As a lab we have been trying to look for interactions between clathrin and other proteins using Hela Cells and Co-IP. Unfortunately, it seems that our protein A and protein G beads seems to non-specifically bind to clathrin. When we do pull-downs of one protein and probe for clathrin, we always see clathrin, even in our negative controls. We concluded that the protein A and G beads are non-specifically binding to clathrin and we found a work around to solve this problem. We still don't know why these beads bind clathrin. Has anyone else ever experienced this?
Charles! Absolutely, I faced the same problem with other set of proteins. This interaction possibly arises from "hanging methyl" or modified groups of target proteins or even antibodies. The way out is to neutralize those groups that makes the whole process more tedious. I tried a modified washing buffer that worked for me. You may want go through this paper.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018218
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