Structure Prediction with FAMS for Proteins Screened Critically to Autoimmune Diseases based upon Bioinformatics

Shigeharu Ishida, Hideaki Umeyama, Mitsuo Iwadate, Y-h. Taguchi

2013

Abstract

Drug discovery for autoimmune diseases is recently recognized to be an important task. In this study, we try to perform structure prediction of proteins whose gene promoter regions were previously reported to be specifically methelysed or demethylased commonly for three autoimmune diseases, systemic lupus erythematosus, rheumatoid arthritis, and dermatomyositis. FAMS were employed for this purpose and we can predict three dimensional structure with significantly small enough P-values. Most of them are suggested to be self immunology related proteins and will be important drug target candidates. We also found some proteins which form complex with each other. The possibility of a new drug target, i.e., suppression of protein complex formation is suggested.

References

  1. Abd-Allah, S. H., el Shal, A. S., Shalaby, S. M., Pasha, H. F., Abou el Saoud, A. M., el Najjar, A. R., and el Shahawy, E. E. (2012). PADI4 polymorphisms and related haplotype in rheumatoid arthritis patients. Joint Bone Spine, 79(2):124-128.
  2. Bingle, C. D. and Vyakarnam, A. (2008). Novel innate immune functions of the whey acidic protein family. Trends Immunol., 29(9):444-453.
  3. Bouma, B. N., Vlooswijk, R. A., and Griffin, J. H. (1983). Immunologic studies of human coagulation factor XI and its complex with high molecular weight kininogen. Blood, 62(5):1123-1131.
  4. Coito, A. J., de Sousa, M., and Kupiec-Weglinski, J. W. (2000). Fibronectin in immune responses in organ transplant recipients. Dev. Immunol., 7(2-4):239-248.
  5. Cronstein, B. N. (2007). Interleukin-6-a key mediator of systemic and local symptoms in rheumatoid arthritis. Bull NYU Hosp Jt Dis, 65 Suppl 1:S11-15.
  6. Dogliotti, G., Galliera, E., Licastro, F., Porcellini, E., and Corsi, M. M. (2010). Serum neutrophil gelatinaseB associated lipocalin (NGAL) levels in Down's syndrome patients. Immun Ageing, 7 Suppl 1:S7.
  7. Fong, L., Ruegg, C. L., Brockstedt, D., Engleman, E. G., and Laus, R. (1997). Induction of tissue-specific autoimmune prostatitis with prostatic acid phosphatase immunization: implications for immunotherapy of prostate cancer. J. Immunol., 159(7):3113-3117.
  8. Frey, T. G., Chan, S. H., and Schatz, G. (1978). Structure and orientation of cytochrome c oxidase in crystalline membranes. Studies by electron microscopy and by labeling with subunit-specific antibodies. J. Biol. Chem., 253(12):4389-4395.
  9. Gabr, A. A., Reed, M., Newman, D. R., Pohl, J., Khosla, J., and Sannes, P. L. (2007). Alterations in cytoskeletal and immune function-related proteome profiles in whole rat lung following intratracheal instillation of heparin. Respir. Res., 8:36.
  10. Gervin, K., Vigeland, M. D., Mattingsdal, M., Hammer?, M., Nygard, H., Olsen, A. O., Brandt, I., Harris, J. R., Undlien, D. E., and Lyle, R. (2012). DNA methylation and gene expression changes in monozygotic twins discordant for psoriasis: identification of epigenetically dysregulated genes. PLoS Genet., 8(1):e1002454.
  11. Heijmans, J., Buller, N. V., Hoff, E., Dihal, A. A., van der Poll, T., van Zoelen, M. A., Bierhaus, A., Biemond, I., Hardwick, J. C., Hommes, D. W., Muncan, V., and van den Brink, G. R. (2012). Rage signalling promotes intestinal tumourigenesis. Oncogene.
