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Simulation Methods in Uncovering New Regulatory Mechanisms in Signaling Pathways

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Book cover Bioinformatics and Computational Biology (BICoB 2009)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5462))

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Abstract

The paper deals with in silico investigation of possible regulatory mechanisms involved in control of signaling pathways. As an example, the Interferon- b activated pathway has been chosen. Though many processes involved in this pathway are known, there are still some that evade explanation. One of them is the nuclear accumulation of the IRF1 protein. Here, three hypotheses are stated and tested numerically, showing that the most likely mechanism involved in this process is an inhibition of IRF1 activation by an yet unrecognized factor.

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References

  1. Alexander, W.S., Hilton, D.J.: The role of suppressors of cytokine signaling (SOCS) proteins in regulation of the immune response. Annu. Rev. Immunol. 22, 503–529 (2004)

    Article  CAS  PubMed  Google Scholar 

  2. Bekisz, J., Schmeisser, H., Hernandez, J., Goldman, N.D., Zoon, K.C.: Human Interferons Alpha, Beta and Omega. Growth Factors 22(4), 243–251 (2004)

    Article  CAS  PubMed  Google Scholar 

  3. Chen, W., Daines, M.O., Khurana Hershey, G.K.: Turning off signal transducer and activator of transcription (STAT): The negative regulation of STAT signaling. J. Allergy Clin. Immunol. 114, 476–489 (2004)

    Article  CAS  PubMed  Google Scholar 

  4. Goodbourn, S., Didcock, L., Randall, R.E.: Interferons: cell signalling, immune modulation, antiviral responses and virus countermeasures. J. Gen. Virol. 81, 2341–2364 (2000)

    Article  CAS  PubMed  Google Scholar 

  5. Kalvakolanu, D.V.: Alternate interferon signaling pathways. Pharmacol Ther. 100, 1–29 (2003)

    Article  CAS  PubMed  Google Scholar 

  6. Levy, D.E., Darnell Jr., J.: STATs: transcriptional control and biological impact. Nat. Rev. Mol. Cell Biol. 3, 651–662 (2002)

    Article  CAS  PubMed  Google Scholar 

  7. Pestka, S., Krause, C.D., Walter, M.R.: Interferons, interferon-like cytokines, and their receptors. Immunol. Rev. 202, 8–32 (2004)

    Article  CAS  PubMed  Google Scholar 

  8. Rogers, R.S., Horvath, C.M., Matunis, M.J.: SUMO Modification of STAT1 and Its Role in PIAS-mediated Inhibition of Gene Activation. J. Biol. Chem. 278(32), 30091–30097 (2003)

    Article  CAS  PubMed  Google Scholar 

  9. O’Shea, J.J., Watford, W.: A peek at PIAS. Nat. Immunol. 5(9), 875–876 (2004)

    Article  PubMed  Google Scholar 

  10. Shuai, K., Liu, B.: Regulation of JAK–STAT signalling in the immune system. Nat. Rev. Immunol. 3, 900–911 (2003)

    Article  CAS  PubMed  Google Scholar 

  11. Smieja, J., Jamaluddin, M., Brasier, A.R., Kimmel, M.: Model-based analysis of Interferon-b induced signaling pathway. Bioinformatics 24(20), 2363–2369 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Taniguchi, T., Ogasawara, K., Takaoka, A., Tanaka, N.: IRF family of transcription factors as regulators of host defense. Annu. Rev. Immunol. 19, 623–655 (2001)

    Article  CAS  PubMed  Google Scholar 

  13. Taniguchi, T., Takaoka, A.: The interferon-α/β system in antiviral responses: a multimodal machinery of gene regulation by the IRF family of transcription factors. Curr. Opin. Immunol. 14, 111–116 (2002)

    Article  CAS  PubMed  Google Scholar 

  14. Vinkemeier, U.: Getting the message across, STAT! Design principles of a molecular signaling circuit. J. Cell Biol. 167(2), 197–201 (2004)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Wormald, S., Hilton, D.J.: Inhibitors of Cytokine Signal Transduction. J. Biol. Chem. 279(2), 821–824 (2004)

    Article  CAS  PubMed  Google Scholar 

  16. Yasukawa, H., Sasaki, A., Yoshimura, A.: Negative Regulation Of Cytokine Signaling Pathways. Annu. Rev. Immunol. 18, 143–164 (2000)

    Article  CAS  PubMed  Google Scholar 

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© 2009 Springer-Verlag Berlin Heidelberg

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Smieja, J. (2009). Simulation Methods in Uncovering New Regulatory Mechanisms in Signaling Pathways. In: Rajasekaran, S. (eds) Bioinformatics and Computational Biology. BICoB 2009. Lecture Notes in Computer Science(), vol 5462. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00727-9_37

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  • DOI: https://doi.org/10.1007/978-3-642-00727-9_37

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-00726-2

  • Online ISBN: 978-3-642-00727-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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