Figure 1.
Schematic overview of FA β-oxidation as it is modeled in this study.
Enzymes are depicted in italics bold face, metabolites in regular and allosteric inhibitors in red. CPT1: carnitine-palmitoyl transferase 1 (E.C. 2.3.1.21), CACT: carnitine-acyl-carnitine translocase, CPT2: carnitine-palmitoyl transferase 2 (E.C. 2.3.1.21), VLCAD: very-long-chain acyl-CoA dehydrogenase (E.C. 1.3.99.3), LCAD: long-chain acyl-CoA dehydrogenase (E.C. 1.3.99.3), MCAD: medium-chain acyl-CoA dehydrogenase (E.C. 1.3.99.3), SCAD short-chain acyl-CoA dehydrogenase (E.C.1.3.8.1 for butanoyl CoA (C4) (was previously E.C. 1.3.99.2) and E.C. 1.3.99.3 for hexanoyl CoA (C6)), MTP: mitochondrial trifunctional protein (E.C. 4.2.1.17, E.C. 1.1.1.211 and E.C. 2.3.1.16), M/SCHAD: medium/short-chain hydroxyacyl-CoA dehydrogenase (E.C. 1.1.1.35), MCKAT: medium-chain ketoacyl-CoA thiolase (E.C. 2.3.1.16). The chain-length specificity as included in the model is indicated for each enzyme (e.g. C6–C12). The boundary metabolites which are kept at fixed concentrations are underlined. The direction of the flux is from the small to large arrow heads.
Figure 2.
Comparison between the model simulations and the experiment with palmitoyl CoA as substrate.
At time point zero the substrate palmitoyl CoA was added to uncoupled mitochondria in the presence of an excess amount of l-carnitine and malic acid. Samples for acyl carnitine analysis were taken at different time points. Error bars on the experimental data represent SEM (n = 4 for the flux data, n = 8 for the acyl-carnitine concentrations). Panel A: Comparison of the experimental and modeled flux through the FA β-oxidation. The reported experimental flux is 2/3 of the oxygen consumption flux averaged from 1.5 to 8 min. The modeled flux equals the production fluxes of NADH plus FADH2 divided by 2 (one O2 oxidizes two NADH or FADH2), averaged over the same time interval. Panel B: experimental acyl-carnitine concentrations in total samples, i.e. including intra- and extramitochondrial metabolites. Panel C: acyl-carnitine concentrations simulated by the computer model, representing the weighted average over the matrix and extramitochondrial concentrations to allow direct comparison to the experiments.
Figure 3.
Steady-state fluxes and concentration of the intermediate metabolite at various concentrations of the substrate palmitoyl CoA.
Panels A and C: Steady-state flux through the FA β-oxidation. Panel B: CoASH concentration (solid lines) and total CoA esters (dashed lines) corresponding to the simulations in A. Panel D: Graphical representation of the differences between the computational models with and without competition. Blue lines in A and B: standard model; red lines in A and B: model without competition; green lines in A and B: model with fixed CoASH concentration (see text). Solid line in C: standard model (malonyl-CoA concentration 0 µM, mitochondrial NAD/NADH ratio 15); short-dashed line in C: standard model but with increased concentration of malonyl CoA of 10 µM; long-dashed line in C: standard model but with increased mitochondrial NAD+/NADH ratio of 40. Different colors in panel D represent the four acyl-CoA dehydrogenases; cyan: SCAD, yellow: MCAD, purple: LCAD and green: VLCAD.