Statistical mechanical concepts in immunology

Annual Review of Physical Chemistry

Volumn 61, Issue , 2010, Pages 283-303

  Chakraborty, Arup K ^a,b,d   Košmrlj, Andrej ^c,d  

^a Chemical Engineering Department   (United States)

^b Departments of Chemistry   (United States)

^c Physics Department Harvard   (United States)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Antigen recognition; B cell; Lymphocyte development; T cell; Theory and computation

Indexed keywords

COMPUTATION THEORY; CYTOLOGY; IMMUNE SYSTEM; PATHOGENS; STATISTICAL MECHANICS;

ADAPTIVE IMMUNE SYSTEMS; ANTIGEN RECOGNITION; B CELLS; CELLULARS; IMMUNE RESPONSE; LYMPHOCYTE DEVELOPMENT; MECHANICAL; MECHANISTICS; MICROBIAL PATHOGENS; THEORY AND COMPUTATION;

T-CELLS;

ADAPTIVE IMMUNITY; ANIMAL; B LYMPHOCYTE; CYTOLOGY; HUMAN; IMMUNOLOGY; MECHANICS; REVIEW; T LYMPHOCYTE;

ADAPTIVE IMMUNITY; ANIMALS; B-LYMPHOCYTES; HUMANS; MECHANICAL PHENOMENA; T-LYMPHOCYTES;

EID: 77951669881     PISSN: 0066426X     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.physchem.59.032607.093537     Document Type: Article

References (110)

