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Research Publications (Applied Sciences)

Permanent URI for this collectionhttp://ir-dev.dut.ac.za/handle/10321/213

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Author: search.filters.author.Ahmad, FaizanSubject: search.filters.subject.Hypothetical proteins

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    Functional insight into Putative Conserved Proteins of Rickettsia rickettsii and their Virulence characterization
    (Bentham Science Publishers, 2015) Shahbaaz, Mohd; Bisetty, Krishna; Ahmad, Faizan
    Abstract: Rickettsia rickettsii is an aerobic, Gram-negative and non-motile coccobacillus known to cause Rocky Mountain spotted fever. The sequenced genome of its 'Sheila Smith' strain contains 1,343 protein-coding genes, 3 rRNA genes and 33 transfer RNA genes. There are 680 hypothetical proteins (HPs) present in the genome of R. rickettsii. Since functions of these proteins are not validated ex-perimentally, characterization of these HPs may play a significant role in understanding the patho-genic mechanisms of R. rickettsii. Hence, functions of these HPs were annotated by in silico methods based on sequence similarity, protein clustering and protein-protein interactions. We have successfully predicted functions of 214 proteins among 680 HPs present in R. rickettsii. These annotated proteins were further classified into 88 enzymes, 59 transport and membrane proteins, 35 binding proteins, 12 structural motifs and the rest of the protein families. Moreo-ver, we identified HPs involved in virulence among 214 functionally annotated proteins. 15 HPs were classified as viru-lence factors and two proteins with the highest scores were selected for further analyses. Additionally, molecular dynam-ics simulations were performed on these selected virulent HPs in order to observe their conformational behaviors. These analyses can further be utilized in the identification of new drug targets for development of better therapeutic agents against the infections caused by R. rickettsii.
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    In silico approaches for the identification of virulence candidates amongst hypothetical proteins of Mycoplasma pneumoniae 309
    (Elsevier, 2015) Shahbaaz, Mohd; Bisetty, Krishna; Ahmad, Faizan; Hassan, Md. Imtaiyaz
    Mycoplasma pneumoniae type 2a strain 309 is a simplest known bacterium and is the primary cause of community acquired pneumonia in the children. It mainly causes severe atypical pneumonia as well as several other non-pulmonary manifestations such as neurological, hepatic, hemolytic anemia, cardiacdiseases and polyarthritis. The size of M. pneumoniae genome (Accession number: NC_016807.1) is relatively smaller as compared to other bacteria and contains 707 functional proteins, in which 204 are classified as hypothetical proteins (HPs) because of the unavailability of experimentally validated functions. The functions of the HPs were predicted by integrating a variety of protein classification systems, motif discovery tools as well as methods that are based on characteristic features obtained from the protein sequence and metabolic pathways. The probable functions of 83HPs were predicted successfully. The accuracy of the diverse tools used in the adopted pipeline was evaluated on the basis of statistical techniques of Receiver Operating Characteristic (ROC), which indicated the reliability of the functional predictions. Furthermore, the virulent HPs present in the set of 83 functionally annotated proteins were predicted by using the Bioinformatics tools and the conformational behaviours of the proteins with highest virulence scores were studied by using the molecular dynamics (MD) simulations. This study will facilitate in the better understanding of various drug resistance and pathogenesis mechanisms present in the M. pneumoniae and can be utilized in designing of better therapeutic agents.