In Silico Binding Interactions Of Dehalogenase (Dehe) With Various Haloalkanoic Acids
Journal Title: Science Heritage Journal | Galeri Warisan Sains (GWS) - Year 2017, Vol 1, Issue 1
Abstract
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.
Authors and Affiliations
Nur Illani Abd Halin, Fahrul Huyop, Tengku Haziyamin Tengku Abdul Hamid, Khairul Bariyyah Abdul Halim, Azzmer Azzar Abdul Hamid
Keywords
Related Articles
- EP ID EP255908
- DOI 10.26480/gws.01.2017.04.06
- Views 128
- Downloads 0
Pcb biodegration using bacteria isolated from landfill leachate
Polychlorinated biphenyls, PCBs are toxic, persistent organic pollutants (POP) which are harmful to human and environment due to their lipophilic characteristic and not easily degraded in the environment. Biodegradation...
Isolation and characterization of biosurfactant producing bacteria isolated from petroleum contaminated sites with the potential to be used in bioremediation
Surfactants have been widely used to facilitate biodegradation of petroleum pollutant; particularly those are being produced by microorganisms which are also known as biosurfactant. Six bacterial isolates from petroleum...
PHYSICOCHEMICAL PARAMETERS AND BACTERIAL COMPOSITION IN SUNGAI PUSU GOMBAK
Sungai Pusu is a river that flows through the campus of the International Islamic University Malaysia (IIUM), Gombak. This river could have been affected by pollution and urbanization making the water to be cloudy in app...
IN-VITRO REGENERATION OF ORTHOSIPHON STAMINEUS (MISAI KUCING) USING AXILLARY BUD
Orthosiphon stamineus or known as Misai kucing is a popular herbal tea plant that helps in treating the ailments of kidney and bladder, diabetes mellitus and gout. Due to high demand of this medicinal plant, a large prop...
RESEARCH ON ARBITRARY VIRTUAL VIEW IMAGE SYNTHESIS METHOD OF TWO VIEWS
This paper proposes an improved virtual view image synthesis algorithm to overcome the drawbacks of conventional virtual view synthesis technologies in dealing with holes and artifacts. First, conduct edge detection and...