1. Janeway C. 2005. Immunobiology: The Immune System in Health and Disease. New York: Garland Sci. 823 pp.
2. Allison JP, McIntyre BW, Bloch D. 1982. Tumor-specific antigen of murine T-lymphoma defined with monoclonal antibody. J. Immunol. 129:2293-2300
3. Dialynas DP, Wilde DB, Marrack P, Pierres A, Wall KA, et al. 1983. Characterization of the murine antigenic determinant, designated L3T4a, recognized by monoclonal antibody GK1. 5: Expression of L3T4a by functional T cell clones appears to correlate primarily with class II MHC antigen reactivity. Immunol. Rev. 74:29-56
4. Hedrick SM, Cohen DI, Nielsen EA, Davis MM. 1984. IsolationofcDNA clones encodingTcell-specific membrane-associated proteins. Nature 308:149-153
5. Yanagi Y, Yoshikai Y, Leggett K, Clark SP, Aleksander I, Mak TW. 1984. A human T cell-specific cDNA clone encodes a protein having extensive homology to immunoglobulin chains. Nature 308:145-149
6. Unanue ER. 1984. Antigen-presenting function of the macrophage. Annu. Rev. Immunol. 2:395-428
7. Chan AC, IwashimaM,Turck CW, Weiss A. 1992. ZAP-70:a70kdprotein-tyrosine kinase that associates with the TCR zeta chain. Cell 71:649-662
8. Irving BA, Weiss A. 1991. The cytoplasmic domain of the T cell receptor zeta chain is sufficient to couple to receptor-associated signal transduction pathways. Cell 64:891-901
9. Gallegos AM, Bevan MJ. 2006. Central tolerance: good but imperfect. Immunol. Rev. 209:290-296
10. Hogquist KA, Baldwin TA, Jameson SC. 2005. Central tolerance: learning self-control in the thymus. Nat. Rev. Immunol. 5:772-782
11. Chakraborty AK, Das J. 2010. Pairing computation with experimentation: a powerful coupling for understanding T cell signalling. Nat. Rev. Immunol. 10:59-71
12. Altan-Bonnet G, Germain RN. 2005. Modeling T cell antigen discrimination based on feedback control of digital ERK responses. PLoS Biol. 3:e356
13. Das J, Ho M, Zikherman J, Govern C, Yang M, et al. 2009. Digital signaling and hysteresis characterize Ras activation in lymphoid cells. Cell 136:337-351
14. Iwashima M, Irving BA, van Oers NS, Chan AC, Weiss A. 1994. Sequential interactions of the TCR with two distinct cytoplasmic tyrosine kinases. Science 263:1136-1139
15. Neumeister EN, Zhu Y, Richard S, Terhorst C, Chan AC, Shaw AS. 1995. Binding of ZAP-70 to phosphorylated T-cell receptor zeta and eta enhances its autophosphorylation and generates specific binding sites for SH2 domain-containing proteins. Mol. Cell Biol. 15:3171-3178
16. Zhang W, Sloan-Lancaster J, Kitchen J, Trible RP, Samelson LE. 1998. LAT: the ZAP-70 tyrosine kinase substrate that links T cell receptor to cellular activation. Cell 92:83-92
17. Houtman JC, Higashimoto Y, Dimasi N, Cho S, Yamaguchi H, et al. 2004. Binding specificity of multiprotein signaling complexes is determined by both cooperative interactions and affinity preferences. Biochemistry 43:4170-4178
18. Lin J, Weiss A. 2001. Identification of the minimal tyrosine residues required for linker for activation of T cell function. J. Biol. Chem. 276:29588-29595 (Pubitemid 37452058)
19. Zhu M, Janssen E, Zhang W. 2003. Minimal requirement of tyrosine residues of linker for activation of T cells in TCR signaling and thymocyte development. J. Immunol. 170:325-333
20. Genot E, Cantrell DA. 2000. Ras regulation and function in lymphocytes. Curr. Opin. Immunol. 12:289-294
21. Ebinu JO, Bottorff DA, Chan EY, Stang SL, Dunn RJ, Stone JC. 1998. RasGRP, a Ras guanyl nucleotide-releasing protein with calcium-and diacylglycerol-binding motifs. Science 280:1082-1086
22. Chardin P, Camonis JH, Gale NW, van Aelst L, Schlessinger J, et al. 1993. Human Sos1: a guanine nucleotide exchange factor for Ras that binds to GRB2. Science 260:1338-1343
23. Margarit SM, Sondermann H, Hall BE, Nagar B, Hoelz A, et al. 2003. Structural evidence for feedback activation by Ras. GTP of the Ras-specific nucleotide exchange factor SOS. Cell 112:685-695
24. Sondermann H, Soisson SM, Boykevisch S, Yang SS, Bar-Sagi D, Kuriyan J. 2004. Structural analysis of autoinhibition in the Ras activator Son of sevenless. Cell 119:393-405
25. Freedman TS, Sondermann H, Friedland GD, Kortemme T, Bar-Sagi D, et al. 2006. A Ras-induced conformational switch in the Ras activator Son of sevenless. Proc. Natl. Acad. Sci. USA 103:16692-16697
