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Online Journal of Bioinformatics©
21(3): 209-224, 2020.
In silico homology model of polyphenolic substrates for Laccase from Pleurotus ostreatus
†P. Ravindra Babu1 PhD, S Siva Rajesh1 MSc, Jayasree G1* PhD, Suhasini Donthi1 MSc, S Siva Thejasree2 MSc, SS Lakshmana Rao1 PhD, KSR Siva Sai1 PhD.
1Department of Biotechnology, Sreenidhi
Institute of Science and Technology, Yamnampet, Hyderabad-501301,
Ravindra Babu P, Siva Rajesh S, Jayasree G, Donthi S, Thejasree SS, Lakshmana Rao SS, Siva Sai KSR, In silico homology model of polyphenolic substrates †for Laccase from Pleurotus ostreatus, Onl J Bioinform., 21(3): 209-224, 2020. Phenol oxidase (benzenediol O2:oxidoreductase [EC 184.108.40.206], Laccase Pleurotus ostreatus catalyzes oxidation of aromatic mono-, di-, and polyphenols, aminophenols, and diamines by reducing molecular oxygen to water through an oxidoreductive multicopper system. Homology modeling of enzyme Laccase from Pleurotus ostreatus based on hits from NCBI BLAST against PDB database was performed. The crystal structures of Laccase of Trametes versicolor (PDB ID 1GYC_A) and Rigidoporus lignosus (PDB ID 1KYA_A, 1V10_A) from PDB were used as templates due to high level of sequence identity. Functional prediction was performed using PFAM and INTERPROSCAN. A comparative assessment of secondary structure using SSM web server revealed greater percentage of residues in beta sheets. A three-dimensional model was generated using MODELLER9v7 based on the multiple Crystal Structures (PDB IDís 1GYC_A, 1KYA_A, 1V10_A). Protein sequence alignment was performed using CLUSTALW 2.0.8. With the aid of molecular mechanics method using force field AMBER the final model was obtained. Inspection and analysis of the final model was made by PROCHECK, VERIFY3D graph, PROVE Program. After the prediction of 3-dimensional model of Laccase, the possible active site of Laccase was determined using CASTp web server. The three dimensional structures of ligands (substrates and pollutants) including all hydrogen atoms, were built and minimized using the Dundee PRODRG2 Server. Toxicity studies were carried out using the web server OSIRIS Property Explorer in which the Mutagenic, Tumorigenic irritation and reproductive effects of the ligands were analysed. The Docked complexes were validated and enumerated based on the GOLD Scoring function to pick out the best substrates for Laccase, suggesting that Laccase might be able to oxidize these pollutants.
Keywords: Laccase, Homology Modeling, Docking, Toxicity risk.