Secondary structural elements as a basis for antibody recognition in the immunodominant region of human immunodeficiency viruses 1 and 2

European Journal of Biochemistry

Volumn 237, Issue 1, 1996, Pages 188-204

  Markert, Robert L M ^a   Ruppach, Horst ^b   Gehring, Stephan ^b   Dietrich, Ursula ^b   Mierke, Dale F ^c   Köck, Matthias ^a   Rübsamen Waigmann, Helga ^d   Griesinger, Christian ^a  

^a GOETHE UNIVERSITY   (Germany)

^b INSTITUTE FOR TUMOR BIOLOGY AND EXPERIMENTAL THERAPY   (Germany)

^c CLARK UNIVERSITY   (United States)

^d BAYER AG   (Germany)

Author keywords

Distance geometry; ELISA; Glycoprotein 120 (gp120) V3 regions; NMR spectroscopy; Peptide synthesis

Indexed keywords

ANTIGEN; GLYCOPROTEIN GP 120; SYNTHETIC PEPTIDE;

AMINO ACID SEQUENCE; ANTIGEN BINDING; ARTICLE; BLOOD ANALYSIS; CIRCULAR DICHROISM; CONTROLLED STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 2; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN VARIANT; RECOGNITION; VIRUS TYPING;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 2;

EID: 0029892305     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1432-1033.1996.0188n.x     Document Type: Article

References (98)

1. Bachmann, M. H., Delwart, E. L., Shpaer, E. G., Lingenfelter, P., Singal, R. & Mullins, J. I. (1994) WHO network for HIV isolation and characterization. Rapid genetic characterization of HIV type 1 from four World Health Organization-sponsored vaccine evaluation sites using heteroduplex mobility assay, AIDS Res. Hum. Retroviruses 10, 1345-1353.
2. Bardaji, H., Torres, J. L., Clapés, P., Albericio, R. Barany, G. & Valencia, G. (1990) Festphasen-Synthese von Glycopeptidamiden unter milden Bedingungen: Morphiceptin-Analoga, Angew. Chem. 102, 311-312.
3. Barlos, K., Chatzi, O., Gatos, D. & Stavropoulos, G. (1991) 2-Chlorotrityl chloride resin, Int. J. Peptide Protein Res. 37, 513-520.
4. Becker, Y. (1992) Computer predictions of functional, topographic, and antigenic domains in human immunodeficiency virus-2 envelope glycoprotein, Virus Genes 6, 79-93.
5. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A. & Haak, J. R. (1984) Molecular dynamics with coupling to an external bath, J. Chem. Phys. 81, 3684-3690.
6. Bjoerling, E., Broliden, K., Bernadi, D., Utter, G., Thorstensson, R., Chiodi, F. & Norrby, E. (1991) Hyperimmune antisera against synthetic peptides representing the glycoprotein of human immunodeficiency virus type 2 can mediate neutralisation and antibody-dependent cytotoxic activity, Proc. Natl Acad. Sci. USA 88, 6082-6086.
7. Bjoerling, E., Chiodi, F., Utter, G. & Norrby, E. (1994) Two neutralizing domains in the V3 region in the envelope glycoprotein gp125 of HIV type 2, J. Immunol. 152, 1952-1959.
8. Boeri, E., Giri, A., Lillo, F., Ferrari, G., Varnier, O. E., Ferro, A., Sabbatani, S., Saxinger, W. C. & Franchini, G. (1992) In vivo genetic variability of the human immunodeficiency virus type 2 V3 region, J. Virol. 66, 4546-4550.
9. Braunschweiler, L. & Ernst, R. R. (1983) Coherence transfer by isotropic mixing: application to proton correlation spectroscopy, J. Magn. Reson, 53, 521-528.
10. Chandrasekhar, K., Profy, A. T. & Dyson, H. J. (1991) Solution conformational preferences of immunogenic peptides derived from the principal neutralizing determinant of the HIV-1 envelope glycoprotein gp120, Biochemistry 30, 9187-9194.
11. Clements, G. J., Price-Jones, M. J., Stephens, P. E., Sutton, C., Schulz, T. F., Clapham, P. R., McKeating, J. A., McClure, M. O., Thomson, S., Marsh, M., Kay, J., Weiss, R. A. & Moore, J. P. (1991) The V3 loops of the HIV-1 and HIV-2 surface glycoproteins contain proteolytic cleavage sites: a possible function in the viral fusion? AIDS Res. Hum. Retroviruses 71, 3-16.
12. + cells, Science 262, 2045-2050.
13. Crippen, G. M. & Havel, T. F. (1988) Distance geometry and molecular conformation, Research Studies Press Ltd., Somerset, England, John Wiley, New York.
14. 1H nuclear magnetic resonance study of AaHIT, an anti-insect toxin from the scorpion Androctonus australis Hector. Sequential resonance assignments and folding of the polypeptide chain, Biochemistry 30, 1836-1845.
15. Dietrich, U., Adamski, M., Kreutz, R., Seipp, A., Kühnel, H. & Rübsamen-Waigmann, H. (1989) A highly divergent HIV-2-related isolate, Nature 342, 948-950.
16. de Wolf, F., Meloen, F. H., Bakker, M., Barin, F. & Goudsmit, J. (1991) Characterization of human antibody-binding sites on the external envelope of human immunodeficiency virus type 2, J. Gen. Virol. 72, 1261-1267.
17. Dyson, H. J., Cross, K. J., Houghten, R. A., Wilson, I. A., Wright, P. E. & Lerner, R. A. (1985) The immunodominant site of a synthetic immunogen has a conformational preference in water for a type-II reverse turn, Nature 318, 480-483.
18. Dyson, H. J., Rance, M., Houghten, R. A., Lerner, R. A. & Wright, P. E. (1988a) Folding of immunogenic peptide fragments of proteins in water solution, J. Mol. Biol. 201, 161-200.
