Computational Characterization of Conformational Transitions in the Voltage-Sensing Domain of Ci-VSP

Abstract

The canonical voltage-sensing domain (VSD) is a conserved structural module that transduces the electric field across cellular membranes into defined protein motions of its charge-rich helix, the S4 segment. Up on depolarization, the VSD rearranges from the ‘resting’ (or ‘down’) state conformation into the ‘active’ (or ‘up’) state conformation, which in turn regulates the motion of downstream modules of the protein, such as opening of the pore domain of a voltage-gated ion channel or the activity of an enzyme. The voltage-sensing process has long attracted much interest and fruitful results have been reported using a variety of functional, spectroscopic and structural approaches. Recently, we solved crystal structures of the VSD of the Ciona intestinalis voltage-sensing phosphatase Ci-VSP in both it resting (Down) and activated (Up) conformations. Comparison of the two structures reveals an ∼ 5-A three-residue displacement of the S4 segment along, together with an ∼ 60° rotation around, its axis (called the one-click gating motion), while the S1-S3 segments remain fairly stable. Using 2-D self-learning umbrella sampling molecular dynamics simulations, combined with homology modeling and the string method, we have now calculated the free energy landscape governing the conformational changes of Ci-VSD. These calculations have allowed us to explore the energetic viability of further up (one-click up) and further down (two-clicks down) conformations, as potential mechanisms for additional charge translocation. These conformations should advance our understanding of the detailed mechanisms of voltage-gating and allow for the design of new experiments aimed to verify the present model of S4 movements and gating charge translocation.