Systematic assignment of thermodynamic constraints in metabolic network models

BMC Bioinformatics

Table 1 Co-substrate groups that were eliminated from the stoichiometric matrix to identify energy producing cycles

selected co-substrate groups
NTP, NDP, NMP
NADH, NAD⁺
NADPH, NADP⁺
FADH₂, FAD⁺
$H_{e x t r a c e l l u l a r}^{+}$ , H⁺

Besides these co-substrates, also the molecules water, oxygen, carbon dioxide, ammonium and inorganic phosphate were removed from the stoichiometric matrix to identify energy producing cycles. This is necessary to elementally balance the resulting net conversion of co-substrates. NTP, NDP and NMP denote nucleoside tri-, di- and monophosphate for adenosine, cytidine, guanosine, inosine and uridine.

ISSN: 1471-2105