Journal
JOURNAL OF PROTEOME RESEARCH
Volume 11, Issue 2, Pages 1454-1459Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr200846y
Keywords
nanodiscs; SILAC; SecYEG; MalFGK(2); YidC; membrane proteome; protein-lipid interactions
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Funding
- NSERC
- British Columbia Proteomics Network
- BC Knowledge Development Fund
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Integral membrane proteins are challenging to work with biochemically given their insoluble nature; the nanodisc circumvents the difficulty by stabilizing them in small patches of lipid bilayer. Here, we show that nanodiscs combined with SILAC-based quantitative proteomics can be used to identify the soluble interacting partners of virtually any membrane protein. As a proof of principle, we applied the method to the bacterial SecYEG protein-conducting channel, the maltose transporter MalFGK(2) and the membrane integrase YidC. In contrast to the detergent micelles, which tend to destabilize interactions, the nanodisc was able to capture out of a complex whole cell extract the proteins SecA, Syd, and MalE with a high degree of confidence and specificity. The method was sensitive enough to isolate these interactors as a function of the lipid composition in the disc and the culture conditions. In agreement with a previous photo-cross linking analysis, YidC did not show any high-affinity interactions with cytosolic or periplasmic proteins. These three examples illustrate the utility of nanoscale lipid bilayers to identify the soluble peripheral partners of proteins intergrated in the lipid bilayer.
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