title: Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin.
abstract: Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3-7 cm(-1) (compared to the experimental value of 10 cm(-1)) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe...CO and Fe...OC) is 0.3 kcal mol(-1) and agrees well with the experimentally estimated value of 0.29 kcal mol(-1). A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.
authors.affiliation: Department of Chemistry, University of Basel, CH-4056 Basel, Switzerland.
authors.forename: David R
authors.initials: DR
authors.lastname: Nutt
authors.forename: Markus
authors.initials: M
authors.lastname: Meuwly
mesh_terms: D001665:Binding Sites; D001703:Biophysics / Q000379:methods; D002244:Carbon; D002248:Carbon Monoxide; D006418:Heme / Q000737:chemistry; D008024:Ligands; D008027:Light; D008956:Models, Chemical; D008958:Models, Molecular; D009154:Mutation; D009211:Myoglobin / Q000737:chemistry*; D010100:Oxygen; D011487:Protein Conformation; D012984:Software; D013997:Time Factors
chemical_list: D008024:Ligands; D009211:Myoglobin; C018013:carboxymyoglobin; D006418:Heme; D002244:Carbon; D002248:Carbon Monoxide; D010100:Oxygen