Molecular dynamic simulation of the Kv1.2 voltage-gated potassium channel in open and closed state conformations

We performed 45 ns atomistic force field based molecular dynamics (MD) simulations to explore the structure and dynamics of the Kvl.2 voltage-dependent potassium ion channel in both open and closed state conformations. The Kvl.2 crystal structure (PDB 2A79) based open state model and homologically derived closed state model are embedded in a hydrated lipid membrane. We present a detailed analysis of the protein stability, the environment of the gating-charge-carrying residues, the salt bridge within the voltage sensor, S4 segment helix movement, helix interaction between S4-S5 linker and S6, interaction between subunits, and interaction between protein and lipid membrane. The four subunits of the channel lost the symmetry from the starting structure during the simulation, especially the voltage sensors. According to our comparative analysis of the open and closed state conformations, S4 in our simulation behaves more near the screw helix model except for the tilt action. The S4 segment azimuthal rotation angle difference between two conformations shifts about 60° after being embedded in a membrane environment. The S4-S5 linker helix remains stable. The contact area between the S4 and S5 from the adjacent subunit increases after transition to the closed state from the open state. The current investigation provided valuable information to our understanding of the structure and dynamics of membrane-associated helices and the gating mechanism of the voltage-dependent potassium ion channel of the Kv channel.