A GRAPH-THEORETIC APPROACH TO THE IDENTIFICATION OF 3-DIMENSIONAL PATTERNS OF AMINO-ACID SIDE-CHAINS IN PROTEIN STRUCTURES
A GRAPH-THEORETIC APPROACH TO THE IDENTIFICATION OF 3-DIMENSIONAL PATTERNS OF AMINO-ACID SIDE-CHAINS IN PROTEIN STRUCTURES
复制标题
DOI：
10.1006/jmbi.1994.1657
复制
发表时间：
1994-10-21
影响因子：
5.6
通讯作者：
WILLETT, P
中科院分区：
文献类型：
--
作者：
ARTYMIUK, PJ;POIRRETTE, AR;WILLETT, P
本文讨论了利用图论方法来表示和搜索蛋白质结构中侧链的三维模式。侧链的位置由假原子表示，侧链对的相对位置由它们之间的距离表示。这种几何形状的描述可以用一个标记图来表示，其中图的节点和边分别表示伪原子和伪原子间距离的集合。给定这样的表示，可以搜索蛋白质的存在下，用户定义的查询模式的侧链通过子图同构算法，这是在程序ASSAM中实现的。一个这样的算法，由于Ullmann的实验表明，它提供了一个有效的和高效的方式搜索模式的侧链。该方法是通过搜索丝氨酸蛋白酶催化三联体，参与葡萄球菌核酸酶的催化活性的残基，和嗜热菌蛋白酶的锌结合侧链来说明。的催化三联体模式搜索显示存在的第二Asp-His-Ser三联体样安排的残基在胰蛋白酶原和胰凝乳蛋白酶原，除了催化残基。此外，该程序可用于搜索假设模式，如三个色氨酸侧链的模式所示。这些搜索表明，搜索算法可以成功地检索到绝大多数预期的蛋白质，以及其他以前未报道的蛋白质，含有。兴趣模式。
This paper discusses the use of graph-theoretic methods for the representation and searching of three-dimensional patterns of side-chains in protein structures. The position of a side-chain is represented by pseudo-atoms, and the relative positions of pairs of side-chains by the distances between them. This description of the geometry can be represented by a labelled graph in which the nodes and the edges of the graph represent the pseudo-atoms and the sets of inter-pseudo-atomic distances, respectively. Given such a representation, a protein can be searched for the presence of a user-defined query pattern of side-chains by means of a subgraph-isomorphism algorithm which is implemented in the program ASSAM. Experiments with one such algorithm, that due to Ullmann, show that it provides both an effective and a highly efficient way of searching for patterns of side-chains. The method is illustrated by searches for the serine protease catalytic triad, for residues involved in the catalytic activity of staphyloccocal nuclease, and for the zinc-binding side-chains of thermolysin. The catalytic triad pattern search revealed the existence of a second Asp-His-Ser triad-like arrangement of residues in trypsinogen and chymotrypsinogen, in addition to the catalytic residues. In addition the program can be used to search for hypothetical patterns, as is shown for a pattern of three tryptophan side-chains. These searches demonstrate that the search algorithm can successfully retrieve the great majority of the expected proteins, as well as other, previously unreported proteins that contain the. pattern of interest.