  12. Jin, T., Perry, A., Jiang, J., Smith, P., Curry, J. A., Unterholzner, L., Jiang, Z., Horvath, G., Rathinam, V. A., Johnstone, R. W., Hornung, V., Latz, E., Bowie, A. G., Fitzgerald, K. A., and Xiao, T. S. (2012). Structures of the HIN Domain:DNA Complexes Reveal Ligand Binding and Activation Mechanisms of the AIM2 Inflammasome and IFI16 Receptor. Immunity, 36(4):561-571.
  13. Latonen, L., Jarvinen, P. M., Suomela, S., Moore, H. M., Saarialho-Kere, U., and Laiho, M. (2010). Ultraviolet B radiation regulates cysteine-rich protein 1 in human keratinocytes. Photodermatol Photoimmunol Photomed, 26(2):70-77.
  14. Lin, J. X., Li, P., Liu, D., Jin, H. T., He, J., Rasheed, M. A., Rochman, Y., Wang, L., Cui, K., Liu, C., Kelsall, B. L., Ahmed, R., and Leonard, W. J. (2012). Critical Role of STAT5 Transcription Factor Tetramerization for Cytokine Responses and Normal Immune Function. Immunity, 36(4):586-599.
  15. Meylan, E., Burns, K., Hofmann, K., Blancheteau, V., Martinon, F., Kelliher, M., and Tschopp, J. (2004). RIP1 is an essential mediator of Toll-like receptor 3-induced NF-kappa B activation. Nat. Immunol., 5(5):503-507.
  16. O-Sullivan, I., Chopra, A., Carr, J., Kim, T. S., and Cohen, E. P. (2008). Immunity to growth factor receptorbound protein 10, a signal transduction molecule, inhibits the growth of breast cancer in mice. Cancer Res., 68(7):2463-2470.
  17. O'Hanlon, T. P., Li, Z., Gan, L., Gourley, M. F., Rider, L. G., and Miller, F. W. (2011a). Plasma proteomic profiles from disease-discordant monozygotic twins suggest that molecular pathways are shared in multiple systemic autoimmune diseases*. Arthritis Res. Ther., 13(6):R181.
  18. O'Hanlon, T. P., Rider, L. G., Gan, L., Fannin, R., Paules, R. S., Umbach, D. M., Weinberg, C. R., Shah, R. R., Mav, D., Gourley, M. F., and Miller, F. W. (2011b). Gene expression profiles from discordant monozygotic twins suggest that molecular pathways are shared among multiple systemic autoimmune diseases. Arthritis Res. Ther., 13(2):R69.
  19. Pan, H. F., Leng, R. X., Tao, J. H., Li, X. P., and Ye, D. Q. (2011). Ets-1: a new player in the pathogenesis of systemic lupus erythematosus? Lupus, 20(3):227-230.
  20. Quek, A. M., Britton, J. W., McKeon, A., So, E., Lennon, V. A., Shin, C., Klein, C. J., Watson, R. E., Kotsenas, A. L., Lagerlund, T. D., Cascino, G. D., Worrell, G. A., Wirrell, E. C., Nickels, K. C., Aksamit, A. J., Noe, K. H., and Pittock, S. J. (2012). Autoimmune Epilepsy: Clinical Characteristics and Response to Immunotherapy. Arch Neurol, 69(5):582-593.
  21. Samadani, U. and Costa, R. H. (1996). The transcriptional activator hepatocyte nuclear factor 6 regulates liver gene expression. Mol. Cell. Biol., 16(11):6273-6284.
  22. Sarkar, S., Song, Y., Sarkar, S., Kipen, H. M., Laumbach, R. J., Zhang, J., Strickland, P. A., Gardner, C. R., and Schwander, S. (2012). Suppression of the NF-B pathway by diesel exhaust particles impairs human antimycobacterial immunity. J. Immunol., 188(6):2778- 2793.
  23. Selvaraj, R. K., Shanmugasundaram, R., and Klasing, K. C. (2010). Effects of dietary lutein and PUFA on PPAR and RXR isomer expression in chickens during an inflammatory response. Comp. Biochem. Physiol., Part A Mol. Integr. Physiol., 157(3):198-203.
