Assays

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

Model prediction of the conversion of 3PG to fructose-6-phosphate and the gluconeogenic pathway intermediates. https://jjj.bio.vu.nl/models/experiments/kouril3_experiment-user/simulate

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

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

Mathematical model for FBPAase kinetics, saturation with DHAP and GAP

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

The stressosome is an important sensor of environmental stresses in B. subtilis. It is formed by three protein types that form an icosahedral geometric protein complex. There are uncertanties how protein interactions take place, what the effects on the response behaviour of activation and inhibition of phosphorylation among proteins is, and what kind of proximal signal activates the stressosome in the first place. To answer these questions a computational modelling approach was developed. This ...

Despite high similarity in sequence and catalytic properties, the L-lactate dehydrogenases (LDH) in lactic acid bacteria (LAB) display differences in their regulation which may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose-1,6-bisphosphate (FBP), phosphate (Pi) and ionic strength (NaCl concentration) on 6 LDHs from 4 LABs studied at pH 6 and pH 7. We find: (1) The extent of activation by FBP (Kact) ...

We here create a kinetic model for a single enzyme within the T. brucei trypanothione synthesis pathway, the enzyme trypanothione synthetase based on the insights from the laboratory experiments

The RNAseq data on mRNA processing and mRNA decay were used to update a previously published model and to interrogate which process should be dependent on mRNA length

Kinetic characterisation en mathematical modelling of HK.

Kinetic characterisation en mathematical modelling of PGI.

Kinetic characterisation en mathematical modelling of PFK.

Kinetic characterisation en mathematical modelling of ALD.

Kinetic characterisation en mathematical modelling of TPI.

Kinetic characterisation en mathematical modelling of G3PDH.

Kinetic characterisation en mathematical modelling of GAPDH.

Kinetic characterisation en mathematical modelling of PGK.

Kinetic characterisation en mathematical modelling of PGM.

Kinetic characterisation en mathematical modelling of ENO.

Kinetic characterisation en mathematical modelling of PK.

Kinetic characterisation and mathematical modelling of LDH.

SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/penkler2aa_experiment-user/simulate

RobOKoD algorithm was, designed then implemented as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain. It was shown to perform better than similar methods (OptKnock, and RobustKnock).