Sequence co-evolution gives 3D contacts and structures of protein complexes
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Abstract
Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution.
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One of the major insights leveraged by AlphaFold comes from the use of evolutionary covariations that can be extracted from large-scale multiple sequence alignments.
“One of the major insights leveraged by AlphaFold 1,2 comes from the use of evolutionary covariations that can be extracted from large-scale multiple sequence alignments.[49][50][51][52][53][54]”
From AlphaFold and Implications for Intrinsically Disordered Proteins (2021) · cites this paper as [52]
Amino acid coevolution has been used to guide modeling of complexes for cases in which the structures of the partners are known, and to systematically identify pairs of interacting proteins in Prokaryotes with accuracy higher than experimental screens.
“Such amino acid coevolution has been used to guide modeling of complexes for cases in which the structures of the partners are known (11,12), and to systematically identify pairs of interacting proteins in Prokaryotes with accuracy higher than experimental screens (9).”
From Computed structures of core eukaryotic protein complexes (2021) · cites this paper as [12]
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Protein oligomer modeling guided by predicted interchain contacts in <scp>CASP14</scp>
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- Authors
- Hopf, T. A., Schärfe, C. P. I., Rodrigues, J. P. G. L. M., Green, A. G., Kohlbacher, O., Sander, C., Bonvin, A. M. J. J., & Marks, D. S.
- Affiliations
- Harvard University (US)
- Utrecht University (NL)
- Quantitative Biology Center (DE)
- Memorial Sloan Kettering Cancer Center (US)
- Corresponding author
- Sander, Chris
- Bonvin, Alexandre M J J
- Marks, Debora S
- ORCID
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2014-09-25
- Volume
- 3
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC4360534
- OpenAlex
- W2120836664
- Cited by
- 515
- References
- 70
- Citations by year
- 2026: 23 · 2025: 31 · 2024: 20 · 2023: 34 · 2022: 46 · 2021: 57 · 2020: 37 · 2019: 62 · 2018: 60 · 2017: 75 · 2016: 36 · 2015: 31 · 2014: 3
- FWCI
- 19.83
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- arXiv (Cornell University)
- Funders
- National Institute of General Medical Sciences (R01 GM106303)
- Fulbright Commission
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- protein-protein interaction, protein complexes, correlated mutations, evolutionary coupling, 3D structure prediction, protein-protein interaction network
- MeSH terms
- Escherichia coli, Models, Molecular, Protein Binding, Protein Conformation, Gene Expression, Genome, Bacterial, Evolution, Molecular, Protein Interaction Mapping, Escherichia coli Proteins, Databases, Protein, Gene Regulatory Networks
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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