Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53

Immunity

Volumn 4, Issue 3, 1996, Pages 215-228

  Smith, Kathrine J ^a,d   Reid, Scott W ^b   Harlos, Karl ^b,c   McMichael, Andrew J ^a   Stuart, David I ^b,c   Bell, John I ^a   Jones, E Yvonne ^b,c  

^a JOHN RADCLIFFE HOSPITAL   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; GAG PROTEIN; HLA B ANTIGEN; WATER;

ARTICLE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 2; MAJOR HISTOCOMPATIBILITY COMPLEX; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY;

EID: 0029969665     PISSN: 10747613     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-7613(00)80430-6     Document Type: Article

References (45)

1. Allsopp, C.E., Hill, A.V., Kwiatkowski, D., Hughes, A., Bunce, M., Taylor, C.J., Pazmany, L., Brewster, D., McMichael, A.J., and Greenwood, B.M. (1991). Sequence analysis of HLA-Bw53, a common West African allele, suggests an origin by gene conversion of HLA-B35. Hum. Immunol. 30, 105-109.
2. Barber, L.D., Gillece Castro, B., Percival, L., Li, X., Clayberger, C., and Parham, P. (1995). Overlap in the repertoires of peptides bound in vivo by a group of related class I HLA-B allotypes. Curr. Biol. 5, 179-190.
3. Bjorkman, P.J., Saper, M.A., Samraoui, B., Bennett, W.S., Strominger, J.L., and Wiley, D.C. (1987). Structure of the human class I histocompatibility antigen, HLA-A2. Nature 329, 506-512.
4. Bruger, A.T., and Krukowski, A. (1990). Slow-cooling procedures for crystallographic refinement by simulated anealing. Acta Cryst. A46, 585-593.
5. Brunger, A. (1992). XPLOR version 3.1. A System for X-Ray Crystallography and NMR (New Haven, Connecticut: Yale University Press).
6. (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D50, 760-763.
7. Collins, E.J., Garboczi, D.N., and Wiley, D.C. (1994). Three-dimensional structure of a peptide extending from one end of a class I MHC binding site. Nature 371, 626-629.
8. Connolly, J.M., Hansen, T.H., Ingold, A.L., and Potter, T.A. (1990). Recognition by CD8 on cytotoxic T lymphocytes is ablated by several substitutions in the class I alpha 3 domain: CD8 and the T-cell receptor recognize the same class I molecule. Proc. Natl. Acad. Sci. USA 87, 2137-2141.
9. ds: sequence motif, quantitative binding, and molecular modeling of the complex. J. Exp. Med. 176, 1681-1692.
10. Elliott, T., Driscoll, P., Smith, M., and McMichael, A. (1993). Peptide epitope selection by class I MHC molecules. Curr. Biol. 3, 854-866.
11. Engh, R.A., and Huber, R. (1991). Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Cryst. A47, 392-400.
12. b. Science 257, 919-927.
13. b-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove. Proc. Natl. Acad. Sci. USA 92, 2479-2483.
14. Garboczi, D.N., Hung, D.T., and Wiley, D.C. (1992). HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides. Proc. Natl. Acad. Sci. USA 89, 3429-3433.
15. Garrett, T.P., Saper, M.A., Bjorkman, P.J., Strominger, J.L., and Wiley, D.C. (1989). Specificity pockets for the side chains of peptide antigens in HLA-AW68. Nature 342, 692-696.
16. Gotch, F., McAdam, S.N., Allsopp, C.E., Gallimore, A., Elvin, J., Kieny, M.P., Hill, A.V., McMichael, A.J., and Whittle, H.C. (1993). Cytotoxic T cells in HIV2 seropositive Gambians: identification of a virus-specific MHC-restricted peptide epitope. J. Immunol. 151, 3361-3369.
17. Guo, H.C., Jardetzky, T.S., Garrett, T.P., Lane, W.S., Strominger, J.L., and Wiley, D.C. (1992). Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle. Nature 360, 364-366.
18. Guo, H.C., Madden, D.R., Silver, M.L., Jardetzky, T.S., Gorga, J.C., Strominger, J.L., and Wiley, D.C. (1993). Comparison of the P2 specificity pocket in three human histocompatibility antigens: HLA-A*6801, HLA-A*0201, and HLA-B*2705. Proc. Natl. Acad. Sci. USA 90, 8053-8057.
19. Hill, A.V., Allsopp, C.E., Kwiatkowski, D., Anstey, N.M., Twumasi, P., Rowe, P.A., Bennett, S., Brewster, D., McMichael, A.J., and Greenwood, B.M. (1991). Common west African HLA antigens are associated with protection from severe malaria. Nature 352, 595-600.
20. Hill, A.V., Elvin, J., Willis, A.C., Aidoo, M., Allsopp, C.E., Gotch, F.M., Gao, X.M., Takiguchi, M., Greenwood, B.M., Townsend, A.R., McMichael, A.J., and Whittle, H.C. (1992). Molecularanalysis of the association of HLA-B53 and resistance to severe malaria. Nature 360, 434-439.
21. Jones, A. (1985). Interactive computer graphics: FRODO. Meth. Enzymol. 115, 157-171.
22. Jones, T.A., Jou, J.W., Cowan, S.W., and Kjeldgaard, M. (1991). Improved methods for building protein models in electron densitiy maps and the location of errors in these models. Acta Cryst. A47, 110-119.
23. Kabsch, W., and Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22, 2577-2637.
24. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
25. Laskowski, R.J., Macarthur, W., Moss, D., and Thornton, J. (1993). Procheck: a program to check stereochemical quality of protein structures. J. Appl. Crystallogr. 26, 283-290.
26. Madden, D.R., Gorga, J.C., Strominger, J.L., and Wiley, D.C. (1991). The structure of HLA-B27 reveals nonamer self-peptides bound in an extended conformation. Nature 353, 321-325.
27. Madden, D.R., Gorga, J.C., Strominger, J.L., and Wiley, D.C. (1992). The three-dimensional structure of HLA-B27 at 2.1 Å resolution suggests a general mechanism for tight peptide binding to MHC. Cell 70, 1035-1048.
28. Madden, D.R., Garboczi, D.N., and Wiley, D.C. (1993). The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2. Cell 75, 693-708.
29. Merritt, E.A., and Murphy, M.E.P. (1994). Raster3D version 2.0: A program for photorealistic molecular graphics. Acta Cryst. D50, 869-873.
30. Navaza, J. (1994). AMoRe: an automated package for molecular replacment. Acta Cryst. A50, 157-163.
31. Nicholls, A., Sharp, K.A., and Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
32. Otwinowski, Z. (1993). Oscillation data reduction program. In Data Collection and Processing, L. Sawyer, N. Issacs, and S. Bailey, eds. (Warrington, United Kingdom: Daresbury Laboratory), pp. 55-62.
33. Potter, T.A., Rajan, T.V., Dick, R.F.D., and Bluestone, J.A. (1989). Substitution at residue 227 of H-2 class I molecules abrogates recognition by CD8-dependent, but not CD8-independent, cytotoxic T lymphocytes. Nature 337, 73-75.
34. Rammensee, H.G., Friede, T., and Stevanoviic, S. (1995). MHC ligands and peptide motifs: first listing. Immunogenetics 41, 178-228.
35. Reid, S.W., Smith, K.J., Jakobsen, B., O'Callaghan, C., Reyburn, H., Harlos, K., Stuart, D., McMichael, A.J., Bell, J.I., and Jones, E.Y. (1996). Production and crystallization of MHC class T B allele single peptide complexes. FEBS Lett., in press.
36. Salter, R.D., Benjamin, R.J., Wesley, P.K., Buxton, S.E., Garrett, T.P., Clayberger, C., Krensky, A.M., Norment, A.M., Littman, D.R., and Parham, P. (1990). A binding site for the T-cell co-receptor CD8 on the alpha 3 domain of HLA-A2. Nature 345, 41-46.
37. Saper, M.A., Bjorkman, P.J., and Wiley, D.C. (1991). Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 Å resolution. J. Mol. Biol. 219, 277-319.
38. Silver, M.L., Guo, H.C., Strominger, J.L., and Wiley, D.C. (1992). Atomic structure of a human MHC molecule presenting an influenza virus peptide. Nature 360, 367-369.
39. Stuart, D.I., Levine, M., Muirhead, M., and Stammers, D. (1979). The crystal structure of cat pyruvate kinase at a resolution of 2.6 Å. J. Mol. Biol. 134, 109-142.
40. Studier, F.W., Rosenberg, A.H., Dunn, J.J., and Dubendorff, J.W. (1990). Use of T7 RNA polymerase to direct expression of cloned genes. Meth. Enzymol. 185, 60-89.
41. Sutton, J., Rowland-Jones, S., Rosenberg, W., Nixon, D., Gotch, F., Gao, M., Murray, N., Spoonas, A., Driscoll, P., Smith, M., Willis, A., and McMichael, A. (1993). A sequence pattern for epitopes presented to cytotoxic T lymphocytes by HLA B8 revealed by analysis of epitopes and eluted peptides. Eur. J. Immunol. 23, 447-453.
42. Townsend, A., and Bodmer, H. (1989). Antigen recognition by class I-restricted T lymphocytes. Annu. Rev. Immunol. 7, 601-624.
43. Yamamoto, J., Kariyone, A., Akiyama, N., Kano, K., and Takiguchi, M. (1990). Presentation of human minor histocompatibility antigens by HLA-B35 and HLA-B38 molecules. Proc. Natl. Acad. Sci. USA 87, 2583-2587.
44. b at 2.4 Å resolution: implications for antigen-determinant selection. Cell 76, 39-50.
45. b molecule containing a single viral peptide: implications for peptide binding and T-cell receptor recognition. Proc. Natl. Acad. Sci. USA 89, 8403-8407.