The primary photochemical reaction of the green-absorbing proteorhodopsin is studied by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The simulations are based on a homology model derived from the blue-absorbing proteorhodopsin crystal structure. The geometry of retinal and the surrounding sidechains in the protein binding pocket were optimized using the QM/MM method. Starting from this geometry the isomerization was studied with a relaxed scan along the C₁₃C₁₄ dihedral. It revealed an “aborted bicycle pedal” mechanism of isomerization that was originally proposed by Warshel for bovine rhodopsin and bacteriorhodopsin. However, the isomerization involved the concerted rotation about C₁₃C₁₄ and C₁₅N, with the latter being highly twisted but not isomerized. Further, the simulation showed an increased steric interaction between the hydrogen at the C₁₄ of the isomerizing bond and the hydroxyl group at the neighbouring tyrosine 200. In addition, we have simulated a nonadiabatic trajectory which showed the timing of the isomerization. In the first 20 fs upon excitation the order of the conjugated double and single bonds is inverted, consecutively the C₁₃C₁₄ rotation is activated for 200 fs until the S₁–S₀ transition is detected. However, the isomerization is reverted due to the specific interaction with the tyrosine as observed along the relaxed scan calculation. Our simulations indicate that the retinal – tyrosine 200 interaction plays an important role in the outcome of the photoisomerization.

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QM / MM研究绿色吸收蛋白视紫红质的初始激发态动力学

通过混合量子力学/分子力学（QM / MM）方法研究了绿色吸收蛋白视紫红质的主要光化学反应。该模拟基于从吸收蓝色的蛋白视紫红质晶体结构衍生的同源性模型。使用QM / MM方法优化了蛋白质结合袋中的视网膜和周围侧链的几何结构。从这种几何形状开始，通过沿C ₁₃ C ₁₄二面体的松弛扫描研究了异构化。它揭示了Warshel最初提出的用于牛视紫红质和细菌视紫红质的“流离失所的自行车踏板”异构化机制。但是，异构化涉及绕C ₁₃ C ₁₄和C的协同旋转。₁₅ N，后者高度扭曲但未异构化。此外，模拟显示异构化键的C ₁₄处的氢与相邻酪氨酸200处的羟基之间的空间相互作用增加。此外，我们还模拟了非绝热轨迹，该轨迹显示了异构化的时间。在激发的前20 fs中，共轭双键和单键的顺序反转，随后C ₁₃ C ₁₄旋转被激活200 fs，直到S ₁ –S ₀检测到转变。然而，由于沿着松弛扫描计算观察到的与酪氨酸的特异性相互作用，异构化得以恢复。我们的模拟表明，视网膜–酪氨酸200的相互作用在光异构化的结果中起着重要的作用。