How can we understand metabolism?

Systems Biology

Volumn , Issue , 2007, Pages 87-101

  Fell, David ^a  

^a OXFORD BROOKES UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 70450121151     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-044452085-2/50006-1     Document Type: Chapter

References (50)

1. Bennett FH, Koza JR, Yu J, Mydlowec W Automatic synthesis, placement and routing of an amplifier circuit by means of genetic programming. Lecture Notes in Computer Science 2000, 1801:1-10.
2. Black S, Wright NG β-aspartokinase and β-aspartyl phosphate. Journal of Biological Chem- istry 1955, 213:27-38.
3. Blackman FF Optima and limiting factors. Annals of Botany 1905, 19:281.
4. Burns JA, Cornish-Bowden A, Groen AK, Heinrich R, Kacser H, Porteous JW, Rapoport SM, Rapoport TA, Stucki JW, Tager JM, Wanders RJA, Westerhoff HV Control analysis of metabolic systems. Trends in Biochemical Sciences 1985, 10:16.
5. Chance B, Holmes W, Higgins JJ, Connelly CM Localization of interaction sites in multi- component transfer systems: Theorems derived from analogues. Nature (London) 1958, 182:1190-1193.
6. Chassagnole C, Fell DA, Rais B, Kudla B, Mazat JP Control of the threonine-synthesis pathway in Escherichia coli: A theoretical and experimental approach. Biochemical Journal 2001, 356:433-444.
7. Control of Metabolic Processes. NATO ASI Series 1990, Plenum Press, New York. A. Cornish-Bowden, M.L. Cárdenas (Eds.).
8. Crabtree B, Newsholme EA A quantitative approach to metabolic control. Current Topics in Cellular Regulation 1985, 25:21-76.
9. Deckard A, Sauro HM Preliminary studies on the in silico evolution of biochemical networks. ChemBioChem 2004, 5:1423-1431.
10. Denton RM, Pogson CI Metabolic Regulation 1976, Chapman Hall, London.
11. Dujon B European Functional Analysis Network (EUROFAN) and the functional analysis of the Saccharomyces cerevisiae genome. Electrophoresis 1998, 19:617-624.
12. Fell DA Understanding the Control of Metabolism 1997, Portland Press, London.
13. Fell DA, Snell K Control analysis of mammalian serine biosynthesis. Biochemical Journal 1988, 256:97-101.
14. Garfinkel D, Hess B Metabolic control mechanisms VII. a detailed computer model of the glycolytic pathway in ascites cells. Journal of Biological Chemistry 1964, 239:971-983.
15. Garry DJ, Ordway GA, Lorenz JN, Radford NB, Chin ER, Grange RW, Bassel-Duby R, Williams RS Mice without myoglobin. Nature 1998, 395:905-908.
16. Grange RW, Meeson A, Chin E, Lau KS, Stull JT, Shelton JM, Williams RS, Garry DJ Functional and molecular adaptations in skeletal muscle of myoglobin-mutant mice. American Journal of Physiological - Cell Physiology 2001, 281:C1487-C1494.
17. Groen AK, Wanders RJA, Westerhoff HV, van der Meer R, Tager JM Quantification of the contribution of various steps to the control of mitochondrial respiration. Journal of Biological Chemistry 1982, 257:2754-2757.
18. Heinrich R, Rapoport TA A linear steady-state treatment of enzymatic chains; general proper- ties, control and effector strength. European Journal of Biochemistry 1974, 42:89-95.
19. Heinrich R, Schuster S The modelling of metabolic systems: Structure, control and optimality. Biosystems 1998, 47:61-77.
20. Higgins J Analysis of sequential reactions. Annals of the New York Academy of Sciences 1963, 108:305-321.
21. Hofmeyr JHS, Cornish-Bowden A Quantitative assessment of regulation in metabolic systems. European Journal of Biochemistry 1991, 200:223-236.
22. Hofmeyr JHS, Cornish-Bowden A Predicting metabolic pathway kinetics with control analysis. BioThermoKinetics of the Living Cell 1996, 155-158. BioThermoKinetics Press, Amsterdam. H.V. Westerhoff, J.L. Snoep, J.E. Wijker, F.E. Sluse, B.N. Kholodenko (Eds.).
23. Kacser H, Beeby R Evolution of catalytic proteins or on the origin of enzyme species by means of natural selection. Journal of Molecular Evolution 1984, 20:38-51.
