Determining The Structural And Functional Importance Of Bio-Molecular Complexes Of Microbial Proteins Using Network Biology, Molecular Modeling And Docking Approaches.

Banerjee, Anindyajit (2017) Determining The Structural And Functional Importance Of Bio-Molecular Complexes Of Microbial Proteins Using Network Biology, Molecular Modeling And Docking Approaches. PhD thesis, University of Calcutta.

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    Supervisors

    SupervisorsEmail
    Chakrabarti, Saikat

    Abstract

    Microbial pathogenesis involves a complex interplay between differential expression of pathogenic virulence and host’s immune system. Pathogenic virulence is characterized by their degree of pathogenicity and capacity to invade host’s defence mechanisms. A dynamic relationship exists between host and pathogen since each modifies the biological functions of the other, and the outcome is mainly dependable on pathogenic virulence and the relative degree of resistance or susceptibility of the host. Pathogens undertake various strategies to infect the host. Upon foreign challenges host evolves immune response in order to initiate the defence mechanism. The progression of the infection mechanism involved in alteration of host’s immune response which initiates the molecular interaction between host-pathogen interactions. The host-pathogen interactions are mainly involved in recognising the proteinprotein interactions (PPI). These PPI perhaps play important role in the disease progression. Identification of such PPI may help in understanding the role of host molecules in pathogenic infection. Insight into such molecular pathogenicity may widen a new aspect in determining the pharmacological intervention of newly identified targets. Pathogens are single celled, responsible for causing a wide array of diseases and they include agents like protozoa, bacteria, virus, prion, fungus etc. Leishmania is an obligatory intracellular protozoan parasite. It is responsible for causing leishmaniasis. Types of leishmaniasis depends upon the types of leishmanial species involved into it. This may range from cutaneous, mucocutaneous to another most destructive form, visceral leishmaniasis. Visceral leishmaniasis is mostly prevailed in the tropical region. It is mostly caused by Leishmania donovani. Leishmaniasis is considered as one of the most neglected tropical disease, which is prevalent in the Indian subcontinent. Although pentavalent antimonials and amphotericin B were the mainstream therapy for past 70 years, however 60% of leishmanial patient currently does not respond to the existing available drugs. Hence, it become essential for us to identify novel target molecules and develop respective new drugs. In order to reach this goal, new target molecules should be evaluated by understanding the complex biological interaction between Leishmania and their host molecules. It is important to understand the complex protein-protein interactions in the pathogenesis of this disease. This in turn can be achieved by the study of host-Leishmania protein-protein interaction network. These networks will aid in identifying proteins and their respective interactions can be used as new targets for drugs and vaccines development. More specifically, understanding this host-pathogen protein-protein interaction network will open a new perspective in analysing how a pathogen exploits a host molecule to setup the infection process. Plasmodium falciparum is responsible to cause one of the most life-threatening disease, malaria. Drug resistance is becoming one of the prime bottleneck in managing this disease, which accounts for millions of deaths annually. Henceforth, to understand its pathogenesis, identification and characterization of novel proteins which can be considered as drug targets are considered as a fundamental approach. Plasmodium genome constitutes family of DNA-binding proteins. These proteins are involved in regulation of its gene expression for virulence. One of the major architectural DNA-binding proteins are Alba family proteins which organizes and regulates the genome of both euryarchea (having histone) as well as crenarchea (having no histone) and is regulated by acetylation and deacetylation. Genome analysis of Plasmodium falciparum revealed that it encodes a putative DNA–RNA-binding protein, PfAlba3, showing the sequence and structural homology with other Alba family proteins. Currently, not much information is known regarding PfAlba3 to elucidate its role in P. falciparum. Therefore, it is important to identify and understand the structural features of PfAlba3 protein which regulates the cellular growth and development of malarial parasite and may be considered one of the possible targets of this global disease. Several Gram-negative bacteria uses a complex protein delivery mechanism known as Type III secretion system (T3SS). It injects the toxins or effectors into the host cells to establish its virulence. Pseudomonas aeruginosa, a gram-negative pathogen, use T3SS translocator proteins, and associates with their common chaperones PcrH to rupture the cholesterol rich host cell membranes and inject toxic effector molecules into the host cell to establish its virulence. However, due to unavailability of crystal structure of the translocator protein, PopB, the exact mode of this chaperone-translocator interaction is deficient. To understand the functional insights into the T3SS translocation mechanism, it is crucial to study the structural aspects of the individual proteins along with the binding mechanism of the full length PopB-PcrH complex. This will help in deciphering the structure-function relationships among T3SS translocator proteins and also encourage the design of PopB protein inhibitors that can combat the pathogenesis into host cell. Another ultimate hitchhiker pathogens are viruses which invades the host immune cells by attaching the virions and hijack the cellular internal machinery to replicate within it.This causes the rupture of the cell and newly-formed virus particles are free to infect other cells. Among these a genus of double-stranded RNA viruses in the family of Reoviridae is rotavirus. Rotavirus is the single most common etiological pathogen. It is responsible for causing severe diarrhea in infants and resulting death of over half a million infants a year. However, till date there is no effective anti-retroviral drug have been successfully implemented for treatment of rotavirus infection. Therefore, an approach can be undertaken in identification and characterization of anti-retroviral drug for rapid recovery. An adenosine analogue, Cordycepin (3’-deoxyadenosine), has been reported to provide protection against HIV infection which further modulate the cell proliferation and platelet aggregation.Moreover, it has potent inhibitory role in inhibiting rotavirus infection. Therefore, a study was undertaken to understand the structural mechanism of binding of cordycepin onto its preferential domain of the molecular target which will affect the cellular signaling. Thus, to understand the complexity of pathogenesis and etiology of host-pathogen relationship in terms of network and structural biology, I have undertaken the following objectives as my studies for dissertation: 1. Understanding the structural and functional dynamics of host-Leishmania protein-protein interaction network. 2. Identification and characterization of novel protein from P. falciparum which is ubiquitously expressed in all the erythrocytic stages of P. falciparum 3. Analyzing the probable mode of binding of the major T3SS PopB from Pseudomonas aeruginosa with its chaperone PcrH. 4. Identifying the efficacy of an anti rotaviral drug in providing the protection against rotavirus.

    Item Type: Thesis (PhD)
    URI: http://www.eprints.iicb.res.in/id/eprint/2742
    Subjects: Structural Biology & Bioinformatics
    Divisions: UNSPECIFIED
    Depositing User: Mr N C Ghosh
    Date Deposited: 22 Feb 2018 14:26
    Last Modified: 22 Feb 2018 14:26
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