Wickstrand Cecilia, Dods Robert, Royant Antoine, Neutze Richard
Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden.
Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France; European Synchrotron Radiation Facility, F-38043 Grenoble, France.
Biochim Biophys Acta. 2015 Mar;1850(3):536-53. doi: 10.1016/j.bbagen.2014.05.021. Epub 2014 Jun 8.
Bacteriorhodopsin (bR) is the simplest known light driven proton pump and has been heavily studied using structural methods: eighty four X-ray diffraction, six electron diffraction and three NMR structures of bR are deposited within the protein data bank. Twenty one X-ray structures report light induced structural changes and changes induced by mutation, changes in pH, thermal annealing or X-ray induced photo-reduction have also been examined.
We argue that light-induced structural changes that are replicated across several studies by independent research groups are those most likely to represent what is happening in reality. We present both internal distance matrix analyses that sort deposited bR structures into hierarchal trees, and difference Fourier analysis of deposited X-ray diffraction data.
An internal distance matrix analysis separates most wild-type bR structures according to their different crystal forms, indicating how the protein's structure is influenced by crystallization conditions. A similar analysis clusters eleven studies of illuminated bR crystals as one branch of a hierarchal tree with reproducible movements of the extracellular portion of helix C towards helix G, and of the cytoplasmic portion of helix F away from helices A, B and G. All crystallographic data deposited for illuminated crystals show negative difference density on a water molecule (Wat402) that forms H-bonds to the retinal Schiff Base and two aspartate residues (Asp85, Asp212) in the bR resting state. Other recurring difference density features indicated reproducible side-chain, backbone and water molecule displacements. X-ray induced radiation damage also disorders Wat402 but acts via cleaving the head-groups of Asp85 and Asp212.
A remarkable level of agreement exists when deposited structures and crystallographic observations are viewed as a whole. From this agreement a unified picture of the structural mechanism of light-induced proton pumping by bR emerges. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
细菌视紫红质（bR）是已知最简单的光驱动质子泵，已通过结构方法进行了大量研究：蛋白质数据库中存有84个bR的X射线衍射结构、6个电子衍射结构和3个核磁共振结构。21个X射线结构报告了光诱导的结构变化以及由突变、pH变化、热退火或X射线诱导的光还原所引起的变化。
我们认为，由独立研究小组在多项研究中重复出现的光诱导结构变化最有可能代表实际发生的情况。我们展示了将存入的bR结构分类为层次树的内部距离矩阵分析，以及对存入的X射线衍射数据的差分傅里叶分析。
内部距离矩阵分析根据不同的晶体形式将大多数野生型bR结构区分开来，表明蛋白质结构是如何受到结晶条件影响的。类似的分析将11项关于光照bR晶体的研究聚类为层次树的一个分支，其中螺旋C的细胞外部分向螺旋G有可重复的移动，螺旋F的细胞质部分远离螺旋A、B和G。所有存入的光照晶体的晶体学数据在一个水分子（Wat402）上显示出负差分密度，该水分子在bR静止状态下与视黄醛席夫碱和两个天冬氨酸残基（Asp85、Asp212）形成氢键。其他反复出现的差分密度特征表明存在可重复的侧链、主链和水分子位移。X射线诱导的辐射损伤也会扰乱Wat402，但通过切割Asp85和Asp212的头部基团起作用。
当将存入的结构和晶体学观察结果作为一个整体来看时，存在着显著程度的一致性。基于这种一致性，出现了bR光诱导质子泵浦结构机制的统一图景。本文是名为“膜蛋白的结构生物化学和生物物理学”的特刊的一部分。
