Stucture of the complex between Mucor pusillus pepsin and the key domain of κ-casein for site-directed mutagenesis: a combined molecular modeling and docking approach.

In the structural-based mutagenesis of Mucor pusillus pepsin (MPP), understanding how κ-casein interacts with MPP is a great challenge for us to explore. Chymosin-sensitive peptide is the key domain of κ-casein that regulates milk clotting through the specific proteolytic cleavage of its peptide bond (Phe¹⁰⁵-Met¹⁰⁶) by MPP to produce insoluble para-κ-casein. Here, we built the model of this large peptide using molecular modeling technique. Docking study showed that MPP can accommodate the designed model with a favorable binding energy and the docked complex has proven to locally resemble the inhibitor-chymosin complex. The catalytic mechanism for the peptide model binding with MPP was explored in terms of substrate-enzyme interaction and property of contacting surface. Some critical amino acid residues in the substrate binding cleft have been identified as an important guide for further site-directed mutagenesis. Glu13 and Leu11 in the S3 region of MPP, predicted as the special mutation sites, were confirmed to retain clotting activity and decrease the proteolytic activity. These novel mutants may provide a promising application for improving cheese flavor.