BioModels Database logo

BioModels Database

spacer

BIOMD0000000254 - Bier2000_GlycolyticOscillation

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 10692299
Bier M, Bakker BM, Westerhoff HV.
How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment.
Biophys. J. 2000 Mar; 78(3): 1087-1093
Section of Plastic and Reconstructive Surgery, Dept. of Surgery MC 6035, University of Chicago, Chicago, Illinois 60637, USA. mbier@surgery.bsd.uchicago.edu  [more]
Model
Original Model: BIOMD0000000254.origin
Submitter: Vijayalakshmi Chelliah
Submission ID: MODEL1007260000
Submission Date: 26 Jul 2010 13:43:05 UTC
Last Modification Date: 08 Apr 2016 16:10:00 UTC
Creation Date: 26 Jul 2010 12:19:53 UTC
Encoders:  Vijayalakshmi Chelliah
   Martin Bier
set #1
bqbiol:isVersionOf Gene Ontology glycolytic process
set #2
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
Notes

This a model from the article:
How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment
Bier M, Bakker BM, Westerhoff HV. Biophys. J2000 Mar;78(3):1087-93. 10692299,
Abstract:
Of all the lifeforms that obtain their energy from glycolysis, yeast cells are among the most basic. Under certain conditions the concentrations of the glycolytic intermediates in yeast cells can oscillate. Individual yeast cells in a suspension can synchronize their oscillations to get in phase with each other. Although the glycolytic oscillations originate in the upper part of the glycolytic chain, the signaling agent in this synchronization appears to be acetaldehyde, a membrane-permeating metabolite at the bottom of the anaerobic part of the glycolytic chain. Here we address the issue of how a metabolite remote from the pacemaking origin of the oscillation may nevertheless control the synchronization. We present a quantitative model for glycolytic oscillations and their synchronization in terms of chemical kinetics. We show that, in essence, the common acetaldehyde concentration can be modeled as a small perturbation on the "pacemaker" whose effect on the period of the oscillations of cells in the same suspension is indeed such that a synchronization develops.

Model
Publication ID: 10692299 Submission Date: 26 Jul 2010 13:43:05 UTC Last Modification Date: 08 Apr 2016 16:10:00 UTC Creation Date: 26 Jul 2010 12:19:53 UTC
Mathematical expressions
Rules
Rate Rule (variable: Glucose_1) Rate Rule (variable: Glucose_2) Rate Rule (variable: ATP_1) Rate Rule (variable: ATP_2)
Assignment Rule (variable: Tsum) Assignment Rule (variable: Tdiff)    
Physical entities
Compartments Species
compartment Glucose_1 ATP_1 Glucose_2
ATP_2    
Global parameters
V_in k1 kp km
epsilon Tsum Tdiff  
Reactions (0)
Rules (6)
 
 Rate Rule (name: G1) d [ Glucose_1] / d t= V_in-k1*G1*T1
 
 Rate Rule (name: G2) d [ Glucose_2] / d t= V_in-k1*G2*T2
 
 Rate Rule (name: T1) d [ ATP_1] / d t= 2*k1*T1*G1-kp*T1/(km+T1)+epsilon*(T2-T1)
 
 Rate Rule (name: T2) d [ ATP_2] / d t= 2*k1*G2*T2-kp*T2/(km+T2)-epsilon*(T2-T1)
 
 Assignment Rule (name: Tsum) Tsum = T2+T1
 
 Assignment Rule (name: Tdiff) Tdiff = T2-T1
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Glucose_1
Compartment: compartment
Initial concentration: 6.6
 
 ATP_1
Compartment: compartment
Initial concentration: 7.6
 
 Glucose_2
Compartment: compartment
Initial concentration: 10.3
 
 ATP_2
Compartment: compartment
Initial concentration: 0.41
 
Global Parameters (7)
 
 V_in
Value: 0.36
Constant
 
 k1
Value: 0.02
Constant
 
   kp
Value: 6.0
Constant
 
   km
Value: 13.0
Constant
 
   epsilon
Value: 0.01
Constant
 
   Tsum
Value: NaN
 
   Tdiff
Value: NaN
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000254

Curator's comment: (updated: 26 Jul 2010 14:44:39 BST)

The model reproduces figure 3 of the reference publication. The model was integrated and simulated using Copasi v4.5.31.

spacer
spacer