The crystal structure of a fab fragment to the melanoma-associated GD2 ganglioside

Journal of Structural Biology

Volumn 119, Issue 1, 1997, Pages 6-16

  Pichla, Susan L ^a   Murali, Ramachandran ^a,b   Burnett, Roger M ^a  

^a WISTAR INSTITUTE   (United States)

^b Department of Otolaryngology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GANGLIOSIDE GD2; IMMUNOGLOBULIN F(AB) FRAGMENT;

ARTICLE; CRYSTAL STRUCTURE; MELANOMA; PRIORITY JOURNAL;

EID: 0031171367     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1006/jsbi.1997.3857     Document Type: Article

References (47)

1. Bentley, G. A., Boulot, G., Riottot, M. M., and Poljak, R. J. (1990) Three-dimensional structure of an idiotope-anti-idiotope complex, Nature 348, 254-257.
2. Bhat, T. N., Bentley, G. A., Fischmann, T. O., Boulot, G., and Poljak, R. J. (1990) Small rearrangements in structures of Fv and Fab fragments of antibody D1.3 on antigen binding, Nature 347, 483-485.
3. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) CHARMM: A Program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem. 4, 187-217.
4. Brünger, A. T. (1990) Extension of molecular replacement: A new search strategy based on Patterson correlation refinement, Acta Crystallogr. A46, 46-57.
5. Brünger, A. T. (1992a) X-PLOR Version 3.1: A system for X-ray Crystallography and NMR, Yale University, New Haven, CT.
6. Brünger, A. T. (1992b) Free R value: A novel statistical quantity for assessing the accuracy of crystal structures, Nature 355, 472-475.
7. Brünger, A. T., Krukowski, A., and Erickson, J. W. (1990) Slow-cooling protocols for crystallographic refinement by simulated annealing, Acta Crystallogr. A46, 585-593.
8. Brünger, A. T., Kuriyan, J., and Karplus, M. (1987) Crystallographic R factor refinement by molecular dynamics, Science 235, 458-460.
9. Bundle, D. R., and Young, N. M. (1992) Carbohydrate-protein interactions in antibodies and lectins, Current Opinion Struct. Biol. 2, 666-673.
10. Collaborative Computational Project, Number 4. (1994) The CCP4 Suite: Programs for Protein Crystallography, Acta Crystallogr. D50, 760-763.
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., and Poljak, R. J. (1989) Conformations of immunoglobulin hypervariable regions, Nature 342, 877-883.
12. Cisar, J., Kabat, E. A., Dorner, M. M., and Liao, J. (1975) Binding properties of immunoglobulin combining sites specific for terminal or nonterminal antigenic determinants in dextran, J. Exp. Med. 142, 435-459.
13. Cygler, M., Rose, D. R., and Bundle, D. R. (1991) Recognition of a cell-surface oligosaccharide of pathogenic Salmonella by an antibody Fab fragment, Science 253, 442-445.
14. Davies, D. R., and Padlan, E. A. (1990) Antibody-antigen complexes, Annu. Rev. Biochem. 59, 439-473.
15. Engh, R. A., and Huber, R. (1991) Accurate bond and angle parameters for X-ray protein structure refinement, Acta Crystallogr. A47, 392-400.
16. Evans, S. V. (1993) SETOR: Hardware-lighted three-dimensional solid model representations of macromolecules, J. Mol. Graphics 11, 134-138.
17. Herlyn, M., and Koprowski, H. (1988) Melanoma antigens: Immunological and biological characterization and clinical significance. Annu. Rev. Immunol. 6, 283-308.
18. Herron, J. N., He, X. M., Ballard, D. W., Blier, P. R., Pace, P. E., Bothwell, A. L. M., Voss, E. W., Jr., and Edmundson, A. B. (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.
19. D3 gangliosides, J. Natl. Cancer Inst. 81, 440-444.
20. Jeffrey, P. D., Bajorath, J., Chang, C. Y., Yelton, D., Hellström, I., Hellström, K. E., and Sheriff, S. (1995) The X-ray structure of an anti-tumour antibody in complex with antigen, Nature Struct. Biol. 2, 466-471.
21. Jones, T. A. (1982). FRODO: A graphics fitting program for macromolecules, in Sayre, D. (Ed.), Computational Crystallography, pp. 303-317, Clarendon Press, Oxford.
