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


METHODS
The mathematical models described here have been submitted to the JWS Online Cellular Systems Modelling Database and can be accessed at http://jjj.biochem.sun.ac.za/database/dupreez/index.html.
Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK.
Franco B
FB
du Preez
David D
DD
van Niekerk
Bob
B
Kooi
Johann M
JM
Rohwer
Jacky L
JL
Snoep
D000079:Acetaldehyde / Q000378:metabolism; D000251:Adenosine Triphosphatases / Q000378:metabolism; D002450:Cell Communication / Q000502:physiology; D003198:Computer Simulation; D016208:Databases, Factual; D006019:Glycolysis; D007700:Kinetics; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D009243:NAD / Q000378:metabolism; D025221:Phosphofructokinases / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D049490:Systems Biology
D009243:NAD; D025221:Phosphofructokinases; D000251:Adenosine Triphosphatases; D000079:Acetaldehyde