Skip to main content

Structural Basis of Antibody–Antigen Interactions

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 524))

Summary

Antibody molecules can be regarded as products of a protein engineering system for the generation of a virtually unlimited repertoire of complementary molecular surfaces. This extreme structural heterogeneity is required for recognition of the nearly infinite array of antigenic determinants. This chapter discusses the structures of antibodies and their specific recognition of antigens, the binding energetics of these interactions, the cross-reactivity and specificity of antibody–antigen interactions, the role of conformational flexibility in antigen recognition, and the structural basis of the antibody affinity maturation process.

This is a preview of subscription content, log in via an institution.

Buying options

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Amzel, L. M., and Poljak, R. J. (1979) Three-dimensional structure of immunoglobulins. Annu. Rev. Biochem. 48, 961–997.

    Article  PubMed  CAS  Google Scholar 

  2. Harris, L. J., Larson, S. B., Hasel, K. W., and McPherson, A. (1997) Refined structure of an intact IgG2a monoclonal antibody. Biochemistry 36, 1581–1597.

    Article  PubMed  CAS  Google Scholar 

  3. Harris, L. J., Skaletsky, E., and McPherson, A. (1998) Crystallographic structure of an intact IgG1 monoclonal antibody. J. Mol. Biol. 275, 861–872.

    Article  PubMed  CAS  Google Scholar 

  4. Wu, T. T., and Kabat, E. A. (1970) An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J. Exp. Med. 132, 211–250.

    Article  PubMed  CAS  Google Scholar 

  5. Al-Lazikani, B., Lesk, A. M., and Chothia, C. (1997) Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol. 273, 927–948.

    Article  PubMed  CAS  Google Scholar 

  6. Chitarra, V., Alzari, P. M., Bentley, G. A., Bhat, T. N., Eiselé, J. L., Houdusse, A., Lescar, J., Souchon, H., and Poljak, R. J. (1993) Three-dimensional structure of a heteroclitic antigen–antibody cross-reaction complex. Proc. Natl. Acad. Sci. USA 90, 7711–7715.

    Article  PubMed  CAS  Google Scholar 

  7. Wilson, I. A., and Stanfield, R. L. (1993) Antibody–antigen interactions. Curr. Opin. Struct. Biol. 3, 113–118.

    Article  CAS  Google Scholar 

  8. Hamers-Casterman, C., Atarhouch, T., Muyldermans, S., Robinson, G., Hamers, C., Songa, E. B., Bendahman, N., and Hamers, R. (1993) Naturally occurring antibodies devoid of light chains. Nature 363, 446–448.

    Article  PubMed  CAS  Google Scholar 

  9. Decanniere, K., Desmyter, A., Lauwereys, M., Ghahroudi, M. A., Muyldermans, S., and Wyns, L. (1999) A single-domain antibody fragment in complex with RNase A: non-canonical loop structures and nanomolar affinity using two CDR loops. Struct. Fold. Des. 7, 361–370.

    Article  CAS  Google Scholar 

  10. Stanfield, R. L., Dooley, H., Flajnik, M. F., and Wilson, I. A. (2004) Crystal structure of a shark single-domain antibody V region in complex with lysozyme. Science 305, 1770–1773.

    Article  PubMed  CAS  Google Scholar 

  11. Chersi, A., Galati, R., Ogino, T., Butler, R. H., and Tanigaki, N. (2002) Anti-peptide antibodies that recognize conformational differences of HLA class I intracytoplasmic domains. Hum. Immunol. 63, 731–741.

    Article  PubMed  CAS  Google Scholar 

  12. Hewer, R., and Meyer, D. (2003) Peptide immunogens based on the envelope region of HIV-1 are recognized by HIV/AIDS patient polyclonal antibodies and induce strong humoral immune responses in mice and rabbits. Mol. Immunol. 40, 327–335.

    Article  PubMed  CAS  Google Scholar 

  13. Metaxas, A., Tzartos, S., and Liakopoulou-Kyriakide, M. (2002) The production of anti-hexapeptide antibodies which recognize the S7, L6 and L13 ribosomal proteins of Escherichia coli. J. Pept. Sci. 8, 118–124.

    Article  PubMed  CAS  Google Scholar 

  14. Wilson, I. A., and Stanfield, R. L. (1994) Antibody–antigen interactions: new structures and new conformational changes. Curr. Opin. Struct. Biol. 4, 857–867.

    Article  PubMed  CAS  Google Scholar 

  15. Chothia, C., Lesk, A. M., Tramontano, A., Levitt, M., Smith-Gill, S. J., Air, G., Sheriff, S., Padlan, E. A., Davies, D., and Tulip, W. R. (1989) Conformations of immunoglobulin hypervariable regions. Nature 342, 877–883.

    Article  PubMed  CAS  Google Scholar 

  16. Conte, L. L., Chothia, C., and Janin, J. (1999) The atomic structure of protein–protein recognition sites. J. Mol. Biol. 285, 2177–2198.

    Article  PubMed  Google Scholar 

  17. MacCallum, R. M., Martin, A. C., and Thornton, J. M. (1996) Antibody–antigen interactions: contact analysis and binding site topography. J. Mol. Biol. 262, 732–745.

    Article  PubMed  CAS  Google Scholar 

  18. Jones, S., and Thornton, J. M. (1996) Principles of protein–protein interactions. Proc. Natl. Acad. Sci. USA 93, 13–20.

    Article  PubMed  CAS  Google Scholar 

  19. Webster, D. M., Henry, A. H., and Rees, A. R. (1994) Antibody–antigen interactions. Curr. Opin. Struct. Biol. 4, 123–129.

    Article  CAS  Google Scholar 

  20. Rini, J. M., Schulze-Gahmen, U., and Wilson, I. A. (1992) Structural evidence for induced fit as a mechanism for antibody–antigen recognition. Science 255, 959–965.

    Article  PubMed  CAS  Google Scholar 

  21. Stanfield, R. L., Fieser, T. M., Lerner, R. A., and Wilson, I. A. (1990) Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 Å. Science 248, 712–719.

    Article  PubMed  CAS  Google Scholar 

  22. Garcia, K. C., Ronco, P. M., Verroust, P. J., Brünger, A. T., and Amzel, L. M. (1992) Three-dimensional structure of an angiotensin II-Fab complex at 3 Å: hormone recognition by an anti-idiotypic antibody. Science 257, 502–507.

    Article  PubMed  CAS  Google Scholar 

  23. Foote, J., and Eisen, H. N. (1995) Kinetic and affinity limits on antibodies produced during immune responses. Proc. Natl. Acad. Sci. USA 92, 1254–1256.

    Article  PubMed  CAS  Google Scholar 

  24. Batista, F. D., and Neuberger, M. S. (1998) Affinity dependence of the B cell response to antigen: a threshold, a ceiling, and the importance of off-rate. Immunity 8, 751–759.

    Article  PubMed  CAS  Google Scholar 

  25. Roost, H. P., Bachmann, M. F., Haag, A., Kalinke, U., Pliska, V., Hengartner, H., and Zinkernagel, R. M. (1995) Early high-affinity neutralizing anti-viral IgG responses without further overall improvements of affinity. Proc. Natl. Acad. Sci. USA 92, 1257–1261.

    Article  PubMed  CAS  Google Scholar 

  26. Batista, F. D., and Neuberger, M. S. (2000) B cells extract and present immobilized antigen: implications for affinity discrimination. EMBO J. 19, 513–520.

    Article  PubMed  CAS  Google Scholar 

  27. Xavier, K. A., McDonald, S. M., McCammon, J. A., and Willson, R. C. (1999) Association and dissociation kinetics of bobwhite quail lysozyme with monoclonal antibody HyHEL-5. Protein Eng. 12, 79–83.

    Article  PubMed  CAS  Google Scholar 

  28. Gerstner, R. B., Carter, P., and Lowman, H. B. (2002) Sequence plasticity in the antigen-binding site of a therapeutic anti-HER2 antibody. J. Mol. Biol. 321, 851–862.

    Article  PubMed  CAS  Google Scholar 

  29. Rajpal, A. and Kirsch, J. F. (2000) Role of the minor energetic determinants of chicken egg white lysozyme (HEWL) to the stability of the HEWL antibody scFv-10 complex. Proteins 40, 49–57.

    Article  PubMed  CAS  Google Scholar 

  30. England, P., Bregegere, F., and Bedouelle, H. (1997) Energetic and kinetic contributions of contact residues of antibody D1.3 in the interaction with lysozyme. Biochemistry 36, 164–172.

    Article  Google Scholar 

  31. Goldbaum, F. A., Schwarz, F. P., Eisenstein, E., Cauerhff, A., Mariuzza, R. A., and Poljak, R. J. (1996) The effect of water activity on the association constant and the enthalpy of reaction between lysozyme and the specific antibodies D1.3 and D44.1. J. Mol. Recognit. 9, 6–12.

    Article  PubMed  CAS  Google Scholar 

  32. Kelley, R. F., O’Connell, M. P., Carter, P., Presta, L., Eigenbrot, C., Covarrubias, M., Snedecor, B., Bourell, J. H., and Vetterlein, D. (1992) Antigen binding thermodynamics and antiproliferative effects of chimeric and humanized anti-p185HER2 antibody Fab fragments. Biochemistry 31, 5434–5441.

    Article  PubMed  CAS  Google Scholar 

  33. Sigurskjold, B. W., Altman, E., and Bundle, D. R. (1991) Sensitive titration microcalorimetric study of the binding of Salmonella O-antigenic oligosaccharides by a monoclonal antibody. Eur. J. Biochem. 197, 239–246.

    Article  PubMed  CAS  Google Scholar 

  34. Gibas, C. J., Subramaniam, S., McCammon, J. A., Braden, B. C., and Poljak, R. J. (1997) pH dependence of antibody/lysozyme complexation. Biochemistry 36, 15599–15614.

    Article  PubMed  CAS  Google Scholar 

  35. Omelyanenko, V. G., Jiskoot, W., and Herron, J. N. (1993) Role of electrostatic interactions in the binding of fluorescein by anti-fluorescein antibody 4–4–20. Biochemistry 32, 10423–10429.

    Article  PubMed  CAS  Google Scholar 

  36. De Genst, E., Areskoug, D., Decanniere, K., Muyldermans, S., and Andersson, K. (2002) Kinetic and affinity predictions of a protein–protein interaction using multivariate experimental design. J. Biol. Chem. 277, 29897–29907.

    Article  PubMed  CAS  Google Scholar 

  37. Kaplan, M. H., and Meyeserian, M. (1962) An immunological cross-reaction between group-A streptococcal cells and human heart tissue. Lancet 1, 706–710.

    Article  PubMed  CAS  Google Scholar 

  38. Oldstone, M. B. (1998) Molecular mimicry and immune-mediated diseases. FASEB J. 12, 1255–1265.

    PubMed  CAS  Google Scholar 

  39. Dall’Acqua, W., Goldman, E. R., Eisenstein, E., and Mariuzza, R. A. (1996) A mutational analysis of the binding of two different proteins to the same antibody. Biochemistry 35, 9667–9676.

    Article  PubMed  Google Scholar 

  40. Poljak, R. J. (1994) An idiotope–anti-idiotope complex and the structural basis of molecular mimicking. Proc. Natl. Acad. Sci. USA 91, 1599–1600.

    Article  PubMed  CAS  Google Scholar 

  41. Pan, Y., Yuhasz, S. C., and Amzel, L. M. (1995) Anti-idiotypic antibodies: biological function and structural studies. FASEB J. 9, 43–49.

    PubMed  CAS  Google Scholar 

  42. Bhat, T. N., Bentley, G. A., Boulot, G., Greene, M. I., Tello, D., Dall’Acqua, W., Souchon, H., Schwarz, F. P., Mariuzza, R. A., and Poljak, R. J. (1994) Bound water molecules and conformational stabilization help mediate an antigen–antibody association. Proc. Natl. Acad. Sci. USA 91, 1089–1093.

    Article  PubMed  CAS  Google Scholar 

  43. Braden, B. C., Fields, B. A., Ysern, X., Dall’Acqua, W., Goldbaum, F. A., Poljak, R. J., and Mariuzza, R. A. (1996) Crystal structure of an Fv-Fv idiotope-anti-idiotope complex at 1.9 Å resolution. J. Mol. Biol. 264, 137–151.

    Article  PubMed  CAS  Google Scholar 

  44. Fields, B. A., Goldbaum, F. A., Ysern, X., Poljak, R. J., and Mariuzza, R. A. (1995) Molecular basis of antigen mimicry by an anti-idiotope. Nature 374, 739–742.

    Article  PubMed  CAS  Google Scholar 

  45. Eshhar, Z., Ofarim, M., and Waks, T. (1980) Generation of hybridomas secreting murine reaginic antibodies of anti-DNP specificity. J. Immunol. 124, 775–780.

    PubMed  CAS  Google Scholar 

  46. Varga, J. M., Kalchschmid, G., Klein, G. F., and Fritsch, P. (1991) Mechanism of allergic cross-reactions – I. Multispecific binding of ligands to a mouse monoclonal anti-DNP IgE antibody. Mol. Immunol. 28, 641–654.

