Molecular Dynamics Simulation of the Kv1.2 Potassium Channel

Abstract

Voltage-gated ion channels are membrane proteins that open and close in response to voltage changes across the membrane. Voltage-gated potassium (Kv) channels are composed of two structurally and functionally separate domains, a voltage-sensing domain (VSD) and the ion conducting pore (PD). The voltage-sensing domain is comprised of four transmembrane segments that are highly charged and move in response to changes in the electric potential resulting in opening of the channel. We have developed complete models of the Kv1.2 channel in the open and closed state using the homology, de novo, and domain assembly methods of the structure prediction program ROSETTA. Molecular dynamics (MD) simulations were carried out to refine selected candidates of the open and closed state models of Kv1.2 in an explicit water-membrane environment. Each model was simulated for 100ns in the presence of a positive or negative voltage using the program NAMD. The magnitude of the gating charge that is transferred across the membrane upon opening of the channel is calculated based on 500ns of MD simulations of the full-channel and the isolated VSDs. In addition FEP simulations were performed to calculate the free energy of neutralizing (transmembrane) charged residues on the voltage-sensing helices, and to determine the fraction of the transmembrane voltage acting on each residue. The contribution of several charged residues (on the S4 and S2 segments) to the gating charge was then obtained by calculating the “electric” displacement of each amino acid side chain in the external field. The results show that the transmembrane electric field is focused inside the voltage sensor domains and that the gating charge arises mainly from the three positively charged residues located on the S4 segment.