Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Raf1_inact Raf1_act Raf1_Activation cell GeneralKinetics
Raf1_act Raf1_inact Raf1_Deactivation cell GeneralKinetics
Raf1_act Raf1_inact Raf1_Deactivation_Akt cell GeneralKinetics

Raf1_Activation Universal ID's

Raf1_Activation Text Annotations

Raf1_Deactivation Universal ID's

Raf1_Deactivation Text Annotations

Raf1_Deactivation_Akt Universal ID's

Raf1_Deactivation_Akt Text Annotations

Expressions for Raf1_Activation

reaction rate

J

(Kcat_act * Ras_act * Raf1_inact / (km_act + Raf1_inact)) [mmol.ml-1.min-1]

Expressions for Raf1_Deactivation

reaction rate

J

(Kcat_inact_PPt * Raf1_PPtase * Raf1_act / (km_inact_PPt + Raf1_act)) [mmol.ml-1.min-1]

Expressions for Raf1_Deactivation_Akt

reaction rate

J

(Kcat_inact_Akt * Akt_act * Raf1_act / (km_inact_Akt + Raf1_act)) [mmol.ml-1.min-1]

Structures

Name
Type
Electrical
cell Compartment (+)   (-)

cell Universal ID's

cell Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Ras_act cell Ras(status~active!-,).
Raf1_act cell Raf(status~active!-,).
Raf1_inact cell Raf(status~inactive!-,).
Akt_act cell Akt(status~active!-,).
Raf1_PPtase cell Raf(status~inactive!-,).Phosphotase().

Ras_act Universal ID's

Ras_act Text Annotations

Raf1_act Universal ID's

Raf1_act Text Annotations

Raf1_inact Universal ID's

Raf1_inact Text Annotations

Akt_act Universal ID's

Akt_act Text Annotations

Raf1_PPtase Universal ID's

Raf1_PPtase Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
Ras Ras(status~active~inactive,)
Raf Raf(status~active~inactive,)
Akt Akt(status~active~inactive,)
Phosphotase Phosphotase()

Ras Universal ID's

Ras Text Annotations

Raf Universal ID's

Raf Text Annotations

Akt Universal ID's

Akt Text Annotations

Phosphotase Universal ID's

Phosphotase Text Annotations

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
Raf_total cell Molecules Raf(status!-,). Multimolecular

Raf_total Universal ID's

Raf_total Text Annotations

Applications

Name
Properties Math Type
Deterministic Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Deterministic Text Annotations

Deterministic Universal ID's

Annotations will come here

RFID | pubmed

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
Ras_act 0.0 0.0 [m2/min]
Raf1_act 0.0 0.0 [m2/min]
Raf1_inact 120000.0 0.0 [m2/min]
Akt_act 0.0 0.0 [m2/min]
Raf1_PPtase 120000.0 0.0 [m2/min]

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
Raf1_Activation included
Raf1_Deactivation included
Raf1_Deactivation_Akt included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options

Global Parameters

Name
Expression
km_act 62464.6[mmol.ml-1]
Kcat_act 0.884096[min-1]
Kcat_inact_PPt 0.126329[min-1]
km_inact_PPt 1061.71[mmol.ml-1]
Kcat_inact_Akt 15.1212[min-1]
km_inact_Akt 119355.0[mmol.ml-1]

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Downloads

Format
File
VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML