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Advances in Bioinformatics
Volume 2016 (2016), Article ID 1276594, 13 pages
http://dx.doi.org/10.1155/2016/1276594
Research Article

Expressing Redundancy among Linear-Epitope Sequence Data Based on Residue-Level Physicochemical Similarity in the Context of Antigenic Cross-Reaction

Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Room 101, Medical Annex Building, 547 Pedro Gil Street, Ermita, 1000 Manila, Philippines

Received 27 October 2015; Revised 29 March 2016; Accepted 10 April 2016

Academic Editor: Gilbert Deleage

Copyright © 2016 Salvador Eugenio C. Caoili. 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. S. E. C. Caoili, “Antidotes, antibody-mediated immunity and the future of pharmaceutical product development,” Human Vaccines and Immunotherapeutics, vol. 9, no. 2, pp. 294–299, 2013. View at Publisher · View at Google Scholar · View at Scopus
  2. S. E. C. Caoili, “Beyond new chemical entities: advancing drug development based on functional versatility of antibodies,” Human Vaccines and Immunotherapeutics, vol. 10, no. 6, pp. 1639–1644, 2014. View at Publisher · View at Google Scholar · View at Scopus
  3. B. Greenwood, “The contribution of vaccination to global health: past, present and future,” Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences, vol. 369, no. 1645, Article ID 20130433, 2014. View at Publisher · View at Google Scholar · View at Scopus
  4. M. H. V. Van Regenmortel, “What is a B-cell epitope?” Methods in Molecular Biology, vol. 524, pp. 3–20, 2009. View at Publisher · View at Google Scholar · View at Scopus
  5. M. H. V. Regenmortel, “Specificity, polyspecificity, and heterospecificity of antibody-antigen recognition,” Journal of Molecular Recognition, vol. 27, no. 11, pp. 627–639, 2014. View at Publisher · View at Google Scholar · View at Scopus
  6. N. Tomar and R. K. De, “Immunoinformatics: a brief review,” Methods in Molecular Biology, vol. 1184, pp. 23–55, 2014. View at Publisher · View at Google Scholar · View at Scopus
  7. S. E. C. Caoili, “An integrative structure-based framework for predicting biological effects mediated by antipeptide antibodies,” Journal of Immunological Methods, vol. 427, pp. 19–29, 2015. View at Publisher · View at Google Scholar · View at Scopus
  8. S. E. C. Caoili, “Immunization with peptide-protein conjugates: impact on benchmarking B-cell epitope prediction for vaccine design,” Protein and Peptide Letters, vol. 17, no. 3, pp. 386–398, 2010. View at Publisher · View at Google Scholar · View at Scopus
  9. S. E. C. Caoili, “Hybrid methods for B-cell epitope prediction,” Methods in Molecular Biology, vol. 1184, pp. 245–283, 2014. View at Publisher · View at Google Scholar · View at Scopus
  10. S. E. C. Caoili, “Benchmarking B-cell epitope prediction with quantitative dose-response data on antipeptide antibodies: towards novel pharmaceutical product development,” BioMed Research International, vol. 2014, Article ID 867905, 13 pages, 2014. View at Publisher · View at Google Scholar · View at Scopus
  11. U. Hobohm, M. Scharf, R. Schneider, and C. Sander, “Selection of representative protein data sets,” Protein Science, vol. 1, no. 3, pp. 409–417, 1992. View at Google Scholar · View at Scopus
  12. U. Lessel and D. Schomburg, “Creation and characterization of a new, non-redundant fragment data bank,” Protein Engineering, vol. 10, no. 6, pp. 659–664, 1997. View at Publisher · View at Google Scholar · View at Scopus
  13. T. Noguchi and Y. Akiyama, “PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003,” Nucleic Acids Research, vol. 31, no. 1, pp. 492–493, 2003. View at Publisher · View at Google Scholar · View at Scopus
  14. P. Motte, G. Alberici, M. Ait-Abdellah, and D. Bellet, “Monoclonal antibodies distinguish synthetic peptides that differ in one chemical group,” The Journal of Immunology, vol. 138, no. 10, pp. 3332–3338, 1987. View at Google Scholar · View at Scopus
