Flexible protein alignment and hinge detection
Flexible protein alignment and hinge detection
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DOI：
10.1002/prot.10100
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发表时间：
2002-08-01
影响因子：
2.9
通讯作者：
Wolfson, HJ
中科院分区：
文献类型：
--
作者：
Shatsky, M;Nussinov, R;Wolfson, HJ
在这里，我们提出了一种新的技术，灵活的蛋白质的对齐。该方法不需要柔性铰链区域的先验知识。FlexProt算法同时检测铰链区并对齐分子的刚性子部分。我们的技术对插入和缺失不敏感。已经开发了许多方法来解决刚性结构比较。与FlexProt不同，所有先前开发的用于解决蛋白质柔性比对的方法都需要铰链区的先验知识。FlexProt方法基于结合了图论技术的3-D模式匹配算法。该算法是高效的。例如，它可以在400 MHz的台式PC上在大约7秒内对一对具有300个氨基酸的蛋白质进行结构比较。我们提供了实验结果与此算法。首先，我们灵活地比对从运动数据库中提取的蛋白质对。通过从相同的SCOP家族中提取额外的蛋白质来扩展这些。接下来，我们提出了一些从详尽的所有对所有灵活的结构比较1329 SCOP家庭的代表。我们的研究结果包括相对高分的灵活的结构之间的C-末端裂殖子表面蛋白与组织因子，II类氨酰-tRNA合成酶，组织相容性抗原与新生儿FC受体，酪氨酸蛋白激酶C-SRC与造血细胞激酶（HCK），酪氨酸蛋白激酶C-SRC与titine蛋白（自抑制丝氨酸激酶结构域），和组织因子与酶结合蛋白。这些都说明和讨论，显示这种结构对齐算法，它允许非预定义的铰链为基础的运动的能力。(C)2002 Wiley-Liss，Inc.
Here we present a novel technique for the alignment of flexible proteins. The method does not require an a priori knowledge of the flexible hinge regions. The FlexProt algorithm simultaneously detects the hinge regions and aligns the rigid subparts of the molecules. Our technique is not sensitive to insertions and deletions. Numerous methods have been developed to solve rigid structural comparisons. Unlike FlexProt, all previously developed methods designed to solve the protein flexible alignment require an a priori knowledge of the hinge regions. The FlexProt method is based on 3-D pattern-matching algorithms combined with graph theoretic techniques. The algorithm is highly efficient. For example, it performs a structural comparison of a pair of proteins with 300 amino acids in about 7 s on a 400-MHz desktop PC. We provide experimental results obtained with this algorithm. First, we flexibly align pairs of proteins taken from the database of motions. These are extended by taking additional proteins from the same SCOP family. Next, we present some of the results obtained from exhaustive all-against-all flexible structural comparisons of 1329 SCOP family representatives. Our results include relatively high-scoring flexible structural alignments between the C-terminal merozoite surface protein vs. tissue factor; class II aminoacyl-tRNA synthase, histocompatibility antigen vs. neonatal FC receptor; tyrosine-protein kinase C-SRC vs. haematopoetic cell kinase (HCK); tyrosine-protein kinase C-SRC vs. titine protein (autoinhibited serine kinase domain); and tissue factor vs. hormone-binding protein. These are illustrated and discussed, showing the capabilities of this structural alignment algorithm, which allows un-predefined hinge-based motions. (C) 2002 Wiley-Liss, Inc.