Finding evolutionary relations beyond superfamilies: Fold‐based superfamilies

Abstract

Superfamily classifications are based variably on similarity of sequences, global folds, local structures, or functions. We have examined the possibility of defining superfamilies purely from the viewpoint of the global fold/function relationship. For this purpose, we first classified protein domains according to the ␤-sheet topology. We then introduced the concept of kinship relations among the classified ␤-sheet topology by assuming that the major elementary event leading to creation of a new ␤-sheet topology is either an addition or deletion of one ␤-strand at the edge of an existing ␤-sheet during the molecular evolution. Based on this kinship relation, a network of protein domains was constructed so that the distance between a pair of domains represents the number of evolutionary events that lead one from the other domain. We then mapped on it all known domains with a specific core chemical function (here taken, as an example, that involving ATP or its analogs). Careful analyses revealed that the domains are found distributed on the network as >20 mutually disjointed clusters. The proteins in each cluster are defined to form a fold-based superfamily. The results indicate that >20 ATP-binding protein superfamilies have been invented independently in the process of molecular evolution, and the conservative evolutionary diffusion of global folds and functions is the origin of the relationship between them.

Classification Modeling and Recognition of Protein Fold Type

“…对自然界存在的数百到数千种 折叠类型进行系统分类和识别, 将有助于揭示蛋白 质的折叠规律. 蛋白质折叠类型识别的研究在国内外已有一些 报道并取得一些进展.Dubchak 等 [8,9] 基于氨基酸序 列用神经网络方法进行折叠识别, 包含 83 个折叠类 型, 平均识别准确率为 71.7%;Ding 等 [10] 用支持向量 机(SVM)进行蛋白质折叠识别, 包含 27 个 SCOP 折 叠子, 平均预测精度为 56%;Karplus 等 [11] [12,13] . 尽管 SCOP、 CATH 等蛋白质折叠分类数据 库可用, 但它们不是为折叠识别而产生的 [14] .…”

Cloning and Characterization of New Protocatechuate Dioxygenase (PCAD) Superfamily Members

“…The term "superfamily" has experienced a series of changes, and has evolved to have a clearer and more explicit definition as a deeper understanding of protein structure and function has developed. (6)(7)(8)(9)(10) The first person to use superfamily and family to systematically classify proteins is Margaret O. Dayhoff for "Atlas of Protein Sequence and Structure" in 1965. Without the invention of techniques to obtain protein structures, proteins are categorized only based upon sequence identities.…”