ArticlePLoS computational biology2014
Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Computational approaches to druggable site identification: Current status and future perspective.Acta pharmaceutica Sinica. B · 2026Review
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- Hidden route of protein damage through oxygen-confined photooxidation.Nature communications · 2024Article
- Capturing the Effects of Single Atom Substitutions on the Inhibition Efficiency of Glycogen Synthase Kinase-3β Inhibitors via Markov State Modeling and Experiments.Journal of chemical theory and computation · 2024Article
- Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites.Journal of chemical theory and computation · 2024Article
- A Kinetic Transition Network Model Reveals the Diversity of Protein Dimer Formation Mechanisms.Biomolecules · 2023Article
- Disease mutations and phosphorylation alter the allosteric pathways involved in autoinhibition of protein phosphatase 2A.The Journal of chemical physics · 2023Article
- Simulation of ligand dissociation kinetics from the protein kinase PYK2.Journal of computational chemistry · 2022Article
- A litmus test for classifying recognition mechanisms of transiently binding proteins.Nature communications · 2022Article
- Qualitative Prediction of Ligand Dissociation Kinetics from Focal Adhesion Kinase Using Steered Molecular Dynamics.Life (Basel, Switzerland) · 2021Article
- Markov State Models to Elucidate Ligand Binding Mechanism.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- Enhanced Jarzynski free energy calculations using weighted ensemble.The Journal of chemical physics · 2020Article
- A combination of machine learning and infrequent metadynamics to efficiently predict kinetic rates, transition states, and molecular determinants of drug dissociation from G protein-coupled receptors.The Journal of chemical physics · 2020Article
- Ligand-bound glutamine binding protein assumes multiple metastable binding sites with different binding affinities.Communications biology · 2020Article
- On Calculating Free Energy Differences Using Ensembles of Transition Paths.Frontiers in molecular biosciences · 2020Article
- Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Dynamic graphical models of molecular kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Simulations of the regulatory ACT domain of human phenylalanine hydroxylase (PAH) unveil its mechanism of phenylalanine binding.The Journal of biological chemistry · 2018Article
- Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics.The Journal of chemical physics · 2018Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-ligand recognition plays key roles in many biological processes. One of the most fascinating questions about protein-ligand recognition is to understand its underlying mechanism, which often results from a combination of induced fit and conformational selection. In this study, we have developed a three-pronged approach of Markov State Models, Molecular Dynamics simulations, and flux analysis to determine the contribution of each model. Using this approach, we have quantified the recognition mechanism of the choline binding protein (ChoX) to be ∼90% conformational selection dominant under experimental conditions. This is achieved by recovering all the necessary parameters for the flux analysis in combination with available experimental data. Our results also suggest that ChoX has several metastable conformational states, of which an apo-closed state is dominant, consistent with previous experimental findings. Our methodology holds great potential to be widely applied to understand recognition mechanisms underlining many fundamental biological processes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.