Role of Channel Fluctuations in Ion Transport and Selectivity in Bacterial Sodium Channel NavAb

Abstract

The elucidation of high-resolution structures of voltage-gated sodium channels has opened the way to elucidating the mechanism of sodium permeation and selectivity. Molecular simulation studies of bacterial sodium channel NavAb (Chakrabarti et al., PNAS 110, 11331-11336, 2013) suggested that Na+ binding and permeation through the selectivity filter are coupled to the conformational isomerization of the Glu177 side chains of the EEEE ring from an outfacing conformation to a lumen-facing conformation, resulting in a high rate of Na+ diffusion through the selectivity filter. To clarify the role of channel dynamics on ion permeation and selectivity, we examine the mechanism of ion permeation in various systems in which either the nature of the EEEE ring or the extent of channel fluctuations have been modified. Specifically, we study how the molecular mechanism of Na+ and K+ permeation in NavAb is affected by protonating a single Glu177 side chain, by replacing all four Glu177 side chains by Asp, by preventing conformational isomerization of Glu177 side chains, by removing the voltage-sensing domains, and by introducing artificial structural restraints on the transmembrane helices of the pore domain. The analysis of unbiased equilibrium simulations totalling over 200 microseconds, including simulations with competitive binding of Na+ and K+, shows how modifying the structure and fluctuations of the selectivity filter, either directly or indirectly, alters both the ion conduction mechanism and the ionic selectivity of the channel. These findings have implications for the study of cation permeation and selectivity in a large class of tetrameric ion channels containing acidic side chains in the conduction pore.