Possible Mechanism of Ion Selectivity in Eukaryotic Voltage-Gated Sodium Channels

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. Here, contacts involving DEKA residues in 15 cryo-EM structures of Nav1.x channels were analyzed and Monte Carlo (MC) energy minimizations of models with the DEKA residues in different protonation states, with or without Na+ or K+, were 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 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 a H-bond involving Glu or/and Asp. When Na+ leaves the outer pore, reprotonated Lys•• would rejoin Glu to complete the permeation cycle.