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.

  • Review Article
  • Published:

Breaking the law: unconventional strategies for antibody diversification

Nature Reviews Immunology volume 19, pages 355–368 (2019)Cite this article

Subjects

Abstract

Antibodies are essential components of adaptive immunity. A typical antibody repertoire comprises an enormous diversity of antigen-binding specificities, which are generated by the genetic processes of recombination and mutation. Accumulating evidence suggests that the immune system can exploit additional strategies to diversify the repertoire of antigen specificities. These unconventional mechanisms exclusively target the antigen-binding sites of immunoglobulins and include the insertion of large amino acid sequences, post-translational modifications, conformational heterogeneity and use of nonprotein cofactor molecules. Here, we describe the different unconventional routes for diversification of antibody specificities. Furthermore, we highlight how the immune system has a much greater level of adaptability and plasticity than previously anticipated, which goes far beyond that encoded in the genome or generated by the acquisition of somatic mutations.

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

Fig. 1: Diversification of antibody specificity by incorporation of non-immunoglobulin sequences in the V region.
Fig. 2: Diversification of antibody specificity through post-translational modifications in the antigen-binding site.
Fig. 3: Diversification of antibody specificity by conformational dynamics and reconfiguration of the antigen-binding site.
Fig. 4: Diversification of antibody specificity by use of cofactor molecules.
Fig. 5: Different levels of diversification of antibody repertoires.

Similar content being viewed by others

References

  1. Flajnik, M. F. A cold-blooded view of adaptive immunity. Nat. Rev. Immunol. 18, 438–453 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Lu, L. L., Suscovich, T. J., Fortune, S. M. & Alter, G. Beyond binding: antibody effector functions in infectious diseases. Nat. Rev. Immunol. 18, 46–61 (2018).

    CAS  PubMed  Google Scholar 

  3. Saada, R., Weinberger, M., Shahaf, G. & Mehr, R. Models for antigen receptor gene rearrangement: CDR3 length. Immunol. Cell Biol. 85, 323–332 (2007).

    CAS  PubMed  Google Scholar 

  4. Collins, A. M. & Jackson, K. J. L. On being the right size: antibody repertoire formation in the mouse and human. Immunogenetics 70, 143–158 (2018).

    CAS  PubMed  Google Scholar 

  5. Wardemann, H. & Busse, C. E. Novel approaches to analyze immunoglobulin repertoires. Trends Immunol. 38, 471–482 (2017).

    CAS  PubMed  Google Scholar 

  6. Imkeller, K. & Wardemann, H. Assessing human B cell repertoire diversity and convergence. Immunol. Rev. 284, 51–66 (2018).

    CAS  PubMed  Google Scholar 

  7. Klein, F. et al. Antibodies in HIV-1 vaccine development and therapy. Science 341, 1199–1204 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Corti, D. & Lanzavecchia, A. Broadly neutralizing antiviral antibodies. Annu. Rev. Immunol. 31, 705–742 (2013).

    CAS  PubMed  Google Scholar 

  9. Tan, J. et al. A LAIR1 insertion generates broadly reactive antibodies against malaria variant antigens. Nature 529, 105–109 (2016). This article demonstrates that some antibodies isolated from patients with malaria have insertions of LAIR1 protein in their V H regions.

    CAS  PubMed  Google Scholar 

  10. Meyaard, L. et al. LAIR-1, a novel inhibitory receptor expressed on human mononuclear leukocytes. Immunity 7, 283–290 (1997).

    CAS  PubMed  Google Scholar 

  11. Hsieh, F. L. & Higgins, M. K. The structure of a LAIR1-containing human antibody reveals a novel mechanism of antigen recognition. eLife 6, e27311 (2017). This paper reveals the crystal structure of an antibody that incorporates LAIR1 in its V region.

