This is a good question that I love to answer. I won't make an example of you though because you legitimately want to know. I'm going to answer this in a long drawn out way to make sure you get something out of it. Because in a forum like this, a simple yes or no doesn't really mean ****. So hopefully you (and others) will get something out of this.
First off, Let's describe what protein denaturation is...
In biochemical terms, it literally means that the polypeptide loses its tertiary (3-dimensional) structure and secondary (think of it has HALF 3-dimensional) structure.
Secondly, lets describe what causes polypeptide/protein denaturation.
1. Heat
2. PH (changes in the various hydrogen Ion species)
3. Radiation
4. Torsional stress (e.g. violent shaking)
5. Harsh solvents (typically throwing off hydrophobic stabilization)
6. High salt content (large concentration of ions throwing off electrostatic stabilization)
This list goes on...
I like to give this analogy. Given the list you have ^^^^ up there think about these things...
cooking chicken on a BBQ (super high heat)
your stomach acid having high salt concentration and a low PH (high hydrogen ion content)
blah blah blah
Lastly: even if the protein you consume through your whey is "native" it will be digested and denatured in your stomach/intestine anyway.
Some people argue that 'native' whey peptides enter the bloodstream faster. This is true, but the overall muscular assimilation is a wash. Because proteins cannot be incorporated into metabolic processes (in our case, anabolic) unless they are broken down into their constitutive amino acids. So, even if it enters your bloodstream faster it STILL needs to be degraded after it enters the bloodstream. So it's a matter of digesting it now or later... in the long run I don't think it will make a difference in the overall musculature (people have been giant since before protein powder existed)
So, in short. Nuke and cook whatever the F#*K you want. You superheat your chicken to 600F on the grill. If that doesn't denature the living **** out of something nothing will. People would have stopped eating cooked meat a long time ago if it didn't correlate with muscle gain... Some nitpickers say that grilling at super high heat can actually react the polypeptide into nitrosamines, which is can. but screw them. It doesn't mess with the nutritive value enough in my opinion.
Unless somebody has a huge argument against this... I think these few paragraphs should be stickied in the nutrition section... because it's something everyone needs to know...