ArticleProceedings of the National Academy of Sciences of the United States of America2014
Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Proline-based tripodal cages with guest-adaptive features for capturing hydrophilic and amphiphilic fluoride substances.Nature communications · 2025Article
- Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure.Protein science : a publication of the Protein Society · 2024Review
- A Kinetic Transition Network Model Reveals the Diversity of Protein Dimer Formation Mechanisms.Biomolecules · 2023Article
- Protein conformational ensembles in function: roles and mechanisms.RSC chemical biology · 2023Review
- Biochemical and biophysical characterization of natural polyreactivity in antibodies.Cell reports · 2023Article
- Folding of Staphylococcal Nuclease Induced by Binding of Chemically Modified Substrate Analogues Sheds Light on Mechanisms of Coupled Folding/Binding Reactions.Biochemistry · 2023Article
- Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs.Journal of molecular biology · 2022Review
- Elucidating the mechanisms underlying protein conformational switching using NMR spectroscopy.Journal of magnetic resonance open · 2022Article
- Structural-Energetic Basis for Coupling between Equilibrium Fluctuations and Phosphorylation in a Protein Native Ensemble.ACS central science · 2022Article
- Induced fit versus conformational selection: From rate constants to fluxes… and back to rate constants.Pharmacology research & perspectives · 2021Article
- Mechanisms of ligand binding.Biophysics reviews · 2020Review
- Challenges in protein docking.Current opinion in structural biology · 2020Review
- Ligand binding free-energy calculations with funnel metadynamics.Nature protocols · 2020Article
- Energetics and kinetics of substrate analog-coupled staphylococcal nuclease folding revealed by a statistical mechanical approach.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Ligand-bound glutamine binding protein assumes multiple metastable binding sites with different binding affinities.Communications biology · 2020Article
- β-Lactamase of Mycobacterium tuberculosis Shows Dynamics in the Active Site That Increase upon Inhibitor Binding.Antimicrobial agents and chemotherapy · 2020Article
- DROIDS 3.0-Detecting Genetic and Drug Class Variant Impact on Conserved Protein Binding Dynamics.Biophysical journal · 2020Article
- Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins.Current research in structural biology · 2020Article
- Binding-induced folding under unfolding conditions: Switching between induced fit and conformational selection mechanisms.The Journal of biological chemistry · 2019Article
- Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding.Protein science : a publication of the Protein Society · 2019Review
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Authors and funding
2 authors.
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Abstract
This study aimed to shed light on the long debate over whether conformational selection (CS) or induced fit (IF) is the governing mechanism for protein-ligand binding. The main difference between the two scenarios is whether the conformational transition of the protein from the unbound form to the bound form occurs before or after encountering the ligand. Here we introduce the IF fraction (i.e., the fraction of binding events achieved via IF), to quantify the binding mechanism. Using simulations of a model protein-ligand system, we demonstrate that both the rate of the conformational transition and the concentration of ligand molecules can affect the IF fraction. CS dominates at slow conformational transition and low ligand concentration. An increase in either quantity results in a higher IF fraction. Despite the many-body nature of the system and the involvement of multiple, disparate types of dynamics (i.e., ligand diffusion, protein conformational transition, and binding reaction), the overall binding kinetics over wide ranges of parameters can be fit to a single exponential, with the apparent rate constant exhibiting a linear dependence on ligand concentration. The present study may guide future kinetics experiments and dynamics simulations in determining the IF fraction.
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