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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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**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

Mathematical model for the analysis of carbon loss of BPG, GAP and DHAP in reconstituted system of S. solfataricus at 70C.

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

**Study:** Model gluconeogenesis

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

**Models:** Mathematical model for the combined four enzyme...

**SOPs:** No SOPs

**Data files:** Metabolite concentrations during reconstituted ...

**Scales:**
Not specified

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

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

**Study:** Model gluconeogenesis

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

**Models:** TIM kinetic model

**SOPs:** No SOPs

**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

Mathematical model for GAPDH kinetics, saturation of GAP, BPG, NADP, NADPH and Pi.

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

**Study:** Model gluconeogenesis

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

**Models:** GAPDH kinetic model

**SOPs:** No SOPs

**Data files:** GAPDH kinetics 3PG, GAPDH kinetics GAP, GAPDH kinetics NADP, GAPDH kinetics NADPH, GAPDH kinetics Pi and 1 hidden item

**Scales:**
Not specified

Mathematical model for PGK kinetics, saturation with ADP, ATP, 3PG and BPG.

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

**Study:** Model gluconeogenesis

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

**Models:** 1 hidden item

**SOPs:** No SOPs

**Data files:** Model simulation and experimental data for ADP,..., PGK kinetics 3PG, PGK kinetics ADP, PGK kinetics ATP, PGK kinetics BPG

**Scales:**
Not specified

Mathematical model for FBPAase kinetics, saturation of GAP and DHAP

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

**Study:** Model gluconeogenesis

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

**Models:** FBPAase kinetic model

**SOPs:** No SOPs

**Data files:** FBPA/ase kinetics DHAP, FBPA/ase kinetics GAP, Model simulation and experimental data for DHAP...

**Scales:**
Not specified

A time simulation of the mathematical model is shown together with the experimental data to which the model was fitted.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

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

**Studies:** Model gluconeogenesis

**Scales:**
Not specified

A time simulation of the mathematical model is shown together with the experimental data to which the model was fitted.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

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

**Studies:** Model gluconeogenesis

**Scales:**
Not specified

GAP concentrations were measured over time at 70C.

**Creators: **None

**Contributor**: Jacky Snoep

**Scales:**
Not specified

DHAP concentrations were measured over time at 70C.

**Creators: **None

**Contributor**: Jacky Snoep

**Scales:**
Not specified

Model simulation and experimental data for DHAP and GAP saturation of FBPA/ase

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

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

**Studies:** Model gluconeogenesis

**Assays:** FBPA/ase, FBPAase model

**Scales:**
Not specified

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

**Creator: **Jacky Snoep

**Contributor**: 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

**Modelling analyses:** Gluconeogenic model, Model reconstituted system, Modelling pathway optimisation

**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

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 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

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

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

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

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

**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