Paper Citing NAMD - Abstract
Song, Hyun Deok; Beck, Thomas L.
Temperature Dependence of Gramicidin Channel Transport and Structure
JOURNAL OF PHYSICAL CHEMISTRY C, 117:3701-3712, FEB 28 2013
The gramicidin dipeptide is a small, cation-selective ion channel. Recent experiments have indicated that gramicidin can conduct ions at elevated temperatures. Since gramicidin is an efficient proton conductor, it is possible that this channel may have applications in fuel cell technology. In this study, we examine the temperature dependence of gramicidin A channel transport and structure with molecular dynamics simulations. In particular, the potentials of mean force (PMFs) for potassium ion motion through the channel are computed at five temperatures in the range 300-360 K. The channel displays a decrease in the free energy barrier height as the temperature increases. In addition, the enthalpic and entropic components of the free energy are computed, indicating a substantial enthalpy-entropy compensation and a positive entropy change when the ion enters the channel. The positive entropy change results from a reduction in fluctuations of ion interaction energies in the pore relative to those in the bulk solvent. The overall dimeric channel structure is maintained at 360 K for time scales up to 100 ns. In addition, higher temperatures affect the distributions of hydrogen bonds at the dimer interface, conformations of the N-terminal domain that may block the pore, channel bending angles, and distances between dimers. These findings may be related to the gating of the channel, although no complete dimer dissociation events were observed in the simulations.
