Construction of kinetic models for metabolic reaction networks: Lessons learned in analysing short-term stimulus response data

References

• Chassagnole , C. , Noisommit-Rizzi , N. , Schmid , J.W. , Mauch , K. and Reuss , M. 2002 . Dynamic modeling of the central carbon metabolism of Escherichia coli . Biotechnol.Bioeng , 79 ( 1 ) : 53 – 73 .
   Google Scholar
• Teusink , B. , Passarge , J. , Reijenga , C.A. , Esgalhado , E. , van der Weijden , C.C. , Schepper , M. , Walsh , M.C. , Bakker , B.M. , van Dam , K. , Westerhoff , H.V. and Snoep , J.L. 2000 . Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry . Eur. J. Biochem. , 267 ( 17 ) : 5313 – 5329 .
   PubMedGoogle Scholar
• Heijnen , J.J. 2005 . Approximative kinetic formats used in metabolic network modeling . Biotechnol. Bioeng. , 91 ( 5 ) : 534 – 545 .
   PubMedGoogle Scholar
• Voit , E.O. 2000 . Computational Analysis of Biochemical Systems , Cambridge : Cambridge University Press .
   Google Scholar
• Liebermeister , W. and Klipp , E. 2006 . Bringing metabolic networks to life: Integration of kinetic, metabolic, and proteomic data . Theor. Biol. Med. Model. , 3 : 42
   Google Scholar
• Hadlich , F. , Noack , S. and Wiechert , W. 2009 . Translating biochemical network models between different kinetic formats . Metab. Eng. , 11 ( 2 ) : 87 – 100 .
   Google Scholar
• Canelas , A.B. , van Gulik , W.M. and Heijnen , J.J. 2008 . Determination of the cytosolic free nad/nadh ratio in Saccharomyces cerevisiae under steady-state and highly dynamic conditions . Biotechnol. Bioeng. , 100 : 734 – 743 .
   PubMed Web of Science ®Google Scholar
• Kresnowati , M.T.A.P. , Suarez-Mendez , C.M. , van Winden , W.A. , van Gulik , W.M. and Heijnen , J.J. 2008 . Quantitative physiological study of the fast dynamics in the intracellular pH of Saccharomyces cerevisiae in response to glucose and ethanol pulses . Metab. Eng. , 10 ( 1 ) : 39 – 54 .
   Google Scholar
• Üçışık , M.H. 2006 . Transient energetic metabolic response of anaerobic Saccharomyces cerevisiae culture to benzoic acid , Delft University of Technology . Master's thesis
   Google Scholar
• Heinrich , R. and Schuster , S. 1996 . The Regulation of Cellular Systems , Dordrecht, , The Netherlands : Kluwer Academic Publishers .
   Google Scholar
• Wu , L. , Wang , W. , van Winden , W.A. , van Gulik , W.M. and Heijnen , J.J. 2004 . A new framework for the estimation of control parameters in metabolic pathways using lin-log kinetics . Eur. J. Biochem. , 271 ( 16 ) : 3348 – 3359 .
   Google Scholar
• Nikerel , I.E. , van Winden , W.A. , van Gulik , W.M. and Heijnen , J.J. 2006 . A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics . BMC Bioinformatics , 7 : 540
   Google Scholar
• Magnus , J.B. , Hollwedel , D. , Oldiges , M. and Takors , R. 2006 . Monitoring and modeling of the reaction dynamics in the valine/leucine synthesis pathway in Corynebacterium glutamicum . Biotechnol. Prog. , 22 ( 4 ) : 1071 – 1083 .
   Google Scholar
• Visser , D. , Schmid , J.W. , Mauch , K. , Reuss , M. and Heijnen , J.J. 2004 . Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics . Metab. Eng. , 6 ( 4 ) : 378 – 390 .
   Google Scholar
• Nikerel , I.E. , van Winden , W.A. , Verheijen , P.J.T. and Heijnen , J.J. 2009 . Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics . Metab. Eng. , 11 : 20 – 30 .
   Google Scholar
• Nevoigt , E. 2008 . Progress in metabolic engineering of Saccharomyces cerevisiae . Microb. Mol. Biol. Rev. , 72 ( 3 ) : 379 – 412 .
   PubMed Web of Science ®Google Scholar
• Rossell , S. , Van Der Weijden , C.C. , Lindenbergh , A. , Van Tuijl , A. , Francke , C. , Bakker , B.M. and Westerhoff , H.V. 2006 . Unraveling the complexity of flux regulation: A new method demonstrated for nutrient starvation in Saccharomyces cerevisiae . Proc. Nat. Acad. Sci. U.S.A , 103 ( 7 ) : 2166
   PubMedGoogle Scholar
• Rizzi , M. , Baltes , M. , Theobald , U. and Reuss , M. 1997 . In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model . Biotechnol. Bioeng. , 55 ( 4 ) : 592 – 608 .
   Google Scholar
• Degenring , D. , Froemel , C. , Dikta , G. and Takors , R. 2004 . Sensitivity analysis for the reduction of complex metabolism models . J. Process Control , 14 ( 7 ) : 729 – 745 .
   Google Scholar
• Galazzo , J.L. and Bailey , J. 1990 . Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae . Enzyme Microb. Technol. , 12 ( 3 ) : 162 – 172 .
   Google Scholar