  15. M. K. Gilson and S. E. Radford, “Protein folding and binding: from biology to physics and back again,” Current Opinion in Structural Biology, vol. 21, no. 1, pp. 1–3, 2011. View at Publisher · View at Google Scholar · View at Scopus
  16. B. Rost, “Twilight zone of protein sequence alignments,” Protein Engineering, vol. 12, no. 2, pp. 85–94, 1999. View at Publisher · View at Google Scholar · View at Scopus
  17. B. Y. Khor, G. J. Tye, T. S. Lim, and Y. S. Choong, “General overview on structure prediction of twilight-zone proteins,” Theoretical Biology and Medical Modelling, vol. 12, article 15, 2015. View at Publisher · View at Google Scholar · View at Scopus
  18. H. Nakamura, “Roles of electrostatic interaction in proteins,” Quarterly Reviews of Biophysics, vol. 29, no. 1, pp. 1–90, 1996. View at Publisher · View at Google Scholar · View at Scopus
  19. P. J. Fleming and G. D. Rose, “Do all backbone polar groups in proteins form hydrogen bonds?” Protein Science, vol. 14, no. 7, pp. 1911–1917, 2005. View at Publisher · View at Google Scholar · View at Scopus
  20. S. Basu, D. Bhattacharyya, and R. Banerjee, “Self-complementarity within proteins: bridging the gap between binding and folding,” Biophysical Journal, vol. 102, no. 11, pp. 2605–2614, 2012. View at Publisher · View at Google Scholar · View at Scopus
  21. Y. Harpaz, M. Gerstein, and C. Chothia, “Volume changes on protein folding,” Structure, vol. 2, no. 7, pp. 641–649, 1994. View at Publisher · View at Google Scholar · View at Scopus
  22. A. Handisurya, S. Gilch, D. Winter et al., “Vaccination with prion peptide-displaying papillomavirus-like particles induces autoantibodies to normal prion protein that interfere with pathologic prion protein production in infected cells,” FEBS Journal, vol. 274, no. 7, pp. 1747–1758, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. M. Plebanski, E. A. M. Lee, C. M. Hannan et al., “Altered peptide ligands narrow the repertoire of cellular immune responses by interfering with T-cell priming,” Nature Medicine, vol. 5, no. 5, pp. 565–571, 1999. View at Publisher · View at Google Scholar · View at Scopus
  24. E. Michaëlsson, M. Andersson, Å. Engström, and R. Holmdahl, “Identification of an immunodominant type-II collagen peptide recognized by T cells in H-2q mice: self tolerance at the level of determinant selection,” European Journal of Immunology, vol. 22, no. 7, pp. 1819–1825, 1992. View at Publisher · View at Google Scholar · View at Scopus
  25. J. M. Greer, C. Klinguer, E. Trifilieff, R. A. Sobel, and M. B. Lees, “Encephalitogenicity of murine, but not bovine, DM20 in SJL mice is due to a single amino acid difference in the immunodominant encephalitogenic epitope,” Neurochemical Research, vol. 22, no. 4, pp. 541–547, 1997. View at Publisher · View at Google Scholar · View at Scopus
  26. A. Gaur, S. A. Boehme, D. Chalmers et al., “Amelioration of relapsing experimental autoimmune encephalomyelitis with altered myelin basic protein peptides involves different cellular mechanisms,” Journal of Neuroimmunology, vol. 74, no. 1-2, pp. 149–158, 1997. View at Publisher · View at Google Scholar · View at Scopus
  27. A. T. Kozhich, Y.-I. Kawano, C. E. Egwuagu et al., “A pathogenic autoimmune process targeted at a surrogate epitope,” The Journal of Experimental Medicine, vol. 180, no. 1, pp. 133–140, 1994. View at Publisher · View at Google Scholar · View at Scopus
  28. H. Masaki, M. Tamura, and I. Kurane, “Induction of cytotoxic T lymphocytes of heterogeneous specificities by immunization with a single peptide derived from influenza A virus,” Viral Immunology, vol. 13, no. 1, pp. 73–81, 2000. View at Publisher · View at Google Scholar · View at Scopus
  29. G. B. Lipford, S. Bauer, H. Wagner, and K. Heeg, “Peptide engineering allows cytotoxic T-cell vaccination against human papilloma virus tumour antigen, E6,” Immunology, vol. 84, no. 2, pp. 298–303, 1995. View at Google Scholar · View at Scopus
