Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

BMC Bioinformatics

Table 1 Rate laws used in the simplified model

v _PTS	$k_{cat} e_{PTS} \frac{c_{pep}}{c_{pyr}}$	v _PGI	$k_{cat} e_{PGI} (1 - \frac{c_{f 6 p}}{c_{g 6 p} K_{eq}})$
v _PFK	k _cat e _PFK C _atp	v _ALDO	$\frac{k_{cat} e_{ALDO} (c_{fdp} - \frac{c_{gap} c_{dhap}}{K_{eq}})}{K_{fdp} + C_{fdp}}$
v _TPI	$k_{cat} e_{TPI} (1 - \frac{c_{gap}}{c_{dhap} K_{eq}})$	v _GAPD	$k_{cat} e_{GAPD} (c_{nad} c_{gap} - \frac{c_{13 dpg} c_{nadh}}{K_{eq}})$
v _PGK	$k_{cat} e_{PGK} (1 - \frac{c_{atp} c_{3 pg}}{c_{adp} c_{13 dpg} K_{eq}})$	v _PGM	$k_{cat} e_{PGM} (1 - \frac{c_{2 pg}}{c_{3 pg} K_{eq}})$
v _ENO	$k_{cat} e_{ENO} (c_{2 pg} - \frac{c_{pep}}{K_{eq}})$	v _PYK	$k_{cat} e_{PYK} \frac{c_{adp}}{c_{atp}}$
v _PDH	$k_{cat} e_{PDH} (\frac{c_{pyr}^{4}}{K_{pyr} + C_{pyr}^{4}})$	v _PPC	$\frac{k_{cat} e_{PPC} c_{pep} (1 + \frac{c_{fdp}}{K_{fdp}})}{K_{pep} + C_{pep}}$
v _{G 6PDH}	k _cat e _{G 6PDH} c _nadp c _{g 6p}	v _GND	$\frac{k_{cat} e_{GND} c_{nadp} c_{6 pgc}}{c_{nadph} c_{atp} (K_{pep} + C_{pep})}$
v _RPE	$k_{cat} e_{RPE} (c_{ru 5 pD} - \frac{c_{xu 5 pD}}{K_{eq}})$	v _RPI	$k_{cat} e_{RPI} (c_{ru 5 pD} - \frac{c_{r 5 p}}{K_{eq}})$
v _{TKT 1}	$k_{cat} e_{TKT 1} (c_{r 5 p} c_{xu 5 pD} - \frac{c_{s 7 p} c_{gap}}{K_{eq}})$	v _TALA	$k_{cat} e_{TALA} (c_{gap} c_{s 7 p} - \frac{c_{e 4 p} c_{f 6 p}}{K_{eq}})$
v _{TKT 2}	$k_{cat} e_{TKT 2} (c_{xu 5 pD} c_{e 4 p} - \frac{c_{f 6 p} c_{gap}}{K_{eq}})$

ISSN: 1471-2105