Analysis of the selectivity filter of the voltage-gated sodium channel NavRh

Abstract

NaChBac is a bacterial voltage-gated sodium (Na v ) channel that shows sequence similarity to voltage-gated calcium channels. To understand the ion-permeation mechanism of Na v channels, we combined molecular dynamics simulation, structural biology and electrophysiological approaches to investigate the recently determined structure of Na v Rh, a marine bacterial NaChBac ortholog. Two Na + binding sites are identified in the selectivity filter (SF) in our simulations: The extracellular Na + ion first approaches site 1 constituted by the side groups of Ser181 and Glu183, and then spontaneously arrives at the energetically more favorable site 2 formed by the carbonyl oxygens of Leu179 and Thr178. In contrast, Ca 2+ ions are prone to being trapped by Glu183 at site 1, which then blocks the entrance of both Na + and Ca 2+ to the vestibule of the SF. In addition, Na + permeates through the selective filter in an asymmetrical manner, a feature that resembles that of the mammalian Na v orthologs. The study reported here provides insights into the mechanism of ion selectivity on Na + over Ca 2+ in mammalian Na v channels.

Bacterial Voltage-Gated Sodium Channels (BacNaVs) from the Soil, Sea, and Salt Lakes Enlighten Molecular Mechanisms of Electrical Signaling and Pharmacology in the Brain and Heart

“…1c) provided crystallographic evidence for an inner ion binding site (Fig. 3d) formed from the backbone carbonyls of Leu (-1) and Thr (-2) at the C-terminal end of the P-helix that could be occupied by a partly hydrated calcium ion 39 , a barium ion 97 , or a rubidium ion 97 . Electron density for a partially hydrated calcium ion coordinated by the SF (+1) serine in the Na V Ae1p structure provided the first direct crystallographic evidence for an outer ion binding site at the mouth of the selectivity filter 41 (Fig.…”

Molecular basis of ion permeability in a voltage‐gated sodium channel

“…The resolution of the first such structure (3.5 Å), however, was too low to determine the details of the sites of the ions in the SF, whilst the latter structures contained channel blocker ligands which interfered with ion binding. The sodium ion binding site locations and mechanisms for ion selectivity have also been predicted by a number of molecular dynamics (MD) studies, although they differ considerably in their details (Amaral et al , 2012; Chakrabarti et al , 2013; Stock et al , 2013; Ulmschneider et al , 2013; Xia et al , 2013; Zhang et al , 2013; Boiteux et al , 2014; Furini et al , 2014). …”

Voltage-Gated Sodium Channels

“…In Na V Rh, all simulations with variable concentrations of Ca 2+ show persistent binding at S1; strong binding determined by electrostatic interactions with Glu183, as well as interactions with S180 result in an insurmountable energy barrier (~11.38 kcal/mol), hindering progression deeper in the selectivity filter (Zhang et al, 2013). Therefore, the authors suggest this site confers selectivity in Na V Rh.…”

“…In Na V Rh, due to the non-conserved selectivity filter sequence, the characteristic inner 'EEEE ring' and outer 'SSSS ring' at the extracellular mouth are in reversed positions. Despite the supposed collapsed conformation of these residues, reorientation at the side chain of the inner ring (S181) leads to spontaneous opening of the selectivity filter in the first stages of the simulation (Zhang et al, 2013).…”