    PubMed  PubMed Central  Google Scholar 

  12. Pieper, K. et al. Public antibodies to malaria antigens generated by two LAIR1 insertion modalities. Nature 548, 597–601 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Robbiani, D. F. et al. Plasmodium infection promotes genomic instability and AID-dependent B cell lymphoma. Cell 162, 727–737 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Briney, B. S., Willis, J. R. & Crowe, J. E. Jr. Location and length distribution of somatic hypermutation-associated DNA insertions and deletions reveals regions of antibody structural plasticity. Genes Immun. 13, 523–529 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Wilson, P. C. et al. Somatic hypermutation introduces insertions and deletions into immunoglobulin V genes. J. Exp. Med. 187, 59–70 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Bowers, P. M. et al. Nucleotide insertions and deletions complement point mutations to massively expand the diversity created by somatic hypermutation of antibodies. J. Biol. Chem. 289, 33557–33567 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Kepler, T. B. et al. Immunoglobulin gene insertions and deletions in the affinity maturation of HIV-1 broadly reactive neutralizing antibodies. Cell Host Microbe 16, 304–313 (2014). This article shows that the frequency of indels in V regions is increased in antibodies from individuals infected with HIV-1 and in bNAbs against HIV-1.

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Krause, J. C. et al. An insertion mutation that distorts antibody binding site architecture enhances function of a human antibody. mBio 2, e00345–10 (2011).

    PubMed  PubMed Central  Google Scholar 

  19. Klein, F. et al. Somatic mutations of the immunoglobulin framework are generally required for broad and potent HIV-1 neutralization. Cell 153, 126–138 (2013). This work reveals the molecular mechanism of indel-mediated optimization of the neutralizing potential of a bNAb against HIV-1.

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Jennewein, M. F. & Alter, G. The immunoregulatory roles of antibody glycosylation. Trends Immunol. 38, 358–372 (2017).

    CAS  PubMed  Google Scholar 

  21. Moore, K. L. The biology and enzymology of protein tyrosine O-sulfation. J. Biol. Chem. 278, 24243–24246 (2003).

    CAS  PubMed  Google Scholar 

  22. Ouyang, Y., Lane, W. S. & Moore, K. L. Tyrosylprotein sulfotransferase: purification and molecular cloning of an enzyme that catalyzes tyrosine O-sulfation, a common posttranslational modification of eukaryotic proteins. Proc. Natl Acad. Sci. USA 95, 2896–2901 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Choe, H. et al. Tyrosine sulfation of human antibodies contributes to recognition of the CCR5 binding region of HIV-1 gp120. Cell 114, 161–170 (2003).

    CAS  PubMed  Google Scholar 

  24. 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).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Farzan, M. et al. Tyrosine sulfation of the amino terminus of CCR5 facilitates HIV-1 entry. Cell 96, 667–676 (1999).

    CAS  PubMed  Google Scholar 

  26. Huang, C. C. et al. Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science 317, 1930–1934 (2007). This article shows molecular details about the role of tyrosine sulfation in the interaction of an antibody with its target antigen.

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Pejchal, R. et al. Structure and function of broadly reactive antibody PG16 reveal an H3 subdomain that mediates potent neutralization of HIV-1. Proc. Natl Acad. Sci. USA 107, 11483–11488 (2010). This work presents evidence for the functional impact of sulfation of tyrosine in the antibody-mediated neutralization of HIV-1.

    PubMed  PubMed Central  Google Scholar 

  28. Changela, A. et al. Crystal structure of human antibody 2909 reveals conserved features of quaternary structure-specific antibodies that potently neutralize HIV-1. J. Virol. 85, 2524–2535 (2011).

    CAS  PubMed  Google Scholar 

  29. van de Bovenkamp, F. S., Hafkenscheid, L., Rispens, T. & Rombouts, Y. The emerging importance of IgG Fab glycosylation in immunity. J. Immunol. 196, 1435–1441 (2016).

    PubMed  Google Scholar 

  30. Hamza, N. et al. Ig gene analysis reveals altered selective pressures on Ig-producing cells in parotid glands of primary Sjogren’s syndrome patients. J. Immunol. 194, 514–521 (2015).

    CAS  PubMed  Google Scholar 

  31. Rombouts, Y. et al. Extensive glycosylation of ACPA-IgG variable domains modulates binding to citrullinated antigens in rheumatoid arthritis. Ann. Rheum. Dis. 75, 578–585 (2016).

    CAS  PubMed  Google Scholar 

  32. Hafkenscheid, L. et al. Structural analysis of variable domain glycosylation of anti-citrullinated protein antibodies in rheumatoid arthritis reveals the presence of highly sialylated glycans. Mol. Cell. Proteom. 16, 278–287 (2017).

    CAS  Google Scholar 

  33. van de Bovenkamp, F. S. et al. Variable domain N-linked glycans acquired during antigen-specific immune responses can contribute to immunoglobulin G antibody stability. Front. Immunol. 9, 740 (2018).

    PubMed  PubMed Central  Google Scholar 

  34. van de Bovenkamp, F. S. et al. Adaptive antibody diversification through N-linked glycosylation of the immunoglobulin variable region. Proc. Natl Acad. Sci. USA 115, 1901–1906 (2018). This study demonstrates the importance of glycosylation of V regions for the diversification of human antibody repertoires.

    PubMed  PubMed Central  Google Scholar 

  35. Wallick, S. C., Kabat, E. A. & Morrison, S. L. Glycosylation of a VH residue of a monoclonal antibody against alpha (1——6) dextran increases its affinity for antigen. J. Exp. Med. 168, 1099–1109 (1988).

    CAS  PubMed  Google Scholar 

  36. Leibiger, H., Wustner, D., Stigler, R. D. & Marx, U. Variable domain-linked oligosaccharides of a human monoclonal IgG: structure and influence on antigen binding. Biochem. J. 338, 529–538 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Khurana, S., Raghunathan, V. & Salunke, D. M. The variable domain glycosylation in a monoclonal antibody specific to GnRH modulates antigen binding. Biochem. Biophys. Res. Commun. 234, 465–469 (1997).

    CAS  PubMed  Google Scholar 

  38. Jacquemin, M. et al. Variable region heavy chain glycosylation determines the anticoagulant activity of a factor VIII antibody. J. Thromb. Haemost. 4, 1047–1055 (2006).

    CAS  PubMed  Google Scholar 

  39. Song, R., Oren, D. A., Franco, D., Seaman, M. S. & Ho, D. D. Strategic addition of an N-linked glycan to a monoclonal antibody improves its HIV-1-neutralizing activity. Nat. Biotechnol. 31, 1047–1052 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Sabouri, Z. et al. Redemption of autoantibodies on anergic B cells by variable-region glycosylation and mutation away from self-reactivity. Proc. Natl Acad. Sci. USA 111, E2567–E2575 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Chuang, G. Y. et al. Eliminating antibody polyreactivity through addition of N-linked glycosylation. Protein Sci. 24, 1019–1030 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Boehr, D. D., Nussinov, R. & Wright, P. E. The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol. 5, 789–796 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Tokuriki, N. & Tawfik, D. S. Protein dynamism and evolvability. Science 324, 203–207 (2009).

    CAS  PubMed  Google Scholar 

  44. James, L. C. & Tawfik, D. S. Conformational diversity and protein evolution—a 60-year-old hypothesis revisited. Trends Biochem. Sci. 28, 361–368 (2003).

    CAS  PubMed  Google Scholar 

  45. Yin, J., Beuscher, A. E. 4th, Andryski, S. E., Stevens, R. C. & Schultz, P. G. Structural plasticity and the evolution of antibody affinity and specificity. J. Mol. Biol. 330, 651–656 (2003).

    CAS  PubMed  Google Scholar 

  46. Manivel, V., Sahoo, N. C., Salunke, D. M. & Rao, K. V. Maturation of an antibody response is governed by modulations in flexibility of the antigen-combining site. Immunity 13, 611–620 (2000).

