Antibody-antigen interactions: Contact analysis and binding site topography

Journal of Molecular Biology

Volumn 262, Issue 5, 1996, Pages 732-745

  MacCallum, Robert M ^a   Martin, Andrew C R ^a   Thornton, Janet M ^a,b  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Antigen type; Complementarity determining region; Molecular recognition; Surface shape

Indexed keywords

IMMUNOGLOBULIN F(AB) FRAGMENT;

ANTIBODY COMBINING SITE; ANTIGEN ANTIBODY REACTION; ARTICLE; BINDING SITE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DATA BASE; IMMUNOLOGY; PRIORITY JOURNAL; PROTEIN CONFORMATION; TOPOGRAPHY;

EID: 0030580057     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0548     Document Type: Article

References (41)

1. Arevalo, J. H., Hassig, C. A., Stura, E. A., Sims, M. J., Taussig, M. J. & Wilson, I. A. (1994). Structural-analysis of antibody specificity - detailed comparison of 5 Fab'-steroid complexes. J. Mol. Biol. 241, 663-690.
2. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
3. Brinkman, K., Termaat, R., Berden, J. H. M. & Smeenk, R. J. T. (1990). Anti-DNA antibodies and lupus nepritis: the complexity of cross-reactivity. Immun. Today, 11, 232-234.
4. Brünger, A. T., Leahy, D. J., Hynes, T. R. & Fox, R. O. (1991). 2.9 Å-resolution structure of an anti-dinitrophenyl-spin-label monoclonal-antibody Fab fragment with bound hapten. J. Mol. Biol. 221, 239-256.
5. Chester, K. A. & Hawkins, R. E. (1995). Clinical issues in antibody design. Trends Biotechnol. 13, 294-300.
6. Chothia, C. & Lesk, A. M. (1987). Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901-917.
7. Chothia, C., Lesk, A. M., Levitt, M., Amit, A. G., Mariuzza, R. A., Phillips, S. E. V. & Poljak, R. J. (1986). The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure. Science, 233, 755-758.
8. Chothia, C., Lesk, A. M., Tramontane, A., Levitt, M., Smith-Gill, S. J., Air, G., Sheriff, S., Padlan, E. A., Davies, D. R., Tulip, W. R., Colman, P. M., Alzri, P. M. & Poljak, R. J. (1989). Conformations of immunoglobulin hypervariable regions. Nature, 342, 877-883.
9. Churchill, M. E. A., Stura, E. A., Pinilla, C., Appel, J. R., Houghten, R. A., Kono, D. H., Balderas, R. S., Fieser, G. G., Schulzegahmen, U. & Wilson, I. A. (1994). Crystal-structure of a peptide complex of antiinfluenza peptide antibody-Fab-26/9 - comparison of two different antibodies bound to the same peptide antigen. J. Mol. Biol. 241, 534-556.
10. Delaney, J. S. (1992). Finding and filling protein cavities using cellular logic operations. J. Mol. Graph. 101, 174.
11. Gerstein, M. (1992). A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen combining sites. Acta Crystallog. sect. A, 48, 271-276.
12. Herron, J. N., He, X. M., Ballard, D. W., Blier, P. R., Pace, P. E., Bothwell, A. L. M., Voss, E. W. & Edmundson, A. B. (1991). An autoantibody to single-stranded-DNA - comparison of the 3-dimensional structures of the unliganded Fab and a deoxynucleotide Fab complex. Proteins: Struct. Funct. Genet. 11, 159-175.
13. Hilvert, D. (1994). Catalytic antibodies. Curr. Opin. Struct. Biol. 4, 612-617.
14. Jeffrey, P. D., Schildbach, J. F., Chang, C. Y. Y., Kussie, P. H., Margolies, M. N. & Sheriff, S. (1995). Structure and specificity of the antidigoxin antibody-40-50. J. Mol. Biol. 248, 344-360.
15. Killard, A. J., Deasy, B., O'Kennedy, R. & Smyth, M. R. (1995). Antibodies - production, functions and applications in biosensors. Trends Anal. Chem. 14, 257-266.
16. Kuhn, L. A., Siani, M. A., Pique, M. E., Fisher, C. L., Getzoff, E. D. & Tainer, J. A. (1992). The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. J. Mol. Biol. 228, 13-22.
17. Lawrence, M. C. & Colman, P. M. (1993). Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946-950.
18. Lee, B. K. & Richards, F. M. (1971). The interpretation of protein structures: Estimation of static accessibility. J. Mol. Biol. 55, 379-400.
19. Lescar, J., Pellegrini, M., Souchon, H., Tello, D., Poljak, R. J., Peterson, N., Greene, M. & Alzari, P. M. (1995). Crystal-structure of a cross-reaction complex between Fab F9.13.7 and guinea-fowl lysozyme. J. Biol. Chem. 270, 18067-18076.
20. Love, R. A., Villafranca, J. E., Aust, R. M., Nakamura, K. K., Jue, R. A., Major, J. G., Radhakrishnan, R. & Butler, W. F. (1993). How the anti-(metal chelate) antibody CHA255 is specific for the metal-ion of its antigen - X-ray structures for 2 Fab' hapten complexes with different metals in the chelate. Biochemistry, 32, 10950-10959.
21. Martin, A. C. R. & Thornton, J. M. (1996). Structural families in loops of homologous proteins: Automatic classification, modelling and application to antibodies. J. Mol. Biol. in the press.
22. Martin, A. C. R., Cheetham, J. C. & Rees, A. R. (1991). Molecular modelling of antibody combining sites. Meth. Enzymol. 203, 121-153.
23. Nicholls, A., Sharp, K. A. & Honig, B. (1991). Protein folding and association - insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11, 281-296.
24. Padlan, E. A., Silverton, E. W., Sheriff, S., Cohen, G. H., Smithgill, S. J. & 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.
25. Padlan, E. A., Abergel, C. & Tipper, J. P. (1995). Identification of specificity-determining residues in antibodies. FASEB J. 9, 133-139.
26. Pokkuluri, P. R., Bouthillier, F., Li, Y. G., Kuderova, A., Lee, J. & Cygler, M. (1994). Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA:crystal-structures of native Fab and three Fab-mononucleotide complexes. J. Mol. Biol. 243, 283-297.
27. Prasad, L., Vandonselaar, M., Lee, J. S. & Delbaere, L. T. J. (1988). Structure determination of a monoclonal Fab fragment specific for histidine-containing protein of the phosphoenolpyruvate - sugar phosphotransferase system of Escherichia coli. J. Biol. Chem. 263, 2571-2574.
28. Rees, A. R., Staunton, D., Webster, D. M., Searle, S. J., Henry, A. H. & Pedersen, J. T. (1994). Antibody design: beyond the natural limits. Trends Biotechnol. 12, 199-206.
29. Rini, J. M., Stanfield, R. L., Stura, E. A., Saunas, P. A., Profy, A. T. & Wilson, I. A. (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.
30. Satow, Y., Cohen, G. H., Padlan, E. A. & Davies, D. R. (1986). Phosphocholine binding immunoglobulin Fab McPC603 an X-ray-diffraction study at 2.7 Å. J. Mol. Biol. 190, 593-604.
31. Schulzegahmen, U., Rini, J. M. & Wilson, I. A. (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.
32. Stanfield, R. L., Takimotokamimura, M., Rini, J. M., Profy, A. T. & Wilson, I. A. (1993). Major antigen-induced domain rearrangements in an antibody. Structure, 1, 83-93.
33. Tulip, W. R., Varghese, J. N., Laver, W. G., Webster, R. G. & Colman, P. M. (1992). Refined crystal-structure of the influenza virus-N9 neuraminidase NC41 Fab complex. J. Mol. Biol. 227, 122-148.
34. Ward, J. H. (1963). Hierachical grouping to optimize an objective function. J. Am. Statist. Assoc. 58, 236-244.
35. Webster, D. M., Henry, A. H. & Rees, A. R. (1994). Antibody-antigen interactions. Curr. Opin. Struct. Biol. 4, 123-129.
36. Wilson, I. A. & Stanfield, R. L. (1993). Antibody-antigen interactions. Curr. Opin. Struct. Biol. 3, 113-118.
37. Wilson, I. A. & Stanfield, R. L. (1994). Antibody-antigen interactions - new structures and new conformational-changes. Curr. Opin. Struct. Biol. 4, 857-867.
38. Winter, G., Griffiths, A. D., Hawkins, R. E. & Hoogenboom, H. R. (1994). Making antibodies by phage display technology. Annu. Rev. Immunol. 12, 433-455.
39. Wishart, D. (1969). An algorithm for hierachical classifications. Biometrics, 25, 165-170.
40. Wong, Y. W., Kussie, P. H., Parhamiseren, B. & Margolies, M. N. (1995). Modulation of antibody-affinity by an engineered amino-acid substitution. J. Immunol. 154, 3351-3358.
41. Wu, T. T. & 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.