clarke1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000112) Biomodels notes: The model reproduces the temporal evolution of four variables depicted in Fig 2a. The solution is generated for median parameter values as given in Table 3. Result shown was generated by MathSBML. 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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Systems theory of Smad signalling.

  • DC Clarke
  • MD Betterton
  • X Liu
IEE Proceedings Systems Biology 2006; 153 (6): 412-424
Abstract
Transforming growth factor-beta (TGFbeta) signalling is an important regulator of cellular growth and differentiation. The principal intracellular mediators of TGFbeta signalling are the Smad proteins, which upon TGFbeta stimulation accumulate in the nucleus and regulate the transcription of target genes. To investigate the mechanisms of Smad nuclear accumulation, we developed a simple mathematical model of canonical Smad signalling. The model was built using both published data and our experimentally determined cellular Smad concentrations (isoforms 2, 3 and 4). We found in mink lung epithelial cells that Smad2 (8.5-12 x 10(4) molecules cell(-1)) was present in similar amounts to Smad4 (9.3-12 x 10(4) molecules cell(-1)), whereas both were in excess of Smad3 (1.1-2.0 x 10(4) molecules cell(-1)). Variation of the model parameters and statistical analysis showed that Smad nuclear accumulation is most sensitive to parameters affecting the rates of R-Smad phosphorylation and dephosphorylation and Smad complex formation/ dissociation in the nucleus. Deleting Smad4 from the model revealed that rate-limiting phospho-R-Smad dephosphorylation could be an important mechanism for Smad nuclear accumulation. Furthermore, we observed that binding factors constitutively localised to the nucleus do not efficiently mediate Smad nuclear accumulation, if dephosphorylation is rapid. We therefore conclude that an imbalance in the rates of R-Smad phosphorylation and dephosphorylation is likely an important mechanism of Smad nuclear accumulation during TGFbeta signalling.

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
60.0 second
1.0 item
0.016666666666666666 second^(-1.0)
0.016666666666666666 item second^(-1.0)
0.016666666666666666 item^(-1.0) second^(-1.0)
Id Name Spatial dimensions Size
cytoplasm cytoplasm 3.0 1.0
nucleus nucleus 3.0 1.0
Id Name Initial quantity Compartment Fixed
Pi Pi 0.0 nucleus (nucleus)
R_smad_P_cyt R-Smad-P_cyt 0.0 cytoplasm (cytoplasm)
R_smad_P_nuc R-Smad-P_nuc 0.0 nucleus (nucleus)
R_smad_P_smad4_cyt R-Smad-P-Smad4_cyt 0.0 cytoplasm (cytoplasm)
R_smad_P_smad4_nuc R-Smad-P-Smad4_nuc 0.0 nucleus (nucleus)
R_smad_cyt R-Smad_cyt 162000.0 cytoplasm (cytoplasm)
R_smad_nuc R-Smad_nuc 18000.0 nucleus (nucleus)
receptor receptors 10000.0 cytoplasm (cytoplasm)
smad4_cyt Smad4_cyt 120000.0 cytoplasm (cytoplasm)
smad4_nuc Smad4_nuc 30000.0 nucleus (nucleus)

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_0 Receptor degradation receptor > ∅

100 * exp(-time / 90)
reaction_1 Phosphorylation R_smad_cyt > R_smad_P_cyt

KCAT * receptor * R_smad_cyt / (K1 + R_smad_cyt)
reaction_2 Complex formation R_smad_P_cyt + smad4_cyt = R_smad_P_smad4_cyt

k2a * R_smad_P_cyt * smad4_cyt - k2d * R_smad_P_smad4_cyt
reaction_3 Complex translocation R_smad_P_smad4_cyt > R_smad_P_smad4_nuc

k3 * R_smad_P_smad4_cyt
reaction_4 Smad4 translocation smad4_nuc = smad4_cyt

k4nc * smad4_nuc - k4cn * smad4_cyt
reaction_5 R-Smad translocation R_smad_nuc = R_smad_cyt

k5nc * R_smad_nuc - k5cn * R_smad_cyt
reaction_6 Complex in nucleus R_smad_P_smad4_nuc = smad4_nuc + R_smad_P_nuc

k6d * R_smad_P_smad4_nuc - k6a * smad4_nuc * R_smad_P_nuc
reaction_7 Dephosphorylation R_smad_P_nuc > R_smad_nuc + Pi

Vmax7 * R_smad_P_nuc / (K7 + R_smad_P_nuc)

Global parameters

Id Value
sum_R_smad_cyt 0.0
sum_R_smad_nuc 0.0
sum_smad4_cyt 0.0
sum_smad4_nuc 0.0

Local parameters

Id Value Reaction
KCAT 3.51 min_inv reaction_1 (Phosphorylation)
K1 289000.0 substance reaction_1 (Phosphorylation)
k5nc 5.63 min_inv reaction_5 (R-Smad translocation)
k5cn 0.563 min_inv reaction_5 (R-Smad translocation)
k4nc 0.783 min_inv reaction_4 (Smad4 translocation)
k4cn 0.00497 min_inv reaction_4 (Smad4 translocation)
k2a 0.000065 reaction_2 (Complex formation)
k2d 0.0399 min_inv reaction_2 (Complex formation)
k3 16.6 min_inv reaction_3 (Complex translocation)
k6d 0.0492 min_inv reaction_6 (Complex in nucleus)
k6a 0.000144 reaction_6 (Complex in nucleus)
Vmax7 17100.0 items per min reaction_7 (Dephosphorylation)
K7 8950.0 substance reaction_7 (Dephosphorylation)

Assignment rules

Definition
sum_smad4_cyt = smad4_cyt + R_smad_P_smad4_cyt
sum_R_smad_cyt = R_smad_cyt + R_smad_P_cyt + R_smad_P_smad4_cyt
sum_smad4_nuc = smad4_nuc + R_smad_P_smad4_nuc
sum_R_smad_nuc = R_smad_nuc + R_smad_P_nuc + R_smad_P_smad4_nuc

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments