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[Ringaling]

The protein I am working with binds to the cell (E. coli BL21(DE3)pLysS) membrane.  How should I separate it from the membrane and purify it?

[labslave]

I think you have encountered insoluble protein expression from your E. coli growth.  When you protein binds to the bacterial cell membrane you have produced inclusion bodies.  Actually inclusion bodies are a good thing since pelleting your bacterial will give you >85% recombinant protein.  Try using Sarkosyl it separate your protein from the inclusion bodies.  For a more detailed explaination please check the Frangioni & Neel paper from Analytical Biochemistry 210, 179-187 (1993)  title of paper: Solubilization and Purification of Enzymatically Active Glutathione S-Transferase (pGEX) Fusion Proteins.

Hope that helps!