ArticleBiophysical journal2015
Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Molecular basis of tRNA substrate recognition and modification by the atypical SPOUT methyltransferase Trm10.Nucleic acids research · 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
- Generation of Pathway Signatures by Combining Normal Modes with Weighted Ensemble Simulations.bioRxiv : the preprint server for biology · 2026Article
- The Ensemble Basis of Allostery and Function: Insights from Models of Local Unfolding.Journal of molecular biology · 2025Review
- Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases.Evolution letters · 2025Article
- Alpha-synuclein interacts with regulators of ATP homeostasis in mitochondria.Nature communications · 2025Article
- Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.Pharmaceuticals (Basel, Switzerland) · 2025Review
- The B22 Dilemma: Structural Basis for Conformational Differences in Proinsulin B-Chain Arg22 Mutants.Biomolecules · 2025Article
- An accelerated molecular dynamics study for investigating protein pathways using the bond-boost hyperdynamics method.Protein science : a publication of the Protein Society · 2025Article
- Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins.Journal of chemical information and modeling · 2025Article
- Allostery can convert binding free energies into concerted domain motions in enzymes.Nature communications · 2024Article
- Predicting binding events in very flexible, allosteric, multi-domain proteins.bioRxiv : the preprint server for biology · 2024Article
- Folding of N-terminally acetylated α-synuclein upon interaction with lipid membranes.Biophysical journal · 2024Article
- Single Molecule Thermodynamic Penalties Applied to Enzymes by Whispering Gallery Mode Biosensors.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Rosetta Energy Analysis of AlphaFold2 models: Point Mutations and Conformational Ensembles.bioRxiv : the preprint server for biology · 2024Article
- 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
- Article
- Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO.Journal of chemical theory and computation · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological operation of the functional domains of AdK. Specifically in the ligand-free AdK, there is no significant energy barrier in the free energy landscape separating the open and closed states. Instead there are multiple intermediate conformational states, which facilitate the rapid transitions of AdK. In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions. The results suggest a perspective for a hybrid of conformational selection and induced fit operations of ligand binding to AdK. These observations, depicted in the most comprehensive and quantitative way to date, to our knowledge, emphasize the underlying intrinsic dynamics of AdK and reveal the sophisticated conformational transitions of AdK in fulfilling its enzymatic functions. The developed methodology can also apply to other proteins and biomolecular systems.
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