Abstract
BackgroundMitochondrial 2-oxoglutarate (α-ketoglutarate) dehydrogenase complex (OGDHC), a key regulatory point of tricarboxylic acid (TCA) cycle, plays vital roles in multiple pathways of energy metabolism and biosynthesis. The catalytic mechanism and allosteric regulation of this large enzyme complex are not fully understood. Here computer simulation is used to test possible catalytic mechanisms and mechanisms of allosteric regulation of the enzyme by nucleotides (ATP, ADP), pH, and metal ion cofactors (Ca2+ and Mg2+).ResultsA model was developed based on an ordered ter-ter enzyme kinetic mechanism combined with con-formational changes that involve rotation of one lipoic acid between three catalytic sites inside the enzyme complex. The model was parameterized using a large number of kinetic data sets on the activity of OGDHC, and validated by comparison of model predictions to independent data.ConclusionsThe developed model suggests a hybrid rapid-equilibrium ping-pong random mechanism for the kinetics of OGDHC, consistent with previously reported mechanisms, and accurately describes the experimentally observed regulatory effects of cofactors on the OGDHC activity. This analysis provides a single consistent theoretical explanation for a number of apparently contradictory results on the roles of phosphorylation potential, NAD (H) oxidation-reduction state ratio, as well as the regulatory effects of metal ions on ODGHC function.
Highlights
Mitochondrial 2-oxoglutarate (a-ketoglutarate) dehydrogenase complex (OGDHC), a key regulatory point of tricarboxylic acid (TCA) cycle, plays vital roles in multiple pathways of energy metabolism and biosynthesis
OGDHC is primarily located within the mitochondrial matrix and is a key regulatory enzyme complex in the TCA cycle, responsible for oxidative decarboxylation of 2-oxoglutarate, transferring a succinyl group to coenzyme A (CoASH4-) and producing reducing equivalents (NADH2-) for the electron transport system
Parameterization of basic kinetic mechanism of OGDHC we present the detailed parameterization and validation of the proposed kinetic model based on the available experimental data on the kinetics of OGDHC, measured in a wide variety of experimental conditions
Summary
Mitochondrial 2-oxoglutarate (a-ketoglutarate) dehydrogenase complex (OGDHC), a key regulatory point of tricarboxylic acid (TCA) cycle, plays vital roles in multiple pathways of energy metabolism and biosynthesis. The molecular organization of OGDHC is similar to that of the pyruvate dehydrogenase complex (PDHC) as it belongs to the same heterogeneous family of 2-oxo acid dehydrogenase multi-enzyme complexes [2]. It consists of multiple copies of three enzyme components: oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2), and dihydro-lipoamide dehydrogenase (E3). Consecutive actions of these enzymes catalyze the oxidation of 2-oxoglutarate and reduction ofNAD-, which results in the production of NADH2- and Succinyl-CoA4- (Figure 1A). Allosteric interactions associated with the E1 component are known to be the predominant target for controlling of OG-DHC activity [3]
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