Dielectric response and vibrational energy relaxation in photoactive yellow protein: A molecular dynamics simulation study

Molecular dynamics simulations of the dielectric response and vibrational energy relaxation (VER) from the chromophore to the protein and solvent environment following photoexcitation of photoactive yellow protein are presented. The computed protein response to photoexcitation appears prominently between times of 0.1 and 0.3 ps. Contributions from individual residues to this response are analyzed. The frequency-dependent VER rate also reveals dynamic coupling between the chromophore and residues that hydrogen bond to it. Resonances in the VER rate appear at frequencies comparable to the oscillations observed in recent fluorescence decay studies.