Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.
This CellML runs in both OpenCell and COR to recreate the published results. The units have been checked and they are consistent. This particular CellML model is based on a Matlab file which, in turn, was exported from the working SBML file in the BioModels database. There are several subtle differences between the published paper and the working Matlab code which have been previously documented by the BioModels curators. In brief these are: in the kinetic law for ADH the species a should denote NAD and b Ethanol the last term in the equation should read bpq/(Kib Kiq Kp) and the rate equation for the PFK contains two errors: the R term should read: R = 1 + lambda1 + lambda2 + gR lambda1 lambda2 and the last term in the L equation should be squared. Also there are slight differences in the parameterisation of the model depending on whether it comes from the JWS or the BioModels database and, for Vmax values, please note that there is a conversion factor of approxinately 270 to convert from U/mg-protein as shown in Table 1 of the paper to mmol/(min*L_cytosol).
ABSTRACT: This paper examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes. In nongrowing, anaerobic, compressed Saccharomyces cerevisiae the values of the kinetic parameters of most glycolytic enzymes were determined. For the other enzymes appropriate literature values were collected. By inserting these values into a kinetic model for glycolysis, fluxes and metabolites were calculated. Under the same conditions fluxes and metabolite levels were measured. In our first model, branch reactions were ignored. This model failed to reach the stable steady state that was observed in the experimental flux measurements. Introduction of branches towards trehalose, glycogen, glycerol and succinate did allow such a steady state. The predictions of this branched model were compared with the empirical behavior. Half of the enzymes matched their predicted flux in vivo within a factor of 2. For the other enzymes it was calculated what deviation between in vivo and in vitro kinetic characteristics could explain the discrepancy between in vitro rate and in vivo flux.
The original paper reference is cited below:
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry, Bas Teusink, Jutta Passarge, Corinne A. Reijenga, Eugenia Esgalhado, Coen C. van der Weijden, Mike Schepper, Michael C. Walsh, Barbara M. Bakker, Karel van Dam, Hans V. Westerhoff, and Jacky L. Snoep, 2000, European Journal of Biochemistry, 267, 5313-5329. PubMed ID: 10951190
|Schematic diagram of the glycolysis pathway model described by Teusink et al. 2000. Reactions in boxes show the branches introduced in the extended model.|