I am looking to perform IP/co-IP studies and possibly downstream mass spectrometry applications from protein lysate. Ideally I would IP/co-IP on cytoplasmic and nuclear fractions.
However, my understanding is that oftentimes the high salt content of the nuclear extraction buffer does not preserve protein-protein interactions very well. Is there a way to perform subcellular fractionations while maintaining these interactions so that I can then do co-IP studies?
Protein-protein interactions (PPI) are in general 'dynamic' - some are transient, some are more or less permanent, and some are ornagelle-specific. Thus it would be difficult to pinpoint which PPIs are preserved and which are not during your cell fractionation experiment. It might be better to do co-immunoprecipitation both before and after the cell fractionation, and then compare the results.
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