  30. C. L. Keech, K. C. Pang, J. McCluskey, and W. Chen, “Direct antigen presentation by DC shapes the functional CD8+ T-cell repertoire against the nuclear self-antigen La-SSB,” European Journal of Immunology, vol. 40, no. 2, pp. 330–338, 2010. View at Publisher · View at Google Scholar · View at Scopus
  31. S. Tangri, G. Y. Ishioka, X. Huang et al., “Structural features of peptide analogs of human histocompatibility leukocyte antigen class I epitopes that are more potent and immunogenic than wild-type peptide,” Journal of Experimental Medicine, vol. 194, no. 6, pp. 833–846, 2001. View at Publisher · View at Google Scholar · View at Scopus
  32. S. J. Turner and F. R. Carbone, “A dominant Vβ bias in the CTL response after HSV-1 infection is determined by peptide residues predicted to also interact with the TCR β- chain CDR3,” Molecular Immunology, vol. 35, no. 5, pp. 307–316, 1998. View at Publisher · View at Google Scholar · View at Scopus
  33. E. Lazoura, J. Lodding, W. Farrugia et al., “Enhanced major histocompatibility complex class I binding and immune responses through anchor modification of the non-canonical tumour-associated mucin 1-8 peptide,” Immunology, vol. 119, no. 3, pp. 306–316, 2006. View at Publisher · View at Google Scholar · View at Scopus
  34. C. E. Shannon, “A mathematical theory of communication,” The Bell System Technical Journal, vol. 27, no. 4, pp. 623–656, 1948. View at Publisher · View at Google Scholar
  35. E. T. Jaynes, “Information theory and statistical mechanics,” Physical Review, vol. 106, no. 4, pp. 620–630, 1957. View at Publisher · View at Google Scholar
  36. E. T. Jaynes, “Information theory and statistical mechanics. II,” Physical Review, vol. 108, no. 2, pp. 171–190, 1957. View at Google Scholar
  37. A. E. Eriksson, W. A. Baase, X.-J. Zhang et al., “Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect,” Science, vol. 255, no. 5041, pp. 178–183, 1992. View at Publisher · View at Google Scholar · View at Scopus
  38. B. Honig and A.-S. Yang, “Free energy balance in protein folding,” Advances in Protein Chemistry, vol. 46, pp. 27–58, 1995. View at Publisher · View at Google Scholar · View at Scopus
  39. R. Vita, J. A. Overton, J. A. Greenbaum et al., “The immune epitope database (IEDB) 3.0,” Nucleic Acids Research, vol. 43, no. 1, pp. D405–D412, 2015. View at Publisher · View at Google Scholar
  40. S. E. C. Caoili, “A structural-energetic basis for B-cell epitope prediction,” Protein and Peptide Letters, vol. 13, no. 7, pp. 743–751, 2006. View at Publisher · View at Google Scholar · View at Scopus
  41. S. E. C. Caoili, “Benchmarking B-cell epitope prediction for the design of peptide-based vaccines: problems and prospects,” Journal of Biomedicine and Biotechnology, vol. 2010, Article ID 910524, 14 pages, 2010. View at Publisher · View at Google Scholar · View at Scopus
  42. S. P. Edgcomb and K. P. Murphy, “Structural energetics of protein folding and binding,” Current Opinion in Biotechnology, vol. 11, no. 1, pp. 62–66, 2000. View at Publisher · View at Google Scholar · View at Scopus
  43. S. E. C. Caoili, “On the meaning of affinity limits in B-cell epitope prediction for antipeptide antibody-mediated immunity,” Advances in Bioinformatics, vol. 2012, Article ID 346765, 17 pages, 2012. View at Publisher · View at Google Scholar · View at Scopus
  44. N. Dalchau, A. Phillips, L. D. Goldstein et al., “A peptide filtering relation quantifies MHC class I peptide optimization,” PLoS Computational Biology, vol. 7, no. 10, Article ID e1002144, 2011. View at Publisher · View at Google Scholar · View at Scopus
  45. L. J. Edwards and B. D. Evavold, “T cell recognition of weak ligands: roles of signaling, receptor number, and affinity,” Immunologic Research, vol. 50, no. 1, pp. 39–48, 2011. View at Publisher · View at Google Scholar · View at Scopus