Rigid domains in proteins: an algorithmic approach to their identification.
Rigid domains in proteins: an algorithmic approach to their identification.
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蛋白质中的刚性结构域：识别其的算法方法。
DOI：
10.1002/prot.340230106
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发表时间：
1995
期刊：
影响因子：
--
通讯作者：
Zimm,BH
中科院分区：
文献类型：
--
作者：
Nichols,WL;Rose,GD;TenEyck,LF;Zimm,BH
刚性结构域，这里定义为两种或更多种不同蛋白质构象共有的三级结构，可以通过找到残基组（每个构象中一个残基）从原子坐标中以数字方式鉴定，使得属于一种构象的组内的任何两个残基之间的距离与属于任何其他构象的组内的两个结构上等同的残基之间的距离相同。两个残基之间的距离被认为是它们各自的α碳原子之间的距离。利用本文的方法，我们在人血红蛋白α1β 1二聚体的脱氧和氧合构象中发现了一个刚性结构域，该刚性结构域与Baldwin和Chothia先前鉴定的结构域密切相关（J. Mol. 129：175- 220，1979）。我们提供了两种算法，都使用差距离矩阵，直接从原子坐标搜索刚性域。第一种方法发现蛋白质中的所有刚性结构域，但随着蛋白质大小的增加，其存储和加工需求变得非常大。第二种方法虽然不一定能找到每个刚性结构域，但对任何大小的蛋白质都是计算上容易处理的。由于它的效率，我们能够递归地搜索蛋白质构象的非交叉结构域组。当通过叠加它们各自的结构域结构进行比对时，可以检查不同蛋白质构象在补充刚性结构域的区域中的结构差异。© 1995 Wiley利斯公司
A rigid domain, defined here as a tertiary structure common to two or more different protein conformations, can be identified numerically from atomic coordinates by finding sets of residues, one in each conformation, such that the distance between any two residues within the set belonging to one conformation is the same as the distance between the two structurally equivalent residues within the set belonging to any other conformation. The distance between two residues is taken to be the distance between their respective α carbon atoms. With the methods of this paper we have found in the deoxy and oxy conformations of the human hemoglobin α1β1dimer a rigid domain closely related to that previously identified by Baldwin and Chothia (J. Mol. Biol. 129:175–220,1979). We provide two algorithms, both using the difference‐distance matrix, with which to search for rigid domains directly from atomic coordinates. The first finds all rigid domains in a protein but has storage and processing demands that become prohibitively large with increasing protein size. The second, although not necessarily finding every rigid domain, is computationally tractable for proteins of any size. Because of its efficiency we are able to search protein conformations recursively for groups of non‐intersecting domains. Different protein conformations, when aligned by superimposing their respective domain structures; can be examined for structural differences in regions complementing a rigid domain. © 1995 Wiley‐Liss, Inc.