Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Rab7_GDP Recruitment of Rab7_GDP endosome GeneralLumpedKinetics
Rab7_GDP Rab7_GTP activation of Rab7 by GEF7 endosome GeneralLumpedKinetics
Rab7_GDP Rab7_GTP activation of Rab7 by GEF5 endosome GeneralLumpedKinetics
Rab7_GDP Extraction of Rab7_GDP endosome GeneralLumpedKinetics
Rab7_GTP Rab7_GDP Hydrolysis of Rab7_GTP endosome GeneralLumpedKinetics

Structures

Name
Type
Electrical
endosome Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
Rab5_GTP endosome RAB5(BS!1,).GTP(BS!1,).
Rab7_GDP endosome Rab7(bs!1,).GDP(BS!1,).
Rab7_GTP endosome Rab7(bs!1,).GTP(BS!1,).

Molecules

Name
BioNetGen Definition
DEPICTION
RAB5 RAB5(BS,)
Rab7 Rab7(bs,)
GTP GTP(BS,)
GDP GDP(BS,)

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_RAB5_tot endosome Molecules RAB5(BS!?,). Multimolecular
O0_Rab7_tot endosome Molecules Rab7(bs!?,). Multimolecular
O0_GTP_tot endosome Molecules GTP(BS!?,). Multimolecular
O0_GDP_tot endosome Molecules GDP(BS!?,). Multimolecular

Applications

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

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
Rab5_GTP 0.001 0.0 [m2/s]
Rab7_GDP 1.0 0.0 [m2/s]
Rab7_GTP 0.001 0.0 [m2/s]

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
Recruitment of Rab7_GDP included
activation of Rab7 by GEF7 included
activation of Rab7 by GEF5 included
Extraction of Rab7_GDP included
Hydrolysis of Rab7_GTP included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
Simulation0 1000.0

KeepEvery 1

KeepAtMost 1000

Global Parameters

Name
Expression

Downloads

Format
File
VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML