ArticleProceedings of the National Academy of Sciences of the United States of America2016
Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 40 citations in OpenAlex.
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration.Scientific reports · 2024Article
- Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences.Nature communications · 2021Article
- Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs.Computational and structural biotechnology journal · 2021Article
- Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes.Computational and structural biotechnology journal · 2021Article
- CoRNeA: A Pipeline to Decrypt the Inter-Protein Interfaces from Amino Acid Sequence Information.Biomolecules · 2020Article
- Comparative Structural Analysis of 20S Proteasome Ortholog Protein Complexes by Native Mass Spectrometry.ACS central science · 2020Article
- Predicted Structural Variability ofFrontiers in microbiology · 2020Article
- A protocol to automatically calculate homo-oligomeric protein structures through the integration of evolutionary constraints and NMR ambiguous contacts.Computational and structural biotechnology journal · 2020Article
- A multi-scale coevolutionary approach to predict interactions between protein domains.PLoS computational biology · 2019Article
- Improved measures for evolutionary conservation that exploit taxonomy distances.Nature communications · 2019Article
- Inter-residue, inter-protein and inter-family coevolution: bridging the scales.Current opinion in structural biology · 2018Review
- Structural Insight Into the Role of Mutual Polymorphism and Conservatism in the Contact Zone of the NFR5-K1 Heterodimer With the Nod Factor.Frontiers in plant science · 2018Article
- Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
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Authors and funding
4 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Protein-protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that coevolution points to structurally conserved contacts at protein-protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a domain-centered protocol to study the interplay between residue coevolution and structural conservation of protein-protein interfaces. We show that sequence-based coevolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein-protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic coevolutionary analysis to the prediction of eukaryotic interfaces further illustrate the potential of this approach.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.