Arginine deiminase is an enzyme that plays an essential role in energy production of bacteria and primitive protozoa. Since its gene is absent in the human genome, it is an attractive target for developing novel antibacterial and antiparasitic drugs. Inhibition of the enzyme might also have biodefense implications concerning a category B pathogen Giardia intestinalis. The recent advances in both enzyme kinetics and structural determination have revealed a unique catalytic scaffold consisting of several well organized charged and polar residues. Superficially similar to cysteine protease, arginine deiminase has a conserved Cys-His-Glu triad and uses Cys in covalent catalysis. However, the drastically different arrangement of the three key residues in the active site of this enzyme suggests a completely different nucleophile activation scheme, which might involve the substrate. In this application, we present a detailed and self-contained research plan for understanding both the catalytic mechanism of arginine deiminase and its inhibition. In particular, we propose to calculate reaction paths and free energy barriers for both the nucleophilic substitution and hydrolysis partial reactions catalyzed by the enzyme, using high level quantum mechanical/molecular mechanical (QM/MM) methods. The proposed research is unique in that the computational work will be closely coupled with experimental studies of the same enzyme. Simulations of the enzymatic reaction will be based on experimental structures while theoretical predictions will in turn provide guidance to further experimental investigations. If successful, this exploratory project will evolve into a comprehensive study of the arginine deiminase superfamily, whose members use the same catalytic strategy in modifying the guanidino group in arginine derivatives. The members of the superfamily, such as dimethylarginine dimethylaminohydrolase and peptidyl-arginine deiminase, are involved in many important human diseases such as cancer, stroke, rheumatoid arthritis, and multiple sclerosis. Hence, the fundamental research proposed here also has potential practical applications.
The research proposed here is aimed at the elucidation of the catalytic mechanism of arginine deiminase, which may help designing new antibacterial and antiparasitic drugs.
