A comprehensive analysis of non-sequential alignments between all protein structures.
A comprehensive analysis of non-sequential alignments between all protein structures.
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DOI：
10.1186/1472-6807-7-78
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发表时间：
2007-11-16
影响因子：
--
通讯作者：
Ilyin VA
中科院分区：
文献类型：
--
作者：
Abyzov A;Ilyin VA
蛋白质之间的大多数关系可以表示为常规的序列比对。然而，许多研究者报道了比较蛋白质中具有不同连接性的不寻常的非顺序比对。理解这些非顺序排列是很有趣的;它们是独特的、零星的还是经常发生的;它们是属于几个特定的折叠还是分布在许多不同的折叠中，作为蛋白质结构的共同特征。在这里，我们提出了一个全面的大规模研究的非序列比对可用的蛋白质结构在蛋白质数据库。该研究是在TOPOFIT方法的帮助下对8，865个蛋白质结构的非冗余集进行的。据估计，17.4%至35.2%的所有比对是非连续的，这取决于参数的变化。对数据的分析表明，蛋白质之间的非顺序关系确实系统地大量发生。已经观察到各种大小和数量的非连续片段，其中发现了由多达12个片段组成的比对的片段重排的所有可能的复杂性。已经发现，非顺序比对不限于任何特定折叠的蛋白质，并且存在于其中的200多个中。此外，它们中的许多在具有不同折叠分配的蛋白质之间被发现。它已被证明，蛋白质结构的对称性不能解释非顺序排列。因此，已经提供了令人信服的证据，表明蛋白质之间的非顺序比对是系统的，并且在整个蛋白质宇宙中广泛存在。蛋白质之间普遍存在的非顺序排列现象可能代表了蛋白质结构组织规则的缺失。对这种现象的更详细的研究将增强我们对蛋白质稳定性、折叠和进化的理解。
The majority of relations between proteins can be represented as a conventional sequential alignment. Nevertheless, unusual non-sequential alignments with different connectivity of the aligned fragments in compared proteins have been reported by many researchers. It is interesting to understand those non-sequential alignments; are they unique, sporadic cases or they occur frequently; do they belong to a few specific folds or spread among many different folds, as a common feature of protein structure. We present here a comprehensive large-scale study of non-sequential alignments between available protein structures in Protein Data Bank. The study has been conducted on a non-redundant set of 8,865 protein structures aligned with the aid of the TOPOFIT method. It has been estimated that between 17.4% and 35.2% of all alignments are non-sequential depending on variations in the parameters. Analysis of the data revealed that non-sequential relations between proteins do occur systematically and in large quantities. Various sizes and numbers of non-sequential fragments have been observed with all possible complexities of fragment rearrangements found for alignments consisting of up to 12 fragments. It has been found that non-sequential alignments are not limited to proteins of any particular fold and are present in more than two hundred of them. Moreover, many of them are found between proteins with different fold assignments. It has been shown that protein structure symmetry does not explain non-sequential alignments. Therefore, compelling evidences have been provided that non-sequential alignments between proteins are systematic and widespread across the protein universe. The phenomenon of the widespread occurrence of non-sequential alignments between proteins might represent a missing rule of protein structure organization. More detailed study of this phenomenon will enhance our understanding of protein stability, folding, and evolution.
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DOI：
10.1073/pnas.97.1.67
发表时间：
2000-01-04
影响因子：
11.1
作者：
Gooptu, B;Hazes, B;Lomas, DA
通讯作者：
Lomas, DA
影响因子：
3.9
作者：
Jeltsch, A
通讯作者：
Jeltsch, A
影响因子：
8
作者：
Jung, J;Lee, B
通讯作者：
Lee, B
影响因子：
15
作者：
Horne, WS;Yadav, MK;Ghadiri, MR
通讯作者：
Ghadiri, MR
DOI：
10.1073/pnas.0401595101
发表时间：
2004-05-11
影响因子：
11.1
作者：
Corbett, KD;Shultzaberger, RK;Berger, JM
通讯作者：
Berger, JM