The Aspartic Proteinases are an important family of hydrolytic enzymes associated with several pathological disorders such as hypertension (renin), gastric ulcers (pepsin), muscular dystrophy and neoplastic diseases (cathepsins D and E).
Crystallographic studies have shown that the active site consists of two carboxyl groups and a tightly bound water molecule.
The rational design of inhibitors of the aspartic proteinases would be greatly facilitated by a deeper understanding of the catalytic mechanism. However, despite numerous experimental studies the exact details of the mechanism are not fully understood, although it is generally believed to involve general acid/general base catalysis.
One of the main weaknesses of protein crystallography is the inability of the method to locate the positions of hydrogen atoms. The problem is particularly acute in the aspartic proteinases because the nucleophilic water molecule can bind to the active site in several different orientations. Hartree-Fock calculations have been used to estimate the relative stability of several possible configurations for the active site of endothiapepsin.
The Hartree-Fock calculations on native endothiapepsin predict that the nucleophilic water molecule is bound in a catalytically inert configuration in the native enzyme. Further calculations have demonstrated that rotating the carboxyl group of Asp-32 enables the water molecule to adopt the optimal orientation prior to catalysis. This result suggests that substrate induced activation of the water molecule occurs prior to catalysis.
The results for native endothiapepsin have been used to construct a model for the Initial Enzyme-Substrate Complex