Chromophore vibrations during isomerization of photoactive yellow protein: analysis of normal modes and energy transfer

Ultrafast studies of fluorescence decay of photoactive yellow protein (PYP) and several mutants by Mataga et al. [Chem. Phys. Lett. 352 (2002) 220] reveal coherent oscillations of about 140 cm−1, attributed to largely chromophore motions, and 50 cm−1, corresponding more to protein matrix vibrations. We identify these vibrations by normal mode analysis. Vibrational modes near 130 cm−1 are relatively localized to the chromophore, consistent with interpretation of the ultrafast data. Dynamical coupling between the chromophore and protein matrix enhances twisting of the thioester group near 130 cm−1 compared to the isolated chromophore. We also compute rates of vibrational energy transfer rates in PYP and discuss its influence on the photoisomerization kinetics.