In silico binding interactions of dehalogenase (Dehe) with various haloalkanoic acids

Synthetic haloalkanoic acid (HA) is one of the synthetics compounds that can be found as active ingredients in herbicides. These compounds are known to pollute our agriculture land due to their toxicity, thus may cause serious environmental and health problems. Biological process such as microbial...

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Main Authors:	Abdul Halin, Nur Illani, Huyop, Fahrul Zaman, Tengku Abdul Hamid, Tengku Haziyamin, Abd Halim, Khairul Bariyyah, Abdul Hamid, Azzmer Azzar
Format:	Article
Language:	English
Published:	Razi Publishing 2017
Subjects:	QR Microbiology
Online Access:	http://irep.iium.edu.my/59640/ http://irep.iium.edu.my/59640/ http://irep.iium.edu.my/59640/1/2.%20In%20Silico%20Binding%20Interactions%20Of%20Dehalogenase%20%28Dehe%29%20With%20Various%20.pdf

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spelling	iium-596402017-11-27T08:34:41Z http://irep.iium.edu.my/59640/ In silico binding interactions of dehalogenase (Dehe) with various haloalkanoic acids Abdul Halin, Nur Illani Huyop, Fahrul Zaman Tengku Abdul Hamid, Tengku Haziyamin Abd Halim, Khairul Bariyyah Abdul Hamid, Azzmer Azzar QR Microbiology Synthetic haloalkanoic acid (HA) is one of the synthetics compounds that can be found as active ingredients in herbicides. These compounds are known to pollute our agriculture land due to their toxicity, thus may cause serious environmental and health problems. Biological process such as microbial dehalogenation degrades the harmful compounds and prevents their migration into groundwater source. For instance, Rhizobial Dehalogenase E (DehE) could catalyze these HA compounds and convert them into hydroxylated compounds which are less harmful to the environment. In previous study, DehE was considered to degrade many HA compounds with different Km values. However, the binding interaction of this enzyme towards many HA substrates is still unclear. In this study, docking simulation has been performed to determine the affinity of active site residues of DehE towards 15 HA compounds. Tribromoacetic acid (TBA) was identified to be the most favourable substrate for DehE which has the lowest binding energy (-6.48 Kcal/mol) compared to other haloalkanoic acids. Size of halogen and hydrogen bond numbers are the contributing factor for dehalogenase affinity towards its substrates. Besides, it was found that Trp34, Phe37 and Ser188 served as binding residues and Phe37 was mostly interacted and bound with all of the tested HA compounds. This findings provides an opportunity for rational design of haloacid dehalogenase especially to DehE. Razi Publishing 2017 Article PeerReviewed application/pdf en http://irep.iium.edu.my/59640/1/2.%20In%20Silico%20Binding%20Interactions%20Of%20Dehalogenase%20%28Dehe%29%20With%20Various%20.pdf Abdul Halin, Nur Illani and Huyop, Fahrul Zaman and Tengku Abdul Hamid, Tengku Haziyamin and Abd Halim, Khairul Bariyyah and Abdul Hamid, Azzmer Azzar (2017) In silico binding interactions of dehalogenase (Dehe) with various haloalkanoic acids. Galeri Warisan Sains, 1 (1). pp. 4-6. ISSN 2521-0858 E-ISSN 2521-0866 http://www.razipublishing.com/archives/GWS/2017-issue1/2.%20In%20Silico%20Binding%20Interactions%20Of%20Dehalogenase%20(Dehe)%20With%20Various%20.pdf
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English
topic	QR Microbiology
spellingShingle	QR Microbiology Abdul Halin, Nur Illani Huyop, Fahrul Zaman Tengku Abdul Hamid, Tengku Haziyamin Abd Halim, Khairul Bariyyah Abdul Hamid, Azzmer Azzar In silico binding interactions of dehalogenase (Dehe) with various haloalkanoic acids
description	Synthetic haloalkanoic acid (HA) is one of the synthetics compounds that can be found as active ingredients in herbicides. These compounds are known to pollute our agriculture land due to their toxicity, thus may cause serious environmental and health problems. Biological process such as microbial dehalogenation degrades the harmful compounds and prevents their migration into groundwater source. For instance, Rhizobial Dehalogenase E (DehE) could catalyze these HA compounds and convert them into hydroxylated compounds which are less harmful to the environment. In previous study, DehE was considered to degrade many HA compounds with different Km values. However, the binding interaction of this enzyme towards many HA substrates is still unclear. In this study, docking simulation has been performed to determine the affinity of active site residues of DehE towards 15 HA compounds. Tribromoacetic acid (TBA) was identified to be the most favourable substrate for DehE which has the lowest binding energy (-6.48 Kcal/mol) compared to other haloalkanoic acids. Size of halogen and hydrogen bond numbers are the contributing factor for dehalogenase affinity towards its substrates. Besides, it was found that Trp34, Phe37 and Ser188 served as binding residues and Phe37 was mostly interacted and bound with all of the tested HA compounds. This findings provides an opportunity for rational design of haloacid dehalogenase especially to DehE.
format	Article
author	Abdul Halin, Nur Illani Huyop, Fahrul Zaman Tengku Abdul Hamid, Tengku Haziyamin Abd Halim, Khairul Bariyyah Abdul Hamid, Azzmer Azzar
author_facet	Abdul Halin, Nur Illani Huyop, Fahrul Zaman Tengku Abdul Hamid, Tengku Haziyamin Abd Halim, Khairul Bariyyah Abdul Hamid, Azzmer Azzar
author_sort	Abdul Halin, Nur Illani
title	In silico binding interactions of dehalogenase (Dehe) with various haloalkanoic acids
title_short	In silico binding interactions of dehalogenase (Dehe) with various haloalkanoic acids
title_full	In silico binding interactions of dehalogenase (Dehe) with various haloalkanoic acids
title_fullStr	In silico binding interactions of dehalogenase (Dehe) with various haloalkanoic acids
title_full_unstemmed	In silico binding interactions of dehalogenase (Dehe) with various haloalkanoic acids
title_sort	in silico binding interactions of dehalogenase (dehe) with various haloalkanoic acids
publisher	Razi Publishing
publishDate	2017
url	http://irep.iium.edu.my/59640/ http://irep.iium.edu.my/59640/ http://irep.iium.edu.my/59640/1/2.%20In%20Silico%20Binding%20Interactions%20Of%20Dehalogenase%20%28Dehe%29%20With%20Various%20.pdf
first_indexed	2023-09-18T21:24:30Z
last_indexed	2023-09-18T21:24:30Z
_version_	1777412101291114496

In silico binding interactions of dehalogenase (Dehe) with various haloalkanoic acids

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