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I. A. Kaliman, A. A. Moskovsky, S. S. Konyukhov, A. V. Nemukhin

Modeling proton transport in the channel of gramicidin A

Abstract

The energy profiles for the proton transfer along the oriented water molecules inside the gramicidin A channel were computed. We use an original implementation of the rigid body molecular dynamics method for description of the peptide groups of the channel as well as of the outer water molecules. In order to simulate the inner water wire, the force field parameters PM6 allowing formation and cleavage of chemical and hydrogen bonds in water molecules are used. We studied the intrinsic stage of the proton H+ translocation, the transfer of the anionic defect OH, and the stage of re-orientation of the water file inside the channel. To facilitate parallel calculations of trajectories, the reaction coordinate is subdivided into segments, and the weighted histogram analysis method is applied. No energy barrier was found for the transfer of an anion defect from the center of the channel, as well as for the proton transfer. The re-orientation of water file inside the channel is the only stage, that has a barrier.
Moscow University Chemistry Bulletin.
2008, Vol. 49, No. 5, P. 291
   

Copyright (C) Chemistry Dept., Moscow State University, 2002
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