Abstract
Many protein functions are coupled to proton transfer, yet the underlying mechanisms remain extremely difficult to resolve by experiment or conventional molecular dynamics (MD) simulations. The human voltage-gated proton channel HV1 (hHV1) plays key roles in human physiology, but how voltage and pH together drive its activation remains unresolved. Experimental structures of hHV1 are limited to the X-ray structure of a mouse chimera and NMR models of a truncated hHV1, both representing an intermediate resting state. Here we determine the activation pathway of hHV1, together with structural models of its resting and activated states, using an approach that integrates all-atom continuous constant-pH MD (CpHMD), weighted-ensemble (WE) path sampling, and AlphaFold modeling. Starting from an AlphaFold model selected for consistency with resting-state experimental data, over 100 μs of simulations reveal a mechanism in which transmembrane voltage, assisted by proton titration, drives an outward displacement of the transmembrane segment S4 accompanied by a one-click reorganization of countercharge pairings. These events are enabled by a delicately balanced electrostatic landscape and pH-modulated breathing motions in the resting state that prime the channel for protonation-state switches upon voltage sensing, a principle that may underlie other proton-coupled voltage-gating processes. The simulations also uncover lipid-binding sites at which POPG selectively stabilizes the S4-up conformation, whereas POPE can stabilize either state. These predictions are validated against extensive electrophysiology, mutagenesis data, and new smFRET experiments, which support the one-click S4 displacement and the lipid effects. WE-CpHMD, implemented in the AMBER package, is applicable to other proton-coupled processes that remain elusive.