Kinetics of carbon monoxide migration and binding in solvated myoglobin as revealed by molecular dynamics simulations and quantum mechanical calculations.
By using multiple (independent) molecular dynamics (MD) trajectories (about 500 ns in total) of photolized carbon monoxide (CO) within solvated myoglobin, a quantitative description of CO migration and corresponding kinetics is obtained. MD results combined with previously reported quantum mechanical calculations on the CO-heme binding-unbinding reaction step in myoglobin allowed construction of a detailed quantitative model, shedding light on the kinetic mechanism and relevant steps of CO migration and geminate binding. Finally, the obtained (unbiased) theoretical-computational model is critically compared with the available computational and experimental data for myoglobin in solution.
D'Abramo
Marco
M
Institut de Recerca Biomèdica, and Barcelona Supercomputing Center Jordi Girona 29, Barcelona, Spain.
Di Nola
Alfredo
A
Amadei
Andrea
A
D002248:Carbon Monoxide / Q000737:chemistry*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009211:Myoglobin / Q000737:chemistry*; D011485:Protein Binding; D011789:Quantum Theory
D009211:Myoglobin; D002248:Carbon Monoxide