T cell receptor variable β20-1 harbors a nucleotide binding pocket in the CDR2β loop


Novel aspects of T cells containing TCRVβ20-1 are numerous, ranging from pathogen specific reactivity to specific tissue homing, or possible T cell subsets. Recently, it was demonstrated that TCR itself could become reactive by binding to small molecules free of the pHLA interface. Our work here was to identify a natural ligand binding to an identified pocket on the CDR2β loop of these TCR. Using docking of suspected ligands, we were able to show Guanine and Adenine diand tri-nucleotides readily bind to the identified site. Comparing these with small molecule sites found on other TCR types, we show this interaction is novel. With further molecular dynamic simulations, these sites are shown to be plausible by conducting simple computational based solubility tests as cross validation. Combined with simple proliferative responses, the identified nucleotides are also shown to have functional consequences by inducing T cell proliferation for CD4/Vβ20-1 + T cells, while failing to induce proliferation in other T cell isolates. Merging computational and simple cell assays, this work establishes a role of nucleotides in T cells found to contain this TCR subtype.

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Watkins, S. and Pichler, W. (2013) T cell receptor variable β20-1 harbors a nucleotide binding pocket in the CDR2β loop. Open Journal of Immunology, 3, 165-174. doi: 10.4236/oji.2013.33021.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Moza, B., Varma, A.K., Buonpane, R.A., Zhu, P., Herfst, C.A., et al. (2007) Structural basis of T-cell specificity and activation by the bacterial superantigen TSST-1. EMBO Journal, 26, 1187-1197. doi:10.1038/sj.emboj.7601531
[2] Watkins, S.L. and Pichler, W.J. (2013) Activating interactions of sulfanilamides with T cell receptors. Open Journal of Immunology, 3, in press.
[3] Engler, O.B., Strasser, I., Naisbitt, D.J., Cerny, A. and Pichler, W.J. (2004) A chemically inert drug can stimulate T cells in vitro by their T cell receptor in non-sensitised individuals. Toxicology, 197, 47-56. doi:10.1016/j.tox.2003.12.008
[4] Ko, T.M., Chung, W.H., Wei, C.Y., Shih, H.Y., Chen, J.K., et al. (2011) Shared and restricted T-cell receptor use is crucial for carbamazepine-induced Stevens-Johnson syndrome. Journal of Allergy and Clinical Immunology, 128, 1266-1276.
[5] Komatsu, T., Moriya, N. and Shiohara, T. (1996) T cell receptor (TCR) repertoire and function of human epidermal T cells: Restricted TCR V alpha-V beta genes are utilized by T cells residing in the lesional epidermis in fixed drug eruption. Clinical & Experimental Immunology, 104, 343-350. doi:10.1046/j.1365-2249.1996.30738.x
[6] Sumida, T., Kita, Y., Yonaha, F., Maeda, T., Iwamoto, I., et al. (1994) T cell receptor V alpha repertoire of infiltrating T cells in labial salivary glands from patients with Sjogren’s syndrome. Journal of Rheumatology, 21, 1655- 1661.
[7] Sumida, T., Yonaha, F., Maeda, T., Tanabe, E., Koike, T., et al. (1992) T cell receptor repertoire of infiltrating T cells in lips of Sjogren’s syndrome patients. Journal of Clinical Investigation, 89, 681-685. doi:10.1172/JCI115635
[8] Wucherpfennig, K.W. and Hafler, D.A. (1995) A review of T-cell receptors in multiple sclerosis: Clonal expansion and persistence of human T-cells specific for an immunodominant myelin basic protein peptide. Annals of the New York Academy of Sciences, 756, 241-258. doi:10.1111/j.1749-6632.1995.tb44522.x
[9] He, X., Rosloniec, E.F., Myers, L.K., McColgan, W.L., Gumanovskaya, M., et al. (2004) T cell receptors recognizing type II collagen in HLA-DR-transgenic mice characterized by highly restricted V beta usage. Arthritis & Rheumatism, 50, 1996-2004. doi:10.1002/art.20289
[10] Thompson, S.D., Murray, K.J., Grom, A.A., Passo, M.H., Choi, E., et al. (1998) Comparative sequence analysis of the human T cell receptor beta chain in juvenile rheumatoid arthritis and juvenile spondylarthropathies: Evidence for antigenic selection of T cells in the synovium. Arthritis & Rheumatism, 41, 482-497. doi:10.1002/1529-0131(199803)41:3<482::AID-ART15>3.0.CO;2-G
[11] Lopez-Sagaseta, J., Dulberger, C.L., Crooks, J.E., Parks, C.D., Luoma, A.M., et al. (2013) The molecular basis for Mucosal-Associated Invariant T cell recognition of MR1 proteins. Proceedings of the National Academy of Sciences of USA, 110, E1771-1778. doi:10.1073/pnas.1222678110
[12] Reantragoon, R., Kjer-Nielsen, L., Patel, O., Chen, Z., Illing, P.T., et al. (2012) Structural insight into MR1-mediated recognition of the mucosal associated invariant T cell receptor. Journal of Experimental Medicine, 209, 761-774. doi:10.1084/jem.20112095
[13] Pichler, W.J. (2003) Delayed drug hypersensitivity reactions. Annals of Internal Medicine, 139, 683-693. doi:10.7326/0003-4819-139-8-200310210-00012
[14] Garcia-Carrasco, M., Fuentes-Alexandro, S., Escarcega, R.O., Salgado, G., Riebeling, C., et al. (2006) Pathophysiology of Sjogren’s syndrome. Archives of Medical Research, 37, 921-932. doi:10.1016/j.arcmed.2006.08.002
[15] de Bakker, P.I., McVean, G., Sabeti, P.C., Miretti, M.M., Green, T., et al. (2006) A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nature Genetics, 38, 1166-1172. doi:10.1038/ng1885
[16] Wei, C.Y., Chung, W.H., Huang, H.W., Chen, Y.T. and Hung, S.I. (2012) Direct interaction between HLA-B and carbamazepine activates T cells in patients with Stevens- Johnson syndrome. Journal of Allergy and Clinical Immunology, 129, 1562-1569.
