A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique
A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique
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DOI：
10.1006/jmbi.1996.0424
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发表时间：
1996-07-26
影响因子：
5.6
通讯作者：
Nussinov, R
中科院分区：
文献类型：
--
作者：
Tsai, CJ;Lin, SL;Nussinov, R
尽管存在许多结构上不冗余的蛋白质单体数据集，但没有蛋白质-蛋白质界面。然而，这样一个数据集的可用性有望为一些调查提供额外的见解。首先也是最重要的是分析界面以获得它们的主要结构、解释蛋白质-蛋白质关联的力以及它们的包装考虑。它们与单体的比较可能会对蛋白质-蛋白质识别和多肽链折叠的另一方面提供更多的信息。对接模拟也有望从这样一个数据集的存在中受益。生成接口数据集的一个主要障碍是接口至少由两个链组成。此外，在接口中，每个链可能由不连续的片段表示。它们在被比较的接口中的顺序也可能不同。这种不连续性源于接口的定义。界面由链之间的相互作用残基，以及在一定距离阈值内的支撑支架中它们附近的残基组成。这必然产生无序的片段，以及孤立的残基。我们的新颖，高效，序列顺序无关的结构比较技术非常适合处理生成结构上无冗余的蛋白质-蛋白质界面库的任务。由于它是基于计算机视觉的，它将原子视为空间中点的集合，而忽略了它们的链式连接。在这项工作中，创建了351个接口族。对这些界面进行比较，并分别对构成这些界面的链进行比较，可以得出一些有趣的例子。在其中一种情况下，虽然两个界面相似，但两个配合物之间只有一条链的结构相似。第一配合物第二链的结构与第二配合物第二链的结构不同。在这里，第一个链上的裂缝结构决定了特定的结合相互作用。在另一种情况下，虽然两个配合物的界面相似，但组成它们的两个链在配合物之间不同。最后，组成复合物的链是相似的，但界面是不同的，为研究蛋白质-蛋白质结合的有利方向提供了一组数据。(C) 1996学术出版社有限公司
White there are a number of-structurally non-redundant datasets of protein monomers, there is none of protein-protein interfaces. Yet, the availability of such a dataset is expected to provide an added insight into a number of investigations. First and foremost among these is analyzing the interfaces to obtain their prevailing architectures, the forces that account for the protein-protein associations and their packing considerations. Their comparisons with those of the monomers are likely to shed additional light on protein-protein recognition on the one hand and on the folding of the polypeptide chain on the other. Docking simulations are also expected to benefit from the existence of such a dataset. A major stumbling block to the generation of a dataset of interfaces has been that the interface is composed of at least two chains. Furthermore, in the interfaces, each of the chains might be represented by non-contiguous pieces. Their order in the interfaces being compared might be different as well. This discontinuity stems from the definition of an interface. An interface consists of interacting residues between the chains, and those that-are in their vicinity in the supporting scaffold, within a certain distance threshold. This necessarily yields unordered fragments, as well as isolated residues. Our novel, efficient, sequence-order-independent structural comparison technique is ideally suited to handle the task of the generation of a library of structurally non-redundant protein-protein interfaces. As it is computer-vision based, it views atoms as collections of points in space, disregarding their chain connectivity. in this work, 351 interface-families are created. Comparisons of the interfaces, and separately, of the chains which contribute to them, yield some interesting cases. In one of the cases, while two interfaces are similar, the structure of only one of the two chains is similar between the two complexes. The structure of the second chain of the first complex differs from that of the second chain of the second complex. Here the structure of the cleft in the first chain dictates the specific binding interactions. Ln another case, while the interfaces in the two complexes are similar, both chains composing them differ between the complexes. Lastly, the chains composing the complexes are similar, but the interfaces are dissimilar, providing a set of data for investigations of the favorable orientations of protein-protein associations. (C) 1996 Academic Press Limited