Jacky Snoep

Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:

• facilitates and maximises the potential for data exchange between SysMO research groups;
• maximises the ‘shelf life’ and ...

Comparative Systems Biology: Lactic Acid Bacteria

Systems analysis of process-induced stresses: towards a quantum increase in process performance of Pseudomonas putida as the cell factory of choice for white biotechnology.

The specific goal of this project is to exploit the full biotechnological efficacy of Pseudomonas putida KT2440 by developing new optimization strategies that increase its performance through a systems biology understanding of key metabolic and regulatory parameters that control callular responses to key stresses generated ...

MOSES (Micro Organism Systems biology: Energy and Saccharomyces cerevisiae) develops a new Systems Biology approach, which is called 'domino systems biology'. It uses this to unravel the role of cellular free energy ('ATP') in the control and regulation of cell function. MOSES operates though continuous iterations between partner groups through a new systems-biology driven data-management workflow. MOSES also tries to serve as a substrate for three or more other SYSMO programs.

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.

Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus

By varying the input or output flux via PGK and FBPAase manipulation respectively the pathway efficiency can be optimised.

Kinetic characterisation of Phosphoglycerokinase

Kinetic characterization of the FBPA/ase with respect to GAP en DHAP saturation.

GAP and DHAP concentrations were measured over time at 70C.

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.

Saturation of PGK with 3PG

Kinetic characterisation of Phosphoglycerokinase. Measures enzyme reaction rate with increasing concentration of ATP

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.

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.

Mathematical model for FBPAase kinetics

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

Mathematical model for TIM kinetics, GAP and DHAP saturation and PEP inhibition.

Cloning and heterologous expression of gluconeogenic enzymes in E. coli

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

The recombinant enzymes were purified from the cell free extracts of E. coli expressing the respective enzymes.