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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

**FAIRDOMHub ID: ** https://seek.sysmo-db.org/studies/112

Central Carbon Metabolism of Sulfolobus solfataricus

**Projects:** SulfoSys

**Experimentalists:**
Theresa Kouril

**Views:** 1602

**Created**: 1st Aug 2013 at 11:03

## Related items

- People (1)
- Projects (1)
- Investigations (1)
- Assays (11)
- Data files (10)
- Models (6)
- SOPs (3)
- Publications (1)

**Projects:** PSYSMO, MOSES, SysMO DB, SysMO-LAB, SulfoSys, SulfoSys - Biotec, Whole body modelling of glucose metabolism in malaria patients, FAIRDOM, Molecular Systems Biology

**Institutions:** Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch, School of Computer Science, University of Manchester

**Disciplines:** Not specified

**Roles:** Not specified

**Expertise:** Not specified

**Tools:** Not specified

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 central carbon metabolism of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.

**Studies:** Carbon Loss at High Temperature, Model Gluconeogenesis

In vitro reconstitution of the PGK, GAPHD, TPI and FBPAase enzymes from S. solfataricus

**Contributor**: Jacky Snoep

**Biological problem addressed**: Metabolic network

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

**Study:** Model Gluconeogenesis

**Organisms**: Sulfolobus solfataricus

**Models:** FBPAase Kinetic Model, GAPDH Kinetic Model, Kinetic Model of Temperature Degradation of Glu..., Model of reconstituted gluconeogenesis system i..., PGK Kinetic Model, TPI Kinetic Model

**SOPs:** No SOPs

**Data files:** No Data files

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

**Contributor**: Jacky Snoep

**Biological problem addressed**: Enzymology

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

**Study:** Model Gluconeogenesis

**Organisms**: Sulfolobus solfataricus

**Models:** GAPDH Kinetic Model

**SOPs:** No SOPs

**Data files:** GAPDH Kinetic Data, GAPDH Kinetics Simulation

Mathematical model for FBPAase kinetics, saturation with DHAP and GAP

**Contributor**: Jacky Snoep

**Biological problem addressed**: Enzymology

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

**Study:** Model Gluconeogenesis

**Organisms**: Sulfolobus solfataricus

**Models:** FBPAase Kinetic Model

**SOPs:** No SOPs

**Data files:** FBPAase Kinetic data, FBPAase Kinetics Simulation

Temperature degradation of BPG, GAP and DHAP

**Contributor**: Jacky Snoep

**Assay type**: Metabolite concentration

**Technology type**: Technology type

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

**Study:** Model Gluconeogenesis

**Organisms**: Sulfolobus solfataricus

**SOPs:** No SOPs

**Data files:** Temperature Degradation of Gluconeogenic Interm...

Modelling the degradation of BPG, GAP and DHAP at high temperature

**Contributor**: Jacky Snoep

**Biological problem addressed**: Metabolism

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

**Study:** Model Gluconeogenesis

**Organisms**: Sulfolobus solfataricus

**Models:** Kinetic Model of Temperature Degradation of Glu...

**SOPs:** No SOPs

**Data files:** Temperature Degradation Kinetics Simulation, Temperature Degradation of Gluconeogenic Interm...

Kinetic characterisation of fructose 1,6-bisphosphate aldolase phosphatase

**Contributor**: Jacky Snoep

**Assay type**: Enzymatic assay

**Technology type**: Initial rate experiment

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

**Study:** Model Gluconeogenesis

Mathematical model for TPI kinetics, saturation with GAP and DHAP, and inhibition by 3PG and PEP

**Contributor**: Jacky Snoep

**Biological problem addressed**: Enzymology

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

**Study:** Model Gluconeogenesis

**Organisms**: Sulfolobus solfataricus

**Models:** TPI Kinetic Model

**SOPs:** No SOPs

**Data files:** TPI Kinetic Data, TPI Kinetics Simulation

Kinetic characterisation of FBPAase. Expermental data for enzyme reaction rates with increasing concentrations of DHAP and GAP.

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

Kinetic characterisation of TPI. Experimental data for enzyme reaction rates with increasing concentrations of DHAP and GAP, and inhibition with 3PG and PEP.

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

Kinetic characterisation of GAPDH. Expermental data for enzyme reaction rates with increasing concentrations of BPG, NADPH, NADP, GAP and Pi.

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

Simulation results of temperature degradation of gluconeogenic intermediates

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

Experimental data for determination of half-life of gluconeogenic intermediates (BPG, GAP and DHAP).

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

Simulation results of TPI experimental data for GAP and DHAP saturation.

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

Simulation results of GAPDH experimental data for BPG, NADPH, NADP, GAP, and Pi

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

Model of reconstituted gluconeogenesis system in S. solfataricus based on the individual kinetic models for PGK, GAPDH, TPI, FBPAase.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Organism**: Sulfolobus solfataricus

**Environment**: JWS Online

Exponential decay model of gluconeogenic intermediates

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

**Organism**: Sulfolobus solfataricus

**Environment**: Not specified

Mathematical model for TPI kinetics, GAP and DHAP saturation, and inhibition with 3PG and PEP.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

**Organism**: Sulfolobus solfataricus

**Environment**: Not specified

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

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

**Organism**: Sulfolobus solfataricus

**Environment**: Not specified

Mathematical model for FBPAase kinetics, saturation with DHAP and GAP

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

**Organism**: Sulfolobus solfataricus

**Environment**: Not specified

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

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

**Organism**: Sulfolobus solfataricus

**Environment**: Not specified

Preparation of cell free extracts of the recombinant E. coli strains expressing the gluconeogenic S. solfataricus enzymes.

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

Cloning and heterologous expression of gluconeogenic enzymes from S. solfataricus in E. coli

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

Purification of gluconeogenic enzymes from S. solfataricus in recombinant E.coli extracts

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

**Abstract** (Expand)

**Authors: **Theresa Kouril, Hans Westerhoff, Bettina Siebers, Jacky Snoep, Esser Dominik,Kort Julia

**Date Published**: 20th Jul 2013

**Journal**: FEBS J.

**PubMed ID**: 23865479

**Citation**: