neumann1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000243) Biomodels notes: The model reproduces figure 5D of the reference publication. The model as such reproduces the plot corresponding to Anti-CD95 conc. 1500ng/ml (black). To obtain plots corresponding to Anti-CD95 conc. 500ng/ml (blue) and Anti-CD95 conc. 250ng/ml (red), the initial concentration of L should be set as 37.74nM and 18.87nM, respectively. The model was integrated and simulated using Copasi v4.5 (Build 30). JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. Only figures C3, C8, NF-KB:IKB and NF-KB:IKB:P were recreated.

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Dynamics within the CD95 death-inducing signaling complex decide life and death of cells.

  • Leo Neumann
  • Carina Pforr
  • Joel Beaudouin
  • Alexander Pappa
  • Nicolai Fricker
  • Peter H Krammer
  • Inna N Lavrik
  • Roland Eils
Mol. Syst. Biol. 2010; 6 : 352
Abstract
This study explores the dilemma in cellular signaling that triggering of CD95 (Fas/APO-1) in some situations results in cell death and in others leads to the activation of NF-kappaB. We established an integrated kinetic mathematical model for CD95-mediated apoptotic and NF-kappaB signaling. Systematic model reduction resulted in a surprisingly simple model well approximating experimentally observed dynamics. The model postulates a new link between c-FLIP(L) cleavage in the death-inducing signaling complex (DISC) and the NF-kappaB pathway. We validated experimentally that CD95 stimulation resulted in an interaction of p43-FLIP with the IKK complex followed by its activation. Furthermore, we showed that the apoptotic and NF-kappaB pathways diverge already at the DISC. Model and experimental analysis of DISC formation showed that a subtle balance of c-FLIP(L) and procaspase-8 determines life/death decisions in a nonlinear manner. We present an integrated model describing the complex dynamics of CD95-mediated apoptosis and NF-kappaB signaling.

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
1e-09 mole
Id Name Spatial dimensions Size
default default 3.0 1.0
Id Name Initial quantity Compartment Fixed
C3 C3 1.443404 default (default)
C3_star C3* 0.0 default (default)
C8 C8 64.47652 default (default)
C8_star C8* 0.0 default (default)
FL FL 7.398562 default (default)
FS FS 5.083923 default (default)
IKK IKK 5.772825 default (default)
L L 113.22 default (default)
L_RF L:RF 0.0 default (default)
L_RF_C8 L:RF:C8 0.0 default (default)
L_RF_C8_FS L:RF:C8:FS 0.0 default (default)
L_RF_FL L:RF:FL 0.0 default (default)
L_RF_FL_FL L:RF:FL:FL 0.0 default (default)
L_RF_FL_FS L:RF:FL:FS 0.0 default (default)
L_RF_FS L:RF:FS 0.0 default (default)
L_RF_FS_FS L:RF:FS:FS 0.0 default (default)
NF_kB_IkB NF-kB:IkB 4.739546 default (default)
NF_kB_IkB_P NF-kB:IkB:P 0.0 default (default)
NF_kB_star NF-kB* 0.0 default (default)
RF RF 91.26592 default (default)
p43_FLIP p43-FLIP 0.0 default (default)
p43_FLIP_IKK_star p43-FLIP:IKK* 0.0 default (default)
p43_p41 p43/p41 0.0 default (default)

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 reaction_1 L + RF > L_RF

default * k1 * L * RF
reaction_10 reaction_10 L_RF_FL + FS > L_RF_FL_FS

default * k7 * L_RF_FL * FS
reaction_11 reaction_11 L_RF_FS + C8 > L_RF_C8_FS

default * k5 * L_RF_FS * C8
reaction_12 reaction_12 L_RF_FS + FL > L_RF_FL_FS

default * k6 * L_RF_FS * FL
reaction_13 reaction_13 L_RF_FS + FS > L_RF_FS_FS

default * k7 * L_RF_FS * FS
reaction_14 reaction_14 p43_p41 + p43_p41 > C8_star

default * k8 * p43_p41 * p43_p41
reaction_15 reaction_15 C3 + C8_star > C3_star + C8_star

default * k9 * C3 * C8_star
reaction_16 reaction_16 C8 + C3_star > p43_p41 + C3_star

default * k10 * C8 * C3_star
reaction_17 reaction_17 C8_star > ∅

default * k11 * C8_star
reaction_18 reaction_18 C3_star > ∅

default * k12 * C3_star
reaction_19 reaction_19 p43_FLIP + IKK > p43_FLIP_IKK_star

default * k13 * p43_FLIP * IKK
reaction_2 reaction_2 L_RF + C8 > L_RF_C8

default * k2 * L_RF * C8
reaction_20 reaction_20 NF_kB_IkB + p43_FLIP_IKK_star > NF_kB_IkB_P + p43_FLIP_IKK_star

default * k14 * NF_kB_IkB * p43_FLIP_IKK_star
reaction_21 reaction_21 NF_kB_IkB_P > NF_kB_star

default * k15 * NF_kB_IkB_P
reaction_22 reaction_22 p43_FLIP_IKK_star > ∅

default * k16 * p43_FLIP_IKK_star
reaction_23 reaction_23 NF_kB_star > ∅

default * k17 * NF_kB_star
reaction_3 reaction_3 L_RF + FL > L_RF_FL

default * k3 * L_RF * FL
reaction_4 reaction_4 L_RF + FS > L_RF_FS

default * k4 * L_RF * FS
reaction_5 reaction_5 L_RF_C8 + C8 > p43_p41 + p43_p41

default * k5 * L_RF_C8 * C8
reaction_6 reaction_6 L_RF_C8 + FL > p43_FLIP

default * k6 * L_RF_C8 * FL
reaction_7 reaction_7 L_RF_C8 + FS > L_RF_C8_FS

default * k7 * L_RF_C8 * FS
reaction_8 reaction_8 L_RF_FL + C8 > p43_FLIP

default * k5 * L_RF_FL * C8
reaction_9 reaction_9 L_RF_FL + FL > L_RF_FL_FL

default * k6 * L_RF_FL * FL

Global parameters

Id Value
k1 1.0
k10 0.1205258
k11 0.02891451
k12 0.1502914
k13 0.0007204261
k14 0.3588224
k15 3.684162
k16 0.02229912
k17 0.0064182
k2 0.0001277248
k3 0.6693316
k4 0.00001
k5 0.0005946569
k6 0.9999999
k7 0.8875063
k8 0.0008044378
k9 0.002249759

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments