Molecular Dynamics Simulation Study of the B-States of Solvated Carbon Monoxymyoglobin

Abstract

Classical molecular dynamics simulation is employed to study the photodissociated B-states of carbon monoxymyoglobin. Four independent 10 ps dynamical trajectories of the fully solvated protein, in a box of 2988 water molecules using periodic boundary conditions, were simulated at 300 K starting from the equilibrium deoxymyoglobin structure. Two prototypical protein conformational substates, defined by the conformation of the distal histidine, were sampled from a 1.5 ns trajectory of solvated, room temperature deoxymyoglobin. The structure and ligand vibrational spectral line shapes and frequency shifts were derived from the simulation trajectories. The simulated structure of the ligand−heme complex shows that the ligand is localized under the C-ring of the heme, which is consistent with the low-temperature X-ray crystal structures of the photolyzed state [Schlichting et al. Nature 1994, 371, 808. Teng; Šrajer; Moffat Nat. Struct. Biol. 1994, 1, 701]. The ligand is found to be parallel to the heme “plane” and confined to a small region displaced from the heme iron in apparent agreement with the low-temperature X-ray crystal structures and room temperature experimental studies [Lim; Jackson; Anfinrud Science 1995, 269, 962]. Stark shifts in the ligand vibrational frequency, induced by the protein electric field in the heme pocket, are estimated using both atomic point charge models with explicit solvent and finite difference Poisson−Boltzmann calculations. Simulated ligand frequency shifts are compared with those of the experimental spectrum as a test of the accuracy of the simulated electric field in the heme pocket. The magnitudes of the induced ligand frequency shifts are in good agreement with experimental results. The largest contribution to the electric field in the heme pocket is due to the heme and proximal histidines not, as it has often been assumed, the distal histidine. The exact value of the protein electric field experienced by the ligand is well correlated with the conformation of the distal His. The dipole induced in the ligand by the protein electric field is found to make a significant contribution to the total ligand dipole moment and is not necessarily aligned with the ligand bond. The proposal that the ligand “docking site” functions to suppress CO binding is examined.