Traditional biochemistry studies individual components of a system in isolation. It is thought that, once all the components have been characterized in vitro, the behaviour of the system can be tackled by using the properties of the individual components. The authors of this model [1] attempt to do justice to this idea by using kinetic properties of individual enzymes determined in vitro to build a computational model of the glycolytic pathway in Saccharomyces cerevisiae, and then compare the behaviour of the computational system, in terms of fluxes and metabolite levels, to that of the system in vivo. This contrasts with usual model building, where the aim tends to be to show the possibility of types of behaviour or to describe behaviour often by fitting rate constants and other parameters until the behaviour of the pathway is correctly simulated. In effect, the authors use a computational model to assess the conception that kinetic properties measured in vitro can be used to determine the behaviour of the system in vivo.

In order to be able to reconstitute the entire glycolytic pathway using individual components, the authors experimentally determined the individual enzyme kinetic properties using the same yeast source and assay conditions for each enzyme. A differential equations model was then constructed using the measured kinetic parameters of each enzyme. Additionally, during model construction and simulation, the authors did not adjust kinetic parameters to fit the model to in vivo pathway behaviour. To compare the systems in vivo behaviour with the model, flux and metabolite levels were measured in both the model and in the yeast source. Two versions of the model were created, one using the unbranched glycolytic pathway and one incorporating branches in the pathway (see Figure 1).

Whereas the unbranched version failed to reach a steady state, as some of the metabolites (fructose-1,6-bisphosphate, D-glyceraldehyde-3-phosphate and glycerol phosphate) rose to very high levels, the branched version did attain a steady state. The failure of the unbranched version to reach a steady state was due to a discrepancy in the flux of the pathway upstream of fructose-1,6-bisphosphate and downstream of D-glyceraldehyde-3-phsophate caused by the moiety conservation of the oxidized species in the lower part of glycolysis. The glycerol and succinate branches in the branched version, relieved this moiety conservation by offering alternative end products. In general, most of the metabolite levels did not differ by more than a factor of two from the experimental values. When the activities of the individual enzymes were compared, half of the enzymes the in vitro kinetics did describe the in vivo activity within a factor of two.

The model of Teusink et al not only offers an unusual approach to modeling by adhering strictly to in vitro determined kinetic parameters, but preparations for the model building has led to a comprehensive and complete description of the glycolytic enzymes under a standard set of conditions.

Figure 1: Scheme of the model, from [1]