Computer-aided molecular modeling of cathepsin E, a possible endothelin-converting enzyme

Abstract

A three-dimensional model of human cathepsin E, a possible endothelin-converting enzyme, is constructed using computer-aided molecular modeling techniques. The structure of porcine pepsin, another aspartic protease, was used as a template. The final structure, after all gaps and deletions were made, was optimized using the AMBER-4 package. A dipeptide (Trp-Val) representing the substrate was docked in the putative active site and the whole structure was optimized after several runs of minimization and dynamics calculations. The result of this modeling study showed that the structure of cathepsin E is similar to that of porcine pepsin and has three disulfide bonds that are conserved in both enzymes. There are two Asp-Thr-Gly sequences at the active site of enzyme. The active site cavity is large enough to accommodate its substrate.