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Dissipative structures for an allosteric model. Application to glycolytic oscillations.

  • Albert Goldbeter
  • R Lefever
Biophys. J. 1972; 12 (10): 1302-1315
Abstract
An allosteric model of an open monosubstrate enzyme reaction is analyzed for the case where the enzyme, containing two protomers, is activated by the product. It is shown that this system can lead to instabilities beyond which a new state organized in time or in space (dissipative structure) can be reached. The conditions for both types of instabilities are presented and the occurrence of a temporal structure, consisting of a limit cycle behavior, is determined numerically as a function of the important parameters involved in the system. Sustained oscillations in the product and substrate concentrations are shown to occur for acceptable values of the allosteric and kinetic constants; moreover, they seem to be favored by substrate activation. The model is applied to phosphofructokinase, which is the enzyme chiefly responsible for glycolytic oscillations and which presents the same pattern of regulation as the allosteric enzyme appearing in the model. A qualitative and quantitative agreement is obtained with the experimental observations concerning glycolytic self-oscillations.

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 default_compartment 3.0 1.0
Id Name Initial quantity Compartment Fixed
alpha alpha 27.0 default_compartment (default_compartment)
alpha2 alpha2 84.0 default_compartment (default_compartment)
gamma gamma 10.0 default_compartment (default_compartment)
gamma2 gamma2 2.0 default_compartment (default_compartment)
p p 0.0 default_compartment (default_compartment)
s s 0.0 default_compartment (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
v1 v1 s = alpha

k1
v12 v12 s = alpha2

k1
v2 v2 alpha = gamma

k2 * (alpha * es * (1 + alpha * es) * pow(1 + gamma, 2) + el * ve * alpha * c * ep * (1 + alpha * c * ep)) / (el * pow(1 + alpha * c * ep, 2) + pow(1 + gamma, 2) * pow(1 + alpha * es, 2))
v22 v22 alpha2 = gamma2

k2 * (alpha2 * es * (1 + alpha2 * es) * pow(1 + gamma2, 2) + el * ve * alpha2 * c * ep * (1 + alpha2 * c * ep)) / (el * pow(1 + alpha2 * c * ep, 2) + pow(1 + gamma2, 2) * pow(1 + alpha2 * es, 2))
v3 v3 gamma = p

k3 * (gamma - p)
v32 v32 gamma2 = p

k3 * (gamma2 - p)
v4 v4 p = ∅

k4 * p

Global parameters

Id Value
EXTERNAL 0.0
c 0.00001
el 1000000.0
ep 0.9090909
es 0.9090909
k1 0.7
k2 3.98
k3 0.07
k4 10.0
ve 1.0

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Definition
Trigger Assignments