Analysis of the antigen combining site: Correlations between length and sequence composition of the hypervariable loops and the nature of the antigen

Journal of Molecular Biology

Volumn 325, Issue 2, 2003, Pages 337-354

  Collis, Abigail V J ^a   Brouwer, Adam P ^a   Martin, Andrew C R ^a  

^a UNIVERSITY OF READING   (United Kingdom)

Author keywords

Antibodies; Antigen combining site; Complementarity determining regions; Sequence composition

Indexed keywords

ANTIGEN; PROTEIN;

ANTIBODY COMBINING SITE; ANTIGEN RECOGNITION; ARTICLE; AUTOIMMUNE DISEASE; COMPLEMENTARITY DETERMINING REGION; CORRELATION ANALYSIS; CROSS REACTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MODIFICATION;

EID: 0037227422     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)01222-6     Document Type: Article

References (37)

1. Chothia, C. & Lesk, A. M. (1987). Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901-917.
2. Riechmann, L., Clark, M., Waldmann, H. & Winter, G. (1988). Reshaping human antibodies for therapy. Nature (London), 332, 323-327.
3. 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.
4. Davies, D. R., Padlan, E. A. & Sheriff, S. (1990). Antibody-antigen complexes. Annu. Rev. Biochem. 59, 439-473.
5. Padlan, E. A. (1977). The structural basis for the specificity of antibody-antigen reactions and structural mechanisms for the diversification of antigen binding specificities. Quart. Rev. Biophys. 10, 35-65.
6. Braden, B. C. & Poljak, R. J. (1995). Structural features of the reactions between antibodies and protein antigens. FASEB J. 9, 9-16.
7. Wilson, I. A. & Stanfield, R. L. (1993). Antibody-antigen interactions. Curr. Opin. Struct. Biol. 3, 113-118.
8. Mariuzza, R. A., Phillips, S. E. V. & Poljak, R. J. (1987). The structural basis of antigen-antibody recognition. Annu. Rev. Biophys. Bioeng., 139-159.
9. MacCallum, R. M., Martin, A. C. R. & Thornton, J. M. (1996). Antibody-antigen interactions: Contact analysis and binding site topography. J. Mol. Biol. 262, 732-745.
10. 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.
11. Lara-Ochoa, F., Almagro, J. C., Vargas-Madrazo, E. & Conrad, M. (1996). Antibody-antigen recognition: A canonical structure paradigm. J. Mol. Evol. 43, 678-684.
12. Vargas-Madrazo, E., Lara-Ochoa, F. & Almagro, J. C. (1995). Canonical structure repertoire of the antigen-binding site of immunoglobulins suggests strong geometrical restrictions associated to the mechanism of immune recognition. J. Mol. Biol. 254, 497-504.
13. Lara-Ochoa, F., Vargas-Madrazo, E. & Almagro, J. C. (1995). Distributions of the use frequencies of amino acids in the hypervariable regions of immunoglobulins. J. Mol. Evol. 41, 98-103.
14. Wu, T. T., Johnson, G. & Kabat, E. A. (1993). Length distribution of CDRH3 in antibodies. Proteins: Struct. Funct. Genet. 16, 1-7.
15. Engberg, J., Jensen, L. B., Yenidunya, A. F., Brandt, K. & Riise, E. (2001). Phage-display libraries of murine antibody Fab fragments. In Antibody Engineering (Kontermann, R. & Dübel, S., eds), pp. 65-92, Springer Verlag, Heidelberg.
16. Winter, G., Griffiths, A. D., Hawkins, R. E. & Hoogenboom, H. R. (1994). Making antibodies by phage display technology. Annu. Rev. Immunol. 12, 433-455.
17. Knappik, A., Ge, L., Honegger, A., Pack, P., Fischer, M., Wellnhofer, G. et al. (2000). Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides. J. Mol. Biol. 296, 57-86.
18. Jespers, L. S., Roberts, A., Mahler, S. M., Winter, G. & Hoogenboom, H. R. (1994). Guiding the selection of human antibodies from phage display repertoires to a single epitope of an antigen. Biotechnology, 12, 899-903.
19. Miyazaki, C., Iba, Y., Yamada, Y., Takahashi, H., Sawada, J. & Kurosawa, Y. (1999). Changes in the specificity of antibodies by site-specific mutagenesis followed by random mutagenesis. Protein Eng. 12, 407-415.
20. Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B. & Thornton, J. M. (1997). CATH - A hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
21. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure. Biopolymers, 22, 2577-2637.
22. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H. et al. (2000). The protein data bank. Nucl. Acids Res. 28, 235-242.
23. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R. et al. (1977). The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
24. Martin, A. C. R., Toda, K., Stirk, H. J. & Thornton, J. M. (1995). Long loops in proteins. Protein Eng. 8, 1093-1101.
25. Martin, A. C. R. & Thornton, J. M. (1996). Structural families of loops in homologous proteins: Automatic classification, modelling and application to antibodies. J. Mol. Biol. 263, 800-815.
26. Swayne, D. F., Cook, D. & Buja, A. (1992). XGobi: interactive dynamic graphics in the X window system with a link to S. In ASA Proceedings of the 1991 American Statistical Association Meetings, pp. 1-8, American Statistical Association, VA.
27. Darsley, M. J. & Rees, A. R. (1985). Nucleotide sequences of five anti-lysozyme monoclonal antibodies. EMBO J. 4, 393-398.
28. Chowdhury, P. S. & Pastan, I. (1999). Improving antibody affinity by mimicking somatic hypermutation in vitro. Nature: Biotechnol. 17, 568-572.
29. Daugherty, P. S., Chen, G., Iverson, B. L. & Georgiou, G. (1999). Quantitative analysis of the effect of the mutation frequency on the affinity maturation of single chain Fv antibodies. Proc. Natl Acad. Sci. USA, 97, 2029-2034.
30. Kalsi, J. K., Martin, A. C. R. & Isenberg, D. A. (1995). Structure-function relation of anti-DNA antibodies. Lupus, 4, 245-248.
31. Martin, A. C. R. (1996). Accessing the Kabat antibody sequence database by computer. Proteins: Struct. Funct. Genet. 25, 130-133.
32. Kaartinen, M. & Makela, O. (1987). Functional analogues of the VKOx1 gene in different strains of mice: Evolutionary conservation but diversity based on V-J joining. J. Immunol. 138, 1613-1617.
33. Kaartinen, M., Solin, M.-L. & Makela, O. (1989). "Allelic" forms of immunoglobulin V genes in different strains of mice. EMBO J. 8, 1743-1748.
34. Williams, S. C., Frippiat, J.-P., Tomlinson, I. M., Ignatovich, O., le Franc, M.-P. & Winter, G. (1996). Sequence and evolution of the human germline V-repertoire. J. Mol. Biol. 264, 220-232.
35. Saul, F. A., Amzel, L. M. & Poljak, R. J. (1978). The preliminary refinement and structural analysis of the Fab fragment from human immunoglobulin New at 2.0 Å resolution. J. Biol. Chem. 253, 585-597.
36. Lamminmaki, U. & Kankare, J. A. (2001). Crystal structure of a recombinant anti-estradiol Fab fragment in complex with 17-β-estradiol. J. Biol. Chem. 276, 36687-36694.
37. Ban, N., Day, J., Wang, X., Ferrone, S. & McPherson, A. (1996). Crystal structure of an anti-anti-idiotype shows it to be self-complementary. J. Mol. Biol. 225, 617-627.