Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by Direct Coupling Analysis

Abstract

Proteins have evolved to perform diverse cellular functions, from serving as reaction catalysts to coordinating cellular propagation and development. Frequently, proteins do not exert their full potential as monomers but rather undergo concerted interactions as either homo-oligomers or with other proteins as hetero-oligomers. The experimental study of such protein complexes and interactions has been arduous. Theoretical structure prediction methods are an attractive alternative. Here, we investigate homo-oligomeric interfaces by tracing residue coevolution via the global statistical Direct Coupling Analysis (DCA). DCA can accurately infer spatial adjacencies between residues. These adjacencies can be included as constraints in structure-prediction techniques to predict high-resolution models. By taking advantage of the on-going exponential growth of sequence databases, we go significantly beyond anecdotal cases of a few protein families and apply DCA to a systematic large-scale study of nearly 2000 PFAM protein families with sufficient sequence information and structurally resolved homo-oligomeric interfaces. We find that large interfaces are commonly identified by DCA. We further demonstrate that DCA can differentiate between subfamilies of different binding modes within one large PFAM family. Sequence derived contact information for the subfamilies proves sufficient to assemble accurate structural models of the diverse protein-oligomers. Thus, we provide an approach to investigate oligomerization for arbitrary protein families leading to structural models complementary to often difficult experimental methods. Combined with ever more abundant sequential data, we anticipate that this study will be instrumental to allow the structural description of many hetero-protein complexes in the future.

arXiv comment18 pages, 6 figures, to appears in PNAS

References in corpus (9)

• Direct-coupling analysis of residue co-evolution captures native contacts across many protein families
• Identification of direct residue contacts in protein-protein interaction by message passing
• Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models
• Sequence co-evolution gives 3D contacts and structures of protein complexes
• Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1
• Inferring interaction partners from protein sequences
• Simultaneous identification of specifically interacting paralogs and inter-protein contacts by Direct-Coupling Analysis
• Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction
• Inter-protein sequence co-evolution predicts known physical interactions in bacterial ribosomes and the trp operon

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