A search for ligand diffusion pathway in myoglobin using a metadynamics simulation

摘要

The carbon monoxide (CO) migration pathways inside myoglobin are investigated by molecular dynamics simulations. In order to identify the pathways of migration inside the protein, we applied a metadynamics method. We succeeded in determining two main pathways from the distal pocket, where CO is initially bound, to a protein surface near a histidine gate, and to a proximal xenon trapping site, Xe1. By a careful refinement of the CO distribution obtained by the metadynamics simulation, the free energy profiles of migration pathways were evaluated. The resultant free energy barriers were found to be small compared to those computed previously.