19. Dyson, H. J., Rance, M., Houghten, R. A., Wright, P. E. & Lerner, R. A. (1988b) Folding of immunogenic peptide fragments of proteins in water solution, J. Mol. Biol. 201, 201-217.
20. Dyson, H. J., Lerner, R. A. & Wright, P. E. (1988c) The physical basis for induction of protein-reactive antipeptide antibodies, Annu. Rev. Biophys. Biophys. Chem. 17, 305-324.
21. Dyson, H. J. & Wright, P. E. (1991) Defining solution conformations of small linear peptides, Annu. Rev. Biophys. Biophys. Chem. 20, 519-538.
22. Feizi, T. & Larkin, M. (1990) AIDS and glycosylation, Glycobiology 1, 17-23.
23. Fields, G. B. & Noble, R. L. (1990) Solid phase peptide synthesis utilizing 9-fluorenylmethoxycarbonyl amino acids, Int. J. Peptide Protein Res. 35, 161-214.
24. Gehring, S. (1995) M. D.thesis, University of Frankfurt.
25. Geyer, H., Holschbach, C., Hunsmann, G. & Schneider, J. (1988) Carbohydrates of human immunodeficiency virus, J. Biol. Chem. 263, 11 760-11 767.
26. Ghiara, J. B., Stura, E. A., Stanfield, R. L., Profy, A. T. & Wilson, I. A. (1994) Crystal structure of the principal neutralisation site of HIV-1, Science 264, 82-85.
27. Goudsmit, J., Debouck, C., Meloen, R. H., Smit, L., Bakker, M., Asher, D. M., Wolff, A. V., Gibbs, C. J. Jr & Gajdusek, D. C. (1988) Human immunodeficiency virus type 1 neutralisation epitope with conserved architecture elicts early type-specific antibodies in experimentally infected chimpanzees, Proc. Natl Acad. Sci. USA 85, 4478-4482.
28. Griesinger, C., Sørensen, O. W. & Ernst, R. R. (1986) Correlation of connected transitions by two-dimensional NMR spectroscopy, J. Chem. Phys. 85, 6837.
29. Grez, M., Dietrich, U., Balfe, P., von Briesen, H., Maniar, J. K., Malianbre, G., Delwart, E. L., Mullins, J. I. & Rübsamen-Waigmann, H. (1994) Genetic analysis of HIV-1/HIV-2 mixed infection in India reveals a recent spread of HIV-1 and HIV-2 from a single ancestor for each of these viruses, J. Virol. 68, 2161-2168.
30. Gubta, G., Anantharamaiah, G. M., Scott, D. R., Eldridge, J. H. & Myers, G. (1993) Solution structure of the V3 loop of a Thailand HIV isolate, J. Biomol. Struct. & Dyn. 11, 2 345-366.
31. Havel, T. F. (1986) DISGEO, Quantum Chemistry Exchange Program, Exchange no. 507, Indiana University.
32. Havel, T. F. (1990) The sampling properties of some distance geometry algorithms applied to unconstrained polypeptide chains: A study of 1830 independently computed conformations, Biopolymers 29, 1565-1585.
33. Havel, T. F. (1991) An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance, Prog. Biophys. Molec. Biol. 56, 43-78.
34. Hore, P. J. (1989) Solvent supression, Methods Enzymol. 176, 64-77.
35. Janssens, W., Heyndrickx, L., Fransen, K., Motte, J., Peeters, M., Nkengasong, J. N., Ndumbe, P. M., Delaporte, E., Perret, J.-L., Atende, C., Piot, P. & van der Groen, G. (1994) Genetic and phylogenetic analysis of env subtypes G and H in Central Africa, AIDS Res. Hum. Retroviruses 10, 877-879.
36. Javaherian, K., Langlois, A. J., McDanal, C., Ross, K. L., Eckler, L. I., Jellis, C. L., Profy, A. T., Rusche, J. R., Bolognesi, D. P., Putney, S. D. & Matthews, T. J. (1989) Principal neutralising domain of the human immunodeficiency virus type 1 envelope protein, Proc. Natl Acad. Sci. USA 86, 6768-6772.
37. Jeener, J., Meier, B. H., Bachmann, P. & Ernst, R. R. (1979) Investigation of exchange processes by two-dimensional NMR spectroscopy, J. Chem. Phys. 71, 4546-4553.
38. Johnson, W. C. Jr (1988) Secondary structure of proteins through circular dichroism spectroscopy, Annu. Rev. Biophys. Biophys. Chem. 17, 145-166.
39. Johnson, W. C. Jr (1990) Protein secondary structure and circular dichroism: a practical guide, Proteins Struct. Funct. Genet. 7, 205-214.
