Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Distinct conformational states of HIV-1 gp41 are recognized by neutralizing and non-neutralizing antibodies

Nature Structural & Molecular Biology volume 17, pages 1486–1491 (2010)Cite this article

Subjects

Abstract

HIV-1 envelope glycoprotein gp41 undergoes large conformational changes to drive fusion of viral and target cell membranes, adopting at least three distinct conformations during the viral entry process. Neutralizing antibodies against gp41 block HIV-1 infection by targeting gp41′s membrane-proximal external region in a fusion-intermediate state. Here we report biochemical and structural evidence that non-neutralizing antibodies, capable of binding with high affinity to an immunodominant segment adjacent to the neutralizing epitopes in the membrane-proximal region, recognize a gp41 conformation that exists only when membrane fusion is complete. We propose that these non-neutralizing antibodies are induced in HIV-1–infected individuals by gp41 in a triggered, postfusion form and contribute to production of ineffective humoral responses. These results have important implications for gp41-based vaccine design.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: HIV-1 envelope constructs and GCN4-gp41-inter.
Figure 2: HIV-1 gp41 cluster II antibodies preferentially bind gp41 in its postfusion conformation.
Figure 3: Analysis of interactions of 1281 Fab with various gp41 constructs.
Figure 4: Crystal structure of the complex of gp41-post and the Fab fragment of cluster II antibody 1281.
Figure 5: Close-up of major contacts between gp41 and 1281 Fab.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Referenced accessions

Protein Data Bank

References

  1. Harrison, S.C. Viral membrane fusion. Nat. Struct. Mol. Biol. 15, 690–698 (2008).

    Article  CAS  Google Scholar 

  2. Wyatt, R. & Sodroski, J. The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens. Science 280, 1884–1888 (1998).

    Article  CAS  Google Scholar 

  3. Allan, J.S. et al. Major glycoprotein antigens that induce antibodies in AIDS patients are encoded by HTLV-III. Science 228, 1091–1094 (1985).

    Article  CAS  Google Scholar 

  4. Veronese, F.D. et al. Characterization of gp41 as the transmembrane protein coded by the HTLV-III/LAV envelope gene. Science 229, 1402–1405 (1985).

    Article  CAS  Google Scholar 

  5. Harrison, S.C. Mechanism of membrane fusion by viral envelope proteins. Adv. Virus Res. 64, 231–261 (2005).

    Article  CAS  Google Scholar 

  6. Chan, D.C. & Kim, P.S. HIV entry and its inhibition. Cell 93, 681–684 (1998).

    Article  CAS  Google Scholar 

  7. Kilby, J.M. & Eron, J.J. Novel therapies based on mechanisms of HIV-1 cell entry. N. Engl. J. Med. 348, 2228–2238 (2003).

    Article  CAS  Google Scholar 

  8. Wild, C., Oas, T., McDanal, C., Bolognesi, D. & Matthews, T. A synthetic peptide inhibitor of human immunodeficiency virus replication: correlation between solution structure and viral inhibition. Proc. Natl. Acad. Sci. USA 89, 10537–10541 (1992).

    Article  CAS  Google Scholar 

  9. Frey, G. et al. A fusion-intermediate state of HIV-1 gp41 targeted by broadly neutralizing antibodies. Proc. Natl. Acad. Sci. USA 105, 3739–3744 (2008).

    Article  CAS  Google Scholar 

  10. Chan, D.C., Fass, D., Berger, J.M. & Kim, P.S. Core structure of gp41 from the HIV envelope glycoprotein. Cell 89, 263–273 (1997).

    Article  CAS  Google Scholar 

  11. Weissenhorn, W., Dessen, A., Harrison, S.C., Skehel, J.J. & Wiley, D.C. Atomic structure of the ectodomain from HIV-1 gp41. Nature 387, 426–430 (1997).

    Article  CAS  Google Scholar 

  12. Richman, D.D., Wrin, T., Little, S.J. & Petropoulos, C.J. Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc. Natl. Acad. Sci. USA 100, 4144–4149 (2003).

