharomyces cerevisiae (ScDbp5p) and X-ray crystal structure of Dbp5p from Schizosaccharomyces pombe (SpDbp5p) in the absence of nucleotides and RNA. The crystal structure clearly shows that SpDbp5p comprises two RecA-like domains that do not interact with each other. NMR results show that the N-terminal flanking region of ScDpbp5 (M1-E70) is intrinsically unstructured and the region Y71-R121 including the Q motif is highly dynamic on millisecond-microsecond timescales in solution. The C-terminal flanking region of ScDbp5p forms a short beta-strand and a long helix. This helix is unique for ScDbp5p and has not been observed in other DEAD-box proteins. Compared with other DEAD-box proteins, Dbp5p has an extra insert with six residues in the CTD. NMR structure reveals that the insert is located in a solvent-exposed loop capable of interacting with other proteins. ATP and ADP titration experiments show that both ADP and ATP bind to the consensus binding site in the NTD of ScDbp5p but do not interact with the CTD at all. Binding of ATP or ADP to NTD induces significant conformational rearrangement too. FAU - Fan, Jing-Song AU - Fan JS AD - Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore. FAU - Cheng, Zhihong AU - Cheng Z FAU - Zhang, Jingfeng AU - Zhang J FAU - Noble, Christian AU - Noble C FAU - Zhou, Zhihong AU - Zhou Z FAU - Song, Haiwei AU - Song H FAU - Yang, Daiwen AU - Yang D LA - eng SI - PDB/2KBE SI - PDB/2KBF SI - PDB/3FHO PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090310 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Nucleocytoplasmic Transport Proteins) RN - 0 (Nucleotides) RN - 0 (RNA, Messenger) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Schizosaccharomyces pombe Proteins) RN - 61D2G4IYVH (Adenosine Diphosphate) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 2.7.7.- (Dbp5 protein, S pombe) RN - EC 3.6.1.- (DBP5 protein, S cerevisiae) RN - EC 3.6.4.13 (DEAD-box RNA Helicases) SB - IM MH - Adenosine Diphosphate/*metabolism MH - Adenosine Triphosphate/*metabolism MH - Binding Sites MH - Crystallography, X-Ray MH - DEAD-box RNA Helicases/*chemistry/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Nucleocytoplasmic Transport Proteins/*chemistry/metabolism MH - Nucleotides/chemistry/metabolism MH - Protein Structure, Secondary MH - RNA, Messenger/metabolism MH - Saccharomyces cerevisiae/enzymology/metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/metabolism MH - Schizosaccharomyces/enzymology/metabolism MH - Schizosaccharomyces pombe Proteins/*chemistry/metabolism EDAT- 2009/03/14 09:00 MHDA- 2009/05/20 09:00 CRDT- 2009/03/14 09:00 PHST- 2008/12/17 [received] PHST- 2009/02/28 [revised] PHST- 2009/03/03 [accepted] PHST- 2009/03/10 [aheadofprint] AID - S0022-2836(09)00269-1 [pii] AID - 10.1016/j.jmb.2009.03.004 [doi] PST - ppublish SO - J Mol Biol. 2009 Apr 24;388(1):1-10. doi: 10.1016/j.jmb.2009.03.004. Epub 2009 Mar 10. PMID- 24523724 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20140213 DCOM- 20140422 LR - 20150104 IS - 1664-462X (Electronic) IS - 1664-462X (Linking) VI - 5 DP - 2014 TI - The CP12 protein family: a thioredoxin-mediated metabolic switch? PG - 9 LID - 10.3389/fpls.2014.00009 [doi] AB - CP12 is a small, redox-sensitive protein, representatives of which are found in most photosynthetic organisms, including cyanobacteria, diatoms, red and green algae, and higher plants. The only clearly defined function for CP12 in any organism is in the thioredoxin-mediated regulation of the Calvin-Benson cycle. CP12 mediates the formation of a complex between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) in response to changes in light intensity. Under low light, the formation of the GAPDH/PRK/CP12 complex results in a reduction in the activity of both PRK and GAPDH and, under high light conditions, thioredoxin mediates the disassociation of the complex resulting in an increase in both GAPDH and PRK activity. Although the role of CP12 in the redox-mediated formation of the GAPDH/PRK/CP12 multiprotein complex has been clearly demonstrated, a number of studies now provide evidence that the CP12 proteins may play a wider role. In Arabidopsis thaliana CP12 is expressed in a range of tissue including roots, flowers, and seeds and antisense suppression of tobacco CP12 disrupts metabolism and impacts on growth and development. Furthermore, in addition to the higher plant genomes which encode up to three forms of CP12, analysis of cyanobacterial genomes has revealed that, not only are there multiple forms of the CP12 protein, but that in these organisms CP12 is also found fused to cystathionine-beta-synthase domain containing proteins. In this review we present the latest information on the CP12 protein family and explore the possibility that CP12 proteins form part of a redox-mediated metabolic switch, allowing organisms to respond to rapid changes in the external environment. FAU - Lopez-Calcagno, Patricia E AU - Lopez-Calcagno PE AD - School of Biological Sciences, University of Essex Colchester, UK. FAU - Howard, Thomas P AU - Howard TP AD - Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK. FAU - Raines, Christine A AU - Raines CA AD - School of Biological Sciences, University of Essex Colchester, UK. LA - eng GR - P19403/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Review DEP - 20140130 PL - Switzerland TA - Front Plant Sci JT - Frontiers in plant science JID - 101568200 PMC - PMC3906501 OID - NLM: PMC3906501 OTO - NOTNLM OT - cystathionine-beta-synthase (CBS)-domains OT - intrinsically unstructured (disordered) protein OT - protein-protein interactions OT - redox OT - thioredoxin EDAT- 2014/02/14 06:00 MHDA- 2014/02/14 06:01 CRDT- 2014/02/14 06:00 PHST- 2014 [ecollection] PHST- 2013/08/27 [received] PHST- 2014/01/07 [accepted] PHST- 2014/01/30 [epublish] AID - 10.3389/fpls.2014.00009 [doi] PST - epublish SO - Front Plant Sci. 2014 Jan 30;5:9. doi: 10.3389/fpls.2014.00009. eCollection 2014. PMID- 25307498 OWN - NLM STAT- In-Process DA - 20150223 IS - 1096-3634 (Electronic) IS - 1084-9521 (Linking) VI - 37 DP - 2015 Jan TI - Intrinsically disordered tubulin tails: complex tuners of microtubule functions? PG - 11-9 LID - 10.1016/j.semcdb.2014.09.026 [doi] LID - S1084-9521(14)00293-6 [pii] AB - Microtubules are essential cellular polymers assembled from tubulin heterodimers. The tubulin dimer consists of a compact folded globular core and intrinsically disordered C-terminal tails. The tubulin tails form a lawn of densely grafted, negatively charged, flexible peptides on the exterior of the microtubule, potentially akin to brush polymers in the field of synthetic materials. These tails are hotspots for conserved, chemically complex posttranslational modifications that have the potential to act in a combinatorial fashion to regulate microtubule polymer dynamics and interactions with microtubule effectors, giving rise to a "tubulin code". In this review, I summarize our current knowledge of the enzymes that generate the astonishing tubulin chemical diversity observed in cells and describe recent advances in deciphering the roles of tubulin C-terminal tails and their posttranslational modifications in regulating the activity of molecular motors and microtubule associated proteins. Lastly, I outline the promises, challenges and potential pitfalls of deciphering the tubulin code. CI - Copyright (c) 2014. Published by Elsevier Ltd. FAU - Roll-Mecak, Antonina AU - Roll-Mecak A AD - Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892, USA; Biophysics Center, National Heart, Lung and Blood Institute, MD 20892, USA. Electronic address: Antonina@mail.nih.gov. LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Review DEP - 20141013 PL - England TA - Semin Cell Dev Biol JT - Seminars in cell & developmental biology JID - 9607332 SB - IM OTO - NOTNLM OT - Brush polymer OT - Intrinsically disordered proteins OT - Microtubule OT - Molecular motors OT - Post-translational modification OT - Tubulin tyrosine ligase EDAT- 2014/10/14 06:00 MHDA- 2014/10/14 06:00 CRDT- 2014/10/14 06:00 PHST- 2014/08/07 [received] PHST- 2014/09/15 [revised] PHST- 2014/09/30 [accepted] PHST- 2014/10/13 [aheadofprint] AID - S1084-9521(14)00293-6 [pii] AID - 10.1016/j.semcdb.2014.09.026 [doi] PST - ppublish SO - Semin Cell Dev Biol. 2015 Jan;37:11-9. doi: 10.1016/j.semcdb.2014.09.026. Epub 2014 Oct 13. PMID- 22514270 OWN - NLM STAT- MEDLINE DA - 20120611 DCOM- 20120921 LR - 20141016 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 24 DP - 2012 Jun 8 TI - Characterization of conformational changes and protein-protein interactions of rod photoreceptor phosphodiesterase (PDE6). PG - 20111-21 LID - 10.1074/jbc.M112.354647 [doi] AB - As the central effector of visual transduction, the regulation of photoreceptor phosphodiesterase (PDE6) is controlled by both allosteric mechanisms and extrinsic binding partners. However, the conformational changes and interactions of PDE6 with known interacting proteins are poorly understood. Using a fluorescence detection system for the analytical ultracentrifuge, we examined allosteric changes in PDE6 structure and protein-protein interactions with its inhibitory gamma-subunit, the prenyl-binding protein (PrBP/delta), and activated transducin. In solution, the PDE6 catalytic dimer (Palphabeta) exhibits a more asymmetric shape (axial ratio of 6.6) than reported previously. The inhibitory Pgamma subunit behaves as an intrinsically disordered protein in solution but binds with high affinity to the catalytic dimer to reconstitute the holoenzyme without a detectable change in shape. Whereas the closely related PDE5 homodimer undergoes a significant change in its sedimentation properties upon cGMP binding to its regulatory cGMP binding site, no such change was detected upon ligand binding to the PDE6 catalytic dimer. However, when Palphabeta was reconstituted with Pgamma truncation mutants lacking the C-terminal inhibitory region, cGMP-dependent allosteric changes were observed. PrBP/delta bound to the PDE6 holoenzyme with high affinity (K(D) = 6.2 nm) and induced elongation of the protein complex. Binding of activated transducin to PDE6 holoenzyme resulted in a concentration-dependent increase in the sedimentation coefficient, reflecting a dynamic equilibrium between transducin and PDE6. We conclude that allosteric regulation of PDE6 is more complex than for PDE5 and is dependent on interactions of regions of Pgamma with the catalytic dimer. FAU - Matte, Suzanne L AU - Matte SL AD - Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, USA. FAU - Laue, Thomas M AU - Laue TM FAU - Cote, Rick H AU - Cote RH LA - eng GR - EY-05798/EY/NEI NIH HHS/United States GR - R01 EY005798/EY/NEI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120418 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Eye Proteins) RN - EC 3.1.4.35 (Cyclic Nucleotide Phosphodiesterases, Type 5) RN - EC 3.1.4.35 (Cyclic Nucleotide Phosphodiesterases, Type 6) RN - EC 3.6.1.- (Transducin) RN - H2D2X058MU (Cyclic GMP) SB - IM MH - Allosteric Regulation/physiology MH - Animals MH - Cattle MH - Cyclic GMP/chemistry/genetics/*metabolism MH - Cyclic Nucleotide Phosphodiesterases, Type 5/chemistry/genetics/metabolism MH - Cyclic Nucleotide Phosphodiesterases, Type 6/chemistry/genetics/*metabolism MH - Eye Proteins/chemistry/genetics/*metabolism MH - Humans MH - Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Retinal Rod Photoreceptor Cells/cytology/*enzymology MH - Transducin/chemistry/genetics/*metabolism PMC - PMC3370194 OID - NLM: PMC3370194 EDAT- 2012/04/20 06:00 MHDA- 2012/09/22 06:00 CRDT- 2012/04/20 06:00 PHST- 2012/04/18 [aheadofprint] AID - M112.354647 [pii] AID - 10.1074/jbc.M112.354647 [doi] PST - ppublish SO - J Biol Chem. 2012 Jun 8;287(24):20111-21. doi: 10.1074/jbc.M112.354647. Epub 2012 Apr 18. PMID- 22514274 OWN - NLM STAT- MEDLINE DA - 20120618 DCOM- 20120824 LR - 20141016 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 25 DP - 2012 Jun 15 TI - Conformational selection and folding-upon-binding of intrinsically disordered protein CP12 regulate photosynthetic enzymes assembly. PG - 21372-83 LID - 10.1074/jbc.M112.350355 [doi] AB - Carbon assimilation in plants is regulated by the reduction of specific protein disulfides by light and their re-oxidation in the dark. The redox switch CP12 is an intrinsically disordered protein that can form two disulfide bridges. In the dark oxidized CP12 forms an inactive supramolecular complex with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase, two enzymes of the carbon assimilation cycle. Here we show that binding of CP12 to GAPDH, the first step of ternary complex formation, follows an integrated mechanism that combines conformational selection with induced folding steps. Initially, a CP12 conformation characterized by a circular structural motif including the C-terminal disulfide is selected by GAPDH. Subsequently, the induced folding of the flexible C-terminal tail of CP12 in the active site of GAPDH stabilizes the binary complex. Formation of several hydrogen bonds compensates the entropic cost of CP12 fixation and terminates the interaction mechanism that contributes to carbon assimilation control. FAU - Fermani, Simona AU - Fermani S AD - Department of Chemistry G Ciamician, University of Bologna, 40126 Bologna, Italy. FAU - Trivelli, Xavier AU - Trivelli X FAU - Sparla, Francesca AU - Sparla F FAU - Thumiger, Anton AU - Thumiger A FAU - Calvaresi, Matteo AU - Calvaresi M FAU - Marri, Lucia AU - Marri L FAU - Falini, Giuseppe AU - Falini G FAU - Zerbetto, Francesco AU - Zerbetto F FAU - Trost, Paolo AU - Trost P LA - eng SI - PDB/2LJ9 SI - PDB/3QV1 SI - PDB/3RVD PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120418 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Arabidopsis Proteins) RN - 0 (Carrier Proteins) RN - 0 (Disulfides) RN - 0 (Multienzyme Complexes) RN - EC 1.2.1.13 (Glyceraldehyde-3-Phosphate Dehydrogenase (NADP+)(Phosphorylating)) RN - EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)) RN - EC 2.7.1.19 (phosphoribulokinase) SB - IM MH - Arabidopsis/genetics/*metabolism MH - Arabidopsis Proteins/genetics/*metabolism MH - Carrier Proteins/genetics/*metabolism MH - Disulfides/metabolism MH - Enzyme Stability/physiology MH - Glyceraldehyde-3-Phosphate Dehydrogenase (NADP+)(Phosphorylating)/genetics/metabolism MH - Multienzyme Complexes/genetics/metabolism MH - Phosphotransferases (Alcohol Group Acceptor)/genetics/metabolism MH - Photosynthesis/*physiology MH - *Protein Folding PMC - PMC3375559 OID - NLM: PMC3375559 EDAT- 2012/04/20 06:00 MHDA- 2012/08/25 06:00 CRDT- 2012/04/20 06:00 PHST- 2012/04/18 [aheadofprint] AID - M112.350355 [pii] AID - 10.1074/jbc.M112.350355 [doi] PST - ppublish SO - J Biol Chem. 2012 Jun 15;287(25):21372-83. doi: 10.1074/jbc.M112.350355. Epub 2012 Apr 18. PMID- 11560511 OWN - NLM STAT- MEDLINE DA - 20010918 DCOM- 20011025 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 40 IP - 38 DP - 2001 Sep 25 TI - Effect of familial Parkinson's disease point mutations A30P and A53T on the structural properties, aggregation, and fibrillation of human alpha-synuclein. PG - 11604-13 AB - Parkinson's disease involves the loss of dopaminergic neurons in the substantia nigra, leading to movement disorders. The pathological hallmark of Parkinson's disease is the presence of Lewy bodies and Lewy neurites, which are intracellular inclusions consisting primarily of alpha-synuclein. Although essentially all cases of sporadic and early-onset Parkinson's disease are of unknown etiology, two point mutations (A53T and A30P) in the alpha-synuclein gene have been identified in familial early-onset Parkinson's disease. Previous reports have shown that mutant alpha-synuclein may form fibrils more rapidly than wild-type protein. To determine the underlying molecular basis for the enhanced fibrillation of the mutants, the structural properties, responses to changes in the environment, and propensity to aggregate of wild-type, A30P, and A53T alpha-synucleins were systematically investigated. A variety of biophysical methods, including far-UV circular dichroism, FTIR, small-angle X-ray scattering, and light scattering, were employed. Neither the natively unfolded nor the partially folded intermediate conformations are affected by the familial Parkinson's disease point mutations. However, both mutants underwent self-association more readily than the wild type (i.e., at much lower protein concentration and more rapidly). We attribute this effect to the increased propensity of their partially folded intermediates to aggregate, rather than to any changes in the monomeric natively unfolded species. This increased propensity of these mutants to aggregate, relative to wild-type alpha-synuclein, would account for the correlation of these mutations with Parkinson's disease. FAU - Li, J AU - Li J AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. FAU - Uversky, V N AU - Uversky VN FAU - Fink, A L AU - Fink AL LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Nerve Tissue Proteins) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Substitution MH - Circular Dichroism MH - Humans MH - Hydrogen-Ion Concentration MH - Light MH - Nerve Tissue Proteins/*chemistry/*genetics/ultrastructure MH - Parkinson Disease/*genetics MH - Phosphoproteins/chemistry/genetics/ultrastructure MH - *Point Mutation MH - Protein Conformation MH - Protein Structure, Secondary MH - Recombinant Fusion Proteins/chemistry/metabolism/ultrastructure MH - Scattering, Radiation MH - Spectroscopy, Fourier Transform Infrared MH - Synucleins MH - Thermodynamics MH - X-Rays MH - alpha-Synuclein EDAT- 2001/09/19 10:00 MHDA- 2001/10/26 10:01 CRDT- 2001/09/19 10:00 AID - bi010616g [pii] PST - ppublish SO - Biochemistry. 2001 Sep 25;40(38):11604-13. PMID- 17531814 OWN - NLM STAT- MEDLINE DA - 20070528 DCOM- 20070801 LR - 20140916 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 26 IP - 4 DP - 2007 May 25 TI - The N terminus of Saccharomyces cerevisiae Msh6 is an unstructured tether to PCNA. PG - 565-78 AB - The eukaryotic MutS homolog complexes, Msh2-Msh6 and Msh2-Msh3, recognize mismatched bases in DNA during mismatch repair (MMR). The eukaryote-specific N-terminal regions (NTRs) of Msh6 and Msh3 have not been characterized other than by demonstrating that they contain an N-terminal PCNA-interacting motif. Here we have demonstrated genetically that the NTR of Msh6 has an important role in MMR that is partially redundant with PCNA binding. Small-angle X-ray scattering (SAXS) was used to determine the solution structure of the complex of PCNA with Msh2-Msh6 and with the isolated Msh6 NTR, revealing that the Msh6 NTR is a natively disordered domain that forms an extended tether between Msh6 and PCNA. Moreover, computational analysis of PCNA-interacting motifs in the S. cerevisiae proteome indicated that flexible linkers are a common theme for PCNA-interacting proteins that may serve to localize these binding partners without tightly restraining them to the immediate vicinity of PCNA. FAU - Shell, Scarlet S AU - Shell SS AD - Ludwig Institute for Cancer Research, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA. FAU - Putnam, Christopher D AU - Putnam CD FAU - Kolodner, Richard D AU - Kolodner RD LA - eng GR - CA92584/CA/NCI NIH HHS/United States GR - GM50006/GM/NIGMS NIH HHS/United States GR - P01 CA092584/CA/NCI NIH HHS/United States GR - P01 CA092584-06/CA/NCI NIH HHS/United States GR - R01 GM050006/GM/NIGMS NIH HHS/United States GR - R01 GM050006-19/GM/NIGMS NIH HHS/United States GR - T32 GM08666/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (DNA, Fungal) RN - 0 (DNA-Binding Proteins) RN - 0 (MSH6 protein, S cerevisiae) RN - 0 (Peptide Fragments) RN - 0 (Proliferating Cell Nuclear Antigen) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Base Pair Mismatch MH - Chromatography, Gel MH - DNA, Fungal/genetics MH - DNA-Binding Proteins/chemistry/genetics/*metabolism MH - Genetic Complementation Test MH - Mass Spectrometry MH - Peptide Fragments/chemistry/*metabolism MH - Plasmids MH - Proliferating Cell Nuclear Antigen/*metabolism MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism MH - Sequence Deletion PMC - PMC2001284 MID - NIHMS25294 OID - NLM: NIHMS25294 OID - NLM: PMC2001284 EDAT- 2007/05/29 09:00 MHDA- 2007/08/02 09:00 CRDT- 2007/05/29 09:00 PHST- 2006/11/24 [received] PHST- 2007/03/27 [revised] PHST- 2007/04/18 [accepted] AID - S1097-2765(07)00262-6 [pii] AID - 10.1016/j.molcel.2007.04.024 [doi] PST - ppublish SO - Mol Cell. 2007 May 25;26(4):565-78. PMID- 8138348 OWN - NLM STAT- MEDLINE DA - 19940425 DCOM- 19940425 LR - 20131121 IS - 0367-8377 (Print) IS - 0367-8377 (Linking) VI - 43 IP - 1 DP - 1994 Jan TI - Interaction with model membrane systems induces secondary structure in amino-terminal fragments of parathyroid hormone related protein. PG - 23-8 AB - The secondary structure of amino terminal fragments of human parathyroid hormone related protein (PTHrP) in aqueous solution, in trifluoroethanol solution and in the presence of model membrane systems has been studied by circular dichroism (CD) spectroscopy. Far-UV CD spectra of PTHrP 1-40, 1-34 amide, 7-34 amide and 1-16 are consistent with a predominantly unordered structure. Addition of trifluoroethanol stabilized alpha-helical structure in the 1-34 amide and 7-34 amide peptides. The effect reached a plateau at a trifluoroethanol concentration of approximately 40%, and a helix content of some 23 residues was determined. PTHrP 1-34 amide interacted with palmitoyloleoylphosphatidyl serine vesicles and exhibited an increased alpha-helix content of approximately 12 helical residues. Similar results were observed for monomyristoyllecithin micelles and sodium dodecyl sulfate micelles. No interaction with dimyristoylphosphatidylcholine vesicles was detected by CD. The ability to bind to palmitoyloleoylphosphotidyl serine vesicles was also a feature of the 1-40 and 7-34 fragments, while the 1-16 fragment was apparently unaffected by interaction with this model membrane system. These results indicate that the conformational properties of the functionally significant amino terminal 1-34 region of PTHrP parallel those reported for the corresponding, but largely nonhomologous, region of parathyroid hormone. Conformational similarities may account for the ability of PTHrP to mimic the functional properties of parathyroid hormone. FAU - Willis, K J AU - Willis KJ AD - Allelix Biopharmaceuticals Inc., Mississauga, Ontario, Canada. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - DENMARK TA - Int J Pept Protein Res JT - International journal of peptide and protein research JID - 0330420 RN - 0 (Liposomes) RN - 0 (Micelles) RN - 0 (PTHLH protein, human) RN - 0 (Parathyroid Hormone-Related Protein) RN - 0 (Peptide Fragments) RN - 0 (Phospholipids) RN - 0 (Proteins) RN - 0 (Solutions) RN - 059QF0KO0R (Water) RN - 75-89-8 (Trifluoroethanol) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Humans MH - Hydrogen-Ion Concentration MH - Liposomes/*metabolism MH - Mass Spectrometry MH - Micelles MH - Molecular Sequence Data MH - Parathyroid Hormone-Related Protein MH - Peptide Fragments/*chemistry/metabolism MH - Phospholipids/metabolism MH - Protein Structure, Secondary MH - Proteins/*chemistry/metabolism MH - Solutions MH - Trifluoroethanol MH - Water EDAT- 1994/01/01 MHDA- 1994/01/01 00:01 CRDT- 1994/01/01 00:00 PST - ppublish SO - Int J Pept Protein Res. 1994 Jan;43(1):23-8. PMID- 16626738 OWN - NLM STAT- MEDLINE DA - 20060508 DCOM- 20060713 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 359 IP - 1 DP - 2006 May 26 TI - Crystal structure of SUMO-3-modified thymine-DNA glycosylase. PG - 137-47 AB - Modification of cellular proteins by the small ubiquitin-like modifier SUMO is important in regulating various cellular events. Many different nuclear proteins are targeted by SUMO, and the functional consequences of this modification are diverse. For most proteins, however, the functional and structural consequences of modification by specific SUMO isomers are unclear. Conjugation of SUMO to thymine-DNA glycosylase (TDG) induces the dissociation of TDG from its product DNA. Structure determination of the TDG central region conjugated to SUMO-1 previously suggested a mechanism in which the SUMOylation-induced conformational change in the C-terminal region of TDG releases TDG from tight binding to its product DNA. Here, we have determined the crystal structure of the central region of TDG conjugated to SUMO-3. The overall structure of SUMO-3-conjugated TDG is similar to the previously reported structure of TDG conjugated to SUMO-1, despite the relatively low level of amino acid sequence similarity between SUMO-3 and SUMO-1. The two structures revealed that the sequence of TDG that resembles the SUMO-binding motif (SBM) can form an intermolecular beta-sheet with either SUMO-1 or SUMO-3. Structural comparison with the canonical SBM shows that this SBM-like sequence of TDG retains all of the characteristic interactions of the SBM, indicating sequence diversity in the SBM. FAU - Baba, Daichi AU - Baba D AD - Graduate School of Integrated Science, Yokohama City University, Japan. FAU - Maita, Nobuo AU - Maita N FAU - Jee, Jun-Goo AU - Jee JG FAU - Uchimura, Yasuhiro AU - Uchimura Y FAU - Saitoh, Hisato AU - Saitoh H FAU - Sugasawa, Kaoru AU - Sugasawa K FAU - Hanaoka, Fumio AU - Hanaoka F FAU - Tochio, Hidehito AU - Tochio H FAU - Hiroaki, Hidekazu AU - Hiroaki H FAU - Shirakawa, Masahiro AU - Shirakawa M LA - eng SI - PDB/2D07 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060331 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Molecular Chaperones) RN - 0 (Nuclear Pore Complex Proteins) RN - 0 (PIAS2 protein, human) RN - 0 (Protein Inhibitors of Activated STAT) RN - 0 (Protein Isoforms) RN - 0 (SUMO3 protein, human) RN - 0 (Ubiquitins) RN - 0 (ran-binding protein 2) RN - EC 3.2.2.- (Thymine DNA Glycosylase) SB - IM MH - Amino Acid Sequence MH - Crystallography, X-Ray MH - Humans MH - Models, Molecular MH - Molecular Chaperones/chemistry/genetics MH - Molecular Sequence Data MH - Nuclear Pore Complex Proteins/chemistry/genetics MH - Protein Inhibitors of Activated STAT/chemistry/genetics MH - Protein Isoforms/chemistry/genetics/metabolism MH - *Protein Structure, Tertiary MH - Sequence Alignment MH - Thymine DNA Glycosylase/*chemistry/genetics/*metabolism MH - Ubiquitins/*chemistry/genetics/*metabolism EDAT- 2006/04/22 09:00 MHDA- 2006/07/14 09:00 CRDT- 2006/04/22 09:00 PHST- 2006/02/09 [received] PHST- 2006/03/14 [revised] PHST- 2006/03/14 [accepted] PHST- 2006/03/31 [aheadofprint] AID - S0022-2836(06)00372-X [pii] AID - 10.1016/j.jmb.2006.03.036 [doi] PST - ppublish SO - J Mol Biol. 2006 May 26;359(1):137-47. Epub 2006 Mar 31. PMID- 7669757 OWN - NLM STAT- MEDLINE DA - 19951013 DCOM- 19951013 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 34 IP - 35 DP - 1995 Sep 5 TI - The Arg7Lys mutant of heat-labile enterotoxin exhibits great flexibility of active site loop 47-56 of the A subunit. PG - 10996-1004 AB - The heat-labile enterotoxin from Escherichia coli (LT) is a member of the cholera toxin family. These and other members of the larger class of AB5 bacterial toxins act through catalyzing the ADP-ribosylation of various intracellular targets including Gs alpha. The A subunit is responsible for this covalent modification, while the B pentamer is involved in receptor recognition. We report here the crystal structure of an inactive single-site mutant of LT in which arginine 7 of the A subunit has been replaced by a lysine residue. The final model contains 103 residues for each of the five B subunits, 175 residues for the A1 subunit, and 41 residues for the A2 subunit. In this Arg7Lys structure the active site cleft within the A subunit is wider by approximately 1 A than is seen in the wild-type LT. Furthermore, a loop near the active site consisting of residues 47-56 is disordered in the Arg7Lys structure, even though the new lysine residue at position 7 assumes a position which virtually coincides with that of Arg7 in the wild-type structure. The displacement of residues 47-56 as seen in the mutant structure is proposed to be necessary for allowing NAD access to the active site of the wild-type LT. On the basis of the differences observed between the wild-type and Arg7Lys structures, we propose a model for a coordinated sequence of conformational changes required for full activation of LT upon reduction of disulfide bridge 187-199 and cleavage of the peptide loop between the two cysteines in the A subunit.(ABSTRACT TRUNCATED AT 250 WORDS) FAU - van den Akker, F AU - van den Akker F AD - Department of Biological Structure and Biochemistry, University of Washington, Seattle, USA. FAU - Merritt, E A AU - Merritt EA FAU - Pizza, M AU - Pizza M FAU - Domenighini, M AU - Domenighini M FAU - Rappuoli, R AU - Rappuoli R FAU - Hol, W G AU - Hol WG LA - eng GR - AI34501/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Toxins) RN - 0 (Enterotoxins) RN - 0 (Escherichia coli Proteins) RN - 0 (heat-labile enterotoxin, E coli) RN - 0U46U6E8UK (NAD) SB - IM MH - Bacterial Toxins/*chemistry/*genetics/metabolism MH - Binding Sites MH - Crystallography, X-Ray MH - Electrochemistry MH - Enterotoxins/*chemistry/*genetics/metabolism MH - Escherichia coli/genetics/metabolism MH - *Escherichia coli Proteins MH - Models, Molecular MH - Molecular Structure MH - NAD/metabolism MH - Point Mutation MH - Protein Conformation EDAT- 1995/09/05 MHDA- 1995/09/05 00:01 CRDT- 1995/09/05 00:00 PST - ppublish SO - Biochemistry. 1995 Sep 5;34(35):10996-1004. PMID- 21545188 OWN - NLM STAT- MEDLINE DA - 20110701 DCOM- 20111026 IS - 1535-3907 (Electronic) IS - 1535-3893 (Linking) VI - 10 IP - 7 DP - 2011 Jul 1 TI - Conformational role for the C-terminal tail of the intrinsically disordered high mobility group A (HMGA) chromatin factors. PG - 3283-91 LID - 10.1021/pr200116w [doi] AB - The architectural factors HMGA are highly connected hubs in the chromatin network and affect key cellular functions. HMGA have a causal involvement in cancer development; in fact, truncated or chimeric HMGA forms, resulting from chromosomal rearrangements, lack the constitutively phosphorylated acidic C-terminal tail and display increased oncogenic potential, suggesting a functional role for this domain. HMGA belong to the intrinsically disordered protein category, and this prevents the use of classical approaches to obtain structural data. Therefore, we combined limited proteolysis, ion mobility separation-mass spectrometry (IMS-MS), and electrospray ionization-mass spectrometry (ESI-MS) to obtain structural information regarding full length and C-terminal truncated HMGA forms. Limited proteolysis indicates that HMGA acidic tail shields the inner portions of the protein. IMS-MS and ESI-MS show that HMGA proteins can assume a compact form and that the degree of compactness is dependent upon the presence of the acidic tail and its constitutive phosphorylations. Moreover, we demonstrate that C-terminal truncated forms and wild type proteins are post-translationally modified in a different manner. Therefore, we propose that the acidic tail and its phosphorylation could affect HMGA post-translational modification status and likely their activity. Finally, the mass spectrometry-based approach adopted here proves to be a valuable new tool to obtain structural data regarding intrinsically disordered proteins. FAU - Maurizio, Elisa AU - Maurizio E AD - Department of Life Sciences, University of Trieste, Trieste, Italy. FAU - Cravello, Laetitia AU - Cravello L FAU - Brady, Liam AU - Brady L FAU - Spolaore, Barbara AU - Spolaore B FAU - Arnoldo, Laura AU - Arnoldo L FAU - Giancotti, Vincenzo AU - Giancotti V FAU - Manfioletti, Guidalberto AU - Manfioletti G FAU - Sgarra, Riccardo AU - Sgarra R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110520 PL - United States TA - J Proteome Res JT - Journal of proteome research JID - 101128775 RN - 0 (Chromatin) RN - 0 (HMGA Proteins) RN - 0 (Recombinant Proteins) SB - IM MH - Amino Acid Sequence MH - Cell Transformation, Neoplastic/genetics/metabolism MH - Chromatin/*chemistry/metabolism MH - HMGA Proteins/*chemistry/genetics/metabolism MH - Humans MH - Methylation MH - Molecular Sequence Data MH - Phosphorylation MH - Protein Processing, Post-Translational MH - Protein Structure, Tertiary MH - Proteomics/*methods MH - Recombinant Proteins/*chemistry/genetics/metabolism MH - Spectrometry, Mass, Electrospray Ionization MH - Static Electricity EDAT- 2011/05/07 06:00 MHDA- 2011/10/27 06:00 CRDT- 2011/05/07 06:00 PHST- 2011/05/20 [aheadofprint] AID - 10.1021/pr200116w [doi] PST - ppublish SO - J Proteome Res. 2011 Jul 1;10(7):3283-91. doi: 10.1021/pr200116w. Epub 2011 May 20. PMID- 18688269 OWN - NLM STAT- MEDLINE DA - 20080808 DCOM- 20081218 LR - 20140903 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 4 IP - 8 DP - 2008 TI - Intramolecular cohesion of coils mediated by phenylalanine--glycine motifs in the natively unfolded domain of a nucleoporin. PG - e1000145 LID - 10.1371/journal.pcbi.1000145 [doi] AB - The nuclear pore complex (NPC) provides the sole aqueous conduit for macromolecular exchange between the nucleus and the cytoplasm of cells. Its diffusion conduit contains a size-selective gate formed by a family of NPC proteins that feature large, natively unfolded domains with phenylalanine-glycine repeats (FG domains). These domains of nucleoporins play key roles in establishing the NPC permeability barrier, but little is known about their dynamic structure. Here we used molecular modeling and biophysical techniques to characterize the dynamic ensemble of structures of a representative FG domain from the yeast nucleoporin Nup116. The results showed that its FG motifs function as intramolecular cohesion elements that impart order to the FG domain and compact its ensemble of structures into native premolten globular configurations. At the NPC, the FG motifs of nucleoporins may exert this cohesive effect intermolecularly as well as intramolecularly to form a malleable yet cohesive quaternary structure composed of highly flexible polypeptide chains. Dynamic shifts in the equilibrium or competition between intra- and intermolecular FG motif interactions could facilitate the rapid and reversible structural transitions at the NPC conduit needed to accommodate passing karyopherin-cargo complexes of various shapes and sizes while simultaneously maintaining a size-selective gate against protein diffusion. FAU - Krishnan, V V AU - Krishnan VV AD - Department of Applied Science, University of California Davis, Davis, California, United States of America. FAU - Lau, Edmond Y AU - Lau EY FAU - Yamada, Justin AU - Yamada J FAU - Denning, Daniel P AU - Denning DP FAU - Patel, Samir S AU - Patel SS FAU - Colvin, Michael E AU - Colvin ME FAU - Rexach, Michael F AU - Rexach MF LA - eng GR - GM061900/GM/NIGMS NIH HHS/United States GR - GM077520/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20080808 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (NUP116 protein, S cerevisiae) RN - 0 (Nuclear Pore Complex Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 47E5O17Y3R (Phenylalanine) RN - TE7660XO1C (Glycine) SB - IM MH - Active Transport, Cell Nucleus/physiology MH - Amino Acid Motifs/physiology MH - Glycine/*chemistry MH - Models, Molecular MH - Molecular Weight MH - Nuclear Pore/chemistry/metabolism/ultrastructure MH - Nuclear Pore Complex Proteins/*chemistry/metabolism/ultrastructure MH - Phenylalanine/*chemistry MH - Protein Binding/physiology MH - *Protein Folding MH - Protein Interaction Domains and Motifs/*physiology MH - Protein Structure, Quaternary MH - Repetitive Sequences, Amino Acid/physiology MH - Saccharomyces cerevisiae/metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/metabolism/ultrastructure MH - Thermodynamics PMC - PMC2475668 OID - NLM: PMC2475668 EDAT- 2008/08/09 09:00 MHDA- 2008/12/19 09:00 CRDT- 2008/08/09 09:00 PHST- 2006/08/29 [received] PHST- 2008/06/26 [accepted] AID - 10.1371/journal.pcbi.1000145 [doi] PST - epublish SO - PLoS Comput Biol. 2008 Aug 8;4(8):e1000145. doi: 10.1371/journal.pcbi.1000145. PMID- 20472935 OWN - NLM STAT- MEDLINE DA - 20100712 DCOM- 20100806 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 29 DP - 2010 Jul 16 TI - The crystal structure of dynein intermediate chain-light chain roadblock complex gives new insights into dynein assembly. PG - 22566-75 LID - 10.1074/jbc.M110.103861 [doi] AB - The roadblock/LC7 dynein light chain is a ubiquitous component of all dyneins and is essential for many diverse processes including proper axonal transport and dendrite growth. In addition, LC7 functions in non-dynein transcriptional activation of the transforming growth factor-beta complex. Crystal structures of Drosophila melanogaster LC7 in the apo form and in complex with a segment of the disordered N-terminal domain of dynein intermediate chain (IC) provide the first definitive identification of the IC sequence recognized by LC7. The site, confirmed by isothermal titration calorimetry studies, overlaps the IC sequence considered in the literature to be an IC self-association domain. The IC peptide binds as two amphipathic helices that lie along an extensive hydrophobic cleft on LC7 and ends with a polar side-chain interaction network that includes conserved residues from both proteins. The LC7 recognition sequence on IC and its interface with LC7 are well conserved and are, thus, likely representative of all IC x LC7 structures. Interestingly, the position of bound IC in the IC x LC7 complex mimics a helix that is integrated into the primary structure in distantly related LC7 homologs. The IC x LC7 structure further shows that the naturally occurring robl(Z) deletion mutation contains the majority of the IC binding site and suggests that promotion of IC binding by phosphorylation of LC7 is an indirect effect. FAU - Hall, Justin AU - Hall J AD - Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA. FAU - Song, Yujuan AU - Song Y FAU - Karplus, P Andrew AU - Karplus PA FAU - Barbar, Elisar AU - Barbar E LA - eng SI - PDB/3L7H SI - PDB/3L9K GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20100515 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Apoproteins) RN - 0 (Carrier Proteins) RN - 0 (Drosophila Proteins) RN - 0 (roadblock protein, Drosophila) RN - EC 3.6.4.2 (Dyneins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Apoproteins/chemistry/metabolism MH - Binding Sites MH - Calorimetry MH - Carrier Proteins/*chemistry MH - Chromatography, Gel MH - Crystallography, X-Ray MH - Drosophila Proteins/*chemistry MH - Drosophila melanogaster/*metabolism MH - Dyneins/*chemistry/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Structure, Secondary MH - Static Electricity MH - Thermodynamics PMC - PMC2903378 OID - NLM: PMC2903378 EDAT- 2010/05/18 06:00 MHDA- 2010/08/07 06:00 CRDT- 2010/05/18 06:00 PHST- 2010/05/15 [aheadofprint] AID - M110.103861 [pii] AID - 10.1074/jbc.M110.103861 [doi] PST - ppublish SO - J Biol Chem. 2010 Jul 16;285(29):22566-75. doi: 10.1074/jbc.M110.103861. Epub 2010 May 15. PMID- 18436957 OWN - NLM STAT- MEDLINE DA - 20080425 DCOM- 20080523 LR - 20140903 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 17 IP - 5 DP - 2008 May TI - Molecular determinants of the aggregation behavior of alpha- and beta-synuclein. PG - 887-98 LID - 10.1110/ps.073181508 [doi] AB - Alpha- and beta-synuclein are closely related proteins, the first of which is associated with deposits formed in neurodegenerative conditions such as Parkinson's disease while the second appears to have no relationship to any such disorders. The aggregation behavior of alpha- and beta-synuclein as well as a series of chimeric variants were compared by exploring the structural transitions that occur in the presence of a widely used lipid mimetic, sodium dodecyl sulfate (SDS). We found that the aggregation rates of all these protein variants are significantly enhanced by low concentrations of SDS. In particular, we inserted the 11-residue sequence of mainly hydrophobic residues from the non-amyloid-beta-component (NAC) region of alpha-synuclein into beta-synuclein and show that the fibril formation rate of this chimeric protein is only weakly altered from that of beta-synuclein. These intrinsic propensities to aggregate are rationalized to a very high degree of accuracy by analysis of the sequences in terms of their associated physicochemical properties. The results begin to reveal that the differences in behavior are primarily associated with a delicate balance between the positions of a range of charged and hydrophobic residues rather than the commonly assumed presence or absence of the highly aggregation-prone region of the NAC region of alpha-synuclein. This conclusion provides new insights into the role of alpha-synuclein in disease and into the factors that regulate the balance between solubility and aggregation of a natively unfolded protein. FAU - Rivers, Robert C AU - Rivers RC AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom. FAU - Kumita, Janet R AU - Kumita JR FAU - Tartaglia, Gian Gaetano AU - Tartaglia GG FAU - Dedmon, Matthew M AU - Dedmon MM FAU - Pawar, Amol AU - Pawar A FAU - Vendruscolo, Michele AU - Vendruscolo M FAU - Dobson, Christopher M AU - Dobson CM FAU - Christodoulou, John AU - Christodoulou J LA - eng GR - Wellcome Trust/United Kingdom PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Amyloid beta-Peptides) RN - 0 (Recombinant Fusion Proteins) RN - 0 (alpha-Synuclein) RN - 0 (beta-Synuclein) RN - 368GB5141J (Sodium Dodecyl Sulfate) SB - IM MH - Amino Acid Sequence MH - Amyloid beta-Peptides/chemistry MH - Humans MH - Molecular Sequence Data MH - Mutagenesis, Insertional MH - Nuclear Magnetic Resonance, Biomolecular MH - Parkinson Disease/metabolism MH - Protein Conformation MH - Protein Folding MH - Recombinant Fusion Proteins/chemistry/genetics MH - Sequence Deletion MH - Sodium Dodecyl Sulfate/chemistry MH - Solubility MH - alpha-Synuclein/*chemistry/genetics MH - beta-Synuclein/*chemistry/genetics PMC - PMC2327276 OID - NLM: PMC2327276 EDAT- 2008/04/26 09:00 MHDA- 2008/05/24 09:00 CRDT- 2008/04/26 09:00 AID - 17/5/887 [pii] AID - 10.1110/ps.073181508 [doi] PST - ppublish SO - Protein Sci. 2008 May;17(5):887-98. doi: 10.1110/ps.073181508. PMID- 15753083 OWN - NLM STAT- MEDLINE DA - 20050509 DCOM- 20050712 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 19 DP - 2005 May 13 TI - 1.6-Angstroms crystal structure of EntA-im. A bacterial immunity protein conferring immunity to the antimicrobial activity of the pediocin-like bacteriocin enterocin A. PG - 19045-50 AB - Many Gram-positive bacteria produce ribosomally synthesized antimicrobial peptides, often termed bacteriocins. Genes encoding pediocin-like bacteriocins are generally cotranscribed with or in close vicinity to a gene encoding a cognate immunity protein that protects the bacteriocin-producer from their own bacteriocin. We present the first crystal structure of a pediocin-like immunity protein, EntA-im, conferring immunity to the bacteriocin enterocin A. Determination of the structure of this 103-amino acid protein revealed that it folds into an antiparallel four-helix bundle with a flexible C-terminal part. The fact that the immunity protein conferring immunity to carnobacteriocin B2 also consists of a four-helix bundle (Sprules, T., Kawulka, K. E., and Vederas, J. C. (2004) Biochemistry 43, 11740-11749) strongly indicates that this is a conserved structural motif in all pediocin-like immunity proteins. The C-terminal half of the immunity protein contains a region that recognizes the C-terminal half of the cognate bacteriocin, and the flexibility in the C-terminal end of the immunity protein might thus be an important characteristic that enables the immunity protein to interact with its cognate bacteriocin. By homology modeling of three other pediocin-like immunity proteins and calculation of the surface charge distribution for EntA-im and the three structure models, different charge distributions were observed. The differences in the latter part of helix 3, the beginning of helix 4, and the loop connecting these helices might also be of importance in determining the specificity. FAU - Johnsen, Line AU - Johnsen L AD - Program for Biochemistry and Molecular Biology, Department of Molecular Biosciences, University of Oslo, 0316 Oslo, Norway. line.johnsen@biokjemi.uio.no FAU - Dalhus, Bjorn AU - Dalhus B FAU - Leiros, Ingar AU - Leiros I FAU - Nissen-Meyer, Jon AU - Nissen-Meyer J LA - eng SI - PDB/2BL7 SI - PDB/2BL8 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050307 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - 0 (Bacteriocins) RN - 0 (enterocin A) RN - 0 (pediocin A) RN - 155982-38-0 (bacteriocin B2 protein, Carnobacterium piscicola) RN - 33X04XA5AT (Lactic Acid) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Bacterial Proteins/chemistry MH - Bacteriocins/*chemistry MH - Crystallography, X-Ray MH - Electrons MH - Enterococcus faecium/metabolism MH - Lactic Acid/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Plasmids/metabolism MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid EDAT- 2005/03/09 09:00 MHDA- 2005/07/13 09:00 CRDT- 2005/03/09 09:00 PHST- 2005/03/07 [aheadofprint] AID - M501386200 [pii] AID - 10.1074/jbc.M501386200 [doi] PST - ppublish SO - J Biol Chem. 2005 May 13;280(19):19045-50. Epub 2005 Mar 7. PMID- 10569936 OWN - NLM STAT- MEDLINE DA - 19991216 DCOM- 19991216 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 38 IP - 47 DP - 1999 Nov 23 TI - Leucine 245 is a critical residue for folding and function of the manganese stabilizing protein of photosystem II. PG - 15528-35 AB - In solution, Manganese Stabilizing Protein, the polypeptide which is responsible for the structural and functional integrity of the manganese cluster in photosystem II, is a natively unfolded protein with a prolate ellipsoid shape [Lydakis-Simantiris et al. (1999) Biochemistry 38, 404-414; Zubrzycki et al. (1998) Biochemistry 37, 13553-13558]. The C-terminal tripeptide of Manganese Stabilizing Protein was shown to be critical for binding to photosystem II and restoration of O(2) evolution activity [Betts et al. (1998) Biochemistry 37, 14230-14236]. Here, we report new biochemical, hydrodynamic, and spectroscopic data on mutants E246K, E246STOP, L245E, L245STOP, and Q244STOP. Truncation of the final dipeptide (E246STOP) or substitution of Glu246 with Lys resulted in no significant changes in secondary and tertiary structures of Manganese Stabilizing Protein as monitored by CD spectroscopy. The apparent molecular mass of the protein remained unchanged, both mutants were able to rebind to photosystem II, and both proteins reactivate O(2) evolution. Manganese Stabilizing Protein lacking the final tripeptide (L245STOP), or substitution of Glu for Leu245 dramatically modified the protein's solution structure. The apparent molecular masses of these mutants increased significantly, which might indicate unfolding of the protein in solution. This was verified by CD spectroscopy. Both mutant proteins rebound to photosystem II with lower affinities, and activation of O(2) evolution was decreased dramatically. Enhancement of these defects was observed upon removal of the final tetrapeptide (Q244STOP). These results indicate that Leu245 is essential to maintaining Manganese Stabilizing Protein's solution structure in a conformation that promotes efficient binding to photosystem II and/or for the subsequent steps that lead to enzyme activation. Based on an analysis of the properties of C-terminal mutations, a hypothesis for structural requirements for functional binding of Manganese Stabilizing Protein to photosystem II is presented. Effects of C-terminal mutations on the UV spectrum of Manganese Stabilizing Protein were also examined. Mutations that alter solution structure also affect a 293 nm absorption shoulder which is assigned to the only tryptophan residue, Trp241, in the protein, and this absorbance feature is shown to be a useful indicator of alterations to the Trp241 environment. FAU - Lydakis-Simantiris, N AU - Lydakis-Simantiris N AD - Department of Biology, The University of Michigan, Ann Arbor 48109-1048, USA. FAU - Betts, S D AU - Betts SD FAU - Yocum, C F AU - Yocum CF LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Metalloproteins) RN - 0 (Photosynthetic Reaction Center Complex Proteins) RN - 0 (Photosystem II Protein Complex) RN - 0 (Proteins) RN - 0 (oxygen-evolving complex, 33 kDa protein) RN - 0 (photosystem II manganese-stabilizing protein) RN - 42Z2K6ZL8P (Manganese) RN - 8DUH1N11BX (Tryptophan) RN - GMW67QNF9C (Leucine) SB - IM MH - Circular Dichroism MH - Leucine/*chemistry/genetics MH - Manganese/*chemistry MH - Metalloproteins/*chemistry/genetics MH - Mutagenesis, Site-Directed MH - Photosynthetic Reaction Center Complex Proteins/*chemistry/genetics MH - *Photosystem II Protein Complex MH - *Protein Folding MH - Protein Structure, Secondary/genetics MH - Proteins/*chemistry/genetics MH - Sequence Deletion MH - Spinacia oleracea MH - Tryptophan/genetics EDAT- 1999/11/26 MHDA- 1999/11/26 00:01 CRDT- 1999/11/26 00:00 AID - bi991599m [pii] PST - ppublish SO - Biochemistry. 1999 Nov 23;38(47):15528-35. PMID- 15639237 OWN - NLM STAT- MEDLINE DA - 20050110 DCOM- 20050223 LR - 20071115 IS - 0003-9861 (Print) IS - 0003-9861 (Linking) VI - 434 IP - 2 DP - 2005 Feb 15 TI - Identification and optimization of an antimicrobial peptide from the ant venom toxin pilosulin. PG - 358-64 AB - A template based on positional residue frequencies in the N-terminal stretch of natural alpha-helical antimicrobial peptides was used to prepare sequence patterns and to scan the Swiss-Prot Database, using the ScanProsite tool. This search identified a segment in pilosulin 1, a cytotoxic peptide from the venom of the jumper ant Myrmecia pilosula, as a potential novel antimicrobial peptide sequence. This segment, corresponding to the 20 N-terminal residues, was synthesized and its structural properties and biological activities were investigated. It showed a potent and broad spectrum antimicrobial activity including standard and multi-drug resistant gram-positive and gram-negative bacteria and Candida albicans, confirming the validity of the search method. A rational redesign approach resulting in four amino acid substitutions yielded a variant with improved antibacterial and significantly reduced hemolytic activity. FAU - Zelezetsky, Igor AU - Zelezetsky I AD - Department of Biochemistry, Biophysics and Macromolecular Chemistry, University of Trieste, 34127 Trieste, Italy. zelezetsky@bbcm.units.it FAU - Pag, Ulrike AU - Pag U FAU - Antcheva, Nikolinka AU - Antcheva N FAU - Sahl, Hans-Georg AU - Sahl HG FAU - Tossi, Alessandro AU - Tossi A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (Ant Venoms) RN - 0 (Antimicrobial Cationic Peptides) RN - 0 (pilosulin 1) SB - IM MH - Amino Acid Sequence MH - Animals MH - Ant Venoms/*chemistry/*metabolism MH - Antimicrobial Cationic Peptides/chemistry/*pharmacology MH - Ants MH - Bacteria/metabolism MH - Candida albicans/metabolism MH - Circular Dichroism MH - Databases as Topic MH - Drug Resistance, Bacterial MH - Drug Resistance, Multiple MH - Erythrocytes/metabolism/microbiology MH - Escherichia coli/metabolism MH - Humans MH - Hydrolysis MH - Kinetics MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Time Factors EDAT- 2005/01/11 09:00 MHDA- 2005/02/24 09:00 CRDT- 2005/01/11 09:00 PHST- 2004/10/28 [received] AID - S0003-9861(04)00654-X [pii] AID - 10.1016/j.abb.2004.11.006 [doi] PST - ppublish SO - Arch Biochem Biophys. 2005 Feb 15;434(2):358-64. PMID- 22579287 OWN - NLM STAT- MEDLINE DA - 20120514 DCOM- 20120702 LR - 20150412 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 149 IP - 4 DP - 2012 May 11 TI - Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization. PG - 860-70 LID - 10.1016/j.cell.2012.02.063 [doi] AB - The mutation and overexpression of the epidermal growth factor receptor (EGFR) are associated with the development of a variety of cancers, making this prototypical dimerization-activated receptor tyrosine kinase a prominent target of cancer drugs. Using long-timescale molecular dynamics simulations, we find that the N lobe dimerization interface of the wild-type EGFR kinase domain is intrinsically disordered and that it becomes ordered only upon dimerization. Our simulations suggest, moreover, that some cancer-linked mutations distal to the dimerization interface, particularly the widespread L834R mutation (also referred to as L858R), facilitate EGFR dimerization by suppressing this local disorder. Corroborating these findings, our biophysical experiments and kinase enzymatic assays indicate that the L834R mutation causes abnormally high activity primarily by promoting EGFR dimerization rather than by allowing activation without dimerization. We also find that phosphorylation of EGFR kinase domain at Tyr845 may suppress the intrinsic disorder, suggesting a molecular mechanism for autonomous EGFR signaling. CI - Copyright (c) 2012 Elsevier Inc. All rights reserved. FAU - Shan, Yibing AU - Shan Y AD - D.E. Shaw Research, New York, NY 10036, USA. yibing.shan@deshawresearch.com FAU - Eastwood, Michael P AU - Eastwood MP FAU - Zhang, Xuewu AU - Zhang X FAU - Kim, Eric T AU - Kim ET FAU - Arkhipov, Anton AU - Arkhipov A FAU - Dror, Ron O AU - Dror RO FAU - Jumper, John AU - Jumper J FAU - Kuriyan, John AU - Kuriyan J FAU - Shaw, David E AU - Shaw DE LA - eng GR - R01 CA096504/CA/NCI NIH HHS/United States GR - R01 CA96504/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (Protein Kinase Inhibitors) RN - 0 (Quinazolines) RN - 0VUA21238F (lapatinib) RN - EC 2.7.10.1 (Receptor, Epidermal Growth Factor) RN - S65743JHBS (gefitinib) SB - IM CIN - Cell. 2012 May 11;149(4):735-7. PMID: 22579278 MH - Amino Acid Sequence MH - Crystallography, X-Ray MH - Humans MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Neoplasms/*metabolism MH - *Point Mutation MH - Protein Folding MH - Protein Kinase Inhibitors/pharmacology MH - Protein Multimerization MH - Protein Structure, Tertiary MH - Quinazolines/pharmacology MH - Receptor, Epidermal Growth Factor/antagonists & inhibitors/*chemistry/*genetics/metabolism MH - Sequence Alignment MH - *Signal Transduction EDAT- 2012/05/15 06:00 MHDA- 2012/07/03 06:00 CRDT- 2012/05/15 06:00 PHST- 2011/08/02 [received] PHST- 2012/01/20 [revised] PHST- 2012/02/23 [accepted] AID - S0092-8674(12)00416-3 [pii] AID - 10.1016/j.cell.2012.02.063 [doi] PST - ppublish SO - Cell. 2012 May 11;149(4):860-70. doi: 10.1016/j.cell.2012.02.063. PMID- 19128030 OWN - NLM STAT- MEDLINE DA - 20090127 DCOM- 20090225 LR - 20140901 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 4 DP - 2009 Feb 3 TI - Dihydroorotase from the hyperthermophile Aquifex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis. PG - 766-78 LID - 10.1021/bi801831r [doi] AB - In prokaryotes, the first three enzymes in pyrimidine biosynthesis, carbamoyl phosphate synthetase (CPS), aspartate transcarbamoylase (ATC), and dihydroorotase (DHO), are commonly expressed separately and either function independently (Escherichia coli) or associate into multifunctional complexes (Aquifex aeolicus). In mammals the enzymes are expressed as a single polypeptide chain (CAD) in the order CPS-DHO-ATC and associate into a hexamer. This study presents the three-dimensional structure of the noncovalent hexamer of DHO and ATC from the hyperthermophile A. aeolicus at 2.3 A resolution. It is the first structure of any multienzyme complex in pyrimidine biosynthesis and is a possible model for the core of mammalian CAD. The structure has citrate, a near isosteric analogue of carbamoyl aspartate, bound to the active sites of both enzymes. Three active site loops that are intrinsically disordered in the free, inactive DHO are ordered in the complex. The reorganization also changes the peptide bond between Asp153, a ligand of the single zinc atom in DHO, and Gly154, to the rare cis conformation. In the crystal structure, six DHO and six ATC chains form a hollow dodecamer, in which the 12 active sites face an internal reaction chamber that is approximately 60 A in diameter and connected to the cytosol by narrow tunnels. The entrances and the interior of the chamber are both electropositive, which suggests that the architecture of this nanoreactor modifies the kinetics of the bisynthase, not only by steric channeling but also by preferential escape of the product, dihydroorotase, which is less negatively charged than its precursors, carbamoyl phosphate, aspartate, or carbamoyl aspartate. FAU - Zhang, Pengfei AU - Zhang P AD - Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, Michigan 48201, USA. FAU - Martin, Philip D AU - Martin PD FAU - Purcarea, Cristina AU - Purcarea C FAU - Vaishnav, Asmita AU - Vaishnav A FAU - Brunzelle, Joseph S AU - Brunzelle JS FAU - Fernando, Roshini AU - Fernando R FAU - Guy-Evans, Hedeel I AU - Guy-Evans HI FAU - Evans, David R AU - Evans DR FAU - Edwards, Brian F P AU - Edwards BF LA - eng SI - PDB/3D6N GR - CA60321/CA/NCI NIH HHS/United States GR - GM47399/GM/NIGMS NIH HHS/United States GR - GM60321/GM/NIGMS NIH HHS/United States GR - HL47399/HL/NHLBI NIH HHS/United States GR - HL57527/HL/NHLBI NIH HHS/United States GR - R01 GM047399/GM/NIGMS NIH HHS/United States GR - R01 HL057527/HL/NHLBI NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (Multienzyme Complexes) RN - 0 (Pyrimidines) RN - 155-54-4 (4,5-dihydroorotic acid) RN - 61H4T033E5 (Orotic Acid) RN - EC 2.1.3.2 (Aspartate Carbamoyltransferase) RN - EC 3.5.2.3 (Dihydroorotase) SB - IM MH - Allosteric Regulation MH - Aspartate Carbamoyltransferase/chemistry/*metabolism MH - Bacteria/*enzymology MH - Bacterial Proteins/chemistry/metabolism MH - Binding Sites/physiology MH - Crystallography, X-Ray MH - Dihydroorotase/chemistry/isolation & purification/*metabolism MH - Multienzyme Complexes/chemistry/*metabolism MH - Orotic Acid/analogs & derivatives/chemistry/metabolism MH - Protein Structure, Tertiary/physiology MH - Pyrimidines/*biosynthesis/chemistry MH - Static Electricity MH - Thermodynamics PMC - PMC3863388 MID - NIHMS529265 OID - NLM: NIHMS529265 OID - NLM: PMC3863388 EDAT- 2009/01/09 09:00 MHDA- 2009/02/26 09:00 CRDT- 2009/01/09 09:00 AID - 10.1021/bi801831r [doi] AID - 10.1021/bi801831r [pii] PST - ppublish SO - Biochemistry. 2009 Feb 3;48(4):766-78. doi: 10.1021/bi801831r. PMID- 19910228 OWN - NLM STAT- MEDLINE DA - 20100203 DCOM- 20100423 LR - 20140921 IS - 1096-0856 (Electronic) IS - 1090-7807 (Linking) VI - 202 IP - 2 DP - 2010 Feb TI - A bioreactor for in-cell protein NMR. PG - 140-6 LID - 10.1016/j.jmr.2009.10.008 [doi] AB - The inside of the cell is a complex environment that is difficult to simulate when studying proteins and other molecules in vitro. We have developed a device and system that provides a controlled environment for nuclear magnetic resonance (NMR) experiments involving living cells. Our device comprises two main parts, an NMR detection region and a circulation system. The flow of medium from the bottom of the device pushes alginate encapsulated cells into the circulation chamber. In the chamber, the exchange of oxygen and nutrients occurs between the media and the encapsulated cells. When the media flow is stopped, the encapsulated cells fall back into the NMR detection region, and spectra can be acquired. We have utilized the bioreactor to study the expression of the natively disordered protein alpha-synuclein, inside Escherichia coli cells. CI - Copyright 2009 Elsevier Inc. All rights reserved. FAU - Sharaf, Naima G AU - Sharaf NG AD - Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. FAU - Barnes, Christopher O AU - Barnes CO FAU - Charlton, Lisa M AU - Charlton LM FAU - Young, Gregory B AU - Young GB FAU - Pielak, Gary J AU - Pielak GJ LA - eng GR - DP1 OD000783/OD/NIH HHS/United States GR - DP1 OD000783-01/OD/NIH HHS/United States GR - DP1 OD000783-02/OD/NIH HHS/United States GR - DP1 OD000783-03/OD/NIH HHS/United States GR - DP1 OD000783-03S1/OD/NIH HHS/United States GR - DP1 OD000783-04/OD/NIH HHS/United States GR - R21 ES010774/ES/NIEHS NIH HHS/United States GR - R21 ES010774-01/ES/NIEHS NIH HHS/United States GR - R21 ES010774-02/ES/NIEHS NIH HHS/United States PT - Journal Article DEP - 20091023 PL - United States TA - J Magn Reson JT - Journal of magnetic resonance (San Diego, Calif. : 1997) JID - 9707935 RN - 0 (Alginates) RN - 0 (Culture Media) RN - 0 (Proteins) RN - 0 (Recombinant Proteins) RN - 0 (alpha-Synuclein) RN - 9002-84-0 (Polytetrafluoroethylene) RN - S88TT14065 (Oxygen) SB - IM MH - Alginates MH - *Bioreactors MH - Culture Media MH - Equipment Design MH - Escherichia coli/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy/*methods MH - Oxygen/chemistry MH - Polytetrafluoroethylene MH - Proteins/*chemistry MH - Recombinant Proteins/chemistry MH - alpha-Synuclein/biosynthesis/chemistry/genetics PMC - PMC2818327 MID - NIHMS154679 OID - NLM: NIHMS154679 OID - NLM: PMC2818327 EDAT- 2009/11/17 06:00 MHDA- 2010/04/24 06:00 CRDT- 2009/11/14 06:00 PHST- 2009/08/25 [received] PHST- 2009/10/12 [revised] PHST- 2009/10/20 [accepted] PHST- 2009/10/23 [aheadofprint] AID - S1090-7807(09)00301-2 [pii] AID - 10.1016/j.jmr.2009.10.008 [doi] PST - ppublish SO - J Magn Reson. 2010 Feb;202(2):140-6. doi: 10.1016/j.jmr.2009.10.008. Epub 2009 Oct 23. PMID- 16166265 OWN - NLM STAT- MEDLINE DA - 20050928 DCOM- 20051121 LR - 20140605 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 102 IP - 39 DP - 2005 Sep 27 TI - Cell entry mechanism of enzymatic bacterial colicins: porin recruitment and the thermodynamics of receptor binding. PG - 13849-54 AB - Binding of enzymatic E colicins to the vitamin B12 receptor, BtuB, is the first stage in a cascade of events that culminate in the translocation of the cytotoxic nuclease into the Escherichia coli cytoplasm and release of its tightly bound immunity protein. A dogma of colicin biology is that the toxin coiled-coil connecting its functional domains must unfold or unfurl to span the periplasm, with recent reports claiming this reaction is initiated by receptor binding. We report isothermal titration calorimetry data of BtuB binding the endonuclease toxin ColE9 and a disulfide form (ColE9S-S) where unfolding of the coiled-coil is prevented and, as a consequence, the toxin is biologically inactive. Contrary to expectation, the thermodynamics of receptor binding, characterized by large negative values for TDeltaS, are identical for the two colicins, arguing against any form of BtuB-induced unfolding. We go on to delineate key features of the "colicin translocon" that assembles at the cell surface after BtuB binding by using a complex of histidine-tagged Im9 bound to ColE9S-S. First, we show that the porin OmpF is recruited directly to the BtuB.colicin complex to form the translocon. Second, recruitment is through the natively unfolded region of the colicin translocation domain, with this domain likely having two contact points for OmpF. Finally, the immunity protein is not released during its assembly. Our study demonstrates that although colicin unfolding is undoubtedly a prerequisite for E. coli cell death, it must occur after assembly of the translocon. FAU - Housden, Nicholas G AU - Housden NG AD - Department of Biology (Area 10), P.O. Box 373, University of York, York YO10 5YW, United Kingdom. FAU - Loftus, Steven R AU - Loftus SR FAU - Moore, Geoffrey R AU - Moore GR FAU - James, Richard AU - James R FAU - Kleanthous, Colin AU - Kleanthous C LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050915 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Bacterial Outer Membrane Proteins) RN - 0 (BtuB protein, E coli) RN - 0 (Colicins) RN - 0 (Disulfides) RN - 0 (Escherichia coli Proteins) RN - 0 (Membrane Transport Proteins) RN - 0 (OmpF protein) RN - 0 (Porins) RN - 0 (Receptors, Peptide) RN - 0 (immE9 protein, E coli) RN - SY7Q814VUP (Calcium) SB - IM MH - Bacterial Outer Membrane Proteins/*metabolism MH - Calcium/metabolism MH - Colicins/*metabolism/pharmacology MH - Disulfides/metabolism MH - Escherichia coli/drug effects/*metabolism MH - Escherichia coli Proteins/*metabolism/pharmacology MH - Membrane Transport Proteins/*metabolism MH - Porins/genetics/*metabolism MH - Protein Folding MH - Protein Structure, Tertiary MH - Protein Transport MH - Receptors, Peptide/metabolism MH - Sequence Deletion MH - Thermodynamics PMC - PMC1236540 OID - NLM: PMC1236540 EDAT- 2005/09/17 09:00 MHDA- 2005/12/13 09:00 CRDT- 2005/09/17 09:00 PHST- 2005/09/15 [aheadofprint] AID - 0503567102 [pii] AID - 10.1073/pnas.0503567102 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13849-54. Epub 2005 Sep 15. PMID- 19540204 OWN - NLM STAT- MEDLINE DA - 20090717 DCOM- 20090804 LR - 20101118 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 386 IP - 3 DP - 2009 Aug 28 TI - Cyclodextrins promote protein aggregation posing risks for therapeutic applications. PG - 526-31 LID - 10.1016/j.bbrc.2009.06.077 [doi] AB - The presence of neurofibrillary tangles (NFTs) is a hallmark feature of various neurodegenerative disorders including Alzheimer's (AD) and Niemann-Pick type C (NPC) diseases. NFTs have been correlated with elevated cholesterol levels and a cholesterol-scavenging compound, cyclodextrin, effectively modulates and traffics cholesterol from cell bodies in NPC disease models. Cyclodextrins are also used as drug carriers to the blood-brain barrier (BBB) and other tissues. While cyclodextrins have potential value in treating brain diseases, it is important to determine how cyclodextrins affect natively unfolded proteins such as beta-amyloid (Abeta) whose aggregation has been correlated with AD. We show that cyclodextrins drastically alter Abeta aggregation kinetics and induce morphological changes to Abeta that can enhance toxicity towards SH-SY5Y human neuroblastoma cells. These results suggest that care must be taken when using cyclodextrins for BBB delivery or for treatment of brain disease because cyclodextrins can promote toxic aggregation of Abeta. FAU - Wang, Min S AU - Wang MS AD - Department of Chemical Engineering, Arizona State University, Tempe, AZ 85287-6006, USA. FAU - Boddapati, Shanta AU - Boddapati S FAU - Sierks, Michael R AU - Sierks MR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090618 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Amyloid beta-Peptides) RN - 0 (Cyclodextrins) SB - IM MH - Alzheimer Disease/metabolism MH - Amyloid beta-Peptides/chemistry/*metabolism/*toxicity MH - Blood-Brain Barrier/metabolism MH - Cell Survival/drug effects MH - Cyclodextrins/chemistry/*metabolism/*toxicity MH - *Drug Delivery Systems MH - Humans MH - Niemann-Pick Disease, Type C/drug therapy/metabolism EDAT- 2009/06/23 09:00 MHDA- 2009/08/06 09:00 CRDT- 2009/06/23 09:00 PHST- 2009/06/05 [received] PHST- 2009/06/15 [accepted] PHST- 2009/06/18 [aheadofprint] AID - S0006-291X(09)01220-0 [pii] AID - 10.1016/j.bbrc.2009.06.077 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2009 Aug 28;386(3):526-31. doi: 10.1016/j.bbrc.2009.06.077. Epub 2009 Jun 18. PMID- 23583779 OWN - NLM STAT- MEDLINE DA - 20130701 DCOM- 20130904 LR - 20131121 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 425 IP - 14 DP - 2013 Jul 24 TI - The H/D-exchange kinetics of the Escherichia coli co-chaperonin GroES studied by 2D NMR and DMSO-quenched exchange methods. PG - 2541-60 LID - 10.1016/j.jmb.2013.04.008 [doi] LID - S0022-2836(13)00239-8 [pii] AB - We studied hydrogen/deuterium-exchange reactions of peptide amide protons of GroES using two different techniques: (1) two-dimensional (1)H-(15)N transverse-optimized NMR spectroscopy and (2) the dimethylsulfoxide-quenched hydrogen-exchange method combined with conventional (1)H-(15)N heteronuclear single quantum coherence spectroscopy. By using these techniques together with direct heteronuclear single quantum coherence experiments, we quantitatively evaluated the exchange rates for 33 out of the 94 peptide amide protons of GroES and their protection factors, and for the remaining 61 residues, we obtained the lower limits of the exchange rates. The protection factors of the most highly protected amide protons were on the order of 10(6)-10(7), and the values were comparable in magnitude to those observed in typical small globular proteins, but the number of the highly protected amide protons with a protection factor larger than 10(6) was only 10, significantly smaller than the numbers reported for the small globular proteins, indicating that significant portions of free heptameric GroES are flexible and natively unfolded. The highly protected amino acid residues with a protection factor larger than 10(5) were mainly located in three beta-strands that form the hydrophobic core of GroES, while the residues in a mobile loop (residues 17-34) were not highly protected. The protection factors of the most highly protected amide protons were orders of magnitude larger than the value expected from the equilibrium unfolding parameters previously reported, strongly suggesting that the equilibrium unfolding of GroES is more complicated than a simple two-state or three-state mechanism and may involve more than a single intermediate. CI - Copyright (c) 2013 Elsevier Ltd. All rights reserved. FAU - Chandak, Mahesh S AU - Chandak MS AD - Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan. FAU - Nakamura, Takashi AU - Nakamura T FAU - Makabe, Koki AU - Makabe K FAU - Takenaka, Toshio AU - Takenaka T FAU - Mukaiyama, Atsushi AU - Mukaiyama A FAU - Chaudhuri, Tapan K AU - Chaudhuri TK FAU - Kato, Koichi AU - Kato K FAU - Kuwajima, Kunihiro AU - Kuwajima K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130411 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Chaperonin 10) RN - 0 (Escherichia coli Proteins) RN - 7YNJ3PO35Z (Hydrogen) RN - YOW8V9698H (Dimethyl Sulfoxide) SB - IM MH - Chaperonin 10/*chemistry/*metabolism MH - Deuterium Exchange Measurement MH - Dimethyl Sulfoxide/metabolism MH - Escherichia coli Proteins/*chemistry/*metabolism MH - Hydrogen/metabolism MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - *Protein Unfolding EDAT- 2013/04/16 06:00 MHDA- 2013/09/05 06:00 CRDT- 2013/04/16 06:00 PHST- 2013/01/17 [received] PHST- 2013/03/29 [revised] PHST- 2013/04/05 [accepted] PHST- 2013/04/11 [aheadofprint] AID - S0022-2836(13)00239-8 [pii] AID - 10.1016/j.jmb.2013.04.008 [doi] PST - ppublish SO - J Mol Biol. 2013 Jul 24;425(14):2541-60. doi: 10.1016/j.jmb.2013.04.008. Epub 2013 Apr 11. PMID- 19020623 OWN - NLM STAT- MEDLINE DA - 20081121 DCOM- 20081218 LR - 20131121 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 456 IP - 7220 DP - 2008 Nov 20 TI - Calcium-bound structure of calpain and its mechanism of inhibition by calpastatin. PG - 409-12 LID - 10.1038/nature07451 [doi] AB - Calpains are non-lysosomal calcium-dependent cysteine proteinases that selectively cleave proteins in response to calcium signals and thereby control cellular functions such as cytoskeletal remodelling, cell cycle progression, gene expression and apoptotic cell death. In mammals, the two best-characterized members of the calpain family, calpain 1 and calpain 2 (micro-calpain and m-calpain, respectively), are ubiquitously expressed. The activity of calpains is tightly controlled by the endogenous inhibitor calpastatin, which is an intrinsically unstructured protein capable of reversibly binding and inhibiting four molecules of calpain, but only in the presence of calcium. To date, the mechanism of inhibition by calpastatin and the basis for its absolute specificity have remained speculative. It was not clear how this unstructured protein inhibits calpains without being cleaved itself, nor was it known how calcium induced changes that facilitated the binding of calpastatin to calpain. Here we report the 2.4-A-resolution crystal structure of the calcium-bound calpain 2 heterodimer bound by one of the four inhibitory domains of calpastatin. Calpastatin is seen to inhibit calpain by occupying both sides of the active site cleft. Although the inhibitor passes through the active site cleft it escapes cleavage in a novel manner by looping out and around the active site cysteine. The inhibitory domain of calpastatin recognizes multiple lower affinity sites present only in the calcium-bound form of the enzyme, resulting in an interaction that is tight, specific and calcium dependent. This crystal structure, and that of a related complex, also reveal the conformational changes that calpain undergoes on binding calcium, which include opening of the active site cleft and movement of the domains relative to each other to produce a more compact enzyme. FAU - Hanna, Rachel A AU - Hanna RA AD - Department of Biochemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6. FAU - Campbell, Robert L AU - Campbell RL FAU - Davies, Peter L AU - Davies PL LA - eng SI - PDB/3BOW PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Calcium-Binding Proteins) RN - 79079-11-1 (calpastatin) RN - EC 3.4.22.- (Calpain) RN - EC 3.4.22.- (m-calpain) RN - SY7Q814VUP (Calcium) SB - IM CIN - Nature. 2008 Nov 20;456(7220):337-8. PMID: 19020611 MH - Animals MH - Calcium/*metabolism MH - Calcium-Binding Proteins/*chemistry/*metabolism MH - Calpain/*antagonists & inhibitors/*chemistry/metabolism MH - Catalytic Domain MH - Crystallography, X-Ray MH - Models, Molecular MH - Protein Binding MH - Protein Multimerization MH - Rats MH - Structure-Activity Relationship EDAT- 2008/11/21 09:00 MHDA- 2008/12/19 09:00 CRDT- 2008/11/21 09:00 PHST- 2008/03/11 [received] PHST- 2008/09/24 [accepted] AID - nature07451 [pii] AID - 10.1038/nature07451 [doi] PST - ppublish SO - Nature. 2008 Nov 20;456(7220):409-12. doi: 10.1038/nature07451. PMID- 15530367 OWN - NLM STAT- MEDLINE DA - 20041108 DCOM- 20050411 LR - 20051226 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 12 IP - 11 DP - 2004 Nov TI - Crystal structures of Ral-GppNHp and Ral-GDP reveal two binding sites that are also present in Ras and Rap. PG - 2025-36 AB - RalA is a GTPase with effectors such as Sec5 and Exo84 in the exocyst complex and RalBP1, a GAP for Rho proteins. We report the crystal structures of Ral-GppNHp and Ral-GDP. Disordered switch I and switch II, located away from crystal contacts, are observed in one of the molecules in the asymmetric unit of the Ral-GppNHp structure. In the other molecule in the asymmetric unit, a second Mg(2+) ion is bound to the GppNHp gamma-phosphate in an environment in which switch I is pulled away from the nucleotide and switch II is found in a tight beta turn. Clustering of conserved residues on the surface of Ral-GppNHp identifies two putative sites for protein-protein interaction. One site is adjacent to switch I. The other is modulated by switch II and is obstructed in Ral-GDP. The Ral structures are discussed in the context of the published structures of the Ral/Sec5 complex, Ras, and Rap. FAU - Nicely, Nathan I AU - Nicely NI AD - Department of Molecular and Structural Biochemistry, 128 Polk Hall-CB 7622, North Carolina State University, Raleigh, NC 27695, USA. FAU - Kosak, Justin AU - Kosak J FAU - de Serrano, Vesna AU - de Serrano V FAU - Mattos, Carla AU - Mattos C LA - eng SI - PDB/1U8Y SI - PDB/1U8Z SI - PDB/1U9O PT - Journal Article PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 146-91-8 (Guanosine Diphosphate) RN - 86-01-1 (Guanosine Triphosphate) RN - EC 3.6.5.2 (rap GTP-Binding Proteins) RN - EC 3.6.5.2 (ras Proteins) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Catalytic Domain MH - Crystallography, X-Ray MH - Guanosine Diphosphate/*chemistry/metabolism MH - Guanosine Triphosphate/analogs & derivatives/*chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Sequence Homology, Amino Acid MH - rap GTP-Binding Proteins/*chemistry/metabolism MH - ras Proteins/*chemistry/metabolism EDAT- 2004/11/09 09:00 MHDA- 2005/04/12 09:00 CRDT- 2004/11/09 09:00 PHST- 2004/06/21 [received] PHST- 2004/08/26 [revised] PHST- 2004/08/28 [accepted] AID - S0969212604003387 [pii] AID - 10.1016/j.str.2004.08.011 [doi] PST - ppublish SO - Structure. 2004 Nov;12(11):2025-36. PMID- 15236960 OWN - NLM STAT- MEDLINE DA - 20040706 DCOM- 20040825 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 340 IP - 5 DP - 2004 Jul 23 TI - Studies of the RNA degradosome-organizing domain of the Escherichia coli ribonuclease RNase E. PG - 965-79 AB - The hydrolytic endoribonuclease RNase E, which is widely distributed in bacteria and plants, plays key roles in mRNA degradation and RNA processing in Escherichia coli. The enzymatic activity of RNase E is contained within the conserved amino-terminal half of the 118 kDa protein, and the carboxy-terminal half organizes the RNA degradosome, a multi-enzyme complex that degrades mRNA co-operatively and processes ribosomal and other RNA. The study described herein demonstrates that the carboxy-terminal domain of RNase E has little structure under native conditions and is unlikely to be extensively folded within the degradosome. However, three isolated segments of 10-40 residues, and a larger fourth segment of 80 residues, are predicted to be regions of increased structural propensity. The larger of these segments appears to be a protein-RNA interaction site while the other segments possibly correspond to sites of self-recognition and interaction with the other degradosome proteins. The carboxy-terminal domain of RNase E may thus act as a flexible tether of the degradosome components. The implications of these and other observations for the organization of the RNA degradosome are discussed. FAU - Callaghan, Anastasia J AU - Callaghan AJ AD - Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAU - Aurikko, Jukka P AU - Aurikko JP FAU - Ilag, Leopold L AU - Ilag LL FAU - Gunter Grossmann, J AU - Gunter Grossmann J FAU - Chandran, Vidya AU - Chandran V FAU - Kuhnel, Karin AU - Kuhnel K FAU - Poljak, Leonora AU - Poljak L FAU - Carpousis, Agamennon J AU - Carpousis AJ FAU - Robinson, Carol V AU - Robinson CV FAU - Symmons, Martyn F AU - Symmons MF FAU - Luisi, Ben F AU - Luisi BF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Multienzyme Complexes) RN - 0 (RNA, Bacterial) RN - 0 (RNA-Binding Proteins) RN - 0 (degradosome) RN - EC 2.7.7.8 (Polyribonucleotide Nucleotidyltransferase) RN - EC 3.1.- (Endoribonucleases) RN - EC 3.1.4.- (ribonuclease E) RN - EC 3.6.4.13 (RNA Helicases) RN - EC 4.2.1.11 (Phosphopyruvate Hydratase) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Circular Dichroism MH - Endoribonucleases/*chemistry/genetics/isolation & purification/*metabolism MH - Escherichia coli/*enzymology/genetics MH - Molecular Sequence Data MH - Multienzyme Complexes/*chemistry/*metabolism MH - Phosphopyruvate Hydratase/isolation & purification/metabolism MH - Polyribonucleotide Nucleotidyltransferase/*chemistry/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - RNA Helicases/*chemistry/*metabolism MH - RNA, Bacterial/chemistry/*metabolism MH - RNA-Binding Proteins/metabolism MH - Spectrometry, Mass, Electrospray Ionization MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization EDAT- 2004/07/09 05:00 MHDA- 2004/08/26 05:00 CRDT- 2004/07/09 05:00 PHST- 2003/12/22 [received] PHST- 2004/05/21 [revised] PHST- 2004/05/21 [accepted] AID - 10.1016/j.jmb.2004.05.046 [doi] AID - S0022283604006163 [pii] PST - ppublish SO - J Mol Biol. 2004 Jul 23;340(5):965-79. PMID- 19800647 OWN - NLM STAT- MEDLINE DA - 20091117 DCOM- 20091124 IS - 1096-0341 (Electronic) IS - 0042-6822 (Linking) VI - 395 IP - 1 DP - 2009 Dec 5 TI - Interaction of a potyviral VPg with anionic phospholipid vesicles. PG - 114-20 LID - 10.1016/j.virol.2009.09.009 [doi] AB - The viral genome-linked protein (VPg) of Potato virus A (PVA) is a multifunctional protein that belongs to a class of intrinsically disordered proteins. Typically, this type of protein gains a more stable structure upon interactions or posttranslational modifications. In a membrane lipid strip overlay binding assay, PVA VPg was found to bind phosphatidylserine (PS), but not phosphatidylcholine (PC). According to circular dichroism spectroscopy, the secondary structure of PVA VPg was stabilized upon interactions with PS and phosphatidylglycerol (PG), but not with PC vesicles. It is possible that this stabilization favored the formation of alpha-helical structures. Limited tryptic digestion showed that the interaction with anionic vesicles protected certain, otherwise accessible, trypsin cleavage sites. An electron microscopy study revealed that interaction with VPg substantially increased the vesicle diameter and caused the formation of pore or plaque-like electron dense spots on the vesicle surface, which gradually led to disruption of the vesicles. FAU - Rantalainen, Kimmo I AU - Rantalainen KI AD - Department of Applied Chemistry and Microbiology, University of Helsinki, Finland. FAU - Christensen, Peter A AU - Christensen PA FAU - Hafren, Anders AU - Hafren A FAU - Otzen, Daniel E AU - Otzen DE FAU - Kalkkinen, Nisse AU - Kalkkinen N FAU - Makinen, Kristiina AU - Makinen K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091002 PL - United States TA - Virology JT - Virology JID - 0110674 RN - 0 (Phospholipids) RN - 0 (Ribonucleoproteins) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Circular Dichroism MH - Phospholipids/*metabolism MH - Potyviridae/*metabolism MH - Protein Processing, Post-Translational MH - Protein Structure, Secondary MH - Ribonucleoproteins/*metabolism MH - Viral Nonstructural Proteins/*metabolism EDAT- 2009/10/06 06:00 MHDA- 2009/12/16 06:00 CRDT- 2009/10/06 06:00 PHST- 2009/07/03 [received] PHST- 2009/07/31 [revised] PHST- 2009/09/07 [accepted] PHST- 2009/10/02 [aheadofprint] AID - S0042-6822(09)00557-1 [pii] AID - 10.1016/j.virol.2009.09.009 [doi] PST - ppublish SO - Virology. 2009 Dec 5;395(1):114-20. doi: 10.1016/j.virol.2009.09.009. Epub 2009 Oct 2. PMID- 19598264 OWN - NLM STAT- MEDLINE DA - 20090826 DCOM- 20090921 LR - 20101118 IS - 1097-0215 (Electronic) IS - 0020-7136 (Linking) VI - 125 IP - 8 DP - 2009 Oct 15 TI - Cytosolic accumulation of HPV16 E7 oligomers supports different transformation routes for the prototypic viral oncoprotein: the amyloid-cancer connection. PG - 1902-11 LID - 10.1002/ijc.24579 [doi] AB - E7 is the major transforming activity in human papillomaviruses, a causal agent for cervical cancer. HPV16 E7 is a small protein with a natively unfolded domain for which dozens of specific cellular targets were described, and represents a prototypical oncoprotein among small DNA tumor viruses. The protein can form spherical oligomers with amyloid-like properties and chaperone activity. Conformation specific antibodies locate endogenous oligomeric E7 species in the cytosol of 3 model cell lines, strongly co-localizing with amyloid structures and dimeric E7 localizes to the nucleus. The cytosolic oligomeric E7 appear as the most abundant species in all cell systems tested. We show that nuclear E7 levels are replenished dynamically from the cytosolic pool and do not result from protein synthesis. Our results suggest that long-term events related to de-repression of E7 would cause accumulation of excess E7 into oligomeric species in the cytosol. These, together with the known target promiscuity of E7, may allow interactions with many of the non-pRb dependent targets described. This hypothesis is further supported by the detection of E7 oligomers in the cytosol of cancerous cells from tissue biopsies. FAU - Dantur, Karina AU - Dantur K AD - Instituto Leloir and Instituto de Investigaciones Bioquimicas Buenos Aires, Conicet, Patricias Argentinas 435, (C1405BWE) Ciudad Autonoma de Buenos Aires, Argentina. FAU - Alonso, Leonardo AU - Alonso L FAU - Castano, Eduardo AU - Castano E FAU - Morelli, Laura AU - Morelli L FAU - Centeno-Crowley, Juan Manuel AU - Centeno-Crowley JM FAU - Vighi, Susana AU - Vighi S FAU - de Prat-Gay, Gonzalo AU - de Prat-Gay G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Int J Cancer JT - International journal of cancer. Journal international du cancer JID - 0042124 RN - 0 (Amyloid) RN - 0 (Oncogene Proteins, Viral) RN - 0 (Papillomavirus E7 Proteins) RN - 0 (oncogene protein E7, Human papillomavirus type 16) SB - IM MH - Amyloid/*chemistry MH - Animals MH - Bone Neoplasms/metabolism/pathology/virology MH - Carcinoma, Endometrioid/*metabolism/pathology/virology MH - Cell Nucleus/metabolism MH - *Cell Transformation, Neoplastic MH - Cytosol/*metabolism MH - Female MH - Fluorescent Antibody Technique MH - Humans MH - Immunoblotting MH - Immunoenzyme Techniques MH - Mice MH - Mice, Inbred BALB C MH - Oncogene Proteins, Viral/genetics/*metabolism MH - Osteosarcoma/*metabolism/pathology/virology MH - Papillomaviridae MH - Papillomavirus E7 Proteins MH - Papillomavirus Infections/metabolism/pathology/virology MH - Transfection MH - Tumor Cells, Cultured MH - Uterine Cervical Neoplasms/*metabolism/pathology/virology EDAT- 2009/07/15 09:00 MHDA- 2009/09/22 06:00 CRDT- 2009/07/15 09:00 AID - 10.1002/ijc.24579 [doi] PST - ppublish SO - Int J Cancer. 2009 Oct 15;125(8):1902-11. doi: 10.1002/ijc.24579. PMID- 2504923 OWN - NLM STAT- MEDLINE DA - 19891005 DCOM- 19891005 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 208 IP - 1 DP - 1989 Jul 5 TI - Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. PG - 83-98 AB - The crystal structure of tyrosyl-tRNA synthetase (EC 6.1.1.1) from Bacillus stearothermophilus has been refined to a crystallographic R-factor of 22.6% at 2.3 A resolution using a restrained least-squares procedure. In the final model the root-mean-square deviation from ideality for bond distances is 0.018 A and for angle distances is 0.044 A. Each monomer consists of three domains: an alpha/beta domain (residues 1 to 220) containing a six-stranded beta-sheet, an alpha-helical domain (248 to 318) containing five helices, and a disordered C-terminal domain (319 to 418) for which the electron density is very weak and where it has not been possible to trace the polypeptide chain. Complexes of the enzyme with the catalytic intermediate tyrosyl adenylate and the inhibitor tyrosinyl adenylate have also been refined to R-factors of 23.9% at 2.8 A resolution and 21.0% at 2.7 A resolution, respectively. Formation of the complexes results in some crystal cracking, but there is no significant difference in the conformation of the polypeptide chain of the three structures described here. The relative orientation of the alpha/beta and alpha-helical domains is similar to that previously observed for the "A" subunit of a deletion mutant lacking the C-terminal domain. Differences between these structures are confined to surface loops that are involved in crystal packing. Tyrosyl adenylate and tyrosinyl adenylate bind in similar conformations within a deep cleft in the alpha/beta domain. The tyrosine moiety is in the equivalent position to that occupied by tyrosine in crystals of the truncated mutant and makes similar strong polar interactions with the enzyme. The alpha-phosphate group interacts with the main-chain nitrogen of Asp38. The two hydroxyl groups of the ribose form strong interactions with the protein. The 2'-hydroxyl group interacts with the carboxylate of Asp194 and the main-chain nitrogen of Gly192 while the 3'-hydroxyl interacts with a tightly bound water molecule (Wat326). The adenine moiety appears to make no significant polar interactions with the protein. The results of site-directed mutagenesis studies are examined in the light of these refined structures. FAU - Brick, P AU - Brick P AD - Blackett Laboratory, Imperial College, London, England. FAU - Bhat, T N AU - Bhat TN FAU - Blow, D M AU - Blow DM LA - eng SI - PDB/UNKNOWN PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Ligands) RN - 0 (Phosphates) RN - 415SHH325A (Adenosine Monophosphate) RN - 42HK56048U (Tyrosine) RN - 6372-08-3 (tyrosinyl-5'-AMP) RN - 681HV46001 (Ribose) RN - EC 6.1.1.- (Amino Acyl-tRNA Synthetases) RN - EC 6.1.1.1 (Tyrosine-tRNA Ligase) RN - JAC85A2161 (Adenine) SB - IM MH - Adenine/metabolism MH - Adenosine Monophosphate/*analogs & derivatives/metabolism MH - *Amino Acyl-tRNA Synthetases MH - Binding Sites MH - Geobacillus stearothermophilus/enzymology MH - Hydrogen Bonding MH - Ligands/metabolism MH - Models, Molecular MH - Models, Structural MH - Molecular Sequence Data MH - Phosphates/metabolism MH - Protein Conformation MH - Ribose/metabolism MH - Tyrosine/*analogs & derivatives/metabolism MH - *Tyrosine-tRNA Ligase MH - X-Ray Diffraction EDAT- 1989/07/05 MHDA- 1989/07/05 00:01 CRDT- 1989/07/05 00:00 AID - 0022-2836(89)90090-9 [pii] PST - ppublish SO - J Mol Biol. 1989 Jul 5;208(1):83-98. PMID- 1619650 OWN - NLM STAT- MEDLINE DA - 19920804 DCOM- 19920804 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 226 IP - 1 DP - 1992 Jul 5 TI - Crystal structure of the factor for inversion stimulation FIS at 2.0 A resolution. PG - 209-26 AB - The factor for inversion stimulation (FIS) binds as a homodimeric molecule to a loose 15 nucleotide consensus sequence in DNA. It stimulates DNA-related processes, such as DNA inversion and excision, it activates transcription of tRNA and rRNA genes and it regulates its own synthesis. FIS crystallizes as a homodimer, with 2 x 98 amino acid residues in the asymmetric unit. The crystal structure was determined with multiple isomorphous replacement and refined to an R-factor of 19.2% against all the 12,719 X-ray data (no sigma-cutoff) extending to 2.0 A resolution. The two monomers are related by a non-crystallographic dyad axis. The structure of the dimer is modular, with the first 23 amino acid residues in molecule M1 and the first 24 in molecule M2 disordered and not "seen" in the electron density. The polypeptide folds into four alpha-helices, with alpha A, alpha A' (amino acid residues 26 to 40) and alpha B, alpha B' (49 to 69) forming the core of the FIS dimer, which is stabilized by hydrophobic forces. To the core are attached "classical" helix-turn-helix motifs, alpha C, alpha D (73 to 81 and 84 to 94) and alpha C', alpha D'. The connections linking the helices are structured by two beta-turns for alpha A/alpha B, and alpha C1 type extensions are observed at the C termini of helices alpha B, alpha C and alpha D. Helices alpha D and alpha D' contain 2 x 6 positive charges; they are separated by 24 A and can bind adjacent major grooves in B-type DNA if it is bent 90 degrees. The modular structure of FIS is also reflected by mutation experiments; mutations in the N-terminal part and alpha A interfere with FIS binding to invertases, and mutations in the helix-turn-helix motif interfere with DNA binding. FAU - Kostrewa, D AU - Kostrewa D AD - Institut fur Kristallographie, Freie Universitat Berlin, Germany. FAU - Granzin, J AU - Granzin J FAU - Stock, D AU - Stock D FAU - Choe, H W AU - Choe HW FAU - Labahn, J AU - Labahn J FAU - Saenger, W AU - Saenger W LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Carrier Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Factor For Inversion Stimulation Protein) RN - 0 (Integration Host Factors) RN - 9007-49-2 (DNA) SB - IM GS - fis MH - Amino Acid Sequence MH - Base Sequence MH - Binding Sites/genetics MH - Carrier Proteins/*chemistry/metabolism MH - DNA/genetics/metabolism MH - DNA-Binding Proteins/*chemistry/metabolism MH - Factor For Inversion Stimulation Protein MH - Integration Host Factors MH - Molecular Sequence Data MH - Protein Conformation MH - X-Ray Diffraction EDAT- 1992/07/05 MHDA- 1992/07/05 00:01 CRDT- 1992/07/05 00:00 AID - 0022-2836(92)90134-6 [pii] PST - ppublish SO - J Mol Biol. 1992 Jul 5;226(1):209-26. PMID- 14759363 OWN - NLM STAT- MEDLINE DA - 20040204 DCOM- 20040310 LR - 20091119 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 13 IP - 2 DP - 2004 Jan 30 TI - The structural basis for autoinhibition of FLT3 by the juxtamembrane domain. PG - 169-78 AB - FLT3 is a type III receptor tyrosine kinase that is thought to play a key role in hematopoiesis. Certain classes of FLT3 mutations cause constitutively activated forms of the receptor that are found in significant numbers of patients with acute myelogenous leukemia (AML). The mutations occur either in the activation loop, for example, as point mutations of Asp835 or as internal tandem duplication (ITD) sequences in the juxtamembrane (JM) domain. To further understand the nature of FLT3 autoinhibition and regulation, we have determined the crystal structure of the autoinhibited form of FLT3. This structure shows the autoinhibitory conformation of a complete JM domain in this class of receptor tyrosine kinases. The detailed inhibitory mechanism of the JM domain is revealed, which is likely utilized by other members of type III receptor tyrosine kinases. FAU - Griffith, James AU - Griffith J AD - Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139, USA. james_griffith@vrtx.com FAU - Black, James AU - Black J FAU - Faerman, Carlos AU - Faerman C FAU - Swenson, Lora AU - Swenson L FAU - Wynn, Michael AU - Wynn M FAU - Lu, Fan AU - Lu F FAU - Lippke, Judith AU - Lippke J FAU - Saxena, Kumkum AU - Saxena K LA - eng SI - PDB/1RJB PT - Journal Article PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Proto-Oncogene Proteins) RN - EC 2.7.10.1 (FLT3 protein, human) RN - EC 2.7.10.1 (Receptor Protein-Tyrosine Kinases) RN - EC 2.7.10.1 (fms-Like Tyrosine Kinase 3) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Cloning, Molecular MH - Gene Library MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Point Mutation MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins/*chemistry/*physiology MH - Receptor Protein-Tyrosine Kinases/*chemistry/*physiology MH - Sequence Homology, Amino Acid MH - fms-Like Tyrosine Kinase 3 EDAT- 2004/02/05 05:00 MHDA- 2004/03/11 05:00 CRDT- 2004/02/05 05:00 PHST- 2003/09/16 [received] PHST- 2003/11/20 [revised] PHST- 2003/11/24 [accepted] AID - S1097276503005057 [pii] PST - ppublish SO - Mol Cell. 2004 Jan 30;13(2):169-78. PMID- 18783251 OWN - NLM STAT- MEDLINE DA - 20080930 DCOM- 20081230 LR - 20101118 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 40 DP - 2008 Oct 7 TI - The natively unfolded character of tau and its aggregation to Alzheimer-like paired helical filaments. PG - 10526-39 LID - 10.1021/bi800783d [doi] AB - The abnormal aggregation of the microtubule-associated protein Tau into paired helical filaments (PHFs) is one of the hallmarks of Alzheimer disease (AD). Tau in solution behaves as a natively unfolded or intrinsically disordered protein while its aggregation is based on the partial structural transition from random coil to beta-structure. Our aim is to understand in more detail the unfolded nature of Tau, to investigate the aggregation of Tau under different conditions and the molecular interactions of Tau in filaments. We show that soluble Tau remains natively unfolded even when its net charge is minimized, in contrast to other unfolded proteins. The CD signature of the random-coil character of Tau shows no major change over wide variations in charge (pH), ionic strength, solvent polarity, and denaturation. Thus there is no indication of a hydrophobicity-driven collapse, neither in the microtubule-binding repeat domain constructs nor in full-length Tau. This argues that the lack of hydrophobic residues but not the net charge accounts for unfolded nature of soluble Tau. The aggregation of the Tau repeat domain (that forms the core of PHFs) in the presence of nucleating polyanionic cofactors (heparin) is efficient in a range of buffers and pH values between approximately 5 and 10 but breaks down beyond that range, presumably because the pattern of charged interactions disappears. Similarly, elevated ionic strength attenuates aggregation, and the temperature dependence is bell-shaped with an optimum around 50 degrees C. Reporter dyes ThS and ANS record the aggregation process but sense different states (cross-beta-structure vs hydrophobic pockets) with different kinetics. Preformed PHFs are surprisingly labile and can be disrupted by denaturants at rather low concentration ( approximately 1.0 M GdnHCl), much less than required to denature globular proteins. Partial disaggregation of Tau filaments at extreme pH values monitored by CD and EM indicate the importance of salt bridges in filament formation. In contrast, Tau filaments are remarkably resistant to high temperature and high ionic strength. Overall, the stability of PHFs appears to depend mainly on directed salt bridges with contributions from hydrophobic interactions as well, consistent with a recent structural model of the PHF core derived from solid state NMR (Andronesi, O. C., von Bergen, M., Biernat, J., Seidel, K., Griesinger, C., Mandelkow, E., and Baldus, M. (2008) Characterization of Alzheimer's-like paired helical filaments from the core domain of tau protein using solid-state NMR spectroscopy. FAU - Jeganathan, Sadasivam AU - Jeganathan S AD - Max Planck Unit for Structural Molecular Biology, Notkestrasse 85, D-22607 Hamburg, Germany. siva@mpasmb.desy.de FAU - von Bergen, Martin AU - von Bergen M FAU - Mandelkow, Eva-Maria AU - Mandelkow EM FAU - Mandelkow, Eckhard AU - Mandelkow E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080911 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Neurofilament Proteins) RN - 0 (Solvents) RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/*metabolism MH - Circular Dichroism MH - Humans MH - Hydrogen-Ion Concentration MH - Hydrophobic and Hydrophilic Interactions MH - Microscopy, Electron, Scanning MH - Models, Biological MH - Neurofilament Proteins/*chemistry/ultrastructure MH - Protein Folding MH - Solvents/chemistry MH - Temperature MH - tau Proteins/*chemistry/ultrastructure EDAT- 2008/09/12 09:00 MHDA- 2008/12/31 09:00 CRDT- 2008/09/12 09:00 PHST- 2008/09/11 [aheadofprint] AID - 10.1021/bi800783d [doi] PST - ppublish SO - Biochemistry. 2008 Oct 7;47(40):10526-39. doi: 10.1021/bi800783d. Epub 2008 Sep 11. PMID- 23417771 OWN - NLM STAT- MEDLINE DA - 20140317 DCOM- 20141112 IS - 1874-270X (Electronic) VI - 8 IP - 1 DP - 2014 Apr TI - Backbone and side-chain assignments of a tethered complex between LMO4 and DEAF-1. PG - 141-4 LID - 10.1007/s12104-013-9470-x [doi] AB - The transcriptional regulator LMO4 and the transcription factor DEAF-1 are both essential for brain and skeletal development. They are also implicated in human breast cancers; overexpression of LMO4 is an indicator of poor prognosis, and overexpression of DEAF-1 promotes epithelial breast cell proliferation. We have generated a stable LMO4-DEAF-1 complex comprising the C-terminal LIM domain of LMO4 and an intrinsically disordered LMO4-interaction domain from DEAF-1 tethered by a glycine/serine linker. Here we report the (1)H, (15)N and (13)C assignments of this construct. Analysis of the assignments indicates the presence of structure in the DEAF-1 part of the complex supporting the presence of a physical interaction between the two proteins. FAU - Joseph, Soumya AU - Joseph S AD - School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia. FAU - Kwan, Ann H Y AU - Kwan AH FAU - Mackay, Joel P AU - Mackay JP FAU - Cubeddu, Liza AU - Cubeddu L FAU - Matthews, Jacqueline M AU - Matthews JM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130216 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Deaf1 protein, mouse) RN - 0 (LIM Domain Proteins) RN - 0 (Lmo4 protein, mouse) RN - 0 (Transcription Factors) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry MH - Amino Acid Sequence MH - Animals MH - Humans MH - LIM Domain Proteins/*chemistry MH - Mice MH - Molecular Sequence Data MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Transcription Factors/*chemistry EDAT- 2013/02/19 06:00 MHDA- 2014/11/13 06:00 CRDT- 2013/02/19 06:00 PHST- 2013/01/03 [received] PHST- 2013/02/08 [accepted] PHST- 2013/02/16 [aheadofprint] AID - 10.1007/s12104-013-9470-x [doi] PST - ppublish SO - Biomol NMR Assign. 2014 Apr;8(1):141-4. doi: 10.1007/s12104-013-9470-x. Epub 2013 Feb 16. PMID- 21108951 OWN - NLM STAT- MEDLINE DA - 20110118 DCOM- 20110224 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 405 IP - 5 DP - 2011 Feb 4 TI - Segmental conformational disorder and dynamics in the intrinsically disordered protein alpha-synuclein and its chain length dependence. PG - 1267-83 LID - 10.1016/j.jmb.2010.11.011 [doi] AB - Conformational ensembles of fully disordered natural polypeptides represent the starting point of protein refolding initiated by transfer to folding conditions. Thus, understanding the transient properties and dimensions of such peptides under folding conditions is a necessary step in the understanding of their subsequent folding behavior. Such ensembles can also undergo alternative folding and form amyloid structures, which are involved in many neurological degenerative diseases. Here, we performed a structural study of this initial state using time-resolved fluorescence resonance energy transfer analysis of a series of eight partially overlapping double-labeled chain segments of the N-terminal and NAC domains of the alpha-synuclein molecule. The distributions of end-to-end distance and segmental intramolecular diffusion coefficients were simultaneously determined for eight labeled chain segments. We used the coefficient of variation, C(v), as a measure of the conformational heterogeneity (i.e., structural disorder). With the exception of two segments, the C(v)s were characteristic of a fully disordered state of the chain. Subtle deviations from this behavior at the segment labeled in the NAC domain and the segment at the N termini reflected subtle conformational bias that might be related to the initiation of transition to amyloid aggregates. The chain length dependence of the mean segmental end-to-end distance followed a power law as predicted by Flory, but the dependence was steeper than previously predicted, probably due to the contribution of the excluded volume effect, which is more dominant for shorter-chain segments. The observed intramolecular diffusion coefficients (<10 to approximately 25 A(2)/ns) are only an order of magnitude lower than the common diffusion coefficients of low molecular weight probes. This diffusion coefficient increased with chain length, probably due to the cumulative contributions of minor bond rotations along the chain. These results gave us a reference both for characteristics of a natural unfolded polypeptide at the moment of initiation of folding and for detection of possible initiation sites of the amyloid transition. CI - Copyright A(c) 2010 Elsevier Ltd. All rights reserved. FAU - Grupi, Asaf AU - Grupi A AD - The Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel. FAU - Haas, Elisha AU - Haas E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101123 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amyloid) RN - 0 (SNCA protein, human) RN - 0 (alpha-Synuclein) SB - IM MH - Amyloid/*chemistry MH - Fluorescence Resonance Energy Transfer MH - Humans MH - Models, Molecular MH - Parkinson Disease/*metabolism MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - alpha-Synuclein/*chemistry/genetics EDAT- 2010/11/27 06:00 MHDA- 2011/02/25 06:00 CRDT- 2010/11/27 06:00 PHST- 2010/06/29 [received] PHST- 2010/10/29 [revised] PHST- 2010/11/04 [accepted] PHST- 2010/11/23 [aheadofprint] AID - S0022-2836(10)01225-8 [pii] AID - 10.1016/j.jmb.2010.11.011 [doi] PST - ppublish SO - J Mol Biol. 2011 Feb 4;405(5):1267-83. doi: 10.1016/j.jmb.2010.11.011. Epub 2010 Nov 23. PMID- 23060071 OWN - NLM STAT- MEDLINE DA - 20121030 DCOM- 20130927 IS - 1439-7633 (Electronic) IS - 1439-4227 (Linking) VI - 13 IP - 16 DP - 2012 Nov 5 TI - Exclusively heteronuclear (13) C-detected amino-acid-selective NMR experiments for the study of intrinsically disordered proteins (IDPs). PG - 2425-32 LID - 10.1002/cbic.201200447 [doi] AB - Carbon-13 direct-detection NMR methods have proved to be very useful for the characterization of intrinsically disordered proteins (IDPs). Here we present a suite of experiments in which amino-acid-selective editing blocks are encoded in CACON- and CANCO-type sequences to give (13) C-detected spectra containing correlations arising from a particular type or group of amino acid(s). These two general types of experiments provide the complementary intra- and inter-residue correlations necessary for sequence-specific assignment of backbone resonance frequencies. We demonstrate the capabilities of these experiments on two IDPs: fully reduced Cox17 and WIP(C) . The proposed approach constitutes an independent strategy to simplify crowded spectra as well as to perform sequence-specific assignment, thereby demonstrating its potential to study IDPs. CI - Copyright (c) 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. FAU - Bermel, Wolfgang AU - Bermel W AD - Bruker BioSpin GmbH, 76287 Rheinstetten, Germany. FAU - Bertini, Ivano AU - Bertini I FAU - Chill, Jordan AU - Chill J FAU - Felli, Isabella C AU - Felli IC FAU - Haba, Noam AU - Haba N FAU - Kumar M V, Vasantha AU - Kumar M V V FAU - Pierattelli, Roberta AU - Pierattelli R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121011 PL - Germany TA - Chembiochem JT - Chembiochem : a European journal of chemical biology JID - 100937360 RN - 0 (Amino Acids) RN - 0 (Carbon Isotopes) RN - 0 (Proteins) SB - IM MH - Amino Acids/*analysis MH - Carbon Isotopes MH - Magnetic Resonance Spectroscopy MH - Proteins/*chemistry EDAT- 2012/10/13 06:00 MHDA- 2013/09/28 06:00 CRDT- 2012/10/13 06:00 PHST- 2012/07/02 [received] PHST- 2012/10/11 [aheadofprint] AID - 10.1002/cbic.201200447 [doi] PST - ppublish SO - Chembiochem. 2012 Nov 5;13(16):2425-32. doi: 10.1002/cbic.201200447. Epub 2012 Oct 11. PMID- 21533121 OWN - NLM STAT- MEDLINE DA - 20110502 DCOM- 20110830 LR - 20140820 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 4 DP - 2011 TI - Directed evolution reveals the binding motif preference of the LC8/DYNLL hub protein and predicts large numbers of novel binders in the human proteome. PG - e18818 LID - 10.1371/journal.pone.0018818 [doi] AB - LC8 dynein light chain (DYNLL) is a eukaryotic hub protein that is thought to function as a dimerization engine. Its interacting partners are involved in a wide range of cellular functions. In its dozens of hitherto identified binding partners DYNLL binds to a linear peptide segment. The known segments define a loosely characterized binding motif: [D/S](-4)K(-3)X(-2)[T/V/I](-1)Q(0)[T/V](1)[D/E](2). The motifs are localized in disordered segments of the DYNLL-binding proteins and are often flanked by coiled coil or other potential dimerization domains. Based on a directed evolution approach, here we provide the first quantitative characterization of the binding preference of the DYNLL binding site. We displayed on M13 phage a naive peptide library with seven fully randomized positions around a fixed, naturally conserved glutamine. The peptides were presented in a bivalent manner fused to a leucine zipper mimicking the natural dimer to dimer binding stoichiometry of DYNLL-partner complexes. The phage-selected consensus sequence V(-5)S(-4)R(-3)G(-2)T(-1)Q(0)T(1)E(2) resembles the natural one, but is extended by an additional N-terminal valine, which increases the affinity of the monomeric peptide twentyfold. Leu-zipper dimerization increases the affinity into the subnanomolar range. By comparing crystal structures of an SRGTQTE-DYNLL and a dimeric VSRGTQTE-DYNLL complex we find that the affinity enhancing valine is accommodated in a binding pocket on DYNLL. Based on the in vitro evolved sequence pattern we predict a large number of novel DYNLL binding partners in the human proteome. Among these EML3, a microtubule-binding protein involved in mitosis contains an exact match of the phage-evolved consensus and binds to DYNLL with nanomolar affinity. These results significantly widen the scope of the human interactome around DYNLL and will certainly shed more light on the biological functions and organizing role of DYNLL in the human and other eukaryotic interactomes. FAU - Rapali, Peter AU - Rapali P AD - Department of Biochemistry, Eotvos Lorand University, Budapest, Hungary. FAU - Radnai, Laszlo AU - Radnai L FAU - Suveges, Daniel AU - Suveges D FAU - Harmat, Veronika AU - Harmat V FAU - Tolgyesi, Ferenc AU - Tolgyesi F FAU - Wahlgren, Weixiao Y AU - Wahlgren WY FAU - Katona, Gergely AU - Katona G FAU - Nyitray, Laszlo AU - Nyitray L FAU - Pal, Gabor AU - Pal G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110418 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Proteome) RN - 9007-49-2 (DNA) RN - EC 3.6.1.- (DYNLL1 protein, human) RN - EC 3.6.4.2 (Cytoplasmic Dyneins) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - Cytoplasmic Dyneins/chemistry/genetics/*metabolism MH - DNA MH - Dimerization MH - *Directed Molecular Evolution MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - *Proteome PMC - PMC3078936 OID - NLM: PMC3078936 EDAT- 2011/05/03 06:00 MHDA- 2011/08/31 06:00 CRDT- 2011/05/03 06:00 PHST- 2010/12/17 [received] PHST- 2011/03/10 [accepted] PHST- 2011/04/18 [epublish] AID - 10.1371/journal.pone.0018818 [doi] PST - epublish SO - PLoS One. 2011 Apr 18;6(4):e18818. doi: 10.1371/journal.pone.0018818. PMID- 19260715 OWN - NLM STAT- MEDLINE DA - 20090826 DCOM- 20090911 LR - 20140901 IS - 1520-6106 (Print) IS - 1520-5207 (Linking) VI - 113 IP - 10 DP - 2009 Mar 12 TI - A kinetic model for beta-amyloid adsorption at the air/solution interface and its implication to the beta-amyloid aggregation process. PG - 3160-8 LID - 10.1021/jp8085792 [doi] AB - At the air/buffer solution interface the kinetics of adsorption of amyloid beta peptide, Abeta(1-42), whose bulk concentration (submicromolar) is more than 2 orders of magnitude lower than that typically used in other in vitro aggregation studies, has been studied using a Langmuir-Blodgett trough. The pressure-time curves exhibit a lag phase, wherein the surface pressure essentially remains at zero, and a rising phase, corresponding to the Abeta adsorption at the interface. The duration of the lag phase was found to be highly dependent on both the Abeta bulk concentration and the solution temperature. A large activation energy (62.2 +/- 4.1 KJ/mol) was determined and the apparent adsorption rate constant was found to be linearly dependent on the Abeta bulk concentration. Attenuated total reflection-IR spectra of the adsorbed Abeta transferred to a solid substrate and circular dichroism measurements of Abeta in the solution layer near the interface reveal that the natively unstructured Abeta in the bulk undergo a conformation change (folding) to mainly the alpha-helical structure. The results suggest that, prior to the adsorption step, an equilibrium between Abeta conformations is established within the subsurface. The kinetic equation derived from this model confirms that the overall Abeta adsorption is kinetically controlled and the apparent rate constant is proportional to the Abeta bulk concentration. This model also indicates that interfaces such as cell membranes and lipid bilayers may facilitate Abeta aggregation/ fibrillation by providing a thin hydrophobic layer adjacent to the interface for the initial A/beta conformation change (misfolding) and accumulation. Such a preconcentration effect offers a plausible explanation of the fact that Abeta fibrillation occurs in vivo at nanomolar concentrations. Another important biological implication from our work is that Abeta misfolding may occur before its adsorption onto a cell membrane. This general kinetic model should also find applications in adsorption studies of other types of biomolecules whose overall kinetics exhibits a lag phase that is dependent on the bulk concentration of the adsorbate. FAU - Jiang, Dianlu AU - Jiang D AD - Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, California 90032, USA. FAU - Dinh, Kim Lien AU - Dinh KL FAU - Ruthenburg, Travis C AU - Ruthenburg TC FAU - Zhang, Yi AU - Zhang Y FAU - Su, Lei AU - Su L FAU - Land, Donald P AU - Land DP FAU - Zhou, Feimeng AU - Zhou F LA - eng GR - GM 08101/GM/NIGMS NIH HHS/United States GR - P20 MD001824-01/MD/NIMHD NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptides) RN - 0 (Solutions) RN - 059QF0KO0R (Water) SB - IM MH - Adsorption MH - Air MH - Amyloid beta-Peptides/*chemistry MH - Biophysics/methods MH - Chemistry, Physical/methods MH - Circular Dichroism MH - Humans MH - Kinetics MH - Microscopy, Atomic Force/methods MH - Peptides/chemistry MH - Protein Binding MH - Solutions MH - Spectroscopy, Fourier Transform Infrared MH - Surface Properties MH - Water/chemistry PMC - PMC3222685 MID - NIHMS96347 OID - NLM: NIHMS96347 OID - NLM: PMC3222685 EDAT- 2009/03/06 09:00 MHDA- 2009/09/12 06:00 CRDT- 2009/03/06 09:00 AID - 10.1021/jp8085792 [doi] PST - ppublish SO - J Phys Chem B. 2009 Mar 12;113(10):3160-8. doi: 10.1021/jp8085792. PMID- 10398682 OWN - NLM STAT- MEDLINE DA - 19990805 DCOM- 19990805 LR - 20140615 IS - 0890-9369 (Print) IS - 0890-9369 (Linking) VI - 13 IP - 13 DP - 1999 Jul 1 TI - Crystal structure of the conserved core of the herpes simplex virus transcriptional regulatory protein VP16. PG - 1692-703 AB - On infection, the herpes simplex virus (HSV) virion protein VP16 (Vmw65; alphaTIF) forms a transcriptional regulatory complex-the VP16-induced complex-with two cellular proteins, HCF and Oct-1, on VP16-responsive cis-regulatory elements in HSV immediate-early promoters called TAATGARAT. Comparison of different HSV VP16 sequences reveals a conserved core region that is sufficient for VP16-induced complex formation. The crystal structure of the VP16 core has been determined at 2.1 A resolution. The results reveal a novel, seat-like protein structure. Together with the activity of mutant VP16 proteins, the structure of free VP16 suggests that it contains (1) a disordered carboxy-terminal region that associates with HCF, Oct-1, and DNA in the VP16-induced complex, and (2) a structured region involved in virion assembly and possessing a novel DNA-binding surface that differentiates among TAATGARAT VP16-response elements. FAU - Liu, Y AU - Liu Y AD - Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA. FAU - Gong, W AU - Gong W FAU - Huang, C C AU - Huang CC FAU - Herr, W AU - Herr W FAU - Cheng, X AU - Cheng X LA - eng GR - CA-13106/CA/NCI NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Genes Dev JT - Genes & development JID - 8711660 RN - 0 (DNA-Binding Proteins) RN - 0 (Herpes Simplex Virus Protein Vmw65) RN - 0 (Host Cell Factor C1) RN - 0 (Macromolecular Substances) RN - 0 (Octamer Transcription Factor-1) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Crystallization MH - Crystallography, X-Ray MH - DNA/metabolism MH - DNA-Binding Proteins/metabolism MH - Gene Expression Regulation, Viral MH - Herpes Simplex Virus Protein Vmw65/*chemistry/genetics/metabolism MH - Herpesviridae/chemistry MH - Host Cell Factor C1 MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Octamer Transcription Factor-1 MH - *Protein Conformation MH - Recombinant Fusion Proteins/genetics MH - Regulatory Sequences, Nucleic Acid MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Simplexvirus/*chemistry/physiology MH - Transcription Factors/metabolism MH - Transcriptional Activation PMC - PMC316849 OID - NLM: PMC316849 EDAT- 1999/07/10 MHDA- 1999/07/10 00:01 CRDT- 1999/07/10 00:00 PST - ppublish SO - Genes Dev. 1999 Jul 1;13(13):1692-703. PMID- 11702069 OWN - NLM STAT- MEDLINE DA - 20011127 DCOM- 20020102 LR - 20081121 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 8 IP - 12 DP - 2001 Dec TI - Crystal structure of an Xrcc4-DNA ligase IV complex. PG - 1015-9 AB - A complex of two proteins, Xrcc4 and DNA ligase IV, plays a fundamental role in DNA non-homologous end joining (NHEJ), a cellular function required for double-strand break repair and V(D)J recombination. Here we report the crystal structure of human Xrcc4 bound to a polypeptide that corresponds to the DNA ligase IV sequence linking its two BRCA1 C-terminal (BRCT) domains. In the complex, a single ligase chain binds asymmetrically to an Xrcc4 dimer. The helical tails of Xrcc4 undergo a substantial conformational change relative to the uncomplexed protein, forming a coiled coil that unwinds upon ligase binding, leading to a flat interaction surface. A buried network of charged hydrogen bonds surrounded by extensive hydrophobic contacts explains the observed tightness of the interaction. The strong conservation of residues at the interface between the two proteins provides evidence that the observed mode of interaction has been maintained in NHEJ throughout evolution. FAU - Sibanda, B L AU - Sibanda BL AD - Department of Biochemistry, Cambridge University, Tennis Court Road, Cambridge CB2 1GA, UK. FAU - Critchlow, S E AU - Critchlow SE FAU - Begun, J AU - Begun J FAU - Pei, X Y AU - Pei XY FAU - Jackson, S P AU - Jackson SP FAU - Blundell, T L AU - Blundell TL FAU - Pellegrini, L AU - Pellegrini L LA - eng SI - PDB/1IK9 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (DNA-Binding Proteins) RN - 0 (Macromolecular Substances) RN - 0 (XRCC4 protein, human) RN - EC 6.5.1.- (DNA Ligases) RN - EC 6.5.1.1 (DNA ligase (ATP)) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - DNA Ligases/*chemistry/*metabolism MH - DNA-Binding Proteins/*chemistry/*metabolism MH - Dimerization MH - Humans MH - Hydrogen Bonding MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Static Electricity EDAT- 2001/11/10 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/11/10 10:00 AID - 10.1038/nsb725 [doi] AID - nsb725 [pii] PST - ppublish SO - Nat Struct Biol. 2001 Dec;8(12):1015-9. PMID- 11702068 OWN - NLM STAT- MEDLINE DA - 20011127 DCOM- 20020102 LR - 20131121 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 8 IP - 12 DP - 2001 Dec TI - Crystal structure and assembly of a eukaryotic small heat shock protein. PG - 1025-30 AB - The 2.7 A structure of wheat HSP16.9, a member of the small heat shock proteins (sHSPs), indicates how its alpha-crystallin domain and flanking extensions assemble into a dodecameric double disk. The folding of the monomer and assembly of the oligomer are mutually interdependent, involving strand exchange, helix swapping, loose knots and hinged extensions. In support of the chaperone mechanism, the substrate-bound dimers, in temperature-dependent equilibrium with higher assembly forms, have unfolded N-terminal arms and exposed conserved hydrophobic binding sites on the alpha-crystallin domain. The structure also provides a model by which members of the sHSP protein family bind unfolded substrates, which are involved in a variety of neurodegenerative diseases and cataract formation. FAU - van Montfort, R L AU - van Montfort RL AD - Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX UK. FAU - Basha, E AU - Basha E FAU - Friedrich, K L AU - Friedrich KL FAU - Slingsby, C AU - Slingsby C FAU - Vierling, E AU - Vierling E LA - eng SI - PDB/1GME SI - PDB/R1GMESF PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Crystallins) RN - 0 (HSP16.9 protein, Triticum aestivum) RN - 0 (Heat-Shock Proteins) RN - 0 (Plant Proteins) RN - 0 (Protein Subunits) RN - 94ZLA3W45F (Arginine) SB - IM MH - Amino Acid Sequence MH - Arginine/genetics/metabolism MH - Binding Sites MH - Conserved Sequence MH - Crystallins/chemistry MH - Crystallography, X-Ray MH - Dimerization MH - Eukaryotic Cells/*chemistry MH - Heat-Shock Proteins/*chemistry/*metabolism MH - Methanococcus/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Plant Proteins/chemistry/metabolism MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Subunits MH - Sequence Alignment MH - Triticum/*chemistry EDAT- 2001/11/10 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/11/10 10:00 AID - 10.1038/nsb722 [doi] AID - nsb722 [pii] PST - ppublish SO - Nat Struct Biol. 2001 Dec;8(12):1025-30. PMID- 20026028 OWN - NLM STAT- MEDLINE DA - 20100217 DCOM- 20100318 IS - 1096-0384 (Electronic) IS - 0003-9861 (Linking) VI - 495 IP - 1 DP - 2010 Mar 1 TI - Role of the 207-218 peptide region of Moloney murine leukemia virus integrase in enzyme catalysis. PG - 28-34 LID - 10.1016/j.abb.2009.12.018 [doi] AB - X-ray diffraction data on a few retroviral integrases show a flexible loop near the active site. By sequence alignment, the peptide region 207-218 of Mo-MLV IN appears to correspond to this flexible loop. In this study, residues H208, Y211, R212, Q214, S215 and S216 of Mo-MLV IN were mutated to determine their role on enzyme activity. We found that Y211A, R212A, R212K and Q214A decreased integration activity, while disintegration and 3'-processing were not significantly affected. By contrast H208A was completely inactive in all the assays. The core domain of Mo-MLV integrase was modeled and the flexibility of the region 207-216 was analyzed. Substitutions with low integration activity showed a lower flexibility than wild type integrase. We propose that the peptide region 207-216 is a flexible loop and that H208, Y211, R212 and Q214 of this loop are involved in the correct assembly of the DNA-integrase complex during integration. CI - 2009 Elsevier Inc. All rights reserved. FAU - Acevedo, Monica L AU - Acevedo ML AD - Programa de Virologia, Instituto de Ciencias Biomedicas, Facultad de Medicina, Universidad de Chile, Independencia 1027, Santiago, Chile. macevedo@med.uchile.cl FAU - Arbildua, Jose Jaime AU - Arbildua JJ FAU - Monasterio, Octavio AU - Monasterio O FAU - Toledo, Hector AU - Toledo H FAU - Leon, Oscar AU - Leon O LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091221 PL - United States TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - EC 2.7.7.- (Integrases) SB - IM MH - Amino Acid Sequence MH - Integrases/chemistry/*genetics/*metabolism MH - Models, Molecular MH - Moloney murine leukemia virus/*enzymology/genetics MH - Mutagenesis, Site-Directed MH - Mutation MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Virus Integration EDAT- 2009/12/23 06:00 MHDA- 2010/03/20 06:00 CRDT- 2009/12/23 06:00 PHST- 2009/09/30 [received] PHST- 2009/12/11 [revised] PHST- 2009/12/13 [accepted] PHST- 2009/12/21 [aheadofprint] AID - S0003-9861(09)00427-5 [pii] AID - 10.1016/j.abb.2009.12.018 [doi] PST - ppublish SO - Arch Biochem Biophys. 2010 Mar 1;495(1):28-34. doi: 10.1016/j.abb.2009.12.018. Epub 2009 Dec 21. PMID- 24020004 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20130910 DCOM- 20130910 LR - 20130912 IS - 1947-6019 (Print) IS - 1947-6019 (Linking) VI - 4 IP - 3-4 DP - 2013 Mar TI - SIRT1 is a Highly Networked Protein That Mediates the Adaptation to Chronic Physiological Stress. PG - 125-34 LID - 10.1177/1947601912474893 [doi] AB - SIRT1 is a NAD(+)-dependent protein deacetylase that has a very large number of established protein substrates and an equally impressive list of biological functions thought to be regulated by its activity. Perhaps as notable is the remarkable number of points of conflict concerning the role of SIRT1 in biological processes. For example, evidence exists suggesting that SIRT1 is a tumor suppressor, is an oncogene, or has no effect on oncogenesis. Similarly, SIRT1 is variably reported to induce, inhibit, or have no effect on autophagy. We believe that the resolution of many conflicting results is possible by considering recent reports indicating that SIRT1 is an important hub interacting with a complex network of proteins that collectively regulate a wide variety of biological processes including cancer and autophagy. A number of the interacting proteins are themselves hubs that, like SIRT1, utilize intrinsically disordered regions for their promiscuous interactions. Many studies investigating SIRT1 function have been carried out on cell lines carrying undetermined numbers of alterations to the proteins comprising the SIRT1 network or on inbred mouse strains carrying fixed mutations affecting some of these proteins. Thus, the effects of modulating SIRT1 amount and/or activity are importantly determined by the genetic background of the cell (or the inbred strain of mice), and the effects attributed to SIRT1 are synthetic with the background of mutations and epigenetic differences between cells and organisms. Work on mice carrying alterations to the Sirt1 gene suggests that the network in which SIRT1 functions plays an important role in mediating physiological adaptation to various sources of chronic stress such as calorie restriction and calorie overload. Whether the catalytic activity of SIRT1 and the nuclear concentration of the co-factor, NAD(+), are responsible for modulating this activity remains to be determined. However, the effect of modulating SIRT1 activity must be interpreted in the context of the cell or tissue under investigation. Indeed, for SIRT1, we argue that context is everything. FAU - McBurney, Michael W AU - McBurney MW AD - Program in Cancer Therapeutics, Ottawa Hospital Research Institute ; Department of Medicine, University of Ottawa, Ottawa, ON, Canada. FAU - Clark-Knowles, Katherine V AU - Clark-Knowles KV FAU - Caron, Annabelle Z AU - Caron AZ FAU - Gray, Douglas A AU - Gray DA LA - eng PT - Journal Article PL - United States TA - Genes Cancer JT - Genes & cancer JID - 101516546 PMC - PMC3764470 OID - NLM: PMC3764470 OTO - NOTNLM OT - nutritional stress OT - oncogenesis OT - protein deacetylation OT - scale-free network EDAT- 2013/09/11 06:00 MHDA- 2013/09/11 06:01 CRDT- 2013/09/11 06:00 AID - 10.1177/1947601912474893 [doi] AID - 10.1177_1947601912474893 [pii] PST - ppublish SO - Genes Cancer. 2013 Mar;4(3-4):125-34. doi: 10.1177/1947601912474893. PMID- 25215518 OWN - NLM STAT- MEDLINE DA - 20141003 DCOM- 20150526 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 118 IP - 39 DP - 2014 Oct 2 TI - Experimental validation of the role of trifluoroethanol as a nanocrowder. PG - 11455-61 LID - 10.1021/jp508056w [doi] AB - Trifluoroethanol (TFE) is commonly used to induce protein secondary structure, especially alpha-helix formation. Due to its amphiphilic nature, however, TFE can also self-associate to form micellelike, nanometer-sized clusters. Herein, we hypothesize that such clusters can act as nanocrowders to increase protein folding rates via the excluded volume effect. To test this hypothesis, we measure the conformational relaxation kinetics of an intrinsically disordered protein, the phosphorylated kinase inducible domain (pKID), which forms a helix-turn-helix in TFE solutions. We find that the conformational relaxation rate of pKID displays a rather complex dependence on TFE percentage (v/v): while it first decreases between 0 and 5%, between 5 and 15% the rate increases and then remains relatively unchanged between 15 and 30% and finally decreases again at higher percentages (i.e., 50%). This trend coincides with the fact that TFE clustering is maximized in the range of 15-30%, thus providing validation of our hypothesis. Another line of supporting evidence comes from the observation that the relaxation rate of a monomeric helical peptide, which due to its predominantly local interactions in the folded state is less affected by crowding, does not show a similar TFE dependence. FAU - Culik, Robert M AU - Culik RM AD - Department of Biochemistry & Biophysics and double daggerDepartment of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States. FAU - Abaskharon, Rachel M AU - Abaskharon RM FAU - Pazos, Ileana M AU - Pazos IM FAU - Gai, Feng AU - Gai F LA - eng GR - GM-008275/GM/NIGMS NIH HHS/United States GR - GM-065978/GM/NIGMS NIH HHS/United States GR - T32-GM008275/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140919 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Peptides) RN - 75-89-8 (Trifluoroethanol) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Molecular Sequence Data MH - Peptides/chemistry/metabolism MH - Phosphorylation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Unfolding MH - Temperature MH - Thermodynamics MH - Trifluoroethanol/*chemistry PMC - PMC4183368 OID - NLM: PMC4183368 [Available on 09/12/15] EDAT- 2014/09/13 06:00 MHDA- 2015/05/27 06:00 CRDT- 2014/09/13 06:00 PMCR- 2015/09/12 00:00 PHST- 2014/09/19 [aheadofprint] AID - 10.1021/jp508056w [doi] PST - ppublish SO - J Phys Chem B. 2014 Oct 2;118(39):11455-61. doi: 10.1021/jp508056w. Epub 2014 Sep 19. PMID- 16373493 OWN - NLM STAT- MEDLINE DA - 20051223 DCOM- 20060203 LR - 20140910 IS - 1355-8382 (Print) IS - 1355-8382 (Linking) VI - 12 IP - 1 DP - 2006 Jan TI - Structural study of the H/ACA snoRNP components Nop10p and the 3' hairpin of U65 snoRNA. PG - 40-52 AB - The H/ACA small nucleolar ribonucleoprotein (snoRNP) complexes guide the modification of uridine to pseudouridine at conserved sites in rRNA. The H/ACA snoRNPs each comprise a target-site-specific snoRNA and four core proteins, Nop10p, Nhp2p, Gar1p, and the pseudouridine synthase, Cbf5p, in yeast. The secondary structure of the H/ACA snoRNAs includes two hairpins that each contain a large internal loop (the pseudouridylation pocket), one or both of which are partially complementary to the target RNA(s). We have determined the solution structure of an RNA hairpin derived from the human U65 box H/ACA snoRNA including the pseudouridylation pocket and adjacent stems, providing the first three-dimensional structural information on these H/ACA snoRNAs. We have also determined the structure of Nop10p and investigated its interaction with RNA using NMR spectroscopy. Nop10p contains a structurally well-defined N-terminal region composed of a beta-hairpin, and the rest of the protein lacks a globular structure. Chemical shift mapping of the interaction of RNA constructs of U65 box H/ACA 3' hairpin with Nop10p shows that the beta-hairpin binds weakly but specifically to RNA. The unstructured region of Nop10p likely interacts with Cbf5p. FAU - Khanna, May AU - Khanna M AD - Department of Chemistry and Biochemistry, 607 Charles Young Drive East, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA. FAU - Wu, Haihong AU - Wu H FAU - Johansson, Carina AU - Johansson C FAU - Caizergues-Ferrer, Michele AU - Caizergues-Ferrer M FAU - Feigon, Juli AU - Feigon J LA - eng GR - GM37254/GM/NIGMS NIH HHS/United States GR - GM48123/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - RNA JT - RNA (New York, N.Y.) JID - 9509184 RN - 0 (GAR1 protein, human) RN - 0 (NOP10 protein, S cerevisiae) RN - 0 (Nuclear Proteins) RN - 0 (RNA-Binding Proteins) RN - 0 (Ribonucleoproteins, Small Nuclear) RN - 0 (Ribonucleoproteins, Small Nucleolar) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 1445-07-4 (Pseudouridine) SB - IM MH - Amino Acid Sequence MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Proteins/*chemistry/*genetics MH - Nucleic Acid Conformation MH - Protein Structure, Tertiary MH - Pseudouridine/*chemistry/metabolism MH - RNA-Binding Proteins/*chemistry/*genetics MH - Ribonucleoproteins, Small Nuclear/*chemistry/genetics MH - Ribonucleoproteins, Small Nucleolar/*chemistry MH - Saccharomyces cerevisiae Proteins/*chemistry/*genetics MH - Sequence Homology PMC - PMC1370884 OID - NLM: PMC1370884 EDAT- 2005/12/24 09:00 MHDA- 2006/02/04 09:00 CRDT- 2005/12/24 09:00 AID - 12/1/40 [pii] AID - 10.1261/rna.2221606 [doi] PST - ppublish SO - RNA. 2006 Jan;12(1):40-52. PMID- 19847913 OWN - NLM STAT- MEDLINE DA - 20100112 DCOM- 20100325 LR - 20131121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 78 IP - 3 DP - 2010 Feb 15 TI - Characterization of intrinsically disordered proteins with electrospray ionization mass spectrometry: conformational heterogeneity of alpha-synuclein. PG - 714-22 LID - 10.1002/prot.22604 [doi] AB - Conformational heterogeneity of alpha-synuclein was studied with electrospray ionization mass spectrometry by analyzing protein ion charge state distributions, where the extent of multiple charging reflects compactness of the protein conformations in solution. Although alpha-synuclein lacks a single well-defined structure under physiological conditions, it was found to sample four distinct conformational states, ranging from a highly structured one to a random coil. The compact highly structured state of alpha-synuclein is present across the entire range of conditions tested (pH ranging from 2.5 to 10, alcohol content from 0% to 60%), but is particularly abundant in acidic solutions. The only other protein state populated in acidic solutions is a partially folded intermediate state lacking stable tertiary structure. Another, more compact intermediate state is induced by significant amounts of ethanol used as a co-solvent and appears to represent a partially folded conformation with high beta-sheet content. Protein dimerization is observed throughout the entire range of conditions tested, although only acidic solutions favor formation of highly structured dimers of alpha-synuclein. These dimers are likely to present the earliest stages in protein aggregation leading to globular oligomers and, subsequently, protofibrils. FAU - Frimpong, Agya K AU - Frimpong AK AD - Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA. FAU - Abzalimov, Rinat R AU - Abzalimov RR FAU - Uversky, Vladimir N AU - Uversky VN FAU - Kaltashov, Igor A AU - Kaltashov IA LA - eng GR - GM071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 LM007688-01A1/LM/NLM NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (alpha-Synuclein) RN - 3K9958V90M (Ethanol) SB - IM MH - Ethanol/chemistry MH - Humans MH - Hydrogen-Ion Concentration MH - Protein Conformation MH - Protein Multimerization MH - Spectrometry, Mass, Electrospray Ionization MH - alpha-Synuclein/*chemistry EDAT- 2009/10/23 06:00 MHDA- 2010/03/26 06:00 CRDT- 2009/10/23 06:00 AID - 10.1002/prot.22604 [doi] PST - ppublish SO - Proteins. 2010 Feb 15;78(3):714-22. doi: 10.1002/prot.22604. PMID- 11566136 OWN - NLM STAT- MEDLINE DA - 20010921 DCOM- 20011207 LR - 20091119 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 9 IP - 9 DP - 2001 Sep TI - Crystal structure of beta-arrestin at 1.9 A: possible mechanism of receptor binding and membrane Translocation. PG - 869-80 AB - BACKGROUND: Arrestins are responsible for the desensitization of many sequence-divergent G protein-coupled receptors. They compete with G proteins for binding to activated phosphorylated receptors, initiate receptor internalization, and activate additional signaling pathways. RESULTS: In order to understand the structural basis for receptor binding and arrestin's function as an adaptor molecule, we determined the X-ray crystal structure of two truncated forms of bovine beta-arrestin in its cytosolic inactive state to 1.9 A. Mutational analysis and chimera studies identify the regions in beta-arrestin responsible for receptor binding specificity. beta-arrestin demonstrates high structural homology with the previously solved visual arrestin. All key structural elements responsible for arrestin's mechanism of activation are conserved. CONCLUSIONS: Based on structural analysis and mutagenesis data, we propose a previously unappreciated part in beta-arrestin's mode of action by which a cationic amphipathic helix may function as a reversible membrane anchor. This novel activation mechanism would facilitate the formation of a high-affinity complex between beta-arrestin and an activated receptor regardless of its specific subtype. Like the interaction between beta-arrestin's polar core and the phosphorylated receptor, such a general activation mechanism would contribute to beta-arrestin's versatility as a regulator of many receptors. FAU - Han, M AU - Han M AD - Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. mhan@mpi.com FAU - Gurevich, V V AU - Gurevich VV FAU - Vishnivetskiy, S A AU - Vishnivetskiy SA FAU - Sigler, P B AU - Sigler PB FAU - Schubert, C AU - Schubert C LA - eng SI - PDB/1G4M SI - PDB/1G4R GR - EY011500/EY/NEI NIH HHS/United States GR - GM22324/GM/NIGMS NIH HHS/United States GR - GM63097/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Arrestins) RN - 0 (Receptors, Cell Surface) RN - 0 (beta-arrestin) RN - EC 3.6.5.1 (Heterotrimeric GTP-Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Arrestins/*chemistry/genetics/*metabolism MH - Binding Sites MH - Biological Transport MH - Cattle MH - Cell Membrane/*metabolism MH - Crystallography, X-Ray MH - Dimerization MH - Heterotrimeric GTP-Binding Proteins/metabolism MH - *Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Point Mutation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Cell Surface/*metabolism MH - Sequence Homology, Amino Acid MH - Structure-Activity Relationship EDAT- 2001/09/22 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/09/22 10:00 AID - S096921260100644X [pii] PST - ppublish SO - Structure. 2001 Sep;9(9):869-80. PMID- 4344990 OWN - NLM STAT- MEDLINE DA - 19730215 DCOM- 19730215 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 247 IP - 24 DP - 1972 Dec 25 TI - The conformation of horse heart apocytochrome c. PG - 8074-7 FAU - Stellwagen, E AU - Stellwagen E FAU - Rysavy, R AU - Rysavy R FAU - Babul, G AU - Babul G LA - eng PT - Journal Article PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Amino Acids) RN - 0 (Apoproteins) RN - 0 (Cytochrome c Group) RN - 0 (Ferricyanides) RN - 0 (Glycols) RN - 0 (Peptides) RN - 0 (Sulfates) RN - 1364PS73AF (Acetone) RN - 3M4G523W1G (Silver) RN - 42HK56048U (Tyrosine) RN - 42VZT0U6YR (Heme) RN - 4QD397987E (Histidine) RN - 60-24-2 (Mercaptoethanol) SB - IM MH - Acetone MH - Alkylation MH - Amino Acids/analysis MH - Animals MH - Apoproteins MH - Circular Dichroism MH - *Cytochrome c Group/analysis MH - Ferricyanides MH - Glycols MH - Heme MH - Histidine MH - Horses MH - Hydrogen-Ion Concentration MH - Mercaptoethanol MH - *Myocardium MH - Oxidation-Reduction MH - Peptides MH - Protein Binding MH - Protein Conformation MH - Silver MH - Spectrophotometry, Ultraviolet MH - Sulfates MH - Tyrosine MH - Ultracentrifugation MH - Viscosity EDAT- 1972/12/25 MHDA- 1972/12/25 00:01 CRDT- 1972/12/25 00:00 PST - ppublish SO - J Biol Chem. 1972 Dec 25;247(24):8074-7. PMID- 17905836 OWN - NLM STAT- MEDLINE DA - 20071026 DCOM- 20080115 LR - 20140904 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 16 IP - 11 DP - 2007 Nov TI - The intrinsically disordered TC-1 interacts with Chibby via regions with high helical propensity. PG - 2510-8 AB - Thyroid cancer 1 (TC-1) is a 106-residue naturally disordered protein that has been found to associate with thyroid, gastric, and breast cancers. Recent studies showed that the protein functions as a positive regulator in the Wnt/beta-catenin signaling pathway, a pathway that is known to play essential roles in developmental processes and causes tumor formation when misregulated. By competing with beta-catenin for binding to Chibby (Cby), a conserved nuclear protein that antagonizes the beta-catenin-mediated transcriptions, TC-1 up-regulates a number of beta-catenin target genes that are known to be involved in the aggressive behavior of cancers. In order to gain a molecular understanding of the role TC-1 plays in regulating the Wnt/beta-catenin signaling pathway, detailed structural studies of the protein and its interaction with Cby are essential. In this work, we used nuclear magnetic resonance (NMR) spectroscopy to elucidate the structure of TC-1 and its interaction with Cby. Our results indicate that even though TC-1 is naturally disordered, the protein adopts fairly compact conformations under nondenaturing conditions. Chemical shift analysis and relaxation measurements show that three regions (D44-R53, K58-A64, and D73-T88) with high-helical propensity are present in the C-terminal portion of TC-1. Upon addition of Cby, significant broadening of resonance signals derived from these helical regions of TC-1 was observed. The result indicates that the intrinsically disordered TC-1 interacts with Cby via its transient helical structure. FAU - Gall, Chris AU - Gall C AD - Department of Biochemistry, University of Western Ontario, London, Canada. FAU - Xu, Hanyu AU - Xu H FAU - Brickenden, Anne AU - Brickenden A FAU - Ai, Xuanjun AU - Ai X FAU - Choy, Wing Yiu AU - Choy WY LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070928 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (C8orf4 protein, human) RN - 0 (CBY1 protein, human) RN - 0 (Carrier Proteins) RN - 0 (Neoplasm Proteins) RN - 0 (Nuclear Proteins) RN - 0 (beta Catenin) SB - IM MH - Amino Acid Sequence MH - Carrier Proteins/*chemistry/metabolism MH - *Gene Expression Regulation, Neoplastic MH - Humans MH - Magnetic Resonance Spectroscopy/*methods MH - Molecular Sequence Data MH - Neoplasm Proteins/*chemistry/metabolism MH - Neoplasms/metabolism MH - Nuclear Proteins/*chemistry/metabolism MH - Plasmids/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Signal Transduction MH - Temperature MH - beta Catenin/metabolism PMC - PMC2211702 OID - NLM: PMC2211702 EDAT- 2007/10/02 09:00 MHDA- 2008/01/16 09:00 CRDT- 2007/10/02 09:00 PHST- 2007/09/28 [aheadofprint] AID - ps.073062707 [pii] AID - 10.1110/ps.073062707 [doi] PST - ppublish SO - Protein Sci. 2007 Nov;16(11):2510-8. Epub 2007 Sep 28. PMID- 3515197 OWN - NLM STAT- MEDLINE DA - 19860501 DCOM- 19860501 LR - 20081023 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 320 IP - 6059 DP - 1986 Mar 20-26 TI - Sequence homology of the yeast regulatory protein ADR1 with Xenopus transcription factor TFIIIA. PG - 283-7 AB - Classical yeast genetics coupled with the cloning of regulatory genes by complementation of function is a powerful means of identifying and isolating trans-acting regulatory elements. One such regulatory gene is ADR1 which encodes a protein required for transcriptional activation of the glucose-repressible alcohol dehydrogenase (ADH2) gene. We now report the nucleotide sequence of ADR1; it encodes a polypeptide chain of 1,323 amino acids, of which the amino-terminal 302 amino acids are sufficient to stimulate ADH2 transcription. This active amino-terminal region shows amino-acid sequence homology with the repetitive DNA-binding domain of TFIIIA, an RNA polymerase III transcription factor of Xenopus laevis. Similar domains are found in proteins encoded at the Kruppel and Serendipity loci of Drosophila melanogaster. We discuss the implications of this structural homology and suggest that a similar domain may exist in other yeast regulatory proteins such as those encoded by GAL4 (ref. 13) and PPR1 (ref.14). FAU - Hartshorne, T A AU - Hartshorne TA FAU - Blumberg, H AU - Blumberg H FAU - Young, E T AU - Young ET LA - eng SI - GENBANK/X03763 GR - 5 T32 GM07270/GM/NIGMS NIH HHS/United States GR - GM26079/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (ADR1 protein, S cerevisiae) RN - 0 (DNA, Fungal) RN - 0 (DNA-Binding Proteins) RN - 0 (Fungal Proteins) RN - 0 (RNA, Ribosomal) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Transcription Factor TFIIIA) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Binding Sites MH - DNA/genetics/metabolism MH - DNA, Fungal/genetics MH - *DNA-Binding Proteins MH - Fungal Proteins/*genetics MH - Molecular Sequence Data MH - RNA, Ribosomal MH - Saccharomyces cerevisiae/*genetics MH - *Saccharomyces cerevisiae Proteins MH - Transcription Factor TFIIIA MH - Transcription Factors/*genetics/metabolism MH - Transcription, Genetic MH - Xenopus laevis/*genetics EDAT- 1986/03/20 MHDA- 1986/03/20 00:01 CRDT- 1986/03/20 00:00 AID - 10.1038/320283a0 [doi] PST - ppublish SO - Nature. 1986 Mar 20-26;320(6059):283-7. PMID- 9722562 OWN - NLM STAT- MEDLINE DA - 19981015 DCOM- 19981015 LR - 20081121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 273 IP - 36 DP - 1998 Sep 4 TI - Structural and transglutaminase substrate properties of the small proline-rich 2 family of cornified cell envelope proteins. PG - 23297-303 AB - The small proline-rich (SPR) proteins are components of the cornified cell envelope of stratified squamous epithelia and become cross-linked to other proteins by transglutaminases (TGases). The SPR2 family is the most complex, as it consists of several differentially expressed members of the same size. To explore their physical and cross-linking properties, we have expressed in bacteria a human SPR2 family member, and purified it to homogeneity. By circular dichroism, it possesses no alpha or beta structure but has some organized structure associated with the central peptide repeat domain. The TGase 1, 2, and 3 enzymes expressed in epithelia use the recombinant SPR2 protein as a complete substrate in vitro, but with widely differing kinetic efficiencies, and in different ways. With TGase 1, only one glutamine on the head domain and one lysine on the tail domain were used for limited interchain cross-linking. With TGase 3, multiple head and tail domain residues were used for extensive interchain cross-linking. The total usage of glutamine and lysine residues in vitro by TGase 3 was similar to that seen in earlier in vivo studies. We conclude that SPR2 proteins are cross-linked in epithelia primarily by the TGase 3 enzyme, a minor extent by TGase 1, and probably not by TGase 2. FAU - Tarcsa, E AU - Tarcsa E AD - Laboratory of Skin Biology, NIAMS, National Institutes of Health, Bethesda, Maryland 20892-2752, USA. FAU - Candi, E AU - Candi E FAU - Kartasova, T AU - Kartasova T FAU - Idler, W W AU - Idler WW FAU - Marekov, L N AU - Marekov LN FAU - Steinert, P M AU - Steinert PM LA - eng PT - Comparative Study PT - Journal Article PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Cornified Envelope Proline-Rich Proteins) RN - 0 (Isoenzymes) RN - 0 (Membrane Proteins) RN - 0 (Proteins) RN - 0 (Recombinant Proteins) RN - EC 2.3.2.13 (Transglutaminases) SB - IM MH - Amino Acid Sequence MH - Animals MH - Circular Dichroism MH - Cornified Envelope Proline-Rich Proteins MH - Epithelial Cells/*metabolism MH - Humans MH - Isoenzymes/*metabolism MH - Membrane Proteins MH - Mice MH - Molecular Sequence Data MH - Protein Conformation MH - Proteins/chemistry/genetics/*metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Substrate Specificity MH - Transglutaminases/*metabolism EDAT- 1998/08/29 MHDA- 1998/08/29 00:01 CRDT- 1998/08/29 00:00 PST - ppublish SO - J Biol Chem. 1998 Sep 4;273(36):23297-303. PMID- 11206074 OWN - NLM STAT- MEDLINE DA - 20010202 DCOM- 20010531 LR - 20140613 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 9 IP - 12 DP - 2000 Dec TI - Rationale for Bcl-xL/Bad peptide complex formation from structure, mutagenesis, and biophysical studies. PG - 2528-34 AB - The three-dimensional structure of the anti-apoptotic protein Bcl-xL complexed to a 25-residue peptide from the death promoting region of Bad was determined using NMR spectroscopy. Although the overall structure is similar to Bcl-xL bound to a 16-residue peptide from the Bak protein (Sattler et al., 1997), the Bad peptide forms additional interactions with Bcl-xL. However, based upon site-directed mutagenesis experiments, these additional contacts do not account for the increased affinity of the Bad 25-mer for Bcl-xL compared to the Bad 16-mer. Rather, the increased helix propensity of the Bad 25-mer is primarily responsible for its greater affinity for Bcl-xL. Based on this observation, a pair of 16-residue peptides were designed and synthesized that were predicted to have a high helix propensity while maintaining the interactions important for complexation with Bcl-xL. Both peptides showed an increase in helix propensity compared to the wild-type and exhibited an enhanced affinity for Bcl-xL. FAU - Petros, A M AU - Petros AM AD - Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064-6098, USA. FAU - Nettesheim, D G AU - Nettesheim DG FAU - Wang, Y AU - Wang Y FAU - Olejniczak, E T AU - Olejniczak ET FAU - Meadows, R P AU - Meadows RP FAU - Mack, J AU - Mack J FAU - Swift, K AU - Swift K FAU - Matayoshi, E D AU - Matayoshi ED FAU - Zhang, H AU - Zhang H FAU - Thompson, C B AU - Thompson CB FAU - Fesik, S W AU - Fesik SW LA - eng PT - Comparative Study PT - Journal Article PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (BAD protein, human) RN - 0 (BCL2L1 protein, human) RN - 0 (Carrier Proteins) RN - 0 (Peptides) RN - 0 (Proto-Oncogene Proteins c-bcl-2) RN - 0 (bcl-Associated Death Protein) RN - 0 (bcl-X Protein) SB - IM MH - Amino Acid Sequence MH - Apoptosis MH - Binding Sites MH - Carrier Proteins/*chemistry/metabolism MH - Humans MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides/chemical synthesis/metabolism MH - Protein Binding MH - Protein Engineering MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-bcl-2/*chemistry/metabolism MH - Structure-Activity Relationship MH - bcl-Associated Death Protein MH - bcl-X Protein PMC - PMC2144516 OID - NLM: PMC2144516 EDAT- 2001/02/24 12:00 MHDA- 2001/06/02 10:01 CRDT- 2001/02/24 12:00 AID - 10.1110/ps.9.12.2528 [doi] PST - ppublish SO - Protein Sci. 2000 Dec;9(12):2528-34. PMID- 18260106 OWN - NLM STAT- MEDLINE DA - 20080715 DCOM- 20080826 LR - 20131121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 72 IP - 3 DP - 2008 Aug 15 TI - Apo-parvalbumin as an intrinsically disordered protein. PG - 822-36 LID - 10.1002/prot.21974 [doi] AB - Recently defined family of intrinsically disordered proteins (IDP) includes proteins lacking rigid tertiary structure meanwhile fulfilling essential biological functions. Here we show that apo-state of pike parvalbumin (alpha- and beta-isoforms, pI 5.0 and 4.2, respectively) belongs to the family of IDP, which is in accord with theoretical predictions. Parvalbumin (PA) is a 12-kDa calcium-binding protein involved into regulation of relaxation of fast muscles. Differential scanning calorimetry measurements of metal-depleted form of PA revealed the absence of any thermally induced transitions with measurable denaturation enthalpy along with elevated specific heat capacity, implying the lack of rigid tertiary structure and exposure of hydrophobic protein groups to the solvent. Calcium removal from the PAs causes more than 10-fold increase in fluorescence intensity of hydrophobic probe bis-ANS and is accompanied by a decrease in alpha-helical content and a marked increase in mobility of aromatic residues environment, as judged by circular dichroism spectroscopy (CD). Guanidinium chloride-induced unfolding of the apo-parvalbumins monitored by CD showed the lack of fixed tertiary structure. Theoretical estimation of energetics of the charge-charge interactions in the PAs indicated their pronounced destabilization upon calcium removal, which is in line with sequence-based predictions of disordered protein chain regions. Far-UV CD studies of apo-alpha-PA revealed hallmarks of cold denaturation of the protein at temperatures below 20 degrees C. Moreover, a cooperative thermal denaturation transition with mid-temperature at 10-15 degrees C is revealed by near-UV CD for both PAs. The absence of detectable enthalpy change in this temperature region suggests continuous nature of the transition. Overall, the theoretical and experimental data obtained show that PA in apo-state is essentially disordered nevertheless demonstrates complex denaturation behavior. The native rigid tertiary structure of PA is attained upon association of one (alpha-PA) or two (beta-PA) calcium ions per protein molecule, as follows from calorimetric and calcium titration data. FAU - Permyakov, Sergei E AU - Permyakov SE AD - Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia. FAU - Bakunts, Anush G AU - Bakunts AG FAU - Denesyuk, Alexander I AU - Denesyuk AI FAU - Knyazeva, Ekaterina L AU - Knyazeva EL FAU - Uversky, Vladimir N AU - Uversky VN FAU - Permyakov, Eugene A AU - Permyakov EA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Apoproteins) RN - 0 (Parvalbumins) RN - 0 (Protein Isoforms) RN - JU58VJ6Y3B (Guanidine) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Apoproteins/*chemistry/*metabolism MH - Calcium/pharmacology MH - Circular Dichroism MH - Esocidae MH - Guanidine/pharmacology MH - Parvalbumins/*chemistry/*metabolism MH - Protein Denaturation/drug effects MH - Protein Folding MH - Protein Isoforms/chemistry/metabolism MH - Static Electricity MH - Temperature MH - Thermodynamics EDAT- 2008/02/09 09:00 MHDA- 2008/08/30 09:00 CRDT- 2008/02/09 09:00 AID - 10.1002/prot.21974 [doi] PST - ppublish SO - Proteins. 2008 Aug 15;72(3):822-36. doi: 10.1002/prot.21974. PMID- 20678071 OWN - NLM STAT- MEDLINE DA - 20110110 DCOM- 20111123 IS - 1875-5828 (Electronic) IS - 1567-2050 (Linking) VI - 7 IP - 8 DP - 2010 Dec TI - Tau truncation is a productive posttranslational modification of neurofibrillary degeneration in Alzheimer's disease. PG - 708-16 AB - Deposits of the misfolded neuronal protein tau are major hallmarks of neurodegeneration in Alzheimer's disease (AD) and other tauopathies. The etiology of the transformation process of the intrinsically disordered soluble protein tau into the insoluble misordered aggregate has attracted much attention. Tau undergoes multiple modifications in AD, most notably hyperphosphorylation and truncation. Hyperphosphorylation is widely regarded as the hottest candidate for the inducer of the neurofibrillary pathology. However, the true nature of the impetus that initiates the whole process in the human brains remains unknown. In AD, several site-specific tau cleavages were identified and became connected to the progression of the disease. In addition, western blot analyses of tau species in AD brains reveal multitudes of various truncated forms. In this review we summarize evidence showing that tau truncation alone is sufficient to induce the complete cascade of neurofibrillary pathology, including hyperphosphorylation and accumulation of misfolded insoluble forms of tau. Therefore, proteolytical abnormalities in the stressed neurons and production of aberrant tau cleavage products deserve closer attention and should be considered as early therapeutic targets for Alzheimer's disease. FAU - Kovacech, B AU - Kovacech B AD - Institute of Neuroimmunology, AD Centre, Slovak Academy of Sciences, Bratislava, Slovakia. FAU - Novak, M AU - Novak M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United Arab Emirates TA - Curr Alzheimer Res JT - Current Alzheimer research JID - 101208441 RN - 0 (MAPT protein, human) RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/genetics/*metabolism/*pathology MH - Animals MH - *Gene Deletion MH - Humans MH - Nerve Degeneration/metabolism/*pathology MH - Neurofibrillary Tangles/metabolism/*pathology MH - Phosphorylation MH - *Protein Processing, Post-Translational/genetics MH - tau Proteins/*genetics/metabolism/physiology EDAT- 2010/08/04 06:00 MHDA- 2011/12/13 00:00 CRDT- 2010/08/04 06:00 PHST- 2009/12/30 [received] PHST- 2010/01/17 [accepted] AID - CAR -87 [pii] PST - ppublish SO - Curr Alzheimer Res. 2010 Dec;7(8):708-16. PMID- 3473966 OWN - NLM STAT- MEDLINE DA - 19870723 DCOM- 19870723 LR - 20131121 IS - 0077-8923 (Print) IS - 0077-8923 (Linking) VI - 493 DP - 1987 TI - Chromogranin A: the primary structure deduced from cDNA clones reveals the presence of pairs of basic amino acids. PG - 351-78 FAU - Grimes, M AU - Grimes M FAU - Iacangelo, A AU - Iacangelo A FAU - Eiden, L E AU - Eiden LE FAU - Godfrey, B AU - Godfrey B FAU - Herbert, E AU - Herbert E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Ann N Y Acad Sci JT - Annals of the New York Academy of Sciences JID - 7506858 RN - 0 (Chromogranin A) RN - 0 (Chromogranins) RN - 0 (Nerve Tissue Proteins) RN - 0 (RNA, Messenger) RN - 9007-49-2 (DNA) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Brain Chemistry MH - Calcium/metabolism MH - Chromaffin Granules/*analysis MH - Chromaffin System/*analysis MH - Chromogranin A MH - Chromogranins/*genetics MH - DNA/*analysis MH - Electrophoresis, Polyacrylamide Gel MH - Endocrine Glands/analysis MH - Molecular Weight MH - Nerve Tissue Proteins/*genetics MH - Nucleic Acid Hybridization MH - RNA, Messenger/analysis EDAT- 1987/01/01 MHDA- 1987/01/01 00:01 CRDT- 1987/01/01 00:00 PST - ppublish SO - Ann N Y Acad Sci. 1987;493:351-78. PMID- 2243113 OWN - NLM STAT- MEDLINE DA - 19901228 DCOM- 19901228 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 265 IP - 33 DP - 1990 Nov 25 TI - Zinc-induced secondary structure transitions in human sperm protamines. PG - 20667-72 AB - Using CD we show that human group II protamines undergo novel zinc-dependent secondary structure transitions. The CD spectra of protamine is characteristic of random coil proteins with a large minima at 197 nm. Upon the addition of 1 mM zinc, the magnitude of this minima is decreased by 44%. This spectral change is not induced by 1 mM calcium or magnesium. Cadmium, which has chemical properties similar to zinc, can also induce the structural transition although not as effectively as zinc. The spectral changes that accompany zinc binding are indicative of an increase in beta-turn and anti-parallel beta-sheet structures. This is consistent with the predicted secondary structure for protamines which is dominated by beta-turns. Our data support a model in which protamine adopts a folded structure in the presence of zinc. We propose that a zinc-modulated structure is physiologically significant considering the relatively high levels of zinc in human sperm. FAU - Gatewood, J M AU - Gatewood JM AD - Department of Chemistry, School of Medicine, University of California, Davis 95616. FAU - Schroth, G P AU - Schroth GP FAU - Schmid, C W AU - Schmid CW FAU - Bradbury, E M AU - Bradbury EM LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Protamines) RN - J41CSQ7QDS (Zinc) SB - IM MH - Amino Acid Sequence MH - Animals MH - Circular Dichroism MH - Humans MH - Kinetics MH - Male MH - Models, Structural MH - Molecular Sequence Data MH - Protamines/*metabolism MH - Protein Binding MH - Protein Conformation MH - Salmon MH - Sequence Homology, Nucleic Acid MH - Spermatozoa/*metabolism MH - Zinc/*pharmacology EDAT- 1990/11/25 MHDA- 1990/11/25 00:01 CRDT- 1990/11/25 00:00 PST - ppublish SO - J Biol Chem. 1990 Nov 25;265(33):20667-72. PMID- 19732855 OWN - NLM STAT- MEDLINE DA - 20100204 DCOM- 20100421 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1799 IP - 1-2 DP - 2010 Jan-Feb TI - HMGA molecular network: From transcriptional regulation to chromatin remodeling. PG - 37-47 LID - 10.1016/j.bbagrm.2009.08.009 [doi] AB - Nuclear functions rely on the activity of a plethora of factors which mostly work in highly coordinated molecular networks. The HMGA proteins are chromatin architectural factors which constitute critical hubs in these networks. HMGA are referred to as oncofetal proteins since they are highly expressed and play essential functions both during embryonic development and neoplastic transformation. A particular feature of HMGA is their intrinsically disordered status, which confers on them an unusual plasticity in contacting molecular partners. Indeed these proteins are able to bind to DNA at the level of AT-rich DNA stretches and to interact with several nuclear factors. In the post-genomic era, and with the advent of proteomic tools for the identification of protein-protein interactions, the number of HMGA molecular partners has increased rapidly. This has led to the extension of our knowledge of the functional involvement of HMGA from the transcriptional regulation field to RNA processing, DNA repair, and chromatin remodeling and dynamics. This review focuses mainly on the protein-protein interaction network of HMGA and its functional outcome. HMGA molecular partners have been functionally classified and all the information collected in a freely available database (http://www.bbcm.units.it/ approximately manfiol/INDEX.HTM). CI - Copyright 2009 Elsevier B.V. All rights reserved. FAU - Sgarra, Riccardo AU - Sgarra R AD - Department of Life Sciences, University of Trieste, via L. Giorgieri, 1-34127 Trieste, Italy. FAU - Zammitti, Salvina AU - Zammitti S FAU - Lo Sardo, Alessandra AU - Lo Sardo A FAU - Maurizio, Elisa AU - Maurizio E FAU - Arnoldo, Laura AU - Arnoldo L FAU - Pegoraro, Silvia AU - Pegoraro S FAU - Giancotti, Vincenzo AU - Giancotti V FAU - Manfioletti, Guidalberto AU - Manfioletti G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20090902 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (HMGA Proteins) SB - IM MH - Animals MH - Chromatin Assembly and Disassembly/*genetics MH - *Gene Regulatory Networks MH - HMGA Proteins/*metabolism MH - Humans MH - Models, Biological MH - *Transcription, Genetic RF - 68 EDAT- 2009/09/08 06:00 MHDA- 2010/04/22 06:00 CRDT- 2009/09/08 06:00 PHST- 2009/08/21 [received] PHST- 2009/08/24 [accepted] PHST- 2009/09/02 [aheadofprint] AID - S1874-9399(09)00103-5 [pii] AID - 10.1016/j.bbagrm.2009.08.009 [doi] PST - ppublish SO - Biochim Biophys Acta. 2010 Jan-Feb;1799(1-2):37-47. doi: 10.1016/j.bbagrm.2009.08.009. Epub 2009 Sep 2. PMID- 24957607 OWN - NLM STAT- MEDLINE DA - 20140801 DCOM- 20141014 LR - 20150603 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 42 IP - 13 DP - 2014 Jul TI - Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function. PG - 8705-18 LID - 10.1093/nar/gku468 [doi] AB - Glycine-rich RNA-binding proteins (GR-RBPs) are involved in cold shock response of plants as RNA chaperones facilitating mRNA transport, splicing and translation. GR-RBPs are bipartite proteins containing a RNA recognition motif (RRM) followed by a glycine-rich region. Here, we studied the structural basis of nucleic acid binding of full-length Nicotiana tabacum GR-RBP1. NMR studies of NtGR-RBP1 show that the glycine-rich domain, while intrinsically disordered, is responsible for mediating self-association by transient interactions with its RRM domain (NtRRM). Both NtGR-RBP1 and NtRRM bind specifically and with low micromolar affinity to RNA and single-stranded DNA. The solution structure of NtRRM shows that it is a canonical RRM domain. A HADDOCK model of the NtRRM-RNA complex, based on NMR chemical shift and NOE data, shows that nucleic acid binding results from a combination of stacking and electrostatic interactions with conserved RRM residues. Finally, DNA melting experiments demonstrate that NtGR-RBP1 is more efficient in melting CTG containing nucleic acids than isolated NtRRM. Together, our study supports the model that self-association of GR-RBPs by the glycine-rich region results in cooperative unfolding of non-native substrate structures, thereby enhancing its chaperone function. CI - (c) The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. FAU - Khan, Fariha AU - Khan F AD - NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Department of Biochemistry, PMAS Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan. FAU - Daniels, Mark A AU - Daniels MA AD - NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. FAU - Folkers, Gert E AU - Folkers GE AD - NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. FAU - Boelens, Rolf AU - Boelens R AD - NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. FAU - Saqlan Naqvi, S M AU - Saqlan Naqvi SM AD - Department of Biochemistry, PMAS Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan hugo.van.ingen@gmail.com. FAU - van Ingen, Hugo AU - van Ingen H AD - NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands hugo.van.ingen@gmail.com. LA - eng SI - PDB/4C7Q PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140623 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (DNA, Single-Stranded) RN - 0 (Plant Proteins) RN - 0 (RNA-Binding Proteins) RN - 0 (glycine-rich RNA-binding protein, plant) RN - 63231-63-0 (RNA) SB - IM MH - Amino Acid Sequence MH - Conserved Sequence MH - DNA, Single-Stranded/chemistry/metabolism MH - Nucleic Acid Denaturation MH - Plant Proteins/*chemistry/metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - RNA/chemistry/metabolism MH - RNA-Binding Proteins/*chemistry/metabolism MH - Static Electricity MH - *Tobacco PMC - PMC4117745 OID - NLM: PMC4117745 EDAT- 2014/06/25 06:00 MHDA- 2014/10/15 06:00 CRDT- 2014/06/25 06:00 PHST- 2014/06/23 [aheadofprint] AID - gku468 [pii] AID - 10.1093/nar/gku468 [doi] PST - ppublish SO - Nucleic Acids Res. 2014 Jul;42(13):8705-18. doi: 10.1093/nar/gku468. Epub 2014 Jun 23. PMID- 15294156 OWN - NLM STAT- MEDLINE DA - 20040805 DCOM- 20040901 LR - 20061115 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 118 IP - 3 DP - 2004 Aug 6 TI - Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription. PG - 297-309 AB - Bacterial transcription is regulated by the alarmone ppGpp, which binds near the catalytic site of RNA polymerase (RNAP) and modulates its activity. We show that the DksA protein is a crucial component of ppGpp-dependent regulation. The 2.0 A resolution structure of Escherichia coli DksA reveals a globular domain and a coiled coil with two highly conserved Asp residues at its tip that is reminiscent of the transcript cleavage factor GreA. This structural similarity suggests that DksA coiled coil protrudes into the RNAP secondary channel to coordinate a ppGpp bound Mg2+ ion with the Asp residues, thereby stabilizing the ppGpp-RNAP complex. Biochemical analysis demonstrates that DksA affects transcript elongation, albeit differently from GreA; augments ppGpp effects on initiation; and binds directly to RNAP, positioning the Asp residues near the active site. Substitution of these residues eliminates the synergy between DksA and ppGpp. Thus, the secondary channel emerges as a common regulatory entrance for transcription factors. FAU - Perederina, Anna AU - Perederina A AD - Cellular Signaling Laboratory, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan. FAU - Svetlov, Vladimir AU - Svetlov V FAU - Vassylyeva, Marina N AU - Vassylyeva MN FAU - Tahirov, Tahir H AU - Tahirov TH FAU - Yokoyama, Shigeyuki AU - Yokoyama S FAU - Artsimovitch, Irina AU - Artsimovitch I FAU - Vassylyev, Dmitry G AU - Vassylyev DG LA - eng SI - PDB/1TJL PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (Bacterial Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (GreA protein, E coli) RN - 0 (Transcription Factors) RN - 0 (dksA protein, E coli) RN - EC 3.1.7.2 (guanosine-3',5'-bis(diphosphate) 3'-pyrophosphatase) RN - EC 3.6.1.- (Pyrophosphatases) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/genetics/metabolism MH - Escherichia coli Proteins/chemistry/genetics/*metabolism MH - Gene Expression Regulation, Bacterial/*physiology MH - Molecular Sequence Data MH - Mutation MH - Protein Structure, Tertiary MH - Pyrophosphatases/*metabolism MH - Sequence Alignment MH - Transcription Factors/genetics MH - Transcription, Genetic/physiology EDAT- 2004/08/06 05:00 MHDA- 2004/09/02 05:00 CRDT- 2004/08/06 05:00 PHST- 2004/04/12 [received] PHST- 2004/06/02 [revised] PHST- 2004/06/04 [accepted] AID - 10.1016/j.cell.2004.06.030 [doi] AID - S0092867404006270 [pii] PST - ppublish SO - Cell. 2004 Aug 6;118(3):297-309. PMID- 9109385 OWN - NLM STAT- MEDLINE DA - 19970515 DCOM- 19970515 LR - 20131121 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 406 IP - 1-2 DP - 1997 Apr 7 TI - Nucleotide and calcium-induced conformational changes in histone H1. PG - 56-60 AB - The principal constituents of chromatin, histone H1 (H1) and the nucleosome have essential roles in regulation of eukaryotic gene expression. However, mechanisms for the H1-dependent inactivation and for the ATP-dependent chromatin remodeling upon activation are largely unelucidated. Using circular dichroism (CD) analysis we show that ATP and other nucleotides and Ca2+ induce structural changes in H1. ATP and Ca2+ also induce changes when H1 is interacting with DNA, and the changes in H1 are accompanied by alterations in its DNA interaction. These results suggest that nucleotide and Ca2+ binding may be important for H1-mediated chromatin changes. FAU - Tarkka, T AU - Tarkka T AD - Department of Applied Cell and Molecular Biology, University of Umea, Sweden. FAU - Oikarinen, J AU - Oikarinen J FAU - Grundstrom, T AU - Grundstrom T LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Adenine Nucleotides) RN - 0 (Histones) RN - 0 (Phosphates) RN - 9007-49-2 (DNA) RN - SY7Q814VUP (Calcium) SB - IM MH - Adenine Nucleotides/*chemistry MH - Animals MH - Calcium/*chemistry MH - Circular Dichroism MH - DNA/chemistry MH - Histones/*chemistry MH - Phosphates/chemistry MH - Protein Conformation MH - Protein Folding MH - Rats EDAT- 1997/04/07 MHDA- 1997/04/07 00:01 CRDT- 1997/04/07 00:00 AID - S0014-5793(97)00238-X [pii] PST - ppublish SO - FEBS Lett. 1997 Apr 7;406(1-2):56-60. PMID- 19235716 OWN - NLM STAT- MEDLINE DA - 20090303 DCOM- 20090504 IS - 1058-8388 (Print) IS - 1058-8388 (Linking) VI - 238 IP - 3 DP - 2009 Mar TI - Tubulin polymerization-promoting protein family member 3, Tppp3, is a specific marker of the differentiating tendon sheath and synovial joints. PG - 685-92 LID - 10.1002/dvdy.21865 [doi] AB - Tppp3, a member of the Tubulin polymerization-promoting protein family, is an intrinsically unstructured protein that induces tubulin polymerization. We show that Tppp3 is a distinct marker in the developing musculoskeletal system. In tendons, Tppp3 is expressed in cells at the circumference of the developing tendons, likely the progenitors of connective tissues that surround tendons: the tendon sheath, epitenon, and paratenon. These tissues form an elastic sleeve around tendons and provide lubrication to minimize friction between tendons and surrounding tissues. Tppp3 is the first molecular marker of the tendon sheath, opening the door for direct examination of these tissues. Tppp3 is also expressed in forming synovial joints. The onset of Tppp3 expression in joints coincides with cavitation, representing a molecular marker that can be used to indicate this stage in joint transition in joint differentiation. In late embryonic stages, Tppp3 expression highlights other demarcation lines that surround differentiating tissues in the forelimb. CI - (c) 2009 Wiley-Liss, Inc. FAU - Staverosky, Julia A AU - Staverosky JA AD - Shriners Hospital for Children, Research Division, Portland, Oregon 97239, USA. FAU - Pryce, Brian A AU - Pryce BA FAU - Watson, Spencer S AU - Watson SS FAU - Schweitzer, Ronen AU - Schweitzer R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Dev Dyn JT - Developmental dynamics : an official publication of the American Association of Anatomists JID - 9201927 RN - 0 (Biological Markers) RN - 0 (Ceacam9 protein, mouse) RN - 0 (Cell Adhesion Molecules) SB - IM MH - Animals MH - Biological Markers MH - Cell Adhesion Molecules/genetics/*metabolism MH - Cell Differentiation MH - Connective Tissue/embryology/metabolism MH - Gene Expression Regulation MH - Mice MH - Synovial Membrane/cytology/embryology/*metabolism MH - Tendons/cytology/embryology/*metabolism EDAT- 2009/02/25 09:00 MHDA- 2009/05/05 09:00 CRDT- 2009/02/25 09:00 AID - 10.1002/dvdy.21865 [doi] PST - ppublish SO - Dev Dyn. 2009 Mar;238(3):685-92. doi: 10.1002/dvdy.21865. PMID- 15667212 OWN - NLM STAT- MEDLINE DA - 20050125 DCOM- 20050308 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 44 IP - 4 DP - 2005 Feb 1 TI - Conformational changes in the alpha-subunit coupled to binding of the beta 2-subunit of tryptophan synthase from Escherichia coli: crystal structure of the tryptophan synthase alpha-subunit alone. PG - 1184-92 AB - When the tryptophan synthase alpha- and beta(2)-subunits combine to form the alpha(2)beta(2)-complex, the enzymatic activity of each subunit is stimulated by 1-2 orders of magnitude. To elucidate the structural basis of this mutual activation, it is necessary to determine the structures of the alpha- and beta-subunits alone and together with the alpha(2)beta(2)-complex. The crystal structures of the tryptophan synthase alpha(2)beta(2)-complex from Salmonella typhimurium (Stalpha(2)beta(2)-complex) have already been reported. However, the structures of the subunit alone from mesophiles have not yet been determined. The structure of the tryptophan synthase alpha-subunit alone from Escherichia coli (Ecalpha-subunit) was determined by an X-ray crystallographic analysis at 2.3 A, which is the first report on the subunits alone from the mesophiles. The biggest difference between the structures of the Ecalpha-subunit alone and the alpha-subunit in the Stalpha(2)beta(2)-complex (Stalpha-subunit) was as follows. Helix 2' in the Stalpha-subunit, including an active site residue (Asp60), was changed to a flexible loop in the Ecalpha-subunit alone. The conversion of the helix to a loop resulted in the collapse of the correct active site conformation. This region is also an important part for the mutual activation in the Stalpha(2)beta(2)-complex and interaction with the beta-subunit. These results suggest that the formation of helix 2'that is essential for the stimulation of the enzymatic activity of the alpha-subunit is constructed by the induced-fit mode involved in conformational changes upon interaction between the alpha- and beta-subunits. This also confirms the prediction of the conformational changes based on the thermodynamic analysis for the association between the alpha- and beta-subunits. FAU - Nishio, Kazuya AU - Nishio K AD - Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. FAU - Morimoto, Yukio AU - Morimoto Y FAU - Ishizuka, Manabu AU - Ishizuka M FAU - Ogasahara, Kyoko AU - Ogasahara K FAU - Tsukihara, Tomitake AU - Tsukihara T FAU - Yutani, Katsuhide AU - Yutani K LA - eng SI - PDB/1V7Y SI - PDB/1WQ5 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Escherichia coli Proteins) RN - 0 (Protein Subunits) RN - EC 4.2.1.20 (Tryptophan Synthase) SB - IM MH - Amino Acid Sequence MH - Crystallization MH - Crystallography, X-Ray MH - Enzyme Activation MH - Escherichia coli Proteins/*chemistry/isolation & purification/metabolism MH - Molecular Sequence Data MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Subunits/*chemistry/isolation & purification/metabolism MH - Salmonella typhimurium/*enzymology MH - Sequence Homology, Amino Acid MH - Thermodynamics MH - Tryptophan Synthase/*chemistry/isolation & purification/metabolism EDAT- 2005/01/26 09:00 MHDA- 2005/03/09 09:00 CRDT- 2005/01/26 09:00 AID - 10.1021/bi047927m [doi] PST - ppublish SO - Biochemistry. 2005 Feb 1;44(4):1184-92. PMID- 22405011 OWN - NLM STAT- MEDLINE DA - 20120312 DCOM- 20120629 LR - 20140220 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 20 IP - 3 DP - 2012 Mar 7 TI - Recognition pliability is coupled to structural heterogeneity: a calmodulin intrinsically disordered binding region complex. PG - 522-33 LID - 10.1016/j.str.2012.01.021 [doi] AB - Protein interactions within regulatory networks should adapt in a spatiotemporal-dependent dynamic environment, in order to process and respond to diverse and versatile cellular signals. However, the principles governing recognition pliability in protein complexes are not well understood. We have investigated a region of the intrinsically disordered protein myelin basic protein (MBP(145-165)) that interacts with calmodulin, but that also promiscuously binds other biomolecules (membranes, modifying enzymes). To characterize this interaction, we implemented an NMR spectroscopic approach that calculates, for each conformation of the complex, the maximum occurrence based on recorded pseudocontact shifts and residual dipolar couplings. We found that the MBP(145-165)-calmodulin interaction is characterized by structural heterogeneity. Quantitative comparative analysis indicated that distinct conformational landscapes of structural heterogeneity are sampled for different calmodulin-target complexes. Such structural heterogeneity in protein complexes could potentially explain the way that transient and promiscuous protein interactions are optimized and tuned in complex regulatory networks. CI - Copyright A(c) 2012 Elsevier Ltd. All rights reserved. FAU - Nagulapalli, Malini AU - Nagulapalli M AD - Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy. FAU - Parigi, Giacomo AU - Parigi G FAU - Yuan, Jing AU - Yuan J FAU - Gsponer, Joerg AU - Gsponer J FAU - Deraos, George AU - Deraos G FAU - Bamm, Vladimir V AU - Bamm VV FAU - Harauz, George AU - Harauz G FAU - Matsoukas, John AU - Matsoukas J FAU - de Planque, Maurits R R AU - de Planque MR FAU - Gerothanassis, Ioannis P AU - Gerothanassis IP FAU - Babu, M Madan AU - Babu MM FAU - Luchinat, Claudio AU - Luchinat C FAU - Tzakos, Andreas G AU - Tzakos AG LA - eng GR - MC_U105185859/Medical Research Council/United Kingdom GR - MOP 74468/Canadian Institutes of Health Research/Canada GR - Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Calmodulin) RN - 0 (Multiprotein Complexes) RN - 0 (Myelin Basic Protein) SB - IM MH - Binding Sites/genetics MH - Calmodulin/*chemistry/metabolism MH - *Models, Molecular MH - Multiprotein Complexes/*chemistry/metabolism MH - Myelin Basic Protein/*chemistry/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - *Protein Conformation EDAT- 2012/03/13 06:00 MHDA- 2012/06/30 06:00 CRDT- 2012/03/13 06:00 PHST- 2011/07/15 [received] PHST- 2011/12/01 [revised] PHST- 2012/01/03 [accepted] AID - S0969-2126(12)00052-4 [pii] AID - 10.1016/j.str.2012.01.021 [doi] PST - ppublish SO - Structure. 2012 Mar 7;20(3):522-33. doi: 10.1016/j.str.2012.01.021. PMID- 23864166 OWN - NLM STAT- MEDLINE DA - 20130816 DCOM- 20140401 IS - 0948-5023 (Electronic) IS - 0948-5023 (Linking) VI - 19 IP - 9 DP - 2013 Sep TI - Modeling and molecular dynamics of the intrinsically disordered e7 proteins from high- and low-risk types of human papillomavirus. PG - 4025-37 LID - 10.1007/s00894-013-1915-8 [doi] AB - Cervical cancer affects millions of women worldwide each year. Most cases of cervical cancer are caused by the sexually transmitted human papillomavirus (HPV). The approximately 40 HPV types that infect the cervix are designated high- or low-risk based on their potential to lead to high-grade lesions and cancer. The HPV E7 oncoprotein is directly involved in the onset of cervical cancer and associates with the pRb protein and other cellular targets that promote cell immortalization and carcinogenesis. This is the first description of the modeling and molecular dynamics analysis of complete three-dimensional structures of high-risk (HPV types 16 and 18), low-risk (HPV type 11), and HPV type 01 E7 proteins. The models were constructed by a hybrid approach using homology (MODELLER) and ab initio (Rosetta) modeling, and the protein dynamics were simulated for 50 ns under normal pressure and temperature (NPT) conditions. The intrinsic disorder of the E7 protein sequence was assessed in silico. Complete models of E7 were obtained despite the predicted intrinsic disorder of the N-termini from the high-risk HPV types. The N-terminal domains of all of the E7 proteins studied, even those from high-risk strains, exhibited secondary structure after modeling. Trajectory analysis of E7 proteins from HPV types 16 and 18 showed higher instability in their N-terminal domains than in those of HPV types 11 and 01; however, this variation did not affect the secondary structure during the simulation. ANCHOR analysis indicated that the CR1 and CR2 regions of HPV types 16 and 18 contain possible targets for future drug-discovery studies. FAU - Nicolau, Nilson Jr AU - Nicolau N Jr AD - Department of Genetics, School of Medicine of Ribeirao Preto, University of Sao Paulo, Av. Bandeirantes, 3900, Ribeirao Preto, SP, 14049-900, Brazil. FAU - Giuliatti, Silvana AU - Giuliatti S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130718 PL - Germany TA - J Mol Model JT - Journal of molecular modeling JID - 9806569 RN - 0 (Amino Acids) RN - 0 (DNA-Binding Proteins) RN - 0 (E7 protein, Human papillomavirus type 18) RN - 0 (E7 protein, human papillomavirus 11) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Oncogene Proteins, Viral) RN - 0 (Papillomavirus E7 Proteins) RN - 0 (oncogene protein E7, Human papillomavirus type 16) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Amino Acids/chemistry MH - Binding Sites MH - DNA-Binding Proteins/chemistry MH - Humans MH - Intrinsically Disordered Proteins/*chemistry MH - *Models, Molecular MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Oncogene Proteins, Viral/chemistry MH - Papillomavirus E7 Proteins/*chemistry MH - Protein Binding MH - Protein Conformation MH - Sequence Alignment EDAT- 2013/07/19 06:00 MHDA- 2014/04/02 06:00 CRDT- 2013/07/19 06:00 PHST- 2012/05/16 [received] PHST- 2013/06/09 [accepted] PHST- 2013/07/18 [aheadofprint] AID - 10.1007/s00894-013-1915-8 [doi] PST - ppublish SO - J Mol Model. 2013 Sep;19(9):4025-37. doi: 10.1007/s00894-013-1915-8. Epub 2013 Jul 18. PMID- 11294863 OWN - NLM STAT- MEDLINE DA - 20010625 DCOM- 20010816 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 26 DP - 2001 Jun 29 TI - Structure of a pilin monomer from Pseudomonas aeruginosa: implications for the assembly of pili. PG - 24186-93 AB - Type IV pilin monomers assemble to form fibers called pili that are required for a variety of bacterial functions. Pilin monomers oligomerize due to the interaction of part of their hydrophobic N-terminal alpha-helix. Engineering of a truncated pilin from Pseudomonas aeruginosa strain K122-4, where the first 28 residues are removed from the N terminus, yields a soluble, monomeric protein. This truncated pilin is shown to bind to its receptor and to decrease morbidity and mortality in mice upon administration 15 min before challenge with a heterologous strain of Pseudomonas. The structure of this truncated pilin reveals an alpha-helix at the N terminus that lies across a 4-stranded antiparallel beta-sheet. A model for a pilus is proposed that takes into account both electrostatic and hydrophobic interactions of pilin subunits as well as previously published x-ray fiber diffraction data. Our model indicates that DNA or RNA cannot pass through the center of the pilus, however, the possibility exists for small organic molecules to pass through indicating a potential mechanism for signal transduction. FAU - Keizer, D W AU - Keizer DW AD - Protein Engineering Network Centres of Excellence (PENCE), 713 Heritage Medical Research Centre, University of Alberta, Edmonton, Alberta T6G 2S2, Canada. FAU - Slupsky, C M AU - Slupsky CM FAU - Kalisiak, M AU - Kalisiak M FAU - Campbell, A P AU - Campbell AP FAU - Crump, M P AU - Crump MP FAU - Sastry, P A AU - Sastry PA FAU - Hazes, B AU - Hazes B FAU - Irvin, R T AU - Irvin RT FAU - Sykes, B D AU - Sykes BD LA - eng SI - PDB/1HPW PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20010409 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Outer Membrane Proteins) RN - 0 (Bacterial Proteins) RN - 0 (Bacterial Vaccines) RN - 0 (Membrane Proteins) RN - 0 (Peptide Fragments) RN - 0 (type IV pilin (29-150), Pseudomonas aeruginosa, K122-4 strain) RN - 147680-16-8 (Fimbriae Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Bacterial Outer Membrane Proteins/*chemistry/genetics/therapeutic use MH - Bacterial Proteins/*chemistry/genetics/*therapeutic use MH - Bacterial Vaccines MH - Binding, Competitive MH - Double-Blind Method MH - Fimbriae Proteins MH - Membrane Proteins/*chemistry/genetics/therapeutic use MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Peptide Fragments/*chemistry/genetics/*therapeutic use MH - Protein Structure, Tertiary MH - Pseudomonas Infections/therapy MH - Pseudomonas aeruginosa/immunology MH - Sequence Deletion MH - Sequence Homology, Amino Acid MH - Survival Rate EDAT- 2001/04/11 10:00 MHDA- 2001/08/17 10:01 CRDT- 2001/04/11 10:00 PHST- 2001/04/09 [aheadofprint] AID - 10.1074/jbc.M100659200 [doi] AID - M100659200 [pii] PST - ppublish SO - J Biol Chem. 2001 Jun 29;276(26):24186-93. Epub 2001 Apr 9. PMID- 21080428 OWN - NLM STAT- MEDLINE DA - 20101224 DCOM- 20110415 LR - 20140821 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 20 IP - 1 DP - 2011 Jan TI - Characterization of the disordered-to-alpha-helical transition of IA(3) by SDSL-EPR spectroscopy. PG - 150-9 LID - 10.1002/pro.547 [doi] AB - Electron paramagnetic resonance (EPR) spectroscopy coupled with site-directed spin labeling (SDSL) is a valuable tool for characterizing the mobility and conformational changes of proteins but has seldom been applied to intrinsically disordered proteins (IDPs). Here, IA(3) is used as a model system demonstrating SDSL-EPR characterization of conformational changes in small IDP systems. IA(3) has 68 amino acids, is unstructured in solution, and becomes alpha-helical upon addition of the secondary structural stabilizer 2,2,2-trifluoroethanol (TFE). Two single cysteine substitutions, one in the N-terminus (S14C) and one in the C-terminus (N58C), were generated and labeled with three different nitroxide spin labels. The resultant EPR line shapes of each of the labels were compared and each reported changes in mobility upon addition of TFE. Specifically, the spectral line shape parameters h((+1))/h((0)), the local tumbling volume (V(L)), and the percent change of the h((-)(1)) intensity were utilized to quantitatively monitor TFE-induced conformational changes. The values of h((+1)/)h((0)) as a function of TFE titration varied in a sigmoidal manner and were fit to a two-state Boltzmann model that provided values for the midpoint of the transition, thus, reporting on the global conformational change of IA(3). The other parameters provide site-specific information and show that S14C-SL undergoes a conformational change resulting in more restricted motion than N58C-SL, which is consistent with previously published results obtained by studies using NMR and circular dichroism spectroscopy indicating a higher degree of alpha-helical propensity of the N-terminal segment of IA(3). Overall, the results provide a framework for data analyzes that can be used to study induced unstructured-to-helical conformations in IDPs by SDSL. FAU - Pirman, Natasha L AU - Pirman NL AD - Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA. FAU - Milshteyn, Eugene AU - Milshteyn E FAU - Galiano, Luis AU - Galiano L FAU - Hewlett, Justin C AU - Hewlett JC FAU - Fanucci, Gail E AU - Fanucci GE LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Nitrogen Oxides) RN - 0 (PAI3 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Spin Labels) RN - 14332-28-6 (nitroxyl) SB - IM MH - Electron Spin Resonance Spectroscopy MH - Nitrogen Oxides/chemistry MH - Protein Structure, Secondary MH - Saccharomyces cerevisiae Proteins/*chemistry MH - Spin Labels PMC - PMC3047071 OID - NLM: PMC3047071 EDAT- 2010/11/17 06:00 MHDA- 2011/04/19 06:00 CRDT- 2010/11/17 06:00 AID - 10.1002/pro.547 [doi] PST - ppublish SO - Protein Sci. 2011 Jan;20(1):150-9. doi: 10.1002/pro.547. PMID- 24161561 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20131126 DCOM- 20131127 IS - 1096-0279 (Electronic) IS - 1046-5928 (Linking) VI - 93 DP - 2014 Jan TI - Novel high-performance purification protocol of recombinant CNBP suitable for biochemical and biophysical characterization. PG - 23-31 LID - 10.1016/j.pep.2013.10.006 [doi] LID - S1046-5928(13)00210-6 [pii] AB - Cellular nucleic acid binding protein (CNBP) is a highly conserved multi-zinc knuckle protein that enhances c-MYC expression, is related to certain human muscular diseases and is required for proper rostral head development. CNBP binds to single-stranded DNA (ssDNA) and RNA and acts as nucleic acid chaperone. Despite the advances made concerning CNBP biological roles, a full knowledge about the structure-function relationship has not yet been achieved, likely due to difficulty in obtaining pure and tag-free CNBP. Here, we report a fast, simple, reproducible, and high-performance expression and purification protocol that provides recombinant tag-free CNBP from Escherichia coli cultures. We determined that tag-free CNBP binds its molecular targets with higher affinity than tagged-CNBP. Furthermore, fluorescence spectroscopy revealed the presence of a unique and conserved tryptophan, which is exposed to the solvent and involved, directly or indirectly, in nucleic acid binding. Size-exclusion HPLC revealed that CNBP forms homodimers independently of nucleic acid binding and coexist with monomers as non-interconvertible forms or in slow equilibrium. Circular dichroism spectroscopy showed that CNBP has a secondary structure dominated by random-coil and beta-sheet coincident with the sequence-predicted repetitive zinc knuckles motifs, which folding is required for CNBP structural stability and biochemical activity. CNBP structural stability increased in the presence of single-stranded nucleic acid targets similar to other unstructured nucleic acid chaperones. Altogether, data suggest that CNBP is a flexible protein with interspersed structured zinc knuckles, and acquires a more rigid structure upon nucleic acid binding. CI - Copyright (c) 2013 Elsevier Inc. All rights reserved. FAU - Challier, Emilse AU - Challier E AD - Instituto de Biologia Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET) - Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, CCT-Rosario, Ocampo y Esmeralda, S2000FHQ Rosario, Argentina. FAU - Lisa, Maria-Natalia AU - Lisa MN FAU - Nerli, Bibiana B AU - Nerli BB FAU - Calcaterra, Nora B AU - Calcaterra NB FAU - Armas, Pablo AU - Armas P LA - eng PT - Journal Article DEP - 20131022 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 OTO - NOTNLM OT - Cellular nucleic acid binding protein OT - Intrinsic fluorescence quenching OT - Intrinsically unstructured protein OT - Nucleic acid binding OT - Proteolysis assay OT - Tag-free OT - Zinc knuckle EDAT- 2013/10/29 06:00 MHDA- 2013/10/29 06:01 CRDT- 2013/10/29 06:00 PHST- 2013/09/16 [received] PHST- 2013/10/13 [accepted] PHST- 2013/10/22 [aheadofprint] AID - S1046-5928(13)00210-6 [pii] AID - 10.1016/j.pep.2013.10.006 [doi] PST - ppublish SO - Protein Expr Purif. 2014 Jan;93:23-31. doi: 10.1016/j.pep.2013.10.006. Epub 2013 Oct 22. PMID- 22080214 OWN - NLM STAT- MEDLINE DA - 20111202 DCOM- 20120320 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Dynamic optimization of signal transduction via intrinsic disorder. PG - 194-7 LID - 10.1039/c1mb05412k [doi] AB - It is widely accepted that the inherent flexibility of intrinsically disordered proteins (IDPs) correlates with essential functions in the cell such as signaling. However, the mechanisms by which disorder dynamically facilitates and optimizes signal transduction remain unclear. In this study, we have used a computational protocol to evaluate the interplay between the intrinsic disorder of p27(kip1) and the collective motions of its binding partners, cyclin dependent kinase 2 (CDK2) and cyclin A (CA). We found that the synergy between intrinsic disorder of p27(kip1) and the essential collective motions of the CDK2-CA complex introduces a set of sequential steps to dynamically optimize signal transduction. Our observations indicate that optimized p27(kip1)-mediated signaling originates from a combination of adaptive folding, and the cooperativity between its residual disorder and the functional collective motions of the CDK2-CA complex. FAU - Espinoza-Fonseca, L Michel AU - Espinoza-Fonseca LM AD - Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA. mef@ddt.biochem.umn.edu LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111114 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Cyclin A) RN - 0 (Proteins) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 2) SB - IM MH - Animals MH - Crystallography, X-Ray MH - Cyclin A/chemistry/metabolism MH - Cyclin-Dependent Kinase 2/chemistry/metabolism MH - Cyclin-Dependent Kinase Inhibitor p27/chemistry/metabolism MH - Humans MH - Models, Molecular MH - Principal Component Analysis MH - Protein Conformation MH - *Protein Folding MH - Proteins/*chemistry/*metabolism MH - *Signal Transduction EDAT- 2011/11/15 06:00 MHDA- 2012/03/21 06:00 CRDT- 2011/11/15 06:00 PHST- 2011/11/14 [aheadofprint] PHST- 2011/12/01 [epublish] AID - 10.1039/c1mb05412k [doi] PST - ppublish SO - Mol Biosyst. 2012 Jan;8(1):194-7. doi: 10.1039/c1mb05412k. Epub 2011 Nov 14. PMID- 16542639 OWN - NLM STAT- MEDLINE DA - 20060327 DCOM- 20060524 LR - 20081121 IS - 0006-291X (Print) IS - 0006-291X (Linking) VI - 343 IP - 1 DP - 2006 Apr 28 TI - Biophysical characterisation reveals structural disorder in the nucleolar protein, Dribble. PG - 311-8 AB - Dribble (DBE) is an essential protein in Drosophila that belongs to the evolutionarily conserved Krr1p protein family. Proteins in this family are localised in the cell nucleolus and are important for the processing of ribosomal RNAs. However, little is known about their structural and biophysical properties. We have expressed and purified full-length DBE protein from Escherichia coli. Consistent with the native role of DBE in RNA processing, recombinant DBE was shown to bind RNA homo-polymers in vitro. By bioinformatics, size-exclusion chromatography, equilibrium sedimentation analysis, controlled proteolysis, and a variety of spectroscopic techniques, we have found that DBE is a monomeric protein in solution containing both alpha- and beta-structures. Moreover, the structure of DBE is expanded and significantly disordered (approximately 45% disordered). Natively disordered proteins are thought to provide a disproportionately large surface area and structural plasticity for nucleic acid binding. We therefore propose that the presence of structural disorder is an important feature of DBE that facilitates the protein to interact with RNAs in the nucleolus. FAU - Yiu, C-P Benny AU - Yiu CP AD - Laboratory of Drosophila Research, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China. FAU - Beavil, Rebecca L AU - Beavil RL FAU - Chan, H Y Edwin AU - Chan HY LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060306 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Drosophila Proteins) RN - 0 (Nuclear Proteins) RN - 0 (RNA-Binding Proteins) RN - 0 (Solvents) RN - 0 (dribble protein, Drosophila) RN - 63231-63-0 (RNA) SB - IM MH - Amino Acid Sequence MH - Animals MH - Biophysical Phenomena MH - Biophysics MH - Drosophila Proteins/biosynthesis/*chemistry/genetics MH - Drosophila melanogaster/metabolism MH - Molecular Sequence Data MH - Nuclear Proteins/biosynthesis/*chemistry/genetics MH - Protein Conformation MH - RNA/chemistry MH - RNA-Binding Proteins/biosynthesis/*chemistry/genetics MH - Solvents/chemistry EDAT- 2006/03/18 09:00 MHDA- 2006/05/25 09:00 CRDT- 2006/03/18 09:00 PHST- 2006/02/14 [received] PHST- 2006/02/24 [accepted] PHST- 2006/03/06 [aheadofprint] AID - S0006-291X(06)00462-1 [pii] AID - 10.1016/j.bbrc.2006.02.153 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2006 Apr 28;343(1):311-8. Epub 2006 Mar 6. PMID- 24043833 OWN - NLM STAT- MEDLINE DA - 20131002 DCOM- 20131203 LR - 20141112 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 110 IP - 40 DP - 2013 Oct 1 TI - Structural features of Argonaute-GW182 protein interactions. PG - E3770-9 LID - 10.1073/pnas.1308510110 [doi] AB - MicroRNAs (miRNAs) guide Argonaute (Ago) proteins to target mRNAs, leading to gene silencing. However, Ago proteins are not the actual mediators of gene silencing but interact with a member of the GW182 protein family (also known as GW proteins), which coordinates all downstream steps in gene silencing. GW proteins contain an N-terminal Ago-binding domain that is characterized by multiple GW repeats and a C-terminal silencing domain with several globular domains. Within the Ago-binding domain, Trp residues mediate the direct interaction with the Ago protein. Here, we have characterized the interaction of Ago proteins with GW proteins in molecular detail. Using biochemical and NMR experiments, we show that only a subset of Trp residues engage in Ago interactions. The Trp residues are located in intrinsically disordered regions, where flanking residues mediate additional weak interactions, that might explain the importance of specific tryptophans. Using cross-linking followed by mass spectrometry, we map the GW protein interactions with Ago2, which allows for structural modeling of Ago-GW182 interaction. Our data further indicate that the Ago-GW protein interaction might be a two-step process involving the sequential binding of two tryptophans separated by a spacer with a minimal length of 10 aa. FAU - Pfaff, Janina AU - Pfaff J AD - Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany. FAU - Hennig, Janosch AU - Hennig J FAU - Herzog, Franz AU - Herzog F FAU - Aebersold, Ruedi AU - Aebersold R FAU - Sattler, Michael AU - Sattler M FAU - Niessing, Dierk AU - Niessing D FAU - Meister, Gunter AU - Meister G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130916 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Argonaute Proteins) RN - 0 (Autoantigens) RN - 0 (EIF2C2 protein, human) RN - 0 (Multiprotein Complexes) RN - 0 (RNA-Binding Proteins) RN - 0 (autoantigen GW182, human) SB - IM MH - Argonaute Proteins/*chemistry/metabolism MH - Autoantigens/*chemistry/metabolism MH - Baculoviridae MH - Circular Dichroism MH - Fluorescence Polarization MH - Gene Expression Regulation/*genetics MH - Genetic Vectors MH - HEK293 Cells MH - Humans MH - Immunoprecipitation MH - Magnetic Resonance Spectroscopy MH - Mass Spectrometry MH - *Models, Molecular MH - Multiprotein Complexes/*chemistry/metabolism MH - Protein Binding MH - *Protein Conformation MH - RNA Interference MH - RNA-Binding Proteins/*chemistry/metabolism PMC - PMC3791723 OID - NLM: PMC3791723 OTO - NOTNLM OT - RNA interference OT - RNAi OT - gene regulation OT - small RNA-mediated gene silencing EDAT- 2013/09/18 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/09/18 06:00 PHST- 2013/09/16 [aheadofprint] AID - 1308510110 [pii] AID - 10.1073/pnas.1308510110 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):E3770-9. doi: 10.1073/pnas.1308510110. Epub 2013 Sep 16. PMID- 15304491 OWN - NLM STAT- MEDLINE DA - 20041108 DCOM- 20050121 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 46 DP - 2004 Nov 12 TI - Structural analysis of the complement control protein (CCP) modules of GABA(B) receptor 1a: only one of the two CCP modules is compactly folded. PG - 48292-306 AB - The gamma-aminobutyric acid type B (GABA(B)) receptor is a heterodimeric G-protein-coupled receptor. In humans, three splice variants of the GABA(B) receptor 1 (R1) subunit differ in having one, both, or neither of two putative complement control protein (CCP) modules at the extracellular N terminus, prior to the GABA-binding domain. The in vivo function of these predicted modules remains to be discovered, but a likely association with extracellular matrix proteins is intriguing. The portion of the GABA(B) R1a variant encompassing both of its CCP module-like sequences has been expressed, as have the sequences corresponding to each individual module. Each putative CCP module exhibits the expected pattern of disulfide formation. However, the second module (CCP2) is more compactly folded than the first, and the three-dimensional structure of this more C-terminal module (expressed alone) was solved on the basis of NMR-derived nuclear Overhauser effects. This revealed a strong similarity to previously determined CCP module structures in the regulators of complement activation. The N-terminal module (CCP1) displayed conformational heterogeneity under a wide range of conditions whether expressed alone or together with CCP2. Several lines of evidence indicated the presence of native disorder in CCP1, despite the fact that recombinant CCP1 contributes to binding to the extracellular matrix protein fibulin-2. Thus, we have shown that the two CCP modules of GABA(B) R1a have strikingly different structural properties, reflecting their different functions. FAU - Blein, Stanislas AU - Blein S AD - Edinburgh Protein Interaction Centre, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, United Kingdom. FAU - Ginham, Rachel AU - Ginham R FAU - Uhrin, Dusan AU - Uhrin D FAU - Smith, Brian O AU - Smith BO FAU - Soares, Dinesh C AU - Soares DC FAU - Veltel, Stefvan AU - Veltel S FAU - McIlhinney, R A Jeffrey AU - McIlhinney RA FAU - White, Julia H AU - White JH FAU - Barlow, Paul N AU - Barlow PN LA - eng SI - PDB/1SRZ SI - PDB/1SS2 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040809 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Calcium-Binding Proteins) RN - 0 (Disulfides) RN - 0 (Extracellular Matrix Proteins) RN - 0 (Peptide Fragments) RN - 0 (Protein Isoforms) RN - 0 (Receptors, GABA-B) RN - 0 (fibulin 2) SB - IM MH - Animals MH - Calcium-Binding Proteins/genetics/metabolism MH - Calorimetry, Differential Scanning MH - Circular Dichroism MH - Disulfides MH - Extracellular Matrix Proteins/genetics/metabolism MH - Humans MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/*chemistry/genetics/metabolism MH - Protein Binding MH - Protein Denaturation MH - Protein Isoforms/chemistry/genetics/metabolism MH - *Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Rats MH - Receptors, GABA-B/*chemistry/genetics/metabolism MH - Two-Hybrid System Techniques EDAT- 2004/08/12 05:00 MHDA- 2005/01/22 09:00 CRDT- 2004/08/12 05:00 PHST- 2004/08/09 [aheadofprint] AID - 10.1074/jbc.M406540200 [doi] AID - M406540200 [pii] PST - ppublish SO - J Biol Chem. 2004 Nov 12;279(46):48292-306. Epub 2004 Aug 9. PMID- 12211008 OWN - NLM STAT- MEDLINE DA - 20020904 DCOM- 20021003 LR - 20071114 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 49 IP - 2 DP - 2002 Nov 1 TI - NMR structure of the Escherichia coli protein YacG: a novel sequence motif in the zinc-finger family of proteins. PG - 289-93 FAU - Ramelot, Theresa A AU - Ramelot TA AD - Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA. FAU - Cort, John R AU - Cort JR FAU - Yee, Adelinda A AU - Yee AA FAU - Semesi, Anthony AU - Semesi A FAU - Edwards, Aled M AU - Edwards AM FAU - Arrowsmith, Cheryl H AU - Arrowsmith CH FAU - Kennedy, Michael A AU - Kennedy MA LA - eng GR - P50-GM62413/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Escherichia coli Proteins) RN - 0 (YacG protein, E coli) SB - IM MH - Amino Acid Sequence MH - Escherichia coli Proteins/*chemistry MH - *Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Sequence Alignment MH - Zinc Fingers EDAT- 2002/09/05 10:00 MHDA- 2002/10/04 04:00 CRDT- 2002/09/05 10:00 AID - 10.1002/prot.10214 [doi] PST - ppublish SO - Proteins. 2002 Nov 1;49(2):289-93. PMID- 7500341 OWN - NLM STAT- MEDLINE DA - 19960118 DCOM- 19960118 LR - 20080814 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 254 IP - 4 DP - 1995 Dec 8 TI - Three-dimensional dimer structure of the lambda-Cro repressor in solution as determined by heteronuclear multidimensional NMR. PG - 668-80 AB - The 1H, 15N and 13C magnetic resonances of the lambda-Cro repressor have been assigned almost completely, mainly through the use of heteronuclear multidimensional NMR methods. Inter-subunit NOEs were distinguished by means of heteronuclear spectral editing technique (13C double half filter technique). Based on the distance and dihedral angle constraints derived from the NMR data, the three-dimensional solution structure of the lambda-Cro repressor in the dimeric form has been calculated by the simulated annealing method. The input for the structure calculations consisted of 1H-1H distance constraints, of which 1536 were intra-subunit and 40 were inter-subunit, and dihedral angle, phi, constraints, which numbered 92. The average root-mean-square deviation (RMSD) for all backbone heavy- atoms of the 20 calculated structures for residues 3 to 59 of the total of 66 amino acid residues in both subunits was 1.57 Angstrum, while the average RMSD for each subunit in the same residue range was 0.66 Angstrum. The subunit is composed of three alpha-helices, residues 7 to 13, 16 to 23 and 27 to 36, and a three-stranded anti-parallel beta-sheet composed of residues 3 to 6, 40 to 44 and 50 to 55. The solution structure of the subunit is essentially the same as that in the crystalline form, but the structure of the dimer form in solution differs from that of the dimer unit in the crystalline form. It is suggested that the solution dimer structure is distorted to fit the recognition helices in the major grooves of DNA on complex formation. FAU - Matsuo, H AU - Matsuo H AD - Institute for Protein Research, Osaka University, Japan. FAU - Shirakawa, M AU - Shirakawa M FAU - Kyogoku, Y AU - Kyogoku Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DNA-Binding Proteins) RN - 0 (Repressor Proteins) RN - 0 (Solutions) RN - 0 (Viral Proteins) RN - 0 (Viral Regulatory and Accessory Proteins) RN - 0 (phage repressor proteins) SB - IM MH - Amino Acid Sequence MH - *DNA-Binding Proteins MH - Magnetic Resonance Spectroscopy/*methods MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Repressor Proteins/*chemistry MH - Solutions MH - Viral Proteins MH - Viral Regulatory and Accessory Proteins EDAT- 1995/12/08 MHDA- 1995/12/08 00:01 CRDT- 1995/12/08 00:00 AID - S0022-2836(85)70646-8 [pii] AID - 10.1006/jmbi.1995.0646 [doi] PST - ppublish SO - J Mol Biol. 1995 Dec 8;254(4):668-80. PMID- 22760334 OWN - NLM STAT- MEDLINE DA - 20120704 DCOM- 20121024 LR - 20131121 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 895 DP - 2012 TI - Fluorescence lifetime measurements of intrinsically unstructured proteins: application to alpha-synuclein. PG - 461-6 LID - 10.1007/978-1-61779-927-3_27 [doi] AB - Lifetimes of fluorescent states and their fluorescence intensities are strictly coupled and very sensitive to the environment of the fluorophores. The advantage of measuring lifetimes, next to intensities, comes from the fact that it can reveal heterogeneity and dynamic properties of this environment. In this way lifetime analysis can be used to characterize static and dynamic conformational properties and heterogeneity of fluorescent groups in different areas of a protein and as a function of time for an evolving protein. The phenomena that determine the lifetime of a label are its intrinsic properties, dynamic quenching by neighboring groups, exposure to the solvent, as well as Forster resonance energy transfer (FRET) between different groups. The basic principles of these fluorescence phenomena can be found extensively described in the excellent book of Lakowicz (Principles of fluorescence spectroscopy, 3rd edn. Springer, New York, 2006). The fluorescent groups involved are either natural amino acid side chains like tryptophan (Trp) or tyrosine (Tyr), or fluorescent labels covalently engineered into the protein. Even a single fluorescent group can show indications of heterogeneity in the local environment. If several natural fluorescent groups are present, the properties of the individual groups can be separated using site-directed mutagenesis, and additivity of their contributions can be analyzed (Engelborghs, Spectrochim Acta A Mol Biomol Spectrosc 57(11):2255-2270, 2001). If no fluorescent group is naturally present, site-directed mutagenesis can be used to introduce either a fluorescent amino acid or a cysteine allowing chemical labeling. FAU - Schreurs, Sarah AU - Schreurs S AD - Laboratory of Biomolecular Dynamics, University of Leuven, Leuven, Belgium. FAU - Kluba, Malgorzata AU - Kluba M FAU - Meuvis, Jessika AU - Meuvis J FAU - Engelborghs, Yves AU - Engelborghs Y LA - eng PT - Journal Article PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (Fluorescent Dyes) RN - 0 (Naphthalenesulfonates) RN - 0 (alpha-Synuclein) RN - 3604-79-3 (3-nitrotyrosine) RN - 42HK56048U (Tyrosine) RN - 6V7G304M5M (1,5-I-AEDANS) RN - 8DUH1N11BX (Tryptophan) SB - IM MH - Algorithms MH - Amino Acid Substitution MH - Anisotropy MH - Fluorescence Resonance Energy Transfer MH - Fluorescent Dyes/chemistry MH - Naphthalenesulfonates/chemistry MH - Protein Conformation MH - Spectrometry, Fluorescence MH - Staining and Labeling MH - Tryptophan/chemistry MH - Tyrosine/analogs & derivatives/chemistry MH - alpha-Synuclein/*chemistry/genetics EDAT- 2012/07/05 06:00 MHDA- 2012/10/25 06:00 CRDT- 2012/07/05 06:00 AID - 10.1007/978-1-61779-927-3_27 [doi] PST - ppublish SO - Methods Mol Biol. 2012;895:461-6. doi: 10.1007/978-1-61779-927-3_27. PMID- 16037492 OWN - NLM STAT- MEDLINE DA - 20060113 DCOM- 20070625 IS - 0959-6658 (Print) IS - 0959-6658 (Linking) VI - 16 IP - 2 DP - 2006 Feb TI - Structures and mechanisms of glycosyltransferases. PG - 29R-37R AB - Glycosyltransferases (GTs) catalyze the transfer of a sugar moiety from an activated donor sugar onto saccharide and nonsaccharide acceptors. A sequence-based classification spreads GTs in many families thus reflecting the variety of molecules that can be used as acceptors. In contrast, this enzyme family is characterized by a more conserved three-dimensional architecture. Until recently, only two different folds (GT-A and GT-B) have been identified for solved crystal structures. The recent report of a structure for a bacterial sialyltransferase allows the definition of a new fold family. Progress in the elucidation of the structures and mechanisms of GTs are discussed in this review. To accommodate the growing number of crystal structures, we created the 3D-Glycosyltransferase database to gather structural information concerning this class of enzymes. FAU - Breton, Christelle AU - Breton C AD - CERMAV-CNRS, Universite Joseph Fourier, PO Box 53,38041 Grenoble cedex 9 France. breton@cermav.cnrs.fr FAU - Snajdrova, Lenka AU - Snajdrova L FAU - Jeanneau, Charlotte AU - Jeanneau C FAU - Koca, Jaroslav AU - Koca J FAU - Imberty, Anne AU - Imberty A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20050721 PL - England TA - Glycobiology JT - Glycobiology JID - 9104124 RN - EC 2.4.- (Glycosyltransferases) SB - IM MH - Animals MH - Glycosyltransferases/*chemistry/*metabolism MH - Humans MH - Models, Molecular MH - Structure-Activity Relationship RF - 73 EDAT- 2005/07/23 09:00 MHDA- 2007/06/26 09:00 CRDT- 2005/07/23 09:00 PHST- 2005/07/21 [aheadofprint] AID - cwj016 [pii] AID - 10.1093/glycob/cwj016 [doi] PST - ppublish SO - Glycobiology. 2006 Feb;16(2):29R-37R. Epub 2005 Jul 21. PMID- 17437522 OWN - NLM STAT- MEDLINE DA - 20070501 DCOM- 20070626 IS - 1742-464X (Print) IS - 1742-464X (Linking) VI - 274 IP - 10 DP - 2007 May TI - Biochemical characterization of the recombinant human Nogo-A ectodomain. PG - 2603-13 AB - Nogo-A is a physiologically relevant inhibitor of neuronal growth and regeneration in the myelin of the adult human central nervous system and has attracted considerable attention as a molecular target for the treatment of spinal cord injuries. To gain insight into the structural and functional properties of the large extramembrane region that is characteristic for the Nogo-A splice form of this member of the Reticulon family of membrane proteins, we cloned and expressed the region comprising residues 334-966 as a soluble homogeneous protein in the periplasm of Escherichia coli. SDS/PAGE, under nonreducing conditions, and a systematic substitution analysis of all six Cys residues of Nogo-A indicated that this domain forms two structural disulfide bonds among Cys residues 424, 464, 559 and 597, whereas the Cys residues at positions 699 and 912 seem to be dispensable for folding. The occurrence of a hot spot for host cell proteases and a limited proteolysis experiment suggest that the N-terminal region of Nogo-A up to residue 373 is structurally disordered. Although analytical gel permeation chromatography revealed a large apparent molecular size for the recombinant Nogo-A fragment, indicating oligomer formation, data from analytical ultracentrifugation and dynamic light scattering support a stable monomeric quaternary structure. Notably, the CD spectrum is indicative of a high content of random coil, such that Nogo-A exhibits--at least in part--features of a natively unfolded protein. Nevertheless, the protein fragment identified in this study, as well as its biochemical analysis, provide a promising starting point for future investigations to track down globular subdomains and functionally important regions as well as putative receptor-binding sites therein. FAU - Zander, Hilke AU - Zander H AD - Lehrstuhl fur Biologische Chemie, Technische Universitat Munchen, Freising, Weihenstephan, Germany. FAU - Hettich, Eva AU - Hettich E FAU - Greiff, Kathrin AU - Greiff K FAU - Chatwell, Lorenz AU - Chatwell L FAU - Skerra, Arne AU - Skerra A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070416 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Disulfides) RN - 0 (Myelin Proteins) RN - 0 (Nogo protein) RN - 0 (Recombinant Proteins) SB - IM MH - Circular Dichroism MH - Cloning, Molecular MH - Disulfides/analysis MH - Electrophoresis, Polyacrylamide Gel MH - Escherichia coli/metabolism MH - Humans MH - Myelin Proteins/*chemistry MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry EDAT- 2007/04/18 09:00 MHDA- 2007/06/27 09:00 CRDT- 2007/04/18 09:00 PHST- 2007/04/16 [aheadofprint] AID - EJB5796 [pii] AID - 10.1111/j.1742-4658.2007.05796.x [doi] PST - ppublish SO - FEBS J. 2007 May;274(10):2603-13. Epub 2007 Apr 16. PMID- 24787448 OWN - NLM STAT- MEDLINE DA - 20140828 DCOM- 20150526 IS - 1756-2651 (Electronic) IS - 0021-924X (Linking) VI - 156 IP - 3 DP - 2014 Sep TI - The staphylococcal elastin-binding protein regulates zinc-dependent growth/biofilm formation. PG - 155-62 LID - 10.1093/jb/mvu027 [doi] AB - Staphylococcus aureus is one of the most important human pathogens because it is a common cause of nosocomial infections. The elastin-binding protein of Staphylococcus aureus (EbpS) is an adhesin that is responsible for attachment to host cells via its binding to elastin. Despite its relatively weak contribution to adhesion, the ebpS gene is highly conserved among S. aureus isolates, suggesting that EbpS may have other crucial functions. Here, we found that EbpS binds Zn(2+) with its N-terminal region, which leads to local conformational changes that result in the assembly of the EbpS protein. The growth rate of the EbpS-deficient strain was considerably decreased. Zn(2+) chelation decreased the growth rate of the wild-type strain but did not alter that of the EbpS-deficient strain. Furthermore, biofilm formation by the EbpS-deficient strain was abnormally enhanced in the Zn(2+) concentration-dependent manner. All the results suggest that ebpS deficiency led to a zinc concentration-dependent inability to modulate the growth/biofilm maturation phase appropriately. Given the high conservation of ebpS and that appropriate regulation of biofilm formation is thought to be essential for effective staphylococcal infection, inhibition of EbpS binding to Zn(2+) could lead to the development of novel therapeutic strategies for controlling S. aureus infections. CI - (c) The Authors 2014. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved. FAU - Nakakido, Makoto AU - Nakakido M AD - Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; Division of Bacteriology, International Research Center for infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; Division of Bacteriology, International Research Center for infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. FAU - Aikawa, Chihiro AU - Aikawa C AD - Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; Division of Bacteriology, International Research Center for infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; Division of Bacteriology, International Research Center for infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato- FAU - Nakagawa, Ichiro AU - Nakagawa I AD - Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; Division of Bacteriology, International Research Center for infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; Division of Bacteriology, International Research Center for infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan ichiro-n.bac@tmd.ac.jp. FAU - Tsumoto, Kouhei AU - Tsumoto K AD - Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; Division of Bacteriology, International Research Center for infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; Division of Bacteriology, International Research Center for infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; and Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato- LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140429 PL - England TA - J Biochem JT - Journal of biochemistry JID - 0376600 RN - 0 (Adhesins, Bacterial) RN - 0 (Bacterial Proteins) RN - 0 (Receptors, Cell Surface) RN - 0 (elastin-binding proteins) RN - 9007-58-3 (Elastin) RN - J41CSQ7QDS (Zinc) SB - IM MH - Adhesins, Bacterial/genetics/*metabolism MH - Bacterial Proteins/genetics/*metabolism/ultrastructure MH - Biofilms/*growth & development MH - Calorimetry/methods MH - Circular Dichroism MH - Elastin/metabolism MH - Electrophoresis, Polyacrylamide Gel MH - Microscopy, Electron, Transmission MH - Mutation MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Receptors, Cell Surface/chemistry/genetics/*metabolism MH - Scattering, Small Angle MH - Staphylococcus aureus/genetics/*metabolism/physiology MH - X-Ray Diffraction MH - Zinc/chemistry/*metabolism OTO - NOTNLM OT - Staphylococcus aureus OT - biofilm OT - elastin-binding protein OT - intrinsically disordered protein OT - zinc EDAT- 2014/05/03 06:00 MHDA- 2015/05/27 06:00 CRDT- 2014/05/03 06:00 PHST- 2014/04/29 [aheadofprint] AID - mvu027 [pii] AID - 10.1093/jb/mvu027 [doi] PST - ppublish SO - J Biochem. 2014 Sep;156(3):155-62. doi: 10.1093/jb/mvu027. Epub 2014 Apr 29. PMID- 12223444 OWN - NLM STAT- MEDLINE DA - 20021031 DCOM- 20021216 LR - 20131121 IS - 1530-6860 (Electronic) IS - 0892-6638 (Linking) VI - 16 IP - 13 DP - 2002 Nov TI - A concerted, rational design of type 1 17beta-hydroxysteroid dehydrogenase inhibitors: estradiol-adenosine hybrids with high affinity. PG - 1829-31 AB - Human estrogenic 17beta-hydroxysteroid dehydrogenase (17beta-HSD type 1) catalyzes the final step in the synthesis of active estrogens that stimulate the proliferation of breast cancer cells. Based on the initial premise to make use of the binding energies of both the substrate and cofactor sites, and molecular modeling starting from the enzyme structure, several estradiol-adenosine hybrids were designed and synthesized. Among these hybrids, EM-1745 with a linker of 8-CH2 groups is proved to be the best competitive inhibitor with a Ki of 3.0 +/- 0.8 nM. The crystal structure of the EM-1745 enzyme complex at 1.6 A provides evidence at atomic resolution of strong interactions between both the steroid and cofactor moieties and the enzyme molecule, as illustrated by a deltaA-weighted 2Fo-Fc electron density map contoured at 3.0 delta. The substrate entry loop is further stabilized in this complex compared with previous complexes of the enzyme. These results confirm our initial strategy of combining studies of structural biology and enzyme mechanism in the inhibitor design, which may be applied to other steroidogenic enzymes involved in human diseases. FAU - Qiu, Wei AU - Qiu W AD - Oncology and Molecular Endocrinology Research Center, Laval University Medical Center (CHUL) and Laval University, Quebec, G1V 4G2, Canada. FAU - Campbell, Robert L AU - Campbell RL FAU - Gangloff, Anne AU - Gangloff A FAU - Dupuis, Philippe AU - Dupuis P FAU - Boivin, Roch P AU - Boivin RP FAU - Tremblay, Martin R AU - Tremblay MR FAU - Poirier, Donald AU - Poirier D FAU - Lin, Sheng-Xiang AU - Lin SX LA - eng PT - Journal Article DEP - 20020905 PL - United States TA - FASEB J JT - FASEB journal : official publication of the Federation of American Societies for Experimental Biology JID - 8804484 RN - 0 (Enzyme Inhibitors) RN - 4TI98Z838E (Estradiol) RN - EC 1.1.- (17-Hydroxysteroid Dehydrogenases) RN - EC 1.1.1.51 (3 (or 17)-beta-hydroxysteroid dehydrogenase) RN - K72T3FS567 (Adenosine) SB - IM MH - 17-Hydroxysteroid Dehydrogenases/*antagonists & inhibitors/chemistry/metabolism MH - Adenosine/chemistry/metabolism/pharmacology MH - Binding, Competitive MH - Crystallography, X-Ray MH - Drug Design MH - Enzyme Inhibitors/*chemistry/metabolism/pharmacology MH - Estradiol/chemistry/metabolism/pharmacology MH - Kinetics MH - Models, Molecular MH - Protein Conformation EDAT- 2002/09/12 10:00 MHDA- 2002/12/18 04:00 CRDT- 2002/09/12 10:00 PHST- 2002/09/05 [aheadofprint] AID - 10.1096/fj.02-0026fje [doi] AID - 02-0026fje [pii] PST - ppublish SO - FASEB J. 2002 Nov;16(13):1829-31. Epub 2002 Sep 5. PMID- 11790096 OWN - NLM STAT- MEDLINE DA - 20020115 DCOM- 20020213 LR - 20091119 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 41 IP - 3 DP - 2002 Jan 22 TI - Functional consequences of preorganized helical structure in the intrinsically disordered cell-cycle inhibitor p27(Kip1). PG - 752-9 AB - p27(Kip1) contributes to cell-cycle regulation by inhibiting cyclin-dependent kinase (Cdk) activity. The p27 Cdk-inhibition domain has an ordered conformation comprising an alpha-helix, a 3(10) helix, and beta-structure when bound to cyclin A-Cdk2. In contrast, the unbound p27 Cdk-inhibition domain is intrinsically disordered (natively unfolded) as shown by circular dichroism spectroscopy, lack of chemical-shift dispersion, and negative heteronuclear nuclear Overhauser effects. The intrinsic disorder is not due to the excision of the Cdk-inhibition domain from p27, since circular dichroism spectra of the full-length protein are also indicative of a largely unfolded protein. Both the inhibition domain and full-length p27 are active as cyclin A-Cdk2 inhibitors. Using circular dichroism and proline mutagenesis, we demonstrate that the unbound p27 Cdk-inhibition domain is not completely unfolded. The domain contains marginally stable helical structure that presages the alpha-helix, but not the 3(10) helix, adopted upon binding cyclin A-Cdk2. Increasing or reducing the stability of the partially preformed alpha-helix in the isolated p27 domain with alanine or proline substitutions did not affect formation of the p27-inhibited cyclin A-Cdk2 complex in energetic terms. However, stabilization of the helix with alanine hindered kinetically the formation of the inhibited complex, suggesting that p27 derives a kinetic advantage from intrinsic structural disorder. FAU - Bienkiewicz, Ewa A AU - Bienkiewicz EA AD - Department of Biochemistry and Molecular Biology, Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1870, USA. FAU - Adkins, Joshua N AU - Adkins JN FAU - Lumb, Kevin J AU - Lumb KJ LA - eng GR - GM55156/GM/NIGMS NIH HHS/United States GR - RR11981/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cell Cycle Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Tumor Suppressor Proteins) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - EC 2.7.11.22 (Cyclin-Dependent Kinases) SB - IM MH - Amino Acid Substitution MH - Binding Sites MH - Cell Cycle Proteins/*chemistry/metabolism MH - Circular Dichroism MH - Cyclin-Dependent Kinase Inhibitor p27 MH - Cyclin-Dependent Kinases/antagonists & inhibitors MH - Humans MH - Kinetics MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Phosphorylation MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Spectrophotometry, Ultraviolet MH - Thermodynamics MH - Tumor Suppressor Proteins/*chemistry/metabolism EDAT- 2002/01/16 10:00 MHDA- 2002/02/14 10:01 CRDT- 2002/01/16 10:00 AID - bi015763t [pii] PST - ppublish SO - Biochemistry. 2002 Jan 22;41(3):752-9. PMID- 19136012 OWN - NLM STAT- MEDLINE DA - 20090209 DCOM- 20090220 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 386 IP - 2 DP - 2009 Feb 20 TI - The desmoglein-specific cytoplasmic region is intrinsically disordered in solution and interacts with multiple desmosomal protein partners. PG - 531-43 LID - 10.1016/j.jmb.2008.12.054 [doi] AB - The desmoglein-specific cytoplasmic region (DSCR) is a conserved region of unknown structure and function that uniquely defines the desmoglein family of cell adhesion molecules. It is the site of caspase cleavage during apoptosis, and its mutation is linked to cardiomyopathy. Here, we reveal that a 276-residue DSCR construct of human desmoglein 1 is intrinsically disordered and forms an interaction hub for desmosomal proteins. In solution, it contains 6.5% helical and 10.3% beta-strand structure based on circular dichroism spectroscopy. A single monomeric state with a predominantly unfolded structure is found by size-exclusion chromatography and analytical ultracentrifugation. Thermal stability assays and nuclear magnetic resonance spectroscopy reveal a nonglobular structure under a range of solution conditions. However, the introduction of detergent micelles increases structure to 18% helical and 16% beta-strand character, suggesting an inducible structure. The DSCR exhibits weak but specific interactions with plakoglobin, the plakin domain of desmoplakin, plakophilin 1, and the cytoplasmic domain of desmocollin 1. The desmoglein 1 membrane proximal region also interacts with all four DSCR ligands, strongly with plakoglobin and plakophilin and more weakly with desmoplakin and desmocollin 1. Thus, the DSCR is an intrinsically disordered functional domain with an inducible structure that, along with the membrane proximal region, forms a flexible scaffold for cytoplasmic assembly at the desmosome. FAU - Kami, Keiichiro AU - Kami K AD - University of Birmingham, UK. FAU - Chidgey, Martyn AU - Chidgey M FAU - Dafforn, Timothy AU - Dafforn T FAU - Overduin, Michael AU - Overduin M LA - eng GR - Biotechnology and Biological Sciences Research Council/United Kingdom GR - Cancer Research UK/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20081230 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DSC1 protein, human) RN - 0 (DSG1 protein, human) RN - 0 (Desmocollins) RN - 0 (Desmoglein 1) RN - 0 (Desmoplakins) RN - 0 (JUP protein, human) RN - 0 (PKP1 protein, human) RN - 0 (Plakophilins) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Desmocollins/*metabolism MH - Desmoglein 1/*chemistry/*metabolism MH - Desmoplakins/*metabolism MH - Humans MH - Molecular Sequence Data MH - Plakophilins/*metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Sequence Alignment EDAT- 2009/01/13 09:00 MHDA- 2009/02/21 09:00 CRDT- 2009/01/13 09:00 PHST- 2008/11/03 [received] PHST- 2008/12/18 [revised] PHST- 2008/12/19 [accepted] PHST- 2008/12/30 [aheadofprint] AID - S0022-2836(08)01576-3 [pii] AID - 10.1016/j.jmb.2008.12.054 [doi] PST - ppublish SO - J Mol Biol. 2009 Feb 20;386(2):531-43. doi: 10.1016/j.jmb.2008.12.054. Epub 2008 Dec 30. PMID- 14654701 OWN - NLM STAT- MEDLINE DA - 20031205 DCOM- 20040114 LR - 20140610 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 31 IP - 24 DP - 2003 Dec 15 TI - Residues 190-210 of human topoisomerase I are required for enzyme activity in vivo but not in vitro. PG - 7255-63 AB - DNA-topoisomerase I (topo I) unwinds the DNA- double helix by cutting one strand and allowing rotation of the other. In vitro, this function does not require the N-terminal domain of the enzyme, which is believed to regulate cellular properties. To assess this role, we studied the cellular distribution and mobility of green fluorescent protein-chimera of human topo I lacking either the entire N-terminal domain or a portion of it. We find that topo I truncated up to position 210 is not stabilized by camptothecin in covalent DNA-complexes inside a living cell, whereas in vitro it retains full DNA-relaxation activity, and is targeted by camptothecin in the usual manner. This difference is not shared with a fragment lacking the N-terminal domain up to position 190, indicating that residues 190-210 play a crucial role for the activity of the enzyme in its physiological environment, but not in vitro. Since it is impossible to discriminate in vivo whether this region is required for topo I to form covalent DNA intermediates in the cell, or just for camptothecin to bind and stabilize such complexes, we could not explain precisely these cellular observations. However, inactivity in vivo of the enzyme lacking this region is indicated by a lesser cytotoxicity. FAU - Christensen, Morten O AU - Christensen MO AD - Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Medical School, Moorenstrasse 5, D-40225 Duesseldorf, Germany. FAU - Barthelmes, Hans U AU - Barthelmes HU FAU - Boege, Fritz AU - Boege F FAU - Mielke, Christian AU - Mielke C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Salts) RN - 0 (Topoisomerase I Inhibitors) RN - 9007-49-2 (DNA) RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) RN - XT3Z54Z28A (Camptothecin) SB - IM MH - Camptothecin/pharmacology MH - Catalytic Domain MH - Cell Line MH - Cell-Free System MH - DNA/metabolism MH - DNA Topoisomerases, Type I/*chemistry/genetics/*metabolism MH - Drug Resistance/genetics MH - Humans MH - Osmolar Concentration MH - Protein Binding MH - Protein Structure, Tertiary MH - Protein Transport MH - Salts/pharmacology MH - Sequence Deletion/*genetics MH - Topoisomerase I Inhibitors PMC - PMC291868 OID - NLM: PMC291868 EDAT- 2003/12/05 05:00 MHDA- 2004/01/15 05:00 CRDT- 2003/12/05 05:00 PST - ppublish SO - Nucleic Acids Res. 2003 Dec 15;31(24):7255-63. PMID- 24120941 OWN - NLM STAT- MEDLINE DA - 20131223 DCOM- 20140224 LR - 20150118 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 426 IP - 1 DP - 2014 Jan 9 TI - The cytoplasmic domain of the T-cell receptor zeta subunit does not form disordered dimers. PG - 62-70 LID - 10.1016/j.jmb.2013.09.036 [doi] LID - S0022-2836(13)00620-7 [pii] AB - Intrinsically disordered regions in proteins play active roles in recognition, signaling and molecular sorting. They often undergo coupled folding and binding giving rise to largely ordered interfaces with their binding partners. The cytoplasmic region of the T-cell receptor zeta subunit (zetacyt) has been previously proposed to specifically dimerize in the absence of a disorder-to-order transition, suggesting an intriguing dimerization mechanism that may involve multiple transient interfaces. We show here using analytical ultracentrifugation, NMR, size-exclusion chromatography (SEC) and multi-angle light scattering that neither zetacyt nor the cytoplasmic region of CD3epsilon significantly populates a dimeric state but that they are mostly monomers in solution up to millimolar concentrations. They experience a salt- and concentration-dependent shift of their elution volume in SEC previously interpreted as dimerization. Our data show that zetacyt does not form a highly disordered protein complex and leaves open the question as to whether completely disordered dimers (or other oligomers) exist in nature. CI - (c) 2013 Elsevier Ltd. All rights reserved. FAU - Nourse, Amanda AU - Nourse A AD - Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 311, Memphis, TN 38105, USA. Electronic address: amanda.nourse@stjude.org. FAU - Mittag, Tanja AU - Mittag T AD - Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 311, Memphis, TN 38105, USA. Electronic address: tanja.mittag@stjude.org. LA - eng GR - P30 CA021765/CA/NCI NIH HHS/United States GR - P30CA21765/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20131010 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Receptors, Antigen, T-Cell) RN - 0 (antigen T cell receptor, zeta chain) SB - IM MH - Chromatography, Gel MH - Magnetic Resonance Spectroscopy MH - *Protein Multimerization MH - Receptors, Antigen, T-Cell/*chemistry/*metabolism MH - Spectrum Analysis, Raman MH - Ultracentrifugation PMC - PMC3919065 MID - NIHMS531999 OID - NLM: NIHMS531999 OID - NLM: PMC3919065 OTO - NOTNLM OT - AUC OT - EDTA OT - HSQC OT - IDP OT - M OT - MALS OT - PRE OT - SE OT - SEC OT - SV OT - analytical ultracentrifugation OT - ethylenediaminetetraacetic acid OT - fuzzy complex OT - heteronuclear single quantum coherence OT - immune receptor OT - intrinsically disordered protein OT - molecular mass OT - multi-angle light scattering OT - paramagnetic relaxation enhancement OT - sedimentation equilibrium OT - sedimentation velocity OT - size-exclusion chromatography EDAT- 2013/10/15 06:00 MHDA- 2014/02/25 06:00 CRDT- 2013/10/15 06:00 PHST- 2013/06/26 [received] PHST- 2013/09/11 [revised] PHST- 2013/09/25 [accepted] PHST- 2013/10/10 [aheadofprint] AID - S0022-2836(13)00620-7 [pii] AID - 10.1016/j.jmb.2013.09.036 [doi] PST - ppublish SO - J Mol Biol. 2014 Jan 9;426(1):62-70. doi: 10.1016/j.jmb.2013.09.036. Epub 2013 Oct 10. PMID- 23050820 OWN - NLM STAT- MEDLINE DA - 20121011 DCOM- 20130104 IS - 1749-6632 (Electronic) IS - 0077-8923 (Linking) VI - 1270 DP - 2012 Oct TI - NMR structural studies of thymosin alpha1 and beta-thymosins. PG - 73-8 LID - 10.1111/j.1749-6632.2012.06656.x [doi] AB - Thymosin proteins, originally isolated from fractionation of thymus tissue, represent a class of compounds that we now know are present in numerous other tissues, are unrelated to each other in a genetic sense, and appear to have different functions within the cell. Thymosin alpha1 (generic drug name thymalfasin; trade name Zadaxin) is derived from a precursor molecule, prothymosin, by proteolytic cleavage, and stimulates the immune system. Although the peptide is natively unstructured in aqueous solution, the helical structure has been observed in the presence of trifluoroethanol or unilamellar vesicles, and these studies are consistent with the presence of a dynamic helical structure whose sides are not completely hydrophilic or hydrophobic. This helical structure may occur in circulation when the peptide comes into contact with membranes. In this report, we discuss the current knowledge of the thymosin alpha1 structure and similar properties of thymosin beta4 and thymosin beta9, in different environments. CI - (c) 2012 New York Academy of Sciences. FAU - Volk, David E AU - Volk DE AD - Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas 77030, USA. David.Volk@uth.tmc.edu FAU - Tuthill, Cynthia W AU - Tuthill CW FAU - Elizondo-Riojas, Miguel-Angel AU - Elizondo-Riojas MA FAU - Gorenstein, David G AU - Gorenstein DG LA - eng PT - Journal Article PL - United States TA - Ann N Y Acad Sci JT - Annals of the New York Academy of Sciences JID - 7506858 RN - 0 (thymalfasin) RN - 61512-21-8 (Thymosin) RN - 77591-33-4 (thymosin beta(4)) RN - 81775-04-4 (thymosin beta(9)) SB - IM MH - Animals MH - Humans MH - Magnetic Resonance Spectroscopy/*methods MH - Thymosin/*analogs & derivatives/*chemistry EDAT- 2012/10/12 06:00 MHDA- 2013/01/05 06:00 CRDT- 2012/10/12 06:00 AID - 10.1111/j.1749-6632.2012.06656.x [doi] PST - ppublish SO - Ann N Y Acad Sci. 2012 Oct;1270:73-8. doi: 10.1111/j.1749-6632.2012.06656.x. PMID- 18198943 OWN - NLM STAT- MEDLINE DA - 20080131 DCOM- 20080324 LR - 20140904 IS - 1545-7885 (Electronic) IS - 1544-9173 (Linking) VI - 6 IP - 1 DP - 2008 Jan TI - Conformational equilibria in monomeric alpha-synuclein at the single-molecule level. PG - e6 LID - 10.1371/journal.pbio.0060006 [doi] AB - Human alpha-Synuclein (alphaSyn) is a natively unfolded protein whose aggregation into amyloid fibrils is involved in the pathology of Parkinson disease. A full comprehension of the structure and dynamics of early intermediates leading to the aggregated states is an unsolved problem of essential importance to researchers attempting to decipher the molecular mechanisms of alphaSyn aggregation and formation of fibrils. Traditional bulk techniques used so far to solve this problem point to a direct correlation between alphaSyn's unique conformational properties and its propensity to aggregate, but these techniques can only provide ensemble-averaged information for monomers and oligomers alike. They therefore cannot characterize the full complexity of the conformational equilibria that trigger the aggregation process. We applied atomic force microscopy-based single-molecule mechanical unfolding methodology to study the conformational equilibrium of human wild-type and mutant alphaSyn. The conformational heterogeneity of monomeric alphaSyn was characterized at the single-molecule level. Three main classes of conformations, including disordered and "beta-like" structures, were directly observed and quantified without any interference from oligomeric soluble forms. The relative abundance of the "beta-like" structures significantly increased in different conditions promoting the aggregation of alphaSyn: the presence of Cu2+, the pathogenic A30P mutation, and high ionic strength. This methodology can explore the full conformational space of a protein at the single-molecule level, detecting even poorly populated conformers and measuring their distribution in a variety of biologically important conditions. To the best of our knowledge, we present for the first time evidence of a conformational equilibrium that controls the population of a specific class of monomeric alphaSyn conformers, positively correlated with conditions known to promote the formation of aggregates. A new tool is thus made available to test directly the influence of mutations and pharmacological strategies on the conformational equilibrium of monomeric alphaSyn. FAU - Sandal, Massimo AU - Sandal M AD - Department of Biochemistry G. Moruzzi, University of Bologna, Bologna, Italy. FAU - Valle, Francesco AU - Valle F FAU - Tessari, Isabella AU - Tessari I FAU - Mammi, Stefano AU - Mammi S FAU - Bergantino, Elisabetta AU - Bergantino E FAU - Musiani, Francesco AU - Musiani F FAU - Brucale, Marco AU - Brucale M FAU - Bubacco, Luigi AU - Bubacco L FAU - Samori, Bruno AU - Samori B LA - eng SI - GENBANK/P37840 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - PLoS Biol JT - PLoS biology JID - 101183755 RN - 0 (Buffers) RN - 0 (alpha-Synuclein) RN - 789U1901C5 (Copper) SB - IM MH - Buffers MH - Circular Dichroism MH - Copper/chemistry/metabolism MH - Entropy MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation/genetics MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - alpha-Synuclein/*chemistry/genetics/*metabolism PMC - PMC2174973 OID - NLM: PMC2174973 EDAT- 2008/01/18 09:00 MHDA- 2008/03/25 09:00 CRDT- 2008/01/18 09:00 PHST- 2007/06/06 [received] PHST- 2007/11/26 [accepted] AID - 07-PLBI-RA-1662 [pii] AID - 10.1371/journal.pbio.0060006 [doi] PST - ppublish SO - PLoS Biol. 2008 Jan;6(1):e6. doi: 10.1371/journal.pbio.0060006. PMID- 17323918 OWN - NLM STAT- MEDLINE DA - 20070313 DCOM- 20070516 LR - 20101118 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 46 IP - 11 DP - 2007 Mar 20 TI - The carboxy-terminal domain of heat-shock factor 1 is largely unfolded but can be induced to collapse into a compact, partially structured state. PG - 3405-15 AB - Heat-shock transcription factor 1 (HSF1) is a key regulator of the expression of heat-shock proteins during the heat-shock response. The C terminus of HSF1 (CT) contains both the regulatory and transcriptional activation domains. Predictors of natural disordered regions analysis predicts and our study demonstrates that CT is predominantly natively unfolded under physiological conditions but can be induced to fold into a number of structured states under different conditions. Under physiological conditions, CT exhibits a very low abundance of secondary and tertiary structures as observed by circular dichroism, no hydrophobic core as monitored by the 6-p-toluidino-2-naphthalenesulfonic acid (TNS)-binding assay, a large hydrodynamic radius as measured by size-exclusion chromatography-high-performance liquid chromatography, and high structural flexibility as probed by limited proteolysis. However, secondary-structure content significantly increases at high temperatures, in acidic pH, or in the presence of trimethylamine N-oxide, trifluoroethanol, or a cationic surfactant. Interestingly, the hydrophobicity of "folded" CT, as monitored by the TNS-binding assay, is enhanced by acidic pH and a cationic surfactant but not by trifluoroethanol. CT also displays different patterns in the proteolytic cleavage in acidic pH and in the presence of a cationic surfactant compared with that under native condition, suggesting that CT undergoes distinct structural rearrangements. FAU - Pattaramanon, Narinporn AU - Pattaramanon N AD - Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0606, USA. FAU - Sangha, Navneet AU - Sangha N FAU - Gafni, Ari AU - Gafni A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070227 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA-Binding Proteins) RN - 0 (Heat-Shock Proteins) RN - 0 (Hsf1 protein, mouse) RN - 0 (Transcription Factors) SB - IM MH - Chromatography, High Pressure Liquid MH - Circular Dichroism MH - Computational Biology/methods MH - DNA-Binding Proteins/*chemistry MH - Heat-Shock Proteins/chemistry/*drug effects MH - Hydrophobic and Hydrophilic Interactions MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary/drug effects MH - Spectrometry, Fluorescence MH - Transcription Factors/*chemistry EDAT- 2007/02/28 09:00 MHDA- 2007/05/17 09:00 CRDT- 2007/02/28 09:00 PHST- 2007/02/27 [aheadofprint] AID - 10.1021/bi061124c [doi] PST - ppublish SO - Biochemistry. 2007 Mar 20;46(11):3405-15. Epub 2007 Feb 27. PMID- 18270511 OWN - NLM STAT- MEDLINE DA - 20080404 DCOM- 20080428 LR - 20081121 IS - 1545-9985 (Electronic) IS - 1545-9985 (Linking) VI - 15 IP - 4 DP - 2008 Apr TI - The ARID domain of the H3K4 demethylase RBP2 binds to a DNA CCGCCC motif. PG - 419-21 LID - 10.1038/nsmb.1400 [doi] AB - The histone H3 lysine 4 demethylase RBP2 contains a DNA binding domain, the AT-rich interaction domain (ARID). We solved the structure of ARID by NMR, identified its DNA binding motif (CCGCCC) and characterized the binding contacts. Immunofluorescence and luciferase assays indicated that ARID is required for RBP2 demethylase activity in cells and that DNA recognition is essential to regulate transcription. FAU - Tu, Shengjiang AU - Tu S AD - Department of Chemistry, Ohio State University, 100 West 18th Ave., Columbus, Ohio 43210, USA. FAU - Teng, Yu-Ching AU - Teng YC FAU - Yuan, Chunhua AU - Yuan C FAU - Wu, Ying-Ta AU - Wu YT FAU - Chan, Meng-Yu AU - Chan MY FAU - Cheng, An-Ning AU - Cheng AN FAU - Lin, Po-Hsun AU - Lin PH FAU - Juan, Li-Jung AU - Juan LJ FAU - Tsai, Ming-Daw AU - Tsai MD LA - eng SI - PDB/2JXJ GR - CA69472/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20080212 PL - United States TA - Nat Struct Mol Biol JT - Nature structural & molecular biology JID - 101186374 RN - 0 (RBP2 protein, human) RN - 0 (Retinol-Binding Proteins, Cellular) RN - 9007-49-2 (DNA) RN - EC 2.7.1.- (BRD2 protein, human) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - DNA/*metabolism MH - Fluorescent Antibody Technique MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Promoter Regions, Genetic MH - Protein Binding MH - Protein-Serine-Threonine Kinases/genetics MH - Retinol-Binding Proteins, Cellular/chemistry/*metabolism MH - Structure-Activity Relationship EDAT- 2008/02/14 09:00 MHDA- 2008/04/29 09:00 CRDT- 2008/02/14 09:00 PHST- 2007/11/20 [received] PHST- 2008/02/06 [accepted] PHST- 2008/02/12 [aheadofprint] AID - nsmb.1400 [pii] AID - 10.1038/nsmb.1400 [doi] PST - ppublish SO - Nat Struct Mol Biol. 2008 Apr;15(4):419-21. doi: 10.1038/nsmb.1400. Epub 2008 Feb 12. PMID- 16489768 OWN - NLM STAT- MEDLINE DA - 20060221 DCOM- 20060428 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 8 DP - 2006 Feb 28 TI - Characterization of oligomers during alpha-synuclein aggregation using intrinsic tryptophan fluorescence. PG - 2752-60 AB - The aggregation of the presynaptic protein alpha-synuclein is associated with Parkinson's disease (PD). The details of the mechanism of aggregation, as well as the cytotoxic species, are currently not well understood. alpha-Synuclein has four tyrosine and no tryptophan residues. We introduced a tyrosine to tryptophan mutation at position 39 to create an intrinsic fluorescence probe and allow additional characterization of the aggregation process. Y39W alpha-synuclein had similar fibrillation kinetics (2-fold slower), pH-induced conformational changes, and fibril morphology to wild-type alpha-synuclein. In addition to intrinsic Trp fluorescence, acrylamide quenching, fluorescence anisotropy, ANS binding, dynamic light scattering, and FTIR were employed to monitor the kinetics of aggregation. These biophysical probes revealed the significant population of two classes of oligomeric intermediates, one formed during the lag period of fibrillation and the other present at the completion of fibrillation. As expected for a natively unfolded protein, Trp 39 was highly solvent-exposed in the monomer and is solvent-exposed in the two oligomeric intermediates; however, it is partially, but not fully, buried in the fibrils. These observations demonstrate the utility of Trp fluorescence labeled alpha-synuclein and demonstrate the existence of an oligomeric intermediate that exists as a transient reservoir of alpha-synuclein for fibrillation. FAU - Dusa, Alexandra AU - Dusa A AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. FAU - Kaylor, Joanna AU - Kaylor J FAU - Edridge, Shauna AU - Edridge S FAU - Bodner, Nika AU - Bodner N FAU - Hong, Dong-Pyo AU - Hong DP FAU - Fink, Anthony L AU - Fink AL LA - eng GR - NS39985/NS/NINDS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Anilino Naphthalenesulfonates) RN - 0 (Solvents) RN - 0 (alpha-Synuclein) RN - 20R035KLCI (Acrylamide) RN - 42HK56048U (Tyrosine) RN - 8DUH1N11BX (Tryptophan) RN - 980-21-2 (dityrosine) SB - IM MH - Acrylamide/metabolism MH - Amino Acid Substitution MH - Amyloid/metabolism MH - Anilino Naphthalenesulfonates/metabolism MH - *Fluorescence MH - Fluorescence Polarization MH - Fluorescence Resonance Energy Transfer MH - Protein Structure, Secondary/genetics MH - Solvents MH - Time Factors MH - Tryptophan/*chemistry/metabolism MH - Tyrosine/analogs & derivatives/metabolism MH - alpha-Synuclein/chemistry/genetics/*metabolism EDAT- 2006/02/24 09:00 MHDA- 2006/04/29 09:00 CRDT- 2006/02/24 09:00 AID - 10.1021/bi051426z [doi] PST - ppublish SO - Biochemistry. 2006 Feb 28;45(8):2752-60. PMID- 10368269 OWN - NLM STAT- MEDLINE DA - 19990415 DCOM- 19990415 LR - 20131121 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 7 IP - 1 DP - 1999 Jan 15 TI - Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center. PG - 13-23 AB - BACKGROUND: Many microorganisms have the ability to either oxidize molecular hydrogen to generate reducing power or to produce hydrogen in order to remove low-potential electrons. These reactions are catalyzed by two unrelated enzymes: the Ni-Fe hydrogenases and the Fe-only hydrogenases. RESULTS: We report here the structure of the heterodimeric Fe-only hydrogenase from Desulfovibrio desulfuricans - the first for this class of enzymes. With the exception of a ferredoxin-like domain, the structure represents a novel protein fold. The so-called H cluster of the enzyme is composed of a typical [4Fe-4S] cubane bridged to a binuclear active site Fe center containing putative CO and CN ligands and one bridging 1, 3-propanedithiol molecule. The conformation of the subunits can be explained by the evolutionary changes that have transformed monomeric cytoplasmic enzymes into dimeric periplasmic enzymes. Plausible electron- and proton-transfer pathways and a putative channel for the access of hydrogen to the active site have been identified. CONCLUSIONS: The unrelated active sites of Ni-Fe and Fe-only hydrogenases have several common features: coordination of diatomic ligands to an Fe ion; a vacant coordination site on one of the metal ions representing a possible substrate-binding site; a thiolate-bridged binuclear center; and plausible proton- and electron-transfer pathways and substrate channels. The diatomic coordination to Fe ions makes them low spin and favors low redox states, which may be required for catalysis. Complex electron paramagnetic resonance signals typical of Fe-only hydrogenases arise from magnetic interactions between the [4Fe-4S] cluster and the active site binuclear center. The paucity of protein ligands to this center suggests that it was imported from the inorganic world as an already functional unit. FAU - Nicolet, Y AU - Nicolet Y AD - Laboratoire de Cristallographie et de Cristallogenese des Proteines, Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS 41, Grenoble, France. FAU - Piras, C AU - Piras C FAU - Legrand, P AU - Legrand P FAU - Hatchikian, C E AU - Hatchikian CE FAU - Fontecilla-Camps, J C AU - Fontecilla-Camps JC LA - eng SI - PDB/1HFE PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNKNOWN TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Iron-Sulfur Proteins) RN - E1UOL152H7 (Iron) RN - EC 1.12.- (nickel-iron hydrogenase) RN - EC 1.12.7.2 (Hydrogenase) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Clostridium/enzymology MH - Computer Simulation MH - Cytoplasm/enzymology MH - Desulfovibrio/*enzymology MH - Electron Spin Resonance Spectroscopy MH - Hydrogenase/*chemistry/metabolism MH - Iron/chemistry/*metabolism MH - Iron-Sulfur Proteins/*chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Sequence Alignment MH - Software MH - Trichomonas vaginalis/enzymology EDAT- 1999/06/16 MHDA- 1999/06/16 00:01 CRDT- 1999/06/16 00:00 PST - ppublish SO - Structure. 1999 Jan 15;7(1):13-23. PMID- 21120859 OWN - NLM STAT- MEDLINE DA - 20110105 DCOM- 20110527 LR - 20131121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 79 IP - 2 DP - 2011 Feb TI - Compact conformations of alpha-synuclein induced by alcohols and copper. PG - 611-21 LID - 10.1002/prot.22909 [doi] AB - The intrinsically disordered protein alpha-synuclein aggregates into amyloid fibrils, a process known to be implicated in several neurodegenerative states. Partially folded forms of the protein are thought to trigger the aggregation process. Here, alpha-synuclein conformers are characterized by analysis of the charge-state distributions observed in electrospray-ionization mass spectrometry under negative-ion mode. It is found that, even at neutral pH, a small fraction of the molecular population is in a compact conformation. Several distinct partially folded forms are then identified under conditions that promote alpha-synuclein aggregation, such as solutions of simple and fluorinated alcohols. Specific intermediates accumulate at increasing concentrations of ethanol, hexafluoro-2-propanol, and trifluoroethanol. Finally, extensive folding induced by Cu(2+) binding is revealed by titrations in the presence of Cu(2+)-glycine. The data confirm the existence of a single, high-affinity binding site for Cu(2+). Because accumulation of this partially folded form correlates with enhancement of fibrillation kinetics, it is likely to represent an amyloidogenic intermediate in alpha-synuclein conformational transitions. CI - (c) 2010 Wiley-Liss, Inc. FAU - Natalello, Antonino AU - Natalello A AD - Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy. FAU - Benetti, Federico AU - Benetti F FAU - Doglia, Silvia Maria AU - Doglia SM FAU - Legname, Giuseppe AU - Legname G FAU - Grandori, Rita AU - Grandori R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Propanols) RN - 0 (alpha-Synuclein) RN - 75-89-8 (Trifluoroethanol) RN - 920-66-1 (hexafluoroisopropanol) RN - LRX7AJ16DT (Copper Sulfate) RN - Y4S76JWI15 (Methanol) SB - IM MH - Copper Sulfate/*chemistry MH - Hydrogen-Ion Concentration MH - Methanol/*chemistry MH - Propanols/*chemistry MH - Protein Folding MH - Protein Structure, Tertiary MH - Spectrometry, Mass, Electrospray Ionization MH - Trifluoroethanol/*chemistry MH - alpha-Synuclein/*chemistry EDAT- 2010/12/02 06:00 MHDA- 2011/05/28 06:00 CRDT- 2010/12/02 06:00 AID - 10.1002/prot.22909 [doi] PST - ppublish SO - Proteins. 2011 Feb;79(2):611-21. doi: 10.1002/prot.22909. PMID- 14980481 OWN - NLM STAT- MEDLINE DA - 20040224 DCOM- 20040401 LR - 20061115 IS - 0042-6822 (Print) IS - 0042-6822 (Linking) VI - 319 IP - 2 DP - 2004 Feb 20 TI - Structure and dynamics of the nucleocapsid-binding domain of the Sendai virus phosphoprotein in solution. PG - 201-11 AB - The RNA-dependent RNA polymerase of the Sendai virus (SeV) consists of the large protein (L) and the phosphoprotein (P). P plays a crucial role in the enzyme by positioning L (which carries the polymerase activity) onto the matrix for transcription and replication formed by the RNA and the nucleoprotein, the N-RNA. P has a modular structure with distinct functional domains: an N-terminal domain involved in binding to N degrees (N that is not yet bound to RNA) and a C-terminal domain that carries the oligomerisation domain, the N-RNA binding domain and the L binding domain and that, combined with L, is active in transcription. Structural data have previously been obtained on the N-terminal domain and on the oligomerisation domain of P, but not yet on its N-RNA binding domain (also-called the X protein). Here we present an NMR and a small angle neutron scattering study of the SeV X protein. We show that this molecule presents two subdomains linked by an 11-residue linker, with the N-subdomain lacking a well-defined conformation. The 3D structure of the C-subdomain consists of three alpha-helices revealing an asymmetric charge distribution that may be important for binding to RNA-bound nucleoprotein. The structure of the entire C-terminal domain of P is modelled from its constituent parts in combination with small angle scattering data on this domain. FAU - Blanchard, Laurence AU - Blanchard L AD - Institut de Biologie Structurale 'Jean-Pierre Ebel' (UMR 5075, CEA-CNRS-UJF), 38027 Grenoble cedex 1, France. Laurence.Blanchard@ibs.fr FAU - Tarbouriech, Nicolas AU - Tarbouriech N FAU - Blackledge, Martin AU - Blackledge M FAU - Timmins, Peter AU - Timmins P FAU - Burmeister, Wilhelm P AU - Burmeister WP FAU - Ruigrok, Rob W H AU - Ruigrok RW FAU - Marion, Dominique AU - Marion D LA - eng PT - Comparative Study PT - Journal Article PL - United States TA - Virology JT - Virology JID - 0110674 RN - 0 (Phosphoproteins) RN - 0 (Viral Proteins) SB - IM MH - Amino Acid Sequence MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleocapsid/*metabolism MH - Phosphoproteins/chemistry/*metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sendai virus/chemistry/*metabolism MH - Sequence Alignment MH - Viral Proteins/chemistry/*metabolism EDAT- 2004/02/26 05:00 MHDA- 2004/04/02 05:00 CRDT- 2004/02/26 05:00 PHST- 2003/08/11 [received] PHST- 2003/10/10 [revised] PHST- 2003/10/17 [accepted] AID - 10.1016/j.virol.2003.10.029 [doi] AID - S0042682203008006 [pii] PST - ppublish SO - Virology. 2004 Feb 20;319(2):201-11. PMID- 10639192 OWN - NLM STAT- MEDLINE DA - 20000223 DCOM- 20000223 LR - 20061115 IS - 0270-4137 (Print) IS - 0270-4137 (Linking) VI - 42 IP - 3 DP - 2000 Feb 15 TI - Crystal structure of human prostatic acid phosphatase . PG - 211-8 AB - BACKGROUND: Prostatic acid phosphatase (hPAP) is a major product of the human prostate gland, yet its physiological substrate remains unknown. METHODS: Human PAP, purified from semen, was crystallized using polyethylene glycol as the precipitant and its crystal structure was determined using X-ray diffraction. The structure was refined at 3.1 A resolution to R = 16% and R(free) = 27%. RESULTS: The structure of hPAP is similar to that of other known histidine phosphatases, and the positions of its catalytic residues are conserved. N-linked carbohydrates are present at each of the possible glycosylation sites. It appears that high-mannose chains are attached to Asn 62 and Asp 301, while complex chains are at Asn 188. CONCLUSIONS: The similarity of the three-dimensional structures of rat PAP and human PAP indicates that the mechanistic analyses of the catalytic mechanism proposed for the rat enzyme should be extended to the human enzyme without reservations. The crystallographic data allowed the correlation of attachment sites of N-linked carbohydrate chains with a given carbohydrate type. The carbohydrates of the protein produced in the prostate cells and in the baculovirus expression system appear to differ at the site of complex carbohydrates attachment. CI - Copyright 2000 Wiley-Liss, Inc. FAU - Jakob, C G AU - Jakob CG AD - Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA. FAU - Lewinski, K AU - Lewinski K FAU - Kuciel, R AU - Kuciel R FAU - Ostrowski, W AU - Ostrowski W FAU - Lebioda, L AU - Lebioda L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - UNITED STATES TA - Prostate JT - The Prostate JID - 8101368 RN - 0 (Carbohydrates) RN - EC 3.1.3.2 (Acid Phosphatase) SB - IM MH - Acid Phosphatase/*chemistry/metabolism MH - Binding Sites MH - Carbohydrates/chemistry MH - Crystallography, X-Ray MH - Glycosylation MH - Humans MH - Male MH - Models, Molecular MH - Prostate/*enzymology MH - Protein Conformation MH - Protein Processing, Post-Translational MH - Semen/enzymology EDAT- 2000/01/19 09:00 MHDA- 2000/02/26 09:00 CRDT- 2000/01/19 09:00 AID - 10.1002/(SICI)1097-0045(20000215)42:3<211::AID-PROS7>3.0.CO;2-U [pii] PST - ppublish SO - Prostate. 2000 Feb 15;42(3):211-8. PMID- 1946369 OWN - NLM STAT- MEDLINE DA - 19911203 DCOM- 19911203 LR - 20131002 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 88 IP - 21 DP - 1991 Nov 1 TI - The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding. PG - 9558-62 AB - The 98-amino acid Fis protein from Escherichia coli functions in a variety of reactions, including promotion of Hin-mediated site-specific DNA inversion when bound to an enhancer sequence. It is unique among site-specific DNA-binding proteins in that it binds to a large number of different DNA sequences, for which a consensus sequence is difficult to establish. X-ray crystal structure analyses have been carried out at 2.3 A resolution for wild-type Fis and for an Arg-89----Cys mutant that does not stimulate DNA inversion. Each monomer of the Fis dimer has four alpha-helices, A-D; the first 19 residues are disordered in the crystal. The end of each C helix is hydrogen bonded to the beginning of helix B' from the opposite subunit in what effectively is one long continuous, although bent, helix. The four helices, C, B', C', and B, together define a platform through the center of the Fis molecule: helices A and A' are believed to be involved with Hin recombinase on one side, and helices D and D' interact with DNA lying on the other side of the platform. Helices C and D of each subunit comprise a helix-turn-helix (HTH) DNA-binding element. The spacing of these two HTH elements in the dimer, 25 A, is too short to allow insertion into adjacent major grooves of a straight B-DNA helix. However, bending the DNA at discrete points, to an overall radius of curvature of 62 A, allows efficient docking of a B-DNA helix with the Fis molecule. The proposed complex explains the experimentally observed patterns of methylation protection and DNase I cleavage hypersensitivity. The x-ray structure accounts for the effects of mutations in the Fis sequence. Those that affect DNA inversion but not DNA binding are located within the N-terminal disordered region and helix A. This inversion activation domain is physically separated in the Fis molecule from the HTH elements and may specify a region of contact with the Hin recombinase. In contrast, mutations that affect HTH helices C and D, or interactions of these with helix B, have the additional effect of decreasing or eliminating binding to DNA. FAU - Yuan, H S AU - Yuan HS AD - Molecular Biology Institute, University of California, Los Angeles 90024. FAU - Finkel, S E AU - Finkel SE FAU - Feng, J A AU - Feng JA FAU - Kaczor-Grzeskowiak, M AU - Kaczor-Grzeskowiak M FAU - Johnson, R C AU - Johnson RC FAU - Dickerson, R E AU - Dickerson RE LA - eng SI - PDB/UNKNOWN GR - GM-07104/GM/NIGMS NIH HHS/United States GR - GM-31299/GM/NIGMS NIH HHS/United States GR - GM-38509/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Factor For Inversion Stimulation Protein) RN - 0 (Integration Host Factors) RN - 0 (integration host factor, E coli) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/metabolism/*ultrastructure MH - Base Sequence MH - Carrier Proteins/metabolism/*ultrastructure MH - Computer Graphics MH - Computer Simulation MH - Crystallography MH - DNA Mutational Analysis MH - DNA-Binding Proteins/physiology/*ultrastructure MH - Escherichia coli MH - *Escherichia coli Proteins MH - Factor For Inversion Stimulation Protein MH - Integration Host Factors MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - *Recombination, Genetic MH - Structure-Activity Relationship PMC - PMC52757 OID - NLM: PMC52757 EDAT- 1991/11/01 MHDA- 1991/11/01 00:01 CRDT- 1991/11/01 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9558-62. PMID- 14536075 OWN - NLM STAT- MEDLINE DA - 20031010 DCOM- 20031125 LR - 20131121 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 12 IP - 2 DP - 2003 Aug TI - Flexible linkers leash the substrate binding domain of SspB to a peptide module that stabilizes delivery complexes with the AAA+ ClpXP protease. PG - 355-63 AB - SspB dimers bind proteins bearing the ssrA-degradation tag and stimulate their degradation by the ClpXP protease. Here, E. coli SspB is shown to contain a dimeric substrate binding domain of 110-120 N-terminal residues, which binds ssrA-tagged substrates but does not stimulate their degradation. The C-terminal 40-50 residues of SspB are unstructured but are required for SspB to form substrate-delivery complexes with ClpXP. A synthetic peptide containing the 10 C-terminal residues of SspB binds ClpX, stimulates its ATPase activity, and prevents SspB-mediated delivery of GFP-ssrA for ClpXP degradation. This tripartite structure--an ssrA-tag binding and dimerization domain, a flexible linker, and a short peptide module that docks with ClpX--allows SspB to deliver tagged substrates to ClpXP without interfering with their denaturation or degradation. FAU - Wah, David A AU - Wah DA AD - Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. FAU - Levchenko, Igor AU - Levchenko I FAU - Rieckhof, Gabrielle E AU - Rieckhof GE FAU - Bolon, Daniel N AU - Bolon DN FAU - Baker, Tania A AU - Baker TA FAU - Sauer, Robert T AU - Sauer RT LA - eng GR - AI-16892/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Adhesins, Bacterial) RN - 0 (Bacterial Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Luminescent Proteins) RN - 0 (Molecular Chaperones) RN - 0 (RNA, Bacterial) RN - 0 (tmRNA) RN - 136250-21-0 (salivary agglutinin receptor, Streptocococcus) RN - 147336-22-9 (Green Fluorescent Proteins) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 3.4.21.- (Serine Endopeptidases) RN - EC 3.4.21.92 (ClpXP protease, E coli) RN - EC 3.4.21.92 (Endopeptidase Clp) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 3.6.1.- (ClpX protein, E coli) SB - IM MH - Adenosine Triphosphatases/*chemistry MH - Adenosine Triphosphate/metabolism MH - Adhesins, Bacterial/*chemistry/metabolism MH - Amino Acid Sequence MH - Bacterial Proteins/physiology MH - Binding Sites MH - Dimerization MH - Dose-Response Relationship, Drug MH - Endopeptidase Clp MH - Escherichia coli/metabolism MH - *Escherichia coli Proteins MH - Green Fluorescent Proteins MH - Hydrolysis MH - Luminescent Proteins/metabolism MH - Models, Biological MH - Molecular Chaperones MH - Molecular Sequence Data MH - Mutation MH - Protein Binding MH - Protein Structure, Tertiary MH - RNA, Bacterial/metabolism MH - Sequence Homology, Amino Acid MH - Serine Endopeptidases/*chemistry MH - Substrate Specificity EDAT- 2003/10/11 05:00 MHDA- 2003/12/03 05:00 CRDT- 2003/10/11 05:00 AID - S1097276503002727 [pii] PST - ppublish SO - Mol Cell. 2003 Aug;12(2):355-63. PMID- 15379539 OWN - NLM STAT- MEDLINE DA - 20040921 DCOM- 20041109 LR - 20120222 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 38 DP - 2004 Sep 28 TI - The long acidic tail of high mobility group box 1 (HMGB1) protein forms an extended and flexible structure that interacts with specific residues within and between the HMG boxes. PG - 11992-7 AB - HMGB1 (high mobility group B1) is a conserved chromosomal protein composed of two similar DNA binding domains (HMG box A and box B) linked by a short basic stretch to an acidic C-terminal tail of 30 residues. The acidic tail modulates the DNA binding properties of HMGB1, and its length differentiates the various HMGB family members. We synthesized a peptide that corresponds to the acidic tail in HMGB1 (T-peptide) and studied its binding to the single boxes and to the fragment corresponding to tailless HMGB1 (designated as AB(bt) fragment). CD spectroscopy showed that T-peptide stabilizes significantly the AB(bt) fragment and that the complex has an identical thermal stability as full-length HMGB1. Calorimetric and NMR data showed that T-peptide binds with a dissociation constant of 9 microM to box A and much more weakly to box B. (1)H-(15)N HSQC spectra of full-length HMGB1 and of the AB(bt) fragment are very similar; the small chemical shift differences that exist correspond to those residues of the AB(bt) fragment that were affected by the addition of the T-peptide. We conclude that the T-peptide mimics closely the acidic tail and that the basic stretch and the acidic tail form an extended and flexible segment. The tail interacts with specific residues in the boxes and shields them from other interactions. FAU - Knapp, Stefan AU - Knapp S AD - Discovery Research Oncology, Department of Chemistry, Pharmacia Corporation, Viale Pasteur 10, 20014 Nerviano, Italy. FAU - Muller, Susanne AU - Muller S FAU - Digilio, Giuseppe AU - Digilio G FAU - Bonaldi, Tiziana AU - Bonaldi T FAU - Bianchi, Marco E AU - Bianchi ME FAU - Musco, Giovanna AU - Musco G LA - eng GR - TCP99035/Telethon/Italy PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (HMGB1 Protein) RN - 0 (Peptide Fragments) SB - IM MH - Circular Dichroism MH - HMGB1 Protein/*chemistry/genetics/*metabolism MH - Hydrogen-Ion Concentration MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/*chemistry/genetics/*metabolism MH - Pliability MH - Protein Binding MH - Protein Structure, Tertiary MH - Static Electricity EDAT- 2004/09/24 05:00 MHDA- 2004/11/13 09:00 CRDT- 2004/09/24 05:00 AID - 10.1021/bi049364k [doi] PST - ppublish SO - Biochemistry. 2004 Sep 28;43(38):11992-7. PMID- 25142030 OWN - NLM STAT- MEDLINE DA - 20150129 DCOM- 20150410 LR - 20150201 IS - 1420-9071 (Electronic) IS - 1420-682X (Linking) VI - 72 IP - 4 DP - 2015 Feb TI - A di-arginine ER retention signal regulates trafficking of HCN1 channels from the early secretory pathway to the plasma membrane. PG - 833-43 LID - 10.1007/s00018-014-1705-1 [doi] AB - Hyperpolarization-activated cyclic nucleotide-gated 1 (HCN1) channels carry Ih, which contributes to neuronal excitability and signal transmission in the nervous system. Controlling the trafficking of HCN1 is an important aspect of its regulation, yet the details of this process are poorly understood. Here, we investigated how the C-terminus of HCN1 regulates trafficking by testing for its ability to redirect the localization of a non-targeted reporter in transgenic Xenopus laevis photoreceptors. We found that HCN1 contains an ER localization signal and through a series of deletion constructs, identified the responsible di-arginine ER retention signal. This signal is located in the intrinsically disordered region of the C-terminus of HCN1. To test the function of the ER retention signal in intact channels, we expressed wild type and mutant HCN1 in HEK293 cells and found this signal negatively regulates surface expression of HCN1. In summary, we report a new mode of regulating HCN1 trafficking: through the use of a di-arginine ER retention signal that monitors processing of the channel in the early secretory pathway. FAU - Pan, Yuan AU - Pan Y AD - Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road, Biochemistry, 4-712 BSB, Iowa City, IA, 52242, USA. FAU - Laird, Joseph G AU - Laird JG FAU - Yamaguchi, David M AU - Yamaguchi DM FAU - Baker, Sheila A AU - Baker SA LA - eng GR - EY020542/EY/NEI NIH HHS/United States GR - R01 EY020542/EY/NEI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140821 PL - Switzerland TA - Cell Mol Life Sci JT - Cellular and molecular life sciences : CMLS JID - 9705402 RN - 0 (Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels) RN - 94ZLA3W45F (Arginine) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Animals MH - Animals, Genetically Modified/metabolism MH - Arginine/chemistry/*metabolism MH - Cell Membrane/*metabolism MH - Endoplasmic Reticulum/*metabolism MH - HEK293 Cells MH - Humans MH - Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels/genetics/*metabolism MH - Molecular Sequence Data MH - Photoreceptor Cells/metabolism MH - Secretory Pathway MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Xenopus laevis/metabolism PMC - PMC4309907 MID - NIHMS650213 OID - NLM: NIHMS650213 OID - NLM: PMC4309907 EDAT- 2014/08/22 06:00 MHDA- 2015/04/11 06:00 CRDT- 2014/08/22 06:00 PHST- 2014/05/09 [received] PHST- 2014/08/12 [accepted] PHST- 2014/07/14 [revised] PHST- 2014/08/21 [aheadofprint] AID - 10.1007/s00018-014-1705-1 [doi] PST - ppublish SO - Cell Mol Life Sci. 2015 Feb;72(4):833-43. doi: 10.1007/s00018-014-1705-1. Epub 2014 Aug 21. PMID- 15448165 OWN - NLM STAT- MEDLINE DA - 20041125 DCOM- 20050111 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 49 DP - 2004 Dec 3 TI - Myristoylation, a protruding loop, and structural plasticity are essential features of a nonenveloped virus fusion peptide motif. PG - 51386-94 AB - Members of the fusion-associated small transmembrane (FAST) protein family are a distinct class of membrane fusion proteins encoded by nonenveloped fusogenic reoviruses. The 125-residue p14 FAST protein of reptilian reovirus has an approximately 38-residue myristoylated N-terminal ectodomain containing a moderately apolar N-proximal region, termed the hydrophobic patch. Mutagenic analysis indicated sequence-specific elements in the N-proximal portion of the p14 hydrophobic patch affected cell-cell fusion activity, independent of overall effects on the relative hydrophobicity of the motif. Circular dichroism (CD) of a myristoylated peptide representing the majority of the p14 ectodomain suggested this region is mostly disordered in solution but assumes increased structure in an apolar environment. From NMR spectroscopic data and simulated annealing, the soluble nonmyristoylated p14 ectodomain peptide consists of an N-proximal extended loop flanked by two proline hinges. The remaining two-thirds of the ectodomain peptide structure is disordered, consistent with predictions based on CD spectra of the myristoylated peptide. The myristoylated p14 ectodomain peptide, but not a nonmyristoylated version of the same peptide nor a myristoylated scrambled peptide, mediated extensive lipid mixing in a liposome fusion assay. Based on the lipid mixing activity, structural plasticity, environmentally induced conformational changes, and kinked structures predicted for the p14 ectodomain and hydrophobic patch (all features associated with fusion peptides), we propose that the majority of the p14 ectodomain is composed of a fusion peptide motif, the first such motif dependent on myristoylation for membrane fusion activity. FAU - Corcoran, Jennifer A AU - Corcoran JA AD - Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada. FAU - Syvitski, Raymond AU - Syvitski R FAU - Top, Deniz AU - Top D FAU - Epand, Richard M AU - Epand RM FAU - Epand, Raquel F AU - Epand RF FAU - Jakeman, David AU - Jakeman D FAU - Duncan, Roy AU - Duncan R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040924 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Lipids) RN - 0 (Peptides) RN - 0 (Viral Fusion Proteins) RN - 0 (Viral Matrix Proteins) RN - 0I3V7S25AW (Myristic Acid) RN - 9DLQ4CIU6V (Proline) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Cercopithecus aethiops MH - Circular Dichroism MH - Cloning, Molecular MH - Immunoprecipitation MH - Lipids/chemistry MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis MH - Mutation MH - Myristic Acid/*chemistry MH - Peptides/chemistry MH - Proline/chemistry MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Reoviridae/metabolism MH - Time Factors MH - Transfection MH - Vero Cells MH - Viral Fusion Proteins/*chemistry MH - Viral Matrix Proteins/*chemistry/metabolism EDAT- 2004/09/28 05:00 MHDA- 2005/01/12 09:00 CRDT- 2004/09/28 05:00 PHST- 2004/09/24 [aheadofprint] AID - 10.1074/jbc.M406990200 [doi] AID - M406990200 [pii] PST - ppublish SO - J Biol Chem. 2004 Dec 3;279(49):51386-94. Epub 2004 Sep 24. PMID- 21129485 OWN - NLM STAT- MEDLINE DA - 20110128 DCOM- 20110531 LR - 20141120 IS - 1096-0279 (Electronic) IS - 1046-5928 (Linking) VI - 76 IP - 2 DP - 2011 Apr TI - Functional expression of milligram quantities of the synthetic human serotonin transporter gene in a tetracycline-inducible HEK293 cell line. PG - 211-20 LID - 10.1016/j.pep.2010.11.015 [doi] AB - The serotonin transporter (SERT), a member of the solute carrier 6 family, is responsible for reuptake of the monoamine neurotransmitter serotonin (5-hydroxytryptamine) from the synaptic cleft on the neural cells, and a vital target for several antidepressants. To investigate biophysical studies of this pharmacologically relevant transporter, we developed a mammalian expression system with tetracycline-inducible HEK293 cells using synthetic human SERT genes produced by PCR-based self-assembly method. Codon-optimization of this de novo constructed genes and construction of stable cell lines improved expression 3.5-fold and single-step immunoaffinity purification with FLAG-epitope tag yielded around one milligram functional SERT per liter culture medium assessed by [(3)H] imipramine ligand binding. Some characterizations including electrospray ionization MS/MS analysis, subcellular localization and cellular-uptake assay demonstrated that expressed human SERT was properly expressed, folded and fully functional. The long cytosolic N-terminal of SERT was predicted as containing 'intrinsically disordered region (IDR)' ( approximately 85 residues) by DISOPRED2 program. We engineered this salient region by step-wise truncation and ligand binding assay determined that dissociation constant for a series of de novo designed truncation constructs was close to the one for full-length wild type SERT. Our expression platform using synthetic codon-optimized gene and mammalian stable cell lines is feasible to produce milligram-scale functional membrane transporter for further biophysical and biochemical studies. CI - Copyright (c) 2010 Elsevier Inc. All rights reserved. FAU - Takayama, Hidehito AU - Takayama H AD - R&D Strategy Department, Corporate Strategy Division, Mitsubishi Chemical Corporation, Yokohama, Japan. FAU - Sugio, Shigetoshi AU - Sugio S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101201 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (Oligopeptides) RN - 0 (Peptides) RN - 0 (Recombinant Fusion Proteins) RN - 0 (SLC6A4 protein, human) RN - 0 (Serotonin Plasma Membrane Transport Proteins) RN - 10028-17-8 (Tritium) RN - 98849-88-8 (FLAG peptide) RN - F8VB5M810T (Tetracycline) RN - OGG85SX4E4 (Imipramine) SB - IM MH - Amino Acid Sequence MH - Blotting, Western MH - Chromatography, Affinity MH - Cloning, Molecular MH - Electrophoresis, Polyacrylamide Gel MH - Glycosylation MH - HEK293 Cells MH - Humans MH - Imipramine/analysis/metabolism MH - Intracellular Space/metabolism MH - Microscopy, Fluorescence MH - Molecular Sequence Annotation MH - Molecular Sequence Data MH - Oligopeptides MH - Peptides/genetics/metabolism MH - Protein Conformation MH - Protein Engineering/methods MH - Recombinant Fusion Proteins/*biosynthesis/chemistry/genetics/metabolism MH - Serotonin Plasma Membrane Transport Proteins/*biosynthesis/chemistry/genetics/metabolism MH - Tandem Mass Spectrometry MH - Tetracycline/*pharmacology MH - Tritium/analysis EDAT- 2010/12/07 06:00 MHDA- 2011/06/01 06:00 CRDT- 2010/12/07 06:00 PHST- 2010/08/24 [received] PHST- 2010/11/17 [revised] PHST- 2010/11/23 [accepted] PHST- 2010/12/01 [aheadofprint] AID - S1046-5928(10)00325-6 [pii] AID - 10.1016/j.pep.2010.11.015 [doi] PST - ppublish SO - Protein Expr Purif. 2011 Apr;76(2):211-20. doi: 10.1016/j.pep.2010.11.015. Epub 2010 Dec 1. PMID- 23286197 OWN - NLM STAT- MEDLINE DA - 20130122 DCOM- 20130314 LR - 20141104 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 52 IP - 3 DP - 2013 Jan 22 TI - Assembly of the SLIP1-SLBP complex on histone mRNA requires heterodimerization and sequential binding of SLBP followed by SLIP1. PG - 520-36 LID - 10.1021/bi301074r [doi] AB - The SLIP1-SLBP complex activates translation of replication-dependent histone mRNAs. In this report, we describe how the activity of the SLIP1-SLBP complex is modulated by phosphorylation and oligomerization. Biophysical characterization of the free proteins shows that whereas SLIP1 is a homodimer that does not bind RNA, human SLBP is an intrinsically disordered protein that is phosphorylated at 23 Ser/Thr sites when expressed in a eukaryotic expression system such as baculovirus. The bacterially expressed unphosphorylated SLIP1-SLBP complex forms a 2:2 high-affinity (K(D) < 0.9 nM) heterotetramer that is also incapable of binding histone mRNA. In contrast, phosphorylated SLBP from baculovirus has a weak affinity (K(D) ~3 muM) for SLIP1. Sequential binding of phosphorylated SLBP to the histone mRNA stem-loop motif followed by association with SLIP1 is required to form an "active" ternary complex. Phosphorylation of SLBP at Thr171 promotes dissociation of the heterotetramer to the SLIP1-SLBP heterodimer. Using alanine scanning mutagenesis, we demonstrate that the binding site on SLIP1 for SLBP lies close to the dimer interface. A single-point mutant near the SLIP1 homodimer interface abolished interaction with SLBP in vitro and reduced the abundance of histone mRNA in vivo. On the basis of these biophysical studies, we propose that oligomerization and SLBP phosphorylation may regulate the SLBP-SLIP1 complex in vivo. SLIP1 may act to sequester SLBP in vivo, protecting it from proteolytic degradation as an inactive heterotetramer, or alternatively, formation of the SLIP1-SLBP heterotetramer may facilitate removal of SLBP from the histone mRNA prior to histone mRNA degradation. FAU - Bansal, Nitin AU - Bansal N AD - Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA. FAU - Zhang, Minyou AU - Zhang M FAU - Bhaskar, Aishwarya AU - Bhaskar A FAU - Itotia, Patrick AU - Itotia P FAU - Lee, EunHee AU - Lee E FAU - Shlyakhtenko, Lyudmila S AU - Shlyakhtenko LS FAU - Lam, TuKiet T AU - Lam TT FAU - Fritz, Andrew AU - Fritz A FAU - Berezney, Ronald AU - Berezney R FAU - Lyubchenko, Yuri L AU - Lyubchenko YL FAU - Stafford, Walter F AU - Stafford WF FAU - Thapar, Roopa AU - Thapar R LA - eng GR - 1P01-GM091743/GM/NIGMS NIH HHS/United States GR - 1R01-GM072131/GM/NIGMS NIH HHS/United States GR - 1R01-GM076660/GM/NIGMS NIH HHS/United States GR - 1R01-GM076660-04S1/GM/NIGMS NIH HHS/United States GR - 1R01-GM096039/GM/NIGMS NIH HHS/United States GR - R01 GM076660/GM/NIGMS NIH HHS/United States GR - R01 GM096039/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130111 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Carrier Proteins) RN - 0 (Histones) RN - 0 (Mutant Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Peptide Fragments) RN - 0 (RNA, Messenger) RN - 0 (Recombinant Proteins) RN - 0 (SLBP protein, human) RN - 0 (SLIP1 protein, human) RN - 0 (mRNA Cleavage and Polyadenylation Factors) RN - 2ZD004190S (Threonine) RN - 42HK56048U (Tyrosine) RN - 452VLY9402 (Serine) SB - IM MH - Carrier Proteins/*chemistry/genetics/*metabolism MH - Histones/chemistry/genetics/*metabolism MH - Humans MH - Kinetics MH - Mutagenesis, Site-Directed MH - Mutant Proteins/chemistry/metabolism MH - Nuclear Proteins/*chemistry/genetics/*metabolism MH - Peptide Fragments/chemistry/genetics/metabolism MH - Phosphorylation MH - Point Mutation MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - Protein Multimerization MH - Protein Processing, Post-Translational MH - RNA Folding MH - RNA, Messenger/*chemistry/*metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Serine/chemistry/metabolism MH - Threonine/chemistry/metabolism MH - Tyrosine/chemistry/metabolism MH - mRNA Cleavage and Polyadenylation Factors/*chemistry/genetics/*metabolism PMC - PMC3580866 MID - NIHMS434265 OID - NLM: NIHMS434265 OID - NLM: PMC3580866 EDAT- 2013/01/05 06:00 MHDA- 2013/03/15 06:00 CRDT- 2013/01/05 06:00 PHST- 2013/01/11 [aheadofprint] AID - 10.1021/bi301074r [doi] PST - ppublish SO - Biochemistry. 2013 Jan 22;52(3):520-36. doi: 10.1021/bi301074r. Epub 2013 Jan 11. PMID- 24960591 OWN - NLM STAT- MEDLINE DA - 20140728 DCOM- 20140912 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1844 IP - 9 DP - 2014 Sep TI - Long-range effects of tag sequence on marginally stabilized structure in HIV-1 p24 capsid protein monitored using NMR. PG - 1638-47 LID - 10.1016/j.bbapap.2014.06.009 [doi] LID - S1570-9639(14)00158-7 [pii] AB - N-terminal domain of HIV-1 p24 capsid protein is a globular fold composed of seven helices and two beta-strands with a flexible structure including the alpha4-5 loop and both N- and C-terminal ends. However, the protein shows a high tendency (48%) for an intrinsically disordered structure based on the PONDR VL-XT prediction from the primary sequence. To assess the possibility of marginally stabilized structure under physiological conditions, the N-terminal domain of p24 was destabilized by the addition of an artificial flexible tag to either N- or C-terminal ends, and it was analyzed using T1, T2, hetero-nuclear NOE, and amide-proton exchange experiments. When the C-terminal tag (12 residues) was attached, the regions of the alpha3-4 loop and helix 6 as well as the alpha4-5 loop attained the flexible structures. Furthermore, in the protein containing the N-terminal tag (27 residues), helix 4 in addition to the above-mentioned area including alpha3-4 and alpha4-5 loops as well as helix 6 exhibited highly disordered structures. Thus, the long-range effects of the existence of tag sequence was observed in the stepwise manner of the appearance of disordered structures (step 1: alpha4-5 loop, step 2: alpha3-4 loop and helix 6, and step 3: helix 4). Furthermore, the disordered regions in tagged proteins were consistent with the PONDR VL-XT disordered prediction. The dynamic structure located in the middle part (alpha3-4 loop to helix 6) of the protein shown in this study may be related to the assembly of the viral particle. CI - Copyright (c) 2014 Elsevier B.V. All rights reserved. FAU - Okazaki, Honoka AU - Okazaki H AD - Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan. FAU - Kaneko, Chie AU - Kaneko C AD - Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan. FAU - Hirahara, Miyuki AU - Hirahara M AD - Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan. FAU - Watanabe, Satoru AU - Watanabe S AD - NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan. FAU - Tochio, Naoya AU - Tochio N AD - NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan. FAU - Kigawa, Takanori AU - Kigawa T AD - NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan. FAU - Nishimura, Chiaki AU - Nishimura C AD - Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan. Electronic address: cnishimura@thu.ac.jp. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140621 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (HIV Core Protein p24) RN - 0 (Recombinant Fusion Proteins) RN - 0 (p24 protein, Human Immunodeficiency Virus Type 1) SB - IM MH - Amino Acid Sequence MH - HIV Core Protein p24/*chemistry MH - HIV-1/*chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Engineering MH - Protein Folding MH - Protein Stability MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/*chemistry/genetics/metabolism OTO - NOTNLM OT - HIV-1 p24 capsid protein OT - Intrinsically disordered protein OT - NMR OT - Protein dynamics OT - Protein folding EDAT- 2014/06/25 06:00 MHDA- 2014/09/13 06:00 CRDT- 2014/06/25 06:00 PHST- 2014/01/07 [received] PHST- 2014/06/10 [revised] PHST- 2014/06/16 [accepted] PHST- 2014/06/21 [aheadofprint] AID - S1570-9639(14)00158-7 [pii] AID - 10.1016/j.bbapap.2014.06.009 [doi] PST - ppublish SO - Biochim Biophys Acta. 2014 Sep;1844(9):1638-47. doi: 10.1016/j.bbapap.2014.06.009. Epub 2014 Jun 21. PMID- 22089506 OWN - NLM STAT- MEDLINE DA - 20111214 DCOM- 20120417 IS - 1463-9084 (Electronic) IS - 1463-9076 (Linking) VI - 14 IP - 2 DP - 2012 Jan 14 TI - Specific recognition between intrinsically disordered LEF and DNA. PG - 538-45 LID - 10.1039/c1cp22610j [doi] AB - Lymphoid enhancer-binding factor-1 (LEF-1) is a sequence-specific and cell type-specific transcription factor in regulation of the human T cell receptor alpha enhancer. It has been shown the minor groove of DNA can bind the intrinsic disordered LEF. To get an insight into the mechanism of how the intrinsic disordered LEF specifically recognizes DNA, we have performed explicit-solvent multiple molecular dynamics (MD) simulations to study the specific recognition between DNA and LEF. Room-temperature MD simulations suggest that the disordered C-tails of LEF have nonspecific and specific interactions with the minor groove of DNA. Kinetic analysis of high-temperature MD simulations shows that bound and apo-states unfold via a two-state process. The specific binding of the disordered C-tails of LEF can accelerate the formation of a complex. Gly38Ala and Met11Gly mutant simulations show that electrostatic interactions between DNA and LEF significantly decrease. Kolmogorov-Smirnov (KS) P test analysis illustrates that the specific recognition between DNA and LEF might follow an induced-fit mechanism. Furthermore, these methods can be used for the research of specific recognition between DNA and other intrinsic disordered proteins. FAU - Qin, Fang AU - Qin F AD - State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China. FAU - Ye, Wei AU - Ye W FAU - Chen, Yue AU - Chen Y FAU - Chen, Xiaodong AU - Chen X FAU - Li, Yixue AU - Li Y FAU - Zhang, Jian AU - Zhang J FAU - Chen, Hai-Feng AU - Chen HF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111116 PL - England TA - Phys Chem Chem Phys JT - Physical chemistry chemical physics : PCCP JID - 100888160 RN - 0 (Lymphoid Enhancer-Binding Factor 1) RN - 9007-49-2 (DNA) SB - IM MH - DNA/chemistry/*metabolism MH - Humans MH - Kinetics MH - Lymphoid Enhancer-Binding Factor 1/chemistry/*metabolism MH - Molecular Dynamics Simulation MH - Protein Binding MH - Protein Structure, Tertiary MH - Protein Unfolding MH - Temperature EDAT- 2011/11/18 06:00 MHDA- 2012/04/18 06:00 CRDT- 2011/11/18 06:00 PHST- 2011/11/16 [aheadofprint] PHST- 2011/12/08 [epublish] AID - 10.1039/c1cp22610j [doi] PST - ppublish SO - Phys Chem Chem Phys. 2012 Jan 14;14(2):538-45. doi: 10.1039/c1cp22610j. Epub 2011 Nov 16. PMID- 21609000 OWN - NLM STAT- MEDLINE DA - 20110705 DCOM- 20110909 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 50 IP - 27 DP - 2011 Jul 12 TI - The metastasis-associated extracellular matrix protein osteopontin forms transient structure in ligand interaction sites. PG - 6113-24 LID - 10.1021/bi200291e [doi] AB - Osteopontin (OPN) is an acidic hydrophilic glycophosphoprotein that was first identified as a major sialoprotein in bones. It functions as a cell attachment protein displaying a RGD cell adhesion sequence and as a cytokine that signals through integrin and CD44 cell adhesion molecules. OPN is also implicated in human tumor progression and cell invasion. OPN has intrinsic transforming activity, and elevated OPN levels promote metastasis. OPN gene expression is also strongly activated in avian fibroblasts simultaneously transformed by the v-myc and v-mil(raf) oncogenes. Here we have investigated the solution structure of a 220-amino acid recombinant OPN protein by an integrated structural biology approach employing bioinformatic sequence analysis, multidimensional nuclear magnetic resonance spectroscopy, synchrotron radiation circular dichroism spectroscopy, and small-angle X-ray scattering. These studies suggest that OPN is an intrinsically unstructured protein in solution. Although OPN does not fold into a single defined structure, its conformational flexibility significantly deviates from random coil-like behavior. OPN comprises distinct local secondary structure elements with reduced conformational flexibility and substantially populates a compact subspace displaying distinct tertiary contacts. These compacted regions of OPN encompass the binding sites for alpha(V)beta(III) integrin and heparin. The conformational flexibility combined with the modular architecture of OPN may represent an important structural prerequisite for its functional diversity. FAU - Platzer, Gerald AU - Platzer G AD - Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria. FAU - Schedlbauer, Andreas AU - Schedlbauer A FAU - Chemelli, Angela AU - Chemelli A FAU - Ozdowy, Przemyslaw AU - Ozdowy P FAU - Coudevylle, Nicolas AU - Coudevylle N FAU - Auer, Renate AU - Auer R FAU - Kontaxis, Georg AU - Kontaxis G FAU - Hartl, Markus AU - Hartl M FAU - Miles, Andrew J AU - Miles AJ FAU - Wallace, B A AU - Wallace BA FAU - Glatter, Otto AU - Glatter O FAU - Bister, Klaus AU - Bister K FAU - Konrat, Robert AU - Konrat R LA - eng GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110616 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Antimicrobial Cationic Peptides) RN - 0 (Avian Proteins) RN - 0 (Blood Proteins) RN - 0 (Carrier Proteins) RN - 0 (Extracellular Matrix Proteins) RN - 0 (Ligands) RN - 0 (Neoplasm Proteins) RN - 0 (cationic antimicrobial protein CAP 37, human) RN - 106441-73-0 (Osteopontin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Antimicrobial Cationic Peptides/chemistry/metabolism MH - Avian Proteins/*chemistry/*metabolism MH - Blood Proteins/chemistry/metabolism MH - Carrier Proteins/chemistry/metabolism MH - Circular Dichroism MH - Extracellular Matrix Proteins/*chemistry/*metabolism MH - Humans MH - Ligands MH - Molecular Sequence Data MH - Neoplasm Metastasis/*pathology MH - Neoplasm Proteins/*physiology MH - Nuclear Magnetic Resonance, Biomolecular MH - Osteopontin/*chemistry/*metabolism MH - Protein Interaction Mapping MH - Protein Unfolding MH - Quail EDAT- 2011/05/26 06:00 MHDA- 2011/09/10 06:00 CRDT- 2011/05/26 06:00 PHST- 2011/06/16 [aheadofprint] AID - 10.1021/bi200291e [doi] PST - ppublish SO - Biochemistry. 2011 Jul 12;50(27):6113-24. doi: 10.1021/bi200291e. Epub 2011 Jun 16. PMID- 21441896 OWN - NLM STAT- MEDLINE DA - 20110519 DCOM- 20110726 LR - 20140820 IS - 1460-2075 (Electronic) IS - 0261-4189 (Linking) VI - 30 IP - 10 DP - 2011 May 18 TI - The cellular prion protein mediates neurotoxic signalling of beta-sheet-rich conformers independent of prion replication. PG - 2057-70 LID - 10.1038/emboj.2011.86 [doi] AB - Formation of aberrant protein conformers is a common pathological denominator of different neurodegenerative disorders, such as Alzheimer's disease or prion diseases. Moreover, increasing evidence indicates that soluble oligomers are associated with early pathological alterations and that oligomeric assemblies of different disease-associated proteins may share common structural features. Previous studies revealed that toxic effects of the scrapie prion protein (PrP(Sc)), a beta-sheet-rich isoform of the cellular PrP (PrP(C)), are dependent on neuronal expression of PrP(C). In this study, we demonstrate that PrP(C) has a more general effect in mediating neurotoxic signalling by sensitizing cells to toxic effects of various beta-sheet-rich (beta) conformers of completely different origins, formed by (i) heterologous PrP, (ii) amyloid beta-peptide, (iii) yeast prion proteins or (iv) designed beta-peptides. Toxic signalling via PrP(C) requires the intrinsically disordered N-terminal domain (N-PrP) and the GPI anchor of PrP. We found that the N-terminal domain is important for mediating the interaction of PrP(C) with beta-conformers. Interestingly, a secreted version of N-PrP associated with beta-conformers and antagonized their toxic signalling via PrP(C). Moreover, PrP(C)-mediated toxic signalling could be blocked by an NMDA receptor antagonist or an oligomer-specific antibody. Our study indicates that PrP(C) can mediate toxic signalling of various beta-sheet-rich conformers independent of infectious prion propagation, suggesting a pathophysiological role of the prion protein beyond of prion diseases. FAU - Resenberger, Ulrike K AU - Resenberger UK AD - Department of Metabolic Biochemistry, Neurobiochemistry, Adolf-Butenandt-Institute, Ludwig-Maximilians-University Munich, Munich, Germany. FAU - Harmeier, Anja AU - Harmeier A FAU - Woerner, Andreas C AU - Woerner AC FAU - Goodman, Jessica L AU - Goodman JL FAU - Muller, Veronika AU - Muller V FAU - Krishnan, Rajaraman AU - Krishnan R FAU - Vabulas, R Martin AU - Vabulas RM FAU - Kretzschmar, Hans A AU - Kretzschmar HA FAU - Lindquist, Susan AU - Lindquist S FAU - Hartl, F Ulrich AU - Hartl FU FAU - Multhaup, Gerd AU - Multhaup G FAU - Winklhofer, Konstanze F AU - Winklhofer KF FAU - Tatzelt, Jorg AU - Tatzelt J LA - eng GR - GM25874/GM/NIGMS NIH HHS/United States GR - NS067782/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20110325 PL - England TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Amyloid beta-Peptides) RN - 0 (Membrane Proteins) RN - 0 (PrPC Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM CIN - EMBO J. 2011 May 18;30(10):1882-4. PMID: 21593729 MH - Amyloid beta-Peptides/chemistry/metabolism/toxicity MH - Cell Death MH - Humans MH - Membrane Proteins/chemistry/*metabolism/*toxicity MH - Neurons/drug effects/physiology MH - PrPC Proteins/chemistry/*metabolism/*toxicity MH - Prion Diseases/*pathology MH - Protein Conformation MH - Protein Interaction Mapping MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae Proteins/chemistry/metabolism/toxicity PMC - PMC3098494 OID - NLM: PMC3098494 EDAT- 2011/03/29 06:00 MHDA- 2011/07/27 06:00 CRDT- 2011/03/29 06:00 PHST- 2010/08/26 [received] PHST- 2011/03/03 [accepted] PHST- 2011/03/25 [aheadofprint] AID - emboj201186 [pii] AID - 10.1038/emboj.2011.86 [doi] PST - ppublish SO - EMBO J. 2011 May 18;30(10):2057-70. doi: 10.1038/emboj.2011.86. Epub 2011 Mar 25. PMID- 22921828 OWN - NLM STAT- MEDLINE DA - 20121015 DCOM- 20130322 LR - 20141105 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 20 IP - 10 DP - 2012 Oct 10 TI - Enterohaemorrhagic Escherichia coli exploits a tryptophan switch to hijack host f-actin assembly. PG - 1692-703 LID - 10.1016/j.str.2012.07.015 [doi] LID - S0969-2126(12)00280-8 [pii] AB - Intrinsically disordered protein (IDP)-mediated interactions are often characterized by low affinity but high specificity. These traits are essential in signaling and regulation that require reversibility. Enterohaemorrhagic Escherichia coli (EHEC) exploit this situation by commandeering host cytoskeletal signaling to stimulate actin assembly beneath bound bacteria, generating "pedestals" that promote intestinal colonization. EHEC translocates two proteins, EspF(U) and Tir, which form a complex with the host protein IRTKS. The interaction of this complex with N-WASP triggers localized actin polymerization. We show that EspF(U) is an IDP that contains a transiently alpha-helical N-terminus and dynamic C-terminus. Our structure shows that single EspF(U) repeat forms a high-affinity trimolecular complex with N-WASP and IRTKS. We demonstrate that bacterial and cellular ligands interact with IRTKS SH3 in a similar fashion, but the bacterial protein has evolved to outcompete cellular targets by utilizing a tryptophan switch that offers superior binding affinity enabling EHEC-induced pedestal formation. CI - Copyright (c) 2012 Elsevier Ltd. All rights reserved. FAU - Aitio, Olli AU - Aitio O AD - Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland. FAU - Hellman, Maarit AU - Hellman M FAU - Skehan, Brian AU - Skehan B FAU - Kesti, Tapio AU - Kesti T FAU - Leong, John M AU - Leong JM FAU - Saksela, Kalle AU - Saksela K FAU - Permi, Perttu AU - Permi P LA - eng SI - PDB/2LNH GR - R01 AI046454/AI/NIAID NIH HHS/United States GR - R01AI46454/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120823 PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Actins) RN - 0 (Carrier Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (EspFU protein, E coli) RN - 0 (IRTKS protein, human) RN - 0 (Microfilament Proteins) RN - 0 (Peptide Fragments) RN - 0 (WASL protein, human) RN - 0 (Wiskott-Aldrich Syndrome Protein, Neuronal) RN - 8DUH1N11BX (Tryptophan) SB - IM CIN - Structure. 2012 Oct 10;20(10):1613-5. PMID: 23063005 MH - Actins/*chemistry MH - Amino Acid Sequence MH - Carrier Proteins/*chemistry MH - Conserved Sequence MH - Enterohemorrhagic Escherichia coli/*physiology MH - Escherichia coli Proteins/*chemistry MH - HEK293 Cells MH - *Host-Pathogen Interactions MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Microfilament Proteins/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemistry MH - Protein Binding MH - Protein Structure, Quaternary MH - Protein Transport MH - Thermodynamics MH - Tryptophan/*chemistry MH - Wiskott-Aldrich Syndrome Protein, Neuronal/chemistry MH - src Homology Domains PMC - PMC3472031 MID - NIHMS400135 OID - NLM: NIHMS400135 OID - NLM: PMC3472031 EDAT- 2012/08/28 06:00 MHDA- 2013/03/23 06:00 CRDT- 2012/08/28 06:00 PHST- 2012/03/23 [received] PHST- 2012/07/25 [revised] PHST- 2012/07/31 [accepted] PHST- 2012/08/23 [aheadofprint] AID - S0969-2126(12)00280-8 [pii] AID - 10.1016/j.str.2012.07.015 [doi] PST - ppublish SO - Structure. 2012 Oct 10;20(10):1692-703. doi: 10.1016/j.str.2012.07.015. Epub 2012 Aug 23. PMID- 9326367 OWN - NLM STAT- MEDLINE DA - 19971106 DCOM- 19971106 LR - 20071114 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 415 IP - 1 DP - 1997 Sep 22 TI - Formation of a yeast SNARE complex is accompanied by significant structural changes. PG - 49-55 AB - The evolutionarily conserved SNARE (SNAP receptor) proteins and their complexes are key players in the docking and fusion of secretory vesicles with their target membrane. Biophysical techniques were used to characterize structural and energetic properties of the cytoplasmic domains of the yeast SNAREs Snc1 and Sso1, of the SNAP-25-like domain of Sec9, and of the Sso1:Sec9 and Sso1:Sec9:Snc1 complexes. Individually, all three SNAREs are monomeric; Sso1 shows significant secondary structure while Snc1 and Sec9 are largely unstructured. Ternary SNARE complex formation (KD <50 nM) is accompanied by a more than two-fold increase in secondary structure. This binding induced structure, the large increase in thermal stability, and the self-association of the ternary complex represent conserved properties of SNAREs that are probably important in vesicle docking and fusion. FAU - Rice, L M AU - Rice LM AD - The Howard Hughes Medical Institute, and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. FAU - Brennwald, P AU - Brennwald P FAU - Brunger, A T AU - Brunger AT LA - eng GR - GM54160-01/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Fungal Proteins) RN - 0 (Membrane Proteins) RN - 0 (Qa-SNARE Proteins) RN - 0 (Qc-SNARE Proteins) RN - 0 (R-SNARE Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SEC9 protein, S cerevisiae) RN - 0 (SNARE Proteins) RN - 0 (SNC1 protein, S cerevisiae) RN - 0 (SSO1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Vesicular Transport Proteins) SB - IM MH - Base Sequence MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Fungal Proteins/chemistry/genetics/*metabolism MH - Genes, Synthetic MH - Membrane Fusion/physiology MH - Membrane Proteins/chemistry/genetics/*metabolism MH - Molecular Sequence Data MH - Protein Binding MH - Protein Conformation MH - Protein Denaturation MH - Protein Structure, Secondary MH - Qa-SNARE Proteins MH - Qc-SNARE Proteins MH - R-SNARE Proteins MH - Recombinant Proteins/chemistry/metabolism MH - SNARE Proteins MH - *Saccharomyces cerevisiae Proteins MH - Spectrometry, Fluorescence MH - Temperature MH - Ultracentrifugation MH - *Vesicular Transport Proteins EDAT- 1997/11/05 MHDA- 1997/11/05 00:01 CRDT- 1997/11/05 00:00 AID - S0014-5793(97)01091-0 [pii] PST - ppublish SO - FEBS Lett. 1997 Sep 22;415(1):49-55. PMID- 22762014 OWN - NLM STAT- MEDLINE DA - 20120704 DCOM- 20130729 LR - 20141015 IS - 2157-1422 (Electronic) VI - 2 IP - 7 DP - 2012 Jul TI - Biochemistry and cell biology of tau protein in neurofibrillary degeneration. PG - a006247 LID - 10.1101/cshperspect.a006247 [doi] AB - Tau represents the subunit protein of one of the major hallmarks of Alzheimer disease (AD), the neurofibrillary tangles, and is therefore of major interest as an indicator of disease mechanisms. Many of the unusual properties of Tau can be explained by its nature as a natively unfolded protein. Examples are the large number of structural conformations and biochemical modifications (phosphorylation, proteolysis, glycosylation, and others), the multitude of interaction partners (mainly microtubules, but also other cytoskeletal proteins, kinases, and phosphatases, motor proteins, chaperones, and membrane proteins). The pathological aggregation of Tau is counterintuitive, given its high solubility, but can be rationalized by short hydrophobic motifs forming beta structures. The aggregation of Tau is toxic in cell and animal models, but can be reversed by suppressing expression or by aggregation inhibitors. This review summarizes some of the structural, biochemical, and cell biological properties of Tau and Tau fibers. Further aspects of Tau as a diagnostic marker and therapeutic target, its involvement in other Tau-based diseases, and its histopathology are covered by other chapters in this volume. FAU - Mandelkow, Eva-Maria AU - Mandelkow EM AD - Max-Planck Unit for Structural Molecular Biology, c/o DESY, 22607 Hamburg, Germany; DZNE, German Center for Neurodegenerative Diseases, and CAESAR Research Center, 53175 Bonn, Germany. mandelkow@mpasmb.desy.de FAU - Mandelkow, Eckhard AU - Mandelkow E LA - eng PT - Journal Article PT - Review PL - United States TA - Cold Spring Harb Perspect Med JT - Cold Spring Harbor perspectives in medicine JID - 101571139 RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/*metabolism/*pathology MH - Animals MH - Humans MH - Microtubules MH - Nerve Degeneration/*metabolism MH - Neurofibrillary Tangles MH - Neurons/metabolism MH - tau Proteins/*chemistry/genetics/*metabolism/ultrastructure PMC - PMC3385935 OID - NLM: PMC3385935 GN - NLM: Original DateCompleted: 20121002 EDAT- 2012/07/05 06:00 MHDA- 2012/07/05 06:01 CRDT- 2012/07/05 06:00 AID - 10.1101/cshperspect.a006247 [doi] AID - a006247 [pii] PST - ppublish SO - Cold Spring Harb Perspect Med. 2012 Jul;2(7):a006247. doi: 10.1101/cshperspect.a006247. PMID- 24029407 OWN - NLM STAT- MEDLINE DA - 20131126 DCOM- 20140915 IS - 1873-4200 (Electronic) IS - 0301-4622 (Linking) VI - 184 DP - 2013 Dec 31 TI - Replica exchange molecular dynamics simulations of an alpha/beta-type small acid soluble protein (SASP). PG - 17-21 LID - 10.1016/j.bpc.2013.07.014 [doi] LID - S0301-4622(13)00134-8 [pii] AB - Small acid soluble proteins (SASPs) of alpha/beta-type play a major role in the resistance of spore DNAs to external assaults. It has been found that alpha/beta-type SASP exhibits intrinsic disorder on isolation, but it acquires a defined native state upon binding to DNA. This disorder to order transition is not yet understood. Other questions related to the role of the thermodynamics and structure of the individual protein in the complex formation remain elusive. Characterization of the unbound state of alpha/beta-type SASP in experiments could be a challenging problem because of the heterogeneous nature of the ensemble. Here, computer simulations can help gain more insights into the unbound state of alpha/beta-type SASP. In the present work, by using replica exchange molecular dynamics (REMD), we simulated an alpha/beta-type SASP on isolation with an implicit solvent. We found that alpha/beta-type SASP undergoes a continuous phase transition with a small free energy barrier, a common feature of intrinsically disordered proteins (IDPs). Additionally, we detected the presence of residual alpha-helical structures at local level and a high degree of plasticity in the chain which can contribute to the fast disorder to order transition by reducing the fly-casting mechanism. CI - (c) 2013 Elsevier B.V. All rights reserved. FAU - Ojeda-May, P AU - Ojeda-May P AD - Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, IN 46202, USA. Electronic address: pojedama@iupui.edu. FAU - Pu, Jingzhi AU - Pu J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130820 PL - Netherlands TA - Biophys Chem JT - Biophysical chemistry JID - 0403171 RN - 0 (Bacterial Proteins) SB - IM MH - Bacillus subtilis/*chemistry MH - Bacterial Proteins/*chemistry MH - Models, Molecular MH - *Molecular Dynamics Simulation MH - Protein Structure, Secondary MH - Thermodynamics OTO - NOTNLM OT - Intrinsic disordered protein OT - MD simulations OT - Molecular simulation OT - Proteins EDAT- 2013/09/14 06:00 MHDA- 2014/09/16 06:00 CRDT- 2013/09/14 06:00 PHST- 2013/07/10 [received] PHST- 2013/07/30 [revised] PHST- 2013/07/31 [accepted] PHST- 2013/08/20 [aheadofprint] AID - S0301-4622(13)00134-8 [pii] AID - 10.1016/j.bpc.2013.07.014 [doi] PST - ppublish SO - Biophys Chem. 2013 Dec 31;184:17-21. doi: 10.1016/j.bpc.2013.07.014. Epub 2013 Aug 20. PMID- 18692067 OWN - NLM STAT- MEDLINE DA - 20080915 DCOM- 20081001 LR - 20081121 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 382 IP - 4 DP - 2008 Oct 17 TI - The affinity of Ets-1 for DNA is modulated by phosphorylation through transient interactions of an unstructured region. PG - 1014-30 LID - 10.1016/j.jmb.2008.07.064 [doi] AB - Binding of the transcription factor Ets-1 to DNA is allosterically regulated by a serine-rich region (SRR) that modulates the dynamic character of the adjacent structured DNA-binding ETS domain and its flanking autoinhibitory elements. Multi-site phosphorylation of the flexible SRR in response to Ca(2+) signaling mediates variable regulation of Ets-1 DNA-binding affinity. In this study, we further investigated the mechanism of this regulation. First, thermal and urea denaturation experiments demonstrated that phosphorylation of the predominantly unstructured SRR imparts enhanced thermodynamic stability on the well-folded ETS domain and its inhibitory module. We next identified a minimal fragment (residues 279-440) that exhibits both enhanced autoinhibition of Ets-1 DNA-binding and allosteric reinforcement by phosphorylation. To test for intramolecular interactions between the SRR and the rest of the fragment that were not detectable by (1)H-(1)H NOE measurements, paramagnetic relaxation enhancements were performed using Cu(2+) bound to the N-terminal ATCUN motif. Increased relaxation detected for specific amide and methyl groups revealed a preferential interaction surface for the flexible SRR extending from the inhibitory module to the DNA-binding interface. Phosphorylation enhanced the localization of the SRR to this surface. We therefore hypothesize that the positioning of the SRR at the DNA-binding interface and its role in shifting Ets-1 to an inhibited conformation are linked. In particular, transient interactions dampen the conformational flexibility of the ETS domain and inhibitory module required for high-affinity binding, as well as possibly occlude the DNA interaction site. Surprisingly, the phosphorylation-dependent effects were relatively insensitive to changes in ionic strength, suggesting that electrostatic forces are not the dominant mechanism for mediating these interactions. The results of this study highlight the role of flexibility and transient binding in the variable regulation of Ets-1 activity. FAU - Lee, Gregory M AU - Lee GM AD - Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3. FAU - Pufall, Miles A AU - Pufall MA FAU - Meeker, Charles A AU - Meeker CA FAU - Kang, Hyun-Seo AU - Kang HS FAU - Graves, Barbara J AU - Graves BJ FAU - McIntosh, Lawrence P AU - McIntosh LP LA - eng GR - CA42014-I/CA/NCI NIH HHS/United States GR - GM08537/GM/NIGMS NIH HHS/United States GR - GM38663/GM/NIGMS NIH HHS/United States GR - T32-CA93247/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20080729 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Peptide Fragments) RN - 0 (Proto-Oncogene Protein c-ets-1) RN - 9007-49-2 (DNA) SB - IM MH - Allosteric Regulation MH - Amino Acid Sequence MH - DNA/*chemistry/genetics MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Nucleic Acid Conformation MH - Peptide Fragments/chemistry/genetics/metabolism MH - Phosphorylation MH - *Protein Conformation MH - *Protein Structure, Tertiary MH - Proto-Oncogene Protein c-ets-1/antagonists & inhibitors/*chemistry/genetics/*metabolism MH - Static Electricity MH - Thermodynamics EDAT- 2008/08/12 09:00 MHDA- 2008/10/02 09:00 CRDT- 2008/08/12 09:00 PHST- 2008/06/07 [received] PHST- 2008/07/24 [revised] PHST- 2008/07/24 [accepted] PHST- 2008/07/29 [aheadofprint] AID - S0022-2836(08)00933-9 [pii] AID - 10.1016/j.jmb.2008.07.064 [doi] PST - ppublish SO - J Mol Biol. 2008 Oct 17;382(4):1014-30. doi: 10.1016/j.jmb.2008.07.064. Epub 2008 Jul 29. PMID- 22291015 OWN - NLM STAT- MEDLINE DA - 20120319 DCOM- 20120612 LR - 20141019 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 12 DP - 2012 Mar 16 TI - Using intramolecular disulfide bonds in tau protein to deduce structural features of aggregation-resistant conformations. PG - 9591-600 LID - 10.1074/jbc.M111.336107 [doi] AB - Because tau aggregation likely plays a role in a number of neurodegenerative diseases, understanding the processes that affect tau aggregation is of considerable importance. One factor that has been shown to influence the aggregation propensity is the oxidation state of the protein itself. Tau protein, which contains two naturally occurring cysteine residues, can form both intermolecular disulfide bonds and intramolecular disulfide bonds. Several studies suggest that intermolecular disulfide bonds can promote tau aggregation in vitro. By contrast, although there are data to suggest that intramolecular disulfide bond formation retards tau aggregation in vitro, the precise mechanism underlying this observation remains unclear. While it has been hypothesized that a single intramolecular disulfide bond in tau leads to compact conformations that cannot form extended structure consistent with tau fibrils, there are few data to support this conjecture. In the present study we generate oxidized forms of the truncation mutant, K18, which contains all four microtubule binding repeats, and isolate the monomeric fraction, which corresponds to K18 monomers that have a single intramolecular disulfide bond. We study the aggregation propensity of the oxidized monomeric fraction and relate these data to an atomistic model of the K18 unfolded ensemble. Our results argue that the main effect of intramolecular disulfide bond formation is to preferentially stabilize conformers within the unfolded ensemble that place the aggregation-prone tau subsequences, PHF6* and PHF6, in conformations that are inconsistent with the formation of cross-beta-structure. These data further our understanding of the precise structural features that retard tau aggregation. FAU - Walker, Sophie AU - Walker S AD - Research Laboratory of Electronics,Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA. FAU - Ullman, Orly AU - Ullman O FAU - Stultz, Collin M AU - Stultz CM LA - eng GR - 5R21NS063185-02/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20120130 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Disulfides) RN - 0 (tau Proteins) SB - IM MH - Disulfides/*chemistry/metabolism MH - Humans MH - Models, Molecular MH - Oxidation-Reduction MH - Protein Folding MH - Protein Structure, Secondary MH - tau Proteins/*chemistry/genetics/metabolism PMC - PMC3308815 OID - NLM: PMC3308815 EDAT- 2012/02/01 06:00 MHDA- 2012/06/13 06:00 CRDT- 2012/02/01 06:00 PHST- 2012/01/30 [aheadofprint] AID - M111.336107 [pii] AID - 10.1074/jbc.M111.336107 [doi] PST - ppublish SO - J Biol Chem. 2012 Mar 16;287(12):9591-600. doi: 10.1074/jbc.M111.336107. Epub 2012 Jan 30. PMID- 12107152 OWN - NLM STAT- MEDLINE DA - 20020710 DCOM- 20020822 LR - 20140612 IS - 0021-9193 (Print) IS - 0021-9193 (Linking) VI - 184 IP - 15 DP - 2002 Aug TI - Structural evidence that the P/Q domain of ZipA is an unstructured, flexible tether between the membrane and the C-terminal FtsZ-binding domain. PG - 4313-5 AB - The cell division protein ZipA has an N-terminal transmembrane domain and a C-terminal globular domain that binds FtsZ. Between them are a charged domain and a P/Q domain rich in proline and glutamine that has been proposed to be an unfolded polypeptide. Here we provide evidence obtained by electron microscopy that the P/Q domain is a flexible tether ranging in length from 8 to 20 nm and invisible in rotary shadowing electron microscopy. We estimated a persistence length of 0.66 nm, which is similar to the persistence lengths of other unfolded and unstructured polypeptides. FAU - Ohashi, Tomoo AU - Ohashi T AD - Department of Cell Biology, Duke University Medical Center, Durham, North Carolina 27710-3709, USA. FAU - Hale, Cynthia A AU - Hale CA FAU - de Boer, Piet A J AU - de Boer PA FAU - Erickson, Harold P AU - Erickson HP LA - eng GR - CA47056/CA/NCI NIH HHS/United States GR - GM-57059/GM/NIGMS NIH HHS/United States GR - R01 GM057059/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - J Bacteriol JT - Journal of bacteriology JID - 2985120R RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (Cell Cycle Proteins) RN - 0 (Cytoskeletal Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (FtsZ protein, Bacteria) RN - 0 (Luminescent Proteins) RN - 0 (ZipA protein, E coli) RN - 0RH81L854J (Glutamine) RN - 147336-22-9 (Green Fluorescent Proteins) RN - 9DLQ4CIU6V (Proline) SB - IM MH - Bacterial Proteins/*chemistry/ultrastructure MH - Carrier Proteins/*chemistry/ultrastructure MH - Cell Cycle Proteins/*chemistry/ultrastructure MH - Cell Division MH - *Cytoskeletal Proteins MH - Escherichia coli MH - *Escherichia coli Proteins MH - Glutamine/chemistry MH - Green Fluorescent Proteins MH - Luminescent Proteins MH - Microscopy, Electron MH - Models, Molecular MH - Proline/chemistry MH - Protein Binding MH - Protein Conformation PMC - PMC135210 OID - NLM: PMC135210 EDAT- 2002/07/11 10:00 MHDA- 2002/08/23 10:01 CRDT- 2002/07/11 10:00 PST - ppublish SO - J Bacteriol. 2002 Aug;184(15):4313-5. PMID- 17355803 OWN - NLM STAT- MEDLINE DA - 20070314 DCOM- 20090924 LR - 20150313 VI - 26 IP - 3 DP - 2007 Mar TI - [Prothymosin alpha and tumor: current status and perspective]. PG - 333-6 AB - Prothymosin alpha (ProTalpha) is a small molecule of natively unstructured acidic protein, and widely exists in mammalian tissues. Nevertheless, its biological functions are still elusive. Recent studies indicate that ProTalpha is involved in carcinogenesis and cancer development. We reviewed current reports on the potential roles of ProTalpha in cell proliferation, carcinogenesis, apoptosis, and immunomodulatory, discussed the regulation of ProTalpha gene expression and possible molecular mechanisms underlying its internal and external actions in cells, and explored its significance in tumor diagnosis and treatment. FAU - Wang, Mei AU - Wang M AD - Department of Bioscience and Biotechnology, Dalian University of Technology, Dalian, Liaoning, PR China. FAU - Pan, Ji-Yong AU - Pan JY LA - chi PT - English Abstract PT - Journal Article PT - Review PL - China TA - Ai Zheng JT - Ai zheng = Aizheng = Chinese journal of cancer JID - 9424852 RN - 0 (Protein Precursors) RN - 0 (Tumor Markers, Biological) RN - 0 (prothymosin alpha) RN - 61512-21-8 (Thymosin) SB - IM MH - Animals MH - *Apoptosis MH - *Cell Proliferation MH - Genetic Therapy MH - Humans MH - Neoplasms/metabolism/*pathology/therapy MH - *Protein Precursors/genetics/immunology/metabolism/physiology MH - Thymosin/*analogs & derivatives/genetics/immunology/metabolism/physiology MH - Tumor Markers, Biological/*analysis RF - 41 EDAT- 2007/03/16 09:00 MHDA- 2009/09/25 06:00 CRDT- 2007/03/16 09:00 AID - 1000-467X200703333 [pii] PST - ppublish SO - Ai Zheng. 2007 Mar;26(3):333-6. PMID- 23204517 OWN - NLM STAT- MEDLINE DA - 20130121 DCOM- 20130326 LR - 20141107 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 3 DP - 2013 Jan 18 TI - The calmodulin regulator protein, PEP-19, sensitizes ATP-induced Ca2+ release. PG - 2040-8 LID - 10.1074/jbc.M112.411314 [doi] AB - PEP-19 is a small, intrinsically disordered protein that binds to the C-domain of calmodulin (CaM) via an IQ motif and tunes its Ca(2+) binding properties via an acidic sequence. We show here that the acidic sequence of PEP-19 has intrinsic Ca(2+) binding activity, which may modulate Ca(2+) binding to CaM by stabilizing an initial Ca(2+)-CaM complex or by electrostatically steering Ca(2+) to and from CaM. Because PEP-19 is expressed in cells that exhibit highly active Ca(2+) dynamics, we tested the hypothesis that it influences ligand-dependent Ca(2+) release. We show that PEP-19 increases the sensitivity of HeLa cells to ATP-induced Ca(2+) release to greatly increase the percentage of cells responding to sub-saturating doses of ATP and increases the frequency of Ca(2+) oscillations. Mutations in the acidic sequence of PEP-19 that inhibit or prevent it from modulating Ca(2+) binding to CaM greatly inhibit its effect on ATP-induced Ca(2+) release. Thus, this cellular effect of PEP-19 does not depend simply on binding to CaM via the IQ motif but requires its acidic metal binding domain. Tuning the activities of Ca(2+) mobilization pathways places PEP-19 at the top of CaM signaling cascades, with great potential to exert broad effects on downstream CaM targets, thus expanding the biological significance of this small regulator of CaM signaling. FAU - Wang, Xu AU - Wang X AD - Department of Biochemistry and Molecular Biology and Structural Biology Imaging Center, University of Texas Medical School, Houston, Texas 77030, USA. FAU - Xiong, Liang Wen AU - Xiong LW FAU - El Ayadi, Amina AU - El Ayadi A FAU - Boehning, Darren AU - Boehning D FAU - Putkey, John A AU - Putkey JA LA - eng GR - GM06961109/GM/NIGMS NIH HHS/United States GR - GM081685/GM/NIGMS NIH HHS/United States GR - GM081685-03S1/GM/NIGMS NIH HHS/United States GR - R01 GM081685/GM/NIGMS NIH HHS/United States GR - R90 DK071504/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20121130 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Calmodulin) RN - 0 (Ligands) RN - 0 (Nerve Tissue Proteins) RN - 106494-08-0 (PCP4 protein, human) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - SY7Q814VUP (Calcium) SB - IM MH - Adenosine Triphosphate/metabolism MH - Amino Acid Motifs MH - Binding Sites MH - Calcium/*metabolism MH - *Calcium Signaling MH - Calmodulin/chemistry/*metabolism MH - HeLa Cells MH - Humans MH - Kinetics MH - Ligands MH - Molecular Imaging MH - Molecular Sequence Data MH - Mutation MH - Nerve Tissue Proteins/chemistry/genetics/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Structure, Tertiary MH - Static Electricity MH - Transfection PMC - PMC3548510 OID - NLM: PMC3548510 EDAT- 2012/12/04 06:00 MHDA- 2013/03/27 06:00 CRDT- 2012/12/04 06:00 PHST- 2012/11/30 [aheadofprint] AID - M112.411314 [pii] AID - 10.1074/jbc.M112.411314 [doi] PST - ppublish SO - J Biol Chem. 2013 Jan 18;288(3):2040-8. doi: 10.1074/jbc.M112.411314. Epub 2012 Nov 30. PMID- 24360766 OWN - NLM STAT- MEDLINE DA - 20140324 DCOM- 20141117 LR - 20150422 IS - 1096-0856 (Electronic) IS - 1090-7807 (Linking) VI - 241 DP - 2014 Apr TI - Homonuclear decoupling for enhancing resolution and sensitivity in NOE and RDC measurements of peptides and proteins. PG - 97-102 LID - 10.1016/j.jmr.2013.11.006 [doi] LID - S1090-7807(13)00289-9 [pii] AB - Application of band-selective homonuclear (BASH) (1)H decoupling pulses during acquisition of the (1)H free induction decay is shown to be an efficient procedure for removal of scalar and residual dipolar couplings between amide and aliphatic protons. BASH decoupling can be applied in both dimensions of a homonuclear 2D NMR experiment and is particularly useful for enhancing spectral resolution in the H(N)-H(alpha) region of NOESY spectra of peptides and proteins, which contain important information on the backbone torsion angles. The method then also prevents generation of zero quantum and Hz(N)-Hz(alpha) terms, thereby facilitating analysis of intraresidue interactions. Application to the NOESY spectrum of a hexapeptide fragment of the intrinsically disordered protein alpha-synuclein highlights the considerable diffusion anisotropy present in linear peptides. Removal of residual dipolar couplings between H(N) and aliphatic protons in weakly aligned proteins increases resolution in the (1)H-(15)N HSQC region of the spectrum and allows measurement of RDCs in samples that are relatively strongly aligned. The approach is demonstrated for measurement of RDCs in protonated (15)N/(13)C-enriched ubiquitin, aligned in Pf1, yielding improved fitting to the ubiquitin structure. CI - Published by Elsevier Inc. FAU - Ying, Jinfa AU - Ying J AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. FAU - Roche, Julien AU - Roche J AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. FAU - Bax, Ad AU - Bax A AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: bax@nih.gov. LA - eng GR - ZIA DK029048-07/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Review DEP - 20131122 PL - United States TA - J Magn Reson JT - Journal of magnetic resonance (San Diego, Calif. : 1997) JID - 9707935 RN - 0 (Proteins) SB - IM MH - Animals MH - Anisotropy MH - Humans MH - Liquid Crystals/chemistry MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Protein Conformation MH - Proteins/*chemistry PMC - PMC3965638 MID - NIHMS544574 OID - NLM: NIHMS544574 OID - NLM: PMC3965638 OTO - NOTNLM OT - Diffusion anisotropy OT - IDP OT - Liquid crystal OT - NOESY OT - RDC OT - Residual dipolar coupling OT - Synuclein OT - Ubiquitin OT - Weak alignment EDAT- 2013/12/24 06:00 MHDA- 2014/11/18 06:00 CRDT- 2013/12/24 06:00 PHST- 2013/10/14 [received] PHST- 2013/11/11 [revised] PHST- 2013/11/12 [accepted] PHST- 2013/11/22 [aheadofprint] AID - S1090-7807(13)00289-9 [pii] AID - 10.1016/j.jmr.2013.11.006 [doi] PST - ppublish SO - J Magn Reson. 2014 Apr;241:97-102. doi: 10.1016/j.jmr.2013.11.006. Epub 2013 Nov 22. PMID- 19081741 OWN - NLM STAT- MEDLINE DA - 20090729 DCOM- 20090826 LR - 20140914 IS - 1874-270X (Electronic) VI - 2 IP - 1 DP - 2008 Jun TI - 1H, 13C, and 15N resonance assignments of murine amelogenin, an enamel biomineralization protein. PG - 89-91 LID - 10.1007/s12104-008-9092-x [doi] AB - Amelogenin is the predominant matrix protein in developing dental enamel. Making extensive use of residue specific 15N-labeled amino acids samples, the majority of the main and side chain resonances for murine amelogenin were assigned in 2% aqueous acetic acid at pH 3.0. FAU - Buchko, Garry W AU - Buchko GW AD - Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. FAU - Bekhazi, Jacky AU - Bekhazi J FAU - Cort, John R AU - Cort JR FAU - Valentine, Nancy B AU - Valentine NB FAU - Snead, Malcolm L AU - Snead ML FAU - Shaw, Wendy J AU - Shaw WJ LA - eng GR - DE-015347/DE/NIDCR NIH HHS/United States GR - R01 DE015347/DE/NIDCR NIH HHS/United States GR - R01 DE015347-03/DE/NIDCR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (Amelogenin) RN - 0 (Carbon Isotopes) RN - 0 (Minerals) RN - 0 (Nitrogen Isotopes) RN - 0 (Protons) SB - IM MH - Amelogenin/*chemistry MH - Amino Acid Sequence MH - Animals MH - Carbon Isotopes/chemistry MH - Dental Enamel/*chemistry MH - Magnetic Resonance Spectroscopy/*methods MH - Mice MH - Minerals/*chemistry MH - Molecular Sequence Data MH - Molecular Weight MH - Nitrogen Isotopes/chemistry MH - Protons PMC - PMC2600544 MID - NIHMS55757 OTO - NOTNLM OT - Amelogenin OT - Biomineralization OT - Enamel OT - Polyproline type II structure OT - Unfolded protein EDAT- 2008/12/17 09:00 MHDA- 2009/08/27 09:00 CRDT- 2008/12/17 09:00 AID - 10.1007/s12104-008-9092-x [doi] PST - ppublish SO - Biomol NMR Assign. 2008 Jun;2(1):89-91. doi: 10.1007/s12104-008-9092-x. PMID- 22528085 OWN - NLM STAT- MEDLINE DA - 20120424 DCOM- 20120808 LR - 20131121 IS - 1940-6029 (Electronic) IS - 1064-3745 (Linking) VI - 849 DP - 2012 TI - Conformations of microtubule-associated protein Tau mapped by fluorescence resonance energy transfer. PG - 85-99 LID - 10.1007/978-1-61779-551-0_7 [doi] AB - The microtubule-associated protein Tau plays a physiological role of stabilizing neuronal microtubules by binding to their lateral surface. Tau belongs to the category of natively unfolded protein as it shows typical features of random coil, as analyzed by various biophysical techniques. In cells, it is subjected to several posttranslational modifications (e.g., phosphorylation, cleavage, ubiquitination, and glycosylation). In neurodegenerative diseases, Tau forms insoluble aggregates called paired helical filaments (PHFs). We have applied fluorescence resonance energy transfer (FRET) to examine the conformations of soluble Tau. We created a series of Tau mutants, each carrying one tryptophan and one cysteine (labeled by IEADANS). This made it possible to measure the distance between these FRET pairs placed in different domains of Tau. This approach enables one to analyze the global folding of soluble Tau and its alteration upon phosphorylation and denaturation. FAU - Jeganathan, Sadasivam AU - Jeganathan S AD - Max-Planck-Unit for Structural Molecular Biology c/o DESY, Hamburg, Germany. FAU - Chinnathambi, Subashchandrabose AU - Chinnathambi S FAU - Mandelkow, Eva-Maria AU - Mandelkow EM FAU - Mandelkow, Eckhard AU - Mandelkow E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Methods Mol Biol JT - Methods in molecular biology (Clifton, N.J.) JID - 9214969 RN - 0 (tau Proteins) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Fluorescence Resonance Energy Transfer/*methods MH - Guanidine/pharmacology MH - Phosphorylation MH - Protein Conformation/drug effects MH - Protein Unfolding/drug effects MH - tau Proteins/*chemistry EDAT- 2012/04/25 06:00 MHDA- 2012/08/09 06:00 CRDT- 2012/04/25 06:00 AID - 10.1007/978-1-61779-551-0_7 [doi] PST - ppublish SO - Methods Mol Biol. 2012;849:85-99. doi: 10.1007/978-1-61779-551-0_7. PMID- 15039431 OWN - NLM STAT- MEDLINE DA - 20040524 DCOM- 20040729 LR - 20041117 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 22 DP - 2004 May 28 TI - Coupling of folding and binding of thymosin beta4 upon interaction with monomeric actin monitored by nuclear magnetic resonance. PG - 23637-45 AB - Thymosin beta4 is a major actin-sequestering protein, yet the structural basis for its biological function is still unknown. This study provides insight regarding the way this 43-amino acid peptide, mostly unstructured in solution, binds to monomeric actin and prevents its assembly in filaments. We show here that the whole backbone of thymosin beta4 is highly affected upon binding to G-actin. The assignment of all amide protons and nitrogens of thymosin in the bound state, obtained using a combination of NMR experiments and selective labelings, shows that thymosin folds completely upon binding and displays a central extended region flanked by two N- and C-terminal helices. The cleavage of actin by subtilisin in the DNase I binding loop does not modify the structure of thymosin beta4 in the complex, showing that the backbone of the peptide is not in close proximity to segment 42-47 of actin. The combination of our NMR results and previously published mutation and cross-link data allows a better characterization of the binding mode of thymosins on G-actin. FAU - Domanski, Michael AU - Domanski M AD - Institut de Chimie des Substances Naturelles, Laboratoire de Chimie et Biologie Structurales, CNRS, 1 Avenue de la Terrasse, F-91190 Gif sur Yvette, France. FAU - Hertzog, Maud AU - Hertzog M FAU - Coutant, Jerome AU - Coutant J FAU - Gutsche-Perelroizen, Irina AU - Gutsche-Perelroizen I FAU - Bontems, Francois AU - Bontems F FAU - Carlier, Marie-France AU - Carlier MF FAU - Guittet, Eric AU - Guittet E FAU - van Heijenoort, Carine AU - van Heijenoort C LA - eng SI - PDB/1UY5 PT - Journal Article DEP - 20040322 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Actins) RN - 61512-21-8 (Thymosin) RN - 77591-33-4 (thymosin beta(4)) SB - IM MH - Actins/*chemistry/metabolism MH - Animals MH - Binding Sites MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Protein Binding MH - Protein Folding MH - Thymosin/*chemistry EDAT- 2004/03/25 05:00 MHDA- 2004/07/30 05:00 CRDT- 2004/03/25 05:00 PHST- 2004/03/22 [aheadofprint] AID - 10.1074/jbc.M311413200 [doi] AID - M311413200 [pii] PST - ppublish SO - J Biol Chem. 2004 May 28;279(22):23637-45. Epub 2004 Mar 22. PMID- 19214739 OWN - NLM STAT- MEDLINE DA - 20090729 DCOM- 20090819 IS - 1573-6830 (Electronic) IS - 0272-4340 (Linking) VI - 29 IP - 6-7 DP - 2009 Sep TI - Chaperone-like antibodies in neurodegenerative tauopathies: implication for immunotherapy. PG - 793-8 LID - 10.1007/s10571-009-9355-9 [doi] AB - Alzheimer's disease (AD) belongs to the category of neurodegenerative tauopathies, which are characterized by intracellular and extracellular accumulation of misfolded tau. Structurally, tau belongs to the family of the intrinsically disordered proteins that are characterized by the absence of well-defined three-dimensional structure of the free protein. In the course of neurodegeneration, intrinsically disordered tau protein gains highly ordered misfolded structure. Currently it is widely accepted that misfolded tau proteins represent viable drug target for prospective therapeutic development. Until now several therapeutic approaches targeting misfolded tau were developed. Monoclonal antibodies with chaperone-like activities that would be able to neutralize the toxic gain of function of misfolded tau represent novel promising immunological concept in the treatment of AD. We suggest that antibodies as specific chaperones targeting misfolded proteins may serve as potent therapeutic drugs of AD as well as others conformational diseases. FAU - Kontsekova, Eva AU - Kontsekova E AD - Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, 845 10, Slovak Republic. FAU - Ivanovova, Natalia AU - Ivanovova N FAU - Handzusova, Martina AU - Handzusova M FAU - Novak, Michal AU - Novak M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20090213 PL - United States TA - Cell Mol Neurobiol JT - Cellular and molecular neurobiology JID - 8200709 RN - 0 (Antibodies, Monoclonal) RN - 0 (Molecular Chaperones) RN - 0 (tau Proteins) SB - IM MH - Animals MH - Antibodies, Monoclonal/*therapeutic use MH - Humans MH - *Immunotherapy MH - Molecular Chaperones/*therapeutic use MH - Tauopathies/*therapy MH - tau Proteins RF - 62 EDAT- 2009/02/14 09:00 MHDA- 2009/08/20 09:00 CRDT- 2009/02/14 09:00 PHST- 2008/11/19 [received] PHST- 2009/01/22 [accepted] PHST- 2009/02/13 [aheadofprint] AID - 10.1007/s10571-009-9355-9 [doi] PST - ppublish SO - Cell Mol Neurobiol. 2009 Sep;29(6-7):793-8. doi: 10.1007/s10571-009-9355-9. Epub 2009 Feb 13. PMID- 22906532 OWN - NLM STAT- MEDLINE DA - 20121226 DCOM- 20130318 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1834 IP - 1 DP - 2013 Jan TI - Structural disorder and local order of hNopp140. PG - 342-50 LID - 10.1016/j.bbapap.2012.08.005 [doi] LID - S1570-9639(12)00178-1 [pii] AB - Human nucleolar phosphoprotein p140 (hNopp 140) is a highly phosphorylated protein inhibitor of casein kinase 2 (CK2). As in the case of many kinase-inhibitor systems, the inhibitor has been described to belong to the family of intrinsically disordered proteins (IDPs), which often utilize transient structural elements to bind their cognate enzyme. Here we investigated the structural status of this protein both to provide distinct lines of evidence for its disorder and to point out its transient structure potentially involved in interactions and also its tendency to aggregate. Structural disorder of hNopp140 is apparent by its anomalous electrophoretic mobility, protease sensitivity, heat stability, hydrodynamic behavior on size-exclusion chromatography, (1)H NMR spectrum and differential scanning calorimetry scan. hNopp140 has a significant tendency to aggregate and the change of its circular dichroism spectrum in the presence of 0-80% TFE suggests a tendency to form local helical structures. Wide-line NMR measurements suggest the overall disordered character of the protein. In all, our data suggest that this protein falls into the pre-molten globule state of IDPs, with a significant tendency to become ordered in the presence of its partner as demonstrated in the presence of transcription factor IIB (TFIIB). CI - Copyright (c) 2012 Elsevier B.V. All rights reserved. FAU - Tantos, Agnes AU - Tantos A AD - Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary. FAU - Szrnka, Kriszta AU - Szrnka K FAU - Szabo, Beata AU - Szabo B FAU - Bokor, Monika AU - Bokor M FAU - Kamasa, Pawel AU - Kamasa P FAU - Matus, Peter AU - Matus P FAU - Bekesi, Angela AU - Bekesi A FAU - Tompa, Kalman AU - Tompa K FAU - Han, Kyou-Hoon AU - Han KH FAU - Tompa, Peter AU - Tompa P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120811 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (NOLC1 protein, human) RN - 0 (Nuclear Proteins) RN - 0 (Phosphoproteins) RN - 0 (Transcription Factor TFIIB) RN - EC 2.7.11.1 (Casein Kinase II) SB - IM MH - Casein Kinase II/antagonists & inhibitors/chemistry/metabolism MH - Circular Dichroism MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*chemistry/metabolism MH - Phosphoproteins/*chemistry/metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Transcription Factor TFIIB/chemistry/metabolism EDAT- 2012/08/22 06:00 MHDA- 2013/03/19 06:00 CRDT- 2012/08/22 06:00 PHST- 2012/03/23 [received] PHST- 2012/08/02 [revised] PHST- 2012/08/04 [accepted] PHST- 2012/08/11 [aheadofprint] AID - S1570-9639(12)00178-1 [pii] AID - 10.1016/j.bbapap.2012.08.005 [doi] PST - ppublish SO - Biochim Biophys Acta. 2013 Jan;1834(1):342-50. doi: 10.1016/j.bbapap.2012.08.005. Epub 2012 Aug 11. PMID- 19759397 OWN - NLM STAT- MEDLINE DA - 20091125 DCOM- 20100121 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 284 IP - 48 DP - 2009 Nov 27 TI - Multivalency in the assembly of intrinsically disordered Dynein intermediate chain. PG - 33115-21 LID - 10.1074/jbc.M109.048587 [doi] AB - Dynein light chains are thought to increase binding efficiency of dynein intermediate chain to both dynein heavy chain and dynactin, but their exact role is not clear. Isothermal titration calorimetry and x-ray crystallography reported herein indicate that multivalency effects underlie efficient dynein assembly and regulation. For a ternary complex of a 60-amino acid segment of dynein intermediate chain (IC) bound to two homodimeric dynein light chains Tctex1 and LC8, there is a 50-fold affinity enhancement for the second light chain binding. For a designed IC construct containing two LC8 sites, observed the 1000-fold enhancement reflects a remarkably pure entropic chelate effect of a magnitude commensurate with theoretical predictions. The lower enhancement in wild-type IC is attributed to unfavorable free energy changes associated with incremental interactions of IC with Tctex1. Our results show assembled dynein IC as an elongated, flexible polybivalent duplex, and suggest that polybivalency is an important general mechanism for constructing stable yet reversible and functionally versatile complexes. FAU - Hall, Justin AU - Hall J AD - Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA. FAU - Karplus, P Andrew AU - Karplus PA FAU - Barbar, Elisar AU - Barbar E LA - eng SI - PDB/3FM7 SI - PDB/3GLW GR - 00210/PHS HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20090916 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Drosophila Proteins) RN - EC 3.6.4.2 (Dyneins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Calorimetry/methods MH - Crystallography, X-Ray MH - Drosophila Proteins/*chemistry/genetics/metabolism MH - Drosophila melanogaster/genetics/metabolism MH - Dyneins/*chemistry/genetics/metabolism MH - Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Folding MH - Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Thermodynamics PMC - PMC2785153 OID - NLM: PMC2785153 EDAT- 2009/09/18 06:00 MHDA- 2010/01/22 06:00 CRDT- 2009/09/18 06:00 PHST- 2009/09/16 [aheadofprint] AID - M109.048587 [pii] AID - 10.1074/jbc.M109.048587 [doi] PST - ppublish SO - J Biol Chem. 2009 Nov 27;284(48):33115-21. doi: 10.1074/jbc.M109.048587. Epub 2009 Sep 16. PMID- 25049401 OWN - NLM STAT- MEDLINE DA - 20140820 DCOM- 20141103 LR - 20150604 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 33 DP - 2014 Aug 19 TI - Dissecting allosteric effects of activator-coactivator complexes using a covalent small molecule ligand. PG - 12061-6 LID - 10.1073/pnas.1406033111 [doi] AB - Allosteric binding events play a critical role in the formation and stability of transcriptional activator-coactivator complexes, perhaps in part due to the often intrinsically disordered nature of one or more of the constituent partners. The kinase-inducible domain interacting (KIX) domain of the master coactivator CREB binding protein/p300 is a conformationally dynamic domain that complexes with transcriptional activators at two discrete binding sites in allosteric communication. The complexation of KIX with the transcriptional activation domain of mixed-lineage leukemia protein leads to an enhancement of binding by the activation domain of CREB (phosphorylated kinase-inducible domain of CREB) to the second site. A transient kinetic analysis of the ternary complex formation aided by small molecule ligands that induce positive or negative cooperative binding reveals that positive cooperativity is largely governed by stabilization of the bound complex as indicated by a decrease in koff. Thus, this suggests the increased binding affinity for the second ligand is not due to an allosteric creation of a more favorable binding interface by the first ligand. This is consistent with data from us and from others indicating that the on rates of conformationally dynamic proteins approach the limits of diffusion. In contrast, negative cooperativity is manifested by alterations in both kon and koff, suggesting stabilization of the binary complex. FAU - Wang, Ningkun AU - Wang N AD - Program in Chemical Biology,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109. FAU - Lodge, Jean M AU - Lodge JM AD - Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109Departments of Chemistry and. FAU - Fierke, Carol A AU - Fierke CA AD - Program in Chemical Biology,Departments of Chemistry andBiological Chemistry, amapp@umich.edu fierke@umich.edu. FAU - Mapp, Anna K AU - Mapp AK AD - Program in Chemical Biology,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109Departments of Chemistry and amapp@umich.edu fierke@umich.edu. LA - eng GR - 2R01 GM65330/GM/NIGMS NIH HHS/United States GR - GM07767/GM/NIGMS NIH HHS/United States GR - R01 GM055387/GM/NIGMS NIH HHS/United States GR - R01 GM55387/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140721 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Ligands) RN - EC 2.3.1.48 (p300-CBP Transcription Factors) SB - IM MH - Allosteric Regulation MH - Ligands MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - p300-CBP Transcription Factors/*chemistry PMC - PMC4143068 OID - NLM: PMC4143068 OTO - NOTNLM OT - IDP OT - protein-protein interaction EDAT- 2014/07/23 06:00 MHDA- 2014/11/05 06:00 CRDT- 2014/07/23 06:00 PHST- 2014/07/21 [aheadofprint] AID - 1406033111 [pii] AID - 10.1073/pnas.1406033111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12061-6. doi: 10.1073/pnas.1406033111. Epub 2014 Jul 21. PMID- 25049402 OWN - NLM STAT- MEDLINE DA - 20140806 DCOM- 20141003 LR - 20150105 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 31 DP - 2014 Aug 5 TI - Pathway of binding of the intrinsically disordered mitochondrial inhibitor protein to F1-ATPase. PG - 11305-10 LID - 10.1073/pnas.1411560111 [doi] AB - The hydrolysis of ATP by the ATP synthase in mitochondria is inhibited by a protein called IF1. Bovine IF1 has 84 amino acids, and its N-terminal inhibitory region is intrinsically disordered. In a known structure of bovine F1-ATPase inhibited with residues 1-60 of IF1, the inhibitory region from residues 1-50 is mainly alpha-helical and buried deeply at the alpha(DP)beta(DP)-catalytic interface, where it forms extensive interactions with five of the nine subunits of F1-ATPase but mainly with the beta(DP)-subunit. As described here, on the basis of two structures of inhibited complexes formed in the presence of large molar excesses of residues 1-60 of IF1 and of a version of IF1 with the mutation K39A, it appears that the intrinsically disordered inhibitory region interacts first with the alphaEbetaE-catalytic interface, the most open of the three catalytic interfaces, where the available interactions with the enzyme allow it to form an alpha-helix from residues 31-49. Then, in response to the hydrolysis of an ATP molecule and the associated partial closure of the interface to the alphaTPbetaTP state, the extent of the folded alpha-helical region of IF1 increases to residues 23-50 as more interactions with the enzyme become possible. Finally, in response to the hydrolysis of a second ATP molecule and a concomitant 120 degrees rotation of the gamma-subunit, the interface closes further to the alpha(DP)beta(DP)-state, allowing more interactions to form between the enzyme and IF1. The structure of IF1 now extends to its maximally folded state found in the previously observed inhibited complex. FAU - Bason, John V AU - Bason JV AD - The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom; and. FAU - Montgomery, Martin G AU - Montgomery MG AD - The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom; and. FAU - Leslie, Andrew G W AU - Leslie AG AD - The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom. FAU - Walker, John E AU - Walker JE AD - The Medical Research Council Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom; and walker@mrc-mbu.cam.ac.uk. LA - eng SI - PDB/4TSF SI - PDB/4TT3 GR - MC_U105184325/Medical Research Council/United Kingdom GR - MC_U105663150/Medical Research Council/United Kingdom GR - Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140721 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (ATPase inhibitory protein) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Mitochondrial Proteins) RN - 0 (Protein Subunits) RN - 0 (Proteins) RN - EC 3.6.3.14 (Proton-Translocating ATPases) SB - IM MH - Animals MH - Cattle MH - Crystallography, X-Ray MH - Intrinsically Disordered Proteins/antagonists & inhibitors/chemistry/*metabolism MH - Mitochondrial Proteins/antagonists & inhibitors/chemistry/*metabolism MH - Protein Binding MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Subunits/chemistry MH - Proteins/chemistry/*metabolism MH - Proton-Translocating ATPases/*antagonists & inhibitors/chemistry PMC - PMC4128166 OID - NLM: PMC4128166 OTO - NOTNLM OT - binding site OT - folding OT - inhibitory path OT - rotary catalysis EDAT- 2014/07/23 06:00 MHDA- 2014/10/04 06:00 CRDT- 2014/07/23 06:00 PHST- 2014/07/21 [aheadofprint] AID - 1411560111 [pii] AID - 10.1073/pnas.1411560111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Aug 5;111(31):11305-10. doi: 10.1073/pnas.1411560111. Epub 2014 Jul 21. PMID- 19249289 OWN - NLM STAT- MEDLINE DA - 20090330 DCOM- 20090428 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 381 IP - 4 DP - 2009 Apr 17 TI - Domain 3 of non-structural protein 5A from hepatitis C virus is natively unfolded. PG - 634-8 LID - 10.1016/j.bbrc.2009.02.108 [doi] AB - Hepatitis C virus (HCV) non-structural protein 5A (NS5A) is involved both in the viral replication and particle production. Its third domain (NS5A-D3), although not absolutely required for replication, is a key determinant for the production and assembly of novel HCV particles. As a prerequisite to elucidate the precise functions of this domain, we report here the first molecular characterization of purified recombinant HCV NS5A-D3. Sequence analysis indicates that NS5A-D3 is mostly unstructured but that short structural elements may exist at its N-terminus. Gel filtration chromatography, circular dichroism and finally NMR spectroscopy all point out the natively unfolded nature of purified recombinant NS5A-D3. This lack of stable folding is thought to be essential for primary interactions of NS5A-D3 domain with other viral or host proteins, which could stabilize some specific conformations conferring new functional features. FAU - Hanoulle, Xavier AU - Hanoulle X AD - UGSF, UMR CNRS, IFR, Universite des Sciences et Technologies de Lille, Villeneuve d'Ascq, France. xavier.hanoulle@univ-lille1.fr FAU - Verdegem, Dries AU - Verdegem D FAU - Badillo, Aurelie AU - Badillo A FAU - Wieruszeski, Jean-Michel AU - Wieruszeski JM FAU - Penin, Francois AU - Penin F FAU - Lippens, Guy AU - Lippens G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090226 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Recombinant Proteins) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Amino Acid Sequence MH - Hepacivirus/*metabolism MH - Molecular Sequence Data MH - Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics MH - Viral Nonstructural Proteins/*chemistry/genetics EDAT- 2009/03/03 09:00 MHDA- 2009/04/29 09:00 CRDT- 2009/03/03 09:00 PHST- 2009/02/13 [received] PHST- 2009/02/20 [accepted] PHST- 2009/02/26 [aheadofprint] AID - S0006-291X(09)00384-2 [pii] AID - 10.1016/j.bbrc.2009.02.108 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2009 Apr 17;381(4):634-8. doi: 10.1016/j.bbrc.2009.02.108. Epub 2009 Feb 26. PMID- 17335006 OWN - NLM STAT- MEDLINE DA - 20070412 DCOM- 20070709 LR - 20071203 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 67 IP - 3 DP - 2007 May 15 TI - Identifying long-range structure in the intrinsically unstructured transactivation domain of p53. PG - 526-30 AB - Paramagnetic relaxation enhancement (PRE) was used to identify a compact dynamic structure for the intrinsically unstructured transactivation domain of the tumor suppressor protein, p53. Our results show that p53 residues essential for binding to the ubiquitin ligase, MDM2, and the 70 kDa subunit of replication protein A, RPA70, are separated by an average distance of 10-15 A. This result suggests that a more extended member of the ensemble must be populated prior to binding either MDM2 or RPA70. We also show that PRE can be used to detect intermolecular distances between p53 and RPA70. CI - 2007 Wiley-Liss, Inc. FAU - Vise, Pamela AU - Vise P AD - Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Moscow, Idaho 83844-3052, USA. FAU - Baral, Bharat AU - Baral B FAU - Stancik, Amber AU - Stancik A FAU - Lowry, David F AU - Lowry DF FAU - Daughdrill, Gary W AU - Daughdrill GW LA - eng GR - P20 RR 16448/RR/NCRR NIH HHS/United States GR - P20 RR 16454-02/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Replication Protein A) RN - 0 (Tumor Suppressor Protein p53) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Magnetic Resonance Spectroscopy MH - Protein Binding MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-mdm2/*chemistry/metabolism MH - Replication Protein A/*chemistry/metabolism MH - Tumor Suppressor Protein p53/*chemistry/metabolism EDAT- 2007/03/06 09:00 MHDA- 2007/07/10 09:00 CRDT- 2007/03/06 09:00 AID - 10.1002/prot.21364 [doi] PST - ppublish SO - Proteins. 2007 May 15;67(3):526-30. PMID- 12416980 OWN - NLM STAT- MEDLINE DA - 20021105 DCOM- 20021217 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 41 IP - 45 DP - 2002 Nov 12 TI - Characterization of large peptide fragments derived from the N-terminal domain of the ribosomal protein L9: definition of the minimum folding motif and characterization of local electrostatic interactions. PG - 13360-9 AB - A set of peptides derived from the N-terminal domain of the ribosomal protein L9 (NTL9) have been characterized in an effort to define the minimum unit of this domain required to fold and to provide model peptides for the analysis of electrostatic interactions in the unfolded state. NTL9 is a 56-residue alpha-beta protein with a beta1-loop-beta2-alpha1-beta3-alpha2 topology. The beta-sheet together with the first helix comprise a simple example of a common supersecondary motif called the split beta-alpha-beta fold. Peptides corresponding to the beta1-loop-beta2 unit are unstructured even when constrained by an introduced disulfide. The pK(a)s of Asp-8 and Glu-17 in these peptides are slightly lower than the values found for shorter peptides but are considerably higher than the values in NTL9. A 34-residue peptide, which represents the beta1-loop-beta2-alpha1 portion of NTL9, is also unstructured. In contrast, a 39-residue peptide corresponding to the entire split beta-alpha-beta motif is folded and monomeric as judged by near- and far-UV CD, two-dimensional NMR, ANS binding experiments, pK(a) measurements, and analytical ultracentrifugation. The fold is very similar to the structure of this region in the intact protein. Thermal and urea unfolding experiments show that it is cooperatively folded with a DeltaG degrees of unfolding of 1.8-2.0 kcal/mol and a T(m) of 58 degrees C. This peptide represents the first demonstration of the independent folding of an isolated split beta-alpha-beta motif, and is one of only four naturally occurring sequences of fewer than 40 residues that has been shown to fold cooperatively in the absence of disulfides or ligand binding. FAU - Horng, Jia-Cherng AU - Horng JC AD - Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, USA. FAU - Moroz, Viktor AU - Moroz V FAU - Rigotti, Daniel J AU - Rigotti DJ FAU - Fairman, Robert AU - Fairman R FAU - Raleigh, Daniel P AU - Raleigh DP LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Naphthalenesulfonates) RN - 0 (Peptide Fragments) RN - 0 (Ribosomal Proteins) RN - 0 (ribosomal protein L9) RN - 30KYC7MIAI (Aspartic Acid) RN - 3KX376GY7L (Glutamic Acid) RN - 82-75-7 (1-naphthylamine-8-sulfonic acid) RN - K3Z4F929H6 (Lysine) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Aspartic Acid/chemistry MH - Circular Dichroism MH - Glutamic Acid/chemistry MH - Hydrogen-Ion Concentration MH - Lysine/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Naphthalenesulfonates/chemistry MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemical synthesis/*chemistry MH - Protein Denaturation MH - *Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Ribosomal Proteins/chemical synthesis/*chemistry MH - Spectrometry, Fluorescence MH - Static Electricity EDAT- 2002/11/06 04:00 MHDA- 2002/12/18 04:00 CRDT- 2002/11/06 04:00 AID - bi026410c [pii] PST - ppublish SO - Biochemistry. 2002 Nov 12;41(45):13360-9. PMID- 9095196 OWN - NLM STAT- MEDLINE DA - 19970430 DCOM- 19970430 LR - 20061115 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 4 IP - 4 DP - 1997 Apr TI - The C-terminal half of the anti-sigma factor, FlgM, becomes structured when bound to its target, sigma 28. PG - 285-91 AB - The interaction between the flagellum specific sigma factor, sigma 28, and its inhibitor, FlgM, was examined using multidimensional heteronuclear NMR. Here we observe that free FlgM is mostly unfolded, but about 50% of the residues become structured when bound to sigma 28. Our analysis suggests that the sigma 28 binding domain of FlgM is contained within the last 57 amino acids of the protein while the first 40 amino acids are unstructured in both the free and bound states. Genetic analysis of flgM mutants that fail to inhibit sigma 28 activity reveal amino acid changes that are also isolated to the C-terminal 57 residues of FlgM. We postulate that the lack of structure in free and bound FlgM is important to its role as an exported protein. FAU - Daughdrill, G W AU - Daughdrill GW AD - Institute of Molecular Biology, University of Oregon, Eugene 97403, USA. FAU - Chadsey, M S AU - Chadsey MS FAU - Karlinsey, J E AU - Karlinsey JE FAU - Hughes, K T AU - Hughes KT FAU - Dahlquist, F W AU - Dahlquist FW LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Bacterial Proteins) RN - 0 (FliA protein, Bacteria) RN - 0 (Sigma Factor) RN - 142462-45-1 (FlgM protein, Bacteria) SB - IM MH - Bacterial Proteins/*antagonists & inhibitors/*chemistry/genetics/secretion MH - Binding Sites/genetics MH - Flagella/*chemistry MH - Magnetic Resonance Spectroscopy MH - Mutation MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Sigma Factor/*antagonists & inhibitors/*chemistry MH - Time Factors EDAT- 1997/04/01 MHDA- 1997/04/01 00:01 CRDT- 1997/04/01 00:00 PST - ppublish SO - Nat Struct Biol. 1997 Apr;4(4):285-91. PMID- 19918058 OWN - NLM STAT- MEDLINE DA - 20091203 DCOM- 20100218 LR - 20140827 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 106 IP - 48 DP - 2009 Dec 1 TI - Dynamic structure of lipid-bound synaptobrevin suggests a nucleation-propagation mechanism for trans-SNARE complex formation. PG - 20306-11 LID - 10.1073/pnas.0908317106 [doi] AB - The synaptic vesicle protein synaptobrevin engages with syntaxin and SNAP-25 to form the SNARE complex, which drives membrane fusion in neuronal exocytosis. In the SNARE complex, the SNARE motif of synaptobrevin forms a 55-residue helix, but it has been assumed to be mostly unstructured in its prefusion form. NMR data for full-length synaptobrevin in dodecylphosphocholine micelles reveals two transient helical segments flanked by natively disordered regions and a third more stable helix. Transient helix I comprises the most N-terminal part of the SNARE motif, transient helix II extends the SNARE motif into the juxtamembrane region, and the more stable helix III is the transmembrane domain. These helices may have important consequences for SNARE complex folding and fusion: helix I likely forms a nucleation site, the C-terminal disordered SNARE motif may act as a folding arrest signal, and helix II likely couples SNARE complex folding and fusion. FAU - Ellena, Jeffrey F AU - Ellena JF AD - Biomolecular Magnetic Resonance Research Core, PO Box 800741, University of Virginia, Charlottesville, VA 22908, USA. FAU - Liang, Binyong AU - Liang B FAU - Wiktor, Maciej AU - Wiktor M FAU - Stein, Alexander AU - Stein A FAU - Cafiso, David S AU - Cafiso DS FAU - Jahn, Reinhard AU - Jahn R FAU - Tamm, Lukas K AU - Tamm LK LA - eng SI - PDB/2KOG GR - P01 GM072694/GM/NIGMS NIH HHS/United States GR - P01 GM72694/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20091116 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Micelles) RN - 0 (R-SNARE Proteins) RN - 0 (SNARE Proteins) SB - IM MH - Animals MH - Cell Membrane/*chemistry MH - Micelles MH - *Models, Molecular MH - Neurons/*chemistry MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - R-SNARE Proteins/*chemistry MH - Rats MH - SNARE Proteins/*chemistry PMC - PMC2787132 OID - NLM: PMC2787132 EDAT- 2009/11/18 06:00 MHDA- 2010/02/19 06:00 CRDT- 2009/11/18 06:00 PHST- 2009/11/16 [aheadofprint] AID - 0908317106 [pii] AID - 10.1073/pnas.0908317106 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20306-11. doi: 10.1073/pnas.0908317106. Epub 2009 Nov 16. PMID- 24758710 OWN - NLM STAT- MEDLINE DA - 20140514 DCOM- 20150514 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 136 IP - 19 DP - 2014 May 14 TI - Internal nanosecond dynamics in the intrinsically disordered myelin basic protein. PG - 6987-94 LID - 10.1021/ja502343b [doi] AB - Intrinsically disordered proteins lack a well-defined folded structure and contain a high degree of structural freedom and conformational flexibility, which is expected to enhance binding to their physiological targets. In solution and in the lipid-free state, myelin basic protein belongs to that class of proteins. Using small-angle scattering, the protein was found to be structurally disordered similar to Gaussian chains. The combination of structural and hydrodynamic information revealed an intermediary compactness of the protein between globular proteins and random coil polymers. Modeling by a coarse-grained structural ensemble gave indications for a compact core with flexible ends. Neutron spin-echo spectroscopy measurements revealed a large contribution of internal dynamics to the overall diffusion. The experimental results showed a high flexibility of the structural ensemble. Displacement patterns along the first two normal modes demonstrated that collective stretching and bending motions dominate the internal modes. The observed dynamics represent nanosecond conformational fluctuations within the reconstructed coarse-grained structural ensemble, allowing the exploration of a large configurational space. In an alternative approach, we investigated if models from polymer theory, recently used for the interpretation of fluorescence spectroscopy experiments on disordered proteins, are suitable for the interpretation of the observed motions. Within the framework of the Zimm model with internal friction (ZIF), a large offset of 81.6 ns is needed as an addition to all relaxation times due to intrachain friction sources. The ZIF model, however, shows small but systematic deviations from the measured data. The large value of the internal friction leads to the breakdown of the Zimm model. FAU - Stadler, Andreas M AU - Stadler AM AD - Julich Centre for Neutron Science JCNS and Institute for Complex Systems ICS, Forschungszentrum Julich GmbH, 52425 Julich, Germany. FAU - Stingaciu, Laura AU - Stingaciu L FAU - Radulescu, Aurel AU - Radulescu A FAU - Holderer, Olaf AU - Holderer O FAU - Monkenbusch, Michael AU - Monkenbusch M FAU - Biehl, Ralf AU - Biehl R FAU - Richter, Dieter AU - Richter D LA - eng PT - Journal Article DEP - 20140501 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Myelin Basic Protein) SB - IM MH - Diffusion MH - Hydrodynamics MH - Models, Molecular MH - Myelin Basic Protein/*chemistry MH - Neutron Diffraction MH - Protein Conformation MH - Scattering, Small Angle MH - X-Ray Diffraction EDAT- 2014/04/25 06:00 MHDA- 2015/05/15 06:00 CRDT- 2014/04/25 06:00 PHST- 2014/05/01 [aheadofprint] AID - 10.1021/ja502343b [doi] PST - ppublish SO - J Am Chem Soc. 2014 May 14;136(19):6987-94. doi: 10.1021/ja502343b. Epub 2014 May 1. PMID- 12437352 OWN - NLM STAT- MEDLINE DA - 20021119 DCOM- 20030109 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 41 IP - 47 DP - 2002 Nov 26 TI - Structurally distinct modes of recognition of the KIX domain of CBP by Jun and CREB. PG - 13956-64 AB - Gene expression is coordinated in part by interactions between transcriptional activators and other transcription factors such as coactivators. The KIX domain of the coactivator and histone acetyltransferase CREB binding protein (CBP) binds numerous mammalian and viral transcriptional activators such as BRCA1, CREB, c-Jun, c-Myb, p53, papillomavirus E2, and HTLV-1 Tax. Formation of the CREB-CBP complex depends on phosphorylation of the KID region of CREB and involves induced folding of KID upon binding a hydrophobic groove of the KIX domain of CBP. Here we investigate the formation of the complex formed by human KIX and the N-terminal activation domain of human c-Jun. The c-Jun activation domain and KID do not share significant sequence similarity. Circular dichroism spectroscopy shows that the Jun N-terminal activation domain is intrinsically disordered in isolation and that KIX binding is independent of Jun phosphorylation. In contrast to the mode of binding exhibited by CREB, NMR chemical shift mapping indicates that the c-Jun activation domain binds to a distinctly different surface of KIX than used by CREB. Moreover, NMR and sedimentation equilibrium studies show that the activation domains of c-Jun and CREB can simultaneously bind the KIX domain of CBP. The results illustrate a new mode of binding and combinatorial recruitment via the KIX domain of CBP by multiple transcriptional activators. FAU - Campbell, Kathleen M AU - Campbell KM AD - Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA. FAU - Lumb, Kevin J AU - Lumb KJ LA - eng GR - RR11847/RR/NCRR NIH HHS/United States GR - RR11981/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (CREBBP protein, human) RN - 0 (Cyclic AMP Response Element-Binding Protein) RN - 0 (Nuclear Proteins) RN - 0 (Proto-Oncogene Proteins c-jun) RN - 0 (Recombinant Proteins) RN - 0 (Trans-Activators) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - CREB-Binding Protein MH - Circular Dichroism MH - Cloning, Molecular MH - Cyclic AMP Response Element-Binding Protein/*chemistry/*metabolism MH - Escherichia coli/genetics MH - Genetic Vectors MH - Humans MH - Molecular Sequence Data MH - Molecular Weight MH - Mutagenesis, Insertional MH - Nuclear Proteins/*chemistry/*metabolism MH - Polymerase Chain Reaction MH - Protein Conformation MH - Protein Structure, Secondary MH - Proto-Oncogene Proteins c-jun/*chemistry/*metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Trans-Activators/*chemistry/*metabolism EDAT- 2002/11/20 04:00 MHDA- 2003/01/10 04:00 CRDT- 2002/11/20 04:00 AID - bi026222m [pii] PST - ppublish SO - Biochemistry. 2002 Nov 26;41(47):13956-64. PMID- 23137297 OWN - NLM STAT- MEDLINE DA - 20130130 DCOM- 20130802 LR - 20141104 IS - 1573-4935 (Electronic) IS - 0144-8463 (Linking) VI - 33 IP - 1 DP - 2013 TI - The folded and disordered domains of human ribosomal protein SA have both idiosyncratic and shared functions as membrane receptors. PG - 113-24 LID - 10.1042/BSR20120103 [doi] LID - e00011 [pii] AB - The human RPSA [ribosomal protein SA; also known as LamR1(laminin receptor 1)] belongs to the ribosome but is also a membrane receptor for laminin, growth factors, prion, pathogens and the anticarcinogen EGCG (epigallocatechin-gallate). It contributes to the crossing of the blood-brain barrier by neurotropic viruses and bacteria, and is a biomarker of metastasis. RPSA includes an N-terminal domain, which is folded and homologous to the prokaryotic RPS2, and a C-terminal extension, which is intrinsically disordered and conserved in vertebrates. We used recombinant derivatives of RPSA and its N- and C-domains to quantify its interactions with ligands by in-vitro immunochemical and spectrofluorimetric methods. Both N- and C-domains bound laminin with K(D) (dissociation constants) of 300 nM. Heparin bound only to the N-domain and competed for binding to laminin with the negatively charged C-domain, which therefore mimicked heparin. EGCG bound only to the N-domain with a K(D) of 100 nM. Domain 3 of the envelope protein from yellow fever virus and serotypes-1 and -2 of dengue virus bound preferentially to the C-domain whereas that from West Nile virus bound only to the N-domain. Our quantitative in-vitro approach should help clarify the mechanisms of action of RPSA, and ultimately fight against cancer and infectious agents. FAU - Zidane, Nora AU - Zidane N AD - Institut Pasteur, Unit of Molecular Prevention and Therapy of Human Diseases, Department of Infection and Epidemiology, rue du Dr. Roux, F-75015 Paris, France. FAU - Ould-Abeih, Mohamed B AU - Ould-Abeih MB FAU - Petit-Topin, Isabelle AU - Petit-Topin I FAU - Bedouelle, Hugues AU - Bedouelle H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121220 PL - United States TA - Biosci Rep JT - Bioscience reports JID - 8102797 RN - 0 (Laminin) RN - 0 (Ligands) RN - 0 (RPSA protein, human) RN - 0 (Receptors, Laminin) RN - 0 (Recombinant Proteins) RN - 0 (Ribosomal Proteins) RN - 0 (Viral Envelope Proteins) RN - 145420-18-4 (glycoprotein E, Flavivirus) RN - 8DUH1N11BX (Tryptophan) RN - 9005-49-6 (Heparin) SB - IM MH - Cell Membrane/*metabolism MH - Enzyme-Linked Immunosorbent Assay MH - Escherichia coli/genetics/metabolism MH - Heparin/metabolism MH - Humans MH - Immunochemistry MH - Laminin/metabolism MH - Ligands MH - Protein Binding MH - *Protein Folding MH - Protein Interaction Mapping/*methods MH - Protein Structure, Tertiary MH - Receptors, Laminin/genetics/*metabolism MH - Recombinant Proteins/genetics/metabolism MH - Ribosomal Proteins/genetics/*metabolism MH - Spectrometry, Fluorescence/methods MH - Tryptophan/metabolism MH - Viral Envelope Proteins/metabolism MH - West Nile virus/metabolism MH - Yellow fever virus/metabolism PMC - PMC4098866 OID - NLM: PMC4098866 EDAT- 2012/11/10 06:00 MHDA- 2013/08/03 06:00 CRDT- 2012/11/10 06:00 AID - BSR20120103 [pii] AID - 10.1042/BSR20120103 [doi] PST - epublish SO - Biosci Rep. 2012 Dec 20;33(1):113-24. doi: 10.1042/BSR20120103. PMID- 6452580 OWN - NLM STAT- MEDLINE DA - 19810625 DCOM- 19810625 LR - 20071114 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 290 IP - 5809 DP - 1981 Apr 30 TI - Structure of the cro repressor from bacteriophage lambda and its interaction with DNA. PG - 754-8 AB - The three-dimensional structure of the 66-amino acid cro repressor protein of bacteriophage lambda suggests how it binds to its operator DNA. We propose that a dimer of cro protein is bound to the B-form of DNA with the 2-fold axis of the dimer coincident with the 2-fold axis of DNA. A pair of 2-fold-related alpha-helices of the repressor, lying within successive major grooves of the DNA, seem to be a major determinant in recognition and binding. In addition, the C-terminal residues of the protein, some of which are disordered in the absence of DNA, appear to contribute to the binding. FAU - Anderson, W F AU - Anderson WF FAU - Ohlendorf, D H AU - Ohlendorf DH FAU - Takeda, Y AU - Takeda Y FAU - Matthews, B W AU - Matthews BW LA - eng GR - GM 20066/GM/NIGMS NIH HHS/United States GR - GM 28138/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Carrier Proteins) RN - 0 (DNA, Viral) RN - 0 (DNA-Binding Proteins) RN - 0 (Macromolecular Substances) RN - 0 (Repressor Proteins) RN - 0 (Transcription Factors) RN - 0 (Viral Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Bacteriophage lambda MH - *Carrier Proteins MH - *DNA MH - DNA, Viral/*metabolism MH - DNA-Binding Proteins MH - Macromolecular Substances MH - Nucleic Acid Conformation MH - Protein Binding MH - Protein Conformation MH - *Repressor Proteins MH - Structure-Activity Relationship MH - *Transcription Factors MH - Viral Proteins MH - X-Ray Diffraction EDAT- 1981/04/30 MHDA- 1981/04/30 00:01 CRDT- 1981/04/30 00:00 PST - ppublish SO - Nature. 1981 Apr 30;290(5809):754-8. PMID- 20103592 OWN - NLM STAT- MEDLINE DA - 20100405 DCOM- 20100504 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 15 DP - 2010 Apr 9 TI - N-terminal domains of DELLA proteins are intrinsically unstructured in the absence of interaction with GID1/gibberellic acid receptors. PG - 11557-71 LID - 10.1074/jbc.M109.027011 [doi] AB - The plant growth-repressing DELLA proteins (DELLAs) are known to represent a convergence point in integration of multiple developmental and environmental signals in planta, one of which is hormone gibberellic acid (GA). Binding of the liganded GA receptor (GID1/GA) to the N-terminal domain of DELLAs is required for GA-induced degradation of DELLAs via the ubiquitin-proteasome pathway, thus derepressing plant growth. However, the conformational changes of DELLAs upon binding to GID1/GA, which are the key to understanding the precise mechanism of GID1/GA-mediated degradation of DELLAs, remain unclear. Using biophysical, biochemical, and bioinformatics approaches, we demonstrated for the first time that the unbound N-terminal domains of DELLAs are intrinsically unstructured proteins under physiological conditions. Within the intrinsically disordered N-terminal domain of DELLAs, we have identified several molecular recognition features, sequences known to undergo disorder-to-order transitions upon binding to interacting proteins in intrinsically unstructured proteins. In accordance with the molecular recognition feature analyses, we have observed the binding-induced folding of N-terminal domains of DELLAs upon interaction with AtGID1/GA. Our results also indicate that DELLA proteins can be divided into two subgroups in terms of their molecular compactness and their interactions with monoclonal antibodies. FAU - Sun, Xiaolin AU - Sun X AD - New Zealand Institute for Plant and Food Research, Private Bag 11 030, Palmerston North, New Zealand. Xiaolin.Sun@plantandfood.co.nz FAU - Jones, William T AU - Jones WT FAU - Harvey, Dawn AU - Harvey D FAU - Edwards, Patrick J B AU - Edwards PJ FAU - Pascal, Steven M AU - Pascal SM FAU - Kirk, Christopher AU - Kirk C FAU - Considine, Therese AU - Considine T FAU - Sheerin, David J AU - Sheerin DJ FAU - Rakonjac, Jasna AU - Rakonjac J FAU - Oldfield, Christopher J AU - Oldfield CJ FAU - Xue, Bin AU - Xue B FAU - Dunker, A Keith AU - Dunker AK FAU - Uversky, Vladimir N AU - Uversky VN LA - eng GR - GM071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 LM007688-01A1/LM/NLM NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20100126 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Antibodies, Monoclonal) RN - 0 (Arabidopsis Proteins) RN - 0 (GID1a protein, Arabidopsis) RN - 0 (Gibberellins) RN - 0 (Plant Proteins) RN - 0 (Receptors, Cell Surface) RN - 0 (Recombinant Proteins) RN - BU0A7MWB6L (gibberellic acid) SB - IM MH - Amino Acid Sequence MH - Antibodies, Monoclonal/chemistry MH - Arabidopsis/metabolism MH - Arabidopsis Proteins/*chemistry/metabolism MH - Gene Expression Regulation, Plant MH - Gibberellins/*chemistry MH - Molecular Sequence Data MH - Mutation MH - Plant Proteins/*metabolism MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Receptors, Cell Surface/*chemistry/metabolism MH - Recombinant Proteins/chemistry MH - Sequence Homology, Amino Acid MH - Signal Transduction PMC - PMC2857034 OID - NLM: PMC2857034 EDAT- 2010/01/28 06:00 MHDA- 2010/05/05 06:00 CRDT- 2010/01/28 06:00 PHST- 2010/01/26 [aheadofprint] AID - M109.027011 [pii] AID - 10.1074/jbc.M109.027011 [doi] PST - ppublish SO - J Biol Chem. 2010 Apr 9;285(15):11557-71. doi: 10.1074/jbc.M109.027011. Epub 2010 Jan 26. PMID- 17676872 OWN - NLM STAT- MEDLINE DA - 20070821 DCOM- 20070926 LR - 20121115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 46 IP - 34 DP - 2007 Aug 28 TI - The BG21 isoform of Golli myelin basic protein is intrinsically disordered with a highly flexible amino-terminal domain. PG - 9700-12 AB - The genes of the oligodendrocyte lineage (Golli) encode a family of developmentally regulated isoforms of myelin basic protein. The "classic" MBP isoforms arise from transcription start site 3, whereas Golli-specific isoforms arise from transcription start site 1, and comprise both Golli-specific and classic MBP sequences. The Golli isoform BG21 has been suggested to play roles in myelination and T cell activation pathways. It is an intrinsically disordered protein, thereby presenting a large effective surface area for interaction with other proteins such as Golli-interacting protein. We have used multidimensional heteronuclear NMR spectroscopy to achieve sequence-specific resonance assignments of the recombinant murine BG21 in physiologically relevant buffer, to analyze its secondary structure using chemical shift indexing (CSI), and to investigate its backbone dynamics using 15N spin relaxation measurements. We have assigned 184 out of 199 residues unambiguously. The CSI analysis revealed little ordered secondary structure under these conditions, with only some small fragments having a slight tendency toward alpha-helicity, which may represent putative recognition motifs. The 15N relaxation and NOE measurements confirmed the general behavior of the protein as an extended polypeptide chain, with the N-terminal Golli-specific portion (residues S5-T69) being exceptionally flexible, even in comparison to other intrinsically disordered proteins that have been studied this way. The high degree of flexibility of this N-terminal region may be to provide additional plasticity, or conformational adaptability, in protein-protein interactions. Another highly mobile segment, A126-S127-G128-G129, may function as a hinge. FAU - Ahmed, Mumdooh A M AU - Ahmed MA AD - Department of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada. FAU - Bamm, Vladimir V AU - Bamm VV FAU - Harauz, George AU - Harauz G FAU - Ladizhansky, Vladimir AU - Ladizhansky V LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070804 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Mbp protein, mouse) RN - 0 (Myelin Basic Protein) RN - 0 (Nerve Tissue Proteins) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) SB - IM MH - Amino Acid Sequence MH - Animals MH - Magnetic Resonance Imaging MH - Mice MH - Molecular Sequence Data MH - Myelin Basic Protein MH - Nerve Tissue Proteins/*chemistry/genetics/isolation & purification MH - Nuclear Magnetic Resonance, Biomolecular MH - Oligodendroglia MH - Protein Isoforms/chemistry/genetics/isolation & purification MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/genetics/isolation & purification MH - Transcription Factors/*chemistry/genetics/isolation & purification EDAT- 2007/08/07 09:00 MHDA- 2007/09/27 09:00 CRDT- 2007/08/07 09:00 PHST- 2007/08/04 [aheadofprint] AID - 10.1021/bi700632x [doi] PST - ppublish SO - Biochemistry. 2007 Aug 28;46(34):9700-12. Epub 2007 Aug 4. PMID- 10704222 OWN - NLM STAT- MEDLINE DA - 20000419 DCOM- 20000419 LR - 20081121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 39 IP - 10 DP - 2000 Mar 14 TI - Intrinsic structural disorder of the C-terminal activation domain from the bZIP transcription factor Fos. PG - 2708-13 AB - The bZIP proto-oncoprotein c-Fos activates transcription of a wide variety of genes involved in cell growth. The C-terminal activation domain of c-Fos is functionally independent of the remainder of the protein. Fos-AD corresponds to the C-terminal activation domain of human c-Fos (residues 216-380). Fos-AD suppresses (squelches) transcription in vitro, as expected for a functional activation domain lacking a DNA-binding domain. Fos-AD is unstructured and highly mobile, as demonstrated by circular dichroism spectra indicative of unfolded proteins, a lack of (1)H chemical shift dispersion, and negative (1)H-(15)N heteronuclear nuclear Overhauser effects. The hydrodynamic properties of Fos-AD are also consistent with an extended structure. We conclude that the C-terminal domain of human c-Fos is biologically active yet intrinsically disordered. Our results suggest that conformational disorder is an integral aspect of the diverse contributions to transcriptional regulation by c-Fos. FAU - Campbell, K M AU - Campbell KM AD - Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA. FAU - Terrell, A R AU - Terrell AR FAU - Laybourn, P J AU - Laybourn PJ FAU - Lumb, K J AU - Lumb KJ LA - eng GR - RR11847/RR/NCRR NIH HHS/United States GR - RR11981/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Basic-Leucine Zipper Transcription Factors) RN - 0 (DNA-Binding Proteins) RN - 0 (G-Box Binding Factors) RN - 0 (Peptide Fragments) RN - 0 (Proto-Oncogene Proteins c-fos) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Transcription Factors) SB - IM MH - Basic-Leucine Zipper Transcription Factors MH - Circular Dichroism MH - DNA-Binding Proteins/*chemistry/*genetics/metabolism/physiology MH - G-Box Binding Factors MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/*chemistry/*genetics/metabolism/physiology MH - Protein Structure, Secondary/genetics MH - Protein Structure, Tertiary/genetics MH - Proto-Oncogene Proteins c-fos/*chemistry/genetics/metabolism/physiology MH - Recombinant Fusion Proteins/chemistry/genetics/metabolism MH - Sequence Deletion MH - Thermodynamics MH - Transcription Factors/*chemistry/*genetics/metabolism/physiology MH - Transcriptional Activation/genetics EDAT- 2000/03/08 09:00 MHDA- 2000/04/25 09:00 CRDT- 2000/03/08 09:00 AID - bi9923555 [pii] PST - ppublish SO - Biochemistry. 2000 Mar 14;39(10):2708-13. PMID- 24739028 OWN - NLM STAT- MEDLINE DA - 20140506 DCOM- 20140619 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 17 DP - 2014 May 6 TI - A revised picture of the Cu(II)-alpha-synuclein complex: the role of N-terminal acetylation. PG - 2815-7 LID - 10.1021/bi5003025 [doi] AB - alpha-Synuclein (alphaS) is an amyloidogenic intrinsically disordered protein implicated in Parkinson's disease, for which copper-mediated pathways of neurodegeneration have been suggested. We have employed nuclear magnetic resonance, circular dichroism, electrospray ionization mass spectrometry, and thioflavin T fluorescence to characterize interactions of Cu(2+) with the physiological acetylated form (Ac-alphaS). Significantly, N-terminal acetylation abolishes Cu(2+) binding at the high-affinity M1-D2 site present in the nonacetylated protein and maintains Cu(2+) interactions around H50/D121. Fibrillation enhancement observed at an equimolar Cu(2+) stoichiometry with the nonacetylated model does not occur with Ac-alphaS. These findings open new avenues of investigation into Cu(2+)-mediated neurodegenerative pathology suggested in vivo. FAU - Moriarty, Gina M AU - Moriarty GM AD - Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States. FAU - Minetti, Conceicao A S A AU - Minetti CA FAU - Remeta, David P AU - Remeta DP FAU - Baum, Jean AU - Baum J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140422 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (alpha-Synuclein) RN - 42Z2K6ZL8P (Manganese) RN - 789U1901C5 (Copper) SB - IM MH - Acetylation MH - Amyloid/biosynthesis MH - Binding Sites MH - Circular Dichroism MH - Copper/*chemistry/*metabolism MH - Humans MH - Manganese/chemistry MH - Nuclear Magnetic Resonance, Biomolecular MH - Parkinson Disease/metabolism MH - alpha-Synuclein/*chemistry/*metabolism EDAT- 2014/04/18 06:00 MHDA- 2014/06/20 06:00 CRDT- 2014/04/18 06:00 PHST- 2014/04/22 [aheadofprint] AID - 10.1021/bi5003025 [doi] PST - ppublish SO - Biochemistry. 2014 May 6;53(17):2815-7. doi: 10.1021/bi5003025. Epub 2014 Apr 22. PMID- 15226509 OWN - NLM STAT- MEDLINE DA - 20040708 DCOM- 20040730 LR - 20140609 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 101 IP - 27 DP - 2004 Jul 6 TI - Structure of the periplasmic component of a bacterial drug efflux pump. PG - 9994-9 AB - Multidrug resistance among Gram-negative bacteria is conferred by three-component membrane pumps that expel diverse antibiotics from the cell. These efflux pumps consist of an inner membrane transporter such as the AcrB proton antiporter, an outer membrane exit duct of the TolC family, and a periplasmic protein known as the adaptor. We present the x-ray structure of the MexA adaptor from the human pathogen Pseudomonas aeruginosa. The elongated molecule contains three linearly arranged subdomains; a 47-A-long alpha-helical hairpin, a lipoyl domain, and a six-stranded beta-barrel. In the crystal, hairpins of neighboring MexA monomers pack side-by-side to form twisted arcs. We discuss the implications of the packing of molecules within the crystal. On the basis of the structure and packing, we suggest a model for the key periplasmic interaction between the outer membrane channel and the adaptor protein in the assembled drug efflux pump. FAU - Higgins, Matthew K AU - Higgins MK AD - Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, United Kingdom. mkh20@hermes.cam.ac.uk FAU - Bokma, Evert AU - Bokma E FAU - Koronakis, Eva AU - Koronakis E FAU - Hughes, Colin AU - Hughes C FAU - Koronakis, Vassilis AU - Koronakis V LA - eng SI - PDB/1T5E PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040628 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Bacterial Outer Membrane Proteins) RN - 0 (Carrier Proteins) RN - 0 (Membrane Transport Proteins) RN - 0 (MexA protein, Pseudomonas aeruginosa) SB - IM MH - Amino Acid Sequence MH - Bacterial Outer Membrane Proteins/*chemistry MH - Carrier Proteins/*chemistry MH - Crystallography MH - *Membrane Transport Proteins MH - Molecular Sequence Data MH - Protein Structure, Secondary PMC - PMC454203 OID - NLM: PMC454203 EDAT- 2004/07/01 05:00 MHDA- 2004/07/31 05:00 CRDT- 2004/07/01 05:00 PHST- 2004/06/28 [aheadofprint] AID - 10.1073/pnas.0400375101 [doi] AID - 0400375101 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):9994-9. Epub 2004 Jun 28. PMID- 23782691 OWN - NLM STAT- MEDLINE DA - 20130805 DCOM- 20131021 LR - 20141113 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 31 DP - 2013 Aug 2 TI - Intrinsically disordered enamel matrix protein ameloblastin forms ribbon-like supramolecular structures via an N-terminal segment encoded by exon 5. PG - 22333-45 LID - 10.1074/jbc.M113.456012 [doi] AB - Tooth enamel, the hardest tissue in the body, is formed by the evolutionarily highly conserved biomineralization process that is controlled by extracellular matrix proteins. The intrinsically disordered matrix protein ameloblastin (AMBN) is the most abundant nonamelogenin protein of the developing enamel and a key element for correct enamel formation. AMBN was suggested to be a cell adhesion molecule that regulates proliferation and differentiation of ameloblasts. Nevertheless, detailed structural and functional studies on AMBN have been substantially limited by the paucity of the purified nondegraded protein. With this study, we have developed a procedure for production of a highly purified form of recombinant human AMBN in quantities that allowed its structural characterization. Using size exclusion chromatography, analytical ultracentrifugation, transmission electron, and atomic force microscopy techniques, we show that AMBN self-associates into ribbon-like supramolecular structures with average widths and thicknesses of 18 and 0.34 nm, respectively. The AMBN ribbons exhibited lengths ranging from tens to hundreds of nm. Deletion analysis and NMR spectroscopy revealed that an N-terminal segment encoded by exon 5 comprises two short independently structured regions and plays a key role in self-assembly of AMBN. FAU - Wald, Tomas AU - Wald T AD - Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czech Republic. FAU - Osickova, Adriana AU - Osickova A FAU - Sulc, Miroslav AU - Sulc M FAU - Benada, Oldrich AU - Benada O FAU - Semeradtova, Alena AU - Semeradtova A FAU - Rezabkova, Lenka AU - Rezabkova L FAU - Veverka, Vaclav AU - Veverka V FAU - Bednarova, Lucie AU - Bednarova L FAU - Maly, Jan AU - Maly J FAU - Macek, Pavel AU - Macek P FAU - Sebo, Peter AU - Sebo P FAU - Slaby, Ivan AU - Slaby I FAU - Vondrasek, Jiri AU - Vondrasek J FAU - Osicka, Radim AU - Osicka R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130619 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (AMBN protein, human) RN - 0 (Dental Enamel Proteins) RN - 0 (Recombinant Proteins) SB - IM MH - Chromatography, Gel MH - Circular Dichroism MH - Dental Enamel Proteins/chemistry/genetics/*metabolism MH - Electrophoresis, Polyacrylamide Gel MH - *Exons MH - Microscopy, Atomic Force MH - Microscopy, Electron, Transmission MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Recombinant Proteins/chemistry/genetics/metabolism PMC - PMC3829324 OID - NLM: PMC3829324 OTO - NOTNLM OT - Ameloblastin OT - Amelogenin OT - Extracellular Matrix Proteins OT - Intrinsically Disordered Proteins OT - Protein Purification OT - Protein Self-assembly OT - Tooth EDAT- 2013/06/21 06:00 MHDA- 2013/10/22 06:00 CRDT- 2013/06/21 06:00 PHST- 2013/06/19 [aheadofprint] AID - M113.456012 [pii] AID - 10.1074/jbc.M113.456012 [doi] PST - ppublish SO - J Biol Chem. 2013 Aug 2;288(31):22333-45. doi: 10.1074/jbc.M113.456012. Epub 2013 Jun 19. PMID- 23782697 OWN - NLM STAT- MEDLINE DA - 20130805 DCOM- 20131021 LR - 20141113 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 31 DP - 2013 Aug 2 TI - Modulating the intrinsic disorder in the cytoplasmic domain alters the biological activity of the N-methyl-D-aspartate-sensitive glutamate receptor. PG - 22506-15 LID - 10.1074/jbc.M113.477810 [doi] AB - The NMDA-sensitive glutamate receptor is a ligand-gated ion channel that mediates excitatory synaptic transmission in the nervous system. Extracellular zinc allosterically regulates the NMDA receptor by binding to the extracellular N-terminal domain, which inhibits channel gating. Phosphorylation of the intrinsically disordered intracellular C-terminal domain alleviates inhibition by extracellular zinc. The mechanism for this functional effect is largely unknown. Proline is a hallmark of intrinsic disorder, so we used proline mutagenesis to modulate disorder in the cytoplasmic domain. Proline depletion selectively uncoupled zinc inhibition with little effect on receptor biogenesis, surface trafficking, or ligand-activated gating. Proline depletion also reduced the affinity for a PDZ domain involved in synaptic trafficking and affected small molecule binding. To understand the origin of these phenomena, we used single molecule fluorescence and ensemble biophysical methods to characterize the structural effects of proline mutagenesis. Proline depletion did not eliminate intrinsic disorder, but the underlying conformational dynamics were changed. Thus, we altered the form of intrinsic disorder, which appears sufficient to affect the biological activity. These findings suggest that conformational dynamics within the intrinsically disordered cytoplasmic domain are important for the allosteric regulation of NMDA receptor gating. FAU - Choi, Ucheor B AU - Choi UB AD - Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA. FAU - Kazi, Rashek AU - Kazi R FAU - Stenzoski, Natalie AU - Stenzoski N FAU - Wollmuth, Lonnie P AU - Wollmuth LP FAU - Uversky, Vladimir N AU - Uversky VN FAU - Bowen, Mark E AU - Bowen ME LA - eng GR - MH081923/MH/NIMH NIH HHS/United States GR - R01 MH081923/MH/NIMH NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130619 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Receptors, N-Methyl-D-Aspartate) SB - IM MH - Allosteric Regulation MH - Cytoplasm/*metabolism MH - Electrophoresis, Polyacrylamide Gel MH - Fluorescence Resonance Energy Transfer MH - HEK293 Cells MH - Humans MH - Protein Binding MH - Receptors, N-Methyl-D-Aspartate/metabolism/*physiology MH - Solubility PMC - PMC3829338 OID - NLM: PMC3829338 OTO - NOTNLM OT - Electrophysiology OT - Fluorescence Resonance Energy Transfer (FRET) OT - Glutamate Receptors Ionotropic (AMPA, NMDA) OT - Intrinsically Disordered Proteins OT - Single Molecule Biophysics EDAT- 2013/06/21 06:00 MHDA- 2013/10/22 06:00 CRDT- 2013/06/21 06:00 PHST- 2013/06/19 [aheadofprint] AID - M113.477810 [pii] AID - 10.1074/jbc.M113.477810 [doi] PST - ppublish SO - J Biol Chem. 2013 Aug 2;288(31):22506-15. doi: 10.1074/jbc.M113.477810. Epub 2013 Jun 19. PMID- 25017730 OWN - NLM STAT- MEDLINE DA - 20140807 DCOM- 20150330 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 22 IP - 8 DP - 2014 Aug 5 TI - Phosphorylation of an intrinsically disordered segment in Ets1 shifts conformational sampling toward binding-competent substates. PG - 1196-203 LID - 10.1016/j.str.2014.06.002 [doi] LID - S0969-2126(14)00175-0 [pii] AB - Functions of many proteins are affected by posttranslational modifications of intrinsically disordered (ID) regions, yet little is known about the underlying molecular mechanisms. By combining molecular dynamics simulations and protein docking, we demonstrate that the addition of phosphates to an ID segment adjacent to the PNT domain of Ets1 directs conformational sampling toward substates that are most compatible with high-affinity binding of the TAZ1 domain of its coactivator CBP. The phosphate charges disrupt salt bridges and thereby open a hydrophobic cleft and expose hydrophobic residues at the ID N terminus. The structure of the PNT-TAZ1 complex that we determined shows that PNT binds to TAZ1 via these hydrophobic regions in a similar manner to how it interacts with other partners. Our calculations reveal a dual effect of phosphorylation in that it changes the dynamics of PNT so that it becomes more compatible for TAZ1 binding and increases complementarity with this binding partner. CI - Copyright (c) 2014 Elsevier Ltd. All rights reserved. FAU - Bui, Jennifer M AU - Bui JM AD - The Qualcomm Institute, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-4040, USA. Electronic address: jennbui@eng.ucsd.edu. FAU - Gsponer, Jorg AU - Gsponer J AD - Department of Biochemistry and Molecular Biology, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada. Electronic address: gsponer@chibi.ubc.ca. LA - eng GR - ES018854/ES/NIEHS NIH HHS/United States GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140710 PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (ETS1 protein, human) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Peptide Fragments) RN - 0 (Proto-Oncogene Protein c-ets-1) RN - 0 (Sialoglycoproteins) RN - 0 (bone sialoprotein (35-62), human) SB - IM MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Intrinsically Disordered Proteins/*chemistry/*metabolism MH - *Models, Molecular MH - Molecular Dynamics Simulation MH - Peptide Fragments/metabolism MH - Phosphorylation MH - Protein Binding MH - Protein Conformation MH - Proto-Oncogene Protein c-ets-1/*chemistry/*metabolism MH - Sialoglycoproteins/metabolism EDAT- 2014/07/16 06:00 MHDA- 2015/03/31 06:00 CRDT- 2014/07/15 06:00 PHST- 2014/03/07 [received] PHST- 2014/05/15 [revised] PHST- 2014/06/04 [accepted] PHST- 2014/07/10 [aheadofprint] AID - S0969-2126(14)00175-0 [pii] AID - 10.1016/j.str.2014.06.002 [doi] PST - ppublish SO - Structure. 2014 Aug 5;22(8):1196-203. doi: 10.1016/j.str.2014.06.002. Epub 2014 Jul 10. PMID- 20403335 OWN - NLM STAT- MEDLINE DA - 20100531 DCOM- 20100707 LR - 20101118 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 396 IP - 2 DP - 2010 May 28 TI - The flexible loop L1 of the H3K4 demethylase JARID1B ARID domain has a crucial role in DNA-binding activity. PG - 323-8 LID - 10.1016/j.bbrc.2010.04.091 [doi] AB - JARID1B, a member of the JmjC demethylase family, has a crucial role in H3K4me3 demethylation. The ARID domain is a potential DNA-binding domain of JARID1B. Previous studies indicate that a GC-rich DNA motif is the specific target of the ARID domain. However, the details of the interaction between the ARID domain and duplex DNA require further study. Here, we utilized NMR spectroscopy to assign the backbone amino acids and mapped the DNA-binding sites of the human JARID1B ARID domain. Perturbations to (1)H-(15)N correlation spectra revealed that the flexible loop L1 of ARID was the main DNA-binding interface. EMSA and intrinsic fluorescence experiments demonstrated that mutations on loop L1 strongly reduced the DNA-binding activity of JARID1B ARID. Furthermore, transfection of mutant forms resulted in a distinct loss of intrinsic H3K4 demethylase activity, implying that the flexible loop L1 made a major contribution to sustaining the DNA-binding ability of JARID1B ARID domain. CI - Copyright (c) 2010 Elsevier Inc. All rights reserved. FAU - Yao, Wenming AU - Yao W AD - Key Laboratory of Optical and Magnetic Resonance Spectroscopy, East China Normal University, Shanghai 200062, China. FAU - Peng, Yu AU - Peng Y FAU - Lin, Donghai AU - Lin D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100418 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Nuclear Proteins) RN - 0 (Repressor Proteins) RN - 9007-49-2 (DNA) RN - EC 1.14.11.- (Histone Demethylases) RN - EC 1.14.11.- (Jumonji Domain-Containing Histone Demethylases) RN - EC 1.14.11.- (KDM5B protein, human) SB - IM MH - Binding Sites MH - DNA/*metabolism MH - DNA Mutational Analysis MH - HeLa Cells MH - Histone Demethylases/genetics/*metabolism MH - Humans MH - Jumonji Domain-Containing Histone Demethylases MH - Mutagenesis, Site-Directed MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/genetics/*metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Repressor Proteins/genetics/*metabolism MH - Sequence Alignment EDAT- 2010/04/21 06:00 MHDA- 2010/07/08 06:00 CRDT- 2010/04/21 06:00 PHST- 2010/04/08 [received] PHST- 2010/04/14 [accepted] PHST- 2010/04/18 [aheadofprint] AID - S0006-291X(10)00771-0 [pii] AID - 10.1016/j.bbrc.2010.04.091 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2010 May 28;396(2):323-8. doi: 10.1016/j.bbrc.2010.04.091. Epub 2010 Apr 18. PMID- 10618385 OWN - NLM STAT- MEDLINE DA - 20000210 DCOM- 20000210 LR - 20140615 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 97 IP - 1 DP - 2000 Jan 4 TI - NMR solution structure of the human prion protein. PG - 145-50 AB - The NMR structures of the recombinant human prion protein, hPrP(23-230), and two C-terminal fragments, hPrP(90-230) and hPrP(121-230), include a globular domain extending from residues 125-228, for which a detailed structure was obtained, and an N-terminal flexibly disordered "tail." The globular domain contains three alpha-helices comprising the residues 144-154, 173-194, and 200-228 and a short anti-parallel beta-sheet comprising the residues 128-131 and 161-164. Within the globular domain, three polypeptide segments show increased structural disorder: i.e., a loop of residues 167-171, the residues 187-194 at the end of helix 2, and the residues 219-228 in the C-terminal part of helix 3. The local conformational state of the polypeptide segments 187-193 in helix 2 and 219-226 in helix 3 is measurably influenced by the length of the N-terminal tail, with the helical states being most highly populated in hPrP(23-230). When compared with the previously reported structures of the murine and Syrian hamster prion proteins, the length of helix 3 coincides more closely with that in the Syrian hamster protein whereas the disordered loop 167-171 is shared with murine PrP. These species variations of local structure are in a surface area of the cellular form of PrP that has previously been implicated in intermolecular interactions related both to the species barrier for infectious transmission of prion disease and to immune reactions. FAU - Zahn, R AU - Zahn R AD - Institut fur Molekularbiologie und Biophysik, Eidgenossische Technische Hochschule Honggerberg, CH-8093 Zurich, Switzerland. FAU - Liu, A AU - Liu A FAU - Luhrs, T AU - Luhrs T FAU - Riek, R AU - Riek R FAU - von Schroetter, C AU - von Schroetter C FAU - Lopez Garcia, F AU - Lopez Garcia F FAU - Billeter, M AU - Billeter M FAU - Calzolai, L AU - Calzolai L FAU - Wider, G AU - Wider G FAU - Wuthrich, K AU - Wuthrich K LA - eng SI - PDB/1QLX SI - PDB/1QLZ SI - PDB/1QM1 SI - PDB/1QM2 SI - PDB/1QM3 SI - PDB/1QMO PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Peptide Fragments) RN - 0 (Prions) RN - 0 (Recombinant Proteins) SB - IM MH - Animals MH - Cloning, Molecular MH - Cricetinae MH - Humans MH - Magnetic Resonance Spectroscopy MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Peptide Fragments/chemistry MH - Prions/*chemistry MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry PMC - PMC26630 OID - NLM: PMC26630 EDAT- 2000/01/05 MHDA- 2000/01/05 00:01 CRDT- 2000/01/05 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):145-50. PMID- 9506949 OWN - NLM STAT- MEDLINE DA - 19980409 DCOM- 19980409 LR - 20070319 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 279 IP - 5358 DP - 1998 Mar 20 TI - Redesigning enzyme topology by directed evolution. PG - 1958-61 AB - Genetic selection was exploited in combination with structure-based design to transform an intimately entwined, dimeric chorismate mutase into a monomeric, four-helix-bundle protein with near native activity. Successful reengineering depended on choosing a thermostable starting protein, introducing point mutations that preferentially destabilize the wild-type dimer, and using directed evolution to optimize an inserted interhelical turn. Contrary to expectations based on studies of other four-helix-bundle proteins, only a small fraction of possible turn sequences (fewer than 0.05 percent) yielded well-behaved, monomeric, and highly active enzymes. Selection for catalytic function thus provides an efficient yet stringent method for rapidly assessing correctly folded polypeptides and may prove generally useful for protein design. FAU - MacBeath, G AU - MacBeath G AD - The Scripps Research Institute, Department of Chemistry, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA. FAU - Kast, P AU - Kast P FAU - Hilvert, D AU - Hilvert D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Recombinant Proteins) RN - EC 5.4.99.5 (Chorismate Mutase) SB - IM CIN - Science. 1998 Mar 20;279(5358):1852. PMID: 9537901 MH - Amino Acid Sequence MH - Binding Sites MH - Catalysis MH - Chorismate Mutase/*chemistry/genetics/*metabolism MH - Circular Dichroism MH - Cloning, Molecular MH - Dimerization MH - *Directed Molecular Evolution MH - Escherichia coli/genetics MH - Models, Molecular MH - Molecular Sequence Data MH - *Protein Conformation MH - *Protein Engineering MH - Protein Folding MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Transformation, Bacterial EDAT- 1998/04/16 MHDA- 1998/04/16 00:01 CRDT- 1998/04/16 00:00 PST - ppublish SO - Science. 1998 Mar 20;279(5358):1958-61. PMID- 16949604 OWN - NLM STAT- MEDLINE DA - 20060918 DCOM- 20070112 LR - 20091119 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 362 IP - 5 DP - 2006 Oct 6 TI - Heteronuclear NMR identifies a nascent helix in intrinsically disordered dynein intermediate chain: implications for folding and dimerization. PG - 1082-93 AB - The intermediate chain of dynein forms a tight subcomplex with dimeric light chains LC8 and Tctex-1, and together they constitute the cargo attachment complex. There is considerable interest in identifying the role of these light chains in the assembly of the two copies of the intermediate chain. The N-terminal domain of the intermediate chain, IC1-289, contains the binding sites for the light chains, and is a highly disordered monomer but gains helical structure upon binding to light chains LC8 and Tctex-1. To provide insights into the structural and dynamic changes that occur in the intermediate chain upon light chains binding, we have used NMR spectroscopy to compare the properties of two distinct sub-domains of IC1-289: IC84-143 which is the light chains binding domain, and IC198-237, which contains a predicted coiled coil necessary for the increase in ordered structure upon light chain binding. Neither construct has stable secondary structure when probed by circular dichroism and amide chemical shift dispersion. Specific residues of IC84-143 involved in binding to the light chains were identified by their increase in resonance line broadening and the corresponding large intensity reduction in 1H-15N HSQC spectra. Interestingly, IC84-143 shows no sign of structure formation after binding to either LC8 or Tctex-1 or to both. IC198-237, on the other hand, contains a population of a nascent helix at low temperature as identified by heteronuclear NMR relaxation measurements, secondary chemical shifts, and sequential amide-amide connectivities. These data are consistent with a model for light chain binding coupled to intermediate chain dimerization through forming a coiled coil distant from the binding site. FAU - Benison, Gregory AU - Benison G AD - Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA. FAU - Nyarko, Afua AU - Nyarko A FAU - Barbar, Elisar AU - Barbar E LA - eng GR - 00210/PHS HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20060804 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - EC 3.6.4.2 (Dyneins) SB - IM MH - Chromatography, Gel MH - Circular Dichroism MH - Dimerization MH - Dyneins/*chemistry/genetics/*metabolism MH - Hydrogen-Ion Concentration MH - Mass Spectrometry MH - Models, Molecular MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - *Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Analysis, Protein MH - Temperature MH - Ultracentrifugation EDAT- 2006/09/05 09:00 MHDA- 2007/01/16 09:00 CRDT- 2006/09/05 09:00 PHST- 2006/06/16 [received] PHST- 2006/07/29 [revised] PHST- 2006/08/01 [accepted] PHST- 2006/08/04 [aheadofprint] AID - S0022-2836(06)00994-6 [pii] AID - 10.1016/j.jmb.2006.08.006 [doi] PST - ppublish SO - J Mol Biol. 2006 Oct 6;362(5):1082-93. Epub 2006 Aug 4. PMID- 19159266 OWN - NLM STAT- MEDLINE DA - 20090624 DCOM- 20090717 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 6 DP - 2009 Feb 17 TI - AP7, a partially disordered pseudo C-RING protein, is capable of forming stabilized aragonite in vitro. PG - 1332-9 LID - 10.1021/bi802148r [doi] AB - AP7 is an extracellular aragonite-associated protein of the nacre layer of the mollusk Haliotis rufescens and possesses a 36-amino acid C-terminal domain that exhibits sequence homology to the C subclass of the RING domain intracellular protein family. We report here novel findings which implicate AP7 as a member of the intrinsically disordered protein class (IDP) and reveal new aspects of AP7 mineralization activity. AP7 is partially disordered but can undergo additional folding in the presence of TFE. AP7 binds Zn(II) ions in a non-tetracoordinate complex but does not require Zn(II) either for folding or for in vitro function. In addition to limiting calcite crystal growth, AP7 is also observed to induce aggregate formation within in vitro mineralization assays, and these aggregates are either amorphous (type A) or crystalline (type B) in appearance. The type A aggregate displays an irregular morphology and round, dark, electron dense deposits that do not give rise to a diffraction pattern. In contrast, the type B aggregates possess either organized parallel crystal clusters or highly dense hexagonal clusters that are confirmed by electron diffraction to be aragonite. This stabilization of aragonite is remarkable in that it occurred in the presence of AP7 alone and did not require typical aragonite stabilization agents such as Mg(II), other nacre proteins, or an organized organic matrix. The ability of a partially disordered C-RING protein to perform inorganic phase stabilization represents a new twist on both the RING domain and IDP stories, and this process of aggregate formation may provide an important clue with regard to the protein-mediated nacre formation process. FAU - Amos, Fairland F AU - Amos FF AD - Laboratory for Chemical Physics, New York University, 345 East 24th Street, New York, New York 10010, USA. FAU - Evans, John Spencer AU - Evans JS LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Ions) RN - 0 (Metals) RN - 0 (Minerals) RN - 0 (Proteins) RN - H0G9379FGK (Calcium Carbonate) SB - IM MH - Calcium Carbonate/*chemistry MH - Circular Dichroism MH - Ions MH - Metals/metabolism MH - Minerals/metabolism MH - Models, Biological MH - Protein Binding MH - Protein Stability MH - Protein Structure, Secondary MH - Proteins/*chemistry/ultrastructure MH - Spectrum Analysis MH - X-Ray Diffraction EDAT- 2009/01/23 09:00 MHDA- 2009/07/18 09:00 CRDT- 2009/01/23 09:00 AID - 10.1021/bi802148r [doi] AID - 10.1021/bi802148r [pii] PST - ppublish SO - Biochemistry. 2009 Feb 17;48(6):1332-9. doi: 10.1021/bi802148r. PMID- 22505609 OWN - NLM STAT- MEDLINE DA - 20120907 DCOM- 20130325 IS - 1477-9137 (Electronic) IS - 0021-9533 (Linking) VI - 125 IP - Pt 14 DP - 2012 Jul 15 TI - Conserved motifs in the Msn2-activating domain are important for Msn2-mediated yeast stress response. PG - 3333-42 LID - 10.1242/jcs.096446 [doi] AB - The Msn2 and Msn4 transcription factors play crucial roles in the yeast general stress response. Previous studies identified several large functional domains of Msn2, mainly through crude truncations. Here, using bioinformatics and experimental approaches to examine Msn2 structure-function relationships, we have identified new functional motifs in the Msn2 transcriptional-activating domain (TAD). Msn2 is predicted to adopt an intrinsically disordered structure with two short structural motifs in its TAD. Mutations in these motifs dramatically decreased Msn2 transcriptional activity, yeast stress survival and Msn2 nuclear localization levels. Using the split-ubiquitin assay, we found that these motifs are important for the interaction of Msn2 with Gal11, a subunit of the mediator complex. Finally, we show that one of these motifs is functionally conserved in several yeast species, highlighting a common mechanism of Msn2 transcriptional activation throughout yeast evolution. FAU - Sadeh, Amit AU - Sadeh A AD - Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel. FAU - Baran, Dror AU - Baran D FAU - Volokh, Misha AU - Volokh M FAU - Aharoni, Amir AU - Aharoni A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120414 PL - England TA - J Cell Sci JT - Journal of cell science JID - 0052457 RN - 0 (DNA-Binding Proteins) RN - 0 (MSN2 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Transcription Factors) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Conserved Sequence MH - DNA Mutational Analysis MH - DNA-Binding Proteins/*genetics/metabolism MH - Mutagenesis, Site-Directed MH - Phosphorylation MH - Protein Folding MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/*genetics/metabolism MH - Saccharomyces cerevisiae Proteins/*genetics/metabolism MH - Stress, Physiological/genetics MH - Structure-Activity Relationship MH - Transcription Factors/*genetics/metabolism MH - Transcriptional Activation MH - Yeasts/*genetics/metabolism EDAT- 2012/04/17 06:00 MHDA- 2013/03/26 06:00 CRDT- 2012/04/17 06:00 PHST- 2012/04/14 [aheadofprint] AID - jcs.096446 [pii] AID - 10.1242/jcs.096446 [doi] PST - ppublish SO - J Cell Sci. 2012 Jul 15;125(Pt 14):3333-42. doi: 10.1242/jcs.096446. Epub 2012 Apr 14. PMID- 23941114 OWN - NLM STAT- MEDLINE DA - 20140204 DCOM- 20141021 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 117 IP - 37 DP - 2013 Sep 19 TI - A relationship between the aggregation rates of alpha-synuclein variants and the beta-sheet populations in their monomeric forms. PG - 10737-41 LID - 10.1021/jp405614j [doi] AB - Intrinsically disordered proteins constitute a significant part of the human proteome and carry out a wide range of different functions, including in particular signaling and regulation. Several of these proteins are vulnerable to aggregation, and their aberrant assemblies have been associated with a variety of neurodegenerative and systemic diseases. It remains unclear, however, the extent to which the conformational properties of intrinsically disordered proteins in their monomeric states influence the aggregation behavior of these molecules. Here we report a relationship between aggregation rates and secondary structure populations in the soluble monomeric states of a series of mutational variants of alpha-synuclein. Overall, we found a correlation of over 90% between the changes in beta-sheet populations calculated from NMR chemical shift data and the changes in aggregation rates for eight human-to-mouse chimeric mutants. These results provide support to the idea of investigating therapeutic strategies based on the stabilization of the monomeric form of intrinsically disordered proteins through the alteration of their conformational properties. FAU - Camilloni, Carlo AU - Camilloni C AD - Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom. FAU - Vendruscolo, Michele AU - Vendruscolo M LA - eng GR - 089703/Wellcome Trust/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130909 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Recombinant Proteins) RN - 0 (alpha-Synuclein) RN - 0 (beta-Synuclein) SB - IM MH - Animals MH - Humans MH - Mice MH - Models, Molecular MH - Mutation MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/genetics MH - alpha-Synuclein/*chemistry/genetics MH - beta-Synuclein/*chemistry/genetics EDAT- 2013/08/15 06:00 MHDA- 2014/10/22 06:00 CRDT- 2013/08/15 06:00 PHST- 2013/09/09 [aheadofprint] AID - 10.1021/jp405614j [doi] PST - ppublish SO - J Phys Chem B. 2013 Sep 19;117(37):10737-41. doi: 10.1021/jp405614j. Epub 2013 Sep 9. PMID- 14741206 OWN - NLM STAT- MEDLINE DA - 20040126 DCOM- 20040302 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 336 IP - 1 DP - 2004 Feb 6 TI - Regions within the N-terminal domain of human topoisomerase I exert important functions during strand rotation and DNA binding. PG - 93-103 AB - The human topoisomerase I N-terminal domain is the only part of the enzyme still not crystallized and the function of this domain remains enigmatical. In the present study, we have addressed the specific functions of individual N-terminal regions of topoisomerase I by characterizing mutants lacking amino acid residues 1-202 or 191-206 or having tryptophane-205 substituted by glycine in a broad variety of in vitro activity assays. As a result of these investigations we find that mutants altered in the region 191-206 distinguished themselves from the wild-type enzyme by a faster strand rotation step, insensitivity towards the anti-cancer drug camptothecin in relaxation and the inability to ligate blunt end DNA fragments. The mutant lacking amino acid residues 1-202 was impaired in blunt end DNA ligation and showed wild-type sensitivity towards camptothecin in relaxation. Taken together, the presented data support a model according to which tryptophane-205 and possibly other residues located between position 191-206 coordinates the restriction of free strand rotation during the topoisomerization step of catalysis. Moreover, tryptophane-205 appears important for the function of the bulk part of the N-terminal domain in direct DNA interaction. FAU - Frohlich, Rikke From AU - Frohlich RF AD - Department of Molecular Biology, University of Aarhus, CF Mollers Alle, Building 130, DK-8000 Aarhus C, Denmark. FAU - Andersen, Felicie Faucon AU - Andersen FF FAU - Westergaard, Ole AU - Westergaard O FAU - Andersen, Anni Hangaard AU - Andersen AH FAU - Knudsen, Birgitta Ruth AU - Knudsen BR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Antineoplastic Agents) RN - 0 (Enzyme Inhibitors) RN - 9007-49-2 (DNA) RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) RN - XT3Z54Z28A (Camptothecin) SB - IM MH - Antineoplastic Agents/metabolism MH - Base Sequence MH - Camptothecin/metabolism MH - DNA/metabolism MH - DNA Topoisomerases, Type I/*chemistry/genetics/*metabolism MH - Enzyme Inhibitors/metabolism MH - Humans MH - Mutation MH - *Protein Structure, Tertiary EDAT- 2004/01/27 05:00 MHDA- 2004/03/03 05:00 CRDT- 2004/01/27 05:00 AID - S0022283603014980 [pii] PST - ppublish SO - J Mol Biol. 2004 Feb 6;336(1):93-103. PMID- 15609993 OWN - NLM STAT- MEDLINE DA - 20041221 DCOM- 20050203 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 51 DP - 2004 Dec 28 TI - Solution structure, backbone dynamics, and association behavior of the C-terminal BRCT domain from the breast cancer-associated protein BRCA1. PG - 15983-95 AB - BRCA1 is a tumor suppressor protein associated with breast and ovarian cancer. The C-terminal region of BRCA1 consists of two closely spaced BRCT domains which mediate essential biological functions, including regulation of transcription and control of cell-cycle progression by their interaction with phosphorylated effector proteins. Here we report the NMR structure of the isolated C-terminal BRCT domain (BRCT-c) from human BRCA1. BRCT-c is well-structured in solution, folding independently in the absence of its BRCT-n counterpart. Ultracentrifugation experiments and size exclusion chromatography reveal that BRCT-c exists as a monomer under near-physiological conditions. Dynamics measurements from NMR data show three loops which coincide with the most variable sequence regions in BRCT domains, to be genuinely flexible in solution. The solution structure of BRCT-c shows subtle conformational changes when compared to the crystal structure of BRCT-c in the tandem repeat of BRCA1. These affect sites involved in formation of the BRCT-n-BRCT-c interface and the binding to phosphoserine-containing peptides. The results suggest that the presence of native BRCT-n and a properly aligned BRCT-n-BRCT-c interface are essential if BRCT-c is to adopt a biologically active conformation. Structural consequences of cancer-associated mutations and biological implications of the dynamic behavior are discussed. FAU - Gaiser, Olaf J AU - Gaiser OJ AD - Max Delbruck Center for Molecular Medicine, Robert-Rossle-Strasse 10, D-13125 Berlin, Germany. FAU - Ball, Linda J AU - Ball LJ FAU - Schmieder, Peter AU - Schmieder P FAU - Leitner, Dietmar AU - Leitner D FAU - Strauss, Holger AU - Strauss H FAU - Wahl, Martin AU - Wahl M FAU - Kuhne, Ronald AU - Kuhne R FAU - Oschkinat, Hartmut AU - Oschkinat H FAU - Heinemann, Udo AU - Heinemann U LA - eng SI - PDB/1OQA PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (BRCA1 Protein) SB - IM MH - Amino Acid Sequence MH - BRCA1 Protein/*chemistry/metabolism MH - Chromatography, Gel MH - Dimerization MH - Humans MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Structure, Tertiary MH - Sequence Alignment EDAT- 2004/12/22 09:00 MHDA- 2005/02/04 09:00 CRDT- 2004/12/22 09:00 AID - 10.1021/bi049550q [doi] PST - ppublish SO - Biochemistry. 2004 Dec 28;43(51):15983-95. PMID- 20361791 OWN - NLM STAT- MEDLINE DA - 20100511 DCOM- 20100616 LR - 20140917 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 19 DP - 2010 May 18 TI - Crystal structures of the glycopeptide sulfotransferase Teg12 in a complex with the teicoplanin aglycone. PG - 4159-68 LID - 10.1021/bi100150v [doi] AB - The TEG gene cluster, a glycopeptide biosynthetic gene cluster that is predicted to encode the biosynthesis of a polysulfated glycopeptide congener, was recently cloned from DNA extracted directly from desert soil. This predicted glycopeptide gene cluster contains three closely related sulfotransferases (Teg12, -13, and -14) that sulfate teicoplanin-like glycopeptides at three unique sites. Here we report a series of structures: an apo structure of Teg12, Teg12 bound to the desulfated cosubstrate 3'-phosphoadenosine 5'-phosphate, and Teg12 bound to the teicoplanin aglycone. Teg12 appears to undergo a series of significant conformational rearrangements during glycopeptide recruitment, binding, and catalysis. Loop regions that exhibit the most conformational flexibility show the least sequence conservation between TEG sulfotransferases. Site-directed mutagenesis guided by our structural studies confirmed the importance of key catalytic residues as well as the importance of residues found throughout the conformationally flexible loop regions. FAU - Bick, Matthew J AU - Bick MJ AD - Howard Hughes Medical Institute, Laboratory of Genetically Encoded Small Molecules, Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA. FAU - Banik, Jacob J AU - Banik JJ FAU - Darst, Seth A AU - Darst SA FAU - Brady, Sean F AU - Brady SF LA - eng GR - GM077516/GM/NIGMS NIH HHS/United States GR - P30 EB009998/EB/NIBIB NIH HHS/United States GR - R01 GM077516/GM/NIGMS NIH HHS/United States GR - R01 GM077516-04/GM/NIGMS NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Glycopeptides) RN - 1053-73-2 (adenosine 3'-phosphate-5'-phosphate) RN - 61036-62-2 (Teicoplanin) RN - 61D2G4IYVH (Adenosine Diphosphate) RN - 89139-42-4 (teicoplanin aglycone) RN - EC 2.8.2.- (Sulfotransferases) SB - IM MH - Adenosine Diphosphate/chemistry/metabolism MH - Amino Acid Sequence MH - Binding Sites MH - Catalysis MH - Crystallography, X-Ray MH - Glycopeptides/*chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Substrate Specificity MH - Sulfotransferases/*chemistry/*metabolism MH - Teicoplanin/*analogs & derivatives/chemistry/metabolism PMC - PMC2888265 MID - NIHMS199664 OID - NLM: NIHMS199664 OID - NLM: PMC2888265 EDAT- 2010/04/07 06:00 MHDA- 2010/06/17 06:00 CRDT- 2010/04/06 06:00 AID - 10.1021/bi100150v [doi] PST - ppublish SO - Biochemistry. 2010 May 18;49(19):4159-68. doi: 10.1021/bi100150v. PMID- 15609997 OWN - NLM STAT- MEDLINE DA - 20041221 DCOM- 20050203 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 51 DP - 2004 Dec 28 TI - NMR structure of transcription factor Sp1 DNA binding domain. PG - 16027-35 AB - To understand the DNA recognition mechanism of zinc finger motifs of transcription factor Sp1, we have determined the solution structure of DNA-binding domain of the Sp1 by solution NMR techniques. The DNA-binding domain of Sp1 consists of three Cys(2)His(2)-type zinc finger motifs. They have typical betabetaalpha zinc finger folds and relatively random orientations. From DNA-binding analysis performed by NMR and comparison between structures determined here and previously reported structures of other zinc fingers, it was assumed that DNA recognition modes of fingers 2 and 3 would be similar to those of fingers of Zif268, in which each finger recognizes four base pairs strictly by using residues at positions -1, 2, 3, and 6 of the recognition helix. On the contrary, finger 1 can use only two residues for DNA recognition, Lys550 and His553 at positions -1 and 3 of the helix, and has more relaxed sequence and site specificity than other Cys(2)His(2) zinc fingers. It is proposed that this relaxed property of finger 1 allows transcription factor Sp1 to bind various DNA sequences with high affinity. FAU - Oka, Shinichiro AU - Oka S AD - Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan. FAU - Shiraishi, Yasuhisa AU - Shiraishi Y FAU - Yoshida, Takuya AU - Yoshida T FAU - Ohkubo, Tadayasu AU - Ohkubo T FAU - Sugiura, Yukio AU - Sugiura Y FAU - Kobayashi, Yuji AU - Kobayashi Y LA - eng SI - PDB/1TF3 SI - PDB/1VA1 SI - PDB/1VA2 SI - PDB/1VA3 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Nitrogen Isotopes) RN - 0 (Sp1 Transcription Factor) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - DNA/*metabolism MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Nitrogen Isotopes MH - Sequence Alignment MH - Sp1 Transcription Factor/*chemistry/metabolism EDAT- 2004/12/22 09:00 MHDA- 2005/02/04 09:00 CRDT- 2004/12/22 09:00 AID - 10.1021/bi048438p [doi] PST - ppublish SO - Biochemistry. 2004 Dec 28;43(51):16027-35. PMID- 21280118 OWN - NLM STAT- MEDLINE DA - 20110131 DCOM- 20110603 LR - 20140821 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 20 IP - 2 DP - 2011 Feb TI - NMR determination of pKa values in alpha-synuclein. PG - 256-69 LID - 10.1002/pro.556 [doi] AB - The intrinsically unfolded protein alpha-synuclein has an N-terminal domain with seven imperfect KTKEGV sequence repeats and a C-terminal domain with a large proportion of acidic residues. We characterized pK(a) values for all 26 sites in the protein that ionize below pH 7 using 2D (1) H-(15) N HSQC and 3D C(CO)NH NMR experiments. The N-terminal domain shows systematically lowered pK(a) values, suggesting weak electrostatic interactions between acidic and basic residues in the KTKEGV repeats. By contrast, the C-terminal domain shows elevated pK(a) values due to electrostatic repulsion between like charges. The effects are smaller but persist at physiological salt concentrations. For alpha-synuclein in the membrane-like environment of sodium dodecylsulfate (SDS) micelles, we characterized the pK(a) of His50, a residue of particular interest since it is flanked within one turn of the alpha-helix structure by the Parkinson's disease-linked mutants E46K and A53T. The pK(a) of His50 is raised by 1.4 pH units in the micelle-bound state. Titrations of His50 in the micelle-bound states of the E46K and A53T mutants show that the pK(a) shift is primarily due to interactions between the histidine and the sulfate groups of SDS, with electrostatic interactions between His50 and Glu46 playing a much smaller role. Our results indicate that the pK(a) values of uncomplexed alpha-synuclein differ significantly from random coil model peptides even though the protein is intrinsically unfolded. Due to the long-range nature of electrostatic interactions, charged residues in the alpha-synuclein sequence may help nucleate the folding of the protein into an alpha-helical structure and confer protection from misfolding. CI - Copyright (c) 2010 The Protein Society. FAU - Croke, Robyn L AU - Croke RL AD - Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269-3125, USA. FAU - Patil, Sharadrao M AU - Patil SM FAU - Quevreaux, Jason AU - Quevreaux J FAU - Kendall, Debra A AU - Kendall DA FAU - Alexandrescu, Andrei T AU - Alexandrescu AT LA - eng PT - Journal Article DEP - 20101213 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Amyloid) RN - 0 (Micelles) RN - 0 (alpha-Synuclein) RN - 7647-14-5 (Sodium Chloride) SB - IM MH - Amino Acid Sequence MH - Amyloid/chemistry/metabolism MH - Humans MH - Hydrogen-Ion Concentration MH - Micelles MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Protein Folding MH - Sodium Chloride/chemistry MH - Static Electricity MH - alpha-Synuclein/*chemistry/metabolism PMC - PMC3048411 OID - NLM: PMC3048411 EDAT- 2011/02/01 06:00 MHDA- 2011/06/04 06:00 CRDT- 2011/02/01 06:00 PHST- 2010/09/20 [received] PHST- 2010/11/03 [revised] PHST- 2010/11/05 [accepted] PHST- 2010/12/13 [aheadofprint] AID - 10.1002/pro.556 [doi] PST - ppublish SO - Protein Sci. 2011 Feb;20(2):256-69. doi: 10.1002/pro.556. Epub 2010 Dec 13. PMID- 17007877 OWN - NLM STAT- MEDLINE DA - 20061103 DCOM- 20070110 LR - 20081121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 364 IP - 2 DP - 2006 Nov 24 TI - Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin CcdA. PG - 170-85 AB - Toxin-antitoxin systems are highly abundant in plasmids and bacterial chromosomes. They ensure plasmid maintenance by killing bacteria that have lost the plasmid. Their expression is autoregulated at the level of transcription. Here, we present the solution structure of CcdA, the antitoxin of the ccd system, as a free protein (16.7 kDa) and in complex with its cognate DNA (25.3 kDa). CcdA is composed of two distinct and independent domains: the N-terminal domain, responsible for DNA binding, which establishes a new family of the ribbon-helix-helix fold and the C-terminal region, which is responsible for the interaction with the toxin CcdB. The C-terminal domain is intrinsically unstructured and forms a tight complex with the toxin. We show that CcdA specifically recognizes a 6 bp palindromic DNA sequence within the operator-promoter (OP) region of the ccd operon and binds to DNA by insertion of the positively charged N-terminal beta-sheet into the major groove. The binding of up to three CcdA dimers to a 33mer DNA of its operator-promoter region was studied by NMR spectroscopy, isothermal titration calorimetry and single point mutation. The highly flexible C-terminal region of free CcdA explains its susceptibility to proteolysis by the Lon ATP-dependent protease. FAU - Madl, Tobias AU - Madl T AD - Institute of Chemistry, University of Graz, Graz 8010, Austria. FAU - Van Melderen, Laurence AU - Van Melderen L FAU - Mine, Natacha AU - Mine N FAU - Respondek, Michal AU - Respondek M FAU - Oberer, Monika AU - Oberer M FAU - Keller, Walter AU - Keller W FAU - Khatai, Leila AU - Khatai L FAU - Zangger, Klaus AU - Zangger K LA - eng SI - PDB/2ADL SI - PDB/2ADN SI - PDB/2H3A SI - PDB/2H3C PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060901 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (Bacterial Toxins) RN - 0 (CcdA protein, Bacteria) RN - 0 (CcdB protein, Plasmid F) RN - 0 (DNA, Bacterial) RN - 0 (Nucleic Acids) RN - 0 (Oligonucleotides) RN - 0 (Solutions) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry MH - Bacterial Toxins/*chemistry MH - Calorimetry MH - Crystallography, X-Ray MH - DNA, Bacterial/*chemistry MH - Dimerization MH - Magnetic Resonance Spectroscopy MH - *Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acids/*chemistry MH - Oligonucleotides/chemistry MH - Point Mutation MH - Promoter Regions, Genetic MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Solutions EDAT- 2006/09/30 09:00 MHDA- 2007/01/11 09:00 CRDT- 2006/09/30 09:00 PHST- 2006/07/17 [received] PHST- 2006/08/25 [revised] PHST- 2006/08/29 [accepted] PHST- 2006/09/01 [aheadofprint] AID - S0022-2836(06)01140-5 [pii] AID - 10.1016/j.jmb.2006.08.082 [doi] PST - ppublish SO - J Mol Biol. 2006 Nov 24;364(2):170-85. Epub 2006 Sep 1. PMID- 24406167 OWN - NLM STAT- MEDLINE DA - 20140211 DCOM- 20140414 LR - 20141120 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 443 IP - 4 DP - 2014 Jan 24 TI - Direct interaction between EFL1 and SBDS is mediated by an intrinsically disordered insertion domain. PG - 1251-6 LID - 10.1016/j.bbrc.2013.12.143 [doi] LID - S0006-291X(14)00004-7 [pii] AB - Removal of anti-association factor, Tif6 (eIF6), by elongation factor-like 1 (EFL1) and Shwachman-Bodian-Diamond syndrome (SBDS) protein is a critical step in the late stage of ribosome maturation. Although EFL1 is known to have GTPase activity that is stimulated by SBDS, how they cooperatively trigger dissociation of Tif6 from the ribosome remains to be elucidated. In the present study, the interaction between EFL1 and SBDS was analyzed by size exclusion chromatography, gel shift assay, and isothermal titration calorimetry (ITC). The results showed that EFL1 interacted directly with SBDS. ITC experiments using domain-truncated mutants showed that the interaction between EFL1 and SBDS is governed by the insertion domain of EFL1 and domains II-III of SBDS. Circular dichroism spectroscopy showed that the insertion domain of EFL1 has a random structure in the absence of SBDS, whereas the disadvantageous entropy change observed on ITC suggested a fixed conformation coupled with complex formation with SBDS. Based on these observations together with those reported previously, we propose roles of EFL1 and SBDS in ribosomal maturation. CI - Copyright (c) 2014 Elsevier Inc. All rights reserved. FAU - Asano, Nozomi AU - Asano N AD - Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan. FAU - Atsuumi, Haruka AU - Atsuumi H AD - Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan. FAU - Nakamura, Akiyoshi AU - Nakamura A AD - Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan. FAU - Tanaka, Yoshikazu AU - Tanaka Y AD - Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan. FAU - Tanaka, Isao AU - Tanaka I AD - Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan. FAU - Yao, Min AU - Yao M AD - Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan. Electronic address: yao@castor.sci.hokudai.ac.jp. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140107 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Peptide Elongation Factor 2) RN - 0 (Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Ribosomal Proteins) RN - 0 (SBDS protein, human) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (TIF6 protein, S cerevisiae) RN - EC 3.6.1.- (GTP Phosphohydrolases) RN - EC 3.6.1.- (RIA1 protein, S cerevisiae) RN - Shwachman syndrome SB - IM MH - Amino Acid Sequence MH - Binding Sites/genetics MH - Bone Marrow Diseases/genetics/metabolism MH - Exocrine Pancreatic Insufficiency/genetics/metabolism MH - GTP Phosphohydrolases/*chemistry/genetics/*metabolism MH - Humans MH - Intrinsically Disordered Proteins/chemistry/genetics/metabolism MH - Lipomatosis/genetics/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Insertional MH - Peptide Elongation Factor 2/chemistry/genetics/metabolism MH - Protein Interaction Domains and Motifs MH - Proteins/*chemistry/genetics/*metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Ribosomal Proteins/chemistry/genetics/metabolism MH - Ribosomes/metabolism MH - Saccharomyces cerevisiae/genetics/metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism MH - Sequence Homology, Amino Acid MH - Thermodynamics OTO - NOTNLM OT - Circular dichroism OT - Interaction OT - Intrinsically disordered protein OT - Isothermal titration calorimetry OT - Ribosome biogenesis EDAT- 2014/01/11 06:00 MHDA- 2014/04/15 06:00 CRDT- 2014/01/11 06:00 PHST- 2013/12/17 [received] PHST- 2013/12/24 [accepted] PHST- 2014/01/07 [aheadofprint] AID - S0006-291X(14)00004-7 [pii] AID - 10.1016/j.bbrc.2013.12.143 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2014 Jan 24;443(4):1251-6. doi: 10.1016/j.bbrc.2013.12.143. Epub 2014 Jan 7. PMID- 12351827 OWN - NLM STAT- MEDLINE DA - 20020927 DCOM- 20030409 LR - 20070724 IS - 0907-4449 (Print) IS - 0907-4449 (Linking) VI - 58 IP - Pt 10 Pt 2 DP - 2002 Oct TI - Purification, crystallization and preliminary X-ray analysis of the BRCT domains of human 53BP1 bound to the p53 tumour suppressor. PG - 1826-9 AB - A complex of the DNA-binding domain of the tumour suppressor p53 bound to the BRCT domains of the p53-binding protein (53BP1) has been prepared and purified. Single crystals have been obtained using the microbatch technique with polyethylene glycol 4 kDa and ammonium sulfate. Crystals diffract X-rays to beyond 2.3 A and belong to the space group P2(1)2(1)2(1). Several complete data sets have been collected from a number of crystals, each with different unit-cell parameters. Partial structures have been produced by successful placement of two copies of the p53 core region into the asymmetric unit. There is clear evidence for the binding protein and a complete structure determination is under way. FAU - Derbyshire, Dean J AU - Derbyshire DJ AD - Structural Medicine Unit, Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, England. FAU - Basu, Balaku P AU - Basu BP FAU - Date, Takayasu AU - Date T FAU - Iwabuchi, Kuniyoshi AU - Iwabuchi K FAU - Doherty, Aidan J AU - Doherty AJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20020928 PL - Denmark TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (Carrier Proteins) RN - 0 (DNA Primers) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Phosphoproteins) RN - 0 (TP53BP1 protein, human) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Carrier Proteins/*chemistry MH - Cloning, Molecular MH - Crystallization MH - Crystallography, X-Ray/methods MH - DNA Primers MH - *Genes, p53 MH - Humans MH - *Intracellular Signaling Peptides and Proteins MH - *Phosphoproteins MH - Sensitivity and Specificity EDAT- 2002/09/28 04:00 MHDA- 2003/04/10 05:00 CRDT- 2002/09/28 04:00 PHST- 2002/04/22 [received] PHST- 2002/06/18 [accepted] PHST- 2002/09/28 [epublish] AID - S0907444902010910 [pii] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2002 Oct;58(Pt 10 Pt 2):1826-9. Epub 2002 Sep 28. PMID- 11119643 OWN - NLM STAT- MEDLINE DA - 20010119 DCOM- 20010201 LR - 20071114 IS - 0887-3585 (Print) IS - 0887-3585 (Linking) VI - 42 IP - 2 DP - 2001 Feb 1 TI - Localization of the C-terminus of rat glutathione S-transferase A1-1: crystal structure of mutants W21F and W21F/F220Y. PG - 192-200 AB - Twelve C-terminal residues of human glutathione S-transferase A1-1 form a helix in the presence of glutathione-conjugate, or substrate alone, and partly cover the active site. According to X-ray structures, the helix is disordered in the absence of glutathione, but it is not known if it is helical and delocalized, or in a random-coil conformation. Mutation to a tyrosine of residue 220 within this helix was previously shown to affect the pK(a) of Tyr-9 at the active site, in the apo form of the enzyme, and it was proposed that an on-face hydrogen bond between Tyr-220 and Tyr-9 provided a means for affecting this pK(a). In the current study, X-ray structures of the W21F and of the C-terminal mutation, W21F/F220Y, with glutathione sulfonate bound, show that the C-terminal helix is disordered (or delocalized) in the W21F crystal but is visible and ordered in a novel location, a crystal packing crevice, in one of three monomers in the W21F/F220Y crystal, and the proposed hydrogen bond is not formed. Fluorescence spectroscopy studies using an engineered F222W mutant show that the C-terminus remains delocalized in the absence of glutathione or when only the glutathione binding site is occupied, but is ordered and localized in the presence of substrate or conjugate, consistent with these and previous crystallographic studies. Proteins 2001;42:192-200. CI - Copyright 2000 Wiley-Liss, Inc. FAU - Adman, E T AU - Adman ET AD - Department of Biological Structure, University of Washington, Seattle, Washington, USA. adman@u.washington.edu FAU - Le Trong, I AU - Le Trong I FAU - Stenkamp, R E AU - Stenkamp RE FAU - Nieslanik, B S AU - Nieslanik BS FAU - Dietze, E C AU - Dietze EC FAU - Tai, G AU - Tai G FAU - Ibarra, C AU - Ibarra C FAU - Atkins, W M AU - Atkins WM LA - eng GR - GM51210/GM/NIGMS NIH HHS/United States GR - P30 ES07033/ES/NIEHS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Isoenzymes) RN - 0 (Peptide Fragments) RN - EC 2.5.1.18 (Glutathione Transferase) RN - EC 2.5.1.18 (glutathione S-transferase alpha) SB - IM MH - Animals MH - Binding Sites MH - Crystallography, X-Ray MH - Glutathione Transferase/*chemistry/genetics MH - Isoenzymes MH - Models, Molecular MH - Mutation MH - Peptide Fragments/chemistry MH - Protein Conformation MH - Rats MH - Spectrometry, Fluorescence EDAT- 2000/12/19 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/12/19 11:00 AID - 10.1002/1097-0134(20010201)42:2<192::AID-PROT60>3.0.CO;2-# [pii] PST - ppublish SO - Proteins. 2001 Feb 1;42(2):192-200. PMID- 21803119 OWN - NLM STAT- MEDLINE DA - 20111128 DCOM- 20120319 LR - 20150521 IS - 1872-8057 (Electronic) IS - 0303-7207 (Linking) VI - 348 IP - 2 DP - 2012 Jan 30 TI - Structural and functional analysis of domains of the progesterone receptor. PG - 418-29 LID - 10.1016/j.mce.2011.07.017 [doi] AB - Steroid hormone receptors are multi-domain proteins composed of conserved well-structured regions, such as ligand (LBD) and DNA binding domains (DBD), plus other naturally unstructured regions including the amino-terminal domain (NTD) and the hinge region between the LBD and DBD. The hinge is more than just a flexible region between the DBD and LBD and is capable of binding co-regulatory proteins and the minor groove of DNA flanking hormone response elements. Because the hinge can directly participate in DNA binding it has also been termed the carboxyl terminal extension (CTE) of the DNA binding domain. The CTE and NTD are dynamic regions of the receptor that can adopt multiple conformations depending on the environment of interacting proteins and DNA. Both regions have important regulatory roles for multiple receptor functions that are related to the ability of the CTE and NTD to form multiple active conformations. This review focuses on studies of the CTE and NTD of progesterone receptor (PR), as well as related work with other steroid/nuclear receptors. CI - Copyright (c) 2011 Elsevier Ireland Ltd. All rights reserved. FAU - Hill, Krista K AU - Hill KK AD - Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206, USA. FAU - Roemer, Sarah C AU - Roemer SC FAU - Churchill, Mair E A AU - Churchill ME FAU - Edwards, Dean P AU - Edwards DP LA - eng GR - CA46938/CA/NCI NIH HHS/United States GR - R01 GM079154/GM/NIGMS NIH HHS/United States GR - R01 GM079154-01A1/GM/NIGMS NIH HHS/United States GR - R01 GM079154-02/GM/NIGMS NIH HHS/United States GR - R01 GM079154-03/GM/NIGMS NIH HHS/United States GR - R01 GM079154-04/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review DEP - 20110722 PL - Ireland TA - Mol Cell Endocrinol JT - Molecular and cellular endocrinology JID - 7500844 RN - 0 (High Mobility Group Proteins) RN - 0 (Receptors, Progesterone) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - DNA/chemistry MH - Gene Expression Regulation MH - High Mobility Group Proteins/chemistry MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Protein Binding MH - Protein Structure, Tertiary MH - Receptors, Progesterone/*chemistry/physiology MH - Response Elements PMC - PMC4437577 MID - NIHMS313758 OID - NLM: NIHMS313758 OID - NLM: PMC4437577 EDAT- 2011/08/02 06:00 MHDA- 2012/03/20 06:00 CRDT- 2011/08/02 06:00 PHST- 2011/03/10 [received] PHST- 2011/06/29 [revised] PHST- 2011/07/07 [accepted] PHST- 2011/07/22 [aheadofprint] AID - S0303-7207(11)00397-2 [pii] AID - 10.1016/j.mce.2011.07.017 [doi] PST - ppublish SO - Mol Cell Endocrinol. 2012 Jan 30;348(2):418-29. doi: 10.1016/j.mce.2011.07.017. Epub 2011 Jul 22. PMID- 21156144 OWN - NLM STAT- MEDLINE DA - 20101215 DCOM- 20110328 LR - 20140821 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 12 DP - 2010 Dec 15 TI - Analysis of the bacterial luciferase mobile loop by replica-exchange molecular dynamics. PG - 4012-9 LID - 10.1016/j.bpj.2010.11.001 [doi] AB - Bacterial luciferase contains an extended 29-residue mobile loop. Movements of this loop are governed by binding of either flavin mononucleotide (FMNH2) or polyvalent anions. To understand this process, loop dynamics were investigated using replica-exchange molecular dynamics that yielded conformational ensembles in either the presence or absence of FMNH2. The resulting data were analyzed using clustering and network analysis. We observed the closed conformations that are visited only in the simulations with the ligand. Yet the mobile loop is intrinsically flexible, and FMNH2 binding modifies the relative populations of conformations. This model provides unique information regarding the function of a crystallographically disordered segment of the loop near the binding site. Structures at or near the fringe of this network were compatible with flavin binding or release. Finally, we demonstrate that the crystallographically observed conformation of the mobile loop bound to oxidized flavin was influenced by crystal packing. Thus, our study has revealed what we believe are novel conformations of the mobile loop and additional context for experimentally determined structures. CI - Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Campbell, Zachary T AU - Campbell ZT AD - Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA. FAU - Baldwin, Thomas O AU - Baldwin TO FAU - Miyashita, Osamu AU - Miyashita O LA - eng PT - Journal Article PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 7N464URE7E (Flavin Mononucleotide) RN - EC 1.14.14.3 (Luciferases, Bacterial) SB - IM MH - Cluster Analysis MH - Flavin Mononucleotide/chemistry/metabolism MH - Luciferases, Bacterial/*chemistry MH - *Molecular Dynamics Simulation MH - Protein Structure, Secondary PMC - PMC3000479 OID - NLM: PMC3000479 EDAT- 2010/12/16 06:00 MHDA- 2011/03/29 06:00 CRDT- 2010/12/16 06:00 PHST- 2010/02/28 [received] PHST- 2010/10/21 [revised] PHST- 2010/11/01 [accepted] AID - S0006-3495(10)01367-6 [pii] AID - 10.1016/j.bpj.2010.11.001 [doi] PST - ppublish SO - Biophys J. 2010 Dec 15;99(12):4012-9. doi: 10.1016/j.bpj.2010.11.001. PMID- 21894929 OWN - NLM STAT- MEDLINE DA - 20111004 DCOM- 20111216 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 50 IP - 40 DP - 2011 Oct 11 TI - Mapping unstructured regions and synergistic folding in intrinsically disordered proteins with amide H/D exchange mass spectrometry. PG - 8722-32 LID - 10.1021/bi200875p [doi] AB - Mapping the structured and disordered regions and identifying disorder-to-order transitions are essential to understanding intrinsically disordered proteins (IDPs). One technique that can provide such information is H/D exchange coupled with mass spectrometry (H/D-MS). To explore the feasibility of H/D-MS for mapping disordered and ordered regions in IDPs, we undertook a systematic evaluation of an unstructured protein, a molten globular protein, and the well-folded complex of the two proteins. Most segments of the unstructured protein, ACTR (activator of thyroid and retinoid receptors, NCOA3_HUMAN, residues 1018-1088), exchange at rates consistent with its assignment as an unstructured protein, but there is slight protection in regions that become helical in the ACTR-CBP complex. The molten globular protein, CBP (the nuclear coactivator binding domain of the CREB binding protein, CBP_MOUSE, residues 2059-2117), is moderately protected from exchange, and the protection is nearly uniform across the length of the protein. The uniformity arises because of rapid interconversion between an ensemble of folded conformers and an ensemble of unstructured conformers. Rapid interconversion causes the H/D exchange kinetics to be dominated by exchange by molecules in unstructured conformations. For the folded ACTR-CBP complex, the exchange data provide a qualitatively accurate description of the complex. Our results provide a useful framework to use in the interpretation of H/D-MS data of intrinsically disordered proteins. FAU - Keppel, Theodore R AU - Keppel TR AD - Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States. FAU - Howard, Brent A AU - Howard BA FAU - Weis, David D AU - Weis DD LA - eng PT - Evaluation Studies PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110919 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Crebbp protein, mouse) RN - 7YNJ3PO35Z (Hydrogen) RN - AR09D82C7G (Deuterium) RN - EC 2.3.1.48 (CREB-Binding Protein) RN - EC 2.3.1.48 (NCOA3 protein, human) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 3) SB - IM EIN - Biochemistry. 2012 Oct 2;51(39):7812 MH - Animals MH - CREB-Binding Protein/*chemistry/genetics/metabolism MH - Deuterium/chemistry MH - Humans MH - Hydrogen/chemistry MH - Isotope Labeling MH - Mass Spectrometry/*methods MH - Models, Molecular MH - Nuclear Receptor Coactivator 3/*chemistry/genetics/metabolism MH - Protein Folding EDAT- 2011/09/08 06:00 MHDA- 2011/12/17 06:00 CRDT- 2011/09/08 06:00 PHST- 2011/09/19 [aheadofprint] AID - 10.1021/bi200875p [doi] PST - ppublish SO - Biochemistry. 2011 Oct 11;50(40):8722-32. doi: 10.1021/bi200875p. Epub 2011 Sep 19. PMID- 19501564 OWN - NLM STAT- MEDLINE DA - 20090714 DCOM- 20090812 LR - 20121115 IS - 1096-0384 (Electronic) IS - 0003-9861 (Linking) VI - 487 IP - 2 DP - 2009 Jul 15 TI - Tropoelastin as a thermodynamically unfolded premolten globule protein: The effect of trimethylamine N-oxide on structure and coacervation. PG - 79-84 LID - 10.1016/j.abb.2009.06.001 [doi] AB - Tropoelastin is the monomer building block of the biopolymer elastin, which is responsible for elasticity in arteries, lung and skin. Previous studies have shown that, in contrast to predictions made based on primary sequence, tropoelastin has little regular secondary structure in aqueous solution and displays considerable flexibility. This investigation defines the level of residual structure present in tropoelastin and uses the naturally-occurring structure-inducing osmolyte trimethylamine N-oxide to examine the potential for regular structure in tropoelastin. Tropoelastin is defined as a thermodynamically unfolded premolten globule, which can account for its ability to elastically deform. FAU - Dyksterhuis, Leanne B AU - Dyksterhuis LB AD - CSIRO Molecular and Health Technologies, Clayton, Vic. 3168, Australia. Leanne.Dyksterhuis@csiro.au FAU - Carter, Elizabeth A AU - Carter EA FAU - Mithieux, Suzanne M AU - Mithieux SM FAU - Weiss, Anthony S AU - Weiss AS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090606 PL - United States TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (Emulsions) RN - 0 (Methylamines) RN - 0 (Tropoelastin) RN - FLD0K1SJ1A (trimethyloxamine) SB - IM MH - Circular Dichroism MH - Emulsions MH - Humans MH - Methylamines/*pharmacology MH - Protein Binding/drug effects MH - Protein Denaturation/*drug effects MH - Spectroscopy, Fourier Transform Infrared MH - Temperature MH - Thermodynamics MH - Tropoelastin/*chemistry/metabolism EDAT- 2009/06/09 09:00 MHDA- 2009/08/13 09:00 CRDT- 2009/06/09 09:00 PHST- 2009/05/14 [received] PHST- 2009/05/29 [revised] PHST- 2009/06/02 [accepted] PHST- 2009/06/06 [aheadofprint] AID - S0003-9861(09)00178-7 [pii] AID - 10.1016/j.abb.2009.06.001 [doi] PST - ppublish SO - Arch Biochem Biophys. 2009 Jul 15;487(2):79-84. doi: 10.1016/j.abb.2009.06.001. Epub 2009 Jun 6. PMID- 17681539 OWN - NLM STAT- MEDLINE DA - 20070903 DCOM- 20071101 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 372 IP - 3 DP - 2007 Sep 21 TI - Structural characterization of the intrinsically unfolded protein beta-synuclein, a natural negative regulator of alpha-synuclein aggregation. PG - 708-22 AB - The synuclein family of intrinsically unfolded proteins is composed of three highly homologous members, alpha-synuclein (alphaS), beta-synuclein (betaS) and gamma-synuclein (gammaS), which are linked to neurodegenerative disorders and cancer. alphaS has been studied intensively after its identification as the major protein component of amyloid-like deposits in Parkinson's disease and dementia with Lewy bodies. betaS, on the other hand, was found to act as a potent inhibitor of alphaS amyloid formation, and it is proposed as a natural regulator of its neurotoxicity. It is then of particular interest to elucidate the structural and dynamic features of the soluble state of betaS as a first step to understand the molecular basis of its anti-amyloidogenic effect on alphaS. We present here the characterization of natively unstructured betaS by high resolution heteronuclear NMR techniques. A combination of pulse-field gradient, three-dimensional heteronuclear correlation, residual dipolar couplings, paramagnetic relaxation enhancement and backbone relaxation experiments were employed to characterize the ensemble of conformations populated by the protein. The results indicate that betaS adopts extended conformations in its native state, characterized by the lack of the long-range contacts as previously reported for alphaS. Despite the lack of defined secondary structure, we found evidence for transient polyproline II conformations clustered at the C-terminal region. The structuring of the backbone at the C terminus is locally encoded, stabilized by the presence of eight proline residues embedded in a polypeptide stretch rich in hydrophilic and negatively charged amino acids. The structural and functional implications of these findings are analyzed via a thorough comparison with its neurotoxic homolog alphaS. FAU - Bertoncini, Carlos W AU - Bertoncini CW AD - Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077, Gottingen, Germany. FAU - Rasia, Rodolfo M AU - Rasia RM FAU - Lamberto, Gonzalo R AU - Lamberto GR FAU - Binolfi, Andres AU - Binolfi A FAU - Zweckstetter, Markus AU - Zweckstetter M FAU - Griesinger, Christian AU - Griesinger C FAU - Fernandez, Claudio O AU - Fernandez CO LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070717 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Nitrogen Isotopes) RN - 0 (Peptides) RN - 0 (Protons) RN - 0 (Solutions) RN - 0 (alpha-Synuclein) RN - 0 (beta-Synuclein) RN - 25191-13-3 (polyproline) SB - IM MH - Amino Acid Sequence MH - Hydrogen-Ion Concentration MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Nitrogen Isotopes MH - Peptides/chemistry MH - *Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protons MH - Solutions MH - Time Factors MH - alpha-Synuclein/*chemistry MH - beta-Synuclein/*chemistry/*metabolism EDAT- 2007/08/08 09:00 MHDA- 2007/11/02 09:00 CRDT- 2007/08/08 09:00 PHST- 2007/05/30 [received] PHST- 2007/07/07 [revised] PHST- 2007/07/09 [accepted] PHST- 2007/07/17 [aheadofprint] AID - S0022-2836(07)00923-0 [pii] AID - 10.1016/j.jmb.2007.07.009 [doi] PST - ppublish SO - J Mol Biol. 2007 Sep 21;372(3):708-22. Epub 2007 Jul 17. PMID- 12815044 OWN - NLM STAT- MEDLINE DA - 20030922 DCOM- 20031117 LR - 20101118 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 39 DP - 2003 Sep 26 TI - Structural organization of alpha-synuclein fibrils studied by site-directed spin labeling. PG - 37530-5 AB - Despite its importance in Parkinson's disease, a detailed understanding of the structure and mechanism of alpha-synuclein fibril formation remains elusive. In this study, we used site-directed spin labeling and electron paramagnetic resonance spectroscopy to study the structural features of monomeric and fibrillar alpha-synuclein. Our results indicate that monomeric alpha-synuclein, in solution, has a highly dynamic structure, in agreement with the notion that alpha-synuclein is a natively unfolded protein. In contrast, fibrillar aggregates of alpha-synuclein exhibit a distinct domain organization. Our data identify a highly ordered and specifically folded central core region of approximately 70 amino acids, whereas the N terminus is structurally more heterogeneous and the C terminus ( approximately 40 amino acids) is completely unfolded. Interestingly, the central core region of alpha-synuclein exhibits several features reminiscent of those observed in the core region of fibrillar Alzheimer's amyloid beta peptide, including an in-register parallel structure. Although the lengths of the respective core regions differ, fibrils from different amyloid proteins nevertheless appear to be able to take up highly similar, and possibly conserved, structures. FAU - Der-Sarkissian, Ani AU - Der-Sarkissian A AD - Department of Molecular Pharmacology and Toxicology, School of Pharmacy, University of Southern California, Los Angeles 90089, USA. FAU - Jao, Christine C AU - Jao CC FAU - Chen, Jeannie AU - Chen J FAU - Langen, Ralf AU - Langen R LA - eng GR - T32 DE07211/DE/NIDCR NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20030618 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Amyloid beta-Peptides) RN - 0 (Nerve Tissue Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Amyloid beta-Peptides/*chemistry MH - Electron Spin Resonance Spectroscopy MH - Humans MH - Models, Molecular MH - Nerve Tissue Proteins/*chemistry MH - Protein Folding MH - Synucleins MH - alpha-Synuclein EDAT- 2003/06/20 05:00 MHDA- 2003/12/03 05:00 CRDT- 2003/06/20 05:00 PHST- 2003/06/18 [aheadofprint] AID - 10.1074/jbc.M305266200 [doi] AID - M305266200 [pii] PST - ppublish SO - J Biol Chem. 2003 Sep 26;278(39):37530-5. Epub 2003 Jun 18. PMID- 12667059 OWN - NLM STAT- MEDLINE DA - 20030401 DCOM- 20030501 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 42 IP - 13 DP - 2003 Apr 8 TI - Beta-synuclein inhibits formation of alpha-synuclein protofibrils: a possible therapeutic strategy against Parkinson's disease. PG - 3696-700 AB - Parkinson's disease (PD) is an age-associated and progressive movement disorder that is characterized by dopaminergic neuronal loss in the substantia nigra and, at autopsy, by fibrillar alpha-synuclein inclusions, or Lewy bodies. Despite the qualitative correlation between alpha-synuclein fibrils and disease, in vitro biophysical studies strongly suggest that prefibrillar alpha-synuclein oligomers, or protofibrils, are pathogenic. Consistent with this proposal, transgenic mice that express human alpha-synuclein develop a Parkinsonian movement disorder concurrent with nonfibrillar alpha-synuclein inclusions and the loss of dopaminergic terminii. Double-transgenic progeny of these mice that also express human beta-synuclein, a homologue of alpha-synuclein, show significant amelioration of all three phenotypes. We demonstrate here that beta- and gamma-synuclein (a third homologue that is expressed primarily in peripheral neurons) are natively unfolded in monomeric form, but structured in protofibrillar form. Beta-synuclein protofibrils do not bind to or permeabilize synthetic vesicles, unlike protofibrils comprising alpha-synuclein or gamma-synuclein. Significantly, beta-synuclein inhibits the generation of A53T alpha-synuclein protofibrils and fibrils. This finding provides a rationale for the phenotype of the double-transgenic mice and suggests a therapeutic strategy for PD. FAU - Park, June-Young AU - Park JY AD - Center for Neurologic Diseases, Brigham and Women's Hospital and Department of Neurology, Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA. FAU - Lansbury, Peter T Jr AU - Lansbury PT Jr LA - eng GR - NS38375/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Nerve Tissue Proteins) RN - 0 (Phospholipids) RN - 0 (SNCA protein, human) RN - 0 (SNCB protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 0 (beta-Synuclein) RN - 0 (gamma-Synuclein) SB - IM MH - Amino Acid Sequence MH - Amyloid/*chemistry MH - Circular Dichroism MH - Humans MH - Light MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*antagonists & inhibitors/*metabolism MH - Parkinson Disease/*metabolism/therapy MH - Permeability MH - Phospholipids/metabolism MH - Protein Binding MH - Sequence Homology, Amino Acid MH - Synucleins MH - alpha-Synuclein MH - beta-Synuclein MH - gamma-Synuclein EDAT- 2003/04/02 05:00 MHDA- 2003/05/02 05:00 CRDT- 2003/04/02 05:00 AID - 10.1021/bi020604a [doi] PST - ppublish SO - Biochemistry. 2003 Apr 8;42(13):3696-700. PMID- 8567649 OWN - NLM STAT- MEDLINE DA - 19960301 DCOM- 19960301 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 271 IP - 4 DP - 1996 Jan 26 TI - Identification of a nucleolin binding site in human topoisomerase I. PG - 1993-7 AB - DNA topoisomerase I (topo I) is involved in the regulation of DNA supercoiling, gene transcription, and rDNA recombination. However, little is known about interactions between topo I and other nuclear proteins. We used affinity chromatography with a topo I fusion protein to screen U-937 leukemic cell extracts and have identified nucleolin as a topo I-binding protein. Coimmunoprecipitation and other studies demonstrate that the interaction between topo I and nucleolin is direct. Furthermore, deletion analyses have identified the 166-210-amino acid region of topo I as sufficient for the interaction with nucleolin. Since nucleolin has been implicated in nuclear transport and in a variety of transcriptional processes, the interaction with topo I may relate to the cellular localization of topo I or to the known role of this topoisomerase in transcription. FAU - Bharti, A K AU - Bharti AK AD - Division of Cancer Pharmacology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Olson, M O AU - Olson MO FAU - Kufe, D W AU - Kufe DW FAU - Rubin, E H AU - Rubin EH LA - eng GR - CA19589/CA/NCI NIH HHS/United States GR - CA70981/CA/NCI NIH HHS/United States GR - GM28349/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA, Superhelical) RN - 0 (Nuclear Proteins) RN - 0 (Phosphoproteins) RN - 0 (RNA-Binding Proteins) RN - 0 (nucleolin) RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Cell Compartmentation MH - DNA Topoisomerases, Type I/*chemistry/metabolism MH - DNA, Superhelical/metabolism MH - Humans MH - Molecular Sequence Data MH - Nuclear Proteins/*chemistry/metabolism MH - Phosphoproteins/*chemistry/metabolism MH - *RNA-Binding Proteins MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Tumor Cells, Cultured EDAT- 1996/01/26 MHDA- 1996/01/26 00:01 CRDT- 1996/01/26 00:00 PST - ppublish SO - J Biol Chem. 1996 Jan 26;271(4):1993-7. PMID- 15004549 OWN - NLM STAT- MEDLINE DA - 20040329 DCOM- 20040519 LR - 20061115 IS - 1545-9993 (Print) IS - 1545-9985 (Linking) VI - 11 IP - 4 DP - 2004 Apr TI - Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein. PG - 323-9 AB - The La protein is a conserved component of eukaryotic ribonucleoprotein complexes that binds the 3' poly(U)-rich elements of nascent RNA polymerase III (pol III) transcripts to assist folding and maturation. This specific recognition is mediated by the N-terminal domain (NTD) of La, which comprises a La motif and an RNA recognition motif (RRM). We have determined the solution structures of both domains and show that the La motif adopts an alpha/beta fold that comprises a winged-helix motif elaborated by the insertion of three helices. Chemical shift mapping experiments show that these insertions are involved in RNA interactions. They further delineate a distinct surface patch on each domain-containing both basic and aromatic residues-that interacts with RNA and accounts for the cooperative binding of short oligonucleotides exhibited by the La NTD. FAU - Alfano, Caterina AU - Alfano C AD - Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, St. Michael's Building, Portsmouth PO1 2DT, UK. FAU - Sanfelice, Domenico AU - Sanfelice D FAU - Babon, Jeff AU - Babon J FAU - Kelly, Geoff AU - Kelly G FAU - Jacks, Amanda AU - Jacks A FAU - Curry, Stephen AU - Curry S FAU - Conte, Maria R AU - Conte MR LA - eng SI - PDB/1S79 SI - PDB/1S7A PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040307 PL - United States TA - Nat Struct Mol Biol JT - Nature structural & molecular biology JID - 101186374 RN - 0 (Autoantigens) RN - 0 (Ribonucleoproteins) RN - 0 (SS-B antigen) RN - 63231-63-0 (RNA) SB - IM CIN - Nat Struct Mol Biol. 2004 Apr;11(4):303-5. PMID: 15048103 MH - Amino Acid Sequence MH - Animals MH - Autoantigens MH - Binding Sites MH - Conserved Sequence MH - Humans MH - Magnetic Resonance Spectroscopy/methods MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA/genetics/*metabolism MH - Ribonucleoproteins/*chemistry/genetics/*metabolism MH - Sequence Alignment MH - Sequence Homology, Amino Acid EDAT- 2004/03/09 05:00 MHDA- 2004/05/20 05:00 CRDT- 2004/03/09 05:00 PHST- 2004/01/26 [received] PHST- 2004/02/19 [accepted] PHST- 2004/03/07 [aheadofprint] AID - 10.1038/nsmb747 [doi] AID - nsmb747 [pii] PST - ppublish SO - Nat Struct Mol Biol. 2004 Apr;11(4):323-9. Epub 2004 Mar 7. PMID- 19821614 OWN - NLM STAT- MEDLINE DA - 20091218 DCOM- 20100222 IS - 1554-8937 (Electronic) IS - 1554-8929 (Linking) VI - 4 IP - 12 DP - 2009 Dec 18 TI - Synergistic interplay between promoter recognition and CBP/p300 coactivator recruitment by FOXO3a. PG - 1017-27 LID - 10.1021/cb900190u [doi] AB - FOXO3a is a transcription factor belonging to the forkhead box O-Class (FOXO) subfamily, and it regulates metabolism, cell-cycle arrest, cell differentiation, and apoptosis through activating or suppressing gene transcription. FOXO3a contains a well-folded DNA-binding forkhead (FH) domain, but a large portion of the remaining protein sequence (75% of the total) is predicted to comprise intrinsically disordered regions (IDRs). Within the IDRs, there are three conserved regions (CR1-CR3), and it has been shown that CR3 (residues D610-N650) is a transactivation domain that recruits the coactivator histone acetyltransferase (HAT) CBP/p300, through binding to its KIX domain. In a previous study, we determined the solution structure of the FH domain and identified an intramolecular interaction between FH and CR3 domains of FOXO3a. Here we illustrate that the KIX domain of CBP interacts with the central core region (L620-A635) of CR3, which also internally interacts with the FH domain. In this heterotypic interplay, FH prevents CR3 from binding to KIX; however, upon binding to the Forkhead response element (FRE) DNA, the FH domain releases the CR3 domain, allowing it to interact with KIX. While previous studies have shown that the transactivation domains of c-Myb and MLL bind to distinct sites on KIX, our results indicate that FOXO3a CR3 has an ability to bind to both of these sites. These results suggest a model of FOXO3a-dependent coactivator recruitment in which the dynamic interplay between KIX and FH domains for binding to CR3 plays a key regulatory role in gene transcription activation. FAU - Wang, Feng AU - Wang F AD - Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 2M9. FAU - Marshall, Christopher B AU - Marshall CB FAU - Li, Guang-Yao AU - Li GY FAU - Yamamoto, Kazuo AU - Yamamoto K FAU - Mak, Tak W AU - Mak TW FAU - Ikura, Mitsuhiko AU - Ikura M LA - eng GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - ACS Chem Biol JT - ACS chemical biology JID - 101282906 RN - 0 (FOXO3 protein, human) RN - 0 (Forkhead Transcription Factors) RN - 9007-49-2 (DNA) RN - EC 2.3.1.48 (p300-CBP Transcription Factors) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - DNA/metabolism MH - Forkhead Transcription Factors/*analysis/*metabolism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Promoter Regions, Genetic MH - Protein Structure, Tertiary MH - Sequence Alignment MH - *Transcriptional Activation MH - p300-CBP Transcription Factors/analysis/*metabolism EDAT- 2009/10/14 06:00 MHDA- 2010/02/23 06:00 CRDT- 2009/10/14 06:00 AID - 10.1021/cb900190u [doi] PST - ppublish SO - ACS Chem Biol. 2009 Dec 18;4(12):1017-27. doi: 10.1021/cb900190u. PMID- 24643059 OWN - NLM STAT- MEDLINE DA - 20140610 DCOM- 20150129 LR - 20150420 IS - 1555-8584 (Electronic) IS - 1547-6286 (Linking) VI - 11 IP - 4 DP - 2014 TI - Novel regulatory principles of the spliceosomal Brr2 RNA helicase and links to retinal disease in humans. PG - 298-312 LID - 10.4161/rna.28353 [doi] AB - For each round of pre-mRNA splicing, a spliceosome is assembled anew on its substrate. RNA-protein remodeling events required for spliceosome assembly, splicing catalysis, and spliceosome disassembly are driven and controlled by a conserved group of ATPases/RNA helicases. The activities of most of these enzymes are timed by their recruitment to the spliceosome. The Brr2 enzyme, however, which mediates spliceosome catalytic activation, is a stable subunit of the spliceosome, and thus, requires special regulation. Recent structural and functional studies have revealed diverse mechanisms whereby an RNaseH-like and a Jab1/MPN-like domain of the Prp8 protein regulate Brr2 activity during splicing both positively and negatively. Reversible Brr2 inhibition might in part be achieved via an intrinsically unstructured element of the Prp8 Jab1/MPN domain, a concept widespread in biological systems. Mutations leading to changes in the Prp8 Jab1/MPN domain, which are linked to a severe form of retinitis pigmentosa, disrupt Jab1/MPN-mediated regulation of Brr2. FAU - Mozaffari-Jovin, Sina AU - Mozaffari-Jovin S AD - Dept. of Cellular Biochemistry; Max Planck Institute for Biophysical Chemistry; Am Fassberg 11; Gottingen, Germany. FAU - Wandersleben, Traudy AU - Wandersleben T AD - Laboratory of Structural Biochemistry; Freie Universitat Berlin; Takustr. 6; Berlin, Germany. FAU - Santos, Karine F AU - Santos KF AD - Laboratory of Structural Biochemistry; Freie Universitat Berlin; Takustr. 6; Berlin, Germany. FAU - Will, Cindy L AU - Will CL AD - Dept. of Cellular Biochemistry; Max Planck Institute for Biophysical Chemistry; Am Fassberg 11; Gottingen, Germany. FAU - Luhrmann, Reinhard AU - Luhrmann R AD - Dept. of Cellular Biochemistry; Max Planck Institute for Biophysical Chemistry; Am Fassberg 11; Gottingen, Germany. FAU - Wahl, Markus C AU - Wahl MC AD - Laboratory of Structural Biochemistry; Freie Universitat Berlin; Takustr. 6; Berlin, Germany. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20140305 PL - United States TA - RNA Biol JT - RNA biology JID - 101235328 RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (PRPF8 protein, human) RN - 0 (RNA Precursors) RN - 0 (RNA-Binding Proteins) RN - 0 (Ribonucleoproteins, Small Nuclear) RN - 0 (SNRNP200 protein, human) RN - EC 3.4.- (Peptide Hydrolases) RN - EC 3.4.-.- (COPS5 protein, human) SB - IM MH - *Gene Expression Regulation MH - Humans MH - Intracellular Signaling Peptides and Proteins/metabolism MH - Peptide Hydrolases/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Interaction Domains and Motifs MH - RNA Precursors/genetics MH - RNA Splicing MH - RNA-Binding Proteins/chemistry/metabolism MH - Retinal Diseases/*genetics/*metabolism MH - Ribonucleoproteins, Small Nuclear/chemistry/*metabolism MH - Spliceosomes/metabolism MH - Substrate Specificity PMC - PMC4075514 OID - NLM: PMC4075514 OTO - NOTNLM OT - Pre-mRNA splicing OT - RNA helicase OT - RNA-protein complex OT - retinitis pigmentosa OT - spliceosome catalytic activation EDAT- 2014/03/20 06:00 MHDA- 2015/01/30 06:00 CRDT- 2014/03/20 06:00 PHST- 2014/03/05 [aheadofprint] AID - 28353 [pii] AID - 10.4161/rna.28353 [doi] PST - ppublish SO - RNA Biol. 2014;11(4):298-312. doi: 10.4161/rna.28353. Epub 2014 Mar 5. PMID- 21859464 OWN - NLM STAT- MEDLINE DA - 20110912 DCOM- 20111209 LR - 20141022 IS - 1476-4598 (Electronic) IS - 1476-4598 (Linking) VI - 10 DP - 2011 TI - Messing up disorder: how do missense mutations in the tumor suppressor protein APC lead to cancer? PG - 101 LID - 10.1186/1476-4598-10-101 [doi] AB - Mutations in the adenomatous polyposis coli (APC) tumor suppressor gene strongly predispose to development of gastro-intestinal tumors. Central to the tumorigenic events in APC mutant cells is the uncontrolled stabilization and transcriptional activation of the protein beta-catenin. Many questions remain as to how APC controls beta-catenin degradation. Remarkably, the large C-terminal region of APC, which spans over 2000 amino acids and includes critical regions in downregulating beta-catenin, is predicted to be natively unfolded. Here we discuss how this uncommonly large disordered region may help to coordinate the multiple cellular functions of APC. Recently, a significant number of germline and somatic missense mutations in the central region of APC were linked to tumorigenesis in the colon as well as extra-intestinal tissues. We classify and localize all currently known missense mutations in the APC structure. The molecular basis by which these mutations interfere with the function of APC remains unresolved. We propose several mechanisms by which cancer-related missense mutations in the large disordered domain of APC may interfere with tumor suppressor activity. Insight in the underlying molecular events will be invaluable in the development of novel strategies to counter dysregulated Wnt signaling by APC mutations in cancer. FAU - Minde, David P AU - Minde DP AD - Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands. FAU - Anvarian, Zeinab AU - Anvarian Z FAU - Rudiger, Stefan Gd AU - Rudiger SG FAU - Maurice, Madelon M AU - Maurice MM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20110822 PL - England TA - Mol Cancer JT - Molecular cancer JID - 101147698 RN - 0 (Adenomatous Polyposis Coli Protein) SB - IM MH - Adenomatous Polyposis Coli/genetics/metabolism MH - Adenomatous Polyposis Coli Protein/chemistry/genetics/physiology MH - Animals MH - Cell Transformation, Neoplastic/genetics/pathology MH - Genes, APC/*physiology MH - Genes, Tumor Suppressor MH - Humans MH - Models, Biological MH - Mutation, Missense/*physiology MH - Neoplasms/*genetics MH - Protein Folding MH - Protein Structure, Tertiary/physiology PMC - PMC3170638 OID - NLM: PMC3170638 EDAT- 2011/08/24 06:00 MHDA- 2011/12/14 06:00 CRDT- 2011/08/24 06:00 PHST- 2011/03/17 [received] PHST- 2011/08/22 [accepted] PHST- 2011/08/22 [aheadofprint] AID - 1476-4598-10-101 [pii] AID - 10.1186/1476-4598-10-101 [doi] PST - epublish SO - Mol Cancer. 2011 Aug 22;10:101. doi: 10.1186/1476-4598-10-101. PMID- 20303863 OWN - NLM STAT- MEDLINE DA - 20100322 DCOM- 20100623 LR - 20140827 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 98 IP - 6 DP - 2010 Mar 17 TI - Conformational analysis of the partially disordered measles virus N(TAIL)-XD complex by SDSL EPR spectroscopy. PG - 1055-64 LID - 10.1016/j.bpj.2009.11.036 [doi] AB - To characterize the structure of dynamic protein systems, such as partly disordered protein complexes, we propose a novel approach that relies on a combination of site-directed spin-labeled electron paramagnetic resonance spectroscopy and modeling of local rotation conformational spaces. We applied this approach to the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N(TAIL)) both free and in complex with the X domain (XD, aa 459-507) of the viral phosphoprotein. By comparing measured and modeled temperature-dependent restrictions of the side-chain conformational spaces of 12 SL cysteine-substituted N(TAIL) variants, we showed that the 490-500 region of N(TAIL) is prestructured in the absence of the partner, and were able to quantitatively estimate, for the first time to our knowledge, the extent of the alpha-helical sampling of the free form. In addition, we showed that the 505-525 region of N(TAIL) conserves a significant degree of freedom even in the bound form. The latter two findings provide a mechanistic explanation for the reported rather high affinity of the N(TAIL)-XD binding reaction. Due to the nanosecond timescale of X-band EPR spectroscopy, we were also able to monitor the disordering in the 488-525 region of N(TAIL), in particular the unfolding of the alpha-helical region when the temperature was increased from 281 K to 310 K. CI - Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Kavalenka, Aleh AU - Kavalenka A AD - Laboratory of Biophysics, Solid State Physics Department, Josef Stefan Institute, Ljubljana, Slovenia. FAU - Urbancic, Iztok AU - Urbancic I FAU - Belle, Valerie AU - Belle V FAU - Rouger, Sabrina AU - Rouger S FAU - Costanzo, Stephanie AU - Costanzo S FAU - Kure, Sandra AU - Kure S FAU - Fournel, Andre AU - Fournel A FAU - Longhi, Sonia AU - Longhi S FAU - Guigliarelli, Bruno AU - Guigliarelli B FAU - Strancar, Janez AU - Strancar J LA - eng GR - R01 NS031693-11A2/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Nucleoproteins) SB - IM MH - Computer Simulation MH - Crystallography/*methods MH - Electron Spin Resonance Spectroscopy/*methods MH - Measles virus/*chemistry MH - *Models, Chemical MH - *Models, Molecular MH - Nucleoproteins/*chemistry/*ultrastructure MH - Protein Conformation PMC - PMC2849088 OID - NLM: PMC2849088 EDAT- 2010/03/23 06:00 MHDA- 2010/06/24 06:00 CRDT- 2010/03/23 06:00 PHST- 2009/04/16 [received] PHST- 2009/10/30 [revised] PHST- 2009/11/17 [accepted] AID - S0006-3495(09)01803-7 [pii] AID - 10.1016/j.bpj.2009.11.036 [doi] PST - ppublish SO - Biophys J. 2010 Mar 17;98(6):1055-64. doi: 10.1016/j.bpj.2009.11.036. PMID- 10409688 OWN - NLM STAT- MEDLINE DA - 19990826 DCOM- 19990826 LR - 20101118 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 274 IP - 30 DP - 1999 Jul 23 TI - The Cap-binding protein eIF4E promotes folding of a functional domain of yeast translation initiation factor eIF4G1. PG - 21297-304 AB - The association of eucaryotic translation initiation factor eIF4G with the cap-binding protein eIF4E establishes a critical link between the mRNA and the ribosome during translation initiation. This association requires a conserved seven amino acid peptide within eIF4G that binds to eIF4E. Here we report that a 98-amino acid fragment of S. cerevisiae eIF4G1 that contains this eIF4E binding peptide undergoes an unfolded to folded transition upon binding to eIF4E. The folding of the eIF4G1 domain was evidenced by the eIF4E-dependent changes in its protease sensitivity and (1)H-(15)N HSQC NMR spectrum. Analysis of a series of charge-to-alanine mutations throughout the essential 55.4-kDa core of yeast eIF4G1 also revealed substitutions within this 98-amino acid region that led to reduced eIF4E binding in vivo and in vitro. These data suggest that the association of yeast eIF4E with eIF4G1 leads to the formation of a structured domain within eIF4G1 that could serve as a specific site for interactions with other components of the translational apparatus. They also suggest that the stability of the native eIF4E-eIF4G complex is determined by amino acid residues outside of the conserved seven-residue consensus sequence. FAU - Hershey, P E AU - Hershey PE AD - Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA. FAU - McWhirter, S M AU - McWhirter SM FAU - Gross, J D AU - Gross JD FAU - Wagner, G AU - Wagner G FAU - Alber, T AU - Alber T FAU - Sachs, A B AU - Sachs AB LA - eng GR - 50308/PHS HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Eukaryotic Initiation Factor-4E) RN - 0 (Eukaryotic Initiation Factor-4G) RN - 0 (Fungal Proteins) RN - 0 (Peptide Fragments) RN - 0 (Peptide Initiation Factors) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (TIF4631 protein, S cerevisiae) SB - IM MH - Amino Acid Sequence MH - Eukaryotic Initiation Factor-4E MH - Eukaryotic Initiation Factor-4G MH - Fungal Proteins/*chemistry/metabolism MH - Molecular Sequence Data MH - Peptide Fragments/*chemistry/metabolism MH - Peptide Initiation Factors/*chemistry/metabolism MH - Protein Binding MH - *Protein Folding MH - Saccharomyces cerevisiae MH - Saccharomyces cerevisiae Proteins EDAT- 1999/07/20 MHDA- 1999/07/20 00:01 CRDT- 1999/07/20 00:00 PST - ppublish SO - J Biol Chem. 1999 Jul 23;274(30):21297-304. PMID- 21603604 OWN - NLM STAT- MEDLINE DA - 20110523 DCOM- 20111021 LR - 20141022 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 5 DP - 2011 TI - Naturally occurring osmolyte, trehalose induces functional conformation in an intrinsically disordered activation domain of glucocorticoid receptor. PG - e19689 LID - 10.1371/journal.pone.0019689 [doi] AB - Intrinsically disordered (ID) regions are frequently found in the activation domains of many transcription factors including nuclear hormone receptors. It is believed that these ID regions promote molecular recognition by creating large surfaces suitable for interactions with their specific protein binding partners, which is a critical component of gene regulation by transcription factors. It has been hypothesized that conditional folding of these activation domains may be a prerequisite for their efficient interaction with specific coregulatory proteins, and subsequent transcriptional activity leading to the regulation of target gene(s). In this study, we tested whether a naturally occurring osmolyte, trehalose can promote functionally ordered conformation in glucocorticoid receptor's major activation function domain, AF1, which is found to exist as an ID protein, and requires an efficient interaction with coregulatory proteins for optimal activity. Our data show that trehalose induces an ordered conformation in AF1 such that its interaction with steroid receptor coactivator-1 (SRC-1), a critical coregulator of glucocorticoid receptor's activity, is greatly enhanced. FAU - Khan, Shagufta H AU - Khan SH AD - Department of Basic Sciences, The Commonwealth Medical College, Scranton, Pennsylvania, United States of America. FAU - Arnott, John A AU - Arnott JA FAU - Kumar, Raj AU - Kumar R LA - eng GR - 1R03AR057193-01/AR/NIAMS NIH HHS/United States GR - R01DK058829/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20110516 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Receptors, Glucocorticoid) RN - B8WCK70T7I (Trehalose) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 1) SB - IM MH - Animals MH - Cell Line MH - Haplorhini MH - Nuclear Receptor Coactivator 1/metabolism MH - Protein Binding/physiology MH - Protein Folding/*drug effects MH - Protein Structure, Tertiary/drug effects MH - Receptors, Glucocorticoid/*chemistry MH - Transcription, Genetic MH - Trehalose/*pharmacology PMC - PMC3095608 OID - NLM: PMC3095608 EDAT- 2011/05/24 06:00 MHDA- 2011/10/22 06:00 CRDT- 2011/05/24 06:00 PHST- 2011/02/10 [received] PHST- 2011/04/04 [accepted] PHST- 2011/05/16 [epublish] AID - 10.1371/journal.pone.0019689 [doi] AID - PONE-D-11-03021 [pii] PST - ppublish SO - PLoS One. 2011;6(5):e19689. doi: 10.1371/journal.pone.0019689. Epub 2011 May 16. PMID- 12086620 OWN - NLM STAT- MEDLINE DA - 20020627 DCOM- 20020802 LR - 20091119 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 9 IP - 6 DP - 2002 Jun TI - Molecular mechanism for the regulation of protein kinase B/Akt by hydrophobic motif phosphorylation. PG - 1227-40 AB - Protein kinase B/Akt plays crucial roles in promoting cell survival and mediating insulin responses. The enzyme is stimulated by phosphorylation at two regulatory sites: Thr 309 of the activation segment and Ser 474 of the hydrophobic motif, a conserved feature of many AGC kinases. Analysis of the crystal structures of the unphosphorylated and Thr 309 phosphorylated states of the PKB kinase domain provides a molecular explanation for regulation by Ser 474 phosphorylation. Activation by Ser 474 phosphorylation occurs via a disorder to order transition of the alphaC helix with concomitant restructuring of the activation segment and reconfiguration of the kinase bilobal structure. These conformational changes are mediated by a phosphorylation-promoted interaction of the hydrophobic motif with a channel on the N-terminal lobe induced by the ordered alphaC helix and are mimicked by peptides corresponding to the hydrophobic motif of PKB and potently by the hydrophobic motif of PRK2. FAU - Yang, Jing AU - Yang J AD - Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK. FAU - Cron, Peter AU - Cron P FAU - Thompson, Vivienne AU - Thompson V FAU - Good, Valerie M AU - Good VM FAU - Hess, Daniel AU - Hess D FAU - Hemmings, Brian A AU - Hemmings BA FAU - Barford, David AU - Barford D LA - eng SI - PDB/1GZK SI - PDB/1GZN SI - PDB/1GZO PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Peptides) RN - 0 (Proto-Oncogene Proteins) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - EC 2.7.11.1 (Proto-Oncogene Proteins c-akt) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - Cyclic AMP-Dependent Protein Kinases/chemistry/genetics MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Peptides/genetics/metabolism MH - Phosphorylation MH - Protein Structure, Tertiary MH - *Protein-Serine-Threonine Kinases MH - Proto-Oncogene Proteins/chemistry/genetics/*metabolism MH - Proto-Oncogene Proteins c-akt MH - Sequence Alignment EDAT- 2002/06/28 10:00 MHDA- 2002/08/03 10:01 CRDT- 2002/06/28 10:00 AID - S1097276502005506 [pii] PST - ppublish SO - Mol Cell. 2002 Jun;9(6):1227-40. PMID- 19913031 OWN - NLM STAT- MEDLINE DA - 20100128 DCOM- 20100303 LR - 20150325 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 395 IP - 3 DP - 2010 Jan 22 TI - Structure of the flexible amino-terminal domain of prion protein bound to a sulfated glycan. PG - 475-90 LID - 10.1016/j.jmb.2009.10.075 [doi] AB - The intrinsically disordered amino-proximal domain of hamster prion protein (PrP) contains four copies of a highly conserved octapeptide sequence, PHGGGWGQ, that is flanked by two polycationic residue clusters. This N-terminal domain mediates the binding of sulfated glycans, which can profoundly influence the conversion of PrP to pathological forms and the progression of prion disease. To investigate the structural consequences of sulfated glycan binding, we performed multidimensional heteronuclear ((1)H, (13)C, (15)N) NMR (nuclear magnetic resonance), circular dichroism (CD), and fluorescence studies on hamster PrP residues 23-106 (PrP 23-106) and fragments thereof when bound to pentosan polysulfate (PPS). While the majority of PrP 23-106 remain disordered upon PPS binding, the octarepeat region adopts a repeating loop-turn structure that we have determined by NMR. The beta-like turns within the repeats are corroborated by CD data demonstrating that these turns are also present, although less pronounced, without PPS. Binding to PPS exposes a hydrophobic surface composed of aligned tryptophan side chains, the spacing and orientation of which are consistent with a self-association or ligand binding site. The unique tryptophan motif was probed by intrinsic tryptophan fluorescence, which displayed enhanced fluorescence of PrP 23-106 when bound to PPS, consistent with the alignment of tryptophan side chains. Chemical-shift mapping identified binding sites on PrP 23-106 for PPS, which include the octarepeat histidine and an N-terminal basic cluster previously linked to sulfated glycan binding. These data may in part explain how sulfated glycans modulate PrP conformational conversions and oligomerizations. CI - Published by Elsevier Ltd. FAU - Taubner, Lara M AU - Taubner LM AD - Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA. taubnerl@niaid.nih.gov FAU - Bienkiewicz, Ewa A AU - Bienkiewicz EA FAU - Copie, Valerie AU - Copie V FAU - Caughey, Byron AU - Caughey B LA - eng SI - PDB/2KKG GR - 1-S10RR13878-01/RR/NCRR NIH HHS/United States GR - ZIA AI000580-20/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't DEP - 20091110 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Ligands) RN - 0 (Macromolecular Substances) RN - 0 (Prions) RN - 0 (Recombinant Proteins) RN - 37300-21-3 (Pentosan Sulfuric Polyester) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Circular Dichroism MH - Cricetinae MH - In Vitro Techniques MH - Ligands MH - Macromolecular Substances MH - Mesocricetus MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Pentosan Sulfuric Polyester/chemistry/metabolism MH - Prions/*chemistry/genetics/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Repetitive Sequences, Amino Acid MH - Spectrometry, Fluorescence MH - Thermodynamics PMC - PMC2830820 MID - NIHMS164246 OID - NLM: NIHMS164246 OID - NLM: PMC2830820 EDAT- 2009/11/17 06:00 MHDA- 2010/03/04 06:00 CRDT- 2009/11/17 06:00 PHST- 2009/06/19 [received] PHST- 2009/09/24 [revised] PHST- 2009/10/28 [accepted] PHST- 2009/11/10 [aheadofprint] AID - S0022-2836(09)01354-0 [pii] AID - 10.1016/j.jmb.2009.10.075 [doi] PST - ppublish SO - J Mol Biol. 2010 Jan 22;395(3):475-90. doi: 10.1016/j.jmb.2009.10.075. Epub 2009 Nov 10. PMID- 9136897 OWN - NLM STAT- MEDLINE DA - 19970520 DCOM- 19970520 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 406 IP - 3 DP - 1997 Apr 14 TI - Identification of the secretory vesicle membrane binding region of chromogranin B. PG - 259-62 AB - In the past a synthetic peptide representing the conserved near N-terminal region of chromogranin B (CGB) (residues 17-36) has been shown to interact with the vesicle membrane. Hence, it was necessary to confirm this observation with CGB deletion proteins. In order to address this need and to confirm the published sequence of CGB, we cloned a CGB gene and produced various CGB deletion proteins. The recombinant CGB protein lacking the first 15 (rCGB 16-626) or 16 amino acid residues (rCGB 17-626) bound to the vesicle membrane as well as the full-length CGB. However, rCGB 49-626, lacking the conserved near N-terminal region, failed to interact with the vesicle membrane, indicating an anchor role for the conserved near the N-terminal region. FAU - Yoo, S H AU - Yoo SH AD - Laboratory of Neurochemistry, NIDCD, National Institutes of Health, Bethesda, MD 20892-3320, USA. syoo@pop.nidcd.nih.gov FAU - Kang, Y K AU - Kang YK LA - eng SI - GENBANK/U88551 SI - GENBANK/X55489 PT - Journal Article PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Chromogranins) RN - 0 (Recombinant Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cattle MH - Chromatography, Affinity MH - Chromogranins/*chemistry/genetics/*metabolism MH - Cloning, Molecular MH - Cytoplasmic Granules/*metabolism MH - Hydrogen-Ion Concentration MH - Intracellular Membranes/*metabolism MH - Molecular Sequence Data MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Deletion EDAT- 1997/04/14 MHDA- 1997/04/14 00:01 CRDT- 1997/04/14 00:00 AID - S0014-5793(97)00276-7 [pii] PST - ppublish SO - FEBS Lett. 1997 Apr 14;406(3):259-62. PMID- 22401494 OWN - NLM STAT- MEDLINE DA - 20120327 DCOM- 20120514 LR - 20141019 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 51 IP - 12 DP - 2012 Mar 27 TI - Interaction of tau protein with model lipid membranes induces tau structural compaction and membrane disruption. PG - 2539-50 LID - 10.1021/bi201857v [doi] AB - The misfolding and aggregation of the intrinsically disordered, microtubule-associated tau protein into neurofibrillary tangles is implicated in the pathogenesis of Alzheimer's disease. However, the mechanisms of tau aggregation and toxicity remain unknown. Recent work has shown that anionic lipid membranes can induce tau aggregation and that membrane permeabilization may serve as a pathway by which protein aggregates exert toxicity, suggesting that the plasma membrane may play dual roles in tau pathology. This prompted our investigation to assess tau's propensity to interact with membranes and to elucidate the mutually disruptive structural perturbations the interactions induce in both tau and the membrane. We show that although highly charged and soluble, the full-length tau (hTau40) is also highly surface active, selectively inserts into anionic DMPG lipid monolayers and induces membrane morphological changes. To resolve molecular-scale structural details of hTau40 associated with lipid membranes, X-ray and neutron scattering techniques are utilized. X-ray reflectivity indicates hTau40s presence underneath a DMPG monolayer and penetration into the lipid headgroups and tailgroups, whereas grazing incidence X-ray diffraction shows that hTau40 insertion disrupts lipid packing. Moreover, both air/water and DMPG lipid membrane interfaces induce the disordered hTau40 to partially adopt a more compact conformation with density similar to that of a folded protein. Neutron reflectivity shows that tau completely disrupts supported DMPG bilayers while leaving the neutral DPPC bilayer intact. Our results show that hTau40s strong interaction with anionic lipids induces tau structural compaction and membrane disruption, suggesting possible membrane-based mechanisms of tau aggregation and toxicity in neurodegenerative diseases. FAU - Jones, Emmalee M AU - Jones EM AD - Department of Chemical and Nuclear Engineering, Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States. FAU - Dubey, Manish AU - Dubey M FAU - Camp, Phillip J AU - Camp PJ FAU - Vernon, Briana C AU - Vernon BC FAU - Biernat, Jacek AU - Biernat J FAU - Mandelkow, Eckhard AU - Mandelkow E FAU - Majewski, Jaroslaw AU - Majewski J FAU - Chi, Eva Y AU - Chi EY LA - eng GR - R25 CA153825/CA/NCI NIH HHS/United States GR - R25 CA153825-01/CA/NCI NIH HHS/United States GR - R25 CA153825-02/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120314 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Lipid Bilayers) RN - 0 (tau Proteins) SB - IM MH - Cell Membrane/*chemistry/*metabolism MH - Humans MH - Lipid Bilayers/*chemistry/*metabolism MH - Neutron Diffraction MH - Protein Binding MH - Protein Conformation MH - Solubility MH - X-Ray Diffraction MH - tau Proteins/*chemistry/*metabolism PMC - PMC3319454 MID - NIHMS364124 OID - NLM: NIHMS364124 OID - NLM: PMC3319454 EDAT- 2012/03/10 06:00 MHDA- 2012/05/15 06:00 CRDT- 2012/03/10 06:00 PHST- 2012/03/14 [aheadofprint] AID - 10.1021/bi201857v [doi] PST - ppublish SO - Biochemistry. 2012 Mar 27;51(12):2539-50. doi: 10.1021/bi201857v. Epub 2012 Mar 14. PMID- 9413984 OWN - NLM STAT- MEDLINE DA - 19980113 DCOM- 19980113 LR - 20061115 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 91 IP - 6 DP - 1997 Dec 12 TI - Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: a model for activator:coactivator interactions. PG - 741-52 AB - The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner. The solution structure of the complex formed by the phosphorylated kinase-inducible domain (pKID) of CREB with KIX reveals that pKID undergoes a coil-->helix folding transition upon binding to KIX, forming two alpha helices. The amphipathic helix alphaB of pKID interacts with a hydrophobic groove defined by helices alpha1 and alpha3 of KIX. The other pKID helix, alphaA, contacts a different face of the alpha3 helix. The phosphate group of the critical phosphoserine residue of pKID forms a hydrogen bond to the side chain of Tyr-658 of KIX. The structure provides a model for interactions between other transactivation domains and their targets. FAU - Radhakrishnan, I AU - Radhakrishnan I AD - Department of Molecular Biology, and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA. FAU - Perez-Alvarado, G C AU - Perez-Alvarado GC FAU - Parker, D AU - Parker D FAU - Dyson, H J AU - Dyson HJ FAU - Montminy, M R AU - Montminy MR FAU - Wright, P E AU - Wright PE LA - eng SI - PDB/1KDX PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Cell JT - Cell JID - 0413066 RN - 0 (CREBBP protein, human) RN - 0 (Cyclic AMP Response Element-Binding Protein) RN - 0 (Nuclear Proteins) RN - 0 (Phosphopeptides) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - CREB-Binding Protein MH - Consensus Sequence MH - Cyclic AMP Response Element-Binding Protein/*chemistry/*metabolism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*metabolism MH - Phosphopeptides/chemistry/metabolism MH - *Protein Conformation MH - Protein Structure, Secondary MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - *Trans-Activators MH - Transcription Factors/*metabolism EDAT- 1997/12/31 MHDA- 1997/12/31 00:01 CRDT- 1997/12/31 00:00 AID - S0092-8674(00)80463-8 [pii] PST - ppublish SO - Cell. 1997 Dec 12;91(6):741-52. PMID- 19508346 OWN - NLM STAT- MEDLINE DA - 20100204 DCOM- 20100421 IS - 1440-1789 (Electronic) IS - 0919-6544 (Linking) VI - 30 IP - 1 DP - 2010 Feb 1 TI - Protein microarray analysis identifies cyclic nucleotide phosphodiesterase as an interactor of Nogo-A. PG - 7-14 LID - 10.1111/j.1440-1789.2009.01035.x [doi] AB - Nogo-A, a neurite outgrowth inhibitor, is expressed exclusively on oligodendrocytes and neurons in the CNS. The central domain of Amino-Nogo spanning amino acids 567-748 in the human Nogo-A designated NIG, mediates persistent inhibition of axonal outgrowth and induces growth cone collapse by signaling through an as yet unidentified NIG receptor. We identified 82 NIG-interacting proteins by screening a high-density human protein microarray composed of 5000 proteins with a recombinant NIG protein as a probe. Following an intensive database search, we selected 12 neuron/oligodendrocyte-associated NIG interactors. Among them, we verified the molecular interaction of NIG with 2', 3'-cyclic nucleotide 3'-phosphodiesterase (CNP), a cell type-specific marker of oligodendrocytes, by immunoprecipitation and cell imaging analysis. Although CNP located chiefly in the cytoplasm of oligodendrocytes might not serve as a cell-surface NIG receptor, it could act as a conformational stabilizer for the intrinsically unstructured large segment of Amino-Nogo. FAU - Sumiyoshi, Kenta AU - Sumiyoshi K AD - Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo 204-8588, Japan. FAU - Obayashi, Shinya AU - Obayashi S FAU - Tabunoki, Hiroko AU - Tabunoki H FAU - Arima, Kunimasa AU - Arima K FAU - Satoh, Jun-ichi AU - Satoh J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090607 PL - Australia TA - Neuropathology JT - Neuropathology : official journal of the Japanese Society of Neuropathology JID - 9606526 RN - 0 (Myelin Proteins) RN - 0 (Nogo protein) RN - 0 (Recombinant Proteins) RN - EC 3.1.4.- (2',3'-Cyclic-Nucleotide Phosphodiesterases) SB - IM MH - 2',3'-Cyclic-Nucleotide Phosphodiesterases/*metabolism MH - Animals MH - Blotting, Western MH - Brain/metabolism MH - Cell Line, Tumor MH - Cells, Cultured MH - Databases, Protein MH - Humans MH - Immunohistochemistry MH - Immunoprecipitation MH - Male MH - Mice MH - Mice, Inbred ICR MH - Middle Aged MH - Myelin Proteins/genetics/*metabolism MH - Neurons/metabolism MH - Oligodendroglia/metabolism MH - Protein Array Analysis MH - Recombinant Proteins/metabolism MH - Reproducibility of Results EDAT- 2009/06/11 09:00 MHDA- 2010/04/22 06:00 CRDT- 2009/06/11 09:00 PHST- 2009/06/07 [aheadofprint] AID - NEU1035 [pii] AID - 10.1111/j.1440-1789.2009.01035.x [doi] PST - ppublish SO - Neuropathology. 2010 Feb 1;30(1):7-14. doi: 10.1111/j.1440-1789.2009.01035.x. Epub 2009 Jun 7. PMID- 17125854 OWN - NLM STAT- MEDLINE DA - 20061215 DCOM- 20070221 LR - 20070813 IS - 0166-6851 (Print) IS - 0166-6851 (Linking) VI - 151 IP - 1 DP - 2007 Jan TI - Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms. PG - 100-10 AB - Parasites from the protozoan phylum Apicomplexa are responsible for diseases, such as malaria, toxoplasmosis and cryptosporidiosis, all of which have significantly higher rates of mortality and morbidity in economically underdeveloped regions of the world. Advances in vaccine development and drug discovery are urgently needed to control these diseases and can be facilitated by production of purified recombinant proteins from Apicomplexan genomes and determination of their 3D structures. To date, both heterologous expression and crystallization of Apicomplexan proteins have seen only limited success. In an effort to explore the effectiveness of producing and crystallizing proteins on a genome-scale using a standardized methodology, over 400 distinct Plasmodium falciparum target genes were chosen representing different cellular classes, along with select orthologues from four other Plasmodium species as well as Cryptosporidium parvum and Toxoplasma gondii. From a total of 1008 genes from the seven genomes, 304 (30.2%) produced purified soluble proteins and 97 (9.6%) crystallized, culminating in 36 crystal structures. These results demonstrate that, contrary to previous findings, a standardized platform using Escherichia coli can be effective for genome-scale production and crystallography of Apicomplexan proteins. Predictably, orthologous proteins from different Apicomplexan genomes behaved differently in expression, purification and crystallization, although the overall success rates of Plasmodium orthologues do not differ significantly. Their differences were effectively exploited to elevate the overall productivity to levels comparable to the most successful ongoing structural genomics projects: 229 of the 468 target genes produced purified soluble protein from one or more organisms, with 80 and 32 of the purified targets, respectively, leading to crystals and ultimately structures from one or more orthologues. FAU - Vedadi, Masoud AU - Vedadi M AD - Structural Genomics Consortium, U. of Toronto, 100 College St. Rm 522B, Toronto, Ont., Canada M5G 1L5. FAU - Lew, Jocelyne AU - Lew J FAU - Artz, Jennifer AU - Artz J FAU - Amani, Mehrnaz AU - Amani M FAU - Zhao, Yong AU - Zhao Y FAU - Dong, Aiping AU - Dong A FAU - Wasney, Gregory A AU - Wasney GA FAU - Gao, Mian AU - Gao M FAU - Hills, Tanya AU - Hills T FAU - Brokx, Stephen AU - Brokx S FAU - Qiu, Wei AU - Qiu W FAU - Sharma, Sujata AU - Sharma S FAU - Diassiti, Angelina AU - Diassiti A FAU - Alam, Zahoor AU - Alam Z FAU - Melone, Michelle AU - Melone M FAU - Mulichak, Anne AU - Mulichak A FAU - Wernimont, Amy AU - Wernimont A FAU - Bray, James AU - Bray J FAU - Loppnau, Peter AU - Loppnau P FAU - Plotnikova, Olga AU - Plotnikova O FAU - Newberry, Kate AU - Newberry K FAU - Sundararajan, Emayavaram AU - Sundararajan E FAU - Houston, Simon AU - Houston S FAU - Walker, John AU - Walker J FAU - Tempel, Wolfram AU - Tempel W FAU - Bochkarev, Alexey AU - Bochkarev A FAU - Kozieradzki, Ivona AU - Kozieradzki I FAU - Edwards, Aled AU - Edwards A FAU - Arrowsmith, Cheryl AU - Arrowsmith C FAU - Roos, David AU - Roos D FAU - Kain, Kevin AU - Kain K FAU - Hui, Raymond AU - Hui R LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20061113 PL - Netherlands TA - Mol Biochem Parasitol JT - Molecular and biochemical parasitology JID - 8006324 RN - 0 (Protozoan Proteins) SB - IM MH - Animals MH - Crystallization MH - Escherichia coli/genetics/metabolism MH - Gene Expression MH - Genome, Protozoan/*genetics MH - Models, Molecular MH - Plasmodium falciparum/*chemistry/genetics/*metabolism MH - Protein Structure, Tertiary MH - Protozoan Proteins/*chemistry/genetics/*metabolism MH - Solubility EDAT- 2006/11/28 09:00 MHDA- 2007/02/22 09:00 CRDT- 2006/11/28 09:00 PHST- 2006/04/26 [received] PHST- 2006/10/19 [revised] PHST- 2006/10/20 [accepted] PHST- 2006/11/13 [aheadofprint] AID - S0166-6851(06)00312-4 [pii] AID - 10.1016/j.molbiopara.2006.10.011 [doi] PST - ppublish SO - Mol Biochem Parasitol. 2007 Jan;151(1):100-10. Epub 2006 Nov 13. PMID- 16565295 OWN - NLM STAT- MEDLINE DA - 20060608 DCOM- 20060828 LR - 20140909 IS - 0032-0889 (Print) IS - 0032-0889 (Linking) VI - 141 IP - 2 DP - 2006 Jun TI - Structural investigation of disordered stress proteins. Comparison of full-length dehydrins with isolated peptides of their conserved segments. PG - 638-50 AB - Dehydrins constitute a class of intrinsically disordered proteins that are expressed under conditions of water-related stress. Characteristic of the dehydrins are some highly conserved stretches of seven to 17 residues that are repetitively scattered in their sequences, the K-, S-, Y-, and Lys-rich segments. In this study, we investigate the putative role of these segments in promoting structure. The analysis is based on comparative analysis of four full-length dehydrins from Arabidopsis (Arabidopsis thaliana; Cor47, Lti29, Lti30, and Rab18) and isolated peptide mimics of the K-, Y-, and Lys-rich segments. In physiological buffer, the circular dichroism spectra of the full-length dehydrins reveal overall disordered structures with a variable content of poly-Pro helices, a type of elongated secondary structure relying on bridging water molecules. Similar disordered structures are observed for the isolated peptides of the conserved segments. Interestingly, neither the full-length dehydrins nor their conserved segments are able to adopt specific structure in response to altered temperature, one of the factors that regulate their expression in vivo. There is also no structural response to the addition of metal ions, increased protein concentration, or the protein-stabilizing salt Na(2)SO(4). Taken together, these observations indicate that the dehydrins are not in equilibrium with high-energy folded structures. The result suggests that the dehydrins are highly evolved proteins, selected to maintain high configurational flexibility and to resist unspecific collapse and aggregation. The role of the conserved segments is thus not to promote tertiary structure, but to exert their biological function more locally upon interaction with specific biological targets, for example, by acting as beads on a string for specific recognition, interaction with membranes, or intermolecular scaffolding. In this perspective, it is notable that the Lys-rich segment in Cor47 and Lti29 shows sequence similarity with the animal chaperone HSP90. FAU - Mouillon, Jean-Marie AU - Mouillon JM AD - Department of Chemistry and Biomedical Sciences, Kalmar University, S-391 82 Kalmar, Sweden. FAU - Gustafsson, Petter AU - Gustafsson P FAU - Harryson, Pia AU - Harryson P LA - eng SI - GENBANK/CAA48178 SI - GENBANK/P31168 SI - GENBANK/P42758 SI - GENBANK/P42759 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060324 PL - United States TA - Plant Physiol JT - Plant physiology JID - 0401224 RN - 0 (Heat-Shock Proteins) RN - 0 (Metals) RN - 0 (Peptides) RN - 0 (Plant Proteins) RN - 0 (Sulfates) RN - 0YPR65R21J (sodium sulfate) RN - 134711-03-8 (dehydrin proteins, plant) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Guanidine MH - Heat-Shock Proteins/*chemistry MH - Metals/chemistry MH - Molecular Sequence Data MH - Peptides/*chemistry MH - Plant Proteins/*chemistry MH - Protein Conformation MH - Protein Denaturation MH - Sequence Homology, Amino Acid MH - Sulfates/chemistry MH - Temperature PMC - PMC1475461 OID - NLM: PMC1475461 EDAT- 2006/03/28 09:00 MHDA- 2006/08/29 09:00 CRDT- 2006/03/28 09:00 PHST- 2006/03/24 [aheadofprint] AID - pp.106.079848 [pii] AID - 10.1104/pp.106.079848 [doi] PST - ppublish SO - Plant Physiol. 2006 Jun;141(2):638-50. Epub 2006 Mar 24. PMID- 18462685 OWN - NLM STAT- MEDLINE DA - 20080508 DCOM- 20080725 LR - 20131121 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 16 IP - 5 DP - 2008 May TI - Crystal structures of human saposins C andD: implications for lipid recognition and membrane interactions. PG - 809-17 LID - 10.1016/j.str.2008.02.016 [doi] AB - Human saposins are essential proteins required for degradation of sphingolipids and lipid antigen presentation. Despite the conserved structural organization of saposins, their distinct modes of interaction with biological membranes are not fully understood. We describe two crystal structures of human saposin C in an "open" configuration with unusual domain swapped homodimers. This form of SapC dimer supports the "clip-on" model for SapC-induced vesicle fusion. In addition, we present the crystal structure of SapD in two crystal forms. They reveal the monomer-monomer interface for the SapD dimer, which was confirmed in solution by analytical ultracentrifugation. The crystal structure of SapD suggests that side chains of Lys10 and Arg17 are involved in initial association with the preferred anionic biological membranes by forming salt bridges with sulfate or phosphate lipid headgroups. FAU - Rossmann, Maxim AU - Rossmann M AD - Institut fur Chemie und Biochemie, Kristallographie, Freie Universitat Berlin, Takustr. 6, 14195 Berlin, Germany. FAU - Schultz-Heienbrok, Robert AU - Schultz-Heienbrok R FAU - Behlke, Joachim AU - Behlke J FAU - Remmel, Natascha AU - Remmel N FAU - Alings, Claudia AU - Alings C FAU - Sandhoff, Konrad AU - Sandhoff K FAU - Saenger, Wolfram AU - Saenger W FAU - Maier, Timm AU - Maier T LA - eng SI - PDB/2QYP SI - PDB/2R0R SI - PDB/2R1Q SI - PDB/2RB3 SI - PDB/2Z9A PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Recombinant Proteins) RN - 0 (Saposins) RN - K848JZ4886 (Cysteine) SB - IM MH - Amino Acid Sequence MH - Cell Membrane/metabolism MH - Cloning, Molecular MH - Conserved Sequence MH - Crystallography, X-Ray MH - Cysteine/chemistry MH - Dimerization MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Lipid Metabolism MH - Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis MH - Pichia/genetics MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/isolation & purification MH - Saposins/*chemistry/genetics/isolation & purification MH - Sequence Homology, Amino Acid EDAT- 2008/05/09 09:00 MHDA- 2008/07/26 09:00 CRDT- 2008/05/09 09:00 PHST- 2007/11/07 [received] PHST- 2008/01/30 [revised] PHST- 2008/02/06 [accepted] AID - S0969-2126(08)00109-3 [pii] AID - 10.1016/j.str.2008.02.016 [doi] PST - ppublish SO - Structure. 2008 May;16(5):809-17. doi: 10.1016/j.str.2008.02.016. PMID- 15567525 OWN - NLM STAT- MEDLINE DA - 20041129 DCOM- 20050414 LR - 20061115 IS - 0248-4900 (Print) IS - 0248-4900 (Linking) VI - 96 IP - 9 DP - 2004 Dec TI - TPPP/p25: from unfolded protein to misfolding disease: prediction and experiments. PG - 701-11 AB - TPPP/p25, the first representative of a new protein family, identified as a brain-specific unfolded protein induces aberrant microtubule assemblies in vitro, suppresses mitosis in Drosophila embryo and is accumulated in inclusion bodies of human pathological brain tissues. In this paper, we present prediction and additional experimental data that validate TPPP/p25 to be a new member of the "intrinsically unstructured" protein family. The comparison of these characteristics with that of alpha-synuclein and tau, involved also in neurodegenerative diseases, suggested that although the primary sequences of these proteins are entirely different, there are similarities in their well-defined unstructured segments interrupted by "stabilization centres", phosphorylation and tubulin binding motives. SK-N-MC neuroblastoma cells were transfected with pEGFP-TPPP/p25 construct and a stable clone denoted K4 was selected and used to establish the effect of this unstructured protein on the energy state/metabolism of the cells. Our data by analyzing the mitochondrial membrane polarization by fluorescence microscopy revealed that the high-energy phosphate production in K4 clone is not damaged by the TPPP/p25 expression. Biochemical analysis with cell homogenates provided quantitative data that the ATP level increased 1.5-fold and the activities of hexokinase, glucosephosphate isomerase, phosphofructokinase, triosephosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase were 1.2 to 2.0-fold higher in K4 as compared to the control. Our modelling using these data and rate equations of the individual enzymes suggests that the TPPP/p25 expression stimulates glucose metabolism. At pathological conditions TPPP/p25 is localized in inclusion bodies in multiple system atrophy, it tightly co-localizes with alpha-synuclein, partially with tubulin and not with vimentin. The previous and the present studies obtained with immunohistochemistry with pathological human brain tissues rendered it possible to classify among pathological inclusions on the basis of immunolabelling of TPPP/p25, and suggest this protein to be a potential linkage between Parkinson's and Alzheimer's diseases. FAU - Orosz, F AU - Orosz F AD - Institute of Enzymology, Biological Research Centre, Hungarian Academy of Sciences, Karolina ut 29, 1113 Budapest, Hungary. FAU - Kovacs, G G AU - Kovacs GG FAU - Lehotzky, A AU - Lehotzky A FAU - Olah, J AU - Olah J FAU - Vincze, O AU - Vincze O FAU - Ovadi, J AU - Ovadi J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biol Cell JT - Biology of the cell / under the auspices of the European Cell Biology Organization JID - 8108529 RN - 0 (Nerve Tissue Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (p25 protein, human) SB - IM MH - Brain/*metabolism/pathology MH - Circular Dichroism MH - Genes, Reporter MH - Humans MH - Immunohistochemistry MH - Nerve Tissue Proteins/chemistry/genetics/*metabolism MH - Neurodegenerative Diseases/*metabolism MH - *Protein Folding MH - Recombinant Fusion Proteins/genetics/metabolism MH - Spectrometry, Fluorescence EDAT- 2004/11/30 09:00 MHDA- 2005/04/15 09:00 CRDT- 2004/11/30 09:00 PHST- 2004/05/28 [received] PHST- 2004/08/12 [accepted] AID - S0248-4900(04)00164-9 [pii] AID - 10.1016/j.biolcel.2004.08.002 [doi] PST - ppublish SO - Biol Cell. 2004 Dec;96(9):701-11. PMID- 12079388 OWN - NLM STAT- MEDLINE DA - 20020624 DCOM- 20020809 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 320 IP - 2 DP - 2002 Jul 5 TI - High pressure NMR reveals that apomyoglobin is an equilibrium mixture from the native to the unfolded. PG - 311-9 AB - Pressure-induced reversible conformational changes of sperm whale apomyoglobin have been studied between 30 bar and 3000 bar on individual residue basis by utilizing 1H/15N hetero nuclear single-quantum coherence two-dimensional NMR spectroscopy at pH 6.0 and 35 degrees C. Apomyoglobin showed a series of pressure-dependent NMR spectra as a function of pressure, assignable to the native (N), intermediates (I), molten globule (MG) and unfolded (U) conformers. At 30 bar, the native fold (N) shows disorder only in the F helix. Between 500 bar and 1200 bar, a series of locally disordered conformers I are produced, in which local disorder occurs in the C helix, the CD loop, the G helix and part of the H helix. At 2000 bar, most cross-peaks exhibit severe line-broadening, suggesting the formation of a molten globule, but at 3000 bar all the cross-peaks reappear, showing that the molten globule turns into a well-hydrated, mobile unfolded conformation U. Since all the spectral changes were reversible with pressure, apomyoglobin is considered to exist as an equilibrium mixture of the N, I, MG and U conformers at all pressures. MG is situated at 2.4+/-(0.1) kcal/mol above N at 1 bar and the unfolding transition from the combined N-I state to MG is accompanied by a loss of partial molar volume by 75+/-(3) ml/mol. On the basis of these observations, we postulate a theorem that the partial molar volume of a protein decreases in parallel with the loss of its conformational order. FAU - Kitahara, Ryo AU - Kitahara R AD - Department of Molecular Science, Graduate School of Science and Technology, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan. FAU - Yamada, Hiroaki AU - Yamada H FAU - Akasaka, Kazuyuki AU - Akasaka K FAU - Wright, Peter E AU - Wright PE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Apoproteins) RN - 0 (Myoglobin) RN - 0 (apomyoglobin) SB - IM MH - Apoproteins/*chemistry MH - Escherichia coli/metabolism MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Myoglobin/*chemistry MH - Protein Conformation MH - Protein Folding MH - Thermodynamics EDAT- 2002/06/25 10:00 MHDA- 2002/08/10 10:01 CRDT- 2002/06/25 10:00 AID - 10.1016/S0022-2836(02)00449-7 [doi] AID - S0022-2836(02)00449-7 [pii] PST - ppublish SO - J Mol Biol. 2002 Jul 5;320(2):311-9. PMID- 15905169 OWN - NLM STAT- MEDLINE DA - 20050829 DCOM- 20051025 LR - 20091119 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 35 DP - 2005 Sep 2 TI - ICln159 folds into a pleckstrin homology domain-like structure. Interaction with kinases and the splicing factor LSm4. PG - 31276-82 AB - ICln is a multifunctional protein involved in regulatory mechanisms as different as membrane ion transport and RNA splicing. The protein is water-soluble, and during regulatory volume decrease after cell swelling, it is able to migrate from the cytosol to the cell membrane. Purified, water-soluble ICln is able to insert into lipid bilayers to form ion channels. Here, we show that ICln159, a truncated ICln mutant, which is also able to form ion channels in lipid bilayers, belongs to the pleckstrin homology (PH) domain superfold family of proteins. The ICln PH domain shows unusual properties as it lacks the electrostatic surface polarization seen in classical PH domains. However, similar to many classical PH domain-containing proteins, ICln interacts with protein kinase C, and in addition, interacts with cAMP-dependent protein kinase and cGMP-dependent protein kinase type II but not cGMP-dependent protein kinase type Ibeta. A major phosphorylation site for all three kinases is Ser-45 within the ICln PH domain. Furthermore, ICln159 interacts with LSm4, a protein involved in splicing and mRNA degradation, suggesting that the ICln159 PH domain may serve as a protein-protein interaction platform. FAU - Furst, Johannes AU - Furst J AD - Department of Physiology and Medical Physics, Innsbruck Medical University, Fritz-Pregl Strasse 3, A-6020 Innsbruck, Austria. FAU - Schedlbauer, Andreas AU - Schedlbauer A FAU - Gandini, Rosaria AU - Gandini R FAU - Garavaglia, Maria Lisa AU - Garavaglia ML FAU - Saino, Stefano AU - Saino S FAU - Gschwentner, Martin AU - Gschwentner M FAU - Sarg, Bettina AU - Sarg B FAU - Lindner, Herbert AU - Lindner H FAU - Jakab, Martin AU - Jakab M FAU - Ritter, Markus AU - Ritter M FAU - Bazzini, Claudia AU - Bazzini C FAU - Botta, Guido AU - Botta G FAU - Meyer, Giuliano AU - Meyer G FAU - Kontaxis, Georg AU - Kontaxis G FAU - Tilly, Ben C AU - Tilly BC FAU - Konrat, Robert AU - Konrat R FAU - Paulmichl, Markus AU - Paulmichl M LA - eng SI - PDB/1ZYI PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050519 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Blood Proteins) RN - 0 (CLNS1A protein, human) RN - 0 (Clns1a protein, mouse) RN - 0 (Ion Channels) RN - 0 (LSM4 protein, human) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Ribonucleoproteins, Small Nuclear) RN - 0 (platelet protein P47) RN - EC 2.7.- (Protein Kinases) SB - IM MH - Amino Acid Sequence MH - Animals MH - Blood Proteins/*chemistry MH - Dogs MH - Humans MH - Ion Channels/*chemistry/genetics/*metabolism MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - NIH 3T3 Cells MH - Nuclear Magnetic Resonance, Biomolecular MH - Patch-Clamp Techniques MH - Phosphoproteins/*chemistry MH - Phosphorylation MH - *Protein Folding MH - Protein Kinases/metabolism MH - *Protein Structure, Tertiary MH - Recombinant Fusion Proteins/chemistry/genetics/metabolism MH - Ribonucleoproteins, Small Nuclear/chemistry/genetics/*metabolism EDAT- 2005/05/21 09:00 MHDA- 2005/10/26 09:00 CRDT- 2005/05/21 09:00 PHST- 2005/05/19 [aheadofprint] AID - M500541200 [pii] AID - 10.1074/jbc.M500541200 [doi] PST - ppublish SO - J Biol Chem. 2005 Sep 2;280(35):31276-82. Epub 2005 May 19. PMID- 20873738 OWN - NLM STAT- MEDLINE DA - 20101014 DCOM- 20110201 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 114 IP - 41 DP - 2010 Oct 21 TI - Modeling the relationship between the p53 C-terminal domain and its binding partners using molecular dynamics. PG - 13201-13 LID - 10.1021/jp1011445 [doi] AB - Fifty percent of all cancer cases result from mutations of the TP53 gene, which encodes the tumor suppressor p53, and it is hypothesized that the p53-mediated checkpoint pathway is compromised in most of the remaining cases. The p53 C-terminal domain (CTD) is an important site of p53 regulation but by nature is difficult to study, as it is intrinsically disordered. In this study, we performed molecular dynamics simulations on the p53 CTD and five known regulatory binding partners. We identified distinct trends in fluctuation within and around the p53 CTD binding site on each partner demonstrating a behavior that facilitates association. Further, we present evidence that the size of the hydrophobic pocket in each p53 CTD binding site governs the secondary structure of the p53 CTD when in the bound state. This information will be useful for predicting new binding partners for the p53 CTD, identifying interacting regions within other known partners, and discovering inhibitors that provide additional points of control over p53 activity. FAU - Allen, William J AU - Allen WJ AD - Department of Biochemistry, Virginia Polytechnic Institute and State University, 111 Engel Hall (0308), Blacksburg, Virginia 24061, United States. FAU - Capelluto, Daniel G S AU - Capelluto DG FAU - Finkielstein, Carla V AU - Finkielstein CV FAU - Bevan, David R AU - Bevan DR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Animals MH - Humans MH - Molecular Dynamics Simulation MH - Protein Binding MH - Protein Structure, Tertiary MH - Tumor Suppressor Protein p53/*chemistry/*metabolism EDAT- 2010/09/30 06:00 MHDA- 2011/02/02 06:00 CRDT- 2010/09/30 06:00 AID - 10.1021/jp1011445 [doi] PST - ppublish SO - J Phys Chem B. 2010 Oct 21;114(41):13201-13. doi: 10.1021/jp1011445. PMID- 23208874 OWN - NLM STAT- MEDLINE DA - 20130102 DCOM- 20130605 IS - 1099-1387 (Electronic) IS - 1075-2617 (Linking) VI - 19 IP - 1 DP - 2013 Jan TI - NMR investigations of structural and dynamics features of natively unstructured drug peptide - salmon calcitonin: implication to rational design of potent sCT analogs. PG - 33-45 LID - 10.1002/psc.2471 [doi] AB - Backbone dynamics and conformational properties of drug peptide salmon calcitonin have been studied in aqueous solution using nuclear magnetic resonance (NMR). Although salmon calcitonin (sCT) is largely unfolded in solution (as has been reported in several circular dichroism studies), the secondary H(alpha) chemical shifts and three bond H(N) -H(alpha) coupling constants indicated that most of the residues of the peptide are populating the alpha-helical region of the Ramachandran (varphi, psi) map. Further, the peptide in solution has been found to exhibit multiple conformational states exchanging slowly on the NMR timescale (10(2) -10(3) s(-1) ), inferred by the multiple chemical shift assignments in the region Leu4-Leu12 and around Pro23 (for residues Gln20-Tyr22 and Arg24). Possibly, these slowly exchanging multiple conformational states might inhibit symmetric self-association of the peptide and, in part, may account for its reduced aggregation propensity compared with human calcitonin (which lacks this property). The (15) N NMR-relaxation data revealed (i) the presence of slow (microsecond-to-millisecond) timescale dynamics in the N-terminal region (Cys1-Ser5) and core residues His17 and Asn26 and (ii) the presence of high frequency (nanosecond-to-picosecond) motions in the C-terminal arm. Put together, the various results suggested that (i) the flexible C-terminal of sCT (from Thr25-Thr31) is involved in identification of specific target receptors, (ii) whereas the N-terminal of sCT (from Cys1-Gln20) in solution - exhibiting significant amount of conformational plasticity and strong bias towards biologically active alpha-helical structure - facilitates favorable conformational adaptations while interacting with the intermembrane domains of these target receptors. Thus, we believe that the structural and dynamics features of sCT presented here will be useful guiding attributes for the rational design of biologically active sCT analogs. CI - Copyright (c) 2012 European Peptide Society and John Wiley & Sons, Ltd. FAU - Rawat, Atul AU - Rawat A AD - Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Raibareli Road, Lucknow-, 226014, India. FAU - Kumar, Dinesh AU - Kumar D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121204 PL - England TA - J Pept Sci JT - Journal of peptide science : an official publication of the European Peptide Society JID - 9506309 RN - 0 (Peptides) RN - 47931-85-1 (salmon calcitonin) RN - 9007-12-9 (Calcitonin) SB - IM MH - Amino Acid Sequence MH - Calcitonin/*chemistry MH - *Drug Design MH - Hydrogen Bonding MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Peptides/*chemistry MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization EDAT- 2012/12/05 06:00 MHDA- 2013/06/06 06:00 CRDT- 2012/12/05 06:00 PHST- 2012/06/14 [received] PHST- 2012/09/30 [revised] PHST- 2012/10/24 [accepted] PHST- 2012/12/04 [aheadofprint] AID - 10.1002/psc.2471 [doi] PST - ppublish SO - J Pept Sci. 2013 Jan;19(1):33-45. doi: 10.1002/psc.2471. Epub 2012 Dec 4. PMID- 12062445 OWN - NLM STAT- MEDLINE DA - 20020613 DCOM- 20020729 LR - 20131121 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 517 IP - 1-3 DP - 2002 Apr 24 TI - Methionine oxidation inhibits fibrillation of human alpha-synuclein in vitro. PG - 239-44 AB - We examined the effect of methionine oxidation of human recombinant alpha-synuclein on its structural properties and propensity to fibrillate. Both oxidized and non-oxidized alpha-synucleins were natively unfolded under conditions of neutral pH, with the oxidized protein being slightly more disordered. Both proteins adopted identical partially folded conformations under conditions of acidic pH. The fibrillation of alpha-synuclein at neutral pH was completely inhibited by methionine oxidation. This inhibitory effect was eliminated at low pH. The addition of oxidized alpha-synuclein to the unoxidized form led to a substantial inhibition of alpha-synuclein fibrillation. FAU - Uversky, Vladimir N AU - Uversky VN AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA. uversky@hydrogen.ucsc.edu FAU - Yamin, Ghiam AU - Yamin G FAU - Souillac, Pierre O AU - Souillac PO FAU - Goers, John AU - Goers J FAU - Glaser, Charles B AU - Glaser CB FAU - Fink, Anthony L AU - Fink AL LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Nerve Tissue Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - AE28F7PNPL (Methionine) SB - IM MH - Escherichia coli MH - Humans MH - Hydrogen-Ion Concentration MH - Methionine/*metabolism MH - Nerve Tissue Proteins/chemistry/*metabolism MH - Oxidation-Reduction MH - Protein Binding MH - Protein Folding MH - Protein Structure, Secondary MH - Synucleins MH - alpha-Synuclein EDAT- 2002/06/14 10:00 MHDA- 2002/07/30 10:01 CRDT- 2002/06/14 10:00 AID - S0014579302026388 [pii] PST - ppublish SO - FEBS Lett. 2002 Apr 24;517(1-3):239-44. PMID- 17313959 OWN - NLM STAT- MEDLINE DA - 20070319 DCOM- 20070510 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 367 IP - 4 DP - 2007 Apr 6 TI - NMR dynamics distinguish between hard and soft hydrophobic cores in the DNA-binding domain of PhoB and demonstrate different roles of the cores in binding to DNA. PG - 1093-117 AB - The transcription factor PhoB contains an N-terminal regulatory domain and a C-terminal DNA-binding/transactivation domain. The DNA-binding/transactivation domain alone can bind specifically to DNA and consequently activate transcription. It consists of an N-terminal four-stranded beta-sheet and a winged helix domain, containing a three-helix bundle and a C-terminal beta-hairpin. The second and third helices, together with the beta-hairpin, contact DNA and the loop between the second and third helices is responsible for the transactivation. Here, we have examined the backbone and side-chain dynamics of the DNA-binding domain in its DNA-free and bound forms by NMR. The side-chain dynamics identified two apparent hydrophobic cores: one, a soft hydrophobic core, shows inherently flexible dynamics on the pico-to nanosecond timescale and maintains the DNA-binding and transactivation surfaces; the other is a hard hydrophobic core formed between the N-terminal beta-sheet and the three-helix bundle, which maintains the other non-functional surface. Upon binding to DNA, the flexibility of the soft core decreases but remains more flexible than the hard core. The winged helix domain itself has inherent flexibility in the DNA-binding and transactivation functions. However, the back surface of both functional surfaces seems to be covered by the N-terminal beta-sheet in order to mask a possible function arising from the inherent flexibility of the winged helix domain. FAU - Okamura, Hideyasu AU - Okamura H AD - Graduate School of Supramolecular Biology, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. FAU - Makino, Kozo AU - Makino K FAU - Nishimura, Yoshifumi AU - Nishimura Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070124 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (DNA, Bacterial) RN - 0 (DNA-Binding Proteins) RN - 104220-36-2 (PhoB protein, Bacteria) RN - GMW67QNF9C (Leucine) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/*metabolism MH - DNA, Bacterial/*metabolism MH - DNA-Binding Proteins/chemistry MH - Escherichia coli MH - *Hydrophobic and Hydrophilic Interactions MH - Leucine/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Structure, Tertiary/physiology EDAT- 2007/02/23 09:00 MHDA- 2007/05/11 09:00 CRDT- 2007/02/23 09:00 PHST- 2006/07/24 [received] PHST- 2007/01/16 [revised] PHST- 2007/01/19 [accepted] PHST- 2007/01/24 [aheadofprint] AID - S0022-2836(07)00104-0 [pii] AID - 10.1016/j.jmb.2007.01.052 [doi] PST - ppublish SO - J Mol Biol. 2007 Apr 6;367(4):1093-117. Epub 2007 Jan 24. PMID- 12643535 OWN - NLM STAT- MEDLINE DA - 20030319 DCOM- 20030416 LR - 20131121 IS - 1535-3893 (Print) IS - 1535-3893 (Linking) VI - 1 IP - 2 DP - 2002 Mar-Apr TI - Effect of zinc and temperature on the conformation of the gamma subunit of retinal phosphodiesterase: a natively unfolded protein. PG - 149-59 AB - The cyclic GMP phosphodiesterase gamma-subunit (PDEgamma) was shown to belong to the family of natively unfolded proteins. Increasing temperature transforms the protein into a more ordered (but still relatively disordered) conformation. The C-terminal part of PDEgamma has a high-affinity zinc-binding site (Kd approximately 1 microM), with His75 and His79 being directly involved into the coordination of Zn2+. Zinc-loaded protein remains effectively unfolded. Possible implications of these findings to the functioning of PDEgamma are discussed. FAU - Uversky, Vladimir N AU - Uversky VN AD - Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Russia. uversky@hydrogen.ucsc.edu FAU - Permyakov, Sergey E AU - Permyakov SE FAU - Zagranichny, Vasily E AU - Zagranichny VE FAU - Rodionov, Igor L AU - Rodionov IL FAU - Fink, Anthony L AU - Fink AL FAU - Cherskaya, Alexandra M AU - Cherskaya AM FAU - Wasserman, Lyubov A AU - Wasserman LA FAU - Permyakov, Eugene A AU - Permyakov EA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Proteome Res JT - Journal of proteome research JID - 101128775 RN - 20R035KLCI (Acrylamide) RN - EC 3.1.4.35 (3',5'-Cyclic-GMP Phosphodiesterases) RN - J41CSQ7QDS (Zinc) SB - IM MH - 3',5'-Cyclic-GMP Phosphodiesterases/chemistry/*metabolism MH - Acrylamide/chemistry MH - Binding Sites MH - Circular Dichroism MH - Protein Binding MH - Protein Conformation MH - Sequence Analysis, Protein MH - Spectrometry, Fluorescence MH - Temperature MH - Zinc/*metabolism EDAT- 2003/03/20 04:00 MHDA- 2003/04/17 05:00 CRDT- 2003/03/20 04:00 PST - ppublish SO - J Proteome Res. 2002 Mar-Apr;1(2):149-59. PMID- 18032507 OWN - NLM STAT- MEDLINE DA - 20080118 DCOM- 20080205 LR - 20140904 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 82 IP - 3 DP - 2008 Feb TI - Bovine viral diarrhea virus core is an intrinsically disordered protein that binds RNA. PG - 1294-304 AB - Pestiviruses, including bovine viral diarrhea virus (BVDV), are important animal pathogens and close relatives of hepatitis C virus. Pestivirus particles are composed of an RNA genome, a host-derived lipid envelope, and four virion-encoded structural proteins, core (C), E(rns), E1, and E2. Core is a small, highly basic polypeptide that is processed by three enzymatic cleavages before its incorporation into virions. Little is known about its biological properties or its role in virion assembly and structure. We have purified BVDV core protein and characterized it biochemically. We have determined that the processed form of core lacks significant secondary structure and is instead intrinsically disordered. Consistent with its highly basic sequence, we observed that core binds to RNA, although with low affinity and little discernible specificity. We found that BVDV core protein was able to functionally replace the nonspecific RNA binding and condensing region of an unrelated viral capsid protein. Together these results suggest that the in vitro properties of core may reflect its mechanism of action in RNA packaging and virion morphogenesis. FAU - Murray, Catherine L AU - Murray CL AD - Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, 1230 York Ave., New York, NY 10065, USA. ricec@rockefeller.edu FAU - Marcotrigiano, Joseph AU - Marcotrigiano J FAU - Rice, Charles M AU - Rice CM LA - eng GR - R01 AI075099/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20071121 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (RNA, Viral) RN - 0 (RNA-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Viral Core Proteins) SB - IM MH - Amino Acid Sequence MH - Diarrhea Viruses, Bovine Viral/*metabolism MH - Molecular Sequence Data MH - Protein Binding MH - Protein Structure, Secondary MH - RNA, Viral/*metabolism MH - RNA-Binding Proteins/*chemistry/*metabolism MH - Recombinant Proteins/chemistry/isolation & purification/metabolism MH - Viral Core Proteins/*chemistry/isolation & purification/*metabolism MH - *Virus Assembly PMC - PMC2224441 OID - NLM: PMC2224441 EDAT- 2007/11/23 09:00 MHDA- 2008/02/06 09:00 CRDT- 2007/11/23 09:00 PHST- 2007/11/21 [aheadofprint] AID - JVI.01815-07 [pii] AID - 10.1128/JVI.01815-07 [doi] PST - ppublish SO - J Virol. 2008 Feb;82(3):1294-304. Epub 2007 Nov 21. PMID- 22342723 OWN - NLM STAT- MEDLINE DA - 20120312 DCOM- 20120507 LR - 20141019 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 419 IP - 2 DP - 2012 Mar 9 TI - Post-translational modification of osteopontin: effects on in vitro hydroxyapatite formation and growth. PG - 333-8 LID - 10.1016/j.bbrc.2012.02.024 [doi] AB - The manuscript tests the hypothesis that posttranslational modification of the SIBLING family of proteins in general and osteopontin in particular modify the abilities of these proteins to regulate in vitro hydroxyapatite (HA) formation. Osteopontin has diverse effects on hydroxyapatite (HA) mineral crystallite formation and growth depending on the extent of phosphorylation. We hypothesized that different regions of full-length OPN would also have distinct effects on the mineralization process. Thrombin fragmentation of milk OPN (mOPN) was used to test this hypothesis. Three fragments were tested in a de novo HA formation assay; an N-terminal fragment (aa 1-147), a central fragment (aa 148-204) denoted SKK-fragment and a C-terminal fragment (aa 205-262). Compared to intact mOPN the C- and N-terminal fragments behaved comparably, promoting HA formation and growth, but the central SKK-fragment acted as a mineralization inhibitor. In a seeded growth experiment all fragments inhibited mineral proliferation, but the SKK-fragment was the most effective inhibitor. These effects, seen in HA-formation and seeded growth assays in a gelatin gel system and in a pH-stat experiment were lost when the protein or fragments were dephosphorylated. Effects of the fully phosphorylated protein and fragments were also altered in the presence of fibrillar collagen. The diverse effects can be explained in terms of the intrinsically disordered nature of OPN and its fragments which enable them to interact with their multiple partners. CI - Copyright (c) 2012 Elsevier Inc. All rights reserved. FAU - Boskey, Adele L AU - Boskey AL AD - Musculoskeletal Integrity Program, Hospital for Special Surgery, New York, NY 10021, USA. boskeya@hss.edu FAU - Christensen, Brian AU - Christensen B FAU - Taleb, Hayat AU - Taleb H FAU - Sorensen, Esben S AU - Sorensen ES LA - eng GR - DE04141/DE/NIDCR NIH HHS/United States GR - R01 DE004141/DE/NIDCR NIH HHS/United States GR - R01 DE004141-35/DE/NIDCR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120210 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Milk Proteins) RN - 106441-73-0 (Osteopontin) RN - 9007-34-5 (Collagen) RN - 91D9GV0Z28 (Durapatite) RN - EC 3.4.21.5 (Thrombin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cattle MH - Collagen/chemistry MH - Durapatite/*chemical synthesis MH - Milk Proteins/*chemistry MH - Molecular Sequence Data MH - Osteopontin/*chemistry MH - *Protein Processing, Post-Translational MH - Thrombin/chemistry PMC - PMC3299831 MID - NIHMS356650 OID - NLM: NIHMS356650 OID - NLM: PMC3299831 EDAT- 2012/02/22 06:00 MHDA- 2012/05/09 06:00 CRDT- 2012/02/21 06:00 PHST- 2012/01/25 [received] PHST- 2012/02/03 [accepted] PHST- 2012/02/10 [aheadofprint] AID - S0006-291X(12)00242-2 [pii] AID - 10.1016/j.bbrc.2012.02.024 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2012 Mar 9;419(2):333-8. doi: 10.1016/j.bbrc.2012.02.024. Epub 2012 Feb 10. PMID- 22815741 OWN - NLM STAT- MEDLINE DA - 20120720 DCOM- 20130326 LR - 20141015 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 7 DP - 2012 TI - VAPC, an human endogenous inhibitor for hepatitis C virus (HCV) infection, is intrinsically unstructured but forms a "fuzzy complex" with HCV NS5B. PG - e40341 LID - 10.1371/journal.pone.0040341 [doi] AB - Nearly 200 million people are infected by hepatitis C virus (HCV) worldwide. For replicating the HCV genome, the membrane-associated machinery needs to be formed by both HCV non-structural proteins (including NS5B) and human host factors such as VAPB. Recently, the 99-residue VAPC, a splicing variant of VAPB, was demonstrated to inhibit HCV replication via binding to NS5B, thus acting as an endogenous inhibitor of HCV infection. So far, the structure of VAPC remains unknown, and its interaction with NS5B has not been biophysically characterized. In this study, we conducted extensive CD and NMR investigations on VAPC which led to several striking findings: 1) although the N-terminal 70 residues are identical in VAPC and VAPB, they constitute the characteristic beta-barrel MSP fold in VAPB, while VAPC is entirely unstructured in solution, only with helical-like conformations weakly populated. 2) VAPC is indeed capable of binding to NS5B, with an average dissociation constant (Kd) of approximately 20 microM. Intriguingly, VAPC remains dynamic even in the complex, suggesting that the VAPC-NS5B is a "fuzzy complex". 3) NMR mapping revealed that the major binding region for NS5B is located over the C-terminal half of VAPC, which is composed of three discrete clusters, of which only the first contains the region identical in VAPC and VAPB. The second region containing approximately 12 residues appears to play a key role in binding since mutation of 4 residues within this region leads to almost complete loss of the binding activity. 4) A 14-residue mimetic, VAPC-14 containing the second region, only has a approximately 3-fold reduction of the affinity. Our study not only provides critical insights into how a human factor mediates the formation of the HCV replication machinery, but also leads to design of VAPC-14 which may be further used to explore the function of VAPC and to develop anti-HCV molecules. FAU - Goyal, Shaveta AU - Goyal S AD - Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore. FAU - Gupta, Garvita AU - Gupta G FAU - Qin, Haina AU - Qin H FAU - Upadya, Megha Haridas AU - Upadya MH FAU - Tan, Yee Joo AU - Tan YJ FAU - Chow, Vincent T K AU - Chow VT FAU - Song, Jianxing AU - Song J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120717 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Peptide Fragments) RN - 0 (VAPB protein, human) RN - 0 (Vesicular Transport Proteins) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Amino Acid Sequence MH - Hepacivirus/*drug effects/*physiology MH - Humans MH - Molecular Sequence Data MH - Peptide Fragments/metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Vesicular Transport Proteins/*chemistry/*metabolism/pharmacology MH - Viral Nonstructural Proteins/chemistry/*metabolism PMC - PMC3398895 OID - NLM: PMC3398895 EDAT- 2012/07/21 06:00 MHDA- 2013/03/27 06:00 CRDT- 2012/07/21 06:00 PHST- 2012/05/03 [received] PHST- 2012/06/04 [accepted] PHST- 2012/07/17 [epublish] AID - 10.1371/journal.pone.0040341 [doi] AID - PONE-D-11-08927 [pii] PST - ppublish SO - PLoS One. 2012;7(7):e40341. doi: 10.1371/journal.pone.0040341. Epub 2012 Jul 17. PMID- 23972852 OWN - NLM STAT- MEDLINE DA - 20130826 DCOM- 20140415 LR - 20141112 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 105 IP - 4 DP - 2013 Aug 20 TI - The arginine-rich RNA-binding motif of HIV-1 Rev is intrinsically disordered and folds upon RRE binding. PG - 1004-17 LID - 10.1016/j.bpj.2013.07.022 [doi] LID - S0006-3495(13)00807-2 [pii] AB - Arginine-rich motifs (ARMs) capable of binding diverse RNA structures play critical roles in transcription, translation, RNA trafficking, and RNA packaging. The regulatory HIV-1 protein Rev is essential for viral replication and belongs to the ARM family of RNA-binding proteins. During the early stages of the HIV-1 life cycle, incompletely spliced and full-length viral mRNAs are very inefficiently recognized by the splicing machinery of the host cell and are subject to degradation in the cell nucleus. These transcripts harbor the Rev Response Element (RRE), which orchestrates the interaction with the Rev ARM and the successive Rev-dependent mRNA export pathway. Based on established criteria for predicting intrinsic disorder, such as hydropathy, combined with significant net charge, the very basic primary sequences of ARMs are expected to adopt coil-like structures. Thus, we initiated this study to investigate the conformational changes of the Rev ARM associated with RNA binding. We used multidimensional NMR and circular dichroism spectroscopy to monitor the observed structural transitions, and described the conformational landscapes using statistical ensemble and molecular-dynamics simulations. The combined spectroscopic and simulated results imply that the Rev ARM is intrinsically disordered not only as an isolated peptide but also when it is embedded into an oligomerization-deficient Rev mutant. RRE recognition triggers a crucial coil-to-helix transition employing an induced-fit mechanism. CI - Copyright (c) 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Casu, Fabio AU - Casu F AD - Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA. FAU - Duggan, Brendan M AU - Duggan BM FAU - Hennig, Mirko AU - Hennig M LA - eng GR - AI081640/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (rev Gene Products, Human Immunodeficiency Virus) RN - 0 (rev protein, Human Immunodeficiency Virus-1) RN - 63231-63-0 (RNA) RN - 94ZLA3W45F (Arginine) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Arginine/*metabolism MH - Intrinsically Disordered Proteins/chemistry/genetics/metabolism MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Mutation MH - Protein Binding MH - *Protein Folding MH - RNA/*metabolism MH - *Response Elements MH - rev Gene Products, Human Immunodeficiency Virus/*chemistry/genetics/*metabolism PMC - PMC3752131 OID - NLM: PMC3752131 EDAT- 2013/08/27 06:00 MHDA- 2014/04/16 06:00 CRDT- 2013/08/27 06:00 PHST- 2013/03/20 [received] PHST- 2013/06/19 [revised] PHST- 2013/07/02 [accepted] AID - S0006-3495(13)00807-2 [pii] AID - 10.1016/j.bpj.2013.07.022 [doi] PST - ppublish SO - Biophys J. 2013 Aug 20;105(4):1004-17. doi: 10.1016/j.bpj.2013.07.022. PMID- 20392693 OWN - NLM STAT- MEDLINE DA - 20100615 DCOM- 20100721 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 25 DP - 2010 Jun 18 TI - Apoptotic regulation by MCL-1 through heterodimerization. PG - 19615-24 LID - 10.1074/jbc.M110.105452 [doi] AB - Myeloid cell leukemia 1 (MCL-1), an anti-apoptotic BCL-2 family member active in the preservation of mitochondrial integrity during apoptosis, has fundamental roles in development and hematopoiesis and is dysregulated in human cancers. It bears a unique, intrinsically unstructured, N-terminal sequence, which leads to its instability in cells and hinders protein production and structural characterization. Here, we present collective data from NMR spectroscopy and titration calorimetry to reveal the selectivity of MCL-1 in binding BCL-2 homology 3 (BH3) ligands of interest for mammalian biology. The N-terminal sequence weakens the BH3 interactions but does not affect selectivity. Its removal by calpain-mediated limited proteolysis results in a stable BCL-2-like core domain of MCL-1 (cMCL-1). This core is necessary and sufficient for BH3 ligand binding. Significantly, we also characterized the in vitro protein-protein interaction between cMCL-1 and activated BID by size exclusion chromatography and NMR titrations. This interaction occurs in a very slow manner in solution but is otherwise similar to the interaction between cMCL-1 and BID-BH3 peptides. We also present the solution structure of complex cMCL-1xhBID-BH3, which completes the family portrait of MCL-1 complexes and may facilitate drug discovery against human tumors. FAU - Liu, Qian AU - Liu Q AD - Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada. FAU - Moldoveanu, Tudor AU - Moldoveanu T FAU - Sprules, Tara AU - Sprules T FAU - Matta-Camacho, Edna AU - Matta-Camacho E FAU - Mansur-Azzam, Nura AU - Mansur-Azzam N FAU - Gehring, Kalle AU - Gehring K LA - eng SI - PDB/2KBW GR - MOP-81277/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100414 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Ligands) RN - 0 (Myeloid Cell Leukemia Sequence 1 Protein) RN - 0 (Proto-Oncogene Proteins c-bcl-2) RN - EC 3.4.22.- (Calpain) SB - IM MH - Amino Acid Sequence MH - *Apoptosis MH - Calorimetry/methods MH - Calpain/chemistry MH - Dimerization MH - Gene Expression Regulation, Neoplastic MH - Humans MH - Ligands MH - Magnetic Resonance Spectroscopy MH - Mitochondria/metabolism MH - Molecular Sequence Data MH - Myeloid Cell Leukemia Sequence 1 Protein MH - Protein Interaction Mapping MH - Proto-Oncogene Proteins c-bcl-2/chemistry/*metabolism MH - Sequence Homology, Amino Acid PMC - PMC2885240 OID - NLM: PMC2885240 EDAT- 2010/04/16 06:00 MHDA- 2010/07/22 06:00 CRDT- 2010/04/16 06:00 PHST- 2010/04/14 [aheadofprint] AID - M110.105452 [pii] AID - 10.1074/jbc.M110.105452 [doi] PST - ppublish SO - J Biol Chem. 2010 Jun 18;285(25):19615-24. doi: 10.1074/jbc.M110.105452. Epub 2010 Apr 14. PMID- 23504368 OWN - NLM STAT- MEDLINE DA - 20130506 DCOM- 20130712 LR - 20141116 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 18 DP - 2013 May 3 TI - Minute time scale prolyl isomerization governs antibody recognition of an intrinsically disordered immunodominant epitope. PG - 13110-23 LID - 10.1074/jbc.M112.444554 [doi] AB - Conformational rearrangements in antibody.antigen recognition are essential events where kinetic discrimination of isomers expands the universe of combinations. We investigated the interaction mechanism of a monoclonal antibody, M1, raised against E7 from human papillomavirus, a prototypic viral oncoprotein and a model intrinsically disordered protein. The mapped 12-amino acid immunodominant epitope lies within a "hinge" region between the N-terminal intrinsically disordered and the C-terminal globular domains. Kinetic experiments show that despite being within an intrinsically disordered region, the hinge E7 epitope has at least two populations separated by a high energy barrier. Nuclear magnetic resonance traced the origin of this barrier to a very slow (t(1/2) approximately 4 min) trans-cis prolyl isomerization event involving changes in secondary structure. The less populated (10%) cis isomer is the binding-competent species, thus requiring the 90% of molecules in the trans configuration to isomerize before binding. The association rate for the cis isomer approaches 6 x 10(7) M(-1) s(-1), a ceiling for antigen-antibody interactions. Mutagenesis experiments showed that Pro-41 in E7Ep was required for both binding and isomerization. After a slow postbinding unimolecular rearrangement, a consolidated complex with K(D) = 1.2 x 10(-7) M is reached. Our results suggest that presentation of this viral epitope by the antigen-presenting cells would have to be "locked" in the cis conformation, in opposition to the most populated trans isomer, in order to select the specific antibody clone that goes through affinity and kinetic maturation. FAU - Fassolari, Marisol AU - Fassolari M AD - Protein Structure-Function and Engineering Laboratory, Fundacion Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435, 1405 Buenos Aires, Argentina. FAU - Chemes, Lucia B AU - Chemes LB FAU - Gallo, Mariana AU - Gallo M FAU - Smal, Clara AU - Smal C FAU - Sanchez, Ignacio E AU - Sanchez IE FAU - de Prat-Gay, Gonzalo AU - de Prat-Gay G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130315 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Antibodies, Monoclonal, Murine-Derived) RN - 0 (Antibodies, Viral) RN - 0 (Epitopes) RN - 0 (Papillomavirus E7 Proteins) RN - 0 (oncogene protein E7, Human papillomavirus type 16) SB - IM MH - Animals MH - Antibodies, Monoclonal, Murine-Derived/*chemistry/immunology MH - Antibodies, Viral/*chemistry/immunology MH - *Antibody Specificity MH - Epitopes MH - Human papillomavirus 16/*chemistry/genetics/immunology MH - Humans MH - Mice MH - Nuclear Magnetic Resonance, Biomolecular MH - Papillomavirus E7 Proteins/*chemistry/genetics/immunology MH - Protein Structure, Secondary PMC - PMC3642352 OID - NLM: PMC3642352 OTO - NOTNLM OT - Antigen OT - Antigen Recognition OT - Biophysics OT - Conformational Selection OT - E7 Oncoprotein OT - Intrinsically Disordered Proteins OT - Pre-steady-state Kinetics OT - Prolyl Isomerization OT - Protein Folding EDAT- 2013/03/19 06:00 MHDA- 2013/07/16 06:00 CRDT- 2013/03/19 06:00 PHST- 2013/03/15 [aheadofprint] AID - M112.444554 [pii] AID - 10.1074/jbc.M112.444554 [doi] PST - ppublish SO - J Biol Chem. 2013 May 3;288(18):13110-23. doi: 10.1074/jbc.M112.444554. Epub 2013 Mar 15. PMID- 9201953 OWN - NLM STAT- MEDLINE DA - 19970721 DCOM- 19970721 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 36 IP - 26 DP - 1997 Jul 1 TI - Solution conformations and interactions of alpha and beta subunits of the Oxytricha nova telomere binding protein: investigation by Raman spectroscopy. PG - 8053-9 AB - Solution conformations of the alpha and beta subunits of the Oxytricha nova telomere binding protein have been investigated by Raman spectroscopy. Raman spectra have also been obtained for a deletion mutant of the beta subunit, betaC232, which retains the N-terminal domain that is active in ternary complex (alpha:beta:DNA) formation but lacks the C-terminal domain that is active in catalyzing guanine quadruplex formation. The Raman spectra show that alpha, beta, and betaC232 are rich in beta-strand secondary structure ( approximately 40-50%) and turns. The Raman signature of the C-terminal 153 amino acids of beta, generated by subtracting the spectrum of betaC232 (residues 1-232) from that of the full subunit, indicates that the domain active in guanine quadruplex formation contains less beta-strand secondary structure and more irregular structure than the domain active in alpha:beta:DNA formation. Raman markers also provide information about the environments and orientations of several key side chains, including tryptophan residues in N- and C-terminal domains of the beta subunit. Both alpha and beta denature between 30 and 40 degrees C, as evidenced by large changes in Raman bands diagnostic of main chain conformation and side chain environments. The Raman spectrum of an equimolar alpha/beta mixture exhibits no evidence of specific interaction between the subunits; further, the denaturation profile of this mixture is indistinguishable from the sum of denaturation profiles of the constituent subunits, consistent with the absence of appreciable interaction between alpha and beta throughout the range 0-50 degrees C. The present results provide insights into the solution conformations of the Oxytricha telomere binding protein subunits and serve as the basis for future study of subunit interactions with telomeric DNA. FAU - Laporte, L AU - Laporte L AD - Division of Cell Biology, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA. FAU - Stultz, J AU - Stultz J FAU - Thomas, G J Jr AU - Thomas GJ Jr LA - eng GR - GM54378/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA-Binding Proteins) RN - 0 (Macromolecular Substances) RN - 0 (Protozoan Proteins) RN - 0 (Solutions) SB - IM MH - Animals MH - DNA-Binding Proteins/*chemistry MH - Drug Stability MH - Heating MH - Macromolecular Substances MH - Mutation MH - Oxytricha/*metabolism MH - Protein Conformation MH - *Protein Structure, Secondary MH - Protozoan Proteins/*chemistry MH - Solutions MH - Spectrum Analysis, Raman MH - Thermodynamics EDAT- 1997/07/01 MHDA- 2001/03/28 10:01 CRDT- 1997/07/01 00:00 AID - 10.1021/bi970283g [doi] AID - bi970283g [pii] PST - ppublish SO - Biochemistry. 1997 Jul 1;36(26):8053-9. PMID- 15465872 OWN - NLM STAT- MEDLINE DA - 20041201 DCOM- 20050426 LR - 20140608 IS - 0006-3495 (Print) IS - 0006-3495 (Linking) VI - 87 IP - 6 DP - 2004 Dec TI - Colicin occlusion of OmpF and TolC channels: outer membrane translocons for colicin import. PG - 3901-11 AB - The interaction of colicins with target cells is a paradigm for protein import. To enter cells, bactericidal colicins parasitize Escherichia coli outer membrane receptors whose physiological purpose is the import of essential metabolites. Colicins E1 and E3 initially bind to the BtuB receptor, whose beta-barrel pore is occluded by an N-terminal globular "plug". The x-ray structure of a complex of BtuB with the coiled-coil BtuB-binding domain of colicin E3 did not reveal displacement of the BtuB plug that would allow passage of the colicin (Kurisu, G., S. D. Zakharov, M. V. Zhalnina, S. Bano, V. Y. Eroukova, T. I. Rokitskaya, Y. N. Antonenko, M. C. Wiener, and W. A. Cramer. 2003. Nat. Struct. Biol. 10:948-954). This correlates with the inability of BtuB to form ion channels in planar bilayers, shown in this work, suggesting that an additional outer membrane protein(s) is required for colicin import across the outer membrane. The identity and interaction properties of this OMP were analyzed in planar bilayer experiments.OmpF and TolC channels in planar bilayers were occluded by colicins E3 and E1, respectively, from the trans-side of the membrane. Occlusion was dependent upon a cis-negative transmembrane potential. A positive potential reversibly opened OmpF and TolC channels. Colicin N, which uses only OmpF for entry, occludes OmpF in planar bilayers with the same orientation constraints as colicins E1 and E3. The OmpF recognition sites of colicins E3 and N, and the TolC recognition site of colicin E1, were found to reside in the N-terminal translocation domains. These data are considered in the context of a two-receptor translocon model for colicin entry into cells. FAU - Zakharov, Stanislav D AU - Zakharov SD AD - Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA. zakharos@purdue.edu FAU - Eroukova, Veronika Y AU - Eroukova VY FAU - Rokitskaya, Tatyana I AU - Rokitskaya TI FAU - Zhalnina, Mariya V AU - Zhalnina MV FAU - Sharma, Onkar AU - Sharma O FAU - Loll, Patrick J AU - Loll PJ FAU - Zgurskaya, Helen I AU - Zgurskaya HI FAU - Antonenko, Yuri N AU - Antonenko YN FAU - Cramer, William A AU - Cramer WA LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20041001 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Bacterial Outer Membrane Proteins) RN - 0 (BtuB protein, E coli) RN - 0 (Colicins) RN - 0 (Escherichia coli Proteins) RN - 0 (Lipid Bilayers) RN - 0 (Membrane Transport Proteins) RN - 0 (Membranes, Artificial) RN - 0 (OmpF protein) RN - 0 (Porins) RN - 0 (Receptors, Peptide) RN - 0 (tolC protein, E coli) SB - IM MH - Bacterial Outer Membrane Proteins/*chemistry MH - Colicins/*chemistry MH - Diffusion MH - Escherichia coli Proteins/*metabolism MH - *Ion Channel Gating MH - Lipid Bilayers/*chemistry MH - Membrane Transport Proteins MH - Membranes, Artificial MH - Porins/*chemistry MH - Protein Binding MH - *Protein Transport MH - Receptors, Peptide/*metabolism PMC - PMC1304901 OID - NLM: PMC1304901 EDAT- 2004/10/07 09:00 MHDA- 2005/04/27 09:00 CRDT- 2004/10/07 09:00 PHST- 2004/10/01 [aheadofprint] AID - S0006-3495(04)73856-4 [pii] AID - 10.1529/biophysj.104.046151 [doi] PST - ppublish SO - Biophys J. 2004 Dec;87(6):3901-11. Epub 2004 Oct 1. PMID- 24278008 OWN - NLM STAT- MEDLINE DA - 20131126 DCOM- 20140714 LR - 20141112 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 9 IP - 11 DP - 2013 TI - Electrostatically accelerated encounter and folding for facile recognition of intrinsically disordered proteins. PG - e1003363 LID - 10.1371/journal.pcbi.1003363 [doi] AB - Achieving facile specific recognition is essential for intrinsically disordered proteins (IDPs) that are involved in cellular signaling and regulation. Consideration of the physical time scales of protein folding and diffusion-limited protein-protein encounter has suggested that the frequent requirement of protein folding for specific IDP recognition could lead to kinetic bottlenecks. How IDPs overcome such potential kinetic bottlenecks to viably function in signaling and regulation in general is poorly understood. Our recent computational and experimental study of cell-cycle regulator p27 (Ganguly et al., J. Mol. Biol. (2012)) demonstrated that long-range electrostatic forces exerted on enriched charges of IDPs could accelerate protein-protein encounter via "electrostatic steering" and at the same time promote "folding-competent" encounter topologies to enhance the efficiency of IDP folding upon encounter. Here, we further investigated the coupled binding and folding mechanisms and the roles of electrostatic forces in the formation of three IDP complexes with more complex folded topologies. The surface electrostatic potentials of these complexes lack prominent features like those observed for the p27/Cdk2/cyclin A complex to directly suggest the ability of electrostatic forces to facilitate folding upon encounter. Nonetheless, similar electrostatically accelerated encounter and folding mechanisms were consistently predicted for all three complexes using topology-based coarse-grained simulations. Together with our previous analysis of charge distributions in known IDP complexes, our results support a prevalent role of electrostatic interactions in promoting efficient coupled binding and folding for facile specific recognition. These results also suggest that there is likely a co-evolution of IDP folded topology, charge characteristics, and coupled binding and folding mechanisms, driven at least partially by the need to achieve fast association kinetics for cellular signaling and regulation. FAU - Ganguly, Debabani AU - Ganguly D AD - Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, United States of America. FAU - Zhang, Weihong AU - Zhang W FAU - Chen, Jianhan AU - Chen J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20131121 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (Intrinsically Disordered Proteins) SB - IM MH - Intrinsically Disordered Proteins/*chemistry/*metabolism MH - Kinetics MH - Molecular Dynamics Simulation MH - Protein Folding MH - Static Electricity MH - Surface Properties MH - Thermodynamics PMC - PMC3836701 OID - NLM: PMC3836701 EDAT- 2013/11/28 06:00 MHDA- 2014/07/16 06:00 CRDT- 2013/11/27 06:00 PHST- 2013/11 [ecollection] PHST- 2013/07/12 [received] PHST- 2013/10/10 [accepted] PHST- 2013/11/21 [epublish] AID - 10.1371/journal.pcbi.1003363 [doi] AID - PCOMPBIOL-D-13-01242 [pii] PST - ppublish SO - PLoS Comput Biol. 2013;9(11):e1003363. doi: 10.1371/journal.pcbi.1003363. Epub 2013 Nov 21. PMID- 16984883 OWN - NLM STAT- MEDLINE DA - 20060920 DCOM- 20061212 LR - 20131121 IS - 1074-5521 (Print) IS - 1074-5521 (Linking) VI - 13 IP - 9 DP - 2006 Sep TI - Alternative O-GlcNAcylation/O-phosphorylation of Ser16 induce different conformational disturbances to the N terminus of murine estrogen receptor beta. PG - 937-44 AB - Serine and threonine residues in many proteins can be modified by either phosphorylation or GlcNAcylation. To investigate the mechanism of O-GlcNAc and O-phosphate's reciprocal roles in modulating the degradation and activity of murine estrogen receptor beta (mER-beta), the conformational changes induced by O-GlcNAcylation and O-phosphorylation of Ser(16) in 17-mer model peptides corresponding to the N-terminal intrinsically disordered (ID) region of mER-beta were studied by NMR techniques, circular dichroism (CD), and molecular dynamics simulations. Our results suggest that O-phosphorylation discourages the turn formation in the S(15)STG(18) fragment. In contrast, O-GlcNAcylation promotes turn formation in this region. Thus, we postulate that the different changes of the local structure in the N-terminal S(15)STG(18) fragment of mER-beta caused by O-phosphate or O-GlcNAc modification might lead to the disturbances to the dynamic ensembles of the ID region of mER-beta, which is related to its modulatory activity. FAU - Chen, Yong-Xiang AU - Chen YX AD - Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China. FAU - Du, Jin-Tang AU - Du JT FAU - Zhou, Lian-Xiu AU - Zhou LX FAU - Liu, Xiao-Hong AU - Liu XH FAU - Zhao, Yu-Fen AU - Zhao YF FAU - Nakanishi, Hiroshi AU - Nakanishi H FAU - Li, Yan-Mei AU - Li YM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Chem Biol JT - Chemistry & biology JID - 9500160 RN - 0 (Estrogen Receptor beta) RN - 0 (Peptides) RN - 452VLY9402 (Serine) RN - V956696549 (Acetylglucosamine) SB - IM CIN - Chem Biol. 2006 Sep;13(9):923-4. PMID: 16984879 MH - Acetylglucosamine/chemistry/metabolism MH - Acylation MH - Animals MH - Circular Dichroism MH - Computer Simulation MH - Estrogen Receptor beta/*chemistry/*metabolism MH - Mice MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides/chemistry/*metabolism MH - Phosphorylation MH - Protein Conformation MH - *Protein Processing, Post-Translational MH - Protein Structure, Secondary MH - Serine/metabolism EDAT- 2006/09/21 09:00 MHDA- 2006/12/13 09:00 CRDT- 2006/09/21 09:00 PHST- 2006/04/12 [received] PHST- 2006/06/16 [revised] PHST- 2006/06/26 [accepted] AID - S1074-5521(06)00232-8 [pii] AID - 10.1016/j.chembiol.2006.06.017 [doi] PST - ppublish SO - Chem Biol. 2006 Sep;13(9):937-44. PMID- 18725412 OWN - NLM STAT- MEDLINE DA - 20081110 DCOM- 20090107 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 46 DP - 2008 Nov 14 TI - Proline-directed pseudo-phosphorylation at AT8 and PHF1 epitopes induces a compaction of the paperclip folding of Tau and generates a pathological (MC-1) conformation. PG - 32066-76 LID - 10.1074/jbc.M805300200 [doi] AB - Tau, a neuronal microtubule-associated protein that aggregates in Alzheimer disease is a natively unfolded protein. In solution, Tau adopts a "paperclip" conformation, whereby the N- and C-terminal domains approach each other and the repeat domain ( Jeganathan, S., von Bergen, M., Brutlach, H., Steinhoff, H. J., and Mandelkow, E. (2006) Biochemistry 45, 2283-2293 ). In AD, Tau is in a hyperphosphorylated state. The consequences for microtubule binding or aggregation are a matter of debate. We therefore tested whether phosphorylation alters the conformation of Tau. To avoid the ambiguities of heterogeneous phosphorylation we cloned "pseudo-phosphorylation" mutants of Tau where combinations of Ser or Thr residues were converted into Glu. These mutations were combined with FRET pairs inserted in different locations to allow distance measurements. The results show that the paperclip conformation becomes tighter or looser, depending on the pseudo-phosphorylation state. In particular, pseudo-phosphorylation at the epitope of the diagnostic antibody AT8* (S199E + S202E + T205E) moves the N-terminal domain away from the C-terminal domain. Pseudo-phosphorylation at the PHF1 epitope (S396E + S404E) moves the C-terminal domain away from the repeat domain. In both cases the paperclip conformation is opened up. By contrast, the combination of AT8* and PHF1 sites leads to compaction of the paperclip, such that the N-terminus approaches the repeat domain. The compaction becomes even stronger by combining pseudo-phosphorylated AT8*, AT100, and PHF1 epitopes. This is accompanied by a strong increase in the reaction with conformation-dependent antibody MC1, suggesting the generation of a pathological conformation characteristic for Tau in AD. Furthermore, the compact paperclip conformation enhances the aggregation to paired helical filaments but has little influence on microtubule interactions. The data provide a framework for the global folding of Tau dependent on proline-directed phosphorylation in the domains flanking the repeats and the consequences for pathological properties of Tau. FAU - Jeganathan, Sadasivam AU - Jeganathan S AD - Max Planck Unit for Structural Molecular Biology, Notkestrasse 85, D-22607 Hamburg, Germany. FAU - Hascher, Antje AU - Hascher A FAU - Chinnathambi, Subashchandrabose AU - Chinnathambi S FAU - Biernat, Jacek AU - Biernat J FAU - Mandelkow, Eva-Maria AU - Mandelkow EM FAU - Mandelkow, Eckhard AU - Mandelkow E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080825 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Antibodies) RN - 0 (Epitopes) RN - 0 (tau Proteins) RN - 9DLQ4CIU6V (Proline) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Alzheimer Disease/*pathology MH - Antibodies/*immunology MH - Circular Dichroism MH - Epitopes/immunology/*metabolism MH - Guanidine/pharmacology MH - Microscopy, Electron, Transmission MH - Mutation/genetics MH - Phosphorylation MH - Proline/genetics/*metabolism MH - Protein Conformation MH - Protein Denaturation/drug effects MH - *Protein Folding MH - Protein Structure, Secondary MH - tau Proteins/*chemistry/*metabolism/ultrastructure EDAT- 2008/08/30 09:00 MHDA- 2009/01/08 09:00 CRDT- 2008/08/30 09:00 PHST- 2008/08/25 [aheadofprint] AID - M805300200 [pii] AID - 10.1074/jbc.M805300200 [doi] PST - ppublish SO - J Biol Chem. 2008 Nov 14;283(46):32066-76. doi: 10.1074/jbc.M805300200. Epub 2008 Aug 25. PMID- 12842046 OWN - NLM STAT- MEDLINE DA - 20030704 DCOM- 20040319 LR - 20061115 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 11 IP - 7 DP - 2003 Jul TI - Structure of the C-terminal domain of human La protein reveals a novel RNA recognition motif coupled to a helical nuclear retention element. PG - 833-43 AB - The La protein is an important component of ribonucleoprotein complexes that acts mainly as an RNA chaperone to facilitate correct processing and maturation of RNA polymerase III transcripts, but can also stimulate translation initiation. We report here the structure of the C-terminal domain of human La, which comprises an atypical RNA recognition motif (La225-334) and a long unstructured C-terminal tail. The central beta sheet of La225-334 reveals novel features: the putative RNA binding surface is formed by a five-stranded beta sheet and, strikingly, is largely obscured by a long C-terminal alpha helix that encompasses a recently identified nuclear retention element. Contrary to previous observations, we find that the La protein does not contain a dimerization domain. FAU - Jacks, Amanda AU - Jacks A AD - Biophysics Laboratories, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, St Michael's Building, PO1 2DT, Portsmouth, United. FAU - Babon, Jeff AU - Babon J FAU - Kelly, Geoff AU - Kelly G FAU - Manolaridis, Ioannis AU - Manolaridis I FAU - Cary, Peter D AU - Cary PD FAU - Curry, Stephen AU - Curry S FAU - Conte, Maria R AU - Conte MR LA - eng SI - PDB/1OXW SI - PDB/1U1A PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Autoantigens) RN - 0 (Ribonucleoproteins) RN - 0 (SS-B antigen) RN - 63231-63-0 (RNA) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Autoantigens MH - Binding Sites MH - Circular Dichroism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - RNA/*metabolism MH - Ribonucleoproteins/*chemistry/metabolism EDAT- 2003/07/05 05:00 MHDA- 2004/03/20 05:00 CRDT- 2003/07/05 05:00 AID - S0969212603001217 [pii] PST - ppublish SO - Structure. 2003 Jul;11(7):833-43. PMID- 11292835 OWN - NLM STAT- MEDLINE DA - 20010618 DCOM- 20010719 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 25 DP - 2001 Jun 22 TI - Circular proteins in plants: solution structure of a novel macrocyclic trypsin inhibitor from Momordica cochinchinensis. PG - 22875-82 AB - Much interest has been generated by recent reports on the discovery of circular (i.e. head-to-tail cyclized) proteins in plants. Here we report the three-dimensional structure of one of the newest such circular proteins, MCoTI-II, a novel trypsin inhibitor from Momordica cochinchinensis, a member of the Cucurbitaceae plant family. The structure consists of a small beta-sheet, several turns, and a cystine knot arrangement of the three disulfide bonds. Interestingly, the molecular topology is similar to that of the plant cyclotides (Craik, D. J., Daly, N. L., Bond, T., and Waine, C. (1999) J. Mol. Biol. 294, 1327-1336), which derive from the Rubiaceae and Violaceae plant families, have antimicrobial activities, and exemplify the cyclic cystine knot structural motif as part of their circular backbone. The sequence, biological activity, and plant family of MCoTI-II are all different from known cyclotides. However, given the structural similarity, cyclic backbone, and plant origin of MCoTI-II, we propose that MCoTI-II can be classified as a new member of the cyclotide class of proteins. The expansion of the cyclotides to include trypsin inhibitory activity and a new plant family highlights the importance and functional variability of circular proteins and the fact that they are more common than has previously been believed. Insights into the possible roles of backbone cyclization have been gained by a comparison of the structure of MCoTI-II with the homologous acyclic trypsin inhibitors CMTI-I and EETI-II from the Cucurbitaceae plant family. FAU - Felizmenio-Quimio, M E AU - Felizmenio-Quimio ME AD - Institute for Molecular Bioscience, University of Queensland, Brisbane, 4072 Queensland, Australia. FAU - Daly, N L AU - Daly NL FAU - Craik, D J AU - Craik DJ LA - eng SI - PDB/1IB9 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20010405 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Plant Proteins) RN - 0 (Trypsin Inhibitors) SB - IM MH - Amino Acid Sequence MH - Cucurbitaceae/*chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Plant Proteins/*chemistry MH - Protein Conformation MH - Sequence Homology, Amino Acid MH - Trypsin Inhibitors/*chemistry EDAT- 2001/04/09 10:00 MHDA- 2001/07/20 10:01 CRDT- 2001/04/09 10:00 PHST- 2001/04/05 [aheadofprint] AID - 10.1074/jbc.M101666200 [doi] AID - M101666200 [pii] PST - ppublish SO - J Biol Chem. 2001 Jun 22;276(25):22875-82. Epub 2001 Apr 5. PMID- 15087392 OWN - NLM STAT- MEDLINE DA - 20040416 DCOM- 20040610 LR - 20071115 IS - 0008-5472 (Print) IS - 0008-5472 (Linking) VI - 64 IP - 8 DP - 2004 Apr 15 TI - TC-1 is a novel tumorigenic and natively disordered protein associated with thyroid cancer. PG - 2766-73 AB - A novel gene, thyroid cancer 1 (TC-1), was found recently to be overexpressed in thyroid cancer. TC-1 shows no homology to any of the known thyroid cancer-associated genes. We have produced stable transformants of normal thyroid cells that express the TC-1 gene, and these cells show increased proliferation rates and anchorage-independent growth in soft agar. Apoptosis rates also are decreased in the transformed cells. We also have expressed recombinant TC-1 protein and have undertaken a structural and functional characterization of the protein. The protein is monomeric and predominantly unstructured under conditions of physiologic salt and pH. This places it in the category of natively disordered proteins, a rapidly expanding group of proteins, many members of which play critical roles in cell regulation processes. We show that the protein can be phosphorylated by cyclic AMP-dependent protein kinase and protein kinase C, and the activity of both of these kinases is up-regulated when cells are stably transfected with TC-1. These results suggest that overexpression of TC-1 may be important in thyroid carcinogenesis. FAU - Sunde, Margaret AU - Sunde M AD - School of Molecular and Microbial Biosciences and Discipline of Medicine, University of Sydney, Australia. FAU - McGrath, Kristine C Y AU - McGrath KC FAU - Young, Lei AU - Young L FAU - Matthews, Jacqueline M AU - Matthews JM FAU - Chua, Elizabeth L AU - Chua EL FAU - Mackay, Joel P AU - Mackay JP FAU - Death, Alison K AU - Death AK LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Cancer Res JT - Cancer research JID - 2984705R RN - 0 (C8orf4 protein, human) RN - 0 (Neoplasm Proteins) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) RN - EC 2.7.11.13 (Protein Kinase C) SB - IM MH - Apoptosis/physiology MH - Cell Adhesion/physiology MH - Cell Division/physiology MH - Cell Line, Tumor MH - Cyclic AMP-Dependent Protein Kinases/metabolism MH - Humans MH - Neoplasm Proteins/*chemistry/genetics/metabolism/*physiology MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphorylation MH - Protein Conformation MH - Protein Kinase C/metabolism MH - Signal Transduction/physiology MH - Thyroid Neoplasms/chemistry/genetics/*metabolism/pathology MH - Transfection EDAT- 2004/04/17 05:00 MHDA- 2004/06/21 10:00 CRDT- 2004/04/17 05:00 PST - ppublish SO - Cancer Res. 2004 Apr 15;64(8):2766-73. PMID- 25092343 OWN - NLM STAT- MEDLINE DA - 20140820 DCOM- 20141103 LR - 20150114 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 33 DP - 2014 Aug 19 TI - Allostery within a transcription coactivator is predominantly mediated through dissociation rate constants. PG - 12055-60 LID - 10.1073/pnas.1405815111 [doi] AB - The kinase-inducible domain interacting (KIX) domain of CREB binding protein binds to multiple intrinsically disordered transcription factors in vivo at two distinct sites on its surface. Several reports have been made of allosteric communication between these two sites in this well-characterized model system. In this work, we have performed fluorescence stopped-flow measurements to investigate the kinetics of binding of five KIX binding proteins. We find that they all have similar association and dissociation rate constants for complex formation, despite their wide range of intrinsic helical propensities. Furthermore, by careful arrangement of pseudofirst-order conditions, we have been able to show that both association and dissociation rate constants are decreased when a partner is bound at the alternative site. These decreases suggest that positive allosteric effects are not mediated by structural changes in binding sites but rather, through a more general mechanism, largely mediated through dissociation, which we propose is largely related to changes in the flexibility of the KIX domain itself. FAU - Shammas, Sarah L AU - Shammas SL AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom sls42@cam.ac.uk. FAU - Travis, Alexandra J AU - Travis AJ AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom. FAU - Clarke, Jane AU - Clarke J AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom. LA - eng GR - 095195/Wellcome Trust/United Kingdom GR - WT095195MA/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140804 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Trans-Activators) SB - IM MH - Allosteric Regulation MH - Fluorescence MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Trans-Activators/*chemistry PMC - PMC4143058 OID - NLM: PMC4143058 OTO - NOTNLM OT - coupled folding and binding OT - dynamic allostery OT - induced fit OT - intrinsic disorder OT - intrinsically disordered protein EDAT- 2014/08/06 06:00 MHDA- 2014/11/05 06:00 CRDT- 2014/08/06 06:00 PHST- 2014/08/04 [aheadofprint] AID - 1405815111 [pii] AID - 10.1073/pnas.1405815111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12055-60. doi: 10.1073/pnas.1405815111. Epub 2014 Aug 4. PMID- 23601177 OWN - NLM STAT- MEDLINE DA - 20130508 DCOM- 20131210 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 18 DP - 2013 May 8 TI - Crystal structure of the complex between prokaryotic ubiquitin-like protein and its ligase PafA. PG - 6794-7 LID - 10.1021/ja4024012 [doi] AB - Prokaryotic ubiquitin-like protein (Pup) is covalently attached to target proteins by the ligase PafA, tagging substrates for proteasomal degradation. The crystal structure of Pup in complex with PafA, reported here, reveals that a long groove wrapping around the enzyme serves as a docking site for Pup. Upon binding, the C-terminal region of the intrinsically disordered Pup becomes ordered to form two helices connected by a linker, positioning the C-terminal glutamate in the active site of PafA. FAU - Barandun, Jonas AU - Barandun J AD - Institute of Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland. FAU - Delley, Cyrille L AU - Delley CL FAU - Ban, Nenad AU - Ban N FAU - Weber-Ban, Eilika AU - Weber-Ban E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130423 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Ubiquitin) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM MH - Corynebacterium glutamicum/enzymology MH - Crystallography, X-Ray MH - Models, Molecular MH - Protein Conformation MH - Ubiquitin/*chemistry/metabolism MH - Ubiquitin-Protein Ligases/*chemistry/metabolism EDAT- 2013/04/23 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/04/23 06:00 PHST- 2013/04/23 [aheadofprint] AID - 10.1021/ja4024012 [doi] PST - ppublish SO - J Am Chem Soc. 2013 May 8;135(18):6794-7. doi: 10.1021/ja4024012. Epub 2013 Apr 23. PMID- 22966050 OWN - NLM STAT- MEDLINE DA - 20121113 DCOM- 20130207 LR - 20141105 IS - 1098-5522 (Electronic) IS - 0019-9567 (Linking) VI - 80 IP - 12 DP - 2012 Dec TI - Antigenic characterization of an intrinsically unstructured protein, Plasmodium falciparum merozoite surface protein 2. PG - 4177-85 LID - 10.1128/IAI.00665-12 [doi] AB - Merozoite surface protein 2 (MSP2) is an abundant glycosylphosphatidylinositol (GPI)-anchored protein of Plasmodium falciparum, which is a potential component of a malaria vaccine. As all forms of MSP2 can be categorized into two allelic families, a vaccine containing two representative forms of MSP2 may overcome the problem of diversity in this highly polymorphic protein. Monomeric recombinant MSP2 is an intrinsically unstructured protein, but its conformational properties on the merozoite surface are unknown. This question is addressed here by analyzing the 3D7 and FC27 forms of recombinant and parasite MSP2 using a panel of monoclonal antibodies raised against recombinant MSP2. The epitopes of all antibodies, mapped using both a peptide array and by nuclear magnetic resonance (NMR) spectroscopy on full-length recombinant MSP2, were shown to be linear. The antibodies revealed antigenic differences, which indicate that the conserved N- and C-terminal regions, but not the central variable region, are less accessible in the parasite antigen. This appears to be an intrinsic property of parasite MSP2 and is not dependent on interactions with other merozoite surface proteins as the loss of some conserved-region epitopes seen using the immunofluorescence assay (IFA) on parasite smears was also seen on Western blot analyses of parasite lysates. Further studies of the structural basis of these antigenic differences are required in order to optimize recombinant MSP2 constructs being evaluated as potential vaccine components. FAU - Adda, Christopher G AU - Adda CG AD - Department of Biochemistry, La Trobe University, Victoria, Australia. FAU - MacRaild, Christopher A AU - MacRaild CA FAU - Reiling, Linda AU - Reiling L FAU - Wycherley, Kaye AU - Wycherley K FAU - Boyle, Michelle J AU - Boyle MJ FAU - Kienzle, Vivian AU - Kienzle V FAU - Masendycz, Paul AU - Masendycz P FAU - Foley, Michael AU - Foley M FAU - Beeson, James G AU - Beeson JG FAU - Norton, Raymond S AU - Norton RS FAU - Anders, Robin F AU - Anders RF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120910 PL - United States TA - Infect Immun JT - Infection and immunity JID - 0246127 RN - 0 (Antibodies, Monoclonal) RN - 0 (Antigens, Protozoan) RN - 0 (Protozoan Proteins) RN - 0 (Recombinant Proteins) RN - 0 (merozoite surface protein 2, Plasmodium) SB - IM MH - Animals MH - Antibodies, Monoclonal/*immunology MH - Antigens, Protozoan/*chemistry/genetics/*immunology MH - *Epitope Mapping MH - Female MH - Magnetic Resonance Spectroscopy MH - Mice MH - Mice, Inbred CBA MH - Plasmodium falciparum/genetics/*immunology MH - Protein Conformation MH - Protozoan Proteins/*chemistry/genetics/*immunology MH - Recombinant Proteins/*immunology PMC - PMC3497424 OID - NLM: PMC3497424 EDAT- 2012/09/12 06:00 MHDA- 2013/02/08 06:00 CRDT- 2012/09/12 06:00 PHST- 2012/09/10 [aheadofprint] AID - IAI.00665-12 [pii] AID - 10.1128/IAI.00665-12 [doi] PST - ppublish SO - Infect Immun. 2012 Dec;80(12):4177-85. doi: 10.1128/IAI.00665-12. Epub 2012 Sep 10. PMID- 9722554 OWN - NLM STAT- MEDLINE DA - 19981015 DCOM- 19981015 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 273 IP - 36 DP - 1998 Sep 4 TI - Structure of cysteine- and glycine-rich protein CRP2. Backbone dynamics reveal motional freedom and independent spatial orientation of the lim domains. PG - 23233-40 AB - Members of the cysteine- and glycine-rich protein family (CRP1, CRP2, and CRP3) contain two zinc-binding LIM domains, LIM1 (amino-terminal) and LIM2 (carboxyl-terminal), and are implicated in diverse cellular processes linked to differentiation, growth control, and pathogenesis. Here we report the solution structure of full-length recombinant quail CRP2 as determined by multi-dimensional triple-resonance NMR spectroscopy. The structural analysis revealed that the global fold of the two LIM domains in the context of the full-length protein is identical to the recently determined solution structures of the isolated individual LIM domains of quail CRP2. There is no preference in relative spatial orientation of the two domains. This supports the view that the two LIM domains are independent structural and presumably functional modules of CRP proteins. This is also reflected by the dynamic properties of CRP2 probed by 15N relaxation values (T1, T2, and nuclear Overhauser effect). A model-free analysis revealed local variations in mobility along the backbone of the two LIM domains in the native protein, similar to those observed for the isolated domains. Interestingly, fast and slow motions observed in the 58-amino acid linker region between the two LIM domains endow extensive motional freedom to CRP2. The dynamic analysis indicates independent backbone mobility of the two LIM domains and rules out correlated LIM domain motion in full-length CRP2. The finding that the LIM domains in a protein encompassing multiple LIM motifs are structurally and dynamically independent from each other supports the notion that these proteins may function as adaptor molecules arranging two or more protein constituents into a macromolecular complex. FAU - Konrat, R AU - Konrat R AD - Institute of Organic Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria. robert.konrat@uibk.ac.at FAU - Krautler, B AU - Krautler B FAU - Weiskirchen, R AU - Weiskirchen R FAU - Bister, K AU - Bister K LA - eng SI - PDB/1A7I SI - PDB/1QLI PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (CRP2 protein, Coturnix japonica) RN - 0 (DNA-Binding Proteins) RN - 0 (Homeodomain Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Solutions) RN - K848JZ4886 (Cysteine) RN - TE7660XO1C (Glycine) SB - IM MH - Amino Acid Sequence MH - Animals MH - *Cysteine MH - DNA-Binding Proteins/*chemistry/genetics MH - *Glycine MH - Homeodomain Proteins/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Motion MH - Nerve Tissue Proteins/chemistry MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Protein Folding MH - Quail MH - Recombinant Proteins/chemistry MH - Sequence Homology, Amino Acid MH - Solutions EDAT- 1998/08/29 MHDA- 1998/08/29 00:01 CRDT- 1998/08/29 00:00 PST - ppublish SO - J Biol Chem. 1998 Sep 4;273(36):23233-40. PMID- 23295967 OWN - NLM STAT- MEDLINE DA - 20130304 DCOM- 20130617 LR - 20131121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1830 IP - 4 DP - 2013 Apr TI - Oxidized quercetin inhibits alpha-synuclein fibrillization. PG - 2872-81 LID - 10.1016/j.bbagen.2012.12.027 [doi] LID - S0304-4165(12)00388-1 [pii] AB - BACKGROUND: alpha-Synucein is a small (14 kDa), abundant, intrinsically disordered presynaptic protein, whose aggregation is believed to be a critical step in Parkinson's disease (PD). Oxidative stress is reported to be a risk factor for dopamine cell degeneration in PD. Flavonoids are suggested to be important antioxidant against oxidative stress. Flavonoids were reported to inhibit fibrillization and disaggregate the preformed fibrils of alpha-synucein, but the molecular mechanism was still not clear. METHODS: Quercetin, a well-recognized flavonoid antioxidant, was tested for its inhibition of alpha-synucein aggregation by thioflavin T assay, light scattering measurement, size-exclusion high performance liquid chromatography, atomic force microscopy, etc. RESULTS: The pre-incubated quercetin exhibited a noticeably stronger inhibition behavior to the fibril formation than that of the freshly prepared. The inhibition is significant in the presence of ortho- and para-benzenediol isomers and inconsiderable in the presence of meta-isomer. The oxidized quercetin species (i.e., chalcantrione, benzyfuranone, quercetinchinone, and other derivatives) cause stronger inhibition than quercetin does because of the elevated polarity and hydrophilicity. Presence of quercetin disaggregates alpha-synucein fibrils, rather than oligomers and amorphous aggregations. CONCLUSIONS: Instead of the antioxidant activity, the 1:1 covalent binding of quercetin with alpha-synucein, and the increased hydophilicity of the covalently modified alpha-synucein oligomers or monomers, account for the inhibition of alpha-synucein fibrillation. GENERAL SIGNIFICANCE: Clarification of the molecular mechanism of the inhibition and disaggregation may help to screen safer and more effective flavonoid therapeutic in combating PD. CI - Copyright (c) 2012. Published by Elsevier B.V. FAU - Zhu, Min AU - Zhu M AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA. FAU - Han, Shubo AU - Han S FAU - Fink, Anthony L AU - Fink AL LA - eng PT - Journal Article DEP - 20130104 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (alpha-Synuclein) RN - 9IKM0I5T1E (Quercetin) SB - IM MH - Microscopy, Atomic Force MH - Oxidation-Reduction MH - Protein Multimerization MH - Quercetin/*pharmacology MH - alpha-Synuclein/*chemistry EDAT- 2013/01/09 06:00 MHDA- 2013/06/19 06:00 CRDT- 2013/01/09 06:00 PHST- 2012/11/10 [received] PHST- 2012/12/18 [revised] PHST- 2012/12/21 [accepted] PHST- 2013/01/04 [aheadofprint] AID - S0304-4165(12)00388-1 [pii] AID - 10.1016/j.bbagen.2012.12.027 [doi] PST - ppublish SO - Biochim Biophys Acta. 2013 Apr;1830(4):2872-81. doi: 10.1016/j.bbagen.2012.12.027. Epub 2013 Jan 4. PMID- 22817985 OWN - NLM STAT- MEDLINE DA - 20120723 DCOM- 20130102 IS - 1934-6069 (Electronic) IS - 1931-3128 (Linking) VI - 12 IP - 1 DP - 2012 Jul 19 TI - Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA. PG - 20-33 LID - 10.1016/j.chom.2012.05.010 [doi] AB - The Helicobacter pylori type IV secretion effector CagA is a major bacterial virulence determinant and critical for gastric carcinogenesis. Upon delivery into gastric epithelial cells, CagA localizes to the inner face of the plasma membrane, where it acts as a pathogenic scaffold/hub that promiscuously recruits host proteins to potentiate oncogenic signaling. We find that CagA comprises a structured N-terminal region and an intrinsically disordered C-terminal region that directs versatile protein interactions. X-ray crystallographic analysis of the N-terminal CagA fragment (residues 1-876) revealed that the region has a structure comprised of three discrete domains. Domain I constitutes a mobile CagA N terminus, while Domain II tethers CagA to the plasma membrane by interacting with membrane phosphatidylserine. Domain III interacts intramolecularly with the intrinsically disordered C-terminal region, and this interaction potentiates the pathogenic scaffold/hub function of CagA. The present work provides a tertiary-structural basis for the pathophysiological/oncogenic action of H. pylori CagA. CI - Copyright (c) 2012 Elsevier Inc. All rights reserved. FAU - Hayashi, Takeru AU - Hayashi T AD - Division of Microbiology, Graduate School of Medicine, University of Tokyo, Japan. FAU - Senda, Miki AU - Senda M FAU - Morohashi, Hiroko AU - Morohashi H FAU - Higashi, Hideaki AU - Higashi H FAU - Horio, Masafumi AU - Horio M FAU - Kashiba, Yui AU - Kashiba Y FAU - Nagase, Lisa AU - Nagase L FAU - Sasaya, Daisuke AU - Sasaya D FAU - Shimizu, Tomohiro AU - Shimizu T FAU - Venugopalan, Nagarajan AU - Venugopalan N FAU - Kumeta, Hiroyuki AU - Kumeta H FAU - Noda, Nobuo N AU - Noda NN FAU - Inagaki, Fuyuhiko AU - Inagaki F FAU - Senda, Toshiya AU - Senda T FAU - Hatakeyama, Masanori AU - Hatakeyama M LA - eng SI - PDB/4DVY SI - PDB/4DVZ GR - Y1-CO-1020/CO/NCI NIH HHS/United States GR - Y1-GM-1104/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Cell Host Microbe JT - Cell host & microbe JID - 101302316 RN - 0 (Antigens, Bacterial) RN - 0 (Bacterial Proteins) RN - 0 (Receptor, PAR-1) RN - 0 (Recombinant Proteins) RN - 0 (cagA protein, Helicobacter pylori) SB - IM CIN - Cell Host Microbe. 2012 Jul 19;12(1):3-5. PMID: 22817982 MH - Amino Acid Sequence MH - Antigens, Bacterial/*chemistry/genetics/*metabolism MH - Bacterial Proteins/*chemistry/genetics/*metabolism MH - Cell Membrane/metabolism MH - Crystallography, X-Ray MH - Helicobacter pylori/metabolism/pathogenicity MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Tertiary MH - Receptor, PAR-1/chemistry/metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Signal Transduction MH - Structure-Activity Relationship MH - Surface Plasmon Resonance EDAT- 2012/07/24 06:00 MHDA- 2013/01/03 06:00 CRDT- 2012/07/24 06:00 PHST- 2011/11/17 [received] PHST- 2012/04/06 [revised] PHST- 2012/05/07 [accepted] AID - S1931-3128(12)00196-5 [pii] AID - 10.1016/j.chom.2012.05.010 [doi] PST - ppublish SO - Cell Host Microbe. 2012 Jul 19;12(1):20-33. doi: 10.1016/j.chom.2012.05.010. PMID- 18059524 OWN - NLM STAT- MEDLINE DA - 20071206 DCOM- 20080307 LR - 20131121 IS - 0829-8211 (Print) IS - 0829-8211 (Linking) VI - 85 IP - 6 DP - 2007 Dec TI - Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family. PG - 649-62 AB - Acyl carrier protein (ACP) is a universal and highly conserved carrier of acyl intermediates during fatty acid synthesis. In yeast and mammals, ACP exists as a separate domain within a large multifunctional fatty acid synthase polyprotein (type I FAS), whereas it is a small monomeric protein in bacteria and plastids (type II FAS). Bacterial ACPs are also acyl donors for synthesis of a variety of products, including endotoxin and acylated homoserine lactones involved in quorum sensing; the distinct and essential nature of these processes in growth and pathogenesis make ACP-dependent enzymes attractive antimicrobial drug targets. Additionally, ACP homologues are key components in the production of secondary metabolites such as polyketides and nonribosomal peptides. Many ACPs exhibit characteristic structural features of natively unfolded proteins in vitro, with a dynamic and flexible conformation dominated by 3 parallel alpha helices that enclose the thioester-linked acyl group attached to a phosphopantetheine prosthetic group. ACP conformation may also be influenced by divalent cations and interaction with partner enzymes through its "recognition" helix II, properties that are key to its ability to alternately sequester acyl groups and deliver them to the active sites of ACP-dependent enzymes. This review highlights recent progress in defining how the structural features of ACP are related to its multiple carrier roles in fatty acid metabolism. FAU - Byers, David M AU - Byers DM AD - Atlantic Research Centre, Departments of Pediatrics and Biochemistry & Molecular Biology, Dalhousie University, 5849 University Avenue, Halifax, Nova Scotia, Canada. david.byers@dal.ca FAU - Gong, Huansheng AU - Gong H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Canada TA - Biochem Cell Biol JT - Biochemistry and cell biology = Biochimie et biologie cellulaire JID - 8606068 RN - 0 (Acyl Carrier Protein) RN - 0 (Fatty Acids) RN - EC 2.3.1.85 (Fatty Acid Synthases) SB - IM MH - Acyl Carrier Protein/*chemistry/classification/*metabolism MH - Amino Acid Sequence MH - Animals MH - *Conserved Sequence MH - Fatty Acid Synthases/metabolism MH - Fatty Acids/biosynthesis MH - Humans MH - Molecular Sequence Data MH - *Multigene Family MH - Structure-Activity Relationship RF - 115 EDAT- 2007/12/07 09:00 MHDA- 2008/03/08 09:00 CRDT- 2007/12/07 09:00 AID - o07-109 [pii] AID - 10.1139/o07-109 [doi] PST - ppublish SO - Biochem Cell Biol. 2007 Dec;85(6):649-62. PMID- 21998307 OWN - NLM STAT- MEDLINE DA - 20111214 DCOM- 20120327 LR - 20141219 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 50 DP - 2011 Dec 16 TI - Structural characterization of Hsp12, the heat shock protein from Saccharomyces cerevisiae, in aqueous solution where it is intrinsically disordered and in detergent micelles where it is locally alpha-helical. PG - 43447-53 LID - 10.1074/jbc.M111.306464 [doi] AB - Hsp12 (heat shock protein 12) belongs to the small heat shock protein family, partially characterized as a stress response, stationary phase entry, late embryonic abundant-like protein located at the plasma membrane to protect membrane from desiccation. Here, we report the structural characterization of Hsp12 by NMR and biophysical techniques. The protein was labeled uniformly with nitrogen-15 and carbon-13 so that its conformation could be determined in detail both in aqueous solution and in two membrane-mimetic environments, SDS and dodecylphosphocholine (DPC) micelles. Secondary structural elements determined from assigned chemical shifts indicated that Hsp12 is dynamically disordered in aqueous solution, whereas it gains four helical stretches in the presence of SDS micelles and a single helix in presence of DPC. These conclusions were reinforced by circular dichroism spectra of the protein in all three environments. The lack of long range interactions in NOESY spectra indicated that the helices present in SDS micelles do not pack together. R(1) and R(2), relaxation and heteronuclear NOE measurements showed that the protein is disordered in aqueous solution but becomes more ordered in presence of detergent micelles. NMR spectra collected in presence of paramagnetic spin relaxation agents (5DSA, 16DSA, and Gd(DTPA-BMA)) indicated that the amphipathic alpha-helices of Hsp12 in SDS micelles lie on the membrane surface. These observations are in agreement with studies suggesting that Hsp12 functions to protect the membrane from desiccation. FAU - Singarapu, Kiran K AU - Singarapu KK AD - National Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin 53705, USA. FAU - Tonelli, Marco AU - Tonelli M FAU - Chow, Darius C AU - Chow DC FAU - Frederick, Ronnie O AU - Frederick RO FAU - Westler, William M AU - Westler WM FAU - Markley, John L AU - Markley JL LA - eng SI - PDB/2L9Q SI - PDB/2LJL GR - 1U54 GM074901/GM/NIGMS NIH HHS/United States GR - P41 GM66326/GM/NIGMS NIH HHS/United States GR - P41 RR002301/RR/NCRR NIH HHS/United States GR - P41 RR02301/RR/NCRR NIH HHS/United States GR - U54 GM074901/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20111013 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (HSP12 protein, S cerevisiae) RN - 0 (Heat-Shock Proteins) RN - 0 (Micelles) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 107-73-3 (Phosphorylcholine) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - 53949-18-1 (dodecylphosphocholine) SB - IM MH - Heat-Shock Proteins/*chemistry MH - Magnetic Resonance Spectroscopy MH - *Micelles MH - Phosphorylcholine/analogs & derivatives/chemistry MH - Protein Structure, Secondary MH - Saccharomyces cerevisiae Proteins/*chemistry MH - Sodium Dodecyl Sulfate/chemistry PMC - PMC3234819 OID - NLM: PMC3234819 EDAT- 2011/10/15 06:00 MHDA- 2012/03/28 06:00 CRDT- 2011/10/15 06:00 PHST- 2011/10/13 [aheadofprint] AID - M111.306464 [pii] AID - 10.1074/jbc.M111.306464 [doi] PST - ppublish SO - J Biol Chem. 2011 Dec 16;286(50):43447-53. doi: 10.1074/jbc.M111.306464. Epub 2011 Oct 13. PMID- 22276948 OWN - NLM STAT- MEDLINE DA - 20120420 DCOM- 20121019 LR - 20141019 IS - 1554-8937 (Electronic) IS - 1554-8929 (Linking) VI - 7 IP - 4 DP - 2012 Apr 20 TI - Mechanism of cell cycle entry mediated by the intrinsically disordered protein p27(Kip1). PG - 678-82 LID - 10.1021/cb200487h [doi] AB - p27(Kip1) (p27), a prototypical intrinsically disordered protein (IDP), regulates eukaryotic cell division through interactions with cyclin-dependent kinase (Cdk)/cyclin complexes. The activity, stability, and subcellular localization of p27 are regulated by phosphorylation. We illustrate how p27 integrates regulatory signals from several non-receptor tyrosine kinases (NRTKs) to activate Cdk4 and initiate cell cycle entry. Unmodified p27 potently inhibits Cdk/cyclin complexes, including Cdk4/cyclin D (IC(50), 1 nM). Some NRTKs (e.g., Abl) phosphorylate p27 on Tyr 88, which facilitates a second modification on Tyr 74 by another NRTK (e.g., Src). Importantly, this second modification causes partial reactivation of Cdk4 within ternary complexes containing doubly Tyr phosphorylated p27. Partial activation of Cdk4 initiates entry into the cell division cycle. Therefore, p27's disordered features enable NRTKs to sequentially promote a phosphorylation cascade that controls cell fate. Beyond cell cycle control, these results illustrate general concepts regarding why IDPs are well-suited for roles in signaling and regulation in biological systems. FAU - Ou, Li AU - Ou L FAU - Waddell, M Brett AU - Waddell MB FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng GR - 2P30CA021765/CA/NCI NIH HHS/United States GR - P30 CA021765/CA/NCI NIH HHS/United States GR - P30 CA021765-34/CA/NCI NIH HHS/United States GR - R01 CA082491/CA/NCI NIH HHS/United States GR - R01 CA082491/CA/NCI NIH HHS/United States GR - R01 CA082491-10/CA/NCI NIH HHS/United States GR - R01 GM083159/GM/NIGMS NIH HHS/United States GR - R01 GM083159-03/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120203 PL - United States TA - ACS Chem Biol JT - ACS chemical biology JID - 101282906 RN - 0 (Cyclins) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 4) RN - EC 2.7.11.22 (Cyclin-Dependent Kinases) SB - IM MH - Animals MH - Cell Cycle MH - *Cell Cycle Checkpoints MH - Cyclin-Dependent Kinase 4 MH - Cyclin-Dependent Kinase Inhibitor p27/*physiology MH - Cyclin-Dependent Kinases MH - Cyclins MH - Humans MH - Phosphorylation PMC - PMC3331940 MID - NIHMS355199 OID - NLM: NIHMS355199 OID - NLM: PMC3331940 EDAT- 2012/01/27 06:00 MHDA- 2012/10/20 06:00 CRDT- 2012/01/27 06:00 PHST- 2012/02/03 [aheadofprint] AID - 10.1021/cb200487h [doi] PST - ppublish SO - ACS Chem Biol. 2012 Apr 20;7(4):678-82. doi: 10.1021/cb200487h. Epub 2012 Feb 3. PMID- 20399178 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20100419 DCOM- 20100727 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 18 IP - 4 DP - 2010 Mar 14 TI - The meandering of disordered proteins in conformational space. PG - 416-9 LID - 10.1016/j.str.2010.03.003 [doi] AB - In this issue, Mittag et al. (2010) provided interesting insights concerning the molecular details of how the meandering of disordered proteins in conformational space can lead to collective binding modes and ultrasensitive probing of cellular kinase activities. CI - Copyright 2010 Elsevier Ltd. All rights reserved. FAU - Konrat, Robert AU - Konrat R AD - Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria. robert.konrat@univie.ac.at LA - eng PT - Comment PT - Journal Article PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 CON - Structure. 2010 Mar 14;18(4):494-506. PMID: 20399186 EDAT- 2010/04/20 06:00 MHDA- 2010/04/20 06:01 CRDT- 2010/04/20 06:00 AID - S0969-2126(10)00112-7 [pii] AID - 10.1016/j.str.2010.03.003 [doi] PST - ppublish SO - Structure. 2010 Mar 14;18(4):416-9. doi: 10.1016/j.str.2010.03.003. PMID- 10606515 OWN - NLM STAT- MEDLINE DA - 20000119 DCOM- 20000119 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 38 IP - 51 DP - 1999 Dec 21 TI - Metal and DNA binding properties of a two-domain fragment of neural zinc finger factor 1, a CCHC-type zinc binding protein. PG - 16826-30 AB - Neural zinc finger factor 1 (NZF-1) is a member of a family of neural-specific transcription factors that contain multiple copies of a relatively uncharacterized zinc binding motif. We have studied the metal binding and DNA binding properties of a fragment of NZF-1 containing two adjacent zinc binding domains. Partial proteolysis with endoproteinase Lys-C identified metal-stabilized fragments containing either one or both of the zinc binding domains. Both domains were required for specific DNA binding to the beta-retinoic acid receptor element, producing a DNase I footprint covering predominantly one strand. The metal binding site was probed via cobalt(II) substitution. The visible absorption spectrum of the cobalt(II) complex is consistent with Cys-Cys-His-Cys coordination of the metal. The two domains appear to have similar affinities for metal and bind cobalt(II) and zinc(II) with dissociation constants of 4 (+/- 2) x 10(-)(7) M and 1.4 (+/- 0.8) x 10(-)(10) M, respectively. The domains fold upon the addition of zinc, as observed by (1)H NMR. However, an additional weak binding site causes line broadening in the presence of excess zinc, presumably due to aggregation. FAU - Berkovits, H J AU - Berkovits HJ AD - Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. FAU - Berg, J M AU - Berg JM LA - eng GR - GM 46257/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA-Binding Proteins) RN - 0 (NZF-1 protein, rat) RN - 0 (Nerve Tissue Proteins) RN - 0 (Peptide Fragments) RN - 0 (Receptors, Retinoic Acid) RN - 0 (Trans-Activators) RN - 0 (retinoic acid receptor beta) RN - 3G0H8C9362 (Cobalt) RN - EC 3.1.21.1 (Deoxyribonuclease I) RN - J41CSQ7QDS (Zinc) SB - IM MH - Animals MH - Binding Sites/genetics MH - Cloning, Molecular MH - Cobalt/chemistry/metabolism MH - DNA Footprinting MH - DNA-Binding Proteins/*chemistry/genetics/metabolism MH - Deoxyribonuclease I/chemistry MH - Hydrolysis MH - Nerve Tissue Proteins/*chemistry/genetics/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemistry/genetics/isolation & purification/metabolism MH - Protein Folding MH - Protein Structure, Tertiary/genetics MH - Rats MH - Receptors, Retinoic Acid/genetics MH - Response Elements MH - Trans-Activators/*chemistry/genetics/metabolism MH - Zinc/*chemistry/metabolism MH - *Zinc Fingers/genetics EDAT- 1999/12/22 MHDA- 1999/12/22 00:01 CRDT- 1999/12/22 00:00 AID - bi991433l [pii] PST - ppublish SO - Biochemistry. 1999 Dec 21;38(51):16826-30. PMID- 17174464 OWN - NLM STAT- MEDLINE DA - 20070326 DCOM- 20070813 LR - 20140908 IS - 0300-9084 (Print) IS - 0300-9084 (Linking) VI - 89 IP - 3 DP - 2007 Mar TI - Binding of intrinsically disordered proteins is not necessarily accompanied by a structural transition to a folded form. PG - 419-21 AB - There are a large number of protein domains and even entire proteins, lacking ordered structure under physiological conditions. Intriguingly, a highly flexible, random coil-like conformation is the native and functional state for many proteins known to be involved in cell signaling. An example is a key component of immune signaling, the cytoplasmic region of the T cell receptor zeta subunit. This domain exhibits specific dimerization that is distinct from non-specific aggregation behavior seen in many systems. In this work, we use diffusion and chemical shift mapping NMR data to show that the protein does not undergo a transition between disordered and ordered states upon dimerization. This finding opposes the generally accepted view on the behavior of intrinsically disordered proteins, provides evidence for the existence of specific dimerization interactions for intrinsically disordered protein species and opens a new line of research in this new and quickly developing field. FAU - Sigalov, Alexander B AU - Sigalov AB AD - Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA. alexander.sigalov@umassmed.edu FAU - Zhuravleva, Anastasia V AU - Zhuravleva AV FAU - Orekhov, Vladislav Yu AU - Orekhov VY LA - eng GR - P30 AI042845/AI/NIAID NIH HHS/United States GR - P30 AI042845-08/AI/NIAID NIH HHS/United States GR - P30 AI42845-08/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20061122 PL - France TA - Biochimie JT - Biochimie JID - 1264604 RN - 0 (Proteins) SB - IM MH - Dimerization MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Tertiary MH - Proteins/*chemistry PMC - PMC2692994 MID - NIHMS21403 OID - NLM: NIHMS21403 OID - NLM: PMC2692994 EDAT- 2006/12/19 09:00 MHDA- 2007/08/19 09:00 CRDT- 2006/12/19 09:00 PHST- 2006/08/02 [received] PHST- 2006/11/16 [accepted] PHST- 2006/11/22 [aheadofprint] AID - S0300-9084(06)00288-4 [pii] AID - 10.1016/j.biochi.2006.11.003 [doi] PST - ppublish SO - Biochimie. 2007 Mar;89(3):419-21. Epub 2006 Nov 22. PMID- 15103328 OWN - NLM STAT- MEDLINE DA - 20040519 DCOM- 20050714 LR - 20140609 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 23 IP - 10 DP - 2004 May 19 TI - NMR of alpha-synuclein-polyamine complexes elucidates the mechanism and kinetics of induced aggregation. PG - 2039-46 AB - The aggregation of alpha-synuclein is characteristic of Parkinson's disease (PD) and other neurodegenerative synucleinopathies. The 140-aa protein is natively unstructured; thus, ligands binding to the monomeric form are of therapeutic interest. Biogenic polyamines promote the aggregation of alpha-synuclein and may constitute endogenous agents modulating the pathogenesis of PD. We characterized the complexes of natural and synthetic polyamines with alpha-synuclein by NMR and assigned the binding site to C-terminal residues 109-140. Dissociation constants were derived from chemical shift perturbations. Greater polyamine charge (+2 --> +5) correlated with increased affinity and enhancement of fibrillation, for which we propose a simple kinetic mechanism involving a dimeric nucleation center. According to the analysis, polyamines increase the extent of nucleation by approximately 10(4) and the rate of monomer addition approximately 40-fold. Significant secondary structure is not induced in monomeric alpha-synuclein by polyamines at 15 degrees C. Instead, NMR reveals changes in a region (aa 22-93) far removed from the polyamine binding site and presumed to adopt the beta-sheet conformation characteristic of fibrillar alpha-synuclein. We conclude that the C-terminal domain acts as a regulator of alpha-synuclein aggregation. FAU - Fernandez, Claudio O AU - Fernandez CO AD - LANAIS RMN 300, Laboratorio Nacional de Resonancia Magnetica, Facultad de Farmacia y Bioquimica, Universidad de Buenos Aires, Buenos Aires, Argentina. cfernand@ffyb.uba.ar FAU - Hoyer, Wolfgang AU - Hoyer W FAU - Zweckstetter, Markus AU - Zweckstetter M FAU - Jares-Erijman, Elizabeth A AU - Jares-Erijman EA FAU - Subramaniam, Vinod AU - Subramaniam V FAU - Griesinger, Christian AU - Griesinger C FAU - Jovin, Thomas M AU - Jovin TM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040422 PL - England TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Fluorescent Dyes) RN - 0 (Nerve Tissue Proteins) RN - 0 (Polyamines) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (Thiazoles) RN - 0 (alpha-Synuclein) RN - 2390-54-7 (thioflavin T) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Fluorescent Dyes/metabolism MH - Humans MH - Molecular Sequence Data MH - Molecular Structure MH - Nerve Tissue Proteins/*chemistry/genetics/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Parkinson Disease/metabolism MH - Polyamines/*chemistry/*metabolism MH - *Protein Structure, Secondary MH - Synucleins MH - Thiazoles/metabolism MH - alpha-Synuclein PMC - PMC424375 OID - NLM: PMC424375 EDAT- 2004/04/23 05:00 MHDA- 2005/07/15 09:00 CRDT- 2004/04/23 05:00 PHST- 2003/10/28 [received] PHST- 2004/03/22 [accepted] PHST- 2004/04/22 [aheadofprint] AID - 10.1038/sj.emboj.7600211 [doi] AID - 7600211 [pii] PST - ppublish SO - EMBO J. 2004 May 19;23(10):2039-46. Epub 2004 Apr 22. PMID- 10555145 OWN - NLM STAT- MEDLINE DA - 19991123 DCOM- 19991123 LR - 20150612 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 99 IP - 3 DP - 1999 Oct 29 TI - The mechanism of membrane insertion for a cholesterol-dependent cytolysin: a novel paradigm for pore-forming toxins. PG - 293-9 AB - Perfringolysin O (PFO), a water-soluble monomeric cytolysin secreted by pathogenic Clostridium perfringens, oligomerizes and forms large pores upon encountering cholesterol-containing membranes. Whereas all pore-forming bacterial toxins examined previously have been shown to penetrate the membrane using a single amphipathic beta hairpin per polypeptide, cysteine-scanning mutagenesis and multiple independent fluorescence techniques here reveal that each PFO monomer contains a second domain involved in pore formation, and that each of the two amphipathic beta hairpins completely spans the membrane. In the soluble monomer, these transmembrane segments are folded into six alpha helices. The insertion of two transmembrane hairpins per toxin monomer and the major change in secondary structure are striking and define a novel paradigm for the mechanism of membrane insertion by a cytolytic toxin. FAU - Shatursky, O AU - Shatursky O AD - Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City 73190, USA. FAU - Heuck, A P AU - Heuck AP FAU - Shepard, L A AU - Shepard LA FAU - Rossjohn, J AU - Rossjohn J FAU - Parker, M W AU - Parker MW FAU - Johnson, A E AU - Johnson AE FAU - Tweten, R K AU - Tweten RK LA - eng GR - AI37657/AI/NIAID NIH HHS/United States GR - R01 AI037657/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Cell JT - Cell JID - 0413066 RN - 0 (Bacterial Toxins) RN - 0 (Fluorescent Dyes) RN - 0 (Hemolysin Proteins) RN - 0 (Liposomes) RN - 0 (Phosphatidylcholines) RN - 0 (Recombinant Proteins) RN - 0 (Spin Labels) RN - 71329-60-7 (Clostridium perfringens theta-toxin) RN - K848JZ4886 (Cysteine) RN - TE895536Y5 (1-palmitoyl-2-oleoylphosphatidylcholine) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Bacterial Toxins/*chemistry/genetics/*metabolism MH - Clostridium perfringens/*physiology MH - Cysteine MH - Fluorescent Dyes MH - Hemolysin Proteins/metabolism MH - *Liposomes MH - Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Phosphatidylcholines MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Spin Labels EDAT- 1999/11/11 MHDA- 1999/11/11 00:01 CRDT- 1999/11/11 00:00 AID - S0092-8674(00)81660-8 [pii] PST - ppublish SO - Cell. 1999 Oct 29;99(3):293-9. PMID- 18311971 OWN - NLM STAT- MEDLINE DA - 20080319 DCOM- 20080527 LR - 20081205 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 130 IP - 12 DP - 2008 Mar 26 TI - Hyperdimensional NMR spectroscopy with nonlinear sampling. PG - 3927-36 LID - 10.1021/ja077282o [doi] AB - An approach is described for joint interleaved recording, real-time processing, and analysis of NMR data sets. The method employs multidimensional decomposition to find common information in a set of conventional triple-resonance spectra recorded in the nonlinear sampling mode, and builds a model of hyperdimensional (HD) spectrum. While preserving sensitivity per unit of measurement time and allowing for maximal spectral resolution, the approach reduces data collection time on average by 2 orders of magnitude compared to the conventional method. The 7-10 dimensional HD spectrum, which is represented as a set of deconvoluted 1D vectors, is easy to handle and amenable for automated analysis. The method is exemplified by automated assignment for two protein systems of low and high spectral complexity: ubiquitin (globular, 8 kDa) and zetacyt (naturally disordered, 13 kDa). The collection and backbone assignment of the data sets are achieved in real time after approximately 1 and 10 h, respectively. The approach removes the most critical time bottlenecks in data acquisition and analysis. Thus, it can significantly increase the value of NMR spectroscopy in structural biology, for example, in high-throughput structural genomics applications. FAU - Jaravine, Victor A AU - Jaravine VA AD - Swedish NMR Centre, Goteborg University, Box 465, 40530 Goteborg, Sweden. FAU - Zhuravleva, Anastasia V AU - Zhuravleva AV FAU - Permi, Perttu AU - Permi P FAU - Ibraghimov, Ilgis AU - Ibraghimov I FAU - Orekhov, Vladislav Yu AU - Orekhov VY LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080301 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Ubiquitin) SB - IM EIN - J Am Chem Soc. 2008 Oct 1;130(39):13182 MH - Algorithms MH - Computer Simulation MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Reference Standards MH - Sensitivity and Specificity MH - Time Factors MH - Ubiquitin/*chemistry EDAT- 2008/03/04 09:00 MHDA- 2008/05/28 09:00 CRDT- 2008/03/04 09:00 PHST- 2008/03/01 [aheadofprint] AID - 10.1021/ja077282o [doi] PST - ppublish SO - J Am Chem Soc. 2008 Mar 26;130(12):3927-36. doi: 10.1021/ja077282o. Epub 2008 Mar 1. PMID- 11350901 OWN - NLM STAT- MEDLINE DA - 20010514 DCOM- 20010719 LR - 20131121 IS - 1078-0432 (Print) IS - 1078-0432 (Linking) VI - 7 IP - 5 DP - 2001 May TI - Overexpression of p8 is inversely correlated with apoptosis in pancreatic cancer. PG - 1320-4 AB - A recently identified gene, p8, has cell growth-promoting activity and is strongly induced in acute pancreatitis. In this study, we detected p8 and single-stranded DNA (ssDNA) for apoptosis by immunohistochemistry in human pancreatic cancer. The p8 was overexpressed (>30% per 1000 cancer cells) in 26 of 44 (59%) pancreatic cancers, and apoptosis (ssDNA-positive cells >10% per 1000 cancer cells) was recognized in 18 of 44 (41%) pancreatic cancers. There was a significant inverse correlation between the p8 overexpression and apoptosis (P < 0.05). Moreover, the expression pattern of high p8 and low ssDNA was seen significantly more often in lower age (<65 years), in moderately or poorly differentiated cancers, and in node-positive cases (P < 0.05). The p8 expression and apoptosis were not significantly correlated with survival. These results suggest that p8 overexpression is involved in antiapoptotic activity and the biological characteristics of pancreatic cancer. FAU - Su, S B AU - Su SB AD - Department of Internal Medicine and Medical Oncology, Cancer Research Institute, Kanazawa University, Kanazawa 921-8044, Japan. FAU - Motoo, Y AU - Motoo Y FAU - Iovanna, J L AU - Iovanna JL FAU - Berthezene, P AU - Berthezene P FAU - Xie, M J AU - Xie MJ FAU - Mouri, H AU - Mouri H FAU - Ohtsubo, K AU - Ohtsubo K FAU - Matsubara, F AU - Matsubara F FAU - Sawabu, N AU - Sawabu N LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Clin Cancer Res JT - Clinical cancer research : an official journal of the American Association for Cancer Research JID - 9502500 RN - 0 (Basic Helix-Loop-Helix Transcription Factors) RN - 0 (DNA, Neoplasm) RN - 0 (DNA, Single-Stranded) RN - 0 (DNA-Binding Proteins) RN - 0 (Fluorescent Dyes) RN - 0 (Growth Substances) RN - 0 (Neoplasm Proteins) RN - 0 (P8 protein, human) RN - LHQ7J5KV9B (Bisbenzimidazole) SB - IM MH - Aged MH - Aged, 80 and over MH - Apoptosis/*genetics MH - Basic Helix-Loop-Helix Transcription Factors MH - Bisbenzimidazole/diagnostic use MH - DNA, Neoplasm/analysis MH - DNA, Single-Stranded/analysis MH - DNA-Binding Proteins/*biosynthesis/physiology MH - Female MH - Fluorescent Dyes/diagnostic use MH - Gene Expression MH - Growth Substances/*biosynthesis/physiology MH - Humans MH - Immunohistochemistry MH - Male MH - Middle Aged MH - *Neoplasm Proteins MH - Pancreatic Neoplasms/genetics/metabolism/mortality/*pathology MH - Survival Analysis EDAT- 2001/05/15 10:00 MHDA- 2001/07/20 10:01 CRDT- 2001/05/15 10:00 PST - ppublish SO - Clin Cancer Res. 2001 May;7(5):1320-4. PMID- 23028280 OWN - NLM STAT- MEDLINE DA - 20121002 DCOM- 20130128 LR - 20141105 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 8 IP - 9 DP - 2012 TI - Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study. PG - e1002682 LID - 10.1371/journal.pcbi.1002682 [doi] AB - The unique ability of intrinsically disordered proteins (IDPs) to fold upon binding to partner molecules makes them functionally well-suited for cellular communication networks. For example, the folding-binding of different IDP sequences onto the same surface of an ordered protein provides a mechanism for signaling in a many-to-one manner. Here, we study the molecular details of this signaling mechanism by applying both Molecular Dynamics and Monte Carlo methods to S100B, a calcium-modulated homodimeric protein, and two of its IDP targets, p53 and TRTK-12. Despite adopting somewhat different conformations in complex with S100B and showing no apparent sequence similarity, the two IDP targets associate in virtually the same manner. As free chains, both target sequences remain flexible and sample their respective bound, natively [Formula: see text]-helical states to a small extent. Association occurs through an intermediate state in the periphery of the S100B binding pocket, stabilized by nonnative interactions which are either hydrophobic or electrostatic in nature. Our results highlight the importance of overall physical properties of IDP segments, such as net charge or presence of strongly hydrophobic amino acids, for molecular recognition via coupled folding-binding. FAU - Staneva, Iskra AU - Staneva I AD - Department of Astronomy and Theoretical Physics, Computational Biology and Biological Physics group, Lund University, Lund, Sweden. FAU - Huang, Yongqi AU - Huang Y FAU - Liu, Zhirong AU - Liu Z FAU - Wallin, Stefan AU - Wallin S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120913 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (CapZ Actin Capping Protein) RN - 0 (Nerve Growth Factors) RN - 0 (Oligopeptides) RN - 0 (Peptide Fragments) RN - 0 (S100 Calcium Binding Protein beta Subunit) RN - 0 (S100 Proteins) RN - 0 (TRTK-12 peptide) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - CapZ Actin Capping Protein MH - Computer Simulation MH - *Models, Chemical MH - Models, Statistical MH - *Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Monte Carlo Method MH - Nerve Growth Factors/*chemistry/*ultrastructure MH - Oligopeptides/*chemistry MH - Peptide Fragments MH - Protein Binding MH - Protein Conformation MH - S100 Calcium Binding Protein beta Subunit MH - S100 Proteins/*chemistry/*ultrastructure MH - Tumor Suppressor Protein p53/*chemistry/*ultrastructure PMC - PMC3441455 OID - NLM: PMC3441455 EDAT- 2012/10/03 06:00 MHDA- 2013/01/29 06:00 CRDT- 2012/10/03 06:00 PHST- 2012/04/02 [received] PHST- 2012/07/20 [accepted] PHST- 2012/09/13 [epublish] AID - 10.1371/journal.pcbi.1002682 [doi] AID - PCOMPBIOL-D-12-00538 [pii] PST - ppublish SO - PLoS Comput Biol. 2012;8(9):e1002682. doi: 10.1371/journal.pcbi.1002682. Epub 2012 Sep 13. PMID- 1549776 OWN - NLM STAT- MEDLINE DA - 19920420 DCOM- 19920420 LR - 20070319 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 255 IP - 5042 DP - 1992 Jan 17 TI - Human growth hormone and extracellular domain of its receptor: crystal structure of the complex. PG - 306-12 AB - Binding of human growth hormone (hGH) to its receptor is required for regulation of normal human growth and development. Examination of the 2.8 angstrom crystal structure of the complex between the hormone and the extracellular domain of its receptor (hGHbp) showed that the complex consists of one molecule of growth hormone per two molecules of receptor. The hormone is a four-helix bundle with an unusual topology. The binding protein contains two distinct domains, similar in some respects to immunoglobulin domains. The relative orientation of these domains differs from that found between constant and variable domains in immunoglobulin Fab fragments. Both hGHbp domains contribute residues that participate in hGH binding. In the complex both receptors donate essentially the same residues to interact with the hormone, even though the two binding sites on hGH have no structural similarity. Generally, the hormone-receptor interfaces match those identified by previous mutational analyses. In addition to the hormone-receptor interfaces, there is also a substantial contact surface between the carboxyl-terminal domains of the receptors. The relative extents of the contact areas support a sequential mechanism for dimerization that may be crucial for signal transduction. FAU - de Vos, A M AU - de Vos AM AD - Department of Protein Engineering, Genentech, Inc., South San Francisco, CA 94080. FAU - Ultsch, M AU - Ultsch M FAU - Kossiakoff, A A AU - Kossiakoff AA LA - eng PT - Journal Article PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Receptors, Somatotropin) RN - 9002-72-6 (Growth Hormone) SB - IM MH - Binding Sites MH - Crystallography MH - Growth Hormone/*chemistry/metabolism MH - Humans MH - Hydrogen Bonding MH - Models, Molecular MH - Molecular Structure MH - Mutation MH - Receptors, Somatotropin/*chemistry/metabolism MH - Signal Transduction EDAT- 1992/01/17 MHDA- 1992/01/17 00:01 CRDT- 1992/01/17 00:00 PST - ppublish SO - Science. 1992 Jan 17;255(5042):306-12. PMID- 22280012 OWN - NLM STAT- MEDLINE DA - 20120127 DCOM- 20120325 LR - 20121115 IS - 1470-8728 (Electronic) IS - 0264-6021 (Linking) VI - 442 IP - 1 DP - 2012 Feb 15 TI - GRAS proteins: the versatile roles of intrinsically disordered proteins in plant signalling. PG - 1-12 LID - 10.1042/BJ20111766 [doi] AB - IDPs (intrinsically disordered proteins) are highly abundant in eukaryotic proteomes and important for cellular functions, especially in cell signalling and transcriptional regulation. An IDR (intrinsically disordered region) within an IDP often undergoes disorder-to-order transitions upon binding to various partners, allowing an IDP to recognize and bind different partners at various binding interfaces. Plant-specific GRAS proteins play critical and diverse roles in plant development and signalling, and act as integrators of signals from multiple plant growth regulatory and environmental inputs. Possessing an intrinsically disordered N-terminal domain, the GRAS proteins constitute the first functionally required unfoldome from the plant kingdom. Furthermore, the N-terminal domains of GRAS proteins contain MoRFs (molecular recognition features), short interaction-prone segments that are located within IDRs and are able to recognize their interacting partners by undergoing disorder-to-order transitions upon binding to these specific partners. These MoRFs represent potential protein-protein binding sites and may be acting as molecular bait in recognition events during plant development. Intrinsic disorder provides GRAS proteins with a degree of binding plasticity that may be linked to their functional versatility. As an overview of structure-function relationships for GRAS proteins, the present review covers the main biological functions of the GRAS family, the IDRs within these proteins and their implications for understanding mode-of-action. FAU - Sun, Xiaolin AU - Sun X AD - The New Zealand Institute for Plant and Food Research, Private Bag 11030, Palmerston North 4474, New Zealand. xiaolin.sun@plantandfood.co.nz FAU - Jones, William T AU - Jones WT FAU - Rikkerink, Erik H A AU - Rikkerink EH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (Phytochrome A) RN - 0 (Plant Proteins) SB - IM MH - Amino Acid Motifs MH - Meristem/growth & development MH - Phosphorylation MH - Phytochrome A/physiology MH - Plant Development MH - Plant Proteins/*physiology MH - Plant Root Nodulation/physiology MH - Plant Roots/growth & development MH - Plants/*metabolism MH - Protein Folding MH - Protein Structure, Tertiary/physiology MH - Signal Transduction/*physiology MH - Transcriptional Activation/*physiology EDAT- 2012/01/28 06:00 MHDA- 2012/03/27 06:00 CRDT- 2012/01/28 06:00 AID - BJ20111766 [pii] AID - 10.1042/BJ20111766 [doi] PST - ppublish SO - Biochem J. 2012 Feb 15;442(1):1-12. doi: 10.1042/BJ20111766. PMID- 20438845 OWN - NLM STAT- MEDLINE DA - 20100823 DCOM- 20101207 IS - 1096-0279 (Electronic) IS - 1046-5928 (Linking) VI - 74 IP - 1 DP - 2010 Nov TI - Overexpression and purification of PWL2D, a mutant of the effector protein PWL2 from Magnaporthe grisea. PG - 24-31 LID - 10.1016/j.pep.2010.04.020 [doi] AB - The rice blast disease caused by the ascomycete Magnaporthe grisea continues to cause a tremendous impact in rice (Oryza sativa) cultures around the world. Elucidating the molecular basis of the fungus interactions with its host might help increase the general understanding of the pathogen-host relationship. At the moment of invasion, the fungus secretes effectors that modify host defenses and cellular processes as they successively invade living rice cells. PWL2, an effector protein, is a known AVR (avirulence) gene product. The PWL2 gene prevents the fungus from infecting weeping lovegrass (Eragrostis curvula). In this study, we identified a PWL2 allele gene (which we termed PWL2D) in a strain of M. grisea. The sequence of PWL2D has only two bases different from that of PWL2, producing alterations in residue 90 and residue 142. However, the alteration of residue 90 (from D(90) to N(90)) is critical to gene function. Here, we cloned the gene PWL2D in a pET System vector, expressed the gene product in Escherichia coli and evaluated by spectroscopic techniques some aspects of the PWL2D structure. While TRX-tagged PWL2D is prone to aggregation, the solubility of PWL2D is improved when it is overexpressed without its original signal peptide. Expression and purification procedures for these constructs are described. Finally, we found out that the protein seems to be an intrinsically disordered protein. Results from these studies will facilitate structural analysis of PWL2D and might contribute to understanding the gene's function and of fungal/plant interactions. CI - Copyright 2010 Elsevier Inc. All rights reserved. FAU - Schneider, D R S AU - Schneider DR AD - Centro de Biologia Molecular e Engenharia Genetica (CBMEG), Universidade Estadual de Campinas, CP 6010, CEP 13083-970 Campinas, SP, Brazil. FAU - Saraiva, A M AU - Saraiva AM FAU - Azzoni, A R AU - Azzoni AR FAU - Miranda, H R C A N AU - Miranda HR FAU - de Toledo, M A S AU - de Toledo MA FAU - Pelloso, A C AU - Pelloso AC FAU - Souza, A P AU - Souza AP LA - eng PT - Journal Article DEP - 20100511 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (Fungal Proteins) RN - 0 (Mutant Proteins) RN - 0 (PWL2 protein, Magnaporthe grisea) RN - 52500-60-4 (Thioredoxins) SB - IM MH - Alleles MH - Amino Acid Sequence MH - Circular Dichroism MH - Cloning, Molecular MH - Escherichia coli/genetics MH - Fungal Proteins/chemistry/*genetics/*isolation & purification MH - Genes, Fungal MH - Genetic Vectors/genetics MH - Magnaporthe/*genetics MH - Molecular Sequence Data MH - Mutant Proteins/chemistry/genetics/isolation & purification MH - *Mutation MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Sequence Alignment MH - Thioredoxins/chemistry MH - Up-Regulation EDAT- 2010/05/05 06:00 MHDA- 2010/12/14 06:00 CRDT- 2010/05/05 06:00 PHST- 2010/01/25 [received] PHST- 2010/04/22 [revised] PHST- 2010/04/23 [accepted] PHST- 2010/05/11 [aheadofprint] AID - S1046-5928(10)00134-8 [pii] AID - 10.1016/j.pep.2010.04.020 [doi] PST - ppublish SO - Protein Expr Purif. 2010 Nov;74(1):24-31. doi: 10.1016/j.pep.2010.04.020. Epub 2010 May 11. PMID- 17309280 OWN - NLM STAT- MEDLINE DA - 20070313 DCOM- 20070516 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 46 IP - 11 DP - 2007 Mar 20 TI - Biochemical studies on Mycobacterium tuberculosis UreG and comparative modeling reveal structural and functional conservation among the bacterial UreG family. PG - 3171-82 AB - Nickel is a fundamental micronutrient for cellular life, but it is toxic in soluble form at nonphysiological concentrations. Such potentially contradictory features required living organisms to develop efficient systems for nickel utilization and homeostasis. This is the case for incorporation of nickel into the active site of urease, a multistep, tightly regulated process, requiring the interplay of various accessory proteins. The understanding of this activation mechanism may find medical applications against ureolytic bacteria, among which Mycobacterium tuberculosis is a deadly pathogen for humans. The topic of this study is UreG, an essential chaperone in the in vivo activation of urease upon insertion of Ni2+ into the active site. The protein was examined using both experimental and computational approaches. In particular, the soluble M. tuberculosis UreG (MtUreG) was overexpressed in Escherichia coli and purified to homogeneity. The identity of the isolated protein was established by mass spectrometry. On-line size-exclusion chromatography and light scattering indicated that MtUreG exists as a dimeric form in solution. Determination of the free thiol concentration revealed that a disulfide bond is present in the dimer. The isolated MtUreG shows low GTPase activity under native conditions, with a kcat of 0.01 min-1. Circular dichroism spectroscopy demonstrated the presence of a well-defined secondary structure (8% alpha-helices, 29% beta-strands) in MtUreG, whereas NMR spectroscopy indicated that this protein does not behave as a rigid three-dimensional fold and thus can be assigned to the class of intrinsically unstructured polypeptides. The molecular model of MtUreG in the fully folded and functional form was built using fold recognition algorithms. An extensive similarity search was performed to determine conservation patterns in all known bacterial UreG sequences. The generation of a multiple-sequence alignment and the related phylogenetic tree allowed us to recognize key residues and motifs that are likely important for protein function. A structural database containing the homology-built models of the most representative UreG proteins was created, confirming the structural analogies among the UreG family. A flexible region, likely to be important for protein function, is identified. The structural conservation among this class of GTPases is discussed on the basis of their function in the urease assembly process. FAU - Zambelli, Barbara AU - Zambelli B AD - Laboratory of Bioinorganic Chemistry, Department of Agro-Environmental Science and Technology, University of Bologna, Viale Giuseppe Fanin 40, 40127 Bologna, Italy. FAU - Musiani, Francesco AU - Musiani F FAU - Savini, Matteo AU - Savini M FAU - Tucker, Paul AU - Tucker P FAU - Ciurli, Stefano AU - Ciurli S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070220 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Molecular Chaperones) RN - 7OV03QG267 (Nickel) RN - EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)) RN - EC 2.7.1.- (guanosine phosphotransferase) RN - K848JZ4886 (Cysteine) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Cysteine/analysis MH - Models, Molecular MH - Molecular Chaperones/genetics/*metabolism MH - Molecular Sequence Data MH - Mycobacterium tuberculosis/*chemistry MH - Nickel/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphotransferases (Alcohol Group Acceptor)/genetics/*metabolism MH - Phylogeny MH - Sequence Alignment EDAT- 2007/02/21 09:00 MHDA- 2007/05/17 09:00 CRDT- 2007/02/21 09:00 PHST- 2007/02/20 [aheadofprint] AID - 10.1021/bi6024676 [doi] PST - ppublish SO - Biochemistry. 2007 Mar 20;46(11):3171-82. Epub 2007 Feb 20. PMID- 23198089 OWN - NLM STAT- MEDLINE DA - 20121130 DCOM- 20130429 LR - 20141104 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 2 DP - 2012 TI - Juxtanodin is an intrinsically disordered F-actin-binding protein. PG - 899 LID - 10.1038/srep00899 [doi] AB - Juxtanodin, also called ermin, is an F-actin-binding protein expressed by oligodendrocytes, the myelin-forming cells of the central nervous system. While juxtanodin carries a short conserved F-actin-binding segment at its C terminus, it otherwise shares no similarity with known protein sequences. We carried out a structural characterization of recombinant juxtanodin in solution. Juxtanodin turned out to be intrinsically disordered, as evidenced by conventional and synchrotron radiation CD spectroscopy. Small-angle X-ray scattering indicated that juxtanodin is a monomeric, highly elongated, unfolded molecule. Ensemble optimization analysis of the data suggested also the presence of more compact forms of juxtanodin. The C terminus was a strict requirement for co-sedimentation of juxtanodin with microfilaments, but juxtanodin had only mild effects on actin polymerization. The disordered nature of juxtanodin may predict functions as a protein interaction hub, although F-actin is its only currently known binding partner. FAU - Ruskamo, Salla AU - Ruskamo S AD - Department of Biochemistry, University of Oulu, Oulu, Finland. FAU - Chukhlieb, Maryna AU - Chukhlieb M FAU - Vahokoski, Juha AU - Vahokoski J FAU - Bhargav, Saligram Prabhakar AU - Bhargav SP FAU - Liang, Fengyi AU - Liang F FAU - Kursula, Inari AU - Kursula I FAU - Kursula, Petri AU - Kursula P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121129 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (Actins) RN - 0 (Carrier Proteins) RN - 0 (F-actin-binding proteins) RN - 0 (Microfilament Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Solutions) RN - 0 (juxtanodin protein, rat) SB - IM MH - Actins/*chemistry/metabolism/ultrastructure MH - Algorithms MH - Amino Acid Sequence MH - Animals MH - Carrier Proteins/*chemistry/metabolism MH - Circular Dichroism MH - Microfilament Proteins/*chemistry/genetics/metabolism MH - Microscopy, Electron MH - Molecular Sequence Data MH - Muscle, Skeletal/metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Rats MH - Recombinant Proteins/*chemistry/metabolism MH - Scattering, Small Angle MH - Sequence Homology, Amino Acid MH - Software MH - Solutions/chemistry MH - Swine MH - X-Ray Diffraction PMC - PMC3509349 OID - NLM: PMC3509349 EDAT- 2012/12/01 06:00 MHDA- 2013/04/30 06:00 CRDT- 2012/12/01 06:00 PHST- 2012/08/17 [received] PHST- 2012/10/15 [accepted] PHST- 2012/11/29 [epublish] AID - 10.1038/srep00899 [doi] PST - ppublish SO - Sci Rep. 2012;2:899. doi: 10.1038/srep00899. Epub 2012 Nov 29. PMID- 18536007 OWN - NLM STAT- MEDLINE DA - 20081121 DCOM- 20081224 LR - 20131121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 73 IP - 4 DP - 2008 Dec TI - Mapping alpha-helical induced folding within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by site-directed spin-labeling EPR spectroscopy. PG - 973-88 LID - 10.1002/prot.22125 [doi] AB - Using site-directed spin-labeling EPR spectroscopy, we mapped the region of the intrinsically disordered C-terminal domain of measles virus nucleoprotein (N(TAIL)) that undergoes induced folding. In addition to four spin-labeled N(TAIL) variants (S407C, S488C, L496C, and V517C) (Morin et al. (2006), J Phys Chem 110: 20596-20608), 10 new single-site cysteine variants were designed, purified from E. coli, and spin-labeled. These 14 spin-labeled variants enabled us to map in detail the gain of rigidity of N(TAIL) in the presence of either the secondary structure stabilizer 2,2,2-trifluoroethanol or the C-terminal domain X (XD) of the viral phosphoprotein. Different regions of N(TAIL) were shown to contribute to a different extent to the binding to XD, while the mobility of the spin labels grafted at positions 407 and 460 was unaffected upon addition of XD; that of the spin labels grafted within the 488-502 and the 505-522 regions was severely and moderately reduced, respectively. Furthermore, EPR experiments in the presence of 30% sucrose allowed us to precisely map to residues 488-502, the N(TAIL) region undergoing alpha-helical folding. The mobility of the 488-502 region was found to be restrained even in the absence of the partner, a behavior that could be accounted for by the existence of a transiently populated folded state. Finally, we show that the restrained motion of the 505-522 region upon binding to XD is due to the alpha-helical transition occurring within the 488-502 region and not to a direct interaction with XD. FAU - Belle, Valerie AU - Belle V AD - Bioenergetique et Ingenierie des Proteines, UPR 9036 CNRS et Universite Aix-Marseille I et II, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 9, France. FAU - Rouger, Sabrina AU - Rouger S FAU - Costanzo, Stephanie AU - Costanzo S FAU - Liquiere, Elodie AU - Liquiere E FAU - Strancar, Janez AU - Strancar J FAU - Guigliarelli, Bruno AU - Guigliarelli B FAU - Fournel, Andre AU - Fournel A FAU - Longhi, Sonia AU - Longhi S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Mutant Proteins) RN - 0 (Nucleoproteins) RN - 0 (Spin Labels) RN - 0 (Viral Proteins) RN - 0 (nucleoprotein, Measles virus) RN - 57-50-1 (Sucrose) RN - 75-89-8 (Trifluoroethanol) RN - K848JZ4886 (Cysteine) SB - IM MH - Amino Acid Substitution MH - Circular Dichroism MH - Crystallography, X-Ray MH - Cysteine/genetics MH - Electron Spin Resonance Spectroscopy MH - Electrophoresis, Polyacrylamide Gel MH - Mutant Proteins/chemistry/isolation & purification/metabolism MH - Nucleoproteins/*chemistry/*metabolism MH - *Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - *Spin Labels MH - Sucrose MH - Temperature MH - Trifluoroethanol/chemistry MH - Viral Proteins/*chemistry/*metabolism EDAT- 2008/06/07 09:00 MHDA- 2008/12/25 09:00 CRDT- 2008/06/07 09:00 AID - 10.1002/prot.22125 [doi] PST - ppublish SO - Proteins. 2008 Dec;73(4):973-88. doi: 10.1002/prot.22125. PMID- 20405910 OWN - NLM STAT- MEDLINE DA - 20100518 DCOM- 20100527 LR - 20140905 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 20 DP - 2010 May 25 TI - Unique physical properties and interactions of the domains of methylated DNA binding protein 2. PG - 4395-410 LID - 10.1021/bi9019753 [doi] AB - Methylated DNA binding protein 2 (MeCP2) is a methyl CpG binding protein whose key role is the recognition of epigenetic information encoded in DNA methylation patterns. Mutation or misregulation of MeCP2 function leads to Rett syndrome as well as a variety of other autism spectrum disorders. Here, we have analyzed in detail the properties of six individually expressed human MeCP2 domains spanning the entire protein with emphasis on their interactions with each other, with DNA, and with nucleosomal arrays. Each domain contributes uniquely to the structure and function of the full-length protein. MeCP2 is approximately 60% unstructured, with nine interspersed alpha-molecular recognition features (alpha-MoRFs), which are polypeptide segments predicted to acquire secondary structure upon forming complexes with binding partners. Large increases in secondary structure content are induced in some of the isolated MeCP2 domains and in the full-length protein by binding to DNA. Interactions between some MeCP2 domains in cis and trans seen in our assays likely contribute to the structure and function of the intact protein. We also show that MeCP2 has two functional halves. The N-terminal portion contains the methylated DNA binding domain (MBD) and two highly disordered flanking domains that modulate MBD-mediated DNA binding. One of these flanking domains is also capable of autonomous DNA binding. In contrast, the C-terminal portion of the protein that harbors at least two independent DNA binding domains and a chromatin-specific binding domain is largely responsible for mediating nucleosomal array compaction and oligomerization. These findings led to new mechanistic and biochemical insights regarding the conformational modulations of this intrinsically disordered protein, and its context-dependent in vivo roles. FAU - Ghosh, Rajarshi P AU - Ghosh RP AD - Department of Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA. FAU - Nikitina, Tatiana AU - Nikitina T FAU - Horowitz-Scherer, Rachel A AU - Horowitz-Scherer RA FAU - Gierasch, Lila M AU - Gierasch LM FAU - Uversky, Vladimir N AU - Uversky VN FAU - Hite, Kristopher AU - Hite K FAU - Hansen, Jeffrey C AU - Hansen JC FAU - Woodcock, Christopher L AU - Woodcock CL LA - eng GR - DP1 OD000945/OD/NIH HHS/United States GR - DP1 OD000945-04/OD/NIH HHS/United States GR - GM027616/GM/NIGMS NIH HHS/United States GR - GM066834/GM/NIGMS NIH HHS/United States GR - GM070897/GM/NIGMS NIH HHS/United States GR - GM071714/GM/NIGMS NIH HHS/United States GR - LM007688/LM/NLM NIH HHS/United States GR - OD945/OD/NIH HHS/United States GR - R01 GM070897-04/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Chromatin) RN - 0 (MECP2 protein, human) RN - 0 (Methyl-CpG-Binding Protein 2) RN - 9007-49-2 (DNA) SB - IM MH - Binding Sites MH - Chromatin/metabolism MH - DNA/metabolism MH - Humans MH - Methyl-CpG-Binding Protein 2/*chemistry/*metabolism/physiology MH - Models, Molecular MH - Protein Binding/physiology MH - Protein Interaction Domains and Motifs/*physiology MH - Protein Stability MH - Protein Structure, Secondary MH - Protein Structure, Tertiary/physiology MH - Substrate Specificity MH - Temperature PMC - PMC2872689 MID - NIHMS199946 OID - NLM: NIHMS199946 OID - NLM: PMC2872689 EDAT- 2010/04/22 06:00 MHDA- 2010/05/28 06:00 CRDT- 2010/04/22 06:00 AID - 10.1021/bi9019753 [doi] PST - ppublish SO - Biochemistry. 2010 May 25;49(20):4395-410. doi: 10.1021/bi9019753. PMID- 25193139 OWN - NLM STAT- MEDLINE DA - 20141006 DCOM- 20150204 LR - 20150401 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 426 IP - 21 DP - 2014 Oct 23 TI - Characterization of the Grp94/OS-9 chaperone-lectin complex. PG - 3590-605 LID - 10.1016/j.jmb.2014.08.024 [doi] LID - S0022-2836(14)00469-0 [pii] AB - Grp94 is a macromolecular chaperone belonging to the hsp90 family and is the most abundant glycoprotein in the endoplasmic reticulum (ER) of mammals. In addition to its essential role in protein folding, Grp94 was proposed to participate in the ER-associated degradation quality control pathway by interacting with the lectin OS-9, a sensor for terminally misfolded proteins. To understand how OS-9 interacts with ER chaperone proteins, we mapped its interaction with Grp94. Glycosylation of the full-length Grp94 protein was essential for OS-9 binding, although deletion of the Grp94 N-terminal domain relieved this requirement suggesting that the effect was allosteric rather than direct. Although yeast OS-9 is composed of a well-established N-terminal mannose recognition homology lectin domain and a C-terminal dimerization domain, we find that the C-terminal domain of OS-9 in higher eukaryotes contains "mammalian-specific insets" that are specifically recognized by the middle and C-terminal domains of Grp94. Additionally, the Grp94 binding domain in OS-9 was found to be intrinsically disordered. The biochemical analysis of the interacting regions provides insight into the manner by which the two associate and it additionally hints at a plausible biological role for the Grp94/OS-9 complex. CI - Copyright (c) 2014 Elsevier Ltd. All rights reserved. FAU - Seidler, Paul M AU - Seidler PM AD - Department of Structural Biology, University at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA; Hauptman Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA. FAU - Shinsky, Stephen A AU - Shinsky SA AD - Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 766 Irving Aveenue, Syracuse, NY 13210, USA. FAU - Hong, Feng AU - Hong F AD - Department of Microbiology and Immunology, Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA. FAU - Li, Zihai AU - Li Z AD - Department of Microbiology and Immunology, Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, Charleston, SC 29425, USA. FAU - Cosgrove, Michael S AU - Cosgrove MS AD - Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 766 Irving Aveenue, Syracuse, NY 13210, USA. FAU - Gewirth, Daniel T AU - Gewirth DT AD - Department of Structural Biology, University at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA; Hauptman Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA. Electronic address: gewirth@hwi.buffalo.edu. LA - eng GR - R01 CA095130/CA/NCI NIH HHS/United States GR - R01-CA095130/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140903 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Lectins) RN - 0 (Membrane Glycoproteins) RN - 0 (Molecular Chaperones) RN - 0 (Neoplasm Proteins) RN - 0 (OS9 protein, human) RN - 0 (OS9 protein, rat) RN - 0 (endoplasmin) SB - IM MH - Allosteric Site MH - Animals MH - Cattle MH - Dogs MH - Escherichia coli/metabolism MH - Glycosylation MH - HEK293 Cells MH - Humans MH - Lectins/*chemistry/physiology MH - Membrane Glycoproteins/*chemistry/physiology MH - Molecular Chaperones/*chemistry MH - Neoplasm Proteins/*chemistry/physiology MH - Protein Binding MH - Protein Processing, Post-Translational MH - Protein Structure, Tertiary MH - Rats MH - Thermodynamics MH - Ultracentrifugation MH - Yeasts PMC - PMC4188734 MID - NIHMS625519 OID - NLM: NIHMS625519 [Available on 10/23/15] OID - NLM: PMC4188734 [Available on 10/23/15] OTO - NOTNLM OT - ER-associated degradation OT - Grp94 OT - Hsp90 OT - chaperone OT - intrinsically disordered protein EDAT- 2014/09/07 06:00 MHDA- 2015/02/05 06:00 CRDT- 2014/09/07 06:00 PMCR- 2015/10/23 00:00 PHST- 2014/07/29 [received] PHST- 2014/08/26 [accepted] PHST- 2014/09/03 [aheadofprint] AID - S0022-2836(14)00469-0 [pii] AID - 10.1016/j.jmb.2014.08.024 [doi] PST - ppublish SO - J Mol Biol. 2014 Oct 23;426(21):3590-605. doi: 10.1016/j.jmb.2014.08.024. Epub 2014 Sep 3. PMID- 22274962 OWN - NLM STAT- MEDLINE DA - 20120410 DCOM- 20120920 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 80 IP - 5 DP - 2012 May TI - The chaperone activity of alpha-synuclein: Utilizing deletion mutants to map its interaction with target proteins. PG - 1316-25 LID - 10.1002/prot.24028 [doi] AB - alpha-Synuclein is the principal component of the Lewy body deposits that are characteristic of Parkinson's disease. In vivo, and under physiological conditions in vitro, alpha-synuclein aggregates to form amyloid fibrils, a process that is likely to be associated with the development of Parkinson's disease. alpha-Synuclein also possesses chaperone activity to prevent the precipitation of amorphously aggregating target proteins, as demonstrated in vitro. alpha-Synuclein is an intrinsically disordered (i.e., unstructured) protein of 140 amino acids in length, and therefore studies on its fragments can be correlated directly to the functional role of these regions in the intact protein. In this study, the fragment containing residues 61-140 [alpha-syn(61-140)] was observed to be highly amyloidogenic and was as effective a chaperone in vitro as the full-length protein, while the N- and C-terminal fragments alpha-syn(1-60) and alpha-syn(96-140) had no intrinsic chaperone activity. Interestingly, full-length fibrillar alpha-synuclein had greater chaperone activity than nonfibrillar alpha-synuclein. It is concluded that the amyloidogenic NAC region (residues 61-95) contains the chaperone-binding site which is optimized for target protein binding as a result of its beta-sheet formation and/or ordered aggregation by alpha-synuclein. On the other hand, the first 60 residues of alpha-synuclein modulate the protein's chaperone-active site, while at the same time protecting alpha-synuclein from fibrillation. On its own, however, this fragment [alpha-syn(1-60)] had a tendency to aggregate amorphously. As a result of this study, the functional roles of the various regions of alpha-synuclein in its chaperone activity have been delineated. CI - Copyright (c) 2012 Wiley Periodicals, Inc. FAU - Rekas, Agata AU - Rekas A AD - National Deuteration Facility, Australian Nuclear Science and Technology Organization, PMB 1, Menai, NSW 2234, Australia. agata.rekas@ansto.gov.au FAU - Ahn, Keun Jae AU - Ahn KJ FAU - Kim, Jongsun AU - Kim J FAU - Carver, John A AU - Carver JA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120210 PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Amyloid) RN - 0 (Molecular Chaperones) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 0 (alpha-Synuclein) SB - IM MH - Amyloid/chemistry/genetics/metabolism MH - Binding Sites MH - Circular Dichroism MH - Humans MH - Light MH - Molecular Chaperones/metabolism MH - Peptide Fragments/chemistry/genetics/*metabolism MH - Protein Interaction Mapping/*methods MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Scattering, Radiation MH - Sequence Deletion MH - alpha-Synuclein/chemistry/genetics/*metabolism EDAT- 2012/01/26 06:00 MHDA- 2012/09/21 06:00 CRDT- 2012/01/26 06:00 PHST- 2011/10/27 [received] PHST- 2011/12/14 [revised] PHST- 2011/12/29 [accepted] PHST- 2012/02/10 [aheadofprint] AID - 10.1002/prot.24028 [doi] PST - ppublish SO - Proteins. 2012 May;80(5):1316-25. doi: 10.1002/prot.24028. Epub 2012 Feb 10. PMID- 19645507 OWN - NLM STAT- MEDLINE DA - 20090901 DCOM- 20090925 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 35 DP - 2009 Sep 8 TI - On the mechanism of nonspecific inhibitors of protein aggregation: dissecting the interactions of alpha-synuclein with Congo red and lacmoid. PG - 8322-34 LID - 10.1021/bi901285x [doi] AB - Increasing evidence links the misfolding and aberrant self-assembly of proteins with the molecular events that underlie a range of neurodegenerative diseases, yet the mechanistical details of these processes are still poorly understood. The fact that many of these proteins are intrinsically unstructured makes it particularly challenging to develop strategies for discovering small molecule inhibitors of their aggregation. We present here a broad biophysical approach that enables us to characterize the mechanisms of interaction between alpha-synuclein, a protein whose aggregation is closely connected with Parkinson's disease, and two small molecules, Congo red and Lacmoid, which inhibit its fibrillization. Both compounds are found to interact with the N-terminal and central regions of the monomeric protein although with different binding mechanisms and affinities. The differences can be attributed to the chemical nature of the compounds as well as their abilities to self-associate. We further show that alpha-synuclein binding and aggregation inhibition are mediated by small oligomeric species of the compounds that interact with distinct regions of the monomeric protein. These findings provide potential explanations of the nonspecific antiamyloid effect observed for these compounds as well as important mechanistical information for future drug discovery efforts targeting the misfolding and aggregation of intrinsically unstructured proteins. FAU - Lendel, Christofer AU - Lendel C AD - Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. FAU - Bertoncini, Carlos W AU - Bertoncini CW FAU - Cremades, Nunilo AU - Cremades N FAU - Waudby, Christopher A AU - Waudby CA FAU - Vendruscolo, Michele AU - Vendruscolo M FAU - Dobson, Christopher M AU - Dobson CM FAU - Schenk, Dale AU - Schenk D FAU - Christodoulou, John AU - Christodoulou J FAU - Toth, Gergely AU - Toth G LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Small Molecule Libraries) RN - 0 (alpha-Synuclein) RN - 3U05FHG59S (Congo Red) SB - IM MH - Congo Red/*metabolism MH - Humans MH - Microscopy, Atomic Force MH - Molecular Sequence Data MH - Molecular Structure MH - Neurodegenerative Diseases/*metabolism MH - Parkinson Disease/metabolism MH - Protein Conformation MH - Protein Folding MH - Signal Transduction MH - Small Molecule Libraries/metabolism MH - Spectrophotometry, Ultraviolet MH - alpha-Synuclein/*chemistry/metabolism EDAT- 2009/08/04 09:00 MHDA- 2009/09/26 06:00 CRDT- 2009/08/04 09:00 AID - 10.1021/bi901285x [doi] PST - ppublish SO - Biochemistry. 2009 Sep 8;48(35):8322-34. doi: 10.1021/bi901285x. PMID- 14559966 OWN - NLM STAT- MEDLINE DA - 20031029 DCOM- 20040105 LR - 20140610 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 100 IP - 22 DP - 2003 Oct 28 TI - Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-Met and its complex with the microbial alkaloid K-252a. PG - 12654-9 AB - The protooncogene c-met codes for the hepatocyte growth factor receptor tyrosine kinase. Binding of its ligand, hepatocyte growth factor/scatter factor, stimulates receptor autophosphorylation, which leads to pleiotropic downstream signaling events in epithelial cells, including cell growth, motility, and invasion. These events are mediated by interaction of cytoplasmic effectors, generally through Src homology 2 (SH2) domains, with two phosphotyrosine-containing sequence motifs in the unique C-terminal tail of c-Met (supersite). There is a strong link between aberrant c-Met activity and oncogenesis, which makes this kinase an important cancer drug target. The furanosylated indolocarbazole K-252a belongs to a family of microbial alkaloids that also includes staurosporine. It was recently shown to be a potent inhibitor of c-Met. Here we report the crystal structures of an unphosphorylated c-Met kinase domain harboring a human cancer mutation and its complex with K-252a at 1.8-A resolution. The structure follows the well established architecture of protein kinases. It adopts a unique, inhibitory conformation of the activation loop, a catalytically noncompetent orientation of helix alphaC, and reveals the complete C-terminal docking site. The first SH2-binding motif (1349YVHV) adopts an extended conformation, whereas the second motif (1356YVNV), a binding site for Grb2-SH2, folds as a type II Beta-turn. The intermediate portion of the supersite (1353NATY) assumes a type I Beta-turn conformation as in an Shc-phosphotyrosine binding domain peptide complex. K-252a is bound in the adenosine pocket with an analogous binding mode to those observed in previously reported structures of protein kinases in complex with staurosporine. FAU - Schiering, Nikolaus AU - Schiering N AD - Departments of Chemistry and Biology, Pharmacia S.p.A., Discovery Research, Viale Pasteur 10, 20014 Nerviano (MI), Italy. nikolaus.schiering@pharma.novartis.com FAU - Knapp, Stefan AU - Knapp S FAU - Marconi, Marina AU - Marconi M FAU - Flocco, Maria M AU - Flocco MM FAU - Cui, Jean AU - Cui J FAU - Perego, Rita AU - Perego R FAU - Rusconi, Luisa AU - Rusconi L FAU - Cristiani, Cinzia AU - Cristiani C LA - eng SI - PDB/1R0P SI - PDB/1R1W PT - Journal Article DEP - 20031014 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Carbazoles) RN - 0 (Enzyme Inhibitors) RN - 0 (Indole Alkaloids) RN - 0 (Recombinant Proteins) RN - 97161-97-2 (staurosporine aglycone) RN - AE28F7PNPL (Methionine) RN - EC 2.7.10.1 (Protein-Tyrosine Kinases) RN - EC 2.7.10.1 (Proto-Oncogene Proteins c-met) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Carbazoles/*chemistry MH - Cloning, Molecular MH - Crystallography, X-Ray/methods MH - Enzyme Inhibitors/*chemistry MH - Indole Alkaloids MH - Methionine MH - Models, Molecular MH - Protein Conformation MH - Protein-Tyrosine Kinases/antagonists & inhibitors/*chemistry MH - Proto-Oncogene Proteins c-met/*chemistry MH - Recombinant Proteins/chemistry MH - Sensitivity and Specificity PMC - PMC240673 OID - NLM: PMC240673 EDAT- 2003/10/16 05:00 MHDA- 2004/01/06 05:00 CRDT- 2003/10/16 05:00 PHST- 2003/10/14 [aheadofprint] AID - 10.1073/pnas.1734128100 [doi] AID - 1734128100 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12654-9. Epub 2003 Oct 14. PMID- 21222437 OWN - NLM STAT- MEDLINE DA - 20110215 DCOM- 20110331 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 50 IP - 7 DP - 2011 Feb 22 TI - Light-induced movement of the LOV2 domain in an Asp720Asn mutant LOV2-kinase fragment of Arabidopsis phototropin 2. PG - 1174-83 LID - 10.1021/bi101689b [doi] AB - Phototropin, a blue-light receptor protein of plants, triggers phototropic responses, chloroplast relocation, and opening of stomata to maximize the efficiency of photosynthesis. Phototropin is composed of two light-oxygen-voltage sensing domains (LOV1 and LOV2) that absorb blue light and a serine/theroine kinase domain responsible for light-dependent autophosphorylation leading to cellular signaling cascades. Although the light-activated LOV2 domain is primarily responsible for subsequent activation of the kinase domain, it is unclear how conformational changes in the former transmit to the latter. To understand this molecular mechanism in Arabidopsis phototropin 2, we performed small-angle X-ray scattering analysis on a fragment composed of the LOV2 and kinase domains, which contained an Asp720Asn mutation that led to an absence of ATP binding activity. The scattering data were collected up to a resolution of 25 A. The apparent molecular weight of the fragment estimated from scattering intensities demonstrated that the fragment existed in a monomeric form in solution. The fragment exhibited photoreversible changes in the scattering profiles, and the radii of gyration under dark and blue-light irradiation conditions were 32.4 and 34.8 A, respectively. In the dark, the molecular shape restored from the scattering profile appeared as an elongated shape of 110 A in length and 45 A in width. The homology modeled LOV2 and kinase domains could be fitted to the molecular shape and appeared to make slight contact. However, under blue-light irradiation, a more extended molecular shape was observed. The changes in the molecular shape and radius of gyration were interpreted as a light-dependent positional shift of the LOV2 domain of approximately 13 A from the kinase domain. Because the region connecting the LOV2 and kinase domains was categorized as a naturally unfolded polypeptide, we propose that the light-activated LOV2 domain triggers conformational changes in the linker region to separate the LOV2 and kinase domains. FAU - Takayama, Yuki AU - Takayama Y AD - Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1Hiyoshi, Kohoku-ku, Kanagawa 223-8522, Japan. FAU - Nakasako, Masayoshi AU - Nakasako M FAU - Okajima, Koji AU - Okajima K FAU - Iwata, Aya AU - Iwata A FAU - Kashojiya, Sachiko AU - Kashojiya S FAU - Matsui, Yuka AU - Matsui Y FAU - Tokutomi, Satoru AU - Tokutomi S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110128 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Arabidopsis Proteins) RN - 0 (Mutant Proteins) RN - 0 (PHOT2 protein, Arabidopsis) RN - 0 (Peptide Fragments) RN - 30KYC7MIAI (Aspartic Acid) RN - 7006-34-0 (Asparagine) RN - EC 2.7.- (Phosphotransferases) SB - IM MH - Amino Acid Substitution/physiology MH - Arabidopsis/*enzymology/genetics/metabolism MH - Arabidopsis Proteins/*chemistry/genetics/*metabolism/physiology MH - Asparagine/genetics MH - Aspartic Acid/genetics MH - *Light MH - Models, Biological MH - Models, Molecular MH - Movement/*radiation effects MH - Mutant Proteins/chemistry/metabolism/physiology MH - Peptide Fragments/chemistry/genetics/metabolism/physiology MH - Phosphotransferases/chemistry/genetics/metabolism/physiology MH - Protein Conformation/radiation effects MH - Protein Folding/*radiation effects MH - Protein Structure, Tertiary/genetics/physiology/radiation effects EDAT- 2011/01/13 06:00 MHDA- 2011/04/01 06:00 CRDT- 2011/01/13 06:00 PHST- 2011/01/28 [aheadofprint] AID - 10.1021/bi101689b [doi] PST - ppublish SO - Biochemistry. 2011 Feb 22;50(7):1174-83. doi: 10.1021/bi101689b. Epub 2011 Jan 28. PMID- 24675874 OWN - NLM STAT- MEDLINE DA - 20140328 DCOM- 20141104 LR - 20141111 IS - 1553-7374 (Electronic) IS - 1553-7366 (Linking) VI - 10 IP - 3 DP - 2014 Mar TI - Structural and functional characterization of a complex between the acidic transactivation domain of EBNA2 and the Tfb1/p62 subunit of TFIIH. PG - e1004042 LID - 10.1371/journal.ppat.1004042 [doi] AB - Infection with the Epstein-Barr virus (EBV) can lead to a number of human diseases including Hodgkin's and Burkitt's lymphomas. The development of these EBV-linked diseases is associated with the presence of nine viral latent proteins, including the nuclear antigen 2 (EBNA2). The EBNA2 protein plays a crucial role in EBV infection through its ability to activate transcription of both host and viral genes. As part of this function, EBNA2 associates with several host transcriptional regulatory proteins, including the Tfb1/p62 (yeast/human) subunit of the general transcription factor IIH (TFIIH) and the histone acetyltransferase CBP(CREB-binding protein)/p300, through interactions with its C-terminal transactivation domain (TAD). In this manuscript, we examine the interaction of the acidic TAD of EBNA2 (residues 431-487) with the Tfb1/p62 subunit of TFIIH and CBP/p300 using nuclear magnetic resonance (NMR) spectroscopy, isothermal titration calorimeter (ITC) and transactivation studies in yeast. NMR studies show that the TAD of EBNA2 binds to the pleckstrin homology (PH) domain of Tfb1 (Tfb1PH) and that residues 448-471 (EBNA2(4)(4)(8)(-)(4)(7)(1)) are necessary and sufficient for this interaction. NMR structural characterization of a Tfb1PH-EBNA2(4)(4)(8)(-)(4)(7)(1) complex demonstrates that the intrinsically disordered TAD of EBNA2 forms a 9-residue alpha-helix in complex with Tfb1PH. Within this helix, three hydrophobic amino acids (Trp458, Ile461 and Phe462) make a series of important interactions with Tfb1PH and their importance is validated in ITC and transactivation studies using mutants of EBNA2. In addition, NMR studies indicate that the same region of EBNA2 is also required for binding to the KIX domain of CBP/p300. This study provides an atomic level description of interactions involving the TAD of EBNA2 with target host proteins. In addition, comparison of the Tfb1PH-EBNA2(4)(4)(8)(-)(4)(7)(1) complex with structures of the TAD of p53 and VP16 bound to Tfb1PH highlights the versatility of intrinsically disordered acidic TADs in recognizing common target host proteins. FAU - Chabot, Philippe R AU - Chabot PR AD - Departement de Biochimie et Medicine Moleculaire, Universite de Montreal, Succursale Centre-Ville, Montreal, Quebec, Canada. FAU - Raiola, Luca AU - Raiola L AD - Departement de Biochimie et Medicine Moleculaire, Universite de Montreal, Succursale Centre-Ville, Montreal, Quebec, Canada. FAU - Lussier-Price, Mathieu AU - Lussier-Price M AD - Departement de Biochimie et Medicine Moleculaire, Universite de Montreal, Succursale Centre-Ville, Montreal, Quebec, Canada. FAU - Morse, Thomas AU - Morse T AD - Departement de Biochimie et Medicine Moleculaire, Universite de Montreal, Succursale Centre-Ville, Montreal, Quebec, Canada. FAU - Arseneault, Genevieve AU - Arseneault G AD - Departement de Biochimie et Medicine Moleculaire, Universite de Montreal, Succursale Centre-Ville, Montreal, Quebec, Canada. FAU - Archambault, Jacques AU - Archambault J AD - Departement de Biochimie et Medicine Moleculaire, Universite de Montreal, Succursale Centre-Ville, Montreal, Quebec, Canada; Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada. FAU - Omichinski, James G AU - Omichinski JG AD - Departement de Biochimie et Medicine Moleculaire, Universite de Montreal, Succursale Centre-Ville, Montreal, Quebec, Canada. LA - eng GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140327 PL - United States TA - PLoS Pathog JT - PLoS pathogens JID - 101238921 RN - 0 (EBNA-2 protein, Human herpesvirus 4) RN - 0 (Epstein-Barr Virus Nuclear Antigens) RN - 0 (Viral Proteins) RN - 148710-81-0 (Transcription Factor TFIIH) SB - IM MH - Animals MH - Epstein-Barr Virus Infections/*metabolism MH - Epstein-Barr Virus Nuclear Antigens/chemistry/*metabolism MH - Herpesvirus 4, Human/*metabolism MH - Host-Pathogen Interactions/*physiology MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Tertiary MH - Structure-Activity Relationship MH - Transcription Factor TFIIH/chemistry/*metabolism MH - Transcriptional Activation MH - Viral Proteins/chemistry/*metabolism PMC - PMC3968163 OID - NLM: PMC3968163 EDAT- 2014/03/29 06:00 MHDA- 2014/11/05 06:00 CRDT- 2014/03/29 06:00 PHST- 2014/03 [ecollection] PHST- 2013/10/31 [received] PHST- 2014/02/15 [accepted] PHST- 2014/03/27 [epublish] AID - 10.1371/journal.ppat.1004042 [doi] AID - PPATHOGENS-D-13-02816 [pii] PST - epublish SO - PLoS Pathog. 2014 Mar 27;10(3):e1004042. doi: 10.1371/journal.ppat.1004042. eCollection 2014 Mar. PMID- 19226187 OWN - NLM STAT- MEDLINE DA - 20090226 DCOM- 20090423 LR - 20140901 IS - 1545-7885 (Electronic) IS - 1544-9173 (Linking) VI - 7 IP - 2 DP - 2009 Feb 17 TI - Structural polymorphism of 441-residue tau at single residue resolution. PG - e34 LID - 10.1371/journal.pbio.1000034 [doi] AB - Alzheimer disease is characterized by abnormal protein deposits in the brain, such as extracellular amyloid plaques and intracellular neurofibrillary tangles. The tangles are made of a protein called tau comprising 441 residues in its longest isoform. Tau belongs to the class of natively unfolded proteins, binds to and stabilizes microtubules, and partially folds into an ordered beta-structure during aggregation to Alzheimer paired helical filaments (PHFs). Here we show that it is possible to overcome the size limitations that have traditionally hampered detailed nuclear magnetic resonance (NMR) spectroscopy studies of such large nonglobular proteins. This is achieved using optimal NMR pulse sequences and matching of chemical shifts from smaller segments in a divide and conquer strategy. The methodology reveals that 441-residue tau is highly dynamic in solution with a distinct domain character and an intricate network of transient long-range contacts important for pathogenic aggregation. Moreover, the single-residue view provided by the NMR analysis reveals unique insights into the interaction of tau with microtubules. Our results establish that NMR spectroscopy can provide detailed insight into the structural polymorphism of very large nonglobular proteins. FAU - Mukrasch, Marco D AU - Mukrasch MD AD - Department for Nuclear Magnetic Resonance (NMR)-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany. FAU - Bibow, Stefan AU - Bibow S FAU - Korukottu, Jegannath AU - Korukottu J FAU - Jeganathan, Sadasivam AU - Jeganathan S FAU - Biernat, Jacek AU - Biernat J FAU - Griesinger, Christian AU - Griesinger C FAU - Mandelkow, Eckhard AU - Mandelkow E FAU - Zweckstetter, Markus AU - Zweckstetter M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - PLoS Biol JT - PLoS biology JID - 101183755 RN - 0 (MAPT protein, human) RN - 0 (Protein Isoforms) RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/*genetics/metabolism MH - Amino Acid Sequence MH - Animals MH - Axons/metabolism MH - Humans MH - Microtubules/chemistry/metabolism MH - Molecular Sequence Data MH - Neurofibrillary Tangles/genetics/metabolism MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Protein Conformation MH - Protein Folding MH - Protein Isoforms MH - Protein Structure, Secondary MH - Swine MH - tau Proteins/*chemistry/genetics/metabolism PMC - PMC2642882 OID - NLM: PMC2642882 EDAT- 2009/02/20 09:00 MHDA- 2009/04/25 09:00 CRDT- 2009/02/20 09:00 PHST- 2008/05/21 [received] PHST- 2009/01/07 [accepted] AID - 08-PLBI-RA-2022 [pii] AID - 10.1371/journal.pbio.1000034 [doi] PST - ppublish SO - PLoS Biol. 2009 Feb 17;7(2):e34. doi: 10.1371/journal.pbio.1000034. PMID- 12235146 OWN - NLM STAT- MEDLINE DA - 20021126 DCOM- 20030108 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 277 IP - 48 DP - 2002 Nov 29 TI - Role of the C-terminal extensions of alpha-crystallins. Swapping the C-terminal extension of alpha-crystallin to alphaB-crystallin results in enhanced chaperone activity. PG - 45821-8 AB - Several small heat shock proteins contain a well conserved alpha-crystallin domain, flanked by an N-terminal domain and a C-terminal extension, both of which vary in length and sequence. The structural and functional role of the C-terminal extension of small heat shock proteins, particularly of alphaA- and alphaB-crystallins, is not well understood. We have swapped the C-terminal extensions between alphaA- and alphaB-crystallins and generated two novel chimeric proteins, alphaABc and alphaBAc. We have investigated the domain-swapped chimeras for structural and functional alterations. We have used thermal and non-thermal models of protein aggregation and found that the chimeric alphaB with the C-terminal extension of alphaA-crystallin, alphaBAc, exhibits dramatically enhanced chaperone-like activity. Interestingly, however, the chimeric alphaA with the C-terminal extension of alphaB-crystallin, alphaABc, has almost lost its activity. Pyrene solubilization and bis-1-anilino-8-naphthalenesulfonate binding studies show that alphaBAc exhibits more solvent-exposed hydrophobic pockets than alphaA, alphaB, or alphaABc. Significant tertiary structural changes are revealed by tryptophan fluorescence and near-UV CD studies upon swapping the C-terminal extensions. The far-UV CD spectrum of alphaBAc differs from that of alphaB-crystallin whereas that of alphaABc overlaps with that of alphaA-crystallin. Gel filtration chromatography shows alteration in the size of the proteins upon swapping the C-terminal extensions. Our study demonstrates that the unstructured C-terminal extensions play a crucial role in the structure and chaperone activity, in addition to generally believed electrostatic "solubilizer" function. FAU - Pasta, Saloni Yatin AU - Pasta SY AD - Centre for Cellular and Molecular Biology, Hyderabad, Andhrapradesh 500 007, India. FAU - Raman, Bakthisaran AU - Raman B FAU - Ramakrishna, Tangirala AU - Ramakrishna T FAU - Rao, Ch Mohan AU - Rao ChM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20020915 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Anilino Naphthalenesulfonates) RN - 0 (DNA Primers) RN - 0 (Fluorescent Dyes) RN - 0 (Molecular Chaperones) RN - 0 (alpha-Crystallins) RN - 82-76-8 (1-anilino-8-naphthalenesulfonate) SB - IM MH - Amino Acid Sequence MH - Anilino Naphthalenesulfonates/chemistry MH - Base Sequence MH - Chromatography, Gel MH - Circular Dichroism MH - DNA Primers MH - Fluorescent Dyes/chemistry MH - Molecular Chaperones/chemistry/*metabolism MH - Molecular Sequence Data MH - Sequence Homology, Amino Acid MH - Spectrometry, Fluorescence MH - Spectrophotometry, Ultraviolet MH - alpha-Crystallins/chemistry/*metabolism EDAT- 2002/09/18 10:00 MHDA- 2003/01/09 04:00 CRDT- 2002/09/18 10:00 PHST- 2002/09/15 [aheadofprint] AID - 10.1074/jbc.M206499200 [doi] AID - M206499200 [pii] PST - ppublish SO - J Biol Chem. 2002 Nov 29;277(48):45821-8. Epub 2002 Sep 15. PMID- 21653825 OWN - NLM STAT- MEDLINE DA - 20110729 DCOM- 20111228 LR - 20141022 IS - 1939-4586 (Electronic) IS - 1059-1524 (Linking) VI - 22 IP - 15 DP - 2011 Aug 1 TI - The yeast kinase Yck2 has a tripartite palmitoylation signal. PG - 2702-15 LID - 10.1091/mbc.E11-02-0115 [doi] AB - The yeast kinase Yck2 tethers to the cytoplasmic surface of the plasma membrane through dual palmitoylation of its C-terminal Cys-Cys dipeptide, mediated by the Golgi-localized palmitoyl-transferase Akr1. Here, the Yck2 palmitoylation signal is found to consist of three parts: 1) a 10-residue-long, conserved C-terminal peptide (CCTP) that includes the C-terminal Cys-Cys dipeptide; 2) the kinase catalytic domain (KD); and mapping between these two elements; and 3) a 176-residue-long, poorly conserved, glutamine-rich sequence. The CCTP, which contains the C-terminal cysteines as well as an important Phe-Phe dipeptide, likely serves as an Akr1 recognition element, because CCTP mutations disrupt palmitoylation within a purified in vitro palmitoylation system. The KD contribution appears to be complex with roles for both KD activity (e.g., Yck2-mediated phosphorylation) and structure (e.g., Akr1 recognition elements). KD and CCTP mutations are strongly synergistic, suggesting that, like the CCTP, the KD may also participate at the Yck2-Akr1 recognition step. The long, glutamine-rich domain, which is located between the KD and CCTP, is predicted to be intrinsically disordered and may function as a flexible, interdomain linker, allowing a coupled interaction of the KD and CCTP with Akr1. Multipart palmitoylation signals may prove to be a general feature of this large class of palmitoylation substrates. These soluble proteins have no clear means of accessing membranes and thus may require active capture out of the cytoplasm for palmitoylation by their membrane-localized transferases. FAU - Roth, Amy F AU - Roth AF AD - Department of Pharmacology, Wayne State University, Detroit, MI 48201, USA. FAU - Papanayotou, Irene AU - Papanayotou I FAU - Davis, Nicholas G AU - Davis NG LA - eng GR - P30CA22453/CA/NCI NIH HHS/United States GR - R01 GM65525/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20110608 PL - United States TA - Mol Biol Cell JT - Molecular biology of the cell JID - 9201390 RN - 0 (Dipeptides) RN - 0 (Oligopeptides) RN - 0 (Protein Sorting Signals) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 18048-87-8 (cysteinylcysteine) RN - 2577-40-4 (phenylalanylphenylalanine) RN - EC 2.3.- (Acyltransferases) RN - EC 2.3.1.- (AKR1 protein, S cerevisiae) RN - EC 2.7.11.1 (Casein Kinase I) RN - EC 2.7.11.1 (YCK2 protein, S cerevisiae) SB - IM MH - Acyltransferases/genetics/*metabolism MH - Casein Kinase I/chemistry/genetics/*metabolism MH - Catalytic Domain MH - Cell Membrane/*metabolism MH - Cloning, Molecular MH - Cytoplasm/*metabolism MH - Dipeptides/chemistry/metabolism MH - Escherichia coli MH - Lipoylation MH - Mutation MH - Oligopeptides/chemistry/metabolism MH - Phosphorylation MH - Plasmids MH - Protein Binding MH - *Protein Interaction Domains and Motifs/genetics MH - Protein Sorting Signals MH - Protein Transport MH - Recombinant Proteins/chemistry/genetics/*metabolism MH - Saccharomyces cerevisiae/genetics/*metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism MH - Signal Transduction/genetics MH - Transformation, Bacterial PMC - PMC3145546 OID - NLM: PMC3145546 EDAT- 2011/06/10 06:00 MHDA- 2011/12/29 06:00 CRDT- 2011/06/10 06:00 PHST- 2011/06/08 [aheadofprint] AID - mbc.E11-02-0115 [pii] AID - 10.1091/mbc.E11-02-0115 [doi] PST - ppublish SO - Mol Biol Cell. 2011 Aug 1;22(15):2702-15. doi: 10.1091/mbc.E11-02-0115. Epub 2011 Jun 8. PMID- 18616282 OWN - NLM STAT- MEDLINE DA - 20080729 DCOM- 20080910 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 31 DP - 2008 Aug 5 TI - Brucella abortus MFP: a trimeric coiled-coil protein with membrane fusogenic activity. PG - 8165-75 LID - 10.1021/bi800462y [doi] AB - The bacterial genus Brucella consists of a group of facultative intracellular pathogens which produces abortion and infertility in animals and a chronic debilitating febrile illness in humans. BMFP is a basic protein of Brucella abortus that belongs to a highly conserved group of homologue proteins of unknown structure and function in proteobacteria (COG2960). In this study, we report the structural and biochemical characterization of this protein. We found that BMFP has two structural domains: a carboxyl-terminal coiled-coil domain through which the protein self-associates as a trimer and a natively disordered amino-terminal domain which has propensity to adopt an amphipathic alpha-helical structure. This natively unfolded domain undergoes a structural rearrangement from unfolded to alpha-helix in the presence of high ionic strength, acidic pH, detergents, and phospholipid vesicles. Moreover, we demonstrated that the interaction of BMFP with phospholipid vesicles promotes in vitro membrane fusion. These results contribute to the elucidation of the structural and functional properties of this protein and its homologues present in most proteobacteria. FAU - Carrica, Mariela del Carmen AU - Carrica Mdel C AD - Instituto de Biotecnologia, CICVyA, INTA, Los reseros y las cabanas s/n, Castelar, Buenos Aires, Agentina. carricamariela@yahoo.com.ar FAU - Craig, Patricio Oliver AU - Craig PO FAU - Alonso, Silvia del Valle AU - Alonso Sdel V FAU - Goldbaum, Fernando Alberto AU - Goldbaum FA FAU - Cravero, Silvio Lorenzo AU - Cravero SL LA - eng GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080711 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (Liposomes) RN - 0 (Membrane Lipids) RN - 0 (Phospholipids) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/chemistry/genetics/*metabolism MH - Brucella abortus/genetics/*metabolism MH - Circular Dichroism MH - Dimerization MH - Liposomes/chemistry MH - Membrane Fusion MH - Membrane Lipids/chemistry/*metabolism MH - Models, Biological MH - Molecular Sequence Data MH - Molecular Weight MH - Phospholipids/chemistry/*metabolism MH - Polymerase Chain Reaction MH - Protein Binding MH - Protein Conformation MH - Sequence Homology, Amino Acid MH - Spectrometry, Fluorescence EDAT- 2008/07/12 09:00 MHDA- 2008/09/11 09:00 CRDT- 2008/07/12 09:00 PHST- 2008/07/11 [aheadofprint] AID - 10.1021/bi800462y [doi] PST - ppublish SO - Biochemistry. 2008 Aug 5;47(31):8165-75. doi: 10.1021/bi800462y. Epub 2008 Jul 11. PMID- 19838685 OWN - NLM STAT- MEDLINE DA - 20100121 DCOM- 20100225 IS - 1618-2650 (Electronic) VI - 395 IP - 8 DP - 2009 Dec TI - Characterization, stoichiometry, and stability of salivary protein-tannin complexes by ESI-MS and ESI-MS/MS. PG - 2535-45 LID - 10.1007/s00216-009-3180-3 [doi] AB - Numerous protein-polyphenol interactions occur in biological and food domains particularly involving proline-rich proteins, which are representative of the intrinsically unstructured protein group (IUP). Noncovalent protein-ligand complexes are readily detected by electrospray ionization mass spectrometry (ESI-MS), which also gives access to ligand binding stoichiometry. Surprisingly, the study of interactions between polyphenolic molecules and proteins is still an area where ESI-MS has poorly benefited, whereas it has been extensively applied to the detection of noncovalent complexes. Electrospray ionization mass spectrometry has been applied to the detection and the characterization of the complexes formed between tannins and a human salivary proline-rich protein (PRP), namely IB5. The study of the complex stability was achieved by low-energy collision-induced dissociation (CID) measurements, which are commonly implemented using triple quadrupole, hybrid quadrupole time-of-flight, or ion trap instruments. Complexes composed of IB5 bound to a model polyphenol EgCG have been detected by ESI-MS and further analyzed by MS/MS. Mild ESI interface conditions allowed us to observe intact noncovalent PRP-tannin complexes with stoichiometries ranging from 1:1 to 1:5. Thus, ESI-MS shows its efficiency for (1) the study of PRP-tannin interactions, (2) the determination of stoichiometry, and (3) the study of complex stability. We were able to establish unambiguously both their stoichiometries and their overall subunit architecture via tandem mass spectrometry and solution disruption experiments. Our results prove that IB5.EgCG complexes are maintained intact in the gas phase. FAU - Canon, Francis AU - Canon F AD - UMR 1083 Sciences Pour l'Oenologie, Polyphenol Interaction Research Group, INRA, Bat 28, 2 place Viala, F-34060, Montpellier, France. FAU - Pate, Franck AU - Pate F FAU - Meudec, Emmanuelle AU - Meudec E FAU - Marlin, Therese AU - Marlin T FAU - Cheynier, Veronique AU - Cheynier V FAU - Giuliani, Alexandre AU - Giuliani A FAU - Sarni-Manchado, Pascale AU - Sarni-Manchado P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091018 PL - Germany TA - Anal Bioanal Chem JT - Analytical and bioanalytical chemistry JID - 101134327 RN - 0 (Salivary Proteins and Peptides) RN - 0 (Tannins) SB - IM MH - Amino Acid Sequence MH - Humans MH - Molecular Sequence Data MH - Proline-Rich Protein Domains MH - Salivary Proteins and Peptides/*chemistry MH - Spectrometry, Mass, Electrospray Ionization/*methods MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods MH - Tannins/*chemistry EDAT- 2009/10/20 06:00 MHDA- 2010/02/26 06:00 CRDT- 2009/10/20 06:00 PHST- 2009/06/09 [received] PHST- 2009/09/21 [accepted] PHST- 2009/09/16 [revised] PHST- 2009/10/18 [aheadofprint] AID - 10.1007/s00216-009-3180-3 [doi] PST - ppublish SO - Anal Bioanal Chem. 2009 Dec;395(8):2535-45. doi: 10.1007/s00216-009-3180-3. Epub 2009 Oct 18. PMID- 24778935 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20140429 DCOM- 20140429 LR - 20150327 IS - 2162-4046 (Print) IS - 2162-4046 (Linking) VI - 2 IP - 3 DP - 2013 Jul 1 TI - The SAS-5 N-terminal domain is a tetramer, with implications for centriole assembly in C. elegans. PG - e25214 LID - 10.4161/worm.25214 [doi] AB - The centriole is a conserved microtubule-based organelle essential for both centrosome formation and cilium biogenesis. It has a unique 9-fold symmetry and its assembly is governed by at least five component proteins (SPD-2, ZYG-1, SAS-5, SAS-6 and SAS-4), which are recruited in a hierarchical order. Recently published structural studies of the SAS-6 N-terminal domain have greatly advanced our understanding of the mechanisms of centriole assembly. However, it remains unclear how the weak interaction between the SAS-6 N-terminal head groups could drive the assembly of a closed ring-like structure, and what determines the stacking of multiple rings on top one another in centriole duplication. We recently reported that SAS-5 binds specifically to a very narrow region of the SAS-6 central coiled coil through its C-terminal domain (CTD, residues 391-404). Here, we further demonstrate by both static light scattering and small angle X-ray scattering that the SAS-5 N-terminal domain (NTD, residues 1-260) forms a tetramer. Specifically, we found that the tetramer is formed by SAS-5 residues 82-260, whereas residues 1-81 are intrinsically disordered. Taking these results together, we propose a working model for SAS-5-mediated assembly of the multi-layered central tube structure. FAU - Shimanovskaya, Ekaterina AU - Shimanovskaya E AD - Max F. Perutz Laboratories; Medical University of Vienna; Vienna, Austria. FAU - Qiao, Renping AU - Qiao R AD - Max F. Perutz Laboratories; Medical University of Vienna; Vienna, Austria. FAU - Lesigang, Johannes AU - Lesigang J AD - Max F. Perutz Laboratories; Medical University of Vienna; Vienna, Austria. FAU - Dong, Gang AU - Dong G AD - Max F. Perutz Laboratories; Medical University of Vienna; Vienna, Austria. LA - eng GR - P 23440-B20/Austrian Science Fund FWF/Austria PT - Journal Article DEP - 20130531 PL - United States TA - Worm JT - Worm JID - 101591366 PMC - PMC3875647 MID - EMS62458 OID - NLM: EMS62458 OID - NLM: PMC3875647 OTO - NOTNLM OT - SAS-5 OT - SAS-6 OT - centriole OT - protein interaction EDAT- 2014/04/30 06:00 MHDA- 2014/04/30 06:01 CRDT- 2014/04/30 06:00 PHST- 2013/02/22 [received] PHST- 2013/05/05 [revised] PHST- 2013/05/29 [accepted] PHST- 2013/05/31 [epublish] AID - 10.4161/worm.25214 [doi] AID - 2012WORM095R [pii] PST - ppublish SO - Worm. 2013 Jul 1;2(3):e25214. doi: 10.4161/worm.25214. Epub 2013 May 31. PMID- 15994560 OWN - NLM STAT- MEDLINE DA - 20050704 DCOM- 20050715 LR - 20101118 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 309 IP - 5731 DP - 2005 Jul 1 TI - Variable control of Ets-1 DNA binding by multiple phosphates in an unstructured region. PG - 142-5 AB - Cell signaling that culminates in posttranslational modifications directs protein activity. Here we report how multiple Ca2+-dependent phosphorylation sites within the transcription activator Ets-1 act additively to produce graded DNA binding affinity. Nuclear magnetic resonance spectroscopic analyses show that phosphorylation shifts Ets-1 from a dynamic conformation poised to bind DNA to a well-folded inhibited state. These phosphates lie in an unstructured flexible region that functions as the allosteric effector of autoinhibition. Variable phosphorylation thus serves as a "rheostat" for cell signaling to fine-tune transcription at the level of DNA binding. FAU - Pufall, Miles A AU - Pufall MA AD - Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, UT 84112-5550, USA. FAU - Lee, Gregory M AU - Lee GM FAU - Nelson, Mary L AU - Nelson ML FAU - Kang, Hyun-Seo AU - Kang HS FAU - Velyvis, Algirdas AU - Velyvis A FAU - Kay, Lewis E AU - Kay LE FAU - McIntosh, Lawrence P AU - McIntosh LP FAU - Graves, Barbara J AU - Graves BJ LA - eng GR - GM08537/GM/NIGMS NIH HHS/United States GR - P01-CA24014/CA/NCI NIH HHS/United States GR - R01 GM38663/GM/NIGMS NIH HHS/United States GR - T32-CA93247/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Ets1 protein, mouse) RN - 0 (Proto-Oncogene Protein c-ets-1) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Proto-Oncogene Proteins c-ets) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) RN - EC 2.7.11.17 (Calcium-Calmodulin-Dependent Protein Kinase Type 2) RN - EC 2.7.11.17 (Calcium-Calmodulin-Dependent Protein Kinases) SB - IM MH - Allosteric Regulation MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Animals MH - Calcium-Calmodulin-Dependent Protein Kinase Type 2 MH - Calcium-Calmodulin-Dependent Protein Kinases/metabolism MH - DNA/*metabolism MH - Hydrophobic and Hydrophilic Interactions MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphorylation MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Protein c-ets-1 MH - Proto-Oncogene Proteins/*chemistry/genetics/*metabolism MH - Proto-Oncogene Proteins c-ets MH - Signal Transduction MH - Transcription Factors/*chemistry/genetics/*metabolism EDAT- 2005/07/05 09:00 MHDA- 2005/07/16 09:00 CRDT- 2005/07/05 09:00 AID - 309/5731/142 [pii] AID - 10.1126/science.1111915 [doi] PST - ppublish SO - Science. 2005 Jul 1;309(5731):142-5. PMID- 22826265 OWN - NLM STAT- MEDLINE DA - 20121101 DCOM- 20130108 LR - 20141105 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 109 IP - 44 DP - 2012 Oct 30 TI - Counteracting chemical chaperone effects on the single-molecule alpha-synuclein structural landscape. PG - 17826-31 LID - 10.1073/pnas.1201802109 [doi] AB - Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Forster resonance energy transfer to test the counteraction hypothesis of counterbalancing effects between the protecting osmolyte trimethylamine-N-oxide (TMAO) and denaturing osmolyte urea for the case of alpha-synuclein, a Parkinson's disease-linked protein whose monomer exhibits significant disorder. The single-molecule experiments, which avoid complications from protein aggregation, do not exhibit clear solvent-induced cooperative protein transitions for these osmolytes, unlike results from previous studies on globular proteins. Our data demonstrate the ability of TMAO and urea to shift alpha-synuclein structures towards either more compact or expanded average dimensions. Strikingly, the experiments directly reveal that a 21 [urea][TMAO] ratio has a net neutral effect on the protein's dimensions, a result that holds regardless of the absolute osmolyte concentrations. Our findings shed light on a surprisingly simple aspect of the interplay between urea and TMAO on alpha-synuclein in the context of intrinsically disordered proteins, with potential implications for the biological roles of such chemical chaperones. The results also highlight the strengths of single-molecule experiments in directly probing the chemical physics of protein structure and disorder in more chemically complex environments. FAU - Ferreon, Allan Chris M AU - Ferreon AC AD - Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. FAU - Moosa, Mahdi Muhammad AU - Moosa MM FAU - Gambin, Yann AU - Gambin Y FAU - Deniz, Ashok A AU - Deniz AA LA - eng GR - GM066833/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20120723 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Methylamines) RN - 0 (Molecular Chaperones) RN - 0 (alpha-Synuclein) RN - 8W8T17847W (Urea) RN - FLD0K1SJ1A (trimethyloxamine) SB - IM MH - Fluorescence Resonance Energy Transfer MH - Methylamines/chemistry MH - Molecular Chaperones/*chemistry MH - Protein Conformation MH - Urea/chemistry MH - alpha-Synuclein/*chemistry PMC - PMC3497778 OID - NLM: PMC3497778 EDAT- 2012/07/25 06:00 MHDA- 2013/01/09 06:00 CRDT- 2012/07/25 06:00 PHST- 2012/07/23 [aheadofprint] AID - 1201802109 [pii] AID - 10.1073/pnas.1201802109 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2012 Oct 30;109(44):17826-31. doi: 10.1073/pnas.1201802109. Epub 2012 Jul 23. PMID- 9187648 OWN - NLM STAT- MEDLINE DA - 19970714 DCOM- 19970714 LR - 20120604 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 4 IP - 6 DP - 1997 Jun TI - X-ray structure of glial cell-derived neurotrophic factor at 1.9 A resolution and implications for receptor binding. PG - 435-8 AB - The crystal structure of glial cell-derived neurotrophic factor (GDNF) reveals two independent copies of the dimer that differ significantly through a hinge bending at the central, disulphide-rich region. GDNF is compared with other members of the TGF-beta family, and potential receptor binding surfaces are identified. FAU - Eigenbrot, C AU - Eigenbrot C FAU - Gerber, N AU - Gerber N LA - eng PT - Comparative Study PT - Letter PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Bone Morphogenetic Protein 7) RN - 0 (Bone Morphogenetic Proteins) RN - 0 (Drosophila Proteins) RN - 0 (Glial Cell Line-Derived Neurotrophic Factor) RN - 0 (Glial Cell Line-Derived Neurotrophic Factor Receptors) RN - 0 (Nerve Growth Factors) RN - 0 (Nerve Tissue Proteins) RN - 0 (Neurturin) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Transforming Growth Factor beta) RN - EC 2.7.10.1 (Proto-Oncogene Proteins c-ret) RN - EC 2.7.10.1 (Receptor Protein-Tyrosine Kinases) RN - EC 2.7.10.1 (Ret oncogene protein, Drosophila) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Bone Morphogenetic Protein 7 MH - Bone Morphogenetic Proteins/chemistry MH - Crystallography, X-Ray MH - Dimerization MH - *Drosophila Proteins MH - Glial Cell Line-Derived Neurotrophic Factor MH - Glial Cell Line-Derived Neurotrophic Factor Receptors MH - Models, Molecular MH - Molecular Sequence Data MH - Nerve Growth Factors/chemistry MH - Nerve Tissue Proteins/*chemistry/*metabolism MH - Neurturin MH - Protein Conformation MH - Proto-Oncogene Proteins/chemistry/*metabolism MH - Proto-Oncogene Proteins c-ret MH - Receptor Protein-Tyrosine Kinases/chemistry/*metabolism MH - Sequence Homology, Amino Acid MH - Transforming Growth Factor beta/chemistry/metabolism EDAT- 1997/06/01 MHDA- 1997/06/01 00:01 CRDT- 1997/06/01 00:00 PST - ppublish SO - Nat Struct Biol. 1997 Jun;4(6):435-8. PMID- 23349712 OWN - NLM STAT- MEDLINE DA - 20130125 DCOM- 20130709 LR - 20141103 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 1 DP - 2013 TI - Temperature-dependent structural changes of Parkinson's alpha-synuclein reveal the role of pre-existing oligomers in alpha-synuclein fibrillization. PG - e53487 LID - 10.1371/journal.pone.0053487 [doi] AB - Amyloid fibrils of alpha-synuclein are the main constituent of Lewy bodies deposited in substantial nigra of Parkinson's disease brains. alpha-Synuclein is an intrinsically disordered protein lacking compact secondary and tertiary structures. To enhance the understanding of its structure and function relationship, we utilized temperature treatment to study alpha-synuclein conformational changes and the subsequent effects. We found that after 1 hr of high temperature pretreatment, >80 degrees C, alpha-synuclein fibrillization was significantly inhibited. However, the temperature melting coupled with circular dichroism spectra showed that alpha-synuclein was fully reversible and the NMR studies showed no observable structural changes of alpha-synuclein after 95 degrees C treatment. By using cross-linking and analytical ultracentrifugation, rare amount of pre-existing alpha-synuclein oligomers were found to decrease after the high temperature treatment. In addition, a small portion of C-terminal truncation of alpha-synuclein also occurred. The reduction of pre-existing oligomers of alpha-synuclein may contribute to less seeding effect that retards the kinetics of amyloid fibrillization. Overall, our results showed that the pre-existing oligomeric species is a key factor contributing to alpha-synuclein fibrillization. Our results facilitate the understanding of alpha-synuclein fibrillization. FAU - Ariesandi, Winny AU - Ariesandi W AD - Genomics Research Center, Academia Sinica, Taipei, Taiwan. FAU - Chang, Chi-Fon AU - Chang CF FAU - Chen, Tseng-Erh AU - Chen TE FAU - Chen, Yun-Ru AU - Chen YR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130122 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (alpha-Synuclein) SB - IM MH - Humans MH - Parkinson Disease/*metabolism MH - Protein Denaturation MH - *Protein Multimerization MH - Protein Structure, Secondary MH - Sequence Deletion MH - *Temperature MH - alpha-Synuclein/*chemistry/genetics PMC - PMC3551866 OID - NLM: PMC3551866 EDAT- 2013/01/26 06:00 MHDA- 2013/07/10 06:00 CRDT- 2013/01/26 06:00 PHST- 2012/09/06 [received] PHST- 2012/11/28 [accepted] PHST- 2013/01/22 [epublish] AID - 10.1371/journal.pone.0053487 [doi] AID - PONE-D-12-27078 [pii] PST - ppublish SO - PLoS One. 2013;8(1):e53487. doi: 10.1371/journal.pone.0053487. Epub 2013 Jan 22. PMID- 25002523 OWN - NLM STAT- MEDLINE DA - 20140723 DCOM- 20140930 LR - 20150509 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 29 DP - 2014 Jul 22 TI - Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation. PG - E2937-46 LID - 10.1073/pnas.1406381111 [doi] AB - Replication-dependent histone mRNAs end with a conserved stem loop that is recognized by stem-loop-binding protein (SLBP). The minimal RNA-processing domain of SLBP is phosphorylated at an internal threonine, and Drosophila SLBP (dSLBP) also is phosphorylated at four serines in its 18-aa C-terminal tail. We show that phosphorylation of dSLBP increases RNA-binding affinity dramatically, and we use structural and biophysical analyses of dSLBP and a crystal structure of human SLBP phosphorylated on the internal threonine to understand the striking improvement in RNA binding. Together these results suggest that, although the C-terminal tail of dSLBP does not contact the RNA, phosphorylation of the tail promotes SLBP conformations competent for RNA binding and thereby appears to reduce the entropic penalty for the association. Increased negative charge in this C-terminal tail balances positively charged residues, allowing a more compact ensemble of structures in the absence of RNA. FAU - Zhang, Jun AU - Zhang J AD - Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; FAU - Tan, Dazhi AU - Tan D AD - Department of Biological Sciences, Columbia University, New York, NY 10027; FAU - DeRose, Eugene F AU - DeRose EF AD - Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; FAU - Perera, Lalith AU - Perera L AD - Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; FAU - Dominski, Zbigniew AU - Dominski Z AD - Department of Biochemistry and Biophysics andIntegrative Program in Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599. FAU - Marzluff, William F AU - Marzluff WF AD - Department of Biochemistry and Biophysics andIntegrative Program in Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599 marzluff@med.unc.edu ltong@columbia.edu hall4@niehs.nih.gov. FAU - Tong, Liang AU - Tong L AD - Department of Biological Sciences, Columbia University, New York, NY 10027; marzluff@med.unc.edu ltong@columbia.edu hall4@niehs.nih.gov. FAU - Hall, Traci M Tanaka AU - Hall TM AD - Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; marzluff@med.unc.edu ltong@columbia.edu hall4@niehs.nih.gov. LA - eng SI - PDB/4QOZ SI - PDB/4TUW SI - PDB/4TUX SI - PDB/4TV0 GR - GM077175/GM/NIGMS NIH HHS/United States GR - GM29832/GM/NIGMS NIH HHS/United States GR - GM58921/GM/NIGMS NIH HHS/United States GR - HHSN273200700046U/PHS HHS/United States GR - P30 CA016086/CA/NCI NIH HHS/United States GR - P41 GM111244/GM/NIGMS NIH HHS/United States GR - R01 GM058921/GM/NIGMS NIH HHS/United States GR - R01 GM077175/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140707 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Drosophila Proteins) RN - 0 (Histones) RN - 0 (Nuclear Proteins) RN - 0 (RNA, Messenger) RN - 0 (RNA-Binding Proteins) RN - 0 (SLBP protein, human) RN - 0 (mRNA Cleavage and Polyadenylation Factors) RN - 0 (stem-loop binding protein, Drosophila) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Calorimetry MH - Crystallography, X-Ray MH - Drosophila Proteins/chemistry/*metabolism MH - Drosophila melanogaster MH - Entropy MH - Fluorescence Resonance Energy Transfer MH - Histones/*metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Nuclear Proteins/chemistry/*metabolism MH - Phosphorylation MH - Protein Binding MH - Protein Structure, Tertiary MH - RNA, Messenger/genetics/metabolism MH - RNA-Binding Proteins/chemistry/*metabolism MH - Sequence Alignment MH - mRNA Cleavage and Polyadenylation Factors/chemistry/*metabolism PMC - PMC4115514 OID - NLM: PMC4115514 OTO - NOTNLM OT - NMR OT - X-ray crystallography OT - intrinsically disordered protein EDAT- 2014/07/09 06:00 MHDA- 2014/10/01 06:00 CRDT- 2014/07/09 06:00 PHST- 2014/07/07 [aheadofprint] AID - 1406381111 [pii] AID - 10.1073/pnas.1406381111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):E2937-46. doi: 10.1073/pnas.1406381111. Epub 2014 Jul 7. PMID- 15023052 OWN - NLM STAT- MEDLINE DA - 20040316 DCOM- 20040713 LR - 20121115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 11 DP - 2004 Mar 23 TI - Induced alpha-helix structure in AF1 of the androgen receptor upon binding transcription factor TFIIF. PG - 3008-13 AB - In recent years, it has become clear that in many proteins, significant regions are encoded by amino acid sequences that do not automatically fold into their fully condensed, functional structures. Characterization of the conformational propensities and function of the nonglobular protein sequences represents a major challenge. Striking among proteins with unfolded regions are numbers of transcription factors, including steroid receptors. In many cases, the unfolded or partially folded regions of such proteins take shape when the protein interacts with its proper binding partner(s), that is, the molecules to which it must bind to carry out its function. The AF1 domain of the androgen receptor (AR) shows little structure, when expressed as a recombinant peptide. It has been shown previously that AF1 interacts with transcription factor TFIIF in vitro. Using Fourier transform infrared (FTIR), we tested whether this interaction can induce structure in the AR AF1. Our results demonstrate that the recombinant AR AF1 can acquire significantly higher helical content after interacting with RAP74, a subunit of the TFIIF complex. We further show that this induced conformation in the AR AF1 is well-suited for its interaction with SRC-1. FAU - Kumar, Raj AU - Kumar R AD - Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, Texas 77555-1068, USA. FAU - Betney, Russell AU - Betney R FAU - Li, Jianquan AU - Li J FAU - Thompson, E Brad AU - Thompson EB FAU - McEwan, Iain J AU - McEwan IJ LA - eng GR - 1R01-DK58829/DK/NIDDK NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Methylamines) RN - 0 (Peptide Fragments) RN - 0 (Receptors, Androgen) RN - 0 (Receptors, Steroid) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) RN - 0 (Transcription Factors, TFII) RN - 0 (transcription factor TFIIF) RN - EC 2.3.1.48 (Histone Acetyltransferases) RN - EC 2.3.1.48 (NCOA1 protein, human) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 1) RN - FLD0K1SJ1A (trimethyloxamine) SB - IM MH - Histone Acetyltransferases MH - Humans MH - Methylamines/chemistry MH - Nuclear Receptor Coactivator 1 MH - Osmolar Concentration MH - Peptide Fragments/*chemistry/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Androgen/*chemistry/metabolism MH - Receptors, Steroid/metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Spectroscopy, Fourier Transform Infrared MH - Transcription Factors/metabolism MH - Transcription Factors, TFII/*chemistry/metabolism EDAT- 2004/03/17 05:00 MHDA- 2004/07/14 05:00 CRDT- 2004/03/17 05:00 AID - 10.1021/bi035934p [doi] PST - ppublish SO - Biochemistry. 2004 Mar 23;43(11):3008-13. PMID- 16856872 OWN - NLM STAT- MEDLINE DA - 20060721 DCOM- 20060914 IS - 0300-5127 (Print) IS - 0300-5127 (Linking) VI - 34 IP - Pt 4 DP - 2006 Aug TI - Structural and functional properties of mouse proNGF. PG - 605-6 AB - The unprocessed pro-form of the NGF (nerve growth factor), proNGF (NGF precursor, without signal peptide), has been suggested to have additional functions distinct from its role as a promoter of protein folding, i.e. apoptosis and/or neurotrophic activity. Aiming to gain insights into the specific molecular interactions that mediate proNGF biological activity and into the structural determinants stabilizing its pro-region, rm-proNGF (recombinant mouse proNGF) was expressed in Escherichia coli, refolded in vitro and characterized by physicochemical methods. X-ray solution scattering measurements (small angle X-ray scattering) revealed that rm-proNGF is dimeric in solution and appears to be anisometric when compared with the compact structure of the NGF dimer. Two structural models, a globular crab-like shape and an elongated rod-like shape, equally fit to the experimental results, pointing to an intrinsically structural disordered pro-region of NGF. The models obtained allowed the interpretation of TrkA (tropomyosin receptor kinase A) binding and activation assays in cell cultures, shedding new light on the key role of proNGF in neuronal survival and neurodegeneration. FAU - Paoletti, F AU - Paoletti F AD - SISSA/ISAS (Scuola Internazionale Superiore di Studi Avanzati/International School of Advanced Studies), Trieste, Italy. paoletti@sissa.it FAU - Konarev, P V AU - Konarev PV FAU - Covaceuszach, S AU - Covaceuszach S FAU - Schwarz, E AU - Schwarz E FAU - Cattaneo, A AU - Cattaneo A FAU - Lamba, D AU - Lamba D FAU - Svergun, D I AU - Svergun DI LA - eng PT - Journal Article PL - England TA - Biochem Soc Trans JT - Biochemical Society transactions JID - 7506897 RN - 0 (Protein Precursors) RN - 0 (pro-nerve growth factor, mouse) RN - 9061-61-4 (Nerve Growth Factor) SB - IM MH - Animals MH - Computational Biology MH - Mice MH - Models, Molecular MH - Nerve Growth Factor/*chemistry/*metabolism MH - Protein Folding MH - Protein Precursors/*chemistry/*metabolism MH - Protein Structure, Tertiary EDAT- 2006/07/22 09:00 MHDA- 2006/09/15 09:00 CRDT- 2006/07/22 09:00 AID - BST0340605 [pii] AID - 10.1042/BST0340605 [doi] PST - ppublish SO - Biochem Soc Trans. 2006 Aug;34(Pt 4):605-6. PMID- 10942772 OWN - NLM STAT- MEDLINE DA - 20001120 DCOM- 20001214 LR - 20051117 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 275 IP - 44 DP - 2000 Nov 3 TI - Parkinson's disease-associated alpha-synuclein is more fibrillogenic than beta- and gamma-synuclein and cannot cross-seed its homologs. PG - 34574-9 AB - Parkinson's disease (PD) is a neurodegenerative disorder that is pathologically characterized by the presence of intracytoplasmic Lewy bodies. Recently, two point mutations in alpha-synuclein were found to be associated with familial PD, but as of yet no mutations have been described in the homologous genes beta- and gamma-synuclein. alpha-Synuclein forms the major fibrillar component of Lewy bodies, but these do not stain for beta- or gamma-synuclein. This result is very surprising, given the extent of sequence conservation and the high similarity in expression and subcellular localization, in particular between alpha- and beta-synuclein. Here we compare in vitro fibrillogenesis of all three purified synucleins. We show that fresh solutions of alpha-, beta-, and gamma- synuclein show the same natively unfolded structure. While over time alpha-synuclein forms the previously described fibrils, no fibrils could be detected for beta- and gamma-synuclein under the same conditions. Most importantly, beta- and gamma-synuclein could not be cross-seeded with alpha-synuclein fibrils. However, under conditions that drastically accelerate aggregation, gamma-synuclein can form fibrils with a lag phase roughly three times longer than alpha-synuclein. These results indicate that beta- and gamma-synuclein are intrinsically less fibrillogenic than alpha-synuclein and cannot form mixed fibrils with alpha-synuclein, which may explain why they do not appear in the pathological hallmarks of PD, although they are closely related to alpha-synuclein and are also abundant in brain. FAU - Biere, A L AU - Biere AL AD - Amgen, Inc., Thousand Oaks, California 91320-1789, USA. abiere@amgen.com FAU - Wood, S J AU - Wood SJ FAU - Wypych, J AU - Wypych J FAU - Steavenson, S AU - Steavenson S FAU - Jiang, Y AU - Jiang Y FAU - Anafi, D AU - Anafi D FAU - Jacobsen, F W AU - Jacobsen FW FAU - Jarosinski, M A AU - Jarosinski MA FAU - Wu, G M AU - Wu GM FAU - Louis, J C AU - Louis JC FAU - Martin, F AU - Martin F FAU - Narhi, L O AU - Narhi LO FAU - Citron, M AU - Citron M LA - eng PT - Journal Article PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA Primers) RN - 0 (Nerve Tissue Proteins) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 0 (beta-Synuclein) RN - 0 (gamma-Synuclein) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Circular Dichroism MH - DNA Primers MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*chemistry/metabolism MH - Parkinson Disease/*metabolism MH - Protein Folding MH - Sequence Homology, Amino Acid MH - Spectrum Analysis/methods MH - Synucleins MH - alpha-Synuclein MH - beta-Synuclein MH - gamma-Synuclein EDAT- 2000/08/16 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/08/16 11:00 AID - 10.1074/jbc.M005514200 [doi] AID - M005514200 [pii] PST - ppublish SO - J Biol Chem. 2000 Nov 3;275(44):34574-9. PMID- 16407174 OWN - NLM STAT- MEDLINE DA - 20060313 DCOM- 20060510 LR - 20081121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 11 DP - 2006 Mar 17 TI - Solution structure of the immunodominant domain of protective antigen GNA1870 of Neisseria meningitidis. PG - 7220-7 AB - GNA1870, a 28-kDa surface-exposed lipoprotein of Neisseria meningitidis recently discovered by reverse vaccinology, is one of the most potent antigens of Meningococcus and a promising candidate for a universal vaccine against a devastating disease. Previous studies of epitope mapping and genetic characterization identified residues critical for bactericidal response within the C-terminal domain of the molecule. To elucidate the conformation of protective epitopes, we used NMR spectroscopy to obtain the solution structure of the immunodominant 18-kDa C-terminal portion of GNA1870. The structure consists of an eight-stranded antiparallel beta-barrel overlaid by a short alpha-helix with an unstructured N-terminal end. Residues previously shown to be important for antibody recognition were mapped on loops facing the same ridge of the molecule. The sequence similarity of GNA1870 with members of the bacterial transferrin receptor family allows one to predict the folding of this class of well known bacterial antigens, providing the basis for the rational engineering of high affinity B cell epitopes. FAU - Cantini, Francesca AU - Cantini F AD - Centro Risonanze Magnetiche (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. FAU - Savino, Silvana AU - Savino S FAU - Scarselli, Maria AU - Scarselli M FAU - Masignani, Vega AU - Masignani V FAU - Pizza, Mariagrazia AU - Pizza M FAU - Romagnoli, Giacomo AU - Romagnoli G FAU - Swennen, Erwin AU - Swennen E FAU - Veggi, Daniele AU - Veggi D FAU - Banci, Lucia AU - Banci L FAU - Rappuoli, Rino AU - Rappuoli R LA - eng SI - PDB/1YS5 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051231 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Antibodies) RN - 0 (Antigens, Bacterial) RN - 0 (Bacterial Proteins) RN - 0 (Epitopes) RN - 0 (Epitopes, B-Lymphocyte) RN - 0 (Immunodominant Epitopes) RN - 0 (Receptors, Transferrin) RN - 0 (antigen 1870, Neisseria meningitidis) SB - IM MH - Amino Acid Sequence MH - Antibodies/chemistry MH - Antigens, Bacterial/*chemistry/metabolism MH - Bacterial Proteins/*chemistry/metabolism MH - Binding Sites MH - Epitope Mapping MH - Epitopes/chemistry MH - Epitopes, B-Lymphocyte/chemistry MH - Escherichia coli/metabolism MH - Immunodominant Epitopes/chemistry MH - Magnetic Resonance Spectroscopy MH - Meningococcal Infections MH - Models, Molecular MH - Molecular Conformation MH - Neisseria meningitidis/*metabolism MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Transferrin/chemistry MH - Sequence Homology, Amino Acid MH - Software MH - Static Electricity EDAT- 2006/01/13 09:00 MHDA- 2006/05/11 09:00 CRDT- 2006/01/13 09:00 PHST- 2005/12/31 [aheadofprint] AID - M508595200 [pii] AID - 10.1074/jbc.M508595200 [doi] PST - ppublish SO - J Biol Chem. 2006 Mar 17;281(11):7220-7. Epub 2005 Dec 31. PMID- 23056243 OWN - NLM STAT- MEDLINE DA - 20121011 DCOM- 20130402 LR - 20141105 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 10 DP - 2012 TI - Cell biological characterization of the malaria vaccine candidate trophozoite exported protein 1. PG - e46112 LID - 10.1371/journal.pone.0046112 [doi] AB - In a genome-wide screen for alpha-helical coiled coil motifs aiming at structurally defined vaccine candidates we identified PFF0165c. This protein is exported in the trophozoite stage and was named accordingly Trophozoite exported protein 1 (Tex1). In an extensive preclinical evaluation of its coiled coil peptides Tex1 was identified as promising novel malaria vaccine candidate providing the rational for a comprehensive cell biological characterization of Tex1. Antibodies generated against an intrinsically unstructured N-terminal region of Tex1 and against a coiled coil domain were used to investigate cytological localization, solubility and expression profile. Co-localization experiments revealed that Tex1 is exported across the parasitophorous vacuole membrane and located to Maurer's clefts. Change in location is accompanied by a change in solubility: from a soluble state within the parasite to a membrane-associated state after export to Maurer's clefts. No classical export motifs such as PEXEL, signal sequence/anchor or transmembrane domain was identified for Tex1. FAU - Kulangara, Caroline AU - Kulangara C AD - Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland. FAU - Luedin, Samuel AU - Luedin S FAU - Dietz, Olivier AU - Dietz O FAU - Rusch, Sebastian AU - Rusch S FAU - Frank, Geraldine AU - Frank G FAU - Mueller, Dania AU - Mueller D FAU - Moser, Mirjam AU - Moser M FAU - Kajava, Andrey V AU - Kajava AV FAU - Corradin, Giampietro AU - Corradin G FAU - Beck, Hans-Peter AU - Beck HP FAU - Felger, Ingrid AU - Felger I LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121008 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Antigens, Protozoan) RN - 0 (Carrier Proteins) RN - 0 (MAHRP-1 protein, Plasmodium falciparum) RN - 0 (Malaria Vaccines) RN - 0 (Membrane Proteins) RN - 0 (Pfsbp1 protein, Plasmodium falciparum) RN - 0 (Protozoan Proteins) RN - 0 (Tex1 protein, Plasmodium falciparum) RN - 20350-15-6 (Brefeldin A) SB - IM MH - Amino Acid Sequence MH - Animals MH - Antigens, Protozoan/genetics/*immunology/*metabolism MH - Base Sequence MH - Blotting, Western MH - Brefeldin A/pharmacology MH - Carrier Proteins/genetics/metabolism MH - Cytosol/drug effects/metabolism MH - Erythrocytes/drug effects/metabolism/*parasitology MH - Gene Expression MH - Malaria/metabolism/*parasitology MH - Malaria Vaccines/immunology MH - Membrane Proteins/genetics/metabolism MH - Mice MH - Microscopy, Confocal MH - Molecular Sequence Data MH - Organelles/metabolism MH - Plasmodium falciparum/genetics/immunology/*metabolism MH - Protein Transport/drug effects MH - Protozoan Proteins/genetics/immunology/*metabolism MH - Rabbits MH - Reverse Transcriptase Polymerase Chain Reaction MH - Vacuoles/metabolism PMC - PMC3466242 OID - NLM: PMC3466242 EDAT- 2012/10/12 06:00 MHDA- 2013/04/03 06:00 CRDT- 2012/10/12 06:00 PHST- 2011/05/13 [received] PHST- 2012/08/28 [accepted] PHST- 2012/10/08 [epublish] AID - 10.1371/journal.pone.0046112 [doi] AID - PONE-D-11-08456 [pii] PST - ppublish SO - PLoS One. 2012;7(10):e46112. doi: 10.1371/journal.pone.0046112. Epub 2012 Oct 8. PMID- 20545323 OWN - NLM STAT- MEDLINE DA - 20100729 DCOM- 20100813 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 28 DP - 2010 Jul 20 TI - Inhibition by flavonoids of amyloid-like fibril formation by Plasmodium falciparum merozoite surface protein 2. PG - 5899-908 LID - 10.1021/bi902197x [doi] AB - Merozoite surface protein 2 (MSP2) is a glycosylphosphatidylinositol (GPI)-anchored protein expressed abundantly on the surface of Plasmodium falciparum merozoites. The results of a phase 2 trial in Papua New Guinean children showed MSP2 to be a promising malaria vaccine candidate. MSP2 is intrinsically unstructured and forms amyloid-like fibrils under physiological conditions. Oligomers containing beta-strand interactions similar to those in amyloid fibrils may be a component of the fibrillar surface coat on P. falciparum merozoites. As the propensity of MSP2 to form fibrils in solution also has the potential to impede its development as a vaccine candidate, finding an inhibitor that specifically inhibits fibrillogenesis may enhance vaccine development. In this study, we tested the ability of three flavonoids, EGCG, baicalein, and resveratrol, to inhibit MSP2 fibrillogenesis and found marked inhibition with EGCG but not with the other two flavonoids. The inhibitory effect and the interactions of the flavonoids with MSP2 were characterized using NMR spectroscopy, thioflavin T fluorescence assays, electron microscopy, and other biophysical methods. EGCG stabilizes soluble oligomers and blocks fibrillogenesis by preventing the conformational transition of MSP2 from a random coil to an amyloidogenic beta-sheet structure. Structural comparison of the three flavonoids indicates an association between their propensity for autoxidation and their fibril inhibitory activity; the activity of EGCG can be attributed to the vicinal hydroxyl groups present in this flavonoid and their ability to form quinones. The molecular mechanism of fibril inhibition by EGCG appears to be complex and involves noncovalent binding followed by covalent modification of the protein. Although the addition of EGCG appears to be an effective means of stabilizing MSP2 in solution, the covalent modification of MSP2 would most likely not be acceptable in a vaccine formulation. However, these small molecule inhibitors of MSP2 fibril formation will be useful as mechanistic probes in studying oligomerization and fibril assembly of MSP2. FAU - Chandrashekaran, Indu R AU - Chandrashekaran IR AD - The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia. FAU - Adda, Christopher G AU - Adda CG FAU - MacRaild, Christopher A AU - MacRaild CA FAU - Anders, Robin F AU - Anders RF FAU - Norton, Raymond S AU - Norton RS LA - eng GR - R01AI59229/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Antigens, Protozoan) RN - 0 (Flavonoids) RN - 0 (Malaria Vaccines) RN - 0 (Membrane Proteins) RN - 0 (Protozoan Proteins) RN - 0 (merozoite surface protein 2, Plasmodium) RN - 8R1V1STN48 (Catechin) RN - BQM438CTEL (epigallocatechin gallate) SB - IM MH - Amyloid/*chemistry/immunology MH - Animals MH - Antigens, Protozoan MH - Catechin/analogs & derivatives MH - Child MH - Flavonoids/immunology MH - Humans MH - Magnetic Resonance Spectroscopy MH - Malaria Vaccines/immunology MH - Membrane Proteins/immunology MH - Merozoites/immunology MH - Plasmodium falciparum/*chemistry/immunology MH - Protozoan Proteins EDAT- 2010/06/16 06:00 MHDA- 2010/08/14 06:00 CRDT- 2010/06/16 06:00 AID - 10.1021/bi902197x [doi] PST - ppublish SO - Biochemistry. 2010 Jul 20;49(28):5899-908. doi: 10.1021/bi902197x. PMID- 15629713 OWN - NLM STAT- MEDLINE DA - 20050104 DCOM- 20050210 LR - 20141120 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 17 IP - 1 DP - 2005 Jan 7 TI - Binding of natively unfolded HIF-1alpha ODD domain to p53. PG - 11-21 AB - Hypoxia-inducible factor-1 (HIF-1) is a heterodimeric transcription factor that plays a crucial role in mediating oxygen response in the cell. Using biophysical techniques, we characterized two fragments of the HIF-1alpha subunit, one the full-length ODD domain (residues 403-603) and the second comprising the N-TAD (N-transactivation domain) and inhibitory domain (residues 530-698). Both were unstructured in solution under physiological conditions and so belong to the family of natively unfolded proteins. The HIF-1alpha ODD domain binds weakly to the isolated p53 core domain but tightly to full-length p53 to give a complex of one HIF-1alpha ODD domain with a p53 dimer. By being unstructured, the HIF-1alpha ODD domain can thread both its binding sites through the p53 multimer and bind tightly by the "chelate effect." These results support the idea that hypoxic p53-mediated apoptosis does involve the direct binding of HIF-1alpha to p53. FAU - Sanchez-Puig, Nuria AU - Sanchez-Puig N AD - Centre for Protein Engineering, Medical Research Council, Hills Road, CB2 2QH, Cambridge, United Kingdom. FAU - Veprintsev, Dmitry B AU - Veprintsev DB FAU - Fersht, Alan R AU - Fersht AR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (DNA-Binding Proteins) RN - 0 (HIF1A protein, human) RN - 0 (Hypoxia-Inducible Factor 1) RN - 0 (Hypoxia-Inducible Factor 1, alpha Subunit) RN - 0 (Multiprotein Complexes) RN - 0 (Nuclear Proteins) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) RN - 0 (Tumor Suppressor Protein p53) RN - 9007-49-2 (DNA) SB - IM MH - Anoxia/metabolism/pathology MH - Apoptosis MH - Base Sequence MH - Binding Sites MH - Circular Dichroism MH - DNA/genetics MH - DNA-Binding Proteins/*chemistry/genetics/*metabolism MH - Humans MH - Hypoxia-Inducible Factor 1 MH - Hypoxia-Inducible Factor 1, alpha Subunit MH - In Vitro Techniques MH - Kinetics MH - Multiprotein Complexes MH - Nuclear Proteins/*chemistry/genetics/*metabolism MH - Osmolar Concentration MH - Peptide Fragments/chemistry/genetics/metabolism MH - Protein Binding MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Transcription Factors/*chemistry/genetics/*metabolism MH - Tumor Suppressor Protein p53/chemistry/genetics/*metabolism EDAT- 2005/01/05 09:00 MHDA- 2005/02/11 09:00 CRDT- 2005/01/05 09:00 PHST- 2004/08/24 [received] PHST- 2004/10/10 [revised] PHST- 2004/10/27 [accepted] AID - S1097276504007105 [pii] AID - 10.1016/j.molcel.2004.11.019 [doi] PST - ppublish SO - Mol Cell. 2005 Jan 7;17(1):11-21. PMID- 23758617 OWN - NLM STAT- MEDLINE DA - 20130710 DCOM- 20140211 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 27 DP - 2013 Jul 10 TI - Modulation of the intrinsic helix propensity of an intrinsically disordered protein reveals long-range helix-helix interactions. PG - 10155-63 LID - 10.1021/ja4045532 [doi] AB - Intrinsically disordered proteins (IDPs) are widespread and important in biology but defy the classical protein structure-function paradigm by being functional in the absence of a stable, folded conformation. Here we investigate the coupling between transient secondary and tertiary structure in the protein activator for thyroid hormone and retinoid receptors (ACTR) by rationally modulating the helical propensity of a partially formed alpha-helix via mutations. Eight mutations predicted to affect the population of a transient helix were produced and investigated by NMR spectroscopy. Chemical shift changes distant to the mutation site are observed in regions containing other transient helices indicating that distant helices are stabilized through long-range hydrophobic helix-helix interactions and demonstrating the coupling of transient secondary and tertiary structure. The long-range structure of ACTR is also probed using paramagnetic relaxation enhancements (PRE) and residual dipolar couplings, which reveal an additional long-range contact between the N- and C-terminal segments. Compared to residual dipolar couplings and PRE, modulation of the helical propensity by mutagenesis thus reveals a different set of long-range interactions that may be obscured by stronger interactions that dominate other NMR measurements. This approach thus offers a complementary and generally applicable strategy for probing long-range structure in disordered proteins. FAU - Iesmantavicius, Vytautas AU - Iesmantavicius V AD - Department of Biology, University of Copenhagen, 1017 Kobenhavn K, Copenhagen, Denmark. FAU - Jensen, Malene Ringkjobing AU - Jensen MR FAU - Ozenne, Valery AU - Ozenne V FAU - Blackledge, Martin AU - Blackledge M FAU - Poulsen, Flemming M AU - Poulsen FM FAU - Kjaergaard, Magnus AU - Kjaergaard M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130625 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Intrinsically Disordered Proteins) SB - IM MH - Intrinsically Disordered Proteins/*chemistry MH - Models, Molecular MH - Protein Conformation EDAT- 2013/06/14 06:00 MHDA- 2014/02/12 06:00 CRDT- 2013/06/14 06:00 PHST- 2013/06/25 [aheadofprint] AID - 10.1021/ja4045532 [doi] PST - ppublish SO - J Am Chem Soc. 2013 Jul 10;135(27):10155-63. doi: 10.1021/ja4045532. Epub 2013 Jun 25. PMID- 24581495 OWN - NLM STAT- MEDLINE DA - 20140303 DCOM- 20140529 LR - 20150311 IS - 1097-4172 (Electronic) IS - 0092-8674 (Linking) VI - 156 IP - 5 DP - 2014 Feb 27 TI - Hsp90-Tau complex reveals molecular basis for specificity in chaperone action. PG - 963-74 LID - 10.1016/j.cell.2014.01.037 [doi] LID - S0092-8674(14)00089-0 [pii] AB - Protein folding in the cell relies on the orchestrated action of conserved families of molecular chaperones, the Hsp70 and Hsp90 systems. Hsp70 acts early and Hsp90 late in the folding path, yet the molecular basis of this timing is enigmatic, mainly because the substrate specificity of Hsp90 is poorly understood. Here, we obtained a structural model of Hsp90 in complex with its natural disease-associated substrate, the intrinsically disordered Tau protein. Hsp90 binds to a broad region in Tau that includes the aggregation-prone repeats. Complementarily, a 106-A-long substrate-binding interface in Hsp90 enables many low-affinity contacts. This allows recognition of scattered hydrophobic residues in late folding intermediates that remain after early burial of the Hsp70 sites. Our model resolves the paradox of how Hsp90 specifically selects for late folding intermediates but also for some intrinsically disordered proteins-through the eyes of Hsp90 they look the same. CI - Copyright (c) 2014 Elsevier Inc. All rights reserved. FAU - Karagoz, G Elif AU - Karagoz GE AD - Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA. FAU - Duarte, Afonso M S AU - Duarte AM AD - Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Instituto de Tecnologia Quimica e Biologica Antonio Xavier, Universidade Nova de Lisboa, Av. da Republica EAN, 2780-157 Oeiras, Portugal. FAU - Akoury, Elias AU - Akoury E AD - Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany. FAU - Ippel, Hans AU - Ippel H AD - Biomolecular NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; CARIM School for Cardiovascular Diseases, Biochemistry Group, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands. FAU - Biernat, Jacek AU - Biernat J AD - DZNE, German Center for Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany. FAU - Moran Luengo, Tania AU - Moran Luengo T AD - Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. FAU - Radli, Martina AU - Radli M AD - Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. FAU - Didenko, Tatiana AU - Didenko T AD - Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. FAU - Nordhues, Bryce A AU - Nordhues BA AD - Department of Pharmaceutical Sciences and Department of Molecular Medicine, University of South Florida Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL 33613, USA. FAU - Veprintsev, Dmitry B AU - Veprintsev DB AD - Laboratory of Biomolecular Research, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland and Department of Biology, ETH Zurich, 8093 Zurich, Switzerland. FAU - Dickey, Chad A AU - Dickey CA AD - Department of Pharmaceutical Sciences and Department of Molecular Medicine, University of South Florida Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL 33613, USA. FAU - Mandelkow, Eckhard AU - Mandelkow E AD - DZNE, German Center for Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany; CAESAR Research Center, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany. FAU - Zweckstetter, Markus AU - Zweckstetter M AD - Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 37077 Gottingen, Germany; Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University Medical Center, 37073 Gottingen, Germany. FAU - Boelens, Rolf AU - Boelens R AD - Biomolecular NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. FAU - Madl, Tobias AU - Madl T AD - Biomolecular NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Institute of Structural Biology, Helmholtz Zentrum Munchen Neuherberg and Biomolecular NMR-Spectroscopy, Technische Universitat Munchen, Lichtenbergstrasse 4, 85747 Garching, Germany; Institute of Chemistry, University of Graz, Heinrichstrasse 28, 8010 Graz, Austria. Electronic address: t.madl@tum.de. FAU - Rudiger, Stefan G D AU - Rudiger SG AD - Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands. Electronic address: s.g.d.rudiger@uu.nl. LA - eng GR - NS073899/NS/NINDS NIH HHS/United States GR - R01 NS073899/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (HSP90 Heat-Shock Proteins) RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/drug therapy MH - Amino Acid Sequence MH - HSP90 Heat-Shock Proteins/chemistry/metabolism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Folding MH - Scattering, Small Angle MH - X-Ray Diffraction MH - tau Proteins/*chemistry/metabolism PMC - PMC4263503 MID - NIHMS642089 OID - NLM: NIHMS642089 OID - NLM: PMC4263503 EDAT- 2014/03/04 06:00 MHDA- 2014/05/30 06:00 CRDT- 2014/03/04 06:00 PHST- 2013/08/29 [received] PHST- 2013/12/11 [revised] PHST- 2014/01/15 [accepted] AID - S0092-8674(14)00089-0 [pii] AID - 10.1016/j.cell.2014.01.037 [doi] PST - ppublish SO - Cell. 2014 Feb 27;156(5):963-74. doi: 10.1016/j.cell.2014.01.037. PMID- 22528768 OWN - NLM STAT- MEDLINE DA - 20130312 DCOM- 20130829 IS - 1874-270X (Electronic) VI - 7 IP - 1 DP - 2013 Apr TI - (1)H-, (13)C- and (15)N-NMR assignment of the N-terminal domain of human cerebral dopamine neurotrophic factor (CDNF). PG - 101-3 LID - 10.1007/s12104-012-9388-8 [doi] AB - Parkinson's disease (PD) is a neurodegenerative disorder that is caused by the death of midbrain dopaminergic neurons. Current therapies for PD do not halt the neurodegeneration nor repair the affected neurons. Therefore, search for novel neurotrophic factors (NTF) for midbrain dopaminergic neurons, which could be used in novel therapeutic approaches, is highly wanted. In 2007, a potent NTF for dopaminergic neurons was described as the conserved dopamine neurotrophic factor (CDNF). Single doses of this protein protect and restore dopaminergic neurons in experimental models of PD. CDNF has two domains; an N-terminal saposin-like domain, which may bind to membranes; and a presumably intrinsically unstructured C-terminal which contains an internal cysteine bridge in a CXXC motif similar to that of thiol/disulphide oxidoreductases and isomerases, and may thus reduce the endoplasmic reticulum stress caused by incorrectly folded proteins. We show for the first time the nuclear magnetic resonance assignment of N-terminal domain of recombinant CDNF (residues 1-105) by solution 2D and 3D NMR spectroscopy. We were able to obtain a nearly complete resonance assignment, which is the first step toward the solution structure determination of this neurotrophic factor. FAU - Latge, Cristiane AU - Latge C AD - Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. FAU - Cabral, Katia M S AU - Cabral KM FAU - Almeida, Marcius S AU - Almeida MS FAU - Foguel, Debora AU - Foguel D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120418 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (CDNF protein, human) RN - 0 (Nerve Growth Factors) SB - IM MH - Amino Acid Sequence MH - Humans MH - Molecular Sequence Data MH - Nerve Growth Factors/*chemistry/metabolism MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Tertiary EDAT- 2012/04/25 06:00 MHDA- 2013/08/30 06:00 CRDT- 2012/04/25 06:00 PHST- 2012/02/16 [received] PHST- 2012/04/06 [accepted] PHST- 2012/04/18 [aheadofprint] AID - 10.1007/s12104-012-9388-8 [doi] PST - ppublish SO - Biomol NMR Assign. 