Bordin Nicola, Sillitoe Ian, Lees Jonathan G, Orengo Christine
Institute of Structural and Molecular Biology, University College London, London, United Kingdom.
Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom.
Front Mol Biosci. 2021 May 10;8:668184. doi: 10.3389/fmolb.2021.668184. eCollection 2021.
This article is dedicated to the memory of Cyrus Chothia, who was a leading light in the world of protein structure evolution. His elegant analyses of protein families and their mechanisms of structural and functional evolution provided important evolutionary and biological insights and firmly established the value of structural perspectives. He was a mentor and supervisor to many other leading scientists who continued his quest to characterise structure and function space. He was also a generous and supportive colleague to those applying different approaches. In this article we review some of his accomplishments and the history of protein structure classifications, particularly SCOP and CATH. We also highlight some of the evolutionary insights these two classifications have brought. Finally, we discuss how the expansion and integration of protein sequence data into these structural families helps reveal the dark matter of function space and can inform the emergence of novel functions in Metazoa. Since we cover 25 years of structural classification, it has not been feasible to review all structure based evolutionary studies and hence we focus mainly on those undertaken by the SCOP and CATH groups and their collaborators.
本文谨献给赛勒斯·乔西亚（Cyrus Chothia），他是蛋白质结构进化领域的领军人物。他对蛋白质家族及其结构和功能进化机制的精妙分析提供了重要的进化和生物学见解，并牢固确立了结构视角的价值。他是许多其他顶尖科学家的导师和指导者，这些科学家继续着他对结构和功能空间进行表征的探索。他也是那些采用不同方法的人的慷慨且支持性的同事。在本文中，我们回顾了他的一些成就以及蛋白质结构分类的历史，特别是蛋白质结构分类数据库（SCOP）和基于结构的蛋白质分类（CATH）。我们还强调了这两种分类所带来的一些进化见解。最后，我们讨论了将蛋白质序列数据扩展并整合到这些结构家族中如何有助于揭示功能空间的暗物质，并为后生动物新功能的出现提供信息。由于我们涵盖了25年的结构分类，因此回顾所有基于结构的进化研究是不可行的，所以我们主要关注由SCOP和CATH团队及其合作者所开展的研究。
