KScience! Comparing GEF-induced GTP binding between the Hlavacek and Faeder models, using Stites 2007 paper rates Eitan Pearl, Stephanie Salarbux, Jennifer.

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Presentation transcript:

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)

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

The Hlavacek Model: 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

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

Hlavacek Model 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)

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

Allosteric Binding in the Hlavacek Model: Changing Rate of Basic SOS1

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.

Hlavacek original model with Stites paper rates (gdat)

Hlavacek allosteric graph with converted rates (gdat)

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

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) kf kr kcat Other semi-tested mutations: Eliminated GAP (GAP-insensitive mutation) Removing the effector binding of Ras-GTP

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

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

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

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

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