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. (C) 2004 Elsevier B.V. All rights reserved.