Physicochemical, functional, and evolutionary characteristics of protein loop regions in human and Escherichia coli proteomes

Abstract

Protein loops play crucial roles in the formation of binding and enzyme active sites. However, general structural and biological characteristics of these loops remain unclear. In this study, we investigated loops from structural and evolutionary perspectives using the entire protein data bank (PDB), Homo sapiens, and Escherichia coli proteins. We found that loop sequences tended to be unique among species. However, loop properties exhibited high similarity or conservation. Class, Architecture, Topology, and Homologous superfamily (CATH) classification analysis, which clusters domains within protein chains into superfamilies indicating an evolutionary relationship, suggested that the terminal residues of most loops connected to the same superfamily. The functions of conserved loops were not consistently conserved. The amino acid composition profiles showed different preferences. Collectively, this study provides an overview of loops from structural, functional, and evolutionary perspectives and a vast natural loop repertoire for future investigations.

Caption of Graphical Abstract

Comprehensive analysis of protein loop properties reveals conserved structural features across species. Four key loop features were characterized: length (number of residues), distance (end-to-end separation), stretch (normalized distance), and amino acid composition. Loops were also classified by CATH superfamily context, distinguishing within-domain loops (A=B, same superfamily) from inter-domain loops (A≠B, different superfamilies). Conserved loop sequences between human and E. coli were also investigated.