Skip to main content
Log in

On the logic of restrictive recognition of peptide by the T-cell antigen receptor

  • Published:
Immunologic Research Aims and scope Submit manuscript

Abstract

This essay provides an analysis of the inadequacy of the current view of restrictive recognition of peptide by the T-cell antigen receptor. A competing model is developed, and the experimental evidence for the prevailing model is reinterpreted in the new framework. The goal is to contrast the two models with respect to their consistency, coverage of the data, explanatory power, and predictability.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Zinkernagel RM, Doherty PC. Immunological surveillance against altered self components by sensitised T lymphocytes in lymphocytic choriomeningitis. Nature. 1974;251:547–8.

    Article  PubMed  CAS  Google Scholar 

  2. Cohn M. The tritope model for restrictive recognition of antigen by T-cells: I. What assumptions about structure are needed to explain function? Mol Immunol. 2005;42:1419–43.

    Article  PubMed  CAS  Google Scholar 

  3. Langman RE, Cohn M. The standard model of T-cell receptor function: a critical reassessment. Scand J Immunol. 1999;49:570–7.

    Article  PubMed  CAS  Google Scholar 

  4. Matzinger P, Bevan MJ. Hypothesis: why do so many lymphocytes respond to major histocompatibility antigens? Cell Immunol. 1977;29:1–5.

    Article  PubMed  CAS  Google Scholar 

  5. Collins EJ, Riddle DS. TCR-MHC docking orientation: natural selection, or thymic selection? Immuol Res. 2008;41:267–94.

    Article  CAS  Google Scholar 

  6. Archbold JK, Macdonald WA, Burrows SR, Rossjohn J, McCluskey J. T-cell allorecognition: a case of mistaken identity or deja vu? Trends Immunol. 2008;29:220–6.

    Article  PubMed  CAS  Google Scholar 

  7. Cohn M. The immune system: a weapon of mass destruction invented by evolution to even the odds during the war of the DNAs. Immunol Rev. 2002;185:24–38.

    Article  PubMed  CAS  Google Scholar 

  8. Cohn M. What are the commonalities governing the behavior of humoral immune recognitive repertoires? Dev Comp Immunol. 2006;30:19–42.

    Article  PubMed  CAS  Google Scholar 

  9. Marrack P, Scott-Browne JP, Dai S, Gapin L, Kappler JW. Evolutionarily conserved amino acids that control TCR-MHC interaction. Annu Rev Immunol. 2008;26:171–203.

    Article  PubMed  CAS  Google Scholar 

  10. Cohn M. On a key postulate of TCR restrictive function: the V-gene loci act as a single pool encoding recognition of the polymorphic alleles of the species MHC. Immunology. 2007;120:140–2.

    Article  PubMed  CAS  Google Scholar 

  11. Cohn M. The Tritope model of restrictive recognition by the TCR. Trends Immunol. 2003;24:127–31.

    Article  PubMed  CAS  Google Scholar 

  12. Huseby ES, White J, Crawford F, Vass T, Becker D, Pinilla C, Marrack P, Kappler JW. How the T cell repertoire becomes peptide and MHC specific. Cell. 2005;122:247–60.

    Article  PubMed  CAS  Google Scholar 

  13. Cohn M. An alternative to current thinking about positive selection, negative selection and activation of T-cells. Immunology. 2004;111:1–6.

    Article  Google Scholar 

  14. Cohn M. On the logic of positive selection. Immunology. 2006;117:452–3.

    Article  PubMed  CAS  Google Scholar 

  15. Müllbacher A, Hill AB, Blanden RV, Cowden WB, King NJC. Alloreactive cytotoxic T cells recognize MHC Class I antigen without peptide specificity. J Immunol. 1991;147:1765–71.

    PubMed  Google Scholar 

  16. Müllbacher A, Lobigs M, Kos FJ, Langman RE. Alloreactive cytotoxic T-cell function, peptide nonspecific. Scand J Immunol. 1999;49:563–9.

    Article  PubMed  Google Scholar 

  17. Cohn M. The tritope model for restrictive recognition of antigen by T-cells: II. Implications for ontogeny, evolution and physiology. Mol Immunol. 2008;45:632–52.

