Chloe Martens, Mrinal Shekhar, Andy M. Lau, Emad Tajkhorshid, and Argyris
Politis.
Integrating hydrogen-deuterium exchange mass spectrometry with
molecular dynamics simulations to probe lipid-modulated conformational
changes in membrane proteins.
Nature Protocols, 14:3183-3204, 2019.
Published.
(PMC: PMC7058097)
MART2019-ET
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.
