Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin.

ABSTRACT: Myoglobin is a globular protein involved in oxygen storage and transport. No consensus yet exists on the atomic level mechanism by which oxygen and other small nonpolar ligands move between the myoglobin's buried heme, which is the ligand binding site, and surrounding solvent. This study uses room temperature molecular dynamics simulations to provide a complete atomic level picture of ligand migration in myoglobin. Multiple trajectories--providing a cumulative total of 7 micros of simulation--are analyzed. Our simulation results are consistent with and tie together previous experimental findings. Specifically, we characterize: (i) Explicit full trajectories in which the CO ligand shuttles between the internal binding site and the solvent and (ii) pattern and structural origins of transient

SUBMITTER: Ruscio JZ 

PROVIDER: S-EPMC2453746 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature