Department of Biology, Darwin Building, University College, University of London, Gower Street, WC1 E 6BT, London, UK.
Photosynth Res. 1992 Nov;34(2):287-300. doi: 10.1007/BF00033446.
A three-dimensional model of the core proteins D1 and D2, including the cofactors, that form the Photosystem II reaction centre of pea (Pisum sativum), has been generated. This model was built with a rule-based computer modelling system using the information from the crystal structures of the photosynthetic reaction centres of Rhodopseudomonas viridis and Rhodobacter sphaeroides. An alignment of the primary sequences of twenty three D1, nine D2, eight bacterial L and eight bacterial M subunits predicts strong similarity between bacterial and higher plant reaction centres, especially in the transmembrane region where the cofactors responsible for electron transport are located. The sequence to be modelled was aligned to the bacterial structures using environment-dependent substitution tables to construct matrices, improving the alignment procedure. The ancestral relationship between the bacteria and higher plant sequences allowed both the L and M subunits to be used as structural templates as they were equally related to the higher plant polypeptides. The regions with the highest predicted structural homology were used as a framework for the construction of the structurally conserved regions. The structurally conserved region of the model shows strong similarity to the bacterial reaction centre in the transmembrane helices. The stromal and lumenal loops show greater sequence variation and are therefore predicted to be the structurally variable regions in the model. The key sidechain assignments and residues that may interact with cofactors are discussed.
已生成形成豌豆（Pisum sativum）光系统 II 反应中心的核心蛋白 D1 和 D2 及其辅助因子的三维模型。该模型是使用基于规则的计算机建模系统，利用来自绿菌（Rhodopseudomonas viridis）和球形红杆菌（Rhodobacter sphaeroides）光合作用反应中心的晶体结构信息构建的。二十三个 D1、九个 D2、八个细菌 L 和八个细菌 M 亚基的一级序列比对表明，细菌和高等植物反应中心之间具有很强的相似性，尤其是在负责电子传递的辅助因子所在的跨膜区域。使用环境相关的替代表构建矩阵对齐模型的序列与细菌结构，以改善对齐过程。细菌和高等植物序列之间的祖先关系允许同时使用 L 和 M 亚基作为结构模板，因为它们与高等植物多肽同样相关。预测具有最高结构同源性的区域被用作构建结构保守区域的框架。模型的结构保守区域与细菌反应中心在跨膜螺旋中显示出很强的相似性。基质和腔环显示出更大的序列变异，因此预计在模型中是结构可变区域。讨论了关键侧链分配和可能与辅助因子相互作用的残基。
