Model reconstituted system

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

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

Class: Modelling Analysis

Submitter: Jacky Snoep

Projects: SulfoSys

Investigation: Central Carbon Metabolism of Sulfolobus solfataricus

Study: Carbon loss at high T

Assay position:

Biological problem addressed: Model Analysis Type

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

Model:

Mathematical model for the combined four enzyme system

Data:

Metabolite concentrations during reconstituted enzyme incubation
Model simulation and Exp data for reconstituted system

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Creators

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Submitter

Jacky Snoep

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Views: 4720

Created: 2nd Feb 2013 at 16:32

Last updated: 26th Oct 2017 at 09:57

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Projects (1)
Investigations (1)
Studies (1)
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Data files (2)
Models (1)
Publications (1)

Jacky Snoep

Projects: SysMO-LAB, PSYSMO, MOSES, SulfoSys, SysMO DB

Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch

SysMO

SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".

The goal pursued by SysMO is to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.

Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...

Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB

Web page: http://sysmo.net/

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/

Organisms: Sulfolobus solfataricus

Central Carbon Metabolism of Sulfolobus solfataricus

SulfoSys

All creators

Jacky Snoep

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.

Submitter: Jacky Snoep

Studies: Carbon loss at high T, Model gluconeogenesis, Pathway optimisation

Assays: Experimental assays of the temperature dependent degradation of GAP and ..., FBPA/ase, FBPAase model, GAPDH, GAPDH modeling, Gluconeogenic model, Model reconstituted system, Modelling pathway optimisation, Modelling temperature dependent degradation of GAP and DHAP, PGK, PGK and FBPAase titrations, PGK modeling, Reconstituted system reference state, TPI, TPI modeling

Snapshots: Snapshot 1

Scales: Not specified

Created: 29th Jan 2013 at 14:09, Last updated: 28th May 2015 at 08:50

Carbon loss at high T

SulfoSys

All creators

Jacky Snoep

No description specified

Submitter: Jacky Snoep

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Assays: Model reconstituted system, Reconstituted system reference state

Snapshots: No snapshots

Scales: Not specified

Created: 29th Jan 2013 at 14:11, Last updated: 28th May 2015 at 08:50

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

Created: 28th Apr 2010 at 16:17, Last updated: 18th Jul 2012 at 12:26

Model simulation and Exp data for reconstituted system

SulfoSys

All creators

Jacky Snoep

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

Creator: Jacky Snoep

Submitter: Jacky Snoep

Relationship type: Validation data

Investigations: Central Carbon Metabolism of Sulfolobus solfata...

Studies: Carbon loss at high T

Assays: Model reconstituted system, Reconstituted system reference state

Scales: Not specified

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Created: 2nd Feb 2013 at 20:55, Last updated: 28th May 2015 at 08:50

Metabolite concentrations during reconstituted enzyme incubation

SulfoSys

All creators

Jacky Snoep

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

Investigations: Central Carbon Metabolism of Sulfolobus solfata...

Studies: Carbon loss at high T, Model gluconeogenesis

Assays: Gluconeogenic model, Model reconstituted system, Reconstituted system reference state

Scales: Not specified

Download

Created: 2nd Feb 2013 at 16:24, Last updated: 28th May 2015 at 08:50

Mathematical model for the combined four enzyme system

SulfoSys

All creators

Jacky Snoep

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

Creator: Jacky Snoep

Submitter: Jacky Snoep

Model type: Ordinary differential equations (ODE)

Model format: SBML

Environment: JWS Online

Organism: Sulfolobus solfataricus

Investigations: Central Carbon Metabolism of Sulfolobus solfata...

Studies: Carbon loss at high T, Model gluconeogenesis, Pathway optimisation

Assays: Gluconeogenic model, Model reconstituted system, Modelling pathway optimisation

Scales: Not specified

Download

Created: 6th Feb 2013 at 10:07, Last updated: 28th May 2015 at 08:50

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

SulfoSys

All creators

Jacky Snoep

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

PubMed ID: 23865479

Citation: FEBS J. 2013 Sep;280(18):4666-80. doi: 10.1111/febs.12438. Epub 2013 Aug 22.

Scales: Not specified

Created: 9th Jun 2015 at 12:00