Computer simulations of carbon monoxide photodissociation in myoglobin: Structural interpretation of the B states

The early diffusion processes of a photodissociated ligand (carbon monoxide) in sperm whale myoglobin and its Phe(29) mutant are studied computationally. An explicit solvent model is employed in which the protein is embedded in a box of at least 2300 water molecules. Electrostatic interactions are accounted for by using the particle mesh Ewald. Two hundred seventy molecular dynamics trajectories are computed for 10 ps, Different models of solvation and the ligand, and their influence on the diffusion are examined. The two B states of the CO are identified as "docking" sites in the heme pocket. The sites have a similar angle with respect to the heme normal, but differ in the orientation in the plane. The computational detection of the B states is stable under a reasonable variation of simulation conditions. However, in some trajectories only one of the states is observed. It is therefore necessary to use extensive simulation data to probe these states. Comparison to diffraction experiments and spectroscopy is performed. The shape of the experimental infrared spectra is computed. The overall linewidth is in an agreement with experiment. The contributions to the linewidth (van der Waals and electrostatic interactions) are discussed.