Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
PDGFR_cyto_mem+PDGF_extraPDGF_PDGFR PDGF_binds_PDGFR cyto_mem MassAction
PDGF_PDGFR_Srccyto_memSrc_active_cyto Src activation cyto_mem HMMIrreversible
Src_active_cytoSrc_cyto Src dephosphorylation in cyto cyto HMMIrreversible
csk_cyto_inactiveCsk_cyto_active r0 cyto MassAction
PDGF_PDGFR+Src_cytoPDGF_PDGFR_Srccyto_mem Src association with receptor cyto_mem MassAction

PDGF_binds_PDGFR Universal ID's

PDGF_binds_PDGFR Text Annotations

Src activation Universal ID's

Src activation Text Annotations

Src dephosphorylation in cyto Universal ID's

Src dephosphorylation in cyto Text Annotations

r0 Universal ID's

r0 Text Annotations

Src association with receptor Universal ID's

Src association with receptor Text Annotations

Expressions for PDGF_binds_PDGFR

reaction rate

J

(((Kf * PDGFR_cyto_mem) * PDGF_extra) - (Kr * PDGF_PDGFR)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

0.0 [1]

forward rate constant

Kf

1.0 [s-1.uM-1]

reverse rate constant

Kr

0.01 [s-1]

Expressions for Src activation

reaction rate

J

((Vmax * PDGF_PDGFR_Srccyto_mem) / (Km + PDGF_PDGFR_Srccyto_mem)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

0.0 [1]

Km (1/2 max)

Km

0.1 [molecules.um-2]

max reaction rate

Vmax

(kcat * PTP) [molecules.um-2.s-1]

local

kcat

(0.01 * n) [molecules.um-2.uM-1.s-1]

global

n

900.0 [molecules.um-2.uM-1]

Expressions for Src dephosphorylation in cyto

reaction rate

J

((Vmax * Src_active_cyto) / (Km + Src_active_cyto)) [uM.s-1]

Km (1/2 max)

Km

1.5 [uM]

max reaction rate

Vmax

(0.3 * Csk_cyto_active) [uM.s-1]

Expressions for r0

reaction rate

J

((Kf * csk_cyto_inactive) - (Kr * Csk_cyto_active)) [uM.s-1]

global

n

900.0 [molecules.um-2.uM-1]

forward rate constant

Kf

0.001 [s-1]

reverse rate constant

Kr

0.0 [s-1]

Expressions for Src association with receptor

reaction rate

J

(((Kf * PDGF_PDGFR) * Src_cyto) - (Kr * PDGF_PDGFR_Srccyto_mem)) [molecules.um-2.s-1]

inward current density

I

0.0 [pA.um-2]

net charge valence

netValence

0.0 [1]

forward rate constant

Kf

1.0 [s-1.uM-1]

reverse rate constant

Kr

0.1 [s-1]

Structures

Name
Type
Electrical
cyto_mem Membrane cyto(+)   extra(-)
extra Compartment (+)   (-)
cyto Compartment (+)   (-)

cyto_mem Universal ID's

cyto_mem Text Annotations

extra Universal ID's

extra Text Annotations

cyto Universal ID's

cyto Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
PDGFR_cyto_mem cyto_mem cyto_mem
PDGF_extra extra extra
PTP cyto cyto
Csk_cyto_active cyto cyto
PDGF_PDGFR_Srccyto_mem cyto_mem cyto_mem
Src_active_cyto cyto cyto
csk_cyto_inactive cyto cyto
Src_cyto cyto cyto
PDGF_PDGFR cyto_mem cyto_mem

PDGFR_cyto_mem Universal ID's

PDGFR_cyto_mem Text Annotations

PDGF_extra Universal ID's

PDGF_extra Text Annotations

PTP Universal ID's

PTP Text Annotations

Csk_cyto_active Universal ID's

Csk_cyto_active Text Annotations

PDGF_PDGFR_Srccyto_mem Universal ID's

PDGF_PDGFR_Srccyto_mem Text Annotations

Src_active_cyto Universal ID's

Src_active_cyto Text Annotations

csk_cyto_inactive Universal ID's

csk_cyto_inactive Text Annotations

Src_cyto Universal ID's

Src_cyto Text Annotations

PDGF_PDGFR Universal ID's

PDGF_PDGFR Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Annotation
compartmental Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental cloned from 'compartmental' owned by user susana compartmental model used for Fig S1
ellipse 0999 Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (2D) (copied from compartmental) cloned from 'compartmental' owned by user susana compartmental model used for Fig S1
circle Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Spatial (2D) (copied from ellipse 0999) (copied from compartmental) cloned from 'compartmental' owned by user susana compartmental model used for Fig S1

compartmental Universal ID's

compartmental Text Annotations

ellipse 0999 Universal ID's

ellipse 0999 Text Annotations

circle Universal ID's

circle Text Annotations

Specifications (Species) - compartmental go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
PDGF_extra 1.0 [uM] 0.0 [um2/s] extra
PTP 0.1 [uM] 0.0 [um2/s] cyto
Csk_cyto_active 0.0 [uM] 0.0 [um2/s] cyto
Src_active_cyto 0.0 [uM] 0.0 [um2/s] cyto
csk_cyto_inactive 0.1 [uM] 0.0 [um2/s] cyto
Src_cyto 1.0 [uM] 0.0 [um2/s] cyto
PDGFR_cyto_mem 250.0 [uM] 0.0 [um2/s] cyto_mem
PDGF_PDGFR_Srccyto_mem 0.0 [uM] 0.0 [um2/s] cyto_mem
PDGF_PDGFR 0.0 [uM] 0.0 [um2/s] cyto_mem

