Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
Rab7_GDP Recruitment of Rab7_GDP endosome GeneralLumpedKinetics
Rab7_GDPRab7_GTP activation of Rab7 by GEF7 endosome GeneralLumpedKinetics
Rab7_GDPRab7_GTP activation of Rab7 by GEF5 endosome GeneralLumpedKinetics
Rab7_GDP Extraction of Rab7_GDP endosome GeneralLumpedKinetics
Rab7_GTPRab7_GDP Hydrolysis of Rab7_GTP endosome GeneralLumpedKinetics

Recruitment of Rab7_GDP Universal ID's

Recruitment of Rab7_GDP Text Annotations

activation of Rab7 by GEF7 Universal ID's

activation of Rab7 by GEF7 Text Annotations

activation of Rab7 by GEF5 Universal ID's

activation of Rab7 by GEF5 Text Annotations

Extraction of Rab7_GDP Universal ID's

Extraction of Rab7_GDP Text Annotations

Hydrolysis of Rab7_GTP Universal ID's

Hydrolysis of Rab7_GTP Text Annotations

Expressions for Recruitment of Rab7_GDP

lumped reaction rate

LumpedJ

(endosome * K1) [mole.s-1]

local

K1

0.483 [mol.s-1.l-1]

Expressions for activation of Rab7 by GEF7

lumped reaction rate

LumpedJ

(endosome * ((Rab7_GDP * ke * pow(Rab7_GTP,h)) / (kg + pow(Rab7_GTP,h)))) [mole.s-1]

local

h

3.0 [1]

local

ke

0.21 [s-1]

local

kg

0.1 [tbd]

Expressions for activation of Rab7 by GEF5

lumped reaction rate

LumpedJ

(endosome * ((ke * Rab7_GDP) / (1.0 + exp(((kg - Rab5_GTP) * kf))))) [mole.s-1]

local

ke

0.021 [s-1]

local

kf

3.0 [M-1]

local

kg

1.0 [M]

Expressions for Extraction of Rab7_GDP

lumped reaction rate

LumpedJ

(endosome * (kminus1 * Rab7_GDP)) [mole.s-1]

local

kminus1

0.483 [s-1]

Expressions for Hydrolysis of Rab7_GTP

lumped reaction rate

LumpedJ

(endosome * (kh * Rab7_GTP)) [mole.s-1]

local

kh

0.15 [s-1]

Structures

Name
Type
Electrical
endosome Compartment (+)   (-)

endosome Universal ID's

endosome Text Annotations

Species

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

Rab5_GTP Universal ID's

Rab5_GTP Text Annotations

Rab7_GDP Universal ID's

Rab7_GDP Text Annotations

Rab7_GTP Universal ID's

Rab7_GTP Text Annotations

Molecules

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

RAB5 Universal ID's

RAB5 Text Annotations

Rab7 Universal ID's

Rab7 Text Annotations

GTP Universal ID's

GTP Text Annotations

GDP Universal ID's

GDP Text Annotations

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

O0_RAB5_tot Universal ID's

O0_RAB5_tot Text Annotations

O0_Rab7_tot Universal ID's

O0_Rab7_tot Text Annotations

O0_GTP_tot Universal ID's

O0_GTP_tot Text Annotations

O0_GDP_tot Universal ID's

O0_GDP_tot Text Annotations

Applications

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

Deterministic Universal ID's

Deterministic Text Annotations

Specifications (Species) - Deterministic go to Simulations

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

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

Deterministic Universal ID's

Deterministic Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Compartmental1388779149

(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 endosome

Events

Name Variable Rate Expression

Global Parameters

Name
Expression

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