Hepatitis Monthly

Published by: Kowsar

GB Virus C/Hepatitis G Virus Envelope Glycoprotein E2: Computational Molecular Features and Immunoinformatics Study

Mohammad Mahdi Ranjbar 1 , Khodayar Ghorban 2 , Seyed Moayed Alavian 3 , 4 , * , Hossein Keyvani 5 , Maryam Dadmanesh 6 , Abbas Roayaei Ardakany 7 , Mohammad Hassan Motedayen 8 and Alireza Sazmand 9
Authors Information
1 Department of Immunology, University of Tehran, Tehran, IR Iran
2 Department of Immunology, School of Medicine, AJA University of Medical Sciences, Tehran, IR Iran
3 Middle East Liver Diseases Center (MELD), Tehran, IR Iran
4 Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallh University of Medical Sciences, Tehran, IR Iran
5 Department of Virology, Tehran University of Medical Sciences, Tehran, IR Iran
6 Department of Infectious Diseases, School of Medicine, AJA University of Medical Sciences, Tehran, IR Iran
7 Department of Computer Sciences, University of Nevada, Reno, USA
8 Razi Vaccine and Serum Research Institute, Karaj Branch, Karaj, IR Iran
9 Department of Agriculture, Payame Noor University, Yazd, IR Iran
Article information
  • Hepatitis Monthly: December 01, 2013, 13 (12); e15342
  • Published Online: December 30, 2013
  • Article Type: Review Article
  • Received: October 9, 2013
  • Revised: December 1, 2013
  • Accepted: December 1, 2013
  • DOI: 10.5812/hepatmon.15342

To Cite: Ranjbar M M, Ghorban K, Alavian S M, Keyvani H, Dadmanesh M, et al. GB Virus C/Hepatitis G Virus Envelope Glycoprotein E2: Computational Molecular Features and Immunoinformatics Study, Hepat Mon. 2013 ;13(12):e15342. doi: 10.5812/hepatmon.15342.

