Fel'dman T B, Kholmurodov Kh T, Ostrovskiĭ M A, Khrenova M G, Nemukhin A V
Biofizika. 2009 Jul-Aug;54(4):660-7.
Based on computer simulation methods, the molecular dynamics of the rhodopsin chromophore group (11-cis-retinal) has been analyzed. The molecular dynamics has been traced within a 3-ns time interval; thereby 3 x 10(6) discrete conformational states of opsin and rhodopsin were compared and analyzed. It was shown that, within a short time of about 0.3-0.4 ns from the start of simulation, the retinal beta-ionone ring becomes twisted around the C6-C7 bond by approximately 60 degrees compared with that of the initial configuration. The influence of retinal conformation on the positions of the maximum of the absorption band of rhodopsin at the conformational states of t=0 and t=3 ns were estimated using the ab initio methods. The results indicated that the absorption maximum for the final (3-ns) state is shifted by 10 nm toward the long wavelength region compared with the initial state. This suggests that the rhodopsin molecule with its twisted chromophore will possess a considerably lower activation energy than the rhodopsin molecule where the beta-ionone ring is in a planar orientation to the retinal polyene chain.
基于计算机模拟方法，对视紫红质发色团（11-顺式视黄醛）的分子动力学进行了分析。在3纳秒的时间间隔内追踪分子动力学；从而对视蛋白和视紫红质的3×10⁶个离散构象状态进行了比较和分析。结果表明，在模拟开始后的约0.3 - 0.4纳秒的短时间内，与初始构型相比，视黄醛的β-紫罗兰酮环围绕C6 - C7键扭转了约60度。使用从头算方法估计了在t = 0和t = 3纳秒的构象状态下视黄醛构象对视紫红质吸收带最大值位置的影响。结果表明，最终（3纳秒）状态的吸收最大值与初始状态相比向长波长区域移动了10纳米。这表明，其发色团扭曲的视紫红质分子将比β-紫罗兰酮环与视黄醛多烯链呈平面取向的视紫红质分子具有低得多的活化能。
