Table 1 Reactions and rate equations used for the model.
From: Entrainment of superoxide rhythm by menadione in HCT116 colon cancer cells
Reaction | Rate equation |
|---|---|
\(MD+NADPH\mathop{\to }\limits^{CP450R}SQ+NAD{P}^{+}\) | \({r}_{1}=\frac{{V}_{m1}[MD][NADPH]}{{K}_{N}[MD]+\,{K}_{M}\,[NADPH]+[MD]\,[NADPH]}\) |
\(SQ+{O}_{2}\underset{{k}_{m1}}{\overset{{k}_{1}}{\rightleftharpoons }}MD+SOX+{H}^{+}\) | \({r}_{2}={k}_{1}[{O}_{2}][SQ]-{k}_{m1}[MD][SOX]\) |
\(ER{K}_{c}+SOX\mathop{\to }\limits^{{k}_{t1}}+\,ER{K}_{n}+\varnothing \) | \({r}_{3}={k}_{t1}{[ERK]}_{C}[SOX]\) |
\(P+p53\underset{phosphatase}{\overset{ERK2}{\rightleftharpoons }}\,p53-P\) | \({r}_{4}=\frac{{k}_{3}{n}_{v}n{[ERK]}_{c}[p53]}{{K}_{p53}}-\frac{{V}_{4}[p53-P]}{{K}_{p53-P}+[p53-P]}\) |
\(2SOX+2{H}^{+}\mathop{\to }\limits^{Mn-SOD}+\,{H}_{2}{O}_{2}+{O}_{2}\) | \({r}_{5}=\frac{{k}_{2}[Mn-SOD][SOX]}{{K}_{SOX}+[SOX]}\) |
\(\varnothing +p53-P+DNA\to mSOD2\) | \({r}_{6}=\frac{{I}_{max}[{D}_{n}]{[p53-P]}^{{n}_{a}}}{{K}_{p53-P}^{{n}_{a}}+{[p53-P]}^{{n}_{a}}}\) |
\(mSOD2\to \varnothing \) | \({r}_{7}=\,{K}_{dm}[mSOD2]\) |
\(\varnothing +mSOD2\,\to Mn-SOD+\,mSOD2\) | \({r}_{8}=\,{K}_{tr}[mSOD2]\) |
\(Mn-SOD\,\to \,\varnothing \) | \({r}_{9}={K}_{dp}[Mn-SOD]\) |
\({H}^{+}+NAD{P}^{+}\mathop{\to }\limits^{FNR}NADPH\) | \({r}_{10}=\frac{{V}_{5}[NAD{P}^{+}]}{{K}_{NAD{P}^{+}}+[NAD{P}^{+}]}\) |
\(\varnothing \mathop{\to }\limits^{MD}p53\) | \(r11={k}_{p}[MD]\) |
\({r}_{oscil}=-\,{\rm{LA}}{e}^{-Lt}+{\rm{A}}{e}^{-Lt}({\rm{wcos}}({\rm{wt}}+{\rm{phi}})-{\rm{Lsin}}({\rm{wt}}+{\rm{phi}}))\) |