2013 Apr;7(1):101-3. doi: 10.1007/s12104-012-9388-8. Epub 2012 Apr 18. PMID- 17299036 OWN - NLM STAT- MEDLINE DA - 20070315 DCOM- 20070412 LR - 20140922 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 104 IP - 8 DP - 2007 Feb 20 TI - A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures. PG - 2649-54 AB - The yeast prion protein Sup35 is a translation termination factor, whose activity is modulated by sequestration into a self-perpetuating amyloid. The prion-determining domain, NM, consists of two distinct regions: an amyloidogenic N terminus domain (N) and a charged solubilizing middle region (M). To gain insight into prion conversion, we used single-molecule fluorescence resonance energy transfer (SM-FRET) and fluorescence correlation spectroscopy to investigate the structure and dynamics of monomeric NM. Low protein concentrations in these experiments prevented the formation of obligate on-pathway oligomers, allowing us to study early folding intermediates in isolation from higher-order species. SM-FRET experiments on a dual-labeled amyloid core variant (N21C/S121C, retaining wild-type prion behavior) indicated that the N region of NM adopts a collapsed form similar to "burst-phase" intermediates formed during the folding of many globular proteins, even though it lacks a typical hydrophobic core. The mean distance between residues 21 and 121 was approximately equal to 43 A. This increased with denaturant in a noncooperative fashion to approximately equal to 63 A, suggesting a multitude of interconverting species rather than a small number of discrete monomeric conformers. Fluorescence correlation spectroscopy analysis of singly labeled NM revealed fast conformational fluctuations on the 20- to 300-ns time scale. Quenching from proximal and distal tyrosines resulted in distinct fast and slower fluctuations. Our results indicate that native monomeric NM is composed of an ensemble of structures, having a collapsed and rapidly fluctuating N region juxtaposed with a more extended M region. The stability of such ensembles is likely to play a key role in prion conversion. FAU - Mukhopadhyay, Samrat AU - Mukhopadhyay S AD - Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. FAU - Krishnan, Rajaraman AU - Krishnan R FAU - Lemke, Edward A AU - Lemke EA FAU - Lindquist, Susan AU - Lindquist S FAU - Deniz, Ashok A AU - Deniz AA LA - eng GR - GM 066883/GM/NIGMS NIH HHS/United States GR - GM 25874/GM/NIGMS NIH HHS/United States GR - R01 GM025874/GM/NIGMS NIH HHS/United States GR - R37 GM025874/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070213 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Peptide Termination Factors) RN - 0 (Peptides) RN - 0 (Prions) RN - 0 (SUP35 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Amino Acid Sequence MH - Computer Simulation MH - Fluorescence Resonance Energy Transfer MH - Molecular Sequence Data MH - Peptide Termination Factors MH - Peptides/chemistry MH - Prions/*chemistry/*metabolism MH - Protein Denaturation MH - *Protein Folding MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/*chemistry MH - Saccharomyces cerevisiae Proteins/*chemistry/*metabolism PMC - PMC1815236 OID - NLM: PMC1815236 EDAT- 2007/02/15 09:00 MHDA- 2007/04/14 09:00 CRDT- 2007/02/15 09:00 PHST- 2007/02/13 [aheadofprint] AID - 0611503104 [pii] AID - 10.1073/pnas.0611503104 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2649-54. Epub 2007 Feb 13. PMID- 8524402 OWN - NLM STAT- MEDLINE DA - 19960123 DCOM- 19960123 LR - 20131121 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 378 IP - 6557 DP - 1995 Dec 7 TI - Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex. PG - 641-4 AB - Calcineurin (CaN) is a calcium- and calmodulin-dependent protein serine/threonine phosphate which is critical for several important cellular processes, including T-cell activation. CaN is the target of the immunosuppressive drugs cyclosporin A and FK506, which inhibit CaN after forming complexes with cytoplasmic binding proteins (cyclophilin and FKBP12, respectively). We report here the crystal structures of full-length human CaN at 2.1 A resolution and of the complex of human CaN with FKBP12-FK506 at 3.5 A resolution. In the native CaN structure, an auto-inhibitory element binds at the Zn/Fe-containing active site. The metal-site geometry and active-site water structure suggest a catalytic mechanism involving nucleophilic attack on the substrate phosphate by a metal-activated water molecule. In the FKBP12-FK506-CaN complex, the auto-inhibitory element is displaced from the active site. The site of binding of FKBP12-FK506 appears to be shared by other non-competitive inhibitors of calcineurin, including a natural anchoring protein. FAU - Kissinger, C R AU - Kissinger CR AD - Agouron Pharmaceuticals Inc., San Diego, California 92121-1121, USA. FAU - Parge, H E AU - Parge HE FAU - Knighton, D R AU - Knighton DR FAU - Lewis, C T AU - Lewis CT FAU - Pelletier, L A AU - Pelletier LA FAU - Tempczyk, A AU - Tempczyk A FAU - Kalish, V J AU - Kalish VJ FAU - Tucker, K D AU - Tucker KD FAU - Showalter, R E AU - Showalter RE FAU - Moomaw, E W AU - Moomaw EW AU - et al. LA - eng PT - Journal Article PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (A Kinase Anchor Proteins) RN - 0 (AKAP5 protein, human) RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Calmodulin-Binding Proteins) RN - 0 (Carrier Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Enzyme Inhibitors) RN - 0 (Heat-Shock Proteins) RN - 0 (Proteins) RN - 0 (Recombinant Proteins) RN - 059QF0KO0R (Water) RN - EC 3.1.3.16 (Calcineurin) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - EC 5.2.1.- (Tacrolimus Binding Proteins) RN - SY7Q814VUP (Calcium) RN - WM0HAQ4WNM (Tacrolimus) SB - IM MH - A Kinase Anchor Proteins MH - *Adaptor Proteins, Signal Transducing MH - Amino Acid Sequence MH - Binding Sites MH - Calcineurin MH - Calcium/metabolism MH - Calmodulin-Binding Proteins/antagonists & inhibitors/*chemistry/metabolism/ultrastructure MH - Carrier Proteins/chemistry/*metabolism MH - Crystallization MH - Crystallography, X-Ray MH - DNA-Binding Proteins/chemistry/*metabolism MH - Enzyme Inhibitors/metabolism/pharmacology MH - Heat-Shock Proteins/chemistry/*metabolism MH - Humans MH - Hydrogen Bonding MH - Models, Molecular MH - Molecular Sequence Data MH - Phosphoprotein Phosphatases/antagonists & inhibitors/*chemistry/metabolism/ultrastructure MH - Protein Conformation MH - Protein Structure, Secondary MH - Proteins/metabolism/pharmacology MH - Recombinant Proteins/chemistry MH - Tacrolimus/chemistry/*metabolism MH - Tacrolimus Binding Proteins MH - Water/metabolism EDAT- 1995/12/07 MHDA- 1995/12/07 00:01 CRDT- 1995/12/07 00:00 AID - 10.1038/378641a0 [doi] PST - ppublish SO - Nature. 1995 Dec 7;378(6557):641-4. PMID- 18326633 OWN - NLM STAT- MEDLINE DA - 20080529 DCOM- 20080627 LR - 20140904 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 94 IP - 12 DP - 2008 Jun TI - Backbone dynamics of the 18.5 kDa isoform of myelin basic protein reveals transient alpha-helices and a calmodulin-binding site. PG - 4847-66 LID - 10.1529/biophysj.107.125823 [doi] AB - The 18.5 kDa isoform of myelin basic protein (MBP) is the predominant form in adult human central nervous system myelin. It is an intrinsically disordered protein that functions both in membrane adhesion, and as a linker connecting the oligodendrocyte membrane to the underlying cytoskeleton; its specific interactions with calmodulin and SH3-domain containing proteins suggest further multifunctionality in signaling. Here, we have used multidimensional heteronuclear nuclear magnetic resonance spectroscopy to study the conformational dependence on environment of the protein in aqueous solution (100 mM KCl) and in a membrane-mimetic solvent (30% TFE-d(2)), particularly to analyze its secondary structure using chemical shift indexing, and to investigate its backbone dynamics using (15)N spin relaxation measurements. Collectively, the data revealed three major segments of the protein with a propensity toward alpha-helicity that was stabilized by membrane-mimetic conditions: T33-D46, V83-T92, and T142-L154 (murine 18.5 kDa sequence numbering). All of these regions corresponded with bioinformatics predictions of ordered secondary structure. The V83-T92 region comprises a primary immunodominant epitope that had previously been shown by site-directed spin labeling and electron paramagnetic resonance spectroscopy to be alpha-helical in membrane-reconstituted systems. The T142-L154 segment overlapped with a predicted calmodulin-binding site. Chemical shift perturbation experiments using labeled MBP and unlabeled calmodulin demonstrated a dramatic conformational change in MBP upon association of the two proteins, and were consistent with the C-terminal segment of MBP being the primary binding site for calmodulin. FAU - Libich, David S AU - Libich DS AD - Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada. FAU - Harauz, George AU - Harauz G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080307 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Calmodulin) RN - 0 (Protein Isoforms) SB - IM MH - Binding Sites MH - Calmodulin/*chemistry/*ultrastructure MH - Computer Simulation MH - *Models, Chemical MH - *Models, Molecular MH - Myelin Sheath/*chemistry/*ultrastructure MH - Protein Binding MH - Protein Isoforms/chemistry/ultrastructure PMC - PMC2397351 OID - NLM: PMC2397351 EDAT- 2008/03/11 09:00 MHDA- 2008/06/28 09:00 CRDT- 2008/03/11 09:00 PHST- 2008/03/07 [aheadofprint] AID - S0006-3495(08)70352-7 [pii] AID - 10.1529/biophysj.107.125823 [doi] PST - ppublish SO - Biophys J. 2008 Jun;94(12):4847-66. doi: 10.1529/biophysj.107.125823. Epub 2008 Mar 7. PMID- 17189335 OWN - NLM STAT- MEDLINE DA - 20070207 DCOM- 20070424 LR - 20140907 IS - 0032-0889 (Print) IS - 0032-0889 (Linking) VI - 143 IP - 2 DP - 2007 Feb TI - Desiccation and zinc binding induce transition of tomato abscisic acid stress ripening 1, a water stress- and salt stress-regulated plant-specific protein, from unfolded to folded state. PG - 617-28 AB - Abscisic acid stress ripening 1 (ASR1) is a low molecular weight plant-specific protein encoded by an abiotic stress-regulated gene. Overexpression of ASR1 in transgenic plants increases their salt tolerance. The ASR1 protein possesses a zinc-dependent DNA-binding activity. The DNA-binding site was mapped to the central part of the polypeptide using truncated forms of the protein. Two additional zinc-binding sites were shown to be localized at the amino terminus of the polypeptide. ASR1 protein is presumed to be an intrinsically unstructured protein using a number of prediction algorithms. The degree of order of ASR1 was determined experimentally using nontagged recombinant protein expressed in Escherichia coli and purified to homogeneity. Purified ASR1 was shown to be unfolded using dynamic light scattering, gel filtration, microcalorimetry, circular dichroism, and Fourier transform infrared spectrometry. The protein was shown to be monomeric by analytical ultracentrifugation. Addition of zinc ions resulted in a global change in ASR1 structure from monomer to homodimer. Upon binding of zinc ions, the protein becomes ordered as shown by Fourier transform infrared spectrometry and microcalorimetry, concomitant with dimerization. Tomato (Solanum lycopersicum) leaf soluble ASR1 is unstructured in the absence of added zinc and gains structure upon binding of the metal ion. The effect of zinc binding on ASR1 folding and dimerization is discussed. FAU - Goldgur, Yehuda AU - Goldgur Y AD - Department of Chemistry, Ben-Gurion University, Beer-Sheva 84105, Israel. FAU - Rom, Slava AU - Rom S FAU - Ghirlando, Rodolfo AU - Ghirlando R FAU - Shkolnik, Doron AU - Shkolnik D FAU - Shadrin, Natalia AU - Shadrin N FAU - Konrad, Zvia AU - Konrad Z FAU - Bar-Zvi, Dudy AU - Bar-Zvi D LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't DEP - 20061222 PL - United States TA - Plant Physiol JT - Plant physiology JID - 0401224 RN - 0 (Asr1 protein, Lycopersicon esculentum) RN - 0 (Plant Proteins) RN - 059QF0KO0R (Water) RN - 7647-14-5 (Sodium Chloride) RN - J41CSQ7QDS (Zinc) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Cytosol/metabolism MH - Gene Expression Regulation, Plant MH - Lycopersicon esculentum/drug effects/*metabolism MH - Plant Leaves/metabolism MH - Plant Proteins/*metabolism MH - Pollen/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Seeds/metabolism MH - Sodium Chloride/*pharmacology MH - Water/*metabolism MH - Zinc/*metabolism PMC - PMC1803749 OID - NLM: PMC1803749 EDAT- 2006/12/26 09:00 MHDA- 2007/04/25 09:00 CRDT- 2006/12/26 09:00 PHST- 2006/12/22 [aheadofprint] PHST- 2006/12/27 [aheadofprint] PHST- 2007/01/05 [aheadofprint] AID - pp.106.092965 [pii] AID - 10.1104/pp.106.092965 [doi] PST - ppublish SO - Plant Physiol. 2007 Feb;143(2):617-28. Epub 2006 Dec 22. PMID- 19146389 OWN - NLM STAT- MEDLINE DA - 20090624 DCOM- 20090717 LR - 20140901 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 6 DP - 2009 Feb 17 TI - Effects of full-length borealin on the composition and protein-protein interaction activity of a binary chromosomal passenger complex. PG - 1156-61 LID - 10.1021/bi801298j [doi] AB - The chromosomal passenger complex (CPC) comprises at least four protein components and functions at various cellular localizations during different mitotic stages to ensure correct chromosome segregation and completion of cytokinesis. Borealin, the most recently identified member of the CPC, is an intrinsically unstructured protein of low solubility and stability. Recent reports have demonstrated the formation of binary or ternary CPC subcomplexes incorporating short Borealin fragments in vitro. Using isothermal titration calorimetry, we show that full-length Borealin, instead of a Borealin fragment possessing the complete Survivin and INCENP recognition sequence, is required for the composition of a Borealin-Survivin complex competent to interact with INCENP. In addition, we show evidence that full-length Borealin, which forms high-order oligomers in its isolated form, is a monomer in the Borealin-Survivin CPC subcomplex. FAU - Zhou, Lihong AU - Zhou L AD - Institute for Structural and Molecular Biology, Division of Biosciences, University College London, UK. FAU - Li, Jiejin AU - Li J FAU - George, Roger AU - George R FAU - Ruchaud, Sandrine AU - Ruchaud S FAU - Zhou, Hong-Gang AU - Zhou HG FAU - Ladbury, John E AU - Ladbury JE FAU - Earnshaw, William C AU - Earnshaw WC FAU - Yuan, Xuemei AU - Yuan X LA - eng GR - 073915/Wellcome Trust/United Kingdom GR - BB/C520820/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BBC5208201/Biotechnology and Biological Sciences Research Council/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cell Cycle Proteins) RN - 0 (Microtubule-Associated Proteins) RN - 0 (Multiprotein Complexes) SB - IM MH - Calorimetry MH - Cell Cycle Proteins/chemistry/*metabolism MH - Chromatography, Gel MH - Chromosomes/*metabolism MH - Microtubule-Associated Proteins/metabolism MH - Multiprotein Complexes/*metabolism MH - Protein Binding MH - Ultracentrifugation PMC - PMC2746994 MID - UKMS27729 OID - NLM: PMC2746994 OID - NLM: UKMS27729 EDAT- 2009/01/17 09:00 MHDA- 2009/07/18 09:00 CRDT- 2009/01/17 09:00 AID - 10.1021/bi801298j [doi] AID - 10.1021/bi801298j [pii] PST - ppublish SO - Biochemistry. 2009 Feb 17;48(6):1156-61. doi: 10.1021/bi801298j. PMID- 8269922 OWN - NLM STAT- MEDLINE DA - 19940203 DCOM- 19940203 LR - 20131121 IS - 0014-2956 (Print) IS - 0014-2956 (Linking) VI - 218 IP - 2 DP - 1993 Dec 1 TI - Conformation of thymosin beta 4 in water determined by NMR spectroscopy. PG - 335-44 AB - The conformational preferences of a 43-amino-acid G-actin-binding peptide, thymosin beta 4, in water at 1, 4 and 14 degrees C, and at pH 3.0 and 6.5 were studied by NMR. NMR showed that thymosin beta 4 lacks a uniquely folded conformation in water. However, some preferential alpha-helical conformations of thymosin beta 4 can be observed in aqueous solutions. The segment at residues 5-16 showed characteristic interactions for conformations in both the beta-strand and alpha-helical regions of the phi-psi space, based on strong C alpha H(i)-NH(i+1) interactions and NH-NH, C alpha H(i)-NH(i+3), and C alpha H(i)-C beta H(i+3) interactions, respectively. At 1-4 degrees C, another segment at residues 31-37 also shows both beta and alpha conformations, forming however a less well-defined helix than the segment at residues 5-16. At 14 degrees C, the conformational population of the helix at positions 5-16 is shifted more towards the random and turn-like structures, whereas the segment at positions 31-37 becomes exclusively a random coil. FAU - Czisch, M AU - Czisch M AD - Max-Planck-Institut fur Biochemie, Germany. FAU - Schleicher, M AU - Schleicher M FAU - Horger, S AU - Horger S FAU - Voelter, W AU - Voelter W FAU - Holak, T A AU - Holak TA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - GERMANY TA - Eur J Biochem JT - European journal of biochemistry / FEBS JID - 0107600 RN - 059QF0KO0R (Water) RN - 61512-21-8 (Thymosin) RN - 77591-33-4 (thymosin beta(4)) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Hydrogen-Ion Concentration MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Structure, Secondary MH - Temperature MH - Thymosin/*chemistry MH - Water EDAT- 1993/12/01 MHDA- 1993/12/01 00:01 CRDT- 1993/12/01 00:00 PST - ppublish SO - Eur J Biochem. 1993 Dec 1;218(2):335-44. PMID- 9684899 OWN - NLM STAT- MEDLINE DA - 19981021 DCOM- 19981021 LR - 20140617 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 7 IP - 7 DP - 1998 Jul TI - The interaction of eIF4E with 4E-BP1 is an induced fit to a completely disordered protein. PG - 1639-42 AB - 4E binding protein 1 (4E-BP1) inhibits translation by binding to the initiation factor eIF4E and is mostly or completely unstructured in both free and bound states. We wished to determine whether the free protein has local structure that could be involved in eIF4E binding. Assignments were obtained using double and triple resonance NMR methods. Residues 4-10, 43-46, and 56-65 could not be assigned, primarily because of a high degree of 1H and 15N chemical shift overlap. Steady-state inverted question mark1H inverted question mark-15N NOEs were measured for 45 residues in the assigned regions. Except for the two C-terminal residues, the NOEs were between -0.77 and - 1.14, indicating a high level of flexibility. Furthermore, the inverted question mark1H inverted question mark-15N NOE spectrum recorded with presaturation contained no strong positive signals, making it likely that no other residues have positive or smaller negative NOEs. This implies that 4E-BP1 has no regions of local order in the absence of eIF4E. The interaction therefore appears to be an induced fit to a completely disordered protein molecule. FAU - Fletcher, C M AU - Fletcher CM AD - Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA. cmf@hugin.med.harvard.edu FAU - Wagner, G AU - Wagner G LA - eng GR - CA68262/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Carrier Proteins) RN - 0 (EIF4EBP1 protein, human) RN - 0 (Eukaryotic Initiation Factor-4E) RN - 0 (Peptide Initiation Factors) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Proteins) SB - IM MH - Adaptor Proteins, Signal Transducing MH - Allosteric Regulation MH - Amino Acid Sequence MH - Amino Acid Substitution MH - Binding Sites MH - *Carrier Proteins MH - Enzyme Stability MH - Escherichia coli MH - Eukaryotic Initiation Factor-4E MH - Gene Deletion MH - Humans MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Initiation Factors/metabolism MH - Phosphoproteins/*chemistry/metabolism MH - Phosphorylation MH - Protein Biosynthesis MH - Protein Conformation MH - *Protein Folding MH - Recombinant Proteins/chemistry/metabolism PMC - PMC2144065 OID - NLM: PMC2144065 EDAT- 1998/07/31 MHDA- 1998/07/31 00:01 CRDT- 1998/07/31 00:00 AID - 10.1002/pro.5560070720 [doi] PST - ppublish SO - Protein Sci. 1998 Jul;7(7):1639-42. PMID- 21875562 OWN - NLM STAT- MEDLINE DA - 20110830 DCOM- 20120216 IS - 1937-6448 (Print) VI - 290 DP - 2011 TI - Control of actin assembly by the WH2 domains and their multifunctional tandem repeats in Spire and Cordon-Bleu. PG - 55-85 LID - 10.1016/B978-0-12-386037-8.00005-3 [doi] AB - The WASP-homology 2 (WH2) domain is a 5-kDa actin-binding protein module that attracts increasing interest by its multifunctional regulation of actin dynamics in motile and morphogenetic processes. Identified by a short consensus sequence LKKT/V originally found in the actin-sequestering ss-thymosin peptides, the ssT/WH2 domains are inserted in a large number of proteins, in particular, the WASP proteins involved in cell protrusions. WH2 are found in tandem repeats in proteins involved in early development and axis-patterning processes, like Spire and Cordon-Bleu. These intrinsically disordered proteins regulate actin assembly in an adaptive and versatile fashion by a fine control of local interaction dynamics within the WH2-actin complex. Versatility is amplified by the protein environment in which the WH2 domain is inserted and by synergy with other adjacent actin-binding modules. Multifunctional activities emerge in WH2 repeats, including filament nucleation, dramatic severing, and barbed end capping or tracking. WH2 domains thus are instrumental in designing customized actin regulators. CI - Copyright (c) 2011 Elsevier Inc. All rights reserved. FAU - Carlier, Marie-France AU - Carlier MF AD - Cytoskeleton Dynamics and Cell Motility group, CNRS Gif-sur-Yvette, France. FAU - Husson, Clotilde AU - Husson C FAU - Renault, Louis AU - Renault L FAU - Didry, Dominique AU - Didry D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Netherlands TA - Int Rev Cell Mol Biol JT - International review of cell and molecular biology JID - 101475846 RN - 0 (Actins) RN - 0 (Microfilament Proteins) RN - 0 (Wiskott-Aldrich Syndrome Protein Family) SB - IM MH - Actins/*metabolism MH - Animals MH - Humans MH - Microfilament Proteins/*chemistry/metabolism MH - Protein Structure, Tertiary MH - Wiskott-Aldrich Syndrome Protein Family/*chemistry/*metabolism EDAT- 2011/08/31 06:00 MHDA- 2012/02/18 06:00 CRDT- 2011/08/31 06:00 AID - B978-0-12-386037-8.00005-3 [pii] AID - 10.1016/B978-0-12-386037-8.00005-3 [doi] PST - ppublish SO - Int Rev Cell Mol Biol. 2011;290:55-85. doi: 10.1016/B978-0-12-386037-8.00005-3. PMID- 18700180 OWN - NLM STAT- MEDLINE DA - 20081020 DCOM- 20090112 LR - 20131121 IS - 1011-1344 (Print) IS - 1011-1344 (Linking) VI - 93 IP - 1 DP - 2008 Oct 16 TI - Interaction with Al and Zn induces structure formation and aggregation in natively unfolded caseins. PG - 36-43 LID - 10.1016/j.jphotobiol.2008.06.011 [doi] AB - Caseins are phosphoproteins that form the principal protein component of milk, their chief function being the transport of inorganic calcium and phosphate to the neonates. The four major members of the casein family are alpha(s1)-, alpha(s2)- (together referred to as alpha(s)-casein), beta- and kappa-casein, each having a characteristic high negative net charge as well as high hydrophobicity and preferring extended conformational states in solution. We have investigated the influence of the polyvalent metal cations Zn(II) and Al(III) on the structure of bovine caseins, using fluorescence and circular dichroic (CD) spectroscopy and light scattering. Changes in Trp and ANS fluorescence parameters (blue shifts of the emission maxima and enhancement of fluorescence intensity) and in the far-UV CD spectra of the caseins caused by the presence of both metals suggest that conformational changes are induced in them by low concentrations (20-40 microM) of the metal cations. These changes lead to formation of solvent-accessible hydrophobic clusters or cavities that, in turn, cause self-association and precipitation of caseins at higher concentration of the metals. These conclusions are supported by increased binding of ThT to the caseins, as well as enhancement of light scattering intensity, observed in presence of Al(III). The chaperonic property of alpha(s)-casein, which enables it to inhibit thermal aggregation of alcohol dehydrogenase, is shown to be partially destroyed by Zn(II)-induced structural alterations, due possibly to loss of flexibility of the natively unfolded casein chains. FAU - Chakraborty, Asima AU - Chakraborty A AD - Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata, West Bengal 700 064, India. FAU - Basak, Soumen AU - Basak S LA - eng PT - Journal Article DEP - 20080705 PL - Switzerland TA - J Photochem Photobiol B JT - Journal of photochemistry and photobiology. B, Biology JID - 8804966 RN - 0 (Caseins) RN - 8DUH1N11BX (Tryptophan) RN - CPD4NFA903 (Aluminum) RN - J41CSQ7QDS (Zinc) SB - IM MH - Aluminum/*pharmacology MH - Caseins/*chemistry/drug effects MH - Circular Dichroism MH - Hydrogen-Ion Concentration MH - Kinetics MH - Protein Denaturation/drug effects MH - Protein Folding/drug effects MH - Spectrometry, Fluorescence MH - Tryptophan MH - Ultraviolet Rays MH - Zinc/*pharmacology EDAT- 2008/08/14 09:00 MHDA- 2009/01/13 09:00 CRDT- 2008/08/14 09:00 PHST- 2008/03/18 [received] PHST- 2008/06/09 [revised] PHST- 2008/06/28 [accepted] PHST- 2008/07/05 [aheadofprint] AID - S1011-1344(08)00139-5 [pii] AID - 10.1016/j.jphotobiol.2008.06.011 [doi] PST - ppublish SO - J Photochem Photobiol B. 2008 Oct 16;93(1):36-43. doi: 10.1016/j.jphotobiol.2008.06.011. Epub 2008 Jul 5. PMID- 21766125 OWN - NLM STAT- MEDLINE DA - 20111202 DCOM- 20120320 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Synergistic folding of two intrinsically disordered proteins: searching for conformational selection. PG - 198-209 LID - 10.1039/c1mb05156c [doi] AB - Intrinsically disordered proteins (IDPs) lack stable structures under physiological conditions but often fold into stable structures upon specific binding. These coupled binding and folding processes underlie the organization of cellular regulatory networks, and a mechanistic understanding is thus of fundamental importance. Here, we investigated the synergistic folding of two IDPs, namely, the NCBD domain of transcription coactivator CBP and the p160 steroid receptor coactivator ACTR, using a topology-based model that was carefully calibrated to balance intrinsic folding propensities and intermolecular interactions. As one of the most structured IDPs, NCBD is a plausible candidate that interacts through conformational selection-like mechanisms, where binding is mainly initiated by pre-existing folded-like conformations. Indeed, the simulations demonstrate that, even though binding and folding of both NCBD and ACTR is highly cooperative on the baseline level, the tertiary folding of NCBD is best described by the "extended conformational selection" model that involves multiple stages of selection and induced folding. The simulations further predict that the NCBD/ACTR recognition is mainly initiated by forming a mini folded core that includes the second and third helices of NCBD and ACTR. These predictions are fully consistent with independent physics-based atomistic simulations as well as a recent experimental mapping of the H/D exchange protection factors. The current work thus adds to the limited number of existing mechanistic studies of coupled binding and folding of IDPs, and provides a first direct demonstration of how conformational selection might contribute to efficient recognition of IDPs. Interestingly, even for highly structured IDPs like NCBD, the recognition is initiated by the more disordered C-terminal segment and with substantial contribution from induced folding. Together with existing studies of IDP interaction mechanisms, this argues that induced folding is likely prevalent in IDP-protein interaction, and emphasizes the importance of understanding how IDPs manage to fold efficiently upon (nonspecific) binding. Success of the current study also further supports the notion that, with careful calibration, topology-based models can be effective tools for mechanistic study of IDP interaction and regulation, especially when combined with physics-based atomistic simulations and experiments. FAU - Ganguly, Debabani AU - Ganguly D AD - Department of Biochemistry, Kansas State University, Manhattan, KS 66506, USA. FAU - Zhang, Weihong AU - Zhang W FAU - Chen, Jianhan AU - Chen J LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110718 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - EC 2.3.1.48 (CREB-Binding Protein) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 3) SB - IM MH - Amino Acid Sequence MH - Animals MH - CREB-Binding Protein/*chemistry/*metabolism MH - Calibration MH - Humans MH - Magnetic Resonance Spectroscopy MH - Mice MH - Models, Molecular MH - Nuclear Receptor Coactivator 3/*chemistry/*metabolism MH - *Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Thermodynamics EDAT- 2011/07/19 06:00 MHDA- 2012/03/21 06:00 CRDT- 2011/07/19 06:00 PHST- 2011/07/18 [aheadofprint] PHST- 2011/12/01 [epublish] AID - 10.1039/c1mb05156c [doi] PST - ppublish SO - Mol Biosyst. 2012 Jan;8(1):198-209. doi: 10.1039/c1mb05156c. Epub 2011 Jul 18. PMID- 15966733 OWN - NLM STAT- MEDLINE DA - 20050621 DCOM- 20050812 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 44 IP - 25 DP - 2005 Jun 28 TI - Forcing nonamyloidogenic beta-synuclein to fibrillate. PG - 9096-107 AB - The fibrillation and aggregation of alpha-synuclein is a key process in the formation of intracellular inclusions, Lewy bodies, in substantia nigral neurons and, potentially, in the pathology of Parkinson's disease and several other neurodegenerative disorders. Alpha-synuclein and its homologue beta-synuclein are both natively unfolded proteins that colocalize in presynaptic terminals of neurons in many regions of the brain, including those of dopamine-producing cells of the substantia nigra. Unlike its homologue, beta-synuclein does not form fibrils and has been shown to inhibit the fibrillation of alpha-synuclein. In this study, we demonstrate that fast and efficient aggregation and fibrillation of beta-synuclein can be induced in the presence of a variety of factors. Certain metals (Zn(2+), Pb(2+), and Cu(2+)) induce a partially folded conformation of beta-synuclein that triggers rapid fibrillation. In the presence of these metals, mixtures of alpha- and beta-synucleins exhibited rapid fibrillation. The metal-induced fibrillation of beta-synuclein was further accelerated by the addition of glycosaminoglycans or high concentrations of macromolecular crowding agents. Beta-synuclein also rapidly formed soluble oligomers and fibrils in the presence of pesticides, whereas the addition of low concentrations of organic solvents induced formation of amorphous aggregates. These new findings demonstrate the potential effect of environmental pollutants in generating an amyloidogenic, and potentially neurotoxic, conformation, in an otherwise benign protein. FAU - Yamin, Ghiam AU - Yamin G AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. FAU - Munishkina, Larissa A AU - Munishkina LA FAU - Karymov, Mikhail A AU - Karymov MA FAU - Lyubchenko, Yuri L AU - Lyubchenko YL FAU - Uversky, Vladimir N AU - Uversky VN FAU - Fink, Anthony L AU - Fink AL LA - eng GR - NS39985/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Glycosaminoglycans) RN - 0 (Nerve Tissue Proteins) RN - 0 (Pesticides) RN - 0 (SNCA protein, human) RN - 0 (SNCB protein, human) RN - 0 (Solvents) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 0 (beta-Synuclein) RN - 0 (glucosaminoglycans) RN - 2P299V784P (Lead) RN - 789U1901C5 (Copper) RN - J41CSQ7QDS (Zinc) SB - IM MH - Amyloid/*chemistry/*metabolism MH - Chromatography, High Pressure Liquid MH - Circular Dichroism MH - Copper/pharmacology MH - Glycosaminoglycans/pharmacology MH - Humans MH - Lead/pharmacology MH - Microscopy, Atomic Force MH - Nerve Tissue Proteins/*chemistry/*metabolism/ultrastructure MH - Pesticides/pharmacology MH - Protein Binding MH - Protein Structure, Quaternary MH - Solvents MH - Spectroscopy, Fourier Transform Infrared MH - Synucleins MH - Zinc/pharmacology MH - alpha-Synuclein MH - beta-Synuclein EDAT- 2005/06/22 09:00 MHDA- 2005/08/13 09:00 CRDT- 2005/06/22 09:00 AID - 10.1021/bi048778a [doi] PST - ppublish SO - Biochemistry. 2005 Jun 28;44(25):9096-107. PMID- 25091206 OWN - NLM STAT- In-Data-Review DA - 20141028 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 103 IP - 1 DP - 2015 Jan TI - The C-terminal calcium-sensitive disordered motifs regulate isoform-specific polymerization characteristics of calsequestrin. PG - 15-22 LID - 10.1002/bip.22534 [doi] AB - Calsequestrin (CASQ) exists as two distinct isoforms CASQ1 and CASQ2 in all vertebrates. Although the isoforms exhibit unique functional characteristic, the structural basis for the same is yet to be fully defined. Interestingly, the C-terminal region of the two isoforms exhibit significant differences both in length and amino acid composition; forming Dn-motif and DEXn-motif in CASQ1 and CASQ2, respectively. Here, we investigated if the unique C-terminal motifs possess Ca(2+) -sensitivity and affect protein function. Sequence analysis shows that both the Dn- and DEXn-motifs are intrinsically disordered regions (IDRs) of the protein, a feature that is conserved from fish to man. Using purified synthetic peptides, we show that these motifs undergo distinctive Ca(2+) -mediated folding suggesting that these disordered motifs are Ca(2+) -sensitivity. We generated chimeric proteins by swapping the C-terminal portions between CASQ1 and CASQ2. Our studies show that the C-terminal portions do not play significant role in protein folding. An interesting finding of the current study is that the switching of the C-terminal portion completely reverses the polymerization kinetics. Collectively, these data suggest that these Ca(2+) -sensitivity IDRs located at the back-to-back dimer interface influence isoform-specific Ca(2+) -dependent polymerization properties of CASQ. (c) 2014 Wiley Periodicals, Inc. Biopolymers 103: 15-22, 2015. CI - (c) 2014 Wiley Periodicals, Inc. FAU - Bal, Naresh C AU - Bal NC AD - Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210. FAU - Jena, Nivedita AU - Jena N FAU - Chakravarty, Harapriya AU - Chakravarty H FAU - Kumar, Amit AU - Kumar A FAU - Chi, Mei AU - Chi M FAU - Balaraju, Tuniki AU - Balaraju T FAU - Rawale, Sharad V AU - Rawale SV FAU - Rawale, Jayashree S AU - Rawale JS FAU - Sharon, Ashoke AU - Sharon A FAU - Periasamy, Muthu AU - Periasamy M LA - eng GR - R01 HL088555/HL/NHLBI NIH HHS/United States PT - Journal Article PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 SB - IM PMC - PMC4213203 MID - NIHMS619978 OID - NLM: NIHMS619978 [Available on 01/01/16] OID - NLM: PMC4213203 [Available on 01/01/16] OTO - NOTNLM OT - calcium binding protein OT - calcium-induced polymerization OT - circular dichroism OT - disordered motifs EDAT- 2014/08/06 06:00 MHDA- 2014/08/06 06:00 CRDT- 2014/08/06 06:00 PMCR- 2016/01/01 00:00 PHST- 2014/06/08 [received] PHST- 2014/07/31 [revised] PHST- 2014/08/01 [accepted] AID - 10.1002/bip.22534 [doi] PST - ppublish SO - Biopolymers. 2015 Jan;103(1):15-22. doi: 10.1002/bip.22534. PMID- 15713458 OWN - NLM STAT- MEDLINE DA - 20050216 DCOM- 20050318 LR - 20141120 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 346 IP - 3 DP - 2005 Feb 25 TI - Molecular recognition via coupled folding and binding in a TPR domain. PG - 717-32 AB - The majority of known tetratricopeptide repeat (TPR) domains consist of three copies of the helix-turn-helix TPR motif, together with a seventh C-terminal helix. TPR domains function as protein-protein recognition modules in intracellular signalling. This function is exemplified by the TPR domain of protein phosphatase 5 (PP5), which binds to the C terminus of the chaperone protein Hsp90. Here, we report NMR and CD spectroscopic studies that reveal that this domain is largely unfolded at physiological temperatures, and that interaction with an MEEVD pentapeptide derived from Hsp90 stabilises a folded structure. This complex, coupled folding-binding mechanism is characterised further by its observed enthalpy change on binding (determined by isothermal titration calorimetry), which displays a markedly non-linear relationship with temperature. A nested Gibbs-Helmholtz model is used in a novel combined analysis of the CD and ITC data to determine separately the thermodynamic contributions of the intrinsic folding and binding events to the overall coupled process. The analysis shows that, despite the expected large entropic opposition to the folding process, a nearly equal favourable folding enthalpy means the net effect of coupled folding on the observed affinity is small across a broad range of temperature. We hypothesise that a coupled folding-binding mechanism is common in this class of domains. FAU - Cliff, Matthew J AU - Cliff MJ AD - Department of Biochemistry and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK. FAU - Williams, Mark A AU - Williams MA FAU - Brooke-Smith, John AU - Brooke-Smith J FAU - Barford, David AU - Barford D FAU - Ladbury, John E AU - Ladbury JE LA - eng GR - MC_U117533887/Medical Research Council/United Kingdom PT - Journal Article DEP - 20050118 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (HSP90 Heat-Shock Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Peptide Fragments) RN - 0 (Proteins) RN - 0 (Recombinant Proteins) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - EC 3.1.3.16 (protein phosphatase 5) SB - IM MH - Amino Acid Sequence MH - Calorimetry MH - Circular Dichroism MH - HSP90 Heat-Shock Proteins/chemistry/genetics/metabolism MH - Humans MH - In Vitro Techniques MH - Mutagenesis, Site-Directed MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/chemistry/genetics/metabolism MH - Peptide Fragments/chemistry/genetics/metabolism MH - Phosphoprotein Phosphatases/chemistry/genetics/metabolism MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Proteins/*chemistry/genetics/*metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Thermodynamics EDAT- 2005/02/17 09:00 MHDA- 2005/03/19 09:00 CRDT- 2005/02/17 09:00 PHST- 2004/09/14 [received] PHST- 2004/12/08 [revised] PHST- 2004/12/08 [accepted] PHST- 2005/01/18 [aheadofprint] AID - S0022-2836(04)01587-6 [pii] AID - 10.1016/j.jmb.2004.12.017 [doi] PST - ppublish SO - J Mol Biol. 2005 Feb 25;346(3):717-32. Epub 2005 Jan 18. PMID- 24327774 OWN - NLM STAT- MEDLINE DA - 20131211 DCOM- 20150417 IS - 1738-0006 (Electronic) IS - 0023-4001 (Linking) VI - 51 IP - 5 DP - 2013 Oct TI - A rapid diagnostic test for toxoplasmosis using recombinant antigenic N-terminal half of SAG1 linked with intrinsically unstructured domain of gra2 protein. PG - 503-10 LID - 10.3347/kjp.2013.51.5.503 [doi] AB - Toxoplasma gondii is an apicomplexan parasite with a broad host range of most warm-blooded mammals including humans, of which one-thirds of the human population has been infected worldwide which can cause congenital defects, abortion, and neonatal complications. Here, we developed a rapid diagnostic test (RDT) for T. gondii infection. Antigenic N-terminal half of the major surface antigen (SAG1) was linked with intrinsically unstructured domain (IUD) of dense granule protein 2 (GRA2). The recombinant GST-GRA2-SAG1A protein was successfully expressed and purified as 51 kDa of molecular weight. Furthermore, antigenicity and solubility of the rGST-GRA2-SAG1A protein were significantly increased. The overall specificity and sensitivity of GST-GRA2-SAG1A loaded RDT (TgRDT) were estimated as 100% and 97.1% by comparing with ELISA result which uses T. gondii whole cell lysates as the antigen. The TgRDT tested with Uganda people sera for field trial and showed 31.9% of seroprevalence against T. gondii antibody. The TgRDT is proved to be a kit for rapid and easy to use with high accuracy, which would be a suitable serodiagnostic tool for toxoplasmosis. FAU - Song, Kyoung Ju AU - Song KJ AD - Department of Parasitology, Catholic Institute of Parasitic Disease, College of Medicine, Catholic University of Korea, Seoul 137-701, Korea. FAU - Yang, Zhaoshou AU - Yang Z FAU - Chong, Chom-Kyu AU - Chong CK FAU - Kim, Jin-Soo AU - Kim JS FAU - Lee, Kyung Chan AU - Lee KC FAU - Kim, Tong-Soo AU - Kim TS FAU - Nam, Ho-Woo AU - Nam HW LA - eng PT - Evaluation Studies PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131031 PL - Korea (South) TA - Korean J Parasitol JT - The Korean journal of parasitology JID - 9435800 RN - 0 (Antibodies, Protozoan) RN - 0 (Antigens, Protozoan) RN - 0 (Gra2 protein, Toxoplasma gondii) RN - 0 (Protozoan Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (SAG1 antigen, Toxoplasma) SB - IM MH - Adolescent MH - Adult MH - Amino Acid Sequence MH - Antibodies, Protozoan/*blood MH - Antigens, Protozoan/genetics/*immunology MH - Child MH - Child, Preschool MH - Female MH - Humans MH - Infant MH - Male MH - Molecular Sequence Data MH - Protozoan Proteins/genetics/*immunology MH - Recombinant Fusion Proteins MH - Reproducibility of Results MH - Republic of Korea/epidemiology MH - Sensitivity and Specificity MH - Serologic Tests MH - Time Factors MH - Toxoplasma/genetics/*immunology/isolation & purification MH - Toxoplasmosis/*diagnosis/epidemiology/parasitology MH - Uganda/epidemiology MH - Young Adult PMC - PMC3857496 OID - NLM: PMC3857496 OTO - NOTNLM OT - ELISA OT - Toxoplasma gondii OT - intrinsically unstructured domain OT - rapid diagnostic test OT - recombinant GST-GRA2-SAG1A OT - serodiagnosis EDAT- 2013/12/12 06:00 MHDA- 2015/04/18 06:00 CRDT- 2013/12/12 06:00 PHST- 2013/07/08 [received] PHST- 2013/08/30 [revised] PHST- 2013/09/02 [accepted] PHST- 2013/10/31 [epublish] AID - 10.3347/kjp.2013.51.5.503 [doi] PST - ppublish SO - Korean J Parasitol. 2013 Oct;51(5):503-10. doi: 10.3347/kjp.2013.51.5.503. Epub 2013 Oct 31. PMID- 24830542 OWN - NLM STAT- In-Process DA - 20150306 IS - 1874-270X (Electronic) VI - 9 IP - 1 DP - 2015 Apr TI - (1)H, (13)C and (15)N resonance assignment of the mature form of monothiol glutaredoxin 1 from the pathogen Trypanosoma brucei. PG - 143-6 LID - 10.1007/s12104-014-9561-3 [doi] AB - Glutaredoxins (Grx) are small proteins, conserved throughout all the kingdoms of life, which are engaged in a wide variety of biological processes. According to the number of cysteines in their active site, Grx are classified as dithiolic or monothiolic (1-C-Grx). In most organisms, 1-C-Grx are implicated in iron-sulfur cluster (FeS) metabolism and utilize glutathione as cofactor. Trypanosomatids are parasitic protozoa of the order Kinetoplastida, which cause severe diseases in humans and domestic animals. These parasites exploit a unique thiol-dependent redox system based on bis(glutathionyl)spermidine (trypanothione) rather than on glutathione. Mitochondrial 1-C-Grx1 from trypanosomes differs from orthologues in several features including the use of trypanothione as ligand for FeS binding and the presence of a parasite-specific N-terminal extension. We have recently shown that 1-C-Grx1 from Trypanosoma brucei is indispensable for parasite survival in mouse, making this protein a potential drug target candidate against trypanosomiasis. However, structural information for the full-length form of 1-C-Grx1 is still lacking. Here, we report the NMR resonance assignment of the mature form of Tb1-C-Grx1 including an N-terminal tail, paving the way to disclose the role of this intrinsically disordered region in the protein function. FAU - Sturlese, Mattia AU - Sturlese M AD - Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy. FAU - Lelli, Moreno AU - Lelli M FAU - Manta, Bruno AU - Manta B FAU - Mammi, Stefano AU - Mammi S FAU - Comini, Marcelo A AU - Comini MA FAU - Bellanda, Massimo AU - Bellanda M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140516 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 SB - IM EDAT- 2014/05/17 06:00 MHDA- 2014/05/17 06:00 CRDT- 2014/05/17 06:00 PHST- 2014/02/26 [received] PHST- 2014/05/06 [accepted] PHST- 2014/05/16 [aheadofprint] AID - 10.1007/s12104-014-9561-3 [doi] PST - ppublish SO - Biomol NMR Assign. 2015 Apr;9(1):143-6. doi: 10.1007/s12104-014-9561-3. Epub 2014 May 16. PMID- 15136044 OWN - NLM STAT- MEDLINE DA - 20040511 DCOM- 20040713 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 339 IP - 2 DP - 2004 May 28 TI - In vitro characterization of FlgB, FlgC, FlgF, FlgG, and FliE, flagellar basal body proteins of Salmonella. PG - 423-35 AB - The bacterial flagellar basal body is a rotary motor. It spans the cytoplasmic and outer membranes and drives rapid rotation of a long helical filament in the cell exterior. The flagellar rod at its central axis is a drive shaft that transmits torque through the hook to the filament to propel the bacterial locomotion. To study the structure of the rod in detail, we have established purification procedures for Salmonella rod proteins, FlgB, FlgC, FlgF, FlgG, and also for FliE, a rod adapter protein, from an Escherichia coli expression system. While FlgF was highly soluble, FlgB, FlgC, FlgG and FliE tended to self or cross-aggregate into fibrils in solutions at neutral pH or below, at high ionic strength, or at high protein concentration. These aggregates were characterized to be beta-amyloid fibrils, unrelated to the rod structure formed in vivo. Under non-aggregative conditions, no protein-protein interactions were detected between any pairs of these five proteins, suggesting that their spontaneous, template-free polymerization is strongly suppressed. Limited proteolyses showed that FlgF and FlgG have natively unfolded N and C-terminal regions of about 100 residues in total just as flagellin does, whereas FlgB, FlgC and FliE, which are little over 100 residues long, are unfolded in their entire peptide chains. These results together with other data indicate that all of the ten flagellar axial proteins share structural characteristics and folding dynamics in relation to the mechanism of their self-assembly into the flagellar axial structure. FAU - Saijo-Hamano, Yumiko AU - Saijo-Hamano Y AD - Protomic NanoMachine Project, ERATO, JST, Seika, Kyoto, Japan. FAU - Uchida, Naoko AU - Uchida N FAU - Namba, Keiichi AU - Namba K FAU - Oosawa, Kenji AU - Oosawa K LA - eng PT - Journal Article PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (DNA Primers) SB - IM MH - Bacterial Proteins/*chemistry/isolation & purification/metabolism/ultrastructure MH - Base Sequence MH - Chromatography, Gel MH - Chromatography, Ion Exchange MH - DNA Primers MH - Flagella/*chemistry MH - Hydrolysis MH - Mass Spectrometry MH - Microscopy, Electron MH - Salmonella/*chemistry EDAT- 2004/05/12 05:00 MHDA- 2004/07/14 05:00 CRDT- 2004/05/12 05:00 PHST- 2003/12/29 [received] PHST- 2004/03/25 [revised] PHST- 2004/03/25 [accepted] AID - 10.1016/j.jmb.2004.03.070 [doi] AID - S0022283604003870 [pii] PST - ppublish SO - J Mol Biol. 2004 May 28;339(2):423-35. PMID- 10064708 OWN - NLM STAT- MEDLINE DA - 19990427 DCOM- 19990427 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 286 IP - 5 DP - 1999 Mar 12 TI - Glycyl-tRNA synthetase uses a negatively charged pit for specific recognition and activation of glycine. PG - 1449-59 AB - The crystal structures of glycyl-tRNA synthetase (GlyRS) from Thermus thermophilus, a homodimeric class II enzyme, were determined in the enzyme-substrate and enzyme-product states corresponding to the first step of aminoacylation. GlyRS was cocrystallized with glycine and ATP, which were transformed by the enzyme into glycyl-adenylate and thus gave the enzyme-product complex. To trap the enzyme-substrate complex, the enzyme was combined with the glycine analog ethanolamine and ATP. The ligands are bound in fixed orientations in the substrate-binding pocket of the N-terminal active site domain, which contains the classical class II aminoacyl-tRNA synthetase (aaRS) fold. Since glycine does not possess a side-chain, much of the specificity of the enzyme is directed toward excluding any additional atoms beyond the alpha-carbon atom. Several carboxylate residues of GlyRS line the glycine binding pocket; two of them interact directly with the alpha-ammonium group. In addition, the enzyme utilizes the acidic character of the pro-L alpha-hydrogen atom by contacting it via a glutamate carboxylic oxygen atom. A guanidino eta-nitrogen atom of the class II aaRS-conserved motif 2 arginine interacts with the substrate carbonyl oxygen atom. These features serve to attract the small amino acid substrate into the active site and to position it in the correct orientation. GlyRS uses class II-conserved residues to interact with the ATP and the adenosine-phosphate moiety of glycyl-adenylate. On the basis of this similarity, we propose that GlyRS utilizes the same general mechanism as that employed by other class II aminoacyl-tRNA synthetases. CI - Copyright 1999 Academic Press. FAU - Arnez, J G AU - Arnez JG AD - Laboratoire de Biologie Structurale, Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch Cedex, 67404, France. FAU - Dock-Bregeon, A C AU - Dock-Bregeon AC FAU - Moras, D AU - Moras D LA - eng SI - PDB/1B76 SI - PDB/1GGM PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Phosphates) RN - 35985-26-3 (glycyladenylate) RN - 415SHH325A (Adenosine Monophosphate) RN - 5KV86114PT (Ethanolamine) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 6.1.1.14 (Glycine-tRNA Ligase) RN - I38ZP9992A (Magnesium) RN - TE7660XO1C (Glycine) SB - IM MH - Adenosine Monophosphate/analogs & derivatives/chemistry/metabolism MH - Adenosine Triphosphate/chemistry/metabolism MH - Binding Sites MH - Crystallization MH - Crystallography, X-Ray MH - Dimerization MH - Electrons MH - Ethanolamine/metabolism MH - Glycine/chemistry/*metabolism MH - Glycine-tRNA Ligase/chemistry/isolation & purification/*metabolism MH - Hydrogen Bonding MH - Magnesium/chemistry/metabolism MH - Models, Chemical MH - Models, Molecular MH - Molecular Sequence Data MH - Phosphates/chemistry/metabolism MH - Protein Conformation MH - Substrate Specificity MH - Thermus thermophilus/*enzymology MH - *Transfer RNA Aminoacylation EDAT- 1999/03/05 MHDA- 1999/03/05 00:01 CRDT- 1999/03/05 00:00 AID - S0022-2836(99)92562-7 [pii] AID - 10.1006/jmbi.1999.2562 [doi] PST - ppublish SO - J Mol Biol. 1999 Mar 12;286(5):1449-59. PMID- 9698548 OWN - NLM STAT- MEDLINE DA - 19980903 DCOM- 19980903 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 281 IP - 2 DP - 1998 Aug 14 TI - High-resolution solution structure of the retinoid X receptor DNA-binding domain. PG - 271-84 AB - The retinoid X receptor (RXR) is a member of the nuclear hormone receptor superfamily of transcriptional regulators and plays a central role in the retinoid and, through its ability to heterodimerize with other nuclear hormone receptors, non-steroid signaling pathways. The DNA-binding and recognition functions of RXR are located in a conserved 83 amino acid residue domain that recognizes the consensus sequence AGGTCA. In order to provide a detailed picture of its structure, we have calculated a high-resolution solution structure of the C195A RXRalpha DNA-binding domain. Structures were calculated using 1131 distance and dihedral angle constraints derived from 1H, 13C and 15N NMR spectra. The structures reveal a perpendicularly packed, "loop-helix" fold similar to other nuclear hormone receptor DNA-binding domains and confirm the existence of the C-terminal helix, which was first observed in the low-resolution NMR structure. The C-terminal helix is well formed and is stabilized by packing interactions with residues in the hydrophobic core. The solution structure of RXR is very similar to that determined by X-ray crystallographic studies of the RXR-TR heterodimer complex with DNA, except that in the latter case no electron density was observed for residues corresponding to the C-terminal helix. Other differences between the X-ray and NMR structures occur in the second zinc-binding loop, which is disordered in solution. Heteronuclear 15N NOE measurements suggest that this loop has enhanced flexibility in the free protein. CI - Copyright 1998 Academic Press FAU - Holmbeck, S M AU - Holmbeck SM AD - Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla,, CA 92037, USA. FAU - Foster, M P AU - Foster MP FAU - Casimiro, D R AU - Casimiro DR FAU - Sem, D S AU - Sem DS FAU - Dyson, H J AU - Dyson HJ FAU - Wright, P E AU - Wright PE LA - eng SI - PDB/1RXR GR - GM36643/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Receptors, Retinoic Acid) RN - 0 (Retinoid X Receptors) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) RN - J41CSQ7QDS (Zinc) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - DNA MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - *Protein Structure, Secondary MH - Receptors, Retinoic Acid/*chemistry MH - Retinoid X Receptors MH - Transcription Factors/*chemistry MH - Zinc/chemistry EDAT- 1998/08/12 MHDA- 1998/08/12 00:01 CRDT- 1998/08/12 00:00 AID - S0022-2836(98)91908-8 [pii] AID - 10.1006/jmbi.1998.1908 [doi] PST - ppublish SO - J Mol Biol. 1998 Aug 14;281(2):271-84. PMID- 21712388 OWN - NLM STAT- MEDLINE DA - 20110822 DCOM- 20111018 LR - 20141022 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 34 DP - 2011 Aug 26 TI - Effect of Src kinase phosphorylation on disordered C-terminal domain of N-methyl-D-aspartic acid (NMDA) receptor subunit GluN2B protein. PG - 29904-12 LID - 10.1074/jbc.M111.258897 [doi] AB - NMDA receptors are ligand-gated ion channels with a regulatory intracellular C-terminal domain (CTD). In GluN2B, the CTD is the largest domain in the protein but is intrinsically disordered. The GluN2B subunit is the major tyrosine-phosphorylated protein in synapses. Src kinase phosphorylates the GluN2B CTD, but it is unknown how this affects channel activity. In disordered proteins, phosphorylation can tip the balance between order and disorder. Transitions can occur in both directions, so it is not currently possible to predict the effects of phosphorylation. We used single molecule fluorescence to characterize the effects of Src phosphorylation on GluN2B. Scanning fluorescent labeling sites throughout the domain showed no positional dependence of the energy transfer. Instead, efficiency only scaled with the separation between labeling sites suggestive of a relatively featureless conformational energy landscape. Src phosphorylation led to a general expansion of the polypeptide, which would result in greater exposure of known protein-binding sites and increase the physical separation between contiguous sites. Phosphorylation makes the CTD more like a random coil leaving open the question of how Src exerts its effects on the NMDA receptor. FAU - Choi, Ucheor B AU - Choi UB AD - Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794-8661, USA. FAU - Xiao, Shifeng AU - Xiao S FAU - Wollmuth, Lonnie P AU - Wollmuth LP FAU - Bowen, Mark E AU - Bowen ME LA - eng GR - MH066892/MH/NIMH NIH HHS/United States GR - MH081923/MH/NIMH NIH HHS/United States GR - R01 MH081923/MH/NIMH NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20110628 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (NR2B NMDA receptor) RN - 0 (Receptors, N-Methyl-D-Aspartate) RN - EC 2.7.10.2 (src-Family Kinases) SB - IM MH - Binding Sites MH - Humans MH - Phosphorylation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, N-Methyl-D-Aspartate/*chemistry/genetics/metabolism MH - src-Family Kinases/*chemistry/genetics/metabolism PMC - PMC3191031 OID - NLM: PMC3191031 EDAT- 2011/06/30 06:00 MHDA- 2011/10/19 06:00 CRDT- 2011/06/30 06:00 PHST- 2011/06/28 [aheadofprint] AID - M111.258897 [pii] AID - 10.1074/jbc.M111.258897 [doi] PST - ppublish SO - J Biol Chem. 2011 Aug 26;286(34):29904-12. doi: 10.1074/jbc.M111.258897. Epub 2011 Jun 28. PMID- 18664522 OWN - NLM STAT- MEDLINE DA - 20081006 DCOM- 20090107 LR - 20131121 IS - 0021-924X (Print) IS - 0021-924X (Linking) VI - 144 IP - 4 DP - 2008 Oct TI - A plasma membrane-associated protein of Arabidopsis thaliana AtPCaP1 binds copper ions and changes its higher order structure. PG - 487-97 LID - 10.1093/jb/mvn092 [doi] AB - PCaP1, a hydrophilic cation-binding protein, is bound to the plasma membrane in Arabidopsis thaliana. We focused on the physicochemical properties of PCaP1 to understand its uniqueness in terms of structure and binding of metal ions. On fluorescence analysis, PCaP1 showed a signal of structural change in the presence of Cu(2+). The near-UV CD spectra showed a marked change of PCaP1 in CuCl(2) solution. The far-UV CD spectra showed the presence of alpha-helices and the intrinsically unstructured region. However, addition of Cu(2+) gave no change in the far-UV CD spectra. These results indicate that Cu(2+) induced a change in the tertiary structure without changing the secondary structure. The protein was sensitive to proteinase in the presence of Cu(2+), supporting that Cu(2+) is involved in the structural change. The PCaP1 solution was titrated with CuCl(2) and the change in the fluorescence spectrum was monitored to characterize Cu(2+)-binding properties. The obtained values of K(d) for Cu(2+) and the ligand-binding number were 10 microM and six ions per molecule, respectively. These findings indicate that PCaP1 has a high Cu(2+)-binding capacity with a relatively high affinity. PCaP1 lacks cysteine and histidine residues. A large number of glutamate residues may be involved in the Cu(2+) binding. FAU - Nagasaki-Takeuchi, Nahoko AU - Nagasaki-Takeuchi N AD - Laboratory of Cell Dynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan. FAU - Miyano, Masashi AU - Miyano M FAU - Maeshima, Masayoshi AU - Maeshima M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080729 PL - Japan TA - J Biochem JT - Journal of biochemistry JID - 0376600 RN - 0 (Arabidopsis Proteins) RN - 0 (Calcium-Binding Proteins) RN - 0 (Carrier Proteins) RN - 0 (Membrane Proteins) RN - 0 (PCaP1 protein, Arabidopsis) RN - 0 (Recombinant Proteins) RN - 789U1901C5 (Copper) SB - IM MH - Arabidopsis/genetics/metabolism MH - Arabidopsis Proteins/*chemistry/genetics/*metabolism MH - Calcium-Binding Proteins MH - Carrier Proteins/*chemistry/genetics/*metabolism MH - Cell Membrane/metabolism MH - Circular Dichroism MH - Copper/*metabolism MH - Kinetics MH - Membrane Proteins/*chemistry/genetics/*metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Spectrometry, Fluorescence MH - Thermodynamics EDAT- 2008/07/31 09:00 MHDA- 2009/01/08 09:00 CRDT- 2008/07/31 09:00 PHST- 2008/07/29 [aheadofprint] AID - mvn092 [pii] AID - 10.1093/jb/mvn092 [doi] PST - ppublish SO - J Biochem. 2008 Oct;144(4):487-97. doi: 10.1093/jb/mvn092. Epub 2008 Jul 29. PMID- 22947936 OWN - NLM STAT- MEDLINE DA - 20120905 DCOM- 20130117 LR - 20141105 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 103 IP - 4 DP - 2012 Aug 22 TI - Identification of minimally interacting modules in an intrinsically disordered protein. PG - 748-57 LID - 10.1016/j.bpj.2012.06.052 [doi] AB - The conformational characterization of intrinsically disordered proteins (IDPs) is complicated by their conformational heterogeneity and flexibility. If an IDP could somehow be divided into smaller fragments and reconstructed later, theoretical and spectroscopic studies could probe its conformational variability in detail. Here, we used replica molecular-dynamics simulations and network theory to explore whether such a divide-and-conquer strategy is feasible for alpha-synuclein, a prototypical IDP. We characterized the conformational variability of alpha-synuclein by conducting >100 unbiased all-atom molecular-dynamics simulations, for a total of >10 mus of trajectories. In these simulations, alpha-synuclein formed a heterogeneous ensemble of collapsed coil states in an aqueous environment. These states were stabilized by heterogeneous contacts between sequentially distant regions. We find that alpha-synuclein contains residual secondary structures in the collapsed states, and the heterogeneity in the collapsed state makes it feasible to split alpha-synuclein into sequentially contiguous minimally interacting fragments. This study reveals previously unknown characteristics of alpha-synuclein and provides a new (to our knowledge) approach for studying other IDPs. CI - Copyright (c) 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Sethi, Anurag AU - Sethi A AD - Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA. FAU - Tian, Jianhui AU - Tian J FAU - Vu, Dung M AU - Vu DM FAU - Gnanakaran, S AU - Gnanakaran S LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Peptide Fragments) RN - 0 (alpha-Synuclein) RN - 059QF0KO0R (Water) SB - IM MH - *Molecular Dynamics Simulation MH - Peptide Fragments/chemistry MH - Protein Structure, Secondary MH - Vibration MH - Water/chemistry MH - alpha-Synuclein/*chemistry/metabolism PMC - PMC3443776 OID - NLM: PMC3443776 EDAT- 2012/09/06 06:00 MHDA- 2013/01/18 06:00 CRDT- 2012/09/06 06:00 PHST- 2011/11/17 [received] PHST- 2012/06/20 [revised] PHST- 2012/06/25 [accepted] AID - S0006-3495(12)00785-0 [pii] AID - 10.1016/j.bpj.2012.06.052 [doi] PST - ppublish SO - Biophys J. 2012 Aug 22;103(4):748-57. doi: 10.1016/j.bpj.2012.06.052. PMID- 19783089 OWN - NLM STAT- MEDLINE DA - 20091027 DCOM- 20100122 IS - 1873-4200 (Electronic) IS - 0301-4622 (Linking) VI - 145 IP - 2-3 DP - 2009 Dec TI - Thermally induced structural changes of intrinsically disordered small heat shock protein Hsp22. PG - 79-85 LID - 10.1016/j.bpc.2009.09.003 [doi] AB - We applied different methods (differential scanning calorimetry, circular dichroism, Fourier transform infrared spectroscopy, and intrinsic fluorescence) to investigate the thermal-induced changes in the structure of small heat shock protein Hsp22. It has been shown that this protein undergoes thermal-induced unfolding that occurs within a very broad temperature range (from 27 degrees C to 80 degrees C and above), and this is accompanied by complete disappearance of alpha-helices, significant decrease in beta-sheets content, and by pronounced changes in the intrinsic fluorescence. The results confirm predictions that Hsp22 belongs to the family of intrinsically disordered proteins (IDP) with certain parts of its molecule (presumably, in the alpha-crystallin domain) retaining folded structure and undergoing reversible thermal unfolding. The results are also discussed in terms of downhill folding scenario. FAU - Kazakov, Alexey S AU - Kazakov AS AD - A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prosp. 33, 119071 Moscow, Russia. FAU - Markov, Denis I AU - Markov DI FAU - Gusev, Nikolai B AU - Gusev NB FAU - Levitsky, Dmitrii I AU - Levitsky DI LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090912 PL - Netherlands TA - Biophys Chem JT - Biophysical chemistry JID - 0403171 RN - 0 (Actins) RN - 0 (Heat-Shock Proteins) RN - 0 (alpha-Crystallins) RN - EC 2.7.1.- (HSPB8 protein, human) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - Actins/metabolism MH - Calorimetry, Differential Scanning MH - Heat-Shock Proteins/*chemistry/genetics/metabolism/pharmacology MH - *Hot Temperature MH - Humans MH - Mutation MH - Protein Binding/drug effects MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein-Serine-Threonine Kinases/*chemistry/genetics/metabolism/pharmacology MH - alpha-Crystallins/chemistry EDAT- 2009/09/29 06:00 MHDA- 2010/01/23 06:00 CRDT- 2009/09/29 06:00 PHST- 2009/06/06 [received] PHST- 2009/08/31 [revised] PHST- 2009/09/05 [accepted] PHST- 2009/09/12 [aheadofprint] AID - S0301-4622(09)00176-8 [pii] AID - 10.1016/j.bpc.2009.09.003 [doi] PST - ppublish SO - Biophys Chem. 2009 Dec;145(2-3):79-85. doi: 10.1016/j.bpc.2009.09.003. Epub 2009 Sep 12. PMID- 22640394 OWN - NLM STAT- MEDLINE DA - 20120823 DCOM- 20120905 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 51 IP - 24 DP - 2012 Jun 19 TI - Multiple folding states and disorder of ribosomal protein SA, a membrane receptor for laminin, anticarcinogens, and pathogens. PG - 4807-21 LID - 10.1021/bi300335r [doi] AB - The human ribosomal protein SA (RPSA) is a multilocus protein, present in most cellular compartments. It is a multifunctional protein, which belongs to the ribosome but is also a membrane receptor for laminin, growth factors, prion, pathogenic microorganisms, toxins, and the anticarcinogen epigallocatechin gallate. It contributes to the crossing of the blood-brain barrier by neurotropic viruses and bacteria and is used as a biomarker of metastasis. RPSA includes an N-terminal domain, which is homologous to the prokaryotic ribosomal proteins S2, and a C-terminal extension, which is conserved in vertebrates. The structure of its N-domain has been determined from crystals grown at 17 degrees C. The structure of its C-domain remains unknown. We produced in Escherichia coli and purified the full-length RPSA and its N- and C-domains. We characterized the folding states of these recombinant proteins mainly by methods of fluorescence and circular dichroism spectrometry, in association with quantitative analyses of their unfolding equilibria, induced with heat or urea. The necessary equations were derived from first principles. The results showed that the N-domain unfolded according to a three-state equilibrium. The monomeric intermediate was predominant at the body temperature of 37 degrees C. It also existed in the full-length RPSA and bound ANS, a small fluorescent molecule. The C-domain was in an intrinsically disordered state. The recombinant N- and C-domains weakly interacted together. These results indicated a high plasticity of RPSA, which could be important for its multiple cellular localizations and functional interactions. FAU - Ould-Abeih, Mohamed B AU - Ould-Abeih MB AD - Institut Pasteur , Unit of Molecular Prevention and Therapy of Human Diseases, Department of Infection and Epidemiology, rue du Dr. Roux, F-75015 Paris, France. FAU - Petit-Topin, Isabelle AU - Petit-Topin I FAU - Zidane, Nora AU - Zidane N FAU - Baron, Bruno AU - Baron B FAU - Bedouelle, Hugues AU - Bedouelle H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120606 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Anticarcinogenic Agents) RN - 0 (Laminin) RN - 0 (RPSA protein, human) RN - 0 (Receptors, Laminin) RN - 0 (Ribosomal Proteins) RN - 8W8T17847W (Urea) SB - IM MH - Amino Acid Sequence MH - Animals MH - Anticarcinogenic Agents/*metabolism MH - Humans MH - Laminin/*metabolism MH - Mice MH - *Microbiology MH - Models, Molecular MH - Molecular Sequence Data MH - *Protein Folding MH - Protein Structure, Tertiary MH - Protein Unfolding/drug effects MH - Receptors, Laminin/*chemistry/isolation & purification/*metabolism MH - Ribosomal Proteins/*chemistry/isolation & purification/*metabolism MH - Spectrometry, Fluorescence MH - Urea/pharmacology EDAT- 2012/05/30 06:00 MHDA- 2012/09/06 06:00 CRDT- 2012/05/30 06:00 PHST- 2012/06/06 [aheadofprint] AID - 10.1021/bi300335r [doi] PST - ppublish SO - Biochemistry. 2012 Jun 19;51(24):4807-21. doi: 10.1021/bi300335r. Epub 2012 Jun 6. PMID- 15951570 OWN - NLM STAT- MEDLINE DA - 20050801 DCOM- 20051012 LR - 20141125 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 31 DP - 2005 Aug 5 TI - The unstructured N-terminal tail of ParG modulates assembly of a quaternary nucleoprotein complex in transcription repression. PG - 28683-91 AB - ParG is the prototype of a group of small (<10 kDa) proteins involved in accurate plasmid segregation. The protein is a dimeric DNA binding factor, which consists of symmetric paired C-terminal domains that interleave into a ribbon-helix-helix fold that is crucial for the interaction with DNA, and unstructured N-terminal domains of previously unknown function. Here the ParG protein is shown to be a transcriptional repressor of the parFG genes. The protein assembles on its operator site initially as a tetramer (dimer of dimers) and, at elevated protein concentrations, as a pair of tetramers. Progressive deletion of the mobile N-terminal tails concomitantly decreased transcriptional repression by ParG and perturbed the DNA binding kinetics of the protein. The flexible tails are not necessary for ParG dimerization but instead modulate the organization of a higher order nucleoprotein complex that is crucial for proper transcriptional repression. This is achieved by transient associations between the flexible and folded domains in complex with the target DNA. Numerous ParG homologs encoded by plasmids of Gram-negative bacteria similarly are predicted to possess N-terminal disordered tails, suggesting that this is a common feature of partition operon autoregulation. The results provide new insights into the role of natively unfolded domains in protein function, the molecular mechanisms of transcription regulation, and the control of plasmid segregation. FAU - Carmelo, Emma AU - Carmelo E AD - Faculty of Life Sciences, The University of Manchester, Manchester M60 1QD, United Kingdom. FAU - Barilla, Daniela AU - Barilla D FAU - Golovanov, Alexander P AU - Golovanov AP FAU - Lian, Lu-Yun AU - Lian LY FAU - Derome, Andrew AU - Derome A FAU - Hayes, Finbarr AU - Hayes F LA - eng GR - G0400287/Medical Research Council/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050612 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (ParG protein, E coli) RN - 0 (Repressor Proteins) SB - IM MH - Base Sequence MH - DNA Mutational Analysis MH - DNA-Binding Proteins/chemistry/genetics/*metabolism MH - Dimerization MH - Escherichia coli/genetics/metabolism MH - Escherichia coli Proteins/chemistry/genetics/*metabolism MH - Gene Expression Regulation, Bacterial MH - Kinetics MH - Molecular Sequence Data MH - Plasmids/*genetics MH - Promoter Regions, Genetic MH - Repressor Proteins/*chemistry/*metabolism MH - *Transcription, Genetic EDAT- 2005/06/14 09:00 MHDA- 2005/10/13 09:00 CRDT- 2005/06/14 09:00 PHST- 2005/06/12 [aheadofprint] AID - M501173200 [pii] AID - 10.1074/jbc.M501173200 [doi] PST - ppublish SO - J Biol Chem. 2005 Aug 5;280(31):28683-91. Epub 2005 Jun 12. PMID- 11162539 OWN - NLM STAT- MEDLINE DA - 20010222 DCOM- 20010322 LR - 20101118 IS - 0006-291X (Print) IS - 0006-291X (Linking) VI - 280 IP - 2 DP - 2001 Jan 19 TI - Flexible structures of SIBLING proteins, bone sialoprotein, and osteopontin. PG - 460-5 AB - Bone sialoprotein (BSP) and osteopontin (OPN) are two members of the SIBLING (Small Integrin-Binding LIgand, N-linked Glycoprotein) family of genetically related proteins that are clustered on human chromosome 4. We present evidence that this entire family is the result of duplication and subsequent divergent evolution of a single ancient gene. The solution structures of these two post-translationally modified recombinant proteins were solved by one dimensional proton NMR and transverse relaxation times. The polypeptide backbones of both free BSP and OPN rapidly sample an ensemble of conformations consistent with them both being completely unstructured in solution. This flexibility appears to enable these relatively small glycoproteins to rapidly associate with a number of different binding partners including other proteins as well as the mineral phase of bones and teeth. These proteins often function by bridging two proteins of fixed structures into a biologically active complex. CI - Copyright 2001 Academic Press. FAU - Fisher, L W AU - Fisher LW AD - Craniofacial and Skeletal Diseases Branch, NIH, Bethesda, Maryland, 20892-4320, USA. lfisher@dir.nidcr.nih.gov FAU - Torchia, D A AU - Torchia DA FAU - Fohr, B AU - Fohr B FAU - Young, M F AU - Young MF FAU - Fedarko, N S AU - Fedarko NS LA - eng PT - Journal Article PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (IBSP protein, human) RN - 0 (Integrin-Binding Sialoprotein) RN - 0 (Integrins) RN - 0 (Ligands) RN - 0 (Recombinant Proteins) RN - 0 (SPP1 protein, human) RN - 0 (Sialoglycoproteins) RN - 0 (Solutions) RN - 106441-73-0 (Osteopontin) SB - IM MH - Amino Acid Sequence MH - Bone and Bones/*chemistry/metabolism MH - Humans MH - Integrin-Binding Sialoprotein MH - Integrins/*metabolism MH - Ligands MH - Magnetic Resonance Spectroscopy MH - Models, Biological MH - Molecular Sequence Data MH - Osteopontin MH - Pliability MH - Protein Binding MH - Protein Conformation MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Alignment MH - Sialoglycoproteins/*chemistry/*metabolism MH - Solutions EDAT- 2001/02/13 11:00 MHDA- 2001/03/27 10:01 CRDT- 2001/02/13 11:00 AID - 10.1006/bbrc.2000.4146 [doi] AID - S0006-291X(00)94146-9 [pii] PST - ppublish SO - Biochem Biophys Res Commun. 2001 Jan 19;280(2):460-5. PMID- 25244701 OWN - NLM STAT- In-Process DA - 20141118 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 82 IP - 12 DP - 2014 Dec TI - Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins. PG - 3373-84 LID - 10.1002/prot.24692 [doi] AB - Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins (IDPs), mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N-terminal region of the p53 protein as an experimental model, a set of proline (PRO) and alanine (ALA) to glycine (GLY) substitution variants were designed to modulate backbone conformational propensities without introducing non-native intramolecular interactions. The hydrodynamic radius (R(h)) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the GLY substitutions decreased polyproline II (PP(II)) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution-induced changes in R(h) were not associated with folding. The experiments showed that changes in local PP(II) structure cause changes in R(h) that are variable and that depend on the intrinsic chain propensities of PRO and ALA residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed PRO and alanine effects on the structures of IDPs. CI - (c) 2014 Wiley Periodicals, Inc. FAU - Perez, Romel B AU - Perez RB AD - Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas. FAU - Tischer, Alexander AU - Tischer A FAU - Auton, Matthew AU - Auton M FAU - Whitten, Steven T AU - Whitten ST LA - eng GR - HL109109/HL/NHLBI NIH HHS/United States GR - R01 HL109109/HL/NHLBI NIH HHS/United States GR - R25 GM102783/GM/NIGMS NIH HHS/United States GR - R25-GM-102783/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20141010 PL - United States TA - Proteins JT - Proteins JID - 8700181 SB - IM PMC - PMC4237723 MID - NIHMS630185 OID - NLM: NIHMS630185 [Available on 12/01/15] OID - NLM: PMC4237723 [Available on 12/01/15] OTO - NOTNLM OT - alanine OT - hydrodynamic radius OT - intrinsically disordered protein OT - polyproline II OT - proline EDAT- 2014/09/23 06:00 MHDA- 2014/09/23 06:00 CRDT- 2014/09/23 06:00 PMCR- 2015/12/01 00:00 PHST- 2014/06/09 [received] PHST- 2014/08/26 [revised] PHST- 2014/09/16 [accepted] PHST- 2014/10/10 [aheadofprint] AID - 10.1002/prot.24692 [doi] PST - ppublish SO - Proteins. 2014 Dec;82(12):3373-84. doi: 10.1002/prot.24692. Epub 2014 Oct 10. PMID- 6194313 OWN - NLM STAT- MEDLINE DA - 19831123 DCOM- 19831123 LR - 20130925 IS - 0022-538X (Print) IS - 0022-538X (Linking) VI - 48 IP - 2 DP - 1983 Nov TI - Comparison of the major antigenic determinants of different serotypes of foot-and-mouth disease virus. PG - 451-9 AB - Complete nucleotide sequences which code for the capsid protein VP1 of two foot-and-mouth disease virus serotypes, O1Campos/Brazil/58 and C3Indaial/Brazil/71, have been determined. Ten available VP1 sequences (three serotype O, three serotype C, and four serotype A) were aligned and compared. Our evidence suggests that O1BFS/Britain/68 and O1K/Germany/66 are closely related to O1Campos/Brazil/58. Significant variations were observed between the nucleotide sequences of C3Indaial determined by two different laboratories. These differences are probably the result of virus adaptation and propagation in different laboratories. In one of the isolates (C3Biogen), a 13-base-pair stem and 13-base-pair loop structure is located in the 134-158 amino acid variable region. Isolates of different serotypes differ at two highly variable regions, amino acid positions 42-60 and 134-158, but isolates of the same serotype show major differences only in the variable region between amino acids 134 and 158. Since the remaining amino acid sequence of VP1 is highly conserved, we conclude that the 134-158 amino acid variable region is involved in subtype specificity, whereas both variable regions contribute to serotype differences. FAU - Cheung, A AU - Cheung A FAU - DeLamarter, J AU - DeLamarter J FAU - Weiss, S AU - Weiss S FAU - Kupper, H AU - Kupper H LA - eng SI - GENBANK/K01201 SI - GENBANK/K01202 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (Antigens, Viral) RN - 0 (DNA, Viral) RN - 0 (Epitopes) RN - 0 (Viral Proteins) RN - 0 (Viral Structural Proteins) SB - IM MH - Amino Acid Sequence MH - Antigens, Viral/genetics/*immunology MH - Aphthovirus/classification/genetics/*immunology MH - Base Sequence MH - DNA, Viral MH - Epitopes MH - Serotyping MH - Viral Proteins/genetics/*immunology MH - Viral Structural Proteins PMC - PMC255370 OID - NLM: PMC255370 EDAT- 1983/11/01 MHDA- 1983/11/01 00:01 CRDT- 1983/11/01 00:00 PST - ppublish SO - J Virol. 1983 Nov;48(2):451-9. PMID- 19022175 OWN - NLM STAT- MEDLINE DA - 20081121 DCOM- 20090206 LR - 20140913 IS - 1879-1301 (Electronic) IS - 1074-5521 (Linking) VI - 15 IP - 11 DP - 2008 Nov 24 TI - Structural rationale for the coupled binding and unfolding of the c-Myc oncoprotein by small molecules. PG - 1149-55 LID - 10.1016/j.chembiol.2008.09.011 [doi] AB - The basic-helix-loop-helix-leucine-zipper domains of the c-Myc oncoprotein and its obligate partner Max are intrinsically disordered (ID) monomers that undergo coupled folding and binding upon heterodimerization. We have identified the binding sites and determined the structural means by which two unrelated small molecules, 10058-F4 and 10074-G5, bind c-Myc and stabilize the ID monomer over the highly ordered c-Myc-Max heterodimer. In solution, the molecules bind to distinct regions of c-Myc and thus limit its ability to interact with Max and assume a more rigid and defined conformation. The identification of multiple, specific binding sites on an ID domain suggests that small molecules may provide a general means for manipulating the structure and function of ID proteins, such as c-Myc. FAU - Follis, Ariele Viacava AU - Follis AV AD - Department of Chemistry, Georgetown University, Washington, DC 20057, USA. FAU - Hammoudeh, Dalia I AU - Hammoudeh DI FAU - Wang, Huabo AU - Wang H FAU - Prochownik, Edward V AU - Prochownik EV FAU - Metallo, Steven J AU - Metallo SJ LA - eng GR - R01 CA140624/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Chem Biol JT - Chemistry & biology JID - 9500160 RN - 0 (10074-G5) RN - 0 (5-(4-ethylbenzylidene)-2-thioxothiazolidin-4-one) RN - 0 (MYC protein, human) RN - 0 (Oxadiazoles) RN - 0 (Proto-Oncogene Proteins c-myc) RN - 0 (Thiazoles) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Humans MH - Molecular Sequence Data MH - Mutation MH - Oxadiazoles/chemistry/*metabolism/*pharmacology MH - Protein Binding/drug effects MH - Protein Conformation/drug effects MH - Protein Denaturation/drug effects MH - Protein Multimerization/drug effects MH - Proto-Oncogene Proteins c-myc/chemistry/genetics/*metabolism MH - Thiazoles/chemistry/*metabolism/*pharmacology EDAT- 2008/11/22 09:00 MHDA- 2009/02/07 09:00 CRDT- 2008/11/22 09:00 PHST- 2008/07/19 [received] PHST- 2008/09/08 [revised] PHST- 2008/09/24 [accepted] AID - S1074-5521(08)00370-0 [pii] AID - 10.1016/j.chembiol.2008.09.011 [doi] PST - ppublish SO - Chem Biol. 2008 Nov 24;15(11):1149-55. doi: 10.1016/j.chembiol.2008.09.011. PMID- 15811367 OWN - NLM STAT- MEDLINE DA - 20050406 DCOM- 20050512 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 348 IP - 2 DP - 2005 Apr 29 TI - Solution structure and backbone dynamics of the KH-QUA2 region of the Xenopus STAR/GSG quaking protein. PG - 265-79 AB - The Quaking protein belongs to the family of STAR/GSG domain RNA-binding proteins and is involved in multiple cell signalling and developmental processes in vertebrates, including the formation of myelin. Heteronuclear NMR methods were used to determine the solution structure of a 134 residue fragment spanning the KH and QUA2 homology regions of the Quaking protein from Xenopus laevis (pXqua) in the absence of RNA. The protein is shown to adopt an extended type I KH domain fold that is connected to a structured alpha-helix in the C-terminal QUA2 region by means of a highly flexible linker. A comparison with the solution structure of the related protein splicing factor 1 (SF1) indicates that most aspects of the RNA-binding interface are conserved in pXqua, although the "variable loop" region that follows the second beta-strand possesses two additional alpha-helices. The structure of pXqua provides an appropriate template for building models of important homologues, such as GLD-1 and Sam68. Measurements of the (15)N relaxation parameters of pXqua confirm that the polypeptide backbone of the QUA2 region is more dynamic than that of the KH portion, and that the C-terminal helix is partially structured in the absence of RNA. By comparison with a random coil reference state, the nascent structure in the QUA2 region is estimated to contribute 15.5kJmol(-1) to the change in conformational free energy that occurs on forming a complex with RNA. Since STAR/GSG proteins may regulate alternative splicing by competing with SF1 in the nucleus for specific branch-point sequences that signal intronic RNA, the formation of secondary structure in the QUA2 region in the unbound state of pXqua has important functional consequences. FAU - Maguire, Mahon L AU - Maguire ML AD - Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAU - Guler-Gane, Gulin AU - Guler-Gane G FAU - Nietlispach, Daniel AU - Nietlispach D FAU - Raine, Andrew R C AU - Raine AR FAU - Zorn, Aaron M AU - Zorn AM FAU - Standart, Nancy AU - Standart N FAU - Broadhurst, R William AU - Broadhurst RW LA - eng SI - PDB/2BL5 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (RNA-Binding Proteins) RN - 0 (Xenopus Proteins) RN - 0 (Xqua protein, Xenopus) SB - IM MH - Amino Acid Sequence MH - Animals MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA-Binding Proteins/*chemistry/*metabolism MH - Sequence Alignment MH - Xenopus Proteins/*chemistry/*metabolism MH - *Xenopus laevis EDAT- 2005/04/07 09:00 MHDA- 2005/05/13 09:00 CRDT- 2005/04/07 09:00 PHST- 2004/10/11 [received] PHST- 2005/02/11 [revised] PHST- 2005/02/25 [accepted] AID - S0022-2836(05)00234-2 [pii] AID - 10.1016/j.jmb.2005.02.058 [doi] PST - ppublish SO - J Mol Biol. 2005 Apr 29;348(2):265-79. PMID- 18757857 OWN - NLM STAT- MEDLINE DA - 20081103 DCOM- 20081223 LR - 20140903 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 45 DP - 2008 Nov 7 TI - Doc of prophage P1 is inhibited by its antitoxin partner Phd through fold complementation. PG - 30821-7 LID - 10.1074/jbc.M805654200 [doi] AB - Prokaryotic toxin-antitoxin modules are involved in major physiological events set in motion under stress conditions. The toxin Doc (death on curing) from the phd/doc module on phage P1 hosts the C-terminal domain of its antitoxin partner Phd (prevents host death) through fold complementation. This Phd domain is intrinsically disordered in solution and folds into an alpha-helix upon binding to Doc. The details of the interactions reveal the molecular basis for the inhibitory action of the antitoxin. The complex resembles the Fic (filamentation induced by cAMP) proteins and suggests a possible evolutionary origin for the phd/doc operon. Doc induces growth arrest of Escherichia coli cells in a reversible manner, by targeting the protein synthesis machinery. Moreover, Doc activates the endogenous E. coli RelE mRNA interferase but does not require this or any other known chromosomal toxin-antitoxin locus for its action in vivo. FAU - Garcia-Pino, Abel AU - Garcia-Pino A AD - Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium. FAU - Christensen-Dalsgaard, Mikkel AU - Christensen-Dalsgaard M FAU - Wyns, Lode AU - Wyns L FAU - Yarmolinsky, Michael AU - Yarmolinsky M FAU - Magnuson, Roy David AU - Magnuson RD FAU - Gerdes, Kenn AU - Gerdes K FAU - Loris, Remy AU - Loris R LA - eng GR - 2 R15 GM67668-03/GM/NIGMS NIH HHS/United States GR - R15 GM067668/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't DEP - 20080830 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Toxins) RN - 0 (Doc protein, Enterobacteria phage P1) RN - 0 (Escherichia coli Proteins) RN - 0 (Phd protein, Enterobacteria phage P1) RN - 0 (RelE protein, E coli) RN - 0 (Viral Proteins) SB - IM MH - Bacterial Toxins/metabolism MH - Bacteriophage P1/*chemistry/metabolism MH - Escherichia coli/growth & development/metabolism/virology MH - Escherichia coli Proteins/metabolism MH - Prophages/*chemistry/metabolism MH - *Protein Folding MH - Protein Structure, Quaternary/physiology MH - Protein Structure, Secondary/physiology MH - Protein Structure, Tertiary/physiology MH - RNA Interference/physiology MH - Viral Proteins PMC - PMC2576525 OID - NLM: PMC2576525 EDAT- 2008/09/02 09:00 MHDA- 2008/12/24 09:00 CRDT- 2008/09/02 09:00 PHST- 2008/08/30 [aheadofprint] AID - M805654200 [pii] AID - 10.1074/jbc.M805654200 [doi] PST - ppublish SO - J Biol Chem. 2008 Nov 7;283(45):30821-7. doi: 10.1074/jbc.M805654200. Epub 2008 Aug 30. PMID- 15983043 OWN - NLM STAT- MEDLINE DA - 20050822 DCOM- 20051003 LR - 20140909 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 34 DP - 2005 Aug 26 TI - Disruption of the coenzyme binding site and dimer interface revealed in the crystal structure of mitochondrial aldehyde dehydrogenase "Asian" variant. PG - 30550-6 AB - Mitochondrial aldehyde dehydrogenase (ALDH2) is the major enzyme that oxidizes ethanol-derived acetaldehyde. A nearly inactive form of the enzyme, ALDH2*2, is found in about 40% of the East Asian population. This variant enzyme is defined by a glutamate to lysine substitution at residue 487 located within the oligomerization domain. ALDH2*2 has an increased Km for its coenzyme, NAD+, and a decreased kcat, which lead to low activity in vivo. Here we report the 2.1 A crystal structure of ALDH2*2. The structure shows a large disordered region located at the dimer interface that includes much of the coenzyme binding cleft and a loop of residues that form the base of the active site. As a consequence of these structural changes, the variant enzyme exhibits rigid body rotations of its catalytic and coenzyme-binding domains relative to the oligomerization domain. These structural perturbations are the direct result of the inability of lysine 487 to form important stabilizing hydrogen bonds with arginines 264 and 475. Thus, the elevated Km for coenzyme exhibited by this variant probably reflects the energetic penalty for reestablishing this site for productive coenzyme binding, whereas the structural alterations near the active site are consistent with the lowered Vmax. FAU - Larson, Heather N AU - Larson HN AD - Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA. FAU - Weiner, Henry AU - Weiner H FAU - Hurley, Thomas D AU - Hurley TD LA - eng SI - PDB/1ZUM GR - R01 AA 11982/AA/NIAAA NIH HHS/United States GR - R01 AA011982/AA/NIAAA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050627 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA, Complementary) RN - 0U46U6E8UK (NAD) RN - 3KX376GY7L (Glutamic Acid) RN - 94ZLA3W45F (Arginine) RN - EC 1.2.1.3 (Aldehyde Dehydrogenase) RN - K3Z4F929H6 (Lysine) SB - IM MH - Aldehyde Dehydrogenase/*chemistry MH - Arginine/chemistry MH - Binding Sites MH - Crystallography, X-Ray MH - DNA, Complementary/metabolism MH - Dimerization MH - Glutamic Acid/chemistry MH - Humans MH - Hydrogen Bonding MH - Kinetics MH - Lysine/chemistry MH - Mitochondria/*enzymology MH - Models, Molecular MH - NAD/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary PMC - PMC1262676 MID - NIHMS5043 OID - NLM: NIHMS5043 OID - NLM: PMC1262676 EDAT- 2005/06/29 09:00 MHDA- 2005/10/04 09:00 CRDT- 2005/06/29 09:00 PHST- 2005/06/27 [aheadofprint] AID - M502345200 [pii] AID - 10.1074/jbc.M502345200 [doi] PST - ppublish SO - J Biol Chem. 2005 Aug 26;280(34):30550-6. Epub 2005 Jun 27. PMID- 21777386 OWN - NLM STAT- MEDLINE DA - 20110819 DCOM- 20111021 LR - 20120711 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 278 IP - 17 DP - 2011 Sep TI - DYNLL/LC8: a light chain subunit of the dynein motor complex and beyond. PG - 2980-96 LID - 10.1111/j.1742-4658.2011.08254.x [doi] AB - The LC8 family members of dynein light chains (DYNLL1 and DYNLL2 in vertebrates) are highly conserved ubiquitous eukaryotic homodimer proteins that interact, besides dynein and myosin 5a motor proteins, with a large (and still incomplete) number of proteins involved in diverse biological functions. Despite an earlier suggestion that LC8 light chains function as cargo adapters of the above molecular motors, they are now recognized as regulatory hub proteins that interact with short linear motifs located in intrinsically disordered protein segments. The most prominent LC8 function is to promote dimerization of their binding partners that are often scaffold proteins of various complexes, including the intermediate chains of the dynein motor complex. Structural and functional aspects of this intriguing hub protein will be highlighted in this minireview. CI - (c) 2011 The Authors Journal compilation (c) 2011 FEBS. FAU - Rapali, Peter AU - Rapali P AD - Department of Biochemistry, Eotvos Lorand University, Budapest, Hungary. FAU - Szenes, Aron AU - Szenes A FAU - Radnai, Laszlo AU - Radnai L FAU - Bakos, Anita AU - Bakos A FAU - Pal, Gabor AU - Pal G FAU - Nyitray, Laszlo AU - Nyitray L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20110808 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Protein Subunits) RN - EC 3.6.4.2 (Cytoplasmic Dyneins) RN - EC 3.6.4.2 (DYNLL2 protein, human) RN - EC 3.6.4.2 (Dyneins) SB - IM MH - Animals MH - Biological Transport MH - Cytoplasmic Dyneins/chemistry/*physiology MH - Cytoskeleton/*metabolism MH - Dyneins/metabolism MH - Humans MH - Protein Interaction Domains and Motifs MH - Protein Subunits/chemistry/*physiology EDAT- 2011/07/23 06:00 MHDA- 2011/10/22 06:00 CRDT- 2011/07/23 06:00 PHST- 2011/08/08 [aheadofprint] AID - 10.1111/j.1742-4658.2011.08254.x [doi] PST - ppublish SO - FEBS J. 2011 Sep;278(17):2980-96. doi: 10.1111/j.1742-4658.2011.08254.x. Epub 2011 Aug 8. PMID- 8941715 OWN - NLM STAT- MEDLINE DA - 19970114 DCOM- 19970114 LR - 20091119 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 397 IP - 1 DP - 1996 Nov 11 TI - The crystal structure of human cyclin H. PG - 65-9 AB - The crystal structure of human cyclin H has been solved at 2.6 A resolution by the MIR method and refined to an R-factor of 23.1%. The core of the molecule consists of two helical repeats adopting the canonical cyclin fold already observed in the structures of cyclin A [Brown et al. (1995) Structure 3, 1235-1247; Jeffrey et al. (1995) Nature 376, 313-320; Russo et al. (1996) Nature 382, 325-331] and TFIIB [Nikoilov et al. (1995) Nature 377, 119-128]. The N-terminal and C-terminal residues form a new domain built on two long helices interacting essentially with the first repeat of the molecule. FAU - Andersen, G AU - Andersen G AD - Institut de Genetique et Biologie Moleculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France. FAU - Poterszman, A AU - Poterszman A FAU - Egly, J M AU - Egly JM FAU - Moras, D AU - Moras D FAU - Thierry, J C AU - Thierry JC LA - eng SI - PDB/UNKNOWN PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (CCNH protein, human) RN - 0 (Cyclin H) RN - 0 (Cyclins) SB - IM MH - Crystallization MH - Crystallography, X-Ray MH - Cyclin H MH - Cyclins/*chemistry MH - Humans MH - Models, Molecular MH - *Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary EDAT- 1996/11/11 MHDA- 1996/11/11 00:01 CRDT- 1996/11/11 00:00 AID - S0014-5793(96)01143-X [pii] PST - ppublish SO - FEBS Lett. 1996 Nov 11;397(1):65-9. PMID- 16293619 OWN - NLM STAT- MEDLINE DA - 20060112 DCOM- 20060228 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 2 DP - 2006 Jan 13 TI - Thermodynamics of beta-catenin-ligand interactions: the roles of the N- and C-terminal tails in modulating binding affinity. PG - 1027-38 AB - beta-Catenin is a structural component of adherens junctions, where it binds to the cytoplasmic domain of cadherin cell adhesion molecules. beta-Catenin is also a transcriptional coactivator in the Wnt signaling pathway, where it binds to Tcf/Lef family transcription factors. In the absence of a Wnt signal, nonjunctional beta-catenin is present in a multiprotein complex containing the proteins axin and adenomatous polyposis coli (APC), both of which bind directly to beta-catenin. The thermodynamics of beta-catenin binding to E-cadherin, Lef-1, APC, axin, and the transcriptional inhibitor ICAT have been determined by isothermal titration calorimetry. Most of the interactions showed large, unfavorable entropy changes, consistent with these ligands being natively unstructured in the absence of beta-catenin. Phosphorylation of serine residues present in a sequence motif common to cadherins and APC increased the affinity for beta-catenin 300-700-fold, and surface plasmon resonance measurements revealed that phosphorylation of E-cadherin both enhanced its on rate and decreased its off rate. The effects of the N- and C-terminal "tails" that flank the beta-catenin armadillo repeat domain on ligand binding have also been investigated using constructs lacking one or both tails. Contrary to earlier studies that employed less direct binding assays, the tails did not affect the affinity of beta-catenin for tight ligands such as E-cadherin, Lef-1, and phosphorylated APC. However, the beta-catenin C-terminal tail was found to decrease the affinity for the weaker ligands APC and axin, suggesting that this region may have a regulatory role in beta-catenin degradation. FAU - Choi, Hee-Jung AU - Choi HJ AD - Department of Structural Biology, Stanford University School of Medicine, CA 94305-5126, USA. FAU - Huber, Andrew H AU - Huber AH FAU - Weis, William I AU - Weis WI LA - eng GR - R01 GM56169/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20051117 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Adenomatous Polyposis Coli Protein) RN - 0 (Cadherins) RN - 0 (Ligands) RN - 0 (Recombinant Proteins) RN - 0 (Wnt Proteins) RN - 0 (beta Catenin) RN - 452VLY9402 (Serine) SB - IM MH - Adenomatous Polyposis Coli Protein/chemistry MH - Animals MH - Biotinylation MH - Cadherins/metabolism MH - Calorimetry MH - Cytoplasm/metabolism MH - Escherichia coli/metabolism MH - Genetic Vectors MH - Kinetics MH - *Ligands MH - Mice MH - Models, Molecular MH - Phosphorylation MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Serine/chemistry MH - Signal Transduction MH - Surface Plasmon Resonance MH - Temperature MH - Thermodynamics MH - Time Factors MH - Transcription, Genetic MH - Transcriptional Activation MH - Wnt Proteins/metabolism MH - beta Catenin/*chemistry/*physiology EDAT- 2005/11/19 09:00 MHDA- 2006/03/01 09:00 CRDT- 2005/11/19 09:00 PHST- 2005/11/17 [aheadofprint] AID - M511338200 [pii] AID - 10.1074/jbc.M511338200 [doi] PST - ppublish SO - J Biol Chem. 2006 Jan 13;281(2):1027-38. Epub 2005 Nov 17. PMID- 22653727 OWN - NLM STAT- MEDLINE DA - 20120716 DCOM- 20120730 LR - 20141016 IS - 1095-9203 (Electronic) IS - 0036-8075 (Linking) VI - 337 IP - 6091 DP - 2012 Jul 13 TI - Crystal structure of the heterodimeric CLOCK:BMAL1 transcriptional activator complex. PG - 189-94 LID - 10.1126/science.1222804 [doi] AB - The circadian clock in mammals is driven by an autoregulatory transcriptional feedback mechanism that takes approximately 24 hours to complete. A key component of this mechanism is a heterodimeric transcriptional activator consisting of two basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) domain protein subunits, CLOCK and BMAL1. Here, we report the crystal structure of a complex containing the mouse CLOCK:BMAL1 bHLH-PAS domains at 2.3 A resolution. The structure reveals an unusual asymmetric heterodimer with the three domains in each of the two subunits--bHLH, PAS-A, and PAS-B--tightly intertwined and involved in dimerization interactions, resulting in three distinct protein interfaces. Mutations that perturb the observed heterodimer interfaces affect the stability and activity of the CLOCK:BMAL1 complex as well as the periodicity of the circadian oscillator. The structure of the CLOCK:BMAL1 complex is a starting point for understanding at an atomic level the mechanism driving the mammalian circadian clock. FAU - Huang, Nian AU - Huang N AD - Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. FAU - Chelliah, Yogarany AU - Chelliah Y FAU - Shan, Yongli AU - Shan Y FAU - Taylor, Clinton A AU - Taylor CA FAU - Yoo, Seung-Hee AU - Yoo SH FAU - Partch, Carrie AU - Partch C FAU - Green, Carla B AU - Green CB FAU - Zhang, Hong AU - Zhang H FAU - Takahashi, Joseph S AU - Takahashi JS LA - eng SI - PDB/4F3L GR - R01 GM081875/GM/NIGMS NIH HHS/United States GR - R01 GM090247/GM/NIGMS NIH HHS/United States GR - R01 GM090247/GM/NIGMS NIH HHS/United States GR - Howard Hughes Medical Institute/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120531 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (ARNTL Transcription Factors) RN - 0 (Arntl protein, mouse) RN - 0 (Mutant Proteins) RN - 0 (Protein Subunits) RN - 9007-49-2 (DNA) RN - EC 2.3.1.48 (CLOCK Proteins) RN - EC 2.3.1.48 (Clock protein, mouse) SB - IM CIN - Science. 2012 Jul 13;337(6091):165-6. PMID: 22798591 MH - ARNTL Transcription Factors/*chemistry/genetics/metabolism MH - Amino Acid Sequence MH - Animals MH - CLOCK Proteins/*chemistry/genetics/metabolism MH - Cells, Cultured MH - *Circadian Rhythm MH - Crystallography, X-Ray MH - DNA/metabolism MH - HEK293 Cells MH - Helix-Loop-Helix Motifs MH - Humans MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Mutant Proteins/chemistry/metabolism MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Subunits/chemistry/metabolism MH - Static Electricity MH - *Transcriptional Activation PMC - PMC3694778 MID - NIHMS483291 OID - NLM: NIHMS483291 OID - NLM: PMC3694778 EDAT- 2012/06/02 06:00 MHDA- 2012/07/31 06:00 CRDT- 2012/06/02 06:00 PHST- 2012/05/31 [aheadofprint] AID - science.1222804 [pii] AID - 10.1126/science.1222804 [doi] PST - ppublish SO - Science. 2012 Jul 13;337(6091):189-94. doi: 10.1126/science.1222804. Epub 2012 May 31. PMID- 22815918 OWN - NLM STAT- MEDLINE DA - 20120720 DCOM- 20130116 LR - 20141015 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 7 DP - 2012 TI - The impact of small molecule binding on the energy landscape of the intrinsically disordered protein C-myc. PG - e41070 LID - 10.1371/journal.pone.0041070 [doi] AB - Intrinsically disordered proteins are attractive therapeutic targets owing to their prevalence in several diseases. Yet their lack of well-defined structure renders ligand discovery a challenging task. An intriguing example is provided by the oncoprotein c-Myc, a transcription factor that is over expressed in a broad range of cancers. Transcriptional activity of c-Myc is dependent on heterodimerization with partner protein Max. This protein-protein interaction is disrupted by the small molecule 10058-F4 (1), that binds to monomeric and disordered c-Myc. To rationalize the mechanism of inhibition, structural ensembles for the segment of the c-Myc domain that binds to 1 were computed in the absence and presence of the ligand using classical force fields and explicit solvent metadynamics molecular simulations. The accuracy of the computed structural ensembles was assessed by comparison of predicted and measured NMR chemical shifts. The small molecule 1 was found to perturb the composition of the apo equilibrium ensemble and to bind weakly to multiple distinct c-Myc conformations. Comparison of the apo and holo equilibrium ensembles reveals that the c-Myc conformations binding 1 are already partially formed in the apo ensemble, suggesting that 1 binds to c-Myc through an extended conformational selection mechanism. The present results have important implications for rational ligand design efforts targeting intrinsically disordered proteins. FAU - Michel, Julien AU - Michel J AD - EastCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom. mail@julienmichel.net FAU - Cuchillo, Remi AU - Cuchillo R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120716 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (5-(4-ethylbenzylidene)-2-thioxothiazolidin-4-one) RN - 0 (Ligands) RN - 0 (Proto-Oncogene Proteins c-myc) RN - 0 (Thiazoles) RN - 0 (Transcription Factors) SB - IM MH - *Gene Expression Regulation MH - Humans MH - Inhibitory Concentration 50 MH - Kinetics MH - Ligands MH - Magnetic Resonance Spectroscopy/methods MH - Models, Biological MH - Models, Chemical MH - Molecular Conformation MH - Molecular Dynamics Simulation MH - Protein Binding MH - Protein Conformation MH - Protein Interaction Mapping/methods MH - Protein Structure, Secondary MH - Proto-Oncogene Proteins c-myc/*chemistry/*metabolism MH - Reproducibility of Results MH - Thiazoles/pharmacology MH - Transcription Factors/metabolism MH - Transcription, Genetic PMC - PMC3397933 OID - NLM: PMC3397933 EDAT- 2012/07/21 06:00 MHDA- 2013/01/17 06:00 CRDT- 2012/07/21 06:00 PHST- 2012/02/05 [received] PHST- 2012/06/18 [accepted] PHST- 2012/07/16 [epublish] AID - 10.1371/journal.pone.0041070 [doi] AID - PONE-D-12-03937 [pii] PST - ppublish SO - PLoS One. 2012;7(7):e41070. doi: 10.1371/journal.pone.0041070. Epub 2012 Jul 16. PMID- 15751971 OWN - NLM STAT- MEDLINE DA - 20050308 DCOM- 20050607 LR - 20091119 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 44 IP - 10 DP - 2005 Mar 15 TI - Primary contact sites in intrinsically unstructured proteins: the case of calpastatin and microtubule-associated protein 2. PG - 3955-64 AB - Intrinsically unstructured proteins (IUPs) exist in a disordered conformational state, often considered to be equivalent with the random-coil structure. We challenge this simplifying view by limited proteolysis, circular dichroism (CD) spectroscopy, and solid-state (1)H NMR, to show short- and long-range structural organization in two IUPs, the first inhibitory domain of calpastatin (CSD1) and microtubule-associated protein 2c (MAP2c). Proteases of either narrow (trypsin, chymotrypsin, and plasmin) or broad (subtilisin and proteinase K) substrate specificity, applied at very low concentrations, preferentially cleaved both proteins in regions, i.e., subdomains A, B, and C in CSD1 and the proline-rich region (PRR) in MAP2c, that are destined to form contacts with their targets. For CSD1, nonadditivity of the CD spectra of its two halves and suboptimal hydration of the full-length protein measured by solid-state NMR demonstrate that long-range tertiary interactions provide the structural background of this structural feature. In MAP2c, such tertiary interactions are absent, which points to the importance of local structural constraints. In fact, urea and temperature dependence of the CD spectrum of its PRR reveals the presence of the extended and rather stiff polyproline II helix conformation that keeps the interaction site exposed. These data suggest that functionally significant residual structure exists in both of these IUPs. This structure, manifest as either transient local and/or global organization, ensures the spatial exposure of short contact segments on the surface. Pertinent data from other IUPs suggest that the presence of such recognition motifs may be a general feature of disordered proteins. To emphasize the possible importance of this structural trait, we propose that these motifs be called primary contact sites in IUPs. FAU - Csizmok, Veronika AU - Csizmok V AD - Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Post Office Box 7, H-1518 Budapest, Hungary. FAU - Bokor, Monika AU - Bokor M FAU - Banki, Peter AU - Banki P FAU - Klement, Eva AU - Klement E FAU - Medzihradszky, Katalin F AU - Medzihradszky KF FAU - Friedrich, Peter AU - Friedrich P FAU - Tompa, Kalman AU - Tompa K FAU - Tompa, Peter AU - Tompa P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Calcium-Binding Proteins) RN - 0 (Microtubule-Associated Proteins) RN - 0 (Peptide Fragments) RN - 79079-11-1 (calpastatin) RN - EC 3.4.21.1 (Chymotrypsin) RN - EC 3.4.21.4 (Trypsin) RN - EC 3.4.21.62 (Subtilisin) RN - EC 3.4.21.64 (Endopeptidase K) RN - EC 3.4.21.7 (Fibrinolysin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Calcium-Binding Proteins/*chemistry/genetics/*metabolism MH - Chymotrypsin/metabolism MH - Circular Dichroism MH - Endopeptidase K/metabolism MH - Fibrinolysin/metabolism MH - Humans MH - Hydrolysis MH - Microtubule-Associated Proteins/*chemistry/genetics/*metabolism MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemistry/genetics/metabolism MH - Protein Structure, Tertiary MH - Rats MH - Structure-Activity Relationship MH - Substrate Specificity MH - Subtilisin/metabolism MH - Trypsin/metabolism EDAT- 2005/03/09 09:00 MHDA- 2005/06/09 09:00 CRDT- 2005/03/09 09:00 AID - 10.1021/bi047817f [doi] PST - ppublish SO - Biochemistry. 2005 Mar 15;44(10):3955-64. PMID- 24489820 OWN - NLM STAT- MEDLINE DA - 20140203 DCOM- 20141222 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 1 DP - 2014 TI - Investigation of intramolecular dynamics and conformations of alpha-, beta- and gamma-synuclein. PG - e86983 LID - 10.1371/journal.pone.0086983 [doi] AB - The synucleins are a family of natively unstructured proteins consisting of alpha-, beta-, and gamma-synuclein which are primarily expressed in neurons. They have been linked to a wide variety of pathologies, including neurological disorders, such as Parkinson's disease (alpha-synuclein) and dementia with Lewy bodies (alpha- and beta-synuclein), as well as various types of cancers (gamma-synuclein). Self-association is a key pathological feature of many of these disorders, with alpha-synuclein having the highest propensity to form aggregates, while beta-synuclein is the least prone. Here, we used a combination of fluorescence correlation spectroscopy and single molecule Forster resonance energy transfer to compare the intrinsic dynamics of different regions of all three synuclein proteins to investigate any correlation with putative functional or dysfunctional interactions. Despite a relatively high degree of sequence homology, we find that individual regions sample a broad range of diffusion coefficients, differing by almost a factor of four. At low pH, a condition that accelerates aggregation of alpha-synuclein, on average smaller diffusion coefficients are measured, supporting a hypothesis that slower intrachain dynamics may be correlated with self-association. Moreover, there is a surprising inverse correlation between dynamics and bulkiness of the segments. Aside from this observation, we could not discern any clear relationship between the physico-chemical properties of the constructs and their intrinsic dynamics. This work suggests that while protein dynamics may play a role in modulating self-association or interactions with other binding partners, other factors, particularly the local cellular environment, may be more important. FAU - Ducas, Vanessa C AU - Ducas VC AD - Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America. FAU - Rhoades, Elizabeth AU - Rhoades E AD - Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America ; Department of Physics, Yale University, New Haven, Connecticut, United States of America. LA - eng GR - GM008283/GM/NIGMS NIH HHS/United States GR - GM067543/GM/NIGMS NIH HHS/United States GR - GM102815/GM/NIGMS NIH HHS/United States GR - NS079955/NS/NINDS NIH HHS/United States GR - R01 NS079955/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140128 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Solutions) RN - 0 (alpha-Synuclein) RN - 0 (beta-Synuclein) RN - 0 (gamma-Synuclein) SB - IM MH - Amino Acid Sequence MH - Diffusion MH - Fluorescence Resonance Energy Transfer MH - Hydrogen-Ion Concentration MH - Molecular Sequence Data MH - Protein Structure, Tertiary MH - Solutions MH - alpha-Synuclein/*chemistry/*metabolism MH - beta-Synuclein/*chemistry/*metabolism MH - gamma-Synuclein/*chemistry/*metabolism PMC - PMC3904966 OID - NLM: PMC3904966 EDAT- 2014/02/04 06:00 MHDA- 2014/12/23 06:00 CRDT- 2014/02/04 06:00 PHST- 2014 [ecollection] PHST- 2013/08/23 [received] PHST- 2013/12/18 [accepted] PHST- 2014/01/28 [epublish] AID - 10.1371/journal.pone.0086983 [doi] AID - PONE-D-13-34897 [pii] PST - epublish SO - PLoS One. 2014 Jan 28;9(1):e86983. doi: 10.1371/journal.pone.0086983. eCollection 2014. PMID- 9488652 OWN - NLM STAT- MEDLINE DA - 19980318 DCOM- 19980318 LR - 20131121 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 279 IP - 5356 DP - 1998 Mar 6 TI - A model for the mechanism of human topoisomerase I. PG - 1534-41 AB - The three-dimensional structure of a 70-kilodalton amino terminally truncated form of human topoisomerase I in complex with a 22-base pair duplex oligonucleotide, determined to a resolution of 2.8 angstroms, reveals all of the structural elements of the enzyme that contact DNA. The linker region that connects the central core of the enzyme to the carboxyl-terminal domain assumes a coiled-coil configuration and protrudes away from the remainder of the enzyme. The positively charged DNA-proximal surface of the linker makes only a few contacts with the DNA downstream of the cleavage site. In combination with the crystal structures of the reconstituted human topoisomerase I before and after DNA cleavage, this information suggests which amino acid residues are involved in catalyzing phosphodiester bond breakage and religation. The structures also lead to the proposal that the topoisomerization step occurs by a mechanism termed "controlled rotation." FAU - Stewart, L AU - Stewart L AD - Biomolecular Structure Center and Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA 98195-7742, USA. emerald_biostructures@rocketmail.com FAU - Redinbo, M R AU - Redinbo MR FAU - Qiu, X AU - Qiu X FAU - Hol, W G AU - Hol WG FAU - Champoux, J J AU - Champoux JJ LA - eng GR - CA65656/CA/NCI NIH HHS/United States GR - GM16713/GM/NIGMS NIH HHS/United States GR - GM49156/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Oligodeoxyribonucleotides) RN - 42HK56048U (Tyrosine) RN - 9007-49-2 (DNA) RN - 94ZLA3W45F (Arginine) RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) SB - IM CIN - Science. 1998 Mar 6;279(5356):1490-1. PMID: 9508726 MH - Amino Acid Sequence MH - Arginine/chemistry/metabolism MH - Binding Sites MH - Catalysis MH - Crystallography, X-Ray MH - DNA/chemistry/*metabolism MH - DNA Topoisomerases, Type I/*chemistry/*metabolism MH - Humans MH - Hydrogen Bonding MH - *Models, Chemical MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Oligodeoxyribonucleotides/chemistry/metabolism MH - *Protein Conformation MH - Protein Structure, Secondary MH - Tyrosine/chemistry/metabolism EDAT- 1998/03/21 MHDA- 1998/03/21 00:01 CRDT- 1998/03/21 00:00 PST - ppublish SO - Science. 1998 Mar 6;279(5356):1534-41. PMID- 25263009 OWN - NLM STAT- In-Process DA - 20150223 LR - 20150408 IS - 1096-3634 (Electronic) IS - 1084-9521 (Linking) VI - 37 DP - 2015 Jan TI - Polybivalency and disordered proteins in ordering macromolecular assemblies. PG - 20-5 LID - 10.1016/j.semcdb.2014.09.016 [doi] LID - S1084-9521(14)00271-7 [pii] AB - Intrinsically disordered proteins (IDPs) are prevalent in macromolecular assemblies and are thought to mediate protein recognition in complex regulatory processes and signaling pathways. The formation of a polybivalent scaffold is a key process by which IDPs drive early steps in macromolecular assemblies. Three intrinsically disordered proteins, IC, Swallow and Nup159, are core components, respectively, of cytoplasmic dynein, bicoid mRNA localization apparatus, and nuclear pore complexes. In all three systems, the hub protein LC8 recognizes on the IDP, short linear motifs that are fully disordered in the apo form, but adopt a beta-strand when bound to LC8. The IDP/LC8 complex forms a bivalent scaffold primed to bind additional bivalent ligands. Scaffold formation also promotes self-association and/or higher order organization of the IDP components at a site distant from LC8 binding. Rigorous thermodynamic analyses imply that association of additional bivalent ligands is driven by entropic effects where the first binding event is weak but subsequent binding of additional ligands occurs with higher affinity. Here, we review specific examples of macromolecular assemblies in which polybivalency of aligned IDP duplexes not only enhances binding affinity and results in formation of a stable complex but also compensates unfavorable steric and enthalpic interactions. We propose that polybivalent scaffold assembly involving IDPs and LC8-like proteins is a general process in the cell biology of a class of multi-protein structures that are stable yet fine-tuned for diverse cellular requirements. CI - Copyright (c) 2014 Elsevier Ltd. All rights reserved. FAU - Barbar, Elisar AU - Barbar E AD - Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, United States. Electronic address: barbare@science.oregonstate.edu. FAU - Nyarko, Afua AU - Nyarko A AD - Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, United States. LA - eng GR - GM 084276/GM/NIGMS NIH HHS/United States GR - R01 GM084276/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review DEP - 20140927 PL - England TA - Semin Cell Dev Biol JT - Seminars in cell & developmental biology JID - 9607332 SB - IM PMC - PMC4339520 MID - NIHMS634091 OID - NLM: NIHMS634091 [Available on 01/01/16] OID - NLM: PMC4339520 [Available on 01/01/16] OTO - NOTNLM OT - Bivalency OT - Enthalpy-entropy compensation OT - Intrinsically disordered proteins OT - LC8 OT - Macromolecular assembly OT - Poly-bivalent scaffold EDAT- 2014/09/30 06:00 MHDA- 2014/09/30 06:00 CRDT- 2014/09/30 06:00 PMCR- 2016/01/01 00:00 PHST- 2014/06/25 [received] PHST- 2014/09/10 [revised] PHST- 2014/09/13 [accepted] PHST- 2014/09/27 [aheadofprint] AID - S1084-9521(14)00271-7 [pii] AID - 10.1016/j.semcdb.2014.09.016 [doi] PST - ppublish SO - Semin Cell Dev Biol. 2015 Jan;37:20-5. doi: 10.1016/j.semcdb.2014.09.016. Epub 2014 Sep 27. PMID- 10595530 OWN - NLM STAT- MEDLINE DA - 20000107 DCOM- 20000107 LR - 20140615 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 8 IP - 11 DP - 1999 Nov TI - The solution structure of the anti-HIV chemokine vMIP-II. PG - 2270-80 AB - We report the solution structure of the chemotactic cytokine (chemokine) vMIP-II. This protein has unique biological activities in that it blocks infection by several different human immunodeficiency virus type 1 (HIV-1) strains. This occurs because vMIP-II binds to a wide range of chemokine receptors, some of which are used by HJV to gain cell entry. vMIP-II is a monomeric protein, unlike most members of the chemokine family, and its structure consists of a disordered N-terminus, followed by a helical turn (Gln25-Leu27), which leads into the first strand of a three-stranded antiparallel beta-sheet (Ser29-Thr34; Gly42-Thr47; Gln52-Asp56). Following the sheet is a C-terminal alpha-helix, which extends from residue Asp60 until Gln68. The final five residues beyond the C-terminal helix (Pro70-Arg74) are in an extended conformation, but several of these C-terminal residues contact the first beta-strand. The structure of vMIP-II is compared to other chemokines that also block infection by HIV-1, and the structural basis of its lack of ability to form a dimer is discussed. FAU - Liwang, A C AU - Liwang AC AD - Texas A&M University, Department of Biochemistry and Biophysics, College Station 77843-2128, USA. FAU - Wang, Z X AU - Wang ZX FAU - Sun, Y AU - Sun Y FAU - Peiper, S C AU - Peiper SC FAU - Liwang, P J AU - Liwang PJ LA - eng SI - PDB/1VMP GR - R01AI41346/AI/NIAID NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Anti-HIV Agents) RN - 0 (CCL11 protein, human) RN - 0 (CXCL12 protein, human) RN - 0 (Chemokine CCL11) RN - 0 (Chemokine CCL4) RN - 0 (Chemokine CXCL12) RN - 0 (Chemokines) RN - 0 (Chemokines, CC) RN - 0 (Chemokines, CXC) RN - 0 (Chemotactic Factors, Eosinophil) RN - 0 (Cytokines) RN - 0 (Macrophage Inflammatory Proteins) RN - 0 (Solutions) RN - 0 (vMIP-II) SB - IM SB - X MH - Amino Acid Sequence MH - Anti-HIV Agents/*chemistry MH - Chemokine CCL11 MH - Chemokine CCL4 MH - Chemokine CXCL12 MH - Chemokines/*chemistry/pharmacology MH - Chemokines, CC/*chemistry MH - Chemokines, CXC/chemistry MH - Chemotactic Factors, Eosinophil/chemistry MH - Cytokines/chemistry MH - HIV-1/drug effects MH - Humans MH - Macrophage Inflammatory Proteins/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Solutions PMC - PMC2144214 OID - NLM: PMC2144214 EDAT- 1999/12/14 MHDA- 1999/12/14 00:01 CRDT- 1999/12/14 00:00 AID - 10.1110/ps.8.11.2270 [doi] PST - ppublish SO - Protein Sci. 1999 Nov;8(11):2270-80. PMID- 15728574 OWN - NLM STAT- MEDLINE DA - 20050425 DCOM- 20050621 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 17 DP - 2005 Apr 29 TI - Structural basis for the unique biological function of small GTPase RHEB. PG - 17093-100 AB - The small GTPase Rheb displays unique biological and biochemical properties different from other small GTPases and functions as an important mediator between the tumor suppressor proteins TSC1 and TSC2 and the mammalian target of rapamycin to stimulate cell growth. We report here the three-dimensional structures of human Rheb in complexes with GDP, GTP, and GppNHp (5'-(beta,gamma-imide)triphosphate), which reveal novel structural features of Rheb and provide a molecular basis for its distinct properties. During GTP/GDP cycling, switch I of Rheb undergoes conformational change while switch II maintains a stable, unusually extended conformation, which is substantially different from the alpha-helical conformation seen in other small GTPases. The unique switch II conformation results in a displacement of Gln64 (equivalent to the catalytic Gln61 of Ras), making it incapable of participating in GTP hydrolysis and thus accounting for the low intrinsic GTPase activity of Rheb. This rearrangement also creates space to accommodate the side chain of Arg15, avoiding its steric hindrance with the catalytic residue and explaining its noninvolvement in GTP hydrolysis. Unlike Ras, the phosphate moiety of GTP in Rheb is shielded by the conserved Tyr35 of switch I, leading to the closure of the GTP-binding site, which appears to prohibit the insertion of a potential arginine finger from its GTPase-activating protein. Taking the genetic, biochemical, biological, and structural data together, we propose that Rheb forms a new group of the Ras/Rap subfamily and uses a novel GTP hydrolysis mechanism that utilizes Asn1643 of the tuberous sclerosis complex 2 GTPase-activating protein domain instead of Gln64 of Rheb as the catalytic residue. FAU - Yu, Yadong AU - Yu Y AD - Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of the Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China. FAU - Li, Sheng AU - Li S FAU - Xu, Xiang AU - Xu X FAU - Li, Yong AU - Li Y FAU - Guan, Kunliang AU - Guan K FAU - Arnold, Eddy AU - Arnold E FAU - Ding, Jianping AU - Ding J LA - eng SI - PDB/1XTQ SI - PDB/1XTR SI - PDB/1XTS PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050223 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Neuropeptides) RN - 0 (RHEB protein, human) RN - 0 (Repressor Proteins) RN - 0 (Tumor Suppressor Proteins) RN - 0 (tuberous sclerosis complex 1 protein) RN - 146-91-8 (Guanosine Diphosphate) RN - 4JG2LF96VF (tuberous sclerosis complex 2 protein) RN - 7006-34-0 (Asparagine) RN - 86-01-1 (Guanosine Triphosphate) RN - 94ZLA3W45F (Arginine) RN - EC 2.7.- (Protein Kinases) RN - EC 2.7.1.1 (MTOR protein, human) RN - EC 2.7.1.1 (TOR Serine-Threonine Kinases) RN - EC 3.6.1.- (GTP Phosphohydrolases) RN - EC 3.6.5.2 (Monomeric GTP-Binding Proteins) RN - EC 3.6.5.2 (ras Proteins) RN - I38ZP9992A (Magnesium) SB - IM MH - Amino Acid Sequence MH - Arginine/chemistry MH - Asparagine/chemistry MH - Binding Sites MH - Catalytic Domain MH - Cell Proliferation MH - Crystallography, X-Ray MH - Databases, Protein MH - GTP Phosphohydrolases/*chemistry MH - Guanosine Diphosphate/metabolism MH - Guanosine Triphosphate/chemistry/metabolism MH - Humans MH - Hydrolysis MH - Magnesium/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Monomeric GTP-Binding Proteins/*chemistry/physiology MH - Neuropeptides/*chemistry/physiology MH - Protein Conformation MH - Protein Kinases/*metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Repressor Proteins/chemistry/metabolism MH - Sequence Homology, Amino Acid MH - TOR Serine-Threonine Kinases MH - Tuberous Sclerosis/metabolism MH - Tumor Suppressor Proteins/chemistry/metabolism MH - X-Ray Diffraction MH - ras Proteins/metabolism EDAT- 2005/02/25 09:00 MHDA- 2005/06/23 09:00 CRDT- 2005/02/25 09:00 PHST- 2005/02/23 [aheadofprint] AID - M501253200 [pii] AID - 10.1074/jbc.M501253200 [doi] PST - ppublish SO - J Biol Chem. 2005 Apr 29;280(17):17093-100. Epub 2005 Feb 23. PMID- 22243255 OWN - NLM STAT- MEDLINE DA - 20120116 DCOM- 20120618 LR - 20131121 IS - 1600-0722 (Electronic) IS - 0909-8836 (Linking) VI - 119 Suppl 1 DP - 2011 Dec TI - Biophysical characterization of recombinant human ameloblastin. PG - 261-9 LID - 10.1111/j.1600-0722.2011.00913.x [doi] AB - Ameloblastin (AMBN) is a protein expressed mainly during dental hard tissue development. Biochemically, it is classified as an intrinsically disordered protein (IDP). Its biological role remains largely unknown; however, the question of AMBN function will undoubtedly be connected to its structural properties and its potential for protein-protein and protein-cell interactions. A basic biophysical characterization of human recombinant ameloblastin (hrAMBN) and its N- and C-terminal domains by means of circular dichroism spectroscopy and dynamic light scattering showed that under physiological conditions ameloblastin is an IDP with a prevalent polyproline-II (PPII) conformation. Both the N- and C-terminal polypeptides, when expressed independently, showed different structural preferences upon heating as well as different behaviour in the presence of trifluoroethanol and CaCl(2) salt. The N-terminal peptide showed a more ordered structure with a strong tendency to adopt a helical conformation upon the addition of trifluorethanol, whereas the C-terminal domain seemed to be primarily responsible for the structural disorder of the entire AMBN molecule. CI - (c) 2011 Eur J Oral Sci. FAU - Wald, Tomas AU - Wald T AD - Institute of Microbiology v.v.i, Academy of Sciences of Czech Republic, Videnska, 1083, 142 20 Prague 4 Czech Republic. FAU - Bednarova, Lucie AU - Bednarova L FAU - Osicka, Radim AU - Osicka R FAU - Pachl, Petr AU - Pachl P FAU - Sulc, Miroslav AU - Sulc M FAU - Lyngstadaas, Stale Petter AU - Lyngstadaas SP FAU - Slaby, Ivan AU - Slaby I FAU - Vondrasek, Jiri AU - Vondrasek J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Denmark TA - Eur J Oral Sci JT - European journal of oral sciences JID - 9504563 RN - 0 (AMBN protein, human) RN - 0 (Cross-Linking Reagents) RN - 0 (Dental Enamel Proteins) RN - 0 (Recombinant Proteins) RN - 75-89-8 (Trifluoroethanol) RN - 7647-14-5 (Sodium Chloride) RN - M4I0D6VV5M (Calcium Chloride) SB - D SB - IM MH - Biophysical Processes MH - Calcium Chloride/pharmacology MH - Circular Dichroism MH - Cross-Linking Reagents MH - Dental Enamel Proteins/*chemistry MH - Humans MH - Osmolar Concentration MH - Protein Conformation/drug effects MH - Protein Interaction Domains and Motifs MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Scattering, Radiation MH - Sequence Analysis, Protein MH - Sodium Chloride/pharmacology MH - Spectrum Analysis MH - Temperature MH - Trifluoroethanol/pharmacology EDAT- 2012/02/22 06:00 MHDA- 2012/06/19 06:00 CRDT- 2012/01/17 06:00 AID - 10.1111/j.1600-0722.2011.00913.x [doi] PST - ppublish SO - Eur J Oral Sci. 2011 Dec;119 Suppl 1:261-9. doi: 10.1111/j.1600-0722.2011.00913.x. PMID- 24769851 OWN - NLM STAT- MEDLINE DA - 20140428 DCOM- 20150120 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 4 DP - 2014 TI - Tyrosine phosphorylation within the intrinsically disordered cytosolic domains of the B-cell receptor: an NMR-based structural analysis. PG - e96199 LID - 10.1371/journal.pone.0096199 [doi] AB - Intrinsically disordered proteins are found extensively in cell signaling pathways where they often are targets of posttranslational modifications e.g. phosphorylation. Such modifications can sometimes induce or disrupt secondary structure elements present in the modified protein. CD79a and CD79b are membrane-spanning, signal-transducing components of the B-cell receptor. The cytosolic domains of these proteins are intrinsically disordered and each has an immunoreceptor tyrosine-based activation motif (ITAM). When an antigen binds to the receptor, conserved tyrosines located in the ITAMs are phosphorylated which initiate further downstream signaling. Here we use NMR spectroscopy to examine the secondary structure propensity of the cytosolic domains of CD79a and CD79b in vitro before and after phosphorylation. The phosphorylation patterns are identified through analysis of changes of backbone chemical shifts found for the affected tyrosines and neighboring residues. The number of the phosphorylated sites is confirmed by mass spectrometry. The secondary structure propensities are calculated using the method of intrinsic referencing, where the reference random coil chemical shifts are measured for the same protein under denaturing conditions. Our analysis revealed that CD79a and CD79b both have an overall propensity for alpha-helical structure that is greatest in the C-terminal region of the ITAM. Phosphorylation of CD79a caused a decrease in helical propensity in the C-terminal ITAM region. For CD79b, the opposite was observed and phosphorylation resulted in an increase of helical propensity in the C-terminal part. FAU - Rosenlow, Joakim AU - Rosenlow J AD - The Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden. FAU - Isaksson, Linnea AU - Isaksson L AD - The Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden. FAU - Mayzel, Maxim AU - Mayzel M AD - The Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden. FAU - Lengqvist, Johan AU - Lengqvist J AD - Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden. FAU - Orekhov, Vladislav Y AU - Orekhov VY AD - The Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140425 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Antigens, CD79) RN - 0 (Intrinsically Disordered Proteins) RN - 42HK56048U (Tyrosine) SB - IM MH - Antigens, CD79/*chemistry/metabolism MH - Humans MH - Intrinsically Disordered Proteins/chemistry/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphorylation MH - *Protein Processing, Post-Translational MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Tyrosine/chemistry PMC - PMC4000212 OID - NLM: PMC4000212 EDAT- 2014/04/29 06:00 MHDA- 2015/01/21 06:00 CRDT- 2014/04/29 06:00 PHST- 2014 [ecollection] PHST- 2014/01/14 [received] PHST- 2014/04/04 [accepted] PHST- 2014/04/25 [epublish] AID - 10.1371/journal.pone.0096199 [doi] AID - PONE-D-14-01932 [pii] PST - epublish SO - PLoS One. 2014 Apr 25;9(4):e96199. doi: 10.1371/journal.pone.0096199. eCollection 2014. PMID- 18410249 OWN - NLM STAT- MEDLINE DA - 20080603 DCOM- 20080903 IS - 0066-4154 (Print) IS - 0066-4154 (Linking) VI - 77 DP - 2008 TI - Structural biology of the tumor suppressor p53. PG - 557-82 LID - 10.1146/annurev.biochem.77.060806.091238 [doi] AB - The tumor suppressor protein p53 induces or represses the expression of a variety of target genes involved in cell cycle control, senescence, and apoptosis in response to oncogenic or other cellular stress signals. It exerts its function as guardian of the genome through an intricate interplay of independently folded and intrinsically disordered functional domains. In this review, we provide insights into the structural complexity of p53, the molecular mechanisms of its inactivation in cancer, and therapeutic strategies for the pharmacological rescue of p53 function in tumors. p53 emerges as a paradigm for a more general understanding of the structural organization of modular proteins and the effects of disease-causing mutations. FAU - Joerger, Andreas C AU - Joerger AC AD - Medical Research Council Centre for Protein Engineering, Cambridge, United Kingdom. acj2@mrc-lmb.cam.ac.uk FAU - Fersht, Alan R AU - Fersht AR LA - eng PT - Journal Article PT - Review PL - United States TA - Annu Rev Biochem JT - Annual review of biochemistry JID - 2985150R RN - 0 (Transcription Factors) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cell Cycle MH - Drug Design MH - Genes, Dominant MH - Genes, p53 MH - Humans MH - Models, Biological MH - Molecular Sequence Data MH - Mutation MH - Neoplasms/metabolism MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Transcription Factors/metabolism MH - Tumor Suppressor Protein p53/*chemistry/*physiology RF - 160 EDAT- 2008/04/16 09:00 MHDA- 2008/09/04 09:00 CRDT- 2008/04/16 09:00 AID - 10.1146/annurev.biochem.77.060806.091238 [doi] PST - ppublish SO - Annu Rev Biochem. 2008;77:557-82. doi: 10.1146/annurev.biochem.77.060806.091238. PMID- 12569097 OWN - NLM STAT- MEDLINE DA - 20030407 DCOM- 20030703 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 15 DP - 2003 Apr 11 TI - Transition from natively unfolded to folded state induced by desiccation in an anhydrobiotic nematode protein. PG - 12977-84 AB - Late embryogenesis abundant (LEA) proteins are associated with desiccation tolerance in resurrection plants and in plant seeds, and the recent discovery of a dehydration-induced Group 3 LEA-like gene in the nematode Aphelenchus avenae suggests a similar association in anhydrobiotic animals. Despite their importance, little is known about the structure of Group 3 LEA proteins, although computer modeling and secondary structure algorithms predict a largely alpha-helical monomer that forms coiled coil oligomers. We have therefore investigated the structure of the nematode protein, AavLEA1, in the first such analysis of a well characterized Group 3 LEA-like protein. Immunoblotting and subunit cross-linking experiments demonstrate limited oligomerization of AavLEA1, but analytical ultracentrifugation and gel filtration show that the vast majority of the protein is monomeric. Moreover, CD, fluorescence emission, and Fourier transform-infrared spectroscopy indicate an unstructured conformation for the nematode protein. Therefore, in solution, no evidence was found to support structure predictions; instead, AavLEA1 seems to be natively unfolded with a high degree of hydration and low compactness. Such proteins can, however, be induced to fold into more rigid structures by partner molecules or by altered physiological conditions. Because AavLEA1 is associated with desiccation stress, its Fourier transform-infrared spectrum in the dehydrated state was examined. A dramatic but reversible increase in alpha-helix and, possibly, coiled coil formation was observed on drying, indicating that computer predictions of secondary structure may be correct for the solid state. This unusual finding offers the possibility that structural shifts in Group 3 LEA proteins occur on dehydration, perhaps consistent with their role in anhydrobiosis. FAU - Goyal, Kshamata AU - Goyal K AD - Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, United Kingdom. FAU - Tisi, Laurence AU - Tisi L FAU - Basran, Amrik AU - Basran A FAU - Browne, John AU - Browne J FAU - Burnell, Ann AU - Burnell A FAU - Zurdo, Jesus AU - Zurdo J FAU - Tunnacliffe, Alan AU - Tunnacliffe A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030204 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Cross-Linking Reagents) RN - 0 (Helminth Proteins) RN - 0 (Macromolecular Substances) RN - 0 (Peptide Fragments) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Animals MH - Chromatography, Gel MH - Circular Dichroism MH - Computer Simulation MH - Cross-Linking Reagents MH - Electrophoresis, Polyacrylamide Gel MH - Helminth Proteins/*chemistry/isolation & purification MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Nematoda MH - Peptide Fragments/chemistry MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Secondary MH - Spectroscopy, Fourier Transform Infrared EDAT- 2003/02/06 04:00 MHDA- 2003/07/04 05:00 CRDT- 2003/02/06 04:00 PHST- 2003/02/04 [aheadofprint] AID - 10.1074/jbc.M212007200 [doi] AID - M212007200 [pii] PST - ppublish SO - J Biol Chem. 2003 Apr 11;278(15):12977-84. Epub 2003 Feb 4. PMID- 22529103 OWN - NLM STAT- MEDLINE DA - 20120501 DCOM- 20120621 LR - 20141016 IS - 1540-8140 (Electronic) IS - 0021-9525 (Linking) VI - 197 IP - 3 DP - 2012 Apr 30 TI - An intrinsically disordered yeast prion arrests the cell cycle by sequestering a spindle pole body component. PG - 369-79 LID - 10.1083/jcb.201108146 [doi] AB - Intrinsically disordered proteins play causative roles in many human diseases. Their overexpression is toxic in many organisms, but the causes of toxicity are opaque. In this paper, we exploit yeast technologies to determine the root of toxicity for one such protein, the yeast prion Rnq1. This protein is profoundly toxic when overexpressed but only in cells carrying the endogenous Rnq1 protein in its [RNQ(+)] prion (amyloid) conformation. Surprisingly, toxicity was not caused by general proteotoxic stress. Rather, it involved a highly specific mitotic arrest mediated by the Mad2 cell cycle checkpoint. Monopolar spindles accumulated as a result of defective duplication of the yeast centrosome (spindle pole body [SPB]). This arose from selective Rnq1-mediated sequestration of the core SPB component Spc42 in the insoluble protein deposit (IPOD). Rnq1 does not normally participate in spindle pole dynamics, but it does assemble at the IPOD when aggregated. Our work illustrates how the promiscuous interactions of an intrinsically disordered protein can produce highly specific cellular toxicities through illicit, yet highly specific, interactions with the proteome. FAU - Treusch, Sebastian AU - Treusch S AD - Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA. FAU - Lindquist, Susan AU - Lindquist S LA - eng GR - 5R37GM025874/GM/NIGMS NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120423 PL - United States TA - J Cell Biol JT - The Journal of cell biology JID - 0375356 RN - 0 (Cell Cycle Proteins) RN - 0 (MAD2 protein, S cerevisiae) RN - 0 (Mad2 Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Prions) RN - 0 (RNA, Small Interfering) RN - 0 (RNQ1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM CIN - Nat Rev Mol Cell Biol. 2012 Jun;13(6):338. PMID: 22572991 MH - Cell Cycle/*physiology MH - Cell Cycle Checkpoints MH - Cell Cycle Proteins/genetics/metabolism MH - Centrosome/*metabolism MH - Genome, Fungal MH - Humans MH - Immunoenzyme Techniques MH - Mad2 Proteins MH - Nuclear Proteins/genetics/metabolism MH - Prions/antagonists & inhibitors/genetics/*metabolism MH - RNA, Small Interfering/*genetics MH - Saccharomyces cerevisiae/genetics/*metabolism MH - Saccharomyces cerevisiae Proteins/antagonists & inhibitors/genetics/*metabolism MH - Spindle Apparatus/*metabolism PMC - PMC3341155 OID - NLM: PMC3341155 EDAT- 2012/04/25 06:00 MHDA- 2012/06/22 06:00 CRDT- 2012/04/25 06:00 PHST- 2012/04/23 [aheadofprint] AID - jcb.201108146 [pii] AID - 10.1083/jcb.201108146 [doi] PST - ppublish SO - J Cell Biol. 2012 Apr 30;197(3):369-79. doi: 10.1083/jcb.201108146. Epub 2012 Apr 23. PMID- 21821043 OWN - NLM STAT- MEDLINE DA - 20110916 DCOM- 20111128 LR - 20141022 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 412 IP - 4 DP - 2011 Sep 30 TI - The bacteriophage lambda gpNu3 scaffolding protein is an intrinsically disordered and biologically functional procapsid assembly catalyst. PG - 723-36 LID - 10.1016/j.jmb.2011.07.045 [doi] AB - Procapsid assembly is a process whereby hundreds of copies of a major capsid protein assemble into an icosahedral protein shell into which the viral genome is packaged. The essential features of procapsid assembly are conserved in both eukaryotic and prokaryotic complex double-stranded DNA viruses. Typically, a portal protein nucleates the co-polymerization of an internal scaffolding protein and the major capsid protein into an icosahedral capsid shell. The scaffolding proteins are essential to procapsid assembly. Here, we describe the solution-based biophysical and functional characterization of the bacteriophage lambda (lambda) scaffolding protein gpNu3. The purified protein possesses significant alpha-helical structure and appears to be partially disordered. Thermally induced denaturation studies indicate that secondary structures are lost in a cooperative, apparent two-state transition (T(m)=40.6+/-0.3 degrees C) and that unfolding is, at least in part, reversible. Analysis of the purified protein by size-exclusion chromatography suggests that gpNu3 is highly asymmetric, which contributes to an abnormally large Stokes radius. The size-exclusion chromatography data further indicate that the protein self-associates in a concentration-dependent manner. This was confirmed by analytical ultracentrifugation studies, which reveal a monomer-dimer equilibrium (K(d,app)~50 muM) and an asymmetric protein structure at biologically relevant concentrations. Purified gpNu3 promotes the polymerization of gpE, the lambda major capsid protein, into virus-like particles that possess a native-like procapsid morphology. The relevance of this work with respect to procapsid assembly in the complex double-stranded DNA viruses is discussed. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Medina, Eva Margarita AU - Medina EM AD - Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA. FAU - Andrews, Benjamin T AU - Andrews BT FAU - Nakatani, Eri AU - Nakatani E FAU - Catalano, Carlos Enrique AU - Catalano CE LA - eng GR - F32 GM090565/GM/NIGMS NIH HHS/United States GR - F32 GM090565-02/GM/NIGMS NIH HHS/United States GR - F32GM-905652/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110729 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Viral Proteins) SB - IM MH - Amino Acid Sequence MH - Bacteriophage lambda/genetics/metabolism/*physiology MH - Capsid/chemistry/*metabolism/physiology MH - Hydrolysis MH - Models, Biological MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - *Protein Folding MH - Protein Stability MH - Protein Structure, Secondary MH - Temperature MH - Ultracentrifugation MH - Viral Proteins/chemistry/genetics/metabolism/*physiology MH - Virus Assembly/*genetics PMC - PMC3247018 MID - NIHMS344518 OID - NLM: NIHMS344518 OID - NLM: PMC3247018 EDAT- 2011/08/09 06:00 MHDA- 2011/12/13 00:00 CRDT- 2011/08/09 06:00 PHST- 2011/04/22 [received] PHST- 2011/07/19 [revised] PHST- 2011/07/21 [accepted] PHST- 2011/07/29 [aheadofprint] AID - S0022-2836(11)00813-8 [pii] AID - 10.1016/j.jmb.2011.07.045 [doi] PST - ppublish SO - J Mol Biol. 2011 Sep 30;412(4):723-36. doi: 10.1016/j.jmb.2011.07.045. Epub 2011 Jul 29. PMID- 19554627 OWN - NLM STAT- MEDLINE DA - 20090917 DCOM- 20091123 LR - 20140828 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 18 IP - 9 DP - 2009 Sep TI - Structural characterization of alpha-synuclein in an aggregation prone state. PG - 1840-6 LID - 10.1002/pro.194 [doi] AB - The relation of alpha-synuclein (alphaS) aggregation to Parkinson's disease has long been recognized, but the pathogenic species and its molecular properties have yet to be identified. To obtain insight into the properties of alphaS in an aggregation-prone state, we studied the structural properties of alphaS at acidic pH using NMR spectroscopy and computation. NMR demonstrated that alphaS remains natively unfolded at lower pH, but secondary structure propensities were changed in proximity to acidic residues. The ensemble of conformations of alphaS at acidic pH is characterized by a rigidification and compaction of the Asp and Glu-rich C-terminal region, an increased probability for proximity between the NAC-region and the C-terminal region and a lower probability for interactions between the N- and C-terminal regions. FAU - Cho, Min-Kyu AU - Cho MK AD - Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany. FAU - Nodet, Gabrielle AU - Nodet G FAU - Kim, Hai-Young AU - Kim HY FAU - Jensen, Malene R AU - Jensen MR FAU - Bernado, Pau AU - Bernado P FAU - Fernandez, Claudio O AU - Fernandez CO FAU - Becker, Stefan AU - Becker S FAU - Blackledge, Martin AU - Blackledge M FAU - Zweckstetter, Markus AU - Zweckstetter M LA - eng PT - Journal Article PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Humans MH - Hydrogen-Ion Concentration MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Parkinson Disease/metabolism MH - Protein Conformation MH - Protein Folding MH - alpha-Synuclein/*chemistry PMC - PMC2777359 OID - NLM: PMC2777359 EDAT- 2009/06/26 09:00 MHDA- 2009/12/16 06:00 CRDT- 2009/06/26 09:00 AID - 10.1002/pro.194 [doi] PST - ppublish SO - Protein Sci. 2009 Sep;18(9):1840-6. doi: 10.1002/pro.194. PMID- 23029651 OWN - NLM STAT- MEDLINE DA - 20121001 DCOM- 20121212 IS - 1437-4315 (Electronic) IS - 1431-6730 (Linking) VI - 393 IP - 4 DP - 2012 Apr TI - Disorder-function relationships for the cell cycle regulatory proteins p21 and p27. PG - 259-74 LID - 10.1515/hsz-2011-0254 [doi] AB - The classic structure-function paradigm has been challenged by a recently identified class of proteins: intrinsically disordered proteins (IDPs). Despite their lack of stable secondary or tertiary structure, IDPs are prevalent in all forms of life and perform myriad cellular functions, including signaling and regulation. Importantly, disruption of IDP homeostasis is associated with numerous human diseases, including cancer and neurodegeneration. Despite wide recognition of IDPs, the molecular mechanisms underlying their functions are not fully understood. Here we review the structural features and disorder-function relationships for p21 and p27, two cyclin-dependent kinase (Cdk) regulators involved in controlling cell division and fate. Studies of p21 bound to Cdk2/cyclin A revealed that a helix stretching mechanism mediates binding promiscuity. Further, investigations of Tyr88-phosphorylated p27 identified a signaling conduit that controls cell division and is disrupted in certain cancers. These mechanisms rely upon a balance between nascent structure in the free state, induced folding upon binding, and persistent flexibility within functional complexes. Although these disorder-function relationships are likely to be recapitulated in other IDPs, it is also likely that the vocabulary of their mechanisms is much more extensive than is currently understood. Further study of the physical properties of IDPs and elucidation of their links with function are needed to fully understand the mechanistic language of IDPs. FAU - Mitrea, Diana M AU - Mitrea DM AD - Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38103, USA. FAU - Yoon, Mi-Kyung AU - Yoon MK FAU - Ou, Li AU - Ou L FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng PT - Journal Article PT - Review PL - Germany TA - Biol Chem JT - Biological chemistry JID - 9700112 RN - 0 (Cyclin-Dependent Kinase Inhibitor p21) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) SB - IM MH - Animals MH - Cyclin-Dependent Kinase Inhibitor p21/genetics/*metabolism MH - Cyclin-Dependent Kinase Inhibitor p27/genetics/*metabolism MH - Humans MH - Phosphorylation MH - Signal Transduction/genetics EDAT- 2012/10/03 06:00 MHDA- 2012/12/13 06:00 CRDT- 2012/10/03 06:00 PST - ppublish SO - Biol Chem. 2012 Apr;393(4):259-74. doi: 10.1515/hsz-2011-0254. PMID- 19134474 OWN - NLM STAT- MEDLINE DA - 20090112 DCOM- 20100222 LR - 20140901 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 96 IP - 1 DP - 2009 Jan TI - Induced secondary structure and polymorphism in an intrinsically disordered structural linker of the CNS: solid-state NMR and FTIR spectroscopy of myelin basic protein bound to actin. PG - 180-91 LID - 10.1016/j.bpj.2008.10.003 [doi] AB - The 18.5 kDa isoform of myelin basic protein (MBP) is a peripheral membrane protein that maintains the structural integrity of the myelin sheath of the central nervous system by conjoining the cytoplasmic leaflets of oligodendrocytes and by linking the myelin membrane to the underlying cytoskeleton whose assembly it strongly promotes. It is a multifunctional, intrinsically disordered protein that behaves primarily as a structural stabilizer, but with elements of a transient or induced secondary structure that represent binding sites for calmodulin or SH3-domain-containing proteins, inter alia. In this study we used solid-state NMR (SSNMR) and Fourier transform infrared (FTIR) spectroscopy to study the conformation of 18.5 kDa MBP in association with actin microfilaments and bundles. FTIR spectroscopy of fully (13)C,(15)N-labeled MBP complexed with unlabeled F-actin showed induced folding of both protein partners, viz., some increase in beta-sheet content in actin, and increases in both alpha-helix and beta-sheet content in MBP, albeit with considerable extended structure remaining. Solid-state NMR spectroscopy revealed that MBP in MBP-actin assemblies is structurally heterogeneous but gains ordered secondary structure elements (both alpha-helical and beta-sheet), particularly in the terminal fragments and in a central immunodominant epitope. The overall conformational polymorphism of MBP is consistent with its in vivo roles as both a linker (membranes and cytoskeleton) and a putative signaling hub. FAU - Ahmed, Mumdooh A M AU - Ahmed MA AD - Department of Physics, University of Guelph, Guelph, Canada. FAU - Bamm, Vladimir V AU - Bamm VV FAU - Shi, Lichi AU - Shi L FAU - Steiner-Mosonyi, Marta AU - Steiner-Mosonyi M FAU - Dawson, John F AU - Dawson JF FAU - Brown, Leonid AU - Brown L FAU - Harauz, George AU - Harauz G FAU - Ladizhansky, Vladimir AU - Ladizhansky V LA - eng GR - MOP 74468/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Actins) RN - 0 (Myelin Basic Protein) RN - 0 (Protein Isoforms) RN - 0 (Protons) RN - 0 (Recombinant Proteins) RN - 0 (Salts) SB - IM MH - Actin Cytoskeleton/*chemistry MH - Actins/*chemistry MH - Amino Acid Sequence MH - Animals MH - Chickens MH - Mice MH - Molecular Sequence Data MH - Myelin Basic Protein/*chemistry/genetics MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Protein Isoforms/chemistry MH - Protein Structure, Secondary MH - Protons MH - Recombinant Proteins/chemistry MH - Salts/chemistry MH - Spectroscopy, Fourier Transform Infrared/methods MH - Temperature PMC - PMC2710047 OID - NLM: PMC2710047 EDAT- 2009/01/13 09:00 MHDA- 2010/02/23 06:00 CRDT- 2009/01/13 09:00 PHST- 2008/07/28 [received] PHST- 2008/10/07 [accepted] AID - S0006-3495(08)00040-4 [pii] AID - 10.1016/j.bpj.2008.10.003 [doi] PST - ppublish SO - Biophys J. 2009 Jan;96(1):180-91. doi: 10.1016/j.bpj.2008.10.003. PMID- 15805597 OWN - NLM STAT- MEDLINE DA - 20050404 DCOM- 20050829 LR - 20070724 IS - 0907-4449 (Print) IS - 0907-4449 (Linking) VI - 61 IP - Pt 4 DP - 2005 Apr TI - Synchrotron X-ray powder diffraction study of hexagonal turkey egg-white lysozyme. PG - 423-32 AB - The structure of turkey egg-white lysozyme (TEWL) has been refined from high-resolution X-ray powder diffraction data. The sample was rapidly obtained as a polycrystalline precipitate at high protein concentration using 0.5 M NaCl solvent pH 6 and was deposited in the PDB with code 1xft. The diffraction data were collected at room temperature. Molecular replacement was shown to give a suitable starting point for refinement, illustrating that powder data can be sufficient for this approach. Crystallographic models were then refined by combined Rietveld and stereochemical restraint analysis of the powder data (d(min) = 3.35 A), resulting in the extraction of reliable lattice parameters and the refinement of the molecular conformation at room temperature. The structure is hexagonal [space group P6(1)22, unit-cell parameters a = 71.0862 (3), c = 85.0276 (5) A] with 12 symmetry-related molecules in the unit cell, in agreement with previous studies. The results of our analysis are indicative of specific amino acids being disordered at this temperature. Upon cooling, a sudden drop in the lattice parameters at approximately 250 K is observed concurrently with the freezing of the mother liquor. The observation of severe peak broadening below this temperature indicates strain effects accompanying the freezing transition, which are found to be reversible. Finally, a correlation between the unit-cell parameters and the pH of the buffer solution is evident, in a similar manner to earlier observations on HEWL. FAU - Margiolaki, Irene AU - Margiolaki I AD - European Synchrotron Radiation Facility, BP-220, F-38043, Grenoble CEDEX 9, France. margiolaki@esrf.fr FAU - Wright, Jonathan P AU - Wright JP FAU - Fitch, Andrew N AU - Fitch AN FAU - Fox, Gavin C AU - Fox GC FAU - Von Dreele, Robert B AU - Von Dreele RB LA - eng PT - Journal Article DEP - 20050324 PL - Denmark TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - EC 3.2.1.17 (Muramidase) SB - IM MH - Animals MH - Crystallization MH - Crystallography, X-Ray/*methods MH - Hydrogen-Ion Concentration MH - Models, Molecular MH - Muramidase/*chemistry MH - Powder Diffraction MH - Synchrotrons MH - Temperature MH - Turkeys EDAT- 2005/04/05 09:00 MHDA- 2005/08/30 09:00 CRDT- 2005/04/05 09:00 PHST- 2004/08/12 [received] PHST- 2005/01/13 [accepted] PHST- 2005/03/24 [epublish] AID - S0907444905001393 [pii] AID - 10.1107/S0907444905001393 [doi] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):423-32. Epub 2005 Mar 24. PMID- 11593006 OWN - NLM STAT- MEDLINE DA - 20011010 DCOM- 20011228 LR - 20140613 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 98 IP - 21 DP - 2001 Oct 9 TI - Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase. PG - 11973-8 AB - A crystal structure of the anaerobic Ni-Fe-S carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum has been determined to 2.8-A resolution. The CODH family, for which the R. rubrum enzyme is the prototype, catalyzes the biological oxidation of CO at an unusual Ni-Fe-S cluster called the C-cluster. The Ni-Fe-S C-cluster contains a mononuclear site and a four-metal cubane. Surprisingly, anomalous dispersion data suggest that the mononuclear site contains Fe and not Ni, and the four-metal cubane has the form [NiFe(3)S(4)] and not [Fe(4)S(4)]. The mononuclear site and the four-metal cluster are bridged by means of Cys(531) and one of the sulfides of the cube. CODH is organized as a dimer with a previously unidentified [Fe(4)S(4)] cluster bridging the two subunits. Each monomer is comprised of three domains: a helical domain at the N terminus, an alpha/beta (Rossmann-like) domain in the middle, and an alpha/beta (Rossmann-like) domain at the C terminus. The helical domain contributes ligands to the bridging [Fe(4)S(4)] cluster and another [Fe(4)S(4)] cluster, the B-cluster, which is involved in electron transfer. The two Rossmann domains contribute ligands to the active site C-cluster. This x-ray structure provides insight into the mechanism of biological CO oxidation and has broader significance for the roles of Ni and Fe in biological systems. FAU - Drennan, C L AU - Drennan CL AD - Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. cdrennan@mit.edu FAU - Heo, J AU - Heo J FAU - Sintchak, M D AU - Sintchak MD FAU - Schreiter, E AU - Schreiter E FAU - Ludden, P W AU - Ludden PW LA - eng SI - PDB/1JQK GR - F32 GM19044/GM/NIGMS NIH HHS/United States GR - GM45162/GM/NIGMS NIH HHS/United States GR - RR07707/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20011002 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Multienzyme Complexes) RN - 70FD1KFU70 (Sulfur) RN - 7OV03QG267 (Nickel) RN - 7U1EE4V452 (Carbon Monoxide) RN - E1UOL152H7 (Iron) RN - EC 1.2.- (Aldehyde Oxidoreductases) RN - EC 1.2.99.2 (carbon monoxide dehydrogenase) SB - IM MH - Aldehyde Oxidoreductases/*chemistry MH - Carbon Monoxide/chemistry MH - Crystallography, X-Ray MH - Dimerization MH - Iron/*chemistry MH - Models, Molecular MH - Multienzyme Complexes/*chemistry MH - Nickel/*chemistry MH - Protein Structure, Tertiary MH - Rhodospirillum rubrum/enzymology MH - Sulfur/*chemistry PMC - PMC59822 OID - NLM: PMC59822 EDAT- 2001/10/11 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/10/11 10:00 PHST- 2001/10/02 [aheadofprint] AID - 10.1073/pnas.211429998 [doi] AID - 211429998 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2001 Oct 9;98(21):11973-8. Epub 2001 Oct 2. PMID- 21031501 OWN - NLM STAT- MEDLINE DA - 20101029 DCOM- 20110609 LR - 20140916 IS - 1521-6551 (Electronic) IS - 1521-6543 (Linking) VI - 62 IP - 10 DP - 2010 Oct TI - Binding of the Rett syndrome protein, MeCP2, to methylated and unmethylated DNA and chromatin. PG - 732-8 LID - 10.1002/iub.386 [doi] AB - Methylated CpG Binding Protein 2 (MeCP2) is a nuclear protein named for its ability to selectively recognize methylated DNA. Much attention has been focused on understanding MeCP2 structure and function in the context of its role in Rett syndrome, a severe neurodevelopmental disorder that afflicts one in 10,000-15,000 girls. Early studies suggested a connection between DNA methylation, MeCP2, and establishment of a repressive chromatin structure at specific gene promoters. However, it is now recognized that MeCP2 can both activate and repress specific genes depending on the context. Likewise, in the cell, MeCP2 is bound to unmethylated DNA and chromatin in addition to methylated DNA. Thus, to understand the molecular basis of MeCP2 functionality, it is necessary to unravel the complex interrelationships between MeCP2 binding to unmethylated and methylated regions of the genome. MeCP2 is unusual and interesting in that it is an intrinsically disordered protein, that is, much of its primary sequence fails to fold into secondary structure and yet is functional. The unique structure of MeCP2 is the subject of the first section of this article. We then discuss recent investigations of the in vitro binding of MeCP2 to unmethylated and methylated DNA, and the potential ramifications of this work for in vivo function. We close by focusing on mechanistic studies indicating that the binding of MeCP2 to chromatin results in compaction into local (secondary) and global (tertiary) higher order structures. MeCP2 also competes with histone H1 for nucleosomal binding sites. The recent finding that MeCP2 is found at near stoichiometric levels with nucleosomes in neuronal cells underscores the multiple modes of engagement of MeCP2 with the genome, which include the cooperative tracking of methylation density. FAU - Hansen, Jeffrey C AU - Hansen JC AD - Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA. jeffrey.c.hansen@colostate.edu FAU - Ghosh, Rajarshi P AU - Ghosh RP FAU - Woodcock, Christopher L AU - Woodcock CL LA - eng GR - GM066834/GM/NIGMS NIH HHS/United States GR - GM070897/GM/NIGMS NIH HHS/United States GR - R01 GM066834/GM/NIGMS NIH HHS/United States GR - R01 GM066834-09/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - IUBMB Life JT - IUBMB life JID - 100888706 RN - 0 (Chromatin) RN - 0 (Histones) RN - 0 (Methyl-CpG-Binding Protein 2) RN - 0 (Nucleosomes) RN - 9007-49-2 (DNA) SB - IM MH - Binding Sites MH - Chromatin/*metabolism MH - DNA/chemistry/genetics/*metabolism MH - DNA Methylation MH - Female MH - Genome, Human MH - Histones/genetics/*metabolism MH - Humans MH - Methyl-CpG-Binding Protein 2/chemistry/genetics/*metabolism MH - Nucleosomes/metabolism MH - Promoter Regions, Genetic MH - Protein Binding MH - Protein Structure, Secondary MH - Rett Syndrome/genetics PMC - PMC3096928 MID - NIHMS290783 OID - NLM: NIHMS290783 OID - NLM: PMC3096928 EDAT- 2010/10/30 06:00 MHDA- 2011/06/10 06:00 CRDT- 2010/10/30 06:00 AID - 10.1002/iub.386 [doi] PST - ppublish SO - IUBMB Life. 2010 Oct;62(10):732-8. doi: 10.1002/iub.386. PMID- 2373370 OWN - NLM STAT- MEDLINE DA - 19900830 DCOM- 19900830 LR - 20081121 IS - 0378-1119 (Print) IS - 0378-1119 (Linking) VI - 89 IP - 2 DP - 1990 May 14 TI - Isolation of a genomic clone encoding the rat histone variant, H1d. PG - 265-9 AB - Mammals contain a family of five closely related H1 histone variants (H1a-e) as well as two less closely related forms, H10 and H1t. We have sequenced a rat genomic clone that encodes one of the standard H1 variants. An RNA transcript of the gene was made with bacteriophage SP6 RNA polymerase and translated in a cell-free system. The protein synthesized in vitro was identified as variant H1d by its electrophoretic mobility. FAU - Cole, K D AU - Cole KD AD - Department of Chemistry, University of South Carolina, Columbia 29208. FAU - Kandala, J C AU - Kandala JC FAU - Kremer, E AU - Kremer E FAU - Kistler, W S AU - Kistler WS LA - eng SI - GENBANK/M31229 GR - HD 10793/HD/NICHD NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - NETHERLANDS TA - Gene JT - Gene JID - 7706761 RN - 0 (Histones) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Chickens MH - Cloning, Molecular MH - *Genes MH - *Genetic Variation MH - Histones/*genetics MH - Mice MH - Molecular Sequence Data MH - Multigene Family MH - Rats MH - Restriction Mapping MH - Sequence Homology, Nucleic Acid MH - Trout EDAT- 1990/05/14 MHDA- 1990/05/14 00:01 CRDT- 1990/05/14 00:00 PST - ppublish SO - Gene. 1990 May 14;89(2):265-9. PMID- 24863370 OWN - NLM STAT- MEDLINE DA - 20140721 DCOM- 20140912 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 281 IP - 14 DP - 2014 Jul TI - Conformational modulation and hydrodynamic radii of CP12 protein and its complexes probed by fluorescence correlation spectroscopy. PG - 3206-17 LID - 10.1111/febs.12854 [doi] AB - Light/dark regulation of the Calvin cycle in oxygenic photosynthetic organisms involves the formation and dissociation of supramolecular complexes between CP12, a nuclear-encoded chloroplast protein, and the two enzymes glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (EC 1.2.1.13) and phosphoribulokinase (PRK) (EC 2.7.1.19). Despite the high importance of understanding the structural basis of the interaction of CP12 with GAPDH and PRK to investigate the regulation of the Calvin cycle, information is still lacking about the structural remodulation of CP12 and its complex formation. Here, we characterize the diffusion dynamics and hydrodynamic radii of CP12 from Chlamydomonas reinhardtii upon binding to GAPDH and PRK using fluorescence correlation spectroscopy experiments. We quantify a hydrodynamic radius of 3.4 +/- 0.2 nm for the CP12 protein with an increase up to 5.2 +/- 0.3 nm upon complex formation with GAPDH and PRK. In addition, unfolding experiments reveal a 1.6- and 2.0-fold increase respectively of the hydrodynamic radii for the N-terminal and C-terminal cysteine CP12 mutant proteins compared with their native folded structures. The different behavior of the CP12 mutant proteins during hydrophobic collapse transition is a direct clue to different structural orientations of the CP12 mutant proteins. These different structures are expected to facilitate the binding of either GAPDH or PRK during binary complex and ternary complex formation. CI - (c) 2014 FEBS. FAU - Moparthi, Satish Babu AU - Moparthi SB AD - Centrale Marseille, Institut Fresnel, Aix Marseille Universite, France. FAU - Thieulin-Pardo, Gabriel AU - Thieulin-Pardo G FAU - Mansuelle, Pascal AU - Mansuelle P FAU - Rigneault, Herve AU - Rigneault H FAU - Gontero, Brigitte AU - Gontero B FAU - Wenger, Jerome AU - Wenger J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140701 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Chloroplast Proteins) RN - 0 (Intrinsically Disordered Proteins) RN - EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases) RN - EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)) RN - EC 2.7.1.19 (phosphoribulokinase) SB - IM MH - Chlamydomonas reinhardtii/metabolism MH - Chloroplast Proteins/*chemistry/*metabolism MH - Chloroplasts/metabolism MH - Glyceraldehyde-3-Phosphate Dehydrogenases/chemistry/*metabolism MH - Hydrodynamics MH - Intrinsically Disordered Proteins/chemistry/*metabolism MH - Phosphotransferases (Alcohol Group Acceptor)/chemistry/*metabolism MH - Photosynthesis MH - Spectrometry, Fluorescence OTO - NOTNLM OT - CP12 OT - GAPDH OT - PRK OT - fluorescence correlation spectroscopy OT - hydrodynamic radius OT - intrinsic disorder proteins EDAT- 2014/05/28 06:00 MHDA- 2014/09/13 06:00 CRDT- 2014/05/28 06:00 PHST- 2014/02/07 [received] PHST- 2014/04/30 [revised] PHST- 2014/05/16 [accepted] PHST- 2014/07/01 [aheadofprint] AID - 10.1111/febs.12854 [doi] PST - ppublish SO - FEBS J. 2014 Jul;281(14):3206-17. doi: 10.1111/febs.12854. Epub 2014 Jul 1. PMID- 23373423 OWN - NLM STAT- MEDLINE DA - 20131205 DCOM- 20140131 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 52 IP - 10 DP - 2013 Mar 12 TI - A folded excited state of ligand-free nuclear coactivator binding domain (NCBD) underlies plasticity in ligand recognition. PG - 1686-93 LID - 10.1021/bi4001062 [doi] AB - Intrinsically disordered proteins are renowned for their structural plasticity when they undergo coupled folding and binding to partner proteins. The nuclear coactivator binding domain of CBP is a remarkable example of this adaptability as it folds into two different conformations depending on the binding partner. To understand the role of the conformational ensemble for plasticity in ligand recognition, we investigated the millisecond dynamics of this domain using relaxation dispersion NMR spectroscopy. All NMR signals originating from the domain are broadened, demonstrating that the whole domain experience conformational exchange. The dispersion data can be described by a global two-state exchange process between a ground state and an excited state populated to 8%. The three helices are still folded in the excited state but have a different packing from the ground state; the contact between helices 2 and 3 found in the ground state is broken in the excited state, and a new one is formed between helices 1 and 3. This suggests that while NCBD in the ground state has a structure similar to the complex with the ligand ACTR, the conformation of NCBD in the excited state has some similarity with that of NCBD in complex with the ligand IRF-3. The energy landscape of this domain is thus proposed to resemble the fold-switching proteins that have two coexisting native states, which may serve as a starting point for binding via conformational selection. FAU - Kjaergaard, Magnus AU - Kjaergaard M AD - Department of Biology, University of Copenhagen , Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark. FAU - Andersen, Lisbeth AU - Andersen L FAU - Nielsen, Lau Dalby AU - Nielsen LD FAU - Teilum, Kaare AU - Teilum K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130301 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Crebbp protein, mouse) RN - 0 (Interferon Regulatory Factor-3) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Irf3 protein, mouse) RN - 0 (Ligands) RN - 0 (Nuclear Proteins) RN - EC 2.3.1.48 (CREB-Binding Protein) RN - EC 2.3.1.48 (Ncoa3 protein, mouse) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 3) SB - IM MH - Animals MH - CREB-Binding Protein/*chemistry/*metabolism MH - Hydrophobic and Hydrophilic Interactions MH - Interferon Regulatory Factor-3/chemistry/metabolism MH - Intrinsically Disordered Proteins/*chemistry/*metabolism MH - Ligands MH - Mice MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*chemistry/*metabolism MH - Nuclear Receptor Coactivator 3/chemistry/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Static Electricity MH - Thermodynamics EDAT- 2013/02/05 06:00 MHDA- 2014/02/01 06:00 CRDT- 2013/02/05 06:00 PHST- 2013/03/01 [aheadofprint] AID - 10.1021/bi4001062 [doi] PST - ppublish SO - Biochemistry. 2013 Mar 12;52(10):1686-93. doi: 10.1021/bi4001062. Epub 2013 Mar 1. PMID- 23477540 OWN - NLM STAT- MEDLINE DA - 20130409 DCOM- 20130920 IS - 1520-5827 (Electronic) IS - 0743-7463 (Linking) VI - 29 IP - 14 DP - 2013 Apr 9 TI - Study of wild-type alpha-synuclein binding and orientation on gold nanoparticles. PG - 4603-15 LID - 10.1021/la400266u [doi] AB - The disruption of alpha-synuclein (alpha-syn) homeostasis in neurons is a potential cause of Parkinson's disease, which is manifested pathologically by the appearance of alpha-syn aggregates, or Lewy bodies. Treatments for neurological diseases are extremely limited. To study the potential use of gold nanoparticles (Au NPs) to limit alpha-syn misfolding, the binding and orientation of alpha-syn on Au NPs were investigated. alpha-Syn was determined to interact with 20 and 90 nm Au NPs via multilayered adsorption: a strong electrostatic interaction between alpha-syn and Au NPs in the hard corona and a weaker noncovalent protein-protein interaction in the soft corona. Spectroscopic and light-scattering titrations led to the determinations of binding constants for the Au NP alpha-syn coronas: for the hard corona on 20 nm Au NPs, the equilibrium association constant was 2.9 +/- 1.1 x 10(9) M(-1) (for 360 +/- 70 alpha-syn/NP), and on 90 nm Au NPs, the hard corona association constant was 9.5 +/- 0.8 x 10(10) M(-1) (for 5300 +/- 700 alpha-syn/NP). The binding of the soft corona was thermodynamically unfavorable and kinetically driven and was in constant exchange with "free" alpha-syn in solution. A protease digestion method was used to deduce the alpha-syn orientation and structure on Au NPs, revealing that alpha-syn absorbs onto negatively charged Au NPs via its N-terminus while apparently retaining its natively unstructured conformation. These results suggest that Au NPs could be used to sequester and regulate alpha-syn homeostasis. FAU - Yang, Jie An AU - Yang JA AD - Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. FAU - Johnson, Brittany J AU - Johnson BJ FAU - Wu, Sway AU - Wu S FAU - Woods, Wendy S AU - Woods WS FAU - George, Julia M AU - George JM FAU - Murphy, Catherine J AU - Murphy CJ LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130325 PL - United States TA - Langmuir JT - Langmuir : the ACS journal of surfaces and colloids JID - 9882736 RN - 0 (alpha-Synuclein) RN - 7440-57-5 (Gold) RN - EC 3.4.21.4 (Trypsin) SB - IM MH - Adsorption MH - Amino Acid Sequence MH - Gold/*chemistry MH - Humans MH - Metal Nanoparticles/*chemistry MH - Molecular Sequence Data MH - Particle Size MH - Protein Binding MH - Proteolysis MH - Spectrometry, Fluorescence MH - Trypsin/metabolism MH - alpha-Synuclein/*chemistry/metabolism EDAT- 2013/03/13 06:00 MHDA- 2013/09/21 06:00 CRDT- 2013/03/13 06:00 PHST- 2013/03/25 [aheadofprint] AID - 10.1021/la400266u [doi] PST - ppublish SO - Langmuir. 2013 Apr 9;29(14):4603-15. doi: 10.1021/la400266u. Epub 2013 Mar 25. PMID- 20973509 OWN - NLM STAT- MEDLINE DA - 20101130 DCOM- 20101228 LR - 20150317 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 48 DP - 2010 Dec 7 TI - Intrinsically disordered PEP-19 confers unique dynamic properties to apo and calcium calmodulin. PG - 10287-97 LID - 10.1021/bi100500m [doi] AB - PEP-19 (Purkinje cell protein 4) is an intrinsically disordered protein with an IQ calmodulin (CaM) binding motif. Expression of PEP-19 was recently shown to protect cells from apoptosis and cell death due to Ca(2+) overload. Our initial studies showed that PEP-19 causes novel and dramatic increases in the rates of association of Ca(2+) with and dissociation of Ca(2+) from the C-domain of CaM. The goal of this work was to study interactions between the C-domain of CaM (C-CaM) and PEP-19 by solution nuclear magnetic resonance (NMR) to identify mechanisms by which PEP-19 regulates binding of Ca(2+) to CaM. Our results show that PEP-19 causes a greater structural change in apo C-CaM than in Ca(2+)-C-CaM, and that the first Ca(2+) binds preferentially to site IV in the presence of PEP-19 with exchange characteristics that are consistent with a decrease in Ca(2+) binding cooperativity. Relatively weak binding of PEP-19 has distinct effects on chemical and conformational exchange on the microsecond to millisecond time scale. In apo C-CaM, PEP-19 binding causes a redistribution of residues that experience conformational exchange, leading to an increase in the number of residues around Ca(2+) binding site IV that undergo conformational exchange on the microsecond to millisecond time scale. This appears to be caused by an allosteric effect because these residues are not localized to the PEP-19 binding site. In contrast, PEP-19 increases the number of residues that exhibit conformational exchange in Ca(2+)-C-CaM. These residues are primarily localized to the PEP-19 binding site but also include Asp93 in site III. These results provide working models for the role of protein dynamics in the regulation of binding of Ca(2+) to CaM by PEP-19. FAU - Wang, Xu AU - Wang X AD - Department of Biochemistry and Molecular Biology and Structural Biology Center, University of Texas-Houston Medical School, 6431 Fannin Street, Houston, TX 77030, USA. FAU - Kleerekoper, Quinn K AU - Kleerekoper QK FAU - Xiong, Liang-wen AU - Xiong LW FAU - Putkey, John A AU - Putkey JA LA - eng GR - R01 GM069611/GM/NIGMS NIH HHS/United States GR - R01 GM069611/GM/NIGMS NIH HHS/United States GR - R01 GM069611-01A2/GM/NIGMS NIH HHS/United States GR - R01 GM069611-04/GM/NIGMS NIH HHS/United States GR - R90 DK071504/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20101112 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Apoproteins) RN - 0 (Calmodulin) RN - 0 (Nerve Tissue Proteins) RN - SY7Q814VUP (Calcium) SB - IM MH - Apoproteins/chemistry/*metabolism MH - Binding Sites MH - Calcium/*metabolism MH - Calmodulin/chemistry/*metabolism MH - Kinetics MH - Models, Molecular MH - Nerve Tissue Proteins/*chemistry/*metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Reproducibility of Results PMC - PMC3001392 MID - NIHMS252506 OID - NLM: NIHMS252506 OID - NLM: PMC3001392 EDAT- 2010/10/27 06:00 MHDA- 2010/12/29 06:00 CRDT- 2010/10/27 06:00 PHST- 2010/11/12 [aheadofprint] AID - 10.1021/bi100500m [doi] PST - ppublish SO - Biochemistry. 2010 Dec 7;49(48):10287-97. doi: 10.1021/bi100500m. Epub 2010 Nov 12. PMID- 24327307 OWN - NLM STAT- MEDLINE DA - 20131220 DCOM- 20140813 IS - 1756-591X (Electronic) IS - 1756-5901 (Linking) VI - 6 IP - 1 DP - 2014 Jan TI - Characterization of UO2(2+) binding to osteopontin, a highly phosphorylated protein: insights into potential mechanisms of uranyl accumulation in bones. PG - 166-76 LID - 10.1039/c3mt00269a [doi] AB - Bones are one of the few organs in which uranyl (UO2(2+)) accumulates. This large dioxo-cation displays affinity for carboxylates, phenolates and phosphorylated functional groups in proteins. The noncollagenous protein osteopontin (OPN) plays an important role in bone homeostasis. It is mainly found in the extracellular matrix of mineralized tissues but also in body fluids such as milk, blood and urine. Furthermore, OPN is an intrinsically disordered protein, which, like other proteins of the SIBLING family, contains a polyaspartic acid sequence and numerous patterns of alternating acidic and phosphorylated residues. All these properties led to the hypothesis that this protein could be prone to UO2(2+) binding. In this work, a simple purification procedure enabling highly purified bovine (bOPN) and human OPN (hOPN) to be obtained was developed. Various biophysical approaches were set up to study the impact of phosphorylations on the affinity of OPN for UO2(2+) as well as the formation of stable complexes originating from structural changes induced by the binding of this metal cation. The results obtained suggest a new mechanism of the interaction of UO2(2+) with bone metabolism and a new role for OPN as a metal transporter. FAU - Qi, Lei AU - Qi L AD - CEA/DSV/iBEB/SBTN, Laboratoire d'Etude des Proteines Cibles, BP 17171, 30207 Bagnols sur Ceze Cedex, France. claude.vidaud@cea.fr. FAU - Basset, Christian AU - Basset C FAU - Averseng, Olivier AU - Averseng O FAU - Quemeneur, Eric AU - Quemeneur E FAU - Hagege, Agnes AU - Hagege A FAU - Vidaud, Claude AU - Vidaud C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Metallomics JT - Metallomics : integrated biometal science JID - 101478346 RN - 0 (Uranium Compounds) RN - 106441-73-0 (Osteopontin) RN - 4OC371KSTK (Uranium) RN - L70487KUZO (uranium dioxide) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding, Competitive MH - Bone and Bones/*metabolism MH - Cattle MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - Mass Spectrometry MH - Molecular Sequence Data MH - Osteopontin/chemistry/isolation & purification/*metabolism MH - Phosphorylation MH - Protein Binding MH - Protein Conformation MH - Uranium/*metabolism MH - Uranium Compounds/*metabolism EDAT- 2013/12/12 06:00 MHDA- 2014/08/15 06:00 CRDT- 2013/12/12 06:00 AID - 10.1039/c3mt00269a [doi] PST - ppublish SO - Metallomics. 2014 Jan;6(1):166-76. doi: 10.1039/c3mt00269a. PMID- 23418572 OWN - NLM STAT- MEDLINE DA - 20130218 DCOM- 20130827 LR - 20141116 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 2 DP - 2013 TI - The N-terminal intrinsically disordered domain of Mgm101p is localized to the mitochondrial nucleoid. PG - e56465 LID - 10.1371/journal.pone.0056465 [doi] AB - The mitochondrial genome maintenance gene, MGM101, is essential for yeasts that depend on mitochondrial DNA replication. Previously, in Saccharomyces cerevisiae, it has been found that the carboxy-terminal two-thirds of Mgm101p has a functional core. Furthermore, there is a high level of amino acid sequence conservation in this region from widely diverse species. By contrast, the amino-terminal region, that is also essential for function, does not have recognizable conservation. Using a bioinformatic approach we find that the functional core from yeast and a corresponding region of Mgm101p from the coral Acropora millepora have an ordered structure, while the N-terminal domains of sequences from yeast and coral are predicted to be disordered. To examine whether ordered and disordered domains of Mgm101p have specific or general functions we made chimeric proteins from yeast and coral by swapping the two regions. We find, by an in vivo assay in S.cerevisiae, that the ordered domain of A.millepora can functionally replace the yeast core region but the disordered domain of the coral protein cannot substitute for its yeast counterpart. Mgm101p is found in the mitochondrial nucleoid along with enzymes and proteins involved in mtDNA replication. By attaching green fluorescent protein to the N-terminal disordered domain of yeast Mgm101p we find that GFP is still directed to the mitochondrial nucleoid where full-length Mgm101p-GFP is targeted. FAU - Hayward, David C AU - Hayward DC AD - Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia. FAU - Dosztanyi, Zsuzsanna AU - Dosztanyi Z FAU - Clark-Walker, George Desmond AU - Clark-Walker GD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130213 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA, Mitochondrial) RN - 0 (MGM1 protein, S cerevisiae) RN - 0 (Mitochondrial Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 147336-22-9 (Green Fluorescent Proteins) RN - EC 3.6.1.- (GTP-Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Anthozoa/genetics MH - Binding Sites/genetics MH - DNA, Mitochondrial/genetics/metabolism MH - GTP-Binding Proteins/chemistry/genetics/*metabolism MH - Genetic Complementation Test MH - Green Fluorescent Proteins/genetics/metabolism MH - Microscopy, Fluorescence MH - Mitochondria/genetics/*metabolism MH - Mitochondrial Proteins/chemistry/genetics/*metabolism MH - Molecular Sequence Data MH - Mutation MH - Saccharomyces cerevisiae/genetics/growth & development/*metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism MH - Sequence Homology, Amino Acid PMC - PMC3572067 OID - NLM: PMC3572067 EDAT- 2013/02/19 06:00 MHDA- 2013/08/28 06:00 CRDT- 2013/02/19 06:00 PHST- 2012/12/02 [received] PHST- 2013/01/14 [accepted] PHST- 2013/02/13 [epublish] AID - 10.1371/journal.pone.0056465 [doi] AID - PONE-D-12-38046 [pii] PST - ppublish SO - PLoS One. 2013;8(2):e56465. doi: 10.1371/journal.pone.0056465. Epub 2013 Feb 13. PMID- 14704153 OWN - NLM STAT- MEDLINE DA - 20040315 DCOM- 20040527 LR - 20071115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 12 DP - 2004 Mar 19 TI - Structural insights into molecular function of the metastasis-associated phosphatase PRL-3. PG - 11882-9 AB - Phosphatases and kinases are the cellular signal transduction enzymes that control protein phosphorylation. PRL phosphatases constitute a novel class of small (20 kDa), prenylated phosphatases with oncogenic activity. In particular, PRL-3 is consistently overexpressed in liver metastasis in colorectal cancer cells and represents a new therapeutic target. Here, we present the solution structure of PRL-3, the first structure of a PRL phosphatase. The structure places PRL phosphatases in the class of dual specificity phosphatases with closest structural homology to the VHR phosphatase. The structure, coupled with kinetic studies of site-directed mutants, identifies functionally important residues and reveals unique features, differentiating PRLs from other phosphatases. These differences include an unusually hydrophobic active site without the catalytically important serine/threonine found in most other phosphatases. The position of the general acid loop indicates the presence of conformational change upon catalysis. The studies also identify a potential regulatory role of Cys(49) that forms an intramolecular disulfide bond with the catalytic Cys(104) even under mildly reducing conditions. Molecular modeling of the highly homologous PRL-1 and PRL-2 phosphatases revealed unique surface elements that are potentially important for specificity. FAU - Kozlov, Guennadi AU - Kozlov G AD - Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada. FAU - Cheng, Jing AU - Cheng J FAU - Ziomek, Edmund AU - Ziomek E FAU - Banville, Denis AU - Banville D FAU - Gehring, Kalle AU - Gehring K FAU - Ekiel, Irena AU - Ekiel I LA - eng SI - PDB/1R6H PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040101 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Immediate-Early Proteins) RN - 0 (Neoplasm Proteins) RN - EC 3.1.3.48 (PTP4A3 protein, human) RN - EC 3.1.3.48 (Protein Tyrosine Phosphatases) SB - IM MH - Amino Acid Sequence MH - Humans MH - Immediate-Early Proteins/chemistry/genetics/*metabolism MH - Kinetics MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Neoplasm Proteins MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Tyrosine Phosphatases/chemistry/genetics/*metabolism MH - Structure-Activity Relationship EDAT- 2004/01/06 05:00 MHDA- 2004/05/28 05:00 CRDT- 2004/01/06 05:00 PHST- 2004/01/01 [aheadofprint] AID - 10.1074/jbc.M312905200 [doi] AID - M312905200 [pii] PST - ppublish SO - J Biol Chem. 2004 Mar 19;279(12):11882-9. Epub 2004 Jan 1. PMID- 25190813 OWN - NLM STAT- MEDLINE DA - 20141025 DCOM- 20150212 LR - 20141224 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 289 IP - 43 DP - 2014 Oct 24 TI - Structural insights into the mechanism of negative regulation of single-box high mobility group proteins by the acidic tail domain. PG - 29817-26 LID - 10.1074/jbc.M114.591115 [doi] AB - The Drosophila and plant (maize) functional counterparts of the abundant vertebrate chromosomal protein HMGB1 (HMG-D and ZmHMGB1, respectively) differ from HMGB1 in having a single HMG box, as well as basic and acidic flanking regions that vary greatly in length and charge. We show that despite these variations, HMG-D and ZmHMGB1 exist in dynamic assemblies in which the basic HMG boxes and linkers associate with their intrinsically disordered, predominantly acidic, tails in a manner analogous to that observed previously for HMGB1. The DNA-binding surfaces of the boxes and linkers are occluded in "auto-inhibited" forms of the protein, which are in equilibrium with transient, more open structures that are "binding-competent." This strongly suggests that the mechanism of auto-inhibition may be a general one. HMG-D and ZmHMGB1 differ from HMGB1 in having phosphorylation sites in their tail and linker regions. In both cases, in vitro phosphorylation of serine residues within the acidic tail stabilizes the assembled form, suggesting another level of regulation for interaction with DNA, chromatin, and other proteins that is not possible for the uniformly acidic (hence unphosphorylatable) tail of HMGB1. CI - (c) 2014 by The American Society for Biochemistry and Molecular Biology, Inc. FAU - Stott, Katherine AU - Stott K AD - From the Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom and. FAU - Watson, Matthew AU - Watson M AD - From the Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom and. FAU - Bostock, Mark J AU - Bostock MJ AD - From the Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom and. FAU - Mortensen, Simon A AU - Mortensen SA AD - the Department of Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitatsstrasse 31, 93053 Regensburg, Germany. FAU - Travers, Andrew AU - Travers A AD - From the Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom and. FAU - Grasser, Klaus D AU - Grasser KD AD - the Department of Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitatsstrasse 31, 93053 Regensburg, Germany. FAU - Thomas, Jean O AU - Thomas JO AD - From the Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom and jot1@cam.ac.uk. LA - eng GR - BB/D002257/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BB/D002257/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140904 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Drosophila Proteins) RN - 0 (High Mobility Group Proteins) RN - 0 (HmgD protein, Drosophila) RN - 0 (Mutant Proteins) RN - 0 (Plant Proteins) SB - IM MH - Animals MH - Drosophila Proteins/*chemistry/*metabolism MH - Drosophila melanogaster MH - High Mobility Group Proteins/*chemistry/*metabolism MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Mutant Proteins/chemistry/metabolism MH - Phosphorylation MH - Plant Proteins/*chemistry/*metabolism MH - Protein Structure, Tertiary MH - Structure-Activity Relationship MH - Zea mays PMC - PMC4207994 OID - NLM: PMC4207994 OTO - NOTNLM OT - Acidic Regulatory Domain OT - Casein Kinase 2 (CK2) OT - Chromatin OT - HMGB Protein OT - Intrinsically Disordered Protein OT - Nuclear Magnetic Resonance (NMR) OT - Paramagnetic Relaxation Enhancement OT - Phosphorylation OT - Protein Kinase C OT - Protein Kinase C (PKC) EDAT- 2014/09/06 06:00 MHDA- 2015/02/13 06:00 CRDT- 2014/09/06 06:00 PHST- 2014/09/04 [aheadofprint] AID - M114.591115 [pii] AID - 10.1074/jbc.M114.591115 [doi] PST - ppublish SO - J Biol Chem. 2014 Oct 24;289(43):29817-26. doi: 10.1074/jbc.M114.591115. Epub 2014 Sep 4. PMID- 16403517 OWN - NLM STAT- MEDLINE DA - 20060130 DCOM- 20060323 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 356 IP - 4 DP - 2006 Mar 3 TI - The N-terminal half of the peroxisomal cycling receptor Pex5p is a natively unfolded domain. PG - 864-75 AB - Targeting of most newly synthesised peroxisomal matrix proteins to the organelle requires Pex5p, the so-called PTS1 receptor. According to current models of peroxisomal biogenesis, Pex5p interacts with these proteins in the cytosol, transports them to the peroxisomal membrane and catalyses their translocation across the membrane. Presently, our knowledge on the structural details behind the interaction of Pex5p with the cargo proteins is reasonably complete. In contrast, information regarding the structure of the Pex5p N-terminal half (a region containing its peroxisomal targeting domain) is still limited. We have recently observed that the Stokes radius of this Pex5p domain is anomalously large, suggesting that this portion of the protein is either a structured elongated domain or that it adopts a low compactness conformation. Here, we address this issue using a combination of biophysical and biochemical approaches. Our results indicate that the N-terminal half of Pex5p is best described as a natively unfolded pre-molten globule-like domain. The implications of these findings on the mechanism of protein import into the peroxisome are discussed. FAU - Carvalho, Andreia F AU - Carvalho AF AD - Instituto de Biologia Molecular e Celular, Rua do Campo Alegre, 823, 4150-180 Porto, Portugal. FAU - Costa-Rodrigues, Joao AU - Costa-Rodrigues J FAU - Correia, Isabel AU - Correia I FAU - Costa Pessoa, Joao AU - Costa Pessoa J FAU - Faria, Tiago Q AU - Faria TQ FAU - Martins, Cristina L AU - Martins CL FAU - Fransen, Marc AU - Fransen M FAU - Sa-Miranda, Clara AU - Sa-Miranda C FAU - Azevedo, Jorge E AU - Azevedo JE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051219 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amino Acids) RN - 0 (Receptors, Cytoplasmic and Nuclear) RN - 0 (peroxisome-targeting signal 1 receptor) SB - IM MH - Amino Acids/chemistry MH - Calorimetry, Differential Scanning MH - Chromatography, Gel MH - Circular Dichroism MH - Humans MH - Protein Folding MH - *Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - Receptors, Cytoplasmic and Nuclear/*chemistry/genetics MH - Spectroscopy, Fourier Transform Infrared EDAT- 2006/01/13 09:00 MHDA- 2006/03/24 09:00 CRDT- 2006/01/13 09:00 PHST- 2005/09/05 [received] PHST- 2005/11/26 [revised] PHST- 2005/12/01 [accepted] PHST- 2005/12/19 [aheadofprint] AID - S0022-2836(05)01541-X [pii] AID - 10.1016/j.jmb.2005.12.002 [doi] PST - ppublish SO - J Mol Biol. 2006 Mar 3;356(4):864-75. Epub 2005 Dec 19. PMID- 10196139 OWN - NLM STAT- MEDLINE DA - 19990517 DCOM- 19990517 LR - 20121115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 274 IP - 16 DP - 1999 Apr 16 TI - Trimethylamine N-oxide-induced cooperative folding of an intrinsically unfolded transcription-activating fragment of human glucocorticoid receptor. PG - 10693-6 AB - A number of biologically important proteins or protein domains identified recently are fully or partially unstructured (unfolded). Methods that allow studies of the propensity of such proteins to fold naturally are valuable. The traditional biophysical approaches using alcohols to drive alpha-helix formation raise serious questions of the relevance of alcohol-induced structure to the biologically important conformations. Recently we illustrated the extraordinary capability of the naturally occurring solute, trimethylamine N-oxide (TMAO), to force two unfolded proteins to fold to native-like species with significant functional activity. In the present work we apply this technique to recombinant human glucocorticoid receptor fragments consisting of residues 1-500 and residues 77-262. CD and fluorescence spectroscopy showed that both were largely disordered in aqueous solution. TMAO induced a condensed structure in the large fragment, indicated by the substantial enhancement in intrinsic fluorescence and blue shift of fluorescent maxima. CD spectroscopy demonstrated that the TMAO-induced structure is different from the alpha-helix-rich conformation driven by trifluoroethanol (TFE). In contrast to TFE, the conformational transition of the 1-500 fragment induced by TMAO is cooperative, a condition characteristic of proteins with unique structures. FAU - Baskakov, I V AU - Baskakov IV AD - Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, Texas 77555-0645, USA. FAU - Kumar, R AU - Kumar R FAU - Srinivasan, G AU - Srinivasan G FAU - Ji, Y S AU - Ji YS FAU - Bolen, D W AU - Bolen DW FAU - Thompson, E B AU - Thompson EB LA - eng GR - CA41407/CA/NCI NIH HHS/United States GR - GM 49760/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Methylamines) RN - 0 (Peptide Fragments) RN - 0 (Receptors, Glucocorticoid) RN - FLD0K1SJ1A (trimethyloxamine) SB - IM MH - Circular Dichroism MH - Humans MH - Methylamines/*pharmacology MH - Peptide Fragments/metabolism MH - *Protein Folding MH - Protein Structure, Secondary MH - Receptors, Glucocorticoid/chemistry/*drug effects/metabolism MH - *Transcription, Genetic EDAT- 1999/04/10 MHDA- 1999/04/10 00:01 CRDT- 1999/04/10 00:00 PST - ppublish SO - J Biol Chem. 1999 Apr 16;274(16):10693-6. PMID- 12488014 OWN - NLM STAT- MEDLINE DA - 20021218 DCOM- 20030717 LR - 20071114 IS - 0301-4622 (Print) IS - 0301-4622 (Linking) VI - 101-102 DP - 2002 Dec 10 TI - The dynamic behavior of CheW from Thermotoga maritima in solution, as determined by nuclear magnetic resonance: implications for potential protein-protein interaction sites. PG - 359-73 AB - Measurements of the 15N relaxation parameters have been used to characterize the backbone dynamics of CheW from Thermotoga maritima. The dynamic nature of residues that appeared disordered in our recent solution structure of CheW is confirmed by these dynamics measurements. We have interpreted the data in terms of the Lipari and Szabo 'model-free' approach. The derived order parameter, S(2), the [1H]-(15)N heteronuclear nuclear Overhauser effect (NOE) values, the chemical exchange rate, R(ex), and the internal correlation time, tau(e), show that CheW exhibits considerable motional freedom from the picosecond to millisecond time scales. These regions of the protein cluster within the framework of the three-dimensional structure and may indicate possible binding sites for other protein components of the bacterial chemotaxis receptor-signaling complex. The structure of CheW consists of two five-stranded beta-barrel domains that pack together with an extensive hydrophobic core between the domains. Regions highlighted by dynamics measurements co-localize to specific regions of the three-dimensional structure of CheW previously implicated in the formation of bacterial chemotaxis receptor signaling complex. The motional properties of domain 2 of CheW suggest that this domain may be able to experience structural rearrangements that allow the exposure of a hydrophobic surface area that could be used as a binding surface for the other members of the receptor complex. Residues within domain 2 have been implicated in binding interactions for two chemotaxis proteins, CheA and the receptor. We further propose that domain 1 interacts with other components of the chemotaxis machinery, such as CheZ, or in the formation of clusters of signaling components. CI - Copyright 2002 Elsevier Science B.V. FAU - Griswold, Ian J AU - Griswold IJ AD - Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR, USA. FAU - Dahlquist, Frederick W AU - Dahlquist FW LA - eng GR - GM57766/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - Netherlands TA - Biophys Chem JT - Biophysical chemistry JID - 0403171 RN - 0 (Bacterial Proteins) RN - 107217-07-2 (CheW protein, Bacteria) SB - IM MH - Bacterial Proteins/*chemistry MH - Binding Sites MH - Nuclear Magnetic Resonance, Biomolecular MH - Thermotoga maritima/*chemistry EDAT- 2002/12/19 04:00 MHDA- 2003/07/18 05:00 CRDT- 2002/12/19 04:00 AID - S0301462202001576 [pii] PST - ppublish SO - Biophys Chem. 2002 Dec 10;101-102:359-73. PMID- 23553631 OWN - NLM STAT- MEDLINE DA - 20130527 DCOM- 20130805 LR - 20141116 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 21 DP - 2013 May 24 TI - Molecular bases of multimodal regulation of a fungal transient receptor potential (TRP) channel. PG - 15303-17 LID - 10.1074/jbc.M112.434795 [doi] AB - Multimodal activation by various stimuli is a fundamental characteristic of TRP channels. We identified a fungal TRP channel, TRPGz, exhibiting activation by hyperosmolarity, temperature increase, cytosolic Ca(2+) elevation, membrane potential, and H2O2 application, and thus it is expected to represent a prototypic multimodal TRP channel. TRPGz possesses a cytosolic C-terminal domain (CTD), primarily composed of intrinsically disordered regions with some regulatory modules, a putative coiled-coil region and a basic residue cluster. The CTD oligomerization mediated by the coiled-coil region is required for the hyperosmotic and temperature increase activations but not for the tetrameric channel formation or other activation modalities. In contrast, the basic cluster is responsible for general channel inhibition, by binding to phosphatidylinositol phosphates. The crystal structure of the presumed coiled-coil region revealed a tetrameric assembly in an offset spiral rather than a canonical coiled-coil. This structure underlies the observed moderate oligomerization affinity enabling the dynamic assembly and disassembly of the CTD during channel functions, which are compatible with the multimodal regulation mediated by each functional module. FAU - Ihara, Makoto AU - Ihara M AD - Molecular Signaling Research Team, Structural Physiology Research Group, RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan. FAU - Hamamoto, Shin AU - Hamamoto S FAU - Miyanoiri, Yohei AU - Miyanoiri Y FAU - Takeda, Mitsuhiro AU - Takeda M FAU - Kainosho, Masatsune AU - Kainosho M FAU - Yabe, Isamu AU - Yabe I FAU - Uozumi, Nobuyuki AU - Uozumi N FAU - Yamashita, Atsuko AU - Yamashita A LA - eng SI - PDB/3VVI PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130403 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Fungal Proteins) RN - 0 (TRPC Cation Channels) RN - SY7Q814VUP (Calcium) SB - IM MH - Calcium/chemistry/metabolism MH - Crystallography, X-Ray MH - Fungal Proteins/*chemistry/genetics/metabolism MH - Gibberella/*chemistry/genetics/metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Structure-Activity Relationship MH - TRPC Cation Channels/*chemistry/genetics/metabolism PMC - PMC3663550 OID - NLM: PMC3663550 OTO - NOTNLM OT - Analytical Ultracentrifugation OT - Calcium Intracellular Release OT - Coiled-coil OT - Crystal Structure OT - Ion Channels OT - NMR OT - Phosphatidylinositol Signaling OT - TRP Channel OT - Whole-vacuole Patch Clamp Recording EDAT- 2013/04/05 06:00 MHDA- 2013/08/06 06:00 CRDT- 2013/04/05 06:00 PHST- 2013/04/03 [aheadofprint] AID - M112.434795 [pii] AID - 10.1074/jbc.M112.434795 [doi] PST - ppublish SO - J Biol Chem. 2013 May 24;288(21):15303-17. doi: 10.1074/jbc.M112.434795. Epub 2013 Apr 3. PMID- 19271754 OWN - NLM STAT- MEDLINE DA - 20090608 DCOM- 20090914 LR - 20141120 IS - 1535-3893 (Print) IS - 1535-3893 (Linking) VI - 8 IP - 6 DP - 2009 Jun TI - CLPH, a novel casein kinase 2-phosphorylated disordered protein, is specifically associated with postmeiotic germ cells in rat spermatogenesis. PG - 2953-65 LID - 10.1021/pr900082m [doi] AB - In a recent proteomic study of rat spermatogenesis, we identified CLPH (for Casein-Like PHosphoprotein), a new testis-specific protein expressed exclusively in postmeiotic germ cells. In situ hybridization showed that the CLPH transcript was mainly present in round spermatids, whereas the protein was specifically detected by immunohistochemistry in elongated spermatids and in residual bodies. Electron microscopy showed the protein to be mostly cytoplasmic, but also frequently associated with the mitochondrial inner membrane during the last steps of spermatid differentiation. The Clph gene was found to be present solely in mammalian genomes, in a chromosomal region syntenic to the mammalian cluster of secretory calcium-binding phosphoprotein (SCPP) genes. CLPH has several distinctive properties in common with SCPPs: calcium overlay experiments showed that CLPH was a calcium-binding protein, whereas trypsin digestion assay, circular dichroism and fluorescence experiments demonstrated its intrinsically disordered structure. We also showed that CLPH was phosphorylated in vitro and in vivo by casein kinase 2, an enzyme critical for spermatid elongation. Given the specific and strong production of CLPH during rat spermiogenesis, together with the particular biochemical properties of this protein, we suggest that CLPH is involved in the extremely complex structural rearrangements occurring in haploid germ cells during spermiogenesis. FAU - Calvel, Pierre AU - Calvel P AD - Inserm, U625, Rennes, Universite Rennes I, Campus de Beaulieu, IFR-140, GERHM, Rennes, F-35042, France. FAU - Kervarrec, Christine AU - Kervarrec C FAU - Lavigne, Regis AU - Lavigne R FAU - Vallet-Erdtmann, Virginie AU - Vallet-Erdtmann V FAU - Guerrois, Myriam AU - Guerrois M FAU - Rolland, Antoine D AU - Rolland AD FAU - Chalmel, Frederic AU - Chalmel F FAU - Jegou, Bernard AU - Jegou B FAU - Pineau, Charles AU - Pineau C LA - eng SI - PDB/AAK57455 SI - RefSeq/NP_081907 PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - J Proteome Res JT - Journal of proteome research JID - 101128775 RN - 0 (Cabs1 protein, rat) RN - 0 (Caseins) RN - EC 2.7.11.1 (Casein Kinase II) SB - IM MH - Amino Acid Sequence MH - Animals MH - Casein Kinase II/metabolism MH - Caseins/chemistry/genetics/*metabolism MH - Computer Simulation MH - Electrophoresis, Gel, Two-Dimensional MH - Humans MH - In Situ Hybridization MH - Male MH - Mass Spectrometry MH - Meiosis MH - Molecular Sequence Data MH - Phosphorylation MH - Protein Folding MH - Proteomics MH - Rats MH - Rats, Sprague-Dawley MH - Reverse Transcriptase Polymerase Chain Reaction MH - Spermatids/*metabolism MH - *Spermatogenesis MH - Testis/cytology/metabolism EDAT- 2009/03/11 09:00 MHDA- 2009/09/15 06:00 CRDT- 2009/03/11 09:00 AID - 10.1021/pr900082m [doi] PST - ppublish SO - J Proteome Res. 2009 Jun;8(6):2953-65. doi: 10.1021/pr900082m. PMID- 11005854 OWN - NLM STAT- MEDLINE DA - 20001103 DCOM- 20001103 LR - 20140615 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 97 IP - 20 DP - 2000 Sep 26 TI - Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: structure-based mechanism of conversion. PG - 10723-8 AB - Mammalian xanthine oxidoreductases, which catalyze the last two steps in the formation of urate, are synthesized as the dehydrogenase form xanthine dehydrogenase (XDH) but can be readily converted to the oxidase form xanthine oxidase (XO) by oxidation of sulfhydryl residues or by proteolysis. Here, we present the crystal structure of the dimeric (M(r), 290,000) bovine milk XDH at 2.1-A resolution and XO at 2.5-A resolution and describe the major changes that occur on the proteolytic transformation of XDH to the XO form. Each molecule is composed of an N-terminal 20-kDa domain containing two iron sulfur centers, a central 40-kDa flavin adenine dinucleotide domain, and a C-terminal 85-kDa molybdopterin-binding domain with the four redox centers aligned in an almost linear fashion. Cleavage of surface-exposed loops of XDH causes major structural rearrangement of another loop close to the flavin ring (Gln 423Lys 433). This movement partially blocks access of the NAD substrate to the flavin adenine dinucleotide cofactor and changes the electrostatic environment of the active site, reflecting the switch of substrate specificity observed for the two forms of this enzyme. FAU - Enroth, C AU - Enroth C AD - Ontario Cancer Institute/Princess Margaret Hospital, Division of Molecular and Structural Biology, 610 University Avenue, Toronto, ON, Canada M5G 2M9. FAU - Eger, B T AU - Eger BT FAU - Okamoto, K AU - Okamoto K FAU - Nishino, T AU - Nishino T FAU - Nishino, T AU - Nishino T FAU - Pai, E F AU - Pai EF LA - eng SI - PDB/1FIQ SI - PDB/1FO4 PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - EC 1.17.1.4 (Xanthine Dehydrogenase) RN - EC 1.17.3.2 (Xanthine Oxidase) SB - IM MH - Animals MH - Cattle MH - Dimerization MH - Milk/*chemistry/enzymology MH - Molecular Sequence Data MH - Protein Conformation MH - Static Electricity MH - Xanthine Dehydrogenase/*chemistry MH - Xanthine Oxidase/*chemistry PMC - PMC27090 OID - NLM: PMC27090 EDAT- 2000/09/27 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/09/27 11:00 AID - 97/20/10723 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2000 Sep 26;97(20):10723-8. PMID- 21209058 OWN - NLM STAT- MEDLINE DA - 20110401 DCOM- 20110603 LR - 20131121 IS - 1530-6860 (Electronic) IS - 0892-6638 (Linking) VI - 25 IP - 4 DP - 2011 Apr TI - Folding stability of amyloid-beta 40 monomer is an important determinant of the nucleation kinetics in fibrillization. PG - 1390-401 LID - 10.1096/fj.10-175539 [doi] AB - Amyloid formation is initiated by protein misfolding, followed by self-association to ultimately form amyloid fibrils. The discovery of toxic prefibrillar oligomers in many amyloidosis underscores the importance of understanding the folding mechanism prior to such aggregation. Here, we investigated the folding properties of the natively unfolded amyloid-beta (Abeta) peptide and the familial variants (A21G, E22Q, E22G, E22K, and D23N) in Alzheimer's disease (AD). In combinations of native electrophoresis, analytical ultracentrifugation, fluorescence emission, and far-UV circular dichroism, we showed that all Abeta40 variants are predominantly monomeric with similar residual secondary structures, but distinct hydrophobic-exposed protein surfaces. Guanidine hydrochloride (GdnHCl) denaturation in the absence and presence of trifluoroethanol (TFE) showed that Abeta variants adopt an apparent 2-state equilibrium model with different stabilities, in which wild type is less stable than A21G but more stable than D23N and E22 mutants. By correlating the folding stability with the nucleation phase in fibrillization, we found the more stable the variant, the slower the nucleation, except for D23N. Besides, the unfolding of Abeta conformation leads to reduced formation of mature fibrils, but an increase in nonfibrillar, amorphous type of aggregates. Overall, we demonstrated that folding stability of Abeta is an important determinant of the nucleation kinetics. FAU - Ni, Chun-Lun AU - Ni CL AD - Genomics Research Center, Academia Sinica, Taipei, Taiwan. FAU - Shi, Hoi-Ping AU - Shi HP FAU - Yu, Hui-Ming AU - Yu HM FAU - Chang, Yun-Chorng AU - Chang YC FAU - Chen, Yun-Ru AU - Chen YR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110105 PL - United States TA - FASEB J JT - FASEB journal : official publication of the Federation of American Societies for Experimental Biology JID - 8804484 RN - 0 (APP protein, human) RN - 0 (Amyloid) RN - 0 (Amyloid beta-Peptides) RN - 0 (Amyloid beta-Protein Precursor) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (1-40)) RN - 75-89-8 (Trifluoroethanol) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Amino Acid Sequence MH - Amyloid/chemistry MH - Amyloid beta-Peptides/*chemistry MH - Amyloid beta-Protein Precursor/*chemistry/genetics MH - Guanidine/pharmacology MH - Humans MH - Kinetics MH - Peptide Fragments/*chemistry MH - Protein Denaturation MH - *Protein Folding MH - Protein Stability MH - Protein Structure, Secondary MH - Trifluoroethanol/pharmacology EDAT- 2011/01/07 06:00 MHDA- 2011/06/04 06:00 CRDT- 2011/01/07 06:00 PHST- 2011/01/05 [aheadofprint] AID - fj.10-175539 [pii] AID - 10.1096/fj.10-175539 [doi] PST - ppublish SO - FASEB J. 2011 Apr;25(4):1390-401. doi: 10.1096/fj.10-175539. Epub 2011 Jan 5. PMID- 20620148 OWN - NLM STAT- MEDLINE DA - 20100920 DCOM- 20101007 LR - 20120113 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 402 IP - 2 DP - 2010 Sep 17 TI - Structure and properties of a complex of alpha-synuclein and a single-domain camelid antibody. PG - 326-43 LID - 10.1016/j.jmb.2010.07.001 [doi] AB - The aggregation of the intrinsically disordered protein alpha-synuclein to form fibrillar amyloid structures is intimately associated with a variety of neurological disorders, most notably Parkinson's disease. The molecular mechanism of alpha-synuclein aggregation and toxicity is not yet understood in any detail, not least because of the paucity of structural probes through which to study the behavior of such a disordered system. Here, we describe an investigation involving a single-domain camelid antibody, NbSyn2, selected by phage display techniques to bind to alpha-synuclein, including the exploration of its effects on the in vitro aggregation of the protein under a variety of conditions. We show using isothermal calorimetric methods that NbSyn2 binds specifically to monomeric alpha-synuclein with nanomolar affinity and by means of NMR spectroscopy that it interacts with the four C-terminal residues of the protein. This latter finding is confirmed by the determination of a crystal structure of NbSyn2 bound to a peptide encompassing the nine C-terminal residues of alpha-synuclein. The NbSyn2:alpha-synuclein interaction is mediated mainly by side-chain interactions while water molecules cross-link the main-chain atoms of alpha-synuclein to atoms of NbSyn2, a feature we believe could be important in intrinsically disordered protein interactions more generally. The aggregation behavior of alpha-synuclein at physiological pH, including the morphology of the resulting fibrillar structures, is remarkably unaffected by the presence of NbSyn2 and indeed we show that NbSyn2 binds strongly to the aggregated as well as to the soluble forms of alpha-synuclein. These results give strong support to the conjecture that the C-terminal region of the protein is not directly involved in the mechanism of aggregation and suggest that binding of NbSyn2 could be a useful probe for the identification of alpha-synuclein aggregation in vitro and possibly in vivo. CI - Copyright (c) 2010. Published by Elsevier Ltd. FAU - De Genst, Erwin J AU - De Genst EJ AD - Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. FAU - Guilliams, Tim AU - Guilliams T FAU - Wellens, Joke AU - Wellens J FAU - O'Day, Elizabeth M AU - O'Day EM FAU - Waudby, Christopher A AU - Waudby CA FAU - Meehan, Sarah AU - Meehan S FAU - Dumoulin, Mireille AU - Dumoulin M FAU - Hsu, Shang-Te Danny AU - Hsu ST FAU - Cremades, Nunilo AU - Cremades N FAU - Verschueren, Koen H G AU - Verschueren KH FAU - Pardon, Els AU - Pardon E FAU - Wyns, Lode AU - Wyns L FAU - Steyaert, Jan AU - Steyaert J FAU - Christodoulou, John AU - Christodoulou J FAU - Dobson, Christopher M AU - Dobson CM LA - eng SI - PDB/2X6M GR - H-0903/Parkinson's UK/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100708 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Antibodies) RN - 0 (Peptide Library) RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Antibodies/*chemistry/*metabolism MH - Antibody Affinity MH - Calorimetry MH - Camelids, New World MH - Crystallography, X-Ray MH - Kinetics MH - Microscopy, Electron, Transmission MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Library MH - Protein Binding MH - Protein Denaturation MH - Protein Interaction Mapping MH - Protein Multimerization MH - Protein Structure, Quaternary MH - alpha-Synuclein/*chemistry/*metabolism EDAT- 2010/07/14 06:00 MHDA- 2010/10/12 06:00 CRDT- 2010/07/13 06:00 PHST- 2010/03/01 [received] PHST- 2010/07/01 [revised] PHST- 2010/07/02 [accepted] PHST- 2010/07/08 [aheadofprint] AID - S0022-2836(10)00742-4 [pii] AID - 10.1016/j.jmb.2010.07.001 [doi] PST - ppublish SO - J Mol Biol. 2010 Sep 17;402(2):326-43. doi: 10.1016/j.jmb.2010.07.001. Epub 2010 Jul 8. PMID- 20816072 OWN - NLM STAT- MEDLINE DA - 20100906 DCOM- 20101217 LR - 20140824 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 5 DP - 2010 Sep 8 TI - An unusual hydrophobic core confers extreme flexibility to HEAT repeat proteins. PG - 1596-603 LID - 10.1016/j.bpj.2010.06.032 [doi] AB - Alpha-solenoid proteins are suggested to constitute highly flexible macromolecules, whose structural variability and large surface area is instrumental in many important protein-protein binding processes. By equilibrium and nonequilibrium molecular dynamics simulations, we show that importin-beta, an archetypical alpha-solenoid, displays unprecedentedly large and fully reversible elasticity. Our stretching molecular dynamics simulations reveal full elasticity over up to twofold end-to-end extensions compared to its bound state. Despite the absence of any long-range intramolecular contacts, the protein can return to its equilibrium structure to within 3 A backbone RMSD after the release of mechanical stress. We find that this extreme degree of flexibility is based on an unusually flexible hydrophobic core that differs substantially from that of structurally similar but more rigid globular proteins. In that respect, the core of importin-beta resembles molten globules. The elastic behavior is dominated by nonpolar interactions between HEAT repeats, combined with conformational entropic effects. Our results suggest that alpha-solenoid structures such as importin-beta may bridge the molecular gap between completely structured and intrinsically disordered proteins. CI - Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Kappel, Christian AU - Kappel C AD - Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany. FAU - Zachariae, Ulrich AU - Zachariae U FAU - Dolker, Nicole AU - Dolker N FAU - Grubmuller, Helmut AU - Grubmuller H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Fungal Proteins) RN - 0 (beta Karyopherins) SB - IM MH - Amino Acid Motifs MH - Elasticity MH - Entropy MH - Fungal Proteins/*chemistry/metabolism MH - *Hydrophobic and Hydrophilic Interactions MH - *Molecular Dynamics Simulation MH - Protein Structure, Secondary MH - Saccharomyces cerevisiae MH - beta Karyopherins/*chemistry/metabolism PMC - PMC2931736 OID - NLM: PMC2931736 EDAT- 2010/09/08 06:00 MHDA- 2010/12/18 06:00 CRDT- 2010/09/07 06:00 PHST- 2010/05/10 [received] PHST- 2010/05/10 [revised] PHST- 2010/06/07 [accepted] AID - S0006-3495(10)00775-7 [pii] AID - 10.1016/j.bpj.2010.06.032 [doi] PST - ppublish SO - Biophys J. 2010 Sep 8;99(5):1596-603. doi: 10.1016/j.bpj.2010.06.032. PMID- 7791872 OWN - NLM STAT- MEDLINE DA - 19950726 DCOM- 19950726 LR - 20091119 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 375 IP - 6532 DP - 1995 Jun 15 TI - The 2.2 A crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue. PG - 554-60 AB - The X-ray crystal structure of the complex between the Ras-related protein Rap1A in the GTP-analogue (GppNHp) form and the Ras-binding domain (RBD) of the Ras effector molecule c-Raf1, a Ser/Thr-specific protein kinase, has been solved to a resolution of 2.2 A. It shows that RBD has the ubiquitin superfold and that the structure of Rap1A is very similar to that of Ras. The interaction between the two proteins is mediated by an apparent central antiparallel beta-sheet formed by strands B1-B2 from RBD and strands beta 2-beta 3 from Rap1A. Complex formation is mediated by main-chain and side-chain interactions of the so-called effector residues in the switch I region of Rap1A. FAU - Nassar, N AU - Nassar N AD - Max-Planck-Institut fur molekulare Physiologie, Abteilung Strukturelle Biologie, Dortmund, Germany. FAU - Horn, G AU - Horn G FAU - Herrmann, C AU - Herrmann C FAU - Scherer, A AU - Scherer A FAU - McCormick, F AU - McCormick F FAU - Wittinghofer, A AU - Wittinghofer A LA - eng PT - Journal Article PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Proto-Oncogene Proteins) RN - 0 (Recombinant Proteins) RN - 34273-04-6 (Guanylyl Imidodiphosphate) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - EC 2.7.11.1 (Proto-Oncogene Proteins c-raf) RN - EC 3.6.1.- (GTP Phosphohydrolases) RN - EC 3.6.1.- (GTP-Binding Proteins) RN - EC 3.6.5.2 (rap GTP-Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Computer Graphics MH - Crystallography, X-Ray MH - Escherichia coli MH - GTP Phosphohydrolases/metabolism MH - GTP-Binding Proteins/*chemistry/metabolism MH - Guanylyl Imidodiphosphate/*chemistry/metabolism MH - Humans MH - Molecular Sequence Data MH - Protein Conformation MH - Protein-Serine-Threonine Kinases/*chemistry/metabolism MH - Proto-Oncogene Proteins/*chemistry/metabolism MH - Proto-Oncogene Proteins c-raf MH - Recombinant Proteins/chemistry/metabolism MH - Signal Transduction MH - rap GTP-Binding Proteins EDAT- 1995/06/15 MHDA- 1995/06/15 00:01 CRDT- 1995/06/15 00:00 AID - 10.1038/375554a0 [doi] PST - ppublish SO - Nature. 1995 Jun 15;375(6532):554-60. PMID- 16632472 OWN - NLM STAT- MEDLINE DA - 20060626 DCOM- 20060818 LR - 20090625 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 26 DP - 2006 Jun 30 TI - Structural, biochemical, and dynamic characterizations of the hRPB8 subunit of human RNA polymerases. PG - 18216-26 AB - The RPB8 subunit is present in all three types of eukaryotic RNA polymerases and is highly conserved during evolution. It is an essential subunit required for the transcription of nuclear genes, but the detailed mechanism including its interactions with different subunits and oligonucleotides remains largely unclear. Herein, we report the three-dimensional structure of human RPB8 (hRPB8) at high resolution determined by NMR spectroscopy. The protein fold comprises an eight-stranded beta-barrel, six short helices, and a large unstructured Omega-loop. The overall structure of hRPB8 is similar to that of yRPB8 from Saccharomyces cerevisiae and belongs to the oligonucleotide/oligosaccharide-binding fold. However, several features of the tertiary structures are notably different between the two proteins. In particular, hRPB8 has a more clustered positively charged binding interface with the largest subunit RPB1 of the RNA polymerases. We employed biochemical methods to detect its interactions with different single-stranded DNA sequences. In addition, single-stranded DNA titration experiments were performed to identify the residues involved in nonspecific binding with different DNA sequences. Furthermore, we characterized the millisecond time scale conformational flexibility of hRPB8 upon its binding to single-stranded DNA. The current results demonstrate that hRPB8 interacts with single-stranded DNA nonspecifically and adopts significant conformational changes, and the hRPB8/single-stranded DNA complex is a fast exchanging system. The solution structure in conjunction with the biochemical and dynamic studies reveal new aspects of this subunit in the molecular assembly and the biological function of the human nuclear RNA polymerases. FAU - Kang, Xue AU - Kang X AD - Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China. FAU - Hu, Yunfei AU - Hu Y FAU - Li, You AU - Li Y FAU - Guo, Xianrong AU - Guo X FAU - Jiang, Xiaolu AU - Jiang X FAU - Lai, Luhua AU - Lai L FAU - Xia, Bin AU - Xia B FAU - Jin, Changwen AU - Jin C LA - eng SI - PDB/2F31 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060421 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA, Single-Stranded) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 2.7.7.- (RNA Polymerase II) RN - EC 2.7.7.6 (DNA-Directed RNA Polymerases) RN - EC 2.7.7.6 (Rpb8 protein, S cerevisiae) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - DNA, Single-Stranded/metabolism MH - DNA-Directed RNA Polymerases/chemistry/metabolism MH - Humans MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA Polymerase II/*chemistry/*metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/metabolism EDAT- 2006/04/25 09:00 MHDA- 2006/08/19 09:00 CRDT- 2006/04/25 09:00 PHST- 2006/04/21 [aheadofprint] AID - M513241200 [pii] AID - 10.1074/jbc.M513241200 [doi] PST - ppublish SO - J Biol Chem. 2006 Jun 30;281(26):18216-26. Epub 2006 Apr 21. PMID- 24559171 OWN - NLM STAT- MEDLINE DA - 20140318 DCOM- 20140615 LR - 20150224 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 10 DP - 2014 Mar 18 TI - Cancer/testis antigen PAGE4, a regulator of c-Jun transactivation, is phosphorylated by homeodomain-interacting protein kinase 1, a component of the stress-response pathway. PG - 1670-9 LID - 10.1021/bi500013w [doi] AB - Prostate-associated gene 4 (PAGE4) is a cancer/testis antigen that is typically restricted to the testicular germ cells but is aberrantly expressed in cancer. Furthermore, PAGE4 is developmentally regulated with dynamic expression patterns in the developing prostate and is also a stress-response protein that is upregulated in response to cellular stress. PAGE4 interacts with c-Jun, which is activated by the stress-response kinase JNK1, and plays an important role in the development and pathology of the prostate gland. Here, we have identified homeodomain-interacting protein kinase 1 (HIPK1), also a component of the stress-response pathway, as a kinase that phosphorylates PAGE4 at T51. We show that phosphorylation of PAGE4 is critical for its transcriptional activity since mutating this T residue abolishes its ability to potentiate c-Jun transactivation. In vitro single molecule FRET indicates phosphorylation results in compaction of (still) intrinsically disordered PAGE4. Interestingly, however, while our previous observations indicated that the wild-type nonphosphorylated PAGE4 protein interacted with c-Jun [Rajagopalan , K. et al. ( 2014 ) Biochim, Biophys. Acta 1842 , 154 -163], here we show that phosphorylation of PAGE4 weakens its interaction with c-Jun in vitro. These data suggest that phosphorylation induces conformational changes in natively disordered PAGE4 resulting in its decreased affinity for c-Jun to promote interaction of c-Jun with another, unidentified, partner. Alternatively, phosphorylated PAGE4 may induce transcription of a novel partner, which then potentiates c-Jun transactivation. Regardless, the present results clearly implicate PAGE4 as a component of the stress-response pathway and uncover a novel link between components of this pathway and prostatic development and disease. FAU - Mooney, Steven M AU - Mooney SM AD - The James Buchanan Brady Urological Institute and Department of Urology, double daggerOncology, section signCellular and Molecular Medicine, and parallelDepartment of Biomedical Engineering, Whiting School of Engineering, The Johns Hopkins University School of Medicine , 733 North Broadway, Baltimore, Maryland 21205, United States. FAU - Qiu, Ruoyi AU - Qiu R FAU - Kim, John J AU - Kim JJ FAU - Sacho, Elizabeth J AU - Sacho EJ FAU - Rajagopalan, Krithika AU - Rajagopalan K FAU - Johng, Dorhyun AU - Johng D FAU - Shiraishi, Takumi AU - Shiraishi T FAU - Kulkarni, Prakash AU - Kulkarni P FAU - Weninger, Keith R AU - Weninger KR LA - eng GR - CA181730/CA/NCI NIH HHS/United States GR - R21 CA181730/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140305 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Antigens, Neoplasm) RN - 0 (PAGE4 protein, human) RN - 0 (Proto-Oncogene Proteins c-jun) RN - EC 2.7.11.1 (HIPK1 protein, human) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - Amino Acid Motifs MH - Antigens, Neoplasm/chemistry/genetics/*metabolism MH - Cell Line, Tumor MH - Humans MH - Male MH - Phosphorylation MH - Prostatic Neoplasms/enzymology/genetics/*metabolism/physiopathology MH - Protein Binding MH - Protein-Serine-Threonine Kinases/genetics/*metabolism MH - Proto-Oncogene Proteins c-jun/*genetics/metabolism MH - Signal Transduction MH - Stress, Physiological MH - Testis/metabolism MH - *Transcriptional Activation PMC - PMC4198062 OID - NLM: PMC4198062 EDAT- 2014/02/25 06:00 MHDA- 2014/06/16 06:00 CRDT- 2014/02/25 06:00 PHST- 2014/03/05 [aheadofprint] AID - 10.1021/bi500013w [doi] PST - ppublish SO - Biochemistry. 2014 Mar 18;53(10):1670-9. doi: 10.1021/bi500013w. Epub 2014 Mar 5. PMID- 23648364 OWN - NLM STAT- MEDLINE DA - 20130604 DCOM- 20131216 IS - 1471-499X (Electronic) IS - 1471-4914 (Linking) VI - 19 IP - 6 DP - 2013 Jun TI - The remarkable conformational plasticity of alpha-synuclein: blessing or curse? PG - 368-77 LID - 10.1016/j.molmed.2013.04.002 [doi] LID - S1471-4914(13)00060-9 [pii] AB - The aggregation of the protein alpha-synuclein (alpha-SYN) is believed to be a critical event in Parkinson's disease (PD). alpha-SYN is characterized by a remarkable conformational plasticity, adopting different conformations depending on the environment. In vitro, alpha-SYN lacks a well-defined structure. Therefore, it was classified as an 'intrinsically disordered protein'. A debate has recently begun over how alpha-SYN behaves in the cell: is it an intrinsically disordered protein or a stable tetramer with a low propensity for aggregation? In this review, we discuss the aggregation of alpha-SYN and describe factors that influence this process and their potential relevance in PD pathogenesis. We address the ways in which aggregated alpha-SYN mediates toxicity and might lead to PD, and propose possible therapeutic strategies. CI - Copyright (c) 2013 Elsevier Ltd. All rights reserved. FAU - Deleersnijder, Angelique AU - Deleersnijder A AD - Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences and Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven, Flanders, Belgium. FAU - Gerard, Melanie AU - Gerard M FAU - Debyser, Zeger AU - Debyser Z FAU - Baekelandt, Veerle AU - Baekelandt V LA - eng PT - Journal Article PT - Review DEP - 20130503 PL - England TA - Trends Mol Med JT - Trends in molecular medicine JID - 100966035 RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Humans MH - Parkinson Disease/genetics/*metabolism MH - Protein Conformation MH - alpha-Synuclein/*chemistry/genetics/metabolism/toxicity EDAT- 2013/05/08 06:00 MHDA- 2013/12/18 06:00 CRDT- 2013/05/08 06:00 PHST- 2012/12/22 [received] PHST- 2013/04/03 [revised] PHST- 2013/04/03 [accepted] PHST- 2013/05/03 [aheadofprint] AID - S1471-4914(13)00060-9 [pii] AID - 10.1016/j.molmed.2013.04.002 [doi] PST - ppublish SO - Trends Mol Med. 2013 Jun;19(6):368-77. doi: 10.1016/j.molmed.2013.04.002. Epub 2013 May 3. PMID- 16361249 OWN - NLM STAT- MEDLINE DA - 20060220 DCOM- 20060504 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 8 DP - 2006 Feb 24 TI - Biochemical characterization of the diaphanous autoregulatory interaction in the formin homology protein FHOD1. PG - 5084-93 AB - Diaphanous related formins (DRFs) are cytoskeleton remodeling proteins that mediate specific upstream GTPase signals to regulate cellular processes such as cytokinesis, cell polarity, and organelle motility. Previous work on the Rho-interacting DRF mDia has established that the biological activity of DRFs is regulated by an autoinhibitory interaction of a C-terminal diaphanous autoregulatory domain (DAD) with the DRF N terminus. This autoinhibition is released upon competitive binding of an activated GTPase to the N terminus of the DRF. Analyzing autoregulation of the Rac1-interacting DRF FHOD1, we utilized in vitro binding studies to identify a 60-amino acid DAD at the protein C terminus that recognizes an N-terminal formin homology (FH) 3 domain. Importantly, the FH3 domain of FHOD1 does not overlap with the proposed Rac1-binding domain. The FHOD1 DAD was found to contain one functional hydrophobic autoregulatory motif, while a previously uncharacterized basic cluster that is conserved in all DRF family DADs also contributed to the FH3-DAD interaction. Simultaneous mutation of both motifs efficiently released autoinhibition of FHOD1 in NIH3T3 cells resulting in the formation of actin stress fibers and increased serum response element transcription. A second putative hydrophobic autoregulatory motif N-terminal of the DAD belongs to a unique FHOD subdomain of yet undefined function. NMR structural analysis and size exclusion chromatography experiments revealed that the FHOD1 DAD is intrinsically unstructured with a tendency for a helical conformation in the hydrophobic autoregulation motif. Together, these data suggest that in FHOD1, DAD acts as signal sequence for binding to the well folded and monomeric FH3 domain and imply an activation mechanism that differs from competitive binding of Rac1 and DAD to one interaction site. FAU - Schonichen, Andre AU - Schonichen A AD - Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry, D-44227 Dortmund, Germany. FAU - Alexander, Michael AU - Alexander M FAU - Gasteier, Judith E AU - Gasteier JE FAU - Cuesta, Fanny E AU - Cuesta FE FAU - Fackler, Oliver T AU - Fackler OT FAU - Geyer, Matthias AU - Geyer M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051216 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (FHOD1 protein, human) RN - 0 (Fetal Proteins) RN - 0 (Nuclear Proteins) RN - 9007-49-2 (DNA) RN - EC 2.5.1.18 (Glutathione Transferase) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Blotting, Western MH - Calorimetry MH - Cell Division MH - Chromatography MH - Chromatography, Gel MH - Cloning, Molecular MH - DNA/metabolism MH - Fetal Proteins/chemistry/*physiology MH - *Gene Expression Regulation MH - Glutathione Transferase/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Mice MH - Molecular Sequence Data MH - Mutation MH - NIH 3T3 Cells MH - Nuclear Proteins/chemistry/*physiology MH - Plasmids/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid EDAT- 2005/12/20 09:00 MHDA- 2006/05/05 09:00 CRDT- 2005/12/20 09:00 PHST- 2005/12/16 [aheadofprint] AID - M509226200 [pii] AID - 10.1074/jbc.M509226200 [doi] PST - ppublish SO - J Biol Chem. 2006 Feb 24;281(8):5084-93. Epub 2005 Dec 16. PMID- 22108848 OWN - NLM STAT- MEDLINE DA - 20111202 DCOM- 20120320 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Compaction and binding properties of the intrinsically disordered C-terminal domain of Henipavirus nucleoprotein as unveiled by deletion studies. PG - 392-410 LID - 10.1039/c1mb05401e [doi] AB - Henipaviruses are recently emerged severe human pathogens within the Paramyxoviridae family. Their genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that recruits the polymerase complex via the phosphoprotein (P). We have previously shown that in Henipaviruses the N protein possesses an intrinsically disordered C-terminal domain, N(TAIL), which undergoes alpha-helical induced folding in the presence of the C-terminal domain (P(XD)) of the P protein. Using computational approaches, we previously identified within N(TAIL) four putative molecular recognition elements (MoREs) with different structural propensities, and proposed a structural model for the N(TAIL)-P(XD) complex where the MoRE encompassing residues 473-493 adopt an alpha-helical conformation at the P(XD) surface. In this work, for each N(TAIL) protein, we designed four deletion constructs bearing different combinations of the predicted MoREs. Following purification of the N(TAIL) truncated proteins from the soluble fraction of E. coli, we characterized them in terms of their conformational, spectroscopic and binding properties. These studies provided direct experimental evidence for the structural state of the four predicted MoREs, and showed that two of them have clear alpha-helical propensities, with the one spanning residues 473-493 being strictly required for binding to P(XD). We also showed that Henipavirus N(TAIL) and P(XD) form heterologous complexes, indicating that the P(XD) binding regions are functionally interchangeable between the two viruses. By combining spectroscopic and conformational analyses, we showed that the content in regular secondary structure is not a major determinant of protein compaction. FAU - Blocquel, David AU - Blocquel D AD - CNRS, UMR 6098, 13288, Marseille, France. FAU - Habchi, Johnny AU - Habchi J FAU - Gruet, Antoine AU - Gruet A FAU - Blangy, Stephanie AU - Blangy S FAU - Longhi, Sonia AU - Longhi S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111123 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Nucleoproteins) RN - 0 (Viral Proteins) SB - IM MH - Amino Acid Sequence MH - Calorimetry MH - Chromatography, Gel MH - Circular Dichroism MH - Henipavirus MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Kinetics MH - Light MH - Molecular Sequence Data MH - Nucleoproteins/*chemistry/*metabolism MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Scattering, Radiation MH - *Sequence Deletion MH - Viral Proteins/*chemistry/*metabolism EDAT- 2011/11/24 06:00 MHDA- 2012/03/21 06:00 CRDT- 2011/11/24 06:00 PHST- 2011/11/23 [aheadofprint] PHST- 2011/12/01 [epublish] AID - 10.1039/c1mb05401e [doi] PST - ppublish SO - Mol Biosyst. 2012 Jan;8(1):392-410. doi: 10.1039/c1mb05401e. Epub 2011 Nov 23. PMID- 16698542 OWN - NLM STAT- MEDLINE DA - 20060515 DCOM- 20060706 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 14 IP - 5 DP - 2006 May TI - Turning up the HEAT on translation. PG - 806-7 FAU - Phillips, Simon E V AU - Phillips SE LA - eng PT - Comment PT - News PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Eukaryotic Initiation Factor-4G) SB - IM CON - Structure. 2006 May;14(5):913-23. PMID: 16698552 MH - Eukaryotic Initiation Factor-4G/*chemistry/genetics MH - Humans MH - *Protein Biosynthesis MH - Protein Conformation EDAT- 2006/05/16 09:00 MHDA- 2006/07/11 09:00 CRDT- 2006/05/16 09:00 AID - S0969-2126(06)00183-3 [pii] AID - 10.1016/j.str.2006.05.002 [doi] PST - ppublish SO - Structure. 2006 May;14(5):806-7. PMID- 18511942 OWN - NLM STAT- MEDLINE DA - 20080604 DCOM- 20080708 LR - 20140219 IS - 1545-9985 (Electronic) IS - 1545-9985 (Linking) VI - 15 IP - 6 DP - 2008 Jun TI - EGCG redirects amyloidogenic polypeptides into unstructured, off-pathway oligomers. PG - 558-66 LID - 10.1038/nsmb.1437 [doi] AB - The accumulation of beta-sheet-rich amyloid fibrils or aggregates is a complex, multistep process that is associated with cellular toxicity in a number of human protein misfolding disorders, including Parkinson's and Alzheimer's diseases. It involves the formation of various transient and intransient, on- and off-pathway aggregate species, whose structure, size and cellular toxicity are largely unclear. Here we demonstrate redirection of amyloid fibril formation through the action of a small molecule, resulting in off-pathway, highly stable oligomers. The polyphenol (-)-epigallocatechin gallate efficiently inhibits the fibrillogenesis of both alpha-synuclein and amyloid-beta by directly binding to the natively unfolded polypeptides and preventing their conversion into toxic, on-pathway aggregation intermediates. Instead of beta-sheet-rich amyloid, the formation of unstructured, nontoxic alpha-synuclein and amyloid-beta oligomers of a new type is promoted, suggesting a generic effect on aggregation pathways in neurodegenerative diseases. FAU - Ehrnhoefer, Dagmar E AU - Ehrnhoefer DE AD - Max Delbrueck Center for Molecular Medicine, AG Neuroproteomics, 13092 Berlin, Germany. FAU - Bieschke, Jan AU - Bieschke J FAU - Boeddrich, Annett AU - Boeddrich A FAU - Herbst, Martin AU - Herbst M FAU - Masino, Laura AU - Masino L FAU - Lurz, Rudi AU - Lurz R FAU - Engemann, Sabine AU - Engemann S FAU - Pastore, Annalisa AU - Pastore A FAU - Wanker, Erich E AU - Wanker EE LA - eng GR - MC_U117533887/Medical Research Council/United Kingdom GR - MC_U117584256/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080530 PL - United States TA - Nat Struct Mol Biol JT - Nature structural & molecular biology JID - 101186374 RN - 0 (Amyloid) RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptide Fragments) RN - 0 (alpha-Synuclein) RN - 0 (amyloid beta-protein (1-34)) RN - 8R1V1STN48 (Catechin) RN - BQM438CTEL (epigallocatechin gallate) SB - IM CIN - Nat Struct Mol Biol. 2008 Jun;15(6):537. PMID: 18523460 CIN - Nat Struct Mol Biol. 2008 Jun;15(6):544-6. PMID: 18523464 MH - Amyloid/chemistry/*drug effects MH - Amyloid Neuropathies/drug therapy/*prevention & control MH - Amyloid beta-Peptides/chemistry MH - Catechin/*analogs & derivatives/chemistry/pharmacology MH - Humans MH - Peptide Fragments/chemistry MH - Plaque, Amyloid/chemistry/*drug effects MH - Protein Binding MH - alpha-Synuclein/chemistry EDAT- 2008/05/31 09:00 MHDA- 2008/07/09 09:00 CRDT- 2008/05/31 09:00 PHST- 2007/12/10 [received] PHST- 2008/04/30 [accepted] PHST- 2008/05/30 [aheadofprint] AID - nsmb.1437 [pii] AID - 10.1038/nsmb.1437 [doi] PST - ppublish SO - Nat Struct Mol Biol. 2008 Jun;15(6):558-66. doi: 10.1038/nsmb.1437. Epub 2008 May 30. PMID- 12554650 OWN - NLM STAT- MEDLINE DA - 20030129 DCOM- 20030326 LR - 20140611 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 22 IP - 3 DP - 2003 Feb 3 TI - Structural basis for recruitment of glycogen synthase kinase 3beta to the axin-APC scaffold complex. PG - 494-501 AB - Glycogen synthase kinase 3beta (GSK3beta) is a serine/threonine kinase involved in insulin, growth factor and Wnt signalling. In Wnt signalling, GSK3beta is recruited to a multiprotein complex via interaction with axin, where it hyperphosphorylates beta-catenin, marking it for ubiquitylation and destruction. We have now determined the crystal structure of GSK3beta in complex with a minimal GSK3beta-binding segment of axin, at 2.4 A resolution. The structure confirms the co-localization of the binding sites for axin and FRAT in the C-terminal domain of GSK3beta, but reveals significant differences in the interactions made by axin and FRAT, mediated by conformational plasticity of the 285-299 loop in GSK3beta. Detailed comparison of the axin and FRAT GSK3beta complexes allows the generation of highly specific mutations, which abrogate binding of one or the other. Quantitative analysis suggests that the interaction of GSK3beta with the axin scaffold enhances phosphorylation of beta-catenin by >20 000-fold. FAU - Dajani, Rana AU - Dajani R AD - Section of Structural Biology and Cancer Research UK Centre for Cell and Molecular Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK. FAU - Fraser, Elizabeth AU - Fraser E FAU - Roe, S Mark AU - Roe SM FAU - Yeo, Maggie AU - Yeo M FAU - Good, Valerie M AU - Good VM FAU - Thompson, Vivienne AU - Thompson V FAU - Dale, Trevor C AU - Dale TC FAU - Pearl, Laurence H AU - Pearl LH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Adenomatous Polyposis Coli Protein) RN - 0 (Axin Protein) RN - 0 (CTNNB1 protein, human) RN - 0 (Carrier Proteins) RN - 0 (Cytoskeletal Proteins) RN - 0 (FRAT1 protein, human) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Macromolecular Substances) RN - 0 (Multiprotein Complexes) RN - 0 (Neoplasm Proteins) RN - 0 (Proteins) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Repressor Proteins) RN - 0 (Trans-Activators) RN - 0 (Wnt Proteins) RN - 0 (Zebrafish Proteins) RN - 0 (beta Catenin) RN - 42HK56048U (Tyrosine) RN - EC 2.7.11.1 (glycogen synthase kinase 3 beta) RN - EC 2.7.11.26 (Glycogen Synthase Kinase 3) SB - IM MH - Adenomatous Polyposis Coli Protein/chemistry/*metabolism MH - Axin Protein MH - Binding Sites MH - *Carrier Proteins MH - Cell Line MH - Crystallography, X-Ray MH - Cytoskeletal Proteins/metabolism MH - Glycogen Synthase Kinase 3/*chemistry/genetics/metabolism MH - Humans MH - Intracellular Signaling Peptides and Proteins MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Structure MH - Multiprotein Complexes MH - Mutation MH - *Neoplasm Proteins MH - Phosphorylation MH - *Protein Structure, Tertiary MH - Proteins/*chemistry/metabolism MH - Proto-Oncogene Proteins/metabolism MH - Recombinant Fusion Proteins/metabolism MH - *Repressor Proteins MH - Signal Transduction/*physiology MH - Trans-Activators/metabolism MH - Tyrosine/metabolism MH - Wnt Proteins MH - *Zebrafish Proteins MH - beta Catenin PMC - PMC140752 OID - NLM: PMC140752 EDAT- 2003/01/30 04:00 MHDA- 2003/03/27 05:00 CRDT- 2003/01/30 04:00 AID - 10.1093/emboj/cdg068 [doi] PST - ppublish SO - EMBO J. 2003 Feb 3;22(3):494-501. PMID- 21303909 OWN - NLM STAT- MEDLINE DA - 20110404 DCOM- 20110719 LR - 20140821 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 14 DP - 2011 Apr 8 TI - The intrinsically disordered nuclear localization signal and phosphorylation segments distinguish the membrane affinity of two cytidylyltransferase isoforms. PG - 12349-60 LID - 10.1074/jbc.M110.201715 [doi] AB - Membrane phosphatidylcholine homeostasis is maintained in part by a sensing device in the key regulatory enzyme, CTP:phosphocholine cytidylyltransferase (CCT). CCT responds to decreases in membrane phosphatidylcholine content by reversible membrane binding and activation. Two prominent isoforms, CCTalpha and -beta2, have nearly identical catalytic domains and very similar membrane binding amphipathic helical (M) domains but have divergent and structurally disordered N-terminal (N) and C-terminal phosphorylation (P) regions. We found that the binding affinity of purified CCTbeta2 for anionic membranes was weaker than CCTalpha by more than an order of magnitude. Using chimeric CCTs, insertion/deletion mutants, and truncated CCTs, we show that the stronger affinity of CCTalpha can be attributed in large part to the electrostatic membrane binding function of the polybasic nuclear localization signal (NLS) motif, present in the unstructured N-terminal segment of CCTalpha but lacking in CCTbeta2. The membrane partitioning of CCTbeta2 in cells enriched with the lipid activator, oleic acid, was also weaker than that of CCTalpha and was elevated by incorporation of the NLS motif. Thus, the polybasic NLS can function as a secondary membrane binding motif not only in vitro but in the context of cell membranes. A comparison of phosphorylated, dephosphorylated, and region P-truncated forms showed that the in vitro membrane affinity of CCTbeta2 is more sensitive than CCTalpha to phosphorylation status, which antagonizes membrane binding of both isoforms. These data provide a model wherein the primary membrane binding motif, an amphipathic helical domain, works in collaboration with other intrinsically disordered segments that modulate membrane binding strength. The NLS reinforces, whereas the phosphorylated tail antagonizes the attraction of domain M for anionic membranes. FAU - Dennis, Melissa K AU - Dennis MK AD - Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada. FAU - Taneva, Svetla G AU - Taneva SG FAU - Cornell, Rosemary B AU - Cornell RB LA - eng GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110208 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Nuclear Localization Signals) RN - 0 (Protein Isoforms) RN - EC 2.7.7.15 (Choline-Phosphate Cytidylyltransferase) SB - IM MH - Animals MH - COS Cells MH - Cell Membrane/*metabolism MH - Cercopithecus aethiops MH - Choline-Phosphate Cytidylyltransferase/genetics/*metabolism MH - Immunoblotting MH - Mutagenesis, Site-Directed MH - Nuclear Localization Signals/genetics/*metabolism MH - Phosphorylation MH - Protein Binding MH - Protein Isoforms/genetics/*metabolism PMC - PMC3069438 OID - NLM: PMC3069438 EDAT- 2011/02/10 06:00 MHDA- 2011/07/20 06:00 CRDT- 2011/02/10 06:00 PHST- 2011/02/08 [aheadofprint] AID - M110.201715 [pii] AID - 10.1074/jbc.M110.201715 [doi] PST - ppublish SO - J Biol Chem. 2011 Apr 8;286(14):12349-60. doi: 10.1074/jbc.M110.201715. Epub 2011 Feb 8. PMID- 20831157 OWN - NLM STAT- MEDLINE DA - 20101012 DCOM- 20101103 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 41 DP - 2010 Oct 19 TI - Secondary structure and solvent accessibility of a calmodulin-binding C-terminal segment of membrane-associated myelin basic protein. PG - 8955-66 LID - 10.1021/bi100988p [doi] AB - Myelin basic protein (MBP), specifically the 18.5 kDa isoform, is a peripheral membrane protein and a major component of mammalian central nervous system myelin. It is an intrinsically disordered and multifunctional protein that binds cytoskeletal and other cytosolic proteins to a membrane surface and thereby acquires ordered structure. These associations are modulated by post-translational modifications of MBP, as well as by interactions of MBP with Ca(2+)-calmodulin (CaM). Enzymatic deimination of usually six arginine residues to citrulline results in a decrease in the net positive charge of the protein from 19 to 7) to 12 at high calcium (pCa <5.5) with a Hill coefficient of ~2.15. The similarity of the curves for excess-actin and excess-myosin data confirms their allosteric relationship. The spatially explicit calculations confirmed variable sizes for the cooperative units and clustering of bound myosins at low calcium concentrations. Moreover, inclusion of negative cooperativity between myosin units predicted the observed slowing of myosin binding at excess-myosin concentrations. FAU - Mijailovich, Srboljub M AU - Mijailovich SM AD - Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115, USA. smijailo@gmail.com FAU - Kayser-Herold, Oliver AU - Kayser-Herold O FAU - Li, Xiaochuan AU - Li X FAU - Griffiths, Hugh AU - Griffiths H FAU - Geeves, Michael A AU - Geeves MA LA - eng GR - 085309/Wellcome Trust/United Kingdom GR - 085309/Wellcome Trust/United Kingdom GR - R01 AR048776/AR/NIAMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20121007 PL - Germany TA - Eur Biophys J JT - European biophysics journal : EBJ JID - 8409413 RN - 0 (Tropomyosin) RN - 0 (Troponin) RN - EC 3.6.4.1 (Myosins) RN - SY7Q814VUP (Calcium) SB - IM MH - Actin Cytoskeleton/chemistry/*metabolism MH - Allosteric Regulation MH - Animals MH - Calcium/metabolism MH - Molecular Dynamics Simulation MH - Myosins/chemistry/*metabolism MH - Protein Binding MH - Static Electricity MH - Tropomyosin/chemistry/*metabolism MH - Troponin/chemistry/*metabolism PMC - PMC3509328 OID - NLM: PMC3509328 EDAT- 2012/10/12 06:00 MHDA- 2013/04/30 06:00 CRDT- 2012/10/12 06:00 PHST- 2012/03/04 [received] PHST- 2012/09/06 [accepted] PHST- 2012/08/30 [revised] PHST- 2012/10/07 [aheadofprint] AID - 10.1007/s00249-012-0859-8 [doi] PST - ppublish SO - Eur Biophys J. 2012 Dec;41(12):1015-32. doi: 10.1007/s00249-012-0859-8. Epub 2012 Oct 7. PMID- 23813793 OWN - NLM STAT- MEDLINE DA - 20130930 DCOM- 20140423 LR - 20150325 IS - 1439-7633 (Electronic) IS - 1439-4227 (Linking) VI - 14 IP - 14 DP - 2013 Sep 23 TI - Impact of hydrostatic pressure on an intrinsically disordered protein: a high-pressure NMR study of alpha-synuclein. PG - 1754-61 LID - 10.1002/cbic.201300244 [doi] AB - The impact of pressure on the backbone (15) N, (1) H and (13) C chemical shifts in N-terminally acetylated alpha-synuclein has been evaluated over a pressure range 1-2500 bar. Even while the chemical shifts fall very close to random coil values, as expected for an intrinsically disordered protein, substantial deviations in the pressure dependence of the chemical shifts are seen relative to those in short model peptides. In particular, the nonlinear pressure response of the (1) H(N) chemical shifts, which commonly is associated with the presence of low-lying "excited states", is much larger in alpha-synuclein than in model peptides. The linear pressure response of (1) H(N) chemical shift, commonly linked to H-bond length change, correlates well with those in short model peptides, and is found to be anticorrelated with its temperature dependence. The pressure dependence of (13) C chemical shifts shows remarkably large variations, even when accounting for residue type, and do not point to a clear shift in population between different regions of the Ramachandran map. However, a nearly universal decrease in (3) JHN-Halpha by 0.22 +/- 0.05 Hz suggests a slight increase in population of the polyproline II region at 2500 bar. The first six residues of N-terminally acetylated synuclein show a transient of approximately 15% population of alpha-helix, which slightly diminishes at 2500 bar. The backbone dynamics of the protein is not visibly affected beyond the effect of slight increase in water viscosity at 2500 bar. CI - Copyright (c) 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. FAU - Roche, Julien AU - Roche J AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892 (USA). FAU - Ying, Jinfa AU - Ying J FAU - Maltsev, Alexander S AU - Maltsev AS FAU - Bax, Ad AU - Bax A LA - eng GR - ZIA DK029047-06/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20130628 PL - Germany TA - Chembiochem JT - Chembiochem : a European journal of chemical biology JID - 100937360 RN - 0 (Carbon Isotopes) RN - 0 (Nitrogen Isotopes) RN - 0 (alpha-Synuclein) RN - 7YNJ3PO35Z (Hydrogen) SB - IM MH - Carbon Isotopes/chemistry MH - Hydrogen/chemistry MH - Hydrostatic Pressure MH - Nitrogen Isotopes/chemistry MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Temperature MH - alpha-Synuclein/*chemistry/metabolism PMC - PMC3874805 MID - NIHMS534457 OID - NLM: NIHMS534457 OID - NLM: PMC3874805 OTO - NOTNLM OT - 15N relaxation OT - intrinsically disordered proteins OT - nonuniform sampling OT - random coils OT - triple resonance EDAT- 2013/07/03 06:00 MHDA- 2014/04/24 06:00 CRDT- 2013/07/02 06:00 PHST- 2013/04/20 [received] PHST- 2013/06/28 [aheadofprint] AID - 10.1002/cbic.201300244 [doi] PST - ppublish SO - Chembiochem. 2013 Sep 23;14(14):1754-61. doi: 10.1002/cbic.201300244. Epub 2013 Jun 28. PMID- 22543239 OWN - NLM STAT- MEDLINE DA - 20120618 DCOM- 20120827 LR - 20131121 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 420 IP - 4-5 DP - 2012 Jul 20 TI - Transient structure and SH3 interaction sites in an intrinsically disordered fragment of the hepatitis C virus protein NS5A. PG - 310-23 LID - 10.1016/j.jmb.2012.04.023 [doi] AB - Understanding the molecular mechanisms involved in virus replication and particle assembly is of primary fundamental and biomedical importance. Intrinsic conformational disorder plays a prominent role in viral proteins and their interaction with other viral and host cell proteins via transiently populated structural elements. Here, we report on the results of an investigation of an intrinsically disordered 188-residue fragment of the hepatitis C virus non-structural protein 5A (NS5A), which contains a classical poly-proline Src homology 3 (SH3) binding motif, using sensitivity- and resolution-optimized multidimensional NMR methods, complemented by small-angle X-ray scattering data. Our study provides detailed atomic-resolution information on transient local and long-range structure, as well as fast time scale dynamics in this NS5A fragment. In addition, we could characterize two distinct interaction modes with the SH3 domain of Bin1 (bridging integrator protein 1), a pro-apoptotic tumor suppressor. Despite being largely disordered, the protein contains three regions that transiently adopt alpha-helical structures, partly stabilized by long-range tertiary interactions. Two of these transient alpha-helices form a noncanonical SH3-binding motif, which allows low-affinity SH3 binding. Our results contribute to a better understanding of the role of the NS5A protein during hepatitis C virus infection. The present work also highlights the power of NMR spectroscopy to characterize multiple binding events including short-lived transient interactions between globular and highly disordered proteins. CI - Copyright (c) 2012 Elsevier Ltd. All rights reserved. FAU - Feuerstein, Sophie AU - Feuerstein S AD - Institut de Biologie Structurale, Universite Grenoble 1, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France. FAU - Solyom, Zsofia AU - Solyom Z FAU - Aladag, Amine AU - Aladag A FAU - Favier, Adrien AU - Favier A FAU - Schwarten, Melanie AU - Schwarten M FAU - Hoffmann, Silke AU - Hoffmann S FAU - Willbold, Dieter AU - Willbold D FAU - Brutscher, Bernhard AU - Brutscher B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120426 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (BIN1 protein, human) RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Nuclear Proteins) RN - 0 (Tumor Suppressor Proteins) RN - 0 (Viral Nonstructural Proteins) RN - 9DLQ4CIU6V (Proline) SB - IM MH - Adaptor Proteins, Signal Transducing/*metabolism MH - Binding Sites MH - Electron Spin Resonance Spectroscopy MH - Humans MH - Magnetic Resonance Spectroscopy MH - Nuclear Proteins/*metabolism MH - Proline/*chemistry MH - Protein Binding MH - Protein Structure, Tertiary MH - Scattering, Small Angle MH - Tumor Suppressor Proteins/*metabolism MH - Viral Nonstructural Proteins/*chemistry/genetics/*metabolism MH - X-Rays MH - src Homology Domains EDAT- 2012/05/01 06:00 MHDA- 2012/08/28 06:00 CRDT- 2012/05/01 06:00 PHST- 2012/04/12 [received] PHST- 2012/04/21 [accepted] PHST- 2012/04/26 [aheadofprint] AID - S0022-2836(12)00352-X [pii] AID - 10.1016/j.jmb.2012.04.023 [doi] PST - ppublish SO - J Mol Biol. 2012 Jul 20;420(4-5):310-23. doi: 10.1016/j.jmb.2012.04.023. Epub 2012 Apr 26. PMID- 23199922 OWN - NLM STAT- MEDLINE DA - 20121203 DCOM- 20130520 LR - 20141104 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 103 IP - 9 DP - 2012 Nov 7 TI - The conformational ensembles of alpha-synuclein and tau: combining single-molecule FRET and simulations. PG - 1940-9 LID - 10.1016/j.bpj.2012.09.032 [doi] LID - S0006-3495(12)01073-9 [pii] AB - Intrinsically disordered proteins (IDPs) are increasingly recognized for their important roles in a range of biological contexts, both in normal physiological function and in a variety of devastating human diseases. However, their structural characterization by traditional biophysical methods, for the purposes of understanding their function and dysfunction, has proved challenging. Here, we investigate the model IDPs alpha-Synuclein (alphaS) and tau, that are involved in major neurodegenerative conditions including Parkinson's and Alzheimer's diseases, using excluded volume Monte Carlo simulations constrained by pairwise distance distributions from single-molecule fluorescence measurements. Using this, to our knowledge, novel approach we find that a relatively small number of intermolecular distance constraints are sufficient to accurately determine the dimensions and polymer conformational statistics of alphaS and tau in solution. Moreover, this method can detect local changes in alphaS and tau conformations that correlate with enhanced aggregation. Constrained Monte Carlo simulations produce ensembles that are in excellent agreement both with experimental measurements on alphaS and tau and with all-atom, explicit solvent molecular dynamics simulations of alphaS, with much lower configurational sampling requirements and computational expense. CI - Copyright (c) 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Nath, Abhinav AU - Nath A AD - Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA. abhinav.nath@yale.edu FAU - Sammalkorpi, Maria AU - Sammalkorpi M FAU - DeWitt, David C AU - DeWitt DC FAU - Trexler, Adam J AU - Trexler AJ FAU - Elbaum-Garfinkle, Shana AU - Elbaum-Garfinkle S FAU - O'Hern, Corey S AU - O'Hern CS FAU - Rhoades, Elizabeth AU - Rhoades E LA - eng GR - GM007223/GM/NIGMS NIH HHS/United States GR - T32 GM007223/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Amyloid) RN - 0 (Synucleins) RN - 0 (tau Proteins) SB - IM MH - Amino Acid Sequence MH - Amyloid/*chemistry MH - Fluorescence Resonance Energy Transfer MH - Humans MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Monte Carlo Method MH - Protein Binding MH - Protein Structure, Tertiary MH - Synucleins/*chemistry MH - tau Proteins/*chemistry PMC - PMC3491709 OID - NLM: PMC3491709 EDAT- 2012/12/04 06:00 MHDA- 2013/05/22 06:00 CRDT- 2012/12/04 06:00 PHST- 2012/01/19 [received] PHST- 2012/07/29 [revised] PHST- 2012/09/17 [accepted] AID - S0006-3495(12)01073-9 [pii] AID - 10.1016/j.bpj.2012.09.032 [doi] PST - ppublish SO - Biophys J. 2012 Nov 7;103(9):1940-9. doi: 10.1016/j.bpj.2012.09.032. PMID- 22212475 OWN - NLM STAT- MEDLINE DA - 20120103 DCOM- 20130226 IS - 1365-2443 (Electronic) IS - 1356-9597 (Linking) VI - 17 IP - 1 DP - 2012 Jan TI - Nucleosome surface containing nucleosomal DNA entry/exit site regulates H3-K36me3 via association with RNA polymerase II and Set2. PG - 65-81 LID - 10.1111/j.1365-2443.2011.01573.x [doi] AB - A nucleosome is composed of intrinsically disordered histone tails and a structured nucleosome core surrounded by DNA. A variety of modifiable residues on the intrinsically disordered histone tails have been identified in the last decade. Mapping of the functional residues on the structured nucleosome core surface was recently initiated by global analysis of a comprehensive histone point mutant library (histone-GLibrary). It stands to reason that a functional relationship exists between modifiable residues on the intrinsically disordered histone tails and functional residues on the structured nucleosome core; however, this matter has been poorly explored. During transcription elongation, trimethylation of histone H3 at lysine 36 (H3-K36me3) is mediated by histone methyltransferase Set2, which binds to RNA polymerase II. Here, we used a histone-GLibrary that encompasses the nucleosomal DNA entry/exit site to show that six residues (H2A-G107, H2A-I112, H2A-L117, H3-T45, H3-R49 and H3-R52) form a surface on the structured nucleosome core and regulate H3-K36me3. Trimethylation at H3-K4 introduced by histone methyltransferase Set1 was not affected by the mutation of any of the six residues. Chromatin immunoprecipitation analysis showed that most of these residues are critical for the chromatin association of RNA polymerase II and Set2, suggesting that these components regulate H3-K36me3 through functional interactions with the structured nucleosome core surface. CI - (c) 2011 The Authors. Journal compilation (c) 2011 by the Molecular Biology Society of Japan/Blackwell Publishing Ltd. FAU - Endo, Hirohito AU - Endo H AD - Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan. FAU - Nakabayashi, Yu AU - Nakabayashi Y FAU - Kawashima, Satoshi AU - Kawashima S FAU - Enomoto, Takemi AU - Enomoto T FAU - Seki, Masayuki AU - Seki M FAU - Horikoshi, Masami AU - Horikoshi M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Genes Cells JT - Genes to cells : devoted to molecular & cellular mechanisms JID - 9607379 RN - 0 (Histones) RN - 0 (Nucleosomes) RN - 9007-49-2 (DNA) RN - EC 2.1.1.43 (Histone-Lysine N-Methyltransferase) RN - EC 2.1.1.43 (Set2 protein, human) RN - EC 2.7.7.- (RNA Polymerase II) SB - IM MH - DNA/*metabolism MH - Gene Expression Regulation, Fungal MH - Histone-Lysine N-Methyltransferase/*metabolism MH - Histones/chemistry/genetics/*metabolism MH - Methylation MH - Nucleosomes/*metabolism MH - RNA Polymerase II/*metabolism EDAT- 2012/01/04 06:00 MHDA- 2013/02/27 06:00 CRDT- 2012/01/04 06:00 AID - 10.1111/j.1365-2443.2011.01573.x [doi] PST - ppublish SO - Genes Cells. 2012 Jan;17(1):65-81. doi: 10.1111/j.1365-2443.2011.01573.x. PMID- 23861868 OWN - NLM STAT- MEDLINE DA - 20130717 DCOM- 20140213 LR - 20141113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 7 DP - 2013 TI - The effects of threonine phosphorylation on the stability and dynamics of the central molecular switch region of 18.5-kDa myelin basic protein. PG - e68175 LID - 10.1371/journal.pone.0068175 [doi] AB - The classic isoforms of myelin basic protein (MBP) are essential for the formation and maintenance of myelin in the central nervous system of higher vertebrates. The protein is involved in all facets of the development, compaction, and stabilization of the multilamellar myelin sheath, and also interacts with cytoskeletal and signaling proteins. The predominant 18.5-kDa isoform of MBP is an intrinsically-disordered protein that is a candidate auto-antigen in the human demyelinating disease multiple sclerosis. A highly-conserved central segment within classic MBP consists of a proline-rich region (murine 18.5-kDa sequence -T92-P93-R94-T95-P96-P97-P98-S99-) containing a putative SH3-ligand, adjacent to a region that forms an amphipathic alpha-helix (P82-I90) upon interaction with membranes, or under membrane-mimetic conditions. The T92 and T95 residues within the proline-rich region can be post-translationally modified through phosphorylation by mitogen-activated protein (MAP) kinases. Here, we have investigated the structure of the alpha-helical and proline-rich regions in dilute aqueous buffer, and have evaluated the effects of phosphorylation at T92 and T95 on the stability and dynamics of the alpha-helical region, by utilizing four 36-residue peptides (S72-S107) with differing phosphorylation status. Nuclear magnetic resonance spectroscopy reveals that both the alpha-helical as well as the proline-rich regions are disordered in aqueous buffer, whereas they are both structured in a lipid environment (cf., Ahmed et al., Biochemistry 51, 7475-9487, 2012). Thermodynamic analysis of trifluoroethanol-titration curves monitored by circular dichroism spectroscopy reveals that phosphorylation, especially at residue T92, impedes formation of the amphipathic alpha-helix. This conclusion is supported by molecular dynamics simulations, which further illustrate that phosphorylation reduces the folding reversibility of the alpha-helix upon temperature perturbation and affect the global structure of the peptides through altered electrostatic interactions. The results support the hypothesis that the central conserved segment of MBP constitutes a molecular switch in which the conformation and/or intermolecular interactions are mediated by phosphorylation/dephosphorylation at T92 and T95. FAU - Vassall, Kenrick A AU - Vassall KA AD - Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada. FAU - Bessonov, Kyrylo AU - Bessonov K FAU - De Avila, Miguel AU - De Avila M FAU - Polverini, Eugenia AU - Polverini E FAU - Harauz, George AU - Harauz G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130705 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Myelin Basic Protein) RN - 0 (Peptides) RN - 0 (Recombinant Proteins) RN - 059QF0KO0R (Water) RN - 2ZD004190S (Threonine) SB - IM MH - Amino Acid Sequence MH - Animals MH - Mice MH - Molecular Conformation MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Myelin Basic Protein/*chemistry/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides/chemistry/metabolism MH - Phosphorylation MH - Proline-Rich Protein Domains MH - Protein Stability MH - Recombinant Proteins MH - Sequence Alignment MH - Thermodynamics MH - Threonine/chemistry/*metabolism MH - Water PMC - PMC3702573 OID - NLM: PMC3702573 EDAT- 2013/07/19 06:00 MHDA- 2014/02/14 06:00 CRDT- 2013/07/18 06:00 PHST- 2013 [ppublish] PHST- 2013/03/14 [received] PHST- 2013/05/24 [accepted] PHST- 2013/07/05 [epublish] AID - 10.1371/journal.pone.0068175 [doi] AID - PONE-D-13-11118 [pii] PST - epublish SO - PLoS One. 2013 Jul 5;8(7):e68175. doi: 10.1371/journal.pone.0068175. Print 2013. PMID- 21818348 OWN - NLM STAT- MEDLINE DA - 20110805 DCOM- 20111206 LR - 20141022 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 7 DP - 2011 TI - Conformational plasticity of proNGF. PG - e22615 LID - 10.1371/journal.pone.0022615 [doi] AB - Nerve Growth Factor is an essential protein that supports neuronal survival during development and influences neuronal function throughout adulthood, both in the central and peripheral nervous system. The unprocessed precursor of NGF, proNGF, seems to be endowed with biological functions distinct from those of the mature protein, such as chaperone-like activities and apoptotic and/or neurotrophic properties. We have previously suggested, based on Small Angle X-ray Scattering data, that recombinant murine proNGF has features typical of an intrinsically unfolded protein. Using complementary biophysical techniques, we show here new evidence that clarifies and widens this hypothesis through a detailed comparison of the structural properties of NGF and proNGF. Our data provide direct information about the dynamic properties of the pro-peptide and indicate that proNGF assumes in solution a compact globular conformation. The N-terminal pro-peptide extension influences the chemical environment of the mature protein and protects the protein from proteolytic digestion. Accordingly, we observe that unfolding of proNGF involves a two-steps mechanism. The distinct structural properties of proNGF as compared to NGF agree with and rationalise a different functional role of the precursor. FAU - Paoletti, Francesca AU - Paoletti F AD - European Brain Research Institute, Rome, Italy. FAU - Malerba, Francesca AU - Malerba F FAU - Kelly, Geoff AU - Kelly G FAU - Noinville, Sylvie AU - Noinville S FAU - Lamba, Doriano AU - Lamba D FAU - Cattaneo, Antonino AU - Cattaneo A FAU - Pastore, Annalisa AU - Pastore A LA - eng GR - MC_U117533887/Medical Research Council/United Kingdom GR - MC_U117584256/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110726 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Culture Media) RN - 0 (Peptides) RN - 0 (Protein Precursors) RN - 0 (Solutions) RN - 0 (pro-nerve growth factor, mouse) RN - 9061-61-4 (Nerve Growth Factor) RN - EC 3.4.21.4 (Trypsin) SB - IM MH - Animals MH - Calorimetry, Differential Scanning MH - Circular Dichroism MH - Culture Media MH - Diffusion MH - Magnetic Resonance Spectroscopy MH - Mice MH - Models, Molecular MH - Molecular Weight MH - Nerve Growth Factor/*chemistry/isolation & purification/metabolism MH - Peptides/chemistry MH - Protein Precursors/*chemistry/isolation & purification/metabolism MH - Protein Refolding MH - Protein Stability MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Unfolding MH - Proteolysis MH - Solutions MH - Spectroscopy, Fourier Transform Infrared MH - Trypsin/metabolism PMC - PMC3144226 OID - NLM: PMC3144226 EDAT- 2011/08/06 06:00 MHDA- 2011/12/13 00:00 CRDT- 2011/08/06 06:00 PHST- 2011/05/05 [received] PHST- 2011/06/26 [accepted] PHST- 2011/07/26 [epublish] AID - 10.1371/journal.pone.0022615 [doi] AID - PONE-D-11-07581 [pii] PST - ppublish SO - PLoS One. 2011;6(7):e22615. doi: 10.1371/journal.pone.0022615. Epub 2011 Jul 26. PMID- 22112013 OWN - NLM STAT- MEDLINE DA - 20111220 DCOM- 20120221 LR - 20120308 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 50 IP - 51 DP - 2011 Dec 27 TI - Dimerization-induced folding of MST1 SARAH and the influence of the intrinsically unstructured inhibitory domain: low thermodynamic stability of monomer. PG - 10990-1000 LID - 10.1021/bi201110h [doi] AB - The serine/threonine mammalian sterile 20-like kinase (MST1) is involved in promotion of caspase-dependent and independent apoptosis. Phosphorylation and oligomerization are required for its activation. The oligomerization domain, denoted as SARAH domain, forms an antiparallel coiled coil dimer, and it is important for both MST1 autophosphorylation and interactions with other proteins like the Rassf proteins containing also a SARAH domain. Here we show that the monomeric state of SARAH is thermodynamically unstable and that homodimerization is coupled with folding. Moreover, the influence of the inhibitory domain on SARAH stability and affinity is addressed. By investigating the thermal denaturation using differential scanning calorimetry and circular dichroism, we have found that the SARAH domain dissociates and unfolds cooperatively, without a stable intermediate monomeric state. Combining the data with information from isothermal titration calorimetry, a low thermodynamic stability of the monomeric species is obtained. Thus, it is proposed that the transition from MST1 SARAH homodimer to some specific heterodimer implies a non-native monomer intermediate. The inhibitory domain is found to be highly flexible and intrinsically unfolded, not only in isolation but also in the dimeric state of the inhibitory-SARAH construct. The existence of two caspase recognition motifs within the inhibitory domain suggests that its structural flexibility might be important for activation of MST1 during apoptosis. Moreover, the inhibitory domain increases the thermodynamic stability of the SARAH dimer and the homodimer affinity, while having almost no effect on the SARAH domain in the monomeric state. These results emphasize the importance of flexibility and binding-induced folding for specificity, affinity, and the capacity to switch from one state to another. FAU - Constantinescu Aruxandei, Diana AU - Constantinescu Aruxandei D AD - Department of Physical Chemistry I, Ruhr University Bochum, Universitatsstrasse 150, 44780 Bochum, Germany. FAU - Makbul, Cihan AU - Makbul C FAU - Koturenkiene, Agne AU - Koturenkiene A FAU - Ludemann, Maik-Borris AU - Ludemann MB FAU - Herrmann, Christian AU - Herrmann C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111202 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cross-Linking Reagents) RN - 0 (Peptide Fragments) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Recombinant Proteins) RN - 0 (macrophage stimulating protein) RN - 67256-21-7 (Hepatocyte Growth Factor) RN - EC 3.4.22.- (Caspases) SB - IM MH - Algorithms MH - Calorimetry MH - Calorimetry, Differential Scanning MH - Caspases/metabolism MH - Circular Dichroism MH - Cross-Linking Reagents/chemistry MH - *Dimerization MH - Enzyme Stability MH - Hepatocyte Growth Factor/*chemistry/genetics/metabolism MH - Humans MH - Models, Molecular MH - Nephelometry and Turbidimetry MH - Osmolar Concentration MH - Peptide Fragments/chemistry/genetics/metabolism MH - Protein Denaturation MH - *Protein Folding MH - Protein Interaction Domains and Motifs MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins/*chemistry/genetics/metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Thermodynamics EDAT- 2011/11/25 06:00 MHDA- 2012/02/22 06:00 CRDT- 2011/11/25 06:00 PHST- 2011/12/02 [aheadofprint] AID - 10.1021/bi201110h [doi] PST - ppublish SO - Biochemistry. 2011 Dec 27;50(51):10990-1000. doi: 10.1021/bi201110h. Epub 2011 Dec 2. PMID- 12110597 OWN - NLM STAT- MEDLINE DA - 20020711 DCOM- 20020905 LR - 20140612 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 21 IP - 14 DP - 2002 Jul 15 TI - Crystal structure of human 53BP1 BRCT domains bound to p53 tumour suppressor. PG - 3863-72 AB - The BRCT (BRCA1 C-terminus) is an evolutionary conserved protein-protein interacting module found as single, tandem or multiple repeats in a diverse range of proteins known to play roles in the DNA-damage response. The BRCT domains of 53BP1 bind to the tumour suppressor p53. To investigate the nature of this interaction, we have determined the crystal structure of the 53BP1 BRCT tandem repeat in complex with the DNA-binding domain of p53. The structure of the 53BP1-p53 complex shows that the BRCT tandem repeats pack together through a conserved interface that also involves the inter-domain linker. A comparison of the structure of the BRCT region of 53BP1 with the BRCA1 BRCT tandem repeat reveals that the interdomain interface and linker regions are remarkably well conserved. 53BP1 binds to p53 through contacts with the N-terminal BRCT repeat and the inter-BRCT linker. The p53 residues involved in this binding are mutated in cancer and are also important for DNA binding. We propose that BRCT domains bind to cellular target proteins through a conserved structural element termed the 'BRCT recognition motif'. FAU - Derbyshire, Dean J AU - Derbyshire DJ AD - Structural Medicine Unit, Cambridge Institute for Medical Research and Department of Haematology, University of Cambridge, Hills Road, Cambridge CB2 2XY, UK. FAU - Basu, Balaku P AU - Basu BP FAU - Serpell, Louise C AU - Serpell LC FAU - Joo, Woo S AU - Joo WS FAU - Date, Takayasu AU - Date T FAU - Iwabuchi, Kuniyoshi AU - Iwabuchi K FAU - Doherty, Aidan J AU - Doherty AJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Carrier Proteins) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Phosphoproteins) RN - 0 (TP53BP1 protein, human) RN - 0 (Tumor Suppressor Protein p53) SB - IM EIN - EMBO J 2002 Nov 1;21(21):5953 MH - Amino Acid Sequence MH - Carrier Proteins/chemistry/*metabolism MH - Humans MH - *Intracellular Signaling Peptides and Proteins MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - *Phosphoproteins MH - Protein Conformation MH - Tumor Suppressor Protein p53/genetics/*metabolism PMC - PMC126127 OID - NLM: PMC126127 EDAT- 2002/07/12 10:00 MHDA- 2002/09/06 10:01 CRDT- 2002/07/12 10:00 AID - 10.1093/emboj/cdf383 [doi] PST - ppublish SO - EMBO J. 2002 Jul 15;21(14):3863-72. PMID- 24688736 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20140401 DCOM- 20140401 LR - 20140404 IS - 2001-0370 (Electronic) IS - 2001-0370 (Linking) VI - 7 DP - 2013 TI - Biochemical and biophysical characterization of recombinant yeast proteasome maturation factor ump1. PG - e201304006 LID - 10.5936/csbj.201304006 [doi] AB - Protein degradation is essential for maintaining cellular homeostasis. The proteasome is the central enzyme responsible for non-lysosomal protein degradation in eukaryotic cells. Although proteasome assembly is not yet completely understood, a number of cofactors required for proper assembly and maturation have been identified. Ump is a short-lived maturation factor required for the efficient biogenesis of the 20S proteasome. Upon the association of the two precursor complexes, Ump is encased and is rapidly degraded after the proteolytic sites in the interior of the nascent proteasome are activated. In order to further understand the mechanisms behind proteasomal maturation, we expressed and purified yeast Ump in E. coli for biophysical and structural analysis. We show that recombinant Ump is purified as a mixture of different oligomeric species and that oligomerization is mediated by intermolecular disulfide bond formation involving the only cysteine residue present in the protein. Furthermore, a combination of bioinformatic, biochemical and structural analysis revealed that Ump shows characteristics of an intrinsically disordered protein, which might become structured only upon interaction with the proteasome subunits. FAU - Sa-Moura, Bebiana AU - Sa-Moura B AD - IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal. FAU - Simoes, Ana Marisa AU - Simoes AM AD - IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal. FAU - Fraga, Joana AU - Fraga J AD - IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal. FAU - Fernandes, Humberto AU - Fernandes H AD - Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, Portugal ; Current address: Biophysics Section, Department of Life Sciences, Imperial College, London, UK. FAU - Abreu, Isabel A AU - Abreu IA AD - IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal ; Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Portugal. FAU - Botelho, Hugo M AU - Botelho HM AD - Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Portugal ; Current address: BioFIG - Centre for Biodiversity, Functional and Integrative Genomics, Faculty of Sciences, University of Lisboa, Campo Grande 1749-016 Lisboa, Portugal. FAU - Gomes, Claudio M AU - Gomes CM AD - Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Portugal. FAU - Marques, Antonio J AU - Marques AJ AD - Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, Portugal ; Current address: Immunodiagnostic Systems, Core Technology, 10 Didcot Way, Boldon, NE35 9PD, UK. FAU - Dohmen, R Jurgen AU - Dohmen RJ AD - Institute for Genetics, University of Cologne, Zulpicher Str. 47, D-50674 Cologne, Germany. FAU - Ramos, Paula C AU - Ramos PC AD - Centre for Molecular and Structural Biomedicine, CBME/IBB, LA, Portugal ; Institute for Genetics, University of Cologne, Zulpicher Str. 47, D-50674 Cologne, Germany. FAU - Macedo-Ribeiro, Sandra AU - Macedo-Ribeiro S AD - IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal. LA - eng PT - Journal Article DEP - 20130910 PL - Sweden TA - Comput Struct Biotechnol J JT - Computational and structural biotechnology journal JID - 101585369 PMC - PMC3962104 OID - NLM: PMC3962104 OTO - NOTNLM OT - Circular dichroism OT - dynamic light scattering OT - intrinsically disordered OT - protein structure EDAT- 2013/01/01 00:00 MHDA- 2013/01/01 00:01 CRDT- 2014/04/02 06:00 PHST- 2013 [ecollection] PHST- 2013/04/27 [received] PHST- 2013/08/16 [revised] PHST- 2013/08/19 [accepted] PHST- 2013/09/10 [epublish] AID - 10.5936/csbj.201304006 [doi] AID - CSBJ-7-e201304006 [pii] PST - epublish SO - Comput Struct Biotechnol J. 2013 Sep 10;7:e201304006. doi: 10.5936/csbj.201304006. eCollection 2013. PMID- 14749181 OWN - NLM STAT- MEDLINE DA - 20040129 DCOM- 20040406 LR - 20061115 IS - 0168-1702 (Print) IS - 0168-1702 (Linking) VI - 99 IP - 2 DP - 2004 Feb TI - The C-terminal domain of measles virus nucleoprotein belongs to the class of intrinsically disordered proteins that fold upon binding to their physiological partner. PG - 157-67 AB - The nucleoprotein of measles virus consists of an N-terminal domain, N(CORE) (aa 1-400), resistant to proteolysis, and a C-terminal domain, N(TAIL) (aa 401-525), hypersensitive to proteolysis and not visible by electron microscopy. Using two complementary computational approaches, we predict that N(TAIL) belongs to the class of natively unfolded proteins. Using different biochemical and biophysical approaches, we show that N(TAIL) is indeed unstructured in solution. In particular, the spectroscopic and hydrodynamic properties of N(TAIL) indicate that this protein domain belongs to the premolten globule subfamily within the class of intrinsically disordered proteins. The isolated N(TAIL) domain was shown to be able to bind to its physiological partner, the phosphoprotein (P), and to undergo an induced folding upon binding to the C-terminal moiety of P [J. Biol. Chem. 278 (2003) 18638]. Using a computational analysis, we have identified within N(TAIL) a putative alpha-helical molecular recognition element (alpha-MoRE, aa 488-499), which could be involved in binding to P via induced folding. We report the bacterial expression and purification of a truncated form of N(TAIL) (N(TAIL2), aa 401-488) devoid of the alpha-MoRE. We show that N(TAIL2) has lost the ability to bind to P, thus supporting the hypothesis that the alpha-MoRE may play a role in binding to P. We have further analyzed the alpha-helical propensities of N(TAIL2) and N(TAIL) using circular dichroism in the presence of 2,2,2-trifluoroethanol. We show that N(TAIL2) has a lower alpha-helical potential compared to N(TAIL), thus suggesting that the alpha-MoRE may be indeed involved in the induced folding of N(TAIL). FAU - Bourhis, Jean-Marie AU - Bourhis JM AD - Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS et Universite Aix-Marseille I et II, ESIL, Campus de Luminy, Cedex 09 13288, Marseille, France. FAU - Johansson, Kenth AU - Johansson K FAU - Receveur-Brechot, Veronique AU - Receveur-Brechot V FAU - Oldfield, Christopher J AU - Oldfield CJ FAU - Dunker, Keith A AU - Dunker KA FAU - Canard, Bruno AU - Canard B FAU - Longhi, Sonia AU - Longhi S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - Virus Res JT - Virus research JID - 8410979 RN - 0 (Nucleoproteins) RN - 0 (P protein, Sendai virus) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Proteins) RN - 0 (Viral Proteins) RN - 0 (nucleoprotein, Measles virus) SB - IM MH - Circular Dichroism MH - Computational Biology MH - Measles virus/*chemistry MH - Nucleoproteins/*chemistry/genetics/isolation & purification/*metabolism MH - Phosphoproteins/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Recombinant Proteins/biosynthesis/chemistry/isolation & purification/metabolism MH - Sequence Deletion MH - Viral Proteins/*chemistry/genetics/isolation & purification/*metabolism EDAT- 2004/01/30 05:00 MHDA- 2004/04/07 05:00 CRDT- 2004/01/30 05:00 AID - S0168170203003411 [pii] PST - ppublish SO - Virus Res. 2004 Feb;99(2):157-67. PMID- 22194938 OWN - NLM STAT- MEDLINE DA - 20111223 DCOM- 20120827 LR - 20141019 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 12 DP - 2011 TI - NMR studies of the C-terminus of alpha4 reveal possible mechanism of its interaction with MID1 and protein phosphatase 2A. PG - e28877 LID - 10.1371/journal.pone.0028877 [doi] AB - Alpha4 is a regulatory subunit of the protein phosphatase family of enzymes and plays an essential role in regulating the catalytic subunit of PP2A (PP2Ac) within the rapamycin-sensitive signaling pathway. Alpha4 also interacts with MID1, a microtubule-associated ubiquitin E3 ligase that appears to regulate the function of PP2A. The C-terminal region of alpha4 plays a key role in the binding interaction of PP2Ac and MID1. Here we report on the solution structure of a 45-amino acid region derived from the C-terminus of alpha4 (alpha45) that binds tightly to MID1. In aqueous solution, alpha45 has properties of an intrinsically unstructured peptide although chemical shift index and dihedral angle estimation based on chemical shifts of backbone atoms indicate the presence of a transient alpha-helix. Alpha45 adopts a helix-turn-helix HEAT-like structure in 1% SDS micelles, which may mimic a negatively charged surface for which alpha45 could bind. Alpha45 binds tightly to the Bbox1 domain of MID1 in aqueous solution and adopts a structure consistent with the helix-turn-helix structure observed in 1% SDS. The structure of alpha45 reveals two distinct surfaces, one that can interact with a negatively charged surface, which is present on PP2A, and one that interacts with the Bbox1 domain of MID1. FAU - Du, Haijuan AU - Du H AD - Department of Chemistry, George Washington University, Washington, DC, United States of America. FAU - Massiah, Michael A AU - Massiah MA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20111214 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (IGBP1 protein, human) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Micelles) RN - 0 (Microtubule Proteins) RN - 0 (Solutions) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - EC 3.1.3.16 (Protein Phosphatase 2) SB - IM MH - Amino Acid Sequence MH - Humans MH - Intracellular Signaling Peptides and Proteins/*chemistry/*metabolism MH - *Magnetic Resonance Spectroscopy MH - Micelles MH - Microtubule Proteins/chemistry/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding/drug effects MH - Protein Phosphatase 2/*metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sodium Dodecyl Sulfate/pharmacology MH - Solutions MH - Static Electricity PMC - PMC3237570 OID - NLM: PMC3237570 EDAT- 2011/12/24 06:00 MHDA- 2012/08/28 06:00 CRDT- 2011/12/24 06:00 PHST- 2011/08/16 [received] PHST- 2011/11/16 [accepted] PHST- 2011/12/14 [epublish] AID - 10.1371/journal.pone.0028877 [doi] AID - PONE-D-11-16065 [pii] PST - ppublish SO - PLoS One. 2011;6(12):e28877. doi: 10.1371/journal.pone.0028877. Epub 2011 Dec 14. PMID- 23722902 OWN - NLM STAT- MEDLINE DA - 20130718 DCOM- 20131001 LR - 20150209 IS - 1558-8238 (Electronic) IS - 0021-9738 (Linking) VI - 123 IP - 7 DP - 2013 Jul TI - An androgen receptor N-terminal domain antagonist for treating prostate cancer. PG - 2948-60 LID - 10.1172/JCI66398 [doi] LID - 66398 [pii] AB - Hormone therapies for advanced prostate cancer target the androgen receptor (AR) ligand-binding domain (LBD), but these ultimately fail and the disease progresses to lethal castration-resistant prostate cancer (CRPC). The mechanisms that drive CRPC are incompletely understood, but may involve constitutively active AR splice variants that lack the LBD. The AR N-terminal domain (NTD) is essential for AR activity, but targeting this domain with small-molecule inhibitors is complicated by its intrinsic disorder. Here we investigated EPI-001, a small-molecule antagonist of AR NTD that inhibits protein-protein interactions necessary for AR transcriptional activity. We found that EPI analogs covalently bound the NTD to block transcriptional activity of AR and its splice variants and reduced the growth of CRPC xenografts. These findings suggest that the development of small-molecule inhibitors that bind covalently to intrinsically disordered proteins is a promising strategy for development of specific and effective anticancer agents. FAU - Myung, Jae-Kyung AU - Myung JK AD - Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada. FAU - Banuelos, Carmen A AU - Banuelos CA FAU - Fernandez, Javier Garcia AU - Fernandez JG FAU - Mawji, Nasrin R AU - Mawji NR FAU - Wang, Jun AU - Wang J FAU - Tien, Amy H AU - Tien AH FAU - Yang, Yu Chi AU - Yang YC FAU - Tavakoli, Iran AU - Tavakoli I FAU - Haile, Simon AU - Haile S FAU - Watt, Kate AU - Watt K FAU - McEwan, Iain J AU - McEwan IJ FAU - Plymate, Stephen AU - Plymate S FAU - Andersen, Raymond J AU - Andersen RJ FAU - Sadar, Marianne D AU - Sadar MD LA - eng GR - 2 P50 CA 097186-06/CA/NCI NIH HHS/United States GR - 2R01 CA105304/CA/NCI NIH HHS/United States GR - MOP79308/Canadian Institutes of Health Research/Canada GR - P01 CA85859/CA/NCI NIH HHS/United States GR - P50 CA097186/CA/NCI NIH HHS/United States GR - PPP90150/Canadian Institutes of Health Research/Canada GR - R01 CA105304/CA/NCI NIH HHS/United States GR - S10-10/Prostate Cancer UK/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130603 PL - United States TA - J Clin Invest JT - The Journal of clinical investigation JID - 7802877 RN - 0 (Androgen Receptor Antagonists) RN - 0 (Antineoplastic Agents, Hormonal) RN - 0 (Benzhydryl Compounds) RN - 0 (Chlorohydrins) RN - 0 (EPI 001) RN - 0 (Receptors, Androgen) RN - EC 1.13.12.- (Luciferases) SB - AIM SB - IM MH - Androgen Receptor Antagonists/chemistry/*pharmacology MH - Animals MH - Antineoplastic Agents, Hormonal/chemistry/*pharmacology MH - Benzhydryl Compounds/chemistry/*pharmacology MH - COS Cells MH - Cell Proliferation/drug effects MH - Cercopithecus aethiops MH - Chlorohydrins/chemistry/*pharmacology MH - Click Chemistry MH - Gene Expression MH - Gene Expression Regulation, Neoplastic/drug effects MH - Genes, Reporter MH - Humans MH - Luciferases/biosynthesis/genetics MH - Male MH - Mice MH - Mice, Inbred NOD MH - Mice, SCID MH - Orchiectomy MH - Prostatic Neoplasms/*drug therapy/metabolism/pathology MH - Protein Binding MH - Protein Structure, Tertiary MH - Receptors, Androgen/chemistry/genetics/*metabolism MH - Stereoisomerism MH - Transcriptional Activation/drug effects MH - Tumor Burden/drug effects MH - Xenograft Model Antitumor Assays PMC - PMC3696543 OID - NLM: PMC3696543 EDAT- 2013/06/01 06:00 MHDA- 2013/10/18 06:00 CRDT- 2013/06/01 06:00 PHST- 2012/08/17 [received] PHST- 2013/03/28 [accepted] PHST- 2013/06/03 [aheadofprint] PHST- 2013/06/03 [epublish] AID - 66398 [pii] AID - 10.1172/JCI66398 [doi] PST - ppublish SO - J Clin Invest. 2013 Jul;123(7):2948-60. doi: 10.1172/JCI66398. Epub 2013 Jun 3. PMID- 208844 OWN - NLM STAT- MEDLINE DA - 19780929 DCOM- 19780929 LR - 20071115 IS - 0014-2956 (Print) IS - 0014-2956 (Linking) VI - 87 IP - 2 DP - 1978 Jun 15 TI - The regulation of glycogen metabolism. Purification and characterisation of protein phosphatase inhibitor-1 from rabbit skeletal muscle. PG - 341-51 AB - Inhibitor-1 is a protein which inhibits phosphorylase phosphatase only when it has been phosphorylated by cyclic-AMP-dependent protein kinase [Huang, F. L. and Glinsmann, W. H. (1976) Eur. J. Biochem. 70, 419--426]. Inhibitor-1 was purified by a heat treatment at 90 degrees C, precipitation with ammonium sulphate, chromatography on DEAE-cellulose, gel filtration on Sephadex G-100, and finally rechromatography of the phosphorylated protein on DEAE-cellulose, The protein was purified 4000-fold and 1.5 mg per 1000 g muscle was obtained in seven days corresponding to an overall yield of 15-20%. The purified protein was in a state approaching homogeneity as judged by the criteria of polyacrylamide-gel electrophoresis and ultracentrifugal analysis. The concentration of inhibitor-1 in vivo was calculated to be 1.5 micron, which is at least as high as the concentration of phosphorylase phosphatase. The amino acid composition of inhibitor-1 showed several unusual features. Glutamic acid and proline accounted for nearly one third of the residues, tyrosine, tryptophan and cysteine were absent, and the content of aromatic amino acids was very low. The molecular weight measured by sedimentation equilibrium centrifugation was 19200 and by amino acid analysis was 20800. These values were lower than the mol. wt 26000 determined empirically by gel electrophoresis in the presence of sodium dodecyl sulphate, and much lower than the apparent molecular weight of 60000 estimated by gel filtration on Sephadex G-100. The gel filtration behaviour, stability to heating at 100 degrees C and amino acid composition suggest that inhibitor-1 may possess little ordered structure. The phosphorylated from of inhibitor-1 contained close to one molecule of covalently bound phosphate per mole of protein, which is consistent with the previous finding of a unique decapeptide sequence at the site of phosphorylation, Ile-Arg-Arg-Arg-Arg-Pro-Thr(P)-Pro-Ala-Thr- [Cohen, P., Rylatt, D. B. and Nimmo, G. A. (1977) FEBS Lett. 76, 182-186].the phosphorylated form of inhibitor-1 inhibited phosphorylase phosphatase activity (0.02U) by 50% at a concentration of only 7.0 nM in the standard assay, but the phosphorylated decapeptide was 1000-2000 times less effective as an inhibitor. FAU - Nimmo, G A AU - Nimmo GA FAU - Cohen, P AU - Cohen P LA - eng PT - Journal Article PL - GERMANY, WEST TA - Eur J Biochem JT - European journal of biochemistry / FEBS JID - 0107600 RN - 0 (Amino Acids) RN - 0 (Muscle Proteins) RN - EC 3.1.3.- (Phosphoric Monoester Hydrolases) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - EC 3.1.3.17 (Phosphorylase Phosphatase) SB - IM MH - Amino Acids/analysis MH - Animals MH - Kinetics MH - Molecular Weight MH - Muscle Proteins/isolation & purification/*physiology MH - Muscles/*enzymology MH - Phosphoprotein Phosphatases/antagonists & inhibitors MH - Phosphoric Monoester Hydrolases/*antagonists & inhibitors MH - Phosphorylase Phosphatase/*antagonists & inhibitors MH - Rabbits EDAT- 1978/06/15 MHDA- 1978/06/15 00:01 CRDT- 1978/06/15 00:00 PST - ppublish SO - Eur J Biochem. 1978 Jun 15;87(2):341-51. PMID- 22683353 OWN - NLM STAT- MEDLINE DA - 20120820 DCOM- 20130116 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 422 IP - 3 DP - 2012 Sep 21 TI - Evolution of linear motifs within the papillomavirus E7 oncoprotein. PG - 336-46 LID - 10.1016/j.jmb.2012.05.036 [doi] AB - Many protein functions can be traced to linear sequence motifs of less than five residues, which are often found within intrinsically disordered domains. In spite of their prevalence, their role in protein evolution is only beginning to be understood. The study of papillomaviruses has provided many insights on the evolution of protein structure and function. We have chosen the papillomavirus E7 oncoprotein as a model system for the evolution of functional linear motifs. The multiple functions of E7 proteins from paradigmatic papillomavirus types can be explained to a large extent in terms of five linear motifs within the intrinsically disordered N-terminal domain and two linear motifs within the globular homodimeric C-terminal domain. We examined the motif inventory of E7 proteins from over 200 known papillomavirus types and found that the motifs reported for paradigmatic papillomavirus types are absent from many uncharacterized E7 proteins. Several motif pairs occur more often than expected, suggesting that linear motifs may evolve and function in a cooperative manner. The E7 linear motifs have appeared or disappeared multiple times during papillomavirus evolution, confirming the evolutionary plasticity of short functional sequences. Four of the motifs appeared several times during papillomavirus evolution, providing direct evidence for convergent evolution. Interestingly, the evolution pattern of a motif is independent of its location in a globular or disordered domain. The correlation between the presence of some motifs and virus host specificity and tissue tropism suggests that linear motifs play a role in the adaptive evolution of papillomaviruses. CI - Copyright (c) 2012 Elsevier Ltd. All rights reserved. FAU - Chemes, Lucia B AU - Chemes LB AD - Protein Structure-Function and Engineering Laboratory, Fundacion Instituto Leloir and IIBBA-CONICET, Patricias Argentinas 435 (1405), Buenos Aires, Argentina. FAU - Glavina, Juliana AU - Glavina J FAU - Faivovich, Julian AU - Faivovich J FAU - de Prat-Gay, Gonzalo AU - de Prat-Gay G FAU - Sanchez, Ignacio E AU - Sanchez IE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120606 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Papillomavirus E7 Proteins) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Evolution, Molecular MH - Molecular Sequence Data MH - Papillomaviridae/*genetics/metabolism MH - Papillomavirus E7 Proteins/*chemistry/*genetics/metabolism MH - Protein Structure, Tertiary MH - Sequence Alignment EDAT- 2012/06/12 06:00 MHDA- 2013/01/17 06:00 CRDT- 2012/06/12 06:00 PHST- 2012/03/09 [received] PHST- 2012/05/07 [revised] PHST- 2012/05/30 [accepted] PHST- 2012/06/06 [aheadofprint] AID - S0022-2836(12)00434-2 [pii] AID - 10.1016/j.jmb.2012.05.036 [doi] PST - ppublish SO - J Mol Biol. 2012 Sep 21;422(3):336-46. doi: 10.1016/j.jmb.2012.05.036. Epub 2012 Jun 6. PMID- 7569978 OWN - NLM STAT- MEDLINE DA - 19951113 DCOM- 19951113 LR - 20131121 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 270 IP - 5234 DP - 1995 Oct 13 TI - Titins: giant proteins in charge of muscle ultrastructure and elasticity. PG - 293-6 AB - In addition to thick and thin filaments, vertebrate striated muscle contains a third filament system formed by the giant protein titin. Single titin molecules extend from Z discs to M lines and are longer than 1 micrometer. The titin filament contributes to muscle assembly and resting tension, but more details are not known because of the large size of the protein. The complete complementary DNA sequence of human cardiac titin was determined. The 82-kilobase complementary DNA predicts a 3-megadalton protein composed of 244 copies of immunoglobulin and fibronectin type III (FN3) domains. The architecture of sequences in the A band region of titin suggests why thick filament structure is conserved among vertebrates. In the I band region, comparison of titin sequences from muscles of different passive tension identifies two elements that correlate with tissue stiffness. This suggests that titin may act as two springs in series. The differential expression of the springs provides a molecular explanation for the diversity of sarcomere length and resting tension in vertebrate striated muscles. FAU - Labeit, S AU - Labeit S AD - European Molecular Biology Laboratory, Heidelberg, Germany. FAU - Kolmerer, B AU - Kolmerer B LA - eng SI - GENBANK/X90568 SI - GENBANK/X90569 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Connectin) RN - 0 (DNA, Complementary) RN - 0 (Fibronectins) RN - 0 (Immunoglobulins) RN - 0 (Muscle Proteins) RN - 0 (TTN protein, human) RN - EC 2.7.- (Protein Kinases) SB - IM CIN - Science. 1995 Oct 13;270(5234):236. PMID: 7569971 MH - Actin Cytoskeleton/chemistry/*ultrastructure MH - Amino Acid Sequence MH - Animals MH - Connectin MH - DNA, Complementary MH - Elasticity MH - Fibronectins/chemistry MH - Humans MH - Immunoglobulins/chemistry MH - Molecular Sequence Data MH - Muscle Contraction MH - Muscle Proteins/*chemistry/physiology MH - Muscle, Skeletal/*chemistry/ultrastructure MH - Myocardium/*chemistry/ultrastructure MH - Protein Kinases/*chemistry/physiology MH - Rabbits MH - Repetitive Sequences, Nucleic Acid MH - Sarcomeres/chemistry/*ultrastructure EDAT- 1995/10/13 MHDA- 1995/10/13 00:01 CRDT- 1995/10/13 00:00 PST - ppublish SO - Science. 1995 Oct 13;270(5234):293-6. PMID- 22226835 OWN - NLM STAT- MEDLINE DA - 20120131 DCOM- 20120405 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 416 IP - 2 DP - 2012 Feb 17 TI - N-terminal segments modulate the alpha-helical propensities of the intrinsically disordered basic regions of bZIP proteins. PG - 287-99 LID - 10.1016/j.jmb.2011.12.043 [doi] AB - Basic region leucine zippers (bZIPs) are modular transcription factors that play key roles in eukaryotic gene regulation. The basic regions of bZIPs (bZIP-bRs) are necessary and sufficient for DNA binding and specificity. Bioinformatic predictions and spectroscopic studies suggest that unbound monomeric bZIP-bRs are uniformly disordered as isolated domains. Here, we test this assumption through a comparative characterization of conformational ensembles for 15 different bZIP-bRs using a combination of atomistic simulations and circular dichroism measurements. We find that bZIP-bRs have quantifiable preferences for alpha-helical conformations in their unbound monomeric forms. This helicity varies from one bZIP-bR to another despite a significant sequence similarity of the DNA binding motifs (DBMs). Our analysis reveals that intramolecular interactions between DBMs and eight-residue segments directly N-terminal to DBMs are the primary modulators of bZIP-bR helicities. We test the accuracy of this inference by designing chimeras of bZIP-bRs to have either increased or decreased overall helicities. Our results yield quantitative insights regarding the relationship between sequence and the degree of intrinsic disorder within bZIP-bRs, and might have general implications for other intrinsically disordered proteins. Understanding how natural sequence variations lead to modulation of disorder is likely to be important for understanding the evolution of specificity in molecular recognition through intrinsically disordered regions (IDRs). CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Das, Rahul K AU - Das RK AD - Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA. FAU - Crick, Scott L AU - Crick SL FAU - Pappu, Rohit V AU - Pappu RV LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20111228 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Basic-Leucine Zipper Transcription Factors) SB - IM MH - Amino Acid Sequence MH - Basic-Leucine Zipper Transcription Factors/*chemistry/metabolism MH - Binding Sites MH - Circular Dichroism MH - Computer Simulation MH - Leucine Zippers MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Structure, Secondary MH - Sequence Alignment MH - Structure-Activity Relationship EDAT- 2012/01/10 06:00 MHDA- 2012/04/06 06:00 CRDT- 2012/01/10 06:00 PHST- 2011/10/21 [received] PHST- 2011/12/16 [revised] PHST- 2011/12/20 [accepted] PHST- 2011/12/28 [aheadofprint] AID - S0022-2836(11)01372-6 [pii] AID - 10.1016/j.jmb.2011.12.043 [doi] PST - ppublish SO - J Mol Biol. 2012 Feb 17;416(2):287-99. doi: 10.1016/j.jmb.2011.12.043. Epub 2011 Dec 28. PMID- 21393250 OWN - NLM STAT- MEDLINE DA - 20110425 DCOM- 20110714 LR - 20140821 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 17 DP - 2011 Apr 29 TI - N-terminal half of the cGMP phosphodiesterase gamma-subunit contributes to stabilization of the GTPase-accelerating protein complex. PG - 15260-7 LID - 10.1074/jbc.M110.210567 [doi] AB - In the visual signal terminating transition state, the cyclic GMP phosphodiesterase (PDE6) inhibitory gamma-subunit (PDEgamma) stimulates GTPase activity of the alpha-subunit of transducin (alphat) by enhancing the interaction between alphat and its regulator of G protein signaling (RGS9), which is constitutively bound to the type 5 G protein beta-subunit (beta5). Although it is known from a crystal structure of partial molecules that the PDEgamma C terminus contacts with both alphat and RGS9, contributions from the intrinsically disordered PDEgamma N-terminal half remain unclear. In this study, we were able to investigate this issue using a photolabel transfer strategy that allows for mapping the interface of full-length proteins. We observed label transfer from PDEgamma N-terminal positions 50, 30, and 16 to RGS9.beta5 in the GTPase-accelerating protein (GAP) complex composed of PDEgamma.alphat.RGS9.beta5. In support of a direct PDEgamma N-terminal interaction with RGS9.beta5, the PDEgamma N-terminal peptide PDEgamma(1-61) abolished label transfer to RGS9.beta5, and another N-terminal peptide, PDEgamma(10-30), disassembled the GAP complex in label transfer and pulldown experiments. Furthermore, we determined that the PDEgamma C-terminal interaction with alphat was enhanced whereas the N-terminal interaction was weakened upon changing the alphat conformation from the signaling state to the transition state. This "rearrangement" of PDEgamma domain interactions with alphat appears to facilitate the interaction of the PDEgamma N-terminal half with RGS9.beta5 and hence its contribution to optimal stabilization of the GAP complex. FAU - Guo, Lian-Wang AU - Guo LW AD - Department of Pharmacology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA. lianwangguo@wisc.edu FAU - Ruoho, Arnold E AU - Ruoho AE LA - eng GR - GM-33138/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20110310 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (RGS Proteins) RN - 0 (regulator of g-protein signaling 9) RN - EC 3.1.4.35 (Cyclic Nucleotide Phosphodiesterases, Type 6) SB - IM MH - Animals MH - Cattle MH - Cyclic Nucleotide Phosphodiesterases, Type 6/*chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Interaction Mapping/methods MH - Protein Stability MH - RGS Proteins/*chemistry PMC - PMC3083170 OID - NLM: PMC3083170 EDAT- 2011/03/12 06:00 MHDA- 2011/07/16 06:00 CRDT- 2011/03/12 06:00 PHST- 2011/03/10 [aheadofprint] AID - M110.210567 [pii] AID - 10.1074/jbc.M110.210567 [doi] PST - ppublish SO - J Biol Chem. 2011 Apr 29;286(17):15260-7. doi: 10.1074/jbc.M110.210567. Epub 2011 Mar 10. PMID- 12149256 OWN - NLM STAT- MEDLINE DA - 20020930 DCOM- 20021120 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 277 IP - 40 DP - 2002 Oct 4 TI - Kinetic studies of amyloid beta-protein fibril assembly. Differential effects of alpha-helix stabilization. PG - 36948-54 AB - Amyloid beta-protein (Abeta) fibril assembly is a defining characteristic of Alzheimer's disease. Fibril formation is a complex nucleation-dependent polymerization process characterized in vitro by an initial lag phase. To a significant degree, this phase is a consequence of the energy barrier that must be overcome in order for Abeta monomers to fold and oligomerize into fibril nuclei. Here we show that low concentrations of 2,2,2-trifluoroethanol (TFE) convert predominately unstructured Abeta monomers into partially ordered, quasistable conformers. Surprisingly, this results in a temporal decrease in the lag phase for fibril formation and a significant increase in the rate of fibril elongation. The TFE effect is concentration dependent and is maximal at approximately 20% (v/v). In the presence of low concentrations of TFE, fibril formation is observed in Abeta samples at nanomolar concentration, well below the critical concentration for Abeta fibril formation in the absence of TFE. As the amount of TFE is increased above 20%, helix content progressively rises to approximately 80%, a change paralleled first by a decrease in elongation rate and then by a complete cessation of fibril growth. These findings are consistent with the hypothesis that a partially folded helix-containing conformer is an intermediate in Abeta fibril assembly. The requirement that Abeta partially folds in order to assemble into fibrils contrasts with the mechanism of amyloidogenesis of natively folded proteins such as transthyretin and lysozyme, in which partial unfolding is a prerequisite. Our results suggest that in vivo, factors that affect helix formation and stability will have significant effects on the kinetics of Abeta fibril formation. FAU - Fezoui, Youcef AU - Fezoui Y AD - Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA. FAU - Teplow, David B AU - Teplow DB LA - eng GR - 1P01AG14366/AG/NIA NIH HHS/United States GR - 1R01NS38328/NS/NINDS NIH HHS/United States GR - T32-AG00222/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20020730 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptides) RN - 75-89-8 (Trifluoroethanol) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Amyloid beta-Peptides/*chemical synthesis/chemistry/*ultrastructure MH - Circular Dichroism MH - Guanidine/pharmacology MH - Kinetics MH - Microfibrils/*metabolism/*ultrastructure MH - Microscopy, Electron MH - Peptides/chemical synthesis/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Denaturation MH - Protein Structure, Secondary MH - Spectrophotometry, Ultraviolet MH - Trifluoroethanol EDAT- 2002/08/01 10:00 MHDA- 2002/11/26 04:00 CRDT- 2002/08/01 10:00 PHST- 2002/07/30 [aheadofprint] AID - 10.1074/jbc.M204168200 [doi] AID - M204168200 [pii] PST - ppublish SO - J Biol Chem. 2002 Oct 4;277(40):36948-54. Epub 2002 Jul 30. PMID- 19556969 OWN - NLM STAT- MEDLINE DA - 20100616 DCOM- 20100629 LR - 20140828 IS - 1460-2075 (Electronic) IS - 0261-4189 (Linking) VI - 28 IP - 15 DP - 2009 Aug 5 TI - Unusual bipartite mode of interaction between the nonsense-mediated decay factors, UPF1 and UPF2. PG - 2293-306 LID - 10.1038/emboj.2009.175 [doi] AB - Nonsense-mediated decay (NMD) is a eukaryotic quality control mechanism that degrades mRNAs carrying premature stop codons. In mammalian cells, NMD is triggered when UPF2 bound to UPF3 on a downstream exon junction complex interacts with UPF1 bound to a stalled ribosome. We report structural studies on the interaction between the C-terminal region of UPF2 and intact UPF1. Crystal structures, confirmed by EM and SAXS, show that the UPF1 CH-domain is docked onto its helicase domain in a fixed configuration. The C-terminal region of UPF2 is natively unfolded but binds through separated alpha-helical and beta-hairpin elements to the UPF1 CH-domain. The alpha-helical region binds sixfold more weakly than the beta-hairpin, whereas the combined elements bind 80-fold more tightly. Cellular assays show that NMD is severely affected by mutations disrupting the beta-hairpin binding, but not by those only affecting alpha-helix binding. We propose that the bipartite mode of UPF2 binding to UPF1 brings the ribosome and the EJC in close proximity by forming a tight complex after an initial weak encounter with either element. FAU - Clerici, Marcello AU - Clerici M AD - European Molecular Biology Laboratory, Grenoble Outstation, Grenoble Cedex 9, France. FAU - Mourao, Andre AU - Mourao A FAU - Gutsche, Irina AU - Gutsche I FAU - Gehring, Niels H AU - Gehring NH FAU - Hentze, Matthias W AU - Hentze MW FAU - Kulozik, Andreas AU - Kulozik A FAU - Kadlec, Jan AU - Kadlec J FAU - Sattler, Michael AU - Sattler M FAU - Cusack, Stephen AU - Cusack S LA - eng SI - PDB/2WJV SI - PDB/2WJY PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090625 PL - England TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (RNA, Messenger) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - 0 (UPF1 protein, human) RN - 0 (UPF2 protein, human) SB - IM MH - Amino Acid Sequence MH - Crystallography, X-Ray MH - DNA Mutational Analysis MH - Microscopy, Electron MH - Molecular Sequence Data MH - Mutation, Missense MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - *Protein Interaction Mapping MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - *RNA Stability MH - RNA, Messenger/*metabolism MH - Scattering, Small Angle MH - Sequence Alignment MH - Trans-Activators/chemistry/*metabolism MH - Transcription Factors/chemistry/*metabolism PMC - PMC2726699 OID - NLM: PMC2726699 EDAT- 2009/06/27 09:00 MHDA- 2010/06/30 06:00 CRDT- 2009/06/27 09:00 PHST- 2008/11/01 [received] PHST- 2009/06/03 [accepted] PHST- 2009/06/25 [aheadofprint] AID - emboj2009175 [pii] AID - 10.1038/emboj.2009.175 [doi] PST - ppublish SO - EMBO J. 2009 Aug 5;28(15):2293-306. doi: 10.1038/emboj.2009.175. Epub 2009 Jun 25. PMID- 8230201 OWN - NLM STAT- MEDLINE DA - 19931209 DCOM- 19931209 LR - 20081121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 234 IP - 1 DP - 1993 Nov 5 TI - Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 A resolution. PG - 222-33 AB - The three-dimensional structure of the seryl-tRNA synthetase from Thermus thermophilus has been determined and refined at 2.5 A resolution. The final model consists of a dimer of 421 residues each and 190 water molecules. The R-factor is 18.4% for all the data between 10 and 2.5 A resolution. The structure is very similar to that of the homologous enzyme from Escherichia coli, with an r.m.s. difference of 1.5 A for the 357 alpha-carbon atoms considered equivalent. The comparison of the two structures indicates increased hydrophobicity, reduced conformational entropy and reduced torsional strain as possible mechanisms by which thermostability is obtained in the enzyme from the thermophile. FAU - Fujinaga, M AU - Fujinaga M AD - EMBL Grenoble Outstation, France. FAU - Berthet-Colominas, C AU - Berthet-Colominas C FAU - Yaremchuk, A D AU - Yaremchuk AD FAU - Tukalo, M A AU - Tukalo MA FAU - Cusack, S AU - Cusack S LA - eng PT - Comparative Study PT - Journal Article PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (Fungal Proteins) RN - EC 6.1.1.11 (Serine-tRNA Ligase) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/ultrastructure MH - Crystallography, X-Ray MH - Escherichia coli/enzymology MH - Fungal Proteins/ultrastructure MH - Hot Temperature MH - Hydrogen Bonding MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Denaturation MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/enzymology MH - Sequence Alignment MH - Sequence Homology MH - Serine-tRNA Ligase/*ultrastructure MH - Surface Properties MH - Thermus thermophilus/*enzymology EDAT- 1993/11/05 MHDA- 1993/11/05 00:01 CRDT- 1993/11/05 00:00 AID - S0022-2836(83)71576-7 [pii] AID - 10.1006/jmbi.1993.1576 [doi] PST - ppublish SO - J Mol Biol. 1993 Nov 5;234(1):222-33. PMID- 25024220 OWN - NLM STAT- MEDLINE DA - 20140730 DCOM- 20141031 LR - 20150130 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 30 DP - 2014 Jul 29 TI - Synergy of aromatic residues and phosphoserines within the intrinsically disordered DNA-binding inhibitory elements of the Ets-1 transcription factor. PG - 11019-24 LID - 10.1073/pnas.1401891111 [doi] AB - The E26 transformation-specific (Ets-1) transcription factor is autoinhibited by a conformationally disordered serine-rich region (SRR) that transiently interacts with its DNA-binding ETS domain. In response to calcium signaling, autoinhibition is reinforced by calmodulin-dependent kinase II phosphorylation of serines within the SRR. Using mutagenesis and quantitative DNA-binding measurements, we demonstrate that phosphorylation-enhanced autoinhibition requires the presence of phenylalanine or tyrosine (varphi) residues adjacent to the SRR phosphoacceptor serines. The introduction of additional phosphorylated Ser-varphi-Asp, but not Ser-Ala-Asp, repeats within the SRR dramatically reinforces autoinhibition. NMR spectroscopic studies of phosphorylated and mutated SRR variants, both within their native context and as separate trans-acting peptides, confirmed that the aromatic residues and phosphoserines contribute to the formation of a dynamic complex with the ETS domain. Complementary NMR studies also identified the SRR-interacting surface of the ETS domain, which encompasses its positively charged DNA-recognition interface and an adjacent region of neutral polar and nonpolar residues. Collectively, these studies highlight the role of aromatic residues and their synergy with phosphoserines in an intrinsically disordered regulatory sequence that integrates cellular signaling and gene expression. FAU - Desjardins, Genevieve AU - Desjardins G AD - Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; FAU - Meeker, Charles A AU - Meeker CA AD - Department of Oncological Sciences, University of Utah School of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112; and. FAU - Bhachech, Niraja AU - Bhachech N AD - Department of Oncological Sciences, University of Utah School of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112; and. FAU - Currie, Simon L AU - Currie SL AD - Department of Oncological Sciences, University of Utah School of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112; and. FAU - Okon, Mark AU - Okon M AD - Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; FAU - Graves, Barbara J AU - Graves BJ AD - Department of Oncological Sciences, University of Utah School of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112; andHoward Hughes Medical Institute, Chevy Chase, MD 20815 barbara.graves@hci.utah.edu mcintosh@chem.ubc.ca. FAU - McIntosh, Lawrence P AU - McIntosh LP AD - Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3; barbara.graves@hci.utah.edu mcintosh@chem.ubc.ca. LA - eng GR - P30 CA042014/CA/NCI NIH HHS/United States GR - R01 GM038663/GM/NIGMS NIH HHS/United States GR - R01 GM38663/GM/NIGMS NIH HHS/United States GR - Canadian Institutes of Health Research/Canada GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140714 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (ETS1 protein, human) RN - 0 (Peptides) RN - 0 (Proto-Oncogene Protein c-ets-1) RN - 17885-08-4 (Phosphoserine) SB - IM MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides MH - Phosphoserine/*chemistry/metabolism MH - Protein Structure, Tertiary MH - Proto-Oncogene Protein c-ets-1/*chemistry/genetics/metabolism MH - Repetitive Sequences, Amino Acid PMC - PMC4121781 OID - NLM: PMC4121781 OTO - NOTNLM OT - fuzz complex OT - intrinsically disordered region OT - protein dynamics OT - transcription factor regulation EDAT- 2014/07/16 06:00 MHDA- 2014/11/02 06:00 CRDT- 2014/07/16 06:00 PHST- 2014/07/14 [aheadofprint] AID - 1401891111 [pii] AID - 10.1073/pnas.1401891111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):11019-24. doi: 10.1073/pnas.1401891111. Epub 2014 Jul 14. PMID- 21220121 OWN - NLM STAT- MEDLINE DA - 20110111 DCOM- 20110418 LR - 20150325 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 19 IP - 1 DP - 2011 Jan 12 TI - SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. PG - 109-16 LID - 10.1016/j.str.2010.10.006 [doi] AB - We developed and implemented an ensemble-refinement method to study dynamic biomolecular assemblies with intrinsically disordered segments. Data from small angle X-ray scattering (SAXS) experiments and from coarse-grained molecular simulations were combined by using a maximum-entropy approach. The method was applied to CHMP3 of ESCRT-III, a protein with multiple helical domains separated by flexible linkers. Based on recent SAXS data by Lata et al. (J. Mol. Biol. 378, 818, 2008), we constructed ensembles of CHMP3 at low- and high-salt concentration to characterize its closed autoinhibited state and open active state. At low salt, helix alpha(5) is bound to the tip of helices alpha(1) and alpha(2), in excellent agreement with a recent crystal structure. Helix alpha(6) remains free in solution and does not appear to be part of the autoinhibitory complex. The simulation-based ensemble refinement is general and effectively increases the resolution of SAXS beyond shape information to atomically detailed structures. CI - Copyright A(c) 2011 Elsevier Ltd. All rights reserved. FAU - Rozycki, Bartosz AU - Rozycki B AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. FAU - Kim, Young C AU - Kim YC FAU - Hummer, Gerhard AU - Hummer G LA - eng GR - ZIA DK029033-11/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (CHMP3 protein, human) RN - 0 (Endosomal Sorting Complexes Required for Transport) SB - IM CIN - Structure. 2011 Jan 12;19(1):3-4. PMID: 21220109 MH - Cluster Analysis MH - Computer Simulation MH - Endosomal Sorting Complexes Required for Transport/*chemistry MH - Entropy MH - Humans MH - Models, Molecular MH - Monte Carlo Method MH - Osmolar Concentration MH - Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Scattering, Small Angle MH - X-Ray Diffraction PMC - PMC3032427 MID - NIHMS254651 OID - NLM: NIHMS254651 OID - NLM: PMC3032427 EDAT- 2011/01/12 06:00 MHDA- 2011/04/19 06:00 CRDT- 2011/01/12 06:00 PHST- 2010/08/12 [received] PHST- 2010/09/22 [revised] PHST- 2010/10/20 [accepted] AID - S0969-2126(10)00395-3 [pii] AID - 10.1016/j.str.2010.10.006 [doi] PST - ppublish SO - Structure. 2011 Jan 12;19(1):109-16. doi: 10.1016/j.str.2010.10.006. PMID- 17190599 OWN - NLM STAT- MEDLINE DA - 20061227 DCOM- 20070126 LR - 20140907 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 127 IP - 7 DP - 2006 Dec 29 TI - UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke. PG - 1349-60 AB - Helicases use the energy derived from nucleoside triphosphate hydrolysis to unwind double helices in essentially every metabolic pathway involving nucleic acids. Earlier crystal structures have suggested that DNA helicases translocate along a single-stranded DNA in an inchworm fashion. We report here a series of crystal structures of the UvrD helicase complexed with DNA and ATP hydrolysis intermediates. These structures reveal that ATP binding alone leads to unwinding of 1 base pair by directional rotation and translation of the DNA duplex, and ADP and Pi release leads to translocation of the developing single strand. Thus DNA unwinding is achieved by a two-part power stroke in a combined wrench-and-inchworm mechanism. The rotational angle and translational distance of DNA define the unwinding step to be 1 base pair per ATP hydrolyzed. Finally, a gateway for ssDNA translocation and an alternative strand-displacement mode may explain the varying step sizes reported previously. FAU - Lee, Jae Young AU - Lee JY AD - Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. FAU - Yang, Wei AU - Yang W LA - eng GR - Z01 DK036119-10/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Intramural PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (DNA, Single-Stranded) RN - 0 (Escherichia coli Proteins) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - 9007-49-2 (DNA) RN - EC 3.6.1.- (UvrD protein, E coli) RN - EC 3.6.4.- (DNA Helicases) SB - IM MH - Adenosine Triphosphate/chemistry MH - Amino Acid Sequence MH - *Base Pairing MH - Conserved Sequence MH - Crystallization MH - DNA/*chemistry/genetics MH - DNA Helicases/*chemistry/genetics MH - DNA Repair MH - DNA, Single-Stranded/chemistry MH - Escherichia coli Proteins/*chemistry/genetics MH - *Models, Genetic MH - Molecular Sequence Data MH - Protein Biosynthesis MH - Protein Structure, Tertiary MH - Recombination, Genetic MH - Sequence Homology, Amino Acid MH - Structure-Activity Relationship PMC - PMC1866287 MID - NIHMS15787 OID - NLM: NIHMS15787 OID - NLM: PMC1866287 EDAT- 2006/12/28 09:00 MHDA- 2007/01/27 09:00 CRDT- 2006/12/28 09:00 PHST- 2006/08/05 [received] PHST- 2006/10/09 [revised] PHST- 2006/10/20 [accepted] AID - S0092-8674(06)01601-1 [pii] AID - 10.1016/j.cell.2006.10.049 [doi] PST - ppublish SO - Cell. 2006 Dec 29;127(7):1349-60. PMID- 16366524 OWN - NLM STAT- MEDLINE DA - 20051221 DCOM- 20060321 LR - 20080117 IS - 0002-7863 (Print) IS - 0002-7863 (Linking) VI - 127 IP - 51 DP - 2005 Dec 28 TI - Defining long-range order and local disorder in native alpha-synuclein using residual dipolar couplings. PG - 17968-9 AB - Intrinsically unstructured proteins play key biochemical roles in a vast range of normal and pathological processes. To study these systems, it is necessary to invoke an ensemble of rapidly interconverting conformations. Residual dipolar couplings (RDCs) are particularly powerful probes of the behavior of unfolded proteins, reporting on time and ensemble-averaged conformations up to and beyond the millisecond time scale. In this study, we present a novel interpretation of RDCs in unfolded systems that simultaneously defines long-range structural order and local conformational sampling. This approach is used to describe the structure and dynamics of alpha-Synuclein (alphaS), a protein that is strongly implicated in the development of Parkinson's disease (PD), allowing unambiguous detection of strongly populated conformers containing long-range contacts between the N- and C-terminal domains. The structural model combines two features required for the description of alphaS in solution: local conformational fluctuation based on random sampling of residue-specific phi/psi distributions, and long-range contacts induced by the presence of nonbonding interactions between domains that are distant in primary sequence. Both aspects are found to be necessary for the reproduction of the nonaveraged RDCs from alphaS. Although RDCs have previously been shown to report on local conformational preferences in unstructured proteins, this study shows the additional sensitivity of these measurements to the presence of long-range order in highly flexible systems. FAU - Bernado, Pau AU - Bernado P AD - Institute de Biologie Structurale Jean-Pierre Ebel, CNRS-CEA-UJF, 41 rue Jules Horowitz, 38027-Grenoble Cedex, France. FAU - Bertoncini, Carlos W AU - Bertoncini CW FAU - Griesinger, Christian AU - Griesinger C FAU - Zweckstetter, Markus AU - Zweckstetter M FAU - Blackledge, Martin AU - Blackledge M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (alpha-Synuclein) SB - IM MH - Protein Conformation MH - Protein Structure, Tertiary MH - Spectrum Analysis/methods MH - alpha-Synuclein/*chemistry EDAT- 2005/12/22 09:00 MHDA- 2006/03/22 09:00 CRDT- 2005/12/22 09:00 AID - 10.1021/ja055538p [doi] PST - ppublish SO - J Am Chem Soc. 2005 Dec 28;127(51):17968-9. PMID- 17947231 OWN - NLM STAT- MEDLINE DA - 20080121 DCOM- 20080326 LR - 20090724 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 4 DP - 2008 Jan 25 TI - Spontaneous assembly of photosynthetic supramolecular complexes as mediated by the intrinsically unstructured protein CP12. PG - 1831-8 AB - CP12 is a protein of 8.7 kDa that contributes to Calvin cycle regulation by acting as a scaffold element in the formation of a supramolecular complex with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) in photosynthetic organisms. NMR studies of recombinant CP12 (isoform 2) of Arabidopsis thaliana show that CP12-2 is poorly structured. CP12-2 is monomeric in solution and contains four cysteines, which can form two intramolecular disulfides with midpoint redox potentials of -326 and -352 mV, respectively, at pH 7.9. Site-specific mutants indicate that the C-terminal disulfide is involved in the interaction between CP12-2 and GAPDH (isoform A(4)), whereas the N-terminal disulfide is involved in the interaction between this binary complex and PRK. In the presence of NAD, oxidized CP12-2 interacts with A(4)-GAPDH (K(D) = 0.18 microm) to form a binary complex of 170 kDa with (A(4)-GAPDH)-(CP12-2)(2) stoichiometry, as determined by isothermal titration calorimetry and multiangle light scattering analysis. PRK is a dimer and by interacting with this binary complex (K(D) = 0.17 microm) leads to a 498-kDa ternary complex constituted by two binary complexes and two PRK dimers, i.e. ((A(4)-GAPDH)-(CP12-2)(2)-(PRK))(2). Thermodynamic parameters indicate that assembly of both binary and ternary complexes is exoergonic although penalized by a decrease in entropy that suggests an induced folding of CP12-2 upon binding to partner proteins. The redox dependence of events leading to supramolecular complexes is consistent with a role of CP12 in coordinating the reversible inactivation of chloroplast enzymes A(4)-GAPDH and PRK during darkness in photosynthetic tissues. FAU - Marri, Lucia AU - Marri L AD - Laboratory of Molecular Plant Physiology, Department of Experimental Evolutionary Biology, University of Bologna, Via Irnerio 42, Bologna 40126, Italy. FAU - Trost, Paolo AU - Trost P FAU - Trivelli, Xavier AU - Trivelli X FAU - Gonnelli, Leonardo AU - Gonnelli L FAU - Pupillo, Paolo AU - Pupillo P FAU - Sparla, Francesca AU - Sparla F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20071018 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Arabidopsis Proteins) RN - 0 (Isoenzymes) RN - 0 (Photosynthetic Reaction Center Complex Proteins) RN - 0 (Plant Proteins) RN - EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases) RN - EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)) RN - EC 2.7.1.19 (phosphoribulokinase) SB - IM MH - Arabidopsis/genetics/*metabolism MH - Arabidopsis Proteins/genetics/*metabolism MH - Glyceraldehyde-3-Phosphate Dehydrogenases/genetics/metabolism MH - Isoenzymes/genetics/metabolism MH - Mutagenesis, Site-Directed MH - Mutation, Missense MH - Oxidation-Reduction MH - Phosphotransferases (Alcohol Group Acceptor)/genetics/metabolism MH - Photosynthesis/*physiology MH - Photosynthetic Reaction Center Complex Proteins/genetics/*metabolism MH - Plant Proteins/genetics/*metabolism MH - Protein Binding/genetics EDAT- 2007/10/20 09:00 MHDA- 2008/03/28 09:00 CRDT- 2007/10/20 09:00 PHST- 2007/10/18 [aheadofprint] AID - M705650200 [pii] AID - 10.1074/jbc.M705650200 [doi] PST - ppublish SO - J Biol Chem. 2008 Jan 25;283(4):1831-8. Epub 2007 Oct 18. PMID- 22253588 OWN - NLM STAT- MEDLINE DA - 20120118 DCOM- 20120608 LR - 20141019 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Residual structures, conformational fluctuations, and electrostatic interactions in the synergistic folding of two intrinsically disordered proteins. PG - e1002353 LID - 10.1371/journal.pcbi.1002353 [doi] AB - To understand the interplay of residual structures and conformational fluctuations in the interaction of intrinsically disordered proteins (IDPs), we first combined implicit solvent and replica exchange sampling to calculate atomistic disordered ensembles of the nuclear co-activator binding domain (NCBD) of transcription coactivator CBP and the activation domain of the p160 steroid receptor coactivator ACTR. The calculated ensembles are in quantitative agreement with NMR-derived residue helicity and recapitulate the experimental observation that, while free ACTR largely lacks residual secondary structures, free NCBD is a molten globule with a helical content similar to that in the folded complex. Detailed conformational analysis reveals that free NCBD has an inherent ability to substantially sample all the helix configurations that have been previously observed either unbound or in complexes. Intriguingly, further high-temperature unbinding and unfolding simulations in implicit and explicit solvents emphasize the importance of conformational fluctuations in synergistic folding of NCBD with ACTR. A balance between preformed elements and conformational fluctuations appears necessary to allow NCBD to interact with different targets and fold into alternative conformations. Together with previous topology-based modeling and existing experimental data, the current simulations strongly support an "extended conformational selection" synergistic folding mechanism that involves a key intermediate state stabilized by interaction between the C-terminal helices of NCBD and ACTR. In addition, the atomistic simulations reveal the role of long-range as well as short-range electrostatic interactions in cooperating with readily fluctuating residual structures, which might enhance the encounter rate and promote efficient folding upon encounter for facile binding and folding interactions of IDPs. Thus, the current study not only provides a consistent mechanistic understanding of the NCBD/ACTR interaction, but also helps establish a multi-scale molecular modeling framework for understanding the structure, interaction, and regulation of IDPs in general. FAU - Zhang, Weihong AU - Zhang W AD - Department of Biochemistry, Kansas State University, Manhattan, Kansas, United States of America. FAU - Ganguly, Debabani AU - Ganguly D FAU - Chen, Jianhan AU - Chen J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120112 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (Proteins) SB - IM MH - Binding Sites MH - *Computer Simulation MH - Models, Molecular MH - *Protein Folding MH - Protein Structure, Tertiary MH - Proteins/*chemistry/metabolism PMC - PMC3257294 OID - NLM: PMC3257294 EDAT- 2012/01/19 06:00 MHDA- 2012/06/09 06:00 CRDT- 2012/01/19 06:00 PHST- 2011/09/20 [received] PHST- 2011/11/30 [accepted] PHST- 2012/01/12 [epublish] AID - 10.1371/journal.pcbi.1002353 [doi] AID - PCOMPBIOL-D-11-01388 [pii] PST - ppublish SO - PLoS Comput Biol. 2012 Jan;8(1):e1002353. doi: 10.1371/journal.pcbi.1002353. Epub 2012 Jan 12. PMID- 24906881 OWN - NLM STAT- MEDLINE DA - 20140704 DCOM- 20140902 LR - 20150606 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 42 IP - 12 DP - 2014 Jul TI - Dynamic condensation of linker histone C-terminal domain regulates chromatin structure. PG - 7553-60 LID - 10.1093/nar/gku491 [doi] AB - The basic and intrinsically disordered C-terminal domain (CTD) of the linker histone (LH) is essential for chromatin compaction. However, its conformation upon nucleosome binding and its impact on chromatin organization remain unknown. Our mesoscale chromatin model with a flexible LH CTD captures a dynamic, salt-dependent condensation mechanism driven by charge neutralization between the LH and linker DNA. Namely, at low salt concentration, CTD condenses, but LH only interacts with the nucleosome and one linker DNA, resulting in a semi-open nucleosome configuration; at higher salt, LH interacts with the nucleosome and two linker DNAs, promoting stem formation and chromatin compaction. CTD charge reduction unfolds the domain and decondenses chromatin, a mechanism in consonance with reduced counterion screening in vitro and phosphorylated LH in vivo. Divalent ions counteract this decondensation effect by maintaining nucleosome stems and expelling the CTDs to the fiber exterior. Additionally, we explain that the CTD folding depends on the chromatin fiber size, and we show that the asymmetric structure of the LH globular head is responsible for the uneven interaction observed between the LH and the linker DNAs. All these mechanisms may impact epigenetic regulation and higher levels of chromatin folding. CI - (c) The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. FAU - Luque, Antoni AU - Luque A AD - Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA. FAU - Collepardo-Guevara, Rosana AU - Collepardo-Guevara R AD - University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK. FAU - Grigoryev, Sergei AU - Grigoryev S AD - Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA. FAU - Schlick, Tamar AU - Schlick T AD - Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA schlick@nyu.edu. LA - eng GR - R01 GM055164/GM/NIGMS NIH HHS/United States PT - Journal Article DEP - 20140606 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Chromatin) RN - 0 (Histones) RN - 0 (Nucleosomes) RN - I38ZP9992A (Magnesium) SB - IM MH - Chromatin/*chemistry MH - Histones/*chemistry MH - Magnesium/chemistry MH - Models, Molecular MH - Nucleosomes/chemistry MH - Protein Structure, Tertiary PMC - PMC4081093 OID - NLM: PMC4081093 EDAT- 2014/06/08 06:00 MHDA- 2014/09/03 06:00 CRDT- 2014/06/08 06:00 PHST- 2014/06/06 [aheadofprint] AID - gku491 [pii] AID - 10.1093/nar/gku491 [doi] PST - ppublish SO - Nucleic Acids Res. 2014 Jul;42(12):7553-60. doi: 10.1093/nar/gku491. Epub 2014 Jun 6. PMID- 15065849 OWN - NLM STAT- MEDLINE DA - 20040406 DCOM- 20040806 LR - 20091119 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 14 DP - 2004 Apr 13 TI - IA3, an aspartic proteinase inhibitor from Saccharomyces cerevisiae, is intrinsically unstructured in solution. PG - 4071-81 AB - IA(3) is a highly specific and potent 68-amino acid endogenous inhibitor of yeast proteinase A (YprA), and X-ray crystallographic studies have shown that IA(3) binds to YprA as an alpha-helix [Li, M., Phylip, L. H., Lees, W. E., Winther, J. R., Dunn, B. M., Wlodawer, A., Kay, J., and Gustchina, A. (2000) Nat. Struct. Biol. 7, 113-117]. Surprisingly, only residues 2-32 of IA(3) are seen in the X-ray structure, and the remaining residues are believed to be disordered in the complex. We have used circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy to show that IA(3) is unstructured in the absence of YprA. Specifically, IA(3) produced a CD spectrum characteristic of an unstructured peptide, and the (15)N HSQC NMR spectra of IA(3) were characteristic of a polypeptide lacking intrinsic structure. We characterized the unstructured state of IA(3) by using singular-value decomposition (SVD) to analyze the CD data in the presence of TFE, by fully assigning the unbound IA(3) protein by NMR and comparing the chemical shifts to published random-coil values, and by measuring (1)H-(15)N heteronuclear NOEs, which are all consistent with an unfolded protein. The IA(3) samples used for NMR analyses were active and inhibited YprA with an inhibition constant (K(i)) of 1.7 nM, and the addition of YprA led to a large spectral transition in IA(3). Calorimetric (ITC) data also show that the overall enthalpy of the interaction between IA(3) and YprA is exothermic. FAU - Green, Terry B AU - Green TB AD - Department of Biochemistry and Molecular Biology, Box 100245, University of Florida, Gainesville, Florida 32610-0245, USA. FAU - Ganesh, Omjoy AU - Ganesh O FAU - Perry, Kyle AU - Perry K FAU - Smith, Leif AU - Smith L FAU - Phylip, Lowri H AU - Phylip LH FAU - Logan, Timothy M AU - Logan TM FAU - Hagen, Stephen J AU - Hagen SJ FAU - Dunn, Ben M AU - Dunn BM FAU - Edison, Arthur S AU - Edison AS LA - eng GR - 1R01AI4903-01/AI/NIAID NIH HHS/United States GR - 5P41RR016105-02/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Ligands) RN - 0 (PAI3 protein, S cerevisiae) RN - 0 (Protease Inhibitors) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Solutions) RN - EC 3.4.23 (aspartic proteinase A) RN - EC 3.4.23.- (Aspartic Acid Endopeptidases) SB - IM MH - Amino Acid Sequence MH - Aspartic Acid Endopeptidases/*antagonists & inhibitors/metabolism MH - Circular Dichroism MH - Ligands MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protease Inhibitors/*chemistry/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Saccharomyces cerevisiae Proteins/*chemistry/metabolism MH - Solutions MH - Substrate Specificity MH - Thermodynamics EDAT- 2004/04/07 05:00 MHDA- 2004/08/07 05:00 CRDT- 2004/04/07 05:00 AID - 10.1021/bi034823n [doi] PST - ppublish SO - Biochemistry. 2004 Apr 13;43(14):4071-81. PMID- 19190183 OWN - NLM STAT- MEDLINE DA - 20090219 DCOM- 20090327 LR - 20140901 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 106 IP - 7 DP - 2009 Feb 17 TI - Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin. PG - 2104-9 LID - 10.1073/pnas.0806872106 [doi] AB - We explore how inherent flexibility of a protein molecule influences the mechanism controlling allosteric transitions by using a variational model inspired from work in protein folding. The striking differences in the predicted transition mechanism for the opening of the two domains of calmodulin (CaM) emphasize that inherent flexibility is key to understanding the complex conformational changes that occur in proteins. In particular, the C-terminal domain of CaM (cCaM), which is inherently less flexible than its N-terminal domain (nCaM), reveals "cracking" or local partial unfolding during the open/closed transition. This result is in harmony with the picture that cracking relieves local stresses caused by conformational deformations of a sufficiently rigid protein. We also compare the conformational transition in a recently studied even-odd paired fragment of CaM. Our results rationalize the different relative binding affinities of the EF-hands in the engineered fragment compared with the intact odd-even paired EF-hands (nCaM and cCaM) in terms of changes in flexibility along the transition route. Aside from elucidating general theoretical ideas about the cracking mechanism, these studies also emphasize how the remarkable intrinsic plasticity of CaM underlies conformational dynamics essential for its diverse functions. FAU - Tripathi, Swarnendu AU - Tripathi S AD - Department of Physics, Kent State University, Kent, OH 44242, USA. FAU - Portman, John J AU - Portman JJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090203 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Calmodulin) RN - SY7Q814VUP (Calcium) SB - IM MH - Allosteric Site MH - Amino Acid Motifs MH - Calcium/metabolism MH - Calmodulin/*chemistry MH - EF Hand Motifs/genetics MH - Humans MH - Kinetics MH - Models, Molecular MH - Models, Statistical MH - Molecular Conformation MH - Pliability MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary PMC - PMC2650115 OID - NLM: PMC2650115 EDAT- 2009/02/05 09:00 MHDA- 2009/03/28 09:00 CRDT- 2009/02/05 09:00 PHST- 2009/02/03 [aheadofprint] AID - 0806872106 [pii] AID - 10.1073/pnas.0806872106 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2104-9. doi: 10.1073/pnas.0806872106. Epub 2009 Feb 3. PMID- 11237626 OWN - NLM STAT- MEDLINE DA - 20010312 DCOM- 20010412 LR - 20101118 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 306 IP - 5 DP - 2001 Mar 9 TI - Thermodynamics of the high-affinity interaction of TCF4 with beta-catenin. PG - 1179-89 AB - The formation of a complex between beta-catenin and members of the TCF/LEF family of high-mobility group proteins is a key regulatory event in the wnt-signaling pathway, essential for embryonal development as well as the growth of normal and malignant colon epithelium. We have characterized the binding of TCF4 to human beta-catenin by steady-state intrinsic fluorescence quenching experiments, surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC). Binding studies in solution and in heterogeneous phase showed that TCF4 binds reversibly to beta-catenin with an affinity (KB) of 3(+/-1) 10(8) M(-1). Site-directed mutagenesis, together with calorimetric measurements, revealed that residue D16 in TCF4 plays a crucial role in high-affinity binding. Mutation of this residue to alanine resulted in a decrease of KB by two orders of magnitude as well as a significant reduction in binding enthalpy. Binding of TCF4 to beta-catenin gave rise to a large negative enthalpy change at 25 degrees C (-29.7 kcal/mol). Binding enthalpies were strongly temperature dependent, which resulted in the determination of a large heat capacity change upon binding of -1.5 kcal/(mol K). The molecular events that take place upon complex formation are discussed using the measured thermodynamic data together with the crystal structure of the beta-catenin arm repeat region/TCF complex. FAU - Knapp, S AU - Knapp S AD - Department of Structural Chemistry, Pharmacia Corporation, Discovery Research Oncology, Nerviano, Italy. stefan.knapp@eu.pnu.com FAU - Zamai, M AU - Zamai M FAU - Volpi, D AU - Volpi D FAU - Nardese, V AU - Nardese V FAU - Avanzi, N AU - Avanzi N FAU - Breton, J AU - Breton J FAU - Plyte, S AU - Plyte S FAU - Flocco, M AU - Flocco M FAU - Marconi, M AU - Marconi M FAU - Isacchi, A AU - Isacchi A FAU - Caiolfa, V R AU - Caiolfa VR LA - eng PT - Journal Article PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (CTNNB1 protein, human) RN - 0 (Cytoskeletal Proteins) RN - 0 (DNA Primers) RN - 0 (Recombinant Fusion Proteins) RN - 0 (TCF Transcription Factors) RN - 0 (TCF7L2 protein, human) RN - 0 (Trans-Activators) RN - 0 (Transcription Factor 7-Like 2 Protein) RN - 0 (Transcription Factors) RN - 0 (beta Catenin) RN - EC 2.5.1.18 (Glutathione Transferase) SB - IM MH - Binding Sites MH - Circular Dichroism MH - Cloning, Molecular MH - Cytoskeletal Proteins/chemistry/*metabolism MH - DNA Primers/chemistry MH - Fluorescence MH - Glutathione Transferase/metabolism MH - Humans MH - Models, Molecular MH - Polymerase Chain Reaction MH - Protein Structure, Secondary MH - Recombinant Fusion Proteins/metabolism MH - Surface Plasmon Resonance/methods MH - TCF Transcription Factors MH - *Thermodynamics MH - *Trans-Activators MH - Transcription Factor 7-Like 2 Protein MH - Transcription Factors/chemistry/genetics/*metabolism MH - beta Catenin EDAT- 2001/03/10 10:00 MHDA- 2001/04/17 10:01 CRDT- 2001/03/10 10:00 AID - 10.1006/jmbi.2001.4463 [doi] AID - S0022-2836(01)94463-8 [pii] PST - ppublish SO - J Mol Biol. 2001 Mar 9;306(5):1179-89. PMID- 16060685 OWN - NLM STAT- MEDLINE DA - 20050802 DCOM- 20051101 LR - 20140916 IS - 0739-1102 (Print) IS - 0739-1102 (Linking) VI - 23 IP - 2 DP - 2005 Oct TI - Secondary structure and dynamics of an intrinsically unstructured linker domain. PG - 113-24 AB - The transient secondary structure and dynamics of an intrinsically unstructured linker domain from the 70 kDa subunit of human replication protein A was investigated using solution state NMR. Stable secondary structure, inferred from large secondary chemical shifts, was observed for a segment of the intrinsically unstructured linker domain when it is attached to an N-terminal protein interaction domain. Results from NMR relaxation experiments showed the rotational diffusion for this segment of the intrinsically unstructured linker domain to be correlated with the N-terminal protein interaction domain. When the N-terminal domain is removed, the stable secondary structure is lost and faster rotational diffusion is observed. The large secondary chemical shifts were used to calculate phi and psi dihedral angles and these dihedral angles were used to build a backbone structural model. Restrained molecular dynamics were performed on this new structure using the chemical shift based dihedral angles and a single NOE distance as restraints. In the resulting family of structures a large, solvent exposed loop was observed for the segment of the intrinsically unstructured linker domain that had large secondary chemical shifts. FAU - Olson, Katie E AU - Olson KE AD - Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Life Science South, Rm. 142, Moscow, ID 83844-3052, USA. FAU - Narayanaswami, Pranesh AU - Narayanaswami P FAU - Vise, Pamela D AU - Vise PD FAU - Lowry, David F AU - Lowry DF FAU - Wold, Marc S AU - Wold MS FAU - Daughdrill, Gary W AU - Daughdrill GW LA - eng GR - P20 RR 16448/RR/NCRR NIH HHS/United States GR - P20 RR 16454-02/RR/NCRR NIH HHS/United States GR - R01 GM044721/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - J Biomol Struct Dyn JT - Journal of biomolecular structure & dynamics JID - 8404176 RN - 0 (DNA-Binding Proteins) RN - 0 (RPA1 protein, human) RN - 0 (Recombinant Proteins) RN - 0 (Replication Protein A) SB - IM MH - DNA Replication MH - DNA-Binding Proteins/*chemistry/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy/methods MH - Models, Molecular MH - *Protein Conformation MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Replication Protein A EDAT- 2005/08/03 09:00 MHDA- 2005/11/03 09:00 CRDT- 2005/08/03 09:00 AID - d=3021&c=4185&p=13080&do=detail [pii] AID - 10.1080/07391102.2005.10507052 [doi] PST - ppublish SO - J Biomol Struct Dyn. 2005 Oct;23(2):113-24. PMID- 23374074 OWN - NLM STAT- MEDLINE DA - 20130320 DCOM- 20131212 LR - 20141103 IS - 1948-7193 (Electronic) IS - 1948-7193 (Linking) VI - 4 IP - 3 DP - 2013 Mar 20 TI - Structures of the E46K mutant-type alpha-synuclein protein and impact of E46K mutation on the structures of the wild-type alpha-synuclein protein. PG - 498-508 LID - 10.1021/cn3002027 [doi] AB - The E46K genetic missense mutation of the wild-type alpha-synuclein protein was recently identified in a family of Spanish origin with hereditary Parkinson's disease. Detailed understanding of the structures of the monomeric E46K mutant-type alpha-synuclein protein as well as the impact of the E46K missense mutation on the conformations and free energy landscapes of the wild-type alpha-synuclein are required for gaining insights into the pathogenic mechanism of Parkinson's disease. In this study, we use extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations to assess the secondary and tertiary structural properties as well as the conformational preferences of the monomeric wild-type and E46K mutant-type alpha-synuclein proteins in an aqueous solution environment. We also present the residual secondary structure component conversion stabilities with dynamics using a theoretical strategy, which we most recently developed. To the best of our knowledge, this study presents the first detailed comparison of the structural and thermodynamic properties of the wild-type and E46K mutant-type alpha-synuclein proteins in an aqueous solution environment at the atomic level with dynamics. We find that the E46K mutation results not only in local but also in long-range changes in the structural properties of the wild-type alpha-synuclein protein. The mutation site shows a significant decrease in helical content as well as a large increase in beta-sheet structure formation upon E46K mutation. In addition, the beta-sheet content of the C-terminal region increases significantly in the E46K mutant-type alphaS in comparison to the wild-type alphaS. Our theoretical strategy developed to assess the thermodynamic preference of secondary structure transitions indicates that this shift in secondary structure is the result of a decrease in the thermodynamic preference of turn to helix conversions while the coil to beta-sheet preference increases for these residues. Long-range intramolecular protein interactions of the C-terminal with the N-terminal and NAC regions increase upon E46K mutation, resulting in more compact structures for the E46K mutant-type rather than wild-type alphaS. However, the E46K mutant-type alphaS structures are less stable than the wild-type alphaS. Overall, our results show that the E46K mutant-type alphaS has a higher propensity to aggregate than the wild-type alphaS and that the N-terminal and C-terminal regions are reactive toward fibrillization and aggregation upon E46K mutation and we explain the associated reasons based on the structural properties herein. Small molecules or drugs that can block the specific residues forming abundant beta-sheet structure, which we report here, might help to reduce the reactivity of these intrinsically disordered fibrillogenic proteins toward aggregation and their toxicity. FAU - Wise-Scira, Olivia AU - Wise-Scira O AD - Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249, USA. FAU - Dunn, Aquila AU - Dunn A FAU - Aloglu, Ahmet K AU - Aloglu AK FAU - Sakallioglu, Isin T AU - Sakallioglu IT FAU - Coskuner, Orkid AU - Coskuner O LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130130 PL - United States TA - ACS Chem Neurosci JT - ACS chemical neuroscience JID - 101525337 RN - 0 (Mutant Proteins) RN - 0 (alpha-Synuclein) SB - IM MH - Humans MH - Mutant Proteins/*chemistry/*genetics MH - Mutation, Missense/*genetics MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - alpha-Synuclein/*chemistry/*genetics PMC - PMC3605821 OID - NLM: PMC3605821 EDAT- 2013/02/05 06:00 MHDA- 2013/12/18 06:00 CRDT- 2013/02/05 06:00 PHST- 2013/01/30 [aheadofprint] AID - 10.1021/cn3002027 [doi] PST - ppublish SO - ACS Chem Neurosci. 2013 Mar 20;4(3):498-508. doi: 10.1021/cn3002027. Epub 2013 Jan 30. PMID- 22972749 OWN - NLM STAT- MEDLINE DA - 20120928 DCOM- 20121205 LR - 20150104 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 109 IP - 39 DP - 2012 Sep 25 TI - Domain-domain interactions in full-length p53 and a specific DNA complex probed by methyl NMR spectroscopy. PG - 15752-6 AB - The tumor suppressor p53 is a homotetramer of 4 x 393 residues. Its core domain and tetramerization domain are linked and flanked by intrinsically disordered sequences, which hinder its full structural characterization. There is an outstanding problem of the state of the tetramerization domain. Structural studies on the isolated tetramerization domain show it is in a folded tetrameric conformation, but there are conflicting models from electron microscopy of the full-length protein, one of which proposes that the domain is not tetramerically folded and the tetrameric protein is stabilized by interactions between the N and C termini. Here, we present methyl-transverse relaxation optimized NMR spectroscopy (methyl-TROSY) investigations on the full-length and separate domains of the protein with its methionine residues enriched with (13)C to probe its quaternary structure. We obtained high-quality spectra of both the full-length tetrameric p53 and its DNA complex, observing the environment at 11 specific methyl sites. The tetramerization domain was as tetramerically folded in the full-length constructs as in the isolated domain. The N and C termini were intrinsically disordered in both the full-length protein and its complex with a 20-residue specific DNA sequence. Additionally, we detected in the interface of the core (DNA-binding) and N-terminal parts of the protein a slow conformational exchange process that was modulated by specific recognition of DNA, indicating allosteric processes. FAU - Bista, Michal AU - Bista M AD - Medical Research Council Laboratory of Molecular Biology, Cambridge, England. FAU - Freund, Stefan M AU - Freund SM FAU - Fersht, Alan R AU - Fersht AR LA - eng GR - G0901534/Medical Research Council/United Kingdom GR - MC_EX_G0901534/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120912 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (TP53 protein, human) RN - 0 (Tumor Suppressor Protein p53) RN - 9007-49-2 (DNA) SB - IM MH - Allosteric Regulation MH - DNA/*chemistry/metabolism MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - *Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Structure-Activity Relationship MH - Tumor Suppressor Protein p53/*chemistry/metabolism PMC - PMC3465378 OID - NLM: PMC3465378 EDAT- 2012/09/14 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/09/14 06:00 PHST- 2012/09/12 [aheadofprint] AID - 1214176109 [pii] AID - 10.1073/pnas.1214176109 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):15752-6. Epub 2012 Sep 12. PMID- 20385841 OWN - NLM STAT- MEDLINE DA - 20100428 DCOM- 20100602 LR - 20140827 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 107 IP - 17 DP - 2010 Apr 27 TI - EGCG remodels mature alpha-synuclein and amyloid-beta fibrils and reduces cellular toxicity. PG - 7710-5 LID - 10.1073/pnas.0910723107 [doi] AB - Protein misfolding and formation of beta-sheet-rich amyloid fibrils or aggregates is related to cellular toxicity and decay in various human disorders including Alzheimer's and Parkinson's disease. Recently, we demonstrated that the polyphenol (-)-epi-gallocatechine gallate (EGCG) inhibits alpha-synuclein and amyloid-beta fibrillogenesis. It associates with natively unfolded polypeptides and promotes the self-assembly of unstructured oligomers of a new type. Whether EGCG disassembles preformed amyloid fibrils, however, remained unclear. Here, we show that EGCG has the ability to convert large, mature alpha-synuclein and amyloid-beta fibrils into smaller, amorphous protein aggregates that are nontoxic to mammalian cells. Mechanistic studies revealed that the compound directly binds to beta-sheet-rich aggregates and mediates the conformational change without their disassembly into monomers or small diffusible oligomers. These findings suggest that EGCG is a potent remodeling agent of mature amyloid fibrils. FAU - Bieschke, Jan AU - Bieschke J AD - Max Delbrueck Center for Molecular Medicine, Robert-Roessle-Strasse 10, 13125 Berlin-Buch, Germany. jbiesch@mdc-berlin.de FAU - Russ, Jenny AU - Russ J FAU - Friedrich, Ralf P AU - Friedrich RP FAU - Ehrnhoefer, Dagmar E AU - Ehrnhoefer DE FAU - Wobst, Heike AU - Wobst H FAU - Neugebauer, Katja AU - Neugebauer K FAU - Wanker, Erich E AU - Wanker EE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100412 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Amyloid) RN - 0 (Amyloid beta-Peptides) RN - 0 (Neuroprotective Agents) RN - 0 (alpha-Synuclein) RN - 8R1V1STN48 (Catechin) RN - BQM438CTEL (epigallocatechin gallate) SB - IM MH - Amyloid/*biosynthesis/drug effects MH - Amyloid Neuropathies/drug therapy/*prevention & control MH - Amyloid beta-Peptides/*metabolism MH - Animals MH - Blotting, Western MH - CHO Cells MH - Catechin/*analogs & derivatives/pharmacology MH - Chromatography, Affinity MH - Circular Dichroism MH - Cricetinae MH - Cricetulus MH - Escherichia coli MH - Humans MH - Microscopy, Atomic Force MH - Microscopy, Electron, Transmission MH - Microscopy, Fluorescence MH - Neuroprotective Agents/*pharmacology MH - PC12 Cells MH - Rats MH - alpha-Synuclein/*metabolism PMC - PMC2867908 OID - NLM: PMC2867908 EDAT- 2010/04/14 06:00 MHDA- 2010/06/03 06:00 CRDT- 2010/04/14 06:00 PHST- 2010/04/12 [aheadofprint] AID - 0910723107 [pii] AID - 10.1073/pnas.0910723107 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2010 Apr 27;107(17):7710-5. doi: 10.1073/pnas.0910723107. Epub 2010 Apr 12. PMID- 20797624 OWN - NLM STAT- MEDLINE DA - 20100827 DCOM- 20100920 IS - 1097-4164 (Electronic) IS - 1097-2765 (Linking) VI - 39 IP - 4 DP - 2010 Aug 27 TI - Hsp12 is an intrinsically unstructured stress protein that folds upon membrane association and modulates membrane function. PG - 507-20 LID - 10.1016/j.molcel.2010.08.001 [doi] AB - Hsp12 of S. cerevisiae is upregulated several 100-fold in response to stress. Our phenotypic analysis showed that this protein is important for survival of a variety of stress conditions, including high temperature. In the absence of Hsp12, we observed changes in cell morphology under stress conditions. Surprisingly, in the cell, Hsp12 exists both as a soluble cytosolic protein and associated to the plasma membrane. The in vitro analysis revealed that Hsp12, unlike all other Hsps studied so far, is completely unfolded; however, in the presence of certain lipids, it adopts a helical structure. The presence of Hsp12 does not alter the overall lipid composition of the plasma membrane but increases membrane stability. CI - Copyright (c) 2010 Elsevier Inc. All rights reserved. FAU - Welker, Sylvia AU - Welker S AD - Munich Center for Integrated Protein Science, Technische Universitat Munchen, Department Chemie, Lichtenbergstrasse 4, 85747 Garching, Germany. FAU - Rudolph, Birgit AU - Rudolph B FAU - Frenzel, Elke AU - Frenzel E FAU - Hagn, Franz AU - Hagn F FAU - Liebisch, Gerhard AU - Liebisch G FAU - Schmitz, Gerd AU - Schmitz G FAU - Scheuring, Johannes AU - Scheuring J FAU - Kerth, Andreas AU - Kerth A FAU - Blume, Alfred AU - Blume A FAU - Weinkauf, Sevil AU - Weinkauf S FAU - Haslbeck, Martin AU - Haslbeck M FAU - Kessler, Horst AU - Kessler H FAU - Buchner, Johannes AU - Buchner J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (HSP12 protein, S cerevisiae) RN - 0 (Heat-Shock Proteins) RN - 0 (Membrane Lipids) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Cell Membrane/*metabolism/ultrastructure MH - Cytosol/metabolism MH - Gene Expression Regulation, Fungal MH - Genotype MH - Heat-Shock Proteins/chemistry/*genetics/metabolism MH - Heat-Shock Response MH - *Membrane Fluidity MH - Membrane Lipids/metabolism MH - Osmotic Pressure MH - Oxidative Stress MH - Phenotype MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Transport MH - Saccharomyces cerevisiae/genetics/growth & development/*metabolism/ultrastructure MH - Saccharomyces cerevisiae Proteins/chemistry/*genetics/metabolism MH - Sequence Deletion MH - Stress, Physiological MH - Structure-Activity Relationship EDAT- 2010/08/28 06:00 MHDA- 2010/09/21 06:00 CRDT- 2010/08/28 06:00 PHST- 2010/01/11 [received] PHST- 2010/07/02 [revised] PHST- 2010/08/04 [accepted] AID - S1097-2765(10)00583-6 [pii] AID - 10.1016/j.molcel.2010.08.001 [doi] PST - ppublish SO - Mol Cell. 2010 Aug 27;39(4):507-20. doi: 10.1016/j.molcel.2010.08.001. PMID- 11320305 OWN - NLM STAT- MEDLINE DA - 20010523 DCOM- 20010712 LR - 20070724 IS - 0907-4449 (Print) IS - 0907-4449 (Linking) VI - 57 IP - Pt 5 DP - 2001 May TI - Ultrahigh-resolution structure of a BPTI mutant. PG - 649-63 AB - The crystal structure of a mutant of bovine pancreatic trypsin inhibitor has been refined to 0.86 A resolution using low-temperature synchrotron data. The variant contains three mutations in the binding loop (Thr11Ala, Pro13Ala, Lys15Arg) and an unrelated Met52Leu substitution. Refinement with anisotropic displacement parameters and with removal of main-chain stereochemical restraints converged with R = 0.1035. The use of full-matrix refinement provided an estimate of the variances in the derived parameters. Some stereochemical parameters, such as the planarity of the peptide group and the value of the N-C(alpha)-C angle, show a wide spread, suggesting that the standard values used as restraints in protein structure refinements may not always be entirely appropriate. Comparison with the recently determined room-temperature structure of the same mutant at 1.42 A resolution confirms the previous observations and provides new details, such as a double conformation of the main chain at Leu29 and at Gly56-Gly57, a high proportion (over 20%) of residues in double conformations, correlation of disorder through lattice contacts and the positions of H atoms, including those in water molecules, and their involvement in C-H...O and N-H...pi hydrogen bonds. FAU - Addlagatta, A AU - Addlagatta A AD - Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland. FAU - Krzywda, S AU - Krzywda S FAU - Czapinska, H AU - Czapinska H FAU - Otlewski, J AU - Otlewski J FAU - Jaskolski, M AU - Jaskolski M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20010424 PL - Denmark TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (Disulfides) RN - 9087-70-1 (Aprotinin) SB - IM MH - Aprotinin/*chemistry/genetics MH - Disulfides/chemistry MH - Hydrogen Bonding MH - Models, Molecular MH - Mutation MH - Protein Conformation EDAT- 2001/04/26 10:00 MHDA- 2001/07/13 10:01 CRDT- 2001/04/26 10:00 PHST- 2000/11/14 [received] PHST- 2001/02/19 [accepted] PHST- 2001/04/24 [epublish] AID - S0907444901003468 [pii] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2001 May;57(Pt 5):649-63. Epub 2001 Apr 24. PMID- 23029259 OWN - NLM STAT- MEDLINE DA - 20121002 DCOM- 20130228 LR - 20141105 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 9 DP - 2012 TI - GAGE cancer-germline antigens are recruited to the nuclear envelope by germ cell-less (GCL). PG - e45819 LID - 10.1371/journal.pone.0045819 [doi] AB - GAGE proteins are highly similar, primate-specific molecules with unique primary structure and undefined cellular roles. They are restricted to cells of the germ line in adult healthy individuals, but are broadly expressed in a wide range of cancers. In a yeast two-hybrid screen we identified the metazoan transcriptional regulator, Germ cell-less (GCL), as an interaction partner of GAGE12I. GCL directly binds LEM-domain proteins (LAP2beta, emerin, MAN1) at the nuclear envelope, and we found that GAGE proteins were recruited to the nuclear envelope inner membrane by GCL. Based on yeast two-hybrid analysis and pull-down experiments of GCL polypeptides, GCL residues 209-320 (which includes the BACK domain) were deduced sufficient for association with GAGE proteins. GAGE mRNAs and GCL mRNA were demonstrated in human testis and most types of cancers, and at the protein level GAGE members and GCL were co-expressed in cancer cell lines. Structural studies of GAGE proteins revealed no distinct secondary or tertiary structure, suggesting they are intrinsically disordered. Interestingly GAGE proteins formed stable complexes with dsDNA in vitro at physiological concentrations, and GAGE12I bound several different dsDNA fragments, suggesting sequence-nonspecific binding. Dual association of GAGE family members with GCL at the nuclear envelope inner membrane in cells, and with dsDNA in vitro, implicate GAGE proteins in chromatin regulation in germ cells and cancer cells. FAU - Gjerstorff, Morten F AU - Gjerstorff MF AD - Department of Cancer and Inflammation Research, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark. mgjerstorff@health.sdu.dk FAU - Rosner, Heike I AU - Rosner HI FAU - Pedersen, Christina B AU - Pedersen CB FAU - Greve, Katrine B V AU - Greve KB FAU - Schmidt, Steffen AU - Schmidt S FAU - Wilson, Katherine L AU - Wilson KL FAU - Mollenhauer, Jan AU - Mollenhauer J FAU - Besir, Huseyin AU - Besir H FAU - Poulsen, Flemming M AU - Poulsen FM FAU - Mollegaard, Niels Erik AU - Mollegaard NE FAU - Ditzel, Henrik J AU - Ditzel HJ LA - eng GR - R01 GM48646/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120920 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Antigens, Neoplasm) RN - 0 (Chromatin) RN - 0 (GAGE7 protein, human) RN - 0 (GMCL1 protein, human) RN - 0 (Neoplasm Proteins) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) SB - IM MH - Antigens, Neoplasm/chemistry/genetics/*metabolism MH - Cell Line MH - Cell Transformation, Neoplastic/metabolism MH - Chromatin/metabolism MH - Circular Dichroism MH - DNA/chemistry MH - Electrophoretic Mobility Shift Assay MH - Gene Expression MH - Humans MH - Male MH - Neoplasm Proteins/chemistry/genetics/*metabolism MH - Nuclear Envelope/*metabolism MH - Organ Specificity MH - Plasmids/chemistry MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Transport MH - Testis/metabolism MH - Transcription Factors/genetics/*metabolism MH - Two-Hybrid System Techniques PMC - PMC3447759 OID - NLM: PMC3447759 EDAT- 2012/10/03 06:00 MHDA- 2013/03/01 06:00 CRDT- 2012/10/03 06:00 PHST- 2012/04/13 [received] PHST- 2012/08/22 [accepted] PHST- 2012/09/20 [epublish] AID - 10.1371/journal.pone.0045819 [doi] AID - PONE-D-12-10440 [pii] PST - ppublish SO - PLoS One. 2012;7(9):e45819. doi: 10.1371/journal.pone.0045819. Epub 2012 Sep 20. PMID- 20028147 OWN - NLM STAT- MEDLINE DA - 20091223 DCOM- 20100302 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 131 IP - 51 DP - 2009 Dec 30 TI - Determination of the free energy landscape of alpha-synuclein using spin label nuclear magnetic resonance measurements. PG - 18314-26 LID - 10.1021/ja904716h [doi] AB - Natively unfolded proteins present a challenge for structure determination because they populate highly heterogeneous ensembles of conformations. A useful source of structural information about these states is provided by paramagnetic relaxation enhancement measurements by nuclear magnetic resonance spectroscopy, from which long-range interatomic distances can be estimated. Here we describe a method for using such distances as restraints in molecular dynamics simulations to obtain a mapping of the free energy landscapes of natively unfolded proteins. We demonstrate the method in the case of alpha-synuclein and validate the results by a comparison with electron transfer measurements. Our findings indicate that our procedure provides an accurate estimate of the relative statistical weights of the different conformations populated by alpha-synuclein in its natively unfolded state. FAU - Allison, Jane R AU - Allison JR AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK. FAU - Varnai, Peter AU - Varnai P FAU - Dobson, Christopher M AU - Dobson CM FAU - Vendruscolo, Michele AU - Vendruscolo M LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Spin Labels) RN - 0 (alpha-Synuclein) SB - IM MH - Magnetic Resonance Spectroscopy/*methods MH - Methods MH - Molecular Dynamics Simulation MH - Protein Conformation MH - Protein Denaturation MH - *Spin Labels MH - *Thermodynamics MH - alpha-Synuclein/*chemistry EDAT- 2009/12/24 06:00 MHDA- 2010/03/03 06:00 CRDT- 2009/12/24 06:00 AID - 10.1021/ja904716h [doi] PST - ppublish SO - J Am Chem Soc. 2009 Dec 30;131(51):18314-26. doi: 10.1021/ja904716h. PMID- 20580965 OWN - NLM STAT- MEDLINE DA - 20100628 DCOM- 20100927 IS - 1557-7988 (Electronic) IS - 0076-6879 (Linking) VI - 472 DP - 2010 TI - Single-molecule fluorescence studies of intrinsically disordered proteins. PG - 179-204 LID - 10.1016/S0076-6879(10)72010-3 [doi] AB - Intrinsically disordered proteins (IDPs) (also referred to as natively unfolded proteins) play critical roles in a variety of cellular processes such as transcription and translation and also are linked to several human diseases. Biophysical studies of IDPs present unusual experimental challenges due in part to their broad conformational heterogeneity and potentially complex binding-induced folding behavior. By minimizing the averaging over an ensemble (which is typical of most conventional experiments), single-molecule fluorescence (SMF) techniques have recently begun to add advanced capabilities for structural studies to the experimental arsenal of IDP investigators. Here, we briefly discuss a few common SMF methods that are particularly useful for IDP studies, including SMF resonance energy transfer and fluorescence correlation spectroscopy, along with site-specific protein-labeling methods that are essential for application of these methods to IDPs. We then present an overview of a few studies in this area, highlighting how SMF methods are being used to gain valuable information about two amyloidogenic IDPs, the Parkinson's disease-linked alpha-synuclein and the NM domain of the yeast prion protein Sup 35. SMF experiments provided new information about the proteins' rapidly fluctuating IDP forms, and the complex alpha-synuclein folding behavior upon its binding to lipid and membrane mimics. We anticipate that SMF and single-molecule methods, in general, will find broad application for structural and mechanistic studies of a wide variety of IDPs, both of their disordered conformations, and their ordered ensembles relevant for function and disease. CI - Copyright 2010 Elsevier Inc. All rights reserved. FAU - Ferreon, Allan Chris M AU - Ferreon AC AD - Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA. FAU - Moran, Crystal R AU - Moran CR FAU - Gambin, Yann AU - Gambin Y FAU - Deniz, Ashok A AU - Deniz AA LA - eng PT - Journal Article PL - United States TA - Methods Enzymol JT - Methods in enzymology JID - 0212271 RN - 0 (Amino Acids) RN - 0 (Fluorescent Dyes) RN - 0 (Peptide Termination Factors) RN - 0 (Proteins) RN - 0 (SUP35 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acids/chemistry MH - Fluorescence Resonance Energy Transfer/instrumentation/methods MH - Fluorescent Dyes/chemistry MH - Humans MH - Models, Molecular MH - Molecular Structure MH - Peptide Termination Factors/chemistry MH - Protein Binding MH - *Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Proteins/*chemistry MH - Saccharomyces cerevisiae Proteins/chemistry MH - Spectrometry, Fluorescence/instrumentation/*methods MH - Staining and Labeling/methods MH - alpha-Synuclein/chemistry EDAT- 2010/06/29 06:00 MHDA- 2010/09/29 06:00 CRDT- 2010/06/29 06:00 AID - S0076-6879(10)72010-3 [pii] AID - 10.1016/S0076-6879(10)72010-3 [doi] PST - ppublish SO - Methods Enzymol. 