kallenberger1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000523) Biomodels notes: This model contain the equations for one "average cell" with median initial concentrations for CD95, FADD, p55, BID, PrNES_mCherry and PrER_mGFP. Figure 4A in the reference publication gives the simulation and experimental results of several cells (80 different cells). As this model is a "average cell" model, trajectories similar to that of Figure 4A has been reproduced, but for the ligand concentration of 500ng/ml (CD95L = 16.6nM (500ng/ml)). The simulation results are checked with the authors. 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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Intra- and interdimeric caspase-8 self-cleavage controls strength and timing of CD95-induced apoptosis.

  • Stefan M Kallenberger
  • Joel Beaudouin
  • Juliane Claus
  • Carmen Fischer
  • Peter K Sorger
  • Stefan Legewie
  • Roland Eils
Sci Signal 2014; 7 (316):
Abstract
Apoptosis in response to the ligand CD95L (also known as Fas ligand) is initiated by caspase-8, which is activated by dimerization and self-cleavage at death-inducing signaling complexes (DISCs). Previous work indicated that the degree of substrate cleavage by caspase-8 determines whether a cell dies or survives in response to a death stimulus. To determine how a death ligand stimulus is effectively translated into caspase-8 activity, we assessed this activity over time in single cells with compartmentalized probes that are cleaved by caspase-8 and used multiscale modeling to simultaneously describe single-cell and population data with an ensemble of single-cell models. We derived and experimentally validated a minimal model in which cleavage of caspase-8 in the enzymatic domain occurs in an interdimeric manner through interaction between DISCs, whereas prodomain cleavage sites are cleaved in an intradimeric manner within DISCs. Modeling indicated that sustained membrane-bound caspase-8 activity is followed by transient cytosolic activity, which can be interpreted as a molecular timer mechanism reflected by a limited lifetime of active caspase-8. The activation of caspase-8 by combined intra- and interdimeric cleavage ensures weak signaling at low concentrations of CD95L and strongly accelerated activation at higher ligand concentrations, thereby contributing to precise control of apoptosis.

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
Id Name Spatial dimensions Size
cell cell 3.0 1.0
Id Name Initial quantity Compartment Fixed
Bid Bid 236.0 cell (cell)
CD95 CD95 116.0 cell (cell)
CD95L CD95L 16.6 cell (cell)
DISC DISC 0.0 cell (cell)
DISCp55 DISCp55 0.0 cell (cell)
FADD FADD 93.0 cell (cell)
PrER PrER 0.0 cell (cell)
PrER_mGFP PrER_mGFP 5178.0 cell (cell)
PrNES PrNES 0.0 cell (cell)
PrNES_mCherry PrNES_mCherry 973.0 cell (cell)
mCherry mCherry 0.0 cell (cell)
mGFP mGFP 0.0 cell (cell)
p18 p18 0.0 cell (cell)
p18inactive p18inactive 0.0 cell (cell)
p30 p30 0.0 cell (cell)
p43 p43 0.0 cell (cell)
p55free p55free 155.0 cell (cell)
tBid tBid 0.0 cell (cell)

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 FADD > DISC

kon_FADD * CD95act * FADD * cell
reaction_10 p18 > p18inactive

kdiss_p18 * p18 * cell
reaction_11 Bid > tBid

kBid * Bid * (p43 + p18) * cell
reaction_12 PrNES_mCherry > PrNES + mCherry

kD374probe * PrNES_mCherry * (p43 + p18) * cell
reaction_13 PrER_mGFP > PrER + mGFP

kD374probe * PrER_mGFP * p18 * cell
reaction_2 DISC > FADD

koff_FADD * DISC * cell
reaction_3 p55free + DISC > DISCp55

kDISC * p55free * DISC * cell
reaction_4 DISCp55 > p30

kD216 * DISCp55 * cell
reaction_5 p43 > p18 + DISC

kD216 * p43 * cell
reaction_6 DISCp55 > p43

kD374trans_p55 * DISCp55 * (DISCp55 + p30) * cell
reaction_7 DISCp55 > p43

kD374trans_p43 * DISCp55 * p43 * cell
reaction_8 p30 > p18 + DISC

kD374trans_p55 * p30 * (DISCp55 + p30) * cell
reaction_9 p30 > p18 + DISC

kD374trans_p43 * p30 * p43 * cell

Global parameters

Id Value
CD95act 0.0
KDL 15.421878766215
KDR 8.98496674617627
kBid 0.00052867403363568
kD216 0.0114186392006403
kD374probe 0.00152252549827479
kD374trans_p43 0.00343995957326369
kD374trans_p55 0.000446994772958953
kDISC 0.000491828591049766
kdiss_p18 0.0949914492651531
koff_FADD 0.00566528253772301
kon_FADD 0.000811711012144556

Local parameters

Id Value Reaction

Assignment rules

Definition
CD95act = pow(CD95, 3.0) * pow(KDL, 2.0) * CD95L / ((CD95L + KDL) * (pow(CD95, 2.0) * pow(KDL, 2.0) + KDR * pow(CD95L, 2.0) + 2.0 * KDR * KDL * CD95L + KDR * pow(KDL, 2.0)))

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments