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Structure to function analysis with antigenic characterization of a hypothetical protein, HPAG1_0576 from Helicobacter pylori HPAG1



Hanan Ashrafi1,3, Muntequa Ishtiaq Siraji3,4, Nazmir Nur Showva1, Md. Mozammel Hossain2, Tareq Hossan2, Md. Ashraful Hasan2, Abdullah Mohammad Shohael1* and Mohammad Mahfuz Ali Khan Shawan2*



1Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh; 2Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh; 3Department of Biomedicine, University of Bergen, Bergen, Norway; 4Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh



Mohammad Mahfuz Ali Khan Shawan - E-mail: mahfuz_026shawan@juniv.edu & amshohael@juniv.edu; *Corresponding author


Article Type

Research Article



Received May 18, 2019; Accepted June 3, 2019; Published July 31, 2019



Helicobacter pylori, a unique gastric pathogen causing chronic inflammation in the gastric mucosa with a possibility to develop gastric cancer has one-third of its proteins still uncharacterized. In this study, a hypothetical protein (HP) namely HPAG1_0576 from H. pylori HPAG1 was chosen for detailed computational analysis of its structural, functional and epitopic properties. The primary, secondary and 3D structure/model of the selected HP was constructed. Then refinement and structure validation were done, which indicated a good quality of the newly constructed model. ProFunc and STRING suggested that HPAG1_0576 shares 98% identity with a carcinogenic factor, TNF-α inducing protein (Tip-α) of H. pylori. IEDB immunoinformatics tool predicted VLMLQACTCPNTSQRNS from position 19-35 as most potential B-cell linear epitope and SFLKSKQL from position 5-12 as most potent conformational epitope. Alternatively, FALVRARGF and FLCGLGVLM were predicted as most immunogenic CD8+ and CD4+ T-cell epitopes respectively. At the same time findings of IFN epitope tool suggests that, HPAG1_0576 had a great potential to evoke interferon-gamma (IFN-γ) mediated immune response. However, this experiment is a primary approach for in silico vaccine designing from a HP, findings of this study will provide significant insights in further investigations and will assist in identifying new drug targets/vaccine candidates.



H. pylori HPAG1, hypothetical protein, B and T cell epitopes, drug target and vaccine candidates.



Ashrafi et al. Bioinformation 15(7): 456-466 (2019)

Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.