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kScience !

kScience !. Comparing GEF-induced GTP binding between the Hlavacek and Faeder models, using Stites 2007 paper rates. Eitan Pearl, Stephanie Salarbux , Jennifer Nam CMACS Workshop 2014. The Stites Paper Minimal Model (no intermediate apo-Ras steps).

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kScience !

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  1. kScience! Comparing GEF-induced GTP binding between the Hlavacek and Faeder models, using Stites 2007 paper rates Eitan Pearl, Stephanie Salarbux, Jennifer Nam CMACS Workshop 2014

  2. The Stites Paper Minimal Model(no intermediate apo-Ras steps)

  3. Inputting the Stites differential equation for the GEF-nt-exchange rate

  4. The HlavacekModel: Allosteric Binding Reactions • We added the rates for positive feedback loop – allosteric SOS1 binding (from Cell 2009) • Ras • Unbound, slow rate • Ras-GDP • Bound, intermediate rate, 5x faster • Ras-GTP • Bound, Max allosteric rate, 75x faster • Then compared the Hlavacek (Mass-Action) and Faeder(Minimal) Models

  5. Hlavacek, Faeder Models with Stites’ Rates: Conversions Required! Stites paper rates into Hlavacek model: Stites paper rates into Faeder model: Added units to be comparable to the Hlavacek model • Increased SOS1 concentrations • Parameter scan and gdat simulations

  6. HlavacekModel • Increased SOS1 binding rates in the model to Stites paper rates/concentrations • Effect: turned off Ras-GDP  Ras-GTP conversion • Possible Mutation: Turned off GAP (GTP hydrolysis)

  7. Allosteric Binding in the Hlavacek Model:Changing Rate of Fast SOS1

  8. Allosteric Binding in the HlavacekModel:Changing Rate of Basic SOS1

  9. What happens when you increase Sos? • Simulation • Gdat shows crossover of GTP and GDP • Parameter Scan • Interpretation: GDP began higher than GTP, but due to allosteric binding, GTP overtakes GDP.

  10. Hlavacek original model with Stites paper rates (gdat)

  11. Hlavacek allosteric graph with converted rates (gdat)

  12. Hlavacek model with converted rates, looking at increased Sos concentration (scan)

  13. Minimal Model: units conversions & mutation effects • Replaced minimal model concentration values with Stites paper conversions to molecules • Mutations • Removing GAP-mediated GTP hydrolysis produces a simulation gdat • Looked mainly at the G12V GAP insensitivity mutation (Stites 2007) • kfkrkcat • Other semi-tested mutations: • Eliminated GAP (GAP-insensitive mutation) • Removing the effector binding of Ras-GTP

  14. Initial: Minimal Model with GAP insensitivity mutation rates (gdat)

  15. Further(1): Minimal Model with GAP insensitivity mutation rates (gdat)

  16. Further(2): Minimal Model with GAP insensitivity mutation rates (gdat)

  17. Acknowledgements Thank you to • Dr. Nancy Griffeth & Naralys • Dr. Jim Faeder • NSF-CMACS • Our fellow workshop members for collaboration!

  18. The End! Any Questions? There he goes again… Yea sure whatever… I’m about to run the model guys!!!

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