    Article  PubMed  CAS  Google Scholar 

  47. James, L. C., Roversi, P., and Tawfik, D. S. (2003) Antibody multispecificity mediated by conformational diversity. Science 299, 1362–1367.

    Article  PubMed  CAS  Google Scholar 

  48. Li, Y., Lipschultz, C. A., Mohan, S., and Smith-Gill, S. J. (2001) Mutations of an epitope hot-spot residue alter rate limiting steps of antigen–antibody protein–protein associations. Biochemistry 40, 2011–2022.

    Article  PubMed  CAS  Google Scholar 

  49. Lipschultz, C. A., Li, Y., and Smith-Gill, S. J. (2000) Experimental design for analysis of complex kinetics using surface plasmon resonance. Methods 20, 310–318.

    Article  PubMed  CAS  Google Scholar 

  50. Tormo, J., Blaas, D., Parry, N. R., Rowlands, D., Stuart, D., and Fita, I. (1994) Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2. EMBO J. 13, 2247–2256.

    PubMed  CAS  Google Scholar 

  51. Herron, J. N., He, X. M., Ballard, D. W., Blier, P. R., Pace, P. E., Bothwell, A. L., Voss, E. W., Jr., and Edmundson, A. B. (1991) An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide–Fab complex. Proteins 11, 159–175.

    Article  PubMed  CAS  Google Scholar 

  52. Prasad, G. S., Earhart, C. A., Murray, D. L., Novick, R. P., Schlievert, P. M., and Ohlendorf, D. H. (1993) Structure of toxic shock syndrome toxin 1. Biochemistry 32, 13761–13766.

    Article  PubMed  CAS  Google Scholar 

  53. Mylvaganam, S. E., Paterson, Y., and Getzoff, E. D. (1998) Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 Å resolution and FabE8 to 2.26 Å resolution. J. Mol. Biol. 281, 301–322.

    Article  PubMed  CAS  Google Scholar 

  54. Li, Y., Li, H., Smith-Gill, S. J., and Mariuzza, R. A. (2000) Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63. Biochemistry 39, 6296–6309.

    Article  PubMed  CAS  Google Scholar 

  55. Braden, B. C., Souchon, H., Eiselé, J. L., Bentley, G. A., Bhat, T. N., Navaza, J., and Poljak, R. J. (1994) Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1. J. Mol. Biol. 243, 767–781.

    Article  PubMed  CAS  Google Scholar 

  56. Faelber, K., Kirchhofer, D., Presta, L., Kelley, R. F., and Muller, Y. A. (2001) The 1.85 Å resolution crystal structures of tissue factor in complex with humanized Fab D3h44 and of free humanized Fab D3h44: revisiting the solvation of antigen combining sites. J. Mol. Biol. 313, 83–97.

    Article  PubMed  CAS  Google Scholar 

  57. Kurinov, I. V., and Harrison, R. W. (1995) The influence of temperature on lysozyme crystals. Structure and dynamics of protein and water. Acta Crystallogr. D 51, 98–109.

    Article  PubMed  CAS  Google Scholar 

  58. Harata, K. (1994) X-ray structure of a monoclinic form of hen egg-white lysozyme crystallized at 313 K. Comparison of two independent molecules. Acta Crystallogr. D 50, 250–257.

    Article  PubMed  CAS  Google Scholar 

  59. Ramanadham, M., Sieker, L. C., and Jensen, L. H. (1990) Refinement of triclinic lysozyme: II. The method of stereochemically restrained least squares. Acta Crystallogr. B 46, 63–69.

    Article  PubMed  Google Scholar 

  60. Padlan, E. A., Silverton, E. W., Sheriff, S., Cohen, G. H., Smith-Gill, S. J., and Davies, D. R. (1989) Structure of an antibody–antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex. Proc. Natl. Acad. Sci. USA 86, 5938–5942.

    Article  PubMed  CAS  Google Scholar 

  61. Hahn, M., Winkler, D., Welfle, K., Misselwitz, R., Welfle, H., Wessner, H., Zahn, G., Scholz, C., Seifert, M., Harkins, R., Schneider-Mergener, J., and Höhne, W. (2001) Cross-reactive binding of cyclic peptides to an anti-TGFalpha antibody Fab fragment: an X-ray structural and thermodynamic analysis. J. Mol. Biol. 314, 293–309.

