Molecular Mechanism Of Ion Selectivity In The Voltage- Gated Sodium Channel

Voltage-gated sodium(Nav) channels belong to voltage-gated ion channel(VGIC) superfamily, and play significant roles in the mammalian neuronal signaling. Mutations and dysfunction of Nav channels may cause a series of critical human diseases. Prokaryotic Nav channels have high structural and functional homology with mammalian Nav channels. Several crystal structures of bacteria sodium channels have been determined recently, which enables the functional studies of Nav channels on the molecular level. In this work, we adopted the structure of Nav Rh, a marine bacteria Nav channel, to investigate the mechanisms of ion permeation and ion selectivity of Nav channels using molecular dynamics simulations.We performed equilibrium simulations and identified two cation binding sites by calculating the free energy profiles for single ions(Na+, Ca2+ or K+) to permeate through the selectivity filter(SF) of Nav Rh. At the first site that is located in the extracellular side, Glu183 and Ser181 attract ions using their side groups, while the ions interact with the backbone carbonyl group of Leu179 and Thr178 at the second site. According to our results, periplasmic Na+ ions can pass the SF of Nav Rh easily. In contrast, the free permeation of Ca2+ ions is precluded by a high free energy barrier present between the two sites, which mainly arises from the extremely strong electrostatic interaction between Ca2+ and the negatively charged Glu183 side chains at site 1. The free energy profile of K+ ions is similar to that of Na+ ions, thus consistent with the experimental observation that the wild type(WT) Nav Rh only possesses weak Na+/K+ selectivity.Previous mutational study shows that the Na+/K+ selectivity in mammalian Na_v channels is mainly determined by the key residues(Lys and Asp/Glu) at the constriction site within the SF, a site that is equivalent to the Ser180 residues in the prokaryotic homotetramer Nav channel Nav Rh. Na+/K+ selectivity in mammalian Nav channels requires the presence of Lys and at least one of Asp and Glu. Although essential in selectivity, these key residues have not been studied by molecular simulations previously. We constructed a structural model for the mammalian Nav channels by mutating Ser180 in the WT Nav Rh and performed a series of molecular dynamics simulations on this model. A highly Na+ selective site was identified at the constriction site, and the roles of Lys and Asp/Glu in Na+/K+ selectivity were interpreted by our work.