    Article  PubMed  CAS  Google Scholar 

  18. Naeher D, Daniels MA, Hausmann B, Guillaume P, Luescher I, Palmer E. A constant affinity threshold for T cell tolerance. J Exp Med. 2007;11:2553–9.

    Article  Google Scholar 

  19. Palmer E, Naeher D. Affinity threshold for thymic selection through a T-cell receptor—co-receptor zipper. Nat Rev Immunol. 2009;9:207–13.

    Article  PubMed  CAS  Google Scholar 

  20. Park J-H, Adoro S, Guinter T, Erman B, Alag AS, Catalfamo M, Kimura MY, Cui Y, Lucas PJ, Gress RE, Kubo M, Hennighausen L, Feigenbaum L, Singer A. Signaling by intrathymic cytokines, not T cell antigen receptors, specifies CD8 lineage choice and promotes the differentiation of cytotoxic-lineage T cells. Nat Immunol. 2010;11:257–64.

    Article  PubMed  CAS  Google Scholar 

  21. Alves NL, Huntington ND, Mention J-J, Richard-Le Goff O, Di Santo JP. A thymocyte-thymic epithelial cell cross-talk dynamically regulates intrathymic IL-7 expression in vivo. J Immunol. 2010;184:5949–53.

    Article  PubMed  CAS  Google Scholar 

  22. Hao Y, Legrand N, Freitas AA. The clone size of peripheral CD8 T cells is regulated by TCR promiscuity. J Exp Med. 2006;203:1643–9.

    Article  PubMed  CAS  Google Scholar 

  23. Bowerman NA, Colf LA, Garcia KC, Kranz DM. Different strategies adopted by Kb and Ld to generate T cell specificity directed against their respective bound peptides. J Biol Chem. 2009;284:32551–61.

    Article  PubMed  CAS  Google Scholar 

  24. Huseby ES, Kappler JW, Marrack P. TCR-MHC/peptide interactions: kissing-cousins or a shotgun wedding? Eur J Immunol. 2004;34:1243–50.

    Article  PubMed  CAS  Google Scholar 

  25. Jerne NK. The somatic generation of immune recognition. Eur J Immunol. 1971;1:1–9.

    Article  PubMed  CAS  Google Scholar 

  26. Dai S, Huseby ES, Rubtsova K, Scott-Browne J, Crawford F, Macdonald WA, Marrack P, Kappler JW. Crossreactive T cells spotlight the germline rules for αβ T cell-receptor interactions with MHC molecules. Immunity. 2008;28:324–34.

    Article  PubMed  CAS  Google Scholar 

  27. Jerne NK. Generation of antibody diversity and self tolerance. In: Smith RT, Landy M, editors. Immune surveillance. Augusta: Academic Press; 1970. p. 343–436.

    Google Scholar 

  28. Wucherpfennig KW, Allen PM, Celada F, Cohen IR, De Boer RJ, Garcia KC, Goldstein B, Greenspan R, Hafler D, Hodgkin PD, Huseby ES, Krakauer DC, Nemazee D, Perelson AS, Pinilla C, Strong RK, Sercarz EE. Polyspecificity of T cell and B cell receptor recognition. Semin Immunol. 2007;19:216–24.

    Article  PubMed  CAS  Google Scholar 

  29. Cohn M. The self-nonself discrimination: reconstructing a cabbage from sauerkraut. Res Immunol. 1992;143:323–34.

    Article  PubMed  CAS  Google Scholar 

  30. Gavin MA, Dere B, Grandea AG, Hogquist KA, Bevan MJ. Major histocompatibility complex class I allele-specific peptide libraries: identification of peptides that mimic an H-Y T cell epitope. Eur J Immunol. 1994;24:2124–33.

    Article  PubMed  CAS  Google Scholar 

  31. Gavin MA, Bevan JJ. Increased peptide promiscuity provides a rationale for the lack of N regions in the neonatal T cell repertoire. Immunity. 1995;3:793–800.

    Article  PubMed  CAS  Google Scholar 

  32. Huseby ES, Crawford F, White J, Kappler JW, Marrack P. Negative selection imparts peptide specificity to the mature T cell repertoire. Proc Natl Acad Sci USA. 2003;100:11565–70.

