Modelling pathway optimisation
Varying the relative amounts of PGK and FBPAase and analyse the 3PG uptake and F6P production rates.
SEEK ID: https://demo.fairdomhub.org/assays/29
Modelling analysis
Projects: SulfoSys
Investigation: Central Carbon Metabolism of Sulfolobus solfataricus
Study: Pathway optimisation
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: Sulfolobus solfataricus : P2 (wild-type / wild-type)
Data:
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Created: 3rd Feb 2013 at 09:56
Last updated: 26th Oct 2017 at 09:57
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SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO is to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB
Web page: http://sysmo.net/
Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Programme: SysMO
Public web page: http://sulfosys.com/
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.
Submitter: Jacky Snoep
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
By varying the input or output flux via PGK and FBPAase manipulation respectively the pathway efficiency can be optimised.
Submitter: Jacky Snoep
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Assays: Modelling pathway optimisation, PGK and FBPAase titrations
Submitter: Not available
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Sulfolobus solfataricus
Genotypes: wild-type
Phenotypes: wild-type
Comment: Not specified
Combined plot fo the model simulations and the experimental data for the PGK and FBPAase titrations.
Model simulation showing the effect of varying PGK or FBPAase concentration on the efficiency for 3PG to F6P conversion.
Increasing the amount of PGK in the incubation assay and measuring the 3PG and F6P fluxes.
Increasing the amount of FBPAase in the reconstituted system and measuring the 3PG and F6P fluxes.
The PGK, GAPDH, TPI and FBPAase were modelled together using the individual rate equations. Closed system.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Abstract (Expand)
Authors: T. Kouril, D. Esser, J. Kort, H. V. Westerhoff, B. Siebers, J. L. Snoep
Date Published: 22nd Aug 2013
Publication Type: Not specified
