A Shannon entropy analysis of immunoglobulin and T cell receptor

Molecular Immunology

Volumn 34, Issue 15, 1997, Pages 1067-1082

  Stewart, Jeffrey J ^a   Lee, Connie Y ^a,d   Ibrahim, Saleh ^a,e   Watts, Perry ^b   Shlomchik, Mark ^c   Weigert, Martin ^a   Litwin, Samuel ^a,b  

^a PRINCETON UNIVERSITY   (United States)

^b FOX CHASE CANCER CENTER   (United States)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

^e UNIVERSITY OF ROSTOCK   (Germany)

Author keywords

Diversity; Framework; Immunoglobulin (Ig); Kabat Wu measure (KW); Shannon entropy; Shannon information theory; T cell receptor (TCR)

Indexed keywords

IMMUNOGLOBULIN; T LYMPHOCYTE RECEPTOR;

AMINO ACID COMPOSITION; ARTICLE; BIODIVERSITY; ENTROPY; HUMAN; MEASUREMENT; MOLECULAR INTERACTION; PRIORITY JOURNAL;

ANIMALS; CYTOCHROME C GROUP; DIMERIZATION; ENTROPY; MICE; MODELS, MOLECULAR; RECEPTORS, ANTIGEN, T-CELL; RECEPTORS, IMMUNOLOGIC;

EID: 0031427052     PISSN: 01615890     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0161-5890(97)00130-2     Document Type: Article

References (54)

