Network-based analysis of metabolic regulation in the human red blood cell

Journal of Theoretical Biology

Volumn 225, Issue 2, 2003, Pages 185-194

  Price, Nathan D ^a   Reed, Jennifer L ^a   Papin, Jason A ^a   Wiback, Sharon J ^a   Palsson, Bernhard O ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Constraint based models; Elementary modes; Extreme pathways; Singular value decomposition; SVD

Indexed keywords

HEMATOLOGY;

ARTICLE; ARTIFICIAL NEURAL NETWORK; BIOLOGICAL MODEL; CALCULATION; ERYTHROCYTE; ERYTHROCYTE METABOLISM; HUMAN; KINETICS; METABOLISM; MODEL; PHYSIOLOGY; PRIORITY JOURNAL; REGULATORY MECHANISM; SIGNAL TRANSDUCTION; STEADY STATE; STOICHIOMETRY;

EID: 0142186707     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-5193(03)00237-6     Document Type: Article

References (31)

1. Arkin A., Ross J., McAdams H.H. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics. 149:1998;1633-1648.
2. Beard D.A., Liang S.D., Qian H. Energy balance for analysis of complex metabolic networks. Biophys. J. 83:2002;79-86.
3. Covert M.W., Schilling C.H., Famili I., Edwards J.S., Goryanin I.I., Selkov E., Palsson B.O. Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26:2001;179-186.
4. Davidson E.H. Genomic Regulatory Systems. Development and Evolution:2001;Academic Press, San Diego.
5. Edwards J.S., Covert M., Palsson B. Metabolic modelling of microbes. the flux-balance approach Environ. Microbiol. 4:2002;133-140.
6. Elowitz M.B., Levine A.J., Siggia E.D., Swain P.S. Stochastic gene expression in a single cell. Science. 297:2002;1183-1186.
7. Gerber G., Preissler H., Heinrich R., Rapoport S.M. Hexokinase of human erythrocytes. Purification, kinetic model and its application to the conditions in the cell. Eur. J. Biochem. 45:1974;39-52.
8. Halestrap A.P. Transport of pyruvate NAD lactate into human erythrocytes. Evidence for the involvement of the chloride carrier and a chloride- independent carrier. Biochem. J. 156:1976;193-207.
9. Heinrich R., Rapaport S.M., Rapaport T.A. Metabolic regulation and mathematical models. Prog. Biophys. Mol. Biol. 32:1977;1-82.
10. Holzhütter H.G., Jacobasch G., Bisdorff A. Mathematical modelling of metabolic pathways affected by an enzyme deficiency. A mathematical model of glycolysis in normal and pyruvate-kinase-deficient red blood cells. Eur. J. Biochem. 149:1985;101-111.
11. Jamshidi N., Edwards J.S., Fahland T., Church G.M., Palsson B.O. Dynamic simulation of the human red blood cell metabolic network. Bioinformaics. 17:2001;286-287.
12. Jamshidi N., Wiback S.J., Palsson B.O. In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism. Genome Res. 12:2002;1687-1692.
13. Joshi A., Palsson B.O. Metabolic dynamics in the human red cell. Part I - A comprehensive kinetic model. J. Theor. Biol. 141:1989;515-528.
14. Joshi A., Palsson B.O. Metabolic dynamics in the human red cell. Part III - metabolic reaction rates. J. Theor. Biol. 142:1990;41-68.
15. Kirkman H.N., Gaetani G.F. Regulation of glucose-6-phosphate dehydrogenase in human erythrocytes. J. Biol. Chem. 261:1986;4033-4038.
16. Lay D.C. Linear Algebra and Its Applications. 2nd Edition:1997;Addison Wesley Longman Inc, Reading, MA.
17. McAdams H.H., Arkin A. Stochastic mechanisms in gene expression. Proc. Natl Acad. Sci. 94:1997;814-819.
18. Palsson B.O. The challenges of in silico biology. Nat. Biotechnol. 18:2000;1147-1150.
19. Palsson B.O. In silico biology through "omics" Nat. Biotechnol. 20:2002;649-650.
20. Papin J.A., Price N.D., Palsson B.O. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res. 12:2002;1889-1900.
21. Papin J.A., Price N.D., Wiback S.J., Fell D., Palsson B. Metabolic pathways in the post-genome era. Trends Biochem. Sci. 28:2003;250-258.
22. Price N.D., Famili I., Beard D.A., Palsson B.O. Extreme pathways and Kirchhoff's second law. Biophys. J. 83:2002;2879-2882.
23. Price N.D., Papin J.A., Schilling C.H., Palsson B. Genome-scale microbial in silico models. the constraints-based approach Trends Biotechnol. 21:2003;162-169.
24. Price N.D., Reed J.L., Papin J.A., Famili I., Palsson B.O. Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices. Biophys. J. 84:2003;794-804.
25. Ptashne M., Gann A. Genes and Signals. Cold Spring Harbor Laboratory Press. 2002;Cold Spring Harbor, New York.
26. Schilling C.H., Letscher D., Palsson B.O. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 203:2000;229-248.
27. Schuster S., Fell D.A., Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nature Biotechnol. 18:2000;326-332.
28. Stelling J., Klamt S., Bettenbrock K., Schuster S., Gilles E.D. Metabolic network structure determines key aspects of functionality and regulation. Nature. 420:2002;190-193.
29. Tomita M., Hashimoto K., Takahashi K., Shimizu T.S., Matsuzaki Y., Miyoshi F., Saito K., Tanida S., Yugi K., Venter J.C., Hutchison C.A.I. E-CELL. software environment for whole-cell simulation Bioinformatics. 15:1999;72-84.
30. Werner A., Heinrich R. A kinetic model for the interaction of energy metabolism and osmotic states of human erythrocytes. Analysis of the stationary "in vivo" state and of time dependent variations under blood preservation conditions. Biomed. Biochim. Acta. 44:1985;185-212.
31. Wiback S.J., Palsson B.O. Extreme pathway analysis of human red blood cell metabolism. Biophys. J. 83:2002;808-818.