Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism

Henry, Christopher S.; Jankowski, Matthew D.; Broadbelt, Linda J.; Hatzimanikatis, Vassily

doi:10.1529/biophysj.105.071720

Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism

Journal Article · Wed Feb 01 04:00:00 EST 2006 · Biophysical Journal

DOI:https://doi.org/10.1529/biophysj.105.071720· OSTI ID:2318570

Henry, Christopher S.; Jankowski, Matthew D.; Broadbelt, Linda J.; Hatzimanikatis, Vassily

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Sponsoring Organization:: USDOE

OSTI ID:: 2318570

Journal Information:: Biophysical Journal, Journal Name: Biophysical Journal Journal Issue: 4 Vol. 90; ISSN 0006-3495

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (35)

Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Covert, Markus W.; Famili, Iman; Palsson, Bernhard O. Biotechnology and Bioengineering, Vol. 84, Issue 7 https://doi.org/10.1002/bit.10849	journal	December 2003
Probing the performance limits of theEscherichia coli metabolic network subject to gene additions or deletions Burgard, Anthony P.; Maranas, Costas D. Biotechnology and Bioengineering, Vol. 74, Issue 5 https://doi.org/10.1002/bit.1127	journal	January 2001
Equations and calculations of product yields and preferred pathways for butanediol and mixed-acid fermentations Papoutsakis, Eleftherios Terry; Meyer, Charles L. Biotechnology and Bioengineering, Vol. 27, Issue 1 https://doi.org/10.1002/bit.260270108	journal	January 1985
Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution Mavrovouniotis, Michael L. Biotechnology and Bioengineering, Vol. 36, Issue 10 https://doi.org/10.1002/bit.260361013	journal	December 1990
Calculation of Standard Transformed Gibbs Energies and Standard Transformed Enthalpies of Biochemical Reactants Alberty, Robert A. Archives of Biochemistry and Biophysics, Vol. 353, Issue 1 https://doi.org/10.1006/abbi.1998.0638	journal	May 1998
Metabolic Capabilities of Escherichia coli: I. Synthesis of Biosynthetic Precursors and Cofactors Varma, Amit; Palsson, Bernhard O. Journal of Theoretical Biology, Vol. 165, Issue 4 https://doi.org/10.1006/jtbi.1993.1202	journal	December 1993
Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns Varma, Amit; Palsson, Bernhard O. Journal of Theoretical Biology, Vol. 165, Issue 4 https://doi.org/10.1006/jtbi.1993.1203	journal	December 1993
Theory for the Systemic Definition of Metabolic Pathways and their use in Interpreting Metabolic Function from a Pathway-Oriented Perspective Schilling, Christophe H.; Letscher, David; Palsson, Bernhard Ø. Journal of Theoretical Biology, Vol. 203, Issue 3 https://doi.org/10.1006/jtbi.2000.1073	journal	April 2000
An equilibrium and calorimetric investigation of the hydrolysis of L-tryptophan to (indole + pyruvate + ammonia) Tewari, Yadu B.; Goldberg, Robert N. Journal of Solution Chemistry, Vol. 23, Issue 2 https://doi.org/10.1007/BF00973544	journal	February 1994
Duality theory for thermodynamic bottlenecks in bioreaction pathways Mavrovouniotis, Michael L. Chemical Engineering Science, Vol. 51, Issue 9 https://doi.org/10.1016/0009-2509(95)00308-8	journal	May 1996
Energy Balance for Analysis of Complex Metabolic Networks Beard, Daniel A.; Liang, Shou-dan; Qian, Hong Biophysical Journal, Vol. 83, Issue 1 https://doi.org/10.1016/S0006-3495(02)75150-3	journal	July 2002
The First Step of Histidine Biosynthesis Ames, Bruce N.; Martin, Robert G.; Garry, Barbara J. Journal of Biological Chemistry, Vol. 236, Issue 7 https://doi.org/10.1016/S0021-9258(18)64123-7	journal	July 1961
Steady state kinetics of ATP synthesis and hydrolysis coupled calcium transport catalyzed by the reconstituted sarcoplasmic reticulum ATPase. Fagan, M. H.; Dewey, T. G. Journal of Biological Chemistry, Vol. 260, Issue 10 https://doi.org/10.1016/S0021-9258(18)88949-9	journal	May 1985
