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Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
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Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here, we describe an extended conformational selection model that embraces a repertoire of selection and adjustment processes. Induced fit can be viewed as a subset of this repertoire, whose contribution is affected by the bond types stabilizing the interaction and the differences between the interacting partners. We argue that protein segments whose dynamics are distinct from the rest of the protein ('discrete breathers') can govern conformational transitions and allosteric propagation that accompany binding processes and, as such, might be more sensitive to mutational events. Additionally, we highlight the dynamic complexity of binding scenarios as they relate to events such as aggregation and signalling, and the crowded cellular environment.
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“The propagation of conformational change at certain locations228–230 can lead to large amplitude fluctuations of the linked domains.231”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [228]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
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“In a long-standing debate between the proponents of the “induced-fit” and the “conformational selection” binding mechanisms [21–23], the evidence pointing to the latter allows one to precompute the conformational ensemble of the interacting molecule(s) and dock the separate conformers with limited conformational search [24,25].”
From Challenges in protein docking (2020) · cites this paper as [22]
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In the citing paper
“Even if we take P (A p ) equal to 1, and thus assume there are no problematic obstacles involved in generating the building blocks; and also eliminate the localization probability by collapsing chance to necessity (selforganization), P(A c ) can still pose huge obstacles to the chance configuration of the quaternary structure of operative biological systems (Csermely et al., 2010).”
From Using statistical methods to model the fine-tuning of molecular machines and systems (2020) · cites this paper as Csermely et al., 2010
Experimental — accuracy not yet measuredIn the citing paper
“In an induced fit scenario, the ligands bind to the single “open” protein structure and the interaction between a protein and a rigid binding partner induces a conformational change in the protein.”
From AlphaFold, Artificial Intelligence (AI), and Allostery (2022) · cites this paper as [184]
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Raper, A. T., & Suo, Z. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00878 · Cited by 12
Zhao, Y., Zhang, W., Hong, J., Yang, L., Wang, Y., Qu, F., & Xu, W. L. (2024) · The Analyst · doi:10.1039/d4an00378k · Cited by 11
DACMF-DTI: Dual attention embedded cross-modality fusion for drug-target interaction prediction
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Metadata
- Authors
- Csermely, P., Palotai, R., & Nussinov, R.
- Affiliations
- Semmelweis University (HU)
- Tel Aviv University (IL)
- ORCID
- Nussinov, Ruth
- Venue
- Trends in Biochemical Sciences
- Publisher
- Elsevier BV
- Published
- 2010-10
- Volume
- 35
- Issue
- 10
- Pages
- 539-546
- ISSN
- 0968-0004 (ISSN-L)
- PMC
- PMC3018770
- OpenAlex
- W2096929343
- Cited by
- 821
- References
- 69
- Citations by year
- 2026: 40 · 2025: 47 · 2024: 33 · 2023: 23 · 2022: 43 · 2021: 36 · 2020: 56 · 2019: 48 · 2018: 44 · 2017: 49 · 2016: 60 · 2015: 58 · 2014: 75 · 2013: 73 · 2012: 72
- FWCI
- 5.87
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Trends in Biochemical Sciences (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- arXiv (Cornell University) (submittedVersion)
- arXiv (Cornell University)
- Funders
- National Institutes of Health (HHSN261200800001C)
- National Cancer Institute (HHSN261200800001E), Z01BC010441)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Interaction Studies and Fluorescence Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Keywords
- induced fit, conformational selection, protein-protein binding, protein dynamics, discrete breathers, conformational change, protein aggregation, cellular crowding
- MeSH terms
- Animals, Humans, Protein Binding, Protein Conformation, Proteins, Signal Transduction, Protein Folding
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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