A Model of Demasking and Hydrolysis of Peptide Bonds During Tryptic Digestion of β-Casein and β-Lactoglobulin.

The prediction of polypeptide chain fragmentation during digestion (proteolysis) of protein substrates by trypsin was carried out for globular β-lactoglobulin (β-LG) and micellar β-casein (β-CN). Despite significant differences in the protein structures of these substrates, the concentrations of peptide fragments are calculated as functions of time or degree of hydrolysis using the same equations derived from the general proteolysis model. This model considers the opening of protein substrates in the course of proteolysis, the so-called demasking process, and the subsequent hydrolysis of specific peptide bonds at different rates determined by the amino acid sequence of hydrolyzed sites. The use of this model for in silico prediction of proteolysis is discussed. An algorithm for calculating demasking rate constants based on the experimental distribution of peptide fragments is presented. The calculated concentration dependence on the degree of hydrolysis of peptide bonds was compared with the experimental data for the intermediate and final peptide fragments of β-LG and β-CN. The predicted and experimental concentration curves for the final products were compared based on their curvatures. For both substrates, the predicted redistribution of peptide fragments in the course of proteolysis was found to be consistent with the experimental one.