Unusual water-mediated antigenic recognition of the proinflammatory cytokine interleukin-18

Journal of Biological Chemistry

Volumn 284, Issue 36, 2009, Pages 24478-24489

  Argiriadi, Maria A ^a   Xiang, Tao ^a   Wu, Chengbin ^a   Ghayur, Tariq ^a   Borhani, David W ^a,b  

^a ABBOTT LABORATORIES   (United States)

^b D E SHAW RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLERGIC DISEASE; ANTIBODY BINDING; AUTOIMMUNE DISEASE; BINDING DATA; CLINICAL DEVELOPMENT; COMPLEMENTARITY-DETERMINING REGIONS; COMPLEX FORMATIONS; CYTOKINES; FAB FRAGMENTS; HUMAN ANTIBODIES; INTERLEUKIN-18; ORDERED WATER; PROINFLAMMATORY CYTOKINES; STRUCTURAL BASIS;

BIOLOGY; PLASTICITY;

ANTIBODIES;

INTERLEUKIN 18; MONOCLONAL ANTIBODY; NEUTRALIZING ANTIBODY;

ANIMAL CELL; ANTIBODY COMBINING SITE; ANTIGEN BINDING; ANTIGEN RECOGNITION; ARTICLE; CHIMERA; COMPLEMENTARITY DETERMINING REGION; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; EPITOPE MAPPING; HUMAN; HYDROPHILICITY; MOLECULAR DOCKING; NONHUMAN; PRIORITY JOURNAL;

ANIMALS; ANTIBODIES, MONOCLONAL; ANTIGENS; CRYSTALLOGRAPHY, X-RAY; EPITOPES; HUMANS; IMMUNOGLOBULIN FAB FRAGMENTS; INTERLEUKIN-18; MICE; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; WATER;

MURINAE;

EID: 69949161901     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.023887     Document Type: Article

References (60)

