ArticleBiophysical journal2019
Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery.
Article in Biophysical journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- Exploring the CNOT1(800-999) HEAT Domain and Its Interactions with Tristetraprolin (TTP) as Revealed by Hydrogen/Deuterium Exchange Mass Spectrometry.Biomolecules · 2025Article
- The Light Chain Allosterically Enhances the Protease Activity of Murine Urokinase-Type Plasminogen Activator.Biochemistry · 2024Article
- Interpretation of Hydrogen/Deuterium Exchange Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2024Article
- Capturing the Dynamic Conformational Changes of Human Isocitrate Dehydrogenase 1 (IDH1) upon Ligand and Metal Binding Using Hydrogen-Deuterium Exchange Mass Spectrometry.Biochemistry · 2023Article
- SARS-CoV-2 spike protein as a bacterial lipopolysaccharide delivery system in an overzealous inflammatory cascade.Journal of molecular cell biology · 2023Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- Enhanced sampling without borders: on global biasing functions and how to reweight them.Physical chemistry chemical physics : PCCP · 2022Review
- How Thrombomodulin Enables W215A/E217A Thrombin to Cleave Protein C but Not Fibrinogen.Biochemistry · 2022Article
- Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.Journal of chemical theory and computation · 2022Article
- Achieving a realistic native protein ensemble by HDX-MS and computational modeling.Biophysical journal · 2021Article
- Regulation of the EphA2 receptor intracellular region by phosphomimetic negative charges in the kinase-SAM linker.Nature communications · 2021Article
- Hydrogen/Deuterium Exchange and Nuclear Magnetic Resonance Spectroscopy Reveal Dynamic Allostery on Multiple Time Scales in the Serine Protease Thrombin.Biochemistry · 2021Article
- Human FoxP Transcription Factors as Tractable Models of the Evolution and Functional Outcomes of Three-Dimensional Domain Swapping.International journal of molecular sciences · 2021Review
- Proton Bridging in Catalysis by and Inhibition of Serine Proteases of the Blood Cascade System.Life (Basel, Switzerland) · 2021Review
- Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0].Living journal of computational molecular science · 2021Article
- Synergistic Allostery in Multiligand-Protein Interactions.Biophysical journal · 2020Article
- Intrinsically Disordered Regions of the DNA-Binding Domain of Human FoxP1 Facilitate Domain Swapping.Journal of molecular biology · 2020Article
- Structure and dynamics of the ASB9 CUL-RING E3 Ligase.Nature communications · 2020Article
- Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles.Biophysical journal · 2020Article
- DECA, A Comprehensive, Automatic Post-processing Program for HDX-MS Data.Molecular & cellular proteomics : MCP · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Amide hydrogen/deuterium exchange mass spectrometry (HDXMS) of proteins has become extremely popular for identifying ligand-binding sites, protein-protein interactions, intrinsic disorder, and allosteric changes upon protein modification. Such phenomena are revealed when amide exchange is measured in the fast limit, that is, within a few minutes of exchange in deuterated buffer. The HDXMS data have a resolution of the length of peptides and are difficult to interpret because many different phenomena lead to changes in hydrogen/deuterium exchange. We present a quantitative analysis of accelerated molecular dynamics simulations that provides impressive agreement with peptide-length HDXMS data. Comparative analysis of thrombin and a single-point mutant reveals that the simulation analysis can distinguish the subtle differences in exchange due to mutation. In addition, the results provide a deeper understanding of the underlying changes in dynamics revealed by the HDXMS that extend far from the site of mutation.
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Registered trials
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