Nonexponential relaxation after ligand dissociation from myoglobin: a molecular dynamics simulation.
Molecular dynamics simulations of myoglobin after ligand photodissociation show that the out-of-plane motion of the heme iron has a rapid subpicosecond phase followed by a slower nonexponential process involving more global protein relaxation. Individual trajectories show rather different behavior, suggesting there is an inhomogeneous component to the relaxation. The calculated time dependence of the iron motion over 100 ps is in excellent agreement with the frequency shift of band III of the heme group [see Lim, M., Jackson, T. A. & Anfinrud, P. A. (1993) Proc. Natl. Acad. Sci. USA 90, 5801-5804]. If that the barrier to rebinding depends on the out-of-plane iron position, the time dependence obtained from the simulation can explain the nonexponential room-temperature geminate recombination of NO.
Kuczera
K
K
Department of Chemistry, Harvard University, Cambridge, MA 02138.
Lambry
J C
JC
Martin
J L
JL
Karplus
M
M
D007700:Kinetics; D008024:Ligands; D008962:Models, Theoretical; D009211:Myoglobin / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D013997:Time Factors
D008024:Ligands; D009211:Myoglobin