In silico subtractive genomics approach characterizes a hypothetical protein (MG_476) from microplasma genitalium G37
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Naznin Jahan 1 2 , Tanvir Ahamed 1 , Arun Das 2 , Md. Arif Khan 2 , Sharif Hossain 1 , Satya Ranjan Sarker 1 , Mohammad Mahfuz Ali Khan Shawan 3 *
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1 Department of Biotechnology & Genetic Engineering, Jahangirnagar University, Dhaka, Bangladesh2 Bio-Bio-1 Bioinformatics Research Foundation, Dhaka, Bangladesh3 Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Bangladesh* Corresponding Author

Abstract

Background: Mycoplasma genitalium is a gram negative, parasitic pathogenic bacterium, usually transmitted sexually into human and frequently causing urethritis in men and women as well as cervicitis and pelvic inflammation in women. This is an extremely small self-replicating entity whose genome has been sequenced. This genome sequencing is advantageous in understanding pathogenesis and identifying therapeutic targets. In this study different bioinformatics tools and databases were adopted to analyze the functions of different hypothetical proteins from M. genitalium G37.
Methodology: A total of 75 hypothetical proteins (HPs) were retrieved from KEGG database, while CDD-BLAST, Pfam, and InterProScan servers were used for conserved domains analysis. After that, those HPs were broadly analyzed for physicochemical properties, subcellular localization, GO annotation, and virulence factors.
Results: Based on best score, hypothetical protein MG_476 was selected for homology modelling which produced a fairly good quality 3D model. The active site within MG_476 was predicted using CASTp server that helps to explore the surface features of the protein. Other approaches include the use of NetCTL, IEDB, Bcepred, and ABCpred servers to predict the location of B and T cell epitopes. Among the CD8+ T cell epitopes tested, ILQIIMFIL scored highest (0.23718) in terms of immunogenicity.
Conclusion: Moreover, this analysis recommended MG_476 as a non-homologous protein and the data generated in this study may facilitate the experimental designing of novel drug and vaccines against M. genitalium.

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Article Type: Research Article

J CLIN EXP INVEST, 2022, Volume 13, Issue 4, Article No: em00805

https://doi.org/10.29333/jcei/12377

Publication date: 18 Aug 2022

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Article Downloads: 409

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