26. Irvine DJ, Purbhoo MA, Krogsgaard M, Davis MM. 2002. Direct observation of ligand recognition by T cells. Nature 419:845-849
27. Sykulev Y, Joo M, Vturina I, Tsomides TJ, Eisen HN. 1996. Evidence that a single peptide-MHC complex on a target cell can elicit a cytolytic T cell response. Immunity 4:565-571
28. Purbhoo MA, Irvine DJ, Huppa JB, Davis MM. 2004. T cell killing does not require the formation of a stable mature immunological synapse. Nat. Immunol. 5:524-530
29. van Kampen NG. 2007. Stochastic Processes in Physics and Chemistry. Amsterdam: Elsevier. 463 pp.
30. Gillespie DT. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81:2340-2361
31. Bortz AB, Kalos MH, Lebowitz JL. 1975. New algorithm for Monte-Carlo simulation of Ising spin systems. J. Comput. Phys. 17:10-18
32. van Zon JS, ten Wolde PR. 2005. Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space. J. Chem. Phys. 123:234910
33. Danos V, Laneve C. 2004. Formal molecular biology. Theor. Comp. Sci. 325:69-110
34. Faeder JR, Blinov ML, Hlavacek WS. 2009. Rule-based modeling of biochemical systems with BioNet-Gen. Methods Mol. Biol. 500:113-167
35. Gillespie CS, Wilkinson DJ, Proctor CJ, Shanley DP, Boys RJ, Kirkwood TB. 2006. Tools for the SBML community. Bioinformatics 22:628-629
36. Hattne J, Fange D, Elf J. 2005. Stochastic reaction-diffusion simulation with MesoRD. Bioinformatics 21:2923-2924
37. Li H, Cao Y, Petzold LR, Gillespie DT. 2008. Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnol. Prog. 24:56-61
38. Lis M, Artyomov MN, Devadas S, Chakraborty AK. 2009. Efficient stochastic simulation of reaction-diffusion processes via direct compilation. Bioinformatics 25:2289-2291
39. Coombs D, Kalergis AM, Nathenson SG, Wofsy C, Goldstein B. 2002. Activated TCRs remain marked for internalization after dissociation from pMHC. Nat. Immunol. 3:926-931
40. Cemerski S, Das J, Locasale J, Arnold P, Giurisato E, et al. 2007. The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse. Immunity 26:345-355
41. Cemerski S, Das J, Giurisato E, Markiewicz MA, Allen PM, et al. 2008. The balance between T cell receptor signaling and degradation at the center of the immunological synapse is determined by antigen quality. Immunity 29:414-422
42. Lee KH, Dinner AR, Tu C, Campi G, Raychaudhuri S, et al. 2003. The immunological synapse balances T cell receptor signaling and degradation. Science 302:1218-1222
43. Grakoui A, Bromley SK, Sumen C, Davis MM, Shaw AS, et al. 1999. The immunological synapse: a molecular machine controlling T cell activation. Science 285:221-227 (Pubitemid 29329988) (Pubitemid 29329988)
44. Monks CR, Freiberg BA, Kupfer H, Sciaky N, Kupfer A. 1998. Three-dimensional segregation of supramolecular activation clusters in T cells. Nature 395:82-86
45. Qi SY, Groves JT, Chakraborty AK. 2001. Synaptic pattern formation during cellular recognition. Proc. Natl. Acad. Sci. USA 98:6548-6553
46. Mossman KD, Campi G, Groves JT, Dustin ML. 2005. Altered TCR signaling from geometrically repatterned immunological synapses. Science 310:1191-1193
47. Irvine DJ, Doh J, Huang B. 2007. Patterned surfaces as tools to study ligand recognition and synapse formation by T cells. Curr. Opin. Immunol. 19:463-469
48. Gutenkunst RN, Waterfall JJ, Casey FP, Brown KS, Myers CR, Sethna JP. 2007. Universally sloppy parameter sensitivities in systems biology models. PLoS Comput. Biol. 3:1871-1878
49. Huseby ES, Crawford F, White J, Marrack P, Kappler JW. 2006. Interface-disrupting amino acids establish specificity between T cell receptors and complexes of major histocompatibility complex and peptide. Nat. Immunol. 7:1191-1199
50. Huseby ES, White J, Crawford F, Vass T, Becker D, et al. 2005. How the T cell repertoire becomes peptide and MHC specific. Cell 122:247-260
51. Hemmer B, Vergelli M, Gran B, Ling N, Conlon P, et al. 1998. Predictable TCR antigen recognition based on peptide scans leads to the identification of agonist ligands with no sequence homology. J. Immunol. 160:3631-3636 (Pubitemid 28176061) (Pubitemid 28176061)
52. Kersh GJ, Allen PM. 1996. Essential flexibility in the T-cell recognition of antigen. Nature 380:495-498
