ArticleScientific reports2015
Energetics and structural characterization of the large-scale functional motion of adenylate kinase.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
31 citing papers in PubMed, 74 citations in OpenAlex.
- Exploring the conformational landscape of adenylate kinase and beyond with protein folding models.Scientific reports · 2026Article
- QM/MM Free Energy Calculations of IRE1 Reveal a Unique Protonation State of the Catalytic Lys599.Journal of computational chemistry · 2025Article
- MDGraphEmb: a toolkit for graph embedding and classification of protein conformational ensembles.Bioinformatics (Oxford, England) · 2025Article
- The progress and prospects of targeting the adenosine pathway in cancer immunotherapy.Biomarker research · 2025Review
- Molecular mechanism of Arp2/3 complex activation by nucleation-promoting factors and an actin monomer.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins.Journal of chemical information and modeling · 2025Article
- Minute-timescale free-energy calculations reveal a pseudo-active state in the adenosine AChem · 2024Article
- Predicting binding events in very flexible, allosteric, multi-domain proteins.bioRxiv : the preprint server for biology · 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
- Whispering-Gallery Mode Optoplasmonic Microcavities: From Advanced Single-Molecule Sensors and Microlasers to Applications in Synthetic Biology.ACS photonics · 2024Review
- Free energy along drug-protein binding pathways interactively sampled in virtual reality.Scientific reports · 2023Article
- Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO.Journal of chemical theory and computation · 2023Article
- 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
- Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins.Journal of chemical information and modeling · 2023Article
- LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories.Journal of chemical information and modeling · 2023Article
- Role of Repeated Conformational Transitions in Substrate Binding of Adenylate Kinase.The journal of physical chemistry. B · 2022Article
- Activation of Abl1 Kinase Explored Using Well-Tempered Metadynamics Simulations on an Essential Dynamics Sampled Path.Journal of chemical theory and computation · 2021Article
- Cryo-EM Analyses Permit Visualization of Structural Polymorphism of Biological Macromolecules.Frontiers in bioinformatics · 2021Review
- A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules.The European physical journal. B · 2021Article
- Explore Protein Conformational Space With Variational Autoencoder.Frontiers in molecular biosciences · 2021Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Adenylate Kinase (AK) is a signal transducing protein that regulates cellular energy homeostasis balancing between different conformations. An alteration of its activity can lead to severe pathologies such as heart failure, cancer and neurodegenerative diseases. A comprehensive elucidation of the large-scale conformational motions that rule the functional mechanism of this enzyme is of great value to guide rationally the development of new medications. Here using a metadynamics-based computational protocol we elucidate the thermodynamics and structural properties underlying the AK functional transitions. The free energy estimation of the conformational motions of the enzyme allows characterizing the sequence of events that regulate its action. We reveal the atomistic details of the most relevant enzyme states, identifying residues such as Arg119 and Lys13, which play a key role during the conformational transitions and represent druggable spots to design enzyme inhibitors. Our study offers tools that open new areas of investigation on large-scale motion in proteins.
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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.