  24. Silva, J. A., Ferrucci, D. L., Peroni, L. A., Abrahao, P. G., Salamene, A. F., Rossa-Junior, C., Carvalho, H. F., and Stach-Machado, D. R. (2012). Sequential IL-23 and IL-17 and increased Mmp8 and Mmp14 expression characterize the progression of an experimental model of periodontal disease in type 1 diabetes. J. Cell. Physiol., 227(6):2441-2450.
  25. Skeie, G. O., Bentsen, P. T., Freiburg, A., Aarli, J. A., and Gilhus, N. E. (1998). Cell-mediated immune response against titin in myasthenia gravis: evidence for the involvement of Th1 and Th2 cells. Scand. J. Immunol., 47(1):76-81.
  26. Taguchi, Y.-h. (2010). A significance test based upon PCA. SIG-DMSM, A903:38-47.
  27. Tripp, R. A., Barskey, A., Goss, L., and Anderson, L. J. (2002). Substance P receptor expression on lymphocytes is associated with the immune response to respiratory syncytial virus infection. J. Neuroimmunol., 129(1-2):141-153.
  28. Tsukazaki, T., Mori, H., Fukai, S., Ishitani, R., Mori, T., Dohmae, N., Perederina, A., Sugita, Y., Vassylyev, D. G., Ito, K., and Nureki, O. (2008). Conformational transition of Sec machinery inferred from bacterial SecYE structures. Nature, 455(7215):988-991.
  29. Tsunoda, T., Takashima, Y., Tanaka, Y., Fujimoto, T., Doi, K., Hirose, Y., Koyanagi, M., Yoshida, Y., Okamura, T., Kuroki, M., Sasazuki, T., and Shirasawa, S. (2010). Immune-related zinc finger gene ZFAT is an essential transcriptional regulator for hematopoietic differentiation in blood islands. Proc. Natl. Acad. Sci. U.S.A., 107(32):14199-14204.
  30. Umeyama, H. and Iwadate, M. (2002). Fams and famsbase for protein structure. In Current Protocols in Bioinformatics. John Wiley & Sons, Inc.
  31. Watson, F. L., Puttmann-Holgado, R., Thomas, F., Lamar, D. L., Hughes, M., Kondo, M., Rebel, V. I., and Schmucker, D. (2005). Extensive diversity of Igsuperfamily proteins in the immune system of insects. Science, 309(5742):1874-1878.
  32. Zhou, X., Tan, F. K., Xiong, M., Arnett, F. C., and FeghaliBostwick, C. A. (2005). Monozygotic twins clinically discordant for scleroderma show concordance for fibroblast gene expression profiles. Arthritis Rheum., 52(10):3305-3314.
  33. Zoller, K. E., MacNeil, I. A., and Brugge, J. S. (1997). Protein tyrosine kinases Syk and ZAP-70 display distinct requirements for Src family kinases in immune response receptor signal transduction. J. Immunol., 158(4):1650-1659.
Download


Paper Citation


in Harvard Style

Ishida S., Umeyama H., Iwadate M. and Taguchi Y. (2013). Structure Prediction with FAMS for Proteins Screened Critically to Autoimmune Diseases based upon Bioinformatics . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013) ISBN 978-989-8565-35-8, pages 261-267. DOI: 10.5220/0004188802610267


in Bibtex Style

@conference{bioinformatics13,
author={Shigeharu Ishida and Hideaki Umeyama and Mitsuo Iwadate and Y-h. Taguchi},
title={Structure Prediction with FAMS for Proteins Screened Critically to Autoimmune Diseases based upon Bioinformatics},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)},
year={2013},
pages={261-267},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0004188802610267},
isbn={978-989-8565-35-8},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2013)
TI - Structure Prediction with FAMS for Proteins Screened Critically to Autoimmune Diseases based upon Bioinformatics
SN - 978-989-8565-35-8
AU - Ishida S.
AU - Umeyama H.
AU - Iwadate M.
AU - Taguchi Y.
PY - 2013
SP - 261
EP - 267
DO - 10.5220/0004188802610267