Denating the protein via heat can decrease the amount of amino acids, generally in proportion to the amount of heat, and the time. So strangely enough, cooking your beef steak in an oven at 800 for 2hours may not be that useful for the amino acids, but neither is the piece of leather you have left over.
Short cooking can help increase the availability of some protein, in others it worsens it. Strangely people have been cooking protein for years and have survived pretty nicely on it.
Acid denaturation during digestion is one thing, the body will also perform enzymatic denaturation. Because if the body does not denature the protein, it cannot get the aminos.
(remember quaternary and tertiary structures of proteins)