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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Razi Publishing
2017
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| Subjects: | |
| 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 |
| Summary: | 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. |
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