Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
Raf1_inactRaf1_act Raf1_Activation cell GeneralKinetics
Raf1_actRaf1_inact Raf1_Deactivation cell GeneralKinetics
Raf1_actRaf1_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]

global

km_act

62464.6 [mmol.ml-1]

global

Kcat_act

0.884096 [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]

global

Kcat_inact_PPt

0.126329 [min-1]

global

km_inact_PPt

1061.71 [mmol.ml-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]

global

Kcat_inact_Akt

15.1212 [min-1]

global

km_inact_Akt

119355.0 [mmol.ml-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!-,). cell
Raf1_act cell Raf(status~active!-,). cell
Raf1_inact cell Raf(status~inactive!-,). cell
Akt_act cell Akt(status~active!-,). cell
Raf1_PPtase cell Raf(status~inactive!-,).Phosphotase(). cell

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
Annotation
Deterministic Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental cloned from 'Deterministic' owned by user savi06 cloned from 'Deterministic' owned by user mblinov cloned from 'Deterministic' owned by user cab15130

Deterministic Universal ID's

Deterministic Text Annotations

Specifications (Species) - Deterministic go to Simulations

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

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

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Compartmental1716227696

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [m])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment cell

Events

Name Variable Rate Expression

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

Model Format
Model Downloads
Virtual Cell Markup Language VCML File
PDF Report Report
COMBINE Archive OMEX File
SEDML SEDML File
File Format
Application Downloads
BNGL Deterministic.bngl
SBML Deterministic.sbml
Matlab Deterministic.m
NFSim XML Deterministic.xml