protein protein interaction discovery - (Dec/30/2010 )
I am trying to design an experiment but I am not sure if it is at all possible to do it. I am trying to find what proteins my protein of interest is interacting with. I know I can tag my protein of interest ...that part is easy breezy ( well in theory anyways) but what i want to know is if it is possible to extract proteins from plants and run in through the pull-down column that already has the tagged protein of interest. I tried searching for article but could not find any that described a similar experiment. All I found were experiments that cloned the "fish" proteins into bacteria/yeast along with the bait protein and tested for interaction that way using pull-down assay.
Even if pull-down column system works, is the interaction going to be strong enough to withstand all the washes?
Maybe if you know the function of your protein you could use it in advantage to shorten the list of possible interaction proteins.