ArticleChemical physics2012
Large-scale motions in the adenylate kinase solution ensemble: coarse-grained simulations and comparison with solution X-ray scattering.
Article in Chemical physics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Allostery can convert binding free energies into concerted domain motions in enzymes.Nature communications · 2024Article
- Conformational dynamics of adenylate kinase in crystals.Structural dynamics (Melville, N.Y.) · 2024Article
- Mechanistic Basis for a Connection between the Catalytic Step and Slow Opening Dynamics of Adenylate Kinase.Journal of chemical information and modeling · 2023Article
- Tracking the ATP-binding response in adenylate kinase in real time.Science advances · 2021Article
- p38α Mitogen-Activated Protein Kinase Is a Druggable Target in Pancreatic Adenocarcinoma.Frontiers in oncology · 2019Article
- Article
- Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities.Protein science : a publication of the Protein Society · 2016Article
- 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
- Characterization of protein flexibility using small-angle x-ray scattering and amplified collective motion simulations.Biophysical journal · 2014Article
- MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins.Journal of applied crystallography · 2014Article
- The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers.The Plant cell · 2014Article
- Fast-SAXS-pro: a unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes.The Journal of chemical physics · 2013Article
- Moving beyond static snapshots: Protein dynamics and the Protein Data Bank.The Journal of biological chemistryReview
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Authors and funding
4 authors.
Funding
Abstract
While coarse-grained (CG) simulations provide an efficient approach to identify small- and large-scale motions important to protein conformational transitions, coupling with appropriate experimental validation is essential. Here, by comparing small-angle X-ray scattering (SAXS) predictions from CG simulation ensembles of adenylate kinase (AK) with a range of energetic parameters, we demonstrate that AK is flexible in solution in the absence of ligand and that a small population of the closed form exists without ligand. In addition, by analyzing variation of scattering patterns within CG simulation ensembles, we reveal that rigid-body motion of the LID domain corresponds to a dominant scattering feature. Thus, we have developed a novel approach for three-dimensional structural interpretation of SAXS data. Finally, we demonstrate that the agreement between predicted and experimental SAXS can be improved by increasing the simulation temperature or by computationally mutating selected residues to glycine, both of which perturb LID rigid-body flexibility.
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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.