ArticlePloS one2013
Conformational dynamics of a ligand-free adenylate kinase.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Upregulation of AK7 in ACC-VTA glutamatergic projections contributes to chronic inflammation pain in male mice.EMBO reports · 2026Article
- Real-time Structural Tracking of Slow P-type ATPase Dynamics.The Journal of membrane biology · 2026Article
- DeepPath: overcoming data scarcity for protein transition pathway prediction using physics-based deep learning.Chemical science · 2026Article
- Rectifying AI-generated protein structure ensembles for equilibrium using physics-based computations.bioRxiv : the preprint server for biology · 2026Article
- Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release.Journal of chemical information and modeling · 2024Article
- Conformational dynamics of adenylate kinase in crystals.Structural dynamics (Melville, N.Y.) · 2024Article
- Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO.Journal of chemical theory and computation · 2023Article
- Role of Repeated Conformational Transitions in Substrate Binding of Adenylate Kinase.The journal of physical chemistry. B · 2022Article
- ADP-Induced Conformational Transition of Human Adenylate Kinase 1 Is Triggered by Suppressing Internal Motion of αBiomolecules · 2022Article
- Investigation of the Importance of Protein 3D Structure for Assessing Conservation of Lysine Acetylation Sites in Protein Homologs.Frontiers in microbiology · 2021Article
- Data-guided Multi-Map variables for ensemble refinement of molecular movies.The Journal of chemical physics · 2020Article
- Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation.Biophysical journal · 2020Article
- The crystal structures of Thermus thermophilus CMP kinase complexed with a phosphoryl group acceptor and donor.PloS one · 2020Article
- Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields.Journal of chemical theory and computation · 2017Article
- Substrate Binding Specifically Modulates Domain Arrangements in Adenylate Kinase.Biophysical journal · 2015Article
- Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case.Biophysical journal · 2015Article
- Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field.Journal of computer-aided molecular design · 2015Article
- Energetics and structural characterization of the large-scale functional motion of adenylate kinase.Scientific reports · 2015Article
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2 authors.
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Abstract
Adenylate kinase (AdK) is a phosphoryl-transfer enzyme with important physiological functions. Based on a ligand-free open structure and a ligand-bound closed structure solved by crystallography, here we use molecular dynamics simulations to examine the stability and dynamics of AdK conformations in the absence of ligands. We first perform multiple simulations starting from the open or the closed structure, and observe their free evolutions during a simulation time of 100 or 200 nanoseconds. In all seven simulations starting from the open structure, AdK remained stable near the initial conformation. The eight simulations initiated from the closed structure, in contrast, exhibited large variation in the subsequent evolutions, with most (seven) undergoing large-scale spontaneous conformational changes and approaching or reaching the open state. To characterize the thermodynamics of the transition, we propose and apply a new sampling method that employs a series of restrained simulations to calculate a one-dimensional free energy along a curved pathway in the high-dimensional conformational space. Our calculated free energy profile features a single minimum at the open conformation, and indicates that the closed state, with a high (∼13 kcal/mol) free energy, is not metastable, consistent with the observed behaviors of the unrestrained simulations. Collectively, our simulations suggest that it is energetically unfavorable for the ligand-free AdK to access the closed conformation, and imply that ligand binding may precede the closure of the enzyme.
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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.