Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study.

A molecular dynamics simulation of lysozyme is used to examine the fluorescence depolarization of tryptophan residues on the picosecond time scale. The calculated time dependence of fluorescence emission anisotropy for the six tryptophans in lysozyme exhibits a wide variety of motional behavior that should correspond to the range expected more generally for tryptophan residues in proteins. It is found that some tryptophans are highly mobile with a large fluorescence anisotropy decay on the picosecond time scale while others are essentially rigid due to the presence of the protein matrix. Further, it is demonstrated that correlations among the internal degrees of freedom (e.g., dihedral angles) play an important role in the observed decay behavior; this suggests that care has to be used in interpreting experimental results in terms of simple motional models. Because the available experimental time resolution is limited to the nanosecond time scale, only the effective zero-time anisotropy can be compared with the calculated values. The results suggest that the study of fluorescence depolarization with femtosecond lasers would provide new insights into the short time dynamics of amino acid side chains in proteins.