Reaction Diagram
Physiology
Universal ID's | Text Annotations |
---|---|
|
|
Reaction |
Name
Structure
|
Kinetics | Depiction |
---|---|---|---|
Rab7_GDP |
Recruitment of Rab7_GDP
endosome
|
GeneralLumpedKinetics | Rab7_GDP |
|
|
lumped reaction rate (LumpedJ): (endosome * K1)[mole.s-1]
user defined (K1): 0.483[mol.s-1.l-1] |
|
Rab7_GDPRab7_GTP |
activation of Rab7 by GEF7
endosome
|
GeneralLumpedKinetics | Rab7_GDPRab7_GTP |
|
|
lumped reaction rate (LumpedJ): (endosome * ((Rab7_GDP * ke * pow(Rab7_GTP,h)) / (kg + pow(Rab7_GTP,h))))[mole.s-1]
user defined (h): 3.0[1] user defined (ke): 0.21[s-1] user defined (kg): 0.1[tbd] |
|
Rab7_GDPRab7_GTP |
activation of Rab7 by GEF5
endosome
|
GeneralLumpedKinetics | Rab7_GDPRab7_GTP |
|
|
lumped reaction rate (LumpedJ): (endosome * ((ke * Rab7_GDP) / (1.0 + exp(((kg - Rab5_GTP) * kf)))))[mole.s-1]
user defined (ke): 0.021[s-1] user defined (kf): 3.0[M-1] user defined (kg): 1.0[M] |
|
Rab7_GDP |
Extraction of Rab7_GDP
endosome
|
GeneralLumpedKinetics | Rab7_GDP |
|
|
lumped reaction rate (LumpedJ): (endosome * (kminus1 * Rab7_GDP))[mole.s-1]
user defined (kminus1): 0.483[s-1] |
|
Rab7_GTPRab7_GDP |
Hydrolysis of Rab7_GTP
endosome
|
GeneralLumpedKinetics | Rab7_GTPRab7_GDP |
|
|
lumped reaction rate (LumpedJ): (endosome * (kh * Rab7_GTP))[mole.s-1]
user defined (kh): 0.15[s-1] |
Name |
Type
Electrical (Membrane Polarity)
|
---|---|
endosome |
Compartment
(+) (-)
|
|
|
Name | Structure | BioNetGen Definition |
---|---|---|
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,). |
|
|
Name | Text Annotations | BioNetGen Definition |
---|---|---|
RAB5 | Text Annotations | RAB5(BS,) |
|
|
|
Rab7 | Text Annotations | Rab7(bs,) |
|
|
|
GTP | Text Annotations | GTP(BS,) |
|
|
|
GDP | Text Annotations | GDP(BS,) |
|
|
Name |
Type
Count
|
BioNetGen Definition |
---|---|---|
O0_RAB5_tot |
Molecules Multimolecular |
RAB5(BS!?,). |
|
|
|
O0_Rab7_tot |
Molecules Multimolecular |
Rab7(bs!?,). |
|
|
|
O0_GTP_tot |
Molecules Multimolecular |
GTP(BS!?,). |
|
|
|
O0_GDP_tot |
Molecules Multimolecular |
GDP(BS!?,). |
|
|
Applications
Name | Math Type | Annotation |
---|---|---|
Deterministic | Deterministic (ODE) Compartmental |
Application - Deterministic
Species | Initial Condition | Diffusion Constant | ||||||
---|---|---|---|---|---|---|---|---|
Rab5_GTP | 0.001 [mole] | 0.0
[m2/s] Rab7_GDP |
1.0
[mole]
|
0.0
[m2/s] | Rab7_GTP |
0.001
[mole]
|
0.0
[m2/s]
|
|
Name | Reaction Mapping |
---|---|
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 |
Name | End Time | Output Options |
---|---|---|
Simulation0 | 1000.0 [s] |
KeepEvery 1 KeepAtMost 1000 |
Dimension | Type | Subdomain | Adjacent Subvolumes | Size | Mapped Compartment |
---|---|---|---|---|---|
Compartmental | Compartment | endosome |
Global Parameters
Name | Expression |
---|