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Advances in Bioinformatics
Volume 2015, Article ID 278197, 8 pages
http://dx.doi.org/10.1155/2015/278197
Research Article

A Highly Conserved GEQYQQLR Epitope Has Been Identified in the Nucleoprotein of Ebola Virus by Using an In Silico Approach

Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh

Received 18 November 2014; Accepted 14 January 2015

Academic Editor: Gilbert Deleage

Copyright © 2015 Mohammad Tuhin Ali and Md Ohedul Islam. 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.

Linked References

  1. Y. Suzuki and T. Gojobori, “The origin and evolution of Ebola and Marburg viruses,” Molecular Biology and Evolution, vol. 14, no. 8, pp. 800–806, 1997. View at Publisher · View at Google Scholar · View at Scopus
  2. T. Ikegami, A. B. Calaor, M. E. Miranda et al., “Genome structure of Ebola virus subtype Reston: differences among Ebola subtypes,” Archives of Virology, vol. 146, no. 10, pp. 2021–2027, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. H. Feldmann and T. W. Geisbert, “Ebola haemorrhagic fever,” The Lancet, vol. 377, no. 9768, pp. 849–862, 2011. View at Publisher · View at Google Scholar · View at Scopus
  4. S. K. Gire, A. Goba, K. G. Andersen et al., “Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak,” Science, vol. 345, no. 6202, pp. 1369–1372, 2014. View at Publisher · View at Google Scholar
  5. J. A. López, C. Weilenman, R. Audran et al., “A synthetic malaria vaccine elicits a potent CD8+ and CD4+ T lymphocyte immune response in humans. Implications for vaccination strategies,” European Journal of Immunology, vol. 31, no. 7, pp. 1989–1998, 2001. View at Google Scholar
  6. K. L. Knutson, K. Schiffman, and M. L. Disis, “Immunization with a HER-2/neu helper peptide vaccine generates HER-2/neu CD8 T-cell immunity in cancer patients,” The Journal of Clinical Investigation, vol. 107, no. 4, pp. 477–484, 2001. View at Publisher · View at Google Scholar · View at Scopus
  7. D. N. Bourdette, E. Edmonds, C. Smith et al., “A highly immunogenic trivalent T cell receptor peptide vaccine for multiple sclerosis,” Multiple Sclerosis, vol. 11, no. 5, pp. 552–561, 2005. View at Publisher · View at Google Scholar · View at Scopus
  8. M. Goujon, H. McWilliam, W. Li et al., “A new bioinformatics analysis tools framework at EMBL-EBI,” Nucleic Acids Research, vol. 38, supplement 2, pp. W695–W699, 2010. View at Publisher · View at Google Scholar · View at Scopus
  9. F. Sievers, A. Wilm, D. Dineen et al., “Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega,” Molecular Systems Biology, vol. 7, no. 1, article 539, 2011. View at Publisher · View at Google Scholar · View at Scopus
  10. J. E. Larsen, O. Lund, and M. Nielsen, “Improved method for predicting linear B-cell epitopes,” Immunome Research, vol. 2, no. 1, article 2, 2006. View at Google Scholar
  11. R. Vita, L. Zarebski, J. A. Greenbaum et al., “The immune epitope database 2.0,” Nucleic Acids Research, vol. 38, no. 1, pp. D854–D862, 2009. View at Publisher · View at Google Scholar · View at Scopus
  12. A. S. Kolaskar and P. C. Tongaonkar, “A semi-empirical method for prediction of antigenic determinants on protein antigens,” FEBS Letters, vol. 276, no. 1-2, pp. 172–174, 1990. View at Publisher · View at Google Scholar · View at Scopus
  13. E. A. Emini, J. V. Hughes, D. S. Perlow, and J. Boger, “Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide,” Journal of Virology, vol. 55, no. 3, pp. 836–839, 1985. View at Google Scholar · View at Scopus
  14. H.-H. Bui, J. Sidney, W. Li, N. Fusseder, and A. Sette, “Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines,” BMC Bioinformatics, vol. 8, article 361, 2007. View at Publisher · View at Google Scholar · View at Scopus
