Molecular dynamics studies of human β-Glucuronidase

Problem statement: The enzyme β-glucuronidase is being used as a reporter molecule in the area of genetic engineering, as a component of prodrug therapy in cancer treatment and in the scouring process of cotton fabrics. However, a detailed understanding of the factors responsible for the stability...

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Main Authors:	Noorbatcha, Ibrahim Ali, Masrur Khan, Ayesha, Mohd. Salleh, Hamzah
Format:	Article
Language:	English
Published:	Science Publications 2010
Subjects:	QP Physiology TP248.13 Biotechnology
Online Access:	http://irep.iium.edu.my/486/ http://irep.iium.edu.my/486/ http://irep.iium.edu.my/486/ http://irep.iium.edu.my/486/1/ajas76823-828.pdf

id	iium-486
recordtype	eprints
spelling	iium-4862017-11-21T07:43:27Z http://irep.iium.edu.my/486/ Molecular dynamics studies of human β-Glucuronidase Noorbatcha, Ibrahim Ali Masrur Khan, Ayesha Mohd. Salleh, Hamzah QP Physiology TP248.13 Biotechnology Problem statement: The enzyme β-glucuronidase is being used as a reporter molecule in the area of genetic engineering, as a component of prodrug therapy in cancer treatment and in the scouring process of cotton fabrics. However, a detailed understanding of the factors responsible for the stability and the activity of this enzyme is still not available. Molecular Dynamics (MD) simulations provide an estimate of equilibrium and dynamic properties of enzyme systems that cannot be calculated analytically. With this perspective, molecular dynamics simulations of human β- glucuronidase (GUS) have been carried out to determine the behavior of this enzyme in vacuum and solvent environments at a defined temperature. Approach: CHARMM force field along with distance dependent dielectric model was used to represent the solvent environment in the MD simulations. The parameters employed in various stages of MD simulations had been selected based on repeated trials under various conditions as a method of choosing the optimum parameters for each stage. Results: It was found that simulations in vacuum caused the backbone of GUS to have smaller fluctuations from their mean values compared with the fluctuation in implicit solvent simulations, due to the fact that vacuum environment did not provide for the electrostatic interactions affecting the backbone of GUS that may otherwise exist in a solvent environment. Conclusion: Inclusion of solvent effects in MD simulations is crucial in understanding structural flexibility and stability of β-glucuronidase. Implicit solvent method can provide a realistic inclusion of backbone flexibility and structural compactness of GUS, which will have profound influence on the stability and activity of the enzymes, with a marginal increase in computational time. Science Publications 2010 Article PeerReviewed application/pdf en http://irep.iium.edu.my/486/1/ajas76823-828.pdf Noorbatcha, Ibrahim Ali and Masrur Khan, Ayesha and Mohd. Salleh, Hamzah (2010) Molecular dynamics studies of human β-Glucuronidase. American Journal of Applied Sciences , 7 (6). pp. 823-828. ISSN 1546-9239 E-ISSN 1554-3641 http://www.thescipub.com/abstract/10.3844/ajassp.2010.823.828 DOI: 10.3844/ajassp.2010.823.828
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English
topic	QP Physiology TP248.13 Biotechnology
spellingShingle	QP Physiology TP248.13 Biotechnology Noorbatcha, Ibrahim Ali Masrur Khan, Ayesha Mohd. Salleh, Hamzah Molecular dynamics studies of human β-Glucuronidase
description	Problem statement: The enzyme β-glucuronidase is being used as a reporter molecule in the area of genetic engineering, as a component of prodrug therapy in cancer treatment and in the scouring process of cotton fabrics. However, a detailed understanding of the factors responsible for the stability and the activity of this enzyme is still not available. Molecular Dynamics (MD) simulations provide an estimate of equilibrium and dynamic properties of enzyme systems that cannot be calculated analytically. With this perspective, molecular dynamics simulations of human β- glucuronidase (GUS) have been carried out to determine the behavior of this enzyme in vacuum and solvent environments at a defined temperature. Approach: CHARMM force field along with distance dependent dielectric model was used to represent the solvent environment in the MD simulations. The parameters employed in various stages of MD simulations had been selected based on repeated trials under various conditions as a method of choosing the optimum parameters for each stage. Results: It was found that simulations in vacuum caused the backbone of GUS to have smaller fluctuations from their mean values compared with the fluctuation in implicit solvent simulations, due to the fact that vacuum environment did not provide for the electrostatic interactions affecting the backbone of GUS that may otherwise exist in a solvent environment. Conclusion: Inclusion of solvent effects in MD simulations is crucial in understanding structural flexibility and stability of β-glucuronidase. Implicit solvent method can provide a realistic inclusion of backbone flexibility and structural compactness of GUS, which will have profound influence on the stability and activity of the enzymes, with a marginal increase in computational time.
format	Article
author	Noorbatcha, Ibrahim Ali Masrur Khan, Ayesha Mohd. Salleh, Hamzah
author_facet	Noorbatcha, Ibrahim Ali Masrur Khan, Ayesha Mohd. Salleh, Hamzah
author_sort	Noorbatcha, Ibrahim Ali
title	Molecular dynamics studies of human β-Glucuronidase
title_short	Molecular dynamics studies of human β-Glucuronidase
title_full	Molecular dynamics studies of human β-Glucuronidase
title_fullStr	Molecular dynamics studies of human β-Glucuronidase
title_full_unstemmed	Molecular dynamics studies of human β-Glucuronidase
title_sort	molecular dynamics studies of human β-glucuronidase
publisher	Science Publications
publishDate	2010
url	http://irep.iium.edu.my/486/ http://irep.iium.edu.my/486/ http://irep.iium.edu.my/486/ http://irep.iium.edu.my/486/1/ajas76823-828.pdf
first_indexed	2023-09-18T20:07:36Z
last_indexed	2023-09-18T20:07:36Z
_version_	1777407263463440384

Molecular dynamics studies of human β-Glucuronidase

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