Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
cdc42_inactcdc42_act r0 cytosol GeneralKinetics
Rac_inactRac_act r1 cytosol GeneralKinetics
Rho_inactRho_act r2 cytosol GeneralKinetics
P1P2 r3 cytosol GeneralKinetics
P2P3 r4 cytosol GeneralKinetics
PIP1 r5 cytosol GeneralKinetics

r0 Universal ID's

r0 Text Annotations

r1 Universal ID's

r1 Text Annotations

r2 Universal ID's

r2 Text Annotations

r3 Universal ID's

r3 Text Annotations

r4 Universal ID's

r4 Text Annotations

r5 Universal ID's

r5 Text Annotations

Expressions for r0

reaction rate

J

((Ic / (1.0 + ((Rho_act / a1) ^ n)) * (cdc42_inact / cdc42_tot) * ((1.0 - f) + (f * P3 / P3b))) - (d_cdc42 * cdc42_act)) [uM.s-1]

global

n

3.0 [1]

global

Ic

(((2.6 + (0.05 * x)) * (t <= 10.0)) + (2.95 * (t > 10.0))) [uM.s-1]

global

P3b

0.05 [uM]

global

f

0.4 [1]

global

cdc42_tot

2.4 [uM]

local

a1

1.25 [uM]

local

d_cdc42

1.0 [s-1]

Expressions for r1

reaction rate

J

(((Ir + (alpha * cdc42_act)) * (Rac_inact / Rac_tot) * ((1.0 - f) + (f * P3 / P3b))) - (d_rac * Rac_act)) [uM.s-1]

global

n

3.0 [1]

global

P3b

0.05 [uM]

global

f

0.4 [1]

global

Rac_tot

7.5 [uM]

local

alpha

4.5 [s-1]

local

d_rac

1.0 [s-1]

local

Ir

0.5 [uM.s-1]

Expressions for r2

reaction rate

J

(((Ip + (Beta * Rac_act)) / (1.0 + ((cdc42_act / a2) ^ n)) * (Rho_inact / Rho_tot)) - (d_rho * Rho_act)) [uM.s-1]

global

n

3.0 [1]

global

Rho_tot

3.1 [uM]

local

d_rho

1.0 [s-1]

local

a2

1.0 [uM]

local

Ip

3.3 [uM.s-1]

local

Beta

0.3 [s-1]

Expressions for r3

reaction rate

J

(( - k21 * P2) + (k_PI5K / 2.0 * (1.0 + (Rac_act / Rb)) * P1)) [uM.s-1]

global

Rb

3.0 [microM]

local

k_PI5K

0.084 [microM.s-1.uM-1]

local

k21

0.014 [s-1]

Expressions for r4

reaction rate

J

((k_PI3K / 2.0 * (1.0 + (Rac_act / Rb)) * P2) - (k_PTEN / 2.0 * (1.0 + (Rho_act / Rho_b)) * P3)) [uM.s-1]

global

Rb

3.0 [microM]

local

k_PI3K

7.2E-4 [microM.s-1.uM-1]

local

k_PTEN

0.432 [microM.s-1.uM-1]

local

Rho_b

1.25 [microM]

Expressions for r5

reaction rate

J

(Ip1 - (delta_P1 * P1)) [uM.s-1]

local

Ip1

10.5 [uM.s-1]

local

delta_P1

0.21 [s-1]

Structures

Name
Type
Electrical
plasma membrane Membrane (+)   (-)
extracellular space Compartment (+)   (-)
cytosol Compartment (+)   (-)

plasma membrane Universal ID's

plasma membrane Text Annotations

extracellular space Universal ID's

extracellular space Text Annotations

cytosol Universal ID's

cytosol Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
cdc42_inact cytosol cytosol
cdc42_act cytosol cytosol
Rac_inact cytosol cytosol
Rac_act cytosol cytosol
Rho_inact cytosol cytosol
Rho_act cytosol cytosol
P1 cytosol cytosol
P2 cytosol cytosol
P3 cytosol cytosol
PI5K cytosol cytosol
PI3K cytosol cytosol
PTEN cytosol cytosol
PI cytosol cytosol

cdc42_inact Universal ID's

cdc42_inact Text Annotations

cdc42_act Universal ID's

cdc42_act Text Annotations

Rac_inact Universal ID's

Rac_inact Text Annotations

Rac_act Universal ID's

Rac_act Text Annotations

Rho_inact Universal ID's

Rho_inact Text Annotations

Rho_act Universal ID's

Rho_act Text Annotations

P1 Universal ID's

P1 Text Annotations

P2 Universal ID's

P2 Text Annotations

P3 Universal ID's

P3 Text Annotations

PI5K Universal ID's

PI5K Text Annotations

PI3K Universal ID's

PI3K Text Annotations

PTEN Universal ID's

PTEN Text Annotations

PI Universal ID's

PI Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
real cell Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (2D) cloned from 'real cell' owned by user aureliecarlier (copied from real cell) (copied from Application0)

real cell Universal ID's

real cell Text Annotations

Specifications (Species) - real cell go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
cdc42_inact 1.4 [uM] 50.0 [um2/s] cytosol
cdc42_act 1.0 [uM] 0.1 [um2/s] cytosol
Rac_inact 4.5 [uM] 50.0 [um2/s] cytosol
Rac_act 3.0 [uM] 0.1 [um2/s] cytosol
Rho_inact 1.85 [uM] 50.0 [um2/s] cytosol
Rho_act 1.25 [uM] 0.1 [um2/s] cytosol
P1 55.0 [uM] 5.0 [um2/s] cytosol
P2 30.0 [uM] 5.0 [um2/s] cytosol
P3 0.05 [uM] 5.0 [um2/s] cytosol
PI5K 10.0 [uM] 10.0 [um2/s] cytosol
PI3K 10.0 [uM] 10.0 [um2/s] cytosol
PTEN 10.0 [uM] 10.0 [um2/s] cytosol
PI 10.0 [uM] 10.0 [um2/s] cytosol

Specifications (Reaction) - real cell go to Simulations

Name
Enabled?
r0 included
r1 included
r2 included
r3 included
r4 included
r5 included

Simulations - real cell go to Specifications

Name
End Time
Output Options
simulation1 500.0

OutputTimeStep 5.0
simulation2 100.0

OutputTimeStep 5.0
simulation3 1000.0

OutputTimeStep 5.0

real cell Universal ID's

real cell Text Annotations

real cell Universal ID's

real cell Text Annotations

real cell Universal ID's

real cell Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry geom_20171120_183216

(Origin: 0.0, 0.0, 0.0; Extent: 50.0, 20.0, 9.0E-7 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Image Cell 640.0005147077745 [um2] cytosol
Volume Image EC 34.62053169313122 [um2] extracellular space
Surface Cell_EC_membrane Cell | EC 19.36700981687842 [um] plasma membrane

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
n 3.0[1]
Ic (((2.6 + (0.05 * x)) * (t <= 10.0)) + (2.95 * (t > 10.0)))[uM.s-1]
P3b 0.05[uM]
f 0.4[1]
cdc42_tot 2.4[uM]
Rac_tot 7.5[uM]
Rho_tot 3.1[uM]
Rb 3.0[microM]

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 real cell.bngl
SBML real cell.sbml
Matlab real cell.m
NFSim XML real cell.xml