22. Jones, T. A., Zou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Crystallogr. A47, 110-119.
23. Kabsch, W. (1988) Automatic indexing of rotation diffraction patterns. J. Appl. Crystallogr. 21, 67-71.
24. Kabat, E. A., Wu, T. T., Reid-Miller, M., Perry, H. M., and Gottesman, K. S. (1987) Sequences of Proteins of Immunological Interest, 4th ed., Public Health Service, NIH, Washington, DC.
25. Kolbinger, F., Saldanha, J., Hardman, N., and Bendig, M. M. (1993) Humanization of a mouse anti-human IgE antibody: A potential therapeutic for IgE-mediated allergies, Protein Eng. 6, 971-980.
26. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures, J. Appl. Crystallogr. 26, 283-291.
27. Lattman, E. E. (1972) Optimal sampling of the rotation function, Acta Crystallogr. B28, 1065-1068.
28. Li, Y.-T., and Li, S.-C. (1989) Ceramide glycanase from leech, Hirudo medicinalis, and earthworm, Lumbricus terrestris, Methods Enzymol. 179, 479-487.
29. Mayworth, R. D., and Quintáns, J. (1990) Designer and catalytic antibodies, N. Engl. J. Med. 323, 173-178.
30. Nicholls, A., Sharp, K. A., and Honig, B. (1991) Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons, Proteins: Struct. Funct. Genet. 11, 281-296.
31. Padlan, E. A. (1990) On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands, Proteins 7, 112-124.
32. Pichla, S. L., Murali, R., and Burnett, R. M. (1995) Preliminary crystallographic data for an Fab to the melanoma-associated GD2 ganglioside, and the purification of a soluble form of this antigen, Acta Crystallogr. D51, 124-126.
33. Pokkuluri, P. R., Bouthillier, F., Li, Y., Kuderova, A., Lee, J., and Cygler, M. (1994) Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA, J. Mol. Biol. 243, 283-297.
34. Priestle, J. P. (1988) RIBBON: A stereo cartoon drawing program for proteins, J. Appl. Crystallogr. 21, 572-576.
35. Quanta (1989) Version 2.1, Polygen Corp., Waltham, Massachusetts.
36. Quiocho, F. A. (1986) Carbohydrate-binding proteins: Tertiary structures and protein-sugar interactions, Annu. Rev. Biochem. 55, 287-315.
37. Ramachandran, G. N., and Sasisekharan, V. (1968) Conformation of polypeptides and proteins, Adv. Protein Chem. 23, 283-438.
38. Ravindranath, M. H., Tsuchida, T., and Irie, R. F. (1989) Diversity of ganglioside expression in human melanoma, in Oettgen, H. F. (Ed.), Gangliosides and Cancer, pp. 79-91, VCH, New York.
39. Rini, J. M., Schulze-Gahmen, U., and Wilson, I. A. (1992) Structural evidence for induced fit as a mechanism for antibody-antigen recognition, Science 255, 959-965.
40. Roitt, I. M., Brostoff, J., and Male, D. K. (1989) Immunology, 2nd ed., Gower Medical, New York.
41. Stanfield, R. L., Fieser, T. M., Lerner, R. A., and Wilson, I. A. (1990) Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 Å, Science 248, 712-719.
42. Stanfield, R. L., Takimoto-Kamimura, M., Rini, J. M., Profy, A. T., and Wilson, I. A. (1993) Major antigen-induced domain rearrangements in an antibody, Structure 1, 83-93.
43. Suh, S. W., Bhat, T. N., Navia, M. A., Cohen, G. H., Rao, D. N., Rudikoff, S., and Davies, D. R. (1986) The galactan-binding immunoglobulin Fab J539: An X-ray diffraction study at 2.6-Å resolution, Proteins 1, 74-80.
44. Tai, T., Cahan, L. D., Tsuchida, T., Saxton, R. E., Irie, R. F., and Morton, D. L. (1985) Immunogenicity of melanoma-associated gangliosides in cancer patients, Int. J. Cancer 35, 607-612.
45. D3 antigens and antibody-mediated cytotoxicity, Cancer Res. 47, 1229-1233.
46. Vyas, N. K. (1991) Atomic features of protein-carbohydrate interactions, Current Opinion Struct. Biol. 1, 732-740.
47. Waldmann, T. A. (1991) Monoclonal antibodies in diagnosis and therapy, Science 252, 1657-1662.