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

Abstract

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.