Prime region subsite specificity characterization of human cathepsin D: The dominant role of position 128

Abstract In order to contribute to our understanding of cathepsin D (CatD) active site specificity, two series of chromogenic octapeptides with systematic substitutions in positions P' 2 and P' 3 were synthesized. This panel was characterized with native human liver cathepsin D (nHuCatD) and yielded information concerning specificity trends within the S'2 and S'3 subsites. The pepstatin inhibited crystal structure of nHuCatD (Baldwin et al., 1993) was then utilized in conjunction with these subsite preference data to identify residues suspected of contributing to “prime” side subsite specificity. These residues were targeted for site‐directed mutagenesis using the re‐engineered recombinant model, “short” pseudocathepsin D (Beyer & Dunn, 1996). As a result of these analyses it was determined that prime region subsites do contribute to the unique specificity of human CatD. Furthermore, it was ascertained that the poly‐proline loop does not have an active role in S'3 subsite specificity. Lastly, it appears that Ile 128 has a dominant role on S'2 subsite specificity whereas Val130 does not.