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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://fairdomhub.org/studies/112

Central Carbon Metabolism of Sulfolobus solfataricus

**Projects:** SulfoSys

**Experimentalists:**
Theresa Kouril

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**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, COMBINE Multicellular Modelling, HOTSOLUTE, Steroid biosynthesis, Yeast glycolytic oscillations, Computational pathway design for biotechnological applications

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

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.

**Snapshots: **No snapshots

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

**Assays:** Experimental Validation Gluconeogenesis in S. solfataricus, FBPAase, FBPAase Modelling, GAPDH, GAPDH Modelling, Model Validation Gluconeogenesis in S. solfataricus, Modelling Metabolite Degradation at High Temperature, PGK, PGK Modelling, Reconstituted Gluconeogenesis System, TPI, TPI Modelling, Temperature Degradation of Gluconeogenic Intermediates

Kinetic characterisation of glyceraldehyde 3-phosphate dehydrogenase

**Contributor**: Jacky Snoep

**Assay type**: Enzymatic Assay

**Technology type**: Initial Rate Experiment

**Snapshots: **No snapshots

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

**Study:** Model Gluconeogenesis

**Organisms**: Sulfolobus solfataricus

**SOPs:** Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts

**Data files:** GAPDH Kinetic Data

Kinetic characterisation of triose phosphate isomerase

**Contributor**: Jacky Snoep

**Assay type**: Enzymatic Assay

**Technology type**: Initial Rate Experiment

**Snapshots: **No snapshots

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

**Study:** Model Gluconeogenesis

**Organisms**: Sulfolobus solfataricus

**SOPs:** Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts

**Data files:** TPI Kinetic Data

Kinetic characterisation of fructose 1,6-bisphosphate aldolase phosphatase

**Contributor**: Jacky Snoep

**Assay type**: Enzymatic Assay

**Technology type**: Initial Rate Experiment

**Snapshots: **No snapshots

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

**Study:** Model Gluconeogenesis

**Organisms**: Sulfolobus solfataricus

**SOPs:** Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts

**Data files:** FBPAase Kinetic data

Temperature degradation of BPG, GAP and DHAP

**Contributor**: Jacky Snoep

**Assay type**: Metabolite Concentration

**Technology type**: Technology Type

**Snapshots: **No snapshots

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

**Study:** Model Gluconeogenesis

**Organisms**: Sulfolobus solfataricus

**SOPs:** No SOPs

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

Kinetic characterisation of phosphoglycerate kinase

**Contributor**: Jacky Snoep

**Assay type**: Enzymatic Assay

**Technology type**: Initial Rate Experiment

**Snapshots: **No snapshots

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

**Study:** Model Gluconeogenesis

**Organisms**: Sulfolobus solfataricus

**SOPs:** Cloning and heterologous expression in E. coli, Preparation of cell extracts of recombinant E.coli, Protein purification from E. coli extracts

**Data files:** PGK Kinetic Data

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

**Models:** PGK Kinetic Model

**SOPs:** No SOPs

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

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

**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

**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 TPI kinetics, saturation with GAP and DHAP, and inhibition by 3PG and PEP

**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

Mathematical model for FBPAase kinetics, saturation with DHAP and GAP

**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

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

**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...

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

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

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

**Studies:** Model Gluconeogenesis

**Assays:** TPI Modelling

Simulation results of temperature degradation of gluconeogenic intermediates

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

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

**Studies:** Model Gluconeogenesis

Simulation results of PGK experimental data for ADP, ATP, 3PG and BPG saturation.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

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

**Studies:** Model Gluconeogenesis

**Assays:** PGK Modelling

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

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

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

**Studies:** Model Gluconeogenesis

**Assays:** GAPDH Modelling

Simulation results of FBPAase of experimental data for DHAP and GAP saturation

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

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

**Studies:** Model Gluconeogenesis

**Assays:** FBPAase Modelling

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

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

**Studies:** Model Gluconeogenesis

**Assays:** FBPAase, FBPAase Modelling

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

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

**Studies:** Model Gluconeogenesis

**Assays:** TPI, TPI Modelling

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

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

**Studies:** Model Gluconeogenesis

**Assays:** GAPDH, GAPDH Modelling

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

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

Kinetic characterisation of PGK. Expermental data for enzyme reaction rates with increasing concentrations of ATP, ADP, BPG and 3PG.

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

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

**Studies:** Model Gluconeogenesis

**Assays:** PGK, PGK Modelling

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

**Environment**: JWS Online

**Organism**: Sulfolobus solfataricus

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

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

**Modelling analyses:** Model Validation Gluconeogenesis in S. solfatar..., Reconstituted Gluconeogenesis System

Exponential decay model of gluconeogenic intermediates

**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:** Modelling Metabolite Degradation at High Temper..., Reconstituted Gluconeogenesis System

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

**Environment**: Not specified

**Organism**: Sulfolobus solfataricus

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

**Studies:** Model Gluconeogenesis

**Modelling analyses:** Reconstituted Gluconeogenesis System, TPI Modelling

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

**Environment**: Not specified

**Organism**: Sulfolobus solfataricus

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

**Studies:** Model Gluconeogenesis

**Modelling analyses:** GAPDH Modelling, Reconstituted Gluconeogenesis System

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

**Environment**: Not specified

**Organism**: Sulfolobus solfataricus

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

**Studies:** Model Gluconeogenesis

**Modelling analyses:** FBPAase Modelling, Reconstituted Gluconeogenesis System

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

**Environment**: Not specified

**Organism**: Sulfolobus solfataricus

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

**Studies:** Model Gluconeogenesis

**Modelling analyses:** PGK Modelling, Reconstituted Gluconeogenesis System

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

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

**Studies:** Model Gluconeogenesis

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

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

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

**Studies:** Model Gluconeogenesis

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

**Creators: **Jacky Snoep, Theresa Kouril

**Contributor**: Jacky Snoep

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

**Studies:** Model Gluconeogenesis

**Abstract** (Expand)

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

**Date Published**: 20th Jul 2013

**Journal**: FEBS J.

**PubMed ID**: 23865479

**Citation**: