kallenberger4

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000526) 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 4B 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 4B 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 224.0 cell (cell)
CD95 CD95 12.0 cell (cell)
CD95L CD95L 16.6 cell (cell)
DISC DISC 0.0 cell (cell)
DISCp55 DISCp55 0.0 cell (cell)
FADD FADD 90.0 cell (cell)
PrER PrER 0.0 cell (cell)
PrER_mGFP PrER_mGFP 3316.0 cell (cell)
PrNES PrNES 0.0 cell (cell)
PrNES_mCherry PrNES_mCherry 1909.0 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 127.0 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 DISCp55 > p43

kD374 * DISCp55 * cell
reaction_11 DISCp55 > p43

kD374trans_p55 * DISCp55 * (DISCp55 + p30) * cell
reaction_12 DISCp55 > p43

kD374trans_p43 * DISCp55 * p43 * cell
reaction_13 p30 > p18 + DISC

kD374 * p30 * cell
reaction_14 p30 > p18 + DISC

kD374trans_p55 * p30 * (DISCp55 + p30) * cell
reaction_15 p30 > p18 + DISC

kD374trans_p43 * p30 * p43 * cell
reaction_16 p18 > p18inactive

kdiss_p18 * p18 * cell
reaction_17 Bid > tBid

kBid * Bid * (p43 + p18) * cell
reaction_18 PrNES_mCherry > PrNES + mCherry

kD374probe * PrNES_mCherry * (p43 + p18) * cell
reaction_19 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 DISCp55 > p30

kD216trans_p55 * DISCp55 * (DISCp55 + p30) * cell
reaction_6 DISCp55 > p30

kD216trans_p43 * DISCp55 * p43 * cell
reaction_7 p43 > p18 + DISC

kD216 * p43 * cell
reaction_8 p43 > p18 + DISC

kD216trans_p55 * p43 * (DISCp55 + p30) * cell
reaction_9 p43 > p18 + DISC

kD216trans_p43 * p43 * p43 * cell

Global parameters

Id Value
CD95act 0.0
KDL 30.0060394758199
KDR 57.2050013008496
kBid 0.00052134055139547
kD216 0.00639775937416746
kD216trans_p43 0.0000529906975294056
kD216trans_p55 0.000223246421372882
kD374 0.000644612643975149
kD374probe 0.00153710001025539
kD374trans_p43 0.00413530054938906
kD374trans_p55 0.000543518631342483
kDISC 0.000364965874405544
kdiss_p18 0.064713651554491
koff_FADD 0.00130854998177646
kon_FADD 0.00108871858684363

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