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GAPDH modeling

Mathematical model for GAPDH kinetics, saturation of GAP, BPG, NADP, NADPH and Pi.

SEEK ID: https://demo.fairdomhub.org/assays/24

Modelling Analysis

Jacky Snoep

Projects: SulfoSys

Investigation: Central Carbon Metabolism of Sulfolobus solfataricus

Study: Model gluconeogenesis

Biological problem addressed: Model Analysis Type

Organisms: Sulfolobus solfataricus : P2 (wild-type / wild-type)

Model:
Data:
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Created: 1st Feb 2013 at 00:11

Last updated: 26th Oct 2017 at 11:57

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SulfoSys

Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Programme: SysMO

Public web page: http://sulfosys.com/

Central Carbon Metabolism of Sulfolobus solfataricus
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An investigation in the CCM of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.

Snapshots: Snapshot 1

Model gluconeogenesis
SulfoSys

Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus

Person responsible: Jacky Snoep

Snapshots: No snapshots

P2

Contributor: Not available

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Sulfolobus solfataricus

Genotypes: wild-type

Phenotypes: wild-type

Comment: Not specified

GAPDH kinetics Pi
SulfoSys
No description specified

Creators: None

Contributor: Jacky Snoep

Relationship type: Construction data

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GAPDH kinetics NADPH
SulfoSys
No description specified

Creators: None

Contributor: Jacky Snoep

Relationship type: Construction data

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GAPDH kinetics NADP
SulfoSys
No description specified

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Relationship type: Construction data

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GAPDH kinetics GAP
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No description specified

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Contributor: Jacky Snoep

Relationship type: Construction data

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GAPDH kinetics 3PG
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No description specified

Creators: None

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Relationship type: Construction data

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1 hidden item
GAPDH kinetic model
SulfoSys

Mathematical model for GAPDH kinetics, saturation for GAP, BPG, NADP, NADPH, Pi.

Creator: Jacky Snoep

Contributor: Jacky Snoep

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Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus
SulfoSys

Abstract (Expand)

Four enzymes of the gluconeogenic pathway in Sulfolobus solfataricus were purified and kinetically characterized. The enzymes were reconstituted in vitro to quantify the contribution of temperature … instability of the pathway intermediates to carbon loss from the system. The reconstituted system, consisting of phosphoglycerate kinase, glyceraldehyde 3-phosphate dehydrogenase, triose phosphate isomerase and the fructose 1,6-bisphosphate aldolase/phosphatase, maintained a constant consumption rate of 3-phosphoglycerate and production of fructose 6-phosphate over a 1-h period. Cofactors ATP and NADPH were regenerated via pyruvate kinase and glucose dehydrogenase. A mathematical model was constructed on the basis of the kinetics of the purified enzymes and the measured half-life times of the pathway intermediates. The model quantitatively predicted the system fluxes and metabolite concentrations. Relative enzyme concentrations were chosen such that half the carbon in the system was lost due to degradation of the thermolabile intermediates dihydroxyacetone phosphate, glyceraldehyde 3-phosphate and 1,3-bisphosphoglycerate, indicating that intermediate instability at high temperature can significantly affect pathway efficiency.

Authors: T. Kouril, D. Esser, J. Kort, H. V. Westerhoff, B. Siebers, Jacky Snoep

Date Published: 22nd Aug 2013

Journal: FEBS J

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