40. Jones, I. M., Morikawa, Y., Fenouillet, E. & Moore, J. P. (1992) Antigenicity of the HIV-2 V3 loop, AIDS 6, 888-889.
41. Kaptein, R., Boelens, R., Scheek, R. M. & van Gunsteren, W. F. (1988) Protein structures from NMR, Biochemistry 27, 5389-5395.
42. Karplus, M. (1959) Contact electron-spin coupling of nuclear magnetic moments, J. Chem. Phys. 30, 11-15.
43. 1H-nuclear magnetic resonance spectroscopy in peptides related to the N terminus of the bovine pancreatic trypsin inhibitor, J. Mol. Biol. 230, 312-322.
44. King, D. S., Fields, C. G. & Fields, G. B. (1990) A cleavage method which minimizes side reactions following Fmoc solid phase peptide synthesis, Int. J. Peptide Protein Res. 36, 255-265.
45. Knorr, R., Trzeciak, A., Bannwarth, W. & Gillessen, D. (1989) New coupling reagents in peptide chemistry, Tetrahedron Lett. 30, 1927-1930.
46. Kühnel, H., von Briesen, H., Dietrich, U., Adamski, M., Mix, D., Biesert, L., Kreutz, R., Immelmann, A., Henco, K., Meichsner, C., Andreesen, R., Gelderbloom, H. & Rübsamen-Waigmann, H. (1989) Molecular cloning of two West African human immunodeficiency virus type 2 isolates that replicate well in macrophages: a Gambian isolate, from a patient with neurologic acquired immunodeficiency syndrome, and a highly divergent Ghanian isolate, Proc. Natl Acad. Sci. USA 86, 2383-2387.
47. Laczko, I., Hollosi, M., Urge, L., Ugen, K. E., Weiner, D. B., Mantsch, H. H., Thurin, J. & Otvos, L. (1992) Synthesis and conformational studies of N-glycosylated analogues of the HIV-1 principal neutralizing determinant, Biochemistry 31, 4282-4288.
48. LaRosa, G. J., Davide, J. P., Weinhold, K., Waterbury, J. A., Profy, A. T., Lewis, J. A., Langlois, A. J., Dreesman, G. R., Boswell, R. N., Shadduck, P., Holley, L. H., Karplus, M., Bolognesi, D. P., Matthews, T. J., Emini, E. A. & Putney, S. D. (1990) Conserved sequence and structural elements in the HIV-1 principal neutralizing determinant, Science 249, 932-935.
49. Lee, K. K., Black, J. A. & Hodges, R. S. (1989) Air oxidation of peptides and separation of their reduced and intra-chain disulfide-bridged forms by RPHPLC, Peptides 1990, 999-1002.
50. Lee, K. K., Black, J. A. & Hodges, R. S. (1991) High performance liquid chromatography of peptides and proteins: separation, analysis and conformation (Mant, C. T. & Hodges, R. S., eds) pp. 389-398, CRC Press.
51. Leonard, C. K., Spellman, M. W., Riddle, L., Harris, R. J., Thomas, J. N. & Gregory, T. J. (1990) Assignment of intrachain disulfide bonds and characterisation of potential glycosylation sites of the type 1 recombinant human immunodeficiency virus envelope glycoprotein (gp120) expressed in Chinese hamster ovary cells, J. Biol. Chem. 265, 10 373-10 382.
52. Lewis, P. N., Momany, F. A. & Scheraga, H. A. (1973) Chain reversals in proteins, Biochim. Biophys. Acta 303, 211-229.
53. Liedtke, S., Adamski, M., Geyer, R., Pfützner, A., Rübsamen-Waigmann, H. & Geyer, H. (1994) Oligosaccharide profiles of HIV-2 external envelope glycoprotein: dependence on host cells and virus isolates, Glycobiology 4, 477-484
54. Louwagie, J., Delwart, E. L., Mullins, J. I., McCutchan, F. E., Eddy, G. & Burke, D. S. (1994) Genetic analysis of HIV-1 isolates from Brazil reveals presence of two distinct genetic subtypes, AIDS Res. Hum. Retroviruses 10, 561-567.
55. Marion, D. & Bax, A. (1988) P. COSY, a sensitive alternative for double-quantum-filtered COSY, J. Magn. Reson. 80, 528-533.
56. Markert, R., Schreiber, A., Eggenberger, U., Lichte, E. & Griesinger, C. (1992) Synthesis, conformational and ELISA study of the immunodominant region of the HIV-1 and HIV-2 glycoprotein gp120, in Peptides (Schneider, C. H. & Eberle, A. N., eds) pp. 567-568, Escom, Leiden.
57. Markert, R. L. M. (1994) Ph. D. thesis, University of Frankfurt.
