Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints

Biophysical Journal
Nathan D PriceBernhard O Palsson

Abstract

Constraint-based modeling has proven to be a useful tool in the analysis of biochemical networks. To date, most studies in this field have focused on the use of linear constraints, resulting from mass balance and capacity constraints, which lead to the definition of convex solution spaces. One additional constraint arising out of thermodynamics is known as the "loop law" for reaction fluxes, which states that the net flux around a closed biochemical loop must be zero because no net thermodynamic driving force exists. The imposition of the loop-law can lead to nonconvex solution spaces making the analysis of the consequences of its imposition challenging. A four-step approach is developed here to apply the loop-law to study metabolic network properties: 1), determine linear equality constraints that are necessary (but not necessarily sufficient) for thermodynamic feasibility; 2), tighten V(max) and V(min) constraints to enclose the remaining nonconvex space; 3), uniformly sample the convex space that encloses the nonconvex space using standard Monte Carlo techniques; and 4), eliminate from the resulting set all solutions that violate the loop-law, leaving a subset of steady-state solutions. This subset of solutions represents a ...Continue Reading

References

Jun 25, 2002·Biophysical Journal·Daniel A BeardHong Qian
Nov 12, 2002·Biophysical Journal·Nathan D PriceBernhard Ø Palsson
Jan 25, 2003·European Journal of Biochemistry·Hong QianShou-dan Liang
Sep 26, 2003·Omics : a Journal of Integrative Biology·Jochen FörsterJens Nielsen
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May 12, 2004·Journal of Theoretical Biology·Daniel A BeardHong Qian
Jul 31, 2004·Trends in Biotechnology·Jason A PapinBernhard O Palsson
Oct 21, 2004·Nature Reviews. Microbiology·Nathan D PriceBernhard Ø Palsson
Dec 2, 2004·The Journal of Biological Chemistry·Ines ThieleBernhard Ø Palsson
May 18, 2005·Proceedings of the National Academy of Sciences of the United States of America·Tomer ShlomiEytan Ruppin
Jun 18, 2005·Biotechnology and Bioengineering·Stephen S FongBernhard O Palsson

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Citations

Jan 9, 2010·Nature Protocols·Ines Thiele, Bernhard Ø Palsson
Mar 1, 2012·Nature Reviews. Microbiology·Nathan E LewisBernhard O Palsson
Jan 21, 2012·Bioinformatics·Mario LatendressePeter D Karp
May 21, 2008·BMC Bioinformatics·Alfredo BraunsteinAndrea Pagnani
Jul 12, 2008·BMC Systems Biology·Jeremiah Wright, Andreas Wagner
Mar 27, 2009·BMC Systems Biology·Monica L MoMarkus J Herrgård
Jul 23, 2011·BMC Systems Biology·Saheed ImamTimothy J Donohue
Feb 21, 2009·PLoS Computational Biology·Fan LiBernhard Ø Palsson
Apr 24, 2012·PloS One·Gunnar SigurdssonInes Thiele
Apr 20, 2011·The Plant Journal : for Cell and Molecular Biology·Jordan Hay, Jörg Schwender
Jan 27, 2015·Mathematical Biosciences·Arne C ReimersAlexander Bockmayr
Jun 28, 2012·PLoS Computational Biology·Daniele De MartinoEnzo Marinari
Aug 20, 2015·PloS One·Arne C Reimers
Nov 18, 2010·Biophysical Journal·Stefan J JolMatthias Heinemann
Feb 8, 2013·Bioinformatics·Arne C Müller, Alexander Bockmayr
Apr 19, 2017·PLoS Computational Biology·Claus Jonathan FritzemeierMartin J Lercher
Oct 23, 2008·The Journal of Biological Chemistry·Jan Schellenberger, Bernhard Ø Palsson
Feb 2, 2011·Biophysical Journal·Jan SchellenbergerBernhard Ø Palsson

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