Issue 32, 2023

Combining native mass spectrometry and lipidomics to uncover specific membrane protein–lipid interactions from natural lipid sources

Abstract

While it is known that lipids play an essential role in regulating membrane protein structure and function, it remains challenging to identify specific protein–lipid interactions. Here, we present an innovative approach that combines native mass spectrometry (MS) and lipidomics to identify lipids retained by membrane proteins from natural lipid extracts. Our results reveal that the bacterial ammonia channel (AmtB) enriches specific cardiolipin (CDL) and phosphatidylethanolamine (PE) from natural headgroup extracts. When the two extracts are mixed, AmtB retains more species, wherein selectivity is tuned to bias headgroup selection. Using a series of natural headgroup extracts, we show TRAAK, a two-pore domain K+ channel (K2P), retains specific acyl chains that is independent of the headgroup. A brain polar lipid extract was then combined with the K2Ps, TRAAK and TREK2, to understand lipid specificity. More than a hundred lipids demonstrated affinity for each protein, and both channels were found to retain specific fatty acids and lysophospholipids known to stimulate channel activity, even after several column washes. Natural lipid extracts provide the unique opportunity to not only present natural lipid diversity to purified membrane proteins but also identify lipids that may be important for membrane protein structure and function.

Graphical abstract: Combining native mass spectrometry and lipidomics to uncover specific membrane protein–lipid interactions from natural lipid sources

Supplementary files

Article information

Article type
Edge Article
Submitted
21 mar 2023
Accepted
19 iyl 2023
First published
21 iyl 2023
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY-NC license

Chem. Sci., 2023,14, 8570-8582

Combining native mass spectrometry and lipidomics to uncover specific membrane protein–lipid interactions from natural lipid sources

Y. Zhu, M. T. Odenkirk, P. Qiao, T. Zhang, S. Schrecke, M. Zhou, M. T. Marty, E. S. Baker and A. Laganowsky, Chem. Sci., 2023, 14, 8570 DOI: 10.1039/D3SC01482G

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