Refinement and Validation of Atomic Models of the Kv1.2 Potassium Channel Through Molecular Dynamics and Gating Charge Calculations

Abstract

Voltage-gated potassium (Kv) channels are membrane proteins that respond to changes in transmembrane potential through voltage-sensing domains (VSD). These domains are composed of highly charged transmembrane segments that move in response to changes in electric potential and control opening of the ion conduction gate. Complete atomistic models of Kv1.2, in the open and closed states, have been constructed using the structure prediction program Rosetta and available crystallographic structures. By means of molecular dynamics simulations, the two models are refined in the presence of an external voltage bias leading to stable conformations of the channel in an explicit membrane-solvent environment. Salt-bridge interactions stabilizing the VSD are identified within the VSD and between the charged residues of the VSD and lipid head groups. Conformational changes in the VSD result in the transfer of electric charge across the membrane, that can be measured as a gating current. The magnitude of the gating charge in Kv1.2 potassium channel is calculated from more than 1microsecond of all-atom molecular dynamics simulation. Free energy calculations are performed to determine the individual contribution of several (nine) charged residues of the VSD to the gating charge. The total gating charge obtained for the refined models of the channel is ∼10.5e, indicating that the refined model of the closed resting state most likely represents an intermediate conformation that precedes closing of the channel. Through steered molecular dynamics (SMD) simulations we identify a closed conformation of the channel, corresponding to a gating charge of 12.7e, in accord with experimental values obtained for the Shaker potassium channel.