Structure-based design of a constrained peptide mimic of the HIV-1 V3 loop neutralization site

Journal of Molecular Biology

Volumn 266, Issue 1, 1997, Pages 31-39

  Ghiara, Jayant B ^a   Ferguson, David C ^a   Satterthwait, Arnold C ^a   Dyson, H Jane ^a   Wilson, Ian A ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Antigenic peptide conformation; Human immunodeficiency virus type 1; NMR; Synthetic vaccines; X ray crystallography; aminoisobutyric acid

Indexed keywords

ALANINE; GLYCOPROTEIN GP 120; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; IMMUNOGLOBULIN F(AB) FRAGMENT; NEUTRALIZING ANTIBODY; SYNTHETIC PEPTIDE; VIRUS PROTEIN;

ANTIGENIC VARIATION; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG DESIGN; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE;

EID: 0031566953     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0768     Document Type: Article

References (48)

1. Alkhatib G., Combadiere C., Broder C. C., Feng Y., Kennedy P. E., Murphy P. M., Berger E. A. CC CKR5: a RANTES, MIP-Iα, MIP-Iβ receptor as a fusion cofactor for macrophage-tropic HIV-1. Science. 272:1996;1955-1958.
2. Baker E. N., Hubbard R. E. Hydrogen bonding in globular proteins. Prog. Biophys. Mol. Biol. 44:1984;97-179.
3. Bax A., Davis D. G. MLEV-17 based two-dimensional homonuclear magnetization transfer spectroscopy. J. Magn. Reson. 65:1985;355-360.
4. Brünger A. T. X-PLOR 3.1: A System for X-Ray Crystallography and NMR. 1992;Yale University Press, New Haven.
5. Cabezas E., Chiang L.-C., Satterthwait A. C. A role for amino acids in the cooperative interactions between an alpha helix nucleation site and appended peptides. Peptides: Chemistry, Structure and Biology. Proceedings of the 13th American Peptide Symposium. 1994;ESCOM, Leiden.
6. Cabezas E., Wang P. L., Satterthwait A. C. Identifying determinants of protein structure with loop peptides. Kaumaya P. T. P., Hodges R. S. Proceedings of the 14th American Peptide Symposium. 1995;Mayflower Scientific Ltd.
7. Chandrasekhar K., Profy A. T., Dyson H. J. Solution conformational preferences of immunogenic peptides derived from the principal neutralizing determinant of the HIV-1 envelope glycoprotein gp120. Biochemistry. 30:1991;9187-9194.
8. Chiang L.-C., Cabezas E., Calvo J. C., Satterthwait A. C. The synthesis of peptide secondary structure mimetics with covalent hydrogen bond mimics on the solid support. Hodges R. S., Smith J. A. Peptides: Chemistry, Structure and Biology. Proceedings of the 13th American Peptide Symposium. 1994;ESCOM, Leiden.
9. Chiengsong-Popov R., Lister S., Callow D., Kaleebu P., Beddows S., Weber J. Serotyping HIV type i by antibody binding to the V3 loop: relationship to viral genotype. AIDS Res. Human Retroviruses. 10:1994;1379-1386.
10. Choe H., Farzan M., Sun Y., Sullivan N., Rollins B., Ponath P. D., Wu L., Mackay C. R., LaRosa G., Newman W., Gerard N., Gerard C., Sodroski J. The β-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell. 85:1996;1135-1148.
11. Coffin J. M. HIV population dynamics in vivo: implications for genetic variation, pathogenesis and therapy. Science. 267:1995;483-489.
12. Conley A. J., Gorny M. K., Kessler J. A., II, Boots L. J., Ossorio-Castro M., Koenig S., Lineberger D. W., Emini E. A., Williams C., Zolla-Pazner S. Neutralization of primary human immunodeficiency virus type 1 isolates by the broadly reactive anti-V3 monoclonal antibody 447-52D. J. Virol. 68:1994;6994-7000.
13. Delaglio F., Grzesiek S., Vuister G. W., Guang Z., Pfeifer J., Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR. 6:1995;277-293.
14. Deng H., Liu R., Ellmeier W., Choe S., Unutmaz D., Burkhart M., Di Marzio P., Marmon S., Sutton R. E., Hill C. M., Davis C. B., Peiper S. C., Schall T. J., Littman D. R., Landau N. R. Identification of a major co-receptor for primary isolates of HIV-1. Nature. 381:1996;661-666.
15. Doranz B. J., Rucker J., Yi Y., Smyth R. J., Samson M., Peiper S. C., Parmentier M., Collman R. G., Doms R. W. A dual-tropic primary HIV-1 isolate that uses fusin and the β-chemokine receptors CKR-5, CKR-3, and CKR-2b as fusion cofactors. Cell. 85:1996;1149-1158.
16. Dragic T., Litwin V., Allaway G. P., Martin S. R., Huang Y., Nagashima K. A., Cayanan C., Maddon P. J., Koup R. A., Moore J. P., Paxton W. A. HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5. Nature. 381:1996;667-673.
17. Dyson H. J., Wright P. E. Defining solution conformations of small linear peptides. Annu. Rev. Biophys. Biophys. Chem. 20:1991;519-538.
18. Dyson H. J., Merutka G., Waltho J. P., Lerner R. A., Wright P. E. Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding I. Myohemerythrin. J. Mol. Biol. 226:1992;795-817.
