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

Structures

Name
Type
Electrical
default Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
Active_GEF default RhoGEF(Active~yes!-,).
RhoGDP default G_protein(State~GDP!-,GDI!-,Effector!-,).
RhoGTP default G_protein(State~GTP!-,GDI!-,Effector!-,).
GDI default GDI(Rho!-,).
GAP default RhoGAP().
Effector default Effector(Rho!-,Active~no!-,).
Effector_RhoGTP default G_protein(State~GTP!-,GDI!-,Effector!1,).Effector(Rho!1,Active~yes!-,).

Molecules

Name
BioNetGen Definition
DEPICTION
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,)

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_RhoGEF_tot default Molecules RhoGEF(Active!?,). Multimolecular
O0_G_protein_tot default Molecules G_protein(State!?,GDI!?,Effector!?,). Multimolecular
O0_GDI_tot default Molecules GDI(Rho!?,). Multimolecular
O0_RhoGAP_tot default Molecules RhoGAP(). Multimolecular
O0_Effector_tot default Molecules Effector(Rho!?,Active!?,). Multimolecular

Applications

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

Specifications (Species) - GDI_integrated go to Simulations

Species
Initial Condition
Diffusion Constant
Active_GEF 0.31 0.0 [m2/min]
RhoGDP 1.3 0.0 [m2/min]
RhoGTP 0.0 0.0 [m2/min]
GDI 0.7 0.0 [m2/min]
GAP 0.1 0.0 [m2/min]
Effector 1.0 0.0 [m2/min]
Effector_RhoGTP 0.0 0.0 [m2/min]

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

KeepEvery 1

KeepAtMost 1000

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]

Downloads

Format
File
VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML