Well...I'm not sure what you are asking. Proteins are polymers of amino acids. Think of amino acids as a Lego and stringing various legos together in a straight line could represent a protein. This straight line of amino acids is called the primary structure of the protein. If you imagined this chain coiling around and sticking together in various places this would be called the secondary structure of a protein.
Now when we eat a protein source we need to break down both the secondary and primary structures of the protein to break the amino acids into single units. We can only absorb individual amino acids into our blood stream from the small intestine so the structure of the proteins MUST be destroyed to digest them.
So the question of cooking and protein quality is a bit ambiguous. Some nutrients such as Vit-C and B-vitamins are destroyed with over cooking but then again some carotenoids are ONLY available after the food is cooked. Human evolution since H. Erectus was a story of both cooked and raw foods. This seems to make sense with regards to nutrient availability.
If this did not answer your question let me know!