Lloyd Catherine May c.lloyd@auckland.ac.nz The University of Auckland The Bioengineering Institute 2002-05-31 Changed the model name so the model loads in the database easier. Cuellar Autumn A 2003-04-05 Added more metadata. Lloyd Catherine May 2002-07-22 The University of Auckland, Bioengineering Institute A Generic Model Of The Pentose Phosphate Pathway Below is a CellML description of a general model of the metabolic pentose phosphate pathway. It is not based on a specific published mathematical model, but instead it is based on a textbook defined pathway. The general sequential structure and all the reactant, product and enzyme components are included. Michaelis-Menten enzyme kinetics are assumed. The purpose of this description is to illustrate how CellML can be used to model a general metabolic pathway. Catherine Lloyd Homo sapiens keyword metabolism Bronk J Ramsey Human Metabolism 1999 Addison Wesley Longman Limited location England $\frac{d \mathrm{Glucose\_6\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Glucose\_6\_phosphate\_rxn0}$ $\frac{d \mathrm{Phosphoglucono\_lactone\_6}}{d \mathrm{time}}=\mathrm{delta\_Phosphoglucono\_lactone\_6\_rxn0}+\mathrm{delta\_Phosphoglucono\_lactone\_6\_rxn1}$ $\frac{d \mathrm{Phosphogluconate\_6}}{d \mathrm{time}}=\mathrm{delta\_Phosphogluconate\_6\_rxn1}+\mathrm{delta\_Phosphogluconate\_6\_rxn2}$ $\frac{d \mathrm{Ribulose\_5\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Ribulose\_5\_phosphate\_rxn2}+\mathrm{delta\_Ribulose\_5\_phosphate\_rxn3}+\mathrm{delta\_Ribulose\_5\_phosphate\_rxn4}$ $\frac{d \mathrm{Xylulose\_5\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Xylulose\_5\_phosphate\_rxn3}+\mathrm{delta\_Xylulose\_5\_phosphate\_rxn7}+\mathrm{delta\_Xylulose\_5\_phosphate\_rxn5}$ $\frac{d \mathrm{Ribose\_5\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Ribose\_5\_phosphate\_rxn4}+\mathrm{delta\_Ribose\_5\_phosphate\_rxn5}$ $\frac{d \mathrm{Glyceraldehyde\_3\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Glyceraldehyde\_3\_phosphate\_rxn5}+\mathrm{delta\_Glyceraldehyde\_3\_phosphate\_rxn10}+\mathrm{delta\_Glyceraldehyde\_3\_phosphate\_rxn6}+\mathrm{delta\_Glyceraldehyde\_3\_phosphate\_rxn7}$ $\frac{d \mathrm{Sedoheptulose\_7\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Sedoheptulose\_7\_phosphate\_rxn5}+\mathrm{delta\_Sedoheptulose\_7\_phosphate\_rxn6}$ $\frac{d \mathrm{Erythrose\_4\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Erythrose\_4\_phosphate\_rxn6}+\mathrm{delta\_Erythrose\_4\_phosphate\_rxn7}$ $\frac{d \mathrm{Fructose\_6\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Fructose\_6\_phosphate\_rxn6}+\mathrm{delta\_Fructose\_6\_phosphate\_rxn9}+\mathrm{delta\_Fructose\_6\_phosphate\_rxn7}+\mathrm{delta\_Fructose\_6\_phosphate\_rxn8}$ $\frac{d \mathrm{NADP}}{d \mathrm{time}}=\mathrm{delta\_NADP\_rxn0}+\mathrm{delta\_NADP\_rxn2}$ $\frac{d \mathrm{NADPH}}{d \mathrm{time}}=\mathrm{delta\_NADPH\_rxn0}+\mathrm{delta\_NADPH\_rxn2}$ $\frac{d H}{d \mathrm{time}}=\mathrm{delta\_H\_rxn0}$ $\frac{d \mathrm{H2O}}{d \mathrm{time}}=\mathrm{delta\_H2O\_rxn1}+\mathrm{delta\_H2O\_rxn9}$ $\frac{d \mathrm{CO2}}{d \mathrm{time}}=\mathrm{delta\_CO2\_rxn2}$ $\frac{d \mathrm{Fructose\_1\_6\_bisphosphate}}{d \mathrm{time}}=\mathrm{delta\_Fructose\_1\_6\_bisphosphate\_rxn8}+\mathrm{delta\_Fructose\_1\_6\_bisphosphate\_rxn9}+\mathrm{delta\_Fructose\_1\_6\_bisphosphate\_rxn10}$ $\frac{d \mathrm{Pi}}{d \mathrm{time}}=\mathrm{delta\_Pi\_rxn9}$ $\frac{d \mathrm{ATP}}{d \mathrm{time}}=\mathrm{delta\_ATP\_rxn8}$ $\frac{d \mathrm{ADP}}{d \mathrm{time}}=\mathrm{delta\_ADP\_rxn8}$ $\mathrm{rate}=\frac{\mathrm{vmax0}\mathrm{Glucose\_6\_phosphate}\mathrm{NADP}}{\mathrm{km0}+\mathrm{Glucose\_6\_phosphate}+\mathrm{NADP}}$ $\mathrm{rate}=\frac{\mathrm{Phosphoglucono\_lactone\_6}\mathrm{H2O}\mathrm{vmax1}}{\mathrm{km1}+\mathrm{H2O}+\mathrm{Phosphoglucono\_lactone\_6}}$ $\mathrm{rate}=\frac{\mathrm{Phosphogluconate\_6}\mathrm{NADP}\mathrm{vmax2}}{\mathrm{km2}+\mathrm{NADP}+\mathrm{Phosphogluconate\_6}}$ $\mathrm{rate}=\frac{\mathrm{ATP}\mathrm{Fructose\_6\_phosphate}\mathrm{vmax8}}{\mathrm{km8}+\mathrm{ATP}+\mathrm{Fructose\_6\_phosphate}}$ $\mathrm{rate}=\frac{\mathrm{H2O}\mathrm{Fructose\_1\_6\_bisphosphate}\mathrm{vmax9}}{\mathrm{km9}+\mathrm{H2O}+\mathrm{Fructose\_1\_6\_bisphosphate}}$