Simulatting interaction of tuberculosis antigen 85B protein with hydrophobic surface graphene

Around two millions people die each year from Tuberculosis. Due to the ability of the pathogen (Mycobacterium tuberculosis) to evade host defense system and remains undetected for decades in the host cell, it is very difficult to control and cure the disease. Therefore, it is a challenge to invent a...

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Main Author:	Sheykhandalibi, Nazanin
Format:	Thesis
Language:	English
Published:	2013
Subjects:	QH301 Biology
Online Access:	http://eprints.utm.my/id/eprint/78291/1/NazaninSheykhandalibiMFBME20131.pdf
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spelling	my-utm-ep.782912018-08-03T08:47:09Z Simulatting interaction of tuberculosis antigen 85B protein with hydrophobic surface graphene 2013-08 Sheykhandalibi, Nazanin QH301 Biology Around two millions people die each year from Tuberculosis. Due to the ability of the pathogen (Mycobacterium tuberculosis) to evade host defense system and remains undetected for decades in the host cell, it is very difficult to control and cure the disease. Therefore, it is a challenge to invent an easy, cheap, and fast detection method to control and cure the disease. The maintenance of the highly hydrophobic cell wall of the pathogen is crucial to the survival of this bacterium in the host cell and the antigen 85, a major secretory protein, of the bacterium helps maintain the integrality of the cell wall. Since antigen 85 protein is directly linked to the survival mechanism of the bacteria, the protein is a very good marker candidate for disease detection and drug target. This study was exploration of the possibilities to immobilize the protein on hydrophobic graphene surface for separating the protein from the blood sample at the initial processing stage of the detection process. Predicting the conformation of the protein adopted on the surface should provide a clue about the possibility to immobilize the protein on the surface. Molecular dynamics (MD) simulation was carried out to study adsorbed conformation of antigen 85 at the graphene (hydrophobic) surface. The preliminary results showed that there were some conformational changes of protein in water phase while the protein was not preferentially adsorbed on the surface at that particular orientation. As the result, there were no significant changes of Ag85B protein conformation. Also the protein preferred to locate middle of water box rather than close to graphene surface. Based on thermodynamic energy findings, the system equilibrated well and the energy of the system is reasonably conserved which is the fundamental requirement for molecular dynamics methodology. 2013-08 Thesis http://eprints.utm.my/id/eprint/78291/ http://eprints.utm.my/id/eprint/78291/1/NazaninSheykhandalibiMFBME20131.pdf application/pdf en public http://dms.library.utm.my:8080/vital/access/manager/Repository/vital:79511 masters Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering Faculty of Biosciences and Medical Engineering
institution	Universiti Teknologi Malaysia
collection	UTM Institutional Repository
language	English
topic	QH301 Biology
spellingShingle	QH301 Biology Sheykhandalibi, Nazanin Simulatting interaction of tuberculosis antigen 85B protein with hydrophobic surface graphene
description	Around two millions people die each year from Tuberculosis. Due to the ability of the pathogen (Mycobacterium tuberculosis) to evade host defense system and remains undetected for decades in the host cell, it is very difficult to control and cure the disease. Therefore, it is a challenge to invent an easy, cheap, and fast detection method to control and cure the disease. The maintenance of the highly hydrophobic cell wall of the pathogen is crucial to the survival of this bacterium in the host cell and the antigen 85, a major secretory protein, of the bacterium helps maintain the integrality of the cell wall. Since antigen 85 protein is directly linked to the survival mechanism of the bacteria, the protein is a very good marker candidate for disease detection and drug target. This study was exploration of the possibilities to immobilize the protein on hydrophobic graphene surface for separating the protein from the blood sample at the initial processing stage of the detection process. Predicting the conformation of the protein adopted on the surface should provide a clue about the possibility to immobilize the protein on the surface. Molecular dynamics (MD) simulation was carried out to study adsorbed conformation of antigen 85 at the graphene (hydrophobic) surface. The preliminary results showed that there were some conformational changes of protein in water phase while the protein was not preferentially adsorbed on the surface at that particular orientation. As the result, there were no significant changes of Ag85B protein conformation. Also the protein preferred to locate middle of water box rather than close to graphene surface. Based on thermodynamic energy findings, the system equilibrated well and the energy of the system is reasonably conserved which is the fundamental requirement for molecular dynamics methodology.
format	Thesis
qualification_level	Master's degree
author	Sheykhandalibi, Nazanin
author_facet	Sheykhandalibi, Nazanin
author_sort	Sheykhandalibi, Nazanin
title	Simulatting interaction of tuberculosis antigen 85B protein with hydrophobic surface graphene
title_short	Simulatting interaction of tuberculosis antigen 85B protein with hydrophobic surface graphene
title_full	Simulatting interaction of tuberculosis antigen 85B protein with hydrophobic surface graphene
title_fullStr	Simulatting interaction of tuberculosis antigen 85B protein with hydrophobic surface graphene
title_full_unstemmed	Simulatting interaction of tuberculosis antigen 85B protein with hydrophobic surface graphene
title_sort	simulatting interaction of tuberculosis antigen 85b protein with hydrophobic surface graphene
granting_institution	Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering
granting_department	Faculty of Biosciences and Medical Engineering
publishDate	2013
url	http://eprints.utm.my/id/eprint/78291/1/NazaninSheykhandalibiMFBME20131.pdf
_version_	1747817953624064000

Simulatting interaction of tuberculosis antigen 85B protein with hydrophobic surface graphene

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