24. Kacser H, Burns JA The control of flux. Symposium Society Experimental Biology 1973, 27:65-104.
25. Biochemical Society Transactions 1995, 23:341-366.
26. Kacser H, Burns JA The molecular basis of dominance. Genetics 1981, 97:639-666.
27. Kahn D, Westerhoff HV Control theory of regulatory cascades. Journal of Theoretical Biology 1991, 153:255-285.
28. Kholodenko BN, Molenaar D, Schuster S, Heinrich R, Westerhoff HV Defining control coeffi- cients in non-ideal metabolic pathways. Biophysical Chemistry 1995, 56:215-226.
29. Klipp E, Heinrich R Competition for enzymes in metabolic pathways: Implications for optimal distributions of enzyme concentrations and for the distribution of flux control. Biosystems 1999, 54:1-14.
30. Koza JR, Andre D, Bennett FH, Keene MA Genetic Programming III: Darwinian Invention &Problem Solving 1999, Morgan Kauffmann, San Francisco.
31. Krebs HA Control of metabolic processes. Endeavour 1957, 16:125-132.
32. Lazebnik Y Can a biologist fix a radio?. Cancer Cell 2002, 2:179-182.
33. Letellier T, Heinrich R, Malgat M, Mazat JP The kinetic basis of threshold effects observed in mitochondrial diseases - a systemic approach. Biochemical Journal 1994, 302:171-174.
34. Newsholme EA, Start C Regulation in Metabolism 1973, Wiley and Sons, London.
35. Park DJM, Wright BE Metasim, a general purpose metabolic simulator for studying cellular transformations. Computer Programs in Biomedicine 1973, 3:10-26.
36. Pizer LI The pathway and control of serine biosynthesis in Escherischia coli. Journal of Biological Chemistry 1963, 238:3934-3944.
37. Porteous JW A rational treatment of Mendelian genetics. Theoretical Biology &Medical Mod- elling 2004, 1:6.
38. Rolleston FS A theoretical background to the use of measured concentrations of intermediates in study of the control of intermediary metabolism. Current Topics in Cell Regulation 1972, 5:47-75.
39. Sauro HM The computational versatility of proteomic signalling networks. Current Proteomics 2004, 1:67-81.
40. Savageau MA Biochemical systems analysis: I. some mathematical properties of the rate law for the component enzyme reactions. Journal of Theoretical Biology 1969, 25:365-369.
41. Savageau MA Optimal design of feedback control by inhibition: Steady state considerations. Journal of Molecular Evolution 1974, 4:139-156.
42. Savageau MA Biochemical Systems Analysis: a Study of Function and Design in Molecular Biology 1976, Addison-Wesley, Reading, Mass.
43. Schaaff I, Heinisch J, Zimmerman FK Overproduction of Glycolytic Enzymes in Yeast. Yeast 1989, 5:285-290.
44. Small JR, Fell DA Covalent modification and Metabolic Control Analysis: Modification to the theorems and their application to metabolic systems containing covalently-modified e. European Journal of Biochemistry 1990, 191:405-411.
45. ter Kuile BH, Westerhoff HV Transcriptome meets metabolome: Hierarchical and metabolic regulation of the glycolytic pathway. FEBS Letters 2001, 500:169-171.
46. Thatcher JW, Shaw JM, Dickinson WJ Marginal fitness contributions of nonessential genes in yeast. Proceedings of the National Academy of Sciences USA 1998, 95:253-257.
47. Thomas S, Mooney PJF, Burrell MM, Fell DA Metabolic Control Analysis of Glycolysis in Tuber Tissue of Potato Solanum tuberosum. Explanation for the Low Control Coefficient of Phosphofructokinase over Flux. The Biochemical Journal 1997, 322:119-127.
48. Umbarger HE Evidence for a negative-feedback mechanism in the biosynthesis of isoleucine. Science 1956, 123:848.
49. Wouters AG Four notions of biological function. Studies in History and Philosophy of Science Part C 2003, 34:633-668.
50. Yates RA, Pardee AB Control of pyrimidine biosynthesis in Escherichia coli by a feed-back mechanism. Journal of Biological Chemistry 1956, 221:757-770.