Dynamics, energy transfer, and the B-states of carbon monoxide in myoglobin

Abstract

Molecular dynamics simulation is used to study the photodissociation of the ligand carbon monoxide from the protein myoglobin with particular emphasis on the dynamics of the unbound ligand. The study seeks to interpret experimental data on the presence of binding sites in the heme pocket (corresponding to three shifts in the ligand vibrational frequency) which are reached by the ligand soon after dissociation, remain stable for upwards of 50 ps, and whose relative populations are strongly dependent on pH. The stochastic boundary approximation is employed to isolate the protein’s heme pocket in the presence of solvent at two effective pH states. A new three-site model for carbon monoxide is presented. The affect of the protonation state model for carbon monoxide is presented. The affect of the protonation state of the distal histidine on the ligand dynamics is examined. Analysis of the center-of-mass, rotational, and vibrational dynamics of the ligand agrees well with the experimental data of Anfinrund, Han and Hochstrasser [Proc. Natl. Acad. Sci. USA 86, 8387 (1989)1. The role of the protonation state of the distal histidine and its effect on the dynamics and conformation of the unbound ligand is discussed. The possibility that hydrogen bonding of the ligand to the distal histidine may account for ligand vibrational frequency shifts observed experimentally is explored thorough ab initio frequency calculations.