58. 2, J. Mol. Struct. 107, 181-198
59. McInnes, C., Sönnichsen, F. D., Kay, C. M., Hodges, R. S. & Sykes, B. D. (1993) NMR solution structure and flexibility of a peptide antigen representing the receptor binding domain of Pseudomonas aeruginosa, Biochemistry 32, 13 432-13 440.
60. Moore, J. P. & Nara, P. L. (1991) The role of the V3 loop of gp120 in HIV infection, AIDS 5, 21-33.
61. Müller, L. (1987) P. E. COSY, a simple alternative to E. COSY, J. Magn. Reson. 72, 191-197.
62. Myers, G., Wain-Hobson, S., Korber, B., Smith, R. F. & Pavlakis, G. N. (1993) Human retroviruses and AIDS, a compilation of nucleic acid and amino acid sequences, Los Alamos National Laboratory, New Mexico.
63. Mierke, D. F., Geyer, A. & Kessler, H. (1994a) Coupling constants and hydrogen bonds as experimental restraints in a distance geometry refinement protocol, Int. J. Peptide Protein Res. 44, 325-331.
64. Mierke, D. F., Scheek, R. M. & Kessler, H. (1994b) Coupling constants as restraints in ensemble distance driven dynamics, Biopolymers 34, 559-563.
65. Mizuochi, T., Spellman, M. W., Larkin, M., Solomon, J., Basa, L. J. & Feizi, T. (1988) Carbohydrate structures of the human-immunodeficiency-virus (HIV) recombinant envelope glycoprotein gp120 produced in Chinese-hamster ovary cells, Biochem J. 254, 599-603.
66. Mizuochi, T., Matthews, T. J., Kato, M., Hamako, J., Titani, K., Solomon, J. & Feizi, T. (1990) Diversity of oligosaccharide structures on the envelope glycoprotein gp120 of human immunodeficiency virus 1 from the lymphoblastoid cell line H, J. Biol. Chem. 265, 8519-8524.
67. Osmanov, S., Hyward, W. L. & Esparza, J. (1994) The World Health Organization network for HIV isolation and characterization: summary of pilot study, AIDS Res. Hum. Retroviruses 10, 1325-1326.
68. Otvos, L. Jr, Wroblewski, K., Kollat, E., Perczel, A., Hollosi, M., Fasman, G. D., Ertl, H. C. J. & Thurin, J. (1989) Coupling strategies in solid-phase synthesis of glycopeptides, Peptide Res. 2, 362-366.
69. Otvos, L. Jr, Urge, L., Hollosi, M., Wroblewski, K., Graczyk, G., Fasman, G. D. & Thurin, J. (1990) Automated solid-phase synthesis of glycopeptides. Incorporation of unprotected mono- and disaccharide units of N-glycoprotein antennae into T cell epitopic peptides, Tetrahedron Lett. 41, 5889-5892.
70. Ou, C.-Y., Takebe, Y., Weniger, B. G., Luo, C.-C., Kalish, M. L., Auwanit, W., Yamazaki, S., Gayle, H., Young, N. L. & Schochetman, G. (1993) Independent introduction of two major HIV-1 genotypes into distinct high-risk populations in Thailand, The Lancet 341, 1171-1174.
71. HN/α in a globular protein, J. Mol. Biol. 180, 741-751.
72. Perczel, A., Kajtar, M., Marcoccia, J.-F. & Csizmadia, I. G. (1991a) The utility of the four-dimensional Ramachandran map for the description of peptide conformations, J. Mol. Struct. 232, 291-319.
73. Perczel, A., Angyan, J. G., Kajtar, M., Viviani, W., Rivail, J.-L., Marcoccia, J.-F. & Csizmadia, I. G. (1991b) Peptide models.1. Topology of selected peptide conformational potential energy surfaces (glycine and alanine derivatives), J. Am. Chem. Soc. 113, 6256-6265.
74. Perczel, A., McAllister, M. A., Császár, P. & Csizmadia, I. G. (1993) New β-turn conformations from ab initio calculations confirmed by X-ray data of proteins, J. Am. Chem. Soc. 115, 4849-4858.
75. Profy, A. T. (1992) Structural basis for antibody recognition of the HIV-1 V3 determinant, Septieme Colloque des Cent Gardes, 123-127.
76. 1H NMR spectra of proteins via double quantum filtering, Biochem. Biophys. Res. Commun. 117, 479-485.
77. Richardson, J. S. (1981) The anatomy and taxonomy of protein structure, Adv. Protein Chem. 34, 167-339.
