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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.
SEEK ID: https://demo.fairdomhub.org/investigations/6
Projects: SulfoSys
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Created: 29th Jan 2013 at 14:09
Last updated: 28th May 2015 at 08:50

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- People (1)
- Projects (1)
- Studies (3)
- Assays (15+1)
- Data files (28+1)
- Models (6+1)
- SOPs (3)
- Publications (1)
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
Person responsible: Jacky Snoep
Snapshots: No snapshots
Scales: Not specified
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
By varying the input or output flux via PGK and FBPAase manipulation respectively the pathway efficiency can be optimised.
Person responsible: Jacky Snoep
Snapshots: No snapshots
Scales: Not specified
Kinetic characterisation of Phosphoglycerokinase
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Initial Rate Experiment
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model gluconeogenesis
Organisms: Sulfolobus solfataricus : P2 (wild-type / wild-type)
SOPs: Expression of S. solfataricus enzymes in E. col..., Preparation of cell free extract of recombinant..., Protein purification from E. coli extracts.
Data files: Model simulation and experimental data for ADP,..., PGK kinetics 3PG, PGK kinetics ADP, PGK kinetics ATP, PGK kinetics BPG
Scales: Not specified
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Initial Rate Experiment
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model gluconeogenesis
Organisms: Sulfolobus solfataricus : P2 (wild-type / wild-type)
SOPs: Expression of S. solfataricus enzymes in E. col..., Preparation of cell free extract of recombinant..., Protein purification from E. coli extracts.
Data files: GAPDH kinetics 3PG, GAPDH kinetics GAP, GAPDH kinetics NADP, GAPDH kinetics NADPH, GAPDH kinetics Pi
Scales: Not specified
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Initial Rate Experiment
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model gluconeogenesis
Organisms: Sulfolobus solfataricus : P2 (wild-type / wild-type)
SOPs: Expression of S. solfataricus enzymes in E. col..., Preparation of cell free extract of recombinant..., Protein purification from E. coli extracts.
Data files: Model simulation and exp data for TIM kinetics,..., TPI kinetics DHAP, TPI kinetics GAP, TPI kinetics PEP inhibition GAP, TPI kinetics PEP inhibition of DHAP
Scales: Not specified
Kinetic characterization of the FBPA/ase with respect to GAP en DHAP saturation.
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Initial Rate Experiment
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model gluconeogenesis
Organisms: Sulfolobus solfataricus : P2 (wild-type / wild-type)
SOPs: Expression of S. solfataricus enzymes in E. col..., Preparation of cell free extract of recombinant..., Protein purification from E. coli extracts.
Data files: FBPA/ase kinetics DHAP, FBPA/ase kinetics GAP, Model simulation and experimental data for DHAP...
Scales: Not specified
GAP and DHAP concentrations were measured over time at 70C.
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Progressive Curve Experiment
Snapshots: No snapshots
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model gluconeogenesis
Organisms: No organisms
SOPs: No SOPs
Data files: T degradation DHAP, T degradation GAP
Scales: Not specified
Combined plot fo the model simulations and the experimental data for the PGK and FBPAase titrations.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Pathway optimisation
Assays: Modelling pathway optimisation, PGK and FBPAase titrations
Scales: Not specified
Model simulation showing the effect of varying PGK or FBPAase concentration on the efficiency for 3PG to F6P conversion.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Pathway optimisation
Assays: Modelling pathway optimisation
Scales: Not specified
Saturation of PGK with 3PG
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Assays: PGK, PGK modeling
Scales: Not specified
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Assays: PGK, PGK modeling
Scales: Not specified
Kinetic characterisation of Phosphoglycerokinase. Measures enzyme reaction rate with increasing concentration of ATP
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Assays: PGK, PGK modeling
Scales: Not specified
An exponential decay model was fitted to the experimental data set of GAP degradation at 70C. The model is uploaded as an SBML file. A data file showing the model fit to the experimental data set is included. The rate constant for GAP degradation at 70C was estimated to be 0.056 1/min, equivalent to a half life time of 12.4 min.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Modelling analyses: Modelling temperature dependent degradation of ...
Scales: Not specified
An exponential decay model was fitted to the experimental data set of DHAP degradation at 70C. The model is uploaded as an SBML file. A data file showing the model fit to the experimental data set is included. The rate constant for DHAP degradation at 70C was estimated to be 0.0225 1/min, equivalent to a half life time of 30.8 min.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Modelling analyses: Modelling temperature dependent degradation of ...
Scales: Not specified
Mathematical model for FBPAase kinetics
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: FBPAase model
Scales: Not specified
Mathematical model for GAPDH kinetics, saturation for GAP, BPG, NADP, NADPH, Pi.
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: GAPDH modeling
Scales: Not specified
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
Cloning and heterologous expression of gluconeogenic enzymes in E. coli
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Scales: Not specified
Preparation of cell free extracts of the recombinant E. coli strains expressing the respective S. solfataricus enzymes.
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Scales: Not specified
The recombinant enzymes were purified from the cell free extracts of E. coli expressing the respective enzymes.
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Scales: Not specified
Abstract (Expand)
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