From interaction networks to interfaces, scanning intrinsically disordered regions using AlphaFold2
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Abstract
The revolution brought about by AlphaFold2 opens promising perspectives to unravel the complexity of protein-protein interaction networks. The analysis of interaction networks obtained from proteomics experiments does not systematically provide the delimitations of the interaction regions. This is of particular concern in the case of interactions mediated by intrinsically disordered regions, in which the interaction site is generally small. Using a dataset of protein-peptide complexes involving intrinsically disordered regions that are non-redundant with the structures used in AlphaFold2 training, we show that when using the full sequences of the proteins, AlphaFold2-Multimer only achieves 40% success rate in identifying the correct site and structure of the interface. By delineating the interaction region into fragments of decreasing size and combining different strategies for integrating evolutionary information, we manage to raise this success rate up to 90%. We obtain similar success rates using a much larger dataset of protein complexes taken from the ELM database. Beyond the correct identification of the interaction site, our study also explores specificity issues. We show the advantages and limitations of using the AlphaFold2 confidence score to discriminate between alternative binding partners, a task that can be particularly challenging in the case of small interaction motifs.
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Together with the extensive interface between the CTF18 complex and POLE1, these interactions would position the catalytic, N-terminal domain of Pol ε adjacent to CMG's rear exit channel.
“Together with the extensive interface between the CTF18 complex and POLE173, these interactions would position the catalytic, N-terminal domain of Pol ε adjacent to CMG’s rear exit channel”
From Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions (2025) · cites this paper as [73]
The Results passages on binding interfaces discuss AlphaFold2 predictions for protein–peptide complexes, not the proposed position of Pol ε beside CMG’s rear exit channel. Searches for CTF18, POLE1, CMG, and the catalytic N-terminal domain found no passage in our copy addressing that arrangement. (LLM, conf=0.77)
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- Authors
- Bret, H., Gao, J., Zea, D. J., Andreani, J., & Guerois, R.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Venue
- Nature Communications
- Published
- 2024-01-18
- Volume
- 15
- Issue
- 1
- Pages
- 597-597
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10796318
- OpenAlex
- W4390986414
- Cited by
- 103
- References
- 71
- Citations by year
- 2026: 24 · 2025: 45 · 2024: 29 · 2023: 4 · 2022: 1
- FWCI
- 13.34
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Agence Nationale de la Recherche (ANR-18-CE45-0005)
- 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
- intrinsically disordered regions, protein-protein interfaces, interaction site prediction, AlphaFold2, AlphaFold2-Multimer, protein-peptide complex, protein complexes, evolutionary information, interaction networks
- MeSH terms
- Biological Evolution, Protein Binding, Proteins, Protein Interaction Maps, Intrinsically Disordered Proteins
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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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