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

The outer pore of Navl.x channels is lined by the selectivityfilter 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 Navl.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 center dot center dot "dunked" to the inner rings. When Na+ was pulled through the outer pore, it was inevitably chelated by Glu and Lys center dot center dot at the narrow pore levels. Lys center dot center dot 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 center dot center dot, 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 center dot center dot, and move down escorted by Lys center dot center dot , whereas the displaced H+ would stay nearby in a H-bond involving Glu or/and Asp. When Na+ leaves the outer pore, reprotonated Lys center dot center dot would rejoin Glu to complete the permeation cycle.