IIUM Repository

Computer Aided Design of Polygalacturonase II from Aspergillus niger

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.

PDF (Computer Aided Design of Polygalacturonase II from Aspergillus niger - ICBioE 2011) - Published Version
Download (450kB) | Preview


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

Item Type: Conference or Workshop Item (UNSPECIFIED)
Additional Information: 3704/3977
Uncontrolled Keywords: computer aided design; polygalacturonse; automated docking; in silico mutations
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
Depositing User: Prof. Dr. Ibrahim Ali Noorbatcha
Date Deposited: 14 Oct 2011 11:28
Last Modified: 29 Jun 2021 10:38
URI: http://irep.iium.edu.my/id/eprint/3977

Actions (login required)

View Item View Item


Downloads per month over past year