In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism

Genome Research

Volumn 12, Issue 11, 2002, Pages 1687-1692

  Jamshidi, Neema ^a   Wiback, Sharon J ^a   Palsson, Bernhard Ø ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ERYTHROCYTE ENZYME; GLUCOSE 6 PHOSPHATE DEHYDROGENASE; PYRUVATE KINASE;

AMINO ACID SEQUENCE; ANEMIA; ARTICLE; CELL FUNCTION; CHEMICAL REACTION; CHRONIC DISEASE; COMPUTER MODEL; CONTROLLED STUDY; ENZYME KINETICS; ERYTHROCYTE METABOLISM; HUMAN; HUMAN CELL; MEDICAL GENETICS; PATHOPHYSIOLOGY; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

COMPUTATIONAL BIOLOGY; ERYTHROCYTES; GLUCOSEPHOSPHATE DEHYDROGENASE DEFICIENCY; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; PYRUVATE KINASE;

EID: 0036851376     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.329302     Document Type: Article

References (38)

1. Adediran, S.A. 1996. Kinetic and thermodynamic properties of two electrophoretically similar genetic variants of human erythrocyte glucose-6-phosphate dehydrogenase. Biochimie 78: 165-170.
2. Atkinson, D.E. 1977. Cellular energy metabolism and its regulation. Academic Press, New York.
3. Au, S.W., Gover, S., Lam, V., and Adams, M.J. 2000. Human glucose-6-phosphate dehydrogenase: The crystal structure reveals a structural NADP molecule and provides insights into enzyme deficiency. Structure 8: 293-303.
4. Betke, K.B.E., Brewer, G.J., Kirkman, H.N., Luzzatto, I., Motulsky, A.G., Ramot, B., and Siniscalco, M. 1967. Standardization of procedures for the study of glucose-6-phosphate dehydrogenase. Report of a WHO scientific group. WHO Tech. Rep. Ser. Ser 366.
5. Beutler, E. 1986. Red cell metabolism. Churchill Livingstone, Edinburgh, England; New York.
6. Beutler, E. 1990. The genetics of glucose-6-posphate dehydrogenase deficiency. Semin. Hematol. 27: 137-164.
7. Beutler, E. and Yoshida, A. 1988. Genetic variations of glucose-6-phosphate dehydrogenase: A catalog and future prospects. Medicine 67: 311-334.
8. Fiorelli, G., Martinez di Montemuros, F., and Domencia Cappellini, M. 2000. Chronc non-spherocytic haemolytic disorders associated with glucose-6-phosphate dehydrogenase variants. Baillieres Clin. Haematol. 13: 35-55.
9. Heinrich, R., Rapaport, S.M., and Rapaport, T.A. 1977. Metabolic regulation and mathematical models. Prog. Biophys. Mol. Biol. 32: 1-82.
10. Hirono, A., Kuhl, W., Gelbart, T., Forman, L., Fairbanks, V. F., and Beutler, E. 1989. Identification of the binding domain for NADP of human glucose-6-phosphate dehydrogenase by sequence analysis of mutants. Proc. Natl. Acad. Sci. 86: 10015-10017.
11. Holzhütter, H.G., Jacobasch, G., and Bisdorff, A. 1985. 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: 101-111.
12. Jacobasch, G. and Rapoport, S.M. 1996. Hemolytic anemias due to erythrocyte enzyme deficiencies. Mol. Aspects Med. 17: 143-170.
13. Jamshidi, N., Edwards, J.S., Fahland, T., Church, G.M., and Palsson, B.Ø. 2001. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics 17: 286-287.
14. Joshi, A. and Palsson, B.Ø. 1989. Metabolic dynamics in the human red cell. Part I-A comprehensive kinetic model. J. Theor. Biol. 141: 515-528.
15. Joshi, A. and Palsson, B.Ø. 1990. Metabolic dynamics in the human red cell. Part IV-Data prediction and some model computations. J. Theor. Biol. 142: 69-85.
16. Kirkman, H.N. 1960. Different enzymic expressions of mutants of human glucose-6-phosphate dehydrogenase. Proc. Natl. Acad. Sci. 46: 938-944.
17. Kirkman, H.N. 1962. Glucose-6-phosphate dehydrogenase from human erythrocytes. I. Further purification and characterization. J. Biol. Chem. 237: 2364-2370.
18. Kirkman, H.N. and Gaetani, G.F. 1986. Regulation of glucose-6-phosphate dehydrogenase in human erythrocytes. J. Biol. Chem. 261: 4033-4038.
19. Kirkman, H.N., Gaetani, G.D., Clemons, E.H., and Mareni, C. 1975. Red cell NADP+ and NADPH in glucose-6-phosphate dehydrogenase deficiency. J. Clin. Inves. 55: 875-878.
20. Lee, I.-D. and Palsson, B.Ø. 1991. A comprehensive model of human erythrocyte metabolism: Extensions to include pH effects. Biomedica Biochimica Acta. 49: 771-789.
21. Martinov, M.V., Plotnikov, A.G, Vitvitsky, V.M., and Ataullakhanov, F.I. 2000. Deficiencies of glycolytic enzymes as a possible cause of hemolytic anemia. Biochim. Biophys. Acta. 1474: 75-87.
22. Miwa, S., Boivin, P., Blume, K.G., Arnold, H., Black, J.A., Kahn, A., Staal, G.E., Nakashima, K., Tanaka, K.R., Paglia, D.E., et al. 1979. Recommended methods for the characterization of red cell pyruvate kinase variants. International Committee for Standardization in Haematology. Brit. J. Haematol. 43: 275-286.
23. Mulquiney, P.J. and Kuchel, P.W. 1999. Model of 2-3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed kinetic equations: Computer simulation and metabolic control analysis. Biochem. J. 342: 597-604.
24. Otto, M., Heinrich, R., Kuhn, B., and Jacobasch, G. 1974. A mathematical model for the influence of frutose-6-phosphate, ATP, potassium, ammonium, and magnesium on the phosphofructokinase from rat erythrocytes. Eur. J. Biochem. 49: 169-178.
25. Palsson, B.Ø. 2000. The challenges of in silico biology. Nat. Biotech. 18: 1147-1150.
26. Rapoport, T.A. and Heinrich, R. 1975. Mathematical analysis of multienzyme systems. I: Modelling of glycolysis of human erythrocytes. Biosystems 7: 120-129.
27. Schauer, M., Heinrich, R., and Rapoport, S.M. 1981. Mathematische modellierung der glykolyse und des adeninnukleotidstoffwechsels menschlicher erythrozyten. Acta. Biological er Medica Germanica 40: 1659-1682.
28. Schilling, C.H., Edwards, J.S., and Palsson, B.Ø. 1999. Towards metabolic phenomics: Analysis of genomic data using flux balances. Biotechnol. Prog. 15: 288-295.
29. Schuster, R. and Holzutter, H.C. 1995. Use of mathematical models for predicting the effect of large scale enzyme activity alterations: Applications to enzyme deficiencies of red blood cells. Eur. J. Biochem. 229: 403-418.
30. Solinge, W.W.v., Kraaijenhagen, R.J., Rijksen, G., van Wijk, R., Stoffer, B.B., and Gajhede, F.C.N.M. 1997. Molecular modeling of human red blood cell pyruvate kinase: Structural implications of a novel G-1091 to A mutation causing severe nonspherocytic hemolytic anemia. Blood 90: 4987-4995.
31. Syvanen, A. 2001. Accessing genetic variation: Genotyping single nucleotide polymorphisms. Nat. Rev. Genet. 2: 930-942.
32. Tanaka, K.R. and Zerez, C.R. 1990. Red cell enzymopathies of the glycolytic pathway. Semin. Hematol. 27: 165-185.
33. Thorburn, D.R. and Kuchel, P.W. 1985. Regulation of the human-erythrocyte hexose-monophosphate shunt under conditions of oxidative stress. A study using NMR spectroscopy, a kinetic isotope effect, a reconstituted system and computer simulation. Eur. J. Biochem. 150: 371-386.
34. Vulliamy, T.J., D'Urso, M., Battistuzzi, G., Estrada, M., Foulkes, N.S., Martini, G., Calabro, V., Poggi, V., Giordano, R., Town, M., et al. 1988. Diverse point mutations in the human glucose-6-phosphate dehydrogenase gene cause enzyme deficiency and mild or severe hemolytic anemia. Proc. Natl. Acad. Sci. 85: 5171-5175.
35. Yamada, K., Chen, Z., Rozen, R., and Matthews, R.G. 2001. Effects of common polymorphisms on the properties of recombinant human methylenetetrahydrofolate reductase. Proc. Natl. Acad. Sci. 98: 14853-14858.
36. Yoshida, A. 1986. Kinetics and molecular abnormalities of human G6PDH variants. In Glucose-6-Phosphate Dehydrogenase, pp. 493-502. Academic Press, Orlando, FL.
37. Yoshida, A. and Lin., M. 1973. Regulation of glucose-6-phosphate dehydrogenase activity in red blood cells from hemolytic and nonhemolytic variant subjects. Blood 41: 877-891.
38. Zanella, A. and Bianchi, P. 2000. Red cell pyruvate kinase deficiency: From genetics to clinical manifestations. Ballieres Clin. Hematol. 13: 57-81.