Dynamic influence of the two membrane-proximal immunoglobulin-like domains upon the peptide-binding platform domain in class I and class II major histocompatibility complexes: Normal mode analysis

Chemical and Pharmaceutical Bulletin

Volumn 57, Issue 11, 2009, Pages 1193-1199

  Nojima, Hiroyuki ^a   Kanou, Kazuhiko ^a   Kamiya, Kenshu ^a   Atsuda, Koichiro ^a   Umeyama, Hideaki ^a   Takeda Shitaka, Mayuko ^a  

^a KITASATO UNIVERSITY   (Japan)

Author keywords

Class I; Class II; Major histocompatibility complex; Membrane proximal immunoglobulin like domain; Normal mode analysis; Peptide binding platform domain

Indexed keywords

IMMUNOGLOBULIN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 2; MEMBRANE PROTEIN; PEPTIDE;

AMINO TERMINAL SEQUENCE; ARTICLE; CELL DIFFERENTIATION; HYDROPHOBICITY; PROTEIN BINDING; T LYMPHOCYTE;

COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HISTOCOMPATIBILITY ANTIGENS CLASS I; HISTOCOMPATIBILITY ANTIGENS CLASS II; HUMANS; IMMUNOGLOBULINS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY;

EID: 71049155498     PISSN: 00092363     EISSN: 13475223     Source Type: Journal    
DOI: 10.1248/cpb.57.1193     Document Type: Article

References (39)

1. Bjorkman P. J., Saper M. A., Samraoui B., Bennett W. S., Strominger J. L., Wiley D. C., Nature (London), 329, 506-512 (1987).
2. 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).
3. 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).
4. Zhang W., Young A. C., Imarai M., Nathenson S. G., Sacchettini J. C., Proc. Natl. Acad. Sci. U.S.A., 89, 8403-8407 (1992).
5. Fremont D. H., Stura E. A., Matsumura M., Peterson P. A., Wilson I. A., Science, 257, 919-927 (1992).
6. Madden D. R., Garboczi D. N., Wiley D. C., Cell, 75, 693-708 (1993).
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. Rudensky A., Perston-Hurlburt P., Hong S. C., Barlow A., Janeway C. A., Jr, Nature (London), 353, 622-627 (1991).
9. Utz U., Koenig S., Coligan J. E., Biddison W. E., J. Immunol., 149, 214-221 (1992).
10. Meng W. S., von Grafenstein H., Haworth I. S., Int. Immunol., 9, 1339-1349 (1997).
11. Bouvier M., Wiley D. C., Nat. Struct. Biol., 5, 377-384 (1998).
12. Hansen T., Nat. Struct. Biol., 5, 340-341 (1998).
13. Meng W. S., von Grafenstein H., Haworth I. S., Int. Immunol., 12, 949-957 (2000).
14. Sato A. K., Zarutskie J. A., Rushe M. M., Lomakin A., Natarajan S. K., Sadegh-Nasseri S., Benedek G. B., Stern L. J., J. Biol. Chem., 275, 2165-21732 (2000).
15. Nojima H., Takeda-Shitaka M., Kurihara Y., Adachi M., Yoneda S., Kamiya K., Umeyama H., Chem. Pharm. Bull., 50, 1209-1214 (2002).
16. Nojima H., Takeda-Shitaka M., Kurihara Y., Kamiya K., Umeyama H., Chem. Pharm. Bull., 51, 923-928 (2003).
17. Zacharias M., Springer S., Biophys. J., 87, 2203-2214 (2004).
18. Gupta S., Höpner S., Rupp B., Günther S., Dickhaut K., Agarwal N., Cardoso M. C., Kühne R., Wiesmüller K. H., Jung G., Falk K., Rötzschke O., PLoS ONE 2008;3:e1814.
19. Painter C. A., Cruz A., López G. E., Stern L. J., Zavala-Ruiz Z., PLoS ONE. 2008;3:e2403.
20. Yaneva R., Springer S., Zacharias. M., Biopolymers, 91, 14-27 (2009).
21. Vitiello A., Potter T. A., Sherman L. A., Science, 250, 1423-1426 (1990).
22. Cook J. R., Myers N. B., Hansen T. H., J. Immunol., 157, 2256-2261 (1996).
23. Kamiya K., Sugawara Y., Umeyama H., J. Comput. Chem., 24, 826-841 (2003).
24. 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).
25. Weiner S. J., Kollman P. A., Nguyen D. T., Case D. A., J. Comput. Chem., 107, 230-252 (1986).
26. Nojima H., Takeda-Shitaka M., Kanou K., Kamiya K., Umeyama H., Chem. Pharm. Bull., 56, 635-641 (2008).
27. Jääskeläinen S., Verma C. S., Hubbard R. E., Linko P., Caves L. S., Protein Sci., 7, 1359-1367 (1998).
28. Adachi M., Kurihara Y., Nojima H., Takeda-Shitaka M., Kamiya K., Umeyama H., Protein Sci., 12, 2125-2131 (2003).
29. Kurihara Y., Watanabe T., Nojima H., Takeda-Shitaka M., Kamiya K., Umeyama H., Chem. Pharm. Bull., 51, 754-758 (2003).
30. Takeda-Shitaka M., Nojima H., Takaya D., Kanou K., Iwadate M., Umeyama H., Chem. Pharm. Bull., 52, 643-645 (2004).
31. Brooks B., Karplus M., Proc. Natl. Acad. Sci. U.S.A., 80, 6571-6575 (1983).
32. Ishida H., Jochi Y., Kidera A., Proteins, 32, 324-333 (1998).
33. Eckart C., Phys. Rev., 47, 552-558 (1935).
34. Go N., Noguti T., Nishikawa T., Proc. Natl. Acad. Sci. U.S.A., 80, 3696-13670 (1983).
35. Levitt M., Sander C., Stern P. S., J. Mol. Biol., 181, 423-447 (1985).
36. Nishikawa T., Go N., Proteins, 2, 308-329 (1987).
37. Wan S., Coveney P., Flower D. R., J. Comput. Chem., 25, 1803-1813 (2004).
38. Collins E. J., Garboczi D. N., Wiley D. C., Nature (London), 371, 626-629 (1994).
39. Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W., Lipman D. J., Nucleic Acids Res., 25, 3389-3402 (1997).