Khrenova M G, Nemukhin A V, Grigorenko B L, Krylov A I, Domratcheva T M
Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation, N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation, Department of Chemistry, University of Southern California, Los Angeles, California 90089, and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany.
J Chem Theory Comput. 2010 Aug 10;6(8):2293-302. doi: 10.1021/ct100179p.
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 QM(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÷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).
利用黄素发色团光感受器蛋白进行蓝光光致反应的推测机制主要基于X射线晶体学和光谱学研究结果。特别有价值的是在形成信号（光诱导）状态时在光学和振动光谱中观察到的谱带位移。然而，同一组实验数据却引发了相互矛盾的解释，暗示了暗态和信号态的不同结构。为了验证涉及黄素发色团附近保守Gln残基的旋转/互变异构转变的光诱导变化的具体机制，我们对模拟黄素蛋白AppA的BLUF结构域的模型系统的平衡结构、振动和吸收带进行了精确的量子化学计算。从代表性的分子动力学（MD）快照开始，采用QM（B3LYP/cc-pVDZ）/MM（AMBER）方法进行几何优化和振动频率计算。MD模拟从AppA蛋白的现有晶体结构开始。使用缩放的相反自旋组态相互作用单取代SOS-CIS（D）方法进行垂直激发能计算，该方法能够有效处理大分子系统中的激发态。计算得到的分子结构以及光谱位移（吸收光谱中红移12÷16 nm，黄素C4═O振动模式下移25 cm(-1)）与实验结果非常吻合，有力地支持了Domratcheva等人提出的机制（《生物物理杂志》2008年，94卷，3872页）。
