Molecular Dynamics Simulation Of Polyhydroxyalkanoate Synthase From Chromobacterium Sp. Usm2

Polyhydroxyalkanoate synthase from locally isolated organism, Chromobacterium sp. (PhaCCs) has been reported as a highly active enzyme in its natural form that is able to produce PHA that have better mechanical and thermal properties compared to the commonly produced P(3HB) homopolymer. In an attemp...

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Main Author:	Annamalai, Nithyanan
Format:	Thesis
Language:	English
Published:	2019
Subjects:	T Technology (General)
Online Access:	http://eprints.usm.my/46622/1/NITHYANAN%20AL%20ANNAMALAI24.pdf
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id	my-usm-ep.46622
record_format	uketd_dc
spelling	my-usm-ep.466222020-06-26T02:55:46Z Molecular Dynamics Simulation Of Polyhydroxyalkanoate Synthase From Chromobacterium Sp. Usm2 2019-05 Annamalai, Nithyanan T Technology (General) Polyhydroxyalkanoate synthase from locally isolated organism, Chromobacterium sp. (PhaCCs) has been reported as a highly active enzyme in its natural form that is able to produce PHA that have better mechanical and thermal properties compared to the commonly produced P(3HB) homopolymer. In an attempt to understand the dimerization of PhaCC, a research been done to predict the monomer and dimer model the PhaCCs. Based on the result obtain via site-directed mutagenesis, it has been postulated that mutation of residue Arg409Ala and Arg490Ala of the PhaCCs disrupt the formation of PhaCCs dimer. However, it is completely unknown how this mutation affects the structure, stability, dynamics, and binding function of the PhaCCs protein. In this research study, molecular dynamics simulation approach has been utilized to address these issues. From the simulation analysis of the native and proposed mutant structures of both monomer and dimer of PhaCC, it has been found that mutation of R409A and R490A has disrupted the hydrogen bond interaction of His404 and Gly480 and the salt bridge interaction between Arg490 and Asp488 respectively which leads to the disorientation of the catalytic triad position of PhaCCs. In addition, the results also demonstrated that there is no direct involvement of Arg409 and Arg490 in dimerization of PhaCCs. 2019-05 Thesis http://eprints.usm.my/46622/ http://eprints.usm.my/46622/1/NITHYANAN%20AL%20ANNAMALAI24.pdf application/pdf en public masters Universiti Sains Malaysia Institut Perubatan & Pergigian Termaju
institution	Universiti Sains Malaysia
collection	USM Institutional Repository
language	English
topic	T Technology (General)
spellingShingle	T Technology (General) Annamalai, Nithyanan Molecular Dynamics Simulation Of Polyhydroxyalkanoate Synthase From Chromobacterium Sp. Usm2
description	Polyhydroxyalkanoate synthase from locally isolated organism, Chromobacterium sp. (PhaCCs) has been reported as a highly active enzyme in its natural form that is able to produce PHA that have better mechanical and thermal properties compared to the commonly produced P(3HB) homopolymer. In an attempt to understand the dimerization of PhaCC, a research been done to predict the monomer and dimer model the PhaCCs. Based on the result obtain via site-directed mutagenesis, it has been postulated that mutation of residue Arg409Ala and Arg490Ala of the PhaCCs disrupt the formation of PhaCCs dimer. However, it is completely unknown how this mutation affects the structure, stability, dynamics, and binding function of the PhaCCs protein. In this research study, molecular dynamics simulation approach has been utilized to address these issues. From the simulation analysis of the native and proposed mutant structures of both monomer and dimer of PhaCC, it has been found that mutation of R409A and R490A has disrupted the hydrogen bond interaction of His404 and Gly480 and the salt bridge interaction between Arg490 and Asp488 respectively which leads to the disorientation of the catalytic triad position of PhaCCs. In addition, the results also demonstrated that there is no direct involvement of Arg409 and Arg490 in dimerization of PhaCCs.
format	Thesis
qualification_level	Master's degree
author	Annamalai, Nithyanan
author_facet	Annamalai, Nithyanan
author_sort	Annamalai, Nithyanan
title	Molecular Dynamics Simulation Of Polyhydroxyalkanoate Synthase From Chromobacterium Sp. Usm2
title_short	Molecular Dynamics Simulation Of Polyhydroxyalkanoate Synthase From Chromobacterium Sp. Usm2
title_full	Molecular Dynamics Simulation Of Polyhydroxyalkanoate Synthase From Chromobacterium Sp. Usm2
title_fullStr	Molecular Dynamics Simulation Of Polyhydroxyalkanoate Synthase From Chromobacterium Sp. Usm2
title_full_unstemmed	Molecular Dynamics Simulation Of Polyhydroxyalkanoate Synthase From Chromobacterium Sp. Usm2
title_sort	molecular dynamics simulation of polyhydroxyalkanoate synthase from chromobacterium sp. usm2
granting_institution	Universiti Sains Malaysia
granting_department	Institut Perubatan & Pergigian Termaju
publishDate	2019
url	http://eprints.usm.my/46622/1/NITHYANAN%20AL%20ANNAMALAI24.pdf
_version_	1747821698901606400

Molecular Dynamics Simulation Of Polyhydroxyalkanoate Synthase From Chromobacterium Sp. Usm2

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