High-Resolution Structural Modeling of Voltage-Dependent Conformational Changes in the Voltage Sensor of NaChBac

Abstract

Progress has been made in determining high-resolution structures of voltage sensors of voltage-gated ion channels in activated and/or inactivated states. However, high-resolution structures of resting and intermediate states of voltage sensors remain unknown. We constructed high-resolution structural models of resting, intermediate, and activated states of the voltage-sensing domain (VSD) of the bacterial sodium channel NaChBac using the Rosetta-Membrane computational method, the Rosetta method-based FoldIt program, the x-ray structure of the Kv1.2-Kv2.1 chimeric channel, and experimental data demonstrating sequential interactions between gating-charge-carrying arginines in S4 segment and negatively charged residues in S1, S2, and S3 segments during activation. The resulting sliding helix model suggests that the S4 is a 3-10 helix from the first or second gating-charge-carrying arginine to the fourth gating-charge-carrying arginine or S125 near its C-terminus during the conformational change between the resting and activated states. The S4 segment slides ∼10 Å through a narrow groove formed by rigid S1, S2 and S3 segments, rotates ∼30-60 degrees with respect to its own axis, and tilts sideways at a pivot point formed by a highly conserved hydrophobic region in the middle of the VSD. During S4 movement, gating-charge-carrying arginines sequentially form ion pairs and hydrogen bonds with highly conserved negatively charged and polar residues in the narrow gating pore and in the intracellular and extracellular water-accessible cavities of the VSD. Conformational changes of the intracellular half of S4 are coupled to lateral movement of the S4-S5 linker that leads to movement of the intracellular half of S5 and S6 segments and either opens or closes the intracellular gate of the ion-conducting pore. Supported by NIH R01 NS015751 to W.A.C. and P20GM076222 to D.B.