Analysing six types of protein-protein interfaces
Analysing six types of protein-protein interfaces
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DOI：
10.1016/s0022-2836(02)01223-8
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发表时间：
2003-01-10
影响因子：
5.6
通讯作者：
Rost, B
中科院分区：
文献类型：
--
作者：
Ofran, Y;Rost, B
非共价残基侧链相互作用存在于许多不同类型的蛋白质中，并促进许多生物功能。这些差异是否表现在界面的序列组成和/或残基-残基接触偏好上？之前的研究分析了小数据集，并给出了相互矛盾的答案。在这里，我们介绍了一种新的数据挖掘方法，它产生了所分析的最大的高分辨率交互数据集。我们介绍了一种基于信息论的分析方法。根据序列特征，我们能够区分六种类型的蛋白质界面，每一种都对应于不同的残基之间的功能或结构结合。特别是，我们发现在同一结构域内的残基之间、不同结构域之间的残基相互作用、永久界面和瞬时界面之间以及同源低聚物和杂寡体之间的相互作用在氨基酸组成和残基偏好方面存在显著差异。这六种类型之间的差异是如此之大，以至于仅使用氨基酸组成，我们就可以统计地预测1000个残基池属于六种类型的界面中的哪一种，准确率为63%-100%。所有界面都与Swiss-Prot中所有残基的背景、表面残基组和未参与非平凡相互作用的内部残基有显著不同。总体而言，我们的结果表明，界面类型可以从序列中预测出来，界面类型的特定平均场势可能足以满足某些应用。(C)2003爱思唯尔科学有限公司。保留所有权利。
Non-covalent residue side-chain interactions occur in many different types of proteins and facilitate many biological functions. Are these differences manifested in the sequence compositions and/or the residue-residue contact preferences of the interfaces? Previous studies analysed small data sets and gave contradictory answers. Here, we introduced a new data-mining method that yielded the largest high-resolution data set of interactions analysed. We introduced an information theory-based analysis method. On the basis of sequence features, we were able to differentiate six types of protein interfaces, each corresponding to a different functional or structural association between residues. Particularly, we found significant differences in amino acid composition and residue-residue preferences between interactions of residues within the same structural domain and between different domains, between permanent and transient interfaces, and between interactions associating homo-oligomers and hetero-oligomers. The differences between the six types were so substantial that, using amino acid composition alone, we could predict statistically to which of the six types of interfaces a pool of 1000 residues belongs at 63-100% accuracy. All interfaces differed significantly from the background of all residues in SWISS-PROT, from the group of surface residues, and from internal residues that were not involved in non-trivial interactions. Overall, our results suggest that the interface type could be predicted from sequence and that interface-type specific mean-field potentials may be adequate for certain applications. (C) 2003 Elsevier Science Ltd. All rights reserved.