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

RhoGDP_GDI_binding Universal ID's

RhoGDP_GDI_binding Text Annotations

RhoGTP_GDI_binding Universal ID's

RhoGTP_GDI_binding Text Annotations

Expressions for RhoGDP_GDI_binding

reaction rate

J

((k4 * RhoGDP * GDI) - (k5 * GDI_RhoGDP)) [umol.l-1.min-1]

global

k5

0.05 [min-1]

global

k4

0.5 [l.umol-1.min-1]

Expressions for RhoGTP_GDI_binding

reaction rate

J

((k6 * RhoGTP * GDI) - (k7 * GDI_RhoGTP)) [umol.l-1.min-1]

global

k6

0.5 [l.umol-1.min-1]

global

k7

0.05 [min-1]

Structures

Name
Type
Electrical
default Compartment (+)   (-)

default Universal ID's

default Text Annotations

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

RhoGDP Universal ID's

RhoGDP Text Annotations

RhoGTP Universal ID's

RhoGTP Text Annotations

GDI Universal ID's

GDI Text Annotations

GDI_RhoGDP Universal ID's

GDI_RhoGDP Text Annotations

GDI_RhoGTP Universal ID's

GDI_RhoGTP Text Annotations

Molecules

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

G_protein Universal ID's

G_protein Text Annotations

GDI Universal ID's

GDI Text Annotations

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

O0_G_protein_tot Universal ID's

O0_G_protein_tot Text Annotations

O0_GDI_tot Universal ID's

O0_GDI_tot Text Annotations

Applications

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

Application Universal ID's

Application Text Annotations

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

Application Universal ID's

Application Text Annotations

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]

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

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

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