From steady-state to synchronized yeast glycolytic oscillations I: model construction.

F.B. du Preez, D.D. van Niekerk, B.W. Kooi, J.M. Rohwer, J.L. Snoep

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. Using a small subset of experimental data, the original model was adapted by adjusting its parameter values in three optimization steps. Only small adaptations to the original model were required for realistic simulation of experimental data for limit-cycle oscillations. The greatest changes were required for parameter values for the phosphofructokinase reaction. The importance of ATP for the oscillatory mechanism and NAD(H) for inter-and intra-cellular communications and synchronization was evident in the optimization steps and simulation experiments. In an accompanying paper [du Preez F et al. (2012) FEBS J279, 2823-2836], we validate the model for a wide variety of experiments on oscillatory yeast cells. The results are important for re-use of detailed kinetic models in modular modeling approaches and for approaches such as that used in the Silicon Cell initiative. © 2012 FEBS.
Original languageEnglish
Pages (from-to)2810-2822
JournalThe FEBS Journal
Volume279
DOIs
Publication statusPublished - 2012

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Yeast
Yeasts
Phosphofructokinases
Glycolysis
Silicon
NAD
Adenosine Triphosphate
Cellular radio systems
Kinetics
Synchronization
Experiments
Cells

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du Preez, F.B. ; van Niekerk, D.D. ; Kooi, B.W. ; Rohwer, J.M. ; Snoep, J.L. / From steady-state to synchronized yeast glycolytic oscillations I: model construction. In: The FEBS Journal. 2012 ; Vol. 279. pp. 2810-2822.
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From steady-state to synchronized yeast glycolytic oscillations I: model construction. / du Preez, F.B.; van Niekerk, D.D.; Kooi, B.W.; Rohwer, J.M.; Snoep, J.L.

In: The FEBS Journal, Vol. 279, 2012, p. 2810-2822.

Research output: Contribution to JournalArticleAcademicpeer-review

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