Computational study of substrates and mediators features of lacasses

摘要

Laccases are enzymes of the family multicopper oxidases, being widely used for biotechnological applications (Canas & Camarero, 2010). The enzymes’ catalytic cycle consists of the oxidation of the substrate with the concomitant reduction of molecular oxygen to water. In this process, the substrate is converted to a free radical, that can oxidize larger substrates acting as a mediator or it can undergo polymerization. Substrate binding is not specific, and there is a large diversity of substrates for laccases. Moreover, the binding site shows important differences among diverse species. The goal of the present work is to characterize the laccase binding pocket of different species, in order to establish their common pharmacophoric characteristics. For this purpose, we have carried out docking studies with a subset of substrates, covering the diversity of substrates using the Glide program (Friesner et al., 2004). We have also analyzed the characteristics of the binding site using diverse probes. We further have rationalized the differential values of km found among diverse species for a specific substrate. Finally, special attention has been devoted to the binding of the mediator 2,2′-azido-di-(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS), commonly used in industrial processes. Figure 1 shows, ABTS docked onto the fungal laccase, whereas Figure 2 shows ABTS docked onto the bacterial laccase. The analysis of the protein–ligand complex together with the corresponding optimized geometries of the possible substrate species carried out using DFT suggest that the bound species is the protonated form of ABTS as previously suggested (Enguita et al., 2004). Furthermore, the results of this study also suggest that its mechanism of oxidation occurs in a similar way to the rest of substrates/mediators, in contrast to previous suggestions