1. Amit, A. G., Mariuzza, R. A., Phillips, S. E. and Poljak, R. J. (1986) Three-dimensional structure of an antigen-antibody complex at 2.8 A resolution. Science 233, 747-753.
2. Arden, B., Clark, S. P., Kabelitz, D. and Mak, T. W. (1995a) Human T cell receptor variable gene segment families. Immunogenetics 42, 455-500.
3. Arden, B., Clark, S. P., Kabelitz, D. and Mak, T. W. (1995b) Mouse T cell receptor variable gene segment families. Immunogenetics 42, 501-530.
4. Baba, M. L., Darga, L. L., Goodman, M. and Czelusniak, J. (1981) Evolution of cytochrome C investigated by the maximum parsimony method. J. Mol. Evol. 17, 197-213.
5. Bentley, G. A., Boulot, G., Karjalainen, K. and Mariuzza, R. A. (1995) Crystal structure of the beta chain of a T cell antigen receptor [see comments]. Science 267, 1984-1987.
6. Bjorkman, P. J., Saper, M. A., Samraoui, B., Bennett, W. S., Strominger, J. L. and Wiley, D. C. (1987) The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens. Nature 329, 512-518.
7. Blackman, M. A. and Woodland, D. L. (1995) In vivo effects of superantigens. Life Sci. 57, 1717-1735.
8. Boitel, B., Ermonval, M., Panina Bordignon, P., Mariuzza, R. A., Lanzavecchia, A. and Acuto, O. (1992) Preferential V beta gene usage and lack of junctional sequence conservation among human T cell receptors specific for a tetanus toxin-derived peptide: evidence for a dominant role of a germline-encoded V region in antigen/major histocompatibility complex recognition. J. Exp. Med 175, 765-777.
9. Capra, J. D. and Kehoe, J. M. (1975) Hypervariable regions, idiotypy and the antibody combining site. Adv. Immunol. 20, 1-40.
10. Chothia, C., Boswell, D. R. and Lesk, A. M. (1988) The outline structure of the T cell alpha beta receptor. Embo J. 7, 3745-3755.
11. Chothia, C. and Lesk, A. M. (1987) Canonical structures for the hypervariable regions of immunoglobulins. J. Mol. Biol. 196, 901-917.
12. Fields, B. A., Ober, B., Malchiodi, E. L., Lebedeva, M. I., Braden, B. C., Ysern, X., Kim, J. K., Shao, X., Ward, E. S. and Mariuzza, R. A. (1995) Crystal structure of the V alpha domain of a T cell antigen receptor. Science 270, 1821-1824.
13. Fraser, J. D. (1989) High-affinity binding of staphylococcal enterotoxins A and B to HLA-DR. Nature 339, 221-223.
14. Garboczi, D. N., Ghosh, P., Utz, U., Fan, Q. R., Biddison, W. E. and Wiley, D. C. (1996a). Structure of the complex between human T cell receptor, viral peptide and HLA-A2 [comment]. Nature 384, 134-141.
15. Garboczi, D. N., Utz, U., Ghosh, P., Seth, A., Kim, J., Van-Tienhoven, E. A., Biddison, W. E., and Wiley, D. C. (1996b). Assembly, specific binding, and crystallization of a human TCR-alphabeta with an antigenic Tax peptide from human T lymphotropic virus type 1 and the class I MHC molecule HLA-A2. J. Immunol 157, 5403-5410.
16. Garcia, K. C., Degano, M., Stanfield, R. L., Brunmark, A., Jackson, M. R., Peterson, P. A., Teyton, L. and Wilson, I. A. (1996) An alphabeta T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex [see comments]. Science 274, 209-219.
17. Gascoigne, N. R. and Ames, K. T. (1991) Direct binding of secreted T cell receptor beta chain to superantigen associated with class II major histocompatibility complex protein. Proc. Natl. Acad. Sci. U.S.A. 88, 613-616.
18. Hay, F. C. (1988) Rheumatoid factor: structural and genetic studies indicating novel binding sites may confer the specificity for IgG Fc. Br. J. Rheumatoll, 157-161.
19. Hay, F. C., Soltys, A. J., Tribbick, G. and Geysen, H. M. (1991) Framework peptides from kappa I lib rheumatoid factor light chains with binding activity for aggregated IgG. Eur. J. Immunol 21, 1837-1841.
20. Hedrick, S. M., Engel, I., McElligott, D. L., Fink, P. J., Hsu, M. L., Hansburg, D. and Matis, L. A. (1988) Selection of amino acid sequences in the beta chain of the T cell antigen receptor. Science 239, 1541-1544.
21. Jores, R., Alzari, P. M. and Meo, T. (1990) Resolution of hypervariable regions in T cell receptor beta chains by a modified Wu-Kabat index of amino acid diversity. Proc. Natl. Acad. Sci. U.S.A. 87, 9138-9142.
22. Jorgensen, J. L., Reay, P. A., Ehrich, E. W. and Davis, M. M. (1992) Molecular components of T cell recognition. Annu. Rev. Immunol. 10, 835-873.
23. Kabat, E. A. (1970) Heterogeneity and structure of antibody-combining sites. Ann. N.Y. Acad. Sci. 169, 43-54.
24. Kabat, E. A., Wu, T. T. and Bilofsky, H. (1977) Unusual distributions of amino acids in complementarity-determining (hypervariable) segments of heavy and light chains of immunoglobulins and their possible roles in specificity of antibody-combining sites. J. Biol. Chem. 252, 6609-6616.
25. Kabat, E. A., Wu, T. T., Reid-Miller, M., Perry, H. M., Gottesman, K. S. and Foeller, C. (1987) Sequences of Proteins of Immunological Interest, 5 ed., NIH, Bethesda, MD.