2010;472:179-204. doi: 10.1016/S0076-6879(10)72010-3. PMID- 19378261 OWN - NLM STAT- MEDLINE DA - 20090507 DCOM- 20090707 LR - 20131121 IS - 1099-1387 (Electronic) IS - 1075-2617 (Linking) VI - 15 IP - 6 DP - 2009 Jun TI - Folding transitions in calpain activator peptides studied by solution NMR spectroscopy. PG - 404-10 LID - 10.1002/psc.1131 [doi] AB - Calpastatin, the endogenous inhibitor of calpain, a cysteine protease in eukaryotic cells, is an intrinsically unstructured protein, which upon binding to the enzyme goes through a conformational change. Peptides calpA (SGKSGMDAALDDLIDTLGG) and calpC (SKPIGPDDAIDALSSDFTS), corresponding to the two conserved subdomains of calpastatin, are known to activate calpain and increase the Ca(2+) sensitivity of the enzyme. Using solution NMR spectroscopy, here we show that calpA and calpC are disordered in water but assume an alpha-helical conformation in 50% CD(3)OH. The position and length of the helices are in agreement with those described in the literature for the bound state of the corresponding segments of calpastatin suggesting that the latter might be structurally primed for the interaction with its target. According to our data, the presence of Ca(2+) induces a backbone rearrangement in the peptides, an effect that may contribute to setting the fine conformational balance required for the interaction of the peptides with calpain. FAU - Toke, Orsolya AU - Toke O AD - Institute of Structural Chemistry, Chemical Research Center, Hungarian Academy of Sciences, 59-67 Pusztaszeri ut, Budapest, H-1025 Hungary. toke@chemres.hu FAU - Banoczi, Zoltan AU - Banoczi Z FAU - Tarkanyi, Gabor AU - Tarkanyi G FAU - Friedrich, Peter AU - Friedrich P FAU - Hudecz, Ferenc AU - Hudecz F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Pept Sci JT - Journal of peptide science : an official publication of the European Peptide Society JID - 9506309 RN - 0 (Calcium-Binding Proteins) RN - 0 (Peptides) RN - 79079-11-1 (calpastatin) RN - EC 3.4.22.- (Calpain) RN - SY7Q814VUP (Calcium) SB - IM MH - Calcium/pharmacology MH - Calcium-Binding Proteins/chemistry MH - Calpain/*metabolism MH - Enzyme Activation/drug effects MH - Magnetic Resonance Spectroscopy/*methods MH - Peptides/*chemistry/*pharmacology MH - Protein Binding/drug effects MH - Protein Conformation/drug effects MH - Protein Folding MH - Protein Structure, Secondary EDAT- 2009/04/21 09:00 MHDA- 2009/07/08 09:00 CRDT- 2009/04/21 09:00 AID - 10.1002/psc.1131 [doi] PST - ppublish SO - J Pept Sci. 2009 Jun;15(6):404-10. doi: 10.1002/psc.1131. PMID- 23762412 OWN - NLM STAT- MEDLINE DA - 20130613 DCOM- 20140114 LR - 20141113 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 6 DP - 2013 TI - The C-terminal V5 domain of Protein Kinase Calpha is intrinsically disordered, with propensity to associate with a membrane mimetic. PG - e65699 LID - 10.1371/journal.pone.0065699 [doi] AB - The C-terminal V5 domain is one of the most variable domains in Protein Kinase C isoforms (PKCs). V5 confers isoform specificity on its parent enzyme through interactions with isoform-specific adaptor proteins and possibly through specific intra-molecular interactions with other PKC domains. The structural information about V5 domains in solution is sparse. The objective of this work was to determine the conformational preferences of the V5 domain from the alpha isoform of PKC (V5alpha) and evaluate its ability to associate with membrane mimetics. We show that V5alpha and its phosphorylation-mimicking variant, dmV5alpha, are intrinsically disordered protein domains. Phosphorylation-mimicking mutations do not alter the overall conformation of the polypeptide backbone, as evidenced by the local nature of chemical shift perturbations and the secondary structure propensity scores. However, the population of the "cis-trans" conformer of the Thr(638)-Pro(639)-Pro(640) turn motif, which has been implicated in the down-regulation of PKCalpha via peptidyl-prolyl isomerase Pin1, increases in dmV5alpha, along with the conformational flexibility of the region between the turn and hydrophobic motifs. Both wild type and dmV5alpha associate with micelles made of a zwitterionic detergent, n-dodecylphosphocholine. Upon micelle binding, V5alpha acquires a higher propensity to form helical structures at the conserved "NFD" motif and the entire C-terminal third of the domain. The ability of V5alpha to partition into the hydrophobic micellar environment suggests that it may serve as a membrane anchor during the PKC maturation process. FAU - Yang, Yuan AU - Yang Y AD - Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas, United States of America. FAU - Igumenova, Tatyana I AU - Igumenova TI LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130606 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Micelles) RN - 0 (Recombinant Fusion Proteins) RN - 107-73-3 (Phosphorylcholine) RN - 53949-18-1 (dodecylphosphocholine) RN - EC 2.7.11.13 (Protein Kinase C-alpha) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Hydrophobic and Hydrophilic Interactions MH - Mice MH - Micelles MH - *Molecular Dynamics Simulation MH - Molecular Mimicry MH - Molecular Sequence Data MH - Phosphorylation MH - Phosphorylcholine/analogs & derivatives/chemistry MH - Protein Binding MH - Protein Kinase C-alpha/*chemistry/genetics MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/*chemistry/genetics MH - Stereoisomerism PMC - PMC3675085 OID - NLM: PMC3675085 EDAT- 2013/06/14 06:00 MHDA- 2014/01/15 06:00 CRDT- 2013/06/14 06:00 PHST- 2013 [ppublish] PHST- 2013/03/14 [received] PHST- 2013/04/26 [accepted] PHST- 2013/06/06 [epublish] AID - 10.1371/journal.pone.0065699 [doi] AID - PONE-D-13-10517 [pii] PST - epublish SO - PLoS One. 2013 Jun 6;8(6):e65699. doi: 10.1371/journal.pone.0065699. Print 2013. PMID- 24338013 OWN - NLM STAT- MEDLINE DA - 20140210 DCOM- 20140407 LR - 20150212 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 289 IP - 6 DP - 2014 Feb 7 TI - N-terminal acetylation stabilizes N-terminal helicity in lipid- and micelle-bound alpha-synuclein and increases its affinity for physiological membranes. PG - 3652-65 LID - 10.1074/jbc.M113.512459 [doi] AB - The Parkinson disease protein alpha-synuclein is N-terminally acetylated, but most in vitro studies have been performed using unacetylated alpha-synuclein. Binding to lipid membranes is considered key to the still poorly understood function of alpha-synuclein. We report the effects of N-terminal acetylation on alpha-synuclein binding to lipid vesicles of different composition and curvature and to micelles composed of the detergents beta-octyl-glucoside (BOG) and SDS. In the presence of SDS, N-terminal acetylation results in a slightly increased helicity for the N-terminal ~10 residues of the protein, likely due to the stabilization of N-terminal fraying through the formation of a helix cap motif. In the presence of BOG, a detergent used in previous isolations of helical oligomeric forms of alpha-synuclein, the N-terminally acetylated protein adopts a novel conformation in which the N-terminal ~30 residues bind the detergent micelle in a partly helical conformation, whereas the remainder of the protein remains unbound and disordered. Binding of alpha-synuclein to lipid vesicles with high negative charge content is essentially unaffected by N-terminal acetylation irrespective of curvature, but binding to vesicles of lower negative charge content is increased, with stronger binding observed for vesicles with higher curvature. Thus, the naturally occurring N-terminally acetylated form of alpha-synuclein exhibits stabilized helicity at its N terminus and increased affinity for lipid vesicles similar to synaptic vesicles, a binding target of the protein in vivo. Furthermore, the novel BOG-bound state of N-terminally acetylated alpha-synuclein may serve as a model of partly helical membrane-bound intermediates with a role in alpha-synuclein function and dysfunction. FAU - Dikiy, Igor AU - Dikiy I AD - From the Department of Biochemistry and Program in Structural Biology, Weill Cornell Medical College, New York, New York 10065. FAU - Eliezer, David AU - Eliezer D LA - eng GR - CO6RR015495/CO/NCI NIH HHS/United States GR - P41GM066354/GM/NIGMS NIH HHS/United States GR - R01AG025440/AG/NIA NIH HHS/United States GR - R37 AG019391/AG/NIA NIH HHS/United States GR - R37AG019391/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20131212 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Glucosides) RN - 0 (Membranes, Artificial) RN - 0 (Micelles) RN - 0 (SNCA protein, human) RN - 0 (alpha-Synuclein) RN - 29836-26-8 (octyl-beta-D-glucoside) RN - 368GB5141J (Sodium Dodecyl Sulfate) SB - IM MH - Acetylation MH - Glucosides/*chemistry MH - Humans MH - *Membranes, Artificial MH - *Micelles MH - *Models, Molecular MH - Protein Stability MH - Protein Structure, Secondary MH - Sodium Dodecyl Sulfate/*chemistry MH - alpha-Synuclein/*chemistry PMC - PMC3916564 OID - NLM: PMC3916564 OTO - NOTNLM OT - Lipid-binding Protein OT - N-terminal Acetylation OT - Parkinson Disease OT - Post Translational Modification OT - Protein Aggregation OT - Synuclein OT - alpha-Synuclein EDAT- 2013/12/18 06:00 MHDA- 2014/04/08 06:00 CRDT- 2013/12/17 06:00 PHST- 2013/12/12 [aheadofprint] AID - M113.512459 [pii] AID - 10.1074/jbc.M113.512459 [doi] PST - ppublish SO - J Biol Chem. 2014 Feb 7;289(6):3652-65. doi: 10.1074/jbc.M113.512459. Epub 2013 Dec 12. PMID- 11829734 OWN - NLM STAT- MEDLINE DA - 20020206 DCOM- 20020322 LR - 20140612 IS - 0264-6021 (Print) IS - 0264-6021 (Linking) VI - 362 IP - Pt 1 DP - 2002 Feb 15 TI - Cross-talk unfolded: MARCKS proteins. PG - 1-12 AB - The proteins of the MARCKS (myristoylated alanine-rich C kinase substrate) family were first identified as prominent substrates of protein kinase C (PKC). Since then, these proteins have been implicated in the regulation of brain development and postnatal survival, cellular migration and adhesion, as well as endo-, exo- and phago-cytosis, and neurosecretion. The effector domain of MARCKS proteins is phosphorylated by PKC, binds to calmodulin and contributes to membrane binding. This multitude of mutually exclusive interactions allows cross-talk between the signal transduction pathways involving PKC and calmodulin. This review focuses on recent, mostly biophysical and biochemical results renewing interest in this protein family. MARCKS membrane binding is now understood at the molecular level. From a structural point of view, there is a consensus emerging that MARCKS proteins are "natively unfolded". Interestingly, domains similar to the effector domain have been discovered in other proteins. Furthermore, since the effector domain enhances the polymerization of actin in vitro, MARCKS proteins have been proposed to mediate regulation of the actin cytoskeleton. However, the recent observations that MARCKS might serve to sequester phosphatidylinositol 4,5-bisphosphate in the plasma membrane of unstimulated cells suggest an alternative model for the control of the actin cytoskeleton. While myristoylation is classically considered to be a co-translational, irreversible event, new reports on MARCKS proteins suggest a more dynamic picture of this protein modification. Finally, studies with mice lacking MARCKS proteins have investigated the functions of these proteins during embryonic development in the intact organism. FAU - Arbuzova, Anna AU - Arbuzova A AD - Department of Physiology and Biophysics, Health Sciences Center, State University of New York, Stony Brook, NY 11794-8661, U.S.A. FAU - Schmitz, Arndt A P AU - Schmitz AA FAU - Vergeres, Guy AU - Vergeres G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Membrane Proteins) RN - 0 (Proteins) RN - 125267-21-2 (myristoylated alanine-rich C kinase substrate) SB - IM MH - Amino Acid Sequence MH - Animals MH - Humans MH - *Intracellular Signaling Peptides and Proteins MH - *Membrane Proteins MH - Molecular Sequence Data MH - Protein Binding MH - Protein Conformation MH - Proteins/chemistry/*metabolism/physiology MH - *Receptor Cross-Talk RF - 124 PMC - PMC1222354 OID - NLM: PMC1222354 EDAT- 2002/02/07 10:00 MHDA- 2002/03/23 10:01 CRDT- 2002/02/07 10:00 PST - ppublish SO - Biochem J. 2002 Feb 15;362(Pt 1):1-12. PMID- 17397058 OWN - NLM STAT- MEDLINE DA - 20070528 DCOM- 20071231 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 68 IP - 1 DP - 2007 Jul 1 TI - The N- and C-termini of the human Nogo molecules are intrinsically unstructured: bioinformatics, CD, NMR characterization, and functional implications. PG - 100-8 AB - RTN4 or Nogo proteins are composed of three alternative splice forms, namely 1192-residue Nogo-A, 373-residue Nogo-B, and 199-residue Nogo-C. Nogo proteins have received intense attentions because they have been implicated in a variety of critical cellular processes including CNS neuronal regeneration, vascular remodeling, apoptosis, interaction with beta-amyloid protein converting enzyme, and generation/maintenance of the tubular network of the endoplasmic reticulum (ER). Despite their significantly-different N-terminal lengths, they share a conserved C-terminal reticulon-homology domain consisting of two transmembrane fragments, a 66-residue extracellular loop Nogo-66 and a 38-residue C-tail carrying ER retention motif. Nogo-A owns the largest N-terminus with 1016 residues while the Nogo-B has an N-terminus almost identical to the first 200 residues of Nogo-A. So far, except for our previous determination of the Nogo-66 solution structure, no structural characterization of the other Nogo regions has been reported. In the present study, we initiated a systematically investigation of structural properties of Nogo molecules by a combined use of bioinformatics, CD, and NMR spectroscopy. The results led to two striking findings: (1) in agreement with bioinformatics prediction, the N- and C-termini of Nogo-B were experimentally demonstrated to be intrinsically unstructured by CD, two-dimensional 1H 15N NMR HSQC, hydrogen exchange, and 15N heteronuclear NOE characterization. (2) Further studies showed that the 1016-residue N-terminus of Nogo-A was again highly disordered. Therefore, it appears that being intrinsically-unstructured allows Nogo molecules to serve as double-faceted functional players, with one set of functions involved in cellular signaling processes essential for CNS neuronal regeneration, vascular remodeling, apoptosis and so forth and with another in generating/maintaining membrane-related structures. We propose that this mechanism may represent a general strategy to place the formation/maintenance of membrane-related structures under the direct regulation of the cellular signaling. CI - 2007 Wiley-Liss, Inc. FAU - Li, Minfen AU - Li M AD - Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260. FAU - Song, Jianxing AU - Song J LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Myelin Proteins) RN - 0 (Nogo protein) SB - IM MH - Alternative Splicing/*genetics MH - Circular Dichroism MH - Computational Biology MH - Humans MH - Myelin Proteins/*chemistry MH - Nuclear Magnetic Resonance, Biomolecular MH - *Protein Structure, Secondary MH - Structure-Activity Relationship EDAT- 2007/04/03 09:00 MHDA- 2008/01/01 09:00 CRDT- 2007/04/03 09:00 AID - 10.1002/prot.21385 [doi] PST - ppublish SO - Proteins. 2007 Jul 1;68(1):100-8. PMID- 17883245 OWN - NLM STAT- MEDLINE DA - 20071206 DCOM- 20080304 IS - 1075-2617 (Print) IS - 1075-2617 (Linking) VI - 13 IP - 12 DP - 2007 Dec TI - A partially structured region of a largely unstructured protein, Plasmodium falciparum merozoite surface protein 2 (MSP2), forms amyloid-like fibrils. PG - 839-48 AB - Merozoite surface protein 2 (MSP2) from the human malaria parasite Plasmodium falciparum is expressed as a GPI-anchored protein on the merozoite surface. It has been implicated in the process of erythrocyte invasion and is a leading vaccine candidate. MSP2 is an intrinsically unstructured protein (IUP), and recombinant MSP2 forms amyloid-like fibrils upon storage. We have examined synthetic peptides corresponding to sequences in the conserved N-terminal region of MSP2 for the presence of local structure and the ability to form fibrils related to those formed by full-length MSP2. In a 25-residue peptide corresponding to the entire N-terminal region of mature MSP2, structures calculated from NMR data show the presence of nascent helical and turn-like structures. An 8-residue peptide from the central region of the N-terminal domain (residues 8-15) also formed a turn-like structure. Both peptides formed fibrils that were similar but not identical to the amyloid-like fibrils formed by full-length MSP2. Notably, the fibrils formed by the peptides bound both Congo Red and Thioflavin T, whereas the fibrils formed by full-length MSP2 bound only Congo Red. The propensity of peptides from the N-terminal conserved region of MSP2 to form amyloid-like fibrils makes it likely that this region contributes to fibril formation by the full-length protein. Thus, in contrast to the more common pathway of amyloid formation by structured proteins, which proceeds via partially unfolded intermediates that then undergo beta-aggregation, MSP2 is an example of a largely unstructured protein with at least one small structured region that has an important role in fibril formation. FAU - Yang, Xiaodong AU - Yang X AD - The Walter & Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3050, Australia. FAU - Adda, Christopher G AU - Adda CG FAU - Keizer, David W AU - Keizer DW FAU - Murphy, Vince J AU - Murphy VJ FAU - Rizkalla, Michael M AU - Rizkalla MM FAU - Perugini, Matthew A AU - Perugini MA FAU - Jackson, David C AU - Jackson DC FAU - Anders, Robin F AU - Anders RF FAU - Norton, Raymond S AU - Norton RS LA - eng GR - R01AI59229/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - J Pept Sci JT - Journal of peptide science : an official publication of the European Peptide Society JID - 9506309 RN - 0 (Amyloid) RN - 0 (Antigens, Protozoan) RN - 0 (Peptide Fragments) RN - 0 (Protozoan Proteins) RN - 0 (Solutions) RN - 0 (merozoite surface protein 2, Plasmodium) SB - IM MH - Amino Acid Sequence MH - Amyloid/*chemistry MH - Animals MH - Antigens, Protozoan/*chemistry MH - Circular Dichroism/methods MH - Magnetic Resonance Spectroscopy/methods MH - Microscopy, Electron/methods MH - Peptide Fragments/chemical synthesis/*chemistry MH - Plasmodium falciparum/*chemistry MH - Protein Structure, Secondary MH - Protozoan Proteins/chemical synthesis/*chemistry MH - Solutions/chemistry EDAT- 2007/09/22 09:00 MHDA- 2008/03/05 09:00 CRDT- 2007/09/22 09:00 AID - 10.1002/psc.910 [doi] PST - ppublish SO - J Pept Sci. 2007 Dec;13(12):839-48. PMID- 18519038 OWN - NLM STAT- MEDLINE DA - 20080616 DCOM- 20080825 LR - 20131121 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 582 IP - 15 DP - 2008 Jun 25 TI - Calcium-induced tripartite binding of intrinsically disordered calpastatin to its cognate enzyme, calpain. PG - 2149-54 LID - 10.1016/j.febslet.2008.05.032 [doi] AB - The activity of calpain is controlled by the free intracellular calcium level and by the protein's intrinsically disordered endogenous inhibitor, calpastatin, mediated by short conserved segments: subdomains A-C. The exact binding mode of calpastatin to the enzyme has until now been unclear. Our NMR data of the 141 amino acid long inhibitor, with and without calcium and calpain, have revealed structural changes and a tripartite binding mode, in which the disordered inhibitor wraps around, and contacts, the enzyme at three points, facilitated by flexible linkers. This unprecedented binding mode permits a unique combination of specificity, speed and binding strength in regulation. FAU - Kiss, Robert AU - Kiss R AD - Institute of Chemistry, Laboratory of Structural Chemistry and Biology, Eotvos Lorand University, Budapest, Hungary. FAU - Bozoky, Zoltan AU - Bozoky Z FAU - Kovacs, Denes AU - Kovacs D FAU - Rona, Gergely AU - Rona G FAU - Friedrich, Peter AU - Friedrich P FAU - Dvortsak, Peter AU - Dvortsak P FAU - Weisemann, Rudiger AU - Weisemann R FAU - Tompa, Peter AU - Tompa P FAU - Perczel, Andras AU - Perczel A LA - eng GR - ISRF067595/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080602 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Calcium-Binding Proteins) RN - 79079-11-1 (calpastatin) RN - EC 3.4.22.- (Calpain) RN - SY7Q814VUP (Calcium) SB - IM EIN - FEBS Lett. 2008 Aug 6;582(18):2816. Weisemann, Rudinger [corrected to Weisemann, Rudiger] MH - Calcium/*chemistry MH - Calcium-Binding Proteins/*chemistry MH - Calpain/*antagonists & inhibitors/*chemistry MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation EDAT- 2008/06/04 09:00 MHDA- 2008/08/30 09:00 CRDT- 2008/06/04 09:00 PHST- 2008/03/29 [received] PHST- 2008/05/02 [revised] PHST- 2008/05/06 [accepted] PHST- 2008/06/02 [aheadofprint] AID - S0014-5793(08)00456-0 [pii] AID - 10.1016/j.febslet.2008.05.032 [doi] PST - ppublish SO - FEBS Lett. 2008 Jun 25;582(15):2149-54. doi: 10.1016/j.febslet.2008.05.032. Epub 2008 Jun 2. PMID- 23358668 OWN - NLM STAT- MEDLINE DA - 20130418 DCOM- 20131031 IS - 1432-0991 (Electronic) IS - 0343-8651 (Linking) VI - 66 IP - 6 DP - 2013 Jun TI - The secretion of an intrinsically disordered protein with different secretion signals in Bacillus subtilis. PG - 566-72 LID - 10.1007/s00284-013-0315-8 [doi] AB - In this study, a naturally unsecretory intrinsically disordered domain of nucleoskeletal-like protein (Nsp) was attempted to be secreted with different types of secretion signals in Bacillus subtilis. The results showed that Nsp can be secreted efficiently by all selected Sec-type signal peptides. Nsp was successfully exported when fused to Tat-type signal peptides but less efficient than Sec-type. The fusion protein with the non-classical extracellular proteins can be detected in the cell and extracellular milieu. This study further demonstrated that the mature protein plays an important role in protein secretion. Moreover, these results indicated that Nsp could be a useful tool to understand the individual roles of mature proteins and signal peptide in protein secretion, to evaluate the effect of conformation of mature proteins on their export pathway when coupled with Tat-type signal peptide, and to seek the signal of non-classical secretory proteins. FAU - Wang, Guangqiang AU - Wang G AD - State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, People's Republic of China. FAU - Chen, Haiqin AU - Chen H FAU - Zhang, Hao AU - Zhang H FAU - Song, Yuanda AU - Song Y FAU - Chen, Wei AU - Chen W LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130129 PL - United States TA - Curr Microbiol JT - Current microbiology JID - 7808448 RN - 0 (Bacterial Proteins) RN - 0 (Protein Sorting Signals) SB - IM MH - Bacillus subtilis/*metabolism MH - Bacterial Proteins/*chemistry/genetics/*metabolism MH - Protein Sorting Signals MH - Protein Transport MH - Signal Transduction EDAT- 2013/01/30 06:00 MHDA- 2013/11/01 06:00 CRDT- 2013/01/30 06:00 PHST- 2012/10/28 [received] PHST- 2013/01/12 [accepted] PHST- 2013/01/29 [aheadofprint] AID - 10.1007/s00284-013-0315-8 [doi] PST - ppublish SO - Curr Microbiol. 2013 Jun;66(6):566-72. doi: 10.1007/s00284-013-0315-8. Epub 2013 Jan 29. PMID- 23670046 OWN - NLM STAT- MEDLINE DA - 20131024 DCOM- 20140403 LR - 20140701 IS - 1554-8635 (Electronic) IS - 1554-8627 (Linking) VI - 9 IP - 7 DP - 2013 Jul TI - What the N-terminal domain of Atg13 looks like and what it does: a HORMA fold required for PtdIns 3-kinase recruitment. PG - 1112-4 LID - 10.4161/auto.24896 [doi] AB - Atg13 is a subunit of the Atg1 complex that is involved in autophagy. The middle and C-terminal regions of Atg13 are intrinsically disordered and rich in regulatory phosphorylation sites. Thus far, there have been no structural data for any part of Atg13, and no function assigned to its N-terminal domain. We crystallized this domain, and found that it has a HORMA (Hop1, Rev7, Mad2) fold. We showed that the Atg13 HORMA domain is required for autophagy and for recruitment of the phosphatidylinositol (PtdIns) 3-kinase subunit Atg14, but is not required for Atg1 interaction or Atg13 recruitment to the PAS. The HORMA domain of Atg13 is similar to the closed conformation of the spindle checkpoint protein Mad2. A pair of conserved arginines was identified in the structure, and tested functionally in yeast. These residues are important for autophagy, as mutations abrogate autophagy and block Atg14 recruitment. The location of these Arg residues in the structure suggests that the Atg13 HORMA domain could act as a phosphorylation-dependent conformational switch. FAU - Jao, Christine C AU - Jao CC AD - Laboratory of Molecular Biology; National Institute of Diabetes and Digestive and Kidney Diseases; National Institutes of Health; Bethesda, MD USA. FAU - Ragusa, Michael J AU - Ragusa MJ FAU - Stanley, Robin E AU - Stanley RE FAU - Hurley, James H AU - Hurley JH LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't DEP - 20130502 PL - United States TA - Autophagy JT - Autophagy JID - 101265188 RN - 0 (Adaptor Proteins, Signal Transducing) RN - EC 2.7.1.137 (Phosphatidylinositol 3-Kinase) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry/*metabolism MH - Models, Molecular MH - Phosphatidylinositol 3-Kinase/*metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Structure-Activity Relationship MH - Yeasts/metabolism PMC - PMC3722324 OID - NLM: PMC3722324 OTO - NOTNLM OT - Atg13 OT - Atg14 OT - HORMA OT - protein crystallography OT - protein degradation OT - protein structure OT - yeast genetics EDAT- 2013/05/15 06:00 MHDA- 2014/04/04 06:00 CRDT- 2013/05/15 06:00 PHST- 2013/05/02 [aheadofprint] AID - 24896 [pii] AID - 10.4161/auto.24896 [doi] PST - ppublish SO - Autophagy. 2013 Jul;9(7):1112-4. doi: 10.4161/auto.24896. Epub 2013 May 2. PMID- 23740998 OWN - NLM STAT- MEDLINE DA - 20130729 DCOM- 20131018 LR - 20141113 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 87 IP - 16 DP - 2013 Aug TI - A novel hepacivirus with an unusually long and intrinsically disordered NS5A protein in a wild Old World primate. PG - 8971-81 LID - 10.1128/JVI.00888-13 [doi] AB - GB virus B (GBV-B; family Flaviviridae, genus Hepacivirus) has been studied in New World primates as a model for human hepatitis C virus infection, but the distribution of GBV-B and its relatives in nature has remained obscure. Here, we report the discovery of a novel and highly divergent GBV-B-like virus in an Old World monkey, the black-and-white colobus (Colobus guereza), in Uganda. The new virus, guereza hepacivirus (GHV), clusters phylogenetically with GBV-B and recently described hepaciviruses infecting African bats and North American rodents, and it shows evidence of ancient recombination with these other hepaciviruses. Direct sequencing of reverse-transcribed RNA from blood plasma from three of nine colobus monkeys yielded near-complete GHV genomes, comprising two distinct viral variants. The viruses contain an exceptionally long nonstructural 5A (NS5A) gene, approximately half of which codes for a protein with no discernible homology to known proteins. Computational structure-based analyses indicate that the amino terminus of the GHV NS5A protein may serve a zinc-binding function, similar to the NS5A of other viruses within the family Flaviviridae. However, the 521-amino-acid carboxy terminus is intrinsically disordered, reflecting an unusual degree of structural plasticity and polyfunctionality. These findings shed new light on the natural history and evolution of the hepaciviruses and on the extent of structural variation within the Flaviviridae. FAU - Lauck, Michael AU - Lauck M AD - Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA. FAU - Sibley, Samuel D AU - Sibley SD FAU - Lara, James AU - Lara J FAU - Purdy, Michael A AU - Purdy MA FAU - Khudyakov, Yury AU - Khudyakov Y FAU - Hyeroba, David AU - Hyeroba D FAU - Tumukunde, Alex AU - Tumukunde A FAU - Weny, Geoffrey AU - Weny G FAU - Switzer, William M AU - Switzer WM FAU - Chapman, Colin A AU - Chapman CA FAU - Hughes, Austin L AU - Hughes AL FAU - Friedrich, Thomas C AU - Friedrich TC FAU - O'Connor, David H AU - O'Connor DH FAU - Goldberg, Tony L AU - Goldberg TL LA - eng SI - GENBANK/KC551800 SI - GENBANK/KC551801 SI - GENBANK/KC551802 GR - R01 AI098420/AI/NIAID NIH HHS/United States GR - TW009237/TW/FIC NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130605 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (RNA, Viral) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Animals MH - Cluster Analysis MH - Colobus MH - Computer Simulation MH - GB virus B/chemistry/*genetics/*isolation & purification MH - Genome, Viral MH - Hepatitis C/*veterinary/virology MH - Models, Molecular MH - Molecular Sequence Data MH - Phylogeny MH - Primate Diseases/*virology MH - Protein Conformation MH - RNA, Viral/genetics MH - Sequence Analysis, DNA MH - Uganda MH - Viral Nonstructural Proteins/chemistry/*genetics PMC - PMC3754081 OID - NLM: PMC3754081 EDAT- 2013/06/07 06:00 MHDA- 2013/10/19 06:00 CRDT- 2013/06/07 06:00 PHST- 2013/06/05 [aheadofprint] AID - JVI.00888-13 [pii] AID - 10.1128/JVI.00888-13 [doi] PST - ppublish SO - J Virol. 2013 Aug;87(16):8971-81. doi: 10.1128/JVI.00888-13. Epub 2013 Jun 5. PMID- 9915794 OWN - NLM STAT- MEDLINE DA - 19990303 DCOM- 19990303 LR - 20081121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 274 IP - 5 DP - 1999 Jan 29 TI - Stability and DNA binding of the phd protein of the phage P1 plasmid addiction system. PG - 2652-7 AB - The plasmid addiction module of bacteriophage P1 encodes two proteins, Doc, a toxin that is stable to proteolytic degradation, and Phd, the toxin's antidote that is proteolytically unstable. Phd has been shown to autoregulate its expression by specific DNA binding. Here, we investigate the secondary structure and thermal stability of Phd, the effect of operator DNA binding on the structure and stability of Phd, and the stoichiometry, affinity, and cooperativity of Phd binding to operator subsites and intact operator DNA. Phd folds as a monomer at low temperatures or in the presence of osmolytes but exists predominantly in an unfolded conformation at 37 degreesC. The native state of Phd is stabilized by operator binding. Two Phd monomers bind to each operator subsite, and four monomers bind to the intact operator. The subsite binding reaction shows a second-order dependence on protein concentration and monomer-bound DNA species are unpopulated, suggesting that two Phd molecules bind cooperatively to each operator subsite. In intact operator binding experiments, both dimer-bound and tetramer-bound DNA species are populated, and binding occurs at protein concentrations similar to those required for subsite binding, suggesting that there is no significant dimer-dimer cooperativity. FAU - Gazit, E AU - Gazit E AD - Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. FAU - Sauer, R T AU - Sauer RT LA - eng GR - AI-15706/AI/NIAID NIH HHS/United States GR - AI-16892/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA, Viral) RN - 0 (Doc protein, Enterobacteria phage P1) RN - 0 (Phd protein, Enterobacteria phage P1) RN - 0 (Viral Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Bacteriophage P1/*metabolism MH - Base Sequence MH - Circular Dichroism MH - DNA/*metabolism MH - DNA, Viral/metabolism MH - Dimerization MH - Escherichia coli MH - Hot Temperature MH - Molecular Sequence Data MH - Operon MH - Plasmids/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Viral Proteins/*metabolism EDAT- 1999/01/23 MHDA- 1999/01/23 00:01 CRDT- 1999/01/23 00:00 PST - ppublish SO - J Biol Chem. 1999 Jan 29;274(5):2652-7. PMID- 15341732 OWN - NLM STAT- MEDLINE DA - 20040902 DCOM- 20050516 LR - 20071114 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 12 IP - 9 DP - 2004 Sep TI - Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with CP-640186. PG - 1683-91 AB - Acetyl-coenzyme A carboxylases (ACCs) are important targets for the development of therapeutic agents against obesity, diabetes, and other diseases. CP-640186 is a potent inhibitor of mammalian ACCs and can reduce body weight and improve insulin sensitivity in test animals. It is believed to target the carboxyltransferase (CT) domain of these enzymes. Here we report the crystal structure of the yeast CT domain in complex with CP-640186. The inhibitor is bound in the active site at the interface of a dimer of the CT domain. CP-640186 has tight interactions with the putative biotin binding site in the CT domain and demonstrates a distinct mode of inhibiting the CT activity as compared to the herbicides that inhibit plant ACCs. The affinity of inhibitors for the CT domain has been assessed using kinetic and fluorescence anisotropy binding studies. The structural information identifies three regions for drug binding in the active site of CT. FAU - Zhang, Hailong AU - Zhang H AD - Department of Biological Sciences, Columbia University, New York, NY 10027, USA. FAU - Tweel, Benjamin AU - Tweel B FAU - Li, Jiang AU - Li J FAU - Tong, Liang AU - Tong L LA - eng SI - PDB/1W2X GR - DK67238/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (3-(2-methoxy-5-trifluoromethoxybenzyl)amino-1-methyl-2-phenylpiperidine) RN - 0 (CP-640186) RN - 0 (Isoenzymes) RN - 0 (Morpholines) RN - 0 (Piperidines) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 6.4.1.2 (Acetyl-CoA Carboxylase) SB - IM MH - Acetyl-CoA Carboxylase/*antagonists & inhibitors/*chemistry/metabolism MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Crystallography, X-Ray MH - Humans MH - Isoenzymes/chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Molecular Structure MH - Morpholines/*chemistry/metabolism MH - Piperidines/*chemistry/metabolism MH - Protein Binding MH - *Protein Structure, Tertiary MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism MH - Sequence Alignment EDAT- 2004/09/03 05:00 MHDA- 2005/05/17 09:00 CRDT- 2004/09/03 05:00 PHST- 2004/05/18 [received] PHST- 2004/07/01 [revised] PHST- 2004/07/02 [accepted] AID - 10.1016/j.str.2004.07.009 [doi] AID - S0969212604002783 [pii] PST - ppublish SO - Structure. 2004 Sep;12(9):1683-91. PMID- 22339436 OWN - NLM STAT- MEDLINE DA - 20120315 DCOM- 20120706 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 116 IP - 10 DP - 2012 Mar 15 TI - Insights into structural properties of denatured human prion 121-230 at melting temperature studied by replica exchange molecular dynamics. PG - 3305-12 LID - 10.1021/jp208433w [doi] AB - Misfolding and aggregation of the prion protein (PrP) is responsible for the development of fatal transmissible neurodegenerative diseases. PrP undergoes structural conversion from a natively folded state into a misfolded state, resulting in aggregated amyloid fibrils. Partial unfolding has been recognized as an essential step in fibrillation, especially at the middle point of unfolding. To study the possible aggregation-prone states, we characterized the structure of the C-terminal globular domain of human prion (huPrP) 121-230 near extended conformation at melting temperature by replica exchange molecular dynamics (REMD) simulation, as the REMD method is the most suited generalized-ensemble algorithm that performs random walk in energy space and promotes a system to escape from local energy traps. Our results revealed that denatured huPrP is partially folded with alpha-helical structure at melting temperature. The simulation results provide further insight into the unfolding of prion, which is essential in pathogenesis of prion diseases. CI - (c) 2012 American Chemical Society FAU - Tang, Jaw-Luen AU - Tang JL AD - Department of Physics, National Chung Cheng University, Ming-Hsiung Chia-Yi, Taiwan 62102, ROC. FAU - Wu, Po-Jen AU - Wu PJ FAU - Wang, Shing-Chuen AU - Wang SC FAU - Lee, Cheng-I AU - Lee CI LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120302 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Prions) RN - 0 (Recombinant Proteins) SB - IM MH - Circular Dichroism MH - Cluster Analysis MH - Humans MH - *Molecular Dynamics Simulation MH - Prions/*chemistry/genetics/metabolism MH - Protein Structure, Secondary MH - Protein Unfolding MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Thermodynamics MH - Transition Temperature EDAT- 2012/02/22 06:00 MHDA- 2012/07/07 06:00 CRDT- 2012/02/21 06:00 PHST- 2012/03/02 [aheadofprint] AID - 10.1021/jp208433w [doi] PST - ppublish SO - J Phys Chem B. 2012 Mar 15;116(10):3305-12. doi: 10.1021/jp208433w. Epub 2012 Mar 2. PMID- 4472093 OWN - NLM STAT- MEDLINE DA - 19741219 DCOM- 19741219 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 249 IP - 18 DP - 1974 Sep 25 TI - Effects of cation binding on the conformation of calsequestrin and the high affinity calcium-binding protein of sarcoplasmic reticulum. PG - 5867-71 FAU - Ostwald, T J AU - Ostwald TJ FAU - MacLennan, D H AU - MacLennan DH FAU - Dorrington, K J AU - Dorrington KJ LA - eng PT - Journal Article PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Muscle Proteins) RN - 42HK56048U (Tyrosine) RN - 47E5O17Y3R (Phenylalanine) RN - 8DUH1N11BX (Tryptophan) RN - SY7Q814VUP (Calcium) SB - IM MH - Animals MH - Calcium/administration & dosage/*metabolism/pharmacology MH - Circular Dichroism MH - Hydrogen-Ion Concentration MH - Muscle Proteins/*metabolism MH - Muscles/cytology MH - Osmolar Concentration MH - Phenylalanine MH - *Protein Binding MH - Protein Conformation MH - Rabbits MH - Sarcoplasmic Reticulum/*metabolism MH - Spectrophotometry, Ultraviolet MH - Tryptophan MH - Tyrosine EDAT- 1974/09/25 MHDA- 1974/09/25 00:01 CRDT- 1974/09/25 00:00 PST - ppublish SO - J Biol Chem. 1974 Sep 25;249(18):5867-71. PMID- 24970895 OWN - NLM STAT- MEDLINE DA - 20140823 DCOM- 20141216 LR - 20150401 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 289 IP - 33 DP - 2014 Aug 15 TI - The C-terminal tails of the bacterial chaperonin GroEL stimulate protein folding by directly altering the conformation of a substrate protein. PG - 23219-32 LID - 10.1074/jbc.M114.577205 [doi] AB - Many essential cellular proteins fold only with the assistance of chaperonin machines like the GroEL-GroES system of Escherichia coli. However, the mechanistic details of assisted protein folding by GroEL-GroES remain the subject of ongoing debate. We previously demonstrated that GroEL-GroES enhances the productive folding of a kinetically trapped substrate protein through unfolding, where both binding energy and the energy of ATP hydrolysis are used to disrupt the inhibitory misfolded states. Here, we show that the intrinsically disordered yet highly conserved C-terminal sequence of the GroEL subunits directly contributes to substrate protein unfolding. Interactions between the C terminus and the non-native substrate protein alter the binding position of the substrate protein on the GroEL apical surface. The C-terminal tails also impact the conformational state of the substrate protein during capture and encapsulation on the GroEL ring. Importantly, removal of the C termini results in slower overall folding, reducing the fraction of the substrate protein that commits quickly to a productive folding pathway and slowing several kinetically distinct folding transitions that occur inside the GroEL-GroES cavity. The conserved C-terminal tails of GroEL are thus important for protein folding from the beginning to the end of the chaperonin reaction cycle. CI - (c) 2014 by The American Society for Biochemistry and Molecular Biology, Inc. FAU - Weaver, Jeremy AU - Weaver J AD - From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843. FAU - Rye, Hays S AU - Rye HS AD - From the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843 haysrye@tamu.edu. LA - eng GR - GM065421/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140625 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Chaperonin 10) RN - 0 (Chaperonin 60) RN - 0 (Escherichia coli Proteins) RN - 0 (Oligopeptides) RN - 103131-69-7 (kinetensin) SB - IM MH - Chaperonin 10/chemistry/genetics/metabolism MH - Chaperonin 60/*chemistry/genetics/metabolism MH - Escherichia coli/*chemistry/genetics/metabolism MH - Escherichia coli Proteins/*chemistry/genetics/metabolism MH - Oligopeptides MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Tertiary PMC - PMC4132819 OID - NLM: PMC4132819 [Available on 08/15/15] OTO - NOTNLM OT - Chaperone OT - Chaperonin OT - GroEL OT - Hsp60 OT - Molecular Chaperone OT - Protein Dynamic OT - Protein Folding OT - Protein Misfolding EDAT- 2014/06/28 06:00 MHDA- 2014/12/17 06:00 CRDT- 2014/06/28 06:00 PMCR- 2015/08/15 00:00 PHST- 2014/06/25 [aheadofprint] AID - M114.577205 [pii] AID - 10.1074/jbc.M114.577205 [doi] PST - ppublish SO - J Biol Chem. 2014 Aug 15;289(33):23219-32. doi: 10.1074/jbc.M114.577205. Epub 2014 Jun 25. PMID- 22700979 OWN - NLM STAT- MEDLINE DA - 20120730 DCOM- 20121011 LR - 20141016 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 31 DP - 2012 Jul 27 TI - The human selenoprotein VCP-interacting membrane protein (VIMP) is non-globular and harbors a reductase function in an intrinsically disordered region. PG - 26388-99 LID - 10.1074/jbc.M112.346775 [doi] AB - The human selenoprotein VIMP (VCP-interacting membrane protein)/SelS (selenoprotein S) localizes to the endoplasmic reticulum (ER) membrane and is involved in the process of ER-associated degradation (ERAD). To date, little is known about the presumed redox activity of VIMP, its structure and how these features might relate to the function of the protein in ERAD. Here, we use the recombinantly expressed cytosolic region of VIMP where the selenocysteine (Sec) in position 188 is replaced with a cysteine (a construct named cVIMP-Cys) to characterize redox and structural properties of the protein. We show that Cys-188 in cVIMP-Cys forms a disulfide bond with Cys-174, consistent with the presence of a Cys174-Sec188 selenosulfide bond in the native sequence. For the disulfide bond in cVIMP-Cys we determined the reduction potential to -200 mV, and showed it to be a good substrate of thioredoxin. Based on a biochemical and structural characterization of cVIMP-Cys using analytical gel filtration, CD and NMR spectroscopy in conjunction with bioinformatics, we propose a comprehensive overall structural model for the cytosolic region of VIMP. The data clearly indicate the N-terminal half to be comprised of two extended alpha-helices followed by a C-terminal region that is intrinsically disordered. Redox-dependent conformational changes in cVIMP-Cys were observed only in the vicinity of the two Cys residues. Overall, the redox properties observed for cVIMP-Cys are compatible with a function as a reductase, and we speculate that the plasticity of the intrinsically disordered C-terminal region allows the protein to access many different and structurally diverse substrates. FAU - Christensen, Lea Cecilie AU - Christensen LC AD - Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N., Denmark. FAU - Jensen, Njal Winther AU - Jensen NW FAU - Vala, Andrea AU - Vala A FAU - Kamarauskaite, Jurate AU - Kamarauskaite J FAU - Johansson, Linda AU - Johansson L FAU - Winther, Jakob Rahr AU - Winther JR FAU - Hofmann, Kay AU - Hofmann K FAU - Teilum, Kaare AU - Teilum K FAU - Ellgaard, Lars AU - Ellgaard L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120614 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Membrane Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Selenoproteins) RN - 0 (VIMP protein, human) RN - 48TCX9A1VT (Cystine) RN - 52500-60-4 (Thioredoxins) RN - EC 1.- (Oxidoreductases) SB - IM MH - Amino Acid Sequence MH - Catalytic Domain MH - Chromatography, Gel MH - Circular Dichroism MH - Cystine/chemistry MH - Escherichia coli MH - Membrane Proteins/biosynthesis/*chemistry/isolation & purification MH - Molecular Sequence Data MH - Molecular Weight MH - Oxidation-Reduction MH - Oxidoreductases/biosynthesis/*chemistry/isolation & purification MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/biosynthesis/chemistry/isolation & purification MH - Selenoproteins/biosynthesis/*chemistry/isolation & purification MH - Thioredoxins/chemistry PMC - PMC3406722 OID - NLM: PMC3406722 EDAT- 2012/06/16 06:00 MHDA- 2012/10/12 06:00 CRDT- 2012/06/16 06:00 PHST- 2012/06/14 [aheadofprint] AID - M112.346775 [pii] AID - 10.1074/jbc.M112.346775 [doi] PST - ppublish SO - J Biol Chem. 2012 Jul 27;287(31):26388-99. doi: 10.1074/jbc.M112.346775. Epub 2012 Jun 14. PMID- 16483603 OWN - NLM STAT- MEDLINE DA - 20060313 DCOM- 20060502 LR - 20140916 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 357 IP - 4 DP - 2006 Apr 7 TI - Modular enzyme design: regulation by mutually exclusive protein folding. PG - 1058-62 AB - A regulatory mechanism is introduced whereupon the catalytic activity of a given enzyme is controlled by ligand binding to a receptor domain of choice. A small enzyme (barnase) and a ligand-binding polypeptide (GCN4) are fused so that a simple topological constraint prevents them from existing simultaneously in their folded states. The two domains consequently engage in a thermodynamic tug-of-war in which the more stable domain forces the less stable domain to unfold. In the absence of ligand, the barnase domain is more stable and is therefore folded and active; the GCN4 domain is substantially unstructured. DNA binding induces folding of GCN4, forcibly unfolding and inactivating the barnase domain. Barnase-GCN4 is thus a "natively unfolded" protein that uses ligand binding to switch between partially folded forms. The key characteristics of each parent protein (catalytic efficiency of barnase, DNA binding affinity and sequence specificity of GCN4) are retained in the chimera. Barnase-GCN4 thus defines a modular approach for assembling enzymes with novel sensor capabilities from a variety of catalytic and ligand binding domains. FAU - Ha, Jeung-Hoi AU - Ha JH AD - Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, 750 E. Adams St, Syracuse, NY 13210, USA. FAU - Butler, James S AU - Butler JS FAU - Mitrea, Diana M AU - Mitrea DM FAU - Loh, Stewart N AU - Loh SN LA - eng GR - GM 069755/GM/NIGMS NIH HHS/United States GR - R01 GM069755/GM/NIGMS NIH HHS/United States GR - R01 GM069755-07/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20060206 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Basic-Leucine Zipper Transcription Factors) RN - 0 (DNA-Binding Proteins) RN - 0 (GCN4 protein, S cerevisiae) RN - 0 (Ligands) RN - 0 (Peptides) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Transcription Factors) RN - EC 3.1.- (Ribonucleases) RN - EC 3.1.4.- (Bacillus amyloliquefaciens ribonuclease) SB - IM MH - Animals MH - Basic-Leucine Zipper Transcription Factors MH - Catalytic Domain MH - DNA-Binding Proteins/*chemistry/genetics/metabolism MH - Ligands MH - Models, Molecular MH - Peptides/chemistry/genetics/metabolism MH - Protein Binding MH - *Protein Conformation MH - *Protein Folding MH - Recombinant Fusion Proteins/*chemistry/genetics/metabolism MH - Ribonucleases/*chemistry/genetics/metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism MH - Thermodynamics MH - Transcription Factors/*chemistry/genetics/metabolism PMC - PMC3145369 MID - NIHMS311540 OID - NLM: NIHMS311540 OID - NLM: PMC3145369 EDAT- 2006/02/18 09:00 MHDA- 2006/05/04 09:00 CRDT- 2006/02/18 09:00 PHST- 2005/11/16 [received] PHST- 2006/01/10 [revised] PHST- 2006/01/19 [accepted] PHST- 2006/02/06 [aheadofprint] AID - S0022-2836(06)00114-8 [pii] AID - 10.1016/j.jmb.2006.01.073 [doi] PST - ppublish SO - J Mol Biol. 2006 Apr 7;357(4):1058-62. Epub 2006 Feb 6. PMID- 21970344 OWN - NLM STAT- MEDLINE DA - 20111101 DCOM- 20111220 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 50 IP - 44 DP - 2011 Nov 8 TI - Phosphorylation of Thellungiella salsuginea dehydrins TsDHN-1 and TsDHN-2 facilitates cation-induced conformational changes and actin assembly. PG - 9587-604 LID - 10.1021/bi201205m [doi] AB - Group 2 late embryogenesis abundant (LEA) proteins, also known as dehydrins, are intrinsically disordered proteins that are expressed in plants experiencing extreme environmental conditions such as drought or low temperatures. These proteins are characterized by the presence of at least one conserved, lysine-rich K-segment and sometimes by one or more serine-rich S-segments that are phosphorylated. Dehydrins may stabilize proteins and membrane structures during environmental stress and can sequester and scavenge metal ions. Here, we investigate how the conformations of two dehydrins from Thellungiella salsuginea, denoted as TsDHN-1 (acidic) and TsDHN-2 (basic), are affected by pH, interactions with cations and membranes, and phosphorylation. Both TsDHN-1 and TsDHN-2 were expressed as SUMO fusion proteins for in vitro phosphorylation by casein kinase II (CKII), and structural analysis by circular dichroism and attenuated total reflection-Fourier transform infrared spectroscopy. We show that the polyproline II conformation can be induced in the dehydrins by their environmental conditions, including changes in the concentration of divalent cations such as Ca(2+). The assembly of actin by these dehydrins was assessed by sedimentation assays and viewed by transmission electron and atomic force microscopy. Phosphorylation allowed both dehydrins to polymerize actin filaments. These results support the hypothesis that dehydrins stabilize the cytoskeleton under stress conditions and further that phosphorylation may be an important feature of this stabilization. FAU - Rahman, Luna N AU - Rahman LN AD - Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada. FAU - Smith, Graham S T AU - Smith GS FAU - Bamm, Vladimir V AU - Bamm VV FAU - Voyer-Grant, Janine A M AU - Voyer-Grant JA FAU - Moffatt, Barbara A AU - Moffatt BA FAU - Dutcher, John R AU - Dutcher JR FAU - Harauz, George AU - Harauz G LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111010 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Actins) RN - 0 (Cations, Divalent) RN - 0 (Plant Proteins) RN - 0 (Protein Isoforms) RN - 134711-03-8 (dehydrin proteins, plant) RN - J41CSQ7QDS (Zinc) RN - SY7Q814VUP (Calcium) SB - IM MH - Actins/*chemistry/*metabolism MH - Brassicaceae/chemistry/metabolism MH - Calcium/*chemistry MH - Cations, Divalent MH - Hydrogen-Ion Concentration MH - Phosphorylation MH - Plant Proteins/*chemistry/*metabolism MH - Protein Conformation MH - Protein Isoforms/chemistry/metabolism MH - Zinc/*chemistry EDAT- 2011/10/06 06:00 MHDA- 2011/12/21 06:00 CRDT- 2011/10/06 06:00 PHST- 2011/10/10 [aheadofprint] AID - 10.1021/bi201205m [doi] PST - ppublish SO - Biochemistry. 2011 Nov 8;50(44):9587-604. doi: 10.1021/bi201205m. Epub 2011 Oct 10. PMID- 12840750 OWN - NLM STAT- MEDLINE DA - 20030703 DCOM- 20030801 LR - 20131121 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 424 IP - 6944 DP - 2003 Jul 3 TI - Structure of the core domain of human cardiac troponin in the Ca(2+)-saturated form. PG - 35-41 AB - Troponin is essential in Ca(2+) regulation of skeletal and cardiac muscle contraction. It consists of three subunits (TnT, TnC and TnI) and, together with tropomyosin, is located on the actin filament. Here we present crystal structures of the core domains (relative molecular mass of 46,000 and 52,000) of human cardiac troponin in the Ca(2+)-saturated form. Analysis of the four-molecule structures reveals that the core domain is further divided into structurally distinct subdomains that are connected by flexible linkers, making the entire molecule highly flexible. The alpha-helical coiled-coil formed between TnT and TnI is integrated in a rigid and asymmetric structure (about 80 angstrom long), the IT arm, which bridges putative tropomyosin-anchoring regions. The structures of the troponin ternary complex imply that Ca(2+) binding to the regulatory site of TnC removes the carboxy-terminal portion of TnI from actin, thereby altering the mobility and/or flexibility of troponin and tropomyosin on the actin filament. FAU - Takeda, Soichi AU - Takeda S AD - Laboratory for Structural Biochemistry, RIKEN Harima Institute at SPring-8, Mikazuki, Sayo, Hyogo, Japan. stakeda@ri.ncvc.go.jp FAU - Yamashita, Atsuko AU - Yamashita A FAU - Maeda, Kayo AU - Maeda K FAU - Maeda, Yuichiro AU - Maeda Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Protein Subunits) RN - 0 (Tropomyosin) RN - 0 (Troponin) RN - 0 (Troponin C) RN - 0 (Troponin I) RN - 0 (Troponin T) RN - SY7Q814VUP (Calcium) SB - IM MH - Calcium/*metabolism MH - Crystallography, X-Ray MH - Humans MH - Models, Molecular MH - Pliability MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Subunits/chemistry/metabolism MH - Tropomyosin/chemistry/metabolism MH - Troponin/*chemistry/*metabolism MH - Troponin C/chemistry/metabolism MH - Troponin I/chemistry/metabolism MH - Troponin T/chemistry/metabolism EDAT- 2003/07/04 05:00 MHDA- 2003/08/02 05:00 CRDT- 2003/07/04 05:00 PHST- 2002/12/24 [received] PHST- 2003/04/28 [accepted] AID - 10.1038/nature01780 [doi] AID - nature01780 [pii] PST - ppublish SO - Nature. 2003 Jul 3;424(6944):35-41. PMID- 9346936 OWN - NLM STAT- MEDLINE DA - 19971209 DCOM- 19971209 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 272 IP - 44 DP - 1997 Oct 31 TI - Crystal structure of rat Bcl-xL. Implications for the function of the Bcl-2 protein family. PG - 27886-92 AB - Bcl-xL is a member of the Bcl-2 protein family, which regulates apoptosis. Preparation of recombinant rat Bcl-xL yielded two forms, one deamidated at -Asn-Gly- sequences to produce isoaspartates and the other not deamidated. The crystal structures of the two forms show that they both adopt an essentially identical backbone structure which resembles the fold of human Bcl-xL: three layers of two alpha-helices each, capped at one end by two short helices. Both forms have a long disordered region, which contains the potential deamidation sites. The molecular structure exhibits a low level of interhelical interactions, the presence of three cavities, and a notable hydrophobic cleft surrounded by walls rich in basic residues. These unique structural features may be favorable for its accommodation into membranes or for possible rearrangement to modulate homo-/heterodimerization. Homology modeling of Bcl-2 and Bax, based on the Bcl-xL structure, suggests that Bax has the strongest potential for membrane insertion. Furthermore, we found a possible interface for interaction with non-Bcl-2 family member proteins, such as CED-4 homologues. FAU - Aritomi, M AU - Aritomi M AD - Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita-city, Osaka 565, Japan. FAU - Kunishima, N AU - Kunishima N FAU - Inohara, N AU - Inohara N FAU - Ishibashi, Y AU - Ishibashi Y FAU - Ohta, S AU - Ohta S FAU - Morikawa, K AU - Morikawa K LA - eng SI - PDB/1AF3 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (BCL2L1 protein, human) RN - 0 (Bcl2l1 protein, rat) RN - 0 (Proto-Oncogene Proteins c-bcl-2) RN - 0 (bcl-X Protein) RN - 30KYC7MIAI (Aspartic Acid) SB - IM MH - Animals MH - Aspartic Acid/*chemistry MH - Crystallography, X-Ray MH - Humans MH - Protein Conformation MH - Proto-Oncogene Proteins c-bcl-2/*chemistry MH - Rats MH - Sequence Homology, Amino Acid MH - bcl-X Protein EDAT- 1997/11/05 MHDA- 1997/11/05 00:01 CRDT- 1997/11/05 00:00 PST - ppublish SO - J Biol Chem. 1997 Oct 31;272(44):27886-92. PMID- 18954556 OWN - NLM STAT- MEDLINE DA - 20081028 DCOM- 20090522 LR - 20140722 IS - 1672-7681 (Print) IS - 1672-7681 (Linking) VI - 5 IP - 5 DP - 2008 Oct TI - Rwdd1, a thymus aging related molecule, is a new member of the intrinsically unstructured protein family. PG - 333-9 LID - 10.1038/cmi.2008.41 [doi] AB - We had previously identified a novel protein termed Rwdd1 whose expression in thymus is decreased in aged or oxidatively stressed mice. In the present study, we found that Rwdd1 expressed in both prokaryotic and eukaryotic cells showed a slower migration rate on SDS-PAGE gel. In addition, Rwdd1 was more sensitive to proteinase proteolysis. Furthermore, being a highly acidic protein which contains an RWD domain, Rwdd1 shared a high level of sequence similarity with Gir2, a member of the intrinsically unstructured protein (IUP). These findings suggest that Rwdd1 is a novel member of the IUP family. FAU - Kang, Ning AU - Kang N AD - Department of Immunology, School of Basic Medicine, Peking Union Medical College, and Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China. FAU - Chen, Dai AU - Chen D FAU - Wang, Li AU - Wang L FAU - Duan, Lian AU - Duan L FAU - Liu, Shirong AU - Liu S FAU - Tang, Long AU - Tang L FAU - Liu, Qingfeng AU - Liu Q FAU - Cui, Lianxian AU - Cui L FAU - He, Wei AU - He W LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - China TA - Cell Mol Immunol JT - Cellular & molecular immunology JID - 101242872 RN - 0 (Proteins) RN - 0 (Rwdd1 protein, mouse) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cell Line MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - Mice MH - Molecular Sequence Data MH - Protein Folding MH - Proteins/*chemistry/genetics MH - Thymus Gland/*physiology PMC - PMC4073699 OID - NLM: PMC4073699 EDAT- 2008/10/29 09:00 MHDA- 2009/05/23 09:00 CRDT- 2008/10/29 09:00 AID - 10.1038/cmi.2008.41 [doi] PST - ppublish SO - Cell Mol Immunol. 2008 Oct;5(5):333-9. doi: 10.1038/cmi.2008.41. PMID- 20025277 OWN - NLM STAT- MEDLINE DA - 20100120 DCOM- 20100325 IS - 1520-5118 (Electronic) IS - 0021-8561 (Linking) VI - 58 IP - 2 DP - 2010 Jan 27 TI - Caseins: utilizing molecular chaperone properties to control protein aggregation in foods. PG - 685-93 LID - 10.1021/jf903072g [doi] AB - Denaturation and aggregation of proteins are reactions that are relevant to functional applications of proteins in foods. Depending on concentration, ionic strength, and pH, aggregation can result in turbidity, precipitation, or gelation. Aggregation may be desirable, as in the case of gelation, or undesirable, as in the case when it causes phase separation in beverages. One approach to improve the stability of globular proteins against heat stresses is through the addition of other compounds that alter aggregation. Numerous studies have shown the ability of molecular chaperones to assist proper folding/unfolding and assembly/disassembly of proteins, especially during stressed conditions. Recently, several papers have reported the molecular chaperone-like properties of caseins, especially using alpha(s)- and beta-caseins. Caseins appear to function like small heat shock proteins (sHSP). We have compared the results among investigations from the perspective of food processing conditions and related them to the mechanism for sHSP. Caseins possess three of the four common features among sHSP; lacking a similar sequence domain. Their function may be explained in part by having structures fitting the intrinsically unfolded class of proteins. With a few exceptions, most investigations were done at solution conditions that poorly represent foods; lacking investigations at pH < 4.5 and concentrations above 20 mg/mL. While it is clear that caseins can alter aggregation at neutral pH, their effectiveness at low pH, high protein concentration, and high thermal treatment (T >or= 100 degrees C) remains to be fully established. FAU - Yong, Yie Hui AU - Yong YH AD - Department of Food, Bioprocessing and Nutrition Sciences, Southeast Dairy Foods Research Center, Box 7624, North Carolina State University, Raleigh, North Carolina 27695-7624, USA. FAU - Foegeding, E Allen AU - Foegeding EA LA - eng PT - Journal Article PL - United States TA - J Agric Food Chem JT - Journal of agricultural and food chemistry JID - 0374755 RN - 0 (Caseins) RN - 0 (Milk Proteins) RN - 0 (Molecular Chaperones) RN - 0 (Proteins) RN - 0 (whey protein) SB - IM MH - Animals MH - Caseins/*chemistry MH - Cattle MH - Chickens MH - *Food Technology MH - Milk Proteins/chemistry MH - Molecular Chaperones/*chemistry MH - Protein Folding MH - Proteins/chemistry EDAT- 2009/12/23 06:00 MHDA- 2010/03/26 06:00 CRDT- 2009/12/23 06:00 AID - 10.1021/jf903072g [doi] PST - ppublish SO - J Agric Food Chem. 2010 Jan 27;58(2):685-93. doi: 10.1021/jf903072g. PMID- 17972286 OWN - NLM STAT- MEDLINE DA - 20080402 DCOM- 20080502 LR - 20081121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 71 IP - 2 DP - 2008 May 1 TI - Modeling the accessible conformations of the intrinsically unstructured transactivation domain of p53. PG - 587-98 AB - Internuclear distances derived from paramagnetic relaxation enhancement (PRE) data were used to restrain molecular dynamics simulations of the intrinsically unstructured transactivation domain of the tumor suppressor protein, p53. About 1000 structures were simulated using ensemble averaging of replicate molecules to compensate for the inherent bias in the PRE-derived distances. Gyration radii measurements on these structures show that the p53 transactivation domain (p53TAD) is statistically predominantly in a partially collapsed state that is unlike the open structure that is found for p53TAD bound to either the E3 ubiquitin ligase, MDM2, or the 70 kDa subunit of replication protein A, RPA70. Contact regions that potentially mediate the collapse were identified and found to consist of mostly hydrophobic residues. The identified contact regions preferentially place the MDM2 and RPA70 binding regions in close proximity. We show that our simulations thoroughly sample the available range of conformations and that a fraction of the molecules are in an open state that would be competent for binding either MDM2 or RPA70. We also show that the Stokes radius estimated from the average gyration radius of the ensemble is in good agreement with the value determined using size exclusion chromatography. Finally, the presence of a persistent loop localized to a PXP motif was identified. Serine residues flanking the PXP motif become phosphorylated in response to DNA damage, and we postulate that this will perturb the equilibrium population to more open conformations. FAU - Lowry, David F AU - Lowry DF AD - Department of Microbiology, Molecular Biology, and Biochemistry, University of Idaho, Life Science South Rm. 140, Moscow, Idaho 83844-3052, USA. FAU - Stancik, Amber AU - Stancik A FAU - Shrestha, Ranjay Mann AU - Shrestha RM FAU - Daughdrill, Gary W AU - Daughdrill GW LA - eng GR - P20 RR 16448/RR/NCRR NIH HHS/United States GR - P20 RR 16454-02/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Spin Labels) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Computer Simulation MH - Humans MH - Models, Chemical MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Protein Structure, Tertiary MH - Spin Labels MH - *Transcriptional Activation MH - Tumor Suppressor Protein p53/*chemistry EDAT- 2007/11/01 09:00 MHDA- 2008/05/03 09:00 CRDT- 2007/11/01 09:00 AID - 10.1002/prot.21721 [doi] PST - ppublish SO - Proteins. 2008 May 1;71(2):587-98. PMID- 21853163 OWN - NLM STAT- MEDLINE DA - 20111202 DCOM- 20120320 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Role of an intrinsically disordered conformation in AMPK-mediated phosphorylation of ULK1 and regulation of autophagy. PG - 91-6 LID - 10.1039/c1mb05265a [doi] AB - Recently, it has been established that there is a direct link between adenosine monophosphate activated protein kinase (AMPK), which is an energy sensor and is activated by glucose starvation, and Unc-51-like kinase 1 (ULK1) in triggering autophagy. Proper phosphorylation of ULK1 is crucial for ULK1/AMPK association and subsequent ULK1 functions in response to nutrient deprivation. Signaling modulated via phosphorylation often involves a flexible/unstructured or an intrinsically disordered (ID) region of proteins. Structural analyses of the ULK1 protein suggest that most of its functionally important phosphorylation sites are located in an ID region. We propose that this ID nature facilitates AMPK-mediated phosphorylation of ULK1, which may provide a mechanism for ULK1 functions in response to nutrient deprivation. Understanding how an ID region of ULK1 modulates its post-translational modifications through AMPK in regulating allosteric coupling will significantly help in defining the cellular and molecular mechanisms involved in ULK1/AMPK functions and in regulation of autophagy. FAU - Khan, Shagufta H AU - Khan SH AD - Department of Basic Sciences, The Commonwealth Medical College, Scranton, PA 18509, USA. FAU - Kumar, Raj AU - Kumar R LA - eng PT - Journal Article PT - Review DEP - 20110818 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - EC 2.7.11.1 (AMP-Activated Protein Kinases) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - AMP-Activated Protein Kinases/*metabolism MH - Animals MH - *Autophagy MH - Humans MH - Phosphorylation MH - Protein Conformation MH - *Protein Folding MH - Protein-Serine-Threonine Kinases/*chemistry/*metabolism EDAT- 2011/08/20 06:00 MHDA- 2012/03/21 06:00 CRDT- 2011/08/20 06:00 PHST- 2011/08/18 [aheadofprint] PHST- 2011/12/01 [epublish] AID - 10.1039/c1mb05265a [doi] PST - ppublish SO - Mol Biosyst. 2012 Jan;8(1):91-6. doi: 10.1039/c1mb05265a. Epub 2011 Aug 18. PMID- 9510255 OWN - NLM STAT- MEDLINE DA - 19980324 DCOM- 19980324 LR - 20061115 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 392 IP - 6671 DP - 1998 Mar 5 TI - The 1.7 A crystal structure of the regulator of chromosome condensation (RCC1) reveals a seven-bladed propeller. PG - 97-101 AB - The gene encoding the regulator of chromosome condensation (RCC1) was cloned by virtue of its ability to complement the temperature-sensitive phenotype of the hamster cell line tsBN2, which undergoes premature chromosome condensation or arrest in the G1 phase of the cell cycle at non-permissive temperatures. RCC1 homologues have been identified in many eukaryotes, including budding and fission yeast. Mutations in the gene affect pre-messenger RNA processing and transport, mating, initiation of mitosis and chromatin decondensation, suggesting that RCC1 is important in the control of nucleo-cytoplasmic transport and the cell cycle. Biochemically, RCC1 is a guanine-nucleotide-exchange factor for the nuclear Ras homologue Ran; it increases the dissociation of Ran-bound GDP by 10(5)-fold. It may also bind to DNAvia a protein-protein complex. Here we show that the structure of human RCC1, solved to 1.7-A resolution by X-ray crystallography, consists of a seven-bladed propeller formed from internal repeats of 51-68 residues per blade. The sequence and structure of the repeats differ from those of WD40-domain proteins, which also form seven-bladed propellers and include the beta-subunits of G proteins. The nature of the structure explains the consequences of a wide range of known mutations. The region of the protein that is involved in guanine-nucleotide exchange is located opposite the region that is thought to be involved in chromosome binding. FAU - Renault, L AU - Renault L AD - Abteilung Strukturelle Biologie, Max-Planck-Institut fur Molekulare Physiologie, Dortmund, Germany. FAU - Nassar, N AU - Nassar N FAU - Vetter, I AU - Vetter I FAU - Becker, J AU - Becker J FAU - Klebe, C AU - Klebe C FAU - Roth, M AU - Roth M FAU - Wittinghofer, A AU - Wittinghofer A LA - eng SI - PDB/A12 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Cell Cycle Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Guanine Nucleotide Exchange Factors) RN - 0 (Nuclear Proteins) RN - 0 (RCC1 protein, human) RN - 0 (Recombinant Proteins) RN - 146-91-8 (Guanosine Diphosphate) SB - IM MH - Amino Acid Sequence MH - Animals MH - *Cell Cycle Proteins MH - Cell Line MH - Cloning, Molecular MH - Cricetinae MH - Crystallography, X-Ray MH - DNA-Binding Proteins/*chemistry/genetics MH - Drosophila MH - *Guanine Nucleotide Exchange Factors MH - Guanosine Diphosphate/metabolism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - *Nuclear Proteins MH - Protein Conformation MH - Recombinant Proteins/chemistry/genetics MH - Schizosaccharomyces/genetics MH - Sequence Homology, Amino Acid EDAT- 1998/03/24 03:02 MHDA- 2001/03/23 10:01 CRDT- 1998/03/24 03:02 AID - 10.1038/32204 [doi] PST - ppublish SO - Nature. 1998 Mar 5;392(6671):97-101. PMID- 17082188 OWN - NLM STAT- MEDLINE DA - 20061225 DCOM- 20070212 LR - 20140907 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 52 DP - 2006 Dec 29 TI - Structural reorganization and the cooperative binding of single-stranded telomere DNA in Sterkiella nova. PG - 40124-34 AB - In Sterkiella nova, alpha and beta telomere proteins bind cooperatively with single-stranded DNA to form a ternary alpha.beta.DNA complex. Association of telomere protein subunits is DNA-dependent, and alpha-beta association enhances DNA affinity. To further understand the molecular basis for binding cooperativity, we characterized several possible stepwise assembly pathways using isothermal titration calorimetry. In one path, alpha and DNA first form a stable alpha.DNA complex followed by the addition of beta in a second step. Binding energy accumulates with nearly equal free energy of association for each of these steps. Heat capacity is nonetheless dramatically different, with DeltaCp = -305 +/- 3 cal mol(-1) K(-1) for alpha binding with DNA and DeltaCp = -2010 +/- 20 cal mol(-1) K(-1) for the addition of beta to complete the alpha.beta.DNA complex. By examining alternate routes including titration of single-stranded DNA with a preformed alpha.beta complex, a significant portion of binding energy and heat capacity could be assigned to structural reorganization involving protein-protein interactions and repositioning of the DNA. Structural reorganization probably affords a mechanism to regulate high affinity binding of telomere single-stranded DNA with important implications for telomere biology. Regulation of telomere complex dissociation is thought to involve post-translational modifications in the lysine-rich C-terminal portion of beta. We observed no difference in binding energetics or crystal structure when comparing complexes prepared with full-length beta or a C-terminally truncated form, supporting interesting parallels between the intrinsically disordered regions of histones and this portion of beta. FAU - Buczek, Pawel AU - Buczek P AD - Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA. FAU - Horvath, Martin P AU - Horvath MP LA - eng SI - PDB/2I0Q GR - 5P30 CA42014/CA/NCI NIH HHS/United States GR - CA92584/CA/NCI NIH HHS/United States GR - R01 GM067994/GM/NIGMS NIH HHS/United States GR - R01 GM067994-01/GM/NIGMS NIH HHS/United States GR - R01 GM067994-02/GM/NIGMS NIH HHS/United States GR - R01 GM067994-03/GM/NIGMS NIH HHS/United States GR - R01 GM067994-04/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20061102 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA, Protozoan) RN - 0 (DNA, Single-Stranded) RN - 0 (Histones) RN - 0 (Telomere-Binding Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Animals MH - Binding Sites/genetics MH - Calorimetry MH - Crystallography, X-Ray MH - DNA/*chemistry/metabolism MH - DNA, Protozoan/*chemistry/metabolism MH - DNA, Single-Stranded/*chemistry/metabolism MH - G-Quadruplexes MH - Histones/chemistry/genetics/metabolism MH - Nucleic Acid Conformation MH - *Oxytricha MH - Protein Processing, Post-Translational/genetics MH - Telomere/*chemistry/metabolism MH - Telomere-Binding Proteins/chemistry/metabolism MH - Thermodynamics PMC - PMC2910716 MID - NIHMS69173 OID - NLM: NIHMS69173 OID - NLM: PMC2910716 EDAT- 2006/11/04 09:00 MHDA- 2007/02/13 09:00 CRDT- 2006/11/04 09:00 PHST- 2006/11/02 [aheadofprint] AID - M607749200 [pii] AID - 10.1074/jbc.M607749200 [doi] PST - ppublish SO - J Biol Chem. 2006 Dec 29;281(52):40124-34. Epub 2006 Nov 2. PMID- 25135664 OWN - NLM STAT- In-Data-Review DA - 20141011 LR - 20150127 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1838 IP - 12 DP - 2014 Dec TI - Conformational heterogeneity of alpha-synuclein in membrane. PG - 3107-17 LID - 10.1016/j.bbamem.2014.08.012 [doi] LID - S0005-2736(14)00294-6 [pii] AB - alpha-Synuclein (alphaS) is a natively disordered protein in solution, thought to be involved in the fusion of neurotransmitter vesicles to cellular membranes during neurotransmission. Monomeric alphaS has been previously characterized in two distinct membrane-associated conformations: a broken-helix structure, and an extended helix. By employing atomistic molecular dynamics and a novel membrane representation with significantly enhanced lipid mobility (HMMM), we investigate the process of spontaneous membrane binding of alphaS and the conformational dynamics of monomeric alphaS in its membrane-bound form. By repeatedly placing helical alphaS monomers in solution above a planar lipid bilayer and observing their spontaneous association and its spontaneous insertion into the membrane during twenty independent unbiased simulations, we are able to characterize alphaS in its membrane-bound state, suggesting that alphaS has a highly variable membrane insertion depth at equilibrium. Our simulations also capture two distinct states of alphaS, the starting broken-helix conformation seen in the micelle bound NMR structures, and a semi-extended helix. Analysis of lipid distributions near alphaS monomers indicates that the transition to a semi-extended helix is facilitated by concentration of phosphatidyl-serine headgroups along the inner edge of the protein. Such a lipid-mediated transition between helix-turn-helix and extended conformations of alphaS may also occur in vivo, and may be important for the physiological function of alphaS. CI - Copyright (c) 2014 Elsevier B.V. All rights reserved. FAU - Vermaas, Josh V AU - Vermaas JV AD - Beckman Institute for Advanced Science and Technology, Department of Biochemistry, College of Medicine, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. FAU - Tajkhorshid, Emad AU - Tajkhorshid E AD - Beckman Institute for Advanced Science and Technology, Department of Biochemistry, College of Medicine, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Electronic address: emad@life.illinois.edu. LA - eng GR - P41 GM104601/GM/NIGMS NIH HHS/United States GR - R01 GM086749/GM/NIGMS NIH HHS/United States GR - R01 GM101048/GM/NIGMS NIH HHS/United States GR - U54 GM087519/GM/NIGMS NIH HHS/United States PT - Journal Article DEP - 20140816 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 SB - IM PMC - PMC4194229 MID - NIHMS623833 OID - NLM: NIHMS623833 [Available on 12/01/15] OID - NLM: PMC4194229 [Available on 12/01/15] OTO - NOTNLM OT - HMMM OT - Membrane binding OT - Molecular dynamics OT - Peripheral membrane protein OT - alpha-Synuclein EDAT- 2014/08/20 06:00 MHDA- 2014/08/20 06:00 CRDT- 2014/08/20 06:00 PMCR- 2015/12/01 00:00 PHST- 2014/03/26 [received] PHST- 2014/08/09 [revised] PHST- 2014/08/11 [accepted] PHST- 2014/08/16 [aheadofprint] AID - S0005-2736(14)00294-6 [pii] AID - 10.1016/j.bbamem.2014.08.012 [doi] PST - ppublish SO - Biochim Biophys Acta. 2014 Dec;1838(12):3107-17. doi: 10.1016/j.bbamem.2014.08.012. Epub 2014 Aug 16. PMID- 23532302 OWN - NLM STAT- MEDLINE DA - 20130508 DCOM- 20140218 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 9 IP - 6 DP - 2013 Jun TI - Molecular dynamic simulations of the tubulin-human gamma synuclein complex: structural insight into the regulatory mechanism involved in inducing resistance against Taxol. PG - 1470-88 LID - 10.1039/c3mb25427e [doi] AB - Members of the synuclein family (alpha, beta and gamma synucleins) are intrinsically disordered in nature and play a crucial role in the progression of various neurodegenerative disorders and cancers. The association of gammaSyn with both BubR1 as well as microtubule subunits renders resistance against various anti-cancer drugs. However, the structural aspects underlying drug resistance have not been explored. In this study, the mechanism involved in the association between gammaSyn and microtubule subunits (alphabetaTub) was investigated and the results reveal a strong interaction between gammaSyn and the tail regions of alphabetaTub. Complexation of gammaSyn induces conformational rearrangements in the nucleotide binding loops (NBL), interdomain and tail regions of both alpha and betaTub. Moreover, in betaTub, the massive displacement observed in M and S loops significantly alters the binding site of microtubule targeting drugs like Taxol. The resulting weak association between Taxol and betaTub of the gammaSyn-alphabetaTub complex was confirmed by molecular dynamic simulation studies. In addition, the effect of Taxol on NBL, M and S loops of alphabetaTub, is reversed in the presence of gammaSyn. These results clearly indicate that the presence of gammaSyn annulled the allosteric regulation imposed by Taxol on the alphabetaTub complex as well as preventing the binding of microtubule targeting drugs, which eventually leads to the development of resistance against these drugs in cancer cells. FAU - Panneerselvam, Manivel AU - Panneerselvam M AD - Centre for Bioinformatics, School of Life sciences, Pondicherry University, Puducherry-605 014, India. FAU - Muthu, Kannan AU - Muthu K FAU - Jayaraman, Muthukumaran AU - Jayaraman M FAU - Sridharan, Upasana AU - Sridharan U FAU - Jenardhanan, Pranitha AU - Jenardhanan P FAU - Ramadas, Krishna AU - Ramadas K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130327 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Antineoplastic Agents) RN - 0 (Tubulin) RN - 0 (gamma-Synuclein) RN - 33069-62-4 (Paclitaxel) RN - EC 2.7.11.1 (BUB1 protein, human) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - Allosteric Regulation MH - Antineoplastic Agents/*metabolism/*pharmacology MH - Binding Sites MH - Drug Resistance, Neoplasm MH - Humans MH - Molecular Dynamics Simulation MH - Paclitaxel/*metabolism/*pharmacology MH - Protein Binding MH - Protein Structure, Quaternary MH - Protein-Serine-Threonine Kinases/metabolism MH - Tubulin/chemistry/*metabolism MH - gamma-Synuclein/chemistry/*metabolism EDAT- 2013/03/28 06:00 MHDA- 2014/02/19 06:00 CRDT- 2013/03/28 06:00 PHST- 2013/03/27 [aheadofprint] PHST- 2013/05/07 [epublish] AID - 10.1039/c3mb25427e [doi] PST - ppublish SO - Mol Biosyst. 2013 Jun;9(6):1470-88. doi: 10.1039/c3mb25427e. Epub 2013 Mar 27. PMID- 7628623 OWN - NLM STAT- MEDLINE DA - 19950907 DCOM- 19950907 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 368 IP - 2 DP - 1995 Jul 17 TI - The three-dimensional structure of thymidine kinase from herpes simplex virus type 1. PG - 289-92 AB - Recombinant thymidine kinase from Herpes simplex virus type 1 (ATP:thymidine 5'-phosphotransferase; EC 2.7.1.21), an enzyme of therapeutic importance, was purified and crystallized in an N-terminally truncated but still fully active form. The three-dimensional structure was solved by X-ray diffraction analysis at 3.0 A resolution using isomorphous replacement. The chain fold is presented together with the bound substrates thymidine and ATP. Three chain segments at the surface could not be located. The chain fold, the location of the substrates and presumbly also the catalytic mechanism resemble the well-known adenylate kinases. FAU - Wild, K AU - Wild K AD - Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Freiburg im Breisgau, Germany. FAU - Bohner, T AU - Bohner T FAU - Aubry, A AU - Aubry A FAU - Folkers, G AU - Folkers G FAU - Schulz, G E AU - Schulz GE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Recombinant Fusion Proteins) RN - EC 2.7.1.21 (Thymidine Kinase) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Crystallization MH - Crystallography, X-Ray MH - Herpesvirus 1, Human/*enzymology MH - Molecular Sequence Data MH - *Protein Conformation MH - Protein Folding MH - Recombinant Fusion Proteins/chemistry MH - Thymidine Kinase/*chemistry EDAT- 1995/07/17 MHDA- 1995/07/17 00:01 CRDT- 1995/07/17 00:00 AID - 0014-5793(95)00680-8 [pii] PST - ppublish SO - FEBS Lett. 1995 Jul 17;368(2):289-92. PMID- 23421682 OWN - NLM STAT- MEDLINE DA - 20130220 DCOM- 20131029 LR - 20141116 IS - 1948-7193 (Electronic) IS - 1948-7193 (Linking) VI - 4 IP - 2 DP - 2013 Feb 20 TI - The structures of the E22Delta mutant-type amyloid-beta alloforms and the impact of E22Delta mutation on the structures of the wild-type amyloid-beta alloforms. PG - 310-20 LID - 10.1021/cn300149j [doi] AB - Structural differences between the intrinsically disordered fibrillogenic wild-type Abeta40 and Abeta42 peptides are linked to Alzheimer's disease. Recently, the E22Delta genetic missense mutation was detected in patients exhibiting Alzheimer's-disease type dementia. However, detailed knowledge about the E22Delta mutant-type Abeta40 and Abeta42 alloform structures as well as the differences from the wild-type Abeta40 and Abeta42 alloform structures is currently lacking. In this study, we present the structures of the E22Delta mutant-type Abeta40 and Abeta42 alloforms as well as the impact of E22Delta mutation on the wild-type Abeta40 and Abeta42 alloform structures. For this purpose, we performed extensive microsecond-time scale parallel tempering molecular dynamics simulations coupled with thermodynamic calculations. For studying the residual secondary structure component transition stabilities, we developed and applied a new theoretical strategy in our studies. We find that the E22Delta mutant-type Abeta40 might have a higher tendency toward aggregation due to more abundant beta-sheet formation in the C-terminal region in comparison to the E22Delta mutant-type Abeta42 peptide. More abundant alpha-helix is formed in the mid-domain regions of the E22Delta mutant-type Abeta alloforms rather than in their wild-type forms. The turn structure at Ala21-Ala30 of the wild-type Abeta, which has been linked to the aggregation process, is less abundant upon E22Delta mutation of both Abeta alloforms. Intramolecular interactions between the N-terminal and central hydrophobic core (CHC), N- and C-terminal, and CHC and C-terminal regions are less abundant or disappear in the E22Delta mutant-type Abeta alloform structures. The thermodynamic trends indicate that the wild-type Abeta42 tends to aggregate more than the wild-type Abeta40 peptide, which is in agreement with experiments. However, this trend is vice versa for the E22Delta mutant-type alloforms. The structural properties of the E22Delta mutant-type Abeta40 and Abeta42 peptides reported herein may prove useful for the development of new drugs to block the formation of toxic E22Delta mutant-type oligomers by either stabilizing helical or destabilizing beta-sheet structure in the C-terminal region of these two mutant alloforms. FAU - Coskuner, Orkid AU - Coskuner O AD - Department of Chemistry, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA. FAU - Wise-Scira, Olivia AU - Wise-Scira O FAU - Perry, George AU - Perry G FAU - Kitahara, Taizo AU - Kitahara T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20121218 PL - United States TA - ACS Chem Neurosci JT - ACS chemical neuroscience JID - 101525337 RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (1-40)) RN - 0 (amyloid beta-protein (1-42)) SB - IM MH - Alzheimer Disease/*genetics MH - Amyloid beta-Peptides/*chemistry/genetics/metabolism MH - Humans MH - Molecular Dynamics Simulation MH - Mutation, Missense MH - Peptide Fragments/*chemistry/genetics/metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary PMC - PMC3582298 OID - NLM: PMC3582298 EDAT- 2013/02/21 06:00 MHDA- 2013/10/30 06:00 CRDT- 2013/02/21 06:00 PHST- 2012/12/18 [aheadofprint] AID - 10.1021/cn300149j [doi] PST - ppublish SO - ACS Chem Neurosci. 2013 Feb 20;4(2):310-20. doi: 10.1021/cn300149j. Epub 2012 Dec 18. PMID- 9653037 OWN - NLM STAT- MEDLINE DA - 19980803 DCOM- 19980803 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 280 IP - 1 DP - 1998 Jul 3 TI - Crystal structure of lambda-Cro bound to a consensus operator at 3.0 A resolution. PG - 137-51 AB - The structure of the Cro protein from bacteriophage lambda in complex with a 19 base-pair DNA duplex that includes the 17 base-pair consensus operator has been determined at 3.0 A resolution. The structure confirms the large changes in the protein and DNA seen previously in a crystallographically distinct low-resolution structure of the complex and, for the first time, reveals the detailed interactions between the side-chains of the protein and the base-pairs of the operator. Relative to the crystal structure of the free protein, the subunits of Cro rotate 53 degrees with respect to each other on binding DNA. At the same time the DNA is bent by 40 degrees through the 19 base-pairs. The intersubunit connection includes a region within the protein core that is structurally reminiscent of the "ball and socket" motif seen in the immunoglobulins and T-cell receptors. The crystal structure of the Cro complex is consistent with virtually all available biochemical and related data. Some of the interactions between Cro and DNA proposed on the basis of model-building are now seen to be correct, but many are different. Tests of the original model by mutagenesis and biochemical analysis corrected some but not all of the errors. Within the limitations of the crystallographic resolution it appears that operator recognition is achieved almost entirely by direct hydrogen-bonding and van der Waals contacts between the protein and the exposed bases within the major groove of the DNA. The discrimination of Cro between the operators OR3 and OR1, which differ in sequence at just three positions, is inferred to result from a combination of small differences, both favorable and unfavorable. A van der Waals contact at one of the positions is of primary importance, while the other two provide smaller, indirect effects. Direct hydrogen bonding is not utilized in this distinction. CI - Copyright 1998 Academic Press. FAU - Albright, R A AU - Albright RA AD - Institute of Molecular Biology Howard Hughes Medical Institute and Department of Physics, University of Oregon, Eugene, OR, 97403-1229, USA. FAU - Matthews, B W AU - Matthews BW LA - eng GR - GM20066/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DNA-Binding Proteins) RN - 0 (Phosphates) RN - 0 (Repressor Proteins) RN - 0 (Viral Proteins) RN - 0 (Viral Regulatory and Accessory Proteins) RN - 0 (phage repressor proteins) RN - 681HV46001 (Ribose) SB - IM MH - Bacteriophage lambda/*metabolism MH - Base Composition MH - Crystallography, X-Ray MH - DNA-Binding Proteins/*chemistry/metabolism MH - Hydrogen Bonding MH - Models, Molecular MH - *Nucleic Acid Conformation MH - *Operator Regions, Genetic MH - Phosphates/metabolism MH - *Protein Conformation MH - Repressor Proteins/*chemistry/metabolism MH - Ribose/metabolism MH - Viral Proteins MH - Viral Regulatory and Accessory Proteins EDAT- 1998/07/07 MHDA- 1998/07/07 00:01 CRDT- 1998/07/07 00:00 AID - S0022-2836(98)91848-4 [pii] AID - 10.1006/jmbi.1998.1848 [doi] PST - ppublish SO - J Mol Biol. 1998 Jul 3;280(1):137-51. PMID- 22301802 OWN - NLM STAT- MEDLINE DA - 20120306 DCOM- 20120629 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 4 DP - 2012 Apr TI - Forced homodimerization of the c-Fos leucine zipper in designed bHLHZ-like hybrid proteins MaxbHLH-Fos and ArntbHLH-Fos. PG - 1286-96 LID - 10.1039/c2mb05354c [doi] AB - Although the c-Fos leucine zipper (LZ) does not form a homodimer in its native basic region/leucine zipper (bZIP) structure, we found that it is capable of homodimerization and promoting protein folding in engineered basic region/helix-loop-helix/leucine zipper (bHLHZ) hybrid proteins MaxbHLH-Fos and ArntbHLH-Fos, in which the bHLH subdomains of Max and Arnt are fused to the c-Fos LZ. By using the in vivo yeast one-hybrid system and in vitro circular dichroism and quantitative fluorescence anisotropy, we demonstrated that attachment of the c-Fos LZ to the otherwise unstructured MaxbHLH resulted in a hybrid bHLHZ-like protein now competent for homodimerization and DNA binding at the cognate E-box site, CACGTG. In ArntbHLH-Fos, the c-Fos LZ promoted proper folding of the HLH structure, although unlike MaxbHLH, ArntbHLH alone is capable of homodimerization and DNA binding. In addition, by comparing the E-box binding and secondary structures of MaxbHLH-Fos and two derivatives containing targeted mutations in the c-Fos LZ, we found that cooperative communication exists between the bHLH and LZ: proper folding of the four-helix bundle in the HLH region could be induced by the c-Fos LZ, and the HLH dimerization region could force homodimerization of the c-Fos LZ. These results demonstrate that although intrinsically unfavorable, the c-Fos LZ can homodimerize, demonstrating that the same c-Fos LZ element can yield orthogonal differences in structure and/or DNA-binding function within different transcription factor families, including the bZIP and bHLHZ. FAU - Chen, Gang AU - Chen G AD - Department of Chemistry, University of Toronto, Mississauga, Ontario, Canada L5L 1C6. FAU - De Jong, Antonia T AU - De Jong AT FAU - Shin, Jumi A AU - Shin JA LA - eng GR - R01 GM069041/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120202 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (DNA-Binding Proteins) RN - 0 (Proto-Oncogene Proteins c-fos) RN - 0 (Recombinant Fusion Proteins) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - DNA-Binding Proteins MH - Dimerization MH - E-Box Elements MH - *Helix-Turn-Helix Motifs MH - *Leucine Zippers MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Folding MH - *Protein Multimerization MH - Protein Structure, Secondary MH - Proto-Oncogene Proteins c-fos/genetics/*metabolism MH - Recombinant Fusion Proteins/genetics/metabolism EDAT- 2012/02/04 06:00 MHDA- 2012/06/30 06:00 CRDT- 2012/02/04 06:00 PHST- 2012/02/02 [aheadofprint] PHST- 2012/04/01 [epublish] AID - 10.1039/c2mb05354c [doi] PST - ppublish SO - Mol Biosyst. 2012 Apr;8(4):1286-96. doi: 10.1039/c2mb05354c. Epub 2012 Feb 2. PMID- 14623073 OWN - NLM STAT- MEDLINE DA - 20031118 DCOM- 20031218 LR - 20111117 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 554 IP - 3 DP - 2003 Nov 20 TI - The PIR domain of Grb14 is an intrinsically unstructured protein: implication in insulin signaling. PG - 240-6 AB - Grb14 belongs to the Grb7 family of adapter proteins and was identified as a negative regulator of insulin signal transduction. Its inhibitory effect on the insulin receptor kinase activity is controlled by a newly discovered domain called PIR. To investigate the biochemical and biophysical characteristics of this new domain, we cloned and purified recombinant PIR-SH2, PIR, and SH2 domains. The isolated PIR and PIR-SH2 domains were physiologically active and inhibited insulin-induced reinitiation of meiosis in the Xenopus oocytes system. However, NMR experiments on (15)N-labelled PIR revealed that it did not present secondary structure. These results suggest that the PIR domain belongs to the growing family of intrinsically unstructured proteins. FAU - Moncoq, Karine AU - Moncoq K AD - Laboratoire de Cristallographie et RMN Biologiques, Faculte de Pharmacie Paris 5, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France. FAU - Broutin, Isabelle AU - Broutin I FAU - Larue, Valery AU - Larue V FAU - Perdereau, Dominique AU - Perdereau D FAU - Cailliau, Katia AU - Cailliau K FAU - Browaeys-Poly, Edith AU - Browaeys-Poly E FAU - Burnol, Anne-Francoise AU - Burnol AF FAU - Ducruix, Arnaud AU - Ducruix A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Grb14 protein, Xenopus) RN - 0 (Insulin) RN - 0 (Nitrogen Isotopes) RN - 0 (Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Xenopus Proteins) RN - EC 2.7.10.1 (Receptor, Insulin) SB - IM MH - Animals MH - Insulin/*physiology MH - Meiosis/drug effects MH - Models, Molecular MH - Nitrogen Isotopes MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Oocytes/drug effects/physiology MH - Phosphorylation MH - Protein Conformation MH - Protein Structure, Tertiary MH - Proteins/*chemistry/genetics/metabolism/pharmacology MH - Receptor, Insulin/genetics/*physiology MH - Recombinant Fusion Proteins/chemistry/genetics/metabolism MH - Signal Transduction/drug effects/physiology MH - *Xenopus Proteins MH - Xenopus laevis MH - src Homology Domains EDAT- 2003/11/19 05:00 MHDA- 2003/12/19 05:00 CRDT- 2003/11/19 05:00 AID - S0014579303010950 [pii] PST - ppublish SO - FEBS Lett. 2003 Nov 20;554(3):240-6. PMID- 15840573 OWN - NLM STAT- MEDLINE DA - 20050620 DCOM- 20050929 LR - 20091119 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 25 DP - 2005 Jun 24 TI - A structural model for the membrane-bound form of the juxtamembrane domain of the epidermal growth factor receptor. PG - 24043-52 AB - The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family involved in the regulation of cellular proliferation and differentiation. Its juxtamembrane domain (JX), the region located between the transmembrane and kinase domains, plays important roles in receptor trafficking. Two sorting signals, a PXXP motif and a 658LL659 motif, are responsible for basolateral sorting in polarized epithelial cells, and a 679LL680 motif targets the ligand-activated receptor for lysosomal degradation. To understand the regulation of these signals, we characterized the structural properties of recombinant JX domain in aqueous solution and in dodecylphosphocholine (DPC) detergent. JX is inherently unstructured in aqueous solution, albeit a nascent helix encompasses the lysosomal sorting signal. In DPC micelles, structures derived from NMR data showed three amphipathic, helical segments. A large, internally inconsistent group of long range nuclear Overhauser effects suggest a close proximity of the helices, and the presence of significant conformational averaging. Models were determined for the average JX conformation using restraints representing the translational restriction due to micelle-surface adsorption, and the helix orientations were determined from residual dipolar couplings. Two equivalent average structural models were obtained that differ only in the relative orientation between first and second helices. In these models, the 658LL659 and 679LL680 motifs are located in the first and second helices and face the micelle surface, whereas the PXXP motif is located in a flexible helix-connecting region. The data suggest that the activity of these signals may be regulated by their membrane association and restricted accessibility in the intact receptor. FAU - Choowongkomon, Kiattawee AU - Choowongkomon K AD - Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4970, USA. FAU - Carlin, Cathleen R AU - Carlin CR FAU - Sonnichsen, Frank D AU - Sonnichsen FD LA - eng SI - PDB/1Z9I GR - DK54178/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050419 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA Primers) RN - 0 (Micelles) RN - 0 (Recombinant Proteins) RN - 0 (Solutions) RN - EC 2.7.10.1 (Receptor, Epidermal Growth Factor) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Cell Membrane/metabolism MH - DNA Primers MH - Micelles MH - *Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Receptor, Epidermal Growth Factor/*chemistry/genetics/metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Solutions EDAT- 2005/04/21 09:00 MHDA- 2005/09/30 09:00 CRDT- 2005/04/21 09:00 PHST- 2005/04/19 [aheadofprint] AID - M502698200 [pii] AID - 10.1074/jbc.M502698200 [doi] PST - ppublish SO - J Biol Chem. 2005 Jun 24;280(25):24043-52. Epub 2005 Apr 19. PMID- 23586525 OWN - NLM STAT- MEDLINE DA - 20130521 DCOM- 20131122 IS - 1520-6882 (Electronic) IS - 0003-2700 (Linking) VI - 85 IP - 10 DP - 2013 May 21 TI - Analysis of disordered proteins using a simple apparatus for millisecond quench-flow H/D exchange. PG - 5161-8 LID - 10.1021/ac4004979 [doi] AB - Measurement of amide H/D exchange on the ms time scale can provide valuable information about the dynamic behavior of the most flexible regions of proteins. We describe here a simple mixing apparatus, assembled solely from off-the-shelf components, that can be used for H/D exchange mass spectrometry to measure exchange on the 50-5000 ms time scale. Our apparatus utilizes flow-injection to minimize sample consumption. Although the mixer operates at low Reynolds numbers (less than 10(2)) where laminar flow is expected, H/D exchange kinetics were well-approximated using the assumption of plug-flow. We validated this approximation using fluorescence imaging of fluorescein-conjugated bovine serum albumin in the delay line and by demonstrating agreement between measured and calculated H/D exchange kinetics for a mixture of peptides. The performance of the apparatus was further validated by measuring rapid H/D exchange kinetics by an intrinsically disordered protein, murine CBP(2059-2117) (UniProt CBP_MOUSE). H/D exchange data from CBP, both free and in complex with human ACTR(1018-1088) (UniProt NCOA3_HUMAN), were consistent with previous biophysical studies of this protein. FAU - Keppel, Theodore R AU - Keppel TR AD - Department of Chemistry and the Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, Kansas 66045, United States. FAU - Weis, David D AU - Weis DD LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130501 PL - United States TA - Anal Chem JT - Analytical chemistry JID - 0370536 RN - 0 (Peptide Fragments) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Amino Acid Sequence MH - Animals MH - CREB-Binding Protein/*chemistry MH - Deuterium Exchange Measurement/*instrumentation MH - Humans MH - Molecular Sequence Data MH - Peptide Fragments/chemistry MH - Time Factors EDAT- 2013/04/17 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/04/17 06:00 PHST- 2013/05/01 [aheadofprint] AID - 10.1021/ac4004979 [doi] PST - ppublish SO - Anal Chem. 2013 May 21;85(10):5161-8. doi: 10.1021/ac4004979. Epub 2013 May 1. PMID- 19162020 OWN - NLM STAT- MEDLINE DA - 20090202 DCOM- 20090216 LR - 20131121 IS - 1873-3468 (Electronic) IS - 0014-5793 (Linking) VI - 583 IP - 3 DP - 2009 Feb 4 TI - Leucine-rich hydrophobic clusters promote folding of the N-terminus of the intrinsically disordered transactivation domain of p53. PG - 556-60 LID - 10.1016/j.febslet.2008.12.060 [doi] AB - Molecular dynamics simulations have been performed on the intrinsically disordered 39-residue N-terminal transactivation domain of p53 (p53(1-39)). Simulations not only revealed that p53(1-39) is natively compact, but also possesses a folded structure. Furthermore, leucine-rich hydrophobic clusters were found to play a crucial role in the formation and stabilization of the folded structure of p53(1-39). Collapsing in the sub-microsecond timescale might allow for rapid conformational turnovers of p53(1-39), necessary for its efficient transactivation activity and modulation. Fast collapsing might be the result of unique conformational landscapes, featuring several energy minima separated by small energy barriers. It is suggested that IDPs with highly specialized functions in the cell, such as transactivation, possibly display more ordered patterns than their less specialized counterparts. FAU - Espinoza-Fonseca, L Michel AU - Espinoza-Fonseca LM AD - Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA. mef@ddt.biochem.umn.edu LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090120 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Tumor Suppressor Protein p53) RN - GMW67QNF9C (Leucine) SB - IM MH - Computer Simulation MH - *Hydrophobic and Hydrophilic Interactions MH - Leucine/metabolism MH - Models, Molecular MH - *Protein Folding MH - Protein Structure, Tertiary MH - Transcriptional Activation/*genetics MH - Tumor Suppressor Protein p53/*chemistry/genetics/*metabolism EDAT- 2009/01/24 09:00 MHDA- 2009/02/17 09:00 CRDT- 2009/01/24 09:00 PHST- 2008/09/03 [received] PHST- 2008/12/08 [revised] PHST- 2008/12/24 [accepted] PHST- 2009/01/20 [aheadofprint] AID - S0014-5793(09)00017-9 [pii] AID - 10.1016/j.febslet.2008.12.060 [doi] PST - ppublish SO - FEBS Lett. 2009 Feb 4;583(3):556-60. doi: 10.1016/j.febslet.2008.12.060. Epub 2009 Jan 20. PMID- 21351181 OWN - NLM STAT- MEDLINE DA - 20110324 DCOM- 20110718 LR - 20140821 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 20 IP - 4 DP - 2011 Apr TI - Probing the self-association, intermolecular contacts, and folding propensity of amelogenin. PG - 724-34 LID - 10.1002/pro.603 [doi] AB - Amelogenins are an intrinsically disordered protein family that plays a major role in the development of tooth enamel, one of the most highly mineralized materials in nature. Monomeric porcine amelogenin possesses random coil and residual secondary structures, but it is not known which sequence regions would be conformationally attractive to potential enamel matrix targets such as other amelogenins (self-assembly), other matrix proteins, cell surfaces, or biominerals. To address this further, we investigated recombinant porcine amelogenin (rP172) using "solvent engineering" techniques to simultaneously promote native-like structure and induce amelogenin oligomerization in a manner that allows identification of intermolecular contacts between amelogenin molecules. We discovered that in the presence of 2,2,2-trifluoroethanol (TFE) significant folding transitions and stabilization occurred primarily within the N- and C-termini, while the polyproline Type II central domain was largely resistant to conformational transitions. Seven Pro residues (P2, P127, P130, P139, P154, P157, P162) exhibited conformational response to TFE, and this indicates these Pro residues act as folding enhancers in rP172. The remaining Pro residues resisted TFE perturbations and thus act as conformational stabilizers. We also noted that TFE induced rP172 self-association via the formation of intermolecular contacts involving P4-H6, V19-P33, and E40-T58 regions of the N-terminus. Collectively, these results confirm that the N- and C-termini of amelogenin are conformationally responsive and represent potential interactive sites for amelogenin-target interactions during enamel matrix mineralization. Conversely, the Pro, Gln central domain is resistant to folding and this may have important functional significance for amelogenin. CI - Copyright (c) 2011 The Protein Society. FAU - Ndao, Moise AU - Ndao M AD - Laboratory for Chemical Physics, New York University, New York, New York 10010, USA. FAU - Dutta, Kaushik AU - Dutta K FAU - Bromley, Keith M AU - Bromley KM FAU - Lakshminarayanan, Rajamani AU - Lakshminarayanan R FAU - Sun, Zhi AU - Sun Z FAU - Rewari, Gita AU - Rewari G FAU - Moradian-Oldak, Janet AU - Moradian-Oldak J FAU - Evans, John Spencer AU - Evans JS LA - eng GR - DE-013414/DE/NIDCR NIH HHS/United States GR - DE-020099/DE/NIDCR NIH HHS/United States GR - P41 GM66354/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Amelogenin) RN - 0 (Peptides) RN - 0 (Recombinant Proteins) RN - 25191-13-3 (polyproline) RN - 75-89-8 (Trifluoroethanol) SB - IM MH - Amelogenin/*chemistry/genetics MH - Amino Acid Sequence MH - Animals MH - Dental Enamel/chemistry MH - Molecular Sequence Data MH - Peptides/chemistry MH - *Protein Folding MH - Protein Multimerization MH - *Protein Structure, Secondary MH - Recombinant Proteins/*chemistry/genetics MH - Swine MH - Trifluoroethanol/chemistry PMC - PMC3081550 OID - NLM: PMC3081550 EDAT- 2011/02/26 06:00 MHDA- 2011/07/19 06:00 CRDT- 2011/02/26 06:00 AID - 10.1002/pro.603 [doi] PST - ppublish SO - Protein Sci. 2011 Apr;20(4):724-34. doi: 10.1002/pro.603. PMID- 19131341 OWN - NLM STAT- MEDLINE DA - 20090309 DCOM- 20090504 LR - 20140901 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 284 IP - 11 DP - 2009 Mar 13 TI - The PN2-3 domain of centrosomal P4.1-associated protein implements a novel mechanism for tubulin sequestration. PG - 6909-17 LID - 10.1074/jbc.M808249200 [doi] AB - Microtubules are cytoskeletal components involved in multiple cell functions such as mitosis, motility, or intracellular traffic. In vivo, these polymers made of alphabeta-tubulin nucleate mostly from the centrosome to establish the interphasic microtubule network or, during mitosis, the mitotic spindle. Centrosomal P4.1-associated protein (CPAP; also named CENPJ) is a centrosomal protein involved in the assembly of centrioles and important for the centrosome function. This protein contains a microtubule-destabilizing region referred to as PN2-3. Here we decrypt the microtubule destabilization activity of PN2-3 at the molecular level and show that it results from the sequestration of tubulin by PN2-3 in a non-polymerizable 1:1 complex. We also map the tubulin/PN2-3 interaction both on the PN2-3 sequence and on the tubulin surface. NMR and CD data on free PN2-3 in solution show that this is an intrinsically unstructured protein that comprises a 23-amino acid residue alpha-helix. This helix is embedded in a 76-residue region that interacts strongly with tubulin. The interference of PN2-3 with well characterized tubulin properties, namely GTPase activity, nucleotide exchange, vinblastine-induced self-assembly, and stathmin family protein binding, highlights the beta subunit surface located at the intermolecular longitudinal interface when tubulin is embedded in a microtubule as a tubulin/PN2-3 interaction area. These findings characterize the PN2-3 fragment of CPAP as a protein with an unprecedented tubulin sequestering mechanism distinct from that of stathmin family proteins. FAU - Cormier, Anthony AU - Cormier A AD - Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, Batiment 34, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France. FAU - Clement, Marie-Jeanne AU - Clement MJ FAU - Knossow, Marcel AU - Knossow M FAU - Lachkar, Sylvie AU - Lachkar S FAU - Savarin, Philippe AU - Savarin P FAU - Toma, Flavio AU - Toma F FAU - Sobel, Andre AU - Sobel A FAU - Gigant, Benoit AU - Gigant B FAU - Curmi, Patrick A AU - Curmi PA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090107 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (CENPJ protein, human) RN - 0 (Microtubule-Associated Proteins) RN - 0 (Tubulin) SB - IM MH - Animals MH - Centrioles/*metabolism MH - Circular Dichroism MH - Humans MH - Microtubule-Associated Proteins/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Tertiary/physiology MH - Sheep MH - Spindle Apparatus/*metabolism MH - Tubulin/*metabolism PMC - PMC2652345 OID - NLM: PMC2652345 EDAT- 2009/01/10 09:00 MHDA- 2009/05/05 09:00 CRDT- 2009/01/10 09:00 PHST- 2009/01/07 [aheadofprint] AID - M808249200 [pii] AID - 10.1074/jbc.M808249200 [doi] PST - ppublish SO - J Biol Chem. 2009 Mar 13;284(11):6909-17. doi: 10.1074/jbc.M808249200. Epub 2009 Jan 7. PMID- 15896712 OWN - NLM STAT- MEDLINE DA - 20050524 DCOM- 20050801 LR - 20061115 IS - 0006-291X (Print) IS - 0006-291X (Linking) VI - 332 IP - 2 DP - 2005 Jul 1 TI - Gir2 is an intrinsically unstructured protein that is present in Saccharomyces cerevisiae as a group of heterogeneously electrophoretic migrating forms. PG - 450-5 AB - Gir2 is a highly acidic cytoplasmic protein of Saccharomyces cerevisiae of unknown function that shows an anomalous migration on SDS-PAGE. Based on its large Stokes radius and thermostability, we have previously suggested that Gir2 lacks extensive secondary structure. Here we report that Gir2 is extremely sensitive to proteolysis when compared to glutathione-S-transferase, a highly structured protein, further indicating its unfolded nature. Prediction based on the FoldIndex program also indicates that Gir2 is a disordered protein. Using truncated forms of Gir2 we show that the N-terminal half of this protein, with its high content of acidic amino acid residues, is responsible for the anomalous electrophoretic behavior of Gir2. Because all these features are hallmarks of intrinsically unstructured proteins (IUP), we propose that Gir2 is another representative of the IUP group of proteins. Additionally, we describe that the endogenous yeast Gir2 shows heterogeneous electrophoretic mobility, which is not due to proteolytic cleavage. FAU - Alves, Viviane S AU - Alves VS AD - Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil. FAU - Castilho, Beatriz A AU - Castilho BA LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Gir2 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Amino Acid Sequence MH - Computer Simulation MH - Electrophoresis/*methods MH - *Models, Chemical MH - *Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Saccharomyces cerevisiae Proteins/analysis/*chemistry MH - Structure-Activity Relationship EDAT- 2005/05/18 09:00 MHDA- 2005/08/02 09:00 CRDT- 2005/05/18 09:00 PHST- 2005/04/27 [received] PHST- 2005/04/29 [accepted] AID - S0006-291X(05)00950-2 [pii] AID - 10.1016/j.bbrc.2005.04.151 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2005 Jul 1;332(2):450-5. PMID- 23964651 OWN - NLM STAT- MEDLINE DA - 20130924 DCOM- 20131126 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 52 IP - 38 DP - 2013 Sep 24 TI - A molecular dynamics simulation-based interpretation of nuclear magnetic resonance multidimensional heteronuclear spectra of alpha-synuclein.dopamine adducts. PG - 6672-83 LID - 10.1021/bi400367r [doi] AB - Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy provides valuable structural information about adducts between naturally unfolded proteins and their ligands. These are often highly pharmacologically relevant. Unfortunately, the determination of the contributions to observed chemical shifts changes upon ligand binding is complicated. Here we present a tool that uses molecular dynamics (MD) trajectories to help interpret two-dimensional (2D) NMR data. We apply this tool to the naturally unfolded protein human alpha-synuclein interacting with dopamine, an inhibitor of fibril formation, and with its oxidation products in water solutions. By coupling 2D NMR experiments with MD simulations of the adducts in explicit water, the tool confirms with experimental data that the ligands bind preferentially to (125)YEMPS(129) residues in the C-terminal region and to a few residues of the so-called NAC region consistently. It also suggests that the ligands might cause conformational rearrangements of distal residues located at the N-terminus. Hence, the performed analysis provides a rationale for the observed changes in chemical shifts in terms of direct contacts with the ligand and conformational changes in the protein. FAU - Dibenedetto, Domenica AU - Dibenedetto D AD - Computational Biophysics, German Research School for Simulation Sciences (joint venture of RWTH Aachen University and Forschungszentrum Julich ), D-52425 Julich, Germany , and Institute for Advanced Simulation IAS-5, Computational Biomedicine, Forschungszentrum Julich , D-52425 Julich, Germany. FAU - Rossetti, Giulia AU - Rossetti G FAU - Caliandro, Rocco AU - Caliandro R FAU - Carloni, Paolo AU - Carloni P LA - eng PT - Journal Article DEP - 20130909 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Ligands) RN - 0 (alpha-Synuclein) RN - VTD58H1Z2X (Dopamine) SB - IM MH - Dopamine/*chemistry MH - Humans MH - Ligands MH - Molecular Dynamics Simulation MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - alpha-Synuclein/*chemistry EDAT- 2013/08/24 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/08/23 06:00 PHST- 2013/09/09 [aheadofprint] AID - 10.1021/bi400367r [doi] PST - ppublish SO - Biochemistry. 2013 Sep 24;52(38):6672-83. doi: 10.1021/bi400367r. Epub 2013 Sep 9. PMID- 21183464 OWN - NLM STAT- MEDLINE DA - 20110426 DCOM- 20110712 LR - 20140821 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 39 IP - 8 DP - 2011 Apr TI - The translational repressor 4E-BP called to order by eIF4E: new structural insights by SAXS. PG - 3496-503 LID - 10.1093/nar/gkq1306 [doi] AB - eIF4E binding protein (4E-BP) inhibits translation of capped mRNA by binding to the initiation factor eIF4E and is known to be mostly or completely unstructured in both free and bound states. Using small angle X-ray scattering (SAXS), we report here the analysis of 4E-BP structure in solution, which reveals that while 4E-BP is intrinsically disordered in the free state, it undergoes a dramatic compaction in the bound state. Our results demonstrate that 4E-BP and eIF4E form a 'fuzzy complex', challenging current visions of eIF4E/4E-BP complex regulation. FAU - Gosselin, Pauline AU - Gosselin P AD - UPMC Univ Paris 06, UMR 7150, Mer et Sante, Equipe Traduction Cycle Cellulaire et Developpement, Station Biologique de Roscoff, 29680 Roscoff, France. gosselin@sb-roscoff.fr FAU - Oulhen, Nathalie AU - Oulhen N FAU - Jam, Murielle AU - Jam M FAU - Ronzca, Justyna AU - Ronzca J FAU - Cormier, Patrick AU - Cormier P FAU - Czjzek, Mirjam AU - Czjzek M FAU - Cosson, Bertrand AU - Cosson B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101222 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Eukaryotic Initiation Factor-4E) RN - 0 (Eukaryotic Initiation Factors) SB - IM MH - Eukaryotic Initiation Factor-4E/*chemistry/metabolism MH - Eukaryotic Initiation Factors/*chemistry/metabolism MH - Models, Molecular MH - Protein Binding MH - Scattering, Small Angle MH - Sequence Analysis, Protein MH - X-Ray Diffraction PMC - PMC3082885 OID - NLM: PMC3082885 EDAT- 2010/12/25 06:00 MHDA- 2011/07/13 06:00 CRDT- 2010/12/25 06:00 PHST- 2010/12/22 [aheadofprint] AID - gkq1306 [pii] AID - 10.1093/nar/gkq1306 [doi] PST - ppublish SO - Nucleic Acids Res. 2011 Apr;39(8):3496-503. doi: 10.1093/nar/gkq1306. Epub 2010 Dec 22. PMID- 11264583 OWN - NLM STAT- MEDLINE DA - 20010326 DCOM- 20010621 LR - 20070724 IS - 0907-4449 (Print) IS - 0907-4449 (Linking) VI - 57 IP - Pt 4 DP - 2001 Apr TI - Structure of the C-terminal sterile alpha-motif (SAM) domain of human p73 alpha. PG - 545-51 AB - p73 is a homologue of the tumour suppressor p53 and contains all three functional domains of p53. The alpha-splice variant of p73 (p73 alpha) contains near its C-terminus an additional structural domain known as the sterile alpha-motif (SAM) that is probably responsible for regulating p53-like functions of p73. Here, the 2.54 A resolution crystal structure of this protein domain is reported. The crystal structure and the published solution structure have the same five-helix bundle fold that is characteristic of all SAM-domain structures, with an overall r.m.s.d. of 1.5 A for main-chain atoms. The hydrophobic core residues are well conserved, yet some large local differences are observed. The crystal structure reveals a dimeric organization, with the interface residues forming a mini four-helix bundle. However, analysis of solvation free energies and the surface area buried upon dimer formation indicated that this arrangement is more likely to be an effect of crystal packing rather than reflecting a physiological state. This is consistent with the solution structure being a monomer. The p73 alpha SAM domain also contains several interesting structural features: a Cys-X-X-Cys motif, a 3(10)-helix and a loop that have elevated B factors, and short tight inter-helical loops including two beta-turns; these elements are probably important in the normal function of this domain. FAU - Wang, W K AU - Wang WK AD - Centre for Protein Engineering and Cambridge University Chemical Laboratory, MRC Centre, Hills Road, Cambridge CB2 2QH, England. FAU - Bycroft, M AU - Bycroft M FAU - Foster, N W AU - Foster NW FAU - Buckle, A M AU - Buckle AM FAU - Fersht, A R AU - Fersht AR FAU - Chen, Y W AU - Chen YW LA - eng SI - PDB/1DXS SI - PDB/1FVK PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Denmark TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (DNA-Binding Proteins) RN - 0 (Disulfides) RN - 0 (Nuclear Proteins) RN - 0 (Tumor Suppressor Proteins) RN - 0 (tumor suppressor protein p73) SB - IM MH - Amino Acid Motifs MH - Crystallography, X-Ray MH - DNA-Binding Proteins/*chemistry/metabolism MH - Dimerization MH - Disulfides/chemistry/metabolism MH - Genes, Tumor Suppressor MH - Humans MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*chemistry/metabolism MH - Protein Binding MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Tumor Suppressor Proteins MH - Ultracentrifugation EDAT- 2001/03/27 10:00 MHDA- 2001/06/22 10:01 CRDT- 2001/03/27 10:00 PHST- 2000/11/16 [received] PHST- 2001/02/05 [accepted] AID - S0907444901002529 [pii] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2001 Apr;57(Pt 4):545-51. PMID- 15099522 OWN - NLM STAT- MEDLINE DA - 20040421 DCOM- 20040521 LR - 20131121 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 14 IP - 2 DP - 2004 Apr 23 TI - Crystal structure and functional analysis of the eukaryotic class II release factor eRF3 from S. pombe. PG - 233-45 AB - Translation termination in eukaryotes is governed by two interacting release factors, eRF1 and eRF3. The crystal structure of the eEF1alpha-like region of eRF3 from S. pombe determined in three states (free protein, GDP-, and GTP-bound forms) reveals an overall structure that is similar to EF-Tu, although with quite different domain arrangements. In contrast to EF-Tu, GDP/GTP binding to eRF3c does not induce dramatic conformational changes, and Mg(2+) is not required for GDP binding to eRF3c. Mg(2+) at higher concentration accelerates GDP release, suggesting a novel mechanism for nucleotide exchange on eRF3 from that of other GTPases. Mapping sequence conservation onto the molecular surface, combined with mutagenesis analysis, identified the eRF1 binding region, and revealed an essential function for the C terminus of eRF3. The N-terminal extension, rich in acidic amino acids, blocks the proposed eRF1 binding site, potentially regulating eRF1 binding to eRF3 in a competitive manner. FAU - Kong, Chunguang AU - Kong C AD - Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609, Japan. FAU - Ito, Koichi AU - Ito K FAU - Walsh, Martin A AU - Walsh MA FAU - Wada, Miki AU - Wada M FAU - Liu, Yuying AU - Liu Y FAU - Kumar, Sundramurthy AU - Kumar S FAU - Barford, David AU - Barford D FAU - Nakamura, Yoshikazu AU - Nakamura Y FAU - Song, Haiwei AU - Song H LA - eng SI - PDB/1R5B SI - PDB/1R5N SI - PDB/1R5O PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Fungal Proteins) RN - 0 (Peptide Fragments) RN - 0 (Peptide Termination Factors) RN - 0 (peptide-chain-release factor 3) RN - 146-91-8 (Guanosine Diphosphate) RN - 86-01-1 (Guanosine Triphosphate) RN - I38ZP9992A (Magnesium) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - Binding, Competitive MH - Conserved Sequence MH - *Crystallography, X-Ray MH - DNA Mutational Analysis MH - Fungal Proteins/*chemistry/genetics/*metabolism MH - Genetic Complementation Test MH - Genetic Variation MH - Guanosine Diphosphate/chemistry MH - Guanosine Triphosphate/chemistry MH - Magnesium/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis MH - Peptide Fragments/metabolism MH - Peptide Termination Factors/*chemistry/genetics/*metabolism MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Schizosaccharomyces/*genetics/growth & development MH - Sequence Homology, Amino Acid MH - Two-Hybrid System Techniques EDAT- 2004/04/22 05:00 MHDA- 2004/05/22 05:00 CRDT- 2004/04/22 05:00 PHST- 2004/01/16 [received] PHST- 2004/03/03 [revised] PHST- 2004/03/10 [accepted] AID - S1097276504002060 [pii] PST - ppublish SO - Mol Cell. 2004 Apr 23;14(2):233-45. PMID- 17598142 OWN - NLM STAT- MEDLINE DA - 20071001 DCOM- 20090721 LR - 20140921 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 69 IP - 2 DP - 2007 Nov 1 TI - Mass spectrometry analysis of HIV-1 Vif reveals an increase in ordered structure upon oligomerization in regions necessary for viral infectivity. PG - 270-84 AB - HIV-1 Vif, an accessory protein in the viral genome, performs an important role in viral pathogenesis by facilitating the degradation of APOBEC3G, an endogenous cellular inhibitor of HIV-1 replication. In this study, intrinsically disordered regions are predicted in HIV-1 Vif using sequence-based algorithms. Intrinsic disorder may explain why traditional structure determination of HIV-1 Vif has been elusive, making structure-based drug design impossible. To characterize HIV-1 Vif's structural topology and to map the domains involved in oligomerization we used chemical cross-linking, proteolysis, and mass spectrometry. Cross-linking showed evidence of monomer, dimer, and trimer species via denaturing gel analysis and an additional tetramer via western blot analysis. We identified 47 unique linear peptides and 24 (13 intramolecular; 11 intermolecular) noncontiguous, cross-linked peptides, among the noncross-linked monomer, cross-linked monomer, cross-linked dimer, and cross-linked trimer samples. Almost complete peptide coverage of the N-terminus is observed in all samples analyzed, however reduced peptide coverage in the C-terminal region is observed in the dimer and trimer samples. These differences in peptide coverage or "protections" between dimer and trimer indicate specific differences in packing between the two oligomeric forms. Intramolecular cross-links within the monomer suggest that the N-terminus is likely folded into a compact domain, while the C-terminus remains intrinsically disordered. Upon oligomerization, as evidenced by the intermolecular cross-links, the C-terminus of one Vif protein becomes ordered by wrapping back on the N-terminal domain of another. In addition, the majority of the intramolecular cross-links map to regions that have been previously reported to be necessary for viral infectivity. Thus, this data suggests HIV-1 Vif is in a dynamic equilibrium between the various oligomers potentially allowing it to interact with other binding partners. CI - (c) 2007 Wiley-Liss, Inc. FAU - Auclair, Jared R AU - Auclair JR AD - Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA. FAU - Green, Karin M AU - Green KM FAU - Shandilya, Shivender AU - Shandilya S FAU - Evans, James E AU - Evans JE FAU - Somasundaran, Mohan AU - Somasundaran M FAU - Schiffer, Celia A AU - Schiffer CA LA - eng GR - 5P3O AI42845/AI/NIAID NIH HHS/United States GR - R21 AI056935/AI/NIAID NIH HHS/United States GR - R21 AI056935/AI/NIAID NIH HHS/United States GR - R21 AI056935-01/AI/NIAID NIH HHS/United States GR - R21 AI067021/AI/NIAID NIH HHS/United States GR - R21 AI067021/AI/NIAID NIH HHS/United States GR - R21 AI067021-01A2/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Cross-Linking Reagents) RN - 0 (Gene Products, vif) RN - EC 3.5.4.5 (APOBEC3G protein, human) RN - EC 3.5.4.5 (Cytidine Deaminase) SB - IM MH - Cross-Linking Reagents/metabolism MH - Cytidine Deaminase/metabolism MH - Gene Products, vif/*chemistry/*metabolism MH - HIV Infections/metabolism/virology MH - HIV-1/*chemistry/metabolism/*pathogenicity MH - Humans MH - Predictive Value of Tests MH - Protein Binding/physiology MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Tandem Mass Spectrometry PMC - PMC3366188 MID - NIHMS92955 OID - NLM: NIHMS92955 OID - NLM: PMC3366188 EDAT- 2007/06/29 09:00 MHDA- 2009/07/22 09:00 CRDT- 2007/06/29 09:00 AID - 10.1002/prot.21471 [doi] PST - ppublish SO - Proteins. 2007 Nov 1;69(2):270-84. PMID- 16529944 OWN - NLM STAT- MEDLINE DA - 20060523 DCOM- 20060921 LR - 20081121 IS - 1046-5928 (Print) IS - 1046-5928 (Linking) VI - 47 IP - 2 DP - 2006 Jun TI - Overexpression and characterization of two human salivary proline rich proteins. PG - 524-32 AB - Proline rich proteins (PRP) are among major human saliva constituents and are known to interact with wine tannins that are involved in astringency. To characterize these interactions, a human salivary proline rich pro-protein, PRB4S, was overexpressed in Pichia pastoris. Six recombinant proteins resulting from maturation in bioreactor were detected by SDS-PAGE analysis between 15 and 45 kDa (apparent molecular weight). Two of them, the 45 and the 15 kDa ones, were isolated from culture supernatant by adsorption and permeation chromatography. They were characterized by N-terminal sequencing and MALDI-TOF analysis after trypsic digestion. The 45 kDa protein is glycosylated while the 15 kDa one was obtained after a furin-like proteolysis. Both of them are similar to human whole saliva PRP resulting from proteolysis of PRB4S pro-protein in Golgi network and known as II-1 and IB-5. Because of their sensitivity to proteolysis or their unusual mobility on SDS-PAGE gel, these recombinant proteins seem to be intrinsically unstructured proteins. FAU - Pascal, Christine AU - Pascal C AD - UMR Sciences Pour l'oenologie (SPO), INRA-ENSAM, equipe Systemes Supramoleculaires Impliquant les Polyphenols, Montpellier, France. FAU - Bigey, Frederic AU - Bigey F FAU - Ratomahenina, Robert AU - Ratomahenina R FAU - Boze, Helene AU - Boze H FAU - Moulin, Guy AU - Moulin G FAU - Sarni-Manchado, Pascale AU - Sarni-Manchado P LA - eng PT - Journal Article DEP - 20060209 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (Peptides) RN - 0 (Protein Precursors) RN - 0 (Recombinant Proteins) RN - 0 (Salivary Proteins and Peptides) SB - IM MH - Glycosylation MH - Golgi Apparatus/metabolism MH - Humans MH - *Peptides/genetics/metabolism MH - Pichia MH - Proline-Rich Protein Domains MH - Protein Modification, Translational/physiology MH - Protein Precursors/*biosynthesis/genetics/metabolism MH - Protein Structure, Tertiary MH - Recombinant Proteins/*biosynthesis/genetics/metabolism MH - Salivary Proteins and Peptides/*biosynthesis/genetics/metabolism EDAT- 2006/03/15 09:00 MHDA- 2006/09/22 09:00 CRDT- 2006/03/15 09:00 PHST- 2005/10/17 [received] PHST- 2006/01/13 [revised] PHST- 2006/01/18 [accepted] PHST- 2006/02/09 [aheadofprint] AID - S1046-5928(06)00031-3 [pii] AID - 10.1016/j.pep.2006.01.012 [doi] PST - ppublish SO - Protein Expr Purif. 2006 Jun;47(2):524-32. Epub 2006 Feb 9. PMID- 22901047 OWN - NLM STAT- MEDLINE DA - 20120912 DCOM- 20130204 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 134 IP - 36 DP - 2012 Sep 12 TI - Mapping the potential energy landscape of intrinsically disordered proteins at amino acid resolution. PG - 15138-48 LID - 10.1021/ja306905s [doi] AB - Intrinsically disordered regions are predicted to exist in a significant fraction of proteins encoded in eukaryotic genomes. The high levels of conformational plasticity of this class of proteins endows them with unique capacities to act in functional modes not achievable by folded proteins, but also places their molecular characterization beyond the reach of classical structural biology. New techniques are therefore required to understand the relationship between primary sequence and biological function in this class of proteins. Although dependences of some NMR parameters such as chemical shifts (CSs) or residual dipolar couplings (RDCs) on structural propensity are known, so that sampling regimes are often inferred from experimental observation, there is currently no framework that allows for a statistical mapping of the available Ramachandran space of each amino acid in terms of conformational propensity. In this study we develop such an approach, combining highly efficient conformational sampling with ensemble selection to map the backbone conformational sampling of IDPs on a residue specific level. By systematically analyzing the ability of NMR data to map the conformational landscape of disordered proteins, we identify combinations of RDCs and CSs that can be used to raise conformational degeneracies inherent to different data types, and apply these approaches to characterize the conformational behavior of two intrinsically disordered proteins, the K18 domain from Tau protein and N(TAIL) from measles virus nucleoprotein. In both cases, we identify the enhanced populations of turn and helical regions in key regions of the proteins, as well as contiguous strands that show clear and enhanced polyproline II sampling. FAU - Ozenne, Valery AU - Ozenne V AD - CEA, CNRS, and UJF-Grenoble 1, Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, Grenoble 38027, France. FAU - Schneider, Robert AU - Schneider R FAU - Yao, Mingxi AU - Yao M FAU - Huang, Jie-rong AU - Huang JR FAU - Salmon, Loic AU - Salmon L FAU - Zweckstetter, Markus AU - Zweckstetter M FAU - Jensen, Malene Ringkjobing AU - Jensen MR FAU - Blackledge, Martin AU - Blackledge M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120828 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Amino Acids) RN - 0 (Nucleoproteins) RN - 0 (tau Proteins) SB - IM MH - Amino Acids/*chemistry MH - *Nuclear Magnetic Resonance, Biomolecular MH - Nucleoproteins/*chemistry MH - Protein Conformation MH - tau Proteins/*chemistry EDAT- 2012/08/21 06:00 MHDA- 2013/02/05 06:00 CRDT- 2012/08/21 06:00 PHST- 2012/08/28 [aheadofprint] AID - 10.1021/ja306905s [doi] PST - ppublish SO - J Am Chem Soc. 2012 Sep 12;134(36):15138-48. doi: 10.1021/ja306905s. Epub 2012 Aug 28. PMID- 12860982 OWN - NLM STAT- MEDLINE DA - 20030929 DCOM- 20031106 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 40 DP - 2003 Oct 3 TI - Thermodynamics of the Op18/stathmin-tubulin interaction. PG - 38926-34 AB - Op18/stathmin (stathmin) is an intrinsically disordered protein involved in the regulation of the microtubule filament system. One function of stathmin is to sequester tubulin dimers into assembly incompetent complexes, and recent studies revealed two tubulin binding sites per stathmin molecule. Using high sensitivity isothermal titration calorimetry, we document that at 10 degrees C and under the conditions of 80 mM PIPES, pH 6.8, 1 mM EGTA, 1 mM MgCl2, 1 mM GTP these two binding sites are of equal affinity with an equilibrium binding constant of K0 = 6.0 x 10(6) m(-1). The obtained large negative molar heat capacity change of deltaCp0 = -860 cal mol(-1) K(-1) (referring to tubulin) for the tubulin-stathmin binding equilibrium suggests that the hydrophobic effect is the major driving force of the binding reaction. Replacing GTP by GDP on beta-tubulin had no significant effect on the thermodynamic parameters of the tubulin-stathmin binding equilibrium. The proposed pH-sensitive dual function of stathmin was further evaluated by circular dichroism spectroscopy and nuclear magnetic resonance. At low temperatures, stathmin was found to be extensively helical but devoid of any stable tertiary structure. However, in complex with two tubulin subunits stathmin adopts a stable conformation. Both the stability and conformation of the individual proteins and complexes were not significantly affected by small changes in pH. A 4-fold decrease in affinity of stathmin for tubulin was revealed at pH 7.5 compared with pH 6.8. This decrease could be attributed to a weaker binding of the C terminus of stathmin. These findings do not support the view that stathmin works as a pH-sensitive protein. FAU - Honnappa, Srinivas AU - Honnappa S AD - Structural Biology, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland. FAU - Cutting, Brian AU - Cutting B FAU - Jahnke, Wolfgang AU - Jahnke W FAU - Seelig, Joachim AU - Seelig J FAU - Steinmetz, Michel O AU - Steinmetz MO LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030714 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA, Complementary) RN - 0 (Microtubule Proteins) RN - 0 (Phosphoproteins) RN - 0 (STMN1 protein, human) RN - 0 (Stathmin) RN - 0 (Tubulin) RN - 146-91-8 (Guanosine Diphosphate) RN - 86-01-1 (Guanosine Triphosphate) RN - PDC6A3C0OX (Glycerol) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Calorimetry MH - Cattle MH - Circular Dichroism MH - DNA, Complementary/metabolism MH - Entropy MH - Glycerol/chemistry MH - Guanosine Diphosphate/chemistry MH - Guanosine Triphosphate/chemistry MH - Humans MH - Hydrogen-Ion Concentration MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Microscopy, Electron MH - *Microtubule Proteins MH - Models, Molecular MH - Models, Statistical MH - Molecular Sequence Data MH - Phosphoproteins/*chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - Stathmin MH - Temperature MH - Thermodynamics MH - Time Factors MH - Tubulin/*chemistry/metabolism EDAT- 2003/07/16 05:00 MHDA- 2003/11/07 05:00 CRDT- 2003/07/16 05:00 PHST- 2003/07/14 [aheadofprint] AID - 10.1074/jbc.M305546200 [doi] AID - M305546200 [pii] PST - ppublish SO - J Biol Chem. 2003 Oct 3;278(40):38926-34. Epub 2003 Jul 14. PMID- 19280601 OWN - NLM STAT- MEDLINE DA - 20090623 DCOM- 20090908 LR - 20140831 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 76 IP - 3 DP - 2009 Aug 15 TI - Order propensity of an intrinsically disordered protein, the cyclin-dependent-kinase inhibitor Sic1. PG - 731-46 LID - 10.1002/prot.22385 [doi] AB - Intrinsically disordered proteins (IDPs) carry out important biological functions and offer an instructive model system for folding and binding studies. However, their structural characterization in the absence of interactors is hindered by their highly dynamic conformation. The cyclin-dependent-kinase inhibitor (Cki) Sic1 from Saccharomyces cerevisiae is a key regulator of the yeast cell cycle, which controls entrance into S phase and coordination between cell growth and proliferation. Its last 70 out of 284 residues display functional and structural homology to the inhibitory domain of mammalian p21 and p27. Sic1 has escaped systematic structural characterization until now. Here, complementary biophysical methods are applied to the study of conformational properties of pure Sic1 in solution. Based on sequence analysis, gel filtration, circular dichroism (CD), electrospray-ionization mass spectrometry (ESI-MS), and limited proteolysis, it can be concluded that the whole molecule exists in a highly disordered state and can, therefore, be classified as an IDP. However, the results of these experiments indicate, at the same time, that the protein displays some content in secondary and tertiary structure, having properties similar to those of molten globules or premolten globules. Proteolysis-hypersensitive sites cluster at the N-terminus and in the middle of the molecule, whereas the most structured region resides at the C-terminus, including part of the inhibitory domain and the casein-kinase-2 (CK2) phosphorylation target S201. The mutations S201A and S201E, which are known to affect Sic1 function, do not have significant effects on the conformational properties of the pure protein. CI - 2009 Wiley-Liss, Inc. FAU - Brocca, Stefania AU - Brocca S AD - Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy. FAU - Samalikova, Maria AU - Samalikova M FAU - Uversky, Vladimir N AU - Uversky VN FAU - Lotti, Marina AU - Lotti M FAU - Vanoni, Marco AU - Vanoni M FAU - Alberghina, Lilia AU - Alberghina L FAU - Grandori, Rita AU - Grandori R LA - eng GR - GM071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 GM071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 LM007688-01A1/LM/NLM NIH HHS/United States GR - R01 LM007688-01A1/LM/NLM NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Cyclin-Dependent Kinase Inhibitor Proteins) RN - 0 (SIC1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Cyclin-Dependent Kinase Inhibitor Proteins/*chemistry/genetics/*metabolism MH - Electrophoresis, Polyacrylamide Gel MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Mutation MH - Protein Folding MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism MH - Spectrometry, Mass, Electrospray Ionization PMC - PMC2754754 MID - NIHMS130537 OID - NLM: NIHMS130537 OID - NLM: PMC2754754 EDAT- 2009/03/13 09:00 MHDA- 2009/09/09 06:00 CRDT- 2009/03/13 09:00 AID - 10.1002/prot.22385 [doi] PST - ppublish SO - Proteins. 2009 Aug 15;76(3):731-46. doi: 10.1002/prot.22385. PMID- 12680753 OWN - NLM STAT- MEDLINE DA - 20030408 DCOM- 20030512 LR - 20051117 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 42 IP - 14 DP - 2003 Apr 15 TI - The Habc domain and the SNARE core complex are connected by a highly flexible linker. PG - 4009-14 AB - Syntaxin 1a is a member of the SNARE superfamily of small, mostly membrane-bound proteins that mediate membrane fusion in all eukaryotic cells. Upon membrane fusion, syntaxin 1 forms a stable complex with its partner SNAREs. Syntaxin contains a C-terminal transmembrane domain, an adjacent SNARE motif that interacts with its partner SNAREs, and an N-terminal Habc domain. The Habc domain reversibly folds back upon the SNARE motif, resulting in a "closed" conformation that is stabilized by binding to the protein munc18. The SNARE motif and the Habc domain are separated by a linker region of about 40 amino acids. When syntaxin is complexed with munc18, the linker is structured and consists of a mix of turns and small alpha-helices. When syntaxin is complexed with its partner SNAREs, the Habc domain is dissociated, but the structure of the linker region is not known. Here we used site-directed spin labeling and EPR spectroscopy to determine the structure of the linker region of syntaxin in the SNARE complex. We found that the entire linker region of syntaxin is unstructured except for three residues at the N-terminal and six residues at the C-terminal boundary whereas the structures of the flanking regions in the Habc domain and the SNARE motif correspond to the high-resolution structures of the isolated fragments. We conclude that the linker region exhibits a high degree of conformational flexibility. FAU - Margittai, Martin AU - Margittai M AD - Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, D-37077 Gottingen, Germany. FAU - Fasshauer, Dirk AU - Fasshauer D FAU - Jahn, Reinhard AU - Jahn R FAU - Langen, Ralf AU - Langen R LA - eng PT - Journal Article PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Membrane Proteins) RN - 0 (Qa-SNARE Proteins) RN - 0 (SNARE Proteins) RN - 0 (Spin Labels) RN - 0 (Vesicular Transport Proteins) SB - IM MH - Amino Acid Motifs MH - Electron Spin Resonance Spectroscopy MH - Membrane Proteins/*chemistry MH - Qa-SNARE Proteins MH - SNARE Proteins MH - Spin Labels MH - *Vesicular Transport Proteins EDAT- 2003/04/19 05:00 MHDA- 2003/05/13 05:00 CRDT- 2003/04/19 05:00 AID - 10.1021/bi027437z [doi] PST - ppublish SO - Biochemistry. 2003 Apr 15;42(14):4009-14. PMID- 18287285 OWN - NLM STAT- MEDLINE DA - 20080221 DCOM- 20080407 LR - 20140904 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 17 IP - 3 DP - 2008 Mar TI - The solution structure of ZNF593 from Homo sapiens reveals a zinc finger in a predominantly unstructured protein. PG - 571-6 LID - 10.1110/ps.073290408 [doi] AB - Here, we report the solution structure of ZNF593, a protein identified in a functional study as a negative modulator of the DNA-binding activity of the Oct-2 transcription factor. ZNF593 contains a classic C(2)H(2) zinc finger domain flanked by about 40 disordered residues on each terminus. Although the protein contains a high degree of intrinsic disorder, the structure of the zinc finger domain was resolved by NMR spectroscopy without a need for N- or C-terminal truncations. The tertiary structure of the zinc finger domain is composed of a beta-hairpin that positions the cysteine side chains for zinc coordination, followed by an atypical kinked alpha-helix containing the two histidine side chain ligands. The structural topology of ZNF593 is similar to a fragment of the double-stranded RNA-binding protein Zfa and the C-terminal zinc finger of MBP-1, a human enhancer binding protein. The structure presented here will provide a guide for future functional studies of how ZNF593 negatively modulates the DNA-binding activity of Oct-2, a POU domain-containing transcription factor. Our work illustrates the unique capacity of NMR spectroscopy for structural analysis of folded domains in a predominantly disordered protein. FAU - Hayes, Paulette L AU - Hayes PL AD - Department of Biochemistry and Center for Eukaryotic Structural Genomics, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA. FAU - Lytle, Betsy L AU - Lytle BL FAU - Volkman, Brian F AU - Volkman BF FAU - Peterson, Francis C AU - Peterson FC LA - eng SI - PDB/1ZR9 GR - P50 GM64598/GM/NIGMS NIH HHS/United States GR - U54 GM074901/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (DNA-Binding Proteins) RN - 0 (Solutions) RN - 0 (Transcription Factors) RN - 0 (ZNF593 protein, human) SB - IM MH - Amino Acid Sequence MH - DNA-Binding Proteins/*chemistry MH - Humans MH - *Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Sequence Alignment MH - Solutions MH - Structural Homology, Protein MH - Transcription Factors/*chemistry MH - *Zinc Fingers PMC - PMC2248319 OID - NLM: PMC2248319 EDAT- 2008/02/22 09:00 MHDA- 2008/04/09 09:00 CRDT- 2008/02/22 09:00 AID - 17/3/571 [pii] AID - 10.1110/ps.073290408 [doi] PST - ppublish SO - Protein Sci. 2008 Mar;17(3):571-6. doi: 10.1110/ps.073290408. PMID- 12384576 OWN - NLM STAT- MEDLINE DA - 20021030 DCOM- 20021209 LR - 20140611 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 99 IP - 22 DP - 2002 Oct 29 TI - Structure of a regulatory complex involving the Abl SH3 domain, the Crk SH2 domain, and a Crk-derived phosphopeptide. PG - 14053-8 AB - On phosphorylation of Y221 by Abelson (Abl) kinase, the Crk-II adapter protein undergoes an intramolecular reorganization initiated by the binding of its own Src homology 2 (SH2) domain to the pY221 site. Conformational changes induced by phosphotyrosine recognition promote the binding of the Src homology 3 (SH3) domain of the Abl tyrosine kinase to a proline-rich loop located between the betaD and betaE strands of the SH2 domain (DE loop). We have determined the NMR solution structure of the ternary complex of the Abl SH3 domain with the Crk SH2 domain bound to a Crk pY221 phosphopeptide. The SH2 domain bridges two ligands that bind at distinct sites. The interaction between the Abl SH3 domain and the Crk SH2 domain is localized to a canonical eight-residue site within the DE loop. From (15)N relaxation experiments, the DE loop of the SH2 domain in the complex displays a significant degree of conformational freedom. The structural and dynamic data therefore indicate that these SH2 and SH3 domains do not assume a unique orientation with respect to one another; rather, they appear to be only tethered via the DE loop. Thus, SH2 domain-SH3 domain interactions do not require additional tertiary contacts or restriction of domain orientation when a recognition motif is presented in a mobile loop. This complex between the Abl SH3 domain, Crk SH2 domain, and Crk phosphopeptide is an example of the extremely modular nature of regulatory proteins that provides a rich repertoire of mechanisms for control of biological function. FAU - Donaldson, Logan W AU - Donaldson LW AD - Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8. FAU - Gish, Gerald AU - Gish G FAU - Pawson, Tony AU - Pawson T FAU - Kay, Lewis E AU - Kay LE FAU - Forman-Kay, Julie D AU - Forman-Kay JD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20021016 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Ligands) RN - 0 (Phosphopeptides) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Proto-Oncogene Proteins c-crk) RN - 0 (Recombinant Fusion Proteins) RN - EC 2.7.10.1 (Protein-Tyrosine Kinases) RN - EC 2.7.10.2 (Proto-Oncogene Proteins c-abl) SB - IM MH - Amino Acid Sequence MH - Humans MH - Ligands MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphopeptides/*chemistry/genetics MH - Protein Structure, Tertiary MH - Protein-Tyrosine Kinases/*chemistry/genetics MH - Proto-Oncogene Proteins/*chemistry/genetics MH - Proto-Oncogene Proteins c-abl/*chemistry MH - Proto-Oncogene Proteins c-crk MH - Recombinant Fusion Proteins/chemistry/genetics MH - Sequence Homology, Amino Acid MH - *src Homology Domains PMC - PMC137835 OID - NLM: PMC137835 EDAT- 2002/10/18 04:00 MHDA- 2002/12/10 04:00 CRDT- 2002/10/18 04:00 PHST- 2002/10/16 [aheadofprint] AID - 10.1073/pnas.212518799 [doi] AID - 212518799 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14053-8. Epub 2002 Oct 16. PMID- 18636772 OWN - NLM STAT- MEDLINE DA - 20080811 DCOM- 20081201 LR - 20131121 IS - 1526-4602 (Electronic) IS - 1525-7797 (Linking) VI - 9 IP - 8 DP - 2008 Aug TI - Starmaker exhibits properties of an intrinsically disordered protein. PG - 2118-25 LID - 10.1021/bm800135m [doi] AB - Fish otoliths composed of calcium carbonate and an organic matrix play a primary role in gravity sensing and the perception of sound. Starmaker (Stm) was the first protein found to be capable of influencing the process of biomineralization of otoliths. Stm dictates the shape, size, and selection of calcium carbonate polymorphs in a concentration-dependent manner. To facilitate exploration of the molecular basis of Stm function, we have developed and optimized a protocol for efficient expression and purification of the homogeneous nontagged Stm. The homogeneous nontagged Stm corresponds to its functional form, which is devoid of a signal peptide. A comprehensive biochemical and biophysical analysis of recombinant Stm, along with in silico examinations, indicate for the first time that Stm exhibits the properties of intrinsically disordered proteins. The functional significance of Stm having intrinsically disordered protein properties and its possible role in controlling the formation of otoliths is discussed. FAU - Kaplon, Tomasz M AU - Kaplon TM AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland. FAU - Rymarczyk, Grzegorz AU - Rymarczyk G FAU - Nocula-Lugowska, Malgorzata AU - Nocula-Lugowska M FAU - Jakob, Michal AU - Jakob M FAU - Kochman, Marian AU - Kochman M FAU - Lisowski, Marek AU - Lisowski M FAU - Szewczuk, Zbigniew AU - Szewczuk Z FAU - Ozyhar, Andrzej AU - Ozyhar A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080718 PL - United States TA - Biomacromolecules JT - Biomacromolecules JID - 100892849 RN - 0 (Protein Sorting Signals) RN - 0 (Recombinant Proteins) RN - 0 (Zebrafish Proteins) RN - 0 (starmaker protein, zebrafish) RN - H0G9379FGK (Calcium Carbonate) SB - IM MH - Animals MH - Biophysics/methods MH - Calcium Carbonate/chemistry MH - Dose-Response Relationship, Drug MH - Fishes MH - Genetic Vectors MH - Otolithic Membrane/*physiology MH - Protein Conformation MH - Protein Sorting Signals MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Spectrometry, Mass, Electrospray Ionization/methods MH - Spectrophotometry, Ultraviolet/methods MH - Zebrafish MH - Zebrafish Proteins/*chemistry EDAT- 2008/07/19 09:00 MHDA- 2008/12/17 09:00 CRDT- 2008/07/19 09:00 PHST- 2008/07/18 [aheadofprint] AID - 10.1021/bm800135m [doi] PST - ppublish SO - Biomacromolecules. 2008 Aug;9(8):2118-25. doi: 10.1021/bm800135m. Epub 2008 Jul 18. PMID- 12846565 OWN - NLM STAT- MEDLINE DA - 20030708 DCOM- 20030812 LR - 20090724 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 42 IP - 27 DP - 2003 Jul 15 TI - The small protein CP12: a protein linker for supramolecular complex assembly. PG - 8163-70 AB - CP12 is an 8.5-kDa nuclear-encoded chloroplast protein, isolated from higher plants. It forms part of a core complex of two dimers of phosphoribulokinase (PRK), two tetramers of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and CP12. The role of CP12 in this complex assembly has not been determined. To address this question, we cloned a cDNA encoding the mature CP12 from the green alga Chlamydomonas reinhardtii and expressed it in Escherichia coli. Sequence alignments show that it is very similar to other CP12s, with four conserved cysteine residues forming two disulfide bridges in the oxidized CP12. On the basis of reconstitution assays and surface plasmon resonance binding studies, we show that oxidized, but not reduced, CP12 acts as a linker in the assembly of the complex, and we propose a model in which CP12 associates with GAPDH, causing its conformation to change. This GAPDH/CP12 complex binds PRK to form a half-complex (one unit). This unit probably dimerizes due partially to interactions between the enzymes of each unit. Reduced CP12 being unable to reconstitute the complex, we studied the structures of oxidized and reduced CP12 by NMR and circular dichroism to determine whether reduction induced structural transitions. Oxidized CP12 is mainly composed of alpha helix and coil segments, and is extremely flexible, while reduced CP12 is mainly unstructured. Remarkably, CP12 has similar physicochemical properties to those of "intrinsically unstructured proteins" that are also involved in regulating macromolecular complexes, or in their assembly. CP12s are thus one of the few protein families of intrinsically unstructured proteins specific to plants. FAU - Graciet, Emmanuelle AU - Graciet E AD - Laboratoire d'ingenierie des proteines et controle metabolique, Departement Biologie des genomes, Institut Jacques Monod, UMR 7592 CNRS, Universites Paris VI -VII, 2 place Jussieu, 75251 Paris Cedex 05, France. FAU - Gans, Pierre AU - Gans P FAU - Wedel, Norbert AU - Wedel N FAU - Lebreton, Sandrine AU - Lebreton S FAU - Camadro, Jean-Michel AU - Camadro JM FAU - Gontero, Brigitte AU - Gontero B LA - eng PT - Journal Article PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA Primers) RN - 0 (Disulfides) RN - 0 (Plant Proteins) RN - 0 (Recombinant Proteins) RN - EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases) RN - EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)) RN - EC 2.7.1.19 (phosphoribulokinase) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Chlamydomonas reinhardtii/*chemistry MH - Circular Dichroism MH - DNA Primers MH - Disulfides/chemistry MH - Glyceraldehyde-3-Phosphate Dehydrogenases/chemistry MH - Molecular Sequence Data MH - Oxidation-Reduction MH - Phosphotransferases (Alcohol Group Acceptor)/chemistry MH - Plant Proteins/*chemistry MH - Recombinant Proteins/chemistry/genetics MH - Sequence Homology, Amino Acid MH - Surface Plasmon Resonance EDAT- 2003/07/09 05:00 MHDA- 2003/08/13 05:00 CRDT- 2003/07/09 05:00 AID - 10.1021/bi034474x [doi] PST - ppublish SO - Biochemistry. 2003 Jul 15;42(27):8163-70. PMID- 16601002 OWN - NLM STAT- MEDLINE DA - 20060627 DCOM- 20060908 LR - 20061115 IS - 1367-4803 (Print) IS - 1367-4803 (Linking) VI - 22 IP - 13 DP - 2006 Jul 1 TI - Intrinsically disordered C-terminal segments of voltage-activated potassium channels: a possible fishing rod-like mechanism for channel binding to scaffold proteins. PG - 1546-50 AB - Membrane-embedded voltage-activated potassium channels (Kv) bind intracellular scaffold proteins, such as the Post Synaptic Density 95 (PSD-95) protein, using a conserved PDZ-binding motif located at the channels' C-terminal tip. This interaction underlies Kv-channel clustering, and is important for the proper assembly and functioning of the synapse. Here we demonstrate that the C-terminal segments of Kv channels adjacent to the PDZ-binding motif are intrinsically disordered. Phylogenetic analysis of the Kv channel family reveals a cluster of channel sequences belonging to three out of the four main channel families, for which an association is demonstrated between the presence of the consensus terminal PDZ-binding motif and the intrinsically disordered nature of the immediately adjacent C-terminal segment. Our observations, combined with a structural analogy to the N-terminal intra-molecular ball-and-chain mechanism for Kv channel inactivation, suggest that the C-terminal disordered segments of these channel families encode an inter-molecular fishing rod-like mechanism for K(+) channel binding to scaffold proteins. FAU - Magidovich, Elhanan AU - Magidovich E AD - Department of Life Sciences and the Zlotowski Center for Neurosciences, Ben Gurion University of the Negev Beer Sheva, Israel. FAU - Fleishman, Sarel J AU - Fleishman SJ FAU - Yifrach, Ofer AU - Yifrach O LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060406 PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 0 (DLG4 protein, human) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Membrane Proteins) RN - 0 (Potassium Channels) RN - 0 (Shaker Superfamily of Potassium Channels) SB - IM MH - Amino Acid Motifs MH - Animals MH - Computational Biology/*methods MH - Humans MH - Intracellular Signaling Peptides and Proteins/chemistry MH - Membrane Proteins/chemistry MH - Models, Biological MH - Phylogeny MH - Potassium Channels/*chemistry MH - Protein Binding MH - Protein Denaturation MH - Protein Structure, Tertiary MH - Shaker Superfamily of Potassium Channels/*chemistry EDAT- 2006/04/08 09:00 MHDA- 2006/09/09 09:00 CRDT- 2006/04/08 09:00 PHST- 2006/04/06 [aheadofprint] AID - btl137 [pii] AID - 10.1093/bioinformatics/btl137 [doi] PST - ppublish SO - Bioinformatics. 2006 Jul 1;22(13):1546-50. Epub 2006 Apr 6. PMID- 16645638 OWN - NLM STAT- MEDLINE DA - 20061214 DCOM- 20070215 LR - 20071114 IS - 1350-9047 (Print) IS - 1350-9047 (Linking) VI - 14 IP - 1 DP - 2007 Jan TI - Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets. PG - 128-36 AB - All BH3-only proteins, key initiators of programmed cell death, interact tightly with multiple binding partners and have sequences of low complexity, properties that are the hallmark of intrinsically unstructured proteins (IUPs). We show, using spectroscopic methods, that the BH3-only proteins Bim, Bad and Bmf are unstructured in the absence of binding partners. Detailed sequence analyses are consistent with this observation and suggest that most BH3-only proteins are unstructured. When Bim binds and inactivates prosurvival proteins, most residues remain disordered, only the BH3 element becomes structured, and the short alpha-helical molecular recognition element can be considered to behave as a 'bead on a string'. Coupled folding and binding is typical of many IUPs that have important signaling roles, such as BH3-only proteins, as the inherent structural plasticity favors interaction with multiple targets. This understanding offers promise for the development of BH3 mimetics, as multiple modes of binding are tolerated. FAU - Hinds, M G AU - Hinds MG AD - The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia. FAU - Smits, C AU - Smits C FAU - Fredericks-Short, R AU - Fredericks-Short R FAU - Risk, J M AU - Risk JM FAU - Bailey, M AU - Bailey M FAU - Huang, D C S AU - Huang DC FAU - Day, C L AU - Day CL LA - eng GR - CA 80188/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20060428 PL - England TA - Cell Death Differ JT - Cell death and differentiation JID - 9437445 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Apoptosis Regulatory Proteins) RN - 0 (BCL2L2 protein, human) RN - 0 (Bad protein, mouse) RN - 0 (Bcl-2-like protein 11) RN - 0 (Bmf protein, mouse) RN - 0 (Membrane Proteins) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (bcl-Associated Death Protein) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry/genetics/isolation & purification/metabolism MH - Animals MH - Apoptosis Regulatory Proteins/*chemistry/genetics/isolation & purification/*metabolism MH - Circular Dichroism MH - Membrane Proteins/*chemistry/genetics/isolation & purification/metabolism MH - Mice MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins/*chemistry/genetics/isolation & purification/metabolism MH - Recombinant Fusion Proteins/chemistry/genetics/isolation & purification/metabolism MH - bcl-Associated Death Protein/*chemistry/genetics/isolation & purification/metabolism EDAT- 2006/04/29 09:00 MHDA- 2007/02/16 09:00 CRDT- 2006/04/29 09:00 PHST- 2006/04/28 [aheadofprint] AID - 4401934 [pii] AID - 10.1038/sj.cdd.4401934 [doi] PST - ppublish SO - Cell Death Differ. 2007 Jan;14(1):128-36. Epub 2006 Apr 28. PMID- 17611012 OWN - NLM STAT- MEDLINE DA - 20070810 DCOM- 20071017 LR - 20131121 IS - 0301-4622 (Print) IS - 0301-4622 (Linking) VI - 129 IP - 2-3 DP - 2007 Sep TI - On the NMR analysis of pKa values in the unfolded state of proteins by extrapolation to zero denaturant. PG - 242-50 AB - Detailed knowledge of the pH-dependence in both folded and unfolded states of proteins is essential to understand the role of electrostatics in protein stability. The increasing number of natively disordered proteins constitutes an excellent source for the NMR analysis of pKa values in the unfolded state of proteins. However, the tendency of many natively disordered proteins to aggregate via intermolecular hydrophobic clusters limits their NMR analysis over a wide pH range. To assess whether the pKa values in natively disordered polypeptides can be extrapolated from NMR measurements in the presence of denaturants, the natively disordered backbone of the C-terminal fragment 75 to 105 of Human Thioredoxin was studied. First, assignments using triple resonance experiments were performed to confirm lack of secondary structure. Then the pH-dependence of the amides and carboxylate side chains of Glu residues (Glu88, Glu95, Glu98, and Glu103) in the pH range from 2.0 to 7.0 was monitored using 2D 1H15N HSQC and 3D C(CO)NH experiments, and the behavior of their amides and corresponding carboxyl groups was compared to confirm the absence of nonlocal interactions. Lastly, the effect of increasing dimethyl urea concentration on the pKa values of these Glu residues was monitored. The results indicate that: (i) the dispersion in the pKa of carboxyl groups and the pH midpoints of amides in Glu residues is about 0.5 pH units and 0.6 pH units, respectively; (ii) the backbone amides of the Glu residues exhibit pH midpoints which are within 0.2 pH units from those of their carboxylates; (iii) the addition of denaturant produces upshifts in the pKa values of Glu residues that are nearly independent of their position in the sequence; and (iv) these upshifts show a nonlinear behavior in denaturant concentration, complicating the extrapolation to zero denaturant. Nevertheless, the relative ordering of the pKa values of Glu residues is preserved over the whole range of denaturant concentrations indicating that measurements at high denaturant concentration (e.g. 4 M dimethyl urea) can yield a qualitatively correct ranking of the pKa of these residues in natively disordered proteins whose pH-dependence cannot be monitored directly by NMR. FAU - Quijada, Jeniffer AU - Quijada J AD - Department of Chemistry, City College of New York, 138th Street and Convent Avenue, New York, NY 10031, USA. FAU - Lopez, Gary AU - Lopez G FAU - Versace, Rodney AU - Versace R FAU - Ramirez, Luis AU - Ramirez L FAU - Tasayco, Maria Luisa AU - Tasayco ML LA - eng GR - 5G12RR03060/RR/NCRR NIH HHS/United States GR - GM66354/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20070614 PL - Netherlands TA - Biophys Chem JT - Biophysical chemistry JID - 0403171 RN - 0 (Amides) RN - 0 (Proteins) RN - 3KX376GY7L (Glutamic Acid) RN - 52500-60-4 (Thioredoxins) SB - IM MH - Amides/chemistry MH - Amino Acid Sequence MH - Glutamic Acid/*chemistry MH - Humans MH - Hydrogen-Ion Concentration MH - *Models, Chemical MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Denaturation MH - *Protein Folding MH - Proteins/*chemistry MH - Static Electricity MH - Thioredoxins/chemistry EDAT- 2007/07/06 09:00 MHDA- 2007/10/18 09:00 CRDT- 2007/07/06 09:00 PHST- 2007/02/09 [received] PHST- 2007/06/04 [revised] PHST- 2007/06/04 [accepted] PHST- 2007/06/14 [aheadofprint] AID - S0301-4622(07)00154-8 [pii] AID - 10.1016/j.bpc.2007.06.004 [doi] PST - ppublish SO - Biophys Chem. 2007 Sep;129(2-3):242-50. Epub 2007 Jun 14. PMID- 23692518 OWN - NLM STAT- MEDLINE DA - 20130708 DCOM- 20140224 LR - 20141113 IS - 1365-2958 (Electronic) IS - 0950-382X (Linking) VI - 89 IP - 2 DP - 2013 Jul TI - A flexible C-terminal linker is required for proper FtsZ assembly in vitro and cytokinetic ring formation in vivo. PG - 249-63 LID - 10.1111/mmi.12272 [doi] AB - Assembly of the cytoskeletal protein FtsZ into a ring-like structure is required for bacterial cell division. Structurally, FtsZ consists of four domains: the globular N-terminal core, a flexible linker, 8-9 conserved residues implicated in interactions with modulatory proteins, and a highly variable set of 4-10 residues at its very C terminus. Largely ignored and distinguished by lack of primary sequence conservation, the linker is presumed to be intrinsically disordered. Here we employ genetics, biochemistry and cytology to dissect the role of the linker in FtsZ function. Data from chimeric FtsZs substituting the native linker with sequences from unrelated FtsZs as well as a helical sequence from human beta-catenin indicate that while variations in the primary sequence are well tolerated, an intrinsically disordered linker is essential for Bacillus subtilis FtsZ assembly. Linker lengths ranging from 25 to 100 residues supported FtsZ assembly, but replacing the B. subtilis FtsZ linker with a 249-residue linker from Agrobacterium tumefaciens FtsZ interfered with cell division. Overall, our results support a model in which the linker acts as a flexible tether allowing FtsZ to associate with the membrane through a conserved C-terminal domain while simultaneously interacting with itself and modulatory proteins in the cytoplasm. CI - (c) 2013 John Wiley & Sons Ltd. FAU - Buske, P J AU - Buske PJ AD - Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA. FAU - Levin, Petra Anne AU - Levin PA LA - eng GR - GM64671/GM/NIGMS NIH HHS/United States GR - R01 GM064671/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20130610 PL - England TA - Mol Microbiol JT - Molecular microbiology JID - 8712028 RN - 0 (Bacterial Proteins) RN - 0 (Cytoskeletal Proteins) RN - 0 (FtsZ protein, Bacteria) SB - IM MH - Bacillus subtilis/cytology/genetics/metabolism MH - Bacterial Proteins/chemistry/genetics/*metabolism MH - Cell Division/physiology MH - *Cytokinesis MH - Cytoskeletal Proteins/chemistry/genetics/*metabolism PMC - PMC3708608 MID - NIHMS485227 OID - NLM: NIHMS485227 OID - NLM: PMC3708608 EDAT- 2013/05/23 06:00 MHDA- 2014/02/25 06:00 CRDT- 2013/05/23 06:00 PHST- 2013/05/18 [accepted] PHST- 2013/06/10 [aheadofprint] AID - 10.1111/mmi.12272 [doi] PST - ppublish SO - Mol Microbiol. 2013 Jul;89(2):249-63. doi: 10.1111/mmi.12272. Epub 2013 Jun 10. PMID- 21851959 OWN - NLM STAT- MEDLINE DA - 20110830 DCOM- 20111027 IS - 1096-0341 (Electronic) IS - 0042-6822 (Linking) VI - 418 IP - 2 DP - 2011 Sep 30 TI - Intrinsic disorder in the common N-terminus of human adenovirus 5 E1B-55K and its related E1BN proteins indicated by studies on E1B-93R. PG - 133-43 LID - 10.1016/j.virol.2011.07.012 [doi] AB - The E1B transcription unit of human adenovirus encodes at least five different proteins generated by alternative splicing of a common E1B precursor mRNA. E1B-156R, -93R and -84R contain individual carboxy termini but share a common amino terminus. To acquire data on the structure of the amino terminus we performed biophysical analyses on E1B-93R. We show that E1B-93R is mostly unstructured and fulfills the criteria of an intrinsically disordered protein (IDP). The intrinsic disorder in the amino terminus of these proteins is evolutionary conserved in all seven human adenovirus species. As IDPs comprise a rapidly growing family of proteins which, despite their lack of a well defined structure, often fulfill essential regulatory functions, the observations described here might open up a new avenue for the understanding of the regulation and functions of E1B proteins, in particular the multifunctional E1B-55K oncoprotein. CI - Copyright (c) 2011 Elsevier Inc. All rights reserved. FAU - Sieber, Timo AU - Sieber T AD - Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany. FAU - Scholz, Roland AU - Scholz R FAU - Spoerner, Michael AU - Spoerner M FAU - Schumann, Frank AU - Schumann F FAU - Kalbitzer, Hans Robert AU - Kalbitzer HR FAU - Dobner, Thomas AU - Dobner T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110817 PL - United States TA - Virology JT - Virology JID - 0110674 RN - 0 (Adenovirus E1B Proteins) RN - 0 (DNA, Complementary) SB - IM MH - Adenovirus E1B Proteins/*genetics/*metabolism MH - Adenoviruses, Human/genetics/*metabolism MH - Amino Acid Sequence MH - DNA, Complementary MH - Gene Expression Regulation, Viral/*physiology MH - HeLa Cells MH - Humans MH - Models, Molecular MH - Mutation MH - Protein Conformation EDAT- 2011/08/20 06:00 MHDA- 2011/10/28 06:00 CRDT- 2011/08/20 06:00 PHST- 2011/04/28 [received] PHST- 2011/07/13 [revised] PHST- 2011/07/18 [accepted] PHST- 2011/08/17 [aheadofprint] AID - S0042-6822(11)00318-7 [pii] AID - 10.1016/j.virol.2011.07.012 [doi] PST - ppublish SO - Virology. 2011 Sep 30;418(2):133-43. doi: 10.1016/j.virol.2011.07.012. Epub 2011 Aug 17. PMID- 18423664 OWN - NLM STAT- MEDLINE DA - 20080429 DCOM- 20080609 LR - 20140917 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 378 IP - 5 DP - 2008 May 16 TI - Characterization of conformational and dynamic properties of natively unfolded human and mouse alpha-synuclein ensembles by NMR: implication for aggregation. PG - 1104-15 LID - 10.1016/j.jmb.2008.03.017 [doi] AB - Conversion of human alpha-synuclein (aS) from the free soluble state to the insoluble fibrillar state has been implicated in the etiology of Parkinson's disease. Human aS is highly homologous in amino acid sequence to mouse aS, which contains seven substitutions including the A53T that has been linked to familial Parkinson's disease, and including five substitutions in the C-terminal region. It has been shown that the rate of fibrillation is highly dependent on the exact sequence of the protein, and mouse aS is reported to aggregate more rapidly than human aS in vitro. Nuclear magnetic resonance experiments of mouse and human aS at supercooled temperatures (263 K) are used to understand the effect of sequence on conformational fluctuations in the disordered ensembles and to relate these to differences in propensities to aggregate. We show that both aS are natively unfolded at low temperature with different propensities to secondary structure, backbone dynamics and long-range contacts across the protein. Mouse aS exhibits a higher propensity to helical conformation around the C-terminal substitutions as well as the loss of transient long-range contacts from the C- to the N-terminal end and hydrophobic central regions of the protein relative to human aS. Lack of back-folding from the C-terminal end of mouse aS exposes the N-terminal region, which is shown, by (15)N relaxation experiments, to be very restricted in mobility relative to human aS. We propose that the restricted mobility in the N-terminal region may arise from transient interchain interactions, suggesting that the N-terminal KTK(E/Q)GV repeats may serve as initiation sites for aggregation in mouse aS. These transient interchain interactions coupled with a non-A beta amyloid component (NAC) region that is both more exposed and has a higher propensity to beta structure may accelerate the rate of fibril formation of aS. FAU - Wu, Kuen-Phon AU - Wu KP AD - Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA. FAU - Kim, Seho AU - Kim S FAU - Fela, David A AU - Fela DA FAU - Baum, Jean AU - Baum J LA - eng GR - R01 GM087012/GM/NIGMS NIH HHS/United States GR - R01 GM087012-02/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20080318 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Animals MH - Humans MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Parkinson Disease/etiology/metabolism/pathology MH - Protein Folding MH - *Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - alpha-Synuclein/*chemistry/metabolism PMC - PMC3064448 MID - NIHMS252169 OID - NLM: NIHMS252169 OID - NLM: PMC3064448 EDAT- 2008/04/22 09:00 MHDA- 2008/06/10 09:00 CRDT- 2008/04/22 09:00 PHST- 2007/12/31 [received] PHST- 2008/03/08 [revised] PHST- 2008/03/11 [accepted] PHST- 2008/03/18 [aheadofprint] AID - S0022-2836(08)00321-5 [pii] AID - 10.1016/j.jmb.2008.03.017 [doi] PST - ppublish SO - J Mol Biol. 2008 May 16;378(5):1104-15. doi: 10.1016/j.jmb.2008.03.017. Epub 2008 Mar 18. PMID- 18423665 OWN - NLM STAT- MEDLINE DA - 20080429 DCOM- 20080609 LR - 20140903 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 378 IP - 5 DP - 2008 May 16 TI - Computational studies reveal phosphorylation-dependent changes in the unstructured R domain of CFTR. PG - 1052-63 LID - 10.1016/j.jmb.2008.03.033 [doi] AB - The cystic fibrosis transmembrane conductance regulator (CFTR) is a cAMP-dependent chloride channel that is mutated in cystic fibrosis, an inherited disease of high morbidity and mortality. The phosphorylation of its approximately 200 amino acid R domain by protein kinase A is obligatory for channel gating under normal conditions. The R domain contains more than ten PKA phosphorylation sites. No individual site is essential but phosphorylation of increasing numbers of sites enables progressively greater channel activity. In spite of numerous studies of the role of the R domain in CFTR regulation, its mechanism of action remains largely unknown. This is because neither its structure nor its interactions with other parts of CFTR have been completely elucidated. Studies have shown that the R domain lacks well-defined secondary structural elements and is an intrinsically disordered region of the channel protein. Here, we have analyzed the disorder pattern and employed computational methods to explore low-energy conformations of the R domain. The specific disorder and secondary structure patterns detected suggest the presence of molecular recognition elements (MoREs) that may mediate phosphorylation-regulated intra- and inter-domain interactions. Simulations were performed to generate an ensemble of accessible R domain conformations. Although the calculated structures may represent more compact conformers than occur in vivo, their secondary structure propensities are consistent with predictions and published experimental data. Equilibrium simulations of a mimic of a phosphorylated R domain showed that it exhibited an increased radius of gyration. In one possible interpretation of these findings, by changing its size, the globally unstructured R domain may act as an entropic spring to perturb the packing of membrane-spanning sequences that constitute the ion permeability pathway and thereby activate channel gating. FAU - Hegedus, Tamas AU - Hegedus T AD - Department of Biochemistry and Biophysics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599, USA. hegedus@med.unc.edu FAU - Serohijos, Adrian W R AU - Serohijos AW FAU - Dokholyan, Nikolay V AU - Dokholyan NV FAU - He, Lihua AU - He L FAU - Riordan, John R AU - Riordan JR LA - eng GR - R01 DK051619/DK/NIDDK NIH HHS/United States GR - R01 DK051619-08/DK/NIDDK NIH HHS/United States GR - R01 DK051870/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20080326 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 126880-72-6 (Cystic Fibrosis Transmembrane Conductance Regulator) SB - IM MH - Algorithms MH - Amino Acid Sequence MH - Animals MH - *Computer Simulation MH - Cystic Fibrosis/genetics MH - Cystic Fibrosis Transmembrane Conductance Regulator/*chemistry/genetics MH - Humans MH - Ion Channel Gating MH - Models, Molecular MH - Molecular Sequence Data MH - Monte Carlo Method MH - Phosphorylation MH - *Protein Structure, Secondary MH - *Protein Structure, Tertiary PMC - PMC2556564 MID - NIHMS50814 OID - NLM: NIHMS50814 OID - NLM: PMC2556564 EDAT- 2008/04/22 09:00 MHDA- 2008/06/10 09:00 CRDT- 2008/04/22 09:00 PHST- 2007/08/27 [received] PHST- 2008/03/11 [revised] PHST- 2008/03/15 [accepted] PHST- 2008/03/26 [aheadofprint] AID - S0022-2836(08)00353-7 [pii] AID - 10.1016/j.jmb.2008.03.033 [doi] PST - ppublish SO - J Mol Biol. 2008 May 16;378(5):1052-63. doi: 10.1016/j.jmb.2008.03.033. Epub 2008 Mar 26. PMID- 11519747 OWN - NLM STAT- MEDLINE DA - 20010824 DCOM- 20020204 LR - 20071114 IS - 0925-2738 (Print) IS - 0925-2738 (Linking) VI - 20 IP - 3 DP - 2001 Jul TI - Backbone dynamics of the natively unfolded pro-peptide of subtilisin by heteronuclear NMR relaxation studies. PG - 233-49 AB - The dynamics of the natively unfolded form of the pro-peptide of subtilisin (PPS) have been characterized at two different pHs (6.0 and 3.0) by 15N relaxation experiments. 15N relaxation data is obtained at multiple field strengths and a detailed comparison of spectral density mapping, the model free approach and the recently proposed Cole-Cole model free (CC-MF) analysis is presented. The CC-MF analysis provides a better fit to the observed magnetic field dependence of 15N relaxation data of unfolded PPS than conventional model free approaches and shows that fluctuations in R2 may be accounted for by a distribution of correlation times on the nanosecond timescale. A new parameter epsilon derives from the analysis and represents the width of the distribution function and the heterogeneity of the dynamics on the nanosecond timescale at a particular site. Particularly interesting is the observation that epsilon is sensitive to pH changes and that PPS samples a wider distribution of nanosecond time scale motions at less acidic pHs than at more acidic pHs. These results suggest that PPS experiences a higher degree of correlated motion at pH 6.0 and that electrostatic interactions may be important for inducing correlated motions on the nanosecond timescale in unfolded PPS. FAU - Buevich, A V AU - Buevich AV AD - Department of Chemistry, Rutgers University, Piscataway, NJ 08854, USA. FAU - Shinde, U P AU - Shinde UP FAU - Inouye, M AU - Inouye M FAU - Baum, J AU - Baum J LA - eng GR - GM-45302/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - Netherlands TA - J Biomol NMR JT - Journal of biomolecular NMR JID - 9110829 RN - 0 (Enzyme Precursors) RN - 0 (Escherichia coli Proteins) RN - 0 (Nitrogen Isotopes) RN - EC 3.4.21.- (Subtilisins) RN - EC 3.4.21.- (preprosubtilisin) SB - IM MH - Amino Acid Sequence MH - Enzyme Precursors/*chemistry MH - Escherichia coli Proteins/*chemistry MH - Hydrogen-Ion Concentration MH - Models, Chemical MH - Molecular Sequence Data MH - Motion MH - Nitrogen Isotopes/analysis MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Protein Denaturation MH - Subtilisins/*chemistry EDAT- 2001/08/25 10:00 MHDA- 2002/02/05 10:01 CRDT- 2001/08/25 10:00 PST - ppublish SO - J Biomol NMR. 2001 Jul;20(3):233-49. PMID- 12732633 OWN - NLM STAT- MEDLINE DA - 20030704 DCOM- 20030814 LR - 20081121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 28 DP - 2003 Jul 11 TI - Molecular and functional characterization of clathrin- and AP-2-binding determinants within a disordered domain of auxilin. PG - 25357-68 AB - Uncoating of clathrin-coated vesicles requires the J-domain protein auxilin for targeting hsc70 to the clathrin coats and for stimulating the hsc70 ATPase activity. This results in the release of hsc70-complexed clathrin triskelia and concomitant dissociation of the coat. To understand the complex role of auxilin in uncoating and clathrin assembly in more detail, we analyzed the molecular organization of its clathrin-binding domain (amino acids 547-813). CD spectroscopy of auxilin fragments revealed that the clathrin-binding domain is almost completely disordered in solution. By systematic mapping using synthetic peptides and by site-directed mutagenesis, we identified short peptide sequences involved in clathrin heavy chain and AP-2 binding and evaluated their significance for the function of auxilin. Some of the binding determinants, including those containing sequences 674DPF and 636WDW, showed dual specificity for both clathrin and AP-2. In contrast, the two DLL motifs within the clathrin-binding domain were exclusively involved in clathrin binding. Surprisingly, they interacted not only with the N-terminal domain of the heavy chain, but also with the distal domain. Moreover, both DLL peptides proved to be essential for clathrin assembly and uncoating. In addition, we found that the motif 726NWQ is required for efficient clathrin assembly activity. Auxilin shares a number of protein-protein interaction motifs with other endocytic proteins, including AP180. We demonstrate that AP180 and auxilin compete for binding to the alpha-ear domain of AP-2. Like AP180, auxilin also directly interacts with the ear domain of beta-adaptin. On the basis of our data, we propose a refined model for the uncoating mechanism of clathrin-coated vesicles. FAU - Scheele, Urte AU - Scheele U AD - Departments of Cell Biology and Biophysical Chemistry, Hannover Medical School, 30625 Hannover, Germany. FAU - Alves, Jurgen AU - Alves J FAU - Frank, Ronald AU - Frank R FAU - Duwel, Michael AU - Duwel M FAU - Kalthoff, Christoph AU - Kalthoff C FAU - Ungewickell, Ernst AU - Ungewickell E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030505 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Auxilins) RN - 0 (Clathrin) RN - 0 (DNA-Binding Proteins) RN - 0 (HSC70 Heat-Shock Proteins) RN - 0 (HSP70 Heat-Shock Proteins) RN - 0 (Peptides) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factor AP-2) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) RN - EC 2.5.1.18 (Glutathione Transferase) RN - EC 3.4.21.4 (Trypsin) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Auxilins/*chemistry/genetics/metabolism MH - Binding Sites MH - Binding, Competitive MH - Circular Dichroism MH - Clathrin/chemistry/*metabolism MH - DNA/metabolism MH - DNA-Binding Proteins/*metabolism MH - Dose-Response Relationship, Drug MH - Electrophoresis, Polyacrylamide Gel MH - Glutathione Transferase/metabolism MH - HSC70 Heat-Shock Proteins MH - HSP70 Heat-Shock Proteins/metabolism MH - Hot Temperature MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Peptides/chemistry MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Transcription Factor AP-2 MH - Transcription Factors/*metabolism MH - Trypsin/pharmacology MH - Ultraviolet Rays EDAT- 2003/05/07 05:00 MHDA- 2003/08/15 05:00 CRDT- 2003/05/07 05:00 PHST- 2003/05/05 [aheadofprint] AID - 10.1074/jbc.M303738200 [doi] AID - M303738200 [pii] PST - ppublish SO - J Biol Chem. 2003 Jul 11;278(28):25357-68. Epub 2003 May 5. PMID- 22910563 OWN - NLM STAT- MEDLINE DA - 20121002 DCOM- 20130430 LR - 20150325 IS - 1096-0279 (Electronic) IS - 1046-5928 (Linking) VI - 85 IP - 2 DP - 2012 Oct TI - Engineering of an elastic scaffolding polyprotein based on an SH3-binding intrinsically disordered titin PEVK module. PG - 187-99 LID - 10.1016/j.pep.2012.08.003 [doi] LID - S1046-5928(12)00212-4 [pii] AB - Titin is a large elastic protein found in muscle that maintains the elasticity and structural integrity of the sarcomere. The PEVK region of titin is intrinsically disordered, highly elastic and serves as a hub to bind signaling proteins. Systematic investigation of the structure and affinity profile of the PEVK region will provide important information about the functions of titin. Since PEVK is highly heterogeneous due to extensive differential splicing from more than one hundred exons, we engineered and expressed polyproteins that consist of a defined number of identical single exon modules. These customized polyproteins reduce heterogeneity, amplify interactions of less dominant modules, and most importantly, provide tags for atomic force microscopy and allow more readily interpretable data from single-molecule techniques. Expression and purification of recombinant polyprotein with repeat regions presented many technical challenges: recombination events in tandem repeats of identical DNA sequences exacerbated by high GC content, toxicity of polymer plasmid and expressed protein to the bacteria; early truncation of proteins expressed with different numbers of modules; and extreme sensitivity to proteolysis. We have investigated a number of in vitro and in vivo bacterial and yeast expression systems, as well as baculoviral systems as potential solutions to these problems. We successfully expressed and purified in gram quantities a polyprotein derived from human titin exon 172 using Pichia pastoris yeast. This study provides valuable insights into the technical challenges regarding the engineering and purification of a tandem repeat sequence of an intrinsically disordered biopolymer. CI - Copyright (c) 2012 Elsevier Inc. All rights reserved. FAU - Tsai, Wanxia Li AU - Tsai WL AD - Muscle Proteomics and Nanotechnology Section, Laboratory of Muscle Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH/DHHS, Bethesda, MD 20892-8024, USA. liwan@mail.nih.gov FAU - Forbes, Jeffrey G AU - Forbes JG FAU - Wang, Kuan AU - Wang K LA - eng GR - Z99 AR999999/Intramural NIH HHS/United States PT - Journal Article DEP - 20120814 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (Connectin) RN - 0 (Muscle Proteins) RN - 0 (Polyproteins) RN - 0 (Recombinant Proteins) RN - 0 (TTN protein, human) RN - EC 2.7.- (Protein Kinases) RN - IY9XDZ35W2 (Glucose) SB - IM MH - Baculoviridae/genetics MH - Blotting, Western MH - Connectin MH - Escherichia coli/genetics MH - Glucose/metabolism MH - Humans MH - Models, Molecular MH - Muscle Proteins/chemistry/*genetics/metabolism MH - Pichia/genetics MH - Plasmids MH - Polyproteins/chemistry/*genetics/metabolism MH - Protein Engineering MH - Protein Kinases/chemistry/*genetics/metabolism MH - Recombinant Proteins/chemistry/*genetics/isolation & purification/metabolism MH - Tandem Repeat Sequences MH - src Homology Domains PMC - PMC3463739 MID - NIHMS401525 OID - NLM: NIHMS401525 OID - NLM: PMC3463739 EDAT- 2012/08/23 06:00 MHDA- 2013/05/01 06:00 CRDT- 2012/08/23 06:00 PHST- 2012/05/07 [received] PHST- 2012/07/24 [revised] PHST- 2012/08/03 [accepted] PHST- 2012/08/14 [aheadofprint] AID - S1046-5928(12)00212-4 [pii] AID - 10.1016/j.pep.2012.08.003 [doi] PST - ppublish SO - Protein Expr Purif. 2012 Oct;85(2):187-99. doi: 10.1016/j.pep.2012.08.003. Epub 2012 Aug 14. PMID- 9488644 OWN - NLM STAT- MEDLINE DA - 19980318 DCOM- 19980318 LR - 20131121 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 279 IP - 5356 DP - 1998 Mar 6 TI - Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. PG - 1504-13 AB - Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. The crystal structures at 2.1 and 2.5 angstrom resolution of reconstituted human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin is proposed on the basis of chemical and biochemical information combined with these three-dimensional structures of topoisomerase I-DNA complexes. FAU - Redinbo, M R AU - Redinbo MR AD - Biomolecular Structure Center and Department of Biological Structure, Box 357742, School of Medicine, University of Washington, Seattle, WA 98195, USA. FAU - Stewart, L AU - Stewart L FAU - Kuhn, P AU - Kuhn P FAU - Champoux, J J AU - Champoux JJ FAU - Hol, W G AU - Hol WG LA - eng GR - CA65656/CA/NCI NIH HHS/United States GR - GM49156/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Antineoplastic Agents, Phytogenic) RN - 0 (DNA-Binding Proteins) RN - 0 (HCFC1 protein, human) RN - 0 (Homeodomain Proteins) RN - 0 (Host Cell Factor C1) RN - 0 (Octamer Transcription Factor-1) RN - 0 (Oligodeoxyribonucleotides) RN - 0 (POU2F1 protein, human) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) RN - 125724-60-9 (HP1 integrase) RN - 42HK56048U (Tyrosine) RN - 9007-49-2 (DNA) RN - EC 2.7.7.- (Integrases) RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) RN - XT3Z54Z28A (Camptothecin) SB - IM CIN - Science. 1998 Mar 6;279(5356):1490-1. PMID: 9508726 MH - Antineoplastic Agents, Phytogenic/metabolism/pharmacology MH - Binding Sites MH - Camptothecin/analogs & derivatives/metabolism/pharmacology MH - Crystallography, X-Ray MH - DNA/chemistry/*metabolism MH - DNA Topoisomerases, Type I/*chemistry/genetics/metabolism MH - *DNA-Binding Proteins MH - Homeodomain Proteins/chemistry MH - Host Cell Factor C1 MH - Humans MH - Hydrogen Bonding MH - Integrases/chemistry MH - Models, Molecular MH - Mutation MH - Nucleic Acid Conformation MH - Octamer Transcription Factor-1 MH - Oligodeoxyribonucleotides/chemistry/metabolism MH - *Protein Conformation MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry MH - Transcription Factors/chemistry MH - Tyrosine/chemistry/metabolism EDAT- 1998/03/21 MHDA- 1998/03/21 00:01 CRDT- 1998/03/21 00:00 PST - ppublish SO - Science. 1998 Mar 6;279(5356):1504-13. PMID- 16288917 OWN - NLM STAT- MEDLINE DA - 20051212 DCOM- 20060203 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 354 IP - 4 DP - 2005 Dec 9 TI - Minimization and stabilization of the Mycobacterium tuberculosis recA intein. PG - 916-26 AB - Many naturally occurring inteins consist of two functionally independent domains, a protein-splicing domain and an endonuclease domain. In a previous study, a 168 amino acid residue mini-intein was generated by removal of the central endonuclease domain of the 440 residue Mycobacterium tuberculosis (Mtu) recA intein. In addition, directed evolution experiments identified a mutation, V67L, that improved the activity of the mini-intein significantly. A recent crystal structure shows that the loop connecting two beta-strands from the N-terminal and C-terminal intein subdomains of the mini-intein is disordered. The goals of the present study were to generate smaller mini-intein derivatives and to understand the basis for reversal of the splicing defect by the V67L mutation. Guided by the structural information, we generated a number of derivatives 135 to 152 residues in length, with V67 or L67. All of the new minimal inteins are functional in splicing. In vivo selection experiments for function showed that by removal of the loop region, 137 residues may be the lower limit for full protein-splicing activity. In addition, the activation effect of the V67L mutation was observed to be universal for mini-inteins longer than 137 residues. Structural and functional analyses indicate that the role of the mutation is in stabilization of the mini-intein core. FAU - Hiraga, Kaori AU - Hiraga K AD - Wadsworth Center, New York State Department of Health, Center for Medical Science, 150 New Scotland Avenue, Albany, NY 12208, USA. FAU - Derbyshire, Victoria AU - Derbyshire V FAU - Dansereau, John T AU - Dansereau JT FAU - Van Roey, Patrick AU - Van Roey P FAU - Belfort, Marlene AU - Belfort M LA - eng GR - GM44844/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20051021 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 8W8T17847W (Urea) RN - EC 2.7.7.- (Rec A Recombinases) RN - EC 3.4.- (Peptide Hydrolases) SB - IM MH - *Directed Molecular Evolution MH - Enzyme Stability MH - *Inteins MH - Mutation, Missense/physiology MH - Mycobacterium tuberculosis/*enzymology MH - Peptide Hydrolases/metabolism MH - Protein Denaturation MH - Protein Splicing MH - Protein Structure, Tertiary MH - Rec A Recombinases/*chemistry/*genetics MH - Sequence Deletion MH - Urea EDAT- 2005/11/18 09:00 MHDA- 2006/02/04 09:00 CRDT- 2005/11/18 09:00 PHST- 2005/07/29 [received] PHST- 2005/09/01 [revised] PHST- 2005/09/09 [accepted] PHST- 2005/10/21 [aheadofprint] AID - S0022-2836(05)01100-9 [pii] AID - 10.1016/j.jmb.2005.09.088 [doi] PST - ppublish SO - J Mol Biol. 2005 Dec 9;354(4):916-26. Epub 2005 Oct 21. PMID- 7664104 OWN - NLM STAT- MEDLINE DA - 19951012 DCOM- 19951012 LR - 20131121 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 2 IP - 6 DP - 1995 Jun TI - Engineering of plasminogen activator inhibitor-1 to reduce the rate of latency transition. PG - 442-5 FAU - Tucker, H M AU - Tucker HM FAU - Mottonen, J AU - Mottonen J FAU - Goldsmith, E J AU - Goldsmith EJ FAU - Gerard, R D AU - Gerard RD LA - eng PT - Letter PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Plasminogen Activator Inhibitor 1) RN - 3KX376GY7L (Glutamic Acid) RN - EC 3.4.21.- (Plasminogen Activators) SB - IM MH - Genetic Vectors MH - Glutamic Acid/chemistry MH - Half-Life MH - Kinetics MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Plasminogen Activator Inhibitor 1/*chemistry/genetics/isolation & purification/metabolism MH - Plasminogen Activators/metabolism MH - Protein Conformation MH - *Protein Engineering MH - Time Factors EDAT- 1995/06/01 MHDA- 1995/06/01 00:01 CRDT- 1995/06/01 00:00 PST - ppublish SO - Nat Struct Biol. 1995 Jun;2(6):442-5. PMID- 16515451 OWN - NLM STAT- MEDLINE DA - 20060306 DCOM- 20060406 LR - 20061115 IS - 0929-8665 (Print) IS - 0929-8665 (Linking) VI - 13 IP - 3 DP - 2006 TI - Studying the natively unfolded neuronal Tau protein by solution NMR spectroscopy. PG - 235-46 AB - The neuronal Tau protein, whose physiological role is to stabilize the microtubules, is found under the form of aggregated filaments and tangles in Alzheimer's diseased neurons. Until recently detailed structural analysis of the natively unfolded Tau protein has been hindered due to its shear size and unfavourable amino acid composition. We review here the recent progress in the assignments of the full-length polypeptide using novel methods of product planes and peptide NMR mapping, and indicate the structural insights that can be obtained from this assignment. Preliminary NMR data on the fibers show that the assignment enables a precise mapping of the rigid core. Future NMR experiments should allow one to gain more insight into the conformational aspects of this intriguing protein. FAU - Lippens, Guy AU - Lippens G AD - CNRS-Universite de Lille2 UMR 8525, Institut Pasteur de Lille, 1 rue du Professeur Calmette, BP 245, 59019 Lille Cedex France. guy.lippens@pasteur-lille.fr FAU - Sillen, Alain AU - Sillen A FAU - Smet, Caroline AU - Smet C FAU - Wieruszeski, Jean-Michel AU - Wieruszeski JM FAU - Leroy, Arnaud AU - Leroy A FAU - Buee, Luc AU - Buee L FAU - Landrieu, Isabelle AU - Landrieu I LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/metabolism MH - Forecasting MH - Humans MH - Neurons/chemistry/*metabolism MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - tau Proteins/*chemistry/metabolism/ultrastructure RF - 61 EDAT- 2006/03/07 09:00 MHDA- 2006/04/07 09:00 CRDT- 2006/03/07 09:00 PST - ppublish SO - Protein Pept Lett. 2006;13(3):235-46. PMID- 22467876 OWN - NLM STAT- MEDLINE DA - 20120521 DCOM- 20120723 LR - 20141106 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 21 DP - 2012 May 18 TI - Multisite phosphorylation disrupts arginine-glutamate salt bridge networks required for binding of cytoplasmic linker-associated protein 2 (CLASP2) to end-binding protein 1 (EB1). PG - 17050-64 LID - 10.1074/jbc.M111.316661 [doi] AB - A group of diverse proteins reversibly binds to growing microtubule plus ends through interactions with end-binding proteins (EBs). These +TIPs control microtubule dynamics and microtubule interactions with other intracellular structures. Here, we use cytoplasmic linker-associated protein 2 (CLASP2) binding to EB1 to determine how multisite phosphorylation regulates interactions with EB1. The central, intrinsically disordered region of vertebrate CLASP proteins contains two SXIP EB1 binding motifs that are required for EB1-mediated plus-end-tracking in vitro. In cells, both EB1 binding motifs can be functional, but most of the binding free energy results from nearby electrostatic interactions. By employing molecular dynamics simulations of the EB1 interaction with a minimal CLASP2 plus-end-tracking module, we find that conserved arginine residues in CLASP2 form extensive hydrogen-bond networks with glutamate residues predominantly in the unstructured, acidic C-terminal tail of EB1. Multisite phosphorylation of glycogen synthase kinase 3 (GSK3) sites near the EB1 binding motifs disrupts this electrostatic "molecular Velcro." Molecular dynamics simulations and (31)P NMR spectroscopy indicate that phosphorylated serines participate in intramolecular interactions with and sequester arginine residues required for EB1 binding. Multisite phosphorylation of these GSK3 motifs requires priming phosphorylation by interphase or mitotic cyclin-dependent kinases (CDKs), and we find that CDK- and GSK3-dependent phosphorylation completely disrupts CLASP2 microtubule plus-end-tracking in mitosis. FAU - Kumar, Praveen AU - Kumar P AD - Department of Cell and Tissue Biology, University of California, San Francisco, California 94143, USA. FAU - Chimenti, Michael S AU - Chimenti MS FAU - Pemble, Hayley AU - Pemble H FAU - Schonichen, Andre AU - Schonichen A FAU - Thompson, Oliver AU - Thompson O FAU - Jacobson, Matthew P AU - Jacobson MP FAU - Wittmann, Torsten AU - Wittmann T LA - eng GR - C06 RR16490/RR/NCRR NIH HHS/United States GR - R01 GM079139/GM/NIGMS NIH HHS/United States GR - R01 GM079139/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120329 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (CLASP2 protein, human) RN - 0 (MAPRE1 protein, human) RN - 0 (Microtubule-Associated Proteins) RN - EC 2.7.11.26 (Glycogen Synthase Kinase 3) SB - IM MH - Amino Acid Motifs MH - Glycogen Synthase Kinase 3/chemistry/genetics/metabolism MH - HeLa Cells MH - Humans MH - Microtubule-Associated Proteins/chemistry/genetics/*metabolism MH - Microtubules/chemistry/genetics/metabolism MH - Mitosis/physiology MH - Molecular Dynamics Simulation MH - Phosphorylation/physiology MH - Protein Structure, Tertiary MH - Static Electricity PMC - PMC3366819 OID - NLM: PMC3366819 EDAT- 2012/04/03 06:00 MHDA- 2012/07/24 06:00 CRDT- 2012/04/03 06:00 PHST- 2012/03/29 [aheadofprint] AID - M111.316661 [pii] AID - 10.1074/jbc.M111.316661 [doi] PST - ppublish SO - J Biol Chem. 2012 May 18;287(21):17050-64. doi: 10.1074/jbc.M111.316661. Epub 2012 Mar 29. PMID- 11124029 OWN - NLM STAT- MEDLINE DA - 20010108 DCOM- 20010118 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 304 IP - 5 DP - 2000 Dec 15 TI - Multiple disordered loops function in corepressor-induced dimerization of the biotin repressor. PG - 821-33 AB - Cooperative association of the Escherichia coli biotin repressor with the biotin operator is allosterically activated by binding of the corepressor, bio-5'-AMP. The corepressor function of the adenylate is due, in part, to its ability to induce repressor dimerization. Since a high-resolution structure of only the apo or unliganded repressor is currently available, the location of the dimerization interface on the protein structure is not known. Here, five mutants in the corepressor-binding domain of the repressor have been analyzed with respect to their DNA-binding and self-assembly properties. Results of these studies reveal that four of the mutant proteins exhibit defects in DNA binding. These same proteins are compromised in self-assembly. Furthermore, in the three-dimensional structure of the apo protein the mutations all lie in partially disordered surface loops, one of which is known to participate directly in corepressor binding. These results suggest that multiple disordered surface loops function in the corepressor-induced dimerization required for sequence-specific DNA binding by the biotin repressor. CI - Copyright 2000 Academic Press. FAU - Kwon, K AU - Kwon K AD - Department of Chemistry and Biochemistry, University of Maryland, MD 20742, USA. FAU - Streaker, E D AU - Streaker ED FAU - Ruparelia, S AU - Ruparelia S FAU - Beckett, D AU - Beckett D LA - eng GR - GM46511/GM/NIGMS NIH HHS/United States GR - RR08937/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (5'-AMP-biotin) RN - 0 (Apoproteins) RN - 0 (Bacterial Proteins) RN - 0 (DNA, Bacterial) RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Repressor Proteins) RN - 0 (Transcription Factors) RN - 0 (biotin repressor) RN - 415SHH325A (Adenosine Monophosphate) RN - 6SO6U10H04 (Biotin) RN - EC 3.1.21.1 (Deoxyribonuclease I) RN - EC 6.3.- (Carbon-Nitrogen Ligases) RN - EC 6.3.4.15 (birA protein, E coli) SB - IM MH - Adenosine Monophosphate/*analogs & derivatives/*metabolism MH - Allosteric Regulation MH - Allosteric Site MH - Apoproteins/chemistry/genetics/metabolism MH - Bacterial Proteins/*chemistry/genetics/*metabolism MH - Base Sequence MH - Biotin/*analogs & derivatives/genetics/*metabolism MH - Carbon-Nitrogen Ligases/*chemistry/genetics/*metabolism MH - DNA Footprinting MH - DNA, Bacterial/genetics/*metabolism MH - DNA-Binding Proteins/chemistry/genetics/metabolism MH - Deoxyribonuclease I/metabolism MH - Dimerization MH - Escherichia coli/*chemistry/*genetics MH - *Escherichia coli Proteins MH - Models, Molecular MH - Mutation MH - Operator Regions, Genetic/genetics MH - Phenotype MH - Protein Binding MH - Protein Structure, Quaternary MH - Repressor Proteins/*chemistry/genetics/*metabolism MH - Structure-Activity Relationship MH - Substrate Specificity MH - Thermodynamics MH - *Transcription Factors EDAT- 2000/12/22 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/12/22 11:00 AID - 10.1006/jmbi.2000.4249 [doi] AID - S0022-2836(00)94249-9 [pii] PST - ppublish SO - J Mol Biol. 2000 Dec 15;304(5):821-33. PMID- 1505678 OWN - NLM STAT- MEDLINE DA - 19920924 DCOM- 19920924 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 309 IP - 2 DP - 1992 Sep 7 TI - X-ray crystal structure of the serine proteinase inhibitor eglin c at 1.95 A resolution. PG - 139-45 AB - The crystal structure of eglin c, naturally occurring in the leech Hirudo medicinalis, is known from its complexes with various serine proteinases, but the crystallization of free eglin c has not yet been reported. A method is described for growing well-diffracting crystals of free eglin c from highly concentrated protein solutions (approximately 200 mg/ml). The space group of the orthorhombic crystals was determined to be P2(1)2(1)2(1) with unit cell parameters a = 32.6, b = 42.0, c = 44.1 A. The structure of free eglin c was resolved at 1.95 A resolution by Patterson search methods. The final model contains all 70 amino acids of eglin c and 125 water molecules. In comparison to the eglin structure known from its complexes with proteinases, only small differences have been observed in free eglin c. However, the reactive site-binding loop and a few residues on the surface of eglin have been found in different conformations due to crystal contacts. In contrast to the complex structures, the first seven amino acids of the highly flexible amino terminus can be located. Crystallographic refinement comprised molecular dynamics refinement, classical restrained least-squares refinement and individual isotropic atomic temperature refinement. The final R-factor is 15.8%. FAU - Hipler, K AU - Hipler K AD - Department of Biotechnology, Pharma Research, Ciba-Geigy Ltd., Basle, Switzerland. FAU - Priestle, J P AU - Priestle JP FAU - Rahuel, J AU - Rahuel J FAU - Grutter, M G AU - Grutter MG LA - eng PT - Journal Article PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Proteins) RN - 0 (Serine Proteinase Inhibitors) RN - 0 (Serpins) RN - 0 (eglin proteinase inhibitors) SB - IM MH - Amino Acid Sequence MH - Models, Molecular MH - Molecular Sequence Data MH - *Protein Conformation MH - Proteins MH - Serine Proteinase Inhibitors/*chemistry MH - *Serpins MH - X-Ray Diffraction EDAT- 1992/09/07 MHDA- 1992/09/07 00:01 CRDT- 1992/09/07 00:00 AID - 0014-5793(92)81082-W [pii] PST - ppublish SO - FEBS Lett. 1992 Sep 7;309(2):139-45. PMID- 2933134 OWN - NLM STAT- MEDLINE DA - 19860106 DCOM- 19860106 LR - 20131121 IS - 0714-7511 (Print) IS - 0714-7511 (Linking) VI - 63 IP - 8 DP - 1985 Aug TI - Trypsin digestion of bovine cardiac troponin C in the presence and absence of calcium. PG - 812-23 AB - The rate of tryptic digestion of cardiac troponin C (cTNC) has been shown to be dependent on Ca2+ as was noted earlier for skeletal TNC (sTNC). Two representative peptides have been characterized on the basis of amino acid composition and partial amino terminal sequence analysis. Circular dichroism and fluorescence studies monitored their response to the presence of Ca2+. Their ability to form complexes with the ATPase inhibitory subunit of cardiac troponin (cTNI) was determined by urea - polyacrylamide gel electrophoresis and fluorescence experiments. The ability of these peptides to substitute for whole cTNC in restoring the ATPase activity of a partially inhibited synthetic actomyosin system was also explored. The N-terminal peptide 1-88 already contains a large amount of ordered structure, which indicates that the alpha-helices flanking binding site II of cTNC exist independently of Ca2+. Consequently this peptide shows limited increase in structure in the presence of Ca2+. It binds to cTNI independently of the presence of Ca2+ and could substitute for whole cTNC by relaxing the inhibitory effect of cTNI. The C-terminal peptide 103-158 has a low amount of secondary structure in the absence of Ca2+ but this increases dramatically in the presence of this cation. This peptide could only form a stable complex with cTNI in the presence of Ca2+ and was unable to release the inhibitory effect of cTNI. FAU - McCubbin, W D AU - McCubbin WD FAU - Kay, C M AU - Kay CM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - CANADA TA - Can J Biochem Cell Biol JT - Canadian journal of biochemistry and cell biology = Revue canadienne de biochimie et biologie cellulaire JID - 8302763 RN - 0 (Amino Acids) RN - 0 (Peptide Fragments) RN - 0 (Troponin) RN - 0 (Troponin C) RN - EC 3.4.21.4 (Trypsin) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - M4I0D6VV5M (Calcium Chloride) RN - SY7Q814VUP (Calcium) SB - IM MH - Adenosine Triphosphatases/metabolism MH - Amino Acid Sequence MH - Amino Acids/analysis MH - Animals MH - Calcium/metabolism MH - Calcium Chloride/*pharmacology MH - Cattle MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Molecular Weight MH - Peptide Fragments/analysis MH - Protein Binding MH - Protein Conformation MH - Troponin/*metabolism MH - Troponin C MH - Trypsin/*metabolism EDAT- 1985/08/01 MHDA- 1985/08/01 00:01 CRDT- 1985/08/01 00:00 AID - 10.1139/o85-103 [doi] PST - ppublish SO - Can J Biochem Cell Biol. 1985 Aug;63(8):812-23. PMID- 23094644 OWN - NLM STAT- MEDLINE DA - 20130207 DCOM- 20130221 LR - 20141105 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 51 IP - 45 DP - 2012 Nov 13 TI - Dss1 release activates DNA binding potential in Brh2. PG - 9137-46 LID - 10.1021/bi3011187 [doi] AB - Dss1 is an intrinsically unstructured polypeptide that partners with the much larger Brh2 protein, the BRCA2 ortholog in Ustilago maydis, to form a tight complex. Mutants lacking Dss1 have essentially the same phenotype as mutants defective in Brh2, implying that through physical interaction Dss1 serves as a positive activator of Brh2. Dss1 associates with Brh2 through an interaction surface in the carboxy-terminal region. Certain derivatives of Brh2 lacking this interaction surface remain highly competent in DNA repair as long as a DNA-binding domain is present. However, the Dss1-independent activity raises the question of what function might be met in the native protein by having Brh2 under Dss1 control. Using a set of Brh2 fusions and truncated derivatives, we show here that Dss1 is capable of exerting control when there is a cognate Dss1-interacting surface present. We find that association of Dss1 attenuates the DNA binding potential of Brh2 and that the amino-terminal domain of Brh2 helps evict Dss1 from its carboxy-terminal interaction surface. The findings presented here add to the notion that Dss1 serves in a regulatory capacity to dictate order in association of Brh2's amino-terminal and carboxy-terminal domains with DNA. FAU - Zhou, Qingwen AU - Zhou Q AD - Department of Microbiology and Immunology and Weill Cornell Cancer Center, Weill Cornell Medical College, New York, New York 10065, United States. FAU - Kojic, Milorad AU - Kojic M FAU - Holloman, William K AU - Holloman WK LA - eng GR - GM42482/GM/NIGMS NIH HHS/United States GR - GM79859/GM/NIGMS NIH HHS/United States GR - R01 GM042482/GM/NIGMS NIH HHS/United States GR - R01 GM079859/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20121102 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA-Binding Proteins) RN - 0 (Fungal Proteins) SB - IM MH - DNA Repair/*physiology MH - DNA-Binding Proteins/*physiology MH - Fungal Proteins/*metabolism MH - Protein Binding/genetics MH - Ustilago/metabolism PMC - PMC3617921 MID - NIHMS442740 OID - NLM: NIHMS442740 OID - NLM: PMC3617921 EDAT- 2012/10/26 06:00 MHDA- 2013/02/22 06:00 CRDT- 2012/10/26 06:00 PHST- 2012/11/02 [aheadofprint] AID - 10.1021/bi3011187 [doi] PST - ppublish SO - Biochemistry. 2012 Nov 13;51(45):9137-46. doi: 10.1021/bi3011187. Epub 2012 Nov 2. PMID- 8101026 OWN - NLM STAT- MEDLINE DA - 19930809 DCOM- 19930809 LR - 20131121 IS - 0884-0431 (Print) IS - 0884-0431 (Linking) VI - 8 IP - 6 DP - 1993 Jun TI - Isolation and complete amino acid sequence of osteocalcin from canine bone. PG - 733-43 AB - Osteocalcin was purified in high yield and to homogeneity from the diaphysis of dog femora by the following steps: (1) acid demineralization of bone powder, (2) solid-phase extraction of acid-soluble proteins on Sep-Pak C18 cartridges, (3) gel filtration on Sephadex G-50, and (4) fast protein liquid chromatography on an Accell-QMA anion-exchange column. Starting from 30 g washed bone powder, approximately 7-10 mg pure protein was obtained in 2 days. The key step is the initial solid-phase extraction of osteocalcin from a large volume of a demineralized bone solution. The primary structure was established by automated sequence analyses of two tryptic peptides, of two endoproteinase Glu-C carboxy-terminal peptides, and of the first 30 amino acid residues of the intact protein. Dog osteocalcin contains 49 amino acids, has a molecular mass of 5654 daltons, contains no Thr, Met, Hyp, or Trp, has a disulfide bond between Cys 23 and 29, and is fully gamma-carboxylated at residues 17, 21, and 24. Dog osteocalcin does not contain a pair of basic amino acids found at positions 43-44 in most other osteocalcins from mammals and birds. A computer search for homology indicated 88, 90, 84, 88, 66, and 57% sequence identity of dog osteocalcin with human, bovine, cat, monkey, chicken, and swordfish osteocalcin, respectively, and weaker homologies with the gamma-carboxylated domains of blood-clotting proteins and the Pro-rich N-terminal extensions of myosin light-chain A1 and beta-crystalline B1. The possible relevance of these homologies to the structure and potential functions of osteocalcin is discussed. FAU - Colombo, G AU - Colombo G AD - Department of Biochemistry, Albert B. Chandler Medical Center, University of Kentucky, Lexington. FAU - Fanti, P AU - Fanti P FAU - Yao, C AU - Yao C FAU - Malluche, H H AU - Malluche HH LA - eng GR - NIAMS AR-35837/AR/NIAMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Bone Miner Res JT - Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research JID - 8610640 RN - 0 (Amino Acids) RN - 0 (Glutamates) RN - 0 (Peptide Fragments) RN - 104982-03-8 (Osteocalcin) RN - 3KX376GY7L (Glutamic Acid) RN - EC 3.4.- (Endopeptidases) RN - EC 3.4.21.4 (Trypsin) SB - IM MH - Amino Acid Sequence MH - Amino Acids/analysis MH - Animals MH - Bone and Bones/chemistry MH - Chromatography, Gel MH - Chromatography, High Pressure Liquid MH - Chromatography, Ion Exchange MH - Dogs MH - Electrophoresis, Polyacrylamide Gel MH - Endopeptidases MH - Glutamates/isolation & purification MH - Glutamic Acid MH - Humans MH - Molecular Sequence Data MH - Osteocalcin/chemistry/*isolation & purification MH - Peptide Fragments/isolation & purification MH - Spectrum Analysis MH - Trypsin EDAT- 1993/06/01 MHDA- 1993/06/01 00:01 CRDT- 1993/06/01 00:00 AID - 10.1002/jbmr.5650080612 [doi] PST - ppublish SO - J Bone Miner Res. 1993 Jun;8(6):733-43. PMID- 21064127 OWN - NLM STAT- MEDLINE DA - 20110105 DCOM- 20110527 LR - 20131121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 79 IP - 2 DP - 2011 Feb TI - Intrinsic disorder of Drosophila melanogaster hormone receptor 38 N-terminal domain. PG - 376-92 LID - 10.1002/prot.22887 [doi] AB - Drosophila hormone receptor 38 (dHR38), an ortholog of the vertebrate NR4A subclass of nuclear receptors, responds to ecdysteroids, which mediate developmental transitions during the Drosophila life cycle. However, this response is independent of the ecdysteroid receptor, and it does not involve binding of ecdysteroids to dHR38. It has been suggested that ecdysteroids may indirectly activate dHR38, perhaps by recruiting specific proteins. There have been recent reports pointing out the decisive role that nuclear receptor N-terminal domains (NTDs) have in protein-protein interactions that are important for regulation of gene expression. It is reasonable to assume that dHR38-NTD may also be involved in some protein-protein interactions that are critical for the ecdysteroid signaling pathway. To facilitate the exploration of the molecular basis of these interactions, we developed and optimized a protocol for the efficient expression and purification of the recombinant dHR38-NTD. Using a diverse array of biochemical and biophysical methods, we carried out the first structural characterization of dHR38-NTD. The results of our study indicate that dHR38-NTD exhibits a characteristic reminiscent of pre-molten globule-like intrinsically disordered proteins existing in a partially unfolded conformation with regions of secondary structures. The dHR38-NTD structure, which apparently comprises some local, ordered, tertiary structure clusters, is pliable and can adopt more ordered conformations in response to changes in environmental conditions. Thus, dHR38-NTD, which exhibits the structural and functional characteristic of a pre-molten globule-like intrinsically disordered protein, could serve as a platform for multiple protein-protein interactions, possibly including interactions with proteins involved in an unusual ecdysteroid signaling pathway. CI - (c) 2010 Wiley-Liss, Inc. FAU - Dziedzic-Letka, Agnieszka AU - Dziedzic-Letka A AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, Wroclaw 50-370, Poland. FAU - Rymarczyk, Grzegorz AU - Rymarczyk G FAU - Kaplon, Tomasz M AU - Kaplon TM FAU - Gorecki, Andrzej AU - Gorecki A FAU - Szamborska-Gbur, Agnieszka AU - Szamborska-Gbur A FAU - Wojtas, Magdalena AU - Wojtas M FAU - Dobryszycki, Piotr AU - Dobryszycki P FAU - Ozyhar, Andrzej AU - Ozyhar A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Drosophila Proteins) RN - 0 (Hr38 protein, Drosophila) RN - 0 (Receptors, Cytoplasmic and Nuclear) RN - 0 (Recombinant Proteins) RN - 75-89-8 (Trifluoroethanol) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Computer Simulation MH - Drosophila Proteins/biosynthesis/*chemistry/isolation & purification MH - Fluorometry MH - Guanidine/chemistry MH - Hydrodynamics MH - Molecular Sequence Data MH - Phosphorylation MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Unfolding MH - Receptors, Cytoplasmic and Nuclear/biosynthesis/*chemistry/isolation & purification MH - Recombinant Proteins/biosynthesis/*chemistry/isolation & purification MH - Trifluoroethanol/chemistry EDAT- 2010/11/11 06:00 MHDA- 2011/05/28 06:00 CRDT- 2010/11/11 06:00 AID - 10.1002/prot.22887 [doi] PST - ppublish SO - Proteins. 2011 Feb;79(2):376-92. doi: 10.1002/prot.22887. PMID- 17503833 OWN - NLM STAT- MEDLINE DA - 20070606 DCOM- 20070912 LR - 20131121 IS - 0021-8561 (Print) IS - 0021-8561 (Linking) VI - 55 IP - 12 DP - 2007 Jun 13 TI - Interactions between a non glycosylated human proline-rich protein and flavan-3-ols are affected by protein concentration and polyphenol/protein ratio. PG - 4895-901 AB - Interactions between salivary proline-rich proteins and tannins are involved in astringency, which is one of the most important organoleptic sensations perceived when drinking wine or tea. This work aimed to study interactions between a recombinant human salivary proline-rich protein, IB-5, and a flavan-3-ol monomer, epigallocatechin gallate (EGCG). IB-5 presented the characteristics of natively unfolded proteins. Interactions were studied by dynamic light scattering, isothermal titration microcalorimetry, and circular dichroism. The interaction mechanism was dependent on protein concentration. At low concentrations, a three-stage mechanism was evidenced. Saturation of the interaction sites (first stage) was followed by protein aggregation into metastable colloids at higher EGCG/protein ratios (second stage). Further increasing this ratio led to haze formation (third stage). At low ratios, a disorder-to-order transition of IB-5 structure upon binding was evidenced. At high protein concentrations, direct bridging between proteins and EGCG was observed, resulting in significantly lower aggregation and turbidity thresholds. FAU - Pascal, Christine AU - Pascal C AD - UMR INRA-Montpellier SupAgro 1083 Sciences Pour l'Oenologie, 2 place Pierre Viala, F-34060 Montpellier, France. FAU - Poncet-Legrand, Celine AU - Poncet-Legrand C FAU - Imberty, Anne AU - Imberty A FAU - Gautier, Catherine AU - Gautier C FAU - Sarni-Manchado, Pascale AU - Sarni-Manchado P FAU - Cheynier, Veronique AU - Cheynier V FAU - Vernhet, Aude AU - Vernhet A LA - eng PT - Journal Article DEP - 20070516 PL - United States TA - J Agric Food Chem JT - Journal of agricultural and food chemistry JID - 0374755 RN - 0 (Flavonoids) RN - 0 (Peptide Fragments) RN - 0 (Peptides) RN - 0 (Phenols) RN - 0 (Polyphenols) RN - 0 (Salivary Proteins and Peptides) RN - 0 (flavan-3-ol) RN - 8R1V1STN48 (Catechin) RN - BQM438CTEL (epigallocatechin gallate) SB - IM MH - Amino Acid Sequence MH - Catechin/analogs & derivatives/metabolism MH - Flavonoids/*metabolism MH - Glycosylation MH - Humans MH - Kinetics MH - Peptide Fragments/chemistry MH - Peptides/*metabolism MH - Phenols/metabolism MH - Polyphenols MH - Proline-Rich Protein Domains MH - Salivary Proteins and Peptides/metabolism EDAT- 2007/05/17 09:00 MHDA- 2007/09/13 09:00 CRDT- 2007/05/17 09:00 PHST- 2007/05/16 [aheadofprint] AID - 10.1021/jf0704108 [doi] PST - ppublish SO - J Agric Food Chem. 2007 Jun 13;55(12):4895-901. Epub 2007 May 16. PMID- 23200054 OWN - NLM STAT- MEDLINE DA - 20121203 DCOM- 20130517 LR - 20141104 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 103 IP - 10 DP - 2012 Nov 21 TI - Slow, reversible, coupled folding and binding of the spectrin tetramerization domain. PG - 2203-14 LID - 10.1016/j.bpj.2012.10.012 [doi] LID - S0006-3495(12)01116-2 [pii] AB - Many intrinsically disordered proteins (IDPs) are significantly unstructured under physiological conditions. A number of these IDPs have been shown to undergo coupled folding and binding reactions whereby they can gain structure upon association with an appropriate partner protein. In general, these systems display weaker binding affinities than do systems with association between completely structured domains, with micromolar K(d) values appearing typical. One such system is the association between alpha- and beta-spectrin, where two partially structured, incomplete domains associate to form a fully structured, three-helix bundle, the spectrin tetramerization domain. Here, we use this model system to demonstrate a method for fitting association and dissociation kinetic traces where, using typical biophysical concentrations, the association reactions are expected to be highly reversible. We elucidate the unusually slow, two-state kinetics of spectrin assembly in solution. The advantages of studying kinetics in this regime include the potential for gaining equilibrium constants as well as rate constants, and for performing experiments with low protein concentrations. We suggest that this approach would be particularly appropriate for high-throughput mutational analysis of two-state reversible binding processes. CI - Copyright (c) 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Shammas, S L AU - Shammas SL AD - Department of Chemistry, University of Cambridge, Cambridge, United Kingdom. FAU - Rogers, J M AU - Rogers JM FAU - Hill, S A AU - Hill SA FAU - Clarke, J AU - Clarke J LA - eng GR - 095195/Wellcome Trust/United Kingdom GR - WT095195/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't DEP - 20121120 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 12634-43-4 (Spectrin) RN - 8DUH1N11BX (Tryptophan) RN - 8W8T17847W (Urea) SB - IM MH - Fluorescence MH - Humans MH - Kinetics MH - Protein Denaturation/drug effects MH - *Protein Folding/drug effects MH - *Protein Multimerization/drug effects MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Spectrin/*chemistry/*metabolism MH - Tryptophan/metabolism MH - Urea/pharmacology PMC - PMC3512043 OID - NLM: PMC3512043 EDAT- 2012/12/04 06:00 MHDA- 2013/05/18 06:00 CRDT- 2012/12/04 06:00 PHST- 2012/08/02 [received] PHST- 2012/10/02 [revised] PHST- 2012/10/10 [accepted] PHST- 2012/11/20 [aheadofprint] AID - S0006-3495(12)01116-2 [pii] AID - 10.1016/j.bpj.2012.10.012 [doi] PST - ppublish SO - Biophys J. 2012 Nov 21;103(10):2203-14. doi: 10.1016/j.bpj.2012.10.012. Epub 2012 Nov 20. PMID- 23214618 OWN - NLM STAT- MEDLINE DA - 20121211 DCOM- 20130524 IS - 1550-2376 (Electronic) IS - 1539-3755 (Linking) VI - 86 IP - 4 Pt 1 DP - 2012 Oct TI - Molecular simulations of the fluctuating conformational dynamics of intrinsically disordered proteins. PG - 041910 AB - Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP alpha-synuclein that include geometric, attractive hydrophobic, and screened electrostatic interactions and are calibrated to the inter-residue separations measured in recent single-molecule fluorescence energy transfer (smFRET) experiments. We find that alpha-synuclein is disordered, with conformational statistics that are intermediate between random walk and collapsed globule behavior. An advantage of calibrated molecular simulations over constraint methods is that physical forces act on all residues, not only on residue pairs that are monitored experimentally, and these simulations can be used to study oligomerization and aggregation of multiple alpha-synuclein proteins that may precede amyloid formation. FAU - Smith, W Wendell AU - Smith WW AD - Department of Physics, Yale University, New Haven, Connecticut 06520-8120, USA. FAU - Schreck, Carl F AU - Schreck CF FAU - Hashem, Nabeem AU - Hashem N FAU - Soltani, Sherwin AU - Soltani S FAU - Nath, Abhinav AU - Nath A FAU - Rhoades, Elizabeth AU - Rhoades E FAU - O'Hern, Corey S AU - O'Hern CS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20121012 PL - United States TA - Phys Rev E Stat Nonlin Soft Matter Phys JT - Physical review. E, Statistical, nonlinear, and soft matter physics JID - 101136452 RN - 0 (Amyloid) RN - 0 (Proteins) RN - 0 (Solvents) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Amyloid/*chemistry MH - Biophysics/*methods MH - Calibration MH - Fluorescence Resonance Energy Transfer/methods MH - Humans MH - Hydrogen-Ion Concentration MH - Hydrophobic and Hydrophilic Interactions MH - Models, Molecular MH - Models, Statistical MH - *Molecular Conformation MH - Molecular Sequence Data MH - Monte Carlo Method MH - Parkinson Disease/metabolism MH - Protein Conformation MH - Protein Structure, Secondary MH - Proteins/*chemistry MH - Solvents/chemistry MH - alpha-Synuclein/*chemistry EDAT- 2012/12/12 06:00 MHDA- 2013/05/28 06:00 CRDT- 2012/12/11 06:00 PHST- 2012/08/09 [received] PHST- 2012/10/12 [aheadofprint] PST - ppublish SO - Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Oct;86(4 Pt 1):041910. Epub 2012 Oct 12. PMID- 22718765 OWN - NLM STAT- MEDLINE DA - 20120813 DCOM- 20121105 LR - 20141016 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 33 DP - 2012 Aug 10 TI - Characterization of the structure and intermolecular interactions between the connexin 32 carboxyl-terminal domain and the protein partners synapse-associated protein 97 and calmodulin. PG - 27771-88 LID - 10.1074/jbc.M112.382572 [doi] AB - In Schwann cells, connexin 32 (Cx32) can oligomerize to form intracellular gap junction channels facilitating a shorter pathway for metabolite diffusion across the layers of the myelin sheath. The mechanisms of Cx32 intracellular channel regulation have not been clearly defined. However, Ca(2+), pH, and the phosphorylation state can regulate Cx32 gap junction channels, in addition to the direct interaction of protein partners with the carboxyl-terminal (CT) domain. In this study, we used different biophysical methods to determine the structure and characterize the interaction of the Cx32CT domain with the protein partners synapse-associated protein 97 (SAP97) and calmodulin (CaM). Our results revealed that the Cx32CT is an intrinsically disordered protein that becomes alpha-helical upon binding CaM. We identified the GUK domain as the minimal SAP97 region necessary for the Cx32CT interaction. The Cx32CT residues affected by the binding of CaM and the SAP97 GUK domain were determined as well as the dissociation constants for these interactions. We characterized three Cx32CT Charcot-Marie-Tooth disease mutants (R219H, R230C, and F235C) and identified that whereas they all formed functional channels, they all showed reduced binding affinity for SAP97 and CaM. Additionally, we report that in RT4-D6P2T rat schwannoma cells, Cx32 is differentially phosphorylated and exists in a complex with SAP97 and CaM. Our studies support the importance of protein-protein interactions in the regulation of Cx32 gap junction channels and myelin homeostasis. FAU - Stauch, Kelly AU - Stauch K AD - Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA. FAU - Kieken, Fabien AU - Kieken F FAU - Sorgen, Paul AU - Sorgen P LA - eng GR - 2P30CA036727/CA/NCI NIH HHS/United States GR - 2R01GM072631/GM/NIGMS NIH HHS/United States GR - R01 GM072631/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120620 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Calmodulin) RN - 0 (Connexins) RN - 0 (Dlgh1 protein, rat) RN - 0 (Membrane Proteins) RN - 0 (Multiprotein Complexes) RN - 0 (connexin 32) RN - EC 2.7.4.8 (Dlgh1 protein, mouse) RN - EC 2.7.4.8 (Guanylate Kinase) SB - IM MH - Adaptor Proteins, Signal Transducing/chemistry/genetics/*metabolism MH - Amino Acid Substitution MH - Animals MH - Calmodulin/chemistry/genetics/*metabolism MH - Cell Line, Tumor MH - Connexins/chemistry/genetics/*metabolism MH - Gap Junctions/chemistry/genetics/*metabolism MH - Guanylate Kinase/chemistry/genetics/*metabolism MH - Membrane Proteins/chemistry/genetics/*metabolism MH - Mice MH - Multiprotein Complexes/chemistry/genetics/metabolism MH - Mutation, Missense MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Rats MH - Schwann Cells/cytology/*metabolism PMC - PMC3431650 OID - NLM: PMC3431650 EDAT- 2012/06/22 06:00 MHDA- 2012/11/06 06:00 CRDT- 2012/06/22 06:00 PHST- 2012/06/20 [aheadofprint] AID - M112.382572 [pii] AID - 10.1074/jbc.M112.382572 [doi] PST - ppublish SO - J Biol Chem. 2012 Aug 10;287(33):27771-88. doi: 10.1074/jbc.M112.382572. Epub 2012 Jun 20. PMID- 16762919 OWN - NLM STAT- MEDLINE DA - 20060814 DCOM- 20060925 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 33 DP - 2006 Aug 18 TI - Regulation of AKAP-membrane interactions by calcium. PG - 23932-44 AB - The AKAP gravin is a scaffold for protein kinases, phosphatases, and adaptor molecules obligate for resensitization and recycling of beta2-adrenergic receptors. Gravin binds to the receptor through well characterized protein-protein interactions. These interactions are facilitated approximately 1000-fold when gravin is anchored to the cytoplasmic leaflet of the plasma membrane. Although the N-terminal region (approximately 550 residues) is highly negatively charged and probably natively unfolded, it could anchor gravin to the inner leaflet through hydrophobic insertion of its N-terminal myristate and electrostatic binding of three short positively charged domains (PCDs). Loss of the site of N-myristoylation was found to affect neither AKAP macroscopic localization nor AKAP function. Synthetic peptides corresponding to PCD1-3 bound in vitro to unilamellar phospholipid vesicles with high affinity, a binding reversed by calmodulin in the presence of Ca2+. In vivo gravin localization is regulated by intracellular Ca2+, a function mapping to the N terminus of the protein harboring PCD1, PCD2, and PCD3. Mutation of any two PCDs eliminates membrane association of the non-myristoylated gravin, the sensitivity to Ca2+/calmodulin, and the ability of this scaffold to catalyze receptor resensitization and recycling. FAU - Tao, Jiangchuan AU - Tao J AD - Department of Pharmacology, School of Medicine, Heath Sciences Center, State University of New York, Stony Brook, New York 11794-8651, USA. FAU - Shumay, Elena AU - Shumay E FAU - McLaughlin, Stuart AU - McLaughlin S FAU - Wang, Hsien-yu AU - Wang HY FAU - Malbon, Craig C AU - Malbon CC LA - eng GR - DK25410/DK/NIDDK NIH HHS/United States GR - GM024971/GM/NIGMS NIH HHS/United States GR - GM69375/GM/NIGMS NIH HHS/United States GR - T32 DK007521/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20060608 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (A Kinase Anchor Proteins) RN - 0 (AKAP12 protein, human) RN - 0 (Calmodulin) RN - 0 (Cell Cycle Proteins) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Lipid Bilayers) RN - 0 (Membrane Proteins) RN - 0 (Receptors, Adrenergic, beta-2) RN - 0I3V7S25AW (Myristic Acid) RN - 125267-21-2 (myristoylated alanine-rich C kinase substrate) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) RN - SY7Q814VUP (Calcium) SB - IM MH - A Kinase Anchor Proteins MH - Amino Acid Sequence MH - Biological Transport MH - Calcium/*chemistry/metabolism MH - Calmodulin/chemistry/metabolism MH - Cell Cycle Proteins/chemistry/*metabolism/physiology MH - Cell Line, Tumor MH - Cell Membrane/*metabolism MH - Cyclic AMP-Dependent Protein Kinases/*metabolism MH - Humans MH - Intracellular Fluid/chemistry/metabolism MH - Intracellular Signaling Peptides and Proteins/chemistry MH - Lipid Bilayers/metabolism MH - Membrane Proteins/chemistry/metabolism MH - Molecular Sequence Data MH - Myristic Acid/metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Receptors, Adrenergic, beta-2/metabolism MH - Static Electricity EDAT- 2006/06/10 09:00 MHDA- 2006/09/26 09:00 CRDT- 2006/06/10 09:00 PHST- 2006/06/08 [aheadofprint] AID - M601813200 [pii] AID - 10.1074/jbc.M601813200 [doi] PST - ppublish SO - J Biol Chem. 2006 Aug 18;281(33):23932-44. Epub 2006 Jun 8. PMID- 15231848 OWN - NLM STAT- MEDLINE DA - 20040920 DCOM- 20041026 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 39 DP - 2004 Sep 24 TI - Disorder in a target for the smad2 mad homology 2 domain and its implications for binding and specificity. PG - 40707-14 AB - The Smad2 Mad homology 2 (MH2) domain binds to a diverse group of proteins which do not share a common sequence motif. We have used NMR to investigate the structure of one of these interacting proteins, the Smad binding domain (SBD) of Smad anchor for receptor activation (SARA). Our results indicate that the unbound SBD is highly disordered and forms no stable secondary or tertiary structures. Additionally we have used fluorescence binding studies to study the interaction between the MH2 domain and SBD and find that no region of the SBD dominates the interaction between the MH2 and the SBD. Our results are consistent with a series of hydrophobic patches on the MH2 that are able to recognize disordered regions of proteins. These findings elucidate a mechanism by which a single domain (MH2) can specifically recognize a diverse set of proteins which are unrelated by sequence, lead to a clearer picture of how MH2 domains function in the transforming growth factor-beta-signaling pathway and suggest possible mechanisms for controlling interactions with MH2 domains. CI - Copyright 2004 American Society for Biochemistry and Molecular Biology, Inc. FAU - Chong, P Andrew AU - Chong PA AD - Department of Structural Biology and Biochemistry, Hospital for Sick Children, Toronto M5G 1X8, Canada. FAU - Ozdamar, Barish AU - Ozdamar B FAU - Wrana, Jeffrey L AU - Wrana JL FAU - Forman-Kay, Julie D AU - Forman-Kay JD LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040701 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Carrier Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Peptides) RN - 0 (Protein Isoforms) RN - 0 (SMAD2 protein, human) RN - 0 (Smad2 Protein) RN - 0 (Trans-Activators) RN - 0 (Transforming Growth Factor beta) RN - EC 2.5.1.18 (Glutathione Transferase) RN - EC 3.4.21- (ZFYVE16 protein, human) RN - EC 3.4.21.- (Serine Endopeptidases) SB - IM MH - Amino Acid Sequence MH - Carrier Proteins/*chemistry/genetics/physiology MH - DNA-Binding Proteins/*metabolism MH - Glutathione Transferase/metabolism MH - Humans MH - *Intracellular Signaling Peptides and Proteins MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Mutation MH - Peptides/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Isoforms MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Serine Endopeptidases/*chemistry/genetics/physiology MH - Signal Transduction MH - Smad2 Protein MH - Trans-Activators/*metabolism MH - Transforming Growth Factor beta/metabolism EDAT- 2004/07/03 05:00 MHDA- 2004/10/27 09:00 CRDT- 2004/07/03 05:00 PHST- 2004/07/01 [aheadofprint] AID - 10.1074/jbc.M404375200 [doi] AID - M404375200 [pii] PST - ppublish SO - J Biol Chem. 2004 Sep 24;279(39):40707-14. Epub 2004 Jul 1. PMID- 11581264 OWN - NLM STAT- MEDLINE DA - 20011212 DCOM- 20020124 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 50 DP - 2001 Dec 14 TI - Mechanism of product chain length determination and the role of a flexible loop in Escherichia coli undecaprenyl-pyrophosphate synthase catalysis. PG - 47474-82 AB - The Escherichia coli undecaprayl-pyrophosphate synthase (UPPs) structure has been solved using the single wavelength anomalous diffraction method. The putative substrate-binding site is located near the end of the betaA-strand with Asp-26 playing a critical catalytic role. In both subunits, an elongated hydrophobic tunnel is found, surrounded by four beta-strands (betaA-betaB-betaD-betaC) and two helices (alpha2 and alpha3) and lined at the bottom with large residues Ile-62, Leu-137, Val-105, and His-103. The product distributions formed by the use of the I62A, V105A, and H103A mutants are similar to those observed for wild-type UPPs. Catalysis by the L137A UPPs, on the other hand, results in predominantly the formation of the C(70) polymer rather than the C(55) polymer. Ala-69 and Ala-143 are located near the top of the tunnel. In contrast to the A143V reaction, the C(30) intermediate is formed to a greater extent and is longer lived in the process catalyzed by the A69L mutant. These findings suggest that the small side chain of Ala-69 is required for rapid elongation to the C(55) product, whereas the large hydrophobic side chain of Leu-137 is required to limit the elongation to the C(55) product. The roles of residues located on a flexible loop were investigated. The S71A, N74A, or R77A mutants displayed 25-200-fold decrease in k(cat) values. W75A showed an 8-fold increase of the FPP K(m) value, and 22-33-fold increases in the IPP K(m) values were observed for E81A and S71A. The loop may function to bridge the interaction of IPP with FPP, needed to initiate the condensation reaction and serve as a hinge to control the substrate binding and product release. FAU - Ko, T P AU - Ko TP AD - Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan. FAU - Chen, Y K AU - Chen YK FAU - Robinson, H AU - Robinson H FAU - Tsai, P C AU - Tsai PC FAU - Gao, Y G AU - Gao YG FAU - Chen, A P AU - Chen AP FAU - Wang, A H AU - Wang AH FAU - Liang, P H AU - Liang PH LA - eng SI - PDB/1JP3 GR - GM 41612/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20011001 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Detergents) RN - 0 (Lipid Bilayers) RN - 30KYC7MIAI (Aspartic Acid) RN - 9002-93-1 (Octoxynol) RN - EC 2.5.- (Alkyl and Aryl Transferases) RN - EC 2.5.1.31 (undecaprenyl pyrophosphate synthetase) RN - OF5P57N2ZX (Alanine) SB - IM MH - Alanine/chemistry MH - Alkyl and Aryl Transferases/*chemistry/genetics/metabolism MH - Amino Acid Sequence MH - Animals MH - Aspartic Acid/chemistry MH - Binding Sites MH - Catalysis MH - Crystallography, X-Ray MH - Detergents/pharmacology MH - Dimerization MH - Escherichia coli/*chemistry/*enzymology MH - Kinetics MH - Lipid Bilayers/metabolism MH - Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Mutation MH - Octoxynol/pharmacology MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Time Factors EDAT- 2001/10/03 10:00 MHDA- 2002/01/25 10:01 CRDT- 2001/10/03 10:00 PHST- 2001/10/01 [aheadofprint] AID - 10.1074/jbc.M106747200 [doi] AID - M106747200 [pii] PST - ppublish SO - J Biol Chem. 2001 Dec 14;276(50):47474-82. Epub 2001 Oct 1. PMID- 24003031 OWN - NLM STAT- MEDLINE DA - 20131209 DCOM- 20140213 LR - 20141112 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 41 IP - 22 DP - 2013 Dec TI - Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein. PG - 9987-98 LID - 10.1093/nar/gkt794 [doi] AB - Previous evidence indicates that a number of proteins are able to interact with cognate mRNAs. These autogenous associations represent important regulatory mechanisms that control gene expression at the translational level. Using the catRAPID approach to predict the propensity of proteins to bind to RNA, we investigated the occurrence of autogenous associations in the human proteome. Our algorithm correctly identified binding sites in well-known cases such as thymidylate synthase, tumor suppressor P53, synaptotagmin-1, serine/ariginine-rich splicing factor 2, heat shock 70 kDa, ribonucleic particle-specific U1A and ribosomal protein S13. In addition, we found that several other proteins are able to bind to their own mRNAs. A large-scale analysis of biological pathways revealed that aggregation-prone and structurally disordered proteins have the highest propensity to interact with cognate RNAs. These findings are substantiated by experimental evidence on amyloidogenic proteins such as TAR DNA-binding protein 43 and fragile X mental retardation protein. Among the amyloidogenic proteins, we predicted that Parkinson's disease-related alpha-synuclein is highly prone to interact with cognate transcripts, which suggests the existence of RNA-dependent factors in its function and dysfunction. Indeed, as aggregation is intrinsically concentration dependent, it is possible that autogenous interactions play a crucial role in controlling protein homeostasis. FAU - Zanzoni, Andreas AU - Zanzoni A AD - Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain. FAU - Marchese, Domenica AU - Marchese D FAU - Agostini, Federico AU - Agostini F FAU - Bolognesi, Benedetta AU - Bolognesi B FAU - Cirillo, Davide AU - Cirillo D FAU - Botta-Orfila, Maria AU - Botta-Orfila M FAU - Livi, Carmen Maria AU - Livi CM FAU - Rodriguez-Mulero, Silvia AU - Rodriguez-Mulero S FAU - Tartaglia, Gian Gaetano AU - Tartaglia GG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130903 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Nuclear Proteins) RN - 0 (RNA, Messenger) RN - 0 (RNA-Binding Proteins) RN - 0 (Ribonucleoproteins) RN - 0 (Tumor Suppressor Protein p53) RN - 0 (alpha-Synuclein) RN - 147153-65-9 (SRSF2 protein, human) RN - 63231-63-0 (RNA) SB - IM MH - Algorithms MH - Binding Sites MH - Gene Expression Regulation MH - Humans MH - Intrinsically Disordered Proteins/chemistry/metabolism MH - Nuclear Proteins/chemistry/genetics/metabolism MH - Protein Biosynthesis MH - RNA/chemistry/*metabolism MH - RNA, Messenger/chemistry/metabolism MH - RNA-Binding Proteins/chemistry/genetics/*metabolism MH - Ribonucleoproteins/chemistry/genetics/metabolism MH - Tumor Suppressor Protein p53/genetics/metabolism MH - alpha-Synuclein/*metabolism PMC - PMC3905859 OID - NLM: PMC3905859 EDAT- 2013/09/05 06:00 MHDA- 2014/02/14 06:00 CRDT- 2013/09/05 06:00 PHST- 2013/09/03 [aheadofprint] AID - gkt794 [pii] AID - 10.1093/nar/gkt794 [doi] PST - ppublish SO - Nucleic Acids Res. 2013 Dec;41(22):9987-98. doi: 10.1093/nar/gkt794. Epub 2013 Sep 3. PMID- 21689790 OWN - NLM STAT- MEDLINE DA - 20110815 DCOM- 20111011 LR - 20131121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1814 IP - 10 DP - 2011 Oct TI - Aggregation and structural changes of alpha(S1)-, beta- and kappa-caseins induced by homocysteinylation. PG - 1234-45 LID - 10.1016/j.bbapap.2011.05.017 [doi] AB - Elevated homocysteine levels are resulting in N-homocysteinylation of lysyl residues in proteins and they correlate with a number of human pathologies. However, the role of homocysteinylation of lysyl residues is still poorly known. In order to study the features of homocysteinylation of intrinsically unstructured proteins (IUP) bovine caseins were used as a model. alpha(S1)-, beta- and kappa-caseins, showing different aggregations and micelle formation, were modified with homocysteine-thiolactone and their physico-chemical properties were studied. Efficiency of homocysteine incorporation was estimated to be about 1.5, 2.1 and 1.3 homocysteyl residues per one beta-, alpha(S1)-, and kappa-casein molecule, respectively. Use of intrinsic and extrinsic fluorescent markers such as Trp, thioflavin T and ANS, reveal structural changes of casein structures after homocysteinylation reflected by an increase in beta-sheet content, which in some cases may be characteristic of amyloid-like transformations. CD spectra also show an increase in beta-sheet content of homocysteinylated caseins. Casein homocysteinylation leads in all cases to aggregation. The sizes of aggregates and aggregation rates were dependent on homocysteine thiolactone concentration and temperature. DLS and microscopic studies have revealed the formation of large aggregates of about 1-3mum. Homocysteinylation of alpha(S1)- and beta-caseins results in formation of regular spheres. Homocysteinylated kappa-casein forms thin unbranched fibrils about 400-800nm long. In case of kappa-casein amyloidogenic effect of homocysteinylation was confirmed by Congo red spectra. Taken together, data indicate that N-homocysteinylation provokes significant changes in properties of native caseins. A comparison of amyloidogenic transformation of 3 different casein types, belonging to the IUP protein family, shows that the efficiency of amyloidogenic transformation upon homocysteinylation depends on micellization capacity, additional disulphide bonds and other structural features. CI - Copyright (c) 2011 Elsevier B.V. All rights reserved. FAU - Stroylova, Yulia Y AU - Stroylova YY AD - Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia. FAU - Zimny, Jaroslaw AU - Zimny J FAU - Yousefi, Reza AU - Yousefi R FAU - Chobert, Jean-Marc AU - Chobert JM FAU - Jakubowski, Hieronim AU - Jakubowski H FAU - Muronetz, Vladimir I AU - Muronetz VI FAU - Haertle, Thomas AU - Haertle T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110612 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Caseins) RN - 0LVT1QZ0BA (Homocysteine) RN - 3U05FHG59S (Congo Red) SB - IM MH - Animals MH - Caseins/*chemistry/*metabolism MH - Cattle MH - Circular Dichroism MH - Congo Red/chemistry/metabolism MH - Homocysteine/*metabolism MH - Humans MH - Microscopy, Electron, Transmission MH - Microscopy, Fluorescence MH - Protein Binding MH - Protein Conformation MH - Protein Multimerization/physiology MH - Protein Processing, Post-Translational MH - Temperature EDAT- 2011/06/22 06:00 MHDA- 2011/10/12 06:00 CRDT- 2011/06/22 06:00 PHST- 2011/02/16 [received] PHST- 2011/05/14 [revised] PHST- 2011/05/26 [accepted] PHST- 2011/06/12 [aheadofprint] AID - S1570-9639(11)00159-2 [pii] AID - 10.1016/j.bbapap.2011.05.017 [doi] PST - ppublish SO - Biochim Biophys Acta. 2011 Oct;1814(10):1234-45. doi: 10.1016/j.bbapap.2011.05.017. Epub 2011 Jun 12. PMID- 20199073 OWN - NLM STAT- MEDLINE DA - 20100324 DCOM- 20100706 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 132 IP - 12 DP - 2010 Mar 31 TI - A stable lipid-induced aggregate of alpha-synuclein. PG - 4080-2 LID - 10.1021/ja909247j [doi] AB - The Parkinson's disease-related protein alpha-Synuclein (alphaS) is a 140 residue intrinsically disordered protein. Its membrane-binding properties are thought to be relevant for its physiological or pathologic activity. Here, the interaction of alphaS with POPG [1-Palmitoyl-2-Oleoyl-sn-Glycero-3-(Phosphorac-(1-glycerol))] small unilamellar vesicles (SUVs) is investigated by spin-label EPR using double electron-electron resonance (DEER). Intermolecular distances between four single mutants reveal that well-defined aggregates are formed. The data suggest a coexistence of two dimer structures with main interactions in the helix 2, encompassing residues 50-100. Previously, the horseshoe conformation was detected by intramolecular restraints obtained by DEER on alphaS double mutants (Drescher et al. J. Am. Chem. Soc. 2008, 130, 7796). The present study suggests that interdigitation of two monomers in the aggregate fills the void between the two helices of each of the monomers thus providing a rationale for the horseshoe structure. This aggregate is lipid induced and affects the structure of the POPG SUVs, which become leaky and diminish in size upon contact with alphaS suggesting a possible origin of conflicting results in the recent literature (Jao et al. Proc. Natl. Acad. Sci. U.S.A. 2008, 105 (50), 19666; Georgieva et al. J. Am. Chem. Soc. 2008, 130 (39), 12856; Bortolus et al. J. Am. Chem. Soc. 2008, 130, 6690). FAU - Drescher, Malte AU - Drescher M AD - Department of Molecular Physics, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands. FAU - van Rooijen, Bart D AU - van Rooijen BD FAU - Veldhuis, Gertjan AU - Veldhuis G FAU - Subramaniam, Vinod AU - Subramaniam V FAU - Huber, Martina AU - Huber M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Lipids) RN - 0 (alpha-Synuclein) SB - IM MH - Dimerization MH - Lipids/*chemistry MH - Models, Molecular MH - alpha-Synuclein/*chemistry/genetics EDAT- 2010/03/05 06:00 MHDA- 2010/07/07 06:00 CRDT- 2010/03/05 06:00 AID - 10.1021/ja909247j [doi] PST - ppublish SO - J Am Chem Soc. 2010 Mar 31;132(12):4080-2. doi: 10.1021/ja909247j. PMID- 8104613 OWN - NLM STAT- MEDLINE DA - 19931123 DCOM- 19931123 LR - 20130922 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 2 IP - 9 DP - 1993 Sep TI - Expression and characterization of catalytic and regulatory domains of rat tyrosine hydroxylase. PG - 1452-60 AB - Phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase constitute a family of tetrahydropterin-dependent aromatic amino acid hydroxylases. Comparison of the amino acid sequences of these three proteins shows that the C-terminal two-thirds are homologous, while the N-terminal thirds are not. This is consistent with a model in which the C-terminal two-thirds constitute a conserved catalytic domain to which has been appended discrete regulatory domains. To test such a model, two mutant proteins have been constructed, expressed in Escherichia coli, purified, and characterized. One protein contains the first 158 amino acids of rat tyrosine hydroxylase. The second lacks the first 155 amino acid residues of this enzyme. The spectral properties of the two domains suggest that their three-dimensional structures are changed only slightly from intact tyrosine hydroxylase. The N-terminal domain mutant binds to heparin and is phosphorylated by cAMP-dependent protein kinase at the same rate as the holoenzyme but lacks any catalytic activity. The C-terminal domain mutant is fully active, with Vmax and Km values identical to the holoenzyme; these results establish that all of the catalytic residues of tyrosine hydroxylase are located in the C-terminal 330 amino acids. The results with the two mutant proteins are consistent with these two segments of tyrosine hydroxylase being two separate domains, one regulatory and one catalytic. FAU - Daubner, S C AU - Daubner SC AD - Department of Biochemistry and Biophysics, Texas A&M University, College Station 77843-2128. FAU - Lohse, D L AU - Lohse DL FAU - Fitzpatrick, P F AU - Fitzpatrick PF LA - eng GR - GM 47291/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - EC 1.14.16.2 (Tyrosine 3-Monooxygenase) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Binding Sites MH - Catalysis MH - Escherichia coli/genetics MH - Gene Expression MH - Kinetics MH - Molecular Sequence Data MH - Molecular Weight MH - Mutagenesis MH - Phosphorylation MH - Plasmids MH - Rats MH - Spectrophotometry MH - Tyrosine 3-Monooxygenase/*chemistry/genetics/metabolism PMC - PMC2142459 OID - NLM: PMC2142459 EDAT- 1993/09/01 MHDA- 1993/09/01 00:01 CRDT- 1993/09/01 00:00 AID - 10.1002/pro.5560020909 [doi] PST - ppublish SO - Protein Sci. 1993 Sep;2(9):1452-60. PMID- 22749949 OWN - NLM STAT- MEDLINE DA - 20120821 DCOM- 20121024 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1818 IP - 11 DP - 2012 Nov TI - Lipid interactions of the malaria antigen merozoite surface protein 2. PG - 2572-8 LID - 10.1016/j.bbamem.2012.06.015 [doi] AB - With more than half the world's population living at risk of malaria infection, there is a strong demand for the development of an effective malaria vaccine. One promising vaccine candidate is merozoite surface protein 2 (MSP2), which is among the most abundant antigens of the blood stage of the Plasmodium falciparum parasite. In solution, MSP2 is intrinsically unstructured, but little is known about the conformation of native MSP2, which is GPI-anchored to the merozoite surface, or of the implications of that conformation for the immune response induced by MSP2. Initial NMR studies have shown that MSP2 interacts with lipid micelles through a highly conserved N-terminal domain. We have further developed these findings by investigating how different lipid environments affect the protein structure. All of the tested lipid preparations perturbed only the N-terminal part of MSP2. In DPC micelles this region adopts an alpha-helical structure which we have characterized in detail. Our findings suggest a possible mechanism by which lipid interactions might modulate immune recognition of the conserved N-terminus of MSP2, potentially explaining the apparent immunodominance of the central variable region of this important malaria antigen. CI - Copyright (c) 2012 Elsevier B.V. All rights reserved. FAU - MacRaild, Christopher A AU - MacRaild CA AD - Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia. FAU - Pedersen, Marie O AU - Pedersen MO FAU - Anders, Robin F AU - Anders RF FAU - Norton, Raymond S AU - Norton RS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120627 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Antigens, Protozoan) RN - 0 (Micelles) RN - 0 (Protozoan Proteins) RN - 0 (merozoite surface protein 2, Plasmodium) SB - IM MH - Antigens, Protozoan/chemistry/*metabolism MH - *Lipid Metabolism MH - Micelles MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Plasmodium falciparum/*metabolism MH - Protein Conformation MH - Protozoan Proteins/chemistry/*metabolism EDAT- 2012/07/04 06:00 MHDA- 2012/10/25 06:00 CRDT- 2012/07/04 06:00 PHST- 2012/04/23 [received] PHST- 2012/06/20 [revised] PHST- 2012/06/21 [accepted] PHST- 2012/06/27 [aheadofprint] AID - S0005-2736(12)00213-1 [pii] AID - 10.1016/j.bbamem.2012.06.015 [doi] PST - ppublish SO - Biochim Biophys Acta. 2012 Nov;1818(11):2572-8. doi: 10.1016/j.bbamem.2012.06.015. Epub 2012 Jun 27. PMID- 23197791 OWN - NLM STAT- MEDLINE DA - 20130206 DCOM- 20130711 LR - 20141104 IS - 1535-9484 (Electronic) IS - 1535-9476 (Linking) VI - 12 IP - 2 DP - 2013 Feb TI - Nepenthesin from monkey cups for hydrogen/deuterium exchange mass spectrometry. PG - 464-72 LID - 10.1074/mcp.M112.025221 [doi] AB - Studies of protein dynamics, structure and interactions using hydrogen/deuterium exchange mass spectrometry (HDX-MS) have sharply increased over the past 5-10 years. The predominant technology requires fast digestion at pH 2-3 to retain deuterium label. Pepsin is used almost exclusively, but it provides relatively low efficiency under the constraints of the experiment, and a selectivity profile that renders poor coverage of intrinsically disordered regions. In this study we present nepenthesin-containing secretions of the pitcher plant Nepenthes, commonly called monkey cups, for use in HDX-MS. We show that nepenthesin is at least 1400-fold more efficient than pepsin under HDX-competent conditions, with a selectivity profile that mimics pepsin in part, but also includes efficient cleavage C-terminal to "forbidden" residues K, R, H, and P. High efficiency permits a solution-based analysis with no detectable autolysis, avoiding the complication of immobilized enzyme reactors. Relaxed selectivity promotes high coverage of disordered regions and the ability to "tune" the mass map for regions of interest. Nepenthesin-enriched secretions were applied to an analysis of protein complexes in the nonhomologous end-joining DNA repair pathway. The analysis of XRCC4 binding to the BRCT domains of Ligase IV points to secondary interactions between the disordered C-terminal tail of XRCC4 and remote regions of the BRCT domains, which could only be identified with a nepenthesin-based workflow. HDX data suggest that stalk-binding to XRCC4 primes a BRCT conformation in these remote regions to support tail interaction, an event which may be phosphoregulated. We conclude that nepenthesin is an effective alternative to pepsin for all HDX-MS applications, and especially for the analysis of structural transitions among intrinsically disordered proteins and their binding partners. FAU - Rey, Martial AU - Rey M AD - Department of Biochemistry and Molecular Biology and the Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada. FAU - Yang, Menglin AU - Yang M FAU - Burns, Kyle M AU - Burns KM FAU - Yu, Yaping AU - Yu Y FAU - Lees-Miller, Susan P AU - Lees-Miller SP FAU - Schriemer, David C AU - Schriemer DC LA - eng GR - 13639/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121129 PL - United States TA - Mol Cell Proteomics JT - Molecular & cellular proteomics : MCP JID - 101125647 RN - 0 (DNA-Binding Proteins) RN - 0 (Plant Proteins) RN - 0 (Recombinant Proteins) RN - 0 (XRCC4 protein, human) RN - 7YNJ3PO35Z (Hydrogen) RN - AR09D82C7G (Deuterium) RN - EC 3.4.- (Peptide Hydrolases) RN - EC 3.4.23.1 (Pepsin A) RN - EC 6.3.2.- (BRAP protein, human) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM MH - Angiosperms/chemistry/*enzymology MH - DNA End-Joining Repair MH - DNA-Binding Proteins/chemistry/metabolism MH - Deuterium/chemistry MH - Deuterium Exchange Measurement/*methods MH - Hydrogen/chemistry MH - Mass Spectrometry/*methods MH - Molecular Sequence Data MH - Molecular Weight MH - Pepsin A/chemistry/metabolism MH - Peptide Hydrolases/chemistry/*metabolism MH - Plant Proteins/chemistry/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Substrate Specificity MH - Ubiquitin-Protein Ligases/chemistry/metabolism PMC - PMC3567866 OID - NLM: PMC3567866 EDAT- 2012/12/01 06:00 MHDA- 2013/07/13 06:00 CRDT- 2012/12/01 06:00 PHST- 2012/11/29 [aheadofprint] AID - M112.025221 [pii] AID - 10.1074/mcp.M112.025221 [doi] PST - ppublish SO - Mol Cell Proteomics. 2013 Feb;12(2):464-72. doi: 10.1074/mcp.M112.025221. Epub 2012 Nov 29. PMID- 24893801 OWN - NLM STAT- MEDLINE DA - 20140918 DCOM- 20141208 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 281 IP - 18 DP - 2014 Sep TI - Edge strand engineering prevents native-like aggregation in Sulfolobus solfataricus acylphosphatase. PG - 4072-84 LID - 10.1111/febs.12861 [doi] AB - beta-proteins are constantly threatened by the risk of aggregation because beta-sheets are inherently structured for edge-to-edge interactions. To avoid native-like aggregation, evolution has resulted in a set of strategies that prevent intermolecular beta-interactions. Acylphosphatase from Sulfolobus solfataricus (Sso AcP) represents a suitable model for the study of such a process. Under conditions promoting aggregation, Sso AcP acquires a native-like conformational state whereby an unstructured N-terminal segment interacts with the edge beta-strand B4 of an adjacent Sso AcP molecule. Because B4 is poorly protected against aggregation, this interaction triggers the aggregation cascade without the need for unfolding. Recently, three single Sso AcP mutants (V84D, Y86E and V84P) were designed to engineer additional protection against aggregation in B4 and were observed to successfully impair native-like aggregation in all three variants at the expense of a lower stability. To understand the structural basis of the reduced aggregation propensity and lower stability, the crystal structures of the Sso AcP variants were determined in the present study. Structural analysis reveals that the V84D and Y86E mutations exert protection by the insertion of an edge negative charge. A conformationally less regular B4 underlies protection against aggregation in the V84P mutant. The thermodynamic basis of instability is discussed. Moreover, kinetic experiments indicate that aggregation of the three mutants is not native-like and is independent of the interaction between B4 and the unstructured N-terminal segment. The reported data rationalize previous evidence regarding Sso AcP native-like aggregation and provide a basis for the design of aggregation-free proteins. DATABASE: The atomic coordinates and related experimental data for the Sso AcP mutants V84P, V84D, DeltaN11 Y86E have been deposited in the Protein Data Bank under accession numbers 4OJ3, 4OJG and 4OJH, respectively. STRUCTURED DIGITAL ABSTRACT: * Sso AcP and Sso AcP bind by fluorescence technology (View interaction). CI - (c) 2014 FEBS. FAU - de Rosa, Matteo AU - de Rosa M AD - Dipartimento di Bioscienze, Universita di Milano, Italy. FAU - Bemporad, Francesco AU - Bemporad F FAU - Pellegrino, Sara AU - Pellegrino S FAU - Chiti, Fabrizio AU - Chiti F FAU - Bolognesi, Martino AU - Bolognesi M FAU - Ricagno, Stefano AU - Ricagno S LA - eng SI - PDB/4OIX SI - PDB/4OJ3 SI - PDB/4OJG SI - PDB/4OJH PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140613 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Archaeal Proteins) RN - EC 3.6.- (Acid Anhydride Hydrolases) RN - EC 3.6.1.7 (acylphosphatase) SB - IM MH - Acid Anhydride Hydrolases/*chemistry/genetics MH - Amino Acid Substitution MH - Archaeal Proteins/*chemistry/genetics MH - Crystallography, X-Ray MH - Enzyme Stability MH - Hydrogen Bonding MH - Kinetics MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Sulfolobus solfataricus/*enzymology OTO - NOTNLM OT - acylphosphatase OT - amyloidosis OT - crystal structure OT - native-like aggregation OT - beta-strand EDAT- 2014/06/05 06:00 MHDA- 2014/12/15 06:00 CRDT- 2014/06/05 06:00 PHST- 2014/04/03 [received] PHST- 2014/05/19 [revised] PHST- 2014/05/23 [accepted] PHST- 2014/06/13 [aheadofprint] AID - 10.1111/febs.12861 [doi] PST - ppublish SO - FEBS J. 2014 Sep;281(18):4072-84. doi: 10.1111/febs.12861. Epub 2014 Jun 13. PMID- 12086608 OWN - NLM STAT- MEDLINE DA - 20020627 DCOM- 20020719 LR - 20061120 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 109 IP - 4 DP - 2002 May 17 TI - Molecular architecture and functional model of the endocytic AP2 complex. PG - 523-35 AB - AP2 is the best-characterized member of the family of heterotetrameric clathrin adaptor complexes that play pivotal roles in many vesicle trafficking pathways within the cell. AP2 functions in clathrin-mediated endocytosis, the process whereby cargo enters the endosomal system from the plasma membrane. We describe the structure of the 200 kDa AP2 "core" (alpha trunk, beta2 trunk, mu2, and sigma2) complexed with the polyphosphatidylinositol headgroup mimic inositolhexakisphosphate at 2.6 A resolution. Two potential polyphosphatidylinositide binding sites are observed, one on alpha and one on mu2. The binding site for Yxxphi endocytic motifs is buried, indicating that a conformational change, probably triggered by phosphorylation in the disordered mu2 linker, is necessary to allow Yxxphi motif binding. A model for AP2 recruitment and activation is proposed. FAU - Collins, Brett M AU - Collins BM AD - Cambridge Institute for Medical Research, University of Cambridge, Department of Clinical Biochemistry, Wellcome Trust/MRC Building, Hills Road, United Kingdom. FAU - McCoy, Airlie J AU - McCoy AJ FAU - Kent, Helen M AU - Kent HM FAU - Evans, Philip R AU - Evans PR FAU - Owen, David J AU - Owen DJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Cell JT - Cell JID - 0413066 RN - 0 (AP1M2 protein, human) RN - 0 (AP3M2 protein, human) RN - 0 (Adaptor Protein Complex 1) RN - 0 (Adaptor Protein Complex 2) RN - 0 (Adaptor Protein Complex 3) RN - 0 (Adaptor Protein Complex mu Subunits) RN - 0 (Adaptor Proteins, Vesicular Transport) RN - 0 (Ap1m2 protein, mouse) RN - 0 (Ap3m2 protein, mouse) RN - 0 (Ap3m2 protein, rat) RN - 0 (Carrier Proteins) RN - 0 (Clathrin) RN - 0 (Membrane Proteins) RN - 0 (Phosphatidylinositols) RN - 0 (adaptor protein complex 1, mu 2 subunit) RN - 0 (adaptor protein complex 2, mu 2 subunit) SB - IM MH - *Adaptor Protein Complex 1 MH - Adaptor Protein Complex 2 MH - *Adaptor Protein Complex 3 MH - *Adaptor Protein Complex mu Subunits MH - Adaptor Proteins, Vesicular Transport MH - Amino Acid Motifs/physiology MH - Animals MH - Binding Sites MH - Carrier Proteins/*metabolism MH - Cell Membrane/*metabolism MH - Clathrin/*metabolism MH - Eukaryotic Cells/cytology/*metabolism MH - Humans MH - Membrane Proteins/*metabolism MH - Mice MH - Models, Biological MH - Molecular Structure MH - Phosphatidylinositols/metabolism MH - Protein Binding/physiology MH - Protein Structure, Tertiary/physiology MH - Protein Transport/*physiology MH - Rats MH - Transport Vesicles/*metabolism EDAT- 2002/06/28 10:00 MHDA- 2002/07/20 10:01 CRDT- 2002/06/28 10:00 AID - S0092867402007353 [pii] PST - ppublish SO - Cell. 2002 May 17;109(4):523-35. PMID- 20123905 OWN - NLM STAT- MEDLINE DA - 20100203 DCOM- 20100301 LR - 20140827 IS - 1549-5477 (Electronic) IS - 0890-9369 (Linking) VI - 24 IP - 3 DP - 2010 Feb 1 TI - Structural insights into the YAP and TEAD complex. PG - 235-40 LID - 10.1101/gad.1865810 [doi] AB - The Yes-associated protein (YAP) transcriptional coactivator is a key regulator of organ size and a candidate human oncogene inhibited by the Hippo tumor suppressor pathway. The TEAD family of transcription factors binds directly to and mediates YAP-induced gene expression. Here we report the three-dimensional structure of the YAP (residues 50-171)-TEAD1 (residues 194-411) complex, in which YAP wraps around the globular structure of TEAD1 and forms extensive interactions via three highly conserved interfaces. Interface 3, including YAP residues 86-100, is most critical for complex formation. Our study reveals the biochemical nature of the YAP-TEAD interaction, and provides a basis for pharmacological intervention of YAP-TEAD hyperactivation in human diseases. FAU - Li, Ze AU - Li Z AD - School of Life Sciences, Fudan University, Shanghai 200433, China. FAU - Zhao, Bin AU - Zhao B FAU - Wang, Ping AU - Wang P FAU - Chen, Fei AU - Chen F FAU - Dong, Zhenghong AU - Dong Z FAU - Yang, Huirong AU - Yang H FAU - Guan, Kun-Liang AU - Guan KL FAU - Xu, Yanhui AU - Xu Y LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Genes Dev JT - Genes & development JID - 8711660 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (DNA-Binding Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Phosphoproteins) RN - 0 (TEAD1 protein, human) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - 0 (YAP1 (Yes-associated) protein, human) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry/metabolism MH - Amino Acid Sequence MH - Binding Sites MH - DNA-Binding Proteins/*chemistry/metabolism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Proteins/*chemistry/metabolism MH - Phosphoproteins/*chemistry/metabolism MH - Protein Conformation MH - Sequence Alignment MH - Trans-Activators/*chemistry/metabolism MH - Transcription Factors/*chemistry/metabolism PMC - PMC2811825 OID - NLM: PMC2811825 EDAT- 2010/02/04 06:00 MHDA- 2010/03/02 06:00 CRDT- 2010/02/04 06:00 AID - 24/3/235 [pii] AID - 10.1101/gad.1865810 [doi] PST - ppublish SO - Genes Dev. 2010 Feb 1;24(3):235-40. doi: 10.1101/gad.1865810. PMID- 23162382 OWN - NLM STAT- Publisher DA - 20121119 IS - 1549-9618 (Print) IS - 1549-9618 (Linking) VI - 8 IP - 10 DP - 2012 Oct 9 TI - Investigation of the Polymeric Properties of alpha-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study. PG - 3929-3942 AB - Intrinsically disordered proteins (IDPs) have been shown to be involved in a number of cellular functions, in addition to their predominance in diseased states. alpha-synuclein may be described as one such IDP implicated in the pathology of Parkinson's disease. Understanding the conformational characteristics of the monomeric state of alpha-synuclein is necessary for understanding the role of the monomer conformation in aggregation. Polymer theories have been applied to investigate the statistical properties of homopolymeric IDPs. Here we use Replica Exchange Molecular Dynamics (REMD) simulations using temperature as a proxy for solvent quality to examine how well these theories developed for homopolymeric chains describe heteropolymeric alpha-synuclein. Our results indicate that alpha-synuclein behaves like a homopolymer at the extremes of solvent quality, while in the intermediate solvent regime, the uneven distribution of charged residues along the sequence strongly influences the conformations adopted by the chain. We refine the ensemble extracted from the REMD simulations of alpha-synuclein, which shows the best qualitative agreement with experiment, by fitting to the experimental NMR Residual Dipolar Couplings (RDCs) and Paramagnetic Relaxation Enhancements (PREs). Our results demonstrate that the detailed shape of the RDC patterns are sensitive to the angular correlations that are local in sequence while longer range anti-correlations which arise from packing constraints affect the RDC magnitudes. FAU - Narayanan, Chitra AU - Narayanan C AD - Graduate Program in Biochemistry, Rutgers University, Piscataway NJ 08854. FAU - Weinstock, Daniel S AU - Weinstock DS FAU - Wu, Kuen-Phon AU - Wu KP FAU - Baum, Jean AU - Baum J FAU - Levy, Ronald M AU - Levy RM LA - ENG GR - R01 GM030580/GM/NIGMS NIH HHS/United States GR - R01 GM045302/GM/NIGMS NIH HHS/United States GR - R01 GM087012/GM/NIGMS NIH HHS/United States PT - JOURNAL ARTICLE DEP - 20120605 TA - J Chem Theory Comput JT - Journal of chemical theory and computation JID - 101232704 PMC - PMC3496295 MID - NIHMS385154 EDAT- 2012/11/20 06:00 MHDA- 2012/11/20 06:00 CRDT- 2012/11/20 06:00 PHST- 2012/06/05 [epublish] AID - 10.1021/ct300241t [doi] PST - ppublish SO - J Chem Theory Comput. 2012 Oct 9;8(10):3929-3942. Epub 2012 Jun 5. PMID- 25246573 OWN - NLM STAT- MEDLINE DA - 20141008 DCOM- 20150430 LR - 20150407 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 40 DP - 2014 Oct 7 TI - alpha-Synuclein assembles into higher-order multimers upon membrane binding to promote SNARE complex formation. PG - E4274-83 LID - 10.1073/pnas.1416598111 [doi] AB - Physiologically, alpha-synuclein chaperones soluble NSF attachment protein receptor (SNARE) complex assembly and may also perform other functions; pathologically, in contrast, alpha-synuclein misfolds into neurotoxic aggregates that mediate neurodegeneration and propagate between neurons. In neurons, alpha-synuclein exists in an equilibrium between cytosolic and membrane-bound states. Cytosolic alpha-synuclein appears to be natively unfolded, whereas membrane-bound alpha-synuclein adopts an alpha-helical conformation. Although the majority of studies showed that cytosolic alpha-synuclein is monomeric, it is unknown whether membrane-bound alpha-synuclein is also monomeric, and whether chaperoning of SNARE complex assembly by alpha-synuclein involves its cytosolic or membrane-bound state. Here, we show using chemical cross-linking and fluorescence resonance energy transfer (FRET) that alpha-synuclein multimerizes into large homomeric complexes upon membrane binding. The FRET experiments indicated that the multimers of membrane-bound alpha-synuclein exhibit defined intermolecular contacts, suggesting an ordered array. Moreover, we demonstrate that alpha-synuclein promotes SNARE complex assembly at the presynaptic plasma membrane in its multimeric membrane-bound state, but not in its monomeric cytosolic state. Our data delineate a folding pathway for alpha-synuclein that ranges from a monomeric, natively unfolded form in cytosol to a physiologically functional, multimeric form upon membrane binding, and show that only the latter but not the former acts as a SNARE complex chaperone at the presynaptic terminal, and may protect against neurodegeneration. FAU - Burre, Jacqueline AU - Burre J AD - Department of Molecular and Cellular Physiology and. FAU - Sharma, Manu AU - Sharma M AD - Department of Molecular and Cellular Physiology and. FAU - Sudhof, Thomas C AU - Sudhof TC AD - Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University Medical School, Stanford, CA 94305 tcs1@stanford.edu. LA - eng GR - AG010770/AG/NIA NIH HHS/United States GR - NS077906/NS/NINDS NIH HHS/United States GR - P01 AG010770/AG/NIA NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140922 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Liposomes) RN - 0 (Multiprotein Complexes) RN - 0 (Phospholipids) RN - 0 (SNARE Proteins) RN - 0 (Vesicle-Associated Membrane Protein 2) RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Cell Membrane/chemistry/*metabolism MH - Fluorescence Resonance Energy Transfer MH - Humans MH - Immunoblotting MH - Liposomes/metabolism MH - Mice MH - Multiprotein Complexes/metabolism MH - Phospholipids/metabolism MH - Presynaptic Terminals/metabolism MH - Protein Binding MH - *Protein Multimerization MH - SNARE Proteins/*metabolism MH - Synaptic Vesicles/metabolism MH - Vesicle-Associated Membrane Protein 2/metabolism MH - alpha-Synuclein/*chemistry/*metabolism PMC - PMC4210039 OID - NLM: PMC4210039 OTO - NOTNLM OT - Parkinson's disease OT - SNARE proteins OT - membrane fusion OT - synapse EDAT- 2014/09/24 06:00 MHDA- 2015/05/01 06:00 CRDT- 2014/09/24 06:00 PHST- 2014/09/22 [aheadofprint] AID - 1416598111 [pii] AID - 10.1073/pnas.1416598111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):E4274-83. doi: 10.1073/pnas.1416598111. Epub 2014 Sep 22. PMID- 6725251 OWN - NLM STAT- MEDLINE DA - 19840702 DCOM- 19840702 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 259 IP - 10 DP - 1984 May 25 TI - Size and shape of rabbit skeletal muscle calsequestrin. PG - 6248-52 AB - Calsequestrin, a calcium-binding protein isolated from rabbit skeletal muscle sarcoplasmic reticulum, was subjected to physiochemical analysis using sodium dodecyl sulfate gel electrophoresis, gel filtration, sedimentation, viscosity, and circular dichroism techniques. The effects of sodium dodecyl sulfate, alkaline pH, guanidine hydrochloride, and calcium ions on the hydrodynamic properties of the protein were studied. Calsequestrin, in the absence of calcium, had a random coil conformation with an alpha-helical content of 11%. Calsequestrin bound 1.7 mg of sodium dodecyl sulfate per mg of protein resulting in an increase in the alpha-helical content to 20%. The protein was completely random coil in guanidine hydrochloride and had a molecular weight of 42,000 as determined by gel filtration in the presence of this denaturant. Sedimentation equilibrium studies showed that calsequestrin was not subjected to aggregation and had a molecular weight of 38,000. Calsequestrin had a low sedimentation coefficient (2.20 S), a high Stokes radius (45 A), and a high intrinsic viscosity (27.1 ml/g) that increased slightly to 32 ml/g in the presence of guanidine hydrochloride, all indicative of a highly extended structure. Similar studies, performed at pH 9.5, revealed that the protein was even more asymmetric at alkaline pH. Calsequestrin bound 50 mol of calcium ions per mol of protein with an affinity of 1 mM as determined by gel filtration. Calcium binding was accompanied by a change of the protein from a highly extended structure (Rs = 45 A) to a much more compact structure (Rs = 35 A). FAU - Cozens, B AU - Cozens B FAU - Reithmeier, R A AU - Reithmeier RA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Calsequestrin) RN - 0 (Macromolecular Substances) RN - 0 (Muscle Proteins) RN - SY7Q814VUP (Calcium) SB - IM MH - Animals MH - Calcium/metabolism MH - Calsequestrin/*isolation & purification/metabolism MH - Circular Dichroism MH - Macromolecular Substances MH - Molecular Weight MH - Muscle Proteins/*isolation & purification MH - Muscles/*analysis MH - Protein Binding MH - Protein Conformation MH - Rabbits MH - Viscosity EDAT- 1984/05/25 MHDA- 1984/05/25 00:01 CRDT- 1984/05/25 00:00 PST - ppublish SO - J Biol Chem. 1984 May 25;259(10):6248-52. PMID- 17081986 OWN - NLM STAT- MEDLINE DA - 20061103 DCOM- 20061205 LR - 20131121 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 24 IP - 3 DP - 2006 Nov 3 TI - Role of SUMO-interacting motif in Daxx SUMO modification, subnuclear localization, and repression of sumoylated transcription factors. PG - 341-54 AB - Small ubiquitin-like modifier (SUMO) modification has emerged as an important posttranslational control of protein functions. Daxx, a transcriptional corepressor, was reported to repress the transcriptional potential of several transcription factors and target to PML oncogenic domains (PODs) via SUMO-dependent interactions. The mechanism by which Daxx binds to sumoylated factors mediating transcriptional and subnuclear compartmental regulation remains unclear. Here, we define a SUMO-interacting motif (SIM) within Daxx and show it to be crucial for targeting Daxx to PODs and for transrepression of several sumoylated transcription factors, including glucocorticoid receptor (GR). In addition, the capability of Daxx SIM to bind SUMO also controls Daxx sumoylation. We further demonstrate that arsenic trioxide-induced sumoylation of PML correlates with a change of endogenous Daxx partitioning from GR-regulated gene promoter to PODs and a relief of Daxx repression on GR target gene expression. Our results provide mechanistic insights into Daxx in SUMO-dependent transcriptional control and subnuclear compartmentalization. FAU - Lin, Ding-Yen AU - Lin DY AD - Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan, Republic of China. FAU - Huang, Yen-Sung AU - Huang YS FAU - Jeng, Jen-Chong AU - Jeng JC FAU - Kuo, Hong-Yi AU - Kuo HY FAU - Chang, Che-Chang AU - Chang CC FAU - Chao, Ting-Ting AU - Chao TT FAU - Ho, Chun-Chen AU - Ho CC FAU - Chen, Yun-Ching AU - Chen YC FAU - Lin, Tong-Ping AU - Lin TP FAU - Fang, Hsin-I AU - Fang HI FAU - Hung, Chih-Chang AU - Hung CC FAU - Suen, Ching-Shu AU - Suen CS FAU - Hwang, Ming-Jing AU - Hwang MJ FAU - Chang, Kun-Sang AU - Chang KS FAU - Maul, Gerd G AU - Maul GG FAU - Shih, Hsiu-Ming AU - Shih HM LA - eng GR - EX95-9529NI/PHS HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Arsenicals) RN - 0 (Carrier Proteins) RN - 0 (DAXX protein, human) RN - 0 (Daxx protein, mouse) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Neoplasm Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Oxides) RN - 0 (Pml protein, mouse) RN - 0 (Receptors, Glucocorticoid) RN - 0 (Repressor Proteins) RN - 0 (Small Ubiquitin-Related Modifier Proteins) RN - 0 (Transcription Factors) RN - 0 (Tumor Suppressor Proteins) RN - 1327-53-3 (arsenic trioxide) RN - 143220-95-5 (PML protein, human) RN - 7S5I7G3JQL (Dexamethasone) SB - IM MH - Adaptor Proteins, Signal Transducing/chemistry/*metabolism MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Arsenicals/pharmacology MH - COS Cells MH - Carrier Proteins/chemistry/*metabolism MH - Cell Nucleus/*metabolism MH - Cercopithecus aethiops MH - Dexamethasone/pharmacology MH - HeLa Cells MH - Humans MH - Intracellular Signaling Peptides and Proteins/chemistry/*metabolism MH - Mice MH - Molecular Sequence Data MH - Neoplasm Proteins/metabolism MH - Nuclear Proteins/chemistry/*metabolism MH - Oxides/pharmacology MH - Protein Binding MH - Protein Structure, Tertiary MH - Protein Transport MH - Receptors, Glucocorticoid/metabolism MH - Repressor Proteins/*metabolism MH - Small Ubiquitin-Related Modifier Proteins/*metabolism MH - Transcription Factors/metabolism MH - Transcription, Genetic/drug effects MH - Tumor Suppressor Proteins/metabolism EDAT- 2006/11/04 09:00 MHDA- 2006/12/09 09:00 CRDT- 2006/11/04 09:00 PHST- 2006/03/24 [received] PHST- 2006/08/23 [revised] PHST- 2006/10/16 [accepted] AID - S1097-2765(06)00709-X [pii] AID - 10.1016/j.molcel.2006.10.019 [doi] PST - ppublish SO - Mol Cell. 2006 Nov 3;24(3):341-54. PMID- 17233114 OWN - NLM STAT- MEDLINE DA - 20070118 DCOM- 20070131 IS - 1044-5498 (Print) IS - 1044-5498 (Linking) VI - 25 IP - 12 DP - 2006 Dec TI - The disordered amino-terminus of SIMPL interacts with members of the 70-kDa heat-shock protein family. PG - 704-14 AB - The p65 coactivator SIMPL is a small protein that lacks any conserved domains of known function. To better understand regulation of SIMPL activity, we sought to identify novel SIMPL interacting proteins using mass spectrometry analysis of SIMPL containing complexes. Two members of the 70-kDa heat-shock protein family, Hsp70 and Hsc70, were identified as SIMPL binding proteins. Subsequent immunocomplexing assays confirmed this interaction and demonstrated that the amino-terminus of SIMPL is required for this interaction. Using a combination of amino acid composition analysis, PONDR VL-XT prediction, charge-hydropathy plots, and cumulative distribution functions, the amino-terminal region of both mouse and human SIMPL proteins was predicted to be intrinsically disordered. These data, taken together, suggest that Hsp70/Hsc70 bind the intrinsically disordered amino-terminal region of SIMPL to stabilize the protein and thereby regulate its activity. Understanding the regulation of SIMPL through its interaction with Hsp70/Hsc70 may serve as a novel means of modulating tumor necrosis factor alpha signaling. FAU - Haag Breese, Erin AU - Haag Breese E AD - Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indiana University Cancer Center, Indianapolis, Indiana 46220, USA. FAU - Uversky, Vladimir N AU - Uversky VN FAU - Georgiadis, Millie M AU - Georgiadis MM FAU - Harrington, Maureen A AU - Harrington MA LA - eng PT - Journal Article PL - United States TA - DNA Cell Biol JT - DNA and cell biology JID - 9004522 RN - 0 (Carrier Proteins) RN - 0 (HSP70 Heat-Shock Proteins) RN - 0 (Mutant Proteins) RN - 0 (SIMPL protein, mouse) SB - IM MH - Amino Acid Sequence MH - Animals MH - Carrier Proteins/*chemistry/*metabolism MH - Cells, Cultured MH - Computational Biology MH - HSP70 Heat-Shock Proteins/*metabolism MH - Humans MH - Mass Spectrometry MH - Mice MH - Mutant Proteins/metabolism MH - Protein Binding MH - Protein Interaction Mapping MH - Protein Structure, Tertiary MH - Sequence Analysis, Protein MH - Transfection EDAT- 2007/01/20 09:00 MHDA- 2007/02/01 09:00 CRDT- 2007/01/20 09:00 PST - ppublish SO - DNA Cell Biol. 2006 Dec;25(12):704-14. PMID- 18587051 OWN - NLM STAT- MEDLINE DA - 20080707 DCOM- 20080731 LR - 20140917 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 105 IP - 26 DP - 2008 Jul 1 TI - Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence-specific mismatch recognition. PG - 8890-5 LID - 10.1073/pnas.0711061105 [doi] AB - Cytosine methylation at CpG dinucleotides produces m(5)CpG, an epigenetic modification that is important for transcriptional regulation and genomic stability in vertebrate cells. However, m(5)C deamination yields mutagenic G.T mispairs, which are implicated in genetic disease, cancer, and aging. Human thymine DNA glycosylase (hTDG) removes T from G.T mispairs, producing an abasic (or AP) site, and follow-on base excision repair proteins restore the G.C pair. hTDG is inactive against normal A.T pairs, and is most effective for G.T mispairs and other damage located in a CpG context. The molecular basis of these important catalytic properties has remained unknown. Here, we report a crystal structure of hTDG (catalytic domain, hTDG(cat)) in complex with abasic DNA, at 2.8 A resolution. Surprisingly, the enzyme crystallized in a 2:1 complex with DNA, one subunit bound at the abasic site, as anticipated, and the other at an undamaged (nonspecific) site. Isothermal titration calorimetry and electrophoretic mobility-shift experiments indicate that hTDG and hTDG(cat) can bind abasic DNA with 1:1 or 2:1 stoichiometry. Kinetics experiments show that the 1:1 complex is sufficient for full catalytic (base excision) activity, suggesting that the 2:1 complex, if adopted in vivo, might be important for some other activity of hTDG, perhaps binding interactions with other proteins. Our structure reveals interactions that promote the stringent specificity for guanine versus adenine as the pairing partner of the target base and interactions that likely confer CpG sequence specificity. We find striking differences between hTDG and its prokaryotic ortholog (MUG), despite the relatively high (32%) sequence identity. FAU - Maiti, Atanu AU - Maiti A AD - Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA. FAU - Morgan, Michael T AU - Morgan MT FAU - Pozharski, Edwin AU - Pozharski E FAU - Drohat, Alexander C AU - Drohat AC LA - eng SI - PDB/2RBA GR - GM072711/GM/NIGMS NIH HHS/United States GR - R01 GM072711/GM/NIGMS NIH HHS/United States GR - R01 GM072711-03/GM/NIGMS NIH HHS/United States GR - R01 GM072711-04/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20080627 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 5Z93L87A1R (Guanine) RN - 9007-49-2 (DNA) RN - EC 3.2.2.- (Thymine DNA Glycosylase) SB - IM MH - *Base Pair Mismatch MH - Base Pairing MH - Base Sequence MH - CpG Islands/genetics MH - Crystallography, X-Ray MH - DNA/genetics/*metabolism MH - Dimerization MH - Guanine/metabolism MH - Humans MH - Kinetics MH - Models, Molecular MH - Molecular Sequence Data MH - Substrate Specificity MH - Thermodynamics MH - Thymine DNA Glycosylase/*chemistry/*metabolism PMC - PMC2449336 OID - NLM: PMC2449336 EDAT- 2008/07/01 09:00 MHDA- 2008/08/01 09:00 CRDT- 2008/07/01 09:00 PHST- 2008/06/27 [aheadofprint] AID - 0711061105 [pii] AID - 10.1073/pnas.0711061105 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8890-5. doi: 10.1073/pnas.0711061105. Epub 2008 Jun 27. PMID- 15733859 OWN - NLM STAT- MEDLINE DA - 20050228 DCOM- 20050401 LR - 20080515 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 579 IP - 6 DP - 2005 Feb 28 TI - The flexible loop of Bcl-2 is required for molecular interaction with immunosuppressant FK-506 binding protein 38 (FKBP38). PG - 1469-76 AB - Bcl-2 contains an unusually long loop between the first and the second helices. This loop has been shown to be highly flexible based on NMR and X-ray crystallographic analyses of this region. Bcl-2 is regulated at the posttranslational level through phosphorylation of specific residues within the flexible loop. The biological role and posttranslational modifications of the loop of Bcl-2 is currently unclear. FK-506 binding protein 38 (FKBP38) has been reported to interact with Bcl-2, suggesting that FKBP38 could act as a docking molecule to localize Bcl-2 at the mitochondrial membrane [Shirane, M. and Nakayama, K.I. (2003) Inherent calcineurin inhibitor FKBP38 targets Bcl-2 to mitochondria and inhibits apoptosis. Nat. Cell Biol. 5, 28-37]. Here, we investigated the molecular interaction between FKBP38 and Bcl-2, and demonstrated that Bcl-2 interacts with FKBP38 through the unstructured loop, and the interaction appears to regulate phosphorylation in the loop of Bcl-2. FAU - Kang, Cong Bao AU - Kang CB AD - Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637511, Singapore. FAU - Tai, Jeff AU - Tai J FAU - Chia, Joel AU - Chia J FAU - Yoon, Ho Sup AU - Yoon HS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (FKBP8 protein, human) RN - 0 (Immunosuppressive Agents) RN - 0 (Proto-Oncogene Proteins c-bcl-2) RN - EC 5.2.1.- (Tacrolimus Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Humans MH - Immunosuppressive Agents/pharmacology MH - Molecular Sequence Data MH - Mutation/genetics MH - Phosphorylation MH - Protein Binding MH - Proto-Oncogene Proteins c-bcl-2/*chemistry/genetics/*metabolism MH - Sequence Alignment MH - Substrate Specificity MH - Tacrolimus Binding Proteins/chemistry/genetics/isolation & purification/*metabolism EDAT- 2005/03/01 09:00 MHDA- 2005/04/02 09:00 CRDT- 2005/03/01 09:00 PHST- 2004/10/17 [received] PHST- 2005/01/20 [revised] PHST- 2005/01/26 [accepted] AID - S0014-5793(05)00154-7 [pii] AID - 10.1016/j.febslet.2005.01.053 [doi] PST - ppublish SO - FEBS Lett. 2005 Feb 28;579(6):1469-76. PMID- 23132854 OWN - NLM STAT- MEDLINE DA - 20121231 DCOM- 20130325 LR - 20150522 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 53 DP - 2012 Dec 28 TI - Binding of the N-terminal region of coactivator TIF2 to the intrinsically disordered AF1 domain of the glucocorticoid receptor is accompanied by conformational reorganizations. PG - 44546-60 LID - 10.1074/jbc.M112.411330 [doi] AB - Control of gene transcription by glucocorticoid receptors (GRs) is important for many physiological processes. Like other steroid hormone receptors, the regulation of target genes by GR is mediated by two transactivation domains: activation function 1 (AF1) in the N-terminal domain and AF2 in the C-terminal ligand-binding domain (LBD). Full receptor activity requires both AF1 and -2 plus assorted coregulatory proteins. Crystal structures of the ligand-bound LBD have provided insight regarding how AF2 interacts with specific coactivators. However, despite its being the major activation domain of GRs, knowledge of AF1 structure/function has languished. This is mainly because of the highly disorganized structure of the GR N-terminal domain. This lack of AF1 structure is shared by all members of the steroid/nuclear receptor superfamily for which it has been examined and AF1 is thought to allow productive interactions with assorted cofactors via protein-induced changes in secondary/tertiary structures. To date, there are no reports of a classical coactivator altering the secondary/tertiary structure of the GR AF1 domain. Earlier, we reported an N-terminal fragment of the p160 coactivator TIF2, called TIF2.0, that binds the GR N-terminal domain and alters GR transcriptional activity. We therefore proposed that TIF2.0 binding to AF1 changes both its conformation and transcriptional activity. We now report that TIF2.0 interacts with the GR AF1 domain to increase the amount of alpha-helical structure in the complex. Furthermore, TIF2 coactivator activity is observed in the absence of the GR LBD in a manner that requires the AF1 domain. This contrasts with previous models where TIF2 receptor interaction domains binding to GR LBD somehow alter AF1 conformation. Our results establish for the first time that coactivators can modify the structure of the AF1 domain directly via the binding of a second region of the coactivator and suggest a molecular explanation for how coactivators increase the transcriptional activity of GR-agonist complexes. FAU - Khan, Shagufta H AU - Khan SH AD - Department of Basic Sciences, The Commonwealth Medical College, Scranton, Pennsylvania 18509, USA. FAU - Awasthi, Smita AU - Awasthi S FAU - Guo, Chunhua AU - Guo C FAU - Goswami, Devrishi AU - Goswami D FAU - Ling, Jun AU - Ling J FAU - Griffin, Patrick R AU - Griffin PR FAU - Simons, S Stoney Jr AU - Simons SS Jr FAU - Kumar, Raj AU - Kumar R LA - eng GR - R01 GM084041/GM/NIGMS NIH HHS/United States GR - S10 RR027270/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20121106 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (NCOA2 protein, human) RN - 0 (Ncoa2 protein, rat) RN - 0 (Nuclear Receptor Coactivator 2) RN - 0 (Receptors, Glucocorticoid) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cell Line MH - Humans MH - Kinetics MH - Molecular Sequence Data MH - Nuclear Receptor Coactivator 2/*chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Rats MH - Receptors, Glucocorticoid/*chemistry/genetics/*metabolism MH - Transcriptional Activation PMC - PMC3531768 OID - NLM: PMC3531768 EDAT- 2012/11/08 06:00 MHDA- 2013/03/26 06:00 CRDT- 2012/11/08 06:00 PHST- 2012/11/06 [aheadofprint] AID - M112.411330 [pii] AID - 10.1074/jbc.M112.411330 [doi] PST - ppublish SO - J Biol Chem. 2012 Dec 28;287(53):44546-60. doi: 10.1074/jbc.M112.411330. Epub 2012 Nov 6. PMID- 2407243 OWN - NLM STAT- MEDLINE DA - 19900320 DCOM- 19900320 LR - 20081121 IS - 0006-291X (Print) IS - 0006-291X (Linking) VI - 166 IP - 3 DP - 1990 Feb 14 TI - Characterization of a functional domain of human calpastatin. PG - 1485-93 AB - Expression plasmids were constructed from the cDNA of human calpastatin to examine the contribution to the inhibition of calpain of highly conserved sequences in each of four repetitive domains. A series of deletion derivatives of domain 1 proteins, truncated at either the amino or carboxy terminus, were produced in E. coli. Deletion from the amino terminus past the amino terminal conserved sequence decreased the inhibition. When the middle conserved sequence, the M-sequence, was further deleted, no inhibition was detected, but deletion from the carboxy terminus past the carboxy terminal conserved sequence did not decrease the inhibition until the M-sequence was reached. Nuclear magnetic resonance and circular dichroism spectra showed that domain 1 has an unfolded structure. Peptides that contained the M-sequence and some neighboring sequences were synthesized to measure the minimum size of the inhibitory peptide, which was the M-sequence with the next six residues on the amino terminal side. FAU - Uemori, T AU - Uemori T AD - Biotechnology Research Laboratories, Takara Shuzo Co, Ltd, Kyoto, Japan. FAU - Shimojo, T AU - Shimojo T FAU - Asada, K AU - Asada K FAU - Asano, T AU - Asano T FAU - Kimizuka, F AU - Kimizuka F FAU - Kato, I AU - Kato I FAU - Maki, M AU - Maki M FAU - Hatanaka, M AU - Hatanaka M FAU - Murachi, T AU - Murachi T FAU - Hanzawa, H AU - Hanzawa H AU - et al. LA - eng SI - GENBANK/M33328 PT - Journal Article PL - UNITED STATES TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Calcium-Binding Proteins) RN - 0 (Peptides) RN - 0 (Recombinant Proteins) RN - 79079-11-1 (calpastatin) RN - EC 3.4.22.- (Calpain) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Calcium-Binding Proteins/*genetics/isolation & purification/pharmacology MH - Calpain/*antagonists & inhibitors MH - Circular Dichroism MH - Cloning, Molecular MH - Escherichia coli/genetics MH - Kinetics MH - Molecular Sequence Data MH - Peptides/chemical synthesis MH - Plasmids MH - Protein Conformation MH - Recombinant Proteins/isolation & purification/pharmacology MH - Restriction Mapping MH - Terminator Regions, Genetic EDAT- 1990/02/14 MHDA- 1990/02/14 00:01 CRDT- 1990/02/14 00:00 PST - ppublish SO - Biochem Biophys Res Commun. 1990 Feb 14;166(3):1485-93. PMID- 18032500 OWN - NLM STAT- MEDLINE DA - 20080118 DCOM- 20080205 LR - 20140904 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 82 IP - 3 DP - 2008 Feb TI - Identification of residues required for RNA replication in domains II and III of the hepatitis C virus NS5A protein. PG - 1073-83 AB - The NS5A protein of hepatitis C virus (HCV) plays an important but undefined role in viral RNA replication. NS5A has been proposed to be a three-domain protein, and the crystal structure of the well-conserved amino-terminal domain I has been determined. The remaining two domains of NS5A, designated domains II and III, and their corresponding interdomain regions are poorly understood. We have conducted a detailed mutagenesis analysis of NS5A domains II and III using the genotype 1b HCV replicon system. The majority of the mutants containing 15 small (8- to 15-amino-acid) deletions analyzed were capable of efficient RNA replication. Only five deletion mutations yielded lethal phenotypes, and these were colinear, spanning a 56-amino-acid region within domain II. This region was further analyzed by combining triple and single alanine scanning mutagenesis to identify individual residues required for RNA replication. Based upon this analysis, 23 amino acids were identified that were found to be essential. In addition, two residues were identified that yielded a small colony phenotype while possessing only a moderate defect in RNA replication. These results indicate that the entire domain III region and large portions of domain II of the NS5A protein are not required for the function of NS5A in HCV RNA replication. FAU - Tellinghuisen, Timothy L AU - Tellinghuisen TL AD - Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, 1230 York Avenue, Box 64, New York, NY 10065, USA. FAU - Foss, Katie L AU - Foss KL FAU - Treadaway, Jason C AU - Treadaway JC FAU - Rice, Charles M AU - Rice CM LA - eng GR - 1 K22 AI067645-01/AI/NIAID NIH HHS/United States GR - 5 R01 CA57973-12/CA/NCI NIH HHS/United States GR - 5F32 AI51820-03/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20071121 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (RNA, Viral) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Amino Acid Substitution/genetics MH - Hepacivirus/*growth & development/physiology MH - Humans MH - Mutagenesis, Site-Directed MH - Protein Structure, Tertiary MH - RNA, Viral/*metabolism MH - Sequence Deletion MH - Viral Nonstructural Proteins/chemistry/genetics/*metabolism MH - *Virus Replication PMC - PMC2224455 OID - NLM: PMC2224455 EDAT- 2007/11/23 09:00 MHDA- 2008/02/06 09:00 CRDT- 2007/11/23 09:00 PHST- 2007/11/21 [aheadofprint] AID - JVI.00328-07 [pii] AID - 10.1128/JVI.00328-07 [doi] PST - ppublish SO - J Virol. 2008 Feb;82(3):1073-83. Epub 2007 Nov 21. PMID- 12562770 OWN - NLM STAT- MEDLINE DA - 20030407 DCOM- 20030703 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 15 DP - 2003 Apr 11 TI - Structure of human carnitine acetyltransferase. Molecular basis for fatty acyl transfer. PG - 13159-65 AB - Carnitine acyltransferases are a family of ubiquitous enzymes that play a pivotal role in cellular energy metabolism. We report here the x-ray structure of human carnitine acetyltransferase to a 1.6-A resolution. This structure reveals a monomeric protein of two equally sized alpha/beta domains. Each domain is shown to have a partially similar fold to other known but oligomeric enzymes that are also involved in group-transfer reactions. The unique monomeric arrangement of the two domains constitutes a central narrow active site tunnel, indicating a likely universal feature for all members of the carnitine acyltransferase family. Superimposition of the substrate complex of a related protein, dihydrolipoyl trans-acetylase, reveals that both substrates localize to the active site tunnel of human carnitine acetyltransferase, suggesting the location of the ligand binding sites for carnitine and coenzyme A. Most significantly, this structure provides critical insights into the molecular basis for fatty acyl chain transfer and a possible common mechanism among a wide range of acyltransferases utilizing a catalytic dyad. FAU - Wu, Donghai AU - Wu D AD - Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, USA. FAU - Govindasamy, Lakshmanan AU - Govindasamy L FAU - Lian, Wei AU - Lian W FAU - Gu, Yunrong AU - Gu Y FAU - Kukar, Thomas AU - Kukar T FAU - Agbandje-McKenna, Mavis AU - Agbandje-McKenna M FAU - McKenna, Robert AU - McKenna R LA - eng SI - PDB/1NM8 GR - R01 GM58197/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20030131 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Fatty Acids) RN - EC 2.3.1.7 (Carnitine O-Acetyltransferase) SB - IM MH - Amino Acid Sequence MH - Carnitine O-Acetyltransferase/*chemistry/*metabolism MH - Crystallography, X-Ray MH - Fatty Acids/metabolism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Structure, Secondary MH - Sensitivity and Specificity MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Software EDAT- 2003/02/04 04:00 MHDA- 2003/07/04 05:00 CRDT- 2003/02/04 04:00 PHST- 2003/01/31 [aheadofprint] AID - 10.1074/jbc.M212356200 [doi] AID - M212356200 [pii] PST - ppublish SO - J Biol Chem. 2003 Apr 11;278(15):13159-65. Epub 2003 Jan 31. PMID- 23363599 OWN - NLM STAT- MEDLINE DA - 20130327 DCOM- 20130920 LR - 20141103 IS - 1939-4586 (Electronic) IS - 1059-1524 (Linking) VI - 24 IP - 7 DP - 2013 Apr TI - Means of self-preservation: how an intrinsically disordered ubiquitin-protein ligase averts self-destruction. PG - 1041-52 LID - 10.1091/mbc.E12-11-0811 [doi] AB - Ubiquitin-protein ligases (E3s) that ubiquitinate substrates for proteasomal degradation are often in the position of ubiquitinating themselves due to interactions with a charged ubiquitin-conjugating enzyme (E2). This can mediate the E3's proteasomal degradation. Many E3s have evolved means to avoid autoubiquitination, including protection by partner or substrate binding, preventative modifications, and deubiquitinating enzyme reversal of ubiquitination. Here we describe another adaptation for E3 self-protection discovered while exploring San1, which ubiquitinates misfolded nuclear proteins in yeast for proteasomal degradation. San1 is highly disordered in its substrate-binding regions N- and C-terminal to its RING domain. In cis autoubiquitination could occur if these flexible regions come in proximity to the E2. San1 prevents this by containing no lysines in its disordered regions; thus the canonical residue used for ubiquitin attachment has been selectively eliminated. San1's target substrates have lost their native structures and expose hydrophobicity. To avoid in trans autoubiquitination, San1 possesses little concentrated hydrophobicity in its disordered regions, and thus the that feature San1 recognizes in misfolded substrates has also been selectively eliminated. Overall the presence of key residues in San1 have been evolutionarily minimized to avoid self-destruction either in cis or in trans. Our work expands the ways in which E3s protect themselves from autoubiquitination. FAU - Fredrickson, Eric K AU - Fredrickson EK AD - Department of Pharmacology, University of Washington, Seattle, WA 98195, USA. FAU - Clowes Candadai, Sarah V AU - Clowes Candadai SV FAU - Tam, Cheuk Ho AU - Tam CH FAU - Gardner, Richard G AU - Gardner RG LA - eng GR - 5T32GM007750/GM/NIGMS NIH HHS/United States GR - R01 AG031136/AG/NIA NIH HHS/United States GR - R01AG031136/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130130 PL - United States TA - Mol Biol Cell JT - Molecular biology of the cell JID - 9201390 RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Ubiquitin) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) RN - EC 6.3.2.19 (SAN1 protein, S cerevisiae) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) RN - K3Z4F929H6 (Lysine) SB - IM MH - Binding Sites/genetics MH - Blotting, Western MH - Hydrophobic and Hydrophilic Interactions MH - Lysine/genetics/metabolism MH - Mutation MH - Proteasome Endopeptidase Complex/*metabolism MH - Protein Stability MH - Proteolysis MH - Saccharomyces cerevisiae/genetics/growth & development/metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism MH - Ubiquitin/genetics/metabolism MH - Ubiquitin-Protein Ligases/chemistry/genetics/*metabolism MH - *Ubiquitination PMC - PMC3608492 OID - NLM: PMC3608492 EDAT- 2013/02/01 06:00 MHDA- 2013/09/21 06:00 CRDT- 2013/02/01 06:00 PHST- 2013/01/30 [aheadofprint] AID - mbc.E12-11-0811 [pii] AID - 10.1091/mbc.E12-11-0811 [doi] PST - ppublish SO - Mol Biol Cell. 2013 Apr;24(7):1041-52. doi: 10.1091/mbc.E12-11-0811. Epub 2013 Jan 30. PMID- 12562774 OWN - NLM STAT- MEDLINE DA - 20030414 DCOM- 20030522 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 16 DP - 2003 Apr 18 TI - Crystal structure of an alpha 1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis. PG - 14420-8 AB - EXTL2, an alpha1,4-N-acetylhexosaminyltransferase, catalyzes the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta1-3[galactose]beta1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans. We have solved the x-ray crystal structure of the catalytic domain of mouse EXTL2 in the apo-form and with donor substrates UDP-N-acetylglucosamine and UDP-N-acetylgalactosamine. In addition, a structure of the ternary complex with UDP and the acceptor substrate analog [glucuronic acid]beta1-3[galactose]beta1-O-naphthalenemethanol has been determined. These structures reveal three highly conserved residues, Asn-243, Asp-246, and Arg-293, located at the active site. Mutation of these residues greatly decreases the activity. In the ternary complex, an interaction exists between the beta-phosphate of the UDP leaving group and the acceptor hydroxyl of the substrate that may play a functional role in catalysis. These structures represent the first structures from the exostosin gene family and provide important insight into the mechanisms of alpha1,4-N-acetylhexosaminyl transfer in heparan biosynthesis. FAU - Pedersen, Lars C AU - Pedersen LC AD - Pharmacogenetics Section, Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, North Carolina 27709, USA. FAU - Dong, Jian AU - Dong J FAU - Taniguchi, Fumiyasu AU - Taniguchi F FAU - Kitagawa, Hiroshi AU - Kitagawa H FAU - Krahn, Joe M AU - Krahn JM FAU - Pedersen, Lee G AU - Pedersen LG FAU - Sugahara, Kazuyuki AU - Sugahara K FAU - Negishi, Masahiko AU - Negishi M LA - eng SI - PDB/1OMX SI - PDB/1OMZ SI - PDB/1ON6 SI - PDB/1ON8 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030131 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Membrane Proteins) RN - 30KYC7MIAI (Aspartic Acid) RN - 528-04-1 (Uridine Diphosphate N-Acetylglucosamine) RN - 7006-34-0 (Asparagine) RN - 9050-30-0 (Heparitin Sulfate) RN - 94ZLA3W45F (Arginine) RN - EC 2.4.1.- (EXTL2 protein, human) RN - EC 2.4.1.- (N-Acetylgalactosaminyltransferases) RN - EC 2.4.1.- (N-Acetylglucosaminyltransferases) RN - EC 2.4.1.- (UDP-N-acetylgalactosamine (GlcUA-GalNAc-4-sulfate)(4) N-acetylgalactosaminyltransferase) SB - IM MH - Amino Acid Sequence MH - Animals MH - Arginine/chemistry MH - Asparagine/chemistry MH - Aspartic Acid/chemistry MH - Binding Sites MH - COS Cells MH - Catalytic Domain MH - Crystallography, X-Ray MH - Heparitin Sulfate/*biosynthesis/chemistry MH - Hydrogen Bonding MH - *Membrane Proteins MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - N-Acetylgalactosaminyltransferases/metabolism MH - N-Acetylglucosaminyltransferases/*chemistry MH - Protein Conformation MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Transfection MH - Uridine Diphosphate N-Acetylglucosamine/metabolism EDAT- 2003/02/04 04:00 MHDA- 2003/05/23 05:00 CRDT- 2003/02/04 04:00 PHST- 2003/01/31 [aheadofprint] AID - 10.1074/jbc.M210532200 [doi] AID - M210532200 [pii] PST - ppublish SO - J Biol Chem. 2003 Apr 18;278(16):14420-8. Epub 2003 Jan 31. PMID- 15474353 OWN - NLM STAT- MEDLINE DA - 20041011 DCOM- 20041221 LR - 20061115 IS - 0969-9961 (Print) IS - 0969-9961 (Linking) VI - 17 IP - 2 DP - 2004 Nov TI - Natively unfolded tubulin polymerization promoting protein TPPP/p25 is a common marker of alpha-synucleinopathies. PG - 155-62 AB - The novel basic, heat-stable tubulin polymerization promoting protein TPPP/p25 is associated with microtubules in vitro and can induce the formation of aberrant microtubule assemblies. We show by 1H-NMR spectroscopy that TPPP/p25 is natively unfolded. Antisera against peptide 186GKGKAGRVDLVDESG200NH2 (186-200) are highly specific to TPPP/p25. Immunohistochemistry and confocal microscopy demonstrates that TPPP/p25 is enriched in filamentous alpha-synuclein bearing Lewy bodies of Parkinson's (PD) and diffuse Lewy body disease (DLBD), as well as glial inclusions of multiple system atrophy (MSA). There is a correlation between TPPP/p25 and alpha-synuclein immunoreactivity in Western blot. In contrast, TPPP/p25 is not associated with abnormally phosphorylated tau in various inclusions of Pick's disease (PiD), progressive supranuclear palsy (PSP), and corticobasal degeneration (CBD). However, electron microscopy confirms clusters of TPPP/p25 immunoreactivity along filaments of unstructured but not compact neurofibrillary tangles in Alzheimer's disease (AD). TPPP/p25 seems to be a novel marker of alpha-synucleinopathies. FAU - Kovacs, Gabor G AU - Kovacs GG AD - Institute of Neurology, Medical University of Vienna, A-1097 Vienna, Austria. FAU - Laszlo, Lajos AU - Laszlo L FAU - Kovacs, Janos AU - Kovacs J FAU - Jensen, Poul Henning AU - Jensen PH FAU - Lindersson, Evo AU - Lindersson E FAU - Botond, Gergo AU - Botond G FAU - Molnar, Tamas AU - Molnar T FAU - Perczel, Andras AU - Perczel A FAU - Hudecz, Ferenc AU - Hudecz F FAU - Mezo, Gabor AU - Mezo G FAU - Erdei, Anna AU - Erdei A FAU - Tirian, Laszlo AU - Tirian L FAU - Lehotzky, Attila AU - Lehotzky A FAU - Gelpi, Ellen AU - Gelpi E FAU - Budka, Herbert AU - Budka H FAU - Ovadi, Judit AU - Ovadi J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Neurobiol Dis JT - Neurobiology of disease JID - 9500169 RN - 0 (Biological Markers) RN - 0 (Immune Sera) RN - 0 (Nerve Tissue Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 0 (p25 protein, human) SB - IM MH - Aged MH - Animals MH - Biological Markers/metabolism MH - Blotting, Western MH - Brain/*metabolism MH - Cattle MH - Female MH - Humans MH - Immune Sera MH - Immunohistochemistry MH - Magnetic Resonance Spectroscopy MH - Male MH - Microscopy, Electron MH - Middle Aged MH - Nerve Tissue Proteins/*metabolism MH - Neurodegenerative Diseases/*metabolism MH - Protein Folding MH - Synucleins MH - alpha-Synuclein EDAT- 2004/10/12 09:00 MHDA- 2004/12/22 09:00 CRDT- 2004/10/12 09:00 PHST- 2003/12/13 [received] PHST- 2004/06/09 [revised] PHST- 2004/06/14 [accepted] AID - S0969-9961(04)00136-6 [pii] AID - 10.1016/j.nbd.2004.06.006 [doi] PST - ppublish SO - Neurobiol Dis. 2004 Nov;17(2):155-62. PMID- 22024360 OWN - NLM STAT- MEDLINE DA - 20120102 DCOM- 20120710 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1822 IP - 2 DP - 2012 Feb TI - Alpha-synuclein misfolding and Parkinson's disease. PG - 261-85 LID - 10.1016/j.bbadis.2011.10.002 [doi] AB - Substantial evidence links alpha-synuclein, a small highly conserved presynaptic protein with unknown function, to both familial and sporadic Parkinson's disease (PD). alpha-Synuclein has been identified as the major component of Lewy bodies and Lewy neurites, the characteristic proteinaceous deposits that are the hallmarks of PD. alpha-Synuclein is a typical intrinsically disordered protein, but can adopt a number of different conformational states depending on conditions and cofactors. These include the helical membrane-bound form, a partially-folded state that is a key intermediate in aggregation and fibrillation, various oligomeric species, and fibrillar and amorphous aggregates. The molecular basis of PD appears to be tightly coupled to the aggregation of alpha-synuclein and the factors that affect its conformation. This review examines the different aggregation states of alpha-synuclein, the molecular mechanism of its aggregation, and the influence of environmental and genetic factors on this process. CI - Copyright (c) 2011 Elsevier B.V. All rights reserved. FAU - Breydo, Leonid AU - Breydo L AD - Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL 33612, USA. FAU - Wu, Jessica W AU - Wu JW FAU - Uversky, Vladimir N AU - Uversky VN LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20111012 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (alpha-Synuclein) SB - IM MH - Humans MH - Lewy Bodies/*metabolism MH - Parkinson Disease/*metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - alpha-Synuclein/*metabolism EDAT- 2011/10/26 06:00 MHDA- 2012/07/11 06:00 CRDT- 2011/10/26 06:00 PHST- 2011/07/22 [received] PHST- 2011/08/26 [revised] PHST- 2011/10/03 [accepted] PHST- 2011/10/12 [aheadofprint] AID - S0925-4439(11)00225-0 [pii] AID - 10.1016/j.bbadis.2011.10.002 [doi] PST - ppublish SO - Biochim Biophys Acta. 2012 Feb;1822(2):261-85. doi: 10.1016/j.bbadis.2011.10.002. Epub 2011 Oct 12. PMID- 23106332 OWN - NLM STAT- MEDLINE DA - 20121128 DCOM- 20130426 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 134 IP - 47 DP - 2012 Nov 28 TI - Small-molecule inhibition of c-MYC:MAX leucine zipper formation is revealed by ion mobility mass spectrometry. PG - 19384-92 LID - 10.1021/ja306519h [doi] AB - The leucine zipper interaction between MAX and c-MYC has been studied using mass spectrometry and drift time ion mobility mass spectrometry (DT IM-MS) in addition to circular dichroism spectroscopy. Peptides comprising the leucine zipper sequence with (c-MYC-Zip residues 402-434) and without a postulated small-molecule binding region (c-MYC-ZipDeltaDT residues 406-434) have been synthesized, along with the corresponding MAX leucine zipper (MAX-Zip residues 74-102). c-MYC-Zip:MAX-Zip complexes are observed both in the absence and in the presence of the reported small-molecule inhibitor 10058-F4 for both forms of c-MYC-Zip. DT IM-MS, in combination with molecular dynamics (MD), shows that the c-MYC-Zip:MAX-Zip complex [M+5H](5+) exists in two conformations, one extended with a collision cross section (CCS) of 1164 +/- 9.3 A(2) and one compact with a CCS of 982 +/- 6.6 A(2); similar values are observed for the two forms of c-MYC-ZipDeltaDT:MAX-Zip. Candidate geometries for the complexes have been evaluated with MD simulations. The helical leucine zipper structure previously determined from NMR measurements (Lavigne, P.; et al. J. Mol. Biol. 1998, 281, 165), altered to include the DT region and subjected to a gas-phase minimization, yields a CCS of 1247 A(2), which agrees with the extended conformation we observe experimentally. More extensive MD simulations provide compact complexes which are found to be highly disordered, with CCSs that correspond to the compact form from experiment. In the presence of the ligand, the leucine zipper conformation is completely inhibited and only the more disordered species is observed, providing a novel method to study the effect of interactions of disordered systems and subsequent inhibition of the formation of an ordered helical complex. FAU - Harvey, Sophie R AU - Harvey SR AD - EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK. FAU - Porrini, Massimiliano AU - Porrini M FAU - Stachl, Christiane AU - Stachl C FAU - MacMillan, Derek AU - MacMillan D FAU - Zinzalla, Giovanna AU - Zinzalla G FAU - Barran, Perdita E AU - Barran PE LA - eng GR - BB/H013636/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121112 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (5-(4-ethylbenzylidene)-2-thioxothiazolidin-4-one) RN - 0 (Proto-Oncogene Proteins c-myc) RN - 0 (Thiazoles) SB - IM MH - Circular Dichroism MH - Leucine Zippers/*drug effects MH - Mass Spectrometry MH - Models, Molecular MH - Molecular Dynamics Simulation MH - Molecular Weight MH - Proto-Oncogene Proteins c-myc/*antagonists & inhibitors MH - Structure-Activity Relationship MH - Thiazoles/chemical synthesis/chemistry/*pharmacology MH - Time Factors EDAT- 2012/10/31 06:00 MHDA- 2013/04/27 06:00 CRDT- 2012/10/31 06:00 PHST- 2012/11/12 [aheadofprint] AID - 10.1021/ja306519h [doi] PST - ppublish SO - J Am Chem Soc. 2012 Nov 28;134(47):19384-92. doi: 10.1021/ja306519h. Epub 2012 Nov 12. PMID- 24671380 OWN - NLM STAT- MEDLINE DA - 20140606 DCOM- 20150420 IS - 1463-9084 (Electronic) IS - 1463-9076 (Linking) VI - 16 IP - 25 DP - 2014 Jul 7 TI - Conformational propensities and dynamics of a betagamma-crystallin, an intrinsically disordered protein. PG - 12703-18 LID - 10.1039/c3cp53558d [doi] AB - The three-dimensional folded structure of a protein has been considered essential for its function. However, recently many proteins have been identified to function without having a definite structure and they have been classified as intrinsically disordered proteins (IDPs). Recently, we have identified a betagamma-crystallin domain in the genome of a marine bacterium called Hahella chejuensis on the basis of known sequence signatures. This protein, called Hahellin, was characterized by NMR spectroscopy as an IDP, which upon Ca(2+)-binding was shown to undergo a large conformational transformation and acquires a typical betagamma-crystallin fold. In this paper, we have characterized this IDP by a combined use of NMR and Replica Exchange Molecular Dynamics simulation and found it to be in a highly dynamic, inter-converting population having a molten globular state with the C-terminal Greek key motif relatively more flexible as compared to its N-terminal counterpart. Network analysis and clustering on the observed conformational ensemble showed a heterogeneous mixture of eleven distinct clusters, classified into near-native and far-native populations, which are not in equilibrium. Several conformational clusters display an increased propensity for helical conformation(s) and a decreased beta-strand propensity, which is consistent with the NMR observations made on this protein. The negatively charged Ca(2+)-coordinating residues form parts of the highly flexible polypeptide stretches, and thus act as seeds for the origin of different conformational clusters observed. This study thus helps us to understand the relationship between the role of conformational dynamics and the structural propensities of the intrinsically disordered state of apo-Hahellin. FAU - Patel, Sunita AU - Patel S AD - Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India. chary@tifr.res.in. FAU - Ramanujam, Venkatraman AU - Ramanujam V FAU - Srivastava, Atul K AU - Srivastava AK FAU - Chary, Kandala V R AU - Chary KV LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Phys Chem Chem Phys JT - Physical chemistry chemical physics : PCCP JID - 100888160 RN - 0 (Crystallins) RN - 0 (Intrinsically Disordered Proteins) SB - IM MH - Crystallins/*chemistry MH - Intrinsically Disordered Proteins/*chemistry MH - Molecular Dynamics Simulation MH - Protein Conformation EDAT- 2014/03/29 06:00 MHDA- 2015/04/22 06:00 CRDT- 2014/03/28 06:00 PHST- 2014/03/27 [aheadofprint] PHST- 2014/06/04 [epublish] AID - 10.1039/c3cp53558d [doi] PST - ppublish SO - Phys Chem Chem Phys. 2014 Jul 7;16(25):12703-18. doi: 10.1039/c3cp53558d. PMID- 18681437 OWN - NLM STAT- MEDLINE DA - 20080822 DCOM- 20081205 LR - 20091119 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 130 IP - 34 DP - 2008 Aug 27 TI - Kinetics of folding and binding of an intrinsically disordered protein: the inhibitor of yeast aspartic proteinase YPrA. PG - 11477-85 LID - 10.1021/ja803221c [doi] AB - The 68 residue peptide IA 3 is an intrinsically unstructured protein that serves as an endogenous inhibitor of the yeast aspartic proteinase A (YPrA). Although unstructured in free solution, IA 3 forms an N-terminal alpha helix as it binds to YPrA, leading to subnanomolar inhibition of the protease. Equilibrium structural and inhibition studies provide little insight into the mechanism and kinetics of the coupled folding and binding interaction. We have used laser temperature jump spectroscopy to study the kinetics of folding of free IA 3 and of the interaction between IA 3 and YPrA. Inducing folding with trifluoroethanol cosolvent allows us to determine the folding rate (kf approximately 0.3 (micros)(-1)) and the unfolding rate (ku approximately 3 (micros)(-1)) for free IA 3 in water at 25 degrees C. A substantially faster relaxation process is observed in the presence of the proteinase; this process appears to be the kinetic signature of an intermediate binding step in the coupled folding and binding interaction of IA 3 and YPrA. FAU - Narayanan, Ranjani AU - Narayanan R AD - Physics Department, University of Florida, P.O. Box 118440, Gainesville, FL 32611-8440, USA. FAU - Ganesh, Omjoy K AU - Ganesh OK FAU - Edison, Arthur S AU - Edison AS FAU - Hagen, Stephen J AU - Hagen SJ LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20080806 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Protease Inhibitors) RN - 0 (Solutions) RN - EC 3.4.23 (aspartic proteinase A) RN - EC 3.4.23.- (Aspartic Acid Endopeptidases) SB - IM MH - Aspartic Acid Endopeptidases/*antagonists & inhibitors MH - Circular Dichroism MH - Fluorescence Resonance Energy Transfer MH - Kinetics MH - Protease Inhibitors/chemistry/*pharmacology MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Secondary MH - Saccharomyces cerevisiae/*enzymology MH - Solutions/chemistry MH - Spectrometry, Fluorescence MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Temperature EDAT- 2008/08/07 09:00 MHDA- 2008/12/17 09:00 CRDT- 2008/08/07 09:00 PHST- 2008/08/06 [aheadofprint] AID - 10.1021/ja803221c [doi] PST - ppublish SO - J Am Chem Soc. 2008 Aug 27;130(34):11477-85. doi: 10.1021/ja803221c. Epub 2008 Aug 6. PMID- 19929855 OWN - NLM STAT- MEDLINE DA - 20100209 DCOM- 20100305 LR - 20100308 IS - 1470-8728 (Electronic) IS - 0264-6021 (Linking) VI - 426 IP - 2 DP - 2010 Mar 1 TI - Biochemical characterization, membrane association and identification of amino acids essential for the function of Alg11 from Saccharomyces cerevisiae, an alpha1,2-mannosyltransferase catalysing two sequential glycosylation steps in the formation of the lipid-linked core oligosaccharide. PG - 205-17 LID - 10.1042/BJ20091121 [doi] AB - The biosynthesis of asparagine-linked glycans occurs in an evolutionarily conserved manner with the assembly of the unique lipid-linked oligosaccharide precursor Glc3Man9GlcNAc2-PP-Dol at the ER (endoplasmic reticulum). In the present study we characterize Alg11 from yeast as a mannosyltransferase catalysing the sequential transfer of two alpha1,2-linked mannose residues from GDP-mannose to Man3GlcNAc2-PP-Dol and subsequently to Man4GlcNAc2-PP-Dol forming the Man5GlcNAc2-PP-Dol intermediate at the cytosolic side of the ER before flipping to the luminal side. Alg11 is predicted to contain three hydrophobic transmembrane-spanning helices. Using Alg11 topology reporter fusion constructs, we show that only the N-terminal domain fulfils this criterion. Surprisingly, this domain can be deleted without disturbing glycosyltransferase function and membrane association, indicating also that the other two hydrophobic domains contribute to ER localization, but in a non-transmembrane manner. By site-directed mutagenesis we investigated amino acids important for transferase activity. We demonstrate that the first glutamate residue in the EX7E motif, conserved in a variety of glycosyltransferases, is more critical than the second, and loss of Alg11 function occurs only when both glutamate residues are exchanged, or when the mutation of the first glutamate residue is combined with replacement of another amino acid in the motif. This indicates that perturbations in EX7E are not restricted to the second glutamate residue. Moreover, Gly85 and Gly87, within a glycine-rich domain as part of a potential flexible loop, were found to be required for Alg11 function. Similarly, a conserved lysine residue, Lys319, was identified as being important for activity, which could be involved in the binding of the phosphate of the glycosyl donor. FAU - Absmanner, Birgit AU - Absmanner B AD - Lehrstuhl fur Zellbiologie und Pflanzenphysiologie, Universitat Regensburg, 93053 Regensburg, Germany. FAU - Schmeiser, Verena AU - Schmeiser V FAU - Kampf, Michael AU - Kampf M FAU - Lehle, Ludwig AU - Lehle L LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100209 PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (Lipopolysaccharides) RN - 0 (Membrane Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (lipid-linked oligosaccharides) RN - EC 2.4.1.- (Alg11 protein, S cerevisiae) RN - EC 2.4.1.- (Mannosyltransferases) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Catalysis MH - Endoplasmic Reticulum/chemistry/genetics/*metabolism MH - Glycosylation MH - Lipopolysaccharides/chemistry/*metabolism MH - Mannosyltransferases/*chemistry/genetics/*metabolism MH - Membrane Proteins/chemistry/genetics/*metabolism MH - Molecular Sequence Data MH - Protein Binding MH - Protein Transport MH - Saccharomyces cerevisiae/chemistry/genetics/*metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism MH - Sequence Alignment EDAT- 2009/11/26 06:00 MHDA- 2010/03/06 06:00 CRDT- 2009/11/26 06:00 AID - BJ20091121 [pii] AID - 10.1042/BJ20091121 [doi] PST - epublish SO - Biochem J. 2010 Feb 9;426(2):205-17. doi: 10.1042/BJ20091121. PMID- 18512959 OWN - NLM STAT- MEDLINE DA - 20100324 DCOM- 20100507 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 25 DP - 2008 Jun 24 TI - The thymine-DNA glycosylase regulatory domain: residual structure and DNA binding. PG - 6519-30 LID - 10.1021/bi7022283 [doi] AB - Thymine-DNA glycosylases (TDGs) initiate base excision repair by debasification of the erroneous thymine or uracil nucleotide in G.T and G.U mispairs which arise at high frequency through spontaneous or enzymatic deamination of methylcytosine and cytosine, respectively. Human TDG has furthermore been shown to have a functional role in transcription and epigenetic regulation through the interaction with transcription factors from the nuclear receptor superfamily, transcriptional coregulators, and a DNA methyltransferase. The TDG N-terminus encodes regulatory functions, as it assures both G.T versus G.U specificity and contains the sites for interaction and posttranslational modification by transcription-related activities. While the molecular function of the evolutionarily conserved central catalytic domain of TDG in base excision repair has been elucidated by determination of its three-dimensional structure, the mechanisms by which the N-terminus exerts its regulatory roles, as well as the function of TDG in transcription regulation, remain to be understood. We describe here the residual structure of the TDG N-terminus in both contexts of the isolated domain and the entire protein. These studies lead to the characterization of a small structural domain in the TDG N-terminal region preceding the catalytic core and coinciding with the region of functional regulation of TDG's activities. This regulatory domain exhibits a small degree of organization and is implicated in dynamic molecular interactions with the catalytic domain and nonselective interactions with double-stranded DNA, providing a molecular explanation for the evolutionarily acquired G.T mismatch processing activity of TDG. FAU - Smet-Nocca, Caroline AU - Smet-Nocca C AD - Institut de Recherche Interdisciplinaire, USR CNRS 3078, Universite de Lille 1, 1 rue du Professeur Calmette, 59021 Lille Cedex, France. FAU - Wieruszeski, Jean-Michel AU - Wieruszeski JM FAU - Chaar, Vicky AU - Chaar V FAU - Leroy, Arnaud AU - Leroy A FAU - Benecke, Arndt AU - Benecke A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 9007-49-2 (DNA) RN - 9DLQ4CIU6V (Proline) RN - EC 3.2.2.- (Thymine DNA Glycosylase) SB - IM MH - Amino Acid Sequence MH - Binding Sites/genetics MH - *Catalytic Domain MH - DNA/chemistry/genetics/metabolism MH - *DNA Repair MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Proline/chemistry/genetics/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - Structure-Activity Relationship MH - Substrate Specificity MH - Thymine DNA Glycosylase/*chemistry/genetics/*metabolism EDAT- 2008/06/03 09:00 MHDA- 2010/05/08 06:00 CRDT- 2008/06/03 09:00 AID - 10.1021/bi7022283 [doi] PST - ppublish SO - Biochemistry. 2008 Jun 24;47(25):6519-30. doi: 10.1021/bi7022283. PMID- 15308688 OWN - NLM STAT- MEDLINE DA - 20041027 DCOM- 20050315 LR - 20061115 IS - 0888-8809 (Print) IS - 0888-8809 (Linking) VI - 18 IP - 11 DP - 2004 Nov TI - C-terminal domain of insulin-like growth factor (IGF) binding protein-6: structure and interaction with IGF-II. PG - 2740-50 AB - IGFs are important mediators of growth. IGF binding proteins (IGFBPs) 1-6 regulate IGF actions and have IGF-independent actions. The C-terminal domains of IGFBPs contribute to high-affinity IGF binding and modulation of IGF actions and confer some IGF-independent properties, but understanding how they achieve this has been constrained by the lack of a three-dimensional structure. We therefore determined the solution structure of the C-domain of IGFBP-6 using nuclear magnetic resonance (NMR). The domain consists of a thyroglobulin type 1 fold comprising an alpha-helix followed by a loop, a three-stranded antiparallel beta-sheet incorporating a second loop, and finally a disulfide-bonded flexible third loop. The IGF-II binding site on the C-domain was identified by examining NMR spectral changes upon complex formation. It consists of a largely hydrophobic surface patch involving the alpha-helix, the first beta-strand, and the first and second loops. The site was confirmed by mutagenesis of several residues, which resulted in decreased IGF binding affinity. The IGF-II binding site lies adjacent to surfaces likely to be involved in glycosaminoglycan binding of IGFBPs, which might explain their decreased IGF affinity when bound to glycosaminoglycans, and nuclear localization. Our structure provides a framework for understanding the roles of IGFBP C-domains in modulating IGF actions and conferring IGF-independent actions, as well as ultimately for the development of therapeutic IGF inhibitors for diseases including cancer. FAU - Headey, Stephen J AU - Headey SJ AD - The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3050, Australia. FAU - Keizer, David W AU - Keizer DW FAU - Yao, Shenggen AU - Yao S FAU - Brasier, Geoffrey AU - Brasier G FAU - Kantharidis, Phillip AU - Kantharidis P FAU - Bach, Leon A AU - Bach LA FAU - Norton, Raymond S AU - Norton RS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040812 PL - United States TA - Mol Endocrinol JT - Molecular endocrinology (Baltimore, Md.) JID - 8801431 RN - 0 (Insulin-Like Growth Factor Binding Protein 6) RN - 67763-97-7 (Insulin-Like Growth Factor II) RN - 9010-34-8 (Thyroglobulin) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites/genetics MH - Binding, Competitive MH - Humans MH - Insulin-Like Growth Factor Binding Protein 6/*chemistry/genetics/*metabolism MH - Insulin-Like Growth Factor II/*metabolism MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed/genetics MH - Mutation/genetics MH - Protein Folding MH - Protein Structure, Tertiary MH - Structure-Activity Relationship MH - Thyroglobulin/chemistry EDAT- 2004/08/17 10:00 MHDA- 2005/03/16 09:00 CRDT- 2004/08/17 10:00 PHST- 2004/08/12 [aheadofprint] AID - 10.1210/me.2004-0248 [doi] AID - me.2004-0248 [pii] PST - ppublish SO - Mol Endocrinol. 2004 Nov;18(11):2740-50. Epub 2004 Aug 12. PMID- 21357425 OWN - NLM STAT- MEDLINE DA - 20110418 DCOM- 20110628 LR - 20140821 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 16 DP - 2011 Apr 22 TI - The cancer/testis antigen prostate-associated gene 4 (PAGE4) is a highly intrinsically disordered protein. PG - 13985-94 LID - 10.1074/jbc.M110.210765 [doi] AB - The cancer/testis antigens (CTAs) are an important group of heterogeneous proteins that are predominantly expressed in the testis in the normal human adult but are aberrantly expressed in several types of cancers. Prostate-associated gene 4 (PAGE4) is a member of the CT-X family of CTAs that in addition to testis, is highly expressed in the fetal prostate, and may also play an important role both in benign and malignant prostate diseases. However, the function of this gene remains poorly understood. Here, we show that PAGE4 is a highly (100%) intrinsically disordered protein (IDP). The primary protein sequence conforms to the features of a typical IDP sequence and the secondary structure prediction algorithm metaPrDOS strongly supported this prediction. Furthermore, SDS-gel electrophoresis and analytical size exclusion chromatography of the recombinant protein revealed an anomalous behavior characteristic of IDPs. UV circular dichroism (CD) and NMR spectroscopy confirmed that PAGE4 is indeed a highly disordered protein. In further bioinformatic analysis, the PredictNLS algorithm uncovered a potential nuclear localization signal, whereas the algorithm DBS-Pred returned a 99.1% probability that PAGE4 is a DNA-binding protein. Consistent with this prediction, biochemical experiments showed that PAGE4 preferentially binds a GC-rich sequence. Silencing PAGE4 expression induced cell death via apoptosis and in mice carrying PCa xenografts, siRNA-mediated knockdown of the PAGE4 mRNA attenuated tumor growth in vivo. Furthermore, overexpressing PAGE4 protected cells from stress-induced death. To our knowledge, PAGE4 is the first example of a CTA that is an IDP with an anti-apoptotic function. FAU - Zeng, Yu AU - Zeng Y AD - Department of Urology, James Buchanan Brady Urological Institute & the George O'Brien Urology Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA. FAU - He, Yanan AU - He Y FAU - Yang, Fan AU - Yang F FAU - Mooney, Steven M AU - Mooney SM FAU - Getzenberg, Robert H AU - Getzenberg RH FAU - Orban, John AU - Orban J FAU - Kulkarni, Prakash AU - Kulkarni P LA - eng GR - 2P50CA058236-16/CA/NCI NIH HHS/United States GR - P50DK082998/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20110225 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Antigens, Neoplasm) RN - 0 (PAGE4 protein, human) RN - 0 (RNA, Small Interfering) SB - IM CIN - J Urol. 2011 Dec;186(6):2494-5. PMID: 22078626 MH - Animals MH - Antigens, Neoplasm/*chemistry/physiology MH - Apoptosis MH - Cell Line, Tumor MH - Circular Dichroism MH - Humans MH - Male MH - Mice MH - Mice, SCID MH - Neoplasm Transplantation MH - Prostatic Neoplasms/pathology MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA, Small Interfering/metabolism MH - Testis/metabolism PMC - PMC3077599 OID - NLM: PMC3077599 EDAT- 2011/03/02 06:00 MHDA- 2011/06/29 06:00 CRDT- 2011/03/02 06:00 PHST- 2011/02/25 [aheadofprint] AID - M110.210765 [pii] AID - 10.1074/jbc.M110.210765 [doi] PST - ppublish SO - J Biol Chem. 2011 Apr 22;286(16):13985-94. doi: 10.1074/jbc.M110.210765. Epub 2011 Feb 25. PMID- 21584876 OWN - NLM STAT- MEDLINE DA - 20110517 DCOM- 20110901 IS - 1099-1352 (Electronic) IS - 0952-3499 (Linking) VI - 24 IP - 4 DP - 2011 Jul-Aug TI - Systematic analysis of tropomodulin/tropomyosin interactions uncovers fine-tuned binding specificity of intrinsically disordered proteins. PG - 647-55 LID - 10.1002/jmr.1093 [doi] AB - An intriguing regulatory mechanism is the ability of some proteins to recognize their binding partners in an isoform-specific manner. In this study we undertook a systematic analysis of the specificity of the tropomodulin (Tmod) interaction with tropomyosin (TM) to show that affinities of different Tmod isoforms to TM are isoform-dependent. Intrinsic disorder predictions, alignment of sequences, and circular dichroism were utilized to establish a structural basis for these isoform-specific interactions. The affinity of model peptides derived from the N-terminus of different TM isoforms to protein fragments that correspond to the two TM-binding sites of different Tmod isoforms were analyzed. Several residues were determined to be responsible for the isoform-dependent differences in affinity. We suggest that changing a set of residues rather than a single residue is needed to alter the binding affinity of one isoform to mimic the affinity of another isoform. The general intrinsic disorder predictor, PONDR(R) VLXT, was shown to be a useful tool for analyzing regions involved in isoform-specific binding and for predicting the residues important for isoform differences in binding. Knowing the residues responsible for isoform-specific affinity creates a tool suitable for studying the influence of Tmod/TM interactions on sarcomere assembly in muscle cells or actin dynamics in non-muscle cells. CI - Copyright (c) 2011 John Wiley & Sons, Ltd. FAU - Uversky, Vladimir N AU - Uversky VN AD - Department of Biochemistry and Molecular Biology, Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA. vuversky@iupui.edu FAU - Shah, Samar P AU - Shah SP FAU - Gritsyna, Yulia AU - Gritsyna Y FAU - Hitchcock-DeGregori, Sarah E AU - Hitchcock-DeGregori SE FAU - Kostyukova, Alla S AU - Kostyukova AS LA - eng GR - GM081688/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Recognit JT - Journal of molecular recognition : JMR JID - 9004580 RN - 0 (Protein Isoforms) RN - 0 (Tropomodulin) RN - 0 (Tropomyosin) SB - IM MH - Binding Sites MH - Circular Dichroism MH - Humans MH - Protein Binding/genetics/physiology MH - Protein Isoforms/genetics/metabolism MH - Tropomodulin/genetics/*metabolism MH - Tropomyosin/genetics/*metabolism EDAT- 2011/05/18 06:00 MHDA- 2011/09/02 06:00 CRDT- 2011/05/18 06:00 AID - 10.1002/jmr.1093 [doi] PST - ppublish SO - J Mol Recognit. 2011 Jul-Aug;24(4):647-55. doi: 10.1002/jmr.1093. PMID- 15769464 OWN - NLM STAT- MEDLINE DA - 20050316 DCOM- 20050420 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 347 IP - 4 DP - 2005 Apr 8 TI - Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping. PG - 707-18 AB - Eukaryotic cells utilize DcpS, a scavenger decapping enzyme, to degrade the residual cap structure following 3'-5' mRNA decay, thereby preventing the premature decapping of the capped long mRNA and misincorporation of methylated nucleotides in nucleic acids. We report the structures of DcpS in ligand-free form and in a complex with m7GDP. apo-DcpS is a symmetric dimer, strikingly different from the asymmetric dimer observed in the structures of DcpS with bound cap analogues. In contrast, and similar to the m7GpppG-DcpS complex, DcpS with bound m7GDP is an asymmetric dimer in which the closed state appears to be the substrate-bound complex, whereas the open state mimics the product-bound complex. Comparisons of these structures revealed conformational changes of both the N-terminal swapped-dimeric domain and the cap-binding pocket upon cap binding. Moreover, Tyr273 in the cap-binding pocket displays remarkable conformational changes upon cap binding. Mutagenesis and biochemical analysis suggest that Tyr273 seems to play an important role in cap binding and product release. Examination of the crystallographic B-factors indicates that the N-terminal domain in apo-DcpS is inherently flexible, and in a dynamic state ready for substrate binding and product release. FAU - Chen, Nan AU - Chen N AD - Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673. FAU - Walsh, Martin A AU - Walsh MA FAU - Liu, Yuying AU - Liu Y FAU - Parker, Roy AU - Parker R FAU - Song, Haiwei AU - Song H LA - eng SI - PDB/1XML SI - PDB/1XMM GR - R37 GM045443-15/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Apoproteins) RN - 0 (Ligands) RN - 0 (RNA Cap Analogs) RN - 0 (RNA Caps) RN - 0 (RNA, Messenger) RN - 0 (Solvents) RN - 104809-16-7 (7-methylguanosine 5'-diphosphate) RN - 146-91-8 (Guanosine Diphosphate) RN - 42HK56048U (Tyrosine) RN - EC 3.1.- (Endoribonucleases) RN - EC 3.1.27.- (DcpS protein, human) SB - IM MH - Apoproteins/chemistry/metabolism MH - Crystallography, X-Ray MH - Dimerization MH - Endoribonucleases/*chemistry/genetics/*metabolism MH - Guanosine Diphosphate/*analogs & derivatives/*metabolism MH - Humans MH - Ligands MH - Models, Molecular MH - Mutation/genetics MH - Pliability MH - Protein Structure, Tertiary MH - RNA Cap Analogs/metabolism MH - RNA Caps/*metabolism MH - RNA, Messenger/*metabolism MH - Solvents MH - Static Electricity MH - Structure-Activity Relationship MH - Substrate Specificity MH - Tyrosine/genetics/metabolism EDAT- 2005/03/17 09:00 MHDA- 2005/04/21 09:00 CRDT- 2005/03/17 09:00 PHST- 2004/12/02 [received] PHST- 2005/01/10 [revised] PHST- 2005/01/25 [accepted] AID - S0022-2836(05)00119-1 [pii] AID - 10.1016/j.jmb.2005.01.062 [doi] PST - ppublish SO - J Mol Biol. 2005 Apr 8;347(4):707-18. PMID- 10224139 OWN - NLM STAT- MEDLINE DA - 19990603 DCOM- 19990603 LR - 20091119 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 274 IP - 19 DP - 1999 May 7 TI - Structural characterization of Saccharomyces cerevisiae prion-like protein Ure2. PG - 13666-74 AB - Sacchromyces cerevisiae prion-like protein Ure2 was expressed in Escherichia coli and was purified to homogeneity. We show here that Ure2p is a soluble protein that can assemble into fibers that are similar to the fibers observed in the case of PrP in its scrapie prion filaments form or that form on Sup35 self-assembly. Ure2p self-assembly is a cooperative process where one can distinguish a lag phase followed by an elongation phase preceding a plateau. A combination of size exclusion chromatography, sedimentation velocity, and electron microscopy demonstrates that the soluble form of Ure2p consists at least of three forms of the protein as follows: a monomeric, dimeric, and tetrameric form whose abundance is concentration-dependent. By the use of limited proteolysis, intrinsic fluorescence, and circular dichroism measurements, we bring strong evidence for the existence of at least two structural domains in Ure2p molecules. Indeed, Ure2p NH2-terminal region is found poorly structured, whereas its COOH-terminal domain appears to be compactly folded. Finally, we show that only slight conformational changes accompany Ure2p assembly into insoluble high molecular weight oligomers. These changes essentially affect the COOH-terminal part of the molecule. The properties of Ure2p are compared in the discussion to that of other prion-like proteins such as Sup35 and mammalian prion protein PrP. FAU - Thual, C AU - Thual C AD - Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette Cedex, France. FAU - Komar, A A AU - Komar AA FAU - Bousset, L AU - Bousset L FAU - Fernandez-Bellot, E AU - Fernandez-Bellot E FAU - Cullin, C AU - Cullin C FAU - Melki, R AU - Melki R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Biopolymers) RN - 0 (DNA Primers) RN - 0 (Fungal Proteins) RN - 0 (Prions) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 1.11.1.9 (Glutathione Peroxidase) RN - EC 1.11.1.9 (URE2 protein, S cerevisiae) SB - IM MH - Base Sequence MH - Biopolymers MH - Cloning, Molecular MH - DNA Primers MH - Escherichia coli/genetics MH - Fungal Proteins/*chemistry/genetics MH - Glutathione Peroxidase MH - Microscopy, Electron MH - Molecular Weight MH - *Prions MH - Protein Conformation MH - Recombinant Proteins/chemistry/genetics MH - Saccharomyces cerevisiae/*chemistry/genetics MH - *Saccharomyces cerevisiae Proteins MH - Solubility EDAT- 1999/05/01 MHDA- 1999/05/01 00:01 CRDT- 1999/05/01 00:00 PST - ppublish SO - J Biol Chem. 1999 May 7;274(19):13666-74. PMID- 22278251 OWN - NLM STAT- MEDLINE DA - 20120312 DCOM- 20120611 LR - 20141019 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 86 IP - 7 DP - 2012 Apr TI - Inhibition of human papillomavirus DNA replication by an E1-derived p80/UAF1-binding peptide. PG - 3486-500 LID - 10.1128/JVI.07003-11 [doi] AB - The papillomavirus E1 helicase is recruited by E2 to the viral origin, where it assembles into a double hexamer that orchestrates replication of the viral genome. We previously identified the cellular WD40 repeat-containing protein p80/UAF1 as a novel interaction partner of E1 from anogenital human papillomavirus (HPV) types. p80 was found to interact with the first 40 residues of HPV type 31 (HPV31) E1, and amino acid substitutions within this domain abrogated the maintenance of the viral episome in keratinocytes. In this study, we report that these p80-binding substitutions reduce by 70% the ability of E1 to support transient viral DNA replication without affecting its interaction with E2 and assembly at the origin in vivo. Microscopy studies revealed that p80 is relocalized from the cytoplasm to discrete subnuclear foci by E1 and E2. Chromatin immunoprecipitation assays further revealed that p80 is recruited to the viral origin in an E1- and E2-dependent manner. Interestingly, overexpression of a 40-amino-acid-long p80-binding peptide, derived from HPV31 E1, was found to inhibit viral DNA replication by preventing the recruitment of endogenous p80 to the origin. Mutant peptides defective for p80 interaction were not inhibitory, demonstrating the specificity of this effect. Characterization of this E1 peptide by nuclear magnetic resonance (NMR) showed that it is intrinsically disordered in solution, while mapping studies indicated that the WD repeats of p80 are required for E1 interaction. These results provide additional evidence for the requirement for p80 in anogenital HPV DNA replication and highlight the potential of E1-p80 interaction as a novel antiviral target. FAU - Lehoux, Michael AU - Lehoux M AD - Laboratory of Molecular Virology, Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada. jacques.archambault@ircm.qc.ca FAU - Fradet-Turcotte, Amelie AU - Fradet-Turcotte A FAU - Lussier-Price, Mathieu AU - Lussier-Price M FAU - Omichinski, James G AU - Omichinski JG FAU - Archambault, Jacques AU - Archambault J LA - eng GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120125 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (DNA-Binding Proteins) RN - 0 (E1 protein, Human papillomavirus type 31) RN - 0 (E2 protein, Human papillomavirus type 31) RN - 0 (Peptides) RN - 0 (Proteins) RN - 0 (Viral Proteins) RN - 0 (WDR48 protein, human) SB - IM MH - Cell Line, Tumor MH - *DNA Replication MH - DNA-Binding Proteins/genetics/metabolism MH - *Down-Regulation MH - Human papillomavirus 31/*genetics/metabolism MH - Humans MH - Papillomavirus Infections/genetics/*metabolism/virology MH - Peptides/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Proteins/genetics/*metabolism MH - Viral Proteins/chemistry/genetics/*metabolism PMC - PMC3302507 OID - NLM: PMC3302507 EDAT- 2012/01/27 06:00 MHDA- 2012/06/12 06:00 CRDT- 2012/01/27 06:00 PHST- 2012/01/25 [aheadofprint] AID - JVI.07003-11 [pii] AID - 10.1128/JVI.07003-11 [doi] PST - ppublish SO - J Virol. 2012 Apr;86(7):3486-500. doi: 10.1128/JVI.07003-11. Epub 2012 Jan 25. PMID- 24811666 OWN - NLM STAT- MEDLINE DA - 20140509 DCOM- 20150413 LR - 20150507 IS - 1089-7690 (Electronic) IS - 0021-9606 (Linking) VI - 140 IP - 17 DP - 2014 May 7 TI - Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model. PG - 175102 LID - 10.1063/1.4873710 [doi] AB - Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an "induced fit" or "conformational selection" mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD. FAU - Knott, Michael AU - Knott M AD - Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom. FAU - Best, Robert B AU - Best RB AD - Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, United Kingdom. LA - eng GR - BB/H006885/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't PL - United States TA - J Chem Phys JT - The Journal of chemical physics JID - 0375360 RN - 0 (Intrinsically Disordered Proteins) SB - IM MH - Biophysical Processes MH - Intrinsically Disordered Proteins/*chemistry/ultrastructure MH - *Molecular Conformation MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Tertiary PMC - PMC4032430 OID - NLM: PMC4032430 EDAT- 2014/05/09 06:00 MHDA- 2015/04/14 06:00 CRDT- 2014/05/10 06:00 AID - 10.1063/1.4873710 [doi] PST - ppublish SO - J Chem Phys. 2014 May 7;140(17):175102. doi: 10.1063/1.4873710. PMID- 22179008 OWN - NLM STAT- MEDLINE DA - 20111219 DCOM- 20120413 LR - 20141019 IS - 1421-9778 (Electronic) IS - 1015-8987 (Linking) VI - 28 IP - 6 DP - 2011 TI - The C-terminus of ICln is natively disordered but displays local structural preformation. PG - 1203-10 LID - 10.1159/000335852 [doi] AB - ICln is a vital, ubiquitously expressed protein with roles in cell volume regulation, angiogenesis, cell morphology, activation of platelets and RNA processing. In previous work we have determined the 3D structure of the N-terminus of ICln (residues 1-159), which folds into a PH-like domain followed by an unstructured region (residues H134 - Q159) containing protein-protein interaction sites. Here we present sequence-specific resonance assignments of the C-terminus (residues Q159 - H235) of ICln by NMR, and show that this region of the protein is intrinsically unstructured. By applying (13)Calpha- (13)Cbeta secondary chemical shifts to detect possible preferences for secondary structure elements we show that the C-terminus of ICln adopts a preferred alpha-helical organization between residues E170 and E187, and exists preferentially in extended conformations (beta-strands) between residues D161 to Y168 and E217 to T223. CI - Copyright (c) 2011 S. Karger AG, Basel. FAU - Schedlbauer, Andreas AU - Schedlbauer A AD - Max F. Perutz Laboratories, University of Vienna, Vienna, Austria. FAU - Gandini, Rosaria AU - Gandini R FAU - Kontaxis, Georg AU - Kontaxis G FAU - Paulmichl, Markus AU - Paulmichl M FAU - Furst, Johannes AU - Furst J FAU - Konrat, Robert AU - Konrat R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111216 PL - Switzerland TA - Cell Physiol Biochem JT - Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology JID - 9113221 RN - 0 (Chloride Channels) RN - 0 (Recombinant Proteins) SB - IM MH - Animals MH - Chloride Channels/*chemistry/genetics/metabolism MH - Dogs MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism PMC - PMC3665938 OID - NLM: PMC3665938 EDAT- 2011/12/20 06:00 MHDA- 2012/04/14 06:00 CRDT- 2011/12/20 06:00 PHST- 2011/12/09 [accepted] PHST- 2011/12/16 [aheadofprint] AID - 000335852 [pii] AID - 000335852 [doi] PST - ppublish SO - Cell Physiol Biochem. 2011;28(6):1203-10. doi: 10.1159/000335852. Epub 2011 Dec 16. PMID- 19768387 OWN - NLM STAT- MEDLINE DA - 20091019 DCOM- 20091216 IS - 1573-5001 (Electronic) IS - 0925-2738 (Linking) VI - 45 IP - 3 DP - 2009 Nov TI - An intraresidual i(HCA)CO(CA)NH experiment for the assignment of main-chain resonances in 15N, 13C labeled proteins. PG - 301-10 LID - 10.1007/s10858-009-9373-4 [doi] AB - An improved pulse sequence, intraresidual i(HCA)CO(CA)NH, is described for establishing solely (13)C'(i), (15)N(i), (1)HN(i) connectivities in uniformly 15N/13C-labeled proteins. In comparison to the "out-and-back" style intra-HN(CA)CO experiment, the new pulse sequence offers at least two-fold higher experimental resolution in the (13)C' dimension and on average 1.6 times higher sensitivity especially for residues in alpha-helices. Performance of the new experiment was tested on a small globular protein ubiquitin and an intrinsically unfolded 110-residue cancer/testis antigen CT16/PAGE5. Use of intraresidual i(HCA)CO(CA)NH experiment in combination with the established HNCO experiment was crucial for the assignment of highly disordered CT16. FAU - Mantylahti, Sampo AU - Mantylahti S AD - Program in Structural Biology and Biophysics, Institute of Biotechnology/NMR Laboratory, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland. FAU - Tossavainen, Helena AU - Tossavainen H FAU - Hellman, Maarit AU - Hellman M FAU - Permi, Perttu AU - Permi P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - J Biomol NMR JT - Journal of biomolecular NMR JID - 9110829 RN - 0 (Carbon Isotopes) RN - 0 (Nitrogen Isotopes) RN - 0 (Proteins) RN - 0 (Ubiquitin) SB - IM MH - Carbon Isotopes/*chemistry MH - Humans MH - Nitrogen Isotopes/*chemistry MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Proteins/*chemistry MH - Ubiquitin/chemistry EDAT- 2009/09/22 06:00 MHDA- 2009/12/17 06:00 CRDT- 2009/09/22 06:00 PHST- 2009/07/01 [received] PHST- 2009/08/05 [accepted] PHST- 2009/09/19 [aheadofprint] AID - 10.1007/s10858-009-9373-4 [doi] PST - ppublish SO - J Biomol NMR. 2009 Nov;45(3):301-10. doi: 10.1007/s10858-009-9373-4. PMID- 22355530 OWN - NLM STAT- MEDLINE DA - 20120222 DCOM- 20130828 LR - 20141019 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 1 DP - 2011 TI - Mechanism of copper(II)-induced misfolding of Parkinson's disease protein. PG - 11 LID - 10.1038/srep00011 [doi] AB - alpha-synuclein (aS) is a natively unfolded pre-synaptic protein found in all Parkinson's disease patients as the major component of fibrillar plaques. Metal ions, and especially Cu(II), have been demonstrated to accelerate aggregation of aS into fibrillar plaques, the precursors to Lewy bodies. In this work, copper binding to aS is investigated by a combination of quantum and molecular mechanics simulations. Starting from the experimentally observed attachment site, several optimized structures of Cu-binding geometries are examined. The most energetically favorable attachment results in significant allosteric changes, making aS more susceptible to misfolding. Indeed, an inverse kinematics investigation of the configuration space uncovers a dynamically stable beta-sheet conformation of Cu-aS that serves as a nucleation point for a second beta-strand. Based on these findings, we propose an atomistic mechanism of copper-induced misfolding of aS as an initial event in the formation of Lewy bodies and thus in PD pathogenesis. FAU - Rose, Frisco AU - Rose F AD - Center for High Performance Simulation and Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-7518, USA. FAU - Hodak, Miroslav AU - Hodak M FAU - Bernholc, Jerzy AU - Bernholc J LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110614 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 RN - 0 (alpha-Synuclein) RN - 789U1901C5 (Copper) SB - IM MH - Binding Sites MH - Copper/*chemistry MH - Humans MH - Parkinson Disease/*metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - alpha-Synuclein/*chemistry/*ultrastructure PMC - PMC3216499 OID - NLM: PMC3216499 GN - NLM: Original DateCompleted: 20120507 EDAT- 2012/02/23 06:00 MHDA- 2012/02/23 06:01 CRDT- 2012/02/23 06:00 PHST- 2011/02/11 [received] PHST- 2011/04/28 [revised] PHST- 2011/05/06 [accepted] PHST- 2011/06/14 [epublish] AID - 10.1038/srep00011 [doi] PST - ppublish SO - Sci Rep. 2011;1:11. doi: 10.1038/srep00011. Epub 2011 Jun 14. PMID- 22424482 OWN - NLM STAT- MEDLINE DA - 20120403 DCOM- 20120521 LR - 20141120 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 51 IP - 13 DP - 2012 Apr 3 TI - Intrinsically disordered N-terminus of calponin homology-associated smooth muscle protein (CHASM) interacts with the calponin homology domain to enable tropomyosin binding. PG - 2694-705 LID - 10.1021/bi2019018 [doi] AB - The calponin homology-associated smooth muscle (CHASM) protein plays an important adaptive role in smooth and skeletal muscle contraction. CHASM is associated with increased muscle contractility and can be localized to the contractile thin filament via its binding interaction with tropomyosin. We sought to define the structural basis for the interaction of CHASM with smooth muscle tropomyosin as a first step to understanding the contribution of CHASM to the contractile capacity of smooth muscle. Herein, we provide a structure-based model for the tropomyosin-binding domain of CHASM using a combination of hydrogen/deuterium exchange mass spectrometry (HDX-MS) and NMR analyses. Our studies provide evidence that a portion of the N-terminal intrinsically disordered region forms intramolecular contacts with the globular C-terminal calponin homology (CH) domain. Ultimately, cooperativeness between these structurally dissimilar regions is required for CHASM binding to smooth muscle tropomyosin. Furthermore, it appears that the type-2 CH domain of CHASM is required for tropomyosin binding and presents a novel function for this protein domain. FAU - MacDonald, Justin A AU - MacDonald JA AD - Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4Z6. jmacdo@ucalgary.ca FAU - Ishida, Hiroaki AU - Ishida H FAU - Butler, Eric I AU - Butler EI FAU - Ulke-Lemee, Annegret AU - Ulke-Lemee A FAU - Chappellaz, Mona AU - Chappellaz M FAU - Tulk, Sarah E AU - Tulk SE FAU - Chik, John K AU - Chik JK FAU - Vogel, Hans J AU - Vogel HJ LA - eng GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120322 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Calcium-Binding Proteins) RN - 0 (Microfilament Proteins) RN - 0 (Muscle Proteins) RN - 0 (Phosphoproteins) RN - 0 (SMTNL1 protein, mouse) RN - 0 (Tropomyosin) RN - 0 (calponin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Calcium-Binding Proteins/chemistry/*metabolism MH - Circular Dichroism MH - Mass Spectrometry MH - Mice MH - Microfilament Proteins/chemistry/*metabolism MH - Molecular Sequence Data MH - Muscle Proteins/chemistry/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphoproteins/chemistry/*metabolism MH - Protein Binding MH - Tropomyosin/chemistry/*metabolism EDAT- 2012/03/20 06:00 MHDA- 2012/05/23 06:00 CRDT- 2012/03/20 06:00 PHST- 2012/03/22 [aheadofprint] AID - 10.1021/bi2019018 [doi] PST - ppublish SO - Biochemistry. 2012 Apr 3;51(13):2694-705. doi: 10.1021/bi2019018. Epub 2012 Mar 22. PMID- 19086274 OWN - NLM STAT- MEDLINE DA - 20081212 DCOM- 20090129 LR - 20140916 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 50 DP - 2008 Dec 16 TI - The intrinsically disordered RNR inhibitor Sml1 is a dynamic dimer. PG - 13428-37 AB - Sml1 is a small ribonucleotide reductase (RNR) regulatory protein in Saccharomyces cerevisiae that binds to and inhibits RNR activation. NMR studies of 15N-labeled Sml1 (104 residues), as well as of a truncated variant (residues 50-104), have allowed characterization of their molecular properties. Sml1 belongs to the class of intrinsically disordered proteins with a high degree of dynamics and very little stable structure. Earlier suggestions for a dimeric structure of Sml1 were confirmed, and from translation diffusion NMR measurements, a dimerization dissociation constant of 0.1 mM at 4 degreesC could be determined. The hydrodynamic radius for the monomeric form of Sml1 was determined to be 23.4 A, corresponding to a protein size between those of a globular protein and a coil. Formation of a dimer results in a hydrodynamic radius of 34.4 A. The observed chemical shifts showed in agreement with previous studies two segments with transient helical structure, residues 4-20 and 60-86, and relaxation studies clearly showed restricted motion in these segments. A spin-label attached to C14 showed long-range interactions with residues 60-70 and 85-95, suggesting that the N-terminal domain folds onto the C-terminal domain. Importantly, protease degradation studies combined with mass spectrometry indicated that the N-terminal domain is degraded before the C-terminal region and thus may serve as a protection against proteolysis of the functionally important C-terminal region. Dimer formation was not associated with significant induction of structure but was found to provide further protection against proteolysis. We propose that this molecular shielding and protection of vital functional structures from degradation by functionally unimportant sites may be a general attribute of other natively disordered proteins. FAU - Danielsson, Jens AU - Danielsson J AD - Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden. FAU - Liljedahl, Leena AU - Liljedahl L FAU - Barany-Wallje, Elsa AU - Barany-Wallje E FAU - Sonderby, Pernille AU - Sonderby P FAU - Kristensen, Line Hyltoft AU - Kristensen LH FAU - Martinez-Yamout, Maria A AU - Martinez-Yamout MA FAU - Dyson, H Jane AU - Dyson HJ FAU - Wright, Peter E AU - Wright PE FAU - Poulsen, Flemming M AU - Poulsen FM FAU - Maler, Lena AU - Maler L FAU - Graslund, Astrid AU - Graslund A FAU - Kragelund, Birthe B AU - Kragelund BB LA - eng GR - GM7374/GM/NIGMS NIH HHS/United States GR - R01 GM057374/GM/NIGMS NIH HHS/United States GR - R01 GM057374-08/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Peptide Fragments) RN - 0 (SML1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 1.17.4.- (Ribonucleotide Reductases) SB - IM MH - Amino Acid Sequence MH - Conserved Sequence MH - Dimerization MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/metabolism/physiology MH - Protein Binding/physiology MH - Protein Structure, Tertiary MH - Ribonucleotide Reductases/*antagonists & inhibitors/*metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/*metabolism/physiology MH - Thermodynamics PMC - PMC2747730 MID - NIHMS86582 OID - NLM: NIHMS86582 OID - NLM: PMC2747730 EDAT- 2008/12/17 09:00 MHDA- 2009/01/30 09:00 CRDT- 2008/12/17 09:00 PST - ppublish SO - Biochemistry. 