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Model reconstituted system

Mathematical model for the reconstituted system with PGK, GAPDH, TPI and FBPAase.

SEEK ID: https://demo.fairdomhub.org/assays/28

Modelling Analysis

Jacky Snoep

Projects: SulfoSys

Investigation: Central Carbon Metabolism of Sulfolobus solfataricus

Study: Carbon loss at high T

Biological problem addressed: Model Analysis Type

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

Model:
Data:
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Created: 2nd Feb 2013 at 16:32

Last updated: 26th Oct 2017 at 09:57

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Related items

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
SulfoSys

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

Carbon loss at high T
SulfoSys
No description specified

Person responsible: Jacky Snoep

Snapshots: No snapshots

P2

Submitter: Not available

Provider Name: Not specified

Provider's strain ID: Not specified

Organism: Sulfolobus solfataricus

Genotypes: wild-type

Phenotypes: wild-type

Comment: Not specified

Model simulation and Exp data for reconstituted system
SulfoSys

Experimental data for the reconstituted system are plotted together with the model prediction

Creator: Jacky Snoep

Submitter: Jacky Snoep

Relationship type: Validation data

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Metabolite concentrations during reconstituted enzyme incubation
SulfoSys

The purified enzymes, PGK, GAPDH, TPI and FBPAase were incubated at 70 C en conversion of 3PG to F6P was followed

Creator: Jacky Snoep

Submitter: Jacky Snoep

Relationship type: Validation data

Download
Mathematical model for the combined four enzyme system
SulfoSys

The PGK, GAPDH, TPI and FBPAase were modelled together using the individual rate equations. Closed system.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Download
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, J. L. Snoep

Date Published: 22nd Aug 2013

Publication Type: Not specified

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