    CAS  PubMed  Google Scholar 

  47. Manivel, V., Bayiroglu, F., Siddiqui, Z., Salunke, D. M. & Rao, K. V. The primary antibody repertoire represents a linked network of degenerate antigen specificities. J. Immunol. 169, 888–897 (2002).

    CAS  PubMed  Google Scholar 

  48. Notkins, A. L. Polyreactivity of antibody molecules. Trends Immunol. 25, 174–179 (2004).

    CAS  PubMed  Google Scholar 

  49. Eisen, H. N. & Chakraborty, A. K. Evolving concepts of specificity in immune reactions. Proc. Natl Acad. Sci. USA 107, 22373–22380 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Wedemayer, G. J., Patten, P. A., Wang, L. H., Schultz, P. G. & Stevens, R. C. Structural insights into the evolution of an antibody combining site. Science 276, 1665–1669 (1997).

    CAS  PubMed  Google Scholar 

  51. Jimenez, R., Salazar, G., Baldridge, K. K. & Romesberg, F. E. Flexibility and molecular recognition in the immune system. Proc. Natl Acad. Sci. USA 100, 92–97 (2003).

    CAS  PubMed  Google Scholar 

  52. Jimenez, R., Salazar, G., Yin, J., Joo, T. & Romesberg, F. E. Protein dynamics and the immunological evolution of molecular recognition. Proc. Natl Acad. Sci. USA 101, 3803–3808 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Nguyen, H. P. et al. Germline antibody recognition of distinct carbohydrate epitopes. Nat. Struct. Biol. 10, 1019–1025 (2003).

    CAS  PubMed  Google Scholar 

  54. Zimmermann, J. et al. Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proc. Natl Acad. Sci. USA 103, 13722–13727 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Thorpe, I. F. & Brooks, C. L. 3rd Molecular evolution of affinity and flexibility in the immune system. Proc. Natl Acad. Sci. USA 104, 8821–8826 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Schmidt, A. G. et al. Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody. Proc. Natl Acad. Sci. USA 110, 264–269 (2013).

    CAS  PubMed  Google Scholar 

  57. Jeliazkov, J. R. et al. Repertoire analysis of antibody CDR-H3 loops suggests affinity maturation does not typically result in rigidification. Front. Immunol. 9, 413 (2018).

    PubMed  PubMed Central  Google Scholar 

  58. Ovchinnikov, V., Louveau, J. E., Barton, J. P., Karplus, M. & Chakraborty, A. K. Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies. eLife 7, e33038 (2018).

    PubMed  PubMed Central  Google Scholar 

  59. Acierno, J. P., Braden, B. C., Klinke, S., Goldbaum, F. A. & Cauerhff, A. Affinity maturation increases the stability and plasticity of the Fv domain of anti-protein antibodies. J. Mol. Biol. 374, 130–146 (2007).

    CAS  PubMed  Google Scholar 

  60. Haynes, B. F. et al. Cardiolipin polyspecific autoreactivity in two broadly neutralizing HIV-1 antibodies. Science 308, 1906–1908 (2005).

    CAS  PubMed  Google Scholar 

  61. Liu, M. et al. Polyreactivity and autoreactivity among HIV-1 antibodies. J. Virol. 89, 784–798 (2015).

    PubMed  Google Scholar 

  62. Mouquet, H. et al. Polyreactivity increases the apparent affinity of anti-HIV antibodies by heteroligation. Nature 467, 591–595 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Prigent, J. et al. Conformational plasticity in broadly neutralizing HIV-1 antibodies triggers polyreactivity. Cell Rep. 23, 2568–2581 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Erijman, A., Aizner, Y. & Shifman, J. M. Multispecific recognition: mechanism, evolution, and design. Biochemistry 50, 602–611 (2011).

