Dynamic Docking Study of the Binding of 1-Chloro-2,4-Dinitrobenzene in the Putative Electrophile Binding Site of Naturally Occurring Human Glutathione S-Transferase pi Allelo-Polymorphic Proteins
ABSTRACT We recently reported the cloning and expression of full-length cDNAs of three closely related human glutathione S-transferase (GST) pi genes,15 and showed the encoded proteins, designated GSTP1a-1a, GSTP1b-1b, and GSTP1c-1c, to differ in catalytic activity toward the GST substrate, 1-chloro-2,4-dinitrobenzene (CDNB). The better to understand the basis of the functional differences between the three polypeptides, we performed flexible (dynamic) docking of CDNB into the putative electrophile (H-) sites of the GST-Pi variant peptides using a Monte Carlo simulation method as implemented in the Affinity automatic docking module of the Insight II 95.0 molecular modeling program package, with the CFF91 force field of the Discover program (Biosym/MSI, San Diego, CA). The computed binding energies of CDNB at the different H-sites showed a remarkable correlation with the experimentally determined Km values for the catalysis of the conjugation CDNB to glutathione (GSH) by the different enzymes. These observations are in agreement with the prevailing view that the rate determining step of GST-pi catalyzed conjugation of CDNB with GSH resides in product release rather than product formation.