Label distribution

Vitaly Selivanov

If substrates of cellular metabolism contain labeled atoms (as 13C isotopes), metabolic networks introduces them into the intermediates and products in accord with the internal metabolic fluxes. Therefore, the resulting label distribution carries the information about the cellular metabolic fluxes. The distribution could be assessed experimentally with NMR or GC/MS technique; analysis of these data requires tracing of huge amount of possible isotopomers (a substance of n carbon atoms is represented by 2n isotopomers).  A method of authomatical construction of the respective huge system of differential equations is described here: V. A. Selivanov, J. Puigjaner, A. Sillero, J.J. Centelles, A. Ramos-Montoya, P.W.N. Lee, M. Cascante. An Optimized Algorithm for Flux Estimation from Isotopomer Distribution in Glucose Metabolites. Bioinformatics, 2004,20,3387-3397.

   This method was realized as a "Mathematica" (Wolfram Inc) program: fitting.nb This program first calculates total metabolite concentrations and fluxes for glycolytic and pentose phosphate pathways and then uses the linked program check1.exe to calculate concentrations of all possible isotopomers. This program was written in C, which makes these time-consuming calculations faster.

The present approach allows implementing in the isotopomer analysis the available "classical" enzyme kinetic information, which restricts ambiguity in the possible estimated sets of fluxes. The software, which accounts for the detailed kinetic mechanism of transketolase (TK) and transaldolase (TA) reactions, is present in several versions, one of which, "Mathematica"-version, is described here: V.A. Selivanov, L.E. Meshalkina, O.N. Solovjeva, P.W. Kuchel, A.Ramos-Montoya, G.A. Kochetov, P.W.N. Lee, M. Cascante. Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells. Bioinformatics, 2005, 21, 3558-3564.

The "Mathematica" program is in the file “rib-ot.nb” located in the archive Bioinform2005Math. This contains also the executable “rrib.exe”, which is linked to the main program; supplementary file “TK-scheme.nb”, which shows the details of implementation of the isotope-exchange fluxes produced in TK and TA reactions. This program also has an algorithm for parameter optimization, which minimizes χ2 by coordinate descent, estimates the goodness of fit and formal standard errors for parameters. Development of new algorithm was necessary because the standard “Mathematica” algorithms for optimization do not work properly with differential equations because of falling to the area of parameters where the system becomes stiff and solution could not be obtained.

The supplementary file “TK-substrate.nb”, simulating substrate accumulation in TK reaction is located in the archive TK-substrate.

A C++ console application “coli530.exe” computes the distribution of all isotopomers (though only mass isotopomers are included in the output) accounting for, in addition to that present in the "Mathematica" version, the competition between the TK substrates, Krebs cycle and anaplerotic reactions. It is located in the archive Bioinform2005-C++, also containing the scheme of the reaction pathway, “reaction scheme.jpg”; the scheme of TK-reaction accounting for the substrate competition implemented in “coli530.exe”, “TK-compet.jpg”; the scheme for the TA-reaction, “TA.jpg”, and other files described in details in the user guide “readme console.doc”, also located in the same archive.  

A “Windows” application (“wst602.exe”) is located in the archive "windows", which contains also all the files necessary for the correct execution of “wst602.exe” and the user guide with the name “readme windows.doc”. This windows application uses the same format of files with experimental data “exper.dat” and parameters “nv.txt” as the console application.

The archive "fit", represents a next generation of the program described in Bioinformatics, 2006, 22, 2806-2812.. It analyses the metabolic network consisted of glucose input, glycolysis, glycogen metabolism, Pentose Phosphate Pathway with detailed scheme for isotope-exchange fluxes created by transketolase and transaldolase catalysis accounting for competition between the substrates, Krebs cycle, anaplerotic reactions, and various fluxes connecting this part  with whole metabolic system. In the present example it is customized for rat liver cell metabolism and simulates different experiments where labeled glucose or labeled lactate were used. It also has a procedure for  χ2 minimization based on Simulated Annealing algorithm for global optimization, which uses Powell's method in a local area. It also analyses the sensitivity to parameters and evaluates formal standard deviations for the adjusted parameters. The brief user guide "readme.doc" describes the most essential details mecessary for using this tool.

Noraybio

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Model of mitochondrial respiration and ROS production is a tool for the analysis of experimental data related with mitochondrial respiration and coupled reactive oxygen species (ROS) production. It describes the redox state of the complex, which is composed of concentrations of 400 different combinations of oxidized or reduced states of electron transporters: cytochrome Bh, cytochrome Bl, cytochrome C1, Fe-S complex of Rieske protein, and ubiquinone/semiquinone/ubiquinol bound on cytosolic or matrix sides of the complex. Click here to download the model.

 

Research Groups of the Department
Department of Biochemistry and Molecular Biology

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Last update: July, 14th  2008