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.