CH/π interactions in the crystal structure of Class I MHC antigens and their complexes with peptides

Bioorganic and Medicinal Chemistry

Volumn 6, Issue 12, 1998, Pages 2507-2515

  Umezawa, Yoji ^a   Nishio, Motohiro ^b  

^a INSTITUTE OF MICROBIAL CHEMISTRY   (Japan)

^b CHIBA UNIVERSITY   (Japan)

Author keywords

CH interaction; Class I MHC antigens; Ligand specificity; PDB; Subunit interface

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN;

ANTIGEN BINDING; ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; CRYSTAL STRUCTURE; HUMAN; PROTEIN PROTEIN INTERACTION;

MURINAE;

EID: 0032436501     PISSN: 09680896     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0968-0896(98)80024-2     Document Type: Article

References (55)

1. Nishio, M.; Hirota, M.; Umezawa, Y. The CH/π Interaction. Evidence, Nature and Consequences, Wiley-VCH: New York, 1998.
2. Umezawa, Y.; Nishio, M. Bioorg. Med. Chem. 1998, 6, 493.
3. Umezawa, Y.; Tsuboyama, S.; Honda, K.; Uzawa, J.; Nishio, M. Bull. Chem. Soc. Jpn. 1998, 71, 1207.
4. The CVFF force field within the modelling package DISCOVER (MSI, San Diego, CA) was used.
5. Pauling, L. The Nature of the Chemical Bonds, Cornell Univ. Press: Ithaca, New York, 1960, p. 260.
6. 5PTI: Wlodawer, A.; Walter, J.; Huber, R.; Sjolin, L. J. Mol. Biol. 1984, 180, 301.
7. Ref. 1, pp. 178-181; Tables 11.1 and 11.2.
8. Wlodawer, A.; Sjolin, L. Biochemistry 1983, 22, 2720.
9. Wlodawer, A.; Svensson, L. A.; Sjolin, L.; Gilliland, G. L. Biochemistry 1988, 27, 2705.
10. Ref. 2, Tables 1 and 2.
11. Bjorkman, P. J.; Perham, P. Ann. Rev. Biochem. 1990, 59, 253.
12. Bjorkman, P. J.; Saper, M. A.; Samraoui, B.; Bennett, W. S.; Strominger, J. L.; Wiley, D. C. Nature 1987, 329, 506.
13. 3HLA, 2.6 Å: Saper, M. A.; Bjorkman, P. J.; Wiley, D. C. J. Mol. Biol. 1991, 219, 277.
14. Collins, E. J.; Garboczi, D. N.; Wiley, D. C. Nature 1994, 371, 626.
15. Two molecules (ABC and DEF) are included in the PDB data (2CLR, 1HHI,. 1HHJ and 1HHK). The results in Figures 2 and 3, and Tables 1-3 were obtained by analyzing molecule ABC.
16. Townsend, A.; Elliott, T.; Cerundolo, V.; Foster, L.; Barber, B.; Tse, A. Cell 1990, 62, 285.
17. The van der Waals force is an ambiguous concept representing a blend of a variety of nonspecific interactions: beside the dispersion force, the attractive part of the van der Waals force is consisted of a number of polar interactions. The CH/π interaction includes the dispersion force, however, contribution from the charge transfer mechanism is most important.
18. Madden, D. R.; Gorga, J. C.; Strominger, J. L.; Wiley, D. C. Cell 1992, 70, 1035.
19. Reid, S. W.; McAdam, S.; Smith, K. J.; Klenerman, P.; O'Callaghan, C. A.; Harlos, K.; Jakobsen, B. K.; McMichael, A. J.; Bell, J. I.; Stuart, D. I.; Jones, E. Y. J. Exp. Med. 1996, 184, 2279.
20. Fremont, D. H.; Matsumura, M.; Stura, E. A.; Peterson, P. A.; Wilson, I. A. Science 1992, 257, 919.
21. Young, A. C. M.; Zhang, W.; Sacchettini, J. C.; Nathenson, S. G. Cell 1994, 76, 39.
22. We do not discuss the hydrogen-bond data unless it becomes necessary, since most papers in the literature have focused on the polar interactions.
23. Madden, D. R.; Garboczi, D. N.; Wiley, D. C. Cell 1993, 75, 693.
