Albany 2013: Book of Abstracts
June 11-15 2013
©Adenine Press (2012)
Computational study of substrates and mediators features of lacasses
Laccases are enzymes of the family of the multicopper oxidases, being widely used for biotechnological applications (Canas & Camarero, 2010). The enzyme catalytic cycle consists in the oxidation of the substrate with the concomitant reduction of molecular oxygen to water. In the 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 analyze 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 (Fabbrini et al., 2002).
This research has been supported by Bioprocel, Spain.
F. J. Enguita, Marçal¸ D., Martins, L. O., Grenha, R., Henriques, A. O., Lindley, P.F.,& Carrondo, M.A. (2004). Substrate and Dioxygen Binding to the Endospore Coat Laccase from Bacillus subtilis. J. Biol. Chem. 279, 23472–23476
M. Fabbrini, Galli, C., Gentili, P. (2002). Comparing the catalytic efficiency of some mediators of laccase. J Mol. Catal. B 16, 231–240
R.A. Friesner, Banks, J.L., Murphy, R.B., Halgren, T.A., Klicic, J.J., Mainz, D.T., Repasky, M.P., Knoll, E.H., Shelley, M., Perry, J.K., Shaw, D.E., Francis, P. & Shenkin, P. (2004). Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy. J Med Chem 47,1739–1749
Department of Chemical Engineering