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- Modelling temperature dependent degradation of GAP and DHAP

The temperature dependent degradation of DHAP and GAP is modelled as an exponential decay process using experimental data for the disintegration at 70C.

**SEEK ID:** https://demo.fairdomhub.org/assays/21

Modelling Analysis

**Projects:** SulfoSys

**Investigation: **
Central Carbon Metabolism of Sulfolobus solfataricus

**Study: **
Model gluconeogenesis

**Biological problem addressed:**
Metabolism

**Organisms**: No organisms

**Models:**

**Data:**

**Views:** 1073

**Created**: 29th Jan 2013 at 22:05

**Last updated**: 26th Oct 2017 at 11:57

## Related items

**Projects:** PSYSMO, MOSES, SysMO DB, SysMO-LAB, SulfoSys

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

**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 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 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

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

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

**Studies:** Model gluconeogenesis

**Scales:**
Not specified

GAP concentrations were measured over time at 70C.

**Scales:**
Not specified

DHAP concentrations were measured over time at 70C.

**Scales:**
Not specified

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

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

**Studies:** Model gluconeogenesis

**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

**Abstract** (Expand)

**Authors: **Jacky Snoep, Kouril T.,Esser D.,Kort J.,Westerhoff H. V.,Siebers B.

**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