Homology Modelling and in silico Characterization of Laccase from Lentinula edodes

Abstract

Introduction: Laccases are phenol oxidases which belong to the superfamily of multicopper oxidases. Laccases are found in almost all wood-rotting fungi. There is evidence that laccases can play an important role in lignin degradation, fruiting body formation, pigment formation during asexual development, competitor interactions and pathogenesis. Laccase from Lentinula edodes is used in variety of applications like to reduce toxicity, partial decolourization of effluent water and decolourization of chemically different dyes like Remazole brilliant blue R, bromophenol blue, methyl red and naphtol blue black. The objectives of this study include prediction of three dimensional (3D) structure of laccase from Lentinula edodes using homology modelling, in silico characterization and analysis of laccase from this organism using computational methods. Methods: The sequence of laccase from Lentinula edodes was retrieved from UniProt database and sequence analysis was carried out using BLAST for the selection of template. The protein 3D structure was modelled using ModWeb server. The obtained 3D model of the laccase from Lentinula edodes was visualized and analyzed using RasMol. The quality of the 3D structure of protein was verified by its energy and stereochemical properties. The erred regions were remodelled by loop modelling using SWISS PDB viewer. Further, the in sillico characterization of the laccase from Lentinula edodes was computed. Results and Discussion: The 3KW7 A of Trametes Sp AH28-2 is used as template for model building of laccase from L. edodes. The atom model obtained in PDB format showed unstable region in the model. These unstable regions were selected and remodelled by loop modelling. The remodelled structure was further evaluated by its stereochemical quality and energy. The quality of the remodelled structure was found to be improved. Conclusion: Evaluated 3D structure of laccase from L. edodes shows that predicted model is of good quality because maximum residues are present in favoured region of Ramachandran plot, which indicates that the stereochemical quality of predicted 3D structure is reasonably good. It suggests that this model can be used to understand molecular interaction of this laccase with the other proteins.