Birtwistle2007_ErbB_Signalling

  public model
Model Identifier
BIOMD0000000175
Short description
Format
SBML (L2V3)
Related Publication
  • Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses.
  • Birtwistle MR, Hatakeyama M, Yumoto N, Ogunnaike BA, Hoek JB, Kholodenko BN
  • Molecular Systems Biology , 0/ 2007 , Volume 3 , pages: 144 , PubMed ID: 18004277
  • Department of Chemical Engineering, University of Delaware, Newark, DE, USA.
  • Deregulation of ErbB signaling plays a key role in the progression of multiple human cancers. To help understand ErbB signaling quantitatively, in this work we combine traditional experiments with computational modeling, building a model that describes how stimulation of all four ErbB receptors with epidermal growth factor (EGF) and heregulin (HRG) leads to activation of two critical downstream proteins, extracellular-signal-regulated kinase (ERK) and Akt. Model analysis and experimental validation show that (i) ErbB2 overexpression, which occurs in approximately 25% of all breast cancers, transforms transient EGF-induced signaling into sustained signaling, (ii) HRG-induced ERK activity is much more robust to the ERK cascade inhibitor U0126 than EGF-induced ERK activity, and (iii) phosphoinositol-3 kinase is a major regulator of post-peak but not pre-peak EGF-induced ERK activity. Sensitivity analysis leads to the hypothesis that ERK activation is robust to parameter perturbation at high ligand doses, while Akt activation is not.
Contributors
null Molecular Systems Biology

Metadata information

is
BioModels Database MODEL5563731079
BioModels Database BIOMD0000000175
isDescribedBy
PubMed 18004277
hasTaxon
Taxonomy Homo sapiens
hasVersion
Gene Ontology MAPK cascade
Reactome Signalling to ERKs
isVersionOf
Gene Ontology ERBB signaling pathway
Curation status
Curated
Tags
Name Description Size Actions

Model files
BIOMD0000000175_url.xml SBML L2V3 representation of Birtwistle2007_ErbB_Signalling 222.10 KB Preview | Download

Additional files
BIOMD0000000175.svg Auto-generated Reaction graph (SVG) 374.34 KB Preview | Download
BIOMD0000000175.xpp Auto-generated XPP file 50.36 KB Preview | Download
BIOMD0000000175.vcml Auto-generated VCML file 916.00 Bytes Preview | Download
BIOMD0000000175.png Auto-generated Reaction graph (PNG) 4.13 MB Preview | Download
BIOMD0000000175_urn.xml Auto-generated SBML file with URNs 219.79 KB Preview | Download
BIOMD0000000175-biopax2.owl Auto-generated BioPAX (Level 2) 190.20 KB Preview | Download
BIOMD0000000175-biopax3.owl Auto-generated BioPAX (Level 3) 335.09 KB Preview | Download
BIOMD0000000175.sci Auto-generated Scilab file 58.85 KB Preview | Download
BIOMD0000000175.m Auto-generated Octave file 66.76 KB Preview | Download
BIOMD0000000175.pdf Auto-generated PDF file 784.48 KB Preview | Download

  • Model originally submitted by : null Molecular Systems Biology
  • Submitted: 18-Jul-2008 14:45:02
  • Last Modified: 08-Apr-2016 16:42:16
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 08-Apr-2016 16:42:16
    • Submitted by: null Molecular Systems Biology
    • With comment: Current version of Birtwistle2007_ErbB_Signalling
  • Version: 1 public model Download this version
    • Submitted on: 18-Jul-2008 14:45:02
    • Submitted by: null Molecular Systems Biology
    • With comment: Original import of ErbB

