The DOI matches its Crossref record; 69 of the 69 references it cites were found in a registry or an index.
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe check wasn’t confident either way, so it gives no verdict — never disputed.
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
“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 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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL.
Monod, J., Wyman, J., & Changeux, J. (1965) · Journal of Molecular Biology · doi:10.1016/s0022-2836(65)80285-6 · Cited by 7,681
The Energy Landscapes and Motions of Proteins
Frauenfelder, H., Sligar, S. G., & Wolynes, P. G. (1991) · Science · doi:10.1126/science.1749933 · Cited by 3,250
Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits *
Koshland, D. E., Némethy, G., & Filmer, D. (1966) · Biochemistry · doi:10.1021/bi00865a047 · Cited by 3,019
Macromolecular crowding: obvious but underappreciated
Ellis, R. J. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(01)01938-7 · Cited by 2,309
Zhou, H., Rivas, G., & Minton, A. P. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.032807.125817 · Cited by 2,160
Application of a Theory of Enzyme Specificity to Protein Synthesis.
Koshland, D. (1958) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.44.2.98 · Cited by 2,140
Intrinsically unstructured proteins
Tompa, P. (2002) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(02)02169-2 · Cited by 2,056
The role of dynamic conformational ensembles in biomolecular recognition
Boehr, D. D., Nussinov, R., & Wright, P. E. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.232 · Cited by 2,008
Self-citationEinfluss der Configuration auf die Wirkung der Enzyme
Fischer, E. (1894) · Berichte der deutschen chemischen Gesellschaft · doi:10.1002/cber.18940270364 · Cited by 1,841
Understanding protein non-folding
Uversky, V. N., & Dunker, A. K. (2010) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2010.01.017 · Cited by 1,221
Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution
Lange, O. F., Lakomek, N., Farès, C., Schroeder, G. F., Walter, K. F. A., Becker, S., Meiler, J., Grubmüller, H., Griesinger, C., & de Groot, B. L. (2008) · Science · doi:10.1126/science.1157092 · Cited by 1,044
Dynamical networks in tRNA:protein complexes
Sethi, A., Eargle, J., Black, A. A., & Luthey-Schulten, Z. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810961106 · Cited by 777
Dynamics of Water in Biological Recognition
Pal, S. K., & Zewail, A. H. (2004) · Chemical Reviews · doi:10.1021/cr020689l · Cited by 761
Protein Sectors: Evolutionary Units of Three-Dimensional Structure
Halabi, N. M., Rivoire, O., Leibler, S., & Ranganathan, R. (2009) · Cell · doi:10.1016/j.cell.2009.07.038 · Cited by 697
Crowding Effects on Diffusion in Solutions and Cells
Dix, J. A., & Verkman, A. S. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.032807.125824 · Cited by 690
Folding funnels, binding funnels, and protein function
Tsai, C., Kumar, S., Ma, B., & Nussinov, R. (1999) · Protein Science · doi:10.1110/ps.8.6.1181 · Cited by 648
Self-citationFolding funnels and binding mechanisms
Ma, B., Kumar, S., Tsai, C.-J., & Nussinov, R. (1999) · Protein Engineering, Design and Selection · doi:10.1093/protein/12.9.713 · Cited by 594
Self-citationConformational selection or induced fit: A flux description of reaction mechanism
Hammes, G. G., Chang, Y.-C., & Oas, T. G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907195106 · Cited by 577
The role of structural disorder in the function of RNA and protein chaperones
Tompa, P., & Csermely, P. (2004) · The FASEB Journal · doi:10.1096/fj.04-1584rev · Cited by 555
Self-citationSmock, R. G., & Gierasch, L. M. (2009) · Science · doi:10.1126/science.1169377 · Cited by 510
Allostery: Absence of a change in shape does not imply that allostery is not at play
Tsai, C.-J., del Sol, A., & Nussinov, R. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.02.034 · Cited by 453
Self-citationProtein aggregation in crowded environments
Ellis, R. J., & Minton, A. P. (2006) · Biological Chemistry · doi:10.1515/bc.2006.064 · Cited by 432
Multiple diverse ligands binding at a single protein site: A matter of pre‐existing populations
Ma, B., Shatsky, M., Wolfson, H. J., & Nussinov, R. (2002) · Protein Science · doi:10.1110/ps.21302 · Cited by 420
Self-citationVisualization of transient encounter complexes in protein–protein association
Tang, C., Iwahara, J., & Clore, G. M. (2006) · Nature · doi:10.1038/nature05201 · Cited by 406
Stochastic focusing: Fluctuation-enhanced sensitivity of intracellular regulation
