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Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus

**SEEK ID:** https://demo.fairdomhub.org/studies/10

Central Carbon Metabolism of Sulfolobus solfataricus

**Projects:** SulfoSys

**Experimentalists:**
Theresa Kouril

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**Views:** 2224

**Created**: 29th Jan 2013 at 15:16

**Last updated**: 28th May 2015 at 10:50

## Related items

- People (1)
- Projects (1)
- Investigations (1)
- Assays (11+1)
- Data files (23+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

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

Kinetic characterisation of Phosphoglycerokinase

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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.

**Contributor**: 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.

**Contributor**: 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

Saturation of PGK with 3PG

**Creators: **None

**Contributor**: Jacky Snoep

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Model gluconeogenesis

**Assays:** PGK, PGK modeling

**Scales:**
Not specified

**Creators: **None

**Contributor**: 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

**Contributor**: Jacky Snoep

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Model gluconeogenesis

**Assays:** PGK, PGK modeling

**Scales:**
Not specified

**Creators: **None

**Contributor**: Jacky Snoep

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Model gluconeogenesis

**Assays:** PGK, PGK modeling

**Scales:**
Not specified

Model simulation and experimental data for ADP, ATP, 3PG and BPG saturation of PGK

**Creator: **Jacky Snoep

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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

**Contributor**: 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, Jacky Snoep

**Date Published**: 22nd Aug 2013

**Journal**: FEBS J

**PubMed ID**: 23865479

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

**Scales:**
Not specified