Paper Citing VMD - Abstract
Khienova, M. G., Nemukhin, A. V., Grigorenko, B. L., Krylov, A. I., Domratcheva, T. M.
Quantum Chemistry Calculations Provide Support to the Mechanism of the Light-Induced Structural Changes in the Flavin-Binding Photoreceptor Proteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:2293-2302, AUG 2010 2010
The proposed mechanisms of photoinduced 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 OM(B3LYP/cc-pVDZ)/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 scaled opposite spin configuration interaction with single substitutions 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 12 divided by 16 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)