    CAS  PubMed  Google Scholar 

  65. Vogt, A. D. & Di Cera, E. Conformational selection or induced fit? A critical appraisal of the kinetic mechanism. Biochemistry 51, 5894–5902 (2012).

    CAS  PubMed  Google Scholar 

  66. Foote, J. & Milstein, C. Conformational isomerism and the diversity of antibodies. Proc. Natl Acad. Sci. USA 91, 10370–10374 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. James, L. C. & Tawfik, D. S. Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition. Proc. Natl Acad. Sci. USA 102, 12730–12735 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. James, L. C., Roversi, P. & Tawfik, D. S. Antibody multispecificity mediated by conformational diversity. Science 299, 1362–1367 (2003). This study provides structural evidence for the existence of conformational isomerism in some antibodies.

    CAS  PubMed  Google Scholar 

  69. Wardemann, H. et al. Predominant autoantibody production by early human B cell precursors. Science 301, 1374–1377 (2003).

    CAS  PubMed  Google Scholar 

  70. Tiller, T. et al. Autoreactivity in human IgG+memory B cells. Immunity 26, 205–213 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Benckert, J. et al. The majority of intestinal IgA+and IgG+plasmablasts in the human gut are antigen-specific. J. Clin. Invest. 121, 1946–1955 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Bunker, J. J. et al. Natural polyreactive IgA antibodies coat the intestinal microbiota. Science 358, eean6619 (2017).

    Google Scholar 

  73. Jones, D. D., DeIulio, G. A. & Winslow, G. M. Antigen-driven induction of polyreactive IgM during intracellular bacterial infection. J. Immunol. 189, 1440–1447 (2012).

    CAS  PubMed  Google Scholar 

  74. Mouquet, H. & Nussenzweig, M. C. Polyreactive antibodies in adaptive immune responses to viruses. Cell. Mol. Life Sci. 69, 1435–1445 (2012).

    CAS  PubMed  Google Scholar 

  75. Warter, L., Appanna, R. & Fink, K. Human poly- and cross-reactive anti-viral antibodies and their impact on protection and pathology. Immunol. Res. 53, 148–161 (2012).

    CAS  PubMed  Google Scholar 

  76. Trama, A. M. et al. HIV-1 envelope gp41 antibodies can originate from terminal ileum B cells that share cross-reactivity with commensal bacteria. Cell Host Microbe 16, 215–226 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Vogt, A. D. & Di Cera, E. Conformational selection is a dominant mechanism of ligand binding. Biochemistry 52, 5723–5729 (2013).

    CAS  PubMed  Google Scholar 

  78. Calarese, D. A. et al. Antibody domain exchange is an immunological solution to carbohydrate cluster recognition. Science 300, 2065–2071 (2003). This paper reveals that a broadly neutralizing HIV-1 antibody uses V-domain swapping for achievement of high-affinity binding to a carbohydrate epitope on the surface of gp120.

    CAS  PubMed  Google Scholar 

  79. Calarese, D. A. et al. Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12. Proc. Natl Acad. Sci. USA 102, 13372–13377 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Barnes, C. O. et al. Structural characterization of a highly-potent V3-glycan broadly neutralizing antibody bound to natively-glycosylated HIV-1 envelope. Nat. Commun. 9, 1251 (2018).

    PubMed  PubMed Central  Google Scholar 

  81. Imkeller, K. et al. Antihomotypic affinity maturation improves human B cell responses against a repetitive epitope. Science 360, 1358–1362 (2018). This study demonstrates that homotypic interaction between V regions of two different antibody molecules facilitates recognition of repetitive antigens.

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Zhou, T., Hamer, D. H., Hendrickson, W. A., Sattentau, Q. J. & Kwong, P. D. Interfacial metal and antibody recognition. Proc. Natl Acad. Sci. USA 102, 14575–14580 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Wojciak, J. M. et al. The crystal structure of sphingosine-1-phosphate in complex with a Fab fragment reveals metal bridging of an antibody and its antigen. Proc. Natl Acad. Sci. USA 106, 17717–17722 (2009). References 82 and 83 show that certain antibodies use Ca 2+ ions as an interfacial cofactor for antigen recognition.

