Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
Depiction
AC+Gi_GTPAC_inact AC_inactivation PM GeneralLumpedKinetics
ACAC_i AC_internalization PM GeneralLumpedKinetics
AC_inactAC+Gi_GDP AC_unbinding PM GeneralLumpedKinetics
AC_i+Gs_GTP_iAC_act AC_activation intmem GeneralLumpedKinetics
Cdk5+p35_actCdk5_p35_act Cdk5_activation PM GeneralLumpedKinetics
DAG DAG_decactivation PM GeneralLumpedKinetics
PKC_actPKC DAG_deactivation_while_bound PM GeneralLumpedKinetics
GIV_GDIGIV Degradation_GDI Cyto GeneralLumpedKinetics
GIV_GEFGIV Degradation_GEF Cyto GeneralLumpedKinetics
EGF_EGFREGF_EGFR_2 Dimerize PM GeneralLumpedKinetics
EGF_EGFR_2EGF_EGFR_2_act Dimerized_receptor_activation PM GeneralLumpedKinetics
EGFi EGF_deg Endosome GeneralLumpedKinetics
EGFRi EGFR_deg intmem GeneralLumpedKinetics
EGFRiEGFR EGFR_to_PM intmem GeneralLumpedKinetics
GEF_EGFRGIV_GDI+EGF_EGFR_2_act EGFR_GEF_to_GDI PM GeneralLumpedKinetics
GIV_GDI+Gs_GDP_iGs_GDI_i GDI_function intmem GeneralLumpedKinetics
GIV_GEF+EGF_EGFR_2_actGEF_EGFR GEF_EGFR_binding PM GeneralLumpedKinetics
GEF_EGFR+Gi_GDPGEF_Gi_EGFR GEF_Gi_Binding PM GeneralLumpedKinetics
GIVGIV_GEF GEF_activation PM GeneralLumpedKinetics
GIV_GEFGIV_GDI GEF_to_GDI PM GeneralLumpedKinetics
GEF_Gi_EGFRGEF_EGFR+Gi_GTP Gi_activation PM GeneralLumpedKinetics
Gi_GTPGi_GDP Gi_hydrolysis PM GeneralLumpedKinetics
EGF_EGFR_i_act Gs_GDI_accel_deg intmem GeneralLumpedKinetics
Gs_protein_ibg_i+Gs_GTP_i Gs_activation intmem GeneralLumpedKinetics
Gs_GTP_iGs_GDP_i Gs_hydrolysis intmem GeneralLumpedKinetics
Gs_proteinGs_protein_i Gs_internalization PM GeneralLumpedKinetics
IP3inositol IP3_degradation Cyto GeneralLumpedKinetics
AC_actAC_i+Gs_GDP_i InactivAC intmem GeneralLumpedKinetics
PDEPDEp PDE_phos Cyto GeneralLumpedKinetics
PIP2DAG+IP3 PIP2_to_DAG PM GeneralLumpedKinetics
PKAPKA_inact PKA_inactivation Cyto GeneralLumpedKinetics
R2uu+PKAR2C2 PKA_reformation Cyto GeneralLumpedKinetics
PKC+DAGPKC_act PKC_activation PM GeneralLumpedKinetics
PLCgPLCg_active PLC_GEF_enhanced PM GeneralLumpedKinetics
PLCgPLCg_active PLC_activation_basal PM GeneralLumpedKinetics
PLCg_activePLCg PLC_deactivation Cyto GeneralLumpedKinetics
R2uR2uu+cAMP R2uUnbind Cyto GeneralLumpedKinetics
R2R2u+cAMP R2Unbind Cyto GeneralLumpedKinetics
R2C2+cAMPR2+PKA cAMP_Activation Cyto GeneralLumpedKinetics
ATPcAMP cAMP_basal PM GeneralLumpedKinetics
ATPcAMP cAMP_basal_production_internal intmem GeneralLumpedKinetics
cAMPAMP cAMP_to_AMP Cyto GeneralLumpedKinetics
cAMPAMP cAMP_to_AMP_PDEp Cyto GeneralLumpedKinetics
PDEpPDE dephos_of_PDEp Cyto GeneralLumpedKinetics
EGF_EGFR_2_actEGF_EGFR_i_act internal_transport PM GeneralLumpedKinetics
bg_i+Gs_GDP_iGs_protein_i internal_trimerize intmem GeneralLumpedKinetics
p35p35_act p35_activation PM GeneralLumpedKinetics
p35_actp35 p35_inactivation PM GeneralLumpedKinetics
ATPcAMP production_cAMP_internal intmem GeneralLumpedKinetics
EGF+EGFREGF_EGFR receptor_ligand_binding PM GeneralLumpedKinetics
EGFi+EGFRiEGF_EGFRi v10 intmem GeneralLumpedKinetics
EGF_EGFRiEGF_EGFR_2i v11 intmem GeneralLumpedKinetics
EGF_EGFR_2iEGF_EGFR_i_act v12 intmem GeneralLumpedKinetics
GIV+Gs_GDP_iGs_GDI_b basalGIVGDI Cyto GeneralLumpedKinetics
GIV89pGIV _89pDEG Cyto GeneralLumpedKinetics
Gs_GDI_i Gs_GDI_accel_deg_copy intmem GeneralLumpedKinetics
Gs_GDP_i Gs_GDI_accel_deg_copy2 intmem GeneralLumpedKinetics
Gs_GTP_i Gs_GDI_accel_deg_copy3 intmem GeneralLumpedKinetics
AC_act Gs_GDI_accel_deg_copy4 intmem GeneralLumpedKinetics
EGF_EGFRi Gs_GDI_accel_deg_copy5 intmem GeneralLumpedKinetics
Gs_GDI_b Gs_GDI_accel_deg_copy6 intmem GeneralLumpedKinetics
I Intfun intmem GeneralLumpedKinetics

AC_inactivation Universal ID's

AC_inactivation Text Annotations

AC_internalization Universal ID's

AC_internalization Text Annotations

AC_unbinding Universal ID's

AC_unbinding Text Annotations

AC_activation Universal ID's

AC_activation Text Annotations

Cdk5_activation Universal ID's

Cdk5_activation Text Annotations

DAG_decactivation Universal ID's

DAG_decactivation Text Annotations

DAG_deactivation_while_bound Universal ID's

DAG_deactivation_while_bound Text Annotations

Degradation_GDI Universal ID's

Degradation_GDI Text Annotations

Degradation_GEF Universal ID's

Degradation_GEF Text Annotations

Dimerize Universal ID's

Dimerize Text Annotations

Dimerized_receptor_activation Universal ID's

Dimerized_receptor_activation Text Annotations

EGF_deg Universal ID's

EGF_deg Text Annotations

EGFR_deg Universal ID's

EGFR_deg Text Annotations

EGFR_to_PM Universal ID's

EGFR_to_PM Text Annotations

EGFR_GEF_to_GDI Universal ID's

EGFR_GEF_to_GDI Text Annotations

GDI_function Universal ID's

GDI_function Text Annotations

GEF_EGFR_binding Universal ID's

GEF_EGFR_binding Text Annotations

GEF_Gi_Binding Universal ID's

GEF_Gi_Binding Text Annotations

GEF_activation Universal ID's

GEF_activation Text Annotations

GEF_to_GDI Universal ID's

GEF_to_GDI Text Annotations

Gi_activation Universal ID's

Gi_activation Text Annotations

Gi_hydrolysis Universal ID's

Gi_hydrolysis Text Annotations

Gs_GDI_accel_deg Universal ID's

Gs_GDI_accel_deg Text Annotations

Gs_activation Universal ID's

Gs_activation Text Annotations

Gs_hydrolysis Universal ID's

Gs_hydrolysis Text Annotations

Gs_internalization Universal ID's

Gs_internalization Text Annotations

IP3_degradation Universal ID's

IP3_degradation Text Annotations

InactivAC Universal ID's

InactivAC Text Annotations

PDE_phos Universal ID's

PDE_phos Text Annotations

PIP2_to_DAG Universal ID's

PIP2_to_DAG Text Annotations

PKA_inactivation Universal ID's

PKA_inactivation Text Annotations

PKA_reformation Universal ID's

PKA_reformation Text Annotations

PKC_activation Universal ID's

PKC_activation Text Annotations

PLC_GEF_enhanced Universal ID's

PLC_GEF_enhanced Text Annotations

PLC_activation_basal Universal ID's

PLC_activation_basal Text Annotations

PLC_deactivation Universal ID's

PLC_deactivation Text Annotations

R2uUnbind Universal ID's

R2uUnbind Text Annotations

R2Unbind Universal ID's

R2Unbind Text Annotations

cAMP_Activation Universal ID's

cAMP_Activation Text Annotations

cAMP_basal Universal ID's

cAMP_basal Text Annotations

cAMP_basal_production_internal Universal ID's

cAMP_basal_production_internal Text Annotations

cAMP_to_AMP Universal ID's

cAMP_to_AMP Text Annotations

cAMP_to_AMP_PDEp Universal ID's

cAMP_to_AMP_PDEp Text Annotations

dephos_of_PDEp Universal ID's

dephos_of_PDEp Text Annotations

internal_transport Universal ID's

internal_transport Text Annotations

internal_trimerize Universal ID's

internal_trimerize Text Annotations

p35_activation Universal ID's

p35_activation Text Annotations

p35_inactivation Universal ID's

p35_inactivation Text Annotations

production_cAMP_internal Universal ID's

production_cAMP_internal Text Annotations

receptor_ligand_binding Universal ID's

receptor_ligand_binding Text Annotations

v10 Universal ID's

v10 Text Annotations

v11 Universal ID's

v11 Text Annotations

v12 Universal ID's

v12 Text Annotations

basalGIVGDI Universal ID's

basalGIVGDI Text Annotations

_89pDEG Universal ID's

_89pDEG Text Annotations

Gs_GDI_accel_deg_copy Universal ID's

Gs_GDI_accel_deg_copy Text Annotations

Gs_GDI_accel_deg_copy2 Universal ID's

Gs_GDI_accel_deg_copy2 Text Annotations

Gs_GDI_accel_deg_copy3 Universal ID's

Gs_GDI_accel_deg_copy3 Text Annotations

Gs_GDI_accel_deg_copy4 Universal ID's

Gs_GDI_accel_deg_copy4 Text Annotations

Gs_GDI_accel_deg_copy5 Universal ID's

Gs_GDI_accel_deg_copy5 Text Annotations

Gs_GDI_accel_deg_copy6 Universal ID's

Gs_GDI_accel_deg_copy6 Text Annotations

Intfun Universal ID's

Intfun Text Annotations

Expressions for AC_inactivation

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * k1 * AC * Gi_GTP) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

3.14951E17 [um2.s-1.umol-1]

Expressions for AC_internalization

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((kfint * AC) - (krint * AC_i))) [umol.s-1]

global

kfint

4.578940789E-5 [tbd]

global

krint

6.66502822995389E-5 [tbd]

net charge valence

netValence

1.0 [1]

Expressions for AC_unbinding

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * k1 * AC_inact) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

0.1667 [s-1]

Expressions for AC_activation

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * k1 * AC_i * Gs_GTP_i) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

1.26462E15 [um2.s-1.umol-1]

Expressions for Cdk5_activation

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((k1 * p35_act * Cdk5) - (k2 * Cdk5_p35_act))) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

45.0 [litre.s-1.umol-1]

local

k2

10.0 [s-1]

Expressions for DAG_decactivation

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * k1 * DAG) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

6.7E-4 [s-1]

Expressions for DAG_deactivation_while_bound

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * k1 * PKC_act) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

0.028 [s-1]

Expressions for Degradation_GDI

lumped reaction rate

LumpedJ

(Cyto * k1 * GIV_GDI) [umol.s-1]

local

k1

0.00107286 [s-1]

Expressions for Degradation_GEF

lumped reaction rate

LumpedJ

(Cyto * k1 * GIV_GEF) [umol.s-1]

local

k1

0.0064638 [s-1]

Expressions for Dimerize

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((k1 * pow(EGF_EGFR,2.0)) - (k2 * EGF_EGFR_2))) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

3.14951E17 [tbd]

local

k2

0.1 [tbd]

Expressions for Dimerized_receptor_activation

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((k1 * EGF_EGFR_2) - (k2 * EGF_EGFR_2_act))) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

1.0 [s-1]

local

k2

0.01 [s-1]

Expressions for EGF_deg

lumped reaction rate

LumpedJ

(Endosome * ((kbase + (kc * (Gs_GDP_i + Gs_GDI_i + Gs_GDI_b))) * EGFi)) [umol.s-1]

global

kbase

1.07E-8 [tbd]

global

kc

1.32E11 [tbd]

Expressions for EGFR_deg

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((kbase + (kc * (Gs_GDP_i + Gs_GDI_i + Gs_GDI_b))) * EGFRi)) [umol.s-1]

global

kbase

1.07E-8 [tbd]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

Expressions for EGFR_to_PM

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((k1 * EGFRi) - (k2 * EGFR))) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

0.005 [s-1]

local

k2

5.0E-5 [s-1]

Expressions for EGFR_GEF_to_GDI

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((kcat * PKC_act * GEF_EGFR) / (Km + GEF_EGFR))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

Km

2.10987E-15 [umol.um-2]

local

kcat

2.53373 [s-1]

Expressions for GDI_function

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((GDI_function_k1 * Gs_GDP_i * GIV_GDI) - (krGDIGIV * Gs_GDI_i))) [umol.s-1]

global

krGDIGIV

3.0E-4 [tbd]

global

GDI_function_k1

2.91 [tbd]

net charge valence

netValence

1.0 [1]

Expressions for GEF_EGFR_binding

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((k1 * EGF_EGFR_2_act * GIV_GEF) - (k2 * GEF_EGFR))) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

0.00145 [litre.s-1.umol-1]

local

k2

1.09025E-7 [s-1]

