Simulation Studies of Ion Permeation and Selectivity in Voltage-Gated Sodium Channels

Voltage-gated ion channels are responsible for the generation and propagation of action potentials in electrically excitable cells. Molecular dynamics simulations have become a useful tool to study the molecular basis of ion transport in atomistic models of voltage-gated ion channels. The elucidation of several three-dimensional structures of bacterial voltage-gated sodium channels (Na-v) in 2011 and 2012 opened the way to detailed computational investigations of this important class of membrane proteins. Here we review the numerous simulation studies of Na+ permeation and selectivity in bacterial Na-v channels published in the past 5 years. These studies use a variety of simulation methodologies differing in force field parameters, molecular models, sampling algorithms, and simulation times. Although results disagree on the details of ion permeation mechanisms, they concur in the presence of two primary Na+ binding sites in the selectivity filter and support a loosely coupled knock-on mechanism of Na+ permeation. Comparative studies of Na+, K+, and Ca2+ permeation reveal sites within Na-v channels that are Na+ selective, yet a consensus model of selectivity has not been established. We discuss the agreement between simulation and experimental results and propose strategies that may be used to resolve discrepancies between simulation studies in order to improve future computational studies of permeation and selectivity in ion channels.