    CAS  PubMed  PubMed Central  Google Scholar 

  84. Stearns, D. J., Kurosawa, S., Sims, P. J., Esmon, N. L. & Esmon, C. T. The interaction of a Ca2+-dependent monoclonal antibody with the protein C activation peptide region. Evidence for obligatory Ca2+ binding to both antigen and antibody. J. Biol. Chem. 263, 826–832 (1988).

    CAS  PubMed  Google Scholar 

  85. Dimitrov, J. D. et al. Ferrous ions and reactive oxygen species increase antigen-binding and anti-inflammatory activities of immunoglobulin G. J. Biol. Chem. 281, 439–446 (2006).

    CAS  PubMed  Google Scholar 

  86. Baker, H., Frank, O., Feingold, S. & Leevy, C. M. Vitamin distribution in human plasma proteins. Nature 215, 84–85 (1967).

    CAS  PubMed  Google Scholar 

  87. Innis, W. S., McCormick, D. B. & Merrill, A. H. Jr. Variations in riboflavin binding by human plasma: identification of immunoglobulins as the major proteins responsible. Biochem. Med. 34, 151–165 (1985).

    CAS  PubMed  Google Scholar 

  88. Watson, C. D. & Ford, H. C. High-affinity binding of riboflavin and FAD by immunoglobulins from normal human serum. Biochem. Int. 16, 1067–1074 (1988).

    CAS  PubMed  Google Scholar 

  89. Nieva, J., Kerwin, L., Wentworth, A. D., Lerner, R. A. & Wentworth, P. Jr. Immunoglobulins can utilize riboflavin (Vitamin B2) to activate the antibody-catalyzed water oxidation pathway. Immunol. Lett. 103, 33–38 (2006).

    CAS  PubMed  Google Scholar 

  90. Stoppini, M. et al. Characterization of the two unique human anti-flavin monoclonal immunoglobulins. Eur. J. Biochem. 228, 886–893 (1995).

    CAS  PubMed  Google Scholar 

  91. Zhu, X. et al. Cofactor-containing antibodies: crystal structure of the original yellow antibody. Proc. Natl Acad. Sci. USA 103, 3581–3585 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Rajagopalan, K. et al. Novel unconventional binding site in the variable region of immunoglobulins. Proc. Natl Acad. Sci. USA 93, 6019–6024 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  93. Karjalainen, K. & Makela, O. Concentrations of three hapten-binding immunoglobulins in pooled normal human serum. Eur. J. Immunol. 6, 88–93 (1976).

    CAS  PubMed  Google Scholar 

  94. McEnaney, P. J., Parker, C. G., Zhang, A. X. & Spiegel, D. A. Antibody-recruiting molecules: an emerging paradigm for engaging immune function in treating human disease. Chem. Biol. 7, 1139–1151 (2012).

    CAS  Google Scholar 

  95. Dimitrov, J. D. et al. Antibodies use heme as a cofactor to extend their pathogen elimination activity and to acquire new effector functions. J. Biol. Chem. 282, 26696–26706 (2007). This study shows that some antibodies use haem as a cofactor for the diversification of antigen-binding specificity.

    CAS  PubMed  Google Scholar 

  96. Wagener, F. A. et al. Different faces of the heme-heme oxygenase system in inflammation. Pharmacol. Rev. 55, 551–571 (2003).

    CAS  PubMed  Google Scholar 

  97. Soares, M. P. & Bozza, M. T. Red alert: labile heme is an alarmin. Curr. Opin. Immunol. 38, 94–100 (2016).

    CAS  PubMed  Google Scholar 

  98. Roumenina, L. T., Rayes, J., Lacroix-Desmazes, S. & Dimitrov, J. D. Heme: modulator of plasma systems in hemolytic diseases. Trends Mol. Med. 22, 200–213 (2016).

