Docking and molecular dynamics simulation of complexes of high and low reactive substrates with peroxidases

Abstract

The activity of enzymes depends on many factors, i.e., the free energy of reaction, substrate docking in the active center, proton tunneling, and other factors. In our study, we investigate docking of luminol (LUM) and 4-(1-imidazolyl) phenol (IMP), which show different reactivity in peroxidase-catalyzed reaction. As peroxidases, Arthromyces ramosus (ARP) and horseradish (HRP) were used. For this study, simulation of substrate docking in active site of enzymes was performed. Enzyme-substrate complexes structural stability was examinated using molecular dynamics simulations. The calculations revealed that LUM exhibits lower affinity to HRP compounds I and II (HRP I/II) than to ARP compounds I and II (ARP I/II). In the active center of ARP I/II, LUM forms hydrogen bonds with Fe=O. This hydrogen bond was not observed in HRP I/II active center. In contrast with LUM, IMP binds to both peroxidases efficiently and forms hydrogen bonds with Fe=O. Molecular dynamics studies revealed that enzyme complexes with LUM and IMP structurally are stable. Thus, arrangement diversities can determine the different substrates reactivity.