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Virus Genes

, Volume 3, Issue 4, pp 323–341 | Cite as

Computer predictions of antigenic domains in human immunodeficiency virus-1 envelope glycoprotein: Comparison with reported experimental data

  • Yechiel Becker
Article

Abstract

Computer analyses of amino acid sequences in the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein revealed that antigenic domains in the viral protein can be predicted on the basis of the physical properties of amino acids in the polypeptide chain. Relatively high values of surface probability, flexibility, and hydrophilicity were used as markers for domains of putative antigenicity. Comparison of the computer-predicted antigenic domains in the HIV-1 envelope with those reported experimentally indicate that computer analyses are able to predict antigenic domains. This study shows the usefulness of computer programs for the prediction of the antigenic domains in the HIV-1 envelope protein.

Key words

antigenic domains computer predictions envelope glycoprotein experimental analysis of antigenicity HIV-1 

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References

  1. 1.
    Sela M., Science166, 1365–1374, 1969.Google Scholar
  2. 2.
    Crumpton M. J. in Sela M. (ed.)The Antigens, Vol 2. Academic Press, New York, 1974, p. 1–78.Google Scholar
  3. 3.
    Arnon R. in Salton R. R. J. (ed.)Immunochemistry of Enzymes and their Antibodies. Wiley, New York, 1977, pp. 1–28.Google Scholar
  4. 4.
    Benjamin D. C., Berezofsky J. A., East I. J., Gurd F. R. N., Hannum C., Leach S. J., Margoliash E., Michael J. G., Miller A., Prager E. M., Reichlin V., Sercarz E. E., Smith-Gill S. J., Todd P. E. and Wilson A. C., Ann Rev Immunol2, 67–101, 1984.Google Scholar
  5. 5.
    Hopp T. P. and Woods K. R., Proc Natl Acad Sci USA78, 3824–3828, 1981.Google Scholar
  6. 6.
    Hopp T. P. and Woods K. R., Molec Immunol20, 483–489, 1983.Google Scholar
  7. 7.
    Padlan E. A., Molec Immunol220, 1243–1254, 1985.Google Scholar
  8. 8.
    Westhof E., Altschuh D., Moras D., Bloomer A. C., Mondragon A., Klug A. and vanRegenmortel M. H. V., Nature (London)311, 123–126, 1984.Google Scholar
  9. 9.
    Tainer J. A., Getzoff E. D., Alexander H., Houghton R. A., Olson A. J., Lerner R. A., and Hendrickson W. A., Nature (London)312, 127–134, 1984.Google Scholar
  10. 10.
    Pfaff F., Mussgay M., Böhm H. O., Schulz G. E. and Schaller H., EMBO J,1, 869–874, 1982.Google Scholar
  11. 11.
    Geysen H. M., Barteling S. J. and Meloen R. H., Proc Natl Acad Sci USA82, 178–182, 1985.Google Scholar
  12. 12.
    Lerner R. A., Nature299, 592–596, 1984.Google Scholar
  13. 13.
    Sutclife J. G., Shinnick T. M., Green N. and Lerner R. A., Science219, 660–666, 1983.Google Scholar
  14. 14.
    Niman H. L., Houghton R. A., Walker L. E., Reisfeld R. A., Wilson J. A., Hogle J. M. and Lerner R. A., Proc Natl Acad Sci USA80, 4949–4953, 1983.Google Scholar
  15. 15.
    Scheraga H. A., Biopolymers20, 1877–1899, 1981.Google Scholar
  16. 16.
    Emini E. A., Hughes J. V., Perlow D. S. and Boger J., J Virol55, 836–839, 1985.Google Scholar
  17. 17.
    Janin J., Wodak S., Levitt M. and Maigret B., J Mol Biol125, 357–386, 1978.Google Scholar
  18. 18.
    Sela M., Biopolymers22, 415–424, 1983.Google Scholar
  19. 19.
    Allan J. S., Coligan J. E., Barin F., Mclane M. F., Sodroski J. G., Rosen C. A., Haseltine W. A., Lee T. H. and Essex M., Science228, 1091–1094, 1985.Google Scholar
  20. 20.
    Gelderblom H. R., Hausmann E. H. S., Ozel M., Pauli G. and Koch M. A., Virology156, 171–176, 1987.Google Scholar
  21. 21.
    Dalgleish A. G., Beverley C. L., Clapham P. R., Crawford D. H., Greaves M. F. and Weiss R. A., Nature312 763–767, 1986.Google Scholar
  22. 22.
    McDougal J. S., Kennedy M. S., Sligh J. M., Cort S. P., Mawle A. and Nicholson J. K. A., Science231, 382–385, 1986.Google Scholar
  23. 23.
    Takahashi H., Cohen J., Hosmalin A., Cease U. B., Houghton R., Cornette J. L., DeLisi C., Moss B., Germain R. N. and Berzofsky J. A., Proc Natl Acad Sci USA85, 3105–3109, 1988.Google Scholar
  24. 24.
    Willey R. L., Smith D. H., Lasky L. A., Theodore T. S., Earl P. L., Moss B., Capon D. J. and Martin M. A., J Virol62, 139–147, 1988.Google Scholar
  25. 25.
    Kennedy R. C., Henkel R. D., Pauletti D., Allan J. S., Lee T. H., Essex M. and Dreesman G. R., Science231, 1556–1559, 1986.Google Scholar
  26. 26.
    Palker T. J., Matthews T. J., Clark M. E., Cianciolo G. J., Randall R. R., Langlois A. J., White G. C., Safai B., Snyderman R., Bolognesi D. P., et al., Proc Natl Acad Sci USA84, 2479–2483, 1987.Google Scholar
  27. 27.
    Palker T. J., Screarce R. M., Copeland T. D., Oraszlan S. and Haynes B. F., J Immunol136, 2393–2397, 1986.Google Scholar
  28. 28.
    Kowalski M., Potz J., Basiripour L., Dorfman T., Goh W. C., Terwilliger E., Dayton A., Rosen C., Haseltine W. and Sodroski J., Science237, 1351–1355, 1987.Google Scholar
  29. 29.
    Gnann J. W., McCormick J. B., Mitchell S., Nelson J. A. and Oldston M. B., Science237, 1346–1349, 1987.Google Scholar
  30. 30.
    Gnann J. W., Schwimmbeck P. L., Nelson J. A., Traux A. B. and Oldstone M. B., J Infect Dis156, 261–267, 1987.Google Scholar
  31. 31.
    Starcich B. R., Hahn B. H., Shaw G. M., McNeely P. D., Modrow S., Wolf H., Parks E. S., Parks W. P., Josephs S. F., Gallo R. C., et al., Cell45, 637–648, 1986.Google Scholar
  32. 32.
    Matsushita S., Robert-Guroff M., Rusche J., Koito A., Hattori T., Hoshino H., Javaherian K., Takatsuki K. and Putney S., J Virol62, 2107–2114, 1988.Google Scholar
  33. 33.
    Ho D. D., Kaplan J. C., Rackanskas I. E. and Gurnery M. E., Science239, 1021–1023, 1988.Google Scholar
  34. 34.
    Rusche J. R., Javaherian K., McDanal C., Petro J., Lynn D. L., Grimaila R., Langlois A., Gallo R. C., Arthur L. O., Fischinger P. J., et al., Proc Natl Acad Sci USA85, 3198–3202, 1988.Google Scholar
  35. 35.
    Wang J. J. G., Steel S., Wisniewolski R. and Wang Y-W., Proc Natl Acad Sci USA83, 6159–6163, 1986.Google Scholar
  36. 36.
    Kemp B. E., Rylatt D. B., Bundesen P. G., Doherty R. R., McPhee D. A., Stapleton D., Cottis L. E., Wilson K., John M. A., Khan J. M., et al., Science241, 1352–1354, 1988.Google Scholar
  37. 37.
    Sarngadharan M. G., Popovic M., Bruch L., Schüpbach J. and Gallo R. C., Science224, 506–508, 1984.Google Scholar
  38. 38.
    Riggin C. H., Beltz G. A., Hung C. H., Thorn R. M. and Marciani D. J., J Clin Microbiol25, 1772–1773, 1987.Google Scholar
  39. 39.
    Wahren B., Rosen J., Sandström E., Mathiesen T., Modrow S. and Wigzell H., J Aids 1989, in press.Google Scholar
  40. 40.
    George D. G., Barker W. C. and Hunt L. T., Nucl Acids Res14, 11–16, 1986.Google Scholar
  41. 41.
    Devereux J., Haberlin P. and Smithies O., Nucl Acids Res12, 387–395, 1984.Google Scholar
  42. 42.
    Wolf H., Modrow S., Motz M., Jameson B. A., Hermann G. and Förtsch B., CABIOS4, 187–191, 1988.Google Scholar
  43. 43.
    Kyte J. and Doolittle R. F., J Mol Biol157, 105–132, 1982.Google Scholar
  44. 44.
    Karplus P. A. and Schulz G. E., Naturwissenschaften72, 212–213, 1985.Google Scholar
  45. 45.
    Chou P. Y. and Fasman G. D., Ann Rev Biochem47, 251–276, 1978.Google Scholar
  46. 46.
    Garnier J., Osguthorpe D. J. and Robson B., J Mol Biol120, 97–120, 1978.Google Scholar
  47. 47.
    Ratner L., Haseltine W., Patarca R., Livak K. J., Starcich B., Josephs S. F., Doran E. R., Rafalski J. A., Whitehorn E. A., Baumeister K., et al., Nature313, 277–284, 1985.Google Scholar
  48. 48.
    Lasky L. A., Nakamura G., Smith D. H., Fennie C., Shimasaki C., Patzer E., Berman P., Gregory T. and Capon D. J., Cell50, 975–985, 1987.Google Scholar
  49. 49.
    Geysen H. M., Meloen R. H. and Barteling S. J., Proc Natl Acad Sci USA81, 3998–4002, 1984.Google Scholar
  50. 50.
    Margalit H., Spouge J. L., Cornette J. L., Cease K. B., Delisi C. and Berzofsky J. A., J Immunol138, 2213–2229, 1987.Google Scholar
  51. 51.
    Balfour B. M., Drexhage H. A., Kamperdijk E. W. A. and Hoefsmit E. C. M. inMicroenvironments in Haematopoietic and Lymphoid Differentiation. Ciba Foundation Symposium84, 281–301, 1981.Google Scholar
  52. 52.
    Tschachler E., Groh V., Popovic M., Marin D. L., Konrad K., Safai B., Eron L., deMarzo Veronese F., Wolff K. and Stingl G., J Invest Dermatol88, 233–237, 1987.Google Scholar
  53. 53.
    Rappersberger K., Gartner S., Schenk P., Stingl G., Groh V., Tschachler E., Mann D. L., Wolff K., Konrad K. and Popovic M., Intervirology29, 185–194, 1988.Google Scholar
  54. 54.
    Sprecher E. and Becker Y., Arch Virol103, 1–14, 1988.Google Scholar

Copyright information

© Kluwer Academic Publishers 1990

Authors and Affiliations

  • Yechiel Becker
    • 1
  1. 1.Department of Molecular Virology, Faculty of MedicineHebrew University of JerusalemJerusalemIsrael

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