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
SigS 0.0 nmol
SigI 0.0 nmol
SigR 0.0 nmol
SigA 0.0 nmol
SigSP 0.0 nmol
E4 PT 0.0 nmol
H E4 PT 0.0 nmol
Reactions
Reactions Rate Parameters
SigAP + S => SigAP_S + SigS; SigSP, SigSP_G membrane*(3*kon43*SigAP*S-koff43*SigAP_S*SigS/(SigS+SigSP+SigSP_G+eps)) koff43 = 0.5441; eps = 1.0E-16; kon43 = 0.0127
E11S + SigS => S membrane*kdeg*E11S kdeg = 0.0259
E34P + I => E34I + SigI membrane*(4*kon28*E34P*I-koff28*E34I) koff28 = 4.6432; kon28 = 0.0074
E44P + I => E44I + SigI membrane*(2*kon36*E44P*I-koff36*E44I) kon36 = 0.0043; koff36 = 1.2567
E13P + I => E13I + SigI membrane*(3*kon67*E13P*I-koff67*E13I) kon67 = 6.6667E-5; koff67 = 1.6142
E11P + R => E11R + SigR; SigRP membrane*(2*kon18*E11P*R-koff18*SigR/(SigR+SigRP+eps)*E11R) kon18 = 0.0117; eps = 1.0E-16; koff18 = 2.2768
E23P + R => E23R + SigR; SigRP membrane*(2*kon25*E23P*R-koff25*SigR/(SigR+SigRP+eps)*E23R) kon25 = 0.0995; eps = 1.0E-16; koff25 = 2.225
E24P + R => E24R + SigR; SigRP membrane*(2*kon33*E24P*R-koff33*SigR/(SigR+SigRP+eps)*E24R) kon33 = 0.0335; eps = 1.0E-16; koff33 = 1.2817
E13P + R => E13R + SigR; SigRP membrane*(2*kon68*E13P*R-koff68*SigR/(SigR+SigRP+eps)*E13R) eps = 1.0E-16; kon68 = 0.0045; koff68 = 2.8871
SigA => SigAP; E11P, E12P, E23P, E24P, E34P, E44P, E13P, E14P, SigT membrane*((kf39*SigA*(E11P+E12P+E23P+E24P+E34P+E44P+E13P+E14P)-VmaxPY*SigAP/(KmPY+SigAP))-kPTP39*SigT*SigAP) kPTP39 = 79.6132; kf39 = 385.7428; KmPY = 486.1398; VmaxPY = 223.8776
SigG + A => SigG_A + SigA; SigAP, SigAP_S, SigAP_R, SigAP_I, SigAP_T membrane*(kon41*SigG*A-koff41*SigG_A*SigA/(eps+SigA+SigAP+SigAP_S+SigAP_R+SigAP_I+SigAP_T)) eps = 1.0E-16; kon41 = 0.0051; koff41 = 7.0487
P3 + A => P3_A + SigA; SigAP, SigAP_S, SigAP_R, SigAP_I, SigAP_T membrane*(kon46*P3*A-koff46*P3_A*SigA/(eps+SigA+SigAP+SigAP_S+SigAP_R+SigAP_I+SigAP_T)) kon46 = 0.0148; koff46 = 0.5194; eps = 1.0E-16
SigS => SigSP; E11P, E12P, E23P, E24P, E34P, E44P, E13P, E14P, SigT membrane*((kf38*SigS*(E11P+E12P+E23P+E24P+E34P+E44P+E13P+E14P)-VmaxPY*SigSP/(KmPY+SigSP))-kPTP38*SigT*SigSP) kf38 = 279.9929; kPTP38 = 83.4465; KmPY = 486.1398; VmaxPY = 223.8776
E4 => E4_PT; ERKstar membrane*(kf83*E4*ERKstar/(Kmf83+E4)-Vmaxr83*E4_PT/(Kmr83+E4_PT)) Kmf83 = 609.4766; Kmr83 = 653.5184; kf83 = 1.7628; Vmaxr83 = 534.0531
E4_PT => H_E4_PT; H membrane*(kon87*H*E4_PT-HRGoff_4*H_E4_PT) HRGoff_4 = 0.0973; kon87 = 8.0E-4
Curator's comment:
(added: 18 Jul 2008, 14:35:48, updated: 18 Jul 2008, 14:35:48)
reproduction of figure 4 using SBMLodeSolver (20080507)