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Research at the interface between chemistry and the -omic sciences and systems biology.
Contents list for Molecular BioSystems, issue 6, 2008
Front cover
Mol. BioSyst., 2008, 4, 445
DOI: 10.1039/b807534b
Inside front cover
Mol. BioSyst., 2008, 4, 446
DOI: 10.1039/b807535m
Contents and Chemical Biology
Mol. BioSyst., 2008, 4, 447
DOI: 10.1039/b807536k
Editorial
Emerging Investigators issue
Mol. BioSyst., 2008, 4, 465
DOI: 10.1039/b806354k
The chair of the Molecular BioSystems Editorial Board, Professor Tom Kodadek, introduces the Emerging Investigators issue.
Profile
Contributors to the Emerging Investigators issue
Mol. BioSyst., 2008, 4, 466
DOI: 10.1039/b806352b
Molecular BioSystems profiles the contributors to the Emerging Investigators issue.
Reviews
Photocrosslinkers illuminate interactions in living cells
Yoshihito Tanaka, Michelle R. Bond and Jennifer J. Kohler,
Mol. BioSyst., 2008, 4, 473
DOI: 10.1039/b803218a
Enhanced HTML article available
This review highlights recent methodological developments that make it possible to introduce photocrosslinking groups into polypeptides or glycans as they are synthesized in cells and how these methods offer a non-invasive way to study macromolecular interactions in a native context.
Enabling methodology for the end functionalisation of glycosaminoglycan oligosaccharides
Emiliano Gemma, Odile Meyer, Du
an Uhrín and Alison N. Hulme,
Mol. BioSyst., 2008, 4, 481
DOI: 10.1039/b801666f Enhanced HTML article available
We review methods for the preparation of end-functionalised glycosaminoglycan (GAG) oligosaccharides which may be used for a wide range of applications, including the study of GAG–protein complexes and the synthesis of GAG arrays.
Communications
Visualization of phosphatase activity in living cells with a FRET-based calcineurin activity sensor
Robert H. Newman and Jin Zhang,
Mol. BioSyst., 2008, 4, 496
DOI: 10.1039/b720034j Enhanced HTML article available
We describe the first genetically-encodable phosphatase activity biosensor designed to specifically track calcineurin activity inside living cells. The successful design of a prototype phosphatase activity sensor lays a foundation for studying targeting and compartmentation of phosphatases.
Direct printing of trichlorosilanes on glass for selective protein adsorption and cell growth
Dawn M. Yanker and Joshua A. Maurer,
Mol. BioSyst., 2008, 4, 502
DOI: 10.1039/b801161c Enhanced HTML article available
Direct patterning of octadecyltrichlorosilane and backfilling with a glycol-terminated trichlorosilane on glass creates a surface on which protein adsorption and cell growth can be manipulated.
2-Methoxycyclopentyl analogues of a Pseudomonas aeruginosa quorum sensing modulator
Lydia Y. W. Lee, Timothy Hupfield, Rebecca L. Nicholson, James T. Hodgkinson, Xianbin Su, Gemma L. Thomas, George P. C. Salmond, Martin Welch and David R. Spring,
Mol. BioSyst., 2008, 4, 505
DOI: 10.1039/b801563e Enhanced HTML article available
Cis- and trans-2-methoxycyclopentyl analogues of a quorum sensing molecule were synthesized and screened in P. aeruginosa and Serratia 39006 phenotypic assays. Both were agonists, but less active relative to a 2-oxocyclopentyl analogue and the cognate ligand.
Light-activated deoxyguanosine: photochemical regulation of peroxidase activity
Hrvoje Lusic, Mark O. Lively and Alexander Deiters,
Mol. BioSyst., 2008, 4, 508
DOI: 10.1039/b800166a Enhanced HTML article available
A novel photocaged deoxyguanosine phosphoramidite was synthesized and incorporated into DNA. Peroxidase deoxyribozymes carrying the caged dG were catalytically inactive due to inhibition of structural organization. Brief UV irradiation efficiently restored the formation of a G-quadruplex wire and peroxidase activity.
Toward autonomously operating molecular machines driven by transition-metal catalyst
Kenichi Tanaka and Kazushi Kinbara,
Mol. BioSyst., 2008, 4, 512
DOI: 10.1039/b801621f Enhanced HTML article available
A Vaska-type complex carrying a ferrocene-appended diphosphine ligand was developed as a prototype of autonomous molecular machines that is able to undergo continuous scissoring motion in the presence of diphenylphosphoryl azide and aldehyde.
DNA packaging via combinative self-assembly
Jennifer Haley, Xiaolin Li, Nicholas Marshall, Jason Locklin and Yan Geng,
Mol. BioSyst., 2008, 4, 515
DOI: 10.1039/b800220g Enhanced HTML article available
A novel and versatile DNA packaging approach was developed by grafting DNA-binding oligopeptides onto a polymer scaffold to combinatively self-assemble with DNA into compact nanostructures.
A simple solid-phase synthesis of the ubiquitous bacterial signaling molecule, c-di-GMP and analogues
Irene Kiburu, Andrew Shurer, Lei Yan and Herman O. Sintim,
Mol. BioSyst., 2008, 4, 518
DOI: 10.1039/b719423d Enhanced HTML article available
Cyclic-di-guanylate (c-di-GMP) has emerged as a general and important signaling molecule uniquely present in bacteria. We herein provide a simple solid-phase synthesis of c-di-GMP using an automated DNA synthesizer for the majority of the synthesis.
Papers
A chemical approach for detecting sulfenic acid-modified proteins in living cells
Khalilah G. Reddie, Young Ho Seo, Wilson B. Muse III, Stephen E. Leonard and Kate S. Carroll,
Mol. BioSyst., 2008, 4, 521
DOI: 10.1039/b719986d Enhanced HTML article available
We have developed a method that enables live cell labeling of sulfenic acid-modified proteins. This method employs a new probe DAz-1 that is chemoselective for sulfenic acids, cell permeable and contains an azide chemical handle that can be selectively detected with bio-orthogonal phosphine reagents for identification and visualization.
Acid cleavable PEG-lipids for applications in a ternary gene delivery vector
John B. Wong, Stephanie Grosse, Alethea B. Tabor, Stephen L. Hart and Helen C. Hailes,
Mol. BioSyst., 2008, 4, 532
DOI: 10.1039/b719782a Enhanced HTML article available
A novel class of pH-sensitive PEG lipids bearing acid-cleavable acetal linkages and short PEG chains have been synthesised and used in ternary vector formulations. The cleavage pH was influenced by structural components including the terminal PEG moiety and spacer length.
Design, synthesis and characterization of 
clickable
4-anilinoquinazoline kinase inhibitors
B. Gayani K. Perera and Dustin J. Maly,
Mol. BioSyst., 2008, 4, 542
DOI: 10.1039/b720014e Enhanced HTML article available
A versatile method for the generation of clickable 4-anilinoquinazoline kinase inhibitors is reported. This methodology was used to generate potent and selective inhibitors of Aurora A, p38 and Src that can be modified via the Huisgen 1,3-dipolar cycloaddition.
Design, synthesis, and evaluation of an isotopic labeling strategy for studying fatty acid–protein binding by NMR
Yong Han, Timothy E. Alexander and Gregory P. Tochtrop,
Mol. BioSyst., 2008, 4, 551
DOI: 10.1039/b800471d Enhanced HTML article available
We illustrate the utility of a fatty acid isotopic labeling strategy to study protein ligand binding using FABP2 as proof of principle.
Chemical site-selective prenylation of proteins
David P. Gamblin, Sander van Kasteren, Gonçalo J. L. Bernardes, Justin M. Chalker, Neil J. Oldham, Antony J. Fairbanks and Benjamin G. Davis,
Mol. BioSyst., 2008, 4, 558
DOI: 10.1039/b802199f Enhanced HTML article available
A direct thionation procedure allows conversion of allylic alcohols into the corresponding thiols, the products of which are immediately compatible with one-pot site-selective selenenyl sulfide mediated protein conjugation.
Visualizing the spatial distribution of secondary metabolites produced by marine cyanobacteria and sponges via MALDI-TOF imaging
Eduardo Esquenazi, Cameron Coates, Luke Simmons, David Gonzalez, William H. Gerwick and Pieter C. Dorrestein,
Mol. BioSyst., 2008, 4, 562
DOI: 10.1039/b720018h Enhanced HTML article available
MALDI-TOF imaging is a promising tool in marine natural products research: it gives us the ability to visualize the presence and distribution of bioactive compounds in both simple and complex assemblages of intact marine organisms.
Bifunctional molecules evade cytochrome P450 metabolism by forming protective complexes with FK506-binding protein
Paul S. Marinec, Jody K. Lancia and Jason E. Gestwicki,
Mol. BioSyst., 2008, 4, 571
DOI: 10.1039/b720011k Enhanced HTML article available
FK506 has a surprisingly good pharmacology, despite its high molecular weight. We modified unrelated compounds, such that they also acquire affinity for FKBP. Strikingly, these derivatives become resistant to metabolism in vitro. These findings suggest one mechanism that is responsible for FK506
s long half-life in vivo.
Conformation and the sodium ion condensation on DNA and RNA structures in the presence of a neutral cosolute as a mimic of the intracellular media
Shu-ichi Nakano, Lei Wu, Hirohito Oka, Hisae Tateishi Karimata, Toshimasa Kirihata, Yuichi Sato, Satoshi Fujii, Hiroshi Sakai, Masayuki Kuwahara, Hiroaki Sawai and Naoki Sugimoto,
Mol. BioSyst., 2008, 4, 579
DOI: 10.1039/b718806d Enhanced HTML article available
Comprehensive studies of the conformations and the thermal stabilities of DNA and RNA structures in cosolute-containing solutions implicated the significance of the intracellular environment on nucleotide structures in a cell.
Prediction of cardiac transcription networks based on molecular data and complex clinical phenotypes
Martje Toenjes, Markus Schueler, Stefanie Hammer, Utz J. Pape, Jenny J. Fischer, Felix Berger, Martin Vingron and Silke Sperling,
Mol. BioSyst., 2008, 4, 589
DOI: 10.1039/b800207j Enhanced HTML article available
An integrative approach to identifying cardiac transcription networks based on correlated gene expression and optimized prediction of transcription factor binding sites can enable explanation of gene expression profiles observed for congenital heart disease.
Re-engineering a split-GFP reassembly screen to examine RING-domain interactions between BARD1 and BRCA1 mutants observed in cancer patients
Mohosin Sarkar and Thomas J. Magliery,
Mol. BioSyst., 2008, 4, 599
DOI: 10.1039/b802481b Enhanced HTML article available
We re-engineered the split-GFP system for fast reassembly and bright fluorescence with whole protein domains. The improved system was used to study interactions of BARD1 with cancer-associated mutants of the tumor suppressor BRCA1.
Estimating P-coverage of biosynthetic pathways in DNA libraries and screening by genetic selection: biotin biosynthesis in the marine microorganism chromohalobacter
Eun Jin Kim, Scott Angell, Jeff Janes and Coran M. H. Watanabe,
Mol. BioSyst., 2008, 4, 606
DOI: 10.1039/b712770g Enhanced HTML article available
An algorism called BPC is put forth to estimate the size of a library necessary to achieve proper coverage of biosynthetic pathways housed within microbial genomes. Genetic selection is demonstrated as a method to identify and localize biosynthetic gene clusters within metagenomic DNA libraries.
Control of bacterial biofilms with marine alkaloid derivatives
Robert W. Huigens III, Luyan Ma, Christopher Gambino, Peter D. R. Moeller, Anne Basso, John Cavanagh, Daniel J. Wozniak and Christian Melander,
Mol. BioSyst., 2008, 4, 614
DOI: 10.1039/b719989a Enhanced HTML article available
Bacterial biofilms are responsible for a plethora of medical problems. Herein we report the identification of bicyclic 2-aminoimidazole derivatives that inhibit and disperse bacterial biofilms.
