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 that possess bounded diffusion, the rates of kinetic energy partitioning for various elements of solvated carboxy-myoglobin were calculated. Energy redistribution 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 results suggest that a possible doorway for energy release from the photolyzed heme involves the interaction of its isopropionate groups with the neighboring 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 computational results are used to analyze a variety of estimates of the internal friction, viscosity or damping invoked to interpret experimental measures of protein dynamics. The concluding discussion includes speculations on the origin of internal viscosity in proteins.