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wolf

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000206). Biomodels notes: "Model reproduces the dynamics of ATP and NADH as depicted in Fig 4 of the paper. Model successfully tested on Jarnac and MathSBML." 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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Manuscript information

Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations.

  • Jana Wolf
  • J Passarge
  • OJ Somsen
  • Jacky L Snoep
  • Reinhart Heinrich
  • Hans V Westerhoff
Biophys. J. 2000; 78 (3): 1145-1153
Abstract
Under certain well-defined conditions, a population of yeast cells exhibits glycolytic oscillations that synchronize through intercellular acetaldehyde. This implies that the dynamic phenomenon of the oscillation propagates within and between cells. We here develop a method to establish by which route dynamics propagate through a biological reaction network. Application of the method to yeast demonstrates how the oscillations and the synchronization signal can be transduced. That transduction is not so much through the backbone of glycolysis, as via the Gibbs energy and redox coenzyme couples (ATP/ADP, and NADH/NAD), and via both intra- and intercellular acetaldehyde.

Unit definitions 0

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

Compartments 1

Id Name Spatial dimensions Size
default_compartment — 3.0 1.0

Species 9

Id Name Initial quantity Compartment Fixed
at ATP 2.0 default_compartment ✘
na NAD 0.6 default_compartment ✘
s1 glucose 1.0 default_compartment ✘
s2 fructose-1,6-bisphosphate 5.0 default_compartment ✘
s3 triose phosphates 0.6 default_compartment ✘
s4 triphosphoglycerate 0.7 default_compartment ✘
s5 pyruvate 8.0 default_compartment ✘
s6 acetaldehyde 0.08 default_compartment ✘
s6o external acetaldehyde 0.02 default_compartment ✘

Initial assignments 0

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
Reactions 11
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
v_1 glucose transporter ∅ = s1

k0
v_10 — s6o = ∅

k9*s6o
v_11 — at = ∅

k7*at
v_2 — s1 + {2.0}at = s2

k1 * s1 * at / (1 + (at / ki)^n)
v_3 — s2 = {2.0}s3

k2*s2
v_4 — s3 = na

k8*s3*(ntot - na)
v_5 — s3 + na = s4 + at

((k31*k32*s3*na*(atot - at) - k33*k34*s4*at*(ntot - na)))/((k33*((ntot - na)) + k32*(atot - at)))
v_6 — s4 = s5 + at

k4*s4*(atot - at)
v_7 — s5 = s6

k5*s5
v_8 — s6 = na

k6*s6*(ntot - na)
v_9 — s6 = {0.1}s6o

k10*(s6 - s6o)

Parameters 0   18

Global parameters

Id Value
atot 4.0
k0 50.0
k1 550.0
k10 375.0
k2 9.8
k31 323.8
k32 76411.1
k33 57823.1
k34 23.7
k4 80.0
k5 9.7
k6 2000.0
k7 28.0
k8 85.7
k9 80.0
ki 1.0
n 4.0
ntot 1.0

Local parameters

Id Value Reaction

Rules 0   0   0

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition

Events 0

Trigger Assignments