Metabolic network simulation using logical loop algorithm and Jacobian matrix |
| |
Authors: | Yang Tae Hoon Wittmann Christoph Heinzle E Elmar |
| |
Affiliation: | Biochemical Engineering Institute, Saarland University, Postfach 151150, Bldg. 2, D-66041 Saarbrücken, Germany. |
| |
Abstract: | A novel method to accomplish efficient numerical simulation of metabolic networks for flux analysis was developed. The only inputs required are the set of stoichiometric balances and the atom mapping matrices of all components of the reaction network. The latter are used to automatically calculate isotopomer mapping matrices. Using the symbolic toolbox of MATLAB the analytical solution of the stoichiometric balance equation system, isotopomer balances and the analytical Jacobian matrix of the total set of stoichiometric and isotopomer balances are created automatically. The number of variables in the isotopomer distribution equation system is significantly reduced applying modified isotopomer mapping matrices. These allow lumping of several consecutive isotopomer reactions into a single one. The solution of the complete system of equations is improved by implementing an iterative logical loop algorithm and using the analytical Jacobian matrix. This new method provided quick and robust convergence to the root of such equation systems in all cases tested. The method was applied to a network of lysine producing Corynebacterium glutamicum. The resulting equation system with the dimension of 546 x 546 was directly derived from 12 isotopomer balance equations. The results obtained yielded identical labeling patterns for metabolites as compared to the relaxation method. |
| |
Keywords: | AcCoA, acetyl-CoA DAP, http://www.sciencedirect.com/cache/MiamiImageURL/B6WN3-4C76CN9-1-8X/0?wchp=dGLbVlz-zSkWb" alt=" Image" title=" Image" style=" vertical-align:bottom" border=" 0" height=10 width=" 11" />, http://www.sciencedirect.com/cache/MiamiImageURL/B6WN3-4C76CN9-1-8Y/0?wchp=dGLbVlz-zSkWb" alt=" Image" title=" Image" style=" vertical-align:bottom" border=" 0" height=10 width=" 9" />-2, 6-diaminopimelate DHAP, dihydroxyacetone phosphate EMP, Embden–Meyerhof–Parnas pathway ICT, isocitrate IDV, isotopomer distribution vector IMM, isotopomer mapping matrix LLA, logical loop algorithm PP, pentose phosphate pathway TCA, tricarboxylic acid cycle GAP, glyceraldehydes 3-phosphate OAA, oxaloacetate Pyr, pyruvate SUC, succinate αKG, α-ketoglutarate ΔPDC, Δ-piperidine-2, 6-dicarboxylate 3PG, 3-phosphoglycerate. |
本文献已被 ScienceDirect PubMed 等数据库收录! |
|