Antibody-Antigen Recognition and Conformational Changes

Handbook of Cell Signaling: Volume 1-3

Volumn 1-3, Issue , 2003, Pages 33-38

  Stanfield, Robyn L ^a   Wilson, Ian A ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34249277583     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-012124546-7/50366-1     Document Type: Chapter

References (73)

1. E.A. Padlan, D.M. Segal, T.F. Spande, D.R. Davies, S. Rudikoff and M. Potter (1973) Structure at 4.5 resolution of a phosphorylcholine-binding fab. Nature New Biol 245 165-167.
2. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov and P.E. Bourne (2000) The Protein Data Bank. Nucl. Acids Res. 28 235-242.
3. E.W. Silverton, M.A. Navia and D.R. Davies (1977) Three-dimensional structure of an intact human immunoglobulin. Proc. Natl. Acad. Sci. USA 74 5140-5144.
4. M. Marquart, J. Deisenhofer, R. Huber and W. Palmm (1980) Crystallographic refinement and atomic models of the intact immunoglobulin molecule Kol and its antigen-binding, fragment at 3.0 and 1.8 resolution. J. Mol. Biol. 141 369-391.
5. L.J. Harris, S.B. Larson, K.W. Hasel, J. Day, A. Greenwood and A. McPherson (1992) The three-dimensional structure of, an intact monoclonal antibody for canine lymphoma. Nature 360 369-372.
6. L.J. Harris, S.B. Larson, K.W. Hasel and A. McPherson (1997) Refined structure of an intact IgG2a monoclonal antibody. Biochemistry 36 1581-1597.
7. E.O. Saphire, P.W. Parren, R. Pantophlet, M.B. Zwick, G.M. Morris, P.M. Rudd, R.A. Dwek, R.L. Stanfield, D.R. Burton and I.A. Wilson (2001) Crystal structure of a neutralizing human IgG against HIV-1: a template for vaccine design. Science 293 1155-1159.
8. P.G. Schultz and R.A. Lerner (1995) From molecular diversity to catalysis: Lessons from the immune system. Science 269 1835-1842.
9. R.A. Lerner, S.J. Benkovic and P.G. Schultz (1991) At the cross-roads of chemistry and immunology: catalytic antibodies. Science 252 659-667.
10. D. Hilvert (2000) Critical analysis of antibody catalysis. Annu. Rev. Biochem. 69 751-793.
11. C. Tellier (2002) Exploiting antibodies as catalysts: potential therapeutic applications. Transfus. Clin. Biol. 9 1-8.
12. R. Stanfield, E. Cabezas, A. Satterthwait, E. Stura, A. Profy and I. Wilson (1999) Dual conformations for the HIV-1 gp 120 V3 loop in complexes with different neutralizing Fabs. Structure Fold. Des. 7 131-142.
13. N. Ban, C. Escobar, K.W. Hasel, J. Day, A. Greenwood and A. McPherson (1995) Structure of an anti-idiotypic Fab against feline peritonitis virus-neutralizing antibody and a comparison with the complexed Fab. FASEB J. 9 107-114.
14. P.D. Kwong, R. Wyatt, J. Robinson, R.W. Sweet, J. Sodroski and W.A. Hendrickson (1998) Structure of an HIV gp120 envelope glycoprotien in complex with the CD4 receptor and a neutralizing human antibody. Nature 393 648-659.
15. J.B. Ghiara, E.A. Stura, R.L. Stanfield, A.T. Profy and I.A. Wilson (1994) Crystal structure of the principal neutralization site of HIV-1. Science 264 82-85.
16. J.B. Ghiara, D.C. Ferguson, A.C. Satterthwait, H.J. Dyson and I.A. Wilson (1997) Structure-based design of a constrained peptide mimic of the HIV-1 V3 loop neutralization site. J. Mol. Biol. 266 31-39.
17. N. Verdaguer, M.G. Mateu, D. Andreu, E. Giralt, E. Domingo and I. Fita (1995) Structure of the major antigenic loop of foot-and-mouth disease virus complexed with a neutralizing antibody: direct involvement of the Arg-Gly-Asp motif in the interaction. EMBO J. 14 1690-1696.
18. H. Liu, T.J. Smith, W.M. Lee, A.G. Mosser, R.R. Rueckert, N.H. Olson, R.H. Cheng and T.S. Baker (1994) Structure determination of a Fab fragment that neutralizes human rhinovirus 14 and analysis of the Fab-virus complex. J. Mol. Biol. 240 127-137.
19. J. Tormo, D. Blaas, N.R. Parry, D. Rowlands, D. Stuart and I. Fita (1994) Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2. EMBO J. 13 2247-2256.
20. J.M. Rini, R.L. Stanfield, E.A. Stura, P.A. Salinas, A.T. Profy and I.A. Wilson (1993) Crystal structure of a human immunodeficiency virus type 1 neutralizing antibody, 50.1, in complex with its V3 loop peptide antigen. Proc. Natl. Acad. Sci. USA 90 6325-6329.
21. E.A. Hewat and D. Blaas (1996) Structure of a neutralizing antibody bound bivalently to human rhinovirus 2. EMBO J. 15 1515-1523.
22. E.A. Hewat, N. Verdaguer, I. Fita, W. Blakemore, S. Brookes, A. King, J. Newman, E. Domingo, M.G. Mateu and D.I. Stuart (1997) Structure of the complex of an Fab fragment of a neutralizing antibody with foot-and-mouth disease virus: positioning of a highly mobile antigenic loop. EMBO J 16 1492-1500.
23. T.J. Smith, E.S. Chase, T.J. Schmidt, N.H. Olson and T.S. Baker (1996) Neutralizing antibody to human rhinovirus 14 penetrates the receptor-binding canyon. Nature 383 350-354.
24. W.R. Wikoff, G. Wang, C.R. Parrish, R.H. Cheng, M.L. Strassheim, T.S. Baker and M.G. Rossmann (1994) The structure of a neutralized virus: canine parvovirus complexed with neutralizing antibody fragment. Structure 2 595-607.
25. J.M. van Den Elsen, D.A. Kuntz, F.J. Hoedemaeker and D.R. Rose (1999) Antibody C219 recognizes and α-helical epitope on P-glycoprotein. Proc. Natl. Acad. Sci. USA 96 13679-13684.
26. M.J. Kaminski, C.R. MacKenzie, M.J. Mooibroek, T.E. Dahms, T. Hirama, A.N. Houghton, P.B. Chapman and S.V. Evans (1999) The role of homophilic binding in anti-tumor antibody R24 recognition of molecular surfaces. Demonstration of an intermolecular β-sheet interaction between Vh domains. J. Biol. Chem. 274 5597-5604.
27. S.L. Pichla, R. Murali and R.M. Burnett (1997) The crystal structure of a Fab fragment to the melanoma-associated GD2 ganglioside. J. Struct. Biol. 119 6-16.
28. P.D. Jeffrey, J. Bajorath, C.Y. Chang, D. Yelton, I. Hellstrom, K.E. Hellstrom and S. Sheriff (1995) The x-ray structure of an anti-tumor antibody in complex with antigen. Nat. Struct. Biol. 2 466-471.
29. L.J. Harris, S.B. Larson, K.W. Hasel, J. Day, A. Greenwood and A. McPherson (1992) The three-dimensional structure of an intact monoclonal antibody for canine lymphoma. Nature 360 369-372.
30. S. Sheriff, C.Y. Chang, P.D. Jeffrey and J. Bajorath (1996) X-ray structure of the uncomplexed anti-tumor antibody BR96 and comparison with its antigen-bound form. J. Mol. Biol. 259 938-946.
31. R.L. Brady, D.J. Edwards, R.E. Hubbard, J.S. Jiang, G. Lange, S.M. Roberts, R.J. Todd, J.R. Adair, J.S. Emtage, D.J. King and R.J. Todd (1992) Crystal structure of a chimeric Fab'fragment of an antibody binding tumour cells. J. Mol. Biol. 227 253-264.
32. S. Tonegawa (1983) Somatic generation of antibody diversity. Nature 302 575-581.
33. I.M. Tomlinson, G. Walter, J.D. Marks, M.B. Llewelyn and G. Winter (1992) The repertoire of human germline VH sequences reveals about fifty groups of VH segments with different hypervariable loops. J. Mol. Biol. 227 776-798.
34. G.P. Cook and I.M. Tomlinson (1995) The human immunoglobulin VH repertoire. Immunol. Today 16 237-242.
35. J.V. Ravetch, U. Siebenlist, S. Korsmeyer, T. Waldmann and P. Leder (1981) Structure of the human immunoglobulin μ locus: characterization of embryonic and rearranged J and D genes. Cell 27 583-591.
36. S.J. Corbett, I.M. Tomlinson, E.L.L. Sonnhammer, D. Buck and G. Winter (1997) Sequence of the human immunoglobulin diversity (D) segment locus: a systematic analysis provides no evidence for the use of DIR segments, inverted D segments, “minor” D segments or D-D recombination. J. Mol. Biol. 270 587-597.
37. S.C. Williams, J.P. Frippiat, I.M. Tomlinson, O. Ignatovich, M.P. Lefranc and G. Winter (1996) Sequence and evolution of the human germline Vλ repertoire. J. Mol. Biol. 264 220-232.
38. K.F. Schable and H.G. Zachau (1993) The variable genes of the human immunoglobulin κ locus. Biol. Chem. Hoppe-Seyler 374 1001-1022.
39. P.A. Hieter, J.V. Maizel Jr. and P. Leder (1982) Evolution of human immunoglobulin κ J region genes. J. Biol. Chem. 257 1516-1522.
40. T.J. Vasicek and P. Leder (1990) Structure and expression of the human immunoglobulin λ genes. J. Exp. Med. 172 609-620.
41. I.A. Wilson and R.L. Stanfield (1994) Antibody-antigen interactions: new structures and new conformational changes. Curr. Opin. Struct. Biol. 4 857-867.
42. F. Lara-Ochoa, J.C. Almagro, E. Vargas-Madrazo and M. Conrad (1996) Antibody-antigen recogtnition: a canonical structure paradigm. J. Mol. Evol. 43 678-684.
43. R.M. MacCallum, A.C. Martin and J.M. Thornton (1996) Antibody-antigen interactions: contact analysis and binding site topography. J. Mol. Biol. 262 732-745.
44. C. Chothia and A.M. Lesk (1987) Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196 901-917.
45. C. Chothia, A.M. Lesk, A. Tramontano, M. Levitt, S.J. Smith-Gill, G. Air, S. Sheriff, E.A. Padlan, D. Davies, W.R. Tulip, P.M. Colman, S. Spinelli, P.M. Alzari and R.J. Poljak (1989) Conformations of immunoglobulin hypervariable regions. Nature 342 877-883.
46. B. Al-Lazikami, A.M. Lesk and C. Chothia (1997) Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol. 273 927-948.
47. A.C. Martin and J.M. Thornton (1996) Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies. J. Mol. Biol. 263 800-815.
48. H. Shirai, A. Kidera and H. Nakamura (1996) Structural classification of CDR-H3 in antibodies. FEBS Lett 399 1-8.
49. J. Foote and C. Milstein (1994) Conformational isomerism and the diversity of antibodies. Proc. Natl. Acad. Sci. USA 91 10370-10374.
50. J.H. Arevalo, M.J. Taussig and I.A. Wilson (1993) Molecular basis of crossreactivity and the limits of antibody-antigen complementarity. Nature 365 859-863.
51. J.H. Arevalo, E.A. Stura, M.J. Taussig and I.A. Wilson (1993) Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex. J. Mol. Biol. 231 103-118.
52. J.H. Arevalo, C.A. Hassig, E.A. Stura, M.J. Sims, M.J. Taussig and I.A. Wilson (1994) Structural analysis of antibody specificity. Detailed comparison of five Fab'-steroid complexes. J. Mol. Biol. 241 663-690.
53. J.M. Rini, U. Schulze-Gahmen and I.A. Wilson (1992) Structural evidence for induced fit as a mechanism for antibody-antigen recognition. Science 255 959-965.
54. U. Schulze-Gahmen, J.M. Rini and I.A. Wilson (1993) Detailed analysis of the free and bound conformations of an antibody. X-ray structures of Fab 17/9 and three different Fab-peptide complexes. J. Mol. Biol. 234 1098-1118.
55. J.N. Herron, X.M. He, D.W. Ballard, P.R. Blier, P.E. Pace, A.L. Bothwell, E.W. Voss Jr. and A.B. Edmundson (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.
56. R.L. Stanfield, T.M. Fieser, R.A. Lerner and I.A. Wilson (1990) Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8. Science 248 712-719.
57. J. Lescar, R. Stouracova, M.M. Riottot, V. Chitarra, J. Brynda, M. Fabry, M. Horejsi, J. Sedlacek and G.A. Bentley (1997) Three-dimensional structure of an Fab-peptide complex: structural basis of HIV-1 protease inhibition by a monoclonal antibody. J. Mol. Biol. 267 1207-1222.
58. T. Simon and K. Rajewsky (1992) A functional antibody mutant with an insertion in the framework region 3 loop of te VH domain: implications for antibody engineering. Protein Eng. 5 229-234.
59. J.B. Charbonnier, E. Carpenter, B. Gigant, B. Golinelli-Pimpaneau, Z. Eshhar, B.S. Green and M. Knossow (1995) Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog: structural similarities in esterase-like catalytic antibodies. Proc. Natl. Acad. Sci. USA 92 11721-11725.
60. G.J. Wedemayer, P.A. Patten, L.H. Wang, P.G. Schultz and R.C. Stevens (1997) Structural insights into the evolution of an antibody combining site. Science 276 1665-1669.
61. R.L. Stanfield, M. Takimoto-Kamimura, J.M. Rini, A.T. Profy and I.A. Wilson (1993) Major antigen-induced domain rearrangements in an antibody. Structure 1 83-93.
62. E.C. Mundorff, M.A. Hanson, A. Varvak, H. Ulrich, P.G. Schultz and R.C. Stevens (2000) Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearragement. Biochemistry 39 627-632.
63. M.A. Holmes and J. Foote (1997) Structural consequences of humanizing an antibody. J. Immunol. 158 2192-2201.
64. Y. Li, H. Li, S.J. Smith-Gill and R.A. Mariuzza (2000) Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63. Biochemistry 39 6296-6309.
65. B. Golinelli-Pimpaneau, B. Gigant, T. Bizebard, J. Navaza, P. Saludjian, R. Zemel, D.S. Tawfik, Z. Eshhar, B.S. Green and M. Knossow (1994) Crystal structure of a catalytic antibody Fab with esterase-like activity. Structure 2 175-183.
66. K. Gruber, B. Zhou, K.N. Houk, R.A. Lerner, C.G. Shevlin and I.A. Wilson (1999) Structural basis for antibody catalysis of a disfavored ring closure reaction. Biochemistry 38 7062-7074.
67. S. Monaco-Malbet, C. Berthet-Colominas, A. Novelli, N. Battai, N. Piga, V. Cheynet, F. Mallet and S. Cusack (2000) Mutual conformational adaptations in antigen and antibody upon complex formation between an Fab and HIV-1 capsid protein p24. Structure Fold. Des. 8 1069-1077.
68. P. Wirsching, J.A. Ashley, C.H. Lo, K.D. Janda and R.A. Lerner (1995) Reactive immunization. Science 270 1775-1782.
69. B.S. Green (1989) Monoclonal antibodies as catalysts and templates for organic chemical reactions. Adv. Biotechnol. Proc. 11 359-393.
70. P.J. Kraulis (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24 946-950.
71. E.A. Merritt and M.E.P. Murphy (1994) Raster3D Version 2.0—a program for photorealistic molecular graphics. Acta Cryst.D 50 869-873.
72. E.A. Merritt and D.J. Bacon (1997) Raster3D photorealistic molecular graphics. Meth. Enzymol. 277 505-524.
73. A. Nicholls, K.A. Sharp and B. Honig (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11 281-296.