goldbeter3

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000004) Biomodels notes: This model represents the inactive forms of CDC-2 Kinase and Cyclin Protease as separate species, unlike the ODEs in the published paper, in which the equations for the inactive forms are substituted into the equations for the active forms using a mass conservation rule M+MI=1,X+XI=1. Mass is still conserved in this model through the explicit reactions M<->MI and X<->XI. The terms in the kinetic laws are identical to the corresponding terms in the kinetic laws in the published paper. JWS Online curation: This model reproduces Figure 3, similar to goldbeter2.

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A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase.

  • Albert Goldbeter
Proc. Natl. Acad. Sci. U.S.A. 1991; 88 (20): 9107-9111
Abstract
A minimal model for the mitotic oscillator is presented. The model, built on recent experimental advances, is based on the cascade of post-translational modification that modulates the activity of cdc2 kinase during the cell cycle. The model pertains to the situation encountered in early amphibian embryos, where the accumulation of cyclin suffices to trigger the onset of mitosis. In the first cycle of the bicyclic cascade model, cyclin promotes the activation of cdc2 kinase through reversible dephosphorylation, and in the second cycle, cdc2 kinase activates a cyclin protease by reversible phosphorylation. That cyclin activates cdc2 kinase while the kinase triggers the degradation of cyclin has suggested that oscillations may originate from such a negative feedback loop [Félix, M. A., Labbé, J. C., Dorée, M., Hunt, T. & Karsenti, E. (1990) Nature (London) 346, 379-382]. This conjecture is corroborated by the model, which indicates that sustained oscillations of the limit cycle type can arise in the cascade, provided that a threshold exists in the activation of cdc2 kinase by cyclin and in the activation of cyclin proteolysis by cdc2 kinase. The analysis shows how miototic oscillations may readily arise from time lags associated with these thresholds and from the delayed negative feedback provided by cdc2-induced cyclin degradation. A mechanism for the origin of the thresholds is proposed in terms of the phenomenon of zero-order ultrasensitivity previously described for biochemical systems regulated by covalent modification.

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
C Cyclin 0.01 cell (cell)
M Active CDC-2 Kinase 0.01 cell (cell)
MI Inactive CDC-2 Kinase 0.99 cell (cell)
X Active Cyclin Protease 0.01 cell (cell)
XI Inactive Cyclin Protease 0.99 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
reaction1 creation of cyclin ∅ > C

cell * vi
reaction2 default degradation of cyclin C > ∅

C * cell * kd
reaction3 cdc2 kinase triggered degration of cyclin C > ∅

C * cell * vd * X * pow(C + Kd, -1)
reaction4 activation of cdc2 kinase MI > M

cell * MI * V1 * pow(K1 + MI, -1)
reaction5 deactivation of cdc2 kinase M > MI

cell * M * V2 * pow(K2 + M, -1)
reaction6 activation of cyclin protease XI > X

cell * V3 * XI * pow(K3 + XI, -1)
reaction7 deactivation of cyclin protease X > XI

cell * V4 * X * pow(K4 + X, -1)

Global parameters

Id Value
Kc 0.5
V1 0.0
V3 0.0
VM1 3.0
VM3 1.0

Local parameters

Id Value Reaction
vd 0.25 reaction3 (cdc2 kinase triggered degration of cyclin)
vi 0.025 reaction1 (creation of cyclin)
kd 0.01 reaction2 (default degradation of cyclin)
Kd 0.02 reaction3 (cdc2 kinase triggered degration of cyclin)
K1 0.005 reaction4 (activation of cdc2 kinase)
V2 1.5 reaction5 (deactivation of cdc2 kinase)
K2 0.005 reaction5 (deactivation of cdc2 kinase)
K3 0.005 reaction6 (activation of cyclin protease)
K4 0.005 reaction7 (deactivation of cyclin protease)
V4 0.5 reaction7 (deactivation of cyclin protease)

Assignment rules

Definition
V3 = M * VM3
V1 = C * VM1 * pow(C + Kc, -1.0)

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments