Lloyd Catherine May c.lloyd@auckland.ac.nz The University of Auckland The Bioengineering Institute 2002-06-14 Added more metadata. Lloyd Catherine May 2002-07-22 The University of Auckland, Bioengineering Institute A Generic Model Of Cholesterol Synthesis Below is a CellML description of a general model of cholesterol 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 $\frac{d \mathrm{Acetyl\_CoA}}{d \mathrm{time}}=\mathrm{delta\_Acetyl\_CoA\_rxn0}+\mathrm{delta\_Acetyl\_CoA\_rxn1}$ $\frac{d \mathrm{CoA\_SH}}{d \mathrm{time}}=\mathrm{delta\_CoA\_SH\_rxn0}+\mathrm{delta\_CoA\_SH\_rxn1}+\mathrm{delta\_CoA\_SH\_rxn2}$ $\frac{d \mathrm{Acetoacetyl\_CoA}}{d \mathrm{time}}=\mathrm{delta\_Acetoacetyl\_CoA\_rxn0}+\mathrm{delta\_Acetoacetyl\_CoA\_rxn1}$ $\frac{d \mathrm{Hydroxymethylglutaryl\_CoA}}{d \mathrm{time}}=\mathrm{delta\_Hydroxymethylglutaryl\_CoA\_rxn1}+\mathrm{delta\_Hydroxymethylglutaryl\_CoA\_rxn2}$ $\frac{d \mathrm{Mevalonate}}{d \mathrm{time}}=\mathrm{delta\_Mevalonate\_rxn2}+\mathrm{delta\_Mevalonate\_rxn3}$ $\frac{d \mathrm{Phosphomevalonate\_5}}{d \mathrm{time}}=\mathrm{delta\_Phosphomevalonate\_5\_rxn3}+\mathrm{delta\_Phosphomevalonate\_5\_rxn4}$ $\frac{d \mathrm{Pyrophosphomevalonate\_5}}{d \mathrm{time}}=\mathrm{delta\_Pyrophosphomevalonate\_5\_rxn4}+\mathrm{delta\_Pyrophosphomevalonate\_5\_rxn5}$ $\frac{d \mathrm{Isopentenyl\_pyrophosphate}}{d \mathrm{time}}=\mathrm{delta\_Isopentenyl\_pyrophosphate\_rxn5}+\mathrm{delta\_Isopentenyl\_pyrophosphate\_rxn6}+\mathrm{delta\_Isopentenyl\_pyrophosphate\_rxn7}+\mathrm{delta\_Isopentenyl\_pyrophosphate\_rxn8}$ $\frac{d \mathrm{Dimethylallyl\_pyrophosphate}}{d \mathrm{time}}=\mathrm{delta\_Dimethylallyl\_pyrophosphate\_rxn6}+\mathrm{delta\_Dimethylallyl\_pyrophosphate\_rxn7}$ $\frac{d \mathrm{NADPH}}{d \mathrm{time}}=\mathrm{delta\_NADPH\_rxn2}+\mathrm{delta\_NADPH\_rxn9}+\mathrm{delta\_NADPH\_rxn10}$ $\frac{d \mathrm{NADP}}{d \mathrm{time}}=\mathrm{delta\_NADP\_rxn2}+\mathrm{delta\_NADP\_rxn9}+\mathrm{delta\_NADP\_rxn10}$ $\frac{d H}{d \mathrm{time}}=\mathrm{delta\_H\_rxn2}+\mathrm{delta\_H\_rxn9}+\mathrm{delta\_H\_rxn10}$ $\frac{d \mathrm{ATP}}{d \mathrm{time}}=\mathrm{delta\_ATP\_rxn3}+\mathrm{delta\_ATP\_rxn4}+\mathrm{delta\_ATP\_rxn5}$ $\frac{d \mathrm{ADP}}{d \mathrm{time}}=\mathrm{delta\_ADP\_rxn3}+\mathrm{delta\_ADP\_rxn4}+\mathrm{delta\_ADP\_rxn5}$ $\frac{d \mathrm{Pi}}{d \mathrm{time}}=\mathrm{delta\_Pi\_rxn5}$ $\frac{d \mathrm{CO2}}{d \mathrm{time}}=\mathrm{delta\_CO2\_rxn5}$ $\frac{d \mathrm{Geranyl\_pyrophosphate}}{d \mathrm{time}}=\mathrm{delta\_Geranyl\_pyrophosphate\_rxn7}+\mathrm{delta\_Geranyl\_pyrophosphate\_rxn8}$ $\frac{d \mathrm{Farnesyl\_pyrophosphate}}{d \mathrm{time}}=\mathrm{delta\_Farnesyl\_pyrophosphate\_rxn8}+\mathrm{delta\_Farnesyl\_pyrophosphate\_rxn9}$ $\frac{d \mathrm{PPi}}{d \mathrm{time}}=\mathrm{delta\_PPi\_rxn7}+\mathrm{delta\_PPi\_rxn8}+\mathrm{delta\_PPi\_rxn9}$ $\frac{d \mathrm{Squalene}}{d \mathrm{time}}=\mathrm{delta\_Squalene\_rxn9}+\mathrm{delta\_Squalene\_rxn10}$ $\frac{d \mathrm{Squalene\_2\_3\_epoxide}}{d \mathrm{time}}=\mathrm{delta\_Squalene\_2\_3\_epoxide\_rxn10}+\mathrm{delta\_Squalene\_2\_3\_epoxide\_rxn11}$ $\frac{d \mathrm{O2}}{d \mathrm{time}}=\mathrm{delta\_O2\_rxn10}$ $\frac{d \mathrm{H2O}}{d \mathrm{time}}=\mathrm{delta\_H2O\_rxn10}$ $\frac{d \mathrm{Lanosterol}}{d \mathrm{time}}=\mathrm{delta\_Lanosterol\_rxn11}+\mathrm{delta\_Lanosterol\_rxn12}$ $\frac{d \mathrm{Cholesterol}}{d \mathrm{time}}=\mathrm{delta\_Cholesterol\_rxn12}$ $\mathrm{rate}=\frac{\mathrm{Acetyl\_CoA}\mathrm{vmax0}}{\mathrm{km0}+\mathrm{Acetyl\_CoA}}$ $\mathrm{rate}=\frac{\mathrm{Acetoacetyl\_CoA}\mathrm{Acetyl\_CoA}\mathrm{vmax1}}{\mathrm{km1}+\mathrm{Acetoacetyl\_CoA}+\mathrm{Acetyl\_CoA}}$ $\mathrm{rate}=\frac{\mathrm{Mevalonate}\mathrm{ATP}\mathrm{vmax3}}{\mathrm{km3}+\mathrm{Mevalonate}+\mathrm{ATP}}$ $\mathrm{rate}=\frac{\mathrm{Phosphomevalonate\_5}\mathrm{ATP}\mathrm{vmax4}}{\mathrm{km4}+\mathrm{Phosphomevalonate\_5}+\mathrm{ATP}}$ $\mathrm{rate}=\frac{\mathrm{ATP}\mathrm{Pyrophosphomevalonate\_5}\mathrm{vmax5}}{\mathrm{km5}+\mathrm{ATP}+\mathrm{Pyrophosphomevalonate\_5}}$ $\mathrm{rate}=\mathrm{k6}\mathrm{Isopentenyl\_pyrophosphate}+-(\mathrm{k6\_}\mathrm{Dimethylallyl\_pyrophosphate})$ $\mathrm{rate}=\frac{\mathrm{Dimethylallyl\_pyrophosphate}\mathrm{Isopentenyl\_pyrophosphate}\mathrm{vmax7}}{\mathrm{km7}+\mathrm{Dimethylallyl\_pyrophosphate}+\mathrm{Isopentenyl\_pyrophosphate}}$ $\mathrm{rate}=\frac{\mathrm{Isopentenyl\_pyrophosphate}\mathrm{Geranyl\_pyrophosphate}\mathrm{vmax8}}{\mathrm{km8}+\mathrm{Isopentenyl\_pyrophosphate}+\mathrm{Geranyl\_pyrophosphate}}$ $\mathrm{rate}=\frac{\mathrm{NADPH}\mathrm{Farnesyl\_pyrophosphate}H\mathrm{vmax9}}{\mathrm{km9}+\mathrm{NADPH}+\mathrm{Farnesyl\_pyrophosphate}+H}$ $\mathrm{rate}=\frac{H\mathrm{Squalene}\mathrm{NADPH}\mathrm{O2}\mathrm{vmax10}}{\mathrm{km10}+H+\mathrm{Squalene}+\mathrm{NADPH}+\mathrm{O2}}$ $\mathrm{rate}=\frac{\mathrm{Squalene\_2\_3\_epoxide}\mathrm{vmax11}}{\mathrm{km11}+\mathrm{Squalene\_2\_3\_epoxide}}$ $\mathrm{rate}=\mathrm{k12}\mathrm{Lanosterol}$