Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA.
J Am Chem Soc. 2011 Apr 6;133(13):4734-7. doi: 10.1021/ja200322w. Epub 2011 Mar 10.
By comparing the results from a hybrid quantum mechanics/molecular mechanics method (SORCI+Q//B3LYP/6-31G*:Amber) between vertebrate (bovine) and invertebrate (squid) visual pigments, the mechanism of molecular rearrangements, energy storage, and origin of the bathochromic shift accompanying the transformation of rhodopsin to bathorhodopsin have been evaluated. The analysis reveals that, in the presence of an unrelaxed binding site, bathorhodopsin was found to carry almost 27 kcal/mol energy in both visual pigments and absorb (λ(max)) at 528 nm in bovine and 554 nm in squid. However, when the residues within 4.0 Å radius of the retinal are relaxed during the isomerization event, almost ∼16 kcal/mol energy is lost in squid compared to only ∼8 kcal/mol in bovine. Loss of a larger amount of energy in squid is attributed to the presence of a flexible binding site compared to a rigid binding site in bovine. Structure of the squid bathorhodopsin is characterized by formation of a direct H-bond between the Schiff base and Asn87.
通过比较脊椎动物（牛）和无脊椎动物（鱿鱼）视觉色素的混合量子力学/分子力学方法（SORCI+Q//B3LYP/6-31G*：Amber）的结果，评估了分子重排、能量存储以及视黄醛向视紫红质转化伴随的红移的机制。分析表明，在存在未松弛结合位点的情况下，在两种视觉色素中，视紫红质都携带几乎 27 kcal/mol 的能量，并在牛中吸收（λ(max))在 528nm，在鱿鱼中吸收在 554nm。然而，当视黄醛周围 4.0Å 半径内的残基在异构化事件中松弛时，与牛相比，鱿鱼中几乎损失了约 16 kcal/mol 的能量。鱿鱼中能量损失更大是由于与牛相比，鱿鱼的结合位点具有柔韧性。鱿鱼视紫红质的结构特征是形成席夫碱和 Asn87 之间的直接氢键。
