The synergetic effects of multiple rhodopsin mutations on color tuning need to be completely elucidated. Systematic genetic studies and spectroscopy have demonstrated an interesting example of synergetic color tuning between two amino acid residues in conger rhodopsin's ancestral pigment (p501): -a double mutation at one nearby and one distant residue led to a significant λ(max) blue shift of 13 nm, whereas neither of the single mutations at these two sites led to meaningful shifts.To analyze the molecular mechanisms of this synergetic color tuning, we performed homology modeling, molecular simulations, and electronic state calculations. For the double mutant, N195A/A292S, in silico mutation analysis demonstrated conspicuous structural changes in the retinal chromophore, whereas that of the single mutant, A292S, was almost unchanged. Using statistical ensembles of QM/MM optimized structures, the excitation energy of retinal chromophore was evaluated for the three visual pigments. As a result, the λ(max) shift of double mutant (DM) from p501 was -8 nm, while that of single mutant (SM) from p501 was +1 nm. Molecular dynamics simulation for DM demonstrated frequent isomerization between 6-s-cis and 6-s-trans conformers. Unexpectedly, however, the two conformers exhibited almost identical excitation energy, whereas principal component analysis (PCA) identified the retinal-counterion cooperative change of BLA (bond length alternation) and retinal-counterion interaction lead to the shift.

中文翻译：

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海藻视紫红质中多个氨基酸残基之间远程协同颜色调节的分子机制。

需要完全阐明多种视紫红质突变对颜色调节的协同作用。系统的遗传研究和光谱学已经证明了一个有趣的例子，即海藻视紫红质的祖先色素 (p501) 中两个氨基酸残基之间协同颜色调整的一个有趣例子： - 在一个附近和一个远处残基的双重突变导致显着的 λ(max) 蓝移13 nm，而这两个位点的单个突变都没有导致有意义的转变。为了分析这种协同颜色调整的分子机制，我们进行了同源建模、分子模拟和电子状态计算。对于双突变体 N195A/A292S，计算机突变分析表明视网膜发色团有明显的结构变化，而单突变体 A292S 的结构变化几乎没有变化。使用 QM/MM 优化结构的统计集成，评估了三种视觉色素的视网膜发色团的激发能量。结果，来自 p501 的双突变体 (DM) 的 λ(max) 偏移为 -8 nm，而来自 p501 的单突变体 (SM) 的 λ(max) 偏移为 +1 nm。DM 的分子动力学模拟证明了 6-s-cis 和 6-s-trans 构象异构体之间的频繁异构化。然而，出乎意料的是，两个构象异构体表现出几乎相同的激发能量，而主成分分析 (PCA) 确定了 BLA（键长交替）的视网膜-反离子协同变化和视网膜-反离子相互作用导致了这种转变。p501 的双突变体 (DM) 的 λ(max) 偏移为 -8 nm，而 p501 的单突变体 (SM) 的 λ(max) 偏移为 +1 nm。DM 的分子动力学模拟证明了 6-s-cis 和 6-s-trans 构象异构体之间的频繁异构化。然而，出乎意料的是，两个构象异构体表现出几乎相同的激发能量，而主成分分析 (PCA) 确定了 BLA（键长交替）的视网膜-反离子协同变化和视网膜-反离子相互作用导致了这种转变。p501 的双突变体 (DM) 的 λ(max) 偏移为 -8 nm，而 p501 的单突变体 (SM) 的 λ(max) 偏移为 +1 nm。DM 的分子动力学模拟证明了 6-s-cis 和 6-s-trans 构象异构体之间的频繁异构化。然而，出乎意料的是，两个构象异构体表现出几乎相同的激发能量，而主成分分析 (PCA) 确定了 BLA（键长交替）的视网膜-反离子协同变化和视网膜-反离子相互作用导致了这种转变。