Agent-based modeling of the context dependency in T cell recognition

Journal of Theoretical Biology

Volumn 236, Issue 4, 2005, Pages 376-391

  Casal, Arancha ^a   Sumen, Cenk ^b   Reddy, Timothy E ^c   Alber, Mark S ^d   Lee, Peter P ^a  

^a STANFORD UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c BOSTON UNIVERSITY   (United States)

^d UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

Agent based simulation; Immune synapse; Receptor clustering; Systems biology; T cell recognition

Indexed keywords

PEPTIDE DERIVATIVE; T LYMPHOCYTE RECEPTOR;

IMMUNE SYSTEM;

AGONIST; ANTIGEN PRESENTING CELL; ARTICLE; CELL FUNCTION; CHEMICAL COMPOSITION; COMPARATIVE STUDY; MAJOR HISTOCOMPATIBILITY COMPLEX; MATHEMATICAL MODEL; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION; SIMULATION; T LYMPHOCYTE; T LYMPHOCYTE ACTIVATION;

ANIMALS; ANTIGEN PRESENTATION; ANTIGENS; COMPUTER SIMULATION; LYMPHOCYTE ACTIVATION; MAJOR HISTOCOMPATIBILITY COMPLEX; MODELS, IMMUNOLOGICAL; PEPTIDES; SELF TOLERANCE; T-LYMPHOCYTES;

EID: 23744434889     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2005.03.019     Document Type: Article

References (50)

