RE: denaturing protien
from what i can remember from the biochem lectures, i don't think denaturation is much of a problem if one is only concern about absorbing amino acids. the ingested protein has to be broken down into individual aa or small peptides for absorption anyway i.e. the tertiary structure of the ingested protein would have been destroyed (denaturated) during digestion.
dentaturation is the destruction of the tertiary structure of protein structure which causes the protein to lose its biological activities (if any) and doesn't affect the bioavailability of the aa that makes up the protein chain.
do have to be concern about denaturation when one wants to preserve the biological activities of certain protein structures e.g. enzymes. not sure if this is possible since the stomach acid is very acidic! should have paid more attention in biochemistry classes.
maybe james cares to confirm and elaborate if possible.