    Article  PubMed  CAS  Google Scholar 

  62. Tonegawa, S. (1983) Somatic generation of antibody diversity. Nature 302, 575–581.

    Article  PubMed  CAS  Google Scholar 

  63. Chothia, C., Lesk, A. M., Gherardi, E., Tomlinson, I. M., Walter, G., Marks, J. D., Llewelyn, M. B., and Winter, G. (1992) Structural repertoire of the human VH segments. J. Mol. Biol. 227, 799–817.

    Article  PubMed  CAS  Google Scholar 

  64. Tomlinson, I. M., Cox, J. P., Gherardi, E., Lesk, A. M., and Chothia, C. (1995) The structural repertoire of the human V kappa domain. EMBO J. 14, 4628–4638.

    PubMed  CAS  Google Scholar 

  65. Tomlinson, I. M., Walter, G., Jones, P. T., Dear, P. H., Sonnhammer, E. L., and Winter, G. (1996) The imprint of somatic hypermutation on the repertoire of human germline V genes. J. Mol. Biol. 256, 813–817.

    Article  PubMed  CAS  Google Scholar 

  66. Rajewsky, K. (1996) Clonal selection and ­learning in the antibody system. Nature 381, 751–758.

    Article  PubMed  CAS  Google Scholar 

  67. Furukawa, K., Akasako-Furukawa, A., Shirai, H., Nakamura, H., and Azuma, T. (1999) Junctional amino acids determine the maturation pathway of an antibody. Immunity 11, 329–338.

    Article  PubMed  CAS  Google Scholar 

  68. Furukawa, K., Shirai, H., Azuma, T., and Nakamura, H. (2001) A role of the third complementarity-determining region in the affinity maturation of an antibody. J. Biol. Chem. 276, 27622–27628.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  70. Wedemayer, G. J., Wang, L. H., Patten, P. A., Schultz, P. G., and Stevens, R. C. (1997) Crystal structures of the free and liganded form of an esterolytic catalytic antibody. J. Mol. Biol. 268, 390–400.

    Article  PubMed  CAS  Google Scholar 

  71. Patten, P. A., Gray, N. S., Yang, P. L., Marks, C. B., Wedemayer, G. J., Boniface, J. J., Stevens, R. C., and Schultz, P. G. (1996) The immunological evolution of catalysis. Science 271, 1086–1091.

    Article  PubMed  CAS  Google Scholar 

  72. Yang, P. L., and Schultz, P. G. (1999) Mutational analysis of the affinity maturation of antibody 48G7. J. Mol. Biol. 294, 1191–1201.

    Article  PubMed  CAS  Google Scholar 

  73. Romesberg, F. E., Spiller, B., Schultz, P. G., and Stevens, R. C. (1998) Immunological origins of binding and catalysis in a Diels-Alderase antibody. Science 279, 1929–1933.

    Article  PubMed  CAS  Google Scholar 

  74. Ulrich, H. D., Mundorff, E., Santarsiero, B. D., Driggers, E. M., Stevens, R. C., and Schultz, P. G. (1997) The interplay between binding energy and catalysis in the evolution of a catalytic antibody. Nature 389, 271–275.

    Article  PubMed  CAS  Google Scholar 

  75. England, P., Nageotte, R., Renard, M., Page, A. L., and Bedouelle, H. (1999) Functional characterization of the somatic hypermutation process leading to antibody D1.3, a high affinity antibody directed against lysozyme. J. Immunol. 162, 2129–2136.

    Google Scholar 

  76. Li, Y., Li, H., Smith-Gill, S. J., and Mariuzza, R. A. (2003) X-ray snapshots of the maturation of an antibody response to a protein antigen. Nat. Struct. Biol. 10, 482–488.

    Article  PubMed  CAS  Google Scholar 

  77. Sundberg, E. J., Urrutia, M., Braden, B. C., Isern, J., Tsuchiya, D., Fields, B. A., Malchiodi, E. L., Tormo, J., Schwarz, F. P., and Mariuzza, R. A. (2000) Estimation of the hydrophobic effect in an antigen–antibody protein–protein interface. Biochemistry 39, 15375–15387.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Eric J. Sundberg .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Sundberg, E.J. (2009). Structural Basis of Antibody–Antigen Interactions. In: Schutkowski, M., Reineke, U. (eds) Epitope Mapping Protocols. Methods in Molecular Biology™, vol 524. Humana Press. https://doi.org/10.1007/978-1-59745-450-6_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-450-6_2

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-934115-17-6

  • Online ISBN: 978-1-59745-450-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics