Unveiling Potential Binding Sites in the Hv1 Four Helix Bundle

Abstract

Hv1 is a voltage-sensor protein that plays essential roles in proton conduction, pH homeostasis and production of high-level superoxide by phagocytes. Unregulated Hv1 activity has pathological implications, such as hyper-proliferation of cancer cells and exacerbation of brain damage in ischemic stroke.Unlike other voltage-gated ion channels, Hv1 is composed by two subunits each containing a voltage-sensing domain (VSD) and lacking the pore domain. On the other hand, Hv1 shares striking similarities with the M2 proton channel of the influenza A virus (A/M2): in both cases a bundle of four helices lines a proton conduction pathway and positively charged “fragment-like” molecules act as blockers.Starting from the recently solved structure of Hv1, we combined homology modeling, molecular dynamics simulations and site finding methods to unveil potential binding pockets in the most relevant conformational states. We discovered that, similarly to the case of A/M2, the distribution of water molecules inside the channel lumen is state-dependent, offering a rationale to designing novel pore blockers.