Computer Aided Design of Polygalacturonase II from Aspergillus niger

Pectin is a complex polysaccharide found in the cell walls of plants and consisting mainly of esterified D-galacturonic acid resides in α-(1-4) chain. In production of fruit juice, pectin contributes to fruit juice viscosity, thereby reducing the juice production and increasing the filtration time...

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Main Authors:	Noorbatcha, Ibrahim Ali, Ismail, Nur Izzah, Mohd. Salleh, Hamzah
Format:	Conference or Workshop Item
Language:	English
Published:	2011
Subjects:	TP248.13 Biotechnology
Online Access:	http://irep.iium.edu.my/3977/ http://irep.iium.edu.my/3977/ http://irep.iium.edu.my/3977/1/CAD_of_PG_II_from_A_niger_pg298-312.pdf

id	iium-3977
recordtype	eprints
spelling	iium-39772012-01-19T00:07:01Z http://irep.iium.edu.my/3977/ Computer Aided Design of Polygalacturonase II from Aspergillus niger Noorbatcha, Ibrahim Ali Ismail, Nur Izzah Mohd. Salleh, Hamzah TP248.13 Biotechnology Pectin is a complex polysaccharide found in the cell walls of plants and consisting mainly of esterified D-galacturonic acid resides in α-(1-4) chain. In production of fruit juice, pectin contributes to fruit juice viscosity, thereby reducing the juice production and increasing the filtration time. Polygalacturonase improves the juice production process by rapid degradation of pectin. In this project we have designed a novel polygalacturonase enzyme using computer aided design approaches. The three dimension structure of polygalacturonase is first modeled on the basis of the known crystal structure. The active site in this enzyme is identified by manual and automated docking methods. Lamarckian genetic algorithm is used for automated docking andthe active site is validated by comparing with existing experimental data. This is followed by in silico mutations of the enzymes and the automated docking process is repeated using the mutant enzymes. The strength of the binding of the ligands inside the active site is evaluated by computing the binding score using Potential Mean Force (PMF) method. The mutations R256Q, K258N and E252A show improvement of the binding score while N186E reduces the binding strength. The R256Q, K258N or E252A mutant enzymes can be used in the fruit juice industry to minimize the cost of juice production 2011-05-17 Conference or Workshop Item PeerReviewed application/pdf en http://irep.iium.edu.my/3977/1/CAD_of_PG_II_from_A_niger_pg298-312.pdf Noorbatcha, Ibrahim Ali and Ismail, Nur Izzah and Mohd. Salleh, Hamzah (2011) Computer Aided Design of Polygalacturonase II from Aspergillus niger. In: International Conference on Biotechnology Engineering, ICBioE’11, 17-19 May, 2011 , Kuala Lumpur. http://www.iium.edu.my/icbioe/2011/
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 Ismail, Nur Izzah Mohd. Salleh, Hamzah Computer Aided Design of Polygalacturonase II from Aspergillus niger
description	Pectin is a complex polysaccharide found in the cell walls of plants and consisting mainly of esterified D-galacturonic acid resides in α-(1-4) chain. In production of fruit juice, pectin contributes to fruit juice viscosity, thereby reducing the juice production and increasing the filtration time. Polygalacturonase improves the juice production process by rapid degradation of pectin. In this project we have designed a novel polygalacturonase enzyme using computer aided design approaches. The three dimension structure of polygalacturonase is first modeled on the basis of the known crystal structure. The active site in this enzyme is identified by manual and automated docking methods. Lamarckian genetic algorithm is used for automated docking andthe active site is validated by comparing with existing experimental data. This is followed by in silico mutations of the enzymes and the automated docking process is repeated using the mutant enzymes. The strength of the binding of the ligands inside the active site is evaluated by computing the binding score using Potential Mean Force (PMF) method. The mutations R256Q, K258N and E252A show improvement of the binding score while N186E reduces the binding strength. The R256Q, K258N or E252A mutant enzymes can be used in the fruit juice industry to minimize the cost of juice production
format	Conference or Workshop Item
author	Noorbatcha, Ibrahim Ali Ismail, Nur Izzah Mohd. Salleh, Hamzah
author_facet	Noorbatcha, Ibrahim Ali Ismail, Nur Izzah Mohd. Salleh, Hamzah
author_sort	Noorbatcha, Ibrahim Ali
title	Computer Aided Design of Polygalacturonase II from Aspergillus niger
title_short	Computer Aided Design of Polygalacturonase II from Aspergillus niger
title_full	Computer Aided Design of Polygalacturonase II from Aspergillus niger
title_fullStr	Computer Aided Design of Polygalacturonase II from Aspergillus niger
title_full_unstemmed	Computer Aided Design of Polygalacturonase II from Aspergillus niger
title_sort	computer aided design of polygalacturonase ii from aspergillus niger
publishDate	2011
url	http://irep.iium.edu.my/3977/ http://irep.iium.edu.my/3977/ http://irep.iium.edu.my/3977/1/CAD_of_PG_II_from_A_niger_pg298-312.pdf
first_indexed	2023-09-18T20:12:00Z
last_indexed	2023-09-18T20:12:00Z
_version_	1777407539376291840

Computer Aided Design of Polygalacturonase II from Aspergillus niger

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