ArticleNature protocols2019
Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins.
Article in Nature protocols, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 58 citations in OpenAlex.
- Probing protein-lipid interactions by hydrogen/deuterium exchange-mass spectrometry: advances, challenges and future directions.Chemical science · 2026Review
- Practical Tips for the Application of HDX-MS to Membrane Proteins, Biomolecular Condensates, and Weak Protein Binders.Journal of the American Society for Mass Spectrometry · 2025Article
- Development of a Thiol-ene Microfluidic Chip for Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS).Analytical chemistry · 2025Article
- Dissecting Large-Scale Structural Transitions in Membrane Transporters Using Advanced Simulation Technologies.The journal of physical chemistry. B · 2025Review
- Salt-Induced Membrane-Bound Conformation of the NAC Domain of α-Synuclein Leads to Structural Polymorphism of Amyloid Fibrils.Biomolecules · 2025Article
- Regulating cellular metabolism and morphology to achieve high-yield synthesis of hyaluronan with controllable molecular weights.Nature communications · 2025Article
- Advancing Structural Biology and Protein-Ligand Interactions through Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS).Methods in molecular biology (Clifton, N.J.) · 2025Article
- Therapeutic Application and Structural Features of Adeno-Associated Virus Vector.Current issues in molecular biology · 2024Review
- Recent Advances in NMR Protein Structure Prediction with ROSETTA.International journal of molecular sciences · 2023Review
- Advances in Mass Spectrometry on Membrane Proteins.Membranes · 2023Review
- 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
- Hydrogen/deuterium exchange-mass spectrometry of integral membrane proteins in native-like environments: current scenario and the way forward.Essays in biochemistry · 2023Article
- Fundamentals of HDX-MS.Essays in biochemistry · 2023Review
- Chromatographic Phospholipid Trapping for Automated H/D Exchange Mass Spectrometry of Membrane Protein-Lipid Assemblies.Analytical chemistry · 2023Article
- HDX-guided EPR spectroscopy to interrogate membrane protein dynamics.STAR protocols · 2022Article
- Insights into the structure and function of the human organic anion transporter 1 in lipid bilayer membranes.Scientific reports · 2022Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- Protein Structure Prediction with Mass Spectrometry Data.Annual review of physical chemistry · 2022Review
- Pocket delipidation induced by membrane tension or modification leads to a structurally analogous mechanosensitive channel state.Structure (London, England : 1993) · 2022Article
- Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
Biological membranes define the boundaries of cells and are composed primarily of phospholipids and membrane proteins. It has become increasingly evident that direct interactions of membrane proteins with their surrounding lipids play key roles in regulating both protein conformations and function. However, the exact nature and structural consequences of these interactions remain difficult to track at the molecular level. Here, we present a protocol that specifically addresses this challenge. First, hydrogen-deuterium exchange mass spectrometry (HDX-MS) of membrane proteins incorporated into nanodiscs of controlled lipid composition is used to obtain information on the lipid species that are involved in modulating the conformational changes in the membrane protein. Then molecular dynamics (MD) simulations in lipid bilayers are used to pinpoint likely lipid-protein interactions, which can be tested experimentally using HDX-MS. By bringing together the MD predictions with the conformational readouts from HDX-MS, we have uncovered key lipid-protein interactions implicated in stabilizing important functional conformations. This protocol can be applied to virtually any integral membrane protein amenable to classic biophysical studies and for which a near-atomic-resolution structure or homology model is available. This protocol takes ~4 d to complete, excluding the time for data analysis and MD simulations, which depends on the size of the protein under investigation.
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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.