In my attempt to create a metabolic model of E. coli, I have found a comprehensive list of metabolic reactions and their stoichiometry. The one I am currently using is E. coli model iJO1366 (more here). What I have not yet found is a comprehensive list of kinetic rate constants associated with these reactions. I also require a data source of concentrations of these enzymes and metabolites at steady state in E. coli. Where can I find information on concentrations and rate constants?
$\begingroup$ why do you want to compile this? Flux analysis is looking pretty useful and does not require all this data. $\endgroup$– shigetaSep 23, 2012 at 4:09
$\begingroup$ I found SABIO: sabio.h-its.org $\endgroup$– BitwiseMar 21, 2013 at 1:02
I would advise you to use the SMBL for iAF1260 E. Coli with a COBRA toolbox on MATLAB. It has all the constants you are looking for optimized for the steady state and have been extensively tested for simulation of single and multiple genes deletion / mutation. Even if you want to stick with your model you will be able to copy the constants from there.
However depending on what you are doing you might not be satisfied by the whole models, since the they are computationally too complicated to simulate and optimize and lead to computationally unstable results, especially when you try to simulate colony collaborative mechanisms.
$\begingroup$ Do you have any literature to support your claim of computational instability? $\endgroup$– CoderMar 21, 2013 at 18:02
$\begingroup$ This is my personal experience. When you use the COBRA toolbox, you use an external module for linear optimization to get your "objective" function. When I computed the base model from iAF1260 E.Coli, it worked well, just as a system of two bacteria living together. But as soon as you started to perform single or double gene deletion analysis, your objective function maximum started to behave erratically. You could make it bit better with it by using a different external linear optimization module, but still no analysis was possible. $\endgroup$ Mar 21, 2013 at 18:52
$\begingroup$ This work was based on this paper and I had an impression that the authors run into pretty much the same limitations: only qualitative analysis is provided with the computational model, whereas they could have gone quantitative with this model and had quantitative experimental results. $\endgroup$ Mar 21, 2013 at 18:57