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首页> 外文期刊>Journal of Molecular Biology >Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.
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Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.

机译：蛋白质-DNA界面的结构比对：洞察结合特异性的决定因素。

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摘要

A new method is introduced to structurally align interfaces observed in protein--DNA complexes. The method is based on a procedure that describes the interfacial geometry in terms of the spatial relationships between individual amino acid--nucleotide pairs. An amino acid--amino acid similarity matrix, S, is defined that provides a quantitative measure of the geometric relationships of amino acids in different interfaces and the entire stretch of "local" DNA within some distance of each amino acid. S is used as a substitution matrix in a dynamic programming algorithm that aligns the interfacial amino acids of the two complexes. The quality of the alignment is determined by an interface alignment score, IAS, that provides a quantitative measure of the similarity in the docking geometry between two protein--DNA complexes. We have clustered a large set of protein--DNA complexes based on their IAS values. In general, proteins within a single family form identifiable clusters. Subgroup clustering is often observed within families offering a fine-grained description of docking geometries. Although proteins with similar folds tend to dock in similar ways, important differences are observed even for structural motifs that almost perfectly align. Relationships are observed between the interfaces formed in cognate and non-cognate complexes involving the same proteins indicating a strong driving force to maintain certain contacts, even if this requires a distortion of the DNA. There are cases where inter-family similarities are greater than intra-family similarities. Our method offers the possibility of comparing different protein--DNA interfaces in a detailed, objective and quantitative fashion. This offers the possibility of new approaches to the description of the determinants of molecular recognition and to the prediction of protein and DNA sequence combinations that are optimal for binding.
机译：引入了一种新方法来在结构上对齐蛋白质-DNA复合物中观察到的界面。该方法基于一种程序，该程序根据单个氨基酸－核苷酸对之间的空间关系来描述界面几何形状。定义了氨基酸-氨基酸相似性矩阵S，该矩阵可定量测量不同界面中氨基酸的几何关系以及每个氨基酸一定距离内的“局部” DNA的整个延伸。 S在动态编程算法中用作置换矩阵，该算法将两个复合物的界面氨基酸对齐。比对的质量由界面比对分数IAS决定，IAS提供了两种蛋白质-DNA复合物之间对接几何形状相似性的定量度量。我们根据其IAS值对大量的蛋白质-DNA复合物进行了聚类。通常，单个家族中的蛋白质形成可识别的簇。经常在家庭中观察到亚组聚类，提供了对接几何的详细描述。尽管具有相似折叠的蛋白质倾向于以相似的方式对接，但是即使对于几乎完美对齐的结构基序，也观察到了重要的差异。观察到在涉及相同蛋白质的同源和非同源复合物中形成的界面之间的关系表明，即使需要DNA的变形，它也具有强大的驱动力来维持某些接触。在某些情况下，家庭之间的相似度大于家庭内部的相似度。我们的方法提供了以详细，客观和定量的方式比较不同蛋白质-DNA界面的可能性。这为描述分子识别决定因素和预测最适合结合的蛋白质和DNA序列组合提供了新的方法。

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