[17] Yang, C.W., Hung, S.I., Juo, C.G., Lin, Y.P., Fang, W.H., et al. (2007) HLA-B*1502-bound peptides: Implications for the pathogenesis of carbamazepine-induced Stevens- Johnson syndrome. Journal of Allergy and Clinical Immunology, 120, 870-877. doi:10.1016/j.jaci.2007.06.017
[18] Hart, B.A., Hintzen, R.Q. and Laman, J.D. (2009) Multiple sclerosis: A response-to-damage model. Trends in Molecular Medicine, 15, 235-244.
[19] Wei, C.Y., Ko, T.M., Shen, C.Y. and Chen, Y.T. (2012) A recent update of pharmacogenomics in drug-induced severe skin reactions. Drug Metabolism and Pharmacokinetics, 27, 132-141. doi:10.2133/dmpk.DMPK-11-RV-116
[20] Adam, J., Pichler, W.J. and Yerly, D. (2011) Delayed drug hypersensitivity: Models of T-cell stimulation. British Journal of Clinical Pharmacology, 71, 701-707. doi:10.1111/j.1365-2125.2010.03764.x
[21] Pichler, W.J., Beeler, A., Keller, M., Lerch, M., Posadas, S., et al. (2006) Pharmacological interaction of drugs with immune receptors: the p-i concept. Allergology International, 55, 17-25. doi:10.2332/allergolint.55.17
[22] von Greyerz, S., Zanni, M.P., Frutig, K., Schnyder, B., Burkhart, C., et al. (1999) Interaction of sulfonamide derivatives with the TCR of sulfamethoxazole-specific human alpha beta + T cell clones. Journal of Immunology, 162, 595-602.
[23] Yamamoto, T., Katayama, I. and Nishioka, K. (1998) Analysis of T cell receptor Vbeta repertoires of annular erythema associated with Sjogren’s syndrome. European Journal of Dermatology, 8, 248-251.
[24] McArthur, C.P., Daniels, P.J., Kragel, P., Howard, P.F. and Julian, L. (1997) Sjogren’s syndrome salivary gland immunopathology: Increased laminin expression precedes lymphocytic infiltration. Journal of Autoimmunity, 10, 59-65. doi:10.1006/jaut.1996.0109
[25] Miceli-Richard, C., Gestermann, N., Ittah, M., Comets, E., Loiseau, P., et al. (2009) The CGGGG insertion/deletion polymorphism of the IRF5 promoter is a strong risk factor for primary Sjogren’s syndrome. Arthritis & Rheumatism, 60, 1991-1997. doi:10.1002/art.24662
[26] Nordmark, G., Kristjansdottir, G., Theander, E., Eriksson, P., Brun, J.G., et al. (2009) Additive effects of the major risk alleles of IRF5 and STAT4 in primary Sjogren’s syndrome. Genes & Immunity, 10, 68-76. doi:10.1038/gene.2008.94
[27] Di Virgilio, F., Boeynaems, J.M. and Robson, S.C. (2009) Extracellular nucleotides as negative modulators of immunity. Current Opinion in Pharmacology, 9, 507-513. doi:10.1016/j.coph.2009.06.021
[28] Di Virgilio, F., Chiozzi, P., Ferrari, D., Falzoni, S., Sanz, J.M., et al. (2001) Nucleotide receptors: An emerging family of regulatory molecules in blood cells. Blood, 97, 587-600. doi:10.1182/blood.V97.3.587
[29] Duhant, X., Schandene, L., Bruyns, C., Gonzalez, N.S., Goldman, M., et al. (2002) Extracellular adenine nucleotides inhibit the activation of human CD4+ T lymphocytes. Journal of Immunology, 169, 15-21. doi:10.1002/med.20067
[30] Alonso, H., Bliznyuk, A.A. and Gready, J.E. (2006) Combining docking and molecular dynamic simulations in drug design. Medicinal Research Reviews, 26, 531-568. doi:10.1002/med.20067
[31] Cichero, E., D'Ursi, P., Moscatelli, M., Bruno, O., Orro, A., et al. (2013) Homology modeling, docking studies and molecular dynamic simulations using GPU architecture to probe the type-11 Phosphodiesterase (PDE11) catalytic site: A computational approach for the rational design of selective inhibitors. Chemical Biology & Drug Design.
[32] Arnold, K., Bordoli, L., Kopp, J. and Schwede, T. (2006) The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22, 195-201. doi:10.1093/bioinformatics/bti770
[33] Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A.E., et al. (2005) GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701-1718. doi:10.1002/jcc.20291
[34] Oostenbrink, C., Soares, T.A., van der Vegt, N.F. and van Gunsteren, W.F. (2005) Validation of the 53A6 GROMOS force field. European Biophysics Journal, 34, 273-284. doi:10.1007/s00249-004-0448-6
[35] von Greyerz, S., Bultemann, G., Schnyder, K., Burkhart, C., Lotti, B., et al. (2001) Degeneracy and additional alloreactivity of drug-specific human alpha beta(+) T cell clones. International Immunology, 13, 877-885. doi:10.1093/intimm/13.7.877
[36] Seeliger, D and de Groot, B.L. (2010) Ligand docking and binding site analysis with PyMOL and Autodock/ Vina. Journal of Computer-Aided Molecular Design, 24, 417-422. doi:10.1007/s10822-010-9352-6
[37] Trott, O. and Olson, A.J. (2010) AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31, 455-461.
[38] Criscitiello, M.F., Ohta, Y., Saltis, M., McKinney, E.C. and Flajnik, M.F. (2010) Evolutionarily conserved TCR binding sites, identification of T cells in primary lymphoid tissues, and surprising trans-rearrangements in nurse shark. The Journal of Immunology, 184, 6950-6960. doi:10.4049/jimmunol.0902774
[39] Dzik, J.M. (2010) The ancestry and cumulative evolution of immune reactions. Acta Biochimica Polonica, 57, 443- 466.
[40] Mikami, T., Miyashita, H., Takatsuka, S., Kuroki, Y. and Matsushima, N. (2012) Molecular evolution of vertebrate Toll-like receptors: Evolutionary rate difference between their leucine-rich repeats and their TIR domains. Gene, 503, 235-243. doi:10.1016/j.gene.2012.04.007
[41] Posadas, S.J. and Pichler, W.J. (2007) Delayed drug hypersensitivity reactions-new concepts. Clinical & Experimental Allergy, 37, 989-999. doi:10.1111/j.1365-2222.2007.02742.x
[42] Naisbitt, D.J., Britschgi, M., Wong, G., Farrell, J., Depta, J.P., et al. (2003) Hypersensitivity reactions to carbamazepine: Characterization of the specificity, phenotype, and cytokine profile of drug-specific T cell clones. Molecular Pharmacology, 63, 732-741.
[43] Mauri-Hellweg, D., Bettens, F., Mauri, D., Brander, C., Hunziker, T., et al. (1995) Activation of drug-specific CD4+ and CD8+ T cells in individuals allergic to sulfonamides, phenytoin, and carbamazepine. Journal of Immunology, 155, 462-472.
[44] Murata, H., Kita, Y., Sakamoto, A., Matsumoto, I., Matsumura, R., et al. (1995) Limited TCR repertoire of infiltrating T cells in the kidneys of Sjogren’s syndrome patients with interstitial nephritis. Journal of Immunology, 155, 4084-4089.
[45] Miah, M.A., Ahmed, S.S., Chowdhury, S.A., Begum, F. and Rahman, S.H. (2008) Fixed drug eruptions due to cotrimoxazole. Mymensingh Medical Journal, 17, S1-S5.
[46] Taqi, S.A., Zaki, S.A., Nilofer, A.R. and Sami, L.B. (2012) Trimethoprim-sulfamethoxazole-induced Steven Johnson syndrome in an HIV-infected patient. Indian Journal of Pharmacology, 44, 533-535. doi:10.4103/0253-7613.99346
[47] Vandenbark, A.A., Culbertson, N.E., Bartholomew, R.M., Huan, J., Agotsch, M., et al. (2008) Therapeutic vaccinetion with a trivalent T-cell receptor (TCR) peptide vaccine restores deficient FoxP3 expression and TCR recognition in subjects with multiple sclerosis. Immunology, 123, 66- 78. doi:10.1111/j.1365-2567.2007.02703.x
[48] de Haan, E.C., Moret, E.E., Wagenaar-Hilbers, J.P., Liskamp, R.M. and Wauben, M.H. (2005) Possibilities and limitations in the rational design of modified peptides for T cell mediated immunotherapy. Molecular Immunology, 42, 365-373. doi:10.1016/j.molimm.2004.07.015

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