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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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Even if P(Ap) is taken equal to 1 and localization probability is eliminated by collapsing chance to necessity, P(Ac) can still pose huge obstacles to the chance configuration of the quaternary structure of operative biological systems.
“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
The section on binding in the crowded cellular environment discusses factors that increase and decrease protein encounters, while the section on chaperones describes how they facilitate protein-complex assembly. Neither addresses P(Ac), the assumption that P(Ap) equals 1, or a claimed probability obstacle to forming functional quaternary structures by chance (searched those terms and paraphrases). (LLM, conf=0.75)
Experimental — accuracy not yet measuredPropagation of conformational change at certain locations can cause large-amplitude fluctuations of linked domains.
“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]
In the induced fit mechanism, ligands bind to the single open protein structure and interaction with a rigid binding partner induces a conformational change.
“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]
Evidence points to the conformational selection binding mechanism, which allows one to precompute the conformational ensemble of the interacting molecule(s) and dock the separate conformers with limited conformational search.
“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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The Underappreciated Role of Allostery in the Cellular Network
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Self-citationOn the role of electrostatics in protein–protein interactions
Zhang, Z., Witham, S., & Alexov, E. G. (2011) · Physical Biology · doi:10.1088/1478-3975/8/3/035001 · Cited by 169
Protein dynamics and function from solution state NMR spectroscopy
Kovermann, M., Rogne, P., & Wolf‐Watz, M. (2016) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583516000019 · Cited by 177
Ras activation by SOS: Allosteric regulation by altered fluctuation dynamics
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Helical Propensity in an Intrinsically Disordered Protein Accelerates Ligand Binding
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Li, W., Wolynes, P. G., & Takada, S. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1018983108 · Cited by 159
The Hydrophobic Effects: Our Current Understanding
Sun, Q. (2022) · Molecules · doi:10.3390/molecules27207009 · Cited by 175
Protein conformational dynamics dictate the binding affinity for a ligand
Seo, M., Park, J., Kim, E., Hohng, S., & Kim, H. (2014) · Nature Communications · doi:10.1038/ncomms4724 · Cited by 161
Passive immunotherapies targeting Aβ and tau in Alzheimer's disease
Plotkin, S. S., & Cashman, N. R. (2020) · Neurobiology of Disease · doi:10.1016/j.nbd.2020.105010 · Cited by 160
Principles of Allosteric Interactions in Cell Signaling
Nussinov, R., Tsai, C.-J., & Liu, J. (2014) · Journal of the American Chemical Society · doi:10.1021/ja510028c · Cited by 154
Self-citationExploring the role of receptor flexibility in structure-based drug discovery
Feixas, F., Lindert, S., Sinko, W., & McCammon, J. A. (2014) · Biophysical Chemistry · doi:10.1016/j.bpc.2013.10.007 · Cited by 156
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Cavalli, A., Spitaleri, A., Saladino, G., & Gervasio, F. L. (2014) · Accounts of Chemical Research · doi:10.1021/ar500356n · Cited by 147
Camacho‐Zarco, A. R., Schnapka, V., Guseva, S., Abyzov, A., Adamski, W., Milles, S., Jensen, M. R., Žı́dek, L., Salvi, N., & Blackledge, M. J. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.1c01023 · Cited by 157
Harnessing Allostery: A Novel Approach to Drug Discovery
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Allo-network drugs: harnessing allostery in cellular networks
Nussinov, R., Tsai, C., & Csermely, P. (2011) · Trends in Pharmacological Sciences · doi:10.1016/j.tips.2011.08.004 · Cited by 144
Self-citationA Double-Walled Knotted Cage for Guest-Adaptive Molecular Recognition
Tamura, Y., Takezawa, H., & Fujita, M. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.0c00459 · Cited by 138
Ni, D., Wei, J., He, X., Rehman, A. U., Li, X., Qiu, Y., Pu, J., Lu, S., & Zhang, J. (2020) · Chemical Science · doi:10.1039/d0sc05131d · Cited by 138
Conformational selection in protein binding and function
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The role of protein conformational fluctuations in allostery, function, and evolution
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Understanding the challenges of protein flexibility in drug design.
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Disordered Proteinaceous Machines
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Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ
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Multiple conformational selection and induced fit events take place in allosteric propagation
Nussinov, R., Ma, B., & Tsai, C. (2013) · Biophysical Chemistry · doi:10.1016/j.bpc.2013.10.002 · Cited by 132
Self-citationNussinov, R., Jang, H., Tsai, C., & Cheng, F. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006658 · Cited by 133
Self-citationSequestration of a β‐Hairpin for Control of α‐Synuclein Aggregation
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A single-molecule dissection of ligand binding to a protein with intrinsic dynamics
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Knott, M., & Best, R. B. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002605 · Cited by 113
The Design of Covalent Allosteric Drugs
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Self-citationWang, Y., Chu, X., Longhi, S., Roche, P., Han, W., Wang, E., & Wang, J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1308381110 · Cited by 110
Predictive energy landscapes for protein–protein association
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Application of NMR to studies of intrinsically disordered proteins
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Disease mutations in disordered regions—exception to the rule?
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Fabre, B., Ramos, A., & de Pascual‐Teresa, B. (2014) · Journal of Medicinal Chemistry · doi:10.1021/jm500505f · Cited by 106
Mechanical modulation of catalytic power on F1-ATPase
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Understanding intramembrane proteolysis: from protein dynamics to reaction kinetics
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Metal binding sites in amyloid oligomers: Complexes and mechanisms
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Self-citationASD v2.0: updated content and novel features focusing on allosteric regulation
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Computational Approaches to Predict Protein–Protein Interactions in Crowded Cellular Environments
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SPACER: server for predicting allosteric communication and effects of regulation
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Advances in all atom sampling methods for modeling protein–ligand binding affinities
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Conformational selection in protein binding and function
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Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome
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Recent advances in atomic molecular dynamics simulation of intrinsically disordered proteins
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Using azobenzene photocontrol to set proteins in motion
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Building a virtual ligand screening pipeline using free software: a survey
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NMR line shapes and multi-state binding equilibria
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Selective Molecular Recognition in Amyloid Growth and Transmission and Cross-Species Barriers
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Self-citationxPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures.
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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
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