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TPI modeling

TPI modeling

Mathematical model for TPI kinetics, saturation of GAP and DHAP.

SEEK ID: https://demo.fairdomhub.org/assays/25

Class: Modelling Analysis

Submitter: 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:

TIM kinetic model

Data:

TPI kinetics DHAP
TPI kinetics GAP
TPI kinetics PEP inhibition GAP
TPI kinetics PEP inhibition of DHAP
Model simulation and exp data for TIM kinetics, GAP and DHAP saturation, and PEP inhibition.

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Creators and Submitter

Creators

Not specified

Submitter

Jacky Snoep

Activity

Views: 4294

Created: 1st Feb 2013 at 23:26

Last updated: 26th Oct 2017 at 09:57

Scales

Not Specified

Related items

People (1)
Projects (1)
Investigations (1)
Studies (1)
Strains (1)
Data files (5)
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

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 contributors

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.

Snapshots: Snapshot 1

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

Scales: Not specified

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

Model gluconeogenesis

SulfoSys

All contributors

Jacky Snoep

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

Investigation: Central Carbon Metabolism of Sulfolobus solfata...

Assays: Experimental assays of the temperature dependent degradation of GAP and ..., FBPA/ase, FBPAase model, GAPDH, GAPDH modeling, Gluconeogenic model, Modelling temperature dependent degradation of GAP and DHAP, PGK, PGK modeling, TPI, TPI modeling

Scales: Not specified

Created: 29th Jan 2013 at 14:16, 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

TPI kinetics DHAP

SulfoSys

All contributors

Jacky Snoep

No description specified

Creators: None

Submitter: Jacky Snoep

Relationship type: Construction data

Investigations: Central Carbon Metabolism of Sulfolobus solfata...

Studies: Model gluconeogenesis

Assays: TPI, TPI modeling

Scales: Not specified

Download

Created: 29th Jan 2013 at 20:46, Last updated: 28th May 2015 at 08:50

TPI kinetics GAP

SulfoSys

All contributors

Jacky Snoep

No description specified

Creators: None

Submitter: Jacky Snoep

Relationship type: Construction data

Investigations: Central Carbon Metabolism of Sulfolobus solfata...

Studies: Model gluconeogenesis

Assays: TPI, TPI modeling

Scales: Not specified

Download

Created: 29th Jan 2013 at 20:47, Last updated: 28th May 2015 at 08:50

TPI kinetics PEP inhibition of DHAP

SulfoSys

All contributors

Jacky Snoep

No description specified

Creators: None

Submitter: Jacky Snoep

Relationship type: Construction data

Investigations: Central Carbon Metabolism of Sulfolobus solfata...

Studies: Model gluconeogenesis

Assays: TPI, TPI modeling

Scales: Not specified

Download

Created: 29th Jan 2013 at 20:47, Last updated: 28th May 2015 at 08:50

TPI kinetics PEP inhibition GAP

SulfoSys

All contributors

Jacky Snoep

No description specified

Creators: None

Submitter: Jacky Snoep

Relationship type: Construction data

Investigations: Central Carbon Metabolism of Sulfolobus solfata...

Studies: Model gluconeogenesis

Assays: TPI, TPI modeling

Scales: Not specified

Download

Created: 29th Jan 2013 at 20:49, Last updated: 28th May 2015 at 08:50

Model simulation and exp data for TIM kinetics, GAP and DHAP saturation, and PEP inhibition.

SulfoSys

All contributors

Jacky Snoep

Model simulation and exp data for TIM kinetics, GAP and DHAP saturation, and PEP inhibition.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Relationship type: Not specified

Investigations: Central Carbon Metabolism of Sulfolobus solfata...

Studies: Model gluconeogenesis

Assays: TPI, TPI modeling

Scales: Not specified

Download

Created: 1st Feb 2013 at 23:42, Last updated: 28th May 2015 at 08:50

TIM kinetic model

SulfoSys

All contributors

Jacky Snoep

Mathematical model for TIM kinetics, GAP and DHAP saturation and PEP inhibition.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Model type: Ordinary differential equations (ODE)

Model format: Mathematica

Environment: Not specified

Organism: Sulfolobus solfataricus

Investigations: Central Carbon Metabolism of Sulfolobus solfata...

Studies: Model gluconeogenesis

Modelling analyses: TPI modeling

Scales: Not specified

Download

Created: 1st Feb 2013 at 23:47, 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 contributors

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