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Molecular docking studies of Pyranose-2-oxidase from trametes multicolor

Noorbatcha, Ibrahim Ali and Nuge, Tamrin and Yusof, Amirulakmal and Othman, Raihan and Mohd. Salleh, Hamzah (2013) Molecular docking studies of Pyranose-2-oxidase from trametes multicolor. In: International Conference on Biotechnology Engineering (ICBioE 2013), 2-4 July 2013, Kuala Lumpur, Malaysia.

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Abstract

Pyranose 2-oxidase (P2Ox) is a FAD dependent enzyme widespread in wood-degrading basidiomycetes. P2Ox has several biotechnological applications, especially in biofuel cells (BFCs). In this research, computational protein design approach is used to design the new variants of P2Ox in order to improve the binding activity of P2Ox from Trametes multicolor (TmP2Ox) for further development of powerful BFCs. As a first step, the active site of P2Ox is identified by analyzing crystal structure of the enzyme complexed with the substrate. Then this active site is validated by automated docking of the substrates and comparing the docking score with the experimental results. Lamarckian genetic algorithm (LGA) is used to search for active sites and potential mean force (PMF) scoring method is used to evaluate different binding sites. The docking of minimum energy sugar conformation and strength of the binding (docking score) was evaluated using potential mean force (PMF) scores. β-D-Glucose, β-D-Galactose, β-D-Xylose, β-D-Allose and β-L-Arabinose were chosen as sugar substrates to investigate the substrate selectivity of wild type TmP2Ox (wtTmP2Ox). β-D-Glucose showed higher docking score compared to the others. The predicted docking scores were found to correlate very well with the experimental binding constant (Km) values with correlation coefficient R2=0.8744. In silico mutations were applied on several residue positions in the wtTmP2Ox to improve the binding activity. The effect of these mutations on binding strength was found to be in good agreement with experimental results.

Item Type: Conference or Workshop Item (Full Paper)
Additional Information: 3704/34143 (ISBN: 978-983-42978-6-2)
Uncontrolled Keywords: pyranose-2-oxidase, Trametes multicolor, Molecular Docking
Subjects: T Technology > TP Chemical technology > TP248.13 Biotechnology
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button): Kulliyyah of Engineering > Department of Biotechnology Engineering
Kulliyyah of Engineering > Department of Science
Depositing User: Prof. Dr. Ibrahim Ali Noorbatcha
Date Deposited: 15 Jan 2014 09:17
Last Modified: 15 Jan 2014 09:18
URI: http://irep.iium.edu.my/id/eprint/34143

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