American Chemical Society, Journal of Physical Chemistry B (Soft Condensed Matter and Biophysical Chemistry), 14(117), p. 3782-3789
DOI: 10.1021/jp401403b
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The crystal structure of NavAb, a bacterial voltage gated Na+ channel, exhibits a selectivity filter (SF) wider than that of analogous 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 presence of a negative potential (inward conduction), a completely different mechanism operates for outward conduction at positive potentials.