Data_Sheet_1_Identification and Analysis of Long Repeats of Proteins at the Domain Level.xlsx

Amino acid repeats play an important role in the structure and function of proteins. Analysis of long repeats in protein sequences enables one to understand their abundance, structure and function in the protein universe. In the present study, amino acid repeats of length >50 (long repeats) were identified in a non-redundant set of UniProt sequences using the RADAR program. The underlying structures and functions of these long repeats were carried out using the Gene3D for structural domains, Pfam for functional domains and enzyme and non-enzyme functional classification for catalytic and binding of the proteins. From a structural perspective, these long repeats seem to predominantly occur in certain architectures such as sandwich, bundle, barrel, and roll and within these architectures abundant in the superfolds. The lengths of the repeats within each fold are not uniform exhibiting different structures for different functions. We also observed that long repeats are in the domain regions of the family and are involved in the function of the proteins. After grouping based on enzyme and non-enzyme classes, we observed the abundant occurrence of long repeats in specific catalytic and binding of the proteins. In this study, we have analyzed the occurrence of long repeats in the protein sequence universe apart from well-characterized short tandem repeats in sequences and their structures and functions of the proteins at the domain level. The present study suggests that long repeats may play an important role in the structure and function of domains of the proteins.

氨基酸重复序列在蛋白质的结构与功能中扮演着关键角色。对蛋白质序列中的长重复序列开展分析，能够帮助我们明晰其在蛋白质全域中的丰度、结构与功能特征。本研究借助RADAR程序，从非冗余的通用蛋白质知识库（UniProt）序列集中，鉴定出长度大于50的氨基酸重复序列（即长重复序列）。针对这些长重复序列的潜在结构与功能，我们分别采用Gene3D结构域数据库、Pfam功能域数据库，以及酶/非酶功能分类体系，对蛋白质的催化与结合特性进行了系统分析。从结构视角来看，这类长重复序列主要富集于特定的折叠架构中，如三明治折叠、束状折叠、桶状折叠与卷绕折叠，且在这些架构内的超折叠（superfolds）区域中分布尤为密集。各折叠类型内部的重复序列长度并不均一，不同长度的重复序列对应着差异化的功能结构。我们还观察到，长重复序列位于蛋白质家族的结构域区域内，并直接参与蛋白质的功能行使过程。在按照酶与非酶类别进行分组后，我们发现长重复序列在特定的蛋白质催化与结合功能类别中呈现出显著的丰度优势。本研究不仅分析了序列中已被充分表征的短串联重复序列（short tandem repeats），还对蛋白质序列全域内的长重复序列的分布情况，及其在结构域层面的蛋白质结构与功能特征进行了深入探究。本研究结果表明，长重复序列可能在蛋白质结构域的结构构建与功能行使中发挥重要作用。