Characterization of TioF, a tryptophan 2,3-dioxygenase involved in 3-hydroxyquinaldic acid formation during thiocoraline biosynthesis
Anita Sheoran, Andrew King, Ana Velasco, Jessica M. Pero and Sylvie Garneau-Tsodikova,
Mol. BioSyst., 2008, 4, 622
DOI: 10.1039/b801391h Enhanced HTML article available
TioF, a new member of the family of tryptophan 2,3-dioxygenases with broader substrate specificity than other TDOs, is involved in the formation of the marine anticancer agent thiocoraline.
Targeting telomerase and telomeres: a click chemistry approach towards highly selective G-quadruplex ligands
Adam D. Moorhouse, Shozeb Haider, Mekala Gunaratnam, Deeksha Munnur, Stephen Neidle and John E. Moses,
Mol. BioSyst., 2008, 4, 629
DOI: 10.1039/b801822g Enhanced HTML article available
A library of new telomerase inhibitors have been discovered utilizing the Cu(I) catalyzed 
Click reaction between a azides and terminal alkynes. These click ligands show promising activity and selectivity in vivo against telomerase.
A quantitative study of the recruitment potential of all intracellular tyrosine residues on EGFR, FGFR1 and IGF1R
Alexis Kaushansky, Andrew Gordus, Bryan Chang, John Rush and Gavin MacBeath,
Mol. BioSyst., 2008, 4, 643
DOI: 10.1039/b801018h Enhanced HTML article available
This paper reports quantitative interaction maps for EGFR, FGFR1 and IGF1R, obtained by probing protein microarrays comprising human SH2 and PTB domains with phosphopeptides representing every intracellular tyrosine residue on each of the three receptors.
A simple strategy for the creation of a recombinant lectin microarray
Ku-Lung Hsu, Jeffrey C. Gildersleeve and Lara K. Mahal,
Mol. BioSyst., 2008, 4, 654
DOI: 10.1039/b800725j Enhanced HTML article available
We describe an efficient strategy for the systematic creation of bacterially-derived recombinant lectins for use in lectin microarray technology. We demonstrate that a recombinant lectin microarray is capable of distinguishing glycopatterns of protein and tumor cell samples.
The unusual macrocycle forming thioesterase of mycolactone
Jordan L. Meier, Tiffany Barrows-Yano, Timothy L. Foley, Candice L. Wike and Michael D. Burkart,
Mol. BioSyst., 2008, 4, 663
DOI: 10.1039/b801397g Enhanced HTML article available
The putative macrocycle forming thioesterase MLSA2 TE was cloned, expressed and biochemically characterized. The findings suggest that the enzyme utilizes a unique biochemical mechanism for macrocycle formation.
Accurate measurements of protein interactions in cells via improved spatial image cross-correlation spectroscopy
Jonathan W. D. Comeau, David L. Kolin and Paul W. Wiseman,
Mol. BioSyst., 2008, 4, 672
DOI: 10.1039/b719826d Enhanced HTML article available
New strategies to overcome some of the limitations of spatial image cross-correlation spectroscopy promise to significantly improve the dynamic range and practical usage of an accurate method for measuring molecular interactions via analysis of fluorescence microscopy images.
Thermodynamic prediction of RNA–DNA duplex-forming regions in the human genome
Julian L. Huppert,
Mol. BioSyst., 2008, 4, 686
DOI: 10.1039/b800354h Enhanced HTML article available
The energetic contributions of both duplex formation and single-strand folding are considered and used to search the entire human genome for regions predicted to form RNA–DNA hybrids, confirming previous experiments.
Back matter
Mol. BioSyst., 2008, 4, 692
DOI: 10.1039/b808153k
Back cover
Mol. BioSyst., 2008, 4, 695
DOI: 10.1039/b807537a
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