How can we identify target proteins endogenous binding partner proteins?
As Raja suggested, I would suggest the BioID method. This method uses a promiscuous biotin ligase fused to your protein-of-interest which then biotinylates interacting and proximal proteins. You can isolate the biotinylated proteins with streptavidin beads, then proceed to on-bead digestion and mass spec analysis. If you have any questions about this method, please feel free to send me a message. I have a typed protocol I can send to you.
Thank you all for nice suggestions. I might go for a traditional Yeast Two Hybrid Screen (Y2H) or Co-IP followed by Mass Spec. Thanks once again.
I used the bacterial adenylate two hybrid system for similar experiment, and it worked perfectly for me.
Good luck
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