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The gluconeogenic conversion of 3-phosphoglycerate via 1,3-bisphosphoglycerate to glyceraldehyde-3-phosphate was compared at 30 C and at 70 C. At 30 C it was possible to produce 1,3-bisphosphoglycerate from 3-phosphoglycerate with phosphoglycerate kinase, but at 70 C, 1,3- bisphosphoglycerate was dephosphorylated rapidly to 3-phosphoglycerate, effectively turning the phosphoglycerate kinase into a futile cycle. At both temperatures it was possible to convert 3-phosphoglycerate to glyceraldehyde 3-phosphate (although the latter was degraded at 70C) using phosphoglycerate kinase and glyceraldehyde 3-phosphate dehydrogenase.
SEEK ID: https://fairdomhub.org/investigations/156
Projects: SulfoSys, SulfoSys - Biotec
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Created: 27th Sep 2017 at 14:36
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Projects: SulfoSys, SulfoSys - Biotec
Institutions: University Duisburg-Essen
Projects: PSYSMO, MOSES, SysMO DB, SysMO-LAB, SulfoSys, SulfoSys - Biotec, Whole body modelling of glucose metabolism in malaria patients, FAIRDOM, Molecular Systems Biology, COMBINE Multicellular Modelling, HOTSOLUTE, Steroid biosynthesis, Yeast glycolytic oscillations
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch, School of Computer Science, University of Manchester, Stellenbosch University
Within the e:Bio - Innovationswettbewerb Systembiologie (Federal Ministry of Education and Research (BMBF)), the SulfoSYSBIOTECH consortium (10 partners), aim to unravel the complexity and regulation of the carbon metabolic network of the thermoacidophilic archaeon Sulfolobus solfataricus (optimal growth at 80°C and pH 3) in order to provide new catalysts ‘extremozymes’ for utilization in White Biotechnology.
Based on the available S. solfataricus genome scale metabolic model (Ulas et al., 2012)
...
Programme: e:Bio
Public web page: http://www.sulfosys.com/
Organisms: Sulfolobus solfataricus
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
PGK-GAPDH reactions were studied in vitro at 30 and 70 using yeast or Sso enzymes
SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig4b/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig4c/simulate
Person responsible: Theresa Kouril
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: PGK - GAPDH models, PGK-GAPDH 30, PGK-GAPDH 70
PGK reaction at 30 C. Yeast PGK was incubated at 30 C, in the presence or absence of the ATP recycling system, and the conversion of 3 PG to BPG was followed.
SED-ML simulations
Fig. 1A: https://jjj.bio.vu.nl/models/experiments/kouril2017_fig1a/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: PGK 30C data, PGK 30C model
PGK reaction at 70C. Sulfolobus solfataricus PGK was incubated at 70C in presence and absence of an ATP recycling system.
Changes in metabolite concentrations was followed via 31P NMR or enzymatic analyses.
SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3b/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3c/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3d/simulate
Person responsible: Theresa Kouril
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: PGK 70 data, PGK 70C model
BPG produced with yeast PGK was incubated at 70 C,upon which BPG rapidly dephosphorylates to 3PG.
SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig2b/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Assays: BPG degradation, BPG stability analysis
Experimental data for the yeast PGK incubations at 30C, with and without recycling of ATP.
Contributor: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-30C
Organisms: No organisms
SOPs: No SOPs
Data files: PGK yeast with recycling of ATP, PGK yeast without recycling of ATP
Changes in metabolite concentrations were either quantified via 31P NMR or enzymatically
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: NMR
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-70C
Organisms: No organisms
SOPs: No SOPs
Data files: Sso PGK (14 ug/ml) in presence of recycling sys..., Sso PGK (28 ug/ml) in presence of recycling sys..., Sso PGK in absence of recycling system, 31P NMR..., Sso PGK in presence of ATP recycling system at ...
BPG degradation at 70C
Contributor: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: BPG stability
Organisms: No organisms
SOPs: No SOPs
Data files: BPG degradation at 70
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-GAPDH 30C & 70C
Organisms: No organisms
SOPs: No SOPs
Data files: PGK-GAPDH 30, 3PG, GAP & BPG, PGK-GAPDH 30, PYR
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-GAPDH 30C & 70C
Organisms: No organisms
SOPs: No SOPs
Data files: PGK-GAPDH 70
A model for the PGK reaction of yeast in presence or absence of the ATP recycling reactions
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-30C
Organisms: No organisms
Models: PGK yeast Fig1a, PGK yeast with/without recycling
SOPs: No SOPs
Data files: No Data files
BPG stability analysis
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: BPG stability
Organisms: No organisms
Models: BPG stability notebook
SOPs: No SOPs
Data files: No Data files
PGK 70C model
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-70C
Organisms: No organisms
Models: PGK 70C SBML, PGK 70C model Fig. 3
SOPs: No SOPs
Data files: No Data files
PGK - GAPDH models
Investigation: Phosphoglycerate kinase acts as a futile cycle ...
Study: PGK-GAPDH 30C & 70C
Organisms: No organisms
Models: PGK-GAPDH model Sulfolobus kouril8, PGK-GAPDH model yeast kouril7, PGK-GAPDH models yeast and Sulfolobus Fig. 4
SOPs: No SOPs
Data files: No Data files
Creators: Theresa Kouril, Jacky Snoep
Contributor: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Assays: PGK 70 data
Creators: Theresa Kouril, Jacky Snoep
Contributor: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Assays: PGK 70 data
Creator: Theresa Kouril
Contributor: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Assays: PGK 70 data
incubations with yeast enzymes at 30C
Creators: Theresa Kouril, Jacky Snoep
Contributor: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Assays: PGK-GAPDH 30
Creators: Theresa Kouril, Jacky Snoep
Contributor: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Assays: PGK-GAPDH 30
Creators: Theresa Kouril, Jacky Snoep
Contributor: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Assays: PGK-GAPDH 70
metabolite quantification via enzymatic analysis
Creators: Theresa Kouril, Jacky Snoep
Contributor: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Assays: PGK 70 data
Creators: Theresa Kouril, Jacky Snoep
Contributor: Theresa Kouril
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: BPG stability
Assays: BPG degradation
PGK yeast without recycling of ATP
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-30C
Assays: PGK 30C data
PGK yeast with recycling of ATP
Creator: Jacky Snoep
Contributor: Jacky Snoep
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-30C
Assays: PGK 30C data
PGK-GAPDH model Sulfolobus kouril8
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Sulfolobus solfataricus
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Modelling analyses: PGK - GAPDH models
PGK-GAPDH model yeast kouril7
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Modelling analyses: PGK - GAPDH models
PGK-GAPDH models yeast and Sulfolobus Fig. 4 in manuscript
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-GAPDH 30C & 70C
Modelling analyses: PGK - GAPDH models
PGK 70C model, Fig 3 in manuscript
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Organism: Sulfolobus solfataricus
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Modelling analyses: PGK 70C model
PGK 70C SBML
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Sulfolobus solfataricus
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-70C
Modelling analyses: PGK 70C model
BPG stability notebook
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Organism: Not specified
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: BPG stability
Modelling analyses: BPG stability analysis
PGK yeast Fig1a
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
Organism: Saccharomyces cerevisiae
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-30C
Modelling analyses: PGK 30C model
PGK yeast with/without recycling
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Saccharomyces cerevisiae
Investigations: Phosphoglycerate kinase acts as a futile cycle ...
Studies: PGK-30C
Modelling analyses: PGK 30C model