QM/MM investigation of the hydrogen-bonding interactions in putative K and early-M intermediates of the bacteriorhodopsin photocycle
QM/MM investigation of the hydrogen-bonding interactions in putative K and early-M intermediates of the bacteriorhodopsin photocycle
复制标题
QM/MM 研究细菌视紫红质光循环的假定 K 和早期 M 中间体中的氢键相互作用
DOI：
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发表时间：
2005
期刊：
影响因子：
--
通讯作者：
Stefan Fischer
中科院分区：
文献类型：
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作者：
A. Bondar;Jeremy C. Smith;Stefan Fischer
细菌视紫红质质子泵的光驱动光循环包含几个中间态，由它们的光谱信号来表征。大量的实验研究，包括高分辨率的X射线结晶学，已经为光循环中结构重排的性质和程度提供了有价值的见解。然而，视网膜席夫碱和参与质子转移的基团之间的详细氢键相互作用仍然存在争议。本文采用量子力学/分子力学(QM/MM)计算方法，研究了K和EARE-M稳定结构的视网膜结合袋中的氢键相互作用。在两个起始坐标集中，视网膜链高度扭曲，席夫碱基指向膜的细胞外侧。通过考虑Schiff碱质子化和Asp85负电荷(即K中间体)来优化K或早期-M态结构，保留了视网膜链的高度扭曲构型。在使用中性Schiff碱和中性Asp85(即，如在M中间体中)进行优化的情况下，发色团松弛，并且Schiff碱朝向细胞质。去质子化的席夫碱指向膜的胞外侧的扭曲的视网膜构型被发现是不稳定的。
The light-driven photocycle of the bacteriorhodopsin proton pump contains several intermediate states characterized by their spectroscopic signals. Numerous experimental investigations, including high-resolution X-ray crystallography, have provided valuable insight into the nature and the extent of the structural rearrangements along the photocycle. Nevertheless, the detailed hydrogen-bonding interactions of the retinal Schiff base and of the groups involved in proton transfer remain under debate. Combined Quantum Mechanical/Molecular Mechanical (QM/MM) calculations are employed here to assess the hydrogen-bonding interactions in the retinal binding pocket of putative K and early-M stable structures. In both of the starting coordinate sets the retinal chain is highly twisted, with the Schiff base pointing towards the extracellular side of the membrane. The optimization of either the K or the early-M state structure by considering the Schiff base protonated and Asp85 negatively charged (i.e., as in the K intermediate) preserves the highly twisted configuration of the retinal chain. In the case where the optimizations are performed with neutral Schiff base and neutral Asp85 (i.e., as in the M intermediate) the chromophore relaxes and the Schiff base orients towards the cytoplasm. The twisted retinal configuration with the deprotonated Schiff base pointing towards the extracellular side of the membrane is found to be unstable.
细菌视紫红质 M 和 N 中间体的晶体结构：Asp-96 和视网膜席夫碱之间水分子氢键链的组装。
影响因子：
5.6
作者：
Schobert,Brigitte;Brown,LeonidS;Lanyi,JanosK
通讯作者：
Lanyi,JanosK
影响因子：
5.6
作者：
Lanyi, JK;Schobert, B
通讯作者：
Schobert, B