53. Misko IS, Cross SM, Khanna R, Elliott SL, Schmidt C, et al. 1999. Crossreactive recognition ofviral, self, and bacterial peptide ligands byhuman class I-restricted cytotoxic T lymphocyte clonotypes: implications for molecular mimicry in autoimmune disease. Proc. Natl. Acad. Sci. USA 96:2279-2284
54. Sloan-Lancaster J, Allen PM. 1996. Altered peptide ligand-induced partial T cell activation: molecular mechanisms and role in T cell biology. Annu. Rev. Immunol. 14:1-27
55. Fischer E. 1894. Einfluss der Configuration auf die Wirkung der Enzyme. Ber. Dtsch. Chem. Ges. 27:2985-2993
56. Starr TK, Jameson SC, Hogquist KA. 2003. Positive and negative selectionofTcells. Annu. Rev. Immunol. 21:139-176
57. von Boehmer H, Aifantis I, Gounari F, Azogui O, Haughn L, et al. 2003. Thymic selection revisited: How essential is it? Immunol. Rev. 191:62-78
58. Werlen G, Hausmann B, Naeher D, Palmer E. 2003. Signaling life and death in the thymus: Timing is everything. Science 299:1859-1863
59. Siggs OM, Makaroff LE, Liston A. 2006. The why and how of thymocyte negative selection. Curr. Opin. Immunol. 18:175-183
60. Daniels MA, Teixeiro E, Gill J, Hausmann B, Roubaty D, et al. 2006. Thymic selection threshold defined by compartmentalization of Ras/MAPK signalling. Nature 444:724-729
61. Prasad A, Zikherman J, Das J, Roose JP, Weiss A, Chakraborty AK. 2009. Origin of the sharp boundary that discriminates positive and negative selection of thymocytes. Proc. Natl. Acad. Sci. USA 106:528-533
62. Kos?mrlj A, Chakraborty AK, Kardar M, Shakhnovich EI. 2009. Thymic selection of T-cell receptors as an extreme value problem. Phys. Rev. Lett. 103:068103
63. Kos?mrlj A, Jha AK, Huseby ES, Kardar M, Chakraborty AK. 2008. How the thymus designs antigen-specific and self-tolerant T cell receptor sequences. Proc. Natl. Acad. Sci. USA 105:16671-16676
64. Chao DL, Davenport MP, Forrest S, Perelson AS. 2005. The effects of thymic selection on the range of T cell cross-reactivity. Eur. J. Immunol. 35:3452-3459
65. DetoursV, Mehr R, Perelson AS. 1999. Aquantitative theory ofaffinity-drivenTcell repertoire selection. J. Theor. Biol. 200:389-403
66. Detours V, Perelson AS. 1999. Explaining high alloreactivity as a quantitative consequence of affinity-driven thymocyte selection. Proc. Natl. Acad. Sci. USA 96:5153-5158
67. Leadbetter MR, Lindgren G, Rootzen H. 1983. Extremes and Related Properties of Random Sequences and Processes. New York: Springer-Verlag. 336 pp.
68. Burroughs NJ, de Boer RJ, Kesmir C. 2004. Discriminating self from nonself with short peptides from large proteomes. Immunogenetics 56:311-320
69. + T cell responses. J. Immunol. 182:1526-1532
70. Garboczi DN, Ghosh P, Utz U, Fan QR, Biddison WE, Wiley DC. 1996. Structure of the complex between human T-cell receptor, viral peptide and HLA-A2. Nature 384:134-141
71. Garcia KC, Degano M, Stanfield RL, Brunmark A, Jackson MR, et al. 1996. An αβ T cell receptor structure at 2. 5 A and its orientation in the TCR-MHC complex. Science 274:209-219
72. Kardar M. 1983. Phase transitions in new solvable Hamiltonians by a Hamiltonian minimization. Phys. Rev. Lett. 51:523-526
73. Burnet FM. 1957. A modification of Jerne's theory of antibody production using the concept of clonal selection. Aust. J. Sci. 20:67-69
74. Talmage DW. 1957. Allergy and immunology. Annu. Rev. Med. 8:239-256
75. Tonegawa S. 1983. Somatic generation of antibody diversity. Nature 302:575-581
76. Oprea M, Perelson AS. 1997. Somatic mutation leads to efficient affinity maturation when centrocytes recycle back to centroblasts. J. Immunol. 158:5155-5162
77. Kepler TB, Perelson AS. 1993. Somatic hypermutation in B cells: an optimal control treatment. J. Theor. Biol. 164:37-64
78. Oprea M, van Nimwegen E, Perelson AS. 2000. Dynamics of one-pass germinal center models: implications for affinity maturation. Bull. Math. Biol. 62:121-153
79. Moreira JS, Faro J. 2006. Re-evaluating the recycling hypothesis in the germinal centre. Immunol. Cell Biol. 84:404-410
80. Kesmir C, De Boer RJ. 2003. A spatial model of germinal center reactions: cellular adhesion based sorting of B cells results in efficient affinity maturation. J. Theor. Biol. 222:9-22
81. Celada F, Seiden PE. 1996. Affinity maturation and hypermutation in a simulation of the humoral immune response. Eur. J. Immunol. 26:1350-1358
82. Kauffman S, Levin S. 1987. Towards a general theory of adaptive walks on rugged landscapes. J. Theor. Biol. 128:11-45
83. Kauffman SA, Weinberger ED. 1989. The NK model of rugged fitness landscapes and its application to maturation of the immune response. J. Theor. Biol. 141:211-245
84. Meyer-Hermann M. 2002. A mathematical model for the germinal center morphology and affinity maturation. J. Theor. Biol. 216:273-300
85. Meyer-Hermann ME, Maini PK. 2005. Cutting edge: back to "one-way" germinal centers. J. Immunol. 174:2489-2493
86. Perelson AS, Oster GF. 1979. Theoretical studies of clonal selection: minimal antibody repertoire size and reliability of self-non-self discrimination. J. Theor. Biol. 81:645-670
87. De Boer RJ, Segel LA, Perelson AS. 1992. Pattern formation in one-and two-dimensional shape-space models of the immune system. J. Theor. Biol. 155:295-333
88. Kepler TB, Perelson AS. 1995. Modeling and optimization of populations subject to time-dependent mutation. Proc. Natl. Acad. Sci. USA 92:8219-8223
89. Berek C, Milstein C. 1987. Mutation drift and repertoire shift in the maturation of the immune response. Immunol. Rev. 96:23-41
90. Jacob J, Kelsoe G, Rajewsky K, Weiss U. 1991. Intraclonal generation of antibody mutants in germinal centres. Nature 354:389-392
91. Kelsoe G. 1996. Life and death in germinal centers (redux). Immunity 4:107-111
92. Przylepa J, Himes C, Kelsoe G. 1998. Lymphocyte development and selection in germinal centers. Curr. Top. Microbiol. Immunol. 229:85-104
93. Choe J, Li L, Zhang X, Gregory CD, Choi YS. 2000. Distinct role of follicular dendritic cells and T cells in the proliferation, differentiation, and apoptosis of a centroblast cell line, L3055. J. Immunol. 164:56-63
94. Lindhout E, Koopman G, Pals ST, de Groot C. 1997. Triple check for antigen specificity of B cells during germinal centre reactions. Immunol. Today 18:573-577
95. Manser T, Tumas-Brundage KM, Casson LP, Giusti AM, Hande S, et al. 1998. The roles of antibody variable region hypermutation and selection in the development of the memory B-cell compartment. Immunol. Rev. 162:183-196
96. Radmacher MD, Kelsoe G, Kepler TB. 1998. Predicted and inferred waiting times for key mutations in the germinal centre reaction: evidence for stochasticity in selection. Immunol. Cell Biol. 76:373-381
97. Kleinstein SH, Singh JP. 2001. Toward quantitative simulation of germinal center dynamics: biological and modeling insights from experimental validation. J. Theor. Biol. 211:253-275
98. Berek C, Berger A, Apel M. 1991. Maturation of the immune response in germinal centers. Cell 67:1121-1129
99. Pontryagin LS, Boltyanskii VG, Gamkrelidze RV, Mischenko EF. 1962. The Mathematical Theory of Optimal Processes. New York: Wiley. 360 pp.
100. Heo M, Zeldovich KB, Shakhnovich EI. Unpublished manuscript
101. Shakhnovich E. 2006. Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem. Rev. 106:1559-1588
102. Liu YJ, Barthelemy C, de Bouteiller O, Banchereau J. 1994. The differences in survival and phenotype between centroblasts and centrocytes. Adv. Exp. Med. Biol. 355:213-218
103. Bogarad LD, Deem MW. 1999. A hierarchical approach to protein molecular evolution. Proc. Natl. Acad. Sci. USA 96:2591-2595
104. Deem MW, Lee HY. 2003. Sequence space localization in the immune system response to vaccination and disease. Phys. Rev. Lett. 91:068101
105. Gupta V, Earl DJ, Deem MW. 2006. Quantifying influenza vaccine efficacy and antigenic distance. Vaccine 24:3881-3888
106. Munoz ET, Deem MW. 2005. Epitope analysis for influenza vaccine design. Vaccine 23:1144-1148
107. Yang M, Park JM, Deem MW. 2006. A theory of multi-site vaccination for cancer. Phys. A Stat. Mech. Appl. 366:347-364
108. Fazekas de St Groth S, Webster RG. 1966. Disquisitions on original Antigenic Sin. I. Evidence in man. J. Exp. Med. 124:331-345
109. Fazekas de St Groth S, Webster RG. 1966. Disquisitions on original Antigenic Sin. II. Proof in lower creatures. J. Exp. Med. 124:347-361
110. Schreiber H, Wu TH, Nachman J, Kast WM. 2002. Immunodominance and tumor escape. Semin. Cancer Biol. 12:25-31