ArticleThe journal of physical chemistry. B2017
A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen-Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- A machine learning method for calculating highly localized protein stabilities.Nature communications · 2026Article
- HDX-MS Detects Steric Protection and Trimeric Compaction of TNFα after It Binds Receptors or Antibodies.ACS omega · 2026Article
- HXMS: a standardized file format for HX-MS data.Bioinformatics (Oxford, England) · 2026Article
- Structural dynamics and immunogenicity of the recombinant and outer membrane vesicle-embedded Meningococcal antigen NadA.Nature communications · 2026Article
- Site-resolved energetic information from HX-MS experiments.Nature chemical biology · 2026Article
- Light-Regulated Agonists Spatiotemporally Activating the Vitamin D Receptor Mitigate Psoriasis-like Inflammation in Mice without Inducing Hypercalcemia.ACS central science · 2025Article
- Inferring residue level hydrogen deuterium exchange with ReX.Communications chemistry · 2025Article
- Structural proteomics defines a sequential priming mechanism for the progesterone receptor.Nature communications · 2025Article
- Tutorial on integrative spatiotemporal modeling by integrative modeling platform.Protein science : a publication of the Protein Society · 2025Article
- Kingfisher: An open-sourced web-based platform for the analysis of hydrogen exchange mass spectrometry data.Protein science : a publication of the Protein Society · 2025Article
- Computational Tools for Hydrogen-Deuterium Exchange Mass Spectrometry Data Analysis.Chemical reviews · 2024Review
- Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver.Briefings in bioinformatics · 2023Article
- A Functional Bayesian Model for Hydrogen-Deuterium Exchange Mass Spectrometry.Journal of proteome research · 2023Article
- Fundamentals of HDX-MS.Essays in biochemistry · 2023Review
- Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction.Nature communications · 2022Article
- High-Resolution Hydrogen-Deuterium Protection Factors from Sparse Mass Spectrometry Data Validated by Nuclear Magnetic Resonance Measurements.Journal of the American Society for Mass Spectrometry · 2022Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- Challenges and Opportunities for Bayesian Statistics in Proteomics.Journal of proteome research · 2022Review
- Interlaboratory Studies Using the NISTmAb to Advance Biopharmaceutical Structural Analytics.Frontiers in molecular biosciences · 2022Review
- Computational Structure Prediction for Antibody-Antigen Complexes From Hydrogen-Deuterium Exchange Mass Spectrometry: Challenges and Outlook.Frontiers in immunology · 2022Review
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Authors and funding
10 authors.
Funding
Abstract
Characterization of interactions between proteins and other molecules is crucial for understanding the mechanisms of action of biological systems and, thus, drug discovery. An increasingly useful approach to mapping these interactions is measurement of hydrogen/deuterium exchange (HDX) using mass spectrometry (HDX-MS), which measures the time-resolved deuterium incorporation of peptides obtained by enzymatic digestion of the protein. Comparison of exchange rates between apo- and ligand-bound conditions results in a mapping of the differential HDX (ΔHDX) of the ligand. Residue-level analysis of these data, however, must account for experimental error, sparseness, and ambiguity due to overlapping peptides. Here, we propose a Bayesian method consisting of a forward model, noise model, prior probabilities, and a Monte Carlo sampling scheme. This method exploits a residue-resolved exponential rate model of HDX-MS data obtained from all peptides simultaneously, and explicitly models experimental error. The result is the best possible estimate of ΔHDX magnitude and significance for each residue given the data. We demonstrate the method by revealing richer structural interpretation of ΔHDX data on two nuclear receptors: vitamin D-receptor (VDR) and retinoic acid receptor gamma (RORγ). The method is implemented in HDX Workbench and as a standalone module of the open source Integrative Modeling Platform.
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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.