WP2.3 Detailed kinetic modelling, identification and analysis of the citric acid cycle and respiratory chains of E. coli

Project leader: Oliver Sawodny
Former Co-Project leader: Thomas Sauter (now University of Luxembourg)
Sub-Project leader: Michael Ederer
Postgraduate / Postdoc : Sebastian Henkel

This workpackage deals with the detailed kinetic modelling, identification and analysis of the TCA cycle (tricarboxylic acid cycle, citric acid cycle) and the ETC (electron transport chains, respiratory chains) of E. coli. In comparison to the reduced order modelling? this work package aims to reproduce the fast dynamic behaviour of these processes by the insertion of detailed mechanistic components as well as the use of fewer reducing assumptions concerning dynamics. Especially for the identification and the analysis of the models fast dynamic measurement data is required.

Primarily the modelling is divided into the establishment of a TCA cycle model and an ETC model as implicated by the WP's title. Probably at a future stage the two systems will be connected.

The following table shows the information about the available models, experiments and the link to the respective sources in the LIMS (ordered by descending date of first upload):

Models & Experiments

date	name & link	short description
2010	Extended ETC principle model 3	Due to recent ArcA~P phosgel measurement data and investigations concerning thermodynamics between quinones and ArcBA another model version was created. It considers only the oxidised quinones and not the quinone redox state being signal for ArcB. Apart from that it resembles the former version. The parameter identification is still in progress.
2009/2010	Model results	This is in-silico data comparing measurement and simulation data used and created by extended ETC principle model 2
2009/2010	Extended ETC principle model 2	Due to the sensitivity analysis and the discussion about possible parameter changes, another ETC model extension was created. In comparison to the last extension again only one unifying oxidase is considered. In addition a simplified growth model was joined allowing the origin of electrons and possible changes due to different dilution rates. The parameter identification is still in progress. Preliminary results can be found here.
2008 Nov. 5th	Simulation/Sensitivity analysis	Simulation and sensitivity analysis of this extended ETC principle model 1.
2008 Nov. 5th	Extended ETC principle model	First extensions of the earlier ETC principle model: a) input of oxygen by aer variable; b) two oxidases (assumed partitioning). Parameter identified due to the use of measurement data. Experiments.
2008 Jul. 10th	ETC principle model	Simplified model of the electron-transport chain of Escherichia coli and its regulation by ArcA and FNR to demonstrate a hypothetical design principle in the regulatory structure.
2007 Sep. 2nd	TCA preliminary work	Preliminary work on the TCA cycle.