Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
RhoGTP Effector Effector_RhoGTP Effector_activation default GeneralKinetics
RhoGTP RhoGDP RhoGTP_to_RhoGDP default GeneralKinetics
RhoGDP RhoGTP RhoGDP_to_RhoGTP default GeneralKinetics

Reaction Name: Effector_activation

Universal ID's

Text Annotations

Reaction Name: RhoGTP_to_RhoGDP

Universal ID's

Text Annotations

Reaction Name: RhoGDP_to_RhoGTP

Universal ID's

Text Annotations

Reaction Name: Effector_activation

Expressions

reaction rate

((k8 * RhoGTP * Effector) - (k9 * Effector_RhoGTP)) [umol.l-1.min-1]

Reaction Name: RhoGTP_to_RhoGDP

Expressions

reaction rate

(kcatGAP * RhoGTP * GAP / ((KmGAPRho * (1.0 + (on5 * GDI / KmGAPGDI))) + (RhoGTP * (1.0 + (on5 * GDI / KmGAPGDI))))) [umol.l-1.min-1]

user defined

1.0 [1]

Reaction Name: RhoGDP_to_RhoGTP

Expressions

reaction rate

(kcatGEF * RhoGDP * Active_GEF / ((KmGEFRho * (1.0 + (on4 * GDI / KmGEFGDI))) + (RhoGDP * (1.0 + (on4 * GDI / KmGEFGDI))))) [umol.l-1.min-1]

user defined

1.0 [1]

Structures

Name
Type
Electrical
default Compartment (+)   (-)

Structure Name: default

Universal ID's

Text Annotations

Species

Name
Structure
Active_GEF default
RhoGDP default
RhoGTP default
GDI default
GAP default
Effector default
Effector_RhoGTP default

Species Name: Active_GEF

Universal ID's

Text Annotations

Species Name: RhoGDP

Universal ID's

Text Annotations

Species Name: RhoGTP

Universal ID's

Text Annotations

Species Name: GDI

Universal ID's

Text Annotations

Species Name: GAP

Universal ID's

Text Annotations

Species Name: Effector

Universal ID's

Text Annotations

Species Name: Effector_RhoGTP

Universal ID's

Text Annotations

Molecules

Name
Description
RhoGEF RhoGEF ( Active ~no ~yes )
G_protein G_protein ( State ~GTP ~GDP GDI Effector )
GDI GDI ( Rho )
RhoGAP RhoGAP ()
Effector Effector ( Rho Active ~yes ~no )

Molucule Name: RhoGEF

Universal ID's

Text Annotations

Molucule Name: G_protein

Universal ID's

Text Annotations

Molucule Name: GDI

Universal ID's

Text Annotations

Molucule Name: RhoGAP

Universal ID's

Text Annotations

Molucule Name: Effector

Universal ID's

Text Annotations

Observables

Name
Domain
Molecular Type
Sequence Type
O0_RhoGEF_tot Molecules RhoGEF Multimolecular
O0_G_protein_tot Molecules G_protein Multimolecular
O0_GDI_tot Molecules GDI Multimolecular
O0_RhoGAP_tot Molecules RhoGAP Multimolecular
O0_Effector_tot Molecules Effector Multimolecular

Observables Name: O0_RhoGEF_tot

Universal ID's

Text Annotations

Observables Name: O0_G_protein_tot

Universal ID's

Text Annotations

Observables Name: O0_GDI_tot

Universal ID's

Text Annotations

Observables Name: O0_RhoGAP_tot

Universal ID's

Text Annotations

Observables Name: O0_Effector_tot

Universal ID's

Text Annotations

Applications

Name
Properties Math Type
GDI_integrated Specs - Species
Specs - Reaction
Simulations

Application Name: GDI_integrated

Text Annotations

Annotations will come here

Universal ID's

RFID | pubmed

Specifications (Species) - GDI_integrated go to Simulations

Species
Initial Condition
Diffusion Constant
Active_GEF 0.31 0.0
RhoGDP 1.3 0.0
RhoGTP 0.0 0.0
GDI 0.7 0.0
GAP 0.1 0.0
Effector 1.0 0.0
Effector_RhoGTP 0.0 0.0

Specifications (Reaction) - GDI_integrated go to Simulations

Name
Enabled?
Effector_activation included
RhoGTP_to_RhoGDP included
RhoGDP_to_RhoGTP included

Simulations - GDI_integrated go to Specifications

Name
End Time
Output Options
Simulation0 600.0 every

Simulation Name: Simulation0

Universal ID's

Text Annotations

Global Parameters

Name
Expression
k3 0.5[min-1]
k2 0.1[min-1]
kcatGEF 5.64[min-1]
KmGEFRho 24.5[umol.l-1]
KmGEFGDI 1.0[umol.l-1]
k1 1.0[l.umol-1.min-1]
kcatGAP 95.9[min-1]
KmGAPGDI 0.1[umol.l-1]
KmGAPRho 4.48[umol.l-1]
k5 0.05[min-1]
k4 0.5[l.umol-1.min-1]
k6 0.5[l.umol-1.min-1]
k7 0.05[min-1]
k8 28.2[l.umol-1.min-1]
k9 0.18[min-1]

Global Parameter Name: k3

Universal ID's

Text Annotations

Global Parameter Name: k2

Universal ID's

Text Annotations

Global Parameter Name: kcatGEF

Universal ID's

Text Annotations

Global Parameter Name: KmGEFRho

Universal ID's

Text Annotations

Global Parameter Name: KmGEFGDI

Universal ID's

Text Annotations

Global Parameter Name: k1

Universal ID's

Text Annotations

Global Parameter Name: kcatGAP

Universal ID's

Text Annotations

Global Parameter Name: KmGAPGDI

Universal ID's

Text Annotations

Global Parameter Name: KmGAPRho

Universal ID's

Text Annotations

Global Parameter Name: k5

Universal ID's

Text Annotations

Global Parameter Name: k4

Universal ID's

Text Annotations

Global Parameter Name: k6

Universal ID's

Text Annotations

Global Parameter Name: k7

Universal ID's

Text Annotations

Global Parameter Name: k8

Universal ID's

Text Annotations

Global Parameter Name: k9

Universal ID's

Text Annotations

Downloads

Format
File
BNGL
Metlab
SBML
Formatted XML
SEDML
Deterministic XML