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Mathematical Investigation of How Oncogenic Ras Mutants Promote Ras Signaling

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Computational Modeling of Signaling Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 880))

Abstract

We have used a mathematical model of the Ras signaling network to link observable biochemical properties with cellular levels of RasGTP. Although there is abundant data characterizing Ras biochemistry, attributing specific changes in biochemical properties to observed phenotypes has been hindered by the scope and complexity of Ras regulation. A mathematical model of the Ras signaling module, therefore, appeared to be of value for this problem. The model described the core architecture shared by pathways that signal through Ras. Mass-action kinetics and ordinary differential equations were used to describe network reactions. Needed parameters were largely available in the published literature and resulted in a model with good agreement to experimental data. Computational analysis of the model resulted in several unanticipated predictions and suggested experiments that subsequently validated some of these predictions.

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References

  1. Malumbres M, Barbacid M (2003) RAS oncogenes: the first 30 years. Nat Rev Cancer 3(6):459–465

    Article  PubMed  CAS  Google Scholar 

  2. Eccleston JF, Moore KJ, Brownbridge GG, Webb MR, Lowe PN (1991) Fluorescence approaches to the study of the p21ras GTPase mechanism. Biochem Soc Trans 19(2):432–437

    PubMed  CAS  Google Scholar 

  3. Chuang E, Barnard D, Hettich L, Zhang XF, Avruch J, Marshall MS (1994) Critical binding and regulatory interactions between Ras and Raf occur through a small, stable N-terminal domain of Raf and specific Ras effector residues. Mol Cell Biol 14(8):5318–5325

    PubMed  CAS  Google Scholar 

  4. Ahmadian MR, Hoffmann U, Goody RS, Wittinghofer A (1997) Individual rate constants for the interaction of Ras proteins with GTPase-activating proteins determined by fluorescence spectroscopy. Biochemistry 36(15):4535–4541

    Article  PubMed  CAS  Google Scholar 

  5. Stites EC, Trampont PC, Ma Z, Ravichandran KS (2007) Network analysis of oncogenic Ras activation in cancer. Science 318(5849):463–467

    Article  PubMed  CAS  Google Scholar 

  6. Gibbs JB, Marshall MS, Scolnick EM, Dixon RA, Vogel US (1990) Modulation of guanine nucleotides bound to Ras in NIH3T3 cells by oncogenes, growth factors, and the GTPase activating protein (GAP). J Biol Chem 265(33):20437–20442

    PubMed  CAS  Google Scholar 

  7. Milburn MV, Tong L, de Vos AM et al (1990) Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic Ras proteins. Science 247(4945):939–945

    Article  PubMed  CAS  Google Scholar 

  8. Macara IG, Lounsbury KM, Richards SA, McKiernan C, Bar-Sagi D (1996) The Ras superfamily of GTPases. FASEB J 10(5):625–630

    PubMed  CAS  Google Scholar 

  9. Bos JL, Rehmann H, Wittinghofer A (2007) GEFs and GAPs: critical elements in the control of small G proteins. Cell 129(5):865–877

    Article  PubMed  CAS  Google Scholar 

  10. Donovan S, Shannon KM, Bollag G (2002) GTPase activating proteins: critical regulators of intracellular signaling. Biochim Biophys Acta 1602(1):23–45

    PubMed  CAS  Google Scholar 

  11. Mistou MY, Jacquet E, Poullet P et al (1992) Mutations of Ha-Ras p21 that define important regions for the molecular mechanism of the SDC25 C-domain, a guanine nucleotide dissociation stimulator. EMBO J 11(7):2391–2397

    PubMed  CAS  Google Scholar 

  12. Sebolt-Leopold JS, Herrera R (2004) Targeting the mitogen-activated protein kinase cascade to treat cancer. Nat Rev Cancer 4(12):937–947

    Article  PubMed  CAS  Google Scholar 

  13. Vivanco I, Sawyers CL (2002) The phosphatidylinositol 3-Kinase AKT pathway in human cancer. Nat Rev Cancer 2(7):489–501

    Article  PubMed  CAS  Google Scholar 

  14. Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70

    Article  PubMed  CAS  Google Scholar 

  15. Schoeberl B, Eichler-Jonsson C, Gilles ED, Muller G (2002) Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol 20(4):370–375

    Article  PubMed  Google Scholar 

  16. Bhalla US, Ram PT, Iyengar R (2002) MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297(5583):1018–1023

    Article  PubMed  CAS  Google Scholar 

  17. Chen WW, Schoeberl B, Jasper PJ et al (2009) Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol 5:239

    PubMed  Google Scholar 

  18. Markevich NI, Moehren G, Demin OV, Kiyatkin A, Hoek JB, Kholodenko BN (2004) Signal processing at the Ras circuit: what shapes Ras activation patterns? Syst Biol (Stevenage) 1(1):104–113

    Article  CAS  Google Scholar 

  19. Das J, Ho M, Zikherman J et al (2009) Digital signaling and hysteresis characterize Ras activation in lymphoid cells. Cell 136(2):337–351

    Article  PubMed  CAS  Google Scholar 

  20. Warne PH, Viciana PR, Downward J (1993) Direct interaction of Ras and the amino-terminal region of Raf-1 in vitro. Nature 364(6435):352–355

    Article  PubMed  CAS  Google Scholar 

  21. Zhang XF, Settleman J, Kyriakis JM et al (1993) Normal and oncogenic p21ras proteins bind to the amino-terminal regulatory domain of c-Raf-1. Nature 364(6435):308–313

    Article  PubMed  CAS  Google Scholar 

  22. Rajakulendran T, Sahmi M, Lefrancois M, Sicheri F, Therrien M (2009) A dimerization-dependent mechanism drives RAF catalytic activation. Nature 461(7263):542–545

    Article  PubMed  CAS  Google Scholar 

  23. Tian T, Harding A, Inder K, Plowman S, Parton RG, Hancock JF (2007) Plasma membrane nanoswitches generate high-fidelity Ras signal transduction. Nat Cell Biol 9(8):905–914

    Article  PubMed  CAS  Google Scholar 

  24. Konstantinopoulos PA, Karamouzis MV, Papavassiliou AG (2007) Post-translational modifications and regulation of the RAS superfamily of GTPases as anticancer targets. Nat Rev Drug Discov 6(7):541–555

    Article  PubMed  CAS  Google Scholar 

  25. Legewie S, Sers C, Herzel H (2009) Kinetic mechanisms for overexpression insensitivity and oncogene cooperation. FEBS Lett 583(1):93–96

    Article  PubMed  CAS  Google Scholar 

  26. Haigis KM, Kendall KR, Wang Y et al (2008) Differential effects of oncogenic K-Ras and N-Ras on proliferation, differentiation and tumor progression in the colon. Nat Genet 40(5):600–608

    Article  PubMed  CAS  Google Scholar 

  27. Basu TN, Gutmann DH, Fletcher JA, Glover TW, Collins FS, Downward J (1992) Aberrant regulation of Ras proteins in malignant tumour cells from type 1 neurofibromatosis patients. Nature 356(6371):713–715

    Article  PubMed  CAS  Google Scholar 

  28. Chiu VK, Bivona T, Hach A et al (2002) Ras signalling on the endoplasmic reticulum and the Golgi. Nat Cell Biol 4(5):343–350

    PubMed  CAS  Google Scholar 

  29. Hancock JF, Parton RG (2005) Ras plasma membrane signalling platforms. Biochem J 389(Pt 1):1–11

    PubMed  CAS  Google Scholar 

  30. Shin SY, Rath O, Choo SM et al (2009) Positive- and negative-feedback regulations coordinate the dynamic behavior of the Ras-Raf-MEK-ERK signal transduction pathway. J Cell Sci 122(Pt 3):425–435

    Article  PubMed  CAS  Google Scholar 

  31. Courtois-Cox S, Genther Williams SM, Reczek EE et al (2006) A negative feedback signaling network underlies oncogene-induced senescence. Cancer Cell 10(6):459–472

    Article  PubMed  CAS  Google Scholar 

  32. Kotting C, Kallenbach A, Suveyzdis Y, Wittinghofer A, Gerwert K (2008) The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy. Proc Natl Acad Sci USA 105(17):6260–6265

    Article  PubMed  Google Scholar 

  33. Bollag G, Adler F, el Masry N et al (1996) Biochemical characterization of a novel KRAS insertion mutation from a human leukemia. J Biol Chem 271(51):32491–32494

    Article  PubMed  CAS  Google Scholar 

  34. Boykevisch S, Zhao C, Sondermann H et al (2006) Regulation of Ras signaling dynamics by Sos-mediated positive feedback. Curr Biol 16(21):2173–2179

    Article  PubMed  CAS  Google Scholar 

  35. Wittinghofer A, Scheffzek K, Ahmadian MR (1997) The interaction of Ras with GTPase-activating proteins. FEBS Lett 410(1):63–67

    Article  PubMed  CAS  Google Scholar 

  36. Der CJ, Finkel T, Cooper GM (1986) Biological and biochemical properties of human rasH genes mutated at codon 61. Cell 44(1):167–176

    Article  PubMed  CAS  Google Scholar 

  37. Keller JW, Haigis KM, Franklin JL, Whitehead RH, Jacks T, Coffey RJ (2007) Oncogenic K-RAS subverts the antiapoptotic role of N-RAS and alters modulation of the N-RAS:gelsolin complex. Oncogene 26(21):3051–3059

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Medical Scientist Training Program, University of Virginia, Charlottesville, VA, USA

    Edward C. Stites

  2. Department of Microbiology, Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, USA

    Kodi S. Ravichandran

Authors
  1. Edward C. Stites
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  2. Kodi S. Ravichandran
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Corresponding author

Correspondence to Edward C. Stites .

Editor information

Editors and Affiliations

  1. Dept. Chemistry & Biochemistry, University of Colorado, Boulder, Boulder, 80309-0215, Colorado, USA

    Xuedong Liu

  2. Dept. Physics, University of Colorado, Boulder, Boulder, 80309, Colorado, USA

    Meredith D. Betterton

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Stites, E.C., Ravichandran, K.S. (2012). Mathematical Investigation of How Oncogenic Ras Mutants Promote Ras Signaling. In: Liu, X., Betterton, M. (eds) Computational Modeling of Signaling Networks. Methods in Molecular Biology, vol 880. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-833-7_5

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  • DOI: https://doi.org/10.1007/978-1-61779-833-7_5

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-832-0

  • Online ISBN: 978-1-61779-833-7

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