Simulation of proton transport in the gramicidin A channel

Abstract

The free energy profiles for proton transfer along the oriented water file inside the gramicidin A channel were calculated. An original implementation of the rigid-body molecular dynamics method was used for describing the peptide groups of the channel and outer water molecules. The inner water wire was simulated using the PM6 force field parameters, which adequately describe the formation and cleavage of chemical and hydrogen bonds in water molecules. Different mechanisms of proton transfer through the gramicidin A channel were considered, namely, proton H⁺ translocation, transfer of the anion defect OH⁻, and reorientation of the water file inside the channel. To facilitate parallel calculations of trajectories, the reaction coordinate was divided into segments, and the results were combined by the weighted histogram analysis method. The first two processes, H⁺ and OH⁻ transfers, were shown to be barrierless. Only the stage of reorientation of the water file inside the channel has an energy barrier.