    Article  PubMed  CAS  Google Scholar 

  33. Huseby ES, Crawford F, White AJ, Marrack P, Kappler JW. Interface-disrupting amino acids establish specificity between T cell receptors and complexes of major histocompatibility complex and peptide. Nat Immunol. 2006;7:1191–9.

    Article  PubMed  CAS  Google Scholar 

  34. Huseby ES, Kappler JW, Marrack P. Thymic selection stifles TCR reactivity with the main chain structure of MHC and forces interactions with the peptide side chains. Mol Immunol. 2008;45:599–606.

    Article  PubMed  CAS  Google Scholar 

  35. Kosmrlj A, Abhishek KJ, Huseby ES, Kardar M, Chakraborty AK. How the thymus designs antigen-specific and self-tolerant T cell receptor sequences. Proc Natl Acad Sci USA. 2008;105:16671–6.

    Article  PubMed  CAS  Google Scholar 

  36. Percus JK, Percus OE, Perelson AS. Predicting the size of the T cell receptor and antibody combining region from consideration of efficient self-nonself discrimination. Proc Natl Acad Sci USA. 1993;90:1691–5.

    Article  PubMed  CAS  Google Scholar 

  37. Nemazee D. Antigen receptor “capacity” and the sensitivity of self-tolerance. Immunol Today. 1996;17:25–9.

    Article  PubMed  CAS  Google Scholar 

  38. Cohn M. Degeneracy, mimicry and crossreactivity in immune recognition. Mol Immunol. 2005;42:651–5.

    Article  PubMed  CAS  Google Scholar 

  39. Cohn M. An in depth analysis of the concept of “polyspecificity” assumed to characterize TCR/BCR recognition. Immunol Res. 2008;40:128–47.

    Article  PubMed  CAS  Google Scholar 

  40. Sha WC, Nelson CA, Newberry RD, Kranz DM, Russell JH, Loh DY. Positive and negative selection of an antigen receptor on T cells in transgenic mice. Nature. 1988;336:73–6.

    Article  PubMed  CAS  Google Scholar 

  41. Capone M, Curnow J, Bouvier G, Ferrier P, Horvat B. T cell development in TCR-ab transgenic mice. J Immunol. 1995;154:5165–72.

    PubMed  CAS  Google Scholar 

  42. Dao T, Blander JM, Sant’Angelo DB. Recognition of a specific self-peptide: Self-MHC Class II complex is critical for positive selection of thymocytes expressing the D10-TCR. J Immunol. 2003;170:48–54.

    PubMed  CAS  Google Scholar 

  43. Hong S-C, Chelouche A, Lin R-h, Shaywitz D, Braunstein NS, Glimcher L, Janeway J, Charles A. An MHC interaction site maps to the amino-terminal half of the T cell receptor α chain variable domain. Cell. 1992;69:999–1009.

    Article  PubMed  CAS  Google Scholar 

  44. Logunova NN, Viret C, Pobezinksy LA, Miller SA, Kazansky DB, Sundberg JP, Chervonsky AV. Restricted MHC-peptide repertoire predisposes to autoimmunity. J Exp Med. 2005;202:73–84.

    Article  PubMed  CAS  Google Scholar 

  45. Felix NJ, Donermeyer DL, Horvath S, Walters JJ, Gross MI, Suri A, Allen PM. Alloreactive T cells respond specifically to multiple distinct peptide-MHC complexes. Nat Immunol. 2007;8:388–97.

    Article  PubMed  CAS  Google Scholar 

  46. Heath WR, Hurd ME, Carbone FR, Sherman LA. Peptide-dependent recognition of H-1 Kb by alloreactive cytotoxic T lymphocytes. Nature. 1989;341:749–52.

    Article  PubMed  CAS  Google Scholar 

  47. Viret C, Janeway CA. Functional and phenotypic evidence for presentation of E alpha 52–68 structurally related self-peptide(s) in I-E alpha-deficient mice. J Immunol. 2000;164:4627–34.

    PubMed  CAS  Google Scholar 

  48. Ewijk WV, Ron Y, Monaco J, et al. Compartmentalization of MHC Class II gene expression in transgenic mice. Cell. 1988;53:357–70.

    Article  PubMed  Google Scholar 

  49. Rubin B, Gouaillard C, Weideranders G, Kuklmann J. The IE allogeneic response of T cells from C57B1/6 mice is associated with genes of the TCRa locus. Scand J Immunol. 1993;37:388–97.

