Paper Citing NAMD - Abstract
Zhu, Fangqiang; Hummer, Gerhard
Theory and Simulation of Ion Conduction in the Pentameric GLIC Channel
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:3759-3768, OCT 2012
GLIC is a bacterial member of the large family of pentameric ligand-gated ion channels. To study ion conduction through GLIC and other membrane channels, we combine the one-dimensional potential of mean force for ion passage with a Smoluchowski diffusion model, making it possible to calculate single-channel conductance in the regime of low ion concentrations from all-atom molecular dynamics (MD) simulations. We then perform MD simulations to examine sodium ion conduction through the GLIC transmembrane pore in two systems with different bulk ion concentrations. The ion potentials of mean force, calculated from umbrella sampling simulations with Hamiltonian replica exchange, reveal a major barrier at the hydrophobic constriction of the pore. The relevance of this barrier for ion transport is confirmed by a committor function that rises sharply in the barrier region. From the free evolution of Na+ ions starting at the barrier top, we estimate the effective diffusion coefficient in the barrier region and subsequently calculate the conductance of the pore. The resulting diffusivity compares well with the position-dependent ion diffusion coefficient obtained from restrained simulations. The ion conductance obtained from the diffusion model agrees with the value determined via a reactive-flux rate calculation. Our results show that the conformation in the GLIC crystal structure, with an estimated conductance of similar to 1 picosiemens at 140 mM ion concentration, is consistent with a physiologically open state of the channel.
