Structural basis for HIV-1 neutralization by a gp41 fusion intermediate–directed antibody (original) (raw)

• Burton, D.R. et al. HIV vaccine design and the neutralizing antibody problem. Nat. Immunol. 5, 233–236 (2004).
  Article CAS PubMed Google Scholar
• Wyatt, R. & Sodroski, J. The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens. Science 280, 1884–1888 (1998).
  Article CAS PubMed Google Scholar
• Wei, X. et al. Antibody neutralization and escape by HIV-1. Nature 422, 307–312 (2003).
  Article CAS PubMed Google Scholar
• 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 PubMed Google Scholar
• Poignard, P., Saphire, E.O., Parren, P.W. & Burton, D.R. gp120: biologic aspects of structural features. Annu. Rev. Immunol. 19, 253–274 (2001).
  Article CAS PubMed Google Scholar
• Zwick, M.B., Saphire, E.O. & Burton, D.R. gp41: HIV's shy protein. Nat. Med. 10, 133–134 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Burton, D.R., Stanfield, R.L. & Wilson, I.A. Antibody vs. HIV in a clash of evolutionary titans. Proc. Natl. Acad. Sci. USA 102, 14943–14948 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Calarese, D.A. et al. Antibody domain exchange is an immunological solution to carbohydrate cluster recognition. Science 300, 2065–2071 (2003).
  Article CAS PubMed Google Scholar
• Saphire, E.O. et al. Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design. Science 293, 1155–1159 (2001).
  Article CAS PubMed Google Scholar
• Stanfield, R.L., Gorny, M.K., Williams, C., Zolla-Pazner, S. & Wilson, I.A. Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447–52D. Structure 12, 193–204 (2004).
  Article CAS PubMed Google Scholar
• Thali, M. et al. Characterization of conserved human immunodeficiency virus type 1 gp120 neutralization epitopes exposed upon gp120–CD4 binding. J. Virol. 67, 3978–3988 (1993).
  CAS PubMed PubMed Central Google Scholar
• Labrijn, A.F. et al. Access of antibody molecules to the conserved coreceptor binding site on glycoprotein gp120 is sterically restricted on primary human immunodeficiency virus type 1. J. Virol. 77, 10557–10565 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Conley, A.J. et al. Neutralization of divergent human immunodeficiency virus type 1 variants and primary isolates by IAM-41–2F5, an anti-gp41 human monoclonal antibody. Proc. Natl. Acad. Sci. USA 91, 3348–3352 (1994).
  Article CAS PubMed PubMed Central Google Scholar
• 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 PubMed PubMed Central Google Scholar
• Zwick, M.B. et al. The long third complementarity-determining region of the heavy chain is important in the activity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5. J. Virol. 78, 3155–3161 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Baba, T.W. et al. Human neutralizing monoclonal antibodies of the IgG1 subtype protect against mucosal simian-human immunodeficiency virus infection. Nat. Med. 6, 200–206 (2000).
  Article CAS PubMed Google Scholar
• Mascola, J.R. et al. Protection of macaques against vaginal transmission of a pathogenic HIV-1/SIV chimeric virus by passive infusion of neutralizing antibodies. Nat. Med. 6, 207–210 (2000).
  Article CAS PubMed Google Scholar
• Veazey, R.S. et al. Prevention of virus transmission to macaque monkeys by a vaginally applied monoclonal antibody to HIV-1 gp120. Nat. Med. 9, 343–346 (2003).
  Article CAS PubMed Google Scholar
• Mascola, J.R. et al. Protection of macaques against pathogenic simian/human immunodeficiency virus 89.6PD by passive transfer of neutralizing antibodies. J. Virol. 73, 4009–4018 (1999).
  CAS PubMed PubMed Central Google Scholar
• Trkola, A. et al. Delay of HIV-1 rebound after cessation of antiretroviral therapy through passive transfer of human neutralizing antibodies. Nat. Med. 11, 615–622 (2005).
  Article CAS PubMed Google Scholar
• Tan, K., Liu, J., Wang, J., Shen, S. & Lu, M. Atomic structure of a thermostable subdomain of HIV-1 gp41. Proc. Natl. Acad. Sci. USA 94, 12303–12308 (1997).
  Article CAS PubMed PubMed Central Google Scholar
• 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 PubMed Google Scholar
• 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 PubMed Google Scholar
• Furuta, R.A., Wild, C.T., Weng, Y. & Weiss, C.D. Capture of an early fusion-active conformation of HIV-1 gp41. Nat. Struct. Biol. 5, 276–279 (1998).
  Article CAS PubMed Google Scholar
• 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 PubMed PubMed Central Google Scholar
• Ferrer, M. et al. Selection of gp41-mediated HIV-1 cell entry inhibitors from biased combinatorial libraries of non-natural binding elements. Nat. Struct. Biol. 6, 953–960 (1999).
