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