New Results on Energy Balance Analysis of Metabolic Networks

  • Qinghua Zhou
  • Simon C. K. Shiu
  • Sankar K. Pal
  • Yan Li
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4815)

Abstract

A central and long-standing objective of cellular physiology has been to understand the metabolic capabilities of living cells. In this paper, we perform optimization of metabolic networks in E.Coli under both flux and energy balance constraints. The impact of the energy balance is investigated on the behavior of metabolic networks. Different from the existing work, the preliminary results showed that the impact of imposing energy balance constraints on the biological metabolic systems is very limited.

Keywords

Metabolic networks Flux Balance Analysis Energy Balance Analysis Constraint optimization 

References

  1. 1.
    Reich, J.G., Sel’kov, E.E.: Energy metabolism of the cell. Academic Press, New YorkGoogle Scholar
  2. 2.
    Savinell, J.M., Palsson, B.O.: Network analysis of intermediary metabolism using linear optimization. II. Interpretation of hybridoma cell metabolism. J. Theor. Biol. 154, 455–473 (1992)CrossRefGoogle Scholar
  3. 3.
    Varma, A., Palsson, B.O.: Metabolic capabilities of Escherichia coli. I. Synthesis of biosynthetic precursors and cofactors. J. Theor. Biol. 165, 477–502 (1993)CrossRefGoogle Scholar
  4. 4.
    Segre, D., Vitkup, D., Church, G.M.: Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 99, 15112–15117 (2002)CrossRefGoogle Scholar
  5. 5.
    Varma, A., Palsson, B.O.: Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl. Environ. Microbiol. 60, 3724–3731 (1994)Google Scholar
  6. 6.
    Edwards, J.S., Ibarra, R.U., Palsson, B.O.: In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nature Biotechnol. 19, 125–130 (2001)CrossRefGoogle Scholar
  7. 7.
    Beard, D.A., Liang, S.-d., Qian, H.: Energy balance for analysis of complex metabolic networks. Biophysical Journal 83, 79–86 (2002)CrossRefGoogle Scholar
  8. 8.
    Savinell, J.M., Palsson, B.O.: Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. J. Theor. Biol. 154, 421–454 (1992)CrossRefGoogle Scholar
  9. 9.
    Beard, D.A., Babson, E., Curtis, E., Qian, H.: Thermodynamics constraints for biochemical networks. J. Theor. Biol. 228, 327–333 (2004)CrossRefMathSciNetGoogle Scholar
  10. 10.
    Edwards, J.S., Palsson, B.O.: Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 1, 1 (2000)CrossRefGoogle Scholar
  11. 11.

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Qinghua Zhou
    • 1
  • Simon C. K. Shiu
    • 2
  • Sankar K. Pal
    • 3
  • Yan Li
    • 1
  1. 1.College of Mathematics and Computer Science, Hebei University, Baoding City 071002, Hebei ProvinceChina
  2. 2.Department of Computing, The Hong Kong Polytechnic University, HungHom, KowloonHong Kong
  3. 3.Indian Statistical Institute, Kolkata 700 108India

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