| Proton translocation (PTL) is studied in the ion channel gramicidin A (gA). Non-dissociable and fully charged dissociable models are found to be insufficient for studying this complex process. The partially charged and dissociable multi-state empirical valence bond (MS-EVB) model is modified to model the proton hopping process between water molecules in gA. A new and general method is developed for measuring the location of the excess charge in a protonated system. Molecular dynamics simulations are run for a system containing gA, a protonated water wire, a model membrane, and bulk water. Both the water turning defect and excess proton hopping defect contributions to PTL are explored. Proton transfers are observed in these simulations, but long range proton translocation is not, and the differences with experimental results are investigated. A large barrier for the hopping defect is observed, with a much smaller barrier being found for the turning defect. The hopping defect is therefore identified as the likely rate determining step for the overall process in this model. The structure, dynamics, and energetics of proton translocation in gA are found to be determined in large part by competition for hydrogen bonding between protonated and unprotonated waters inside the channel and the carbonyl oxygens lining the channel. |
