The human voltage-gated proton channel Hv1 has an intriguing architecture, as (i) its voltage-sensing unit contributes to the proton permeation pathway and (ii) the single channel proton flux is too large to be supplied solely by diffusion from the aqueous surroundings, and it likely involves both titratable residues and protein-bound water molecules. The paths followed by protons being transferred through the channel, and the identity of the protein groups that can transiently bind protons, remain unclear. To investigate the dynamic hydrogen-bond paths sampled at the channel mouths and inside the pore we carried out extensive atomic-level molecular dynamics simulations and graph-based analyses. We found that the inter-helical region of the channel hosts an extensive water-mediated hydrogen-bond network that includes the key aspartic residue essential for proton selectivity and additional titratable sidechains. We implemented a graph-based protocol to identify continuous hydrogen-bond paths that can connect the aspartic residue to either side of the membrane. We report that the internal H-bond network connects to lipid headgroups at both membrane interfaces, which could provide a mechanism for (i) the surrounding lipid membrane to influence the protein conformational dynamics and the internal hydrogen-bond network, and (ii) channeling rapidly diffusing protons from the membrane surface into and out of the Hv1 pore.

Dynamic hydrogen-bond network

Proton channel

Lipid-protein hydrogen bonding

Hv1

© 2025 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.