Birge R R, Hubbard L M
Biophys J. 1981 Jun;34(3):517-34. doi: 10.1016/S0006-3495(81)84865-5.
Semiempirical molecular dynamics procedures are used to theoretically investigate the trajectories and quantum yields of the rhodopsin leads to bathorhodopsin and bathorhodopsin leads to rhodopsin photoisomerizations. The calculations are based on the semiclassical trajectory formalism and rhodopsin binding site model proposed by Birge and Hubbard (1980. J. Am. Chem. Soc. 102: 2195-2205). The rhodopsin leads to bathorhodopsin photoisomerization is predicted to occur in approximately 2.2 ps with a quantum yield of 0.62 in reasonable agreement with experiment (less than 6 ps, phi = 0.67). The bathorhodopsin leads to rhodopsin photoisomerization is predicted to occur in approximately 1.8 ps with a quantum yield of 0.48. The latter number is in good agreement with the observed quantum yield for cattle bathorhodopsin (phi = 0.5) but in poor agreement with the observed value for squid bathorhodopsin (phi = 0.36). Our calculations suggest that the observed photochemical preference of the chromophore in cattle bathorhodopsin to isomerize to form rhodopsin (phi = 0.5), instead of isorhodopsin (phi - 0.054), is associated with a significant out-of-plane distortion (9-17 degrees) of the 11,12-trans dihedral angle in the batho chromophore.
采用半经验分子动力学方法从理论上研究视紫红质转化为视紫红质中间体以及视紫红质中间体转化为视紫红质的光异构化过程的轨迹和量子产率。计算基于Birge和Hubbard（1980年，《美国化学会志》102: 2195 - 2205）提出的半经典轨迹形式和视紫红质结合位点模型。预测视紫红质转化为视紫红质中间体的光异构化过程大约在2.2皮秒内发生，量子产率为0.62，与实验结果（小于6皮秒，φ = 0.67）合理吻合。预测视紫红质中间体转化为视紫红质的光异构化过程大约在1.8皮秒内发生，量子产率为0.48。后一个数值与牛视紫红质中间体观察到的量子产率（φ = 0.5）吻合良好，但与鱿鱼视紫红质中间体观察到的值（φ = 0.36）吻合较差。我们的计算表明，观察到的牛视紫红质中间体中发色团光化学异构化形成视紫红质（φ = 0.5）而非异视紫红质（φ = 0.054）的偏好，与视紫红质中间体中11,12 - 反式二面角显著的面外扭曲（9 - 17度）有关。
