Here's a good little easy to understand article about what denaturing means of a whey protein.

the article was on allnaturalprevantion.com

The Truth about Whey Protein and Glutathione


Understanding Cysteine, Cystine,
and Native Whey Proteins



Many whey protein products on the market advertise their ability to affect glutathione production within the body. This is a growing area of consumer interest due to clinical studies heralding Glutathione’s role as the body’s master antioxidant and defender against disease and aging.
Because the amino acid Cysteine is the critical rate-limiting factor in the body’s ability to produce Glutathione, its availability in whey protein has become an area of competitive comparison among high-quality whey proteins.
This article is intended to help clear up any confusion regarding the two forms of Cysteine and how it relates to the quality and biological activity of a whey protein.
Native Proteins:
A “native” protein is a protein that is still in its original, natural structure. It has not been altered by heat, chemicals, enzyme action, or distress.
Therefore, it is imperative to understand that a native protein represents the ideal biological function for which it was designed by nature. In regard to whey protein, a native whey protein would represent the exact form of protein that was intended to nourish a newborn mammal from its mother’s milk.
Amino Acids:
Amino acids are critical to life, and have a variety of roles in metabolism. One of their most important functions is to serve as the building blocks of proteins. All proteins in all species, from bacteria to humans, are constructed from the same set of twenty amino acids.
A protein is formed by amino acid subunits linked together in a chain. The bond between two amino acids is called a peptide bond and the chain of amino acids is called a peptide (20 amino acids or less), or a polypeptide (more than 20).
Figure 1: Primary Protein Structure


Protein Structure: Each protein consists of one or more unique polypeptide chains. These chains then undergo a folding process which results in a configuration that is the most stable for its particular chemical structure and environment. The final 3-D arrangement is called the protein’s conformation and typically assumes a globular appearance. To understand this very complex conformation, scientists describe four levels of how the amino acid peptide chains arrange themselves: Primary, Secondary, Tertiary, and Quaternary.
  • Primary Structure refers to the linear sequence of amino acids that make up the polypeptide chain. This sequence is determined by the genetic code. The bond between two amino acids (a peptide bond) is formed by the removal of a water molecule from the two different amino acids, forming a dipeptide. The sequence of amino acids determines the way that the protein folds into its final structure, or conformation. (See Figure 1)
  • Secondary Structure refers to the formation of a regular pattern of twists or kinks of the polypeptide chain. This pattern is due to hydrogen bonds forming between the atoms of the amino acid backbone. (See Figure 1)
  • Tertiary Structure refers to the three dimensional globular structure formed by the folding of these polypeptide chains. This typically results in a compact globular structure. The folding of the polypeptide chain is stabilized by multiple weak, non-covalent interactions. (See Figure 1) These interactions include:
    • Hydrogen bonds that form when a Hydrogen atom is shared by two other atoms.
    • Electrostatic interactions that occur between charged amino acid side chains.
    • Hydrophobic/Hydrophilic interactions: During the folding process, amino acids with a polar (water soluble) side chain are often found on the surface of the molecule while amino acids with non-polar (water insoluble) side chain are buried in the interior. This affects the water solubility of a protein.
  • Quaternary Structure refers to the fact that some proteins contain more than one polypeptide chain, adding an additional level of structural organization
Figure 1: The Four Levels of a Protein Structure Formation

Cysteine vs. Cystine: Covalent bonds may also contribute to the stability of the folding structure. The amino acid Cysteine is unique in that it has a Sulfur-Hydrogen (thiol group) as part of its side chain (R group). Therefore, at points where two Cysteines align within the folding process, a disulfide bond (Sulfur-Sulfur) can form. This molecule formed by two bonded Cysteines is called Cystine.
Cysteine


Cystine
Therefore, Cysteine can be found in both forms within the naturally occurring native whey protein. Because each protein folds into its unique and specific conformation based upon its genetic code, a specific ratio of Cysteine to Cystine is representative of an unaltered native whey protein. The human body is able to use both forms in the production of Glutathione. Thus, it is important to nourish the body with this ratio as prescribed by the naturally occurring native protein.
Cysteine is the preferred form for synthesis of glutathione in the Lymphocytes and neurons, while Cystine is the preferred form for the synthesis of glutathione in macrophages and astrocytes.
Denatured Proteins:
Proteins can denature, or unfold, so that their 3-D structure is altered or damaged, but their primary peptide chain remains intact. (See Figure 3) Many of the interactions that stabilize the 3-D conformation of the protein are relatively weak and are sensitive to various factors including high temperature, low or high pH, high ionic strength, or organic solvents. Proteins vary greatly in the degree of their sensitivity to these factors.
Denaturation is a process in which proteins or nucleic acids lose their 3-D structure (tertiary structure) by application of some external stress or compound. The protein is forced to literally unfold as shown below. (See Figure 3)
Figure 3: Denaturing of a Native Protein

Since the native structure of a protein determines its biological function, the protein can no longer fully perform its original function after it has been denatured. The original amino acid peptide chains may remain intact. However, the denatured protein has now lost its native form, and will now re-associate itself into varying random (non-native) structures.
As a part of that process, sulfur groups on the Cysteines are likely to undergo oxidation to form disulfide bonds thus creating additional Cystines that were not normally present in the native form.
This drastically diminishes the availability of naturally-occurring (native) Cysteine. As a result, the original native whey protein ratio of Cysteine to Cystine is dramatically shifted in favor of Cystine within the denatured protein structure.
Although the body can and does utilize Cystine, it is a larger and less water-soluble molecule making it more difficult to utilize than the native form of Cysteine.
Therefore, in order for the body to provide proper levels of Cysteine to the lymphocytes and neurons, the macrophages and astrocytes must reduce the Cystine into Cysteine. This requires a multi-step process and decreases the efficiency of optimal glutathione production.
Conclusion:
The natural design and structure of a native whey protein specifies its intended biological function. However, the native structure is fragile and requires great care to preserve the integrity of its structure and biological function. The ultra-high heat pasteurization methods used in the production of commercial whey proteins severely denatures the native proteins and diminishes the availability of naturally-occurring Cysteine.
Therefore, in order to achieve the full spectrum of nourishment and biological function intended by nature, whey protein should be consumed in its native, unaltered form.