Allosteric conformational ensembles have unlimited capacity for integrating information
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Abstract
Integration of binding information by macromolecular entities is fundamental to cellular functionality. Recent work has shown that such integration cannot be explained by pairwise cooperativities, in which binding is modulated by binding at another site. Higher-order cooperativities (HOCs), in which binding is collectively modulated by multiple other binding events, appear to be necessary but an appropriate mechanism has been lacking. We show here that HOCs arise through allostery, in which effective cooperativity emerges indirectly from an ensemble of dynamically interchanging conformations. Conformational ensembles play important roles in many cellular processes but their integrative capabilities remain poorly understood. We show that sufficiently complex ensembles can implement any form of information integration achievable without energy expenditure, including all patterns of HOCs. Our results provide a rigorous biophysical foundation for analysing the integration of binding information through allostery. We discuss the implications for eukaryotic gene regulation, where complex conformational dynamics accompanies widespread information integration.
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AlphaFold, which predicts single ranked structures for a protein sequence, is unable to address directly allosteric mechanisms, which are based on populations of conformational states in ensembles.
“AlphaFold, which predicts single ranked structures for a protein sequence, is unable to address directly allosteric mechanisms, which are based on the populations of conformational states in the ensembles.”
From AlphaFold, Artificial Intelligence (AI), and Allostery (2022) · cites this paper as [101]
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AlphaFold, Artificial Intelligence (AI), and Allostery
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- Authors
- Biddle, J. W., Martinez-Corral, R., Wong, F., & Gunawardena, J.
- Affiliations
- Harvard University (US)
- Broad Institute (US)
- Corresponding author
- Gunawardena, Jeremy
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2021-06-09
- Volume
- 10
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC8189718
- OpenAlex
- W3171773865
- Cited by
- 41
- References
- 102
- Citations by year
- 2026: 7 · 2025: 5 · 2024: 5 · 2023: 9 · 2022: 12 · 2021: 3
- FWCI
- 2.26
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Science Foundation (1462629, DGE1144152)
- National Institutes of Health (GM122928)
- European Molecular Biology Organization (ALTF683-2019)
- James S. McDonnell Foundation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- allosteric regulation, conformational ensembles, conformational dynamics, gene expression regulation
- MeSH terms
- Machine Learning, Allosteric Regulation, Animals, Gene Expression Regulation, Models, Biological, Protein Binding, Protein Conformation, Biophysical Phenomena
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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