Abstract
The analysis of pathways in metabolic networks has become an important approach for understanding metabolic systems. Constraint-based approaches recently brought new insight into our understanding of metabolism. Here we introduce a method for identifying optimal metabolic pathways. The method, generates data on reaction fluxes based on biomass conservation constraint and formulates constraints incorporating weighting coefficients corresponding to concentration of enzymes catalyzing the reactions. The effectiveness of the present method is demonstrated on the pentose phosphate pathway (PPP) in T. cruzi and on a large network of the plant polyamine pathway existing in the literature. A comparative study with the existing extreme pathway analysis (EPA) also forms a part of this investigation.
Chapter PDF
Similar content being viewed by others
References
Papin, J.A., Price, N.D., Wiback, S.J., Fell, D.A., Palsson, B.O.: Metabolic path-ways in the post-genome era. Trends in Biochemical Sciences 28, 250–258 (2003)
Lee, J.M., Gianchandani, E.P., Papin, J.A.: Flux balance analysis in the era of metabolomics. Briefings in Bioinformatics 7, 1–11 (2006)
Schilling, C.H., Letscher, D., Palsson, B.O.: Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 203, 229–248 (2000)
Stryer, L., Berg, J.M., Tymoczko, J.L., Clarke, N.D. (eds.): Biochemistry. W H Freeman, New York (1998)
Montoya, A.R., Lee, W.P., Bassilian, S., Lim, S., Trebukhina, R.V., Kazhyna, M.V., Ciudad, C.J., Noe, V., Centelles, J.J., Cascante, M.: Pentose phosphate cycle oxidative and nonoxidative balance: A new vulnerable target for overcoming drug resistance in cancer. Int. J. Cancer 119, 2733–2741 (2006)
Mapelli, S., Brambilla, I.M., Radyukina, N.L., Ivanov, Y.V., Kartashov, A.V.: Free and bound polyamines changes in different plants as a consequence of uv-b light irradiation. Gen. Appl. Plant Physiology (special issue 34), 55–66 (2008)
Kumar, A., Altabella, T., Taylor, M.A., Tiburcio, A.F.: Recent advances in polyamine research. Trends Plant Sci. 2, 124–130 (1997)
Malmberg, R.L., Watson, M.B., Galloway, G.L., Yu, W.: Molecular genetic analyses of plant polyamines. Critical Reviews in Plant Sciences 17, 199–224 (1998)
Ponce, M., Martinez, L., Galmarini, C.: Influence of ccc, putrescine and gellam gum concentration on gynogenic embryo induction in allium cepa. Biologia Plantarum 50(3), 425–428 (2006)
Igoillo-Esteve, M., Maugeri, D., Stern, L., Beluardi, P., Cazzulo, M.J.: The pentose phosphate pathway in trypanosoma cruzi: a potential target for the chemotherapy of chagas disease. Annals of the Brazilian Academy of Sciences 79, 649–663 (2007)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Das, M., Mukhopadhyay, S., De, R.K. (2009). A Constraint Based Method for Optimization in Metabolic Pathways. In: Chaudhury, S., Mitra, S., Murthy, C.A., Sastry, P.S., Pal, S.K. (eds) Pattern Recognition and Machine Intelligence. PReMI 2009. Lecture Notes in Computer Science, vol 5909. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-11164-8_31
Download citation
DOI: https://doi.org/10.1007/978-3-642-11164-8_31
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-11163-1
Online ISBN: 978-3-642-11164-8
eBook Packages: Computer ScienceComputer Science (R0)