Pore Gating of K+ Channels Studied by Essential Dynamics Simulations using the Simplified Bacterial K+ Channel KcsA

Abstract

Voltage gated K+ channels open and close in response to voltage changes. While crystal structures capture a limited number of gating conformations (open, closed), the transition steps and mechanism are still unknown. A limited number of voltage gated potassium channels structures in either open or closed conformation have been crystallized. Since the bacterial K+ channel KcsA has been crystallized in open, intermediate (Cuello et al., 2010) and closed (Zhou et al., 2001) states, this channel offers an ideal model for pore gating simulations. Consequently, we applied essential dynamics simulations to study the gating pathway and energetics underlying pore gating. Essential dynamics simulations were performed at timescales ranging from 1 to 100 ns. Gating simulations were considered complete when the RMSD was below 1.5 A to the target structure. This criterion was reached in most runs, however shorter simulation times usually resulted in lower RMSD values. In agreement with structural data (Cuello et al., 2010), all available KcsA transition structures (PDB identifier: 3fb5, 3fb6, 3f7y) were sampled with our essential dynamics protocol. Furthermore, molecular dynamics runs revealed that channel opening and closing sampled the same conformations along the transition pathway. Removal of pH-Sensor residues (H25, E120, R121, R122, H124) led to spontaneous channel openings on the nanosecond timescale. These unbiased opening simulations sampled the same conformations as our essential dynamics simulations, further supporting the validity of our method. Finally, umbrella sampling was used to estimate the energy profiles of the various gating states and the transition pathways of WT and mutant channels. As expected, the energy needed to open the channel is significantly decreased in the pH-Sensor deleted KcsA.