aguda1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000169) Biomodels notes: The plots correspond to the time profiles of p27, E2F and cycE/CDK2 as depicted in Fig 5c of the paper. MathSBML was used to obtain simulation results. 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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The kinetic origins of the restriction point in the mammalian cell cycle.

  • BD Aguda
  • Y Tang
Cell Prolif. 1999; 32 (5): 321-335
Abstract
A detailed model mechanism for the G1/S transition in the mammalian cell cycle is presented and analysed by computer simulation to investigate whether the kinetic origins of the restriction point (R-point) can be identified. The R-point occurs in mid-to-late G1 phase and marks the transition between mitogen-dependent to mitogen-independent progression of the cell cycle. For purposes of computer simulations, the R-point is defined as the first point in time after mitosis where cutting off mitogen stimulation does not prevent the cell reaching the threshold activity of cyclin-E/cdk2 required for entry into S phase. The key components of the network that generate a dynamic switching behaviour associated with the R-point include a positive feedback loop between cyclin-E/cdk2 and Cdc25A, along with the mutually negative interaction between the cdk inhibitor p27Kip1 and cyclin-E/cdk2. Simulations of the passage through the R-point were carried out and the factors affecting the position of the R-point in G1 are determined. The detailed model also shows various points in the network where the activation of cyclin-E/cdk2 can be initiated with or without the involvement of the retinoblastoma protein.

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
default_compartment 3.0 1.0
Id Name Initial quantity Compartment Fixed
CYCDcdk4 0.0 default_compartment
CYCDcdk4p27 0.0 default_compartment
CYCEcdk2p27 1.0 default_compartment
E2F 0.0 default_compartment
aCYCEcdk2 0.0 default_compartment
aCYCEcdk20 5.0 default_compartment
aCYCEcdk21 0.01 default_compartment
iCYCEcdk2 0.01 default_compartment
p27 2.0 default_compartment
pRB 0.05 default_compartment
pRBE2F 1.95 default_compartment
xvar 0.0 default_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
v_1 v_1 pRBE2F = aCYCEcdk21 + E2F

k1*aCYCEcdk2*pRBE2F + k1a*CYCDcdk4*pRBE2F + k1aa*CYCDcdk4p27*pRBE2F
v_10 CYCDcdk4 = xvar

kmin6*CYCDcdk4
v_11 xvar = p27

k7
v_12 v_12 p27 = xvar

k8*aCYCEcdk2*p27
v_13 aCYCEcdk2 + p27 = CYCEcdk2p27

k9*aCYCEcdk2*p27
v_14 CYCEcdk2p27 = aCYCEcdk2 + p27

k10*CYCEcdk2p27
v_15 aCYCEcdk20 + CYCDcdk4 = xvar

k17*aCYCEcdk20*CYCDcdk4
v_16 xvar = E2F

k18*E2F
v_17 CYCDcdk4 + p27 = CYCDcdk4p27

k19*CYCDcdk4*p27
v_18 CYCDcdk4p27 = CYCDcdk4 + p27

k20*CYCDcdk4p27
v_19 aCYCEcdk2 = xvar

k21*aCYCEcdk2^2
v_2 E2F + pRB = pRBE2F

kmin1*E2F*pRB
v_20 p27 = xvar

k22*p27
v_21 xvar = aCYCEcdk20

k23
v_22 aCYCEcdk20 = xvar

k24*aCYCEcdk20
v_23 v_23 xvar = aCYCEcdk20

k25/(1 + k25a*pRB)
v_24 v_24 xvar = pRB

k26/(1 + k26a*aCYCEcdk20)
v_25 xvar = pRB

k27
v_26 pRB = xvar

k28*pRB
v_27 aCYCEcdk21 = pRB

k29*aCYCEcdk21
v_3 iCYCEcdk2 = aCYCEcdk2

k2*aCYCEcdk2*iCYCEcdk2
v_4 aCYCEcdk2 = iCYCEcdk2

kmin2*aCYCEcdk2
v_5 v_5 xvar = iCYCEcdk2

k3a + k3*E2F
v_6 xvar = E2F

k4
v_7 E2F = xvar

kmin4*E2F
v_8 iCYCEcdk2 = xvar

k5*iCYCEcdk2
v_9 xvar = CYCDcdk4

k6

Global parameters

Id Value
k1 0.1
k10 0.035
k17 3.5
k18 0.00001
k19 0.05
k1a 0.5
k1aa 0.5
k2 0.1
k20 0.01
k21 0.1
k22 0.001
k23 0.2
k24 0.1
k25 0.01
k25a 0.02
k26 0.01
k26a 0.1
k27 0.01
k28 0.01
k29 0.001
k3 1.42
k3a 0.0
k4 0.000001
k5 0.02
k6 0.018
k7 0.00001
k8 2.0
k9 2.0
kmin1 0.001
kmin2 1.0
kmin4 0.016
kmin6 5.0

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments