Lloyd Catherine May c.lloyd@auckland.ac.nz The University of Auckland The Bioengineering Institute 2002-06-14 The University of Auckland, Bioengineering Institute A Generic Model Of Fatty Acid Activation And Oxidation Below is a CellML description of a general model of fatty acid activation and oxidation. 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 $\frac{d \mathrm{fatty\_acid}}{d \mathrm{time}}=\mathrm{delta\_fatty\_acid\_rxn0}$ $\frac{d \mathrm{ATP}}{d \mathrm{time}}=\mathrm{delta\_ATP\_rxn0}$ $\frac{d \mathrm{Pyrophosphate}}{d \mathrm{time}}=\mathrm{delta\_Pyrophosphate\_rxn0}$ $\frac{d \mathrm{Fatty\_acyl\_CoA}}{d \mathrm{time}}=\mathrm{delta\_Fatty\_acyl\_CoA\_rxn1}+\mathrm{delta\_Fatty\_acyl\_CoA\_rxn2}$ $\frac{d \mathrm{AMP}}{d \mathrm{time}}=\mathrm{delta\_AMP\_rxn1}$ $\frac{d \mathrm{CoA\_SH}}{d \mathrm{time}}=\mathrm{delta\_CoA\_SH\_rxn1}+\mathrm{delta\_CoA\_SH\_rxn5}$ $\frac{d \mathrm{Acyladenylate\_mixed\_anhydride}}{d \mathrm{time}}=\mathrm{delta\_Acyladenylate\_mixed\_anhydride\_rxn0}+\mathrm{delta\_Acyladenylate\_mixed\_anhydride\_rxn1}$ $\frac{d \mathrm{trans\_Enol\_CoA}}{d \mathrm{time}}=\mathrm{delta\_trans\_Enol\_CoA\_rxn2}+\mathrm{delta\_trans\_Enol\_CoA\_rxn3}$ $\frac{d \mathrm{L\_3\_Hydroxyacyl\_CoA}}{d \mathrm{time}}=\mathrm{delta\_L\_3\_Hydroxyacyl\_CoA\_rxn3}+\mathrm{delta\_L\_3\_Hydroxyacyl\_CoA\_rxn4}$ $\frac{d \mathrm{beta\_Ketoacyl\_CoA}}{d \mathrm{time}}=\mathrm{delta\_beta\_Ketoacyl\_CoA\_rxn4}+\mathrm{delta\_beta\_Ketoacyl\_CoA\_rxn5}$ $\frac{d \mathrm{Acetyl\_CoA}}{d \mathrm{time}}=\mathrm{delta\_Acetyl\_CoA\_rxn5}$ $\frac{d \mathrm{Fatty\_acyl\_CoA\_minus\_2C}}{d \mathrm{time}}=\mathrm{delta\_Fatty\_acyl\_CoA\_minus\_2C\_rxn5}$ $\frac{d \mathrm{FAD}}{d \mathrm{time}}=\mathrm{delta\_FAD\_rxn2}$ $\frac{d \mathrm{FADH2}}{d \mathrm{time}}=\mathrm{delta\_FADH2\_rxn2}$ $\frac{d \mathrm{H2O}}{d \mathrm{time}}=\mathrm{delta\_H2O\_rxn3}$ $\frac{d \mathrm{NAD}}{d \mathrm{time}}=\mathrm{delta\_NAD\_rxn4}$ $\frac{d \mathrm{NADH}}{d \mathrm{time}}=\mathrm{delta\_NADH\_rxn4}$ $\frac{d H}{d \mathrm{time}}=\mathrm{delta\_H\_rxn4}$ $\mathrm{rate}=\frac{\mathrm{fatty\_acid}\mathrm{ATP}\mathrm{vmax0}}{\mathrm{km0}+\mathrm{fatty\_acid}+\mathrm{ATP}}$ $\mathrm{rate}=\frac{\mathrm{Acyladenylate\_mixed\_anhydride}\mathrm{CoA\_SH}\mathrm{vmax1}}{\mathrm{km1}+\mathrm{Acyladenylate\_mixed\_anhydride}+\mathrm{CoA\_SH}}$ $\mathrm{rate}=\frac{\mathrm{FAD}\mathrm{Fatty\_acyl\_CoA}\mathrm{vmax2}}{\mathrm{km2}+\mathrm{FAD}+\mathrm{Fatty\_acyl\_CoA}}$ $\mathrm{rate}=\frac{\mathrm{trans\_Enol\_CoA}\mathrm{H2O}\mathrm{vmax3}}{\mathrm{km3}+\mathrm{trans\_Enol\_CoA}+\mathrm{H2O}}$ $\mathrm{rate}=\frac{\mathrm{L\_3\_Hydroxyacyl\_CoA}\mathrm{NAD}\mathrm{vmax4}}{\mathrm{km4}+\mathrm{L\_3\_Hydroxyacyl\_CoA}+\mathrm{NAD}}$ $\mathrm{rate}=\frac{\mathrm{CoA\_SH}\mathrm{beta\_Ketoacyl\_CoA}\mathrm{vmax5}}{\mathrm{km5}+\mathrm{CoA\_SH}+\mathrm{beta\_Ketoacyl\_CoA}}$