Specifications (Reaction) - compartmental go to Simulations

Name
Enabled?
PDGF_binds_PDGFR included
Src activation included
Src dephosphorylation in cyto included
r0 included
Src association with receptor included

Simulations - compartmental go to Specifications

Name
End Time
Output Options
compartmental 2700.0

OutputTimeStep 10.0

compartmental Universal ID's

compartmental Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry non-spatial969899354

(Origin: 0.0, 0.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Compartmental Compartment cyto_mem

Events

Name Variable Rate Expression

Specifications (Species) - ellipse 0999 go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
PDGF_extra 1.0 [uM] 10.0 [um2/s] extra
PTP 0.1 [uM] 10.0 [um2/s] cyto
Csk_cyto_active 0.0 [uM] 10.0 [um2/s] cyto
Src_active_cyto 0.0 [uM] 1.0 [um2/s] cyto
csk_cyto_inactive 0.1 [uM] 10.0 [um2/s] cyto
Src_cyto 1.0 [uM] 10.0 [um2/s] cyto
PDGFR_cyto_mem 250.0 [uM] 0.041 [um2/s] cyto_mem
PDGF_PDGFR_Srccyto_mem 0.0 [uM] 0.041 [um2/s] cyto_mem
PDGF_PDGFR 0.0 [uM] 0.0 [um2/s] cyto_mem

Specifications (Reaction) - ellipse 0999 go to Simulations

Name
Enabled?
PDGF_binds_PDGFR included
Src activation included
Src dephosphorylation in cyto included
r0 included
Src association with receptor included

Simulations - ellipse 0999 go to Specifications

Name
End Time
Output Options
Simulation0 1800.0

OutputTimeStep 10.0

ellipse 0999 Universal ID's

ellipse 0999 Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry ellipse sep 08 0999

(Origin: -23.5, -1.25, 0.0; Extent: 47.0, 2.5, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical Cell 74.97675 [um2] cyto
Volume Analytical ECM 42.52324999999999 [um2] extra
Surface Cell_ECM_membrane Cell | ECM 93.46482136095845 [um] cyto_mem

Events

Name Variable Rate Expression

Specifications (Species) - circle go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
PDGF_extra 1.0 [uM] 10.0 [um2/s] extra
PTP 0.1 [uM] 10.0 [um2/s] cyto
Csk_cyto_active 0.0 [uM] 10.0 [um2/s] cyto
Src_active_cyto 0.0 [uM] 1.0 [um2/s] cyto
csk_cyto_inactive 0.1 [uM] 10.0 [um2/s] cyto
Src_cyto 1.0 [uM] 10.0 [um2/s] cyto
PDGFR_cyto_mem 250.0 [uM] 0.041 [um2/s] cyto_mem
PDGF_PDGFR_Srccyto_mem 0.0 [uM] 0.041 [um2/s] cyto_mem
PDGF_PDGFR 0.0 [uM] 0.0 [um2/s] cyto_mem

Specifications (Reaction) - circle go to Simulations

Name
Enabled?
PDGF_binds_PDGFR included
Src activation included
Src dephosphorylation in cyto included
r0 included
Src association with receptor included

Simulations - circle go to Specifications

Name
End Time
Output Options
Simulation1 1800.0

OutputTimeStep 10.0
Copy of Simulation1 300.0

OutputTimeStep 10.0

circle Universal ID's

circle Text Annotations

circle Universal ID's

circle Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment

Geometry circle sep 08

(Origin: -5.0, -5.0, 0.0; Extent: 10.0, 10.0, 10.0 [um])

Dimension Type Subdomain Adjacent Subvolumes Size Mapped Compartment
Volume Analytical Cell 78.39 [um2] cyto
Volume Analytical ECM 5.4125000000000005 [um2] extra
Surface Cell_ECM_membrane Cell | ECM 7.704697811481667 [um] cyto_mem

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
n 900.0[molecules.um-2.uM-1]

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 compartmental.bngl , ellipse 0999.bngl , circle.bngl
SBML compartmental.sbml , ellipse 0999.sbml , circle.sbml
Matlab compartmental.m , ellipse 0999.m , circle.m
NFSim XML compartmental.xml , ellipse 0999.xml , circle.xml