Structural families in loops of homologous proteins: Automatic classification, modelling and application to antibodies

Journal of Molecular Biology

Volumn 263, Issue 5, 1996, Pages 800-815

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

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Canonicals; Cluster analysis; Complementarity determining regions; Loops; Modelling

Indexed keywords

ANTIBODY; POLYPEPTIDE;

ANTIBODY STRUCTURE; ARTICLE; CLASSIFICATION; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FAMILY;

EID: 0030589039     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0617     Document Type: Article

References (56)

1. Baker, E. N. & Hubbard, R. E. (1984). Hydrogen bonding in globular proteins. Prog. Biophys. Mol. Biol. 44, 97-179.
2. Barré, S., Greenberg, A. S., Flajnk, M. F. & Chothia, C. (1994). Structural conservation of hypervariable regions in immunoglobulins' evolution. Nature Struct. Biol. 1, 915-920.
3. 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.
4. Brady, R. L., Edwards, D. J., Hubbard, R. E., Jiang, J. S., Lange, G., Roberts, S. M., Todd, R. J., Adair, J. R., Emtage, J. S., King, D. J. & Low, D. C. (1992). Crystal structure of a chimeric Fab' fragment of an antibody binding tumor-cells. J. Mol. Biol. 227, 253-264.
5. Bruccoleri, R. E. & Karplus, M. (1987). Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers, 26, 137-168.
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., 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.
9. H segments. J. Mol. Biol. 227, 799-817.
10. Claessens, M., Vancutsem, E., Lasters, I. & Wodak, S. (1989). Modeling the polypeptide backbone with spare parts from known protein structures. Protein Eng. 2, 335-345.
11. Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C. (1978). A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure (Dayhoff, M. O., ed.), vol. 5, suppl. 3, National Biomedical Research Foundation, Silver Spring, Washington DC.
12. Fidelis, K., Stern, P. S., Bacon, S. & Moult, J. (1994). Comparison of systematic search and database methods for constructing segments of protein-structure. Protein Eng. 7, 953-960.
13. Fine, R. M., Wang, H., Shenkin, P. S., Yarmush, D. L. & Levinthal, C. (1986). Predicting antibody hypervariable loop conformations II: minimization and molecular dynamics studies of McPC603 from many randomly generated loop conformations. Proteins: Struct. Funct. Genet. 1, 342-362.
14. Golinelli-Pimpaneua, B., Gigant, B., Bizebard, T., Navaza, J., Saludjian, P., Zemel, R., Tawfik, D. S., Eshhar, Z., Green, B. S. & Knossow, M. (1994). Crystal structure of a catalytic antibody Fab with esterase-like activity. Structure, 2, 175-183.
15. Gregory, D. S. (1992). Prediction, design and characterisation of metal binding sites in antibodies. D. Phil. thesis, University of Oxford.
16. Gregory, D. S., Martin, A. C. R., Cheetham, J. C. & Ress, A. R. (1993). The prediction and characterization of metal binding sites in proteins. Protein Eng. 6, 29-35.
17. Guddat, L. W., Shan, L., Anchin, J. M., Linthicum, D. S. & Edmundson, A. B. (1994). Local and transmitted conformational changes on complexation of an anti-sweetener Fab. J. Mol. Biol. 236, 247-274.
18. Haynes, M. R., Stura, E. A., Hilvert, D. & Wilson, I. A. (1994). Routes to catalysis: structure of a catalytic antibody and comparison with its natural counterpart. Science, 263, 646-652.
19. Herron, J. N., He, X. M., Mason, M. L., Voss, E. W. & Edmundson, A. B. (1989). 3-Dimensional structure of a fluorescein Fab complex crystallized in 2-methyl-2,4-pentanediol. Proteins: Struct. Funct. Genet. 5, 271-280.
20. 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.
21. Jedrzejas, M. J., Miglietta, J., Griffin, J. A. & Luo, M. (1995). Structure of a monoclonal anti-ICAM-1 antibody R6.5 Fab fragment at 2.8 Ångström resolution. Acta Crystallog. sect. D, 51, 380-385.
22. Jeffrey, P. D., Strong, R. K., Sieker, L. C., Chang, C. Y. Y., Campbell, R. L., Petsko, G. A., Haber, E., Margolies, M. N. & Sheriff, S. (1993). 26-10 Fab-digoxin complex - affinity and specificity due to surface complementarity. Proc. Natl Acad. Sci. USA, 90, 10310-10314.
23. Jones, T. A. & Thirup, S. (1986). Using known substructures in protein model building and crystallography. EMBO J. 5, 819-822.
24. Kabat, E. A., Wu, T. T., Perry, H. M., Gottesman, K. S. & Foeller, C. (1991). Sequences of Proteins of Immunological Interest. 5th edit., U. S. Department of Health and Human Services, National Institutes for Health, Bethesda, MD.
25. Lee, B. K. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379-400.