1. A.K. Abbas, and A.H. Lichtman Cellular and Molecular Immunology 2000 W.B. Saunders London
2. S.M. Alam, and G.M. Davies Qualitative and quantitative differences in T cell receptor binding of agonist and antagonist ligands Immunity 10 2 1999 227 237
3. A. Bhandoola, and A.S. Rosenberg CD4(+) T-cell responses to self-peptide-MHC Trends Immunol. 24 4 2003 171
4. N.J. Burroughs, and C. Wulfing Differential segregation in a cell-cell contact interface: the dynamics of the immunological synapse Biophys. J. 83 4 2002 1784 1796
5. A. Casal, and C. Sumen A cellular automata model of early T cell recognition Lecture Notes Comput. Sci. 3305 2004 553 560
6. C. Chan, and A.J. George Cooperative enhancement of specificity in a lattice of T cell receptors Proc. Natl Acad. Sci. USA 98 10 2001 5758 5763
7. C. Chan, and J. Stark Feedback control of T-cell receptor activation Proc. R. Soc. Lond. B Biol. Sci. 271 1542 2004 931 939
8. D. Coombs, and A.M. Kalergis Activated TCRs remain marked for internalization after dissociation from pMHC Nat. Immunol. 3 10 2002 926 931
9. M.M. Davis, and J.J. Boniface Ligand recognition by alpha beta T cell receptors Annu. Rev. Immunol. 16 1998 523 544
10. B.N. Dittel, and I. Stefanova Cross-antagonism of a T cell clone expressing two distinct T cell receptors Immunity 11 3 1999 289 298
11. M. Faroudi, and R. Zaru Cutting edge: T lymphocyte activation by repeated immunological synapse formation and intermittent signaling J. Immunol. 171 3 2003 1128 1132
12. K.C. Garcia, and M. Degano An alphabeta T cell receptor structure at 2.5 A and its orientation in the TCR-MHC complex Science 274 5285 1996 209 219
13. R.N. Germain T-cell activation: the power of one Curr. Biol. 13 4 2003 R137 R139
14. R.N. Germain, and I. Stefanova The dynamics of T cell receptor signaling: complex orchestration and the key roles of tempo and cooperation Annu. Rev. Immunol. 17 1999 467 522
15. L.H. Glimcher, and C.J. Kara Sequences and factors: a guide to MHC class-II transcription Annu. Rev. Immunol. 10 1992 13 49
16. B. Goldstein, and J.R. Faeder Mathematical and computational models of immune-receptor signalling Nat. Rev. Immunol. 4 6 2004 445 456
17. A. Grakoui, and S.K. Bromley The immunological synapse: a molecular machine controlling T cell activation Science 285 5425 1999 221 227
18. M. Gunzer, and A. Schafer Antigen presentation in extracellular matrix: interactions of T cells with dendritic cells are dynamic, short lived, and sequential Immunity 13 3 2000 323 332
19. K.A. Hogquist, and T.K. Starr Receptor sensitivity: when T cells lose their sense of self Curr. Biol. 13 6 2003 R239 R241
20. P.D. Holler, and A.R. Lim CD8(-) T cell transfectants that express a high affinity T cell receptor exhibit enhanced peptide-dependent activation J. Exp. Med. 194 8 2001 1043 1052
21. J.E. Hopcroft, R. Motwani, and J.D. Ullman Introduction to Automata Theory, Languages and Computation 2001 Addison Wesley Reading, MA
22. D.J. Irvine, and M.A. Purbhoo Direct observation of ligand recognition by T cells Nature 419 6909 2002 845 849
23. S.C. Jameson T cell receptor antagonism in vivo, at last Proc. Natl Acad. Sci. USA 95 24 1998 14001 14002
24. L.P. Kane, and J. Lin Signal transduction by the TCR for antigen Curr. Opin. Immunol. 12 3 2000 242 249
25. M. Krosgaard, and Q.J. Li Agonist/endogenous peptide-MHC heterodimers drive T cell activation and sensitivity Nature 434 7030 2005 238 243
26. E. Lai Lipid Rafts make for slippery platforms J. Cell Biol. 162 3 2003 365 370
27. S.J. Lee, and Y. Hori Correlation of a dynamic model for immunological synapse formation with effector functions: two pathways to synapse formation Trends Immunol. 23 10 2002 492 499
28. Q.J. Li, and A.R. Dinner CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse Nat. Immunol. 5 8 2004 791 799
29. D.G. Lim, and J.M. Slavik Allelic variation of MHC structure alters peptide ligands to induce atypical partial agonistic CD8+ T cell function J. Exp. Med. 198 1 2003 99 109
30. D.S. Lyons, and S.A. Lieberman A TCR binds to antagonist ligands with lower affinities and faster dissociation rates than to agonists Immunity 5 1 1996 53 61
31. B. Malissen Les liaisons dangereuses Nat. Immunol. 2 3 2001 196 198
32. B. Malissen An evolutionary and structural perspective on T cell antigen receptor function Immunol. Rev. 191 2003 7 27
33. T.W. McKeithan Kinetic proofreading in T-cell receptor signal transduction Proc. Natl Acad. Sci. USA 92 11 1995 5042 5046
34. D.L. Mueller Tuning the immune system: competing positive and negative feedback loops Nat. Immunol. 4 3 2003 210 211
35. S.Y. Qi, and J.T. Groves Synaptic pattern formation during cellular recognition Proc. Natl Acad. Sci. USA 98 12 2001 6548 6553
36. Z. Reich, and J.J. Boniface Ligand-specific oligomerization of T-cell receptor molecules Nature 387 6633 1997 617 620
37. E.L. Reinherz, and K. Tan The crystal structure of a T cell receptor in complex with peptide and MHC class II Science 286 5446 1999 1913 1921
38. J.B. Reiser, and C. Darnault CDR3 loop flexibility contributes to the degeneracy of TCR recognition Nat. Immunol. 4 3 2003 241 247
39. S.D. Saibil, and T. Ohteki Weak agonist self-peptides promote selection and tuning of virus-specific T cells Eur. J. Immunol. 33 3 2003 685 696
40. A. Sette, and J. Alexander Antigen analogs/MHC complexes as specific T cell receptor antagonists Annu. Rev. Immunol. 12 1994 413 431
41. J. Sloan-Lancaster, and P.M. Allen Altered peptide ligand-induced partial T cell activation: molecular mechanisms and role in T cell biology Annu. Rev. Immunol. 14 1996 1 27
42. J. Sloan-Lancaster, and B.D. Evavold Induction of T-cell anergy by altered T-cell-receptor ligand on live antigen-presenting cells Nature 363 6425 1993 156 159
43. P.R. Smith, and I.E. Morrison Anomalous diffusion of major histocompatibility complex class I molecules on HeLa cells determined by single particle tracking Biophys. J. 76 6 1999 3331 3344
44. J. Sousa, and J. Carneiro A mathematical analysis of TCR serial triggering and down-regulation Eur. J. Immunol. 30 11 2000 3219 3227
45. I. Stefanova, and J.R. Dorfman Self-recognition promotes the foreign antigen sensitivity of naive T lymphocytes Nature 420 6914 2002 429 434
46. S. Valitutti, and A. Lanzavecchia Serial triggering of TCRs: a basis for the sensitivity and specificity of antigen recognition Immunol. Today 18 6 1997 299 304
47. H.A. van den Berg, and N.J. Burroughs Quantifying the strength of ligand antagonism in TCR triggering Bull. Math. Biol. 64 4 2002 781 808
48. H.A. van den Berg, and N.J. Burroughs A reliable and safe T cell repertoire based on low-affinity T cell receptors J. Theor. Biol. 209 4 2001 465 486
49. P.A. van der Merwe Do T cell receptors do it alone? Nat. Immunol. 3 12 2002 1122 1123
50. C. Wulfing, and C. Sumen Costimulation and endogenous MHC ligands contribute to T cell recognition Nat. Immunol. 3 1 2002 42 47