Quantum chemistry calculations provide support to the mechanism of the light-induced structural changes in the flavin-binding photoreceptor protein

M. Khrenova, A.V. Nemukhin, B. Grigorenko, A.I. Krylov, and T. Domratcheva
J. Chem. Theor. Comput. 6, 2293 – 2302 (2010)

The proposed mechanisms of photo-induced reactions in the blue light using flavin chromophore photoreceptor proteins are primarily based on the results of X-ray crystallography and spectroscopy studies. Of particular value are the observed band shifts in optical and vibrational spectra upon formation of the signaling (light-induced) state. However, the same set of experimental data has given rise to contradictory interpretations suggesting different structures of the dark and signaling states. To verify the specific mechanism of light-induced changes involving the rotation/tautomerization transformations with the conserved Gln residue near the flavin chromophore we performed accurate quantum chemical calculations of the equilibrium structures, vibrational and absorption bands of the model systems mimicking the BLUF domain of flavoprotein AppA. Geometry optimization and calculations of vibrational frequencies were carried out with the QM(B3LYP/ccpVDZ)/ MM(AMBER) approach starting from the representative molecular dynamics (MD) snapshots. The MD simulations were initiated from the available crystal structures of the AppA protein. Calculations of the vertical excitation energies were performed with the SOS-CIS(D) method that enables efficient treatment of excited states in large molecular systems. The computed molecular structures as well as the spectral shifts (the red shift by 15 nm in absorption and the downshift by 25 cm-1 for the C4=O flavin vibrational mode) are in excellent agreement with the experimental results lending a strong support to the mechanism proposed by Domratcheva et al. (Biophys.J. 2008, 94, 3872).

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