Abstract
Copyright © 2013, Kowsar Corp. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/) which permits copy and redistribute the material just in noncommercial usages, provided the original work is properly cited.
1. Introduction
2. Evidence Acquisition
3. Results
5. Discussion
Acknowledgements
Footnotes
References
  • 1. Linnen J, Wages J, Jr, Zhang-Keck ZY, Fry KE, Krawczynski KZ, Alter H, et al. Molecular cloning and disease association of hepatitis G virus: a transfusion-transmissible agent. Science. 1996; 271(5248): 505-8[PubMed]
  • 2. Stapleton JT, Foung S, Muerhoff AS, Bukh J, Simmonds P. The GB viruses: a review and proposed classification of GBV-A, GBV-C (HGV), and GBV-D in genus Pegivirus within the family Flaviviridae. J Gen Virol. 2011; 92: 233-46[DOI][PubMed]
  • 3. Naito H, Abe K. Genotyping system of GBV-C/HGV type 1 to type 4 by the polymerase chain reaction using type-specific primers and geographical distribution of viral genotypes. J Virol Methods. 2001; 91(1): 3-9[PubMed]
  • 4. Berzsenyi MD, Bowden DS, Roberts SK. GB virus C: insights into co-infection. J Clin Virol. 2005; 33(4): 257-66[DOI][PubMed]
  • 5. Fallahian F, Alavian SM, Rasoulinejad M. Epidemiology and transmission of hepatitis G virus infection in dialysis patients. Saudi J Kidney Dis Transpl. 2010; 21(5): 831-4[PubMed]
  • 6. Alavian SM, Adibi P, Zali MR. Hepatitis C virus in Iran: Epidemiology of an emerging infection. Arch Iranian Med. 2005; 8(2): 84-90
  • 7. Tillmann HL, Heiken H, Knapik-Botor A, Heringlake S, Ockenga J, Wilber JC, et al. Infection with GB virus C and reduced mortality among HIV-infected patients. N Engl J Med. 2001; 345(10): 715-24[DOI][PubMed]
  • 8. Xiang J, Wunschmann S, Diekema DJ, Klinzman D, Patrick KD, George SL, et al. Effect of coinfection with GB virus C on survival among patients with HIV infection. N Engl J Med. 2001; 345(10): 707-14[DOI][PubMed]
  • 9. Lau JY, Qian K, Detmer J, Collins ML, Orito E, Kolberg JA, et al. Effect of interferon-alpha and ribavirin therapy on serum GB virus C/hepatitis G virus (GBV-C/HGV) RNA levels in patients chronically infected with hepatitis C virus and GBV-C/HGV. J Infect Dis. 1997; 176(2): 421-6[PubMed]
  • 10. Alvarado-Mora MV, Botelho L, Nishiya A, Neto RA, Gomes-Gouvea MS, Gutierrez MF, et al. Frequency and genotypic distribution of GB virus C (GBV-C) among Colombian population with Hepatitis B (HBV) or Hepatitis C (HCV) infection. Virol J. 2011; 8: 345[DOI][PubMed]
  • 11. Choo QL, Kuo G, Ralston R, Weiner A, Chien D, Van Nest G, et al. Vaccination of chimpanzees against infection by the hepatitis C virus. Proc Natl Acad Sci U S A. 1994; 91(4): 1294-8[PubMed]
  • 12. Yan Q. Bioinformatics databases and tools in virology research: an overview. In Silico Biol. 2008; 8(2): 71-85[PubMed]
  • 13. Sollner J, Grohmann R, Rapberger R, Perco P, Lukas A, Mayer B. Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins. Immunome Res. 2008; 4: 1[DOI][PubMed]
  • 14. Yang X, Yu X. An introduction to epitope prediction methods and software. Rev Med Virol. 2009; 19(2): 77-96[DOI][PubMed]
  • 15. Vigerust DJ, Shepherd VL. Virus glycosylation: role in virulence and immune interactions. Trends Microbiol. 2007; 15(5): 211-8[DOI][PubMed]
  • 16. Wan J, Roth AF, Bailey AO, Davis NG. Palmitoylated proteins: purification and identification. Nat Protoc. 2007; 2(7): 1573-84[DOI][PubMed]
  • 17. Draper JM, Xia Z, Smith CD. Cellular palmitoylation and trafficking of lipidated peptides. J Lipid Res. 2007; 48(8): 1873-84[DOI][PubMed]
  • 18. Chakrabandhu K, Herincs Z, Huault S, Dost B, Peng L, Conchonaud F, et al. Palmitoylation is required for efficient Fas cell death signaling. EMBO J. 2007; 26(1): 209-20[DOI][PubMed]
  • 19. Ingrell CR, Miller ML, Jensen ON, Blom N. NetPhosYeast: prediction of protein phosphorylation sites in yeast. Bioinformatics. 2007; 23(7): 895-7[DOI][PubMed]
  • 20. Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Fiser A, Pazos F, et al. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics. 2001; 17(12): 1242-3[PubMed]
  • 21. Rychlewski L, Fischer D. LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. Protein Sci. 2005; 14(1): 240-5[DOI][PubMed]
  • 22. Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res. 2005; 33-6[DOI][PubMed]
  • 23. Idrees S, Ashfaq UA, Khaliq S. HCV Envelope protein 2 sequence comparison of Pakistani isolate and In-silico prediction of conserved epitopes for vaccine development. J Transl Med. 2013; 11: 105[DOI][PubMed]
  • 24. Sautto G, Tarr AW, Mancini N, Clementi M. Structural and antigenic definition of hepatitis C virus E2 glycoprotein epitopes targeted by monoclonal antibodies. Clin Dev Immunol. 2013; 2013: 450963[DOI][PubMed]
  • 25. McCaffrey K, Gouklani H, Boo I, Poumbourios P, Drummer HE. The variable regions of hepatitis C virus glycoprotein E2 have an essential structural role in glycoprotein assembly and virion infectivity. J Gen Virol. 2011; 92: 112-21[DOI][PubMed]
  • 26. The Bioinformatics Analysis of Hepatitis C Virus E2 Protein.; Advances in Intelligent Systems Research. : 1875-6883
  • 27. Mondelli MU, Cerino A, Meola A, Nicosia A. Variability or conservation of hepatitis C virus hypervariable region 1? Implications for immune responses. J Biosci. 2003; 28(3): 305-10[PubMed]
  • 28. Petit MA, Jolivet-Reynaud C, Peronnet E, Michal Y, Trepo C. Mapping of a conformational epitope shared between E1 and E2 on the serum-derived human hepatitis C virus envelope. J Biol Chem. 2003; 278(45): 44385-92[DOI][PubMed]
  • 29. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001; 305(3): 567-80[DOI][PubMed]
  • 30. Pelte C, Cherepnev G, Wang Y, Schoenemann C, Volk HD, Kern F. Random screening of proteins for HLA-A*0201-binding nine-amino acid peptides is not sufficient for identifying CD8 T cell epitopes recognized in the context of HLA-A*0201. J Immunol. 2004; 172(11): 6783-9[PubMed]
  • 31. Kolaskar AS, Tongaonkar PC. A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett. 1990; 276(1-2): 172-4[PubMed]
  • 32. Saha S, Raghava GPS. BcePred: Prediction of continuous B-cell epitopes in antigenic sequences using physico-chemical properties. Artificial Immune Systems.: 2004; : 197-204
  • 33. Larsen JE, Lund O, Nielsen M. Improved method for predicting linear B-cell epitopes. Immunome Res. 2006; 2: 2[DOI][PubMed]
  • 34. Saha S, Raghava GP. Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins. 2006; 65(1): 40-8[DOI][PubMed]
  • 35. El-Manzalawy Y, Dobbs D, Honavar V. Predicting linear B-cell epitopes using string kernels. J Mol Recognit. 2008; 21(4): 243-55[DOI][PubMed]
  • 36. Lovell SC, Davis IW, Arendall WB, 3rd, de Bakker PI, Word JM, Prisant MG, et al. Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins. 2003; 50(3): 437-50[DOI][PubMed]
  • 37. Leary TP, Muerhoff AS, Simons JN, Pilot-Matias TJ, Erker JC, Chalmers ML, et al. Sequence and genomic organization of GBV-C: a novel member of the flaviviridae associated with human non-A-E hepatitis. J Med Virol. 1996; 48(1): 60-7[DOI][PubMed]
  • 38. Ogata N, Alter HJ, Miller RH, Purcell RH. Nucleotide sequence and mutation rate of the H strain of hepatitis C virus. Proc Natl Acad Sci U S A. 1991; 88(8): 3392-6[PubMed]
  • 39. Okamoto H, Kojima M, Okada S, Yoshizawa H, Iizuka H, Tanaka T, et al. Genetic drift of hepatitis C virus during an 8.2-year infection in a chimpanzee: variability and stability. Virology. 1992; 190(2): 894-9[PubMed]
  • 40. Manzin A, Solforosi L, Petrelli E, Macarri G, Tosone G, Piazza M, et al. Evolution of hypervariable region 1 of hepatitis C virus in primary infection. J Virol. 1998; 72(7): 6271-6[PubMed]
  • 41. Farci P, Shimoda A, Coiana A, Diaz G, Peddis G, Melpolder JC, et al. The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies. Science. 2000; 288(5464): 339-44[PubMed]
  • 42. Kato T, Furusaka A, Miyamoto M, Date T, Yasui K, Hiramoto J, et al. Sequence analysis of hepatitis C virus isolated from a fulminant hepatitis patient. J Med Virol. 2001; 64(3): 334-9[PubMed]
  • 43. Ducoulombier D, Roque-Afonso AM, Di Liberto G, Penin F, Kara R, Richard Y, et al. Frequent compartmentalization of hepatitis C virus variants in circulating B cells and monocytes. Hepatology. 2004; 39(3): 817-25[DOI][PubMed]
  • 44. Puntoriero G, Meola A, Lahm A, Zucchelli S, Ercole BB, Tafi R, et al. Towards a solution for hepatitis C virus hypervariability: mimotopes of the hypervariable region 1 can induce antibodies cross-reacting with a large number of viral variants. EMBO J. 1998; 17(13): 3521-33[DOI][PubMed]
  • 45. Jusoh SA, Welsch C, Siu SW, Bockmann RA, Helms V. Contribution of charged and polar residues for the formation of the E1-E2 heterodimer from Hepatitis C Virus. J Mol Model. 2010; 16(10): 1625-37[DOI][PubMed]
  • 46. Cocquerel L, Wychowski C, Minner F, Penin F, Dubuisson J. Charged residues in the transmembrane domains of hepatitis C virus glycoproteins play a major role in the processing, subcellular localization, and assembly of these envelope proteins. J Virol. 2000; 74(8): 3623-33[PubMed]
  • 47. Ciczora Y, Callens N, Penin F, Pecheur EI, Dubuisson J. Transmembrane domains of hepatitis C virus envelope glycoproteins: residues involved in E1E2 heterodimerization and involvement of these domains in virus entry. J Virol. 2007; 81(5): 2372-81[DOI][PubMed]
  • 48. Veit M, Schmidt MF. Palmitoylation of influenza virus proteins. Berl Munch Tierarztl Wochenschr. 2006; 119(3-4): 112-22[PubMed]
  • 49. Goffard A, Dubuisson J. Glycosylation of hepatitis C virus envelope proteins. Biochimie. 2003; 85(3-4): 295-301[PubMed]
  • 50. Zhang M, Gaschen B, Blay W, Foley B, Haigwood N, Kuiken C, et al. Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin. Glycobiology. 2004; 14(12): 1229-46[DOI][PubMed]
  • 51. Abro SH, Ullman K, Belak S, Baule C. Bioinformatics and evolutionary insight on the spike glycoprotein gene of QX-like and Massachusetts strains of infectious bronchitis virus. Virol J. 2012; 9: 211[DOI][PubMed]
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