Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43403, United States.
Departamento de Química Física, Universidad de Alcalá , E-28871 Alcalá de Henares, Madrid, Spain.
J Chem Theory Comput. 2016 Feb 9;12(2):839-50. doi: 10.1021/acs.jctc.5b00945. Epub 2016 Jan 6.
While the light-induced population dynamics of different photoresponsive proteins has been investigated spectroscopically, systematic computational studies have not yet been possible due to the phenomenally high cost of suitable high level quantum chemical methods and the need of propagating hundreds, if not thousands, of nonadiabatic trajectories. Here we explore the possibility of studying the photodynamics of rhodopsins by constructing and investigating quantum mechanics/molecular mechanics (QM/MM) models featuring reduced retinal chromophores. In order to do so we use the sensory rhodopsin found in the cyanobacterium Anabaena PCC7120 (ASR) as a benchmark system. We find that the basic mechanistic features associated with the excited state dynamics of ASR QM/MM models are reproduced using models incorporating a minimal (i.e., three double-bond) chromophore. Furthermore, we show that ensembles of nonadiabatic ASR trajectories computed using the same abridged models replicate, at both the CASPT2 and CASSCF levels of theory, the trends in spectroscopy and lifetimes estimated using unabridged models and observed experimentally at room temperature. We conclude that a further expansion of these studies may lead to low-cost QM/MM rhodopsin models that may be used as effective tools in high-throughput in silico mutant screening.
虽然不同光响应蛋白的光诱导种群动力学已经通过光谱学进行了研究，但由于合适的高精度量子化学方法成本极高，并且需要传播数百甚至数千条非绝热轨迹，因此系统的计算研究尚未成为可能。在这里，我们通过构建和研究具有简化视黄醛发色团的量子力学/分子力学（QM/MM）模型，探索了研究视蛋白光动力学的可能性。为此，我们使用在蓝细菌集胞藻 PCC7120 中发现的感觉视蛋白（ASR）作为基准系统。我们发现，使用包含最小（即三个双键）发色团的模型可以再现与 ASR QM/MM 模型激发态动力学相关的基本机制特征。此外，我们表明，使用相同简化模型计算的非绝热 ASR 轨迹的集合在 CASPT2 和 CASSCF 理论水平上复制了使用未简化模型估算的光谱和寿命趋势，以及在室温下观察到的实验结果。我们得出结论，进一步扩展这些研究可能会导致低成本的 QM/MM 视蛋白模型，这些模型可用作高通量计算突变筛选的有效工具。
