Paper Citing NAMD - Abstract
Stock, Leticia; Delemotte, Lucie; Carnevale, Vincenzo; Treptow, Werner; Klein, Michael L.
Conduction in a Biological Sodium Selective Channel
JOURNAL OF PHYSICAL CHEMISTRY B, 117:3782-3789, APR 11 2013
The crystal structure of NavAb, a bacterial voltage gated Na+ channel, exhibits a selectivity filter (SF) wider than that of K+ channels. This new structure provides the opportunity to explore the mechanism of conduction and help rationalize its selectivity for sodium. Recent molecular dynamics (MD) simulations of single- and two-ion permeation processes have revealed that a partially hydrated Na+ permeates the channel by exploring three SF binding sites while being loosely coupled to other ions and/or water molecules; a finding that differs significantly from the behavior of K+ selective channels. Herein, we present results derived from a combination of metadynamics and voltage-biased MD simulations that throws more light on the nature of the Na+ conduction mechanism. Conduction under 0 mV bias explores several distinct pathways involving the binding of two ions to three possible SF sites. While these pathways are very similar to those observed in the presence of a negative potential (inward conduction), a completely different mechanism operates for outward conduction at positive potentials.
