ArticleFrontiers in molecular biosciences2017
Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.
Article in Frontiers in molecular biosciences, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 24 citations in OpenAlex.
- High resolution mapping of protein motions in time and space with RMSX and Flipbook.Scientific reports · 2026Article
- Integrating Hydrogen Deuterium Exchange-Mass Spectrometry with Molecular Simulations Enables Quantification of the Conformational Populations of the Sugar Transporter XylE.Journal of the American Chemical Society · 2023Article
- Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules.PNAS nexus · 2022Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- 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
- DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins.Computers in biology and medicine · 2021Article
- Computational analysis of complement inhibitor compstatin using molecular dynamics.Journal of molecular modeling · 2020Article
- Calcitonin Receptor N-Glycosylation Enhances Peptide Hormone Affinity by Controlling Receptor Dynamics.Journal of molecular biology · 2020Article
- Structural Modeling and Molecular Dynamics of the Immune Checkpoint Molecule HLA-G.Frontiers in immunology · 2020Article
- Estimating Constraints for Protection Factors from HDX-MS Data.Biophysical journal · 2019Article
- Quantitative Evaluation of Native Protein Folds and Assemblies by Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS).Journal of the American Society for Mass Spectrometry · 2019Article
- Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data.International journal of molecular sciences · 2018Article
- Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Monitoring hydrogen/deuterium exchange (HDX) undergone by a protein in solution produces experimental data that translates into valuable information about the protein's structure. Data produced by HDX experiments is often interpreted using a crystal structure of the protein, when available. However, it has been shown that the correspondence between experimental HDX data and crystal structures is often not satisfactory. This creates difficulties when trying to perform a structural analysis of the HDX data. In this paper, we evaluate several strategies to obtain a conformation providing a good fit to the experimental HDX data, which is a premise of an accurate structural analysis. We show that performing molecular dynamics simulations can be inadequate to obtain such conformations, and we propose a novel methodology involving a coarse-grained conformational sampling approach instead. By extensively exploring the intrinsic flexibility of a protein with this approach, we produce a conformational ensemble from which we extract a
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