  Article CAS PubMed Google Scholar
• Eckert, D.M., Malashkevich, V.N., Hong, L.H., Carr, P.A. & Kim, P.S. Inhibiting HIV-1 entry: discovery of D-peptide inhibitors that target the gp41 coiled-coil pocket. Cell 99, 103–115 (1999).
  Article CAS PubMed Google Scholar
• Lalezari, J.P. et al. Enfuvirtide, an HIV-1 fusion inhibitor, for drug-resistant HIV infection in North and South America. N. Engl. J. Med. 348, 2175–2185 (2003).
  Article CAS PubMed Google Scholar
• Sanders, R.W., Korber, B., Lu, M., Berkhout, B. & Moore, J.P. Mutational analyses and natural variability of the gp41 ectodomain. in HIV Sequence Compendium (eds. Kuiken C. et al.) 43–68 (Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA, 2002).
• Hamburger, A.E., Kim, S., Welch, B.D. & Kay, M.S. Steric accessibility of the HIV-1 gp41 N-trimer region. J. Biol. Chem. 280, 12567–12572 (2005).
  Article CAS PubMed Google Scholar
• Louis, J.M., Nesheiwat, I., Chang, L., Clore, G.M. & Bewley, C.A. Covalent trimers of the internal N-terminal trimeric coiled-coil of gp41 and antibodies directed against them are potent inhibitors of HIV envelope-mediated cell fusion. J. Biol. Chem. 278, 20278–20285 (2003).
  Article CAS PubMed Google Scholar
• Miller, M.D. et al. A human monoclonal antibody neutralizes diverse HIV-1 isolates by binding a critical gp41 epitope. Proc. Natl. Acad. Sci. USA 102, 14759–14764 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Root, M.J., Kay, M.S. & Kim, P.S. Protein design of an HIV-1 entry inhibitor. Science 291, 884–888 (2001).
  Article CAS PubMed Google Scholar
• Eckert, D.M. & Kim, P.S. Design of potent inhibitors of HIV-1 entry from the gp41 N-peptide region. Proc. Natl. Acad. Sci. USA 98, 11187–11192 (2001).
  Article CAS PubMed PubMed Central Google Scholar
• Al-Lazikani, B., Lesk, A.M. & Chothia, C. Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol. 273, 927–948 (1997).
  Article CAS PubMed Google Scholar
• Sundberg, E.J. & Mariuzza, R.A. Molecular recognition in antibody-antigen complexes. Adv. Protein Chem. 61, 119–160 (2002).
  Article PubMed Google Scholar
• Lawrence, M.C. & Colman, P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946–950 (1993).
  Article CAS PubMed Google Scholar
• Davies, D.R. & Cohen, G.H. Interactions of protein antigens with antibodies. Proc. Natl. Acad. Sci. USA 93, 7–12 (1996).
  Article CAS PubMed PubMed Central Google Scholar
• Zhou, G. et al. The structure of an HIV-1 specific cell entry inhibitor in complex with the HIV-1 gp41 trimeric core. Bioorg. Med. Chem. 8, 2219–2227 (2000).
  Article CAS PubMed Google Scholar
• Huang, C.C. et al. Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120. Proc. Natl. Acad. Sci. USA 101, 2706–2711 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Yang, X., Kurteva, S., Lee, S. & Sodroski, J. Stoichiometry of antibody neutralization of human immunodeficiency virus type 1. J. Virol. 79, 3500–3508 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, M.Y. et al. Identification and characterization of a new cross-reactive human immunodeficiency virus type 1-neutralizing human monoclonal antibody. J. Virol. 78, 9233–9242 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Munoz-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 CAS PubMed PubMed Central Google Scholar
• Selzer, T., Albeck, S. & Schreiber, G. Rational design of faster associating and tighter binding protein complexes. Nat. Struct. Biol. 7, 537–541 (2000).
  Article CAS PubMed Google Scholar
• MacCallum, R.M., Martin, A.C. & Thornton, J.M. Antibody-antigen interactions: contact analysis and binding site topography. J. Mol. Biol. 262, 732–745 (1996).
  Article CAS PubMed Google Scholar
• Lobo, E.D., Hansen, R.J. & Balthasar, J.P. Antibody pharmacokinetics and pharmacodynamics. J. Pharm. Sci. 93, 2645–2668 (2004).
  Article CAS PubMed Google Scholar
• Li, A. et al. Synergistic neutralization of a chimeric SIV/HIV type 1 virus with combinations of human anti-HIV type 1 envelope monoclonal antibodies or hyperimmune globulins. AIDS Res. Hum. Retroviruses 13, 647–656 (1997).
  Article CAS PubMed Google Scholar
• Bianchi, E. et al. Covalent stabilization of coiled coils of the HIV gp41 N region yields extremely potent and broad inhibitors of viral infection. Proc. Natl. Acad. Sci. USA 102, 12903–12908 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).
• Perrakis, A., Morris, R. & Lamzin, V.S. Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458–463 (1999).
  Article CAS PubMed Google Scholar