A theoretical study of the initial stages of catalysis in the aspartic proteinases

We have studied the initial stages of hydrolysis in the aspartic proteinases by performing ab initio Hartree-Fock calculations on a small portion of the active site of endothiapepsin. The crystallographic coordinates of a difluorostatone inhibitor complexed with endothiapepsin were used to generate a template for the initial enzyme-substrate complex. The active site was modelled as a formic acid-formate anion moiety (representing the catalytic aspartates, Asp-32 and -215) and a bound water molecule. Residues Gly-34, Ser-35, Gly-217, and Thr-218, which all form hydrogen bonds to the active site, were modelled using two acetamide and two methanol molecules. The calculations predict that nucleophilic attack by the active site water results in the formation of a tetrahedral oxyanion intermediate which subsequently abstracts the acidic proton from Asp-32 to form a gem-diol intermediate. Thr-218 appears to play an important role in catalysis by forming an additional hydrogen bond with the water oxygen during the early stages of nucleophilic attack. Ser-35 lowers the pK(a) of Asp-32 and this facilitates the formation of the gem-diol intermediate. (C) 1998 Elsevier Science B.V. All rights reserved.