Transduction of Intracellular and Intercellular Dynamics in Yeast Glycolytic Oscillations
Catherine
Lloyd
Auckland Bioengineering Institute, The University of Auckland
Model Status
This model runs to reproduce published results in COR and OpenCell. The units are consistent throughout. This model currently reproduces Figure 4. The initial conditions were estimated and the model run to steady state to yield precise values, changing any parameters will necessitate repeating this procedure.
Model Structure
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.
The original paper reference is cited below:
Transduction of Intracellular and Intercellular Dynamics in Yeast Glycolytic Oscillations, Jana Wolf, Jutta Passarge, Oscar J.G. Somsen, Jacky L. Snoep, Reinhart Heinrich and Hans V. Westerhoff, 2000, Biophysical Journal, 78, 1145-1153. PubMed ID: 10692304
schematic diagram
Schematic representation of the model. The nine variable model includes all shown metabolites as variables where S1 represents glucose, S2 represents fructose-1,6-bisphosphate, S3 represents the triphopshate pool, S4 represents 3-phosphoglycerate, S5 represents pyruvate, S6 represents intracellular acetaldehyde, S6,ex represents extracellular acetaldehyde, A2 is ADP, A3 is ATP, N1 is NAD+ and N2 is NADH.
HeinrichReinhartAtotal adenosine phosphates2000-03S6_exextracellular acetaldehydeCatherine Lloydoscillatorintercellular dynamicsmetabolismglycolysisintracellular dynamicssignal transduction10692304VWesterhoffHans115378Transduction of Intracellular and Intercellular Dynamics in Yeast Glycolytic Oscillations1145c.lloyd@auckland.ac.nzPassargeJutta100000.15S5pyruvateThis is the CellML description of Wolf et al's mathematical model of
intracellular and intercellular dynamics in yeast glycolytic
oscillations.2007-06-01T00:00:00+00:00N2NADHS1glucoseS2fructose-1,6-bisphosphateWolfJanaThe new version of this model has been re-coded to remove the reaction element and replace it with a simple MathML description of the model reaction kinetics. This is thought to be truer to the original publication, and information regarding the enzyme kinetics etc will later be added to the metadata through use of an ontology.
The model runs in the PCEnv simulator but gives a flat output.S43-phosphoglycerateS3triose phosphate poolA dynamic model of glycolytic oscillations in yeastyeastS6intracellular acetaldehydeLSnoepJackyBiophysical JournalMayLloydCatherine2007-06-05T10:49:58+12:00A3ATPMayLloydCatherinekeywordGJSomsenOscarThe University of Auckland, Auckland Bioengineering InstituteAuckland Bioengineering InstituteThe University of Auckland