Effect of substrate competition in kinetic models of metabolic networks

FEBS Letters

Volumn 587, Issue 17, 2013, Pages 2818-2824

  Schäuble, Sascha ^a   Stavrum, Anne Kristin ^b   Puntervoll, Pål ^c   Schuster, Stefan ^a   Heiland, Ines ^d  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

^b UNIVERSITY OF BERGEN   (Norway)

^c Uni Research   (Norway)

^d UNIVERSITY OF TROMSØ   (Norway)

Author keywords

Kinetic rate laws; Metabolic pathway; Modelling; Substrate competition

Indexed keywords

INDOLEAMINE 2,3 DIOXYGENASE;

AMINO ACID METABOLISM; AMINO ACID TRANSPORT; ARTICLE; BINDING COMPETITION; BINDING SITE; COMPUTER MODEL; CONTROLLED STUDY; ENZYME BINDING; ENZYME KINETICS; ENZYME MECHANISM; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; MICHAELIS CONSTANT; PRIORITY JOURNAL; SUBSTRATE;

KINETIC RATE LAWS; METABOLIC PATHWAY; MODELLING; SUBSTRATE COMPETITION;

ALGORITHMS; BINDING, COMPETITIVE; COMPUTER SIMULATION; ENZYMES; HUMANS; KINETICS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MODELS, CHEMICAL; PROTEIN BINDING;

EID: 84883050265     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2013.06.025     Document Type: Article

References (25)

1. Ö. Kartal, S. Mahlow, A. Skupin, and O. Ebenhöh Carbohydrate-active enzymes exemplify entropic principles in metabolism Mol. Syst. Biol. 7 2011 542
2. B. Knoke, S. Textor, J. Gershenzon, and S. Schuster Mathematical modelling of aliphatic glucosinolate chain length distribution in Arabidopsis thaliana leaves Phytochem. Rev. 8 1 2009 39 51
3. B. Marquez, and F. Van Bambeke ABC multidrug transporters: target for modulation of drug pharmacokinetics and drug-drug interactions Curr. Drug Targets 12 2011 600 620
4. W.M. Pardridge, and T.B. Choi Neutral amino acid transport at the human blood-brain barrier Fed. Proc. 45 1986 2073 2078
5. M. Salter, R.G. Knowles, and C.I. Pogson Quantification of the importance of individual steps in the control of aromatic amino acid metabolism Biochem. J. 234 1986 635 647
6. Y. Kim, M.J. Andreu, B. Lim, K. Chung, M. Terayama, G. Jiménez, C.A. Berg, H. Lu, and S.Y. Shvartsman Gene regulation by MAPK substrate competition Dev. Cell 20 6 2011 880 887
7. S.P. Lee, M.L. Censullo, H.G. Kim, and M.K. Han Substrate-length- dependent activities of human immunodeficiency virus type 1 integrase in vitro: differential DNA binding affinities associated with different lengths of substrates Biochemistry 34 1995 10215 10223
8. L. Jöres, and R. Wagner Essential steps in the ppGpp-dependent regulation of bacterial ribosomal RNA promoters can be explained by substrate competition J. Biol. Chem. 278 2003 16834 16843
9. J.M. Bratt, A.A. Zeki, J.A. Last, and N.J. Kenyon Competitive metabolism of l-arginine: arginase as a therapeutic target in asthma J. Biomed. Res. 25 2011 299 308
10. O.A. Ulanovskaya, A.M. Zuhl, and B.F. Cravatt NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink Nat. Chem. Biol. 9 5 2013 300 306
11. V. Henri Théorie générale de l'action de quelques diastases Compt. Rend. Hebd. Acad. Sci. Paris 135 1902 916 919
12. V. Henri Lois générales de l'action des diastases 1903 Herman
13. L. Michaelis, and M. Menten Die Kinetik der Invertinwirkung Biochem. Z. 49 1913 333 369
14. T.C. Chou, and P. Talaly A simple generalized equation for the analysis of multiple inhibitions of Michaelis-Menten kinetic systems J. Biol. Chem. 252 1977 6438 6442
15. V.L.S. Dingerkus, T.J. Gaber, K. Helmbold, S. Bubenzer, A. Eis-ert, C.L. Sánchez, and F.D. Zepf Acute tryptophan depletion in accordance with body weight: influx of amino acids across the blood-brain barrier J. Neural Transm. 119 2012 1037 1045
16. I.H. Segel Enzyme Kinetics 1993 John Wiley & Sons
17. A. Cornish-Bowden Fundamentals of Enzyme Kinetics 2012 Wiley-VCH
18. S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Men des, and U. Kummer Copasi - a complex pathway simulator Bioinformatics 22 2006 3067 3074
19. J.A. Emery, K. Hermon, N.K.A. Hamid, J.A. Donald, and G.M. Turchini Δ-6 Desaturase substrate competition: dietary linoleic acid (18:2n-6) has only trivial effects on α-linolenic acid (18:3n-3) bioconversion in the teleost rainbow trout PLoS One 8 2013 e57463
20. T. Baks, A.E.M. Janssen, and R.M. Boom A kinetic model to explain the maximum in alpha-amylase activity measurements in the presence of small carbohydrates Biotechnol. Bioeng. 94 2006 431 440
21. D. De Vos, F.J. Bruggeman, H.V. Westerhoff, and B.M. Bakker How molecular competition influences fluxes in gene expression networks PLoS ONE 6 12 2011 e28494
22. J.R. Pomerening Uncovering mechanisms of bistability in biological systems Curr. Opin. Biotechnol. 19 2008 381 388
23. L. Venkatraman, H. Li, C.F. Dewey, J.K. White, S.S. Bhowmick, H. Yu, and L. Tucker-Kellogg Steady states and dynamics of urokinase-mediated plasmin activation in silico and in vitro Biophys. J. 101 2011 1825 1834
24. M. Cascante, E.I. Canela, and R. Franco Control analysis of systems having two steps catalyzed by the same protein molecule in unbranched chains Eur. J. Biochem. 192 1990 369 371
25. M.C. McKenna Substrate competition studies demonstrate oxidative metabolism of glucose, glutamate, glutamine, lactate and 3-hydroxybutyrate in cortical astrocytes from rat brain Neurochem. Res. 37 2012 2613 2626