Scientists in Israel have used computer simulations to understand how protons transfer across the surfaces of proteins.

Proton transfer at the surfaces of biological systems is one of the most prevalent reactions in the biosphere - it is used in the aerobic generation of ATP and oxygen. The mechanism of proton transfer has been studied by researchers for many years. However, modelling protons requires difficult quantum mechanical calculations to be solved. Menachem Gutman and colleagues at Tel Aviv University simplified the problem, using ions as models for protons. This reduced their calculations to simpler classical molecular dynamics ones. 

Gutman and colleagues used the model to analyse the paths of ions on protein surfaces. They found that the ions can enter 'detained states'. Ions in these states can move but are confined within regions near charged residues called attractors. The team used the calculations to show that ions can move between neighbouring attractors, giving an insight into the mechanism of proton transfer in proteins.

Gutman's results take researchers a step closer to understanding proton transfer at the atomic level. The next challenge is to combine these simulative techniques with kinetic measurements 'in order to understand how the proton-driven machines that are populating the bio-membranes really do operate,' he said.

Sarah Dixon