Paulsson, J. F., Berg, O. G., & Ehrenberg, M. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.110057697 · Cited by 391
Dynamic activation of an allosteric regulatory protein
Tzeng, S., & Kalodimos, C. G. (2009) · Nature · doi:10.1038/nature08560 · Cited by 384
Edgetic perturbation models of human inherited disorders
Zhong, Q., Simonis, N., Li, Q., Charloteaux, B., Heuze, F., Klitgord, N., Tam, S., Yu, H., Venkatesan, K., Mou, D., et al. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.80 · Cited by 359
Anchor residues in protein–protein interactions
Rajamani, D., Thiel, S., Vajda, S., & Camacho, C. J. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401942101 · Cited by 341
Okazaki, K.-I., & Takada, S. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0802524105 · Cited by 320
Insufficiently dehydrated hydrogen bonds as determinants of protein interactions
Fernández, A., & Scheraga, H. A. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0136888100 · Cited by 258
Network analysis of protein dynamics
Böde, C., Kovács, I. A., Szalay, M., Palotai, R., Korcsmáros, T., & Csermely, P. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.05.021 · Cited by 227
Self-citationLevy, Y., Cho, S. S., Onuchic, J. N., & Wolynes, P. G. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.12.021 · Cited by 213
Ligand-Dependent Equilibrium Fluctuations of Single Calmodulin Molecules
Junker, J. P., Ziegler, F., & Rief, M. (2009) · Science · doi:10.1126/science.1166191 · Cited by 211
Structured disorder and conformational selection
Tsai, C., Ma, B., Sham, Y. Y., Kumar, S., & Nussinov, R. (2001) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.1107 · Cited by 202 · cited 1×
“a purely induced fit type binding mechanism is not characteristic even in these cases, because IDPs also have a broad fluctuating conformational ensemble, and conformational selection can take place [49, 50, 51]. The initial binding event of IDPs was proposed to be assisted by a ‘fly-casting’-like search mechanism, wh…”
Self-citationMultiple native states reveal persistent ruggedness of an RNA folding landscape
Solomatin, S. V., Greenfeld, M., Chu, S., & Herschlag, D. (2010) · Nature · doi:10.1038/nature08717 · Cited by 200
Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation
Bailor, M. H., Sun, X., & Al‐Hashimi, H. M. (2010) · Science · doi:10.1126/science.1181085 · Cited by 194
Włodarski, T., & Žagrović, B. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906966106 · Cited by 194
Complementarity of Structure Ensembles in Protein-Protein Binding
Grünberg, R., Leckner, J., & Nilges, M. (2004) · Structure · doi:10.1016/j.str.2004.09.014 · Cited by 187
Selected‐fit versus induced‐fit protein binding: Kinetic differences and mutational analysis
Weikl, T. R., & von Deuster, C. I. E. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22223 · Cited by 173
Schrank, T. P., Bolen, D. W., & Hilser, V. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906510106 · Cited by 171
The origins and evolution of functional modules: lessons from protein complexes
Pereira‐Leal, J. B., Levy, E. D., & Teichmann, S. A. (2006) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2005.1807 · Cited by 165
Pechmann, S., Levy, E. D., Tartaglia, G. G., & Vendruscolo, M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0812414106 · Cited by 162
Boehr, D. D., McElheny, D., Dyson, H. J., & Wright, P. E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914163107 · Cited by 142
A Coupled Equilibrium Shift Mechanism in Calmodulin-Mediated Signal Transduction
Gsponer, J. A., Christodoulou, J. C., Cavalli, A., Bui, J. M., Richter, B., Dobson, C. M., & Vendruscolo, M. (2008) · Structure · doi:10.1016/j.str.2008.02.017 · Cited by 134
Csermely, P. (2008) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2008.09.006 · Cited by 129
Self-citationBashir, Q., Volkov, A. N., Ullmann, G. M., & Ubbink, M. (2009) · Journal of the American Chemical Society · doi:10.1021/ja9064574 · Cited by 124
Transient Non-native Hydrogen Bonds Promote Activation of a Signaling Protein
Gardino, A. K., Villali, J., Kivenson, A., Lei, M., Liu, C. F., Steindel, P. A., Eisenmesser, E. Z., Labeikovsky, W., Wolf‐Watz, M., Clarkson, M. W., et al. (2009) · Cell · doi:10.1016/j.cell.2009.11.022 · Cited by 109
Toward a quantitative theory of intrinsically disordered proteins and their function
Liu, J., Faeder, J. R., & Camacho, C. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907710106 · Cited by 106
Reichheld, S. E., Yu, Z., & Davidson, A. (2009) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0911566106 · Cited by 106
Formaneck, M. S., Ma, L., & Cui, Q. (2006) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20893 · Cited by 106
