ArticleBiophysical journal2010
On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 55 citations in OpenAlex.
- Simulating biomolecules for physiological timescales.Current opinion in structural biology · 2025Review
- Allostery can convert binding free energies into concerted domain motions in enzymes.Nature communications · 2024Article
- Role of Repeated Conformational Transitions in Substrate Binding of Adenylate Kinase.The journal of physical chemistry. B · 2022Article
- Integration of Adenylate Kinase 1 with Its Peptide Conformational Imprint.International journal of molecular sciences · 2022Article
- Structure-mechanics statistical learning uncovers mechanical relay in proteins.Chemical science · 2022Article
- Tracking the ATP-binding response in adenylate kinase in real time.Science advances · 2021Article
- Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC.Molecules (Basel, Switzerland) · 2021Article
- Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation.Biophysical journal · 2020Article
- Structural basis for ligand binding to an enzyme by a conformational selection pathway.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Active-Loop Dynamics within the Michaelis Complex of Lactate Dehydrogenase from Bacillus stearothermophilus.Biochemistry · 2016Article
- 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
- Structural basis for catalytically restrictive dynamics of a high-energy enzyme state.Nature communications · 2015Article
- Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field.Journal of computer-aided molecular design · 2015Article
- WEBnm@ v2.0: Web server and services for comparing protein flexibility.BMC bioinformatics · 2014Article
- Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model.PLoS computational biology · 2014Article
- Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase.Biophysical journal · 2013Article
- Transitions to catalytically inactive conformations in EGFR kinase.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations.Topics in current chemistry · 2013Review
- Molecular dynamics studies on the conformational transitions of adenylate kinase: a computational evidence for the conformational selection mechanism.BioMed research international · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier works of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro(177) on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro(177) hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.
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Registered trials
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.