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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/concentrationsEffect: 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

0.00E+00 5.00E+02 1.00E+03 1.50E+03 2.00E+03 2.50E+03 3.00E+03 3.50E+030.00E+00

5.00E+04

1.00E+05

1.50E+05

2.00E+05

2.50E+05

RasGTPRasGDP

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

0.00E+00 5.00E+02 1.00E+03 1.50E+03 2.00E+03 2.50E+03 3.00E+03 3.50E+030.00E+00

5.00E+04

1.00E+05

1.50E+05

2.00E+05

2.50E+05

RasGTPRasGDP

What happens when you increase Sos?Simulation

Gdat shows crossover of GTP and GDPParameter Scan

Interpretation: GDP began higher than GTP, but due to allosteric binding, GTP overtakes GDP.

Hlavacek original model with Stites paper rates (gdat)

0.00E+00 5.00E+02 1.00E+03 1.50E+03 2.00E+03 2.50E+03 3.00E+03 3.50E+030.00E+00

5.00E+04

1.00E+05

1.50E+05

2.00E+05

2.50E+05

RasGTPRasGDP

Hlavacek allosteric graph with converted rates (gdat)

0.00E+00 5.00E+02 1.00E+03 1.50E+03 2.00E+03 2.50E+03 3.00E+03 3.50E+030.00E+00

5.00E+04

1.00E+05

1.50E+05

2.00E+05

2.50E+05

RasGTPRasGDP

Hlavacek model with converted rates, looking at increased Sos concentration

(scan)

0.00E+00 5.00E+09 1.00E+10 1.50E+10 2.00E+10 2.50E+100.00E+00

5.00E+04

1.00E+05

1.50E+05

2.00E+05

2.50E+05

3.00E+05

RasGTPRasGDP

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 gdatLooked 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)

0.00E+00 5.00E+02 1.00E+03 1.50E+03 2.00E+03 2.50E+03 3.00E+03 3.50E+030.00E+00

1.00E+02

2.00E+02

3.00E+02

4.00E+02

5.00E+02

6.00E+02

7.00E+02

8.00E+02

9.00E+02

RasActRasGDP

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

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

AcknowledgementsThank you to

Dr. Nancy Griffeth & NaralysDr. 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…