SOCKET: A program for identifying and analysing coiled-coil motifs within protein structures
SOCKET: A program for identifying and analysing coiled-coil motifs within protein structures
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DOI：
10.1006/jmbi.2001.4545
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发表时间：
2001-04-13
影响因子：
5.6
通讯作者：
Woolfson, DN
中科院分区：
文献类型：
--
作者：
Walshaw, J;Woolfson, DN
卷曲螺旋可以说是最简单的蛋白质结构基序，可能是蛋白质-蛋白质相互作用的最普遍的促进剂。螺旋线圈包括两个Or。更多的α-螺旋相互缠绕形成“超螺旋”。大多数卷曲螺旋的标志是被称为七肽重复的规则序列模式。尽管在序列水平上这种明显的简单性和相关性，卷曲螺旋显示出相当程度的结构多样性：螺旋可以平行或反平行排列，并可以形成各种寡聚体状态。为了帮助卷曲螺旋的研究，我们开发了SOCKET，一个计算机程序来自动识别蛋白质结构中的这些基序。我们使用SOCKET从RCSB蛋白质数据库中收集了一组明确的卷曲螺旋结构。该算法不是搜索序列特征，而是识别卷曲螺旋的特征性旋钮到孔侧链包装;这被证明是直接实现的，并且能够将卷曲螺旋与在球状域中观察到的绝大多数螺旋-螺旋包装排列区分开。SOCKET明确定义卷曲螺旋螺旋边界，寡聚化状态和螺旋方向，并分配七肽寄存器。从蛋白质数据库检索的结构包括两个、三个和四个链卷曲螺旋的平行和反平行变体，平行五聚体的一个实例和少量扩展卷曲螺旋的经典描述的结构。我们预计，我们收集的结构数据库和相关序列数据将用于确定卷曲螺旋组装、预测和设计的原则。为了说明这一点，我们给出的结构，可能使用新的数据库的序列和结构分析的例子，我们提出了不同的基序的七肽重复的氨基酸谱。(C)北京：科学出版社.
The coiled coil is arguably the simplest protein-structure motif and probably the most ubiquitous facilitator of protein-protein interactions. Coiled coils comprise two Or. more a-helices that wind around each other to form "supercoils". The hallmark of most coiled coils is a regular sequence pattern known as the heptad repeat. Despite this apparent simplicity and relatedness at the sequence level, coiled coils display a considerable degree of structural diversity: the helices may be arranged parallel or anti-parallel and may form a variety of oligomer states. To aid studies of coiled coils, we developed SOCKET, a computer program to identify these motifs automatically in protein structures. We used SOCKET to gather a set of unambiguous coiled-coil structures from the RCSB Protein Data Bank. Rather than searching for sequence features, the algorithm recognises the characteristic knobs-into-holes side-chain packing of coiled coils; this proved to be straightforward to implement and was able to distinguish coiled coils from the great majority of helix-helix packing arrangements observed in globular domains. SOCKET unambiguously defines coiled-coil helix boundaries, oligomerisation states and helix orientations, and also assigns heptad registers. Structures retrieved from the Protein Data Bank included parallel and anti-parallel variants of two, three and four-stranded coiled coils, one example of a parallel pentamer and a small number of structures that extend the classical description of a coiled coil. We anticipate that our structural database and the associated sequence data that we have gathered will be of use in identifying principles for coiled-coil assembly, prediction and design. To illustrate this we give examples of sequence and structural analyses of the structures that are possible using the new data bases, and we present amino acid profiles for the heptad repeats of different motifs. (C) 2001 Academic Press.