26. Leszczynski, J. F. & Rose, G. D. (1986). Loops in globular proteins: a novel category of secondary structure. Science, 234, 849-855.
27. 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.
28. 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.
29. Martin, A. C. R., Cheetham, J. C. & Rees, A. R. (1989). Modelling antibody hypervariable loops: a combined algorithm. Proc. Natl Acad. Sci. USA, 86, 9268-9272.
30. Martin, A. C. R., Toda, K., Stirk, H. & Thornton, J. M. (1995). Long loops in proteins. Protein Eng. 8, 1093-1101.
31. Milner-White, E. J. (1986). Classification of β-hairpin turns. Biochem. Soc. Trans. 14, 877.
32. Milner-White, E. J. & Poet, R. (1986). Four classes of β-hairpins in proteins. Biochem. J. 240, 289-292.
33. Milner-White, E. J. & Poet, R. (1987). Loops, bulges, turns and hairpins in proteins. Trends Biochem. Sci. 12, 189-192.
34. 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 HyHe1-10 Fab-lysozyme complex. Proc. Natl Acad. Sci. USA, 86, 5938-5942.
35. Pedersen, J. T. (1993). Molecular modelling of antibody combining sites. PhD thesis, University of Bath.
36. Prasad, L., Sharma, S., van Donselaar, M., Quail, J. W., Lee, J. S., Waygood, E. B., Wilson, K. S., Dauter, Z. & Delbaere, L. T. J. (1993). Evaluation of mutagenesis for epitope mapping: structure of an antibody-protein antigen complex. J. Biol. Chem. 268, 10705-10708.
37. Reczko, M., Martin, A. C. R., Bohr, H. & Suhai, S. (1995). Prediction of hypervariable CDR-H3 loop structures in antibodies. Protein Eng. 9, 389-395.
38. Rooman, M. J., Wodak, S. J. & Thornton, J. M. (1989). Amino-acid sequence templates derived from recurrent turn motifs in proteins - critical-evaluation of their predictive power. Protein Eng. 3, 23-27.
39. Saul, F. A. & Poljak, R. J. (1992). Crystal-structure of human-immunoglobulin fragment Fab NEW refined at 2.0 Ångström resolution. Proteins: Struct. Funct. Genet. 14, 363-371.
40. Schiffer, M., Ainsworth, C., Xu, Z. B., Carperos, W., Olsen, K., Solomon, A., Stevens, F. J. & Chang, C. H. (1989). Structure of a 2nd crystal form of Bence-Jones protein Loc - strikingly different domain associations in 2 crystal forms of a single protein. Biochemistry, 28, 4066-4072.
41. Searle, S. J., Pedersen, J. T., Henry, A. H., Webster, D. A. & Rees, A. R. (1994). Antibody structure and function. In Antibody Engineering (Borreback, C. A. K., ed.), pp. 3-51, Oxford University Press, Oxford, UK.
42. Sheriff, S., Silverton, E. W., Padlan, E. A., Cohen, G. H., Smithgill, S. J., Finzel, B. C. & Davies, D. R. (1987). 3-Dimensional structure of an antibody-antigen complex. Proc. Natl Acad. Sci. USA, 84, 8075-8079.
43. Sibanda, B. L. & Thornton, J. M. (1985). β-Hairpin families in globular proteins. Nature, 316, 170-174.
44. Sibanda, B. L., Blundell, T. L. & Thornton, J. M. (1989). Conformation of β-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J. Mol. Biol. 206, 759-777.
45. Staunton, D., Jones, A. E. & Rees, A. R. (1993). Creation of a metal-binding site within the antibody combining site. Protein Eng. 6 (Special Supplement), 93.
46. Strong, R. K., Campbell, R., Rose, D. R., Petsko, G. A., Sharon, J. & Margolies, M. N. (1991). 3-Dimensional structure of murine anti-para-azophenylarsonate Fab-36-71. 1. X-ray crystallography, site-directed mutagenesis, and modelling of the complex with hapten. Biochemistry, 30, 3739-3748.
47. Sutcliffe, M. J. (1988). An automated approach to the systematic model building of homologous proteins. PhD thesis, University of London, Birkbeck College.
48. Sutcliffe, M. J., Haneef, I., Carney, D. & Blundell, T. L. (1987). Knowledge based modelling of homologous proteins. Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1, 377-384.
49. Swayne, D. F., Cook, D. & Buja, A. (1991). User's Manual for XGobi, a Dynamic Graphics Program for Data Analysis Implemented in the X Window System. Bellcore Technical Memorandum.
50. Taylor, W. R. & Orengo, C. A. (1989). Protein structure alignment. J. Mol. Biol. 208, 208-229.
51. κ domain. EMBO J. 14, 4628-4638.
52. Tramontano, A., Chothia, C. & Lesk, A. M. (1989). Structural determinants of the conformations of medium-sized loops in proteins. Proteins: Struct. Funct. Genet. 6, 382-394.
53. H domains of immunoglobulins. J. Mol. Biol. 215, 175-182.
54. Unger, R., Harel, D., Wherland, S. & Sussman, J. L. (1989). A 3D building-blocks approach to analyzing and predicting structure of proteins. Proteins: Struct. Funct. Genet. 5, 355-373.
55. Ward, J. H. (1963). Hierarchical grouping to optimize an objective function. J. Am. Statist. Assoc. 58, 236-244.
56. Wintjens, R., Rooman, M. J. & Wodak, S. J. (1996). Automatic classification and analysis of αα-turn motifs in proteins. J. Mol. Biol. 255, 235-253.