Expressions for GEF_Gi_Binding

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((kfGi * GEF_EGFR * Gi_GDP) - (krGi * GEF_Gi_EGFR))) [umol.s-1]

global

kfGi

3.0102889041494098E18 [tbd]

global

krGi

((0.24 * ModelValue_4 * Compartment_2) / Compartment_1) [tbd]

net charge valence

netValence

1.0 [1]

Expressions for GEF_activation

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((kcat * Cdk5_p35_act * GIV) / (Km + GIV))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

Km

6.0 [umol.litre-1]

local

kcat

0.6 [s-1]

Expressions for GEF_to_GDI

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((kcat * PKC_act * GIV_GEF) / (Km + GIV_GEF))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

Km

6.0 [umol.litre-1]

local

kcat

0.999995 [s-1]

Expressions for Gi_activation

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * k1 * GEF_Gi_EGFR) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

14.4682 [s-1]

Expressions for Gi_hydrolysis

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * k1 * Gi_GTP) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

0.139 [s-1]

Expressions for Gs_GDI_accel_deg

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((kbase + (kc * (Gs_GDP_i + Gs_GDI_i + Gs_GDI_b))) * EGF_EGFR_i_act)) [umol.s-1]

global

kbase

1.07E-8 [tbd]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

Expressions for Gs_activation

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((kcat * EGF_EGFR_i_act * Gs_protein_i) / (Km + Gs_protein_i))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

Km

5.0E-15 [umol.um-2]

local

kcat

0.4 [s-1]

Expressions for Gs_hydrolysis

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * k1 * Gs_GTP_i) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

0.139 [s-1]

Expressions for Gs_internalization

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((kfint * Gs_protein) - (krint * Gs_protein_i))) [umol.s-1]

global

kfint

4.578940789E-5 [tbd]

global

krint

6.66502822995389E-5 [tbd]

net charge valence

netValence

1.0 [1]

Expressions for IP3_degradation

lumped reaction rate

LumpedJ

(Cyto * k1 * IP3) [umol.s-1]

local

k1

2.5 [s-1]

Expressions for InactivAC

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * k1 * AC_act) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

0.1667 [s-1]

Expressions for PDE_phos

lumped reaction rate

LumpedJ

(Cyto * ((kcat * PKA * PDE) / (Km + PDE))) [umol.s-1]

global

kc

1.32E11 [tbd]

local

Km

0.5 [umol.litre-1]

local

kcat

5.0 [s-1]

Expressions for PIP2_to_DAG

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((kcat * PLCg_active * PIP2) / (Km + PIP2))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

Km

8.3E-15 [umol.um-2]

local

kcat

2.3E-17 [litre.s-1.um-2]

Expressions for PKA_inactivation

lumped reaction rate

LumpedJ

(Cyto * ((k1 * PKA) - (k2 * PKA_inact))) [umol.s-1]

local

k1

1.0E-4 [s-1]

local

k2

1.0 [s-1]

Expressions for PKA_reformation

lumped reaction rate

LumpedJ

(Cyto * k1 * R2uu * pow(PKA,2.0)) [umol.s-1]

local

k1

10.0 [tbd]

Expressions for PKC_activation

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((k1 * DAG * PKC) - (k2 * PKC_act))) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

0.1 [litre.s-1.umol-1]

local

k2

1.0E-5 [s-1]

Expressions for PLC_GEF_enhanced

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((kcat * GEF_EGFR * PLCg) / (Km + PLCg))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

Km

1.0 [umol.litre-1]

local

kcat

0.103589 [s-1]

Expressions for PLC_activation_basal

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((kcat * EGF_EGFR_2_act * PLCg) / (Km + PLCg))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

Km

1.0 [umol.litre-1]

local

kcat

1.00002E-4 [s-1]

Expressions for PLC_deactivation

lumped reaction rate

LumpedJ

(Cyto * k1 * PLCg_active) [umol.s-1]

local

k1

1.00002E-5 [s-1]

Expressions for R2uUnbind

lumped reaction rate

LumpedJ

(Cyto * k1 * R2u) [umol.s-1]

local

k1

2.78E-4 [s-1]

Expressions for R2Unbind

lumped reaction rate

LumpedJ

(Cyto * k1 * R2) [umol.s-1]

local

k1

0.0167 [s-1]

Expressions for cAMP_Activation

lumped reaction rate

LumpedJ

(Cyto * ((V * R2C2 * pow((cAMP / Shalve),h)) / (1.0 + pow((cAMP / Shalve),h)))) [umol.s-1]

local

V

0.05 [s-1]

local

Shalve

0.54 [umol.litre-1]

local

h

1.75 [1]

Expressions for cAMP_basal

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((kcat * AC * ATP) / (Km + ATP))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

Km

1030.0 [umol.litre-1]

local

kcat

0.12 [s-1]

Expressions for cAMP_basal_production_internal

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((kcat * AC_i * ATP) / (Km + ATP))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

