An α-π transition in S6 shapes the conformational cycle of the bacterial sodium channel NavAb

Abstract

Voltage gated sodium channels play an important role in electrical signaling in excitable cells. In response to changes in membrane potential, they cycle between nonconducting and conducting conformations. With recent advances in structural biology, structures of sodium channels have been captured in several distinct conformations, thought to represent different functional states. However, it has been difficult to capture the intrinsically transient open state. We recently showed that a proposed open state of the bacterial sodium channel NavMs was not conductive, and that a conformational change involving a transition to a π helix in the pore-lining S6 helix converted this structure into a conducting state. However, the relevance of this structural feature in other sodium channels, and its implications for the broader gating cycle, remained unclear. Here, we propose a comparable open state of another class of bacterial channel from Aliarcobacter butzleri (NavAb), with characteristic pore hydration, ion permeation and drug binding properties. Furthermore, we show that a π-helix transition is essential for pore opening, and that such a conformational change blocks fenestrations in the inner helix bundle. We also discover that a region in the C-terminal domain can undergo a disordering transition proposed to be important for pore opening. These results support a role for a π-helix transition in the opening of NavAb, enabling new proposals for the structural annotation and drug modulation mechanisms in this important model sodium channel.

Modulation of Pore Opening of Eukaryotic Sodium Channels by π-Helices in S6

“…11 The water density profile along the pore axis shows that the pores are continuously hydrated. Although the water density near the activation gate drops to a value below that of bulk water density (Figures 2B and S1B), it is substantially higher than that in models of the open state of bacterial channels obtained experimentally, 23,24,29 leading us to hypothesize that the presence of π-helices correlates with an increased water density. Indeed, the experimentally resolved open-state model of Nav1.5 featured two π-helixes in DI-S6 and DIII-S6.…”

“…3 More recent structures feature a short π-helix in either DI, DII, and DIII S6 or DI, DIII, DIV S6. 3,17−19 In our recent studies of bacterial Nav channels NavMs 23 and NavAb, 24 we found that introducing a short π-helical stretch in S6 of the channel resulted in the rotation of the S6 C-terminus and in increased pore hydration, allowing sodium ion permeation. This mechanism is consistent with that described in some TRP channels.…”