Consistency analysis of similarity between multiple alignments: Prediction of protein function and fold structure from analysis of local sequence motifs
Consistency analysis of similarity between multiple alignments: Prediction of protein function and fold structure from analysis of local sequence motifs
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DOI：
10.1006/jmbi.2001.4466
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发表时间：
2001-03-30
影响因子：
5.6
通讯作者：
Pietrokovski, S
中科院分区：
文献类型：
--
作者：
Kunin, V;Chan, B;Pietrokovski, S
提出了一种新的分析多序列蛋白质模体（块）之间相似性的方法。它标识一致对齐的块的集合。这些被发现是出现在不同环境中的具有相似功能和结构的蛋白质区域。例如，Rossmann折叠配体结合区域被发现类似于TIM桶和甲基化酶区域，预测各种蛋白质家族具有TIM桶折叠，并且从它们的序列中鉴定ClpP蛋白酶和巴豆酸酶折叠之间的结构关系。除了识别局部结构特征之外，短序列区域（少于20个氨基酸区域）之间的序列相似性还预测几百个氨基酸残基长的整个结构域（折叠）的结构相似性。这些关系中的大多数不能通过其他先进的序列对序列或序列对多重比对比较来确定。我们描述的方法（称为CYRCA），目前的例子，我们的研究结果，并讨论其影响。(C)北京：科学出版社.
A new method to analyze the similarity between multiply aligned protein motifs (blocks) was developed. It identifies sets of consistently aligned blocks. These are found to be protein regions of similar function and structure that appear in different contexts. For example, the Rossmann fold ligand-binding region is found similar to TIM barrel and methylase regions, various protein families are predicted to have a TIM-barrel fold and the structural relation between the ClpP protease and crotonase folds is identified from their sequence. Besides identifying local structure features, sequence similarity across short sequence-regions (less than 20 amino acid regions) also predicts structure similarity of whole domains (folds) a few hundred amino acid reidues long. Most of these relations could not be identified by other advanced sequence-to-sequence or sequence-to-multiple alignments comparisons. We describe the method (termed CYRCA), present examples of our findings, and discuss their implications. (C) 2001 Academic Press.