    Article  CAS  Google Scholar 

  13. Kwong, P.D. et al. HIV-1 evades antibody-mediated neutralization through conformational masking of receptor-binding sites. Nature 420, 678–682 (2002).

    Article  CAS  Google Scholar 

  14. Wei, X. et al. Antibody neutralization and escape by HIV-1. Nature 422, 307–312 (2003).

    Article  CAS  Google Scholar 

  15. Stamatatos, L., Morris, L., Burton, D.R. & Mascola, J.R. Neutralizing antibodies generated during natural HIV-1 infection: good news for an HIV-1 vaccine? Nat. Med. 15, 866–870 (2009).

    Article  CAS  Google Scholar 

  16. Wu, X. et al. Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science 329, 856–861 (2010).

    Article  CAS  Google Scholar 

  17. Zhou, T. et al. Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Science 329, 811–817 (2010).

    Article  CAS  Google Scholar 

  18. Walker, L.M. et al. Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target. Science 326, 285–289 (2009).

    Article  CAS  Google Scholar 

  19. Trkola, A. et al. Human monoclonal antibody 2G12 defines a distinctive neutralization epitope on the gp120 glycoprotein of human immunodeficiency virus type 1. J. Virol. 70, 1100–1108 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Burton, D.R. et al. Efficient neutralization of primary isolates of HIV-1 by a recombinant human monoclonal antibody. Science 266, 1024–1027 (1994).

    Article  CAS  Google Scholar 

  21. Hioe, C.E. et al. Anti-V3 monoclonal antibodies display broad neutralizing activities against multiple HIV-1 subtypes. PLoS ONE 5, e10254 (2010).

    Article  Google Scholar 

  22. Zolla-Pazner, S. & Cardozo, T. Structure-function relationships of HIV-1 envelope sequence-variable regions refocus vaccine design. Nat. Rev. Immunol. 10, 527–535 (2010).

    Article  CAS  Google Scholar 

  23. Stiegler, G. et al. A potent cross-clade neutralizing human monoclonal antibody against a novel epitope on gp41 of human immunodeficiency virus type 1. AIDS Res. Hum. Retroviruses 17, 1757–1765 (2001).

    Article  CAS  Google Scholar 

  24. Muster, T. et al. A conserved neutralizing epitope on gp41 of human immunodeficiency virus type 1. J. Virol. 67, 6642–6647 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Zwick, M.B. et al. Broadly neutralizing antibodies targeted to the membrane-proximal external region of human immunodeficiency virus type 1 glycoprotein gp41. J. Virol. 75, 10892–10905 (2001).

    Article  CAS  Google Scholar 

  26. Alam, S.M. et al. Role of HIV membrane in neutralization by two broadly neutralizing antibodies. Proc. Natl. Acad. Sci. USA 106, 20234–20239 (2009).

    Article  CAS  Google Scholar 

  27. Xu, J.Y., Gorny, M.K., Palker, T., Karwowska, S. & Zolla-Pazner, S. Epitope mapping of two immunodominant domains of gp41, the transmembrane protein of human immunodeficiency virus type 1, using ten human monoclonal antibodies. J. Virol. 65, 4832–4838 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Hioe, C.E. et al. Neutralization of HIV-1 primary isolates by polyclonal and monoclonal human antibodies. Int. Immunol. 9, 1281–1290 (1997).

    Article  CAS  Google Scholar 

  29. Holl, V. et al. Nonneutralizing antibodies are able to inhibit human immunodeficiency virus type 1 replication in macrophages and immature dendritic cells. J. Virol. 80, 6177–6181 (2006).

    Article  CAS  Google Scholar 

  30. Gorny, M.K., Gianakakos, V., Sharpe, S. & Zolla-Pazner, S. Generation of human monoclonal antibodies to human immunodeficiency virus. Proc. Natl. Acad. Sci. USA 86, 1624–1628 (1989).

    Article  CAS  Google Scholar 

  31. Gorny, M.K., VanCott, T.C., Williams, C., Revesz, K. & Zolla-Pazner, S. Effects of oligomerization on the epitopes of the human immunodeficiency virus type 1 envelope glycoproteins. Virology 267, 220–228 (2000).

