Röhrig Ute F, Sebastiani Daniel
Ludwig Institute for Cancer Research, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland.
J Phys Chem B. 2008 Jan 31;112(4):1267-74. doi: 10.1021/jp075662q. Epub 2008 Jan 5.
We investigate nuclear magnetic resonance (NMR) parameters of the rhodopsin chromophore in the dark state of the protein and in the early photointermediate bathorhodopsin via first-principles molecular dynamics simulations and NMR chemical shift calculations in a hybrid quantum/classical (QM/MM) framework. NMR parameters are particularly sensitive to structural properties and to the chemical environment, which allows us to address different questions about the retinal chromophore in situ. Our calculations show that both the 13C and the 1H NMR chemical shifts are rather insensitive to the protonation state of Glu181, an ionizable amino acid side chain located in the vicinity of the isomerizing 11-cis bond. Thus, other techniques should be better suited to establish its protonation state. The calculated chemical shifts for bathorhodopsin further support our previously published theoretical structure, which is in very good agreement with more recent X-ray data.
我们通过在量子/经典混合（QM/MM）框架下的第一性原理分子动力学模拟和核磁共振化学位移计算，研究了视紫红质发色团在蛋白质暗态和早期光中间体视紫红质中的核磁共振（NMR）参数。核磁共振参数对结构性质和化学环境特别敏感，这使我们能够原位解决关于视网膜发色团的不同问题。我们的计算表明，13C和1H核磁共振化学位移对位于异构化11-顺式键附近的可电离氨基酸侧链Glu181的质子化状态相当不敏感。因此，其他技术应该更适合确定其质子化状态。视紫红质的计算化学位移进一步支持了我们之前发表的理论结构，该结构与最近的X射线数据非常吻合。
