The conformational cycle of a prototypical voltage-gated sodium channel

Abstract

Electrical signaling was a dramatic development in evolution, allowing complex single-cell organisms like Paramecium to coordinate movement and early metazoans like worms and jellyfish to send regulatory signals rapidly over increasing distances. But how are electrical signals generated in biology? In fact, voltage-gated sodium channels conduct sodium currents that initiate electrical signals in all kingdoms of life, from bacteria to man. They are responsible for generating the action potential in vertebrate nerve and muscle, neuroendocrine cells, and other cell types^1,2. Because of the high level of conservation of their core structure, it is likely that their fundamental mechanisms of action are conserved as well. Here we describe the complete cycle of conformational changes that a bacterial sodium channel undergoes as it transitions from resting to activated/open and inactivated/closed states, based on high-resolution structural studies of a single sodium channel. We further relate this conformational cycle of the ancestral sodium channel to the function of its vertebrate orthologs. The strong conservation of amino acid sequence and three-dimensional structure suggests that this model, at a fundamental level, is relevant for both prokaryotic and eukaryotic sodium channels, as well as voltage-gated calcium and potassium channels.

Figure 1.. Structure of Na_VAb.

a, Na_VAb structure in top view. Pore module, blue; voltage sensor, green; S4-S5 linker, red. b, Na_VAb structure in side view, colored as in panel a. c, Architecture of the Na_VAb pore. Glu177 side-chains (purple sticks); pore volume, grey; P loops, yellow. d, Voltage sensor. Side view illustrating the extracellular negative cluster (red, ENC), the intracellular negative cluster (red, INC), hydrophobic constriction site (purple, HCS). The Arg gating charges (R1-R4) are in blue.

Figure 2.. Comparison of Na_VAb structures in the resting state and the activated state^,.

a, Structural transition between resting/closed and activated/open states. Structures in the resting/closed state (left) and activated/open state (right) are captured from Movie S1 and illustrated as backbone cartoons with only one voltage sensor shown for clarity. S4 is green, and important sidechains in the voltage sensor are shown as sticks colored as in Figure 1. b, Gating charge movement. Four Arg gating charges R1-R4 are shown in blue, the extracellular negative cluster (ENC) of E32 and N49 and intracellular negative cluster (INC) of E59 and E80 in red. Phe in the hydrophobic constriction site (HCS) is shown in purple. S4 (green) moves outward by 11.5 Å, passing two gating charges through the HCS. Part of S3 is omitted for clarity. c, Side view of the structures focusing on S4 (green) and the S4-S5 linker (red). The S4 segment moves outward across the membrane from the resting to the activated states while the S1 to S3 segments rotate slightly but remain essentially unchanged with respect to their original transmembrane position. The S4-S5 linker is illustrated as an elbow that connects the S4 movement to gating of the pore.

Figure 3.. The activation gate and the pore in resting, activated, and inactivated states^–.

a, Solvent accessible surface of Na_VAb in the resting/closed state (left), adapted from. Interactions between the S4-S5 linker and S6 near the activation gate in the resting state (right). b, Solvent accessible surface of Na_VAb in the activated/open state (left), adapted from. Interactions between the S4-S5 linker and S6 near the activation gate in the activated state (right). The pore is tightly closed at the activation gate in the resting/closed state (red, panel a) but wide open in the activated/open state (green, panel b). The movement of the S4-S5 linker from the resting/closed state to the activated/open state unbends the elbow and causes an exchange of interactions between the S4-S5 linker residues (red) and the S6 residues (blue), which surround the activation gate formed by the S6 segments. c, Solvent accessible surface of Na_VAb in the slow-inactivated/closed state (left). Interactions between the S4-S5 linker and S6 near the activation gate in the slow-inactivated state (right). d, Structural transition between pre-open and inactivated states viewed in cross-section at three levels of the pore: top, ion selectivity filter; center S4 is green, central cavity; bottom, activation gate, adapted from.

Figure 4.. Mammalian Na_V and bacterial Na_VAb are structurally conserved.

a-b, Superposition between rat Na_V1.5 (light gray) and Na_VAb (blue) from side view (a) and bottom view (b). The fast inactivation gate and its key Isoleucine-Phenylalanine-Methionine (IFM) motif are highlighted in purple. c-d, Superposition of the selectivity filter of Na_V1.5 domains I and III (c), and domains II and IV (d) with the selectivity filter of Na_VAb from side view. e, Key specialized and conserved side chains at the selectivity filter viewed from extracellular side. Na_V1.5 uses specific “DEKA” side chains while Na_VAb uses four glutamates to partially dehydrate and conduct sodium ions. f-g, Superposition of the activation gate of Na_V1.5 domains I and III (f), and domains II and IV (g) with the activation gate of Na_VAb from side view. h, Key specialized side chains in Na_V1.5 and Na_VAb that modulate the shape and diameter of the activation gate.

Figure 5.. Drug access to the pore via the hydrophobic fenestrations.

Top view of a cross section below the selectivity filter of the pore module shows fenestrations and hydrophobic access to the drug receptor site in the central cavity of the pore. a, Fenestrations of Na_VAb in resting state, b, activated state, and c, inactivated state. d, Fenestrations of rat apo-Na_V1.5. PM, pore module.