For Pete's sake, why don't you guys just listen to a food scientist for once?!

Do you guys even know what does "denature" means? Only braindead got it right. Denatured protein can coagulate, form crosslinks, becomes gelation, etc...
Unless you super heat the protein at very high temperature, OR you char/carbonise the protein... the amino acids are still intact.
I'll give you guys an analogy:
Unfolding a large map but unable to fold it back to ori configurations. The map is still useful even if it's folded wrongly, right?
Replace the word "map" with "protein" and it's the same thing...
because proteins are very long chains/sheets of amino acids that are folded here and there and cross linked & bonded here and there.
Heat, pressure, enzymes, catalysts, acids can weaken these bonds ---> once weakened, the protein strings/sheets will unfold.
The problem is, the proteins cannot fold themselves back into ori configurations because it's a very complicated biological process. So they just
cincai bundle back together.
Will this denatured form make it hard for your stomach to digest? Yes and no. Depends.
However, remember than acids will denature it? You stomach acid (which is damn powerful) will denature/unfold it again, so that enzyme can digest them.
The problem with over cooking the proteins is that precious vitamins might be lost.
Else, it's basically the same thing in a different look.
P.S. how come no one make noise about eating their meat/chicken RAW?!
P.S.S Old-skool BB'ers didn't know about protein denaturation... yet. You don't see any BB'ers advocating raw eggs nowadays, don't you? =)