Within reason, protein denaturation is fine, as long as the amino acids remain intact. The whole purpose of digesting proteins is to denature them into peptides small enough to be absobed. Extreme denaturation (such as charcoaled/burnt meat) will destroy the amino acids as well as produce heterocyclic amines which are pretty bad for ya! Acidic denaturation is one of the main methods of making cheeses and tofu. These foods maintain high quality protein/amino acid profiles.