Vaseghi, Baumeister, Rizzi, Reuss, 1999

Model Status

This CellML model is known to run in both PCEnv and COR, however at present it does not seem to be recreating the published results - possibly beause we need to include a description of a glucose pulse in the CellML model. We are continuing to work on the model. The units have been checked and they are consistent.

Model Structure

Metabolic networks are highly complex nonlinear reaction systems whose functions are tightly co-ordinated and regulated by feedback mechanisms to meet the physiological demands of living organisms. Dynamic mathematical models of metabolic networks allow prediction as to how metabolism will respond to manipulation.

The pentose phosphate pathway can provide an alternative to glycolysis plus the TCA cycle for the complete oxidation of glucose. However, it is thought that its main role is not glucose oxidation, but to provide the cell with a source of NADPH for biosynthetic reactions and to supply pentose phosphate for the synthesis of nucleotides.

In 1999, Sam Vaseghi, Anja Baumeister, Manfred Rizzi and Matthias Reuss published a kinetic model of the pentose phosphate pathway in the yeast Saccharomyces cerevisiae (see below). They studied the in vivo dynamics of the pathway under conditions of continuous culture in order to elucidate important regulation phenomena responsible for co-ordinating the fluxes between glycolysis and the pentose phosphate pathway. They constructed the model by combining knowledge about enzyme kinetics with the stoichiometry of metabolic pathways based on the same principles used by Rizzi et al in their model of glycolysis (1997) (see The Glycolysis Pathway Model, 1997).

The complete original paper reference is cited below:

In Vivo Dynamics of the Pentose Phosphate Pathway in Saccharomyces cerevisiae , Sam Vaseghi, Anja Baumeister, Manfred Rizzi and Matthias Reuss, 1999, Metabolic Engineering , 1, 128-140. (A PDF version of the article is available to subscribers on the Metabolic Engineering website.) PubMed ID: 10935926

The raw CellML description of the pentose phosphate pathway model can be downloaded in various formats as described in . For an example of a more complete documentation of another real reaction pathway, see The Bhalla Iyengar EGF Pathway Model, 1999.

A rendering of the pentose phosphate pathway in Saccharomyces cerevisiae. Metabolites are represented by rounded rectangles, catalysts are represented by ellipses and reactions by arrows. The action of the inhibitor MgATP on the enzymes G6PDH and 6PGDH is represented by dashed lines.

In CellML, models are thought of as connected networks of discrete components. These components may correspond to physiologically separated regions or chemically distinct objects, or may be useful modelling abstractions. This model has 36 components representing chemically distinct objects (15 metabolites, 10 enzymes one inhibitor and 10 reactions) and one component defined for modelling convenience which stores the universal variable time. Because this model has so many components, its CellML rendering would be complex. For an example of a CellML rendering of a reaction pathway see The Bhalla Iyengar EGF Pathway Model, 1999.

Source
Derived from workspace Vaseghi, Baumeister, Rizzi, Reuss, 1999 at changeset babcfa697e8f.
Collaboration
To begin collaborating on this work, please use your git client and issue this command: