Structural Modeling of Intermediate States of the Gating Pore of NaChBac

Abstract

Voltage-gated sodium channels initiate action potentials in excitable cells. Despite progress in determining the structures of voltage-gated potassium channels, the high-resolution structure of the voltage-gated sodium channels remains unknown. We used the Rosetta-Membrane method (Yarov-Yarovoy et al. Proteins 62, 1010, PNAS 103, 7292) and experimental data suggesting proximity between E70 in S2 and R4 in S4 during activation of NaChBac to construct structural models of intermediate states during channel gating. The structure of the Kv1.2-Kv2.1 chimera channel in the open state (Long et al. (2007) Nature 450, 376) was used as a template and proximity between Cβ atoms of E70 in S2 and R4 in S4 was favored during modeling. The resulting structural models suggest a molecular mechanism of the voltage-dependent activation of NaChBac in which S4 rotates clockwise (as viewed from the extracellular side of the membrane) and translates outward, as proposed in the ‘sliding helix’ model of gating, while gating-charge-carrying arginines in S4 sequentially interact with negatively charged residues in the S1, S2, and S3 segments. Transition through a local 3-10 helical conformation of a short segment of S4 containing two gating-charge-carrying arginines in the narrow part of the gating pore is required for simultaneous interaction with their ion pair partners during activation. The side chain of highly conserved F67 in S2 is oriented sideways away from the gating pore to allow the long side chains of arginines in S4 to pass through the middle of the gating pore. Outward motion of the S4 segment is coupled to lateral movement of the S4-S5 linker and movements of the S5 and S6 segments that open the intracellular gate of the pore-forming module. Supported by NIMH Grant K01 MH67625 (to V.Y.-Y.) and NIH Grant R01 NS15751 (to W.A.C.).