Integrating hydrogen–deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins

Chloe Martens, Mrinal Shekhar, Andy M. Lau, Emad Tajkhorshid, Argyris Politis

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)3183-3204
Number of pages22
JournalNature Protocols
Volume14
Issue number11
DOIs
StatePublished - Nov 1 2019

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Molecular Dynamics Simulation
Mass spectrometry
Molecular dynamics
Mass Spectrometry
Membrane Proteins
Lipids
Computer simulation
Conformations
Biological membranes
Protein Conformation
Lipid bilayers
Lipid Bilayers
Phospholipids
Proteins
Membranes
Chemical analysis

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Integrating hydrogen–deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins. / Martens, Chloe; Shekhar, Mrinal; Lau, Andy M.; Tajkhorshid, Emad; Politis, Argyris.

In: Nature Protocols, Vol. 14, No. 11, 01.11.2019, p. 3183-3204.

Research output: Contribution to journalArticle

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