Proteins 
are comprised of amino acids arranged like beads on a string (primary structure) which are then folded upon themselves by means of hydrogen bonds (secondary, tertiary and quaternary structures). This intricate folding can be very complex, conferring specificity which defines a protein’s biological activity. If such higher structures are disrupted, such as by temperature extremes, altered salt concentration or changes in pH, a protein’s biological activity can be reduced or completely obliterated.
When most proteins are heated beyond 41 degrees Celsius (105.8 degrees Fahrenheit), the bonds are broken, thus resulting in denaturing of proteins. When you consider the fact that normal body temperature is 37 degrees Celsius or 98.6 degrees Fahrenheit, not much heat is required to break down a protein. Most stoves have broiling air temperatures up to 500 degrees Fahrenheit, with the surface temperatures of food reaching higher temperatures as a result of direct radiation from the heating elements. In essence, normal cooking practices heat proteins well above the temperatures at which they become denatured.
In addition to denaturing, cooking temperatures can cause cross-linking of some proteins, best exemplified by hardening of bread or eggs during the cooking process. This reduces the digestibility of the proteins, but it is important to consider that the majority of those proteins is absorbed and utilized by the body. Most whey protein has been processed at temperatures exceeding 160 degrees Fahrenheit or 72 degrees Celsius, qualifying it as hydrolyzed protein. However, despite the fact that the peptide bonds in the protein are broken during pasteurization, denatured protein still contains all of the amino acids that are found in unhydrolyzed protein and which provide the building blocks for muscle.
What this translates to is the fact that there is still nutritional benefit to be gained from denatured protein despite the argument by some that such proteins are useless. During the critical post-workout window, the body needs protein in order to repair and build muscle. Most of this is absorbed and utilized by the body, with a small portion excreted as waste which is often characterized by a particularly pungent “protein bomb” odor.
Why have I brought up the subject of denatured protein? Because I have heard people argue that hydrolyzed whey protein is useless because it is not bioactive. It seems to me that the considerable muscle mass found on individuals who ingest large amounts of whey protein flies directly in the face of such a short-sided argument. Furthermore, I do not believe that the baking process to which whey protein used in high protein breads is subjected poses any greater risks on the constituent amino acids themselves since they are already hydrolyzed to begin with. Until I see an individual who shows no increase in muscle mass despite proper weight training and sufficient protein intake which relies heavily on whey protein sources, I will continue to hail hydrolyzed whey protein as an excellent source of protein for those who are trying to gain muscle.
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