Multi-Microsecond Molecular Dynamics Simulations of the HV1 Proton Channel

Abstract

The voltage-gated proton channel, Hv1, is a membrane protein that plays roles in a variety of cellular processes including proton extrusion, pH regulation, and the production of reactive oxygen species. Like the voltage-gated potassium channels, it contains a voltage-sensing domain (VSD) but lacks a separate pore domain. The crystal structure of a chimera of mouse Hv1 (mHv1cc) in a non-native trimeric construct was recently reported. In order to characterize the structure and transition between the closed and open states of Hv1 in a realistic membrane environment, we used multi-microsecond molecular dynamics (MD) simulations. Specifically, we carried out MD simulations of the mouse chimera trimer and monomer in a fully hydrated POPC bilayer, as well as human Hv1 (hHv1; starting from a homology model built from mmHv1cc). We found that all three of the constructs considered (mHv1cc trimer, mHv1cc monomer, and hHv1 monomer) were stable at zero potential on the timescale of several microseconds. Additionally, the monomer hHv1 model was subjected to hyperpolarizing and depolarizing transmembrane potentials. The structure underwent only minor changes under hyperpolarizing potential. However, under a depolarizing potential, we observed a large conformational change of the protein through the outward movement of the S4 helix by approximately 8 Angstroms. This transition led to a rearrangement of the internal salt-bridge network and allowed more waters into the pore as well as an increased stability in the hydrogen bond pathways, suggesting that it is an open state. We validated our atomistic hHv1 models with a variety of experimental data, including gating charge measurements and binding of the known inhibitor, 2-GBI, at the intracellular side of the selectivity filter. Additional simulations of selected mutants under a depolarizing potential constructed from the generated open state model suggest lower proton conductivity.