24. Two other complexes (1HHG and 1HHH) are omitted because of their low resolution.
25. Perutz, M. F. Phil. Trans. R. Soc. A 1993, 345, 105.
26. Zhang, W.; Young, A.C. M.; Imarai, M.; Nathenson, S. G.; Saccettini, J. C. Proc. Natl. Acad. Sci. USA 1992, 89, 8403.
27. Fremont, D. H.; Matsumura, M.; Stura, E. A.; Peterson, P. A.; Wilson, I. A. Science 1992, 257, 919.
28. Fremont, D. H.; Stura, E. A.; Matsumura, M.; Peterson, P. A.; Wilson, I. A. Proc. Natl. Acad. Sci. USA 1995, 92, 2479.
29. Falk, K.; Rötzschke, O.; Stevanovic, S.; Jung, G.; Rammensee, H.-G. Nature, 1991, 351, 290.
30. Shibata, K.; Imarai, M.; van Bleek, G. M.; Joyce, S.; Nathenson, S. G. Proc. Natl. Acad. Sci. USA 1992 , 89, 3135.
31. Asp98β and Met99β appear in a few cases. The residues are present at the C-terminal of the β-subunit; Asp98β is hydrogen-bonded with the side-chain of His192α and Met99β with the main chain carbonyl group of Trp244α.
32. There are a few exceptions; they might occur as artifacts by low resolution of the crystallographic determinations.
33. (a) Ref. 1, Chapter 11.
34. (b) Nishio, M.; Hirota, M.; Umezawa, Y. Kagaku to Seibustu 1995, 33, 311.
35. Nishio, M.; Umezawa, Y.; Hirota, M.; Takeuchi, Y. Tetrahedron 1995, 51, 8665.
36. (a) Yun, M.; Park, C.; Kim, S.; Nam, D.; Kim, D. H. J. Am. Chem. Soc. 1992, 114, 2281.
37. (b) Morisaki, N.; Funabashi, H.; Shimazawa, R.; Furukawa, J.; Kawaguchi, A.; Okuda, S.; Iwasaki, S. Eur. J. Biochem. 1993, 211, 111.
38. (c) Chakrabarti, P.; Samanta, U. J. Mol. Biol. 1995, 251, 9.
39. (d) Shimohigashi, Y.; Maeda, I.; Nose, T.; Ikesue, K.; Sakamoto, H.; Ogawa, T.; Ide, Y.; Kawahara, M.; Nezu, T.; Terada, Y.; Kawano, K.; Ohno, M. J. Chem. Soc. Perkins Trans. 1 1996, 2479.
40. (e) Maeda, I.; Shimohigashi, Y.; Ikesue, K.; Nose, T.; Ide, Y.; Kawano, K.; Ohno, M. J. Biochem. 1996, 119, 870.
41. (f) Kawasaki, T.; Horimai, E.; Ohta, H. Bull. Chem. Soc. Jpn. 1996, 69, 3591.
42. (g) Kawasaki, T.; Saito, K.; Ohta, H. Chem. Lett. 1997, 351.
43. (h) Harata, K.; Muraki, M. Acta Crystallogr. Sect. D 1997, 53, 650.
44. (i) Zographos, S. E.; Oikonomakos, N. G.; Tsitsanou, K. E.; Leonidas, D. D.; Chrysina, E. D.; Skamnaki, V. T.; Bischoff, H.; Goldman, S.; Watson, K. A.; Johnson, L.N. Structure 1997, 5, 1413.
45. (j) Sato, T.; Kanai, Y.; Hoshino, T. Biosci. Biotech. Biochem. 1998, 62, 407.
46. (a) Tanaka, T.; Hirama, M.; Fujita, K.; Imajo, S.; Ishiguro, M. Chem. Commun. 1993, 1205.
47. (b) Kim, K. H.; Kwon, B. M.; Meyers, A. G.; Rees, D. C. Science 1993, 262, 1042.
48. (c) Takahashi, K.; Tanaka, T.; Suzuki, T.; Hirama, M. Tetrahedron 1994, 50, 1327.
49. (a) Kodama, Y.; Nishihata, K.; Nishio, M.; Nakagawa, N. Tetrahedron Lett. 1977, 2105.
50. (b) Nishio, M. Kagaku no Ryoiki 1977, 31, 998; 1979, 33, 422.
51. (b) Nishio, M. Kagaku no Ryoiki 1977, 31, 998; 1979, 33, 422.
52. (c) Kodama, Y.; Nishihata, K.; Zushi, S.; Nishio, M.; Uzawa, J.; Sakamoto, K.; Iwamura, H. Bull. Chem. Soc. Jpn. 1979, 52, 2661.
53. (d) Zushi, S.; Kodama, Y.; Nishihata, K.; Umemura, K.; Nishio, M.; Uzawa, J.; Hirota, M. Bull. Chem. Soc. Jpn. 1980, 53, 3631.
54. Nishio, M.; Hirota, M. Tetrahedron 1989, 45, 7201.
55. See Ref. 1, Chapter 4 for detail.