Computer simulation of proteolysis. Peptic hydrolysis of partially demasked β-Lactoglobulin

Computer assistance was used for simulation of proteolysis of partially demasked β-Lactoglobulin by pepsin. Total proteolysis kinetics and kinetics for intermediate peptides were computed by PROTEOLYSIS program for different rates of demasking. The increase of demasking rate by a factor of 100 gives twofold increase in the total hydrolysis rate. The identification of cleavage sites on the basis of limited number of peptides was found to depend on the depth of hydrolysis. When the number of identified peptides was only 10, the computer simulation has allowed to predict a half of experimentally determined cleavage sites. The influence of the dimension of enzyme active site and of the secondary structure of substrate on the efficiency of prediction of cleavage sites was analysed.