Lloyd Catherine May c.lloyd@auckland.ac.nz The University of Auckland The Bioengineering Institute 2002-06-05 Including the species N-Formylglycinamidine ribonucleotide which is the intermediate species from Rxn 4 to Rxn 5. Cuellar Autumn A 2003-09-11 Changed the model name so the model loads in the database easier. Cuellar Autumn A 2003-04-05 The University of Auckland, Bioengineering Institute A Generic Model Of Purine Nucleotide Synthesis Below is a CellML description of a general model of purine nucleotide synthesis. 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 $\frac{d \mathrm{PRPP}}{d \mathrm{time}}=\mathrm{delta\_PRPP\_rxn0}$ $\frac{d \mathrm{Glutamine}}{d \mathrm{time}}=\mathrm{delta\_Glutamine\_rxn1}+\mathrm{delta\_Glutamine\_rxn0}+\mathrm{delta\_Glutamine\_rxn4}+\mathrm{delta\_Glutamine\_rxn13}$ $\frac{d \mathrm{Glutamate}}{d \mathrm{time}}=\mathrm{delta\_Glutamate\_rxn0}+\mathrm{delta\_Glutamate\_rxn4}+\mathrm{delta\_Glutamate\_rxn13}+\mathrm{delta\_Glutamate\_rxn1}$ $\frac{d \mathrm{Phosphoribosylamine}}{d \mathrm{time}}=\mathrm{delta\_Phosphoribosylamine\_rxn0}+\mathrm{delta\_Phosphoribosylamine\_rxn2}$ $\frac{d \mathrm{Glycinamide\_ribonucleotide}}{d \mathrm{time}}=\mathrm{delta\_Glycinamide\_ribonucleotide\_rxn2}+\mathrm{delta\_Glycinamide\_ribonucleotide\_rxn3}$ $\frac{d \mathrm{Glycine}}{d \mathrm{time}}=\mathrm{delta\_Glycine\_rxn2}$ $\frac{d \mathrm{ATP}}{d \mathrm{time}}=\mathrm{delta\_ATP\_rxn1}+\mathrm{delta\_ATP\_rxn2}+\mathrm{delta\_ATP\_rxn4}+\mathrm{delta\_ATP\_rxn5}+\mathrm{delta\_ATP\_rxn7}+\mathrm{delta\_ATP\_rxn13}$ $\frac{d \mathrm{ADP}}{d \mathrm{time}}=\mathrm{delta\_ADP\_rxn1}+\mathrm{delta\_ADP\_rxn2}+\mathrm{delta\_ADP\_rxn4}+\mathrm{delta\_ADP\_rxn5}+\mathrm{delta\_ADP\_rxn7}$ $\frac{d \mathrm{Pi}}{d \mathrm{time}}=\mathrm{delta\_Pi\_rxn1}+\mathrm{delta\_Pi\_rxn2}+\mathrm{delta\_Pi\_rxn4}+\mathrm{delta\_Pi\_rxn5}+\mathrm{delta\_Pi\_rxn7}+\mathrm{delta\_Pi\_rxn10}+\mathrm{delta\_Pi\_rxn13}$ $\frac{d \mathrm{NH4}}{d \mathrm{time}}=\mathrm{delta\_NH4\_rxn1}$ $\frac{d H}{d \mathrm{time}}=\mathrm{delta\_H\_rxn1}+\mathrm{delta\_H\_rxn12}$ $\frac{d \mathrm{H2O}}{d \mathrm{time}}=\mathrm{delta\_H2O\_rxn6}+\mathrm{delta\_H2O\_rxn9}+\mathrm{delta\_H2O\_rxn4}+\mathrm{delta\_H2O\_rxn12}+\mathrm{delta\_H2O\_rxn13}$ $\frac{d \mathrm{HCO3}}{d \mathrm{time}}=\mathrm{delta\_HCO3\_rxn6}$ $\frac{d \mathrm{THF}}{d \mathrm{time}}=\mathrm{delta\_THF\_rxn3}+\mathrm{delta\_THF\_rxn8}$ $\frac{d \mathrm{N\_Formyl\_THF}}{d \mathrm{time}}=\mathrm{delta\_N\_Formyl\_THF\_rxn3}+\mathrm{delta\_N\_Formyl\_THF\_rxn8}$ $\frac{d \mathrm{N\_Formylglycinamide\_ribonucleotide}}{d \mathrm{time}}=\mathrm{delta\_N\_Formylglycinamide\_ribonucleotide\_rxn3}+\mathrm{delta\_N\_Formylglycinamide\_ribonucleotide\_rxn4}$ $\frac{d \mathrm{N\_Formylglycinamidine\_ribonucleotide}}{d \mathrm{time}}=\mathrm{delta\_N\_Formylglycinamidine\_ribonucleotide\_rxn4}+\mathrm{delta\_N\_Formylglycinamidine\_ribonucleotide\_rxn5}$ $\frac{d \mathrm{Aminoimidazole\_ribonucleotide}}{d \mathrm{time}}=\mathrm{delta\_Aminoimidazole\_ribonucleotide\_rxn5}+\mathrm{delta\_Aminoimidazole\_ribonucleotide\_rxn6}$ $\frac{d \mathrm{Carboxyaminoimidazole\_ribonucleotide}}{d \mathrm{time}}=\mathrm{delta\_Carboxyaminoimidazole\_ribonucleotide\_rxn6}+\mathrm{delta\_Carboxyaminoimidazole\_ribonucleotide\_rxn7}$ $\frac{d \mathrm{Aminoimidazole\_carboxamide\_ribonucleotide}}{d \mathrm{time}}=\mathrm{delta\_Aminoimidazole\_carboxamide\_ribonucleotide\_rxn7}+\mathrm{delta\_Aminoimidazole\_carboxamide\_ribonucleotide\_rxn8}$ $\frac{d \mathrm{Formamidoimidazole\_carboxamide\_ribonucleotide}}{d \mathrm{time}}=\mathrm{delta\_Formamidoimidazole\_carboxamide\_ribonucleotide\_rxn8}+\mathrm{delta\_Formamidoimidazole\_carboxamide\_ribonucleotide\_rxn9}$ $\frac{d \mathrm{IMP}}{d \mathrm{time}}=\mathrm{delta\_IMP\_rxn9}+\mathrm{delta\_IMP\_rxn10}+\mathrm{delta\_IMP\_rxn12}$ $\frac{d \mathrm{Pyrophosphate}}{d \mathrm{time}}=\mathrm{delta\_Pyrophosphate\_rxn1}$ $\frac{d \mathrm{Aspartate}}{d \mathrm{time}}=\mathrm{delta\_Aspartate\_rxn7}+\mathrm{delta\_Aspartate\_rxn10}$ $\frac{d \mathrm{Fumarate}}{d \mathrm{time}}=\mathrm{delta\_Fumarate\_rxn7}+\mathrm{delta\_Fumarate\_rxn11}$ $\frac{d \mathrm{Adenylosuccinate}}{d \mathrm{time}}=\mathrm{delta\_Adenylosuccinate\_rxn10}+\mathrm{delta\_Adenylosuccinate\_rxn11}$ $\frac{d \mathrm{AMP}}{d \mathrm{time}}=\mathrm{delta\_AMP\_rxn11}+\mathrm{delta\_AMP\_rxn13}$ $\frac{d \mathrm{GTP}}{d \mathrm{time}}=\mathrm{delta\_GTP\_rxn10}$ $\frac{d \mathrm{GDP}}{d \mathrm{time}}=\mathrm{delta\_GDP\_rxn10}$ $\frac{d \mathrm{Xanthine\_5\_phosphate}}{d \mathrm{time}}=\mathrm{delta\_Xanthine\_5\_phosphate\_rxn12}+\mathrm{delta\_Xanthine\_5\_phosphate\_rxn13}$ $\frac{d \mathrm{NAD}}{d \mathrm{time}}=\mathrm{delta\_NAD\_rxn12}$ $\frac{d \mathrm{NADH}}{d \mathrm{time}}=\mathrm{delta\_NADH\_rxn12}$ $\frac{d \mathrm{GMP}}{d \mathrm{time}}=\mathrm{delta\_GMP\_rxn13}$ $\mathrm{rate}=\frac{\mathrm{vmax0}\mathrm{PRPP}\mathrm{Glutamine}}{\mathrm{km0}+\mathrm{PRPP}+\mathrm{Glutamine}}$ $\mathrm{rate}=\mathrm{k1}\mathrm{Glutamate}\mathrm{NH4}\mathrm{Pyrophosphate}\mathrm{ATP}$ $\mathrm{rate}=\frac{\mathrm{Glycine}\mathrm{Phosphoribosylamine}\mathrm{ATP}\mathrm{vmax2}}{\mathrm{km2}+\mathrm{Glycine}+\mathrm{Phosphoribosylamine}+\mathrm{ATP}}$ $\mathrm{rate}=\frac{\mathrm{Glycinamide\_ribonucleotide}\mathrm{N\_Formyl\_THF}\mathrm{vmax3}}{\mathrm{km3}+\mathrm{Glycinamide\_ribonucleotide}+\mathrm{N\_Formyl\_THF}}$ $\mathrm{rate}=\frac{\mathrm{N\_Formylglycinamide\_ribonucleotide}\mathrm{H2O}\mathrm{Glutamine}\mathrm{ATP}\mathrm{vmax4}}{\mathrm{km4}+\mathrm{N\_Formylglycinamide\_ribonucleotide}+\mathrm{H2O}+\mathrm{Glutamine}+\mathrm{ATP}}$ $\mathrm{rate}=\frac{\mathrm{N\_Formylglycinamidine\_ribonucleotide}\mathrm{ATP}\mathrm{vmax5}}{\mathrm{km5}+\mathrm{N\_Formylglycinamidine\_ribonucleotide}+\mathrm{ATP}}$ $\mathrm{rate}=\frac{\mathrm{Aminoimidazole\_ribonucleotide}\mathrm{HCO3}\mathrm{vmax6}}{\mathrm{km6}+\mathrm{Aminoimidazole\_ribonucleotide}+\mathrm{HCO3}}$ $\mathrm{rate}=\frac{\mathrm{Carboxyaminoimidazole\_ribonucleotide}\mathrm{ATP}\mathrm{Aspartate}\mathrm{vmax7}}{\mathrm{km7}+\mathrm{Carboxyaminoimidazole\_ribonucleotide}+\mathrm{ATP}+\mathrm{Aspartate}}$ $\mathrm{rate}=\frac{\mathrm{N\_Formyl\_THF}\mathrm{Aminoimidazole\_carboxamide\_ribonucleotide}\mathrm{vmax8}}{\mathrm{km8}+\mathrm{Aminoimidazole\_carboxamide\_ribonucleotide}+\mathrm{vmax8}}$ $\mathrm{rate}=\frac{\mathrm{Formamidoimidazole\_carboxamide\_ribonucleotide}\mathrm{vmax9}}{\mathrm{km9}+\mathrm{Formamidoimidazole\_carboxamide\_ribonucleotide}}$ $\mathrm{rate}=\frac{\mathrm{GTP}\mathrm{Aspartate}\mathrm{IMP}\mathrm{vmax10}}{\mathrm{km10}+\mathrm{GTP}+\mathrm{Aspartate}+\mathrm{IMP}}$ $\mathrm{rate}=\frac{\mathrm{Adenylosuccinate}\mathrm{vmax11}}{\mathrm{km11}+\mathrm{Adenylosuccinate}}$ $\mathrm{rate}=\frac{\mathrm{IMP}\mathrm{H2O}\mathrm{NAD}\mathrm{vmax12}}{\mathrm{km12}+\mathrm{IMP}+\mathrm{H2O}+\mathrm{NAD}}$ $\mathrm{rate}=\frac{\mathrm{Xanthine\_5\_phosphate}\mathrm{H2O}\mathrm{Glutamine}\mathrm{ATP}\mathrm{vmax13}}{\mathrm{km13}+\mathrm{Xanthine\_5\_phosphate}+\mathrm{H2O}+\mathrm{Glutamine}+\mathrm{ATP}}$