nakakuki2

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000251) Biomodels notes: reproduction of the 10 nM HRG stimlations depicted in figures 4BCD of the original publication. The results were obtained using SBML ODESolver. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.

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Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics.

  • Takashi Nakakuki
  • Marc R Birtwistle
  • Yuko Saeki
  • Noriko Yumoto
  • Kaori Ide
  • Takeshi Nagashima
  • Lutz Brusch
  • Babatunde A Ogunnaike
  • Mariko Okada-Hatakeyama
  • Boris N Kholodenko
Cell 2010; 141 (5): 884-896
Abstract
Activation of ErbB receptors by epidermal growth factor (EGF) or heregulin (HRG) determines distinct cell-fate decisions, although signals propagate through shared pathways. Using mathematical modeling and experimental approaches, we unravel how HRG and EGF generate distinct, all-or-none responses of the phosphorylated transcription factor c-Fos. In the cytosol, EGF induces transient and HRG induces sustained ERK activation. In the nucleus, however, ERK activity and c-fos mRNA expression are transient for both ligands. Knockdown of dual-specificity phosphatases extends HRG-stimulated nuclear ERK activation, but not c-fos mRNA expression, implying the existence of a HRG-induced repressor of c-fos transcription. Further experiments confirmed that this repressor is mainly induced by HRG, but not EGF, and requires new protein synthesis. We show how a spatially distributed, signaling-transcription cascade robustly discriminates between transient and sustained ERK activities at the c-Fos system level. The proposed control mechanisms are general and operate in different cell types, stimulated by various ligands.

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
0.001 litre
60.0 second
0.001 mole
Id Name Spatial dimensions Size
compartment compartment 3.0 1.0
Id Name Initial quantity Compartment Fixed
DUSP DUSP 0.0 compartment (compartment)
cFOS cFOS 0.0 compartment (compartment)
cFOSm cFOSmRNA 0.0 compartment (compartment)
cFOSp cFOS preRNA 0.0 compartment (compartment)
pRSKn pRSKn 0.0 compartment (compartment)
pcFOS pc-FOS 0.0 compartment (compartment)
ppERKc ppERK(cytosol) 0.0 compartment (compartment)
ppERKn ppERK(nucleus) 0.0 compartment (compartment)
x1 x1 0.0 compartment (compartment)
x2 x2 0.0 compartment (compartment)

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
reaction_1 1 PhIM 1 ∅ > x1

compartment * (-x1 / tau1 + K1 * L / tau1)
reaction_2 1 PhIM 2 ∅ > x2

compartment * (-x2 / tau2 + K2 * L / tau2)
reaction_3 2a ppERKn ∅ > ppERKn

compartment * (k1 * ppERKc - k2 * ppERKn - k3 * DUSP * ppERKn)
reaction_4 2b DUSP ∅ > DUSP

compartment * k * ppERKn
reaction_5 3 pRSKn ∅ > pRSKn

compartment * (k4 * ppERKn - k5 * pRSKn)
reaction_6 4 cFOSp ∅ > cFOSp

compartment * (pow(ppERKn * pRSKn, n) / (pow(k6, n) + pow(ppERKn * pRSKn, n)) - k7 * cFOSp)
reaction_7 5 cFOSm ∅ > cFOSm

compartment * (k7 * cFOSp - k8 * cFOSm)
reaction_8 6 cFOS ∅ > cFOS

compartment * (k9 * cFOSm - k10 * cFOS - k11 * cFOS * ppERKc + k13 * pcFOS)
reaction_9 7 pcFOS ∅ > pcFOS

compartment * (k11 * cFOS * ppERKc - k12 * pcFOS - k13 * pcFOS)

Global parameters

Id Value
K1 1.09
K2 2.89
L 1.0
k11 0.11
k13 0.06
k7 0.5
tau1 3.07
tau2 472.0

Local parameters

Id Value Reaction
k1 15.0 reaction_3 (2a ppERKn)
k2 50.0 reaction_3 (2a ppERKn)
k3 14.0 reaction_3 (2a ppERKn)
k 1.0 reaction_4 (2b DUSP)
k4 0.1 reaction_5 (3 pRSKn)
k5 0.15 reaction_5 (3 pRSKn)
k6 0.13 reaction_6 (4 cFOSp)
n 1.1 reaction_6 (4 cFOSp)
k8 0.08 reaction_7 (5 cFOSm)
k10 0.3 reaction_8 (6 cFOS)
k9 0.3 reaction_8 (6 cFOS)
k12 0.001 reaction_9 (7 pcFOS)

Assignment rules

Definition
ppERKc = x1 - x2

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments