Distal cavity fluctuations in myoglobin: protein motion and ligand diffusion.
Experimentally, distal mutations in myoglobin substantially affect the contribution of fast and slow phases to picosecond geminate recombination of NO following flash photolysis. Earlier simulations of ligand diffusion among distal pocket mutants showed greatly differing rates of collisions between the ligands and the heme iron, suggesting that distal residues affect recombination by controlling ligand access to the iron [Gibson, Q. H., Regan, R., Elber, R., Olson, J. S., & Carver, T. (1992) J. Biol. Chem. 267, 22022-22034). In this work, molecular dynamics simulations of sperm whale myoglobin and mutations at positions 68 (E11) and 107 (G8) have been examined to investigate the structural mechanism that controls ligand diffusion and iron accessibility. Visualization of the distal ligand-accessible spaces shows a pattern of cavities (common to other hemoglobins and myoglobins) that fluctuate and interconnect due to protein motions. Access to the iron atom is highly sensitive to these fluctuations in the native structure, perhaps a reason for the strong conservation of distal residues. The positions of the helices surrounding the distal heme site were monitored to assess the involvement of more collective protein motions in ligand diffusion. Ligand migrations and collisions with the iron appear related to expansion of the distal protein matrix due to helix movements. The helices surrounding the distal site also make relative adjustments on the order of 0.5 A to accommodate the presence of a mobile diatomic ligand, suggesting a mechanism for communication between the heme site and the exterior of the protein.
Carlson
M L
ML
Department of Biochemistry and Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, USA.
Regan
R M
RM
Gibson
Q H
QH
D000818:Animals; D003198:Computer Simulation; D004058:Diffusion; D007501:Iron / Q000737:chemistry; D008024:Ligands; D008958:Models, Molecular; D009038:Motion; D009154:Mutation; D009211:Myoglobin / Q000737:chemistry* / Q000235:genetics; D014907:Whales
D008024:Ligands; D009211:Myoglobin; D007501:Iron