Best ways to limit protein denaturization during cooking?

There are also chemical methods to denature proteins (altering pH or introducing some sort of reducing agent); but since you are concerned with maintaining a +N balance at the cellular level - namely in your skeletal muscle tissue, why are you concerned with protein denaturation? All of the proteins you consume must be catabolized into individual amino acids before your cells can use them so it seems that denaturation (breaking the non-covalent bonds that organize the peptide chains) would be good because then your body has less work to do. That is also why single aa supplements are helpful to athletes (particularly those that our body cannot make - threonine, methionine, lysine, etc) - ingesting these makes less work for metabolic pathways (in the digestive system and in each individ. cell).