Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
RhoGDP GDI GDI_RhoGDP RhoGDP_GDI_binding default GeneralKinetics
RhoGTP GDI GDI_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]

Expressions for RhoGTP_GDI_binding

reaction rate

J

((k6 * RhoGTP * GDI) - (k7 * GDI_RhoGTP)) [umol.l-1.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!-,).
RhoGTP default G_protein(State~GTP!-,GDI!-,Effector!-,).
GDI default GDI(Rho!-,).
GDI_RhoGDP default G_protein(State~GDP!-,GDI!1,Effector!-,).GDI(Rho!1,).
GDI_RhoGTP default G_protein(State~GTP!-,GDI!1,Effector!-,).GDI(Rho!1,).

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
Application Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Application Text Annotations

Application Universal ID's

Annotations will come here

RFID | pubmed

Specifications (Species) - Application go to Simulations

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

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

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

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

Text Annotations

Universal ID's

Text Annotations

Downloads

Format
File
VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML