Mathematical Investigation of How Oncogenic Ras Mutants Promote Ras Signaling

  • Edward C. StitesEmail author
  • Kodi S. Ravichandran
Part of the Methods in Molecular Biology book series (MIMB, volume 880)


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.

Key words

Ras Cancer Oncogene ODE model Simulation Module Network 


  1. 1.
    Malumbres M, Barbacid M (2003) RAS oncogenes: the first 30 years. Nat Rev Cancer 3(6):459–465PubMedCrossRefGoogle Scholar
  2. 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):432–437PubMedGoogle Scholar
  3. 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):5318–5325PubMedGoogle Scholar
  4. 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):4535–4541PubMedCrossRefGoogle Scholar
  5. 5.
    Stites EC, Trampont PC, Ma Z, Ravichandran KS (2007) Network analysis of oncogenic Ras activation in cancer. Science 318(5849):463–467PubMedCrossRefGoogle Scholar
  6. 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):20437–20442PubMedGoogle Scholar
  7. 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):939–945PubMedCrossRefGoogle Scholar
  8. 8.
    Macara IG, Lounsbury KM, Richards SA, McKiernan C, Bar-Sagi D (1996) The Ras superfamily of GTPases. FASEB J 10(5):625–630PubMedGoogle Scholar
  9. 9.
    Bos JL, Rehmann H, Wittinghofer A (2007) GEFs and GAPs: critical elements in the control of small G proteins. Cell 129(5):865–877PubMedCrossRefGoogle Scholar
  10. 10.
    Donovan S, Shannon KM, Bollag G (2002) GTPase activating proteins: critical regulators of intracellular signaling. Biochim Biophys Acta 1602(1):23–45PubMedGoogle Scholar
  11. 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):2391–2397PubMedGoogle Scholar
  12. 12.
    Sebolt-Leopold JS, Herrera R (2004) Targeting the mitogen-activated protein kinase cascade to treat cancer. Nat Rev Cancer 4(12):937–947PubMedCrossRefGoogle Scholar
  13. 13.
    Vivanco I, Sawyers CL (2002) The phosphatidylinositol 3-Kinase AKT pathway in human cancer. Nat Rev Cancer 2(7):489–501PubMedCrossRefGoogle Scholar
  14. 14.
    Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70PubMedCrossRefGoogle Scholar
  15. 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):370–375PubMedCrossRefGoogle Scholar
  16. 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):1018–1023PubMedCrossRefGoogle Scholar
  17. 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 5:239PubMedGoogle Scholar
  18. 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):104–113CrossRefGoogle Scholar
  19. 19.
    Das J, Ho M, Zikherman J et al (2009) Digital signaling and hysteresis characterize Ras activation in lymphoid cells. Cell 136(2):337–351PubMedCrossRefGoogle Scholar
  20. 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):352–355PubMedCrossRefGoogle Scholar
  21. 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):308–313PubMedCrossRefGoogle Scholar
  22. 22.
    Rajakulendran T, Sahmi M, Lefrancois M, Sicheri F, Therrien M (2009) A dimerization-dependent mechanism drives RAF catalytic activation. Nature 461(7263):542–545PubMedCrossRefGoogle Scholar
  23. 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):905–914PubMedCrossRefGoogle Scholar
  24. 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):541–555PubMedCrossRefGoogle Scholar
  25. 25.
    Legewie S, Sers C, Herzel H (2009) Kinetic mechanisms for overexpression insensitivity and oncogene cooperation. FEBS Lett 583(1):93–96PubMedCrossRefGoogle Scholar
  26. 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):600–608PubMedCrossRefGoogle Scholar
  27. 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):713–715PubMedCrossRefGoogle Scholar
  28. 28.
    Chiu VK, Bivona T, Hach A et al (2002) Ras signalling on the endoplasmic reticulum and the Golgi. Nat Cell Biol 4(5):343–350PubMedGoogle Scholar
  29. 29.
    Hancock JF, Parton RG (2005) Ras plasma membrane signalling platforms. Biochem J 389(Pt 1):1–11PubMedGoogle Scholar
  30. 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):425–435PubMedCrossRefGoogle Scholar
  31. 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):459–472PubMedCrossRefGoogle Scholar
  32. 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):6260–6265PubMedCrossRefGoogle Scholar
  33. 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):32491–32494PubMedCrossRefGoogle Scholar
  34. 34.
    Boykevisch S, Zhao C, Sondermann H et al (2006) Regulation of Ras signaling dynamics by Sos-mediated positive feedback. Curr Biol 16(21):2173–2179PubMedCrossRefGoogle Scholar
  35. 35.
    Wittinghofer A, Scheffzek K, Ahmadian MR (1997) The interaction of Ras with GTPase-activating proteins. FEBS Lett 410(1):63–67PubMedCrossRefGoogle Scholar
  36. 36.
    Der CJ, Finkel T, Cooper GM (1986) Biological and biochemical properties of human rasH genes mutated at codon 61. Cell 44(1):167–176PubMedCrossRefGoogle Scholar
  37. 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):3051–3059PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Medical Scientist Training ProgramUniversity of VirginiaCharlottesvilleUSA
  2. 2.Department of Microbiology, Beirne B. Carter Center for Immunology ResearchUniversity of VirginiaCharlottesvilleUSA

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