Computational Study of Ion Selectivity in Eukaryotic Voltage-Gated Sodium Channels

Abstract

The outer pore of Nav1.x channels is lined by the selectivity-filter ring Asp-Glu-Lys-Ala (DEKA), an outer ring of carboxylates, and two inner rings of backbone carbonyls. A key role of Lys in the Na/K selectivity is known, but the mechanism is unclear. The DEKA residues may exist in different protonation forms. Here contacts involving DEKA residues in 15 cryo-EM structures of Nav1.x channels were analyzed. The analysis suggests that either Asp or Glu are protonated in the majority of the structures. Monte Carlo (MC) energy minimizations of models with the DEKA residues in different protonation states, with or without Na+ or K+ were further performed. In MC-minimized structures protonated Lys+ was salt bridged with Glu-, whereas deprotonated Lys·· “dunked” to the inner rings. When Na+ was pulled through the outer pore, it was inevitably chelated by Glu- and Lys·· at the narrow pore levels. Lys·· further escorted Na+ to the inner rings and in several steps mutual dispositions of the DEKA residues are similar to those seen in cryo-EM structures. Analogous results were obtained in models with DEKA mutants, which have high, but not low Na/K selectivity. When K+ was pulled through the pore, it was also chelated between Glu- and Lys··, but respective distances were expectedly larger and K+ energy was higher than in models with Na+. The computations suggest that salt-bridged Lys+ and Glu- block the pore. Approaching Na+ would knock-out H+, squeeze between Glu- and Lys·· and move down escorted by Lys··, whereas the displaced H+ would stay nearby in an H-bond involving Glu or/and Asp. When Na+ leaves the outer pore, Lys·· would be re-protonated and rejoin Glu- to complete the permeation cycle. Supported by NSERC (RGPIN-2020-07100) and RSF (17-15-01292-П).