Modeling structure and spectra of the kindling fluorescent protein asFP595

Abstract

Modern computational approaches based on quantum mechanical methods to characterize structures and optical spectra of biological chromophores in proteins are intensively used to gain knowledge of events occurring upon of their photoexcitation. Primary attention is paid to the species from the family of the green fluorescent protein applied as biomarkers in living cells. We apply quantum chemical approaches for accurate calculations of the structures of the chromophore binding pockets and to estimate spectral bands corresponding to the S₀-S₁ optical transitions of the intriguing kindling protein asFP595. Its precursor, the chromoprotein asCP from the sea anemony <i>Anemonia sulcata</i> is characterized by distinctive spectral properties: at low light intensities the wild-type protein is weakly fluorescent with the very low quantum yield, however, high intensity irradiation with green light leads to a drastic increase of quantum yield. This phenomenon is now termed "kindling". In simulations, the model system is designed as a molecular cluster constructed on the basis of available crystal structures of the related protein. The equilibrium geometry of the cluster is optimized using density functional theory approximations. The vertical excitation energies corresponding to the S₀-S₁ transitions are computed by using the semiempirical ZINDO technique. A special attention is paid to evaluate effects of point mutations in the vicinity of the chromophore group. Theoretical data provide important information on the chromophore properties aiming to interpret the results of experimental studies and applications of this fluorescent protein.