    CAS  PubMed  Google Scholar 

  99. McIntyre, J. A. The appearance and disappearance of antiphospholipid autoantibodies subsequent to oxidation—reduction reactions. Thromb. Res. 114, 579–587 (2004).

    CAS  PubMed  Google Scholar 

  100. McIntyre, J. A., Wagenknecht, D. R. & Faulk, W. P. Autoantibodies unmasked by redox reactions. J. Autoimmun. 24, 311–317 (2005).

    CAS  PubMed  Google Scholar 

  101. McIntyre, J. A., Wagenknecht, D. R. & Faulk, W. P. Redox-reactive autoantibodies: detection and physiological relevance. Autoimmun. Rev. 5, 76–83 (2006).

    CAS  PubMed  Google Scholar 

  102. McIntyre, J. A. & Faulk, W. P. Redox-reactive autoantibodies: biochemistry, characterization, and specificities. Clin. Rev. Allergy Immunol. 37, 49–54 (2009).

    CAS  PubMed  Google Scholar 

  103. Lecerf, M. et al. Prevalence and gene characteristics of antibodies with cofactor-induced HIV-1 specificity. J. Biol. Chem. 290, 5203–5213 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  104. Gupta, N. et al. Neutralization of Japanese encephalitis virus by heme-induced broadly reactive human monoclonal antibody. Sci. Rep. 5, 16248 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. Hadzhieva, M. et al. Mechanism and functional implications of the heme-induced binding promiscuity of IgE. Biochemistry 54, 2061–2072 (2015).

    CAS  PubMed  Google Scholar 

  106. Dimitrov, J. D. et al. A cryptic polyreactive antibody recognizes distinct clades of HIV-1 glycoprotein 120 by an identical binding mechanism. J. Biol. Chem. 289, 17767–17779 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Kuhl, T. & Imhof, D. Regulatory Fe(II/III) heme: the reconstruction of a molecule’s biography. Chembiochem 15, 2024–2035 (2014).

    PubMed  Google Scholar 

  108. Djoumerska-Alexieva, I., Roumenina, L. T., Stefanova, T., Vassilev, T. & Dimitrov, J. D. Heme-exposed pooled therapeutic IgG improves endotoxemia survival. Inflammation 40, 117–122 (2017).

    CAS  PubMed  Google Scholar 

  109. Pavlovic, S. et al. Intravenous immunoglobulins exposed to heme (heme IVIG) are more efficient than IVIG in attenuating autoimmune diabetes. Clin. Immunol. 138, 162–171 (2010).

    PubMed  Google Scholar 

  110. Vihinen, M., Torkkila, E. & Riikonen, P. Accuracy of protein flexibility predictions. Proteins 19, 141–149 (1994).

    CAS  PubMed  Google Scholar 

  111. Radivojac, P. et al. Protein flexibility and intrinsic disorder. Protein Sci. 13, 71–80 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Sigounas, G., Harindranath, N., Donadel, G. & Notkins, A. L. Half-life of polyreactive antibodies. J. Clin. Immunol. 14, 134–140 (1994).

    CAS  PubMed  Google Scholar 

  113. Robin, G. et al. Restricted diversity of antigen binding residues of antibodies revealed by computational alanine scanning of 227 antibody-antigen complexes. J. Mol. Biol. 426, 3729–3743 (2014).

    CAS  PubMed  Google Scholar 

  114. Hong, B. et al. In-depth analysis of human neonatal and adult IgM antibody repertoires. Front. Immunol. 9, 128 (2018).

    PubMed  PubMed Central  Google Scholar 

  115. Brooks, C. L., Rossotti, M. A. & Henry, K. A. Immunological functions and evolutionary emergence of heavy-chain antibodies. Trends Immunol. 39, 956–960 (2018).