19. Engh R. A., Huber R. Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Crystallog. sect. A. 47:1991;392-400.
20. Feng Y., Broder C. C., Kennedy P. E., Berger E. A. HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane G-protein coupled receptor. Science. 272:1996;872-877.
21. Ghiara J. B., Stura E. A., Stanfield R. L., Profy A. T., Wilson I. A. Crystal structure of the principal neutralization site of HIV-1. Science. 264:1994;82-85.
22. Jeener J., Meier B. H., Bachmann P., Ernst R. R. Investigation of exchange processes by two-dimensional NMR spectroscopy. J. Chem. Phys. 71:1979;4546-4553.
23. Jones T. A. A graphics model-building and refinement system for macromolecules. J. Appl. Crystallog. 11:1978;268-272.
24. Jones T. A. FRODO: A graphics fitting program for macromolecules. Sayre D. Computational Chemistry. 1982;Clarendon Press, Oxford.
25. Kabat E. A., Wu T. T., Perry H. M., Gottesman K. S., Foeller C. Sequences of Proteins of Immunological Interest. 1991;National Institutes of Health, Bethesda.
26. Karle I. L. Folding, aggregation and molecular recognition in peptides. Acta Crystallog. sect. B. 48:1992;341-356.
27. Karle I. L., Balaram P. Structural characteristics of α-helical peptide molecules containing Aib residues. Biochemistry. 29:1990;6747-6756.
28. LaRosa G. J., Davide J. P., Weinhold K., Waterbury J. A., Profy A. T., Lewis J. A., Langlois A. J., Dressman G. R., Boswell R. N., Shadduck P., Holley L. H., Karplus M., Bolognesi D. P., Matthews T. J., Emini E. A., Putney S. D. Conserved sequence and structural elements in the HIV-1 principal neutralizing domain. Science. 249:1990;932-935.
29. Leslie A. G. W., Brick P., Wonacott A. T. MOSFLM. Daresbury Lab. Inf. Quart. Protein Crystallog. 18:1986). 33-39.
30. Levy J. A. HIV and the Pathogenesis of AIDS. 1994a;ASM Press, Washington, DC.
31. Levy J. A. HIV and the Pathogenesis of AIDS. 1994b;ASM Press, Washington DC.
32. Marion D., Ikura M., Tschudin R., Bax A. Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins. J. Magn. Reson. 85:1989;393-399.
33. Myers G., Berzofsky J. A., Korber B., Smith R. F. Human Retroviruses and AIDS: a Compilation and Analysis of Nucleic Acid and Amino Acid Sequences. 1991;Los ALamos National Laboratory, Los Alamos.
34. Poignard P., Klasse P. J., Sattentau Q. J. Antibody neutralization of HIV-1. Immunol. Today. 17:1996;239-246.
35. Rance M. Improved techniques for homonuclear rotating-frame and isotropic mixing experiments. J. Magn. Reson. 74:1987;557-564.
36. 1H NMR spectra of proteins via double quantum filtering. Biochem. Biophys. Res. Commun. 117:1983;479-485.
37. 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., Ivanoff L., Petteway S. R., Jr, Pearson M. L., Lautenberger J. A., Papas T. S., Ghrayeb G., Chang N. T., Gallo R. C., Wong-Staal F. Complete nucleotide sequence of the AIDS virus, HTLV-III. Nature. 313:1985;277-284.
38. Rini J. M., Stanfield R. L., Stura E. A., Salinas P. A., Profy A. T., Wilson I. A. 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. 90:1993;6325-6329.
39. Rizo J., Gierasch L. M. Constrained peptides: models of bioactive peptides and protein substructures. Annu. Rev. Biochem. 61:1992;387-418.
40. Schnölzer M., Alewood P., Jones A., Alewood D., Kent S. B. H. In situ neutralization in Boc-chemistry solid phase peptide synthesis. Rapid, high yield assembly of difficult sequences. Int. J. Pept. Protein Res. 40:1992;180-193.
41. Sheriff S. Some methods of examining the interactions between two molecules. Immunomethods. 3:1993;191-196.
42. Sheriff S., Hendrickson W. A., Smith J. L. Structure of myohemerythrin in the azidomet state at 1.7/1.3 Å resolution. J. Mol. Biol. 197:1987;273-296.
43. Trkola A., Dragic T., Arthos J., Binley J. M., Olson W. C., Allaway G. P., Cheng-Mayer C., Robinson J., Maddon P. J., Moore J. P. CD4-dependent, antibody-sensitive interactions between HIV-1 and its co-receptor CCR-5. Nature. 384:1996;184-187.
44. White-Scharf M. E., Potts B. J., Smith L. M., Sokolowski K. A., Rusche J. R., Silver S. Broadly neutralizing monoclonal antibodies to the V3 region of HIV-1 can be elicited by peptide immunization. Virology. 192:1993;197-206.
45. Wilmot C. M., Thornton J. M. Analysis and prediction of the different types of β-turn in proteins. J. Mol. Biol. 203:1988;221-232.
46. Wilmot C. M., Thornton J. M. β-Turns and their distortions: a proposed new nomenclature. Protein Eng. 3:1990;479-493.
47. Wu L., Gerard N. P., Wyatt R., Choe H., Parolin C., Ruffing N., Borsetti A., Cardoso A. A., Desjardin E., Newman W., Gerard C., Sodroski J. CD4-induced interaction of primary HIV-1 gp120 glycoproteins with the chemokine receptor CCR-5. Nature. 384:1996;179-183.
48. Wüthrich K. NMR of Proteins and Nucleic Acids. 1986;John Wiley and Sons, New York.