Structural basis of antibody-antigen interactions

Methods in Molecular Biology

Volumn 524, Issue , 2009, Pages 23-36

  Sundberg, Eric J ^a  

^a BOSTON BIOMEDICAL RESEARCH INSTITUTE   (United States)

Author keywords

Affinity maturation; Antibody; Antigen; Binding energetics; X ray crystallography

Indexed keywords

ANTIBODY; ANTIGEN;

ANIMAL; ANTIBODY COMBINING SITE; ANTIGEN ANTIBODY COMPLEX; ARTICLE; CHEMISTRY; CROSS REACTION; GENETICS; HUMAN; IMMUNOLOGY; MUTATION; PROTEIN CONFORMATION; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

ANIMALS; ANTIBODIES; ANTIGEN-ANTIBODY COMPLEX; ANTIGENS; BINDING SITES, ANTIBODY; CROSS REACTIONS; CRYSTALLOGRAPHY, X-RAY; HUMANS; MUTATION; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 67650228031     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-450-6_2     Document Type: Article

References (74)

1. Amzel, L. M., and Poljak, R. J. (1979) Threedimensional structure of immunoglobulins. Annu. Rev. Biochem. 48, 961-997.
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. (Pubitemid 27086254)
3. Harris, L. J., Skaletsky, E., and McPherson, A. (1998) Crystallographic structure of an intact IgG1 monoclonal antibody. J. Mol. Biol. 275, 861-872. (Pubitemid 28077701)
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.
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. (Pubitemid 27493729)
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. (Pubitemid 23250020)
7. Wilson, I. A., and Stanfield, R. L. (1993) Antibody-antigen interactions. Curr. Opin. Struct. Biol. 3, 113-118. (Pubitemid 23058391)
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. (Pubitemid 23179389)
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. (Pubitemid 29190470)
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. (Pubitemid 39249643)
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. (Pubitemid 34983304)
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. (Pubitemid 37176897)
13. Metaxas, A., Tzartos, S., and Liakopoulou-Kyriakide, M. (2002) The production of antihexapeptide antibodies which recognize the S7, L6 and L13 ribosomal proteins of Escherichia coli. J. Pept. Sci. 8, 118-124. (Pubitemid 34211184)
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.
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. (Pubitemid 20021331)
16. Conte, L. L., Chothia, C., and Janin, J. (1999) The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285, 2177-2198. (Pubitemid 29078179)
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. (Pubitemid 26343518)
18. Jones, S., and Thornton, J. M. (1996) Principles of protein-protein interactions. Proc. Natl. Acad. Sci. USA 93, 13-20. (Pubitemid 26038096)
19. Webster, D. M., Henry, A. H., and Rees, A. R. (1994) Antibody-antigen interactions. Curr. Opin. Struct. Biol. 4, 123-129. (Pubitemid 24067254)
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.
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 A. Science 248, 712-719.
22. Garcia, K. C., Ronco, P. M., Verroust, P. J., Brünger, A. T., and Amzel, L. M. (1992) Threedimensional structure of an angiotensin II-Fab complex at 3 A: hormone recognition by an anti-idiotypic antibody. Science 257, 502-507.
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.
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. (Pubitemid 28294522)
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.
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. (Pubitemid 30093724)
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. (Pubitemid 29050545)
28. Gerstner, R. B., Carter, P., and Lowman, H. B. (2002) Sequence plasticity in the antigenbinding site of a therapeutic anti-HER2 antibody. J. Mol. Biol. 321, 851-862.
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. (Pubitemid 30368581)
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. (Pubitemid 27024689)
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. Biochemistry 32, 10423-10429.
32. 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.
33. Kaplan, M. H., and Meyeserian, M. (1962) An immunological cross-reaction between group-A streptococcal cells and human heart tissue. Lancet 1, 706-710.
34. Oldstone, M. B. (1998) Molecular mimicry and immune-mediated diseases. FASEB J. 12, 1255-1265. (Pubitemid 28475568)
35. 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. (Pubitemid 26302979)
36. Poljak, R. J. (1994) An idiotope-anti-idiotope complex and the structural basis of molecular mimicking. Proc. Natl. Acad. Sci. USA 91, 1599-1600. (Pubitemid 24080251)
37. Pan, Y., Yuhasz, S. C., and Amzel, L. M. (1995) Anti-idiotypic antibodies: biological function and structural studies. FASEB J. 9, 43-49.
38. 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. (Pubitemid 24048514)
39. 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 A resolution. J. Mol. Biol. 264, 137-151. (Pubitemid 26399999)
40. Fields, B. A., Goldbaum, F. A., Ysern, X., Poljak, R. J., and Mariuzza, R. A. (1995) Molecular basis of antigen mimicry by an antiidiotope. Nature 374, 739-742.
41. Eshhar, Z., Ofarim, M., and Waks, T. (1980) Generation of hybridomas secreting murine reaginic antibodies of anti-DNP specificity. J. Immunol. 124, 775-780. (Pubitemid 10135320)
42. 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.
43. James, L. C., Roversi, P., and Tawfik, D. S. (2003) Antibody multispecificity mediated by conformational diversity. Science 299, 1362-1367. (Pubitemid 36254643)
44. 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. (Pubitemid 32165670)
45. 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. (Pubitemid 32905165)
46. 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. (Pubitemid 24157598)
47. 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.
48. 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. (Pubitemid 2023165)
49. 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 A resolution and FabE8 to 2.26 A resolution. J. Mol. Biol. 281, 301-322. (Pubitemid 28360596)
50. 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. (Pubitemid 30347133)
51. 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. (Pubitemid 24341717)
52. Faelber, K., Kirchhofer, D., Presta, L., Kelley, R. F., and Muller, Y. A. (2001) The 1.85 A 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. (Pubitemid 33001167)
53. 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.
54. 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. (Pubitemid 2082181)
55. 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.
56. 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. (Pubitemid 19217563)
57. 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. (Pubitemid 33107377)
58. Tonegawa, S. (1983) Somatic generation of antibody diversity. Nature 302, 575-581.
59. 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.
60. 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.
61. 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. (Pubitemid 26108820)
62. Rajewsky, K. (1996) Clonal selection and learning in the antibody system. Nature 381, 751-758. (Pubitemid 26243107)
63. 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. (Pubitemid 29463241)
64. 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.
65. 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. (Pubitemid 27421966)
66. 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. (Pubitemid 27208062)
67. 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. (Pubitemid 26075223)
68. Yang, P. L., and Schultz, P. G. (1999) Mutational analysis of the affinity maturation of antibody 48G7. J. Mol. Biol. 294, 1191-1201. (Pubitemid 30008792)
69. 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. (Pubitemid 28168647)
70. 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. (Pubitemid 27406637)
71. 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. (Pubitemid 29288834)
72. 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. (Pubitemid 36637647)
73. 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. (Pubitemid 32002764)
74. 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.