Conformational analysis of the first observed non-proline cis-peptide bond occurring within the complementarity determining region (CDR) of an antibody

Journal of Molecular Biology

Volumn 284, Issue 3, 1998, Pages 549-555

  Bates, Paul A ^a   Dokurno, Pawel ^a   Freemont, Paul S ^a   Sternberg, Michael J E ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

Anti tumour antibody; Non proline cis peptide bond; Novel antibody to peptide recognition

Indexed keywords

ANTIBODY; CANCER ANTIBODY; IMMUNOGLOBULIN HEAVY CHAIN;

ANTIBODY STRUCTURE; ARTICLE; COMPLEMENTARITY DETERMINING REGION; ISOMERISM; PRIORITY JOURNAL; PROTEIN CONFORMATION;

EID: 0032484160     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2210     Document Type: Article

References (34)

1. Al-Lazikani, B., Lesk, A. M. & Chothia, C. (1997). Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol. 273, 927-948.
2. Barclay, A. N., Birkeland, M. L., Brown, M. H., Beyers, A. D., Davis, S. J., Somoza, C. & Williams, A. F. (1993). The Leukocyte Antigen Facts Book, Academic Press.
3. Bates, P. A., Jackson, R. M. & Sternberg, M. J. E. (1998). Model building by comparison: a combination of expert knowledge and computer automation. Proteins: Struct. Funct. Genet. Suppl. 1, 59-67.
4. Bernstein, F. C., Koetzle, T. F., Williams, G., Meyer, D. J., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1997). The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
5. Braden, B. C., Fields, B. A., Ysern, X., Goldbaum, F. A., Dall'Acqua, W., Schwarz, F. P., Poljak, R. J. & Mariuzza, R. A. (1996). Crystal structure of the complex of the variable domain of antibody D1.3 and turkey egg white lysozyme: A novel conformation change in antibody CDR-L3 selects for antigen. J. Mol. Biol. 257, 889-894.
6. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983). CHARMM: A program for macromolecular energy minimization and dynamics calculations. J. Comp. Chem. 4, 187-217.
7. Bruccoleri, R. E. & Karplus, M. (1987). Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers, 26, 137-168.
8. Brunger, 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.
9. Chothia, C. & Lesk, A. M. (1987). Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901-918.
10. Chothia, C., Novotny. J., Bruccoleri, R. & Karplus, M. (1985). Domain association in immunoglobulin molecules. The packing of variable domains. J. Mol. Biol. 186, 651-663.
11. Chothia, C., Lesk, A. M., Tramontano, A., Levitt, M., Smith-Gill, S. J., Air, G., Sheriff, S., Padlan, E. A., Davies, D., Tulip, W. R., Colman, P. M., Spinelli, S., Alzari, P. M. & Poljak, R. J. (1989). Conformations of immunoglobulin hypervariable regions. Nature, 342, 877-883.
12. Connolly, M. L. (1983). Analytical molecular surface calculation. J. Appl. Crystallog. 16, 548-558.
13. Dokurno, P., Bates, P. A., Band, H. A., Stewart, L. M. D., Lally, J. M., Burchell, J. M., Taylour-Papadimitriou, J., Snary, D., Sternberg, M. J. E. & Freemont, P. S. (1998). Crystal structure at 1.95 Å resolution of the breast tumour-specific antibody SM3 complexed with its peptide epitope reveals novel hypervariable loop recognition. J. Mol. Biol. 284, 691-706.
14. Drakenberg, T., Dahlqvist, K. I. & Forsen, S. (1972). The barrier to internal rotation in amides. IV. N.N-Dimethylamides; substituents ans solvent effects. J. Phys. Chem. 76, 2178-2183.
15. Fidelis, K., Stern, P. S., Bacon, D. & Moult, J. (1994). Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng. 7, 953-960.
16. Herzberg, O. & Moult, J. (1991). Analysis of the steric strain in the polypeptide backbone of protein molecules. Proteins: Struct. Funct. Genet. 11, 223-229.
17. Jones, T. A. & Thirup, S. (1986). Using known substructures in protein model building and crystallography. EMBO J. 5, 819-823.
18. Kabat, E. A., Wu, T. T., Perry, H. M., Gottesman, K. S. & Foeller, C. (1991). Sequences of Proteins of Immunological Interest, 5th edit., Natl. Inst. of Health, Bethesda, MD.
19. Keitel, T., Kramer, A., Wessner, H., Scholz, C., Schneider-Mergener, J. & Wolfgang, H. (1997). Crystallographic analysis of anti-p24 (HIV-1) monoclonal antibody cross-reactivity and polyspecificity. Cell, 91, 811-820.
20. Laskowski, R. A., McArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26, 283-291.
21. MacArthur, M. W. & Thornton, J. M. (1991). Influence of proline residues on protein conformation. J. Mol. Biol. 218, 397-412.
22. Morea, V., Tramontano, A., Rustici, M., Chothia, C. & Lesk, A. M. (1998). Conformations of the third hypervariable region in the VH domain of immunoglobulins. J. Mol. Biol. 275, 269-294.
23. Moult, J. & James, M. N. (1986). An algorithm for the determining the conformation of polypeptide segments in proteins by systematic search. Proteins: Struct. Funct. Genet. 1, 146-163.
24. Olivia, B., Bates, P. A., Querol, E., Aviles, F. X. & Sternberg, M. J. E. (1998). Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction. J. Mol. Biol. 279, 1193-1210.
25. Pokkuluri, P. R., Bouthiller, F., Li, Y., Kuderova, A., Lee, J. & Cygler, M. (1994). Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. J. Mol. Biol. 243, 283-297.
26. Ramachandran, G. N. & Mitra, A. K. (1976). An Explanation for the rare occurrence of cis peptide units in proteins and polypeptides. J. Mol. Biol. 107, 85-92.
27. Rini, J. M., Stanfield, R. L., Stura, E. A., Salinas, 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.
28. Shiria, H., Kidera, A. & Nakamura, H. (1996). Structural classification of H3 in antibodies. FEBS Letters, 399, 1-8.
29. Sibanda, B. L., Blundell, T. L. & Thornton, J. N. (1989). Conformation of ß-hairpins in protein structure. J. Mol. Biol. 206, 759-777.
30. Stanfield, R. L. & Wilson, I. A. (1993). X-ray crystallographic studies of antibody-peptide complexes. ImmunoMethods, 3, 211-221.
31. Stanfield, R. L. & Wilson, I. A. (1995). Protein-peptide interactions. Curr. Opin. Struct. Biol. 5, 103-113.
32. Stanfield, R. L., Takimoto-Kamimura, M., Rini, J. M., Profy, A. T. & Wilson, I. A. (1993). Major antigen-induced domain rearrangements in an antibody. Structure, 1, 83-93.
33. Stewart, D. E., Sarkar, A. & Wampler, J. E. (1990). Occurrence and role of cis-peptide-bonds in protein structures. J. Mol. Biol. 214, 253-260.
34. Wu, T. T., Johnson, G. & Kabat, E. A. (1993). Length distribution of CDRH3 in antibodies. Proteins: Struct. Funct. Genet. 16, 1-7.