Secondary substrate binding in aspartic proteinases: contributions of subsites S3 and S'2 to kcat

The kinetic parameters kcat and Km were determined at 25 degrees C and pH 5.5 for endothiapepsin and rhizopuspepsin acting on the series of substrates Ac-Ala(m)-Lys-Nph-Ala(n)-amide where Nph is p-nitrophenylalanine, and m and n equal 0-4. Kinetic parameters were also determined at 25 degrees C and pH 3.5 for pig pepsin acting on the series of substrates Ac-Ala(m)-Phe-Nph-Argn-Ala(n)-amide, where m equals 0 to 2 and n equals 0 or 1, and another series based on -Ile-Glu-Phe-Nph-Arg-, which is the core of a series of peptides designed by Dunn et al. (1986, Biochem. J. 237, 899-906). Km values were found to be largely independent of increases in the chain length of the substrates whereas kcat values showed large increases with increasing chain length. With endothiapepsin and rhizopuspepsin the largest increases (between 13-fold and over 150-fold) were obtained when alanine residues were added in positions P3 and P'2 and thus are similar to those observed previously with penicillopepsin. Additions of alanines to positions P2, P'3, and P'4 gave much smaller increases. In the case of pig pepsin the results were not as clearcut. Whereas the largest increases were seen for positions P3 and P'2 only with some of the peptides, the increases were strongly dependent on the length of the peptides. With some of the longer peptides the increases were comparable to those seen for positions P2 and P'3. Thus, whereas the addition of two alanines in position P3 to the dipeptide Ac-Phe-Nph-amide caused a large proportional increase in kcat, the increase was much smaller when the addition was made to the homologous tetrapeptide and even smaller when made to the pentapeptide Ac-Ala-Phe-Nph-Arg-Ala-amide. Additions of arginine in position P'2 gave large increases in kcat for all three peptides of the series.