How to Use Protease/s for Protein Proteolysis Protein Proteolysis refers to the use of hydrochloric acid to destroy peptide bonds between the amino acids that make up a protein. When carried out with proteases (also known as proteinases), which are enzymes, the process is termed proteolysis. Depending on how efficient the enzyme is or what links it breaks, the proteolysis can be limited or unlimited. Proteolysis can begin either from one end of the chain of amino acids that comprise the protein or somewhere in the middle of it. Unlimited proteolysis produces individual amino acids while limited proteolysis produces short chains of polypeptides.