    CAS  PubMed  Google Scholar 

  116. Wang, F. et al. Reshaping antibody diversity. Cell 153, 1379–1393 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  117. de Villartay, J. P., Fischer, A. & Durandy, A. The mechanisms of immune diversification and their disorders. Nat. Rev. Immunol. 3, 962–972 (2003).

    PubMed  Google Scholar 

  118. Westra, E. R., Sunderhauf, D., Landsberger, M. & Buckling, A. Mechanisms and consequences of diversity-generating immune strategies. Nat. Rev. Immunol. 17, 719–728 (2017).

    CAS  PubMed  Google Scholar 

  119. Benedict, C. L., Gilfillan, S., Thai, T. H. & Kearney, J. F. Terminal deoxynucleotidyl transferase and repertoire development. Immunol. Rev. 175, 150–157 (2000).

    CAS  PubMed  Google Scholar 

  120. Neuberger, M. S. Antibody diversification by somatic mutation: from Burnet onwards. Immunol. Cell. Biol. 86, 124–132 (2008).

    CAS  PubMed  Google Scholar 

  121. Peled, J. U. et al. The biochemistry of somatic hypermutation. Annu. Rev. Immunol. 26, 481–511 (2008).

    CAS  PubMed  Google Scholar 

  122. Scheid, J. F. et al. Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding. Science 333, 1633–1637 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  123. Pettersen, E. F. et al. UCSF Chimera — a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    CAS  PubMed  Google Scholar 

  124. Dimitrov, J. D. & Vassilev, T. L. Cofactor-mediated protein promiscuity. Nat. Biotechnol. 27, 892 (2009).

    CAS  PubMed  Google Scholar 

  125. Sivasubramanian, A., Sircar, A., Chaudhury, S. & Gray, J. J. Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins 74, 497–514 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  126. Grosdidier, A., Zoete, V. & Michielin, O. SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res. 39, W270–W277 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This work was supported by INSERM, France, and a European Research Council Starting Grant (Project CoBABATI ERC-StG-678905 to J.D.D.).

Reviewer information

Nature Reviews Immunology thanks G. Alter, P. Wilson and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Author information

Authors and Affiliations

  1. Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France

    Alexia Kanyavuz, Annaelle Marey-Jarossay, Sébastien Lacroix-Desmazes & Jordan D. Dimitrov

  2. INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France

    Alexia Kanyavuz, Annaelle Marey-Jarossay, Sébastien Lacroix-Desmazes & Jordan D. Dimitrov

  3. Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France

    Alexia Kanyavuz, Annaelle Marey-Jarossay, Sébastien Lacroix-Desmazes & Jordan D. Dimitrov

Authors
  1. Alexia Kanyavuz
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Annaelle Marey-Jarossay
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sébastien Lacroix-Desmazes
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jordan D. Dimitrov
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

All authors contributed to writing the article. J.D.D. and S.L.-D. were involved in discussing the content of the article and in researching data for the article. J.D.D., A.K. and S.L.-D. contributed to the review and editing of the manuscript before submission.

Corresponding author

Correspondence to Jordan D. Dimitrov.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Related links

ROSIE: http://rosie.rosettacommons.org

SwissDock: http://www.swissdock.ch

Glossary

Elbow region

A region of immunoglobulin molecule situated between the variable domain and the first constant domain.

Activation-induced cytidine deaminase

(AID). An enzyme responsible for the introduction of somatic mutations in variable regions and for a class switch of immunoglobulins.

Paratope

The part of the antigen-binding site of an antibody molecule that is directly involved in interaction with the target antigen.

Epitope

The part of the antigen that is recognized by the paratope of an antibody, that is, the complementary part of the paratope.

γ-Globulin fraction

A fraction of human serum that consists mainly of immunoglobulins.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kanyavuz, A., Marey-Jarossay, A., Lacroix-Desmazes, S. et al. Breaking the law: unconventional strategies for antibody diversification. Nat Rev Immunol 19, 355–368 (2019). https://doi.org/10.1038/s41577-019-0126-7

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41577-019-0126-7

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