2008 Dec 16;47(50):13428-37. PMID- 17256089 OWN - NLM STAT- MEDLINE DA - 20070412 DCOM- 20070522 IS - 1420-682X (Print) IS - 1420-682X (Linking) VI - 64 IP - 7-8 DP - 2007 Apr TI - Scavenger, transducer, RNA chaperone? What ligands of the prion protein teach us about its function. PG - 815-29 AB - Prion protein, a misfolded isoform of which is the essential component of the agent of prion diseases, still remains an enigmatic protein whose physiological functions are at best hypothetical. To gain a better insight into its putative role, many studies were undertaken to look for molecules that bind prion protein, and have notably identified divalent metal ions, several proteins, and nucleic acids. At first sight, the diversity of prion protein's ligands seems of little help to infer a plausible function. However, the intrinsically disordered property of its N-terminal tail and the potential of the protein to adopt a transmembrane topology, can both be taken into account to predict its different states during its cellular cycle and its possible functions, of which the most promising correspond to a general scavenger, a sensor or adaptor in a signaling cascade, and an RNA chaperone. FAU - Marc, D AU - Marc D AD - Infectiologie Animale et Sante Publique, IASP, INRA, UR1282, Nouzilly, France. Daniel.Marc@tours.inra.fr FAU - Mercey, R AU - Mercey R FAU - Lantier, F AU - Lantier F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Switzerland TA - Cell Mol Life Sci JT - Cellular and molecular life sciences : CMLS JID - 9705402 RN - 0 (Ligands) RN - 0 (Metals) RN - 0 (Molecular Chaperones) RN - 0 (Prions) RN - 0 (Proteins) RN - 63231-63-0 (RNA) SB - IM MH - Amino Acid Sequence MH - Animals MH - Humans MH - Ligands MH - Lipid Metabolism MH - Metals/metabolism MH - Molecular Chaperones/metabolism MH - Molecular Sequence Data MH - Prion Diseases/*metabolism MH - Prions/chemistry/*metabolism MH - Proteins/metabolism MH - RNA/metabolism MH - Sequence Alignment RF - 174 EDAT- 2007/01/27 09:00 MHDA- 2007/05/23 09:00 CRDT- 2007/01/27 09:00 AID - 10.1007/s00018-007-6370-1 [doi] PST - ppublish SO - Cell Mol Life Sci. 2007 Apr;64(7-8):815-29. PMID- 23665109 OWN - NLM STAT- MEDLINE DA - 20130626 DCOM- 20140123 IS - 1879-1107 (Electronic) IS - 1096-4959 (Linking) VI - 165 IP - 4 DP - 2013 Aug TI - The adhesive skin exudate of Notaden bennetti frogs (Anura: Limnodynastidae) has similarities to the prey capture glue of Euperipatoides sp. velvet worms (Onychophora: Peripatopsidae). PG - 250-9 LID - 10.1016/j.cbpb.2013.04.008 [doi] LID - S1096-4959(13)00077-8 [pii] AB - The dorsal adhesive secretion of the frog Notaden bennetti and the prey-capture "slime" ejected by Euperipatoides sp. velvet worms look and handle similarly. Both consist largely of protein (55-60% of dry weight), which provides the structural scaffold. The major protein of the onychophoran glue (Er_P1 for Euperipatoides rowelli) and the dominant frog glue protein (Nb-1R) are both very large (260-500 kDa), and both give oddly "turbulent" electrophoresis bands. Both major proteins, which are rich in Gly (16-17 mol%) and Pro (7-12 mol%) and contain 4-hydroxyproline (Hyp, 4 mol%), have the composition of intrinsically unstructured proteins. Their propensities for elastomeric or amyloid structures are discussed in light of Er_P1's large content of intrinsically disordered long tandem repeats. The low carbohydrate content of both glues is consistent with conventional protein glycosylation, which in the N. bennetti adhesive was explored by 2D PAGE. The N-linked sugars of Nb-1R appear to prevent inappropriate self-aggregation. Some peptide sequences from Nb-1R are presented. Overall, there are enough similarities between the frog and the velvet worm glues to suspect that they employ related mechanisms for setting and adhesion. A common paradigm is proposed for amphibian and onychophoran adhesives, which, if correct, points to convergent evolution. CI - Copyright (c) 2013 Elsevier Inc. All rights reserved. FAU - Graham, Lloyd D AU - Graham LD AD - CSIRO Animal, Food and Health Sciences, PO Box 52, North Ryde, Sydney, New South Wales 1670, Australia. lloyd.graham@csiro.au FAU - Glattauer, Veronica AU - Glattauer V FAU - Li, Dongmei AU - Li D FAU - Tyler, Michael J AU - Tyler MJ FAU - Ramshaw, John A M AU - Ramshaw JA LA - eng PT - Comparative Study PT - Journal Article DEP - 20130507 PL - England TA - Comp Biochem Physiol B Biochem Mol Biol JT - Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology JID - 9516061 RN - 0 (Proteins) SB - IM MH - Adhesiveness MH - Amino Acid Sequence MH - Animals MH - Anura/*metabolism MH - Base Sequence MH - Blotting, Western MH - Electrophoresis, Gel, Two-Dimensional MH - Exudates and Transudates/*chemistry MH - Glycosylation MH - Invertebrates/*metabolism MH - Linear Models MH - Molecular Sequence Data MH - Proteins/*genetics MH - Scattering, Radiation MH - Sequence Analysis, DNA MH - Skin/*chemistry MH - Species Specificity EDAT- 2013/05/15 06:00 MHDA- 2014/01/24 06:00 CRDT- 2013/05/14 06:00 PHST- 2013/02/12 [received] PHST- 2013/04/09 [revised] PHST- 2013/04/30 [accepted] PHST- 2013/05/07 [aheadofprint] AID - S1096-4959(13)00077-8 [pii] AID - 10.1016/j.cbpb.2013.04.008 [doi] PST - ppublish SO - Comp Biochem Physiol B Biochem Mol Biol. 2013 Aug;165(4):250-9. doi: 10.1016/j.cbpb.2013.04.008. Epub 2013 May 7. PMID- 8433374 OWN - NLM STAT- MEDLINE DA - 19930316 DCOM- 19930316 LR - 20041117 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 229 IP - 3 DP - 1993 Feb 5 TI - Crystallization and preliminary X-ray analysis of the periplasmic fragment of CyoA-a subunit of the Escherichia coli cytochrome o complex. PG - 794-6 AB - CyoA, an integral membrane protein, is a subunit of the Escherichia coli cytochrome o quinol oxidase complex. The C-terminal periplasmic domain of CyoA has been expressed in E. coli, purified and crystallized. Crystals were grown using ammonium sulphate as a precipitant. They have space group I222 or I2(1)2(1)2(1) and diffract X-rays to 2.3 A resolution. FAU - van der Oost, J AU - van der Oost J AD - European Molecular Biology Laboratory, Heidelberg, Germany. FAU - Musacchio, A AU - Musacchio A FAU - Pauptit, R A AU - Pauptit RA FAU - Ceska, T A AU - Ceska TA FAU - Wierenga, R K AU - Wierenga RK FAU - Saraste, M AU - Saraste M LA - eng PT - Journal Article PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Cytochrome b Group) RN - 0 (Cytochromes) RN - 0 (Escherichia coli Proteins) RN - 9035-48-7 (cytochrome bo, E coli) SB - IM MH - Crystallization MH - *Cytochrome b Group MH - Cytochromes/*chemistry MH - Escherichia coli/*enzymology MH - *Escherichia coli Proteins MH - X-Ray Diffraction EDAT- 1993/02/05 MHDA- 1993/02/05 00:01 CRDT- 1993/02/05 00:00 AID - S0022-2836(83)71083-1 [pii] AID - 10.1006/jmbi.1993.1083 [doi] PST - ppublish SO - J Mol Biol. 1993 Feb 5;229(3):794-6. PMID- 8618822 OWN - NLM STAT- MEDLINE DA - 19960607 DCOM- 19960607 LR - 20131121 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 92 IP - 26 DP - 1995 Dec 19 TI - Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center. PG - 11955-9 AB - Cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. The electron entry site in subunit II is a mixed-valence dinuclear copper center in enzymes that oxidize cytochrome c. This center has been lost during the evolution of the quinoloxidizing branch of cytochrome oxidases but can be restored by engineering. Herein we describe the crystal structures of the periplasmic fragment from the wild-type subunit II (CyoA) of Escherichia coli quinol oxidase at 2.5-A resolution and of the mutant with the engineered dinuclear copper center (purple CyoA) at 2.3-A resolution. CyoA is folded as an 11-stranded mostly antiparallel beta-sandwich followed by three alpha-helices. The dinuclear copper center is located at the loops between strands beta 5-beta 6 and beta 9-beta 10. The two coppers are at a 2.5-A distance and symmetrically coordinated to the main ligands that are two bridging cysteines and two terminal histidines. The residues that are distinct in cytochrome c and quinol oxidases are around the dinuclear copper center. Structural comparison suggests a common ancestry for subunit II of cytochrome oxidase and blue copper-binding proteins. FAU - Wilmanns, M AU - Wilmanns M AD - European Molecular Biology Laboratory, Heidelberg, Germany. FAU - Lappalainen, P AU - Lappalainen P FAU - Kelly, M AU - Kelly M FAU - Sauer-Eriksson, E AU - Sauer-Eriksson E FAU - Saraste, M AU - Saraste M LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Recombinant Proteins) RN - 789U1901C5 (Copper) RN - EC 1.- (Oxidoreductases) RN - EC 1.- (duroquinol oxidase) RN - EC 1.9.3.1 (Electron Transport Complex IV) SB - IM CIN - Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):11949-51. PMID: 8618820 MH - Amino Acid Sequence MH - Binding Sites MH - Conserved Sequence MH - Copper/*metabolism MH - Crystallography, X-Ray MH - Electron Transport Complex IV/*chemistry/isolation & purification/*metabolism MH - Escherichia coli/enzymology MH - Models, Structural MH - Molecular Sequence Data MH - Oxidoreductases/*chemistry/isolation & purification/*metabolism MH - Paracoccus denitrificans/enzymology MH - Protein Engineering MH - *Protein Structure, Secondary MH - Recombinant Proteins/chemistry/isolation & purification/metabolism PMC - PMC40274 OID - NLM: PMC40274 EDAT- 1995/12/19 MHDA- 1995/12/19 00:01 CRDT- 1995/12/19 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):11955-9. PMID- 19607839 OWN - NLM STAT- MEDLINE DA - 20090828 DCOM- 20090923 LR - 20140912 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 392 IP - 1 DP - 2009 Sep 11 TI - Prokaryotic ubiquitin-like protein pup is intrinsically disordered. PG - 208-17 LID - 10.1016/j.jmb.2009.07.018 [doi] AB - The prokaryotic ubiquitin-like protein Pup targets substrates for degradation by the Mycobacterium tuberculosis proteasome through its interaction with Mpa, an ATPase that is thought to abut the 20S catalytic subunit. Ubiquitin, which is assembled into a polymer to similarly signal for proteasomal degradation in eukaryotes, adopts a stable and compact structural fold that is adapted into other proteins for diverse biological functions. We used NMR spectroscopy to demonstrate that, unlike ubiquitin, the 64-amino-acid protein Pup is intrinsically disordered with small helical propensity in the C-terminal region. We found that the Pup:Mpa interaction involves an extensive contact surface that spans S21-K61 and that the binding is in the "slow exchange" regime on the NMR time scale, thus demonstrating higher affinity than most ubiquitin:ubiquitin receptor pairs. Interestingly, during the titration experiment, intermediate Pup species were observable, suggesting the formation of one or more transient state(s) upon binding. Moreover, Mpa selected one configuration for a region undergoing chemical exchange in the free protein. These findings provide mechanistic insights into Pup's functional role as a degradation signal. FAU - Chen, Xiang AU - Chen X AD - Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, 55455, USA. FAU - Solomon, William C AU - Solomon WC FAU - Kang, Yang AU - Kang Y FAU - Cerda-Maira, Francisca AU - Cerda-Maira F FAU - Darwin, K Heran AU - Darwin KH FAU - Walters, Kylie J AU - Walters KJ LA - eng GR - CA097004/CA/NCI NIH HHS/United States GR - HL092774/HL/NHLBI NIH HHS/United States GR - R01 CA097004/CA/NCI NIH HHS/United States GR - R01 CA097004-07/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090714 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (Pup protein, Mycobacterium tuberculosis) RN - 0 (Ubiquitins) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 3.6.1.3 (Mpa protein, Mycobacterium tuberculosis) SB - IM MH - Adenosine Triphosphatases/metabolism MH - Bacterial Proteins/*chemistry/metabolism MH - Models, Molecular MH - Mycobacterium tuberculosis/chemistry MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Interaction Mapping MH - Protein Structure, Tertiary MH - Ubiquitins/*chemistry/metabolism PMC - PMC2734869 MID - NIHMS132719 OID - NLM: NIHMS132719 OID - NLM: PMC2734869 EDAT- 2009/07/18 09:00 MHDA- 2009/09/24 06:00 CRDT- 2009/07/18 09:00 PHST- 2009/06/09 [received] PHST- 2009/07/06 [revised] PHST- 2009/07/06 [accepted] PHST- 2009/07/14 [aheadofprint] AID - S0022-2836(09)00837-7 [pii] AID - 10.1016/j.jmb.2009.07.018 [doi] PST - ppublish SO - J Mol Biol. 2009 Sep 11;392(1):208-17. doi: 10.1016/j.jmb.2009.07.018. Epub 2009 Jul 14. PMID- 25011696 OWN - NLM STAT- In-Process DA - 20141115 LR - 20141224 IS - 1572-994X (Electronic) IS - 0920-8569 (Linking) VI - 49 IP - 3 DP - 2014 Dec TI - Modelling the structure of full-length Epstein-Barr virus nuclear antigen 1. PG - 358-72 LID - 10.1007/s11262-014-1101-9 [doi] AB - Epstein-Barr virus is a clinically important human virus associated with several cancers and is the etiologic agent of infectious mononucleosis. The viral nuclear antigen-1 (EBNA1) is central to the replication and propagation of the viral genome and likely contributes to tumourigenesis. We have compared EBNA1 homologues from other primate lymphocryptoviruses and found that the central glycine/alanine repeat (GAr) domain as well as predicted cellular protein (USP7 and CK2) binding sites are present in homologues in the Old World primates, but not the marmoset, suggesting that these motifs may have co-evolved. Using the resolved structure of the C-terminal one-third of EBNA1 (homodimerization and DNA binding domain), we have gone on to develop monomeric and dimeric models in silico of the full-length protein. The C-terminal domain is predicted to be structurally highly similar between homologues, indicating conserved function. Zinc could be stably incorporated into the model, bonding with two N-terminal cysteines predicted to facilitate multimerisation. The GAr contains secondary structural elements in the models, while the protein binding regions are unstructured, irrespective of the prediction approach used and sequence origin. These intrinsically disordered regions may facilitate the diversity observed in partner interactions. We hypothesize that the structured GAr could mask the disordered regions, thereby protecting the protein from default degradation. In the dimer conformation, the C-terminal tails of each monomer wrap around a proline-rich protruding loop of the partner monomer, providing dimer stability, a feature which could be exploited in therapeutic design. FAU - Hussain, Mushtaq AU - Hussain M AD - College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. FAU - Gatherer, Derek AU - Gatherer D FAU - Wilson, Joanna B AU - Wilson JB LA - eng GR - MC_U130184136/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140711 PL - United States TA - Virus Genes JT - Virus genes JID - 8803967 SB - IM EDAT- 2014/07/12 06:00 MHDA- 2014/07/12 06:00 CRDT- 2014/07/12 06:00 PHST- 2014/03/06 [received] PHST- 2014/06/27 [accepted] PHST- 2014/07/11 [aheadofprint] AID - 10.1007/s11262-014-1101-9 [doi] PST - ppublish SO - Virus Genes. 2014 Dec;49(3):358-72. doi: 10.1007/s11262-014-1101-9. Epub 2014 Jul 11. PMID- 12271132 OWN - NLM STAT- MEDLINE DA - 20021002 DCOM- 20021113 LR - 20140611 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 99 IP - 20 DP - 2002 Oct 1 TI - FlgM gains structure in living cells. PG - 12681-4 AB - Intrinsically disordered proteins such as FlgM play important roles in biology, but little is known about their structure in cells. We use NMR to show that FlgM gains structure inside living Escherichia coli cells and under physiologically relevant conditions in vitro, i.e., in solutions containing high concentrations (>/=400 g/liter) of glucose, BSA, or ovalbumin. Structure formation represents solute-induced changes in the equilibrium between the structured and disordered forms of FlgM. The results provide insight into how the environment of intrinsically disordered proteins could dictate their structure and, in turn, emphasize the relevance of studying proteins in living cells and in vitro under physiologically realistic conditions. FAU - Dedmon, Matthew M AU - Dedmon MM AD - Departments of Chemistry, and Biochemistry and Biophysics, and Lineberger Cancer Research Center, University of North Carolina, Chapel Hill, NC 27599, USA. FAU - Patel, Chetan N AU - Patel CN FAU - Young, Gregory B AU - Young GB FAU - Pielak, Gary J AU - Pielak GJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20020923 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Bacterial Proteins) RN - 0 (Serum Albumin, Bovine) RN - 142462-45-1 (FlgM protein, Bacteria) RN - 7YNJ3PO35Z (Hydrogen) RN - 9006-59-1 (Ovalbumin) RN - IY9XDZ35W2 (Glucose) SB - IM MH - Bacterial Proteins/*chemistry/*physiology MH - Circular Dichroism MH - Escherichia coli/metabolism MH - Glucose/metabolism/pharmacology MH - Hydrogen/pharmacology MH - Magnetic Resonance Spectroscopy MH - Ovalbumin/pharmacology MH - Protein Conformation MH - Serum Albumin, Bovine/pharmacology MH - Ultraviolet Rays PMC - PMC130520 OID - NLM: PMC130520 EDAT- 2002/09/25 06:00 MHDA- 2002/11/26 04:00 CRDT- 2002/09/25 06:00 PHST- 2002/09/23 [aheadofprint] AID - 10.1073/pnas.202331299 [doi] AID - 202331299 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12681-4. Epub 2002 Sep 23. PMID- 15711789 OWN - NLM STAT- MEDLINE DA - 20050330 DCOM- 20050517 LR - 20081121 IS - 0040-5752 (Print) IS - 0040-5752 (Linking) VI - 110 IP - 5 DP - 2005 Mar TI - Barley Dhn13 encodes a KS-type dehydrin with constitutive and stress responsive expression. PG - 852-8 AB - Dehydrins (DHNs) compose a family of intrinsically unstructured proteins that have high water solubility and accumulate during late seed development, low temperature or water deficit conditions, and are thought to play a protective role in freezing and drought tolerance in plants. Twelve Dhn genes were previously described in the barley genome. Here, we report an additional member of this multigene family, Dhn13. The Dhn13 gene is located in chromosome 4 near marker MWG634 and encodes a 107-amino acid KS-type DHN. Semi-quantitative reverse transcriptase PCR data indicated that Dhn13 is constitutively expressed in seedling tissues and embryos of developing seeds. Microarray data were consistent with these results and showed a considerable increase of Dhn13 transcripts when plants were subjected to chilling and freezing temperatures. The highest transcript levels where observed in anthers. The presence of ABRE, MYC, DRE, and POLLEN1LELAT52 regulatory elements in the putative Dhn13 promoter region is in agreement with expression data. FAU - Rodriguez, E M AU - Rodriguez EM AD - Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA. FAU - Svensson, J T AU - Svensson JT FAU - Malatrasi, M AU - Malatrasi M FAU - Choi, D-W AU - Choi DW FAU - Close, T J AU - Close TJ LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20050212 PL - Germany TA - Theor Appl Genet JT - TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik JID - 0145600 RN - 0 (DNA Primers) RN - 0 (Plant Proteins) RN - 134711-03-8 (dehydrin proteins, plant) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Chromosome Mapping MH - DNA Primers MH - *Gene Expression Regulation, Plant MH - Genes, Regulator/genetics MH - Hordeum/*genetics MH - Molecular Sequence Data MH - Multigene Family/genetics MH - Oligonucleotide Array Sequence Analysis MH - Plant Proteins/*genetics/*metabolism MH - Promoter Regions, Genetic/genetics MH - Reverse Transcriptase Polymerase Chain Reaction MH - Seeds/genetics/*metabolism MH - Sequence Alignment MH - Sequence Analysis, DNA MH - Temperature EDAT- 2005/02/16 09:00 MHDA- 2005/05/18 09:00 CRDT- 2005/02/16 09:00 PHST- 2004/09/17 [received] PHST- 2004/11/08 [accepted] PHST- 2005/02/12 [aheadofprint] AID - 10.1007/s00122-004-1877-4 [doi] PST - ppublish SO - Theor Appl Genet. 2005 Mar;110(5):852-8. Epub 2005 Feb 12. PMID- 10555983 OWN - NLM STAT- MEDLINE DA - 19991220 DCOM- 19991220 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 38 IP - 45 DP - 1999 Nov 9 TI - Natively unfolded human prothymosin alpha adopts partially folded collapsed conformation at acidic pH. PG - 15009-16 AB - Prothymosin alpha has previously been shown to be unfolded at neutral pH, thus belonging to a growing family of "natively unfolded" proteins. The structural properties and conformational stability of recombinant human prothymosin alpha were characterized at neutral and acidic pH by gel filtration, SAXS, circular dichroism, ANS fluorescence, (1)H NMR, and resistance to urea-induced unfolding. Interestingly, prothymosin alpha underwent a cooperative transition from the unfolded state into a partially folded conformation on lowering the pH. This conformation of prothymosin alpha is a compact denatured state, with structural properties different from those of the molten globule. The formation of alpha-helical structure by the glutamic acid-rich elements of the protein accompanied by the partial hydrophobic collapse is expected at lower pH due to the neutralization of the negatively charged residues. It is possible that such conformational changes may be associated with the protein function. FAU - Uversky, V N AU - Uversky VN AD - Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia. uversky@hydrogen.ucsc.edu FAU - Gillespie, J R AU - Gillespie JR FAU - Millett, I S AU - Millett IS FAU - Khodyakova, A V AU - Khodyakova AV FAU - Vasiliev, A M AU - Vasiliev AM FAU - Chernovskaya, T V AU - Chernovskaya TV FAU - Vasilenko, R N AU - Vasilenko RN FAU - Kozlovskaya, G D AU - Kozlovskaya GD FAU - Dolgikh, D A AU - Dolgikh DA FAU - Fink, A L AU - Fink AL FAU - Doniach, S AU - Doniach S FAU - Abramov, V M AU - Abramov VM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Protein Precursors) RN - 0 (Recombinant Proteins) RN - 0 (Solutions) RN - 0 (prothymosin alpha) RN - 61512-21-8 (Thymosin) SB - IM MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Escherichia coli MH - Humans MH - Hydrogen-Ion Concentration MH - Magnetic Resonance Spectroscopy MH - Protein Conformation MH - *Protein Folding MH - Protein Precursors/*chemistry MH - Recombinant Proteins/chemistry MH - Solutions MH - Thymosin/*analogs & derivatives/chemistry EDAT- 1999/11/11 MHDA- 1999/11/11 00:01 CRDT- 1999/11/11 00:00 AID - bi990752+ [pii] PST - ppublish SO - Biochemistry. 1999 Nov 9;38(45):15009-16. PMID- 22049338 OWN - NLM STAT- MEDLINE DA - 20111117 DCOM- 20120126 LR - 20150522 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 108 IP - 46 DP - 2011 Nov 15 TI - Disorder-to-order transition underlies the structural basis for the assembly of a transcriptionally active PGC-1alpha/ERRgamma complex. PG - 18678-83 LID - 10.1073/pnas.1113813108 [doi] AB - Peroxisome proliferator activated receptor (PPAR) gamma coactivator-1alpha (PGC-1alpha) is a potent transcriptional coactivator of oxidative metabolism and is induced in response to a variety of environmental cues. It regulates a broad array of target genes by coactivating a whole host of transcription factors. The estrogen-related receptor (ERR) family of nuclear receptors are key PGC-1alpha partners in the regulation of mitochondrial and tissue-specific oxidative metabolic pathways; these receptors also demonstrate strong physical and functional interactions with this coactivator. Here we perform comprehensive biochemical, biophysical, and structural analyses of the complex formed between PGC-1alpha and ERRgamma. PGC-1alpha activation domain (PGC-1alpha(2-220)) is intrinsically disordered with limited secondary and no defined tertiary structure. Complex formation with ERRgamma induces significant changes in the conformational mobility of both partners, highlighted by significant stabilization of the ligand binding domain (ERRgammaLBD) as determined by HDX (hydrogen/deuterium exchange) and an observed disorder-to-order transition in PGC-1alpha(2-220). Small-angle X-ray scattering studies allow for modeling of the solution structure of the activation domain in the absence and presence of ERRgammaLBD, revealing a stable and compact binary complex. These data show that PGC-1alpha(2-220) undergoes a large-scale conformational change when binding to the ERRgammaLBD, leading to substantial compaction of the activation domain. This change results in stable positioning of the N-terminal part of the activation domain of PGC-1alpha, favorable for assembly of an active transcriptional complex. These data also provide structural insight into the versatile coactivation profile of PGC-1alpha and can readily be extended to understand other transcriptional coregulators. FAU - Devarakonda, Srikripa AU - Devarakonda S AD - Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. FAU - Gupta, Kushol AU - Gupta K FAU - Chalmers, Michael J AU - Chalmers MJ FAU - Hunt, John F AU - Hunt JF FAU - Griffin, Patrick R AU - Griffin PR FAU - Van Duyne, Gregory D AU - Van Duyne GD FAU - Spiegelman, Bruce M AU - Spiegelman BM LA - eng GR - R01 DK061562/DK/NIDDK NIH HHS/United States GR - R01 DK54477/DK/NIDDK NIH HHS/United States GR - R01 GM084041/GM/NIGMS NIH HHS/United States GR - R01 GM084041/GM/NIGMS NIH HHS/United States GR - S10 RR027270/RR/NCRR NIH HHS/United States GR - U54 MH084512/MH/NIMH NIH HHS/United States GR - U54GM094597/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20111102 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (ESRRG protein, human) RN - 0 (Heat-Shock Proteins) RN - 0 (Ligands) RN - 0 (PPARGC1A protein, human) RN - 0 (Receptors, Estrogen) RN - 0 (Transcription Factors) RN - S88TT14065 (Oxygen) SB - IM MH - Biophysics/methods MH - Heat-Shock Proteins/*chemistry MH - Humans MH - Ligands MH - Mitochondria/metabolism MH - Models, Molecular MH - Molecular Conformation MH - Oxygen/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - Receptors, Estrogen/*chemistry MH - Scattering, Radiation MH - Transcription Factors/*chemistry MH - Transcription, Genetic MH - X-Rays PMC - PMC3219099 OID - NLM: PMC3219099 EDAT- 2011/11/04 06:00 MHDA- 2012/01/27 06:00 CRDT- 2011/11/04 06:00 PHST- 2011/11/02 [aheadofprint] AID - 1113813108 [pii] AID - 10.1073/pnas.1113813108 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):18678-83. doi: 10.1073/pnas.1113813108. Epub 2011 Nov 2. PMID- 22356687 OWN - NLM STAT- MEDLINE DA - 20120904 DCOM- 20121119 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 279 IP - 18 DP - 2012 Sep TI - Sic1 as a timer of Clb cyclin waves in the yeast cell cycle--design principle of not just an inhibitor. PG - 3386-410 LID - 10.1111/j.1742-4658.2012.08542.x [doi] AB - Cellular systems biology aims to uncover design principles that describe the properties of biological networks through interaction of their components in space and time. The cell cycle is a complex system regulated by molecules that are integrated into functional modules to ensure genome integrity and faithful cell division. In budding yeast, cyclin-dependent kinases (Cdk1/Clb) drive cell cycle progression, being activated and inactivated in a precise temporal sequence. In this module, which we refer to as the 'Clb module', different Cdk1/Clb complexes are regulated to generate waves of Clb activity, a functional property of cell cycle control. The inhibitor Sic1 plays a critical role in the Clb module by binding to and blocking Cdk1/Clb activity, ultimately setting the timing of DNA replication and mitosis. Fifteen years of research subsequent to the identification of Sic1 have lead to the development of an integrative approach that addresses its role in regulating the Clb module. Sic1 is an intrinsically disordered protein and achieves its inhibitory function by cooperative binding, where different structural regions stretch on the Cdk1/Clb surface. Moreover, Sic1 promotes S phase entry, facilitating Cdk1/Clb5 nuclear transport, and therefore revealing a double function of inhibitor/activator that rationalizes a mechanism to prevent precocious DNA replication. Interestingly, the investigation of Clb temporal dynamics by mathematical modelling and experimental validation provides evidence that Sic1 acts as a timer to coordinate oscillations of Clb cyclin waves. Here we review these findings, focusing on the design principle underlying the Clb module, which highlights the role of Sic1 in regulating phase-specific Cdk1/Clb activities. CI - (c) 2012 The Authors Journal compilation (c) 2012 FEBS. FAU - Barberis, Matteo AU - Barberis M AD - Institute for Biology, Theoretical Biophysics, Humboldt University Berlin, Germany. matteo.barberis@biologie.hu-berlin.de LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20120321 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Cyclin B) RN - 0 (Cyclin-Dependent Kinase Inhibitor Proteins) RN - 0 (SIC1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 2.7.11.22 (Cyclin-Dependent Kinases) SB - IM MH - Cell Cycle/physiology MH - Cell Cycle Checkpoints MH - Cyclin B/*metabolism MH - Cyclin-Dependent Kinase Inhibitor Proteins/*physiology MH - Cyclin-Dependent Kinases/metabolism MH - Phosphorylation MH - Saccharomyces cerevisiae/*physiology MH - Saccharomyces cerevisiae Proteins/*physiology MH - Systems Biology EDAT- 2012/02/24 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/02/24 06:00 PHST- 2012/03/21 [aheadofprint] AID - 10.1111/j.1742-4658.2012.08542.x [doi] PST - ppublish SO - FEBS J. 2012 Sep;279(18):3386-410. doi: 10.1111/j.1742-4658.2012.08542.x. Epub 2012 Mar 21. PMID- 22003412 OWN - NLM STAT- MEDLINE DA - 20111017 DCOM- 20120202 LR - 20141021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 10 DP - 2011 TI - Binding-folding induced regulation of AF1 transactivation domain of the glucocorticoid receptor by a cofactor that binds to its DNA binding domain. PG - e25875 LID - 10.1371/journal.pone.0025875 [doi] AB - Intrinsically disordered (ID) regions of proteins commonly exist within transcription factors, including the N-terminal domain (NTD) of steroid hormone receptors (SHRs) that possesses a powerful activation function, AF1 region. The mechanisms by which SHRs pass signals from a steroid hormone to control gene expression remain a central unresolved problem. The role of N-terminal activation function AF1, which exists in an intrinsically disordered (ID) conformation, in this process is of immense importance. It is hypothesized that under physiological conditions, ID AF1 undergoes disorder/order transition via inter- and intra-molecular communications, which allows AF1 surfaces to interact with specific co-regulatory proteins, critical for the final outcome of target gene expression regulated by SHRs. However, the means by which AF1 acquires functionally folded conformations is not well understood. In this study, we tested whether binding of jun dimerization protein 2 (JDP2) within the DNA binding domain (DBD) of the glucocorticoid receptor (GR) leads to acquisition of functionally active structure in its AF1/NTD. Our results show that signals mediated from GR DBD:JDP2 interactions in a two domain GR fragment, consisting of the entire NTD and little beyond DBD, significantly increased secondary/tertiary structure formation in the NTD/AF1. This increased structure formation facilitated AF1's interaction with specific co-regulatory proteins and subsequent glucocorticoid response element-mediated AF1 promoter:reporter activity. These results support the hypothesis that inter- and intra-molecular signals give a functionally active structure(s) to the GR AF1, which is important for its transcriptional activity. FAU - Garza, Anna S AU - Garza AS AD - Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America. FAU - Khan, Shagufta H AU - Khan SH FAU - Moure, Carmen M AU - Moure CM FAU - Edwards, Dean P AU - Edwards DP FAU - Kumar, Raj AU - Kumar R LA - eng GR - CA046938/CA/NCI NIH HHS/United States GR - DK049030/DK/NIDDK NIH HHS/United States GR - R01DK058829/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20111007 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Receptors, Glucocorticoid) RN - 0 (Repressor Proteins) RN - 0 (TATA-Box Binding Protein) RN - 9007-49-2 (DNA) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 1) SB - IM MH - Animals MH - Cell Line MH - DNA/*metabolism MH - Nuclear Receptor Coactivator 1/metabolism MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Tertiary MH - Receptors, Glucocorticoid/*chemistry/genetics/*metabolism MH - Repressor Proteins/metabolism MH - TATA-Box Binding Protein/metabolism MH - Transcription, Genetic MH - *Transcriptional Activation PMC - PMC3189220 OID - NLM: PMC3189220 EDAT- 2011/10/18 06:00 MHDA- 2012/02/03 06:00 CRDT- 2011/10/18 06:00 PHST- 2011/07/31 [received] PHST- 2011/09/12 [accepted] PHST- 2011/10/07 [epublish] AID - 10.1371/journal.pone.0025875 [doi] AID - PONE-D-11-15014 [pii] PST - ppublish SO - PLoS One. 2011;6(10):e25875. doi: 10.1371/journal.pone.0025875. Epub 2011 Oct 7. PMID- 14527388 OWN - NLM STAT- MEDLINE DA - 20031006 DCOM- 20040603 LR - 20070724 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 11 IP - 10 DP - 2003 Oct TI - NMR structure of the apoptosis- and inflammation-related NALP1 pyrin domain. PG - 1199-205 AB - Signaling in apoptosis and inflammation is often mediated by proteins of the death domain superfamily in the Fas/FADD/Caspase-8 or the Apaf-1/Caspase-9 pathways. This superfamily currently comprises the death domain (DD), death effector domain (DED), caspase recruitment domain (CARD), and pyrin domain (PYD) subfamilies. The PYD subfamily is most abundant, but three-dimensional structures are only available for the subfamilies DD, DED, and CARD, which have an antiparallel arrangement of six alpha helices as common fold. This paper presents the NMR structure of PYD of NALP1, a protein that is involved in the innate immune response and is a component of the inflammasome. The structure of NALP1 PYD differs from all other known death domain superfamily structures in that the third alpha helix is replaced by a flexibly disordered loop. This unique feature appears to relate to the molecular basis of familial Mediterranean fever (FMF), a genetic disease caused by single-point mutations. FAU - Hiller, Sebastian AU - Hiller S AD - Institut fur Molekularbiologie und Biophysik, Eidgenossische Technische Hochschule Zurich, CH-8093, Zurich, Switzerland. FAU - Kohl, Andreas AU - Kohl A FAU - Fiorito, Francesco AU - Fiorito F FAU - Herrmann, Torsten AU - Herrmann T FAU - Wider, Gerhard AU - Wider G FAU - Tschopp, Jurg AU - Tschopp J FAU - Grutter, Markus G AU - Grutter MG FAU - Wuthrich, Kurt AU - Wuthrich K LA - eng SI - PDB/1PN5 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Apoptosis Regulatory Proteins) RN - 0 (Cytoskeletal Proteins) RN - 0 (NLRP1 protein, human) RN - 0 (Proteins) RN - 0 (marenostrin) SB - IM CIN - Structure. 2003 Oct;11(10):1190-1. PMID: 14527383 MH - *Adaptor Proteins, Signal Transducing MH - Apoptosis/*physiology MH - Apoptosis Regulatory Proteins MH - Cytoskeletal Proteins MH - Humans MH - Inflammation/*metabolism MH - Magnetic Resonance Spectroscopy MH - Multigene Family MH - Protein Structure, Tertiary MH - Proteins/*chemistry/metabolism EDAT- 2003/10/07 05:00 MHDA- 2004/06/04 05:00 CRDT- 2003/10/07 05:00 AID - S0969212603001989 [pii] PST - ppublish SO - Structure. 2003 Oct;11(10):1199-205. PMID- 10756111 OWN - NLM STAT- MEDLINE DA - 20000510 DCOM- 20000510 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 298 IP - 1 DP - 2000 Apr 21 TI - Mechanisms for auto-inhibition and forced product release in glycine N-methyltransferase: crystal structures of wild-type, mutant R175K and S-adenosylhomocysteine-bound R175K enzymes. PG - 149-62 AB - Glycine N-methyltransferase (S-adenosyl-l-methionine: glycine methyltransferase, EC 2.1.1.20; GNMT) catalyzes the AdoMet-dependent methylation of glycine to form sarcosine (N-methylglycine). Unlike most methyltransferases, GNMT is a tetrameric protein showing a positive cooperativity in AdoMet binding and weak inhibition by S-adenosylhomocysteine (AdoHcy). The first crystal structure of GNMT complexed with AdoMet showed a unique "closed" molecular basket structure, in which the N-terminal section penetrates and corks the entrance of the adjacent subunit. Thus, the apparent entrance or exit of the active site is not recognizable in the subunit structure, suggesting that the enzyme must possess a second, enzymatically active, "open" structural conformation. A new crystalline form of the R175K enzyme has been grown in the presence of an excess of AdoHcy, and its crystal structure has been determined at 3.0 A resolution. In this structure, the N-terminal domain (40 amino acid residues) of each subunit has moved out of the active site of the adjacent subunit, and the entrances of the active sites are now opened widely. An AdoHcy molecule has entered the site occupied in the "closed" structure by Glu15 and Gly16 of the N-terminal domain of the adjacent subunit. An AdoHcy binds to the consensus AdoMet binding site observed in the other methyltransferase. This AdoHcy binding site supports the glycine binding site (Arg175) deduced from a chemical modification study and site-directed mutagenesis (R175K). The crystal structures of WT and R175K enzymes were also determined at 2.5 A resolution. These enzyme structures have a closed molecular basket structure and are isomorphous to the previously determined AdoMet-GNMT structure. By comparing the open structure to the closed structure, mechanisms for auto-inhibition and for the forced release of the product AdoHcy have been revealed in the GNMT structure. The N-terminal section of the adjacent subunit occupies the AdoMet binding site and thus inhibits the methyltransfer reaction, whereas the same N-terminal section forces the departure of the potentially potent inhibitor AdoHcy from the active site and thus facilitates the methyltransfer reaction. Consequently GNMT is less active at a low level of AdoMet concentration, and is only weakly inhibited by AdoHcy. These properties of GNMT are particularly suited for regulation of the cellular AdoMet/AdoHcy ratio. CI - Copyright 2000 Academic Press. FAU - Huang, Y AU - Huang Y AD - Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045-2106, USA. FAU - Komoto, J AU - Komoto J FAU - Konishi, K AU - Konishi K FAU - Takata, Y AU - Takata Y FAU - Ogawa, H AU - Ogawa H FAU - Gomi, T AU - Gomi T FAU - Fujioka, M AU - Fujioka M FAU - Takusagawa, F AU - Takusagawa F LA - eng SI - PDB/1D2C SI - PDB/1D2G SI - PDB/1D2H GR - GM37233/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 7LP2MPO46S (S-Adenosylmethionine) RN - 979-92-0 (S-Adenosylhomocysteine) RN - EC 2.1.1.- (Methyltransferases) RN - EC 2.1.1.20 (Glycine N-Methyltransferase) RN - EC 2.1.1.20 (Gnmt protein, rat) RN - TE7660XO1C (Glycine) SB - IM MH - Allosteric Regulation MH - Amino Acid Sequence MH - Amino Acid Substitution/genetics MH - Animals MH - Binding Sites MH - Catalysis MH - Consensus Sequence MH - Crystallography, X-Ray MH - Glycine/metabolism MH - Glycine N-Methyltransferase MH - Kinetics MH - Methylation MH - Methyltransferases/*antagonists & inhibitors/*chemistry/genetics/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation/*genetics MH - Protein Conformation MH - S-Adenosylhomocysteine/chemistry/*metabolism MH - S-Adenosylmethionine/metabolism MH - Structure-Activity Relationship EDAT- 2000/04/11 09:00 MHDA- 2000/05/16 09:00 CRDT- 2000/04/11 09:00 AID - 10.1006/jmbi.2000.3637 [doi] AID - S0022-2836(00)93637-4 [pii] PST - ppublish SO - J Mol Biol. 2000 Apr 21;298(1):149-62. PMID- 25246715 OWN - NLM STAT- MEDLINE DA - 20140923 DCOM- 20150406 IS - 1738-0006 (Electronic) IS - 0023-4001 (Linking) VI - 52 IP - 4 DP - 2014 Aug TI - High expression of water-soluble recombinant antigenic domains of Toxoplasma gondii secretory organelles. PG - 367-76 LID - 10.3347/kjp.2014.52.4.367 [doi] AB - Recombinant antigenic proteins of Toxoplasma gondii are alternative source of antigens which are easily obtainable for serodiagnosis of toxoplasmosis. In this study, highly antigenic secretory organellar proteins, dense granular GRA2 and GRA3, rhoptrial ROP2, and micronemal MIC2, were analyzed by bioinformatics approach to express as water-soluble forms of antigenic domains. The transmembrane region and disorder tendency of 4 secretory proteins were predicted to clone the genes into pGEX-4T-1 vector. Recombinant plasmids were transformed into BL21 (DE3) pLysS E. coli, and GST fusion proteins were expressed with IPTG. As a result, GST fusion proteins with GRA225-105, GRA339-138, ROP2324-561, and MIC21-284 domains had respectively higher value of IgG avidity. The rGST-GRA225-105 and rGST-GRA339-138 were soluble, while rGST-ROP2324-561 and rGST-MIC21-284 were not. GRA231-71, intrinsically unstructured domain (IUD) of GRA2, was used as a linker to enhance the solubility. The rGST-GRA231-71-ROP2324-561, a chimeric protein, appeared to be soluble. Moreover, rGST-GRA231-71-MIC21-284 was also soluble and had higher IgG avidity comparing to rGST-MIC21-284. These 4 highly expressed and water-soluble recombinant antigenic proteins may be promising candidates to improve the serodiagnosis of toxoplasmosis in addition to the major surface antigen of SAG1. FAU - Yang, Zhaoshou AU - Yang Z AD - Department of Parasitology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Korea. FAU - Ahn, Hye-Jin AU - Ahn HJ AD - Department of Parasitology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Korea. FAU - Nam, Ho-Woo AU - Nam HW AD - Department of Parasitology, College of Medicine, The Catholic University of Korea, Seoul 137-701, Korea. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140829 PL - Korea (South) TA - Korean J Parasitol JT - The Korean journal of parasitology JID - 9435800 RN - 0 (Antibodies, Protozoan) RN - 0 (Antigens, Protozoan) RN - 0 (Immunoglobulin G) RN - 0 (Recombinant Proteins) SB - IM MH - Animals MH - Antibodies, Protozoan/immunology MH - Antibody Affinity MH - Antigens, Protozoan/chemistry/*diagnostic use/genetics/immunology MH - *Gene Expression MH - Immunoglobulin G/blood/immunology MH - Mice, Inbred BALB C MH - Recombinant Proteins/chemistry/*diagnostic use/genetics/immunology MH - Serologic Tests/methods MH - Solubility MH - Toxoplasma/genetics/immunology/*metabolism MH - Toxoplasmosis/diagnosis PMC - PMC4170032 OID - NLM: PMC4170032 OTO - NOTNLM OT - GRA2 OT - GRA3 OT - IgG avidity OT - MIC2 OT - ROP2 OT - Toxoplasma gondii OT - antigenic domain OT - bioinformatics OT - intrinsically unstructured domain EDAT- 2014/09/24 06:00 MHDA- 2015/04/07 06:00 CRDT- 2014/09/24 06:00 PHST- 2014/04/17 [received] PHST- 2014/06/10 [revised] PHST- 2014/06/15 [accepted] PHST- 2014/08/29 [epublish] AID - 10.3347/kjp.2014.52.4.367 [doi] PST - ppublish SO - Korean J Parasitol. 2014 Aug;52(4):367-76. doi: 10.3347/kjp.2014.52.4.367. Epub 2014 Aug 29. PMID- 18177895 OWN - NLM STAT- MEDLINE DA - 20080205 DCOM- 20080219 LR - 20140912 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 376 IP - 3 DP - 2008 Feb 22 TI - Role of intrinsic flexibility in signal transduction mediated by the cell cycle regulator, p27 Kip1. PG - 827-38 LID - 10.1016/j.jmb.2007.12.016 [doi] AB - p27(Kip1) (p27), which controls eukaryotic cell division through interactions with cyclin-dependent kinases (Cdks), integrates and transduces promitogenic signals from various nonreceptor tyrosine kinases by orchestrating its own phosphorylation, ubiquitination and degradation. Intrinsic flexibility allows p27 to act as a "conduit" for sequential signaling mediated by tyrosine and threonine phosphorylation and ubiquitination. While the structural features of the Cdk/cyclin-binding domain of p27 are understood, how the C-terminal regulatory domain coordinates multistep signaling leading to p27 degradation is poorly understood. We show that the 100-residue p27 C-terminal domain is extended and flexible when p27 is bound to Cdk2/cyclin A. We propose that the intrinsic flexibility of p27 provides a molecular basis for the sequential signal transduction conduit that regulates p27 degradation and cell division. Other intrinsically unstructured proteins possessing multiple sites of posttranslational modification may participate in similar signaling conduits. FAU - Galea, Charles A AU - Galea CA AD - Department of Structural Biology, St. Jude Children's Research Hospital, 332 North Lauderdale St., Memphis, TN 38105, USA. FAU - Nourse, Amanda AU - Nourse A FAU - Wang, Yuefeng AU - Wang Y FAU - Sivakolundu, Sivashankar G AU - Sivakolundu SG FAU - Heller, William T AU - Heller WT FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng GR - 2R01CA082491/CA/NCI NIH HHS/United States GR - 5P30CA021765/CA/NCI NIH HHS/United States GR - R01 CA082491/CA/NCI NIH HHS/United States GR - R01 CA082491-01A2/CA/NCI NIH HHS/United States GR - R01 CA082491-02/CA/NCI NIH HHS/United States GR - R01 CA082491-03/CA/NCI NIH HHS/United States GR - R01 CA082491-04/CA/NCI NIH HHS/United States GR - R01 CA082491-05/CA/NCI NIH HHS/United States GR - R01 CA082491-06A2/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20071214 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (CDKN1B protein, human) RN - 0 (Cyclin A) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - EC 2.7.11.22 (CDK2 protein, human) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 2) SB - IM MH - Cyclin A/metabolism MH - Cyclin-Dependent Kinase 2/metabolism MH - Cyclin-Dependent Kinase Inhibitor p27 MH - Intracellular Signaling Peptides and Proteins/*chemistry/*metabolism MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphorylation MH - Signal Transduction PMC - PMC2350195 MID - NIHMS40762 OID - NLM: NIHMS40762 OID - NLM: PMC2350195 EDAT- 2008/01/08 09:00 MHDA- 2008/02/20 09:00 CRDT- 2008/01/08 09:00 PHST- 2007/09/12 [received] PHST- 2007/11/27 [revised] PHST- 2007/12/07 [accepted] PHST- 2007/12/14 [aheadofprint] AID - S0022-2836(07)01621-X [pii] AID - 10.1016/j.jmb.2007.12.016 [doi] PST - ppublish SO - J Mol Biol. 2008 Feb 22;376(3):827-38. doi: 10.1016/j.jmb.2007.12.016. Epub 2007 Dec 14. PMID- 23665563 OWN - NLM STAT- MEDLINE DA - 20130624 DCOM- 20130906 LR - 20141116 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 25 DP - 2013 Jun 21 TI - A ubiquitin-like domain recruits an oligomeric chaperone to a retrotranslocation complex in endoplasmic reticulum-associated degradation. PG - 18068-76 LID - 10.1074/jbc.M112.449199 [doi] AB - The Bag6-Ubl4A-Trc35 complex is a multifunctional chaperone that regulates various cellular processes. The diverse functions of Bag6 are supported by its ubiquitous localization to the cytoplasm, the nucleus, and membranes of the endoplasmic reticulum (ER) in cells. In ER-associated degradation (ERAD) pathways, Bag6 can interact with the membrane-associated ubiquitin ligase gp78 via its ubiquitin-like (UBL) domain, but the relative low affinity of this interaction does not reconcile with the fact that a fraction of Bag6 is tightly bound to the membranes. Here, we demonstrate that the UBL domain of Bag6 is required for interaction with the ER membranes. We find that in addition to gp78, the Bag6 UBL domain also binds a UBL-binding motif in UbxD8, an essential component of the gp78 ubiquitinating machinery. Importantly, Bag6 contains a proline-rich (PR) domain termed PDP (Proline rich-DUF3587-Proline rich) that forms homo-oligomer, allowing the UBL domain to form multivalent interactions with gp78 and UbxD8, which are essential for recruitment of Bag6 to the ER membrane. Furthermore, the PR domain comprises largely intrinsically disordered segments, which are sufficient for interaction with an unfolded substrate. We propose that simultaneous association with multiple ERAD factors helps to anchor a disordered chaperone oligomer to the site of retrotranslocation to prevent protein aggregation in ERAD. FAU - Xu, Yue AU - Xu Y AD - Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA. FAU - Liu, Yanfen AU - Liu Y FAU - Lee, Jin-gu AU - Lee JG FAU - Ye, Yihong AU - Ye Y LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20130512 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (BAG6 protein, human) RN - 0 (Blood Proteins) RN - 0 (ETEA protein, human) RN - 0 (Membrane Proteins) RN - 0 (Molecular Chaperones) RN - 0 (Multiprotein Complexes) RN - 0 (Trc35 protein, human) RN - 0 (Ubiquitin) RN - 0 (Ubiquitins) RN - 0 (Ubl4A protein, human) RN - EC 6.3.2.19 (AMFR protein, human) RN - EC 6.3.2.19 (Receptors, Autocrine Motility Factor) SB - IM MH - Binding Sites/genetics MH - Blood Proteins/genetics/metabolism MH - Endoplasmic Reticulum/*metabolism MH - *Endoplasmic Reticulum-Associated Degradation MH - HEK293 Cells MH - Humans MH - Immunoblotting MH - Membrane Proteins/genetics/metabolism MH - Models, Biological MH - Molecular Chaperones/genetics/*metabolism MH - Multiprotein Complexes/genetics/*metabolism MH - Protein Binding MH - Protein Transport MH - RNA Interference MH - Receptors, Autocrine Motility Factor/genetics/metabolism MH - Ubiquitin/genetics/*metabolism MH - Ubiquitins/genetics/*metabolism PMC - PMC3689951 OID - NLM: PMC3689951 OTO - NOTNLM OT - Bag6/Bat3/Scythe OT - E3 Ubiquitin Ligase OT - ER-associated Degradation OT - Endoplasmic Reticulum Stress OT - Endoplasmic Reticulum(ER) OT - Holdase OT - Molecular Chaperone OT - Retrotranslocation OT - gp78 EDAT- 2013/05/15 06:00 MHDA- 2013/09/07 06:00 CRDT- 2013/05/14 06:00 PHST- 2013/05/12 [aheadofprint] AID - M112.449199 [pii] AID - 10.1074/jbc.M112.449199 [doi] PST - ppublish SO - J Biol Chem. 2013 Jun 21;288(25):18068-76. doi: 10.1074/jbc.M112.449199. Epub 2013 May 12. PMID- 15701513 OWN - NLM STAT- MEDLINE DA - 20050209 DCOM- 20050328 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 346 IP - 4 DP - 2005 Mar 4 TI - Control of bacteriophage T4 tail lysozyme activity during the infection process. PG - 1013-20 AB - Bacteriophage T4 has an efficient mechanism for injecting the host Escherichiacoli cell with genomic DNA. Its gene product 5 (gp5) has a needle-like structure attached to the end of a tube through which the DNA passes on its way out of the head and into the host. The gp5 needle punctures the outer cell membrane and then digests the peptidoglycan cell wall in the periplasmic space. gp5 is normally post-translationally cleaved between residues 351 and 352. The function of this process in controlling the lysozyme activity of gp5 has now been investigated. When gp5 is over-expressed in E.coli, two mutants (S351H and S351A) showed a reduction of cleavage products and five other mutants (S351L, S351K, S351Y, S351Q, and S351T) showed no cleavage. Furthermore, in a complementation assay at 20 degrees C, the mutants that had no cleavage of gp5 produced a reduced number of plaques compared to wild-type T4. The crystal structure of the non-cleavage phenotype mutant of gp5, S351L, complexed with gene product 27, showed that the 18 residues in the vicinity of the potential cleavage site (disordered in the wild-type structure) had visible electron density. The polypeptide around the potential cleavage site is exposed, thus allowing access for an E.coli protease. The lysozyme activity is inhibited in the wild-type structure by a loop from the adjacent gp5 monomer that binds into the substrate-binding site. The same inhibition is apparent in the mutant structure, showing that the lysozyme is inhibited before gp5 is cleaved and, presumably, the lysozyme is activated only after gp5 has penetrated the outer membrane. FAU - Kanamaru, Shuji AU - Kanamaru S AD - Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA. skanamar@bio.titech.ac.jp FAU - Ishiwata, Yasutaka AU - Ishiwata Y FAU - Suzuki, Toshiharu AU - Suzuki T FAU - Rossmann, Michael G AU - Rossmann MG FAU - Arisaka, Fumio AU - Arisaka F LA - eng SI - PDB/1WTH PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20050125 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 452VLY9402 (Serine) RN - EC 3.2.1.17 (Muramidase) SB - IM MH - Bacteriophage T4/*enzymology/genetics/*physiology MH - Crystallography, X-Ray MH - Enzyme Activation MH - Enzyme Stability MH - Escherichia coli/*virology MH - Genetic Complementation Test MH - Models, Molecular MH - Muramidase/*chemistry/genetics/*metabolism MH - Mutation/genetics MH - Protein Binding MH - Protein Structure, Quaternary MH - Serine/genetics/metabolism MH - Temperature EDAT- 2005/02/11 09:00 MHDA- 2005/03/29 09:00 CRDT- 2005/02/11 09:00 PHST- 2004/09/17 [received] PHST- 2004/12/12 [revised] PHST- 2004/12/15 [accepted] PHST- 2005/01/25 [aheadofprint] AID - S0022-2836(04)01612-2 [pii] AID - 10.1016/j.jmb.2004.12.042 [doi] PST - ppublish SO - J Mol Biol. 2005 Mar 4;346(4):1013-20. Epub 2005 Jan 25. PMID- 20088881 OWN - NLM STAT- MEDLINE DA - 20100209 DCOM- 20100308 LR - 20101118 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 277 IP - 4 DP - 2010 Feb TI - Targeting mechanism of the retinoblastoma tumor suppressor by a prototypical viral oncoprotein. Structural modularity, intrinsic disorder and phosphorylation of human papillomavirus E7. PG - 973-88 LID - 10.1111/j.1742-4658.2009.07540.x [doi] AB - DNA tumor viruses ensure genome amplification by hijacking the cellular replication machinery and forcing infected cells to enter the S phase. The retinoblastoma (Rb) protein controls the G1/S checkpoint, and is targeted by several viral oncoproteins, among these the E7 protein from human papillomaviruses (HPVs). A quantitative investigation of the interaction mechanism between the HPV16 E7 protein and the RbAB domain in solution revealed that 90% of the binding energy is determined by the LxCxE motif, with an additional binding determinant (1.0 kcal.mol(-1)) located in the C-terminal domain of E7, establishing a dual-contact mode. The stoichiometry and subnanomolar affinity of E7 indicated that it can bind RbAB as a monomer. The low-risk HPV11 E7 protein bound 2.0 kcal.mol(-1) more weakly than the high-risk HPV16 and HPV18 type counterparts, but the modularity and binding mode were conserved. Phosphorylation at a conserved casein kinase II site in the natively unfolded N-terminal domain of E7 affected the local conformation by increasing the polyproline II content and stabilizing an extended conformation, which allowed for a tighter interaction with the Rb protein. Thus, the E7-RbAB interaction involves multiple motifs within the N-terminal domain of E7 and at least two conserved interaction surfaces in RbAB. We discussed a mechanistic model of the interaction of the Rb protein with a viral target in solution, integrated with structural data and the analysis of other cellular and viral proteins, which provided information about the balance of interactions involving the Rb protein and how these determine the progression into either the normal cell cycle or transformation. FAU - Chemes, Lucia B AU - Chemes LB AD - Protein Structure-Function and Engineering Laboratory, Fundacion Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina. FAU - Sanchez, Ignacio E AU - Sanchez IE FAU - Smal, Clara AU - Smal C FAU - de Prat-Gay, Gonzalo AU - de Prat-Gay G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100120 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Oncogene Proteins, Viral) RN - 0 (Papillomavirus E7 Proteins) RN - 0 (Peptide Fragments) RN - 0 (Retinoblastoma Protein) RN - 0 (oncogene protein E7, Human papillomavirus type 16) RN - EC 2.7.11.1 (Casein Kinase II) SB - IM MH - Amino Acid Sequence MH - Casein Kinase II/genetics MH - Conserved Sequence MH - *Human papillomavirus 16 MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Oncogene Proteins, Viral/genetics/*metabolism MH - Papillomavirus E7 Proteins MH - Peptide Fragments/genetics/metabolism MH - Phosphorylation MH - Protein Structure, Tertiary MH - Retinoblastoma Protein/genetics/*metabolism EDAT- 2010/01/22 06:00 MHDA- 2010/03/10 06:00 CRDT- 2010/01/22 06:00 PHST- 2010/01/20 [aheadofprint] AID - EJB7540 [pii] AID - 10.1111/j.1742-4658.2009.07540.x [doi] PST - ppublish SO - FEBS J. 2010 Feb;277(4):973-88. doi: 10.1111/j.1742-4658.2009.07540.x. Epub 2010 Jan 20. PMID- 17696362 OWN - NLM STAT- MEDLINE DA - 20070828 DCOM- 20071127 LR - 20150602 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 46 IP - 35 DP - 2007 Sep 4 TI - Structure and sodium channel activity of an excitatory I1-superfamily conotoxin. PG - 9929-40 AB - Conotoxin iota-RXIA, from the fish-hunting species Conus radiatus, is a member of the recently characterized I1-superfamily, which contains eight cysteine residues arranged in a -C-C-CC-CC-C-C- pattern. iota-RXIA (formerly designated r11a) is one of three characterized I1 peptides in which the third last residue is posttranslationally isomerized to the d configuration. Naturally occurring iota-RXIA with d-Phe44 is significantly more active as an excitotoxin than the l-Phe analogue both in vitro and in vivo. We have determined the solution structures of both forms by NMR spectroscopy, the first for an I1-superfamily member. The disulfide connectivities were determined from structure calculations and confirmed chemically as 5-19, 12-22, 18-27, and 21-38, suggesting that iota-RXIA has an ICK structural motif with one additional disulfide (21-38). Indeed, apart from the first few residues, the structure is well defined up to around residue 35 and does adopt an ICK structure. The C-terminal region, including Phe44, is disordered. Comparison of the d-Phe44 and l-Phe44 forms indicates that the switch from one enantiomer to the other has very little effect on the structure, even though it is clearly important for receptor interaction based on activity data. Finally, we identify the target of iota-RXIA as a voltage-gated sodium channel; iota-RXIA is an agonist, shifting the voltage dependence of activation of mouse NaV1.6 expressed in Xenopus oocytes to more hyperpolarized potentials. Thus, there is a convergence of structure and function in iota-RXIA, as its disulfide pairing and structure resemble those of funnel web spider toxins that also target sodium channels. FAU - Buczek, Olga AU - Buczek O AD - Department of Biology, University of Utah, Salt Lake City, Utah 84112, USA. FAU - Wei, Daxiu AU - Wei D FAU - Babon, Jeffrey J AU - Babon JJ FAU - Yang, Xiaodong AU - Yang X FAU - Fiedler, Brian AU - Fiedler B FAU - Chen, Ping AU - Chen P FAU - Yoshikami, Doju AU - Yoshikami D FAU - Olivera, Baldomero M AU - Olivera BM FAU - Bulaj, Grzegorz AU - Bulaj G FAU - Norton, Raymond S AU - Norton RS LA - eng SI - PDB/2JRY SI - PDB/2P4L GR - GM 48677/GM/NIGMS NIH HHS/United States GR - P01 GM048677/GM/NIGMS NIH HHS/United States GR - P01 GM048677-16/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070814 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Conotoxins) RN - 0 (Disulfides) RN - 0 (Peptides, Cyclic) RN - 0 (Sodium Channel Agonists) RN - 0 (Sodium Channels) RN - 0 (Spider Venoms) RN - 0 (conotoxin iota-RXIA, Conus radiatus) RN - 47E5O17Y3R (Phenylalanine) SB - IM EIN - Biochemistry. 2007 Nov 6;46(44):12887 MH - Amino Acid Sequence MH - Animals MH - Conotoxins/*chemistry/metabolism/*pharmacology MH - Disulfides/chemistry MH - Membrane Potentials/drug effects MH - Mice MH - *Models, Molecular MH - Molecular Sequence Data MH - Mollusca MH - Oocytes/metabolism MH - Peptides, Cyclic/*chemical synthesis/*chemistry MH - Phenylalanine/analogs & derivatives MH - Protein Folding MH - Protein Processing, Post-Translational MH - Protein Structure, Secondary MH - Sequence Homology, Amino Acid MH - *Sodium Channel Agonists MH - Sodium Channels/*chemistry/metabolism MH - Spider Venoms/chemistry/pharmacology MH - Structure-Activity Relationship MH - Xenopus PMC - PMC2566796 MID - NIHMS62633 OID - NLM: NIHMS62633 OID - NLM: PMC2566796 EDAT- 2007/08/19 09:00 MHDA- 2007/12/06 09:00 CRDT- 2007/08/19 09:00 PHST- 2007/08/14 [aheadofprint] AID - 10.1021/bi700797f [doi] PST - ppublish SO - Biochemistry. 2007 Sep 4;46(35):9929-40. Epub 2007 Aug 14. PMID- 15169953 OWN - NLM STAT- MEDLINE DA - 20040624 DCOM- 20050125 LR - 20140609 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 13 IP - 7 DP - 2004 Jul TI - The C-terminal domain of full-length E. coli SSB is disordered even when bound to DNA. PG - 1942-7 AB - The crystal structure of full-length homotetrameric single-stranded DNA (ssDNA)-binding protein from Escherichia coli (SSB) has been determined to 3.3 A resolution and reveals that the entire C-terminal domain is disordered even in the presence of ssDNA. To our knowledge, this is the first experimental evidence that the C-terminal domain of SSB may be inherently disordered. The N-terminal DNA-binding domain of the protein is well ordered and is virtually indistinguishable from the previously determined structure of the chymotryptic fragment of SSB (SSBc) in complex with ssDNA. The absence of observable interactions with the core protein and the crystal packing of SSB together suggest that the disordered C-terminal domains likely extend laterally away from the DNA- binding domains, which may facilitate interactions with components of the replication machinery in vivo. The structure also reveals the conservation of molecular contacts between successive tetramers mediated by the L(45) loops as seen in two other crystal forms of SSBc, suggesting a possible functional relevance of this interaction. FAU - Savvides, Savvas N AU - Savvides SN AD - Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA. FAU - Raghunathan, Srinivasan AU - Raghunathan S FAU - Futterer, Klaus AU - Futterer K FAU - Kozlov, Alex G AU - Kozlov AG FAU - Lohman, Timothy M AU - Lohman TM FAU - Waksman, Gabriel AU - Waksman G LA - eng GR - GM54033/GM/NIGMS NIH HHS/United States GR - R01 GM030498/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20040528 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (DNA, Single-Stranded) RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (SSB protein, E coli) SB - IM MH - Crystallography, X-Ray MH - DNA, Single-Stranded/*chemistry/metabolism MH - DNA-Binding Proteins/*chemistry/metabolism MH - Escherichia coli Proteins/*chemistry/metabolism MH - Protein Binding MH - Protein Structure, Tertiary PMC - PMC2279931 OID - NLM: PMC2279931 EDAT- 2004/06/01 05:00 MHDA- 2005/01/26 09:00 CRDT- 2004/06/01 05:00 PHST- 2004/05/28 [aheadofprint] AID - 10.1110/ps.04661904 [doi] AID - ps.04661904 [pii] PST - ppublish SO - Protein Sci. 2004 Jul;13(7):1942-7. Epub 2004 May 28. PMID- 9405613 OWN - NLM STAT- MEDLINE DA - 19980202 DCOM- 19980202 LR - 20140617 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 94 IP - 26 DP - 1997 Dec 23 TI - Thermodynamic stability of wild-type and mutant p53 core domain. PG - 14338-42 AB - Some 50% of human cancers are associated with mutations in the core domain of the tumor suppressor p53. Many mutations are thought just to destabilize the protein. To assess this and the possibility of rescue, we have set up a system to analyze the stability of the core domain and its mutants. The use of differential scanning calorimetry or spectroscopy to measure its melting temperature leads to irreversible denaturation and aggregation and so is useful as only a qualitative guide to stability. There are excellent two-state denaturation curves on the addition of urea that may be analyzed quantitatively. One Zn2+ ion remains tightly bound in the holo-form of p53 throughout the denaturation curve. The stability of wild type is 6.0 kcal (1 kcal = 4.18 kJ)/mol at 25 degrees C and 9.8 kcal/mol at 10 degrees C. The oncogenic mutants R175H, C242S, R248Q, R249S, and R273H are destabilized by 3.0, 2.9, 1.9, 1.9, and 0.4 kcal/mol, respectively. Under certain denaturing conditions, the wild-type domain forms an aggregate that is relatively highly fluorescent at 340 nm on excitation at 280 nm. The destabilized mutants give this fluorescence under milder denaturation conditions. FAU - Bullock, A N AU - Bullock AN AD - Cambridge University Chemical Laboratory and Cambridge Centre for Protein Engineering, Medical Research Council Centre, Hills Road, Cambridge CB2 2QH, United Kingdom. FAU - Henckel, J AU - Henckel J FAU - DeDecker, B S AU - DeDecker BS FAU - Johnson, C M AU - Johnson CM FAU - Nikolova, P V AU - Nikolova PV FAU - Proctor, M R AU - Proctor MR FAU - Lane, D P AU - Lane DP FAU - Fersht, A R AU - Fersht AR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Animals MH - Genes, Tumor Suppressor MH - Humans MH - Mutation MH - Thermodynamics MH - Tumor Suppressor Protein p53/*chemistry/genetics PMC - PMC24967 OID - NLM: PMC24967 EDAT- 1998/02/07 MHDA- 1998/02/07 00:01 CRDT- 1998/02/07 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 1997 Dec 23;94(26):14338-42. PMID- 24704038 OWN - NLM STAT- MEDLINE DA - 20140428 DCOM- 20140626 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1844 IP - 6 DP - 2014 Jun TI - Homodimerization propensity of the intrinsically disordered N-terminal domain of Ultraspiracle from Aedes aegypti. PG - 1153-66 LID - 10.1016/j.bbapap.2014.03.010 [doi] LID - S1570-9639(14)00078-8 [pii] AB - The mosquito Aedes aegypti is the principal vector of dengue, one of the most devastating arthropod-borne viral infections in humans. The isoform specific A/B region, called the N-terminal domain (NTD), is hypervariable in sequence and length and is poorly conserved within the Ultraspiracle (Usp) family. The Usp protein together with ecdysteroid receptor (EcR) forms a heterodimeric complex. Up until now, there has been little data on the molecular properties of the isolated Usp-NTD. Here, we describe the biochemical and biophysical properties of the recombinant NTD of the Usp isoform B (aaUsp-NTD) from A. aegypti. These results, in combination with in silico bioinformatics approaches, indicate that aaUsp-NTD exhibits properties of an intrinsically disordered protein (IDP). We also present the first experimental evidence describing the dimerization propensity of the isolated NTD of Usp. These characteristics also appear for other members of the Usp family in different species, for example, in the Usp-NTD from Drosophila melanogaster and Bombyx mori. However, aaUsp-NTD exhibits the strongest homodimerization potential. We postulate that the unique dimerization of the NTD might be important for Usp function by providing an additional platform for interactions, in addition to the nuclear receptor superfamily dimerization via DNA binding domains and ligand binding domains that has already been extensively documented. Furthermore, the unique NTD-NTD interaction that was observed might contribute new insight into the dimerization propensities of nuclear receptors. CI - Copyright (c) 2014 Elsevier B.V. All rights reserved. FAU - Pieprzyk, Joanna AU - Pieprzyk J AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland. FAU - Zbela, Agnieszka AU - Zbela A AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland. FAU - Jakob, Michal AU - Jakob M AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland. FAU - Ozyhar, Andrzej AU - Ozyhar A AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland. FAU - Orlowski, Marek AU - Orlowski M AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland. Electronic address: marek.orlowski@pwr.edu.pl. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140402 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (DNA-Binding Proteins) RN - 0 (Drosophila Proteins) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Receptors, Steroid) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) RN - 0 (ecdysteroid receptor) RN - 0 (ultraspiracle protein, Drosophila) SB - IM MH - Aedes/*chemistry/genetics MH - Animals MH - Bombyx/*chemistry/genetics MH - DNA-Binding Proteins/*chemistry/genetics MH - Drosophila Proteins/*chemistry/genetics MH - Drosophila melanogaster/*chemistry/genetics MH - Escherichia coli MH - Hydrodynamics MH - Intrinsically Disordered Proteins/*chemistry/genetics MH - Kinetics MH - Protein Folding MH - Protein Multimerization MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Steroid/*chemistry/genetics MH - Recombinant Proteins/chemistry/genetics MH - Sequence Homology, Amino Acid MH - Transcription Factors/*chemistry/genetics MH - Transcriptional Activation OTO - NOTNLM OT - Aedes aegypti OT - Ecdysteroid receptor OT - Intrinsically disordered protein OT - N-terminal domain OT - Ultraspiracle protein EDAT- 2014/04/08 06:00 MHDA- 2014/06/27 06:00 CRDT- 2014/04/08 06:00 PHST- 2014/01/11 [received] PHST- 2014/03/21 [revised] PHST- 2014/03/25 [accepted] PHST- 2014/04/02 [aheadofprint] AID - S1570-9639(14)00078-8 [pii] AID - 10.1016/j.bbapap.2014.03.010 [doi] PST - ppublish SO - Biochim Biophys Acta. 2014 Jun;1844(6):1153-66. doi: 10.1016/j.bbapap.2014.03.010. Epub 2014 Apr 2. PMID- 17190613 OWN - NLM STAT- MEDLINE DA - 20061227 DCOM- 20070126 IS - 0065-3233 (Print) IS - 0065-3233 (Linking) VI - 73 DP - 2006 TI - Structure, function, and amyloidogenesis of fungal prions: filament polymorphism and prion variants. PG - 125-80 AB - Infectious proteins (prions) became an important medical issue when they were identified as agents of the transmissible spongiform encephalopathies. More recently, prions have been found in fungi and their investigation has been facilitated by greater experimental tractability. In each case, the normal form of the prion protein may be converted into the infectious form (the prion itself) in an autocatalytic process; conversion may either occur spontaneously or by transmission from an already infected cell. Four fungal prion proteins have been studied in some depth-Ure2p, Sup35p, and Rnq1p of Saccharomyces cerevisiae and HET-s of Podospora anserina. Each has a "prion domain" that governs infectivity and a "functional domain" that contributes the protein's activity in a wild-type cell, if it has one. This activity is repressed in prion-infected cells for loss-of-activity prions, [URE3] (the prion of Ure2p) and [PSI] (the prion of Sup35p). For gain-of-activity prions, [PIN] (the prion of Rnq1p) and [Het-s] (the prion of HET-s), the prion domain is also involved in generating a new activity in infected cells. In prion conversion, prion domains polymerize into an amyloid filament, switching from a "natively unfolded" conformation into an amyloid conformation (stable, protease-resistant, rich in cross-beta structure). For Ure2p and probably also Sup35p, the functional domain retains its globular fold but is inactivated by a steric mechanism. We review the evidence on which this scenario is based with emphasis on filament structure, summarizing current experimental constraints and appraising proposed models. We conclude that the parallel superpleated beta-structure and a specific beta-helical formulation are valid candidates while other proposals are excluded. In both the Ure2p and Sup35p systems, prion domain amyloid filaments exhibit polymorphic variation. However, once a certain structure is nucleated, it is maintained throughout that filament. Electron microscopy of several Ure2p-related constructs indicates that the basis for polymorphism lies mainly if not entirely in the prion domain. Filament polymorphism appears to underlie the phenomenon of prion "variants" which differ in the severity of their phenotype, that is, for Ure2p and Sup35p, the stringency with which their activity is switched off. We discuss a possible structural basis for this phenomenon. FAU - Baxa, Ulrich AU - Baxa U AD - Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA. FAU - Cassese, Todd AU - Cassese T FAU - Kajava, Andrey V AU - Kajava AV FAU - Steven, Alasdair C AU - Steven AC LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Adv Protein Chem JT - Advances in protein chemistry JID - 0116732 RN - 0 (Fungal Proteins) RN - 0 (Prions) SB - IM MH - Amino Acid Sequence MH - Fungal Proteins/*chemistry MH - Molecular Sequence Data MH - Prions/*chemistry MH - Protein Conformation RF - 120 EDAT- 2006/12/28 09:00 MHDA- 2007/01/27 09:00 CRDT- 2006/12/28 09:00 AID - S0065-3233(06)73005-4 [pii] AID - 10.1016/S0065-3233(06)73005-4 [doi] PST - ppublish SO - Adv Protein Chem. 2006;73:125-80. PMID- 24122746 OWN - NLM STAT- In-Data-Review DA - 20140326 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 101 IP - 6 DP - 2014 Jun TI - Limited proteolysis of natively unfolded protein 4E-BP1 in the presence of trifluoroethanol. PG - 591-602 LID - 10.1002/bip.22422 [doi] AB - Natively unfolded (intrinsically disordered (ID) proteins) have been attracting an increasing attention due to their involvement in many regulatory processes. Natively unfolded proteins can fold upon binding to their metabolic partners. Coupled folding and binding events usually involve only relatively short motifs (binding motifs). These binding motifs which are able to fold should have an increased propensity to form a secondary structure. The aim of the present work was to probe the conformation of the intrinsically disordered protein 4E-BP1 in the native and partly folded states by limited proteolysis and to reveal regions with a high propensity to form an ordered structure. Trifuoroethanol (TFE) in low concentrations (up to 15 vol%) was applied to increase the helical population of protein regions with a high intrinsic propensity to fold. When forming helical structures, these regions lose mobility and become more protected from proteases than random/unfolded protein regions. Limited proteolysis followed by mass spectrometry analysis allows identification of the regions with decreased mobility in TFE solutions. Trypsin and V8 proteases were used to perform limited proteolysis of the 4E-BP1 protein in buffer and in solutions with low TFE concentrations at 37 degrees C and at elevated temperatures (42 and 50 degrees C). Comparison of the results obtained with the previously established 4E-BP1 structure and the binding motif illustrates the ability of limited proteolysis in the presence of a folding assistant (TFE) to map the regions with high and low propensities to form a secondary structure revealing potential binding motifs inside the intrinsically disordered protein. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 591-602, 2014. CI - Copyright (c) 2013 Wiley Periodicals, Inc. FAU - Hackl, Ellen V AU - Hackl EV AD - Department of Biomolecular Sciences, Faculty of Life Sciences, The University of Manchester, Manchester M60 1QD, UK. LA - eng PT - Journal Article PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 SB - IM OTO - NOTNLM OT - 2,2,2-trifluoroethanol OT - 4E-BP1 protein OT - intrinsically disordered proteins OT - limited proteolysis OT - protease OT - protein folding OT - thermolysin OT - trypsin EDAT- 2013/10/15 06:00 MHDA- 2013/10/15 06:00 CRDT- 2013/10/15 06:00 PHST- 2013/06/24 [received] PHST- 2013/09/26 [revised] PHST- 2013/09/27 [accepted] AID - 10.1002/bip.22422 [doi] PST - ppublish SO - Biopolymers. 2014 Jun;101(6):591-602. doi: 10.1002/bip.22422. PMID- 18282005 OWN - NLM STAT- MEDLINE DA - 20080219 DCOM- 20080519 IS - 0739-1102 (Print) IS - 0739-1102 (Linking) VI - 25 IP - 5 DP - 2008 Apr TI - Conformational characteristics of unstructured peptides: alpha-synuclein. PG - 505-15 AB - We have performed replica-exchange molecular dynamics simulations on 41 residue peptides containing NAC region of alpha-synuclein in various force fields and solvent conditions. Alpha-synuclein is known to be the major cause of Parkinson's disease by amyloid-like aggregation, and one of the natively unfolded proteins. To investigate conformational characteristics of intrinsically unstructured peptides, we carried out structural analysis by introducing 'representative structure' for ensemble of structures occurring during the overall trajectory. Representative structures may be defined by using either coordinate averaging or distance averaging. When applied to the natively folded proteins such as villin headpiece, structural analysis based on representative structure was found to yield consistent results with those obtained from conventional analysis. Individual conformations obtained from the simulations of NAC peptide for various conditions show flexible structures close to random coil. Secondary structure contents and free energy surfaces showed dependency on solvent conditions, which may be interpreted as another manifestation of structural diversity. It is found that representative structures can provide useful information about structural characteristics of intrinsically unstructured proteins. FAU - Yoon, Jeseong AU - Yoon J AD - School of Chemistry, Seoul National University, Seoul 151-747, Korea. FAU - Park, Joonho AU - Park J FAU - Jang, Soonmin AU - Jang S FAU - Lee, Kyunghee AU - Lee K FAU - Shin, Seokmin AU - Shin S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Biomol Struct Dyn JT - Journal of biomolecular structure & dynamics JID - 8404176 RN - 0 (Neurofilament Proteins) RN - 0 (Peptide Fragments) RN - 0 (Peptides) RN - 0 (Solvents) RN - 0 (alpha-Synuclein) RN - 0 (villin headpiece subdomain peptide) SB - IM MH - Amino Acid Sequence MH - Computer Simulation MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Neurofilament Proteins/chemistry MH - Peptide Fragments/chemistry MH - Peptides/*chemistry MH - Protein Folding MH - *Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - Solvents/chemistry MH - alpha-Synuclein/*chemistry EDAT- 2008/02/20 09:00 MHDA- 2008/05/20 09:00 CRDT- 2008/02/20 09:00 AID - d=3031&c=4251&p=16434&do=detail [pii] AID - 10.1080/07391102.2008.10507197 [doi] PST - ppublish SO - J Biomol Struct Dyn. 2008 Apr;25(5):505-15. PMID- 25286318 OWN - NLM STAT- MEDLINE DA - 20141007 DCOM- 20150610 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 10 DP - 2014 TI - The intrinsically disordered regions of the Drosophila melanogaster Hox protein ultrabithorax select interacting proteins based on partner topology. PG - e108217 LID - 10.1371/journal.pone.0108217 [doi] AB - Interactions between structured proteins require a complementary topology and surface chemistry to form sufficient contacts for stable binding. However, approximately one third of protein interactions are estimated to involve intrinsically disordered regions of proteins. The dynamic nature of disordered regions before and, in some cases, after binding calls into question the role of partner topology in forming protein interactions. To understand how intrinsically disordered proteins identify the correct interacting partner proteins, we evaluated interactions formed by the Drosophila melanogaster Hox transcription factor Ultrabithorax (Ubx), which contains both structured and disordered regions. Ubx binding proteins are enriched in specific folds: 23 of its 39 partners include one of 7 folds, out of the 1195 folds recognized by SCOP. For the proteins harboring the two most populated folds, DNA-RNA binding 3-helical bundles and alpha-alpha superhelices, the regions of the partner proteins that exhibit these preferred folds are sufficient for Ubx binding. Three disorder-containing regions in Ubx are required to bind these partners. These regions are either alternatively spliced or multiply phosphorylated, providing a mechanism for cellular processes to regulate Ubx-partner interactions. Indeed, partner topology correlates with the ability of individual partner proteins to bind Ubx spliceoforms. Partners bind different disordered regions within Ubx to varying extents, creating the potential for competition between partners and cooperative binding by partners. The ability of partners to bind regions of Ubx that activate transcription and regulate DNA binding provides a mechanism for partners to modulate transcription regulation by Ubx, and suggests that one role of disorder in Ubx is to coordinate multiple molecular functions in response to tissue-specific cues. FAU - Hsiao, Hao-Ching AU - Hsiao HC AD - Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America. FAU - Gonzalez, Kim L AU - Gonzalez KL AD - Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America. FAU - Catanese, Daniel J Jr AU - Catanese DJ Jr AD - Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America. FAU - Jordy, Kristopher E AU - Jordy KE AD - Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America. FAU - Matthews, Kathleen S AU - Matthews KS AD - Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America. FAU - Bondos, Sarah E AU - Bondos SE AD - Reynolds Medical Building, Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, United States of America; Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141006 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Drosophila Proteins) RN - 0 (Homeodomain Proteins) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Mutant Proteins) RN - 0 (Protein Isoforms) RN - 0 (Proteome) RN - 0 (Transcription Factors) RN - 0 (Ubx protein, Drosophila) RN - 9007-49-2 (DNA) SB - IM MH - Alternative Splicing/genetics MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Binding Sites MH - DNA/metabolism MH - Drosophila Proteins/chemistry/*metabolism MH - Drosophila melanogaster/*metabolism MH - Homeodomain Proteins/chemistry/*metabolism MH - Intrinsically Disordered Proteins/chemistry/*metabolism MH - Molecular Sequence Data MH - Mutant Proteins/metabolism MH - Protein Binding MH - Protein Interaction Mapping MH - Protein Isoforms/chemistry/metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proteome/metabolism MH - Transcription Factors/chemistry/*metabolism PMC - PMC4186791 OID - NLM: PMC4186791 EDAT- 2014/10/07 06:00 MHDA- 2015/06/11 06:00 CRDT- 2014/10/07 06:00 PHST- 2014 [ecollection] PHST- 2013/04/04 [received] PHST- 2014/08/27 [accepted] PHST- 2014/10/06 [epublish] AID - 10.1371/journal.pone.0108217 [doi] AID - PONE-D-13-13735 [pii] PST - epublish SO - PLoS One. 2014 Oct 6;9(10):e108217. doi: 10.1371/journal.pone.0108217. eCollection 2014. PMID- 11734834 OWN - NLM STAT- MEDLINE DA - 20011205 DCOM- 20020125 LR - 20091119 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 414 IP - 6863 DP - 2001 Nov 29 TI - Six steps to destruction. PG - 498-9 FAU - Ferrell, J E Jr AU - Ferrell JE Jr LA - eng PT - Comment PT - News PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Cyclin-Dependent Kinase Inhibitor Proteins) RN - 0 (Cyclins) RN - 0 (Fungal Proteins) RN - 0 (SIC1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 2.7.11.22 (CDC28 Protein Kinase, S cerevisiae) SB - IM CON - Nature. 2001 Nov 29;414(6863):514-21. PMID: 11734846 MH - CDC28 Protein Kinase, S cerevisiae/*metabolism MH - Cell Division/*physiology MH - Cyclin-Dependent Kinase Inhibitor Proteins MH - Cyclins/*metabolism MH - Fungal Proteins/*metabolism MH - G1 Phase/physiology MH - Phosphorylation MH - S Phase/physiology MH - *Saccharomyces cerevisiae Proteins MH - Saccharomycetales EDAT- 2001/12/06 10:00 MHDA- 2002/01/26 10:01 CRDT- 2001/12/06 10:00 AID - 10.1038/35107180 [doi] AID - 35107180 [pii] PST - ppublish SO - Nature. 2001 Nov 29;414(6863):498-9. PMID- 25310299 OWN - NLM STAT- MEDLINE DA - 20141014 DCOM- 20150629 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 10 DP - 2014 TI - The structure of an LIM-only protein 4 (LMO4) and Deformed epidermal autoregulatory factor-1 (DEAF1) complex reveals a common mode of binding to LMO4. PG - e109108 LID - 10.1371/journal.pone.0109108 [doi] AB - LIM-domain only protein 4 (LMO4) is a widely expressed protein with important roles in embryonic development and breast cancer. It has been reported to bind many partners, including the transcription factor Deformed epidermal autoregulatory factor-1 (DEAF1), with which LMO4 shares many biological parallels. We used yeast two-hybrid assays to show that DEAF1 binds both LIM domains of LMO4 and that DEAF1 binds the same face on LMO4 as two other LMO4-binding partners, namely LIM domain binding protein 1 (LDB1) and C-terminal binding protein interacting protein (CtIP/RBBP8). Mutagenic screening analysed by the same method, indicates that the key residues in the interaction lie in LMO4LIM2 and the N-terminal half of the LMO4-binding domain in DEAF1. We generated a stable LMO4LIM2-DEAF1 complex and determined the solution structure of that complex. Although the LMO4-binding domain from DEAF1 is intrinsically disordered, it becomes structured on binding. The structure confirms that LDB1, CtIP and DEAF1 all bind to the same face on LMO4. LMO4 appears to form a hub in protein-protein interaction networks, linking numerous pathways within cells. Competitive binding for LMO4 therefore most likely provides a level of regulation between those different pathways. FAU - Joseph, Soumya AU - Joseph S AD - School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia. FAU - Kwan, Ann H AU - Kwan AH AD - School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia. FAU - Stokes, Philippa H AU - Stokes PH AD - School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia. FAU - Mackay, Joel P AU - Mackay JP AD - School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia. FAU - Cubeddu, Liza AU - Cubeddu L AD - School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia; School of Science and Health, University of Western Sydney, Campbelltown, NSW Australia. FAU - Matthews, Jacqueline M AU - Matthews JM AD - School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141013 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (DEAF1 protein, human) RN - 0 (LIM Domain Proteins) RN - 0 (LMO4 protein, human) RN - 0 (Nuclear Proteins) SB - IM MH - Adaptor Proteins, Signal Transducing/*metabolism MH - Humans MH - LIM Domain Proteins/*metabolism MH - Nuclear Proteins/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Two-Hybrid System Techniques PMC - PMC4195752 OID - NLM: PMC4195752 EDAT- 2014/10/14 06:00 MHDA- 2015/06/30 06:00 CRDT- 2014/10/14 06:00 PHST- 2014 [ecollection] PHST- 2014/06/26 [received] PHST- 2014/08/27 [accepted] PHST- 2014/10/13 [epublish] AID - 10.1371/journal.pone.0109108 [doi] AID - PONE-D-14-28511 [pii] PST - epublish SO - PLoS One. 2014 Oct 13;9(10):e109108. doi: 10.1371/journal.pone.0109108. eCollection 2014. PMID- 15809432 OWN - NLM STAT- MEDLINE DA - 20050413 DCOM- 20050603 LR - 20141120 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 102 IP - 15 DP - 2005 Apr 12 TI - Conformational variability of matrix metalloproteinases: beyond a single 3D structure. PG - 5334-9 AB - The structures of the catalytic domain of matrix metalloproteinase 12 in the presence of acetohydroxamic acid and N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid have been solved by x-ray diffraction in the crystalline state at 1.0 and 1.3-A resolution, respectively, and compared with the previously published x-ray structure at 1.2-A resolution of the adduct with batimastat. The structure of the N-isobutyl-N-[4-methoxyphenylsulfonyl]glycyl hydroxamic acid adduct has been solved by NMR in solution. The three x-ray structures and the solution structure are similar but not identical to one another, the differences being sizably higher in the loops. We propose that many of the loops show a dynamical behavior in solution on a variety of time scales. Different conformations of some flexible regions of the protein can be observed as "frozen" in different crystalline environments. The mobility in solution studied by NMR reveals conformational equilibria in accessible time scales, i.e., from 10(-5) s to ms and more. Averaging of some residual dipolar couplings is consistent with further motions down to 10(-9) s. Finally, local thermal motions of each frozen conformation in the crystalline state at 100 K correlate well with local motions on the picosecond time scale. Flexibility/conformational heterogeneity in crucial parts of the catalytic domain is a rule rather than an exception in matrix metalloproteinases, and its extent may be underestimated by inspection of one x-ray structure. Backbone flexibility may play a role in the difficulties encountered in the design of selective inhibitors, whereas it may be a requisite for substrate binding and broad substrate specificity. FAU - Bertini, Ivano AU - Bertini I AD - Magnetic Resonance Center (Centro di Risonanze Magnetiche), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy. bertini@cerm.inifi.it FAU - Calderone, Vito AU - Calderone V FAU - Cosenza, Marta AU - Cosenza M FAU - Fragai, Marco AU - Fragai M FAU - Lee, Yong-Min AU - Lee YM FAU - Luchinat, Claudio AU - Luchinat C FAU - Mangani, Stefano AU - Mangani S FAU - Terni, Beatrice AU - Terni B FAU - Turano, Paola AU - Turano P LA - eng SI - PDB/1RMZ SI - PDB/1Y93 SI - PDB/1YCM SI - PDB/1Z3J PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050404 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Hydroxamic Acids) RN - 0 (N-isobutyl-N-(4-methoxyphenylsulfonyl)glycylhydroxamic acid) RN - 0 (Sulfonamides) RN - 4RZ82L2GY5 (acetohydroxamic acid) RN - EC 3.4.24.- (Metalloendopeptidases) RN - EC 3.4.24.65 (Matrix Metalloproteinase 12) SB - IM MH - Catalytic Domain MH - Crystallography, X-Ray MH - Hydroxamic Acids/chemistry/metabolism MH - Matrix Metalloproteinase 12 MH - Metalloendopeptidases/*chemistry/*metabolism MH - Models, Molecular MH - Movement MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Sulfonamides/chemistry/metabolism MH - Time Factors PMC - PMC556229 OID - NLM: PMC556229 EDAT- 2005/04/06 09:00 MHDA- 2005/06/04 09:00 CRDT- 2005/04/06 09:00 PHST- 2005/04/04 [aheadofprint] AID - 0407106102 [pii] AID - 10.1073/pnas.0407106102 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5334-9. Epub 2005 Apr 4. PMID- 21634433 OWN - NLM STAT- MEDLINE DA - 20110628 DCOM- 20110909 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 50 IP - 26 DP - 2011 Jul 5 TI - Protein disorder prevails under crowded conditions. PG - 5834-44 LID - 10.1021/bi200365j [doi] AB - Crowding caused by the high concentrations of macromolecules in the living cell changes chemical equilibria, thus promoting aggregation and folding reactions of proteins. The possible magnitude of this effect is particularly important with respect to the physiological structure of intrinsically disordered proteins (IDPs), which are devoid of well-defined three-dimensional structures in vitro. To probe this effect, we have studied the structural state of three IDPs, alpha-casein, MAP2c, and p21(Cip1), in the presence of the crowding agents Dextran and Ficoll 70 at concentrations up to 40%, and also the small-molecule osmolyte, trimethylamine N-oxide (TMAO), at concentrations up to 3.6 M. The structures of IDPs under highly diluted and crowded conditions were compared by a variety of techniques, fluorescence spectroscopy, acrylamide quenching, 1-anilino-8-naphthalenesulfonic acid (ANS) binding, fluorescence correlation spectroscopy (FCS), and far-UV and near-UV circular dichroism (CD) spectroscopy, which allow us to visualize various levels of structural organization within these proteins. We observed that crowding causes limited structural changes, which seem to reflect the functional requirements of these IDPs. alpha-Casein, a protein of nutrient function in milk, changes least under crowded conditions. On the other hand, MAP2c and, to a lesser degree, p21(Cip1), which carry out their functions by partner binding and accompanying partially induced folding, show signs of local structuring and also some global compaction upon crowded conditions, in particular in the presence of TMAO. The observations are compatible with the possible preformation of binding-competent conformations in these proteins. The magnitude of these changes, however, is far from that of the cooperative folding transitions elicited by crowding in denatured globular proteins; i.e., these IDPs do remain in a state of rapidly interconverting structural ensemble. Altogether, our results underline that structural disorder is the physiological state of these proteins. FAU - Szasz, C S AU - Szasz CS AD - Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary. FAU - Alexa, A AU - Alexa A FAU - Toth, K AU - Toth K FAU - Rakacs, M AU - Rakacs M FAU - Langowski, J AU - Langowski J FAU - Tompa, P AU - Tompa P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110614 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Anilino Naphthalenesulfonates) RN - 0 (Proteins) RN - 20R035KLCI (Acrylamide) RN - 25702-74-3 (Ficoll) RN - 82-76-8 (1-anilino-8-naphthalenesulfonate) RN - K3R6ZDH4DU (Dextrans) SB - IM MH - Acrylamide/chemistry MH - Anilino Naphthalenesulfonates/metabolism MH - Circular Dichroism MH - Dextrans/*chemistry MH - Ficoll/*chemistry MH - Protein Conformation MH - Proteins/*chemistry/metabolism MH - Spectrometry, Fluorescence EDAT- 2011/06/04 06:00 MHDA- 2011/09/10 06:00 CRDT- 2011/06/04 06:00 PHST- 2011/06/14 [aheadofprint] AID - 10.1021/bi200365j [doi] PST - ppublish SO - Biochemistry. 2011 Jul 5;50(26):5834-44. doi: 10.1021/bi200365j. Epub 2011 Jun 14. PMID- 10850798 OWN - NLM STAT- MEDLINE DA - 20001107 DCOM- 20001107 LR - 20140615 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 9 IP - 5 DP - 2000 May TI - Conformational flexibility in the apolipoprotein E amino-terminal domain structure determined from three new crystal forms: implications for lipid binding. PG - 886-97 AB - An amino-terminal fragment of human apolipoprotein E3 (residues 1-165) has been expressed and crystallized in three different crystal forms under similar crystallization conditions. One crystal form has nearly identical cell dimensions to the previously reported orthorhombic (P2(1)2(1)2(1)) crystal form of the amino-terminal 22 kDa fragment of apolipoprotein E (residues 1-191). A second orthorhombic crystal form (P2(1)2(1)2(1) with cell dimensions differing from the first form) and a trigonal (P3(1)21) crystal form were also characterized. The structures of the first orthorhombic and the trigonal form were determined by seleno-methionine multiwavelength anomalous dispersion, and the structure of the second orthorhombic form was determined by molecular replacement using the structure from the trigonal form as a search model. A combination of modern experimental and computational techniques provided high-quality electron-density maps, which revealed new features of the apolipoprotein E structure, including an unambiguously traced loop connecting helices 2 and 3 in the four-helix bundle and a number of multiconformation side chains. The three crystal forms contain a common intermolecular, antiparallel packing arrangement. The electrostatic complimentarity observed in this antiparallel packing resembles the interaction of apolipoprotein E with the monoclonal antibody 2E8 and the low density lipoprotein receptor. Superposition of the model structures from all three crystal forms reveals flexibility and pronounced kinks in helices near one end of the four-helix bundle. This mobility at one end of the molecule provides new insights into the structural changes in apolipoprotein E that occur with lipid association. FAU - Segelke, B W AU - Segelke BW AD - Lawrence Livermore National Laboratory, Biology and Biotechnology Research Program, University of California, Livermore 94550, USA. FAU - Forstner, M AU - Forstner M FAU - Knapp, M AU - Knapp M FAU - Trakhanov, S D AU - Trakhanov SD FAU - Parkin, S AU - Parkin S FAU - Newhouse, Y M AU - Newhouse YM FAU - Bellamy, H D AU - Bellamy HD FAU - Weisgraber, K H AU - Weisgraber KH FAU - Rupp, B AU - Rupp B LA - eng GR - NS35939/NS/NINDS NIH HHS/United States GR - RR01614/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Apolipoproteins) RN - 0 (Apolipoproteins E) RN - 0 (Receptors, LDL) RN - 0 (apolipophorin III) SB - IM MH - Animals MH - Apolipoproteins/chemistry MH - Apolipoproteins E/*chemistry MH - Crystallography, X-Ray MH - Electrons MH - Grasshoppers MH - Humans MH - *Lipid Metabolism MH - Models, Molecular MH - Moths MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, LDL/chemistry/metabolism PMC - PMC2144644 OID - NLM: PMC2144644 EDAT- 2000/06/13 09:00 MHDA- 2001/02/28 10:01 CRDT- 2000/06/13 09:00 AID - 10.1110/ps.9.5.886 [doi] PST - ppublish SO - Protein Sci. 2000 May;9(5):886-97. PMID- 24055875 OWN - NLM STAT- MEDLINE DA - 20131014 DCOM- 20131203 LR - 20141112 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 440 IP - 1 DP - 2013 Oct 11 TI - Structure and expression of a novel compact myelin protein - small VCP-interacting protein (SVIP). PG - 173-8 LID - 10.1016/j.bbrc.2013.09.056 [doi] LID - S0006-291X(13)01537-4 [pii] AB - SVIP (small p97/VCP-interacting protein) was initially identified as one of many cofactors regulating the valosin containing protein (VCP), an AAA+ ATPase involved in endoplasmic-reticulum-associated protein degradation (ERAD). Our previous study showed that SVIP is expressed exclusively in the nervous system. In the present study, SVIP and VCP were seen to be co-localized in neuronal cell bodies. Interestingly, we also observed that SVIP co-localizes with myelin basic protein (MBP) in compact myelin, where VCP was absent. Furthermore, using nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopic measurements, we determined that SVIP is an intrinsically disordered protein (IDP). However, upon binding to the surface of membranes containing a net negative charge, the helical content of SVIP increases dramatically. These findings provide structural insight into interactions between SVIP and myelin membranes. CI - Published by Elsevier Inc. FAU - Wu, Jiawen AU - Wu J AD - Department of Neurology, Vanderbilt University School of Medicine, United States. FAU - Peng, Dungeng AU - Peng D FAU - Voehler, Markus AU - Voehler M FAU - Sanders, Charles R AU - Sanders CR FAU - Li, Jun AU - Li J LA - eng GR - 1S-10RR025677-01/RR/NCRR NIH HHS/United States GR - R01 NS058815/NS/NINDS NIH HHS/United States GR - R01 NS058815/NS/NINDS NIH HHS/United States GR - R01 NS066927/NS/NINDS NIH HHS/United States GR - R01NS066927/NS/NINDS NIH HHS/United States GR - R21 NS081364/NS/NINDS NIH HHS/United States GR - R21NS081364/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130918 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Anions) RN - 0 (Carrier Proteins) RN - 0 (DNA, Complementary) RN - 0 (Membrane Proteins) RN - 0 (Nuclear Proteins) RN - 0 (SVIP protein, human) RN - 0 (SVIP protein, mouse) RN - 0 (small VCP-p97-interacting protein, rat) SB - IM MH - Amino Acid Sequence MH - Animals MH - Anions/chemistry MH - Carrier Proteins/*analysis/genetics MH - DNA, Complementary/genetics MH - Escherichia coli/genetics MH - Gene Expression MH - Humans MH - Membrane Proteins/*analysis/genetics MH - Mice MH - Molecular Sequence Data MH - Nuclear Proteins/*analysis/genetics MH - Plasmids/genetics MH - Protein Structure, Secondary MH - Rats MH - Sciatic Nerve/ultrastructure PMC - PMC3828079 MID - NIHMS526049 OID - NLM: NIHMS526049 OID - NLM: PMC3828079 OTO - NOTNLM OT - Compact myelin OT - Intrinsically disordered protein OT - Myelin basic protein OT - Protein-membrane interaction OT - Small VCP-interacting protein OT - Valosin containing protein EDAT- 2013/09/24 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/09/24 06:00 PHST- 2013/09/06 [received] PHST- 2013/09/10 [accepted] PHST- 2013/09/18 [aheadofprint] AID - S0006-291X(13)01537-4 [pii] AID - 10.1016/j.bbrc.2013.09.056 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2013 Oct 11;440(1):173-8. doi: 10.1016/j.bbrc.2013.09.056. Epub 2013 Sep 18. PMID- 24442277 OWN - NLM STAT- MEDLINE DA - 20140529 DCOM- 20140718 IS - 1617-4623 (Electronic) IS - 1617-4623 (Linking) VI - 289 IP - 3 DP - 2014 Jun TI - DRM1 and DRM2 expression regulation: potential role of splice variants in response to stress and environmental factors in Arabidopsis. PG - 317-32 LID - 10.1007/s00438-013-0804-2 [doi] AB - The DRM1/ARP gene family is increasingly exhibiting associations with stress conditions at the transcript level. Traditionally correlated with dormancy, increases in transcript levels in response to various treatments have also been reported in various species. As alternative transcript splicing is common in stress conditions, the splice variants of AtDRM1 and AtDRM2 were assessed further in this study. A previously undescribed splice variant of AtDRM1 (AtDRM1.6) is introduced in this work. In silico analyses of predicted protein sequence of all splice variants showed that all variants retain the predicted intrinsically disordered nature. Transcriptional studies of AtDRM1 and AtDRM2 in response to a wide range of abiotic, physical and hormonal treatments showed that AtDRM1.6 is differentially regulated at the transcriptional level compared with other splice variants. Promoter analyses demonstrated AtDRM1 light regulation via the upstream promoter sequence. FAU - Rae, Georgina M AU - Rae GM AD - The New Zealand Institute for Plant and Food Research Limited, Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland, 1142, New Zealand, georgina.rae@plantandfood.co.nz. FAU - Uversky, Vladimir N AU - Uversky VN FAU - David, Karine AU - David K FAU - Wood, Marion AU - Wood M LA - eng PT - Journal Article DEP - 20140118 PL - Germany TA - Mol Genet Genomics JT - Molecular genetics and genomics : MGG JID - 101093320 RN - 0 (Intrinsically Disordered Proteins) RN - EC 2.1.1.- (Methyltransferases) RN - EC 2.1.1.37 (DRM1 protein, Arabidopsis) RN - EC 2.1.1.37 (DRM2 protein, Arabidopsis) SB - IM MH - Alternative Splicing MH - Amino Acid Sequence MH - Arabidopsis/*genetics/growth & development/metabolism MH - Gene Expression Profiling MH - *Gene Expression Regulation, Plant MH - Gene-Environment Interaction MH - Intrinsically Disordered Proteins/chemistry/genetics/metabolism MH - Light MH - Methyltransferases/chemistry/*genetics/metabolism MH - Molecular Sequence Data MH - Organ Specificity MH - Phenotype MH - Promoter Regions, Genetic MH - Salt-Tolerance/genetics MH - Sequence Alignment MH - Stress, Physiological MH - Transcription, Genetic EDAT- 2014/01/21 06:00 MHDA- 2014/07/19 06:00 CRDT- 2014/01/21 06:00 PHST- 2013/06/05 [received] PHST- 2013/12/13 [accepted] PHST- 2014/01/18 [aheadofprint] AID - 10.1007/s00438-013-0804-2 [doi] PST - ppublish SO - Mol Genet Genomics. 2014 Jun;289(3):317-32. doi: 10.1007/s00438-013-0804-2. Epub 2014 Jan 18. PMID- 10377061 OWN - NLM STAT- MEDLINE DA - 19990903 DCOM- 19990903 LR - 20061115 IS - 0006-3363 (Print) IS - 0006-3363 (Linking) VI - 61 IP - 1 DP - 1999 Jul TI - Complementary deoxyribonucleic acid cloning and tissue expression of BSP-A3 and BSP-30-kDa: phosphatidylcholine and heparin-binding proteins of bovine seminal plasma. PG - 288-97 AB - BSP-A1, BSP-A2, BSP-A3, and BSP-30-kDa are four major proteins of bovine seminal plasma (BSP protein family). These heparin- and phosphatidylcholine-binding proteins potentiate the capacitation of spermatozoa. Here we determined the complete sequences of the two cDNAs coding for the BSP-A3 and BSP-30-kDa proteins. Degenerate oligonucleotides designed on the basis of the primary sequences of the proteins were used as primers in reverse transcription-polymerase chain reaction, with cDNA preparations of bovine seminal vesicles as templates, to amplify an internal fragment of each BSP cDNA. Specific oligonucleotides designed on the basis of these partial cDNA sequences were used to clone the two complete cDNAs by using the 3' rapid amplification of cDNA ends (RACE) and 5' RACE methods. We also verified the expression of all members of the bovine BSP protein family in several adult bovine tissues by RNase protection assays. The results indicated that each BSP protein mRNA is expressed only in seminal vesicles and in the ampullae. Homologous genes were detected in human, rat, hamster, and rabbit genomic DNA, using high-stringency Southern hybridization with a specific BSP-30-kDa cDNA probe. FAU - Salois, D AU - Salois D AD - Departments of Medicine and of Biochemistry, University of Montreal, Guy-Bernier Research Centre, Montreal, Quebec, Canada H1T 2M4. FAU - Menard, M AU - Menard M FAU - Paquette, Y AU - Paquette Y FAU - Manjunath, P AU - Manjunath P LA - eng SI - GENBANK/AF057133 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biol Reprod JT - Biology of reproduction JID - 0207224 RN - 0 (DNA, Complementary) RN - 0 (Prostatic Secretory Proteins) RN - 0 (Proteins) RN - 0 (RNA, Messenger) RN - 0 (Seminal Plasma Proteins) RN - 0 (Sperm Immobilizing Agents) RN - 0 (beta-microseminoprotein) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Cattle MH - *Cloning, Molecular MH - DNA, Complementary/*chemistry MH - *Gene Expression MH - Humans MH - Male MH - Molecular Sequence Data MH - *Prostatic Secretory Proteins MH - Proteins/*genetics MH - RNA, Messenger/analysis MH - Reverse Transcriptase Polymerase Chain Reaction MH - Semen/chemistry MH - Seminal Plasma Proteins MH - Sequence Alignment MH - Species Specificity MH - Sperm Capacitation MH - Sperm Immobilizing Agents MH - Tissue Distribution EDAT- 1999/06/22 MHDA- 1999/06/22 00:01 CRDT- 1999/06/22 00:00 PST - ppublish SO - Biol Reprod. 1999 Jul;61(1):288-97. PMID- 25075982 OWN - NLM STAT- MEDLINE DA - 20140731 DCOM- 20150330 IS - 1422-0067 (Electronic) IS - 1422-0067 (Linking) VI - 15 IP - 8 DP - 2014 TI - Bioinformatics study of cancer-related mutations within p53 phosphorylation site motifs. PG - 13275-98 LID - 10.3390/ijms150813275 [doi] AB - p53 protein has about thirty phosphorylation sites located at the N- and C-termini and in the core domain. The phosphorylation sites are relatively less mutated than other residues in p53. To understand why and how p53 phosphorylation sites are rarely mutated in human cancer, using a bioinformatics approaches, we examined the phosphorylation site and its nearby flanking residues, focusing on the consensus phosphorylation motif pattern, amino-acid correlations within the phosphorylation motifs, the propensity of structural disorder of the phosphorylation motifs, and cancer mutations observed within the phosphorylation motifs. Many p53 phosphorylation sites are targets for several kinases. The phosphorylation sites match 17 consensus sequence motifs out of the 29 classified. In addition to proline, which is common in kinase specificity-determining sites, we found high propensity of acidic residues to be adjacent to phosphorylation sites. Analysis of human cancer mutations in the phosphorylation motifs revealed that motifs with adjacent acidic residues generally have fewer mutations, in contrast to phosphorylation sites near proline residues. p53 phosphorylation motifs are mostly disordered. However, human cancer mutations within phosphorylation motifs tend to decrease the disorder propensity. Our results suggest that combination of acidic residues Asp and Glu with phosphorylation sites provide charge redundancy which may safe guard against loss-of-function mutations, and that the natively disordered nature of p53 phosphorylation motifs may help reduce mutational damage. Our results further suggest that engineering acidic amino acids adjacent to potential phosphorylation sites could be a p53 gene therapy strategy. FAU - Ji, Xiaona AU - Ji X AD - State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China. xiaonaji@163.com. FAU - Huang, Qiang AU - Huang Q AD - State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China. huangqiang@fudan.edu.cn. FAU - Yu, Long AU - Yu L AD - State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China. longyu@fudan.edu.cn. FAU - Nussinov, Ruth AU - Nussinov R AD - Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA. nussinor@helix.nih.gov. FAU - Ma, Buyong AU - Ma B AD - Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, USA. mabuyong@mail.nih.gov. LA - eng GR - HHSN261200800001E/PHS HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140729 PL - Switzerland TA - Int J Mol Sci JT - International journal of molecular sciences JID - 101092791 RN - 0 (Tumor Suppressor Protein p53) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Amino Acid Motifs MH - Binding Sites MH - *Computational Biology MH - Humans MH - Molecular Sequence Data MH - Mutation MH - Neoplasms/genetics/metabolism/pathology MH - Phosphorylation MH - Protein Binding MH - Proto-Oncogene Proteins c-mdm2/chemistry/metabolism MH - Tumor Suppressor Protein p53/chemistry/*genetics/*metabolism PMC - PMC4159794 OID - NLM: PMC4159794 EDAT- 2014/07/31 06:00 MHDA- 2015/03/31 06:00 CRDT- 2014/07/31 06:00 PHST- 2014/06/10 [received] PHST- 2014/07/23 [revised] PHST- 2014/07/24 [accepted] AID - ijms150813275 [pii] AID - 10.3390/ijms150813275 [doi] PST - epublish SO - Int J Mol Sci. 2014 Jul 29;15(8):13275-98. doi: 10.3390/ijms150813275. PMID- 22427660 OWN - NLM STAT- MEDLINE DA - 20120514 DCOM- 20120713 LR - 20141019 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 20 DP - 2012 May 11 TI - Human cyclin-dependent kinase 2-associated protein 1 (CDK2AP1) is dimeric in its disulfide-reduced state, with natively disordered N-terminal region. PG - 16541-9 LID - 10.1074/jbc.M112.343863 [doi] AB - CDK2AP1 (cyclin-dependent kinase 2-associated protein 1), corresponding to the gene doc-1 (deleted in oral cancer 1), is a tumor suppressor protein. The doc-1 gene is absent or down-regulated in hamster oral cancer cells and in many other cancer cell types. The ubiquitously expressed CDK2AP1 protein is the only known specific inhibitor of CDK2, making it an important component of cell cycle regulation during G(1)-to-S phase transition. Here, we report the solution structure of CDK2AP1 by combined methods of solution state NMR and amide hydrogen/deuterium exchange measurements with mass spectrometry. The homodimeric structure of CDK2AP1 includes an intrinsically disordered 60-residue N-terminal region and a four-helix bundle dimeric structure with reduced Cys-105 in the C-terminal region. The Cys-105 residues are, however, poised for disulfide bond formation. CDK2AP1 is phosphorylated at a conserved Ser-46 site in the N-terminal "intrinsically disordered" region by IkappaB kinase epsilon. FAU - Ertekin, Asli AU - Ertekin A AD - Center for Advanced Biotechnology and Medicine and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA. FAU - Aramini, James M AU - Aramini JM FAU - Rossi, Paolo AU - Rossi P FAU - Leonard, Paul G AU - Leonard PG FAU - Janjua, Haleema AU - Janjua H FAU - Xiao, Rong AU - Xiao R FAU - Maglaqui, Melissa AU - Maglaqui M FAU - Lee, Hsiau-Wei AU - Lee HW FAU - Prestegard, James H AU - Prestegard JH FAU - Montelione, Gaetano T AU - Montelione GT LA - eng SI - PDB/2KW6 GR - 5 R90 DK071502/DK/NIDDK NIH HHS/United States GR - U54 GM094597/GM/NIGMS NIH HHS/United States GR - U54-GM-094597/GM/NIGMS NIH HHS/United States GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120314 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (CDK2AP1 protein, human) RN - 0 (Disulfides) RN - 0 (Tumor Suppressor Proteins) RN - EC 2.7.11.22 (CDK2 protein, human) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 2) SB - IM MH - Animals MH - Cell Line, Tumor MH - Cricetinae MH - Cyclin-Dependent Kinase 2/chemistry/genetics/metabolism MH - Disulfides/chemistry/metabolism MH - G1 Phase/physiology MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Oxidation-Reduction MH - *Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - S Phase/physiology MH - Tumor Suppressor Proteins/*chemistry/genetics/metabolism PMC - PMC3351331 OID - NLM: PMC3351331 EDAT- 2012/03/20 06:00 MHDA- 2012/07/14 06:00 CRDT- 2012/03/20 06:00 PHST- 2012/03/14 [aheadofprint] AID - M112.343863 [pii] AID - 10.1074/jbc.M112.343863 [doi] PST - ppublish SO - J Biol Chem. 2012 May 11;287(20):16541-9. doi: 10.1074/jbc.M112.343863. Epub 2012 Mar 14. PMID- 14769047 OWN - NLM STAT- MEDLINE DA - 20040210 DCOM- 20040617 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 6 DP - 2004 Feb 17 TI - Tau paired helical filaments from Alzheimer's disease brain and assembled in vitro are based on beta-structure in the core domain. PG - 1694-703 AB - Tau protein, a neuronal microtubule-associated protein, forms insoluble fibers ("paired helical filaments") in Alzheimer's disease and other tauopathies. Conflicting views on the structure of the fibers have been proposed recently, ranging from mainly alpha-helical structure to mainly beta-sheet, or a mixture of mostly random coil and beta-sheet. We have addressed this issue by studying tau fibers immunopurified from Alzheimer brain tissue by a conformation-specific antibody and comparing them with fibers reassembled from recombinant tau or tau constructs in vitro, using a combination of electron microscopy and spectroscopic methods. Brain-derived fibers and reassembled fibers both exhibit a typical twisted appearance when examined by electron microscopy. The soluble tau protein is a natively unfolded protein dominated by random coil structure, whereas Alzheimer PHFs and reassembled fibers show a shift toward an increase in the level of beta-structure. The results support a model in which the repeat domain of tau (which lies within the core of PHFs) adopts an increasing level of beta-structure during aggregation, whereas the N- and C-terminal domains projecting away from the PHF core are mostly random coil. FAU - Barghorn, Stefan AU - Barghorn S AD - Max-Planck-Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany. FAU - Davies, Peter AU - Davies P FAU - Mandelkow, Eckhard AU - Mandelkow E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Neurofilament Proteins) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Proteins) RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/*metabolism/pathology MH - Amyloid/chemistry MH - Blotting, Western MH - *Brain Chemistry MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - Neurofibrillary Tangles/chemistry/ultrastructure MH - Neurofilament Proteins/*chemistry/ultrastructure MH - Protein Isoforms/chemistry/isolation & purification/ultrastructure MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/*chemistry/isolation & purification/ultrastructure MH - Spectroscopy, Fourier Transform Infrared MH - tau Proteins/*chemistry/isolation & purification/ultrastructure EDAT- 2004/02/11 05:00 MHDA- 2004/06/18 05:00 CRDT- 2004/02/11 05:00 AID - 10.1021/bi0357006 [doi] PST - ppublish SO - Biochemistry. 2004 Feb 17;43(6):1694-703. PMID- 22820150 OWN - NLM STAT- MEDLINE DA - 20120821 DCOM- 20121024 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1818 IP - 11 DP - 2012 Nov TI - Alpha-synuclein pore forming activity upon membrane association. PG - 2876-83 LID - 10.1016/j.bbamem.2012.07.007 [doi] AB - Alpha-synuclein is a natively unfolded protein widely expressed in neurons at the presynaptic level. It is linked to Parkinson's disease by two lines of evidence: amyloid fibrils of the protein accumulate in patients' brains and three genetic mutants cause autosomal dominant forms of the disease. The biological role of the protein and the mechanisms involved in the etiopathogenesis of Parkinson's disease are still unknown. Membrane binding causes the formation of an amphipathic alpha-helix, which lies on the surface without crossing the bilayer. Recent observations however reported that the application of a voltage induces a pore-like activity of alpha-synuclein. This study aims to characterize the pore forming activity of the protein starting from its monomeric form. In particular, experiments with planar lipid membranes allowed recording of conductance activity bursts with a defined and reproducible fingerprint. Additional experiments with deletion mutants and covalently bound alpha-synuclein dimers were performed to understand both pore assembly and stoichiometry. The information acquired allowed formulation of a model for pore formation at different conductance levels. CI - Copyright (c) 2012 Elsevier B.V. All rights reserved. FAU - Tosatto, Laura AU - Tosatto L AD - Istituto di Biofisica, Consiglio Nazionale delle Ricerche & Fondazione Bruno Kessler, Trento, Italy. FAU - Andrighetti, Alberto O AU - Andrighetti AO FAU - Plotegher, Nicoletta AU - Plotegher N FAU - Antonini, Valeria AU - Antonini V FAU - Tessari, Isabella AU - Tessari I FAU - Ricci, Leonardo AU - Ricci L FAU - Bubacco, Luigi AU - Bubacco L FAU - Dalla Serra, Mauro AU - Dalla Serra M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120720 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Lipid Bilayers) RN - 0 (alpha-Synuclein) SB - IM MH - *Cell Membrane/metabolism MH - Dimerization MH - Lipid Bilayers MH - alpha-Synuclein/*metabolism EDAT- 2012/07/24 06:00 MHDA- 2012/10/25 06:00 CRDT- 2012/07/24 06:00 PHST- 2011/12/14 [received] PHST- 2012/07/09 [revised] PHST- 2012/07/11 [accepted] PHST- 2012/07/20 [aheadofprint] AID - S0005-2736(12)00239-8 [pii] AID - 10.1016/j.bbamem.2012.07.007 [doi] PST - ppublish SO - Biochim Biophys Acta. 2012 Nov;1818(11):2876-83. doi: 10.1016/j.bbamem.2012.07.007. Epub 2012 Jul 20. PMID- 17385861 OWN - NLM STAT- MEDLINE DA - 20070418 DCOM- 20070709 IS - 0002-7863 (Print) IS - 0002-7863 (Linking) VI - 129 IP - 16 DP - 2007 Apr 25 TI - Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation. PG - 5235-43 AB - Tau, a natively unstructured protein that regulates the organization of neuronal microtubules, is also found in high concentrations in neurofibrillary tangles of Alzheimer's disease and other neurodegenerative disorders. The conformational transition between these vastly different healthy and pathological forms remains poorly understood. We have measured residual dipolar couplings (RDCs), J-couplings, and nuclear Overhauser enhancement (NOE) in construct K18 of tau, containing all four repeat domains R1-R4. NHN RDCs were compared with prediction on the basis of a statistical model describing the intrinsic conformational sampling of unfolded proteins in solution. While local variation and relative amplitude of RDCs agrees with propensity-based prediction for most of the protein, homologous sequences in each repeat domain (DLKN, DLSN, DLSK, and DKFD in repeats R1-R4) show strong disagreement characterized by inversion of the sign of the central couplings. Accelerated molecular dynamic simulations (AMD) in explicit solvent revealed strong tendencies to form turns, identified as type I beta-turns for repeats R1-R3. Incorporation of the backbone dihedral sampling resulting from AMD into the statistical coil model closely reproduces experimental RDC values. These localized sequence-dependent conformational tendencies interrupt the propensity to sample more extended conformations in adjacent strands and are remarkably resistant to local environmental factors, as demonstrated by the persistence of the RDC signature even under harsh denaturing conditions (8 M urea). The role that this specific conformational behavior may play in the transition to the pathological form is discussed. FAU - Mukrasch, Marco D AU - Mukrasch MD AD - Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany. FAU - Markwick, Phineus AU - Markwick P FAU - Biernat, Jacek AU - Biernat J FAU - Bergen, Martin von AU - Bergen Mv FAU - Bernado, Pau AU - Bernado P FAU - Griesinger, Christian AU - Griesinger C FAU - Mandelkow, Eckhard AU - Mandelkow E FAU - Zweckstetter, Markus AU - Zweckstetter M FAU - Blackledge, Martin AU - Blackledge M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070327 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/etiology/metabolism MH - Amino Acid Sequence MH - Humans MH - Molecular Sequence Data MH - Protein Folding MH - Protein Structure, Secondary MH - tau Proteins/*chemistry/genetics EDAT- 2007/03/28 09:00 MHDA- 2007/07/10 09:00 CRDT- 2007/03/28 09:00 PHST- 2007/03/27 [aheadofprint] AID - 10.1021/ja0690159 [doi] PST - ppublish SO - J Am Chem Soc. 2007 Apr 25;129(16):5235-43. Epub 2007 Mar 27. PMID- 22310049 OWN - NLM STAT- MEDLINE DA - 20120416 DCOM- 20120608 LR - 20150217 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 418 IP - 5 DP - 2012 May 18 TI - Kinetic basis for the competitive recruitment of TolB by the intrinsically disordered translocation domain of colicin E9. PG - 269-80 LID - 10.1016/j.jmb.2012.01.039 [doi] AB - TolB and Pal are members of the Tol-Pal system that spans the cell envelope of Gram-negative bacteria and contributes to the stability and integrity of the bacterial outer membrane (OM). Lipoylated Pal is tethered to the OM and binds the beta-propeller domain of periplasmic TolB, which, as recent evidence suggests, disengages TolB from its interaction with other components of the Tol system in the inner membrane. Antibacterial nuclease colicins such as colicin E9 (ColE9) also bind the beta-propeller domain of TolB in order to catalyze their translocation across the bacterial OM. In contrast to Pal, however, colicin binding to TolB promotes its interaction with other components of the Tol system. Here, through a series of pre-steady-state kinetic experiments utilizing fluorescence resonance energy transfer pairs within the individual protein-protein complexes, we establish the kinetic basis for such 'competitive recruitment' by the TolB-binding epitope (TBE) of ColE9. Surprisingly, the 16-residue disordered ColE9 TBE associates more rapidly with TolB than Pal, a folded 13-kDa protein. Moreover, we demonstrate that calcium ions, which bind within the confines of the TolB beta-propeller domain tunnel and are known to increase the affinity of the TolB-ColE9 complex, do not exert their influence through long-range electrostatic effects, as had been predicted, but through short-range effects that slow the dissociation rate of ColE9 TBE from its complex with TolB. Our study demonstrates that an intrinsically disordered protein undergoing binding-induced folding can compete effectively with a globular protein for a common target by associating more rapidly than the globular protein. CI - Copyright (c) 2012 Elsevier Ltd. All rights reserved. FAU - Papadakos, Grigorios AU - Papadakos G AD - Department of Biology (Area 10), University of York, Wentworth Way, Heslington, York YO10 5DD, UK. FAU - Housden, Nicholas G AU - Housden NG FAU - Lilly, Katie J AU - Lilly KJ FAU - Kaminska, Renata AU - Kaminska R FAU - Kleanthous, Colin AU - Kleanthous C LA - eng GR - BB/G020671/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BB/G020671/2/Biotechnology and Biological Sciences Research Council/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120130 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Colicins) RN - 0 (Escherichia coli Proteins) RN - 0 (Periplasmic Proteins) RN - 0 (tolB protein, E coli) SB - IM CIN - J Mol Biol. 2012 May 18;418(5):267-8. PMID: 22381408 MH - Binding Sites MH - Colicins/*chemistry/metabolism MH - Escherichia coli/genetics/metabolism MH - Escherichia coli Proteins/*chemistry/metabolism MH - Fluorescence Resonance Energy Transfer MH - Kinetics MH - Models, Molecular MH - Periplasmic Proteins/*chemistry/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Protein Transport EDAT- 2012/02/09 06:00 MHDA- 2012/06/09 06:00 CRDT- 2012/02/08 06:00 PHST- 2011/11/18 [received] PHST- 2012/01/11 [revised] PHST- 2012/01/24 [accepted] PHST- 2012/01/30 [aheadofprint] AID - S0022-2836(12)00093-9 [pii] AID - 10.1016/j.jmb.2012.01.039 [doi] PST - ppublish SO - J Mol Biol. 2012 May 18;418(5):269-80. doi: 10.1016/j.jmb.2012.01.039. Epub 2012 Jan 30. PMID- 10329190 OWN - NLM STAT- MEDLINE DA - 19990625 DCOM- 19990625 LR - 20090929 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 288 IP - 5 DP - 1999 May 21 TI - Oct-1 POU and octamer DNA co-operate to recognise the Bob-1 transcription co-activator via induced folding. PG - 941-52 AB - The expression of immunoglobulin genes is controlled in part by the DNA-binding protein Oct-1 and the B cell-specific transcription co-activator, Bob1 (also known as OCA-B or OBF-1) that together form a complex on the Igkappa promoter. We have characterised the assembly of the ternary complex using biophysical methods. Bob1 binds specifically as a monomer to the complex of the Oct-1 DNA-binding domain (Oct-1 POU) and the Igkappa promoter, but binds weakly to either Oct-1 POU or the Igkappa promoter alone, indicating that both are required to make an avid complex. Ternary complex formation requires a defined DNA sequence, as the stability of the complex can be strongly affected by a single base-pair change or by removing 5-methyl groups from selected thymine bases.In isolation, Bob1 appears to have little secondary structure, but may become partially structured upon recruitment into the ternary complex as demonstrated by circular dichroism spectra and calorimetry. These and other findings suggest that ternary complex formation requires a defined geometry of the POU/DNA complex, and that the co-activator makes stereo-specific contacts to both the POU protein and the major groove of the DNA that induces its fold. CI - Copyright 1998 Academic Press. FAU - Chang, J F AU - Chang JF AD - Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK. FAU - Phillips, K AU - Phillips K FAU - Lundback, T AU - Lundback T FAU - Gstaiger, M AU - Gstaiger M FAU - Ladbury, J E AU - Ladbury JE FAU - Luisi, B AU - Luisi B LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DNA-Binding Proteins) RN - 0 (Host Cell Factor C1) RN - 0 (Octamer Transcription Factor-1) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) SB - IM MH - Base Sequence/physiology MH - Calorimetry MH - Circular Dichroism MH - Crystallography, X-Ray MH - DNA-Binding Proteins/*physiology MH - Host Cell Factor C1 MH - Kinetics MH - Models, Genetic MH - Models, Molecular MH - Octamer Transcription Factor-1 MH - Protein Folding MH - Protein Structure, Secondary MH - Recombinant Fusion Proteins MH - Thermodynamics MH - Time Factors MH - Trans-Activators/*physiology MH - Transcription Factors/*physiology EDAT- 1999/05/18 MHDA- 1999/05/18 00:01 CRDT- 1999/05/18 00:00 AID - S0022-2836(99)92711-0 [pii] AID - 10.1006/jmbi.1999.2711 [doi] PST - ppublish SO - J Mol Biol. 1999 May 21;288(5):941-52. PMID- 24121686 OWN - NLM STAT- MEDLINE DA - 20140128 DCOM- 20140325 LR - 20141112 IS - 1362-4962 (Electronic) IS - 0305-1048 (Linking) VI - 42 IP - 2 DP - 2014 Jan TI - The intrinsically disordered distal face of nucleoplasmin recognizes distinct oligomerization states of histones. PG - 1311-25 LID - 10.1093/nar/gkt899 [doi] AB - The role of Nucleoplasmin (NP) as a H2A-H2B histone chaperone has been extensively characterized. To understand its putative interaction with other histone ligands, we have characterized its ability to bind H3-H4 and histone octamers. We find that the chaperone forms distinct complexes with histones, which differ in the number of molecules that build the assembly and in their spatial distribution. When complexed with H3-H4 tetramers or histone octamers, two NP pentamers form an ellipsoidal particle with the histones located at the center of the assembly, in stark contrast with the NP/H2A-H2B complex that contains up to five histone dimers bound to one chaperone pentamer. This particular assembly relies on the ability of H3-H4 to form tetramers either in solution or as part of the octamer, and it is not observed when a variant of H3 (H3C110E), unable to form stable tetramers, is used instead of the wild-type protein. Our data also suggest that the distal face of the chaperone is involved in the interaction with distinct types of histones, as supported by electron microscopy analysis of the different NP/histone complexes. The use of the same structural region to accommodate all type of histones could favor histone exchange and nucleosome dynamics. FAU - Ramos, Isbaal AU - Ramos I AD - Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencia y Tecnologia, Universidad del PaisVasco, P. O. Box 644, 48080 Bilbao, Spain, Unidad de Biofisica (Consejo Superior de Investigaciones Cientificas-Universidad del Pais Vasco/Euskal Herriko Unibertsitatea), Barrio Sarriena s/n, 48080 Leioa Spain, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049 Madrid, Spain and Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada. FAU - Fernandez-Rivero, Noelia AU - Fernandez-Rivero N FAU - Arranz, Rocio AU - Arranz R FAU - Aloria, Kerman AU - Aloria K FAU - Finn, Ron AU - Finn R FAU - Arizmendi, Jesus M AU - Arizmendi JM FAU - Ausio, Juan AU - Ausio J FAU - Valpuesta, Jose Maria AU - Valpuesta JM FAU - Muga, Arturo AU - Muga A FAU - Prado, Adelina AU - Prado A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131010 PL - England TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Histones) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Nucleoplasmins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Histones/*chemistry/metabolism MH - Intrinsically Disordered Proteins/chemistry/metabolism MH - Molecular Sequence Data MH - Nucleoplasmins/*chemistry/metabolism MH - Protein Multimerization MH - Proteolysis MH - Xenopus laevis PMC - PMC3902905 OID - NLM: PMC3902905 EDAT- 2013/10/15 06:00 MHDA- 2014/03/26 06:00 CRDT- 2013/10/15 06:00 PHST- 2013/10/10 [aheadofprint] AID - gkt899 [pii] AID - 10.1093/nar/gkt899 [doi] PST - ppublish SO - Nucleic Acids Res. 2014 Jan;42(2):1311-25. doi: 10.1093/nar/gkt899. Epub 2013 Oct 10. PMID- 17929838 OWN - NLM STAT- MEDLINE DA - 20071106 DCOM- 20071227 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 46 IP - 45 DP - 2007 Nov 13 TI - Effects of zinc binding on the structure and dynamics of the intrinsically disordered protein prothymosin alpha: evidence for metalation as an entropic switch. PG - 13120-30 AB - Prothymosin alpha (ProTalpha) is a small acidic protein that is highly conserved among mammals. The human form has 110 amino acid residues (M.W. 12.1 kDa; pI approximately 3.5) and is found to be expressed in a wide variety of tissues. ProTalpha plays an essential role in cell proliferation and apoptosis, and it is involved in transcriptional regulation of oxidative stress-protecting genes. Despite the multiple biological functions ProTalpha has, the protein does not adopt a well-defined three-dimensional structure under physiological conditions. Previous studies have shown that the interaction between ProTalpha and some of its protein targets is significantly enhanced in the presence of zinc ions, suggesting that zinc binding plays a crucial role in the protein's function. In this work, we use nuclear magnetic resonance spectroscopy and electrospray ionization mass spectrometry to characterize the structure and dynamics of ProTalpha and its complexation with Zn2+. We found that zinc binding causes partial folding of the C-terminal half of ProTalpha, especially the Glu-rich region, while the N-terminal portion of the protein remains largely unstructured. The metalated protein also exhibits a significantly reduced flexibility. ProTalpha shows a high specificity for Zn2+, and the interactions with other divalent cations (Ca2+, Mg2+) are much weaker. On the basis of the site-specific information obtained here, as well as the results from previous studies, we propose that the conformational and dynamic changes upon zinc binding may act as an entropic switch that greatly facilitates the binding to other proteins. FAU - Yi, Shiluan AU - Yi S AD - Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1. FAU - Boys, Brian L AU - Boys BL FAU - Brickenden, Anne AU - Brickenden A FAU - Konermann, Lars AU - Konermann L FAU - Choy, Wing-Yiu AU - Choy WY LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20071011 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Protein Precursors) RN - 0 (prothymosin alpha) RN - 61512-21-8 (Thymosin) RN - J41CSQ7QDS (Zinc) SB - IM MH - Circular Dichroism MH - Electron Spin Resonance Spectroscopy MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Precursors/*chemistry MH - Spectrometry, Mass, Electrospray Ionization MH - Thymosin/*analogs & derivatives/chemistry MH - Zinc/*chemistry EDAT- 2007/10/13 09:00 MHDA- 2007/12/28 09:00 CRDT- 2007/10/13 09:00 PHST- 2007/10/11 [aheadofprint] AID - 10.1021/bi7014822 [doi] PST - ppublish SO - Biochemistry. 2007 Nov 13;46(45):13120-30. Epub 2007 Oct 11. PMID- 20872101 OWN - NLM STAT- MEDLINE DA - 20110307 DCOM- 20110621 LR - 20140917 IS - 1874-270X (Electronic) VI - 5 IP - 1 DP - 2011 Apr TI - Backbone assignment and dynamics of human alpha-synuclein in viscous 2 M glucose solution. PG - 43-6 LID - 10.1007/s12104-010-9263-4 [doi] AB - We present (1)H(N), (15)N, (13)C(alpha), (13)C(beta) and (13)C' assignments and (15)N transverse relaxation rates (R(2)) of a Parkinson's disease-related intrinsically disordered protein, alpha-synuclein, in the presence of 2 M (360 g/l) glucose solution. FAU - Wu, Kuen-Phon AU - Wu KP AD - Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA. FAU - Baum, Jean AU - Baum J LA - eng GR - 5R90DK071502/DK/NIDDK NIH HHS/United States GR - GM087012/GM/NIGMS NIH HHS/United States GR - R01 GM087012/GM/NIGMS NIH HHS/United States GR - R01 GM087012-02/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20100925 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (SNCA protein, human) RN - 0 (Solutions) RN - 0 (alpha-Synuclein) RN - IY9XDZ35W2 (Glucose) SB - IM MH - Glucose/*chemistry MH - Humans MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Secondary MH - Solutions MH - Viscosity MH - alpha-Synuclein/*chemistry PMC - PMC3064444 MID - NIHMS250309 OID - NLM: NIHMS250309 OID - NLM: PMC3064444 EDAT- 2010/09/28 06:00 MHDA- 2011/06/22 06:00 CRDT- 2010/09/28 06:00 PHST- 2010/05/24 [received] PHST- 2010/08/02 [accepted] PHST- 2010/09/25 [aheadofprint] AID - 10.1007/s12104-010-9263-4 [doi] PST - ppublish SO - Biomol NMR Assign. 2011 Apr;5(1):43-6. doi: 10.1007/s12104-010-9263-4. Epub 2010 Sep 25. PMID- 8875929 OWN - NLM STAT- MEDLINE DA - 19961206 DCOM- 19961206 LR - 20081121 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 274 IP - 5289 DP - 1996 Nov 8 TI - Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. PG - 948-53 AB - The MDM2 oncoprotein is a cellular inhibitor of the p53 tumor suppressor in that it can bind the transactivation domain of p53 and downregulate its ability to activate transcription. In certain cancers, MDM2 amplification is a common event and contributes to the inactivation of p53. The crystal structure of the 109-residue amino-terminal domain of MDM2 bound to a 15-residue transactivation domain peptide of p53 revealed that MDM2 has a deep hydrophobic cleft on which the p53 peptide binds as an amphipathic alpha helix. The interface relies on the steric complementarity between the MDM2 cleft and the hydrophobic face of the p53 alpha helix and, in particular, on a triad of p53 amino acids-Phe19, Trp23, and Leu26-which insert deep into the MDM2 cleft. These same p53 residues are also involved in transactivation, supporting the hypothesis that MDM2 inactivates p53 by concealing its transactivation domain. The structure also suggests that the amphipathic alpha helix may be a common structural motif in the binding of a diverse family of transactivation factors to the TATA-binding protein-associated factors. FAU - Kussie, P H AU - Kussie PH AD - Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. nikola@xray2.mskcc.org FAU - Gorina, S AU - Gorina S FAU - Marechal, V AU - Marechal V FAU - Elenbaas, B AU - Elenbaas B FAU - Moreau, J AU - Moreau J FAU - Levine, A J AU - Levine AJ FAU - Pavletich, N P AU - Pavletich NP LA - eng SI - PDB/1YCQ SI - PDB/1YCR GR - CA65698/CA/NCI NIH HHS/United States PT - Comment PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Nuclear Proteins) RN - 0 (Proto-Oncogene Proteins) RN - 0 (Transcription Factors) RN - 0 (Tumor Suppressor Protein p53) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM CON - Science. 1996 Nov 8;274(5289):921-2. PMID: 8966571 MH - Binding Sites MH - Crystallization MH - Crystallography, X-Ray MH - Hydrogen Bonding MH - Models, Molecular MH - *Nuclear Proteins MH - Protein Binding MH - *Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins/*chemistry/metabolism MH - Proto-Oncogene Proteins c-mdm2 MH - Transcription Factors/chemistry/metabolism MH - *Transcriptional Activation MH - Tumor Suppressor Protein p53/*chemistry/metabolism EDAT- 1996/11/08 MHDA- 1996/11/08 00:01 CRDT- 1996/11/08 00:00 PST - ppublish SO - Science. 1996 Nov 8;274(5289):948-53. PMID- 11886217 OWN - NLM STAT- MEDLINE DA - 20020311 DCOM- 20020703 LR - 20061115 IS - 1047-8477 (Print) IS - 1047-8477 (Linking) VI - 136 IP - 2 DP - 2001 Nov TI - Crystallization and preliminary X-ray diffraction analysis of the Rab escort protein-1 in complex with Rab geranylgeranyltransferase. PG - 158-61 AB - Posttranslational prenylation of proteins is a widespread phenomenon and the majority of prenylated proteins are geranylgeranylated members of the Rab GTPase family. Geranylgeranylation is catalyzed by Rab geranylgeranyltransferase (RabGGTase) and is critical for the ability of Rab protein to mediate vesicular docking and fusion of various intracellular vesicles. RabGGTase consists of a catalytic alpha/beta heterodimer and an accessory protein termed Rab escort protein (REP-1) that delivers the newly prenylated Rab proteins to their target membrane. Mutations in the REP-1 gene in humans lead to an X-chromosome-linked defect known as choroideremia--a debilitating disease that inevitably culminates in complete blindness. Here we report in vitro assembly and purification of the stoichiometric ternary complex of RabGGTase with REP-1 stabilized by a hydrolysis-resistant phosphoisoprenoid analog--farnesyl phosphonyl(methyl)phoshonate. The complex formed crystals of extended plate morphology under low ionic-strength conditions. X-ray diffraction data were collected to 2.8 A resolution at the ESRF. The crystals belong to the monoclinic space group P2(1), with unit-cell parameters a = 68.7, b = 197.7, c = 86.1 A, beta = 113.4 degrees. Preliminary structural analysis revealed the presence of one molecule in the asymmetric unit. CI - (C)2001 Elsevier Science (USA). FAU - Rak, A AU - Rak A AD - Max-Plank-Institute for Molecular Physiology, Dortmund, Germany. FAU - Reents, R AU - Reents R FAU - Pylypenko, O AU - Pylypenko O FAU - Niculae, A AU - Niculae A FAU - Sidorovitch, V AU - Sidorovitch V FAU - Thoma, N H AU - Thoma NH FAU - Waldmann, H AU - Waldmann H FAU - Schlichting, I AU - Schlichting I FAU - Goody, R S AU - Goody RS FAU - Alexandrov, K AU - Alexandrov K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - EC 2.5.- (Alkyl and Aryl Transferases) RN - EC 2.5.1.- (Rab geranylgeranyltransferase) RN - EC 3.6.1.- (rab GTP-Binding Proteins) SB - IM MH - Alkyl and Aryl Transferases/*chemistry MH - Crystallization MH - Crystallography, X-Ray MH - Electrophoresis, Polyacrylamide Gel MH - Protein Binding MH - Protein Conformation MH - X-Ray Diffraction MH - rab GTP-Binding Proteins/*chemistry EDAT- 2002/03/12 10:00 MHDA- 2002/07/04 10:01 CRDT- 2002/03/12 10:00 AID - 10.1006/jsbi.2001.4433 [doi] AID - S1047-8477(01)94433-8 [pii] PST - ppublish SO - J Struct Biol. 2001 Nov;136(2):158-61. PMID- 12621042 OWN - NLM STAT- MEDLINE DA - 20030512 DCOM- 20030625 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 20 DP - 2003 May 16 TI - The C-terminal domain of the measles virus nucleoprotein is intrinsically disordered and folds upon binding to the C-terminal moiety of the phosphoprotein. PG - 18638-48 AB - The nucleoprotein of measles virus consists of an N-terminal moiety, N(CORE), resistant to proteolysis and a C-terminal moiety, N(TAIL), hypersensitive to proteolysis and not visible as a distinct domain by electron microscopy. We report the bacterial expression, purification, and characterization of measles virus N(TAIL). Using nuclear magnetic resonance, circular dichroism, gel filtration, dynamic light scattering, and small angle x-ray scattering, we show that N(TAIL) is not structured in solution. Its sequence and spectroscopic and hydrodynamic properties indicate that N(TAIL) belongs to the premolten globule subfamily within the class of intrinsically disordered proteins. The same epitopes are exposed in N(TAIL) and within the nucleoprotein, which rules out dramatic conformational changes in the isolated N(TAIL) domain compared with the full-length nucleoprotein. Most unstructured proteins undergo some degree of folding upon binding to their partners, a process termed "induced folding." We show that N(TAIL) is able to bind its physiological partner, the phosphoprotein, and that it undergoes such an unstructured-to-structured transition upon binding to the C-terminal moiety of the phosphoprotein. The presence of flexible regions at the surface of the viral nucleocapsid would enable plastic interactions with several partners, whereas the gain of structure arising from induced folding would lead to modulation of these interactions. These results contribute to the study of the emerging field of natively unfolded proteins. FAU - Longhi, Sonia AU - Longhi S AD - Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS et Universite Aix-Marseille I et II, ESIL, Campus de Luminy, 13288 Marseille Cedex 09, France. longhi@afmb.cnrs-mrs.fr FAU - Receveur-Brechot, Veronique AU - Receveur-Brechot V FAU - Karlin, David AU - Karlin D FAU - Johansson, Kenth AU - Johansson K FAU - Darbon, Herve AU - Darbon H FAU - Bhella, David AU - Bhella D FAU - Yeo, Robert AU - Yeo R FAU - Finet, Stephanie AU - Finet S FAU - Canard, Bruno AU - Canard B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030305 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Epitopes) RN - 0 (Nucleoproteins) RN - 0 (Viral Proteins) RN - 0 (nucleoprotein, Measles virus) SB - IM MH - Chromatography, Gel MH - Circular Dichroism MH - Epitopes MH - Escherichia coli/metabolism MH - Light MH - Magnetic Resonance Spectroscopy MH - Mass Spectrometry MH - Nucleoproteins/*chemistry/metabolism MH - Plasmids/metabolism MH - Precipitin Tests MH - Protein Binding MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Scattering, Radiation MH - Viral Proteins/*chemistry/metabolism MH - X-Rays EDAT- 2003/03/07 04:00 MHDA- 2003/06/26 05:00 CRDT- 2003/03/07 04:00 PHST- 2003/03/05 [aheadofprint] AID - 10.1074/jbc.M300518200 [doi] AID - M300518200 [pii] PST - ppublish SO - J Biol Chem. 2003 May 16;278(20):18638-48. Epub 2003 Mar 5. PMID- 24021816 OWN - NLM STAT- MEDLINE DA - 20131111 DCOM- 20140102 LR - 20141202 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 425 IP - 23 DP - 2013 Nov 29 TI - Multiple C-terminal tails within a single E. coli SSB homotetramer coordinate DNA replication and repair. PG - 4802-19 LID - 10.1016/j.jmb.2013.08.021 [doi] LID - S0022-2836(13)00541-X [pii] AB - Escherichia coli single-stranded DNA binding protein (SSB) plays essential roles in DNA replication, recombination and repair. SSB functions as a homotetramer with each subunit possessing a DNA binding domain (OB-fold) and an intrinsically disordered C-terminus, of which the last nine amino acids provide the site for interaction with at least a dozen other proteins that function in DNA metabolism. To examine how many C-termini are needed for SSB function, we engineered covalently linked forms of SSB that possess only one or two C-termini within a four-OB-fold "tetramer". Whereas E. coli expressing SSB with only two tails can survive, expression of a single-tailed SSB is dominant lethal. E. coli expressing only the two-tailed SSB recovers faster from exposure to DNA damaging agents but accumulates more mutations. A single-tailed SSB shows defects in coupled leading and lagging strand DNA replication and does not support replication restart in vitro. These deficiencies in vitro provide a plausible explanation for the lethality observed in vivo. These results indicate that a single SSB tetramer must interact simultaneously with multiple protein partners during some essential roles in genome maintenance. CI - (c) 2013. FAU - Antony, Edwin AU - Antony E AD - Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, Box 8231, St. Louis, MO 63110-1093, USA. FAU - Weiland, Elizabeth AU - Weiland E FAU - Yuan, Quan AU - Yuan Q FAU - Manhart, Carol M AU - Manhart CM FAU - Nguyen, Binh AU - Nguyen B FAU - Kozlov, Alexander G AU - Kozlov AG FAU - McHenry, Charles S AU - McHenry CS FAU - Lohman, Timothy M AU - Lohman TM LA - eng GR - GM30498/GM/NIGMS NIH HHS/United States GR - R01 GM030498/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130907 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (DNA, Bacterial) RN - 0 (DNA, Single-Stranded) RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (SSB protein, E coli) SB - IM MH - DNA Mutational Analysis MH - *DNA Repair MH - *DNA Replication MH - DNA, Bacterial/metabolism MH - DNA, Single-Stranded/metabolism MH - DNA-Binding Proteins/genetics/*metabolism MH - Escherichia coli/*enzymology/genetics/metabolism MH - Escherichia coli Proteins/genetics/*metabolism MH - Microbial Viability MH - Models, Molecular MH - Protein Binding MH - Protein Conformation MH - Protein Multimerization MH - Recombinant Fusion Proteins/genetics/metabolism PMC - PMC3832242 MID - NIHMS524023 OID - NLM: NIHMS524023 OID - NLM: PMC3832242 OTO - NOTNLM OT - DNA binding OT - DNA repair OT - DNA replication OT - EDTA OT - FRET OT - PBS OT - SIP OT - SSB OT - SSB interacting protein OT - ethylenediaminetetraacetic acid OT - fluorescence resonance energy transfer OT - phosphate-buffered saline OT - single stranded DNA binding protein OT - single-stranded DNA OT - single-stranded DNA binding protein OT - ssDNA OT - wild type OT - wt EDAT- 2013/09/12 06:00 MHDA- 2014/01/03 06:00 CRDT- 2013/09/12 06:00 PHST- 2013/06/13 [received] PHST- 2013/08/01 [revised] PHST- 2013/08/16 [accepted] PHST- 2013/09/07 [aheadofprint] AID - S0022-2836(13)00541-X [pii] AID - 10.1016/j.jmb.2013.08.021 [doi] PST - ppublish SO - J Mol Biol. 2013 Nov 29;425(23):4802-19. doi: 10.1016/j.jmb.2013.08.021. Epub 2013 Sep 7. PMID- 24474217 OWN - NLM STAT- MEDLINE DA - 20140331 DCOM- 20150109 LR - 20150422 IS - 1573-6881 (Electronic) IS - 0145-479X (Linking) VI - 46 IP - 2 DP - 2014 Apr TI - Linking alpha-synuclein properties with oxidation: a hypothesis on a mechanism underling cellular aggregation. PG - 93-8 LID - 10.1007/s10863-014-9540-5 [doi] AB - alpha-Synuclein is a small, natively unstructured protein with propensity to aggregate. alpha-Synuclein fibrils are major components of Lewy bodies that are hallmarks of many neurodegenerative diseases. The solution properties and aggregation behavior of alpha-synuclein has been well characterized, but despite numerous studies that address the role of alpha-synuclein in cells, a clear physiological function of this protein remains a mystery. Over a hundred review articles of alpha-synuclein have been written in the last decade, making it difficult to list all of the important studies that have added to our insight of alpha-synuclein physiology. Instead, we briefly review the status of alpha-synuclein research and propose a model based on the idea that alpha-synuclein may not have an intrinsic activity in cells but rather, it modifies the function of a group of protein partners that in turn affect cell processes. We propose that it is the loss of its cellular partners under oxidative conditions that promotes alpha-synuclein aggregation accelerating neuronal death. FAU - Scarlata, Suzanne AU - Scarlata S AD - Department of Physiology & Biophysics, Stony Brook University, Stony Brook, NY, 11794-8661, USA, suzanne.scarlata@stonybrook.edu. FAU - Golebiewska, Urszula AU - Golebiewska U LA - eng GR - GM05312/GM/NIGMS NIH HHS/United States GR - P41 RR003155/RR/NCRR NIH HHS/United States GR - R01 GM053132/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review DEP - 20140129 PL - United States TA - J Bioenerg Biomembr JT - Journal of bioenergetics and biomembranes JID - 7701859 RN - 0 (Nerve Tissue Proteins) RN - 0 (alpha-Synuclein) RN - EC 3.1.4.- (Type C Phospholipases) SB - IM EIN - J Bioenerg Biomembr. 2014 Apr;46(2):157 MH - Humans MH - Nerve Tissue Proteins/*metabolism MH - Oxidation-Reduction MH - Oxidative Stress MH - Type C Phospholipases/*metabolism MH - alpha-Synuclein/*metabolism PMC - PMC4000690 MID - NIHMS571953 OID - NLM: NIHMS571953 OID - NLM: PMC4000690 EDAT- 2014/01/30 06:00 MHDA- 2015/01/13 06:00 CRDT- 2014/01/30 06:00 PHST- 2014/01/17 [received] PHST- 2014/01/20 [accepted] PHST- 2014/01/29 [aheadofprint] AID - 10.1007/s10863-014-9540-5 [doi] PST - ppublish SO - J Bioenerg Biomembr. 2014 Apr;46(2):93-8. doi: 10.1007/s10863-014-9540-5. Epub 2014 Jan 29. PMID- 21640124 OWN - NLM STAT- MEDLINE DA - 20110725 DCOM- 20110921 LR - 20141022 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 411 IP - 1 DP - 2011 Aug 5 TI - Consequences of stabilizing the natively disordered f helix for the folding pathway of apomyoglobin. PG - 248-63 LID - 10.1016/j.jmb.2011.05.028 [doi] AB - The F helix region of sperm whale apomyoglobin is disordered, undergoing conformational fluctuations between a folded helical conformation and one or more locally unfolded states. To examine the effects of F helix stabilization on the folding pathway of apomyoglobin, we have introduced mutations to augment intrinsic helical structure in the F helix of the kinetic folding intermediate and to increase its propensity to fold early in the pathway, using predictions based on plots of the average area buried upon folding (AABUF) derived from the primary sequence. Two mutant proteins were prepared: a double mutant, P88K/S92K (F2), and a quadruple mutant, P88K/A90L/S92K/A94L (F4). Whereas the AABUF for F2 predicts that the F helix will not fold early in the pathway, the F helix in F4 shows a significantly increased AABUF and is therefore predicted to fold early. Protection of amide protons by formation of hydrogen-bonded helical structure during the early folding events has been analyzed by pH-pulse labeling. Consistent with the AABUF prediction, many of the F helix residues for F4 are significantly protected in the kinetic intermediate but are not protected in the F2 mutant. F4 folds via a kinetically trapped burst-phase intermediate that contains stabilized secondary structure in the A, B, F, G, and H helix regions. Rapid folding of the F helix stabilizes the central core of the misfolded intermediate and inhibits translocation of the H helix back to its native position, thereby decreasing the overall folding rate. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Nishimura, Chiaki AU - Nishimura C AD - Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla CA 92037, USA. FAU - Dyson, H Jane AU - Dyson HJ FAU - Wright, Peter E AU - Wright PE LA - eng GR - R01 DK034909/DK/NIDDK NIH HHS/United States GR - R01 DK034909-24/DK/NIDDK NIH HHS/United States GR - R01 DK34909/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20110527 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Apoproteins) RN - 0 (Mutant Proteins) RN - 0 (Myoglobin) RN - 0 (apomyoglobin) SB - IM MH - Amino Acid Substitution/genetics MH - Animals MH - Apoproteins/*chemistry/genetics/*metabolism MH - Circular Dichroism MH - Kinetics MH - Mutagenesis, Site-Directed MH - Mutant Proteins/chemistry/genetics/metabolism MH - Myoglobin/*chemistry/genetics/*metabolism MH - Protein Conformation MH - *Protein Folding MH - Spectrometry, Fluorescence MH - Sperm Whale PMC - PMC3143293 MID - NIHMS300323 OID - NLM: NIHMS300323 OID - NLM: PMC3143293 EDAT- 2011/06/07 06:00 MHDA- 2011/09/22 06:00 CRDT- 2011/06/07 06:00 PHST- 2011/04/08 [received] PHST- 2011/05/16 [revised] PHST- 2011/05/18 [accepted] PHST- 2011/05/27 [aheadofprint] AID - S0022-2836(11)00578-X [pii] AID - 10.1016/j.jmb.2011.05.028 [doi] PST - ppublish SO - J Mol Biol. 2011 Aug 5;411(1):248-63. doi: 10.1016/j.jmb.2011.05.028. Epub 2011 May 27. PMID- 19995078 OWN - NLM STAT- MEDLINE DA - 20091209 DCOM- 20100316 LR - 20140922 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 131 IP - 49 DP - 2009 Dec 16 TI - NMR structure in a membrane environment reveals putative amyloidogenic regions of the SEVI precursor peptide PAP(248-286). PG - 17972-9 LID - 10.1021/ja908170s [doi] AB - Semen is the main vector for HIV transmission worldwide. Recently, a peptide fragment (PAP(248-286)) has been isolated from seminal fluid that dramatically enhances HIV infectivity by up to 4-5 orders of magnitude. PAP(248-286) appears to enhance HIV infection by forming amyloid fibers known as SEVI, which are believed to enhance the attachment of the virus by bridging interactions between virion and host-cell membranes. We have solved the atomic-level resolution structure of the SEVI precursor PAP(248-286) using NMR spectroscopy in SDS micelles, which serve as a model membrane system. PAP(248-286), which does not disrupt membranes like most amyloid proteins, binds superficially to the surface of the micelle, in contrast to other membrane-disruptive amyloid peptides that generally penetrate into the core of the membrane. The structure of PAP(248-286) is unlike most amyloid peptides in that PAP(248-286) is mostly disordered when bound to the surface of the micelle, as opposed to the alpha-helical structures typically found of most amyloid proteins. The highly disordered nature of the SEVI peptide may explain the unique ability of SEVI amyloid fibers to enhance HIV infection as partially disordered amyloid fibers will have a greater capture radius for the virus than compact amyloid fibers. Two regions of nascent structure (an alpha-helix from V262-H270 and a dynamic alpha/3(10) helix from S279-L283) match the prediction of highly amyloidogenic sequences and may serve as nuclei for aggregation and amyloid fibril formation. The structure presented here can be used for the rational design of mutagenesis studies on SEVI amyloid formation and viral infection enhancement. FAU - Nanga, Ravi P R AU - Nanga RP AD - Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA. FAU - Brender, Jeffrey R AU - Brender JR FAU - Vivekanandan, Subramanian AU - Vivekanandan S FAU - Popovych, Nataliya AU - Popovych N FAU - Ramamoorthy, Ayyalusamy AU - Ramamoorthy A LA - eng GR - DK078885/DK/NIDDK NIH HHS/United States GR - GM084018/GM/NIGMS NIH HHS/United States GR - R01 GM084018/GM/NIGMS NIH HHS/United States GR - R01 GM084018-01A1/GM/NIGMS NIH HHS/United States GR - R21 DK078885/DK/NIDDK NIH HHS/United States GR - R21 DK078885-01A2/DK/NIDDK NIH HHS/United States GR - RR023597/RR/NCRR NIH HHS/United States GR - S10 RR023597/RR/NCRR NIH HHS/United States GR - S10 RR023597-01/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Amyloid) RN - 0 (Membranes, Artificial) RN - 0 (Peptide Fragments) SB - IM MH - Amyloid/*chemistry MH - HIV Infections/virology MH - Magnetic Resonance Spectroscopy MH - *Membranes, Artificial MH - Peptide Fragments/*chemistry MH - Semen/*chemistry/virology PMC - PMC2792124 MID - NIHMS160023 OID - NLM: NIHMS160023 OID - NLM: PMC2792124 EDAT- 2009/12/10 06:00 MHDA- 2010/03/17 06:00 CRDT- 2009/12/10 06:00 AID - 10.1021/ja908170s [doi] PST - ppublish SO - J Am Chem Soc. 2009 Dec 16;131(49):17972-9. doi: 10.1021/ja908170s. PMID- 9628486 OWN - NLM STAT- MEDLINE DA - 19980630 DCOM- 19980630 LR - 20061115 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 5 IP - 6 DP - 1998 Jun TI - Crystal structure of calsequestrin from rabbit skeletal muscle sarcoplasmic reticulum. PG - 476-83 AB - Calsequestrin, the major Ca2+ storage protein of muscle, coordinately binds and releases 40-50 Ca2+ ions per molecule for each contraction-relaxation cycle by an uncertain mechanism. We have determined the structure of rabbit skeletal muscle calsequestrin. Three very negative thioredoxin-like domains surround a hydrophilic center. Each monomer makes two extensive dimerization contacts, both of which involve the approach of many negative groups. This structure suggests a mechanism by which calsequestrin may achieve high capacity Ca2+ binding. The suggested mechanism involves Ca2+-induced collapse of the three domains and polymerization of calsequestrin monomers arising from three factors: N-terminal arm exchange, helix-helix contacts and Ca2+ cross bridges. This proposed structure-based mechanism accounts for the observed coupling of high capacity Ca2+ binding with protein precipitation. FAU - Wang, S AU - Wang S AD - Department of Biochemistry and Biophysics, Washington State University, Pullman 99164-4660, USA. FAU - Trumble, W R AU - Trumble WR FAU - Liao, H AU - Liao H FAU - Wesson, C R AU - Wesson CR FAU - Dunker, A K AU - Dunker AK FAU - Kang, C H AU - Kang CH LA - eng SI - PDB/1A8Y PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Biopolymers) RN - 0 (Calcium-Binding Proteins) RN - 0 (Calsequestrin) SB - IM CIN - Nat Struct Biol. 1998 Jun;5(6):409-11. PMID: 9628471 MH - Animals MH - Biopolymers/chemistry MH - Calcium-Binding Proteins/chemistry MH - Calsequestrin/*chemistry MH - Crystallization MH - Crystallography, X-Ray MH - Dimerization MH - Models, Biological MH - Rabbits MH - Sarcoplasmic Reticulum/*chemistry EDAT- 1998/06/17 MHDA- 1998/06/17 00:01 CRDT- 1998/06/17 00:00 PST - ppublish SO - Nat Struct Biol. 1998 Jun;5(6):476-83. PMID- 20714568 OWN - NLM STAT- MEDLINE DA - 20100902 DCOM- 20101227 LR - 20140922 IS - 1364-548X (Electronic) IS - 1359-7345 (Linking) VI - 46 IP - 36 DP - 2010 Sep 28 TI - Alpha-synuclein in alpha-helical conformation at air-water interface: implication of conformation and orientation changes during its accumulation/aggregation. PG - 6702-4 LID - 10.1039/c0cc02098b [doi] AB - Alpha-synuclein, a natively unstructured protein important in the neuropathology of Parkinson's disease, was found to form a Langmuir monolayer in an alpha-helical conformation with its helical axis parallel to the air-water interface. This study sheds light on the role of vesicles in neuronal cells in the accumulation/aggregation of alpha-synuclein. FAU - Wang, Chengshan AU - Wang C AD - California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA. FAU - Shah, Nilam AU - Shah N FAU - Thakur, Garima AU - Thakur G FAU - Zhou, Feimeng AU - Zhou F FAU - Leblanc, Roger M AU - Leblanc RM LA - eng GR - P20-MD001824-01/MD/NIMHD NIH HHS/United States GR - SC1 NS070155/NS/NINDS NIH HHS/United States GR - SC1NS070155-01/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20100816 PL - England TA - Chem Commun (Camb) JT - Chemical communications (Cambridge, England) JID - 9610838 RN - 0 (alpha-Synuclein) RN - 059QF0KO0R (Water) SB - IM MH - *Air MH - Humans MH - Parkinson Disease/metabolism MH - Protein Structure, Secondary MH - Spectrophotometry, Infrared MH - Water/*chemistry MH - alpha-Synuclein/*chemistry PMC - PMC3186058 MID - NIHMS322352 OID - NLM: NIHMS322352 OID - NLM: PMC3186058 EDAT- 2010/08/18 06:00 MHDA- 2010/12/28 06:00 CRDT- 2010/08/18 06:00 PHST- 2010/08/16 [aheadofprint] PHST- 2010/08/31 [epublish] AID - 10.1039/c0cc02098b [doi] PST - ppublish SO - Chem Commun (Camb). 2010 Sep 28;46(36):6702-4. doi: 10.1039/c0cc02098b. Epub 2010 Aug 16. PMID- 3427055 OWN - NLM STAT- MEDLINE DA - 19880318 DCOM- 19880318 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 26 IP - 22 DP - 1987 Nov 3 TI - Calcium binding domains and calcium-induced conformational transition of SPARC/BM-40/osteonectin, an extracellular glycoprotein expressed in mineralized and nonmineralized tissues. PG - 6958-65 AB - SPARC, BM-40, and osteonectin are identical or very closely related extracellular proteins of apparent Mr 43,000 (Mr 33,000 predicted from sequence). They were originally isolated from parietal endoderm cells, basement membrane producing tumors, and bone, respectively, but are rather widely distributed in various tissues. In view of the calcium binding activity reported for osteonectin, we analyzed the SPARC sequence and found two putative calcium binding domains. One is an N-terminal acidic region with clusters of glutamic acid residues. This region, although neither gamma-carboxylated nor homologous, resembles the gamma-carboxyglutamic acid (Gla) domain of vitamin K dependent proteins of the blood clotting system in charge density, size of negatively charged clusters, and linkage to the rest of the molecule by a cysteine-rich domain. The other region is an EF-hand calcium binding domain located near the C-terminus. A disulfide bond between the E and F helix is predicted from modeling the EF-hand structure with the known coordinates of intestinal calcium binding protein. The disulfide bridge apparently serves to stabilize the isolated calcium loop in the extracellular protein. As observed for cytoplasmic EF-hand-containing proteins and for Gla domain containing proteins, a major conformational transition is induced in BM-40 upon binding of several Ca2+ ions. This is accompanied by a 35% increase in alpha-helicity. A pronounced sigmoidicity of the dependence of the circular dichroism signal at 220 nm on calcium concentration indicates that the process is cooperative. In view of its properties, abundance, and wide distribution, it is proposed that SPARC/BM-40/osteonectin has a rather general regulatory function in calcium-dependent processes of the extracellular matrix. FAU - Engel, J AU - Engel J AD - Department of Biophysical Chemistry, Biozentrum, Basel, Switzerland. FAU - Taylor, W AU - Taylor W FAU - Paulsson, M AU - Paulsson M FAU - Sage, H AU - Sage H FAU - Hogan, B AU - Hogan B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Carrier Proteins) RN - 0 (Glycoproteins) RN - 0 (Osteonectin) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Calcium/*pharmacology MH - Carrier Proteins/isolation & purification/*metabolism MH - Cell Line MH - Circular Dichroism MH - Glycoproteins/*metabolism MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Molecular Weight MH - Osteonectin MH - Protein Conformation EDAT- 1987/11/03 MHDA- 1987/11/03 00:01 CRDT- 1987/11/03 00:00 PST - ppublish SO - Biochemistry. 1987 Nov 3;26(22):6958-65. PMID- 25129622 OWN - NLM STAT- MEDLINE DA - 20140903 DCOM- 20150512 LR - 20150325 IS - 1573-5001 (Electronic) IS - 0925-2738 (Linking) VI - 60 IP - 1 DP - 2014 Sep TI - (1)(3)Calpha decoupling during direct observation of carbonyl resonances in solution NMR of isotopically enriched proteins. PG - 15-21 LID - 10.1007/s10858-014-9853-z [doi] AB - Direct detection of (13)C can be advantageous when studying uniformly enriched proteins, in particular for paramagnetic proteins or when hydrogen exchange with solvent is fast. A scheme recently introduced for long-observation-window band-selective homonuclear decoupling in solid state NMR, LOW-BASHD (Struppe et al. in J Magn Reson 236:89-94, 2013) is shown to be effective for (13)C(alpha) decoupling during direct (13)C' observation in solution NMR experiments too. For this purpose, adjustment of the decoupling pulse parameters and delays is demonstrated to be important for increasing spectral resolution, to reduce three-spin effects, and to decrease the intensity of decoupling side-bands. LOW-BASHD then yields (13)C' line widths comparable to those obtained with the popular IPAP method, while enhancing sensitivity by ca 35 %. As a practical application of LOW-BASHD decoupling, requiring quantitative intensity measurement over a wide dynamic range, the impact of lipid binding on the (13)C'-detected NCO spectrum of the intrinsically disordered protein alpha-synuclein is compared with that on the (1)H-detected (1)H-(15)N HSQC spectrum. Results confirm that synuclein's "dark state" behavior is not caused by paramagnetic relaxation or rapid hydrogen exchange. FAU - Ying, Jinfa AU - Ying J AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA. FAU - Li, Fang AU - Li F FAU - Lee, Jung Ho AU - Lee JH FAU - Bax, Ad AU - Bax A LA - eng GR - ZIA DK029046-07/Intramural NIH HHS/United States GR - ZIA DK029047-07/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't DEP - 20140817 PL - Netherlands TA - J Biomol NMR JT - Journal of biomolecular NMR JID - 9110829 RN - 0 (Carbon Isotopes) RN - 0 (Lipids) RN - 0 (Proteins) RN - 0 (alpha-Synuclein) SB - IM MH - Carbon Isotopes/*chemistry MH - Lipids/chemistry MH - Models, Chemical MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Proteins/*chemistry MH - alpha-Synuclein PMC - PMC4156133 MID - NIHMS621738 OID - NLM: NIHMS621738 [Available on 09/01/15] OID - NLM: PMC4156133 [Available on 09/01/15] EDAT- 2014/08/19 06:00 MHDA- 2015/05/13 06:00 CRDT- 2014/08/18 06:00 PMCR- 2015/09/01 00:00 PHST- 2014/06/12 [received] PHST- 2014/08/04 [accepted] PHST- 2014/08/17 [aheadofprint] AID - 10.1007/s10858-014-9853-z [doi] PST - ppublish SO - J Biomol NMR. 2014 Sep;60(1):15-21. doi: 10.1007/s10858-014-9853-z. Epub 2014 Aug 17. PMID- 6854633 OWN - NLM STAT- MEDLINE DA - 19830729 DCOM- 19830729 LR - 20071114 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 166 IP - 1 DP - 1983 May 5 TI - Subunit interactions in southern bean mosaic virus. PG - 37-73 FAU - Rossmann, M G AU - Rossmann MG FAU - Abad-Zapatero, C AU - Abad-Zapatero C FAU - Hermodson, M A AU - Hermodson MA FAU - Erickson, J W AU - Erickson JW LA - eng GR - AI 11219/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (RNA, Viral) RN - 0 (Viral Proteins) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Models, Molecular MH - Mosaic Viruses/*analysis MH - Protein Conformation MH - RNA, Viral MH - *Viral Proteins MH - X-Ray Diffraction EDAT- 1983/05/05 MHDA- 1983/05/05 00:01 CRDT- 1983/05/05 00:00 PST - ppublish SO - J Mol Biol. 1983 May 5;166(1):37-73. PMID- 16049787 OWN - NLM STAT- MEDLINE DA - 20050728 DCOM- 20060111 LR - 20131121 IS - 0166-8595 (Print) IS - 0166-8595 (Linking) VI - 84 IP - 1-3 DP - 2005 Jun TI - Assembly and function of the photosystem II manganese stabilizing protein: lessons from its natively unfolded behavior. PG - 283-8 AB - The Photosystem II (PS II) manganese stabilizing protein (MSP) possesses characteristics, including thermostability, ascribed to the natively unfolded class of proteins (Lydakis-Simantiris et al. (1999) Biochemistry 38: 404-414). A site-directed mutant of MSP, C28A, C51A, which lacks the -S-S- bridge, also binds to PS II at wild-type levels and reconstitutes oxygen evolution activity [Betts et al. (1996) Biochim Biophys Acta 1274: 135-142], although the mutant protein is even more disordered in solution. Both WT and C28A, C51A MSP aggregate upon heating, but an examination of the effects of protein concentration and pH on heat-induced aggregation showed that each MSP species exhibited greater resistance to aggregation at a pH near their pI (5.2) than do either bovine serum albumin (BSA) or carbonic anhydrase, which were used as model water soluble proteins. Increases in pH above the pI of the MSPs and BSA enhanced their aggregation resistance, a behavior which can be predicted from their charge (MSP) or a combination of charge and stabilization by -S-S- bonds (BSA). In the case of aggregation resistance by MSP, this is likely to be an important factor in its ability to avoid unproductive self-association reactions in favor of formation of the protein-protein interactions that lead to formation of the functional oxygen evolving complex. FAU - Wyman, Aaron J AU - Wyman AJ AD - Department of Molecular, Cellular, and Developmental Biology, The University of Michigan-Ann Arbor, MI 48109, USA. FAU - Yocum, Charles F AU - Yocum CF LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - Netherlands TA - Photosynth Res JT - Photosynthesis research JID - 100954728 RN - 0 (Disulfides) RN - 0 (Photosystem II Protein Complex) RN - 0 (Serum Albumin, Bovine) RN - 0 (photosystem II manganese-stabilizing protein) RN - 42Z2K6ZL8P (Manganese) RN - EC 4.2.1.1 (Carbonic Anhydrases) SB - IM MH - Animals MH - Carbonic Anhydrases/chemistry MH - Cattle MH - Circular Dichroism MH - Disulfides/metabolism MH - Hot Temperature MH - Hydrogen-Ion Concentration MH - Manganese/*chemistry MH - Mutagenesis, Site-Directed MH - Photosystem II Protein Complex/*chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Denaturation MH - *Protein Folding MH - Serum Albumin, Bovine/chemistry EDAT- 2005/07/29 09:00 MHDA- 2006/01/13 09:00 CRDT- 2005/07/29 09:00 PHST- 2004/12/16 [received] PHST- 2004/12/16 [accepted] AID - 10.1007/s11120-004-7759-4 [doi] PST - ppublish SO - Photosynth Res. 2005 Jun;84(1-3):283-8. PMID- 11896058 OWN - NLM STAT- MEDLINE DA - 20020528 DCOM- 20020702 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 277 IP - 22 DP - 2002 May 31 TI - Conformational analysis of the androgen receptor amino-terminal domain involved in transactivation. Influence of structure-stabilizing solutes and protein-protein interactions. PG - 20079-86 AB - The androgen receptor (AR) is a member of the nuclear receptor superfamily. Sequences within the large amino-terminal domain of the receptor have been shown to be important for transactivation and protein-protein interactions; however, little is known about the structure and folding of this region. In the present study we show that a 344-amino acid polypeptide representing the main determinants for transactivation has the propensity to form alpha-helical structure and that mutations which disrupt putative helical regions alter conformation. Folding of the AR was observed in the presence of the helix-stabilizing solvent trifluoroethanol and the natural osmolyte trimethylamine N-oxide (TMAO). TMAO resulted in the movement of two tryptophan residues to a less solvent-exposed environment and the formation of secondary/tertiary structure resistant to protease cleavage. Critically, binding to the RAP74 subunit of the general transcription factor TFIIF resulted in extensive protease resistance, consistent with induced folding of the receptor transactivation domain. These data indicate that this region of the AR is structurally flexible and folds into a stable conformation upon interactions with a component of the general transcription machinery. FAU - Reid, James AU - Reid J AD - Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom. FAU - Kelly, Sharon M AU - Kelly SM FAU - Watt, Kate AU - Watt K FAU - Price, Nicholas C AU - Price NC FAU - McEwan, Iain J AU - McEwan IJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20020314 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Ligands) RN - 0 (Methylamines) RN - 0 (Receptors, Androgen) RN - 8DUH1N11BX (Tryptophan) RN - EC 2.5.1.18 (Glutathione Transferase) RN - EC 3.4.21.4 (Trypsin) RN - FLD0K1SJ1A (trimethyloxamine) SB - IM MH - Circular Dichroism MH - Glutathione Transferase/metabolism MH - Humans MH - Ligands MH - Methylamines/pharmacology MH - Mutagenesis, Site-Directed MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Receptors, Androgen/*chemistry MH - Spectrometry, Fluorescence MH - *Transcriptional Activation MH - Trypsin/pharmacology MH - Tryptophan/chemistry EDAT- 2002/03/16 10:00 MHDA- 2002/07/03 10:01 CRDT- 2002/03/16 10:00 PHST- 2002/03/14 [aheadofprint] AID - 10.1074/jbc.M201003200 [doi] AID - M201003200 [pii] PST - ppublish SO - J Biol Chem. 2002 May 31;277(22):20079-86. Epub 2002 Mar 14. PMID- 25267253 OWN - NLM STAT- In-Process DA - 20141201 IS - 1875-5305 (Electronic) IS - 0929-8665 (Linking) VI - 22 IP - 1 DP - 2015 TI - Assessment of the effect of macromolecular crowding on aggregation behaviour of a model amyloidogenic Peptide. PG - 87-93 AB - Accumulation of ordered protein aggregates (or amyloids) represents a hallmark of many diseases (e.g., Alzheimer's disease, type II diabetes, Parkinson's diseases etc.), results from intermolecular association of partially unfolded proteins/ peptides. Such associations usually take place in highly crowded conditions. The aggregates, which are formed under in vitro and in vivo conditions exhibit substantial variations in their structure and function. Such heterogeneities in amyloids might arise due to macromolecular crowding that is usually omitted under in vitro conditions. The current study is an attempt to assess the effects of macromolecular crowding on amyloid formation using a model amyloidogenic peptide. The sequence of the peptide was derived from C-terminal region (RATQIPSYKKLIMY) of PAP(248-286), which naturally occurs in human semen as amyloid aggregates and is known for boosting HIV infectivity. This model peptide forms sedimentable and fibrillar aggregates in aqueous buffer and shows the characteristic features of amyloids. In the presence of macromolecular crowders the morphological features of the amyloids are significantly altered and resulted in the formation of shorter amyloid aggregates. The current study assumes the hypothesis that macromolecular crowding in the biological system favours formation of heterogeneous classes of aggregates and each of them might differ in their biophysical and biological properties. FAU - Gaharwar, Bharti AU - Gaharwar B FAU - Gour, Shalini AU - Gour S FAU - Kaushik, Vibha AU - Kaushik V FAU - Gupta, Nimisha AU - Gupta N FAU - Kumar, Vijay AU - Kumar V FAU - Hause, Gerd AU - Hause G FAU - Yadav, Jay Kant AU - Yadav JK AD - Department of Biotechnology, Central University of Rajasthan, Bandersindri, NH-8 Jaipur- Ajmer Highway, Dist.- Ajmer. PIN 305 801, Rajasthan, India. jaykantyadav@curaj.ac.in. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 SB - IM EDAT- 2014/10/01 06:00 MHDA- 2014/10/01 06:00 CRDT- 2014/10/01 06:00 PHST- 2014/06/30 [received] PHST- 2014/09/20 [revised] PHST- 2014/09/20 [accepted] AID - PPL-EPUB-62530 [pii] PST - ppublish SO - Protein Pept Lett. 2015;22(1):87-93. PMID- 22166445 OWN - NLM STAT- MEDLINE DA - 20111214 DCOM- 20120827 IS - 1873-5126 (Electronic) IS - 1353-8020 (Linking) VI - 18 Suppl 1 DP - 2012 Jan TI - Synucleinopathies from bench to bedside. PG - S24-7 LID - 10.1016/S1353-8020(11)70010-4 [doi] AB - Accumulation of alpha-synuclein is a pathological feature in several neurological diseases. Its characterization has allowed for a re-grouping of diseases according to the expected pathology. The clinical syndrome of PD can now be classified into forms with and without alpha-synuclein pathology. DLB and PDD are synucleinopathies, and MSA shows alpha-synuclein pathology with glial inclusions. ADHD symptoms commonly occur in persons that will subsequently develop DLB. A similar phenomenon may be the early personality changes and frontotemporal atrophy in patients with SNCA multiplication. RLS is not known to have alpha-synuclein pathology, but as PD and ADHD, involves a hypodopaminergic state. Furthermore, PD and RLS co-occur in families in a way that suggests common inheritance. A proportion of patients with ET have brainstem Lewy body pathology. Gaucher disease and other lysosomal storage disorders also have alpha-synuclein pathology. Alpha-synuclein is a naturally unfolded protein. Non-fibrillar oligomeres may be the toxic species, and Lewy body formation may in fact be protective. Inhibiting alpha-synuclein toxicity seems to be an attractive novel treatment strategy and several approaches are being developed. When such treatments become available, clinicians will need to be familiar with the clinical features that distinguish the synucleinopathies from their look-alikes. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Puschmann, Andreas AU - Puschmann A AD - Department for Geriatric Psychiatry, Lund University, Sweden. andreas.puschmann@med.lu.se FAU - Bhidayasiri, Roongroj AU - Bhidayasiri R FAU - Weiner, William J AU - Weiner WJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Parkinsonism Relat Disord JT - Parkinsonism & related disorders JID - 9513583 RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Brain Chemistry/genetics/physiology MH - Humans MH - Lewy Body Disease/genetics/*metabolism/*pathology MH - Parkinson Disease/genetics/*metabolism/*pathology MH - Synucleins/*adverse effects/genetics/physiology MH - alpha-Synuclein/*adverse effects/genetics/metabolism EDAT- 2011/12/23 06:00 MHDA- 2012/08/28 06:00 CRDT- 2011/12/15 06:00 AID - S1353-8020(11)70010-4 [pii] AID - 10.1016/S1353-8020(11)70010-4 [doi] PST - ppublish SO - Parkinsonism Relat Disord. 2012 Jan;18 Suppl 1:S24-7. doi: 10.1016/S1353-8020(11)70010-4. PMID- 15341725 OWN - NLM STAT- MEDLINE DA - 20040902 DCOM- 20050516 LR - 20071114 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 12 IP - 9 DP - 2004 Sep TI - The crystal and solution structure of a putative transcriptional antiterminator from Mycobacterium tuberculosis. PG - 1595-605 AB - We describe the crystal structure of Rv1626 from Mycobacterium tuberculosis at 1.48 A resolution and the corresponding solution structure determined from small angle X-ray scattering. The N-terminal domain shows structural homology to the receiver domains found in bacterial two-component systems. The C-terminal domain has high structural homology to a recently discovered RNA binding domain involved in transcriptional antitermination. The molecule in solution was found to be monomeric as it is in the crystal, but in solution it undergoes a conformational change that is triggered by changes in ionic strength. This is the first structure that links the phosphorylation cascade of the two-component systems with the antitermination event in the transcriptional machinery. Rv1626 belongs to a family of proteins, which we propose calling phosphorylation-dependent transcriptional antitermination regulators, so far only found in bacteria, and includes NasT, a protein from the assimilatory nitrate/nitrite reductase operon of Azetobacter vinelandii. FAU - Morth, J Preben AU - Morth JP AD - EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, Germany. FAU - Feng, Vicki AU - Feng V FAU - Perry, L Jeanne AU - Perry LJ FAU - Svergun, Dmitri I AU - Svergun DI FAU - Tucker, Paul A AU - Tucker PA LA - eng SI - PDB/1S8N SI - PDB/1SD5 GR - N01 AI-75320/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Bacterial Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (NAST protein, Azotobacter vinelandii) RN - 0 (RNA-Binding Proteins) RN - 0 (Trans-Activators) RN - 0 (antiterminator proteins, Bacteria) RN - 123940-13-6 (NarL protein, E coli) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/genetics/*metabolism MH - Crystallography, X-Ray MH - DNA-Binding Proteins/chemistry MH - Escherichia coli Proteins/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Mycobacterium tuberculosis/*chemistry/genetics MH - Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - RNA-Binding Proteins/*chemistry/genetics/*metabolism MH - Sequence Alignment MH - Trans-Activators/chemistry/genetics EDAT- 2004/09/03 05:00 MHDA- 2005/05/17 09:00 CRDT- 2004/09/03 05:00 PHST- 2004/05/18 [received] PHST- 2004/06/22 [revised] PHST- 2004/06/24 [accepted] AID - 10.1016/j.str.2004.06.018 [doi] AID - S0969212604002710 [pii] PST - ppublish SO - Structure. 2004 Sep;12(9):1595-605. PMID- 21856750 OWN - NLM STAT- MEDLINE DA - 20111010 DCOM- 20111212 LR - 20141022 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 41 DP - 2011 Oct 14 TI - Senescence-associated barley NAC (NAM, ATAF1,2, CUC) transcription factor interacts with radical-induced cell death 1 through a disordered regulatory domain. PG - 35418-29 LID - 10.1074/jbc.M111.247221 [doi] AB - Senescence in plants involves massive nutrient relocation and age-related cell death. Characterization of the molecular components, such as transcription factors (TFs), involved in these processes is required to understand senescence. We found that HvNAC005 and HvNAC013 of the plant-specific NAC (NAM, ATAF1,2, CUC) TF family are up-regulated during senescence in barley (Hordeum vulgare). Both HvNAC005 and HvNAC013 bound the conserved NAC DNA target sequence. Computational and biophysical analyses showed that both proteins are intrinsically disordered in their large C-terminal domains, which are transcription regulatory domains (TRDs) in many NAC TFs. Using motif searches and interaction studies in yeast we identified an evolutionarily conserved sequence, the LP motif, in the TRD of HvNAC013. This motif was sufficient for transcriptional activity. In contrast, HvNAC005 did not function as a transcriptional activator suggesting that an involvement of HvNAC013 and HvNAC005 in senescence will be different. HvNAC013 interacted with barley radical-induced cell death 1 (RCD1) via the very C-terminal part of its TRD, outside of the region containing the LP motif. No significant secondary structure was induced in the HvNAC013 TRD upon interaction with RCD1. RCD1 also interacted with regions dominated by intrinsic disorder in TFs of the MYB and basic helix-loop-helix families. We propose that RCD1 is a regulatory protein capable of interacting with many different TFs by exploiting their intrinsic disorder. In addition, we present the first structural characterization of NAC C-terminal domains and relate intrinsic disorder and sequence motifs to activity and protein-protein interactions. FAU - Kjaersgaard, Trine AU - Kjaersgaard T AD - Department of Biology, University of Copenhagen, Ole Maaloesvej 5, Copenhagen DK-2200, Denmark. FAU - Jensen, Michael K AU - Jensen MK FAU - Christiansen, Michael W AU - Christiansen MW FAU - Gregersen, Per AU - Gregersen P FAU - Kragelund, Birthe B AU - Kragelund BB FAU - Skriver, Karen AU - Skriver K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110819 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Nuclear Proteins) RN - 0 (Plant Proteins) RN - 0 (Transcription Factors) SB - IM MH - Cell Aging/*physiology MH - Evolution, Molecular MH - Helix-Loop-Helix Motifs MH - Hordeum/genetics/*metabolism MH - Nuclear Proteins/genetics/*metabolism MH - Plant Proteins/genetics/*metabolism MH - Protein Structure, Tertiary MH - Transcription Factors/genetics/*metabolism PMC - PMC3195629 OID - NLM: PMC3195629 EDAT- 2011/08/23 06:00 MHDA- 2011/12/14 06:00 CRDT- 2011/08/23 06:00 PHST- 2011/08/19 [aheadofprint] AID - M111.247221 [pii] AID - 10.1074/jbc.M111.247221 [doi] PST - ppublish SO - J Biol Chem. 2011 Oct 14;286(41):35418-29. doi: 10.1074/jbc.M111.247221. Epub 2011 Aug 19. PMID- 11756460 OWN - NLM STAT- MEDLINE DA - 20020304 DCOM- 20020415 LR - 20081121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 277 IP - 10 DP - 2002 Mar 8 TI - Unusual structural organization of the endocytic proteins AP180 and epsin 1. PG - 8209-16 AB - Epsin and AP180/CALM are important endocytic accessory proteins that are believed to be involved in the formation of clathrin coats. Both proteins associate with phosphorylated membrane inositol lipids through their epsin N-terminal homology domains and with other components of the endocytic machinery through short peptide motifs in their carboxyl-terminal segments. Using hydrodynamic and spectroscopic methods, we demonstrate that the parts of epsin 1 and AP180 that are involved in protein-protein interactions behave as poorly structured flexible polypeptide chains with little or no conventional secondary structure. The predominant cytosolic forms of both proteins are monomers. Furthermore, we show that recombinant epsin 1, like AP180, drives in vitro assembly of clathrin cages. We conclude that the epsin N-terminal homology domain-containing proteins AP180/CALM and epsin 1 have a very similar molecular architecture that is designed for the rapid and efficient recruitment of the principal coat components clathrin and AP-2 at the sites of coated pit assembly. FAU - Kalthoff, Christoph AU - Kalthoff C AD - Department of Cell Biology, Center of Anatomy, Hannover Medical School, D-30125 Hannover, Germany. FAU - Alves, Jurgen AU - Alves J FAU - Urbanke, Claus AU - Urbanke C FAU - Knorr, Ruth AU - Knorr R FAU - Ungewickell, Ernst J AU - Ungewickell EJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20011226 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Adaptor Proteins, Vesicular Transport) RN - 0 (Carrier Proteins) RN - 0 (Membrane Proteins) RN - 0 (Monomeric Clathrin Assembly Proteins) RN - 0 (Neuropeptides) RN - 0 (PICALM protein, human) RN - 0 (Peptides) RN - 0 (Recombinant Proteins) RN - 0 (Vesicular Transport Proteins) RN - 0 (clathrin assembly protein AP180) RN - 0 (epsin) RN - 57-50-1 (Sucrose) SB - IM MH - Adaptor Proteins, Vesicular Transport MH - Animals MH - Brain/metabolism MH - Carrier Proteins/*chemistry MH - Cell Membrane/metabolism MH - Centrifugation, Density Gradient MH - Chromatography, Gel MH - Circular Dichroism MH - Cytosol/metabolism MH - Electrophoresis, Polyacrylamide Gel MH - *Endocytosis MH - Hot Temperature MH - Kinetics MH - Membrane Proteins/*chemistry MH - Models, Molecular MH - *Monomeric Clathrin Assembly Proteins MH - Neuropeptides/*chemistry MH - Peptides/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Sucrose/pharmacology MH - Swine MH - *Vesicular Transport Proteins EDAT- 2002/01/05 10:00 MHDA- 2002/04/16 10:01 CRDT- 2002/01/05 10:00 PHST- 2001/12/26 [aheadofprint] AID - 10.1074/jbc.M111587200 [doi] AID - M111587200 [pii] PST - ppublish SO - J Biol Chem. 2002 Mar 8;277(10):8209-16. Epub 2001 Dec 26. PMID- 23811056 OWN - NLM STAT- MEDLINE DA - 20130826 DCOM- 20131210 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 425 IP - 18 DP - 2013 Sep 23 TI - Dissecting partner recognition by an intrinsically disordered protein using descriptive random mutagenesis. PG - 3495-509 LID - 10.1016/j.jmb.2013.06.025 [doi] LID - S0022-2836(13)00405-1 [pii] AB - In view of getting insights into the molecular determinants of the binding efficiency of intrinsically disordered proteins (IDPs), we used random mutagenesis. As a proof of concept, we chose the interaction between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) and the X domain (XD) of the viral phosphoprotein and assessed how amino acid substitutions introduced at random within NTAIL affect partner recognition. In contrast with directed evolution approaches, we did not apply any selection and used the gene library approach not for production purposes but for achieving a better understanding of the NTAIL/XD interaction. For that reason, and to differentiate our approach from similar approaches that make use of systematic (i.e., targeted) mutagenesis, we propose to call it "descriptive random mutagenesis" (DRM). NTAIL variants generated by error-prone PCR were picked at random in the absence of selection pressure and were characterized in terms of sequence and binding abilities toward XD. DRM not only identified determinants of NTAIL/XD interaction that were in good agreement with previous work but also provided new insights. In particular, we discovered that the primary interaction site is poorly evolvable in terms of binding abilities toward XD. We also identified a critical NTAIL residue whose role in stabilizing the NTAIL/XD complex had previously escaped detection, and we identified NTAIL regulatory sites that dampen the interaction while being located outside the primary interaction site. Results show that DRM is a valuable approach to study binding abilities of IDPs. CI - (c) 2013 Elsevier Ltd. All rights reserved. FAU - Gruet, Antoine AU - Gruet A AD - CNRS and Aix-Marseille Universite, Architecture et Fonction des Macromolecules Biologiques, UMR 7257, 13288 Marseille, France. FAU - Dosnon, Marion AU - Dosnon M FAU - Vassena, Andrea AU - Vassena A FAU - Lombard, Vincent AU - Lombard V FAU - Gerlier, Denis AU - Gerlier D FAU - Bignon, Christophe AU - Bignon C FAU - Longhi, Sonia AU - Longhi S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130625 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Peptide Library) RN - 0 (Recombinant Fusion Proteins) RN - 147336-22-9 (Green Fluorescent Proteins) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution/physiology MH - Fluorescence MH - Green Fluorescent Proteins/chemistry/genetics/metabolism MH - Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis/*physiology MH - Mutation/physiology MH - Peptide Library MH - Protein Binding MH - *Protein Folding MH - Protein Interaction Mapping/*methods MH - Protein Stability MH - Recombinant Fusion Proteins/chemistry/genetics/metabolism OTO - NOTNLM OT - DRM OT - GFP OT - IDP OT - Intrinsically disordered protein OT - MeV OT - MoRE OT - descriptive random mutagenesis OT - green fluorescent protein OT - library OT - measles virus OT - molecular recognition element OT - partner recognition OT - protein complementation assay OT - protein-protein interactions OT - split-GFP reassembly EDAT- 2013/07/03 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/07/02 06:00 PHST- 2013/03/26 [received] PHST- 2013/06/14 [revised] PHST- 2013/06/18 [accepted] PHST- 2013/06/25 [aheadofprint] AID - S0022-2836(13)00405-1 [pii] AID - 10.1016/j.jmb.2013.06.025 [doi] PST - ppublish SO - J Mol Biol. 2013 Sep 23;425(18):3495-509. doi: 10.1016/j.jmb.2013.06.025. Epub 2013 Jun 25. PMID- 23811057 OWN - NLM STAT- MEDLINE DA - 20130826 DCOM- 20131210 LR - 20141113 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 425 IP - 18 DP - 2013 Sep 23 TI - Abeta monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach. PG - 3338-59 LID - 10.1016/j.jmb.2013.06.021 [doi] LID - S0022-2836(13)00401-4 [pii] AB - Amyloid beta (Abeta) peptides are a primary component of fibrils and oligomers implicated in the etiology of Alzheimer's disease (AD). However, the intrinsic flexibility of these peptides has frustrated efforts to investigate the secondary and tertiary structure of Abeta monomers, whose conformational landscapes directly contribute to the kinetics and thermodynamics of Abeta aggregation. In this work, de novo replica exchange molecular dynamics (REMD) simulations on the microseconds-per-replica timescale are used to characterize the structural ensembles of Abeta42, Abeta40, and M35-oxidized Abeta42, three physiologically relevant isoforms with substantially different aggregation properties. J-coupling data calculated from the REMD trajectories were compared to corresponding NMR-derived values acquired through two different pulse sequences, revealing that all simulations converge on the order of hundreds of nanoseconds-per-replica toward ensembles that yield good agreement with experiment. Though all three Abeta species adopt highly heterogeneous ensembles, these are considerably more structured compared to simulations on shorter timescales. Prominent in the C-terminus are antiparallel beta-hairpins between L17-A21, A30-L36, and V39-I41, similar to oligomer and fibril intrapeptide models that expose these hydrophobic side chains to solvent and may serve as hotspots for self-association. Compared to reduced Abeta42, the absence of a second beta-hairpin in Abeta40 and the sampling of alternate beta topologies by M35-oxidized Abeta42 may explain the reduced aggregation rates of these forms. A persistent V24-K28 bend motif, observed in all three species, is stabilized by buried backbone to side-chain hydrogen bonds with D23 and a cross-region salt bridge between E22 and K28, highlighting the role of the familial AD-linked E22 and D23 residues in Abeta monomer folding. These characterizations help illustrate the conformational landscapes of Abeta monomers at atomic resolution and provide insight into the early stages of Abeta aggregation pathways. CI - Copyright (c) 2013 Elsevier Ltd. All rights reserved. FAU - Rosenman, David J AU - Rosenman DJ AD - Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA. FAU - Connors, Christopher R AU - Connors CR FAU - Chen, Wen AU - Chen W FAU - Wang, Chunyu AU - Wang C FAU - Garcia, Angel E AU - Garcia AE LA - eng GR - 5T32 GM067545-08/GM/NIGMS NIH HHS/United States GR - T32 GM067545/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130625 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amyloid beta-Peptides) SB - IM MH - Amino Acid Sequence MH - Amyloid beta-Peptides/*chemistry/*metabolism MH - Humans MH - Hydrogen Bonding MH - Hydrophobic and Hydrophilic Interactions MH - Models, Biological MH - Models, Molecular MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Protein Conformation MH - Protein Interaction Mapping/methods MH - Protein Multimerization MH - Thermodynamics PMC - PMC3780797 MID - NIHMS500656 OID - NLM: NIHMS500656 OID - NLM: PMC3780797 OTO - NOTNLM OT - (3)J(HNHA) couplings OT - AD OT - Alzheimer's disease OT - Abeta OT - CHC OT - FAD OT - HSQC OT - IDP OT - PCC OT - PDB OT - Pearson correlation coefficient OT - Protein Data Bank OT - RDC OT - REMD OT - amyloid beta OT - central hydrophobic cluster OT - familial Alzheimer's disease OT - free-energy landscape OT - heteronuclear single quantum coherence OT - iRED OT - intrinsically disordered protein OT - isotropic reorientational eigenmode dynamics OT - molecular dynamics simulations OT - replica exchange molecular dynamics OT - residual dipolar coupling OT - residual dipolar couplings EDAT- 2013/07/03 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/07/02 06:00 PHST- 2013/01/28 [received] PHST- 2013/05/15 [revised] PHST- 2013/06/12 [accepted] PHST- 2013/06/25 [aheadofprint] AID - S0022-2836(13)00401-4 [pii] AID - 10.1016/j.jmb.2013.06.021 [doi] PST - ppublish SO - J Mol Biol. 2013 Sep 23;425(18):3338-59. doi: 10.1016/j.jmb.2013.06.021. Epub 2013 Jun 25. PMID- 22280219 OWN - NLM STAT- MEDLINE DA - 20120229 DCOM- 20120626 LR - 20141019 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 134 IP - 8 DP - 2012 Feb 29 TI - Quantitative analysis of multisite protein-ligand interactions by NMR: binding of intrinsically disordered p53 transactivation subdomains with the TAZ2 domain of CBP. PG - 3792-803 LID - 10.1021/ja209936u [doi] AB - Determination of affinities and binding sites involved in protein-ligand interactions is essential for understanding molecular mechanisms in biological systems. Here we combine singular value decomposition and global analysis of NMR chemical shift perturbations caused by protein-protein interactions to determine the number and location of binding sites on the protein surface and to measure the binding affinities. Using this method we show that the isolated AD1 and AD2 binding motifs, derived from the intrinsically disordered N-terminal transactivation domain of the tumor suppressor p53, both interact with the TAZ2 domain of the transcriptional coactivator CBP at two binding sites. Simulations of titration curves and line shapes show that a primary dissociation constant as small as 1-10 nM can be accurately estimated by NMR titration methods, provided that the primary and secondary binding processes are coupled. Unexpectedly, the site of binding of AD2 on the hydrophobic surface of TAZ2 overlaps with the binding site for AD1, but AD2 binds TAZ2 more tightly. The results highlight the complexity of interactions between intrinsically disordered proteins and their targets. Furthermore, the association rate of AD2 to TAZ2 is estimated to be 1.7 x 10(10) M(-1) s(-1), approaching the diffusion-controlled limit and indicating that intrinsic disorder plus complementary electrostatics can significantly accelerate protein binding interactions. CI - (c) 2012 American Chemical Society FAU - Arai, Munehito AU - Arai M AD - Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. FAU - Ferreon, Josephine C AU - Ferreon JC FAU - Wright, Peter E AU - Wright PE LA - eng GR - CA96865/CA/NCI NIH HHS/United States GR - R01 CA096865/CA/NCI NIH HHS/United States GR - R01 CA096865-10/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120215 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Ligands) RN - 0 (Tumor Suppressor Protein p53) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Binding Sites MH - CREB-Binding Protein/*chemistry MH - Ligands MH - Models, Molecular MH - *Nuclear Magnetic Resonance, Biomolecular MH - *Protein Interaction Domains and Motifs MH - Tumor Suppressor Protein p53/*chemistry PMC - PMC3290704 MID - NIHMS354230 OID - NLM: NIHMS354230 OID - NLM: PMC3290704 EDAT- 2012/01/28 06:00 MHDA- 2012/06/27 06:00 CRDT- 2012/01/28 06:00 PHST- 2012/02/15 [aheadofprint] AID - 10.1021/ja209936u [doi] PST - ppublish SO - J Am Chem Soc. 2012 Feb 29;134(8):3792-803. doi: 10.1021/ja209936u. Epub 2012 Feb 15. PMID- 23827411 OWN - NLM STAT- MEDLINE DA - 20130910 DCOM- 20140320 IS - 1873-4200 (Electronic) IS - 0301-4622 (Linking) VI - 180-181 DP - 2013 Oct-Nov TI - P130Cas substrate domain is intrinsically disordered as characterized by single-molecule force measurements. PG - 37-43 LID - 10.1016/j.bpc.2013.06.008 [doi] LID - S0301-4622(13)00097-5 [pii] AB - P130Cas is a docking protein essentially coordinating tyrosine-kinase-based signaling pathways associated with cell adhesion and migration etc. Its central substrate domain (CasSD) can bind to Crk and includes 15 YxxP motifs, where most tyrosine phosphorylation happens. It has been shown that CasSD can be stretched to promote phosphorylation, the mechanism of which needs to be explored in detail. Thus, it is important to uncover the native structure(s) of CasSD and the structural changes associated with mechanical stretching, both of which are still unclear. Here, we used atomic force microscopy force mode and magnetic tweezers to stretch individual molecules of CasSD constructs. Our results showed that the CasSD domain was intrinsically disordered. Natively, CasSD domains took many conformations beside random coils, while most of these conformations possessed limited mechanical stability. In magnetic tweezers experiments, the intramolecular interactions stabilizing the varied native conformations of CasSD were found similar in strength. Such diversity in native conformations of CasSD domains, as discovered here, should play important role in their signaling functions and their limited strength should be relevant to the mechanical activation of those signaling pathways. CI - Copyright (c) 2013 Elsevier B.V. All rights reserved. FAU - Lu, Chen AU - Lu C AD - College of Physics, Chongqing University, No. 55 Daxuecheng South Road, Shapingba District, Chongqing 401331, China; Department of Physics, National University of Singapore, 2 Science Drive 3 117551, Singapore; Mechanobiology Institute, National University of Singapore, 5A Engineering Drive 1 117411, Singapore. FAU - Wu, Fei AU - Wu F FAU - Qiu, Wu AU - Qiu W FAU - Liu, Ruchuan AU - Liu R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130618 PL - Netherlands TA - Biophys Chem JT - Biophysical chemistry JID - 0403171 RN - 0 (BCAR1 protein, human) RN - 0 (Crk-Associated Substrate Protein) RN - 0 (Recombinant Proteins) SB - IM MH - Amino Acid Motifs MH - Crk-Associated Substrate Protein/*chemistry/genetics/metabolism MH - Humans MH - Microscopy, Atomic Force MH - Phosphorylation MH - Protein Denaturation MH - Protein Structure, Tertiary MH - Recombinant Proteins/biosynthesis/chemistry/genetics MH - Signal Transduction MH - Substrate Specificity OTO - NOTNLM OT - AFM OT - Intrinsically disordered protein OT - Magnetic tweezer OT - Mechano-transduction OT - Tyrosine phosphorylation OT - p130Cas EDAT- 2013/07/06 06:00 MHDA- 2014/03/22 06:00 CRDT- 2013/07/06 06:00 PHST- 2013/05/02 [received] PHST- 2013/06/09 [revised] PHST- 2013/06/11 [accepted] PHST- 2013/06/18 [aheadofprint] AID - S0301-4622(13)00097-5 [pii] AID - 10.1016/j.bpc.2013.06.008 [doi] PST - ppublish SO - Biophys Chem. 2013 Oct-Nov;180-181:37-43. doi: 10.1016/j.bpc.2013.06.008. Epub 2013 Jun 18. PMID- 11707391 OWN - NLM STAT- MEDLINE DA - 20011114 DCOM- 20020117 LR - 20140613 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 20 IP - 22 DP - 2001 Nov 15 TI - Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture. PG - 6191-202 AB - The recently published human genome with its relatively modest number of genes has highlighted the importance of post-transcriptional and post-translational modifications, such as alternative splicing or glycosylation, in generating the complexities of human biology. The human UDP-N-acetylglucosamine (UDPGlcNAc) pyrophosphorylases AGX1 and AGX2, which differ in sequence by an alternatively spliced 17 residue peptide, are key enzymes synthesizing UDPGlcNAc, an essential precursor for protein glycosylation. To better understand the catalytic mechanism of these enzymes and the role of the alternatively spliced segment, we have solved the crystal structures of AGX1 and AGX2 in complexes with UDPGlcNAc (at 1.9 and 2.4 A resolution, respectively) and UDPGalNAc (at 2.2 and 2.3 A resolution, respectively). Comparison with known structures classifies AGX1 and AGX2 as two new members of the SpsA-GnT I Core superfamily and, together with mutagenesis analysis, helps identify residues critical for catalysis. Most importantly, our combined structural and biochemical data provide evidence for a change in the oligomeric assembly accompanied by a significant modification of the active site architecture, a result suggesting that the two isoforms generated by alternative splicing may have distinct catalytic properties. FAU - Peneff, C AU - Peneff C AD - AFMB, UMR 6098 CNRS, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. FAU - Ferrari, P AU - Ferrari P FAU - Charrier, V AU - Charrier V FAU - Taburet, Y AU - Taburet Y FAU - Monnier, C AU - Monnier C FAU - Zamboni, V AU - Zamboni V FAU - Winter, J AU - Winter J FAU - Harnois, M AU - Harnois M FAU - Fassy, F AU - Fassy F FAU - Bourne, Y AU - Bourne Y LA - eng SI - PDB/1JV1 SI - PDB/1JV3 SI - PDB/1JVD SI - PDB/1JVG PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Monosaccharide Transport Proteins) RN - 0 (Protein Isoforms) RN - 0 (SLC35D1 protein, human) RN - EC 2.7.7.10 (UTP-Hexose-1-Phosphate Uridylyltransferase) SB - IM MH - Alternative Splicing MH - Amino Acid Sequence MH - Animals MH - Astrocytes/metabolism MH - Binding Sites MH - Cartilage/metabolism MH - Catalysis MH - Catalytic Domain MH - Chromatography, Gel MH - Crystallography, X-Ray MH - Dimerization MH - Expressed Sequence Tags MH - Glycosylation MH - Humans MH - Kinetics MH - Models, Chemical MH - Models, Molecular MH - Molecular Sequence Data MH - Monosaccharide Transport Proteins/*chemistry/*metabolism MH - Mutagenesis, Site-Directed MH - Protein Binding MH - Protein Folding MH - Protein Isoforms MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - UTP-Hexose-1-Phosphate Uridylyltransferase/*chemistry/*genetics/metabolism PMC - PMC125729 OID - NLM: PMC125729 EDAT- 2001/11/15 10:00 MHDA- 2002/01/18 10:01 CRDT- 2001/11/15 10:00 AID - 10.1093/emboj/20.22.6191 [doi] PST - ppublish SO - EMBO J. 2001 Nov 15;20(22):6191-202. PMID- 16787768 OWN - NLM STAT- MEDLINE DA - 20060726 DCOM- 20060926 LR - 20131121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1764 IP - 7 DP - 2006 Jul TI - The pH-dependence of amide chemical shift of Asp/Glu reflects its pKa in intrinsically disordered proteins with only local interactions. PG - 1227-33 AB - Detailed knowledge of the pH-dependence of ionizable residues in both folded and unfolded states of proteins is essential to understand the role of electrostatics in protein folding and stability. The reassembly of E. coli Thioredoxin (Trx) by complementation of its two disordered fragments (1-37/38-108) provides a folded heterodimer in equilibrium with its unfolded state which, based on circular dichroism and NMR spectroscopy, consists of two unfolded monomers. To gain insight into the role of electrostatics in protein folding and stability, we compared the pH-dependence of the carboxylate sidechain chemical shift of each Asp/Glu against that of its backbone amide chemical shift in the unfolded heterodimer. We monitored via C(CO)NH experiments four Asp and four Glu in fragments 38 to 108 (C37) of Trx in the pH range from 2.0 to 7.0 and compared them with results from (1)H(15)N HSQC experiments [Pujato et al., Biophys. J., 89 (2005) 3293-3302]. The (1)H(15)N HSQC analysis indicates two segments with quite distinct behavior: (A) a segment from Ala57 to Ala108 in which ionizable residues have up to three contiguous neighbors with pH-dependent backbone amide shifts, and (B) a segment of fifteen contiguous pH-dependent backbone amide shifts (Leu42 to Val56) in which two Asp and two Glu are implicated in medium range interactions. In all cases, the titration curves are simple modified sigmoidals from which a pH-midpoint (pH(m)) can be obtained by fitting. In segment A, the pH(m) of a given backbone amide of Asp/Glu mirrors within 0.15 pH-units that of its carboxylate sidechain (i.e., the pK(a)). In contrast, segment B shows significant differences with absolute values of 0.46 and 0.74 pH-units for Asp and Glu, respectively. The dispersion in the pH(m) of the backbone amide of Asp/Glu is also different in the two segments. Segment A shows a dispersion of 0.31 and 0.17 pH-units for Asp and Glu, respectively. Segment B shows a substantially larger dispersion (0.50 and 1.08 pH-units for Asp and Glu, respectively). In both segments, the dispersion in the pH(m) of its backbone amide is larger than in the pK(a) of the carboxylate sidechain (the latter is only 0.17 and 0.52 pH-units for Asp and Glu, respectively). Our results indicate that the pH(m) of the backbone amide chemical shift of Asp/Glu in a disordered polypeptide segment is a good predictor of its pK(a) whenever there are none or few neighboring backbone amides with similar pH-dependence. FAU - Pujato, Mario AU - Pujato M AD - Department of Chemistry, City College of New York, New York, NY 10031, USA. FAU - Navarro, Abel AU - Navarro A FAU - Versace, Rodney AU - Versace R FAU - Mancusso, Romina AU - Mancusso R FAU - Ghose, Ranajeet AU - Ghose R FAU - Tasayco, Maria Luisa AU - Tasayco ML LA - eng GR - 5G12RR03060/RR/NCRR NIH HHS/United States GR - GM66354/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20060513 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Amides) RN - 0 (Escherichia coli Proteins) RN - 0 (Peptide Fragments) RN - 30KYC7MIAI (Aspartic Acid) RN - 3KX376GY7L (Glutamic Acid) RN - 52500-60-4 (Thioredoxins) SB - IM MH - Amides/*chemistry MH - Amino Acid Sequence MH - Aspartic Acid/*chemistry MH - Escherichia coli Proteins/chemistry MH - Glutamic Acid/*chemistry MH - Hydrogen-Ion Concentration MH - Molecular Sequence Data MH - *Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemistry MH - *Protein Conformation MH - Protein Folding MH - Static Electricity MH - Thioredoxins/chemistry EDAT- 2006/06/22 09:00 MHDA- 2006/09/27 09:00 CRDT- 2006/06/22 09:00 PHST- 2005/12/26 [received] PHST- 2006/03/22 [revised] PHST- 2006/04/24 [accepted] PHST- 2006/05/13 [aheadofprint] AID - S1570-9639(06)00173-7 [pii] AID - 10.1016/j.bbapap.2006.04.014 [doi] PST - ppublish SO - Biochim Biophys Acta. 2006 Jul;1764(7):1227-33. Epub 2006 May 13. PMID- 20510170 OWN - NLM STAT- MEDLINE DA - 20100719 DCOM- 20101018 LR - 20101118 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1798 IP - 9 DP - 2010 Sep TI - Interaction of two intrinsically disordered plant stress proteins (COR15A and COR15B) with lipid membranes in the dry state. PG - 1812-20 LID - 10.1016/j.bbamem.2010.05.015 [doi] AB - COR15A and COR15B form a tandem repeat of highly homologous genes in Arabidopsis thaliana. Both genes are highly cold induced and the encoded proteins belong to the Pfam LEA_4 group (group 3) of the late embryogenesis abundant (LEA) proteins. Both proteins were predicted to be intrinsically disordered in solution. Only COR15A has previously been characterized and it was shown to be localized in the soluble stroma fraction of chloroplasts. Ectopic expression of COR15A in Arabidopsis resulted in increased freezing tolerance of both chloroplasts after freezing and thawing of intact leaves and of isolated protoplasts frozen and thawed in vitro. In the present study we have generated recombinant mature COR15A and COR15B for a comparative study of their structure and possible function as membrane protectants. CD spectroscopy showed that both proteins are predominantly unstructured in solution and mainly alpha-helical after drying. Both proteins showed similar effects on the thermotropic phase behavior of dry liposomes. A decrease in the gel to liquid-crystalline phase transition temperature depended on both the unsaturation of the fatty acyl chains and lipid headgroup structure. FTIR spectroscopy indicated no strong interactions between the proteins and the lipid phosphate and carbonyl groups, but significant interactions with the galactose headgroup of the chloroplast lipid monogalactosyldiacylglycerol. These findings were rationalized by modeling the secondary structure of COR15A and COR15B. Helical wheel projection indicated the presence of amphipathic alpha-helices in both proteins. The helices lacked a clear separation of positive and negative charges on the hydrophilic face, but contained several hydroxylated amino acids. CI - 2010 Elsevier B.V. All rights reserved. FAU - Thalhammer, Anja AU - Thalhammer A AD - Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, D-14476 Potsdam, Germany. FAU - Hundertmark, Michaela AU - Hundertmark M FAU - Popova, Antoaneta V AU - Popova AV FAU - Seckler, Robert AU - Seckler R FAU - Hincha, Dirk K AU - Hincha DK LA - eng PT - Journal Article DEP - 20100525 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Arabidopsis Proteins) RN - 0 (COR15 protein, Arabidopsis) RN - 0 (Membrane Lipids) SB - IM MH - Amino Acid Sequence MH - Arabidopsis/*chemistry MH - Arabidopsis Proteins/*chemistry MH - Circular Dichroism MH - Hydrogen Bonding MH - Hydrophobic and Hydrophilic Interactions MH - Membrane Lipids/*chemistry MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Sequence Alignment MH - Spectroscopy, Fourier Transform Infrared EDAT- 2010/06/01 06:00 MHDA- 2010/10/19 06:00 CRDT- 2010/06/01 06:00 PHST- 2010/03/19 [received] PHST- 2010/04/27 [revised] PHST- 2010/05/14 [accepted] PHST- 2010/05/25 [aheadofprint] AID - S0005-2736(10)00164-1 [pii] AID - 10.1016/j.bbamem.2010.05.015 [doi] PST - ppublish SO - Biochim Biophys Acta. 2010 Sep;1798(9):1812-20. doi: 10.1016/j.bbamem.2010.05.015. Epub 2010 May 25. PMID- 12754258 OWN - NLM STAT- MEDLINE DA - 20030721 DCOM- 20030826 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 30 DP - 2003 Jul 25 TI - Certain metals trigger fibrillation of methionine-oxidized alpha-synuclein. PG - 27630-5 AB - The aggregation and fibrillation of alpha-synuclein has been implicated as a key step in the etiology of Parkinson's disease and several other neurodegenerative disorders. In addition, oxidative stress and certain environmental factors, including metals, are believed to play an important role in Parkinson's disease. Previously, we have shown that methionine-oxidized human alpha-synuclein does not fibrillate and also inhibits fibrillation of unmodified alpha-synuclein (Uversky, V. N., Yamin, G., Souillac, P. O., Goers, J., Glaser, C. B., and Fink, A. L. (2002) FEBS Lett. 517, 239-244). Using dynamic light scattering, we show that the inhibition results from stabilization of the monomeric form of Met-oxidized alpha-synuclein. We have now examined the effect of several metals on the structural properties of methionine-oxidized human alpha-synuclein and its propensity to fibrillate. The presence of metals induced partial folding of both oxidized and non-oxidized alpha-synucleins, which are intrinsically unstructured under conditions of neutral pH. Although the fibrillation of alpha-synuclein was completely inhibited by methionine oxidation, the presence of certain metals (Ti3+, Zn2+, Al3+, and Pb2+) overcame this inhibition. These findings indicate that a combination of oxidative stress and environmental metal pollution could play an important role in triggering the fibrillation of alpha-synuclein and thus possibly Parkinson's disease. FAU - Yamin, Ghiam AU - Yamin G AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. FAU - Glaser, Charles B AU - Glaser CB FAU - Uversky, Vladimir N AU - Uversky VN FAU - Fink, Anthony L AU - Fink AL LA - eng GR - NS39985/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20030516 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Metals) RN - 0 (Nerve Tissue Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - BBX060AN9V (Hydrogen Peroxide) RN - S88TT14065 (Oxygen) SB - IM MH - Circular Dichroism MH - Escherichia coli/metabolism MH - Humans MH - Hydrogen Peroxide/pharmacology MH - Hydrogen-Ion Concentration MH - Kinetics MH - Light MH - Metals/*pharmacology MH - Microscopy, Electron MH - Nerve Tissue Proteins/chemistry/*metabolism MH - Oxidative Stress MH - Oxygen/*metabolism MH - Protein Conformation MH - Scattering, Radiation MH - Synucleins MH - Temperature MH - Time Factors MH - alpha-Synuclein EDAT- 2003/05/20 05:00 MHDA- 2003/08/27 05:00 CRDT- 2003/05/20 05:00 PHST- 2003/05/16 [aheadofprint] AID - 10.1074/jbc.M303302200 [doi] AID - M303302200 [pii] PST - ppublish SO - J Biol Chem. 2003 Jul 25;278(30):27630-5. Epub 2003 May 16. PMID- 19322774 OWN - NLM STAT- MEDLINE DA - 20090603 DCOM- 20090902 LR - 20141120 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 91 IP - 8 DP - 2009 Aug TI - Chaperone-like activities of different molecular forms of beta-casein. Importance of polarity of N-terminal hydrophilic domain. PG - 623-32 LID - 10.1002/bip.21190 [doi] AB - As a member of intrinsically unstructured protein family, beta-casein (beta-CN) contains relatively high amount of prolyl residues, adopts noncompact and flexible structure and exhibits chaperone-like activity in vitro. Like many chaperones, native beta-CN does not contain cysteinyl residues and exhibits strong tendencies for self-association. The chaperone-like activities of three recombinant beta-CNs wild type (WT) beta-CN, C4 beta-CN (with cysteinyl residue in position 4) and C208 beta-CN (with cysteinyl residue in position 208), expressed and purified from E. coli, which, consequently, lack the phosphorylated residues, were examined and compared with that of native beta-CN using insulin and alcohol dehydrogenase as target/substrate proteins. The dimers (beta-CND) of C4-beta-CN and C208 beta-CN were also studied and their chaperone-like activities were compared with those of their monomeric forms. Lacking phosphorylation, WT beta-CN, C208 beta-CN, C4 beta-CN and C4 beta-CND exhibited significantly lower chaperone-like activities than native beta-CN. Dimerization of C208 beta-CN with two distal hydrophilic domains considerably improved its chaperone-like activity in comparison with its monomeric form. The obtained results demonstrate the significant role played by the polar contributions of phosphorylated residues and N-terminal hydrophilic domain as important functional elements in enhancing the chaperone-like activity of native beta-CN. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 623-632, 2009.This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com. FAU - Yousefi, Reza AU - Yousefi R AD - Biopolymeres Interactions Assemblages, INRA, equipe Fonctions et Interactions des Proteines Laitieres, Nantes Cedex 3, France. FAU - Shchutskaya, Yulia Y AU - Shchutskaya YY FAU - Zimny, Jaroslaw AU - Zimny J FAU - Gaudin, Jean-Charles AU - Gaudin JC FAU - Moosavi-Movahedi, Ali A AU - Moosavi-Movahedi AA FAU - Muronetz, Vladimir I AU - Muronetz VI FAU - Zuev, Yuriy F AU - Zuev YF FAU - Chobert, Jean-Marc AU - Chobert JM FAU - Haertle, Thomas AU - Haertle T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 RN - 0 (Caseins) RN - 0 (DNA Primers) RN - 0 (Molecular Chaperones) RN - 0 (Recombinant Proteins) SB - IM MH - Animals MH - Base Sequence MH - Caseins/*chemistry/genetics/metabolism MH - Cattle MH - DNA Primers/genetics MH - Dimerization MH - In Vitro Techniques MH - Molecular Chaperones/chemistry/genetics/metabolism MH - Mutagenesis, Site-Directed MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism EDAT- 2009/03/27 09:00 MHDA- 2009/09/03 06:00 CRDT- 2009/03/27 09:00 AID - 10.1002/bip.21190 [doi] PST - ppublish SO - Biopolymers. 2009 Aug;91(8):623-32. doi: 10.1002/bip.21190. PMID- 12538870 OWN - NLM STAT- MEDLINE DA - 20030205 DCOM- 20030318 LR - 20140611 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 100 IP - 3 DP - 2003 Feb 4 TI - Crystal structure of the MurG:UDP-GlcNAc complex reveals common structural principles of a superfamily of glycosyltransferases. PG - 845-9 AB - MurG is an essential glycosyltransferase that forms the glycosidic linkage between N-acetyl muramyl pentapeptide and N-acetyl glucosamine in the biosynthesis of the bacterial cell wall. This enzyme is a member of a major superfamily of NDP-glycosyltransferases for which no x-ray structures containing intact substrates have been reported. Here we present the 2.5-A crystal structure of Escherichia coli MurG in complex with its donor substrate, UDP-GlcNAc. Combined with genomic analysis of other superfamily members and site-specific mutagenesis of E. coli MurG, this structure sheds light on the molecular basis for both donor and acceptor selectivity for the superfamily. This structural analysis suggests that it will be possible to evolve new glycosyltransferases from prototypical superfamily members by varying two key loops while maintaining the overall architecture of the family and preserving key residues. FAU - Hu, Yanan AU - Hu Y AD - Department of Chemistry, Princeton University, Princeton, NJ 08540, USA. FAU - Chen, Lan AU - Chen L FAU - Ha, Sha AU - Ha S FAU - Gross, Ben AU - Gross B FAU - Falcone, Brian AU - Falcone B FAU - Walker, Deborah AU - Walker D FAU - Mokhtarzadeh, Maryam AU - Mokhtarzadeh M FAU - Walker, Suzanne AU - Walker S LA - eng SI - PDB/1NLM GR - R01A144854/PHS HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20030121 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Bacterial Outer Membrane Proteins) RN - 528-04-1 (Uridine Diphosphate N-Acetylglucosamine) RN - EC 2.4.1.- (N-Acetylglucosaminyltransferases) RN - EC 2.4.1.227 (UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecapreno l N-acetylglucosamine transferase) SB - IM MH - Amino Acid Sequence MH - *Bacterial Outer Membrane Proteins MH - Binding Sites MH - Catalysis MH - Crystallography, X-Ray MH - Escherichia coli/enzymology MH - Kinetics MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - N-Acetylglucosaminyltransferases/*chemistry MH - Uridine Diphosphate N-Acetylglucosamine/*chemistry PMC - PMC298689 OID - NLM: PMC298689 EDAT- 2003/01/23 04:00 MHDA- 2003/03/19 04:00 CRDT- 2003/01/23 04:00 PHST- 2003/01/21 [aheadofprint] AID - 10.1073/pnas.0235749100 [doi] AID - 0235749100 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):845-9. Epub 2003 Jan 21. PMID- 23266002 OWN - NLM STAT- MEDLINE DA - 20130213 DCOM- 20130723 LR - 20141104 IS - 1879-033X (Electronic) IS - 0959-440X (Linking) VI - 23 IP - 1 DP - 2013 Feb TI - Aggregation of islet amyloid polypeptide: from physical chemistry to cell biology. PG - 82-9 LID - 10.1016/j.sbi.2012.11.003 [doi] LID - S0959-440X(12)00183-2 [pii] AB - Amyloid formation in the pancreas by islet amyloid polypeptide (IAPP) leads to beta-cell death and dysfunction, contributing to islet transplant failure and to type-2 diabetes. IAPP is stored in the beta-cell insulin secretory granules and cosecreted with insulin in response to beta-cell secretagogues. IAPP is believed to play a role in the control of food intake, in controlling gastric emptying and in glucose homeostasis. The polypeptide is natively unfolded in its monomeric state, but is one of the most amyloidogenic sequences known. The mechanisms of IAPP amyloid formation in vivo and in vitro are not understood; the mechanisms of IAPP induced cell death are unclear; and the nature of the toxic species is not completely defined. Recent work is shedding light on these important issues. CI - Copyright (c) 2012. Published by Elsevier Ltd. FAU - Cao, Ping AU - Cao P AD - Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11794-3400, United States. FAU - Abedini, Andisheh AU - Abedini A FAU - Raleigh, Daniel P AU - Raleigh DP LA - eng GR - F32 DK089734-02/DK/NIDDK NIH HHS/United States GR - GM078114/GM/NIGMS NIH HHS/United States GR - R01 GM078114/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review DEP - 20121222 PL - England TA - Curr Opin Struct Biol JT - Current opinion in structural biology JID - 9107784 RN - 0 (Amyloid) RN - 0 (Islet Amyloid Polypeptide) RN - 0 (Lipopeptides) SB - IM MH - Amino Acid Sequence MH - Amyloid/chemistry/metabolism MH - Animals MH - Biophysics MH - Extracellular Matrix/chemistry MH - Humans MH - Insulin-Secreting Cells/drug effects MH - Islet Amyloid Polypeptide/*chemistry/*metabolism/toxicity MH - Lipopeptides/chemistry MH - Protein Structure, Secondary PMC - PMC3969731 MID - NIHMS449228 OID - NLM: NIHMS449228 OID - NLM: PMC3969731 EDAT- 2012/12/26 06:00 MHDA- 2013/07/24 06:00 CRDT- 2012/12/26 06:00 PHST- 2012/09/18 [received] PHST- 2012/11/15 [accepted] PHST- 2012/12/22 [aheadofprint] AID - S0959-440X(12)00183-2 [pii] AID - 10.1016/j.sbi.2012.11.003 [doi] PST - ppublish SO - Curr Opin Struct Biol. 2013 Feb;23(1):82-9. doi: 10.1016/j.sbi.2012.11.003. Epub 2012 Dec 22. PMID- 18954090 OWN - NLM STAT- MEDLINE DA - 20090220 DCOM- 20090316 LR - 20140921 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 47 IP - 47 DP - 2008 Nov 25 TI - Detailed structural characterization of unbound protein phosphatase 1 inhibitors. PG - 12346-56 LID - 10.1021/bi801308y [doi] AB - Protein phosphatase 1 (PP1) is an essential and ubiquitous serine/threonine protein phosphatase that is regulated by more than 100 known inhibitor and targeting proteins. It is currently unclear how protein inhibitors distinctly and specifically regulate PP1 to enable rapid responses to cellular alterations. We demonstrate that two PP1 inhibitors, I-2 and DARPP-32, belong to the class of intrinsically unstructured proteins (IUPs). We show that both inhibitors have distinct preferences for transient local and long-range structure. These preferences are likely their structural signature for their interaction with PP1. Furthermore, we show that upon phosphorylation of Thr(34) in DARPP-32, which turns DARPP-32 into a potent inhibitor of PP1, neither local nor long-range structure of DARPP-32 is altered. Therefore, our data suggest a role for these transient three-dimensional topologies in binding mechanisms that enable extensive contacts with PP1's invariant surfaces. Together, these interactions enable potent and selective inhibition of PP1. FAU - Dancheck, Barbara AU - Dancheck B AD - Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island 02912, USA. FAU - Nairn, Angus C AU - Nairn AC FAU - Peti, Wolfgang AU - Peti W LA - eng GR - 1S10RR020923/RR/NCRR NIH HHS/United States GR - P50 MH074866/MH/NIMH NIH HHS/United States GR - R01 NS056128/NS/NINDS NIH HHS/United States GR - R01 NS056128-02/NS/NINDS NIH HHS/United States GR - R01NS056128/NS/NINDS NIH HHS/United States GR - S10-RR017269/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Dopamine and cAMP-Regulated Phosphoprotein 32) RN - 0 (Enzyme Inhibitors) RN - EC 3.1.3.16 (Protein Phosphatase 1) SB - IM MH - Amino Acid Sequence MH - Animals MH - Dopamine and cAMP-Regulated Phosphoprotein 32/*chemistry/metabolism/pharmacology MH - Enzyme Inhibitors/*chemistry/metabolism/*pharmacology MH - Humans MH - Molecular Sequence Data MH - Phosphorylation MH - Protein Phosphatase 1/*antagonists & inhibitors/metabolism MH - Protein Structure, Secondary MH - Rats MH - Substrate Specificity PMC - PMC2645960 MID - NIHMS86446 OID - NLM: NIHMS86446 OID - NLM: PMC2645960 EDAT- 2008/10/29 09:00 MHDA- 2009/03/17 09:00 CRDT- 2008/10/29 09:00 AID - 10.1021/bi801308y [doi] PST - ppublish SO - Biochemistry. 2008 Nov 25;47(47):12346-56. doi: 10.1021/bi801308y. PMID- 14699011 OWN - NLM STAT- MEDLINE DA - 20040206 DCOM- 20040426 LR - 20131121 IS - 1524-4571 (Electronic) IS - 0009-7330 (Linking) VI - 94 IP - 2 DP - 2004 Feb 6 TI - Regulation of connexin43 protein complexes by intracellular acidification. PG - 215-22 AB - Ischemia-induced acidification of astrocytes or cardiac myocytes reduces intercellular communication by closing gap junction channels and subsequently internalizing gap junction proteins. To determine whether such coupling changes might be attributable to altered interactions between connexin43 (Cx43) and other proteins, we applied the nigericin/high K+ method to vary intracellular pH (pHi) in cultured cortical astrocytes. Intracellular acidification was accompanied by internalization of Cx43 with retention of Cx43 scaffolding protein Zonula Occludens-1 (ZO-1) at cell surfaces, suggesting that ZO-1 and Cx43 dissociate at low pHi. Coimmunoprecipitation studies revealed decreased binding of ZO-1 and increased binding of c-Src to Cx43 at low pHi. Resonant mirror spectroscopy was used to quantify binding of the SH3 domain of c-Src and the PDZ domains of ZO-1 to the carboxyl terminal domain of Cx43 (Cx43CT). Data indicate that the c-Src/Cx43CT interaction is highly pH dependent whereas the ZO-1/Cx43CT interaction is not. Moreover, binding of c-Src to Cx43CT prevented and reversed ZO-1/Cx43CT binding. We hypothesize that increased affinity of c-Src for Cx43 at low pHi aids in separation of Cx43 from ZO-1 and that this may facilitate internalization of Cx43. These data suggest that protracted acidification may remodel protein-protein interactions involving Cx43 and thus provide an important protective mechanism to limit lesion spread after ischemic injury. FAU - Duffy, Heather S AU - Duffy HS AD - Department of Neuroscience, Albert Einstein College of Medicine, 1410 Pelham Pkwy S, Bronx, NY 10464, USA. hduffy@aecom.yu.edu FAU - Ashton, Anthony W AU - Ashton AW FAU - O'Donnell, Phyllis AU - O'Donnell P FAU - Coombs, Wanda AU - Coombs W FAU - Taffet, Steve M AU - Taffet SM FAU - Delmar, Mario AU - Delmar M FAU - Spray, David C AU - Spray DC LA - eng GR - GM57691/GM/NIGMS NIH HHS/United States GR - MH65495/MH/NIMH NIH HHS/United States GR - NS07098/NS/NINDS NIH HHS/United States GR - NS41282/NS/NINDS NIH HHS/United States GR - P01-HL39707/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20031229 PL - United States TA - Circ Res JT - Circulation research JID - 0047103 RN - 0 (Connexin 43) RN - 0 (Macromolecular Substances) RN - 0 (Membrane Proteins) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Tjp1 protein, mouse) RN - 0 (Tjp1 protein, rat) RN - 0 (Zonula Occludens-1 Protein) RN - EC 2.7.10.2 (Proto-Oncogene Proteins pp60(c-src)) RN - RRU6GY95IS (Nigericin) RN - RWP5GA015D (Potassium) SB - IM MH - Animals MH - Astrocytes/drug effects/*metabolism/ultrastructure MH - Cells, Cultured/drug effects/metabolism/ultrastructure MH - Connexin 43/chemistry/*metabolism MH - Gap Junctions/drug effects/*metabolism MH - *Hydrogen-Ion Concentration MH - Intracellular Fluid/chemistry MH - Ischemia/metabolism MH - Kinetics MH - Macromolecular Substances MH - Membrane Proteins/chemistry/*metabolism MH - Mice MH - Mice, Inbred C57BL MH - Nigericin/pharmacology MH - Phosphoproteins/chemistry/*metabolism MH - Potassium/pharmacology MH - Protein Binding MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins pp60(c-src)/chemistry/*metabolism MH - Rats MH - Recombinant Fusion Proteins/chemistry/metabolism MH - Zonula Occludens-1 Protein MH - src Homology Domains EDAT- 2003/12/31 05:00 MHDA- 2004/04/27 05:00 CRDT- 2003/12/31 05:00 PHST- 2003/12/29 [aheadofprint] AID - 10.1161/01.RES.0000113924.06926.11 [doi] AID - 01.RES.0000113924.06926.11 [pii] PST - ppublish SO - Circ Res. 2004 Feb 6;94(2):215-22. Epub 2003 Dec 29. PMID- 20141569 OWN - NLM STAT- MEDLINE DA - 20100416 DCOM- 20100504 LR - 20131121 IS - 1471-4159 (Electronic) IS - 0022-3042 (Linking) VI - 113 IP - 3 DP - 2010 May TI - Copper binding regulates intracellular alpha-synuclein localisation, aggregation and toxicity. PG - 704-14 LID - 10.1111/j.1471-4159.2010.06638.x [doi] AB - Alpha-synuclein is a natively unfolded protein that aggregates and forms inclusions that are associated with a range of diseases that include Parkinson's Disease and Dementia with Lewy Bodies. The mechanism behind the formation of these inclusions and their possible role in disease remains unclear. Alpha-synuclein has also been shown to bind metals including copper and iron. We used a cell culture model of alpha-synuclein aggregation to examine the relationship between metals and formation of aggregates of the protein. While the levels of iron appear to have no role in aggregate formation or localisation of the protein in cells, copper appears to be important for both aggregation and cellular localisation of alpha-synuclein. Reduction in cellular copper resulted in a great decrease in aggregate formation both in terms of large aggregates visible in cells and oligomers observed in western blot analysis of cell extracts. Reduction in copper also resulted in a change in localisation of the protein which became more intensely localised to the plasma membrane in medium with low copper. These changes were reversed when copper was restored to the cells. Mutants of the copper binding domains altered the response to copper. Deletion of either the N- or C-termini resulted in a loss of aggregation while deletion of the C-termini also resulted in a loss of membrane association. Increased expression of alpha-synuclein also increased cell sensitivity to the toxicity of copper. These results suggest that the potential pathological role of alpha-synuclein aggregates is dependent upon the copper binding capacity of the protein. FAU - Wang, Xiaoyan AU - Wang X AD - Department of Biology and Biochemistry, University of Bath, Bath, UK. FAU - Moualla, Dima AU - Moualla D FAU - Wright, Josephine A AU - Wright JA FAU - Brown, David R AU - Brown DR LA - eng PT - Journal Article DEP - 20100205 PL - England TA - J Neurochem JT - Journal of neurochemistry JID - 2985190R RN - 0 (alpha-Synuclein) RN - 789U1901C5 (Copper) SB - IM MH - Binding Sites/drug effects MH - Blotting, Western MH - Cell Aggregation/drug effects MH - Cell Death/physiology MH - Cell Line, Tumor MH - Cell Membrane/drug effects/metabolism MH - Cell Survival/drug effects MH - Cloning, Molecular MH - Copper/*metabolism/*physiology MH - Humans MH - Microscopy, Confocal MH - Mutagenesis MH - Point Mutation/physiology MH - Transfection MH - alpha-Synuclein/genetics/*metabolism/*toxicity EDAT- 2010/02/10 06:00 MHDA- 2010/05/05 06:00 CRDT- 2010/02/10 06:00 PHST- 2010/02/05 [aheadofprint] AID - JNC6638 [pii] AID - 10.1111/j.1471-4159.2010.06638.x [doi] PST - ppublish SO - J Neurochem. 2010 May;113(3):704-14. doi: 10.1111/j.1471-4159.2010.06638.x. Epub 2010 Feb 5. PMID- 23883055 OWN - NLM STAT- MEDLINE DA - 20130725 DCOM- 20140205 LR - 20141204 IS - 1089-7690 (Electronic) IS - 0021-9606 (Linking) VI - 139 IP - 3 DP - 2013 Jul 21 TI - Identification of small-molecule binding pockets in the soluble monomeric form of the Abeta42 peptide. PG - 035101 LID - 10.1063/1.4811831 [doi] AB - The aggregation of intrinsically disordered peptides and proteins is associated with a wide range of highly debilitating neurological and systemic disorders. In this work we explored the potential of a structure-based drug discovery procedure to target one such system, the soluble monomeric form of the Abeta42 peptide. We utilised for this purpose a set of structures of the Abeta42 peptide selected from clusters of conformations within an ensemble generated by molecular dynamics simulations. Using these structures we carried out fragment mapping calculations to identify binding "hot spots" on the monomeric form of the Abeta42 peptide. This procedure provided a set of hot spots with ligand efficiencies comparable to those observed for structured proteins, and clustered into binding pockets. Such binding pockets exhibited a propensity to bind small molecules known to interact with the Abeta42 peptide. Taken together these results provide an initial indication that fragment-based drug discovery may represent a potential therapeutic strategy for diseases associated with the aggregation of intrinsically disordered proteins. FAU - Zhu, Maximillian AU - Zhu M AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom. FAU - De Simone, Alfonso AU - De Simone A FAU - Schenk, Dale AU - Schenk D FAU - Toth, Gergely AU - Toth G FAU - Dobson, Christopher M AU - Dobson CM FAU - Vendruscolo, Michele AU - Vendruscolo M LA - eng GR - 089703/Wellcome Trust/United Kingdom GR - BB/H003843/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - MC_G1000734/Medical Research Council/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Chem Phys JT - The Journal of chemical physics JID - 0375360 RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (1-42)) SB - IM MH - Amino Acid Sequence MH - Amyloid beta-Peptides/*chemistry/metabolism MH - Binding Sites MH - Drug Design MH - *Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Peptide Fragments/*chemistry/metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Solubility EDAT- 2013/07/26 06:00 MHDA- 2014/02/06 06:00 CRDT- 2013/07/26 06:00 AID - 10.1063/1.4811831 [doi] PST - ppublish SO - J Chem Phys. 2013 Jul 21;139(3):035101. doi: 10.1063/1.4811831. PMID- 16113108 OWN - NLM STAT- MEDLINE DA - 20051028 DCOM- 20060222 LR - 20140606 IS - 0006-3495 (Print) IS - 0006-3495 (Linking) VI - 89 IP - 5 DP - 2005 Nov TI - pH dependence of amide chemical shifts in natively disordered polypeptides detects medium-range interactions with ionizable residues. PG - 3293-302 AB - A growing number of natively disordered proteins undergo a folding/binding process that is essential for their biological function. An interesting question is whether these proteins have incompletely solvated regions that drive the folding/binding process. Although the presence of predominantly hydrophobic buried regions can be easily ascertained by high-sensitivity differential scanning calorimetry analysis, the identification of those residues implicated in the burial requires NMR analysis. We have selected a partially solvated natively disordered fragment of Escherichia coli, thioredoxin, C37 (38-108), for full NMR spectral assignment. The secondary chemical shifts, temperature coefficients, and relaxation rates (R(1) and R(2)) of this fragment indicate the presence of a flexible backbone without a stable hydrogen bond network near neutral pH. (1)H-(15)N heteronuclear single quantum coherence analysis of the pH dependence of amide chemical shifts in fragment C37 within pH 2.0 and 7.0 suggests the presence of interactions between nonionizable residues and the carboxylate groups of four Asp and four Glu residues. The pH midpoints (pH(m)) of the amides in the ionizable residues (Asp or Glu) and, consequently, the shifts in the pH(m) (DeltapH(m)) of these residues with respect to model tetrapeptides, are sequence-dependent; and the nonionizable residues that show pH dependence cluster around the ionizable ones. The same pH dependence has been observed in two fragments: M37 (38-73) and C73 (74-108), ruling out the participation of long-range interactions. Our studies indicate the presence of a 15-residue pH-dependent segment with the highest density of ionizable sites in the disordered ensembles of fragments C37 and M37. The observed correlations between ionizable and nonionizable residues in this segment suggest the organization of the backbone and side chains through local and medium-range interactions up to nine residues apart, in contrast to only a few interactions in fragment C73. These results agree qualitatively with the predominantly hydrophobic buried surface detected only in fragments C37 and M37 by highly sensitive differential scanning calorimetry analysis. This work offers a sensitive and rapid new tool to obtain clues about local and nonlocal interactions between ionizable and nonionizable residues in the growing family of natively disordered small proteins with full NMR assignments. FAU - Pujato, Mario AU - Pujato M AD - Department of Chemistry, The City College of New York, New York, NY 10031, USA. FAU - Bracken, Clay AU - Bracken C FAU - Mancusso, Romina AU - Mancusso R FAU - Cataldi, Marcela AU - Cataldi M FAU - Tasayco, Maria Luisa AU - Tasayco ML LA - eng GR - 5G12 RR 03060/RR/NCRR NIH HHS/United States GR - GM 66354/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20050819 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Amides) RN - 0 (Ions) RN - 0 (Peptides) RN - 0 (Protons) RN - 30KYC7MIAI (Aspartic Acid) RN - 3KX376GY7L (Glutamic Acid) RN - 52500-60-4 (Thioredoxins) SB - IM MH - Amides/*chemistry MH - Aspartic Acid/chemistry MH - Calorimetry, Differential Scanning MH - Escherichia coli/metabolism MH - Glutamic Acid/chemistry MH - Hydrogen Bonding MH - Hydrogen-Ion Concentration MH - Ions MH - Magnetic Resonance Spectroscopy/methods MH - Mutagenesis MH - Peptides/*chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Protons MH - Temperature MH - Thioredoxins/*chemistry MH - Time Factors PMC - PMC1366825 OID - NLM: PMC1366825 EDAT- 2005/08/23 09:00 MHDA- 2006/02/24 09:00 CRDT- 2005/08/23 09:00 PHST- 2005/08/19 [aheadofprint] AID - S0006-3495(05)72971-4 [pii] AID - 10.1529/biophysj.105.060384 [doi] PST - ppublish SO - Biophys J. 2005 Nov;89(5):3293-302. Epub 2005 Aug 19. PMID- 22676969 OWN - NLM STAT- MEDLINE DA - 20120815 DCOM- 20121029 IS - 1470-8728 (Electronic) IS - 0264-6021 (Linking) VI - 446 IP - 2 DP - 2012 Sep 1 TI - Structural basis for the protective effect of the human prion protein carrying the dominant-negative E219K polymorphism. PG - 243-51 LID - 10.1042/BJ20111940 [doi] AB - The most common form of prion disease in humans is sCJD (sporadic Creutzfeldt-Jakob disease). The naturally occurring E219K polymorphism in the HuPrP (human prion protein) is considered to protect against sCJD. To gain insight into the structural basis of its protective influence we have determined the NMR structure of recombinant HuPrP (residues 90-231) carrying the E219K polymorphism. The structure of the HuPrP(E219K) protein consists of a disordered N-terminal tail (residues 90-124) and a well-structured C-terminal segment (residues 125-231) containing three alpha-helices and two short antiparallel beta-strands. Comparison of NMR structures of the wild-type and HuPrPs with pathological mutations under identical experimental conditions revealed that, although the global architecture of the protein remains intact, replacement of Glu(2)(1)(9) with a lysine residue introduces significant local structural changes. The structural findings of the present study suggest that the protective influence of the E219K polymorphism is due to the alteration of surface charge distribution, in addition to subtle structural rearrangements localized within the epitopes critical for prion conversion. FAU - Biljan, Ivana AU - Biljan I AD - Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia. FAU - Giachin, Gabriele AU - Giachin G FAU - Ilc, Gregor AU - Ilc G FAU - Zhukov, Igor AU - Zhukov I FAU - Plavec, Janez AU - Plavec J FAU - Legname, Giuseppe AU - Legname G LA - eng SI - PDB/2LFT SI - PDB/2LSB PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (Epitopes) RN - 0 (Mutant Proteins) RN - 0 (Peptide Fragments) RN - 0 (Prions) RN - 0 (Recombinant Proteins) RN - 0 (prion protein (91-231), human) SB - IM MH - Alleles MH - Amino Acid Substitution MH - Creutzfeldt-Jakob Syndrome/*genetics/metabolism MH - Epitopes MH - Genetic Predisposition to Disease MH - Heterozygote MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Mutant Proteins/chemistry/metabolism MH - Peptide Fragments/chemistry/genetics/metabolism MH - *Polymorphism, Genetic MH - Prions/*chemistry/*genetics/metabolism MH - Protein Conformation MH - Recombinant Proteins/chemistry/metabolism MH - Static Electricity MH - Surface Properties EDAT- 2012/06/09 06:00 MHDA- 2012/10/30 06:00 CRDT- 2012/06/09 06:00 AID - BJ20111940 [pii] AID - 10.1042/BJ20111940 [doi] PST - ppublish SO - Biochem J. 2012 Sep 1;446(2):243-51. doi: 10.1042/BJ20111940. PMID- 7548085 OWN - NLM STAT- MEDLINE DA - 19951109 DCOM- 19951109 LR - 20141120 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 34 IP - 40 DP - 1995 Oct 10 TI - Prothymosin alpha: a biologically active protein with random coil conformation. PG - 13211-8 AB - Prothymosin is an acidic protein with an unusual amino acid composition. Though its exact function is not yet known, its high evolutionary conservation and wide tissue distribution suggest an essential biological role. Its physical state, which is controversially discussed in previous publications, was investigated using small-angle X-ray scattering, dynamic light scattering, mass spectrometry, and circular dichroism (CD). Our results unequivocally demonstrate that prothymosin is a monomer under physiological conditions. The protein adopts a random coillike conformation but exhibits persistence of direction and curvature. No regular secondary structure is detectable by CD. The Stokes radius, Rs = 3.07 nm, and the radius of gyration, RG = 4.76 nm, are 1.77 and 3.42 times larger, respectively, than those expected for a compactly folded protein consisting of 109 amino acid residues. A remarkable amount of secondary structure is formed only in the presence of trifluoroethanol at low pH. The finding that a biologically active protein molecule with 109 amino acid residues adopts a random coil conformation under physiological conditions raises the question whether this is a rare or a hitherto-overlooked but widespread phenomenon in the field of macromolecular polypeptides. FAU - Gast, K AU - Gast K AD - Max-Delbruck-Center for Molecular Medicine, Berlin, Germany. FAU - Damaschun, H AU - Damaschun H FAU - Eckert, K AU - Eckert K FAU - Schulze-Forster, K AU - Schulze-Forster K FAU - Maurer, H R AU - Maurer HR FAU - Muller-Frohne, M AU - Muller-Frohne M FAU - Zirwer, D AU - Zirwer D FAU - Czarnecki, J AU - Czarnecki J FAU - Damaschun, G AU - Damaschun G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Protein Precursors) RN - 0 (prothymosin alpha) RN - 61512-21-8 (Thymosin) SB - IM MH - Animals MH - Cattle MH - Circular Dichroism MH - In Vitro Techniques MH - Mass Spectrometry MH - Protein Precursors/*chemistry MH - *Protein Structure, Secondary MH - Scattering, Radiation MH - Thymosin/*analogs & derivatives/chemistry MH - Thymus Gland/enzymology EDAT- 1995/10/10 MHDA- 1995/10/10 00:01 CRDT- 1995/10/10 00:00 PST - ppublish SO - Biochemistry. 1995 Oct 10;34(40):13211-8. PMID- 20356930 OWN - NLM STAT- MEDLINE DA - 20100401 DCOM- 20100624 LR - 20140827 IS - 1477-9137 (Electronic) IS - 0021-9533 (Linking) VI - 123 IP - Pt 8 DP - 2010 Apr 15 TI - Prion-like disorders: blurring the divide between transmissibility and infectivity. PG - 1191-201 LID - 10.1242/jcs.051672 [doi] AB - Prions are proteins that access self-templating amyloid forms, which confer phenotypic changes that can spread from individual to individual within or between species. These infectious phenotypes can be beneficial, as with yeast prions, or deleterious, as with mammalian prions that transmit spongiform encephalopathies. However, the ability to form self-templating amyloid is not unique to prion proteins. Diverse polypeptides that tend to populate intrinsically unfolded states also form self-templating amyloid conformers that are associated with devastating neurodegenerative disorders. Moreover, two RNA-binding proteins, FUS and TDP-43, which form cytoplasmic aggregates in amyotrophic lateral sclerosis, harbor a 'prion domain' similar to those found in several yeast prion proteins. Can these proteins and the neurodegenerative diseases to which they are linked become 'infectious' too? Here, we highlight advances that define the transmissibility of amyloid forms connected with Alzheimer's disease, Parkinson's disease and Huntington's disease. Collectively, these findings suggest that amyloid conformers can spread from cell to cell within the brains of afflicted individuals, thereby spreading the specific neurodegenerative phenotypes distinctive to the protein being converted to amyloid. Importantly, this transmissibility mandates a re-evaluation of emerging neuronal graft and stem-cell therapies. In this Commentary, we suggest how these treatments might be optimized to overcome the transmissible conformers that confer neurodegeneration. FAU - Cushman, Mimi AU - Cushman M AD - Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 805b Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104, USA. FAU - Johnson, Brian S AU - Johnson BS FAU - King, Oliver D AU - King OD FAU - Gitler, Aaron D AU - Gitler AD FAU - Shorter, James AU - Shorter J LA - eng GR - 1DP2OD002177/OD/NIH HHS/United States GR - 1DP2OD002177-01/OD/NIH HHS/United States GR - 1DP2OD004417/OD/NIH HHS/United States GR - 1R01NS065317/NS/NINDS NIH HHS/United States GR - 1R01NS065317-01/NS/NINDS NIH HHS/United States GR - 1R21NS067354/NS/NINDS NIH HHS/United States GR - 1R21NS067354-0110/NS/NINDS NIH HHS/United States GR - AG00255/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - England TA - J Cell Sci JT - Journal of cell science JID - 0052457 RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptides) RN - 0 (Prions) RN - 0 (alpha-Synuclein) RN - 0 (tau Proteins) RN - 26700-71-0 (polyglutamine) SB - IM MH - Amyloid beta-Peptides/metabolism MH - Animals MH - Humans MH - Neurons/transplantation MH - Peptides/metabolism MH - Prion Diseases/*transmission MH - Prions/metabolism/*pathogenicity MH - Stem Cell Transplantation MH - alpha-Synuclein/metabolism MH - tau Proteins/metabolism PMC - PMC2848109 OID - NLM: PMC2848109 EDAT- 2010/04/02 06:00 MHDA- 2010/06/25 06:00 CRDT- 2010/04/02 06:00 AID - 123/8/1191 [pii] AID - 10.1242/jcs.051672 [doi] PST - ppublish SO - J Cell Sci. 2010 Apr 15;123(Pt 8):1191-201. doi: 10.1242/jcs.051672. PMID- 16522184 OWN - NLM STAT- MEDLINE DA - 20060308 DCOM- 20060328 LR - 20140915 IS - 0929-8665 (Print) IS - 0929-8665 (Linking) VI - 12 IP - 7 DP - 2005 Oct TI - Predicted and measured disorder in peripherin/rds, a retinal tetraspanin. PG - 677-86 AB - Vertebrate photoreceptor outer segment (OS) morphogenesis requires peripherin/rds (P/rds). We have characterized this protein's C-terminus and present evidence that suggests it is intrinsically disordered. We propose that structural flexibility may underlie the multifunctionality proposed for this domain previously. The extremely short C-termini present in other tetraspanin family members suggest that intrinsic disorder may also play a role for those proteins. FAU - Ritter, L M AU - Ritter LM AD - Eye Research Institute, Oakland University, Rochester, MI 48309, USA. FAU - Arakawa, T AU - Arakawa T FAU - Goldberg, A F X AU - Goldberg AF LA - eng GR - R01 EY013246/EY/NEI NIH HHS/United States PT - Journal Article PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 RN - 0 (Intermediate Filament Proteins) RN - 0 (Membrane Glycoproteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Peripherins) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Gene Expression/genetics MH - Hydrophobic and Hydrophilic Interactions MH - Intermediate Filament Proteins/*chemistry/genetics/isolation & purification/*metabolism MH - Membrane Glycoproteins/*chemistry/genetics/isolation & purification/*metabolism MH - Molecular Sequence Data MH - Molecular Weight MH - Nerve Tissue Proteins/*chemistry/genetics/isolation & purification/*metabolism MH - Peripherins MH - Pliability MH - Protein Denaturation MH - Retina/*chemistry MH - Solubility MH - Ultracentrifugation PMC - PMC1398073 MID - NIHMS7647 OID - NLM: NIHMS7647 OID - NLM: PMC1398073 EDAT- 2006/03/09 09:00 MHDA- 2006/03/29 09:00 CRDT- 2006/03/09 09:00 PST - ppublish SO - Protein Pept Lett. 2005 Oct;12(7):677-86. PMID- 14648763 OWN - NLM STAT- MEDLINE DA - 20031203 DCOM- 20040204 LR - 20131121 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 70 IP - 4 DP - 2003 Dec TI - Characterization of two molluscan crystal-modulating biomineralization proteins and identification of putative mineral binding domains. PG - 522-33 AB - Ethylenediamine-tetraacetic acid extracted water-soluble matrix proteins in molluscan shells secreted from the mantle epithelia are believed to control crystal nucleation, morphology, orientation, and phase of the deposited mineral. Previously, atomic force microscopy demonstrated that abalone nacre proteins bind to growing step edges and to specific crystallographic faces of calcite, suggesting that inhibition of calcite growth may be one of the molecular processes required for growth of the less thermodynamically stable aragonite phase. Previous experiments were done with protein mixtures. To elucidate the role of single proteins, we have characterized two proteins isolated from the aragonitic component of nacre of the red abalone, Haliotis rufescens. These proteins, purified by hydrophobic interaction chromatography, are designated AP7 and AP24 (aragonitic protein of molecular weight 7 kDa and 24 kDa, respectively). Degenerate oligonucleotide primers corresponding to N-terminal and internal peptide sequences were used to amplify cDNA clones by a polymerase chain reaction from a mantle cDNA library; the deduced primary amino acid sequences are presented. Preliminary crystal growth experiments demonstrate that protein fractions enriched in AP7 and AP24 produced CaCO(3) crystals with morphology distinct from crystals grown in the presence of the total mixture of soluble aragonite-specific proteins. Peptides corresponding to the first 30 residues of the N-terminal sequences of both AP7 and AP24 were generated. The synthetic peptides frustrate the progression of step edges of a growing calcite surface, indicating that sequence features within the N-termini of AP7 and AP24 include domains that interact with CaCO(3). CD analyses demonstrate that the N-terminal peptide sequences do not possess significant percentages of alpha-helix or beta-strand secondary structure in solution. Instead, in both the presence and absence of Ca(II), the peptides retain unfolded conformations that may facilitate protein-mineral interaction. CI - Copyright 2003 Wiley Periodicals, Inc. Biopolymers 70: 522-533, 2003 FAU - Michenfelder, Martina AU - Michenfelder M AD - Biomolecular Science and Engineering Program and the Materials Research Laboratory, University of California, Santa Barbara, CA 93106, USA. FAU - Fu, Germaine AU - Fu G FAU - Lawrence, Camille AU - Lawrence C FAU - Weaver, James C AU - Weaver JC FAU - Wustman, Brandon A AU - Wustman BA FAU - Taranto, Laura AU - Taranto L FAU - Evans, John Spencer AU - Evans JS FAU - Morse, Daniel E AU - Morse DE LA - eng SI - GENBANK/AF225915 SI - GENBANK/AF225916 PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 RN - 0 (Peptides) RN - 0 (Proteins) RN - H0G9379FGK (Calcium Carbonate) SB - IM EIN - Biopolymers. 2004 Feb 5;73(2):291 MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Calcium Carbonate/*chemistry/metabolism MH - Circular Dichroism MH - Models, Molecular MH - Molecular Sequence Data MH - Mollusca/*chemistry/metabolism MH - Peptides/chemistry/metabolism MH - Protein Binding MH - Proteins/*chemistry/isolation & purification/metabolism EDAT- 2003/12/04 05:00 MHDA- 2004/02/05 05:00 CRDT- 2003/12/04 05:00 AID - 10.1002/bip.10536 [doi] PST - ppublish SO - Biopolymers. 2003 Dec;70(4):522-33. PMID- 23888783 OWN - NLM STAT- MEDLINE DA - 20130729 DCOM- 20130812 IS - 0026-8984 (Print) IS - 0026-8984 (Linking) VI - 47 IP - 3 DP - 2013 May-Jun TI - [Comparative characteristics of the structure and function for syndecan-1 from animal organisms]. PG - 505-12 AB - Syndecan-1 is a general representative of transmembrane proteoglycans known for their ability to perform diverse functions in multicellular organisms: to influence on cell interactions, to be act as a co-receptor and bind with to a large number ofligands and integrate them on the receptors, to fulfill the protective function, and to affect on wound repair and oncogenesis. Moreover, syndecan-1 as similar to the extracellular matrix plays an essential role in the development of organisms. Such a diversity of functions is associated with its structure. In this work we demonstrate that intracellular and intercellular domains of syndecan-1 are intrinsically disordered regions. Such structural feature allows them to bind with adapter proteins in the cytoplasm and be extended with glycosaminoglicans in the extracellular matrix, and to take part in the diverse and important cellular processes. The comparison of the occurrence of 20 amino acids for syndecan-1 from 32 animal organisms and 17 animal proteomes demonstrated that for the first such amino acids as glycine, treonine, glutamine, glutamic acid, and proline predominate on amount in the content of the former that results to the appearance of disordered regions in the proteins. FAU - Leonova, E I AU - Leonova EI FAU - Galzitskaia, O V AU - Galzitskaia OV LA - rus PT - Comparative Study PT - English Abstract PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Russia (Federation) TA - Mol Biol (Mosk) JT - Molekuliarnaia biologiia JID - 0105454 RN - 0 (Glycosaminoglycans) RN - 0 (SDC1 protein, human) RN - 0 (Syndecan-1) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cytoplasm/chemistry/genetics/metabolism MH - Databases, Protein MH - Glycosaminoglycans/chemistry/genetics/metabolism MH - Humans MH - Protein Binding/physiology MH - Protein Structure, Tertiary MH - Structure-Activity Relationship MH - *Syndecan-1/chemistry/genetics/metabolism EDAT- 2013/07/31 06:00 MHDA- 2013/08/13 06:00 CRDT- 2013/07/30 06:00 PST - ppublish SO - Mol Biol (Mosk). 2013 May-Jun;47(3):505-12. PMID- 19843162 OWN - NLM STAT- MEDLINE DA - 20100127 DCOM- 20100218 LR - 20140827 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 276 IP - 22 DP - 2009 Nov TI - The N-terminus of mature human frataxin is intrinsically unfolded. PG - 6669-76 LID - 10.1111/j.1742-4658.2009.07381.x [doi] AB - Frataxin is a highly conserved nuclear-encoded mitochondrial protein whose deficiency is the primary cause of Friedreich's ataxia, an autosomal recessive neurodegenerative disease. The frataxin structure comprises a well-characterized globular domain that is present in all species and is preceded in eukaryotes by a non-conserved N-terminal tail that contains the mitochondrial import signal. Little is known about the structure and dynamic properties of the N-terminal tail. Here, we show that this region is flexible and intrinsically unfolded in human frataxin. It does not alter the iron-binding or self-aggregation properties of the globular domain. It is therefore very unlikely that this region could be important for the conserved functions of the protein. FAU - Prischi, Filippo AU - Prischi F AD - Dipartimento di Biologia Molecolare, University of Siena, Siena, Italy. FAU - Giannini, Clelia AU - Giannini C FAU - Adinolfi, Salvatore AU - Adinolfi S FAU - Pastore, Annalisa AU - Pastore A LA - eng GR - MC_U117533887/Medical Research Council/United Kingdom GR - MC_U117584256/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091016 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Iron-Binding Proteins) RN - 0 (frataxin) SB - IM MH - Amino Acid Sequence MH - Humans MH - Iron-Binding Proteins/*chemistry MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Folding MH - Sequence Alignment MH - Sequence Homology, Amino Acid PMC - PMC3430858 OID - NLM: PMC3430858 EDAT- 2009/10/22 06:00 MHDA- 2010/02/19 06:00 CRDT- 2009/10/22 06:00 PHST- 2009/10/16 [aheadofprint] AID - EJB7381 [pii] AID - 10.1111/j.1742-4658.2009.07381.x [doi] PST - ppublish SO - FEBS J. 2009 Nov;276(22):6669-76. doi: 10.1111/j.1742-4658.2009.07381.x. Epub 2009 Oct 16. PMID- 23470734 OWN - NLM STAT- MEDLINE DA - 20130325 DCOM- 20130917 LR - 20131121 IS - 1347-6947 (Electronic) IS - 0916-8451 (Linking) VI - 77 IP - 3 DP - 2013 TI - Effects of Fe3+ and Zn2+ on the structural and thermodynamic properties of a soybean ASR protein. PG - 475-81 AB - Abscisic acid-, stress-, and ripening-induced (ASR) protein play important roles in protecting plants from abiotic stress. The functions of some ASR proteins are known to be modulated by binding to metal ions. In this study, we demonstrated that the non-tagged full-length soybean (Glycine max) ASR protein (GmASR) can bind Fe(3+), Ni(2+), Cu(2+), and Zn(2+). The direct binding properties of GmASR to Fe(3+) and Zn(2+) were further confirmed by intrinsic fluorescence assays. The GmASR protein was found to have three Fe(3+) binding sites but only two Zn(2+) binding sites. Natively disordered in aqueous solution, GmASR remained disordered in the presence of Fe(3+), but was found to aggregate in the presence of Zn(2+). The aggregated GmASR protein was partially resolubilized after Zn(2+) was chelated by EDTA. GmASR exhibited Fe(3+)-binding-dependent antioxidant activity in vitro. We speculate that GmASR thus protects against oxidation damage by buffering metal ions, thus alleviating metal toxicity in plant cells under stressed conditions. FAU - Li, Ran-Hui AU - Li RH AD - Institute of Genetics and Cytology, School of Life Sciences, Northeast Normal University, Changchun, PR China. FAU - Liu, Guo-Bao AU - Liu GB FAU - Wang, Hui AU - Wang H FAU - Zheng, Yi-Zhi AU - Zheng YZ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130307 PL - Japan TA - Biosci Biotechnol Biochem JT - Bioscience, biotechnology, and biochemistry JID - 9205717 RN - 0 (Antioxidants) RN - 0 (Plant Proteins) RN - E1UOL152H7 (Iron) RN - J41CSQ7QDS (Zinc) SB - IM MH - Antioxidants/*chemistry/*metabolism MH - Iron/metabolism/*pharmacology MH - Plant Proteins/*chemistry/*metabolism MH - *Soybeans MH - Thermodynamics MH - Zinc/metabolism/*pharmacology EDAT- 2013/03/09 06:00 MHDA- 2013/09/18 06:00 CRDT- 2013/03/09 06:00 PHST- 2013/03/07 [aheadofprint] AID - DN/JST.JSTAGE/bbb/120666 [pii] AID - 10.1271/bbb.120666 [doi] PST - ppublish SO - Biosci Biotechnol Biochem. 2013;77(3):475-81. Epub 2013 Mar 7. PMID- 20709081 OWN - NLM STAT- MEDLINE DA - 20101004 DCOM- 20101019 LR - 20101118 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 403 IP - 1 DP - 2010 Oct 15 TI - Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-beta peptide in aqueous solution and its implications for Abeta aggregation. PG - 148-65 LID - 10.1016/j.jmb.2010.08.003 [doi] AB - Aggregation of amyloid-beta (Abeta) peptide, a 39- to 43-residue fragment of the amyloid precursor protein, is associated with Alzheimer's disease, the most common form of dementia in the elderly population. Several experimental studies have tried to characterize the atomic details of amyloid fibrils, which are the final product of Abeta aggregation. Much less is known about species forming during the early stages of aggregation, in particular about the monomeric state of the Abeta peptide that may be viewed as the product of the very first step in the hypothesized amyloid cascade. Here, the equilibrium ensembles of monomeric Abeta alloforms Abeta(1-40) and Abeta(1-42) are investigated by Monte Carlo simulations using an atomistic force field and implicit solvent model that have been shown previously to correctly reproduce the ensemble properties of other intrinsically disordered polypeptides. Our simulation results indicate that at physiological temperatures, both alloforms of Abeta assume a largely collapsed globular structure. Conformations feature a fluid hydrophobic core formed, on average, by contacts both within and between the two segments comprising residues 12-21 and 24-40/42, respectively. Furthermore, the 11 N-terminal residues are completely unstructured, and all charged side chains, in particular those of Glu22 and Asp23, remain exposed to solvent. Taken together, these observations indicate a micelle-likedagger architecture at the monomer level whose implications for oligomerization, as well as fibril formation and elongation, are discussed. We establish quantitatively the intrinsic disorder of Abeta and find the propensity to form regular secondary structure to be low but sequence specific. In the presence of a global and unspecific bias for backbone conformations to populate the beta-basin, the beta-sheet propensity along the sequence is consistent with the arrangement of the monomer within the fibril, as derived from solid-state NMR data. These observations indicate that the primary sequence partially encodes fibril structure, but that fibril elongation must be thought of as a templated assembly step. CI - Copyright (c) 2010 Elsevier Ltd. All rights reserved. FAU - Vitalis, Andreas AU - Vitalis A AD - Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland. a.vitalis@bioc.uzh.ch FAU - Caflisch, Amedeo AU - Caflisch A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100813 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amyloid beta-Peptides) RN - 0 (Emulsions) RN - 0 (Micelles) SB - IM MH - Amyloid beta-Peptides/*chemistry/metabolism MH - Computer Simulation MH - Emulsions/*chemistry MH - *Micelles MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Denaturation MH - *Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary EDAT- 2010/08/17 06:00 MHDA- 2010/10/20 06:00 CRDT- 2010/08/17 06:00 PHST- 2010/06/22 [received] PHST- 2010/07/27 [revised] PHST- 2010/08/02 [accepted] PHST- 2010/08/13 [aheadofprint] AID - S0022-2836(10)00851-X [pii] AID - 10.1016/j.jmb.2010.08.003 [doi] PST - ppublish SO - J Mol Biol. 2010 Oct 15;403(1):148-65. doi: 10.1016/j.jmb.2010.08.003. Epub 2010 Aug 13. PMID- 25209675 OWN - NLM STAT- In-Process DA - 20141125 IS - 1439-7633 (Electronic) IS - 1439-4227 (Linking) VI - 15 IP - 17 DP - 2014 Nov 24 TI - Alpha-synuclein binds to the inner membrane of mitochondria in an alpha-helical conformation. PG - 2499-502 LID - 10.1002/cbic.201402281 [doi] AB - The human alpha-Synuclein (alphaS) protein is of significant interest because of its association with Parkinson's disease and related neurodegenerative disorders. The intrinsically disordered protein (140 amino acids) is characterized by the absence of a well-defined structure in solution. It displays remarkable conformational flexibility upon macromolecular interactions, and can associate with mitochondrial membranes. Site-directed spin-labeling in combination with electron paramagnetic resonance spectroscopy enabled us to study the local binding properties of alphaS on artificial membranes (mimicking the inner and outer mitochondrial membranes), and to evaluate the importance of cardiolipin in this interaction. With pulsed, two-frequency, double-electron electron paramagnetic resonance (DEER) approaches, we examined, to the best of our knowledge for the first time, the conformation of alphaS bound to isolated mitochondria. CI - (c) 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. FAU - Robotta, Marta AU - Robotta M AD - Department of Chemistry and Biology, Konstanz Research School Chemical Biology (KoRS-CB) and the Zukunftskolleg, University of Konstanz, 78457 Konstanz (Germany). FAU - Gerding, Hanne R AU - Gerding HR FAU - Vogel, Antonia AU - Vogel A FAU - Hauser, Karin AU - Hauser K FAU - Schildknecht, Stefan AU - Schildknecht S FAU - Karreman, Christiaan AU - Karreman C FAU - Leist, Marcel AU - Leist M FAU - Subramaniam, Vinod AU - Subramaniam V FAU - Drescher, Malte AU - Drescher M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140910 PL - Germany TA - Chembiochem JT - Chembiochem : a European journal of chemical biology JID - 100937360 SB - IM OTO - NOTNLM OT - DEER OT - alpha-synuclein OT - helical structures OT - membranes OT - mitochondria OT - site-directed spin labeling EDAT- 2014/09/12 06:00 MHDA- 2014/09/12 06:00 CRDT- 2014/09/12 06:00 PHST- 2014/06/03 [received] PHST- 2014/09/10 [aheadofprint] AID - 10.1002/cbic.201402281 [doi] PST - ppublish SO - Chembiochem. 2014 Nov 24;15(17):2499-502. doi: 10.1002/cbic.201402281. Epub 2014 Sep 10. PMID- 12890024 OWN - NLM STAT- MEDLINE DA - 20030731 DCOM- 20040308 LR - 20091119 IS - 0950-382X (Print) IS - 0950-382X (Linking) VI - 49 IP - 4 DP - 2003 Aug TI - Prion protein gene polymorphisms in Saccharomyces cerevisiae. PG - 1005-17 AB - The yeast Saccharomyces cerevisiae genome encodes several proteins that, in laboratory strains, can take up a stable, transmissible prion form. In each case, this requires the Asn/Gln-rich prion-forming domain (PrD) of the protein to be intact. In order to further understand the evolutionary significance of this unusual property, we have examined four different prion genes and their corresponding PrDs, from a number of naturally occurring strains of S. cerevisiae. In 4 of the 16 strains studied we identified a new allele of the SUP35 gene (SUP35delta19) that contains a 19-amino-acid deletion within the N-terminal PrD, a deletion that eliminates the prion property of Sup35p. In these strains a second prion gene, RNQ1, was found to be highly polymorphic, with eight different RNQ1 alleles detected in the six diploid strains studied. In contrast, for one other prion gene (URE2) and the sequence of the NEW1 gene encoding a PrD, no significant degree of DNA polymorphism was detected. Analysis of the naturally occurring alleles of RNQ1 and SUP35 indicated that the various polymorphisms identified were associated with DNA tandem repeats (6, 12, 33, 42 or 57 bp) within the coding sequences. The expansion and contraction of DNA repeats within the RNQ1 gene may provide an evolutionary mechanism that can ensure rapid change between the [PRION+] and [prion-] states. FAU - Resende, Catarina G AU - Resende CG AD - Research School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK. FAU - Outeiro, Tiago F AU - Outeiro TF FAU - Sands, Laina AU - Sands L FAU - Lindquist, Susan AU - Lindquist S FAU - Tuite, Mick F AU - Tuite MF LA - eng SI - GENBANK/AY028674 SI - GENBANK/AY028675 SI - GENBANK/AY028676 SI - GENBANK/AY028677 SI - GENBANK/AY028678 SI - GENBANK/AY028679 SI - GENBANK/AY028680 SI - GENBANK/AY028681 SI - GENBANK/AY028682 SI - GENBANK/AY028683 SI - GENBANK/AY028684 SI - GENBANK/AY028685 SI - GENBANK/AY028686 SI - GENBANK/AY028687 SI - GENBANK/AY028688 SI - GENBANK/AY028689 SI - GENBANK/AY028690 SI - GENBANK/AY028691 SI - GENBANK/AY028692 SI - GENBANK/AY028693 SI - GENBANK/AY028694 SI - GENBANK/AY028695 SI - GENBANK/AY028696 SI - GENBANK/AY028697 PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Mol Microbiol JT - Molecular microbiology JID - 8712028 RN - 0 (Peptide Termination Factors) RN - 0 (Prions) RN - 0 (SUP35 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Alleles MH - Amino Acid Sequence MH - Animals MH - Evolution, Molecular MH - Molecular Sequence Data MH - Peptide Termination Factors MH - *Polymorphism, Genetic MH - Prions/*genetics/metabolism MH - Saccharomyces cerevisiae/*genetics/metabolism MH - Saccharomyces cerevisiae Proteins/*genetics/metabolism MH - Sequence Alignment MH - Tandem Repeat Sequences EDAT- 2003/08/02 05:00 MHDA- 2004/03/09 05:00 CRDT- 2003/08/02 05:00 AID - 3608 [pii] PST - ppublish SO - Mol Microbiol. 2003 Aug;49(4):1005-17. PMID- 20199682 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20100316 DCOM- 20110714 LR - 20141113 IS - 1756-0500 (Electronic) IS - 1756-0500 (Linking) VI - 3 DP - 2010 TI - Identification of a new mechanism for targeting myosin II heavy chain phosphorylation by Dictyostelium myosin heavy chain kinase B. PG - 56 LID - 10.1186/1756-0500-3-56 [doi] AB - BACKGROUND: Heavy chain phosphorylation plays a central role in regulating myosin II bipolar filament assembly in Dictyostelium, as well as in higher eukaryotic nonmuscle cells. Our previous work has demonstrated that the WD-repeat domain of Dictyostelium myosin II heavy chain kinase B (MHCK-B), unlike its counterpart in MHCK-A, is not absolutely required for targeting of the kinase to phosphorylate MHC. Thus, we tested the hypothesis that an asparagine-rich and structurally disordered region that is unique to MHCK-B can by itself function in substrate targeting. FINDINGS: Biochemical assays comparing the activities of full-length MHCK-B, a truncation lacking only the WD-repeat domain (B-Delta-WD), and a truncation lacking both the N-rich region and the WD-repeat domain (B-Delta-N-WD) revealed that the N-rich region targets MHCK-B to phosphorylate MHC in a manner that leads to bipolar filament disassembly. This targeting is physiologically relevant since cellular over-expression of the B-Delta-WD truncation, but not the B-Delta-N-WD truncation, leads to dramatically reduced levels of myosin II filament assembly and associated defects in cytokinesis and multicellular development. CONCLUSIONS: The results presented here demonstrate that an intrinsically unstructured, and asparagine-rich, region of a MHCK-B can mediate specific targeting of the kinase to phosphorylate myosin II heavy chain. This targeting involves a direct binding interaction with myosin II filaments. In terms of regulating myosin bipolar filament assembly, our results suggest that factors affecting the activity of this unique region of MHCK-B could allow for regulation of MHCK-B in a manner that is distinct from the other MHCKs in Dictyostelium. FAU - Underwood, Julie AU - Underwood J AD - Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina, USA. p_steiml@uncg.edu. FAU - Greene, Jonathan AU - Greene J FAU - Steimle, Paul A AU - Steimle PA LA - eng GR - R15 GM066789/GM/NIGMS NIH HHS/United States GR - R15 GM066789-02/GM/NIGMS NIH HHS/United States PT - Journal Article DEP - 20100303 PL - England TA - BMC Res Notes JT - BMC research notes JID - 101462768 PMC - PMC2838905 OID - NLM: PMC2838905 EDAT- 2010/03/05 06:00 MHDA- 2010/03/05 06:01 CRDT- 2010/03/05 06:00 PHST- 2009/07/21 [received] PHST- 2010/03/03 [accepted] PHST- 2010/03/03 [aheadofprint] AID - 1756-0500-3-56 [pii] AID - 10.1186/1756-0500-3-56 [doi] PST - epublish SO - BMC Res Notes. 2010 Mar 3;3:56. doi: 10.1186/1756-0500-3-56. PMID- 17904099 OWN - NLM STAT- MEDLINE DA - 20071010 DCOM- 20080211 LR - 20131121 IS - 0006-291X (Print) IS - 0006-291X (Linking) VI - 363 IP - 3 DP - 2007 Nov 23 TI - Ultra-high field NMR studies of antibody binding and site-specific phosphorylation of alpha-synuclein. PG - 795-9 AB - Although biological importance of intrinsically disordered proteins is becoming recognized, NMR analyses of this class of proteins remain as tasks with more challenge because of poor chemical shift dispersion. It is expected that ultra-high field NMR spectroscopy offers improved resolution to cope with this difficulty. Here, we report an ultra-high field NMR study of alpha-synuclein, an intrinsically disordered protein identified as the major component of the Lewy bodies. Based on NMR spectral data collected at a 920 MHz proton frequency, we performed epitope mapping of an anti-alpha-synuclein monoclonal antibody, and furthermore, characterized conformational effects of phosphorylation at Ser129 of alpha-synuclein. FAU - Sasakawa, Hiroaki AU - Sasakawa H AD - Department of Structural Biology and Biomolecular Engineering, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan. FAU - Sakata, Eri AU - Sakata E FAU - Yamaguchi, Yoshiki AU - Yamaguchi Y FAU - Masuda, Masami AU - Masuda M FAU - Mori, Tetsuya AU - Mori T FAU - Kurimoto, Eiji AU - Kurimoto E FAU - Iguchi, Takeshi AU - Iguchi T FAU - Hisanaga, Shin-ichi AU - Hisanaga S FAU - Iwatsubo, Takeshi AU - Iwatsubo T FAU - Hasegawa, Masato AU - Hasegawa M FAU - Kato, Koichi AU - Kato K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070921 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Antibodies, Monoclonal) RN - 0 (Epitopes) RN - 0 (alpha-Synuclein) RN - 452VLY9402 (Serine) SB - IM MH - Antibodies, Monoclonal/immunology/*metabolism MH - Binding Sites MH - Epitope Mapping MH - Epitopes/immunology/metabolism MH - Humans MH - Magnetic Resonance Spectroscopy/*methods MH - Mutation MH - Phosphorylation MH - Serine/genetics/metabolism MH - alpha-Synuclein/genetics/immunology/*metabolism EDAT- 2007/10/02 09:00 MHDA- 2008/02/12 09:00 CRDT- 2007/10/02 09:00 PHST- 2007/09/09 [received] PHST- 2007/09/11 [accepted] PHST- 2007/09/21 [aheadofprint] AID - S0006-291X(07)02007-4 [pii] AID - 10.1016/j.bbrc.2007.09.048 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2007 Nov 23;363(3):795-9. Epub 2007 Sep 21. PMID- 24446368 OWN - NLM STAT- MEDLINE DA - 20140121 DCOM- 20140529 IS - 0065-2598 (Print) IS - 0065-2598 (Linking) VI - 805 DP - 2014 TI - Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics. PG - 331-51 LID - 10.1007/978-3-319-02970-2_14 [doi] AB - We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning. FAU - Higo, Junichi AU - Higo J AD - Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan, higo@protein.osaka-u.ac.jp. FAU - Umezawa, Koji AU - Umezawa K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Adv Exp Med Biol JT - Advances in experimental medicine and biology JID - 0121103 RN - 0 (CREB1 protein, human) RN - 0 (Cyclic AMP Response Element-Binding Protein) RN - 0 (Ligands) RN - EC 2.3.1.48 (CREB-Binding Protein) RN - EC 3.5.1.98 (Histone Deacetylases) SB - IM MH - Binding Sites MH - CREB-Binding Protein/*chemistry MH - Cyclic AMP Response Element-Binding Protein/*chemistry MH - Histone Deacetylases/*chemistry MH - Humans MH - Kinetics MH - Ligands MH - *Molecular Dynamics Simulation MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Thermodynamics EDAT- 2014/01/22 06:00 MHDA- 2014/05/30 06:00 CRDT- 2014/01/22 06:00 AID - 10.1007/978-3-319-02970-2_14 [doi] PST - ppublish SO - Adv Exp Med Biol. 2014;805:331-51. doi: 10.1007/978-3-319-02970-2_14. PMID- 22628309 OWN - NLM STAT- MEDLINE DA - 20120525 DCOM- 20120925 IS - 1437-4315 (Electronic) IS - 1431-6730 (Linking) VI - 393 IP - 6 DP - 2012 May TI - The composite nature of the interaction between nuclear receptors EcR and DHR38. PG - 457-71 LID - 10.1515/hsz-2011-0283 [doi] LID - /j/bchm.2012.393.issue-6/hsz-2011-0283/hsz-2011-0283.xml [pii] AB - Ecdysteroids coordinate essential biological processes in Drosophila through a complex of two nuclear receptors, the ecdysteroid receptor (EcR) and the ultraspiracle protein (Usp). Biochemical experiments have shown that, in contrast to Usp, the EcR molecule is characterized by high intramolecular plasticity. To investigate whether this plasticity is sufficient to form EcR complexes with nuclear receptors other than Usp, we studied the interaction of EcR with the DHR38 nuclear receptor. Previous in vitro experiments suggested that DHR38 can form complexes with Usp and thus disrupt Usp-EcR interaction with the specific hsp27pal response element. This article provides the experimental evidence that EcR is able to form complexes with DHR38 as well. The recombinant DNA-binding domains (DBDs) of EcR and DHR38 interact specifically on hsp27pal. However, the interaction between the receptors is not restricted to their isolated DBDs. We pre\xadsent data that indicate that the full-length EcR and DHR38 can also form specific complexes within the nuclei of living cells. This interaction is mediated by the hinge region of EcR, which was recently classified as an intrinsically disordered region. Our results indicate that DHR38 might modulate the activity of the Usp-EcR heterodimer by forming complexes with both of its components. FAU - Zoglowek, Anna AU - Zoglowek A AD - Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland. FAU - Orlowski, Marek AU - Orlowski M FAU - Pakula, Szymon AU - Pakula S FAU - Dutko-Gwozdz, Joanna AU - Dutko-Gwozdz J FAU - Pajdzik, Dorota AU - Pajdzik D FAU - Gwozdz, Tomasz AU - Gwozdz T FAU - Rymarczyk, Grzegorz AU - Rymarczyk G FAU - Wieczorek, Elzbieta AU - Wieczorek E FAU - Dobrucki, Jurek AU - Dobrucki J FAU - Dobryszycki, Piotr AU - Dobryszycki P FAU - Ozyhar, Andrzej AU - Ozyhar A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Biol Chem JT - Biological chemistry JID - 9700112 RN - 0 (Drosophila Proteins) RN - 0 (HSP27 Heat-Shock Proteins) RN - 0 (Hr38 protein, Drosophila) RN - 0 (Receptors, Cytoplasmic and Nuclear) RN - 0 (Receptors, Steroid) RN - 0 (ecdysteroid receptor) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Cell Line MH - Cell Survival MH - DNA/genetics/metabolism MH - Drosophila Proteins/chemistry/*metabolism MH - Drosophila melanogaster/cytology/metabolism MH - HSP27 Heat-Shock Proteins/genetics MH - Humans MH - Molecular Sequence Data MH - Promoter Regions, Genetic/genetics MH - Protein Binding MH - Protein Structure, Tertiary MH - Receptors, Cytoplasmic and Nuclear/chemistry/*metabolism MH - Receptors, Steroid/chemistry/*metabolism MH - Substrate Specificity EDAT- 2012/05/26 06:00 MHDA- 2012/09/26 06:00 CRDT- 2012/05/26 06:00 PHST- 2011/12/09 [received] PHST- 2012/03/05 [accepted] AID - 10.1515/hsz-2011-0283 [doi] AID - /j/bchm.2012.393.issue-6/hsz-2011-0283/hsz-2011-0283.xml [pii] PST - ppublish SO - Biol Chem. 2012 May;393(6):457-71. doi: 10.1515/hsz-2011-0283. PMID- 22952038 OWN - NLM STAT- MEDLINE DA - 20120906 DCOM- 20121105 LR - 20141111 IS - 1940-087X (Electronic) IS - 1940-087X (Linking) IP - 66 DP - 2012 TI - Purification and aggregation of the amyloid precursor protein intracellular domain. PG - e4204 LID - 10.3791/4204 [doi] LID - 4204 [pii] AB - Amyloid precursor protein (APP) is a type I transmembrane protein associated with the pathogenesis of Alzheimer's disease (AD). APP is characterized by a large extracellular domain and a short cytosolic domain termed the APP intracellular domain (AICD). During maturation through the secretory pathway, APP can be cleaved by proteases termed alpha, beta, and gamma-secretases. Sequential proteolytic cleavage of APP with beta and gamma-secretases leads to the production of a small proteolytic peptide, termed Abeta, which is amyloidogenic and the core constituent of senile plaques. The AICD is also liberated from the membrane after secretase processing, and through interactions with Fe65 and Tip60, can translocate to the nucleus to participate in transcription regulation of multiple target genes. Protein-protein interactions involving the AICD may affect trafficking, processing, and cellular functions of holo-APP and its C-terminal fragments. We have recently shown that AICD can aggregate in vitro, and this process is inhibited by the AD-implicated molecular chaperone ubiquilin-1. Consistent with these findings, the AICD has exposed hydrophobic domains and is intrinsically disordered in vitro, however it obtains stable secondary structure when bound to Fe65. We have proposed that ubiquilin-1 prevents inappropriate inter- and intramolecular interactions of AICD, preventing aggregation in vitro and in intact cells. While most studies focus on the role of APP in the pathogenesis of AD, the role of AICD in this process is not clear. Expression of AICD has been shown to induce apoptosis, to modulate signaling pathways, and to regulate calcium signaling. Over-expression of AICD and Fe65 in a transgenic mouse model induces Alzheimer's like pathology, and recently AICD has been detected in brain lysates by western blotting when using appropriate antigen retrieval techniques. To facilitate structural, biochemical, and biophysical studies of the AICD, we have developed a procedure to produce recombinantly large amounts of highly pure AICD protein. We further describe a method for inducing the in vitro thermal aggregation of AICD and analysis by atomic force microscopy. The methods described are useful for biochemical, biophysical, and structural characterization of the AICD and the effects of molecular chaperones on AICD aggregation. FAU - El Ayadi, Amina AU - El Ayadi A AD - Department of Surgery, University of Texas Medical Branch, USA. FAU - Stieren, Emily S AU - Stieren ES FAU - Barral, Jose M AU - Barral JM FAU - Oberhauser, Andres F AU - Oberhauser AF FAU - Boehning, Darren AU - Boehning D LA - eng GR - F30AG030878/AG/NIA NIH HHS/United States GR - P30 AG024832/AG/NIA NIH HHS/United States GR - P30-AG-024832/AG/NIA NIH HHS/United States GR - R01DK073394/DK/NIDDK NIH HHS/United States GR - R21 AG031948/AG/NIA NIH HHS/United States GR - R21AG031948/AG/NIA NIH HHS/United States GR - UL1 TR000071/TR/NCATS NIH HHS/United States GR - UL1RR029876/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Video-Audio Media DEP - 20120828 PL - United States TA - J Vis Exp JT - Journal of visualized experiments : JoVE JID - 101313252 RN - 0 (Amyloid beta-Protein Precursor) RN - 0 (Recombinant Proteins) SB - IM MH - Amyloid beta-Protein Precursor/*biosynthesis/*chemistry/genetics/isolation & purification MH - Escherichia coli/genetics/metabolism MH - Humans MH - Protein Structure, Tertiary MH - Recombinant Proteins/biosynthesis/chemistry/genetics/isolation & purification PMC - PMC3478677 MID - NIHMS407735 OID - NLM: NIHMS407735 OID - NLM: PMC3478677 EDAT- 2012/09/07 06:00 MHDA- 2012/11/06 06:00 CRDT- 2012/09/07 06:00 AID - 4204 [pii] AID - 10.3791/4204 [doi] PST - epublish SO - J Vis Exp. 2012 Aug 28;(66):e4204. doi: 10.3791/4204. PMID- 23798407 OWN - NLM STAT- MEDLINE DA - 20130710 DCOM- 20131018 LR - 20150425 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 110 IP - 28 DP - 2013 Jul 9 TI - Probing the transient dark state of substrate binding to GroEL by relaxation-based solution NMR. PG - 11361-6 LID - 10.1073/pnas.1305715110 [doi] AB - The mechanism whereby the prototypical chaperonin GroEL performs work on substrate proteins has not yet been fully elucidated, hindered by lack of detailed structural and dynamic information on the bound substrate. Previous investigations have produced conflicting reports on the state of GroEL-bound polypeptides, largely due to the transient and dynamic nature of these complexes. Here, we present a unique approach, based on combined analysis of four complementary relaxation-based NMR experiments, to probe directly the "dark" NMR-invisible state of the model, intrinsically disordered, polypeptide amyloid beta (Abeta40) bound to GroEL. The four NMR experiments, lifetime line-broadening, dark-state exchange saturation transfer, relaxation dispersion, and small exchange-induced chemical shifts, are dependent in different ways on the overall exchange rates and populations of the free and bound states of the substrate, as well as on residue-specific dynamics and structure within the bound state as reported by transverse magnetization relaxation rates and backbone chemical shifts, respectively. Global fitting of all the NMR data shows that the complex is transient with a lifetime of <1 ms, that binding involves two predominantly hydrophobic segments corresponding to predicted GroEL consensus binding sequences, and that the structure of the bound polypeptide remains intrinsically and dynamically disordered with minimal changes in secondary structure propensity relative to the free state. Our results establish a unique method to observe NMR-invisible dynamic states of GroEL-bound substrates and to describe at atomic resolution the events between substrate binding and encapsulation that are crucial for understanding the normal and stress-related metabolic function of chaperonins. FAU - Libich, David S AU - Libich DS AD - Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA. FAU - Fawzi, Nicolas L AU - Fawzi NL FAU - Ying, Jinfa AU - Ying J FAU - Clore, G Marius AU - Clore GM LA - eng GR - P20 GM104937/GM/NIGMS NIH HHS/United States GR - P20 RR024484/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural DEP - 20130624 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Chaperonin 60) RN - 0 (Escherichia coli Proteins) RN - 0 (Molecular Probes) SB - IM MH - Chaperonin 60/chemistry/*metabolism MH - Escherichia coli/metabolism MH - Escherichia coli Proteins/chemistry/*metabolism MH - Molecular Probes MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Protein Binding MH - Protein Structure, Secondary PMC - PMC3710837 OID - NLM: PMC3710837 OTO - NOTNLM OT - conformational sampling OT - protein-protein interactions OT - supramolecular machine EDAT- 2013/06/27 06:00 MHDA- 2013/10/19 06:00 CRDT- 2013/06/27 06:00 PHST- 2013/06/24 [aheadofprint] AID - 1305715110 [pii] AID - 10.1073/pnas.1305715110 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11361-6. doi: 10.1073/pnas.1305715110. Epub 2013 Jun 24. PMID- 25251363 OWN - NLM STAT- MEDLINE DA - 20141206 DCOM- 20150212 LR - 20150401 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1848 IP - 1 Pt B DP - 2015 Jan TI - Effects of naturally occurring arginine 14 deletion on phospholamban conformational dynamics and membrane interactions. PG - 315-22 LID - 10.1016/j.bbamem.2014.09.007 [doi] LID - S0005-2736(14)00322-8 [pii] AB - Phospholamban (PLN) is a single-pass membrane protein that regulates the sarco(endo)plasmic reticulum Ca(2)(+)-ATPase (SERCA). Phosphorylation of PLN at Ser16 reverses its inhibitory function under beta-adrenergic stimulation, augmenting Ca(2)(+) uptake in the sarcoplasmic reticulum and muscle contractility. PLN exists in two conformations; a T state, where the cytoplasmic domain is helical and adsorbed on the membrane surface, and an R state, where the cytoplasmic domain is unfolded and membrane detached. Previous studies have shown that the PLN conformational equilibrium is crucial to SERCA regulation. Here, we used a combination of solution and solid-state NMR to compare the structural topology and conformational dynamics of monomeric PLN (PLN(AFA)) with that of the PLN(R14del), a naturally occurring deletion mutant that is linked to the progression of dilated cardiomyopathy. We found that the behavior of the inhibitory transmembrane domain of PLN(R14del) is similar to that of the native sequence. Conversely, the conformational dynamics of R14del both in micelles and lipid membranes are enhanced. We conclude that the deletion of Arg14 in the cytoplasmic region weakens the interactions with the membrane and shifts the conformational equilibrium of PLN toward the disordered R state. This conformational transition is correlated with the loss-of-function character of this mutant and is corroborated by SERCA's activity assays. These findings support our hypothesis that SERCA function is fine-tuned by PLN conformational dynamics and begin to explain the aberrant regulation of SERCA by the R14del mutant. CI - Copyright (c) 2014 Elsevier B.V. All rights reserved. FAU - Vostrikov, Vitaly V AU - Vostrikov VV AD - Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA. FAU - Soller, Kailey J AU - Soller KJ AD - Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA. FAU - Ha, Kim N AU - Ha KN AD - Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Department of Chemistry and Biochemistry, St. Catherine University, St. Paul, MN 55105, USA. FAU - Gopinath, T AU - Gopinath T AD - Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA. FAU - Veglia, Gianluigi AU - Veglia G AD - Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address: vegli001@umn.edu. LA - eng GR - 5F31HL095361/HL/NHLBI NIH HHS/United States GR - GM072701/GM/NIGMS NIH HHS/United States GR - R01 GM072701/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140922 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Calcium-Binding Proteins) RN - 0 (Lipid Bilayers) RN - 0 (Membrane Proteins) RN - 0 (Micelles) RN - 0 (phospholamban) RN - 94ZLA3W45F (Arginine) RN - EC 3.6.3.8 (Sarcoplasmic Reticulum Calcium-Transporting ATPases) SB - IM MH - Arginine/*chemistry MH - Calcium-Binding Proteins/*chemistry MH - Lipid Bilayers/chemistry MH - Membrane Proteins/*chemistry MH - Micelles MH - Protein Conformation MH - Sarcoplasmic Reticulum Calcium-Transporting ATPases/metabolism PMC - PMC4258429 MID - NIHMS632031 OID - NLM: NIHMS632031 [Available on 01/01/16] OID - NLM: PMC4258429 [Available on 01/01/16] OTO - NOTNLM OT - Dilated cardiomyopathy OT - Membrane proteins OT - Phospholamban OT - R14 deletion OT - SERCA OT - Solid-state NMR EDAT- 2014/09/25 06:00 MHDA- 2015/02/13 06:00 CRDT- 2014/09/25 06:00 PMCR- 2016/01/01 00:00 PHST- 2014/06/30 [received] PHST- 2014/09/12 [revised] PHST- 2014/09/13 [accepted] PHST- 2014/09/22 [aheadofprint] AID - S0005-2736(14)00322-8 [pii] AID - 10.1016/j.bbamem.2014.09.007 [doi] PST - ppublish SO - Biochim Biophys Acta. 2015 Jan;1848(1 Pt B):315-22. doi: 10.1016/j.bbamem.2014.09.007. Epub 2014 Sep 22. PMID- 9398519 OWN - NLM STAT- MEDLINE DA - 19980106 DCOM- 19980106 LR - 20061115 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 274 IP - 1 DP - 1997 Nov 21 TI - The RNA binding domain of ribosomal protein L11: three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNA. PG - 101-13 AB - The three-dimensional solution structure has been determined by NMR spectroscopy of the 75 residue C-terminal domain of ribosomal protein L11 (L11-C76) in its RNA-bound state. L11-C76 recognizes and binds tightly to a highly conserved 58 nucleotide domain of 23 S ribosomal RNA, whose secondary structure consists of three helical stems and a central junction loop. The NMR data reveal that the conserved structural core of the protein, which consists of a bundle of three alpha-helices and a two-stranded parallel beta-sheet four residues in length, is nearly the same as the solution structure determined for the non-liganded form of the protein. There are however, substantial chemical shift perturbations which accompany RNA binding, the largest of which map onto an extended loop which bridges the C-terminal end of alpha-helix 1 and the first strand of parallel beta-sheet. Substantial shift perturbations are also observed in the N-terminal end of alpha-helix 1, the intervening loop that bridges helices 2 and 3, and alpha-helix 3. The four contact regions identified by the shift perturbation data also displayed protein-RNA NOEs, as identified by isotope-filtered three-dimensional NOE spectroscopy. The shift perturbation and NOE data not only implicate helix 3 as playing an important role in RNA binding, but also indicate that regions flanking helix 3 are involved as well. Loop 1 is of particular interest as it was found to be flexible and disordered for L11-C76 free in solution, but not in the RNA-bound form of the protein, where it appears rigid and adopts a specific conformation as a result of its direct contact to RNA. CI - Copyright 1997 Academic Press Limited. FAU - Hinck, A P AU - Hinck AP AD - National Institute of Dental Research, Bethesda, MD 20892-4326, USA. FAU - Markus, M A AU - Markus MA FAU - Huang, S AU - Huang S FAU - Grzesiek, S AU - Grzesiek S FAU - Kustonovich, I AU - Kustonovich I FAU - Draper, D E AU - Draper DE FAU - Torchia, D A AU - Torchia DA LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (RNA, Ribosomal, 23S) RN - 0 (RNA-Binding Proteins) RN - 0 (Ribosomal Proteins) RN - 0 (Solutions) RN - 0 (ribosomal protein L11) RN - 63231-63-0 (RNA) SB - IM MH - Amino Acid Sequence MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - *Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA/*metabolism MH - RNA, Ribosomal, 23S/*metabolism MH - RNA-Binding Proteins/*chemistry MH - Ribosomal Proteins/*chemistry/*metabolism MH - Solutions EDAT- 1998/01/10 MHDA- 1998/01/10 00:01 CRDT- 1998/01/10 00:00 AID - S0022-2836(97)91379-6 [pii] AID - 10.1006/jmbi.1997.1379 [doi] PST - ppublish SO - J Mol Biol. 1997 Nov 21;274(1):101-13. PMID- 19858290 OWN - NLM STAT- MEDLINE DA - 20091216 DCOM- 20100114 LR - 20140827 IS - 1098-5549 (Electronic) IS - 0270-7306 (Linking) VI - 30 IP - 1 DP - 2010 Jan TI - A bifunctional regulatory element in human somatic Wee1 mediates cyclin A/Cdk2 binding and Crm1-dependent nuclear export. PG - 116-30 LID - 10.1128/MCB.01876-08 [doi] AB - Sophisticated models for the regulation of mitotic entry are lacking for human cells. Inactivating human cyclin A/Cdk2 complexes through diverse approaches delays mitotic entry and promotes inhibitory phosphorylation of Cdk1 on tyrosine 15, a modification performed by Wee1. We show here that cyclin A/Cdk2 complexes physically associate with Wee1 in U2OS cells. Mutation of four conserved RXL cyclin A/Cdk binding motifs (RXL1 to RXL4) in Wee1 diminished stable binding. RXL1 resides within a large regulatory region of Wee1 that is predicted to be intrinsically disordered (residues 1 to 292). Near RXL1 is T239, a site of inhibitory Cdk phosphorylation in Xenopus Wee1 proteins. We found that T239 is phosphorylated in human Wee1 and that this phosphorylation was reduced in an RXL1 mutant. RXL1 and T239 mutants each mediated greater Cdk phosphorylation and G(2)/M inhibition than the wild type, suggesting that cyclin A/Cdk complexes inhibit human Wee1 through these sites. The RXL1 mutant uniquely also displayed increased nuclear localization. RXL1 is embedded within sequences homologous to Crm1-dependent nuclear export signals (NESs). Coimmunoprecipitation showed that Crm1 associated with Wee1. Moreover, treatment with the Crm1 inhibitor leptomycin B or independent mutation of the potential NES (NESm) abolished Wee1 nuclear export. Export was also reduced by Cdk inhibition or cyclin A RNA interference, suggesting that cyclin A/Cdk complexes contribute to Wee1 export. Somewhat surprisingly, NESm did not display increased G(2)/M inhibition. Thus, nuclear export of Wee1 is not essential for mitotic entry though an important functional role remains likely. These studies identify a novel bifunctional regulatory element in Wee1 that mediates cyclin A/Cdk2 association and nuclear export. FAU - Li, Changqing AU - Li C AD - Department of Medicine, Epigenetics and Progenitor Cell Keystone Program, Fox Chase Cancer Center, Philadelphia, Pennyslvania 19111, USA. FAU - Andrake, Mark AU - Andrake M FAU - Dunbrack, Roland AU - Dunbrack R FAU - Enders, Greg H AU - Enders GH LA - eng GR - P30 CA006927/CA/NCI NIH HHS/United States GR - R01 GM065514/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (Cell Cycle Proteins) RN - 0 (Cyclin A) RN - 0 (Cyclin E) RN - 0 (Karyopherins) RN - 0 (Nuclear Proteins) RN - 0 (Receptors, Cytoplasmic and Nuclear) RN - 0 (exportin 1 protein) RN - EC 2.7.10.1 (Protein-Tyrosine Kinases) RN - EC 2.7.10.2 (WEE1 protein, human) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 2) SB - IM MH - Active Transport, Cell Nucleus MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Cell Cycle Proteins/*physiology MH - Cell Line MH - Cell Nucleus/*metabolism MH - Conserved Sequence MH - Cyclin A/genetics/*metabolism MH - Cyclin E/metabolism MH - Cyclin-Dependent Kinase 2/*metabolism MH - G2 Phase MH - Humans MH - Karyopherins/antagonists & inhibitors/*physiology MH - Mitosis MH - Molecular Sequence Data MH - Nuclear Proteins/*physiology MH - Phosphorylation MH - Protein Binding MH - Protein Structure, Tertiary MH - Protein-Tyrosine Kinases/*physiology MH - RNA Interference MH - Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors/*physiology MH - S Phase PMC - PMC2798281 OID - NLM: PMC2798281 EDAT- 2009/10/28 06:00 MHDA- 2010/01/15 06:00 CRDT- 2009/10/28 06:00 PHST- 2009/10/26 [aheadofprint] AID - MCB.01876-08 [pii] AID - 10.1128/MCB.01876-08 [doi] PST - ppublish SO - Mol Cell Biol. 2010 Jan;30(1):116-30. doi: 10.1128/MCB.01876-08. Epub . PMID- 21665998 OWN - NLM STAT- MEDLINE DA - 20110729 DCOM- 20120308 LR - 20141022 IS - 1532-298X (Electronic) IS - 1040-4651 (Linking) VI - 23 IP - 6 DP - 2011 Jun TI - Tunable membrane binding of the intrinsically disordered dehydrin Lti30, a cold-induced plant stress protein. PG - 2391-404 LID - 10.1105/tpc.111.085183 [doi] AB - Dehydrins are intrinsically disordered plant proteins whose expression is upregulated under conditions of desiccation and cold stress. Their molecular function in ensuring plant survival is not yet known, but several studies suggest their involvement in membrane stabilization. The dehydrins are characterized by a broad repertoire of conserved and repetitive sequences, out of which the archetypical K-segment has been implicated in membrane binding. To elucidate the molecular mechanism of these K-segments, we examined the interaction between lipid membranes and a dehydrin with a basic functional sequence composition: Lti30, comprising only K-segments. Our results show that Lti30 interacts electrostatically with vesicles of both zwitterionic (phosphatidyl choline) and negatively charged phospholipids (phosphatidyl glycerol, phosphatidyl serine, and phosphatidic acid) with a stronger binding to membranes with high negative surface potential. The membrane interaction lowers the temperature of the main lipid phase transition, consistent with Lti30's proposed role in cold tolerance. Moreover, the membrane binding promotes the assembly of lipid vesicles into large and easily distinguishable aggregates. Using these aggregates as binding markers, we identify three factors that regulate the lipid interaction of Lti30 in vitro: (1) a pH dependent His on/off switch, (2) phosphorylation by protein kinase C, and (3) reversal of membrane binding by proteolytic digest. FAU - Eriksson, Sylvia K AU - Eriksson SK AD - Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, 106 91 Stockholm, Sweden. FAU - Kutzer, Michael AU - Kutzer M FAU - Procek, Jan AU - Procek J FAU - Grobner, Gerhard AU - Grobner G FAU - Harryson, Pia AU - Harryson P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110610 PL - United States TA - Plant Cell JT - The Plant cell JID - 9208688 RN - 0 (Arabidopsis Proteins) RN - 0 (Cold Shock Proteins and Peptides) RN - 0 (Phospholipids) RN - 0 (XERO2 protein, Arabidopsis) SB - IM MH - Amino Acid Sequence MH - Arabidopsis/cytology/metabolism MH - Arabidopsis Proteins/*chemistry/genetics/*metabolism MH - Calorimetry, Differential Scanning MH - Cell Membrane/chemistry/*metabolism MH - Cold Shock Proteins and Peptides/*chemistry/genetics/*metabolism MH - Hydrogen-Ion Concentration MH - Molecular Sequence Data MH - Phospholipids/chemistry/metabolism MH - Protein Binding MH - Protein Conformation MH - Static Electricity MH - Surface Plasmon Resonance MH - Temperature MH - Thylakoids/chemistry/ultrastructure PMC - PMC3160030 OID - NLM: PMC3160030 EDAT- 2011/06/15 06:00 MHDA- 2012/03/09 06:00 CRDT- 2011/06/14 06:00 PHST- 2011/06/10 [aheadofprint] AID - tpc.111.085183 [pii] AID - 10.1105/tpc.111.085183 [doi] PST - ppublish SO - Plant Cell. 2011 Jun;23(6):2391-404. doi: 10.1105/tpc.111.085183. Epub 2011 Jun 10. PMID- 14514667 OWN - NLM STAT- MEDLINE DA - 20031208 DCOM- 20040115 LR - 20141120 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 50 DP - 2003 Dec 12 TI - Crystal structure of the yeast Phox homology (PX) domain protein Grd19p complexed to phosphatidylinositol-3-phosphate. PG - 50371-6 AB - Phox homology (PX) domains have been recently identified in a number of different proteins and are involved in various cellular functions such as vacuolar targeting and membrane protein trafficking. It was shown that these modules of about 130 amino acids specifically binding to phosphoinositides and that this interaction is crucial for their cellular function. The yeast genome contains 17 PX domain proteins. One of these, Grd19p, is involved in the localization of the late Golgi membrane proteins DPAP A and Kex2p. Grd19p consists of the PX domain with 30 extra residues at the N-terminal and is homologous to the functionally characterized human sorting nexin protein SNX3. We determined the 2.0 A crystal structure of Grd19p in the free form and in complex with d-myo-phosphatidylinositol 3-phosphate (diC4PtdIns(3)P), representing the first case of both free and ligand-bound conformations of the same PX module. The ligand occupies a well defined positively charged binding pocket at the interface between the beta-sheet and alpha-helical parts of the molecule. The structure of the free and bound protein are globally similar but show some significant differences in a region containing a polyproline peptide and a putative membrane attachment site. FAU - Zhou, Cong-Zhao AU - Zhou CZ AD - Institut de Biochimie et de Biophysique Moleculaire et Cellulaire (CNRS-Unite Mixte de Recherche 8619), Universite Paris-Sud, Bat. 430, 91405 Orsay, France. FAU - Li de La Sierra-Gallay, Ines AU - Li de La Sierra-Gallay I FAU - Quevillon-Cheruel, Sophie AU - Quevillon-Cheruel S FAU - Collinet, Bruno AU - Collinet B FAU - Minard, Philippe AU - Minard P FAU - Blondeau, Karine AU - Blondeau K FAU - Henckes, Gilles AU - Henckes G FAU - Aufrere, Robert AU - Aufrere R FAU - Leulliot, Nicolas AU - Leulliot N FAU - Graille, Marc AU - Graille M FAU - Sorel, Isabelle AU - Sorel I FAU - Savarin, Philippe AU - Savarin P FAU - de la Torre, Francoise AU - de la Torre F FAU - Poupon, Anne AU - Poupon A FAU - Janin, Joel AU - Janin J FAU - van Tilbeurgh, Herman AU - van Tilbeurgh H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030926 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Carrier Proteins) RN - 0 (Fungal Proteins) RN - 0 (Ligands) RN - 0 (Peptides) RN - 0 (Phosphates) RN - 0 (SNX3 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Vesicular Transport Proteins) RN - 25191-13-3 (polyproline) RN - EC 3.1.3.- (Phosphoric Monoester Hydrolases) RN - EC 3.1.3.64 (phosphatidylinositol-3-phosphatase) SB - IM MH - Amino Acid Sequence MH - Carrier Proteins/*chemistry/metabolism MH - Cell Membrane/metabolism MH - Cloning, Molecular MH - Crystallography, X-Ray MH - Fungal Proteins/chemistry MH - Genome, Fungal MH - Golgi Apparatus/metabolism MH - Intracellular Membranes/metabolism MH - Ligands MH - Models, Molecular MH - Molecular Sequence Data MH - Open Reading Frames MH - Peptides/chemistry MH - Phosphates/*chemistry MH - Phosphoric Monoester Hydrolases/*chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae Proteins/*chemistry/metabolism MH - Sequence Homology, Amino Acid MH - *Vesicular Transport Proteins EDAT- 2003/09/30 05:00 MHDA- 2004/01/16 05:00 CRDT- 2003/09/30 05:00 PHST- 2003/09/26 [aheadofprint] AID - 10.1074/jbc.M304392200 [doi] AID - M304392200 [pii] PST - ppublish SO - J Biol Chem. 2003 Dec 12;278(50):50371-6. Epub 2003 Sep 26. PMID- 24077017 OWN - NLM STAT- MEDLINE DA - 20140820 DCOM- 20150423 IS - 1546-4156 (Electronic) IS - 0893-0341 (Linking) VI - 28 IP - 3 DP - 2014 Jul-Sep TI - Altered levels of amyloid precursor protein intracellular domain-interacting proteins in Alzheimer disease. PG - 283-90 LID - 10.1097/WAD.0000000000000011 [doi] AB - BACKGROUND: The amyloid precursor protein intracellular domain (AICD) is an intrinsically unstructured molecule with functional promiscuity that plays an important role in determining the fate of the neurons during its degeneration. Its association with Alzheimer disease (AD) recently played a key role in propelling scientists to choose AICD as a major molecule of interest. Although several studies have been conducted elucidating AICD's participation in inducing neurodegenerative outcomes in AD condition, much remains to be deciphered regarding the linkage of AICD with cellular pathways in the AD scenario. RESULTS: In the present study, we have pulled down interactors of nonphosphorylated AICD from the cerebrospinal fluid of AD subjects, identified them by matrix assisted laser desorption ionization mass spectrometry, and subsequently studied the differential expression of these interactors in AD and control cases by 2-dimensional difference gel electrophoresis. The study has yielded some AICD-interactors that are differentially expressed in the AD cases and are involved in diverse cellular functions. CONCLUSIONS: This proteomic-based approach highlights the first step in finding the possible cellular pathways engaged in AD pathophysiology on the basis of interaction of one or more of their members with AICD. FAU - Chakrabarti, Arunabha AU - Chakrabarti A AD - *Structural Genomics Division, Saha Institute of Nuclear Physics daggerDepartment of Medicine, Nilratan Sircar Medical College, Kolkata, West Bengal, India. FAU - Chatterjee, Atri AU - Chatterjee A FAU - Sengupta, Mohor B AU - Sengupta MB FAU - Chattopadhyay, Partha AU - Chattopadhyay P FAU - Mukhopadhyay, Debashis AU - Mukhopadhyay D LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Alzheimer Dis Assoc Disord JT - Alzheimer disease and associated disorders JID - 8704771 RN - 0 (Amyloid beta-Protein Precursor) RN - 0 (Biological Markers) SB - IM MH - Aged MH - Alzheimer Disease/*metabolism/pathology MH - Amyloid beta-Protein Precursor/*metabolism MH - Biological Markers/*cerebrospinal fluid MH - Blotting, Western MH - Electrophoresis, Gel, Two-Dimensional MH - Female MH - Humans MH - Immunoprecipitation MH - Male MH - Phosphorylation MH - Protein Structure, Tertiary MH - Proteomics MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization EDAT- 2013/10/01 06:00 MHDA- 2015/04/24 06:00 CRDT- 2013/10/01 06:00 AID - 10.1097/WAD.0000000000000011 [doi] PST - ppublish SO - Alzheimer Dis Assoc Disord. 2014 Jul-Sep;28(3):283-90. doi: 10.1097/WAD.0000000000000011. PMID- 24977921 OWN - NLM STAT- MEDLINE DA - 20140715 DCOM- 20140909 LR - 20150630 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 27 DP - 2014 Jul 15 TI - The intrinsically disordered C-RING biomineralization protein, AP7, creates protein phases that introduce nanopatterning and nanoporosities into mineral crystals. PG - 4317-9 LID - 10.1021/bi500664w [doi] AB - We report an interesting process whereby the formation of nanoparticle assemblies on and nanoporosities within calcite crystals is directed by an intrinsically disordered C-RING mollusk shell nacre protein, AP7. Under mineralization conditions, AP7 forms protein phases that direct the nucleation of ordered calcite nanoparticles via a repetitive protein phase deposition process onto calcite crystals. These organized nanoparticles are separated by gaps or spaces that become incorporated into the forming bulk crystal as nanoporosities. This is an unusual example of organized nanoparticle biosynthesis and mineral modification directed by a C-RING protein phase. FAU - Chang, Eric P AU - Chang EP AD - Laboratory for Chemical Physics, Department of Skeletal Biology, New York University , New York, New York 10012, United States. FAU - Russ, Jennie A AU - Russ JA FAU - Verch, Andreas AU - Verch A FAU - Kroger, Roland AU - Kroger R FAU - Estroff, Lara A AU - Estroff LA FAU - Evans, John Spencer AU - Evans JS LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140702 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Nacre) SB - IM MH - Animal Shells/*chemistry MH - Animals MH - Calcification, Physiologic MH - Crystallization MH - Intrinsically Disordered Proteins/*chemistry MH - *Mollusca MH - Nacre/*chemistry MH - Nanoparticles/*chemistry MH - Porosity PMC - PMC4215888 OID - NLM: PMC4215888 EDAT- 2014/07/01 06:00 MHDA- 2014/09/10 06:00 CRDT- 2014/07/01 06:00 PHST- 2014/07/02 [aheadofprint] AID - 10.1021/bi500664w [doi] PST - ppublish SO - Biochemistry. 2014 Jul 15;53(27):4317-9. doi: 10.1021/bi500664w. Epub 2014 Jul 2. PMID- 11408620 OWN - NLM STAT- MEDLINE DA - 20010625 DCOM- 20010712 LR - 20131121 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 292 IP - 5525 DP - 2001 Jun 22 TI - The human nuclear xenobiotic receptor PXR: structural determinants of directed promiscuity. PG - 2329-33 AB - The human nuclear pregnane X receptor (hPXR) activates cytochrome P450-3A expression in response to a wide variety of xenobiotics and plays a critical role in mediating dangerous drug-drug interactions. We present the crystal structures of the ligand-binding domain of hPXR both alone and in complex with the cholesterol-lowering drug SR12813 at resolutions of 2.5 and 2.75 angstroms, respectively. The hydrophobic ligand-binding cavity of hPXR contains a small number of polar residues, permitting SR12813 to bind in three distinct orientations. The position and nature of these polar residues were found to be critical for establishing the precise pharmacologic activation profile of PXR. Our findings provide important insights into how hPXR detects xenobiotics and may prove useful in predicting and avoiding drug-drug interactions. FAU - Watkins, R E AU - Watkins RE AD - Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, NC 27599, USA. FAU - Wisely, G B AU - Wisely GB FAU - Moore, L B AU - Moore LB FAU - Collins, J L AU - Collins JL FAU - Lambert, M H AU - Lambert MH FAU - Williams, S P AU - Williams SP FAU - Willson, T M AU - Willson TM FAU - Kliewer, S A AU - Kliewer SA FAU - Redinbo, M R AU - Redinbo MR LA - eng SI - PDB/1ILG SI - PDB/1ILH PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20010614 PL - United States TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Diphosphonates) RN - 0 (Ligands) RN - 0 (Receptors, Cytoplasmic and Nuclear) RN - 0 (Receptors, Steroid) RN - 0 (SR 12813) RN - 0 (Xenobiotics) RN - 0 (pregnane X receptor) RN - VJT6J7R4TR (Rifampin) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - Diphosphonates/chemistry/*metabolism MH - Humans MH - Ligands MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Cytoplasmic and Nuclear/*chemistry/*metabolism MH - Receptors, Steroid/*chemistry/*metabolism MH - Rifampin/metabolism MH - Xenobiotics/*metabolism EDAT- 2001/06/16 10:00 MHDA- 2001/07/13 10:01 CRDT- 2001/06/16 10:00 PHST- 2001/06/14 [aheadofprint] AID - 10.1126/science.1060762 [doi] AID - 1060762 [pii] PST - ppublish SO - Science. 2001 Jun 22;292(5525):2329-33. Epub 2001 Jun 14. PMID- 21457718 OWN - NLM STAT- MEDLINE DA - 20110520 DCOM- 20110803 LR - 20140820 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 409 IP - 3 DP - 2011 Jun 10 TI - Interaction of the p53 DNA-binding domain with its n-terminal extension modulates the stability of the p53 tetramer. PG - 358-68 LID - 10.1016/j.jmb.2011.03.047 [doi] AB - The tetrameric tumor suppressor p53 plays a pivotal role in the control of the cell cycle and provides a paradigm for an emerging class of oligomeric, multidomain proteins with structured and intrinsically disordered regions. Many of its biophysical and functional properties have been extrapolated from truncated variants, yet the exact structural and functional role of certain segments of the protein is unclear. We found from NMR and X-ray crystallography that the DNA-binding domain (DBD) of human p53, usually defined as residues 94-292, extends beyond these domain boundaries. Trp91, in the hinge region between the disordered proline-rich N-terminal domain and the DBD, folds back onto the latter and has a cation-pi interaction with Arg174. These additional interactions increase the melting temperature of the DBD by up to 2 degrees C and inhibit aggregation of the p53 tetramer. They also modulate the dissociation of the p53 tetramer. The absence of the Trp91/Arg174 packing presumably allows nonnative DBD-DBD interactions that both nucleate aggregation and stabilize the interface. These data have important implications for studies of multidomain proteins in general, highlighting the fact that weak ordered-disordered domain interactions can modulate the properties of proteins of complex structure. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Natan, Eviatar AU - Natan E AD - MRC Laboratory of Molecular Biology, Cambridge, UK. FAU - Baloglu, Cetin AU - Baloglu C FAU - Pagel, Kevin AU - Pagel K FAU - Freund, Stefan M V AU - Freund SM FAU - Morgner, Nina AU - Morgner N FAU - Robinson, Carol V AU - Robinson CV FAU - Fersht, Alan R AU - Fersht AR FAU - Joerger, Andreas C AU - Joerger AC LA - eng GR - G0901534/Medical Research Council/United Kingdom GR - MC_UP_A024_1010/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110330 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Amino Acid Sequence MH - Crystallography, X-Ray MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Folding MH - *Protein Interaction Domains and Motifs MH - Protein Stability MH - Tumor Suppressor Protein p53/*chemistry/genetics PMC - PMC3176915 OID - NLM: PMC3176915 EDAT- 2011/04/05 06:00 MHDA- 2011/08/04 06:00 CRDT- 2011/04/05 06:00 PHST- 2011/02/11 [received] PHST- 2011/03/22 [revised] PHST- 2011/03/23 [accepted] PHST- 2011/03/30 [aheadofprint] AID - S0022-2836(11)00336-6 [pii] AID - 10.1016/j.jmb.2011.03.047 [doi] PST - ppublish SO - J Mol Biol. 2011 Jun 10;409(3):358-68. doi: 10.1016/j.jmb.2011.03.047. Epub 2011 Mar 30. PMID- 14982446 OWN - NLM STAT- MEDLINE DA - 20040225 DCOM- 20040519 LR - 20131121 IS - 0002-7863 (Print) IS - 0002-7863 (Linking) VI - 126 IP - 8 DP - 2004 Mar 3 TI - Raman spectroscopic characterization of secondary structure in natively unfolded proteins: alpha-synuclein. PG - 2399-408 AB - The application of Raman spectroscopy to characterize natively unfolded proteins has been underdeveloped, even though it has significant technical advantages. We propose that a simple three-component band fitting of the amide I region can assist in the conformational characterization of the ensemble of structures present in natively unfolded proteins. The Raman spectra of alpha-synuclein, a prototypical natively unfolded protein, were obtained in the presence and absence of methanol, sodium dodecyl sulfate (SDS), and hexafluoro-2-propanol (HFIP). Consistent with previous CD studies, the secondary structure becomes largely alpha-helical in HFIP and SDS and predominantly beta-sheet in 25% methanol in water. In SDS, an increase in alpha-helical conformation is indicated by the predominant Raman amide I marker band at 1654 cm(-1) and the typical double minimum in the CD spectrum. In 25% HFIP the amide I Raman marker band appears at 1653 cm(-1) with a peak width at half-height of approximately 33 cm(-1), and in 25% methanol the amide I Raman band shifts to 1667 cm(-1) with a peak width at half-height of approximately 26 cm(-1). These well-characterized structural states provide the unequivocal assignment of amide I marker bands in the Raman spectrum of alpha-synuclein and by extrapolation to other natively unfolded proteins. The Raman spectrum of monomeric alpha-synuclein in aqueous solution suggests that the peptide bonds are distributed in both the alpha-helical and extended beta-regions of Ramachandran space. A higher frequency feature of the alpha-synuclein Raman amide I band resembles the Raman amide I band of ionized polyglutamate and polylysine, peptides which adopt a polyproline II helical conformation. Thus, a three-component band fitting is used to characterize the Raman amide I band of alpha-synuclein, phosvitin, alpha-casein, beta-casein, and the non-A beta component (NAC) of Alzheimer's plaque. These analyses demonstrate the ability of Raman spectroscopy to characterize the ensemble of secondary structures present in natively unfolded proteins. FAU - Maiti, Nakul C AU - Maiti NC AD - Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA. FAU - Apetri, Mihaela M AU - Apetri MM FAU - Zagorski, Michael G AU - Zagorski MG FAU - Carey, Paul R AU - Carey PR FAU - Anderson, Vernon E AU - Anderson VE LA - eng GR - AG14249/AG/NIA NIH HHS/United States GR - GM 54072/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Amides) RN - 0 (Amyloid) RN - 0 (Caseins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Propanols) RN - 0 (Recombinant Proteins) RN - 0 (SNCA protein, human) RN - 0 (Solutions) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - 9008-96-2 (Phosvitin) RN - 920-66-1 (hexafluoroisopropanol) RN - Y4S76JWI15 (Methanol) SB - IM MH - Amides/chemistry MH - Amino Acid Sequence MH - Amyloid/chemistry MH - Caseins/chemistry MH - Circular Dichroism MH - Humans MH - Methanol/chemistry MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*chemistry MH - Phosvitin/chemistry MH - Propanols/chemistry MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry MH - Sodium Dodecyl Sulfate/chemistry MH - Solutions MH - Spectrum Analysis, Raman/*methods MH - Synucleins MH - alpha-Synuclein EDAT- 2004/02/26 05:00 MHDA- 2004/05/20 05:00 CRDT- 2004/02/26 05:00 AID - 10.1021/ja0356176 [doi] PST - ppublish SO - J Am Chem Soc. 2004 Mar 3;126(8):2399-408. PMID- 24497973 OWN - NLM STAT- MEDLINE DA - 20140205 DCOM- 20141222 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 1 DP - 2014 TI - TDP-43 inclusion bodies formed in bacteria are structurally amorphous, non-amyloid and inherently toxic to neuroblastoma cells. PG - e86720 LID - 10.1371/journal.pone.0086720 [doi] AB - Accumulation of ubiquitin-positive, tau- and alpha-synuclein-negative intracellular inclusions of TDP-43 in the central nervous system represents the major hallmark correlated to amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitin-positive inclusions. Such inclusions have variably been described as amorphous aggregates or more structured deposits having an amyloid structure. Following the observations that bacterial inclusion bodies generally consist of amyloid aggregates, we have overexpressed full-length TDP-43 and C-terminal TDP-43 in E. coli, purified the resulting full-length and C-terminal TDP-43 containing inclusion bodies (FL and Ct TDP-43 IBs) and subjected them to biophysical analyses to assess their structure/morphology. We show that both FL and Ct TDP-43 aggregates contained in the bacterial IBs do not bind amyloid dyes such as thioflavin T and Congo red, possess a disordered secondary structure, as inferred using circular dichroism and infrared spectroscopies, and are susceptible to proteinase K digestion, thus possessing none of the hallmarks for amyloid. Moreover, atomic force microscopy revealed an irregular structure for both types of TDP-43 IBs and confirmed the absence of amyloid-like species after proteinase K treatment. Cell biology experiments showed that FL TDP-43 IBs were able to impair the viability of cultured neuroblastoma cells when added to their extracellular medium and, more markedly, when transfected into their cytosol, where they are at least in part ubiquitinated and phosphorylated. These data reveal an inherently high propensity of TDP-43 to form amorphous aggregates, which possess, however, an inherently high ability to cause cell dysfunction. This indicates that a gain of toxic function caused by TDP-43 deposits is effective in TDP-43 pathologies, in addition to possible loss of function mechanisms originating from the cellular mistrafficking of the protein. FAU - Capitini, Claudia AU - Capitini C AD - Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy. FAU - Conti, Simona AU - Conti S AD - Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy. FAU - Perni, Michele AU - Perni M AD - Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy. FAU - Guidi, Francesca AU - Guidi F AD - Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy. FAU - Cascella, Roberta AU - Cascella R AD - Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy. FAU - De Poli, Angela AU - De Poli A AD - Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy. FAU - Penco, Amanda AU - Penco A AD - Department of Physics, University of Genoa, Genoa, Italy. FAU - Relini, Annalisa AU - Relini A AD - Department of Physics, University of Genoa, Genoa, Italy. FAU - Cecchi, Cristina AU - Cecchi C AD - Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy. FAU - Chiti, Fabrizio AU - Chiti F AD - Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140130 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Amyloid) RN - 0 (DNA-Binding Proteins) RN - 0 (protein TDP-43) RN - EC 3.4.21.64 (Endopeptidase K) SB - IM MH - Amyloid/chemistry MH - Cell Line, Tumor MH - Cell Survival MH - DNA-Binding Proteins/*chemistry/physiology/ultrastructure MH - Endopeptidase K/chemistry MH - Escherichia coli MH - Humans MH - Inclusion Bodies/ultrastructure MH - Microscopy, Atomic Force MH - Neuroblastoma MH - Phosphorylation MH - Protein Binding MH - Protein Structure, Secondary MH - Proteolysis MH - Transfection MH - Ubiquitination PMC - PMC3907574 OID - NLM: PMC3907574 EDAT- 2014/02/06 06:00 MHDA- 2014/12/23 06:00 CRDT- 2014/02/06 06:00 PHST- 2014 [ecollection] PHST- 2013/10/17 [received] PHST- 2013/12/13 [accepted] PHST- 2014/01/30 [epublish] AID - 10.1371/journal.pone.0086720 [doi] AID - PONE-D-13-42582 [pii] PST - epublish SO - PLoS One. 2014 Jan 30;9(1):e86720. doi: 10.1371/journal.pone.0086720. eCollection 2014. PMID- 12679809 OWN - NLM STAT- MEDLINE DA - 20030425 DCOM- 20030616 LR - 20061115 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 10 IP - 5 DP - 2003 May TI - Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport. PG - 386-93 AB - GGAs are critical for trafficking soluble proteins from the trans-Golgi network (TGN) to endosomes/lysosomes through interactions with TGN-sorting receptors, ADP-ribosylation factor (ARF) and clathrin. ARF-GTP bound to TGN membranes recruits its effector GGA by binding to the GAT domain, thus facilitating recognition of GGA for cargo-loaded receptors. Here we report the X-ray crystal structures of the human GGA1-GAT domain and the complex between ARF1-GTP and the N-terminal region of the GAT domain. When unbound, the GAT domain forms an elongated bundle of three a-helices with a hydrophobic core. Structurally, this domain, combined with the preceding VHS domain, resembles CALM, an AP180 homolog involved in endocytosis. In the complex with ARF1-GTP, a helix-loop-helix of the N-terminal part of GGA1-GAT interacts with the switches 1 and 2 of ARF1 predominantly in a hydrophobic manner. These data reveal a molecular mechanism underlying membrane recruitment of adaptor proteins by ARF-GTP. FAU - Shiba, Tomoo AU - Shiba T AD - Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan. FAU - Kawasaki, Masato AU - Kawasaki M FAU - Takatsu, Hiroyuki AU - Takatsu H FAU - Nogi, Terukazu AU - Nogi T FAU - Matsugaki, Naohiro AU - Matsugaki N FAU - Igarashi, Noriyuki AU - Igarashi N FAU - Suzuki, Mamoru AU - Suzuki M FAU - Kato, Ryuichi AU - Kato R FAU - Nakayama, Kazuhisa AU - Nakayama K FAU - Wakatsuki, Soichi AU - Wakatsuki S LA - eng SI - PDB/1HFV SI - PDB/1J2H SI - PDB/1J2I SI - PDB/1J2J PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Adaptor Proteins, Vesicular Transport) RN - 0 (Carrier Proteins) RN - 0 (GGA adaptor proteins) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 86-01-1 (Guanosine Triphosphate) RN - EC 3.6.5.2 (ADP-Ribosylation Factor 1) RN - EC 3.6.5.2 (ADP-Ribosylation Factors) SB - IM MH - ADP-Ribosylation Factor 1/chemistry/metabolism MH - ADP-Ribosylation Factors/*chemistry/isolation & purification/*metabolism MH - *Adaptor Proteins, Vesicular Transport MH - Amino Acid Sequence MH - Binding Sites MH - Carrier Proteins/chemistry/isolation & purification/*metabolism MH - Circular Dichroism MH - Cloning, Molecular MH - Crystallography, X-Ray MH - Guanosine Triphosphate/metabolism MH - Humans MH - Kinetics MH - Lysosomes/metabolism/ultrastructure MH - Models, Molecular MH - Molecular Sequence Data MH - Peptide Fragments/metabolism MH - Protein Structure, Secondary MH - Protein Transport MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - trans-Golgi Network/*metabolism/ultrastructure EDAT- 2003/04/08 05:00 MHDA- 2003/06/17 05:00 CRDT- 2003/04/08 05:00 PHST- 2003/01/21 [received] PHST- 2003/03/19 [accepted] AID - 10.1038/nsb920 [doi] AID - nsb920 [pii] PST - ppublish SO - Nat Struct Biol. 2003 May;10(5):386-93. PMID- 20173328 OWN - NLM STAT- MEDLINE DA - 20100414 DCOM- 20100721 LR - 20140730 IS - 1660-2862 (Electronic) IS - 1660-2854 (Linking) VI - 7 IP - 1-3 DP - 2010 TI - Acetylcholinesterase variants in Alzheimer's disease: from neuroprotection to programmed cell death. PG - 60-3 LID - 10.1159/000285507 [doi] AB - BACKGROUND: In Alzheimer's disease (AD), cholinergic neurons are particularly vulnerable for as yet unclear reasons. Here, we report that modified composition, localization and properties of alternative splice variants encoding the acetylcholine-hydrolyzing enzyme acetylcholinesterase (AChE) may be variably involved in disease progression or in systemic efforts to attenuate its progression. OBJECTIVE: The purpose of this study was to explore the implications for AD of the cellular and biochemical properties of the various AChE proteins, differing in their N and C termini. METHODS: We have used cell transfection with genetically engineered vectors as well as microinjection to overexpress specific AChE variants and explore the consequences to cellular well-being and survival. Additionally, we employed highly purified recombinant AChE-R and AChE-S to explore putative interactions with the AD beta-amyloid peptide. RESULTS: Our findings demonstrate distinct, and in certain cases inverse cell fate outcome under enforced expression of the human N- and C-terminally modified AChE variants, all of which have similar enzymatic activities. CONCLUSION: The N-terminal extension in conjunction with the primary helical C-terminal peptide of 'tailed' AChE-S facilitates, whereas the shorter, naturally unfolded C-terminus of the stress-induced AChE-R variant attenuates Alzheimer's pathology. CI - Copyright 2010 S. Karger AG, Basel. FAU - Greenberg, David S AU - Greenberg DS AD - Department of Biological Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, Israel. FAU - Toiber, Debra AU - Toiber D FAU - Berson, Amit AU - Berson A FAU - Soreq, Hermona AU - Soreq H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100218 PL - Switzerland TA - Neurodegener Dis JT - Neuro-degenerative diseases JID - 101189034 RN - 0 (Amyloid beta-Protein Precursor) RN - 0 (Peptides) RN - 0 (RNA, Messenger) RN - EC 3.1.1.7 (Acetylcholinesterase) SB - IM MH - Acetylcholinesterase/*genetics/metabolism MH - *Alzheimer Disease/genetics/metabolism/pathology MH - Amyloid beta-Protein Precursor/genetics MH - Animals MH - Apoptosis/*genetics MH - Case-Control Studies MH - Cells, Cultured MH - Hippocampus/pathology MH - Humans MH - Mice MH - Mice, Transgenic MH - Neurons/metabolism/*pathology MH - Peptides/genetics/metabolism MH - RNA, Messenger/metabolism MH - Statistics, Nonparametric EDAT- 2010/02/23 06:00 MHDA- 2010/07/22 06:00 CRDT- 2010/02/23 06:00 PHST- 2010/02/18 [aheadofprint] AID - 000285507 [pii] AID - 10.1159/000285507 [doi] PST - ppublish SO - Neurodegener Dis. 2010;7(1-3):60-3. doi: 10.1159/000285507. Epub 2010 Feb 18. PMID- 8602259 OWN - NLM STAT- MEDLINE DA - 19960508 DCOM- 19960508 LR - 20140219 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 380 IP - 6575 DP - 1996 Apr 18 TI - Crystal structure of a mammalian phosphoinositide-specific phospholipase C delta. PG - 595-602 AB - Mammalian phosphoinositide-specific phospholipase C enzymes (PI-PLC) act as signal transducers that generate two second messengers, inositol-1,4,5-trisphosphate and diacylglycerol. The 2.4-A structure of phospholipase C delta 1 reveals a multidomain protein incorporating modules shared by many signalling proteins. The structure suggests a mechanism for membrane attachment and Ca2+-dependent hydrolysis of second-messenger precursors. The regulation and reversible membrane association of PI-PLC may serve as a model for understanding other multidomain enzymes involved in phospholipid signalling. FAU - Essen, L O AU - Essen LO AD - Center for Protein Engineering, MRC Centre, Cambridge, UK. FAU - Perisic, O AU - Perisic O FAU - Cheung, R AU - Cheung R FAU - Katan, M AU - Katan M FAU - Williams, R L AU - Williams RL LA - eng GR - MC_U105184308/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Isoenzymes) RN - 0 (Recombinant Proteins) RN - 85166-31-0 (Inositol 1,4,5-Trisphosphate) RN - EC 3.1.4.- (Phosphoric Diester Hydrolases) RN - EC 3.1.4.11 (Phosphoinositide Phospholipase C) RN - EC 3.1.4.11 (Phospholipase C delta) SB - IM CIN - Nature. 1996 Apr 18;380(6575):581-3. PMID: 8602254 MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Catalysis MH - Cell Membrane/metabolism MH - Crystallography, X-Ray MH - Humans MH - Hydrolysis MH - Inositol 1,4,5-Trisphosphate/metabolism MH - Isoenzymes/*chemistry/metabolism MH - Models, Molecular MH - Molecular Conformation MH - Molecular Sequence Data MH - Phosphoinositide Phospholipase C MH - Phospholipase C delta MH - Phosphoric Diester Hydrolases/*chemistry/metabolism MH - Protein Binding MH - Protein Conformation MH - Rats MH - Recombinant Proteins/chemistry/metabolism MH - Second Messenger Systems MH - Sequence Homology, Amino Acid EDAT- 1996/04/18 MHDA- 1996/04/18 00:01 CRDT- 1996/04/18 00:00 AID - 10.1038/380595a0 [doi] PST - ppublish SO - Nature. 1996 Apr 18;380(6575):595-602. PMID- 24810720 OWN - NLM STAT- In-Process DA - 20140509 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 4 DP - 2014 TI - Transcriptional repressor domain of MBD1 is intrinsically disordered and interacts with its binding partners in a selective manner. PG - 4896 LID - 10.1038/srep04896 [doi] AB - Methylation of DNA CpG sites is a major mechanism of epigenetic gene silencing and plays important roles in cell division, development and carcinogenesis. One of its regulators is the 64-residue C-terminal Transcriptional Repressor Domain (the TRD) of MBD1, which recruits several repressor proteins such as MCAF1, HDAC3 and MPG that are essential for the gene silencing. Using NMR spectroscopy, we have characterized the solution structure of the C-terminus of MBD1 (MBD1-c, residues D507 to Q605), which included the TRD (A529 to P592). Surprisingly, the MBD1-c is intrinsically disordered. Despite its lack of a tertiary folding, MBD1-c could still bind to different partner proteins in a selective manner. MPG and MCAF1Delta8 showed binding to both the N-terminal and C-terminal residues of MBD1-c but HDAC3 preferably bound to the C-terminal region. This study reveals how MBD1-c discriminates different binding partners, and thus, expands our understanding of the mechanisms of gene regulation by MBD1. FAU - Hameed, Umar Farook Shahul AU - Hameed UF AD - 1] Department of Biological Sciences, National University of Singapore, Singapore 117543 [2]. FAU - Lim, Jackwee AU - Lim J AD - 1] Department of Biological Sciences, National University of Singapore, Singapore 117543 [2]. FAU - Zhang, Qian AU - Zhang Q AD - Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. FAU - Wasik, Mariusz A AU - Wasik MA AD - Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. FAU - Yang, Daiwen AU - Yang D AD - Department of Biological Sciences, National University of Singapore, Singapore 117543. FAU - Swaminathan, Kunchithapadam AU - Swaminathan K AD - Department of Biological Sciences, National University of Singapore, Singapore 117543. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140509 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM PMC - PMC4014985 OID - NLM: PMC4014985 EDAT- 2014/05/09 06:00 MHDA- 2014/05/09 06:00 CRDT- 2014/05/10 06:00 PHST- 2013/07/17 [received] PHST- 2014/02/28 [accepted] AID - srep04896 [pii] AID - 10.1038/srep04896 [doi] PST - epublish SO - Sci Rep. 2014 May 9;4:4896. doi: 10.1038/srep04896. PMID- 20536449 OWN - NLM STAT- MEDLINE DA - 20100611 DCOM- 20100701 LR - 20111117 IS - 1749-6632 (Electronic) IS - 0077-8923 (Linking) VI - 1194 DP - 2010 Apr TI - Multifunctionality of the beta-thymosin/WH2 module: G-actin sequestration, actin filament growth, nucleation, and severing. PG - 44-52 LID - 10.1111/j.1749-6632.2010.05473.x [doi] AB - The beta-thymosin/WH2 actin-binding module shows an amazing adaptation to multifunctionality. The beta-thymosins are genuine G-actin sequesterers of moderate affinity for G-actin, allowing an efficient regulation of the G-actin/F-actin ratio in cells by amplifying changes in the critical concentration for filament assembly. In contrast, the first beta-thymosin domain of the protein Ciboulot makes with G-actin a complex that supports filament growth, such as profilin-actin. We illustrate how the use of engineered chimeric proteins, actin-binding and polymerization assays, crystallographic, NMR, and SAXS structural approaches complement each other to decipher the molecular basis for the functional versatility of these intrinsically disordered domains when they form various 1:1 complexes with G-actin. Multifunctionality is expanded in tandem repeats of WH2 domains present in WASP family proteins and proteins involved in axis patterning like Cordon-Bleu and Spire. The tandem repeats generate new functions such as filament nucleation and severing, as well as barbed end binding, which add up to the G-actin sequestering activity. Novel regulation pathways in actin assembly emerge from these additional activities. FAU - Husson, Clotilde AU - Husson C AD - Centre de Recherche de Gif, Gif-sur-Yvette, France. FAU - Cantrelle, Francois-Xavier AU - Cantrelle FX FAU - Roblin, Pierre AU - Roblin P FAU - Didry, Dominique AU - Didry D FAU - Le, Kim Ho Diep AU - Le KH FAU - Perez, Javier AU - Perez J FAU - Guittet, Eric AU - Guittet E FAU - Van Heijenoort, Carine AU - Van Heijenoort C FAU - Renault, Louis AU - Renault L FAU - Carlier, Marie-France AU - Carlier MF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Ann N Y Acad Sci JT - Annals of the New York Academy of Sciences JID - 7506858 RN - 0 (Actins) RN - 0 (Drosophila Proteins) RN - 0 (Microfilament Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (Profilins) RN - 0 (Proteins) RN - 0 (Wiskott-Aldrich Syndrome Protein Family) RN - 0 (ciboulot protein, Drosophila) RN - 61512-21-8 (Thymosin) RN - 77591-33-4 (thymosin beta(4)) SB - IM MH - Actin Cytoskeleton/*metabolism MH - Actins/chemistry/*metabolism MH - Animals MH - Cytoskeleton/metabolism MH - Drosophila Proteins MH - Humans MH - Microfilament Proteins/chemistry/metabolism MH - Nerve Tissue Proteins MH - Profilins/metabolism MH - Protein Binding MH - Proteins/metabolism MH - Scattering, Small Angle MH - Thymosin/chemistry/*metabolism MH - Wiskott-Aldrich Syndrome Protein Family/*metabolism RF - 40 EDAT- 2010/06/12 06:00 MHDA- 2010/07/02 06:00 CRDT- 2010/06/12 06:00 AID - NYAS5473 [pii] AID - 10.1111/j.1749-6632.2010.05473.x [doi] PST - ppublish SO - Ann N Y Acad Sci. 2010 Apr;1194:44-52. doi: 10.1111/j.1749-6632.2010.05473.x. PMID- 23359453 OWN - NLM STAT- MEDLINE DA - 20130422 DCOM- 20130624 IS - 1097-4652 (Electronic) IS - 0021-9541 (Linking) VI - 228 IP - 8 DP - 2013 Aug TI - First evidence of prothymosin alpha localization in the acrosome of mammalian male gametes. PG - 1629-37 LID - 10.1002/jcp.24332 [doi] AB - Prothymosin alpha (PTMA) is a highly acidic intrinsically unstructured protein. Its expression in male gonads is evolutionary conserved; in rat testis it is specifically localized in the cytoplasm of post-meiotic germ cells, in association with the developing acrosome system. In the present paper we investigated on PTMA localization inside the head of mammalian spermatozoa (SPZ). We chose a confocal approach to ascertain whether PTMA is expressed in the acrosome or in the perinuclear theca, two regions that are tightly linked and partially overlapped in the mature haploid cells. The obtained results showed that PTMA is specifically localized in the acrosome of rat epididymal SPZ; the same experimental approach evidenced, for the first time, PTMA presence in human ejaculated SPZ. A Western blot analysis on protein extracts from human sperm head fractions confirmed the confocal data and demonstrated that the peptide is specifically associated with the inner acrosomal membrane fraction. Finally, when the acrosome reaction was induced in vitro by progesterone treatment on both rat and human sperm, PTMA signal was retained in the apical region of reacted SPZ. In conclusion, this study confirms the conservation of PTMA distribution in vertebrate male gametes and strongly supports a role for this polypeptide in their physiology. CI - Copyright (c) 2013 Wiley Periodicals, Inc. FAU - Ferrara, Diana AU - Ferrara D AD - Dipartimento di Medicina Sperimentale, Sez. Fisiologia Umana e Funzioni Biologiche Integrate F. Bottazzi, Seconda Universita di Napoli, Napoli, Italy. diana.ferrara@unina2.it FAU - Pariante, Paolo AU - Pariante P FAU - Di Matteo, Loredana AU - Di Matteo L FAU - Serino, Ismene AU - Serino I FAU - Oko, Richard AU - Oko R FAU - Minucci, Sergio AU - Minucci S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Cell Physiol JT - Journal of cellular physiology JID - 0050222 RN - 0 (Peptides) RN - 0 (Protein Precursors) RN - 0 (prothymosin alpha) RN - 61512-21-8 (Thymosin) SB - IM MH - Acrosome/*metabolism MH - Acrosome Reaction MH - Animals MH - Blotting, Western MH - Cell Compartmentation MH - Cell Fractionation/methods MH - Epididymis/cytology/metabolism MH - Humans MH - Male MH - Microscopy, Fluorescence MH - Peptides/metabolism MH - Protein Precursors/*metabolism MH - Rats MH - Rats, Sprague-Dawley MH - Species Specificity MH - Spermatozoa/*metabolism MH - Thymosin/*analogs & derivatives/metabolism EDAT- 2013/01/30 06:00 MHDA- 2013/06/26 06:00 CRDT- 2013/01/30 06:00 PHST- 2012/06/21 [received] PHST- 2013/01/16 [accepted] AID - 10.1002/jcp.24332 [doi] PST - ppublish SO - J Cell Physiol. 2013 Aug;228(8):1629-37. doi: 10.1002/jcp.24332. PMID- 20102160 OWN - NLM STAT- MEDLINE DA - 20100223 DCOM- 20100316 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 8 DP - 2010 Mar 2 TI - The basic helix-loop-helix region of human neurogenin 1 is a monomeric natively unfolded protein which forms a "fuzzy" complex upon DNA binding. PG - 1577-89 LID - 10.1021/bi901616z [doi] AB - Neuronal specification is regulated by the activity of transcription factors containing the basic helix-loop-helix motif (bHLH); these regulating proteins include, among others, the neurogenin (Ngn) family, related to the atonal family of genes. Neurogenin 1 (NGN1) is a 237-residue protein that contains a bHLH domain and is involved in neuronal differentiation. In this work, we synthesized the bHLH region of NGN1 (bHLHN) comprising residues 90-150 of the full-length NGN1. The domain is a monomeric natively unfolded protein with a pH-dependent premolten globule conformation, as shown by several spectroscopic techniques (namely, NMR, fluorescence, FTIR, and circular dichroism). The unfolded character of the domain also explains, first, the impossibility of its overexpression in several Escherichia coli strains and, second, its insolubility in aqueous buffers. To the best of our knowledge, this is the first extensive study of the conformational preferences of a bHLH domain under different solution conditions. Upon binding to two DNA E-boxes, the protein forms "fuzzy" complexes (that is, the complexes were not fully folded). The affinities of bHLHN for both DNA boxes were smaller than those of other bHLH domains, which might explain why the protein-DNA complexes were not fully folded. FAU - Aguado-Llera, David AU - Aguado-Llera D AD - Instituto de Biologia Molecular y Celular, Universidad Miguel Hernandez, 03202 Elche (Alicante), Spain. FAU - Goormaghtigh, Erik AU - Goormaghtigh E FAU - de Geest, Natalie AU - de Geest N FAU - Quan, Xiao-Jiang AU - Quan XJ FAU - Prieto, Alicia AU - Prieto A FAU - Hassan, Bassen A AU - Hassan BA FAU - Gomez, Javier AU - Gomez J FAU - Neira, Jose L AU - Neira JL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Basic Helix-Loop-Helix Transcription Factors) RN - 0 (NEUROG1 protein, human) RN - 0 (Nerve Tissue Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Basic Helix-Loop-Helix Transcription Factors/*chemistry/genetics/*metabolism MH - Circular Dichroism MH - DNA/*metabolism MH - Helix-Loop-Helix Motifs/genetics/physiology MH - Humans MH - Nerve Tissue Proteins/*chemistry/genetics/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Folding MH - Spectroscopy, Fourier Transform Infrared EDAT- 2010/01/28 06:00 MHDA- 2010/03/17 06:00 CRDT- 2010/01/28 06:00 AID - 10.1021/bi901616z [doi] PST - ppublish SO - Biochemistry. 2010 Mar 2;49(8):1577-89. doi: 10.1021/bi901616z. PMID- 18713862 OWN - NLM STAT- MEDLINE DA - 20080827 DCOM- 20081024 LR - 20141014 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 105 IP - 34 DP - 2008 Aug 26 TI - Crystal structures of fibronectin-binding sites from Staphylococcus aureus FnBPA in complex with fibronectin domains. PG - 12254-8 LID - 10.1073/pnas.0803556105 [doi] AB - Staphylococcus aureus can adhere to and invade endothelial cells by binding to the human protein fibronectin (Fn). FnBPA and FnBPB, cell wall-attached proteins from S. aureus, have multiple, intrinsically disordered, high-affinity binding repeats (FnBRs) for Fn. Here, 30 years after the first report of S. aureus/Fn interactions, we present four crystal structures that together comprise the structures of two complete FnBRs, each in complex with four of the N-terminal modules of Fn. Each approximately 40-residue FnBR forms antiparallel strands along the triple-stranded beta-sheets of four sequential F1 modules ((2-5)F1) with each FnBR/(2-5)F1 interface burying a total surface area of approximately 4,300 A(2). The structures reveal the roles of residues conserved between S. aureus and Streptococcus pyogenes FnBRs and show that there are few linker residues between FnBRs. The ability to form large intermolecular interfaces with relatively few residues has been proposed to be a feature of disordered proteins, and S. aureus/Fn interactions provide an unusual illustration of this efficiency. FAU - Bingham, Richard J AU - Bingham RJ AD - Department of Biology, University of York, PO Box 373, York YO10 5YW, United Kingdom. FAU - Rudino-Pinera, Enrique AU - Rudino-Pinera E FAU - Meenan, Nicola A G AU - Meenan NA FAU - Schwarz-Linek, Ulrich AU - Schwarz-Linek U FAU - Turkenburg, Johan P AU - Turkenburg JP FAU - Hook, Magnus AU - Hook M FAU - Garman, Elspeth F AU - Garman EF FAU - Potts, Jennifer R AU - Potts JR LA - eng SI - PDB/2RKY SI - PDB/2RKZ SI - PDB/2RLO SI - PDB/3CAL GR - BB/D010608/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - FS/07/034/22969/British Heart Foundation/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom GR - British Heart Foundation/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080819 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Adhesins, Bacterial) RN - 0 (Fibronectins) RN - 0 (fibronectin-binding proteins, bacterial) SB - IM MH - Adhesins, Bacterial/*chemistry MH - Binding Sites MH - Crystallography, X-Ray MH - Fibronectins/*chemistry MH - Humans MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Staphylococcus aureus/*chemistry PMC - PMC2518095 OID - NLM: PMC2518095 EDAT- 2008/08/21 09:00 MHDA- 2008/10/25 09:00 CRDT- 2008/08/21 09:00 PHST- 2008/08/19 [aheadofprint] AID - 0803556105 [pii] AID - 10.1073/pnas.0803556105 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12254-8. doi: 10.1073/pnas.0803556105. Epub 2008 Aug 19. PMID- 22347381 OWN - NLM STAT- MEDLINE DA - 20120220 DCOM- 20120731 LR - 20141019 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 2 DP - 2012 TI - Inherent structural disorder and dimerisation of murine norovirus NS1-2 protein. PG - e30534 LID - 10.1371/journal.pone.0030534 [doi] AB - Human noroviruses are highly infectious viruses that cause the majority of acute, non-bacterial epidemic gastroenteritis cases worldwide. The first open reading frame of the norovirus RNA genome encodes for a polyprotein that is cleaved by the viral protease into six non-structural proteins. The first non-structural protein, NS1-2, lacks any significant sequence similarity to other viral or cellular proteins and limited information is available about the function and biophysical characteristics of this protein. Bioinformatic analyses identified an inherently disordered region (residues 1-142) in the highly divergent N-terminal region of the norovirus NS1-2 protein. Expression and purification of the NS1-2 protein of Murine norovirus confirmed these predictions by identifying several features typical of an inherently disordered protein. These were a biased amino acid composition with enrichment in the disorder promoting residues serine and proline, a lack of predicted secondary structure, a hydrophilic nature, an aberrant electrophoretic migration, an increased Stokes radius similar to that predicted for a protein from the pre-molten globule family, a high sensitivity to thermolysin proteolysis and a circular dichroism spectrum typical of an inherently disordered protein. The purification of the NS1-2 protein also identified the presence of an NS1-2 dimer in Escherichia coli and transfected HEK293T cells. Inherent disorder provides significant advantages including structural flexibility and the ability to bind to numerous targets allowing a single protein to have multiple functions. These advantages combined with the potential functional advantages of multimerisation suggest a multi-functional role for the NS1-2 protein. FAU - Baker, Estelle S AU - Baker ES AD - Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand. FAU - Luckner, Sylvia R AU - Luckner SR FAU - Krause, Kurt L AU - Krause KL FAU - Lambden, Paul R AU - Lambden PR FAU - Clarke, Ian N AU - Clarke IN FAU - Ward, Vernon K AU - Ward VK LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120207 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Animals MH - Escherichia coli MH - HEK293 Cells MH - Humans MH - Mice MH - Norovirus/*chemistry MH - Open Reading Frames MH - *Protein Multimerization MH - Protein Structure, Secondary MH - Viral Nonstructural Proteins/*chemistry/physiology PMC - PMC3274520 OID - NLM: PMC3274520 EDAT- 2012/02/22 06:00 MHDA- 2012/08/01 06:00 CRDT- 2012/02/21 06:00 PHST- 2011/10/17 [received] PHST- 2011/12/23 [accepted] PHST- 2012/02/07 [epublish] AID - 10.1371/journal.pone.0030534 [doi] AID - PONE-D-11-20607 [pii] PST - ppublish SO - PLoS One. 2012;7(2):e30534. doi: 10.1371/journal.pone.0030534. Epub 2012 Feb 7. PMID- 22208199 OWN - NLM STAT- MEDLINE DA - 20120102 DCOM- 20120418 LR - 20141019 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 101 IP - 12 DP - 2011 Dec 21 TI - Atomistic ensemble modeling and small-angle neutron scattering of intrinsically disordered protein complexes: applied to minichromosome maintenance protein. PG - 2999-3007 LID - 10.1016/j.bpj.2011.11.006 [doi] AB - The minichromosome maintenance (MCM) proteins are thought to function as the replicative helicases in archaea and eukarya. In this work we determined the solution structure of the N-terminal portion of the MCM complex from the archaeon Methanothermobacter thermautotrophicus (N-mtMCM) in the presence and absence of DNA using small-angle neutron scattering (SANS). N-mtMCM is a multimeric protein complex that consists of 12 monomers, each of which contains three distinct domains and two unstructured regions. Using an all-atom approach incorporating modern force field and Monte Carlo methods to allow the unstructured regions of each monomer to be varied independently, we generated an ensemble of biologically relevant structures for the complex. An examination of the subsets of structures that were most consistent with the SANS data revealed that large movements between the three domains of N-mtMCM can occur in solution. Furthermore, changes in the SANS curves upon DNA binding could be correlated to the motion of a particular N-mtMCM domain. These results provide structural support to the previously reported biochemical observations that large domain motions are required for the activation of the MCM helicase in archaea and eukarya. The methods developed here for N-mtMCM solution structure modeling should be suitable for other large protein complexes with unstructured flexible regions. CI - Copyright (c) 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Krueger, S AU - Krueger S AD - National Institute of Standards and Technology Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, USA. susan.krueger@nist.gov FAU - Shin, J-H AU - Shin JH FAU - Raghunandan, S AU - Raghunandan S FAU - Curtis, J E AU - Curtis JE FAU - Kelman, Z AU - Kelman Z LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20111220 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Chromosomal Proteins, Non-Histone) RN - 9007-49-2 (DNA) SB - IM MH - Chromosomal Proteins, Non-Histone/*chemistry/*ultrastructure MH - Computer Simulation MH - DNA/*chemistry/*ultrastructure MH - Models, Chemical MH - *Models, Molecular MH - Neutron Diffraction/*methods MH - Protein Conformation MH - Protein Structure, Tertiary MH - *Scattering, Small Angle PMC - PMC3244067 OID - NLM: PMC3244067 EDAT- 2012/01/03 06:00 MHDA- 2012/04/19 06:00 CRDT- 2012/01/03 06:00 PHST- 2011/08/23 [received] PHST- 2011/10/21 [revised] PHST- 2011/11/01 [accepted] PHST- 2011/12/20 [aheadofprint] AID - S0006-3495(11)01319-1 [pii] AID - 10.1016/j.bpj.2011.11.006 [doi] PST - ppublish SO - Biophys J. 2011 Dec 21;101(12):2999-3007. doi: 10.1016/j.bpj.2011.11.006. Epub 2011 Dec 20. PMID- 8876648 OWN - NLM STAT- MEDLINE DA - 19961122 DCOM- 19961122 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 262 IP - 5 DP - 1996 Oct 11 TI - The three-dimensional structure of mammalian ribonucleotide reductase protein R2 reveals a more-accessible iron-radical site than Escherichia coli R2. PG - 706-20 AB - The three-dimensional structure of mouse ribonucleotide reductase R2 has been determined at 2.3 A resolution using molecular replacement and refined to an R-value of 19.1% (Rfree = 25%) with good stereo-chemistry. The overall tertiary structure architecture of mouse R2 is similar to that from Escherichia coli R2. However, several important structural differences are observed. Unlike the E. coli protein, the mouse dimer is completely devoid of beta-strands. The sequences differ significantly between the mouse and E. coli R2s, but there is high sequence identity among the eukaryotic R2 proteins, and the identities are localized over the whole sequence. Therefore, the three-dimensional structures of other mammalian ribonucleotide reductase R2 proteins are expected to be very similar to that of the mouse enzyme. In mouse R2 a narrow hydrophobic channel leads to the proposed binding site for molecular oxygen near to the iron-radical site in the interior of the protein. In E. coli R2 this channel is blocked by the phenyl ring of a tyrosine residue, which in mouse R2 is a serine. These structural variations may explain the observed differences in sensitivity to radical scavengers. The structure determination is based on diffraction data from crystals grown at pH 4.7. Unexpectedly, the protein is not iron-free, but contains one iron ion bound at one of the dinuclear iron sites. This ferric ion is bound with partial occupancy and is coordinated by three glutamic acids (one bidentate) and one histidine in a bipyramidal coordination that has a free apical coordination position. Soaking of crystals in a solution of ferrous salt at pH 4.7 increased the occupancy on the already occupied site, but without any detectable binding at the second site. FAU - Kauppi, B AU - Kauppi B AD - Department of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Center, Uppsala, Sweden. FAU - Nielsen, B B AU - Nielsen BB FAU - Ramaswamy, S AU - Ramaswamy S FAU - Larsen, I K AU - Larsen IK FAU - Thelander, M AU - Thelander M FAU - Thelander, L AU - Thelander L FAU - Eklund, H AU - Eklund H LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (Free Radical Scavengers) RN - 42HK56048U (Tyrosine) RN - E1UOL152H7 (Iron) RN - EC 1.17.4.- (Ribonucleotide Reductases) RN - X6Q56QN5QC (Hydroxyurea) SB - IM MH - Animals MH - Bacterial Proteins/*ultrastructure MH - Crystallography, X-Ray MH - Escherichia coli/chemistry MH - Free Radical Scavengers/chemistry MH - Hydroxyurea/chemistry MH - Iron/chemistry MH - Mice MH - Models, Molecular MH - Oxidation-Reduction MH - Protein Conformation MH - Protein Structure, Secondary MH - Ribonucleotide Reductases/chemistry/*ultrastructure MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Tyrosine/chemistry EDAT- 1996/10/11 MHDA- 1996/10/11 00:01 CRDT- 1996/10/11 00:00 AID - S002228369690546X [pii] PST - ppublish SO - J Mol Biol. 1996 Oct 11;262(5):706-20. PMID- 22683627 OWN - NLM STAT- MEDLINE DA - 20120709 DCOM- 20120920 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 423 IP - 3 DP - 2012 Jul 6 TI - The binding mechanism of eIF2beta with its partner proteins, eIF5 and eIF2Bepsilon. PG - 515-9 LID - 10.1016/j.bbrc.2012.05.155 [doi] AB - The eukaryotic translation initiation factor eIF2 delivers Met-tRNAiMet to the ribosomal small subunit in GTP-bound form associated with eIF1, eIF1A, eIF3 and eIF5, and dissociates together with eIF5 as eIF5-eIF2-GDP complex from the ribosomal small subunit after formation of start codon-anticodon base pairing between Met-tRNAiMet and mRNA. The inactive form eIF2-GDP is then exchanged for the active form eIF2-GTP by eIF2B for further initiation cycle. Previous studies showed that the C-terminal domains of eIF5 (eIF5-CTD) and eIF2Bepsilon (eIF2Bepsilon-CTD) have a common eIF2beta-binding site for interacting with an N-terminal region of eIF2beta (eIF2beta-NTD). Here we have reconstructed the complexes of (eIF5-CTD)-(eIF2beta-NTD) and (eIF2Bepsilon-CTD)-(eIF2beta-NTD) in vitro, and investigated binding mechanism by circular dichroism spectroscopy and small angle X-ray scattering in solution. The results showed the conformation of eIF2beta-NTD was changed when bound to partner proteins, whereas the structures of eIF5-CTD and eIF2Bepsilon-CTD were similar in both isolated and complex states. We propose that eIF2beta-NTD works as an intrinsically disordered domain which is disorder in the isolated state, but folds into a definite structure when bound to its partner proteins. Such flexibility of eIF2beta-NTD is expected to be responsible for its binding capability. CI - Copyright (c) 2012 Elsevier Inc. All rights reserved. FAU - Gai, Zuoqi AU - Gai Z AD - Graduate School of Life Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan. FAU - Kitagawa, Yumie AU - Kitagawa Y FAU - Tanaka, Yoshikazu AU - Tanaka Y FAU - Shimizu, Nobutaka AU - Shimizu N FAU - Komoda, Keisuke AU - Komoda K FAU - Tanaka, Isao AU - Tanaka I FAU - Yao, Min AU - Yao M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120605 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Eukaryotic Initiation Factor-2B) RN - 0 (Peptide Initiation Factors) RN - 0 (RNA-Binding Proteins) RN - 0 (eukaryotic translation initiation factor 5A) SB - IM MH - Circular Dichroism MH - Eukaryotic Initiation Factor-2B/*chemistry MH - Models, Chemical MH - Peptide Initiation Factors/*chemistry MH - Protein Binding MH - Protein Structure, Tertiary MH - RNA-Binding Proteins/*chemistry MH - Saccharomyces cerevisiae MH - Scattering, Small Angle MH - X-Ray Diffraction EDAT- 2012/06/12 06:00 MHDA- 2012/09/21 06:00 CRDT- 2012/06/12 06:00 PHST- 2012/05/21 [received] PHST- 2012/05/28 [accepted] PHST- 2012/06/05 [aheadofprint] AID - S0006-291X(12)01054-6 [pii] AID - 10.1016/j.bbrc.2012.05.155 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2012 Jul 6;423(3):515-9. doi: 10.1016/j.bbrc.2012.05.155. Epub 2012 Jun 5. PMID- 25264250 OWN - NLM STAT- MEDLINE DA - 20141008 DCOM- 20150611 LR - 20150416 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 24 IP - 19 DP - 2014 Oct 6 TI - alpha-synuclein multimers cluster synaptic vesicles and attenuate recycling. PG - 2319-26 LID - 10.1016/j.cub.2014.08.027 [doi] LID - S0960-9822(14)01040-9 [pii] AB - The normal functions and pathologic facets of the small presynaptic protein alpha-synuclein (alpha-syn) are of exceptional interest. In previous studies, we found that alpha-syn attenuates synaptic exo/endocytosis; however, underlying mechanisms remain unknown. More recent evidence suggests that alpha-syn exists as metastable multimers and not solely as a natively unfolded monomer. However, conformations of alpha-syn at synapses--its physiologic locale--are unclear, and potential implications of such higher-order conformations to synaptic function are unknown. Exploring alpha-syn conformations and synaptic function in neurons, we found that alpha-syn promptly organizes into physiological multimers at synapses. Furthermore, our experiments indicate that alpha-syn multimers cluster synaptic vesicles and restrict their motility, suggesting a novel role for these higher-order structures. Supporting this, alpha-syn mutations that disrupt multimerization also fail to restrict synaptic vesicle motility or attenuate exo/endocytosis. We propose a model in which alpha-syn multimers cluster synaptic vesicles, restricting their trafficking and recycling, and consequently attenuate neurotransmitter release. CI - Copyright (c) 2014 Elsevier Ltd. All rights reserved. FAU - Wang, Lina AU - Wang L AD - Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. FAU - Das, Utpal AU - Das U AD - Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. FAU - Scott, David A AU - Scott DA AD - McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. FAU - Tang, Yong AU - Tang Y AD - Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. FAU - McLean, Pamela J AU - McLean PJ AD - Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA. FAU - Roy, Subhojit AU - Roy S AD - Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address: s1roy@ucsd.edu. LA - eng GR - P50 AG005131/AG/NIA NIH HHS/United States GR - P50AG005131/AG/NIA NIH HHS/United States GR - R01 NS073740/NS/NINDS NIH HHS/United States GR - R01 NS073740/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140925 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 RN - 0 (alpha-Synuclein) SB - IM MH - Animals MH - Cells, Cultured MH - HEK293 Cells MH - Hippocampus/metabolism MH - Humans MH - Mice MH - Microscopy, Fluorescence MH - Neurons/*metabolism MH - *Synaptic Transmission MH - Synaptic Vesicles/*metabolism MH - alpha-Synuclein/*genetics/metabolism PMC - PMC4190006 MID - NIHMS631185 OID - NLM: NIHMS631185 [Available on 10/06/15] OID - NLM: PMC4190006 [Available on 10/06/15] EDAT- 2014/09/30 06:00 MHDA- 2015/06/13 06:00 CRDT- 2014/09/30 06:00 PMCR- 2015/10/06 00:00 PHST- 2014/07/05 [received] PHST- 2014/08/01 [revised] PHST- 2014/08/13 [accepted] PHST- 2014/09/25 [aheadofprint] AID - S0960-9822(14)01040-9 [pii] AID - 10.1016/j.cub.2014.08.027 [doi] PST - ppublish SO - Curr Biol. 2014 Oct 6;24(19):2319-26. doi: 10.1016/j.cub.2014.08.027. Epub 2014 Sep 25. PMID- 9067253 OWN - NLM STAT- MEDLINE DA - 19970512 DCOM- 19970512 LR - 20061115 IS - 1431-6730 (Print) IS - 1431-6730 (Linking) VI - 377 IP - 9 DP - 1996 Sep TI - The recombinant dehydrin-like desiccation stress protein from the resurrection plant Craterostigma plantagineum displays no defined three-dimensional structure in its native state. PG - 555-61 AB - Dehydration stress in the drought-tolerant resurrection plant Craterostigma plantagineum is accompanied by the accumulation of a large number of desiccation stress proteins (Dsp). One abundant class of these is represented by the dehydrin-related Dsp16 protein which contains 15 amino acid conserved lysine-rich repeats and a stretch of eight serine residues providing extremely hydrophilic characteristics. Recombinant Dsp16 from Craterostigma plantagineum has been cloned and expressed in Escherichia coli. The protein was purified and characterized regarding its physicochemical properties. Irrespective of successful crystallization experiments, dilute aqueous buffer solutions do not display a well-defined three-dimensional structure in terms of the canonical secondary structural elements. 1H-NMR (nuclear magnetic resonance) spectra in aqueous solution are characterized by a small chemical shift dispersion typical for an unfolded protein; however, the observed line-widths are not typical for a highly mobile random coil structure. Instead they indicate an equilibrium between conformational states with preferentially extended substructures. As a consequence of its loose structure, Dsp16 is extremely sensitive towards proteolysis unless its structure is stabilized by structure-making additives such as trifluoroethanol. Denaturants such as guanidinium chloride do not induce cooperative structural transitions. pH-dependent fluorescence changes reflect protonation/deprotonation rather than conformational changes. Sedimentation/diffusion experiments confirm the predicted molecular mass of 16 kDa. Due to the high serine/threonine content and its loose structure, Dsp16 is accessible to phosphorylation, supporting the idea that in situ the structurally relatively undefined protein may be involved in both water binding and phosphorylation. FAU - Lisse, T AU - Lisse T AD - Institut fur Biophysik und Physikalische Biochemie, Universitat Regensburg, Germany. FAU - Bartels, D AU - Bartels D FAU - Kalbitzer, H R AU - Kalbitzer HR FAU - Jaenicke, R AU - Jaenicke R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - GERMANY TA - Biol Chem JT - Biological chemistry JID - 9700112 RN - 0 (Heat-Shock Proteins) RN - 0 (Recombinant Proteins) SB - IM MH - Cloning, Molecular MH - Desiccation MH - Escherichia coli/metabolism MH - Heat-Shock Proteins/*genetics/isolation & purification MH - Molecular Weight MH - Plants/*genetics MH - Protein Conformation MH - Recombinant Proteins/genetics/isolation & purification MH - Spectrophotometry, Ultraviolet EDAT- 1996/09/01 MHDA- 1996/09/01 00:01 CRDT- 1996/09/01 00:00 PST - ppublish SO - Biol Chem. 1996 Sep;377(9):555-61. PMID- 15735309 OWN - NLM STAT- MEDLINE DA - 20050425 DCOM- 20050621 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 17 DP - 2005 Apr 29 TI - Energetics of structural transitions of the addiction antitoxin MazE: is a programmed bacterial cell death dependent on the intrinsically flexible nature of the antitoxins? PG - 17397-407 AB - The Escherichia coli mazEF addiction module plays a crucial role in the cell death program that is triggered under various stress conditions. It codes for the toxin MazF and the antitoxin MazE, which interferes with the lethal action of the toxin. To better understand the role of various conformations of MazE in bacterial life, its order-disorder transitions were monitored by differential scanning calorimetry, spectropolarimetry, and fluorimetry. The changes in spectral and thermodynamic properties accompanying MazE dimer denaturation can be described in terms of a compensating reversible process of the partial folding of the unstructured C-terminal half (high mean net charge, low mean hydrophobicity) and monomerization coupled with the partial unfolding of the structured N-terminal half (low mean net charge, high mean hydrophobicity). At pHA polymorphism giving rise to a weak B phenotype. This polymorphism is predicted to cause a M186V amino-acid mutation within a highly conserved series of 16 amino acids present both in both blood group A- and blood group B-synthesizing enzymes. These residues are known as the disordered loop because their location cannot be determined in the crystal structure of the enzyme. Another patient has been identified with a 556G>A B(w) allele and the kinetics of the resulting mutant glycosyltransferase were studied. STUDY DESIGN AND METHODS: Serologic testing with murine and human reagents, amplification of the coding regions of exons 6 and 7, and DNA sequencing were performed with standard protocols. Enzyme kinetic studies utilized a model of human GTB M186V expressed in Escherichia coli with radiolabeled UDP-galactose and UDP-N-acetylgalactosamine as donor substrates and synthetic H-disaccharide as acceptor following standard protocols. RESULTS: The patient's red blood cells demonstrated a weak, but not mixed-field, B phenotype. Kinetic studies on the mutant enzyme revealed diminished activity (k(cat) = 0.15 per sec with UDP-galactose compared to 5.1 per sec for wild-type GTB) and elevated K(m) values for all substrates. CONCLUSION: This enzyme with a mutation in the disordered loop produces weak B antigen expression because of greatly decreased enzyme activity and reduced affinity for B-donor and acceptor substances. FAU - Yazer, Mark H AU - Yazer MH AD - Institute for Transfusion Medicine and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA. FAU - Denomme, Greg A AU - Denomme GA FAU - Rose, Natisha L AU - Rose NL FAU - Palcic, Monica M AU - Palcic MM LA - eng PT - Case Reports PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Transfusion JT - Transfusion JID - 0417360 RN - 0 (ABO Blood-Group System) RN - 2956-16-3 (Uridine Diphosphate Galactose) RN - EC 2.4.1.- (Galactosyltransferases) RN - EC 2.4.1.