del Sol, A., Araúzo-Bravo, M. J., Amoros, D., & Nussinov, R. (2007) · Genome biology · doi:10.1186/gb-2007-8-5-r92 · Cited by 92
Self-citationCapillarity theory for the fly-casting mechanism
Trizac, E., Levy, Y., & Wolynes, P. G. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914727107 · Cited by 82
Confinement effects on the kinetics and thermodynamics of protein dimerization
Wang, W., Xu, W., Levy, Y., Trizac, E., & Wolynes, P. G. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809649106 · Cited by 77
Use of Game-Theoretical Methods in Biochemistry and Biophysics
Schuster, S., Kreft, J., Schroeter, A., & Pfeiffer, T. (2008) · Journal of Biological Physics · doi:10.1007/s10867-008-9101-4 · Cited by 76
Discrete breathers in protein structures
Piazza, F., & Sanejouand, Y.-H. (2008) · Physical Biology · doi:10.1088/1478-3975/5/2/026001 · Cited by 75
Haliloǧlu, T., Keskin, Ö., Ma, B., & Nussinov, R. (2005) · Biophysical Journal · doi:10.1529/biophysj.104.051342 · Cited by 70
Self-citationKovács, I. A., Szalay, M., & Csermely, P. (2005) · FEBS Letters · doi:10.1016/j.febslet.2005.03.056 · Cited by 66
Self-citationA finite element framework for computation of protein normal modes and mechanical response
Bathe, M. (2007) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21708 · Cited by 66
Long-range energy transfer in proteins
Piazza, F., & Sanejouand, Y.-H. (2009) · Physical Biology · doi:10.1088/1478-3975/6/4/046014 · Cited by 58
Antal, M., Böde, C., & Csermely, P. (2009) · Current Protein and Peptide Science · doi:10.2174/138920309787847617 · Cited by 58
Self-citationDecomposition of Gene Expression State Space Trajectories
Mar, J. C., & Quackenbush, J. F. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000626 · Cited by 40
Gorfe, A. A., Baron, R., & McCammon, J. A. (2008) · Biophysical Journal · doi:10.1529/biophysj.108.136481 · Cited by 34
Materese, C. K., Goldmon, C. C., & Papoian, G. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801850105 · Cited by 33
Desolvation shell of hydrogen bonds in folded proteins, protein complexes and folding pathways
Fernández, A. (2002) · FEBS Letters · doi:10.1016/s0014-5793(02)03204-0 · Cited by 19
The Goldbeter-Koshland Switch in the First-Order Region and Its Response to Dynamic Disorder
Xing, J., & Chen, J. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002140 · Cited by 19
Games network and application to PAs system
Chettaoui, C., Delaplace, F., Manceny, M., & Malo, M. (2006) · Biosystems · doi:10.1016/j.biosystems.2006.09.006 · Cited by 17
Wu, Z., Elgart, V., Qian, H., & Xing, J. (2009) · The Journal of Physical Chemistry B · doi:10.1021/jp903548d · Cited by 12
Závodszky, P., Biszku, E., Lv, A., & Szabolcsi, G. (1972) · PubMed · Cited by 4
Finite Element Framework for Mechanics and Dynamics of Supramolecular Protein Assemblies
Kim, D., Sedeh, R. S., Nguyen, C.-T., & Bathe, M. (2010) · ASME Global Congress on NanoEngineering for Medicine and Biology (NEMB) · doi:10.1115/nemb2010-13312 · Cited by 3
Research works printed but not linked: 2
- Straub, F. B. and Szabolcsi, G. (1964) O dinamicseszkij aszpektah sztukturü fermentov. (On the dynamic aspects of protein structure) In: Molecular Biology, Problems and Perspectives (Braunstein, A. E., ed.), pp. 182–187 (in Russian), Izdat. Nauka
- Závodszky, 1966, Structure of glyceraldehyde-3-phosphate dehydrogenase and its alteration by coenzyme binding, Acta Biochim. Biophys. Acad. Sci. Hung., 1, 389
Cited by
Sorted by citations
Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods
Du, X., Li, Y., Xia, Y.-L., Ai, S.-M., Liang, J., Sang, P., Ji, X., & Liu, S.-Q. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17020144 · Cited by 1,765
Vital nodes identification in complex networks
Lü, L., Chen, D., Ren, X.-L., Zhang, Q.-M., Zhang, Y., & Zhou, T. (2016) · Physics Reports · doi:10.1016/j.physrep.2016.06.007 · Cited by 1,310
Molecular dynamics simulations: advances and applications
Gelpí, J. L., Hospital, A., Goñi, R., & Orozco, M. (2015) · Advances and Applications in Bioinformatics and Chemistry · doi:10.2147/aabc.s70333 · Cited by 996
Structure and dynamics of molecular networks: A novel paradigm of drug discovery
Csermely, P., Korcsmáros, T., Kiss, H., London, G., & Nussinov, R. (2013) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2013.01.016 · Cited by 911
Self-citationAllostery in Disease and in Drug Discovery
Nussinov, R., & Tsai, C. (2013) · Cell · doi:10.1016/j.cell.2013.03.034 · Cited by 769
Self-citation
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.
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 ›
Are you an author, or do you see a problem with this page? Request a review
