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

• Published in: Proceedings of the National Academy of Sciences
• Main Authors: Ruscio, Jory Z., Kumar, Deept, Shukla, Maulik, Prisant, Michael G., Murali, T. M., Onufriev, Alexey V.
• Format: Text
• Language: English
• Published: National Academy of Sciences 2008
• Subjects: Physical Sciences; Sperm whale
• Online Access: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2453746; http://www.ncbi.nlm.nih.gov/pubmed/18599444; https://doi.org/10.1073/pnas.0710825105

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 μs 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 voids available for ligand migration. The computations are performed both in sperm whale myoglobin wild-type and in sperm whale V68F myoglobin mutant, which is experimentally known to slow ligand-binding kinetics. On the basis of these independent, but mutually consistent ligand migration and transient void computations, we find that there are two discrete dynamical pathways for ligand migration in myoglobin. Trajectory hops between these pathways are limited to two bottleneck regions. Ligand enters and exits the protein matrix in common identifiable portals on the protein surface. The pathways are located in the “softer” regions of the protein matrix and go between its helices and in its loop regions. Localized structural fluctuations are the primary physical origin of the simulated CO migration pathways inside the protein.