78. Rini, J. M. (1993) Crystal structure of a human immunodeficiency virus type 1 neutralizing antibody, 50. 1, in complex with its V3 loop peptide antigen, Proc. Natl Acad. Sci. USA 90, 6325-6329.
79. Roberts, G. C. K. (1993) NMR of macromolecules, Chapter 2, Oxford University Press.
80. Rose, G. D., Gierasch, L. M. & Smith, J. A. (1985) Turns in peptides and proteins, Adv. Protein Chem. 37, 1-109.
81. Ruppach, H., Gehring, S., Markert, R., Gerte, S., Brede, H. D., von Briesen, H., Griesinger, C., Rübsamen-Waigmann, H. & Dietrich, U. (1994) Poster contribution at Tagung d. Gesellschaft für Virologie, Frankfurt.
82. 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., Bolognesi, D. P., Putney, S. D. & Matthews, T. J. (1988) Antibodies that inhibit fusion of human immunodeficiency virus-infected cells bind a 24-amino acid sequence of the viral envelope, gp120, Proc. Natl Acad. Sci. USA 85, 3198-3202.
83. Ryckaert, J. P., Ciccotti, G. & Berendsen, H. J. C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints. Molecular dynamics of n-alkanes, J. Comput. Phys. 23, 327-341.
84. Scheek, R. M., van Gunsteren, W. F. & Kaptein, R. (1989) Molecular dynamics simulation techniques for determination of molecular structures from nuclear magnetic resonance data, Methods Enzymol. 177, 204-218.
85. Scheck, R. M., Torda, A. E., Kenmink, J. & van Gunsteren, W. F. (1991) Structure determination by NMR: the modeling of NMR parameters as ensemble averages, in Computational aspects of the study of biological macromolecules by nuclear magnetic resonance spectroscopy (Hoch, J. C., ed.) pp. 209-217, Plenum Press, New York.
86. Schreiber, A. (1991) Diploma thesis, University of Frankfurt.
87. Shioda, T., Levy, J. A. & Cheng-Mayer, C. (1992) Small amino acid changes in the V3 hypervariable region of gp120 can effect T-cell-line and macrophage tropism of human immundeficiency virus 1, Proc. Natl Acad. Sci. USA 89, 9434-9438.
88. Stanfield, R. L., Takimoto-Kamimura, M., Rini, J. M., Profy, A. T. & Wilson, I. A. (1993) Major antigen-induced domain rearrangements in an antibody, Structure 1, 83-93.
89. Stura, E. A., Stanfield, R. L., Fieser, G. G., Silver, S., Roguska, M., Hincapie, L. M., Simmerman, H. K. B., Profy A. T. & Wilson, I. A. (1992) Crystallisation, sequence, and preliminary crystallographic data for an antipeptide Fab 50.1 and peptide complexes with the principal neutralizing determinant of HIV-1 gp120, Proteins Struct. Funct. Genet. 14, 499-508.
90. Titman, J. J. & Keeler, J. (1990) Measurement of homonuclear coupling constants from NMR correlation spectra, J. Magn. Reson. 89, 640-646.
91. Tolle, T., Petry, H., Bachmann, B., Hunsmann, G. & Lueke, W. (1994) Variability of the env gene in cynomolgus macaques persistently infected with human immunodeficiency virus type 2 strain ben, J. Virol. 68, 2765-2771.
92. Urge, L., Corbics, L. & Otvos, L. Jr (1992) Chemical glycosylation of peptide T at natural and artificial glycosylation sites stabilizes or rearranges the dominant reverse turn structure, Biochem. Biophys. Res. Commun. 184, 1125-1132.
93. Vranken, W., Budesinsky, M., Fant, F., Boulez, K. & Borremans, F. (1994) Conformational preferences of HIV-1 V3 loop derived peptides, poster contribution (W104) EENC, Finland.
94. Wilmot, C. M. & Thornton, J. M. (1988) Analysis and prediction of the different types of β-turn in proteins, J. Mol. Biol. 203, 221-232.
95. Wilmot, C. M. & Thornton, J. M. (1990) β-Turns and their distortions: a proposed new nomenclature, Protein Eng. 3, 479-493.
96. Wishart, D. S., Sykes, B. D. & Richards, F. M. (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure, J. Mol. Biol. 222, 311-333.
97. Wüthrich, K. (1986) NMR of proteins and nucleic acids, Wiley, New York.
98. IIIB: a two-dimensional NMR study, Biochemistry 31, 6972-6979.