Leveraging molecular docking to understand Congo red degradation by Staphylococcus caprae MB400

Abstract

Congo red (CR) is a genotoxic, sulphonated azo dye and poses significant pollution problem. We hereby report its degradation by Staphylococcus caprae MB400. The bacterium initially propagated as a suspected contaminant upon CR dye supplemented nutrient agar plates, forming zones of clearance around its growth area. The bacterium was purified, gram stained and identified as Staphylococcus caprae via 16S rRNA gene sequencing. Dye decolourization was analysed in liquid culture, and Fourier-transform infrared spectroscopy (FTIR) was conducted for analysis of degraded product/metabolites. A decolourization of ~ 96.0% at 100 µg/ml concentration and pH 7 after 24 h of incubation was observed. Structure of the azoreductase enzyme, responsible for breakage of the bond in the dye and ultimately decolourization, was predicted, and molecular docking was harnessed for understanding the mechanism behind the reduction of azo bond (-N=N-) and conversion to metabolites. Our analysis revealed 12 residues critical for structural interaction of the azoreductase enzyme with this dye. Among these, protein backbone region surrounding four residues, i.e. Lys65, Phe122, Ile166 and Phe169, showed major displacement changes, upon binding with the dye. However, overall the conformational changes were not large.

Keywords: Azoreductase; Bioinformatics; Bioremediation; Congo red; Molecular docking.