  15. J. M. R. Parker, D. Guo, and R. S. Hodges, “New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites,” Biochemistry, vol. 25, no. 19, pp. 5425–5432, 1986. View at Publisher · View at Google Scholar · View at Scopus
  16. L. A. Kelley and M. J. E. Sternberg, “Protein structure prediction on the Web: a case study using the Phyre server,” Nature Protocols, vol. 4, no. 3, pp. 363–371, 2009. View at Publisher · View at Google Scholar · View at Scopus
  17. S. C. Lovell, I. W. Davis, W. B. Arendall III et al., “Structure validation by Cα geometry: ϕ,ψ and Cβ deviation,” Proteins: Structure, Function and Genetics, vol. 50, no. 3, pp. 437–450, 2003. View at Publisher · View at Google Scholar · View at Scopus
  18. W. L. DeLano, The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, Calif, USA, 2002.
  19. S. E. C. Caoili, “B-cell epitope prediction for peptide-based vaccine design: towards a paradigm of biological outcomes for global health,” Immunome Research, vol. 7, no. 2, article 2, 2010. View at Google Scholar
  20. N. J. Sullivan, A. Sanchez, P. E. Rollin, Z.-Y. Yang, and G. J. Nabel, “Development of a preventive vaccine for Ebola virus infection in primates,” Nature, vol. 408, no. 6812, pp. 605–609, 2000. View at Publisher · View at Google Scholar · View at Scopus
  21. S. M. Jones, H. Feldmann, U. Ströher et al., “Live attenuated recombinant vaccine protects nonhuman primates against Ebola and Marburg viruses,” Nature Medicine, vol. 11, no. 7, pp. 786–790, 2005. View at Publisher · View at Google Scholar · View at Scopus
  22. A. Marzi and H. Feldmann, “Ebola virus vaccines: an overview of current approaches,” Expert Review of Vaccines, vol. 13, no. 4, pp. 521–531, 2014. View at Publisher · View at Google Scholar · View at Scopus
  23. J. M. Gershoni, A. Roitburd-Berman, D. D. Siman-Tov, N. T. Freund, and Y. Weiss, “Epitope mapping,” BioDrugs, vol. 21, no. 3, pp. 145–156, 2007. View at Publisher · View at Google Scholar · View at Scopus
  24. J. A. Wilson, M. Hevey, R. Bakken et al., “Epitopes involved in antibody-mediated protection from Ebola virus,” Science, vol. 287, no. 5458, pp. 1664–1666, 2000. View at Publisher · View at Google Scholar · View at Scopus
  25. S. Shahhosseini, D. Das, X. Qiu, H. Feldmann, S. M. Jones, and M. R. Suresh, “Production and characterization of monoclonal antibodies against different epitopes of Ebola virus antigens,” Journal of Virological Methods, vol. 143, no. 1, pp. 29–37, 2007. View at Publisher · View at Google Scholar · View at Scopus
  26. P. Becquart, T. Mahlakõiv, D. Nkoghe, E. M. Leroy, and J. H. Kuhn, “Identification of continuous human B-cell epitopes in the VP35, VP40, nucleoprotein and glycoprotein of Ebola virus,” PLoS ONE, vol. 9, no. 6, Article ID e96360, 2014. View at Publisher · View at Google Scholar
  27. M. Niikura, T. Ikegami, M. Saijo, T. Kurata, I. Kurane, and S. Morikawa, “Analysis of linear B-cell epitopes of the nucleoprotein of Ebola virus that distinguish Ebola virus subtypes,” Clinical and Diagnostic Laboratory Immunology, vol. 10, no. 1, pp. 83–87, 2003. View at Publisher · View at Google Scholar · View at Scopus
  28. M. Niikura, T. Ikegami, M. Saijo, I. Kurane, M. E. Miranda, and S. Morikawa, “Detection of Ebola viral antigen by enzyme-linked immunosorbent assay using a novel monoclonal antibody to nucleoprotein,” Journal of Clinical Microbiology, vol. 39, no. 9, pp. 3267–3271, 2001. View at Publisher · View at Google Scholar · View at Scopus
  29. O. F. Olesen, A. Lonnroth, and B. Mulligan, “Human vaccine research in the European Union,” Vaccine, vol. 27, no. 5, pp. 640–645, 2009. View at Publisher · View at Google Scholar · View at Scopus
  30. T. Toyoda, K. Masunaga, Y. Ohtsu et al., “Antibody-scanning and epitope-tagging methods; molecular mapping of proteins using antibodies,” Current Protein and Peptide Science, vol. 1, no. 3, pp. 303–308, 2000. View at Publisher · View at Google Scholar · View at Scopus