Probing Polar Solvation Dynamics in Proteins: A Molecular Dynamics Simulation Analysis

Measurements of time-​resolved Stokes shifts on picosecond to nanosecond time scales have been used to probe the polar solvation dynamics of biol. systems. Since it is difficult to decomp. the measurements into protein and solvent contributions, computer simulations are useful to aid in understanding the details of the mol. behavior. Here the authors report the anal. of simulations of the electrostatic interactions of the rest of the protein and the solvent with 11 residues of the Ig binding domain B1 of protein G. It is shown that the polar solvation dynamics are position-​dependent and highly heterogeneous. The contributions due to interactions with the protein and with the solvent are detd. The solvent contributions are found to vary from negligible after a few picoseconds to dominant on a scale of hundreds of picoseconds. The origin for the latter is found to involve coupled hydration and protein conformational dynamics. The resulting microscopic picture demonstrates that a wide range of possibilities have to be considered in the interpretation of time-​resolved Stokes shift measurements.