|MadSci Network: Biochemistry|
Freeze-drying a protein _should_ not denature your protein, as far as I am aware. In theory, all that is happening is that water is being sublimed off your folded protein, leaving the folded protein behind.
HOWEVER, that is assuming that your protein was folded to begin with (i.e. before you froze the sample). When you say that you "cooked" something, if that means you cooked the protein sample, then THAT will denature the protein for sure. Even after you cooled the sample down again it may not have folded correctly, and then when you freeze-dried the sample it would have remained folded wrong.
Try the links in the MadSci Library for more information on Biochemistry.