Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Rab5_GDP Recruitment of Rab5_GDP endosome GeneralLumpedKinetics
Rab5_GDP Rab5_GTP Activation of Rab5 endosome GeneralLumpedKinetics
Rab5_GDP extraction of Rab5_GDP endosome GeneralLumpedKinetics
Rab5_GTP Rab5_GDP Hydrolysis of Rab5_GTP endosome GeneralLumpedKinetics
Rab5_GTP Rab5_GDP Hydrolysis of Rab5_GTP_d endosome GeneralLumpedKinetics

Structures

Name
Type
Electrical
endosome Compartment (+)   (-)

Species

Name
Structure
BioNetGen Definition
Depiction
Rab5_GDP endosome Rab5(BS!1,).GDP(BS!1,).
Rab5_GTP endosome Rab5(BS!1,).GTP(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_GTP_tot endosome Molecules GTP(BS!?,). Multimolecular
O0_GDP_tot endosome Molecules GDP(BS!?,). Multimolecular

Applications

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
Rab5_GDP 1.0 0.0
Rab5_GTP 0.001 0.0
Rab7_GTP 0.001 0.0

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
Recruitment of Rab5_GDP included
Activation of Rab5 included
extraction of Rab5_GDP included
Hydrolysis of Rab5_GTP included
Hydrolysis of Rab5_GTP_d included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
Simulation0 1000.0 every

Global Parameters

Name
Expression

Downloads

Format
File
VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML