Distribution function implied dynamics versus residence times and correlations: solvation shells of myoglobin.
The dynamics of water at the protein-solvent interface is investigated through the analysis of a molecular dynamics simulation of metmyoglobin in explicit aqueous environment. Distribution implied dynamics, harmonic and quasi-harmonic, are compared with the simulated macroscopic dynamics. The distinction between distinguishable solvent molecules and hydration sites developed in the previous paper is used. The simulated hydration region within 7 A from the protein surface is analyzed using a set of 551 hydration sites characterized by occupancy weights and temperature B-factors determined from the simulation trajectory. The precision of the isotropic harmonic and anisotropic harmonic models for the description of proximal solvent fluctuations is examined. Residence times and dipole reorientation times of water around the protein surface are compared with NMR and ESR results. A correlation between diffraction experiment quantities such as the occupancy weights and temperature factors and the residence and correlation times resulting from magnetic resonance experiments is found via comparison with simulation.
Lounnas
V
V
Department of Chemistry, University of Houston, Texas 77204-5641.
Pettitt
B M
BM
D000818:Animals; D016880:Anisotropy; D001665:Binding Sites; D003198:Computer Simulation; D008786:Metmyoglobin / Q000737:chemistry*; D008956:Models, Chemical; D015394:Molecular Structure; D011487:Protein Conformation; D012997:Solvents; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D012997:Solvents; D014867:Water; D008786:Metmyoglobin