Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
RhoGTP+EffectorEffector_RhoGTP Effector_activation default GeneralKinetics
RhoGTPRhoGDP RhoGTP_to_RhoGDP default GeneralKinetics
RhoGDPRhoGTP RhoGDP_to_RhoGTP default GeneralKinetics

Effector_activation Universal ID's

Effector_activation Text Annotations

RhoGTP_to_RhoGDP Universal ID's

RhoGTP_to_RhoGDP Text Annotations

RhoGDP_to_RhoGTP Universal ID's

RhoGDP_to_RhoGTP Text Annotations

Expressions for Effector_activation

reaction rate

J

((k8 * RhoGTP * Effector) - (k9 * Effector_RhoGTP)) [umol.l-1.min-1]

global

k8

28.2 [l.umol-1.min-1]

global

k9

0.18 [min-1]

Expressions for RhoGTP_to_RhoGDP

reaction rate

J

(kcatGAP * RhoGTP * GAP / ((KmGAPRho * (1.0 + (on5 * GDI / KmGAPGDI))) + (RhoGTP * (1.0 + (on5 * GDI / KmGAPGDI))))) [umol.l-1.min-1]

global

kcatGAP

95.9 [min-1]

global

KmGAPGDI

0.1 [umol.l-1]

global

KmGAPRho

4.48 [umol.l-1]

local

on5

1.0 [1]

Expressions for RhoGDP_to_RhoGTP

reaction rate

J

(kcatGEF * RhoGDP * Active_GEF / ((KmGEFRho * (1.0 + (on4 * GDI / KmGEFGDI))) + (RhoGDP * (1.0 + (on4 * GDI / KmGEFGDI))))) [umol.l-1.min-1]

global

kcatGEF

5.64 [min-1]

global

KmGEFRho

24.5 [umol.l-1]

global

KmGEFGDI

1.0 [umol.l-1]

local

on4

1.0 [1]

Structures

Name
Type
Electrical
default Compartment (+)   (-)

default Universal ID's

default Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
Active_GEF default RhoGEF(Active~yes!-,). default
RhoGDP default G_protein(State~GDP!-,GDI!-,Effector!-,). default
RhoGTP default G_protein(State~GTP!-,GDI!-,Effector!-,). default
GDI default GDI(Rho!-,). default
GAP default RhoGAP(). default
Effector default Effector(Rho!-,Active~no!-,). default
Effector_RhoGTP default G_protein(State~GTP!-,GDI!-,Effector!1,).Effector(Rho!1,Active~yes!-,). default

Active_GEF Universal ID's

Active_GEF Text Annotations

RhoGDP Universal ID's

RhoGDP Text Annotations

RhoGTP Universal ID's

RhoGTP Text Annotations

GDI Universal ID's

GDI Text Annotations

GAP Universal ID's

GAP Text Annotations

Effector Universal ID's

Effector Text Annotations

Effector_RhoGTP Universal ID's

Effector_RhoGTP Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
RhoGEF RhoGEF(Active~no~yes,)
G_protein G_protein(State~GTP~GDP,GDI,Effector,)
GDI GDI(Rho,)
RhoGAP RhoGAP()
Effector Effector(Rho,Active~yes~no,)

RhoGEF Universal ID's

RhoGEF Text Annotations

G_protein Universal ID's

G_protein Text Annotations

GDI Universal ID's

GDI Text Annotations

RhoGAP Universal ID's

RhoGAP Text Annotations

Effector Universal ID's

Effector Text Annotations

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION
O0_RhoGEF_tot default Molecules RhoGEF(Active!?,). Multimolecular
O0_G_protein_tot default Molecules G_protein(State!?,GDI!?,Effector!?,). Multimolecular
O0_GDI_tot default Molecules GDI(Rho!?,). Multimolecular
O0_RhoGAP_tot default Molecules RhoGAP(). Multimolecular
O0_Effector_tot default Molecules Effector(Rho!?,Active!?,). Multimolecular

O0_RhoGEF_tot Universal ID's

O0_RhoGEF_tot Text Annotations

O0_G_protein_tot Universal ID's

O0_G_protein_tot Text Annotations

O0_GDI_tot Universal ID's

O0_GDI_tot Text Annotations

O0_RhoGAP_tot Universal ID's

O0_RhoGAP_tot Text Annotations

O0_Effector_tot Universal ID's

O0_Effector_tot Text Annotations

Applications

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

GDI_integrated Universal ID's

GDI_integrated Text Annotations

Specifications (Species) - GDI_integrated go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
Active_GEF 0.31 [umol] 0.0 [m2/min] default
RhoGDP 1.3 [umol] 0.0 [m2/min] default
RhoGTP 0.0 [umol] 0.0 [m2/min] default
GDI 0.7 [umol] 0.0 [m2/min] default
GAP 0.1 [umol] 0.0 [m2/min] default
Effector 1.0 [umol] 0.0 [m2/min] default
Effector_RhoGTP 0.0 [umol] 0.0 [m2/min] default

Specifications (Reaction) - GDI_integrated go to Simulations

Name
Enabled?
Effector_activation included
RhoGTP_to_RhoGDP included
RhoGDP_to_RhoGTP included

Simulations - GDI_integrated go to Specifications

Name
End Time
Output Options
Simulation0 600.0

KeepEvery 1

KeepAtMost 1000

GDI_integrated Universal ID's

GDI_integrated Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry Compartmental1055847981

(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 default

Events

Name Variable Rate Expression

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

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

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