- (N-Acetylgalactosaminyltransferases) RN - EC 2.4.1.37 (blood-group-substance alpha-D-galactosyltransferase) SB - IM MH - ABO Blood-Group System/*chemistry/classification/*genetics/isolation & purification/metabolism MH - Adult MH - Amino Acid Sequence MH - *Amino Acid Substitution MH - Animals MH - Computer Simulation MH - Conserved Sequence MH - Escherichia coli/genetics MH - Exons MH - Female MH - Galactosyltransferases/*chemistry/classification/*genetics/isolation & purification/metabolism MH - Humans MH - Imaging, Three-Dimensional MH - Kinetics MH - Mice MH - Models, Molecular MH - N-Acetylgalactosaminyltransferases/metabolism MH - Nucleic Acid Amplification Techniques MH - *Phenotype MH - Polymorphism, Genetic MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Analysis, DNA MH - Substrate Specificity MH - Uridine Diphosphate Galactose/metabolism EDAT- 2005/07/01 09:00 MHDA- 2005/08/27 09:00 CRDT- 2005/07/01 09:00 AID - TRF00170 [pii] AID - 10.1111/j.1537-2995.2005.00170.x [doi] PST - ppublish SO - Transfusion. 2005 Jul;45(7):1178-82. PMID- 18773118 OWN - NLM STAT- MEDLINE DA - 20080905 DCOM- 20081118 LR - 20140903 IS - 1553-7374 (Electronic) IS - 1553-7366 (Linking) VI - 4 IP - 9 DP - 2008 TI - The cysteine-rich interdomain region from the highly variable plasmodium falciparum erythrocyte membrane protein-1 exhibits a conserved structure. PG - e1000147 LID - 10.1371/journal.ppat.1000147 [doi] AB - Plasmodium falciparum malaria parasites, living in red blood cells, express proteins of the erythrocyte membrane protein-1 (PfEMP1) family on the red blood cell surface. The binding of PfEMP1 molecules to human cell surface receptors mediates the adherence of infected red blood cells to human tissues. The sequences of the 60 PfEMP1 genes in each parasite genome vary greatly from parasite to parasite, yet the variant PfEMP1 proteins maintain receptor binding. Almost all parasites isolated directly from patients bind the human CD36 receptor. Of the several kinds of highly polymorphic cysteine-rich interdomain region (CIDR) domains classified by sequence, only the CIDR1alpha domains bind CD36. Here we describe the CD36-binding portion of a CIDR1alpha domain, MC179, as a bundle of three alpha-helices that are connected by a loop and three additional helices. The MC179 structure, containing seven conserved cysteines and 10 conserved hydrophobic residues, predicts similar structures for the hundreds of CIDR sequences from the many genome sequences now known. Comparison of MC179 with the CIDR domains in the genome of the P. falciparum 3D7 strain provides insights into CIDR domain structure. The CIDR1alpha three-helix bundle exhibits less than 20% sequence identity with the three-helix bundles of Duffy-binding like (DBL) domains, but the two kinds of bundles are almost identical. Despite the enormous diversity of PfEMP1 sequences, the CIDR1alpha and DBL protein structures, taken together, predict that a PfEMP1 molecule is a polymer of three-helix bundles elaborated by a variety of connecting helices and loops. From the structures also comes the insight that DBL1alpha domains are approximately 100 residues larger and that CIDR1alpha domains are approximately 100 residues smaller than sequence alignments predict. This new understanding of PfEMP1 structure will allow the use of better-defined PfEMP1 domains for functional studies, for the design of candidate vaccines, and for understanding the molecular basis of cytoadherence. FAU - Klein, Michael M AU - Klein MM AD - Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America. FAU - Gittis, Apostolos G AU - Gittis AG FAU - Su, Hua-Poo AU - Su HP FAU - Makobongo, Morris O AU - Makobongo MO FAU - Moore, Jaime M AU - Moore JM FAU - Singh, Sanjay AU - Singh S FAU - Miller, Louis H AU - Miller LH FAU - Garboczi, David N AU - Garboczi DN LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20080905 PL - United States TA - PLoS Pathog JT - PLoS pathogens JID - 101238921 RN - 0 (Antigens, CD36) RN - 0 (Protozoan Proteins) RN - 0 (erythrocyte membrane protein 1, Plasmodium falciparum) RN - K848JZ4886 (Cysteine) SB - IM MH - Animals MH - Antigens, CD36/metabolism MH - Binding Sites MH - *Cysteine MH - Plasmodium falciparum/*chemistry MH - Protein Binding MH - Protein Conformation MH - Protozoan Proteins/*chemistry/metabolism PMC - PMC2518858 OID - NLM: PMC2518858 EDAT- 2008/09/06 09:00 MHDA- 2008/11/19 09:00 CRDT- 2008/09/06 09:00 PHST- 2008/03/13 [received] PHST- 2008/08/07 [accepted] AID - 10.1371/journal.ppat.1000147 [doi] PST - epublish SO - PLoS Pathog. 2008 Sep 5;4(9):e1000147. doi: 10.1371/journal.ppat.1000147. PMID- 21528875 OWN - NLM STAT- MEDLINE DA - 20110825 DCOM- 20111212 LR - 20140915 IS - 1520-5215 (Electronic) IS - 1089-5639 (Linking) VI - 115 IP - 34 DP - 2011 Sep 1 TI - Direct observations of conformational distributions of intrinsically disordered p53 peptides using UV Raman and explicit solvent simulations. PG - 9520-7 LID - 10.1021/jp112235d [doi] AB - We report the first experimental measurements of Ramachandran Psi-angle distributions for intrinsically disordered peptides: the N-terminal peptide fragment of tumor suppressor p53 and its P27S mutant form. To provide atomically detailed views of the conformational distributions, we performed classical, explicit-solvent molecular dynamics simulations on the microsecond time scale. Upon binding its partner protein, MDM2, wild-type p53 peptide adopts an alpha-helical conformation. Mutation of Pro27 to serine results in the highest affinity yet observed for MDM2-binding of the p53 peptide. Both UV resonance Raman spectroscopy (UVRR) and simulations reveal that the P27S mutation decreases the extent of PPII helical content and increases the probability for conformations that are similar to the alpha-helical MDM2-bound conformation. In addition, UVRR measurements were performed on peptides that were isotopically labeled at the Leu26 residue preceding the Pro27 in order to determine the conformational distributions of Leu26 in the wild-type and mutant peptides. The UVRR and simulation results are in quantitative agreement in terms of the change in the population of non-PPII conformations involving Leu26 upon mutation of Pro27 to serine. Finally, our simulations reveal that the MDM2-bound conformation of the peptide is significantly populated in both the wild-type and mutant isolated peptide ensembles in their unbound states, suggesting that MDM2 binding of the p53 peptides may involve conformational selection. CI - (c) 2011 American Chemical Society FAU - Xiong, Kan AU - Xiong K AD - Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA. FAU - Zwier, Matthew C AU - Zwier MC FAU - Myshakina, Nataliya S AU - Myshakina NS FAU - Burger, Virginia M AU - Burger VM FAU - Asher, Sanford A AU - Asher SA FAU - Chong, Lillian T AU - Chong LT LA - eng GR - 1R01EB009089/EB/NIBIB NIH HHS/United States GR - R01 EB009089/EB/NIBIB NIH HHS/United States GR - R01 EB009089-04/EB/NIBIB NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110429 PL - United States TA - J Phys Chem A JT - The journal of physical chemistry. A JID - 9890903 RN - 0 (Peptide Fragments) RN - 0 (Solvents) RN - 0 (Tumor Suppressor Protein p53) RN - 452VLY9402 (Serine) RN - 9DLQ4CIU6V (Proline) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) RN - GMW67QNF9C (Leucine) SB - IM MH - Binding Sites MH - *Chemistry, Physical MH - Computer Simulation MH - Humans MH - Leucine/chemistry/metabolism MH - Models, Molecular MH - Peptide Fragments/*chemistry/genetics/metabolism MH - Proline/chemistry/metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-mdm2/*chemistry/genetics/metabolism MH - Serine/chemistry/metabolism MH - Solvents/chemistry MH - Spectrum Analysis, Raman MH - Tumor Suppressor Protein p53/*chemistry/genetics/metabolism PMC - PMC3161171 MID - NIHMS293208 OID - NLM: NIHMS293208 OID - NLM: PMC3161171 EDAT- 2011/05/03 06:00 MHDA- 2011/12/14 06:00 CRDT- 2011/05/03 06:00 PHST- 2011/04/29 [aheadofprint] AID - 10.1021/jp112235d [doi] PST - ppublish SO - J Phys Chem A. 2011 Sep 1;115(34):9520-7. doi: 10.1021/jp112235d. Epub 2011 Apr 29. PMID- 10228169 OWN - NLM STAT- MEDLINE DA - 19990628 DCOM- 19990628 LR - 20140617 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 18 IP - 9 DP - 1999 May 4 TI - Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding. PG - 2563-79 AB - NHP6A is a chromatin-associated protein from Saccharomyces cerevisiae belonging to the HMG1/2 family of non-specific DNA binding proteins. NHP6A has only one HMG DNA binding domain and forms relatively stable complexes with DNA. We have determined the solution structure of NHP6A and constructed an NMR-based model structure of the DNA complex. The free NHP6A folds into an L-shaped three alpha-helix structure, and contains an unstructured 17 amino acid basic tail N-terminal to the HMG box. Intermolecular NOEs assigned between NHP6A and a 15 bp 13C,15N-labeled DNA duplex containing the SRY recognition sequence have positioned the NHP6A HMG domain onto the minor groove of the DNA at a site that is shifted by 1 bp and in reverse orientation from that found in the SRY-DNA complex. In the model structure of the NHP6A-DNA complex, the N-terminal basic tail is wrapped around the major groove in a manner mimicking the C-terminal tail of LEF1. The DNA in the complex is severely distorted and contains two adjacent kinks where side chains of methionine and phenylalanine that are important for bending are inserted. The NHP6A-DNA model structure provides insight into how this class of architectural DNA binding proteins may select preferential binding sites. FAU - Allain, F H AU - Allain FH AD - Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095-1569, USA. FAU - Yen, Y M AU - Yen YM FAU - Masse, J E AU - Masse JE FAU - Schultze, P AU - Schultze P FAU - Dieckmann, T AU - Dieckmann T FAU - Johnson, R C AU - Johnson RC FAU - Feigon, J AU - Feigon J LA - eng GR - GM08042/GM/NIGMS NIH HHS/United States GR - GM38509/GM/NIGMS NIH HHS/United States GR - GM48123/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (DNA-Binding Proteins) RN - 0 (Fungal Proteins) RN - 0 (HMGN Proteins) RN - 0 (High Mobility Group Proteins) RN - 0 (Lymphoid Enhancer-Binding Factor 1) RN - 0 (NHP6A protein, S cerevisiae) RN - 0 (Nuclear Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Sex-Determining Region Y Protein) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - Binding Sites MH - Computer Simulation MH - DNA/chemistry/metabolism MH - DNA-Binding Proteins/*chemistry/genetics/metabolism MH - Fungal Proteins/*chemistry/genetics/metabolism MH - HMGN Proteins MH - High Mobility Group Proteins/*chemistry/genetics/metabolism MH - Lymphoid Enhancer-Binding Factor 1 MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*chemistry/genetics/metabolism MH - Protein Binding MH - Protein Conformation MH - Saccharomyces cerevisiae MH - *Saccharomyces cerevisiae Proteins MH - Sequence Homology, Amino Acid MH - Sex-Determining Region Y Protein MH - Transcription Factors/chemistry PMC - PMC1171337 OID - NLM: PMC1171337 EDAT- 1999/05/06 MHDA- 1999/05/06 00:01 CRDT- 1999/05/06 00:00 AID - 10.1093/emboj/18.9.2563 [doi] PST - ppublish SO - EMBO J. 1999 May 4;18(9):2563-79. PMID- 12005430 OWN - NLM STAT- MEDLINE DA - 20020513 DCOM- 20021209 LR - 20091119 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 10 IP - 3 DP - 2002 Mar TI - Structure and dynamics of the anticodon arm binding domain of Bacillus stearothermophilus Tyrosyl-tRNA synthetase. PG - 311-7 AB - The structure of a recombinant protein, TyrRS(delta4), corresponding to the anticodon arm binding domain of Bacillus stearothermophilus tyrosyl-tRNA synthetase, has been solved, and its dynamics have been studied by nuclear magnetic resonance (NMR). It is the first structure described for such a domain of a tyrosyl-tRNA synthetase. It consists of a five-stranded beta sheet, packed against two alpha helices on one side and one alpha helix on the other side. A large part of the domain is structurally similar to other functionally unrelated RNA binding proteins. The basic residues known to be essential for tRNA binding and charging are exposed to the solvent on the same face of the molecule. The structure of TyrRS(delta4), together with previous mutagenesis data, allows one to delineate the region of interaction with tRNATyr. FAU - Guijarro, J Inaki AU - Guijarro JI AD - Unite de RMN des Biomolecules, CNRS URA 2185, Institut Pasteur, Paris, France. FAU - Pintar, Alessandro AU - Pintar A FAU - Prochnicka-Chalufour, Ada AU - Prochnicka-Chalufour A FAU - Guez, Valerie AU - Guez V FAU - Gilquin, Bernard AU - Gilquin B FAU - Bedouelle, Hugues AU - Bedouelle H FAU - Delepierre, Muriel AU - Delepierre M LA - eng SI - PDB/1JH3 PT - Journal Article PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Anticodon) RN - 0 (RNA-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 9014-25-9 (RNA, Transfer) RN - EC 6.1.1.1 (Tyrosine-tRNA Ligase) SB - IM MH - Amino Acid Sequence MH - *Anticodon MH - Crystallography, X-Ray MH - Geobacillus stearothermophilus/chemistry/*enzymology MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - *Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - RNA, Transfer/metabolism MH - RNA-Binding Proteins/chemistry/genetics/metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Sequence Alignment MH - Tyrosine-tRNA Ligase/*chemistry/genetics/metabolism EDAT- 2002/05/15 10:00 MHDA- 2002/12/10 04:00 CRDT- 2002/05/15 10:00 PST - ppublish SO - Structure. 2002 Mar;10(3):311-7. PMID- 24263171 OWN - NLM STAT- MEDLINE DA - 20140109 DCOM- 20140416 LR - 20141112 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1842 IP - 2 DP - 2014 Feb TI - The Stress-response protein prostate-associated gene 4, interacts with c-Jun and potentiates its transactivation. PG - 154-63 LID - 10.1016/j.bbadis.2013.11.014 [doi] LID - S0925-4439(13)00339-6 [pii] AB - The Cancer/Testis Antigen (CTA), Prostate-associated Gene 4 (PAGE4), is a stress-response protein that is upregulated in prostate cancer (PCa) especially in precursor lesions that result from inflammatory stress. In cells under stress, translocation of PAGE4 to mitochondria increases while production of reactive oxygen species decreases. Furthermore, PAGE4 is also upregulated in human fetal prostate, underscoring its potential role in development. However, the proteins that interact with PAGE4 and the mechanisms underlying its pleiotropic functions in prostatic development and disease remain unknown. Here, we identified c-Jun as a PAGE4 interacting partner. We show that both PAGE4 and c-Jun are overexpressed in the human fetal prostate; and in cell-based assays, PAGE4 robustly potentiates c-Jun transactivation. Single-molecule Forster resonance energy transfer experiments indicate that upon binding to c-Jun, PAGE4 undergoes conformational changes. However, no interaction is observed in presence of BSA or unilamellar vesicles containing the mitochondrial inner membrane diphosphatidylglycerol lipid marker cardiolipin. Together, our data indicate that PAGE4 specifically interacts with c-Jun and that, conformational dynamics may account for its observed pleiotropic functions. To our knowledge, this is the first report demonstrating crosstalk between a CTA and a proto-oncogene. Disrupting PAGE4/c-Jun interactions using small molecules may represent a novel therapeutic strategy for PCa. CI - Copyright (c) 2013 Elsevier B.V. All rights reserved. FAU - Rajagopalan, Krithika AU - Rajagopalan K AD - Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. FAU - Qiu, Ruoyi AU - Qiu R AD - Department of Physics, North Carolina State University, Raleigh, NC 27695, USA. FAU - Mooney, Steven M AU - Mooney SM AD - Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. FAU - Rao, Shweta AU - Rao S AD - Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. FAU - Shiraishi, Takumi AU - Shiraishi T AD - Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. FAU - Sacho, Elizabeth AU - Sacho E AD - Department of Physics, North Carolina State University, Raleigh, NC 27695, USA. FAU - Huang, Hongying AU - Huang H AD - Department of Urology, New York University School of Medicine, New York, NY 10016, USA. FAU - Shapiro, Ellen AU - Shapiro E AD - Department of Urology, New York University School of Medicine, New York, NY 10016, USA. FAU - Weninger, Keith R AU - Weninger KR AD - Department of Physics, North Carolina State University, Raleigh, NC 27695, USA. Electronic address: krwening@ncsu.edu. FAU - Kulkarni, Prakash AU - Kulkarni P AD - Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Electronic address: pkulkar4@jhmi.edu. LA - eng GR - P30 CA006973/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131118 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (3' Untranslated Regions) RN - 0 (Antigens, Neoplasm) RN - 0 (MIRN221 microRNA, human) RN - 0 (MIRN222 microRNA, human) RN - 0 (MicroRNAs) RN - 0 (PAGE4 protein, human) RN - 0 (Proto-Oncogene Proteins c-jun) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) SB - IM MH - 3' Untranslated Regions/genetics MH - Antigens, Neoplasm/chemistry/genetics/*metabolism MH - Cell Line, Tumor MH - Cyclin-Dependent Kinase Inhibitor p27/genetics/metabolism MH - Fluorescence Resonance Energy Transfer MH - Gene Expression Regulation, Neoplastic MH - Humans MH - Immunohistochemistry MH - Male MH - MicroRNAs/genetics/metabolism MH - Mutation MH - Prostate/embryology/growth & development/*metabolism MH - Prostatic Neoplasms/genetics/metabolism/pathology MH - Protein Binding MH - Protein Conformation MH - Proto-Oncogene Proteins c-jun/genetics/*metabolism MH - Reverse Transcriptase Polymerase Chain Reaction MH - Stress, Physiological MH - *Transcriptional Activation PMC - PMC4086653 MID - NIHMS563177 OID - NLM: NIHMS563177 OID - NLM: PMC4086653 OTO - NOTNLM OT - BPH OT - BSA OT - CD OT - Cancer/Testis Antigen OT - DBD OT - DLS OT - DMSO OT - DNA-binding domain OT - Dimethyl sulfoxide OT - IPTG OT - Intrinsically disordered protein OT - Isopropyl 1-thio-beta-d-galactopyranoside OT - NMR OT - PAGE4 OT - PBS OT - PC OT - PCa OT - PE OT - PIA OT - PIN OT - PINs OT - PVP OT - Phosphate Buffered Saline OT - Prostate Associated Gene 4 OT - Prostate cancer OT - QY OT - SDS-PAGE OT - SEC OT - Sodium Dodecyl sulfate poly-acrylamide gel electrophoresis OT - TCEP.HCl OT - Tris(2-carboxyethyl)phosphine hydrochloride OT - benign prostatic hyperplasia OT - bovine serum albumin OT - c-Jun OT - circular dichroism OT - dynamic light scattering OT - nuclear magnetic resonance OT - phosphatidylcholine OT - phosphatidylethanolamine OT - polyvinyl pyrollidone OT - proliferative inflammatory atrophy OT - prostate cancer OT - prostatic intraepithelial neoplasia OT - protein interaction networks OT - quantum yield OT - single-molecule Forster resonance energy transfer OT - size exclusion chromatography OT - smFRET EDAT- 2013/11/23 06:00 MHDA- 2014/04/17 06:00 CRDT- 2013/11/23 06:00 PHST- 2013/07/15 [received] PHST- 2013/10/26 [revised] PHST- 2013/11/13 [accepted] PHST- 2013/11/18 [aheadofprint] AID - S0925-4439(13)00339-6 [pii] AID - 10.1016/j.bbadis.2013.11.014 [doi] PST - ppublish SO - Biochim Biophys Acta. 2014 Feb;1842(2):154-63. doi: 10.1016/j.bbadis.2013.11.014. Epub 2013 Nov 18. PMID- 9659905 OWN - NLM STAT- MEDLINE DA - 19980724 DCOM- 19980724 LR - 20071114 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 1 IP - 1 DP - 1997 Dec TI - Domain interactions in E. coli SRP: stabilization of M domain by RNA is required for effective signal sequence modulation of NG domain. PG - 79-87 AB - The E. coli protein, Fth, binds to 4.5S RNA through its M domain to form the signal recognition particle (SRP). The other domain of Fth (NG) is a GTPase, which binds and is coordinately regulated by its receptor, FtsY. We find that the helical M domain is inherently flexible. Binding of 4.5S RNA to Fth stabilizes the M domain yet has little apparent effect on the binding of signal peptides. However, in the absence of the RNA, signal peptide binding results in a global destabilization of Fth, which is prevented by binding of 4.5S RNA. Signal peptide binding to isolated NG domain also causes a pronounced destabilization, implicating the NG domain in direct recognition of signal peptide. FAU - Zheng, N AU - Zheng N AD - Molecular Biophysics Program, University of Texas Southwestern Medical Center at Dallas 75235, USA. FAU - Gierasch, L M AU - Gierasch LM LA - eng GR - GM34962/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Bacterial Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Ffh protein, E coli) RN - 0 (RNA, Bacterial) RN - 0 (Signal Recognition Particle) RN - EC 3.6.1.- (GTP Phosphohydrolases) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/genetics/metabolism MH - Binding Sites/physiology MH - Escherichia coli/*chemistry/genetics/metabolism MH - *Escherichia coli Proteins MH - GTP Phosphohydrolases/metabolism MH - Molecular Sequence Data MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RNA, Bacterial/*metabolism MH - Signal Recognition Particle/*chemistry/genetics/metabolism EDAT- 1998/07/11 MHDA- 1998/07/11 00:01 CRDT- 1998/07/11 00:00 AID - S1097-2765(00)80009-X [pii] PST - ppublish SO - Mol Cell. 1997 Dec;1(1):79-87. PMID- 20359221 OWN - NLM STAT- MEDLINE DA - 20100421 DCOM- 20100805 LR - 20140917 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 132 IP - 16 DP - 2010 Apr 28 TI - Detection of transient interchain interactions in the intrinsically disordered protein alpha-synuclein by NMR paramagnetic relaxation enhancement. PG - 5546-7 LID - 10.1021/ja9105495 [doi] AB - NMR paramagnetic relaxation enhancement experiments were applied to the intrinsically disordered protein alpha-synuclein, the primary protein in Parkinson's disease, to directly characterize transient intermolecular complexes at neutral and low pH. At neutral pH, we observed weak N- to C-terminal interchain contacts driven by electrostatic interactions, while at low pH, the C- to C-terminal interchain interactions are significantly stronger and driven by hydrophobic contacts. Characterization of these first interchain interactions will provide fundamental insight into the mechanism of amyloid formation. FAU - Wu, Kuen-Phon AU - Wu KP AD - Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA. FAU - Baum, Jean AU - Baum J LA - eng GR - GM087012/GM/NIGMS NIH HHS/United States GR - GM45302/GM/NIGMS NIH HHS/United States GR - R01 GM045302/GM/NIGMS NIH HHS/United States GR - R01 GM045302-17/GM/NIGMS NIH HHS/United States GR - R01 GM087012/GM/NIGMS NIH HHS/United States GR - R01 GM087012-02/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (alpha-Synuclein) SB - IM MH - Models, Molecular MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - alpha-Synuclein/*chemistry/*metabolism PMC - PMC3064441 MID - NIHMS250317 OID - NLM: NIHMS250317 OID - NLM: PMC3064441 EDAT- 2010/04/03 06:00 MHDA- 2010/08/06 06:00 CRDT- 2010/04/03 06:00 AID - 10.1021/ja9105495 [doi] PST - ppublish SO - J Am Chem Soc. 2010 Apr 28;132(16):5546-7. doi: 10.1021/ja9105495. PMID- 9914248 OWN - NLM STAT- MEDLINE DA - 19990212 DCOM- 19990212 LR - 20071114 IS - 0959-440X (Print) IS - 0959-440X (Linking) VI - 8 IP - 6 DP - 1998 Dec TI - Glutamine PRPP amidotransferase: snapshots of an enzyme in action. PG - 686-94 AB - Recent studies of glutamine PRPP amidotransferase have provided a new understanding of the function and mechanism of this rather complicated enzyme that may be a paradigm for other complex enzymes. New insights have been gained into the mechanisms of catalysis in the active sites of the two half-reactions, catalytic coupling, allosteric control by feedback inhibitors and the channeling of reaction and metabolic intermediates. FAU - Smith, J L AU - Smith JL AD - Department of Biological Sciences Purdue University West Lafayette IN 47907-1392 USA. smithj@bragg.bio.purdue.edu LA - eng GR - DK-42303/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PT - Review PL - ENGLAND TA - Curr Opin Struct Biol JT - Current opinion in structural biology JID - 9107784 RN - EC 2.4.2.14 (Amidophosphoribosyltransferase) SB - IM MH - Allosteric Regulation MH - Amidophosphoribosyltransferase/chemistry/*metabolism MH - Binding Sites MH - Catalytic Domain MH - Feedback MH - Protein Conformation MH - Signal Transduction RF - 47 EDAT- 1999/01/23 MHDA- 1999/01/23 00:01 CRDT- 1999/01/23 00:00 AID - S0959-440X(98)80087-0 [pii] PST - ppublish SO - Curr Opin Struct Biol. 1998 Dec;8(6):686-94. PMID- 22639284 OWN - NLM STAT- MEDLINE DA - 20121112 DCOM- 20130425 IS - 1436-2236 (Electronic) IS - 1436-2228 (Linking) VI - 14 IP - 6 DP - 2012 Dec TI - The SbASR-1 gene cloned from an extreme halophyte Salicornia brachiata enhances salt tolerance in transgenic tobacco. PG - 782-92 LID - 10.1007/s10126-012-9442-7 [doi] AB - Salinity severely affects plant growth and development. Plants evolved various mechanisms to cope up stress both at molecular and cellular levels. Halophytes have developed better mechanism to alleviate the salt stress than glycophytes, and therefore, it is advantageous to study the role of different genes from halophytes. Salicornia brachiata is an extreme halophyte, which grows luxuriantly in the salty marshes in the coastal areas. Earlier, we have isolated SbASR-1 (abscisic acid stress ripening-1) gene from S. brachiata using cDNA subtractive hybridisation library. ASR-1 genes are abscisic acid (ABA) responsive, whose expression level increases under abiotic stresses, injury, during fruit ripening and in pollen grains. The SbASR-1 transcript showed up-regulation under salt stress conditions. The SbASR-1 protein contains 202 amino acids of 21.01-kDa molecular mass and has 79 amino acid long signatures of ABA/WDS gene family. It has a maximum identity (73 %) with Solanum chilense ASR-1 protein. The SbASR-1 has a large number of disorder-promoting amino acids, which make it an intrinsically disordered protein. The SbASR-1 gene was over-expressed under CaMV 35S promoter in tobacco plant to study its physiological functions under salt stress. T(0) transgenic tobacco seeds showed better germination and seedling growth as compared to wild type (Wt) in a salt stress condition. In the leaf tissues of transgenic lines, Na(+) and proline contents were significantly lower, as compared to Wt plant, under salt treatment, suggesting that transgenic plants are better adapted to salt stress. FAU - Jha, Bhavanath AU - Jha B AD - Discipline of Marine Biotechnology and Ecology, CSIR- Central Salt and Marine Chemicals Research Institute, G.B. Road, Bhavnagar, 364 002, Gujarat, India. bjha@csmcri.org FAU - Lal, Sanjay AU - Lal S FAU - Tiwari, Vivekanand AU - Tiwari V FAU - Yadav, Sweta Kumari AU - Yadav SK FAU - Agarwal, Pradeep K AU - Agarwal PK LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120526 PL - United States TA - Mar Biotechnol (NY) JT - Marine biotechnology (New York, N.Y.) JID - 100892712 RN - 0 (Plant Proteins) RN - 7647-14-5 (Sodium Chloride) SB - IM MH - Cloning, Molecular MH - Plant Proteins/*genetics/metabolism MH - Plants, Genetically Modified/*drug effects/*physiology MH - Salt-Tolerance/*genetics MH - Salt-Tolerant Plants/genetics/*metabolism MH - Sodium Chloride/*pharmacology MH - Tobacco/*drug effects/*physiology EDAT- 2012/05/29 06:00 MHDA- 2013/04/26 06:00 CRDT- 2012/05/29 06:00 PHST- 2011/10/04 [received] PHST- 2012/03/24 [accepted] PHST- 2012/05/26 [aheadofprint] AID - 10.1007/s10126-012-9442-7 [doi] PST - ppublish SO - Mar Biotechnol (NY). 2012 Dec;14(6):782-92. doi: 10.1007/s10126-012-9442-7. Epub 2012 May 26. PMID- 23606624 OWN - NLM STAT- MEDLINE DA - 20130911 DCOM- 20140320 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 81 IP - 10 DP - 2013 Oct TI - Structural divergence is more extensive than sequence divergence for a family of intrinsically disordered proteins. PG - 1686-98 LID - 10.1002/prot.24303 [doi] AB - The p53 transactivation domain (p53TAD) is an intrinsically disordered protein (IDP) domain that undergoes coupled folding and binding when interacting with partner proteins like the E3 ligase, MDM2, and the 70 kDa subunit of replication protein A, RPA70. The secondary structure and dynamics of six closely related mammalian homologues of p53TAD were investigated using nuclear magnetic resonance (NMR) spectroscopy. Differences in both transient secondary structure and backbone dynamics were observed for the homologues. Many of these differences were localized to the binding sites for MDM2 and RPA70. The amount of transient helical secondary structure observed for the MDM2 binding site was lower for the dog and mouse homologues, compared with human, and the amount of transient helical secondary structure observed for the RPA70 binding site was higher for guinea pig and rabbit, compared with human. Differences in the amount of transient helical secondary structure observed for the MDM2 binding site were directly related to amino acid substitutions occurring on the solvent exposed side of the amphipathic helix that forms during the p53TAD/MDM2 interaction. Differences in the amount of transient helical secondary structure were not as easily explained for the RPA70 binding site because of its extensive sequence divergence. Clustering analysis shows that the divergence in the transient secondary structure of the p53TAD homologues exceeds the amino acid sequence divergence. In contrast, strong correlations were observed between the backbone dynamics of the homologues and the sequence identity matrix, suggesting that the dynamic behavior of IDPs is a conserved evolutionary feature. CI - Copyright (c) 2013 Wiley Periodicals, Inc. FAU - Borcherds, Wade AU - Borcherds W AD - Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 3720 Spectrum Blvd., Suite 321, Tampa, Florida, 33612; The Center for Drug Discovery and Innovation, University of South Florida, 3720 Spectrum Blvd., Suite 321, Tampa, Florida, 33612. FAU - Kashtanov, Stepan AU - Kashtanov S FAU - Wu, Hongwei AU - Wu H FAU - Daughdrill, Gary W AU - Daughdrill GW LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130723 PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - *Amino Acid Sequence MH - Animals MH - Cluster Analysis MH - Dogs MH - Evolution, Molecular MH - Guinea Pigs MH - Humans MH - Intrinsically Disordered Proteins/*chemistry MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - *Protein Structure, Secondary MH - *Protein Structure, Tertiary MH - Rabbits MH - Sequence Alignment MH - Tumor Suppressor Protein p53/chemistry OTO - NOTNLM OT - intrinsically disordered proteins OT - protein dynamics OT - structural divergence OT - structural evolution EDAT- 2013/04/23 06:00 MHDA- 2014/03/22 06:00 CRDT- 2013/04/23 06:00 PHST- 2012/12/14 [received] PHST- 2013/03/11 [revised] PHST- 2013/03/26 [accepted] PHST- 2013/07/23 [aheadofprint] AID - 10.1002/prot.24303 [doi] PST - ppublish SO - Proteins. 2013 Oct;81(10):1686-98. doi: 10.1002/prot.24303. Epub 2013 Jul 23. PMID- 19846660 OWN - NLM STAT- MEDLINE DA - 20091216 DCOM- 20100309 LR - 20140827 IS - 1939-4586 (Electronic) IS - 1059-1524 (Linking) VI - 20 IP - 24 DP - 2009 Dec TI - Binding the atypical RA domain of Ste50p to the unfolded Opy2p cytoplasmic tail is essential for the high-osmolarity glycerol pathway. PG - 5117-26 LID - 10.1091/mbc.E09-07-0645 [doi] AB - Activation of the high-osmolarity glycerol (HOG) pathway for osmoregulation in the yeast Saccharomyces cerevisiae involves interaction of the adaptor Ste50p with the cytoplasmic tail of single-transmembrane protein Opy2p. We have determined the solution structure of the Ste50p-RA (Ras association) domain, and it shows an atypical RA fold lacking the beta1 and beta2 strands of the canonical motif. Although the core of the RA domain is fully functional in the pheromone response, an additional region is required for the HOG pathway activation. Two peptide motifs within the intrinsically disordered cytoplasmic tail of Opy2p defined by NMR spectroscopy physically interact with the Step50p-RA domain. These Opy2p-derived peptides bind overlapping regions of the Step50p-RA domain with similarly weak affinities, suggesting a multivalent interaction of these proteins as a crucial point of control of the HOG pathway. As well, overall selection of signaling pathways depends on functionally distinct regions of the Ste50p-RA domain, implicating this element in the control of global regulatory decisions. FAU - Ekiel, Irena AU - Ekiel I AD - Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada. FAU - Sulea, Traian AU - Sulea T FAU - Jansen, Gregor AU - Jansen G FAU - Kowalik, Maria AU - Kowalik M FAU - Minailiuc, Ovidiu AU - Minailiuc O FAU - Cheng, Jing AU - Cheng J FAU - Harcus, Doreen AU - Harcus D FAU - Cygler, Miroslaw AU - Cygler M FAU - Whiteway, Malcolm AU - Whiteway M FAU - Wu, Cunle AU - Wu C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Biol Cell JT - Molecular biology of the cell JID - 9201390 RN - 0 (Membrane Proteins) RN - 0 (Opy2 protein, S cerevisiae) RN - 0 (Peptides) RN - 0 (STE50 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - PDC6A3C0OX (Glycerol) SB - IM MH - Amino Acid Sequence MH - Cytoplasm/chemistry MH - Glycerol/*metabolism MH - Membrane Proteins/*chemistry/*metabolism MH - Molecular Sequence Data MH - Osmolar Concentration MH - Osmosis MH - Peptides/chemistry/metabolism MH - Protein Binding MH - *Protein Folding MH - Protein Interaction Mapping MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/*metabolism MH - Sequence Deletion MH - Signal Transduction MH - Stress, Physiological MH - Structure-Activity Relationship PMC - PMC2793289 OID - NLM: PMC2793289 EDAT- 2009/10/23 06:00 MHDA- 2010/03/10 06:00 CRDT- 2009/10/23 06:00 PHST- 2009/10/21 [aheadofprint] AID - E09-07-0645 [pii] AID - 10.1091/mbc.E09-07-0645 [doi] PST - ppublish SO - Mol Biol Cell. 2009 Dec;20(24):5117-26. doi: 10.1091/mbc.E09-07-0645. Epub . PMID- 25101991 OWN - NLM STAT- MEDLINE DA - 20140821 DCOM- 20150512 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 118 IP - 33 DP - 2014 Aug 21 TI - Hot spot of structural ambivalence in prion protein revealed by secondary structure principal component analysis. PG - 9826-33 LID - 10.1021/jp5034245 [doi] AB - The conformational conversion of proteins into an aggregation-prone form is a common feature of various neurodegenerative disorders including Alzheimer's, Huntington's, Parkinson's, and prion diseases. In the early stage of prion diseases, secondary structure conversion in prion protein (PrP) causing beta-sheet expansion facilitates the formation of a pathogenic isoform with a high content of beta-sheets and strong aggregation tendency to form amyloid fibrils. Herein, we propose a straightforward method to extract essential information regarding the secondary structure conversion of proteins from molecular simulations, named secondary structure principal component analysis (SSPCA). The definite existence of a PrP isoform with an increased beta-sheet structure was confirmed in a free-energy landscape constructed by mapping protein structural data into a reduced space according to the principal components determined by the SSPCA. We suggest a "spot" of structural ambivalence in PrP-the C-terminal part of helix 2-that lacks a strong intrinsic secondary structure, thus promoting a partial alpha-helix-to-beta-sheet conversion. This result is important to understand how the pathogenic conformational conversion of PrP is initiated in prion diseases. The SSPCA has great potential to solve various challenges in studying highly flexible molecular systems, such as intrinsically disordered proteins, structurally ambivalent peptides, and chameleon sequences. FAU - Yamamoto, Norifumi AU - Yamamoto N AD - Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology , 2-17-1 Tsudanuma, Narashino 275-0016, Japan. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140807 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Prions) SB - IM MH - Amino Acid Sequence MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Principal Component Analysis MH - Prions/*chemistry/metabolism MH - Protein Structure, Secondary MH - Thermodynamics EDAT- 2014/08/08 06:00 MHDA- 2015/05/13 06:00 CRDT- 2014/08/08 06:00 PHST- 2014/08/07 [aheadofprint] AID - 10.1021/jp5034245 [doi] PST - ppublish SO - J Phys Chem B. 2014 Aug 21;118(33):9826-33. doi: 10.1021/jp5034245. Epub 2014 Aug 7. PMID- 20921991 OWN - NLM STAT- MEDLINE DA - 20101005 DCOM- 20110208 IS - 1208-6002 (Electronic) IS - 0829-8211 (Linking) VI - 88 IP - 5 DP - 2010 Oct TI - Interactions of intrinsically disordered Thellungiella salsuginea dehydrins TsDHN-1 and TsDHN-2 with membranes - synergistic effects of lipid composition and temperature on secondary structure. PG - 791-807 LID - 10.1139/o10-026 [doi] AB - Dehydrins are intrinsically disordered (unstructured) proteins that are expressed in plants experiencing stressful conditions such as drought or low temperature. Dehydrins are typically found in the cytosol and nucleus, but also associate with chloroplasts, mitochondria, and the plasma membrane. Although their role is not completely understood, it has been suggested that they stabilize proteins or membrane structures during environmental stress, the latter association mediated by formation of amphipathic α-helices by conserved regions called the K-segments. Thellungiella salsuginea is a crucifer that thrives in the Canadian sub-Arctic (Yukon Territory) where it grows on saline-rich soils and experiences periods of both extreme cold and drought. We have cloned and expressed in Escherichia coli two dehydrins from this plant, denoted TsDHN-1 (acidic) and TsDHN-2 (basic). Here, we show using transmission-Fourier transform infrared (FTIR) spectroscopy that ordered secondary structure is induced and stabilized in these proteins by association with large unilamellar vesicles emulating the lipid compositions of plant plasma and organellar membranes. Moreover, this induced folding is enhanced at low temperatures, lending credence to the hypothesis that dehydrins stabilize plant outer and organellar membranes in conditions of cold. FAU - Rahman, Luna N AU - Rahman LN AD - Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada. FAU - Chen, Lin AU - Chen L FAU - Nazim, Sumaiya AU - Nazim S FAU - Bamm, Vladimir V AU - Bamm VV FAU - Yaish, Mahmoud W AU - Yaish MW FAU - Moffatt, Barbara A AU - Moffatt BA FAU - Dutcher, John R AU - Dutcher JR FAU - Harauz, George AU - Harauz G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Canada TA - Biochem Cell Biol JT - Biochemistry and cell biology = Biochimie et biologie cellulaire JID - 8606068 RN - 0 (Membrane Lipids) RN - 0 (Plant Proteins) RN - 134711-03-8 (dehydrin proteins, plant) SB - IM MH - Amino Acid Sequence MH - Brassicaceae MH - Cell Membrane/*chemistry/*metabolism MH - Circular Dichroism MH - Hydrophobic and Hydrophilic Interactions MH - Membrane Lipids/chemistry/*metabolism MH - Molecular Sequence Data MH - Plant Proteins/*chemistry/*metabolism MH - Protein Folding MH - Protein Structure, Secondary MH - Sequence Homology, Amino Acid MH - Spectroscopy, Fourier Transform Infrared MH - Temperature EDAT- 2010/10/06 06:00 MHDA- 2011/02/09 06:00 CRDT- 2010/10/06 06:00 AID - o10-026 [pii] AID - 10.1139/o10-026 [doi] PST - ppublish SO - Biochem Cell Biol. 2010 Oct;88(5):791-807. doi: 10.1139/o10-026. PMID- 9016717 OWN - NLM STAT- MEDLINE DA - 19970227 DCOM- 19970227 LR - 20061115 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 5 IP - 1 DP - 1997 Jan 15 TI - The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe. PG - 59-68 AB - BACKGROUND: In the translation of the genetic code each aminoacyl-tRNA synthetase (aaRS) must recognize its own (cognate) tRNA and attach the corresponding amino acid to the acceptor end of tRNA, discriminating all the others. The(alphabeta)2 phenylalanyl-tRNA synthetase (PheRS) is one of the most complex enzymes in the aaRS family and is characterized by anomalous charging properties. Structurally, the enzyme belongs to class II aaRSs, as its catalytic domain is built around an antiparallel beta sheet, but functionally it resembles class I as it aminoacylates the 2'OH of the terminal ribose of tRNA (class II aaRSs aminoacylate the 3'OH). With the availability of the three-dimensional structure of the complex between multisubunit PheRS and tRNAPhe, a fuller picture of the specific tRNA-aaRS interactions is beginning to emerge. RESULTS: The crystal structure of Thermus thermophilus PheRS complexed with cognate tRNA has been solved at 3.28 A resolution. It reveals that one tRNAPhe molecule binds across all four PheRS subunits. The interactions of PheRS with tRNA stabilize the flexible N-terminal part of the alpha subunit, which appeared to form the enzyme's 11th domain, comprising a coiled-coil structure (helical arm) built up of two long antiparallel alpha helices. The helical arms are similar to those observed in SerRS and are in the same relative orientation with respect to the catalytic domain. Anticodon recognition upon tRNA binding is performed by the B8 domain, the structure of which is similar to that of the RNA-binding domain (RBD) of the small spliceosomal protein U1A. The Th. thermophilus PheRS approaches the anticodon loop from the minor groove side. CONCLUSIONS: The mode of interactions with tRNA explains the absolute necessity for the (alphabeta)2 architecture of PheRS. The interactions of tRNAPhe with PheRS and particularly with the coiled-coil domain of the alpha subunit result in conformational changes in TPsiC and D loops seen by comparison with uncomplexed yeast tRNAPhe. The tRNAPhe is a newly recognized type of RNA molecule specifically interacting with the RBD fold. In addition, a new type of anticodon-binding domain emerges in the aaRS family. The uniqueness of PheRS in charging 2'OH of tRNA is dictated by the size of its adenine-binding pocket and by the local conformation of the tRNA's CCA end. FAU - Goldgur, Y AU - Goldgur Y AD - Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel. FAU - Mosyak, L AU - Mosyak L FAU - Reshetnikova, L AU - Reshetnikova L FAU - Ankilova, V AU - Ankilova V FAU - Lavrik, O AU - Lavrik O FAU - Khodyreva, S AU - Khodyreva S FAU - Safro, M AU - Safro M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Anticodon) RN - 0 (RNA, Transfer, Phe) RN - 0 (RNA-Binding Proteins) RN - EC 6.1.1.- (Amino Acyl-tRNA Synthetases) SB - IM MH - Amino Acyl-tRNA Synthetases/*chemistry MH - Anticodon/genetics MH - Base Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - Hydrogen Bonding MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Protein Conformation MH - RNA, Transfer, Phe/*chemistry/metabolism MH - RNA-Binding Proteins/chemistry/metabolism MH - Thermus thermophilus/*enzymology EDAT- 1997/01/15 MHDA- 1997/01/15 00:01 CRDT- 1997/01/15 00:00 PST - ppublish SO - Structure. 1997 Jan 15;5(1):59-68. PMID- 15316022 OWN - NLM STAT- MEDLINE DA - 20041101 DCOM- 20041228 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 45 DP - 2004 Nov 5 TI - A biophysical analysis of the tetratricopeptide repeat-rich mitochondrial import receptor, Tom70, reveals an elongated monomer that is inherently flexible, unstable, and unfolds via a multistate pathway. PG - 46448-54 AB - Proteins destined for all submitochondrial compartments are translocated across the outer mitochondrial membrane by the TOM (translocase of the outer membrane) complex, which consists of a number of specialized receptor subunits that bind mitochondrial precursor proteins for delivery into the translocation channel. One receptor, Tom70, binds large, hydrophobic mitochondrial precursors. The current model of Tom70-mediated import involves multiple dimers of the receptor recognizing a single molecule of substrate. Here we show via a battery of biophysical and spectroscopic techniques that the cytosolic domain of Tom70 is an elongated monomer. Thermal and urea-induced denaturation revealed that the receptor, which unfolds via a multistate pathway, is a relatively unstable molecule undergoing major conformational change at physiological temperatures. The data suggest that the malleability of the monomeric Tom70 receptor is an important factor in mitochondrial import. FAU - Beddoe, Travis AU - Beddoe T AD - Protein Crystallography Unit, The ARC Centre for Structural and Functional Microbial Genomics, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia. FAU - Bushell, Simon R AU - Bushell SR FAU - Perugini, Matthew A AU - Perugini MA FAU - Lithgow, Trevor AU - Lithgow T FAU - Mulhern, Terrence D AU - Mulhern TD FAU - Bottomley, Stephen P AU - Bottomley SP FAU - Rossjohn, Jamie AU - Rossjohn J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040816 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Ligands) RN - 0 (Membrane Proteins) RN - 0 (Mitochondrial Membrane Transport Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (TOM70 protein, S cerevisiae) RN - 8W8T17847W (Urea) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Motifs MH - Binding Sites MH - Circular Dichroism MH - Cytosol/metabolism MH - DNA/metabolism MH - Dimerization MH - Dose-Response Relationship, Drug MH - Electrophoresis, Polyacrylamide Gel MH - Hot Temperature MH - Ligands MH - Membrane Proteins/*physiology MH - Mitochondria/*metabolism MH - Mitochondrial Membrane Transport Proteins MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Saccharomyces cerevisiae/metabolism MH - Saccharomyces cerevisiae Proteins/*physiology MH - Spectrometry, Fluorescence MH - Temperature MH - Thermodynamics MH - Ultracentrifugation MH - Urea/pharmacology EDAT- 2004/08/19 05:00 MHDA- 2004/12/29 09:00 CRDT- 2004/08/19 05:00 PHST- 2004/08/16 [aheadofprint] AID - 10.1074/jbc.M405639200 [doi] AID - M405639200 [pii] PST - ppublish SO - J Biol Chem. 2004 Nov 5;279(45):46448-54. Epub 2004 Aug 16. PMID- 24383916 OWN - NLM STAT- MEDLINE DA - 20140204 DCOM- 20140819 IS - 1520-6882 (Electronic) IS - 0003-2700 (Linking) VI - 86 IP - 3 DP - 2014 Feb 4 TI - Probing conformational change of intrinsically disordered alpha-synuclein to helical structures by distinctive regional interactions with lipid membranes. PG - 1909-16 LID - 10.1021/ac404132g [doi] AB - alpha-Synuclein (alpha-Syn) is an intrinsically disordered protein, whose fibrillar aggregates are associated with the pathogenesis of Parkinson's disease. alpha-Syn associates with lipid membranes and forms helical structures upon membrane binding. In this study, we explored the helix formation of alpha-Syn in solution containing trifluoroethanol using small-angle X-ray scattering and electrospray ionization ion mobility mass spectrometry. We then investigated the structural transitions of alpha-Syn to helical structures via association with large unilamellar vesicles as model lipid membrane systems. Hydrogen-deuterium exchange combined with electrospray ionization mass spectrometry was further utilized to understand the details of the regional interaction mechanisms of alpha-Syn with lipid vesicles based on the polarity of the lipid head groups. The characteristics of the helical structures were observed with alpha-Syn by adsorption onto the anionic phospholipid vesicles via electrostatic interactions between the N-terminal region of the protein and the anionic head groups of the lipids. alpha-Syn also associates with zwitterionic lipid vesicles and forms helical structures via hydrophobic interactions. These experimental observations provide an improved understanding of the distinct structural change mechanisms of alpha-Syn that originate from different regional interactions of the protein with lipid membranes and subsequently provide implications regarding diverse protein-membrane interactions related to their fibrillation kinetics. FAU - Lee, Shin Jung C AU - Lee SJ AD - Department of Chemistry, double daggerPohang Accelerator Laboratory, section signDivision of Advanced Materials Science, Pohang University of Science and Technology (POSTECH) , Pohang, North Gyeongsang 790-784, South Korea. FAU - Lee, Jong Wha AU - Lee JW FAU - Choi, Tae Su AU - Choi TS FAU - Jin, Kyeong Sik AU - Jin KS FAU - Lee, Seonghwan AU - Lee S FAU - Ban, Changill AU - Ban C FAU - Kim, Hugh I AU - Kim HI LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140113 PL - United States TA - Anal Chem JT - Analytical chemistry JID - 0370536 RN - 0 (Lipid Bilayers) RN - 0 (Phospholipids) RN - 0 (Unilamellar Liposomes) RN - 0 (alpha-Synuclein) SB - IM MH - Cell Membrane/chemistry/*metabolism MH - Lipid Bilayers/chemistry/metabolism MH - Phospholipids/chemistry/metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Unilamellar Liposomes/chemistry/metabolism MH - alpha-Synuclein/*chemistry/*metabolism EDAT- 2014/01/05 06:00 MHDA- 2014/08/20 06:00 CRDT- 2014/01/04 06:00 PHST- 2014/01/13 [aheadofprint] AID - 10.1021/ac404132g [doi] PST - ppublish SO - Anal Chem. 2014 Feb 4;86(3):1909-16. doi: 10.1021/ac404132g. Epub 2014 Jan 13. PMID- 23648480 OWN - NLM STAT- MEDLINE DA - 20130610 DCOM- 20130827 LR - 20141116 IS - 1098-5549 (Electronic) IS - 0270-7306 (Linking) VI - 33 IP - 13 DP - 2013 Jul TI - The protein level of PGC-1alpha, a key metabolic regulator, is controlled by NADH-NQO1. PG - 2603-13 LID - 10.1128/MCB.01672-12 [doi] AB - PGC-1alpha is a key transcription coactivator regulating energy metabolism in a tissue-specific manner. PGC-1alpha expression is tightly regulated, it is a highly labile protein, and it interacts with various proteins--the known attributes of intrinsically disordered proteins (IDPs). In this study, we characterize PGC-1alpha as an IDP and demonstrate that it is susceptible to 20S proteasomal degradation by default. We further demonstrate that PGC-1alpha degradation is inhibited by NQO1, a 20S gatekeeper protein. NQO1 binds and protects PGC-1alpha from degradation in an NADH-dependent manner. Using different cellular physiological settings, we also demonstrate that NQO1-mediated PGC-1alpha protection plays an important role in controlling both basal and physiologically induced PGC-1alpha protein level and activity. Our findings link NQO1, a cellular redox sensor, to the metabolite-sensing network that tunes PGC-1alpha expression and activity in regulating energy metabolism. FAU - Adamovich, Yaarit AU - Adamovich Y AD - Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. FAU - Shlomai, Amir AU - Shlomai A FAU - Tsvetkov, Peter AU - Tsvetkov P FAU - Umansky, Kfir B AU - Umansky KB FAU - Reuven, Nina AU - Reuven N FAU - Estall, Jennifer L AU - Estall JL FAU - Spiegelman, Bruce M AU - Spiegelman BM FAU - Shaul, Yosef AU - Shaul Y LA - eng GR - P30 DK057521/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130506 PL - United States TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (Heat-Shock Proteins) RN - 0 (PPARGC1A protein, human) RN - 0 (Ppargc1a protein, mouse) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - 0U46U6E8UK (NAD) RN - 7QID3E7BG7 (Dicumarol) RN - 98600C0908 (Cycloheximide) RN - EC 1.6.5.2 (NAD(P)H Dehydrogenase (Quinone)) RN - EC 1.6.5.2 (NQO1 protein, human) RN - EC 1.6.5.2 (Nqo1 protein, mouse) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Animals MH - Cell Line/drug effects MH - Cycloheximide/pharmacology MH - Dicumarol/pharmacology MH - Fasting MH - Gene Knockdown Techniques MH - Heat-Shock Proteins/*metabolism MH - Hepatocytes/metabolism MH - Humans MH - Liver/drug effects/metabolism MH - Male MH - Mice MH - Mice, Inbred C57BL MH - Myoblasts/metabolism MH - NAD/metabolism MH - NAD(P)H Dehydrogenase (Quinone)/antagonists & inhibitors/genetics/*metabolism MH - Proteasome Endopeptidase Complex/metabolism MH - Trans-Activators/*metabolism MH - Transcription Factors/*metabolism PMC - PMC3700121 OID - NLM: PMC3700121 EDAT- 2013/05/08 06:00 MHDA- 2013/08/28 06:00 CRDT- 2013/05/08 06:00 PHST- 2013/05/06 [aheadofprint] AID - MCB.01672-12 [pii] AID - 10.1128/MCB.01672-12 [doi] PST - ppublish SO - Mol Cell Biol. 2013 Jul;33(13):2603-13. doi: 10.1128/MCB.01672-12. Epub 2013 May 6. PMID- 15571721 OWN - NLM STAT- MEDLINE DA - 20041201 DCOM- 20050111 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 345 IP - 2 DP - 2005 Jan 14 TI - Characterization of segments from the central region of BRCA1: an intrinsically disordered scaffold for multiple protein-protein and protein-DNA interactions? PG - 275-87 AB - The BRCA1 tumor suppressor gene encodes an 1863 amino acid gene product that is implicated in many cellular pathways including transcription, cell-cycle checkpoint control, apoptosis and DNA repair. Much attention has been focused on the structural and biochemical characterization of the N-terminal RING and tandem C-terminal BRCT domains of BRCA1. Here we used NMR spectroscopy in conjunction with CD spectroscopy and limited proteolysis to investigate the biophysical properties of the approximately 1500 residue central region of BRCA1. Our results show that although there are a few small, mildly protease-resistant regions, the majority of the BRCA1 central region lacks any pre-existing independently folded globular domains. Electrophoretic mobility shift assay and intrinsic tryptophan fluorescence experiments also demonstrate that, although intrinsically disordered, polypeptides from the central region are able to mediate interactions with DNA and p53 with affinities in the low micromolar range. This supports a model in which the central region may act as a long flexible scaffold for intermolecular interactions, thereby helping to integrate multiple signals in the DNA damage response pathway. FAU - Mark, Wen-Ying AU - Mark WY AD - Division of Molecular and Structural Biology, Department of Medical Biophysics, Ontario Cancer Institute, University of Toronto, Toronto, Ont., Canada M5G 2M9. FAU - Liao, Jack C C AU - Liao JC FAU - Lu, Ying AU - Lu Y FAU - Ayed, Ayeda AU - Ayed A FAU - Laister, Rob AU - Laister R FAU - Szymczyna, Blair AU - Szymczyna B FAU - Chakrabartty, Avi AU - Chakrabartty A FAU - Arrowsmith, Cheryl H AU - Arrowsmith CH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (BRCA1 Protein) RN - 0 (Tumor Suppressor Protein p53) RN - 8DUH1N11BX (Tryptophan) RN - 9007-49-2 (DNA) SB - IM MH - Apoptosis MH - BRCA1 Protein/*chemistry/metabolism MH - Biophysical Phenomena MH - Biophysics MH - Breast Neoplasms/metabolism MH - Cell Cycle MH - Circular Dichroism MH - DNA/*chemistry MH - DNA Repair MH - Dose-Response Relationship, Drug MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Genetic MH - Mutation, Missense MH - Polymerase Chain Reaction MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Tertiary MH - Transcription, Genetic MH - Tryptophan/chemistry MH - Tumor Suppressor Protein p53/chemistry/metabolism EDAT- 2004/12/02 09:00 MHDA- 2005/01/12 09:00 CRDT- 2004/12/02 09:00 PHST- 2004/07/07 [received] PHST- 2004/09/28 [revised] PHST- 2004/10/14 [accepted] AID - S0022-2836(04)01337-3 [pii] AID - 10.1016/j.jmb.2004.10.045 [doi] PST - ppublish SO - J Mol Biol. 2005 Jan 14;345(2):275-87. PMID- 16766517 OWN - NLM STAT- MEDLINE DA - 20060911 DCOM- 20061031 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 281 IP - 37 DP - 2006 Sep 15 TI - Titin as a giant scaffold for integrating stress and Src homology domain 3-mediated signaling pathways: the clustering of novel overlap ligand motifs in the elastic PEVK segment. PG - 27539-56 AB - The richness of proline sequences in titins qualifies these giant proteins as the largest source of intrinsically disordered structures in nature. An extensive search and analysis for Src homology domain 3 (SH3) ligand motifs revealed a myriad of broadly distributed SH3 ligand motifs, with the highest density in the PEVK segments of human titin. Besides the canonical class I and II motifs with opposite orientations, novel overlapping motifs consisting of one or more of each canonical motif are abundant. Experimentally, the binding affinity and critical residues of these putative titin-based SH3 ligands toward nebulin SH3 and other SH3-containing proteins in muscle and non-muscle cell extracts were validated with peptide array technology and by the sarcomere distribution of SH3-containing proteins. A 28-mer overlapping motif-containing PEVK module binds to nebulin SH3 in and around the canonical cleft, especially to the acidic residues in the loops, as revealed by NMR titration. Molecular dynamics and molecular docking studies indicated that the overlapping motif can bind in opposite orientations with comparable energy and contact areas and predicts correctly orientation-specific contacts in NMR data. We propose that the overlap ligand motifs are a new class of ligands with innate ability to dictate SH3 domain orientation and to facilitate the rate, strength, and stereospecificity of receptor interactions. Proline-rich sequences of titins are candidates as major hubs of SH3-dependent signaling pathways. The interplay of elasticity and dense clustering of mixed receptor orientations in titin PEVK segment have important implications for the mechanical sensing, force sensitivity, and inter-adapter interactions in signaling pathways. FAU - Ma, Kan AU - Ma K AD - Muscle Proteomics and Nanotechnology Section, Laboratory of Muscle Biology, NIAMS, National Institutes of Health, Bethesda, Maryland 20892, USA. FAU - Forbes, Jeffrey G AU - Forbes JG FAU - Gutierrez-Cruz, Gustavo AU - Gutierrez-Cruz G FAU - Wang, Kuan AU - Wang K LA - eng PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20060608 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Connectin) RN - 0 (Ligands) RN - 0 (Muscle Proteins) RN - 0 (TTN protein, human) RN - 0 (nebulin) RN - EC 2.7.- (Protein Kinases) SB - IM MH - Amino Acid Sequence MH - Animals MH - Connectin MH - HeLa Cells MH - Humans MH - Ligands MH - Molecular Sequence Data MH - Muscle Proteins/*chemistry MH - Muscles/metabolism MH - Protein Kinases/*chemistry MH - Protein Structure, Tertiary MH - Rabbits MH - Sequence Homology, Amino Acid MH - Signal Transduction MH - src Homology Domains EDAT- 2006/06/13 09:00 MHDA- 2006/11/01 09:00 CRDT- 2006/06/13 09:00 PHST- 2006/06/08 [aheadofprint] AID - M604525200 [pii] AID - 10.1074/jbc.M604525200 [doi] PST - ppublish SO - J Biol Chem. 2006 Sep 15;281(37):27539-56. Epub 2006 Jun 8. PMID- 9230043 OWN - NLM STAT- MEDLINE DA - 19970808 DCOM- 19970808 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 36 IP - 30 DP - 1997 Jul 29 TI - Regional polysterism in the GTP-bound form of the human c-Ha-Ras protein. PG - 9109-19 AB - The backbone 1H, 13C, and 15N resonances of the c-Ha-Ras protein [a truncated version consisting of residues 1-171, Ras(1-171)] bound with GMPPNP (a slowly hydrolyzable analogue of GTP) were assigned and compared with those of the GDP-bound Ras(1-171). The backbone amide resonances of amino acid residues 10-13, 21, 31-39, 57-64, and 71 of Ras(1-171).GMPPNP, but not those of Ras(1-171).GDP, were extremely broadened, whereas other residues of Ras(1-171).GMPPNP exhibited amide resonances nearly as sharp as those of Ras(1-171). GDP. The residues exhibiting the extreme broadening, except for residues 21 and 71, are localized in three functional loop regions [loops L1, L2 (switch I), and L4 (switch II)], which are involved in hydrolysis of GTP and interactions with other proteins. From the temperature and magnetic field strength dependencies of the backbone amide resonance intensities, the extreme broadening was ascribed to the exchange at an intermediate rate on the NMR time scale. It was shown that the Ras(1-171) protein bound with GTP or GTPgammaS (another slowly hydrolyzable analogue of GTP) exhibits the same type of broadening. Therefore, it is a characteristic feature of the GTP-bound form of Ras that the L1, L2, and L4 loop regions, but not other regions, are in a rather slow interconversion between two or more stable conformers. This phenomenon, termed a "regional polysterism", of these loop regions may be related with their multifunctionality: the GTP-dependent interactions with several downstream target groups such as the Raf and RalGDS families and also with the GTPase activating protein (GAP) family. In fact, the binding of Ras(1-171).GMPPNP with the Ras-binding domain (residues 51-131) of c-Raf-1 was shown to eliminate the regional polysterism nearly completely. It was indicated, therefore, that each target/regulator selects its appropriate conformer among those presented by the "polysteric" binding interface of Ras. As the downstream target groups exhibit no apparent sequence homology to each other, it is possible that one target group prefers a conformer different from that preferred by another group. The involvement of loop L1 in the regional polysterism might suggest that the negative regulators, GAPs, bind to the polysteric binding interface (loops L2 and L4) of Ras and cooperatively select a conformer suitable for transition of the GTPase catalytic center, involving loops L1 and L4, into the highly active state. FAU - Ito, Y AU - Ito Y AD - Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Japan. FAU - Yamasaki, K AU - Yamasaki K FAU - Iwahara, J AU - Iwahara J FAU - Terada, T AU - Terada T FAU - Kamiya, A AU - Kamiya A FAU - Shirouzu, M AU - Shirouzu M FAU - Muto, Y AU - Muto Y FAU - Kawai, G AU - Kawai G FAU - Yokoyama, S AU - Yokoyama S FAU - Laue, E D AU - Laue ED FAU - Walchli, M AU - Walchli M FAU - Shibata, T AU - Shibata T FAU - Nishimura, S AU - Nishimura S FAU - Miyazawa, T AU - Miyazawa T LA - eng SI - PDB/1AA9 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Carbon Isotopes) RN - 0 (Nitrogen Isotopes) RN - 0 (Proto-Oncogene Proteins) RN - 0 (guanosine 5'-O-(1-thiotriphosphate)) RN - 37589-80-3 (Guanosine 5'-O-(3-Thiotriphosphate)) RN - 7YNJ3PO35Z (Hydrogen) RN - 86-01-1 (Guanosine Triphosphate) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - EC 2.7.11.1 (Proto-Oncogene Proteins c-raf) RN - EC 3.6.5.2 (HRAS protein, human) RN - EC 3.6.5.2 (Proto-Oncogene Proteins p21(ras)) SB - IM MH - Carbon Isotopes MH - Crystallography, X-Ray MH - Guanosine 5'-O-(3-Thiotriphosphate)/analogs & derivatives/chemistry MH - Guanosine Triphosphate/*chemistry MH - Humans MH - Hydrogen MH - Magnetic Resonance Spectroscopy MH - Nitrogen Isotopes MH - Protein Binding MH - Protein-Serine-Threonine Kinases/chemistry/metabolism MH - Proto-Oncogene Proteins/chemistry/metabolism MH - Proto-Oncogene Proteins c-raf MH - Proto-Oncogene Proteins p21(ras)/*chemistry/metabolism MH - Temperature EDAT- 1997/07/29 MHDA- 1997/07/29 00:01 CRDT- 1997/07/29 00:00 AID - 10.1021/bi970296u [doi] AID - bi970296u [pii] PST - ppublish SO - Biochemistry. 1997 Jul 29;36(30):9109-19. PMID- 20152802 OWN - NLM STAT- MEDLINE DA - 20100315 DCOM- 20100412 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 393 IP - 3 DP - 2010 Mar 12 TI - NMR characterization of intramolecular interaction of osteopontin, an intrinsically disordered protein with cryptic integrin-binding motifs. PG - 487-91 LID - 10.1016/j.bbrc.2010.02.030 [doi] AB - Osteopontin (OPN) is an integrin-binding protein found in a variety of tissues and physiological fluids and is involved in divergent biological processes such as migration, adhesion and signaling in integrin-independent as well as dependent manners. The adhesive activity of this protein is modulated upon cleavage by thrombin at the central part of the molecule, in the vicinity of the integrin-binding sequences. Although detailed structural characterization is crucial for further understanding of the regulatory mechanisms of the OPN functions, its intrinsically disordered property hampers in-depth conformational analyses. Here we report an NMR study of mouse OPN and its N-terminal thrombin-cleavage product to characterize intramolecular interaction of this molecule. Paramagnetic relaxation enhancement experiment revealed that OPN exhibits a long-range intramolecular interaction between the N- and C-terminal regions. Furthermore, our NMR data showed that anti-OPN antibody OPN1.2, whose reactivity is impaired by deletion or amino acid substitutions of the arginine-aspartate-glycine integrin-binding motif, binds the N-terminal side of the integrin-binding motifs suggesting the existence of intramolecular interaction. These data suggest that functional interactions of OPN with integrins and the other binding partners can be modulated by the intramolecular interactions. CI - 2010 Elsevier Inc. All rights reserved. FAU - Yamaguchi, Yoshiki AU - Yamaguchi Y AD - Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan. FAU - Hanashima, Shinya AU - Hanashima S FAU - Yagi, Hirokazu AU - Yagi H FAU - Takahashi, Yutaka AU - Takahashi Y FAU - Sasakawa, Hiroaki AU - Sasakawa H FAU - Kurimoto, Eiji AU - Kurimoto E FAU - Iguchi, Takeshi AU - Iguchi T FAU - Kon, Shigeyuki AU - Kon S FAU - Uede, Toshimitsu AU - Uede T FAU - Kato, Koichi AU - Kato K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100210 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Antibodies, Monoclonal) RN - 0 (Integrins) RN - 0 (Recombinant Proteins) RN - 106441-73-0 (Osteopontin) SB - IM MH - Amino Acid Motifs MH - Animals MH - Antibodies, Monoclonal/immunology MH - Binding Sites MH - Circular Dichroism MH - Epitope Mapping MH - Integrins/*metabolism MH - Mice MH - Nuclear Magnetic Resonance, Biomolecular MH - Osteopontin/*chemistry/immunology/metabolism MH - Protein Conformation MH - Recombinant Proteins/chemistry/immunology/metabolism EDAT- 2010/02/16 06:00 MHDA- 2010/04/13 06:00 CRDT- 2010/02/16 06:00 PHST- 2010/02/02 [received] PHST- 2010/02/08 [accepted] PHST- 2010/02/10 [aheadofprint] AID - S0006-291X(10)00241-X [pii] AID - 10.1016/j.bbrc.2010.02.030 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2010 Mar 12;393(3):487-91. doi: 10.1016/j.bbrc.2010.02.030. Epub 2010 Feb 10. PMID- 20727855 OWN - NLM STAT- MEDLINE DA - 20100927 DCOM- 20101013 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 400 IP - 3 DP - 2010 Sep 24 TI - The Dad1 subunit of the yeast kinetochore Dam1 complex is an intrinsically disordered protein. PG - 313-7 LID - 10.1016/j.bbrc.2010.08.050 [doi] AB - The Dam1 complex is an important part of the yeast kinetochore. It mediates attachment of the chromosome to the mitotic spindle and is involved in chromatid separation initiated at anaphase. It is comprised of 10 individual subunits and has been observed to oligomerize in various ways as it interacts with microtubules, including forming a ring. This work explores the biochemical and biophysical properties of Dad1, one of the Dam1 complex subunits from the human fungal pathogen Candida albicans. Unlike its Saccharomyces cerevisiae counterpart, C. albicans Dad1 can be expressed as a soluble protein in Escherichia coli. Analysis of this protein's hydrodynamic properties, thermostability and primary sequence have been conducted. As a result, we conclude that isolated Dad1 is an intrinsically disordered protein. CI - Copyright (c) 2010 Elsevier Inc. All rights reserved. FAU - Waldo, Jennifer Turner AU - Waldo JT AD - State University of New York at New Paltz, Biology Department, 1 Hawk Drive, New Paltz, NY 12561, USA. waldoj@newpaltz.edu FAU - Greagor, Stacy A AU - Greagor SA FAU - Iqbal, Aruba J AU - Iqbal AJ FAU - Gittens, Abiola S A AU - Gittens AS FAU - Grant, Kemone K AU - Grant KK LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20100819 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Dad1 protein, S cerevisiae) RN - 0 (Microtubule-Associated Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Candida albicans/genetics/*metabolism MH - Hot Temperature MH - Kinetochores/*metabolism MH - Microtubule-Associated Proteins/chemistry/genetics/*metabolism MH - Protein Folding MH - Protein Stability MH - Saccharomyces cerevisiae/genetics/*metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism EDAT- 2010/08/24 06:00 MHDA- 2010/10/14 06:00 CRDT- 2010/08/24 06:00 PHST- 2010/08/13 [received] PHST- 2010/08/14 [accepted] PHST- 2010/08/19 [aheadofprint] AID - S0006-291X(10)01545-7 [pii] AID - 10.1016/j.bbrc.2010.08.050 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2010 Sep 24;400(3):313-7. doi: 10.1016/j.bbrc.2010.08.050. Epub 2010 Aug 19. PMID- 11171981 OWN - NLM STAT- MEDLINE DA - 20010226 DCOM- 20010419 LR - 20140613 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 98 IP - 4 DP - 2001 Feb 13 TI - The quorum-sensing transcriptional regulator TraR requires its cognate signaling ligand for protein folding, protease resistance, and dimerization. PG - 1507-12 AB - Complexes between the quorum-sensing regulator TraR and its inducing ligand autoinducer (AAI) are soluble in Escherichia coli, whereas apo-TraR is almost completely insoluble. Here we show that the lack of soluble TraR is due in large part to rapid proteolysis, inasmuch as apo-TraR accumulated to high levels in an E. coli strain deficient in Clp and Lon proteases. In pulse labeling experiments, AAI protected TraR against proteolysis only when it was added before the radiolabel. This observation indicates that TraR proteins can productively bind AAI only during their own synthesis on polysomes, whereas fully synthesized apo-TraR proteins are not functional AAI receptors. Purified apo-TraR was rapidly degraded by trypsin to oligopeptides, whereas TraR-AAI complexes were more resistant to trypsin and were cleaved at discrete interdomain linkers, indicating that TraR requires AAI to attain its mature tertiary structure. TraR-AAI complexes eluted from a gel filtration column as dimers and bound DNA as dimers. In contrast, apo-TraR was monomeric, and incubation with AAI under a variety of conditions did not cause dimerization. We conclude that AAI is critical for the folding of nascent TraR protein into its mature tertiary structure and that full-length apo-TraR cannot productively bind AAI and is consequently targeted for rapid proteolysis. FAU - Zhu, J AU - Zhu J AD - Department of Microbiology, Cornell University, Ithaca, NY 14853, USA. FAU - Winans, S C AU - Winans SC LA - eng GR - GM 42893/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Heat-Shock Proteins) RN - 0 (Lactones) RN - 0 (Ligands) RN - 0 (Maltose-Binding Proteins) RN - 0 (Monosaccharide Transport Proteins) RN - 0 (N-octanoylhomoserine lactone) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Solutions) RN - 0 (TraR protein, Agrobacterium tumefaciens) RN - 0 (Transcription Factors) RN - 0 (maltose transport system, E coli) RN - 6KA95X0IVO (Homoserine) RN - EC 3.4.21.- (ATP-Dependent Proteases) RN - EC 3.4.21.- (Serine Endopeptidases) RN - EC 3.4.21.4 (Trypsin) RN - EC 3.4.21.53 (Lon protein, E coli) RN - EC 3.4.21.53 (Protease La) RN - EC 3.4.21.92 (Endopeptidase Clp) RN - EC 3.6.1.- (Adenosine Triphosphatases) SB - IM MH - *ATP-Binding Cassette Transporters MH - ATP-Dependent Proteases MH - Adenosine Triphosphatases/metabolism MH - Bacterial Proteins/genetics/*metabolism MH - Carrier Proteins/metabolism MH - Dimerization MH - Endopeptidase Clp MH - *Escherichia coli Proteins MH - Heat-Shock Proteins/metabolism MH - Homoserine/*analogs & derivatives/*metabolism MH - Lactones/*metabolism MH - Ligands MH - Maltose-Binding Proteins MH - *Monosaccharide Transport Proteins MH - *Protease La MH - Protein Denaturation MH - *Protein Folding MH - Recombinant Fusion Proteins/genetics/metabolism MH - Serine Endopeptidases/metabolism MH - Signal Transduction MH - Solutions MH - Transcription Factors/*metabolism MH - Trypsin/*metabolism PMC - PMC29287 OID - NLM: PMC29287 EDAT- 2001/02/15 11:00 MHDA- 2001/04/21 10:01 CRDT- 2001/02/15 11:00 AID - 10.1073/pnas.98.4.1507 [doi] AID - 98/4/1507 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2001 Feb 13;98(4):1507-12. PMID- 19841061 OWN - NLM STAT- MEDLINE DA - 20091216 DCOM- 20100114 LR - 20140827 IS - 1098-5549 (Electronic) IS - 0270-7306 (Linking) VI - 30 IP - 1 DP - 2010 Jan TI - Site-specific phosphorylation induces functionally active conformation in the intrinsically disordered N-terminal activation function (AF1) domain of the glucocorticoid receptor. PG - 220-30 LID - 10.1128/MCB.00552-09 [doi] AB - Intrinsically disordered (ID) regions are disproportionately higher in cell signaling proteins and are predicted to have much larger frequency of phosphorylation sites than ordered regions, suggesting an important role in their regulatory capacity. In this study, we show that AF1, an ID activation domain of the glucocorticoid receptor (GR), adopts a functionally folded conformation due to its site-specific phosphorylation by p38 mitogen-activated protein kinase, which is involved in apoptotic and gene-inductive events initiated by the GR. Further, we show that site-specific phosphorylation-induced secondary and tertiary structure formation specifically facilitates AF1's interaction with critical coregulatory proteins and subsequently its transcriptional activity. These data demonstrate a mechanism through which ID activation domain of the steroid receptors and other similar transcription factors may adopt a functionally active conformation under physiological conditions. FAU - Garza, Anna M S AU - Garza AM AD - Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas 77555, USA. FAU - Khan, Shagufta H AU - Khan SH FAU - Kumar, Raj AU - Kumar R LA - eng GR - DK058829/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (Receptors, Glucocorticoid) RN - 0 (Recombinant Proteins) RN - 0 (TATA-Box Binding Protein) RN - EC 2.3.1.48 (CREB-Binding Protein) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 1) RN - EC 2.7.11.24 (p38 Mitogen-Activated Protein Kinases) SB - IM MH - Animals MH - CREB-Binding Protein/metabolism MH - Cell Line MH - Cercopithecus aethiops MH - Humans MH - Nuclear Receptor Coactivator 1/metabolism MH - Phosphorylation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Glucocorticoid/chemistry/*metabolism MH - Recombinant Proteins/chemistry MH - TATA-Box Binding Protein/metabolism MH - Transcription, Genetic MH - p38 Mitogen-Activated Protein Kinases/antagonists & inhibitors/chemistry/metabolism PMC - PMC2798295 OID - NLM: PMC2798295 EDAT- 2009/10/21 06:00 MHDA- 2010/01/15 06:00 CRDT- 2009/10/21 06:00 PHST- 2009/10/19 [aheadofprint] AID - MCB.00552-09 [pii] AID - 10.1128/MCB.00552-09 [doi] PST - ppublish SO - Mol Cell Biol. 2010 Jan;30(1):220-30. doi: 10.1128/MCB.00552-09. Epub . PMID- 15299951 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20040809 DCOM- 20050217 LR - 20070724 IS - 0907-4449 (Print) IS - 0907-4449 (Linking) VI - 53 IP - Pt 2 DP - 1997 Mar 1 TI - Structure of human plasminogen kringle 4 at 1.68 a and 277 K. A possible structural role of disordered residues. PG - 169-78 AB - Despite considerable effort to elucidate the functional role of the kringle domains, relatively little is known about interactions with other protein domains. Most of the crystal structures describe the interactions at the kringle active site. This study suggests a novel way to interpret structural results such as disorder located away from an active site. The crystal structure of human plasminogen kringle 4 (PGK4) has been refined against 10-1.68 A resolution X-ray data (R(merge) = 3.7%) to the standard crystallographic R = 14.7% using the program X-PLOR. The crystals of PGK4 showed significant instability in cell dimensions (changes more than 1.5 A) even at 277 K. The refinement revealed structural details not observed before [Mulichak, Tulinsky & Ravichandran (1991). Biochemistry, 30, 10576-10588], such as clear density for additional side chains and more extensive disorder. Discrete disorder was detected for residues S73, S78, T80, S89, S91, S92, Ml12, S132, C138 and K142. Most of the disordered residues form two patches on the surface of the protein. This localized disorder suggests that these residues may play a role in quaternary interactions and possibly form an interface with the other domains of proteins that contain kringles, such as plasminogen. Although, an additional residue D65 was refined at the beginning of the sequence, still more residues near the peptide cleavage site must be disordered in the crystal. FAU - Stec, B AU - Stec B AD - Department of Chemistry, Boston College, Chestnut Hill, MA 02167, USA. stec@bcchem.bc.edu FAU - Yamano, A AU - Yamano A FAU - Whitlow, M AU - Whitlow M FAU - Teeter, M M AU - Teeter MM LA - eng PT - Journal Article PL - Denmark TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 EDAT- 1997/03/01 00:00 MHDA- 1997/03/01 00:01 CRDT- 1997/03/01 00:00 AID - 10.1107/S0907444996012267 [doi] AID - S0907444996012267 [pii] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 1997 Mar 1;53(Pt 2):169-78. PMID- 10545102 OWN - NLM STAT- MEDLINE DA - 20000104 DCOM- 20000104 LR - 20120605 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 18 IP - 21 DP - 1999 Nov 1 TI - Distinct structural elements in GDNF mediate binding to GFRalpha1 and activation of the GFRalpha1-c-Ret receptor complex. PG - 5901-10 AB - Ligand-induced receptor oligomerization is a widely accepted mechanism for activation of cell-surface receptors. We investigated ligand-receptor interactions in the glial cell-line derived neurotrophic factor (GDNF) receptor complex, formed by the c-Ret receptor tyrosine kinase and the glycosylphosphatidylinositol (GPI)-anchored subunit GDNF family receptor alpha-1 (GFRalpha1). As only GFRalpha1 can bind GDNF directly, receptor complex formation is thought to be initiated by GDNF binding to this receptor. Here we identify an interface in GDNF formed by exposed acidic and hydrophobic residues that is critical for binding to GFRalpha1. Unexpectedly, several GDNF mutants deficient in GFRalpha1 binding retained the ability to bind and activate c-Ret at normal levels. Although impaired in binding GFRalpha1 efficiently, these mutants still required GFRalpha1 for c-Ret activation. These findings support a role for c-Ret in ligand binding and indicate that GDNF does not initiate receptor complex formation, but rather interacts with a pre-assembled GFRalpha1- c-Ret complex. FAU - Eketjall, S AU - Eketjall S AD - Division of Molecular Neurobiology, Department of Neuroscience, Karolinska Institute, 17177 Stockholm, Sweden. FAU - Fainzilber, M AU - Fainzilber M FAU - Murray-Rust, J AU - Murray-Rust J FAU - Ibanez, C F AU - Ibanez CF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Cross-Linking Reagents) RN - 0 (Drosophila Proteins) RN - 0 (Gdnf protein, mouse) RN - 0 (Gfra1 protein, mouse) RN - 0 (Glial Cell Line-Derived Neurotrophic Factor) RN - 0 (Glial Cell Line-Derived Neurotrophic Factor Receptors) RN - 0 (Nerve Growth Factors) RN - 0 (Nerve Tissue Proteins) RN - 0 (Proto-Oncogene Proteins) RN - 21820-51-9 (Phosphotyrosine) RN - EC 2.7.10.1 (Proto-Oncogene Proteins c-ret) RN - EC 2.7.10.1 (Receptor Protein-Tyrosine Kinases) RN - EC 2.7.10.1 (Ret oncogene protein, Drosophila) RN - EC 2.7.10.1 (Ret protein, mouse) SB - IM MH - Animals MH - Binding Sites MH - Cell Line MH - Cross-Linking Reagents MH - Dimerization MH - *Drosophila Proteins MH - Glial Cell Line-Derived Neurotrophic Factor MH - Glial Cell Line-Derived Neurotrophic Factor Receptors MH - Mice MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - *Nerve Growth Factors MH - Nerve Tissue Proteins/*chemistry/genetics MH - Phosphorylation MH - Phosphotyrosine/analysis MH - Protein Binding/genetics MH - Protein Conformation MH - Protein Structure, Secondary MH - Proto-Oncogene Proteins/*metabolism MH - Proto-Oncogene Proteins c-ret MH - Receptor Protein-Tyrosine Kinases/*metabolism MH - Structure-Activity Relationship PMC - PMC1171656 OID - NLM: PMC1171656 EDAT- 1999/11/02 MHDA- 1999/11/02 00:01 CRDT- 1999/11/02 00:00 AID - 10.1093/emboj/18.21.5901 [doi] PST - ppublish SO - EMBO J. 1999 Nov 1;18(21):5901-10. PMID- 11056169 OWN - NLM STAT- MEDLINE DA - 20010523 DCOM- 20010621 LR - 20071115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 4 DP - 2001 Jan 26 TI - Human p8 is a HMG-I/Y-like protein with DNA binding activity enhanced by phosphorylation. PG - 2742-51 AB - We have studied the biochemical features, the conformational preferences in solution, and the DNA binding properties of human p8 (hp8), a nucleoprotein whose expression is affected during acute pancreatitis. Biochemical studies show that hp8 has properties of the high mobility group proteins, HMG-I/Y. Structural studies have been carried out by using circular dichroism (near- and far-ultraviolet), Fourier transform infrared, and NMR spectroscopies. All the biophysical probes indicate that hp8 is monomeric (up to 1 mm concentration) and partially unfolded in solution. The protein seems to bind DNA weakly, as shown by electrophoretic gel shift studies. On the other hand, hp8 is a substrate for protein kinase A (PKA). The phosphorylated hp8 (PKAhp8) has a higher content of secondary structure than the nonphosphorylated protein, as concluded by Fourier transform infrared studies. PKAhp8 binds DNA strongly, as shown by the changes in circular dichroism spectra, and gel shift analysis. Thus, although there is not a high sequence homology with HMG-I/Y proteins, hp8 can be considered as a HMG-I/Y-like protein. FAU - Encinar, J A AU - Encinar JA AD - Centro de Biologia Molecular y Celular, Universidad Miguel Hernandez, 03202, Elche, Alicante, Spain. FAU - Mallo, G V AU - Mallo GV FAU - Mizyrycki, C AU - Mizyrycki C FAU - Giono, L AU - Giono L FAU - Gonzalez-Ros, J M AU - Gonzalez-Ros JM FAU - Rico, M AU - Rico M FAU - Canepa, E AU - Canepa E FAU - Moreno, S AU - Moreno S FAU - Neira, J L AU - Neira JL FAU - Iovanna, J L AU - Iovanna JL LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20001030 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Basic Helix-Loop-Helix Transcription Factors) RN - 0 (DNA-Binding Proteins) RN - 0 (Growth Substances) RN - 0 (High Mobility Group Proteins) RN - 0 (Neoplasm Proteins) RN - 0 (P8 protein, human) RN - 0 (Transcription Factors) RN - 124544-67-8 (HMGA1a Protein) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) SB - IM MH - Amino Acid Sequence MH - Basic Helix-Loop-Helix Transcription Factors MH - Circular Dichroism MH - Conserved Sequence MH - Cyclic AMP-Dependent Protein Kinases/metabolism MH - DNA-Binding Proteins/genetics/*metabolism MH - Growth Substances/genetics/*metabolism MH - HMGA1a Protein MH - *High Mobility Group Proteins MH - Humans MH - Molecular Sequence Data MH - *Neoplasm Proteins MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphorylation MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Spectroscopy, Fourier Transform Infrared MH - *Transcription Factors EDAT- 2000/11/01 MHDA- 2001/06/22 10:01 CRDT- 2000/11/01 00:00 PHST- 2000/10/30 [aheadofprint] AID - 10.1074/jbc.M008594200 [doi] AID - M008594200 [pii] PST - ppublish SO - J Biol Chem. 2001 Jan 26;276(4):2742-51. Epub 2000 Oct 30. PMID- 15642262 OWN - NLM STAT- MEDLINE DA - 20050111 DCOM- 20050519 LR - 20101118 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 13 IP - 1 DP - 2005 Jan TI - A vinculin binding domain from the talin rod unfolds to form a complex with the vinculin head. PG - 65-74 AB - The cytoskeletal protein talin plays a key role in activating integrins and in coupling them to the actin cytoskeleton. Its N-terminal globular head, which binds beta integrins, is linked to an extended rod having a C-terminal actin binding site and several vinculin binding sites (VBSs). The NMR structure of residues 755-889 of the rod (containing a VBS) is shown to be an amphipathic four-helix bundle with a left-handed topology. A talin peptide corresponding to the VBS binds the vinculin head; the X-ray crystallographic structure of this complex shows that the residues which interact with vinculin are buried in the hydrophobic core of the talin fragment. NMR shows that the interaction involves a major structural change in the talin fragment, including unfolding of one of its helices, making the VBS accessible to vinculin. Interestingly, the talin 755-889 fragment binds more than one vinculin head molecule, suggesting that the talin rod may contain additional as yet unrecognized VBSs. FAU - Fillingham, Ian AU - Fillingham I AD - Department of Biochemistry, University of Leicester, Leicester LE1 7RH, UK. FAU - Gingras, Alexandre R AU - Gingras AR FAU - Papagrigoriou, Evangelos AU - Papagrigoriou E FAU - Patel, Bipin AU - Patel B FAU - Emsley, Jonas AU - Emsley J FAU - Critchley, David R AU - Critchley DR FAU - Roberts, Gordon C K AU - Roberts GC FAU - Barsukov, Igor L AU - Barsukov IL LA - eng SI - PDB/1U6H SI - PDB/1U89 SI - PDB/1XWX PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Actins) RN - 0 (Cytoskeletal Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Solutions) RN - 0 (Talin) RN - 125361-02-6 (Vinculin) SB - IM MH - Actins/chemistry MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - Cytoskeletal Proteins/chemistry MH - Electrophoresis, Polyacrylamide Gel MH - Hydrophobic and Hydrophilic Interactions MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Homology, Amino Acid MH - Solutions MH - Spectrum Analysis, Raman MH - Talin/*chemistry/genetics/*metabolism MH - Vinculin/*chemistry/*metabolism EDAT- 2005/01/12 09:00 MHDA- 2005/05/20 09:00 CRDT- 2005/01/12 09:00 PHST- 2004/09/30 [received] PHST- 2004/11/02 [revised] PHST- 2004/11/05 [accepted] AID - S0969-2126(04)00382-X [pii] AID - 10.1016/j.str.2004.11.006 [doi] PST - ppublish SO - Structure. 2005 Jan;13(1):65-74. PMID- 23307074 OWN - NLM STAT- MEDLINE DA - 20131015 DCOM- 20131202 IS - 1420-9071 (Electronic) IS - 1420-682X (Linking) VI - 70 IP - 21 DP - 2013 Nov TI - Transcriptional/epigenetic regulator CBP/p300 in tumorigenesis: structural and functional versatility in target recognition. PG - 3989-4008 LID - 10.1007/s00018-012-1254-4 [doi] AB - In eukaryotic cells, gene transcription is regulated by sequence-specific DNA-binding transcription factors that recognize promoter and enhancer elements near the transcriptional start site. Some coactivators promote transcription by connecting transcription factors to the basal transcriptional machinery. The highly conserved coactivators CREB-binding protein (CBP) and its paralog, E1A-binding protein (p300), each have four separate transactivation domains (TADs) that interact with the TADs of a number of DNA-binding transcription activators as well as general transcription factors (GTFs), thus mediating recruitment of basal transcription machinery to the promoter. Most promoters comprise multiple activator-binding sites, and many activators contain tandem TADs, thus multivalent interactions may stabilize CBP/p300 at the promoter, and intrinsically disordered regions in CBP/p300 and many activators may confer adaptability to these multivalent complexes. CBP/p300 contains a catalytic histone acetyltransferase (HAT) domain, which remodels chromatin to 'relax' its superstructure and enables transcription of proximal genes. The HAT activity of CBP/p300 also acetylates some transcription factors (e.g., p53), hence modulating the function of key transcriptional regulators. Through these numerous interactions, CBP/p300 has been implicated in complex physiological and pathological processes, and, in response to different signals, can drive cells towards proliferation or apoptosis. Dysregulation of the transcriptional and epigenetic functions of CBP/p300 is associated with leukemia and other types of cancer, thus it has been recognized as a potential anti-cancer drug target. In this review, we focus on recent exciting findings in the structural mechanisms of CBP/p300 involving multivalent and dynamic interactions with binding partners, which may pave new avenues for anti-cancer drug development. FAU - Wang, Feng AU - Wang F AD - Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada. FAU - Marshall, Christopher B AU - Marshall CB FAU - Ikura, Mitsuhiko AU - Ikura M LA - eng GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20130111 PL - Switzerland TA - Cell Mol Life Sci JT - Cellular and molecular life sciences : CMLS JID - 9705402 RN - 0 (Chromatin) RN - 0 (Histones) RN - EC 2.3.1.48 (E1A-Associated p300 Protein) RN - EC 2.3.1.48 (EP300 protein, human) RN - EC 2.3.1.48 (Histone Acetyltransferases) SB - IM MH - Animals MH - Apoptosis MH - *Carcinogenesis MH - Cell Proliferation MH - Chromatin/chemistry MH - E1A-Associated p300 Protein/*genetics/*physiology MH - *Epigenesis, Genetic MH - *Gene Expression Regulation, Neoplastic MH - Histone Acetyltransferases/metabolism MH - Histones/chemistry MH - Humans MH - Protein Binding MH - Protein Structure, Tertiary MH - Proteomics/methods MH - Transcription, Genetic MH - Transcriptional Activation EDAT- 2013/01/12 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/01/12 06:00 PHST- 2012/09/25 [received] PHST- 2012/12/20 [accepted] PHST- 2012/11/08 [revised] PHST- 2013/01/11 [aheadofprint] AID - 10.1007/s00018-012-1254-4 [doi] PST - ppublish SO - Cell Mol Life Sci. 2013 Nov;70(21):3989-4008. doi: 10.1007/s00018-012-1254-4. Epub 2013 Jan 11. PMID- 20026206 OWN - NLM STAT- MEDLINE DA - 20100209 DCOM- 20100414 LR - 20140827 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1802 IP - 3 DP - 2010 Mar TI - Methionine oxidation stabilizes non-toxic oligomers of alpha-synuclein through strengthening the auto-inhibitory intra-molecular long-range interactions. PG - 322-30 LID - 10.1016/j.bbadis.2009.12.004 [doi] AB - Oxidative stress and aggregation of the presynaptic protein alpha-synuclein (alpha-Syn) are implied in the pathogenesis of Parkinson's disease and several other neurodegenerative diseases. Various posttranslational modifications, such as oxidation, nitration and truncation, have significant effects on the kinetics of alpha-Syn fibrillation in vitro. alpha-Syn is a typical natively unfolded protein, which possesses some residual structure. The existence of long-range intra-molecular interactions between the C-terminal tail (residues 120-140) and the central part of alpha-Syn (residues 30-100) was recently established (Bertoncini et al. (2005) Proc Natl Acad Sci U S A 102, 1430-1435). Since alpha-Syn has four methionines, two of which (Met 1 and 5) are at the N-terminus and the other two (Met 116 and 127) are in the hydrophobic cluster at the C-terminus of protein, the perturbation of these residues via their oxidation represents a good model for studying the effect of long-range interaction on alpha-Syn fibril formation. In this paper we show that Met 1, 116, and 127 are more protected from the oxidation than Met 5 likely due to the residual structure in the natively unfolded alpha-Syn. In addition to the hydrophobic interactions between the C-terminal hydrophobic cluster and hydrophobic central region of alpha-Syn, there are some long-range electrostatic interactions in this protein. Both of these interactions likely serve as auto-inhibitors of alpha-Syn fibrillation. Methionine oxidation affects both electrostatic and hydrophobic long-range interactions in alpha-Syn. Finally, oxidation of methionines by H2O2 greatly inhibited alpha-Syn fibrillation in vitro, leading to the formation of relatively stable oligomers, which are not toxic to dopaminergic and GABAergic neurons. CI - 2009 Elsevier B.V. All rights reserved. FAU - Zhou, Wenbo AU - Zhou W AD - Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA 95064, USA. FAU - Long, Chunmei AU - Long C FAU - Reaney, Stephen H AU - Reaney SH FAU - Di Monte, Donato A AU - Di Monte DA FAU - Fink, Anthony L AU - Fink AL FAU - Uversky, Vladimir N AU - Uversky VN LA - eng GR - GM071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 LM007688-01A1/LM/NLM NIH HHS/United States GR - R01 LM007688-01A1S1/LM/NLM NIH HHS/United States GR - R01 NS039985-03/NS/NINDS NIH HHS/United States GR - R01 NS39985/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20091221 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Oxidants) RN - 0 (alpha-Synuclein) RN - AE28F7PNPL (Methionine) RN - BBX060AN9V (Hydrogen Peroxide) SB - IM MH - Amino Acid Substitution MH - Chromatography, High Pressure Liquid MH - Circular Dichroism MH - Humans MH - Hydrogen Peroxide/pharmacology MH - Methionine/*chemistry/metabolism MH - Mutagenesis, Site-Directed MH - Mutation/genetics MH - Oxidants/pharmacology MH - Oxidation-Reduction MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - alpha-Synuclein/*chemistry/genetics/*metabolism PMC - PMC2814895 MID - NIHMS166434 OID - NLM: NIHMS166434 OID - NLM: PMC2814895 EDAT- 2009/12/23 06:00 MHDA- 2010/04/15 06:00 CRDT- 2009/12/23 06:00 PHST- 2009/08/25 [received] PHST- 2009/11/16 [revised] PHST- 2009/12/08 [accepted] PHST- 2009/12/21 [aheadofprint] AID - S0925-4439(09)00297-X [pii] AID - 10.1016/j.bbadis.2009.12.004 [doi] PST - ppublish SO - Biochim Biophys Acta. 2010 Mar;1802(3):322-30. doi: 10.1016/j.bbadis.2009.12.004. Epub 2009 Dec 21. PMID- 24140056 OWN - NLM STAT- MEDLINE DA - 20131118 DCOM- 20140117 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 441 IP - 2 DP - 2013 Nov 15 TI - Evolutionary aspects of the synuclein super-family and sub-families based on large-scale phylogenetic and group-discrimination analysis. PG - 308-17 LID - 10.1016/j.bbrc.2013.09.132 [doi] LID - S0006-291X(13)01637-9 [pii] AB - Over the last decade, many genetic studies have suggested that the synucleins, which are small, natively unfolded proteins, are closely related to Parkinson's disease and cancer. Less is known about the molecular basis of this role. A comprehensive analysis of the evolutionary path of the synuclein protein family may reveal the relationship between evolutionarily conserved residues and protein function or structure. The phylogeny of 252 unique synuclein sequences from 73 organisms suggests that gamma-synuclein is the common ancestor of alpha- and beta-synuclein. Although all three sub-families remain highly conserved, especially at the N-terminal, nearly 15% of the residues in each sub family clearly diverged during evolution, providing crucial guidance for investigations of the different properties of the members of the superfamily. His50 is found to be an alpha-specific conserved residue (91%) and, based on mutagenesis, evolutionarily developed a secondary copper binding site in the alpha synuclein family. Surprisingly, this site is located between two well-known polymorphisms of alpha-synuclein, E46K and A53T, which are linked to early-onset Parkinson's disease, suggesting that the mutation-induced impairment of copper binding could be a mechanism responsible for alpha-synuclein aggregation. CI - Copyright (c) 2013 Elsevier Inc. All rights reserved. FAU - Yuan, Jiawen AU - Yuan J AD - Department of Neurology, Shanghai Sixth People's Hospital affiliated to Shanghai Jiao Tong University, Shanghai 200233, China. FAU - Zhao, Yuwu AU - Zhao Y LA - eng PT - Journal Article DEP - 20131015 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (alpha-Synuclein) RN - 0 (beta-Synuclein) RN - 0 (gamma-Synuclein) RN - 789U1901C5 (Copper) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Conserved Sequence MH - Copper/chemistry MH - *Evolution, Molecular MH - Humans MH - Molecular Sequence Data MH - *Phylogeny MH - Sequence Alignment MH - alpha-Synuclein/chemistry/*classification/genetics MH - beta-Synuclein/chemistry/*classification/genetics MH - gamma-Synuclein/chemistry/*classification/genetics OTO - NOTNLM OT - His50 OT - Parkinson's disease OT - Phylogenetic tree OT - Synuclein EDAT- 2013/10/22 06:00 MHDA- 2014/01/18 06:00 CRDT- 2013/10/22 06:00 PHST- 2013/09/23 [received] PHST- 2013/09/29 [accepted] PHST- 2013/10/15 [aheadofprint] AID - S0006-291X(13)01637-9 [pii] AID - 10.1016/j.bbrc.2013.09.132 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2013 Nov 15;441(2):308-17. doi: 10.1016/j.bbrc.2013.09.132. Epub 2013 Oct 15. PMID- 22807444 OWN - NLM STAT- MEDLINE DA - 20120903 DCOM- 20121119 LR - 20141015 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 36 DP - 2012 Aug 31 TI - Competitive binding between dynamic p53 transactivation subdomains to human MDM2 protein: implications for regulating the p53.MDM2/MDMX interaction. PG - 30376-84 LID - 10.1074/jbc.M112.369793 [doi] AB - The interaction between the transactivation domain of p53 (p53TAD) and the N-terminal domain of MDM2 and MDMX plays an essential role for cell function. Mutations in these proteins have been implicated in many forms of cancer. The intrinsically disordered p53TAD contains two subdomains, TAD1 and TAD2. Using NMR spectroscopy, site-directed mutagenesis, and molecular dynamics simulations, we demonstrate that TAD2 directly interacts with MDM2, adopting transient structures that bind to the same hydrophobic pocket of MDM2 as TAD1. Our data show that binding of TAD1 and TAD2 to MDM2 is competitive, which is further supported by the observation that the interaction of TAD2 with MDM2 can be blocked by the small molecule inhibitor nutlin-3. Our data further indicate that TAD2 interacts with MDMX in a fashion very similar to MDM2. Because TAD2 is known to have transcriptional activity, the interaction of TAD2 with MDM2/MDMX may play a direct role in the inhibition of p53 transactivation. FAU - Shan, Bing AU - Shan B AD - Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, FL 32306, USA. FAU - Li, Da-Wei AU - Li DW FAU - Bruschweiler-Li, Lei AU - Bruschweiler-Li L FAU - Bruschweiler, Rafael AU - Bruschweiler R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120717 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Imidazoles) RN - 0 (Piperazines) RN - 0 (TP53 protein, human) RN - 0 (Tumor Suppressor Protein p53) RN - 0 (nutlin 3) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Imidazoles/chemistry MH - Mutagenesis, Site-Directed MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Piperazines/chemistry MH - Protein Binding MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-mdm2/antagonists & inhibitors/*chemistry/genetics/metabolism MH - Transcriptional Activation/physiology MH - Tumor Suppressor Protein p53/*chemistry/genetics/metabolism PMC - PMC3436289 OID - NLM: PMC3436289 EDAT- 2012/07/19 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/07/19 06:00 PHST- 2012/07/17 [aheadofprint] AID - M112.369793 [pii] AID - 10.1074/jbc.M112.369793 [doi] PST - ppublish SO - J Biol Chem. 2012 Aug 31;287(36):30376-84. doi: 10.1074/jbc.M112.369793. Epub 2012 Jul 17. PMID- 22536782 OWN - NLM STAT- MEDLINE DA - 20120530 DCOM- 20120730 LR - 20141016 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 279 IP - 12 DP - 2012 Jun TI - Bivalent binding drives the formation of the Grb2-Gab1 signaling complex in a noncooperative manner. PG - 2156-73 LID - 10.1111/j.1742-4658.2012.08600.x [doi] AB - Although the growth factor receptor binder 2 (Grb2)-Grb2-associated binder (Gab)1 macromolecular complex mediates a multitude of cellular signaling cascades, the molecular basis of its assembly has hitherto remained largely elusive. Herein, using an array of biophysical techniques, we show that, whereas Grb2 exists in a monomer-dimer equilibrium, the proline-rich (PR) domain of Gab1 is a monomer in solution. Of particular interest is the observation that although the PR domain appears to be structurally disordered, it nonetheless adopts a more or less compact conformation reminiscent of natively folded globular proteins. Importantly, the structurally flexible conformation of the PR domain appears to facilitate the binding of Gab1 to Grb2 with a 1:2 stoichiometry. More specifically, the formation of the Grb2-Gab1 signaling complex is driven via a bivalent interaction through the binding of the C-terminal homology 3 (cSH3) domain within each monomer of Grb2 homodimer to two distinct RXXK motifs, herein designated G1 and G2, located within the PR domain of Gab1. Strikingly, in spite of the key role of bivalency in driving this macromolecular assembly, the cSH3 domains bind to the G1 and G2 motifs in an independent manner with zero cooperativity. Taken together, our findings shed new light on the physicochemical forces driving the assembly of a key macromolecular signaling complex that is relevant to cellular health and disease. CI - (c) 2012 The Authors Journal compilation (c) 2012 FEBS. FAU - McDonald, Caleb B AU - McDonald CB AD - Department of Biochemistry & Molecular Biology and the USylvester Braman Family Breast Cancer Institute, Leonard Miller School of Medicine, University of Miami, FL 33136, USA. FAU - Bhat, Vikas AU - Bhat V FAU - Mikles, David C AU - Mikles DC FAU - Deegan, Brian J AU - Deegan BJ FAU - Seldeen, Kenneth L AU - Seldeen KL FAU - Farooq, Amjad AU - Farooq A LA - eng GR - R01 GM083897/GM/NIGMS NIH HHS/United States GR - R01 GM083897-04/GM/NIGMS NIH HHS/United States GR - R01-GM083897/GM/NIGMS NIH HHS/United States GR - T32-CA119929/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120509 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (GAB1 protein, human) RN - 0 (GRB2 Adaptor Protein) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry/genetics/*metabolism MH - GRB2 Adaptor Protein/*chemistry/genetics/*metabolism MH - Humans MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Protein Binding MH - Protein Structure, Secondary PMC - PMC3365654 MID - NIHMS369920 OID - NLM: NIHMS369920 OID - NLM: PMC3365654 EDAT- 2012/04/28 06:00 MHDA- 2012/07/31 06:00 CRDT- 2012/04/28 06:00 PHST- 2012/05/09 [aheadofprint] AID - 10.1111/j.1742-4658.2012.08600.x [doi] PST - ppublish SO - FEBS J. 2012 Jun;279(12):2156-73. doi: 10.1111/j.1742-4658.2012.08600.x. Epub 2012 May 9. PMID- 17391701 OWN - NLM STAT- MEDLINE DA - 20070420 DCOM- 20070723 LR - 20140907 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 368 IP - 4 DP - 2007 May 11 TI - Isolation of a human single chain antibody fragment against oligomeric alpha-synuclein that inhibits aggregation and prevents alpha-synuclein-induced toxicity. PG - 1132-44 AB - Protein misfolding and aggregation are pathological aspects of numerous neurodegenerative diseases. Aggregates of alpha-synuclein are major components of the Lewy bodies and Lewy neurites associated with Parkinson's Disease (PD). A natively unfolded protein, alpha-synuclein can adopt different aggregated morphologies, including oligomers, protofibrils and fibrils. The small oligomeric aggregates have been shown to be particularly toxic. Antibodies that neutralize the neurotoxic aggregates without interfering with beneficial functions of monomeric alpha-synuclein can be useful therapeutics. We were able to isolate single chain antibody fragments (scFvs) from a phage displayed antibody library against the target antigen morphology using a novel biopanning technique that utilizes atomic force microscopy (AFM) to image and immobilize specific morphologies of alpha-synuclein. The scFv described here binds only to an oligomeric form of alpha-synuclein and inhibits both aggregation and toxicity of alpha-synuclein in vitro. This scFv can have potential therapeutic value in controlling misfolding and aggregation of alpha-synuclein in vivo when expressed intracellularly in dopaminergic neurons as an intrabody. FAU - Emadi, Sharareh AU - Emadi S AD - Department of Chemical and Materials Engineering, Arizona State University, Tempe, AZ 85287-6006, USA. FAU - Barkhordarian, Hedieh AU - Barkhordarian H FAU - Wang, Min S AU - Wang MS FAU - Schulz, Philip AU - Schulz P FAU - Sierks, Michael R AU - Sierks MR LA - eng GR - AG17984/AG/NIA NIH HHS/United States GR - R01 AG017984-01/AG/NIA NIH HHS/United States GR - R01 AG017984-02/AG/NIA NIH HHS/United States GR - R01 AG017984-03/AG/NIA NIH HHS/United States GR - R01 AG017984-04/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20070307 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Immunoglobulin Variable Region) RN - 0 (Peptide Library) RN - 0 (alpha-Synuclein) SB - IM MH - Cell Line, Tumor MH - Humans MH - Immunoglobulin Variable Region/*isolation & purification/pharmacology MH - Microscopy, Atomic Force MH - Peptide Library MH - Protein Binding/drug effects MH - *Protein Folding MH - alpha-Synuclein/immunology/*metabolism/ultrastructure PMC - PMC2235820 MID - NIHMS22525 OID - NLM: NIHMS22525 OID - NLM: PMC2235820 EDAT- 2007/03/30 09:00 MHDA- 2007/07/24 09:00 CRDT- 2007/03/30 09:00 PHST- 2006/11/27 [received] PHST- 2007/02/19 [revised] PHST- 2007/02/26 [accepted] PHST- 2007/03/07 [aheadofprint] AID - S0022-2836(07)00307-5 [pii] AID - 10.1016/j.jmb.2007.02.089 [doi] PST - ppublish SO - J Mol Biol. 2007 May 11;368(4):1132-44. Epub 2007 Mar 7. PMID- 17234772 OWN - NLM STAT- MEDLINE DA - 20070119 DCOM- 20070220 LR - 20131121 IS - 0008-5472 (Print) IS - 0008-5472 (Linking) VI - 67 IP - 2 DP - 2007 Jan 15 TI - Synuclein-gamma targeting peptide inhibitor that enhances sensitivity of breast cancer cells to antimicrotubule drugs. PG - 626-33 AB - Synuclein-gamma (SNCG) plays oncogenic roles in breast carcinogenesis. Although the expression of SNCG is abnormally high in advanced and metastatic breast carcinomas, SNCG is not expressed in normal or benign breast tissues. SNCG is an intrinsically disordered protein known to interact with BubR1, a mitotic checkpoint kinase. The SNCG-BubR1 interaction inhibits mitotic checkpoint control upon spindle damage caused by anticancer drugs, such as nocodazole and taxol. Antimicrotubule drugs that cause mitotic arrest and subsequent apoptosis of cancer cells are frequently used to treat breast cancer patients with advanced or metastatic diseases. However, patient response rates to this class of chemotherapeutic agents vary significantly. In this study, we have designed a novel peptide (ANK) and shown its interaction with SNCG using fluorometry, surface plasmon resonance, and isothermal titration calorimetry. Binding of the ANK peptide did not induce folding of SNCG, suggesting that SNCG can function biologically in its intrinsically disordered state. Microinjection of the ANK peptide in breast cancer cell line overexpressing SNCG (MCF7-SNCG) exhibited a similar cell killing response by nocodazole as in the SNCG-negative MCF7 cells. Overexpression of enhanced green fluorescent protein-tagged ANK reduces SNCG-mediated resistance to paclitaxel treatment by approximately 3.5-fold. Our coimmunoprecipitation and colocalization results confirmed the intracellular association of the ANK peptide with SNCG. This is likely due to the disruption of the interaction of SNCG with BubR1 interaction. Our findings shed light on the molecular mechanism of the ANK peptide in releasing SNCG-mediated drug resistance. FAU - Singh, Vinay K AU - Singh VK AD - Department of Biochemistry, Queen's University, Kingston, Ontario, and Molecular Structure and Function, Hospital for Sick Children, Toronto, Canada. FAU - Zhou, Yue AU - Zhou Y FAU - Marsh, Joseph A AU - Marsh JA FAU - Uversky, Vladimir N AU - Uversky VN FAU - Forman-Kay, Julie D AU - Forman-Kay JD FAU - Liu, Jingwen AU - Liu J FAU - Jia, Zongchao AU - Jia Z LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Cancer Res JT - Cancer research JID - 2984705R RN - 0 (Ankyrins) RN - 0 (Antineoplastic Agents) RN - 0 (Neoplasm Proteins) RN - 0 (Peptide Fragments) RN - 0 (SNCG protein, human) RN - 0 (gamma-Synuclein) RN - EC 2.7.- (Protein Kinases) RN - EC 2.7.11.1 (BUB1 protein, human) RN - EC 2.7.11.1 (Bub1 spindle checkpoint protein) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - SH1WY3R615 (Nocodazole) SB - IM MH - Amino Acid Sequence MH - Animals MH - Ankyrins/*chemistry/genetics/metabolism MH - Antineoplastic Agents/*pharmacology MH - Breast Neoplasms/*drug therapy/metabolism/pathology MH - COS Cells MH - Cell Line, Tumor MH - Cercopithecus aethiops MH - Conserved Sequence MH - Drug Resistance, Neoplasm MH - Humans MH - Kinetics MH - Microtubules/drug effects MH - Mitosis/drug effects MH - Molecular Sequence Data MH - Neoplasm Proteins/*antagonists & inhibitors/metabolism MH - Nocodazole/*pharmacology MH - Peptide Fragments/chemistry/genetics/metabolism/*pharmacology MH - Protein Folding MH - Protein Kinases/metabolism MH - Protein-Serine-Threonine Kinases MH - gamma-Synuclein/*antagonists & inhibitors/metabolism EDAT- 2007/01/20 09:00 MHDA- 2007/02/21 09:00 CRDT- 2007/01/20 09:00 AID - 67/2/626 [pii] AID - 10.1158/0008-5472.CAN-06-1820 [doi] PST - ppublish SO - Cancer Res. 2007 Jan 15;67(2):626-33. PMID- 11956202 OWN - NLM STAT- MEDLINE DA - 20020617 DCOM- 20020719 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 277 IP - 25 DP - 2002 Jun 21 TI - Interchangeable enzyme modules. Functional replacement of the essential linker of the biotinylated subunit of acetyl-CoA carboxylase with a linker from the lipoylated subunit of pyruvate dehydrogenase. PG - 22520-7 AB - Biotin carboxyl carrier protein (BCCP) is the small biotinylated subunit of Escherichia coli acetyl-CoA carboxylase, the enzyme that catalyzes the first committed step of fatty acid synthesis. E. coli BCCP is a member of a large family of protein domains modified by covalent attachment of biotin. In most biotinylated proteins, the biotin moiety is attached to a lysine residue located about 35 residues from the carboxyl terminus of the protein, which lies in the center of a strongly conserved sequence that forms a tightly folded anti-parallel beta-barrel structure. Located upstream of the conserved biotinoyl domain sequence are proline/alanine-rich sequences of varying lengths, which have been proposed to act as flexible linkers. In E. coli BCCP, this putative linker extends for about 42 residues with over half of the residues being proline or alanine. I report that deletion of the 30 linker residues located adjacent to the biotinoyl domain resulted in a BCCP species that was defective in function in vivo, although it was efficiently biotinylated. Expression of this BCCP species failed to restore normal growth and fatty acid synthesis to a temperature-sensitive E. coli strain that lacks BCCP when grown at nonpermissive temperatures. In contrast, replacement of the deleted BCCP linker with a linker derived from E. coli pyruvate dehydrogenase gave a chimeric BCCP species that had normal in vivo function. Expression of BCCPs having deletions of various segments of the linker region of the chimeric protein showed that some deletions of up to 24 residues had significant or full biological activity, whereas others had very weak or no activity. The inactive deletion proteins all lacked an APAAAAA sequence located adjacent to the tightly folded biotinyl domain, whereas deletions that removed only upstream linker sequences remained active. Deletions within the linker of the wild type BCCP protein also showed that the residues adjacent to the tightly folded domain play an essential role in protein function, although in this case some proteins with deletions within this region retained activity. Retention of activity was due to fusion of the domain to upstream sequences. These data provide new evidence for the functional and structural similarities of biotinylated and lipoylated proteins and strongly support a common evolutionary origin of these enzyme subunits. FAU - Cronan, John E Jr AU - Cronan JE Jr AD - Department of Microbiology, University of Illinois, Urbana, Illinois 61801, USA. j-cronan@life.uiuc.edu LA - eng GR - AI15650/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20020415 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Carrier Proteins) RN - 6SO6U10H04 (Biotin) RN - EC 1.2.4.1 (Pyruvate Dehydrogenase (Lipoamide)) RN - EC 6.- (Fatty Acid Synthase, Type II) RN - EC 6.4.1.2 (Acetyl-CoA Carboxylase) RN - EC 6.4.1.2 (biotin carboxyl carrier protein) SB - IM MH - Acetyl-CoA Carboxylase/*chemistry/genetics MH - Amino Acid Sequence MH - Biotin/chemistry MH - Biotinylation MH - Carrier Proteins/*chemistry/genetics MH - Escherichia coli/enzymology MH - Fatty Acid Synthase, Type II MH - Gene Deletion MH - Models, Chemical MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Plasmids/metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Pyruvate Dehydrogenase (Lipoamide)/*chemistry/genetics MH - Sequence Homology, Amino Acid MH - Temperature EDAT- 2002/04/17 10:00 MHDA- 2002/07/20 10:01 CRDT- 2002/04/17 10:00 PHST- 2002/04/15 [aheadofprint] AID - 10.1074/jbc.M201249200 [doi] AID - M201249200 [pii] PST - ppublish SO - J Biol Chem. 2002 Jun 21;277(25):22520-7. Epub 2002 Apr 15. PMID- 8943276 OWN - NLM STAT- MEDLINE DA - 19970117 DCOM- 19970117 LR - 20041117 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 271 IP - 50 DP - 1996 Dec 13 TI - Crystal structure of an antagonist mutant of human growth hormone, G120R, in complex with its receptor at 2.9 A resolution. PG - 32197-203 AB - Human growth hormone binds two receptor molecules and thereby induces signal transduction through receptor dimerization. At high concentrations, growth hormone acts as an antagonist because of a large difference in affinities at the respective binding sites. This antagonist action can be enhanced further by reducing binding in the low affinity binding site. A growth hormone antagonist mutant Gly-120 --> Arg, has been crystallized with its receptor as a 1:1 complex and the crystal structure determined at 2.9 A resolution. The 1:1 complex is remarkably similar to the native growth hormone-receptor 1:2 complex. A comparison between the two structures reveals only minimal differences in the conformations of the hormone or its receptor in the two complexes, including the angle between the two immunoglobulin-like domains of the receptor. Further, two symmetry-related 1:1 complexes in the crystal form a 2:2 complex with a large solvent inaccessible area between two receptor molecules. In addition, we present here a native human growth hormone-human growth hormone-binding protein 1:2 complex structure at 2.5 A resolution. One important difference between our structure and the previously published crystal structure at 2.8 A is revealed. Trp-104 in the receptor, a key residue in the hormone-receptor interaction, has an altered conformation in the low affinity site enabling a favorable hydrogen bond to be formed with Asp-116 of the hormone. FAU - Sundstrom, M AU - Sundstrom M AD - Department of Structural Biochemistry, Pharmacia and Upjohn, Preclinical Research and Development, S-112 87 Stockholm, Sweden. michael.sundstrom@sto.pharmacia.se FAU - Lundqvist, T AU - Lundqvist T FAU - Rodin, J AU - Rodin J FAU - Giebel, L B AU - Giebel LB FAU - Milligan, D AU - Milligan D FAU - Norstedt, G AU - Norstedt G LA - eng SI - PDB/1HWG SI - PDB/1HWH PT - Journal Article PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (G120R protein, human) RN - 0 (Hormone Antagonists) RN - 0 (Receptors, Somatotropin) RN - 0 (Recombinant Proteins) RN - 12629-01-5 (Human Growth Hormone) RN - 9002-72-6 (Growth Hormone) SB - IM MH - Crystallography, X-Ray MH - Growth Hormone/*analogs & derivatives/chemistry/metabolism MH - Hormone Antagonists/*chemistry/metabolism MH - Human Growth Hormone/chemistry/metabolism MH - Humans MH - Hydrogen Bonding MH - Models, Molecular MH - Molecular Sequence Data MH - Receptors, Somatotropin/*metabolism MH - *Recombinant Proteins EDAT- 1996/12/13 MHDA- 1996/12/13 00:01 CRDT- 1996/12/13 00:00 PST - ppublish SO - J Biol Chem. 1996 Dec 13;271(50):32197-203. PMID- 24021976 OWN - NLM STAT- MEDLINE DA - 20131015 DCOM- 20131223 IS - 1879-0038 (Electronic) IS - 0378-1119 (Linking) VI - 531 IP - 2 DP - 2013 Dec 1 TI - Patterns of evolutionary selection pressure in the immune signaling protein TRAF3IP2 in mammals. PG - 403-10 LID - 10.1016/j.gene.2013.08.074 [doi] LID - S0378-1119(13)01134-7 [pii] AB - TRAF3 interacting protein 2 (TRAF3IP2) is important for immune responses to pathogens, inflammatory signals and autoimmunity in mammals. In the present study, we collected 19 mammalian TRAF3IP2 sequences and investigated the various types of selection pressure acting on them. Maximum likelihood estimations of nonsynonymous (dN) to synonymous (dS) substitution (dN/dS) ratios for the aligned coding sequences indicated that, as a whole, TRAF3IP2 has been subject to purifying selection. However, the N-terminus of the protein has been subject to higher selection pressure than the C-terminal domain. While eight amino acid residues within the N-terminus appear to have evolved under positive selection, no evidence for such selection was found in the C-terminus. The positively selected residues, which fall outside the currently known functional sites within TRAF3IP2, may have novel functions. The different selection pressures acting on the N- and C-terminal regions are consistent with their protein structures: the C-terminal structure is an ordered structure, whereas the N-terminus is disordered. Taken together with the results of previous studies, it is plausible that positive selection on the N-terminus of TRAF3IP2 may have occurred by competitive coevolution between mammalian hosts and viruses. CI - (c) 2013 Elsevier B.V. All rights reserved. FAU - Wu, Baojun AU - Wu B AD - Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA. FAU - Gong, Jing AU - Gong J FAU - Yuan, Shoudao AU - Yuan S FAU - Zhang, Ying AU - Zhang Y FAU - Wei, Tiandi AU - Wei T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130907 PL - Netherlands TA - Gene JT - Gene JID - 7706761 RN - 0 (TRAF3IP2 protein, human) RN - 0 (Tumor Necrosis Factor Receptor-Associated Peptides and Proteins) SB - IM MH - Animals MH - Cattle MH - Evolution, Molecular MH - Guinea Pigs MH - Host-Pathogen Interactions/genetics/immunology MH - Humans MH - Immunity/*genetics MH - Mammals/*genetics/immunology MH - Mice MH - Models, Molecular MH - Rabbits MH - Rats MH - *Selection, Genetic MH - Signal Transduction/genetics/immunology MH - Tumor Necrosis Factor Receptor-Associated Peptides and Proteins/chemistry/*genetics OTO - NOTNLM OT - Adaptive evolution OT - B-cell-activating factor receptor OT - BAFFR OT - CC OT - CIKS OT - Competitive coevolution OT - FEL OT - FUBAR OT - HLH OT - IDR OT - IKKi OT - IL17R OT - Immune defense OT - IkappaB kinase I OT - MEME OT - Mammalian TRAF3IP2 OT - NF-kappaB OT - NG OT - NJ OT - Nei-Gojobori OT - SAPK/JNK OT - SEF/interleukin 17 receptor OT - SEFIR OT - SLAC OT - TIR OT - TNF receptor associated factor 3 interacting protein 2 OT - TNF receptor associated factor 6 OT - TRAF3IP2 OT - TRAF6 OT - Toll/interleukin 1 receptor OT - coiled-coil OT - dN/dS OT - fast unconstrained Bayesian approximation OT - fixed effects likelihood OT - helix-loop-helix OT - interleukin 17 receptor OT - intrinsically disordered region OT - mixed effects model of evolution OT - neighbor-joining OT - nonsynonymous/synonymous substitution rate ratio OT - nuclear factor-kappa B OT - single likelihood ancestor counting EDAT- 2013/09/12 06:00 MHDA- 2013/12/24 06:00 CRDT- 2013/09/12 06:00 PHST- 2013/04/17 [received] PHST- 2013/08/21 [revised] PHST- 2013/08/22 [accepted] PHST- 2013/09/07 [aheadofprint] AID - S0378-1119(13)01134-7 [pii] AID - 10.1016/j.gene.2013.08.074 [doi] PST - ppublish SO - Gene. 2013 Dec 1;531(2):403-10. doi: 10.1016/j.gene.2013.08.074. Epub 2013 Sep 7. PMID- 20483339 OWN - NLM STAT- MEDLINE DA - 20100520 DCOM- 20100915 LR - 20140827 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 98 IP - 10 DP - 2010 May 19 TI - Amyloid-beta fibrillogenesis seeded by interface-induced peptide misfolding and self-assembly. PG - 2299-308 LID - 10.1016/j.bpj.2010.01.056 [doi] AB - The amphipathicity of the natively unstructured amyloid-beta (Abeta40) peptide may play an important role in its aggregation into beta-sheet rich fibrils, which is linked to the pathogenesis of Alzheimer's disease. Using the air/subphase interface as a model interface, we characterized Abeta's surface activity and its conformation, assembly, and morphology at the interface. Abeta readily adsorbed to the air/subphase interface to form a 20 A thick film and showed a critical micelle concentration of approximately 120 nM. Abeta adsorbed at the air/subphase exhibited in-plane ordering that gave rise to Bragg peaks in grazing-incidence x-ray diffraction measurements. Analysis of the peaks showed that the air/subphase interface induced Abeta to fold into a beta-sheet conformation and to self-assemble into approximately 100 A-sized ordered clusters. The formation of these clusters at the air/subphase interface was not affected by pH, salts, or the presence of sucrose or urea, which are known to stabilize or denature native proteins, suggesting that interface-driven Abeta misfolding and assembly are strongly favored. Furthermore, Abeta at the interface seeded the growth of fibrils in the bulk with a distinct morphology compared to those formed by homogeneous nucleation. Our results indicate that interface-induced Abeta misfolding may serve as a heterogeneous, nucleation-controlled aggregation mechanism for Abeta fibrillogenesis in vivo. CI - Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Chi, Eva Y AU - Chi EY AD - Department of Chemical and Nuclear Engineering, Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico, USA. FAU - Frey, Shelli L AU - Frey SL FAU - Winans, Amy AU - Winans A FAU - Lam, Kin Lok H AU - Lam KL FAU - Kjaer, Kristian AU - Kjaer K FAU - Majewski, Jaroslaw AU - Majewski J FAU - Lee, Ka Yee C AU - Lee KY LA - eng GR - AG025649/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Amyloid) RN - 0 (Amyloid beta-Peptides) RN - 0 (Amyloid beta-Protein Precursor) RN - 0 (Lipid Bilayers) RN - 0 (Peptide Fragments) RN - 0 (Peptides) RN - 0 (Protease Nexins) RN - 0 (Receptors, Cell Surface) SB - IM MH - Amyloid/adverse effects/*chemistry MH - Amyloid beta-Peptides/*adverse effects/chemistry MH - Amyloid beta-Protein Precursor MH - Binding Sites MH - Circular Dichroism/methods MH - Lipid Bilayers/pharmacology MH - Microscopy, Atomic Force/methods MH - Peptide Fragments/*pharmacology MH - Peptides/*adverse effects/pharmacology MH - Protease Nexins MH - Protein Conformation MH - Protein Folding/*drug effects MH - Proteostasis Deficiencies/*etiology MH - Receptors, Cell Surface MH - Surface Properties PMC - PMC2872264 OID - NLM: PMC2872264 EDAT- 2010/05/21 06:00 MHDA- 2010/09/16 06:00 CRDT- 2010/05/21 06:00 PHST- 2009/07/30 [received] PHST- 2010/01/18 [revised] PHST- 2010/01/20 [accepted] AID - S0006-3495(10)00221-3 [pii] AID - 10.1016/j.bpj.2010.01.056 [doi] PST - ppublish SO - Biophys J. 2010 May 19;98(10):2299-308. doi: 10.1016/j.bpj.2010.01.056. PMID- 20949632 OWN - NLM STAT- MEDLINE DA - 20101109 DCOM- 20110215 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 78 IP - 16 DP - 2010 Dec TI - Smoothing molecular interactions: the "kinetic buffer" effect of intrinsically disordered proteins. PG - 3251-9 LID - 10.1002/prot.22820 [doi] AB - Intrinsically disordered proteins (IDPs) widely participate in molecular recognition and signaling processes in cells by interacting with other molecules. Compared with ordered proteins, IDPs usually possess stronger intermolecular interactions in binding. As a result, the interface structure of IDPs in complexes is distinct from that of ordered-protein complexes, and this difference may have essential effect on the response to various perturbations in a cell. In this study, we examined the perturbations of intermolecular interactions and temperature on the coupled folding and binding processes of pKID to KIX domains by performing molecular dynamics simulations. By comparing a series of virtual pKID systems with various degree of disorder, we found that the complex stability and the binding kinetics of the disordered systems were less sensitive to the perturbations than the ordered systems. The origin of the lower response sensitivity of IDPs was attributed to their higher flexibility in the complex interface, which was further supported by an analysis on protein complex structures. On the basis of our simulations and results from the literature, we speculate IDPs may not only interact with their biological partners with high specificity and low affinity but also may be resistant to the perturbations in the environment and transmit signals fast and smooth. We proposed to name it the "kinetic buffer" effect. CI - Copyright (c) 2010 Wiley-Liss, Inc. FAU - Huang, Yongqi AU - Huang Y AD - State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, and Center for Theoretical Biology, Peking University, Beijing 100871, People's Republic of China. FAU - Liu, Zhirong AU - Liu Z LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Buffers) RN - 0 (Proteins) SB - IM MH - Buffers MH - Kinetics MH - Protein Binding MH - Protein Structure, Tertiary MH - Proteins/*chemistry/*metabolism MH - Thermodynamics EDAT- 2010/10/16 06:00 MHDA- 2011/02/16 06:00 CRDT- 2010/10/16 06:00 AID - 10.1002/prot.22820 [doi] PST - ppublish SO - Proteins. 2010 Dec;78(16):3251-9. doi: 10.1002/prot.22820. PMID- 19198564 OWN - NLM STAT- MEDLINE DA - 20090209 DCOM- 20090305 IS - 0070-217X (Print) IS - 0070-217X (Linking) VI - 329 DP - 2009 TI - Nucleocapsid structure and function. PG - 103-28 AB - Measles virus belongs to the Paramyxoviridae family within the Mononegavirales order. Its nonsegmented, single-stranded, negative-sense RNA genome is encapsidated by the nucleoprotein (N) to form a helical nucleocapsid. This ribonucleoproteic complex is the substrate for both transcription and replication. The RNA-dependent RNA polymerase binds to the nucleocapsid template via its co-factor, the phosphoprotein (P). This chapter describes the main structural information available on the nucleoprotein, showing that it consists of a structured core (N(CORE)) and an intrinsically disordered C-terminal domain (N(TAIL)). We propose a model where the dynamic breaking and reforming of the interaction between N(TAIL) and P would allow the polymerase complex (L-P) to cartwheel on the nucleocapsid template. We also propose a model where the flexibility of the disordered N and P domains allows the formation of a tripartite complex (No-P-L) during replication, followed by the delivery of N monomers to the newly synthesized genomic RNA chain. Finally, the functional implications of structural disorder are also discussed in light of the ability of disordered regions to establish interactions with multiple partners, thus leading to multiple biological effects. FAU - Longhi, S AU - Longhi S AD - Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS et Universites Aix-Marseille I et II, 163 avenue de Luminy, Case 932, 13288 Marseille Cedex 09, France. Sonia.Longhi@afmb.univ-mrs.fr LA - eng GR - R01 NS031693-11A2/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review PL - Germany TA - Curr Top Microbiol Immunol JT - Current topics in microbiology and immunology JID - 0110513 RN - 0 (Nucleocapsid Proteins) SB - IM MH - Animals MH - Humans MH - Measles/*virology MH - Measles virus/*chemistry/genetics/physiology MH - Nucleocapsid/*chemistry/genetics/metabolism MH - Nucleocapsid Proteins/*chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Virus Replication RF - 132 EDAT- 2009/02/10 09:00 MHDA- 2009/03/06 09:00 CRDT- 2009/02/10 09:00 PST - ppublish SO - Curr Top Microbiol Immunol. 2009;329:103-28. PMID- 24415668 OWN - NLM STAT- MEDLINE DA - 20140325 DCOM- 20141115 LR - 20141120 IS - 1949-3592 (Electronic) IS - 1949-3592 (Linking) VI - 71 IP - 3 DP - 2014 Mar TI - Mutagenetic and electron microscopy analysis of actin filament severing by Cordon-Bleu, a WH2 domain protein. PG - 170-83 LID - 10.1002/cm.21161 [doi] AB - Cordon-Bleu (Cobl) is a regulator of actin dynamics in neural development and ciliogenesis. Its function is associated with three adjacent actin binding WASP Homology 2 (WH2) domains. We showed that these WH2 repeats confer multifunctional regulation of actin dynamics, which makes Cobl a << dynamizer >> of actin assembly, inducing fast turnover of actin filaments and oscillatory polymerization regime via nucleation, severing, and rapid depolymerization activities. Cobl is the most efficient severer of actin filaments characterized so far. To understand which primary sequence elements determine the filament severing activity of the WH2 repeats, here we combine a mutagenetic/domain swapping approach of the minimal fully active Cobl-KAB construct, which comprises the lysine rich region K preceding the two first WH2 domains A and B. The mutated Cobl constructs display variable loss of the original filament nucleating activities of native Cobl-KAB, without any strict correlation with a loss in actin binding, which emphasizes the functional importance of the electrostatic environment of WH2 domains. Filament severing displayed the greatest stringency and was abolished in all mutated forms of Cobl-KAB. Filament severing and re-annealing by Cobl-KAB, which is key in its rapid remodeling of a population of actin filaments, and most likely responsible for its function in ciliogenesis, was analyzed by electron microscopy in comparison with Spire and ADF. CI - Copyright (c) 2014 Wiley Periodicals, Inc. FAU - Jiao, Yue AU - Jiao Y AD - Cytoskeleton Dynamics and Cell Motility Team, Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, 91198, Gif-sur-Yvette, France. FAU - Walker, Matt AU - Walker M FAU - Trinick, John AU - Trinick J FAU - Pernier, Julien AU - Pernier J FAU - Montaville, Pierre AU - Montaville P FAU - Carlier, Marie-France AU - Carlier MF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140312 PL - United States TA - Cytoskeleton (Hoboken) JT - Cytoskeleton (Hoboken, N.J.) JID - 101523844 RN - 0 (Actin Depolymerizing Factors) RN - 0 (Actins) RN - 0 (Cobl protein, human) RN - 0 (Microfilament Proteins) RN - 0 (Mutant Proteins) RN - 0 (Wiskott-Aldrich Syndrome Protein) SB - IM MH - Actin Cytoskeleton/metabolism/*ultrastructure MH - Actin Depolymerizing Factors/metabolism MH - Actins/metabolism MH - Amino Acid Sequence MH - Animals MH - Chromatography, Gel MH - Humans MH - Hydrodynamics MH - Microfilament Proteins/*chemistry/*metabolism MH - *Microscopy, Electron MH - Molecular Sequence Data MH - Mutagenesis/*genetics MH - Mutant Proteins/metabolism MH - Protein Structure, Tertiary MH - Rabbits MH - Sequence Alignment MH - Wiskott-Aldrich Syndrome Protein/chemistry OTO - NOTNLM OT - Cordon-Bleu OT - WASP homology 2 domain OT - actin OT - electron microscopy OT - intrinsically disordered proteins OT - mutagenesis OT - protein complexes EDAT- 2014/01/15 06:00 MHDA- 2014/11/16 06:00 CRDT- 2014/01/14 06:00 PHST- 2013/10/04 [received] PHST- 2013/11/11 [revised] PHST- 2013/12/30 [accepted] PHST- 2014/03/12 [aheadofprint] AID - 10.1002/cm.21161 [doi] PST - ppublish SO - Cytoskeleton (Hoboken). 2014 Mar;71(3):170-83. doi: 10.1002/cm.21161. Epub 2014 Mar 12. PMID- 19590096 OWN - NLM STAT- MEDLINE DA - 20090921 DCOM- 20091106 LR - 20140828 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 284 IP - 39 DP - 2009 Sep 25 TI - Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p. PG - 26918-27 LID - 10.1074/jbc.M109.028431 [doi] AB - SH3 domains, which are among the most frequently occurring protein interaction modules in nature, bind to peptide targets ranging in length from 7 to more than 25 residues. Although the bulk of studies on the peptide binding properties of SH3 domains have focused on interactions with relatively short peptides (less than 10 residues), a number of domains have been recently shown to require much longer sequences for optimal binding affinity. To gain greater insight into the binding mechanism and biological importance of interactions between an SH3 domain and extended peptide sequences, we have investigated interactions of the yeast Abp1p SH3 domain (AbpSH3) with several physiologically relevant 17-residue target peptide sequences. To obtain a molecular model for AbpSH3 interactions, we solved the structure of the AbpSH3 bound to a target peptide from the yeast actin patch kinase, Ark1p. Peptide target complexes from binding partners Scp1p and Sjl2p were also characterized, revealing that the AbpSH3 uses a common extended interface for interaction with these peptides, despite K(d) values for these peptides ranging from 0.3 to 6 mum. Mutagenesis studies demonstrated that residues across the whole 17-residue binding site are important both for maximal in vitro binding affinity and for in vivo function. Sequence conservation analysis revealed that both the AbpSH3 and its extended target sequences are highly conserved across diverse fungal species as well as higher eukaryotes. Our data imply that the AbpSH3 must bind extended target sites to function efficiently inside the cell. FAU - Stollar, Elliott J AU - Stollar EJ AD - Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. FAU - Garcia, Bianca AU - Garcia B FAU - Chong, P Andrew AU - Chong PA FAU - Rath, Arianna AU - Rath A FAU - Lin, Hong AU - Lin H FAU - Forman-Kay, Julie D AU - Forman-Kay JD FAU - Davidson, Alan R AU - Davidson AR LA - eng SI - PDB/2RPN PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090709 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (ABP1 protein, S cerevisiae) RN - 0 (Microfilament Proteins) RN - 0 (Peptides) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Amino Acid Sequence MH - Binding Sites/genetics MH - Computational Biology MH - Microfilament Proteins/chemistry/genetics/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Peptides/chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism MH - Sequence Homology, Amino Acid MH - *src Homology Domains PMC - PMC2785379 OID - NLM: PMC2785379 EDAT- 2009/07/11 09:00 MHDA- 2009/11/07 06:00 CRDT- 2009/07/11 09:00 PHST- 2009/07/09 [aheadofprint] AID - M109.028431 [pii] AID - 10.1074/jbc.M109.028431 [doi] PST - ppublish SO - J Biol Chem. 2009 Sep 25;284(39):26918-27. doi: 10.1074/jbc.M109.028431. Epub 2009 Jul 9. PMID- 20865513 OWN - NLM STAT- MEDLINE DA - 20100924 DCOM- 20110203 IS - 0065-2598 (Print) IS - 0065-2598 (Linking) VI - 680 DP - 2010 TI - An integrated methodology for mining promiscuous proteins: a case study of an integrative bioinformatics approach for hepatitis C virus non-structural 5A protein. PG - 299-305 LID - 10.1007/978-1-4419-5913-3_34 [doi] AB - A methodology for elucidation of structural, functional, and mechanistic knowledge on promiscuous proteins is proposed that constitutes a workflow of integrated bioinformatics analysis. Sequence alignments with closely related homologues can reveal conserved regions which are functionally important. Scanning protein motif databases, along with secondary and surface accessibility predictions integrated with post-translational modification sites (PTMs) prediction reveal functional and protein-binding motifs. Integrating this information about the protein with the GO, SCOP, and CATH annotations of the templates can help to formulate a 3D model with reasonable accuracy even in the case of distant sequence homology. A novel integrative model of the non-structural protein 5A of Hepatitis C virus: a hub promiscuous protein with roles in virus replication and host interactions is proposed. The 3D structure for domain II was predicted based on, the Homo sapiens Replication factor-A protein-1 (RPA1), as a template using consensus meta-servers results. Domain III is an intrinsically unstructured domain with a fold from the retroviral matrix protein, which conducts diverse protein interactions and is involved in viral replication and protein interactions. It also has a single-stranded DNA-binding protein motif (SSDP) signature for pyrimidine binding during viral replication. Two protein-binding motifs with high sequence conservation and disordered regions are proposed; the first corresponds to an Interleukin-8B receptor signature (IL-8R-B), while the second has a lymphotoxin beta receptor (LTbetaR) high local similarity. A mechanism is proposed to their contribution to NS5A Interferon signaling pathway interception. Lastly, the overlapping between LTbetaR and SSDP is considered as a sign for NS5A date hubs. FAU - Elhefnawi, Mahmoud M AU - Elhefnawi MM AD - Informatics and Systems Department, National Research Center, Cairo, Egypt. FAU - Youssif, Aliaa A AU - Youssif AA FAU - Ghalwash, Atef Z AU - Ghalwash AZ FAU - Behaidy, Wessam H El AU - Behaidy WH LA - eng PT - Journal Article PL - United States TA - Adv Exp Med Biol JT - Advances in experimental medicine and biology JID - 0121103 RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Amino Acid Motifs MH - Binding Sites MH - Computational Biology MH - Data Mining/*methods MH - Databases, Protein MH - Hepacivirus/*chemistry/*genetics MH - Humans MH - Protein Structure, Tertiary MH - Sequence Alignment/*methods MH - Software Design MH - Structural Homology, Protein MH - Viral Nonstructural Proteins/*chemistry/*genetics EDAT- 2010/09/25 06:00 MHDA- 2011/02/04 06:00 CRDT- 2010/09/25 06:00 AID - 10.1007/978-1-4419-5913-3_34 [doi] PST - ppublish SO - Adv Exp Med Biol. 2010;680:299-305. doi: 10.1007/978-1-4419-5913-3_34. PMID- 12605403 OWN - NLM STAT- MEDLINE DA - 20030226 DCOM- 20030507 LR - 20121115 IS - 0360-4012 (Print) IS - 0360-4012 (Linking) VI - 71 IP - 6 DP - 2003 Mar 15 TI - Expression and properties of the recombinant murine Golli-myelin basic protein isoform J37. PG - 777-84 AB - A recombinant form of the murine Golli-myelin basic protein (MBP) isoform J37 (rmJ37) has been expressed in Escherichia coli and isolated to 95% purity via metal chelation and ion exchange chromatography. The protein did not aggregate lipid vesicles containing acidic phospholipids, unlike the 18.5 kDa isoform of MBP. This result is consistent with J37 having a functional role prior to the assembly of compact myelin. Circular dichroic spectroscopy showed that rmJ37 had a large proportion of random coil in aqueous solution but gained alpha-helix and beta-sheet in the presence of monosialoganglioside G(M1) and PI(4)P. Thus, like "classic" MBP, J37 is intrinsically unstructured, and its conformation depends on its environment and bound ligands. Analyses of the amino acid sequence of rmJ37 predicted an N-terminal calmodulin (CaM)-binding site. It was determined via a gel-shift assay and fluorescence spectroscopy that rmJ37 and CaM interacted in a 1:1 ratio in a Ca(2+)-dependent manner. However, the interaction was weak compared with 18.5 kDa MBP. CI - Copyright 2003 Wiley-Liss, Inc. FAU - Kaur, Jaspreet AU - Kaur J AD - Department of Molecular Biology and Genetics, and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada. FAU - Libich, David S AU - Libich DS FAU - Campagnoni, Celia W AU - Campagnoni CW FAU - Wood, D Denise AU - Wood DD FAU - Moscarello, Mario A AU - Moscarello MA FAU - Campagnoni, Anthony T AU - Campagnoni AT FAU - Harauz, George AU - Harauz G LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Neurosci Res JT - Journal of neuroscience research JID - 7600111 RN - 0 (Calmodulin) RN - 0 (Mbp protein, mouse) RN - 0 (Myelin Basic Protein) RN - 0 (Nerve Tissue Proteins) RN - 0 (Protein Isoforms) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) SB - IM MH - Animals MH - Binding Sites MH - Calmodulin/metabolism MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Mass Spectrometry MH - Mice MH - Myelin Basic Protein/biosynthesis/*chemistry/*isolation & purification/metabolism MH - Nerve Tissue Proteins/biosynthesis/*chemistry/*isolation & purification/metabolism MH - Protein Binding MH - Protein Isoforms/biosynthesis/chemistry/isolation & purification/metabolism MH - Protein Structure, Secondary MH - Recombinant Proteins/*biosynthesis/chemistry/isolation & purification/metabolism MH - Structure-Activity Relationship MH - Transcription Factors/biosynthesis/*chemistry/*isolation & purification/metabolism EDAT- 2003/02/28 04:00 MHDA- 2003/05/08 05:00 CRDT- 2003/02/28 04:00 AID - 10.1002/jnr.10547 [doi] PST - ppublish SO - J Neurosci Res. 2003 Mar 15;71(6):777-84. PMID- 15741346 OWN - NLM STAT- MEDLINE DA - 20050317 DCOM- 20050802 LR - 20140608 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 14 IP - 4 DP - 2005 Apr TI - Solution structure of At3g04780.1-des15, an Arabidopsis thaliana ortholog of the C-terminal domain of human thioredoxin-like protein. PG - 1059-63 AB - The structure of At3g04780.1-des15, an Arabidopsis thaliana ortholog of the C-terminal domain of human thioredoxin-like protein, was determined by NMR spectroscopy. The structure is dominated by a beta-barrel sandwich. A two-stranded anti-parallel beta-sheet, which seals off one end of the beta-barrel, is flanked by two flexible loops rich in acidic amino acids. Although this fold often provides a ligand binding site, the structure did not reveal an appreciable cavity inside the beta-barrel. The three-dimensional structure of At3g04780.1-des15 provides an entry point for understanding its functional role and those of its mammalian homologs. FAU - Song, Jikui AU - Song J AD - Center for Eukaryotic Structural Genomics, Department of Biochemistry, 433 Babcock Drive, University of Wisconsin-Madison, Madison, WI 53706-1544, USA. FAU - Tyler, Robert C AU - Tyler RC FAU - Wrobel, Russell L AU - Wrobel RL FAU - Frederick, Ronnie O AU - Frederick RO FAU - Vojtek, Frank C AU - Vojtek FC FAU - Jeon, Won Bae AU - Jeon WB FAU - Lee, Min S AU - Lee MS FAU - Markley, John L AU - Markley JL LA - eng SI - PDB/1XOY GR - 1P50 GM 64598/GM/NIGMS NIH HHS/United States GR - P41 GM 66326/GM/NIGMS NIH HHS/United States GR - P41 RR 02301/RR/NCRR NIH HHS/United States GR - RR 02781/RR/NCRR NIH HHS/United States GR - RR 08438/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050301 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Arabidopsis Proteins) RN - 0 (At3g04780.1-des15 protein, Arabidopsis) RN - 52500-60-4 (Thioredoxins) SB - IM MH - Arabidopsis Proteins/*chemistry MH - Humans MH - *Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Tertiary MH - Thioredoxins/*chemistry PMC - PMC2253455 OID - NLM: PMC2253455 EDAT- 2005/03/03 09:00 MHDA- 2005/08/03 09:00 CRDT- 2005/03/03 09:00 PHST- 2005/03/01 [aheadofprint] AID - ps.041246805 [pii] AID - 10.1110/ps.041246805 [doi] PST - ppublish SO - Protein Sci. 2005 Apr;14(4):1059-63. Epub 2005 Mar 1. PMID- 1944569 OWN - NLM STAT- MEDLINE DA - 19911211 DCOM- 19911211 LR - 20101118 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 354 IP - 6348 DP - 1991 Nov 7 TI - Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion. PG - 37-43 AB - Sindbis virus consists of a nucleocapsid core surrounded by a lipid membrane through which penetrate 80 glycoprotein trimers. The structure of the core protein comprising the coat surrounding the genomic RNA has been determined. The polypeptide fold from residue 114 to residue 264 is homologous to that of chymotrypsin-like serine proteinases with catalytic residues His 141, Asp 163 and Ser 215 of the core protein positioned as in other serine proteinases. The C-terminal tryptophan remains in the P1 substrate site subsequent to the autocatalytic cis cleavage of the capsid protein, thus rendering the proteinase inactive. Model building of the Sindbis core protein dimer shows that the nucleocapsid is likely to have T = 4 quasisymmetry. FAU - Choi, H K AU - Choi HK AD - Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907. FAU - Tong, L AU - Tong L FAU - Minor, W AU - Minor W FAU - Dumas, P AU - Dumas P FAU - Boege, U AU - Boege U FAU - Rossmann, M G AU - Rossmann MG FAU - Wengler, G AU - Wengler G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Viral Core Proteins) RN - EC 3.4.21.- (Serine Endopeptidases) RN - EC 3.4.21.1 (Chymotrypsin) SB - IM CIN - Nature. 1991 Nov 7;354(6348):22-3. PMID: 1944564 MH - Amino Acid Sequence MH - Biological Evolution MH - Chymotrypsin/chemistry MH - Molecular Sequence Data MH - Molecular Structure MH - Serine Endopeptidases/*chemistry MH - Sindbis Virus/*chemistry MH - Viral Core Proteins/*chemistry MH - X-Ray Diffraction EDAT- 1991/11/07 MHDA- 1991/11/07 00:01 CRDT- 1991/11/07 00:00 AID - 10.1038/354037a0 [doi] PST - ppublish SO - Nature. 1991 Nov 7;354(6348):37-43. PMID- 24654952 OWN - NLM STAT- MEDLINE DA - 20140409 DCOM- 20150420 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 136 IP - 14 DP - 2014 Apr 9 TI - Coupled folding and binding of the disordered protein PUMA does not require particular residual structure. PG - 5197-200 LID - 10.1021/ja4125065 [doi] AB - Many cellular proteins are 'disordered' in isolation. A subset of these intrinsically disordered proteins (IDPs) can, upon binding another molecule, fold to a well-defined three-dimensional structure. In the structurally heterogeneous, unbound ensemble of these IDPs, conformations are likely to exist that, in part, resemble the final bound form. It has been suggested that these conformations, displaying 'residual structure', could be important for the mechanism of such coupled folding and binding reactions. PUMA, of the BCL-2 family, is an IDP in isolation but will form a single, contiguous alpha-helix upon binding the folded protein MCL-1. Using the helix-breaking residue proline, we systematically target each potential turn of helix of unbound PUMA and assess the binding to MCL-1 using time-resolved stopped-flow techniques. All proline-containing mutants bound, and although binding was weaker than the wild-type protein, association rate constants were largely unaffected. We conclude that population of particular residual structure, containing a specific helical turn, is neither required for the binding nor for fast association of PUMA and MCL-1. FAU - Rogers, Joseph M AU - Rogers JM AD - Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, United Kingdom. FAU - Wong, Chi T AU - Wong CT FAU - Clarke, Jane AU - Clarke J LA - eng GR - 095195/Wellcome Trust/United Kingdom GR - WT095195MA/Wellcome Trust/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140331 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Apoptosis Regulatory Proteins) RN - 0 (BBC3 protein, human) RN - 0 (MCL1 protein, human) RN - 0 (Myeloid Cell Leukemia Sequence 1 Protein) RN - 0 (Proto-Oncogene Proteins) SB - IM MH - Apoptosis Regulatory Proteins/*chemistry MH - Binding Sites MH - Humans MH - Models, Molecular MH - Myeloid Cell Leukemia Sequence 1 Protein/*chemistry MH - Protein Conformation MH - Protein Folding MH - Proto-Oncogene Proteins/*chemistry PMC - PMC4017604 OID - NLM: PMC4017604 EDAT- 2014/03/25 06:00 MHDA- 2015/04/22 06:00 CRDT- 2014/03/25 06:00 PHST- 2014/03/31 [aheadofprint] AID - 10.1021/ja4125065 [doi] PST - ppublish SO - J Am Chem Soc. 2014 Apr 9;136(14):5197-200. doi: 10.1021/ja4125065. Epub 2014 Mar 31. PMID- 21327389 OWN - NLM STAT- MEDLINE DA - 20110614 DCOM- 20111003 LR - 20131121 IS - 1432-203X (Electronic) IS - 0721-7714 (Linking) VI - 30 IP - 7 DP - 2011 Jul TI - MpAsr encodes an intrinsically unstructured protein and enhances osmotic tolerance in transgenic Arabidopsis. PG - 1219-30 LID - 10.1007/s00299-011-1030-1 [doi] AB - Abscisic acid-, stress- and ripening (ASR) -induced proteins are plant-specific proteins whose expression is up-regulated under abiotic stresses or during fruit ripening. In this study, we characterized an ASR protein from plantain to explore its physiological roles under osmotic stress. The expression pattern of MpAsr gene shows that MpAsr gene changed little at the mRNA level, while the MpASR protein accumulates under osmotic treatment. Through bioinformatic-based predictions, circular dichroism spectrometry, and proteolysis and heat-stability assays, we determined that the MpASR protein is an intrinsically unstructured protein in solution. We demonstrated that the hydrophilic MpASR protein could protect L: -lactate dehydrogenase (L: -LDH) from cold-induced aggregation. Furthermore, heterologous expression of MpAsr in Escherichia coli and Arabidopsis enhanced the tolerance of transformants to osmotic stress. Transgenic 35S::MpAsr Arabidopsis seeds had a higher germination frequency than wild-type seeds under unfavorable conditions. At the physiological level, 35S::MpAsr Arabidopsis showed increased soluble sugars and decreased cell membrane damage under osmotic stress. Thus, our results suggest that the MpASR protein may act as an osmoprotectant and water-retaining molecule to help cell adjustment to water deficit caused by osmotic stress. FAU - Dai, Jin-Ran AU - Dai JR AD - The State Key Laboratory of Biocontrol and The Key Laboratory of Gene Engineering, Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China. FAU - Liu, Bing AU - Liu B FAU - Feng, Dong-Ru AU - Feng DR FAU - Liu, Hai-yan AU - Liu HY FAU - He, Yan-ming AU - He YM FAU - Qi, Kang-biao AU - Qi KB FAU - Wang, Hong-Bin AU - Wang HB FAU - Wang, Jin-Fa AU - Wang JF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110215 PL - Germany TA - Plant Cell Rep JT - Plant cell reports JID - 9880970 RN - 0 (Plant Proteins) RN - 0 (RNA, Messenger) RN - 0 (Recombinant Fusion Proteins) RN - 059QF0KO0R (Water) RN - 4Y8F71G49Q (Malondialdehyde) RN - EC 1.1.1.27 (L-Lactate Dehydrogenase) RN - J41CSQ7QDS (Zinc) SB - IM MH - *Adaptation, Physiological MH - Amino Acid Sequence MH - Arabidopsis/genetics/growth & development/*metabolism MH - Cell Membrane/metabolism MH - Escherichia coli/genetics/metabolism MH - Gene Expression Regulation, Plant MH - Germination MH - L-Lactate Dehydrogenase/metabolism MH - Malondialdehyde/analysis MH - Molecular Sequence Data MH - Musa/*genetics/metabolism MH - Osmosis MH - Plant Proteins/chemistry/genetics/*metabolism MH - Plant Roots/genetics/growth & development/metabolism MH - Plants, Genetically Modified/genetics/growth & development/metabolism MH - Protein Stability MH - RNA, Messenger/genetics/metabolism MH - Recombinant Fusion Proteins/metabolism MH - Seeds/genetics/*growth & development/metabolism MH - Stress, Physiological MH - Water/metabolism MH - Zinc/metabolism EDAT- 2011/02/18 06:00 MHDA- 2011/10/04 06:00 CRDT- 2011/02/18 06:00 PHST- 2010/12/01 [received] PHST- 2011/01/26 [accepted] PHST- 2011/01/26 [revised] PHST- 2011/02/15 [aheadofprint] AID - 10.1007/s00299-011-1030-1 [doi] PST - ppublish SO - Plant Cell Rep. 2011 Jul;30(7):1219-30. doi: 10.1007/s00299-011-1030-1. Epub 2011 Feb 15. PMID- 7589490 OWN - NLM STAT- MEDLINE DA - 19951130 DCOM- 19951130 LR - 20131121 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 373 IP - 3 DP - 1995 Oct 16 TI - Crystallization and crystallographic investigations of the small subunit of mouse ribonucleotide reductase. PG - 310-2 AB - The R2 protein component of mouse ribonucleotide reductase has been obtained from overproducing Escherichia coli bacteria. It has been crystallized using NaCl as precipitant. The crystals are orthorhombic, space group C222(1), with cell dimensions a = 76.9 A, b = 108.9 A, c = 92.7 A and diffract to at least 2.5 A. The asymmetric unit of the crystals contains one monomer. Rotation and translation function searches using a model based on the weakly homologous E. coli R2 gave one significant peak. Rotation about a crystallographic 2-fold axis parallel to the a-axis produces an R2 dimer with dimer interactions very similar to those found for E. coli R2. FAU - Nielsen, B B AU - Nielsen BB AD - Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden. FAU - Kauppi, B AU - Kauppi B FAU - Thelander, M AU - Thelander M FAU - Thelander, L AU - Thelander L FAU - Larsen, I K AU - Larsen IK FAU - Eklund, H AU - Eklund H LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Recombinant Proteins) RN - E1UOL152H7 (Iron) RN - EC 1.17.4.- (Ribonucleotide Reductases) SB - IM MH - Animals MH - Crystallization MH - Crystallography, X-Ray MH - Fourier Analysis MH - Iron/analysis MH - Mice MH - Protein Conformation MH - Recombinant Proteins/chemistry MH - Ribonucleotide Reductases/*chemistry EDAT- 1995/10/16 MHDA- 1995/10/16 00:01 CRDT- 1995/10/16 00:00 AID - 0014-5793(95)01067-O [pii] PST - ppublish SO - FEBS Lett. 1995 Oct 16;373(3):310-2. PMID- 14635127 OWN - NLM STAT- MEDLINE DA - 20031124 DCOM- 20040121 LR - 20101118 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 53 IP - 4 DP - 2003 Dec 1 TI - Natively unfolded C-terminal domain of caldesmon remains substantially unstructured after the effective binding to calmodulin. PG - 855-62 AB - The structure of C-terminal domain (CaD136, C-terminal residues 636-771) of chicken gizzard caldesmon has been analyzed by a variety of physico-chemical methods. We are showing here that CaD136 does not have globular structure, has low secondary structure content, is essentially noncompact, as it follows from high R(g) and R(S) values, and is characterized by the absence of distinct heat absorption peaks, i.e. it belongs to the family of natively unfolded (or intrinsically unstructured) proteins. Surprisingly, effective binding of single calmodulin molecule (K(d) = 1.4 +/- 0.2 microM) leads only to a very moderate folding of this protein and CaD136 remains substantially unfolded within its tight complex with calmodulin. The biological significance of these observations is discussed. CI - Copyright 2003 Wiley-Liss, Inc. FAU - Permyakov, Sergei E AU - Permyakov SE AD - Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. FAU - Millett, Ian S AU - Millett IS FAU - Doniach, Sebastian AU - Doniach S FAU - Permyakov, Eugene A AU - Permyakov EA FAU - Uversky, Vladimir N AU - Uversky VN LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Amino Acids) RN - 0 (Calmodulin) RN - 0 (Calmodulin-Binding Proteins) SB - IM MH - Amino Acids/chemistry MH - Animals MH - Calmodulin/*chemistry/metabolism MH - Calmodulin-Binding Proteins/*chemistry/metabolism MH - Chickens MH - Circular Dichroism MH - Hydrophobic and Hydrophilic Interactions MH - Protein Binding MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Spectrometry, Fluorescence/methods EDAT- 2003/11/25 05:00 MHDA- 2004/01/22 05:00 CRDT- 2003/11/25 05:00 AID - 10.1002/prot.10481 [doi] PST - ppublish SO - Proteins. 2003 Dec 1;53(4):855-62. PMID- 24576674 OWN - NLM STAT- MEDLINE DA - 20140428 DCOM- 20140703 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1840 IP - 6 DP - 2014 Jun TI - G-quadruplex DNA recognition by nucleophosmin: new insights from protein dissection. PG - 2050-9 LID - 10.1016/j.bbagen.2014.02.017 [doi] LID - S0304-4165(14)00078-6 [pii] AB - BACKGROUND: Nucleophosmin (NPM1, B23) is a multifunctional protein that is involved in a variety of fundamental biological processes. NPM1/B23 deregulation is implicated in the pathogenesis of several human malignancies. This protein exerts its functions through the interaction with a multiplicity of biological partners. Very recently it is has been shown that NPM1/B23 specifically recognizes DNA G-quadruplexes through its C-terminal region. METHODS: Through a rational dissection approach of protein here we show that the intrinsically unfolded regions of NPM1/B23 significantly contribute to the binding of c-MYC G-quadruplex motif. Interestingly, the analysis of the ability of distinct NPM1/B23 fragments to bind this quadruplex led to the identifications of distinct NPM1/B23-based peptides that individually present a high affinity for this motif. RESULTS: These results suggest that the tight binding of NPM1/B23 to the G-quadruplex is achieved through the cooperation of both folded and unfolded regions that are individually able to bind it. The dissection of NPM1/B23 also unveils that its H1 helix is intrinsically endowed with an unusual thermal stability. CONCLUSIONS: These findings have implications for the unfolding mechanism of NPM1/B23, for the G-quadruplex affinity of the different NPM1/B23 isoforms and for the design of peptide-based molecules able to interact with this DNA motif. GENERAL OBSERVATION: This study sheds new light in the molecular mechanism of the complex NPM1/G-quadruplex involved in acute myeloid leukemia (AML) disease. CI - Copyright (c) 2014 Elsevier B.V. All rights reserved. FAU - Scognamiglio, Pasqualina Liana AU - Scognamiglio PL AD - Department of Pharmacy, University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy; Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), 80125 Naples, Italy. FAU - Di Natale, Concetta AU - Di Natale C AD - Department of Pharmacy, University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy; Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), 80125 Naples, Italy. FAU - Leone, Marilisa AU - Leone M AD - Institute of Biostructures and Bioimaging, CNR, 80134 Naples, Italy; CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy. FAU - Poletto, Mattia AU - Poletto M AD - Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy. FAU - Vitagliano, Luigi AU - Vitagliano L AD - Institute of Biostructures and Bioimaging, CNR, 80134 Naples, Italy. FAU - Tell, Gianluca AU - Tell G AD - Department of Medical and Biological Sciences, University of Udine, 33100 Udine, Italy. FAU - Marasco, Daniela AU - Marasco D AD - Department of Pharmacy, University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy; CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", DFM-Scarl, 80134 Naples, Italy. Electronic address: daniela.marasco@unina.it. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140224 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (MYC protein, human) RN - 0 (Nuclear Proteins) RN - 0 (Proto-Oncogene Proteins c-myc) RN - 117896-08-9 (nucleophosmin) SB - IM MH - Amino Acid Sequence MH - *G-Quadruplexes MH - Humans MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Nuclear Proteins/chemistry/*physiology MH - Protein Folding MH - Proto-Oncogene Proteins c-myc/metabolism OTO - NOTNLM OT - Disordered protein region OT - Helical stability OT - Surface Plasmon Resonance EDAT- 2014/03/01 06:00 MHDA- 2014/07/06 06:00 CRDT- 2014/03/01 06:00 PHST- 2013/12/16 [received] PHST- 2014/02/13 [revised] PHST- 2014/02/18 [accepted] PHST- 2014/02/24 [aheadofprint] AID - S0304-4165(14)00078-6 [pii] AID - 10.1016/j.bbagen.2014.02.017 [doi] PST - ppublish SO - Biochim Biophys Acta. 2014 Jun;1840(6):2050-9. doi: 10.1016/j.bbagen.2014.02.017. Epub 2014 Feb 24. PMID- 15576552 OWN - NLM STAT- MEDLINE DA - 20041220 DCOM- 20050509 LR - 20140608 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 14 IP - 1 DP - 2005 Jan TI - Contribution of the intrinsic disulfide to the assembly mechanism of islet amyloid. PG - 231-9 AB - Amyloidogenesis from soluble protein requires conformational and oligomeric assembly steps. In systems where the precursor protein is natively unfolded, such as islet amyloid polypeptide (IAPP), forces and structural changes relevant to protein unfolding are not thought to participate in the assembly mechanism. Thus, fiber core structure elements should provide the dominant contributions to assembly kinetics. Here we show, however, that residues outside the amyloid core can influence the mechanism of IAPP fiber assembly. IAPP possesses an intramolecular disulfide bond between residues 2 and 7. This short-range disulfide prohibits the N-terminal region from adopting the beta-strand structure of an amyloid. We examined the role of this disulfide in fiber formation by generating a truncated construct (IAPP(8-37)) and a stable reduced form of the full-length protein (IAPP(CAM)). The fiber structures and assembly kinetics of these variants were assessed via optical and mass spectroscopy. Our data confirm that the disulfide does not contribute to the amyloid fiber core structure. Remarkably, however, it plays a central role in the assembly mechanism. First, loss of the disulfide substantially reduces fiber formation by secondary nucleation, i.e., the ability of pre-existing fibers to participate in the formation of new fibers. Second, the bypass of nucleation by seed addition is a two-step process, termed activation. Loss of the disulfide eliminates this two-step nature of seeded kinetics. FAU - Koo, Bon W AU - Koo BW AD - Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Ave., New Haven, CT 06520-8114, USA. FAU - Miranker, Andrew D AU - Miranker AD LA - eng GR - DK54899/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20041202 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Amyloid) RN - 0 (Disulfides) RN - 0 (Islet Amyloid Polypeptide) SB - IM MH - Amino Acid Sequence MH - Amyloid/*chemistry MH - Disulfides/*chemistry MH - Islet Amyloid Polypeptide MH - Kinetics MH - Molecular Sequence Data MH - Protein Binding MH - Sequence Homology, Amino Acid MH - Time Factors PMC - PMC2253339 OID - NLM: PMC2253339 EDAT- 2004/12/04 09:00 MHDA- 2005/05/10 09:00 CRDT- 2004/12/04 09:00 PHST- 2004/12/02 [aheadofprint] AID - ps.041051205 [pii] AID - 10.1110/ps.041051205 [doi] PST - ppublish SO - Protein Sci. 2005 Jan;14(1):231-9. Epub 2004 Dec 2. PMID- 11827516 OWN - NLM STAT- MEDLINE DA - 20020205 DCOM- 20020328 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 41 IP - 6 DP - 2002 Feb 12 TI - Functional roles of conserved residues in the unstructured loop of Vibrio harveyi bacterial luciferase. PG - 1724-31 AB - Residues 257-291 of the Vibrio harveyi bacterial luciferase alpha subunit comprise a highly conserved, protease-labile, disordered loop region, most of which is unresolved in the previously determined X-ray structures of the native enzyme. This loop region has been shown to display a time- dependent proteolysis resistance upon single catalytic turnover and was postulated to undergo conformational changes during catalysis ([AbouKhair, N. K., Ziegler, M. M., and Baldwin, T. O. (1985) Biochemistry 24, 3942-3947]. To investigate the role of this region in catalysis, we have performed site-specific mutations of different conserved loop residues. In comparison with V(max) and V(max)/K(m,flavin) of the native luciferase, the bioluminescence activities of alphaG284P were decreased to 1-2% whereas those of alphaG275P and alphaF261D were reduced by 4-6 orders of magnitude. Stopped-flow results indicate that both alphaG275P and alphaF261D were able to form the 4a-hydroperoxy-FMN intermediate II but at lower yields. Both mutants also had enhanced rates for the intermediate II nonproductive dark decay and significantly compromised abilities to oxidize the decanal substrate. Additional mutations were introduced into the alphaG275 and alphaF261 positions, and the activities of the resulting mutants were characterized. Results indicate that the torsional flexibility of the alphaG275 residue and the bulky and hydrophobic nature of the alphaF261 residue were critical to the luciferase activity. Our results also support a functional role for the alpha subunit unstructured loop itself, possibly by serving as a mobile gating mechanism in shielding critical intermediates (including the excited flavin emitter) from exposure to medium. FAU - Low, John C AU - Low JC AD - Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA. FAU - Tu, Shiao-Chun AU - Tu SC LA - eng GR - GM25953/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Protein Subunits) RN - 0 (Recombinant Proteins) RN - 7N464URE7E (Flavin Mononucleotide) RN - EC 1.13.12.- (Luciferases) SB - IM MH - Amino Acid Sequence MH - Catalytic Domain/genetics MH - Conserved Sequence MH - Enzyme Stability MH - Flavin Mononucleotide MH - Kinetics MH - Luciferases/*chemistry/genetics/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Protein Subunits MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Sequence Homology, Amino Acid MH - Vibrio/*enzymology/genetics EDAT- 2002/02/06 10:00 MHDA- 2002/03/29 10:01 CRDT- 2002/02/06 10:00 AID - bi011958p [pii] PST - ppublish SO - Biochemistry. 2002 Feb 12;41(6):1724-31. PMID- 15654739 OWN - NLM STAT- MEDLINE DA - 20050118 DCOM- 20050412 LR - 20081121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 44 IP - 3 DP - 2005 Jan 25 TI - Structural properties of the promiscuous VP16 activation domain. PG - 827-39 AB - Herpes simplex virion protein 16 (VP16) contains two strong activation regions that can independently and cooperatively activate transcription in vivo. We have identified the regions and residues involved in the interaction with the human transcriptional coactivator positive cofactor 4 (PC4) and the general transcription factor TFIIB. NMR and biochemical experiments revealed that both VP16 activation regions are required for the interaction and undergo a conformational transition from random coil to alpha-helix upon binding to its target PC4. The interaction is strongly electrostatically driven and the binding to PC4 is enhanced by the presence of its amino-terminal domain. We propose models for binding of VP16 to the core domains of PC4 and TFIIB that are based on two independent docking approaches using NMR chemical shift changes observed in titration experiments. The models are consistent with results from site-directed mutagenesis and provide an explanation for the contribution of both acidic and hydrophobic residues for transcriptional activation by VP16. Both intrinsically unstructured activation domains are attracted to their interaction partner by electrostatic interactions, and adopt an alpha-helical conformation around the important hydrophobic residues. The models showed multiple distinct binding surfaces upon interaction with various partners, providing an explanation for the promiscuous properties, cooperativity, and the high activity of this activation domain. FAU - Jonker, Hendrik R A AU - Jonker HR AD - Bijvoet Center for Biomolecular Research, section NMR spectroscopy, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. FAU - Wechselberger, Rainer W AU - Wechselberger RW FAU - Boelens, Rolf AU - Boelens R FAU - Folkers, Gert E AU - Folkers GE FAU - Kaptein, Rob AU - Kaptein R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Herpes Simplex Virus Protein Vmw65) RN - 0 (Transcription Factor TFIIB) SB - IM MH - Herpes Simplex Virus Protein Vmw65/chemistry/*metabolism MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - Static Electricity MH - Transcription Factor TFIIB/metabolism EDAT- 2005/01/19 09:00 MHDA- 2005/04/13 09:00 CRDT- 2005/01/19 09:00 AID - 10.1021/bi0482912 [doi] PST - ppublish SO - Biochemistry. 2005 Jan 25;44(3):827-39. PMID- 20647002 OWN - NLM STAT- MEDLINE DA - 20100816 DCOM- 20100902 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 399 IP - 1 DP - 2010 Aug 13 TI - Solution structure of the N-terminal transactivation domain of ERM modified by SUMO-1. PG - 104-10 LID - 10.1016/j.bbrc.2010.07.049 [doi] AB - ERM is a member of the PEA3 group of the Ets transcription factor family that plays important roles in development and tumorigenesis. The PEA3s share an N-terminal transactivation domain (TADn) whose activity is inhibited by small ubiquitin-like modifier (SUMO). However, the consequences of sumoylation and its underlying molecular mechanism remain unclear. The domain structure of ERM TADn alone or modified by SUMO-1 was analyzed using small-angle X-ray scattering (SAXS). Low resolution shapes determined ab initio from the scattering data indicated an elongated shape and an unstructured conformation of TADn in solution. Covalent attachment of SUMO-1 does not perturb the structure of TADn as indicated by the linear arrangement of the SUMO moiety with respect to TADn. Thus, ERM belongs to the growing family of proteins that contain intrinsically unstructured regions. The flexible nature of TADn may be instrumental for ERM recognition and binding to diverse molecular partners. CI - 2010 Elsevier Inc. All rights reserved. FAU - Lens, Zoe AU - Lens Z AD - IRI USR CNRS, Parc CNRS de la Haute Borne, Villeneuve d'Ascq, France. FAU - Dewitte, Frederique AU - Dewitte F FAU - Monte, Didier AU - Monte D FAU - Baert, Jean-Luc AU - Baert JL FAU - Bompard, Coralie AU - Bompard C FAU - Senechal, Magalie AU - Senechal M FAU - Van Lint, Carine AU - Van Lint C FAU - de Launoit, Yvan AU - de Launoit Y FAU - Villeret, Vincent AU - Villeret V FAU - Verger, Alexis AU - Verger A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100718 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (DNA-Binding Proteins) RN - 0 (ETV5 protein, human) RN - 0 (SUMO-1 Protein) RN - 0 (SUMO1 protein, human) RN - 0 (Transcription Factors) SB - IM MH - DNA-Binding Proteins/*chemistry/genetics/metabolism MH - Humans MH - Protein Structure, Tertiary MH - SUMO-1 Protein/*metabolism MH - Scattering, Small Angle MH - Transcription Factors/*chemistry/genetics/metabolism MH - *Transcriptional Activation MH - X-Ray Diffraction EDAT- 2010/07/22 06:00 MHDA- 2010/09/03 06:00 CRDT- 2010/07/22 06:00 PHST- 2010/07/07 [received] PHST- 2010/07/15 [accepted] PHST- 2010/07/18 [aheadofprint] AID - S0006-291X(10)01360-4 [pii] AID - 10.1016/j.bbrc.2010.07.049 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2010 Aug 13;399(1):104-10. doi: 10.1016/j.bbrc.2010.07.049. Epub 2010 Jul 18. PMID- 16164372 OWN - NLM STAT- MEDLINE DA - 20051215 DCOM- 20060609 LR - 20091119 IS - 0031-8655 (Print) IS - 0031-8655 (Linking) VI - 81 IP - 6 DP - 2005 Nov-Dec TI - Photochemistry and photobiology of cryptochrome blue-light photopigments: the search for a photocycle. PG - 1291-304 AB - Cryptochromes are flavoproteins that exhibit high sequence and structural similarity to the light-dependent DNA-repair enzyme, photolyase. Cryptochromes have lost the ability to repair DNA; instead, they use the energy from near-UV/blue light to regulate a variety of growth and adaptive processes in organisms ranging from bacteria to humans. The photocycle of cryptochrome is not yet known, although it is hypothesized that it may share some similarity to that of photolyase, which utilizes light-driven electron transfer from the catalytic flavin chromophore. In this review, we present genetic evidence for the photoreceptive role of cryptochromes and discuss recent biochemical studies that have furthered our understanding of the cryptochrome photocycle. In particular, the role of the unique C-terminal domain in cryptochrome phototransduction is discussed. FAU - Partch, Carrie L AU - Partch CL AD - Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA. FAU - Sancar, Aziz AU - Sancar A LA - eng PT - Journal Article PT - Review PL - United States TA - Photochem Photobiol JT - Photochemistry and photobiology JID - 0376425 RN - 0 (Cryptochromes) RN - 0 (Flavoproteins) SB - IM MH - Animals MH - Circadian Rhythm MH - Cryptochromes MH - Flavoproteins/classification/*genetics/metabolism MH - Humans MH - *Photobiology MH - *Photochemistry MH - Plants MH - *Signal Transduction RF - 152 EDAT- 2005/09/17 09:00 MHDA- 2006/06/10 09:00 CRDT- 2005/09/17 09:00 AID - 2005-07-08-IR-607 [pii] AID - 10.1562/2005-07-08-IR-607 [doi] PST - ppublish SO - Photochem Photobiol. 2005 Nov-Dec;81(6):1291-304. PMID- 15219899 OWN - NLM STAT- MEDLINE DA - 20040628 DCOM- 20040909 LR - 20121115 IS - 0968-4328 (Print) IS - 0968-4328 (Linking) VI - 35 IP - 7 DP - 2004 TI - Myelin basic protein-diverse conformational states of an intrinsically unstructured protein and its roles in myelin assembly and multiple sclerosis. PG - 503-42 AB - The 18.5 kDa isoform of myelin basic protein (MBP) is a major component of the myelin sheath in the central nervous system of higher vertebrates, and a member of a larger family of proteins with a multiplicity of forms and post-translational modifications (PTMs). The 18.5 kDa protein is the exemplar of the family, being most abundant in adult myelin, and thus the most-studied. It is peripherally membrane-associated, but has generally been investigated in isolated form. MBP is an 'intrinsically unstructured' protein with a high proportion (approximately 75%) of random coil, but postulated to have core elements of beta-sheet and alpha-helix. We review here the properties of the MBP family, especially of the 18.5 kDa isoform, and discuss how its three-dimensional (3D) structure may be resolved by direct techniques available to us, viz., X-ray and electron crystallography, and solution and solid-state NMR spectrometry. In particular, we emphasise that creating an appropriate environment in which the protein can adopt a physiologically relevant fold is crucial to such endeavours. By solving the 3D structure of 18.5 kDa MBP and the effects of PTMs, we will attain a better understanding of myelin architecture, and of the molecular mechanisms that transpire in demyelinating diseases such as multiple sclerosis. CI - Copyright 2004 Elsevier Ltd. FAU - Harauz, George AU - Harauz G AD - Department of Molecular Biology and Genetics, Biophysics Interdepartmental Group, University of Guelph, Room 230, Axelrod Building, 50 Stone Road East, Guelph, Ont., Canada N1G 2W1. gharauz@uoguelph.ca FAU - Ishiyama, Noboru AU - Ishiyama N FAU - Hill, Christopher M D AU - Hill CM FAU - Bates, Ian R AU - Bates IR FAU - Libich, David S AU - Libich DS FAU - Fares, Christophe AU - Fares C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Micron JT - Micron (Oxford, England : 1993) JID - 9312850 RN - 0 (Myelin Basic Protein) SB - IM MH - Amino Acid Sequence MH - Animals MH - Crystallography, X-Ray MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Multiple Sclerosis/*metabolism/physiopathology MH - Myelin Basic Protein/*chemistry/metabolism MH - Myelin Sheath/*metabolism MH - Protein Conformation MH - Structure-Activity Relationship RF - 500 EDAT- 2004/06/29 05:00 MHDA- 2004/09/10 05:00 CRDT- 2004/06/29 05:00 AID - 10.1016/j.micron.2004.04.005 [doi] AID - S0968432804000964 [pii] PST - ppublish SO - Micron. 2004;35(7):503-42. PMID- 12964161 OWN - NLM STAT- MEDLINE DA - 20030909 DCOM- 20040507 LR - 20091119 IS - 1439-4227 (Print) IS - 1439-4227 (Linking) VI - 4 IP - 9 DP - 2003 Sep 5 TI - The structural plasticity of the C terminus of p21Cip1 is a determinant for target protein recognition. PG - 863-9 AB - The cyclin-dependent kinase inhibitory protein p21(Cip1) might play multiple roles in cell-cycle regulation through interaction of its C-terminal domain with a defined set of cellular proteins such as proliferating cell nuclear antigen (PCNA), calmodulin (CaM), and the oncoprotein SET. p21(Cip1) could be described as an intrinsically unstructured protein in solution although the C-terminal domain adopts a well-defined extended conformation when bound to PCNA. However, the molecular mechanism of the interaction with CaM and the oncoprotein SET is not well understood, partly because of the lack of structural information. In this work, a peptide derived from the C-terminal domain of p21(Cip1) that covers the binding domain of the three above-mentioned proteins was used to demonstrate that the C-terminal domain of p21 recognizes multiple ligands through its ability to adopt multiple conformations. The conformation is dictated by tertiary contacts rather than by the primary sequence of the protein. Our results suggest that the C-terminal domain of p21(Cip1) adopts an extended structure when bound to PCNA and probably when bound to the oncoprotein SET, but an alpha helix when bound to CaM. FAU - Esteve, Vicent AU - Esteve V AD - Dept. Bioquimica i Biologia Molecular, Universitat de Valencia, 46100 Burjassot, Valencia, Spain. FAU - Canela, Nuria AU - Canela N FAU - Rodriguez-Vilarrupla, Aina AU - Rodriguez-Vilarrupla A FAU - Aligue, Rosa AU - Aligue R FAU - Agell, Neus AU - Agell N FAU - Mingarro, Ismael AU - Mingarro I FAU - Bachs, Oriol AU - Bachs O FAU - Perez-Paya, Enrique AU - Perez-Paya E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Germany TA - Chembiochem JT - Chembiochem : a European journal of chemical biology JID - 100937360 RN - 0 (CDKN1A protein, human) RN - 0 (Calmodulin) RN - 0 (Chromosomal Proteins, Non-Histone) RN - 0 (Cyclin-Dependent Kinase Inhibitor p21) RN - 0 (Cyclins) RN - 0 (Histone Chaperones) RN - 0 (Ligands) RN - 0 (Peptide Fragments) RN - 0 (Proliferating Cell Nuclear Antigen) RN - 0 (Proteins) RN - 0 (SET protein, human) RN - 0 (Transcription Factors) SB - IM MH - Binding, Competitive MH - Calmodulin/*metabolism MH - Cell Cycle/physiology MH - Chromosomal Proteins, Non-Histone MH - Circular Dichroism MH - Cyclin-Dependent Kinase Inhibitor p21 MH - Cyclins/*chemistry/metabolism MH - Escherichia coli/genetics MH - Histone Chaperones MH - Humans MH - Ligands MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Peptide Fragments/chemistry/metabolism MH - Proliferating Cell Nuclear Antigen/*metabolism MH - Protein Conformation MH - Proteins/*metabolism MH - Transcription Factors EDAT- 2003/09/10 05:00 MHDA- 2004/05/08 05:00 CRDT- 2003/09/10 05:00 AID - 10.1002/cbic.200300649 [doi] PST - ppublish SO - Chembiochem. 2003 Sep 5;4(9):863-9. PMID- 23471103 OWN - NLM STAT- In-Process DA - 20130308 IS - 2050-084X (Electronic) IS - 2050-084X (Linking) VI - 2 DP - 2013 TI - The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat. PG - e00327 LID - 10.7554/eLife.00327 [doi] AB - Human positive transcription elongation factor b (P-TEFb) phosphorylates RNA polymerase II and regulatory proteins to trigger elongation of many gene transcripts. The HIV-1 Tat protein selectively recruits P-TEFb as part of a super elongation complex (SEC) organized on a flexible AFF1 or AFF4 scaffold. To understand this specificity and determine if scaffold binding alters P-TEFb conformation, we determined the structure of a tripartite complex containing the recognition regions of P-TEFb and AFF4. AFF4 meanders over the surface of the P-TEFb cyclin T1 (CycT1) subunit but makes no stable contacts with the CDK9 kinase subunit. Interface mutations reduced CycT1 binding and AFF4-dependent transcription. AFF4 is positioned to make unexpected direct contacts with HIV Tat, and Tat enhances P-TEFb affinity for AFF4. These studies define the mechanism of scaffold recognition by P-TEFb and reveal an unanticipated intersubunit pocket on the AFF4 SEC that potentially represents a target for therapeutic intervention against HIV/AIDS. DOI:http://dx.doi.org/10.7554/eLife.00327.001. FAU - Schulze-Gahmen, Ursula AU - Schulze-Gahmen U AD - Department of Molecular and Cell Biology , University of California, Berkeley , Berkeley , United States. FAU - Upton, Heather AU - Upton H FAU - Birnberg, Andrew AU - Birnberg A FAU - Bao, Katherine AU - Bao K FAU - Chou, Seemay AU - Chou S FAU - Krogan, Nevan J AU - Krogan NJ FAU - Zhou, Qiang AU - Zhou Q FAU - Alber, Tom AU - Alber T LA - eng GR - P50 GM081879/GM/NIGMS NIH HHS/United States GR - P50 GM082250/GM/NIGMS NIH HHS/United States GR - P50GM82250/GM/NIGMS NIH HHS/United States GR - R01 AI041757/AI/NIAID NIH HHS/United States GR - R01 AI095057/AI/NIAID NIH HHS/United States GR - R01AI095057/AI/NIAID NIH HHS/United States GR - R01AI41757-11/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130305 PL - United States TA - Elife JT - eLife JID - 101579614 SB - IM PMC - PMC3589825 OID - NLM: PMC3589825 OTO - NOTNLM OT - Human OT - SEC OT - intrinsically disordered proteins OT - super elongation complex OT - transcription elongation GN - NLM: Original DateCompleted: 20130311 GN - NLM: Original DateCompleted: 20140206 EDAT- 2013/03/09 06:00 MHDA- 2013/03/09 06:01 CRDT- 2013/03/09 06:00 PHST- 2012/10/19 [received] PHST- 2013/01/16 [accepted] PHST- 2013/03/05 [epublish] AID - 10.7554/eLife.00327 [doi] AID - 00327 [pii] PST - epublish SO - Elife. 2013 Mar 5;2:e00327. doi: 10.7554/eLife.00327. PMID- 11344324 OWN - NLM STAT- MEDLINE DA - 20010509 DCOM- 20010927 LR - 20140613 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 10 IP - 3 DP - 2001 Mar TI - Identification of intrinsic order and disorder in the DNA repair protein XPA. PG - 560-71 AB - The DNA-repair protein XPA is required to recognize a wide variety of bulky lesions during nucleotide excision repair. Independent NMR solution structures of a human XPA fragment comprising approximately 40% of the full-length protein, the minimal DNA-binding domain, revealed that one-third of this molecule was disordered. To better characterize structural features of full-length XPA, we performed time-resolved trypsin proteolysis on active recombinant Xenopus XPA (xXPA). The resulting proteolytic fragments were analyzed by electrospray ionization interface coupled to a Fourier transform ion cyclotron resonance mass spectrometry and SDS-PAGE. The molecular weight of the full-length xXPA determined by mass spectrometry (30922.02 daltons) was consistent with that calculated from the sequence (30922.45 daltons). Moreover, the mass spectrometric data allowed the assignment of multiple xXPA fragments not resolvable by SDS-PAGE. The neural network program Predictor of Natural Disordered Regions (PONDR) applied to xXPA predicted extended disordered N- and C-terminal regions with an ordered internal core. This prediction agreed with our partial proteolysis results, thereby indicating that disorder in XPA shares sequence features with other well-characterized intrinsically unstructured proteins. Trypsin cleavages at 30 of the possible 48 sites were detected and no cleavage was observed in an internal region (Q85-I179) despite 14 possible cut sites. For the full-length xXPA, there was strong agreement among PONDR, partial proteolysis data, and the NMR structure for the corresponding XPA fragment. FAU - Iakoucheva, L M AU - Iakoucheva LM AD - Pacific Northwest National Laboratory, Molecular Biosciences Department, Richland, WA 99352, USA. FAU - Kimzey, A L AU - Kimzey AL FAU - Masselon, C D AU - Masselon CD FAU - Bruce, J E AU - Bruce JE FAU - Garner, E C AU - Garner EC FAU - Brown, C J AU - Brown CJ FAU - Dunker, A K AU - Dunker AK FAU - Smith, R D AU - Smith RD FAU - Ackerman, E J AU - Ackerman EJ LA - eng PT - Journal Article PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (DNA-Binding Proteins) RN - 0 (Xeroderma Pigmentosum Group A Protein) RN - EC 3.4.21.4 (Trypsin) SB - IM MH - Amino Acid Motifs/genetics/physiology MH - Amino Acid Sequence MH - Animals MH - DNA Repair/*physiology MH - DNA-Binding Proteins/*chemistry/*physiology MH - Electrophoresis, Polyacrylamide Gel MH - Hydrolysis MH - Neural Networks (Computer) MH - Protein Structure, Secondary MH - Spectrometry, Mass, Electrospray Ionization MH - Spectroscopy, Fourier Transform Infrared MH - Trypsin MH - Xenopus laevis MH - Xeroderma Pigmentosum Group A Protein PMC - PMC2374143 OID - NLM: PMC2374143 EDAT- 2001/05/10 10:00 MHDA- 2001/09/28 10:01 CRDT- 2001/05/10 10:00 AID - 10.1110/ps.29401 [doi] PST - ppublish SO - Protein Sci. 2001 Mar;10(3):560-71. PMID- 15581372 OWN - NLM STAT- MEDLINE DA - 20041207 DCOM- 20050126 LR - 20121115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 43 IP - 49 DP - 2004 Dec 14 TI - The intermediate chain of cytoplasmic dynein is partially disordered and gains structure upon binding to light-chain LC8. PG - 15595-603 AB - The N-terminal domain of dynein intermediate chain, IC(1-289), is highly disordered, but upon binding to dynein light-chain LC8, it undergoes a significant conformational change to a more ordered structure. Using circular dichroism and fluorescence spectroscopy, we demonstrate that the change in conformation is due to an increase in the helical structure and to enhanced compactness in the environment of tryptophan 161. An increase in helical structure and compactness is also observed with trimethylamine-N-oxide (TMAO), a naturally occurring osmolyte used here as a probe to identify regions with a propensity for induced folding. Global protection of IC(1-289) from protease digestion upon LC8 binding was localized to a segment that includes residues downstream of the LC8-binding site. Several smaller constructs of IC(1-289) containing the LC8-binding site and one of the predicted helix or coiled-coil segments were made. IC(1-143) shows no increase in helical structure upon binding, while IC(114-260) shows an increase in helical structure similar to what is observed with IC(1-289). Binding of IC(114-260) to LC8 was monitored by fluorescence and native gel electrophoresis and shows saturation of binding, a stoichiometry of 1:1, and moderate binding affinity. The induced folding of IC(1-289) upon LC8 binding suggests that LC8 could act through the intermediate chain to facilitate dynein assembly or regulate cargo-binding interactions. FAU - Nyarko, Afua AU - Nyarko A AD - Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, USA. FAU - Hare, Michael AU - Hare M FAU - Hays, Thomas S AU - Hays TS FAU - Barbar, Elisar AU - Barbar E LA - eng GR - ES00210/ES/NIEHS NIH HHS/United States GR - GM44757/GM/NIGMS NIH HHS/United States GR - GM60969/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Carrier Proteins) RN - 0 (Drosophila Proteins) RN - 0 (Methylamines) RN - 0 (Peptide Fragments) RN - 0 (Protein Subunits) RN - EC 3.4.21.64 (Endopeptidase K) RN - EC 3.6.4.2 (Dyneins) RN - FLD0K1SJ1A (trimethyloxamine) SB - IM MH - Animals MH - Carrier Proteins/chemical synthesis/genetics/*metabolism MH - Circular Dichroism MH - Cytoplasm/chemistry/enzymology/genetics MH - Drosophila Proteins/chemical synthesis/genetics/*metabolism MH - Drosophila melanogaster MH - Dyneins/chemical synthesis/genetics/*metabolism MH - Endopeptidase K/metabolism MH - Hydrolysis MH - Methylamines/metabolism MH - Mutagenesis, Site-Directed MH - Peptide Fragments/chemistry/genetics/metabolism MH - Protein Binding/genetics MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary/genetics MH - Protein Subunits/chemical synthesis/genetics/*metabolism MH - Water-Electrolyte Balance EDAT- 2004/12/08 09:00 MHDA- 2005/01/27 09:00 CRDT- 2004/12/08 09:00 AID - 10.1021/bi048451+ [doi] PST - ppublish SO - Biochemistry. 2004 Dec 14;43(49):15595-603. PMID- 9346956 OWN - NLM STAT- MEDLINE DA - 19971209 DCOM- 19971209 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 272 IP - 44 DP - 1997 Oct 31 TI - Structural changes are associated with soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor complex formation. PG - 28036-41 AB - SNAP-25, syntaxin, and synaptobrevin play a key role in the regulated exocytosis of synaptic vesicles, but their mechanism of action is not understood. In vitro, the proteins spontaneously assemble into a ternary complex that can be dissociated by the ATPase N-ethylmaleimide-sensitive fusion protein and the cofactors alpha-, beta-, and gamma-SNAP. Since the structural changes associated with these reactions probably form the basis of membrane fusion, we have embarked on biophysical studies aimed at elucidating such changes in vitro using recombinant proteins. All proteins were purified in a monomeric form. Syntaxin showed significant alpha-helicity, whereas SNAP-25 and synaptobrevin exhibited characteristics of largely unstructured proteins. Formation of the ternary complex induced dramatic increases in alpha-helicity and in thermal stability. This suggests that structure is induced in SNAP-25 and synaptobrevin upon complex formation. In addition, the stoichiometry changed from 2:1 in the syntaxin-SNAP-25 complex to 1:1:1 in the ternary complex. We propose that the transition from largely unstructured monomers to a tightly packed, energetically favored ternary complex connecting two membranes is a key step in overcoming energy barriers for membrane fusion. FAU - Fasshauer, D AU - Fasshauer D AD - Howard Hughes Medical Institute, New Haven, Connecticut 06510, USA. FAU - Otto, H AU - Otto H FAU - Eliason, W K AU - Eliason WK FAU - Jahn, R AU - Jahn R FAU - Brunger, A T AU - Brunger AT LA - eng GR - 5 RO1 NS33709-02/NS/NINDS NIH HHS/United States GR - GM54160-01/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (BET1L protein, human) RN - 0 (Carrier Proteins) RN - 0 (Membrane Proteins) RN - 0 (Qc-SNARE Proteins) RN - 0 (Vesicular Transport Proteins) SB - IM MH - Carrier Proteins/chemistry/*metabolism MH - Chromatography, Gel MH - Circular Dichroism MH - Light MH - Membrane Proteins/chemistry/*metabolism MH - Molecular Weight MH - Protein Conformation MH - Qc-SNARE Proteins MH - Scattering, Radiation MH - *Vesicular Transport Proteins EDAT- 1997/11/05 MHDA- 1997/11/05 00:01 CRDT- 1997/11/05 00:00 PST - ppublish SO - J Biol Chem. 1997 Oct 31;272(44):28036-41. PMID- 15994900 OWN - NLM STAT- MEDLINE DA - 20050829 DCOM- 20060105 LR - 20140606 IS - 0006-3495 (Print) IS - 0006-3495 (Linking) VI - 89 IP - 3 DP - 2005 Sep TI - Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. PG - 2113-20 AB - An approach is introduced to characterize conformational ensembles of intrinsically unstructured peptides on the atomic level using two-dimensional solid-state NMR data and their combination with molecular dynamics simulations. For neurotensin, a peptide that binds with high affinity to a G-protein coupled receptor, this method permits the investigation of the changes in conformational preferences of a neurotransmitter transferred from a frozen aqueous solution via a lipid model phase to the receptor-bound form. The results speak against a conformational pre-organization of the ligand in detergents in which the receptor has been shown to be functional. Further extensions to the study of protein folding are possible. FAU - Heise, Henrike AU - Heise H AD - Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, 37077 Gottingen, Germany. FAU - Luca, Sorin AU - Luca S FAU - de Groot, Bert L AU - de Groot BL FAU - Grubmuller, Helmut AU - Grubmuller H FAU - Baldus, Marc AU - Baldus M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050701 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Detergents) RN - 0 (Ligands) RN - 0 (Lipids) RN - 0 (Peptides) RN - 0 (Proteins) RN - 059QF0KO0R (Water) RN - 39379-15-2 (Neurotensin) SB - IM MH - Detergents/pharmacology MH - Freezing MH - Humans MH - Ligands MH - Lipids/chemistry MH - Magnetic Resonance Spectroscopy/*methods MH - Models, Molecular MH - Molecular Conformation MH - Neurotensin/*chemistry MH - Peptides/chemistry MH - Protein Conformation MH - Protein Folding MH - Proteins/chemistry MH - Software MH - Water/chemistry PMC - PMC1366713 OID - NLM: PMC1366713 EDAT- 2005/07/05 09:00 MHDA- 2006/01/06 09:00 CRDT- 2005/07/05 09:00 PHST- 2005/07/01 [aheadofprint] AID - S0006-3495(05)72855-1 [pii] AID - 10.1529/biophysj.105.059964 [doi] PST - ppublish SO - Biophys J. 2005 Sep;89(3):2113-20. Epub 2005 Jul 1. PMID- 22270696 OWN - NLM STAT- MEDLINE DA - 20120828 DCOM- 20121219 IS - 1618-0860 (Electronic) IS - 0918-9440 (Linking) VI - 125 IP - 5 DP - 2012 Sep TI - The Zea mays glycine-rich RNA-binding protein MA16 is bound to a ribonucleotide(s) by a stable linkage. PG - 653-60 LID - 10.1007/s10265-012-0476-8 [doi] AB - Expression of the gene encoding the maize glycine-rich RNA-binding protein MA16 is developmentally regulated and it is involved in environmental stress responses. The MA16 protein shows a wide spectrum of RNA-binding activities. On the basis of in vivo labelling, where a [(3)(2)P]phosphate label was linked to the MA16 protein, Freire and Pages (Plant Mol Biol 29:797-807, 1995) suggested that the protein may be post-translationally modified by phosphorylation. However, further analysis showed that the [(3)(2)P]phosphate label was sensitive to different treatments, suggesting that modification distinct from protein phosphorylation might occur in the MA16 protein. Biochemical analysis revealed that this [(3)(2)P]phosphate labelling was resistant to phenol extraction and denaturing SDS-PAGE but sensitive to micrococcal nuclease, RNase A and RNase T1 treatments. The mobility of [(3)(5)S] labelled MA16 protein on SDS-PAGE did not significantly changed after the nuclease treatments suggesting that the [(3)(2)P]phosphate label associated to MA16 protein could be a ribonucleotide or a very short ribonucleotide chain. In addition, immunoprecipitation of labelled extracts showed that the ribonucleotide(s) linked to the MA16 protein was removed by phosphorolytic activity. This activity could be catalysed by a phosphate-dependent ribonuclease. The C-terminus of MA16 protein harbouring a glycine-rich domain was predicted to be an intrinsically disordered region. FAU - Freire, Miguel Angel AU - Freire MA AD - Facultad de Ciencias Exactas, Fisicas y Naturales, Instituto Multidisciplinario de Biologia Vegetal, CONICET, Universidad Nacional de Cordoba, Edificio de Investigaciones Biologicas y Tecnologicas, 5000 Cordoba, Argentina. mig.frei@yahoo.com.ar LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120121 PL - Japan TA - J Plant Res JT - Journal of plant research JID - 9887853 RN - 0 (Heat-Shock Proteins) RN - 0 (Plant Proteins) RN - 147257-76-9 (GRP protein, Zea mays) SB - IM MH - Heat-Shock Proteins/*chemistry/*metabolism MH - Plant Proteins/*chemistry/*metabolism MH - Protein Binding MH - Protein Conformation MH - Zea mays/*metabolism EDAT- 2012/01/25 06:00 MHDA- 2012/12/20 06:00 CRDT- 2012/01/25 06:00 PHST- 2011/09/30 [received] PHST- 2012/01/03 [accepted] PHST- 2012/01/21 [aheadofprint] AID - 10.1007/s10265-012-0476-8 [doi] PST - ppublish SO - J Plant Res. 2012 Sep;125(5):653-60. doi: 10.1007/s10265-012-0476-8. Epub 2012 Jan 21. PMID- 8310056 OWN - NLM STAT- MEDLINE DA - 19940311 DCOM- 19940311 LR - 20130919 IS - 0032-0889 (Print) IS - 0032-0889 (Linking) VI - 101 IP - 3 DP - 1993 Mar TI - The three-dimensional structure of canavalin from jack bean (Canavalia ensiformis). PG - 729-44 AB - The three-dimensional structure of the vicilin storage protein canavalin, from Canavalia ensiformis, has been determined in a hexagonal crystal by x-ray diffraction methods. The model has been refined at 2.6 A resolution to an R factor of 0.197 with acceptable geometry. Because of proteolysis, 58 of 419 amino acids of the canavalin polypeptide are not visible in the electron density map. The canavalin subunit is composed of two extremely similar structural domains that reflect the tandem duplication observed in the cDNA and in the amino acid sequence. Each domain consists of two elements, a compact, eight-stranded beta-barrel having the "Swiss roll" topology and an extended loop containing several short alpha-helices. The root mean square deviation between 84 pairs of corresponding C alpha atoms making up the strands of the two beta-barrels in a subunit is 0.78 A, and for 112 pairs of structurally equivalent C alpha atoms of the two domains the deviation is 1.37 A. The interface between domains arises from the apposition of broad hydrophobic surfaces formed by side chains originating from one side of the beta-barrels, supplemented by at least four salt bridges. The interfaces between subunits in the trimer are supplied by the extended loop elements. These interfaces are also composed primarily of hydrophobic residues supplemented by six salt bridges. The canavalin subunits have dimensions about 40 x 40 x 86 A, and the oligomer is a disk-shaped molecule about 88 A in diameter with a thickness of about 40 A. The distribution of domains lends a high degree of pseudo-32-point group symmetry to the molecule. There is a large channel of 18 A diameter, lined predominantly by hydrophilic and charged amino acids, running through the molecule along the 3-fold axis. The majority of residues conserved between domains and among vicilins occur at the interface between subunits but appear otherwise arbitrarily distributed within the subunit, although predominantly on its exterior. FAU - Ko, T P AU - Ko TP AD - Department of Biochemistry, University of California, Riverside 92521. FAU - Ng, J D AU - Ng JD FAU - McPherson, A AU - McPherson A LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Plant Physiol JT - Plant physiology JID - 0401224 RN - 0 (Plant Proteins) RN - 0 (canavalin protein, Canavalia ensiformis) SB - IM MH - Amino Acid Sequence MH - Computer Graphics MH - Fabaceae/*chemistry MH - Molecular Sequence Data MH - Plant Proteins/*chemistry MH - *Plants, Medicinal MH - Protein Conformation MH - Protein Structure, Secondary MH - X-Ray Diffraction PMC - PMC158685 OID - NLM: PMC158685 EDAT- 1993/03/01 MHDA- 1993/03/01 00:01 CRDT- 1993/03/01 00:00 AID - 101/3/729 [pii] PST - ppublish SO - Plant Physiol. 1993 Mar;101(3):729-44. PMID- 24722239 OWN - NLM STAT- MEDLINE DA - 20140411 DCOM- 20141208 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 10 IP - 4 DP - 2014 Apr TI - Biophysical properties of intrinsically disordered p130Cas substrate domain--implication in mechanosensing. PG - e1003532 LID - 10.1371/journal.pcbi.1003532 [doi] AB - Mechanical stretch-induced tyrosine phosphorylation in the proline-rich 306-residue substrate domain (CasSD) of p130Cas (or BCAR1) has eluded an experimentally validated structural understanding. Cellular p130Cas tyrosine phosphorylation is shown to function in areas without internal actomyosin contractility, sensing force at the leading edge of cell migration. Circular dichroism shows CasSD is intrinsically disordered with dominant polyproline type II conformations. Strongly conserved in placental mammals, the proline-rich sequence exhibits a pseudo-repeat unit with variation hotspots 2-9 residues before substrate tyrosine residues. Atomic-force microscopy pulling experiments show CasSD requires minimal extension force and exhibits infrequent, random regions of weak stability. Proteolysis, light scattering and ultracentrifugation results show that a monomeric intrinsically disordered form persists for CasSD in solution with an expanded hydrodynamic radius. All-atom 3D conformer sampling with the TraDES package yields ensembles in agreement with experiment when coil-biased sampling is used, matching the experimental radius of gyration. Increasing beta-sampling propensities increases the number of prolate conformers. Combining the results, we conclude that CasSD has no stable compact structure and is unlikely to efficiently autoinhibit phosphorylation. Taking into consideration the structural propensity of CasSD and the fact that it is known to bind to LIM domains, we propose a model of how CasSD and LIM domain family of transcription factor proteins may function together to regulate phosphorylation of CasSD and effect machanosensing. FAU - Hotta, Kinya AU - Hotta K AD - Department of Biological Sciences, National University of Singapore, Singapore; School of Biosciences, The University of Nottingham Malaysia Campus, Selangor, Malaysia. FAU - Ranganathan, Soumya AU - Ranganathan S AD - Department of Biological Sciences, National University of Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore. FAU - Liu, Ruchuan AU - Liu R AD - Mechanobiology Institute, National University of Singapore, Singapore; Department of Physics, National University of Singapore, Singapore. FAU - Wu, Fei AU - Wu F AD - Department of Physics, National University of Singapore, Singapore. FAU - Machiyama, Hiroaki AU - Machiyama H AD - Department of Biological Sciences, National University of Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore. FAU - Gao, Rong AU - Gao R AD - Department of Biological Sciences, National University of Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore. FAU - Hirata, Hiroaki AU - Hirata H AD - Mechanobiology Institute, National University of Singapore, Singapore. FAU - Soni, Neelesh AU - Soni N AD - Indian Institute of Science Education and Research, Pune, India. FAU - Ohe, Takashi AU - Ohe T AD - Locomotive Syndrome Research Institute, Nadogaya Hospital, Kashiwa, Japan. FAU - Hogue, Christopher W V AU - Hogue CW AD - Department of Biological Sciences, National University of Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore. FAU - Madhusudhan, M S AU - Madhusudhan MS AD - Department of Biological Sciences, National University of Singapore, Singapore; Indian Institute of Science Education and Research, Pune, India; Bioinformatics Institute, Singapore. FAU - Sawada, Yasuhiro AU - Sawada Y AD - Department of Biological Sciences, National University of Singapore, Singapore; Mechanobiology Institute, National University of Singapore, Singapore; Locomotive Syndrome Research Institute, Nadogaya Hospital, Kashiwa, Japan. LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140410 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (Crk-Associated Substrate Protein) RN - 0 (Intrinsically Disordered Proteins) SB - IM MH - Biophysics MH - Crk-Associated Substrate Protein/*chemistry MH - Intrinsically Disordered Proteins/*chemistry MH - *Mechanotransduction, Cellular MH - Microscopy, Atomic Force MH - Protein Unfolding PMC - PMC3983058 OID - NLM: PMC3983058 EDAT- 2014/04/12 06:00 MHDA- 2014/12/15 06:00 CRDT- 2014/04/12 06:00 PHST- 2014/04 [ecollection] PHST- 2012/10/10 [received] PHST- 2014/02/05 [accepted] PHST- 2014/04/10 [epublish] AID - 10.1371/journal.pcbi.1003532 [doi] AID - PCOMPBIOL-D-12-01625 [pii] PST - epublish SO - PLoS Comput Biol. 2014 Apr 10;10(4):e1003532. doi: 10.1371/journal.pcbi.1003532. eCollection 2014 Apr. PMID- 21784057 OWN - NLM STAT- MEDLINE DA - 20110817 DCOM- 20111014 LR - 20141022 IS - 1096-0384 (Electronic) IS - 0003-9861 (Linking) VI - 513 IP - 2 DP - 2011 Sep 15 TI - EGCG disaggregates amyloid-like fibrils formed by Plasmodium falciparum merozoite surface protein 2. PG - 153-7 LID - 10.1016/j.abb.2011.07.008 [doi] AB - Merozoite surface protein 2 (MSP2), one of the most abundant proteins on the surface of Plasmodium falciparum merozoites, is a promising malaria vaccine candidate. MSP2 is intrinsically unstructured and forms amyloid-like fibrils in solution. As this propensity of MSP2 to form fibrils in solution has the potential to impede its development as a vaccine candidate, finding an inhibitor that inhibits fibrillogenesis may enhance vaccine development. We have shown previously that EGCG inhibits the formation of MSP2 fibrils. Here we show that EGCG can alter the beta-sheet-like structure of the fibril and disaggregate pre-formed fibrils of MSP2 into soluble oligomers. The fibril remodelling effects of EGCG and other flavonoids were characterised using Thioflavin T fluorescence assays, electron microscopy and other biophysical methods. CI - Copyright (c) 2011 Elsevier Inc. All rights reserved. FAU - Chandrashekaran, Indu R AU - Chandrashekaran IR AD - Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia. FAU - Adda, Christopher G AU - Adda CG FAU - Macraild, Christopher A AU - Macraild CA FAU - Anders, Robin F AU - Anders RF FAU - Norton, Raymond S AU - Norton RS LA - eng GR - R01 AI059229-01A1/AI/NIAID NIH HHS/United States GR - R01AI59229/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20110719 PL - United States TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (Amyloid) RN - 0 (Antigens, Protozoan) RN - 0 (Flavonoids) RN - 0 (Malaria Vaccines) RN - 0 (Protozoan Proteins) RN - 0 (merozoite surface protein 2, Plasmodium) RN - 8R1V1STN48 (Catechin) RN - BQM438CTEL (epigallocatechin gallate) SB - IM MH - Amyloid/chemistry/drug effects/ultrastructure MH - Antigens, Protozoan/*chemistry/*drug effects/ultrastructure MH - Biophysical Phenomena MH - Catechin/*analogs & derivatives/pharmacology MH - Flavonoids/pharmacology MH - Malaria Vaccines/chemistry MH - Merozoites/chemistry/drug effects MH - Microscopy, Electron, Transmission MH - Plasmodium falciparum/*chemistry/*drug effects MH - Protein Multimerization/drug effects MH - Protein Structure, Secondary/drug effects MH - Protozoan Proteins/*chemistry/*drug effects/ultrastructure PMC - PMC3157577 MID - NIHMS313043 OID - NLM: NIHMS313043 OID - NLM: PMC3157577 EDAT- 2011/07/26 06:00 MHDA- 2011/10/15 06:00 CRDT- 2011/07/26 06:00 PHST- 2011/03/09 [received] PHST- 2011/06/21 [revised] PHST- 2011/07/07 [accepted] PHST- 2011/07/19 [aheadofprint] AID - S0003-9861(11)00260-8 [pii] AID - 10.1016/j.abb.2011.07.008 [doi] PST - ppublish SO - Arch Biochem Biophys. 2011 Sep 15;513(2):153-7. doi: 10.1016/j.abb.2011.07.008. Epub 2011 Jul 19. PMID- 19106612 OWN - NLM STAT- MEDLINE DA - 20090123 DCOM- 20090225 LR - 20121115 IS - 1551-4005 (Electronic) IS - 1551-4005 (Linking) VI - 8 IP - 1 DP - 2009 Jan 1 TI - Identification of two independent SUMO-interacting motifs in Daxx: evolutionary conservation from Drosophila to humans and their biochemical functions. PG - 76-87 AB - Daxx is essential for embryonic development and implicated in apoptosis and transcriptional regulation. It is found only in the animal kingdom and appears to arise first in insects. In the Drosophila genus, the Daxx orthologs are much larger than those in other species. Here we show that in addition to a conserved core of approximately 200 residues, Daxx possesses several conserved domains and two essentially invariable short SUMO-interacting motifs (SIMs), each located at one or the other terminus of the protein. Both can independently interact with SUMO. The Daxx I7/733K double mutant with one mutation in each of the two SIMs no longer interacts with SUMO. Daxx interacts with Ubc9 and this interaction strictly requires at least one SIM. Interestingly, the Ubc9 H20D mutation that abolishes non-covalent Ubc9-SUMO interaction also interrupts Daxx-Ubc9 interaction. Thus, SUMO serves as the intermediate for Daxx-Ubc9 interaction. Surprisingly, Daxx I7/733K double mutant could still colocalize with PML. Furthermore, wt Daxx also strongly colocalizes with PMLDeltaS mutant, in which all three sumoylation sites are mutated, whereas PMLDeltaS only weakly colocalizes with Daxx I7/733K mutant, suggesting that SIM-SUMO interaction is not essential for but enhances PML-Daxx interaction. Remarkably, Daxx strongly stimulates c-Jun-mediated transcription and both SIMs are required for this stimulation. PML also activates c-Jun, which requires all three sumoylation sites. Coexpression of Daxx and PML revealed that they independently regulate c-Jun, with Daxx exerting a dominant role. These results suggest that the conserved SIMs are involved in mediating protein-protein interactions that underlie Daxx's diverse cellular functions. FAU - Santiago, Aleixo AU - Santiago A AD - Department of Anatomy and Cell Biology, Shands Cancer Center, University of Florida College of Medicine, 1376 Mowry Road, Gainesville, FL 32611, USA. FAU - Godsey, Adam C AU - Godsey AC FAU - Hossain, Jamil AU - Hossain J FAU - Zhao, Lisa Y AU - Zhao LY FAU - Liao, Daiqing AU - Liao D LA - eng GR - CA 092236/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Cell Cycle JT - Cell cycle (Georgetown, Tex.) JID - 101137841 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (DAXX protein, human) RN - 0 (Daxx-like protein, Drosophila) RN - 0 (Hydroxamic Acids) RN - 0 (Mutant Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Proto-Oncogene Proteins c-jun) RN - 0 (Small Ubiquitin-Related Modifier Proteins) RN - 0 (Transcription Factors) RN - 0 (Tumor Suppressor Proteins) RN - 143220-95-5 (PML protein, human) RN - 3X2S926L3Z (trichostatin A) RN - EC 6.3.2.19 (Ubiquitin-Conjugating Enzymes) RN - EC 6.3.2.19 (ubiquitin-conjugating enzyme UBC9) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry/*metabolism MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - *Conserved Sequence MH - Drosophila melanogaster/*metabolism MH - *Evolution, Molecular MH - Humans MH - Hydroxamic Acids/pharmacology MH - Molecular Sequence Data MH - Mutant Proteins/metabolism MH - Nuclear Proteins/*chemistry/*metabolism MH - Protein Binding/drug effects MH - Protein Structure, Tertiary MH - Protein Transport/drug effects MH - Proto-Oncogene Proteins c-jun/metabolism MH - Sequence Homology, Amino Acid MH - Small Ubiquitin-Related Modifier Proteins/*metabolism MH - Transcription Factors/metabolism MH - Transcription, Genetic/drug effects MH - Tumor Suppressor Proteins/metabolism MH - Ubiquitin-Conjugating Enzymes/metabolism EDAT- 2008/12/25 09:00 MHDA- 2009/02/26 09:00 CRDT- 2008/12/25 09:00 AID - 7493 [pii] PST - ppublish SO - Cell Cycle. 2009 Jan 1;8(1):76-87. PMID- 7305393 OWN - NLM STAT- MEDLINE DA - 19820109 DCOM- 19820109 LR - 20131121 IS - 0003-9861 (Print) IS - 0003-9861 (Linking) VI - 211 IP - 2 DP - 1981 Oct 15 TI - Secondary structure of bovine alpha s1- and beta-casein in solution. PG - 689-96 FAU - Creamer, L K AU - Creamer LK FAU - Richardson, T AU - Richardson T FAU - Parry, D A AU - Parry DA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (Caseins) RN - 0 (Guanidines) RN - 0 (Solutions) RN - 8W8T17847W (Urea) RN - EC 3.4.- (Carboxypeptidases) RN - EC 3.4.17.1 (Carboxypeptidases A) RN - M4I0D6VV5M (Calcium Chloride) SB - IM MH - Animals MH - Calcium Chloride/pharmacology MH - Carboxypeptidases/pharmacology MH - Carboxypeptidases A MH - *Caseins MH - Cattle MH - Circular Dichroism MH - Female MH - Guanidines/pharmacology MH - Hydrogen-Ion Concentration MH - Protein Conformation/drug effects MH - Solutions MH - Urea/pharmacology EDAT- 1981/10/15 MHDA- 1981/10/15 00:01 CRDT- 1981/10/15 00:00 PST - ppublish SO - Arch Biochem Biophys. 1981 Oct 15;211(2):689-96. PMID- 20157636 OWN - NLM STAT- Publisher DA - 20111130 IS - 1349-0079 (Print) IS - 1349-0079 (Linking) VI - 51 IP - 3 DP - 2009 Sep 10 TI - Dentinogenesis and Dentin Sialophosphoprotein (DSPP). PG - 134 AB - Dentin sialophosphoprotein (DSPP) is critical for proper mineralization of tooth dentin, and understanding its structure and function should yield important insights into how dentin biomineralization is controlled. During the recent six years, I have focused on characterizing DSPP-derived proteins isolated from developing porcine teeth. Porcine DSPP is expressed and secreted by odontoblasts and is processed by BMP-1, MMP-20 and MMP-2 into three main parts: dentin sialoprotein (DSP), dentin glycoprotein (DGP), and dentin phosphoprotein (DPP). We have learned that DSP is a proteoglycan that forms covalent dimers, DGP is a phosphorylated glycoprotein, and DPP is a highly phosphorylated intrinsically disordered protein that shows extensive length polymorphisms due to the genetic heterogeneity of its coding region. FAU - Yamakoshi, Yasuo AU - Yamakoshi Y AD - Department of Biologic and Materials Sciences, University of Michigan Dental Research Lab, 1210 Eisenhower Place, Ann Arbor, MI 48108, Tel: 734-975-9358 (Office); Tel: 734-975-9326 (Lab); 734-975-9329 (Fax), yamasan@umich.edu. LA - ENG GR - R01 DE011301/DE/NIDCR NIH HHS/United States GR - R01 DE011301-10/DE/NIDCR NIH HHS/United States GR - R01 DE015846/DE/NIDCR NIH HHS/United States GR - R01 DE015846-05/DE/NIDCR NIH HHS/United States GR - R01 DE016276/DE/NIDCR NIH HHS/United States GR - R01 DE016276-04/DE/NIDCR NIH HHS/United States GR - R01 DE016376/DE/NIDCR NIH HHS/United States GR - R01 DE016376-05/DE/NIDCR NIH HHS/United States GR - R01 DE018020/DE/NIDCR NIH HHS/United States GR - R01 DE018020-03/DE/NIDCR NIH HHS/United States PT - JOURNAL ARTICLE TA - J Oral Biosci JT - Journal of oral biosciences / JAOB, Japanese Association for Oral Biology JID - 101226721 PMC - PMC2821091 MID - NIHMS169027 EDAT- 2010/02/17 06:00 MHDA- 2010/02/17 06:00 CRDT- 2010/02/17 06:00 AID - 10.2330/joralbiosci.51.134 [doi] PST - ppublish SO - J Oral Biosci. 2009 Sep 10;51(3):134. PMID- 12842879 OWN - NLM STAT- MEDLINE DA - 20030915 DCOM- 20031120 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 38 DP - 2003 Sep 19 TI - Solution structure of the recombinant penaeidin-3, a shrimp antimicrobial peptide. PG - 36859-67 AB - Penaeidins are a family of antimicrobial peptides of 47-63 residues isolated from several species of shrimp. These peptides display a proline-rich domain (N-terminal part) and a cysteine-rich domain (C-terminal part) stabilized by three conserved disulfide bonds whose arrangement has not yet been characterized. The recombinant penaeidin-3a of Litopenaeus vannamei (63 residues) and its [T8A]-Pen-3a analogue were produced in Saccharomyces cerevisiae and showed similar antimicrobial activity. The solution structure of the [T8A]-Pen-3a analogue was determined by using two-dimensional 1H NMR and simulated annealing calculations. The proline-rich domain, spanning residues 1-28 was found to be unconstrained. In contrast, the cysteine-rich domain, spanning residues 29-58, displays a well defined structure, which consists of an amphipathic helix (41-50) linked to the upstream and the downstream coils by two disulfide bonds (Cys32-Cys47 and Cys48-Cys55). These two coils are in turn linked together by the third disulfide bond (Cys36-Cys54). Such a disulfide bond packing, which is in agreement with the analysis of trypsin digests by ESI-MS, contributes to the highly hydrophobic core. Side chains of Arg45 and Arg50, which belong to the helix, and side chains of Arg37 and Arg53, which belong to the upstream and the downstream coils, are located in two opposite parts of this globular and compact structure. The environment of these positively charged residues, either by hydrophobic clusters at the surface of the cysteine-rich domain or by sequential hydrophobic residues in the unconstrained proline-rich domain, gives rise to the amphipathic character required for antimicrobial peptides. We hypothesize that the antimicrobial activity of penaeidins can be explained by a cooperative effect between the proline-rich and cysteine-rich features simultaneously present in their sequences. FAU - Yang, Yinshan AU - Yang Y AD - Centre de Biochimie Structurale, CNRS UMR 5048, INSERM U414, Universite Montpellier 1, Faculte de Pharmacie, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France. FAU - Poncet, Joel AU - Poncet J FAU - Garnier, Julien AU - Garnier J FAU - Zatylny, Celine AU - Zatylny C FAU - Bachere, Evelyne AU - Bachere E FAU - Aumelas, Andre AU - Aumelas A LA - eng SI - PDB/1UEO PT - Journal Article DEP - 20030703 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Anti-Infective Agents) RN - 0 (Disulfides) RN - 0 (Peptides) RN - 0 (Proteins) RN - 0 (Recombinant Proteins) RN - 0 (penaeidin 3) RN - 94ZLA3W45F (Arginine) RN - 9DLQ4CIU6V (Proline) RN - EC 3.4.21.4 (Trypsin) RN - K848JZ4886 (Cysteine) SB - IM MH - Amino Acid Sequence MH - Animals MH - Anti-Infective Agents/*chemistry/*pharmacology MH - Arginine/chemistry MH - Cysteine/chemistry MH - Disulfides/chemistry MH - Magnetic Resonance Spectroscopy MH - Mass Spectrometry MH - Models, Molecular MH - Molecular Sequence Data MH - Penaeidae/metabolism MH - Peptides/chemistry MH - Proline/chemistry MH - Protein Conformation MH - Protein Structure, Tertiary MH - Proteins/*chemistry MH - Recombinant Proteins/*chemistry/metabolism MH - Saccharomyces cerevisiae/metabolism MH - Sequence Homology, Amino Acid MH - Trypsin/chemistry/pharmacology EDAT- 2003/07/05 05:00 MHDA- 2003/12/03 05:00 CRDT- 2003/07/05 05:00 PHST- 2003/07/03 [aheadofprint] AID - 10.1074/jbc.M305450200 [doi] AID - M305450200 [pii] PST - ppublish SO - J Biol Chem. 2003 Sep 19;278(38):36859-67. Epub 2003 Jul 3. PMID- 21524106 OWN - NLM STAT- MEDLINE DA - 20110518 DCOM- 20110824 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 133 IP - 20 DP - 2011 May 25 TI - Folding of a salivary intrinsically disordered protein upon binding to tannins. PG - 7847-52 LID - 10.1021/ja200534f [doi] AB - We used ion mobility spectrometry to explore conformational adaptability of intrinsically disordered proteins bound to their targets in complex mixtures. We investigated the interactions between a human salivary proline-rich protein IB5 and a model of wine and tea tannin: epigallocatechin gallate (EgCG). Collisional cross sections of naked IB5 and IB5 complexed with N = 1-15 tannins were recorded. The data demonstrate that IB5 undergoes an unfolded to folded structural transition upon binding with EgCG. FAU - Canon, Francis AU - Canon F AD - INRA, UMR1083 Science Pour l'Oenologie, Polyphenol Interaction, Bat 28, 2 place Viala F-34060 Montpellier, France. FAU - Ballivian, Renaud AU - Ballivian R FAU - Chirot, Fabien AU - Chirot F FAU - Antoine, Rodolphe AU - Antoine R FAU - Sarni-Manchado, Pascale AU - Sarni-Manchado P FAU - Lemoine, Jerome AU - Lemoine J FAU - Dugourd, Philippe AU - Dugourd P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110427 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Salivary Proteins and Peptides) RN - 0 (Tannins) SB - IM MH - Circular Dichroism MH - Mass Spectrometry/methods MH - Protein Binding MH - Protein Folding MH - Salivary Proteins and Peptides/*metabolism MH - Tannins/*metabolism EDAT- 2011/04/29 06:00 MHDA- 2011/08/25 06:00 CRDT- 2011/04/29 06:00 PHST- 2011/04/27 [aheadofprint] AID - 10.1021/ja200534f [doi] PST - ppublish SO - J Am Chem Soc. 2011 May 25;133(20):7847-52. doi: 10.1021/ja200534f. Epub 2011 Apr 27. PMID- 24853747 OWN - NLM STAT- MEDLINE DA - 20140523 DCOM- 20141231 LR - 20150601 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 106 IP - 10 DP - 2014 May 20 TI - Characterization of the connexin45 carboxyl-terminal domain structure and interactions with molecular partners. PG - 2184-95 LID - 10.1016/j.bpj.2014.03.045 [doi] LID - S0006-3495(14)00381-6 [pii] AB - Mechanisms underlying the initiation and persistence of lethal cardiac rhythms are of significant clinical and scientific interests. Gap junctions are principally involved in forming the electrical connections between myocytes, and changes in distribution, density, and properties are consistent characteristics in arrhythmic heart disease. Therefore, understanding the structure and function of gap junctions during normal and abnormal impulse propagation are essential in the control of arrhythmias. For example, Cx45 is predominately expressed in the specialized myocytes of the impulse generation and conduction system. In both ventricular and atrial human working myocytes, Cx45 is present in very low quantities. However, a reduction in Cx43 coupled with an increased Cx45 protein levels within the ventricles have been observed after myocardial infarction and end-stage heart failure. Cx45 may influence electrical and/or metabolic coupling as a result of pathophysiological overexpression. Our goal was to identify mechanisms that could cause cellular coupling to be different between the cardiac connexins. Based upon the conserved transmembrane and extracellular loop segments, our focus was on identifying features within the divergent cytoplasmic portions. Here, we biophysically characterize the carboxyl-terminal domain of Cx45 (Cx45CT). Purification revealed the possibility of oligomeric species, which was confirmed by analytical ultracentrifugation experiments. Sedimentation equilibrium and circular dichroism studies of different Cx45CT constructs identified one region of alpha-helical structure (A333-N361) that mediates CT dimerization through hydrophobic contacts. Interestingly, the binding affinity of Cx45CT dimerization is 1000-fold stronger than Cx43CT dimerization. Cx45CT resonance assignments were also used to identify the binding sites and affinities of molecular partners involved in the Cx45 regulation; although none disrupted dimerization, many of these proteins interacted within one intrinsically disordered region (P278-P285). This domain has similarities with other cardiac connexins, and we propose they constitute a master regulatory domain, which contains overlapping molecular partner binding, cis-trans proline isomerization, and phosphorylation sites. CI - Copyright (c) 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Kopanic, Jennifer L AU - Kopanic JL AD - Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. FAU - Al-mugotir, Mona H AU - Al-mugotir MH AD - Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. FAU - Kieken, Fabien AU - Kieken F AD - Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. FAU - Zach, Sydney AU - Zach S AD - Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. FAU - Trease, Andrew J AU - Trease AJ AD - Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. FAU - Sorgen, Paul L AU - Sorgen PL AD - Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. Electronic address: psorgen@unmc.edu. LA - eng GR - 5P0RR016469/RR/NCRR NIH HHS/United States GR - 8P20GM103427/GM/NIGMS NIH HHS/United States GR - GM072631/GM/NIGMS NIH HHS/United States GR - P30 CA036727/CA/NCI NIH HHS/United States GR - P30CA036727/CA/NCI NIH HHS/United States GR - R01 GM072631/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Connexin 43) RN - 0 (Connexins) RN - 0 (connexin 40) RN - 0 (connexin 45) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cell Membrane/metabolism MH - Connexin 43/metabolism MH - Connexins/*chemistry/*metabolism MH - Gap Junctions/metabolism MH - Humans MH - Mice MH - Molecular Sequence Data MH - Protein Binding MH - Protein Multimerization MH - Protein Structure, Tertiary PMC - PMC4052358 OID - NLM: PMC4052358 EDAT- 2014/05/24 06:00 MHDA- 2015/01/01 06:00 CRDT- 2014/05/24 06:00 PHST- 2013/10/01 [received] PHST- 2014/03/19 [revised] PHST- 2014/03/31 [accepted] AID - S0006-3495(14)00381-6 [pii] AID - 10.1016/j.bpj.2014.03.045 [doi] PST - ppublish SO - Biophys J. 2014 May 20;106(10):2184-95. doi: 10.1016/j.bpj.2014.03.045. PMID- 16427310 OWN - NLM STAT- MEDLINE DA - 20060523 DCOM- 20060921 IS - 1046-5928 (Print) IS - 1046-5928 (Linking) VI - 47 IP - 2 DP - 2006 Jun TI - Gene synthesis, expression, purification, and characterization of human Jagged-1 intracellular region. PG - 398-404 AB - Notch signaling plays a key role in cell differentiation and is very well conserved from Drosophila to humans. Ligands of Notch receptors are type I, membrane spanning proteins composed of a large extracellular region and a 100-150 residue cytoplasmic tail. We report here, for the first time, the expression, purification, and characterization of the intracellular region of a Notch ligand. Starting from a set of synthetic oligonucleotides, we assembled a synthetic gene optimized for Escherichia coli codon usage and encoding the cytoplasmic region of human Jagged-1 (residues 1094-1218). The protein containing a N-terminal His(6)-tag was over-expressed in E. coli, and purified by affinity and reversed phase chromatography. After cleavage of the His(6)-tag by a dipeptidyl aminopeptidase, the protein was purified to homogeneity and characterized by spectroscopic techniques. Far-UV circular dichroism, fluorescence emission spectra, fluorescence anisotropy measurements, and (1)H nuclear magnetic resonance spectra, taken together, suggest that the cytoplasmic tail of human Jagged-1 behaves as an intrinsically unstructured domain in solution. This result was confirmed by the high susceptibility of the recombinant protein to proteolytic cleavage. The significance of this finding is discussed in relation to the recently proposed role of the intracellular region of Notch ligands in bi-directional signaling. FAU - Popovic, Matija AU - Popovic M AD - International Centre for Genetic Engineering and Biotechnology (ICGEB), Protein Structure and Bioinformatics Group, AREA Science Park, Trieste, Italy. FAU - Coglievina, Maristella AU - Coglievina M FAU - Guarnaccia, Corrado AU - Guarnaccia C FAU - Verdone, Giuliana AU - Verdone G FAU - Esposito, Gennaro AU - Esposito G FAU - Pintar, Alessandro AU - Pintar A FAU - Pongor, Sandor AU - Pongor S LA - eng PT - Journal Article DEP - 20051228 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (Calcium-Binding Proteins) RN - 0 (Intercellular Signaling Peptides and Proteins) RN - 0 (Membrane Proteins) RN - 0 (Receptors, Notch) RN - 0 (Recombinant Proteins) RN - 134324-36-0 (Serrate proteins) SB - IM MH - Calcium-Binding Proteins/*biosynthesis/chemistry/genetics/*isolation & purification MH - Chromatography, Liquid MH - Circular Dichroism MH - Escherichia coli/genetics MH - Gene Expression/genetics MH - *Genes, Synthetic/genetics MH - Humans MH - Intercellular Signaling Peptides and Proteins/*biosynthesis/chemistry/genetics/*isolation & purification MH - Membrane Proteins/*biosynthesis/chemistry/genetics/*isolation & purification MH - Protein Binding/genetics MH - Protein Structure, Tertiary/genetics MH - Receptors, Notch/genetics MH - Recombinant Proteins/*biosynthesis/chemistry/genetics/*isolation & purification EDAT- 2006/01/24 09:00 MHDA- 2006/09/22 09:00 CRDT- 2006/01/24 09:00 PHST- 2005/09/26 [received] PHST- 2005/11/25 [revised] PHST- 2005/11/30 [accepted] PHST- 2005/12/28 [aheadofprint] AID - S1046-5928(05)00425-0 [pii] AID - 10.1016/j.pep.2005.11.027 [doi] PST - ppublish SO - Protein Expr Purif. 2006 Jun;47(2):398-404. Epub 2005 Dec 28. PMID- 10971589 OWN - NLM STAT- MEDLINE DA - 20001016 DCOM- 20001107 LR - 20131121 IS - 0014-2956 (Print) IS - 0014-2956 (Linking) VI - 267 IP - 18 DP - 2000 Sep TI - Changes to the length of the flexible linker region of the Rieske protein impair the interaction of ubiquinol with the cytochrome bc1 complex. PG - 5777-82 AB - Crystal structures of the cytochrome bc1 complex indicate that the catalytic domain of the Rieske iron-sulfur protein, which carries the [2Fe-2S] cluster, is connected to a transmembrane anchor by a flexible linker region. This flexible linker allows the catalytic domain to move between two positions, proximal to cytochrome b and cytochrome c1. Addition of an alanine residue to the flexible linker region of the Rieske protein lowers the ubiquinol-cytochrome c reductase activity of the mitochondrial membranes by one half and causes the apparent Km for ubiquinol to decrease from 9.3 to 2.6 microM. Addition of two alanine residues lowers the activity by 90% and the apparent Km decreases to 1.9 microM. Deletion of an alanine residue lowers the activity by approximately 40% and the apparent Km decreases to 5.0 microM. Addition or deletion of an alanine residue also causes a pronounced decrease in efficacy of inhibition of ubiquinol-cytochrome c reductase activity by stigmatellin, which binds analogous to reaction intermediates of ubiquinol oxidation. These results indicate that the length of the flexible linker region is critical for interaction of ubiquinol with the bc1 complex, consistent with electron transfer mechanisms in which ubiquinol must simultaneously interact with the iron-sulfur protein and cytochrome b. FAU - Nett, J H AU - Nett JH AD - Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755, USA. FAU - Hunte, C AU - Hunte C FAU - Trumpower, B L AU - Trumpower BL LA - eng GR - GM 20379/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - GERMANY TA - Eur J Biochem JT - European journal of biochemistry / FEBS JID - 0107600 RN - 0 (Iron-Sulfur Proteins) RN - 0 (Polyenes) RN - 0 (Rieske iron-sulfur protein) RN - 11118-72-2 (antimycin) RN - 1339-63-5 (Ubiquinone) RN - 30KYC7MIAI (Aspartic Acid) RN - 56275-39-9 (ubiquinol) RN - 642-15-9 (Antimycin A) RN - 91682-96-1 (stigmatellin) RN - EC 1.10.2.2 (Electron Transport Complex III) RN - EC 1.6.99.3 (NADH Dehydrogenase) RN - OF5P57N2ZX (Alanine) SB - IM MH - Alanine/chemistry/genetics MH - Amino Acid Sequence MH - Antimycin A/*analogs & derivatives/chemistry MH - Aspartic Acid/chemistry/genetics MH - Blotting, Western MH - Catalysis MH - Crystallography, X-Ray MH - Electron Transport Complex III/*chemistry/genetics/metabolism MH - Electrons MH - Intracellular Membranes/chemistry MH - Iron-Sulfur Proteins/*chemistry/genetics/metabolism MH - Kinetics MH - Mitochondria/chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - NADH Dehydrogenase/metabolism MH - Polyenes/chemistry/metabolism MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/chemistry MH - Sequence Homology, Amino Acid MH - Ubiquinone/*analogs & derivatives/*chemistry/genetics/metabolism EDAT- 2000/09/06 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/09/06 11:00 AID - ejb1650 [pii] PST - ppublish SO - Eur J Biochem. 2000 Sep;267(18):5777-82. PMID- 18793646 OWN - NLM STAT- MEDLINE DA - 20081020 DCOM- 20081106 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 383 IP - 3 DP - 2008 Nov 14 TI - Crystal structure of Mycobacterium tuberculosis YefM antitoxin reveals that it is not an intrinsically unstructured protein. PG - 482-93 LID - 10.1016/j.jmb.2008.08.067 [doi] AB - Toxin-antitoxin modules are present on chromosomes of almost all free-living prokaryotes. Some are implicated to act as stress-responsive elements, among their many functional roles. The YefM-YoeB toxin-antitoxin system is present in many bacterial species, where YefM belongs to the Phd family antidote of phage P1, whereas YoeB is a homolog of the RelE toxin of the RelBE system, rather than the Doc system of phage P1. YoeB, a ribonuclease, is believed to be conformationally stable, whereas YefM has been proposed to be a member of intrinsically disordered proteins. The ribonucleolytic activity of YoeB is neutralized by YefM upon formation of the YefM-YoeB complex. We report here the crystal structure of Mycobacterium tuberculosis YefM from two crystal isoforms. Our crystallographic and biophysical studies reveal that YefM is not an intrinsically unfolded protein and instead forms a well-defined structure with significant secondary and tertiary structure conformations. The residues involved in core formation of the folded structure are evolutionarily conserved among many bacterial species, supporting our observation. The C-terminal end of its polypeptide is highly pliable, which adopts different conformations in different monomers. Since at the physiological level YefM controls the activity of YoeB through intricate protein-protein interactions, the conformational heterogeneity in YefM revealed by our structure suggests that these might act a master switch in controlling YoeB activity. FAU - Kumar, Pramod AU - Kumar P AD - Laboratory of Structural Biology, Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad 500 076, India. FAU - Issac, Biju AU - Issac B FAU - Dodson, Eleanor J AU - Dodson EJ FAU - Turkenburg, Johan P AU - Turkenburg JP FAU - Mande, Shekhar C AU - Mande SC LA - eng SI - PDB/3CTO SI - PDB/3D55 GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080904 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Antitoxins) RN - 0 (Bacterial Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Multiprotein Complexes) RN - 0 (Protein Isoforms) RN - 0 (YefM protein, E coli) SB - IM MH - Amino Acid Sequence MH - Antitoxins/chemistry/genetics MH - Bacterial Proteins/*chemistry/genetics MH - Circular Dichroism MH - Crystallography, X-Ray MH - Dimerization MH - *Escherichia coli Proteins/chemistry/genetics MH - Hydrogen-Ion Concentration MH - Models, Molecular MH - Molecular Sequence Data MH - Multiprotein Complexes/chemistry/genetics MH - Mycobacterium tuberculosis/chemistry MH - Protein Isoforms/*chemistry/genetics MH - *Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Sequence Alignment EDAT- 2008/09/17 09:00 MHDA- 2008/11/07 09:00 CRDT- 2008/09/17 09:00 PHST- 2008/05/21 [received] PHST- 2008/08/17 [revised] PHST- 2008/08/21 [accepted] PHST- 2008/09/04 [aheadofprint] AID - S0022-2836(08)01085-1 [pii] AID - 10.1016/j.jmb.2008.08.067 [doi] PST - ppublish SO - J Mol Biol. 2008 Nov 14;383(3):482-93. doi: 10.1016/j.jmb.2008.08.067. Epub 2008 Sep 4. PMID- 12832790 OWN - NLM STAT- MEDLINE DA - 20030630 DCOM- 20040325 LR - 20070724 IS - 0907-4449 (Print) IS - 0907-4449 (Linking) VI - 59 IP - Pt 7 DP - 2003 Jul TI - Crystallization and preliminary X-ray data investigation of the bacterial enterocin A immunity protein at 1.65 A resolution. PG - 1291-3 AB - Crystals of the bacterial enterocin A immunity protein have been prepared by the hanging-drop vapour-diffusion technique at 293 K. The crystals diffract to better than 1.7 A resolution and X-ray diffraction data to 1.65 A have been collected at 110 K using synchrotron radiation. The enterocin A immunity protein crystals belong to the monoclinic crystal system, with unit-cell parameters a = 116.32, b = 42.35, c = 66.17 A, beta = 111.3 degrees. The symmetry and systematic absences in the diffraction pattern are consistent with space group C2. The presence of two molecules in the asymmetric unit with a molecular weight of approximately 12.2 kDa gives a crystal volume per protein mass (V(M)) of approximately 3.1 A(3) Da(-1) and a solvent content of approximately 60% by volume. FAU - Dalhus, Bjorn AU - Dalhus B AD - Department of Chemistry, University of Oslo, PO Box 1033, Blindern, N-0315 Oslo, Norway. bjornda@kjemi.uio.no FAU - Johnsen, Line AU - Johnsen L FAU - Nissen-Meyer, Jon AU - Nissen-Meyer J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030627 PL - Denmark TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (Bacteriocins) RN - 0 (enterocin A) SB - IM MH - Bacteriocins/*chemistry/genetics/isolation & purification MH - Circular Dichroism MH - Cloning, Molecular MH - Crystallization MH - Protein Structure, Secondary MH - X-Ray Diffraction EDAT- 2003/07/02 05:00 MHDA- 2004/03/26 05:00 CRDT- 2003/07/02 05:00 PHST- 2003/03/21 [received] PHST- 2003/05/06 [accepted] PHST- 2003/06/27 [epublish] AID - S0907444903009879 [pii] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2003 Jul;59(Pt 7):1291-3. Epub 2003 Jun 27. PMID- 21549498 OWN - NLM STAT- MEDLINE DA - 20110531 DCOM- 20110916 LR - 20131121 IS - 1873-4200 (Electronic) IS - 0301-4622 (Linking) VI - 157 IP - 1-3 DP - 2011 Aug TI - Conformational heterogeneity and dynamics in a betagamma-crystallin from Hahella chejuensis. PG - 7-15 LID - 10.1016/j.bpc.2011.04.001 [doi] AB - Most of the betagamma-crystallins are structural proteins with high intrinsic stability, which gets enhanced by Ca(2+)-binding in microbial members. Functions of most of these proteins are yet to be known. However, a few of them were reported to be involved in Ca(2+)-dependent and stress-related functions. Hahellin, a microbial homolog, is a natively unfolded protein that acquires a well-folded structure upon Ca(2+) binding. Although the structure of betagamma-crystallin domains is well understood, the dynamical features are yet to be explored. We have investigated for the first time the equilibrium dynamics, conformational heterogeneity and associated low-lying free-energy states of hahellin in its Ca(2+)-bound form using NMR spectroscopy to understand the dynamics of a betagamma-crystallin domain. Hahellin shows large conformational heterogeneity with nearly 40% of the residues, some of which are part of Ca(2+)-binding loops, accessing alternative states. Further, out of the two Greek key motifs, which together constitute the betagamma-crystallin domain, the second Greek key motif is floppy as compared to its relatively rigid counterpart. Taken together, we believe that these characteristics might be of importance to understand the stability and functions of betagamma-crystallin domains. CI - Copyright (c) 2011 Elsevier B.V. All rights reserved. FAU - Srivastava, Atul K AU - Srivastava AK AD - Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India. atulks@tifr.res.in FAU - Chary, Kandala V R AU - Chary KV LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110409 PL - Netherlands TA - Biophys Chem JT - Biophysical chemistry JID - 0403171 RN - 0 (Crystallins) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Calcium/chemistry/metabolism MH - Calorimetry, Differential Scanning MH - Crystallins/*chemistry/isolation & purification/metabolism MH - Gammaproteobacteria/*chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Protein Folding MH - Temperature MH - Thermodynamics EDAT- 2011/05/10 06:00 MHDA- 2011/09/17 06:00 CRDT- 2011/05/10 06:00 PHST- 2011/02/14 [received] PHST- 2011/04/03 [revised] PHST- 2011/04/03 [accepted] PHST- 2011/04/09 [aheadofprint] AID - S0301-4622(11)00070-6 [pii] AID - 10.1016/j.bpc.2011.04.001 [doi] PST - ppublish SO - Biophys Chem. 2011 Aug;157(1-3):7-15. doi: 10.1016/j.bpc.2011.04.001. Epub 2011 Apr 9. PMID- 15247256 OWN - NLM STAT- MEDLINE DA - 20040906 DCOM- 20041019 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 37 DP - 2004 Sep 10 TI - NMR solution structure of Ole e 6, a major allergen from olive tree pollen. PG - 39035-41 AB - Ole e 6 is a pollen protein from the olive tree (Olea europaea) that exhibits allergenic activity with a high prevalence among olive-allergic individuals. The three-dimensional structure of Ole e 6 has been determined in solution by NMR methods. This is the first experimentally determined structure of an olive tree pollen allergen. The structure of this 50-residue protein is based on 486 upper limit distance constraints derived from nuclear Overhauser effects and 24 torsion angle restraints. The global fold of Ole e 6 consists of two nearly antiparallel alpha-helices, spanning residues 3-19 and 23-33, that are connected by a short loop and followed by a long, unstructured C-terminal tail. Viewed edge-on, the structured N terminus has a dumbbell-like shape with the two helices on the outside and with the hydrophobic core, mainly composed of 3 aromatic and 6 cysteine residues, on the inside. All the aromatic rings lie on top of and pack against the three disulfide bonds. The lack of thermal unfolding, even at 85 degrees C, indicates a high conformational stability. Based on the analysis of the molecular surface, we propose five plausible epitopes for IgE recognition. The results presented here provide the structural foundation for future experiments to verify the antigenicity of the proposed epitopes, as well as to design novel hypoallergenic forms of the protein suitable for diagnosis and treatment of type-I allergies. In addition, three-dimensional structure features of Ole e 6 are discussed to provide a basis for future functional studies. FAU - Trevino, Miguel Angel AU - Trevino MA AD - Departamento de Espectroscopia y Estructura Molecular, Instituto de Quimica Fisica "Rocasolano," Consejo Superior de Investigaciones Cientificas, Serrano 119, 28006 Madrid, Spain. FAU - Garcia-Mayoral, Maria Flor AU - Garcia-Mayoral MF FAU - Barral, Patricia AU - Barral P FAU - Villalba, Mayte AU - Villalba M FAU - Santoro, Jorge AU - Santoro J FAU - Rico, Manuel AU - Rico M FAU - Rodriguez, Rosalia AU - Rodriguez R FAU - Bruix, Marta AU - Bruix M LA - eng SI - PDB/1SS3 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20040707 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Allergens) RN - 0 (DNA, Complementary) RN - 0 (Epitopes) RN - 0 (OLE6 protein, Olea europaea) RN - 0 (Plant Proteins) RN - 37341-29-0 (Immunoglobulin E) SB - IM MH - Allergens/chemistry MH - Circular Dichroism MH - Crystallography, X-Ray MH - DNA, Complementary/metabolism MH - Epitopes/chemistry MH - Immunoglobulin E/chemistry MH - Magnetic Resonance Spectroscopy/*methods MH - Models, Molecular MH - Olea/*metabolism MH - Plant Proteins/*chemistry MH - Pollen/*chemistry MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Stereoisomerism MH - Temperature EDAT- 2004/07/13 05:00 MHDA- 2004/10/20 09:00 CRDT- 2004/07/13 05:00 PHST- 2004/07/07 [aheadofprint] AID - 10.1074/jbc.M406045200 [doi] AID - M406045200 [pii] PST - ppublish SO - J Biol Chem. 2004 Sep 10;279(37):39035-41. Epub 2004 Jul 7. PMID- 14622018 OWN - NLM STAT- MEDLINE DA - 20031118 DCOM- 20040106 LR - 20120222 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 42 IP - 46 DP - 2003 Nov 25 TI - Structural characterization by NMR of the natively unfolded extracellular domain of beta-dystroglycan: toward the identification of the binding epitope for alpha-dystroglycan. PG - 13717-24 AB - Dystroglycan (DG) is an adhesion molecule playing a crucial role for tissue stability during both early embriogenesis and adulthood and is composed by two tightly interacting subunits: alpha-DG, membrane-associated and highly glycosylated, and the transmembrane beta-DG. Recently, by solid-phase binding assays and NMR experiments, we have shown that the C-terminal domain of alpha-DG interacts with a recombinant extracellular fragment of beta-DG (positions 654-750) independently from glycosylation and that the linear binding epitope is located between residues 550 and 565 of alpha-DG. In order to elucidate which moieties of beta-DG are specifically involved in the complex with alpha-DG, the ectodomain has been recombinantly expressed and purified in a labeled ((13)C,(15)N) form and studied by multidimensional NMR. Although it represents a natively unfolded protein domain, we obtained an almost complete backbone assignment. Chemical shift index, (1)H-(15)N heteronuclear single-quantum coherence and nuclear Overhauser effect (HSQC-NOESY) spectra and (3)J(HN,H)(alpha) coupling constant values confirm that this protein is highly disordered, but (1)H-(15)N steady-state NOE experiments indicate that the protein presents two regions of different mobility. The first one, between residues 659 and 722, is characterized by a limited degree of mobility, whereas the C-terminal portion, containing about 30 amino acids, is highly flexible. The binding of beta-DG(654-750) to the C-terminal region of the alpha subunit, alpha-DG(485-620), has been investigated, showing that the region of beta-DG(654-750) between residues 691 and 719 is involved in the interaction. FAU - Bozzi, Manuela AU - Bozzi M AD - Istituto di Chimica del Riconoscimento Molecolare c/o Istituto di Biochimica e Biochimica Clinica, Consiglio Nazionale della Ricerche, Universita Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy. FAU - Bianchi, Marzia AU - Bianchi M FAU - Sciandra, Francesca AU - Sciandra F FAU - Paci, Maurizio AU - Paci M FAU - Giardina, Bruno AU - Giardina B FAU - Brancaccio, Andrea AU - Brancaccio A FAU - Cicero, Daniel O AU - Cicero DO LA - eng GR - GGP030332/Telethon/Italy PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Cytoskeletal Proteins) RN - 0 (Epitopes) RN - 0 (Membrane Glycoproteins) RN - 0 (Recombinant Fusion Proteins) RN - 146888-27-9 (Dystroglycans) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cytoskeletal Proteins/*chemistry/immunology/metabolism MH - Dystroglycans MH - Epitopes/*analysis MH - Membrane Glycoproteins/*chemistry/immunology/metabolism MH - Mice MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/chemistry/immunology/metabolism MH - Sequence Homology, Amino Acid EDAT- 2003/11/19 05:00 MHDA- 2004/01/07 05:00 CRDT- 2003/11/19 05:00 AID - 10.1021/bi034867w [doi] PST - ppublish SO - Biochemistry. 2003 Nov 25;42(46):13717-24. PMID- 17949994 OWN - NLM STAT- MEDLINE DA - 20071126 DCOM- 20080310 LR - 20131121 IS - 1046-5928 (Print) IS - 1046-5928 (Linking) VI - 57 IP - 1 DP - 2008 Jan TI - A new protocol for high-yield purification of recombinant human prothymosin alpha expressed in Escherichia coli for NMR studies. PG - 1-8 AB - Human prothymosin alpha (ProTalpha) is a small acidic protein (12.1 kDa; pI approximately 3.5) ubiquitously expressed in a wide variety of tissues. The amino acid composition of this protein is highly unusual. While close to half of its sequence is composed of acidic amino acids, the protein does not contain any aromatic residues. ProTalpha has been shown to play crucial roles in different biological processes including cell proliferation, transcriptional regulation and apoptosis. Despite the multiple functions this protein has, it does not adopt a stable tertiary fold under physiological conditions. In order to understand how ProTalpha functions, detailed structural characterization of this protein is essential. Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for elucidating the protein structure and dynamics at the atomic level. However, milligrams of isotopically labeled protein with high purity are usually required for the studies. In this work, we developed a high-yield protocol for purifying recombinant ProTalpha expressed in Escherichia coli by exploiting the intrinsically disordered and acidic natures of this protein. By combining the heat-cooling extraction, ammonium sulfate precipitation, and anion exchange chromatography, we were able to obtain over 20 mg of ProTalpha with >97% purity from 1L of M9 minimal media culture. The new purification protocol provides a cost effective and an efficient way to produce large quantities of high purity recombinant human ProTalpha in various isotopically labeled forms, which will greatly facilitate the structural studies of this protein by NMR and other biophysical methods. FAU - Yi, Shiluan AU - Yi S AD - Department of Biochemistry, The University of Western Ontario, London, Ont., Canada N6A 5C1. FAU - Brickenden, Anne AU - Brickenden A FAU - Choy, Wing-Yiu AU - Choy WY LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070914 PL - United States TA - Protein Expr Purif JT - Protein expression and purification JID - 9101496 RN - 0 (Amino Acids, Acidic) RN - 0 (Protein Precursors) RN - 0 (Recombinant Proteins) RN - 0 (prothymosin alpha) RN - 61512-21-8 (Thymosin) RN - SU46BAM238 (Ammonium Sulfate) SB - IM MH - Amino Acid Sequence MH - Amino Acids, Acidic MH - Ammonium Sulfate/chemistry MH - Chemical Precipitation MH - Chromatography, Ion Exchange MH - Circular Dichroism MH - Escherichia coli/genetics MH - Humans MH - Isotope Labeling MH - Molecular Weight MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Protein Precursors/chemistry/genetics/*isolation & purification MH - Recombinant Proteins/chemistry/isolation & purification MH - Thymosin/*analogs & derivatives/chemistry/genetics/isolation & purification MH - Ultracentrifugation EDAT- 2007/10/24 09:00 MHDA- 2008/03/11 09:00 CRDT- 2007/10/24 09:00 PHST- 2007/07/27 [received] PHST- 2007/08/28 [revised] PHST- 2007/09/03 [accepted] PHST- 2007/09/14 [aheadofprint] AID - S1046-5928(07)00220-3 [pii] AID - 10.1016/j.pep.2007.09.005 [doi] PST - ppublish SO - Protein Expr Purif. 2008 Jan;57(1):1-8. Epub 2007 Sep 14. PMID- 12834338 OWN - NLM STAT- MEDLINE DA - 20030701 DCOM- 20030822 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 42 IP - 26 DP - 2003 Jul 8 TI - Zeroing in on the pathogenic form of alpha-synuclein and its mechanism of neurotoxicity in Parkinson's disease. PG - 7871-8 AB - Parkinson's disease (PD) is linked to mutations in the protein alpha-synuclein, which can exist in vitro in several aggregation states, including a natively unfolded monomer, a beta-sheet rich oligomer, or protofibril, and a stable amyloid fibril. This work reviews the current literature that is relevant to two linked questions: which of these species is pathogenic, and what is the mechanism of neurotoxicity? The amyloid fibril, fibrillar aggregates, Lewy bodies, and the alpha-synuclein monomer, which is normally expressed at high levels, are all unlikely to be pathogenic, for reasons discussed here. We therefore favor a toxic protofibril scenario, and propose that the pathogenic species is transiently populated during the process of fibrillization. Toxicity may arise from pore-like protofibrils that cause membrane permeabilization. An approach to testing this hypothesis is discussed. FAU - Volles, Michael J AU - Volles MJ AD - Center for Neurologic Diseases, Brigham and Women's Hospital, and Department of Neurology, Harvard Medical School, 65 Landsdowne Street, Cambridge, Massachusetts 02139, USA. FAU - Lansbury, Peter T Jr AU - Lansbury PT Jr LA - eng GR - NS38375/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PT - Review PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Nerve Tissue Proteins) RN - 0 (SNCA protein, human) RN - 0 (Snca protein, mouse) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Amino Acid Sequence MH - Amyloid/chemistry/*metabolism MH - Animals MH - Brain/*physiology MH - Disease Models, Animal MH - Humans MH - Mice MH - Molecular Sequence Data MH - Mutation MH - Nerve Tissue Proteins/*physiology MH - Parkinson Disease/genetics/*metabolism/pathology MH - Synucleins MH - alpha-Synuclein RF - 119 EDAT- 2003/07/02 05:00 MHDA- 2003/08/23 05:00 CRDT- 2003/07/02 05:00 AID - 10.1021/bi030086j [doi] PST - ppublish SO - Biochemistry. 2003 Jul 8;42(26):7871-8. PMID- 23202419 OWN - NLM STAT- MEDLINE DA - 20121203 DCOM- 20130510 IS - 1434-3207 (Electronic) IS - 1386-6338 (Linking) VI - 11 IP - 5-6 DP - 2011-2012 TI - Coordinated evolution of the hepatitis B virus polymerase. PG - 175-82 LID - 10.3233/ISB-2012-0452 [doi] AB - The detection of compensatory mutations that abrogate negative fitness effects of drug-resistance and vaccine-escape mutations indicates the important role of epistatic connectivity in evolution of viruses, especially under the strong selection pressures. Mapping of epistatic connectivity in the form of coordinated substitutions should help to characterize molecular mechanisms shaping viral evolution and provides a tool for the development of novel anti-viral drugs and vaccines. We analyzed coordinated variation among amino acid sites in 370 the hepatitis B virus (HBV) polymerase sequences using Bayesian networks. Among the HBV polymerase domains the spacer domain separating terminal protein from the reverse-transcriptase domain, showed the highest network centrality. Coordinated substitutions preserve the hydrophobicity and charge of Spacer. Maximum likelihood estimates of codon selection showed that Spacer contains the highest number of positively selected sites. Identification of 67% of the domain lacking an ordered structure suggests that Spacer belongs to the class of intrinsically disordered domains and proteins whose crucial functional role in the regulation of transcription, translation and cellular signal transduction has only recently been recognized. Spacer plays a central role in the epistatic network associating substitutions across the HBV genome, including those conferring viral virulence, drug resistance and vaccine escape. The data suggest that Spacer is extensively involved in coordination of HBV evolution. FAU - Campo, D S AU - Campo DS AD - Laboratory Branch, Division of Viral Hepatitis, Center for Disease Control and Prevention, Atlanta, GA 30300, USA. fyv6@cdc.gov FAU - Dimitrova, Z AU - Dimitrova Z FAU - Lara, J AU - Lara J FAU - Purdy, M AU - Purdy M FAU - Thai, H AU - Thai H FAU - Ramachandran, S AU - Ramachandran S FAU - Ganova-Raeva, L AU - Ganova-Raeva L FAU - Zhai, X AU - Zhai X FAU - Forbi, J C AU - Forbi JC FAU - Teo, C G AU - Teo CG FAU - Khudyakov, Y AU - Khudyakov Y LA - eng PT - Journal Article PL - Netherlands TA - In Silico Biol JT - In silico biology JID - 9815902 RN - 0 (Viral Proteins) RN - EC 2.7.7.7 (DNA-Directed DNA Polymerase) SB - IM MH - DNA-Directed DNA Polymerase/*chemistry/genetics MH - *Evolution, Molecular MH - Hepatitis B virus/*enzymology MH - Protein Structure, Tertiary MH - Viral Proteins/*chemistry/genetics EDAT- 2012/12/04 06:00 MHDA- 2013/05/11 06:00 CRDT- 2012/12/04 06:00 AID - H778181V2K364516 [pii] AID - 10.3233/ISB-2012-0452 [doi] PST - ppublish SO - In Silico Biol. 2011-2012;11(5-6):175-82. doi: 10.3233/ISB-2012-0452. PMID- 24099487 OWN - NLM STAT- MEDLINE DA - 20140204 DCOM- 20141008 LR - 20150325 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 43 DP - 2013 Oct 30 TI - Membrane remodeling by alpha-synuclein and effects on amyloid formation. PG - 15970-3 LID - 10.1021/ja405993r [doi] AB - alpha-Synuclein (alpha-Syn), an intrinsically disordered protein, is associated with Parkinson's disease. Though molecular pathogenic mechanisms are ill-defined, mounting evidence connects its amyloid forming and membrane binding propensities to disease etiology. Contrary to recent data suggesting that membrane remodeling by alpha-syn involves anionic phospholipids and helical structure, we discovered that the protein deforms vesicles with no net surface charge (phosphatidylcholine, PC) into tubules (average diameter approximately 20 nm). No discernible secondary structural changes were detected by circular dichroism spectroscopy upon the addition of vesicles. Notably, membrane remodeling inhibits alpha-syn amyloid formation affecting both lag and growth phases. Using five single tryptophan variants and time-resolved fluorescence anisotropy measurements, we determined that alpha-syn influences bilayer structure with surprisingly weak interaction and no site specificity (partition constant, Kp approximately 300 M(-1)). Vesicle deformation by alpha-syn under a variety of different lipid/protein conditions is characterized via transmission electron microscopy. As cellular membranes are enriched in PC lipids, these results support possible biological consequences for alpha-syn induced membrane remodeling related to both function and pathogenesis. FAU - Jiang, Zhiping AU - Jiang Z AD - Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States. FAU - de Messieres, Michel AU - de Messieres M FAU - Lee, Jennifer C AU - Lee JC LA - eng GR - ZIA HL001055-06/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Intramural DEP - 20131017 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (1-palmitoyl-2-oleoyl-phosphatidyl-3-adenosine) RN - 0 (Amyloid) RN - 0 (Glycerophospholipids) RN - 0 (Indicators and Reagents) RN - 0 (Lipid Bilayers) RN - 0 (Lipids) RN - 0 (Membranes, Artificial) RN - 0 (Phosphatidylcholines) RN - 0 (alpha-Synuclein) RN - 8DUH1N11BX (Tryptophan) RN - 97C5T2UQ7J (Cholesterol) RN - K72T3FS567 (Adenosine) RN - TE895536Y5 (1-palmitoyl-2-oleoylphosphatidylcholine) SB - IM MH - Adenosine/analogs & derivatives/chemistry MH - Amyloid/*chemistry MH - Cholesterol/chemistry MH - Circular Dichroism MH - Glycerophospholipids/chemistry MH - Indicators and Reagents MH - Lipid Bilayers MH - Lipids/chemistry MH - *Membranes, Artificial MH - Microscopy, Electron, Transmission MH - Microtubules MH - Neutrons MH - Phosphatidylcholines MH - Spectrophotometry, Ultraviolet MH - Tryptophan/chemistry MH - alpha-Synuclein/*chemistry PMC - PMC3859146 MID - NIHMS532860 OID - NLM: NIHMS532860 OID - NLM: PMC3859146 EDAT- 2013/10/09 06:00 MHDA- 2014/10/09 06:00 CRDT- 2013/10/09 06:00 PHST- 2013/10/17 [aheadofprint] AID - 10.1021/ja405993r [doi] PST - ppublish SO - J Am Chem Soc. 2013 Oct 30;135(43):15970-3. doi: 10.1021/ja405993r. Epub 2013 Oct 17. PMID- 7979373 OWN - NLM STAT- MEDLINE DA - 19941207 DCOM- 19941207 LR - 20061115 IS - 0003-9861 (Print) IS - 0003-9861 (Linking) VI - 314 IP - 2 DP - 1994 Nov 1 TI - Kappa-casein and beta-caseins in human milk micelles: structural studies. PG - 329-36 AB - The function of human milk micelles is to deliver nutrients, particularly insoluble minerals such as the necessary calcium phosphate, to the child in a readily ingested suspension that meets the special requirements of the human infant digestive system. The micelle structure which fulfills that function is not known. However, the development of ion-exchange and reverse-phase HPLC methods for the purification and quantitation of the kappa- and beta-caseins, along with tritium labeling of the carbohydrate of the kappa-casein in human milk to aid in its detection, provided the tools for probing micelle structure by examining the composition of micelles fractionated according to size by differential centrifugation. The relative amount of kappa-casein increased as micelle size decreased, and thus as surface area/volume increased. Since kappa-casein also stabilizes the micelles against precipitation by Ca2+ ions, a surface position for most of the kappa-casein is implied. The relative amounts of the various phosphorylation levels of the human beta-caseins remained essentially constant except for the nonphosphorylated (O-P) form, which apparently decreased as micelle size decreased. These data suggest that the beta-caseins are linked in the micelles partially through electrostatic interactions involving the organic phosphoryl groups, lacking in the O-P, so that O-P can dissociate into the whey. That further implies that the complete surface is not protected by the kappa -casein but that the beta-caseins are also accessible to the solution. FAU - Dev, B C AU - Dev BC AD - Department of Biochemistry, Loma Linda University School of Medicine, California 92350. FAU - Sood, S M AU - Sood SM FAU - DeWind, S AU - DeWind S FAU - Slattery, C W AU - Slattery CW LA - eng PT - Journal Article PL - UNITED STATES TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (Caseins) RN - 0 (Micelles) RN - 10028-17-8 (Tritium) SB - IM MH - Caseins/*chemistry/isolation & purification MH - Chromatography, High Pressure Liquid MH - Electrophoresis, Polyacrylamide Gel MH - Female MH - Humans MH - Micelles MH - Milk, Human/*chemistry MH - Scintillation Counting MH - Tritium MH - Ultracentrifugation EDAT- 1994/11/01 MHDA- 1994/11/01 00:01 CRDT- 1994/11/01 00:00 AID - S0003-9861(84)71450-0 [pii] AID - 10.1006/abbi.1994.1450 [doi] PST - ppublish SO - Arch Biochem Biophys. 1994 Nov 1;314(2):329-36. PMID- 21098297 OWN - NLM STAT- MEDLINE DA - 20110322 DCOM- 20110512 LR - 20141223 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 107 IP - 50 DP - 2010 Dec 14 TI - Directed epitope delivery across the Escherichia coli outer membrane through the porin OmpF. PG - 21412-7 LID - 10.1073/pnas.1010780107 [doi] AB - The porins OmpF and OmpC are trimeric beta-barrel proteins with narrow channels running through each monomer that exclude molecules > 600 Da while mediating the passive diffusion of small nutrients and metabolites across the Gram-negative outer membrane (OM). Here, we elucidate the mechanism by which an entire soluble protein domain (> 6 kDa) is delivered through the lumen of such porins. Following high-affinity binding to the vitamin B(12) receptor in Escherichia coli, the bacteriocin ColE9 recruits OmpF or OmpC using an 83-residue intrinsically unstructured translocation domain (IUTD) to deliver a 16-residue TolB-binding epitope (TBE) in the center of the IUTD to the periplasm where it triggers toxin entry. We demonstrate that the IUTD houses two OmpF-binding sites, OBS1 (residues 2-18) and OBS2 (residues 54-63), which flank the TBE and bind with K(d)s of 2 and 24 muM, respectively, at pH 6.5 and 25 masculineC. We show the two OBSs share the same binding site on OmpF and that the colicin must house at least one of them for antibiotic activity. Finally, we report the structure of the OmpF-OBS1 complex that shows the colicin bound within the porin lumen spanning the membrane bilayer. Our study explains how colicins exploit porins to deliver epitope signals to the bacterial periplasm and, more broadly, how the inherent flexibility and narrow cross-sectional area of an IUP domain can endow it with the ability to traverse a biological membrane via the constricted lumen of a beta-barrel membrane protein. FAU - Housden, Nicholas G AU - Housden NG AD - Department of Biology, Area 10, and York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom. FAU - Wojdyla, Justyna A AU - Wojdyla JA FAU - Korczynska, Justyna AU - Korczynska J FAU - Grishkovskaya, Irina AU - Grishkovskaya I FAU - Kirkpatrick, Nadine AU - Kirkpatrick N FAU - Brzozowski, A Marek AU - Brzozowski AM FAU - Kleanthous, Colin AU - Kleanthous C LA - eng SI - PDB/3O0E GR - BB/G020671/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101122 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Bacterial Outer Membrane Proteins) RN - 0 (Colicins) RN - 0 (Epitopes) RN - 0 (Escherichia coli Proteins) RN - 0 (OmpF protein) RN - 0 (Porins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (immE9 protein, E coli) SB - IM MH - Bacterial Outer Membrane Proteins/chemistry/*metabolism MH - Cell Membrane/*metabolism MH - Colicins/chemistry/genetics/metabolism MH - Crystallography, X-Ray MH - *Epitopes MH - Escherichia coli/cytology/*metabolism MH - Escherichia coli Proteins/chemistry/*metabolism MH - Models, Molecular MH - Porins/chemistry/genetics/*metabolism MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/chemistry/genetics/metabolism PMC - PMC3003033 EDAT- 2010/11/26 06:00 MHDA- 2011/05/13 06:00 CRDT- 2010/11/25 06:00 PHST- 2010/11/22 [aheadofprint] AID - 1010780107 [pii] AID - 10.1073/pnas.1010780107 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21412-7. doi: 10.1073/pnas.1010780107. Epub 2010 Nov 22. PMID- 1659663 OWN - NLM STAT- MEDLINE DA - 19911231 DCOM- 19911231 LR - 20061115 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 354 IP - 6351 DP - 1991 Nov 28 TI - Structure of simian virus 40 at 3.8-A resolution. PG - 278-84 AB - The crystallographically determined structure of simian virus 40 shows that the 72 pentamers of viral protein VP1, which form the outer shell, have identical conformations except for the C-terminal arms of their subunits. Five arms emerge from each pentamer and insert into neighbouring pentamers. This tying together of standard building blocks allows for the required variability in packing geometry without sacrificing specificity. FAU - Liddington, R C AU - Liddington RC AD - Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138. FAU - Yan, Y AU - Yan Y FAU - Moulai, J AU - Moulai J FAU - Sahli, R AU - Sahli R FAU - Benjamin, T L AU - Benjamin TL FAU - Harrison, S C AU - Harrison SC LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Calcium-Binding Proteins) RN - 0 (Capsid Proteins) RN - 0 (Disulfides) RN - 0 (Macromolecular Substances) RN - 0 (VP1 protein, polyomavirus) SB - IM MH - Amino Acid Sequence MH - Calcium-Binding Proteins/ultrastructure MH - Capsid/*ultrastructure MH - *Capsid Proteins MH - Computer Graphics MH - Crystallography MH - Disulfides/chemistry MH - Humans MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Morphogenesis MH - Protein Conformation MH - Sequence Alignment MH - Simian virus 40/*ultrastructure MH - Virion/ultrastructure MH - X-Ray Diffraction EDAT- 1991/11/28 MHDA- 1991/11/28 00:01 CRDT- 1991/11/28 00:00 AID - 10.1038/354278a0 [doi] PST - ppublish SO - Nature. 1991 Nov 28;354(6351):278-84. PMID- 23807285 OWN - NLM STAT- MEDLINE DA - 20130628 DCOM- 20140114 IS - 1750-2799 (Electronic) IS - 1750-2799 (Linking) VI - 8 IP - 7 DP - 2013 TI - Site-specific NMR mapping and time-resolved monitoring of serine and threonine phosphorylation in reconstituted kinase reactions and mammalian cell extracts. PG - 1416-32 LID - 10.1038/nprot.2013.083 [doi] AB - We outline NMR protocols for site-specific mapping and time-resolved monitoring of protein phosphorylation reactions using purified kinases and mammalian cell extracts. These approaches are particularly amenable to intrinsically disordered proteins and unfolded, regulatory protein domains. We present examples for the (1)(5)N isotope-labeled N-terminal transactivation domain of human p53, which is either sequentially reacted with recombinant enzymes or directly added to mammalian cell extracts and phosphorylated by endogenous kinases. Phosphorylation reactions with purified enzymes are set up in minutes, whereas NMR samples in cell extracts are prepared within 1 h. Time-resolved NMR measurements are performed over minutes to hours depending on the activities of the probed kinases. Phosphorylation is quantitatively monitored with consecutive 2D (1)H-(1)(5)N band-selective optimized-flip-angle short-transient (SOFAST)-heteronuclear multiple-quantum (HMQC) NMR experiments, which provide atomic-resolution insights into the phosphorylation levels of individual substrate residues and time-dependent changes thereof, thereby offering unique advantages over western blotting and mass spectrometry. FAU - Theillet, Francois-Xavier AU - Theillet FX AD - In-Cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany. FAU - Rose, Honor May AU - Rose HM FAU - Liokatis, Stamatios AU - Liokatis S FAU - Binolfi, Andres AU - Binolfi A FAU - Thongwichian, Rossukon AU - Thongwichian R FAU - Stuiver, Marchel AU - Stuiver M FAU - Selenko, Philipp AU - Selenko P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130627 PL - England TA - Nat Protoc JT - Nature protocols JID - 101284307 RN - 0 (Cell Extracts) RN - 0 (Proteins) RN - 0 (Tumor Suppressor Protein p53) RN - 2ZD004190S (Threonine) RN - 452VLY9402 (Serine) RN - EC 2.7.- (Protein Kinases) SB - IM MH - Animals MH - Cell Extracts/*analysis MH - Humans MH - Nuclear Magnetic Resonance, Biomolecular/*methods MH - Phosphorylation MH - Protein Kinases/chemistry/metabolism MH - Protein Structure, Tertiary MH - Proteins/analysis/*metabolism MH - Serine/analysis/*metabolism MH - Threonine/analysis/*metabolism MH - Time Factors MH - Tumor Suppressor Protein p53/metabolism EDAT- 2013/06/29 06:00 MHDA- 2014/01/15 06:00 CRDT- 2013/06/29 06:00 PHST- 2013/06/27 [aheadofprint] AID - nprot.2013.083 [pii] AID - 10.1038/nprot.2013.083 [doi] PST - ppublish SO - Nat Protoc. 2013;8(7):1416-32. doi: 10.1038/nprot.2013.083. Epub 2013 Jun 27. PMID- 19292861 OWN - NLM STAT- MEDLINE DA - 20090401 DCOM- 20090519 IS - 1742-4658 (Electronic) IS - 1742-464X (Linking) VI - 276 IP - 8 DP - 2009 Apr TI - Solubility-dependent structural formation of a 25-residue, natively unfolded protein, induced by addition of a seven-residue peptide fragment. PG - 2336-47 LID - 10.1111/j.1742-4658.2009.06961.x [doi] AB - To elucidate the architectural principle of protein structure, we focused on sequestration from solvent, which is a common characteristic of folding and self-associative precipitation. Because protein solubility can be regarded as a basis for the potential ability to sequester from solvent, we assume that poorly soluble proteins tend not only to precipitate, but also to form solution structures. To examine this, the solubility of a 25-residue, natively unfolded protein, modified from a zinc-finger domain of transcription factor Sp1, was disturbed by adding a seven-residue hydrophobic peptide fragment to the C-terminus. NMR and ultracentrifuge measurements of the resulting sequence showed that a dissolved species forms an alpha-helical structure in a 15-20 molecule oligomer. To elucidate the mechanism by which the structure forms, we prepared two variants in which the added fragments are less hydrophobic; the structural stabilities were then measured at various pH values. A fairly good correlation was observed between stability and hydration potential, whereas a much stronger correlation was observed between stability and solubility, indicating that the stability is more strongly dependent on the ability to precipitate than on dehydration. These results show that, among poorly soluble protein molecules, dissolved species can be transformed from the solvent-exposed unfolded state into a loosely packed structure via intermolecular interactions. Because decreasing the protein solubility does not require the primary sequence to have a sophisticated design, such a protein structure might form readily and frequently, compared with the well-packed structure found in native proteins. FAU - Araki, Mitsugu AU - Araki M AD - Graduate School of Science, Kobe University, Kobe, Nada, Japan. FAU - Tamura, Atsuo AU - Tamura A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090309 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (Peptide Fragments) SB - IM MH - Binding Sites MH - Hydrogen-Ion Concentration MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/*chemistry/metabolism MH - Protein Conformation MH - *Protein Folding MH - Solubility MH - Thermodynamics EDAT- 2009/03/19 09:00 MHDA- 2009/05/20 09:00 CRDT- 2009/03/19 09:00 PHST- 2009/03/09 [aheadofprint] AID - EJB6961 [pii] AID - 10.1111/j.1742-4658.2009.06961.x [doi] PST - ppublish SO - FEBS J. 2009 Apr;276(8):2336-47. doi: 10.1111/j.1742-4658.2009.06961.x. Epub 2009 Mar 9. PMID- 24723374 OWN - NLM STAT- MEDLINE DA - 20140620 DCOM- 20150130 LR - 20150701 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 23 IP - 7 DP - 2014 Jul TI - General flexible nature of the cytosolic regions of fungal transient receptor potential (TRP) channels, revealed by expression screening using GFP-fusion techniques. PG - 923-31 LID - 10.1002/pro.2474 [doi] AB - Transient receptor potential (TRP) channels are members of the voltage gated ion channel superfamily and display the unique characteristic of activation by diverse stimuli. We performed an expression analysis of fungal TRP channels, which possess relatively simple structures yet share the common functional characteristics with the other members, using a green fluorescent protein-based screening methodology. The analysis revealed that all the tested fungal TRP channels were severely digested in their cytosolic regions during expression, implying the common flexibility of this region, as observed in the recent structural analyses of the fungal member, TRPGz. These characteristics are likely to be important for their diverse functions. CI - (c) 2014 The Protein Society. FAU - Ihara, Makoto AU - Ihara M AD - Molecular Signaling Research Team, Structural Physiology Research Group, RIKEN SPring-8 Center, Sayo, Hyogo, 679-5148, Japan; Division of Social and Environmental Sciences, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan. FAU - Takano, Yoshitaka AU - Takano Y FAU - Yamashita, Atsuko AU - Yamashita A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140422 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Fungal Proteins) RN - 0 (Transient Receptor Potential Channels) RN - 147336-22-9 (Green Fluorescent Proteins) SB - IM MH - Fungal Proteins/chemistry/genetics/*metabolism MH - Gene Expression MH - Green Fluorescent Proteins/genetics/metabolism MH - Sequence Analysis, Protein MH - Transient Receptor Potential Channels/chemistry/genetics/*metabolism PMC - PMC4088976 OID - NLM: PMC4088976 OTO - NOTNLM OT - GFP-fusion technique OT - TRP channels OT - intrinsically disordered protein EDAT- 2014/04/12 06:00 MHDA- 2015/01/31 06:00 CRDT- 2014/04/12 06:00 PHST- 2013/11/25 [received] PHST- 2014/03/04 [revised] PHST- 2014/04/03 [accepted] PHST- 2014/04/22 [aheadofprint] AID - 10.1002/pro.2474 [doi] PST - ppublish SO - Protein Sci. 2014 Jul;23(7):923-31. doi: 10.1002/pro.2474. Epub 2014 Apr 22. PMID- 17567691 OWN - NLM STAT- MEDLINE DA - 20070816 DCOM- 20070928 LR - 20140904 IS - 0022-538X (Print) IS - 0022-538X (Linking) VI - 81 IP - 17 DP - 2007 Sep TI - Ebola virus VP30 is an RNA binding protein. PG - 8967-76 AB - The Ebola virus (EBOV) genome encodes for several proteins that are necessary and sufficient for replication and transcription of the viral RNAs in vitro; NP, VP30, VP35, and L. VP30 acts in trans with an RNA secondary structure upstream of the first transcriptional start site to modulate transcription. Using a bioinformatics approach, we identified a region within the N terminus of VP30 with sequence features that typify intrinsically disordered regions and a putative RNA binding site. To experimentally assess the ability of VP30 to directly interact with the viral RNA, we purified recombinant EBOV VP30 to >90% homogeneity and assessed RNA binding by UV cross-linking and filter-binding assays. VP30 is a strongly acidophilic protein; RNA binding became stronger as pH was decreased. Zn(2+), but not Mg(2+), enhanced activity. Enhancement of transcription by VP30 requires a RNA stem-loop located within nucleotides 54 to 80 of the leader region. VP30 showed low binding affinity to the predicted stem-loop alone or to double-stranded RNA but showed a good binding affinity for the stem-loop when placed in the context of upstream and downstream sequences. To map the region responsible for interacting with RNA, we constructed, purified, and assayed a series of N-terminal deletion mutations of VP30 for RNA binding. The key amino acids supporting RNA binding activity map to residues 26 to 40, a region rich in arginine. Thus, we show for the first time the direct interaction of EBOV VP30 with RNA and the importance of the N-terminal region for binding RNA. FAU - John, Sinu P AU - John SP AD - Graduate Program in Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA. FAU - Wang, Tan AU - Wang T FAU - Steffen, Scott AU - Steffen S FAU - Longhi, Sonia AU - Longhi S FAU - Schmaljohn, Connie S AU - Schmaljohn CS FAU - Jonsson, Colleen B AU - Jonsson CB LA - eng PT - Journal Article DEP - 20070613 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (Coenzymes) RN - 0 (RNA, Double-Stranded) RN - 0 (RNA, Viral) RN - 0 (RNA-Binding Proteins) RN - 0 (Transcription Factors) RN - 0 (VP30 protein, ebola virus) RN - 0 (Viral Proteins) RN - I38ZP9992A (Magnesium) RN - J41CSQ7QDS (Zinc) SB - IM MH - Amino Acid Sequence MH - Binding Sites/genetics MH - Coenzymes/pharmacology MH - Computational Biology MH - Ebolavirus/chemistry/metabolism MH - Hydrogen-Ion Concentration MH - Magnesium/pharmacology MH - Molecular Sequence Data MH - Nucleic Acid Conformation MH - Protein Binding MH - RNA, Double-Stranded/metabolism MH - RNA, Viral/chemistry/*metabolism MH - RNA-Binding Proteins/chemistry/genetics/isolation & purification/*metabolism MH - Sequence Deletion MH - Transcription Factors/chemistry/genetics/isolation & purification/*metabolism MH - Viral Proteins/chemistry/genetics/isolation & purification/*metabolism MH - Zinc/pharmacology PMC - PMC1951390 OID - NLM: PMC1951390 EDAT- 2007/06/15 09:00 MHDA- 2007/09/29 09:00 CRDT- 2007/06/15 09:00 PHST- 2007/06/13 [aheadofprint] AID - JVI.02523-06 [pii] AID - 10.1128/JVI.02523-06 [doi] PST - ppublish SO - J Virol. 2007 Sep;81(17):8967-76. Epub 2007 Jun 13. PMID- 11994149 OWN - NLM STAT- MEDLINE DA - 20020507 DCOM- 20020722 LR - 20061115 IS - 0950-382X (Print) IS - 0950-382X (Linking) VI - 44 IP - 3 DP - 2002 May TI - The Bacillus subtilis cell division proteins FtsL and DivIC are intrinsically unstable and do not interact with one another in the absence of other septasomal components. PG - 663-74 AB - The bacterial septum appears to comprise a macromolecular assembly of essential cell division proteins (the 'septasome') that are responsible for physically dividing the cell during cytokinesis. FtsL and DivIC are essential components of this division machinery in Bacillus subtilis. We used yeast two-hybrid analysis as well as a variety of biochemical and biophysical methods to examine the proposed interaction between Bacillus subtilis FtsL and DivIC. We show that FtsL and DivIC are thermodynamically unstable proteins that are likely to be unfolded and therefore targeted for degradation unless stabilized by interactions with other components of the septasome. However, we show that this stabilization does not result from a direct interaction between FtsL and DivIC. We propose that the observed interdependence of DivIC and FtsL stability is a result of indirect interactions that are mediated by other septasomal proteins. FAU - Robson, Scott A AU - Robson SA AD - Department of Biochemistry, University of Connecticut Health Center, Farmington 06032, USA. FAU - Michie, Katharine A AU - Michie KA FAU - Mackay, Joel P AU - Mackay JP FAU - Harry, Elizabeth AU - Harry E FAU - King, Glenn F AU - King GF LA - eng PT - Comparative Study PT - Journal Article PL - England TA - Mol Microbiol JT - Molecular microbiology JID - 8712028 RN - 0 (Bacterial Proteins) RN - 0 (Cell Cycle Proteins) RN - 0 (DivIC protein, Bacillus subtilis) RN - 0 (Escherichia coli Proteins) RN - 0 (Macromolecular Substances) RN - 0 (Membrane Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (ftsL protein, E coli) SB - IM MH - Amino Acid Sequence MH - Bacillus subtilis/cytology/*metabolism MH - Bacterial Proteins/chemistry/*metabolism MH - Cell Cycle Proteins/chemistry/*metabolism MH - Cell Division MH - Circular Dichroism MH - *Escherichia coli Proteins MH - Isoelectric Point MH - Macromolecular Substances MH - Membrane Proteins/chemistry/*metabolism MH - Molecular Sequence Data MH - Nephelometry and Turbidimetry MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Denaturation MH - Protein Folding MH - Protein Interaction Mapping MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/chemistry/metabolism MH - Saccharomyces cerevisiae/metabolism MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Structure-Activity Relationship MH - Thermodynamics MH - Two-Hybrid System Techniques MH - Ultracentrifugation EDAT- 2002/05/08 10:00 MHDA- 2002/07/23 10:01 CRDT- 2002/05/08 10:00 AID - 2920 [pii] PST - ppublish SO - Mol Microbiol. 2002 May;44(3):663-74. PMID- 8634266 OWN - NLM STAT- MEDLINE DA - 19960705 DCOM- 19960705 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 35 IP - 5 DP - 1996 Feb 6 TI - Specific recognition of coiled coils by infrared spectroscopy: analysis of the three structural domains of type III intermediate filament proteins. PG - 1375-82 AB - The central domain of cytoplasmic intermediate filament (IF) proteins from vertebrates contains some 310 residues and forms a double-stranded coiled coil (rod) with a length of about 46 nm. The flanking terminal domains show a high cell type specific variability both in sequence and in length. Using Fourier transform infrared (FTIR) spectroscopy we measured secondary structures of isolated domains of type III and IV IF proteins and of the soluble tetramers and the filaments formed by type III IF proteins. The amide I spectrum of the desmin rod is virtually identical to the spectra of other coiled-coil proteins such as tropomyosin and the myosin rod. All these double-stranded coiled coils reveal spectra distinctly different from classical alpha-helical spectra. The spectrum of coiled coils is a triplet of approximately equally strong bands. One band occurs at normal alpha-helix position, while the other two are found at lower wavenumbers. Theoretical aspects of these findings are discussed in the accompanying paper by W. C. Reisdorf and S. Krimm [(1996) Biochemistry 35, 1383-1386]. The amino-terminal head domain of desmin has a multicomponent spectrum with major fractions of beta-sheet. The carboxy-terminal tail domains of desmin and the neurofilament proteins L and H, the latter in the phosphorylated and in the dephosphorylated forms, have very similar FTIR spectra, indicating mostly random structure. The spectrum of desmin type III protofilaments is very similar to the sum of the spectra of the three isolated domains. Polymerization into filaments seems to induce a small change in secondary structure. FAU - Heimburg, T AU - Heimburg T AD - Max Planck Institute for Biophysical Chemistry, Department of Spectroscopy, Gottingen, Federal Republic of Germany. FAU - Schuenemann, J AU - Schuenemann J FAU - Weber, K AU - Weber K FAU - Geisler, N AU - Geisler N LA - eng PT - Comparative Study PT - Journal Article PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Desmin) RN - 0 (Intermediate Filament Proteins) RN - 0 (Tropomyosin) RN - 0 (Vimentin) SB - IM MH - Desmin/chemistry MH - Intermediate Filament Proteins/*chemistry MH - *Protein Structure, Tertiary MH - Spectroscopy, Fourier Transform Infrared MH - Tropomyosin/chemistry MH - Vimentin/chemistry EDAT- 1996/02/06 MHDA- 1996/02/06 00:01 CRDT- 1996/02/06 00:00 AID - 10.1021/bi9515883 [doi] AID - bi9515883 [pii] PST - ppublish SO - Biochemistry. 1996 Feb 6;35(5):1375-82. PMID- 11967569 OWN - NLM STAT- MEDLINE DA - 20020528 DCOM- 20020618 LR - 20061115 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 9 IP - 6 DP - 2002 Jun TI - Structural insights into the pro-apoptotic function of mitochondrial serine protease HtrA2/Omi. PG - 436-41 AB - HtrA2/Omi, a mitochondrial serine protease in mammals, is important in programmed cell death. However, the underlining mechanism of HtrA2/Omi-mediated apoptosis remains unclear. Analogous to the bacterial homolog HtrA (DegP), the mature HtrA2 protein contains a central serine protease domain and a C-terminal PDZ domain. The 2.0 A crystal structure of HtrA2/Omi reveals the formation of a pyramid-shaped homotrimer mediated exclusively by the serine protease domains. The peptide-binding pocket of the PDZ domain is buried in the intimate interface between the PDZ and the protease domains. Mutational analysis reveals that the monomeric HtrA2/Omi mutants are unable to induce cell death and are deficient in protease activity. The PDZ domain modulates HtrA2/Omi-mediated cell death activity by regulating its serine protease activity. These structural and biochemical observations provide an important framework for deciphering the mechanisms of HtrA2/Omi-mediated apoptosis. FAU - Li, Wenyu AU - Li W AD - Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, New Jersey 08544, USA. FAU - Srinivasula, Srinivasa M AU - Srinivasula SM FAU - Chai, Jijie AU - Chai J FAU - Li, Pingwei AU - Li P FAU - Wu, Jia-Wei AU - Wu JW FAU - Zhang, ZhiJia AU - Zhang Z FAU - Alnemri, Emad S AU - Alnemri ES FAU - Shi, Yigong AU - Shi Y LA - eng SI - PDB/1LCY PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Mitochondrial Proteins) RN - EC 3.4.21.- (Omi serine protease) RN - EC 3.4.21.- (Serine Endopeptidases) RN - EC 3.4.22.- (Caspases) SB - IM CIN - Nat Struct Biol. 2002 Jun;9(6):410-2. PMID: 12032552 MH - Amino Acid Sequence MH - *Apoptosis MH - Caspases/metabolism MH - Cell Line MH - Crystallography, X-Ray MH - Enzyme Activation MH - Humans MH - Mitochondria/*enzymology MH - Mitochondrial Proteins MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Serine Endopeptidases/*chemistry/*metabolism MH - Structure-Activity Relationship EDAT- 2002/04/23 10:00 MHDA- 2002/06/19 10:01 CRDT- 2002/04/23 10:00 AID - 10.1038/nsb795 [doi] AID - nsb795 [pii] PST - ppublish SO - Nat Struct Biol. 2002 Jun;9(6):436-41. PMID- 10675326 OWN - NLM STAT- MEDLINE DA - 20000320 DCOM- 20000320 LR - 20141120 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 19 IP - 4 DP - 2000 Feb 15 TI - Op18/stathmin caps a kinked protofilament-like tubulin tetramer. PG - 572-80 AB - Oncoprotein 18/stathmin (Op18), a regulator of microtubule dynamics, was recombinantly expressed and its structure and function analysed. We report that Op18 by itself can fold into a flexible and extended alpha-helix, which is in equilibrium with a less ordered structure. In complex with tubulin, however, all except the last seven C-terminal residues of Op18 are tightly bound to tubulin. Digital image analysis of Op18:tubulin electron micrographs revealed that the complex consists of two longitudinally aligned alpha/beta-tubulin heterodimers. The appearance of the complex was that of a kinked protofilament-like structure with a flat and a ribbed side. Deletion mapping of Op18 further demonstrated that (i) the function of the N-terminal part of the molecule is to 'cap' tubulin subunits to ensure the specificity of the complex and (ii) the complete C-terminal alpha-helical domain of Op18 is necessary and sufficient for stable Op18:tubulin complex formation. Together, our results suggest that besides sequestering tubulin, the structural features of Op18 enable the protein specifically to recognize microtubule ends to trigger catastrophes. FAU - Steinmetz, M O AU - Steinmetz MO AD - M.E. Muller Institute for Microscopy, Biozentrum, University of Basel, CH-4056 Basel, Switzerland. FAU - Kammerer, R A AU - Kammerer RA FAU - Jahnke, W AU - Jahnke W FAU - Goldie, K N AU - Goldie KN FAU - Lustig, A AU - Lustig A FAU - van Oostrum, J AU - van Oostrum J LA - eng PT - Journal Article PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (DNA Primers) RN - 0 (Macromolecular Substances) RN - 0 (Microtubule Proteins) RN - 0 (Phosphoproteins) RN - 0 (Recombinant Proteins) RN - 0 (STMN1 protein, human) RN - 0 (Stathmin) RN - 0 (Tubulin) SB - IM MH - Base Sequence MH - Circular Dichroism MH - DNA Primers/genetics MH - Humans MH - In Vitro Techniques MH - Macromolecular Substances MH - Magnetic Resonance Spectroscopy MH - Microscopy, Electron MH - Microscopy, Electron, Scanning Transmission MH - *Microtubule Proteins MH - Microtubules/chemistry/ultrastructure MH - Models, Biological MH - Phosphoproteins/*chemistry/genetics/ultrastructure MH - Protein Folding MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/ultrastructure MH - Stathmin MH - Tubulin/*chemistry/ultrastructure PMC - PMC305595 OID - NLM: PMC305595 EDAT- 2000/02/17 09:00 MHDA- 2000/03/25 09:00 CRDT- 2000/02/17 09:00 AID - 10.1093/emboj/19.4.572 [doi] PST - ppublish SO - EMBO J. 2000 Feb 15;19(4):572-80. PMID- 25142785 OWN - NLM STAT- MEDLINE DA - 20141013 DCOM- 20150616 IS - 1526-4602 (Electronic) IS - 1525-7797 (Linking) VI - 15 IP - 10 DP - 2014 Oct 13 TI - Molecular description of the LCST behavior of an elastin-like polypeptide. PG - 3522-30 LID - 10.1021/bm500658w [doi] AB - Elastin-like polypeptides (ELPs) with the repeat sequence of VPGVG are widely used as a model system for investigation of lower critical solution temperature (LCST) transition behavior. In this paper, the effect of temperature on the structure, dynamics and association of (VPGVG)18 in aqueous solution is investigated using atomistic molecular dynamics simulations. Our simulations show that as the temperature increases the ELP backbones undergo gradual conformational changes, which are attributed to the formation of more ordered secondary structures such as beta-strands. In addition, increasing temperature changes the hydrophobicity of the ELP by exposure of hydrophobic valine-side chains to the solvent and hiding of proline residues. Based on our simulations, we conclude that the transition behavior of (VPGVG)18 can be attributed to a combination of thermal disruption of the water network that surrounds the polypeptide, reduction of solvent accessible surface area of the polypeptide, and increase in its hydrophobicity. Simulations of the association of two (VPGVG)18 molecules demonstrated that the observed gradual changes in the structural properties of the single polypeptide chain are enough to cause the aggregation of polypeptides above the LCST. These results lead us to propose that the LCST phase behavior of poly(VPGVG) is a collective phenomenon that originates from the correlated gradual changes in single polypeptide structure and the abrupt change in properties of hydration water around the peptide and is a result of a competition between peptide-peptide and peptide-water interactions. This is a computational study of an important intrinsically disordered peptide system that provides an atomic-level description of structural features and interactions that are relevant in the LCST phase behavior. FAU - Li, Nan K AU - Li NK AD - Department of Materials Science and Engineering and section signDepartment of Chemical and Biomolecular Engineering, North Carolina State University , 911 Partners Way, Raleigh, North Carolina 27695, United States. FAU - Garcia Quiroz, Felipe AU - Garcia Quiroz F FAU - Hall, Carol K AU - Hall CK FAU - Chilkoti, Ashutosh AU - Chilkoti A FAU - Yingling, Yaroslava G AU - Yingling YG LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140902 PL - United States TA - Biomacromolecules JT - Biomacromolecules JID - 100892849 RN - 0 (Oligopeptides) RN - 0 (Peptides) RN - 0 (Solutions) RN - 0 (Solvents) RN - 059QF0KO0R (Water) RN - 52231-42-2 (valyl-prolyl-glycyl-valyl-glycine) RN - 9007-58-3 (Elastin) SB - IM MH - Cold Temperature MH - Elastin/*chemistry MH - Hydrophobic and Hydrophilic Interactions MH - Oligopeptides/chemistry MH - Peptides/*chemistry MH - Protein Structure, Secondary MH - Solutions/chemistry MH - Solvents/chemistry MH - Transition Temperature MH - Water/chemistry EDAT- 2014/08/22 06:00 MHDA- 2015/06/17 06:00 CRDT- 2014/08/22 06:00 PHST- 2014/09/02 [aheadofprint] AID - 10.1021/bm500658w [doi] PST - ppublish SO - Biomacromolecules. 2014 Oct 13;15(10):3522-30. doi: 10.1021/bm500658w. Epub 2014 Sep 2. PMID- 15545613 OWN - NLM STAT- MEDLINE DA - 20041124 DCOM- 20041227 LR - 20141120 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 101 IP - 47 DP - 2004 Nov 23 TI - TATA box binding protein induces structure in the recombinant glucocorticoid receptor AF1 domain. PG - 16425-30 AB - A number of transcription factor proteins contain domains that are fully or partially unstructured. The means by which such proteins acquire naturally folded conformations are not well understood. When they encounter their proper binding partner(s), several of these proteins adopt a folded conformation through an induced-fit mechanism. The glucocorticoid receptor (GR) is a ligand-activated transcription factor. Expressed independently as a recombinant peptide, the N-terminal transactivation domain (AF1) of the GR shows little structure and appears to exist as a collection of random coil configurations. The GR AF1 is known to interact with other transcription factors, including a critical component of the general transcription machinery proteins, the TATA box binding protein (TBP). We tested whether this interaction can lead to acquisition of structure in the GR AF1. Our results show that recombinant GR AF1 acquires a significant amount of helical content when it interacts with TBP. These structural changes were monitored by Fourier transform infrared and NMR spectroscopies, and by proteolytic digestions. Our results support a model in which TBP binding interaction with the GR AF1 induces significantly greater helical structure in the AF1 domain. This increased helical content in the GR AF1 appears to come mostly at the expense of random coil conformation. These results are in accordance with the hypothesis that an induced-fit mechanism gives structure to the GR AF1 when it encounters TBP. FAU - Kumar, Raj AU - Kumar R AD - Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, Galveston, TX 77555, USA. FAU - Volk, David E AU - Volk DE FAU - Li, Jianquan AU - Li J FAU - Lee, James C AU - Lee JC FAU - Gorenstein, David G AU - Gorenstein DG FAU - Thompson, E Brad AU - Thompson EB LA - eng GR - 1R01 DK58829/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20041115 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Receptors, Glucocorticoid) RN - 0 (Recombinant Proteins) RN - 0 (TATA-Box Binding Protein) SB - IM MH - Circular Dichroism MH - Humans MH - In Vitro Techniques MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Glucocorticoid/*chemistry/genetics/*metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Spectroscopy, Fourier Transform Infrared MH - TATA-Box Binding Protein/genetics/*metabolism PMC - PMC534534 OID - NLM: PMC534534 EDAT- 2004/11/17 09:00 MHDA- 2004/12/28 09:00 CRDT- 2004/11/17 09:00 PHST- 2004/11/15 [aheadofprint] AID - 0407160101 [pii] AID - 10.1073/pnas.0407160101 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16425-30. Epub 2004 Nov 15. PMID- 24952945 OWN - NLM STAT- MEDLINE DA - 20140802 DCOM- 20141215 LR - 20150401 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 289 IP - 31 DP - 2014 Aug 1 TI - Synergic role of nucleophosmin three-helix bundle and a flanking unstructured tail in the interaction with G-quadruplex DNA. PG - 21230-41 LID - 10.1074/jbc.M114.565010 [doi] AB - Nucleophosmin (NPM1) is a nucleocytoplasmic shuttling protein, mainly localized at nucleoli, that plays a number of functions in ribosome biogenesis and export, cell cycle control, and response to stress stimuli. NPM1 is the most frequently mutated gene in acute myeloid leukemia; mutations map to the C-terminal domain of the protein and cause its denaturation and aberrant cytoplasmic translocation. NPM1 C-terminal domain binds G-quadruplex regions at ribosomal DNA and at gene promoters, including the well characterized sequence from the nuclease-hypersensitive element III region of the c-MYC promoter. These activities are lost by the leukemic variant. Here we analyze the NPM1/G-quadruplex interaction, focusing on residues belonging to both the NPM1 terminal three-helix bundle and a lysine-rich unstructured tail, which has been shown to be necessary for high affinity recognition. We performed extended site-directed mutagenesis and measured binding rate constants through surface plasmon resonance analysis. These data, supported by molecular dynamics simulations, suggest that the unstructured tail plays a double role in the reaction mechanism. On the one hand, it facilitates the formation of an encounter complex through long range electrostatic interactions; on the other hand, it directly contacts the G-quadruplex scaffold through multiple and transient electrostatic interactions, significantly enlarging the contact surface. CI - (c) 2014 by The American Society for Biochemistry and Molecular Biology, Inc. FAU - Arcovito, Alessandro AU - Arcovito A AD - From the Istituto di Biochimica e Biochimica Clinica, Universita Cattolica del Sacro Cuore, 00168 Rome, Italy. FAU - Chiarella, Sara AU - Chiarella S AD - Ce.S.I. Centro Scienze dell'Invecchiamento, "Fondazione Universita D'Annunzio," 66013 Chieti, Italy, Dipartimento di Scienze Biochimiche, Sapienza Universita di Roma, 00185 Rome, Italy. FAU - Della Longa, Stefano AU - Della Longa S AD - Dipartimento di Medicina Clinica, Sanita Pubblica, Scienze della Vita e dell'Ambiente, Universita dell'Aquila, 67100 Coppito (L'Aquila), Italy. FAU - Di Matteo, Adele AU - Di Matteo A AD - Istituto di Biologia, Medicina Molecolare e NanoBiotecnologie, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy, and. FAU - Lo Sterzo, Carlo AU - Lo Sterzo C AD - Dipartimento di Scienze Biochimiche, Sapienza Universita di Roma, 00185 Rome, Italy. FAU - Scaglione, Giovanni Luca AU - Scaglione GL AD - From the Istituto di Biochimica e Biochimica Clinica, Universita Cattolica del Sacro Cuore, 00168 Rome, Italy. FAU - Federici, Luca AU - Federici L AD - Ce.S.I. Centro Scienze dell'Invecchiamento, "Fondazione Universita D'Annunzio," 66013 Chieti, Italy, Dipartimento di Scienze Sperimentali e Cliniche, Universita di Chieti "G. D'Annunzio," 66013 Chieti, Italy lfederici@unich.it. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140621 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA Primers) RN - 0 (Nuclear Proteins) RN - 117896-08-9 (nucleophosmin) SB - IM MH - Amino Acid Sequence MH - Base Sequence MH - DNA Primers MH - *G-Quadruplexes MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Nuclear Proteins/chemistry/metabolism/*physiology MH - Protein Binding MH - Sequence Homology, Amino Acid MH - Surface Plasmon Resonance PMC - PMC4118085 OID - NLM: PMC4118085 [Available on 08/01/15] OTO - NOTNLM OT - Encounter Complex OT - Flanking Fuzziness OT - Intrinsically Disordered Protein OT - Leukemia OT - Molecular Dynamics OT - Protein-DNA Interaction OT - Surface Plasmon Resonance (SPR) EDAT- 2014/06/24 06:00 MHDA- 2014/12/17 06:00 CRDT- 2014/06/23 06:00 PMCR- 2015/08/01 00:00 PHST- 2014/06/21 [aheadofprint] AID - M114.565010 [pii] AID - 10.1074/jbc.M114.565010 [doi] PST - ppublish SO - J Biol Chem. 2014 Aug 1;289(31):21230-41. doi: 10.1074/jbc.M114.565010. Epub 2014 Jun 21. PMID- 10339551 OWN - NLM STAT- MEDLINE DA - 19990624 DCOM- 19990624 LR - 20140615 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 96 IP - 11 DP - 1999 May 25 TI - Solution structure and peptide binding studies of the C-terminal src homology 3-like domain of the diphtheria toxin repressor protein. PG - 6119-24 AB - The diphtheria toxin repressor (DtxR) is the best-characterized member of a family of homologous proteins that regulate iron uptake and virulence gene expression in the Gram-positive bacteria. DtxR contains two domains that are separated by a short, unstructured linker. The N-terminal domain is structurally well-defined and is responsible for Fe2+ binding, dimerization, and DNA binding. The C-terminal domain adopts a fold similar to eukaryotic Src homology 3 domains, but the functional role of the C-terminal domain in repressor activity is unknown. The solution structure of the C-terminal domain, consisting of residues N130-L226 plus a 13-residue N-terminal extension, has been determined by using NMR spectroscopy. Residues before A147 are highly mobile and adopt a random coil conformation, but residues A147-L226 form a single structured domain consisting of five beta-strands and three helices arranged into a partially orthogonal, two-sheet beta-barrel, similar to the structure observed in the crystalline Co2+ complex of full-length DtxR. Chemical shift perturbation studies demonstrate that a proline-rich peptide corresponding to residues R125-G139 of intact DtxR binds to the C-terminal domain in a pocket formed by residues in beta-strands 2, 3, and 5, and helix 3. Binding of the proline-rich peptide by the C-terminal domain of DtxR presents an example of peptide binding by a prokaryotic Src homology 3-like protein. The results of this study, combined with previous x-ray studies of intact DtxR, provide insights into a possible biological function of the C-terminal domain in regulating repressor activity. FAU - Wang, G AU - Wang G AD - Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA. FAU - Wylie, G P AU - Wylie GP FAU - Twigg, P D AU - Twigg PD FAU - Caspar, D L AU - Caspar DL FAU - Murphy, J R AU - Murphy JR FAU - Logan, T M AU - Logan TM LA - eng SI - PDB/1BYM GR - CA47439/CA/NCI NIH HHS/United States GR - GM54035/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Bacterial Proteins) RN - 0 (DNA-Binding Proteins) RN - 0 (DtxR protein, Corynebacterium diphtheriae) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 0 (Solutions) RN - E1UOL152H7 (Iron) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/*metabolism MH - Binding Sites MH - Conserved Sequence MH - DNA-Binding Proteins/*chemistry/*metabolism MH - Gram-Positive Bacteria/metabolism MH - Iron/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/*chemistry/*metabolism MH - *Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Solutions MH - src Homology Domains PMC - PMC26845 OID - NLM: PMC26845 EDAT- 1999/05/26 MHDA- 1999/05/26 00:01 CRDT- 1999/05/26 00:00 PST - ppublish SO - Proc Natl Acad Sci U S A. 1999 May 25;96(11):6119-24. PMID- 19808665 OWN - NLM STAT- MEDLINE DA - 20091130 DCOM- 20091222 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 284 IP - 49 DP - 2009 Dec 4 TI - Characterization of the structure and intermolecular interactions between the connexin40 and connexin43 carboxyl-terminal and cytoplasmic loop domains. PG - 34257-71 LID - 10.1074/jbc.M109.039594 [doi] AB - Gap junctions are intercellular channels that allow the passage of ions, small molecules, and second messengers that are essential for the coordination of cellular function. They are formed by two hemichannels, each constituted by the oligomerization of six connexins (Cx). Among the 21 different human Cx isoforms, studies have suggested that in the heart, Cx40 and Cx43 can oligomerize to form heteromeric hemichannels. The mechanism of heteromeric channel regulation has not been clearly defined. Tissue ischemia leads to intracellular acidification and closure of Cx43 and Cx40 homomeric channels. However, coexpression of Cx40 and Cx43 in Xenopus oocytes enhances the pH sensitivity of the channel. This phenomenon requires the carboxyl-terminal (CT) part of both connexins. In this study we used different biophysical methods to determine the structure of the Cx40CT and characterize the Cx40CT/Cx43CT interaction. Our results revealed that the Cx40CT is an intrinsically disordered protein similar to the Cx43CT and that the Cx40CT and Cx43CT can interact. Additionally, we have identified an interaction between the Cx40CT and the cytoplasmic loop of Cx40 as well as between the Cx40CT and the cytoplasmic loop of Cx43 (and vice versa). Our studies support the "particle-receptor" model for pH gating of Cx40 and Cx43 gap junction channels and suggest that interactions between cytoplasmic regulatory domains (both homo- and hetero-connexin) could be important for the regulation of heteromeric channels. FAU - Bouvier, Denis AU - Bouvier D AD - Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA. FAU - Spagnol, Gaelle AU - Spagnol G FAU - Chenavas, Sylvie AU - Chenavas S FAU - Kieken, Fabien AU - Kieken F FAU - Vitrac, Heidi AU - Vitrac H FAU - Brownell, Sarah AU - Brownell S FAU - Kellezi, Admir AU - Kellezi A FAU - Forge, Vincent AU - Forge V FAU - Sorgen, Paul L AU - Sorgen PL LA - eng SI - PDB/2K7M GR - GM072631/GM/NIGMS NIH HHS/United States GR - HL039707/HL/NHLBI NIH HHS/United States GR - P30CA036727/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20091005 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Connexin 43) RN - 0 (Connexins) RN - 0 (Protein Isoforms) RN - 0 (connexin 40) SB - IM MH - Amino Acid Sequence MH - Animals MH - Connexin 43/*chemistry/metabolism MH - Connexins/*chemistry/metabolism MH - Cytoplasm/*metabolism MH - Gap Junctions/metabolism MH - Humans MH - Hydrogen-Ion Concentration MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Oocytes/metabolism MH - Protein Isoforms MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Xenopus PMC - PMC2797195 OID - NLM: PMC2797195 EDAT- 2009/10/08 06:00 MHDA- 2009/12/23 06:00 CRDT- 2009/10/08 06:00 PHST- 2009/10/05 [aheadofprint] AID - M109.039594 [pii] AID - 10.1074/jbc.M109.039594 [doi] PST - ppublish SO - J Biol Chem. 2009 Dec 4;284(49):34257-71. doi: 10.1074/jbc.M109.039594. Epub 2009 Oct 5. PMID- 11121423 OWN - NLM STAT- MEDLINE DA - 20010411 DCOM- 20010524 LR - 20071114 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 15 DP - 2001 Apr 13 TI - The cadherin cytoplasmic domain is unstructured in the absence of beta-catenin. A possible mechanism for regulating cadherin turnover. PG - 12301-9 AB - Cadherins are single pass transmembrane proteins that mediate Ca(2+)-dependent homophilic cell-cell adhesion by linking the cytoskeletons of adjacent cells. In adherens junctions, the cytoplasmic domain of cadherins bind to beta-catenin, which in turn binds to the actin-associated protein alpha-catenin. The physical properties of the E-cadherin cytoplasmic domain and its interactions with beta-catenin have been investigated. Proteolytic sensitivity, tryptophan fluorescence, circular dichroism, and (1)H NMR measurements indicate that murine E-cadherin cytoplasmic domain is unstructured. Upon binding to beta-catenin, the domain becomes resistant to proteolysis, suggesting that it structures upon binding. Cadherin-beta-catenin complex stability is modestly dependent on ionic strength, indicating that, contrary to previous proposals, the interaction is not dominated by electrostatics. Comparison of 18 cadherin sequences indicates that their cytoplasmic domains are unlikely to be structured in isolation. This analysis also reveals the presence of PEST sequences, motifs associated with ubiquitin/proteosome degradation, that overlap the previously identified beta-catenin-binding site. It is proposed that binding of cadherins to beta-catenin prevents recognition of degradation signals that are exposed in the unstructured cadherin cytoplasmic domain, favoring a cell surface population of catenin-bound cadherins capable of participating in cell adhesion. FAU - Huber, A H AU - Huber AH AD - Departments of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA. FAU - Stewart, D B AU - Stewart DB FAU - Laurents, D V AU - Laurents DV FAU - Nelson, W J AU - Nelson WJ FAU - Weis, W I AU - Weis WI LA - eng GR - GM35227/GM/NIGMS NIH HHS/United States GR - GM56169/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20001219 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (CTNNB1 protein, human) RN - 0 (Cadherins) RN - 0 (Cytoskeletal Proteins) RN - 0 (DNA Primers) RN - 0 (Recombinant Proteins) RN - 0 (Trans-Activators) RN - 0 (beta Catenin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Cadherins/chemistry/*metabolism MH - Cell Adhesion MH - Circular Dichroism MH - Cytoplasm/*metabolism MH - Cytoskeletal Proteins/*metabolism MH - DNA Primers MH - Humans MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Recombinant Proteins/metabolism MH - Sequence Homology, Amino Acid MH - Spectrometry, Fluorescence MH - *Trans-Activators MH - beta Catenin EDAT- 2000/12/31 19:15 MHDA- 2001/05/26 10:01 CRDT- 2000/12/31 19:15 PHST- 2000/12/19 [aheadofprint] AID - 10.1074/jbc.M010377200 [doi] AID - M010377200 [pii] PST - ppublish SO - J Biol Chem. 2001 Apr 13;276(15):12301-9. Epub 2000 Dec 19. PMID- 18533220 OWN - NLM STAT- MEDLINE DA - 20080623 DCOM- 20080924 LR - 20140903 IS - 0042-6822 (Print) IS - 0042-6822 (Linking) VI - 377 IP - 2 DP - 2008 Aug 1 TI - Potato virus A genome-linked protein VPg is an intrinsically disordered molten globule-like protein with a hydrophobic core. PG - 280-8 LID - 10.1016/j.virol.2008.04.025 [doi] AB - Genome-linked protein VPg of Potato virus A (PVA; genus Potyvirus) has essential functions in all critical steps of PVA infection, i.e. replication, movement, and virulence. Structural features of the recombinant PVA VPg were investigated with the aim to create an outline for structure-function relationships. Circular dichroism data of PVA VPg revealed a distinct near-UV spectrum indicating that the environment around its aromatic residues is structured but rather flexible, and a far-UV spectrum that was characterized by features typical for intrinsically disordered proteins. Temperature-induced denaturation followed a typical all-or-none transition whereas urea- and GdmHCl-induced denaturation proceeded via a route best described by a three-state-model. The conclusion drawn was that the overall structure of PVA VPg is significantly unstable even in the absence of denaturants. Acrylamide fluorescence quenching and 1-anilino-8-naphthalene sulfonate binding experiments together with 1D and 2D NMR data further verified that PVA VPg behaves as a partially folded species that contains a hydrophobic core domain. Regions predicted to be disordered in PVA VPg were the ones that were cut the fastest by trypsin whereas regions predicted to be structured and to contain the most conserved amino acids among potyvirus VPgs were trypsin-resistant. Amino acid composition analysis of potyvirus VPgs revealed a clear enrichment of disorder and depletion of structure-promoting residues. Taken together it seems that the native structure of PVA VPg, and probably that of potyviral VPg in general, resembles a partially disordered molten globule. Further experimentation is required to understand the functional regulation achieved via this property. FAU - Rantalainen, Kimmo I AU - Rantalainen KI AD - Department of Applied Chemistry and Microbiology, PO Box 27, FIN-00014, University of Helsinki, Finland. FAU - Uversky, Vladimir N AU - Uversky VN FAU - Permi, Perttu AU - Permi P FAU - Kalkkinen, Nisse AU - Kalkkinen N FAU - Dunker, A Keith AU - Dunker AK FAU - Makinen, Kristiina AU - Makinen K LA - eng GR - R01 GM071714-03/GM/NIGMS NIH HHS/United States GR - R01 LM007688-01A1S1/LM/NLM NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080603 PL - United States TA - Virology JT - Virology JID - 0110674 RN - 0 (Proteins) RN - 0 (Ribonucleoproteins) RN - 0 (Viral Nonstructural Proteins) RN - 0 (genome-linked viral protein, potato virus Y) SB - IM MH - *Genome, Viral MH - Hydrophobic and Hydrophilic Interactions MH - Magnetic Resonance Spectroscopy MH - Potyvirus/genetics/*metabolism MH - Proteins/chemistry/genetics/*metabolism MH - Ribonucleoproteins/chemistry/genetics/*metabolism MH - Solanaceae/metabolism/*virology MH - Temperature MH - Viral Nonstructural Proteins/chemistry/genetics/*metabolism PMC - PMC2796300 MID - NIHMS105698 OID - NLM: NIHMS105698 OID - NLM: PMC2796300 EDAT- 2008/06/06 09:00 MHDA- 2008/09/25 09:00 CRDT- 2008/06/06 09:00 PHST- 2008/01/21 [received] PHST- 2008/02/17 [revised] PHST- 2008/04/19 [accepted] PHST- 2008/06/03 [aheadofprint] AID - S0042-6822(08)00264-X [pii] AID - 10.1016/j.virol.2008.04.025 [doi] PST - ppublish SO - Virology. 2008 Aug 1;377(2):280-8. doi: 10.1016/j.virol.2008.04.025. Epub 2008 Jun 3. PMID- 19553667 OWN - NLM STAT- MEDLINE DA - 20090831 DCOM- 20091005 LR - 20150407 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 284 IP - 36 DP - 2009 Sep 4 TI - A progesterone receptor co-activator (JDP2) mediates activity through interaction with residues in the carboxyl-terminal extension of the DNA binding domain. PG - 24415-24 LID - 10.1074/jbc.M109.003244 [doi] AB - Progesterone receptor (PR) belongs to the nuclear receptor family of ligand-dependent transcription factors and mediates the major biological effects of progesterone. Transcriptional co-activators that are recruited by PR through the carboxyl-terminal ligand binding domain have been studied extensively. Much less is known about co-activators that interact with other regions of receptors. Jun dimerization protein 2 (JDP2) is a PR co-activator that enhances the transcriptional activity of the amino-terminal domain by increasing the alpha-helical content and stability of the intrinsically disordered amino-terminal domain. To gain insights into the mechanism of JDP2 co-activation of PR, the structural basis of JDP2-PR interaction was analyzed using NMR. The smallest regions of each protein needed for efficient protein interaction were used for NMR and included the basic region plus leucine zipper (bZIP) domain of JDP2 and the core zinc modules of the PR DNA binding domain plus the intrinsically disordered carboxyl-terminal extension (CTE) of the DNA binding domain. Chemical shift changes in PR upon titration with JDP2 revealed that most of the residues involved in binding of JDP2 reside within the CTE. The importance of the CTE for binding JDP2 was confirmed by peptide competition and mutational analyses. Point mutations within CTE sites identified by NMR and a CTE domain swapping experiment also confirmed the functional importance of JDP2 interaction with the CTE for enhancement of PR transcriptional activity. These studies provide insights into the role and functional importance of the CTE for co-activator interactions. FAU - Hill, Krista K AU - Hill KK AD - Molecular Biology Program, School of Medicine, University of Colorado Denver, Aurora, Colorado 80045, USA. FAU - Roemer, Sarah C AU - Roemer SC FAU - Jones, David N M AU - Jones DN FAU - Churchill, Mair E A AU - Churchill ME FAU - Edwards, Dean P AU - Edwards DP LA - eng GR - P30 CA046934/CA/NCI NIH HHS/United States GR - R01 GM059456/GM/NIGMS NIH HHS/United States GR - R01 GM079154/GM/NIGMS NIH HHS/United States GR - R01 GM079154-04/GM/NIGMS NIH HHS/United States PT - Journal Article DEP - 20090624 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (JDP2 protein, human) RN - 0 (Receptors, Progesterone) RN - 0 (Repressor Proteins) RN - 0 (Trans-Activators) SB - IM MH - Animals MH - COS Cells MH - Cercopithecus aethiops MH - Humans MH - Leucine Zippers MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary/physiology MH - Receptors, Progesterone/*chemistry/metabolism MH - Repressor Proteins/*chemistry/metabolism MH - Structure-Activity Relationship MH - Trans-Activators/*chemistry/metabolism PMC - PMC2782034 OID - NLM: PMC2782034 EDAT- 2009/06/26 09:00 MHDA- 2009/10/06 06:00 CRDT- 2009/06/26 09:00 PHST- 2009/06/24 [aheadofprint] AID - M109.003244 [pii] AID - 10.1074/jbc.M109.003244 [doi] PST - ppublish SO - J Biol Chem. 2009 Sep 4;284(36):24415-24. doi: 10.1074/jbc.M109.003244. Epub 2009 Jun 24. PMID- 24650897 OWN - NLM STAT- MEDLINE DA - 20140429 DCOM- 20140630 LR - 20141120 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 426 IP - 10 DP - 2014 May 15 TI - Intrinsic disorder mediates cooperative signal transduction in STIM1. PG - 2082-97 LID - 10.1016/j.jmb.2014.03.006 [doi] LID - S0022-2836(14)00130-2 [pii] AB - Intrinsically disordered domains have been reported to play important roles in signal transduction networks by introducing cooperativity into protein-protein interactions. Unlike intrinsically disordered domains that become ordered upon binding, the EF-SAM domain in the stromal interaction molecule (STIM) 1 is distinct in that it is ordered in the monomeric state and partially unfolded in its oligomeric state, with the population of the two states depending on the local Ca(2+) concentration. The oligomerization of STIM1, which triggers extracellular Ca(2+) influx, exhibits cooperativity with respect to the local endoplasmic reticulum Ca(2+) concentration. Although the physiological importance of the oligomerization reaction is well established, the mechanism of the observed cooperativity is not known. Here, we examine the response of the STIM1 EF-SAM domain to changes in Ca(2+) concentration using mathematical modeling based on in vitro experiments. We find that the EF-SAM domain partially unfolds and dimerizes cooperatively with respect to Ca(2+) concentration, with Hill coefficients and half-maximal activation concentrations very close to the values observed in vivo for STIM1 redistribution and extracellular Ca(2+) influx. Our mathematical model of the dimerization reaction agrees quantitatively with our analytical ultracentrifugation-based measurements and previously published free energies of unfolding. A simple interpretation of these results is that Ca(2+) loss effectively acts as a denaturant, enabling cooperative dimerization and robust signal transduction. We present a structural model of the Ca(2+)-unbound EF-SAM domain that is consistent with a wide range of evidence, including resistance to proteolytic cleavage of the putative dimerization portion. CI - Copyright (c) 2014 The Authors. Published by Elsevier Ltd.. All rights reserved. FAU - Furukawa, Yukio AU - Furukawa Y AD - Nanobiology Laboratories, Protonic NanoMachine Group, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan. FAU - Teraguchi, Shunsuke AU - Teraguchi S AD - Laboratory of Host Defense, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan; Quantitative Immunology Research Unit, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan. FAU - Ikegami, Takahisa AU - Ikegami T AD - Laboratory of Advanced Protein Characterization, Research Center for State-of-the-Art Functional Protein Analysis, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan. FAU - Dagliyan, Onur AU - Dagliyan O AD - Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. FAU - Jin, Lin AU - Jin L AD - Laboratory of Systems Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan. FAU - Hall, Damien AU - Hall D AD - Laboratory of Systems Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan; Research School of Chemistry, Australian National University Section on Biophysical Chemistry, Acton, 0200 ACT, Australia. FAU - Dokholyan, Nikolay V AU - Dokholyan NV AD - Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. FAU - Namba, Keiichi AU - Namba K AD - Nanobiology Laboratories, Protonic NanoMachine Group, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan. FAU - Akira, Shizuo AU - Akira S AD - Laboratory of Host Defense, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan. FAU - Kurosaki, Tomohiro AU - Kurosaki T AD - Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan. FAU - Baba, Yoshihiro AU - Baba Y AD - Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan. FAU - Standley, Daron M AU - Standley DM AD - Laboratory of Systems Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan. Electronic address: standley@ifrec.osaka-u.ac.jp. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140317 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Calcium Channels) RN - 0 (Membrane Glycoproteins) RN - 0 (Stim1 protein, mouse) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Calcium/metabolism MH - Calcium Channels MH - Membrane Glycoproteins/*chemistry/*metabolism MH - Mice MH - Models, Molecular MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - *Protein Folding MH - Protein Interaction Domains and Motifs MH - Protein Multimerization MH - Proteolysis MH - Signal Transduction OTO - NOTNLM OT - STIM1 OT - cooperativity OT - intrinsic disorder OT - store-operated calcium entry EDAT- 2014/03/22 06:00 MHDA- 2014/07/01 06:00 CRDT- 2014/03/22 06:00 PHST- 2013/11/03 [received] PHST- 2014/02/10 [revised] PHST- 2014/03/12 [accepted] PHST- 2014/03/17 [aheadofprint] AID - S0022-2836(14)00130-2 [pii] AID - 10.1016/j.jmb.2014.03.006 [doi] PST - ppublish SO - J Mol Biol. 2014 May 15;426(10):2082-97. doi: 10.1016/j.jmb.2014.03.006. Epub 2014 Mar 17. PMID- 21212361 OWN - NLM STAT- MEDLINE DA - 20110126 DCOM- 20110426 LR - 20150129 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 108 IP - 4 DP - 2011 Jan 25 TI - An intrinsically disordered C terminus allows the La protein to assist the biogenesis of diverse noncoding RNA precursors. PG - 1308-13 LID - 10.1073/pnas.1017085108 [doi] AB - The La protein binds the 3' ends of many newly synthesized noncoding RNAs, protecting these RNAs from nucleases and influencing folding, maturation, and ribonucleoprotein assembly. Although 3' end binding by La involves the N-terminal La domain and adjacent RNA recognition motif (RRM), the mechanisms by which La stabilizes diverse RNAs from nucleases and assists subsequent events in their biogenesis are unknown. Here we report that a conserved feature of La proteins, an intrinsically disordered C terminus, is required for the accumulation of certain noncoding RNA precursors and for the role of the Saccharomyces cerevisiae La protein Lhp1p in assisting formation of correctly folded pre-tRNA anticodon stems in vivo. Footprinting experiments using purified Lhp1p reveal that the C terminus is required to protect a pre-tRNA anticodon stem from chemical modification. Although the C terminus of Lhp1p is hypersensitive to proteases in vitro, it becomes protease-resistant upon binding pre-tRNAs, U6 RNA, or pre-5S rRNA. Thus, while high affinity binding to 3' ends requires the La domain and RRM, a conformationally flexible C terminus allows La to interact productively with a diversity of noncoding RNA precursors. We propose that intrinsically disordered domains adjacent to well characterized RNA-binding motifs in other promiscuous RNA-binding proteins may similarly contribute to the ability of these proteins to influence the cellular fates of multiple distinct RNA targets. FAU - Kucera, Nathan J AU - Kucera NJ AD - Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA. FAU - Hodsdon, Michael E AU - Hodsdon ME FAU - Wolin, Sandra L AU - Wolin SL LA - eng GR - CA108992/CA/NCI NIH HHS/United States GR - GM048410/GM/NIGMS NIH HHS/United States GR - R01 GM048410/GM/NIGMS NIH HHS/United States GR - T32 GM008730/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20110106 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Anticodon) RN - 0 (LHP1 protein, S cerevisiae) RN - 0 (RNA Precursors) RN - 0 (RNA, Fungal) RN - 0 (RNA, Ribosomal) RN - 0 (RNA, Small Nuclear) RN - 0 (RNA, Untranslated) RN - 0 (RNA-Binding Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (U6 small nuclear RNA) RN - 9014-25-9 (RNA, Transfer) RN - EC 3.4.21.1 (Chymotrypsin) RN - EC 3.4.21.4 (Trypsin) SB - IM MH - Amino Acid Sequence MH - Anticodon/genetics/metabolism MH - Chymotrypsin/metabolism MH - Electrophoretic Mobility Shift Assay MH - Immunoblotting MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Nucleic Acid Conformation MH - Protein Binding MH - Protein Structure, Tertiary MH - RNA Precursors/genetics/*metabolism MH - RNA, Fungal/genetics/*metabolism MH - RNA, Ribosomal/genetics/metabolism MH - RNA, Small Nuclear/genetics/metabolism MH - RNA, Transfer/genetics/metabolism MH - RNA, Untranslated/chemistry/genetics/*metabolism MH - RNA-Binding Proteins/chemistry/genetics/*metabolism MH - Saccharomyces cerevisiae/genetics/metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism MH - Sequence Homology, Amino Acid MH - Trypsin/metabolism PMC - PMC3029687 OID - NLM: PMC3029687 EDAT- 2011/01/08 06:00 MHDA- 2011/04/27 06:00 CRDT- 2011/01/08 06:00 PHST- 2011/01/06 [aheadofprint] AID - 1017085108 [pii] AID - 10.1073/pnas.1017085108 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1308-13. doi: 10.1073/pnas.1017085108. Epub 2011 Jan 6. PMID- 21925568 OWN - NLM STAT- MEDLINE DA - 20111128 DCOM- 20120319 LR - 20141022 IS - 1872-8057 (Electronic) IS - 0303-7207 (Linking) VI - 348 IP - 2 DP - 2012 Jan 30 TI - Nuclear hormone receptor co-repressors: structure and function. PG - 440-9 LID - 10.1016/j.mce.2011.08.033 [doi] AB - Co-repressor proteins, such as SMRT and NCoR, mediate the repressive activity of unliganded nuclear receptors and other transcription factors. They appear to act as intrinsically disordered "hub proteins" that integrate the activities of a range of transcription factors with a number of histone modifying enzymes. Although these co-repressor proteins are challenging targets for structural studies due to their largely unstructured character, a number of structures have recently been determined of co-repressor interaction regions in complex with their interacting partners. These have yielded considerable insight into the mechanism of assembly of these complexes, the structural basis for the specificity of the interactions and also open opportunities for targeting these interactions therapeutically. CI - Copyright (c) 2011 Elsevier Ireland Ltd. All rights reserved. FAU - Watson, Peter J AU - Watson PJ AD - Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester LE1 9HN, UK. FAU - Fairall, Louise AU - Fairall L FAU - Schwabe, John W R AU - Schwabe JW LA - eng GR - 085408/Wellcome Trust/United Kingdom GR - 100237/Wellcome Trust/United Kingdom GR - WT085408/Wellcome Trust/United Kingdom GR - WT091820/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20110908 PL - Ireland TA - Mol Cell Endocrinol JT - Molecular and cellular endocrinology JID - 7500844 RN - 0 (Multiprotein Complexes) RN - 0 (Nuclear Receptor Co-Repressor 1) RN - 0 (Nuclear Receptor Co-Repressor 2) RN - 0 (Receptors, Cytoplasmic and Nuclear) RN - EC 3.5.1.98 (Histone Deacetylases) SB - IM MH - Animals MH - Enzyme Activation MH - Gene Expression Regulation MH - Histone Deacetylases/metabolism MH - Humans MH - Multiprotein Complexes/chemistry MH - Nuclear Receptor Co-Repressor 1/*metabolism MH - Nuclear Receptor Co-Repressor 2/*metabolism MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - Receptors, Cytoplasmic and Nuclear/*metabolism PMC - PMC3315023 OID - NLM: PMC3315023 EDAT- 2011/09/20 06:00 MHDA- 2012/03/20 06:00 CRDT- 2011/09/20 06:00 PHST- 2011/04/19 [received] PHST- 2011/08/17 [revised] PHST- 2011/08/25 [accepted] PHST- 2011/09/08 [aheadofprint] AID - S0303-7207(11)00515-6 [pii] AID - 10.1016/j.mce.2011.08.033 [doi] PST - ppublish SO - Mol Cell Endocrinol. 2012 Jan 30;348(2):440-9. doi: 10.1016/j.mce.2011.08.033. Epub 2011 Sep 8. PMID- 22848679 OWN - NLM STAT- MEDLINE DA - 20120731 DCOM- 20130110 LR - 20141105 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 7 DP - 2012 TI - NMR structure of Hsp12, a protein induced by and required for dietary restriction-induced lifespan extension in yeast. PG - e41975 LID - 10.1371/journal.pone.0041975 [doi] AB - Dietary restriction (DR) extends lifespan in yeast, worms, flies and mammals, suggesting that it may act via conserved processes. However, the downstream mechanisms by which DR increases lifespan remain unclear. We used a gel based proteomic strategy to identify proteins whose expression was induced by DR in yeast and thus may correlate with longevity. One protein up-regulated by DR was Hsp12, a small heat shock protein induced by various manipulations known to retard ageing. Lifespan extension by growth on 0.5% glucose (DR) was abolished in an hsp12Delta strain, indicating that Hsp12 is essential for the longevity effect of DR. In contrast, deletion of HSP12 had no effect on growth under DR conditions or a variety of environmental stresses, indicating that the effect of Hsp12 on lifespan is not due to increased general stress resistance. Unlike other small heat shock proteins, recombinant Hsp12 displayed negligible in vitro molecular chaperone activity, suggesting that its cellular function does not involve preventing protein aggregation. NMR analysis indicated that Hsp12 is monomeric and intrinsically unfolded in solution, but switches to a 4-helical conformation upon binding to membrane-mimetic SDS micelles. The structure of micelle-bound Hsp12 reported here is consistent with its recently proposed function as a membrane-stabilising 'lipid chaperone'. Taken together, our data suggest that DR-induced Hsp12 expression contributes to lifespan extension, possibly via membrane alterations. FAU - Herbert, Andrew P AU - Herbert AP AD - Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom. FAU - Riesen, Michele AU - Riesen M FAU - Bloxam, Leanne AU - Bloxam L FAU - Kosmidou, Effie AU - Kosmidou E FAU - Wareing, Brian M AU - Wareing BM FAU - Johnson, James R AU - Johnson JR FAU - Phelan, Marie M AU - Phelan MM FAU - Pennington, Stephen R AU - Pennington SR FAU - Lian, Lu-Yun AU - Lian LY FAU - Morgan, Alan AU - Morgan A LA - eng GR - 090077/Z/09/Z/Wellcome Trust/United Kingdom GR - ERA16235/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120727 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (HSP12 protein, S cerevisiae) RN - 0 (Heat-Shock Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - IY9XDZ35W2 (Glucose) SB - IM MH - Gene Expression Regulation, Fungal MH - Glucose/*metabolism MH - Heat-Shock Proteins/*chemistry/*metabolism MH - Models, Molecular MH - *Nuclear Magnetic Resonance, Biomolecular MH - Phenotype MH - Protein Structure, Secondary MH - Proteomics MH - Saccharomyces cerevisiae/cytology/*metabolism/physiology MH - Saccharomyces cerevisiae Proteins/*chemistry/*metabolism MH - Time Factors PMC - PMC3407059 OID - NLM: PMC3407059 EDAT- 2012/08/01 06:00 MHDA- 2013/01/11 06:00 CRDT- 2012/08/01 06:00 PHST- 2012/05/13 [received] PHST- 2012/06/26 [accepted] PHST- 2012/07/27 [epublish] AID - 10.1371/journal.pone.0041975 [doi] AID - PONE-D-11-08927 [pii] PST - ppublish SO - PLoS One. 2012;7(7):e41975. doi: 10.1371/journal.pone.0041975. Epub 2012 Jul 27. PMID- 25116152 OWN - NLM STAT- In-Process DA - 20140813 IS - 0948-5023 (Electronic) IS - 0948-5023 (Linking) VI - 20 IP - 8 DP - 2014 Aug TI - Computational approaches for evaluating the effect of sequence variations and the intrinsically disordered C-terminal region of the Helicobacter pylori CagA protein on the interaction with tyrosine kinase Src. PG - 2406 LID - 10.1007/s00894-014-2406-2 [doi] AB - The Helicobacter pylori CagA protein was the first bacterial oncoprotein to be identified as important in the development of human malignancies such as gastric cancer. It is not clear how it is able to deregulate a set of cell control mechanisms to induce carcinogenesis following translocation into human gastric epithelial cells. It is likely, however, that structural variations in the CagA sequence alter its affinity with the host proteins inducing differences in the pathogenicity of different H. pylori strains. Using the recently elucidated N-terminal 3D structure of H. pylori CagA, information on the full cagA gene sequence, and intrinsically disordered protein structure predictions methods we evaluated the interaction of different CagA variants with the kinase Src. An automated docking followed by molecular dynamics simulations were performed to explore CagA interaction modes with Src, one of its cellular partners. The computational approach let us establish that even in the presence of the same number and type of EPIYA motifs, CagA protein can reveal different spatial distributions. Based on the lowest affinity energy and higher number of interactions it was established that the principal forces governing the CagA-Src interaction are electrostatic. Results showed that EPIYA-D models presents higher affinity with some host proteins than EPIYA-C. Thus, we highlight the importance and advantage of the use of computational tools in combining chemical and biological data with bioinformatics for modeling and prediction purposes in some cases where experimental techniques present limitations. FAU - Delgado, Paula AU - Delgado P AD - Grupo de Diseno de Productos y Procesos, Chemical Engineering Department, Universidad de los Andes, Bogota, Colombia. FAU - Penaranda, Natalia AU - Penaranda N FAU - Zamora, Maria Antonia AU - Zamora MA FAU - del Pilar Delgado, Maria AU - del Pilar Delgado M FAU - Bohorquez, Eliana AU - Bohorquez E FAU - Castro, Harold AU - Castro H FAU - Barrios, Andres Fernando Gonzalez AU - Barrios AF FAU - Jaramillo, Carlos AU - Jaramillo C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140814 PL - Germany TA - J Mol Model JT - Journal of molecular modeling JID - 9806569 SB - IM EDAT- 2014/08/15 06:00 MHDA- 2014/08/15 06:00 CRDT- 2014/08/14 06:00 PHST- 2013/07/17 [received] PHST- 2014/07/29 [accepted] PHST- 2014/08/14 [aheadofprint] AID - 10.1007/s00894-014-2406-2 [doi] PST - ppublish SO - J Mol Model. 2014 Aug;20(8):2406. doi: 10.1007/s00894-014-2406-2. Epub 2014 Aug 14. PMID- 17176085 OWN - NLM STAT- MEDLINE DA - 20070306 DCOM- 20080111 LR - 20140924 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 45 IP - 51 DP - 2006 Dec 26 TI - Micelle-induced folding of spinach thylakoid soluble phosphoprotein of 9 kDa and its functional implications. PG - 15633-43 AB - Thylakoid soluble phosphoprotein of 9 kDa (TSP9) has been identified as a plant-specific protein in the photosynthetic thylakoid membrane (Carlberg et al. (2003) Proc. Natl. Acad. Sci. 100, 757-762). Nonphosphorylated TSP9 is associated with the membrane, whereas, after light-induced phosphorylation, a fraction of the phosphorylated TSP9 is released into the aqueous stroma. By NMR spectroscopy, we have determined the structural features of nonphosphorylated TSP9 both in aqueous solution and in membrane mimetic micelles. The results show that both wild type nonphosphorylated TSP9 and a triple-mutant (T46E + T53E + T60E) mimic of the triphosphorylated form of TSP9 are disordered under aqueous conditions, but adopt an ordered conformation in the presence of detergent micelles. The micelle-induced structural features, which are similar in micelles either of SDS or dodecylphosphocholine (DPC), consist of an N-terminal alpha-helix, which may represent the primary site of interaction between TSP9 and binding partners, and a less structured helical turn near the C-terminus. These structured elements contain mainly hydrophobic residues. NMR relaxation data for nonphosphorylated TSP9 in SDS micelles indicated that the molecule is highly flexible with the highest order in the N-terminal alpha-helix. Intermolecular NOE signals, as well as spin probe-induced broadening of NMR signals, demonstrated that the SDS micelles contact both the structured and a portion of the unstructured regions of TSP9, in particular, those containing the three phosphorylation sites (T46, T53, and T60). This interaction may explain the selective dissociation of phosphorylated TSP9 from the membrane. Our study presents a structural model for the role played by the structured and unstructured regions of TSP9 in its membrane association and biological function. FAU - Song, Jikui AU - Song J AD - Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706-1544, USA. FAU - Lee, Min S AU - Lee MS FAU - Carlberg, Inger AU - Carlberg I FAU - Vener, Alexander V AU - Vener AV FAU - Markley, John L AU - Markley JL LA - eng SI - PDB/2FFT GR - P41 GM066326/GM/NIGMS NIH HHS/United States GR - P41 GM066326-05/GM/NIGMS NIH HHS/United States GR - P41 GM66326/GM/NIGMS NIH HHS/United States GR - P41 RR002301/RR/NCRR NIH HHS/United States GR - P41 RR002301-200133/RR/NCRR NIH HHS/United States GR - P41 RR02301/RR/NCRR NIH HHS/United States GR - P50 GM64598/GM/NIGMS NIH HHS/United States GR - U54 GM074901/GM/NIGMS NIH HHS/United States GR - U54 GM074901/GM/NIGMS NIH HHS/United States GR - U54 GM074901-03/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20061208 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Membrane Proteins) RN - 0 (Micelles) RN - 0 (Phosphoproteins) RN - 0 (Photosystem II Protein Complex) SB - IM MH - Crystallography, X-Ray MH - Magnetic Resonance Spectroscopy MH - Membrane Proteins/chemistry/genetics/physiology MH - *Micelles MH - Molecular Weight MH - Mutagenesis, Site-Directed MH - Phosphoproteins/*chemistry/genetics/physiology MH - Phosphorylation MH - Photosystem II Protein Complex/*chemistry/genetics/physiology MH - Protein Conformation MH - *Protein Folding MH - Solubility MH - *Spinacia oleracea MH - Thermodynamics MH - Thylakoids/*chemistry/genetics PMC - PMC2533273 MID - NIHMS61717 OID - NLM: NIHMS61717 OID - NLM: PMC2533273 EDAT- 2006/12/21 09:00 MHDA- 2008/01/12 09:00 CRDT- 2006/12/21 09:00 PHST- 2006/12/08 [aheadofprint] AID - 10.1021/bi062148m [doi] PST - ppublish SO - Biochemistry. 2006 Dec 26;45(51):15633-43. Epub 2006 Dec 8. PMID- 14530265 OWN - NLM STAT- MEDLINE DA - 20031222 DCOM- 20040210 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 52 DP - 2003 Dec 26 TI - The kinesin family member BimC contains a second microtubule binding region attached to the N terminus of the motor domain. PG - 52315-22 AB - The kinesin family member BimC has a highly positively charged domain of approximately 70 amino acids at the N terminus of the motor domain. Motor domain constructs of BimC were prepared with and without this extra domain to determine its influence. The level of microtubules needed for half saturation of the ATPase of BimC motor domain constructs is reduced by approximately 7000-fold at low ionic strength upon addition of this extra N-terminal extension. Although the change in microtubule affinity is less at higher salt, addition of the N-terminal domain still produces a 20-fold increase in affinity for microtubules in 200 mm potassium acetate. A fusion protein of the N-terminal domain and thioredoxin binds tightly to MTs at low salt, consistent with the increased affinity of motor domain constructs (which contain the N-terminal domain) being due to the additional binding of the N-terminal domain to the microtubule. Hydrodynamic analysis indicates that the N-terminal extension is in a highly extended conformation, suggesting that it may be intrinsically disordered. Fusion of the N-terminal extension of BimC onto the motor domain of conventional kinesin produces a similar large increase in microtubule affinity without significant reduction in kcat or velocity in an in vitro motility assay, suggesting that the N-terminal extension can act in a modular manner to increase the microtubule affinity of kinesin motor domains without a decrease in velocity. FAU - Stock, Maryanne F AU - Stock MF AD - Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA. FAU - Chu, Jessica AU - Chu J FAU - Hackney, David D AU - Hackney DD LA - eng GR - NS28562/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20031006 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (BimC protein, Aspergillus nidulans) RN - 0 (DNA, Complementary) RN - 0 (Fungal Proteins) RN - 0 (Ions) RN - 0 (Recombinant Fusion Proteins) RN - 059QF0KO0R (Water) RN - 52500-60-4 (Thioredoxins) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 3.6.1.- (Kinesin) RN - JAC85A2161 (Adenine) RN - M911911U02 (Potassium Acetate) RN - P39Y9652YJ (Kinetin) SB - IM MH - Adenine/*analogs & derivatives/chemistry MH - Adenosine Triphosphatases/chemistry MH - Amino Acid Sequence MH - Animals MH - Aspergillus nidulans/metabolism MH - Cell Movement MH - Chromatography, Gel MH - DNA, Complementary/metabolism MH - Dose-Response Relationship, Drug MH - Drosophila MH - Escherichia coli/metabolism MH - Fungal Proteins/*chemistry MH - Ions MH - Kinesin/*chemistry MH - Kinetics MH - Kinetin MH - Microtubules/*metabolism MH - Plasmids/metabolism MH - Potassium Acetate/chemistry MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - Rats MH - Recombinant Fusion Proteins/metabolism MH - Sequence Homology, Amino Acid MH - Thioredoxins/chemistry MH - Water/chemistry EDAT- 2003/10/08 05:00 MHDA- 2004/02/11 05:00 CRDT- 2003/10/08 05:00 PHST- 2003/10/06 [aheadofprint] AID - 10.1074/jbc.M309419200 [doi] AID - M309419200 [pii] PST - ppublish SO - J Biol Chem. 2003 Dec 26;278(52):52315-22. Epub 2003 Oct 6. PMID- 9398523 OWN - NLM STAT- MEDLINE DA - 19980114 DCOM- 19980114 LR - 20101019 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 274 IP - 2 DP - 1997 Nov 28 TI - NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein. PG - 152-9 AB - A 130-residue fragment of the Staphylococcus aureus fibronectin-binding protein has been found to exist in a highly unfolded conformation at neutral pH. Measurement of experimental NMR 3JHNalpha coupling constants provides evidence for individual residues having distinct main-chain conformational preferences that are dependent both on the amino acid concerned and on neighbouring residues in the sequence. Analysis shows that these variations in the populations of individual residues can be explained in detail in terms of statistical distributions of conformational states derived from the protein data base. In particular, when the preceding residue has a beta-branched or aromatic side-chain, a significant increase occurs in the population of the less sterically restricted b region of phi,psi space. The results indicate that the local structure of the fibronectin binding protein in solution, under conditions where it displays full activity, approximates very closely to a statistical random coil structure. This may be an important feature in the biological role of this and other polypeptides involved in protein-protein interactions. CI - Copyright 1997 Academic Press Limited. FAU - Penkett, C J AU - Penkett CJ AD - Oxford Centre for Molecular Sciences and New Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK. FAU - Redfield, C AU - Redfield C FAU - Dodd, I AU - Dodd I FAU - Hubbard, J AU - Hubbard J FAU - McBay, D L AU - McBay DL FAU - Mossakowska, D E AU - Mossakowska DE FAU - Smith, R A AU - Smith RA FAU - Dobson, C M AU - Dobson CM FAU - Smith, L J AU - Smith LJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Adhesins, Bacterial) RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (Peptide Fragments) RN - 0 (fibronectin-binding proteins, bacterial) SB - IM MH - *Adhesins, Bacterial MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry MH - Carrier Proteins/*chemistry MH - Computer Simulation MH - Databases as Topic MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/chemistry MH - *Protein Conformation MH - *Protein Folding MH - Staphylococcus aureus/*chemistry EDAT- 1998/02/12 MHDA- 1998/02/12 00:01 CRDT- 1998/02/12 00:00 AID - S0022-2836(97)91369-3 [pii] AID - 10.1006/jmbi.1997.1369 [doi] PST - ppublish SO - J Mol Biol. 1997 Nov 28;274(2):152-9. PMID- 8070397 OWN - NLM STAT- MEDLINE DA - 19940929 DCOM- 19940929 LR - 20130922 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 13 IP - 16 DP - 1994 Aug 15 TI - Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. PG - 3669-77 AB - The crystal structure of Thermus thermophilus elongation factor G without guanine nucleotide was determined to 2.85 A. This GTPase has five domains with overall dimensions of 50 x 60 x 118 A. The GTP binding domain has a core common to other GTPases with a unique subdomain which probably functions as an intrinsic nucleotide exchange factor. Domains I and II are homologous to elongation factor Tu and their arrangement, both with and without GDP, is more similar to elongation factor Tu in complex with a GTP analogue than with GDP. Domains III and V show structural similarities to ribosomal proteins. Domain IV protrudes from the main body of the protein and has an extraordinary topology with a left-handed cross-over connection between two parallel beta-strands. FAU - AEvarsson, A AU - AEvarsson A AD - Department of Molecular Biophysics, University of Lund, Sweden. FAU - Brazhnikov, E AU - Brazhnikov E FAU - Garber, M AU - Garber M FAU - Zheltonosova, J AU - Zheltonosova J FAU - Chirgadze, Y AU - Chirgadze Y FAU - al-Karadaghi, S AU - al-Karadaghi S FAU - Svensson, L A AU - Svensson LA FAU - Liljas, A AU - Liljas A LA - eng SI - GENBANK/P33998 PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (Peptide Elongation Factor G) RN - 0 (Peptide Elongation Factors) RN - 0 (RNA-Binding Proteins) RN - 0 (Ribosomal Proteins) RN - 146-91-8 (Guanosine Diphosphate) RN - 86-01-1 (Guanosine Triphosphate) RN - EC 3.6.1.- (GTP Phosphohydrolase-Linked Elongation Factors) SB - IM MH - Amino Acid Sequence MH - Crystallography, X-Ray MH - GTP Phosphohydrolase-Linked Elongation Factors/*chemistry/metabolism MH - Guanosine Diphosphate/metabolism MH - Guanosine Triphosphate/metabolism MH - Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Peptide Elongation Factor G MH - Peptide Elongation Factors/*chemistry/metabolism MH - Protein Conformation MH - RNA-Binding Proteins/chemistry MH - Ribosomal Proteins/chemistry MH - Thermus thermophilus/chemistry/*enzymology PMC - PMC395277 OID - NLM: PMC395277 EDAT- 1994/08/15 MHDA- 1994/08/15 00:01 CRDT- 1994/08/15 00:00 PST - ppublish SO - EMBO J. 1994 Aug 15;13(16):3669-77. PMID- 16894158 OWN - NLM STAT- MEDLINE DA - 20060816 DCOM- 20061107 LR - 20141223 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 103 IP - 33 DP - 2006 Aug 15 TI - Competitive recruitment of the periplasmic translocation portal TolB by a natively disordered domain of colicin E9. PG - 12353-8 AB - The natively disordered N-terminal 83-aa translocation (T) domain of E group nuclease colicins recruits OmpF to a colicin-receptor complex in the outer membrane (OM) as well as TolB in the periplasm of Escherichia coli, the latter triggering translocation of the toxin across the OM. We have identified the 16-residue TolB binding epitope in the natively disordered T-domain of the nuclease colicin E9 (ColE9) and solved the crystal structure of the complex. ColE9 folds into a distorted hairpin within a canyon of the six-bladed beta-propeller of TolB, using two tryptophans to bolt the toxin to the canyon floor and numerous intramolecular hydrogen bonds to stabilize the bound conformation. This mode of binding enables colicin side chains to hydrogen-bond TolB residues in and around the channel that runs through the beta-propeller and that constitutes the binding site of peptidoglycan-associated lipoprotein (Pal). Pal is a globular binding partner of TolB, and their association is known to be important for OM integrity. The structure is therefore consistent with translocation models wherein the colicin disrupts the TolB-Pal complex causing local instability of the OM as a prelude to toxin import. Intriguingly, Ca(2+) ions, which bind within the beta-propeller channel and switch the surface electrostatics from negative to positive, are needed for the negatively charged T-domain to bind TolB with an affinity equivalent to that of Pal and competitively displace it. Our study demonstrates that natively disordered proteins can compete with globular proteins for binding to folded scaffolds but that this can require cofactors such as metal ions to offset unfavorable interactions. FAU - Loftus, Steven R AU - Loftus SR AD - Department of Biology (Area 10), University of York, York YO10 5YW, United Kingdom. FAU - Walker, Daniel AU - Walker D FAU - Mate, Maria J AU - Mate MJ FAU - Bonsor, Daniel A AU - Bonsor DA FAU - James, Richard AU - James R FAU - Moore, Geoffrey R AU - Moore GR FAU - Kleanthous, Colin AU - Kleanthous C LA - eng SI - PDB/2IVZ GR - BB/C516236/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060807 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Colicins) RN - 0 (Escherichia coli Proteins) RN - 0 (Periplasmic Proteins) RN - 0 (immE9 protein, E coli) RN - 0 (tolB protein, E coli) RN - SY7Q814VUP (Calcium) SB - IM MH - Binding Sites MH - Calcium/metabolism MH - Colicins/*chemistry/genetics/*metabolism MH - Crystallography, X-Ray MH - Escherichia coli Proteins/*chemistry/genetics/*metabolism MH - Hydrogen Bonding MH - Models, Molecular MH - Molecular Sequence Data MH - Periplasmic Proteins/*chemistry/genetics/*metabolism MH - *Protein Structure, Tertiary MH - Thermodynamics PMC - PMC1567883 OID - NLM: PMC1567883 EDAT- 2006/08/09 09:00 MHDA- 2006/11/09 09:00 CRDT- 2006/08/09 09:00 PHST- 2006/08/07 [aheadofprint] AID - 0603433103 [pii] AID - 10.1073/pnas.0603433103 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12353-8. Epub 2006 Aug 7. PMID- 10807923 OWN - NLM STAT- MEDLINE DA - 20000831 DCOM- 20000831 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 275 IP - 30 DP - 2000 Jul 28 TI - Interaction of inhibitor-2 with the catalytic subunit of type 1 protein phosphatase. Identification of a sequence analogous to the consensus type 1 protein phosphatase-binding motif. PG - 22635-44 AB - Inhibitor-2 (I-2) is the regulatory subunit of a cytosolic type 1 Ser/Thr protein phosphatase (PP1) and potently inhibits the activity of the free catalytic subunit (CS1). Previous work from the laboratory had proposed that the interaction of I-2 with CS1 involved multiple sites (Park, I. K., and DePaoli-Roach, A. A. (1994) J. Biol. Chem. 269, 28919-28928). The present study refines the earlier analysis and arrives at a more detailed model for the interaction between I-2 and CS1. Although the NH(2)-terminal I-2 regions containing residues 1-35 and 1-64 have no inhibitory activity on their own, they increase the IC(50) for I-2 by approximately 30-fold, indicating the presence of a CS1-interacting site. Based on several experimental approaches, we have also identified the sequence Lys(144)-Leu-His-Tyr(147) as a second site of interaction that corresponds to the RVXF motif present in many CS1-binding proteins. The peptide I-2(135-151) significantly increases the IC(50) for I-2 and attenuates CS1 inhibition. Replacement of Leu and Tyr with Ala abolishes the ability to counteract inhibition by I-2. The I-2(135-151) peptide, but not I-2(1-35), also antagonizes inhibition of CS1 by DARPP-32 in a pattern similar to that of I-2. Furthermore, a peptide derived from the glycogen-binding subunit, R(GL)/G(M)(61-80), which contains a consensus CS1-binding motif, completely counteracts CS1 inhibition by I-2 and DARPP-32. The NH(2)-terminal 35 residues of I-2 bind to CS1 at a site that is specific for I-2, whereas the KLHY sequence interacts with CS1 at a site shared with other interacting proteins. Other results suggest the presence of yet more sites of interaction. A model is presented in which multiple "anchoring interactions" serve to position a segment of I-2 such that it sterically occludes the catalytic pocket but need not make high affinity contacts itself. FAU - Yang, J AU - Yang J AD - Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5122, USA. FAU - Hurley, T D AU - Hurley TD FAU - DePaoli-Roach, A A AU - DePaoli-Roach AA LA - eng GR - DK36569/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA Primers) RN - 0 (Enzyme Inhibitors) RN - 0 (Proteins) RN - 0 (Recombinant Proteins) RN - 0 (protein phosphatase inhibitor-2) RN - 1W21G5Q4N2 (Okadaic Acid) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Binding Sites MH - Catalytic Domain MH - DNA Primers MH - Enzyme Inhibitors/chemistry/*metabolism MH - Humans MH - Molecular Sequence Data MH - Mutagenesis MH - Okadaic Acid/pharmacology MH - Phosphoprotein Phosphatases/*antagonists & inhibitors/metabolism MH - Protein Binding MH - Proteins/chemistry/genetics/*metabolism MH - Rabbits MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Deletion EDAT- 2000/05/16 09:00 MHDA- 2000/09/02 11:01 CRDT- 2000/05/16 09:00 AID - 10.1074/jbc.M003082200 [doi] AID - M003082200 [pii] PST - ppublish SO - J Biol Chem. 2000 Jul 28;275(30):22635-44. PMID- 18534616 OWN - NLM STAT- MEDLINE DA - 20080616 DCOM- 20080721 LR - 20140903 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 380 IP - 2 DP - 2008 Jul 4 TI - Intrinsically disordered human C/EBP homologous protein regulates biological activity of colon cancer cells during calcium stress. PG - 313-26 LID - 10.1016/j.jmb.2008.04.069 [doi] AB - Intrinsically disordered proteins are emerging as substantial functional constituents of mammalian proteomes. Although the abundance of these proteins has been established by bioinformatics approaches, the vast majority have not been characterized structurally or functionally. The C/EBP homologous protein (CHOP) is a proto-oncogene, traditionally shown as a dominant-negative inhibitor of C/EBPs and a transcriptional activator of activating protein-1. We report here the in vitro characterization of CHOP, where our computational analyses and experimental evidences show for the first time that CHOP is an intrinsically disordered protein. Intrinsic fluorescence, NMR spectroscopy, and analytical size-exclusion chromatography studies indicate that CHOP contains extensive disordered regions and self-associate in solution. Interestingly, the disordered N-terminal region has a key role in the oligomerization of CHOP and is vital for its biological activity. We report a novel mechanistic role of CHOP in the inhibition of Wnt/TCF signaling and stimulation of c-Jun and sucrase-isomaltase reporter activity in intestinal colon cancer cells. These findings are discussed in the context of oligomerization of intrinsically disordered proteins as one of the mechanisms through which they exert their biological function. FAU - Singh, Vinay K AU - Singh VK AD - Department of Biochemistry, Queen's University, Kingston, Ontario, Canada. FAU - Pacheco, Ivan AU - Pacheco I FAU - Uversky, Vladimir N AU - Uversky VN FAU - Smith, Steven P AU - Smith SP FAU - MacLeod, R John AU - MacLeod RJ FAU - Jia, Zongchao AU - Jia Z LA - eng GR - R01 GM071714-04/GM/NIGMS NIH HHS/United States GR - R01 LM007688-04/LM/NLM NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080503 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (CASR protein, human) RN - 0 (CCAAT-Enhancer-Binding Proteins) RN - 0 (Receptors, Calcium-Sensing) RN - 0 (Recombinant Fusion Proteins) RN - 0 (beta Catenin) RN - 147336-12-7 (Transcription Factor CHOP) RN - EC 2.7.11.24 (JNK Mitogen-Activated Protein Kinases) RN - EC 3.2.1.- (Sucrase-Isomaltase Complex) RN - SY7Q814VUP (Calcium) SB - IM MH - Adenocarcinoma/metabolism/pathology MH - CCAAT-Enhancer-Binding Proteins/genetics/metabolism MH - Calcium/*metabolism MH - Cell Line, Tumor MH - Colonic Neoplasms/*metabolism/pathology MH - Genes, Reporter MH - Humans MH - JNK Mitogen-Activated Protein Kinases/genetics/metabolism MH - Promoter Regions, Genetic MH - Protein Conformation MH - RNA Interference MH - Receptors, Calcium-Sensing/genetics/metabolism MH - Recombinant Fusion Proteins/chemistry/genetics/metabolism MH - Sucrase-Isomaltase Complex/genetics/metabolism MH - Transcription Factor CHOP/*chemistry/genetics/*metabolism MH - beta Catenin/genetics/metabolism PMC - PMC2676882 MID - NIHMS108105 OID - NLM: NIHMS108105 OID - NLM: PMC2676882 EDAT- 2008/06/07 09:00 MHDA- 2008/07/22 09:00 CRDT- 2008/06/07 09:00 PHST- 2008/01/14 [received] PHST- 2008/04/24 [revised] PHST- 2008/04/28 [accepted] PHST- 2008/05/03 [aheadofprint] AID - S0022-2836(08)00536-6 [pii] AID - 10.1016/j.jmb.2008.04.069 [doi] PST - ppublish SO - J Mol Biol. 2008 Jul 4;380(2):313-26. doi: 10.1016/j.jmb.2008.04.069. Epub 2008 May 3. PMID- 17715947 OWN - NLM STAT- MEDLINE DA - 20070911 DCOM- 20071106 LR - 20101118 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 46 IP - 37 DP - 2007 Sep 18 TI - The N-terminal module of HPV16 E7 is an intrinsically disordered domain that confers conformational and recognition plasticity to the oncoprotein. PG - 10405-12 AB - The HPV16 E7 oncoprotein is an extended dimer, with a stable and cooperative fold, but that displays properties of "natively unfolded" proteins. Two regions of conserved sequence are found in E7 proteins, where the N-terminus (1-40) includes the retinoblastoma tumor suppressor binding and casein kinase II phosphorylation sites. A fragment containing the highly acidic N-terminal half shows an apparently disordered conformation by far-UV-circular dichroism (CD) at neutral pH, and its hydrodynamic radius is much larger than a neutral peptide of the same length. Trifluoroethanol and micellar concentrations of sodium dodecyl sulfate stabilize a much more helical structure at pH 4.0 than at pH 7.5, while submicellar concentrations of the detergent yield a beta-strand. The shape, pH, and temperature dependence of the CD spectrum at pH 7.5 are indicative of a poly proline type II structure. This structure is stabilized by phosphorylation, which would translate into increased transforming activity in the cell. Thus, the intrinsically disordered properties of the N-terminal module of E7 are responsible for the structural plasticity of the oncoprotein. Although the domain is not a compact and cooperatively folded unit, it is a bona fide functional domain, evolved to maintain a dynamic but extended structure in the cell. These properties allow adaptation to a variety of protein targets and expose the PEST degradation sequence that regulates its turnover in the cell, a modification of which leads to the accumulation of E7 species with consequences in the transformation process. FAU - Garcia-Alai, Maria M AU - Garcia-Alai MM AD - Instituto Leloir and IIB-BA CONICET, Patricias Argentinas 435, (1405) Buenos Aires, Argentina. FAU - Alonso, Leonardo G AU - Alonso LG FAU - de Prat-Gay, Gonzalo AU - de Prat-Gay G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070823 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Detergents) RN - 0 (Oncogene Proteins, Viral) RN - 0 (Papillomavirus E7 Proteins) RN - 0 (Peptides) RN - 0 (oncogene protein E7, Human papillomavirus type 16) SB - IM MH - Amino Acid Sequence MH - Chromatography, Gel MH - Circular Dichroism MH - Detergents/pharmacology MH - Hydrophobic and Hydrophilic Interactions MH - Molecular Sequence Data MH - Oncogene Proteins, Viral/*chemistry/*metabolism MH - Papillomavirus E7 Proteins MH - Peptides/chemistry MH - Phosphorylation/drug effects MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Structure-Activity Relationship EDAT- 2007/08/25 09:00 MHDA- 2007/11/07 09:00 CRDT- 2007/08/25 09:00 PHST- 2007/08/23 [aheadofprint] AID - 10.1021/bi7007917 [doi] PST - ppublish SO - Biochemistry. 2007 Sep 18;46(37):10405-12. Epub 2007 Aug 23. PMID- 19847292 OWN - NLM STAT- MEDLINE DA - 20091022 DCOM- 20100312 LR - 20140827 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 4 IP - 10 DP - 2009 TI - p53 Amino-terminus region (1-125) stabilizes and restores heat denatured p53 wild phenotype. PG - e7159 LID - 10.1371/journal.pone.0007159 [doi] AB - BACKGROUND: The intrinsically disordered N-ter domain (NTD) of p53 encompasses approximately hundred amino acids that contain a transactivation domain (1-73) and a proline-rich domain (64-92) and is responsible for transactivation function and apoptosis. It also possesses an auto-inhibitory function as its removal results in remarkable reduction in dissociation of p53 from DNA. PRINCIPAL FINDINGS/METHODOLOGY: In this report, we have discovered that p53-NTD spanning amino acid residues 1-125 (NTD125) interacted with WT p53 and stabilized its wild type conformation under physiological and elevated temperatures, both in vitro and in cellular systems. NTD125 prevented irreversible thermal aggregation of heat denatured p53, enhanced p21-5'-DBS binding and further restored DBS binding activity of heat-denatured p53, in vitro, in a dose-dependent manner. In vivo ELISA and immunoprecipitation analysis of NTD125-transfected cells revealed that NTD125 shifted equilibrium from p53 mutant to wild type under heat stress conditions. Further, NTD125 initiated nuclear translocation of cytoplasmic p53 in transcriptionally active state in order to activate p53 downstream genes such as p21, Bax, PUMA, Noxa and SUMO. CONCLUSION/SIGNIFICANCE: Here, we showed that a novel chaperone-like activity resides in p53-N-ter region. This study might have significance in understanding the role of p53-NTD in p53 stabilization, conformational activation and apoptosis under heat-stress conditions. FAU - Sharma, Anuj Kumar AU - Sharma AK AD - Transcription and Human Biology Lab, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India. FAU - Ali, Amjad AU - Ali A FAU - Gogna, Rajan AU - Gogna R FAU - Singh, Amir Kumar AU - Singh AK FAU - Pati, Uttam AU - Pati U LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20091022 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Tumor Suppressor Protein p53) RN - 9DLQ4CIU6V (Proline) SB - IM MH - Apoptosis MH - Cell Nucleus/metabolism MH - Circular Dichroism MH - Cytoplasm/metabolism MH - Dose-Response Relationship, Drug MH - *Gene Expression Regulation MH - Genes, p53 MH - Hot Temperature MH - Humans MH - Phenotype MH - Proline/chemistry MH - Protein Conformation MH - Protein Denaturation MH - Protein Structure, Tertiary MH - Tumor Suppressor Protein p53/*chemistry/physiology PMC - PMC2760748 OID - NLM: PMC2760748 EDAT- 2009/10/23 06:00 MHDA- 2010/03/13 06:00 CRDT- 2009/10/23 06:00 PHST- 2009/06/08 [received] PHST- 2009/08/19 [accepted] PHST- 2009/10/22 [epublish] AID - 10.1371/journal.pone.0007159 [doi] PST - epublish SO - PLoS One. 2009 Oct 22;4(10):e7159. doi: 10.1371/journal.pone.0007159. PMID- 20331968 OWN - NLM STAT- MEDLINE DA - 20100419 DCOM- 20100513 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 394 IP - 4 DP - 2010 Apr 16 TI - The N-terminal part of Binder of SPerm 5 (BSP5), which promotes sperm capacitation in bovine species is intrinsically disordered. PG - 1036-41 LID - 10.1016/j.bbrc.2010.03.118 [doi] AB - Bovine BSP5 belongs to the Binder of SPerm (BSP) family. BSP5 plays a role in the bovine sperm capacitation by promoting cholesterol and phospholipid efflux. The variable N-terminal part in the BSP proteins is the uncharacterized region with no known function. Full-length, N-terminal part, and individual fibronectin type II domains of bovine BSP5 were cloned, expressed and purified from Escherichia coli. His-S tagged N-terminal part showed large variation in migration on SDS-PAGE in comparison to other constructs. Using mass spectrometry it was demonstrated that the His-S-N-terminal part has the expected molecular mass (13 kDa). The recombinant N-terminal part was sensitive to E. coli endogenous proteases during purification. Denaturing purification involving boiling lysis of cells was carried out, as the protein was thermostable. The His-S-N-terminal part lacked structure as determined by CD analysis. Bioinformatics analyses confirmed that the N-terminal part of bovine BSP5 is intrinsically disordered. In addition, bioinformatics analysis indicated that rabbit BSP and multiple forms of BSP proteins of bovine and equine species possess partially or completely disordered N-terminus. The conservation of disorder at the N-terminus in BSP members belonging to different species suggests a role in biological process such as sperm capacitation and/or sperm-egg interactions. CI - 2010 Elsevier Inc. All rights reserved. FAU - Jois, Prashanth Sirigeri AU - Jois PS AD - Maisonneuve-Rosemont Hospital Research Center, 5415 L'Assomption Boulevard, Montreal, Quebec, Canada H1T 2M4. FAU - Manjunath, Puttaswamy AU - Manjunath P LA - eng GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100321 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (BSP-30-kDa protein, Bos taurus) RN - 0 (Seminal Vesicle Secretory Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cattle MH - Conserved Sequence MH - Male MH - Molecular Sequence Data MH - Protein Structure, Tertiary MH - Rabbits MH - Seminal Vesicle Secretory Proteins/chemistry/genetics/*metabolism MH - *Sperm Capacitation MH - Spermatozoa/metabolism/*physiology EDAT- 2010/03/25 06:00 MHDA- 2010/05/14 06:00 CRDT- 2010/03/25 06:00 PHST- 2010/03/10 [received] PHST- 2010/03/17 [accepted] PHST- 2010/03/21 [aheadofprint] AID - S0006-291X(10)00582-6 [pii] AID - 10.1016/j.bbrc.2010.03.118 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2010 Apr 16;394(4):1036-41. doi: 10.1016/j.bbrc.2010.03.118. Epub 2010 Mar 21. PMID- 16605275 OWN - NLM STAT- MEDLINE DA - 20060411 DCOM- 20060531 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 15 DP - 2006 Apr 18 TI - The intrinsically unstructured domain of PC4 modulates the activity of the structured core through inter- and intramolecular interactions. PG - 5067-81 AB - Proteins frequently contain unstructured regions apart from a functionally important and well-conserved structured domain. Functional and structural aspects for these regions are frequently less clear. The general human positive cofactor 4 (PC4), has such a domain organization and can interact with various DNA substrates, transcriptional activators, and basal transcription factors. While essential for the cofactor function, structural and functional knowledge about these interactions is limited. Using biochemical, nuclear magnetic resonance (NMR), and docking experiments, we show that the carboxy-terminal structured core domain (PC4ctd) is required and sufficient for binding to single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and the herpes simplex virion protein 16 (VP16) activation domain (VP16ad). We determined the interaction surfaces within PC4 and showed that VP16 and DNA binding are mutually exclusive. Although the amino-terminal domain of PC4 (PC4ntd) alone is devoid of any bioactivity, it increases the interaction with VP16ad. While it decreases the ssDNA-binding and DNA-unwinding activity, it does not influence dsDNA binding. Structural characterization of this domain showed that it is highly flexible and mostly unstructured both in the free form and in the complex. NMR titration experiments using various protein and DNA substrates of the individual domains and the full-length PC4 revealed local conformational or environmental changes in both the structured and unstructured subdomains, which are interpreted to be caused by inter- and intramolecular interactions. We propose that the unstructured PC4ntd regulates the PC4 cofactor function by specific interactions with the activator and through modulation and/or shielding of the interaction surface in the structured core of PC4ctd. FAU - Jonker, Hendrik R A AU - Jonker HR AD - Bijvoet Center for Biomolecular Research, Section NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. henry@vinden.nl FAU - Wechselberger, Rainer W AU - Wechselberger RW FAU - Boelens, Rolf AU - Boelens R FAU - Kaptein, Rob AU - Kaptein R FAU - Folkers, Gert E AU - Folkers GE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (DNA, Single-Stranded) RN - 0 (DNA-Binding Proteins) RN - 0 (Herpes Simplex Virus Protein Vmw65) RN - 0 (SUB1 protein, human) RN - 0 (Trans-Activators) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) RN - K3Z4F929H6 (Lysine) SB - IM MH - Binding Sites MH - DNA/chemistry/metabolism MH - DNA, Single-Stranded/chemistry/metabolism MH - DNA-Binding Proteins/*chemistry/*metabolism MH - Herpes Simplex Virus Protein Vmw65/chemistry/metabolism MH - Humans MH - Lysine/chemistry/metabolism MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Mutation MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - Structure-Activity Relationship MH - Trans-Activators/chemistry/metabolism MH - Transcription Factors/*chemistry/*metabolism EDAT- 2006/04/12 09:00 MHDA- 2006/06/01 09:00 CRDT- 2006/04/12 09:00 AID - 10.1021/bi052531b [doi] PST - ppublish SO - Biochemistry. 2006 Apr 18;45(15):5067-81. PMID- 18076027 OWN - NLM STAT- MEDLINE DA - 20080602 DCOM- 20080806 LR - 20131121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 71 IP - 4 DP - 2008 Jun TI - Huntingtin interacting protein HYPK is intrinsically unstructured. PG - 1686-98 AB - To characterize HYPK, originally identified as a novel huntingtin (Htt) interacting partner by yeast two hybrid assay, we used various biophysical and biochemical techniques. The molecular weight of the protein, determined by gel electrophoresis, was found to be about 1.3-folds ( approximately 22 kDa) higher than that obtained from mass spectrometric analysis (16.9 kDa). In size exclusion chromatography experiment, HYPK was eluted in three fractions, the hydrodynamic radii for which were calculated to be approximately 1.5-folds (23.06 A) higher than that expected for globular proteins of equivalent mass (17.3 A). The protein exhibited predominantly (63%) random coil characteristics in circular dichroism spectroscopy and was highly sensitive to limited proteolysis by trypsin and papain, indicating absence of any specific domain. Experimental evidences with theoretical analyses of amino acids composition of HYPK and comparison with available published data predicts that HYPK is an intrinsically unstructured protein (IUP) with premolten globule like conformation. In presence of increasing concentration of Ca(2+), HYPK showed conformational alterations as well as concomitant reduction of hydrodynamic radius. Even though any link between the natively unfolded nature of HYPK, its conformational sensitivity towards Ca(2+) and interaction with Htt is yet to be established, its possible involvement in Huntington's disease pathogenesis is discussed. CI - (c) 2007 Wiley-Liss, Inc. FAU - Raychaudhuri, Swasti AU - Raychaudhuri S AD - Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700 064, India. FAU - Majumder, Pritha AU - Majumder P FAU - Sarkar, Somosree AU - Sarkar S FAU - Giri, Kalyan AU - Giri K FAU - Mukhopadhyay, Debashis AU - Mukhopadhyay D FAU - Bhattacharyya, Nitai P AU - Bhattacharyya NP LA - eng PT - Journal Article PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Cross-Linking Reagents) RN - 0 (HTT protein, human) RN - 0 (Nerve Tissue Proteins) RN - 0 (Nuclear Proteins) RN - EC 3.4.21.4 (Trypsin) RN - EC 3.4.22.2 (Papain) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Calcium/pharmacology MH - Chromatography, Gel MH - Circular Dichroism MH - Computer Simulation MH - Cross-Linking Reagents/chemistry MH - Dose-Response Relationship, Drug MH - Humans MH - Huntington Disease/*etiology/genetics/pathology MH - Hydrolysis MH - Hydrophobic and Hydrophilic Interactions MH - Light MH - Mass Spectrometry MH - Molecular Sequence Data MH - Molecular Weight MH - Nerve Tissue Proteins/analysis/*chemistry/isolation & purification/metabolism MH - Nuclear Proteins/analysis/*chemistry/isolation & purification/metabolism MH - Papain/pharmacology MH - Protein Conformation/drug effects MH - Protein Denaturation MH - Protein Structure, Secondary MH - Scattering, Radiation MH - Spectrometry, Fluorescence MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Spectrophotometry, Ultraviolet MH - Time Factors MH - Trypsin/pharmacology EDAT- 2007/12/14 09:00 MHDA- 2008/08/07 09:00 CRDT- 2007/12/14 09:00 AID - 10.1002/prot.21856 [doi] PST - ppublish SO - Proteins. 2008 Jun;71(4):1686-98. PMID- 15746104 OWN - NLM STAT- MEDLINE DA - 20050503 DCOM- 20050902 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 18 DP - 2005 May 6 TI - Mg2+ and Ca2+ differentially regulate DNA binding and dimerization of DREAM. PG - 18008-14 AB - DREAM (calsenilin/KChIP3) is an EF-hand calcium-binding protein that represses transcription of prodynorphin and c-fos genes. Here we present structural and binding studies on single-site mutants of DREAM designed to disable Ca(2+) binding to each of the functional EF-hands (EF-2: D150N; EF-3: E186Q; and EF-4: E234Q). Isothermal titration calorimetry (ITC) analysis of Ca(2+) binding to the various mutants revealed that, in the absence of Mg(2+), Ca(2+) binds independently and sequentially to EF-3 (DeltaH = -2.4 kcal/mol), EF-4 (DeltaH = +5.2 kcal/mol), and EF-2 (DeltaH = +1 kcal/mol). By contrast, only two Ca(2+) bind to DREAM in the presence of physiological levels of Mg(2+) for both wild-type and D150N, suggesting that EF-2 binds constitutively to Mg(2+). ITC measurements demonstrate that one Mg(2+) binds enthalpically with high affinity (K(d) = 13 mum and DeltaH = -0.79 kcal/mol) and two or more Mg(2+) bind entropically in the millimolar range. Size-exclusion chromatography studies revealed that Mg(2+) stabilizes DREAM as a monomer, whereas Ca(2+) induces protein dimerization. Electrophoretic mobility shift assays indicated that Mg(2+) is essential for sequence-specific binding of DREAM to DNA response elements (DREs) in prodynorphin and c-fos genes. The EF-hand mutants bind specifically to DRE, suggesting they are functionally intact. None of the EF-hand mutants bind DRE at saturating Ca(2+) levels, suggesting that binding of a single Ca(2+) at either EF-3 or EF-4 is sufficient to drive conformational changes that abolish DNA binding. NMR structural analysis indicates that metal-free DREAM adopts a folded yet flexible molten globule-like structure. Both Ca(2+) and Mg(2+) induce distinct conformational changes, which stabilize tertiary structure of DREAM. We propose that Mg(2+) binding at EF-2 may structurally bridge DREAM to DNA targets and that Ca(2+)-induced protein dimerization disrupts DNA binding. FAU - Osawa, Masanori AU - Osawa M AD - Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA. FAU - Dace, Alexandra AU - Dace A FAU - Tong, Kit I AU - Tong KI FAU - Valiveti, Aswani AU - Valiveti A FAU - Ikura, Mitsuhiko AU - Ikura M FAU - Ames, James B AU - Ames JB LA - eng GR - EY12347/EY/NEI NIH HHS/United States GR - NS45909/NS/NINDS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050303 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Calcium-Binding Proteins) RN - 0 (Csen protein, mouse) RN - 0 (DNA-Binding Proteins) RN - 0 (Kv Channel-Interacting Proteins) RN - 0 (Repressor Proteins) RN - 9007-49-2 (DNA) RN - I38ZP9992A (Magnesium) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Calcium/*chemistry MH - Calcium-Binding Proteins/genetics/*metabolism MH - DNA/genetics/*metabolism MH - DNA-Binding Proteins/*metabolism MH - Dimerization MH - Kv Channel-Interacting Proteins MH - Magnesium/*chemistry MH - Mice MH - Molecular Sequence Data MH - Protein Binding/physiology MH - Repressor Proteins/genetics/*metabolism EDAT- 2005/03/05 09:00 MHDA- 2005/09/03 09:00 CRDT- 2005/03/05 09:00 PHST- 2005/03/03 [aheadofprint] AID - M500338200 [pii] AID - 10.1074/jbc.M500338200 [doi] PST - ppublish SO - J Biol Chem. 2005 May 6;280(18):18008-14. Epub 2005 Mar 3. PMID- 20306540 OWN - NLM STAT- MEDLINE DA - 20100823 DCOM- 20101208 LR - 20131121 IS - 1520-6033 (Electronic) IS - 1520-6033 (Linking) VI - 26 IP - 4 DP - 2010 Jul-Aug TI - Antifibrillizing agents catalyze the formation of unstable intermediate aggregates of beta-amyloid. PG - 1172-9 LID - 10.1002/btpr.396 [doi] AB - Although Alzheimer's disease (AD) is characterized by the extracellular deposition of fibrillar aggregates of beta-amyloid (Abeta), transient oligomeric species of Abeta are increasingly implicated in the pathogenesis of AD. Natively unfolded monomeric Abeta can misfold and progressively assemble into fibrillar aggregates, following a well-established "on pathway" seeded-nucleation mechanism. Here, we show that three simple saccharides, mannose, sucrose, and raffinose, alter Abeta aggregation kinetics and morphology. The saccharides inhibit formation of Abeta fibrils but promote formation of various oligomeric aggregate species through different "off pathway" aggregation mechanisms at 37 degrees C but not at 60 degrees C. The various oligomeric Abeta aggregates formed when coincubated with the different saccharides are morphologically distinct but all are toxic toward SH-SY5Y human neuroblastoma cells, increasing the level of toxicity and greatly prolonging toxicity compared with Abeta alone. As a wide variety of anti-Abeta aggregation strategies are being actively pursued as potential therapeutics for AD, these studies suggest that care must be taken to ensure that the therapeutic agents also block toxic oligomeric Abeta assembly as well as inhibit fibril formation. CI - (c) 2010 American Institute of Chemical Engineers FAU - Wang, Min S AU - Wang MS AD - Department, of Chemical Engineering, Arizona State University, Tempe, AZ 85287, USA. FAU - Boddapati, Shanta AU - Boddapati S FAU - Sierks, Michael R AU - Sierks MR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biotechnol Prog JT - Biotechnology progress JID - 8506292 RN - 0 (Amyloid) RN - 0 (Amyloid beta-Peptides) RN - 57-50-1 (Sucrose) RN - N5O3QU595M (Raffinose) RN - PHA4727WTP (Mannose) SB - IM MH - Amyloid/*drug effects/*metabolism MH - Amyloid beta-Peptides/*drug effects/*metabolism MH - Cell Line, Tumor MH - Humans MH - Kinetics MH - Mannose/pharmacology MH - Microscopy, Atomic Force MH - Raffinose/pharmacology MH - Sucrose/pharmacology MH - Temperature EDAT- 2010/03/23 06:00 MHDA- 2010/12/14 06:00 CRDT- 2010/03/23 06:00 AID - 10.1002/btpr.396 [doi] PST - ppublish SO - Biotechnol Prog. 2010 Jul-Aug;26(4):1172-9. doi: 10.1002/btpr.396. PMID- 19655784 OWN - NLM STAT- MEDLINE DA - 20090908 DCOM- 20090928 LR - 20140905 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 36 DP - 2009 Sep 15 TI - 19F NMR studies of alpha-synuclein conformation and fibrillation. PG - 8578-84 LID - 10.1021/bi900872p [doi] AB - Fibrils of the intrinsically disordered protein alpha-synuclein are hallmarks of Parkinson's disease. The fluorescent dye thioflavin T is often used to characterize fibrillation, but this assay may not provide quantitative information about structure and mechanism. To gain such information, we incorporated the 19F-labeled amino acid, 3-fluorotyrosine, into recombinant human alpha-synuclein at its endogenous tyrosine residues. Tyrosine 39 is in the positively charged N-terminal region of this 140-residue protein. The other three tyrosines, 125, 133, and 136, are near the C-terminus. 19F nuclear magnetic resonance spectroscopy was used to study several properties of labeled alpha-synuclein, including its conformation, conformational changes induced by urea, spermine, and sodium dodecyl sulfate (SDS), its interaction with SDS micelles, and the kinetics of fibril formation. The results show that the tyrosines are in disordered regions but that there is some structure near position 39 that is disrupted by urea. SDS binding alters the conformation near position 39, but the C-terminal tyrosines are disordered under all conditions. The NMR data also indicate that SDS-micelle-bound alpha-synuclein and the free protein exchange on the 10 ms time scale. Studies of fibrillation show the utility of 19F-labeled NMR. The data indicate that fibrillation is not accompanied by the formation of large quantities of low molecular weight intermediates. Although dye binding and 19F NMR data show that 1 mM SDS and 1 mM spermine accelerate aggregation compared to buffer alone, only the NMR data indicate that the species formed in SDS are smaller than those formed in buffer or buffer plus spermine. We conclude that 19F NMR spectroscopy is useful for obtaining residue-level, quantitative information about the structure, binding, and aggregation of alpha-synuclein. FAU - Li, Conggang AU - Li C AD - Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA. FAU - Lutz, Evan A AU - Lutz EA FAU - Slade, Kristin M AU - Slade KM FAU - Ruf, Rebecca A S AU - Ruf RA FAU - Wang, Gui-Fang AU - Wang GF FAU - Pielak, Gary J AU - Pielak GJ LA - eng GR - DP1 OD000783/OD/NIH HHS/United States GR - DP1 OD000783-01/OD/NIH HHS/United States GR - DP1 OD000783-02/OD/NIH HHS/United States GR - DP1 OD000783-03/OD/NIH HHS/United States GR - DP1 OD000783-04/OD/NIH HHS/United States GR - DP1OD783/OD/NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Buffers) RN - 0 (Drug Combinations) RN - 0 (Fluorine Radioisotopes) RN - 0 (alpha-Synuclein) RN - 139-26-4 (3-fluorotyrosine) RN - 2FZ7Y3VOQX (Spermine) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - 42HK56048U (Tyrosine) SB - IM MH - Buffers MH - Drug Combinations MH - Fluorine Radioisotopes/*metabolism MH - Fluorometry MH - Humans MH - Magnetic Resonance Spectroscopy/methods MH - Molecular Weight MH - Mutagenesis, Site-Directed MH - Protein Binding MH - Protein Conformation MH - Sodium Dodecyl Sulfate/chemistry MH - Spectrometry, Mass, Electrospray Ionization MH - Spermine/chemistry MH - Tyrosine/analogs & derivatives/metabolism MH - alpha-Synuclein/*chemistry/genetics/*metabolism PMC - PMC2749620 MID - NIHMS140490 OID - NLM: NIHMS140490 OID - NLM: PMC2749620 EDAT- 2009/08/07 09:00 MHDA- 2009/09/29 06:00 CRDT- 2009/08/07 09:00 AID - 10.1021/bi900872p [doi] PST - ppublish SO - Biochemistry. 2009 Sep 15;48(36):8578-84. doi: 10.1021/bi900872p. PMID- 23176512 OWN - NLM STAT- MEDLINE DA - 20121126 DCOM- 20130509 IS - 1470-8752 (Electronic) IS - 0300-5127 (Linking) VI - 40 IP - 6 DP - 2012 Dec 1 TI - Intrinsically disordered proteins: lessons from colicins. PG - 1534-8 LID - 10.1042/BST20120198 [doi] AB - Defining structural features of IDPs (intrinsically disordered proteins) and relating these to biological function requires characterization of their dynamical properties. In the present paper, we review what is known about the IDPs of colicins, protein antibiotics that use their IDPs to enter bacterial cells. The structurally characterized colicin IDPs we consider contain linear binding epitopes for proteins within their target cells that the colicin hijacks during entry. We show that these binding epitopes take part in intramolecular interactions in the absence of protein partners, i.e. self-recognition, and consider the structural origins of this and its functional implications. We suggest that self-recognition is common in other IDPs that contain similar types of binding epitopes. FAU - Hecht, Oliver AU - Hecht O AD - Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, UK. FAU - Macdonald, Colin AU - Macdonald C FAU - Moore, Geoffrey R AU - Moore GR LA - eng GR - Biotechnology and Biological Sciences Research Council/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Biochem Soc Trans JT - Biochemical Society transactions JID - 7506897 RN - 0 (Colicins) SB - IM MH - Colicins/*chemistry MH - Escherichia coli MH - Hydrogen Bonding MH - Hydrophobic and Hydrophilic Interactions MH - Models, Molecular MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - Protein Structure, Secondary EDAT- 2012/11/28 06:00 MHDA- 2013/05/10 06:00 CRDT- 2012/11/27 06:00 AID - BST20120198 [pii] AID - 10.1042/BST20120198 [doi] PST - ppublish SO - Biochem Soc Trans. 2012 Dec 1;40(6):1534-8. doi: 10.1042/BST20120198. PMID- 9611241 OWN - NLM STAT- MEDLINE DA - 19980729 DCOM- 19980729 LR - 20140617 IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 26 IP - 12 DP - 1998 Jun 15 TI - Interaction between the N-terminal domain of human DNA topoisomerase I and the arginine-serine domain of its substrate determines phosphorylation of SF2/ASF splicing factor. PG - 2955-62 AB - Human DNA topoisomerase I, known for its DNA-relaxing activity, is possibly one of the kinases phosphorylating members of the SR protein family of splicing factors, in vivo. Little is known about the mechanism of action of this novel kinase. Using the prototypical SR protein SF2/ASF (SRp30a) as model substrate, we demonstrate that serine residues phosphorylated by topo I/kinase exclusively located within the most extended arginine-serine repeats of the SF2/ASF RS domain. Unlike other kinases such as cdc2 and SRPK1, which also phosphorylated serines at the RS domain, topo I/kinase required several SR dipeptide repeats. These repeats possibly contribute to a versatile structure in the RS domain thereby facilitating phosphorylation. Furthermore, far-western, fluorescence spectroscopy and kinase assays using the SF2/ASF mutants, demonstrated that kinase activity and binding were tightly coupled. Since the deletion of N-terminal 174 amino acids of Topo I destroys SF2/ASF binding and kinase activity but not ATP binding, we conclude that at least two distinct domains of Topo I are necessary for kinase activity: one in the C-terminal region contributing to the ATP binding site and the other one in the N-terminal region that allows binding of SF2/ASF. FAU - Labourier, E AU - Labourier E AD - Institut de Genetique Moleculaire de Montpellier (IGM), UMR 5535 CNRS, Universite Montpellier II, CNRS - BP 5051, 1919, route de Mende, F34293 Montpellier Cedex 5, France. FAU - Rossi, F AU - Rossi F FAU - Gallouzi, I E AU - Gallouzi IE FAU - Allemand, E AU - Allemand E FAU - Divita, G AU - Divita G FAU - Tazi, J AU - Tazi J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (Azides) RN - 0 (Cross-Linking Reagents) RN - 0 (DNA, Superhelical) RN - 0 (Nuclear Proteins) RN - 0 (Peptide Fragments) RN - 0 (RNA-Binding Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 170974-22-8 (serine-arginine-rich splicing proteins) RN - 452VLY9402 (Serine) RN - 53696-59-6 (8-azidoadenosine 5'-triphosphate) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - 94ZLA3W45F (Arginine) RN - EC 2.7.- (Protein Kinases) RN - EC 2.7.1.- (SRPK1 protein, human) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) RN - EC 2.7.11.22 (CDC2 Protein Kinase) RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) SB - IM MH - Adenosine Triphosphate/analogs & derivatives MH - Animals MH - Arginine/chemistry MH - Azides MH - CDC2 Protein Kinase/metabolism MH - Cattle MH - Cross-Linking Reagents MH - DNA Topoisomerases, Type I/genetics/*metabolism MH - DNA, Superhelical/metabolism MH - Humans MH - Nuclear Proteins/genetics/*metabolism MH - Peptide Fragments/analysis MH - Phosphorylation MH - Protein Kinases/genetics/*metabolism MH - Protein-Serine-Threonine Kinases/genetics/metabolism MH - RNA-Binding Proteins MH - Recombinant Fusion Proteins MH - Repetitive Sequences, Nucleic Acid MH - Sequence Deletion MH - Serine/chemistry MH - Substrate Specificity MH - Thymus Gland PMC - PMC147637 OID - NLM: PMC147637 EDAT- 1998/06/05 MHDA- 1998/06/05 00:01 CRDT- 1998/06/05 00:00 AID - gkb470 [pii] PST - ppublish SO - Nucleic Acids Res. 1998 Jun 15;26(12):2955-62. PMID- 23398399 OWN - NLM STAT- MEDLINE DA - 20130313 DCOM- 20130903 LR - 20141111 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 10 DP - 2013 Mar 13 TI - The dynamic structure of alpha-synuclein multimers. PG - 3865-72 LID - 10.1021/ja310518p [doi] AB - alpha-Synuclein, a protein that forms ordered aggregates in the brains of patients with Parkinson's disease, is intrinsically disordered in the monomeric state. Several studies, however, suggest that it can form soluble multimers in vivo that have significant secondary structure content. A number of studies demonstrate that alpha-synuclein can form beta-strand-rich oligomers that are neurotoxic, and recent observations argue for the existence of soluble helical tetrameric species in cellulo that do not form toxic aggregates. To gain further insight into the different types of multimeric states that this protein can adopt, we generated an ensemble for an alpha-synuclein construct that contains a 10-residue N-terminal extension, which forms multimers when isolated from Escherichia coli. Data from NMR chemical shifts and residual dipolar couplings were used to guide the construction of the ensemble. Our data suggest that the dominant state of this ensemble is a disordered monomer, complemented by a small fraction of helical trimers and tetramers. Interestingly, the ensemble also contains trimeric and tetrameric oligomers that are rich in beta-strand content. These data help to reconcile seemingly contradictory observations that indicate the presence of a helical tetramer in cellulo on the one hand, and a disordered monomer on the other. Furthermore, our findings are consistent with the notion that the helical tetrameric state provides a mechanism for storing alpha-synuclein when the protein concentration is high, thereby preventing non-membrane-bound monomers from aggregating. FAU - Gurry, Thomas AU - Gurry T AD - Computational and Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA. FAU - Ullman, Orly AU - Ullman O FAU - Fisher, Charles K AU - Fisher CK FAU - Perovic, Iva AU - Perovic I FAU - Pochapsky, Thomas AU - Pochapsky T FAU - Stultz, Collin M AU - Stultz CM LA - eng PT - Journal Article DEP - 20130227 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (alpha-Synuclein) SB - IM MH - Dimerization MH - Escherichia coli/chemistry MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - *Thermodynamics MH - alpha-Synuclein/*chemistry EDAT- 2013/02/13 06:00 MHDA- 2013/09/04 06:00 CRDT- 2013/02/13 06:00 PHST- 2013/02/27 [aheadofprint] AID - 10.1021/ja310518p [doi] PST - ppublish SO - J Am Chem Soc. 2013 Mar 13;135(10):3865-72. doi: 10.1021/ja310518p. Epub 2013 Feb 27. PMID- 11734199 OWN - NLM STAT- MEDLINE DA - 20011205 DCOM- 20020122 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 509 IP - 1 DP - 2001 Nov 30 TI - alpha-synuclein metabolism and aggregation is linked to ubiquitin-independent degradation by the proteasome. PG - 22-6 AB - alpha-Synuclein has been implicated in the pathogenesis of Parkinson's disease based on mutations in familial cases of the disease and its presence in Lewy bodies. Here we show that over-expression of wild-type human alpha-synuclein is sufficient to induce inclusion formation in SH-SY5Y cells. In this cellular model, proteasome inhibition leads to an increase of alpha-synuclein accumulation in vivo without ubiquitylation. In accordance, we find that in vitro, unmodified alpha-synuclein can be directly degraded by the 20S proteasome. These findings suggest an ubiquitin-independent mechanism of proteasomal degradation for alpha-synuclein and other natively unfolded proteins. FAU - Tofaris, G K AU - Tofaris GK AD - Cambridge Centre for Brain Repair and Neurology Department, University of Cambridge, Forvie Site, Robinson Way, CB2 2PY, Cambridge, UK. FAU - Layfield, R AU - Layfield R FAU - Spillantini, M G AU - Spillantini MG LA - eng PT - Journal Article PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (DNA, Complementary) RN - 0 (Multienzyme Complexes) RN - 0 (Nerve Tissue Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (Ubiquitin) RN - 0 (alpha-Synuclein) RN - EC 3.4.22.- (Cysteine Endopeptidases) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Cysteine Endopeptidases/*metabolism MH - DNA, Complementary/metabolism MH - Humans MH - Immunoblotting MH - Immunohistochemistry MH - Microscopy, Electron MH - Multienzyme Complexes/*metabolism MH - Nerve Tissue Proteins/*metabolism MH - Parkinson Disease/metabolism MH - Plasmids/metabolism MH - Proteasome Endopeptidase Complex MH - Protein Binding MH - Protein Denaturation MH - Protein Folding MH - Recombinant Proteins/metabolism MH - Synucleins MH - Time Factors MH - Transfection MH - Tumor Cells, Cultured MH - Ubiquitin/*metabolism MH - alpha-Synuclein EDAT- 2001/12/06 10:00 MHDA- 2002/01/23 10:01 CRDT- 2001/12/06 10:00 AID - S0014-5793(01)03115-5 [pii] PST - ppublish SO - FEBS Lett. 2001 Nov 30;509(1):22-6. PMID- 15477096 OWN - NLM STAT- MEDLINE DA - 20041012 DCOM- 20050421 LR - 20131121 IS - 1047-8477 (Print) IS - 1047-8477 (Linking) VI - 148 IP - 2 DP - 2004 Nov TI - Intrinsic versus mutation dependent instability/flexibility: a comparative analysis of the structure and dynamics of wild-type transthyretin and its pathogenic variants. PG - 153-68 AB - Transthyretin (TTR) is one of the about 20 known human proteins associated with amyloidosis which is characterized by the accumulation of amyloid fibrils in tissues or extracellular matrix surrounding vital organs. Unlike Alzheimer's fibrils that comprise a fragment of a large precursor protein, TTR amyloid fibrils are composed of both full-length protein and fragments of the molecule. The native state of TTR is a homotetramer with eight beta-strands organized into a beta-sandwich in each monomer. To elucidate the structural reorganization mechanisms preceding amyloid formation, it is important to characterize the dynamic features of the wild-type native state as well as to reveal the influence of disease-associated mutations on the structure and dynamics. Molecular dynamics (MD) simulations complement X-ray crystallography and D-H exchange to capture the intrinsically unstable/flexible sites of the wild-type as well as the mutation dependent unstable sites of the pathogenic variants. Our results of MD simulations have shown that the Leu55-->Pro (L55P) mutation occurs in an intrinsically unstable site, leading to substantial local and global structural changes. This observation supports the early speculation that the C-strand-loop-D-strand rearrangement leads to the formation of amyloidogenic intermediates. In addition to the D strand, the alpha-helical region and the strands at the monomer-monomer interface are also intrinsically unstable. The central channel of L55P-TTR undergoes opening and closing fluctuations, which may provide an explanation for the fact that while the mutation is far from the channel, the mutant shows a substantial low binding affinity of thyroxine. FAU - Lei, Ming AU - Lei M AD - Gustaf H. Carlson school of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, USA. FAU - Yang, Mingfeng AU - Yang M FAU - Huo, Shuanghong AU - Huo S LA - eng GR - P41 RR-01081/RR/NCRR NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - 0 (Prealbumin) RN - Q51BO43MG4 (Thyroxine) SB - IM MH - Binding Sites MH - Crystallography, X-Ray MH - Dimerization MH - Genetic Variation MH - Humans MH - Hydrogen Bonding MH - Models, Molecular MH - *Mutation MH - Prealbumin/*chemistry/*genetics MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Thyroxine/chemistry MH - Time Factors EDAT- 2004/10/13 09:00 MHDA- 2005/04/22 09:00 CRDT- 2004/10/13 09:00 PHST- 2004/04/27 [received] AID - S1047-8477(04)00125-X [pii] AID - 10.1016/j.jsb.2004.06.007 [doi] PST - ppublish SO - J Struct Biol. 2004 Nov;148(2):153-68. PMID- 23891935 OWN - NLM STAT- MEDLINE DA - 20130924 DCOM- 20140321 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1830 IP - 11 DP - 2013 Nov TI - The conformational ensemble of the disordered and aggregation-protective 182-291 region of ataxin-3. PG - 5236-47 LID - 10.1016/j.bbagen.2013.07.007 [doi] LID - S0304-4165(13)00310-3 [pii] AB - BACKGROUND: Intrinsically disordered proteins (IDPs) are an emerging part of structural biology that has challenged the classic paradigm of structure-function relationship. Indeed, IDPs have been associated with different physiological functions and associated with several pathologies, such as polyglutamine (polyQ) related diseases. Ataxin-3 (AT3) is the smallest polyQ protein, composed by the N-terminal folded Josephin domain (JD), which is amyloidogenic on its own, and a C-terminal unstructured part. The disordered region between the polyQ and the JD, AT3182-291 plays a key role in the development of the disease. METHODS: We integrated different biophysical experimental techniques, atomistic explicit-solvent molecular dynamics (MD) simulations and graph theory to study AT3182-291 structure. RESULTS: AT3182-291 is a monomeric intrinsically disordered (ID) domain in solution and it is characterized by different conformational states, ascribable to pre-molten globule populations with different degrees of compactness. If isolated, it decreases the aggregation of the entire AT3. CONCLUSIONS: We provided the first structural description of an ID domain associated to a polyQ protein and we also showed that it exerts protective effects against AT3 aggregation. This effect is likely to be induced by intermolecular interactions between AT3 and the ubiquitin-interacting motifs of AT3182-291. Electrostatic interactions play a pivotal role in regulating the topology and tertiary propensity of the fragment and hub residues have been identified. GENERAL SIGNIFICANCE: Synergistic use of atomistic simulations and biophysical techniques should be more generally applied to the study of IDPs. Since ID domains and polyQ-proteins are intimately connected, the study here provided can be of interest for other members of the group. CI - (c) 2013 Elsevier B.V. All rights reserved. FAU - Invernizzi, Gaetano AU - Invernizzi G AD - Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy. Electronic address: gaetano.invernizzi@unimib.it. FAU - Lambrughi, Matteo AU - Lambrughi M FAU - Regonesi, Maria Elena AU - Regonesi ME FAU - Tortora, Paolo AU - Tortora P FAU - Papaleo, Elena AU - Papaleo E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130725 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Nerve Tissue Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Peptide Fragments) RN - 0 (Peptides) RN - 0 (Repressor Proteins) RN - 26700-71-0 (polyglutamine) SB - IM MH - Models, Molecular MH - Nerve Tissue Proteins/*chemistry MH - Nuclear Proteins/*chemistry MH - Peptide Fragments/*chemistry MH - Peptides/chemistry MH - Protein Folding MH - Protein Structure, Tertiary MH - Repressor Proteins/*chemistry OTO - NOTNLM OT - Aggregation OT - Ataxin-3 OT - Intrinsically disordered OT - Molecular dynamics OT - Polyglutamine OT - Ubiquitin interacting motif EDAT- 2013/07/31 06:00 MHDA- 2014/03/22 06:00 CRDT- 2013/07/30 06:00 PHST- 2013/03/05 [received] PHST- 2013/06/10 [revised] PHST- 2013/07/10 [accepted] PHST- 2013/07/25 [aheadofprint] AID - S0304-4165(13)00310-3 [pii] AID - 10.1016/j.bbagen.2013.07.007 [doi] PST - ppublish SO - Biochim Biophys Acta. 2013 Nov;1830(11):5236-47. doi: 10.1016/j.bbagen.2013.07.007. Epub 2013 Jul 25. PMID- 24114119 OWN - NLM STAT- In-Data-Review DA - 20140304 LR - 20150501 IS - 0006-3525 (Print) IS - 0006-3525 (Linking) VI - 101 IP - 5 DP - 2014 May TI - Structural adaptation of tooth enamel protein amelogenin in the presence of SDS micelles. PG - 525-35 LID - 10.1002/bip.22415 [doi] AB - Amelogenin, the major extracellular matrix protein of developing tooth enamel is intrinsically disordered. Through its interaction with other proteins and mineral, amelogenin assists enamel biomineralization by controlling the formation of highly organized enamel crystal arrays. We used circular dichroism (CD), dynamic light scattering (DLS), fluorescence, and NMR spectroscopy to investigate the folding propensity of recombinant porcine amelogenin rP172 following its interaction with SDS, at levels above critical micelle concentration. The rP172-SDS complex formation was confirmed by DLS, while an increase in the structure moiety of rP172 was noted through CD and fluorescence experiments. Fluorescence quenching analyses performed on several rP172 mutants where all but one Trp was replaced by Tyr at different sequence regions confirmed that the interaction of amelogenin with SDS micelles occurs via the N-terminal region close to Trp25 where helical segments can be detected by NMR. NMR spectroscopy and structural refinement calculations using CS-Rosetta modeling confirm that the highly conserved N-terminal domain is prone to form helical structure when bound to SDS micelles. Our findings reported here reveal interactions leading to significant changes in the secondary structure of rP172 upon treatment with SDS. These interactions may reflect the physiological relevance of the flexible nature of amelogenin and its sequence specific helical propensity that might enable it to structurally adapt with charged and potential targets such as cell surface, mineral, and other proteins during enamel biomineralization. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 525-535, 2014. CI - Copyright (c) 2013 Wiley Periodicals, Inc. FAU - Chandrababu, Karthik Balakrishna AU - Chandrababu KB AD - Division of Biomedical Sciences, Center for Craniofacial Molecular Biology, University of Southern California, School of Dentistry, Los Angeles, CA, 90033. FAU - Dutta, Kaushik AU - Dutta K FAU - Lokappa, Sowmya Bekshe AU - Lokappa SB FAU - Ndao, Moise AU - Ndao M FAU - Evans, John Spencer AU - Evans JS FAU - Moradian-Oldak, Janet AU - Moradian-Oldak J LA - eng GR - P41 GM103481/GM/NIGMS NIH HHS/United States GR - R01 DE013414/DE/NIDCR NIH HHS/United States GR - R01 DE020099/DE/NIDCR NIH HHS/United States PT - Journal Article PL - United States TA - Biopolymers JT - Biopolymers JID - 0372525 SB - IM PMC - PMC3947416 MID - NIHMS548426 OID - NLM: NIHMS548426 OID - NLM: PMC3947416 OTO - NOTNLM OT - CS-Rosetta OT - SDS OT - amelogenin OT - enamel OT - intrinsically disordered protein EDAT- 2013/10/12 06:00 MHDA- 2013/10/12 06:00 CRDT- 2013/10/12 06:00 PHST- 2013/08/16 [received] PHST- 2013/09/13 [accepted] AID - 10.1002/bip.22415 [doi] PST - ppublish SO - Biopolymers. 2014 May;101(5):525-35. doi: 10.1002/bip.22415. PMID- 19580545 OWN - NLM STAT- MEDLINE DA - 20090811 DCOM- 20090910 IS - 1470-8728 (Electronic) IS - 0264-6021 (Linking) VI - 422 IP - 2 DP - 2009 Sep 1 TI - Pup, a prokaryotic ubiquitin-like protein, is an intrinsically disordered protein. PG - 207-15 LID - 10.1042/BJ20090738 [doi] AB - Pup (prokaryotic ubiquitin-like protein) from Mycobacterium tuberculosis is the first ubiquitin-like protein identified in non-eukaryotic cells. Although different ubiquitin-like proteins from eukaryotes share low sequence similarity, their 3D (three-dimensional) structures exhibit highly conserved typical ubiquitin-like folds. Interestingly, our studies reveal that Pup not only shares low sequence similarity, but also presents a totally distinguished structure compared with other ubiquitin-like superfamily proteins. Diverse structure predictions combined with CD and NMR spectroscopic studies all demonstrate that Pup is an intrinsically disordered protein. Moreover, 1H-15N NOE (nuclear Overhauser effect) data and CSI (chemical shift index) analyses indicate that there is a residual secondary structure at the C-terminus of Pup. In M. tuberculosis, Mpa (mycobacterium proteasomal ATPase) is the regulatory cap ATPase of the proteasome that interacts with Pup and brings the substrates to the proteasome for degradation. In the present paper, SPR (surface plasmon resonance) and NMR perturbation studies imply that the C-terminus of Pup, ranging from residues 30 to 59, binds to Mpa probably through a hydrophobic interface. In addition, phylogenetic analysis clearly shows that the Pup family belongs to a unique and divergent evolutionary branch, suggesting that it is the most ancient and deeply branched family among ubiquitin-like proteins. This might explain the structural distinction between Pup and other ubiquitin-like superfamily proteins. FAU - Liao, Shanhui AU - Liao S AD - Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China. FAU - Shang, Qiang AU - Shang Q FAU - Zhang, Xuecheng AU - Zhang X FAU - Zhang, Jiahai AU - Zhang J FAU - Xu, Chao AU - Xu C FAU - Tu, Xiaoming AU - Tu X LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090813 PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (Bacterial Proteins) RN - 0 (Pup protein, Mycobacterium tuberculosis) RN - 0 (Ubiquitins) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/*metabolism MH - Molecular Sequence Data MH - Phylogeny MH - Prokaryotic Cells/*chemistry/metabolism MH - Protein Binding/physiology MH - Ubiquitins/*chemistry/metabolism EDAT- 2009/07/08 09:00 MHDA- 2009/09/11 06:00 CRDT- 2009/07/08 09:00 AID - BJ20090738 [pii] AID - 10.1042/BJ20090738 [doi] PST - epublish SO - Biochem J. 2009 Aug 13;422(2):207-15. doi: 10.1042/BJ20090738. PMID- 21760925 OWN - NLM STAT- MEDLINE DA - 20110715 DCOM- 20111013 LR - 20141022 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 7 DP - 2011 TI - TBP binding-induced folding of the glucocorticoid receptor AF1 domain facilitates its interaction with steroid receptor coactivator-1. PG - e21939 LID - 10.1371/journal.pone.0021939 [doi] AB - The precise mechanism by which glucocorticoid receptor (GR) regulates the transcription of its target genes is largely unknown. This is, in part, due to the lack of structural and functional information about GR's N-terminal activation function domain, AF1. Like many steroid hormone receptors (SHRs), the GR AF1 exists in an intrinsically disordered (ID) conformation or an ensemble of conformers that collectively appears to be unstructured. The GR AF1 is known to recruit several coregulatory proteins, including those from the basal transcriptional machinery, e.g., TATA box binding protein (TBP) that forms the basis for the multiprotein transcription initiation complex. However, the precise mechanism of this process is unknown. We have earlier shown that conditional folding of the GR AF1 is the key for its interactions with critical coactivator proteins. We hypothesize that binding of TBP to AF1 results in the structural rearrangement of the ID AF1 domain such that its surfaces become easily accessible for interaction with other coactivators. To test this hypothesis, we determined whether TBP binding-induced structure formation in the GR AF1 facilitates its interaction with steroid receptor coactivator-1 (SRC-1), a critical coactivator that is important for GR-mediated transcriptional activity. Our data show that stoichiometric binding of TBP induces significantly higher helical content at the expense of random coil configuration in the GR AF1. Further, we found that this induced AF1 conformation facilitates its interaction with SRC-1, and subsequent AF1-mediated transcriptional activity. Our results may provide a potential mechanism through which GR and by large other SHRs may regulate the expression of the GR-target genes. FAU - Khan, Shagufta H AU - Khan SH AD - Department of Basic Sciences, The Commonwealth Medical College, Scranton, Pennsylvania, United States of America. FAU - Ling, Jun AU - Ling J FAU - Kumar, Raj AU - Kumar R LA - eng GR - R01 DK058829/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20110707 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Receptors, Glucocorticoid) RN - 0 (TATA-Box Binding Protein) RN - EC 2.3.1.48 (Nuclear Receptor Coactivator 1) SB - IM MH - HeLa Cells MH - Humans MH - Kinetics MH - Nuclear Receptor Coactivator 1/*metabolism MH - Promoter Regions, Genetic/genetics MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Receptors, Glucocorticoid/*chemistry/*metabolism MH - Structure-Activity Relationship MH - Surface Plasmon Resonance MH - TATA-Box Binding Protein/*metabolism MH - Transcription, Genetic MH - Transcriptional Activation/genetics PMC - PMC3131385 OID - NLM: PMC3131385 EDAT- 2011/07/16 06:00 MHDA- 2011/10/14 06:00 CRDT- 2011/07/16 06:00 PHST- 2011/02/26 [received] PHST- 2011/06/13 [accepted] PHST- 2011/07/07 [epublish] AID - 10.1371/journal.pone.0021939 [doi] AID - PONE-D-11-03960 [pii] PST - ppublish SO - PLoS One. 2011;6(7):e21939. doi: 10.1371/journal.pone.0021939. Epub 2011 Jul 7. PMID- 22046250 OWN - NLM STAT- MEDLINE DA - 20111102 DCOM- 20120326 LR - 20141021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 10 DP - 2011 TI - Proteasomal degradation of p53 by human papillomavirus E6 oncoprotein relies on the structural integrity of p53 core domain. PG - e25981 LID - 10.1371/journal.pone.0025981 [doi] AB - The E6 oncoprotein produced by high-risk mucosal HPV stimulates ubiquitinylation and proteasome-dependent degradation of the tumour suppressor p53 via formation of a trimeric complex comprising E6, p53, and E6-AP. p53 is also degraded by its main cellular regulator MDM2. The main binding site of p53 to MDM2 is situated in the natively unfolded N-terminal region of p53. By contrast, the regions of p53 implicated in the degradation by viral E6 are not fully identified to date. Here we generated a series of mutations (Y103G, Y107G, T155A, T155V, T155D, L264A, L265A) targeting the central folded core domain of p53 within a region opposite to its DNA-binding site. We analysed by in vitro and in vivo assays the impact of these mutations on p53 degradation mediated by viral E6 oncoprotein. Whereas all mutants remained susceptible to MDM2-mediated degradation, several of them (Y103G, Y107G, T155D, L265A) became resistant to E6-mediated degradation, confirming previous works that pointed to the core domain as an essential region for the degradation of p53. In parallel, we systematically checked the impact of the mutations on the transactivation activity of p53 as well as on the conformation of p53, analysed by Nuclear Magnetic Resonance (NMR), circular dichroism (CD), and antibody probing. These measurements suggested that the conformational integrity of the core domain is an essential parameter for the degradation of p53 by E6, while it is not essential for the degradation of p53 by MDM2. Thus, the intracellular stability of a protein may or may not rely on its biophysical stability depending on the degradation pathway taken into consideration. FAU - Bernard, Xavier AU - Bernard X AD - Oncoproteines, UMR 7242 CNRS, Ecole Superieure de Biotechnologie de Strasbourg, Universite de Strasbourg, Illkirch, France. FAU - Robinson, Philip AU - Robinson P FAU - Nomine, Yves AU - Nomine Y FAU - Masson, Murielle AU - Masson M FAU - Charbonnier, Sebastian AU - Charbonnier S FAU - Ramirez-Ramos, Juan Ramon AU - Ramirez-Ramos JR FAU - Deryckere, Francois AU - Deryckere F FAU - Trave, Gilles AU - Trave G FAU - Orfanoudakis, Georges AU - Orfanoudakis G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111027 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (E6 protein, Human papillomavirus type 16) RN - 0 (Oncogene Proteins, Viral) RN - 0 (Repressor Proteins) RN - 0 (TP53 protein, human) RN - 0 (Tumor Suppressor Protein p53) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Binding Sites MH - Humans MH - Mutagenesis, Site-Directed MH - Oncogene Proteins, Viral/*metabolism MH - Proteasome Endopeptidase Complex/*metabolism MH - Protein Conformation MH - Protein Stability MH - Proto-Oncogene Proteins c-mdm2/metabolism MH - Repressor Proteins/*metabolism MH - Tumor Suppressor Protein p53/chemistry/genetics/*metabolism PMC - PMC3203139 OID - NLM: PMC3203139 EDAT- 2011/11/03 06:00 MHDA- 2012/03/27 06:00 CRDT- 2011/11/03 06:00 PHST- 2011/06/21 [received] PHST- 2011/09/14 [accepted] PHST- 2011/10/27 [epublish] AID - 10.1371/journal.pone.0025981 [doi] AID - PONE-D-11-11083 [pii] PST - ppublish SO - PLoS One. 2011;6(10):e25981. doi: 10.1371/journal.pone.0025981. Epub 2011 Oct 27. PMID- 8901511 OWN - NLM STAT- MEDLINE DA - 19961203 DCOM- 19961203 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 35 IP - 43 DP - 1996 Oct 29 TI - NACP, a protein implicated in Alzheimer's disease and learning, is natively unfolded. PG - 13709-15 AB - The "non-A beta component of Alzheimer's disease amyloid plaque" (NAC) is a minor peptide component of the insoluble fibrillar core of the Alzheimer's disease (AD) neuritic plaque. NAC amyloid fibrils seed the polymerization of A beta 1-40, the major AD amyloid protein. NAC is derived from a 14 kDa precursor protein, designated NACP, a member of a highly conserved family of heat-stable brain-specific acidic proteins which have been suggested to be involved in synapse formation and/or stabilization. NACP has also been suggested to play a role in AD. We present herein a conformational analysis of human NACP. NACP has a much larger Stokes radius (34 A) but sedimented more slowly (s20,w = 1.7S) than globular proteins of similar molecular weight, indicating that the native protein is elongated. Circular dichroism (CD) and Fourier-transform infrared spectroscopy (FTIR) indicate the absence of significant amounts of secondary structure in NACP, while CD and ultraviolet spectroscopy suggest the lack of a hydrophobic core. The conformational properties of NACP were unchanged by boiling and were independent of concentration, pH, salt, and chemical denaturants. These features indicate that NACP exists as a mixture of rapidly equilibrating extended conformers and is representative of a class of "natively unfolded" proteins, many of which potentiate protein-protein interactions. FAU - Weinreb, P H AU - Weinreb PH AD - Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA. FAU - Zhen, W AU - Zhen W FAU - Poon, A W AU - Poon AW FAU - Conway, K A AU - Conway KA FAU - Lansbury, P T Jr AU - Lansbury PT Jr LA - eng GR - AG08470/AG/NIA NIH HHS/United States GR - RR00317/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Amyloid) RN - 0 (Nerve Tissue Proteins) RN - 0 (Protein Precursors) RN - 0 (Recombinant Proteins) RN - 0 (Synucleins) SB - IM MH - Alzheimer Disease/*metabolism MH - Amino Acid Sequence MH - Amyloid/chemical synthesis/*chemistry/isolation & purification/metabolism MH - Circular Dichroism MH - Cloning, Molecular MH - Escherichia coli/genetics MH - Humans MH - Molecular Sequence Data MH - Molecular Weight MH - *Nerve Tissue Proteins MH - Protein Conformation MH - *Protein Folding MH - Protein Precursors/chemical synthesis/*chemistry/isolation & purification/metabolism MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Spectroscopy, Fourier Transform Infrared MH - Synucleins MH - Ultracentrifugation EDAT- 1996/10/29 MHDA- 2001/03/28 10:01 CRDT- 1996/10/29 00:00 AID - 10.1021/bi961799n [doi] AID - bi961799n [pii] PST - ppublish SO - Biochemistry. 1996 Oct 29;35(43):13709-15. PMID- 17438265 OWN - NLM STAT- MEDLINE DA - 20070425 DCOM- 20070606 LR - 20140907 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 104 IP - 17 DP - 2007 Apr 24 TI - Four domains of p300 each bind tightly to a sequence spanning both transactivation subdomains of p53. PG - 7009-14 AB - The transcriptional coactivator p300 binds to and mediates the transcriptional functions of the tetrameric tumor suppressor p53. Both proteins consist of independently folded domains linked by intrinsically disordered sequences. A well studied short sequence of the p53 transactivation domain, p53(15-29), binds weakly to four folded domains of p300 [Taz1/cysteine-histidine-rich region 1 (CH1), Kix, Taz2/CH3, IBiD], with dissociation constants (K(D)) in the 100 muM region. However, we found that a longer N-terminal transactivation domain construct p53(1-57) bound tightly to each p300 domain. Taz2/CH3 had the greatest affinity (K(D) = 27 nM) and competes with the N-terminal domain of Mdm2 for the p53 N terminus. p300 thus can protect the N terminus of p53 against the binding of other proteins. Mutations of p53 that abrogate transactivation (L22Q/W23S, W53Q/F54S) greatly weakened binding to each p300 domain, linking phenotypic defects to weakened coactivator binding. We propose a complex between tetrameric p53 and p300 in which four domains of p300 wrap around the four transactivation domains of p53. FAU - Teufel, Daniel P AU - Teufel DP AD - MRC Centre for Protein Engineering and Department of Chemistry, Cambridge University, MRC Centre, Hills Road, Cambridge, UK. FAU - Freund, Stefan M AU - Freund SM FAU - Bycroft, Mark AU - Bycroft M FAU - Fersht, Alan R AU - Fersht AR LA - eng GR - MC_U105459896/Medical Research Council/United Kingdom GR - MC_U105474168/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20070416 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Mutant Proteins) RN - 0 (Peptides) RN - 0 (Tumor Suppressor Protein p53) RN - EC 2.3.1.48 (E1A-Associated p300 Protein) RN - EC 2.3.1.48 (EP300 protein, human) RN - EC 6.3.2.19 (MDM2 protein, human) RN - EC 6.3.2.19 (Proto-Oncogene Proteins c-mdm2) SB - IM MH - Amino Acid Sequence MH - Binding, Competitive MH - E1A-Associated p300 Protein/*chemistry/*metabolism MH - Humans MH - Kinetics MH - Magnetic Resonance Spectroscopy MH - Models, Biological MH - Molecular Sequence Data MH - Mutant Proteins/chemistry/metabolism MH - Peptides/metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-mdm2/chemistry/metabolism MH - *Transcriptional Activation MH - Tumor Suppressor Protein p53/*chemistry/*metabolism PMC - PMC1855428 OID - NLM: PMC1855428 EDAT- 2007/04/18 09:00 MHDA- 2007/06/07 09:00 CRDT- 2007/04/18 09:00 PHST- 2007/04/16 [aheadofprint] AID - 0702010104 [pii] AID - 10.1073/pnas.0702010104 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7009-14. Epub 2007 Apr 16. PMID- 18495933 OWN - NLM STAT- MEDLINE DA - 20080529 DCOM- 20080616 LR - 20140903 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 105 IP - 21 DP - 2008 May 27 TI - Complementary dimerization of microtubule-associated tau protein: Implications for microtubule bundling and tau-mediated pathogenesis. PG - 7445-50 LID - 10.1073/pnas.0802036105 [doi] AB - Tau is an intrinsically unstructured microtubule (MT)-associated protein capable of binding to and organizing MTs into evenly spaced parallel assemblies known as "MT bundles." How tau achieves MT bundling is enigmatic because each tau molecule possesses only one MT-binding region. To dissect this complex behavior, we have used a surface forces apparatus to measure the interaction forces of the six CNS tau isoforms when bound to mica substrates in vitro. Two types of measurements were performed for each isoform: symmetric configuration experiments measured the interactions between two tau-coated mica surfaces, whereas "asymmetric" experiments examined tau-coated surfaces interacting with a smooth bare mica surface. Depending on the configuration (of which there were 12), the forces were weakly adhesive, strongly adhesive, or purely repulsive. The equilibrium spacing was determined mainly by the length of the tau projection domain, in contrast to the adhesion force/energy, which was determined by the number of repeats in the MT-binding region. Taken together, the data are incompatible with tau acting as a monomer; rather, they indicate that two tau molecules associate in an antiparallel configuration held together by an electrostatic "zipper" of complementary salt bridges composed of the N-terminal and central regions of each tau monomer, with the C-terminal MT-binding regions extending outward from each end of the dimeric backbone. This tau dimer determines the length and strength of the linker holding two MTs together and could be the fundamental structural unit of tau, underlying both its normal and pathological action. FAU - Rosenberg, Kenneth J AU - Rosenberg KJ AD - Department of Physics, University of California, Santa Barbara, CA 93106, USA. FAU - Ross, Jennifer L AU - Ross JL FAU - Feinstein, H Eric AU - Feinstein HE FAU - Feinstein, Stuart C AU - Feinstein SC FAU - Israelachvili, Jacob AU - Israelachvili J LA - eng GR - R01 NS 35010/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20080521 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Aluminum Silicates) RN - 0 (MAPT protein, human) RN - 0 (Protein Isoforms) RN - 0 (tau Proteins) RN - 12001-26-2 (mica) SB - IM MH - Alternative Splicing MH - Aluminum Silicates/chemistry MH - Amino Acid Sequence MH - Dimerization MH - Humans MH - Microtubules/metabolism MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Isoforms/chemistry/genetics/metabolism MH - Surface Tension MH - tau Proteins/*chemistry/genetics/metabolism PMC - PMC2396711 OID - NLM: PMC2396711 EDAT- 2008/05/23 09:00 MHDA- 2008/06/17 09:00 CRDT- 2008/05/23 09:00 PHST- 2008/05/21 [aheadofprint] AID - 0802036105 [pii] AID - 10.1073/pnas.0802036105 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2008 May 27;105(21):7445-50. doi: 10.1073/pnas.0802036105. Epub 2008 May 21. PMID- 18565540 OWN - NLM STAT- MEDLINE DA - 20080707 DCOM- 20080723 LR - 20141210 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 380 IP - 5 DP - 2008 Jul 25 TI - Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex. PG - 917-31 LID - 10.1016/j.jmb.2008.05.048 [doi] AB - The mechanism of inhibition of the transcriptional activator nuclear factor kappaB (NF-kappaB) by the inhibitor IkappaB* is central to the understanding of the control of transcriptional activity via this widely employed pathway. Previous studies suggested that IkappaB* , a modular protein with an NF-kappaB binding domain consisting of six ankyrin repeat domains (ANKs), shows differential flexibility, with ANK 1-4 apparently more rigid in solution in the absence of NF-kappaB than ANK 5 and 6. Here we report NMR studies that confirm the enhanced flexibility of ANK 5 and 6 in free IkappaB* . Upon binding of NF-kappaB, ANK 5 and 6 become well structured and rigid, but, somewhat surprisingly, other domains of the IkappaB* , which were relatively rigid in the free protein, become significantly more flexible. Due to the high molecular masses of the component proteins and the complexes, we employ a hierarchical experimental plan to maximize the available information on local flexibility in the ankyrin repeat domains. Backbone resonances of the 221-residue IkappaB* protein were assigned firstly in a smaller construct consisting of ankyrin repeats 1-4. These assignments could be readily transferred to the spectra of the construct containing six repeats, both free and complexed with various combinations of the NF-kappaB p50 and p65 domains. Transverse relaxation optimized spectroscopy-type NMR experiments on differentially labeled proteins enabled information on backbone structure and dynamics to be obtained, even in complexes with molecular masses approaching 100 kDa. Changes in the flexibility and stability of the various ankyrin repeat domains of IkappaB* complex formation take a variety of forms depending on the position of the domain in the complex, providing a variety of examples of the structural and functional utility of intrinsically unstructured or partly folded protein domains. FAU - Sue, Shih-Che AU - Sue SC AD - Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. FAU - Cervantes, Carla AU - Cervantes C FAU - Komives, Elizabeth A AU - Komives EA FAU - Dyson, H Jane AU - Dyson HJ LA - eng GR - P01 GM071862/GM/NIGMS NIH HHS/United States GR - P01 GM071862-01A20004/GM/NIGMS NIH HHS/United States GR - P01 GM071862-020004/GM/NIGMS NIH HHS/United States GR - P01 GM071862-030004/GM/NIGMS NIH HHS/United States PT - Journal Article DEP - 20080529 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (I-kappa B Proteins) RN - 0 (NF-kappa B) RN - 0 (Nuclear Localization Signals) RN - 0 (Protein Subunits) RN - 139874-52-5 (NF-kappaB inhibitor alpha) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Ankyrin Repeat MH - Binding Sites MH - Deuterium Exchange Measurement/methods MH - Dimerization MH - I-kappa B Proteins/chemistry/isolation & purification/*metabolism MH - Mass Spectrometry/methods MH - Models, Molecular MH - Molecular Sequence Data MH - Molecular Weight MH - NF-kappa B/biosynthesis/isolation & purification/*metabolism MH - Nuclear Localization Signals/chemistry MH - Nuclear Magnetic Resonance, Biomolecular/methods MH - Protein Binding MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Subunits/chemistry/metabolism PMC - PMC2603615 MID - NIHMS59284 OID - NLM: NIHMS59284 OID - NLM: PMC2603615 EDAT- 2008/06/21 09:00 MHDA- 2008/07/24 09:00 CRDT- 2008/06/21 09:00 PHST- 2008/04/10 [received] PHST- 2008/05/16 [revised] PHST- 2008/05/21 [accepted] PHST- 2008/05/29 [aheadofprint] AID - S0022-2836(08)00629-3 [pii] AID - 10.1016/j.jmb.2008.05.048 [doi] PST - ppublish SO - J Mol Biol. 2008 Jul 25;380(5):917-31. doi: 10.1016/j.jmb.2008.05.048. Epub 2008 May 29. PMID- 21489988 OWN - NLM STAT- MEDLINE DA - 20110606 DCOM- 20110805 LR - 20140820 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 286 IP - 23 DP - 2011 Jun 10 TI - Domain 3 of NS5A protein from the hepatitis C virus has intrinsic alpha-helical propensity and is a substrate of cyclophilin A. PG - 20441-54 LID - 10.1074/jbc.M110.182436 [doi] AB - Nonstructural protein 5A (NS5A) is essential for hepatitis C virus (HCV) replication and constitutes an attractive target for antiviral drug development. Although structural data for its in-plane membrane anchor and domain D1 are available, the structure of domains 2 (D2) and 3 (D3) remain poorly defined. We report here a comparative molecular characterization of the NS5A-D3 domains of the HCV JFH-1 (genotype 2a) and Con1 (genotype 1b) strains. Combining gel filtration, CD, and NMR spectroscopy analyses, we show that NS5A-D3 is natively unfolded. However, NS5A-D3 domains from both JFH-1 and Con1 strains exhibit a propensity to partially fold into an alpha-helix. NMR analysis identifies two putative alpha-helices, for which a molecular model could be obtained. The amphipathic nature of the first helix and its conservation in all genotypes suggest that it might correspond to a molecular recognition element and, as such, promote the interaction with relevant biological partner(s). Because mutations conferring resistance to cyclophilin inhibitors have been mapped into NS5A-D3, we also investigated the functional interaction between NS5A-D3 and cyclophilin A (CypA). CypA indeed interacts with NS5A-D3, and this interaction is completely abolished by cyclosporin A. NMR heteronuclear exchange experiments demonstrate that CypA has in vitro peptidyl-prolyl cis/trans-isomerase activity toward some, but not all, of the peptidyl-prolyl bonds in NS5A-D3. These studies lead to novel insights into the structural features of NS5A-D3 and its relationships with CypA. FAU - Verdegem, Dries AU - Verdegem D AD - Universite Lille Nord de France, F-59000 Lille, France. FAU - Badillo, Aurelie AU - Badillo A FAU - Wieruszeski, Jean-Michel AU - Wieruszeski JM FAU - Landrieu, Isabelle AU - Landrieu I FAU - Leroy, Arnaud AU - Leroy A FAU - Bartenschlager, Ralf AU - Bartenschlager R FAU - Penin, Francois AU - Penin F FAU - Lippens, Guy AU - Lippens G FAU - Hanoulle, Xavier AU - Hanoulle X LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110413 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Viral Nonstructural Proteins) RN - EC 5.2.1.- (Cyclophilin A) SB - IM MH - Cyclophilin A/*chemistry/genetics/metabolism MH - Hepacivirus/*chemistry/genetics/metabolism MH - Humans MH - Mutation MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Mapping/methods MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Structure-Activity Relationship MH - Viral Nonstructural Proteins/*chemistry/genetics/metabolism MH - Virus Replication/physiology PMC - PMC3121464 OID - NLM: PMC3121464 EDAT- 2011/04/15 06:00 MHDA- 2011/08/06 06:00 CRDT- 2011/04/15 06:00 PHST- 2011/04/13 [aheadofprint] AID - M110.182436 [pii] AID - 10.1074/jbc.M110.182436 [doi] PST - ppublish SO - J Biol Chem. 2011 Jun 10;286(23):20441-54. doi: 10.1074/jbc.M110.182436. Epub 2011 Apr 13. PMID- 18565542 OWN - NLM STAT- MEDLINE DA - 20080630 DCOM- 20080725 LR - 20131121 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 380 IP - 4 DP - 2008 Jul 18 TI - Folding of the KIX domain: characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. PG - 726-41 LID - 10.1016/j.jmb.2008.05.040 [doi] AB - The KIX domain of the transcription co-activator CBP is a three-helix bundle protein that folds via rapid accumulation of an intermediate state, followed by a slower folding phase. Recent NMR relaxation dispersion studies revealed the presence of a low-populated (excited) state of KIX that exists in equilibrium with the natively folded form under non-denaturing conditions, and likely represents the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium exchange measurements using rapid NMR data acquisition techniques with backbone (15)N and (13)C relaxation dispersion experiments to further investigate the equilibrium folding of the KIX domain. Residual structure within the folding intermediate is detected by both methods, and their combination enables reliable quantification of the amount of persistent residual structure. Three well-defined folding subunits are found, which display variable stability and correspond closely to the individual helices in the native state. While two of the three helices (alpha(2) and alpha(3)) are partially formed in the folding intermediate (to approximately 50% and approximately 80%, respectively, at 20 degrees C), the third helix is disordered. The observed helical content within the excited state exceeds the helical propensities predicted for the corresponding peptide regions, suggesting that the two helices are weakly mutually stabilized, while methyl (13)C relaxation dispersion data indicate that a defined packing arrangement is unlikely. Temperature-dependent experiments reveal that the largest enthalpy and entropy changes along the folding reaction occur during the final transition from the intermediate to the native state. Our experimental data are consistent with a folding mechanism where helices alpha(2) and alpha(3) form rapidly, although to different extents, while helix alpha(1) consolidates only as folding proceeds to complete the native state-structure. FAU - Schanda, Paul AU - Schanda P AD - Institut de Biologie Structurale Jean-Pierre Ebel, CNRS, CEA, UJF, 41 rue Jules Horowitz, F-38027 Grenoble, France. FAU - Brutscher, Bernhard AU - Brutscher B FAU - Konrat, Robert AU - Konrat R FAU - Tollinger, Martin AU - Tollinger M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080524 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amides) RN - 7YNJ3PO35Z (Hydrogen) RN - AR09D82C7G (Deuterium) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Amides/*chemistry MH - CREB-Binding Protein/chemistry/genetics/metabolism MH - Deuterium/chemistry/*metabolism MH - Hydrogen/chemistry/*metabolism MH - Models, Molecular MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - *Protein Folding MH - Protein Structure, Tertiary MH - Thermodynamics EDAT- 2008/06/21 09:00 MHDA- 2008/07/26 09:00 CRDT- 2008/06/21 09:00 PHST- 2008/03/21 [received] PHST- 2008/05/16 [revised] PHST- 2008/05/17 [accepted] PHST- 2008/05/24 [aheadofprint] AID - S0022-2836(08)00606-2 [pii] AID - 10.1016/j.jmb.2008.05.040 [doi] PST - ppublish SO - J Mol Biol. 2008 Jul 18;380(4):726-41. doi: 10.1016/j.jmb.2008.05.040. Epub 2008 May 24. PMID- 3297162 OWN - NLM STAT- MEDLINE DA - 19870729 DCOM- 19870729 LR - 20061115 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 913 IP - 2 DP - 1987 Jun 17 TI - The tertiary structure of salt-extracted ribosomal proteins from Escherichia coli as studied by proton magnetic resonance spectroscopy and limited proteolysis experiments. PG - 245-55 AB - Ribosomal proteins from Escherichia coli have been isolated by a mild purification procedure. Their tertiary structure has been explored by two techniques, proton magnetic resonance and limited proteolysis. A number of proteins when subjected to limited proteolysis produce resistant fragments in good yields. In most cases this does not depend on the specificity of the enzyme used. The proteins S15, S16, S17 and L30 are not degraded at all, whereas a few proteins are very susceptible to proteolysis. 1H-NMR experiments show that the majority of the ribosomal proteins have a uniquely folded tertiary structure. This is particularly pronounced in the four proteins mentioned above which resist proteolysis. In general, a good agreement is observed between the degree of proteolytic resistance and the amount of folding indicated by NMR spectroscopy. Similar studies on a few ribosomal proteins purified under denaturing conditions show that, in contrast, these protein preparations are not structurally homogeneous and that they contain a mixture of denatured and renatured molecules. The results are interpreted in terms of a compactly folded tertiary structure for the four proteinase-resistant proteins while the majority of the other proteins appear to have two domains, one compactly folded and resistant to proteinase and the other flexible and susceptible to proteolysis. A few proteins seem to have a completely flexible structure and can therefore be easily degraded. FAU - Littlechild, J AU - Littlechild J FAU - Malcolm, A AU - Malcolm A FAU - Paterakis, K AU - Paterakis K FAU - Ackermann, I AU - Ackermann I FAU - Dijk, J AU - Dijk J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Bacterial Proteins) RN - 0 (Peptides) RN - 0 (Ribosomal Proteins) RN - EC 3.4.- (Peptide Hydrolases) SB - IM MH - *Bacterial Proteins/isolation & purification MH - Escherichia coli/*analysis MH - Hydrolysis MH - Magnetic Resonance Spectroscopy MH - Peptide Hydrolases/metabolism MH - Peptides/isolation & purification MH - Protein Conformation MH - *Ribosomal Proteins/isolation & purification EDAT- 1987/06/17 MHDA- 1987/06/17 00:01 CRDT- 1987/06/17 00:00 PST - ppublish SO - Biochim Biophys Acta. 1987 Jun 17;913(2):245-55. PMID- 17222345 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20070129 DCOM- 20070723 LR - 20091118 IS - 1745-6150 (Electronic) IS - 1745-6150 (Linking) VI - 2 DP - 2007 TI - pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model. PG - 1 AB - BACKGROUND: Protein kinase A (cAMP-dependent kinase, PKA) is a serine/threonine kinase, for which ca. 150 substrate proteins are known. Based on a refinement of the recognition motif using the available experimental data, we wished to apply the simplified substrate protein binding model for accurate prediction of PKA phosphorylation sites, an approach that was previously successful for the prediction of lipid posttranslational modifications and of the PTS1 peroxisomal translocation signal. RESULTS: Approximately 20 sequence positions flanking the phosphorylated residue on both sides have been found to be restricted in their sequence variability (region -18...+23 with the site at position 0). The conserved physical pattern can be rationalized in terms of a qualitative binding model with the catalytic cleft of the protein kinase A. Positions -6...+4 surrounding the phosphorylation site are influenced by direct interaction with the kinase in a varying degree. This sequence stretch is embedded in an intrinsically disordered region composed preferentially of hydrophilic residues with flexible backbone and small side chain. This knowledge has been incorporated into a simplified analytical model of productive binding of substrate proteins with PKA. CONCLUSION: The scoring function of the pkaPS predictor can confidently discriminate PKA phosphorylation sites from serines/threonines with non-permissive sequence environments (sensitivity of appoximately 96% at a specificity of approximately 94%). The tool "pkaPS" has been applied on the whole human proteome. Among new predicted PKA targets, there are entirely uncharacterized protein groups as well as apparently well-known families such as those of the ribosomal proteins L21e, L22 and L6. AVAILABILITY: The supplementary data as well as the prediction tool as WWW server are available at http://mendel.imp.univie.ac.at/sat/pkaPS. REVIEWERS: Erik van Nimwegen (Biozentrum, University of Basel, Switzerland), Sandor Pongor (International Centre for Genetic Engineering and Biotechnology, Trieste, Italy), Igor Zhulin (University of Tennessee, Oak Ridge National Laboratory, USA). FAU - Neuberger, Georg AU - Neuberger G AD - IMP - Research Institute of Molecular Pathology, Dr, Bohr-Gasse 7, A-1030 Vienna, Austria. neuberger@imp.univie.ac.at FAU - Schneider, Georg AU - Schneider G FAU - Eisenhaber, Frank AU - Eisenhaber F LA - eng PT - Journal Article DEP - 20070112 PL - England TA - Biol Direct JT - Biology direct JID - 101258412 PMC - PMC1783638 OID - NLM: PMC1783638 EDAT- 2007/01/16 09:00 MHDA- 2007/01/16 09:01 CRDT- 2007/01/16 09:00 PHST- 2007/01/09 [received] PHST- 2007/01/12 [accepted] PHST- 2007/01/12 [aheadofprint] AID - 1745-6150-2-1 [pii] AID - 10.1186/1745-6150-2-1 [doi] PST - epublish SO - Biol Direct. 2007 Jan 12;2:1. PMID- 19524537 OWN - NLM STAT- MEDLINE DA - 20090615 DCOM- 20090717 LR - 20140916 IS - 1097-4164 (Electronic) IS - 1097-2765 (Linking) VI - 34 IP - 5 DP - 2009 Jun 12 TI - An unfolded CH1 domain controls the assembly and secretion of IgG antibodies. PG - 569-79 LID - 10.1016/j.molcel.2009.04.028 [doi] AB - A prerequisite for antibody secretion and function is their assembly into a defined quaternary structure, composed of two heavy and two light chains for IgG. Unassembled heavy chains are actively retained in the endoplasmic reticulum (ER). Here, we show that the C(H)1 domain of the heavy chain is intrinsically disordered in vitro, which sets it apart from other antibody domains. It folds only upon interaction with the light-chain C(L) domain. Structure formation proceeds via a trapped intermediate and can be accelerated by the ER-specific peptidyl-prolyl isomerase cyclophilin B. The molecular chaperone BiP recognizes incompletely folded states of the C(H)1 domain and competes for binding to the C(L) domain. In vivo experiments demonstrate that requirements identified for folding the C(H)1 domain in vitro, including association with a folded C(L) domain and isomerization of a conserved proline residue, are essential for antibody assembly and secretion in the cell. FAU - Feige, Matthias J AU - Feige MJ AD - Center for Integrated Protein Science Munich and Department Chemie, Technische Universitat Munchen, Lichtenbergstrasse 4, 85747 Garching, Germany. FAU - Groscurth, Sandra AU - Groscurth S FAU - Marcinowski, Moritz AU - Marcinowski M FAU - Shimizu, Yuichiro AU - Shimizu Y FAU - Kessler, Horst AU - Kessler H FAU - Hendershot, Linda M AU - Hendershot LM FAU - Buchner, Johannes AU - Buchner J LA - eng GR - CA21765/CA/NCI NIH HHS/United States GR - GM54068/GM/NIGMS NIH HHS/United States GR - R01 GM054068/GM/NIGMS NIH HHS/United States GR - R01 GM054068-15/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Heat-Shock Proteins) RN - 0 (Immunoglobulin G) RN - 0 (molecular chaperone GRP78) RN - 9DLQ4CIU6V (Proline) SB - IM CIN - Mol Cell. 2009 Jun 26;34(6):635-6. PMID: 19560414 MH - Animals MH - COS Cells MH - Cercopithecus aethiops MH - Cricetinae MH - Endoplasmic Reticulum/metabolism MH - Heat-Shock Proteins/metabolism/physiology MH - Humans MH - Immunoglobulin G/chemistry/*metabolism MH - Mice MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Proline/metabolism MH - *Protein Folding MH - Protein Structure, Quaternary PMC - PMC2908990 MID - NIHMS218912 OID - NLM: NIHMS218912 OID - NLM: PMC2908990 EDAT- 2009/06/16 09:00 MHDA- 2009/07/18 09:00 CRDT- 2009/06/16 09:00 PHST- 2008/11/10 [received] PHST- 2009/03/05 [revised] PHST- 2009/04/28 [accepted] AID - S1097-2765(09)00304-9 [pii] AID - 10.1016/j.molcel.2009.04.028 [doi] PST - ppublish SO - Mol Cell. 2009 Jun 12;34(5):569-79. doi: 10.1016/j.molcel.2009.04.028. PMID- 22496840 OWN - NLM STAT- MEDLINE DA - 20120412 DCOM- 20120823 LR - 20141016 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 4 DP - 2012 TI - Free cysteine modulates the conformation of human C/EBP homologous protein. PG - e34680 LID - 10.1371/journal.pone.0034680 [doi] AB - The C/EBP Homologous Protein (CHOP) is a nuclear protein that is integral to the unfolded protein response culminating from endoplasmic reticulum stress. Previously, CHOP was shown to comprise extensive disordered regions and to self-associate in solution. In the current study, the intrinsically disordered nature of this protein was characterized further by comprehensive in silico analyses. Using circular dichroism, differential scanning calorimetry and nuclear magnetic resonance, we investigated the global conformation and secondary structure of CHOP and demonstrated, for the first time, that conformational changes in this protein can be induced by the free amino acid L-cysteine. Addition of L-cysteine caused a significant dose-dependent decrease in the protein helicity--dropping from 69.1% to 23.8% in the presence of 1 mM of L-cysteine--and a sequential transition to a more disordered state, unlike that caused by thermal denaturation. Furthermore, the presence of small amounts of free amino acid (80 microM, an 8:1 cysteineratioCHOP ratio) during CHOP thermal denaturation altered the molecular mechanism of its melting process, leading to a complex, multi-step transition. On the other hand, high levels (4 mM) of free L-cysteine seemed to cause a complete loss of rigid cooperatively melting structure. These results suggested a potential regulatory function of L-cysteine which may lead to changes in global conformation of CHOP in response to the cellular redox state and/or endoplasmic reticulum stress. FAU - Singh, Vinay K AU - Singh VK AD - Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada. FAU - Rahman, Mona N AU - Rahman MN FAU - Munro, Kim AU - Munro K FAU - Uversky, Vladimir N AU - Uversky VN FAU - Smith, Steven P AU - Smith SP FAU - Jia, Zongchao AU - Jia Z LA - eng GR - MOP-77810/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120404 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 147336-12-7 (Transcription Factor CHOP) RN - K848JZ4886 (Cysteine) SB - IM MH - Circular Dichroism MH - Cysteine/*chemistry/pharmacology MH - Endoplasmic Reticulum Stress MH - Humans MH - Oxidation-Reduction MH - Protein Conformation MH - Protein Denaturation/drug effects MH - Transcription Factor CHOP/*chemistry PMC - PMC3319616 OID - NLM: PMC3319616 EDAT- 2012/04/13 06:00 MHDA- 2012/08/24 06:00 CRDT- 2012/04/13 06:00 PHST- 2012/02/13 [received] PHST- 2012/03/08 [accepted] PHST- 2012/04/04 [epublish] AID - 10.1371/journal.pone.0034680 [doi] AID - PONE-D-12-04648 [pii] PST - ppublish SO - PLoS One. 2012;7(4):e34680. doi: 10.1371/journal.pone.0034680. Epub 2012 Apr 4. PMID- 24316221 OWN - NLM STAT- MEDLINE DA - 20131230 DCOM- 20140220 LR - 20141231 IS - 1097-4164 (Electronic) IS - 1097-2765 (Linking) VI - 52 IP - 6 DP - 2013 Dec 26 TI - Conserved RNA helicase FRH acts nonenzymatically to support the intrinsically disordered neurospora clock protein FRQ. PG - 832-43 LID - 10.1016/j.molcel.2013.11.005 [doi] LID - S1097-2765(13)00830-7 [pii] AB - Protein conformation dictates a great deal of protein function. A class of naturally unstructured proteins, termed intrinsically disordered proteins (IDPs), demonstrates that flexibility in structure can be as important mechanistically as rigid structure. At the core of the circadian transcription/translation feedback loop in Neurospora crassa is the protein FREQUENCY (FRQ), shown here shown to share many characteristics of IDPs. FRQ in turn binds to FREQUENCY-Interacting RNA Helicase (FRH), whose clock function has been assumed to relate to its predicted helicase function. However, mutational analyses reveal that the helicase function of FRH is not essential for the clock, and a region of FRH distinct from the helicase region is essential for stabilizing FRQ against rapid degradation via a pathway distinct from its typical ubiquitin-mediated turnover. These data lead to the hypothesis that FRQ is an IDP and that FRH acts nonenzymatically, stabilizing FRQ to enable proper clock circuitry/function. CI - Copyright (c) 2013 Elsevier Inc. All rights reserved. FAU - Hurley, Jennifer M AU - Hurley JM AD - Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. FAU - Larrondo, Luis F AU - Larrondo LF AD - Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Alameda 340, Santiago, Chile. FAU - Loros, Jennifer J AU - Loros JJ AD - Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. FAU - Dunlap, Jay C AU - Dunlap JC AD - Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. Electronic address: jay.c.dunlap@dartmouth.edu. LA - eng GR - F32 GM096574/GM/NIGMS NIH HHS/United States GR - P01 GM068087/GM/NIGMS NIH HHS/United States GR - P01 GM68087/GM/NIGMS NIH HHS/United States GR - R01 GM034985/GM/NIGMS NIH HHS/United States GR - R01 GM083336/GM/NIGMS NIH HHS/United States GR - R01 GM083336/GM/NIGMS NIH HHS/United States GR - R01 GM34985/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20131205 PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (FRQ protein, Neurospora crassa) RN - 0 (Fungal Proteins) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Recombinant Proteins) RN - EC 2.3.1.48 (CLOCK Proteins) RN - EC 3.6.4.13 (RNA Helicases) SB - IM MH - CLOCK Proteins/genetics/*metabolism MH - *Circadian Rhythm/genetics MH - Escherichia coli/genetics/metabolism MH - Fungal Proteins/genetics/*metabolism MH - Genotype MH - Intrinsically Disordered Proteins/genetics/*metabolism MH - Mutation MH - Neurospora crassa/*enzymology/genetics/growth & development MH - Phenotype MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - Protein Stability MH - Proteolysis MH - RNA Helicases/genetics/*metabolism MH - Recombinant Proteins/metabolism MH - Time Factors PMC - PMC3900029 MID - NIHMS546541 OID - NLM: NIHMS546541 OID - NLM: PMC3900029 EDAT- 2013/12/10 06:00 MHDA- 2014/02/22 06:00 CRDT- 2013/12/10 06:00 PHST- 2013/07/02 [received] PHST- 2013/10/08 [revised] PHST- 2013/10/31 [accepted] PHST- 2013/12/05 [aheadofprint] AID - S1097-2765(13)00830-7 [pii] AID - 10.1016/j.molcel.2013.11.005 [doi] PST - ppublish SO - Mol Cell. 2013 Dec 26;52(6):832-43. doi: 10.1016/j.molcel.2013.11.005. Epub 2013 Dec 5. PMID- 18359842 OWN - NLM STAT- MEDLINE DA - 20080429 DCOM- 20080903 LR - 20140904 IS - 0032-0889 (Print) IS - 0032-0889 (Linking) VI - 147 IP - 1 DP - 2008 May TI - Chaperone activity of ERD10 and ERD14, two disordered stress-related plant proteins. PG - 381-90 LID - 10.1104/pp.108.118208 [doi] AB - ERD10 and ERD14 (for early response to dehydration) proteins are members of the dehydrin family that accumulate in response to abiotic environmental stresses, such as high salinity, drought, and low temperature, in Arabidopsis (Arabidopsis thaliana). Whereas these proteins protect cells against the consequences of dehydration, the exact mode(s) of their action remains poorly understood. Here, detailed evidence is provided that ERD10 and ERD14 belong to the family of intrinsically disordered proteins, and it is shown in various assays that they act as chaperones in vitro. ERD10 and ERD14 are able to prevent the heat-induced aggregation and/or inactivation of various substrates, such as lysozyme, alcohol dehydrogenase, firefly luciferase, and citrate synthase. It is also demonstrated that ERD10 and ERD14 bind to acidic phospholipid vesicles without significantly affecting membrane fluidity. Membrane binding is strongly influenced by ionic strength. Our results show that these intrinsically disordered proteins have chaperone activity of rather wide substrate specificity and that they interact with phospholipid vesicles through electrostatic forces. We suggest that these findings provide the rationale for the mechanism of how these proteins avert the adverse effects of dehydration stresses. FAU - Kovacs, Denes AU - Kovacs D AD - Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary H-1113. FAU - Kalmar, Eva AU - Kalmar E FAU - Torok, Zsolt AU - Torok Z FAU - Tompa, Peter AU - Tompa P LA - eng GR - ISRF 067595/Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080321 PL - United States TA - Plant Physiol JT - Plant physiology JID - 0401224 RN - 0 (Arabidopsis Proteins) RN - 0 (ERD10 protein, Arabidopsis) RN - 0 (ERD14 protein, Arabidopsis) RN - 0 (Molecular Chaperones) RN - 0 (Plant Proteins) RN - 0 (late embryogenesis abundant protein, plant) RN - 059QF0KO0R (Water) RN - EC 1.1.1.1 (Alcohol Dehydrogenase) RN - EC 1.13.12.7 (Luciferases, Firefly) RN - EC 2.3.3.1 (Citrate (si)-Synthase) RN - EC 3.2.1.17 (Muramidase) SB - IM MH - Alcohol Dehydrogenase/metabolism MH - Arabidopsis/metabolism/*physiology MH - Arabidopsis Proteins/*physiology MH - Citrate (si)-Synthase/metabolism MH - Hot Temperature MH - Intracellular Membranes/metabolism MH - Luciferases, Firefly/metabolism MH - Molecular Chaperones/metabolism/*physiology MH - Muramidase/metabolism MH - Plant Proteins/physiology MH - Substrate Specificity MH - Water/physiology PMC - PMC2330285 OID - NLM: PMC2330285 EDAT- 2008/03/25 09:00 MHDA- 2008/09/04 09:00 CRDT- 2008/03/25 09:00 PHST- 2008/03/21 [aheadofprint] AID - pp.108.118208 [pii] AID - 10.1104/pp.108.118208 [doi] PST - ppublish SO - Plant Physiol. 2008 May;147(1):381-90. doi: 10.1104/pp.108.118208. Epub 2008 Mar 21. PMID- 21647611 OWN - NLM STAT- MEDLINE DA - 20120312 DCOM- 20120628 LR - 20141022 IS - 1874-270X (Electronic) VI - 6 IP - 1 DP - 2012 Apr TI - Backbone and side chain NMR assignments for the intrinsically disordered cytoplasmic domain of human neuroligin-3. PG - 15-8 LID - 10.1007/s12104-011-9315-4 [doi] AB - Neuroligins act as heterophilic adhesion molecules at neuronal synapses. Their cytoplasmic domains interact with synaptic scaffolding proteins, and have been shown to be intrinsically disordered. Here we report the backbone and side chain (1)H, (13)C and (15)N resonance assignments for the cytoplasmic domain of human neuroligin 3. FAU - Wood, Kathleen AU - Wood K AD - Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands. FAU - Paz, Aviv AU - Paz A FAU - Dijkstra, Klaas AU - Dijkstra K FAU - Scheek, Ruud M AU - Scheek RM FAU - Otten, Renee AU - Otten R FAU - Silman, Israel AU - Silman I FAU - Sussman, Joel L AU - Sussman JL FAU - Mulder, Frans A A AU - Mulder FA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110607 PL - Netherlands TA - Biomol NMR Assign JT - Biomolecular NMR assignments JID - 101472371 RN - 0 (Cell Adhesion Molecules, Neuronal) RN - 0 (Membrane Proteins) RN - 0 (Nerve Tissue Proteins) RN - 0 (neuroligin 3) SB - IM MH - Amino Acid Sequence MH - Cell Adhesion Molecules, Neuronal/*chemistry/metabolism MH - Cytoplasm/*metabolism MH - Humans MH - Membrane Proteins/*chemistry/metabolism MH - Molecular Sequence Data MH - Nerve Tissue Proteins/*chemistry/metabolism MH - *Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Tertiary PMC - PMC3298649 OID - NLM: PMC3298649 EDAT- 2011/06/08 06:00 MHDA- 2012/06/29 06:00 CRDT- 2011/06/08 06:00 PHST- 2011/03/25 [received] PHST- 2011/05/23 [accepted] PHST- 2011/06/07 [aheadofprint] AID - 10.1007/s12104-011-9315-4 [doi] PST - ppublish SO - Biomol NMR Assign. 2012 Apr;6(1):15-8. doi: 10.1007/s12104-011-9315-4. Epub 2011 Jun 7. PMID- 15740751 OWN - NLM STAT- MEDLINE DA - 20050302 DCOM- 20050418 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 347 IP - 2 DP - 2005 Mar 25 TI - Nucleotide dependent motion and mechanism of action of p97/VCP. PG - 437-52 AB - The AAA (ATPases associated with a variety of cellular activities) family of proteins bind, hydrolyze, and release ATP to effect conformational changes, assembly, or disassembly upon their binding partners and substrate molecules. One of the members of this family, the hexameric p97/valosin-containing protein p97/VCP, is essential for the dislocation of misfolded membrane proteins from the endoplasmic reticulum. Here, we observe large motions and dynamic changes of p97/VCP as it proceeds through the ATP hydrolysis cycle. The analysis is based on crystal structures of four representative ATP hydrolysis states: APO, AMP-PNP, hydrolysis transition state ADP x AlF3, and ADP bound. Two of the structures presented herein, ADP and AMP-PNP bound, are new structures, and the ADP x AlF3 structure was re-refined to higher resolution. The largest motions occur at two stages during the hydrolysis cycle: after, but not upon, nucleotide binding and then following nucleotide release. The motions occur primarily in the D2 domain, the D1 alpha-helical domain, and the N-terminal domain, relative to the relatively stationary and invariant D1alpha/beta domain. In addition to the motions, we observed a transition from a rigid state to a flexible state upon loss of the gamma-phosphate group, and a further increase in flexibility within the D2 domains upon nucleotide release. The domains within each protomer of the hexameric p97/VCP deviate from strict 6-fold symmetry, with the more flexible ADP state exhibiting greater asymmetry compared to the relatively rigid ADP x AlF3 state, suggesting a mechanism of action in which hydrolysis and conformational changes move about the hexamer in a processive fashion. FAU - DeLaBarre, Byron AU - DeLaBarre B AD - Howard Hughes Medical Institute, and Department of Molecular and Cellular Physiology, and Stanford Synchrotron Radiation Laboratory, Stanford University, J.H. Clark Center E300-C, 318 Campus Drive, Stanford, CA 94305-5432, USA. FAU - Brunger, Axel T AU - Brunger AT LA - eng SI - PDB/1YPW SI - PDB/1YQI SI - PDB/1YQO PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Cell Cycle Proteins) RN - 0 (Nucleotides) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 3.6.1.- (CDC48 protein) SB - IM MH - Adenosine Triphosphatases MH - Adenosine Triphosphate/chemistry/*metabolism MH - Animals MH - Binding Sites MH - Cell Cycle Proteins/*chemistry/genetics/*metabolism MH - Crystallography, X-Ray MH - Humans MH - Models, Molecular MH - Nucleotides/*metabolism MH - *Protein Conformation EDAT- 2005/03/03 09:00 MHDA- 2005/04/19 09:00 CRDT- 2005/03/03 09:00 PHST- 2004/12/07 [received] PHST- 2005/01/18 [revised] PHST- 2005/01/21 [accepted] AID - S0022-2836(05)00091-4 [pii] AID - 10.1016/j.jmb.2005.01.060 [doi] PST - ppublish SO - J Mol Biol. 2005 Mar 25;347(2):437-52. PMID- 11406578 OWN - NLM STAT- MEDLINE DA - 20010614 DCOM- 20010726 LR - 20140613 IS - 0261-4189 (Print) IS - 0261-4189 (Linking) VI - 20 IP - 12 DP - 2001 Jun 15 TI - The B-box dominates SAP-1-SRF interactions in the structure of the ternary complex. PG - 3018-28 AB - The serum response element (SRE) is found in several immediate-early gene promoters. This DNA sequence is necessary and sufficient for rapid transcriptional induction of the human c-fos proto-oncogene in response to stimuli external to the cell. Full activation of the SRE requires the cooperative binding of a ternary complex factor (TCF) and serum response factor (SRF) to their specific DNA sites. The X-ray structure of the human SAP-1-SRF-SRE DNA ternary complex was determined (Protein Data Bank code 1hbx). It shows SAP-1 TCF bound to SRF through interactions between the SAP-1 B-box and SRF MADS domain in addition to contacts between their respective DNA-binding motifs. The SAP-1 B-box is part of a flexible linker of which 21 amino acids become ordered upon ternary complex formation. Comparison with a similar region from the yeast MATalpha2-MCM1-DNA complex suggests a common binding motif through which MADS-box proteins may interact with additional factors such as Fli-1. FAU - Hassler, M AU - Hassler M AD - ETH Zurich, Institut fur Molekularbiologie und Biophysik, ETH-Honggerberg, CH-8093 Zurich, Switzerland. FAU - Richmond, T J AU - Richmond TJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - EMBO J JT - The EMBO journal JID - 8208664 RN - 0 (DNA-Binding Proteins) RN - 0 (Glycoproteins) RN - 0 (Nuclear Proteins) RN - 0 (PSAP protein, human) RN - 0 (Saposins) RN - 0 (Serum Response Factor) RN - 0 (Sphingolipid Activator Proteins) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - DNA/*chemistry/metabolism MH - DNA-Binding Proteins/*chemistry/metabolism MH - Glycoproteins/*chemistry/metabolism MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Proteins/*chemistry/metabolism MH - Nucleic Acid Conformation MH - Protein Structure, Secondary MH - Regulatory Sequences, Nucleic Acid MH - Saposins MH - Serum Response Factor MH - Sphingolipid Activator Proteins PMC - PMC150215 OID - NLM: PMC150215 EDAT- 2001/06/19 10:00 MHDA- 2001/07/28 10:01 CRDT- 2001/06/19 10:00 AID - 10.1093/emboj/20.12.3018 [doi] PST - ppublish SO - EMBO J. 2001 Jun 15;20(12):3018-28. PMID- 23708362 OWN - NLM STAT- MEDLINE DA - 20130527 DCOM- 20131217 LR - 20141113 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 104 IP - 10 DP - 2013 May 21 TI - Phosphorylation-coupled intramolecular dynamics of unstructured regions in chromatin remodeler FACT. PG - 2222-34 LID - 10.1016/j.bpj.2013.04.007 [doi] LID - S0006-3495(13)00433-5 [pii] AB - The intrinsically disordered region (IDR) of a protein is an important topic in molecular biology. The functional significance of IDRs typically involves gene-regulation processes and is closely related to posttranslational modifications such as phosphorylation. We previously reported that the Drosophila facilitates chromatin transcription (FACT) protein involved in chromatin remodeling contains an acidic ID fragment (AID) whose phosphorylation modulates FACT binding to nucleosomes. Here, we performed dynamic atomic force microscopy and NMR analyses to clarify how the densely phosphorylated AID masks the DNA binding interface of the high-mobility-group domain (HMG). Dynamic atomic force microscopy of the nearly intact FACT revealed that a small globule temporally appears but quickly vanishes within each mobile tail-like image, corresponding to the HMG-containing IDR. The lifespan of the globule increases upon phosphorylation. NMR analysis indicated that phosphorylation induces no ordered structure but increases the number of binding sites in AID to HMG with an adjacent basic segment, thereby retaining the robust electrostatic intramolecular interaction within FACT even in the presence of DNA. These data lead to the conclusion that the inhibitory effect of nucleosome binding is ascribed to the increase in the probability of encounter between HMG and the phosphorylated IDR. CI - Copyright (c) 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Hashimoto, Manami AU - Hashimoto M AD - Department of Mathematical and Life Sciences, Hiroshima University, Hiroshima, Japan. FAU - Kodera, Noriyuki AU - Kodera N FAU - Tsunaka, Yasuo AU - Tsunaka Y FAU - Oda, Masayuki AU - Oda M FAU - Tanimoto, Mitsuru AU - Tanimoto M FAU - Ando, Toshio AU - Ando T FAU - Morikawa, Kosuke AU - Morikawa K FAU - Tate, Shin-ichi AU - Tate S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (Carrier Proteins) RN - 0 (Drosophila Proteins) RN - 0 (FACT protein, Drosophila) RN - 0 (Nucleosomes) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Motifs MH - Animals MH - Binding Sites MH - Carrier Proteins/chemistry/genetics/*metabolism MH - Chromatin Assembly and Disassembly MH - DNA/metabolism MH - Drosophila/chemistry/metabolism MH - Drosophila Proteins/chemistry/genetics/*metabolism MH - Nucleosomes/chemistry/*metabolism MH - Phosphorylation MH - Protein Structure, Tertiary MH - Static Electricity PMC - PMC3660632 OID - NLM: PMC3660632 EDAT- 2013/05/28 06:00 MHDA- 2013/12/18 06:00 CRDT- 2013/05/28 06:00 PHST- 2012/10/10 [received] PHST- 2013/03/30 [revised] PHST- 2013/04/04 [accepted] AID - S0006-3495(13)00433-5 [pii] AID - 10.1016/j.bpj.2013.04.007 [doi] PST - ppublish SO - Biophys J. 2013 May 21;104(10):2222-34. doi: 10.1016/j.bpj.2013.04.007. PMID- 7664121 OWN - NLM STAT- MEDLINE DA - 19951012 DCOM- 19951012 LR - 20131121 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 2 IP - 7 DP - 1995 Jul TI - Structure of phenylalanyl-tRNA synthetase from Thermus thermophilus. PG - 537-47 AB - The crystal structure of phenylalanyl-tRNA synthetase from Thermus thermophilus, solved at 2.9 A resolution, displays (alpha beta)2 subunit organization. Unexpectedly, both the catalytic alpha- and the non-catalytic beta-subunits comprise the characteristic fold of the class II active-site domains. The alpha beta heterodimer contains most of the building blocks so far identified in the class II synthetases. The presence of an RNA-binding domain, similar to that of the U1A spliceosomal protein, in the beta-subunit is indicative of structural relationships among different families of RNA-binding proteins. The structure suggests a plausible catalytic mechanism which explains why the primary site of tRNA aminoacylation is different from that of the other class II enzymes. FAU - Mosyak, L AU - Mosyak L AD - Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel. FAU - Reshetnikova, L AU - Reshetnikova L FAU - Goldgur, Y AU - Goldgur Y FAU - Delarue, M AU - Delarue M FAU - Safro, M G AU - Safro MG LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (Bacterial Proteins) RN - 0 (Macromolecular Substances) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 6.1.1.20 (Phenylalanine-tRNA Ligase) SB - IM MH - Adenosine Triphosphate/metabolism MH - Bacillus subtilis/enzymology MH - Bacterial Proteins/ultrastructure MH - Base Sequence MH - Binding Sites MH - Biological Evolution MH - Crystallography, X-Ray MH - Escherichia coli/enzymology MH - Macromolecular Substances MH - Models, Molecular MH - Molecular Sequence Data MH - Phenylalanine-tRNA Ligase/*ultrastructure MH - Protein Conformation MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Thermus thermophilus/*enzymology EDAT- 1995/07/01 MHDA- 1995/07/01 00:01 CRDT- 1995/07/01 00:00 PST - ppublish SO - Nat Struct Biol. 1995 Jul;2(7):537-47. PMID- 15164081 OWN - NLM STAT- MEDLINE DA - 20040617 DCOM- 20040716 LR - 20131216 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 429 IP - 6993 DP - 2004 Jun 17 TI - Structural basis of protein phosphatase 1 regulation. PG - 780-4 AB - The coordinated and reciprocal action of serine/threonine (Ser/Thr) protein kinases and phosphatases produces transient phosphorylation, a fundamental regulatory mechanism for many biological processes. The human genome encodes a far greater number of Ser/Thr protein kinases than of phosphatases. Protein phosphatase 1 (PP1), in particular, is ubiquitously distributed and regulates a broad range of cellular functions, including glycogen metabolism, cell-cycle progression and muscle relaxation. PP1 has evolved effective catalytic machinery but lacks substrate specificity. Substrate specificity is conferred upon PP1 through interactions with a large number of regulatory subunits. The regulatory subunits are generally unrelated, but most possess the RVxF motif, a canonical PP1-binding sequence. Here we reveal the crystal structure at 2.7 A resolution of the complex between PP1 and a 34-kDa N-terminal domain of the myosin phosphatase targeting subunit MYPT1. MYPT1 is the protein that regulates PP1 function in smooth muscle relaxation. Structural elements amino- and carboxy-terminal to the RVxF motif of MYPT1 are positioned in a way that leads to a pronounced reshaping of the catalytic cleft of PP1, contributing to the increased myosin specificity of this complex. The structure has general implications for the control of PP1 activity by other regulatory subunits. FAU - Terrak, Mohammed AU - Terrak M AD - Boston Biomedical Research Institute, 64 Grove Street, Watertown, Massachusetts 02472, USA. FAU - Kerff, Frederic AU - Kerff F FAU - Langsetmo, Knut AU - Langsetmo K FAU - Tao, Terence AU - Tao T FAU - Dominguez, Roberto AU - Dominguez R LA - eng SI - PDB/1FJM SI - PDB/1IHB SI - PDB/1S70 GR - P01 AR041637/AR/NIAMS NIH HHS/United States GR - R01 AR046524/AR/NIAMS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20040526 PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Peptide Fragments) RN - 0 (Protein Subunits) RN - EC 3.1.3.16 (Phosphoprotein Phosphatases) RN - EC 3.1.3.16 (Protein Phosphatase 1) RN - EC 3.1.3.53 (Myosin-Light-Chain Phosphatase) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - *Chickens MH - Models, Molecular MH - Molecular Sequence Data MH - Myosin-Light-Chain Phosphatase/metabolism MH - Peptide Fragments/chemistry/metabolism MH - Phosphoprotein Phosphatases/*chemistry/*metabolism MH - Protein Binding MH - Protein Phosphatase 1 MH - Protein Structure, Tertiary MH - Protein Subunits/*chemistry/*metabolism MH - Static Electricity MH - Structure-Activity Relationship MH - Substrate Specificity EDAT- 2004/05/28 05:00 MHDA- 2004/07/17 05:00 CRDT- 2004/05/28 05:00 PHST- 2004/01/30 [received] PHST- 2004/04/16 [accepted] PHST- 2004/05/26 [aheadofprint] AID - 10.1038/nature02582 [doi] AID - nature02582 [pii] PST - ppublish SO - Nature. 2004 Jun 17;429(6993):780-4. Epub 2004 May 26. PMID- 21268115 OWN - NLM STAT- MEDLINE DA - 20110309 DCOM- 20110713 LR - 20131121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 79 IP - 4 DP - 2011 Apr TI - Topology-based modeling of intrinsically disordered proteins: balancing intrinsic folding and intermolecular interactions. PG - 1251-66 LID - 10.1002/prot.22960 [doi] AB - Coupled binding and folding is frequently involved in specific recognition of so-called intrinsically disordered proteins (IDPs), a newly recognized class of proteins that rely on a lack of stable tertiary fold for function. Here, we exploit topology-based Go-like modeling as an effective tool for the mechanism of IDP recognition within the theoretical framework of minimally frustrated energy landscape. Importantly, substantial differences exist between IDPs and globular proteins in both amino acid sequence and binding interface characteristics. We demonstrate that established Go-like models designed for folded proteins tend to over-estimate the level of residual structures in unbound IDPs, whereas under-estimating the strength of intermolecular interactions. Such systematic biases have important consequences in the predicted mechanism of interaction. A strategy is proposed to recalibrate topology-derived models to balance intrinsic folding propensities and intermolecular interactions, based on experimental knowledge of the overall residual structure level and binding affinity. Applied to pKID/KIX, the calibrated Go-like model predicts a dominant multistep sequential pathway for binding-induced folding of pKID that is initiated by KIX binding via the C-terminus in disordered conformations, followed by binding and folding of the rest of C-terminal helix and finally the N-terminal helix. This novel mechanism is consistent with key observations derived from a recent NMR titration and relaxation dispersion study and provides a molecular-level interpretation of kinetic rates derived from dispersion curve analysis. These case studies provide important insight into the applicability and potential pitfalls of topology-based modeling for studying IDP folding and interaction in general. CI - Copyright (c) 2011 Wiley-Liss, Inc. FAU - Ganguly, Debabani AU - Ganguly D AD - Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506, USA. FAU - Chen, Jianhan AU - Chen J LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110125 PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Nerve Growth Factors) RN - 0 (Proteins) RN - 0 (S100 Calcium Binding Protein beta Subunit) RN - 0 (S100 Proteins) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - CREB-Binding Protein/chemistry MH - Computational Biology MH - *Molecular Dynamics Simulation MH - Nerve Growth Factors/chemistry MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - *Protein Folding MH - Protein Interaction Domains and Motifs MH - Proteins/*chemistry/metabolism MH - S100 Calcium Binding Protein beta Subunit MH - S100 Proteins/chemistry MH - Thermodynamics EDAT- 2011/01/27 06:00 MHDA- 2011/07/14 06:00 CRDT- 2011/01/27 06:00 PHST- 2010/10/30 [received] PHST- 2010/11/23 [revised] PHST- 2010/11/30 [accepted] PHST- 2011/01/25 [aheadofprint] AID - 10.1002/prot.22960 [doi] PST - ppublish SO - Proteins. 2011 Apr;79(4):1251-66. doi: 10.1002/prot.22960. Epub 2011 Jan 25. PMID- 20336261 OWN - NLM STAT- MEDLINE DA - 20100325 DCOM- 20100719 LR - 20101118 IS - 1463-9084 (Electronic) IS - 1463-9076 (Linking) VI - 12 IP - 14 DP - 2010 Apr 14 TI - Structural diversity of dimers of the Alzheimer amyloid-beta(25-35) peptide and polymorphism of the resulting fibrils. PG - 3622-9 LID - 10.1039/c000755m [doi] AB - The 25-35 fragment of the Alzheimer amyloid beta (Abeta) peptide is a naturally occurring proteolytic by-product that retains the toxicity of its larger, better-known counterpart, Abeta (1-40). Soluble oligomers of the amyloid-beta peptide have been implicated in the pathogenesis of Alzheimer's disease as a primary source of neurotoxicity. These oligomers are difficult to characterize experimentally due to their transient nature. As a result, a detailed knowledge of oligomeric structures at the atomic level is lacking. Using replica exchange molecular dynamics simulations, we investigated the conformations adopted by dimers, the smallest soluble oligomers of Abeta(25-35). Our simulations, which total 4 mus in length, reveal a diverse ensemble of well-organized dimers with high beta-sheet content coexisting with unstructured dimer complexes. The structured dimers comprise parallel and antiparallel extended beta-strand, beta-hairpin, and V-shaped beta-strand conformations. Protofibril models constructed from the extended and V-shaped dimers lead to stable structures consistent with experimentally available data from H/D exchange NMR and AFM spectroscopy. Our simulations suggest that fibril polymorphism may be encoded in the early stages of aggregation for the Abeta(25-35) peptide. FAU - Wei, Guanghong AU - Wei G AD - Department of Physics, Fudan University, Shanghai 200433, China. FAU - Jewett, Andrew I AU - Jewett AI FAU - Shea, Joan-Emma AU - Shea JE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20100311 PL - England TA - Phys Chem Chem Phys JT - Physical chemistry chemical physics : PCCP JID - 100888160 RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (25-35)) SB - IM MH - Alzheimer Disease MH - Amyloid beta-Peptides/*chemistry MH - Dimerization MH - Molecular Dynamics Simulation MH - Peptide Fragments/*chemistry MH - Protein Conformation EDAT- 2010/03/26 06:00 MHDA- 2010/07/20 06:00 CRDT- 2010/03/26 06:00 PHST- 2010/03/11 [aheadofprint] PHST- 2010/03/24 [epublish] AID - 10.1039/c000755m [doi] PST - ppublish SO - Phys Chem Chem Phys. 2010 Apr 14;12(14):3622-9. doi: 10.1039/c000755m. Epub 2010 Mar 11. PMID- 15878177 OWN - NLM STAT- MEDLINE DA - 20050517 DCOM- 20050621 LR - 20141125 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 349 IP - 3 DP - 2005 Jun 10 TI - Engineering the structural stability and functional properties of the GI domain into the intrinsically unfolded GII domain of the yeast linker histone Hho1p. PG - 608-20 AB - Yeast Hho1p contains two domains, GI and GII, that are homologous to the single globular domain of the linker histone H1 (GH1). We showed previously that the isolated GI and GII domains have different structural stabilities and functional properties. GI, like GH1 and the related GH5, is stably folded at low ionic strength (10 mM sodium phosphate) and gives strong protection of chromatosome-length DNA ( approximately 166 bp) during micrococcal nuclease digestion of chromatin. GII is intrinsically unfolded in 10 mM sodium phosphate and gives weak chromatosome protection, but in 250 mM sodium phosphate has a structure very similar to that of GI as determined by NMR spectroscopy. We now show that the loop between helices II and III in GII is the cause of both its instability and its inability to confer strong chromatosome protection. A mutant GII, containing the loop of GI, termed GII-L, is stable in 10 mM sodium phosphate and is as effective as GI in chromatosome protection. Two GII mutants with selected mutations within the original loop were also slightly more stable than GII. In GII, two of the four basic residues conserved at the second DNA binding site ("site II") on the globular domain of canonical linker histones, and in GI, are absent. Introduction of the two "missing" site II basic residues into GII or GII-L destabilised the protein and led to decreased chromatosome protection relative to the protein without the basic residues. In general, the ability to confer chromatosome protection in vitro is closely related to structural stability (the relative population of structured and unstructured states). We have determined the structure of GII-L by NMR spectroscopy. GII-L is very similar to GII folded in 250 mM sodium phosphate, with the exception of the substituted loop region, which, as in GI, contains a single helical turn. FAU - Sanderson, Andrew AU - Sanderson A AD - Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. FAU - Stott, Katherine AU - Stott K FAU - Stevens, Timothy J AU - Stevens TJ FAU - Thomas, Jean O AU - Thomas JO LA - eng SI - PDB/1YQA GR - B19489/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050419 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (HHO1 protein, S cerevisiae) RN - 0 (Histones) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Amino Acid Sequence MH - Computer Simulation MH - Histones/*chemistry/genetics/*metabolism MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - *Protein Engineering MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Saccharomyces cerevisiae/genetics/metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism MH - Spectrum Analysis EDAT- 2005/05/10 09:00 MHDA- 2005/06/23 09:00 CRDT- 2005/05/10 09:00 PHST- 2005/02/05 [received] PHST- 2005/03/30 [revised] PHST- 2005/03/31 [accepted] PHST- 2005/04/19 [aheadofprint] AID - S0022-2836(05)00386-4 [pii] AID - 10.1016/j.jmb.2005.03.085 [doi] PST - ppublish SO - J Mol Biol. 2005 Jun 10;349(3):608-20. Epub 2005 Apr 19. PMID- 19445677 OWN - NLM STAT- MEDLINE DA - 20090527 DCOM- 20090612 LR - 20140829 IS - 1743-422X (Electronic) IS - 1743-422X (Linking) VI - 6 DP - 2009 TI - The interaction between the measles virus nucleoprotein and the Interferon Regulator Factor 3 relies on a specific cellular environment. PG - 59 LID - 10.1186/1743-422X-6-59 [doi] AB - BACKGROUND: The genome of measles virus consists of a non-segmented single-stranded RNA molecule of negative polarity, which is encapsidated by the viral nucleoprotein (N) within a helical nucleocapsid. The N protein possesses an intrinsically disordered C-terminal domain (aa 401-525, N(TAIL)) that is exposed at the surface of the viral nucleopcapsid. Thanks to its flexible nature, N(TAIL) interacts with several viral and cellular partners. Among these latter, the Interferon Regulator Factor 3 (IRF-3) has been reported to interact with N, with the interaction having been mapped to the regulatory domain of IRF-3 and to N(TAIL). This interaction was described to lead to the phosphorylation-dependent activation of IRF-3, and to the ensuing activation of the pro-immune cytokine RANTES gene. RESULTS: After confirming the reciprocal ability of IRF-3 and N to be co-immunoprecipitated in 293T cells, we thoroughly investigated the N(TAIL)-IRF-3 interaction using a recombinant, monomeric form of the regulatory domain of IRF-3. Using a large panel of spectroscopic approaches, including circular dichroism, fluorescence spectroscopy, nuclear magnetic resonance and electron paramagnetic resonance spectroscopy, we failed to detect any direct interaction between IRF-3 and either full-length N or NTAIL under conditions where these latter interact with the C-terminal X domain of the viral phosphoprotein. Furthermore, such interaction was neither detected in E. coli nor in a yeast two hybrid assay. CONCLUSION: Altogether, these data support the requirement for a specific cellular environment, such as that provided by 293T human cells, for the N(TAIL)-IRF-3 interaction to occur. This dependence from a specific cellular context likely reflects the requirement for a human or mammalian cellular co-factor. FAU - Colombo, Matteo AU - Colombo M AD - Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS et Universites Aix-Marseille I et II, 163 Avenue de Luminy, Case 932, 13288 Marseille Cedex 09, France. Matteo.Colombo@unimi.it FAU - Bourhis, Jean-Marie AU - Bourhis JM FAU - Chamontin, Celia AU - Chamontin C FAU - Soriano, Carine AU - Soriano C FAU - Villet, Stephanie AU - Villet S FAU - Costanzo, Stephanie AU - Costanzo S FAU - Couturier, Marie AU - Couturier M FAU - Belle, Valerie AU - Belle V FAU - Fournel, Andre AU - Fournel A FAU - Darbon, Herve AU - Darbon H FAU - Gerlier, Denis AU - Gerlier D FAU - Longhi, Sonia AU - Longhi S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20090515 PL - England TA - Virol J JT - Virology journal JID - 101231645 RN - 0 (Interferon Regulatory Factor-3) RN - 0 (Nucleoproteins) RN - 0 (Viral Proteins) RN - 0 (nucleoprotein, Measles virus) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - Cell Line MH - Humans MH - Interferon Regulatory Factor-3/chemistry/genetics/*metabolism MH - Measles/genetics/*metabolism/virology MH - Measles virus/chemistry/genetics/*metabolism MH - Molecular Sequence Data MH - Nucleoproteins/chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Two-Hybrid System Techniques MH - Viral Proteins/chemistry/genetics/*metabolism PMC - PMC2686699 OID - NLM: PMC2686699 EDAT- 2009/05/19 09:00 MHDA- 2009/06/13 09:00 CRDT- 2009/05/19 09:00 PHST- 2009/03/11 [received] PHST- 2009/05/15 [accepted] PHST- 2009/05/15 [aheadofprint] AID - 1743-422X-6-59 [pii] AID - 10.1186/1743-422X-6-59 [doi] PST - epublish SO - Virol J. 2009 May 15;6:59. doi: 10.1186/1743-422X-6-59. PMID- 11601975 OWN - NLM STAT- MEDLINE DA - 20011016 DCOM- 20011205 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 40 IP - 42 DP - 2001 Oct 23 TI - Crystal structure of native chicken fibrinogen at 2.7 A resolution. PG - 12515-23 AB - The crystal structure of native chicken fibrinogen (320 kDa) complexed with two synthetic peptides has been determined at a resolution of 2.7 A. The structure provides the first atomic-resolution view of the polypeptide chain arrangement in the central domain where the two halves of the molecule are joined, as well as of a putative thrombin-binding site. The amino-terminal segments of the alpha and beta chains, including fibrinopeptides A and B, are not visible in electron density maps, however, and must be highly disordered. The alphaC domain is also very disordered. A residue by residue analysis of the coiled coils with regard to temperature factor shows a strong correlation between mobility and plasmin attack sites. It is concluded that structural flexibility is an inherent feature of fibrinogen that plays a key role in both its conversion to fibrin and its subsequent destruction by plasmin. FAU - Yang, Z AU - Yang Z AD - Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0634, USA. FAU - Kollman, J M AU - Kollman JM FAU - Pandi, L AU - Pandi L FAU - Doolittle, R F AU - Doolittle RF LA - eng SI - PDB/1JFE GR - GM 007240/GM/NIGMS NIH HHS/United States GR - HL-26873/HL/NHLBI NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Disulfides) RN - 0 (Peptide Fragments) RN - 9001-32-5 (Fibrinogen) RN - EC 3.4.21.5 (Thrombin) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cattle MH - Chickens MH - Crystallization MH - *Crystallography, X-Ray MH - Disulfides/chemistry MH - Fibrinogen/*chemistry/metabolism MH - Humans MH - Lampreys MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Thrombin/metabolism EDAT- 2001/10/17 10:00 MHDA- 2002/01/05 10:01 CRDT- 2001/10/17 10:00 AID - bi011394p [pii] PST - ppublish SO - Biochemistry. 2001 Oct 23;40(42):12515-23. PMID- 25223890 OWN - NLM STAT- In-Process DA - 20141205 IS - 1638-6183 (Electronic) IS - 0300-9084 (Linking) VI - 107 Pt B DP - 2014 Dec TI - Identification of phosphatidylcholine transfer protein-like in the parasite Entamoeba histolytica. PG - 223-34 LID - 10.1016/j.biochi.2014.09.007 [doi] LID - S0300-9084(14)00256-9 [pii] AB - Caveolin is the protein marker of caveola-mediated endocytosis. Previously, we demonstrated by immunoblotting and immunofluorescence that an anti-chick embryo caveolin-1 monoclonal antibody (mAb) recognizes a protein in amoeba extracts. Nevertheless, the caveolin-1 gene is absent in the Entamoeba histolytica genome database. In this work, the goal was to isolate, identify and characterize the protein that cross-reacts with chick embryo caveolin-1. We identified the protein using a proteomic approach, and the complete gene was cloned and sequenced. The identified protein, E. histolytica phosphatidylcholine transfer protein-like (EhPCTP-L), is a member of the StAR-related lipid transfer (START) protein superfamily. The human homolog binds and transfers phosphatidylcholine (PC) and phosphatidylethanolamine (PE) between model membranes in vitro; however, the physiological role of PCTP-L remains elusive. Studies in silico showed that EhPCTP-L has a central START domain and also contains a C-terminal intrinsically disordered region. The anti-rEhPCTP-L antibody demonstrated that EhPCTP-L is found in the plasma membrane and cytosol, which is in agreement with previous reports on the human counterpart. This result points to the plasma membrane as one possible target membrane for EhPCTP-L. Furthermore, assays using filipin and nystatin showed down regulation of EhPCTP-L, in an apparently cholesterol-independent way. Interestingly, EhPCTP-L binds primarily to anionic phospholipids phosphatidylserine (PS) and phosphatidic acid (PA), while its mammalian counterpart HsPCTP-L binds neutral phospholipids PC and PE. The present study provides information that helps reveal the possible function and regulation of PCTP-L expression in the primitive eukaryotic parasite E. histolytica. CI - Copyright (c) 2014 Elsevier B.V. and Societe francaise de biochimie et biologie Moleculaire (SFBBM). All rights reserved. FAU - Pina-Vazquez, Carolina AU - Pina-Vazquez C AD - Departamento de Biologia Celular, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional (CINVESTAV-IPN), Ave. IPN # 2508, Col. San Pedro Zacatenco, Mexico DF C.P. 07360, Mexico. FAU - Reyes-Lopez, Magda AU - Reyes-Lopez M AD - Departamento de Biologia Celular, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional (CINVESTAV-IPN), Ave. IPN # 2508, Col. San Pedro Zacatenco, Mexico DF C.P. 07360, Mexico. FAU - Mendoza-Hernandez, Guillermo AU - Mendoza-Hernandez G AD - Departamento de Bioquimica, Facultad de Medicina, Universidad Nacional Autonoma de Mexico (UNAM), Ave. Universidad # 3000, Ciudad Universitaria, Mexico DF C.P. 04510, Mexico. FAU - Bermudez-Cruz, Rosa Maria AU - Bermudez-Cruz RM AD - Departamento de Genetica y Biologia Molecular, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional (CINVESTAV-IPN), Ave. IPN # 2508, Col. San Pedro Zacatenco, Mexico DF C.P. 07360, Mexico. Electronic address: roberm@cinvestav.mx. FAU - de la Garza, Mireya AU - de la Garza M AD - Departamento de Biologia Celular, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional (CINVESTAV-IPN), Ave. IPN # 2508, Col. San Pedro Zacatenco, Mexico DF C.P. 07360, Mexico. Electronic address: mireya@cell.cinvestav.mx. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140916 PL - France TA - Biochimie JT - Biochimie JID - 1264604 SB - IM OTO - NOTNLM OT - Cholesterol-independent regulation OT - Entamoeba histolytica OT - Non-vesicular lipid transport OT - PCTP-L OT - STARD10 EDAT- 2014/09/17 06:00 MHDA- 2014/09/17 06:00 CRDT- 2014/09/17 06:00 PHST- 2014/02/22 [received] PHST- 2014/09/04 [accepted] PHST- 2014/09/16 [aheadofprint] AID - S0300-9084(14)00256-9 [pii] AID - 10.1016/j.biochi.2014.09.007 [doi] PST - ppublish SO - Biochimie. 2014 Dec;107 Pt B:223-34. doi: 10.1016/j.biochi.2014.09.007. Epub 2014 Sep 16. PMID- 10675525 OWN - NLM STAT- MEDLINE DA - 20000331 DCOM- 20000331 LR - 20131121 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 467 IP - 2-3 DP - 2000 Feb 11 TI - Is the manganese stabilizing 33 kDa protein of photosystem II attaining a 'natively unfolded' or 'molten globule' structure in solution? PG - 137-40 AB - This study compares the properties of the extrinsic 33 kDa subunit acting as 'manganese stabilizing protein' (MSP) of the water oxidizing complex with characteristic features of proteins that are known to attain a 'natively unfolded' or a 'molten globule' structure. The analysis leads to the conclusion that the MSP in solution is most likely a 'molten globule' with well defined compact regions of beta structure. The possible role of these structural peculiarities of MSP in solution for its function as important constituent of the WOC is discussed. FAU - Shutova, T AU - Shutova T AD - Max-Volmer-Institute for Biophysical Chemistry, Technical University Berlin, Strasse des 17. Juni 135, D-10623, Berlin, Germany. FAU - Irrgang, K AU - Irrgang K FAU - Klimov, V V AU - Klimov VV FAU - Renger, G AU - Renger G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Photosynthetic Reaction Center Complex Proteins) RN - 0 (Photosystem II Protein Complex) RN - 0 (Proteins) RN - 0 (Solutions) RN - 0 (photosystem II manganese-stabilizing protein) RN - 42Z2K6ZL8P (Manganese) SB - IM EIN - FEBS Lett 2000 Mar 10;469(2-3):214 MH - Manganese/*chemistry MH - Oxidation-Reduction MH - Photosynthetic Reaction Center Complex Proteins/*chemistry MH - *Photosystem II Protein Complex MH - Protein Conformation MH - Proteins/*chemistry MH - Solutions EDAT- 2000/02/17 09:00 MHDA- 2000/06/03 09:00 CRDT- 2000/02/17 09:00 AID - S0014579300011157 [pii] PST - ppublish SO - FEBS Lett. 2000 Feb 11;467(2-3):137-40. PMID- 22789567 OWN - NLM STAT- MEDLINE DA - 20120924 DCOM- 20130104 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 423 IP - 2 DP - 2012 Oct 19 TI - Ensemble structure of the modular and flexible full-length vesicular stomatitis virus phosphoprotein. PG - 182-97 LID - 10.1016/j.jmb.2012.07.003 [doi] LID - S0022-2836(12)00550-5 [pii] AB - The phosphoprotein (P) is an essential component of the viral replication machinery of non-segmented negative-strand RNA viruses, connecting the viral polymerase to its nucleoprotein-RNA template and acting as a chaperone of the nucleoprotein by preventing nonspecific encapsidation of cellular RNAs. The phosphoprotein of vesicular stomatitis virus (VSV) forms homodimers and possesses a modular organization comprising two stable, well-structured domains concatenated with two intrinsically disordered regions. Here, we used a combination of nuclear magnetic resonance spectroscopy and small-angle X-ray scattering to depict VSV P as an ensemble of continuously exchanging conformers that captures the dynamic character of this protein. We discuss the implications of the dynamics and the large conformational space sampled by VSV P in the assembly and functioning of the viral transcription/replication machinery. CI - Copyright (c) 2012 Elsevier Ltd. All rights reserved. FAU - Leyrat, Cedric AU - Leyrat C AD - Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, BP 181, 38042 Grenoble Cedex 9, France. FAU - Schneider, Robert AU - Schneider R FAU - Ribeiro, Euripedes A Jr AU - Ribeiro EA Jr FAU - Yabukarski, Filip AU - Yabukarski F FAU - Yao, Mingxi AU - Yao M FAU - Gerard, Francine C A AU - Gerard FC FAU - Jensen, Malene Ringkjobing AU - Jensen MR FAU - Ruigrok, Rob W H AU - Ruigrok RW FAU - Blackledge, Martin AU - Blackledge M FAU - Jamin, Marc AU - Jamin M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120709 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Phosphoproteins) RN - 0 (RNA, Viral) RN - 0 (Viral Structural Proteins) SB - IM MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Phosphoproteins/*chemistry/metabolism MH - Protein Conformation MH - RNA, Viral/chemistry/metabolism MH - Vesicular stomatitis Indiana virus/*metabolism MH - Viral Structural Proteins/*chemistry/metabolism MH - Virus Replication EDAT- 2012/07/14 06:00 MHDA- 2013/01/05 06:00 CRDT- 2012/07/14 06:00 PHST- 2012/02/03 [received] PHST- 2012/06/15 [revised] PHST- 2012/07/01 [accepted] PHST- 2012/07/09 [aheadofprint] AID - S0022-2836(12)00550-5 [pii] AID - 10.1016/j.jmb.2012.07.003 [doi] PST - ppublish SO - J Mol Biol. 2012 Oct 19;423(2):182-97. doi: 10.1016/j.jmb.2012.07.003. Epub 2012 Jul 9. PMID- 8989327 OWN - NLM STAT- MEDLINE DA - 19970129 DCOM- 19970129 LR - 20061115 IS - 1072-8368 (Print) IS - 1072-8368 (Linking) VI - 4 IP - 1 DP - 1997 Jan TI - High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA. PG - 70-7 AB - The structure of the C-terminal RNA recognition domain of ribosomal protein L11 has been solved by heteronuclear three-dimensional nuclear magnetic resonance spectroscopy. Although the structure can be considered high resolution in the core, 15 residues between helix alpha 1 and strand beta 1 form an extended, unstructured loop. 15N transverse relaxation measurements suggest that the loop is moving on a picosecond-to-nanosecond time scale in the free protein but not in the protein bound to RNA. Chemical shifts differences between the free protein and the bound protein suggest that the loop as well as the C-terminal end of helix alpha 3 are involved in RNA binding. FAU - Markus, M A AU - Markus MA AD - Molecular Structural Biology Unit, National Institute of Dental Research, Bethesda, Maryland 20892-4320, USA. FAU - Hinck, A P AU - Hinck AP FAU - Huang, S AU - Huang S FAU - Draper, D E AU - Draper DE FAU - Torchia, D A AU - Torchia DA LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Nat Struct Biol JT - Nature structural biology JID - 9421566 RN - 0 (RNA-Binding Proteins) RN - 0 (Ribosomal Proteins) RN - 0 (Solutions) RN - 0 (ribosomal protein L11) RN - 63231-63-0 (RNA) SB - IM MH - Amino Acid Sequence MH - Hydrogen Bonding MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Conformation MH - RNA/*metabolism MH - RNA-Binding Proteins/chemistry/metabolism MH - Ribosomal Proteins/*chemistry/metabolism MH - Solutions EDAT- 1997/01/01 MHDA- 1997/01/01 00:01 CRDT- 1997/01/01 00:00 PST - ppublish SO - Nat Struct Biol. 1997 Jan;4(1):70-7. PMID- 19208933 OWN - NLM STAT- MEDLINE DA - 20090211 DCOM- 20090319 LR - 20150503 IS - 1478-3975 (Electronic) IS - 1478-3967 (Linking) VI - 6 IP - 1 DP - 2009 TI - A role for helical intermediates in amyloid formation by natively unfolded polypeptides? PG - 015005 LID - 10.1088/1478-3975/6/1/015005 [doi] AB - Amyloid formation and aberrant protein aggregation have been implicated in more than 15 different human diseases and an even wider range of proteins form amyloid in vitro. From a structural perspective the proteins which form amyloid can be divided into two classes: those which adopt a compact globular fold and must presumably at least partially unfold to form amyloid and those which are unstructured in their monomeric state. Important examples of the latter include the Abeta peptide of Alzheimer's disease, atrial natriuretic factor, calcitonin, pro-calcitonin, islet amyloid polypeptide (IAPP, amylin), alpha-synuclein and the medin polypeptide. The kinetics of amyloid assembly are complex and typically involve a lag phase during which little or no fibril material is formed, followed by a rapid growth stage leading to the beta-sheet-rich amyloid structure. Increasing evidence suggests that some natively unfolded polypeptides populate a helical intermediate during the lag phase. We propose a model in which early oligomerization is linked to helix formation and is promoted by helix-helix association. Recent work has highlighted the potential importance of polypeptide membrane interactions in amyloid formation and helical intermediates appear to play an important role here as well. Characterization of helical intermediates is experimentally challenging but new spectroscopic techniques are emerging which hold considerable promise and even have the potential to provide residue specific information. FAU - Abedini, Andisheh AU - Abedini A AD - Joslin Diabetes Center, Division of Cellular and Molecular Physiology, Harvard Medical School, One Joslin Place, Boston, MA 02250, USA. Andisheh.Abedini@joslin.harvard.edu FAU - Raleigh, Daniel P AU - Raleigh DP LA - eng GR - GM078114/GM/NIGMS NIH HHS/United States GR - R01 GM078114/GM/NIGMS NIH HHS/United States GR - R01 GM078114-02/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090210 PL - England TA - Phys Biol JT - Physical biology JID - 101197454 RN - 0 (Amyloid) RN - 0 (Peptides) SB - IM MH - Amyloid/*chemistry/metabolism MH - Humans MH - Models, Molecular MH - Peptides/*chemistry/metabolism MH - Protein Folding MH - Protein Structure, Secondary PMC - PMC3215505 MID - NIHMS201551 OID - NLM: NIHMS201551 OID - NLM: PMC3215505 EDAT- 2009/02/12 09:00 MHDA- 2009/03/20 09:00 CRDT- 2009/02/12 09:00 AID - S1478-3975(09)87434-4 [pii] AID - 10.1088/1478-3975/6/1/015005 [doi] PST - epublish SO - Phys Biol. 2009 Feb 10;6(1):015005. doi: 10.1088/1478-3975/6/1/015005. PMID- 16302811 OWN - NLM STAT- MEDLINE DA - 20051123 DCOM- 20060209 LR - 20121115 IS - 0022-2623 (Print) IS - 0022-2623 (Linking) VI - 48 IP - 24 DP - 2005 Dec 1 TI - Binding of the anticancer prodrug CB1954 to the activating enzyme NQO2 revealed by the crystal structure of their complex. PG - 7714-9 AB - CB1954 is an attractive prodrug for directed-enzyme prodrug therapy (DEPT) and a conventional prodrug against tumors in which the enzyme NQO2 is highly expressed. We have determined the crystal structure of the NQO2-CB1954 complex to 2.0 A resolution. The binding of the prodrug is governed by hydrophobic forces, while two key electrostatic contacts determine the specific orientation of the ligand. The structure also reveals an unfavorable interaction, therefore suggesting possible avenues for DEPT-tailored engineering studies. FAU - AbuKhader, Majed AU - AbuKhader M AD - School of Pharmacy and The Institute of Infection, Immunity and Inflammation, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK. FAU - Heap, John AU - Heap J FAU - De Matteis, Cristina AU - De Matteis C FAU - Kellam, Barrie AU - Kellam B FAU - Doughty, Stephen W AU - Doughty SW FAU - Minton, Nigel AU - Minton N FAU - Paoli, Massimo AU - Paoli M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Med Chem JT - Journal of medicinal chemistry JID - 9716531 RN - 0 (Antineoplastic Agents) RN - 0 (Aziridines) RN - 0 (Prodrugs) RN - 7865D5D01M (tretazicar) RN - EC 1.6.99.- (NRH - quinone oxidoreductase2) RN - EC 1.6.99.- (Quinone Reductases) SB - IM MH - Antineoplastic Agents/*chemistry MH - Aziridines/*chemistry MH - Crystallization MH - Crystallography, X-Ray MH - Models, Molecular MH - Molecular Conformation MH - Prodrugs/*chemistry MH - Protein Binding MH - Quinone Reductases/*chemistry EDAT- 2005/11/24 09:00 MHDA- 2006/02/10 09:00 CRDT- 2005/11/24 09:00 AID - 10.1021/jm050730n [doi] PST - ppublish SO - J Med Chem. 2005 Dec 1;48(24):7714-9. PMID- 9009196 OWN - NLM STAT- MEDLINE DA - 19970212 DCOM- 19970212 LR - 20061115 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 385 IP - 6615 DP - 1997 Jan 30 TI - The structure of the GTPase-activating domain from p50rhoGAP. PG - 458-61 AB - Members of the Rho family of small G proteins transduce signals from plasma-membrane receptors and control cell adhesion, motility and shape by actin cytoskeleton formation. They also activate other kinase cascades. Like all other GTPases, Rho proteins act as molecular switches, with an active GTP-bound form and an inactive GDP-bound form. The active conformation is promoted by guanine-nucleotide exchange factors, and the inactive state by GTPase-activating proteins (GAPs) which stimulate the intrinsic GTPase activity of small G proteins. Rho-specific GAP domains are found in a wide variety of large, multi-functional proteins. Here we report the crystal structure of an active 242-residue C-terminal fragment of human p50rhoGAP. The structure is an unusual arrangement of nine alpha-helices, the core of which includes a four-helix bundle. Residues conserved across the rhoGAP family are largely confined to one face of this bundle, which may be an interaction site for target G proteins. In particular, we propose that Arg 85 and Asn 194 are involved in binding G proteins and enhancing GTPase activity. FAU - Barrett, T AU - Barrett T AD - National Institute for Medical Research, London, UK. FAU - Xiao, B AU - Xiao B FAU - Dodson, E J AU - Dodson EJ FAU - Dodson, G AU - Dodson G FAU - Ludbrook, S B AU - Ludbrook SB FAU - Nurmahomed, K AU - Nurmahomed K FAU - Gamblin, S J AU - Gamblin SJ FAU - Musacchio, A AU - Musacchio A FAU - Smerdon, S J AU - Smerdon SJ FAU - Eccleston, J F AU - Eccleston JF LA - eng SI - GENBANK/A28765 SI - GENBANK/A38218 SI - GENBANK/P15882 SI - GENBANK/P27986 SI - GENBANK/X87671 SI - GENBANK/Z23024 SI - PDB/1RGP PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (GTPase-Activating Proteins) RN - 0 (rho GTPase-activating protein) RN - EC 3.6.1.- (GTP Phosphohydrolases) RN - EC 3.6.1.- (GTP-Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Crystallography, X-Ray MH - Enzyme Activation MH - GTP Phosphohydrolases/*metabolism MH - GTP-Binding Proteins/*chemistry MH - *GTPase-Activating Proteins MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - *Protein Conformation MH - Sequence Homology, Amino Acid EDAT- 1997/01/30 MHDA- 1997/01/30 00:01 CRDT- 1997/01/30 00:00 AID - 10.1038/385458a0 [doi] PST - ppublish SO - Nature. 1997 Jan 30;385(6615):458-61. PMID- 19435287 OWN - NLM STAT- MEDLINE DA - 20090630 DCOM- 20090813 LR - 20140918 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 26 DP - 2009 Jul 7 TI - Crystal structure of the bacterial luciferase/flavin complex provides insight into the function of the beta subunit. PG - 6085-94 LID - 10.1021/bi900003t [doi] AB - Bacterial luciferase from Vibrio harveyi is a heterodimer composed of a catalytic alpha subunit and a homologous but noncatalytic beta subunit. Despite decades of enzymological investigation, structural evidence defining the active center has been elusive. We report here the crystal structure of V. harveyi luciferase bound to flavin mononucleotide (FMN) at 2.3 A. The isoalloxazine ring is coordinated by an unusual cis-Ala-Ala peptide bond. The reactive sulfhydryl group of Cys106 projects toward position C-4a, the site of flavin oxygenation. This structure also provides the first data specifying the conformations of a mobile loop that is crystallographically disordered in both prior crystal structures [(1995) Biochemistry 34, 6581-6586; (1996) J. Biol. Chem. 271, 21956 21968]. This loop appears to be a boundary between solvent and the active center. Within this portion of the protein, a single contact was observed between Phe272 of the alpha subunit, not seen in the previous structures, and Tyr151 of the beta subunit. Substitutions at position 151 on the beta subunit caused reductions in activity and total quantum yield. Several of these mutants were found to have decreased affinity for reduced flavin mononucleotide (FMNH(2)). These findings partially address the long-standing question of how the beta subunit stabilizes the active conformation of the alpha subunit, thereby participating in the catalytic mechanism. FAU - Campbell, Zachary T AU - Campbell ZT AD - Department of Biochemistry and Molecular Biophysics, University of Arizona, 1041 East Lowell Street, Biological Sciences West, Tucson, Arizona 85721-0088, USA. FAU - Weichsel, Andrzej AU - Weichsel A FAU - Montfort, William R AU - Montfort WR FAU - Baldwin, Thomas O AU - Baldwin TO LA - eng SI - PDB/3FGC GR - HL62969/HL/NHLBI NIH HHS/United States GR - R01 HL062969/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Hydroquinones) RN - 0 (Protein Subunits) RN - 0 (Recombinant Proteins) RN - 0 (flavin mononucleotide hydroquinone) RN - 42HK56048U (Tyrosine) RN - 7N464URE7E (Flavin Mononucleotide) RN - EC 1.14.14.3 (Luciferases, Bacterial) SB - IM MH - Amino Acid Substitution MH - Biocatalysis MH - Catalytic Domain MH - *Crystallography, X-Ray MH - Flavin Mononucleotide/*chemistry/metabolism MH - Hydrogen Bonding MH - Hydroquinones/chemistry/metabolism MH - Kinetics MH - Luciferases, Bacterial/*chemistry/genetics/metabolism MH - Models, Molecular MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Subunits/*chemistry/*metabolism MH - Recombinant Proteins/chemistry MH - Tyrosine/chemistry/genetics MH - Vibrio/*enzymology EDAT- 2009/05/14 09:00 MHDA- 2009/08/14 09:00 CRDT- 2009/05/14 09:00 AID - 10.1021/bi900003t [doi] PST - ppublish SO - Biochemistry. 2009 Jul 7;48(26):6085-94. doi: 10.1021/bi900003t. PMID- 23166627 OWN - NLM STAT- MEDLINE DA - 20121120 DCOM- 20130506 LR - 20141104 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 11 DP - 2012 TI - A new protein superfamily: TPPP-like proteins. PG - e49276 LID - 10.1371/journal.pone.0049276 [doi] AB - The introduction of the term 'Tubulin Polymerization Promoting Protein (TPPP)-like proteins' is suggested. They constitute a eukaryotic protein superfamily, characterized by the presence of the p25alpha domain (Pfam05517, IPR008907), and named after the first identified member, TPPP/p25, exhibiting microtubule stabilizing function. TPPP-like proteins can be grouped on the basis of two characteristics: the length of their p25alpha domain, which can be long, short, truncated or partial, and the presence or absence of additional domain(s). TPPPs, in the strict sense, contain no other domains but one long or short p25alpha one (long- and short-type TPPPs, respectively). Proteins possessing truncated p25alpha domain are first described in this paper. They evolved from the long-type TPPPs and can be considered as arthropod-specific paralogs of long-type TPPPs. Phylogenetic analysis shows that the two groups (long-type and truncated TPPPs) split in the common ancestor of arthropods. Incomplete p25alpha domains can be found in multidomain TPPP-like proteins as well. The various subfamilies occur with a characteristic phyletic distribution: e. g., animal genomes/proteomes contain almost without exception long-type TPPPs; the multidomain apicortins occur almost exclusively in apicomplexan parasites. There are no data about the physiological function of these proteins except two human long-type TPPP paralogs which are involved in developmental processes of the brain and the musculoskeletal system, respectively. I predict that the superfamily members containing long or partial p25alpha domain are often intrinsically disordered proteins, while those with short or truncated domain(s) are structurally ordered. Interestingly, members of this superfamily connected or maybe connected to diseases are intrinsically disordered proteins. FAU - Orosz, Ferenc AU - Orosz F AD - Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary. orosz@enzim.hu LA - eng PT - Journal Article DEP - 20121114 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Nerve Tissue Proteins) RN - 0 (p25 protein, human) SB - IM MH - Amino Acid Sequence MH - Animals MH - Base Sequence MH - Bayes Theorem MH - Data Mining MH - Databases, Genetic MH - *Evolution, Molecular MH - Expressed Sequence Tags MH - Humans MH - Invertebrates/*genetics MH - Microtubules/*metabolism MH - Models, Genetic MH - Molecular Sequence Data MH - Multigene Family/*genetics MH - Nerve Tissue Proteins/classification/*genetics/metabolism MH - *Phylogeny MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Vertebrates/*genetics PMC - PMC3498115 OID - NLM: PMC3498115 EDAT- 2012/11/21 06:00 MHDA- 2013/05/07 06:00 CRDT- 2012/11/21 06:00 PHST- 2012/07/24 [received] PHST- 2012/10/08 [accepted] PHST- 2012/11/14 [epublish] AID - 10.1371/journal.pone.0049276 [doi] AID - PONE-D-12-21595 [pii] PST - ppublish SO - PLoS One. 2012;7(11):e49276. doi: 10.1371/journal.pone.0049276. Epub 2012 Nov 14. PMID- 24974286 OWN - NLM STAT- MEDLINE DA - 20140630 DCOM- 20150212 IS - 1557-7988 (Electronic) IS - 0076-6879 (Linking) VI - 544 DP - 2014 TI - The structural biology of BH3-only proteins. PG - 49-74 LID - 10.1016/B978-0-12-417158-9.00003-0 [doi] LID - B978-0-12-417158-9.00003-0 [pii] AB - B-cell lymphoma-2 (Bcl-2) homology-3 (BH3)-only proteins are considered members of the Bcl-2 family, though they bear little sequence or structural identity with the multi-BH motif prosurvival or proapoptotic Bcl-2 proteins like Bcl-2 or Bax. They are better considered a separate phylogenetic entity. In combination, results from biophysical, biochemical, cell biological, and animal studies in conjunction with structural investigations have elucidated the function and mechanism of action of these proteins. Either by antagonizing prosurvival Bcl-2 proteins or directly activating proapoptotic Bcl-2 proteins (Bax or Bak) they initiate apoptosis. BH3-only proteins are intrinsically disordered and fold and bind into a groove provided by their cognate receptor Bcl-2 family proteins. Our detailed molecular understanding of BH3-only protein action has aided the development of novel chemical entities that initiate cell death by mimicking the properties of BH3-only proteins. CI - (c) 2014 Elsevier Inc. All rights reserved. FAU - Kvansakul, Marc AU - Kvansakul M AD - La Trobe Institute for Medical Science, La Trobe University, Bundoora, Victoria, Australia. Electronic address: m.kvansakul@latrobe.edu.au. FAU - Hinds, Mark G AU - Hinds MG AD - School of Chemistry, The University of Melbourne, Parkville, Victoria, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia. Electronic address: mhinds@unimelb.edu.au. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Methods Enzymol JT - Methods in enzymology JID - 0212271 RN - 0 (Proto-Oncogene Proteins c-bcl-2) SB - IM MH - Amino Acid Sequence MH - Animals MH - Apoptosis MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Neoplasms/metabolism MH - Protein Conformation MH - Protein Interaction Mapping/methods MH - Protein Interaction Maps MH - Proto-Oncogene Proteins c-bcl-2/*analysis/*metabolism OTO - NOTNLM OT - Apoptosis OT - BH3-only OT - Bcl-2 OT - Cancer OT - Protein structure EDAT- 2014/06/30 06:00 MHDA- 2015/02/13 06:00 CRDT- 2014/06/30 06:00 AID - B978-0-12-417158-9.00003-0 [pii] AID - 10.1016/B978-0-12-417158-9.00003-0 [doi] PST - ppublish SO - Methods Enzymol. 2014;544:49-74. doi: 10.1016/B978-0-12-417158-9.00003-0. PMID- 20687558 OWN - NLM STAT- MEDLINE DA - 20100825 DCOM- 20101208 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 132 IP - 34 DP - 2010 Sep 1 TI - Automatic assignment of the intrinsically disordered protein Tau with 441-residues. PG - 11906-7 LID - 10.1021/ja105657f [doi] AB - Intrinsically disordered proteins carry out many important functions in the cell. However, the lack of an ordered structure causes dramatic signal overlap and complicates the NMR-based characterization of their structure and dynamics. Here we demonstrate that the resonance assignment of 441-residue Tau and its smaller isoforms, htau24 (383 residues) and htau23 (352 residues), three prototypes of intrinsically disordered proteins, which bind to microtubules and play a key role in Alzheimer disease, can be obtained within 5 days by a combination of seven-dimensional NMR spectra with optimized methods for automatic assignment. Chemical shift differences between the three isoforms provide evidence for the global folding of Tau in solution. FAU - Narayanan, Rhagavendran L AU - Narayanan RL AD - Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany. FAU - Durr, Ulrich H N AU - Durr UH FAU - Bibow, Stefan AU - Bibow S FAU - Biernat, Jacek AU - Biernat J FAU - Mandelkow, Eckhard AU - Mandelkow E FAU - Zweckstetter, Markus AU - Zweckstetter M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Protein Isoforms) RN - 0 (tau Proteins) SB - IM MH - Amino Acid Sequence MH - *Automatic Data Processing MH - Computational Biology MH - Databases, Protein MH - Humans MH - Magnetic Resonance Spectroscopy/standards MH - Protein Conformation MH - Protein Isoforms/chemistry MH - Reference Standards MH - tau Proteins/*chemistry EDAT- 2010/08/07 06:00 MHDA- 2010/12/14 06:00 CRDT- 2010/08/07 06:00 AID - 10.1021/ja105657f [doi] PST - ppublish SO - J Am Chem Soc. 2010 Sep 1;132(34):11906-7. doi: 10.1021/ja105657f. PMID- 20858207 OWN - NLM STAT- MEDLINE DA - 20110225 DCOM- 20110603 IS - 1875-5305 (Electronic) IS - 0929-8665 (Linking) VI - 18 IP - 3 DP - 2011 Mar TI - Characterization of the non-fibrillar alpha-synuclein oligomers. PG - 230-40 AB - Under certain in vitro conditions, alpha-Synuclein is an abundant 14 kDa presynaptic intrinsically disordered protein, involved in the pathogenesis of Parkinson's disease (PD) forms amyloid fibrils which resemble those found in Lewy bodies of PD patients. However, a substantial fraction of alpha-synuclein molecules (10-20 %) does not form fibrils during fibrillation and exists in a form of soluble oligomers. In this study, we examined these soluble oligomers by a variety of biophysical techniques including atomic force microscopy (AFM), circular dichroism, Fourier-transform infrared spectroscopy and thioflavin T fluorescence. We observed that the fibrillation kinetics is affected by the variation in salt and protein concentrations. Although both high salt and high protein concentrations noticeably accelerated alpha-synuclein fibrillation, the amount of non-fibrillar oligomers is independent of the salt content. The oligomers formed at low salt concentration adopt more beta-sheet structure and are smaller in size than those formed at high salt concentration. AFM analysis shows that the low salt oligomers represent a mixture of small oligomers and some amorphous aggregates, whereas oligomers formed at high salt concentrations are noticeably larger, more homogenous, and are mostly spherical in shape. All the late stage non-fibrillar oligomers do not form fibrils even when seeded with pre-formed fibrils, are characterized by negligible rates of dissociation, likely due to their intertwined structure, and are able to disrupt the integrity of the biological membrane. These findings suggest that these soluble oligomers are important players in the multi-pathway aggregation of alpha-synuclein and should be taken into account in studies on the molecular mechanisms of this protein fibrillation. FAU - Hong, Dong-Pyo AU - Hong DP AD - Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA 95064, USA. FAU - Han, Shubo AU - Han S FAU - Fink, Anthony L AU - Fink AL FAU - Uversky, Vladimir N AU - Uversky VN LA - eng GR - GM071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 LM007688-01A1/LM/NLM NIH HHS/United States GR - R01 NS39985/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 RN - 0 (Salts) RN - 0 (Thiazoles) RN - 0 (Unilamellar Liposomes) RN - 0 (alpha-Synuclein) RN - 2390-54-7 (thioflavin T) SB - IM MH - Cell Membrane/chemistry/metabolism MH - Dose-Response Relationship, Drug MH - Kinetics MH - *Protein Multimerization/drug effects MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Salts/pharmacology MH - Solubility MH - Thiazoles/metabolism MH - Unilamellar Liposomes/chemistry/metabolism MH - alpha-Synuclein/*chemistry/metabolism EDAT- 2010/09/23 06:00 MHDA- 2011/06/04 06:00 CRDT- 2010/09/23 06:00 PHST- 2009/11/12 [received] PHST- 2010/09/02 [accepted] AID - BSP/ PPL/ E pub/0214 [pii] PST - ppublish SO - Protein Pept Lett. 2011 Mar;18(3):230-40. PMID- 23009354 OWN - NLM STAT- MEDLINE DA - 20130207 DCOM- 20130401 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 51 IP - 41 DP - 2012 Oct 16 TI - Novel protease inhibitors via computational redesign of subtilisin BPN' propeptide. PG - 8247-55 LID - 10.1021/bi300832v [doi] AB - The propeptide domain of subtilisin BPN' functions as a molecular chaperone for its cognate protease yet quickly assumes a predominantly unfolded structure following cleavage by the mature protease. In contrast, structural stabilization of the propeptide domain has been proposed to competitively inhibit protease self-cleavage, suggesting the possibility for the generation of novel proteinaceous subtilisin inhibitors. Using a Rosetta fixed backbone design, we have redesigned the subtilisin BPN' propeptide structure to generate synthetic peptide sequences with increased and tunable structural stability. Molecular dynamics simulations provide supporting evidence that the artificial sequences retain structure without its protease cognate unlike the inherently disordered wild-type propeptide. Experimental evaluation of two designer domains by spectroscopic methods verified their structural integrity. Furthermore, the novel propeptide domains were shown to possess significantly enhanced thermostability. Nevertheless, their modest functional performance as protease inhibitors raises doubt that propeptide stability alone is sufficient for effective inhibitor design. FAU - Daugherty, Ashley B AU - Daugherty AB AD - Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA. FAU - Muthu, Pravin AU - Muthu P FAU - Lutz, Stefan AU - Lutz S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20121004 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Protease Inhibitors) RN - EC 3.4.21.- (Subtilisins) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Models, Molecular MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Protease Inhibitors/*chemistry MH - Proteolysis MH - Sequence Homology, Amino Acid MH - Spectrometry, Fluorescence MH - Subtilisins/*chemistry/genetics EDAT- 2012/09/27 06:00 MHDA- 2013/04/02 06:00 CRDT- 2012/09/27 06:00 PHST- 2012/10/04 [aheadofprint] AID - 10.1021/bi300832v [doi] PST - ppublish SO - Biochemistry. 2012 Oct 16;51(41):8247-55. doi: 10.1021/bi300832v. Epub 2012 Oct 4. PMID- 22767608 OWN - NLM STAT- MEDLINE DA - 20120827 DCOM- 20121119 LR - 20150325 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 35 DP - 2012 Aug 24 TI - Remodeling of lipid vesicles into cylindrical micelles by alpha-synuclein in an extended alpha-helical conformation. PG - 29301-11 LID - 10.1074/jbc.M112.365817 [doi] AB - alpha-Synuclein (alphaS) is a protein with multiple conformations and interactions. Natively unfolded in solution, alphaS accumulates as amyloid in neurological tissue in Parkinson disease and interacts with membranes under both physiological and pathological conditions. Here, we used cryoelectron microscopy in conjunction with electron paramagnetic resonance (EPR) and other techniques to characterize the ability of alphaS to remodel vesicles. At molar ratios of 1:5 to 1:40 for protein/lipid (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol), large spherical vesicles are converted into cylindrical micelles ~50 A in diameter. Other lipids of the same charge (negative) exhibit generally similar behavior, although bilayer tubes of 150-500 A in width are also produced, depending on the lipid acyl chains. At higher protein/lipid ratios, discoid particles, 70-100 A across, are formed. EPR data show that, on cylindrical micelles, alphaS adopts an extended amphipathic alpha-helical conformation, with its long axis aligned with the tube axis. The observed geometrical relationship between alphaS and the micelle suggests that the wedging of its long alpha-helix into the outer leaflet of a membrane may cause curvature and an anisotropic partition of lipids, leading to tube formation. FAU - Mizuno, Naoko AU - Mizuno N AD - Laboratory of Structural Biology, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA. mizuno@biochem.mpg.de FAU - Varkey, Jobin AU - Varkey J FAU - Kegulian, Natalie C AU - Kegulian NC FAU - Hegde, Balachandra G AU - Hegde BG FAU - Cheng, Naiqian AU - Cheng N FAU - Langen, Ralf AU - Langen R FAU - Steven, Alasdair C AU - Steven AC LA - eng GR - 2 R01 GM063915/GM/NIGMS NIH HHS/United States GR - R01 GM063915/GM/NIGMS NIH HHS/United States GR - Z01 AR027015-13/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural DEP - 20120705 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Lipid Bilayers) RN - 0 (Micelles) RN - 0 (Phosphatidylglycerols) RN - 0 (alpha-Synuclein) RN - 81490-05-3 (1-palmitoyl-2-oleoylglycero-3-phosphoglycerol) SB - IM MH - Electron Spin Resonance Spectroscopy MH - Humans MH - Lipid Bilayers/*chemistry/metabolism MH - *Micelles MH - Parkinson Disease/genetics/metabolism MH - Phosphatidylglycerols/*chemistry/metabolism MH - *Protein Folding MH - Protein Structure, Secondary MH - alpha-Synuclein/*chemistry/genetics/metabolism PMC - PMC3436199 OID - NLM: PMC3436199 EDAT- 2012/07/07 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/07/07 06:00 PHST- 2012/07/05 [aheadofprint] AID - M112.365817 [pii] AID - 10.1074/jbc.M112.365817 [doi] PST - ppublish SO - J Biol Chem. 2012 Aug 24;287(35):29301-11. doi: 10.1074/jbc.M112.365817. Epub 2012 Jul 5. PMID- 11785981 OWN - NLM STAT- MEDLINE DA - 20020111 DCOM- 20020211 LR - 20061115 IS - 0006-291X (Print) IS - 0006-291X (Linking) VI - 290 IP - 2 DP - 2002 Jan 18 TI - HSP90, HSP70, and GAPDH directly interact with the cytoplasmic domain of macrophage scavenger receptors. PG - 858-64 AB - The macrophage scavenger receptor (MSR) is a trimeric membrane protein which binds to modified low-density lipoprotein (LDL) and has been indicated in the development of atherosclerosis. It has recently been demonstrated that the N-terminal cytoplasmic domain of MSR has an important role in the efficient internalization and cell-surface expression of the receptor. This study shows that the N-terminal cytoplasmic domain in bovine was constructed using a peptide architecture technique in which the peptide chain was bundled at their C-terminus to yield a trimeric form and that this did not form an ordered structure. Furthermore, the binding proteins to the cytoplasmic domain of MSR were determined for the first time using a peptide affinity column. Sequence analyses of the specific binding proteins in bovine revealed that heat shock protein 90 (HSP90), heat shock protein 70 (HSP70), leucine aminopeptidase (LAP), adenocylhomocysteinase, and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were included. GST-pull-down assay and immunoprecipitation analyses on HSP90, HSP70, and GAPDH showed that all these proteins could bind to the cytoplasmic domain of MSR in vitro and in vivo. These proteins interact with the cytoplasmic domain directly and may have an effect on the functions of MSR such as internalization, cell-surface expression, and signal transduction. FAU - Nakamura, Toshinobu AU - Nakamura T AD - Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan. FAU - Hinagata, Jun-ichi AU - Hinagata J FAU - Tanaka, Toshiki AU - Tanaka T FAU - Imanishi, Takeshi AU - Imanishi T FAU - Wada, Youichiro AU - Wada Y FAU - Kodama, Tatsuhiko AU - Kodama T FAU - Doi, Takefumi AU - Doi T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (HSP70 Heat-Shock Proteins) RN - 0 (HSP90 Heat-Shock Proteins) RN - 0 (MSR1 protein, human) RN - 0 (Peptide Fragments) RN - 0 (Receptors, Immunologic) RN - 0 (Receptors, Scavenger) RN - 0 (Scavenger Receptors, Class A) RN - EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases) SB - IM MH - Animals MH - Blotting, Western MH - COS Cells MH - Cattle MH - Chromatography, Affinity MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Glyceraldehyde-3-Phosphate Dehydrogenases/genetics/*metabolism MH - HSP70 Heat-Shock Proteins/genetics/*metabolism MH - HSP90 Heat-Shock Proteins/genetics/*metabolism MH - Humans MH - Lung/chemistry/metabolism MH - Peptide Fragments/chemical synthesis/chemistry/metabolism MH - Precipitin Tests MH - Protein Binding/physiology MH - Protein Structure, Tertiary/physiology MH - Receptors, Immunologic/*chemistry/genetics/*metabolism MH - Receptors, Scavenger MH - Scavenger Receptors, Class A MH - Structure-Activity Relationship EDAT- 2002/01/12 10:00 MHDA- 2002/02/12 10:01 CRDT- 2002/01/12 10:00 AID - 10.1006/bbrc.2001.6271 [doi] AID - S0006291X01962710 [pii] PST - ppublish SO - Biochem Biophys Res Commun. 2002 Jan 18;290(2):858-64. PMID- 16475817 OWN - NLM STAT- MEDLINE DA - 20060214 DCOM- 20060410 LR - 20121115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 7 DP - 2006 Feb 21 TI - Global hairpin folding of tau in solution. PG - 2283-93 AB - The microtubule-associated protein tau stabilizes microtubules in its physiological role, whereas it forms insoluble aggregates (paired helical filaments) in Alzheimer's disease. Soluble tau is considered a natively unfolded protein whose residual folding and intramolecular interactions are largely undetermined. In this study, we have applied fluorescence resonance energy transfer (FRET) and electron paramagnetic resonance (EPR) to examine the proximity and flexibility of tau domains and the global folding. FRET pairs spanning the tau molecule were created by inserting tryptophans (donor) and cysteines (labeled with IAEDANS as an acceptor) by site-directed mutagenesis. The observed FRET distances were significantly different from those expected for a random coil. Notably, the C-terminal end of tau folds over into the vicinity of the microtubule-binding repeat domain, the N-terminus remains outside the FRET distance of the repeat domain, yet both ends of the molecule approach one another. The interactions between the domains were obliterated by denaturation in GdnHCl. Paramagnetic spin-labels attached in various domains of tau were analyzed by EPR and exhibited a high mobility throughout. The data indicate that tau retains some global folding even in its "natively unfolded" state, combined with the high flexibility of the chain. FAU - Jeganathan, Sadasivam AU - Jeganathan S AD - Max Planck Unit for Structural Molecular Biology, Notkestrasse 85, D-22607 Hamburg, Germany. FAU - von Bergen, Martin AU - von Bergen M FAU - Brutlach, Henrik AU - Brutlach H FAU - Steinhoff, Heinz-Jurgen AU - Steinhoff HJ FAU - Mandelkow, Eckhard AU - Mandelkow E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Naphthalenesulfonates) RN - 0 (Solutions) RN - 0 (tau Proteins) RN - 6V7G304M5M (1,5-I-AEDANS) SB - IM MH - Circular Dichroism MH - Electron Spin Resonance Spectroscopy MH - Fluorescence Resonance Energy Transfer MH - Mutagenesis, Site-Directed MH - Naphthalenesulfonates/chemistry MH - Protein Folding MH - Solutions MH - tau Proteins/*chemistry/genetics EDAT- 2006/02/16 09:00 MHDA- 2006/04/11 09:00 CRDT- 2006/02/16 09:00 AID - 10.1021/bi0521543 [doi] PST - ppublish SO - Biochemistry. 2006 Feb 21;45(7):2283-93. PMID- 10372360 OWN - NLM STAT- MEDLINE DA - 19990802 DCOM- 19990802 LR - 20060501 IS - 0076-6879 (Print) IS - 0076-6879 (Linking) VI - 304 DP - 1999 TI - Purification and assays for high mobility group HMG-I(Y) protein function. PG - 155-88 FAU - Reeves, R AU - Reeves R AD - Department of Biochemistry/Biophysics, Washington State University, Pullman 99164-4660, USA. FAU - Nissen, M S AU - Nissen MS LA - eng PT - Journal Article PL - UNITED STATES TA - Methods Enzymol JT - Methods in enzymology JID - 0212271 RN - 0 (Chromatin) RN - 0 (DNA, Superhelical) RN - 0 (High Mobility Group Proteins) RN - 0 (Indicators and Reagents) RN - 0 (Neoplasm Proteins) RN - 0 (Receptors, Interleukin-2) RN - 0 (Recombinant Proteins) RN - 0 (Transcription Factors) RN - 124544-67-8 (HMGA1a Protein) RN - 207137-56-2 (Interleukin-4) RN - EC 3.1.21.1 (Deoxyribonuclease I) SB - IM MH - Animals MH - Base Sequence MH - Cell Fractionation/methods MH - Cell Nucleus/chemistry/ultrastructure MH - Centrifugation/methods MH - Chromatin/chemistry/ultrastructure MH - Chromatography, High Pressure Liquid/methods MH - Chromatography, Ion Exchange/methods MH - DNA Footprinting/methods MH - DNA, Superhelical/chemistry/isolation & purification/metabolism MH - Deoxyribonuclease I MH - HMGA1a Protein MH - HeLa Cells MH - High Mobility Group Proteins/analysis/*isolation & purification/*metabolism MH - Humans MH - Indicators and Reagents MH - Interleukin-4/genetics MH - Leukemia, Erythroblastic, Acute/metabolism/pathology MH - Mice MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Neoplasm Proteins/isolation & purification MH - Plasmids MH - Receptors, Interleukin-2/genetics MH - Recombinant Proteins/analysis/isolation & purification/metabolism MH - Transcription Factors/analysis/*isolation & purification/*metabolism MH - Transfection MH - Tumor Cells, Cultured EDAT- 1999/06/18 MHDA- 1999/06/18 00:01 CRDT- 1999/06/18 00:00 AID - S0076-6879(99)04011-2 [pii] PST - ppublish SO - Methods Enzymol. 1999;304:155-88. PMID- 21031484 OWN - NLM STAT- MEDLINE DA - 20101224 DCOM- 20110415 LR - 20140821 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 20 IP - 1 DP - 2011 Jan TI - Cryoprotective mechanism of a small intrinsically disordered dehydrin protein. PG - 42-50 LID - 10.1002/pro.534 [doi] AB - Dehydration proteins (Dehydrins) are expressed during dehydration stress in plants and are thought to protect plant proteins and membranes from the loss of water during drought and at cold temperatures. Several different dehydrins have been shown to protect lactate dehydrogenase (LDH) from damage from being frozen and thawed. We show here that a 48 residue K(2) dehydrin from Vitis riparia protects LDH more effectively than bovine serum albumin, a protein with known cryoprotective function. Light scattering and 8-anilino-1-naphthalene sulfonate fluorescence experiments show that dehydrins prevent aggregation and unfolding of the enzyme. The cryoprotective effects of LDH are reduced by the addition of salt, suggesting that the positively charged K-segments are attracted to a negatively charged surface but this does not result in binding. Overall K(2) is an intrinsically disordered protein; nuclear magnetic resonance relaxation experiments indicate that the two-terminal, Lys-rich K-segments show a weak propensity for alpha-helicity and are flexible, and that the central, polar rich phi-segment has no secondary structure preference and is highly flexible. We propose that the phi-segments in dehydrins are important for maintaining the disordered structure so that the protein can act as a molecular shield to prevent partially denatured proteins from interacting with one another, whereas the K-segments may help to localize the dehydrin near the enzyme surface. FAU - Hughes, Stephanie AU - Hughes S AD - Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1. FAU - Graether, Steffen P AU - Graether SP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Cold Shock Proteins and Peptides) RN - 0 (Plant Proteins) RN - 134711-03-8 (dehydrin proteins, plant) RN - EC 1.1.1.27 (L-Lactate Dehydrogenase) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cattle MH - Cold Shock Proteins and Peptides/*chemistry MH - Cold Temperature MH - Enzyme Assays MH - Enzyme Stability MH - L-Lactate Dehydrogenase/*chemistry MH - Molecular Sequence Data MH - Plant Proteins/*chemistry MH - Protein Conformation MH - Protein Denaturation MH - Sequence Alignment MH - Vitis PMC - PMC3047060 OID - NLM: PMC3047060 EDAT- 2010/10/30 06:00 MHDA- 2011/04/19 06:00 CRDT- 2010/10/30 06:00 AID - 10.1002/pro.534 [doi] PST - ppublish SO - Protein Sci. 2011 Jan;20(1):42-50. doi: 10.1002/pro.534. PMID- 24127726 OWN - NLM STAT- MEDLINE DA - 20131107 DCOM- 20140617 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 117 IP - 44 DP - 2013 Nov 7 TI - The conformational landscape of an intrinsically disordered DNA-binding domain of a transcription regulator. PG - 13842-50 LID - 10.1021/jp408350v [doi] AB - Delineating the conformational features of intrinsically disordered proteins (IDPs) is an area of work that challenges current experimental and simulation protocols. It is therefore imperative to combine multiple methodologies to arrive at a coherent picture of the heterogeneous IDP ensembles. Here, we present a comprehensive study drawing from structure-based statistical mechanical model, explicit-solvent MD and implicit-solvent REMD simulations, and mutational analysis to characterize, in combination with experimental observables, the functional landscape of the intrinsically disordered DNA-binding domain (DBD) of the Escherichia coli transcription regulator CytR in its free-state. The resulting landscape of CytR DBD populates multiple distinct conformations and shows signs of residual frustration from native interactions that are critical for promoting partial structure in the DNA-binding second helix. We thus find evidence for a unique combination of conformational selection and induced-fit mechanism that enables CytR to bind DNA. Functionally deficient mutations affect the IDP landscape in a nontrivial manner highlighting the importance of using an ensemble-based structural representation of IDPs. In effect, our results reveal a functional role for structural frustration, and provide a novel avenue to characterize IDP landscapes combining simple structural probes and multimodel approaches. FAU - Naganathan, Athi N AU - Naganathan AN AD - Department of Biotechnology, Indian Institute of Technology Madras , Chennai 600036, India. FAU - Orozco, Modesto AU - Orozco M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131028 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (CytR protein, E coli) RN - 0 (Escherichia coli Proteins) RN - 0 (Repressor Proteins) RN - 9007-49-2 (DNA) SB - IM MH - DNA/chemistry/*metabolism MH - Escherichia coli/metabolism MH - Escherichia coli Proteins/chemistry/*metabolism MH - Molecular Dynamics Simulation MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Repressor Proteins/chemistry/*metabolism MH - Thermodynamics EDAT- 2013/10/17 06:00 MHDA- 2014/06/18 06:00 CRDT- 2013/10/17 06:00 PHST- 2013/10/28 [aheadofprint] AID - 10.1021/jp408350v [doi] PST - ppublish SO - J Phys Chem B. 2013 Nov 7;117(44):13842-50. doi: 10.1021/jp408350v. Epub 2013 Oct 28. PMID- 23060620 OWN - NLM STAT- MEDLINE DA - 20121210 DCOM- 20130729 LR - 20131121 IS - 1367-4811 (Electronic) IS - 1367-4803 (Linking) VI - 28 IP - 24 DP - 2012 Dec 15 TI - Aragonite-associated biomineralization proteins are disordered and contain interactive motifs. PG - 3182-5 LID - 10.1093/bioinformatics/bts604 [doi] AB - MOTIVATION: The formation of aragonite mineral in the mollusk shell or pearl nacre requires the participation of a diverse set of proteins that form the mineralized extracellular matrix. Although self-assembly processes have been identified for several nacre proteins, these proteins do not contain known globular protein-protein binding domains. Thus, we hypothesize that other sequence features are responsible for nacre matrix protein-protein assembly processes and ultimately aragonite biosynthesis. RESULTS: Of 39 mollusk aragonite-associated protein sequences, 100% contain at least one region of intrinsic disorder or unfolding, with the highest percentages found in framework and pearl-associated proteins relative to the intracrystalline proteins. In some instances, these intrinsically disordered regions were identified as bind/fold sequences, and a limited number correlate with known biomineral-relevant sequences. Interestingly, 95% of the aragonite-associated protein sequences were found to contain at least one occurrence of amyloid-like or cross-beta strand aggregation-prone supersecondary motifs, and this correlates with known aggregation and aragonite formation functions in three experimentally tested protein sequences. Collectively, our findings indicate that aragonite-associated proteins have evolved signature sequence traits of intrinsic disorder and aggregation-prone regions that are important for their role(s) in matrix assembly and mineralization. FAU - Evans, John Spencer AU - Evans JS AD - Laboratory for Chemical Physics, Department of Basic Sciences and Craniofacial Biology, New York University, New York, NY 10012, USA. jse1@nyu.edu LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20121011 PL - England TA - Bioinformatics JT - Bioinformatics (Oxford, England) JID - 9808944 RN - 0 (Extracellular Matrix Proteins) RN - 0 (Nacre) RN - H0G9379FGK (Calcium Carbonate) SB - IM MH - Animals MH - Calcification, Physiologic MH - Calcium Carbonate/*chemistry/metabolism MH - Extracellular Matrix Proteins/*chemistry MH - Mollusca/*chemistry/metabolism MH - Nacre/chemistry MH - Protein Conformation MH - Protein Interaction Domains and Motifs MH - Sequence Analysis, Protein EDAT- 2012/10/13 06:00 MHDA- 2013/07/31 06:00 CRDT- 2012/10/13 06:00 PHST- 2012/10/11 [aheadofprint] AID - bts604 [pii] AID - 10.1093/bioinformatics/bts604 [doi] PST - ppublish SO - Bioinformatics. 2012 Dec 15;28(24):3182-5. doi: 10.1093/bioinformatics/bts604. Epub 2012 Oct 11. PMID- 20360609 OWN - NLM STAT- MEDLINE DA - 20100524 DCOM- 20100617 LR - 20140827 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 22 DP - 2010 May 28 TI - Regulation of single-stranded DNA binding by the C termini of Escherichia coli single-stranded DNA-binding (SSB) protein. PG - 17246-52 LID - 10.1074/jbc.M110.118273 [doi] AB - The homotetrameric Escherichia coli single-stranded DNA-binding (SSB) protein plays a central role in DNA replication, repair, and recombination. In addition to its essential activity of binding to transiently formed single-stranded (ss) DNA, SSB also binds an array of partner proteins and recruits them to their sites of action using its four intrinsically disordered C-terminal tails. Here we show that the binding of ssDNA to SSB is inhibited by the SSB C-terminal tails, specifically by the last 8 highly acidic amino acids that comprise the binding site for its multiple partner proteins. We examined the energetics of ssDNA binding to short oligodeoxynucleotides and find that at moderate salt concentration, removal of the acidic C-terminal ends increases the intrinsic affinity for ssDNA and enhances the negative cooperativity between ssDNA binding sites, indicating that the C termini exert an inhibitory effect on ssDNA binding. This inhibitory effect decreases as the salt concentration increases. Binding of ssDNA to approximately half of the SSB subunits relieves the inhibitory effect for all of the subunits. The inhibition by the C termini is due primarily to a less favorable entropy change upon ssDNA binding. These observations explain why ssDNA binding to SSB enhances the affinity of SSB for its partner proteins and suggest that the C termini of SSB may interact, at least transiently, with its ssDNA binding sites. This inhibition and its relief by ssDNA binding suggest a mechanism that enhances the ability of SSB to selectively recruit its partner proteins to sites on DNA. FAU - Kozlov, Alexander G AU - Kozlov AG AD - Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri 63110, USA. FAU - Cox, Michael M AU - Cox MM FAU - Lohman, Timothy M AU - Lohman TM LA - eng GR - GM30498/GM/NIGMS NIH HHS/United States GR - GM32335/GM/NIGMS NIH HHS/United States GR - R01 GM030498/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20100401 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Buffers) RN - 0 (DNA, Single-Stranded) RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (SSB protein, E coli) RN - 0 (Salts) SB - IM MH - Binding Sites MH - Buffers MH - Calorimetry/methods MH - DNA, Single-Stranded/*metabolism MH - DNA-Binding Proteins/*chemistry/genetics/*physiology MH - Escherichia coli/*genetics/*metabolism MH - Escherichia coli Proteins/*chemistry/genetics/*physiology MH - Gene Deletion MH - *Gene Expression Regulation, Bacterial MH - Molecular Conformation MH - Protein Binding MH - Protein Structure, Tertiary MH - Salts/chemistry MH - Spectrometry, Fluorescence/methods MH - Thermodynamics PMC - PMC2878057 OID - NLM: PMC2878057 EDAT- 2010/04/03 06:00 MHDA- 2010/06/18 06:00 CRDT- 2010/04/03 06:00 PHST- 2010/04/01 [aheadofprint] AID - M110.118273 [pii] AID - 10.1074/jbc.M110.118273 [doi] PST - ppublish SO - J Biol Chem. 2010 May 28;285(22):17246-52. doi: 10.1074/jbc.M110.118273. Epub 2010 Apr 1. PMID- 21732203 OWN - NLM STAT- MEDLINE DA - 20110913 DCOM- 20111219 LR - 20121115 IS - 1573-5028 (Electronic) IS - 0167-4412 (Linking) VI - 77 IP - 3 DP - 2011 Oct TI - A functionally required unfoldome from the plant kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development. PG - 205-23 LID - 10.1007/s11103-011-9803-z [doi] AB - The intrinsic disorder is highly abundant in eukaryotic genomes. In the animal kingdom, numerous intrinsically disordered proteins (IDPs) have been characterized, especially in cell signalling and transcription regulation. An intrinsically disordered region often folds in different structures allowing an IDP to recognize and bind different partners at various binding interfaces. In contrast, there have only been a few reports of IDPs from the plant kingdom. Plant-specific GRAS proteins play critical and diverse roles in plant development and signalling and often act as integrators of signals from multiple plant growth regulatory inputs. Using computational and bioinformatics tools, we demonstrate here that the GRAS proteins are intrinsically disordered, thus forming the first functionally required unfoldome in the plant kingdom. Furthermore, the N-terminal domains of GRAS proteins are predicted to contain numerous Molecular Recognition Features (MoRFs), short interaction-prone segments that are located within extended disorder regions and are able to recognize their interacting partners and to undergo disorder-to-order transitions upon binding to these specific partners. Overlapping with the relatively conserved motifs in the N-terminal domains of GRAS proteins, these predicted MoRFs represent the potential protein-protein binding sites and may be involved in molecular recognition during plant development. This study enables us to propose a conceptual framework that guides future experimental approaches to understand structure-function relationships of the entire GRAS family. FAU - Sun, Xiaolin AU - Sun X AD - The New Zealand Institute for Plant and Food Research, Private Bag 11030, Palmerston North, New Zealand. Xiaolin.Sun@plantandfood.co.nz FAU - Xue, Bin AU - Xue B FAU - Jones, William T AU - Jones WT FAU - Rikkerink, Erik AU - Rikkerink E FAU - Dunker, A Keith AU - Dunker AK FAU - Uversky, Vladimir N AU - Uversky VN LA - eng PT - Journal Article DEP - 20110706 PL - Netherlands TA - Plant Mol Biol JT - Plant molecular biology JID - 9106343 RN - 0 (Arabidopsis Proteins) RN - 0 (GAI protein, Arabidopsis) RN - 0 (RGA protein, Arabidopsis) RN - 0 (Repressor Proteins) RN - 0 (SCR protein, Arabidopsis) SB - IM MH - Amino Acid Sequence MH - Arabidopsis/*genetics/growth & development/metabolism MH - Arabidopsis Proteins/*genetics/metabolism MH - Binding Sites/genetics MH - Gene Expression Regulation, Developmental MH - Gene Expression Regulation, Plant MH - Models, Genetic MH - Molecular Sequence Data MH - Phosphorylation MH - Phylogeny MH - Plant Development MH - Plants/genetics/metabolism MH - Protein Binding MH - Repressor Proteins/*genetics/metabolism MH - Sequence Homology, Amino Acid MH - Signal Transduction/genetics EDAT- 2011/07/07 06:00 MHDA- 2011/12/20 06:00 CRDT- 2011/07/07 06:00 PHST- 2011/04/29 [received] PHST- 2011/06/08 [accepted] PHST- 2011/07/06 [aheadofprint] AID - 10.1007/s11103-011-9803-z [doi] PST - ppublish SO - Plant Mol Biol. 2011 Oct;77(3):205-23. doi: 10.1007/s11103-011-9803-z. Epub 2011 Jul 6. PMID- 11668184 OWN - NLM STAT- MEDLINE DA - 20020211 DCOM- 20020321 LR - 20091119 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 277 IP - 7 DP - 2002 Feb 15 TI - Unusual binding properties of the SH3 domain of the yeast actin-binding protein Abp1: structural and functional analysis. PG - 5290-8 AB - Abp1p is an actin-binding protein that plays a central role in the organization of Saccharomyces cerevisiae actin cytoskeleton. By a combination of two-hybrid and phage-display approaches, we have identified six new ligands of the Abp1-SH3 domain. None of these SH3-mediated novel interactions was detected in recent all genome high throughput protein interaction projects. Here we show that the SH3-mediated association of Abp1p with the Ser/Thr kinases Prk1p and Ark1p is essential for their localization to actin cortical patches. The Abp1-SH3 domain has a rather unusual binding specificity, because its target peptides contain the tetrapentapeptide +XXXPXXPX+PXXL with positive charges flanking the polyproline core on both sides. Here we present the structure of the Abp1-SH3 domain solved at 1.3-A resolution. The peptide-binding pockets in the SH3 domain are flanked by two acidic residues that are uncommon at those positions in the SH3 domain family. We have shown by site-directed mutagenesis that one of these negatively charged side chains may be the key determinant for the preference for non-classical ligands. FAU - Fazi, Barbara AU - Fazi B AD - Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Roma, Italy. FAU - Cope, M Jamie T V AU - Cope MJ FAU - Douangamath, Alice AU - Douangamath A FAU - Ferracuti, Silvia AU - Ferracuti S FAU - Schirwitz, Katja AU - Schirwitz K FAU - Zucconi, Adriana AU - Zucconi A FAU - Drubin, David G AU - Drubin DG FAU - Wilmanns, Matthias AU - Wilmanns M FAU - Cesareni, Gianni AU - Cesareni G FAU - Castagnoli, Luisa AU - Castagnoli L LA - eng SI - PDB/1JO8 GR - GM42759/GM/NIGMS NIH HHS/United States GR - GM50399/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20011019 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (ABF1 protein, S cerevisiae) RN - 0 (Actins) RN - 0 (DNA-Binding Proteins) RN - 0 (Ligands) RN - 0 (Peptide Library) RN - 0 (Peptides) RN - 0 (Plant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Schizosaccharomyces pombe Proteins) RN - 0 (Transcription Factors) RN - 0 (cbp1 protein, S pombe) RN - EC 2.7.1.- (PRK1 protein, Petunia inflata) RN - EC 2.7.10.1 (Receptor Protein-Tyrosine Kinases) SB - IM MH - Actins/chemistry/metabolism MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - Cytoskeleton MH - DNA-Binding Proteins/*chemistry/*metabolism MH - Endocytosis MH - Enzyme-Linked Immunosorbent Assay MH - Gene Library MH - Ligands MH - Models, Biological MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Peptide Library MH - Peptides/chemistry MH - *Plant Proteins MH - Plasmids/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Tertiary MH - Receptor Protein-Tyrosine Kinases/chemistry MH - Saccharomyces cerevisiae/metabolism MH - *Saccharomyces cerevisiae Proteins MH - *Schizosaccharomyces pombe Proteins MH - Structure-Activity Relationship MH - *Transcription Factors MH - Two-Hybrid System Techniques MH - src Homology Domains EDAT- 2001/10/23 10:00 MHDA- 2002/03/22 10:01 CRDT- 2001/10/23 10:00 PHST- 2001/10/19 [aheadofprint] AID - 10.1074/jbc.M109848200 [doi] AID - M109848200 [pii] PST - ppublish SO - J Biol Chem. 2002 Feb 15;277(7):5290-8. Epub 2001 Oct 19. PMID- 11714921 OWN - NLM STAT- MEDLINE DA - 20011120 DCOM- 20020214 LR - 20140613 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 10 IP - 12 DP - 2001 Dec TI - pH-induced folding of an apoptotic coiled coil. PG - 2531-40 AB - Par-4 is a 38-kD protein pivotal to the apoptotic pathways of various cell types, most notably prostate cells and neurons, where it has been linked to prostate cancer and various neurodegenerative disorders including Alzheimer's and Huntington's diseases and HIV encephalitis. The C-terminal region of Par-4 is responsible for homodimerization and the ability of Par-4 to interact with proposed effector molecules. In this study, we show that the C-terminal 47 residues of Par-4 are natively unfolded at physiological pH and temperature. Evidence is rapidly accumulating that natively unfolded proteins play an important role in various cellular functions and signaling pathways, and that folding can often be induced on complexation with effector molecules or alteration of environment. Here we use primarily CD studies to show that changes in the environment, particularly pH and temperature, can induce the Par-4 C terminus to form a self-associated coiled coil. FAU - Dutta, K AU - Dutta K AD - Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA. kaushik_dutta@urmc.rochester.edu FAU - Alexandrov, A AU - Alexandrov A FAU - Huang, H AU - Huang H FAU - Pascal, S M AU - Pascal SM LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Apoptosis Regulatory Proteins) RN - 0 (Carrier Proteins) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (prostate apoptosis response-4 protein) SB - IM MH - Amino Acid Sequence MH - *Apoptosis MH - Apoptosis Regulatory Proteins MH - Carrier Proteins/*chemistry MH - Circular Dichroism MH - Humans MH - Hydrogen-Ion Concentration MH - *Intracellular Signaling Peptides and Proteins MH - Models, Statistical MH - Molecular Sequence Data MH - Protein Conformation MH - *Protein Folding MH - Protein Structure, Tertiary MH - Temperature PMC - PMC2374040 OID - NLM: PMC2374040 EDAT- 2001/11/21 10:00 MHDA- 2002/02/15 10:01 CRDT- 2001/11/21 10:00 AID - 10.1110/ps.28801 [doi] PST - ppublish SO - Protein Sci. 2001 Dec;10(12):2531-40. PMID- 17706248 OWN - NLM STAT- MEDLINE DA - 20070903 DCOM- 20071101 LR - 20140904 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 372 IP - 3 DP - 2007 Sep 21 TI - Molecular basis of tropomyosin binding to tropomodulin, an actin-capping protein. PG - 608-18 AB - The tropomodulin (Tmod) family of proteins that cap the pointed, slow-growing end of actin filaments require tropomyosin (TM) for optimal function. Earlier studies identified two regions in Tmod1 that bind the N terminus of TM, though the ability of different isoforms to bind the two sites is controversial. We used model peptides to determine the affinity and define the specificity of the highly conserved N termini of three short, non-muscle TMs (alpha, gamma, delta-TM) for the two Tmod1 binding sites using circular dichroism spectroscopy, native gel electrophoresis, and chemical crosslinking. All TM peptides have high affinity for the second Tmod1 binding site (within residues 109-144; alpha-TM, 2.5 nM; gamma-TM, delta-TM, 40-90 nM), but differ >100-fold for the first site (residues 1-38; alpha-TM, 90 nM; undetectable at 10 microM, gamma-TM, delta-TM). Residue 14 (R in alpha; Q in gamma and delta) and, to a lesser extent, residue 4 (S in alpha; T in gamma and delta) are primarily responsible for the differences. The functional consequence of the sequence differences is reflected in more effective inhibition of actin filament elongation by full-length alpha-TMs than gamma-TM in the presence of Tmod1. The binding sites of the two Tmod1 peptides on a model TM peptide differ, as defined by comparing (15)N,(1)H HSQC spectra of a (15)N-labeled model TM peptide in both the absence and presence of Tmod1 peptide. The NMR and CD studies show that there is an increase in alpha-helix upon Tmod1-TM complex formation, indicating that intrinsically disordered regions of the two proteins become ordered upon binding. A model proposed for the binding of Tmod to actin and TM at the pointed end of the filament shows how the Tmod-TM accentuates the asymmetry of the pointed end and suggests how subtle differences among TM isoforms may modulate actin filament dynamics. FAU - Kostyukova, Alla S AU - Kostyukova AS AD - Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ 08854, USA. FAU - Hitchcock-Degregori, Sarah E AU - Hitchcock-Degregori SE FAU - Greenfield, Norma J AU - Greenfield NJ LA - eng GR - GM36326/GM/NIGMS NIH HHS/United States GR - GM63257/GM/NIGMS NIH HHS/United States GR - R01 GM036326/GM/NIGMS NIH HHS/United States GR - R01 GM036326-19/GM/NIGMS NIH HHS/United States GR - R01 GM063257/GM/NIGMS NIH HHS/United States GR - R01 GM063257-17/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070602 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amino Acids) RN - 0 (Cross-Linking Reagents) RN - 0 (Gelsolin) RN - 0 (Mutant Proteins) RN - 0 (Nitrogen Isotopes) RN - 0 (Peptide Fragments) RN - 0 (Protein Isoforms) RN - 0 (Protons) RN - 0 (Tropomodulin) RN - 0 (Tropomyosin) SB - IM MH - Actin Cytoskeleton/metabolism MH - Amino Acid Sequence MH - Amino Acids MH - Animals MH - Chickens MH - Circular Dichroism MH - Cross-Linking Reagents/pharmacology MH - Gelsolin/metabolism MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Mutant Proteins/metabolism MH - Nitrogen Isotopes MH - Peptide Fragments/chemistry MH - Protein Binding/drug effects MH - Protein Isoforms/chemistry/metabolism MH - Protons MH - Sequence Alignment MH - Tropomodulin/chemistry/*metabolism MH - Tropomyosin/chemistry/*metabolism PMC - PMC2134803 MID - NIHMS30377 OID - NLM: NIHMS30377 OID - NLM: PMC2134803 EDAT- 2007/08/21 09:00 MHDA- 2007/11/02 09:00 CRDT- 2007/08/21 09:00 PHST- 2007/03/12 [received] PHST- 2007/05/19 [revised] PHST- 2007/05/26 [accepted] PHST- 2007/06/02 [aheadofprint] AID - S0022-2836(07)00757-7 [pii] AID - 10.1016/j.jmb.2007.05.084 [doi] PST - ppublish SO - J Mol Biol. 2007 Sep 21;372(3):608-18. Epub 2007 Jun 2. PMID- 18550524 OWN - NLM STAT- MEDLINE DA - 20080804 DCOM- 20080917 LR - 20140903 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 32 DP - 2008 Aug 8 TI - Structure-function analysis of the C3 binding region of Staphylococcus aureus immune subversion protein Sbi. PG - 22113-20 LID - 10.1074/jbc.M802636200 [doi] AB - Among the recently discovered Staphylococcus aureus immune evasion proteins, Sbi is unique in its ability to interact with components of both the adaptive and innate immune systems of the host. Sbi domains I and II (Sbi-I and Sbi-II) bind IgG. Sbi domain IV (residues 198-266) binds the central complement protein C3. When linked to Sbi-III, Sbi-IV induces a futile consumption of complement via alternative pathway activation, whereas isolated Sbi-IV specifically inhibits the alternative pathway without complement consumption. Here we have determined the three-dimensional structure of Sbi-IV by NMR spectroscopy, showing that Sbi-IV adopts a three-helix bundle fold similar to those of the S. aureus complement inhibitors Efb-C, Ehp, and SCIN. The (1)H-(15)N HSQC spectrum of Sbi-III indicates that this domain, essential for futile complement consumption, is natively unfolded, at least when isolated from the rest of Sbi. Sbi-IV and Sbi-III-IV both bind C3dg with 1:1 stoichiometry and submicromolar affinity. Despite low overall sequence identity, Sbi possesses the same residues as Efb at two positions essential for Efb-C binding to C3d. Mutation to alanine of either of these residues, Arg-231 and Asn-238, abolishes both Sbi-IV binding to C3dg and Sbi-IV alternative pathway inhibition. The almost complete conservation of Sbi-III and Sbi-IV amino acid sequences across more than 30 strains isolated from human and animal hosts indicates that the unique mechanism of Sbi in complement system subversion is a feature of infections of both humans and economically important animals. FAU - Upadhyay, Abhishek AU - Upadhyay A AD - Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom. FAU - Burman, Julia D AU - Burman JD FAU - Clark, Elizabeth A AU - Clark EA FAU - Leung, Elisa AU - Leung E FAU - Isenman, David E AU - Isenman DE FAU - van den Elsen, Jean M H AU - van den Elsen JM FAU - Bagby, Stefan AU - Bagby S LA - eng SI - PDB/2JVG SI - PDB/2JVH GR - 076124/Wellcome Trust/United Kingdom GR - BBS/B/12121/Biotechnology and Biological Sciences Research Council/United Kingdom GR - MC_U117533887/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080611 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (Complement Inactivator Proteins) RN - 0 (Ehp protein, Staphylococcus aureus) RN - 0 (Sbi protein, Staphylococcus aureus) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/immunology/*metabolism MH - Binding Sites MH - Carrier Proteins/*chemistry/immunology/*metabolism MH - Complement Inactivator Proteins/chemistry/metabolism MH - Complement Pathway, Alternative MH - Humans MH - *Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Staphylococcus aureus/*chemistry/immunology/*metabolism MH - Structure-Activity Relationship PMC - PMC2494919 OID - NLM: PMC2494919 EDAT- 2008/06/14 09:00 MHDA- 2008/09/18 09:00 CRDT- 2008/06/14 09:00 PHST- 2008/06/11 [aheadofprint] AID - M802636200 [pii] AID - 10.1074/jbc.M802636200 [doi] PST - ppublish SO - J Biol Chem. 2008 Aug 8;283(32):22113-20. doi: 10.1074/jbc.M802636200. Epub 2008 Jun 11. PMID- 24947141 OWN - NLM STAT- In-Process DA - 20140620 IS - 2045-2322 (Electronic) IS - 2045-2322 (Linking) VI - 4 DP - 2014 TI - Atomic force microscopy based nanoassay: a new method to study alpha-Synuclein-dopamine bioaffinity interactions. PG - 5366 LID - 10.1038/srep05366 [doi] AB - Intrinsically Disordered Proteins (IDPs) are characterized by the lack of well-defined 3-D structure and show high conformational plasticity. For this reason, they are a strong challenge for the traditional characterization of structure, supramolecular assembly and biorecognition phenomena. We show here how the fine tuning of protein orientation on a surface turns useful in the reliable testing of biorecognition interactions of IDPs, in particular alpha-Synuclein. We exploited atomic force microscopy (AFM) for the selective, nanoscale confinement of alpha-Synuclein on gold to study the early stages of alpha-Synuclein aggregation and the effect of small molecules, like dopamine, on the aggregation process. Capitalizing on the high sensitivity of AFM topographic height measurements we determined, for the first time in the literature, the dissociation constant of dopamine-alpha-Synuclein adducts. FAU - Corvaglia, Stefania AU - Corvaglia S AD - 1] NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy [2] Life Science Department, University of Trieste, via Giorgieri 1, I-34127 Trieste, Italy. FAU - Sanavio, Barbara AU - Sanavio B AD - 1] NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy [2] Department of Biological and Medical Science, University of Udine, Ospedale della Misericordia, Piazzale Santa Maria della Misericordia, 15 -33100 Udine, Italy [3]. FAU - Hong Enriquez, Rolando P AU - Hong Enriquez RP AD - Department of Biological and Medical Science, University of Udine, Ospedale della Misericordia, Piazzale Santa Maria della Misericordia, 15 -33100 Udine, Italy. FAU - Sorce, Barbara AU - Sorce B AD - 1] Center for Bio-Molecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia, Via Barsanti-73010 Arnesano, Lecce, Italy [2]. FAU - Bosco, Alessandro AU - Bosco A AD - NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy. FAU - Scaini, Denis AU - Scaini D AD - 1] NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy [2] Life Science Department, University of Trieste, via Giorgieri 1, I-34127 Trieste, Italy. FAU - Sabella, Stefania AU - Sabella S AD - Center for Bio-Molecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia, Via Barsanti-73010 Arnesano, Lecce, Italy. FAU - Pompa, Pier Paolo AU - Pompa PP AD - Center for Bio-Molecular Nanotechnologies@UniLe, Istituto Italiano di Tecnologia, Via Barsanti-73010 Arnesano, Lecce, Italy. FAU - Scoles, Giacinto AU - Scoles G AD - 1] NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy [2] Department of Biological and Medical Science, University of Udine, Ospedale della Misericordia, Piazzale Santa Maria della Misericordia, 15 -33100 Udine, Italy. FAU - Casalis, Loredana AU - Casalis L AD - NanoInnovation Laboratory, Elettra Sincrotrone Trieste S.C.p.A., S.S.14 Km 163.5, 34149 Basovizza, Trieste, Italy. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140620 PL - England TA - Sci Rep JT - Scientific reports JID - 101563288 SB - IM PMC - PMC4064358 OID - NLM: PMC4064358 EDAT- 2014/06/21 06:00 MHDA- 2014/06/21 06:00 CRDT- 2014/06/21 06:00 PHST- 2014/01/13 [received] PHST- 2014/05/28 [accepted] AID - srep05366 [pii] AID - 10.1038/srep05366 [doi] PST - epublish SO - Sci Rep. 2014 Jun 20;4:5366. doi: 10.1038/srep05366. PMID- 20160453 OWN - NLM STAT- MEDLINE DA - 20100414 DCOM- 20100721 IS - 1660-2862 (Electronic) IS - 1660-2854 (Linking) VI - 7 IP - 1-3 DP - 2010 TI - Transition of tau protein from disordered to misordered in Alzheimer's disease. PG - 24-7 LID - 10.1159/000283478 [doi] AB - The neuronal protein tau, a member of the class of intrinsically disordered proteins, is characterized by the absence of any firm 3-D structure and high solubility when free in solution. The tau protein forms insoluble fibrils in the brain of people suffering from Alzheimer's disease (AD) and other tauopathies and plays a key role in the neurodegenerative process. Posttranslational events leading to the transition of tau from a disordered highly soluble protein to the insoluble aggregate seem to be associated with hyperphosphorylation, truncation or a combination of both. These modifications are assumed to change the native disorder of tau into a preaggregation state, which then directly initiates the fibrillization process. Conformation-specific anti-tau antibody DC11 detects pathological truncated tau forms present in AD brains but not in the normal human brain. A truncated tau protein selected from this pool of DC11-positive molecules was sufficient to initiate and drive the complete tau cascade of neurofibrillary pathology in a rat model of tauopathy. Thus, DC11 antibody recognizes the AD-specific conformation of tau not found in the normal human brain. We propose the term 'misdisordered' for this distinct conformational state of tau, which is the first step in the transition of tau from a soluble disordered protein to its insoluble, misordered aggregated form. CI - Copyright 2010 S. Karger AG, Basel. FAU - Kovacech, Branislav AU - Kovacech B AD - Institute of Neuroimmunology, AD Centre, Slovak Academy of Sciences, Bratislava, Slovakia. FAU - Skrabana, Rostislav AU - Skrabana R FAU - Novak, Michal AU - Novak M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100213 PL - Switzerland TA - Neurodegener Dis JT - Neuro-degenerative diseases JID - 101189034 RN - 0 (tau Proteins) SB - IM MH - Alzheimer Disease/*metabolism/pathology MH - Animals MH - Brain/metabolism MH - Humans MH - Phosphorylation/physiology MH - Protein Conformation MH - Rats MH - tau Proteins/*metabolism EDAT- 2010/02/18 06:00 MHDA- 2010/07/22 06:00 CRDT- 2010/02/18 06:00 PHST- 2010/02/13 [aheadofprint] AID - 000283478 [pii] AID - 10.1159/000283478 [doi] PST - ppublish SO - Neurodegener Dis. 2010;7(1-3):24-7. doi: 10.1159/000283478. Epub 2010 Feb 13. PMID- 8805591 OWN - NLM STAT- MEDLINE DA - 19961107 DCOM- 19961107 LR - 20131121 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 4 IP - 9 DP - 1996 Sep 15 TI - Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site. PG - 1053-64 AB - BACKGROUND: Ribonucleotide reductases (RNRs) catalyze the formation of the deoxyribonucleotides that are essential for DNA synthesis. The R2 subunit of Escherichia coli RNR is a homodimer containing one dinuclear iron centre per monomer. A tyrosyl radical is essential for catalysis, and is formed via a reaction in which the reduced, diferrous form of the iron centre activates dioxygen. To help understand the mechanism of oxygen activation, we examined the structure of the diferrous form of R2. RESULTS: The crystal structures of reduced forms of both wild type R2 and a mutant of R2 (Ser211--> Ala) have been determined at 1.7 A and 2.2 A resolution, respectively. The diferrous iron centre was compared to the previously determined structure of the oxidized, diferric form of R2. In both forms of R2 the iron centre is coordinated by the same carboxylate dominated ligand sphere, but in the reduced form there are clear conformational changes in three of the carboxylate ligands and the bridging mu-oxo group and two water molecules are lost. In the reduced form of R2 the coordination number decreases from six to four for both ferrous ions, explaining their high reactivity towards dioxygen. The structure of the mutant Ser211--> Ala, known to have impaired reduction kinetics, shows a large conformational change in one of the neighbouring helices although the iron coordination is very similar to the wild type protein. CONCLUSIONS: Carboxylate shifts are often important for carboxylate coordinated metal clusters; they allow the metals to achieve different coordination modes in redox reactions. In the case of reduced R2 these carboxylate shifts allow the formation of accessible reaction sites for dioxygen. The Ser211--> Ala mutant displays a conformational change in the helix containing the mutation, explaining its altered reduction kinetics. FAU - Logan, D T AU - Logan DT AD - Department of Molecular Biology University of Stockholm S-106 91 Stockholm Sweden. FAU - Su, X D AU - Su XD FAU - Aberg, A AU - Aberg A FAU - Regnstrom, K AU - Regnstrom K FAU - Hajdu, J AU - Hajdu J FAU - Eklund, H AU - Eklund H FAU - Nordlund, P AU - Nordlund P LA - eng SI - PDB/1XIK SI - PDB/R1XIKSF PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Carboxylic Acids) RN - E1UOL152H7 (Iron) RN - EC 1.17.4.- (Ribonucleotide Reductases) RN - S88TT14065 (Oxygen) SB - IM MH - Carboxylic Acids/chemistry MH - Crystallography, X-Ray MH - Iron/*metabolism MH - Kinetics MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Oxidation-Reduction MH - Oxygen/*metabolism MH - Ribonucleotide Reductases/*chemistry/genetics/metabolism EDAT- 1996/09/15 MHDA- 1996/09/15 00:01 CRDT- 1996/09/15 00:00 PST - ppublish SO - Structure. 1996 Sep 15;4(9):1053-64. PMID- 8073283 OWN - NLM STAT- MEDLINE DA - 19940928 DCOM- 19940928 LR - 20131121 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 265 IP - 5177 DP - 1994 Sep 2 TI - Structures of active conformations of Gi alpha 1 and the mechanism of GTP hydrolysis. PG - 1405-12 AB - Mechanisms of guanosine triphosphate (GTP) hydrolysis by members of the G protein alpha subunit-p21ras superfamily of guanosine triphosphatases have been studied extensively but have not been well understood. High-resolution x-ray structures of the GTP gamma S and GDP.AlF4- complexes formed by the G protein Gi alpha 1 demonstrate specific roles in transition-state stabilization for two highly conserved residues. Glutamine204 (Gln61 in p21ras) stabilizes and orients the hydrolytic water in the trigonal-bipyramidal transition state. Arginine 178 stabilizes the negative charge at the equatorial oxygen atoms of the pentacoordinate phosphate intermediate. Conserved only in the G alpha family, this residue may account for the higher hydrolytic rate of G alpha proteins relative to those of the p21ras family members. The fold of Gi alpha 1 differs from that of the homologous Gt alpha subunit in the conformation of a helix-loop sequence located in the alpha-helical domain that is characteristic of these proteins; this site may participate in effector binding. The amino-terminal 33 residues are disordered in GTP gamma S-Gi alpha 1, suggesting a mechanism that may promote release of the beta gamma subunit complex when the alpha subunit is activated by GTP. FAU - Coleman, D E AU - Coleman DE AD - Howard Hughes Medical Institute, Dallas, TX. FAU - Berghuis, A M AU - Berghuis AM FAU - Lee, E AU - Lee E FAU - Linder, M E AU - Linder ME FAU - Gilman, A G AU - Gilman AG FAU - Sprang, S R AU - Sprang SR LA - eng GR - DK 46371/DK/NIDDK NIH HHS/United States GR - GM34497/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Aluminum Compounds) RN - 0RH81L854J (Glutamine) RN - 146-91-8 (Guanosine Diphosphate) RN - 21340-02-3 (tetrafluoroaluminate) RN - 37589-80-3 (Guanosine 5'-O-(3-Thiotriphosphate)) RN - 86-01-1 (Guanosine Triphosphate) RN - 94ZLA3W45F (Arginine) RN - EC 3.6.1.- (GTP-Binding Proteins) RN - Q80VPU408O (Fluorides) SB - IM MH - Aluminum Compounds/metabolism MH - Arginine/chemistry MH - Binding Sites MH - Catalysis MH - Computer Graphics MH - Crystallography, X-Ray MH - Fluorides/metabolism MH - GTP-Binding Proteins/*chemistry/metabolism MH - Glutamine/chemistry MH - Guanosine 5'-O-(3-Thiotriphosphate)/metabolism MH - Guanosine Diphosphate/metabolism MH - Guanosine Triphosphate/*metabolism MH - Helix-Loop-Helix Motifs MH - Hydrogen Bonding MH - Hydrolysis MH - Models, Molecular MH - *Protein Conformation MH - Protein Structure, Secondary EDAT- 1994/09/02 MHDA- 1994/09/02 00:01 CRDT- 1994/09/02 00:00 PST - ppublish SO - Science. 1994 Sep 2;265(5177):1405-12. PMID- 23189058 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20121128 DCOM- 20121129 LR - 20130813 IS - 1664-042X (Electronic) IS - 1664-042X (Linking) VI - 3 DP - 2012 TI - Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation. PG - 435 LID - 10.3389/fphys.2012.00435 [doi] AB - Cyclin-dependent kinase inhibitors (CKIs) are key regulatory proteins of the eukaryotic cell cycle, which modulate cyclin-dependent kinase (Cdk) activity. CKIs perform their inhibitory effect by the formation of ternary complexes with a target kinase and its cognate cyclin. These regulators generally belong to the class of intrinsically disordered proteins (IDPs), which lack a well-defined and organized three-dimensional (3D) structure in their free state, undergoing folding upon binding to specific partners. Unbound IDPs are not merely random-coil structures, but can present intrinsically folded structural units (IFSUs) and collapsed conformations. These structural features can be relevant to protein function in vivo. The yeast CKI Sic1 is a 284-amino acid IDP that binds to Cdk1 in complex with the Clb5,6 cyclins, preventing phosphorylation of G1 substrates and, therefore, entrance to the S phase. Sic1 degradation, triggered by multiple phosphorylation events, promotes cell-cycle progression. Previous experimental studies pointed out a propensity of Sic1 and its isolated domains to populate both extended and compact conformations. The present contribution provides models for compact conformations of the Sic1 kinase-inhibitory domain (KID) by all-atom molecular dynamics (MD) simulations in explicit solvent and in the absence of interactors. The results are integrated by spectroscopic and spectrometric data. Helical IFSUs are identified, along with networks of intramolecular interactions. The results identify a group of putative hub residues and networks of electrostatic interactions, which are likely to be involved in the stabilization of the globular states. FAU - Lambrughi, Matteo AU - Lambrughi M AD - Department of Biotechnology and Biosciences, University of Milano-Bicocca Milan, Italy. FAU - Papaleo, Elena AU - Papaleo E FAU - Testa, Lorenzo AU - Testa L FAU - Brocca, Stefania AU - Brocca S FAU - De Gioia, Luca AU - De Gioia L FAU - Grandori, Rita AU - Grandori R LA - eng PT - Journal Article DEP - 20121122 PL - Switzerland TA - Front Physiol JT - Frontiers in physiology JID - 101549006 PMC - PMC3504315 OID - NLM: PMC3504315 OTO - NOTNLM OT - Sic1 OT - cyclin-dependent kinase OT - electrospray ionization mass spectrometry OT - electrostatic interactions OT - intrinsically disordered proteins OT - molecular dynamics simulations EDAT- 2012/11/29 06:00 MHDA- 2012/11/29 06:01 CRDT- 2012/11/29 06:00 PHST- 2012/07/05 [received] PHST- 2012/10/28 [accepted] PHST- 2012/11/22 [epublish] AID - 10.3389/fphys.2012.00435 [doi] PST - epublish SO - Front Physiol. 2012 Nov 22;3:435. doi: 10.3389/fphys.2012.00435. eCollection 2012. PMID- 18625543 OWN - NLM STAT- MEDLINE DA - 20080811 DCOM- 20081008 LR - 20131121 IS - 0301-4622 (Print) IS - 0301-4622 (Linking) VI - 137 IP - 1 DP - 2008 Sep TI - Influence of fluorinated and hydrogenated nanoparticles on the structure and fibrillogenesis of amyloid beta-peptide. PG - 35-42 LID - 10.1016/j.bpc.2008.06.010 [doi] AB - Peptide aggregation in amyloid fibrils is implicated in the pathogenesis of several diseases such as Alzheimer's disease. There is a strong correlation between amyloid fibril formation and a decrease in conformational stability of the native state. Amyloid-beta peptide (Abeta), the aggregating peptide in Alzheimer's disease, is natively unfolded. The deposits found in Alzheimer's disease are composed of Abeta fibrillar aggregates rich in beta-sheet structure. The influence of fluorinated complexes on the secondary structure and fibrillogenesis of Abeta peptide was studied by circular dichroism (CD) spectroscopy and transmission electron microscopy (TEM). CD spectra show that complexes of polyampholyte and fluorinated dodecanoic acid induce alpha-helix structure in Abeta, but their hydrogenated analogous lead to beta-sheet formation and aggregation. The fluorinated nanoparticles with highly negative zeta potential and hydrophobic fluorinated core have the fundamental characteristics to prevent Abeta fibrillogenesis. FAU - Rocha, Sandra AU - Rocha S AD - LEPAE, Dept. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal. sandra.rocha@fe.up.pt FAU - Thunemann, Andreas F AU - Thunemann AF FAU - Pereira, Maria do Carmo AU - Pereira Mdo C FAU - Coelho, Manuel AU - Coelho M FAU - Mohwald, Helmuth AU - Mohwald H FAU - Brezesinski, Gerald AU - Brezesinski G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080627 PL - Netherlands TA - Biophys Chem JT - Biophysical chemistry JID - 0403171 RN - 0 (Amyloid beta-Peptides) RN - 0 (Amyloid beta-Protein Precursor) RN - 0 (Protease Nexins) RN - 0 (Receptors, Cell Surface) RN - 284SYP0193 (Fluorine) RN - 7YNJ3PO35Z (Hydrogen) SB - IM MH - Amyloid beta-Peptides/*chemistry/metabolism MH - Amyloid beta-Protein Precursor/chemistry MH - Fluorine/*chemistry MH - Hydrogen/*chemistry MH - Nanoparticles/*chemistry MH - Protease Nexins MH - Receptors, Cell Surface/chemistry EDAT- 2008/07/16 09:00 MHDA- 2008/10/09 09:00 CRDT- 2008/07/16 09:00 PHST- 2008/05/14 [received] PHST- 2008/06/21 [revised] PHST- 2008/06/23 [accepted] PHST- 2008/06/27 [aheadofprint] AID - S0301-4622(08)00140-3 [pii] AID - 10.1016/j.bpc.2008.06.010 [doi] PST - ppublish SO - Biophys Chem. 2008 Sep;137(1):35-42. doi: 10.1016/j.bpc.2008.06.010. Epub 2008 Jun 27. PMID- 16870210 OWN - NLM STAT- MEDLINE DA - 20060814 DCOM- 20061004 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 361 IP - 4 DP - 2006 Aug 25 TI - Structural determinants of natriuretic peptide receptor specificity and degeneracy. PG - 698-714 AB - Cardiovascular homeostasis and blood pressure regulation are reliant, in part, on interactions between natriuretic peptide (NP) hormones and natriuretic peptide receptors (NPR). The C-type NPR (NPR-C) is responsible for clearance of NP hormones from the circulation, and displays a cross-reactivity for all NP hormones (ANP, BNP, and CNP), in contrast to other NPRs, which are more restricted in their specificity. In order to elucidate the structural determinants for the binding specificity and cross-reactivity of NPR-C with NP hormones, we have determined the crystal structures of the complexes of NPR-C with atrial natriuretic peptide (ANP), and with brain natriuretic peptide (BNP). A structural comparison of these complexes, with the previous structure of the NPR-C/CNP complex, reveals that NPR-C uses a conformationally inflexible surface to bind three different, highly flexible, NP ligands. The complex structures support a mechanism of rigid promiscuity rather than conformational plasticity by the receptor. While ANP and BNP appear to adopt similar receptor-bound conformations, the CNP structure diverges, yet shares sets of common receptor contacts with the other ligands. The degenerate versus selective hormone recognition properties of different NPRs appears to derive largely from two cavities on the receptor surfaces, pocket I and pocket II, that serve as anchoring sites for hormone side-chains and modulate receptor selectivity. FAU - He, Xiao-lin AU - He XL AD - Department of Microbiology & Immunology, Howard Hughes Medical Institute, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 94305-5124, USA. FAU - Dukkipati, Abhiram AU - Dukkipati A FAU - Garcia, K Christopher AU - Garcia KC LA - eng SI - PDB/1YK0 SI - PDB/1YK1 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060710 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Ligands) RN - 114471-18-0 (Natriuretic Peptide, Brain) RN - 127869-51-6 (Natriuretic Peptide, C-Type) RN - 47E5O17Y3R (Phenylalanine) RN - 85637-73-6 (Atrial Natriuretic Factor) RN - EC 4.6.1.2 (Receptors, Atrial Natriuretic Factor) RN - EC 4.6.1.2 (atrial natriuretic factor receptor C) SB - IM MH - Amino Acid Sequence MH - Animals MH - Atrial Natriuretic Factor/chemistry/*metabolism MH - Binding Sites MH - Crystallography, X-Ray MH - Dimerization MH - Drosophila melanogaster MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Ligands MH - Models, Molecular MH - Molecular Sequence Data MH - Natriuretic Peptide, Brain/chemistry/*metabolism MH - Natriuretic Peptide, C-Type/chemistry/*metabolism MH - Phenylalanine/chemistry MH - Protein Conformation MH - Receptors, Atrial Natriuretic Factor/*chemistry/genetics/*metabolism MH - Sequence Alignment EDAT- 2006/07/28 09:00 MHDA- 2006/10/05 09:00 CRDT- 2006/07/28 09:00 PHST- 2006/02/08 [received] PHST- 2006/06/22 [revised] PHST- 2006/06/22 [accepted] PHST- 2006/07/10 [aheadofprint] AID - S0022-2836(06)00802-3 [pii] AID - 10.1016/j.jmb.2006.06.060 [doi] PST - ppublish SO - J Mol Biol. 2006 Aug 25;361(4):698-714. Epub 2006 Jul 10. PMID- 11604398 OWN - NLM STAT- MEDLINE DA - 20011225 DCOM- 20020131 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 52 DP - 2001 Dec 28 TI - Parathyroid hormone (PTH)-(1-14) and -(1-11) analogs conformationally constrained by alpha-aminoisobutyric acid mediate full agonist responses via the juxtamembrane region of the PTH-1 receptor. PG - 49003-12 AB - The N-terminal portion of parathyroid hormone is critical for PTH-1 receptor (P1R) activation and has been postulated to be alpha-helical when bound to the receptor. We investigated whether substitution of the sterically hindered and helix-promoting amino acid alpha-aminoisobutyric acid (Aib) in N-terminal PTH oligopeptides would improve the capacity of the peptide to activate the P1R. Analysis of the effects of individual Aib substitutions at each position in [Ala(3,12),Gln(10),Har(11),Trp(14)]PTH(1-14)NH(2) ([M]PTH(1-14)) on cAMP-stimulating potency in HKRK-B28 cells revealed that Aib at most positions diminished potency; however, Aib at positions 1 and 3 enhanced potency. Thus [Aib(1,3),M]PTH(1-14) was approximately 100-fold more potent than [M]PTH(1-14) (EC(50) = 1.1 +/- 0.1 and 100 +/- 20 nm, respectively), approximately 100,000-fold more potent than native PTH(1-14), and 2-fold more potent than PTH(1-34). The shorter peptide, [Aib(1,3),M]PTH(1-11), was also fully efficacious and 1,000-fold more potent than [M]PTH(1-11) (EC(50) 4 +/- 1 nm versus 3 +/- 1 microm). In cAMP stimulation assays performed in COS-7 cells expressing P1R-delNt, a receptor that lacks most of the N-terminal extracellular domain, [Aib(1,3),M]PTH(1-14) was 50-fold more potent than [M]PTH(1-14) (EC(50) = 0.7 +/- 0.2 versus 40 +/- 2 nm) and 1,000-fold more potent than PTH(1-34) (EC(50) = 700 nm). [Aib(1,3),M]PTH(1-14), but not PTH(1-34), inhibited the binding of (125)I-[Aib(1,3),Nle(8),Gln(10),Har(11),Ala(12),Trp(14),Arg(19),Tyr(21)]PTH(1-21) NH(2) to hP1R-delNt (IC(50) = 1,600 +/- 200 nm). The Aib(1,3) substitutions in otherwise unmodified PTH(1-34) enhanced potency and binding affinity on hP1R-delNt, but they had no effect for this peptide on hP1R-WT. Circular dichroism spectroscopy demonstrated that the Aib-1,3 substitutions increased helicity in all peptides tested, including PTH(1-34). The overall data thus suggest that the N-terminal residues of PTH are intrinsically disordered but become conformationally constrained, possibly as an alpha-helix, upon interaction with the activation domain of the PTH-1 receptor. FAU - Shimizu, N AU - Shimizu N AD - Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA. FAU - Guo, J AU - Guo J FAU - Gardella, T J AU - Gardella TJ LA - eng GR - DK-11794/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. DEP - 20011016 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Aminoisobutyric Acids) RN - 0 (Parathyroid Hormone) RN - 0 (Peptide Fragments) RN - 0 (Receptors, Parathyroid Hormone) RN - 1E7ZW41IQU (2-aminoisobutyric acid) RN - E0399OZS9N (Cyclic AMP) SB - IM MH - Aminoisobutyric Acids/chemistry/*metabolism MH - Animals MH - Bone and Bones/cytology/metabolism MH - COS Cells MH - Calcification, Physiologic/drug effects MH - Cell Differentiation MH - Cell Line MH - Chondrocytes/cytology/drug effects MH - Circular Dichroism MH - Cyclic AMP/metabolism MH - Embryo, Mammalian MH - Humans MH - Mice MH - Parathyroid Hormone/chemistry/*metabolism/pharmacology MH - Peptide Fragments/chemistry/*metabolism/pharmacology MH - Protein Binding MH - Protein Conformation MH - Receptors, Parathyroid Hormone/genetics/*metabolism MH - Signal Transduction/physiology MH - Swine MH - Tumor Cells, Cultured EDAT- 2001/10/18 10:00 MHDA- 2002/02/01 10:01 CRDT- 2001/10/18 10:00 PHST- 2001/10/16 [aheadofprint] AID - 10.1074/jbc.M106827200 [doi] AID - M106827200 [pii] PST - ppublish SO - J Biol Chem. 2001 Dec 28;276(52):49003-12. Epub 2001 Oct 16. PMID- 9622505 OWN - NLM STAT- MEDLINE DA - 19980630 DCOM- 19980630 LR - 20041117 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 37 IP - 23 DP - 1998 Jun 9 TI - Solution structure of the cytoplasmic domain of the human CD4 glycoprotein by CD and 1H NMR spectroscopy: implications for biological functions. PG - 8527-38 AB - The human T cell receptor CD4 is a type I integral membrane glycoprotein that is involved in T cell activation and also acts as the primary coreceptor for human immunodeficiency viruses (HIV). Here the structure of a synthetic 38 amino acid peptide corresponding to the complete cytoplasmic domain of CD4 (CD4CYTO) has been investigated under a variety of solution conditions using a combination of circular dichroism and homonuclear two-dimensional 1H nuclear magnetic resonance spectroscopy. In the presence of the membrane mimetic 2,2,2-trifluoroethanol (TFE), a conformational change of CD4CYTO from a random coil to an alpha-helical structure was observed. In keeping with this, CD4CYTO has the potential to associate with membranes as demonstrated by binding studies of in vitro phosphorylated CD4CYTO with microsomal membranes. Both chemical shift and nuclear Overhauser enhancement data in 50% 2,2, 2-trifluoroethanol solution provide direct experimental evidence for the predominance of a short amphiphatic alpha-helix that is approximately 4 turns in length and extends from positions Arg-402 to Lys-417. The present data provide, for the first time, compelling experimental evidence that only a fraction of CD4CYTO has a propensity for adopting secondary structure under conditions that are assumed to exist at or near to the membrane surface and that this alpha-helical structure is located in the membrane-proximal region of CD4CYTO. The N-terminal residues, that link the alpha-helix to the transmembrane anchor of CD4, and a substantial C-terminal portion (14-18 residues) of CD4CYTO are unstructured under the solution conditions investigated. Correlation of our structural data with recent studies on the biological activity of CD4CYTO indicates that the alpha-helix is of crucial importance for the interaction of CD4 with Nef and Vpu in the process of HIV-mediated CD4 down-regulation. FAU - Wray, V AU - Wray V AD - Department of Molecular Structure Research, Gesellschaft fur Biotechnologische Forschung, Braunschweig, Germany. vwr@gbf-braunschweig.de FAU - Mertins, D AU - Mertins D FAU - Kiess, M AU - Kiess M FAU - Henklein, P AU - Henklein P FAU - Trowitzsch-Kienast, W AU - Trowitzsch-Kienast W FAU - Schubert, U AU - Schubert U LA - eng PT - Journal Article PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Antigens, CD4) RN - 0 (Peptides) RN - 0 (Solutions) RN - 75-89-8 (Trifluoroethanol) SB - IM SB - X MH - Amino Acid Sequence MH - Antigens, CD4/*chemistry/isolation & purification/metabolism MH - Circular Dichroism MH - Cytoplasm/chemistry/immunology/*metabolism MH - Humans MH - Intracellular Membranes/metabolism MH - Microsomes/metabolism MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides/chemical synthesis/isolation & purification/metabolism MH - Protein Structure, Secondary/drug effects MH - Solutions MH - Trifluoroethanol/pharmacology EDAT- 1998/06/19 MHDA- 1998/06/19 00:01 CRDT- 1998/06/19 00:00 AID - 10.1021/bi9723111 [doi] AID - bi9723111 [pii] PST - ppublish SO - Biochemistry. 1998 Jun 9;37(23):8527-38. PMID- 20925409 OWN - NLM STAT- MEDLINE DA - 20101105 DCOM- 20110307 IS - 1535-3907 (Electronic) IS - 1535-3893 (Linking) VI - 9 IP - 11 DP - 2010 Nov 5 TI - Extensive phosphorylation flanking the C-terminal functional domains of the measles virus nucleoprotein. PG - 5598-609 LID - 10.1021/pr100407w [doi] AB - The measles virus nucleoprotein (vNP) is the first and most abundant protein in infected cells. It plays numerous important roles including the encapsidation of genomic viral RNA and the transcription of viral proteins. Intricate interactions with host cell proteins rely on the structural integrity of its functional domains. Although some of these functional domains are known, their structural features are still poorly understood. Here we identified multiple isoforms of measles vNP by two-dimensional differential gel electrophoresis (2D-DIGE) and 2D Western blot. These isoforms were further analyzed by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF)/TOF using MS (PMF) and MSMS (PSD) and electrospray ionization (ESI)-ion trap using LC-ESI-ion trap MS(1), MS(2) (neutral loss), MS(3) (phosphosite). Both recombinant NP (rNP) and vNP were alpha-acetylated at the N-terminus. After tryptic or chymotryptic digestion, phosphopeptides were enriched and nine phosphorylation sites were identified and localized in the rNP, seven of which were also phosphorylated in vNP, probably by casein kinase 2. The phosphosites were all found within the intrinsically unstructured C-terminal domain. They clustered around functional domains involved in transcription and replication, as well as in sequences interacting with host-cell proteins. This underlines the importance of these post-translational modifications. FAU - Prodhomme, Emmanuel J F AU - Prodhomme EJ AD - Institute of Immunology, Laboratoire National de Sante and Centre de Recherche Public-Sante, L-1011 Luxembourg, Grand-Duchy of Luxembourg. FAU - Fack, Fred AU - Fack F FAU - Revets, Dominique AU - Revets D FAU - Pirrotte, Patrick AU - Pirrotte P FAU - Kremer, Jacques R AU - Kremer JR FAU - Muller, Claude P AU - Muller CP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101006 PL - United States TA - J Proteome Res JT - Journal of proteome research JID - 101128775 RN - 0 (Nucleoproteins) RN - 0 (Protein Isoforms) RN - 0 (Viral Proteins) RN - 0 (nucleoprotein, Measles virus) SB - IM MH - Acetylation MH - Measles virus/*chemistry MH - Nucleoproteins/*analysis/chemistry MH - Phosphorylation MH - Protein Isoforms/analysis MH - *Protein Processing, Post-Translational MH - Protein Structure, Tertiary MH - Proteomics/*methods MH - Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization MH - Two-Dimensional Difference Gel Electrophoresis MH - Viral Proteins/*analysis/chemistry EDAT- 2010/10/12 06:00 MHDA- 2011/03/08 06:00 CRDT- 2010/10/08 06:00 PHST- 2010/10/06 [aheadofprint] AID - 10.1021/pr100407w [doi] PST - ppublish SO - J Proteome Res. 2010 Nov 5;9(11):5598-609. doi: 10.1021/pr100407w. Epub 2010 Oct 6. PMID- 8631793 OWN - NLM STAT- MEDLINE DA - 19960703 DCOM- 19960703 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 271 IP - 13 DP - 1996 Mar 29 TI - Biochemical and biophysical analyses of recombinant forms of human topoisomerase I. PG - 7593-601 AB - Amino acid sequence comparisons of human topoisomerase I (Topo I) with seven other cellular Topo I enzymes reveal that the enzyme can be divided into four major domains: the unconserved NH2-terminal domain (24 kDa), the conserved core domain (54 kDa), a poorly conserved linker region (5 kDa), and the highly conserved COOH-terminal domain (8 kDa), which contains the active site tyrosine. To investigate this predicted domain organization, recombinant baculoviruses were engineered to express the 91-kDa full-length enzyme, a 70-kDa NH2-terminally truncated enzyme that is missing the first 174 residues, and a 58-kDa NH2- and COOH-terminally truncated core fragment encompassing residues 175-659. The specific activity of the full-length and Topo70 enzymes are indistinguishable from the native human Topo I purified from HeLa cells. Each protein is inhibited by camptothecin, topotecan, and 9-aminocamptothecin, but not by ATP. Activity is stimulated by Mg2+, Ba2+, Ca2+, Mn2+, spermine, and spermidine. The magnitude of the stimulatory effect of Mg2+ is inversely proportional to the salt concentration. Furthermore, at KCl concentrations of 300 mM or greater, the addition of Mg2+ is inhibitory. The effects of Mg2+ and the polycations spermine and spermidine are partially additive, an indication that the stimulatory mechanisms of the two substances are different. Activity was strongly inhibited or abolished by Ni2+, Zn2+, Cu2+, Cd2+, and Co2+. An examination of the hydrodynamic properties of full-length Topo I, Topo70, and Topo58 demonstrates that the core, linker, and COOH-terminal domains fold into a globular structure, while the NH2-terminal domain is highly extended. A comparison of the circular dichroism spectra of full-length Topo I and Topo70 demonstrates that residues 1-174 (approximately 21 kDa) of Topo I are largely if not completely unfolded. This observation is consistent with the fact that the NH2-terminal domain is dispensable for activity. FAU - Stewart, L AU - Stewart L AD - Department of Microbiology, School of Medicine, University of Washington, Seattle, 98195-7242, USA. FAU - Ireton, G C AU - Ireton GC FAU - Parker, L H AU - Parker LH FAU - Madden, K R AU - Madden KR FAU - Champoux, J J AU - Champoux JJ LA - eng GR - GM49156/GM/NIGMS NIH HHS/United States GR - T32-GM07207/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Cations, Divalent) RN - 0 (Oligodeoxyribonucleotides) RN - 0 (Recombinant Proteins) RN - 0 (Topoisomerase I Inhibitors) RN - 5MB77ICE2Q (9-aminocamptothecin) RN - 660YQ98I10 (Potassium Chloride) RN - 7M7YKX2N15 (Topotecan) RN - 8L70Q75FXE (Adenosine Triphosphate) RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) RN - I38ZP9992A (Magnesium) RN - XT3Z54Z28A (Camptothecin) SB - IM MH - Adenosine Triphosphate/pharmacology MH - Amino Acid Sequence MH - Base Sequence MH - Camptothecin/analogs & derivatives/pharmacology MH - Cations, Divalent/pharmacology MH - Circular Dichroism MH - Conserved Sequence MH - DNA Topoisomerases, Type I/*chemistry/*metabolism MH - Humans MH - Kinetics MH - Magnesium/pharmacology MH - Molecular Sequence Data MH - Oligodeoxyribonucleotides MH - Potassium Chloride/pharmacology MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Recombinant Proteins/antagonists & inhibitors/chemistry/metabolism MH - Topoisomerase I Inhibitors MH - Topotecan EDAT- 1996/03/29 MHDA- 1996/03/29 00:01 CRDT- 1996/03/29 00:00 PST - ppublish SO - J Biol Chem. 1996 Mar 29;271(13):7593-601. PMID- 1311056 OWN - NLM STAT- MEDLINE DA - 19920325 DCOM- 19920325 LR - 20131121 IS - 0028-0836 (Print) IS - 0028-0836 (Linking) VI - 355 IP - 6362 DP - 1992 Feb 20 TI - Crystal structure of a dUTPase. PG - 740-3 AB - The enzyme dUTPase catalyses the hydrolysis of dUTP and maintains a low intracellular concentration of dUTP so that uracil cannot be incorporated into DNA. dUTPase from Escherichia coli is strictly specific for its dUTP substrate, the active site discriminating between nucleotides with respect to the sugar moiety as well as the pyrimidine base. Here we report the three-dimensional structure of E. coli dUTPase determined by X-ray crystallography at a resolution of 1.9 A. The enzyme is a symmetrical trimer, and of the 152 amino acid residues in the subunit, the first 136 are visible in the crystal structure. The tertiary structure resembles a jelly-roll fold and does not show the 'classical' nucleotide-binding domain. In the quaternary structure there is a complex interaction between the subunits that may be important in catalysis. This possibility is supported by the location of conserved elements in the sequence. FAU - Cedergren-Zeppezauer, E S AU - Cedergren-Zeppezauer ES AD - Department of Zoological Cell Biology, Wenner-Gren Institute, University of Stockholm, Sweden. FAU - Larsson, G AU - Larsson G FAU - Nyman, P O AU - Nyman PO FAU - Dauter, Z AU - Dauter Z FAU - Wilson, K S AU - Wilson KS LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Nature JT - Nature JID - 0410462 RN - 0 (Cations, Divalent) RN - 0 (Macromolecular Substances) RN - EC 3.6.1.- (Pyrophosphatases) RN - EC 3.6.1.23 (dUTP pyrophosphatase) RN - I38ZP9992A (Magnesium) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Cations, Divalent MH - Crystallization MH - Escherichia coli/*enzymology MH - Macromolecular Substances MH - Magnesium/pharmacology MH - Models, Molecular MH - Molecular Sequence Data MH - Molecular Structure MH - Protein Conformation MH - Pyrophosphatases/*chemistry MH - X-Ray Diffraction EDAT- 1992/02/20 MHDA- 1992/02/20 00:01 CRDT- 1992/02/20 00:00 AID - 10.1038/355740a0 [doi] PST - ppublish SO - Nature. 1992 Feb 20;355(6362):740-3. PMID- 8631794 OWN - NLM STAT- MEDLINE DA - 19960703 DCOM- 19960703 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 271 IP - 13 DP - 1996 Mar 29 TI - The domain organization of human topoisomerase I. PG - 7602-8 AB - Using limited proteolysis, we show that the domain boundaries of human topoisomerase I closely parallel those predicted from sequence comparisons with other cellular Topo I enzymes. The enzyme is comprised of (i) an NH2-terminal domain (approximately 24 kDa), which is known to be dispensable for activity, (ii) the core domain (approximately 54 kDa), (iii) a linker region (approximately 3 kDa), and (iv) the COOH-terminal domain (approximately 10 kDa), which contains the active site tyrosine. The highly conserved core and COOH-terminal domains are resistant to proteolysis, while the unconserved NH2-terminal and linker domains are sensitive. Noncovalent binding of Topo I to plasmid DNA or to short duplex oligonucleotides decreases the sensitivity of the linker to proteolysis by approximately a factor of 10 but has no effect on proteolysis of the NH2-terminal domain. When the enzyme is covalently complexed to an 18 base pair single-stranded oligonucleotide, the linker region is sensitive to proteolysis whether or not duplex DNA is present. The net positive charge of the linker domain suggests that at a certain point in catalysis the linker may bind directly to DNA. Further, we show that limited subtilisin cleavage can generate a mixture of 60-kDa core and approximately 10-kDa COOH-terminal fragments, which retain a level of topoisomerase activity that is nearly equal to undigested control samples, presumably because the two fragments remain associated after proteolytic cleavage. Thus, despite its potential role in DNA binding, the linker domain (in addition to the NH2-terminal domain) appears to be dispensable for topoisomerase activity. Finally, the limited proteolysis pattern of the human enzyme differs substantially from the limited proteolysis pattern of the vaccinia viral Topo I, indicating that the two enzymes belong to separate eukaryotic topoisomerase I subfamilies. FAU - Stewart, L AU - Stewart L AD - Department of Microbiology, School of Medicine, University of Washington, Seattle, 98195-7242, USA. FAU - Ireton, G C AU - Ireton GC FAU - Champoux, J J AU - Champoux JJ LA - eng GR - GM49156/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Oligodeoxyribonucleotides) RN - 0 (Recombinant Proteins) RN - EC 3.4.- (Endopeptidases) RN - EC 3.4.21.- (Subtilisins) RN - EC 3.4.21.4 (Trypsin) RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) RN - I38ZP9992A (Magnesium) SB - IM MH - Base Sequence MH - DNA Topoisomerases, Type I/*chemistry/*metabolism MH - Endopeptidases MH - Humans MH - Kinetics MH - Magnesium/pharmacology MH - Molecular Sequence Data MH - Molecular Weight MH - Oligodeoxyribonucleotides MH - Peptide Mapping MH - Plasmids MH - Recombinant Proteins/chemistry/metabolism MH - Substrate Specificity MH - Subtilisins/metabolism MH - Trypsin/metabolism EDAT- 1996/03/29 MHDA- 1996/03/29 00:01 CRDT- 1996/03/29 00:00 PST - ppublish SO - J Biol Chem. 1996 Mar 29;271(13):7602-8. PMID- 25084333 OWN - NLM STAT- MEDLINE DA - 20140802 DCOM- 20150330 IS - 1399-0047 (Electronic) IS - 0907-4449 (Linking) VI - 70 IP - Pt 8 DP - 2014 Aug TI - Structure of the virulence-associated protein VapD from the intracellular pathogen Rhodococcus equi. PG - 2139-51 LID - 10.1107/S1399004714012632 [doi] AB - Rhodococcus equi is a multi-host pathogen that infects a range of animals as well as immune-compromised humans. Equine and porcine isolates harbour a virulence plasmid encoding a homologous family of virulence-associated proteins associated with the capacity of R. equi to divert the normal processes of endosomal maturation, enabling bacterial survival and proliferation in alveolar macrophages. To provide a basis for probing the function of the Vap proteins in virulence, the crystal structure of VapD was determined. VapD is a monomer as determined by multi-angle laser light scattering. The structure reveals an elliptical, compact eight-stranded beta-barrel with a novel strand topology and pseudo-twofold symmetry, suggesting evolution from an ancestral dimer. Surface-associated octyl-beta-D-glucoside molecules may provide clues to function. Circular-dichroism spectroscopic analysis suggests that the beta-barrel structure is preceded by a natively disordered region at the N-terminus. Sequence comparisons indicate that the core folds of the other plasmid-encoded virulence-associated proteins from R. equi strains are similar to that of VapD. It is further shown that sequences encoding putative R. equi Vap-like proteins occur in diverse bacterial species. Finally, the functional implications of the structure are discussed in the light of the unique structural features of VapD and its partial structural similarity to other beta-barrel proteins. FAU - Whittingham, Jean L AU - Whittingham JL AD - Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England. FAU - Blagova, Elena V AU - Blagova EV AD - Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England. FAU - Finn, Ciaran E AU - Finn CE AD - UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, Dublin, Ireland. FAU - Luo, Haixia AU - Luo H AD - UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, Dublin, Ireland. FAU - Miranda-CasoLuengo, Raul AU - Miranda-CasoLuengo R AD - UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, Dublin, Ireland. FAU - Turkenburg, Johan P AU - Turkenburg JP AD - Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England. FAU - Leech, Andrew P AU - Leech AP AD - Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England. FAU - Walton, Paul H AU - Walton PH AD - Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England. FAU - Murzin, Alexey G AU - Murzin AG AD - MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England. FAU - Meijer, Wim G AU - Meijer WG AD - UCD School of Biomolecular and Biomedical Science and UCD Conway Institute, University College Dublin, Dublin, Ireland. FAU - Wilkinson, Anthony J AU - Wilkinson AJ AD - Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England. LA - eng SI - PDB/4CSB GR - BB/J007900/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - MC_U105192716/Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140725 PL - United States TA - Acta Crystallogr D Biol Crystallogr JT - Acta crystallographica. Section D, Biological crystallography JID - 9305878 RN - 0 (Bacterial Proteins) RN - 0 (DNA Primers) RN - 0 (Membrane Glycoproteins) RN - 147571-30-0 (VapD protein, Bacteria) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/*chemistry/genetics MH - Base Sequence MH - Cloning, Molecular MH - DNA Primers MH - Membrane Glycoproteins/*chemistry/genetics MH - Molecular Sequence Data MH - Protein Conformation MH - Rhodococcus equi/*chemistry/pathogenicity MH - Sequence Homology, Amino Acid PMC - PMC4118825 OID - NLM: PMC4118825 OTO - NOTNLM OT - Rhodococcus equi OT - VapD OT - bacterial pathogenesis OT - virulence factors EDAT- 2014/08/02 06:00 MHDA- 2015/03/31 06:00 CRDT- 2014/08/02 06:00 PHST- 2014/05/07 [received] PHST- 2014/05/30 [accepted] PHST- 2014/07/25 [epublish] AID - S1399004714012632 [pii] AID - 10.1107/S1399004714012632 [doi] PST - ppublish SO - Acta Crystallogr D Biol Crystallogr. 2014 Aug;70(Pt 8):2139-51. doi: 10.1107/S1399004714012632. Epub 2014 Jul 25. PMID- 24751520 OWN - NLM STAT- MEDLINE DA - 20140513 DCOM- 20140813 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 447 IP - 4 DP - 2014 May 16 TI - Regulatory effect of the glial Golli-BG21 protein on the full-length murine small C-terminal domain phosphatase (SCP1, or Golli-interacting protein). PG - 633-7 LID - 10.1016/j.bbrc.2014.04.050 [doi] LID - S0006-291X(14)00692-5 [pii] AB - The gene in the oligodendrocyte lineage (golli) encodes a number of proteins essential for myelination, comprising Golli and classic isoforms that are expressed in a developmentally-regulated manner. The Golli-interacting-protein (GIP) was previously discovered in a search for potential interacting partners of the Golli-isoform BG21, and was realised to be an acidic phosphatase belonging to the family of RNA-polymerase-2, small-subunit, C-terminal phosphatases (viz., SCP1). Here, we refer to this protein as mSCP1/GIP. In subsequent in vitro studies of recombinant murine SCP1/GIP, the inability to produce an active full-length version of the protein under native conditions necessitated the study of a truncated form DeltaN-rmSCP1/GIP, but with inconclusive results regarding its interaction with BG21 [13]. We have since developed a new SUMO-expression and purification protocol for the preparation of a functional, full-length mGIP/SCP1, with no additional purification tags. Here, the interaction between mSCP1/GIP (with intact N-terminus) and BG21 is shown to be different than for the truncation mutant studied previously. Specifically, this interaction shows a dual effect on the enzymatic activity of mSCP1/GIP by BG21: BG21 enhanced mSCP1/GIP phosphatase activity (Ka = 30 muM), whereas PKCalpha-phosphorylated BG21 inhibited its activity (Ki = 2.9 muM), suggesting a potential role of BG21 as a molecular switch ("quick-brake mechanism") on mSCP1/GIP. The successful production of an active, full-length mSCP1/GIP thus demonstrates a role for its N-terminus in regulation of phosphatase activity, in events such as the regulation of transcription in oligodendrocytes. CI - Copyright (c) 2014 Elsevier Inc. All rights reserved. FAU - Jaramillo-Tatis, Sergio AU - Jaramillo-Tatis S AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada. FAU - Vassall, Kenrick A AU - Vassall KA AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada. FAU - Bamm, Vladimir V AU - Bamm VV AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada. FAU - Harauz, George AU - Harauz G AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada. Electronic address: gharauz@uoguelph.ca. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140418 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Mbp protein, mouse) RN - 0 (Myelin Basic Protein) RN - 0 (Nerve Tissue Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - 0 (golli-interacting protein, mouse) RN - EC 2.7.11.13 (Protein Kinase C-alpha) RN - EC 3.1.3.- (Phosphoric Monoester Hydrolases) SB - IM MH - Animals MH - Gene Expression Regulation, Developmental MH - Intrinsically Disordered Proteins/chemistry/genetics/metabolism MH - Kinetics MH - Mice MH - Models, Biological MH - Myelin Basic Protein/chemistry/*genetics/*metabolism MH - Nerve Tissue Proteins/chemistry/*genetics/*metabolism MH - Nuclear Proteins/chemistry/*genetics/*metabolism MH - Oligodendroglia/cytology/metabolism MH - Peptide Fragments/chemistry/genetics/metabolism MH - Phosphoric Monoester Hydrolases/chemistry/genetics/metabolism MH - Phosphorylation MH - Protein Interaction Domains and Motifs MH - Protein Kinase C-alpha/metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism OTO - NOTNLM OT - Golli (gene in the oligodendrocyte lineage) OT - Golli-interacting protein OT - Intrinsically-disordered protein OT - Myelin basic protein OT - Oligodendrocyte OT - Small C-terminal domain phosphatase EDAT- 2014/04/23 06:00 MHDA- 2014/08/15 06:00 CRDT- 2014/04/23 06:00 PHST- 2014/04/07 [received] PHST- 2014/04/10 [accepted] PHST- 2014/04/18 [aheadofprint] AID - S0006-291X(14)00692-5 [pii] AID - 10.1016/j.bbrc.2014.04.050 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2014 May 16;447(4):633-7. doi: 10.1016/j.bbrc.2014.04.050. Epub 2014 Apr 18. PMID- 14572476 OWN - NLM STAT- MEDLINE DA - 20031023 DCOM- 20040702 LR - 20141120 IS - 1047-8477 (Print) IS - 1047-8477 (Linking) VI - 143 IP - 3 DP - 2003 Sep TI - Structure and metal binding studies of the second copper binding domain of the Menkes ATPase. PG - 209-18 AB - Biological utilisation of copper requires that the metal, in its ionic forms, be meticulously transported, inserted into enzymes and regulatory proteins, and excess be excreted. To understand the trafficking process, it is crucial that the structures of the proteins involved in the varied processes be resolved. To investigate copper binding to a family of structurally related copper-binding proteins, we have characterised the second Menkes N-terminal domain (MNKr2). The structure, determined using 1H and 15N heteronuclear NMR, of the reduced form of MNKr2 has revealed two alpha-helices lying over a single beta-sheet and shows that the binding site, a Cys(X)2Cys pair, is located on an exposed loop. 1H-15N HSQC experiments demonstrate that binding of Cu(I) causes changes that are localised to conserved residues adjacent to the metal binding site. Residues in this area are important to the delivery of copper by the structurally related Cu(I) chaperones. Complementary site-directed mutagenesis of the adjacent residues has been used to probe the structural roles of conserved residues. FAU - Jones, Christopher E AU - Jones CE AD - The National Research Centre for Environmental Toxicology, The University of Queensland, 39 Kessels Road, Coopers Plains, Qld 4108, Australia. FAU - Daly, Norelle L AU - Daly NL FAU - Cobine, Paul A AU - Cobine PA FAU - Craik, David J AU - Craik DJ FAU - Dameron, Charles T AU - Dameron CT LA - eng SI - PDB/1Q8L PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - 0 (Bacterial Proteins) RN - 0 (Cation Transport Proteins) RN - 0 (CopZ protein, Enterococcus hirae) RN - 0 (Molecular Chaperones) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Trans-Activators) RN - 47E5O17Y3R (Phenylalanine) RN - 789U1901C5 (Copper) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - EC 3.6.3.4 (ATP7A protein, human) SB - IM MH - Adenosine Triphosphatases/*chemistry/genetics/*metabolism MH - Amino Acid Sequence MH - Bacterial Proteins/chemistry/metabolism MH - Binding Sites MH - Cation Transport Proteins/*chemistry/genetics/*metabolism MH - Conserved Sequence MH - Copper/metabolism MH - Humans MH - In Vitro Techniques MH - Kinetics MH - Menkes Kinky Hair Syndrome/enzymology/genetics MH - Models, Molecular MH - Molecular Chaperones/chemistry/metabolism MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Nuclear Magnetic Resonance, Biomolecular MH - Phenylalanine/chemistry MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/*chemistry/genetics/*metabolism MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Trans-Activators/chemistry/metabolism EDAT- 2003/10/24 05:00 MHDA- 2004/07/03 05:00 CRDT- 2003/10/24 05:00 AID - S1047847703001497 [pii] PST - ppublish SO - J Struct Biol. 2003 Sep;143(3):209-18. PMID- 22955105 OWN - NLM STAT- MEDLINE DA - 20121003 DCOM- 20130225 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 11 DP - 2012 Nov TI - CP12 residues involved in the formation and regulation of the glyceraldehyde-3-phosphate dehydrogenase-CP12-phosphoribulokinase complex in Chlamydomonas reinhardtii. PG - 2994-3002 LID - 10.1039/c2mb25244a [doi] AB - CP12, a member of the intrinsically disordered protein family, forms a stable complex with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK). To understand the function of conserved residues of CP12 in the formation of the GAPDH-CP12-PRK complex and in the regulation of the enzymes within this complex, we have produced mutants of CP12 by site-directed mutagenesis. The GAPDH, CP12 and PRK recombinant proteins are able to reconstitute spontaneously the ternary complex that has been described in Chlamydomonas reinhardtii. Our analysis reveals that the central part ((35)WXXVEE(47)) of CP12 is required to form the GAPDH-CP12-PRK complex. Using the same series of single amino acid replacements, we have identified individual residues, which seem to represent also contact points for GAPDH. Most notably, substitution of glutamate 74 prevents the binding of GAPDH to CP12. This is similar to the mutant C66S, with which the GAPDH-CP12-PRK complex is not formed. In contrast, replacement of the three last residues ((78)YED(80)) of CP12 has no effect on the formation of the ternary supra-molecular complex. However, our findings strongly suggest that Y78 and D80 are involved in the regulation of the GAPDH activity within the supra-molecular complex, since the mutants, D80K and Y78S, do not down-regulate the activity of GAPDH. The replacement of the amino acid E79 weakens the interaction between GAPDH and CP12 as no GAPDH-CP12 sub-complex is formed. In this case, nevertheless, the supra-molecular complex is formed when PRK is present indicating that PRK strengthens the interaction between GAPDH and CP12 within the supra-molecular complex. FAU - Avilan, Luisana AU - Avilan L AD - Laboratoire de Bioenergetique et Ingenierie des Proteines CNRS-UMR 7281-Aix-Marseille Universite. Institut de Microbiologie de la Mediterranee, CNRS, 31 Chemin Joseph Aiguier, BP71, 13 402 Marseille Cedex 20, France. FAU - Puppo, Carine AU - Puppo C FAU - Erales, Jenny AU - Erales J FAU - Woudstra, Mireille AU - Woudstra M FAU - Lebrun, Regine AU - Lebrun R FAU - Gontero, Brigitte AU - Gontero B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Plant Proteins) RN - EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases) RN - EC 1.2.1.12 (Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)) RN - EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)) RN - EC 2.7.1.19 (phosphoribulokinase) SB - IM MH - Chlamydomonas reinhardtii/genetics/*metabolism MH - Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)/metabolism MH - Glyceraldehyde-3-Phosphate Dehydrogenases/genetics/*metabolism MH - Phosphotransferases (Alcohol Group Acceptor)/genetics/*metabolism MH - Plant Proteins/genetics/*metabolism MH - Protein Binding EDAT- 2012/09/08 06:00 MHDA- 2013/02/26 06:00 CRDT- 2012/09/08 06:00 AID - 10.1039/c2mb25244a [doi] PST - ppublish SO - Mol Biosyst. 2012 Nov;8(11):2994-3002. doi: 10.1039/c2mb25244a. PMID- 10995239 OWN - NLM STAT- MEDLINE DA - 20001016 DCOM- 20001107 LR - 20111117 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 39 IP - 38 DP - 2000 Sep 26 TI - Structure, microtubule interactions, and paired helical filament aggregation by tau mutants of frontotemporal dementias. PG - 11714-21 AB - We have studied biochemical and structural parameters of several missense and deletion mutants of tau protein (G272V, N279K, DeltaK280, P301L, V337M, R406W) found in frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17). The mutant proteins were expressed on the basis of both full-length tau (htau40) and constructs derived from the repeat domain. They were analyzed with respect to the capacity to enhance microtubule assembly, binding of tau to microtubules, secondary structure content, and aggregation into Alzheimer-like paired helical or straight filaments. We find that the mutations cause a moderate decrease in microtubule interactions and stabilization, and they show no gross structural changes compared with the natively unfolded conformation of the wild-type protein, but the aggregation into PHFs is strongly enhanced, particularly for the mutants DeltaK280 and P301L. This gain of pathological aggregation would be consistent with the autosomal dominant nature of the disease. FAU - Barghorn, S AU - Barghorn S AD - Max-Planck-Unit for Structural Molecular Biology, c/o DESY, Notkestrasse 85, D-22607 Hamburg, Germany. FAU - Zheng-Fischhofer, Q AU - Zheng-Fischhofer Q FAU - Ackmann, M AU - Ackmann M FAU - Biernat, J AU - Biernat J FAU - von Bergen, M AU - von Bergen M FAU - Mandelkow, E M AU - Mandelkow EM FAU - Mandelkow, E AU - Mandelkow E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Thiazoles) RN - 0 (tau Proteins) RN - 2390-54-7 (thioflavin T) RN - 33069-62-4 (Paclitaxel) SB - IM MH - Actin Cytoskeleton/chemistry/genetics/*metabolism/ultrastructure MH - Circular Dichroism MH - Dementia/*genetics/*metabolism/pathology MH - Humans MH - Microscopy, Electron MH - Microtubules/chemistry/genetics/*metabolism/ultrastructure MH - Mutagenesis, Site-Directed MH - *Mutation MH - Mutation, Missense MH - Neuropil Threads/genetics/metabolism/ultrastructure MH - Paclitaxel/chemistry MH - Protein Binding/genetics MH - Protein Structure, Secondary/genetics MH - Scattering, Radiation MH - Sequence Deletion MH - Spectrometry, Fluorescence MH - Thiazoles/chemistry MH - tau Proteins/*chemistry/*genetics/metabolism/ultrastructure EDAT- 2000/09/20 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/09/20 11:00 AID - bi000850r [pii] PST - ppublish SO - Biochemistry. 2000 Sep 26;39(38):11714-21. PMID- 2063194 OWN - NLM STAT- MEDLINE DA - 19910802 DCOM- 19910802 LR - 20071114 IS - 0036-8075 (Print) IS - 0036-8075 (Linking) VI - 252 IP - 5014 DP - 1991 Jun 28 TI - Three-dimensional structure of the LDL receptor-binding domain of human apolipoprotein E. PG - 1817-22 AB - Human apolipoprotein E, a blood plasma protein, mediates the transport and uptake of cholesterol and lipid by way of its high affinity interaction with different cellular receptors, including the low-density lipoprotein (LDL) receptor. The three-dimensional structure of the LDL receptor-binding domain of apoE has been determined at 2.5 angstrom resolution by x-ray crystallography. The protein forms an unusually elongated (65 angstroms) four-helix bundle, with the helices apparently stabilized by a tightly packed hydrophobic core that includes leucine zipper-type interactions and by numerous salt bridges on the mostly charged surface. Basic amino acids important for LDL receptor binding are clustered into a surface patch on one long helix. This structure provides the basis for understanding the behavior of naturally occurring mutants that can lead to atherosclerosis. FAU - Wilson, C AU - Wilson C AD - Howard Hughes Medical Institute, University of California, San Francisco 94143-0448. FAU - Wardell, M R AU - Wardell MR FAU - Weisgraber, K H AU - Weisgraber KH FAU - Mahley, R W AU - Mahley RW FAU - Agard, D A AU - Agard DA LA - eng GR - HL-41633/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Science JT - Science (New York, N.Y.) JID - 0404511 RN - 0 (Apolipoproteins E) RN - 0 (Receptors, LDL) SB - IM MH - Amino Acid Sequence MH - Apolipoproteins E/*chemistry/genetics/metabolism MH - Binding Sites MH - Computer Graphics MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Receptors, LDL/*metabolism MH - X-Ray Diffraction EDAT- 1991/06/28 MHDA- 1991/06/28 00:01 CRDT- 1991/06/28 00:00 PST - ppublish SO - Science. 1991 Jun 28;252(5014):1817-22. PMID- 15744056 OWN - NLM STAT- MEDLINE DA - 20050525 DCOM- 20060606 LR - 20140608 IS - 0016-6731 (Print) IS - 0016-6731 (Linking) VI - 170 IP - 1 DP - 2005 May TI - Alpha-synuclein targets the plasma membrane via the secretory pathway and induces toxicity in yeast. PG - 47-59 AB - A pathological feature of Parkinson's disease is the presence of Lewy bodies within selectively vulnerable neurons. These are ubiquitinated cytoplasmic inclusions containing alpha-synuclein, an abundant protein normally associated with presynaptic terminals. Point mutations in the alpha-synuclein gene (A30P and A53T), as well as triplication of the wild-type (WT) locus, have been linked to autosomal dominant Parkinson's. How these alterations might contribute to disease progression is unclear. Using the genetically tractable yeast Saccharomyces cerevisiae as a model system, we find that both the WT and the A53T isoforms of alpha-synuclein initially localize to the plasma membrane, to which they are delivered via the classical secretory pathway. In contrast, the A30P mutant protein disperses within the cytoplasm and does not associate with the plasma membrane, and its intracellular distribution is unaffected by mutations in the secretory pathway. When their expression is elevated, WT and A53T, but not A30P, are toxic to cells. At moderate levels of expression, WT and A53T induce the cellular stress (heat-shock) response and are toxic to cells bearing mutations in the 20S proteasome. Our results reveal a link between plasma membrane targeting of alpha-synuclein and its toxicity in yeast and suggest a role for the quality control (QC) system in the cell's effort to deal with this natively unfolded protein. FAU - Dixon, Cheryl AU - Dixon C AD - Department of Biochemistry and Molecular Biology, Louisiana State University Health Science Center, Shreveport, 71130-3932, USA. FAU - Mathias, Neal AU - Mathias N FAU - Zweig, Richard M AU - Zweig RM FAU - Davis, Donnie A AU - Davis DA FAU - Gross, David S AU - Gross DS LA - eng GR - GM-45842/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050302 PL - United States TA - Genetics JT - Genetics JID - 0374636 RN - 0 (Recombinant Fusion Proteins) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Amino Acid Substitution MH - Cell Membrane/*metabolism MH - Cytoplasm/*metabolism MH - Genes, Reporter MH - Hot Temperature MH - Mutation MH - Parkinson Disease/metabolism MH - Proteasome Endopeptidase Complex/genetics/physiology MH - Recombinant Fusion Proteins/genetics/physiology MH - Saccharomyces cerevisiae/*metabolism PMC - PMC1449710 OID - NLM: PMC1449710 EDAT- 2005/03/04 09:00 MHDA- 2006/06/07 09:00 CRDT- 2005/03/04 09:00 PHST- 2005/03/02 [aheadofprint] PHST- 2005/03/21 [aheadofprint] AID - genetics.104.035493 [pii] AID - 10.1534/genetics.104.035493 [doi] PST - ppublish SO - Genetics. 2005 May;170(1):47-59. Epub 2005 Mar 2. PMID- 19008353 OWN - NLM STAT- MEDLINE DA - 20081121 DCOM- 20081217 LR - 20140902 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 105 IP - 46 DP - 2008 Nov 18 TI - Dynamic equilibrium engagement of a polyvalent ligand with a single-site receptor. PG - 17772-7 LID - 10.1073/pnas.0809222105 [doi] AB - Intrinsically disordered proteins play critical but often poorly understood roles in mediating protein interactions. The interactions of disordered proteins studied to date typically entail structural stabilization, whether as a global disorder-to-order transition or minimal ordering of short linear motifs. The disordered cyclin-dependent kinase (CDK) inhibitor Sic1 interacts with a single site on its receptor Cdc4 only upon phosphorylation of its multiple dispersed CDK sites. The molecular basis for this multisite-dependent interaction with a single receptor site is not known. By NMR analysis, we show that multiple phosphorylated sites on Sic1 interact with Cdc4 in dynamic equilibrium with only local ordering around each site. Regardless of phosphorylation status, Sic1 exists in an intrinsically disordered state but is surprisingly compact with transient structure. The observation of this unusual binding mode between Sic1 and Cdc4 extends the understanding of protein interactions from predominantly static complexes to include dynamic ensembles of intrinsically disordered states. FAU - Mittag, Tanja AU - Mittag T AD - Program in Molecular Structure and Function, Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada M5G 1X8. FAU - Orlicky, Stephen AU - Orlicky S FAU - Choy, Wing-Yiu AU - Choy WY FAU - Tang, Xiaojing AU - Tang X FAU - Lin, Hong AU - Lin H FAU - Sicheri, Frank AU - Sicheri F FAU - Kay, Lewis E AU - Kay LE FAU - Tyers, Mike AU - Tyers M FAU - Forman-Kay, Julie D AU - Forman-Kay JD LA - eng GR - Howard Hughes Medical Institute/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20081113 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (CDC4 protein, S cerevisiae) RN - 0 (Cell Cycle Proteins) RN - 0 (Cyclin-Dependent Kinase Inhibitor Proteins) RN - 0 (F-Box Proteins) RN - 0 (Ligands) RN - 0 (SIC1 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM MH - Binding Sites MH - Cell Cycle Proteins/chemistry/*metabolism MH - Cyclin-Dependent Kinase Inhibitor Proteins MH - F-Box Proteins/chemistry/*metabolism MH - Isomerism MH - Ligands MH - Phosphorylation MH - Protein Conformation MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/*metabolism MH - Ubiquitin-Protein Ligases/chemistry/*metabolism PMC - PMC2582940 OID - NLM: PMC2582940 EDAT- 2008/11/15 09:00 MHDA- 2008/12/18 09:00 CRDT- 2008/11/15 09:00 PHST- 2008/11/13 [aheadofprint] AID - 0809222105 [pii] AID - 10.1073/pnas.0809222105 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2008 Nov 18;105(46):17772-7. doi: 10.1073/pnas.0809222105. Epub 2008 Nov 13. PMID- 21935523 OWN - NLM STAT- MEDLINE DA - 20111202 DCOM- 20120320 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Order and disorder in large multi-site docking proteins of the Gab family--implications for signalling complex formation and inhibitor design strategies. PG - 33-46 LID - 10.1039/c1mb05272a [doi] AB - Large multi-site docking (LMD) proteins of the Gab, IRS, FRS, DOK and Cas families consist of one or two folded N-terminal domains, followed by a predominantly disordered C-terminal extension. Their primary function is to provide a docking platform for signalling molecules (including PI3K, PLC, Grb2, Crk, RasGAP, SHP2) in intracellular signal transmission from activated cell-surface receptors, to which they become coupled. A detailed analysis of the structural nature and intrinsic disorder propensity of LMD proteins, with Gab proteins as specific examples, is presented. By primary sequence analysis and literature review the varying levels of disorder and hidden order are predicted, revealing properties and a physical architecture that help to explain their biological function and characteristics, common for network hub proteins. The virulence factor, CagA, from Helicobacter pylori is able to mimic Gab function once injected by this human pathogen into stomach epithelial cells. Its predicted differential structure is compared to Gab1 with respect to its functional mimicry. Lastly, we discuss how LMD proteins, in particular Gab1 and Gab2, and their protein partners, such as SH2 and SH3 domain-containing adaptors like Grb2, might qualify for future anti-cancer strategies in developing protein-protein interaction (PPI) inhibitors towards binary interactors consisting of an intrinsically disordered epitope and a structured domain surface. FAU - Simister, Philip C AU - Simister PC AD - Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK. philip.simister@imm.ox.ac.uk FAU - Feller, Stephan M AU - Feller SM LA - eng GR - Cancer Research UK/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20110920 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Multiprotein Complexes) SB - IM MH - Adaptor Proteins, Signal Transducing/*antagonists & inhibitors/*chemistry/metabolism MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - *Drug Design MH - Humans MH - Molecular Sequence Data MH - Multiprotein Complexes/*antagonists & inhibitors/*chemistry/metabolism MH - *Protein Folding MH - *Signal Transduction EDAT- 2011/09/22 06:00 MHDA- 2012/03/21 06:00 CRDT- 2011/09/22 06:00 PHST- 2011/09/20 [aheadofprint] PHST- 2011/12/01 [epublish] AID - 10.1039/c1mb05272a [doi] PST - ppublish SO - Mol Biosyst. 2012 Jan;8(1):33-46. doi: 10.1039/c1mb05272a. Epub 2011 Sep 20. PMID- 18440296 OWN - NLM STAT- MEDLINE DA - 20080616 DCOM- 20080703 LR - 20140909 IS - 1096-0384 (Electronic) IS - 0003-9861 (Linking) VI - 475 IP - 1 DP - 2008 Jul 1 TI - A glycosylated form of the human cardiac hormone pro B-type natriuretic peptide is an intrinsically unstructured monomeric protein. PG - 36-41 LID - 10.1016/j.abb.2008.04.007 [doi] AB - The N-terminal fragment of pro B-type natriuretic peptide (NT-proBNP) and proBNP are used as gold standard clinical markers of myocardial dysfunction such as cardiac hypertrophy and left ventricle heart failure. The actual circulating molecular forms of these peptides have been the subject of intense investigation particularly since these analytes are measured in clinical assays. Conflicting data has been reported and no firm consensus on the exact nature of the molecular species exists. Because these clinical assays are immunoassay-based, specific epitopes are detected. It is conceivable then that certain epitopes may be masked and therefore unavailable for antibody binding, thus the importance of determining the nature of the circulating molecular forms of these analytes. This situation is an unavoidable Achilles' heel of immunoassays in general. A recombinant O-linked glycosylated form of proBNP has been show to mimic some of the properties of extracted plasma from a heart failure patient. In particular the recombinant and native material co-migrated as diffuse Western-immunostained bands on SDS-PAGE and each band collapsed to an apparent homogeneous band following deglycosylation. Thus, glycosylated-proBNP may be one such circulating form. Here we provide extensive physiochemical characterization for this O-linked protein and compare these results to other described circulating species, non-glycosylated-proBNP and NT-proBNP. It will be shown that glycosylation has no influence on the secondary and quaternary structure of proBNP. In fact, at moderate concentration in benign physiological neutral pH buffer, all three likely circulating species are essentially devoid of major secondary structure, i.e., are intrinsically unstructured proteins (IUPs). Furthermore, all three proteins exist as monomers in solution. These results may have important implications in the design of NT-proBNP/BNP immunoassays. FAU - Crimmins, Dan L AU - Crimmins DL AD - Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA. crimmins@pathology.wustl.edu FAU - Kao, Jeffrey L-F AU - Kao JL LA - eng GR - P30 DK056341/DK/NIDDK NIH HHS/United States GR - P30 DK056341-069003/DK/NIDDK NIH HHS/United States GR - P30 DK056341-07/DK/NIDDK NIH HHS/United States GR - P30 DK056341-08/DK/NIDDK NIH HHS/United States GR - P30-DK56341/DK/NIDDK NIH HHS/United States GR - P41-RR00954/RR/NCRR NIH HHS/United States GR - P60 DK020579/DK/NIDDK NIH HHS/United States GR - P60 DK020579-219005/DK/NIDDK NIH HHS/United States GR - P60 DK020579-307484/DK/NIDDK NIH HHS/United States GR - P60-DK20579/DK/NIDDK NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20080413 PL - United States TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (Hormones) RN - 0 (Peptide Fragments) RN - 0 (Protein Precursors) RN - 0 (Recombinant Proteins) RN - 0 (pro-brain natriuretic peptide (1-76)) RN - 114471-18-0 (Natriuretic Peptide, Brain) SB - IM MH - Glycosylation MH - Hormones/*chemistry/genetics/metabolism MH - Humans MH - Myocardium/*chemistry/metabolism MH - Natriuretic Peptide, Brain/*chemistry/genetics/metabolism MH - Peptide Fragments/*chemistry/genetics/metabolism MH - Protein Precursors/*chemistry/genetics/metabolism MH - Recombinant Proteins/chemistry/metabolism PMC - PMC2659528 MID - NIHMS95501 OID - NLM: NIHMS95501 OID - NLM: PMC2659528 EDAT- 2008/04/29 09:00 MHDA- 2008/07/04 09:00 CRDT- 2008/04/29 09:00 PHST- 2008/03/12 [received] PHST- 2008/04/08 [accepted] PHST- 2008/04/13 [aheadofprint] AID - S0003-9861(08)00192-6 [pii] AID - 10.1016/j.abb.2008.04.007 [doi] PST - ppublish SO - Arch Biochem Biophys. 2008 Jul 1;475(1):36-41. doi: 10.1016/j.abb.2008.04.007. Epub 2008 Apr 13. PMID- 18573254 OWN - NLM STAT- MEDLINE DA - 20080714 DCOM- 20080915 LR - 20141125 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 582 IP - 17 DP - 2008 Jul 23 TI - Self-recognition by an intrinsically disordered protein. PG - 2673-7 LID - 10.1016/j.febslet.2008.06.022 [doi] AB - The intrinsically disordered translocation domain (T-domain) of the protein antibiotic colicin N binds to periplasmic receptors of target Escherichia coli cells in order to penetrate their inner membranes. We report here that the specific 27 consecutive residues of the T-domain of colicin N known to bind to the helper protein TolA in target cells also interacts intramolecularly with folded regions of colicin N. We suggest that this specific self-recognition helps intrinsically disordered domains to bury their hydrophobic recognition motifs and protect them against degradation, showing that an impaired self-recognition leads to increased protease susceptibility. FAU - Hecht, Oliver AU - Hecht O AD - School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich. FAU - Ridley, Helen AU - Ridley H FAU - Boetzel, Ruth AU - Boetzel R FAU - Lewin, Allison AU - Lewin A FAU - Cull, Nick AU - Cull N FAU - Chalton, David A AU - Chalton DA FAU - Lakey, Jeremy H AU - Lakey JH FAU - Moore, Geoffrey R AU - Moore GR LA - eng GR - 082045/Wellcome Trust/United Kingdom GR - 40422/Wellcome Trust/United Kingdom GR - 55979/Wellcome Trust/United Kingdom GR - 56232/Wellcome Trust/United Kingdom GR - 66850/Wellcome Trust/United Kingdom GR - BB/C507396/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BB/F005768/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - MC_U117533887/Medical Research Council/United Kingdom GR - bb/c507402/Wellcome Trust/United Kingdom GR - British Heart Foundation/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080623 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Colicins) RN - 0 (Escherichia coli Proteins) RN - 0 (tolA protein, E coli) RN - 42HK56048U (Tyrosine) SB - IM MH - Amino Acid Sequence MH - Colicins/chemistry/*metabolism MH - Escherichia coli Proteins/metabolism MH - Hydrolysis MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Folding MH - Protein Structure, Tertiary MH - Tyrosine/chemistry EDAT- 2008/06/25 09:00 MHDA- 2008/09/16 09:00 CRDT- 2008/06/25 09:00 PHST- 2008/05/13 [received] PHST- 2008/06/12 [revised] PHST- 2008/06/13 [accepted] PHST- 2008/06/23 [aheadofprint] AID - S0014-5793(08)00521-8 [pii] AID - 10.1016/j.febslet.2008.06.022 [doi] PST - ppublish SO - FEBS Lett. 2008 Jul 23;582(17):2673-7. doi: 10.1016/j.febslet.2008.06.022. Epub 2008 Jun 23. PMID- 16339893 OWN - NLM STAT- MEDLINE DA - 20051221 DCOM- 20060131 LR - 20140910 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 102 IP - 51 DP - 2005 Dec 20 TI - Solution structure of a multifunctional DNA- and protein-binding motif of human Werner syndrome protein. PG - 18379-84 AB - Werner syndrome (WS) is an autosomal recessive disease that results in premature aging. Mutations in the WS gene (WRN) result in a loss of expression of the WRN protein and predispose WS patients to accelerated aging. As a helicase and a nuclease, WRN is unique among the five human RecQ helicase family members and is capable of multiple functions involved in DNA replication, repair, recombination, and telomere maintenance. A 144-residue fragment of WRN was previously determined to be a multifunctional DNA- and protein-binding domain (DPBD) that interacts with structure-specific DNA and a variety of DNA-processing proteins. In addition, DPBD functions as a nucleolar targeting sequence of WRN. The solution structure of the DPBD, the first of a WRN fragment, has been solved by NMR. DPBD consists of a winged helix-like motif and an unstructured C-terminal region of approximately 20 aa. The putative DNA-binding surface of DPBD has been identified by using known structural and biochemical data. Based on the structural data and on the biochemical data, we suggest a surface on the DPBD for interacting with other proteins. In this structural model, a single winged helix domain binds to both DNA and other proteins. Furthermore, we propose that DPBD functions as a regulatory domain to regulate the enzymatic activity of WRN and to direct cellular localization of WRN through protein-protein interaction. FAU - Hu, Jin-Shan AU - Hu JS AD - Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA. jhu1@umail.umd.edu FAU - Feng, Hanqiao AU - Feng H FAU - Zeng, Wangyong AU - Zeng W FAU - Lin, Guang-Xin AU - Lin GX FAU - Xi, Xu Guang AU - Xi XG LA - eng SI - PDB/2AXL PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051209 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 9007-49-2 (DNA) RN - EC 3.1.- (Exodeoxyribonucleases) RN - EC 3.6.1.- (WRN protein, human) RN - EC 3.6.4.- (DNA Helicases) RN - EC 3.6.4.12 (RecQ Helicases) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - DNA/*metabolism MH - DNA Helicases/*chemistry/genetics/*metabolism MH - Enzyme Activation MH - Exodeoxyribonucleases MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - RecQ Helicases MH - Sequence Alignment PMC - PMC1317980 OID - NLM: PMC1317980 EDAT- 2005/12/13 09:00 MHDA- 2006/02/01 09:00 CRDT- 2005/12/13 09:00 PHST- 2005/12/09 [aheadofprint] AID - 0509380102 [pii] AID - 10.1073/pnas.0509380102 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18379-84. Epub 2005 Dec 9. PMID- 15501818 OWN - NLM STAT- MEDLINE DA - 20041231 DCOM- 20050721 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 280 IP - 1 DP - 2005 Jan 7 TI - Crystal structure of the human cytosolic sialidase Neu2. Evidence for the dynamic nature of substrate recognition. PG - 469-75 AB - Gangliosides play key roles in cell differentiation, cell-cell interactions, and transmembrane signaling. Sialidases hydrolyze sialic acids to produce asialo compounds, which is the first step of degradation processes of glycoproteins and gangliosides. Sialidase involvement has been implicated in some lysosomal storage disorders such as sialidosis and galactosialidosis. Neu2 is a recently identified human cytosolic sialidase. Here we report the first high resolution x-ray structures of mammalian sialidase, human Neu2, in its apo form and in complex with an inhibitor, 2-deoxy-2,3-dehydro-N-acetylneuraminic acid (DANA). The structure shows the canonical six-blade beta-propeller observed in viral and bacterial sialidases with its active site in a shallow crevice. In the complex structure, the inhibitor lies in the catalytic crevice surrounded by ten amino acids. In particular, the arginine triad, conserved among sialidases, aids in the proper positioning of the carboxylate group of DANA within the active site region. The tyrosine residue, Tyr(334), conserved among mammalian and bacterial sialidases as well as in viral neuraminidases, facilitates the enzymatic reaction by stabilizing a putative carbonium ion in the transition state. The loops containing Glu(111) and the catalytic aspartate Asp(46) are disordered in the apo form but upon binding of DANA become ordered to adopt two short alpha-helices to cover the inhibitor, illustrating the dynamic nature of substrate recognition. The N-acetyl and glycerol moieties of DANA are recognized by Neu2 residues not shared by bacterial sialidases and viral neuraminidases, which can be regarded as a key structural difference for potential drug design against bacteria, influenza, and other viruses. FAU - Chavas, Leonard M G AU - Chavas LM AD - Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan. FAU - Tringali, Cristina AU - Tringali C FAU - Fusi, Paola AU - Fusi P FAU - Venerando, Bruno AU - Venerando B FAU - Tettamanti, Guido AU - Tettamanti G FAU - Kato, Ryuichi AU - Kato R FAU - Monti, Eugenio AU - Monti E FAU - Wakatsuki, Soichi AU - Wakatsuki S LA - eng SI - PDB/1SNT SI - PDB/1SO7 SI - PDB/1VCU PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20041022 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 24967-27-9 (2-deoxy-2,3-dehydro-N-acetylneuraminic acid) RN - EC 3.2.1.18 (NEU2 protein, human) RN - EC 3.2.1.18 (Neuraminidase) RN - GZP2782OP0 (N-Acetylneuraminic Acid) SB - IM MH - Animals MH - Catalytic Domain MH - Crystallography, X-Ray MH - Humans MH - *Models, Molecular MH - Molecular Structure MH - N-Acetylneuraminic Acid/*analogs & derivatives/chemistry/metabolism MH - Neuraminidase/*chemistry/metabolism MH - Protein Structure, Secondary MH - Static Electricity MH - Structure-Activity Relationship MH - Substrate Specificity EDAT- 2004/10/27 09:00 MHDA- 2005/07/22 09:00 CRDT- 2004/10/27 09:00 PHST- 2004/10/22 [aheadofprint] AID - M411506200 [pii] AID - 10.1074/jbc.M411506200 [doi] PST - ppublish SO - J Biol Chem. 2005 Jan 7;280(1):469-75. Epub 2004 Oct 22. PMID- 15912356 OWN - NLM STAT- MEDLINE DA - 20051017 DCOM- 20060112 LR - 20081121 IS - 0032-0935 (Print) IS - 0032-0935 (Linking) VI - 222 IP - 3 DP - 2005 Oct TI - Two naturally occurring deletion mutants of 12S seed storage proteins in Arabidopsis thaliana. PG - 512-20 AB - Two naturally occurring Arabidopsis mutants, Cape Verde Islands and Monte (Mr-0), with aberrant 12S seed storage protein (SSP) profiles have been identified by SDS-PAGE. In both mutants, one of the 12S globulin bands is missing while a new band of lower molecular mass is present. Tandem mass spectrometry-mass spectrometry (MS/MS) analyses of the mutant peptides have revealed that both are shorter variants of 12S globulin with deletion sites detected within the alpha-subunits of 12S globulin cruciferin B (CRB) and C (CRC), respectively. Sequence analyses of the genomic DNA flanking the deletion sites have demonstrated that both deletions occurred at the genomic level. These two mutants are referred to as CRBDelta12 and CRCDelta13 with the delta sign indicating a deletion and the number indicating amino acids deleted. Alignment of these two mutant sequences with that of soybean A3B4 subunit, for which the crystal structure was determined recently, have revealed that the CRCDelta13 deletion is located in a hypervariable/disordered region, and will probably not affect the structure of the hexameric globulin. The CRBDelta12 deletion, however, is located in a binding region that is thought to be important for the hexamer formation. However, CRBDelta12 appears to accumulate normally as judged by its band intensity relative to the other SSP subunits on the protein gels. Thus it seems that the seed can, to a certain extent, tolerate some mutations in its storage proteins. FAU - Hou, Anfu AU - Hou A AD - Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada. FAU - Liu, Kede AU - Liu K FAU - Catawatcharakul, Niramol AU - Catawatcharakul N FAU - Tang, Xurong AU - Tang X FAU - Nguyen, Vi AU - Nguyen V FAU - Keller, Wilfred A AU - Keller WA FAU - Tsang, Edward W T AU - Tsang EW FAU - Cui, Yuhai AU - Cui Y LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050524 PL - Germany TA - Planta JT - Planta JID - 1250576 RN - 0 (Arabidopsis Proteins) RN - 0 (Globulins) RN - 0 (Protein Subunits) RN - 0 (Seed Storage Proteins) RN - 0 (cruciferin B, Arabidopsis) RN - 0 (cruciferin C, Arabidopsis) SB - IM MH - Amino Acid Sequence MH - Arabidopsis/*genetics MH - Arabidopsis Proteins/chemistry/*genetics MH - Base Sequence MH - *Gene Deletion MH - Globulins/*genetics MH - Molecular Sequence Data MH - Protein Subunits/genetics MH - Seed Storage Proteins MH - Seeds/*genetics MH - Sequence Alignment MH - Sequence Homology, Amino Acid EDAT- 2005/05/25 09:00 MHDA- 2006/01/13 09:00 CRDT- 2005/05/25 09:00 PHST- 2005/01/12 [received] PHST- 2005/04/02 [accepted] PHST- 2005/05/24 [aheadofprint] AID - 10.1007/s00425-005-1555-z [doi] PST - ppublish SO - Planta. 2005 Oct;222(3):512-20. Epub 2005 May 24. PMID- 20961098 OWN - NLM STAT- MEDLINE DA - 20101116 DCOM- 20101230 LR - 20140912 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 46 DP - 2010 Nov 23 TI - Structure of the p53 transactivation domain in complex with the nuclear receptor coactivator binding domain of CREB binding protein. PG - 9964-71 LID - 10.1021/bi1012996 [doi] AB - The activity and stability of the tumor suppressor p53 are regulated by interactions with key cellular proteins such as MDM2 and CBP/p300. The transactivation domain (TAD) of p53 contains two subdomains (AD1 and AD2) and interacts directly with the N-terminal domain of MDM2 and with several domains of CBP/p300. Here we report the NMR structure of the full-length p53 TAD in complex with the nuclear coactivator binding domain (NCBD) of CBP. Both the p53 TAD and NCBD are intrinsically disordered and fold synergistically upon binding, as evidenced by the observed increase in helicity and increased level of dispersion of the amide proton resonances. The p53 TAD folds to form a pair of helices (denoted Palpha1 and Palpha2), which extend from Phe19 to Leu25 and from Pro47 to Trp53, respectively. In the complex, the NCBD forms a bundle of three helices (Calpha1, residues 2066-2075; Calpha2, residues 2081-2092; and Calpha3, residues 2095-2105) with a hydrophobic groove into which p53 helices Palpha1 and Palpha2 dock. The polypeptide chain between the p53 helices remains flexible and makes no detectable intermolecular contacts with the NCBD. Complex formation is driven largely by hydrophobic contacts that form a stable intermolecular hydrophobic core. A salt bridge between D49 of p53 and R2105 of NCBD may contribute to the binding specificity. The structure provides the first insights into simultaneous binding of the AD1 and AD2 motifs to a target protein. FAU - Lee, Chul Won AU - Lee CW AD - Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States. FAU - Martinez-Yamout, Maria A AU - Martinez-Yamout MA FAU - Dyson, H Jane AU - Dyson HJ FAU - Wright, Peter E AU - Wright PE LA - eng GR - CA96865/CA/NCI NIH HHS/United States GR - R01 CA096865/CA/NCI NIH HHS/United States GR - R01 CA096865-10/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20101029 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Nuclear Receptor Coactivators) RN - 0 (Tumor Suppressor Protein p53) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Animals MH - Binding Sites MH - CREB-Binding Protein/*chemistry/metabolism MH - Humans MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Receptor Coactivators/*chemistry/metabolism MH - Protein Structure, Tertiary MH - Tumor Suppressor Protein p53/*chemistry/metabolism PMC - PMC2982890 MID - NIHMS248372 OID - NLM: NIHMS248372 OID - NLM: PMC2982890 EDAT- 2010/10/22 06:00 MHDA- 2010/12/31 06:00 CRDT- 2010/10/22 06:00 PHST- 2010/10/29 [aheadofprint] AID - 10.1021/bi1012996 [doi] PST - ppublish SO - Biochemistry. 2010 Nov 23;49(46):9964-71. doi: 10.1021/bi1012996. Epub 2010 Oct 29. PMID- 22078626 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20111114 DCOM- 20120103 IS - 1527-3792 (Electronic) IS - 0022-5347 (Linking) VI - 186 IP - 6 DP - 2011 Dec TI - Re: The cancer/testis antigen prostate-associated gene 4 (PAGE4) is a highly intrinsically disordered protein. PG - 2494-5 LID - 10.1016/j.juro.2011.08.120 [doi] FAU - Atala, Anthony AU - Atala A LA - eng PT - Comment PT - Journal Article DEP - 20111026 PL - United States TA - J Urol JT - The Journal of urology JID - 0376374 CON - J Biol Chem. 2011 Apr 22;286(16):13985-94. PMID: 21357425 EDAT- 2011/11/15 06:00 MHDA- 2011/11/15 06:01 CRDT- 2011/11/15 06:00 PHST- 2011/10/26 [aheadofprint] AID - S0022-5347(11)04941-X [pii] AID - 10.1016/j.juro.2011.08.120 [doi] PST - ppublish SO - J Urol. 2011 Dec;186(6):2494-5. doi: 10.1016/j.juro.2011.08.120. Epub 2011 Oct 26. PMID- 18336901 OWN - NLM STAT- MEDLINE DA - 20080408 DCOM- 20080728 IS - 0141-8130 (Print) IS - 0141-8130 (Linking) VI - 42 IP - 4 DP - 2008 May 1 TI - Chaperone activities of bovine and camel beta-caseins: Importance of their surface hydrophobicity in protection against alcohol dehydrogenase aggregation. PG - 392-9 LID - 10.1016/j.ijbiomac.2008.01.008 [doi] AB - Beta-casein (beta-CN) showing properties of intrinsically unstructured proteins (IUP) displays many similarities with molecular chaperones and shows anti-aggregation activity in vitro. Chaperone activities of bovine and camel beta-CN were studied using alcohol dehydrogenase (ADH) as a substrate. To obtain an adequate relevant information about the chaperone capacities of studied caseins, three different physical parameters including chaperone constant (k(c), microM(-1)), thermal aggregation constant (k(T), degrees C(-1)) and aggregation rate constant (k(t), min(-1)) were measured. Bovine beta-CN displays greater chaperone activity than camel beta-CN. Fluorescence studies of 8-anilino-1-naphthalenesulfonic acid (ANS) binding demonstrated that bovine beta-CN is doted with larger effective hydrophobic surfaces at all studied temperatures than camel beta-CN. Greater relative hydrophobicity of bovine beta-CN than camel beta-CN may be a factor responsible for stronger interactions of bovine beta-CN with the aggregation-prone pre denatured molecular species of the substrate ADH, which resulted in greater chaperone activity of bovine beta-CN. FAU - Barzegar, Abolfazl AU - Barzegar A AD - Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. FAU - Yousefi, Reza AU - Yousefi R FAU - Sharifzadeh, Ahmad AU - Sharifzadeh A FAU - Dalgalarrondo, Michele AU - Dalgalarrondo M FAU - Chobert, Jean-Marc AU - Chobert JM FAU - Ganjali, Mohammad Reza AU - Ganjali MR FAU - Norouzi, Parviz AU - Norouzi P FAU - Ehsani, Mohammad Reza AU - Ehsani MR FAU - Niasari-Naslaji, Amir AU - Niasari-Naslaji A FAU - Saboury, Ali Akbar AU - Saboury AA FAU - Haertle, Thomas AU - Haertle T FAU - Moosavi-Movahedi, Ali Akbar AU - Moosavi-Movahedi AA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080207 PL - England TA - Int J Biol Macromol JT - International journal of biological macromolecules JID - 7909578 RN - 0 (8-anilino-1-naphthalenesulfonic acid) RN - 0 (Anilino Naphthalenesulfonates) RN - 0 (Caseins) RN - 0 (Micelles) RN - 0 (Molecular Chaperones) RN - EC 1.1.1.1 (Alcohol Dehydrogenase) SB - IM MH - Alcohol Dehydrogenase/*chemistry MH - Amino Acid Sequence MH - Anilino Naphthalenesulfonates/chemistry MH - Animals MH - Camels MH - Caseins/*chemistry MH - Cattle MH - Dose-Response Relationship, Drug MH - Horses MH - Liver/metabolism MH - Micelles MH - Molecular Chaperones/*chemistry MH - Molecular Sequence Data MH - Sequence Homology, Amino Acid MH - Temperature EDAT- 2008/03/14 09:00 MHDA- 2008/07/29 09:00 CRDT- 2008/03/14 09:00 PHST- 2007/11/18 [received] PHST- 2008/01/25 [revised] PHST- 2008/01/28 [accepted] PHST- 2008/02/07 [aheadofprint] AID - S0141-8130(08)00030-5 [pii] AID - 10.1016/j.ijbiomac.2008.01.008 [doi] PST - ppublish SO - Int J Biol Macromol. 2008 May 1;42(4):392-9. doi: 10.1016/j.ijbiomac.2008.01.008. Epub 2008 Feb 7. PMID- 24970188 OWN - NLM STAT- PubMed-not-MEDLINE DA - 20140627 DCOM- 20140627 LR - 20140630 IS - 2218-273X (Electronic) IS - 2218-273X (Linking) VI - 3 IP - 3 DP - 2013 TI - Biophysical Characterization of alpha-Synuclein and Rotenone Interaction. PG - 703-32 LID - 10.3390/biom3030703 [doi] AB - Previous studies revealed that pesticides interact with alpha-synuclein and accelerate the rate of fibrillation. These results are consistent with the prevailing hypothesis that the direct interaction of alpha-synuclein with pesticides is one of many suspected factors leading to alpha-synuclein fibrillation and ultimately to Parkinson's disease. In this study, the biophysical properties and fibrillation kinetics of alpha-synuclein in the presence of rotenone were investigated and, more specifically, the effects of rotenone on the early-stage misfolded forms of alpha-synuclein were considered. The thioflavine T (ThT) fluorescence assay studies provide evidence that early-phase misfolded alpha-synuclein forms are affected by rotenone and that the fibrillation process is accelerated. Further characterization by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) shows that rotenone increases the amount of ordered secondary structure in this intrinsically disordered protein. Morphological characterization by transmission electron microscopy (TEM) and atomic force microscopy (AFM) provide visualization of the differences in the aggregated alpha-synuclein species developing during the early kinetics of the fibrillation process in the absence and presence of rotenone. We believe that these data provide useful information for a better understanding of the molecular basis of rotenone-induced misfolding and aggregation of alpha-synuclein. FAU - Silva, Blanca A AU - Silva BA AD - Department of Chemistry and Biochemistry, University of California, 156 High Street, Santa Cruz, CA 95064, USA. blancasilva@hotmail.com. FAU - Einarsdottir, Olof AU - Einarsdottir O AD - Department of Chemistry and Biochemistry, University of California, 156 High Street, Santa Cruz, CA 95064, USA. olof@ucsc.edu. FAU - Fink, Anthony L AU - Fink AL AD - Department of Chemistry and Biochemistry, University of California, 156 High Street, Santa Cruz, CA 95064, USA. FAU - Uversky, Vladimir N AU - Uversky VN AD - Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida; 12901 Bruce B. Downs Blvd., MDC 7, Tampa, FL 33612, USA. vuversky@health.usf.edu. LA - eng PT - Journal Article DEP - 20130924 PL - Switzerland TA - Biomolecules JT - Biomolecules JID - 101596414 PMC - PMC4030960 OID - NLM: PMC4030960 EDAT- 2013/01/01 00:00 MHDA- 2013/01/01 00:01 CRDT- 2014/06/28 06:00 PHST- 2013/09/13 [received] PHST- 2013/09/21 [revised] PHST- 2013/09/23 [accepted] AID - biom3030703 [pii] AID - 10.3390/biom3030703 [doi] PST - epublish SO - Biomolecules. 2013 Sep 24;3(3):703-32. doi: 10.3390/biom3030703. PMID- 24410358 OWN - NLM STAT- MEDLINE DA - 20140620 DCOM- 20150518 IS - 1520-5207 (Electronic) IS - 1520-5207 (Linking) VI - 118 IP - 24 DP - 2014 Jun 19 TI - Comparison of structure determination methods for intrinsically disordered amyloid-beta peptides. PG - 6405-16 LID - 10.1021/jp410275y [doi] AB - Intrinsically disordered proteins (IDPs) represent a new frontier in structural biology since the primary characteristic of IDPs is that structures need to be characterized as diverse ensembles of conformational substates. We compare two general but very different ways of combining NMR spectroscopy with theoretical methods to derive structural ensembles for the disease IDPs amyloid-beta 1-40 and amyloid-beta 1-42, which are associated with Alzheimer's Disease. We analyze the performance of de novo molecular dynamics and knowledge-based approaches for generating structural ensembles by assessing their ability to reproduce a range of NMR experimental observables. In addition to the comparison of computational methods, we also evaluate the relative value of different types of NMR data for refining or validating the IDP structural ensembles for these important disease peptides. FAU - Ball, K Aurelia AU - Ball KA AD - Graduate Group in Biophysics , Berkeley, California 94720, United States. FAU - Wemmer, David E AU - Wemmer DE FAU - Head-Gordon, Teresa AU - Head-Gordon T LA - eng GR - T32 GM008295/GM/NIGMS NIH HHS/United States GR - T32 GM08295/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140128 PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Amyloid beta-Peptides) RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (1-40)) RN - 0 (amyloid beta-protein (1-42)) SB - IM MH - Amyloid beta-Peptides/*chemistry MH - Intrinsically Disordered Proteins/*chemistry MH - Molecular Dynamics Simulation MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptide Fragments/*chemistry MH - Protein Structure, Secondary PMC - PMC4066902 MID - NIHMS601845 OID - NLM: NIHMS601845 OID - NLM: PMC4066902 EDAT- 2014/01/15 06:00 MHDA- 2015/05/20 06:00 CRDT- 2014/01/14 06:00 PHST- 2014/01/28 [aheadofprint] AID - 10.1021/jp410275y [doi] PST - ppublish SO - J Phys Chem B. 2014 Jun 19;118(24):6405-16. doi: 10.1021/jp410275y. Epub 2014 Jan 28. PMID- 19293380 OWN - NLM STAT- MEDLINE DA - 20090408 DCOM- 20090506 LR - 20140831 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 106 IP - 14 DP - 2009 Apr 7 TI - Interplay of alpha-synuclein binding and conformational switching probed by single-molecule fluorescence. PG - 5645-50 LID - 10.1073/pnas.0809232106 [doi] AB - We studied the coupled binding and folding of alpha-synuclein, an intrinsically disordered protein linked with Parkinson's disease. Using single-molecule fluorescence resonance energy transfer and correlation methods, we directly probed protein membrane association, structural distributions, and dynamics. Results revealed an intricate energy landscape on which binding of alpha-synuclein to amphiphilic small molecules or membrane-like partners modulates conformational transitions between a natively unfolded state and multiple alpha-helical structures. Alpha-synuclein conformation is not continuously tunable, but instead partitions into 2 main classes of folding landscape structural minima. The switch between a broken and an extended helical structure can be triggered by changing the concentration of binding partners or by varying the curvature of the binding surfaces presented by micelles or bilayers composed of the lipid-mimetic SDS. Single-molecule experiments with lipid vesicles of various composition showed that a low fraction of negatively charged lipids, similar to that found in biological membranes, was sufficient to drive alpha-synuclein binding and folding, resulting here in the induction of an extended helical structure. Overall, our results imply that the 2 folded structures are preencoded by the alpha-synuclein amino acid sequence, and are tunable by small-molecule supramolecular states and differing membrane properties, suggesting novel control elements for biological and amyloid regulation of alpha-synuclein. FAU - Ferreon, Allan Chris M AU - Ferreon AC AD - Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. FAU - Gambin, Yann AU - Gambin Y FAU - Lemke, Edward A AU - Lemke EA FAU - Deniz, Ashok A AU - Deniz AA LA - eng GR - GM066833/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20090317 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Lipid Bilayers) RN - 0 (Micelles) RN - 0 (alpha-Synuclein) RN - 368GB5141J (Sodium Dodecyl Sulfate) SB - IM MH - *Fluorescence Resonance Energy Transfer MH - Lipid Bilayers MH - Micelles MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Sodium Dodecyl Sulfate MH - alpha-Synuclein/*chemistry PMC - PMC2667048 OID - NLM: PMC2667048 EDAT- 2009/03/19 09:00 MHDA- 2009/05/07 09:00 CRDT- 2009/03/19 09:00 PHST- 2009/03/17 [aheadofprint] AID - 0809232106 [pii] AID - 10.1073/pnas.0809232106 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5645-50. doi: 10.1073/pnas.0809232106. Epub 2009 Mar 17. PMID- 21322033 OWN - NLM STAT- MEDLINE DA - 20110309 DCOM- 20110713 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 79 IP - 4 DP - 2011 Apr TI - Is there nascent structure in the intrinsically disordered region of troponin I? PG - 1240-50 LID - 10.1002/prot.22959 [doi] AB - In striated muscle, the binding of calcium to troponin C (TnC) results in the removal of the C-terminal region of the inhibitory protein troponin I (TnI) from actin. While structural studies of the muscle system have been successful in determining the overall organization of most of the components involved in force generation at the atomic level, the structure and dynamics of the C-terminal region of TnI remains controversial. This domain of TnI is highly flexible, and it has been proposed that this intrinsically disordered region (IDR) regulates contraction via a "fly-casting" mechanism. Different structures have been presented for this region using different methodologies: a single alpha-helix, a "mobile domain" containing a small beta-sheet, an unstructured region, and a two helix segment. To investigate whether this IDR has in fact any nascent structure, we have constructed a skeletal TnC-TnI chimera that contains the N-domain of TnC (1-90), a short linker (GGAGG), and the C-terminal region of TnI (97-182) and have acquired (1)(5)N NMR relaxation data for this chimera. We compare the experimental relaxation parameters with those calculated from molecular dynamic simulations using four models based upon the structural studies. Our experimental results suggest that the C-terminal region of TnI does not contain any defined secondary structure, supporting the "fly-casting" mechanism. We interpret the presence of a "plateau" in the (1)(5)N NMR relaxation data as being an intrinsic property of IDRs. We also identified a more rigid adjacent region of TnI that has implications for muscle performance under ischemic conditions. CI - Copyright (c) 2011 Wiley-Liss, Inc. FAU - Julien, Olivier AU - Julien O AD - Department of Biochemistry, University of Alberta, Edmonton, AB, Canada. FAU - Mercier, Pascal AU - Mercier P FAU - Allen, Claire N AU - Allen CN FAU - Fisette, Olivier AU - Fisette O FAU - Ramos, Carlos H I AU - Ramos CH FAU - Lague, Patrick AU - Lague P FAU - Blumenschein, Tharin M A AU - Blumenschein TM FAU - Sykes, Brian D AU - Sykes BD LA - eng GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110214 PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Troponin C) RN - 0 (Troponin I) SB - IM MH - Computational Biology MH - Entropy MH - Humans MH - Molecular Dynamics Simulation MH - Nuclear Magnetic Resonance, Biomolecular MH - Pliability MH - Protein Structure, Tertiary MH - Temperature MH - Troponin C/chemistry/metabolism MH - Troponin I/*chemistry/metabolism EDAT- 2011/02/16 06:00 MHDA- 2011/07/14 06:00 CRDT- 2011/02/16 06:00 PHST- 2010/10/05 [received] PHST- 2010/11/20 [revised] PHST- 2010/11/27 [accepted] PHST- 2011/02/14 [aheadofprint] AID - 10.1002/prot.22959 [doi] PST - ppublish SO - Proteins. 2011 Apr;79(4):1240-50. doi: 10.1002/prot.22959. Epub 2011 Feb 14. PMID- 21760931 OWN - NLM STAT- MEDLINE DA - 20110715 DCOM- 20111013 LR - 20141022 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 7 DP - 2011 TI - Mapping of protein-protein interaction sites in the plant-type [2Fe-2S] ferredoxin. PG - e21947 LID - 10.1371/journal.pone.0021947 [doi] AB - Knowing the manner of protein-protein interactions is vital for understanding biological events. The plant-type [2Fe-2S] ferredoxin (Fd), a well-known small iron-sulfur protein with low redox potential, partitions electrons to a variety of Fd-dependent enzymes via specific protein-protein interactions. Here we have refined the crystal structure of a recombinant plant-type Fd I from the blue green alga Aphanothece sacrum (AsFd-I) at 1.46 A resolution on the basis of the synchrotron radiation data. Incorporating the revised amino-acid sequence, our analysis corrects the 3D structure previously reported; we identified the short alpha-helix (67-71) near the active center, which is conserved in other plant-type [2Fe-2S] Fds. Although the 3D structures of the four molecules in the asymmetric unit are similar to each other, detailed comparison of the four structures revealed the segments whose conformations are variable. Structural comparison between the Fds from different sources showed that the distribution of the variable segments in AsFd-I is highly conserved in other Fds, suggesting the presence of intrinsically flexible regions in the plant-type [2Fe-2S] Fd. A few structures of the complexes with Fd-dependent enzymes clearly demonstrate that the protein-protein interactions are achieved through these variable regions in Fd. The results described here will provide a guide for interpreting the biochemical and mutational studies that aim at the manner of interactions with Fd-dependent enzymes. FAU - Kameda, Haruka AU - Kameda H AD - Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan. FAU - Hirabayashi, Kei AU - Hirabayashi K FAU - Wada, Kei AU - Wada K FAU - Fukuyama, Keiichi AU - Fukuyama K LA - eng SI - PDB/3AV8 PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110708 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (2Fe-2S ferredoxin) RN - 0 (Ferredoxins) SB - IM MH - Conserved Sequence/genetics MH - Crystallography, X-Ray MH - Cyanobacteria/*metabolism MH - Ferredoxins/*chemistry/*metabolism MH - Models, Molecular MH - Protein Binding MH - *Protein Interaction Mapping MH - Protein Structure, Secondary MH - Structural Homology, Protein PMC - PMC3132287 OID - NLM: PMC3132287 EDAT- 2011/07/16 06:00 MHDA- 2011/10/14 06:00 CRDT- 2011/07/16 06:00 PHST- 2011/04/18 [received] PHST- 2011/06/13 [accepted] PHST- 2011/07/08 [epublish] AID - 10.1371/journal.pone.0021947 [doi] AID - PONE-D-11-07061 [pii] PST - ppublish SO - PLoS One. 2011;6(7):e21947. doi: 10.1371/journal.pone.0021947. Epub 2011 Jul 8. PMID- 18433059 OWN - NLM STAT- MEDLINE DA - 20081001 DCOM- 20090309 LR - 20131121 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 73 IP - 2 DP - 2008 Nov 1 TI - Isoform-specific variation in the intrinsic disorder of troponin I. PG - 338-50 LID - 10.1002/prot.22063 [doi] AB - Various intrinsic disorder (ID) prediction algorithms were applied to the three tissue isoforms of troponin I (TnI). The results were interpreted in terms of the known structure and dynamics of troponin. In line with previous results, all isoforms of TnI were predicted to have large stretches of ID. The predictions show that the C-termini of all isoforms are extensively disordered as is the N-terminal extension of the cardiac isoform. Cardiac TnI likely belongs to the group of intrinsically disordered signalling hub proteins. For a given portion of the protein sequence, most ID prediction approaches indicate isoform-dependent variations in the probability of disorder. Comparison of machine learning and physically based approaches suggests the ID variations are only partially attributable to local variations in the ratio of charged to hydrophobic residues. The VSL2B algorithm predicts the largest variations in ID across the isoforms, with the cardiac isoform having the highest probability of structured regions, and the fast-skeletal isoform having no intrinsic structure. The region corresponding to residues 57-95 of the fast-skeletal isoform, known to form a coiled coil substructure with troponin T, was highly variable between isoforms. The isoform-specific ID variations may have mechanistic significance, modulating the extent to which conformational fluctuations in tropomyosin are communicated to the troponin complex. We discuss structural mechanisms for this communication. Overall, the results motivate the development of predictors designed to address relative levels of disorder between highly similar proteins. CI - (c) 2008 Wiley-Liss, Inc. FAU - Hoffman, Ryan M B AU - Hoffman RM AD - Department of Biochemistry, University of Alberta, Edmonton, Canada. FAU - Sykes, Brian D AU - Sykes BD LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Protein Isoforms) RN - 0 (Tropomyosin) RN - 0 (Troponin I) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Calcium/*metabolism MH - Humans MH - Molecular Sequence Data MH - Muscle Fibers, Fast-Twitch/*metabolism MH - Myocardium/*metabolism MH - Protein Isoforms/metabolism MH - Sequence Alignment MH - Tropomyosin/*metabolism MH - Troponin I/chemistry/*metabolism EDAT- 2008/04/25 09:00 MHDA- 2009/03/10 09:00 CRDT- 2008/04/25 09:00 AID - 10.1002/prot.22063 [doi] PST - ppublish SO - Proteins. 2008 Nov 1;73(2):338-50. doi: 10.1002/prot.22063. PMID- 21163351 OWN - NLM STAT- MEDLINE DA - 20110307 DCOM- 20110909 LR - 20131121 IS - 1095-9130 (Electronic) IS - 1046-2023 (Linking) VI - 53 IP - 3 DP - 2011 Mar TI - Assays for alpha-synuclein aggregation. PG - 295-305 LID - 10.1016/j.ymeth.2010.12.008 [doi] AB - This review describes different ways to achieve and monitor reproducible aggregation of alpha-synuclein, a key protein in the development of Parkinson's disease. For most globular proteins, aggregation is promoted by partially denaturing conditions which compromise the native state without destabilizing the intermolecular contacts required for accumulation of regular amyloid structure. As a natively disordered protein, alpha-synuclein can fibrillate under physiological conditions and this process is actually stimulated by conditions that promote structure formation, such as low pH, ions, polyamines, anionic surfactants, fluorinated alcohols and agitation. Reproducibility is a critical issue since alpha-synuclein shows erratic fibrillation behavior on its own. Agitation in combination with glass beads significantly reduces the variability of aggregation time curves, but the most reproducible aggregation is achieved by sub-micellar concentrations of SDS, which promote the rapid formation of small clusters of alpha-synuclein around shared micelles. Although the fibrils produced this way have a different appearance and secondary structure, they are rich in cross-beta structure and are amenable to high-throughput screening assays. Although such assays at best provide a very simplistic recapitulation of physiological conditions, they allow the investigator to focus on well-defined molecular events and may provide the opportunity to identify, e.g. small molecule inhibitors of aggregation that affect these steps. Subsequent experiments in more complex cellular and whole-organism environments can then validate whether there is any relation between these molecular interactions and the broader biological context. CI - Copyright (c) 2010 Elsevier Inc. All rights reserved. FAU - Giehm, Lise AU - Giehm L AD - Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, Gustav Wieds Vej 10C, DK - 8000 Aarhus C, Denmark. FAU - Lorenzen, Nikolai AU - Lorenzen N FAU - Otzen, Daniel E AU - Otzen DE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20101214 PL - United States TA - Methods JT - Methods (San Diego, Calif.) JID - 9426302 RN - 0 (Amyloid) RN - 0 (alpha-Synuclein) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - 75-89-8 (Trifluoroethanol) SB - IM MH - Amyloid/chemistry MH - Humans MH - Parkinson Disease/pathology MH - Reproducibility of Results MH - Research Design MH - Sodium Dodecyl Sulfate/chemistry MH - Trifluoroethanol/chemistry MH - alpha-Synuclein/*chemistry/isolation & purification/metabolism EDAT- 2010/12/18 06:00 MHDA- 2011/09/10 06:00 CRDT- 2010/12/18 06:00 PHST- 2010/11/01 [received] PHST- 2010/12/08 [revised] PHST- 2010/12/08 [accepted] PHST- 2010/12/14 [aheadofprint] AID - S1046-2023(10)00291-4 [pii] AID - 10.1016/j.ymeth.2010.12.008 [doi] PST - ppublish SO - Methods. 2011 Mar;53(3):295-305. doi: 10.1016/j.ymeth.2010.12.008. Epub 2010 Dec 14. PMID- 15284189 OWN - NLM STAT- MEDLINE DA - 20040823 DCOM- 20050310 LR - 20071114 IS - 1524-4571 (Electronic) IS - 0009-7330 (Linking) VI - 95 IP - 4 DP - 2004 Aug 20 TI - Modifications in the biophysical properties of connexin43 channels by a peptide of the cytoplasmic loop region. PG - e22-8 AB - Connexin43 (Cx43) channels reside in at least 3 states: closed, open, or residual. It is hypothesized that the residual state results from the interaction of an intracellular "gating element" with structures at the vestibule of the pore. Recently, we showed in vitro that there is an intramolecular interaction of the carboxyl-terminal domain (referred to as "CT") with a region in the cytoplasmic loop of Cx43 (amino acids 119 to 144; referred to as "L2"). Here, we assessed whether the L2 region was able to interact with the gating particle in a functional channel. Cx43 channels were recorded in the presence of a peptide corresponding to the L2 region, delivered via the patch pipette. This manipulation did not modify unitary conductance, but decreased the frequency of transitions into the residual state, prolonged open time, and altered the voltage dependence of the channel in a manner analogous to that observed after truncation of the CT domain. The latter correlated with the ability of the peptide to bind to the CT domain, as determined by mirror resonance spectroscopy. Overall, we propose that the L2 acts as a "receptor" that interacts with a flexible intracellular gating element during channel gating. The full text of this article is available online at http://circres.ahajournals.org. FAU - Seki, Akiko AU - Seki A AD - Department of Pharmacology, State University of New York Upstate Medical University, Syracuse 13210, USA. FAU - Duffy, Heather S AU - Duffy HS FAU - Coombs, Wanda AU - Coombs W FAU - Spray, David C AU - Spray DC FAU - Taffet, Steven M AU - Taffet SM FAU - Delmar, Mario AU - Delmar M LA - eng GR - MH65459/MH/NIMH NIH HHS/United States GR - NS07098/NS/NINDS NIH HHS/United States GR - NS41282/NS/NINDS NIH HHS/United States GR - P01-HL-39707/HL/NHLBI NIH HHS/United States GR - R01-GM-5769/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20040729 PL - United States TA - Circ Res JT - Circulation research JID - 0047103 RN - 0 (Connexin 43) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Fusion Proteins) RN - 0 (enhanced green fluorescent protein) RN - 147336-22-9 (Green Fluorescent Proteins) SB - IM MH - Animals MH - Cell Line, Tumor/pathology MH - Connexin 43/*chemistry/genetics MH - Gap Junctions/drug effects/*physiology MH - Genes, Reporter MH - Green Fluorescent Proteins/analysis/genetics MH - Ion Channel Gating/drug effects/*physiology MH - Mice MH - Mutation MH - Neuroblastoma/pathology MH - Peptide Fragments/chemical synthesis/chemistry/genetics/pharmacology MH - Protein Structure, Tertiary MH - Rats MH - Recombinant Fusion Proteins/chemistry MH - Structure-Activity Relationship MH - Transfection EDAT- 2004/07/31 05:00 MHDA- 2005/03/11 09:00 CRDT- 2004/07/31 05:00 PHST- 2004/07/29 [aheadofprint] AID - 10.1161/01.RES.0000140737.62245.c5 [doi] AID - 01.RES.0000140737.62245.c5 [pii] PST - ppublish SO - Circ Res. 2004 Aug 20;95(4):e22-8. Epub 2004 Jul 29. id: 218966563 Error occurred: The following PMID is not available: 218966563 PMID- 19260013 OWN - NLM STAT- MEDLINE DA - 20090310 DCOM- 20090904 IS - 1521-1878 (Electronic) IS - 0265-9247 (Linking) VI - 31 IP - 3 DP - 2009 Mar TI - Close encounters of the third kind: disordered domains and the interactions of proteins. PG - 328-35 LID - 10.1002/bies.200800151 [doi] AB - Protein-protein interactions are thought to be mediated by domains, which are autonomous folding units of proteins. Recently, a second type of interaction has been suggested, mediated by short segments termed linear motifs, which are related to recognition elements of intrinsically disordered regions. Here, we propose a third kind of protein-protein recognition mechanism, mediated by disordered regions longer than 20-30 residues. Bioinformatics predictions and well-characterized examples, such as the kinase-inhibitory domain of Cdk inhibitors and the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 of actin-binding proteins, show that these disordered regions conform to the definition of domains rather than motifs, i.e., they represent functional, evolutionary, and structural units. Their functions are distinct from those of short motifs and ordered domains, and establish a third kind of interaction principle. With these points, we argue that these long disordered regions should be recognized as a distinct class of biologically functional protein domains. FAU - Tompa, Peter AU - Tompa P AD - Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary. tompa@enzim.hu FAU - Fuxreiter, Monika AU - Fuxreiter M FAU - Oldfield, Christopher J AU - Oldfield CJ FAU - Simon, Istvan AU - Simon I FAU - Dunker, A Keith AU - Dunker AK FAU - Uversky, Vladimir N AU - Uversky VN LA - eng GR - 067595/Wellcome Trust/United Kingdom GR - R01 GM071714-01A2/GM/NIGMS NIH HHS/United States GR - R01 LM007688-01A1/LM/NLM NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Bioessays JT - BioEssays : news and reviews in molecular, cellular and developmental biology JID - 8510851 RN - 0 (Proteins) SB - IM MH - Adsorption MH - Amino Acid Motifs MH - Animals MH - Humans MH - Protein Binding MH - Protein Folding MH - Protein Structure, Tertiary MH - Proteins/*chemistry/*metabolism EDAT- 2009/03/05 09:00 MHDA- 2009/09/05 06:00 CRDT- 2009/03/05 09:00 AID - 10.1002/bies.200800151 [doi] PST - ppublish SO - Bioessays. 2009 Mar;31(3):328-35. doi: 10.1002/bies.200800151. PMID- 20209636 OWN - NLM STAT- MEDLINE DA - 20100421 DCOM- 20100713 LR - 20131121 IS - 1521-6551 (Electronic) IS - 1521-6543 (Linking) VI - 62 IP - 5 DP - 2010 May TI - Oligomeric alpha-synuclein and its role in neuronal death. PG - 334-9 LID - 10.1002/iub.316 [doi] AB - Alpha-synuclein is a natively unfolded protein associated with a number of neurodegenerative disorders that include Parkinson's disease. In the past, research has focused on the fibrillar form of the protein. Current research now indicates that oligomeric alpha-synuclein is the form of the protein most likely to causes neuronal death. Recent research has suggested that a unique oligomer associated with the copper binding capacity of the protein is the neurotoxic form of the protein. This review looks at the evidence for this possibility. FAU - Brown, David R AU - Brown DR AD - Department of Biology and Biochemistry, University of Bath, Bath, UK. bssdrb@bath.ac.uk LA - eng PT - Journal Article PT - Review PL - England TA - IUBMB Life JT - IUBMB life JID - 100888706 RN - 0 (alpha-Synuclein) RN - 789U1901C5 (Copper) RN - E1UOL152H7 (Iron) SB - IM MH - Animals MH - Copper/metabolism MH - Humans MH - Inclusion Bodies/metabolism MH - Iron/metabolism MH - Neurodegenerative Diseases/*etiology MH - Neurons/*pathology MH - Parkinson Disease/genetics/physiopathology MH - Protein Multimerization MH - alpha-Synuclein/metabolism/*toxicity RF - 52 EDAT- 2010/03/09 06:00 MHDA- 2010/07/14 06:00 CRDT- 2010/03/09 06:00 AID - 10.1002/iub.316 [doi] PST - ppublish SO - IUBMB Life. 2010 May;62(5):334-9. doi: 10.1002/iub.316. PMID- 11734201 OWN - NLM STAT- MEDLINE DA - 20011205 DCOM- 20020122 LR - 20121115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 509 IP - 1 DP - 2001 Nov 30 TI - Trimethylamine-N-oxide-induced folding of alpha-synuclein. PG - 31-5 AB - The effect of the natural osmolyte trimethylamine-N-oxide (TMAO) on the structural properties and fibril formation of the natively unfolded protein human alpha-synuclein was studied using several physico-chemical methods. TMAO induced folding of alpha-synuclein: at moderate concentrations, a partially folded intermediate with enhanced propensity for fibrillation accumulated; at higher concentrations, alpha-synuclein was tightly folded and underwent self-association to form oligomers. The latter conformation was significantly helical and probably represents the physiologically folded form of the protein. FAU - Uversky, V N AU - Uversky VN AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA. uversky@hydrogen.ucsc.edu FAU - Li, J AU - Li J FAU - Fink, A L AU - Fink AL LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Acrylamides) RN - 0 (Methylamines) RN - 0 (Nerve Tissue Proteins) RN - 0 (Oxidants) RN - 0 (Peptides) RN - 0 (Recombinant Proteins) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - FLD0K1SJ1A (trimethyloxamine) SB - IM MH - Acrylamides/pharmacology MH - Circular Dichroism MH - Dose-Response Relationship, Drug MH - Methylamines/*chemistry/pharmacology MH - Nerve Tissue Proteins/*chemistry/metabolism MH - Oxidants/*chemistry/pharmacology MH - Peptides/chemistry MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Recombinant Proteins/metabolism MH - Scattering, Radiation MH - Spectrometry, Fluorescence MH - Synucleins MH - Time Factors MH - X-Rays MH - alpha-Synuclein EDAT- 2001/12/06 10:00 MHDA- 2002/01/23 10:01 CRDT- 2001/12/06 10:00 AID - S0014-5793(01)03121-0 [pii] PST - ppublish SO - FEBS Lett. 2001 Nov 30;509(1):31-5. PMID- 12065587 OWN - NLM STAT- MEDLINE DA - 20020902 DCOM- 20021029 LR - 20081121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 277 IP - 36 DP - 2002 Sep 6 TI - The Saccharomyces cerevisiae nucleoporin Nup2p is a natively unfolded protein. PG - 33447-55 AB - Little is known about the structure of the individual nucleoporins that form eukaryotic nuclear pore complexes (NPCs). We report here in vitro physical and structural characterizations of a full-length nucleoporin, the Saccharomyces cerevisiae protein Nup2p. Analyses of the Nup2p structure by far-UV circular dichroism (CD) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, protease sensitivity, gel filtration, and sedimentation velocity experiments indicate that Nup2p is a "natively unfolded protein," belonging to a class of proteins that exhibit little secondary structure, high flexibility, and low compactness. Nup2p possesses a very large Stokes radius (79 A) in gel filtration columns, sediments slowly in sucrose gradients as a 2.9 S particle, and is highly sensitive to proteolytic digestion by proteinase K; these characteristics suggest a structure of low compactness and high flexibility. Spectral analyses (CD and FTIR spectroscopy) provide additional evidence that Nup2p contains extensive regions of structural disorder with comparatively small contributions of ordered secondary structure. We address the possible significance of natively unfolded nucleoporins in the mechanics of nucleocytoplasmic trafficking across NPCs. FAU - Denning, Daniel P AU - Denning DP AD - Department of Biological Sciences, Stanford University, Stanford, California 94305, USA. FAU - Uversky, Vladimir AU - Uversky V FAU - Patel, Samir S AU - Patel SS FAU - Fink, Anthony L AU - Fink AL FAU - Rexach, Michael AU - Rexach M LA - eng PT - Journal Article DEP - 20020613 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (NUP2 protein, S cerevisiae) RN - 0 (Nuclear Pore Complex Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 57-50-1 (Sucrose) RN - EC 3.4.21.64 (Endopeptidase K) SB - IM MH - Blotting, Western MH - Centrifugation, Density Gradient MH - Chromatography, Gel MH - Circular Dichroism MH - Cytoplasm/metabolism MH - Endopeptidase K/pharmacology MH - Hot Temperature MH - Nuclear Pore Complex Proteins/*metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Transport MH - Recombinant Proteins/metabolism MH - Saccharomyces cerevisiae/*metabolism MH - Saccharomyces cerevisiae Proteins/*metabolism MH - Spectroscopy, Fourier Transform Infrared MH - Sucrose/pharmacology MH - Time Factors MH - Ultraviolet Rays EDAT- 2002/06/18 10:00 MHDA- 2002/10/31 04:00 CRDT- 2002/06/18 10:00 PHST- 2002/06/13 [aheadofprint] AID - 10.1074/jbc.M203499200 [doi] AID - M203499200 [pii] PST - ppublish SO - J Biol Chem. 2002 Sep 6;277(36):33447-55. Epub 2002 Jun 13. PMID- 20192271 OWN - NLM STAT- MEDLINE DA - 20100330 DCOM- 20100520 LR - 20140914 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 13 DP - 2010 Apr 6 TI - Characterization of recombinant lysyl oxidase propeptide. PG - 2962-72 LID - 10.1021/bi902218p [doi] AB - Lysyl oxidase enzyme activity is critical for the biosynthesis of mature and functional collagens and elastin. In addition, lysyl oxidase has tumor suppressor activity that has been shown to depend on the propeptide region (LOX-PP) derived from pro-lysyl oxidase (Pro-LOX) and not on lysyl oxidase enzyme activity. Pro-LOX is secreted as a 50 kDa proenzyme and then undergoes biosynthetic proteolytic processing to active approximately 30 kDa LOX enzyme and LOX-PP. The present study reports the efficient recombinant expression and purification of rat LOX-PP. Moreover, using enzymatic deglycosylation and DTT derivatization combined with mass spectrometry technologies, it is shown for the first time that rLOX-PP and naturally occurring LOX-PP contain both N- and O-linked carbohydrates. Structure predictions furthermore suggest that LOX-PP is a mostly disordered protein, which was experimentally confirmed in circular dichroism studies. Due to its high isoelectric point and its disordered structure, we propose that LOX-PP can associate with extracellular and intracellular binding partners to affect its known biological activities as a tumor suppressor and inhibitor of cell proliferation. FAU - Vora, Siddharth R AU - Vora SR AD - Department of Periodontology and Oral Biology, Boston University Henry M. Goldman School of Dental Medicine, Boston, Massachusetts 02118, USA. FAU - Guo, Ying AU - Guo Y FAU - Stephens, Danielle N AU - Stephens DN FAU - Salih, Erdjan AU - Salih E FAU - Vu, Emile D AU - Vu ED FAU - Kirsch, Kathrin H AU - Kirsch KH FAU - Sonenshein, Gail E AU - Sonenshein GE FAU - Trackman, Philip C AU - Trackman PC LA - eng GR - CA82742/CA/NCI NIH HHS/United States GR - R01 CA082742/CA/NCI NIH HHS/United States GR - R01 CA082742-10/CA/NCI NIH HHS/United States GR - R01 DE014066/DE/NIDCR NIH HHS/United States GR - R01 DE014066-07/DE/NIDCR NIH HHS/United States GR - R01 DE14066/DE/NIDCR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Enzyme Precursors) RN - 0 (Recombinant Proteins) RN - EC 1.4.3.13 (Protein-Lysine 6-Oxidase) SB - IM MH - Animals MH - Circular Dichroism MH - Cloning, Molecular/methods MH - Enzyme Precursors MH - Glycosylation MH - Mass Spectrometry MH - Protein Binding MH - Protein Conformation MH - Protein-Lysine 6-Oxidase/*chemistry/genetics/isolation & purification MH - Rats MH - Recombinant Proteins PMC - PMC2847845 MID - NIHMS184746 OID - NLM: NIHMS184746 OID - NLM: PMC2847845 EDAT- 2010/03/03 06:00 MHDA- 2010/05/21 06:00 CRDT- 2010/03/03 06:00 AID - 10.1021/bi902218p [doi] PST - ppublish SO - Biochemistry. 2010 Apr 6;49(13):2962-72. doi: 10.1021/bi902218p. PMID- 20929244 OWN - NLM STAT- MEDLINE DA - 20101109 DCOM- 20101222 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 45 DP - 2010 Nov 16 TI - A natively unfolded betagamma-crystallin domain from Hahella chejuensis. PG - 9746-55 LID - 10.1021/bi101000m [doi] AB - To date, very few betagamma-crystallins have been identified and structurally characterized. Several of them have been shown to bind Ca(2+) and thereby enhance their stability without any significant change in structure. Although Ca(2+)-induced conformational changes have been reported in two putative betagamma-crystallins from Caulobacter crescentus and Yersinia pestis, they are shown to be partially unstructured, and whether they acquire a betagamma-crystallin fold is not known. We describe here a betagamma-crystallin domain, hahellin, its Ca(2+) binding properties and NMR structure. Unlike any other betagamma-crystallin, hahellin is characterized as a pre-molten globule (PMG) type of natively unfolded protein domain. It undergoes drastic conformational change and acquires a typical betagamma-crystallin fold upon Ca(2+) binding and hence acts as a Ca(2+)-regulated conformational switch. However, it does not bind Mg(2+). The intrinsically disordered Ca(2+)-free state and the close structural similarity of Ca(2+)-bound hahellin to a microbial betagamma-crystallin homologue, Protein S, which shows Ca(2+)-dependent stress response, make it a potential candidate for the cellular functions. This study indicates the presence of a new class of natively unfolded betagamma-crystallins and therefore the commencement of the possible functional roles of such proteins in this superfamily. FAU - Srivastava, Atul K AU - Srivastava AK AD - Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India. FAU - Sharma, Yogendra AU - Sharma Y FAU - Chary, Kandala V R AU - Chary KV LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101022 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Crystallins) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Calcium/metabolism/pharmacology MH - Calorimetry MH - Caulobacter/metabolism MH - Circular Dichroism MH - Crystallins/*chemistry/metabolism MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Conformation MH - Protein Denaturation MH - Protein Folding MH - Sequence Alignment MH - Yersinia pestis/metabolism EDAT- 2010/10/12 06:00 MHDA- 2010/12/24 06:00 CRDT- 2010/10/09 06:00 PHST- 2010/10/22 [aheadofprint] AID - 10.1021/bi101000m [doi] PST - ppublish SO - Biochemistry. 2010 Nov 16;49(45):9746-55. doi: 10.1021/bi101000m. Epub 2010 Oct 22. PMID- 24144701 OWN - NLM STAT- MEDLINE DA - 20131231 DCOM- 20140820 IS - 1477-9137 (Electronic) IS - 0021-9533 (Linking) VI - 127 IP - Pt 1 DP - 2014 Jan 1 TI - Entry into the nuclear pore complex is controlled by a cytoplasmic exclusion zone containing dynamic GLFG-repeat nucleoporin domains. PG - 124-36 LID - 10.1242/jcs.133272 [doi] AB - Nuclear pore complexes (NPCs) mediate nucleocytoplasmic movement. The central channel contains proteins with phenylalanine-glycine (FG) repeats, or variations (GLFG, glycine-leucine-phenylalanine-glycine). These are 'intrinsically disordered' and often represent weak interaction sites that become ordered upon interaction. We investigated this possibility during nuclear transport. Using electron microscopy of S. cerevisiae, we show that NPC cytoplasmic filaments form a dome-shaped structure enclosing GLFG domains. GLFG domains extend out of this structure and are part of an 'exclusion zone' that might act as a partial barrier to entry of transport-inert proteins. The anchor domain of a GLFG nucleoporin locates exclusively to the central channel. By contrast, the localisation of the GLFG domains varied between NPCs and could be cytoplasmic, central or nucleoplasmic and could stretch up to 80 nm. These results suggest a dynamic exchange between ordered and disordered states. In contrast to diffusion through the NPC, transport cargoes passed through the exclusion zone and accumulated near the central plane. We also show that movement of cargo through the NPC is accompanied by relocation of GLFG domains, suggesting that binding, restructuring and movement of these domains could be part of the translocation mechanism. FAU - Fiserova, Jindriska AU - Fiserova J AD - School of Biological and Biomedical Sciences, Durham University, Science Laboratories, South Road, Durham DH1 3LE, UK. FAU - Spink, Matthew AU - Spink M FAU - Richards, Shane A AU - Richards SA FAU - Saunter, Christopher AU - Saunter C FAU - Goldberg, Martin W AU - Goldberg MW LA - eng GR - BB/E015735/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - BB/G011818/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131021 PL - England TA - J Cell Sci JT - Journal of cell science JID - 0052457 RN - 0 (Nuclear Pore Complex Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) SB - IM MH - Active Transport, Cell Nucleus MH - Cell Nucleus/*metabolism/ultrastructure MH - Cytoplasm/*metabolism/ultrastructure MH - Microscopy, Electron MH - Nuclear Pore/*chemistry/metabolism MH - Nuclear Pore Complex Proteins/*chemistry/metabolism MH - Protein Structure, Tertiary MH - Protein Transport MH - Repetitive Sequences, Amino Acid MH - Saccharomyces cerevisiae/*metabolism/ultrastructure MH - Saccharomyces cerevisiae Proteins/*chemistry/metabolism OTO - NOTNLM OT - GLFG OT - Nuclear pore OT - Phenylalanine-glycine repeat OT - Transport EDAT- 2013/10/23 06:00 MHDA- 2014/08/21 06:00 CRDT- 2013/10/23 06:00 PHST- 2013/10/21 [aheadofprint] AID - jcs.133272 [pii] AID - 10.1242/jcs.133272 [doi] PST - ppublish SO - J Cell Sci. 2014 Jan 1;127(Pt 1):124-36. doi: 10.1242/jcs.133272. Epub 2013 Oct 21. PMID- 7649277 OWN - NLM STAT- MEDLINE DA - 19950922 DCOM- 19950922 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 369 IP - 2-3 DP - 1995 Aug 7 TI - 1H NMR spectroscopy reveals that mouse Hsp25 has a flexible C-terminal extension of 18 amino acids. PG - 305-10 AB - The small heat-shock proteins (Hsps) exist as large aggregates and function by interacting and stabilising non-native proteins in a chaperone-like manner. Two-dimensional 1H NMR spectroscopy of mouse Hsp25 reveals that the last 18 amino acids have great flexibility with motion that is essentially independent of the domain core of the protein. The lens protein, alpha-crystallin, is homologous to Hsp25 and its two subunits also have flexible C-terminal extensions. The flexible region in Hsp25 encompasses exactly that expected from sequence comparison with alpha-crystallin implying that both proteins have similar structures and that the C-terminal extensions could be of functional importance for both proteins. FAU - Carver, J A AU - Carver JA AD - Australian Cataract Research Foundation, Department of Chemistry, University of Wollongong, NSW, Australia. FAU - Esposito, G AU - Esposito G FAU - Schwedersky, G AU - Schwedersky G FAU - Gaestel, M AU - Gaestel M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Crystallins) RN - 0 (Heat-Shock Proteins) RN - 0 (Hspb1 protein, mouse) RN - 0 (Neoplasm Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Crystallins/chemistry MH - Heat-Shock Proteins/*chemistry MH - Magnetic Resonance Spectroscopy MH - Mice MH - Molecular Sequence Data MH - Neoplasm Proteins/*chemistry MH - *Protein Conformation MH - Sequence Homology, Amino Acid EDAT- 1995/08/07 MHDA- 1995/08/07 00:01 CRDT- 1995/08/07 00:00 AID - 0014-5793(95)00770-A [pii] PST - ppublish SO - FEBS Lett. 1995 Aug 7;369(2-3):305-10. PMID- 20450482 OWN - NLM STAT- MEDLINE DA - 20100726 DCOM- 20101019 LR - 20110331 IS - 1875-5305 (Electronic) IS - 0929-8665 (Linking) VI - 17 IP - 8 DP - 2010 Aug TI - Structural disorder in proteins of the rhabdoviridae replication complex. PG - 979-87 AB - Rhabdoviridae are single stranded negative sense RNA viruses. The viral RNA condensed by the nucleoprotein (N), the phosphoprotein (P) and the large subunit (L) of the RNA-dependent RNA polymerase are the viral components of the transcription/replication machineries. Both P and N contain intrinsically disordered regions (IDRs) that play different roles in the virus life cycle. Here, we describe the modular organization of P based on recent structural, biophysical and bioinformatics data. We show how flexible loops in N participate in the attachment of P to the N-RNA template by an induced-fit mechanism. Finally, we discuss the roles of IDRs in the mechanism of replication/transcription, and propose a new model for the interaction of the L subunit with its N-RNA template. FAU - Leyrat, Cedric AU - Leyrat C AD - Unit of Virus Host Cell Interactions, UMI 3265 UJF-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9, France. FAU - Gerard, Francine C A AU - Gerard FC FAU - de Almeida Ribeiro, Euripedes Jr AU - de Almeida Ribeiro E Jr FAU - Ivanov, Ivan AU - Ivanov I FAU - Ruigrok, Rob W H AU - Ruigrok RW FAU - Jamin, Marc AU - Jamin M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 RN - 0 (Nucleoproteins) RN - 0 (Phosphoproteins) SB - IM MH - Genome, Viral MH - Models, Molecular MH - Nucleoproteins/*chemistry MH - Phosphoproteins/*chemistry MH - Protein Structure, Tertiary MH - Rhabdoviridae/*chemistry/genetics/*physiology MH - Transcription, Genetic MH - *Virus Replication EDAT- 2010/05/11 06:00 MHDA- 2010/10/20 06:00 CRDT- 2010/05/11 06:00 PHST- 2009/12/10 [received] PHST- 2010/04/08 [accepted] AID - BSP/ PPL/ E pub/0159 [pii] PST - ppublish SO - Protein Pept Lett. 2010 Aug;17(8):979-87. PMID- 20450481 OWN - NLM STAT- MEDLINE DA - 20100726 DCOM- 20101019 LR - 20110331 IS - 1875-5305 (Electronic) IS - 0929-8665 (Linking) VI - 17 IP - 8 DP - 2010 Aug TI - Structural disorder within the measles virus nucleoprotein and phosphoprotein. PG - 961-78 AB - In this review, we summarize the main experimental data showing the abundance of structural disorder within the measles virus (MeV) nucleoprotein (N) and phosphoprotein (P), and focus on the molecular mechanisms governing the disorder-to-order transition of the intrinsically disordered C-terminal domain of MeV N (N(TAIL)) upon binding to the C-terminal X domain of P (XD). The functional implications of structural disorder are discussed in light of the ability of disordered regions to establish a complex molecular partnership, thereby leading to a variety of biological effects, including tethering of the polymerase complex onto the nucleocapsid template, stimulation of viral transcription and replication, and virus assembly. We also discuss the ability of N(TAIL) to establish interactions with additional cellular co-factors, including the major inducible heat shock protein, which can modulate the strength of the N(TAIL)-XD interaction. Taking into account the promiscuity that typifies disordered regions, we propose that the main functional advantage of the abundance of disorder within viruses would reside in pleiotropy and genetic compaction, where a single gene would encode a single (regulatory) protein product able to establish multiple interactions via its disordered regions, and hence to exert multiple concomitant biological effects. FAU - Longhi, Sonia AU - Longhi S AD - Architecture et Fonction des Macromolecules Biologiques, UMR 6098 CNRS et Universites d'Aix-Marseille I et II, 163, Avenue de Luminy, Case 932, 13288 Marseille Cedex 09, France. Sonia.Longhi@afmb.univ-mrs.fr FAU - Oglesbee, Michael AU - Oglesbee M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 RN - 0 (Nuclear Proteins) RN - 0 (Nucleoproteins) RN - 0 (Phosphoproteins) RN - 0 (Viral Proteins) RN - 0 (nucleoprotein, Measles virus) SB - IM MH - Animals MH - Humans MH - Measles virus/*chemistry/genetics/physiology MH - Nuclear Proteins/chemistry MH - Nucleoproteins/*chemistry MH - Phosphoproteins/*chemistry MH - Transcription, Genetic MH - Viral Proteins/*chemistry MH - Virus Replication EDAT- 2010/05/11 06:00 MHDA- 2010/10/20 06:00 CRDT- 2010/05/11 06:00 PHST- 2009/12/03 [received] PHST- 2010/04/08 [accepted] AID - BSP/ PPL/ E pub/0160 [pii] PST - ppublish SO - Protein Pept Lett. 2010 Aug;17(8):961-78. PMID- 20450486 OWN - NLM STAT- MEDLINE DA - 20100726 DCOM- 20101019 LR - 20110331 IS - 1875-5305 (Electronic) IS - 0929-8665 (Linking) VI - 17 IP - 8 DP - 2010 Aug TI - Structural disorder within sendai virus nucleoprotein and phosphoprotein: insight into the structural basis of molecular recognition. PG - 952-60 AB - Intrinsically disordered regions of significant length are present throughout eukaryotic genomes, and are particularly prevalent in viral proteins. Due to their inherent flexibility, these proteins inhabit a conformational landscape that is too complex to be described by classical structural biology. The elucidation of the role that conformational flexibility plays in molecular function will redefine our understanding of the molecular basis of biological function, and the development of appropriate technology to achieve this aim remains one of the major challenges for the future of structural biology. NMR is the technique of choice for studying intrinsically disordered proteins, providing information about structure, flexibility and interactions at atomic resolution even in completely disordered proteins. In particular residual dipolar couplings (RDCs) are sensitive and powerful tools for determining local and long-range structural behaviour in flexible proteins. Here we describe recent applications of the use of RDCs to quantitatively describe the level of local structure in intrinsically disordered proteins involved in replication and transcription in Sendai virus. FAU - Jensen, Malene Ringkjobing AU - Jensen MR AD - Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS-UJF, UMR 5075, 41 Rue Jules Horowitz, 38027 Grenoble, France. FAU - Bernado, Pau AU - Bernado P FAU - Houben, Klaartje AU - Houben K FAU - Blanchard, Laurence AU - Blanchard L FAU - Marion, Dominque AU - Marion D FAU - Ruigrok, Rob W H AU - Ruigrok RW FAU - Blackledge, Martin AU - Blackledge M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 RN - 0 (Nucleoproteins) RN - 0 (Phosphoproteins) SB - IM MH - Humans MH - Nucleoproteins/*chemistry/metabolism MH - Phosphoproteins/*chemistry/metabolism MH - Protein Binding MH - Protein Interaction Domains and Motifs MH - Sendai virus/*chemistry/metabolism EDAT- 2010/05/11 06:00 MHDA- 2010/10/20 06:00 CRDT- 2010/05/11 06:00 PHST- 2009/12/09 [received] PHST- 2010/04/08 [accepted] AID - BSP/ PPL/ E pub/0155 [pii] PST - ppublish SO - Protein Pept Lett. 2010 Aug;17(8):952-60. PMID- 20450485 OWN - NLM STAT- MEDLINE DA - 20100726 DCOM- 20101019 LR - 20110331 IS - 1875-5305 (Electronic) IS - 0929-8665 (Linking) VI - 17 IP - 8 DP - 2010 Aug TI - Structural disorder in the HIV-1 Vif protein and interaction-dependent gain of structure. PG - 988-98 AB - The HIV-1 Vif protein (192 residues) is required for HIV-1 infection of many target cells. Vif overcomes the anti-viral cellular defense by antagonizing the cellular cytosine deaminase APOBEC-3G through impairing APOBEC-3G production, inhibiting its enzymatic activity and targeting it for degradation. Vif interacts with several viral and cellular molecules, particularly via its C-terminal domain (residues 100-192). The structure of full-length Vif has not yet been determined. The structure of Vif and its domains was studied using computational and experimental methods. Computational predictions resulted in two suggested homology models for the full length protein. Experimental studies have shown that the Vif C-terminal domain is mainly unstructured. Residues 108-139 have mainly random coil conformation in the unbound state. This region includes an HCCH Zn(2+)-binding motif that also mediates Vif binding to Cul5, a protein in the E3 ubiquitin ligase complex. The C-terminal domain residues 141-192, which mediate interactions with both ElonginC and Cul5, are intrinsically disordered. This region also includes several phosphorylation sites and regions associated with the ability of Vif to undergo self-oligomerization. The unstructured nature of these regions enables them to interact with several ligands, and probably adopt various conformations as is typical for intrinsically disordered proteins. This was demonstrated by a conformational change induced by Zn(2+) binding to the HCCH motif and a conformational change that the C-terminal domain underwent in the presence of dodecylphosphocholine. The only available crystal structure of Vif includes residues 140-155, which are helical when bound to the ElonginBC complex. Overall, empirical structures, predictions and other experimental data for Vif did not always indicate the same degree or type of structure for any given region. This ambiguity is likely to be the tenet of structurally unfolded proteins, which have the propensity to adopt a multitude of biologically relevant and active conformations. FAU - Reingewertz, Tali H AU - Reingewertz TH AD - Institute of Chemistry, Hebrew University of Jerusalem, Safra Campus, Givat Ram, 91904 Jerusalem, Israel. FAU - Shalev, Deborah E AU - Shalev DE FAU - Friedler, Assaf AU - Friedler A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Review PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 RN - 0 (vif Gene Products, Human Immunodeficiency Virus) RN - 0 (vif protein, Human immunodeficiency virus 1) SB - IM MH - Animals MH - HIV-1/*chemistry/metabolism MH - Humans MH - Protein Binding MH - *Protein Interaction Domains and Motifs MH - Unfolded Protein Response MH - vif Gene Products, Human Immunodeficiency Virus/*chemistry/metabolism EDAT- 2010/05/11 06:00 MHDA- 2010/10/20 06:00 CRDT- 2010/05/11 06:00 PHST- 2010/01/03 [received] PHST- 2010/04/08 [accepted] AID - BSP/ PPL/ E pub/0156 [pii] PST - ppublish SO - Protein Pept Lett. 2010 Aug;17(8):988-98. PMID- 20450484 OWN - NLM STAT- MEDLINE DA - 20100726 DCOM- 20101019 LR - 20110331 IS - 1875-5305 (Electronic) IS - 0929-8665 (Linking) VI - 17 IP - 8 DP - 2010 Aug TI - The domain 2 of the HCV NS5A protein is intrinsically unstructured. PG - 1012-8 AB - We present here our current understanding of the NS5A-D2 domain of the hepatitis C virus. Whereas this protein domain is globally unstructured as assessed by macroscopic techniques such as size exclusion chromatography, circular dichroism and homonuclear NMR spectroscopy, high resolution triple resonance spectroscopy allows the identification of a small region of residual structure. This region corresponds moreover to the most conserved sequence over the different genotypes of the virus, underscoring its functional importance. We show that it forms an anchoring point for the host cell cyclophilin prolyl cis/trans isomerase, providing a molecular basis for the use of cyclophilin inhibitors in an antiviral strategy. FAU - Hanoulle, Xavier AU - Hanoulle X AD - Unite de glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, IFR 147, Universite Lille1 - Sciences et Technologies, 59655 Villeneuve d'Ascq, France. Xavier.hanoulle@univ-lille1.fr FAU - Badillo, Aurelie AU - Badillo A FAU - Verdegem, Dries AU - Verdegem D FAU - Penin, Francois AU - Penin F FAU - Lippens, Guy AU - Lippens G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 RN - 0 (Antiviral Agents) RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Viral Nonstructural Proteins) RN - EC 5.2.1.- (Cyclophilins) SB - IM MH - Antiviral Agents/chemistry MH - Cyclophilins/antagonists & inhibitors/metabolism MH - Hepacivirus/*chemistry/metabolism MH - Humans MH - Protein Binding MH - Protein Structure, Tertiary MH - Viral Nonstructural Proteins/*chemistry/metabolism EDAT- 2010/05/11 06:00 MHDA- 2010/10/20 06:00 CRDT- 2010/05/11 06:00 PHST- 2009/12/04 [received] PHST- 2010/04/08 [accepted] AID - BSP/ PPL/ E pub/0157 [pii] PST - ppublish SO - Protein Pept Lett. 2010 Aug;17(8):1012-8. PMID- 15327979 OWN - NLM STAT- MEDLINE DA - 20040825 DCOM- 20041008 LR - 20131121 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 573 IP - 1-3 DP - 2004 Aug 27 TI - Role of amino-acid residue 95 in substrate specificity of phosphagen kinases. PG - 78-82 AB - The purpose of this study is to elucidate the mechanisms of guanidine substrate specificity in phosphagen kinases, including creatine kinase (CK), glycocyamine kinase (GK), lombricine kinase (LK), taurocyamine kinase (TK) and arginine kinase (AK). Among these enzymes, LK is unique in that it shows considerable enzyme activity for taurocyamine in addition to its original target substrate, lombricine. We earlier proposed several candidate amino acids associated with guanidine substrate recognition. Here, we focus on amino-acid residue 95, which is strictly conserved in phosphagen kinases: Arg in CK, Ile in GK, Lys in LK and Tyr in AK. This residue is not directly associated with substrate binding in CK and AK crystal structures, but it is located close to the binding site of the guanidine substrate. We replaced amino acid 95 Lys in LK isolated from earthworm Eisenia foetida with two amino acids, Arg or Tyr, expressed the modified enzymes in Escherichia coli as a fusion protein with maltose-binding protein, and determined the kinetic parameters. The K95R mutant enzyme showed a stronger affinity for both lombricine (Km=0.74 mM and kcat/Km=19.34 s(-1) mM(-1)) and taurocyamine (Km=2.67 and kcat/Km=2.81), compared with those of the wild-type enzyme (Km=5.33 and kcat/Km=3.37 for lombricine, and Km=15.31 and kcat/ Km=0.48for taurocyamine). Enzyme activity of the other mutant, K95Y, was dramatically altered. The affinity for taurocyamine (Km=1.93 and kcat/Km=6.41) was enhanced remarkably and that for lombricine (Km=14.2 and kcat/Km=0.72) was largely decreased, indicating that this mutant functions as a taurocyamine kinase. This mutant also had a lower but significant enzyme activity for the substrate arginine (Km=33.28 and kcat/Km=0.01). These results suggest that Eisenia LK is an inherently flexible enzyme and that substrate specificity is strongly controlled by the amino-acid residue at position 95. FAU - Tanaka, Kumiko AU - Tanaka K AD - Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi 780-8520, Japan. FAU - Suzuki, Tomohiko AU - Suzuki T LA - eng PT - Journal Article PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (Amino Acids) RN - 0 (Recombinant Proteins) RN - 452VLY9402 (Serine) RN - 625-20-7 (lombricine) RN - EC 2.7.3.- (Phosphotransferases (Nitrogenous Group Acceptor)) RN - EC 2.7.3.2 (Creatine Kinase) RN - EC 2.7.3.3 (Arginine Kinase) RN - EC 2.7.3.4 (taurocyamine kinase) RN - EC 2.7.3.5 (lombricine kinase) RN - GO52O1A04E (glycocyamine) RN - TE7660XO1C (Glycine) SB - IM MH - Amino Acid Sequence MH - Amino Acid Substitution/genetics MH - Amino Acids/genetics/*metabolism MH - Animals MH - Arginine Kinase/chemistry/metabolism MH - Binding Sites MH - Creatine Kinase/chemistry/metabolism MH - Glycine/*analogs & derivatives/metabolism MH - Kinetics MH - Models, Molecular MH - Molecular Sequence Data MH - Oligochaeta/enzymology/genetics MH - Phosphotransferases (Nitrogenous Group Acceptor)/*chemistry/genetics/*metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Serine/*analogs & derivatives/metabolism MH - Structure-Activity Relationship MH - Substrate Specificity MH - Thermodynamics EDAT- 2004/08/26 05:00 MHDA- 2004/10/09 09:00 CRDT- 2004/08/26 05:00 PHST- 2004/06/16 [received] PHST- 2004/07/17 [revised] PHST- 2004/07/27 [accepted] AID - 10.1016/j.febslet.2004.07.061 [doi] AID - S0014579304009494 [pii] PST - ppublish SO - FEBS Lett. 2004 Aug 27;573(1-3):78-82. PMID- 9366272 OWN - NLM STAT- MEDLINE DA - 19971208 DCOM- 19971208 LR - 20131121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1342 IP - 1 DP - 1997 Sep 26 TI - A circular dichroism study of preferential hydration and alcohol effects on a denatured protein, pig calpastatin domain I. PG - 73-82 AB - Pig calpastatin domain I (CSD1), a proteinase inhibitor that specifically blocks activity of calpain I and II, is a good candidate protein for studying conformational variations in the denatured form of protein. An extensive structural characterization of CSD1 reported in the first part of this work has shown that CSD1 at neutral pH is in an expanded and flexible conformation without secondary and tertiary structures. Next, we further studied cosolvent effects of protein-stabilizers, polyols and sulfate salts, as well as protein-destabilizers, alcohols, on the conformation of CSD1 monitored by far- and near-UV CD spectroscopy. We found that both groups of cosolvents at high concentration induce highly helical structures of CSD1, but without specific tertiary interactions. Based on the results on the polyols and the sulfate salts, we have suggested that the preferential hydration is one of the thermodynamic forces to induce secondary structures in the denatured state of protein. Variations in isodichroic points of changes in far-UV CD spectrum as functions of cosolvent species and their concentration have exhibited complexity of the processes. The present study implies that protein stability in the presence of cosolvents is often determined by free energy difference between the folded and the highly structured denatured state, not between the folded and the random state. FAU - Konno, T AU - Konno T AD - National Institute for Physiological Science, Myodaiji, Japan. konno@nips.ac.jp FAU - Tanaka, N AU - Tanaka N FAU - Kataoka, M AU - Kataoka M FAU - Takano, E AU - Takano E FAU - Maki, M AU - Maki M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Apoproteins) RN - 0 (Calcium-Binding Proteins) RN - 0 (Cytochrome c Group) RN - 0 (Myoglobin) RN - 0 (Solvents) RN - 0 (apomyoglobin) RN - 506T60A25R (Sorbitol) RN - 75-89-8 (Trifluoroethanol) RN - 79079-11-1 (calpastatin) RN - PDC6A3C0OX (Glycerol) RN - Y4S76JWI15 (Methanol) SB - IM MH - Animals MH - Apoproteins/chemistry MH - Calcium-Binding Proteins/*chemistry MH - Circular Dichroism MH - Cytochrome c Group/chemistry MH - Glycerol MH - Hydrogen-Ion Concentration MH - Methanol MH - Myoglobin/chemistry MH - Nuclear Magnetic Resonance, Biomolecular MH - *Protein Conformation MH - Protein Denaturation MH - Solvents MH - Sorbitol MH - Swine MH - Trifluoroethanol MH - X-Ray Diffraction EDAT- 1997/11/20 MHDA- 1997/11/20 00:01 CRDT- 1997/11/20 00:00 AID - S0167-4838(97)00092-7 [pii] PST - ppublish SO - Biochim Biophys Acta. 1997 Sep 26;1342(1):73-82. PMID- 17176117 OWN - NLM STAT- MEDLINE DA - 20061219 DCOM- 20080111 LR - 20090723 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 45 IP - 51 DP - 2006 Dec 26 TI - Domain organization and quaternary structure of the Saccharomyces cerevisiae silent information regulator 3 protein, Sir3p. PG - 15941-8 AB - The silent information regulator protein 3 (Sir3p) functions in the initiation, propagation, and maintenance of transcriptionally silenced chromatin in Saccharomyces cerevisiae. To better understand the physicochemical basis for its effects on chromatin architecture, recombinant full-length S. cerevisiae Sir3p has been purified to near homogeneity on the large-scale and characterized by circular dichroism, limited protease digestion, and analytical ultracentrifugation. Results indicate that the Sir3p monomer has a unique tripartite domain organization, including a nearly 300-amino-acid residue stretch of intrinsically disordered residues that lies internal to its structured N- and C-terminal regions. Sir3p self-associates extensively in moderate salt and at micromolar protein concentrations producing a broad range of oligomers that sediment from 8 to in excess of 85 S. These results provide new insight into Sir3p domain organization and quaternary structure and support a nucleosome bridging model for Sir3p-dependent regulation of chromatin architecture. FAU - McBryant, Steven J AU - McBryant SJ AD - Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA. FAU - Krause, Christine AU - Krause C FAU - Hansen, Jeffrey C AU - Hansen JC LA - eng PT - Journal Article PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Chromatin) RN - 0 (Nucleosomes) RN - 0 (Recombinant Proteins) RN - 0 (SIR3 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Silent Information Regulator Proteins, Saccharomyces cerevisiae) SB - IM MH - Animals MH - Cells, Cultured MH - Chickens MH - Chromatin/chemistry/physiology MH - Nucleosomes/chemistry/physiology MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Saccharomyces cerevisiae Proteins/*chemistry/physiology MH - Silent Information Regulator Proteins, Saccharomyces cerevisiae/*chemistry/physiology MH - Spodoptera/genetics EDAT- 2006/12/21 09:00 MHDA- 2008/01/12 09:00 CRDT- 2006/12/21 09:00 AID - 10.1021/bi061693k [doi] PST - ppublish SO - Biochemistry. 2006 Dec 26;45(51):15941-8. PMID- 19099437 OWN - NLM STAT- MEDLINE DA - 20090109 DCOM- 20090317 LR - 20140916 IS - 1520-6106 (Print) IS - 1520-5207 (Linking) VI - 113 IP - 2 DP - 2009 Jan 15 TI - Synchronous vs asynchronous chain motion in alpha-synuclein contact dynamics. PG - 522-30 LID - 10.1021/jp806727e [doi] AB - alpha-Synuclein (alpha-syn) is an intrinsically unstructured 140-residue neuronal protein of uncertain function that is implicated in the etiology of Parkinson's disease. Tertiary contact formation rate constants in alpha-syn, determined from diffusion-limited electron-transfer kinetics measurements, are poorly approximated by simple random polymer theory. One source of the discrepancy between theory and experiment may be that interior-loop formation rates are not well approximated by end-to-end contact dynamics models. We have addressed this issue with Monte Carlo simulations to model asynchronous and synchronous motion of contacting sites in a random polymer. These simulations suggest that a dynamical drag effect may slow interior-loop formation rates by about a factor of 2 in comparison to end-to-end loops of comparable size. The additional deviations from random coil behavior in alpha-syn likely arise from clustering of hydrophobic residues in the disordered polypeptide. FAU - Urie, Kristopher G AU - Urie KG AD - Department of Chemistry, DePaul University, 243 South Wabash Ave, Chicago, Illinois 60604-2301, USA. FAU - Angulo, David AU - Angulo D FAU - Lee, Jennifer C AU - Lee JC FAU - Kozak, John J AU - Kozak JJ FAU - Gray, Harry B AU - Gray HB FAU - Winkler, Jay R AU - Winkler JR LA - eng GR - DK19038/DK/NIDDK NIH HHS/United States GR - GM068461/GM/NIGMS NIH HHS/United States GR - R01 GM068461/GM/NIGMS NIH HHS/United States GR - R01 GM068461-06/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural PT - Research Support, Non-U.S. Gov't PL - United States TA - J Phys Chem B JT - The journal of physical chemistry. B JID - 101157530 RN - 0 (Micelles) RN - 0 (alpha-Synuclein) SB - IM MH - Computer Simulation MH - Micelles MH - Models, Molecular MH - Monte Carlo Method MH - *Motion MH - Protein Structure, Tertiary MH - alpha-Synuclein/*chemistry PMC - PMC2743092 MID - NIHMS127854 OID - NLM: NIHMS127854 OID - NLM: PMC2743092 EDAT- 2008/12/23 09:00 MHDA- 2009/03/18 09:00 CRDT- 2008/12/23 09:00 AID - 10.1021/jp806727e [doi] AID - 10.1021/jp806727e [pii] PST - ppublish SO - J Phys Chem B. 2009 Jan 15;113(2):522-30. doi: 10.1021/jp806727e. PMID- 22294343 OWN - NLM STAT- MEDLINE DA - 20120320 DCOM- 20120718 LR - 20141019 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 21 IP - 4 DP - 2012 Apr TI - Coil-to-helix transitions in intrinsically disordered methyl CpG binding protein 2 and its isolated domains. PG - 531-8 LID - 10.1002/pro.2037 [doi] AB - Methyl CpG binding protein 2 (MeCP2) is a canonical intrinsically disordered protein (IDP), that is, it lacks stable secondary structure throughout its entire polypeptide chain. Because IDPs often have the propensity to become locally ordered, we tested whether full-length MeCP2 and its constituent domains would gain secondary structure in 2,2,2-trifluoroethanol (TFE), a cosolvent that stabilizes intramolecular hydrogen bonding in proteins. The alpha-helix, beta-strand/turn, and unstructured content were determined as a function of TFE concentration by deconvolution of circular dichroism data. Results indicate that approximately two-thirds of the unstructured residues present in full-length MeCP2 were converted to alpha-helix in 70% TFE without a change in beta-strand/turn. Thus, much of the MeCP2 polypeptide chain undergoes coil-to-helix transitions under conditions that favor intrachain hydrogen bond formation. The unstructured residues of the N-terminal (NTD) and C-terminal (CTD) domains were partially converted to alpha-helix in 70% TFE. In contrast, the central transcription regulation domain (TRD) became almost completely alpha-helical in 70% TFE. Unlike the NTD, CTD, and TRD, the unstructured content of the methyl DNA binding domain and the intervening domain did not change with increasing TFE concentration. These results indicate that the coil-to-helix transitions that occur in full-length MeCP2 are localized to the NTD, CTD, and TRD, with the TRD showing the greatest tendency for helix formation. The potential relationships between intrinsic disorder, coil-to-helix transitions, and MeCP2 structure and function are discussed. CI - Copyright (c) 2012 The Protein Society. FAU - Hite, Kristopher C AU - Hite KC AD - Department of Biochemistry and Molecular Biology, Campus Delivery 1870, Colorado State University, Fort Collins, Colorado 80523, USA. FAU - Kalashnikova, Anna A AU - Kalashnikova AA FAU - Hansen, Jeffrey C AU - Hansen JC LA - eng GR - GM68834/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20120309 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (DNA-Binding Proteins) RN - 0 (Histones) RN - 0 (Methyl-CpG-Binding Protein 2) RN - 0 (Solvents) RN - 75-89-8 (Trifluoroethanol) SB - IM MH - Animals MH - Chickens MH - DNA-Binding Proteins/*chemistry/isolation & purification MH - Dose-Response Relationship, Drug MH - Histones/chemistry MH - Humans MH - Hydrogen Bonding MH - Methyl-CpG-Binding Protein 2/*chemistry/isolation & purification MH - *Protein Folding MH - Protein Stability MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Solvents/chemistry MH - Structure-Activity Relationship MH - Trifluoroethanol/*chemistry/pharmacology PMC - PMC3375753 OID - NLM: PMC3375753 EDAT- 2012/02/02 06:00 MHDA- 2012/07/19 06:00 CRDT- 2012/02/02 06:00 PHST- 2011/11/10 [received] PHST- 2011/12/25 [revised] PHST- 2011/12/27 [accepted] PHST- 2012/03/09 [aheadofprint] AID - 10.1002/pro.2037 [doi] PST - ppublish SO - Protein Sci. 2012 Apr;21(4):531-8. doi: 10.1002/pro.2037. Epub 2012 Mar 9. PMID- 10794405 OWN - NLM STAT- MEDLINE DA - 20000614 DCOM- 20000614 LR - 20140615 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 9 IP - 4 DP - 2000 Apr TI - A helix-turn motif in the C-terminal domain of histone H1. PG - 627-36 AB - The structural study of peptides belonging to the terminal domains of histone H1 can be considered as a step toward the understanding of the function of H1 in chromatin. The conformational properties of the peptide Ac-EPKRSVAFKKTKKEVKKVATPKK (CH-1), which belongs to the C-terminal domain of histone H1(o) (residues 99-121) and is adjacent to the central globular domain of the protein, were examined by means of 1H-NMR and circular dichroism. In aqueous solution, CH-1 behaved as a mainly unstructured peptide, although turn-like conformations in rapid equilibrium with the unfolded state could be present. Addition of trifluoroethanol resulted in a substantial increase of the helical content. The helical limits, as indicated by (i,i + 3) nuclear Overhauser effect (NOE) cross correlations and significant up-field conformational shifts of the C(alpha) protons, span from Pro100 to Val116, with Glu99 and Ala117 as N- and C-caps. A structure calculation performed on the basis of distance constraints derived from NOE cross peaks in 90% trifluoroethanol confirmed the helical structure of this region. The helical region has a marked amphipathic character, due to the location of all positively charged residues on one face of the helix and all the hydrophobic residues on the opposite face. The peptide has a TPKK motif at the C-terminus, following the alpha-helical region. The observed NOE connectivities suggest that the TPKK sequence adopts a type (I) beta-turn conformation, a sigma-turn conformation or a combination of both, in fast equilibrium with unfolded states. Sequences of the kind (S/T)P(K/R)(K/R) have been proposed as DNA binding motifs. The CH-1 peptide, thus, combines a positively charged amphipathic helix and a turn as potential DNA-binding motifs. FAU - Vila, R AU - Vila R AD - Departamento de Bioquimica y Biologia Molecular, Facultad de Ciencias, Universidad Autonoma de Barcelona, Bellaterra, Spain. FAU - Ponte, I AU - Ponte I FAU - Jimenez, M A AU - Jimenez MA FAU - Rico, M AU - Rico M FAU - Suau, P AU - Suau P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Histones) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - *Helix-Turn-Helix Motifs MH - Histones/*chemistry MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Protein Conformation PMC - PMC2144612 OID - NLM: PMC2144612 EDAT- 2000/05/04 09:00 MHDA- 2000/06/17 09:00 CRDT- 2000/05/04 09:00 AID - 10.1110/ps.9.4.627 [doi] PST - ppublish SO - Protein Sci. 2000 Apr;9(4):627-36. PMID- 20969867 OWN - NLM STAT- MEDLINE DA - 20101115 DCOM- 20101220 LR - 20140912 IS - 1873-3468 (Electronic) IS - 0014-5793 (Linking) VI - 584 IP - 22 DP - 2010 Nov 19 TI - Leu628 of the KIX domain of CBP is a key residue for the interaction with the MLL transactivation domain. PG - 4500-4 LID - 10.1016/j.febslet.2010.10.024 [doi] AB - Physical interaction between the transactivation domain (TAD) of the mixed-lineage leukemia protein (MLL) and the KIX domain of the cyclic-AMP response element binding protein (CREB) binding protein (CBP) is necessary for MLL-mediated transcriptional activation. We show by alanine-scanning mutagenesis that hydrophobic surface residues of KIX, especially L628, are energetically important for binding the MLL TAD. NMR studies of the KIX-L628A mutant suggest that L628 plays a crucial role in conformational transitions at the MLL binding site, necessary for high affinity interactions with MLL. Unexpectedly, MLL also binds to the c-Myb/phosphorylated kinase-inducible domain of CREB (pKID) site of KIX, highlighting the complex nature of interactions involving intrinsically disordered transcriptional activators. CI - Copyright (c) 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. FAU - Arai, Munehito AU - Arai M AD - Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. FAU - Dyson, H Jane AU - Dyson HJ FAU - Wright, Peter E AU - Wright PE LA - eng GR - CA96865/CA/NCI NIH HHS/United States GR - R01 CA096865/CA/NCI NIH HHS/United States GR - R01 CA096865-10/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20101020 PL - Netherlands TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 149025-06-9 (Myeloid-Lymphoid Leukemia Protein) RN - EC 2.3.1.48 (CREB-Binding Protein) RN - GMW67QNF9C (Leucine) SB - IM MH - Animals MH - Binding Sites MH - CREB-Binding Protein/*chemistry/genetics/*metabolism MH - Humans MH - *Leucine MH - Mice MH - Models, Molecular MH - Mutagenesis MH - Mutation MH - Myeloid-Lymphoid Leukemia Protein/*chemistry/genetics/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Structure, Tertiary MH - *Transcriptional Activation PMC - PMC2993637 MID - NIHMS251300 OID - NLM: NIHMS251300 OID - NLM: PMC2993637 EDAT- 2010/10/26 06:00 MHDA- 2010/12/21 06:00 CRDT- 2010/10/26 06:00 PHST- 2010/09/07 [received] PHST- 2010/10/01 [accepted] PHST- 2010/10/20 [aheadofprint] AID - S0014-5793(10)00828-8 [pii] AID - 10.1016/j.febslet.2010.10.024 [doi] PST - ppublish SO - FEBS Lett. 2010 Nov 19;584(22):4500-4. doi: 10.1016/j.febslet.2010.10.024. Epub 2010 Oct 20. PMID- 11238886 OWN - NLM STAT- MEDLINE DA - 20010312 DCOM- 20010412 LR - 20140613 IS - 0270-7306 (Print) IS - 0270-7306 (Linking) VI - 21 IP - 5 DP - 2001 Mar TI - Insight into mammalian selenocysteine insertion: domain structure and ribosome binding properties of Sec insertion sequence binding protein 2. PG - 1491-8 AB - The cotranslational incorporation of the unusual amino acid selenocysteine (Sec) into both prokaryotic and eukaryotic proteins requires the recoding of a UGA stop codon as one specific for Sec. The recognition of UGA as Sec in mammalian selenoproteins requires a Sec insertion sequence (SECIS) element in the 3' untranslated region as well as the SECIS binding protein SBP2. Here we report a detailed analysis of SBP2 structure and function using truncation and site-directed mutagenesis. We have localized the RNA binding domain to a conserved region shared with several ribosomal proteins and eukaryotic translation termination release factor 1. We also identified a separate and novel functional domain N-terminal to the RNA binding domain which was required for Sec insertion but not for SECIS binding. Conversely, we showed that the RNA binding domain was necessary but not sufficient for Sec insertion and that the conserved glycine residue within this domain was required for SECIS binding. Using glycerol gradient sedimentation, we found that SBP2 was stably associated with the ribosomal fraction of cell lysates and that this interaction was not dependent on its SECIS binding activity. This interaction also occurred with purified components in vitro, and we present data which suggest that the SBP2-ribosome interaction occurs via 28S rRNA. SBP2 may, therefore, have a distinct function in selecting the ribosomes to be used for Sec insertion. FAU - Copeland, P R AU - Copeland PR AD - Department of Cell Biology, Cleveland Clinic Foundation, Lerner Research Institute, Cleveland, Ohio 44195, USA. FAU - Stepanik, V A AU - Stepanik VA FAU - Driscoll, D M AU - Driscoll DM LA - eng GR - F32 DK09878-01/DK/NIDDK NIH HHS/United States GR - HL29582/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (3' Untranslated Regions) RN - 0 (Codon, Terminator) RN - 0 (ETF1 protein, human) RN - 0 (Etf1 protein, rat) RN - 0 (Peptide Termination Factors) RN - 0 (RNA, Ribosomal, 28S) RN - 0 (RNA-Binding Proteins) RN - 0 (Recombinant Proteins) RN - 0 (SECISBP2 protein, human) RN - 0 (Secisbp2 protein, rat) RN - 0CH9049VIS (Selenocysteine) RN - 63231-63-0 (RNA) RN - PDC6A3C0OX (Glycerol) SB - IM MH - 3' Untranslated Regions MH - Amino Acid Sequence MH - Animals MH - Centrifugation, Density Gradient MH - Codon, Terminator MH - Electrophoresis, Polyacrylamide Gel MH - Glycerol/metabolism MH - Humans MH - Models, Genetic MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Peptide Termination Factors/metabolism MH - Point Mutation MH - Protein Binding MH - Protein Biosynthesis MH - Protein Structure, Tertiary MH - RNA/metabolism MH - RNA, Ribosomal, 28S/metabolism MH - RNA-Binding Proteins/*chemistry/*genetics/physiology MH - Rats MH - Recombinant Proteins/metabolism MH - Ribosomes/*metabolism MH - Selenocysteine/*chemistry/*genetics MH - Sequence Homology, Amino Acid MH - Tumor Cells, Cultured PMC - PMC86695 OID - NLM: PMC86695 EDAT- 2001/03/10 10:00 MHDA- 2001/04/17 10:01 CRDT- 2001/03/10 10:00 AID - 10.1128/MCB.21.5.1491-1498.2001 [doi] PST - ppublish SO - Mol Cell Biol. 2001 Mar;21(5):1491-8. PMID- 9108480 OWN - NLM STAT- MEDLINE DA - 19970515 DCOM- 19970515 LR - 20131121 IS - 0092-8674 (Print) IS - 0092-8674 (Linking) VI - 89 IP - 2 DP - 1997 Apr 18 TI - Structure of RGS4 bound to AlF4--activated G(i alpha1): stabilization of the transition state for GTP hydrolysis. PG - 251-61 AB - RGS proteins are GTPase activators for heterotrimeric G proteins. We report here the 2.8 A resolution crystal structure of the RGS protein RGS4 complexed with G(i alpha1)-Mg2+-GDP-AlF4 . Only the core domain of RGS4 is visible in the crystal. The core domain binds to the three switch regions of G(i alpha1), but does not contribute catalytic residues that directly interact with either GDP or AlF4-. Therefore, RGS4 appears to catalyze rapid hydrolysis of GTP primarily by stabilizing the switch regions of G(i alpha1), although the conserved Asn-128 from RGS4 could also play a catalytic role by interacting with the hydrolytic water molecule or the side chain of Gln-204. The binding site for RGS4 on G(i alpha1) is also consistent with the activity of RGS proteins as antagonists of G(alpha) effectors. FAU - Tesmer, J J AU - Tesmer JJ AD - Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235, USA. FAU - Berman, D M AU - Berman DM FAU - Gilman, A G AU - Gilman AG FAU - Sprang, S R AU - Sprang SR LA - eng GR - DK46371/DK/NIDDK NIH HHS/United States GR - GM07062/GM/NIGMS NIH HHS/United States GR - GM34497/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Cell JT - Cell JID - 0413066 RN - 0 (Aluminum Compounds) RN - 0 (Proteins) RN - 0 (RGS Proteins) RN - 146-91-8 (Guanosine Diphosphate) RN - 175335-35-0 (RGS4 protein) RN - 21340-02-3 (tetrafluoroaluminate) RN - 86-01-1 (Guanosine Triphosphate) RN - EC 3.6.1.- (GTP Phosphohydrolases) RN - EC 3.6.5.1 (GTP-Binding Protein alpha Subunits, Gi-Go) RN - I38ZP9992A (Magnesium) RN - Q80VPU408O (Fluorides) SB - IM MH - Aluminum Compounds/chemistry MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Crystallography, X-Ray MH - Fluorides/chemistry MH - GTP Phosphohydrolases/metabolism MH - GTP-Binding Protein alpha Subunits, Gi-Go/*chemistry/metabolism MH - Guanosine Diphosphate/chemistry MH - Guanosine Triphosphate/*metabolism MH - Hydrolysis MH - Magnesium/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - *Protein Conformation MH - Proteins/*chemistry/metabolism MH - *RGS Proteins MH - Rats EDAT- 1997/04/18 MHDA- 1997/04/18 00:01 CRDT- 1997/04/18 00:00 AID - S0092-8674(00)80204-4 [pii] PST - ppublish SO - Cell. 1997 Apr 18;89(2):251-61. PMID- 22493266 OWN - NLM STAT- MEDLINE DA - 20120425 DCOM- 20120709 LR - 20141016 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 109 IP - 17 DP - 2012 Apr 24 TI - The E. coli CsgB nucleator of curli assembles to beta-sheet oligomers that alter the CsgA fibrillization mechanism. PG - 6502-7 LID - 10.1073/pnas.1204161109 [doi] AB - Curli are extracellular proteinaceous functional amyloid aggregates produced by Escherichia coli, Salmonella spp., and other enteric bacteria. Curli mediate host cell adhesion and invasion and play a critical role in biofilm formation. Curli filaments consist of CsgA, the major subunit, and CsgB, the minor subunit. In vitro, purified CsgA and CsgB exhibit intrinsically disordered properties, and both are capable of forming amyloid fibers similar in morphology to those formed in vivo. However, in vivo, CsgA alone cannot form curli fibers, and CsgB is required for filament growth. Thus, we studied the aggregation of CsgA and CsgB both alone and together in vitro to investigate the different roles of CsgA and CsgB in curli formation. We found that though CsgA and CsgB individually are able to self-associate to form aggregates/fibrils, they do so using different mechanisms and with different kinetic behavior. CsgB rapidly forms structured oligomers, whereas CsgA aggregation is slower and appears to proceed through large amorphous aggregates before forming filaments. Substoichiometric concentrations of CsgB induce a change in the mechanism of CsgA aggregation from that of forming amorphous aggregates to that of structured intermediates similar to those of CsgB alone. Oligomeric CsgB accelerated the aggregation of CsgA, in contrast to monomeric CsgB, which had no effect. The structured beta-strand oligomers formed by CsgB serve as nucleators for CsgA aggregation. These results provide insights into the formation of curli in vivo, especially the nucleator function of CsgB. FAU - Shu, Qin AU - Shu Q AD - Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA. FAU - Crick, Scott L AU - Crick SL FAU - Pinkner, Jerome S AU - Pinkner JS FAU - Ford, Bradley AU - Ford B FAU - Hultgren, Scott J AU - Hultgren SJ FAU - Frieden, Carl AU - Frieden C LA - eng GR - AI48689/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20120409 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Biopolymers) RN - 0 (CsgB protein, E coli) RN - 0 (Escherichia coli Proteins) SB - IM MH - Biopolymers/chemistry/*metabolism MH - Circular Dichroism MH - Escherichia coli/*metabolism MH - Escherichia coli Proteins/chemistry/*metabolism MH - Fluorescence MH - Kinetics MH - Microscopy, Atomic Force MH - Protein Conformation MH - Spectrometry, Fluorescence MH - Spectrophotometry, Ultraviolet PMC - PMC3340089 OID - NLM: PMC3340089 EDAT- 2012/04/12 06:00 MHDA- 2012/07/10 06:00 CRDT- 2012/04/12 06:00 PHST- 2012/04/09 [aheadofprint] AID - 1204161109 [pii] AID - 10.1073/pnas.1204161109 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6502-7. doi: 10.1073/pnas.1204161109. Epub 2012 Apr 9. PMID- 23618134 OWN - NLM STAT- MEDLINE DA - 20130426 DCOM- 20131112 IS - 1873-3573 (Electronic) IS - 0039-9140 (Linking) VI - 109 DP - 2013 May 15 TI - Coupled solid phase extraction and microparticle-based stability and purity-indicating immunosensor for the determination of recombinant human myelin basic protein in transgenic milk. PG - 7-12 LID - 10.1016/j.talanta.2013.03.043 [doi] LID - S0039-9140(13)00192-6 [pii] AB - An optical immunosensor was developed and validated on the surface of microparticles for the determination of a biopharmaceutical protein. The recombinant human myelin basic protein (rhMBP) was produced in milk of transgenic cows as a His-tagged fusion protein. Previous work indicated exclusive association of rhMBP with milk casein micelles that hindered direct determination of the protein in milk. In this work, a solid phase extraction using a cation exchange matrix was developed in order to liberate rhMBP from casein micelles. A sandwich-type immunoassay was then used for in-process monitoring of the full-length protein in the presence of major milk proteins. The assay was successfully employed for detection of ultra-traces of rhMBP (LOD=6.04 ng mL(-1) approximately 0.3 n mol L(-1)) and for quantitative determination over a wide concentration range (10.00-10,000.00 ng mL(-1)). The assay was able also to detect the rhMBP in the presence of its human counterpart that lacks the His-tag. The high sensitivity along with the ability of the assay to determine the full length protein enabled monitoring of the stability of rhMBP. The testing protocol is particularly useful for intrinsically unstructured proteins that are extremely sensitive to proteolysis and lack a traceable enzymatic activity. This immunosensor provides a specific, ultrasensitive high throughput tool for in-process monitoring in biopharmaceutical industry. CI - Copyright (c) 2013 Elsevier B.V. All rights reserved. FAU - Al-Ghobashy, Medhat A AU - Al-Ghobashy MA AD - Analytical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt. medhat.alghobashy@cu.edu.eg FAU - Williams, Martin A K AU - Williams MA FAU - Laible, Gotz AU - Laible G FAU - Harding, David R K AU - Harding DR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130322 PL - Netherlands TA - Talanta JT - Talanta JID - 2984816R RN - 0 (MBP protein, human) RN - 0 (Milk Proteins) RN - 0 (Myelin Basic Protein) RN - 0 (Recombinant Fusion Proteins) SB - IM MH - Animals MH - *Animals, Genetically Modified MH - Biopharmaceutics/instrumentation/methods MH - Biosensing Techniques/instrumentation/*methods MH - Cattle MH - High-Throughput Screening Assays MH - Humans MH - Microspheres MH - Milk/*chemistry MH - Milk Proteins/chemistry MH - Myelin Basic Protein/*analysis MH - Protein Conformation MH - Protein Stability MH - Recombinant Fusion Proteins/*analysis MH - Reference Standards MH - Solid Phase Extraction/instrumentation/*methods EDAT- 2013/04/27 06:00 MHDA- 2013/11/13 06:00 CRDT- 2013/04/27 06:00 PHST- 2013/02/02 [received] PHST- 2013/03/14 [revised] PHST- 2013/03/16 [accepted] PHST- 2013/03/22 [aheadofprint] AID - S0039-9140(13)00192-6 [pii] AID - 10.1016/j.talanta.2013.03.043 [doi] PST - ppublish SO - Talanta. 2013 May 15;109:7-12. doi: 10.1016/j.talanta.2013.03.043. Epub 2013 Mar 22. PMID- 2339072 OWN - NLM STAT- MEDLINE DA - 19900615 DCOM- 19900615 LR - 20131002 IS - 0305-1048 (Print) IS - 0305-1048 (Linking) VI - 18 IP - 9 DP - 1990 May 11 TI - Sequence of EMB-1, an mRNA accumulating specifically in embryos of carrot. PG - 2826 FAU - Ulrich, T U AU - Ulrich TU AD - Department of Botany, Iowa State University, Ames 50011. FAU - Wurtele, E S AU - Wurtele ES FAU - Nikolau, B J AU - Nikolau BJ LA - eng SI - GENBANK/X17608 PT - Journal Article PL - ENGLAND TA - Nucleic Acids Res JT - Nucleic acids research JID - 0411011 RN - 0 (RNA, Messenger) SB - IM MH - Base Sequence MH - Molecular Sequence Data MH - Plant Development MH - Plants/*genetics MH - RNA, Messenger/*genetics PMC - PMC330784 OID - NLM: PMC330784 EDAT- 1990/05/11 MHDA- 1990/05/11 00:01 CRDT- 1990/05/11 00:00 PST - ppublish SO - Nucleic Acids Res. 1990 May 11;18(9):2826. PMID- 12428728 OWN - NLM STAT- MEDLINE DA - 20021113 DCOM- 20021216 LR - 20071114 IS - 0161-813X (Print) IS - 0161-813X (Linking) VI - 23 IP - 4-5 DP - 2002 Oct TI - Conformational behavior of human alpha-synuclein is modulated by familial Parkinson's disease point mutations A30P and A53T. PG - 553-67 AB - Structural properties and response to changes in the environment of wild-type (WT), A30P and A53T alpha-synucleins, as well as their propensity to aggregate orform fibrils, were compared by a variety of biophysical methods, including far-UV CD, FTIR, SAXS, static light scattering and Thioflavin T (TFT) fluorescence. All three proteins were natively unfolded under physiological conditions but adopted identical partially-folded conformations under conditions of acidic pH or high temperature. The initial kinetic event in the fibrillation of all three alpha-synucleins was shown to be the formation of a partially-folded intermediate with properties close to those described for these proteins at acidic pH or at high temperatures. Both mutants showed a greater propensity to form non-fibrillar aggregates than wild-type protein. All three proteins formed fibrils faster in the presence of heparin, although substantially higher concentrations were required for the A30P mutant. In contrast to the wild-type and A53T proteins, in which fibrillation was further accelerated by the presence of the pesticide diethyldithiocarbamate (DDC), the A30P mutant was inhibited by DDC. The mutant proteins had significantly lower affinity for DDC than the WT. A model of the effect of mutations on the aggregation behavior of alpha-synuclein is proposed, which explains the different effects of exogenous agents on the three proteins, based on different kinetic partitioning along pathways leading to fibrils and to non-fibrillar aggregates. FAU - Li, Jie AU - Li J AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA. FAU - Uversky, Vladimir N AU - Uversky VN FAU - Fink, Anthony L AU - Fink AL LA - eng GR - NS39985/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - Netherlands TA - Neurotoxicology JT - Neurotoxicology JID - 7905589 RN - 0 (Indicators and Reagents) RN - 0 (Nerve Tissue Proteins) RN - 0 (Pesticides) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) SB - IM MH - Algorithms MH - Circular Dichroism MH - Humans MH - Indicators and Reagents MH - Kinetics MH - Nerve Tissue Proteins/*chemistry/isolation & purification MH - Parkinson Disease/*genetics/*metabolism MH - Pesticides/chemistry MH - Point Mutation/*genetics MH - Protein Conformation MH - Protein Folding MH - Scattering, Radiation MH - Spectrometry, Fluorescence MH - Spectroscopy, Fourier Transform Infrared MH - Synucleins MH - X-Rays MH - alpha-Synuclein EDAT- 2002/11/14 04:00 MHDA- 2002/12/18 04:00 CRDT- 2002/11/14 04:00 AID - S0161-813X(02)00066-9 [pii] PST - ppublish SO - Neurotoxicology. 2002 Oct;23(4-5):553-67. PMID- 23352839 OWN - NLM STAT- MEDLINE DA - 20130304 DCOM- 20130617 LR - 20141103 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1834 IP - 4 DP - 2013 Apr TI - FlgM proteins from different bacteria exhibit different structural characteristics. PG - 808-16 LID - 10.1016/j.bbapap.2013.01.010 [doi] LID - S1570-9639(13)00021-6 [pii] AB - Intrinsically disordered proteins (IDPs) are a unique class of proteins that do not require a stable structure for function. The importance of IDPs in many biological processes has been established but there remain unanswered questions about their evolution and conservation of their disordered state within a protein family. Our group has been studying the structural similarities among orthologous FlgM proteins, a model class of IDPs. We have previously shown that the FlgM protein from the thermophile Aquifex aeolicus has more structure at A. aeolicus' physiological temperature (85 degrees C) than is observed for the Salmonella typhimurium FlgM, suggesting that the disordered nature of FlgM varies among organisms and is not universally conserved. In this work, we extend these studies to the FlgM proteins from Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis, and Bacillus subtilis. We demonstrate that the B. subtilis, E. coli, and S. typhimurium FlgMs exist in a premolten globule-like conformation, though the B. subtilis FlgM is in a more compacted conformation than the other two. The P. aeruginosa and P. mirabilis FlgM proteins exist in a currently unknown conformation that is not either coil-like or premolten globule-like. The P. aeruginosa FlgM appears to contain more weak intramolecular contacts given its more compacted state than the P. mirabilis FlgM. These results provide experimental evidence that members of the same protein family can exhibit different degrees of disorder, though understanding how different disordered states evolve in the same protein family will require more study. CI - Copyright (c) 2013 Elsevier B.V. All rights reserved. FAU - Ma, Wai Kit AU - Ma WK AD - Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ 86011, USA. FAU - Hendrix, Rachel AU - Hendrix R FAU - Stewart, Claire AU - Stewart C FAU - Campbell, Eric V AU - Campbell EV FAU - Lavarias, Mitchell AU - Lavarias M FAU - Morris, Kolyn AU - Morris K FAU - Nichol, Shauna AU - Nichol S FAU - Gage, Matthew J AU - Gage MJ LA - eng GR - 5U54CA096320-05/CA/NCI NIH HHS/United States GR - U54 CA096320/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20130122 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Bacterial Proteins) RN - 142462-45-1 (FlgM protein, Bacteria) SB - IM MH - Amino Acid Sequence MH - Bacillus subtilis/chemistry/genetics MH - *Bacterial Proteins/chemistry/metabolism MH - Escherichia coli/chemistry/genetics MH - Molecular Sequence Data MH - Promoter Regions, Genetic MH - *Protein Stability MH - Pseudomonas aeruginosa/chemistry MH - *Salmonella typhimurium/chemistry/genetics PMC - PMC3650836 MID - NIHMS438404 OID - NLM: NIHMS438404 OID - NLM: PMC3650836 EDAT- 2013/01/29 06:00 MHDA- 2013/06/19 06:00 CRDT- 2013/01/29 06:00 PHST- 2012/09/04 [received] PHST- 2013/01/09 [revised] PHST- 2013/01/14 [accepted] PHST- 2013/01/22 [aheadofprint] AID - S1570-9639(13)00021-6 [pii] AID - 10.1016/j.bbapap.2013.01.010 [doi] PST - ppublish SO - Biochim Biophys Acta. 2013 Apr;1834(4):808-16. doi: 10.1016/j.bbapap.2013.01.010. Epub 2013 Jan 22. PMID- 23352836 OWN - NLM STAT- MEDLINE DA - 20130304 DCOM- 20130617 LR - 20141103 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1834 IP - 4 DP - 2013 Apr TI - Intrinsically disordered regions of p53 family are highly diversified in evolution. PG - 725-38 LID - 10.1016/j.bbapap.2013.01.012 [doi] LID - S1570-9639(13)00023-X [pii] AB - Proteins of the p53 family are expressed in vertebrates and in some invertebrate species. The main function of these proteins is to control and regulate cell cycle in response to various cellular signals, and therefore to control the organism's development. The regulatory functions of the p53 family members originate mostly from their highly-conserved and well-structured DNA-binding domains. Many human diseases (including various types of cancer) are related to the missense mutations within this domain. The ordered DNA-binding domains of the p53 family members are surrounded by functionally important intrinsically disordered regions. In this study, substitution rates and propensities in different regions of p53 were analyzed. The analyses revealed that the ordered DNA-binding domain is conserved, whereas disordered regions are characterized by high sequence diversity. This diversity was reflected both in the number of substitutions and in the types of substitutions to which each amino acid was prone. These results support the existence of a positive correlation between protein intrinsic disorder and sequence divergence during the evolutionary process. This higher sequence divergence provides strong support for the existence of disordered regions in p53 in vivo for if they were structured, they would evolve at similar rates as the rest of the protein. CI - Copyright (c) 2013 Elsevier B.V. All rights reserved. FAU - Xue, Bin AU - Xue B AD - Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA. FAU - Brown, Celeste J AU - Brown CJ FAU - Dunker, A Keith AU - Dunker AK FAU - Uversky, Vladimir N AU - Uversky VN LA - eng GR - 5P20RR16448/RR/NCRR NIH HHS/United States GR - 8P20GM103397/GM/NIGMS NIH HHS/United States GR - P20 RR016448/RR/NCRR NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20130122 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (DNA-Binding Proteins) RN - 0 (TP53 protein, human) RN - 0 (Tumor Suppressor Protein p53) SB - IM MH - Amino Acid Sequence MH - Animals MH - Cell Cycle Checkpoints MH - Conserved Sequence/*genetics MH - DNA-Binding Proteins/genetics MH - Databases, Protein MH - *Evolution, Molecular MH - Genetic Variation MH - Humans MH - Molecular Sequence Data MH - Mutation, Missense/genetics MH - Protein Conformation MH - Protein Structure, Tertiary/*genetics MH - *Tumor Suppressor Protein p53/genetics/metabolism PMC - PMC3905691 MID - NIHMS448158 OID - NLM: NIHMS448158 OID - NLM: PMC3905691 EDAT- 2013/01/29 06:00 MHDA- 2013/06/19 06:00 CRDT- 2013/01/29 06:00 PHST- 2012/11/28 [received] PHST- 2012/12/28 [revised] PHST- 2013/01/11 [accepted] PHST- 2013/01/22 [aheadofprint] AID - S1570-9639(13)00023-X [pii] AID - 10.1016/j.bbapap.2013.01.012 [doi] PST - ppublish SO - Biochim Biophys Acta. 2013 Apr;1834(4):725-38. doi: 10.1016/j.bbapap.2013.01.012. Epub 2013 Jan 22. PMID- 15925383 OWN - NLM STAT- MEDLINE DA - 20050614 DCOM- 20050727 LR - 20101118 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 350 IP - 2 DP - 2005 Jul 8 TI - Prediction of "aggregation-prone" and "aggregation-susceptible" regions in proteins associated with neurodegenerative diseases. PG - 379-92 AB - Increasing evidence indicates that many peptides and proteins can be converted in vitro into highly organised amyloid structures, provided that the appropriate experimental conditions can be found. In this work, we define intrinsic propensities for the aggregation of individual amino acids and develop a method for identifying the regions of the sequence of an unfolded peptide or protein that are most important for promoting amyloid formation. This method is applied to the study of three polypeptides associated with neurodegenerative diseases, Abeta42, alpha-synuclein and tau. In order to validate the approach, we compare the regions of proteins that are predicted to be most important in driving aggregation, either intrinsically or as the result of mutations, with those determined experimentally. The knowledge of the location and the type of the "sensitive regions" for aggregation is important both for rationalising the effects of sequence changes on the aggregation of polypeptide chains and for the development of targeted strategies to combat diseases associated with amyloid formation. FAU - Pawar, Amol P AU - Pawar AP AD - Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. FAU - Dubay, Kateri F AU - Dubay KF FAU - Zurdo, Jesus AU - Zurdo J FAU - Chiti, Fabrizio AU - Chiti F FAU - Vendruscolo, Michele AU - Vendruscolo M FAU - Dobson, Christopher M AU - Dobson CM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amyloid beta-Peptides) RN - 0 (Nerve Tissue Proteins) RN - 0 (Peptide Fragments) RN - 0 (Peptides) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 0 (amyloid beta-protein (1-42)) RN - 0 (tau Proteins) SB - IM MH - Amino Acid Substitution/genetics MH - Amyloid beta-Peptides/*chemistry/genetics/metabolism MH - Amyloidosis/*metabolism MH - Hydrogen-Ion Concentration MH - Hydrophobic and Hydrophilic Interactions MH - Nerve Tissue Proteins/*chemistry/metabolism MH - Neurodegenerative Diseases/*metabolism MH - Peptide Fragments/*chemistry/genetics/metabolism MH - Peptides/chemistry/genetics/metabolism MH - Protein Binding MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Synucleins MH - alpha-Synuclein MH - tau Proteins/*chemistry/genetics/metabolism EDAT- 2005/06/01 09:00 MHDA- 2005/07/28 09:00 CRDT- 2005/06/01 09:00 PHST- 2005/02/10 [received] PHST- 2005/04/11 [revised] PHST- 2005/04/11 [accepted] AID - S0022-2836(05)00426-2 [pii] AID - 10.1016/j.jmb.2005.04.016 [doi] PST - ppublish SO - J Mol Biol. 2005 Jul 8;350(2):379-92. PMID- 16981679 OWN - NLM STAT- MEDLINE DA - 20060919 DCOM- 20070517 IS - 0001-4842 (Print) IS - 0001-4842 (Linking) VI - 39 IP - 9 DP - 2006 Sep TI - The aggregation and fibrillation of alpha-synuclein. PG - 628-34 AB - alpha-Synuclein is a small (14 kDa), abundant, intrinsically disordered presynaptic protein, whose aggregation is believed to be a critical step in Parkinson's disease (PD). The kinetics of alpha-synuclein fibrillation are consistent with a nucleation-dependent mechanism, in which the critical early stage of the structural transformation involves a partially folded intermediate. Although the basis for the toxic effects of aggregated alpha-synuclein are unknown, it has been proposed that transient oligomers are responsible, possibly by forming pores in membranes. In this Account, I discuss our investigations into the molecular basis for alpha-synuclein aggregation/fibrillation, including factors that either accelerate or inhibit fibrillation, effects of molecular crowding, oxidation, point mutations, and lipid membranes, as well as the variety of conformational and oligomeric states that alpha-synuclein can adopt. It is apparent that neuronal cells must have a very fine balance of factors that control the levels and potential aggregation of alpha-synuclein. FAU - Fink, Anthony L AU - Fink AL AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA. enzyme@cats.ucsc.edu LA - eng PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review PL - United States TA - Acc Chem Res JT - Accounts of chemical research JID - 0157313 RN - 0 (Biopolymers) RN - 0 (alpha-Synuclein) SB - IM MH - Biopolymers/chemistry MH - Humans MH - Kinetics MH - Microscopy, Atomic Force MH - Oxidation-Reduction MH - Parkinson Disease/metabolism MH - Protein Conformation MH - alpha-Synuclein/*chemistry RF - 70 EDAT- 2006/09/20 09:00 MHDA- 2007/05/18 09:00 CRDT- 2006/09/20 09:00 AID - 10.1021/ar050073t [doi] PST - ppublish SO - Acc Chem Res. 2006 Sep;39(9):628-34. PMID- 24945760 OWN - NLM STAT- MEDLINE DA - 20140620 DCOM- 20140812 IS - 1097-4199 (Electronic) IS - 0896-6273 (Linking) VI - 82 IP - 6 DP - 2014 Jun 18 TI - Tau propagation, different tau phenotypes, and prion-like properties of tau. PG - 1189-90 LID - 10.1016/j.neuron.2014.06.004 [doi] LID - S0896-6273(14)00494-2 [pii] AB - Sanders et al. (2014) demonstrate in this issue of Neuron that the natively unfolded protein tau can propagate indefinitely in distinct stable strains, therefore supporting the general idea that tau has prion-like properties, with implications for Alzheimer's disease and other tauopathies. CI - Copyright (c) 2014 Elsevier Inc. All rights reserved. FAU - Hyman, Bradley T AU - Hyman BT AD - Neurology Service, Massachusetts General Hospital, 114 16(th) Street, Charlestown, MA 02129, USA. Electronic address: bhyman@mgh.harvard.edu. LA - eng PT - Comment PT - Journal Article PL - United States TA - Neuron JT - Neuron JID - 8809320 RN - 0 (Prions) RN - 0 (tau Proteins) SB - IM CON - Neuron. 2014 Jun 18;82(6):1271-88. PMID: 24857020 MH - Animals MH - Hippocampus/*pathology MH - Humans MH - Neurodegenerative Diseases/*pathology MH - Prions/*physiology MH - Tauopathies/*pathology MH - tau Proteins/*physiology EDAT- 2014/06/20 06:00 MHDA- 2014/08/13 06:00 CRDT- 2014/06/20 06:00 AID - S0896-6273(14)00494-2 [pii] AID - 10.1016/j.neuron.2014.06.004 [doi] PST - ppublish SO - Neuron. 2014 Jun 18;82(6):1189-90. doi: 10.1016/j.neuron.2014.06.004. PMID- 16269153 OWN - NLM STAT- MEDLINE DA - 20051121 DCOM- 20051228 LR - 20141120 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 354 IP - 3 DP - 2005 Dec 2 TI - Crystal structures of active LytM. PG - 578-90 AB - Lysostaphin-type enzymes are metalloendopeptidases that are present in bacteriophages and in bacteria. They share the catalytic domain, but normally contain other domains as well. The well-characterized enzymes in this group are all specific for the pentaglycine crosslinks in the cell walls of some Gram-positive bacterial species. Lysostaphin-type enzymes are synthesized as secreted preproenzymes and require proteolytic activation for maturation. Although lysostaphin, the prototypical peptidase in the group, is widely used as a tool in biotechnology and developed as an antistaphylococcal agent, the detailed structure of this enzyme is unknown. So far, only one lysostaphin-type enzyme, the Staphylococcus aureus autolysin LytM, has been crystallized in its full-length, inactive form. Here, we describe the synthesis of a convenient reporter substrate, characterize the metal and pH-dependence of an active LytM fragment, and present its crystal structure in three crystal forms at different pH values that either support or do not support activity. In all structures, we find an extended, long and narrow groove that has the active site at its bottom and is delineated on the sides by the most flexible regions of the molecule. In two cases, the groove is partially filled by a loop of a neighbouring molecule in the crystal. As the loop contains three consecutive glycine residues, this crystal packing effect supports the interpretation that the groove is the substrate-binding cleft. To characterize the substrate-binding mode more closely, a phosphinate analogue of tetraglycine was synthesized. Although tetraglycine is a substrate of the active LytM fragment, the phosphinate analogue turned out to be a very poor inhibitor. Crystals that were grown in its presence contained an L+-tartrate molecule from the crystallization buffer and not the phosphinate in the active site. FAU - Firczuk, Malgorzata AU - Firczuk M AD - International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland. FAU - Mucha, Artur AU - Mucha A FAU - Bochtler, Matthias AU - Bochtler M LA - eng SI - PDB/2B13 SI - PDB/2B44 SI - PDB/2BOP PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20051018 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Bacterial Proteins) RN - 0 (Cations, Divalent) RN - 0 (Dicarboxylic Acids) RN - 0 (Ethylenediamines) RN - 0 (Metals, Heavy) RN - 0 (Phosphinic Acids) RN - 60V9STC53F (ethylenediamine) RN - EC 3.4.- (Endopeptidases) RN - EC 3.4.99.- (LytM protein, Staphylococcus aureus) RN - TE7660XO1C (Glycine) SB - IM MH - Bacterial Proteins/*chemistry/genetics/*metabolism MH - Binding Sites MH - Cations, Divalent/chemistry MH - Crystallography, X-Ray MH - Dicarboxylic Acids/chemistry MH - Endopeptidases/*chemistry/genetics/*metabolism MH - Enzyme Activation/drug effects MH - Ethylenediamines/chemistry/metabolism MH - Glycine/chemistry MH - Hydrogen-Ion Concentration MH - Metals, Heavy/chemistry/pharmacology MH - Models, Molecular MH - Mutation/genetics MH - Phosphinic Acids/chemistry/metabolism MH - Protein Structure, Tertiary MH - Staphylococcus aureus/*enzymology MH - Substrate Specificity EDAT- 2005/11/05 09:00 MHDA- 2005/12/29 09:00 CRDT- 2005/11/05 09:00 PHST- 2005/07/05 [received] PHST- 2005/09/23 [revised] PHST- 2005/09/27 [accepted] PHST- 2005/10/18 [aheadofprint] AID - S0022-2836(05)01161-7 [pii] AID - 10.1016/j.jmb.2005.09.082 [doi] PST - ppublish SO - J Mol Biol. 2005 Dec 2;354(3):578-90. Epub 2005 Oct 18. PMID- 22660624 OWN - NLM STAT- MEDLINE DA - 20120803 DCOM- 20121130 LR - 20141016 IS - 1535-9786 (Electronic) IS - 1535-9786 (Linking) VI - 11 IP - 8 DP - 2012 Aug TI - Solubility-promoting function of Hsp90 contributes to client maturation and robust cell growth. PG - 1033-41 LID - 10.1128/EC.00099-12 [doi] AB - The Hsp90 chaperone is required for the maturation of signal transduction clients, including many kinases and nuclear steroid hormone receptors. The binding and hydrolysis of ATP by Hsp90 drive conformational rearrangements in three structure domains. Two intrinsically disordered regions of Hsp90 located between these domains and at the C terminus have traditionally been considered to impart flexibility. We discovered that the charged nature of these acid-rich disordered regions imparts a solubility-promoting function to Hsp90 that is important for its cellular activity in yeast. Both the solubility-promoting function and ATPase activity must occur in the same Hsp90 molecule in order to support robust growth, suggesting that the solubility-promoting function is required during the ATP-driven client maturation process. Expression of model clients together with Hsp90 variants indicated interdependent solubilities mediated by the aggregation propensities of both the client and Hsp90. We propose a model whereby the charge-rich disordered regions of Hsp90 serve a solubility-promoting function important for complexes with aggregation-prone clients. These findings demonstrate a novel biological function of the intrinsically disordered regions in Hsp90 and provide a compelling rationale for why their charged properties are conserved throughout eukaryotic evolution. FAU - Pursell, Natalie W AU - Pursell NW AD - Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA. FAU - Mishra, Parul AU - Mishra P FAU - Bolon, Daniel N A AU - Bolon DN LA - eng GR - R01 GM083038/GM/NIGMS NIH HHS/United States GR - R01-GM083038/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120601 PL - United States TA - Eukaryot Cell JT - Eukaryotic cell JID - 101130731 RN - 0 (HSP82 protein, S cerevisiae) RN - 0 (HSP90 Heat-Shock Proteins) RN - 0 (Receptors, Glucocorticoid) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 2.7.10.2 (src-Family Kinases) SB - IM MH - Amino Acid Sequence MH - Cell Enlargement MH - HSP90 Heat-Shock Proteins/chemistry/genetics/*metabolism MH - Hydrolysis MH - Molecular Sequence Data MH - Mutation MH - Protein Processing, Post-Translational MH - Protein Structure, Tertiary MH - Receptors, Glucocorticoid/metabolism MH - Saccharomyces cerevisiae/genetics/*growth & development/*metabolism MH - Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism MH - Solubility MH - src-Family Kinases/metabolism PMC - PMC3416057 OID - NLM: PMC3416057 EDAT- 2012/06/05 06:00 MHDA- 2012/12/10 06:00 CRDT- 2012/06/05 06:00 PHST- 2012/06/01 [aheadofprint] AID - EC.00099-12 [pii] AID - 10.1128/EC.00099-12 [doi] PST - ppublish SO - Eukaryot Cell. 2012 Aug;11(8):1033-41. doi: 10.1128/EC.00099-12. Epub 2012 Jun 1. PMID- 19733547 OWN - NLM STAT- MEDLINE DA - 20090929 DCOM- 20091014 LR - 20140908 IS - 1090-2104 (Electronic) IS - 0006-291X (Linking) VI - 389 IP - 2 DP - 2009 Nov 13 TI - Membrane binding mode of intrinsically disordered cytoplasmic domains of T cell receptor signaling subunits depends on lipid composition. PG - 388-93 LID - 10.1016/j.bbrc.2009.09.002 [doi] AB - Intrinsically disordered cytoplasmic domains of T cell receptor (TCR) signaling subunits including zeta(cyt) and CD3epsilon(cyt) all contain one or more copies of an immunoreceptor tyrosine-based activation motif (ITAM), tyrosine residues of which are phosphorylated upon receptor triggering. Membrane binding-induced helical folding of zeta(cyt) and CD3epsilon(cyt) ITAMs is thought to control TCR activation. However, the question whether or not lipid binding of zeta(cyt) and CD3epsilon(cyt) is necessarily accompanied by a folding transition of ITAMs remains open. In this study, we investigate whether the membrane binding mechanisms of zeta(cyt) and CD3epsilon(cyt) depend on the membrane model used. Circular dichroic and fluorescence data indicate that binding of zeta(cyt) and CD3epsilon(cyt) to detergent micelles and unstable vesicles is accompanied by a disorder-to-order transition, whereas upon binding to stable vesicles these proteins remain unfolded. Using electron microscopy and dynamic light scattering, we show that upon protein binding, unstable vesicles fuse and rupture. In contrast, stable vesicles remain intact under these conditions. This suggests different membrane binding modes for zeta(cyt) and CD3epsilon(cyt) depending on the bilayer stability: (1) coupled binding and folding, and (2) binding without folding. These findings explain the long-standing puzzle in the literature and highlight the importance of the choice of an appropriate membrane model for protein-lipid interactions studies. FAU - Sigalov, Alexander B AU - Sigalov AB AD - University of Massachusetts Medical School, Worcester, MA 01655, USA. Alexander.sigalov@umassmed.edu FAU - Hendricks, Gregory M AU - Hendricks GM LA - eng GR - P30 AI042845/AI/NIAID NIH HHS/United States GR - P30 AI042845-08/AI/NIAID NIH HHS/United States GR - P30 AI42845-08/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090904 PL - United States TA - Biochem Biophys Res Commun JT - Biochemical and biophysical research communications JID - 0372516 RN - 0 (Antigens, CD3) RN - 0 (CD3 antigen, zeta chain) RN - 0 (Lipids) RN - 0 (Protein Subunits) RN - 0 (Receptors, Antigen, T-Cell) RN - 42HK56048U (Tyrosine) SB - IM MH - Amino Acid Sequence MH - Antigens, CD3/*metabolism MH - Cell Membrane/chemistry/*metabolism MH - Cytoplasm/metabolism MH - Lipids/*chemistry MH - Molecular Sequence Data MH - Protein Structure, Tertiary MH - Protein Subunits MH - Receptors, Antigen, T-Cell/genetics/*metabolism MH - Signal Transduction MH - Tyrosine/metabolism PMC - PMC2795782 MID - NIHMS143835 OID - NLM: NIHMS143835 OID - NLM: PMC2795782 EDAT- 2009/09/08 06:00 MHDA- 2009/10/15 06:00 CRDT- 2009/09/08 06:00 PHST- 2009/08/14 [received] PHST- 2009/09/01 [accepted] PHST- 2009/09/04 [aheadofprint] AID - S0006-291X(09)01782-3 [pii] AID - 10.1016/j.bbrc.2009.09.002 [doi] PST - ppublish SO - Biochem Biophys Res Commun. 2009 Nov 13;389(2):388-93. doi: 10.1016/j.bbrc.2009.09.002. Epub 2009 Sep 4. PMID- 17315997 OWN - NLM STAT- MEDLINE DA - 20070314 DCOM- 20070424 IS - 0002-7863 (Print) IS - 0002-7863 (Linking) VI - 129 IP - 11 DP - 2007 Mar 21 TI - Amino acid bulkiness defines the local conformations and dynamics of natively unfolded alpha-synuclein and tau. PG - 3032-3 FAU - Cho, Min-Kyu AU - Cho MK AD - Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany. FAU - Kim, Hai-Young AU - Kim HY FAU - Bernado, Pau AU - Bernado P FAU - Fernandez, Claudio O AU - Fernandez CO FAU - Blackledge, Martin AU - Blackledge M FAU - Zweckstetter, Markus AU - Zweckstetter M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070223 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Amino Acids) RN - 0 (alpha-Synuclein) RN - 0 (tau Proteins) SB - IM MH - Amino Acid Sequence MH - Amino Acids/*chemistry MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Conformation MH - Protein Folding MH - Structure-Activity Relationship MH - alpha-Synuclein/*chemistry MH - tau Proteins/*chemistry EDAT- 2007/02/24 09:00 MHDA- 2007/04/25 09:00 CRDT- 2007/02/24 09:00 PHST- 2007/02/23 [aheadofprint] AID - 10.1021/ja067482k [doi] PST - ppublish SO - J Am Chem Soc. 2007 Mar 21;129(11):3032-3. Epub 2007 Feb 23. PMID- 17892493 OWN - NLM STAT- MEDLINE DA - 20071003 DCOM- 20071212 IS - 1742-464X (Print) IS - 1742-464X (Linking) VI - 274 IP - 20 DP - 2007 Oct TI - Molecular mechanisms of the phospho-dependent prolyl cis/trans isomerase Pin1. PG - 5211-22 AB - Since its discovery 10 years ago, Pin1, a prolyl cis/trans isomerase essential for cell cycle progression, has been implicated in a large number of molecular processes related to human diseases, including cancer and Alzheimer's disease. Pin1 is made up of a WW interaction domain and a C-terminal catalytic subunit, and several high-resolution structures are available that have helped define its function. The enzymatic activity of Pin1 towards short peptides containing the pSer/Thr-Pro motif has been well documented, and we discuss the available evidence for the molecular mechanisms of its isomerase activity. We further focus on those studies that examine its cis/trans isomerase function using full-length protein substrates. The interpretation of this research has been further complicated by the observation that many of its pSer/Thr-Pro substrate motifs are located in natively unstructured regions of polypeptides, and are characterized by minor populations of the cis conformer. Finally, we review the data on the possibility of alternative modes of substrate binding and the complex role that Pin1 plays in the degradation of its substrates. After considering the available work, it seems that further analysis is required to determine whether binding or catalysis is the primary mechanism through which Pin1 affects cell cycle progression. FAU - Lippens, G AU - Lippens G AD - CNRS UMR 8576 Unite de Glycobiologie Structurale et Fonctionnelle, Universite des Sciences et Technologies de Lille 1-59655, Villeneuve d'Ascq, France. Guy.Lippens@univ-lille1.fr FAU - Landrieu, I AU - Landrieu I FAU - Smet, C AU - Smet C LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20070924 PL - England TA - FEBS J JT - The FEBS journal JID - 101229646 RN - 0 (NIMA-interacting peptidylprolyl isomerase) RN - EC 5.2.1.8 (Peptidylprolyl Isomerase) SB - IM MH - Humans MH - Peptidylprolyl Isomerase/chemistry/*physiology MH - Phosphorylation RF - 91 EDAT- 2007/09/26 09:00 MHDA- 2007/12/13 09:00 CRDT- 2007/09/26 09:00 PHST- 2007/09/24 [aheadofprint] AID - EJB6057 [pii] AID - 10.1111/j.1742-4658.2007.06057.x [doi] PST - ppublish SO - FEBS J. 2007 Oct;274(20):5211-22. Epub 2007 Sep 24. PMID- 17176095 OWN - NLM STAT- MEDLINE DA - 20070306 DCOM- 20080111 LR - 20140908 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 45 IP - 51 DP - 2006 Dec 26 TI - Lipid-binding activity of intrinsically unstructured cytoplasmic domains of multichain immune recognition receptor signaling subunits. PG - 15731-9 AB - Multichain immune recognition receptors (MIRRs) found on the surface of T cells, B cells, mast cells, natural killer cells, basophils, and other immune cells are formed by the association of several single-pass transmembrane proteins, with immunoglobulin-like ligand recognition domains and signal-transducing domains present on separate subunits. The MIRR signaling subunits all have cytoplasmic domains containing one or more copies of an immunoreceptor tyrosine-based activation motif (ITAM), tyrosine residues of which are phosphorylated upon receptor engagement in an early and obligatory event in the signaling cascade. Despite the proximity to the cell membrane and crucial role in transmembrane signal transduction, little is known about the structure and lipid-binding activity of the ITAM-containing cytoplasmic domains. Here we investigate the conformation and lipid-binding activity of several MIRR cytoplasmic domains, namely, T cell receptor zetacyt, CD3epsiloncyt, CD3deltacyt, and CD3gammacyt, B cell receptor Igalphacyt and Igbetacyt, and Fc receptor FcepsilonRIgammacyt, using purified recombinant proteins. Secondary structure prediction analysis and experimental circular dichroism spectra identify each of these cytoplasmic domains as natively unfolded proteins. We also report that zetacyt, CD3epsiloncyt, and FcepsilonRIgammacyt bind to acidic and mixed phospholipid vesicles and that the binding strength correlates with the protein net charge and the presence of clustered basic amino acid residues. Circular dichroism analysis reveals the lack of secondary structure for these domains in lipid-bound form. Phosphorylation of zetacyt and FcepsilonRIgammacyt does not alter their random-coil conformation but weakens binding to membranes. The implications of these results for transmembrane signal transduction by immune receptors are discussed. FAU - Sigalov, Alexander B AU - Sigalov AB AD - Department of Pathology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, USA. Alexander.Sigalov@umassmed.edu FAU - Aivazian, Dikran A AU - Aivazian DA FAU - Uversky, Vladimir N AU - Uversky VN FAU - Stern, Lawrence J AU - Stern LJ LA - eng GR - P30 AI042845/AI/NIAID NIH HHS/United States GR - P30 AI042845-08/AI/NIAID NIH HHS/United States GR - P30 AI42845-08/AI/NIAID NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20061219 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Antigens, CD3) RN - 0 (CD3E protein, human) RN - 0 (Membrane Proteins) RN - 0 (Phospholipids) RN - 0 (Protein Subunits) RN - 0 (Receptors, Antigen, B-Cell) RN - 0 (Receptors, Antigen, T-Cell) RN - 0 (Receptors, Antigen, T-Cell, gamma-delta) RN - 0 (Receptors, Immunologic) RN - 0 (Unilamellar Liposomes) RN - 0 (antigen T cell receptor, zeta chain) SB - IM MH - Amino Acid Sequence MH - Antigens, CD3/chemistry/metabolism MH - Cytoplasm/chemistry/*metabolism MH - Humans MH - Membrane Proteins/chemistry/metabolism MH - Molecular Sequence Data MH - Phospholipids/chemistry/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Protein Subunits/chemistry/*metabolism/physiology MH - Receptors, Antigen, B-Cell/chemistry/metabolism/physiology MH - Receptors, Antigen, T-Cell/chemistry/metabolism/physiology MH - Receptors, Antigen, T-Cell, gamma-delta/chemistry/metabolism MH - Receptors, Immunologic/chemistry/*metabolism/physiology MH - Signal Transduction/*physiology MH - Unilamellar Liposomes/chemistry/*metabolism PMC - PMC2528957 MID - NIHMS61690 OID - NLM: NIHMS61690 OID - NLM: PMC2528957 EDAT- 2006/12/21 09:00 MHDA- 2008/01/12 09:00 CRDT- 2006/12/21 09:00 PHST- 2006/12/19 [aheadofprint] AID - 10.1021/bi061108f [doi] PST - ppublish SO - Biochemistry. 2006 Dec 26;45(51):15731-9. Epub 2006 Dec 19. PMID- 21376144 OWN - NLM STAT- MEDLINE DA - 20110503 DCOM- 20110719 LR - 20140821 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1814 IP - 5 DP - 2011 May TI - The neurotransmitter serotonin interrupts alpha-synuclein amyloid maturation. PG - 553-61 LID - 10.1016/j.bbapap.2011.02.008 [doi] AB - Indolic derivatives can affect fibril growth of amyloid forming proteins. The neurotransmitter serotonin (5-HT) is of particular interest, as it is an endogenous molecule with a possible link to neuropsychiatric symptoms of Parkinson disease. A key pathomolecular mechanism of Parkinson disease is the misfolding and aggregation of the intrinsically unstructured protein alpha-synuclein. We performed a biophysical study to investigate an influence between these two molecules. In an isolated in vitro system, 5-HT interfered with alpha-synuclein amyloid fiber maturation, resulting in the formation of partially structured, SDS-resistant intermediate aggregates. The C-terminal region of alpha-synuclein was essential for this interaction, which was driven mainly by electrostatic forces. 5-HT did not bind directly to monomeric alpha-synuclein molecules and we propose a model where 5-HT interacts with early intermediates of alpha-synuclein amyloidogenesis, which disfavors their further conversion into amyloid fibrils. CI - Copyright (c) 2011 Elsevier B.V. All rights reserved. FAU - Falsone, S Fabio AU - Falsone SF AD - Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria. fabio.falsone@uni-graz.at FAU - Leitinger, Gerd AU - Leitinger G FAU - Karner, Anita AU - Karner A FAU - Kungl, Andreas J AU - Kungl AJ FAU - Kosol, Simone AU - Kosol S FAU - Cappai, Roberto AU - Cappai R FAU - Zangger, Klaus AU - Zangger K LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110302 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 0 (Amyloid) RN - 0 (Neurotransmitter Agents) RN - 0 (alpha-Synuclein) RN - 333DO1RDJY (Serotonin) SB - IM MH - Amyloid/*chemistry/*metabolism/ultrastructure MH - Circular Dichroism MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - Magnetic Resonance Spectroscopy MH - Microscopy, Electron, Transmission MH - Neurotransmitter Agents/*pharmacology MH - Protein Binding/drug effects MH - Serotonin/*pharmacology MH - alpha-Synuclein/*chemistry/*metabolism/ultrastructure PMC - PMC3092864 OID - NLM: PMC3092864 EDAT- 2011/03/08 06:00 MHDA- 2011/07/20 06:00 CRDT- 2011/03/08 06:00 PHST- 2010/07/21 [received] PHST- 2011/02/10 [revised] PHST- 2011/02/17 [accepted] PHST- 2011/03/02 [aheadofprint] AID - S1570-9639(11)00033-1 [pii] AID - 10.1016/j.bbapap.2011.02.008 [doi] PST - ppublish SO - Biochim Biophys Acta. 2011 May;1814(5):553-61. doi: 10.1016/j.bbapap.2011.02.008. Epub 2011 Mar 2. PMID- 11955070 OWN - NLM STAT- MEDLINE DA - 20020416 DCOM- 20020509 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 41 IP - 16 DP - 2002 Apr 23 TI - Structure of the pyruvate dehydrogenase multienzyme complex E1 component from Escherichia coli at 1.85 A resolution. PG - 5213-21 AB - The crystal structure of the recombinant thiamin diphosphate-dependent E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc) has been determined at a resolution of 1.85 A. The E. coli PDHc E1 component E1p is a homodimeric enzyme and crystallizes with an intact dimer in an asymmetric unit. Each E1p subunit consists of three domains: N-terminal, middle, and C-terminal, with all having alpha/beta folds. The functional dimer contains two catalytic centers located at the interface between subunits. The ThDP cofactors are bound in the "V" conformation in clefts between the two subunits (binding involves the N-terminal and middle domains), and there is a common ThDP binding fold. The cofactors are completely buried, as only the C2 atoms are accessible from solution through the active site clefts. Significant structural differences are observed between individual domains of E1p relative to heterotetrameric multienzyme complex E1 components operating on branched chain substrates. These differences may be responsible for reported alternative E1p binding modes to E2 components within the respective complexes. This paper represents the first structural example of a functional pyruvate dehydrogenase E1p component from any species. It also provides the first representative example for the entire family of homodimeric (alpha2) E1 multienzyme complex components, and should serve as a model for this class of enzymes. FAU - Arjunan, Palaniappa AU - Arjunan P AD - Biocrystallography Laboratory, Veterans Affairs Medical Center, P. O. Box 12055, University Drive C, Pittsburgh, Pennsylvania 15240, USA. FAU - Nemeria, Natalia AU - Nemeria N FAU - Brunskill, Andrew AU - Brunskill A FAU - Chandrasekhar, Krishnamoorthy AU - Chandrasekhar K FAU - Sax, Martin AU - Sax M FAU - Yan, Yan AU - Yan Y FAU - Jordan, Frank AU - Jordan F FAU - Guest, John R AU - Guest JR FAU - Furey, William AU - Furey W LA - eng SI - PDB/1L8A GR - GM-50380/GM/NIGMS NIH HHS/United States GR - GM-61791/GM/NIGMS NIH HHS/United States GR - GM-62330/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Pyruvate Dehydrogenase Complex) RN - 0 (Solvents) RN - 0 (pyruvate dehydrogenase multienzyme complex E1) RN - 059QF0KO0R (Water) RN - I38ZP9992A (Magnesium) RN - Q57971654Y (Thiamine Pyrophosphate) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Computer Simulation MH - Crystallography, X-Ray MH - Dimerization MH - Escherichia coli/*enzymology MH - Magnesium/chemistry/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Pyruvate Dehydrogenase Complex/*chemistry/metabolism MH - Solvents MH - Thiamine Pyrophosphate/chemistry/metabolism MH - Water EDAT- 2002/04/17 10:00 MHDA- 2002/05/10 10:01 CRDT- 2002/04/17 10:00 AID - bi0118557 [pii] PST - ppublish SO - Biochemistry. 2002 Apr 23;41(16):5213-21. PMID- 11178911 OWN - NLM STAT- MEDLINE DA - 20010222 DCOM- 20010405 LR - 20131121 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 306 IP - 3 DP - 2001 Feb 23 TI - Solution structure of Grb2 reveals extensive flexibility necessary for target recognition. PG - 527-37 AB - Grb2 is an adaptor protein composed of a single SH2 domain flanked by two SH3 domains. Grb2 functions as an important evolutionary conserved link between a variety of cell membrane receptors and the Ras/MAP kinase-signaling cascade. Here, we describe the solution structure of Grb2 as revealed by NMR and small angle X-ray scattering measurements. We demonstrate that Grb2 is a flexible protein in which the C-terminal SH3 domain is connected to the SH2 domain via a flexible linker. This is in contrast to the previously described Grb2 crystal structure, which showed a compact structure with intramolecular contact between two SH3 domains. Binding experiments on Grb2 and peptides containing two different proline-rich sequences indicate that Grb2 adapts the relative position and orientation of the two SH3 domains to bind bivalently to the target peptide sequences. FAU - Yuzawa, S AU - Yuzawa S AD - Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan. FAU - Yokochi, M AU - Yokochi M FAU - Hatanaka, H AU - Hatanaka H FAU - Ogura, K AU - Ogura K FAU - Kataoka, M AU - Kataoka M FAU - Miura , K AU - Miura K FAU - Mandiyan, V AU - Mandiyan V FAU - Schlessinger, J AU - Schlessinger J FAU - Inagaki, F AU - Inagaki F LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (GRB2 Adaptor Protein) RN - 0 (GRB2 protein, human) RN - 0 (Ligands) RN - 0 (Proteins) RN - 0 (Solutions) RN - 9DLQ4CIU6V (Proline) SB - IM MH - *Adaptor Proteins, Signal Transducing MH - Amino Acid Sequence MH - Computer Simulation MH - GRB2 Adaptor Protein MH - Humans MH - Ligands MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Pliability MH - Proline/genetics/metabolism MH - Protein Binding MH - Protein Structure, Secondary MH - Proteins/*chemistry/genetics/*metabolism MH - Sequence Alignment MH - Software MH - Solutions MH - Substrate Specificity MH - X-Ray Diffraction MH - *src Homology Domains EDAT- 2001/02/17 11:00 MHDA- 2001/04/06 10:01 CRDT- 2001/02/17 11:00 AID - 10.1006/jmbi.2000.4396 [doi] AID - S0022283600943961 [pii] PST - ppublish SO - J Mol Biol. 2001 Feb 23;306(3):527-37. PMID- 24072065 OWN - NLM STAT- MEDLINE DA - 20131030 DCOM- 20150303 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 9 IP - 12 DP - 2013 Dec TI - Solvent interaction analysis of intrinsically disordered proteins in aqueous two-phase systems. PG - 3068-79 LID - 10.1039/c3mb70329k [doi] AB - In an aqueous two-phase system (ATPS), the partitioning of a protein is defined by the differential interactions of the protein with aqueous media in the two phases. Our study shows that partitioning of proteins in a set of ATPSs of different ionic compositions can be used to quantify structural differences between alpha-synuclein, its variants and several globular proteins. Since application of ATPSs implies the use of high concentrations of two polymers in water when a certain threshold concentration of the polymers is exceeded, and since these levels of polymer concentrations are similar to those commonly used to mimic the effects of macromolecular crowding on proteins, we used circular dichroism spectroscopy to evaluate the structural consequences of placing proteins in solutions with high polymer concentrations and various ionic compositions. FAU - Breydo, Leonid AU - Breydo L AD - Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA. vuversky@health.usf.edu. FAU - Mikheeva, Larissa M AU - Mikheeva LM FAU - Madeira, Pedro P AU - Madeira PP FAU - Zaslavsky, Boris Y AU - Zaslavsky BY FAU - Uversky, Vladimir N AU - Uversky VN LA - eng PT - Journal Article DEP - 20130927 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Ions) RN - 0 (Polyethylene Glycols) RN - 0 (Polymers) RN - 0 (Solvents) RN - 0 (alpha-Synuclein) RN - K3R6ZDH4DU (Dextrans) SB - IM MH - Animals MH - Circular Dichroism MH - Dextrans/chemistry MH - Genetic Variation MH - Humans MH - Hydrogen-Ion Concentration MH - Intrinsically Disordered Proteins/*chemistry/genetics MH - Ions/chemistry MH - Polyethylene Glycols/chemistry MH - Polymers/*chemistry MH - Solvents/*chemistry MH - alpha-Synuclein/*chemistry/genetics EDAT- 2013/09/28 06:00 MHDA- 2015/03/04 06:00 CRDT- 2013/09/28 06:00 PHST- 2013/09/27 [aheadofprint] PHST- 2013/10/29 [epublish] AID - 10.1039/c3mb70329k [doi] PST - ppublish SO - Mol Biosyst. 2013 Dec;9(12):3068-79. doi: 10.1039/c3mb70329k. Epub 2013 Sep 27. PMID- 23947833 OWN - NLM STAT- MEDLINE DA - 20131210 DCOM- 20140211 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 52 IP - 36 DP - 2013 Sep 10 TI - Interaction of nonstructural protein 5A of the hepatitis C virus with Src homology 3 domains using noncanonical binding sites. PG - 6160-8 LID - 10.1021/bi400363v [doi] AB - Src homology 3 (SH3) domains are widely known for their ability to interact with other proteins using the canonical PxxP binding motif. Besides those well-characterized interaction modes, there is an increasing number of SH3 domain-containing complexes that lack this motif. Here we characterize the interaction of SH3 domains, in particular the Bin1-SH3 domain, with the intrinsically disordered part of nonstructural protein 5A of the hepatitis C virus using noncanonical binding sites in addition to its PxxP motif. These binding regions partially overlap with regions that have previously been identified as having an increased propensity to form alpha-helices. Remarkably, upon interaction with the Bin1-SH3 domain, the alpha-helical propensity decreases and a fuzzy complex is formed. FAU - Schwarten, Melanie AU - Schwarten M AD - Institut de Biologie Structurale, Universite Grenoble 1 , 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France. FAU - Solyom, Zsofia AU - Solyom Z FAU - Feuerstein, Sophie AU - Feuerstein S FAU - Aladag, Amine AU - Aladag A FAU - Hoffmann, Silke AU - Hoffmann S FAU - Willbold, Dieter AU - Willbold D FAU - Brutscher, Bernhard AU - Brutscher B LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130826 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (NS-5 protein, hepatitis C virus) RN - 0 (Viral Nonstructural Proteins) SB - IM MH - Adaptor Proteins, Signal Transducing/metabolism MH - Binding Sites MH - Hepacivirus/metabolism MH - Models, Molecular MH - Viral Nonstructural Proteins/*chemistry/metabolism MH - src Homology Domains/*physiology EDAT- 2013/08/21 06:00 MHDA- 2014/02/12 06:00 CRDT- 2013/08/17 06:00 PHST- 2013/08/26 [aheadofprint] AID - 10.1021/bi400363v [doi] PST - ppublish SO - Biochemistry. 2013 Sep 10;52(36):6160-8. doi: 10.1021/bi400363v. Epub 2013 Aug 26. PMID- 23947342 OWN - NLM STAT- MEDLINE DA - 20130909 DCOM- 20140325 IS - 1526-4602 (Electronic) IS - 1525-7797 (Linking) VI - 14 IP - 9 DP - 2013 Sep 9 TI - Lipid-specific beta-sheet formation in a mussel byssus protein domain. PG - 3238-45 LID - 10.1021/bm400860y [doi] AB - Intrinsically disordered proteins (IDP) or regions (IDR) can adopt multiple conformational states, depending on the interaction partners they encounter. This enables proteins or individual domains to fulfill multiple functions. Here, we analyzed the flank sequences of preCol-NG, one of three collagenous proteins of a mussel byssus thread governing its mechanical performance. preCol-NG comprises a collagen domain and nonrepetitive termini enclosing specific flank regions characterized by tandem repeats known from silk proteins, protein elastomers, and plant cell wall-associated proteins. We recombinantly produced a protein mimicking the M. galloprovincialis preCol-NG C-terminal flank region. The protein was intrinsically unfolded in solution, even at elevated temperatures. However, upon contact with small unilamellar vesicles (SUVs) reversible beta-structure formation occurred, reminiscent of partitioning-folding coupling. This behavior of preCol-NG flank domains likely impacts byssogenesis and sheds new light on a distinct mechanism of how fibrous protein materials might be achieved by lipid-induced self-assembly in nature. FAU - Heim, Markus AU - Heim M AD - Fakultat fur Ingenieurwissenschaften, Lehrstuhl Biomaterialien, Universitat Bayreuth, Universitatsstrasse 30, 95440 Bayreuth, Germany. FAU - Elsner, Martina B AU - Elsner MB FAU - Scheibel, Thomas AU - Scheibel T LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130829 PL - United States TA - Biomacromolecules JT - Biomacromolecules JID - 100892849 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Micelles) RN - 0 (Phospholipids) RN - 0 (Surface-Active Agents) RN - 0 (Unilamellar Liposomes) RN - 368GB5141J (Sodium Dodecyl Sulfate) SB - IM MH - Amino Acid Sequence MH - Animals MH - Intrinsically Disordered Proteins/*chemistry MH - Micelles MH - Molecular Mimicry MH - Molecular Sequence Data MH - Mytilus/*chemistry MH - Phospholipids/*chemistry MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sodium Dodecyl Sulfate/chemistry MH - Surface-Active Agents/chemistry MH - Unilamellar Liposomes/chemistry EDAT- 2013/08/21 06:00 MHDA- 2014/03/26 06:00 CRDT- 2013/08/17 06:00 PHST- 2013/08/29 [aheadofprint] AID - 10.1021/bm400860y [doi] PST - ppublish SO - Biomacromolecules. 2013 Sep 9;14(9):3238-45. doi: 10.1021/bm400860y. Epub 2013 Aug 29. PMID- 19456123 OWN - NLM STAT- MEDLINE DA - 20090623 DCOM- 20090720 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 25 DP - 2009 Jun 30 TI - A new function of GAPDH from Chlamydomonas reinhardtii: a thiol-disulfide exchange reaction with CP12. PG - 6034-40 LID - 10.1021/bi900569h [doi] AB - CP12 is a flexible protein that is well-known to interact with GAPDH, and this association is crucial to the regulation of enzyme activity. This regulation is likely related to structural transitions of both proteins, but the molecular bases of these changes are not yet understood. To answer this issue, we undertook a study based on the use of paramagnetic probes grafted on cysteine residues and followed by EPR spectroscopy. We present a new application of this approach that enables us to probe the functional role of cysteine residues in protein-protein interactions. Algal CP12 contains four cysteine residues involved in two disulfide bridges in its oxidized state and has some alpha-helical secondary structural elements. In contrast, in its reduced state, CP12 is mainly unstructured and shares some physical properties with intrinsically disordered proteins. Treatment of CP12 with a methane thiosulfonate derivative spin-label (MTSL) led to the labeling of the cysteine residues involved in the C-terminal bridge only as revealed by mass spectrometry. Surprisingly, the partner protein GAPDH induced the cleavage of the disulfide bridge between the cysteine residues of CP12 and the spin-label, resulting in the full release of the label. We showed the existence of a transitory interaction between both proteins and proposed a mechanism based on a thiol-disulfide exchange reaction. The results of this study point out a novel role of the algal GAPDH which is often termed a "moonlighting" protein. FAU - Erales, Jenny AU - Erales J AD - Bioenergetique et Ingenierie des Proteines, UPR 9036 CNRS et Aix-Marseille Universites, IFR 88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. FAU - Lorenzi, Magali AU - Lorenzi M FAU - Lebrun, Regine AU - Lebrun R FAU - Fournel, Andre AU - Fournel A FAU - Etienne, Emilien AU - Etienne E FAU - Courcelle, Carine AU - Courcelle C FAU - Guigliarelli, Bruno AU - Guigliarelli B FAU - Gontero, Brigitte AU - Gontero B FAU - Belle, Valerie AU - Belle V LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Disulfides) RN - 0 (Plant Proteins) RN - 0 (Recombinant Proteins) RN - 0 (Spin Labels) RN - 0 (Sulfhydryl Compounds) RN - EC 1.2.1.- (Glyceraldehyde-3-Phosphate Dehydrogenases) RN - K848JZ4886 (Cysteine) SB - IM MH - Animals MH - Chlamydomonas reinhardtii/*enzymology/metabolism MH - Cysteine/metabolism MH - Disulfides/chemistry/*metabolism MH - Glyceraldehyde-3-Phosphate Dehydrogenases/*metabolism MH - Hydrolysis MH - Plant Proteins/*metabolism MH - Recombinant Proteins/metabolism MH - Spin Labels MH - Sulfhydryl Compounds/chemistry/*metabolism EDAT- 2009/05/22 09:00 MHDA- 2009/07/21 09:00 CRDT- 2009/05/22 09:00 AID - 10.1021/bi900569h [doi] PST - ppublish SO - Biochemistry. 2009 Jun 30;48(25):6034-40. doi: 10.1021/bi900569h. PMID- 9790669 OWN - NLM STAT- MEDLINE DA - 19981117 DCOM- 19981117 LR - 20071114 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 37 IP - 43 DP - 1998 Oct 27 TI - A 1.4 A crystal structure for the hypoxanthine phosphoribosyltransferase of Trypanosoma cruzi. PG - 15066-75 AB - The hypoxanthine phosphoribosyltransferase (HPRT) from Trypanosoma cruzi, etiologic agent of Chagas' disease, was cocrystallized with the inosine analogue Formycin B (FmB) and the structure determined to 1.4 A resolution. This is the highest resolution structure yet reported for a phosphoribosyltransferase (PRT), and the asymmetric unit of the crystal contains a dimer of closely associated, nearly identical subunits. A conserved nonproline cis peptide in one active-site loop exposes the main-chain nitrogen to the enzyme active site, while the adjacent lysine side chain interacts with the other subunit of the dimer, thereby providing a possible mechanism for communication between the subunits and their active sites. The three-dimensional coordinates for the invariant Ser103-Tyr104 dipeptide are reported here for the first time. These are the only highly conserved residues in a second active-site loop, termed the long flexible loop, which is predicted to close over the active site of HPRTs to protect a labile transition state [Eads et al. (1994) Cell 78, 325-334]. This structure represents a major step forward in efforts to design/discover potent selective inhibitors of the HPRT of T. cruzi. FAU - Focia, P J AU - Focia PJ AD - Laboratory of Molecular Parasitology & Drug Design, School of Pharmacy, University of North Carolina, Chapel Hill 27599-7360, USA. FAU - Craig, S P 3rd AU - Craig SP 3rd FAU - Nieves-Alicea, R AU - Nieves-Alicea R FAU - Fletterick, R J AU - Fletterick RJ FAU - Eakin, A E AU - Eakin AE LA - eng SI - PDB/1TC1 SI - PDB/R1TC1SF GR - AI34326/AI/NIAID NIH HHS/United States GR - AI38919/AI/NIAID NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Recombinant Proteins) RN - EC 2.4.2.8 (Hypoxanthine Phosphoribosyltransferase) SB - IM MH - Animals MH - Binding Sites MH - Crystallization MH - Crystallography, X-Ray MH - Dimerization MH - Escherichia coli/enzymology/genetics MH - Humans MH - Hypoxanthine Phosphoribosyltransferase/*chemistry/genetics/isolation & purification MH - Models, Molecular MH - Protein Structure, Secondary MH - Recombinant Proteins/biosynthesis/chemistry/isolation & purification MH - Trypanosoma cruzi/*enzymology EDAT- 1998/10/28 03:03 MHDA- 2001/03/28 10:01 CRDT- 1998/10/28 03:03 AID - 10.1021/bi981052s [doi] AID - bi981052s [pii] PST - ppublish SO - Biochemistry. 1998 Oct 27;37(43):15066-75. PMID- 16981712 OWN - NLM STAT- MEDLINE DA - 20060919 DCOM- 20061108 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 38 DP - 2006 Sep 26 TI - Conformational properties of the SDS-bound state of alpha-synuclein probed by limited proteolysis: unexpected rigidity of the acidic C-terminal tail. PG - 11523-31 AB - Alpha-synuclein (alpha-syn) is a "natively unfolded" protein constituting the major component of intracellular inclusions in several neurodegenerative disorders. Here, we describe proteolysis experiments conducted on human alpha-syn in the presence of SDS micelles. Our aim was to unravel molecular features of micelle-bound alpha-syn using the limited proteolysis approach. The nonspecific proteases thermolysin and proteinase K, as well as the Glu-specific V8-protease, were used as proteolytic probes. While alpha-syn at neutral pH is easily degraded to a variety of relatively small fragments, in the presence of 10 mM SDS the proteolysis of the protein is rather selective. Complementary fragments 1-111 and 112-140, 1-113 and 114-140, and 1-123 and 124-140 are obtained when thermolysin, proteinase K, and V8 protease, respectively, are used. These results are in line with a conformational model of alpha-syn in which it acquires a folded helical structure in the N-terminal region in its membrane-bound state. At the same time, they indicate that the C-terminal portion of the molecule is rather rigid, as seen in its relative resistance to extensive proteolytic degradation. It is likely that, under the specific experimental conditions of proteolysis in the presence of SDS, the negatively charged C-terminal region can be rigidified by binding a calcium ion, as shown before with intact alpha-syn. In this study, some evidence of calcium binding properties of isolated C-terminal fragments 112-140, 114-140, and 124-140 was obtained by mass spectrometry measurements, since molecular masses for calcium-loaded fragments were obtained. Our results indicate that the C-terminal portion of the membrane-bound alpha-syn is quite rigid and structured, at variance from current models of the membrane-bound protein deduced mostly from NMR. Considering that the aggregation process of alpha-syn is modulated by its C-terminal tail, the results of this study may provide useful insights into the behavior of alpha-syn in a membrane-mimetic environment. FAU - de Laureto, Patrizia Polverino AU - de Laureto PP AD - CRIBI Biotechnology Centre, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy. FAU - Tosatto, Laura AU - Tosatto L FAU - Frare, Erica AU - Frare E FAU - Marin, Oriano AU - Marin O FAU - Uversky, Vladimir N AU - Uversky VN FAU - Fontana, Angelo AU - Fontana A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Peptide Fragments) RN - 0 (alpha-Synuclein) RN - 368GB5141J (Sodium Dodecyl Sulfate) RN - EC 3.4.21.64 (Endopeptidase K) RN - EC 3.4.24.27 (Thermolysin) SB - IM MH - Amino Acid Sequence MH - Circular Dichroism MH - Endopeptidase K/metabolism MH - Humans MH - Models, Biological MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/metabolism MH - Protein Binding MH - *Protein Processing, Post-Translational MH - Protein Structure, Secondary MH - Sodium Dodecyl Sulfate/*metabolism MH - Spectrometry, Mass, Electrospray Ionization MH - Structure-Activity Relationship MH - Thermolysin/metabolism MH - alpha-Synuclein/*chemistry/*metabolism EDAT- 2006/09/20 09:00 MHDA- 2006/11/10 09:00 CRDT- 2006/09/20 09:00 AID - 10.1021/bi052614s [doi] PST - ppublish SO - Biochemistry. 2006 Sep 26;45(38):11523-31. PMID- 18463100 OWN - NLM STAT- MEDLINE DA - 20080630 DCOM- 20080819 LR - 20120224 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 27 DP - 2008 Jul 4 TI - The solution structure of EMILIN1 globular C1q domain reveals a disordered insertion necessary for interaction with the alpha4beta1 integrin. PG - 18947-56 LID - 10.1074/jbc.M801085200 [doi] AB - The extracellular matrix protein EMILIN1 (elastin microfibril interface located protein 1) is implicated in maintaining blood pressure homeostasis via the N-terminal elastin microfibril interface domain and in trophoblast invasion of the uterine wall via the globular C1q (gC1q) domain. Here, we describe the first NMR-based homology model structure of the human 52-kDa homotrimer of the EMILIN1 gC1q domain. In contrast to all of the gC1q (crystal) structures solved to date, the 10-stranded beta-sandwich fold of the gC1q domain is reduced to nine beta strands with a consequent increase in the size of the central cavity lumen. An unstructured loop, resulting from an insertion unique to EMILIN1 and EMILIN2 family members and located at the trimer apex upstream of the missing strand, specifically engages the alpha4beta1 integrin. Using both Jurkat T and EA.hy926 endothelial cells as well as site-directed mutagenesis, we demonstrate that the ability of alpha4beta1 integrins to recognize the trimeric EMILIN1 gC1q domain mainly depends on a single glutamic acid residue (Glu(933)). Static and flow adhesion of T cells and haptotactic migration of endothelial cells on gC1q is fully dependent on this residue. Thus, EMILIN1 gC1q-alpha4beta1 represents a unique ligand/receptor system, with a requirement for a 3-fold arrangement of the interaction site. FAU - Verdone, Giuliana AU - Verdone G AD - Dipartimento di Scienze e Tecnologie Biomediche, Centro di Eccellenza MATI, Universita di Udine, 33100 Udine, Italy. FAU - Doliana, Roberto AU - Doliana R FAU - Corazza, Alessandra AU - Corazza A FAU - Colebrooke, Simon A AU - Colebrooke SA FAU - Spessotto, Paola AU - Spessotto P FAU - Bot, Simonetta AU - Bot S FAU - Bucciotti, Francesco AU - Bucciotti F FAU - Capuano, Alessandra AU - Capuano A FAU - Silvestri, Alessandra AU - Silvestri A FAU - Viglino, Paolo AU - Viglino P FAU - Campbell, Iain D AU - Campbell ID FAU - Colombatti, Alfonso AU - Colombatti A FAU - Esposito, Gennaro AU - Esposito G LA - eng GR - E.1256/Telethon/Italy GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080507 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (EMILIN2 protein, human) RN - 0 (Glycoproteins) RN - 0 (Integrin alpha4beta1) RN - 0 (Membrane Glycoproteins) RN - 0 (elastin microfibril interface located protein) SB - IM MH - Blood Pressure/physiology MH - Cell Adhesion/physiology MH - Cell Movement/*physiology MH - Female MH - Glycoproteins/chemistry/genetics/metabolism MH - Homeostasis/physiology MH - Humans MH - Integrin alpha4beta1/*chemistry/genetics/*metabolism MH - Jurkat Cells MH - Membrane Glycoproteins/*chemistry/genetics/*metabolism MH - *Models, Molecular MH - Mutagenesis, Site-Directed MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Structure, Quaternary/physiology MH - Protein Structure, Secondary/physiology MH - Protein Structure, Tertiary/physiology MH - Structure-Activity Relationship MH - Trophoblasts/metabolism MH - Uterus/metabolism EDAT- 2008/05/09 09:00 MHDA- 2008/08/20 09:00 CRDT- 2008/05/09 09:00 PHST- 2008/05/07 [aheadofprint] AID - M801085200 [pii] AID - 10.1074/jbc.M801085200 [doi] PST - ppublish SO - J Biol Chem. 2008 Jul 4;283(27):18947-56. doi: 10.1074/jbc.M801085200. Epub 2008 May 7. PMID- 24367999 OWN - NLM STAT- MEDLINE DA - 20140121 DCOM- 20140710 LR - 20150122 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 53 IP - 2 DP - 2014 Jan 21 TI - Defining the oligomerization state of gamma-synuclein in solution and in cells. PG - 293-9 LID - 10.1021/bi401479a [doi] AB - gamma-Synuclein is expressed at high levels in neuronal cells and in multiple invasive cancers. Like its family member alpha-synuclein, gamma-synuclein is thought to be natively unfolded but does not readily form fibrils. The function of gamma-synuclein is unknown, but we have found that it interacts strongly with the enzyme phospholipase Cbeta (PLCbeta), altering its interaction with G proteins. As a first step in determining its role, we have characterized its oligomerization using fluorescence homotransfer, photon-counting histogram analysis, and native gel electrophoresis. We found that when its expressed in Escherichia coli and purified, gamma-synuclein appears monomeric on chromatographs under denaturing conditions, but under native conditions, it appears as oligomers of varying sizes. We followed the monomer-to-tetramer association by labeling the protein with fluorescein and following the concentration-dependent loss in fluorescence anisotropy resulting from fluorescence homotransfer. We also performed photon-counting histogram analysis at increasing concentrations of fluorescein-labeled gamma-synuclein and found concentration-dependent oligomerization. Addition of PLCbeta2, a strong gamma-synuclein binding partner whose cellular expression is correlated with gamma-synuclein, results in disruption of gamma-synuclein oligomers. Similarly, its binding to lipid membranes promotes the monomer form. When we exogenously express gamma-synuclein or microinject purified protein into cells, the protein appears monomeric. Our studies show that even though purified gamma-synuclein form oligomers, when binding partners are present, as in cells, it dissociates to a monomer to bind these partners, which in turn may modify protein function and integrity. FAU - Golebiewska, Urszula AU - Golebiewska U AD - Department of Physiology & Biophysics, Stony Brook University , Stony Brook, New York 11794, United States. FAU - Zurawsky, Cassandra AU - Zurawsky C FAU - Scarlata, Suzanne AU - Scarlata S LA - eng GR - GM053132/GM/NIGMS NIH HHS/United States GR - R01 GM053132/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20140106 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Solutions) RN - 0 (gamma-Synuclein) RN - EC 3.1.4.11 (Phospholipase C beta) SB - IM MH - Cell Line, Tumor MH - Cells/*metabolism MH - HEK293 Cells MH - HeLa Cells MH - Humans MH - Phospholipase C beta/chemistry/metabolism MH - Solutions MH - gamma-Synuclein/*chemistry/isolation & purification/*metabolism PMC - PMC3932107 MID - NIHMS553912 OID - NLM: NIHMS553912 OID - NLM: PMC3932107 EDAT- 2013/12/26 06:00 MHDA- 2014/07/11 06:00 CRDT- 2013/12/26 06:00 PHST- 2014/01/06 [aheadofprint] AID - 10.1021/bi401479a [doi] PST - ppublish SO - Biochemistry. 2014 Jan 21;53(2):293-9. doi: 10.1021/bi401479a. Epub 2014 Jan 6. PMID- 21134643 OWN - NLM STAT- MEDLINE DA - 20101207 DCOM- 20110331 LR - 20120119 IS - 1878-4186 (Electronic) IS - 0969-2126 (Linking) VI - 18 IP - 12 DP - 2010 Dec 8 TI - Structural characterization of the DAXX N-terminal helical bundle domain and its complex with Rassf1C. PG - 1642-53 LID - 10.1016/j.str.2010.09.016 [doi] AB - DAXX is a scaffold protein with diverse roles including transcription and cell cycle regulation. Using NMR spectroscopy, we demonstrate that the C-terminal half of DAXX is intrinsically disordered, whereas a folded domain is present near its N terminus. This domain forms a left-handed four-helix bundle (H1, H2, H4, H5). However, due to a crossover helix (H3), this topology differs from that of the Sin3 PAH domain, which to date has been used as a model for DAXX. The N-terminal residues of the tumor suppressor Rassf1C fold into an amphipathic alpha helix upon binding this DAXX domain via a shallow cleft along the flexible helices H2 and H5 (K(D) approximately 60 muM). Based on a proposed DAXX recognition motif as hydrophobic residues preceded by negatively charged groups, we found that peptide models of p53 and Mdm2 also bound the helical bundle. These data provide a structural foundation for understanding the diverse functions of DAXX. CI - Copyright (c) 2010 Elsevier Ltd. All rights reserved. FAU - Escobar-Cabrera, Eric AU - Escobar-Cabrera E AD - Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T1Z3, Canada. FAU - Lau, Desmond K W AU - Lau DK FAU - Giovinazzi, Serena AU - Giovinazzi S FAU - Ishov, Alexander M AU - Ishov AM FAU - McIntosh, Lawrence P AU - McIntosh LP LA - eng GR - R01 CA127378-01A1/CA/NCI NIH HHS/United States GR - R01 CA127378-01A1/CA/NCI NIH HHS/United States GR - R01 CA127378-02/CA/NCI NIH HHS/United States GR - R01 CA127378-03/CA/NCI NIH HHS/United States GR - R01 CA127378-04/CA/NCI NIH HHS/United States GR - R01 CA127378-05/CA/NCI NIH HHS/United States GR - Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (DAXX protein, human) RN - 0 (Multiprotein Complexes) RN - 0 (Mutant Proteins) RN - 0 (Nuclear Proteins) RN - 0 (RASSF1 protein, human) RN - 0 (Tumor Suppressor Proteins) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry/genetics/*metabolism MH - Binding Sites MH - Humans MH - Hydrophobic and Hydrophilic Interactions MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Multiprotein Complexes/chemistry/metabolism MH - Mutant Proteins/chemistry/genetics/metabolism MH - Nuclear Proteins/*chemistry/genetics/*metabolism MH - Protein Interaction Domains and Motifs/physiology MH - Protein Interaction Mapping MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Analysis, Protein MH - Sequence Deletion MH - Tumor Suppressor Proteins/*chemistry/*metabolism EDAT- 2010/12/08 06:00 MHDA- 2011/04/01 06:00 CRDT- 2010/12/08 06:00 PHST- 2010/07/02 [received] PHST- 2010/09/06 [revised] PHST- 2010/09/08 [accepted] AID - S0969-2126(10)00369-2 [pii] AID - 10.1016/j.str.2010.09.016 [doi] PST - ppublish SO - Structure. 2010 Dec 8;18(12):1642-53. doi: 10.1016/j.str.2010.09.016. PMID- 15629534 OWN - NLM STAT- MEDLINE DA - 20050104 DCOM- 20050628 LR - 20131121 IS - 0196-9781 (Print) IS - 0196-9781 (Linking) VI - 26 IP - 2 DP - 2005 Feb TI - Solution structure of a peptide derived from the oncogenic protein beta-Catenin in its phosphorylated and nonphosphorylated states. PG - 227-41 AB - Beta-Catenin plays an essential role in the Wingless/Wnt signaling cascade. Phosphorylation of beta-Catenin in its N-terminal region by the kinase GSK-3beta is required for the interaction with the SCF-beta-TrCP protein complex that targets beta-Catenin for proteasome degradation. In the present work, we used two peptides of 32 amino acids referred to beta-Cat17-48 and P-beta-Cat17-48 for the phosphorylated peptide at the two sites Ser33 and Ser37. Circular dichroism and NMR techniques were used to assess the influence of the phosphorylation. The spectra of the peptides at pH 7.2 were completely assigned. Analysis of the medium-range NOE connectivities indicated that beta-Cat17-48 seems to be only poorly folded. These data are in agreement with the result of structure calculations. P-beta-Cat17-48 possesses two helical segments around the DpSGXXpS motif, which forms a large bent with the phosphate groups pointing out of the structure. On the contrary, beta-Cat17-48 shows less well-defined secondary structures and appears as a more flexible peptide, but adopts in the motif DSGXXS a more compact conformation than P-beta-Cat17-48. Differences in this molecular region suggest that conformational changes of phosphorylated beta-Catenin play an important role for the interaction with the SCF-beta-TrCP protein complex. FAU - Megy, Simon AU - Megy S AD - Universite Rene Descartes-Paris V, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, 45 Rue des Saints-Peres, 75270 Paris Cedex 06, France. FAU - Bertho, Gildas AU - Bertho G FAU - Gharbi-Benarous, Josyane AU - Gharbi-Benarous J FAU - Baleux, Francoise AU - Baleux F FAU - Benarous, Richard AU - Benarous R FAU - Girault, Jean-Pierre AU - Girault JP LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Peptides JT - Peptides JID - 8008690 RN - 0 (Cytoskeletal Proteins) RN - 0 (Hydrocarbons, Fluorinated) RN - 0 (Peptides) RN - 0 (Solutions) RN - 0 (Trans-Activators) RN - 0 (beta Catenin) RN - 059QF0KO0R (Water) RN - 359-11-5 (trifluoroethene) RN - 452VLY9402 (Serine) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - Circular Dichroism MH - Consensus Sequence MH - Cytoskeletal Proteins/*chemistry MH - Hydrocarbons, Fluorinated/chemistry MH - Hydrogen-Ion Concentration MH - Models, Molecular MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides/chemical synthesis/*chemistry/isolation & purification MH - Phosphorylation MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Serine/chemistry MH - Solutions MH - Spectrum Analysis, Raman MH - Trans-Activators/*chemistry MH - Water/chemistry MH - beta Catenin EDAT- 2005/01/05 09:00 MHDA- 2005/06/29 09:00 CRDT- 2005/01/05 09:00 PHST- 2004/07/20 [received] PHST- 2004/09/27 [revised] PHST- 2004/09/28 [accepted] AID - S0196-9781(04)00444-9 [pii] AID - 10.1016/j.peptides.2004.09.021 [doi] PST - ppublish SO - Peptides. 2005 Feb;26(2):227-41. PMID- 8898894 OWN - NLM STAT- MEDLINE DA - 19961205 DCOM- 19961205 LR - 20070723 IS - 0014-2956 (Print) IS - 0014-2956 (Linking) VI - 241 IP - 1 DP - 1996 Oct 1 TI - Analysis of the solution structure of the homeodomain of rat thyroid transcription factor 1 by 1H-NMR spectroscopy and restrained molecular mechanics. PG - 101-13 AB - The solution structure of the rat thyroid transcription factor 1 (TTF-1) homeodomain has been elucidated by 1H-NMR and restrained modeling. The TTF-1 homeodomain folds in the same manner as classical homeodomains, with three helices, a loose loop between the first two helices, and a tight turn between helix II and helix III. The typical assembly of the hydrophobic core is maintained and N-capping motifs are identified in helix I and helix III. The N-terminal stretch of helix II exhibits some mobility, similar to the preceding loop region, which may be related to its anomalous capping. The N-terminal decapeptide and the C-terminal octapeptide of the molecule (68 residues long) are disordered. All the previous characteristics are shared by all known isolated homeodomain structures. An important difference among these structures occurs at the C-terminal extension of helix III, which is either disordered or helically folded. In the TTF-1 homeodomain, the C-terminal extension of helix III (residues 51-59) appears structured, albeit not as rigidly as the preceding portion. Analysis of the NOEs and hydrogendeuterium exchange of backbone amides provides evidence for discontinuity between the two moieties of helix III, which is introduced by a tightening or a kink of residues 51-53. FAU - Esposito, G AU - Esposito G AD - Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy. FAU - Fogolari, F AU - Fogolari F FAU - Damante, G AU - Damante G FAU - Formisano, S AU - Formisano S FAU - Tell, G AU - Tell G FAU - Leonardi, A AU - Leonardi A FAU - Di Lauro, R AU - Di Lauro R FAU - Viglino, P AU - Viglino P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - GERMANY TA - Eur J Biochem JT - European journal of biochemistry / FEBS JID - 0107600 RN - 0 (DNA-Binding Proteins) RN - 0 (Homeodomain Proteins) RN - 0 (Nuclear Proteins) RN - 0 (Transcription Factors) RN - 0 (thyroid nuclear factor 1) SB - IM MH - Animals MH - DNA-Binding Proteins/chemistry MH - Homeodomain Proteins/*chemistry MH - Hydrogen Bonding MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Nuclear Proteins/*chemistry MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Rats MH - Transcription Factors/*chemistry EDAT- 1996/10/01 MHDA- 1996/10/01 00:01 CRDT- 1996/10/01 00:00 PST - ppublish SO - Eur J Biochem. 1996 Oct 1;241(1):101-13. PMID- 20453917 OWN - NLM STAT- MEDLINE DA - 20100510 DCOM- 20100928 LR - 20140827 IS - 1208-6002 (Electronic) IS - 0829-8211 (Linking) VI - 88 IP - 2 DP - 2010 Apr TI - Fuzzy complexes of myelin basic protein: NMR spectroscopic investigations of a polymorphic organizational linker of the central nervous system. PG - 143-55 LID - 10.1139/o09-123 [doi] AB - The classic 18.5 kDa isoform of myelin basic protein (MBP) is central to maintaining the structural homeostasis of the myelin sheath of the central nervous system. It is an intrinsically disordered, promiscuous, multifunctional, peripheral membrane protein, whose conformation adapts to its particular environment. Its study requires the selective and complementary application of diverse approaches, of which solution and solid-state NMR spectroscopy are the most powerful to elucidate site-specific features. We review here several recent solution and solid-state NMR spectroscopic studies of 18.5 kDa MBP, and the induced partial disorder-to-order transitions that it has been demonstrated to undergo when complexed with calmodulin, actin, and phospholipid membranes. FAU - Libich, David S AU - Libich DS AD - Centre for Structural Biology, Institute of Fundamental Sciences, Department of Physics, Massey University, Palmerston North, New Zealand. d.s.libich@massey.ac.nz FAU - Ahmed, Mumdooh A M AU - Ahmed MA FAU - Zhong, Ligang AU - Zhong L FAU - Bamm, Vladimir V AU - Bamm VV FAU - Ladizhansky, Vladimir AU - Ladizhansky V FAU - Harauz, George AU - Harauz G LA - eng GR - 74468/Canadian Institutes of Health Research/Canada GR - MOP74468/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - Canada TA - Biochem Cell Biol JT - Biochemistry and cell biology = Biochimie et biologie cellulaire JID - 8606068 RN - 0 (Myelin Basic Protein) RN - 0 (Protein Isoforms) SB - IM MH - Animals MH - Central Nervous System/*chemistry MH - Humans MH - Magnetic Resonance Spectroscopy MH - Myelin Basic Protein/*chemistry MH - Protein Conformation MH - Protein Isoforms/*chemistry RF - 90 PMC - PMC3517781 MID - CAMS2553 OID - NLM: CAMS2553 OID - NLM: PMC3517781 EDAT- 2010/05/11 06:00 MHDA- 2010/09/30 06:00 CRDT- 2010/05/11 06:00 AID - o09-123 [pii] AID - 10.1139/o09-123 [doi] PST - ppublish SO - Biochem Cell Biol. 2010 Apr;88(2):143-55. doi: 10.1139/o09-123. PMID- 22125611 OWN - NLM STAT- MEDLINE DA - 20111129 DCOM- 20120402 LR - 20141021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 6 IP - 11 DP - 2011 TI - Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response. PG - e27371 LID - 10.1371/journal.pone.0027371 [doi] AB - Intrinsically disordered proteins (IDPs) are abundant in cells and have central roles in protein-protein interaction networks. Interactions between the IDP Prothymosin alpha (ProTalpha) and the Neh2 domain of Nuclear factor erythroid 2-related factor 2 (Nrf2), with a common binding partner, Kelch-like ECH-associated protein 1(Keap1), are essential for regulating cellular response to oxidative stress. Misregulation of this pathway can lead to neurodegenerative diseases, premature aging and cancer. In order to understand the mechanisms these two disordered proteins employ to bind to Keap1, we performed extensive 0.5-1.0 microsecond atomistic molecular dynamics (MD) simulations and isothermal titration calorimetry experiments to investigate the structure/dynamics of free-state ProTalpha and Neh2 and their thermodynamics of bindings. The results show that in their free states, both ProTalpha and Neh2 have propensities to form bound-state-like beta-turn structures but to different extents. We also found that, for both proteins, residues outside the Keap1-binding motifs may play important roles in stabilizing the bound-state-like structures. Based on our findings, we propose that the binding of disordered ProTalpha and Neh2 to Keap1 occurs synergistically via preformed structural elements (PSEs) and coupled folding and binding, with a heavy bias towards PSEs, particularly for Neh2. Our results provide insights into the molecular mechanisms Neh2 and ProTalpha bind to Keap1, information that is useful for developing therapeutics to enhance the oxidative stress response. FAU - Cino, Elio A AU - Cino EA AD - Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada. FAU - Wong-ekkabut, Jirasak AU - Wong-ekkabut J FAU - Karttunen, Mikko AU - Karttunen M FAU - Choy, Wing-Yiu AU - Choy WY LA - eng GR - MOP#74679/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111118 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (KEAP1 protein, human) RN - 0 (NF-E2-Related Factor 2) RN - 0 (Protein Precursors) RN - 0 (prothymosin alpha) RN - 61512-21-8 (Thymosin) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Calorimetry/methods MH - Crystallography, X-Ray MH - Humans MH - Intracellular Signaling Peptides and Proteins/*chemistry/metabolism MH - Models, Molecular MH - *Molecular Dynamics Simulation MH - Molecular Sequence Data MH - NF-E2-Related Factor 2/*chemistry/metabolism MH - Protein Binding MH - Protein Precursors/*chemistry/metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Thermodynamics MH - Thymosin/*analogs & derivatives/chemistry/metabolism MH - Time Factors PMC - PMC3220680 OID - NLM: PMC3220680 EDAT- 2011/11/30 06:00 MHDA- 2012/04/03 06:00 CRDT- 2011/11/30 06:00 PHST- 2011/07/20 [received] PHST- 2011/10/15 [accepted] PHST- 2011/11/18 [epublish] AID - 10.1371/journal.pone.0027371 [doi] AID - PONE-D-11-13828 [pii] PST - ppublish SO - PLoS One. 2011;6(11):e27371. doi: 10.1371/journal.pone.0027371. Epub 2011 Nov 18. PMID- 20593886 OWN - NLM STAT- MEDLINE DA - 20100810 DCOM- 20100827 LR - 20121115 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 49 IP - 32 DP - 2010 Aug 17 TI - Interaction of myelin basic protein with actin in the presence of dodecylphosphocholine micelles. PG - 6903-15 LID - 10.1021/bi100308d [doi] AB - The 18.5 kDa myelin basic protein (MBP), the most abundant splice isoform in human adult myelin, is a multifunctional, intrinsically disordered protein that maintains compact assembly of the myelin sheath in the central nervous system. Protein deimination and phosphorylation are two key posttranslational modifications whose balance determines local myelin microdomain stability and function. It has previously been shown that MBP in solution causes both polymerization of G-actin to F-actin and bundling of the microfilaments, and binds them to a negatively charged membrane. However, the binding parameters, and the roles of different possible interacting domains of membrane-associated MBP, have not yet been investigated. Here, we compared the interaction of unmodified (rmC1) and pseudodeiminated (rmC8) recombinant murine MBP (full-length charge variants), and of two terminal deletion variants (rmDeltaC and rmDeltaN), with actin in the presence of DPC (dodecylphosphocholine) to mimic a membrane environment. Our results show that although both charge variants polymerized and bundled actin, the maximal polymerization/bundling due to rmC1 occurred at a lower molar ratio compared to rmC8. In the presence of DPC, rmC1 appeared to be more active than rmC8 in its ability to polymerize and bundle actin, and the binding affinity of both charge variants to G-actin became higher. Moreover, of the two deletion variants studied in the presence of DPC, the one lacking the C-terminal domain (rmDeltaC) was more active compared to the variant lacking the N-terminal domain (rmDeltaN) but exhibited weaker binding to actin. Thus, whereas the N-terminal domain of MBP can be more important for the MBP's actin polymerization activity and membrane-association, the C-terminal domain can regulate its interaction with actin. FAU - Bamm, Vladimir V AU - Bamm VV AD - Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada. FAU - Ahmed, Mumdooh A M AU - Ahmed MA FAU - Harauz, George AU - Harauz G LA - eng GR - MOP 74468/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Actins) RN - 0 (Micelles) RN - 0 (Myelin Basic Protein) RN - 107-73-3 (Phosphorylcholine) RN - 53949-18-1 (dodecylphosphocholine) SB - IM MH - Actins/*chemistry/*metabolism MH - Animals MH - Chickens MH - Magnetic Resonance Spectroscopy MH - Mice MH - *Micelles MH - Microscopy, Electron, Transmission MH - Myelin Basic Protein/*chemistry/*metabolism MH - Phosphorylcholine/*analogs & derivatives/chemistry MH - Protein Binding/physiology EDAT- 2010/07/03 06:00 MHDA- 2010/08/28 06:00 CRDT- 2010/07/03 06:00 AID - 10.1021/bi100308d [doi] PST - ppublish SO - Biochemistry. 2010 Aug 17;49(32):6903-15. doi: 10.1021/bi100308d. PMID- 20178990 OWN - NLM STAT- MEDLINE DA - 20100412 DCOM- 20100506 LR - 20141120 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 285 IP - 16 DP - 2010 Apr 16 TI - Calcium-dependent conformational flexibility of a CUB domain controls activation of the complement serine protease C1r. PG - 11863-9 LID - 10.1074/jbc.M109.098541 [doi] AB - C1, the first component of the complement system, is a Ca(2+)-dependent heteropentamer complex of C1q and two modular serine proteases, C1r and C1s. Current functional models assume significant flexibility of the subcomponents. Noncatalytic modules in C1r have been proposed to provide the flexibility required for function. Using a recombinant CUB2-CCP1 domain pair and the individual CCP1 module, we showed that binding of Ca(2+) induces the folding of the CUB2 domain and stabilizes its structure. In the presence of Ca(2+), CUB2 shows a compact, folded structure, whereas in the absence of Ca(2+), it has a flexible, disordered conformation. CCP1 module is Ca(2+)-insensitive. Isothermal titration calorimetry revealed that CUB2 binds a single Ca(2+) with a relatively high K(D) (430 mum). In blood, the CUB2 domain of C1r is only partially (74%) saturated by Ca(2+), therefore the disordered, Ca(2+)-free form could provide the flexibility required for C1 activation. In accordance with this assumption, the effect of Ca(2+) on the autoactivation of native, isolated C1r zymogen was proved. In the case of infection-inflammation when the local Ca(2+) concentration decreases, this property of CUB2 domain could serve as subtle means to trigger the activation of the classical pathway of complement. The CUB2 domain of C1r is a novel example for globular protein domains with marginal stability, high conformational flexibility, and proteolytic sensitivity. The physical nature of the behavior of this domain is similar to that of intrinsically unstructured proteins, providing a further example of functionally relevant ligand-induced reorganization of a polypeptide chain. FAU - Major, Balazs AU - Major B AD - Institute of Enzymology, Hungarian Academy of Sciences, Budapest H-1113, Hungary. FAU - Kardos, Jozsef AU - Kardos J FAU - Kekesi, Katalin Adrienna AU - Kekesi KA FAU - Lorincz, Zsolt AU - Lorincz Z FAU - Zavodszky, Peter AU - Zavodszky P FAU - Gal, Peter AU - Gal P LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20100223 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA Primers) RN - 0 (Peptide Fragments) RN - 0 (Recombinant Proteins) RN - EC 3.4.21.41 (Complement C1r) RN - SY7Q814VUP (Calcium) SB - IM MH - Base Sequence MH - Calcium/metabolism MH - Complement C1r/*chemistry/genetics/*metabolism MH - DNA Primers/genetics MH - Enzyme Activation MH - Humans MH - In Vitro Techniques MH - Peptide Fragments/chemistry/genetics/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Stability MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/metabolism MH - Thermodynamics PMC - PMC2852923 OID - NLM: PMC2852923 EDAT- 2010/02/25 06:00 MHDA- 2010/05/07 06:00 CRDT- 2010/02/25 06:00 PHST- 2010/02/23 [aheadofprint] AID - M109.098541 [pii] AID - 10.1074/jbc.M109.098541 [doi] PST - ppublish SO - J Biol Chem. 2010 Apr 16;285(16):11863-9. doi: 10.1074/jbc.M109.098541. Epub 2010 Feb 23. PMID- 8755740 OWN - NLM STAT- MEDLINE DA - 19960916 DCOM- 19960916 LR - 20081121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 35 IP - 29 DP - 1996 Jul 23 TI - Functional interaction of the c-Myc transactivation domain with the TATA binding protein: evidence for an induced fit model of transactivation domain folding. PG - 9584-93 AB - c-Myc is a member of a family of sequence specific-DNA binding proteins that are thought to regulate the transcription of genes involved in normal cell growth, differentiation, and apoptosis. In order to understand how human c-myc functions as a transcription factor, we have studied the mechanism of action and structure of the N-terminal transactivation domain, amino acids 1-143. In a protein interaction assay, c-myc1-143 bound selectively to two basal transcription factors, the TATA binding protein (TBP) and the RAP74 subunit of TFIIF. Furthermore, the isolated c-myc transactivation domain competed for limiting factors required for the assembly of a functional preinitiation complex. This squelching of basal transcription was reversed in a dose-dependent manner by recombinant TBP. Taken together, these results identify TBP as an important target for the c-myc transactivation domain, during transcriptional initiation. Similar to other transactivation domains, the c-myc1-143 polypeptide showed little or no evidence of secondary structure, when measured by circular dichroism spectroscopy (CD) in aqueous solution. However, significant alpha-helical conformation was observed in the presence of the hydrophobic solvent trifluoroethanol. Strikingly, addition of TBP caused changes in the CD spectra consistent with induction of protein conformation in c-myc1-143 during interaction with the target factor. This change was specific for TBP as a similar effect was not observed in the presence of TFIIB. These data support a model in which target factors induce or stabilize a structural conformation in activator proteins during transcriptional transactivation. FAU - McEwan, I J AU - McEwan IJ AD - Department of Biosciences, Karolinska Institute, NOVUM, Huddinge, Sweden. iain.mcewan@cbt.ki.se FAU - Dahlman-Wright, K AU - Dahlman-Wright K FAU - Ford, J AU - Ford J FAU - Wright, A P AU - Wright AP LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Bacterial Proteins) RN - 0 (DNA Primers) RN - 0 (DNA-Binding Proteins) RN - 0 (LexA protein, Bacteria) RN - 0 (Peptide Fragments) RN - 0 (Proto-Oncogene Proteins c-myc) RN - 0 (Recombinant Fusion Proteins) RN - 0 (Repressor Proteins) RN - 0 (TATA-Box Binding Protein) RN - 0 (Transcription Factors) RN - 0 (Transcription Factors, TFII) RN - 0 (transcription factor TFIIF) RN - EC 3.4.21.- (Serine Endopeptidases) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/metabolism MH - Base Sequence MH - Circular Dichroism MH - DNA Primers MH - DNA-Binding Proteins/*metabolism MH - Humans MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/metabolism MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Proto-Oncogene Proteins c-myc/*chemistry/metabolism MH - Recombinant Fusion Proteins/metabolism MH - Repressor Proteins/metabolism MH - Serine Endopeptidases/metabolism MH - TATA Box MH - TATA-Box Binding Protein MH - Transcription Factors/*metabolism MH - *Transcription Factors, TFII MH - Transcription, Genetic MH - *Transcriptional Activation EDAT- 1996/07/23 MHDA- 1996/07/23 00:01 CRDT- 1996/07/23 00:00 AID - 10.1021/bi960793v [doi] AID - bi960793v [pii] PST - ppublish SO - Biochemistry. 1996 Jul 23;35(29):9584-93. PMID- 24835459 OWN - NLM STAT- In-Process DA - 20140618 LR - 20150617 IS - 1879-0445 (Electronic) IS - 0960-9822 (Linking) VI - 24 IP - 12 DP - 2014 Jun 16 TI - Genome-wide analysis reveals novel and discrete functions for tubulin carboxy-terminal tails. PG - 1295-303 LID - 10.1016/j.cub.2014.03.078 [doi] LID - S0960-9822(14)00400-X [pii] AB - BACKGROUND: Microtubules (MTs) support diverse transport and force generation processes in cells. Both alpha- and beta-tubulin proteins possess carboxy-terminal tail regions (CTTs) that are negatively charged, intrinsically disordered, and project from the MT surface where they interact with motors and other proteins. Although CTTs are presumed to play important roles in MT networks, these roles have not been determined in vivo. RESULTS: We examined the function of CTTs in vivo by using a systematic collection of mutants in budding yeast. We find that CTTs are not essential; however, loss of either alpha- or beta-CTT sensitizes cells to MT-destabilizing drugs. beta-CTT, but not alpha-CTT, regulates MT dynamics by increasing frequencies of catastrophe and rescue events. In addition, beta-CTT is critical for the assembly of the mitotic spindle and its elongation during anaphase. We use genome-wide genetic interaction screens to identify roles for alpha- and beta-CTTs, including a specific role for beta-CTT in supporting kinesin-5/Cin8. Our genetic screens also identified novel interactions with pathways not related to canonical MT functions. CONCLUSIONS: We conclude that alpha- and beta-CTTs play important and largely discrete roles in MT networks. beta-CTT promotes MT dynamics. beta-CTT also regulates force generation in the mitotic spindle by supporting kinesin-5/Cin8 and dampening dynein. Our genetic screens identify links between alpha- and beta-CTT and additional cellular pathways and suggest novel functions. CI - Copyright (c) 2014 Elsevier Ltd. All rights reserved. FAU - Aiken, Jayne AU - Aiken J AD - Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA. FAU - Sept, David AU - Sept D AD - Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA. FAU - Costanzo, Michael AU - Costanzo M AD - Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada. FAU - Boone, Charles AU - Boone C AD - Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada. FAU - Cooper, John A AU - Cooper JA AD - Department of Cell Biology and Physiology, Washington University, St. Louis, MO 63110, USA. FAU - Moore, Jeffrey K AU - Moore JK AD - Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address: jeffrey.moore@ucdenver.edu. LA - eng GR - GM076177/GM/NIGMS NIH HHS/United States GR - GM092968/GM/NIGMS NIH HHS/United States GR - GM38542/GM/NIGMS NIH HHS/United States GR - GM47337/GM/NIGMS NIH HHS/United States GR - HG005853/HG/NHGRI NIH HHS/United States GR - MOP-57830/Canadian Institutes of Health Research/Canada GR - R00 GM092968/GM/NIGMS NIH HHS/United States GR - R01 GM038542/GM/NIGMS NIH HHS/United States GR - R01 GM047337/GM/NIGMS NIH HHS/United States GR - R01 GM076177/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140515 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM PMC - PMC4070440 MID - NIHMS584421 OID - NLM: NIHMS584421 OID - NLM: PMC4070440 EDAT- 2014/05/20 06:00 MHDA- 2014/05/20 06:00 CRDT- 2014/05/20 06:00 PHST- 2013/10/29 [received] PHST- 2014/02/27 [revised] PHST- 2014/03/31 [accepted] PHST- 2014/05/15 [aheadofprint] AID - S0960-9822(14)00400-X [pii] AID - 10.1016/j.cub.2014.03.078 [doi] PST - ppublish SO - Curr Biol. 2014 Jun 16;24(12):1295-303. doi: 10.1016/j.cub.2014.03.078. Epub 2014 May 15. PMID- 17399679 OWN - NLM STAT- MEDLINE DA - 20070508 DCOM- 20070626 IS - 0003-9861 (Print) IS - 0003-9861 (Linking) VI - 461 IP - 2 DP - 2007 May 15 TI - The human cardiac hormone fragment N-terminal pro B-type natriuretic peptide is an intrinsically unstructured protein. PG - 242-6 AB - The cardiac hormone B-type natriuretic peptide (BNP) is synthesized as a prepro 134 residue molecule which is further proteolytically processed into a 76 residue fragment termed N-terminal proBNP (NT-proBNP) and the active portion of this hormone, a 32-residue disulfide-linked peptide (BNP-32). The active hormone regulates cardiac hemodynamic output while as yet no biological function has been attributed to NT-proBNP. Some solution properties of synthetically generated NT-proBNP in benign media are known. The protein is monomeric, elutes aberrantly on size-exclusion chromatography as an apparent larger molecular species, and possesses little global secondary structure as assessed by circular dichroism. To explore the solution structure of NT-proBNP in greater detail, we use 2D-NOESY and 2D-TOCSY NMR on recombinant NT-proBNP to obtain a high resolution solution conformation at the alpha-carbon level. Importantly, NH(i)-NH(i+1) coupling is virtually absent at room temperature implying that large stretches of primary sequence are unordered. Together, the results of these physicochemical measurements classify NT-proBNP as a naturally unfolded protein referred to as an Intrinsically Unstructured Protein (IUP). The calculations of FoldIndex, a computer program which predicts disorder, were compared to the experimental results described here for NT-proBNP in addition to proBNP. NT-proBNP thus appears to be an ideal candidate for the study of native, unfolded proteins. FAU - Crimmins, Dan L AU - Crimmins DL AD - Department of Pathology and Immunology, Division of Laboratory Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA. FAU - Kao, Jeffrey L-F AU - Kao JL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070315 PL - United States TA - Arch Biochem Biophys JT - Archives of biochemistry and biophysics JID - 0372430 RN - 0 (Peptide Fragments) RN - 0 (pro-brain natriuretic peptide (1-76)) RN - 114471-18-0 (Natriuretic Peptide, Brain) SB - IM MH - Computational Biology MH - Humans MH - Myocardium/*chemistry/metabolism MH - Natriuretic Peptide, Brain/*chemistry/metabolism MH - Peptide Fragments/*chemistry/metabolism MH - Protein Folding EDAT- 2007/04/03 09:00 MHDA- 2007/06/27 09:00 CRDT- 2007/04/03 09:00 PHST- 2007/01/05 [received] PHST- 2007/02/13 [revised] PHST- 2007/02/16 [accepted] PHST- 2007/03/15 [aheadofprint] AID - S0003-9861(07)00101-4 [pii] AID - 10.1016/j.abb.2007.02.024 [doi] PST - ppublish SO - Arch Biochem Biophys. 2007 May 15;461(2):242-6. Epub 2007 Mar 15. PMID- 10792060 OWN - NLM STAT- MEDLINE DA - 20000613 DCOM- 20000613 LR - 20140615 IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 97 IP - 10 DP - 2000 May 9 TI - A functional R domain from cystic fibrosis transmembrane conductance regulator is predominantly unstructured in solution. PG - 5657-62 AB - Phosphorylation of the regulatory (R) domain initiates cystic fibrosis transmembrane conductance regulator (CFTR) Cl(-) channel activity. To discover how the function of this domain is determined by its structure, we produced an R domain protein (R8) that spanned residues 708-831 of CFTR. Phosphorylated, but not unphosphorylated, R8 stimulated activity of CFTR channels lacking this domain, indicating that R8 is functional. Unexpectedly, this functional R8 was predominantly random coil, as revealed by CD and limited proteolysis. The CD spectra of both phosphorylated and nonphosphorylated R8 were similar in aqueous buffer. The folding agent trimethylamine N-oxide induced only a small increase in the helical content of nonphosphorylated R8 and even less change in the helical content of phosphorylated R8. These data, indicating that the R domain is predominantly random coil, may explain the seemingly complex way in which phosphorylation regulates CFTR channel activity. FAU - Ostedgaard, L S AU - Ostedgaard LS AD - Howard Hughes Medical Institute, Department of Internal Medicine, University of Iowa College of Medicine, Iowa City, IA 52242, USA. FAU - Baldursson, O AU - Baldursson O FAU - Vermeer, D W AU - Vermeer DW FAU - Welsh, M J AU - Welsh MJ FAU - Robertson, A D AU - Robertson AD LA - eng GR - HL42835/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (CFTR protein, human) RN - 0 (Recombinant Proteins) RN - 0 (Solutions) RN - 126880-72-6 (Cystic Fibrosis Transmembrane Conductance Regulator) RN - EC 2.7.11.11 (Cyclic AMP-Dependent Protein Kinases) SB - IM MH - Circular Dichroism MH - Cloning, Molecular MH - Cyclic AMP-Dependent Protein Kinases/metabolism MH - Cystic Fibrosis Transmembrane Conductance Regulator/*chemistry/genetics/*physiology MH - Escherichia coli MH - Humans MH - Models, Molecular MH - Mutagenesis, Site-Directed MH - Phosphorylation MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/metabolism MH - Sequence Deletion MH - Solutions PMC - PMC25884 OID - NLM: PMC25884 EDAT- 2000/05/03 09:00 MHDA- 2000/06/17 09:00 CRDT- 2000/05/03 09:00 AID - 10.1073/pnas.100588797 [doi] AID - 100588797 [pii] PST - ppublish SO - Proc Natl Acad Sci U S A. 2000 May 9;97(10):5657-62. PMID- 4040872 OWN - NLM STAT- MEDLINE DA - 19851017 DCOM- 19851017 LR - 20061115 IS - 0014-5793 (Print) IS - 0014-5793 (Linking) VI - 188 IP - 2 DP - 1985 Sep 2 TI - Characterization of the chymotryptic core of the adenovirus DNA-binding protein. PG - 248-52 AB - A fragment of the DNA-binding protein of adenovirus type 5 has been obtained by controlled chymotryptic digestion of the entire molecule. Partial sequence determination indicates that the fragment consists of amino acids 174-525. The fragment is biologically active as measured by its ability to substitute for the entire molecule in a reconstituted DNA replication system. Crystals have been obtained that show diffraction to 2 A. FAU - Tsernoglou, D AU - Tsernoglou D FAU - Tsugita, A AU - Tsugita A FAU - Tucker, A D AU - Tucker AD FAU - van der Vliet, P C AU - van der Vliet PC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - NETHERLANDS TA - FEBS Lett JT - FEBS letters JID - 0155157 RN - 0 (DNA-Binding Proteins) RN - 0 (Peptide Fragments) RN - 0 (Viral Proteins) RN - EC 3.4.21.1 (Chymotrypsin) SB - IM MH - Adenoviridae/*analysis MH - Amino Acid Sequence MH - Chymotrypsin MH - Crystallization MH - Crystallography MH - DNA Replication MH - DNA-Binding Proteins/*analysis MH - Peptide Fragments/analysis MH - Viral Proteins/*analysis EDAT- 1985/09/02 MHDA- 1985/09/02 00:01 CRDT- 1985/09/02 00:00 AID - 0014-5793(85)80381-1 [pii] PST - ppublish SO - FEBS Lett. 1985 Sep 2;188(2):248-52. PMID- 9650074 OWN - NLM STAT- MEDLINE DA - 19980923 DCOM- 19980923 LR - 20141120 IS - 0141-8130 (Print) IS - 0141-8130 (Linking) VI - 22 IP - 3-4 DP - 1998 May-Jun TI - NMR spectroscopy of alpha-crystallin. Insights into the structure, interactions and chaperone action of small heat-shock proteins. PG - 197-209 AB - The subunit molecular mass of alpha-crystallin, like many small heat-shock proteins (sHsps), is around 20 kDa although the protein exists as a large aggregate of average mass around 800 kDa. Despite this large size, a well-resolved 1H NMR spectrum is observed for alpha-crystallin which arises from short, polar, highly-flexible and solvent-exposed C-terminal extensions in each of the subunits, alpha A- and alpha B-crystallin. These extensions are not involved in interactions with other proteins (e.g. beta- and gamma-crystallins) under non-chaperone conditions. As determined by NMR studies on mutants of alpha A-crystallin with alterations in its C-terminal extension, the extensions have an important role in acting as solubilising agents for the relatively-hydrophobic alpha-crystallin molecule and the high-molecular-weight (HMW) complex that forms during the chaperone action. The related sHsp, Hsp25, also exhibits a flexible C-terminal extension. Under chaperone conditions, and in the HMW complex isolated from old lenses, the C-terminal extension of the alpha A-crystallin subunit maintains its flexibility whereas the alpha B-crystallin subunit loses, at least partially, its flexibility, implying that it is involved in interaction with the 'substrate' protein. The conformation of 'substrate' proteins when they interact with alpha-crystallin has been probed by 1H NMR spectroscopy and it is concluded that alpha-crystallin interacts with 'substrate' proteins that are in a disordered molten globule state, but only when this state is on its way to large-scale aggregation and precipitation. By monitoring the 1H and 31P NMR spectra of alpha-crystallin in the presence of increasing concentrations of urea, it is proposed that alpha-crystallin adopts a two-domain structure with the larger C-terminal domain unfolding first in the presence of denaturant. All these data have been combined into a model for the quaternary structure of alpha-crystallin. The model has two layers each of approximately 40 subunits arranged in an annulus or toroid. A large central cavity is present whose entrance is ringed by the flexible C-terminal extensions. A large hydrophobic region in the aggregate is exposed to solution and is available for interaction with 'substrate' proteins during the chaperone action. FAU - Carver, J A AU - Carver JA AD - Department of Chemistry, University of Wollongong, NSW, Australia. john_carver@uow.edu.au FAU - Lindner, R A AU - Lindner RA LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - ENGLAND TA - Int J Biol Macromol JT - International journal of biological macromolecules JID - 7909578 RN - 0 (Crystallins) RN - 0 (Heat-Shock Proteins) RN - 0 (Hspb1 protein, mouse) RN - 0 (Macromolecular Substances) RN - 0 (Molecular Chaperones) RN - 0 (Neoplasm Proteins) RN - 8W8T17847W (Urea) SB - IM MH - Aging/metabolism MH - Amino Acid Sequence MH - Animals MH - Crystallins/*chemistry/metabolism MH - Heat-Shock Proteins/*chemistry/genetics/metabolism MH - In Vitro Techniques MH - Macromolecular Substances MH - Magnetic Resonance Spectroscopy MH - Mice MH - Models, Molecular MH - Molecular Chaperones/*chemistry/genetics/metabolism MH - Molecular Sequence Data MH - Molecular Weight MH - Mutation MH - Neoplasm Proteins/chemistry/genetics/metabolism MH - Protein Conformation MH - Protein Denaturation MH - Urea EDAT- 1998/07/03 MHDA- 1998/07/03 00:01 CRDT- 1998/07/03 00:00 PST - ppublish SO - Int J Biol Macromol. 1998 May-Jun;22(3-4):197-209. PMID- 24223932 OWN - NLM STAT- MEDLINE DA - 20131113 DCOM- 20140818 LR - 20141112 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 8 IP - 11 DP - 2013 TI - Conformational analysis of isolated domains of Helicobacter pylori CagA. PG - e79367 LID - 10.1371/journal.pone.0079367 [doi] AB - The CagA protein of Helicobacter pylori is associated with increased virulence and gastric cancer risk. CagA is translocated into the host cell by a H. pylori type IV secretion system via mechanisms that are poorly understood. Translocated CagA interacts with numerous host factors, altering a variety of host signalling pathways. The recently determined crystal structure of C-terminally-truncated CagA indicated the presence of two domains: the smaller, flexible N-terminal domain and the larger, middle domain. In this study, we have investigated the conformation, oligomeric state and stability of the N-terminal, middle and glutamate-proline-isoleucine-tyrosine-alanine (EPIYA)-repeats domains. All three domains are monomeric, suggesting that the multimerisation of CagA observed in infected cells is likely to be mediated not by CagA itself but by its interacting partners. The middle and the C-terminal domains, but not the N-terminal domain, are capable of refolding spontaneously upon heat denaturation, lending support to the hypothesis that unfolded CagA is threaded C-terminus first through the type IV secretion channel with its N-terminal domain, which likely requires interactions with other domains to refold, being threaded last. Our findings also revealed that the C-terminal EPIYA-repeats domain of CagA exists in an intrinsically disordered premolten globule state with regions in PPII conformation--a feature that is shared by many scaffold proteins that bind multiple protein components of signalling pathways. Taken together, these results provide a deeper understanding of the physicochemical properties of CagA that underpin its complex cellular and oncogenic functions. FAU - Woon, Amanda P AU - Woon AP AD - Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia. FAU - Tohidpour, Abolghasem AU - Tohidpour A FAU - Alonso, Hernan AU - Alonso H FAU - Saijo-Hamano, Yumiko AU - Saijo-Hamano Y FAU - Kwok, Terry AU - Kwok T FAU - Roujeinikova, Anna AU - Roujeinikova A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20131101 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Antigens, Bacterial) RN - 0 (Bacterial Proteins) RN - 0 (cagA protein, Helicobacter pylori) SB - IM MH - Amino Acid Sequence MH - Antigens, Bacterial/*chemistry/metabolism MH - Bacterial Proteins/*chemistry/metabolism MH - Crystallography, X-Ray MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Denaturation MH - Protein Multimerization MH - Protein Stability MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proteolysis MH - Repetitive Sequences, Amino Acid MH - Temperature PMC - PMC3815135 OID - NLM: PMC3815135 EDAT- 2013/11/14 06:00 MHDA- 2014/08/19 06:00 CRDT- 2013/11/14 06:00 PHST- 2013 [ecollection] PHST- 2013/08/09 [received] PHST- 2013/09/26 [accepted] PHST- 2013/11/01 [epublish] AID - 10.1371/journal.pone.0079367 [doi] AID - PONE-D-13-32760 [pii] PST - epublish SO - PLoS One. 2013 Nov 1;8(11):e79367. doi: 10.1371/journal.pone.0079367. eCollection 2013. PMID- 18197970 OWN - NLM STAT- MEDLINE DA - 20080228 DCOM- 20080314 LR - 20140904 IS - 1471-2202 (Electronic) IS - 1471-2202 (Linking) VI - 9 DP - 2008 TI - Evolution of NMDA receptor cytoplasmic interaction domains: implications for organisation of synaptic signalling complexes. PG - 6 LID - 10.1186/1471-2202-9-6 [doi] AB - BACKGROUND: Glutamate gated postsynaptic receptors in the central nervous system (CNS) are essential for environmentally stimulated behaviours including learning and memory in both invertebrates and vertebrates. Though their genetics, biochemistry, physiology, and role in behaviour have been intensely studied in vitro and in vivo, their molecular evolution and structural aspects remain poorly understood. To understand how these receptors have evolved different physiological requirements we have investigated the molecular evolution of glutamate gated receptors and ion channels, in particular the N-methyl-D-aspartate (NMDA) receptor, which is essential for higher cognitive function. Studies of rodent NMDA receptors show that the C-terminal intracellular domain forms a signalling complex with enzymes and scaffold proteins, which is important for neuronal and behavioural plasticity RESULTS: The vertebrate NMDA receptor was found to have subunits with C-terminal domains up to 500 amino acids longer than invertebrates. This extension was specific to the NR2 subunit and occurred before the duplication and subsequent divergence of NR2 in the vertebrate lineage. The shorter invertebrate C-terminus lacked vertebrate protein interaction motifs involved with forming a signaling complex although the terminal PDZ interaction domain was conserved. The vertebrate NR2 C-terminal domain was predicted to be intrinsically disordered but with a conserved secondary structure. CONCLUSION: We highlight an evolutionary adaptation specific to vertebrate NMDA receptor NR2 subunits. Using in silico methods we find that evolution has shaped the NMDA receptor C-terminus into an unstructured but modular intracellular domain that parallels the expansion in complexity of an NMDA receptor signalling complex in the vertebrate lineage. We propose the NR2 C-terminus has evolved to be a natively unstructured yet flexible hub organising postsynaptic signalling. The evolution of the NR2 C-terminus and its associated signalling complex may contribute to species differences in behaviour and in particular cognitive function. FAU - Ryan, Tomas J AU - Ryan TJ AD - Genes to Cognition Program, Wellcome Trust Sanger Institute, Cambridge, UK. tr1@sanger.ac.uk FAU - Emes, Richard D AU - Emes RD FAU - Grant, Seth Gn AU - Grant SG FAU - Komiyama, Noboru H AU - Komiyama NH LA - eng GR - G90/112/Medical Research Council/United Kingdom GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080115 PL - England TA - BMC Neurosci JT - BMC neuroscience JID - 100966986 RN - 0 (N-methyl D-aspartate receptor subtype 2A) RN - 0 (NR2B NMDA receptor) RN - 0 (Receptors, N-Methyl-D-Aspartate) SB - IM MH - Amino Acid Sequence MH - Animals MH - Conserved Sequence MH - Cytoplasm/*metabolism MH - *Evolution, Molecular MH - Invertebrates/genetics MH - Mice MH - Models, Molecular MH - Molecular Sequence Data MH - PDZ Domains/genetics MH - Protein Binding MH - Protein Interaction Mapping MH - Receptors, N-Methyl-D-Aspartate/*chemistry/*metabolism MH - Sequence Alignment MH - Sequence Analysis, Protein MH - Species Specificity MH - Synaptic Transmission/*genetics PMC - PMC2257970 OID - NLM: PMC2257970 EDAT- 2008/01/17 09:00 MHDA- 2008/03/15 09:00 CRDT- 2008/01/17 09:00 PHST- 2007/08/17 [received] PHST- 2008/01/15 [accepted] PHST- 2008/01/15 [aheadofprint] AID - 1471-2202-9-6 [pii] AID - 10.1186/1471-2202-9-6 [doi] PST - epublish SO - BMC Neurosci. 2008 Jan 15;9:6. doi: 10.1186/1471-2202-9-6. PMID- 21635954 OWN - NLM STAT- MEDLINE DA - 20110803 DCOM- 20120126 LR - 20141022 IS - 1095-8657 (Electronic) IS - 1047-8477 (Linking) VI - 175 IP - 3 DP - 2011 Sep TI - Structure and stability of the lamin A tail domain and HGPS mutant. PG - 425-33 LID - 10.1016/j.jsb.2011.05.015 [doi] AB - Hutchinson-Gilford progeria syndrome (HGPS) is a premature aging syndrome caused by the expression and accumulation of a mutant form of lamin A, Delta50 lamin A. As a component of the cell's nucleoskeleton, lamin A plays an important role in the mechanical stabilization of the nuclear envelope and in other nuclear functions. It is largely unknown how the characteristic 50 amino acid deletion affects the conformation of the mostly intrinsically disordered tail domain of lamin A. Here we perform replica exchange molecular dynamics simulations of the tail domain and determine an ensemble of semi-stable structures. Based on these structures we show that the ZMPSTE 24 cleavage site on the precursor form of the lamin A tail domain orients itself in such a way as to facilitate cleavage during the maturation process. We confirm our simulated structures by comparing the thermodynamic properties of the ensemble structures to in vitro stability measurements. Using this combination of experimental and computational techniques, we compare the size, heterogeneity of size, thermodynamic stability of the Ig-fold, as well as the mechanisms of force-induced denaturation. Our data shows that the Delta50 lamin A tail domain is more compact and displays less heterogeneity than the mature lamin A tail domain. Altogether these results suggest that the altered structure and stability of the tail domain can explain changed protein-protein and protein-DNA interactions and may represent an etiology of the disease. Also, this study provides the first molecular structure(s) of the lamin A tail domain, which is confirmed by thermodynamic tests in experiment. CI - Copyright (c) 2011 Elsevier Inc. All rights reserved. FAU - Qin, Zhao AU - Qin Z AD - Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Mass. Ave., Room 1-235A&B, Cambridge, MA 02139, USA. FAU - Kalinowski, Agnieszka AU - Kalinowski A FAU - Dahl, Kris Noel AU - Dahl KN FAU - Buehler, Markus J AU - Buehler MJ LA - eng GR - F30 AG030905-01A2/AG/NIA NIH HHS/United States GR - F30 AG030905-02/AG/NIA NIH HHS/United States GR - F30 AG030905-03/AG/NIA NIH HHS/United States GR - F30 AG030905-04/AG/NIA NIH HHS/United States GR - F30AG030905/AG/NIA NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20110524 PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - 0 (Lamin Type A) SB - IM MH - Amino Acid Sequence MH - Animals MH - Fluorometry MH - Lamin Type A/*chemistry/*genetics MH - Mice MH - Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Mutation MH - Progeria/*genetics MH - Protein Stability MH - Protein Structure, Secondary PMC - PMC3150306 MID - NIHMS300088 OID - NLM: NIHMS300088 OID - NLM: PMC3150306 EDAT- 2011/06/04 06:00 MHDA- 2012/01/27 06:00 CRDT- 2011/06/04 06:00 PHST- 2011/03/08 [received] PHST- 2011/05/13 [revised] PHST- 2011/05/17 [accepted] PHST- 2011/05/24 [aheadofprint] AID - S1047-8477(11)00163-8 [pii] AID - 10.1016/j.jsb.2011.05.015 [doi] PST - ppublish SO - J Struct Biol. 2011 Sep;175(3):425-33. doi: 10.1016/j.jsb.2011.05.015. Epub 2011 May 24. PMID- 19464966 OWN - NLM STAT- MEDLINE DA - 20090811 DCOM- 20091104 LR - 20140917 IS - 1568-7856 (Electronic) IS - 1568-7856 (Linking) VI - 8 IP - 9 DP - 2009 Sep 2 TI - A tale of two tails: activation of DNA damage checkpoint kinase Mec1/ATR by the 9-1-1 clamp and by Dpb11/TopBP1. PG - 996-1003 LID - 10.1016/j.dnarep.2009.03.011 [doi] AB - The DNA damage and replication checkpoint kinase Mec1/ATR is a member of the PI3-kinase related kinases that function in response to various genotoxic stresses. The checkpoint clamp 9-1-1 (Rad9-Rad1-Hus1 in S. pombe and mammals; Ddc1-Rad17-Mec3 in S. cerevisiae) executes two distinct checkpoint functions. In S. cerevisiae, DNA-bound 9-1-1 directly activates Mec1 kinase activity, a function that has not been demonstrated in other organisms. A second, conserved activity of 9-1-1 is that of TopBP1/Cut5/Dpb11 recruitment to stalled replication sites; subsequent activation of Mec1/ATR is carried out by TopBP1/Cut5/Dpb11. Biochemical studies indicate that the mode of Mec1/ATR activation by S. cerevisiae 9-1-1 is analogous to activation by S. cerevisiae Dpb11 or by vertebrate TopBP1: activation is mediated by the intrinsically disordered C-terminal tail of each activator. The relative contributions made by multiple activators of Mec1/ATR are discussed. FAU - Navadgi-Patil, Vasundhara M AU - Navadgi-Patil VM AD - Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States. FAU - Burgers, Peter M AU - Burgers PM LA - eng GR - GM32431/GM/NIGMS NIH HHS/United States GR - R01 GM032431/GM/NIGMS NIH HHS/United States GR - R01 GM032431-24/GM/NIGMS NIH HHS/United States GR - R01 GM083970/GM/NIGMS NIH HHS/United States GR - R01 GM083970-01A1/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review DEP - 20090522 PL - Netherlands TA - DNA Repair (Amst) JT - DNA repair JID - 101139138 RN - 0 (Cell Cycle Proteins) RN - 0 (DPB11 protein, S cerevisiae) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - EC 2.7.11.1 (MEC1 protein, S cerevisiae) RN - EC 2.7.11.1 (Protein-Serine-Threonine Kinases) SB - IM MH - Cell Cycle Proteins/*metabolism MH - *DNA Damage MH - Enzyme Activation MH - Intracellular Signaling Peptides and Proteins/*metabolism MH - Protein-Serine-Threonine Kinases/*metabolism MH - Saccharomyces cerevisiae/*enzymology MH - Saccharomyces cerevisiae Proteins/*metabolism RF - 92 PMC - PMC2725207 MID - NIHMS114293 OID - NLM: NIHMS114293 OID - NLM: PMC2725207 EDAT- 2009/05/26 09:00 MHDA- 2009/11/05 06:00 CRDT- 2009/05/26 09:00 PHST- 2009/03/25 [received] PHST- 2009/03/25 [accepted] PHST- 2009/05/22 [aheadofprint] AID - S1568-7864(09)00099-8 [pii] AID - 10.1016/j.dnarep.2009.03.011 [doi] PST - ppublish SO - DNA Repair (Amst). 2009 Sep 2;8(9):996-1003. doi: 10.1016/j.dnarep.2009.03.011. Epub 2009 May 22. PMID- 22988850 OWN - NLM STAT- MEDLINE DA - 20120919 DCOM- 20130226 LR - 20141121 IS - 1470-8752 (Electronic) IS - 0300-5127 (Linking) VI - 40 IP - 5 DP - 2012 Oct TI - Interplay between allostery and intrinsic disorder in an ensemble. PG - 975-80 AB - Allostery is a biological phenomenon of critical importance in metabolic regulation and cell signalling. The fundamental premise of classical models that describe allostery is that structure mediates 'action at a distance'. Recently, this paradigm has been challenged by the enrichment of IDPs (intrinsically disordered proteins) or ID (intrinsically disordered) segments in transcription factors and signalling pathways of higher organisms, where an allosteric response from external signals is requisite for regulated function. This observation strongly suggests that IDPs elicit the capacity for finely tunable allosteric regulation. Is there a set of transferable ground rules that reconcile these disparate allosteric phenomena? We focus on findings from the human GR (glucocorticoid receptor) which is a nuclear transcription factor in the SHR (steroid hormone receptor) family. GR contains an intrinsically disordered NTD (N-terminal domain) that is obligatory for transcription activity. Different GR translational isoforms have various lengths of NTD and by studying these isoforms we found that the full-length ID NTD consists of two thermodynamically distinct coupled regions. The data are interpreted in the context of an EAM (ensemble allosteric model) that considers only the intrinsic and measurable energetics of allosteric systems. Expansion of the EAM is able to reconcile the paradox that ligands for SHRs can be agonists and antagonists in a cell-context-dependent manner. These findings suggest a mechanism by which SHRs in particular, and IDPs in general, may have evolved to couple thermodynamically distinct ID segments. The ensemble view of allostery that is illuminated provides organizing principles to unify the description of all allosteric systems and insight into 'how' allostery works. FAU - Motlagh, Hesam N AU - Motlagh HN AD - T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA. FAU - Li, Jing AU - Li J FAU - Thompson, E Brad AU - Thompson EB FAU - Hilser, Vincent J AU - Hilser VJ LA - eng GR - T32 GM008403/GM/NIGMS NIH HHS/United States GR - T32-GM008403/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Review PL - England TA - Biochem Soc Trans JT - Biochemical Society transactions JID - 7506897 RN - 0 (Ligands) RN - 0 (Receptors, Glucocorticoid) SB - IM MH - Allosteric Regulation/drug effects MH - Animals MH - Humans MH - Ligands MH - Models, Molecular MH - Receptors, Glucocorticoid/agonists/antagonists & inhibitors/*metabolism MH - Thermodynamics PMC - PMC4231872 MID - NIHMS639959 OID - NLM: NIHMS639959 OID - NLM: PMC4231872 EDAT- 2012/09/20 06:00 MHDA- 2013/02/27 06:00 CRDT- 2012/09/20 06:00 AID - BST20120163 [pii] AID - 10.1042/BST20120163 [doi] PST - ppublish SO - Biochem Soc Trans. 2012 Oct;40(5):975-80. PMID- 22988851 OWN - NLM STAT- MEDLINE DA - 20120919 DCOM- 20130226 IS - 1470-8752 (Electronic) IS - 0300-5127 (Linking) VI - 40 IP - 5 DP - 2012 Oct TI - Cell cycle regulation by the intrinsically disordered proteins p21 and p27. PG - 981-8 AB - Today, it is widely accepted that proteins that lack highly defined globular three-dimensional structures, termed IDPs (intrinsically disordered proteins), play key roles in myriad biological processes. Our understanding of how intrinsic disorder mediates biological function is, however, incomplete. In the present paper, we review disorder-mediated cell cycle regulation by two intrinsically disordered proteins, p21 and p27. A structural adaptation mechanism involving a stretchable dynamic linker helix allows p21 to promiscuously recognize the various Cdk (cyclin-dependent kinase)-cyclin complexes that regulate cell division. Disorder within p27 mediates transmission of an N-terminal tyrosine phosphorylation signal to a C-terminal threonine phosphorylation, constituting a signalling conduit. These mechanisms are mediated by folding upon binding p21/p27's regulatory targets. However, residual disorder within the bound state contributes critically to these functional mechanisms. Our studies provide insights into how intrinsic protein disorder mediates regulatory processes and opportunities for designing drugs that target cancer-associated IDPs. FAU - Yoon, Mi-Kyung AU - Yoon MK AD - St. Jude Children's Research Hospital, Department of Structural Biology, 262 Danny Thomas Place, Memphis TN, 38105, U.S.A. FAU - Mitrea, Diana M AU - Mitrea DM FAU - Ou, Li AU - Ou L FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng GR - 5P30CA021765/CA/NCI NIH HHS/United States GR - 5R01CA082491/CA/NCI NIH HHS/United States GR - 5R01GM083159/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Biochem Soc Trans JT - Biochemical Society transactions JID - 7506897 RN - 0 (Cyclin-Dependent Kinase Inhibitor p21) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) SB - IM MH - *Cell Cycle MH - Cyclin-Dependent Kinase Inhibitor p21/chemistry/*metabolism MH - Cyclin-Dependent Kinase Inhibitor p27/chemistry/*metabolism MH - Humans MH - Models, Molecular EDAT- 2012/09/20 06:00 MHDA- 2013/02/27 06:00 CRDT- 2012/09/20 06:00 AID - BST20120092 [pii] AID - 10.1042/BST20120092 [doi] PST - ppublish SO - Biochem Soc Trans. 2012 Oct;40(5):981-8. PMID- 22988853 OWN - NLM STAT- MEDLINE DA - 20120919 DCOM- 20130226 IS - 1470-8752 (Electronic) IS - 0300-5127 (Linking) VI - 40 IP - 5 DP - 2012 Oct TI - An intrinsically disordered protein, CP12: jack of all trades and master of the Calvin cycle. PG - 995-9 AB - Many proteins contain disordered regions under physiological conditions and lack specific three-dimensional structure. These are referred to as IDPs (intrinsically disordered proteins). CP12 is a chloroplast protein of approximately 80 amino acids and has a molecular mass of approximately 8.2-8.5 kDa. It is enriched in charged amino acids and has a small number of hydrophobic residues. It has a high proportion of disorder-promoting residues, but has at least two (often four) cysteine residues forming one (or two) disulfide bridge(s) under oxidizing conditions that confers some order. However, CP12 behaves like an IDP. It appears to be universally distributed in oxygenic photosynthetic organisms and has recently been detected in a cyanophage. The best studied role of CP12 is its regulation of the Calvin cycle responsible for CO2 assimilation. Oxidized CP12 forms a supramolecular complex with two key Calvin cycle enzymes, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and PRK (phosphoribulokinase), down-regulating their activity. Association-dissociation of this complex, induced by the redox state of CP12, allows the Calvin cycle to be inactive in the dark and active in the light. CP12 is promiscuous and interacts with other enzymes such as aldolase and malate dehydrogenase. It also plays other roles in plant metabolism such as protecting GAPDH from inactivation and scavenging metal ions such as copper and nickel, and it is also linked to stress responses. Thus CP12 seems to be involved in many functions in photosynthetic cells and behaves like a jack of all trades as well as being a master of the Calvin cycle. FAU - Gontero, Brigitte AU - Gontero B AD - Laboratoire de Bioenergetique et Ingenierie des Proteines (BIP), CNRS-UMR 7281, Aix-Marseille Universite (AMU), Institut de Microbiologie de la Mediterranee, CNRS, 31 Chemin Joseph Aiguier, B.P. 71, 13402 Marseille Cedex 20, France. bmeunier@imm.cnrs.fr FAU - Maberly, Stephen C AU - Maberly SC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review PL - England TA - Biochem Soc Trans JT - Biochemical Society transactions JID - 7506897 RN - 0 (Chloroplast Proteins) SB - IM MH - Amino Acid Sequence MH - Chloroplast Proteins/chemistry/*metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - *Photosynthesis EDAT- 2012/09/20 06:00 MHDA- 2013/02/27 06:00 CRDT- 2012/09/20 06:00 AID - BST20120097 [pii] AID - 10.1042/BST20120097 [doi] PST - ppublish SO - Biochem Soc Trans. 2012 Oct;40(5):995-9. PMID- 22988856 OWN - NLM STAT- MEDLINE DA - 20120919 DCOM- 20130226 LR - 20141105 IS - 1470-8752 (Electronic) IS - 0300-5127 (Linking) VI - 40 IP - 5 DP - 2012 Oct TI - Native disorder mediates binding of dynein to NudE and dynactin. PG - 1009-13 AB - In the present paper, I report the molecular overlap of the linkage of three essential protein complexes that co-ordinate the formation of the mitotic spindle. These proteins are dynein, a large motor complex that moves machinery inside cells, and two of its regulators: a protein complex called dynactin, a dynein activator, and a protein called NudE whose depletion in mice produces a small brain and mental retardation. What is intriguing about the dynein-dynactin-NudE interplay is that dynactin and NudE bind to a common segment of dynein that is intrinsically disordered. Elucidating differences in their binding modes may explain how one regulator can be selected over the other even when both are present in the same cellular compartment. These results not only have a far-reaching impact on our understanding of processes essential for the formation and orientation of the spindle, but also offer a novel role for protein disorder in controlling cellular processes, and highlight the advantages of NMR spectroscopy in elucidating atomic-level characterization of extremely complex dynamic cellular assemblies. FAU - Barbar, Elisar AU - Barbar E AD - Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA. barbare@science.oregonstate.edu LA - eng GR - GM 084276/GM/NIGMS NIH HHS/United States GR - R01 GM084276/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Review PL - England TA - Biochem Soc Trans JT - Biochemical Society transactions JID - 7506897 RN - 0 (Fungal Proteins) RN - 0 (Microtubule-Associated Proteins) RN - 0 (RO-11 protein, Neurospora crassa) RN - 144198-36-7 (dynactin) RN - EC 3.6.4.2 (Dyneins) SB - IM MH - Animals MH - Binding Sites MH - Dyneins/chemistry/*metabolism MH - Fungal Proteins/chemistry/*metabolism MH - Humans MH - Microtubule-Associated Proteins/chemistry/*metabolism MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular PMC - PMC3785714 MID - NIHMS511289 OID - NLM: NIHMS511289 OID - NLM: PMC3785714 EDAT- 2012/09/20 06:00 MHDA- 2013/02/27 06:00 CRDT- 2012/09/20 06:00 AID - BST20120180 [pii] AID - 10.1042/BST20120180 [doi] PST - ppublish SO - Biochem Soc Trans. 2012 Oct;40(5):1009-13. PMID- 22544803 OWN - NLM STAT- MEDLINE DA - 20120625 DCOM- 20120920 LR - 20141016 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 287 IP - 26 DP - 2012 Jun 22 TI - Effect of DNA binding on geminate CO recombination kinetics in CO-sensing transcription factor CooA. PG - 21729-40 LID - 10.1074/jbc.M112.345090 [doi] AB - Carbon monoxide oxidation activator (CooA) proteins are heme-based CO-sensing transcription factors. Here we study the ultrafast dynamics of geminate CO rebinding in two CooA homologues, Rhodospirillum rubrum (RrCooA) and Carboxydothermus hydrogenoformans (ChCooA). The effects of DNA binding and the truncation of the DNA-binding domain on the CO geminate recombination kinetics were specifically investigated. The CO rebinding kinetics in these CooA complexes take place on ultrafast time scales but remain non-exponential over many decades in time. We show that this non-exponential kinetic response is due to a quenched enthalpic barrier distribution resulting from a distribution of heme geometries that is frozen or slowly evolving on the time scale of CO rebinding. We also show that, upon CO binding, the distal pocket of the heme in the CooA proteins relaxes to form a very efficient hydrophobic trap for CO. DNA binding further tightens the narrow distal pocket and slightly weakens the iron-proximal histidine bond. Comparison of the CO rebinding kinetics of RrCooA, truncated RrCooA, and DNA-bound RrCooA proteins reveals that the uncomplexed and inherently flexible DNA-binding domain adds additional structural heterogeneity to the heme doming coordinate. When CooA forms a complex with DNA, the flexibility of the DNA-binding domain decreases, and the distribution of the conformations available in the heme domain becomes restricted. The kinetic studies also offer insights into how the architecture of the heme environment can tune entropic barriers in order to control the geminate recombination of CO in heme proteins, whereas spin selection rules play a minor or non-existent role. FAU - Benabbas, Abdelkrim AU - Benabbas A AD - Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA. FAU - Karunakaran, Venugopal AU - Karunakaran V FAU - Youn, Hwan AU - Youn H FAU - Poulos, Thomas L AU - Poulos TL FAU - Champion, Paul M AU - Champion PM LA - eng GR - DK35090/DK/NIDDK NIH HHS/United States GR - GM42614/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120428 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Bacterial Proteins) RN - 0 (CooA protein, Rhodospirillum rubrum) RN - 0 (DNA-Binding Proteins) RN - 0 (Hemeproteins) RN - 0 (Ligands) RN - 0 (Recombinant Proteins) RN - 0 (Trans-Activators) RN - 42VZT0U6YR (Heme) RN - 7U1EE4V452 (Carbon Monoxide) RN - 9007-49-2 (DNA) SB - IM MH - Allosteric Site MH - Bacteria/*metabolism MH - Bacterial Proteins/*chemistry MH - Carbon Monoxide/*chemistry MH - DNA/*chemistry MH - DNA-Binding Proteins/chemistry MH - Heme/chemistry MH - Hemeproteins/*chemistry MH - Kinetics MH - Ligands MH - Models, Molecular MH - Models, Statistical MH - Molecular Conformation MH - Protein Binding MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry MH - Rhodospirillum rubrum/*metabolism MH - Time Factors MH - Trans-Activators/*chemistry MH - Transcription, Genetic PMC - PMC3381135 OID - NLM: PMC3381135 EDAT- 2012/05/01 06:00 MHDA- 2012/09/21 06:00 CRDT- 2012/05/01 06:00 PHST- 2012/04/28 [aheadofprint] AID - M112.345090 [pii] AID - 10.1074/jbc.M112.345090 [doi] PST - ppublish SO - J Biol Chem. 2012 Jun 22;287(26):21729-40. doi: 10.1074/jbc.M112.345090. Epub 2012 Apr 28. PMID- 22620680 OWN - NLM STAT- MEDLINE DA - 20120830 DCOM- 20120917 LR - 20131121 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 51 IP - 23 DP - 2012 Jun 12 TI - gamma-Synuclein: seeding of alpha-synuclein aggregation and transmission between cells. PG - 4743-54 LID - 10.1021/bi300478w [doi] AB - Protein misfolding and aggregation is a ubiquitous phenomenon associated with a wide range of diseases. The synuclein family comprises three small naturally unfolded proteins implicated in neurodegenerative diseases and some forms of cancer. alpha-Synuclein is a soluble protein that forms toxic inclusions associated with Parkinson's disease and several other synucleinopathies. However, the triggers inducing its conversion into noxious species are elusive. Here we show that another member of the family, gamma-synuclein, can be easily oxidized and form annular oligomers that accumulate in cells in the form of deposits. Importantly, oxidized gamma-synuclein can initiate alpha-synuclein aggregation. Two amino acid residues in gamma-synuclein, methionine and tyrosine located in neighboring positions (Met(38) and Tyr(39)), are most easily oxidized. Their oxidation plays a key role in the ability of gamma-synuclein to aggregate and seed the aggregation of alpha-synuclein. gamma-Synuclein secreted from neuronal cells into conditioned medium in the form of exosomes can be transmitted to glial cells and cause the aggregation of intracellular proteins. Our data suggest that post-translationally modified gamma-synuclein possesses prion-like properties and may induce a cascade of events leading to synucleinopathies. FAU - Surgucheva, Irina AU - Surgucheva I AD - Veterans Administration Medical Center, Kansas City, MO 66148, USA. FAU - Sharov, Victor S AU - Sharov VS FAU - Surguchov, Andrei AU - Surguchov A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20120530 PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Aniline Compounds) RN - 0 (Antibodies) RN - 0 (Benzylidene Compounds) RN - 0 (GW 4869) RN - 0 (Glial Fibrillary Acidic Protein) RN - 0 (alpha-Synuclein) RN - 0 (beta-Cyclodextrins) RN - 0 (gamma-Synuclein) RN - 0 (methyl-beta-cyclodextrin) RN - AE28F7PNPL (Methionine) SB - IM MH - Aniline Compounds/pharmacology MH - Animals MH - Antibodies MH - Astrocytes MH - Benzylidene Compounds/pharmacology MH - Cell Line MH - Gene Expression Regulation MH - Glial Fibrillary Acidic Protein/genetics/metabolism MH - Mass Spectrometry MH - Methionine MH - Models, Molecular MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Rats MH - T-Lymphocytes MH - alpha-Synuclein/*metabolism MH - beta-Cyclodextrins/pharmacology MH - gamma-Synuclein/*metabolism EDAT- 2012/05/25 06:00 MHDA- 2012/09/18 06:00 CRDT- 2012/05/25 06:00 PHST- 2012/05/30 [aheadofprint] AID - 10.1021/bi300478w [doi] PST - ppublish SO - Biochemistry. 2012 Jun 12;51(23):4743-54. doi: 10.1021/bi300478w. Epub 2012 May 30. PMID- 25080056 OWN - NLM STAT- In-Process DA - 20140819 IS - 1520-4898 (Electronic) IS - 0001-4842 (Linking) VI - 47 IP - 8 DP - 2014 Aug 19 TI - The ongoing search for small molecules to study metal-associated amyloid-beta species in Alzheimer's disease. PG - 2475-82 LID - 10.1021/ar500152x [doi] AB - The development of a cure for Alzheimer's disease (AD) has been impeded by an inability to pinpoint the root cause of this disorder. Although numerous potential pathological factors have been indicated, acting either individually or mutually, the molecular mechanisms leading to disease onset and progression have not been clear. Amyloid-beta (Abeta), generated from proteolytic processing of the amyloid precursor protein (APP), and its aggregated forms, particularly oligomers, are suggested as key pathological features in AD-affected brains. Historically, highly concentrated metals are found colocalized within Abeta plaques. Metal binding to Abeta (metal-Abeta) generates/stabilizes potentially toxic Abeta oligomers, and produces reactive oxygen species (ROS) in vitro (redox active metal ions; plausible contribution to oxidative stress). Consequently, clarification of the relationship between Abeta, metal ions, and toxicity, including oxidative stress via metal-Abeta, can lead to a deeper understanding of AD development. To probe the involvement of metal-Abeta in AD pathogenesis, rationally designed and naturally occurring molecules have been examined as chemical tools to target metal-Abeta species, modulate the interaction between the metal and Abeta, and subsequently redirect their aggregation into nontoxic, off-pathway unstructured aggregates. These ligands are also capable of attenuating the generation of redox active metal-Abeta-induced ROS to mitigate oxidative stress. One rational design concept, the incorporation approach, installs a metal binding site into a framework known to interact with Abeta. This approach affords compounds with the simultaneous ability to chelate metal ions and interact with Abeta. Natural products capable of Abeta interaction have been investigated for their influence on metal-induced Abeta aggregation and have inspired the construction of synthetic analogues. Systematic studies of these synthetic or natural molecules could uncover relationships between chemical structures, metal/Abeta/metal-Abeta interactions, and inhibition of Abeta/metal-Abeta reactivity (i.e., aggregation modes of Abeta/metal-Abeta; associated ROS production), suggesting mechanisms to refine the design strategy. Interdisciplinary investigations have demonstrated that the designed molecules and natural products control the aggregation pathways of metal-Abeta species transforming their size/conformation distribution. The aptitude of these molecules to impact metal-Abeta aggregation pathways, either via inhibition of Abeta aggregate formation, most importantly of oligomers, or disaggregation of preformed fibrils, could originate from their formation of complexes with metal-Abeta. Potentially, these molecules could direct metal-Abeta size/conformational states into alternative nontoxic unstructured oligomers, and control the geometry at the Abeta-ligated metal center for limited ROS formation to lessen the overall toxicity induced by metal-Abeta. Complexation between small molecules and Abeta/metal-Abeta has been observed by nuclear magnetic resonance spectroscopy (NMR) and ion mobility-mass spectrometry (IM-MS) pointing to molecular level interactions, validating the design strategy. In addition, these molecules exhibit other attractive properties, such as antioxidant capacity, prevention of ROS production, potential blood-brain barrier (BBB) permeability, and reduction of Abeta-/metal-Abeta-induced cytotoxicity, making them desirable tools for unraveling AD complexity. In this Account, we summarize the recent development of small molecules, via both rational design and the selection and modification of natural products, as tools for investigating metal-Abeta complexes, to advance our understanding of their relation to AD pathology. FAU - Savelieff, Masha G AU - Savelieff MG AD - Life Sciences Institute and double daggerDepartment of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States. FAU - DeToma, Alaina S AU - DeToma AS FAU - Derrick, Jeffrey S AU - Derrick JS FAU - Lim, Mi Hee AU - Lim MH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20140731 PL - United States TA - Acc Chem Res JT - Accounts of chemical research JID - 0157313 SB - IM EDAT- 2014/08/01 06:00 MHDA- 2014/08/01 06:00 CRDT- 2014/08/01 06:00 PHST- 2014/07/31 [aheadofprint] AID - 10.1021/ar500152x [doi] PST - ppublish SO - Acc Chem Res. 2014 Aug 19;47(8):2475-82. doi: 10.1021/ar500152x. Epub 2014 Jul 31. PMID- 23145047 OWN - NLM STAT- MEDLINE DA - 20121112 DCOM- 20130724 LR - 20141104 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 11 DP - 2012 TI - Variation in the mechanical unfolding pathway of p53DBD induced by interaction with p53 N-terminal region or DNA. PG - e49003 LID - 10.1371/journal.pone.0049003 [doi] AB - The tumor suppressor p53 plays a crucial role in the cell cycle checkpoints, DNA repair, and apoptosis. p53 consists of a natively unfolded N-terminal region (NTR), central DNA binding domain (DBD), C-terminal tetramerization domain, and regulatory region. In this paper, the interactions between the DBD and the NTR, and between the DBD and DNA were investigated by measuring changes in the mechanical unfolding trajectory of the DBD using atomic force microscopy (AFM)-based single molecule force spectroscopy. In the absence of DNA, the DBD (94-293, 200 amino acids (AA)) showed two different mechanical unfolding patterns. One indicated the existence of an unfolding intermediate consisting of approximately 60 AA, and the other showed a 100 AA intermediate. The DBD with the NTR did not show such unfolding patterns, but heterogeneous unfolding force peaks were observed. Of the heterogeneous patterns, we observed a high frequency of force peaks indicating the unfolding of a domain consisting of 220 AA, which is apparently larger than that of a sole DBD. This observation implies that a part of NTR binds to the DBD, and the mechanical unfolding happens not solely on the DBD but also accompanying a part of NTR. When DNA is bound, the mechanical unfolding trajectory of p53NTR+DBD showed a different pattern from that without DNA. The pattern was similar to that of the DBD alone, but two consecutive unfolding force peaks corresponding to 60 and 100 AA sub-domains were observed. These results indicate that interactions with the NTR or DNA alter the mechanical stability of DBD and result in drastic changes in the mechanical unfolding trajectory of the DBD. FAU - Taniguchi, Yukinori AU - Taniguchi Y AD - School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), Nomi, Ishikawa, Japan. FAU - Kawakami, Masaru AU - Kawakami M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121108 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (DNA-Binding Proteins) RN - 0 (Recombinant Fusion Proteins) RN - 0 (TP53 protein, human) RN - 0 (Tumor Suppressor Protein p53) RN - 9007-49-2 (DNA) SB - IM MH - DNA/*metabolism MH - DNA-Binding Proteins/chemistry/*metabolism MH - Humans MH - Microscopy, Atomic Force/methods MH - Protein Denaturation MH - Protein Folding MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/chemistry/metabolism MH - Tumor Suppressor Protein p53/chemistry/*metabolism PMC - PMC3493487 OID - NLM: PMC3493487 EDAT- 2012/11/13 06:00 MHDA- 2013/07/25 06:00 CRDT- 2012/11/13 06:00 PHST- 2012/07/26 [received] PHST- 2012/10/03 [accepted] PHST- 2012/11/08 [epublish] AID - 10.1371/journal.pone.0049003 [doi] AID - PONE-D-12-22106 [pii] PST - ppublish SO - PLoS One. 2012;7(11):e49003. doi: 10.1371/journal.pone.0049003. Epub 2012 Nov 8. PMID- 16155205 OWN - NLM STAT- MEDLINE DA - 20050930 DCOM- 20051229 LR - 20140605 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 14 IP - 10 DP - 2005 Oct TI - In vitro study of stability and amyloid-fibril formation of two mutants of human stefin B (cystatin B) occurring in patients with EPM1. PG - 2713-22 AB - Myoclonus epilepsy of type 1 (EPM1) is a rare monogenic progressive and degenerative epilepsy, also known under the name Unverricht-Lundborg disease. With the aim of comparing their behavior in vitro, wild-type (wt) human stefin B (cystatin B) and the G4R and the R68X mutants observed in EPM1 were expressed and isolated from the Escherichia coli lysate. The R68X mutant (Arg68Stop) is a peptide of 67 amino acids from the N terminus of stefin B. CD spectra have shown that the R68X peptide is not folded, in contrast to the G4R mutant, which folds like wild type. The wild type and the G4R mutant were unfolded by urea and by trifluoroethanol (TFE). It has been shown that both proteins have closely similar stability and that at pH 4.8, where a native-like intermediate was demonstrated, TFE induces unfolding intermediates prior to the major transition to the all-alpha-helical state. Kinetics of fibril formation were followed by Thioflavin T fluorescence while the accompanying changes of morphology were followed by the transmission electron microscopy (TEM). For the two folded proteins the optimal concentration of TFE producing extensive lag phases and high fibril yields was predenaturational, 9% (v/v). The unfolded R68X peptide, which is highly prone to aggregate, formed amyloid fibrils in aqueous solution and in predenaturing 3% TFE. The G4R mutant exhibited a much longer lag phase than the wild type, with the accumulation of prefibrillar aggregates. Implications for pathology in view of the higher toxicity of prefibrillar aggregates to cells are discussed. FAU - Rabzelj, Sabina AU - Rabzelj S AD - Department of Biochemistry and Molecular Biology, JoZef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia. FAU - Turk, Vito AU - Turk V FAU - Zerovnik, Eva AU - Zerovnik E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20050909 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Amyloid) RN - 0 (CSTB protein, human) RN - 0 (Cystatins) RN - 0 (Recombinant Proteins) RN - 88844-95-5 (Cystatin B) SB - IM MH - Amino Acid Substitution/*genetics MH - Amyloid/*chemistry/ultrastructure MH - Circular Dichroism/methods MH - Cystatin B MH - Cystatins/*chemistry/genetics MH - Humans MH - Microscopy, Electron, Transmission/methods MH - *Point Mutation MH - Protein Denaturation/genetics MH - Protein Folding MH - Protein Structure, Secondary MH - Recombinant Proteins/chemistry/genetics MH - *Unverricht-Lundborg Syndrome/genetics PMC - PMC2253288 OID - NLM: PMC2253288 EDAT- 2005/09/13 09:00 MHDA- 2005/12/31 09:00 CRDT- 2005/09/13 09:00 PHST- 2005/09/09 [aheadofprint] AID - ps.051609705 [pii] AID - 10.1110/ps.051609705 [doi] PST - ppublish SO - Protein Sci. 2005 Oct;14(10):2713-22. Epub 2005 Sep 9. PMID- 21922108 OWN - NLM STAT- MEDLINE DA - 20111202 DCOM- 20120320 LR - 20131121 IS - 1742-2051 (Electronic) IS - 1742-2051 (Linking) VI - 8 IP - 1 DP - 2012 Jan TI - Insights in the (un)structural organization of Bacillus pasteurii UreG, an intrinsically disordered GTPase enzyme. PG - 220-8 LID - 10.1039/c1mb05227f [doi] AB - In the past, enzymatic activity has always been expected to be dependent on overall protein rigidity, necessary for substrate recognition and optimal orientation. However, increasing evidence is now accumulating, revealing that some proteins characterized by intrinsic disorder are actually able to perform catalysis. Among them, the only known natural intrinsically disordered enzyme is UreG, a GTPase that, in plants and bacteria, is involved in the protein interaction network leading to Ni(2+) ions delivery into the active site of urease. In this paper, we report a detailed analysis of the unfolding behaviour of UreG from Bacillus pasteurii (BpUreG), following its thermal and chemical denaturation with a combination of fluorescence spectroscopy, calorimetry, CD and NMR. The results demonstrate that BpUreG exists as an ensemble of inter-converting conformations, whose degrees of secondary structure depend on temperature and denaturant concentration. In particular, three major types of conformational ensembles with different degrees of residual structure were identified, with major structural characteristics resembling those of a molten globule (low temperature, absence of denaturant), pre-molten globule (high temperature, absence or presence of denaturant) and random coil (low temperature, presence of denaturant). Transitions among these ensembles of conformational states occur non-cooperatively although reversibly, with a gradual loss or acquisition of residual structure depending on the conditions. A possible role of disorder in the biological function of UreG is envisaged and discussed. FAU - Zambelli, Barbara AU - Zambelli B AD - Laboratory of Bioinorganic Chemistry, University of Bologna, Bologna, Italy. barbara.zambelli@unibo.it FAU - Cremades, Nunilo AU - Cremades N FAU - Neyroz, Paolo AU - Neyroz P FAU - Turano, Paola AU - Turano P FAU - Uversky, Vladimir N AU - Uversky VN FAU - Ciurli, Stefano AU - Ciurli S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110916 PL - England TA - Mol Biosyst JT - Molecular bioSystems JID - 101251620 RN - 0 (Bacterial Proteins) RN - 0 (Carrier Proteins) RN - 0 (ureG protein, Bacteria) RN - EC 3.6.1.- (GTP Phosphohydrolases) RN - JU58VJ6Y3B (Guanidine) SB - IM MH - Bacillus/drug effects/*enzymology MH - Bacterial Proteins/*chemistry/*metabolism MH - Calorimetry, Differential Scanning MH - Carrier Proteins/*chemistry/*metabolism MH - Circular Dichroism MH - GTP Phosphohydrolases/*chemistry/*metabolism MH - Guanidine/pharmacology MH - Magnetic Resonance Spectroscopy MH - Protein Conformation MH - Protein Denaturation/drug effects MH - *Protein Folding/drug effects MH - Spectrometry, Fluorescence MH - Temperature EDAT- 2011/09/17 06:00 MHDA- 2012/03/21 06:00 CRDT- 2011/09/17 06:00 PHST- 2011/09/16 [aheadofprint] PHST- 2011/12/01 [epublish] AID - 10.1039/c1mb05227f [doi] PST - ppublish SO - Mol Biosyst. 2012 Jan;8(1):220-8. doi: 10.1039/c1mb05227f. Epub 2011 Sep 16. PMID- 21220295 OWN - NLM STAT- MEDLINE DA - 20110126 DCOM- 20110426 LR - 20141210 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 108 IP - 4 DP - 2011 Jan 25 TI - Detection of a ternary complex of NF-kappaB and IkappaBalpha with DNA provides insights into how IkappaBalpha removes NF-kappaB from transcription sites. PG - 1367-72 LID - 10.1073/pnas.1014323108 [doi] AB - It has been axiomatic in the field of NF-kappaB signaling that the formation of a stable complex between NF-kappaB and the ankyrin repeat protein IkappaBalpha precludes the interaction of NF-kappaB with DNA. Contradicting this assumption, we present stopped-flow fluorescence and NMR experiments that give unequivocal evidence for the presence of a ternary DNA-NF-kappaB-IkappaBalpha complex in solution. Stepwise addition of a DNA fragment containing the kappaB binding sequence to the IkappaBalpha-NF-kappaB complex results in changes in the IkappaBalpha NMR spectrum that are consistent with dissociation of the region rich in proline, glutamate, serine, and threonine (PEST) and C-terminal ankyrin repeat sequences of IkappaBalpha from the complex. However, even at high concentrations of DNA, IkappaBalpha remains associated with NF-kappaB, indicated by the absence of resonances of the free N-terminal ankyrin repeats of IkappaBalpha. The IkappaBalpha-mediated release of NF-kappaB from its DNA-bound state may be envisioned as the reverse of this process. The initial step would consist of the coupled folding and binding of the intrinsically disordered nuclear localization sequence of the p65 subunit of NF-kappaB to the well-structured N-terminal ankyrin repeats of IkappaBalpha. Subsequently the poorly folded C-terminal ankyrin repeats of IkappaBalpha would fold upon binding to the p50 and p65 dimerization domains of NF-kappaB, permitting the negatively charged C-terminal PEST sequence of IkappaBalpha to displace the bound DNA through a process of local mass action. FAU - Sue, Shih-Che AU - Sue SC AD - Department of Molecular Biology MB2, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037-1000, USA. FAU - Alverdi, Vera AU - Alverdi V FAU - Komives, Elizabeth A AU - Komives EA FAU - Dyson, H Jane AU - Dyson HJ LA - eng GR - GM71862/GM/NIGMS NIH HHS/United States GR - P01 GM071862/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20110110 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (I-kappa B Proteins) RN - 0 (Multiprotein Complexes) RN - 0 (NF-kappa B) RN - 0 (NF-kappa B p50 Subunit) RN - 0 (Transcription Factor RelA) RN - 139874-52-5 (NF-kappaB inhibitor alpha) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Animals MH - Ankyrin Repeat/genetics MH - Base Sequence MH - Binding Sites MH - Binding, Competitive MH - DNA/*chemistry/genetics/metabolism MH - Humans MH - I-kappa B Proteins/*chemistry/genetics/metabolism MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Multiprotein Complexes/*chemistry/metabolism MH - NF-kappa B/*chemistry/genetics/metabolism MH - NF-kappa B p50 Subunit/chemistry/genetics/metabolism MH - Protein Binding MH - Protein Multimerization MH - Protein Structure, Quaternary MH - Protein Structure, Tertiary MH - Transcription Factor RelA/chemistry/genetics/metabolism MH - Transcription, Genetic/genetics PMC - PMC3029698 OID - NLM: PMC3029698 EDAT- 2011/01/12 06:00 MHDA- 2011/04/27 06:00 CRDT- 2011/01/12 06:00 PHST- 2011/01/10 [aheadofprint] AID - 1014323108 [pii] AID - 10.1073/pnas.1014323108 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1367-72. doi: 10.1073/pnas.1014323108. Epub 2011 Jan 10. PMID- 20036826 OWN - NLM STAT- MEDLINE DA - 20091228 DCOM- 20100423 LR - 20140722 IS - 1093-4715 (Electronic) IS - 1093-4715 (Linking) VI - 15 DP - 2010 TI - Methods and models in neurodegenerative and systemic protein aggregation diseases. PG - 373-96 AB - Protein misfolding and aggregation are implicated in a wide range of increasingly prevalent human diseases ranging from dementia to diabetes. In this review we discuss the current experimental strategies that are being employed in the investigation of the pathogenesis of three important protein misfolding disorders. The first, Alzheimer's disease (AD), is the most prevalent neurodegenerative disease and is thought to be initiated by the aggregation of a natively unstructured peptide called amyloid beta (Abeta). We discuss methods for the characterization of the aggregation properties of Abeta in vitro and how the results of such experiments can be correlated with data from animal models of disease. We then consider another form of amyloidosis, where a systemic distribution of amyloid deposit is caused by aggregation and deposition of mutational variants of lysozyme. We describe how experiments in vitro, and more recently in vivo, have provided insights into the origins of this disease. Finally we outline the varied paradigms that have been employed in the study of the serpinopathies, and in particular, a dementia caused by neuroserpin polymerization. FAU - Brorsson, Ann-Christin AU - Brorsson AC AD - Molecular Biotechnology/IFM, Linkoping University, SE-581 83, Linkoping, Sweden. FAU - Kumita, Janet R AU - Kumita JR FAU - MacLeod, Ian AU - MacLeod I FAU - Bolognesi, Benedetta AU - Bolognesi B FAU - Speretta, Elena AU - Speretta E FAU - Luheshi, Leila M AU - Luheshi LM FAU - Knowles, Tuomas P J AU - Knowles TP FAU - Dobson, Christopher M AU - Dobson CM FAU - Crowther, Damian C AU - Crowther DC LA - eng GR - BB/E019927/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - G0700990/Medical Research Council/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom GR - Medical Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Review DEP - 20100101 PL - United States TA - Front Biosci (Landmark Ed) JT - Frontiers in bioscience (Landmark edition) JID - 101612996 RN - 0 (Amyloid beta-Peptides) RN - EC 3.2.1.17 (Muramidase) SB - IM MH - Alzheimer Disease/*metabolism/pathology MH - Amyloid beta-Peptides/*chemistry/metabolism/ultrastructure MH - Amyloidosis/*metabolism/pathology MH - Animals MH - Circular Dichroism MH - Humans MH - Microscopy, Electron, Transmission MH - Muramidase/*chemistry/metabolism MH - Protein Conformation MH - Protein Folding RF - 164 EDAT- 2009/12/29 06:00 MHDA- 2010/04/24 06:00 CRDT- 2009/12/29 06:00 AID - 3626 [pii] PST - epublish SO - Front Biosci (Landmark Ed). 2010 Jan 1;15:373-96. PMID- 24928493 OWN - NLM STAT- MEDLINE DA - 20140805 DCOM- 20150330 IS - 1873-2763 (Electronic) IS - 1873-2763 (Linking) VI - 66 DP - 2014 Sep TI - Osteopontin binds multiple calcium ions with high affinity and independently of phosphorylation status. PG - 90-5 LID - 10.1016/j.bone.2014.05.020 [doi] LID - S8756-3282(14)00198-7 [pii] AB - Osteopontin (OPN) is an acidic, intrinsically disordered extracellular matrix protein with a capacity to modulate biomineralization in vitro and in vivo. The role of posttranslational modification of osteopontin has been intensively studied. Phosphorylation of OPN has been demonstrated to play a role in inhibition of biomineral formation and growth in vitro. Here, we used isothermal titration calorimetry (ITC) to investigate the ability of OPN to bind the divalent cations Ca(2+) and Mg(2+), both essential components of inorganic minerals in vivo. We found, that bovine OPN binds ~10 Ca(2+) ions with an apparent affinity ~50-fold tighter than Mg(2+), both regardless of OPN phosphorylation, and with affinities significantly stronger than previously reported. These results were confirmed using human derived OPN. This implies that a majority of the acidic residues within OPN must be engaged in calcium interaction under physiological conditions. CI - Copyright (c) 2014 Elsevier Inc. All rights reserved. FAU - Klaning, Eva AU - Klaning E AD - Department of Molecular Biology and Genetics, Aarhus University, Denmark; Department of Biomedicine, Aarhus University, Denmark. FAU - Christensen, Brian AU - Christensen B AD - Department of Molecular Biology and Genetics, Aarhus University, Denmark. FAU - Sorensen, Esben S AU - Sorensen ES AD - Department of Molecular Biology and Genetics, Aarhus University, Denmark. FAU - Vorup-Jensen, Thomas AU - Vorup-Jensen T AD - Department of Biomedicine, Aarhus University, Denmark. FAU - Jensen, Jan K AU - Jensen JK AD - Department of Molecular Biology and Genetics, Aarhus University, Denmark; Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Denmark. Electronic address: jkj@mb.au.dk. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140610 PL - United States TA - Bone JT - Bone JID - 8504048 RN - 0 (Cations, Divalent) RN - 0 (Ions) RN - 106441-73-0 (Osteopontin) RN - 9G34HU7RV0 (Edetic Acid) RN - I38ZP9992A (Magnesium) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Calcium/*metabolism MH - Calorimetry MH - Cations, Divalent/metabolism MH - Cattle MH - Edetic Acid/metabolism MH - Humans MH - Ions MH - Magnesium/metabolism MH - Molecular Sequence Data MH - Osteopontin/chemistry/*metabolism MH - Phosphorylation MH - Protein Binding MH - Thermodynamics OTO - NOTNLM OT - Calcium OT - EDTA OT - Intrinsically disordered OT - Magnesium OT - Metal affinity OT - Milk protein EDAT- 2014/06/15 06:00 MHDA- 2015/03/31 06:00 CRDT- 2014/06/15 06:00 PHST- 2014/01/20 [received] PHST- 2014/05/15 [revised] PHST- 2014/05/27 [accepted] PHST- 2014/06/10 [aheadofprint] AID - S8756-3282(14)00198-7 [pii] AID - 10.1016/j.bone.2014.05.020 [doi] PST - ppublish SO - Bone. 2014 Sep;66:90-5. doi: 10.1016/j.bone.2014.05.020. Epub 2014 Jun 10. PMID- 22057845 OWN - NLM STAT- MEDLINE DA - 20111216 DCOM- 20120419 LR - 20141021 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 21 IP - 1 DP - 2012 Jan TI - Roles of the N- and C-terminal sequences in Hsp27 self-association and chaperone activity. PG - 122-33 LID - 10.1002/pro.761 [doi] AB - The small heat shock protein 27 (Hsp27 or HSPB1) is an oligomeric molecular chaperone in vitro that is associated with several neuromuscular, neurological, and neoplastic diseases. Although aspects of Hsp27 biology are increasingly well known, understanding of the structural basis for these involvements or of the functional properties of the protein remains limited. As all 11 human small heat shock proteins (sHsps) possess an alpha-crystallin domain, their varied functional and physiological characteristics must arise from contributions of their nonconserved sequences. To evaluate the role of two such sequences in Hsp27, we have studied three Hsp27 truncation variants to assess the functional contributions of the nonconserved N- and C-terminal sequences. The N-terminal variants Delta1-14 and Delta1-24 exhibit little chaperone activity, somewhat slower but temperature-dependent subunit exchange kinetics, and temperature-independent self-association with formation of smaller oligomers than wild-type Hsp27. The C-terminal truncation variants exhibit chaperone activity at 40 degrees C but none at 20 degrees C, limited subunit exchange, and temperature-independent self-association with an oligomer distribution at 40 degrees C that is very similar to that of wild-type Hsp27. We conclude that more of the N-terminal sequence than simply the WPDF domain is essential in the formation of larger, native-like oligomers after binding of substrate and/or in binding of Hsp27 to unfolding peptides. On the other hand, the intrinsically flexible C-terminal region drives subunit exchange and thermally-induced unfolding, both of which are essential to chaperone activity at low temperature and are linked to the temperature dependence of Hsp27 self-association. CI - Copyright (c) 2011 The Protein Society. FAU - Lelj-Garolla, Barbara AU - Lelj-Garolla B AD - Department of Biochemistry and Molecular Biology and the Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada. FAU - Mauk, A Grant AU - Mauk AG LA - eng GR - MCP-14021/Canadian Institutes of Health Research/Canada PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111207 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (HSP27 Heat-Shock Proteins) RN - 0 (HSPB1 protein, human) RN - 0 (Protein Subunits) RN - 0 (alpha-Crystallins) SB - IM MH - HSP27 Heat-Shock Proteins/*chemistry/*metabolism MH - Humans MH - Kinetics MH - Models, Molecular MH - Molecular Weight MH - Protein Binding MH - Protein Denaturation MH - Protein Multimerization MH - Protein Stability MH - Protein Structure, Tertiary MH - Protein Subunits MH - Temperature MH - alpha-Crystallins/chemistry/metabolism PMC - PMC3323787 OID - NLM: PMC3323787 EDAT- 2011/11/08 06:00 MHDA- 2012/04/20 06:00 CRDT- 2011/11/08 06:00 PHST- 2011/10/03 [received] PHST- 2011/10/31 [accepted] PHST- 2011/12/07 [aheadofprint] AID - 10.1002/pro.761 [doi] PST - ppublish SO - Protein Sci. 2012 Jan;21(1):122-33. doi: 10.1002/pro.761. Epub 2011 Dec 7. PMID- 23640306 OWN - NLM STAT- MEDLINE DA - 20130606 DCOM- 20140113 IS - 1432-1017 (Electronic) IS - 0175-7571 (Linking) VI - 42 IP - 7 DP - 2013 Jul TI - Characterization of the internal dynamics and conformational space of zinc-bound amyloid beta peptides by replica-exchange molecular dynamics simulations. PG - 575-86 LID - 10.1007/s00249-013-0906-0 [doi] AB - Amyloid beta (Abeta) peptides and metal ions have been associated with the pathogenesis of Alzheimer's disease. The conformational space of Abeta fragments of different length with and without binding of metal ions has been extensively investigated by replica-exchange molecular dynamics (REMD) simulation. However, only trajectories extracted at relatively low temperatures have been used for this analysis. The capability of REMD simulations to characterize the internal dynamics of such intrinsically disordered proteins (IDPs) as Abeta has been overlooked. In this work, we use an approach recently developed by Xue and Skrynnikov (J Am Chem Soc 133:14614-14628, 2011) to calculate NMR observables, including (15)N relaxation rates and (15)N-(1)H nuclear Overhauser enhancement (NOE), from the high-temperature trajectory of REMD simulations for zinc-bound Abeta peptides. The time axis of the trajectory was rescaled to correct for the effect of the high temperature (408 K) compared with the experimental temperature (278 K). Near-quantitative agreement between simulated values and experimental results was obtained. When the structural properties and free-energy surfaces of zinc-bound Abeta(1-40) and Abeta(1-42) were compared at the physiological temperature 310 K it was found that zinc-bound Abeta(1-42) was more rigid than Abeta(1-40) at the C terminus, and its conformational transitions were also more preferred. The self-consistent results derived from trajectories at high and low temperatures demonstrate the capability of REMD simulations to capture the internal dynamics of IDPs. FAU - Xu, Liang AU - Xu L AD - School of Chemistry, Dalian University of Technology, Dalian 116023, China. xuliang@dlut.edu.cn FAU - Wang, Xiaojuan AU - Wang X FAU - Wang, Xicheng AU - Wang X LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130503 PL - Germany TA - Eur Biophys J JT - European biophysics journal : EBJ JID - 8409413 RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (1-40)) RN - 0 (amyloid beta-protein (1-42)) RN - J41CSQ7QDS (Zinc) SB - IM MH - Amyloid beta-Peptides/*chemistry/*metabolism MH - Magnetic Resonance Spectroscopy MH - *Molecular Dynamics Simulation MH - Peptide Fragments/*chemistry/*metabolism MH - Protein Structure, Secondary MH - Temperature MH - Zinc/*metabolism EDAT- 2013/05/04 06:00 MHDA- 2014/01/15 06:00 CRDT- 2013/05/04 06:00 PHST- 2013/02/21 [received] PHST- 2013/04/12 [accepted] PHST- 2013/04/07 [revised] PHST- 2013/05/03 [aheadofprint] AID - 10.1007/s00249-013-0906-0 [doi] PST - ppublish SO - Eur Biophys J. 2013 Jul;42(7):575-86. doi: 10.1007/s00249-013-0906-0. Epub 2013 May 3. PMID- 12743116 OWN - NLM STAT- MEDLINE DA - 20030721 DCOM- 20030826 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 30 DP - 2003 Jul 25 TI - Crystal structure of the intrinsically flexible addiction antidote MazE. PG - 28252-7 AB - A specific camel VHH (variable domain of dromedary heavy chain antibody) fragment was used to crystallize the intrinsically flexible addiction antidote MazE. Only 45% of the polypeptide chain is found ordered in the crystal. The MazE monomer consisting of two beta-hairpins connected by a short alpha-helix has no hydrophobic core on its own and represents only one half of a typical protein domain. A complete domain structure is formed by the association of two chains, creating a hydrophobic core between two four-stranded beta-sheets. This hydrophobic core consists exclusively of short aliphatic residues. The folded part of MazE contains a novel DNA binding motif. A model for DNA binding that is consistent with the available biochemical data is presented. FAU - Loris, Remy AU - Loris R AD - Laboratorium voor Ultrastructuur en Vlaams instituut voor Biotechnologie, Vrije Universiteit Brussel, Gebouw E, Pleinlaan 2, 1050 Brussel, Belgium. reloris@vub.ac.be FAU - Marianovsky, Irina AU - Marianovsky I FAU - Lah, Jurij AU - Lah J FAU - Laeremans, Toon AU - Laeremans T FAU - Engelberg-Kulka, Hanna AU - Engelberg-Kulka H FAU - Glaser, Gad AU - Glaser G FAU - Muyldermans, Serge AU - Muyldermans S FAU - Wyns, Lode AU - Wyns L LA - eng SI - PDB/1MVF PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030512 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (MazE protein, E coli) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Camels MH - Crystallography, X-Ray MH - DNA/metabolism MH - DNA-Binding Proteins/chemistry/*physiology MH - Escherichia coli/metabolism MH - *Escherichia coli Proteins MH - Models, Molecular MH - Molecular Sequence Data MH - Mutation MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid EDAT- 2003/05/14 05:00 MHDA- 2003/08/27 05:00 CRDT- 2003/05/14 05:00 PHST- 2003/05/12 [aheadofprint] AID - 10.1074/jbc.M302336200 [doi] AID - M302336200 [pii] PST - ppublish SO - J Biol Chem. 2003 Jul 25;278(30):28252-7. Epub 2003 May 12. PMID- 18788774 OWN - NLM STAT- MEDLINE DA - 20081006 DCOM- 20081113 IS - 1535-3893 (Print) IS - 1535-3893 (Linking) VI - 7 IP - 10 DP - 2008 Oct TI - Human regulatory protein Ki-1/57 has characteristics of an intrinsically unstructured protein. PG - 4465-74 LID - 10.1021/pr8005342 [doi] AB - The human protein Ki-1/57 was first identified through the cross reactivity of the anti-CD30 monoclonal antibody Ki-1, in Hodgkin lymphoma cells. The expression of Ki-1/57 in diverse cancer cells and its phosphorylation in peripheral blood leukocytes after mitogenic activation suggested its possible role in cell signaling. Ki-1/57 interacts with several other regulatory proteins involved in cellular signaling, transcriptional regulation and RNA metabolism, suggesting it may have pleiotropic functions. In a previous spectroscopic analysis, we observed a low content of secondary structure for Ki-1/57 constructs. Here, Circular dichroism experiments, in vitro RNA binding analysis, and limited proteolysis assays of recombinant Ki-1/57(122-413) and proteolysis assays of endogenous full length protein from human HEK293 cells suggested that Ki-1/57 has characteristics of an intrinsically unstructured protein. Small-angle X-ray scattering (SAXS) experiments were performed with the C-terminal fragment Ki-1/57(122-413). These results indicated an elongated shape and a partially unstructured conformation of the molecule in solution, confirming the characteristics of an intrinsically unstructured protein. Experimental curves together with ab initio modeling approaches revealed an extended and flexible molecule in solution. An elongated shape was also observed by analytical gel filtration. Furthermore, sedimentation velocity analysis suggested that Ki-1/57 is a highly asymmetric protein. These findings may explain the functional plasticity of Ki-1/57, as suggested by the wide array of proteins with which it is capable of interacting in yeast two-hybrid interaction assays. FAU - Bressan, Gustavo C AU - Bressan GC AD - National Synchrotron Light Laboratory - LNLS, 13083-970, Campinas, SP, Brazil. FAU - Silva, Julio C AU - Silva JC FAU - Borges, Julio C AU - Borges JC FAU - Dos Passos, Dario O AU - Dos Passos DO FAU - Ramos, Carlos H I AU - Ramos CH FAU - Torriani, Iris L AU - Torriani IL FAU - Kobarg, Jorg AU - Kobarg J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080913 PL - United States TA - J Proteome Res JT - Journal of proteome research JID - 101128775 RN - 0 (HABP4 protein, human) RN - 0 (Myogenic Regulatory Factors) RN - EC 3.4.21.64 (Endopeptidase K) SB - IM MH - Amino Acid Sequence MH - Cell Line MH - Endopeptidase K/metabolism MH - Humans MH - Models, Molecular MH - Myogenic Regulatory Factors/*chemistry/genetics/metabolism MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Scattering, Small Angle MH - Signal Transduction EDAT- 2008/09/16 09:00 MHDA- 2008/11/14 09:00 CRDT- 2008/09/16 09:00 PHST- 2008/09/13 [aheadofprint] AID - 10.1021/pr8005342 [doi] PST - ppublish SO - J Proteome Res. 2008 Oct;7(10):4465-74. doi: 10.1021/pr8005342. Epub 2008 Sep 13. PMID- 15479804 OWN - NLM STAT- MEDLINE DA - 20041013 DCOM- 20041116 LR - 20140608 IS - 0022-538X (Print) IS - 0022-538X (Linking) VI - 78 IP - 21 DP - 2004 Nov TI - Measles virus phosphoprotein gene products: conformational flexibility of the P/V protein amino-terminal domain and C protein infectivity factor function. PG - 11632-40 AB - The measles virus (MV) P gene codes for three proteins: P, an essential polymerase cofactor, and V and C, which have multiple functions but are not strictly required for viral propagation in cultured cells. V shares the amino-terminal domain with P but has a zinc-binding carboxyl-terminal domain, whereas C is translated from an overlapping reading frame. During replication, the P protein binds incoming monomeric nucleocapsid (N) proteins with its amino-terminal domain and positions them for assembly into the nascent ribonucleocapsid. The P protein amino-terminal domain is natively unfolded; to probe its conformational flexibility, we fused it to the green fluorescent protein (GFP), thereby also silencing C protein expression. A recombinant virus (MV-GFP/P) expressing hybrid GFP/P and GFP/V proteins in place of standard P and V proteins and not expressing the C protein was rescued and produced normal ratios of mono-, bi-, and tricistronic RNAs, but its replication was slower than that of the parental virus. Thus, the P protein retained nearly intact polymerase cofactor function, even with a large domain added to its amino terminus. Having noted that titers of cell-associated and especially released MV-GFP/P were reduced and knowing that the C protein of the related Sendai virus has particle assembly and infectivity factor functions, we produced an MV-GFP/P derivative expressing C. Intracellular titers of this virus were almost completely restored, and those of released virus were partially restored. Thus, the MV C protein is an infectivity factor. FAU - Devaux, Patricia AU - Devaux P AD - Molecular Medicine Program and Virology and Gene Therapy Graduate Track, Mayo Clinic College, Rochester, MN, USA. FAU - Cattaneo, Roberto AU - Cattaneo R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (P protein, Sendai virus) RN - 0 (Phosphoproteins) RN - 0 (V protein, measles virus) RN - 0 (Viral Proteins) SB - IM MH - Animals MH - Cercopithecus aethiops MH - Measles virus/*pathogenicity MH - Phosphoproteins/*chemistry MH - Protein Conformation MH - Vero Cells MH - Viral Proteins/*chemistry/*physiology MH - Virus Replication PMC - PMC523285 OID - NLM: PMC523285 EDAT- 2004/10/14 09:00 MHDA- 2004/11/17 09:00 CRDT- 2004/10/14 09:00 AID - 78/21/11632 [pii] AID - 10.1128/JVI.78.21.11632-11640.2004 [doi] PST - ppublish SO - J Virol. 2004 Nov;78(21):11632-40. PMID- 16581765 OWN - NLM STAT- MEDLINE DA - 20060403 DCOM- 20060503 LR - 20140909 IS - 0270-7306 (Print) IS - 0270-7306 (Linking) VI - 26 IP - 8 DP - 2006 Apr TI - Keap1 recruits Neh2 through binding to ETGE and DLG motifs: characterization of the two-site molecular recognition model. PG - 2887-900 AB - The expression of the phase 2 detoxification enzymes and antioxidant proteins is induced at the transcriptional level by Nrf2 and negatively regulated at the posttranslational level by Keap1 through protein-protein interactions with and subsequent proteolysis of Nrf2. We found that the Neh2 domain of Nrf2 is an intrinsically disordered but biologically active regulatory domain containing a 33-residue central alpha-helix followed by a mini antiparallel beta-sheet. Isothermal calorimetry analysis indicated that one Neh2 molecule interacts with two molecules of Keap1 via two binding sites, the stronger binding ETGE motif and the weaker binding DLG motif. Nuclear magnetic resonance titration study showed that these two motifs of the Neh2 domain bind to an overlapping site on the bottom surface of the beta-propeller structure of Keap1. In contrast, the central alpha-helix of the Neh2 domain does not have any observable affinity to Keap1, suggesting that this region may serve as a bridge connecting the two motifs for the association with the two beta-propeller structures of a dimer of Keap1. Based on these observations, we propose that Keap1 recruits Nrf2 by the ETGE motif and that the DLG motif of the Neh2 domain locks its lysine-rich central alpha-helix in a correct position to benefit ubiquitin signaling. FAU - Tong, Kit I AU - Tong KI AD - Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8572, Japan. FAU - Katoh, Yasutake AU - Katoh Y FAU - Kusunoki, Hideki AU - Kusunoki H FAU - Itoh, Ken AU - Itoh K FAU - Tanaka, Toshiyuki AU - Tanaka T FAU - Yamamoto, Masayuki AU - Yamamoto M LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Cytoskeletal Proteins) RN - 0 (Keap1 protein, mouse) RN - 0 (NF-E2-Related Factor 2) RN - 0 (Recombinant Fusion Proteins) SB - IM MH - Adaptor Proteins, Signal Transducing/genetics/*metabolism MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Calorimetry MH - Conserved Sequence MH - Cytoskeletal Proteins/genetics/*metabolism MH - Escherichia coli/genetics MH - Mice MH - Models, Chemical MH - Models, Molecular MH - Molecular Sequence Data MH - NF-E2-Related Factor 2/*chemistry/genetics/isolation & purification/*metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Point Mutation MH - Protein Binding MH - Protein Processing, Post-Translational MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/chemistry/metabolism MH - Sequence Homology, Amino Acid MH - Thermodynamics MH - Ultracentrifugation PMC - PMC1446969 OID - NLM: PMC1446969 EDAT- 2006/04/04 09:00 MHDA- 2006/05/04 09:00 CRDT- 2006/04/04 09:00 AID - 26/8/2887 [pii] AID - 10.1128/MCB.26.8.2887-2900.2006 [doi] PST - ppublish SO - Mol Cell Biol. 2006 Apr;26(8):2887-900. PMID- 9375414 OWN - NLM STAT- MEDLINE DA - 19971218 DCOM- 19971218 LR - 20131121 IS - 1386-1425 (Print) IS - 1386-1425 (Linking) VI - 53A IP - 11 DP - 1997 Oct TI - Spectroscopic studies on the conformational transitions of a bovine growth hormone releasing factor analog. PG - 1889-900 AB - The secondary structure of the bovine growth hormone releasing factor analog, [Ile2, Ser8.28, Ala15, Leu27, Hse30] bGRF(1-30)-NH-Ethyl, acetate salt (U-90699F) was studied in solution by Fourier transform infrared and Raman spectroscopies. Spectroscopic studies revealed that concentrated aqueous solutions of U-90699F (100 mg ml-1) undergo a secondary structure transition from disordered coil/alpha-helix to intermolecular beta-sheet. Disordered coil and alpha-helical structure were grouped together in the infrared and Raman studies since the amide I vibrations are close in frequency and overlap in assignments was possible. Before the conformational transition, the facile exchange of the peptide's amide hydrogens for deuterium indicated that the majority of amide hydrogens were readily accessible to solvent. The kinetics of the conformational transition coincided with an increase in solution viscosity and turbidity. An initiation phase preceded the conformational transition during which only minor spectral changes were observed by infrared spectroscopy. The initiation phase and reaction kinetics were consistent with a highly cooperative nucleation ultimately leading to a network of intermolecular beta-sheet structure and gel formation. Increased temperature accelerated the conformational transition. The conformational transition was thermally irreversible but the beta-sheet structure of aggregated or gelled peptide could be disrupted by dilution and agitation. FAU - Sarver, R W Jr AU - Sarver RW Jr AD - Pharmacia and Upjohn Inc., Kalamazoo, MI 49001, USA. Ronald.Sarver@am.pnu.com FAU - Friedman, A R AU - Friedman AR FAU - Thamann, T J AU - Thamann TJ LA - eng PT - Journal Article PL - ENGLAND TA - Spectrochim Acta A Mol Biomol Spectrosc JT - Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy JID - 9602533 RN - 9034-39-3 (Growth Hormone-Releasing Hormone) RN - AR09D82C7G (Deuterium) SB - IM MH - Deuterium MH - Growth Hormone-Releasing Hormone/*analogs & derivatives/*chemistry MH - Protein Conformation MH - Spectrophotometry, Infrared MH - Spectrum Analysis, Raman MH - Temperature EDAT- 1997/12/31 23:38 MHDA- 2001/03/28 10:01 CRDT- 1997/12/31 23:38 PST - ppublish SO - Spectrochim Acta A Mol Biomol Spectrosc. 1997 Oct;53A(11):1889-900. PMID- 16288455 OWN - NLM STAT- MEDLINE DA - 20060316 DCOM- 20070111 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 63 IP - 2 DP - 2006 May 1 TI - Natively unfolded regions of the vertebrate fibrinogen molecule. PG - 391-7 AB - Although it has long been realized that a large portion of the fibrinogen alpha chain has little if any defined structure, the physiological significance of this flexible appendage remains mysterious. CI - 2005 Wiley-Liss, Inc. FAU - Doolittle, Russell F AU - Doolittle RF AD - Division of Biological Sciences, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0634, USA. rdoolittle@ucsd.edu FAU - Kollman, Justin M AU - Kollman JM LA - eng PT - Journal Article PT - Review PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Peptide Fragments) RN - 9001-32-5 (Fibrinogen) RN - 9013-56-3 (Factor XIII) SB - IM MH - Amino Acid Sequence MH - Animals MH - Factor XIII/metabolism MH - Fibrinogen/*chemistry/genetics/*metabolism/ultrastructure MH - Humans MH - Molecular Sequence Data MH - Peptide Fragments/genetics/metabolism MH - Protein Binding MH - Protein Folding RF - 71 EDAT- 2005/11/17 09:00 MHDA- 2007/01/12 09:00 CRDT- 2005/11/17 09:00 AID - 10.1002/prot.20758 [doi] PST - ppublish SO - Proteins. 2006 May 1;63(2):391-7. PMID- 9659923 OWN - NLM STAT- MEDLINE DA - 19980727 DCOM- 19980727 LR - 20081121 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 1 IP - 2 DP - 1998 Jan TI - Independent ligand-induced folding of the RNA-binding domain and two functionally distinct antitermination regions in the phage lambda N protein. PG - 265-75 AB - The transcriptional antitermination protein N of bacteriophage lambda binds the boxB component of the RNA enhancer nut (boxA + boxB) and the E. coli elongation factor NusA. Efficient antitermination by N requires an RNA-binding domain (amino acids 1-22) and two activating regions for antitermination: a newly identified NusA-binding region (amino acids 34-47) that suppresses NusA's enhancement of termination, and a carboxy-terminal region (amino acids 73-107) that interacts directly with RNA polymerase. Heteronuclear magnetic resonance experiments demonstrate that N is a disordered protein. Interaction with boxB RNA induces only the RNA-binding domain of N to adopt a folded conformation, while the activating regions of the protein remain disordered in the absence of their target proteins. FAU - Mogridge, J AU - Mogridge J AD - Banting and Best Department of Medical Research, Department of Molecular and Medical Genetics, University of Toronto, Ontario, Canada. FAU - Legault, P AU - Legault P FAU - Li, J AU - Li J FAU - Van Oene, M D AU - Van Oene MD FAU - Kay, L E AU - Kay LE FAU - Greenblatt, J AU - Greenblatt J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Bacterial Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Ligands) RN - 0 (N protein, Bacteriophage lambda) RN - 0 (Peptide Elongation Factors) RN - 0 (Peptide Fragments) RN - 0 (RNA, Viral) RN - 0 (Transcription Factors) RN - 0 (Viral Regulatory and Accessory Proteins) RN - 0 (nusA protein, E coli) RN - EC 2.7.7.6 (DNA-Directed RNA Polymerases) SB - IM MH - Amino Acid Sequence MH - Bacterial Proteins/chemistry/metabolism MH - Bacteriophage lambda/*chemistry/enzymology/*genetics MH - Binding Sites/physiology MH - DNA-Directed RNA Polymerases/metabolism MH - Enhancer Elements, Genetic/physiology MH - Escherichia coli Proteins MH - *Gene Expression Regulation, Viral MH - Ligands MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - *Peptide Elongation Factors MH - Peptide Fragments/metabolism MH - Protein Structure, Tertiary MH - RNA, Viral/chemistry/genetics/metabolism MH - Regulatory Sequences, Nucleic Acid MH - Transcription Factors/chemistry/metabolism MH - Viral Regulatory and Accessory Proteins/*chemistry/genetics/*metabolism EDAT- 1998/07/11 MHDA- 1998/07/11 00:01 CRDT- 1998/07/11 00:00 AID - S1097-2765(00)80027-1 [pii] PST - ppublish SO - Mol Cell. 1998 Jan;1(2):265-75. PMID- 17446086 OWN - NLM STAT- MEDLINE DA - 20070730 DCOM- 20080225 LR - 20131121 IS - 1047-8477 (Print) IS - 1047-8477 (Linking) VI - 159 IP - 2 DP - 2007 Aug TI - Nanomechanical interactions of phenylalanine-glycine nucleoporins studied by single molecule force-volume spectroscopy. PG - 277-89 AB - Phenylalanine-glycine (FG)-repeat nucleoporins (Nups) form the major components of the selective gating mechanism in the nuclear pore complex (NPC). Hence, a primary requirement is to understand how they vacillate between preventing the access of passively diffusing molecules and promoting the translocation of receptor-bound cargo into the NPC. To shed light on such behavior, we have studied the nanomechanical properties of a cysteine-modified FG-rich C-terminal domain of hNup153 (i.e., cNup153) and its interactions with importin-beta. This is carried out using single molecule force spectroscopy (SMFS) with the atomic force microscope (AFM). In the absence of importin-beta, cNup153 is highly flexible and can be reversibly stretched and relaxed without any change to its intrinsic entropic elasticity, indicating a lack of intra-FG interactions, i.e., natively unfolded. Importin-beta-modified AFM tips reveal complex binding topologies with cNup153, and provide evidence for binding promiscuity in FG-receptor interactions. These differences suggest that cooperativity between FG-domains arises from FG-receptor interactions instead of FG-FG interactions. On a technical note, this work highlights an improved SMFS technique which involves pre-passivating the underlying substrate surface with polyethylene glycol to reduce undesirable AFM tip-surface effects. A high yield of acceptable data is subsequently obtained from the low surface coverage of target molecules by implementing SMFS measurements in force-volume (FV) mode. FAU - Lim, Roderick Y H AU - Lim RY AD - M.E. Muller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, Basel 4056, Switzerland. roderick.lim@unibas.ch FAU - Koser, Joachim AU - Koser J FAU - Huang, Ning-Ping AU - Huang NP FAU - Schwarz-Herion, Kyrill AU - Schwarz-Herion K FAU - Aebi, Ueli AU - Aebi U LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070216 PL - United States TA - J Struct Biol JT - Journal of structural biology JID - 9011206 RN - 0 (Nuclear Pore Complex Proteins) RN - 0 (beta Karyopherins) RN - 47E5O17Y3R (Phenylalanine) RN - TE7660XO1C (Glycine) SB - IM MH - Glycine/*chemistry MH - Humans MH - Nuclear Pore Complex Proteins/*chemistry/genetics/metabolism MH - Phenylalanine/*chemistry MH - Spectrum Analysis MH - beta Karyopherins/chemistry/genetics/metabolism EDAT- 2007/04/21 09:00 MHDA- 2008/02/26 09:00 CRDT- 2007/04/21 09:00 PHST- 2006/10/20 [received] PHST- 2007/01/17 [revised] PHST- 2007/01/26 [accepted] PHST- 2007/02/16 [aheadofprint] AID - S1047-8477(07)00036-6 [pii] AID - 10.1016/j.jsb.2007.01.018 [doi] PST - ppublish SO - J Struct Biol. 2007 Aug;159(2):277-89. Epub 2007 Feb 16. PMID- 10892800 OWN - NLM STAT- MEDLINE DA - 20001103 DCOM- 20001103 LR - 20140615 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 9 IP - 6 DP - 2000 Jun TI - Three-dimensional structures of Drosophila melanogaster acetylcholinesterase and of its complexes with two potent inhibitors. PG - 1063-72 AB - We have crystallized Drosophila melanogaster acetylcholinesterase and solved the structure of the native enzyme and of its complexes with two potent reversible inhibitors, 1,2,3,4-tetrahydro-N-(phenylmethyl)-9-acridinamine and 1,2,3,4-tetrahydro-N-(3-iodophenyl-methyl)-9-acridinamine--all three at 2.7 A resolution. The refined structure of D. melanogaster acetylcholinesterase is similar to that of vertebrate acetylcholinesterases, for example, human, mouse, and fish, in its overall fold, charge distribution, and deep active-site gorge, but some of the surface loops deviate by up to 8 A from their position in the vertebrate structures, and the C-terminal helix is shifted substantially. The active-site gorge of the insect enzyme is significantly narrower than that of Torpedo californica AChE, and its trajectory is shifted several angstroms. The volume of the lower part of the gorge of the insect enzyme is approximately 50% of that of the vertebrate enzyme. Upon binding of either of the two inhibitors, nine aromatic side chains within the active-site gorge change their conformation so as to interact with the inhibitors. Some differences in activity and specificity between the insect and vertebrate enzymes can be explained by comparison of their three-dimensional structures. FAU - Harel, M AU - Harel M AD - Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel. FAU - Kryger, G AU - Kryger G FAU - Rosenberry, T L AU - Rosenberry TL FAU - Mallender, W D AU - Mallender WD FAU - Lewis, T AU - Lewis T FAU - Fletcher, R J AU - Fletcher RJ FAU - Guss, J M AU - Guss JM FAU - Silman, I AU - Silman I FAU - Sussman, J L AU - Sussman JL LA - eng SI - PDB/1DX4 SI - PDB/1QO9 SI - PDB/1QON GR - NS-16577/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PT - Research Support, U.S. Gov't, P.H.S. PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (1,2,3,4-tetrahydro-N-(3-iodophenyl-methyl)-9-acridinamine) RN - 0 (1,2,3,4-tetrahydro-N-(phenyl-methyl)-9-acridinamine) RN - 0 (Aminoacridines) RN - 0 (Cholinesterase Inhibitors) RN - EC 3.1.1.7 (Acetylcholinesterase) SB - IM MH - Acetylcholinesterase/*chemistry/metabolism MH - Amino Acid Sequence MH - Aminoacridines/*chemistry/metabolism MH - Animals MH - Cholinesterase Inhibitors/*chemistry/metabolism MH - Drosophila melanogaster/*enzymology MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Conformation MH - Sequence Homology, Amino Acid MH - Substrate Specificity PMC - PMC2144661 OID - NLM: PMC2144661 EDAT- 2000/07/13 11:00 MHDA- 2001/02/28 10:01 CRDT- 2000/07/13 11:00 AID - 10.1110/ps.9.6.1063 [doi] PST - ppublish SO - Protein Sci. 2000 Jun;9(6):1063-72. PMID- 21112302 OWN - NLM STAT- MEDLINE DA - 20101129 DCOM- 20110307 LR - 20140821 IS - 1542-0086 (Electronic) IS - 0006-3495 (Linking) VI - 99 IP - 11 DP - 2010 Dec 1 TI - The O-glycosylated linker from the Trichoderma reesei Family 7 cellulase is a flexible, disordered protein. PG - 3773-81 LID - 10.1016/j.bpj.2010.10.032 [doi] AB - Fungi and bacteria secrete glycoprotein cocktails to deconstruct cellulose. Cellulose-degrading enzymes (cellulases) are often modular, with catalytic domains for cellulose hydrolysis and carbohydrate-binding modules connected by linkers rich in serine and threonine with O-glycosylation. Few studies have probed the role that the linker and O-glycans play in catalysis. Since different expression and growth conditions produce different glycosylation patterns that affect enzyme activity, the structure-function relationships that glycosylation imparts to linkers are relevant for understanding cellulase mechanisms. Here, the linker of the Trichoderma reesei Family 7 cellobiohydrolase (Cel7A) is examined by simulation. Our results suggest that the Cel7A linker is an intrinsically disordered protein with and without glycosylation. Contrary to the predominant view, the O-glycosylation does not change the stiffness of the linker, as measured by the relative fluctuations in the end-to-end distance; rather, it provides a 16 A extension, thus expanding the operating range of Cel7A. We explain observations from previous biochemical experiments in the light of results obtained here, and compare the Cel7A linker with linkers from other cellulases with sequence-based tools to predict disorder. This preliminary screen indicates that linkers from Family 7 enzymes from other genera and other cellulases within T. reesei may not be as disordered, warranting further study. CI - Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved. FAU - Beckham, Gregg T AU - Beckham GT AD - National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado, USA Gregg.Beckham@nrel.gov FAU - Bomble, Yannick J AU - Bomble YJ FAU - Matthews, James F AU - Matthews JF FAU - Taylor, Courtney B AU - Taylor CB FAU - Resch, Michael G AU - Resch MG FAU - Yarbrough, John M AU - Yarbrough JM FAU - Decker, Steve R AU - Decker SR FAU - Bu, Lintao AU - Bu L FAU - Zhao, Xiongce AU - Zhao X FAU - McCabe, Clare AU - McCabe C FAU - Wohlert, Jakob AU - Wohlert J FAU - Bergenstrahle, Malin AU - Bergenstrahle M FAU - Brady, John W AU - Brady JW FAU - Adney, William S AU - Adney WS FAU - Himmel, Michael E AU - Himmel ME FAU - Crowley, Michael F AU - Crowley MF LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - EC 3.2.1.4 (Cellulase) SB - IM MH - Amino Acid Sequence MH - Cellulase/*chemistry/*metabolism MH - Glycosylation MH - Kinetics MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Structure, Tertiary MH - Thermodynamics MH - Trichoderma/*enzymology PMC - PMC2998629 OID - NLM: PMC2998629 EDAT- 2010/11/30 06:00 MHDA- 2011/03/08 06:00 CRDT- 2010/11/30 06:00 PHST- 2010/09/24 [received] PHST- 2010/10/19 [revised] PHST- 2010/10/20 [accepted] AID - S0006-3495(10)01320-2 [pii] AID - 10.1016/j.bpj.2010.10.032 [doi] PST - ppublish SO - Biophys J. 2010 Dec 1;99(11):3773-81. doi: 10.1016/j.bpj.2010.10.032. PMID- 16581798 OWN - NLM STAT- MEDLINE DA - 20060403 DCOM- 20060503 LR - 20140909 IS - 0270-7306 (Print) IS - 0270-7306 (Linking) VI - 26 IP - 8 DP - 2006 Apr TI - Structure and function of the Saccharomyces cerevisiae Sir3 BAH domain. PG - 3256-65 AB - Previous work has shown that the N terminus of the Saccharomyces cerevisiae Sir3 protein is crucial for the function of Sir3 in transcriptional silencing. Here, we show that overexpression of N-terminal fragments of Sir3 in strains lacking the full-length protein can lead to some silencing of HML and HMR. Sir3 contains a BAH (bromo-adjacent homology) domain at its N terminus. Overexpression of this domain alone can lead to silencing as long as Sir1 is overexpressed and Sir2 and Sir4 are present. Overexpression of the closely related Orc1 BAH domain can also silence in the absence of any Sir3 protein. A previously characterized hypermorphic sir3 mutation, D205N, greatly improves silencing by the Sir3 BAH domain and allows it to bind to DNA and oligonucleosomes in vitro. A previously uncharacterized region in the Sir1 N terminus is required for silencing by both the Sir3 and Orc1 BAH domains. The structure of the Sir3 BAH domain has been determined. In the crystal, the molecule multimerizes in the form of a left-handed superhelix. This superhelix may be relevant to the function of the BAH domain of Sir3 in silencing. FAU - Connelly, Jessica J AU - Connelly JJ AD - W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA . FAU - Yuan, Peihua AU - Yuan P FAU - Hsu, Hao-Chi AU - Hsu HC FAU - Li, Zhizhong AU - Li Z FAU - Xu, Rui-Ming AU - Xu RM FAU - Sternglanz, Rolf AU - Sternglanz R LA - eng SI - PDB/2FYU GR - GM 28220/GM/NIGMS NIH HHS/United States GR - GM 63716/GM/NIGMS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - Mol Cell Biol JT - Molecular and cellular biology JID - 8109087 RN - 0 (Nucleosomes) RN - 0 (Recombinant Fusion Proteins) RN - 0 (SIR3 protein, S cerevisiae) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Silent Information Regulator Proteins, Saccharomyces cerevisiae) RN - 4QD397987E (Histidine) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Chromatin Immunoprecipitation MH - Conserved Sequence MH - Crystallography, X-Ray MH - Dimerization MH - Escherichia coli/genetics MH - Gene Silencing MH - Histidine/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Nucleosomes/metabolism MH - Plasmids/metabolism MH - Point Mutation MH - Protein Binding MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/chemistry/metabolism MH - Saccharomyces cerevisiae/*chemistry/genetics/*metabolism MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism MH - Silent Information Regulator Proteins, Saccharomyces cerevisiae/*chemistry/genetics/*metabolism MH - Static Electricity PMC - PMC1446965 OID - NLM: PMC1446965 EDAT- 2006/04/04 09:00 MHDA- 2006/05/04 09:00 CRDT- 2006/04/04 09:00 AID - 26/8/3256 [pii] AID - 10.1128/MCB.26.8.3256-3265.2006 [doi] PST - ppublish SO - Mol Cell Biol. 2006 Apr;26(8):3256-65. PMID- 12032141 OWN - NLM STAT- MEDLINE DA - 20020805 DCOM- 20020909 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 277 IP - 32 DP - 2002 Aug 9 TI - Distinct roles of the N-terminal-binding domain and the C-terminal-solubilizing domain of alpha-synuclein, a molecular chaperone. PG - 28512-20 AB - alpha-Synuclein, an acidic neuronal protein of 140 amino acids, is extremely heat-resistant and is natively unfolded. Recent studies have demonstrated that alpha-synuclein has chaperone activity both in vitro and in vivo, and that this activity is lost upon removing its C-terminal acidic tail. However, the detailed mechanism of the chaperone action of alpha-synuclein remains unknown. In this study, we investigated the molecular mechanism of the chaperone action of alpha-synuclein by analyzing the roles of its N-terminal and C-terminal domains. The N-terminal domain (residues 1-95) was found to bind to substrate proteins to form high molecular weight complexes, whereas the C-terminal acidic tail (residues 96-140) appears to be primarily involved in solubilizing the high molecular weight complexes. Because the substrate-binding domain and the solubilizing domain for chaperone function are well separated in alpha-synuclein, the N-terminal-binding domain can be substituted by other proteins or peptides. Interestingly, the resultant engineered chaperone proteins appeared to display differential efficiency and specificity in terms of the chaperone function, which depended upon the nature of the binding domain. This finding implies that the C-terminal acidic tail of alpha-synuclein can be fused with other proteins or peptides to engineer synthetic chaperones for specific purposes. FAU - Park, Sang Myun AU - Park SM AD - Department of Microbiology and Brain Korea 21 Project of Medical Sciences, Yonsei University College of Medicine, Seoul 120-752, Korea. FAU - Jung, Han Young AU - Jung HY FAU - Kim, Thomas D AU - Kim TD FAU - Park, Jeon Han AU - Park JH FAU - Yang, Chul-Hak AU - Yang CH FAU - Kim, Jongsun AU - Kim J LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20020524 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Nerve Tissue Proteins) RN - 0 (Peptides) RN - 0 (Recombinant Fusion Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - EC 1.5.1.3 (Tetrahydrofolate Dehydrogenase) RN - EC 2.5.1.18 (Glutathione Transferase) SB - IM MH - Animals MH - Chromatography, Gel MH - Cloning, Molecular MH - Escherichia coli/metabolism MH - Genetic Vectors MH - Glutathione Transferase/metabolism MH - Humans MH - Mutagenesis, Site-Directed MH - Nerve Tissue Proteins/*chemistry MH - Peptides/chemistry MH - Protein Binding MH - Protein Structure, Tertiary MH - Recombinant Fusion Proteins/metabolism MH - Substrate Specificity MH - Synucleins MH - Temperature MH - Tetrahydrofolate Dehydrogenase/chemistry MH - Time Factors MH - alpha-Synuclein EDAT- 2002/05/29 10:00 MHDA- 2002/09/11 10:01 CRDT- 2002/05/29 10:00 PHST- 2002/05/24 [aheadofprint] AID - 10.1074/jbc.M111971200 [doi] AID - M111971200 [pii] PST - ppublish SO - J Biol Chem. 2002 Aug 9;277(32):28512-20. Epub 2002 May 24. PMID- 15907702 OWN - NLM STAT- MEDLINE DA - 20050523 DCOM- 20060317 LR - 20071114 IS - 1044-0305 (Print) IS - 1044-0305 (Linking) VI - 16 IP - 6 DP - 2005 Jun TI - Transient structural disorder as a facilitator of protein-ligand binding: native H/D exchange-mass spectrometry study of cellular retinoic acid binding protein I. PG - 869-79 AB - Binding of all-trans Retinoic Acid (RA) to Cellular Retinoic Acid Binding Protein I (CRABP I) does not result in significant changes of the protein tertiary structure, even though the binding site is inaccessible in a static apo-protein conformation. One of the proposed scenarios for the protein-ligand binding process invokes the notion of a flexible portal region adjacent to the binding site, while another model suggests that the requisite dynamic events are induced by dimerization of the apo-protein in solution. In this work, RA binding to CRABP I is studied in dilute solutions (low micro-molar range), where no dimer and/or oligomer formation occurs. Modulation of backbone dynamics within various segments of the protein by its ligand is assessed using a combination of hydrogen exchange, electrospray ionization mass spectrometry, and collision-induced dissociation of protein ions in the gas phase. Consistent with the portal model of ligand entry, several protein segments (most of them containing residues making hydrophobic contacts to RA in the holo-form of the protein) are flexible in the absence of the ligand. At the same time, the two segments containing arginine residues forming a salt bridge with RA form the least flexible region in the apo-form of the protein. Although the presence of RA in solution reduces flexibility of all protein segments, the largest effect is observed within four strands that form one of the two beta-sheets enveloping a cavity which houses the ligand-binding site. These results are consistent with a model in which ligand binding occurs through a partially unstructured state of the protein with unobstructed access to the ligand-binding site. This intermediate (whose core is formed by the two stable arginine-containing strands) corresponds to a relatively low-energy local minimum on the apo-protein energy surface and is frequently sampled under native conditions. FAU - Xiao, Hui AU - Xiao H AD - Department of Chemistry, University of Massachusetts at Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA. FAU - Kaltashov, Igor A AU - Kaltashov IA LA - eng GR - R01 GM 61666/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, P.H.S. DEP - 20050413 PL - United States TA - J Am Soc Mass Spectrom JT - Journal of the American Society for Mass Spectrometry JID - 9010412 RN - 0 (Ligands) RN - 0 (Receptors, Retinoic Acid) RN - 0 (retinoic acid binding protein I, cellular) SB - IM MH - Amino Acid Sequence MH - Deuterium Exchange Measurement MH - Ligands MH - Mass Spectrometry MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Conformation MH - Receptors, Retinoic Acid/analysis/*chemistry/*metabolism MH - Spectrometry, Mass, Electrospray Ionization EDAT- 2005/05/24 09:00 MHDA- 2006/03/18 09:00 CRDT- 2005/05/24 09:00 PHST- 2004/12/28 [received] PHST- 2005/02/14 [revised] PHST- 2005/02/17 [accepted] PHST- 2005/04/13 [aheadofprint] AID - S1044-0305(05)00197-2 [pii] AID - 10.1016/j.jasms.2005.02.020 [doi] PST - ppublish SO - J Am Soc Mass Spectrom. 2005 Jun;16(6):869-79. Epub 2005 Apr 13. PMID- 22927976 OWN - NLM STAT- MEDLINE DA - 20120828 DCOM- 20130129 LR - 20141105 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 8 DP - 2012 TI - Quantitative analysis of alpha-synuclein solubility in living cells using split GFP complementation. PG - e43505 LID - 10.1371/journal.pone.0043505 [doi] AB - Presently incurable, Parkinson's disease (PD) is the most common neurodegenerative movement disorder and affects 1% of the population over 60 years of age. The hallmarks of PD pathogenesis are the loss of dopaminergic neurons in the substantia nigra pars compacta, and the occurrence of proteinaceous cytoplasmic inclusions (Lewy bodies) in surviving neurons. Lewy bodies are mainly composed of the pre-synaptic protein alpha-synuclein (alphasyn), an intrinsically unstructured, misfolding-prone protein with high propensity to aggregate. Quantifying the pool of soluble alphasyn and monitoring alphasyn aggregation in living cells is fundamental to study the molecular mechanisms of alphasyn-induced cytotoxicity and develop therapeutic strategies to prevent alphasyn aggregation. In this study, we report the use of a split GFP complementation assay to quantify alphasyn solubility. Particularly, we investigated a series of naturally occurring and rationally designed alphasyn variants and showed that this method can be used to study how alphasyn sequence specificity affects its solubility. Furthermore, we demonstrated the utility of this assay to explore the influence of the cellular folding network on alphasyn solubility. The results presented underscore the utility of the split GFP assay to quantify alphasyn solubility in living cells. FAU - Kothawala, Ahmed AU - Kothawala A AD - Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, United States of America. FAU - Kilpatrick, Kiri AU - Kilpatrick K FAU - Novoa, Jose Andres AU - Novoa JA FAU - Segatori, Laura AU - Segatori L LA - eng PT - Journal Article DEP - 20120822 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (alpha-Synuclein) RN - 147336-22-9 (Green Fluorescent Proteins) RN - EC 3.4.25.1 (Proteasome Endopeptidase Complex) SB - IM MH - Cell Survival MH - Green Fluorescent Proteins/*chemistry/genetics MH - HeLa Cells MH - Humans MH - Mutation MH - Proteasome Endopeptidase Complex/metabolism MH - Protein Multimerization MH - Proteolysis/drug effects MH - Solubility/drug effects MH - Spectrometry, Fluorescence/*methods MH - alpha-Synuclein/*chemistry/genetics/metabolism PMC - PMC3425482 OID - NLM: PMC3425482 EDAT- 2012/08/29 06:00 MHDA- 2013/01/30 06:00 CRDT- 2012/08/29 06:00 PHST- 2012/01/06 [received] PHST- 2012/07/24 [accepted] PHST- 2012/08/22 [epublish] AID - 10.1371/journal.pone.0043505 [doi] AID - PONE-D-12-00609 [pii] PST - ppublish SO - PLoS One. 2012;7(8):e43505. doi: 10.1371/journal.pone.0043505. Epub 2012 Aug 22. PMID- 9147986 OWN - NLM STAT- MEDLINE DA - 19970509 DCOM- 19970509 LR - 20131121 IS - 0142-4319 (Print) IS - 0142-4319 (Linking) VI - 18 IP - 1 DP - 1997 Feb TI - An insert in the motor domain determines the functional properties of expressed smooth muscle myosin isoforms. PG - 103-10 AB - Smooth muscle myosin isoforms of the heavy chain and the essential light chain have been hypothesized to contribute to the different shortening velocities of phasic and tonic smooth muscles, and to their different affinities for MgADP. We used the baculovirus/insect cell system to express homogeneous heavy meromyosin molecules differing only in seven amino acid insert (QGPSFSY) in the motor domain near the active site, or in the type of essential light chain isoform. Myosin from tonic rabbit uterine smooth muscle lacks the heavy chain insert, while myosin from phasic chicken gizzard contains it. The properties of a mutant uterine heavy meromyosin with added insert, and a mutant gizzard heavy meromyosin with the insert deleted, were compared with their wild type progenitors. Phosphorylated heavy meromyosins with the insert have a twofold higher enzymatic activity and in vitro motility han heavy meromyosins without the insert. These functional properties were not altered by the essential light chain isoforms. The altered motility caused by the insert implies that it modulates the rate of ADP release, the molecular step believed to limit shortening velocity. The insert may thus account in part for both the lower sensitivity to MgADP and the higher shortening velocity of phasic compared to tonic smooth muscles. FAU - Rovner, A S AU - Rovner AS AD - Department of Molecular Physiology and Biophysics, University of Vermont, College of Medicine, Burlington 05405-0068, USA. FAU - Freyzon, Y AU - Freyzon Y FAU - Trybus, K M AU - Trybus KM LA - eng GR - HL38113/HL/NHLBI NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Muscle Res Cell Motil JT - Journal of muscle research and cell motility JID - 8006298 RN - 0 (Actins) RN - 0 (DNA, Complementary) RN - 0 (Isoenzymes) RN - 0 (Myosin Subfragments) RN - 61D2G4IYVH (Adenosine Diphosphate) RN - EC 3.6.4.1 (Myosins) SB - IM MH - Actins/metabolism MH - Adenosine Diphosphate/metabolism MH - Amino Acid Sequence MH - Animals MH - DNA, Complementary/chemistry MH - Isoenzymes/*chemistry/metabolism MH - Molecular Sequence Data MH - Muscle Contraction/*physiology MH - Muscle, Smooth/*enzymology MH - Myosin Subfragments/chemistry/metabolism MH - Myosins/*chemistry/metabolism MH - Rabbits MH - Spodoptera EDAT- 1997/02/01 MHDA- 1997/02/01 00:01 CRDT- 1997/02/01 00:00 PST - ppublish SO - J Muscle Res Cell Motil. 1997 Feb;18(1):103-10. PMID- 17001643 OWN - NLM STAT- MEDLINE DA - 20061123 DCOM- 20070220 IS - 1097-0134 (Electronic) IS - 0887-3585 (Linking) VI - 65 IP - 4 DP - 2006 Dec 1 TI - Intrinsically unstructured N-terminal domain of bZIP transcription factor HY5. PG - 856-66 AB - The Arabidopsis HY5 protein is a basic leucine zipper (bZIP) transcription factor that promotes photomorphogenesis. HY5 binds directly to the promoters of light responsible element containing the G-box and thus regulates their transcriptional activity. The level and activity of HY5 are negatively regulated, in a light-dependent manner, by interaction with the COP1 protein, which targets HY5 for proteasome-mediated degradation in the nucleus. Despite its essential roles in plant development, no structural information exists for HY5. In this article, we report the first structural and biophysical characterization of HY5. Using limited proteolysis in combination with mass spectrometry, circular dichroism, and nuclear magnetic resonance spectroscopy, we have deduced that the N-terminal 77 amino acids of HY5 form a premolten globular structure, while amino acids 78-110, which constitute the basic region (BR) of the protein, exist in a molten globule state. Our studies also revealed that the overall structural features of full-length HY5 are dominated largely by the disordered N-terminal domain, despite the existence of a bZIP domain at its C-terminus. We propose that HY5 is a member of the intrinsically unstructured protein (IUP) family, and that HY5 functions as an unstructured protein and benefits from being the same, in vivo. CI - (c) 2006 Wiley-Liss, Inc. FAU - Yoon, Mi-Kyung AU - Yoon MK AD - Department of Chemistry and National Creative Research Initiative Center, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejon 305-701, Republic of Korea. FAU - Shin, Jieun AU - Shin J FAU - Choi, Giltsu AU - Choi G FAU - Choi, Byong-Seok AU - Choi BS LA - eng PT - Journal Article PL - United States TA - Proteins JT - Proteins JID - 8700181 RN - 0 (Arabidopsis Proteins) RN - 0 (Basic-Leucine Zipper Transcription Factors) RN - 0 (HY5 protein, Arabidopsis) RN - 0 (Nuclear Proteins) RN - 0 (Recombinant Proteins) SB - IM MH - Amino Acid Sequence MH - Arabidopsis Proteins/*chemistry/isolation & purification MH - Basic-Leucine Zipper Transcription Factors/*chemistry/isolation & purification MH - Circular Dichroism MH - Magnetic Resonance Spectroscopy MH - Mass Spectrometry MH - Models, Genetic MH - Nuclear Proteins/*chemistry/isolation & purification MH - Protein Structure, Tertiary MH - Recombinant Proteins/chemistry/genetics/isolation & purification MH - Temperature EDAT- 2006/09/27 09:00 MHDA- 2007/02/21 09:00 CRDT- 2006/09/27 09:00 AID - 10.1002/prot.21089 [doi] PST - ppublish SO - Proteins. 2006 Dec 1;65(4):856-66. PMID- 10211825 OWN - NLM STAT- MEDLINE DA - 19990714 DCOM- 19990714 LR - 20140617 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 8 IP - 4 DP - 1999 Apr TI - Helicity of alpha(404-451) and beta(394-445) tubulin C-terminal recombinant peptides. PG - 788-99 AB - We have investigated the solution conformation of the functionally relevant C-terminal extremes of alpha- and beta-tubulin, employing the model recombinant peptides RL52alpha3 and RL33beta6, which correspond to the amino acid sequences 404-451(end) and 394-445(end) of the main vertebrate isotypes of alpha- and beta-tubulin, respectively, and synthetic peptides with the alpha-tubulin(430-443) and beta-tubulin(412-431) internal sequences. Alpha(404-451) and beta(394-445) are monomeric in neutral aqueous solution (as indicated by sedimentation equilibrium), and have circular dichroism (CD) spectra characteristic of nearly disordered conformation, consistent with low scores in peptide helicity prediction. Limited proteolysis of beta(394-445) with subtilisin, instead of giving extensive degradation, resulted in main cleavages at positions Thr409-Glu410 and Tyr422-Gln423-Gln424, defining the proteolysis resistant segment 410-422, which corresponds to the central part of the predicted beta-tubulin C-terminal helix. Both recombinant peptides inhibited microtubule assembly, probably due to sequestration of the microtubule stabilizing associated proteins. Trifluoroethanol (TFE)-induced markedly helical CD spectra in alpha(404-451) and beta(394-445). A substantial part of the helicity of beta(394-445) was found to be in the CD spectrum of the shorter peptide beta(412-431) with TFE. Two-dimensional 1H-NMR parameters (nonsequential nuclear Overhauser effects (NOE) and conformational C alphaH shifts) in 30% TFE permitted to conclude that about 25% of alpha(404-451) and 40% of beta(394-451) form well-defined helices encompassing residues 418-432 and 408-431, respectively, flanked by disordered N- and C-segments. The side chains of beta(394-451) residues Leu418, Val419, Ser420, Tyr422, Tyr425, and Gln426 are well defined in structure calculations from the NOE distance constraints. The apolar faces of the helix in both alpha and beta chains share a characteristic sequence of conserved residues Ala,Met(+4),Leu(+7),Tyr(+11). The helical segment of alpha(404-451) is the same as that described in the electron crystallographic model structure of alphabeta-tubulin, while in beta(394-451) it extends for nine residues more, supporting the possibility of a functional coil --> helix transition at the C-terminus of beta-tubulin. These peptides may be employed to construct model complexes with microtubule associated protein binding sites. FAU - Jimenez, M A AU - Jimenez MA AD - Instituto de Estructura de la Materia, CSIC, Madrid, Spain. FAU - Evangelio, J A AU - Evangelio JA FAU - Aranda, C AU - Aranda C FAU - Lopez-Brauet, A AU - Lopez-Brauet A FAU - Andreu, D AU - Andreu D FAU - Rico, M AU - Rico M FAU - Lagos, R AU - Lagos R FAU - Andreu, J M AU - Andreu JM FAU - Monasterio, O AU - Monasterio O LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Recombinant Proteins) RN - 0 (Tubulin) RN - 75-89-8 (Trifluoroethanol) RN - J41CSQ7QDS (Zinc) SB - IM MH - Amino Acid Sequence MH - Animals MH - Chickens MH - Chromatography, High Pressure Liquid MH - Circular Dichroism MH - Computer Simulation MH - Humans MH - Magnetic Resonance Spectroscopy MH - Models, Molecular MH - Molecular Sequence Data MH - Plasmids MH - *Protein Structure, Secondary MH - Recombinant Proteins/chemistry MH - Time Factors MH - Trifluoroethanol/chemistry MH - Tubulin/*chemistry MH - Ultracentrifugation MH - Zinc/chemistry PMC - PMC2144297 OID - NLM: PMC2144297 EDAT- 1999/04/22 MHDA- 1999/04/22 00:01 CRDT- 1999/04/22 00:00 AID - 10.1110/ps.8.4.788 [doi] PST - ppublish SO - Protein Sci. 1999 Apr;8(4):788-99. PMID- 11749217 OWN - NLM STAT- MEDLINE DA - 20011225 DCOM- 20030107 LR - 20091119 IS - 1525-7797 (Print) IS - 1525-7797 (Linking) VI - 2 IP - 2 DP - 2001 Summer TI - Effects of macromolecular crowding on the intrinsically disordered proteins c-Fos and p27(Kip1). PG - 538-40 AB - A number of biologically active proteins exhibit intrinsic structural disorder in vitro under thermodynamically ideal conditions. In vivo, however, proteins exist in a crowded, thermodynamically nonideal environment. We tested the hypothesis that intrinsically disordered proteins adopt stable structure under crowded conditions in which excluded volume is predicted to stabilize compact, native conformations. In the presence of macromolecular crowding agents, neither the intrinsically disordered C-terminal activation domain of c-Fos nor the kinase-inhibition domain of p27(Kip1) undergoes any significant conformational change that is detected by changes in either circular dichroism or fluorescence spectra. We conclude that molecular crowding effects are not necessarily sufficient to induce ordered structure in intrinsically disordered proteins. FAU - Flaugh, S L AU - Flaugh SL AD - Department of Biochemistry and Molecular Biology and Department of Chemistry, Colorado State University, Fort Collins, Colorado, 80523-1870, USA. FAU - Lumb, K J AU - Lumb KJ LA - eng GR - GM55156/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Biomacromolecules JT - Biomacromolecules JID - 100892849 RN - 0 (Cell Cycle Proteins) RN - 0 (Macromolecular Substances) RN - 0 (Proto-Oncogene Proteins c-fos) RN - 0 (Tumor Suppressor Proteins) RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - EC 2.7.11.22 (Cyclin-Dependent Kinases) SB - IM MH - Cell Cycle Proteins/*chemistry/metabolism MH - Cyclin-Dependent Kinase Inhibitor p27 MH - Cyclin-Dependent Kinases/antagonists & inhibitors MH - Escherichia coli MH - Humans MH - Macromolecular Substances MH - Protein Folding MH - Protein Structure, Secondary MH - Proto-Oncogene Proteins c-fos/*chemistry/metabolism MH - Tumor Suppressor Proteins/*chemistry/metabolism EDAT- 2001/12/26 10:00 MHDA- 2003/01/08 04:00 CRDT- 2001/12/26 10:00 AID - bm015502z [pii] PST - ppublish SO - Biomacromolecules. 2001 Summer;2(2):538-40. PMID- 24844634 OWN - NLM STAT- MEDLINE DA - 20140725 DCOM- 20140929 IS - 1470-8728 (Electronic) IS - 0264-6021 (Linking) VI - 462 IP - 1 DP - 2014 Aug 15 TI - Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain. PG - 53-65 LID - 10.1042/BJ20140521 [doi] AB - The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the beta2-strand and the alpha1-helix parallel to the beta2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule. FAU - Kung, Camy C-H AU - Kung CC FAU - Naik, Mandar T AU - Naik MT AD - *Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan. FAU - Wang, Szu-Huan AU - Wang SH AD - section signScientific Instrument Center, Academia Sinica, Taipei 11529, Taiwan. FAU - Shih, Hsiu-Ming AU - Shih HM AD - *Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan. FAU - Chang, Che-Chang AU - Chang CC AD - parallelGraduate Institute of Translational Medicine, Taipei Medical University, Taipei 110, Taiwan. FAU - Lin, Li-Ying AU - Lin LY AD - paragraph signGenomics Research Center, Academia Sinica, Taipei 11529, Taiwan. FAU - Chen, Chia-Lin AU - Chen CL FAU - Ma, Che AU - Ma C AD - paragraph signGenomics Research Center, Academia Sinica, Taipei 11529, Taiwan. FAU - Chang, Chi-Fon AU - Chang CF AD - paragraph signGenomics Research Center, Academia Sinica, Taipei 11529, Taiwan. FAU - Huang, Tai-Huang AU - Huang TH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - England TA - Biochem J JT - The Biochemical journal JID - 2984726R RN - 0 (Nuclear Proteins) RN - 0 (RNF4 protein, human) RN - 0 (Small Ubiquitin-Related Modifier Proteins) RN - 0 (Transcription Factors) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM MH - Amino Acid Motifs/physiology MH - Nuclear Magnetic Resonance, Biomolecular MH - Nuclear Proteins/*metabolism MH - Protein Binding MH - Protein Structure, Tertiary MH - Scattering, Small Angle MH - Small Ubiquitin-Related Modifier Proteins/*metabolism MH - Transcription Factors/*metabolism MH - Ubiquitin-Protein Ligases/metabolism MH - X-Ray Diffraction EDAT- 2014/05/23 06:00 MHDA- 2014/09/30 06:00 CRDT- 2014/05/22 06:00 AID - BJ20140521 [pii] AID - 10.1042/BJ20140521 [doi] PST - ppublish SO - Biochem J. 2014 Aug 15;462(1):53-65. doi: 10.1042/BJ20140521. PMID- 23941183 OWN - NLM STAT- MEDLINE DA - 20130814 DCOM- 20140305 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 135 IP - 32 DP - 2013 Aug 14 TI - Molecular crowding stabilizes both the intrinsically disordered calcium-free state and the folded calcium-bound state of a repeat in toxin (RTX) protein. PG - 11929-34 LID - 10.1021/ja404790f [doi] AB - Macromolecular crowding affects most chemical equilibria in living cells, as the presence of high concentrations of macromolecules sterically restricts the available space. Here, we characterized the influence of crowding on a prototypical RTX protein, RC(L). RTX (Repeat in ToXin) motifs are calcium-binding nonapeptide sequences that are found in many virulence factors produced by Gram-negative bacteria and secreted by dedicated type 1 secretion systems. RC(L) is an attractive model to investigate the effect of molecular crowding on ligand-induced protein folding, as it shifts from intrinsically disordered conformations (apo-form) to a stable structure upon calcium binding (holo-form). It thus offers the rare opportunity to characterize the crowding effects on the same polypeptide chain under two drastically distinct folding states. We showed that the crowding agent Ficoll70 did not affect the structural content of the apo-state and holo-state of RC(L) but increased the protein affinity for calcium. Moreover, Ficoll70 strongly stabilized both states of RC(L), increasing their half-melting temperature, without affecting enthalpy changes. The power law dependence of the melting temperature increase (DeltaT(m)) on the volume fraction (phi) followed theoretical excluded volume predictions and allowed the estimation of the Flory exponent (nu) of the thermally unfolded polypeptide chain in both states. Altogether, our data suggest that, in the apo-state as found in the crowded bacterial cytosol, RTX proteins adopt extended unfolded conformations that may facilitate protein export by the type I secretion machinery. Subsequently, crowding also enhances the calcium-dependent folding and stability of RTX proteins once secreted in the extracellular milieu. FAU - Sotomayor-Perez, Ana-Cristina AU - Sotomayor-Perez AC AD - Unite de Biochimie des Interactions Macromoleculaires, CNRS UMR 3528, Departement de Biologie Structurale et Chimie, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France. FAU - Subrini, Orso AU - Subrini O FAU - Hessel, Audrey AU - Hessel A FAU - Ladant, Daniel AU - Ladant D FAU - Chenal, Alexandre AU - Chenal A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20130731 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Adenylate Cyclase Toxin) RN - 25702-74-3 (Ficoll) RN - SY7Q814VUP (Calcium) SB - IM MH - Adenylate Cyclase Toxin/*chemistry/metabolism MH - Bordetella pertussis/*chemistry/metabolism MH - Calcium/metabolism MH - Ficoll/metabolism MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Stability MH - Whooping Cough/microbiology EDAT- 2013/08/15 06:00 MHDA- 2014/03/07 06:00 CRDT- 2013/08/15 06:00 PHST- 2013/07/31 [aheadofprint] AID - 10.1021/ja404790f [doi] PST - ppublish SO - J Am Chem Soc. 2013 Aug 14;135(32):11929-34. doi: 10.1021/ja404790f. Epub 2013 Jul 31. PMID- 12842038 OWN - NLM STAT- MEDLINE DA - 20030704 DCOM- 20040319 LR - 20061115 IS - 0969-2126 (Print) IS - 0969-2126 (Linking) VI - 11 IP - 7 DP - 2003 Jul TI - Organic solvents order the dynamic switch II in Ras crystals. PG - 747-51 AB - Room temperature crystal structures of crosslinked H-Ras bound to GMPPNP were solved in 50% 2,2,2-trifluoroethanol, 60% 1,6-hexanediol, and 50% isopropanol. The disordered switch II region of Ras is ordered in the presence of 2,2,2-trifluoroethanol or 1,6-hexanediol. The overall backbone conformation of switch II in these organic solvents is the same as in the Ras-GMPPNP complexes with RalGDS, PI(3) kinase, and RasGAP, indicating a biologically relevant form. Key polar interactions that stabilize the ordered switch are enhanced in the presence of hydrophobic cosolvents. These results suggest that hydrophobic solvents can be used in general to order short biologically relevant segments of disordered regions in protein crystals by favoring H-bonding interactions between atoms that are highly solvated and mobile in aqueous solution. FAU - Buhrman, Greg AU - Buhrman G AD - Department of Molecular and Structural Biochemistry, North Carolina State University, 128 Polk Hall, Raleigh, NC 27695, USA. FAU - de Serrano, Vesna AU - de Serrano V FAU - Mattos, Carla AU - Mattos C LA - eng SI - PDB/1P2S SI - PDB/1P2T SI - PDB/1P2U PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Structure JT - Structure (London, England : 1993) JID - 101087697 RN - 0 (Organic Chemicals) RN - 0 (Solvents) RN - 86-01-1 (Guanosine Triphosphate) RN - EC 3.6.5.2 (ras Proteins) SB - IM MH - Crystallization MH - Guanosine Triphosphate/*analogs & derivatives/chemistry MH - Organic Chemicals/*chemistry MH - Solvents/*chemistry MH - ras Proteins/*chemistry EDAT- 2003/07/05 05:00 MHDA- 2004/03/20 05:00 CRDT- 2003/07/05 05:00 AID - S096921260300128X [pii] PST - ppublish SO - Structure. 2003 Jul;11(7):747-51. PMID- 21087614 OWN - NLM STAT- MEDLINE DA - 20110107 DCOM- 20110207 LR - 20111117 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 405 IP - 3 DP - 2011 Jan 21 TI - Critical scaffolding regions of the tumor suppressor Axin1 are natively unfolded. PG - 773-86 LID - 10.1016/j.jmb.2010.11.013 [doi] AB - The Wnt pathway tumor-suppressor protein Axin coordinates the formation of a critical multiprotein destruction complex that serves to downregulate beta-catenin protein levels, thereby preventing target gene activation. Given the lack of structural information on some of the major functional parts of Axin, it remains unresolved how the recruitment and positioning of Wnt pathway kinases, such as glycogen synthase kinase 3beta, are coordinated to bring about beta-catenin phosphorylation. Using various biochemical and biophysical methods, we demonstrate here that the central region of Axin that is implicated in binding glycogen synthase kinase 3beta and beta-catenin is natively unfolded. Our results support a model in which the unfolded nature of these critical scaffolding regions in Axin facilitates dynamic interactions with a kinase and its substrate, which in turn act upon each other. CI - Copyright A(c) 2010. Published by Elsevier Ltd. FAU - Noutsou, Maria AU - Noutsou M AD - Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands. FAU - Duarte, Afonso M S AU - Duarte AM FAU - Anvarian, Zeinab AU - Anvarian Z FAU - Didenko, Tatiana AU - Didenko T FAU - Minde, David P AU - Minde DP FAU - Kuper, Ineke AU - Kuper I FAU - de Ridder, Isabel AU - de Ridder I FAU - Oikonomou, Christina AU - Oikonomou C FAU - Friedler, Assaf AU - Friedler A FAU - Boelens, Rolf AU - Boelens R FAU - Rudiger, Stefan G D AU - Rudiger SG FAU - Maurice, Madelon M AU - Maurice MM LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20101116 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (AXIN1 protein, human) RN - 0 (Adaptor Proteins, Signal Transducing) RN - 0 (Axin Protein) RN - 0 (Repressor Proteins) RN - 0 (Tumor Suppressor Proteins) RN - 0 (Wnt Proteins) RN - 0 (beta Catenin) RN - EC 2.7.11.1 (glycogen synthase kinase 3 beta) RN - EC 2.7.11.26 (Glycogen Synthase Kinase 3) SB - IM MH - Adaptor Proteins, Signal Transducing/*chemistry MH - Axin Protein MH - Binding Sites MH - Glycogen Synthase Kinase 3/chemistry MH - Humans MH - *Matrix Attachment Regions MH - Models, Molecular MH - Protein Binding MH - *Protein Unfolding MH - Repressor Proteins/*chemistry MH - Tumor Suppressor Proteins/*chemistry MH - Wnt Proteins/chemistry/metabolism MH - beta Catenin/chemistry EDAT- 2010/11/23 06:00 MHDA- 2011/02/08 06:00 CRDT- 2010/11/20 06:00 PHST- 2010/06/30 [received] PHST- 2010/11/05 [revised] PHST- 2010/11/05 [accepted] PHST- 2010/11/16 [aheadofprint] AID - S0022-2836(10)01227-1 [pii] AID - 10.1016/j.jmb.2010.11.013 [doi] PST - ppublish SO - J Mol Biol. 2011 Jan 21;405(3):773-86. doi: 10.1016/j.jmb.2010.11.013. Epub 2010 Nov 16. PMID- 17543868 OWN - NLM STAT- MEDLINE DA - 20070604 DCOM- 20070730 LR - 20150325 IS - 1534-5807 (Print) IS - 1534-5807 (Linking) VI - 12 IP - 6 DP - 2007 Jun TI - The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting. PG - 973-86 AB - The yeast Vps27/Hse1 complex and the homologous mammalian Hrs/STAM complex deliver ubiquitinated transmembrane proteins to the ESCRT endosomal-sorting pathway. The Vps27/Hse1 complex directly binds to ubiquitinated transmembrane proteins and recruits both ubiquitin ligases and deubiquitinating enzymes. We have solved the crystal structure of the core responsible for the assembly of the Vps27/Hse1 complex at 3.0 A resolution. The structure consists of two intertwined GAT domains, each consisting of two helices from one subunit and one from the other. The two GAT domains are connected by an antiparallel coiled coil, forming a 90 A-long barbell-like structure. This structure places the domains of Vps27 and Hse1 that recruit ubiquitinated cargo and deubiquitinating enzymes close to each other. Coarse-grained Monte Carlo simulations of the Vps27/Hse1 complex on a membrane show how the complex binds cooperatively to lipids and ubiquitinated membrane proteins and acts as a scaffold for ubiquitination reactions. FAU - Prag, Gali AU - Prag G AD - Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20892, USA. FAU - Watson, Hadiya AU - Watson H FAU - Kim, Young C AU - Kim YC FAU - Beach, Bridgette M AU - Beach BM FAU - Ghirlando, Rodolfo AU - Ghirlando R FAU - Hummer, Gerhard AU - Hummer G FAU - Bonifacino, Juan S AU - Bonifacino JS FAU - Hurley, James H AU - Hurley JH LA - eng GR - Z01 DK036118-14/Intramural NIH HHS/United States GR - Z01 DK036126-01/Intramural NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, N.I.H., Intramural PL - United States TA - Dev Cell JT - Developmental cell JID - 101120028 RN - 0 (Endosomal Sorting Complexes Required for Transport) RN - 0 (Hse1 protein, S cerevisiae) RN - 0 (Receptors, Cytoplasmic and Nuclear) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Ubiquitin) RN - 0 (VPS27 protein, S cerevisiae) RN - 0 (Vesicular Transport Proteins) SB - IM MH - Amino Acid Sequence MH - Chromatography, Gel MH - Crystallography, X-Ray MH - Endosomal Sorting Complexes Required for Transport MH - Immunoprecipitation MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Mutation/genetics MH - Protein Binding MH - Protein Structure, Tertiary MH - Protein Transport MH - Receptors, Cytoplasmic and Nuclear/*chemistry/genetics/metabolism MH - Saccharomyces cerevisiae/*chemistry/genetics MH - Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism MH - Sequence Homology, Amino Acid MH - Ubiquitin/metabolism MH - Vesicular Transport Proteins/*chemistry/genetics/metabolism PMC - PMC2292400 MID - NIHMS44474 OID - NLM: NIHMS44474 OID - NLM: PMC2292400 EDAT- 2007/06/05 09:00 MHDA- 2007/07/31 09:00 CRDT- 2007/06/05 09:00 PHST- 2006/12/12 [received] PHST- 2007/02/20 [revised] PHST- 2007/04/18 [accepted] AID - S1534-5807(07)00160-8 [pii] AID - 10.1016/j.devcel.2007.04.013 [doi] PST - ppublish SO - Dev Cell. 2007 Jun;12(6):973-86. PMID- 19899809 OWN - NLM STAT- MEDLINE DA - 20091222 DCOM- 20100112 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 51 DP - 2009 Dec 29 TI - Receptor and subunit specific interactions of RIC-3 with nicotinic acetylcholine receptors. PG - 12329-36 LID - 10.1021/bi901234a [doi] AB - RIC-3 belongs to a conserved family of proteins influencing maturation of nicotinic acetylcholine receptors (nAChRs). RIC-3 homologues were shown to differently affect different nAChRs. Here we show that coexpression with RIC-3 increases the level of surface expression of DEG-3 while slightly reducing the level of surface expression of DES-2, both subunits of the DEG-3/DES-2 nAChRs. Those different effects are a likely explanation for the previously demonstrated effects of RIC-3, an endoplasmic reticulum resident protein, on properties of this receptor. To understand how RIC-3 interacts with different nAChR subunits, we identified and characterized domains and residues enabling this interaction. This analysis shows that conserved residues in the second RIC-3 transmembrane domain are needed for its interactions with two different Caenorhabditis elegans nAChRs, DEG-3/DES-2 and ACR-16. These conserved residues do not, however, function alone; rather, we show that additional domains also enable RIC-3's interactions with these receptors. Interestingly, the relative importance of these residues or of other domains mediating interactions of RIC-3 with nAChRs differs for the two different receptors. Differences in the way that RIC-3, predicted to be an intrinsically disordered protein, interacts with different receptors and receptor subunits suggest that it may adopt different conformations to enable these interactions. Such differences may explain both the effects of RIC-3 on receptor properties and the differences in its effects on different receptors. FAU - Cohen Ben-Ami, Hagit AU - Cohen Ben-Ami H AD - Department of Medical Neurobiology, Institute for Medical Research-Israel-Canada, Hebrew University, Hadassah Medical School, Jerusalem 91120, Israel. FAU - Biala, Yoav AU - Biala Y FAU - Farah, Hanna AU - Farah H FAU - Elishevitz, Esty AU - Elishevitz E FAU - Battat, Emil AU - Battat E FAU - Treinin, Millet AU - Treinin M LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Caenorhabditis elegans Proteins) RN - 0 (DEG-3 protein, C elegans) RN - 0 (Protein Subunits) RN - 0 (Receptors, Nicotinic) RN - 0 (acr-16 protein, C elegans) RN - 0 (ric-3 protein, C elegans) SB - IM MH - Amino Acid Sequence MH - Animals MH - Caenorhabditis elegans/chemistry/genetics/*metabolism MH - Caenorhabditis elegans Proteins/chemistry/genetics/*metabolism MH - Molecular Sequence Data MH - Oocytes/metabolism MH - Protein Binding MH - Protein Subunits/chemistry/genetics/*metabolism MH - Receptors, Nicotinic/genetics/*metabolism MH - Sequence Homology, Amino Acid MH - Xenopus EDAT- 2009/11/11 06:00 MHDA- 2010/01/13 06:00 CRDT- 2009/11/11 06:00 AID - 10.1021/bi901234a [doi] PST - ppublish SO - Biochemistry. 2009 Dec 29;48(51):12329-36. doi: 10.1021/bi901234a. PMID- 18448430 OWN - NLM STAT- MEDLINE DA - 20080630 DCOM- 20080819 LR - 20131121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 283 IP - 27 DP - 2008 Jul 4 TI - The structure and interactions of the proline-rich domain of ASPP2. PG - 18990-9 LID - 10.1074/jbc.M708717200 [doi] AB - ASPP2 is a pro-apoptotic protein that stimulates the p53-mediated apoptotic response. The C terminus of ASPP2 contains ankyrin (Ank) repeats and a SH3 domain, which mediate its interactions with numerous partner proteins such as p53, NFkappaB, and Bcl-2. It also contains a proline-rich domain (ASPP2 Pro), whose structure and function are unclear. Here we used biophysical and biochemical methods to study the structure and the interactions of ASPP2 Pro, to gain insight into its biological role. We show, using biophysical and computational methods, that the ASPP2 Pro domain is natively unfolded. We found that the ASPP2 Pro domain interacts with the ASPP2 Ank-SH3 domains, and mapped the interaction sites in both domains. Using a combination of peptide array screening, biophysical and biochemical techniques, we found that ASPP2 Ank-SH3, but not ASPP2 Pro, mediates interactions of ASPP2 with peptides derived from its partner proteins. ASPP2 Pro-Ank-SH3 bound a peptide derived from its partner protein NFkappaB weaker than ASPP2 Ank-SH3 bound this peptide. This suggested that the presence of the proline-rich domain inhibited the interactions mediated by the Ank-SH3 domains. Furthermore, a peptide from ASPP2 Pro competed with a peptide derived from NFkappaB on binding to ASPP2 Ank-SH3. Based on our results, we propose a model in which the interaction between the ASPP2 domains regulates the intermolecular interactions of ASPP2 with its partner proteins. FAU - Rotem, Shahar AU - Rotem S AD - Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel. FAU - Katz, Chen AU - Katz C FAU - Benyamini, Hadar AU - Benyamini H FAU - Lebendiker, Mario AU - Lebendiker M FAU - Veprintsev, Dmitry AU - Veprintsev D FAU - Rudiger, Stefan AU - Rudiger S FAU - Danieli, Tsafi AU - Danieli T FAU - Friedler, Assaf AU - Friedler A LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080430 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Apoptosis Regulatory Proteins) RN - 0 (Carrier Proteins) RN - 0 (NF-kappa B) RN - 0 (Proto-Oncogene Proteins c-bcl-2) RN - 0 (TP53 protein, human) RN - 0 (TP53BP2 protein, human) RN - 0 (Tumor Suppressor Protein p53) RN - 9DLQ4CIU6V (Proline) SB - IM MH - Animals MH - Apoptosis Regulatory Proteins MH - Carrier Proteins/*chemistry/metabolism MH - Humans MH - *Models, Molecular MH - NF-kappa B/chemistry/metabolism MH - Peptide Mapping/methods MH - Proline/*chemistry MH - Protein Binding/physiology MH - Proto-Oncogene Proteins c-bcl-2/chemistry/metabolism MH - Structure-Activity Relationship MH - Tumor Suppressor Protein p53/chemistry/metabolism MH - src Homology Domains/physiology EDAT- 2008/05/02 09:00 MHDA- 2008/08/20 09:00 CRDT- 2008/05/02 09:00 PHST- 2008/04/30 [aheadofprint] AID - M708717200 [pii] AID - 10.1074/jbc.M708717200 [doi] PST - ppublish SO - J Biol Chem. 2008 Jul 4;283(27):18990-9. doi: 10.1074/jbc.M708717200. Epub 2008 Apr 30. PMID- 21271977 OWN - NLM STAT- MEDLINE DA - 20110530 DCOM- 20110919 IS - 1875-5305 (Electronic) IS - 0929-8665 (Linking) VI - 18 IP - 6 DP - 2011 Jun TI - Isolation and compositional analysis of a CP12-associated complex of calvin cycle enzymes from Nicotiana tabacum. PG - 618-24 AB - Two Calvin Cycle enzymes, NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and phosphoribulokinase (PRK) form a multiprotein complex with CP12, a small intrinsically-unstructured protein. Under oxidizing conditions, association with CP12 confers redox-sensitivity to the otherwise redox-insensitive A isoform of GAPDH (GapA) and provides an additional level of down-regulation to the redox-regulated PRK. To determine if CP12-mediated regulation is specific for GAPDH and PRK in vivo, a high molecular weight complex containing CP12 was isolated from tobacco chloroplasts and leaves and its protein composition was characterized. Gel electrophoresis and immunoblot analyses after separation of stromal proteins by size fractionation verified that the GAPDH (both isoforms) and PRK co-migrated with CP12 in dark- but not light-adapted chloroplasts. Nano-liquid-chromatography-mass-spectrometry of the isolated complex identified only CP12, GAPDH and PRK. Since nearly all of the CP12 from darkened chloroplasts migrates with GADPH and PRK as a high molecular mass species, these data indicate that the tight association of tobacco CP12 with GAPDH and PRK is specific and involves no other Calvin Cycle enzymes. FAU - Carmo-Silva, A Elizabete AU - Carmo-Silva AE AD - Arid-Land Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, 21881 N. Cardon Lane, Maricopa, Arizona 85138, USA. FAU - Marri, Lucia AU - Marri L FAU - Sparla, Francesca AU - Sparla F FAU - Salvucci, Michael E AU - Salvucci ME LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. PL - Netherlands TA - Protein Pept Lett JT - Protein and peptide letters JID - 9441434 RN - 0 (Plant Proteins) RN - EC 1.2.1.9 (Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)) RN - EC 2.7.1.- (Phosphotransferases (Alcohol Group Acceptor)) RN - EC 2.7.1.19 (phosphoribulokinase) SB - IM MH - Amino Acid Sequence MH - Chloroplasts/enzymology MH - Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)/metabolism MH - Molecular Sequence Data MH - Phosphotransferases (Alcohol Group Acceptor)/metabolism MH - *Photosynthesis MH - Plant Proteins/chemistry/*isolation & purification/*metabolism MH - Tobacco/*enzymology/metabolism EDAT- 2011/01/29 06:00 MHDA- 2011/09/20 06:00 CRDT- 2011/01/29 06:00 PHST- 2010/12/10 [received] PHST- 2011/01/24 [accepted] AID - BSP/ PPL/ E pub/0282 [pii] PST - ppublish SO - Protein Pept Lett. 2011 Jun;18(6):618-24. PMID- 16458085 OWN - NLM STAT- MEDLINE DA - 20060228 DCOM- 20060419 LR - 20131121 IS - 0006-3002 (Print) IS - 0006-3002 (Linking) VI - 1764 IP - 2 DP - 2006 Feb TI - Thermodynamic characterization of interactions between p27(Kip1) and activated and non-activated Cdk2: intrinsically unstructured proteins as thermodynamic tethers. PG - 182-9 AB - The cyclin-dependent kinase inhibitor (CKI) p27Kip1 plays a critical role in cell cycle regulation by binding and inhibiting (or activating) various cyclin-dependent kinase (Cdk)/cyclin complexes. Thermal denaturation monitored by circular dichroism (CD) and isothermal titration calorimetry (ITC) were used to determine the relative stabilities and affinities of p27-KID (p27 kinase inhibitory domain) complexes with activated Cdk2 (phosphorylated at Thr160; P-Cdk2) and non-activated forms of Cdk2 and/or cyclin A. Phosphorylation of residue Thr160 only slightly increases the thermal stability of Cdk2, and its binary complexes with cyclin A and p27-KID. The p27-KID/P-Cdk2/cyclin A or p27-KID/Cdk2/cyclin A ternary complexes exhibited significantly higher thermal stabilities compared to the binary complexes (P-Cdk2/cyclin A or Cdk2/cyclin A). Differences in T(m) values between the binary and ternary complexes with P-Cdk2 and Cdk2 were +25.9 and +20.4 degrees C, respectively. These results indicate that the ternary complex with phosphorylated Cdk2 is stabilized to a larger extent than the non-phosphorylated complex. The free energy of association (deltaG(A)) for formation of the two ternary complexes was more favorable than for the binary complexes, indicating that a significantly smaller population of free components existed when all three components were present. These data indicate that p27-KID, which is intrinsically disordered in solution, acts as a thermodynamic tether when bound within the ternary complexes. It is proposed that thermodynamic tethering may be a general phenomena associated with intrinsically unstructured proteins (IUPs) which often function by binding to multiple partners in multi-protein assemblies. FAU - Bowman, Prentice AU - Bowman P AD - Department of Structural Biology, St. Jude Children's Research Hospital, 332 North Lauderdale St., Memphis, TN 38105, USA. FAU - Galea, Charles A AU - Galea CA FAU - Lacy, Eilyn AU - Lacy E FAU - Kriwacki, Richard W AU - Kriwacki RW LA - eng GR - CA21765/CA/NCI NIH HHS/United States GR - CA82491/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20060111 PL - Netherlands TA - Biochim Biophys Acta JT - Biochimica et biophysica acta JID - 0217513 RN - 147604-94-2 (Cyclin-Dependent Kinase Inhibitor p27) RN - 2ZD004190S (Threonine) RN - EC 2.7.11.22 (Cyclin-Dependent Kinase 2) SB - IM MH - Cyclin-Dependent Kinase 2/*chemistry MH - Cyclin-Dependent Kinase Inhibitor p27/*chemistry MH - Enzyme Activation MH - Humans MH - Phosphorylation MH - Protein Conformation MH - Protein Denaturation MH - Temperature MH - *Thermodynamics MH - Threonine/chemistry EDAT- 2006/02/07 09:00 MHDA- 2006/04/20 09:00 CRDT- 2006/02/07 09:00 PHST- 2005/06/26 [received] PHST- 2005/12/10 [revised] PHST- 2005/12/13 [accepted] PHST- 2006/01/11 [aheadofprint] AID - S1570-9639(05)00448-6 [pii] AID - 10.1016/j.bbapap.2005.12.016 [doi] PST - ppublish SO - Biochim Biophys Acta. 2006 Feb;1764(2):182-9. Epub 2006 Jan 11. PMID- 16628001 OWN - NLM STAT- MEDLINE DA - 20060511 DCOM- 20060809 LR - 20061115 IS - 1551-4005 (Electronic) IS - 1551-4005 (Linking) VI - 5 IP - 8 DP - 2006 Apr TI - p8 and prothymosin alpha: unity is strength. PG - 829-30 AB - p8 and prothymosin alpha are two natively unstructured proteins with anti-apoptotic activity. We showed that their interaction results in the formation of a one-to-one heterodimer complex with stable structure. To test whether the heterodimer bears the function previously attributed to both proteins, we monitored the consequences on apoptosis of modulating in vitro the concentrations of both proteins. Overexpression was obtained by transfection of appropriate vectors and inhibition by using specific siRNAs. In all conditions inhibition of apoptosis correlated with the level of the partner with lowest concentration, demonstrating that the anti-apoptotic effect previously attributed to each proteins was in fact borne by the p8/ProTalpha complex, the two proteins, being individually inactive. These results show that the function attributed to a natively unfolded protein might actually belong to a multi-protein complex in which the protein of interest is engaged. FAU - Malicet, Cedric AU - Malicet C AD - INSERM U.624, Stress Cellulaire, Marseille, France. FAU - Dagorn, Jean Charles AU - Dagorn JC FAU - Neira, Jose Luis AU - Neira JL FAU - Iovanna, Juan L AU - Iovanna JL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20060417 PL - United States TA - Cell Cycle JT - Cell cycle (Georgetown, Tex.) JID - 101137841 RN - 0 (Basic Helix-Loop-Helix Transcription Factors) RN - 0 (Neoplasm Proteins) RN - 0 (P8 protein, human) RN - 0 (Protein Precursors) RN - 0 (RNA, Small Interfering) RN - 0 (prothymosin alpha) RN - 61512-21-8 (Thymosin) SB - IM MH - Apoptosis MH - Basic Helix-Loop-Helix Transcription Factors/*physiology MH - Circular Dichroism MH - Humans MH - Magnetic Resonance Spectroscopy MH - Neoplasm Proteins/*physiology MH - Protein Binding MH - Protein Denaturation MH - Protein Precursors/*physiology MH - RNA, Small Interfering/metabolism MH - Thymosin/*analogs & derivatives/physiology MH - Transfection EDAT- 2006/04/22 09:00 MHDA- 2006/08/10 09:00 CRDT- 2006/04/22 09:00 PHST- 2006/04/17 [aheadofprint] AID - 2686 [pii] PST - ppublish SO - Cell Cycle. 2006 Apr;5(8):829-30. Epub 2006 Apr 17. PMID- 23118886 OWN - NLM STAT- MEDLINE DA - 20121102 DCOM- 20130509 LR - 20141104 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 7 IP - 10 DP - 2012 TI - Sequence evolution of the intrinsically disordered and globular domains of a model viral oncoprotein. PG - e47661 LID - 10.1371/journal.pone.0047661 [doi] AB - In the present work, we have used the papillomavirus E7 oncoprotein to pursue structure-function and evolutionary studies that take into account intrinsic disorder and the conformational diversity of globular domains. The intrinsically disordered (E7N) and globular (E7C) domains of E7 show similar degrees of conservation and co-evolution. We found that E7N can be described in terms of conserved and coevolving linear motifs separated by variable linkers, while sequence evolution of E7C is compatible with the known homodimeric structure yet suggests other activities for the domain. Within E7N, inter-residue relationships such as residue co-evolution and restricted intermotif distances map functional coupling and co-occurrence of linear motifs that evolve in a coordinate manner. Within E7C, additional cysteine residues proximal to the zinc-binding site may allow redox regulation of E7 function. Moreover, we describe a conserved binding site for disordered domains on the surface of E7C and suggest a putative target linear motif. Both homodimerization and peptide binding activities of E7C are also present in the distantly related host PHD domains, showing that these two proteins share not only structural homology but also functional similarities, and strengthening the view that they evolved from a common ancestor. Finally, we integrate the multiple activities and conformations of E7 into a hierarchy of structure-function relationships. FAU - Chemes, Lucia B AU - Chemes LB AD - Protein Structure-Function and Engineering Laboratory, Fundacion Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina. FAU - Glavina, Juliana AU - Glavina J FAU - Alonso, Leonardo G AU - Alonso LG FAU - Marino-Buslje, Cristina AU - Marino-Buslje C FAU - de Prat-Gay, Gonzalo AU - de Prat-Gay G FAU - Sanchez, Ignacio E AU - Sanchez IE LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20121031 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (Papillomavirus E7 Proteins) RN - J41CSQ7QDS (Zinc) SB - IM MH - *Amino Acid Motifs MH - Amino Acid Sequence MH - Binding Sites MH - Dimerization MH - *Evolution, Molecular MH - Humans MH - *Papillomavirus E7 Proteins/chemistry/genetics MH - Protein Conformation MH - Protein Structure, Tertiary MH - Sequence Alignment MH - *Structure-Activity Relationship MH - Zinc/chemistry PMC - PMC3485249 OID - NLM: PMC3485249 EDAT- 2012/11/03 06:00 MHDA- 2013/05/10 06:00 CRDT- 2012/11/03 06:00 PHST- 2012/07/21 [received] PHST- 2012/09/14 [accepted] PHST- 2012/10/31 [epublish] AID - 10.1371/journal.pone.0047661 [doi] AID - PONE-D-12-21195 [pii] PST - ppublish SO - PLoS One. 2012;7(10):e47661. doi: 10.1371/journal.pone.0047661. Epub 2012 Oct 31. PMID- 22083130 OWN - NLM STAT- MEDLINE DA - 20120313 DCOM- 20120723 IS - 1572-8773 (Electronic) IS - 0966-0844 (Linking) VI - 25 IP - 2 DP - 2012 Apr TI - Cooperative folding of tau peptide by coordination of group IIB metal cations during heparin-induced aggregation. PG - 361-72 LID - 10.1007/s10534-011-9505-7 [doi] AB - The group IIB elements, especially Cd(II) and Hg(II), are increasingly considered as potential environmental neurotoxins. This study demonstrates that the Alzheimer's tau fragment R2, corresponding to the second repeat of the microtubule-binding domain, can bind to Zn(II), Cd(II) and Hg(II). Isothermal titration calorimetry experiments suggest that the most likely coordination site is the thiol group of Cys291, and this is further confirmed by a control experiment using a C291A mutant peptide. Circular dichroism spectrum reveals that the coordination of group IIB cations, especially Hg(II), can induce pronounced conformational conversions in natively unfolded R2, from random coil to other ordered structures. ThS fluorescence assays and electron microscopy indicate that the group IIB cations promote heparin-induced aggregation of R2, giving relatively small R2 filaments. The efficiency in promoting aggregation, as well as inducing conformational conversion, varies strongly with the cation's polarizability. Based on these results, a model is proposed in which the cooperative folding of R2 through cross-bridging of group IIB cations is suggested to be a key factor in promoting aggregation, in addition to the effective neutralization of coulombic charge-charge repulsion by heparin, the poly-anion inducer. Our results provide clues to understanding the potential pathogenic role of group IIB metals in the development of neurofibrillary tangles, a typical hallmark of Alzheimer's disease. FAU - Yang, Dan-Jing AU - Yang DJ AD - Department of Chemistry, Tongji University, Shanghai, China. FAU - Shi, Shuo AU - Shi S FAU - Yao, Tian-Ming AU - Yao TM FAU - Ji, Liang-Nian AU - Ji LN LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20111115 PL - Netherlands TA - Biometals JT - Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine JID - 9208478 RN - 0 (Metals) RN - 0 (tau Proteins) RN - 9005-49-6 (Heparin) SB - IM MH - Alzheimer Disease/etiology MH - Amino Acid Sequence MH - Circular Dichroism MH - Heparin/*chemistry MH - Metals/*chemistry MH - Microscopy, Electron MH - Molecular Sequence Data MH - Protein Conformation MH - *Protein Folding MH - Thermodynamics MH - tau Proteins/*chemistry EDAT- 2011/11/16 06:00 MHDA- 2012/07/24 06:00 CRDT- 2011/11/16 06:00 PHST- 2011/06/20 [received] PHST- 2011/11/01 [accepted] PHST- 2011/11/15 [aheadofprint] AID - 10.1007/s10534-011-9505-7 [doi] PST - ppublish SO - Biometals. 2012 Apr;25(2):361-72. doi: 10.1007/s10534-011-9505-7. Epub 2011 Nov 15. PMID- 21570984 OWN - NLM STAT- MEDLINE DA - 20110725 DCOM- 20110921 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 411 IP - 1 DP - 2011 Aug 5 TI - Time-resolved FRET detection of subtle temperature-induced conformational biases in ensembles of alpha-synuclein molecules. PG - 234-47 LID - 10.1016/j.jmb.2011.04.056 [doi] AB - The alpha-synuclein (alphaS) molecule, a polypeptide of 140 residues, is an intrinsically disordered protein that is involved in the onset of Parkinson's disease. We applied time-resolved excitation energy transfer measurements in search of specific deviations from the disordered state in segments of the alphaS backbone that might be involved in the initiation of aggregation. Since at higher temperatures, the alphaS molecule undergoes accelerated aggregation, we studied the temperature dependence of the distributions of intramolecular segmental end-to-end distances and their fast fluctuations in eight labeled chain segments of the alphaS molecule. Over the temperature range of 5-40 degrees C, no temperature-induced unfolding or folding was detected at the N-terminal domain (residues 1-66) of the alphaS molecule. The intramolecular diffusion coefficient of the segments' ends relative to each other increased monotonously with temperature. A common very high upper limiting value of approximately 25 A(2)/ns was reached at 40 degrees C, another indication of a fully disordered state. Three exceptions were two segments with reduced values of the diffusion coefficients (the shortest segment where the excluded volume effect is dominant and the segment labeled in the NAC domain) and a nonlinear cooperative transition in the N-terminal segment. These specific subtle deviations from the common pattern of temperature dependence reflect specific structural constraints that could be critical in controlling the stability of the soluble monomer, or for its aggregation. Such very weak effects might be dominant in determination of the fate of ensembles of disordered polypeptides either to folding or to misfolding. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Grupi, Asaf AU - Grupi A AD - The Goodman Faculty of Life Sciences, Bar-Ilan University, 52900 Ramat Gan, Israel. FAU - Haas, Elisha AU - Haas E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110506 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Multiprotein Complexes) RN - 0 (alpha-Synuclein) SB - IM MH - Fluorescence Resonance Energy Transfer/methods MH - Multiprotein Complexes/*chemistry MH - Protein Conformation MH - Temperature MH - Time Factors MH - alpha-Synuclein/*chemistry EDAT- 2011/05/17 06:00 MHDA- 2011/09/22 06:00 CRDT- 2011/05/17 06:00 PHST- 2011/02/10 [received] PHST- 2011/04/07 [revised] PHST- 2011/04/21 [accepted] PHST- 2011/05/06 [aheadofprint] AID - S0022-2836(11)00489-X [pii] AID - 10.1016/j.jmb.2011.04.056 [doi] PST - ppublish SO - J Mol Biol. 2011 Aug 5;411(1):234-47. doi: 10.1016/j.jmb.2011.04.056. Epub 2011 May 6. PMID- 15790533 OWN - NLM STAT- MEDLINE DA - 20050325 DCOM- 20050613 LR - 20131121 IS - 0169-328X (Print) IS - 0169-328X (Linking) VI - 134 IP - 1 DP - 2005 Mar 24 TI - Effects of nitration on the structure and aggregation of alpha-synuclein. PG - 84-102 AB - Substantial evidence suggests that the aggregation of the presynaptic protein alpha-synuclein is a key step in the etiology of Parkinson's disease (PD). Although the molecular mechanisms underlying alpha-synuclein aggregation remain unknown, oxidative stress has been implicated in the pathogenesis of PD. Here, we report the effects of tyrosine nitration on the propensity of human recombinant alpha-synuclein to fibrillate in vitro. The properties of nitrated alpha-synuclein were investigated using a variety of biophysical and biochemical techniques, which revealed that nitration led to formation of a partially folded conformation with increased secondary structure relative to the intrinsically disordered structure of the monomer, and to oligomerization at neutral pH. The degree of self-association was concentration-dependent, but at 1 mg/mL, nitrated alpha-synuclein was predominantly an octamer. At low pH, small-angle X-ray scattering data indicated that the nitrated protein was monomeric. alpha-Synuclein fibrillation at neutral pH was completely inhibited by nitrotyrosination and is attributed to the formation of stable soluble oligomers. The presence of heparin or metals did not overcome the inhibition; however, the inhibitory effect was eliminated at low pH. The addition of nitrated alpha-synuclein inhibited fibrillation of non-modified alpha-synuclein at neutral pH. Potential implications of these findings to the etiology of Parkinson's disease are discussed. FAU - Uversky, Vladimir N AU - Uversky VN AD - Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA. enzyme@ucsc.edu FAU - Yamin, Ghiam AU - Yamin G FAU - Munishkina, Larissa A AU - Munishkina LA FAU - Karymov, Mikhail A AU - Karymov MA FAU - Millett, Ian S AU - Millett IS FAU - Doniach, Sebastian AU - Doniach S FAU - Lyubchenko, Yuri L AU - Lyubchenko YL FAU - Fink, Anthony L AU - Fink AL LA - eng GR - NS39985/NS/NINDS NIH HHS/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, P.H.S. PL - Netherlands TA - Brain Res Mol Brain Res JT - Brain research. Molecular brain research JID - 8908640 RN - 0 (Nerve Tissue Proteins) RN - 0 (Oxidants) RN - 0 (Recombinant Proteins) RN - 0 (SNCA protein, human) RN - 0 (Synucleins) RN - 0 (alpha-Synuclein) RN - 42HK56048U (Tyrosine) RN - K1G7CKU98F (Tetranitromethane) SB - IM MH - Animals MH - Circular Dichroism/methods MH - Dose-Response Relationship, Drug MH - Humans MH - Microscopy, Atomic Force/methods MH - Microscopy, Electron, Scanning/methods MH - Models, Molecular MH - Nerve Tissue Proteins/chemistry/*metabolism/ultrastructure MH - Oxidants/*pharmacology MH - Recombinant Proteins/chemistry/drug effects/metabolism/ultrastructure MH - Spectrometry, X-Ray Emission/methods MH - Spectroscopy, Fourier Transform Infrared/methods MH - Spectrum Analysis/methods MH - Stress Fibers/drug effects/metabolism/ultrastructure MH - Synucleins MH - Tetranitromethane/*pharmacology MH - Time Factors MH - Tyrosine/metabolism MH - alpha-Synuclein EDAT- 2005/03/26 09:00 MHDA- 2005/06/14 09:00 CRDT- 2005/03/26 09:00 PHST- 2004/08/12 [received] PHST- 2004/11/17 [revised] PHST- 2004/11/17 [accepted] AID - S0169-328X(04)00599-6 [pii] AID - 10.1016/j.molbrainres.2004.11.014 [doi] PST - ppublish SO - Brain Res Mol Brain Res. 2005 Mar 24;134(1):84-102. PMID- 16000119 OWN - NLM STAT- MEDLINE DA - 20050707 DCOM- 20050902 LR - 20131121 IS - 1397-002X (Print) IS - 1397-002X (Linking) VI - 66 IP - 2 DP - 2005 Aug TI - Protein dynamics of bovine dentin phosphophoryn. PG - 59-67 AB - Bovine dentin phosphophoryn (BDP), a protein rich in aspartyl (Asp) and o-phosphoseryl [Ser(P)] residues, is synthesized by odontoblasts and believed to be involved in matrix-mediated biomineralization of dentin. The elucidation of the structure-function relationship of phosphophoryn has been a challenge because of its high-molecular weight, high negative charge, repetitive sequence, and lability. We have used the dynamic behavior of the (1)H NMR signal at 600 MHz to provide insight into the molecular dynamics of phosphophoryn. Our results indicate that phosphophoryn is a molecule of uniformly high mobility, thus belonging to a recently identified class of intrinsically disordered proteins that are characterized by sequences of low complexity and rich in polar and charged residues. The significance of our results is that phosphophoryn, because of its uniform nature has the potential to be replaced by biomimetic synthetic peptide analogs that together with amorphous calcium phosphate may lead to the development of novel, nontoxic, apatite-based dental restorative materials. FAU - Cross, K J AU - Cross KJ AD - Cooperative Research Centre for Oral Health Science, School of Dental Science, The University of Melbourne, Melbourne, Australia. FAU - Huq, N L AU - Huq NL FAU - Reynolds, E C AU - Reynolds EC LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - Denmark TA - J Pept Res JT - The journal of peptide research : official journal of the American Peptide Society JID - 9707067 RN - 0 (Phosphoproteins) RN - 0 (phosphophoryn) RN - SY7Q814VUP (Calcium) SB - IM MH - Amino Acid Motifs MH - Amino Acid Sequence MH - Animals MH - Calcium/metabolism MH - Cattle MH - Dentin/chemistry MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - Magnetic Resonance Spectroscopy MH - Molecular Sequence Data MH - Odontoblasts MH - Phosphoproteins/*chemistry/metabolism MH - Sequence Analysis, Protein MH - Structure-Activity Relationship EDAT- 2005/07/08 09:00 MHDA- 2005/09/03 09:00 CRDT- 2005/07/08 09:00 AID - JPP273 [pii] AID - 10.1111/j.1399-3011.2005.00273.x [doi] PST - ppublish SO - J Pept Res. 2005 Aug;66(2):59-67. PMID- 23714328 OWN - NLM STAT- MEDLINE DA - 20130708 DCOM- 20140224 LR - 20141113 IS - 1365-2958 (Electronic) IS - 0950-382X (Linking) VI - 89 IP - 2 DP - 2013 Jul TI - The C-terminal linker of Escherichia coli FtsZ functions as an intrinsically disordered peptide. PG - 264-75 LID - 10.1111/mmi.12279 [doi] AB - The tubulin homologue FtsZ provides the cytoskeletal framework and constriction force for bacterial cell division. FtsZ has an 50-amino-acid (aa) linker between the protofilament-forming globular domain and the C-terminal (Ct) peptide that binds FtsA and ZipA, tethering FtsZ to the membrane. This Ct-linker is widely divergent across bacterial species and thought to be an intrinsically disordered peptide (IDP). We confirmed that the Ct-linkers from three bacterial species behaved as IDPs in vitro by circular dichroism and trypsin proteolysis. We made chimeras, swapping the Escherichia coli linker for Ct-linkers from other bacteria, and even for an unrelated IDP from human alpha-adducin. Most substitutions allowed for normal cell division, suggesting that sequence of the IDP did not matter. With few exceptions, almost any sequence appears to work. Length, however, was important: IDPs shorter than 43 or longer than 95 aa had compromised or no function. We conclude that the Ct-linker functions as a flexible tether between the globular domain of FtsZ in the protofilament, and its attachment to FtsA/ZipA at the membrane. Modelling the Ct-linker as a worm-like chain, we predict that it functions as a stiff entropic spring linking the bending protofilaments to the membrane. CI - (c) 2013 John Wiley & Sons Ltd. FAU - Gardner, Kiani A J Arkus AU - Gardner KA AD - Department of Cell Biology, Duke University Medical Center, Box 3709, Durham, NC 27710, USA. FAU - Moore, Desmond A AU - Moore DA FAU - Erickson, Harold P AU - Erickson HP LA - eng GR - F31 GM090677/GM/NIGMS NIH HHS/United States GR - R01 GM066014/GM/NIGMS NIH HHS/United States GR - R01 GM66014/GM/NIGMS NIH HHS/United States GR - T32 GM008487/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20130617 PL - England TA - Mol Microbiol JT - Molecular microbiology JID - 8712028 RN - 0 (Bacterial Proteins) RN - 0 (Calmodulin-Binding Proteins) RN - 0 (Cytoskeletal Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (FtsZ protein, Bacteria) RN - 0 (Peptides) RN - 0 (adducin) SB - IM MH - Bacterial Proteins/*chemistry/genetics/*metabolism MH - Calmodulin-Binding Proteins/chemistry/genetics/metabolism MH - Cell Division MH - Cytoskeletal Proteins/*chemistry/genetics/*metabolism MH - Escherichia coli/cytology/genetics/*metabolism MH - Escherichia coli Proteins/chemistry/genetics/metabolism MH - Humans MH - Models, Molecular MH - Peptides/chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Conformation PMC - PMC3725778 MID - NIHMS489575 OID - NLM: NIHMS489575 OID - NLM: PMC3725778 EDAT- 2013/05/30 06:00 MHDA- 2014/02/25 06:00 CRDT- 2013/05/30 06:00 PHST- 2013/05/25 [accepted] PHST- 2013/06/17 [aheadofprint] AID - 10.1111/mmi.12279 [doi] PST - ppublish SO - Mol Microbiol. 2013 Jul;89(2):264-75. doi: 10.1111/mmi.12279. Epub 2013 Jun 17. PMID- 23708605 OWN - NLM STAT- MEDLINE DA - 20130704 DCOM- 20130910 LR - 20141113 IS - 1545-9985 (Electronic) IS - 1545-9985 (Linking) VI - 20 IP - 7 DP - 2013 Jul TI - Electron microscopy structure of human APC/C(CDH1)-EMI1 reveals multimodal mechanism of E3 ligase shutdown. PG - 827-35 LID - 10.1038/nsmb.2593 [doi] AB - The anaphase-promoting complex/cyclosome (APC/C) is a ~1.5-MDa multiprotein E3 ligase enzyme that regulates cell division by promoting timely ubiquitin-mediated proteolysis of key cell-cycle regulatory proteins. Inhibition of human APC/C(CDH1) during interphase by early mitotic inhibitor 1 (EMI1) is essential for accurate coordination of DNA synthesis and mitosis. Here, we report a hybrid structural approach involving NMR, electron microscopy and enzymology, which reveal that EMI1's 143-residue C-terminal domain inhibits multiple APC/C(CDH1) functions. The intrinsically disordered D-box, linker and tail elements, together with a structured zinc-binding domain, bind distinct regions of APC/C(CDH1) to synergistically both block the substrate-binding site and inhibit ubiquitin-chain elongation. The functional importance of intrinsic structural disorder is explained by enabling a small inhibitory domain to bind multiple sites to shut down various functions of a 'molecular machine' nearly 100 times its size. FAU - Frye, Jeremiah J AU - Frye JJ AD - 1Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. FAU - Brown, Nicholas G AU - Brown NG FAU - Petzold, Georg AU - Petzold G FAU - Watson, Edmond R AU - Watson ER FAU - Grace, Christy R R AU - Grace CR FAU - Nourse, Amanda AU - Nourse A FAU - Jarvis, Marc A AU - Jarvis MA FAU - Kriwacki, Richard W AU - Kriwacki RW FAU - Peters, Jan-Michael AU - Peters JM FAU - Stark, Holger AU - Stark H FAU - Schulman, Brenda A AU - Schulman BA LA - eng GR - 1R01GM08315/GM/NIGMS NIH HHS/United States GR - P30 CA021765/CA/NCI NIH HHS/United States GR - P30CA021765/CA/NCI NIH HHS/United States GR - R01 CA082491/CA/NCI NIH HHS/United States GR - R01 GM069530/GM/NIGMS NIH HHS/United States GR - R01 GM083159/GM/NIGMS NIH HHS/United States GR - R01CA082491/CA/NCI NIH HHS/United States GR - R01GM065930/GM/NIGMS NIH HHS/United States GR - Howard Hughes Medical Institute/United States GR - Howard Hughes Medical Institute/United States PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20130526 PL - United States TA - Nat Struct Mol Biol JT - Nature structural & molecular biology JID - 101186374 RN - 0 (CDH1 protein, human) RN - 0 (Cadherins) RN - 0 (Cell Cycle Proteins) RN - 0 (F-Box Proteins) RN - 0 (FBXO5 protein, human) RN - 0 (Ubiquitinated Proteins) RN - EC 6.3.2.19 (Anaphase-Promoting Complex-Cyclosome) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligase Complexes) RN - EC 6.3.2.19 (Ubiquitin-Protein Ligases) SB - IM CIN - Nat Struct Mol Biol. 2013 Jul;20(7):773-4. PMID: 23984442 MH - Amino Acid Sequence MH - Anaphase-Promoting Complex-Cyclosome MH - Cadherins/*chemistry MH - Cell Cycle Proteins/*chemistry/metabolism/pharmacology/ultrastructure MH - F-Box Proteins/*chemistry/metabolism/pharmacology/ultrastructure MH - Humans MH - Microscopy, Electron MH - Models, Molecular MH - Molecular Sequence Data MH - Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Processing, Post-Translational MH - Protein Structure, Tertiary MH - Sequence Alignment MH - Sequence Homology, Amino Acid MH - Structure-Activity Relationship MH - Substrate Specificity MH - Ubiquitin-Protein Ligase Complexes/antagonists & inhibitors/*chemistry/metabolism/ultrastructure MH - Ubiquitin-Protein Ligases/antagonists & inhibitors MH - Ubiquitinated Proteins/metabolism MH - Ubiquitination MH - Ultracentrifugation PMC - PMC3742808 MID - NIHMS466269 OID - NLM: NIHMS466269 OID - NLM: PMC3742808 EDAT- 2013/05/28 06:00 MHDA- 2013/09/11 06:00 CRDT- 2013/05/28 06:00 PHST- 2013/01/04 [received] PHST- 2013/04/09 [accepted] PHST- 2013/05/26 [aheadofprint] AID - nsmb.2593 [pii] AID - 10.1038/nsmb.2593 [doi] PST - ppublish SO - Nat Struct Mol Biol. 2013 Jul;20(7):827-35. doi: 10.1038/nsmb.2593. Epub 2013 May 26. PMID- 11545740 OWN - NLM STAT- MEDLINE DA - 20010907 DCOM- 20011018 LR - 20041117 IS - 1097-2765 (Print) IS - 1097-2765 (Linking) VI - 8 IP - 2 DP - 2001 Aug TI - Crystal structure of the human nuclear cap binding complex. PG - 383-96 AB - The heterodimeric nuclear cap binding complex (CBC) binds to 5'-capped polymerase II transcripts. It enhances the efficiency of several mRNA maturation steps and is essential for U snRNA nuclear export in multicellular eukaryotes. The 2A crystal structure of human CBC shows that the large subunit, CBP80, comprises three domains, each containing consecutive helical hairpins and resembling the so-called MIF4G domain found in several other proteins involved in RNA metabolism. The small subunit, CPB20, has an RNP fold and associates with the second and third domains of CBP80. Site-directed mutagenesis revealed 4 residues of CBP20 which are critical for cap binding. A model for cap binding is proposed based on these results and the known mode of binding of RNA to RNP domains. FAU - Mazza, C AU - Mazza C AD - European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, BP181, F-38042 9, Grenoble Cedex, France. FAU - Ohno, M AU - Ohno M FAU - Segref, A AU - Segref A FAU - Mattaj, I W AU - Mattaj IW FAU - Cusack, S AU - Cusack S LA - eng SI - PDB/1H6K PT - Journal Article PL - United States TA - Mol Cell JT - Molecular cell JID - 9802571 RN - 0 (Cross-Linking Reagents) RN - 0 (Protein Subunits) RN - 0 (RNA Cap-Binding Proteins) RN - 0 (RNA Caps) RN - 0 (RNA-Binding Proteins) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Cross-Linking Reagents/chemistry/metabolism MH - Crystallography, X-Ray MH - Humans MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Protein Binding MH - Protein Conformation MH - *Protein Structure, Quaternary MH - Protein Subunits MH - RNA Cap-Binding Proteins MH - RNA Caps/chemistry MH - RNA-Binding Proteins/*chemistry/genetics/metabolism MH - Sequence Alignment EDAT- 2001/09/08 10:00 MHDA- 2001/10/19 10:01 CRDT- 2001/09/08 10:00 AID - S1097-2765(01)00299-4 [pii] PST - ppublish SO - Mol Cell. 2001 Aug;8(2):383-96. PMID- 18761102 OWN - NLM STAT- MEDLINE DA - 20090116 DCOM- 20091207 LR - 20141120 IS - 1878-5875 (Electronic) IS - 1357-2725 (Linking) VI - 41 IP - 3 DP - 2009 Mar TI - A dihydropyridine receptor alpha1s loop region critical for skeletal muscle contraction is intrinsically unstructured and binds to a SPRY domain of the type 1 ryanodine receptor. PG - 677-86 LID - 10.1016/j.biocel.2008.08.004 [doi] AB - The II-III loop of the dihydropyridine receptor (DHPR) alpha(1s) subunit is a modulator of the ryanodine receptor (RyR1) Ca(2+) release channel in vitro and is essential for skeletal muscle contraction in vivo. Despite its importance, the structure of this loop has not been reported. We have investigated its structure using a suite of NMR techniques which revealed that the DHPR II-III loop is an intrinsically unstructured protein (IUP) and as such belongs to a burgeoning structural class of functionally important proteins. The loop does not possess a stable tertiary fold: it is highly flexible, with a strong N-terminal helix followed by nascent helical/turn elements and unstructured segments. Its residual structure is loosely globular with the N and C termini in close proximity. The unstructured nature of the II-III loop may allow it to easily modify its interaction with RyR1 following a surface action potential and thus initiate rapid Ca(2+) release and contraction. The in vitro binding partner for the II-III was investigated. The II-III loop interacts with the second of three structurally distinct SPRY domains in RyR1, whose function is unknown. This interaction occurs through two preformed N-terminal alpha-helical regions and a C-terminal hydrophobic element. The A peptide corresponding to the helical N-terminal region is a common probe of RyR function and binds to the same SPRY domain as the full II-III loop. Thus the second SPRY domain is an in vitro binding site for the II-III loop. The possible in vivo role of this region is discussed. FAU - Cui, Yanfang AU - Cui Y AD - Division of Molecular Bioscience, John Curtin School of Medical Research, Australian National University, PO Box 334, Canberra, ACT 2601, Australia. FAU - Tae, Han-Shen AU - Tae HS FAU - Norris, Nicole C AU - Norris NC FAU - Karunasekara, Yamuna AU - Karunasekara Y FAU - Pouliquin, Pierre AU - Pouliquin P FAU - Board, Philip G AU - Board PG FAU - Dulhunty, Angela F AU - Dulhunty AF FAU - Casarotto, Marco G AU - Casarotto MG LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20080808 PL - England TA - Int J Biochem Cell Biol JT - The international journal of biochemistry & cell biology JID - 9508482 RN - 0 (Calcium Channels, L-Type) RN - 0 (Membrane Proteins) RN - 0 (Mutant Chimeric Proteins) RN - 0 (Phosphoproteins) RN - 0 (Ryanodine Receptor Calcium Release Channel) RN - 0 (SPRY1 protein, human) SB - IM MH - Animals MH - Binding Sites MH - Calcium Channels, L-Type/chemistry/genetics/*metabolism MH - Crystallization MH - Humans MH - In Vitro Techniques MH - Magnetic Resonance Imaging MH - Membrane Proteins/chemistry/*metabolism MH - Muscle Contraction/physiology MH - Muscle, Skeletal/*physiology MH - Mutagenesis, Site-Directed MH - Mutant Chimeric Proteins/chemistry/genetics/*metabolism MH - Phosphoproteins/chemistry/*metabolism MH - Protein Binding MH - Protein Interaction Domains and Motifs/physiology MH - Protein Structure, Secondary MH - Ryanodine Receptor Calcium Release Channel/chemistry/*metabolism EDAT- 2008/09/02 09:00 MHDA- 2009/12/16 06:00 CRDT- 2008/09/02 09:00 PHST- 2008/05/20 [received] PHST- 2008/07/21 [revised] PHST- 2008/08/04 [accepted] PHST- 2008/08/08 [aheadofprint] AID - S1357-2725(08)00321-X [pii] AID - 10.1016/j.biocel.2008.08.004 [doi] PST - ppublish SO - Int J Biochem Cell Biol. 2009 Mar;41(3):677-86. doi: 10.1016/j.biocel.2008.08.004. Epub 2008 Aug 8. PMID- 23476017 OWN - NLM STAT- MEDLINE DA - 20130422 DCOM- 20130613 LR - 20150202 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 16 DP - 2013 Apr 19 TI - Biochemical and biophysical properties of a putative hub protein expressed by vaccinia virus. PG - 11470-81 LID - 10.1074/jbc.M112.442012 [doi] AB - H5 is a constitutively expressed, phosphorylated vaccinia virus protein that has been implicated in viral DNA replication, post-replicative gene expression, and virus assembly. For the purpose of understanding the role of H5 in vaccinia biology, we have characterized its biochemical and biophysical properties. Previously, we have demonstrated that H5 is associated with an endoribonucleolytic activity. In this study, we have shown that this cleavage results in a 3'-OH end suitable for polyadenylation of the nascent transcript, corroborating a role for H5 in vaccinia transcription termination. Furthermore, we have shown that H5 is intrinsically disordered, with an elongated rod-shaped structure that preferentially binds double-stranded nucleic acids in a sequence nonspecific manner. The dynamic phosphorylation status of H5 influences this structure and has implications for the role of H5 in multiple processes during virus replication. FAU - Kay, Nicole E AU - Kay NE AD - Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610-0266, USA. FAU - Bainbridge, Travis W AU - Bainbridge TW FAU - Condit, Richard C AU - Condit RC FAU - Bubb, Michael R AU - Bubb MR FAU - Judd, Reuben E AU - Judd RE FAU - Venkatakrishnan, Balasubramanian AU - Venkatakrishnan B FAU - McKenna, Robert AU - McKenna R FAU - D'Costa, Susan M AU - D'Costa SM LA - eng GR - R01 18094/PHS HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20130308 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA, Viral) RN - 0 (Viral Proteins) RN - EC 3.1.- (Endoribonucleases) SB - IM MH - DNA Replication/physiology MH - DNA, Viral/biosynthesis/genetics MH - Endoribonucleases/genetics/*metabolism MH - HeLa Cells MH - Humans MH - Phosphorylation/physiology MH - Protein Structure, Tertiary MH - Transcription Termination, Genetic/*physiology MH - Vaccinia/genetics/metabolism MH - Vaccinia virus/*physiology MH - Viral Proteins/genetics/*metabolism MH - Virus Replication/*physiology PMC - PMC3630899 OID - NLM: PMC3630899 EDAT- 2013/03/12 06:00 MHDA- 2013/06/14 06:00 CRDT- 2013/03/12 06:00 PHST- 2013/03/08 [aheadofprint] AID - M112.442012 [pii] AID - 10.1074/jbc.M112.442012 [doi] PST - ppublish SO - J Biol Chem. 2013 Apr 19;288(16):11470-81. doi: 10.1074/jbc.M112.442012. Epub 2013 Mar 8. PMID- 19430464 OWN - NLM STAT- MEDLINE DA - 20090612 DCOM- 20090805 LR - 20140922 IS - 1476-4687 (Electronic) IS - 0028-0836 (Linking) VI - 459 IP - 7248 DP - 2009 Jun 11 TI - Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger. PG - 847-51 LID - 10.1038/nature08036 [doi] AB - Histone H3 lysine 4 methylation (H3K4me) has been proposed as a critical component in regulating gene expression, epigenetic states, and cellular identities1. The biological meaning of H3K4me is interpreted by conserved modules including plant homeodomain (PHD) fingers that recognize varied H3K4me states. The dysregulation of PHD fingers has been implicated in several human diseases, including cancers and immune or neurological disorders. Here we report that fusing an H3K4-trimethylation (H3K4me3)-binding PHD finger, such as the carboxy-terminal PHD finger of PHF23 or JARID1A (also known as KDM5A or RBBP2), to a common fusion partner nucleoporin-98 (NUP98) as identified in human leukaemias, generated potent oncoproteins that arrested haematopoietic differentiation and induced acute myeloid leukaemia in murine models. In these processes, a PHD finger that specifically recognizes H3K4me3/2 marks was essential for leukaemogenesis. Mutations in PHD fingers that abrogated H3K4me3 binding also abolished leukaemic transformation. NUP98-PHD fusion prevented the differentiation-associated removal of H3K4me3 at many loci encoding lineage-specific transcription factors (Hox(s), Gata3, Meis1, Eya1 and Pbx1), and enforced their active gene transcription in murine haematopoietic stem/progenitor cells. Mechanistically, NUP98-PHD fusions act as 'chromatin boundary factors', dominating over polycomb-mediated gene silencing to 'lock' developmentally critical loci into an active chromatin state (H3K4me3 with induced histone acetylation), a state that defined leukaemia stem cells. Collectively, our studies represent, to our knowledge, the first report that deregulation of the PHD finger, an 'effector' of specific histone modification, perturbs the epigenetic dynamics on developmentally critical loci, catastrophizes cellular fate decision-making, and even causes oncogenesis during mammalian development. FAU - Wang, Gang G AU - Wang GG AD - Laboratory of Chromatin Biology & Epigenetics, The Rockefeller University, New York, New York 10065, USA. FAU - Song, Jikui AU - Song J FAU - Wang, Zhanxin AU - Wang Z FAU - Dormann, Holger L AU - Dormann HL FAU - Casadio, Fabio AU - Casadio F FAU - Li, Haitao AU - Li H FAU - Luo, Jun-Li AU - Luo JL FAU - Patel, Dinshaw J AU - Patel DJ FAU - Allis, C David AU - Allis CD LA - eng SI - PDB/2KGG SI - PDB/2KGI SI - PDB/3GL6 GR - K99 CA151683/CA/NCI NIH HHS/United States GR - R37 GM053512/GM/NIGMS NIH HHS/United States GR - R37 GM053512-30/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - England TA - Nature JT - Nature JID - 0410462 RN - 0 (Chromatin) RN - 0 (Histones) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Nuclear Pore Complex Proteins) RN - 0 (Oncogene Proteins, Fusion) RN - 0 (Tumor Suppressor Proteins) RN - 0 (nuclear pore complex protein 98) RN - EC 1.14.11.- (KDM5A protein, human) RN - EC 1.14.11.- (Retinoblastoma-Binding Protein 2) RN - K3Z4F929H6 (Lysine) SB - IM MH - Amino Acid Motifs/genetics/physiology MH - Animals MH - Cell Transformation, Neoplastic MH - Cells, Cultured MH - Chromatin/*metabolism MH - Epigenesis, Genetic MH - Gene Expression Regulation, Developmental MH - Genes, Homeobox/genetics MH - Hematologic Neoplasms/genetics/*metabolism/*pathology MH - Hematopoiesis/genetics MH - Hematopoietic Stem Cells/metabolism/pathology MH - Histones/chemistry/metabolism MH - Humans MH - Intracellular Signaling Peptides and Proteins/*chemistry/genetics/*metabolism MH - Lysine/metabolism MH - Magnetic Resonance Spectroscopy MH - Methylation MH - Mice MH - Models, Molecular MH - Nuclear Pore Complex Proteins/chemistry/genetics/metabolism MH - Oncogene Proteins, Fusion/*chemistry/genetics/*metabolism MH - Protein Binding MH - Protein Conformation MH - Retinoblastoma-Binding Protein 2 MH - Transcription, Genetic MH - Tumor Suppressor Proteins/*chemistry/genetics/*metabolism PMC - PMC2697266 MID - NIHMS107550 OID - NLM: NIHMS107550 OID - NLM: PMC2697266 EDAT- 2009/05/12 09:00 MHDA- 2009/08/06 09:00 CRDT- 2009/05/12 09:00 PHST- 2008/11/30 [received] PHST- 2009/06/11 [revised] PHST- 2009/04/02 [accepted] PHST- 2009/05/10 [aheadofprint] AID - nature08036 [pii] AID - 10.1038/nature08036 [doi] PST - ppublish SO - Nature. 2009 Jun 11;459(7248):847-51. doi: 10.1038/nature08036. PMID- 16734427 OWN - NLM STAT- MEDLINE DA - 20060531 DCOM- 20060804 LR - 20131121 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 45 IP - 22 DP - 2006 Jun 6 TI - Hsc70 contacts helix III of the J domain from polyomavirus T antigens: addressing a dilemma in the chaperone hypothesis of how they release E2F from pRb. PG - 6917-29 AB - Hsc70's expected binding site on helix II of the J domain of T antigens appears to be blocked in its structure bound to tumor suppressor pRb. We used NMR to map where mammalian Hsc70 binds the J domain of murine polyomavirus T antigens (PyJ). The ATPase domain of Hsc70 unexpectedly has its biggest effects on the NMR peak positions of the C-terminal end of helix III of PyJ. The Hsc70 ATPase domain protects the C-terminal end of helix III of PyJ from an uncharged paramagnetic probe of chelated Gd(III), clearly suggesting the interface. Effects on the conserved HPD loop and helix II of PyJ are smaller. The NMR results are supported by a novel assay of Hsc70's ATP hydrolysis showing that mutations of surface residues in PyJ helix III impair PyJ-dependent stimulation of Hsc70 activity. Evolutionary trace analysis of J domains suggests that helix III usually may join helix II in contributing specificities for cognate hsp70s. Our novel evidence implicating helix III differs from evidence that Escherichia coli DnaK primarily affects helix II and the HPD loop of DnaJ. We find the pRb-binding fragment of E2F1 to be intrinsically unfolded and a good substrate for Hsc70 in vitro. This suggests that E2F1 could be a substrate for Hsc70 recruited by T antigen to an Rb family member. Importantly, our results strengthen the chaperone hypothesis for E2F release from an Rb family member by Hsc70 recruited by large T antigen. That is, it now appears that Hsc70 can freely access helix III and the HPD motif of large T antigen bound to an Rb family member. FAU - Garimella, Ravindranath AU - Garimella R AD - Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri 65211, USA. FAU - Liu, Xin AU - Liu X FAU - Qiao, Wei AU - Qiao W FAU - Liang, Xiangyang AU - Liang X FAU - Zuiderweg, Erik R P AU - Zuiderweg ER FAU - Riley, Michael I AU - Riley MI FAU - Van Doren, Steven R AU - Van Doren SR LA - eng GR - R01GM5728/GM/NIGMS NIH HHS/United States GR - R01GM63027/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Antigens, Viral, Tumor) RN - 0 (E2F1 Transcription Factor) RN - 0 (E2F1 protein, human) RN - 0 (HSC70 Heat-Shock Proteins) RN - 0 (Molecular Chaperones) RN - 0 (Retinoblastoma Protein) RN - 2ZD004190S (Threonine) RN - EC 3.6.1.- (Adenosine Triphosphatases) RN - K3Z4F929H6 (Lysine) SB - IM MH - Adenosine Triphosphatases/chemistry MH - Amino Acid Sequence MH - Animals MH - Antigens, Viral, Tumor/*chemistry/genetics MH - E2F1 Transcription Factor/*chemistry/metabolism MH - Evolution, Molecular MH - HSC70 Heat-Shock Proteins/*chemistry MH - Humans MH - Lysine/chemistry/genetics MH - Magnetic Resonance Spectroscopy MH - Mice MH - Molecular Chaperones/chemistry/metabolism MH - Polyomavirus/*immunology MH - Protein Conformation MH - Protein Folding MH - Protein Interaction Mapping MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Retinoblastoma Protein/*chemistry/metabolism MH - Threonine/chemistry/genetics EDAT- 2006/06/01 09:00 MHDA- 2006/08/05 09:00 CRDT- 2006/06/01 09:00 AID - 10.1021/bi060411d [doi] PST - ppublish SO - Biochemistry. 2006 Jun 6;45(22):6917-29. PMID- 11283003 OWN - NLM STAT- MEDLINE DA - 20010604 DCOM- 20010712 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 276 IP - 23 DP - 2001 Jun 8 TI - Residues within the N-terminal domain of human topoisomerase I play a direct role in relaxation. PG - 20220-7 AB - All eukaryotic forms of DNA topoisomerase I contain an extensive and highly charged N-terminal domain. This domain contains several nuclear localization sequences and is essential for in vivo function of the enzyme. However, so far no direct function of the N-terminal domain in the in vitro topoisomerase I reaction has been reported. In this study we have compared the in vitro activities of a truncated form of human topoisomerase I lacking amino acids 1-206 (p67) with the full-length enzyme (p91). Using these enzyme forms, we have identified for the first time a direct role of residues within the N-terminal domain in modulating topoisomerase I catalysis, as revealed by significant differences between p67 and p91 in DNA binding, cleavage, strand rotation, and ligation. A comparison with previously published studies showing no effect of deleting the first 174 or 190 amino acids of topoisomerase I (Stewart, L., Ireton, G. C., and Champoux, J. J. (1999) J. Biol. Chem. 274, 32950-32960; Bronstein, I. B., Wynne-Jones, A., Sukhanova, A., Fleury, F., Ianoul, A., Holden, J. A., Alix, A. J., Dodson, G. G., Jardillier, J. C., Nabiev, I., and Wilkinson, A. J. (1999) Anticancer Res. 19, 317-327) suggests a pivotal role of amino acids 191-206 in catalysis. Taken together the presented data indicate that at least part(s) of the N-terminal domain regulate(s) enzyme/DNA dynamics during relaxation most probably by controlling non-covalent DNA binding downstream of the cleavage site either directly or by coordinating DNA contacts by other parts of the enzyme. FAU - Lisby, M AU - Lisby M AD - Department of Molecular and Structural Biology, University of Aarhus, C.F. Mollers Alle, Building 130, DK-8000, Aarhus C, Denmark. FAU - Olesen, J R AU - Olesen JR FAU - Skouboe, C AU - Skouboe C FAU - Krogh, B O AU - Krogh BO FAU - Straub, T AU - Straub T FAU - Boege, F AU - Boege F FAU - Velmurugan, S AU - Velmurugan S FAU - Martensen, P M AU - Martensen PM FAU - Andersen, A H AU - Andersen AH FAU - Jayaram, M AU - Jayaram M FAU - Westergaard, O AU - Westergaard O FAU - Knudsen, B R AU - Knudsen BR LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. DEP - 20010329 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - EC 5.99.1.2 (DNA Topoisomerases, Type I) SB - IM MH - Catalysis MH - DNA Topoisomerases, Type I/chemistry/isolation & purification/*metabolism MH - Electrophoresis, Polyacrylamide Gel MH - Humans MH - Protein Conformation EDAT- 2001/04/03 10:00 MHDA- 2001/07/13 10:01 CRDT- 2001/04/03 10:00 PHST- 2001/03/29 [aheadofprint] AID - 10.1074/jbc.M010991200 [doi] AID - M010991200 [pii] PST - ppublish SO - J Biol Chem. 2001 Jun 8;276(23):20220-7. Epub 2001 Mar 29. PMID- 16046624 OWN - NLM STAT- MEDLINE DA - 20050727 DCOM- 20051027 LR - 20140606 IS - 0961-8368 (Print) IS - 0961-8368 (Linking) VI - 14 IP - 8 DP - 2005 Aug TI - The intrinsically disordered C-terminal domain of the measles virus nucleoprotein interacts with the C-terminal domain of the phosphoprotein via two distinct sites and remains predominantly unfolded. PG - 1975-92 AB - Measles virus is a negative-sense, single-stranded RNA virus within the Mononegavirales order,which includes several human pathogens, including rabies, Ebola, Nipah, and Hendra viruses. The measles virus nucleoprotein consists of a structured N-terminal domain, and of an intrinsically disordered C-terminal domain, N(TAIL) (aa 401-525), which undergoes induced folding in the presence of the C-terminal domain (XD, aa 459-507) of the viral phosphoprotein. With in N(TAIL), an alpha-helical molecular recognition element (alpha-MoRE, aa 488-499) involved in binding to P and in induced folding was identified and then observed in the crystal structure of XD. Using small-angle X-ray scattering, we have derived a low-resolution structural model of the complex between XD and N(TAIL), which shows that most of N(TAIL) remains disordered in the complex despite P-induced folding within the alpha-MoRE. The model consists of an extended shape accommodating the multiple conformations adopted by the disordered N-terminal region of N(TAIL), and of a bulky globular region, corresponding to XD and to the C terminus of N(TAIL) (aa 486-525). Using surface plasmon resonance, circular dichroism, fluorescence spectroscopy, and heteronuclear magnetic resonance, we show that N(TAIL) has an additional site (aa 517-525) involved in binding to XD but not in the unstructured-to-structured transition. This work provides evidence that intrinsically disordered domains can establish complex interactions with their partners, and can contact them through multiple sites that do not all necessarily gain regular secondary structure. FAU - Bourhis, Jean-Marie AU - Bourhis JM AD - Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 6098 CNRS at Universites Aix-Marseille I et II, ESIL, Campus de Luminy, 13288 Marseille Cedex 09, France. FAU - Receveur-Brechot, Veronique AU - Receveur-Brechot V FAU - Oglesbee, Michael AU - Oglesbee M FAU - Zhang, Xinsheng AU - Zhang X FAU - Buccellato, Matthew AU - Buccellato M FAU - Darbon, Herve AU - Darbon H FAU - Canard, Bruno AU - Canard B FAU - Finet, Stephanie AU - Finet S FAU - Longhi, Sonia AU - Longhi S LA - eng GR - R01 NS31693/NS/NINDS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Nucleoproteins) RN - 0 (P protein, Sendai virus) RN - 0 (Phosphoproteins) RN - 0 (Viral Proteins) RN - 0 (nucleoprotein, Measles virus) SB - IM MH - Binding Sites MH - Cloning, Molecular MH - Models, Molecular MH - Nuclear Magnetic Resonance, Biomolecular MH - Nucleoproteins/*chemistry/genetics/metabolism MH - Phosphoproteins/*chemistry/metabolism MH - Protein Folding MH - Protein Structure, Tertiary MH - Scattering, Radiation MH - Sequence Deletion MH - Spectrometry, Fluorescence MH - Surface Plasmon Resonance MH - Viral Proteins/*chemistry/genetics/metabolism MH - X-Rays PMC - PMC2279309 OID - NLM: PMC2279309 EDAT- 2005/07/28 09:00 MHDA- 2005/10/28 09:00 CRDT- 2005/07/28 09:00 AID - 14/8/1975 [pii] AID - 10.1110/ps.051411805 [doi] PST - ppublish SO - Protein Sci. 2005 Aug;14(8):1975-92. PMID- 25018569 OWN - NLM STAT- Publisher DA - 20140714 IS - 0096-3003 (Print) IS - 0096-3003 (Linking) VI - 224 DP - 2013 Nov 1 TI - Stability analysis of 4-species A aggregation model: A novel approach to obtaining physically meaningful rate constants. PG - 205-215 AB - Protein misfolding and concomitant aggregation towards amyloid formation is the underlying biochemical commonality among a wide range of human pathologies. Amyloid formation involves the conversion of proteins from their native monomeric states (intrinsically disordered or globular) to well-organized, fibrillar aggregates in a nucleation-dependent manner. Understanding the mechanism of aggregation is important not only to gain better insight into amyloid pathology but also to simulate and predict molecular pathways. One of the main impediments in doing so is the stochastic nature of interactions that impedes thorough experimental characterization and the development of meaningful insights. In this study, we have utilized a well-known intermediate state along the amyloid-beta peptide aggregation pathway called protofibrils as a model system to investigate the molecular mechanisms by which they form fibrils using stability and perturbation analysis. Investigation of protofibril aggregation mechanism limits both the number of species to be modeled (monomers, and protofibrils), as well as the reactions to two (elongation by monomer addition, and protofibril-protofibril lateral association). Our new model is a reduced order four species model grounded in mass action kinetics. Our prior study required 3200 reactions, which makes determining the reaction parameters prohibitively difficult. Using this model, along with a linear perturbation argument, we rigorously determine stable ranges of rate constants for the reactions and ensure they are physically meaningful. This was accomplished by finding the ranges in which the perturbations dieout in a five-parameter sweep, which includes the monomer and protofibril equilibrium concentrations and three of the rate constants. The results presented are a proof-of-concept method in determining meaningful rate constants that can be used as a bonafide way for determining accurate rate constants for other models involving complex biological reactions such as amyloid aggregation. FAU - Ghag, G AU - Ghag G AD - Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Dr, # 5043, Hattiesburg, MS 39406, United States. FAU - Ghosh, P AU - Ghosh P AD - Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23220, United States. FAU - Mauro, A AU - Mauro A AD - Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ 07043, United States. FAU - Rangachari, V AU - Rangachari V AD - Department of Chemistry and Biochemistry, University of Southern Mississippi, 118 College Dr, # 5043, Hattiesburg, MS 39406, United States. FAU - Vaidya, A AU - Vaidya A AD - Department of Mathematical Science, Montclair State University, Montclair, NJ 07043, United States. LA - ENG GR - P20 GM103476/GM/NIGMS NIH HHS/United States PT - JOURNAL ARTICLE TA - Appl Math Comput JT - Applied mathematics and computation JID - 7509323 PMC - PMC4092007 MID - NIHMS596111 OTO - NOTNLM OT - Abeta OT - Mathematical model OT - Protein aggregation OT - Rate constants OT - Stability EDAT- 2014/07/16 06:00 MHDA- 2014/07/16 06:00 CRDT- 2014/07/15 06:00 PST - ppublish SO - Appl Math Comput. 2013 Nov 1;224:205-215. PMID- 9642072 OWN - NLM STAT- MEDLINE DA - 19980721 DCOM- 19980721 LR - 20081023 IS - 0022-2836 (Print) IS - 0022-2836 (Linking) VI - 279 IP - 4 DP - 1998 Jun 19 TI - A disorder-to-order transition coupled to DNA binding in the essential zinc-finger DNA-binding domain of yeast ADR1. PG - 929-43 AB - The motional dynamics and solvent-exchange behavior of free and DNA-bound forms of the minimal zinc-finger DNA-binding domain of the yeast transcription factor ADR1 (ADR1-DBD) are investigated using NMR. The parameters measured include the 1H-15N heteronuclear NOE, 15N and 1H T1 relaxation rates, 15N T2 relaxation rates, and solvent-exchange rates. The spin relaxation parameters, spectral density maps, and solvent-exchange behavior show that, exclusive of the N and C termini, three distinct regions of free ADR1-DBD exhibit different motions on multiple timescales. The N-terminal proximal, or accessory, region appears to be unstructured and highly flexible: it exhibits large amplitude motions on a picosecond timescale, little or no protection from solvent exchange, and random-coil proton chemical shifts. The two zinc fingers tumble anisotropically as folded domains, with the tumbling of the individual fingers being only partly correlated to each other, and are modestly protected from solvent exchange except near the tips of the fingers and in the linker joining them. Free ADR1-DBD exhibits exchange broadening around P97 in the proximal region, at the tip of finger 1, and throughout finger 2. Upon binding, most of the proximal region and both zinc fingers tumble as a single domain and exhibit significantly reduced picosecond timescale motions. This region becomes more protected from solvent exchange. The bound portion of the proximal region is proposed to lie exposed on the surface of the DNA. Exchange broadening remains around P97 but also becomes evident for residues in direct contact with the DNA and in the linker. We conclude that the region of ADR1-DBD essential for high-affinity binding undergoes a disorder-to-order transition upon binding to its cognate DNA and, together with the zinc fingers, forms a cohesive molecular complex with the nucleic acid. CI - Copyright 1998 Academic Press Limited. FAU - Hyre, D E AU - Hyre DE AD - Department of Biochemistry and Biomolecular Structure Center, University of Washington, Seattle, WA, 98195-7742, USA. FAU - Klevit, R E AU - Klevit RE LA - eng GR - R01-GM55369/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, P.H.S. PL - ENGLAND TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (ADR1 protein, S cerevisiae) RN - 0 (DNA-Binding Proteins) RN - 0 (Fungal Proteins) RN - 0 (Saccharomyces cerevisiae Proteins) RN - 0 (Transcription Factors) RN - 9007-49-2 (DNA) SB - IM MH - Binding Sites MH - DNA/metabolism MH - DNA-Binding Proteins/*chemistry/metabolism MH - Fungal Proteins/chemistry/metabolism MH - Magnetic Resonance Spectroscopy MH - Saccharomyces cerevisiae/*chemistry/metabolism MH - *Saccharomyces cerevisiae Proteins MH - Transcription Factors/*chemistry/metabolism MH - Zinc Fingers EDAT- 1998/06/27 MHDA- 1998/06/27 00:01 CRDT- 1998/06/27 00:00 AID - S0022-2836(98)91811-3 [pii] AID - 10.1006/jmbi.1998.1811 [doi] PST - ppublish SO - J Mol Biol. 1998 Jun 19;279(4):929-43. PMID- 19804783 OWN - NLM STAT- MEDLINE DA - 20091125 DCOM- 20091221 LR - 20141223 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 394 IP - 5 DP - 2009 Dec 18 TI - The structure of the N-terminus of kindlin-1: a domain important for alphaiibbeta3 integrin activation. PG - 944-56 LID - 10.1016/j.jmb.2009.09.061 [doi] AB - The integrin family of heterodimeric cell adhesion molecules exists in both low- and high-affinity states, and integrin activation requires binding of the talin FERM (four-point-one, ezrin, radixin, moesin) domain to membrane-proximal sequences in the beta-integrin cytoplasmic domain. However, it has recently become apparent that the kindlin family of FERM domain proteins is also essential for talin-induced integrin activation. FERM domains are typically composed of F1, F2, and F3 domains, but the talin FERM domain is atypical in that it contains a large insert in F1 and is preceded by a previously unrecognized domain, F0. Initial sequence alignments showed that the kindlin FERM domain was most similar to the talin FERM domain, but the homology appeared to be restricted to the F2 and F3 domains. Based on a detailed characterization of the talin FERM domain, we have reinvestigated the sequence relationship with kindlins and now show that kindlins do indeed contain the same domain structure as the talin FERM domain. However, the kindlin F1 domain contains an even larger insert than that in talin F1 that disrupts the sequence alignment. The insert, which varies in length between different kindlins, is not conserved and, as in talin, is largely unstructured. We have determined the structure of the kindlin-1 F0 domain by NMR, which shows that it adopts the same ubiquitin-like fold as the talin F0 and F1 domains. Comparison of the kindlin-1 and talin F0 domains identifies the probable interface with the kindlin-1 F1 domain. Potential sites of interaction of kindlin F0 with other proteins are discussed, including sites that differ between kindlin-1, kindlin-2, and kindlin-3. We also demonstrate that F0 is required for the ability of kindlin-1 to support talin-induced alphaIIbbeta3 integrin activation and for the localization of kindlin-1 to focal adhesions. FAU - Goult, Benjamin T AU - Goult BT AD - Department of Biochemistry, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK. FAU - Bouaouina, Mohamed AU - Bouaouina M FAU - Harburger, David S AU - Harburger DS FAU - Bate, Neil AU - Bate N FAU - Patel, Bipin AU - Patel B FAU - Anthis, Nicholas J AU - Anthis NJ FAU - Campbell, Iain D AU - Campbell ID FAU - Calderwood, David A AU - Calderwood DA FAU - Barsukov, Igor L AU - Barsukov IL FAU - Roberts, Gordon C AU - Roberts GC FAU - Critchley, David R AU - Critchley DR LA - eng SI - PDB/2KMC GR - BB/G003637/1/Biotechnology and Biological Sciences Research Council/United Kingdom GR - R01 GM068600/GM/NIGMS NIH HHS/United States GR - R21 HL089433/HL/NHLBI NIH HHS/United States GR - U54 GM64346/GM/NIGMS NIH HHS/United States GR - Cancer Research UK/United Kingdom GR - Wellcome Trust/United Kingdom PT - Comparative Study PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20091003 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (FERMT1 protein, human) RN - 0 (Membrane Proteins) RN - 0 (Neoplasm Proteins) RN - 0 (Platelet Glycoprotein GPIIb-IIIa Complex) RN - 0 (Talin) SB - IM MH - Amino Acid Sequence MH - Membrane Proteins/*chemistry/*genetics/metabolism MH - Models, Molecular MH - Molecular Sequence Data MH - Mutagenesis, Insertional MH - Neoplasm Proteins/*chemistry/*genetics/metabolism MH - Nuclear Magnetic Resonance, Biomolecular MH - Platelet Glycoprotein GPIIb-IIIa Complex/*metabolism MH - Protein Interaction Domains and Motifs MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Talin/chemistry/genetics/metabolism PMC - PMC2963925 OID - NLM: PMC2963925 EDAT- 2009/10/07 06:00 MHDA- 2009/12/22 06:00 CRDT- 2009/10/07 06:00 PHST- 2009/07/27 [received] PHST- 2009/09/25 [revised] PHST- 2009/09/27 [accepted] PHST- 2009/10/03 [aheadofprint] AID - S0022-2836(09)01211-X [pii] AID - 10.1016/j.jmb.2009.09.061 [doi] PST - ppublish SO - J Mol Biol. 2009 Dec 18;394(5):944-56. doi: 10.1016/j.jmb.2009.09.061. Epub 2009 Oct 3. PMID- 19113838 OWN - NLM STAT- MEDLINE DA - 20090114 DCOM- 20090212 IS - 1520-4995 (Electronic) IS - 0006-2960 (Linking) VI - 48 IP - 2 DP - 2009 Jan 20 TI - Intrinsically unstructured phosphoprotein TSP9 regulates light harvesting in Arabidopsis thaliana. PG - 499-509 LID - 10.1021/bi8016334 [doi] AB - Thylakoid-soluble phosphoprotein of 9 kDa, TSP9, is an intrinsically unstructured plant-specific protein [Song, J., et al. (2006) Biochemistry 45, 15633-15643] with unknown function but established associations with light-harvesting proteins and peripheries of both photosystems [Hansson, M., et al. (2007) J. Biol. Chem. 282, 16214-16222]. To investigate the function of this protein, we used a combination of reverse genetics and biochemical and fluorescence measurement methods in Arabidopsis thaliana. Differential gene expression analysis of plants with a T-DNA insertion in the TSP9 gene using an array of 24000 Arabidopsis genes revealed disappearance of high light-dependent induction of a specific set of mostly signaling and unknown proteins. TSP9-deficient plants had reduced levels of in vivo phosphorylation of light-harvesting complex II polypeptides. Recombinant TSP9 was phosphorylated in light by thylakoid membranes isolated from the wild-type and mutant plants lacking STN8 protein kinase but not by the thylakoids deficient in STN7 kinase, essential for photosynthetic state transitions. TSP9-lacking mutant and RNAi plants with downregulation of TSP9 showed reduced ability to perform state transitions. The nonphotochemical quenching of chlorophyll fluorescence at high light intensities was also less efficient in the mutant compared to wild-type plants. Blue native electrophoresis of thylakoid membrane protein complexes revealed that TSP9 deficiency increased relative stability of photosystem II dimers and supercomplexes. It is concluded that TSP9 regulates plant light harvesting acting as a membrane-binding protein facilitating dissociation of light-harvesting proteins from photosystem II. FAU - Fristedt, Rikard AU - Fristedt R AD - Department of Clinical and Experimental Medicine, Linkoping University, SE-581 85 Linkoping, Sweden. FAU - Carlberg, Inger AU - Carlberg I FAU - Zygadlo, Agnieszka AU - Zygadlo A FAU - Piippo, Mirva AU - Piippo M FAU - Nurmi, Markus AU - Nurmi M FAU - Aro, Eva-Mari AU - Aro EM FAU - Scheller, Henrik Vibe AU - Scheller HV FAU - Vener, Alexander V AU - Vener AV LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - Biochemistry JT - Biochemistry JID - 0370623 RN - 0 (Arabidopsis Proteins) RN - 0 (Light-Harvesting Protein Complexes) RN - 0 (Phosphoproteins) RN - 0 (Photosystem II Protein Complex) RN - 0 (Recombinant Proteins) SB - IM MH - Arabidopsis/genetics/*metabolism MH - Arabidopsis Proteins/chemistry/genetics/*metabolism MH - *Gene Expression Regulation, Plant MH - Hydroponics MH - Light-Harvesting Protein Complexes/chemistry/genetics/*metabolism MH - Molecular Weight MH - Phosphoproteins/chemistry/genetics/*metabolism MH - Phosphorylation MH - Photosystem II Protein Complex/chemistry/genetics/metabolism MH - Recombinant Proteins/chemistry/metabolism MH - Thylakoids/chemistry/genetics/metabolism EDAT- 2008/12/31 09:00 MHDA- 2009/02/13 09:00 CRDT- 2008/12/31 09:00 AID - 10.1021/bi8016334 [doi] AID - 10.1021/bi8016334 [pii] PST - ppublish SO - Biochemistry. 2009 Jan 20;48(2):499-509. doi: 10.1021/bi8016334. PMID- 14672926 OWN - NLM STAT- MEDLINE DA - 20040223 DCOM- 20040503 LR - 20061115 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 279 IP - 9 DP - 2004 Feb 27 TI - The YefM antitoxin defines a family of natively unfolded proteins: implications as a novel antibacterial target. PG - 8252-61 AB - Although natively unfolded proteins are being observed increasingly, their physiological role is not well understood. Here, we demonstrate that the Escherichia coli YefM protein is a natively unfolded antitoxin, lacking secondary structure even at low temperature or in the presence of a stabilizing agent. This conformation of the protein is suggested to have a key role in its physiological regulatory activity. Because of the unfolded state of the protein, a linear determinant rather than a conformational one is presumably being recognized by its toxin partner, YoeB. A peptide array technology allowed the identification and validation of such a determinant. This recognition element may provide a novel antibacterial target. Indeed, a pair-constrained bioinformatic analysis facilitated the definite determination of novel YefM-YoeB toxin-antitoxin systems in a large number of bacteria including major pathogens such as Staphylococcus aureus, Streptococcus pneumoniae, and Mycobacterium tuberculosis. Taken together, the YefM protein defines a new family of natively unfolded proteins. The existence of a large and conserved group of proteins with a clear physiologically relevant unfolded state serves as a paradigm to understand the structural basis of this state. FAU - Cherny, Izhack AU - Cherny I AD - Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel. FAU - Gazit, Ehud AU - Gazit E LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20031214 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Escherichia coli Proteins) RN - 0 (Peptide Fragments) RN - 0 (YefM protein, E coli) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Circular Dichroism MH - Escherichia coli/*chemistry MH - Escherichia coli Proteins/*chemistry/genetics/metabolism MH - Molecular Sequence Data MH - Peptide Fragments/chemistry/metabolism MH - *Protein Folding MH - Protein Structure, Secondary MH - Sequence Alignment MH - Surface Plasmon Resonance MH - Temperature EDAT- 2003/12/16 05:00 MHDA- 2004/05/05 05:00 CRDT- 2003/12/16 05:00 PHST- 2003/12/14 [aheadofprint] AID - 10.1074/jbc.M308263200 [doi] AID - M308263200 [pii] PST - ppublish SO - J Biol Chem. 2004 Feb 27;279(9):8252-61. Epub 2003 Dec 14. PMID- 9424114 OWN - NLM STAT- MEDLINE DA - 19980106 DCOM- 19980106 LR - 20061115 IS - 0006-2960 (Print) IS - 0006-2960 (Linking) VI - 36 IP - 49 DP - 1997 Dec 9 TI - Entropic exclusion by neurofilament sidearms: a mechanism for maintaining interfilament spacing. PG - 15035-40 AB - A long-range repulsive force near isolated neurofilaments was detected by exclusion of large molecules and by direct force measurements with atomic force microscopy. Adsorption of isolated native neurofilaments to a solid substrate in a high-salt solution (170 mM NaCl), in the presence of coisolating contaminants, shows that the contaminants are excluded from a zone that extends from 50-100 nm from the core of the filament. Force-distance measurements by AFM show the presence of a weak repulsive force that extends >50 nm from the core of the filament; this repulsive force is absent in homopolymers of neurofilament L or trypsinized native filaments that lack the long sidearms present in native filaments. These results suggest that neurofilament sidearms form an entropic brush, thereby providing a mechanism for maintaining interfilament spacing. FAU - Brown, H G AU - Brown HG AD - Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. FAU - Hoh, J H AU - Hoh JH LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - UNITED STATES TA - Biochemistry JT - Biochemistry JID - 0370623 SB - IM MH - Animals MH - Cattle MH - Entropy MH - Microscopy, Atomic Force MH - Neurofibrils/*chemistry MH - Spinal Cord/chemistry EDAT- 1998/01/10 MHDA- 1998/01/10 00:01 CRDT- 1998/01/10 00:00 AID - 10.1021/bi9721748 [doi] AID - bi9721748 [pii] PST - ppublish SO - Biochemistry. 1997 Dec 9;36(49):15035-40. PMID- 23940038 OWN - NLM STAT- MEDLINE DA - 20131007 DCOM- 20131203 LR - 20141113 IS - 1083-351X (Electronic) IS - 0021-9258 (Linking) VI - 288 IP - 40 DP - 2013 Oct 4 TI - An intrinsically disordered photosystem II subunit, PsbO, provides a structural template and a sensor of the hydrogen-bonding network in photosynthetic water oxidation. PG - 29056-68 LID - 10.1074/jbc.M113.487561 [doi] AB - Photosystem II (PSII) is a membrane-bound enzyme that utilizes solar energy to catalyze the photooxidation of water. Molecular oxygen is evolved after four sequential light-driven oxidation reactions at the Mn4CaO5 oxygen-evolving complex, producing five sequentially oxidized states, Sn. PSII is composed of 17 membrane-spanning subunits and three extrinsic subunits, PsbP, PsbQ, and PsbO. PsbO is intrinsically disordered and plays a role in facilitation of the water oxidizing cycle. Native PsbO can be removed and substituted with recombinant PsbO, thereby restoring steady-state activity. In this report, we used reaction-induced Fourier transform infrared spectroscopy to obtain information concerning the role of PsbP, PsbQ, and PsbO during the S state cycle. Light-minus-dark difference spectra were acquired, monitoring structural changes associated with each accessible flash-induced S state transition in a highly purified plant PSII preparation (Triton X-100, octylthioglucoside). A comparison of S2 minus S1 spectra revealed that removal of PsbP and PsbQ had no significant effect on the data, whereas amide frequency and intensity changes were associated with PsbO removal. These data suggest that PsbO acts as an organizational template for the PSII reaction center. To identify any coupled conformational changes arising directly from PsbO, global (13)C-PsbO isotope editing was employed. The reaction-induced Fourier transform infrared spectra of accessible S states provide evidence that PsbO spectral contributions are temperature (263 and 277 K) and S state dependent. These experiments show that PsbO undergoes catalytically relevant structural dynamics, which are coupled over long distance to hydrogen-bonding changes at the Mn4CaO5 cluster. FAU - Offenbacher, Adam R AU - Offenbacher AR AD - From the School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332. FAU - Polander, Brandon C AU - Polander BC FAU - Barry, Bridgette A AU - Barry BA LA - eng PT - Journal Article PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20130812 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (Carbon Isotopes) RN - 0 (Photosystem II Protein Complex) RN - 0 (Protein Subunits) RN - 0 (photosystem II manganese-stabilizing protein) RN - 059QF0KO0R (Water) RN - S88TT14065 (Oxygen) SB - IM MH - Carbon Isotopes MH - Crystallography, X-Ray MH - Electrophoresis, Polyacrylamide Gel MH - Hydrogen Bonding MH - Kinetics MH - Oxidation-Reduction MH - Oxygen/metabolism MH - *Photosynthesis MH - Photosystem II Protein Complex/*chemistry/*metabolism MH - Protein Subunits/*chemistry/*metabolism MH - Spectroscopy, Fourier Transform Infrared MH - Spinacia oleracea/*metabolism MH - Water/*metabolism PMC - PMC3790005 OID - NLM: PMC3790005 OTO - NOTNLM OT - Conformational Landscape OT - Intrinsically Disordered Proteins OT - Metalloproteins OT - Photosynthesis OT - Protein Dynamics OT - Protein-Protein Interactions EDAT- 2013/08/14 06:00 MHDA- 2013/12/16 06:00 CRDT- 2013/08/14 06:00 PHST- 2013/08/12 [aheadofprint] AID - M113.487561 [pii] AID - 10.1074/jbc.M113.487561 [doi] PST - ppublish SO - J Biol Chem. 2013 Oct 4;288(40):29056-68. doi: 10.1074/jbc.M113.487561. Epub 2013 Aug 12. PMID- 18230733 OWN - NLM STAT- MEDLINE DA - 20080206 DCOM- 20080307 LR - 20140904 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 105 IP - 5 DP - 2008 Feb 5 TI - Intrinsically disordered gamma-subunit of cGMP phosphodiesterase encodes functionally relevant transient secondary and tertiary structure. PG - 1505-10 LID - 10.1073/pnas.0709558105 [doi] AB - The retinal phosphodiesterase (PDE6) inhibitory gamma-subunit (PDEgamma) plays a central role in vertebrate phototransduction through alternate interactions with the catalytic alphabeta-subunits of PDE6 and the alpha-subunit of transducin (alpha(t)). Detailed structural analysis of PDEgamma has been hampered by its intrinsic disorder. We present here the NMR solution structure of PDEgamma, which reveals a loose fold with transient structural features resembling those seen previously in the x-ray structure of PDEgamma(46-87) when bound to alpha(t) in the transition-state complex. NMR mapping of the interaction between PDEgamma(46-87) and the chimeric PDE5/6 catalytic domain confirmed that C-terminal residues 74-87 of PDEgamma are involved in the association and demonstrated that its W70 indole group, which is critical for subsequent binding to alpha(t), is left free at this stage. These results indicate that the interaction between PDEgamma and alpha(t) during the phototransduction cascade involves the selection of preconfigured transient conformations. FAU - Song, Jikui AU - Song J AD - Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA. FAU - Guo, Lian-Wang AU - Guo LW FAU - Muradov, Hakim AU - Muradov H FAU - Artemyev, Nikolai O AU - Artemyev NO FAU - Ruoho, Arnold E AU - Ruoho AE FAU - Markley, John L AU - Markley JL LA - eng SI - PDB/2JU4 GR - EY10843/EY/NEI NIH HHS/United States GR - GM033138/GM/NIGMS NIH HHS/United States GR - P41 GM66326/GM/NIGMS NIH HHS/United States GR - P41 RR02301/RR/NCRR NIH HHS/United States GR - P50 GM64598/GM/NIGMS NIH HHS/United States GR - U54 GM074901/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20080129 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Protein Subunits) RN - EC 3.1.4.35 (Cyclic Nucleotide Phosphodiesterases, Type 6) SB - IM MH - Animals MH - Catalytic Domain MH - Cyclic Nucleotide Phosphodiesterases, Type 6/*chemistry MH - Humans MH - Mice MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Protein Subunits PMC - PMC2234174 OID - NLM: PMC2234174 EDAT- 2008/01/31 09:00 MHDA- 2008/03/08 09:00 CRDT- 2008/01/31 09:00 PHST- 2008/01/29 [aheadofprint] AID - 0709558105 [pii] AID - 10.1073/pnas.0709558105 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1505-10. doi: 10.1073/pnas.0709558105. Epub 2008 Jan 29. PMID- 19357160 OWN - NLM STAT- MEDLINE DA - 20090521 DCOM- 20090528 LR - 20140831 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 83 IP - 12 DP - 2009 Jun TI - Analysis of the varicella-zoster virus IE62 N-terminal acidic transactivating domain and its interaction with the human mediator complex. PG - 6300-5 LID - 10.1128/JVI.00054-09 [doi] AB - The varicella-zoster virus major transactivator, IE62, contains a potent N-terminal acidic transcriptional activation domain (TAD). Our experiments revealed that the minimal IE62 TAD encompasses amino acids (aa) 19 to 67. We showed that the minimal TAD interacts with the human Mediator complex. Site-specific mutations revealed residues throughout the minimal TAD that are important for both activation and Mediator interaction. The TAD interacts directly with aa 402 to 590 of the MED25 subunit, and site-specific TAD mutations abolished this interaction. Two-dimensional nuclear magnetic resonance spectroscopy revealed that the TAD is intrinsically unstructured. Our studies suggest that transactivation may involve the TAD adopting a defined structure upon binding MED25. FAU - Yamamoto, Shinobu AU - Yamamoto S AD - Departments of Microbiology and Immunology, University at Buffalo SUNY, Buffalo, New York 14214, USA. FAU - Eletsky, Alexander AU - Eletsky A FAU - Szyperski, Thomas AU - Szyperski T FAU - Hay, John AU - Hay J FAU - Ruyechan, William T AU - Ruyechan WT LA - eng GR - AI18449/AI/NIAID NIH HHS/United States GR - U54-GM074958/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural DEP - 20090408 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (IE62 protein, Human herpesvirus 3) RN - 0 (Immediate-Early Proteins) RN - 0 (MED25 protein, human) RN - 0 (Mediator Complex) RN - 0 (Trans-Activators) RN - 0 (Viral Envelope Proteins) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - Herpesvirus 3, Human/*metabolism MH - Humans MH - Immediate-Early Proteins/*metabolism MH - Mediator Complex MH - Molecular Sequence Data MH - Mutagenesis, Site-Directed MH - Mutation MH - Protein Structure, Secondary MH - Trans-Activators/*metabolism MH - Transcriptional Activation MH - Viral Envelope Proteins/*metabolism PMC - PMC2687382 OID - NLM: PMC2687382 EDAT- 2009/04/10 09:00 MHDA- 2009/05/29 09:00 CRDT- 2009/04/10 09:00 PHST- 2009/04/08 [aheadofprint] AID - JVI.00054-09 [pii] AID - 10.1128/JVI.00054-09 [doi] PST - ppublish SO - J Virol. 2009 Jun;83(12):6300-5. doi: 10.1128/JVI.00054-09. Epub 2009 Apr 8. PMID- 12533537 OWN - NLM STAT- MEDLINE DA - 20030414 DCOM- 20030522 LR - 20081121 IS - 0021-9258 (Print) IS - 0021-9258 (Linking) VI - 278 IP - 16 DP - 2003 Apr 18 TI - Recognition of the intrinsically flexible addiction antidote MazE by a dromedary single domain antibody fragment. Structure, thermodynamics of binding, stability, and influence on interactions with DNA. PG - 14101-11 AB - The Escherichia coli mazEF operon defines a chromosomal addiction module that programs cell death under various stress conditions. It encodes the toxic and long-lived MazF and the labile antidote MazE. The denaturation of MazE is a two-state reversible dimer-monomer transition. At lower concentrations the denatured state is significantly populated. This leads to a new aspect of the regulation of MazE concentration, which may decide about the life and death of the cell. Interactions of MazE with a dromedary antibody domain, cAbMaz1 (previously used as a crystallization aid), as well as with promoter DNA were studied using microcalorimetric and spectroscopic techniques. Unique features of cAbMaz1 enable a specific enthalpy-driven recognition of MazE and, thus, a significant stabilization of its dimeric native conformation. The MazE dimer and the MazE dimer-cAbMaz1 complex show very similar binding characteristics with promoter DNA, i.e. three binding sites with apparent affinities in micromolar range and highly exothermic binding accompanied by large negative entropy contributions. A working model for the MazE-DNA assembly is proposed on the basis of the structural and binding data. Both binding and stability studies lead to a picture of MazE solution structure that is significantly more unfolded than the structure observed in a crystal of the MazE-cAbMaz1 complex. FAU - Lah, Jurij AU - Lah J AD - Department of Ultrastructure, Vrije Universiteit Brussel, Paardenstraat 65, B-1640 St. Genesius Rode, Belgium. jurij.lah@uni-lj.si FAU - Marianovsky, Irina AU - Marianovsky I FAU - Glaser, Gad AU - Glaser G FAU - Engelberg-Kulka, Hanna AU - Engelberg-Kulka H FAU - Kinne, Jorg AU - Kinne J FAU - Wyns, Lode AU - Wyns L FAU - Loris, Remy AU - Loris R LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20030117 PL - United States TA - J Biol Chem JT - The Journal of biological chemistry JID - 2985121R RN - 0 (DNA-Binding Proteins) RN - 0 (Escherichia coli Proteins) RN - 0 (Immunoglobulin Fragments) RN - 0 (MazE protein, E coli) RN - 0 (Peptides) RN - 9007-49-2 (DNA) SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Biochemistry/methods MH - Calorimetry MH - Calorimetry, Differential Scanning MH - Camels MH - Circular Dichroism MH - DNA/metabolism MH - DNA-Binding Proteins/*chemistry/metabolism MH - Dimerization MH - Entropy MH - Escherichia coli/metabolism MH - *Escherichia coli Proteins MH - Immunoglobulin Fragments/chemistry MH - Models, Molecular MH - Molecular Sequence Data MH - Peptides/chemistry MH - Promoter Regions, Genetic MH - Protein Binding MH - Protein Conformation MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Sequence Homology, Amino Acid MH - Temperature MH - Thermodynamics MH - Time Factors EDAT- 2003/01/21 04:00 MHDA- 2003/05/23 05:00 CRDT- 2003/01/21 04:00 PHST- 2003/01/17 [aheadofprint] AID - 10.1074/jbc.M209855200 [doi] AID - M209855200 [pii] PST - ppublish SO - J Biol Chem. 2003 Apr 18;278(16):14101-11. Epub 2003 Jan 17. PMID- 25100849 OWN - NLM STAT- MEDLINE DA - 20141007 DCOM- 20150219 LR - 20150501 IS - 1098-5514 (Electronic) IS - 0022-538X (Linking) VI - 88 IP - 21 DP - 2014 Nov TI - trans-Protease activity and structural insights into the active form of the alphavirus capsid protease. PG - 12242-53 LID - 10.1128/JVI.01692-14 [doi] AB - The alphavirus capsid protein (CP) is a serine protease that possesses cis-proteolytic activity essential for its release from the nascent structural polyprotein. The released CP further participates in viral genome encapsidation and nucleocapsid core formation, followed by its attachment to glycoproteins and virus budding. Thus, protease activity of the alphavirus capsid is a potential antialphaviral target to arrest capsid release, maturation, and structural polyprotein processing. However, the discovery of capsid protease inhibitors has been hampered due to the lack of a suitable screening assay and of the crystal structure in its active form. Here, we report the development of a trans-proteolytic activity assay for Aura virus capsid protease (AVCP) based on fluorescence resonance energy transfer (FRET) for screening protease inhibitors. Kinetic parameters using fluorogenic peptide substrates were estimated, and the K(m) value was found to be 2.63 +/- 0.62 muM while the k(cat)/K(m) value was 4.97 x 10(4) M(-1) min(-1). Also, the crystal structure of the trans-active form of AVCP has been determined to 1.81-A resolution. Structural comparisons of the active form with the crystal structures of available substrate-bound mutant and inactive blocked forms of the capsid protease identify conformational changes in the active site, the oxyanion hole, and the substrate specificity pocket residues, which could be critical for rational drug design. IMPORTANCE The alphavirus capsid protease is an attractive antiviral therapeutic target. In this study, we have described the formerly unappreciated trans-proteolytic activity of the enzyme and for the first time have developed a FRET-based protease assay for screening capsid protease inhibitors. Our structural studies unveil the structural features of the trans-active protease, which has been previously proposed to exist in the natively unfolded form (M. Morillas, H. Eberl, F. H. Allain, R. Glockshuber, and E. Kuennemann, J. Mol. Biol. 376:721-735, 2008, doi:http://dx.doi.org/10.1016/j.jmb.2007.11.055). The different enzymatic forms have been structurally compared to reveal conformational variations in the active and substrate binding sites. The flexible active-site residue Ser218, the disordered C-terminal residues after His261, and the presence of a water molecule in the oxyanion hole of AVCPDelta2 (AVCP with a deletion of the last two residues at the C terminus) reveal the effect of the C-terminal Trp267 deletion on enzyme structure. New structural data reported in this study along with the fluorogenic assay will be useful in substrate specificity characterization, high-throughput protease inhibitor screening, and structure-based development of antiviral drugs. CI - Copyright (c) 2014, American Society for Microbiology. All Rights Reserved. FAU - Aggarwal, Megha AU - Aggarwal M AD - Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India. FAU - Dhindwal, Sonali AU - Dhindwal S AD - Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India. FAU - Kumar, Pravindra AU - Kumar P AD - Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India. FAU - Kuhn, Richard J AU - Kuhn RJ AD - Department of Biological Sciences and Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, USA. FAU - Tomar, Shailly AU - Tomar S AD - Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India shailfbt@iitr.ac.in. LA - eng SI - PDB/4UON GR - GM56279/GM/NIGMS NIH HHS/United States GR - R01 GM056279/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20140806 PL - United States TA - J Virol JT - Journal of virology JID - 0113724 RN - 0 (Capsid Proteins) RN - 0 (Protease Inhibitors) RN - EC 3.4.- (Peptide Hydrolases) SB - IM MH - Alphavirus/*enzymology MH - Capsid Proteins/*chemistry/*metabolism MH - Crystallography, X-Ray MH - Drug Evaluation, Preclinical MH - Fluorescence Resonance Energy Transfer MH - Kinetics MH - Models, Molecular MH - Peptide Hydrolases/*chemistry/*metabolism MH - Protease Inhibitors/*isolation & purification MH - Protein Conformation PMC - PMC4248945 OID - NLM: PMC4248945 EDAT- 2014/08/08 06:00 MHDA- 2015/02/20 06:00 CRDT- 2014/08/08 06:00 PHST- 2014/08/06 [aheadofprint] AID - JVI.01692-14 [pii] AID - 10.1128/JVI.01692-14 [doi] PST - ppublish SO - J Virol. 2014 Nov;88(21):12242-53. doi: 10.1128/JVI.01692-14. Epub 2014 Aug 6. PMID- 17449672 OWN - NLM STAT- MEDLINE DA - 20070625 DCOM- 20070820 LR - 20140907 IS - 0006-3495 (Print) IS - 0006-3495 (Linking) VI - 93 IP - 2 DP - 2007 Jul 15 TI - Conformation of the EPEC Tir protein in solution: investigating the impact of serine phosphorylation at positions 434/463. PG - 586-96 AB - The translocated intimin receptor (Tir) is a key virulence factor of enteropathogenic Escherichia coli and related bacteria. During infection, Tir is translocated via a type III secretion system into host intestinal epithelial cells, where it inserts into the target cell membrane and acts as a receptor for the bacterial adhesin intimin. The effects of phosphorylation by cAMP-dependent kinase at two serine residues (Ser-434 and Ser-463) within the C-terminal domain of Tir, which may be involved in mediating structural/electrostatic changes in the protein to promote membrane insertion or intermolecular interactions, have previously been investigated. This study has focused on defining the conformation of Tir in solution and assessing any conformational changes associated with serine phosphorylation at positions 434/463. In addition to phosphorylated protein, combinations of Ala (unphosphorylatable) and Asp (phosphate-mimic) mutations of Ser-434 and Ser-463 have been generated, and a range of techniques (sodium dodecyl sulfate polyacrylamide gel electrophoresis, circular dichroism spectroscopy, analytical ultracentrifugation) used to further dissect the structural role and functional implications of changes in residue size/charge at these positions. The results have shown that under physiological NaCl concentrations, Tir is a monomer and adopts a highly elongated state in solution, consistent with a natively unfolded conformation. Despite this, perturbations in the structure in response to buffer conditions and the nature of the residues at positions 434 and 463 are apparent, and may be functionally relevant. FAU - Race, Paul R AU - Race PR AD - Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom. FAU - Solovyova, Alexandra S AU - Solovyova AS FAU - Banfield, Mark J AU - Banfield MJ LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20070420 PL - United States TA - Biophys J JT - Biophysical journal JID - 0370626 RN - 0 (DNA Primers) RN - 0 (Escherichia coli Proteins) RN - 0 (Receptors, Cell Surface) RN - 0 (Recombinant Proteins) RN - 0 (Solutions) RN - 0 (Tir protein, E coli) RN - 452VLY9402 (Serine) SB - IM MH - Amino Acid Substitution MH - Base Sequence MH - Biophysical Phenomena MH - Biophysics MH - Circular Dichroism MH - DNA Primers/genetics MH - Escherichia coli/chemistry/genetics/pathogenicity MH - Escherichia coli Proteins/*chemistry/genetics MH - Molecular Weight MH - Mutagenesis, Site-Directed MH - Phosphorylation MH - Protein Conformation MH - Protein Structure, Quaternary MH - Protein Structure, Secondary MH - Receptors, Cell Surface/*chemistry/genetics MH - Recombinant Proteins/chemistry/genetics MH - Serine/chemistry MH - Solutions MH - Thermodynamics PMC - PMC1896257 OID - NLM: PMC1896257 EDAT- 2007/04/24 09:00 MHDA- 2007/08/21 09:00 CRDT- 2007/04/24 09:00 PHST- 2007/04/20 [aheadofprint] AID - S0006-3495(07)71310-3 [pii] AID - 10.1529/biophysj.106.101766 [doi] PST - ppublish SO - Biophys J. 2007 Jul 15;93(2):586-96. Epub 2007 Apr 20. PMID- 20201512 OWN - NLM STAT- MEDLINE DA - 20100324 DCOM- 20100706 LR - 20150503 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 132 IP - 12 DP - 2010 Mar 31 TI - Ester to amide switch peptides provide a simple method for preparing monomeric islet amyloid polypeptide under physiologically relevant conditions and facilitate investigations of amyloid formation. PG - 4052-3 LID - 10.1021/ja910763m [doi] AB - A major issue in studies of amyloid formation is the difficulty of preparing the polypeptide of interest in an initially monomeric state under physiologically relevant conditions. This is particularly problematic for polypeptides which are natively unfolded in their unaggregated state, and perhaps the most challenging such system is islet amyloid polypeptide (Amylin), the causative agent of amyloid formation in type-2 diabetes. Preparation of islet amyloid polypeptide with the Ser-19 Ser-20 amide bond replaced by an ester circumvents these problems. The modified peptide is unstructured and monomeric at slightly acidic pH's as judged by analytical ultracentrifugation, gel filtration, dynamic light scattering, and CD. A rapid pH jump leads to deprotonation of the Ser-20 amide group, and a subsequent rapid O to N acyl shift regenerates normal human islet amyloid polypeptide. The half time, t(1/2), for the conversion to normal islet amyloid polypeptide is 70 s at pH 7.4. The amyloid fibrils which are formed by the regenerated islet amyloid polypeptide are indistinguishable from those formed by the wild type polypeptide. The approach allows studies of amyloid formation by islet amyloid polypeptide to be carried out from a well-defined, physiologically relevant starting state in the absence of denaturants or organic cosolvents. FAU - Cao, Ping AU - Cao P AD - Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, USA. FAU - Raleigh, Daniel P AU - Raleigh DP LA - eng GR - GM078114/GM/NIGMS NIH HHS/United States GR - R01 GM078114/GM/NIGMS NIH HHS/United States GR - R01 GM078114-01A2/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Amides) RN - 0 (Amyloid) RN - 0 (Esters) RN - 0 (Islet Amyloid Polypeptide) RN - 0 (Peptides) SB - IM MH - Amides/*chemistry MH - Amino Acid Sequence MH - Amyloid/*analysis/*chemistry MH - Esters/*chemistry MH - Humans MH - Hydrogen-Ion Concentration MH - Islet Amyloid Polypeptide MH - Microscopy, Electron, Transmission MH - Molecular Sequence Data MH - Peptides/*chemistry MH - Protein Folding PMC - PMC2882296 MID - NIHMS185706 OID - NLM: NIHMS185706 OID - NLM: PMC2882296 EDAT- 2010/03/06 06:00 MHDA- 2010/07/07 06:00 CRDT- 2010/03/06 06:00 AID - 10.1021/ja910763m [doi] PST - ppublish SO - J Am Chem Soc. 2010 Mar 31;132(12):4052-3. doi: 10.1021/ja910763m. PMID- 20095651 OWN - NLM STAT- MEDLINE DA - 20100305 DCOM- 20100601 LR - 20140915 IS - 1535-3907 (Electronic) IS - 1535-3893 (Linking) VI - 9 IP - 3 DP - 2010 Mar 5 TI - Proteomic identification of Hsc70 as a mediator of RGS9-2 degradation by in vivo interactome analysis. PG - 1510-21 LID - 10.1021/pr901022m [doi] AB - Changes in interactions between signaling proteins underlie many cellular functions. In the mammalian nervous system, a member of the Regulator of G protein Signaling family, RGS9-2 (Regulator of G protein Signaling, type 9), is a key regulator of dopamine and opioid signaling pathways that mediate motor control and reward behavior. Dynamic association of RGS9-2 with a neuronal protein R7BP (R7 family Binding Protein) has been found to be critically important for the regulation of the expression level of the complex by proteolytic mechanisms. Changes in RGS9-2 expression are observed in response to a number of signaling events and are thought to contribute to the plasticity of the neurotransmitter action. In this study, we report an identification of molecular chaperone Hsc70 (Heat shock cognate protein 70) as a critical mediator of RGS9-2 expression that is specifically recruited to the intrinsically disordered C-terminal domain of RGS9-2 following its dissociation from R7BP. Hsc70 was identified by a novel application of the quantitative proteomics approach developed to monitor interactome dynamics in mice using a set of controls contributed by knockout strains. We propose this application to be a useful tool for studying the dynamics of protein assemblies in complex models, such as signaling in the mammalian nervous system. FAU - Posokhova, Ekaterina AU - Posokhova E AD - Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, USA. FAU - Uversky, Vladimir AU - Uversky V FAU - Martemyanov, Kirill A AU - Martemyanov KA LA - eng GR - DA021743/DA/NIDA NIH HHS/United States GR - DA026405/DA/NIDA NIH HHS/United States GR - GM071714/GM/NIGMS NIH HHS/United States GR - K02 DA026405/DA/NIDA NIH HHS/United States GR - K02 DA026405-03/DA/NIDA NIH HHS/United States GR - LM007688/LM/NLM NIH HHS/United States GR - R01 DA021743/DA/NIDA NIH HHS/United States GR - R01 DA021743-03/DA/NIDA NIH HHS/United States GR - R01 EY018139/EY/NEI NIH HHS/United States GR - R01 EY018139-03/EY/NEI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PL - United States TA - J Proteome Res JT - Journal of proteome research JID - 101128775 RN - 0 (HSC70 Heat-Shock Proteins) RN - 0 (R7BP protein, mouse) RN - 0 (RGS Proteins) RN - 0 (regulator of g-protein signaling 9) SB - IM MH - Animals MH - Brain/metabolism MH - Brain Chemistry MH - Cell Line MH - Cerebrum/metabolism MH - HSC70 Heat-Shock Proteins/chemistry/*metabolism MH - Humans MH - Isotope Labeling MH - Mice MH - Mice, Knockout MH - Protein Interaction Mapping/methods MH - Proteomics/*methods MH - RGS Proteins/chemistry/*metabolism PMC - PMC2890236 MID - NIHMS207958 OID - NLM: NIHMS207958 OID - NLM: PMC2890236 EDAT- 2010/01/26 06:00 MHDA- 2010/06/02 06:00 CRDT- 2010/01/26 06:00 AID - 10.1021/pr901022m [doi] PST - ppublish SO - J Proteome Res. 2010 Mar 5;9(3):1510-21. doi: 10.1021/pr901022m. PMID- 21787785 OWN - NLM STAT- MEDLINE DA - 20110825 DCOM- 20111019 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 412 IP - 2 DP - 2011 Sep 16 TI - Kinetic recognition of the retinoblastoma tumor suppressor by a specific protein target. PG - 267-84 LID - 10.1016/j.jmb.2011.07.015 [doi] AB - The retinoblastoma tumor suppressor (Rb) plays a key role in cell cycle control and is linked to various types of human cancer. Rb binds to the LxCxE motif, present in a number of cellular and viral proteins such as AdE1A, SV40 large T-antigen and human papillomavirus (HPV) E7, all instrumental in revealing fundamental mechanisms of tumor suppression, cell cycle control and gene expression. A detailed kinetic study of RbAB binding to the HPV E7 oncoprotein shows that an LxCxE-containing E7 fragment binds through a fast two-state reaction strongly favored by electrostatic interactions. Conversely, full-length E7 binds through a multistep process involving a pre-equilibrium between E7 conformers, a fast electrostatically driven association step guided by the LxCxE motif and a slow conformational rearrangement. This kinetic complexity arises from the conformational plasticity and intrinsically disordered nature of E7 and from multiple interaction surfaces present in both proteins. Affinity differences between E7N domains from high- and low-risk types are explained by their dissociation rates. In fact, since Rb is at the center of a large protein interaction network, fast and tight recognition provides an advantage for disruption by the viral proteins, where the balance of physiological and pathological interactions is dictated by kinetic ligand competition. The localization of the LxCxE motif within an intrinsically disordered domain provides the fast, diffusion-controlled interaction that allows viral proteins to outcompete physiological targets. We describe the interaction mechanism of Rb with a protein ligand, at the same time an LxCxE-containing model target, and a paradigmatic intrinsically disordered viral oncoprotein. CI - Copyright (c) 2011 Elsevier Ltd. All rights reserved. FAU - Chemes, Lucia B AU - Chemes LB AD - Protein Structure-Function and Engineering Laboratory, Fundacion Instituto Leloir and IIBBA-CONICET, Avenida Patricias Argentinas 435, 1405 Buenos Aires, Argentina. FAU - Sanchez, Ignacio E AU - Sanchez IE FAU - de Prat-Gay, Gonzalo AU - de Prat-Gay G LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20110726 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Papillomavirus E7 Proteins) RN - 0 (Retinoblastoma Protein) RN - 0 (oncogene protein E7, Human papillomavirus type 16) SB - IM MH - Amino Acid Sequence MH - Kinetics MH - Models, Molecular MH - Molecular Sequence Data MH - Papillomavirus E7 Proteins/chemistry/*metabolism MH - Protein Binding MH - Retinoblastoma Protein/*metabolism MH - Sequence Homology, Amino Acid MH - Thermodynamics EDAT- 2011/07/27 06:00 MHDA- 2011/10/20 06:00 CRDT- 2011/07/27 06:00 PHST- 2011/05/23 [received] PHST- 2011/07/04 [revised] PHST- 2011/07/11 [accepted] PHST- 2011/07/26 [aheadofprint] AID - S0022-2836(11)00769-8 [pii] AID - 10.1016/j.jmb.2011.07.015 [doi] PST - ppublish SO - J Mol Biol. 2011 Sep 16;412(2):267-84. doi: 10.1016/j.jmb.2011.07.015. Epub 2011 Jul 26. PMID- 19711988 OWN - NLM STAT- MEDLINE DA - 20090828 DCOM- 20091014 IS - 1520-6025 (Electronic) IS - 0163-3864 (Linking) VI - 72 IP - 8 DP - 2009 Aug TI - Isolation and characterization of peptides from Momordica cochinchinensis seeds. PG - 1453-8 LID - 10.1021/np900174n [doi] AB - The plant Momordica cochinchinensis has traditionally been used in Chinese medicine to treat a variety of illnesses. A range of bioactive molecules have been isolated from this plant, including peptides, which are the focus of this study. Here we report the isolation and characterization of two novel peptides, MCoCC-1 and MCoCC-2, containing 33 and 32 amino acids, respectively, which are toxic against three cancer cell lines. The two peptides are highly homologous to one another, but show no sequence similarity to known peptides. Elucidation of the three-dimensional structure of MCoCC-1 suggests the presence of a cystine knot motif, also found in a family of trypsin inhibitor peptides from this plant. However, unlike its structural counterparts, MCoCC-1 does not inhibit trypsin. MCoCC-1 has a well-defined structure, characterized mainly by a triple-stranded antiparallel beta-sheet, but unlike the majority of cystine knot proteins MCoCC-1 contains a disordered loop presumably as a result of flexibility in a localized region of the molecule. Of the cell lines tested, MCoCC-1 is the most toxic against a human melanoma cell line (MM96L) and is nonhemolytic to human erythrocytes. The role of these peptides within the plant remains to be determined. FAU - Chan, Lai Y AU - Chan LY AD - The University of Queensland, Institute for Molecular Bioscience, Brisbane QLD 4072, Australia. FAU - Wang, Conan K L AU - Wang CK FAU - Major, Jodie M AU - Major JM FAU - Greenwood, Kathryn P AU - Greenwood KP FAU - Lewis, Richard J AU - Lewis RJ FAU - Craik, David J AU - Craik DJ FAU - Daly, Norelle L AU - Daly NL LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't PL - United States TA - J Nat Prod JT - Journal of natural products JID - 7906882 RN - 0 (Antineoplastic Agents, Phytogenic) RN - 0 (MCoCC-1 peptide) RN - 0 (MCoCC-2 peptide) RN - 0 (Peptides) RN - 0 (Peptides, Cyclic) RN - 0 (Trypsin Inhibitors) SB - IM MH - Amino Acid Sequence MH - Antineoplastic Agents, Phytogenic/*chemistry/*isolation & purification/pharmacology MH - Drug Screening Assays, Antitumor MH - Erythrocytes/drug effects MH - Hemolysis/drug effects MH - Humans MH - Momordica/*chemistry MH - Nuclear Magnetic Resonance, Biomolecular MH - Peptides/*chemistry/*isolation & purification/pharmacology MH - Peptides, Cyclic/*chemistry/*isolation & purification/pharmacology MH - Plants, Medicinal/*chemistry MH - Seeds/chemistry MH - Sequence Homology, Amino Acid MH - Trypsin Inhibitors/chemistry MH - Vietnam EDAT- 2009/08/29 09:00 MHDA- 2009/10/15 06:00 CRDT- 2009/08/29 09:00 AID - 10.1021/np900174n [doi] PST - ppublish SO - J Nat Prod. 2009 Aug;72(8):1453-8. doi: 10.1021/np900174n. PMID- 22829760 OWN - NLM STAT- MEDLINE DA - 20120725 DCOM- 20130123 LR - 20141105 IS - 1553-7358 (Electronic) IS - 1553-734X (Linking) VI - 8 IP - 7 DP - 2012 TI - A preformed binding interface in the unbound ensemble of an intrinsically disordered protein: evidence from molecular simulations. PG - e1002605 LID - 10.1371/journal.pcbi.1002605 [doi] AB - Intrinsically disordered proteins play an important role in cellular signalling, mediated by their interactions with other biomolecules. A key question concerns the nature of their binding mechanism, and whether the bound structure is induced only by proximity to the binding partner. This is difficult to answer through experiment alone because of the very heterogeneous nature of the unbound ensemble, and the probable rapid interconversion of the various unbound structures. Here we report the most extensive set of simulations on NCBD to date: we use large-scale replica exchange molecular dynamics to explore the unbound state. An important feature of the study is the use of an atomistic force field that has been parametrised against experimental data for weakly structured peptides, together with an accurate explicit water model. Neither the force field nor the starting conformations are biased towards a particular structure. The regions of NCBD that have high helical propensity in the simulations correspond closely to helices in the 'core' unbound conformation determined by NMR, although no single member of the simulated unbound ensemble closely resembles the core conformation, or either of the two known bound conformations. We have validated the results against NMR spectroscopy and SAXS measurements, obtaining reasonable agreement. The two helices which most stabilise the binding of NCBD with ACTR are formed readily; the third helix, which is less important for binding but is involved in most of the intraprotein contacts of NCBD in the bound conformation, is formed more rarely, and tends not to coexist with the other helices. These results support a mechanism by which NCBD gains the advantages of disorder, while forming binding-competent structures in the unbound state. We obtain support for this mechanism from coarse-grained simulations of NCBD with, and without, its binding partner. FAU - Knott, Michael AU - Knott M AD - University of Cambridge, Department of Chemistry, Cambridge, United Kingdom. FAU - Best, Robert B AU - Best RB LA - eng GR - BB/H006885/1/Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20120719 PL - United States TA - PLoS Comput Biol JT - PLoS computational biology JID - 101238922 RN - 0 (Proteins) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Amino Acid Sequence MH - Binding Sites MH - CREB-Binding Protein/chemistry/metabolism MH - Humans MH - *Molecular Dynamics Simulation MH - Molecular Sequence Data MH - Nuclear Magnetic Resonance, Biomolecular MH - Protein Binding MH - Protein Conformation MH - Proteins/*chemistry/*metabolism MH - Reproducibility of Results PMC - PMC3400577 OID - NLM: PMC3400577 EDAT- 2012/07/26 06:00 MHDA- 2013/01/24 06:00 CRDT- 2012/07/26 06:00 PHST- 2011/12/06 [received] PHST- 2012/05/28 [accepted] PHST- 2012/07/19 [epublish] AID - 10.1371/journal.pcbi.1002605 [doi] AID - PCOMPBIOL-D-11-01837 [pii] PST - ppublish SO - PLoS Comput Biol. 2012;8(7):e1002605. doi: 10.1371/journal.pcbi.1002605. Epub 2012 Jul 19. PMID- 24753318 OWN - NLM STAT- MEDLINE DA - 20140620 DCOM- 20150130 LR - 20150701 IS - 1469-896X (Electronic) IS - 0961-8368 (Linking) VI - 23 IP - 7 DP - 2014 Jul TI - The mechanism of binding of the KIX domain to the mixed lineage leukemia protein and its allosteric role in the recognition of c-Myb. PG - 962-9 LID - 10.1002/pro.2480 [doi] AB - The KIX domain is a mediator of the interaction between different transcription factors. This complex function is carried out via two distinct binding sites located on opposite sides of the protein; namely, the 'c-Myb site' and the 'MLL site', named after their characteristic ligands-the transactivation domain of c-Myb and the mixed lineage leukemia protein (MLL). Both these ligands are unstructured in isolation and fold only upon binding, posing the KIX domain as an ideal candidate to explore the binding induced folding reaction of intrinsically unstructured proteins. Here, we complement the recent kinetic description on the interaction between KIX and c-Myb, by characterizing the binding kinetics between KIX and MLL, at different pH and ionic strength conditions. Furthermore, we analyze quantitatively the mechanism of allosteric communication between the topologically distinct c-Myb and MLL sites. The implications of our results are discussed in the light of previous work on other intrinsically unstructured systems. CI - (c) 2014 The Protein Society. FAU - Toto, Angelo AU - Toto A AD - Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, 00185, Rome, Italy. FAU - Giri, Rajanish AU - Giri R FAU - Brunori, Maurizio AU - Brunori M FAU - Gianni, Stefano AU - Gianni S LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140509 PL - United States TA - Protein Sci JT - Protein science : a publication of the Protein Society JID - 9211750 RN - 0 (Proto-Oncogene Proteins c-myb) RN - 149025-06-9 (Myeloid-Lymphoid Leukemia Protein) RN - EC 2.3.1.48 (CREB-Binding Protein) SB - IM MH - Animals MH - Binding Sites MH - CREB-Binding Protein/*chemistry/genetics/*metabolism MH - Mice MH - Models, Molecular MH - Myeloid-Lymphoid Leukemia Protein/*metabolism MH - *Protein Binding MH - Protein Conformation MH - Protein Folding MH - Protein Structure, Secondary MH - Protein Structure, Tertiary MH - Proto-Oncogene Proteins c-myb/*metabolism PMC - PMC4088980 OID - NLM: PMC4088980 OTO - NOTNLM OT - folding upon binding OT - intrinsically disordered proteins OT - kinetics OT - reaction mechanism EDAT- 2014/04/23 06:00 MHDA- 2015/01/31 06:00 CRDT- 2014/04/23 06:00 PHST- 2014/02/17 [received] PHST- 2014/04/14 [revised] PHST- 2014/04/15 [accepted] PHST- 2014/05/09 [aheadofprint] AID - 10.1002/pro.2480 [doi] PST - ppublish SO - Protein Sci. 2014 Jul;23(7):962-9. doi: 10.1002/pro.2480. Epub 2014 May 9. PMID- 22998648 OWN - NLM STAT- MEDLINE DA - 20121010 DCOM- 20130301 LR - 20141105 IS - 1520-5126 (Electronic) IS - 0002-7863 (Linking) VI - 134 IP - 40 DP - 2012 Oct 10 TI - Identification of an aggregation-prone structure of tau. PG - 16607-13 LID - 10.1021/ja305206m [doi] AB - The aggregation and deposition of normally soluble proteins is the hallmark of several devastating neurodegenerative disorders. For proteins such as tau in Alzheimer's disease and alpha-synuclein in Parkinson's disease, aggregation involves a transition from an intrinsically disordered monomer to a highly structured fiber. While understanding the role of these proteins in neurodegeneration requires elucidation of the structural basis of self-association, the conformational heterogeneity of disordered proteins makes their structural characterization inherently challenging. Here we use single molecule Forster resonance energy transfer to measure the conformational ensemble of tau in the absence and presence of heparin to identify critical conformational changes relevant to the initiation of aggregation. We find that different domains of tau display distinct conformational properties that are strongly correlated with their degree of disorder and that may relate to their roles in aggregation. Moreover, we observe that heparin binding induces a distinct two-state structural transition in tau characterized by a loss of long-range contacts and a concomitant compaction of the microtubule binding domain. Our results describe a conformational intermediate of tau that precedes the formation of aggregates and could serve as a target for tau-focused therapeutics. FAU - Elbaum-Garfinkle, Shana AU - Elbaum-Garfinkle S AD - Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520-8114, USA. FAU - Rhoades, Elizabeth AU - Rhoades E LA - eng GR - 5T32GM007223-35/GM/NIGMS NIH HHS/United States GR - T32 GM007223/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20121001 PL - United States TA - J Am Chem Soc JT - Journal of the American Chemical Society JID - 7503056 RN - 0 (Anticoagulants) RN - 0 (tau Proteins) RN - 9005-49-6 (Heparin) SB - IM MH - Alzheimer Disease/metabolism MH - Anticoagulants/*pharmacology MH - Fluorescence Resonance Energy Transfer MH - Heparin/*pharmacology MH - Humans MH - Protein Conformation/*drug effects MH - tau Proteins/*chemistry/*metabolism PMC - PMC3477793 MID - NIHMS410804 OID - NLM: NIHMS410804 OID - NLM: PMC3477793 EDAT- 2012/09/25 06:00 MHDA- 2013/03/02 06:00 CRDT- 2012/09/25 06:00 PHST- 2012/10/01 [aheadofprint] AID - 10.1021/ja305206m [doi] PST - ppublish SO - J Am Chem Soc. 2012 Oct 10;134(40):16607-13. doi: 10.1021/ja305206m. Epub 2012 Oct 1. PMID- 22427633 OWN - NLM STAT- MEDLINE DA - 20120411 DCOM- 20120621 IS - 1550-6606 (Electronic) IS - 0022-1767 (Linking) VI - 188 IP - 8 DP - 2012 Apr 15 TI - MARCKS as a negative regulator of lipopolysaccharide signaling. PG - 3893-902 LID - 10.4049/jimmunol.1003605 [doi] AB - Myristoylated alanine-rich C kinase substrate (MARCKS) is an intrinsically unfolded protein with a conserved cationic effector domain, which mediates the cross-talk between several signal transduction pathways. Transcription of MARCKS is increased by stimulation with bacterial LPS. We determined that MARCKS and MARCKS-related protein specifically bind to LPS and that the addition of the MARCKS effector peptide inhibited LPS-induced production of TNF-alpha in mononuclear cells. The LPS binding site within the effector domain of MARCKS was narrowed down to a heptapeptide that binds to LPS in an extended conformation as determined by nuclear magnetic resonance spectroscopy. After LPS stimulation, MARCKS moved from the plasma membrane to FYVE-positive endosomes, where it colocalized with LPS. MARCKS-deficient mouse embryonic fibroblasts (MEFs) responded to LPS with increased IL-6 production compared with the matched wild-type MEFs. Similarly, small interfering RNA knockdown of MARCKS also increased LPS signaling, whereas overexpression of MARCKS inhibited LPS signaling. TLR4 signaling was enhanced by the ablation of MARCKS, which had no effect on stimulation by TLR2, TLR3, and TLR5 agonists. These findings demonstrate that MARCKS contributes to the negative regulation of the cellular response to LPS. FAU - Mancek-Keber, Mateja AU - Mancek-Keber M AD - Department of Biotechnology, National Institute of Chemistry, Ljubljana 1000, Slovenia. FAU - Bencina, Mojca AU - Bencina M FAU - Japelj, Bostjan AU - Japelj B FAU - Panter, Gabriela AU - Panter G FAU - Andra, Jorg AU - Andra J FAU - Brandenburg, Klaus AU - Brandenburg K FAU - Triantafilou, Martha AU - Triantafilou M FAU - Triantafilou, Kathy AU - Triantafilou K FAU - Jerala, Roman AU - Jerala R LA - eng GR - Wellcome Trust/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20120316 PL - United States TA - J Immunol JT - Journal of immunology (Baltimore, Md. : 1950) JID - 2985117R RN - 0 (Interleukin-6) RN - 0 (Intracellular Signaling Peptides and Proteins) RN - 0 (Lipopolysaccharides) RN - 0 (Membrane Proteins) RN - 0 (Peptides) RN - 0 (RNA, Small Interfering) RN - 0 (Toll-Like Receptors) RN - 0 (Tumor Necrosis Factor-alpha) RN - 125267-21-2 (myristoylated alanine-rich C kinase substrate) SB - AIM SB - IM MH - Amino Acid Sequence MH - Animals MH - Binding Sites MH - Endosomes/immunology MH - Fibroblasts/immunology MH - Gene Expression Regulation MH - HEK293 Cells MH - Humans MH - Immunity, Innate MH - Interleukin-6/biosynthesis/immunology MH - Intracellular Signaling Peptides and Proteins/chemistry/*immunology/metabolism MH - Leukocytes, Mononuclear/*immunology MH - Lipopolysaccharides/*immunology/metabolism/pharmacology MH - Membrane Proteins/chemistry/*immunology/metabolism MH - Mice MH - Molecular Sequence Data MH - Peptides/chemistry/pharmacology MH - Protein Binding MH - Protein Transport/immunology MH - RNA, Small Interfering/genetics MH - Signal Transduction MH - Toll-Like Receptors/genetics/immunology MH - Tumor Necrosis Factor-alpha/biosynthesis/immunology EDAT- 2012/03/20 06:00 MHDA- 2012/06/22 06:00 CRDT- 2012/03/20 06:00 PHST- 2012/03/16 [aheadofprint] AID - jimmunol.1003605 [pii] AID - 10.4049/jimmunol.1003605 [doi] PST - ppublish SO - J Immunol. 2012 Apr 15;188(8):3893-902. doi: 10.4049/jimmunol.1003605. Epub 2012 Mar 16. PMID- 25313042 OWN - NLM STAT- MEDLINE DA - 20141029 DCOM- 20150417 LR - 20150113 IS - 1091-6490 (Electronic) IS - 0027-8424 (Linking) VI - 111 IP - 43 DP - 2014 Oct 28 TI - Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein. PG - 15420-5 LID - 10.1073/pnas.1409122111 [doi] AB - Protein-protein interactions are at the heart of regulatory and signaling processes in the cell. In many interactions, one or both proteins are disordered before association. However, this disorder in the unbound state does not prevent many of these proteins folding to a well-defined, ordered structure in the bound state. Here we examine a typical system, where a small disordered protein (PUMA, p53 upregulated modulator of apoptosis) folds to an alpha-helix when bound to a groove on the surface of a folded protein (MCL-1, induced myeloid leukemia cell differentiation protein). We follow the association of these proteins using rapid-mixing stopped flow, and examine how the kinetic behavior is perturbed by denaturant and carefully chosen mutations. We demonstrate the utility of methods developed for the study of monomeric protein folding, including beta-Tanford values, Leffler alpha, Phi-value analysis, and coarse-grained simulations, and propose a self-consistent mechanism for binding. Folding of the disordered protein before binding does not appear to be required and few, if any, specific interactions are required to commit to association. The majority of PUMA folding occurs after the transition state, in the presence of MCL-1. We also examine the role of the side chains of folded MCL-1 that make up the binding groove and find that many favor equilibrium binding but, surprisingly, inhibit the association process. FAU - Rogers, Joseph M AU - Rogers JM AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom. FAU - Oleinikovas, Vladimiras AU - Oleinikovas V AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom. FAU - Shammas, Sarah L AU - Shammas SL AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom. FAU - Wong, Chi T AU - Wong CT AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom. FAU - De Sancho, David AU - De Sancho D AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom. FAU - Baker, Christopher M AU - Baker CM AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom. FAU - Clarke, Jane AU - Clarke J AD - Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom jc162@cam.ac.uk. LA - eng GR - 095195/Wellcome Trust/United Kingdom GR - WT/095195/Wellcome Trust/United Kingdom GR - Biotechnology and Biological Sciences Research Council/United Kingdom PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20141013 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Intrinsically Disordered Proteins) RN - 0 (Ligands) RN - 0 (Mutant Proteins) RN - 0 (Myeloid Cell Leukemia Sequence 1 Protein) RN - 0 (Proto-Oncogene Proteins) SB - IM MH - Intrinsically Disordered Proteins/*chemistry/*metabolism MH - Kinetics MH - Ligands MH - Molecular Dynamics Simulation MH - Mutant Proteins/chemistry/metabolism MH - Mutation/genetics MH - Myeloid Cell Leukemia Sequence 1 Protein/chemistry/metabolism MH - Protein Binding MH - *Protein Folding MH - Protein Structure, Secondary MH - Proto-Oncogene Proteins/chemistry/genetics/metabolism PMC - PMC4217413 OID - NLM: PMC4217413 OTO - NOTNLM OT - BCL-2 OT - Protein folding OT - coarse-grained simulation OT - protein-protein interactions OT - stopped flow EDAT- 2014/10/15 06:00 MHDA- 2015/04/18 06:00 CRDT- 2014/10/15 06:00 PHST- 2014/10/13 [aheadofprint] AID - 1409122111 [pii] AID - 10.1073/pnas.1409122111 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15420-5. doi: 10.1073/pnas.1409122111. Epub 2014 Oct 13. PMID- 21056574 OWN - NLM STAT- MEDLINE DA - 20110107 DCOM- 20110217 LR - 20140821 IS - 1089-8638 (Electronic) IS - 0022-2836 (Linking) VI - 405 IP - 2 DP - 2011 Jan 14 TI - Atomic-level characterization of the ensemble of the Abeta(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms. PG - 570-83 LID - 10.1016/j.jmb.2010.10.015 [doi] AB - Abeta(1-42) is the highly pathologic isoform of amyloid-beta, the peptide constituent of fibrils and neurotoxic oligomers involved in Alzheimer's disease. Recent studies on the structural features of Abeta in water have suggested that the system can be described as an ensemble of distinct conformational species in fast exchange. Here, we use replica exchange molecular dynamics (REMD) simulations to characterize the conformations accessible to Abeta42 in explicit water solvent, under the ff99SB force field. Monitoring the correlation between J-coupling((3)J(H(N))(H(alpha))) and residual dipolar coupling (RDC) data calculated from the REMD trajectories to their experimental values, as determined by NMR, indicates that the simulations converge towards sampling an ensemble that is representative of the experimental data after 60 ns/replica of simulation time. We further validate the converged MD-derived ensemble through direct comparison with (3)J(H(N))(H(alpha)) and RDC experimental data. Our analysis indicates that the ff99SB-derived REMD ensemble can reproduce the experimental J-coupling values with high accuracy and further provide good agreement with the RDC data. Our results indicate that the peptide is sampling a highly diverse range of conformations: by implementing statistical learning techniques (Laplacian eigenmaps, spectral clustering, and Laplacian scores), we are able to obtain an otherwise hidden structure in the complex conformational space of the peptide. Using these methods, we characterize the peptide conformations and extract their intrinsic characteristics, identify a small number of different conformations that characterize the whole ensemble, and identify a small number of protein interactions (such as contacts between the peptide termini) that are the most discriminative of the different conformations and thus can be used in designing experimental probes of transitions between such molecular states. This is a study of an important intrinsically disordered peptide system that provides an atomic-level description of structural features and interactions that are relevant during the early stages of the oligomerization and fibril nucleation pathways. CI - Copyright A(c) 2010. Published by Elsevier Ltd. FAU - Sgourakis, Nikolaos G AU - Sgourakis NG AD - Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, NY 12180, USA. FAU - Merced-Serrano, Myrna AU - Merced-Serrano M FAU - Boutsidis, Christos AU - Boutsidis C FAU - Drineas, Petros AU - Drineas P FAU - Du, Zheming AU - Du Z FAU - Wang, Chunyu AU - Wang C FAU - Garcia, Angel E AU - Garcia AE LA - eng GR - IP20HG003899-01/HG/NHGRI NIH HHS/United States GR - R01 GM054537/GM/NIGMS NIH HHS/United States GR - R01 GM054537-13/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20101105 PL - England TA - J Mol Biol JT - Journal of molecular biology JID - 2985088R RN - 0 (Amyloid beta-Peptides) RN - 0 (Peptide Fragments) RN - 0 (amyloid beta-protein (1-42)) RN - 059QF0KO0R (Water) SB - IM MH - *Algorithms MH - Amyloid beta-Peptides/*chemistry MH - Humans MH - *Magnetic Resonance Spectroscopy MH - Models, Molecular MH - *Molecular Dynamics Simulation MH - Peptide Fragments/*chemistry MH - Protein Conformation MH - Water/*chemistry PMC - PMC3060569 MID - NIHMS261025 OID - NLM: NIHMS261025 OID - NLM: PMC3060569 EDAT- 2010/11/09 06:00 MHDA- 2011/02/18 06:00 CRDT- 2010/11/09 06:00 PHST- 2010/07/05 [received] PHST- 2010/10/06 [revised] PHST- 2010/10/13 [accepted] PHST- 2010/11/05 [aheadofprint] AID - S0022-2836(10)01123-X [pii] AID - 10.1016/j.jmb.2010.10.015 [doi] PST - ppublish SO - J Mol Biol. 2011 Jan 14;405(2):570-83. doi: 10.1016/j.jmb.2010.10.015. Epub 2010 Nov 5.