Recovering metabolic pathways via optimization

A metabolic pathway is a coherent set of enzyme catalysed biochemical reactions by which a living organism transforms an initial (source) compound into a final (target) compound. Some of the different metabolic pathways adopted within organisms have been experimentally determined. In this paper, we show that a number of experimentally determined metabolic pathways can be recovered by a mathematical optimization model.

[1]  An-Ping Zeng,et al.  Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms , 2003, Bioinform..

[2]  E. Meléndez-Hevia,et al.  The game of the pentose phosphate cycle. , 1985, Journal of theoretical biology.

[3]  J E Bailey,et al.  MPS: An artificially intelligent software system for the analysis and synthesis of metabolic pathways , 1988, Biotechnology and bioengineering.

[4]  J. C. Nuño,et al.  Optimal stoichiometric designs of ATP-producing systems as determined by an evolutionary algorithm. , 1999, Journal of theoretical biology.

[5]  Ross D. King,et al.  On the use of qualitative reasoning to simulate and identify metabolic pathway , 2005, Bioinform..

[6]  Jason A. Papin,et al.  Metabolic pathways in the post-genome era. , 2003, Trends in biochemical sciences.

[7]  B. Clarke,et al.  Designing metabolism: Alternative connectivities for the pentose phosphate pathway , 1998 .

[8]  S. Rao,et al.  PathMiner: predicting metabolic pathways by heuristic search , 2003, Bioinform..

[9]  Andrew R. Dalby,et al.  Constructing an enzyme-centric view of metabolism , 2004, Bioinform..

[10]  R Heinrich,et al.  Kinetic and thermodynamic principles determining the structural design of ATP-producing systems , 1998, Bulletin of mathematical biology.

[11]  Reinhart Heinrich,et al.  Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems , 2001, Bulletin of mathematical biology.

[12]  Marta Cascante,et al.  The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution , 1996, Journal of Molecular Evolution.

[13]  Steffen Klamt,et al.  Two approaches for metabolic pathway analysis? , 2003, Trends in biotechnology.

[14]  M. Mavrovouniotis.  Synthesis of reaction mechanisms consisting of reversible and irreversible steps. 2. Formalization and analysis of the synthesis algorithm , 1992 .

[15]  James E. Bailey,et al.  MPS: An algorithm and data base for metabolic pathway synthesis , 1986, Biotechnology Letters.

[16]  Shoshana J. Wodak,et al.  Metabolic PathFinding: inferring relevant pathways in biochemical networks , 2005, Nucleic Acids Res..

[17]  Oliver Ebenhöh,et al.  Stoichiometric design of metabolic networks: Multifunctionality, clusters, optimization, weak and strong robustness , 2003, Bulletin of mathematical biology.

[18]  R. Albert,et al.  The large-scale organization of metabolic networks , 2000, Nature.

[19]  G. Stephanopoulos,et al.  Computer‐aided synthesis of biochemical pathways , 1990, Biotechnology and bioengineering.

[20]  Thomas Lengauer,et al.  Pathway analysis in metabolic databases via differetial metabolic display (DMD) , 2000, German Conference on Bioinformatics.

[21]  D. Fell,et al.  The small world inside large metabolic networks , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[22]  Peter D. Karp,et al.  EcoCyc: a comprehensive database resource for Escherichia coli , 2004, Nucleic Acids Res..

[23]  F. Montero,et al.  Optimization of Metabolism: The Evolution of Metabolic Pathways Toward Simplicity Through the Game of the Pentose Phosphate Cycle , 1994 .

[24]  E. Meléndez-Hevia,et al.  The game of the pentose phosphate cycle: a mathematical approach to study the optimization in design of metabolic pathways during evolution. , 1990, Biomedica biochimica acta.

[25]  A. Lehninger.  Principles of Biochemistry , 1984 .

[26]  S. Schuster,et al.  Metabolic network structure determines key aspects of functionality and regulation , 2002, Nature.

[27]  B. Palsson,et al.  Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. , 2000, Journal of theoretical biology.

[28]  D. Nelson,et al.  Lehninger Principles of Biochemistry (5th edition) , 2008 .

[29]  R. Heinrich,et al.  Mathematical analysis of enzymic reaction systems using optimization principles. , 1991, European journal of biochemistry.

[30]  S. Wodak,et al.  Inferring meaningful pathways in weighted metabolic networks. , 2006, Journal of molecular biology.

[31]  Yves Deville,et al.  Constrained metabolic network analysis: discovering pathways using CP(Graph) , 2005 .

[32]  Reinhart Heinrich,et al.  Theoretical approaches to the evolutionary optimization of glycolysis--chemical analysis. , 1997, European journal of biochemistry.

[33]  R Heinrich,et al.  Theoretical approaches to the evolutionary optimization of glycolysis: thermodynamic and kinetic constraints. , 1997, European journal of biochemistry.

[34]  E. Meléndez-Hevia,et al.  Economy of design in metabolic pathways: further remarks on the game of the pentose phosphate cycle. , 1988, Journal of theoretical biology.

[35]  D. Fell,et al.  A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks , 2000, Nature Biotechnology.

[36]  R. Heinrich,et al.  Metabolic Pathway Analysis: Basic Concepts and Scientific Applications in the Post‐genomic Era , 1999, Biotechnology progress.

[37]  B. Palsson,et al.  An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) , 2003, Genome Biology.