Prediction of epitopes and structural properties of Iranian HPV-16 E6 by bioinformatics methods

Asian Pacific Journal of Cancer Prevention

Volumn 8, Issue 4, 2007, Pages 602-606

  Mohabatkar, Hassan ^a  

^a SHIRAZ UNIVERSITY   (Iran)

Author keywords

B cell epitopes; Bioinformatics; Computational analysis; Structure prediction; T cell epitopes

Indexed keywords

E6 PROTEIN, HUMAN PAPILLOMAVIRUS TYPE 16; EPITOPE; ONCOPROTEIN; REPRESSOR PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CHEMISTRY; HUMAN; IMMUNOLOGY; IRAN; METHODOLOGY; MOLECULAR GENETICS;

AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; EPITOPES, B-LYMPHOCYTE; EPITOPES, T-LYMPHOCYTE; HUMANS; IRAN; MOLECULAR SEQUENCE DATA; ONCOGENE PROTEINS, VIRAL; REPRESSOR PROTEINS;

EID: 58249092569     PISSN: 15137368     EISSN: 2476762X     Source Type: Journal    
DOI: None     Document Type: Article

References (42)

1. Bairoch A, Bucher P, Hofmann K (1997). The PROSITE database, its status in 1997. Nuc Aci Res, 25, 217-23.
2. Bause E (1983). Structural requirements of N-glycosylation of proteins. Studies with proline peptides as conformational probes. Biochem J, 209, 331-6.
3. Bian H, Reidhaar-Olson JF, Hammer J (2003). The use of bioinformatics for identifying class II-restricted T-cell epitopes. Methods, 29, 299-309.
4. Bourgault Villada I, Bénéton N, Bony C, et al (2000). Identification in humans of HPV-16 E6 and E7 protein epitopes recognized by cytolytic T lymphocytes in association with HLA-B18 and determination of the HLAB18-specific binding motif. Eur J Immunol, 30, 2281-9.
5. Burd EM, (2003). Human Papillomavirus and Cervical Cancer. Clinical Microbiology Reviews, 16, 1-17.
6. Conrad-Stöppler MCK, Ching H, Stöppler K, et al (1996). Natural variants of the human papillomavirus type 16 E6 protein differ in their abilities to alter keratinocyte differentiation and to induce p53 degradation. J Virol, 70, 6987-93.
7. Giannoudis A, Herrington CS (2001). Human papillomavirus variants and squamous neoplasia of the cervix. J Pathol, 193, 295-302.
8. Harro CD, Pang Y-Y S, Roden RBS (2001). Safety and immunogenicity trial in adult volunteers of a human papillomavirus 16 L1 virus-like particle vaccine. J Natl Cancer Inst, 93, 284-92.
9. Chen CC, Hwang JK, Yang JM (2006). (PS)2: protein structure prediction server. Nuc Aci Res, 34 (Web Server issue), 152-7.
10. Doytchinova IA, Flower DR (2002). Quantitative approaches to computational vaccinology. Immunol Cell Biol, 80, 270-9.
11. Emini EA, Hughes JV, Perlow DS, et al (1985). Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol, 55, 836-9.
12. Garnier J, Osguthorpe DJ, Robson B (1978). Analysis and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol, 120, 97-120.
13. Goedert M, Jakes TR, Crowther A, et al (1994). Epitope mapping of monoclonal antibodies to the paired helical filaments of Alzheimer's disease: identification of phosphorylation sites in tau protein. Biochem J, 301, 871-7.
14. Guan P, Doytchinova IA, Zygouri C, et al (2003). MHCPred: bringing a quantitative dimension to the online prediction of MHC binding. Appl Bioinformatics, 2, 63-6.
15. Guan P, Hattotuwagama CK, Doytchinova IA, et al (2006). MHCPred 2.0: an updated quantitative T-cell epitope prediction server. Appl Bioinformatics, 5, 55-61.
16. Hansen JE, Lund O, Neilsen JO, et al (1996). Prediction of the secondary structure of HIV-1 gp120. Proteins, 25, 1-11.
17. Huang X, Barchi JJ Jr, Lung FD, et al (1997). Glycosylation affects both the three dimensional structure and antibody binding properties of the HIV-1IIIB GP120 peptide RP135. Biochemistry, 36, 10846-56.
18. Hubbard SC, Ivatt RJ (1981). Synthesis and processing of asparagine-linked oligosaccharides. Annu Rev Biochem, 50, 555-83.
19. Janin J, Wodak S (1978). Conformation of amino acid side-chains in proteins.J Mol Biol, 125, 357-86.
20. Kanjanavirojkul N, Pairojkul C, Yuenyao P, et al (2006). Risk Factors and Histological Outcome of Abnormal Cervix with Human Papilloma Infection in Northeastern Thai-women. Asian Pacific J Cancer Prev, 7, 567-70.
21. Karplus PA, Schulz GE (1985). Prediction of chain flexibility in proteins: A tool for the selection of peptide antigens. Naturwissenschaften, 72, 212-13.
22. Kaufmann AM, Stern PL, Rankin EM, et al (2002). Safety and immunogenicity of TA-HPV, a recombinant vaccinia virus expressing modified human papillomavirus (HPV)-16 and HPV-18 E6 and E7 genes, in women with progressive cervical cancer. Clin Cancer Res, 8, 3676-85.
23. Kim H, Park H (2003). Protein secondary structure prediction based on an improved support vector machines approach. Protein Eng, 16, 553-60.
24. Kim SH, Kim KS, Lee EJ, et al (2004). Human keratin 14 driven HPV 16 E6/E7 transgenic mice exhibit hyperkeratinosis. Life Sci, 75, 3035-42.
25. Kolaskar AS, Tongaonkar PC (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett, 276, 172-4.
26. Li GF, Wang Y, Zhang ZS, et al (2005). Identification of immunodominant Th1-type T cell epitopes from Schistosoma japonicum 28 kDa glutathione-S-transferase, a vaccine candidate. Acta Biochim Biophys Sin (Shanghai), 37, 751-8.
27. Liang X, Fu T, Xie H, et al (2002). Development of HIV-1 Nef vaccine components: immunogenicity study of Nef mutants lacking myristoylation and dileucine motif in mice. Vaccine, 20, 3413-21.
28. Liu Y, Li JZ, Yuan XH, et al (2002). An AP-1 binding site mutation in HPV-16 LCR enhances E6/E7 promoter activity in human oral epithelial cells. Virus Genes, 24, 29-37.
29. Mohabatkar H, Kar SK (2004). Prediction of exposed domains of envelope glycoprotein in Indian HIV-1 isolates and experimental confirmation of their immunogenicity in humans. Braz J Med Res, 36, 675-81.
30. Parker JM, Guo D, Hodges RS (1986). 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, 23, 5425-32.
31. Pellequer JL, Westhof E, Regenmortel MHV (1991). Predicting location of continuous epitopes in proteins from their primary structures. Methods Enzymol, 203, 176-201.
32. Pellequer JL, Westhof E, Van Regenmortel MH (1993). Correlation between the location of antigenic sites and the prediction of turns in proteins. Immunol Lett, 36, 83-99.
33. Peng S, Trimble C, Ji H, et al (2005). Characterization of HPV- 16 E6 DNA vaccines employing intracellular targeting and intercellular spreading strategies. J Biomed Sci, 12, 689-700.
34. Ponnuswamy PK, Prabhakaran M, Manavalan P (1980). Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins. Biochim Biophys Acta, 623, 301-16.
35. Samorski R, Gissmann L, Osen W (2006). Codon optimized expression of HPV 16 E6 renders target cells susceptible to E6-specific CTL recognition. Immunol Lett, 7, 41-9.
36. Sang BC, Barbosa MS (1992). Single amino acid substitutions in "low-risk" human papillomavirus (HPV) type 6 E7 protein enhance features characteristic of the "high-risk" HPV E7 oncoproteins. Proc Natl Acad Sci USA, 89, 8063-7.
37. Sarkar AK, Tortolero-Luna G, Follen M, et al (2005). Inverse correlation of cellular immune responses specific to synthetic peptides from the E6 and E7 oncoproteins of HPV-16 with recurrence of cervical intraepithelial neoplasia in a crosssectional study. Gynecol Oncol, 99 (3 Suppl 1), S251-61.
38. Schlosser G, Mezo G, Kiss R, et al (2003). Synthesis, solution structure analysis and antibody binding of cyclic epitope peptides from glycoprotein D of Herpes simplex virus type I. Biophys Chem, 106, 155-71.
39. Schuman J, Campbell AP, Koganty RR, et al (2003). Probing the conformational and dynamical effects of O-glycosylation within the immunodominant region of a MUC1 peptide tumor antigen. J Pept Res, 61, 91-108.
40. Veress G, Szarka K, Dong XP, et al. (1999). Functional significance of sequence variation in the E2 gene and the long control region of human papillomavirus type 16. J Gen Virol, 80, 1053-143.
41. Vullo A, Frasconi P (2004). Disulfide connectivity prediction using recursive neural networks and evolutionary information. Bioinformatics, 20, 653-60.
42. Warnock LJ, Raines SA, Mee TR, et al (2005). Role of phosphorylation in p53 acetylation and PAb421 epitope recognition in baculoviral and mammalian expressed proteins. FEBS J, 272, 1669-75.