26. Kappler, J., White, J., Kozono, H., Clements, J. and Marrack, P. (1994) Binding of a soluble alpha beta T cell receptor to superantigen/major histocompatibilily complex ligands. Proc. Natl. Acad. Sci. U.S.A. 91, 8462-8466.
27. Kotzin, B. L., Leung, D. Y., Kappler, J. and Marrack, P. (1993) Superantigens and their potential role in human disease. Adv. Immunol. 54, 99-166.
28. Litman, G. W., Hinds, K., Berger, L., Murphy, K. and Litman, R. (1985) Structure and organization of immunoglobulin VH genes in Heterodontus, a phylogenetically primitive shark. Dev. Comp. Immunol. 9, 749-758.
29. Litwin, S. and Jores, R. (1992) In Theoretical and experimental insights into immunology, (Edited by Perelson A. S. and Weisbuch G.), Springer-Verlag, Berlin.
30. Lloyd-Evans, P (1993) Dev. Comp. Immunol. 17, 501-524.
31. MacCallum, R. M, Martin, A. C. and Thornton, J. M. (1996) Antibody-antigen interactions: contact analysis and binding site topography. J. Mol. Biol. 262, 732-745.
32. Malchiodi, E. L., Eisenstein, E., Fields, B. A., Ohlendorf, D. H., Schlievert, P. M., Karjalainen, K. and Mariuzza, R. A. (1995) Superantigen binding to a T cell receptor beta chain of known three-dimensional structure. J. Exp. Med. 182, 1833-1845.
33. Marrack, P. and Kappler, J. (1990) The staphyloccal enterotoxins and their relatives. Science 248, 705-715.
34. Mollick, J. A., Cook, R. G. and Rich, R. R. (1989) Class II MHC molecules are specific receptors for staphylococcus enterotoxin A. Science 244, 817-820.
35. Nicholls, A. (1992) Columbia University, New York City.
36. Nitta, T., Oksenberg, J. R., Rao, N. A. and Steinman, L. (1990) Predominant expression of T cell receptor V alpha 7 in tumor-infiltrating lymphocytes of uveal melanoma. Science 249, 672-674.
37. Padlan, E. A., Abergel, C. and Tipper, J. P (1995) Identification of specificity-determining residues in antibodies. Faseb J. 9, 133-139.
38. Padovan, E., Casorati, G., Dellabona, P., Meyer, S., Brockhaus, M. and Lanzavecchia, A. (1993) Expression of two T cell receptor alpha chains: dual receptor T cells. Science 262, 422-424.
39. Plaksin, D., Chacko, S., McPhie, P., Bax, A., Padlan, E. A. and Margulies, D. H. (1996) A T cell receptor V alpha domain expressed in bacteria: does it dimerize in solution? J. Exp. Med. 184, 1251-1258.
40. Pullen, A. M., Bill, J., Kubo, R. T., Marrack, P. and Kappler, J.W. (1991) Analysis of the interaction site for the self super-antigen MIs-1a on T cell receptor V beta. J. Exp. Med. 173, 1183-1192.
41. Pullen, A. M., Wade, T., Marrack, P. and Kappler, J. W. (1990) Identification of the region of T cell receptor beta chain that interacts with the self-superantigen MIs-1a Cell 61, 1365-1374.
42. Pulsford, A., Morrow, W. J. W. and Fange, R. (1984) J. Fish. Biol. 25, 353-360.
43. Sant'Angelo, D. B., Waterbury, G., Preston Hurlburt, P., Yoon, S. T., Medzhitov, R., Hong, S. C. and Janeway, C. A., Jr. (1996) The specificity and orientation of a TCR to its peptide-MHC class II ligands. Immunity 4, 367-376.
44. Seth, A., Stern, L. J., Ottenhoff, T. H., Engel, I., Owen, M. J., Lamb, J. R., Klausner, R. D. and Wiley, D. C. (1994) Binary and ternary complexes between T cell receptor, class II MHC and superantigen in vitro. Nature 369, 324-327.
45. Shannon, C. E. (1949) The mathematical theory of communication. University of Illinois Press.
46. Shlomchik, M. J., Nemazee, D. A., Sato, V. L., Van Snick, J., Carson, D. A. and Weigert, M. G. (1986) Variable region sequences of murine IgM anti-IgG monoclonal autoantibodies (rheumatoid factors). A structural explanation for the high frequency of IgM anti-IgG B cells. J. Exp. Med. 164, 407-427.
47. Stanfield, R. L., Takimoto Kamimura, M., Rini, J. M., Profy, A. T. and Wilson, I. A. (1993) Major antigen-induced domain rearrangements in an antibody. Structure 1, 83-93.
48. Stern, L. J., Brown, J. H., Jardetzky, T. S., Gorga, J. C., Urban, R. G., Strominger, J. L. and 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.
49. Stern, L. J. and Wiley, D. C. (1994) Antigenic peptide binding by class I and class II histocompatibility proteins. Behring Inst. Mitt. 94, 1-10.
50. Strohal, R., Helmberg, A., Kroemer, G. and Kofler, R. (1989) Mouse Vk gene classification by nucleic acid sequence similarity Immunogenetics 30, 475-493.
51. Wilson, I. A. and Stanfield, R. L. (1993) Antibody-antigen interactions. Curr. Opin. Struct. Biol. 3, 113-118.
52. Wu, C. I., Li, W. H., Shen, J. J., Scarpulla, R. C., Limbach, K. J. and Wu, R. (1986) Evolution of cytochrome c genes and pseudogenes. J. Mol. Evol. 23, 61-75.
53. Wu, T. T. and Kabat, E. A. (1970) An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J. Exp. Med. 132, 211-250.
54. Yockey, H. P. (1992) Information Theory and Molecular Biology. Cambridge University Press, New York City.