Time scales and pathways for kinetic energy relaxation in solvated proteins: Application to carbonmonoxy myoglobin

Using a novel method for determining the coordinate friction for systems th at possess bounded diffusion, the rates of kinetic energy partitioning for various elements of solvated carboxy-myoglobin were calculated. Energy redi stribution within the heme group and solvent is found to be rapid compared with energy redistribution within the protein. Within the protein, charged residues exhibit much more rapid dispersal than neutral residues. The resul ts suggest that a possible doorway for energy release from the photolyzed h eme involves the interaction of its isopropionate groups with the neighbori ng solvent molecules. The results are analyzed as a function of atom type, protein residue and residue group (charged, polar, aliphatic, and aromatic) leading to general observations relating to the inherent inhomogeneity in the spatially dependent relaxation rate of the solvated protein. The comput ational results are used to analyze a variety of estimates of the internal friction, viscosity or damping invoked to interpret experimental measures o f protein dynamics. The concluding discussion includes speculations on the origin of internal viscosity in proteins. (C) 2000 American Institute of Ph ysics. [S0021-9606(00)52141-2].