ArticleThe Journal of chemical physics2011
Theory and simulation on the kinetics of protein-ligand binding coupled to conformational change.
Article in The Journal of chemical physics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Transient non-local interactions dominate the dynamics of measles virus NCommunications chemistry · 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
- Folding of Staphylococcal Nuclease Induced by Binding of Chemically Modified Substrate Analogues Sheds Light on Mechanisms of Coupled Folding/Binding Reactions.Biochemistry · 2023Article
- 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
- Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions.Frontiers in physics · 2020Article
- Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins.Current research in structural biology · 2020Article
- Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT).PLoS computational biology · 2018Article
- Rate Constants and Mechanisms of Protein-Ligand Binding.Annual review of biophysics · 2017Review
- Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics.Biochemical and biophysical research communications · 2017Article
- Article
- Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics.Journal of chemical theory and computation · 2015Article
- Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate.Journal of chemical theory and computation · 2015Article
- Both protein dynamics and ligand concentration can shift the binding mechanism between conformational selection and induced fit.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Homotropic cooperativity from the activation pathway of the allosteric ligand-responsive regulatory trp RNA-binding attenuation protein.Biochemistry · 2013Article
- Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA.Computational science & discovery · 2012Article
- BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from brownian dynamics simulations.The Journal of chemical physics · 2012Article
- A suite of modular fluorescence assays interrogate the human immunodeficiency virus glycoprotein-41 coiled coil and assist in determining binding mechanism of low molecular weight fusion inhibitors.Assay and drug development technologies · 2012Article
- Rate constants and mechanisms of intrinsically disordered proteins binding to structured targets.Physical chemistry chemical physics : PCCP · 2012Review
- Theory and simulation of diffusion-influenced, stochastically gated ligand binding to buried sites.The Journal of chemical physics · 2011Article
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2 authors.
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Abstract
Conformational change during protein-ligand binding may significantly affect both the binding mechanism and the rate constant. Most earlier theories and simulations treated conformational change as stochastic gating with transition rates between reactive and nonreactive conformations uncoupled to ligand binding. Recently, we introduced a dual-transition-rates model in which the transition rates between reactive and nonreactive conformations depend on the protein-ligand distance [H.-X. Zhou, Biophys. J. 98, L15 (2010)]. Analytical results of that model showed that the apparent binding mechanism switches from conformational selection to induced fit, when the rates of conformational transitions increase from being much slower than the diffusional approach of the protein-ligand pair to being much faster. The conformational-selection limit (k(CS)) and the induced-fit limit (k(IF)) provide lower and upper bounds, respectively, for the binding rate constant. Here we introduce a general model in which the energy surface of the protein in conformational space is coupled to ligand binding, and present a method for calculating the binding rate constant from Brownian dynamics simulations. Analytical and simulation results show that, for an energy surface that switches from favoring the nonreactive conformation while the ligand is away to favoring the reactive conformation while the ligand is near, k(CS) and k(IF) become close and, thus, provide tight bounds to the binding rate constant. This finding has significant mechanistic implications and presents routes for obtaining good estimates of the rate constant at low cost.
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