Km

1030.0 [umol.litre-1]

local

kcat

0.12 [s-1]

Expressions for cAMP_to_AMP

lumped reaction rate

LumpedJ

(Cyto * ((kcat * PDE * cAMP) / (Km + cAMP))) [umol.s-1]

global

kc

1.32E11 [tbd]

local

Km

1.51 [umol.litre-1]

local

kcat

2.0 [s-1]

Expressions for cAMP_to_AMP_PDEp

lumped reaction rate

LumpedJ

(Cyto * ((kcat * PDEp * cAMP) / (Km + cAMP))) [umol.s-1]

global

kc

1.32E11 [tbd]

local

Km

1.26 [umol.litre-1]

local

kcat

5.0 [s-1]

Expressions for dephos_of_PDEp

lumped reaction rate

LumpedJ

(Cyto * ((kcat * PP_PDE * PDEp) / (Km + PDEp))) [umol.s-1]

global

kc

1.32E11 [tbd]

local

Km

8.0 [umol.litre-1]

local

kcat

10.0 [s-1]

Expressions for internal_transport

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * intrec * EGF_EGFR_2_act) [umol.s-1]

global

intrec

0.002 [tbd]

net charge valence

netValence

1.0 [1]

Expressions for internal_trimerize

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * k1 * bg_i * Gs_GDP_i) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

8.91256E14 [um2.s-1.umol-1]

Expressions for p35_activation

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((kcat * EGF_EGFR_2_act * p35) / (Km + p35))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

Km

1.589E-15 [umol.um-2]

local

kcat

0.1 [s-1]

Expressions for p35_inactivation

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * k1 * p35_act) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

0.001 [s-1]

Expressions for production_cAMP_internal

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((kcat * AC_act * ATP) / (Km + ATP))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

Km

315.0 [umol.litre-1]

local

kcat

13.0 [s-1]

Expressions for receptor_ligand_binding

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(PM * ((k1 * EGFR * EGF) - (k2 * EGF_EGFR))) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

3.0 [litre.s-1.umol-1]

local

k2

0.014 [s-1]

Expressions for v10

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((k1 * EGFRi * EGFi) - (k2 * EGF_EGFRi))) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

0.14 [litre.s-1.umol-1]

local

k2

0.0195 [s-1]

Expressions for v11

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((k1 * pow(EGF_EGFRi,2.0)) - (k2 * EGF_EGFR_2i))) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

4.0E-5 [tbd]

local

k2

0.1 [tbd]

Expressions for v12

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((k1 * EGF_EGFR_2i) - (k2 * EGF_EGFR_i_act))) [umol.s-1]

net charge valence

netValence

1.0 [1]

local

k1

1.0 [s-1]

local

k2

0.01 [s-1]

Expressions for basalGIVGDI

lumped reaction rate

LumpedJ

(Cyto * ((bindingGDIGIV * GIV * Gs_GDP_i) - (krGDIGIV * Gs_GDI_b))) [umol.s-1]

global

bindingGDIGIV

(0.05 * GDI_function_k1) [tbd]

global

krGDIGIV

3.0E-4 [tbd]

Expressions for _89pDEG

lumped reaction rate

LumpedJ

(Cyto * k1 * GIV89p) [umol.s-1]

local

k1

0.01 [s-1]

Expressions for Gs_GDI_accel_deg_copy

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * (I * Gs_GDI_i)) [umol.s-1]

net charge valence

netValence

1.0 [1]

Expressions for Gs_GDI_accel_deg_copy2

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * (Gs_GDP_i * Gs_GDP_i)) [umol.s-1]

net charge valence

netValence

1.0 [1]

Expressions for Gs_GDI_accel_deg_copy3

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * (Gs_GDP_i * Gs_GTP_i)) [umol.s-1]

net charge valence

netValence

1.0 [1]

Expressions for Gs_GDI_accel_deg_copy4

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((kbase + (kc * (Gs_GDP_i + Gs_GDI_i + Gs_GDI_b))) * AC_act)) [umol.s-1]

global

kbase

1.07E-8 [tbd]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

Expressions for Gs_GDI_accel_deg_copy5

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * ((kbase + (kc * (Gs_GDP_i + Gs_GDI_i + Gs_GDI_b))) * EGF_EGFRi)) [umol.s-1]

global

kbase

1.07E-8 [tbd]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

Expressions for Gs_GDI_accel_deg_copy6

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * (I * Gs_GDI_b)) [umol.s-1]

net charge valence

netValence

1.0 [1]

Expressions for Intfun

lumped current

LumpedI

0.0 [pA]

lumped reaction rate

LumpedJ

(intmem * (kc * (Gs_GDP_i + Gs_GDI_i + Gs_GDI_b))) [umol.s-1]

global

kc

1.32E11 [tbd]

net charge valence

netValence

1.0 [1]

local

kc

4.2968E7 [s-1]

