Isotopomer subspaces as indicators of metabolic-pathway structure

Journal of Theoretical Biology

Volumn 252, Issue 3, 2008, Pages 391-401

  Kuchel, Philip W ^a   Philp, David J ^b  

^a UNIVERSITY OF SYDNEY   (Australia)

^b The Australian National University   (Australia)

Author keywords

13C NMR; Combinatorics; Erythrocyte metabolism; Isotopomers; Mathematica; Pentose phosphate pathway

Indexed keywords

CARBON 13; GLUCOSE; ISOTOPE; LACTIC ACID;

BIOCHEMISTRY; CARBON ISOTOPE; CYTOLOGY; EXPERIMENTAL STUDY; GLUCOSE; MATHEMATICAL ANALYSIS; METABOLITE; NUCLEAR MAGNETIC RESONANCE; SOFTWARE;

ARTICLE; COMPUTER MODEL; ERYTHROCYTE; GLYCOLYSIS; HUMAN; ISOMER; METABOLISM; METABOLITE; NUCLEAR MAGNETIC RESONANCE; PENTOSE PHOSPHATE CYCLE; PRIORITY JOURNAL; SIMULATION;

CARBON ISOTOPES; COMBINATORIAL CHEMISTRY TECHNIQUES; COMPUTER SIMULATION; ERYTHROCYTES; HUMANS; ISOMERISM; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; PENTOSE PHOSPHATE PATHWAY;

EID: 43449091889     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2007.05.039     Document Type: Article

References (41)

1. Barnett M.P., Capitani J.F., von zur Gathen J., and Gerhard J. Symbolic calculation in chemistry: selected examples. Int. J. Quantum Chem. 100 (2004) 80-104
2. 13C NMR isotopomer and computer simulation studies of the non-oxidative pentose phosphate pathway of human erythrocytes. Biochem. J. 296 (1993) 379-387
3. 1H spin echo NMR. FEBS Lett 82 (1977) 12-16
4. Burns J.A. Steady states of general multi-enzyme networks and their associated properties. Computational approaches. FEBS Lett. 2 (1969) S30-S33
5. 13C NMR studies in perfused rat hearts. J. Biol. Chem. 258 (1983) 13785-13794
6. Cowin G.J., Willgoss D.A., Bartley J., and Endre Z.H. Serine isotopomer analysis by C-13-NMR defines glycine-serine interconversion in situ in the renal proximal tubule. Biochim. Biophys. Acta 1310 (1994) 32-40
7. Garfinkel D., Garfinkel L., Pring M., Green S.B., and Chance B. Computer applications to biochemical kinetics. Ann. Rev. Biochem. 39 (1970) 473-498
8. Heinrich, R., 1979. Heinrich of Seiffersdorf 1839-1979 Gottlob and Anna Rosina Heinrich and their Descendants 140 Years in Australia. Lutheran Publishing House, Adelaide, South Australia.
9. Heinrich R., and Rapoport T.A. A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 42 (1974) 89-95
10. Heinrich R., and Rapoport T.A. A linear steady-state treatment of enzymatic chains. Critique of the cross-over theorem and a general procedure to identify sites with an effector. Eur. J. Biochem. 42 (1974) 97-105
11. Heinrich R., Rapoport T.A., and Rapoport S.M. Metabolic regulation and mathematical models. Prog. Biophys. Mol. Biol. 32 (1977) 1-82
12. Heinrich R., and Schuster S. The Regulation of Cellular Systems (1996), Chapman & Hall, New York
13. Horecker B.L. The pentose phosphate pathway. J. Biol. Chem. 277 (2002) 47965-47971
14. 31P nuclear magnetic resonance. Nature 252 (1974) 285-287
15. Kacser H., and Burns J.A. The control of flux. Symp. Soc. Exp. Biol. 32 (1973) 65-107
16. Kauffman K.J., Pajerowski J.D., Jamshidi N., Palsson B.O., and Edwards J.S. Description and analysis of metabolic connectivity and dynamics in the human red blood cell. Biophys. J. 83 (2002) 646-662
17. Kuchel P.W., Roberts D.V., and Nichol L.W. The simulation of the urea cycle: correlation of effects due to inborn errors in the catalytic properties of the enzymes with clinical-biochemical observations. Aust. J. Expt. Biol. Med. Sci. 55 (1977) 309-326
18. Kuchel P.W. Current status and challenges in connecting models of erythrocyte metabolism to experimental reality. Prog. Biophys. Mol. Biol. 85 (2004) 325-342
19. 13C labeling in studies of metabolic regulation. Prog. NMR Spectr. 20 (1988) 337-383
20. 31P-NMR experimental data from human erythrocytes. Eur. J. Biochem. 180 (1989) 399-420
21. Maher A.D., Kuchel P.W., Ortega F., Atauri J.C., and Cascante M. Mathematical modelling of the urea cycle. Eur. J. Biochem. 270 (2003) 3953-3961
22. 13C NMR spectroscopy. J. Biol. Chem. 263 (1988) 6964-6971
23. Meléndez-Hevia E., and Isidoro A. The game of the pentose phosphate cycle. J. Theoret. Biol. 117 (1985) 251-263
24. Montero F., Nuño J.C., Valdenebro I., Pérez-Iratxeta C., and Meléndez-Hevia E. Stoichiometric properties of the non oxidative phase of the pentose phosphate cycle. Nonlinear Anal. Meth. Appl. 30 (1997) 1865-1874
25. 31P magnetic resonance. J. Biol. Chem. 248 (1973) 7276-7278
26. 31P NMR. Biochem. J. 342 (1999) 567-580
27. Mulquiney P.J., and Kuchel P.W. Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations 2: equations and parameter refinement. Biochem. J. 342 (1999) 581-596
28. Mulquiney P.J., and Kuchel P.W. Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations 3: computer simulation and metabolic control analysis. Biochem. J. 342 (1999) 597-604
29. Mulquiney P.J., and Kuchel P.W. Modelling Metabolism with Mathematica: Detailed Examples Including Erythrocyte Metabolism (2003), CRC Press, Boca Raton, FL, USA pp. 1-309
30. Rapoport T.A., Heinrich R., Jacobasch G., and Rapoport S. A linear steady-state treatment of enzymatic chains. Critique of the cross-over theorem and a general procedure to identify sites with an effector. Eur. J. Biochem. 42 (1974) 97-105
31. Rapoport T.A., Heinrich R., and Rapoport S.M. The regulatory principles of glycolysis in erythrocytes in vivo and in vitro. A minimal comprehensive model describing steady states, quasi-steady states and time-dependent processes. Biochem. J. 154 (1974) 449-469
32. Selivanov V.A., Puigjaner J., Sillero A., Centelles J.J., Ramos-Montoya A., Lee P.W.-N., and Cascante M. An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites. BioInformatics 20 (2004) 3387-3397
33. Selivanov V.A., Meshalkina L.E., Solovjeva O.N., Kuchel P.W., Ramos-Montoya A., Kochetov G.A., Lee P.W.-N., and Cascante M. Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells. BioInformatics 21 (2005) 3551-3564
34. 13C]enriched monosaccharides. Signal assignments and orientational dependence of geminal and vicinal carbon-carbon and carbon-hydrogen spin-spin coupling constants. J. Am. Chem. Soc. 98 (1976) 5807-5813
35. 15N]glutamate by Brevibacterium flavum. Appl. Environ. Microbiol. 53 (1987) 92-98
36. 13C nuclear magnetic resonance studies of the biosynthesis by Microbacterium ammoniaphilum of l-glutamate selectively enriched with carbon-13. J. Biol. Chem. 257 (1982) 1189-1195
37. 13C metabolic flux analysis. Metab. Eng. 3 (2001) 195-206
38. 13C metabolic flux analysis. Metab. Eng. 3 (2001) 265-283
39. Williams J.F., Arora K.K., and Longenecker J.P. The pentose pathway: a random harvest. Impediments which oppose acceptance of the classical (F-type) pentose cycle for liver, some neoplasms and photosynthetic tissue. The case for the L-type pentose pathway. Int. J. Biochem. 19 (1987) 749-817
40. Wolfram S. The Mathematica Book. third ed (2003), Wolfram Media, Champaign, IL
41. Zupke C., and Stephanopoulos G. Modeling of isotope distributions and intracellular fluxes in metabolic networks using atom mapping matrices. Biotechnol. Prog. 10 (1994) 489-498