Dynamic flexibility of a peptide-binding groove of human HLA-DR1 class II MHC molecules: Normal mode analysis of the antigen peptide-class II MHC complex

Chemical and Pharmaceutical Bulletin

Volumn 51, Issue 8, 2003, Pages 923-928

  Nojima, Hiroyuki ^a   Takeda Shitaka, Mayuko ^a   Kurihara, Youji ^a   Kamiya, Kenshu ^a   Umeyama, Hideaki ^a  

^a KITASATO UNIVERSITY   (Japan)

Author keywords

Anti correlative motion; Class II major histocompatibility complex; Normal mode analysis; Peptide binding groove

Indexed keywords

HLA DR1 ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; PEPTIDE;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ANTIGEN BINDING; ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; MAJOR HISTOCOMPATIBILITY COMPLEX; PEPTIDE ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; BINDING SITE; CHEMISTRY; IMMUNOLOGY; METABOLISM; PHYSIOLOGY; PLIABILITY; PROTEIN BINDING;

BINDING SITES; HLA-DR1 ANTIGEN; PEPTIDES; PLIABILITY; PROTEIN BINDING;

EID: 2142661662     PISSN: 00092363     EISSN: 13475223     Source Type: Journal    
DOI: 10.1248/cpb.51.923     Document Type: Article

References (34)

1. Germain R. N., Margulies D. H., Annu. Rev. Immunol., 11, 403-450 (1993).
2. Jorgensen J. L., Reay P. A., Ehrivh E. W., Davis M. M., Annu. Rev. Immunol., 10, 835-873 (1992).
3. Bjorkman P. J., Saper M. A., Samraoui B., Bennett W. S., Strominger J. L., Wiley D. C., Nature (London), 329, 506-512 (1987).
4. Brown J. H., Jardetzky T. S., Gorga J. C., Stern L. J., Urban R. G., Strominger J. L., Wiley D. C., Nature (London), 364, 33-39 (1993).
5. Madden D. R., Garboczi D. N., Wiley D. C., Cell, 75, 693-708 (1993).
6. Stern L. J., Brown J. H., Jardetzky T. S., Gorga J. C., Urban R. G., Strominger J. L., Wiley D. C., Nature (London), 368, 215-221 (1994).
7. Chicz R. M., Urban R. G., Lane W. S., Gorga J. C., Stern L. J., Vignali D. A., Strominger J. L., Nature (London), 358, 764-768 (1992).
8. Falk K., Rötzschke O., Stevanoić S., Jung G., Rammensee H.-G., Nature (London), 351, 290-296 (1991).
9. Gosh P., Amaya M., Mellins E., Wiley D. C., Nature (London), 378, 457-462 (1995).
10. Hunt D. F., Henderson R. A., Shabanowitz J., Sakaguchi K., Michel H., Sevilir N., Cox A. L., Appella E., Engelhard V. H., Science, 255, 1261-1263 (1992).
11. Jardetzky T. S., Lane W. S., Robinson R. A., Madden D. R., Wiley D. C., Nature (London), 353, 326-329 (1991).
12. Matsumura M., Fremont D. H., Peterson P. A.,Wilson I. A., Science, 257, 927-934 (1992).
13. Murthy V. L., Stern L. J., Structure, 5, 1385-1396 (1997).
14. Bouvier M., Wiley D. C., Nature Struct. Biol., 5 377-384 (1998).
15. Nakagawa M., Chiba-Kamoshida K., Udaka K., Nakanishi H., Biochem. Biophys. Res. Commun., 278, 609-613 (2000).
16. Nojima H., Takeda-Shitaka M., Kurihara Y., Adachi M., Yoneda S., Kamiya K., Umeyama H., Chem. Pharm. Bull., 50, 1209-1214 (2002).
17. Bouvier M., Wiley D. C., Science, 265, 398-402 (1994).
18. Madden D. R., Gorga J. C., Strominger J. L., Wiley D. C., Cell, 70, 1035-1048 (1992).
19. Madden D. R., Wiley D. C., Curr. Opin. Struct. Biol., 2, 300-304 (1992).
20. Collins E. J., Garboczi D. N, Karpusas M. N., Wiley D. C., Proc. Natl. Acad. Sci. U.S.A., 92, 1218-1221 (1995).
21. Guo H. C., Jardetzky T. S., Garrett T. P. J., Lane W. S., Strominger J. L., Wiley D. C., Nature (London), 360, 364-366 (1992).
22. Batalia M. A., Collins E. J., Biopolymers, 43, 281-302 (1997).
23. Garrett T. P. J., Saper M. A., Bjorkman P. J., Strominger J. L., Wiley D. C., Nature (London), 342, 692-696 (1989).
24. Saper M. A., Bjorkman P. J., Wiley D. C., J. Mol. Biol., 219, 277-319 (1991).
25. Collins E. J., Garboczi D. N., Wiley D. C., Nature (London), 371, 626-629 (1994).
26. Go N., Noguti T., Nishikawa T., Proc. Natl. Acad. Sci. U.S.A., 80, 3696-3700 (1983).
27. Weiner S. J., Kollman P. A., Case D. A., Singh U. C., Ghio C., Alagona G., Profeta S. J., Weiner P., J. Am. Chem. Soc., 106, 765-784 (1984).
28. Kamiya K., Umeyama H., 19th Kozo Kassei Soukan Symposium, 1991, p. 308.
29. Kamiya K., Sugawara Y., Umeyama H., J. Comp. Chem., 24, 826-841 (2003).
30. Loncharich R. J., Brooks B. R., Proteins, 6, 32-45 (1989).
31. Soejima K., Kurihara Y., Kamiya K., Umeyama H., FEBS Lett., 463, 19-23 (1999).
32. Sumikawa H., Suzuki E., Fukuhara K., Nakajima Y., Kamiya K., Umeyama H., Chem. Pharm. Bull., 46, 1069-1077 (1998).
33. Takeda-Shitaka M., Kamiya K., Miyata T., Ohkura N., Madoiwa S., Sakata Y., Umeyama H., Chem. Pharm. Bull., 47, 322-328 (1999).
34. Eckart C., Phys. Rev., 47, 552-558 (1935).