Identifying Membrane Protein–Lipid Interactions with Lipidomic Lipid Exchange-Mass Spectrometry

Lipids can play important roles in modulating membrane
protein
structure and function. However, it is challenging to identify natural
lipids bound to membrane proteins in complex bilayers. Here, we developed
lipidomic lipid exchange-mass spectrometry (LX-MS) to study the lipid
affinity for membrane proteins on a lipidomic scale. We first mix
membrane protein nanodiscs with empty nanodiscs that have no embedded
membrane proteins. After allowing lipids to passively exchange between
the two populations, we separate the two types of nanodiscs and perform
lipidomic analysis on each with liquid chromatography and MS. Enrichment
of lipids in the membrane protein nanodiscs reveals the affinity of
individual lipids for binding the target membrane protein. We apply
this approach to study three membrane proteins. With the Escherichia coli ammonium transporter AmtB and aquaporin
AqpZ in nanodiscs with E. coli polar
lipid extracts, we detected binding of cardiolipin and phosphatidyl-glycerol
lipids to the proteins. With the acetylcholine receptor in nanodiscs
with brain polar lipid extracts, we discovered a complex set of lipid
interactions that depended on the head group and tail composition.
Overall, lipidomic LX-MS provides a detailed understanding of the
lipid-binding affinity and thermodynamics for membrane proteins in
complex bilayers and provides a unique perspective on the chemical
environment surrounding membrane proteins.