Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.
Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.
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蛋白质-配体、蛋白质-蛋白质和蛋白质-核酸相互作用的功能结构基序及其与超二级结构的联系。
DOI：
10.1007/978-1-62703-065-6_18
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发表时间：
2013
影响因子：
--
通讯作者：
Haruki Nakamura
中科院分区：
文献类型：
--
作者：
A. Kinjo;Haruki Nakamura
蛋白质的功能是由蛋白质和其他分子之间的相互作用介导的。对蛋白质相互作用界面的结构进行比较和分类是分析蛋白质功能的一种有效方法。在这里，我们描述的程序编译接口结构的数据库，并有效地比较接口结构。要做到这一点，需要对蛋白质数据库（PDB）的数据结构有很好的理解。因此，我们还提供了一个详细的说明PDB交换字典必要的提取数据，是相关的分析交互界面和二级结构。我们通过对相似的界面结构进行分类来识别重复出现的结构基序，并且我们定义了一种粗粒度的超二级结构（SSS）表示，它表示两个或三个二级结构元素的序列，包括它们的相对方向，作为一串四到七个字母。通过研究结构基序和SSS字符串之间的对应关系，我们发现，没有SSS字符串具有特别高的倾向，被发现的相互作用界面一般，表明任何SSS可以被用作绑定接口。当检查单个结构基序时，有一些SSS串对特定的结构基序组具有高倾向性。此外，它示出，而SSS字符串中发现的非聚合物和蛋白质接口的特定结构基序是丰富的其他结构基序，属于相同的亚基，核酸接口的结构基序表现出更强的偏好SSS字符串。对于蛋白质折叠，在许多折叠中发现了许多基序特异性的SSS串，这表明SSS可能是一个有用的描述来研究配体结合模式的普遍性。
Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.