Heteronuclear NMR and soft docking:: An experimental approach for a structural model of the cytochrome c553-ferredoxin complex
Heteronuclear NMR and soft docking:: An experimental approach for a structural model of the cytochrome c553-ferredoxin complex
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DOI：
10.1021/bi992306s
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发表时间：
2000-03-14
期刊：
影响因子：
2.9
通讯作者：
Guerlesquin, F
中科院分区：
文献类型：
--
作者：
Morelli, X;Dolla, A;Guerlesquin, F
将对接算法与NMR数据相结合已经被广泛地用于蛋白质-配体相互作用的研究。然而，为了将这一发展扩展到蛋白质-蛋白质相互作用的研究，所需的分子间NOE约束更难获得。在目前的工作中，我们描述了一种新的方法，结合了从头对接计算和映射的相互作用位点，使用化学位移变化分析。细胞色素c（553）-铁氧还蛋白复合物被用作许多电子转移复合物的模型。已经获得了两种分子的N-15-标记，并且使用HSQC实验分别对每个伴侣上的相互作用位点进行了映射。H-1和N-15化学位移分析定义了参与识别界面的两种分子的面积。复合物的模型由从头对接软件BiGGER程序（具有全局评估和排名的双分子复合物生成）生成。该程序生成了一个人口的蛋白质-蛋白质对接的几何形状排列的评分函数，结合相关的稳定参数，如几何互补表面，静电相互作用，去溶剂化能，和成对的氨基酸侧链的亲和力。我们已经实现了一个新的模块，其中包括实验输入（在这里，相互作用位点的NMR映射）作为过滤器进行选择。准确的模型。使用X-PLOR软件使最终结构的能量最小化，然后进行分析。最佳溶液具有接近通常观察到的识别界面范围的界面面积（1037.4埃（2）），氧化还原中心之间的距离为10.0埃。
The combination of docking algorithms with NMR data has been developed extensively for the studies of protein-ligand interactions. However, to extend this development for the studies of protein-protein interactions, the intermolecular NOE constraints, which are needed, are more difficult to access. In the present work, we describe a new approach that combines an ab initio docking calculation and the mapping of an interaction site using chemical shift variation analysis. The cytochrome c(553)-ferredoxin complex is used as a model of numerous electron-transfer complexes. The N-15-labeling of both molecules has been obtained, and the mapping of the interacting site on each partner, respectively, has been done using HSQC experiments. H-1 and N-15 chemical shift analysis defines the area of both molecules involved in the recognition interface. Models of the complex were generated by an ab initio docking software, the BiGGER program (bimolecular complex generation with global evaluation and ranking). This program generates a population of protein-protein docked geometries ranked by a scoring function, combining relevant stabilization parameters such as geometric complementarity surfaces, electrostatic interactions, desolvation energy, and pairwise affinities of amino acid side chains. We have implemented a new module that includes experimental input (here, NMR mapping of the interacting site) as a filter to select. the accurate models. Final structures were energy minimized using the X-PLOR software and then analyzed. The best solution has an interface area (1037.4 Angstrom(2)) falling close to the range of generally observed recognition interfaces, with a distance of 10.0 Angstrom between the redox centers.