Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
RhoGDP+GDIGDI_RhoGDP RhoGDP_GDI_binding default GeneralKinetics
RhoGTP+GDIGDI_RhoGTP RhoGTP_GDI_binding default GeneralKinetics

Structures

Name
Type
Electrical
default Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
RhoGDP default G_protein(State~GDP!-,GDI!-,Effector!-,). default
RhoGTP default G_protein(State~GTP!-,GDI!-,Effector!-,). default
GDI default GDI(Rho!-,). default
GDI_RhoGDP default G_protein(State~GDP!-,GDI!1,Effector!-,).GDI(Rho!1,). default
GDI_RhoGTP default G_protein(State~GTP!-,GDI!1,Effector!-,).GDI(Rho!1,). default

Molecules

Name
BioNetGen Definition
DEPICTION
G_protein G_protein(State~GTP~GDP,GDI,Effector,)
GDI GDI(Rho,)

Observables

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

Applications

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

Specifications (Species) - Application go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
RhoGDP 1.0 [umol] 0.0 [m2/min] default
RhoGTP 1.0 [umol] 0.0 [m2/min] default
GDI 0.7 [umol] 0.0 [m2/min] default
GDI_RhoGDP 0.0 [umol] 0.0 [m2/min] default
GDI_RhoGTP 0.0 [umol] 0.0 [m2/min] default

Specifications (Reaction) - Application go to Simulations

Name
Enabled?
RhoGDP_GDI_binding included
RhoGTP_GDI_binding included

Simulations - Application go to Specifications

Name
End Time
Output Options
Simulation0 600.0

KeepEvery 1

KeepAtMost 1000

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Compartmental1800508731

(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 default

Events

Name Variable Rate Expression

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

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 Application.bngl
SBML Application.sbml
Matlab Application.m
NFSim XML Application.xml