ArticleThe journal of physical chemistry. B2022
Role of Repeated Conformational Transitions in Substrate Binding of Adenylate Kinase.
Article in The journal of physical chemistry. B, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Exploring the conformational landscape of adenylate kinase and beyond with protein folding models.Scientific reports · 2026Article
- Accelerating Quantum Mechanical/Molecular Mechanical (QM/MM) Simulations with Stochastic Iso-Kinetic Nosé-Hoover Multiple Time Step Integrator in CHARMM.The journal of physical chemistry. B · 2026Article
- Allosteric regulation of enzymatic catalysis by molecular crowding.Communications chemistry · 2026Article
- Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Allostery can convert binding free energies into concerted domain motions in enzymes.Nature communications · 2024Article
- Enzyme activation by urea reveals the interplay between conformational dynamics and substrate binding: a single-molecule FRET study.bioRxiv : the preprint server for biology · 2024Article
- Magnesium induced structural reorganization in the active site of adenylate kinase.Science advances · 2024Article
- Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release.Journal of chemical information and modeling · 2024Article
- Insights into Enzymatic Catalysis from Binding and Hydrolysis of Diadenosine Tetraphosphate byBiochemistry · 2023Article
- From Microstates to Macrostates in the Conformational Dynamics of GroEL: A Single-Molecule Förster Resonance Energy Transfer Study.The journal of physical chemistry letters · 2023Article
- Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO.Journal of chemical theory and computation · 2023Article
- Perspective: How Fast Dynamics Affect Slow Function in Protein Machines.The journal of physical chemistry. B · 2023Review
- Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Mechanistic Basis for a Connection between the Catalytic Step and Slow Opening Dynamics of Adenylate Kinase.Journal of chemical information and modeling · 2023Article
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Authors and funding
5 authors.
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Abstract
The catalytic cycle of the enzyme adenylate kinase involves large conformational motions between open and closed states. A previous single-molecule experiment showed that substrate binding tends to accelerate both the opening and the closing rates and that a single turnover event often involves multiple rounds of conformational switching. In this work, we showed that the repeated conformational transitions of adenylate kinase are essential for the relaxation of incorrectly bound substrates into the catalytically competent conformation by combining all-atom and coarse-grained molecular simulations. In addition, free energy calculations based on all-atom and coarse-grained models demonstrated that the enzyme with incorrectly bound substrates has much a lower free energy barrier for domain opening compared to that with the correct substrate conformation, which may explain the the acceleration of the domain opening rate by substrate binding. The results of this work provide mechanistic understanding to previous experimental observations and shed light onto the interplay between conformational dynamics and enzyme catalysis.
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