As whey concentrate is further processed and purified into whey protein isolate, these 3-d structures can degraded and lose their biologic activity. You should note, however, that the amino acid sequences do not change when protein is denatured, and whether a protein is denatured during processing does not affect its muscle-building qualities. All large proteins are broken down during digestion into smaller protein chains and individual amino acids (denatured), and whether this process occurs in the gut or in the manufacturing plant is irrelevant to the muscle fibers getting these proteins.