Structures

Name
Type
Electrical
intmem Membrane (+)   (-)
PM Membrane (+)   (-)
Endosome Compartment (+)   (-)
Cyto Compartment (+)   (-)
ECM Compartment (+)   (-)

intmem Universal ID's

intmem Text Annotations

PM Universal ID's

PM Text Annotations

Endosome Universal ID's

Endosome Text Annotations

Cyto Universal ID's

Cyto Text Annotations

ECM Universal ID's

ECM Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
EGF ECM ECM
EGFR PM PM
p35 PM PM
p35_act PM PM
Gi_GTP PM PM
Gi_GDP PM PM
EGF_EGFR PM PM
PLCg Cyto Cyto
IP3 Cyto Cyto
inositol Cyto Cyto
PKC Cyto Cyto
PKC_act PM PM
AC PM PM
AC_act intmem intmem
ATP Cyto Cyto
cAMP Cyto Cyto
PKA Cyto Cyto
PDE Cyto Cyto
R2C2 Cyto Cyto
AMP Cyto Cyto
PDEp Cyto Cyto
PIP2 PM PM
EGF_EGFR_2_act PM PM
EGF_EGFR_2 PM PM
PP_PDE Cyto Cyto
DAG PM PM
PLCg_active Cyto Cyto
GEF_EGFR PM PM
GEF_Gi_EGFR PM PM
GIV Cyto Cyto
GIV_GEF Cyto Cyto
GIV_GDI Cyto Cyto
Cdk5 Cyto Cyto
Gs_GTP_i intmem intmem
Gs_GDP_i intmem intmem
Gs_GDI_i intmem intmem
EGF_EGFR_i_act intmem intmem
AC_i intmem intmem
bg_i intmem intmem
AC_inact PM PM
Gs_protein PM PM
EGFi Endosome Endosome
EGFRi intmem intmem
R2 Cyto Cyto
R2u Cyto Cyto
R2uu Cyto Cyto
EGF_EGFRi intmem intmem
EGF_EGFR_2i intmem intmem
Cdk5_p35_act PM PM
Gs_protein_i intmem intmem
PKA_inact Cyto Cyto
Gs_GDI_b intmem intmem
GIV89p Cyto Cyto
I intmem intmem

EGF Universal ID's

EGF Text Annotations

EGFR Universal ID's

EGFR Text Annotations

p35 Universal ID's

p35 Text Annotations

p35_act Universal ID's

p35_act Text Annotations

Gi_GTP Universal ID's

Gi_GTP Text Annotations

Gi_GDP Universal ID's

Gi_GDP Text Annotations

EGF_EGFR Universal ID's

EGF_EGFR Text Annotations

PLCg Universal ID's

PLCg Text Annotations

IP3 Universal ID's

IP3 Text Annotations

inositol Universal ID's

inositol Text Annotations

PKC Universal ID's

PKC Text Annotations

PKC_act Universal ID's

PKC_act Text Annotations

AC Universal ID's

AC Text Annotations

AC_act Universal ID's

AC_act Text Annotations

ATP Universal ID's

ATP Text Annotations

cAMP Universal ID's

cAMP Text Annotations

PKA Universal ID's

PKA Text Annotations

PDE Universal ID's

PDE Text Annotations

R2C2 Universal ID's

R2C2 Text Annotations

AMP Universal ID's

AMP Text Annotations

PDEp Universal ID's

PDEp Text Annotations

PIP2 Universal ID's

PIP2 Text Annotations

EGF_EGFR_2_act Universal ID's

EGF_EGFR_2_act Text Annotations

EGF_EGFR_2 Universal ID's

EGF_EGFR_2 Text Annotations

PP_PDE Universal ID's

PP_PDE Text Annotations

DAG Universal ID's

DAG Text Annotations

PLCg_active Universal ID's

PLCg_active Text Annotations

GEF_EGFR Universal ID's

GEF_EGFR Text Annotations

GEF_Gi_EGFR Universal ID's

GEF_Gi_EGFR Text Annotations

GIV Universal ID's

GIV Text Annotations

GIV_GEF Universal ID's

GIV_GEF Text Annotations

GIV_GDI Universal ID's

GIV_GDI Text Annotations

Cdk5 Universal ID's

Cdk5 Text Annotations

Gs_GTP_i Universal ID's

Gs_GTP_i Text Annotations

Gs_GDP_i Universal ID's

Gs_GDP_i Text Annotations

Gs_GDI_i Universal ID's

Gs_GDI_i Text Annotations

EGF_EGFR_i_act Universal ID's

EGF_EGFR_i_act Text Annotations

AC_i Universal ID's

AC_i Text Annotations

bg_i Universal ID's

bg_i Text Annotations

AC_inact Universal ID's

AC_inact Text Annotations

Gs_protein Universal ID's

Gs_protein Text Annotations

EGFi Universal ID's

EGFi Text Annotations

EGFRi Universal ID's

EGFRi Text Annotations

R2 Universal ID's

R2 Text Annotations

R2u Universal ID's

R2u Text Annotations

R2uu Universal ID's

R2uu Text Annotations

EGF_EGFRi Universal ID's

EGF_EGFRi Text Annotations

EGF_EGFR_2i Universal ID's

EGF_EGFR_2i Text Annotations

Cdk5_p35_act Universal ID's

Cdk5_p35_act Text Annotations

Gs_protein_i Universal ID's

Gs_protein_i Text Annotations

PKA_inact Universal ID's

PKA_inact Text Annotations

Gs_GDI_b Universal ID's

Gs_GDI_b Text Annotations

GIV89p Universal ID's

GIV89p Text Annotations

I Universal ID's

I Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

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

unnamed Universal ID's

unnamed Text Annotations

Specifications (Species) - unnamed go to Simulations

Species
Initial Condition
Diffusion Constant
Structure
EGFi 0.0 [umol] 0.0 [um2/s] Endosome
PLCg 0.1 [umol] 0.0 [um2/s] Cyto
IP3 0.0 [umol] 0.0 [um2/s] Cyto
inositol 0.0 [umol] 0.0 [um2/s] Cyto
PKC 0.1 [umol] 0.0 [um2/s] Cyto
ATP 5000.0 [umol] 0.0 [um2/s] Cyto
cAMP 0.00463445029560112 [umol] 0.0 [um2/s] Cyto
PKA 0.00663502149436935 [umol] 0.0 [um2/s] Cyto
PDE 0.3454122887 [umol] 0.0 [um2/s] Cyto
R2C2 0.0963501127833185 [umol] 0.0 [um2/s] Cyto
AMP 1000.0 [umol] 0.0 [um2/s] Cyto
PDEp 0.0545877112954137 [umol] 0.0 [um2/s] Cyto
PP_PDE 0.2 [umol] 0.0 [um2/s] Cyto
PLCg_active 0.0 [umol] 0.0 [um2/s] Cyto
GIV ((totalGIV - (GDImult * totalGIV)) - GIV_GEF) [umol] 0.0 [um2/s] Cyto
GIV_GEF (GEFmult * totalGIV) [umol] 0.0 [um2/s] Cyto
GIV_GDI 0.0 [umol] 0.0 [um2/s] Cyto
Cdk5 0.05 [umol] 0.0 [um2/s] Cyto
R2 6.97924584116095E-5 [umol] 0.0 [um2/s] Cyto
R2u 0.00419256840426028 [umol] 0.0 [um2/s] Cyto
R2uu 0.00264752635400966 [umol] 0.0 [um2/s] Cyto
PKA_inact 0.0 [umol] 0.0 [um2/s] Cyto
GIV89p (GDImult * totalGIV) [umol] 0.0 [um2/s] Cyto
EGF 0.05 [umol] 0.0 [um2/s] ECM
AC_act 0.0 [umol] 0.0 [um2/s] intmem
Gs_GTP_i 0.0 [umol] 0.0 [um2/s] intmem
Gs_GDP_i 0.0 [umol] 0.0 [um2/s] intmem
Gs_GDI_i 0.0 [umol] 0.0 [um2/s] intmem
EGF_EGFR_i_act 0.0 [umol] 0.0 [um2/s] intmem
AC_i 0.0 [umol] 0.0 [um2/s] intmem
bg_i 0.0 [umol] 0.0 [um2/s] intmem
EGFRi 0.0 [umol] 0.0 [um2/s] intmem
EGF_EGFRi 0.0 [umol] 0.0 [um2/s] intmem
EGF_EGFR_2i 0.0 [umol] 0.0 [um2/s] intmem
Gs_protein_i 0.0 [umol] 0.0 [um2/s] intmem
Gs_GDI_b 1.30617460365262E-15 [umol] 0.0 [um2/s] intmem
I 0.0 [umol] 0.0 [um2/s] intmem
EGFR 3.985E-16 [umol] 0.0 [um2/s] PM
p35 1.589E-15 [umol] 0.0 [um2/s] PM
p35_act 0.0 [umol] 0.0 [um2/s] PM
Gi_GTP 0.0 [umol] 0.0 [um2/s] PM
Gi_GDP 7.97E-17 [umol] 0.0 [um2/s] PM
EGF_EGFR 0.0 [umol] 0.0 [um2/s] PM
PKC_act 0.0 [umol] 0.0 [um2/s] PM
AC 4.98E-17 [umol] 0.0 [um2/s] PM
PIP2 1.589E-14 [umol] 0.0 [um2/s] PM
EGF_EGFR_2_act 0.0 [umol] 0.0 [um2/s] PM
EGF_EGFR_2 0.0 [umol] 0.0 [um2/s] PM
DAG 0.0 [umol] 0.0 [um2/s] PM
GEF_EGFR 0.0 [umol] 0.0 [um2/s] PM
GEF_Gi_EGFR 2.0E-20 [umol] 0.0 [um2/s] PM
AC_inact 0.0 [umol] 0.0 [um2/s] PM
Gs_protein 2.49E-15 [umol] 0.0 [um2/s] PM
Cdk5_p35_act 0.0 [umol] 0.0 [um2/s] PM

Specifications (Reaction) - unnamed go to Simulations

Name
Enabled?
AC_inactivation included
AC_internalization included
AC_unbinding included
AC_activation included
Cdk5_activation included
DAG_decactivation included
DAG_deactivation_while_bound included
Degradation_GDI included
Degradation_GEF included
Dimerize included
Dimerized_receptor_activation included
EGF_deg included
EGFR_deg included
EGFR_to_PM included
EGFR_GEF_to_GDI included
GDI_function included
GEF_EGFR_binding included
GEF_Gi_Binding included
GEF_activation included
GEF_to_GDI included
Gi_activation included
Gi_hydrolysis included
Gs_GDI_accel_deg included
Gs_activation included
Gs_hydrolysis included
Gs_internalization included
IP3_degradation included
InactivAC included
PDE_phos included
PIP2_to_DAG included
PKA_inactivation included
PKA_reformation included
PKC_activation included
PLC_GEF_enhanced included
PLC_activation_basal included
PLC_deactivation included
R2uUnbind included
R2Unbind included
cAMP_Activation included
cAMP_basal included
cAMP_basal_production_internal included
cAMP_to_AMP included
cAMP_to_AMP_PDEp included
dephos_of_PDEp included
internal_transport included
internal_trimerize included
p35_activation included
p35_inactivation included
production_cAMP_internal included
receptor_ligand_binding included
v10 included
v11 included
v12 included
basalGIVGDI included
_89pDEG included
Gs_GDI_accel_deg_copy included
Gs_GDI_accel_deg_copy2 included
Gs_GDI_accel_deg_copy3 included
Gs_GDI_accel_deg_copy4 included
Gs_GDI_accel_deg_copy5 included
Gs_GDI_accel_deg_copy6 included
Intfun included

Simulations - unnamed go to Specifications

Name
End Time
Output Options
Simulation0 3600.0

OutputTimeStep 5.0
GIV+EGFR variation 3600.0

OutputTimeStep 5.0

unnamed Universal ID's

unnamed Text Annotations

unnamed Universal ID's

unnamed Text Annotations

Assignments

Name Variable Assignment Function Expression

Events

Name Trigger Type Variable Assignment
EGFoff on condition: 0.0 EGF --> 0.0

Geometry Compartmental

(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 PM

Events

Name Variable Rate Expression

Global Parameters

Name
Expression
kfint 4.578940789E-5[tbd]
krint 6.66502822995389E-5[tbd]
kbase 1.07E-8[tbd]
kc 1.32E11[tbd]
kfGi 3.0102889041494098E18[tbd]
krGi ((0.24 * ModelValue_4 * Compartment_2) / Compartment_1)[tbd]
intrec 0.002[tbd]
normcAMP (cAMP / Metabolite_15)[tbd]
normGDI ((Gs_GDI_i + Gs_GDI_b) / (Metabolite_35 + Metabolite_51))[tbd]
normGEF (GEF_Gi_EGFR / Metabolite_28)[tbd]
normGEFc ((GIV_GEF + GIV_GDI) / (Metabolite_30 + Metabolite_31))[tbd]
normGDIc ((GIV_GDI + GIV89p) / (Metabolite_31 + Metabolite_52))[tbd]
totalGIV 1.0[tbd]
GDImult (2.0 * GEFmult)[tbd]
bindingGDIGIV (0.05 * GDI_function_k1)[tbd]
krGDIGIV 3.0E-4[tbd]
GEFmult 0.0511120195467634[tbd]
GDI_function_k1 2.91[tbd]
Compartment_2 Cyto[tbd]
Metabolite_52 GIV89p[tbd]
Metabolite_31 GIV_GDI[tbd]
Metabolite_30 GIV_GEF[tbd]
Metabolite_15 cAMP[tbd]
Compartment_1 PM[tbd]
Metabolite_28 GEF_Gi_EGFR[tbd]
Metabolite_51 Gs_GDI_b[tbd]
Metabolite_35 Gs_GDI_i[tbd]
ModelValue_4 kfGi[tbd]

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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Universal ID's

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