    Article  Google Scholar 

  50. LaFuse WP, Savariravan S, McCormick JF, David CS. Identification of 1-E alpha genes in H-2 recombinant mouse strains by F1 complementation. Transplantation. 1987;43:297–301.

    Article  PubMed  CAS  Google Scholar 

  51. Zy-Tmg E, Chu C, Carswell C, Cole BC, Jones PP. The minimal polymorphism of Class II Ealpha chains is not due to the functional neutrality of mutations. Genetics. 1994;40:9–20.

    Google Scholar 

  52. Schilham MW, Lang R, Benner R, Zinkernagel RM, Hengartner H. Characterization of an Lyt-2+ alloreactive cytotoxic T cell clone specific for H-2Db that crossreacts with I-Ek. J Immunol. 1986;137:2748–54.

    PubMed  CAS  Google Scholar 

  53. Morris GP, Allen PM. Cutting edge: highly alloreactive dual TCR T cells play a dominant role in graft-versus-host disease. J Immunol. 2009;182:6639–43.

    Article  PubMed  CAS  Google Scholar 

  54. Felix NJ, Suri A, Walters JJ, Horvath S, Gross ML, Allen PA. I-Ep-bound self-peptides: identification, characterization, and role in alloreactivity. J Immunol. 2006;176:1062–71.

    PubMed  CAS  Google Scholar 

  55. Daniel C, Grakoui A, Allen PA. Inhibition of an in vitro CD4+ T cell alloresponse using altered peptide ligands. J Immunol. 1998;160:3244–50.

    PubMed  CAS  Google Scholar 

  56. Daniel C, Horvath S, Allen PM. A basis for alloreactivity: MHC helical residues broaden peptide recognition by the TCR. Immunity. 1998;8:543–52.

    Article  PubMed  CAS  Google Scholar 

  57. Correia-Neves M, Waltzinger C, Mathis D, Benoist C. The shaping of the T cell repertoire. Immunity. 2001;14:21–32.

    Article  PubMed  CAS  Google Scholar 

  58. Matis LA, Sorger SB, McElligott DL, Fink PJ, Hedrick SM. The molecular basis of alloreactivity in antigen-specific, major histocompatibility complex-restricted T cell clones. Cell. 1987;51:59–69.

    Article  PubMed  CAS  Google Scholar 

  59. Nakajima PB, Betz CJ, Hansburg D. Expression of identical VαVβ gene pairs by IE-alloreactive and IE-restricted, antigen-specific T cells from MHC disparate mice. J Immunol. 1990;144:348–57.

    PubMed  CAS  Google Scholar 

  60. Cohn M. Distinguishing the tritope from the interaction antigen models. Trends Immunol. 2004;25:8–9.

    Article  PubMed  CAS  Google Scholar 

  61. Eshima K, Suzuki H, Shinohara N. Cross-positive selection of thymocytes expressing a single TCR by multiple major histocompatibility complex molecules of both classes: implications for CD4+ versus CD8+ lineage commitment. J Immunol. 2006;176:1628–36.

    PubMed  CAS  Google Scholar 

  62. Suzuki H, Eshima K, Takagaki Y, Hanaoka S, Katsuki M, Yokoyama M, Hasegawa T, Yamazaki S, Shinohara N. Origin of a T cell clone with a mismatched combination of MHC restriction and coreceptor expression. J Immunol. 1994;153:4496–507.

    PubMed  CAS  Google Scholar 

  63. Ge Q, Holler PD, Mahajan VS, Nuygen T, Eisen HN, Chen J. Development of CD4+ T cells expressing a nominally MHC class I-restricted T cell receptor by two different mechanisms. Proc Natl Acad Sci USA. 2006;103:1822–7.

    Article  PubMed  CAS  Google Scholar 

  64. Gilfillan S, Dierich A, Lemeur M, Benoist C, Mathis D. Mice lacking TdT: mature animals with an immature lymphocyte repertoire. Science. 1993;261:1175–8.

    Article  PubMed  CAS  Google Scholar 

  65. Komori T, Okada A, Stewart V, Alt FW. Lack of N regions in antigen receptor variable region genes of TdT-deficient lymphocytes. Science. 1993;261:1171–5.

    Article  PubMed  CAS  Google Scholar 

  66. Gilfillan S, Bachmann M, Trembleau S, Adorini L, Kalinke U, Zinkernagel R, Benoist C, Mathis D. Efficient immune responses in mice lacking N-region diversity. Eur J Immunol. 1995;25:3115–22.

    Article  PubMed  CAS  Google Scholar 

  67. Gilfillan S, Waltzinger C, Benoist C, Mathis D. More efficient positive selection of thymocytes in mice lacking terminal deoxynucleotidyl transferase. Int Immunol. 1994;6:1681–6.

    Article  PubMed  CAS  Google Scholar 

  68. Cohn M. A hypothesis accounting for the paradoxical expression of the D gene segment in the BCR and the TCR. Eur J Immunol. 2008;38:1779–87.

    Article  PubMed  CAS  Google Scholar 

  69. Langman RE. Cell-mediated immunity and the major histocompatibility complex. Rev Physiol Biochem Pharmacol. 1978;81:1–37.

    Article  PubMed  CAS  Google Scholar 

  70. Cohn M, Epstein R. T-cell inhibition of humoral responsiveness. II. Theory on the role of restrictive recognition in immune regulation. Cellular Immunol. 1978;39:125–53.

    Article  CAS  Google Scholar 

  71. Feng D, Bond CJ, Ely LI, Maynard J, Garcia KC. Structural evidence for a germline-encoded T cell receptor - major histocompatibility complex interaction ‘codon’. Nat. Immunol. 2007;8:975–83.

    Article  PubMed  CAS  Google Scholar 

  72. Garcia KC, Adams JJ, Feng D, Ely LK. The molecular basis of TCR germline bias for MHC is surprisingly simple. Nat Immunol. 2009;10:143–7.

    Article  PubMed  CAS  Google Scholar 

  73. Cohn M. What does the T-cell receptor recognize when it docks on an MHC-encoded restricting element? Mol Immunol. 2008;45:3264–7.

    Article  PubMed  CAS  Google Scholar 

  74. Armstrong KM, Piepenbrink KH, Baker BM. Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes. Biochem J. 2008;415:183–96.

    Article  PubMed  CAS  Google Scholar 

  75. Beddoe T, Chen Z, Clements CS, Ely LK, Bushell SR, Vivian JP, Kjer-Nielsen L, Pang SS, Dunstone MA, Liu YC, Macdonald WA, Perugini MA, Wilce MCJ, Burrows SR, Purcell AW, Tiganis T, Bottomley SP, McCluskey J, Rossjohn J. Antigen ligation triggers a conformational change within the constant domain of the αβ T cell receptor. Immunity. 2009;30:777–88.

    Article  PubMed  CAS  Google Scholar 

  76. Rojo JM, Bello R, Portoles P. T-cell receptor. In: Sigalov AB, editor. Multichain immune recognition receptor signaling: from spatiotemporal organization to human disease, Heidelberg: Springer; 2008. p. 1–11.

  77. Risueno RM, Ortiz AR, Alarcon B. Conformational model.; In Sigalov AB, editor. Multichain immune recognition receptor signaling: from spatiotemporal organization to human disease, Heidelberg: Spinger; 2008. P. 103–120.

  78. Minguet S, Schamel WWA. Permissive geometry model. In: Sigalov AB, editor. Multichain immune recognition receptor signaling: from spatiotemporal organization to human disease. Heidelberg: Springer; 2008. P. 113–120.

  79. Portoles P, Rojo JJ, Janeway CA Jr. Asymmetry in the recognition of antigen: self class II MHC and non-self class II MHC molecules by the same T-cell receptor. J Mol Cell Immunol. 1989;4:129–37.

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by a grant (RR07716) from the National Center For Research Resources (NCRR), a component of the National Institutes of Health (NIH) and its contents are solely the responsibility of the author and does not represent the official view of NCRR or NIH.

Conflict of interest

The author has no financial conflict of interest.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Melvin Cohn.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cohn, M. On the logic of restrictive recognition of peptide by the T-cell antigen receptor. Immunol Res 50, 49–68 (2011). https://doi.org/10.1007/s12026-010-8173-y

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12026-010-8173-y

Keywords

Navigation