Evolution of protein architectures inferred from phylogenomic analysis of CATH

S. A. Bukhari, G. Caetano-Anollés
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引用次数: 1

Abstract

Protein architecture refers to similar secondary structural arrangements irrespective of their connectivity. Here we aim to explore the evolution of protein architectures by benchmarking CATH and SCOP annotations. For example, we explore the appearance and diversification of protein architectures such as sandwiches, bundles, barrels, solenoids, ribbons, trefoils, prisms and propellers. Structural phylogenies generated at CATH “A”, “T” and “H” levels of structural abstraction revealed patterns of reductive evolution and three epochs in the evolution of protein world. Although CATH and SCOP differ significantly in their protein domain definitions and in the hierarchical partitioning of fold space, our findings strongly support the fact that both protein structural classification systems classify a protein on a very similar theoretical basis by taking into account their structural, functional and evolutionary roles. The tree of “A” showed that the 3-layer (aba) sandwich (3.40), the orthogonal bundle (1.10) and the alpha-beta complex (3.90) harbor simple secondary structure arrangements that are the most ancient, popular and abundant architectures in the protein world.
从CATH的系统基因组分析推断蛋白质结构的进化
蛋白质结构是指相似的二级结构排列,而不考虑它们的连通性。在这里,我们的目标是通过对CATH和SCOP注释进行基准测试来探索蛋白质结构的演变。例如,我们探索蛋白质结构的外观和多样化,如三明治,束,桶,螺线管,丝带,三叶草,棱镜和螺旋桨。在结构抽象的CATH“A”、“T”和“H”水平上产生的结构系统发育揭示了蛋白质世界进化的还原进化模式和三个时代。尽管CATH和SCOP在蛋白质结构域定义和折叠空间的分层划分方面存在显著差异,但我们的研究结果强烈支持这一事实,即两种蛋白质结构分类系统通过考虑其结构、功能和进化作用,在非常相似的理论基础上对蛋白质进行分类。“A”树表明,3层(aba)三明治(3.40)、正交束(1.10)和α - β复合物(3.90)具有简单的二级结构排列,是蛋白质世界中最古老、最流行和最丰富的结构。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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