A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment.
An analysis of a molecular dynamics simulation of metmyoglobin in an explicit solvent environment of 3,128 water molecules has been performed. Both statics and dynamics of the protein-solvent interface are addressed in a comparison with experiment. Three-dimensional density distributions, temperature factors, and occupancy weights are computed for the solvent by using the trajectory coordinates. Analysis of the hydration leads to the localization of more than 500 hydration sites distributed into multiple layers of solvation located between 2.6 and 6.8 A from the atomic protein surface. After locating the local solvent density maxima or hydration sites we conclude that water molecules of hydration positions and hydration sites are distinct concepts. Both global and detailed properties of the hydration cluster around myoglobin are compared with recent neutron and X-ray data on myoglobin. Questions arising from differences between X-ray and neutron data concerning the locations of the protein-bound water are investigated. Analysis of water site differences found from X-ray and neutron experiments compared with our simulation shows that the simulation gives a way to unify the hydration picture given by the two experiments.
Lounnas
V
V
Department of Chemistry, University of Houston, Texas 77204-5641.
Pettitt
B M
BM
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D003198:Computer Simulation; D003461:Crystallography; D018360:Crystallography, X-Ray; D008786:Metmyoglobin / Q000737:chemistry* / Q000235:genetics; D008956:Models, Chemical; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009502:Neutrons; D011487:Protein Conformation; D012997:Solvents; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D012997:Solvents; D014867:Water; D008786:Metmyoglobin