Model construction

PoLiMeR is funded through the EU Marie Skłodowska-Curie Innovative Training Network (ITN), which drives scientific excellence and innovation. ITNs bring together universities, research institutes, industry and clinical partners from across the world to train researchers to doctorate level.

Metabolic diseases are a burden on the European population and health care system. It is increasingly recognised that individual differences with respect to history, lifestyle, and genetic make-up affect disease ...

Minireviews about each enzyme in the mitochindrial beta-oxidation model on which the final parameter choices (fixed-parameter model) and parameter sampling distributions (ensemble) were based.

Adjusted model to test the model's ability to oxygen consumption rate by permeabilised HepG2 cells in an Oroboros oxygraph. Data from Fletcher et al. (2019).

Adjusted model to test the model's ability to predict palmitoyl-CoA and octanoyl-CoA dehydrogenation in human liver lysate, with and without anti-MCAD and anti-VLCAD antibodies. Data from Aoyama et al. (1995).

Human mitochondrial fatty acid oxidation of saturated, even chain acyl-Coas beginning at C16. See Model description for detail.

Unzip model notebooks and keep in the same folder. Notebook names state which notebooks need to be run before them in order for them to word, e.g. "[needs-(1)]" indicates that the notebook numbered 1 must be run and its exported output generated before the given notebook can work. This has to do with the model being generated in only one notebook to avoid duplication.

Medium-/short-chain hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)

Medium-chain ketoacyl-CoA thiolase (EC 2.3.1.16)

Mitochondrial trifunctional protein (UniProt: P40939)

Acyl-CoA thioesterases (EC 3.1.2.1. and EC 3.1.2.2)

L-carnitine as conserved moiety

CoA as conserved moiety

Acetyl-CoA in the mitochondrion as constant metabolite

NADH and NAD+ (Nicotinamide adinine dinucleotide) as constant values.

Oxidised and reduced electron transferring flavoprotein as constant values.

Volume per mg mitochondrial protein of mitochondrion and cytosol.

Carnitine palmitoyltransferase 1 (EC 2.3.1.21)

The theory, calculations, and conditions that went into estimating the Keqs.

Carnitine acylcarnitine translocase (UniProt: O43772)

Carnitine palmitoyltransferase 2 (EC 2.3.1.21)

Carnitine acetyltransferase (EC 2.3.1.7)

Short-chain acyl-CoA dehydrogenase (EC 1.3.99.2)

Medium-chain acyl-CoA dehydrogenase (EC 1.3.99.3)

Very long-chain acyl-CoA dehydrogenase (EC 1.3.8.9)

Crotonase / Enoyl-CoA hydratase (EC 4.2.1.17)