    Article  CAS  Google Scholar 

  32. Pinter, A. et al. Oligomeric structure of gp41, the transmembrane protein of human immunodeficiency virus type 1. J. Virol. 63, 2674–2679 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Gorny, M.K. & Zolla-Pazner, S. Recognition by human monoclonal antibodies of free and complexed peptides representing the prefusogenic and fusogenic forms of human immunodeficiency virus type 1 gp41. J. Virol. 74, 6186–6192 (2000).

    Article  CAS  Google Scholar 

  34. Yuan, W. et al. Oligomer-specific conformations of the human immunodeficiency virus (HIV-1) gp41 envelope glycoprotein ectodomain recognized by human monoclonal antibodies. AIDS Res. Hum. Retroviruses 25, 319–328 (2009).

    Article  CAS  Google Scholar 

  35. Nelson, J.D. et al. An affinity-enhanced neutralizing antibody against the membrane-proximal external region of human immunodeficiency virus type 1 gp41 recognizes an epitope between those of 2F5 and 4E10. J. Virol. 81, 4033–4043 (2007).

    Article  CAS  Google Scholar 

  36. Harbury, P.B., Kim, P.S. & Alber, T. Crystal structure of an isoleucine-zipper trimer. Nature 371, 80–83 (1994).

    Article  CAS  Google Scholar 

  37. Aoki, S.T. et al. Structure of rotavirus outer-layer protein VP7 bound with a neutralizing Fab. Science 324, 1444–1447 (2009).

    Article  CAS  Google Scholar 

  38. Caffrey, M. et al. Three-dimensional solution structure of the 44kDa ectodomain of SIV gp41. EMBO J. 17, 4572–4584 (1998).

    Article  CAS  Google Scholar 

  39. Yang, Z.N. et al. The crystal structure of the SIV gp41 ectodomain at 1.47 A resolution. J. Struct. Biol. 126, 131–144 (1999).

    Article  CAS  Google Scholar 

  40. Ofek, G. et al. Structure and mechanistic analysis of the anti-human immunodeficiency virus type 1 antibody 2F5 in complex with its gp41 epitope. J. Virol. 78, 10724–10737 (2004).

    Article  CAS  Google Scholar 

  41. Pitisuttithum, P. et al. Randomized, double-blind, placebo-controlled efficacy trial of a bivalent recombinant glycoprotein 120 HIV-1 vaccine among injection drug users in Bangkok, Thailand. J. Infect. Dis. 194, 1661–1671 (2006).

    Article  CAS  Google Scholar 

  42. Rerks-Ngarm, S. et al. Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. N. Engl. J. Med. 361, 2209–2220 (2009).

    Article  CAS  Google Scholar 

  43. Nyambi, P.N. et al. Conserved and exposed epitopes on intact, native, primary human immunodeficiency virus type 1 virions of group M. J. Virol. 74, 7096–7107 (2000).

    Article  CAS  Google Scholar 

  44. Schülke, N. et al. Oligomeric and conformational properties of a proteolytically mature, disulfide-stabilized human immunodeficiency virus type 1 gp140 envelope glycoprotein. J. Virol. 76, 7760–7776 (2002).

    Article  Google Scholar 

  45. Muñoz-Barroso, I., Durell, S., Sakaguchi, K., Appella, E. & Blumenthal, R. Dilation of the human immunodeficiency virus-1 envelope glycoprotein fusion pore revealed by the inhibitory action of a synthetic peptide from gp41. J. Cell Biol. 140, 315–323 (1998).

    Article  Google Scholar 

  46. Steger, H.K. & Root, M.J. Kinetic dependence to HIV-1 entry inhibition. J. Biol. Chem. 281, 25813–25821 (2006).

    Article  CAS  Google Scholar 

  47. Moore, P.L. et al. Nature of nonfunctional envelope proteins on the surface of human immunodeficiency virus type 1. J. Virol. 80, 2515–2528 (2006).

