Mechanisms of ligand binding
Open accessAbstract
Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.
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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 [108]
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AlphaFold, Artificial Intelligence (AI), and Allostery
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Cryo-EM structure of the prothrombin-prothrombinase complex
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Structure‐Based Drug Discovery with Deep Learning**
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“The protein structure contains key information for SBDD, since it relates to protein function [43,44], and it determines ligand binding [45].”
BackgroundAllergens and their associated small molecule ligands—their dual role in sensitization
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Cryo-EM structures of human coagulation factors V and Va
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“7 First, the “conformational selection” paradigm suggests that ligands can bind and stabilize pre-existing conformations that proteins adopt 8 even in the apo state.”
Extending the New Generation of Structure Predictors to Account for Dynamics and Allostery
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Analysis of the Equilibrium Distribution of Ligands in Heterogeneous Media–Approaches and Pitfalls
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Databases of ligand-binding pockets and protein-ligand interactions
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Allostery Frustrates the Experimentalist
Gianni, S., & Jemth, P. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167934 · Cited by 25 · see citing works
Design of facilitated dissociation enables timing of cytokine signalling
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“This function describes the slow relaxation rate constant of binding by conformational selection 64 .”
Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators
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Deep sea osmolytes in action: their effect on protein–ligand binding under high pressure stress
Kamali, A., Jahmidi‐Azizi, N., Oliva, R., & Winter, R. (2022) · Physical Chemistry Chemical Physics · doi:10.1039/d2cp01769e · Cited by 21 · see citing works
A structural perspective on enzymes and their catalytic mechanisms
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Global comparative structural analysis of responses to protein phosphorylation
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“We appreciate the reviewer’s concern regarding the low variance explained by the first two principal components in some Pfam domains.”
Cryo‐EM structures of coagulation factors
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Switchable Zinc(II)-Responsive Globular β-Sheet Peptide.
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No dance, no partner! A tale of receptor flexibility in docking and virtual screening
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Modulation of SARS-CoV-2 spike binding to ACE2 through conformational selection
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“We propose thus a conformational selection model describing a serial, two-step mechanism 61,62 .”
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The active site region plays a critical role in Na+ binding to thrombin
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“Resolution of the four independent rate constants in Equation 1 in the general case demands measurements of both relaxations and analysis through mathematical expressions discussed at length elsewhere (26).”
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The Prothrombin-Prothrombinase Interaction
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Microfluidic Applications in Prostate Cancer Research
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“At present time it should be proposed that our understanding of ligand binding mechanisms has been evolved not only course according to the description of the induced fit (when initial binding stage assumes following conformational changes for optimization of complex between high molecular and ligand components) but w…”
BackgroundLe, Q. D., Le, A. T. H., Wang, T. Y., Krylova, S. M., & Krylov, S. N. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.5c03911 · Cited by 6 · see citing works
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“The behavior of a small molecule within the binding pocket of its target is crucial in understanding its binding affinity, therapeutic efficacy, safety and pharmacokinetics (Di Cera, 2020).”
Induced Fit Describes Ligand Binding to Membrane-Associated Cytochrome P450 3A4
Sweeney, D. T., Zárate-Pérez, F., Stokowa‐Sołtys, K., & Hackett, J. C. (2023) · Molecular Pharmacology · doi:10.1124/molpharm.123.000698 · Cited by 6 · see citing works
“(Di Cera 2020) First, both mechanisms assume that there are no equilibria between oligomers of the enzyme or account for potentially different characteristics to bind ligands.”
Kinetics of Intermediate Release Enhances P450 11B2-Catalyzed Aldosterone Synthesis
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How Osmolytes Regulate Protein–Ligand Interactions: The Case of α-Chymotrypsin and Proflavine
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Targeting Gene Transcription Prevents Antibiotic Resistance
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“Also resulting was hydrophobic For molecular docking, a target molecule considered in fl exible requires minimal re fi nement at the site of the ligand binding [26].”
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“Although diffusion-controlled association rate constants may be approximated analytically, most ligand–protein systems have slower association rates than the diffusion-limited rate because the association event involves multiple steps (Di Cera, 2017; Pang and Zhou, 2017).”
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The Streptococcus phage protein paratox is an intrinsically disordered protein
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“…obtained in a complex with various ligands, all this indicates significant fluctuations in the volume and shape of the target pocket, which, in turn, demonstrates a significant contribution of the factor of ligand-protein fitting or ligand-protein adaptation (Ballante et al., 2021; Di Cera, 2020).”
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“The classical “rapid equilibrium” paradigm for IF and CS binding stipulates that the binding proceeds faster than the transconformation or, more precisely, that the pseudo-first order association rate constant (kobs) of the isolated binding step exceeds the kobs of the isolated transconformation step [36, 48].”
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Estimation of Ligand Binding Free Energy Using Multi-eGO
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“7,9 Accordingly, the result of the assays vary, since ligands may have different preferences for distinct protein conformations.”
Welcome to Biophysics Reviews, a big tent for the biophysics community
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- Authors
- Di Cera, E.
- Affiliations
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine , St. Louis, Missouri 63104, USA
- ORCID
- Di Cera, Enrico
- Venue
- Biophysics Reviews
- Publisher
- AIP Publishing
- Published
- 2020-11-16
- Volume
- 1
- Issue
- 1
- Pages
- 011303-011303
- ISSN
- 2688-4089 (ISSN-L)
- PMC
- PMC7714259
- OpenAlex
- W3105542907
- Cited by
- 73
- References
- 181
- Citations by year
- 2026: 12 · 2025: 17 · 2024: 15 · 2023: 6 · 2022: 11 · 2021: 10 · 2020: 2
- FWCI
- 0.69
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Biophysics Reviews (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Heart, Lung, and Blood Institute (HL049413, HL139554, HL147821)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Interaction Studies and Fluorescence Analysis
- Keywords
- ligand binding, induced fit, conformational selection, molecular recognition, conformational change, binding kinetics, reaction scheme, free energy landscape, protein-ligand interactions, conformational equilibrium
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