Catalysis and Selectivity of Na+ Permeation in Bacterial Sodium Channel NaVAb

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The determination of a high-resolution 3D structure of voltage-gated sodium channel NaVAb opens the way to elucidating the mechanism of ion conductance and selectivity. To examine the selective permeation of Na+ over K+ through the selectivity filter of the channel, we performed large-scale molecular dynamics simulations of NaVAb in an explicit, hydrated lipid bilayer at 0mV successively in 150mM NaCl, 150mM KCl, and a combination of both, for a total simulation time of more than 70 microseconds. Although the cytoplasmic end of the pore is closed, reversible influx and efflux of Na+ and K+ through the selectivity filter occurred spontaneously during simulations, leading to equilibrium movement of these cations between the extracellular medium and the central cavity of the channel. Analysis of Na+ dynamics reveals a knock-on mechanism of ion permeation characterized by alternating occupancy of the channel by 2 and 3 Na+ ions, with a computed rate of translocation of (6±1) × 106 ions per second that is consistent with expectations from electrophysiological studies. The binding of Na+ is intimately coupled to conformational isomerization of the four E177 side chains lining the extracellular end of the selectivity filter. The reciprocal coordination of variable numbers of Na+ ions and carboxylate groups leads to their condensation into ionic clusters of variable charge and spatial arrangement. By stabilizing multiple ionic occupancy states while helping Na+ ions diffuse within the selectivity filter, the conformational flexibility of E177 side chains underpins the knock-on mechanism of Na+ permeation. K+ also forms ionic complexes with E177 but, contrary to Na+, K+ ions pass through the selectivity filter in single file. The analysis of competitive binding of Na+ and K+ in mixed-cation simulations provides detailed mechanistic insight into the molecular basis of ion selectivity in NaVAb.