    Article  CAS  Google Scholar 

  48. Alsmadi, O. & Tilley, S.A. Antibody-dependent cellular cytotoxicity directed against cells expressing human immunodeficiency virus type 1 envelope of primary or laboratory-adapted strains by human and chimpanzee monoclonal antibodies of different epitope specificities. J. Virol. 72, 286–293 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Tyler, D.S. et al. Identification of sites within gp41 that serve as targets for antibody-dependent cellular cytotoxicity by using human monoclonal antibodies. J. Immunol. 145, 3276–3282 (1990).

    CAS  PubMed  Google Scholar 

  50. Forthal, D.N., Landucci, G., Gorny, M.K., Zolla-Pazner, S. & Robinson, W.E. Jr. Functional activities of 20 human immunodeficiency virus type 1 (HIV-1)-specific human monoclonal antibodies. AIDS Res. Hum. Retroviruses 11, 1095–1099 (1995).

    Article  CAS  Google Scholar 

  51. Pietzsch, J. et al. Anti-gp41 antibodies cloned from HIV-infected patients with broadly neutralizing serologic activity. J. Virol. 84, 5032–5042 (2010).

    Article  CAS  Google Scholar 

  52. Vagin, A. & Teplyakov, A. Molecular replacement with MOLREP. Acta Crystallogr. D Biol. Crystallogr. 66, 22–25 (1997).

    Article  Google Scholar 

  53. McCoy, A.J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).

    Article  CAS  Google Scholar 

  54. Strong, M. et al. Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 103, 8060–8065 (2006).

    Article  CAS  Google Scholar 

  55. Jones, T.A. & Kjeldgaard, M. Electron-density map interpretation. Methods Enzymol. 277, 173–208 (1997).

    Article  CAS  Google Scholar 

  56. Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article  CAS  Google Scholar 

  57. Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  Google Scholar 

  58. Murshudov, G.N. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).

    Article  CAS  Google Scholar 

  59. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

  60. DeLano, W.L. The PyMOL User's Manual (DeLano Scientific, San Carlos, California, USA, 2002).

Download references

Acknowledgements

We thank S. Harrison, H. Peng, A. Carfi, A. Dey, J. Mascola, M. Alam and B.F. Haynes for advice and assistance, and the staff of the Northeastern Collaborative Access Team at Advanced Photon Source, Argonne National Laboratory, for assistance with X-ray data collection. We acknowledge support from US National Institutes of Health grants GM083680 (to B.C.), AI084794 (to B.C. and Dan H. Barouch) and AI36085 (to S.Z.-P.); a Collaboration for AIDS Vaccine Discovery grant (to Barton F. Haynes) from the Bill and Melinda Gates Foundation; the Center for HIV/AIDS Vaccine Immunology (to Barton F. Haynes); and the Department of Veterans Affairs. J.C. is supported by a fellowship from the Ragon Institute of MGH, MIT and Harvard.

Author information

Author notes

  1. Gary Frey and Jia Chen: These authors contributed equally to this work.

Authors and Affiliations

  1. Division of Molecular Medicine, Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA

    Gary Frey, Jia Chen, Sophia Rits-Volloch, Michael M Freeman & Bing Chen

  2. Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA

    Gary Frey, Jia Chen, Sophia Rits-Volloch, Michael M Freeman & Bing Chen

  3. Department of Pathology, New York University School of Medicine, New York, New York, USA

    Susan Zolla-Pazner

  4. New York Veterans Affairs Medical Center, New York, New York, USA

    Susan Zolla-Pazner

Authors
  1. Gary Frey
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jia Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sophia Rits-Volloch
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michael M Freeman
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Susan Zolla-Pazner
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Bing Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

G.F., J.C. and B.C. designed research; G.F., J.C., S.R.-V. and M.M.F. performed the experiments; S.Z.-P. provided antibodies; G.F., J.C., S.R.-V., M.M.F. and B.C. analyzed data; and G.F., J.C., S.Z.-P. and B.C. wrote the manuscript.

Corresponding author

Correspondence to Bing Chen.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Table 1 and Supplementary Methods (PDF 3003 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Frey, G., Chen, J., Rits-Volloch, S. et al. Distinct conformational states of HIV-1 gp41 are recognized by neutralizing and non-neutralizing antibodies. Nat Struct Mol Biol 17, 1486–1491 (2010). https://doi.org/10.1038/nsmb.1950

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1950

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing