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Chymotrypsinogen A is used as a serine protease that hydrolyzes peptide bonds with aromatic or large hydrophobic side chains (Tyr, Trp, Phe, Met) on the carboxyl end of the peptide bond, used in the non-invasive determination of solid-state protein conformation using near infrared (NIR) spectroscopy. It has been used to study the partitioning of protein in polymer/polymer aqueous two-phase systems. The enzyme has also been used for self-interaction chromatography applications, to test the rapid measurement of protein osmotic second virial coefficients. In this technique, the protein is immobilized on chromatographic particles and its retention is measured using isocratic elution.

Chymotrypsinogen A requires limited proteolysis for its activation. Chymotrypsinogen A may be activated by trypsin and chymotrypsin (autolytic activation) to form m α, β, γ, δ and π chymotrypsin (depending upon the conditions of activation). Chymotrypsin is a protease that will preferentially cleave peptides on the carboxyl side of aromatic amino acids including tryptophan, tyrosine, and phenylalanine. It will also hydrolyze peptides on the carboxyl side of leucine, methionine, and alanine.