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

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 impro...

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Main Authors:	Noorbatcha, Ibrahim Ali, Nuge, Tamrin, Yusof, Amirulakmal, Othman, Raihan, Mohd. Salleh, Hamzah
Format:	Conference or Workshop Item
Language:	English
Published:	2013
Subjects:	TP248.13 Biotechnology
Online Access:	http://irep.iium.edu.my/34143/ http://irep.iium.edu.my/34143/ http://irep.iium.edu.my/34143/1/Molecular_docking.pdf

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recordtype	eprints
spelling	iium-341432014-01-15T01:18:45Z http://irep.iium.edu.my/34143/ Molecular docking studies of Pyranose-2-oxidase from trametes multicolor Noorbatcha, Ibrahim Ali Nuge, Tamrin Yusof, Amirulakmal Othman, Raihan Mohd. Salleh, Hamzah TP248.13 Biotechnology 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. 2013-07-02 Conference or Workshop Item PeerReviewed application/pdf en http://irep.iium.edu.my/34143/1/Molecular_docking.pdf 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. http://www.iium.edu.my/icbioe/2013/
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English
topic	TP248.13 Biotechnology
spellingShingle	TP248.13 Biotechnology Noorbatcha, Ibrahim Ali Nuge, Tamrin Yusof, Amirulakmal Othman, Raihan Mohd. Salleh, Hamzah Molecular docking studies of Pyranose-2-oxidase from trametes multicolor
description	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.
format	Conference or Workshop Item
author	Noorbatcha, Ibrahim Ali Nuge, Tamrin Yusof, Amirulakmal Othman, Raihan Mohd. Salleh, Hamzah
author_facet	Noorbatcha, Ibrahim Ali Nuge, Tamrin Yusof, Amirulakmal Othman, Raihan Mohd. Salleh, Hamzah
author_sort	Noorbatcha, Ibrahim Ali
title	Molecular docking studies of Pyranose-2-oxidase from trametes multicolor
title_short	Molecular docking studies of Pyranose-2-oxidase from trametes multicolor
title_full	Molecular docking studies of Pyranose-2-oxidase from trametes multicolor
title_fullStr	Molecular docking studies of Pyranose-2-oxidase from trametes multicolor
title_full_unstemmed	Molecular docking studies of Pyranose-2-oxidase from trametes multicolor
title_sort	molecular docking studies of pyranose-2-oxidase from trametes multicolor
publishDate	2013
url	http://irep.iium.edu.my/34143/ http://irep.iium.edu.my/34143/ http://irep.iium.edu.my/34143/1/Molecular_docking.pdf
first_indexed	2023-09-18T20:49:15Z
last_indexed	2023-09-18T20:49:15Z
_version_	1777409883856961536

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

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