The Journal of Biological Physics and Chemistry

Normal mode analysis and calculation of the cooling rates of the chromophore vibrations during isomerization of photoactive yellow protein

Gia G. Maisuradze,* Xin Yu and David M. Leitner

Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, NV 89557, USA

Photoactive yellow protein (PYP) is a water-soluble photoreceptor protein consisting of 125 amino acids with a p-coumaric acid anion cofactor. Recent ultrafast studies of fluorescence decay of PYP and several mutants by Mataga et al. revealed coherent oscillations at about 140 cm^-1 and 50 cm^-1 largely attributed to chromophore motions and protein matrix vibrations, respectively. Using normal mode analysis with a new force field, with an adjusted torsional part obtained by fitting the resulting vibrational modes of the isolated chromophore up to 200 cm^-1 to those of ab initio Density Functional Theory (DFT) calculations for PYP in the S₁ excited state, we find that modes with frequencies near 130 cm^-1 project strongly onto the chromophore and largely correspond to isomerization of the chromophore, strongly enhanced in this direction compared to nearby vibrational modes of the isolated chromophore. We also calculate rates of vibrational cooling of the chromophore and find that this process probably influences the photoisomerization kinetics. We present here an analysis of the vibrations of PYP and a mutant, with emphasis on the dynamical coupling between the chromophore and the surrounding protein matrix, calculated by means of the new force field. We also discuss molecular dynamics (MD) simulations for hydrated PYP and the influence of hydration on energy transfer and dynamical coupling between the chromophore and surrounding protein matrix.

Keywords: fluorescence decay, mutant, new force field, vibrational energy flow.