I am working with a membrane protein (A) which is supposed to interact with a membrane receptor (B). I can overexpress A with a tag but don't know the B. I am planning to cross link A with B in vivo followed by membrane purification, Co-Ip and Mass spec analysis to identifty any interacting partners.
I will highly appreciate any suggestions on this.
Thanks.
Any cross-linker will by definition be toxic, you cannot use them in whole organisms. You may get away with using them in cell culture for a short time, if you harvest before the cells get killed. In that case you'd obviously need a protein-free growth medium and a non-membrane permeable cross-linker.
If you purify the membranes first, then you don't have to worry about the toxicity of the crosslinker. Try varying the crosslinker concentration. A specific association will be detectable at lower crosslinker concentrations, but at higher concentrations there will be more non-specific crosslinking.
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