1. Kato, Z., Jee, J., Shikano, H., Mishima, M., Ohki, I., Ohnishi, H., Li, A., Hashimoto, K., Matsukuma, E., Omoya, K., Yamamoto, Y., Yoneda, T., Hara, T., Kondo, N., and Shirakawa, M. (2003) Nat. Struct. Biol. 10, 966-971
2. Okamura, H., Tsutsi, H., Komatsu, T., Yutsudo, M., Hakura, A., Tanimoto, T., Torigoe, K., Okura, T., Nukada, Y., and Hattori, K. (1995) Nature 378, 88-91
3. Nakanishi, K., Yoshimoto, T., Tsutsui, H., and Okamura, H. (2001) Annu. Rev. Immunol. 19, 423-474
4. Plater-Zyberk, C., Joosten, L. A., Helsen, M. M., Sattonnet-Roche, P., Siegfried, C., Alouani, S., van De Loo, F. A., Graber, P., Aloni, S., Cirillo, R., Lubberts, E., Dinarello, C. A., van Den Berg, W. B., and Chvatchko, Y. (2001) J. Clin. Invest. 108, 1825-1832
5. Siegmund, B., Fantuzzi, G., Rieder, F., Gamboni-Robertson, F., Lehr, H. A., Hartmann, G., Dinarello, C. A., Endres, S., and Eigler, A. (2001) Am. J. Physiol. Regul. Integr. Comp. Physiol. 281, R1264-R1273
6. Yamamura, M., Kawashima, M., Taniai, M., Yamauchi, H., Tanimoto, T., Kurimoto, M., Morita, Y., Ohmoto, Y., and Makino, H. (2001) Arthritis Rheum. 44, 275-285
7. Losy, J., and Niezgoda, A. (2001) Acta Neurol. Scand. 104, 171-173
8. Karni, A., Koldzic, D. N., Bharanidharan, P., Khoury, S. J., and Weiner, H. L. (2002) J. Neuroimmunol. 125, 134-140
9. Ludwiczek, O., Kaser, A., Novick, D., Dinarello, C. A., Rubinstein, M., and Tilg, H. (2005) Eur. Cytokine Netw. 16, 27-33
10. Bombardieri, M., McInnes, I. B., and Pitzalis, C. (2007) Expert Opin. Biol. Ther. 7, 31-40
11. Yoshimoto, T., Takeda, K., Tanaka, T., Ohkusu, K., Kashiwamura, S., Okamura, H., Akira, S., and Nakanishi, K. (1998) J. Immunol. 161, 3400-3407
12. Azam, T., Novick, D., Bufler, P., Yoon, D. Y., Rubinstein, M., Dinarello, C. A., and Kim, S. H. (2003) J. Immunol. 171, 6574-6580
13. Vigers, G. P., Anderson, L. J., Caffes, P., and Brandhuber, B. J. (1997) Nature 386, 190-194
14. Wu, C., Sakorafas, P., Miller, R., McCarthy, D., Scesney, S., Dixon, R., and Ghayur, T. (2003) J. Immunol. 170, 5571-5577
15. Brady, K. D. (1998) Biochemistry 37, 8508-8515
16. Taniguchi, M., Nagaoka, K., Kunikata, T., Kayano, T., Yamauchi, H., Nakamura, S., Ikeda, M., Orita, K., and Kurimoto, M. (1997) J. Immunol. Methods 206, 107-113
17. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326
18. Leslie, A. G. W. (1992) CCP4 and ESF-EACMB Newsletter on Protein Crystallography 26
19. Evans, P. R. (1997) Joint CCP4 and ESF-EACBM Newsletter 33
20. French, S., and Wilson, K. (1978) Acta Crystallogr. Sect. A 34, 517-525
21. Brünger, A. T. (1992) Nature 355, 472-475
22. (1994) Acta Crystallogr. D Biol. Crystallogr. 50, 760-763
23. Navaza, J. (1994) Acta Crystallogr. Sect. A 50, 157-163
24. Celikel, R., Ruggeri, Z. M., and Varughese, K. I. (2000) Nat. Struct. Biol. 7, 881-884
25. Storoni, L. C., McCoy, A. J., and Read, R. J. (2004) Acta Crystallogr. D Biol. Crystallogr. 60, 432-438
26. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C., and Read, R. J. (2005) Acta Crystallogr. D Biol. Crystallogr. 61, 458-464
27. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Acta Crystallogr. D Biol. Crystallogr. 54, 905-921
28. Lamzin, V. S., and Wilson, K. S. (1993) Acta Crystallogr. D Biol. Crystallogr. 49, 129-147
29. Brünger, A. T., Kuriyan, J., and Karplus, M. (1987) Science 235, 458-460
30. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjelgaard, M. (1991) Acta Crystallogr. Sect. A 47, 110-119
31. Read, R. J. (1986) Acta Crystallogr. D Biol. Crystallogr. A42, 140-149
32. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Acta Crystallogr. D Biol. Crystallogr. 53, 240-255
33. Winn, M. D., Isupov, M. N., and Murshudov, G. N. (2001) Acta Crystallogr. D Biol. Crystallogr. 57, 122-133
34. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1983) J. Appl. Crystallogr. 26, 283-291
35. Hooft, R. W., Vriend, G., Sander, C., and Abola, E. E. (1996) Nature 381, 272
36. Lawrence, M. C., and Colman, P. M. (1993) J. Mol. Biol. 234, 946-950
37. Kleywegt, G. J. (1996) Acta Crystallogr. D Biol. Crystallogr. 52, 842-857
38. Kleywegt, G. J., and Jones, T. A. (1994) Acta Crystallogr. D Biol. Crystallogr. 50, 178-185
39. Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y., and Liang, J. (2006) Nucleic Acids Res. 34, W116-W118
40. Binkowski, T. A., and Joachimiak, A. (2008) BMC Struct. Biol. 8, 45
41. Humphrey, W., Dalke, A., and Schulten, K. (1996) J. Mol. Graphics 14, 33-38
42. Sanner, M. F., Olson, A. J., and Spehner, J. C. (1996) Biopolymers 38, 305-320
43. Baker, N. A., Sept, D., Joseph, S., Holst, M. J., and McCammon, J. A. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 10037-10041
44. Yamamoto, Y., Kato, Z., Matsukuma, E., Li, A., Omoya, K., Hashimoto, K., Ohnishi, H., and Kondo, N. (2004) Biochem. Biophys. Res. Commun. 317, 181-186
45. Wu, C., Ying, H., Grinnell, C., Bryant, S., Miller, R., Clabbers, A., Bose, S., McCarthy, D., Zhu, R. R., Santora, L., Davis-Taber, R., Kunes, Y., Fung, E., Schwartz, A., Sakorafas, P., Gu, J., Tarcsa, E., Murtaza, A., and Ghayur, T. (2007) Nat. Biotechnol. 25, 1290-1297
46. Lo Conte, L., Chothia, C., and Janin, J. (1999) J. Mol. Biol. 285, 2177-2198
47. Rajamani, D., Thiel, S., Vajda, S., and Camacho, C. J. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 11287-11292
48. Cohen, G. H., Silverton, E. W., Padlan, E. A., Dyda, F., Wibbenmeyer, J. A., Willson, R. C., and Davies, D. R. (2005) Acta Crystallogr. D Biol. Crystallogr. 61, 628-633
49. Bhat, T. N., Bentley, G. A., Boulot, G., Greene, M. I., Tello, D., Dall'Acqua, W., Souchon, H., Schwarz, F. P., Mariuzza, R. A., and Poljak, R. J. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 1089-1093
50. Mazza, G., Housset, D., Piras, C., Grégoire, C., Fontecilla-Camps, J. C., and Malissen, B. (1999) J. Mol. Biol. 287, 773-780
51. Sonavane, S., and Chakrabarti, P. (2008) PLoS Comput. Biol. 4, e1000188
52. Ghayur, T., Labkovsky, B., Voss, J. W., Green, L., Babcock, J., Jia, X.-C., Wieler, J., Kang, J. S., and Hedberg, B. (2005) World Patent WO May 26, 2005/047307
53. Kim, S. H., Eisenstein, M., Reznikov, L., Fantuzzi, G., Novick, D., Rubinstein, M., and Dinarello, C. A. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 1190-1195
54. Kim, S. H., Azam, T., Novick, D., Yoon, D. Y., Reznikov, L. L., Bufler, P., Rubinstein, M., and Dinarello, C. A. (2002) J. Biol. Chem. 277, 10998-11003
55. Krumm, B., Meng, X., Li, Y., Xiang, Y., and Deng, J. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 20711-20715
56. Chen, R., Li, L., and Weng, Z. (2003) Proteins 52, 80-87
57. Comeau, S. R., Gatchell, D. W., Vajda, S., and Camacho, C. J. (2004) Bioinformatics 20, 45-50
58. Comeau, S. R., Gatchell, D. W., Vajda, S., and Camacho, C. J. (2004) Nucleic Acids Res. 32, W96-W99
59. Tovchigrechko, A., and Vakser, I. A. (2006) Nucleic Acids Res. 34, W310-W314
60. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, DeLano Scientific LLC, Palo Alto, CA