The class II MHC protein HLA-DR1 in complex with an endogenous peptide: Implications for the structural basis of the specificity of peptide binding

Structure

Volumn 5, Issue 10, 1997, Pages 1385-1396

  Murthy, Venkatesh L ^a   Stern, Lawrence J ^b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Antigen presentation; Histocompatibility; MHC; Motif; Peptide binding

Indexed keywords

EID: 0031572833     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(97)00288-8     Document Type: Article

References (61)

1. Germain, R.N. & Margulies, D.H. (1993). The biochemistry and cell biology of antigen processing and presentation. Annu. Rev. Immunol. 11, 403-450.
2. Chicz, R.M., et al., & Strominger, J.L. (1992). Predominant naturally processed peptides bound to HLA-DR1 are derived from MHC-related molecules and are heterogeneous in size. Nature 358, 764-768.
3. Rudensky, A.Y., Preston-Hurlburt, P, Al-Ramadi, B.K., Rothbard, J. & Janeway, C.A.J. (1992). Truncation variants of peptides isolated from MHC class II molecules suggest sequence motifs. Nature 359, 429-431.
4. d. Science 256, 1817-1820.
5. Sette, A., et al., & Grey, H.M. (1989). Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis. Proc. Natl. Acad. Sci. USA 86, 3296-3300.
6. Hammer, J., Takacs, B. & Sinigaglia, F. (1992). Identification of a motif for HLA-DR1 binding peptides using M13 display libraries. J. Exp. Med. 176, 1007-1013.
7. Rammensee, H.-G. (1995). Chemistry of peptides associated with MHC class I and class II molecules. Curr. Opin. Immunol. 7, 85-96.
8. Jardetzky, T.S., et al., & Wiley, D.C. (1996). Crystallographic analysis of endogenous peptides associated with HLA-DR1 suggests a common, polyproline II-like conformation for bound peptides. Proc. Natl. Acad. Sci. USA 93, 734-728.
9. Brown, J.H., et al., & Wiley, D.C. (1993). The three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364, 33-39.
10. Stern, L.J., et al., & Wiley, D.C. (1994). Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 368, 215-221.
11. Ghosh, P., Amaya, M., Mellins, E. & Wiley, D.C. (1995). The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3. Nature 378, 457-462.
12. Fremont, D.H., Hendrickson, W.A., Marrack, P. & Kappler, J. (1996). Structures of an MHC class II molecule with covalently bound single peptides. Science 272, 1001-1004.
13. Madden, D.R. (1995). The three-dimensional structure of peptide-MHC complexes. Annu. Rev. Immunol. 13, 587-622.
14. Stern, L.J. & Wiley, D.C. (1994). Antigenic peptide binding by class I and class II histocompatibility proteins. Structure 15, 245-251.
15. Kim, J., Urban, R.G., Strominger, J.L. & Wiley, D.C. (1994). Toxic shock syndrome toxin-1 complexed with a class II MHC protein HLA-DR1. Science 266, 1870-1874.
16. Jardetzky, T.S., et al., & Wiley, D.C. (1993). Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen. Nature 368, 711-718.
17. Connolly, M.L. (1983). Analytical molecular surface calculation. J. Appl. Cryst. 16, 548-558.
18. O'Sullivan, D., et al., & Sette, A. (1991). On the interaction of promiscuous antigenic peptides with different alleles. J. Immunol. 147, 2663-2669.
19. Jardetzky, T.S., Gorga, J.C., Busch, R., Rothbard, J., Strominger, J.L. & Wiley, D.C. (1990). Peptide binding to HLA-DR1: a peptide with most residues substituted to alanine retains MHC binding. EMBO J. 9, 1797-1803.
20. Burley, S.K. & Petsko, G.A. (1986). Amino-aromatic interactions in proteins. FEBS Lett. 203, 139-143.
21. Dougherty, D.A. (1996). Cation-· interactions in chemistry and biology: a new view of benzene, Phe, Tyr and Trp. Science 271, 163-168.
22. Perutz, M.F. (1993). The role of aromatic rings as hydrogen-bond acceptors in molecular recognition. Phil. Trans. Phys. Sci. 345, 1674-1779.
23. Hammer, J., et al., & Nagy, Z. (1994). High-affinity binding of short peptides to major histocompatibility complex class II molecules by anchor combinations. Proc. Natl. Acad. Sci. USA 91, 4456-4460.
24. Hammer, J., et al., & Sinigaglia, F. (1993). Promiscuous and allelespecific anchors in HLA-DR-binding peptides. Cell 74, 197-203.
25. b. Science 257, 919-927.
26. Saper, M.A., Bjorkman, P.J. & Wiley, D.C. (1991). Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 Å resolution. J. Mol. Biol. 219, 277-319.
27. Braunstein, N.S., Weber, D.A., Wang, X.-C., Long, E.O. & Karp, D. (1992). Sequences in both class II major histocompatibility complex · and · ·chains contribute to the binding of the superantigen toxic shock syndrome toxin 1. J. Exp. Med. 175, 1301-1305.
28. Karp, D.R., Teletski, C.L., Jaraquemade, D., Maloy, W.L., Coligan, J.E. & Long, E.O. (1990). Structural requirements for pairing of · and · chains in HLA-DR and DP molecules. J. Exp. Med 171, 615-628.
29. Kwok, W.W., Kovats, S., Thurtle, P. & Nepom, G.T. (1993). HLA-DQ allelic polymorphisms constrain patterns of class II heterodimer formation. J. Immunol. 150, 2263-2272.
30. Madden, D.R., Gorga, J.C., Strominger, J.L. & 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.
31. Gao, G.F., et al., & Jakobsen, B.K. (1997). Crystal structure of the complex between human CD8· · and HLA-A2. Nature 387, 630-634.
32. 3 domain of HLA-A2. Nature 345, 41-46.
33. Konig, R., Huang, L.-Y. & Germain, R.N. (1992). MHC class II interaction with CD4 mediated by a region analogous to the MHC class I binding site for CD8. Nature 356, 796-798.
34. Tiwari, J.L. & Terasaki, P.I. (1985). HLA and Disease Associations. Springer-Verlag, NY.
35. Garboczi, D.N, Ghosh, P., Utz, U., Fan, Q.R., Biddison, W.E. & Wiley, D.C. (1996). Structure of the complex between human T-cell receptor, viral peptide, and HLA-A2. Nature 384, 134-141.
36. Newton-Nash, D.K. & Eckels, D.D. (1993). Differential effect of polymorphism at HLA-DR1 beta-chain positions 85 and 86 on binding and recognition of DR1-restricted antigenic peptides. J. Immunol. 150, 1813-1821.
37. Boehncke, W.-H., et al., & Germain, R.N. (1993). The importance of dominant negative effects of amino acid sidechain substitution in peptide-MHC molecule interactions and T cell recognition. J. Immunol. 150, 331-341.
38. 86 HLA-DR· dimorphism in autoantigen presentation to human T cells. Proc. Natl. Acad. Sci. USA 88, 7343-7347.
39. Wu, S., Gorski, J., Eckels, D.D. & Newton-Nash, D.K. (1996). T cell recognition of MHC class II-associated peptides is independent of peptide affinity for MHC and sodium dodecylsulfate stability of the peptide/MHC complex. J. Immunol. 156, 3815-3820.
40. Vignali, D.A.A. & Strominger, J.L. (1994). Amino acid residues that flank core peptide epitopes and the extracellular domains of CD4 modulate differential signaling through the T cell receptor. J. Exp. Med. 179, 1945-1956.
41. Hudson, K.R., Tiedemann, R.E., Urban, R.G., Lowe, S.C., Strominger, J.L. & Fraser, J.D. (1995). Staphylococcal enterotoxin A has two cooperative binding sites on major histocompatibility complex class II. J. Exp. Med 182, 711-720.
42. Herman, A., Labrecque, N., Thibodeau, J., Marrack, P., Kappler, J.W. & Sekaly, R.P. (1991). Identification of the staphylococcal enterotoxin A superantigen binding site in the b1 domain of the human histocompatibility antigen HLA-DR. Proc. Natl. Acad. Sci. USA 88, 9954-9958.
43. Karp, D.R. & Long, E.O. (1992). Identification of HLA-DR1 · chain residues critical for binding staphylococcal enterotoxin A and E. J. Exp. Med 175, 415-424.
44. Stern, L.J. & Wiley, D.C. (1992). The human class II MHC protein HLA-DR1 assembles as empty ·· heterodimers in the absence of antigenic peptide. Cell 68, 465-477.
45. Navazza, J. (1994). AMoRE: an automated package for molecular replacement. Acta Cryst. A 50, 157-163.
46. Kleywegt, G.J. & Jones, T.A. (1993). Masks made easy. CCP4/ESF-EACBM Newsletter on Protein Crystallography. 28, 56-59.
47. Jones, T.A. (1992). A, yaap, asap, @#*? a set of averaging programs. In Molecular Replacement. (Dobson, E.J., Gover, S. & Wolf, W., eds), pp. 91-105, SERC Daresbury Laboratory, Warrington, UK.
48. Brünger, AT. (1992). X-PLOR Version 3.1: a System for X-ray Crystallography and NMR. Yale University Press, New Haven, CT.
49. Collaborative Computational Project, No.4. (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D 50, 760-763.
50. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). Automated refinement of protein models. Acta Cryst. D 49, 127-149.
51. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291.
52. Luzzati, V. (1952). Traitement statistique des erreurs dans la determination des structures cristallines. Acta Cryst. 5, 802-810.
53. Read, R.J. (1986). Improved Fourier coefficients for maps using phases from partial structures with errors. Acta Cryst. A 42, 140-149.
54. Jones, T.A., Zou, J.-Y., Cowan, S.W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A 47, 110-119.
55. Richards, F.M. & Lee, B. (1971). The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379-400.
56. Kleywegt, G.J. & Jones, T.A. (1994). A super position. CCP4/ESF-EACBM Newsletter on Protein Crystallography. 31, 9-14.
57. Kabsch, W. (1978). A discussion of the solution for the best rotation to relate two sets of vectors. Acta Cryst. A 34, 827-828.
58. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24, 946-950.
59. Carson, M. (1987). Ribbon models of macromolecules. J. Mol. Graph. 5, 103-106.
60. Merritt, E.A. & Murphy, M.E.P. (1994). Raster3D version 2.0, a program for photorealistic molecular graphics. Acta Cryst. D 50, 869-873.
61. Nicholls, A. & Honig, B. (1991). A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comput. Chem. 12, 435-445.