I am to isolate the retina and run a SDS-PAGE western blot. Is it better to store the isolated tissue directly at -80C or to extract the protein immediately and store the extract at -80?
Duration of storage is estimated to be around 3 weeks of time. The protein extract is prepared by sonicating the tissue in RIPA buffer with PI and then centrifuging it.
Is the protein more stable when in its native form (bound to the tissue) or when in a suspension?
I have never worked with something like a retina before but when using E.coli/insect/mammalian cell culture it is standard practice to freeze the cell pellet at -80C before purifying a protein. Storing a protein at -80C is a lot more tricky, it can destabilse the protein due to the salt gradients/ice crystals produced by freezing and thawing. My instinct would be to keep the protein inside the tissue until it is needed.
If you freeze the tissue in the buffer with freshly-prepared protease inhibitors cocktail (you don't know which protease might degrade your protein) you might go with this option. The way you did it is also good, as long as the exposure of your protein in solution is short and the t° ~ 4°C. But it always depends on each particular protein: membrane vs cytoplasmic, sensitivity to pH changes, sensitivity to salt concentration and so on. The general rule is to keep your protein in the buffer (+PI) where this protein shows its highest functionality.
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