Mechanism and energetics of charybdotoxin unbinding from a potassium channel from molecular dynamics simulations.

ABSTRACT: Ion channel-toxin complexes are ideal systems for computational studies of protein-ligand interactions, because, in most cases, the channel axis provides a natural reaction coordinate for unbinding of a ligand and a wealth of physiological data is available to check the computational results. We use a recently determined structure of a potassium channel-charybdotoxin complex in molecular dynamics simulations to investigate the mechanism and energetics of unbinding. Pairs of residues on the channel protein and charybdotoxin that are involved in the binding are identified, and their behavior is traced during umbrella-sampling simulations as charybdotoxin is moved away from the binding site. The potential of mean force for the unbinding of charybdotoxin is constructed from the umbrella sampli

SUBMITTER: Chen PC 

PROVIDER: S-EPMC2711292 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature