ArticleJournal of molecular biology2009
Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.
Article in Journal of molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed, 167 citations in OpenAlex.
- Hierarchical geometric deep learning enables scalable analysis of molecular dynamics.The Journal of chemical physics · 2026Article
- Exploring the conformational landscape of adenylate kinase and beyond with protein folding models.Scientific reports · 2026Article
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- Generation of Pathway Signatures by Combining Normal Modes with Weighted Ensemble Simulations.bioRxiv : the preprint server for biology · 2026Article
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- An accelerated molecular dynamics study for investigating protein pathways using the bond-boost hyperdynamics method.Protein science : a publication of the Protein Society · 2025Article
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- Allostery can convert binding free energies into concerted domain motions in enzymes.Nature communications · 2024Article
- Exploring Protein Conformational Changes Using a Large-Scale Biophysical Sampling Augmented Deep Learning Strategy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- The mechanism and energetics of the dynein priming stroke.Structure (London, England : 1993) · 2024Article
- Nuclear receptor interdomain communication is mediated by the hinge with ligand specificity.bioRxiv : the preprint server for biology · 2024Article
- Rosetta Energy Analysis of AlphaFold2 models: Point Mutations and Conformational Ensembles.bioRxiv : the preprint server for biology · 2024Article
- Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO.Journal of chemical theory and computation · 2023Article
- Omicron BA.1 and BA.2 variants increase the interactions of SARS-CoV-2 spike glycoprotein with ACE2.Journal of molecular graphics & modelling · 2022Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Adenylate kinase (AdK), a phosphotransferase enzyme, plays an important role in cellular energy homeostasis. It undergoes a large conformational change between an open and a closed state, even in the absence of substrate. We investigate the apo-AdK transition at the atomic level both with free-energy calculations and with our new dynamic importance sampling (DIMS) molecular dynamics method. DIMS is shown to sample biologically relevant conformations as verified by comparing an ensemble of hundreds of DIMS transitions to AdK crystal structure intermediates. The simulations reveal in atomic detail how hinge regions partially and intermittently unfold during the transition. Conserved salt bridges are seen to have important structural and dynamic roles; in particular, four ionic bonds that open in a sequential, zipper-like fashion and, thus, dominate the free-energy landscape of the transition are identified. Transitions between the closed and open conformations only have to overcome moderate free-energy barriers. Unexpectedly, the closed state and the open state encompass broad free-energy basins that contain conformations differing in domain hinge motions by up to 40 degrees . The significance of these extended states is discussed in relation to recent experimental Förster resonance energy transfer measurements. Taken together, these results demonstrate how a small number of cooperative key interactions can shape the overall dynamics of an enzyme and suggest an "all-or-nothing" mechanism for the opening and closing of AdK. Our efficient DIMS molecular dynamics computer simulation approach can provide a detailed picture of a functionally important macromolecular transition and thus help to interpret and suggest experiments to probe the conformational landscape of dynamic proteins such as AdK.
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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.