Estimation of standard Gibbs energy changes of biotransformations Mavrovouniotis, M. L. Journal of Biological Chemistry, Vol. 266, Issue 22 https://doi.org/10.1016/S0021-9258(18)98705-3	journal	August 1991
Enzymes of Clostridial Purine Fermentation Uyeda, Kosaku; Rabinowitz, Jesse C. Journal of Biological Chemistry, Vol. 242, Issue 19 https://doi.org/10.1016/S0021-9258(18)99549-9	journal	October 1967
The First Enzyme in Histidine Biosynthesis: The Nature of Feedback Inhibition by Histidine Martin, Robert G. Journal of Biological Chemistry, Vol. 238, Issue 1 https://doi.org/10.1016/S0021-9258(19)83989-3	journal	January 1963
Cellular concentrations of enzymes and their substrates Albe, Kathy R.; Butler, Margaret H.; Wright, Barbara E. Journal of Theoretical Biology, Vol. 143, Issue 2 https://doi.org/10.1016/S0022-5193(05)80266-8	journal	March 1990
Flux analysis of underdetermined metabolic networks: the quest for the missing constraints Bonarius, Hendrik P. J.; Schmid, Georg; Tramper, Johannes Trends in Biotechnology, Vol. 15, Issue 8 https://doi.org/10.1016/S0167-7799(97)01067-6	journal	August 1997
Enzymatic reaction rate limits with constraints on equilibrium constants and experimental parameters Bish, Douglas R.; Mavrovouniotis, Michael L. Biosystems, Vol. 47, Issue 1-2 https://doi.org/10.1016/S0303-2647(98)00012-4	journal	June 1998
Thermodynamic constraints for biochemical networks Beard, Daniel A.; Babson, Eric; Curtis, Edward Journal of Theoretical Biology, Vol. 228, Issue 3 https://doi.org/10.1016/j.jtbi.2004.01.008	journal	June 2004
Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space Wiback, Sharon J.; Famili, Iman; Greenberg, Harvey J. Journal of Theoretical Biology, Vol. 228, Issue 4 https://doi.org/10.1016/j.jtbi.2004.02.006	journal	June 2004
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models Mahadevan, R.; Schilling, C. H. Metabolic Engineering, Vol. 5, Issue 4 https://doi.org/10.1016/j.ymben.2003.09.002	journal	October 2003
Robustness Analysis of the Escherichia coli Metabolic Network Edwards, J. S.; Palsson, B. O. Biotechnology Progress, Vol. 16, Issue 6 https://doi.org/10.1021/bp0000712	journal	December 2000
Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets Alper, Hal; Miyaoku, Kohei; Stephanopoulos, Gregory Nature Biotechnology, Vol. 23, Issue 5 https://doi.org/10.1038/nbt1083	journal	April 2005
Stoichiometric network theory for nonequilibrium biochemical systems Qian, Hong; Beard, Daniel A.; Liang, Shou-dan European Journal of Biochemistry, Vol. 270, Issue 3 https://doi.org/10.1046/j.1432-1033.2003.03357.x	journal	February 2003
Endothelial cell surface F ₁ -F _O ATP synthase is active in ATP synthesis and is inhibited by angiostatin Moser, Tammy L.; Kenan, Daniel J.; Ashley, Timothy A. Proceedings of the National Academy of Sciences, Vol. 98, Issue 12 https://doi.org/10.1073/pnas.131067798	journal	May 2001
Estimation of Upper Bounds for the Rates of Enzymatic Reactions Mavrovouniotis, Michael L.; Stephanopoulos, George; Stephanopoulos, Gregory Chemical Engineering Communications, Vol. 93, Issue 1 https://doi.org/10.1080/00986449008911447	journal	June 1990
KEGG: Kyoto Encyclopedia of Genes and Genomes Ogata, H.; Goto, S.; Sato, K. Nucleic Acids Research, Vol. 27, Issue 1 https://doi.org/10.1093/nar/27.1.29	journal	January 1999
KEGG: Kyoto Encyclopedia of Genes and Genomes Kanehisa, Minoru; Goto, Susumu Nucleic Acids Research, Vol. 28, Issue 1, p. 27-30 https://doi.org/10.1093/nar/28.1.27	journal	January 2000
Genome-Scale In Silico Models of E. coli Have Multiple Equivalent Phenotypic States: Assessment of Correlated Reaction Subsets That Comprise Network States Reed, J. L. Genome Research, Vol. 14, Issue 9 https://doi.org/10.1101/gr.2546004	journal	September 2004
Metabolic Flux Ratio Analysis of Genetic and Environmental Modulations of Escherichia coli Central Carbon Metabolism Sauer, Uwe; Lasko, Daniel R.; Fiaux, Jocelyne Journal of Bacteriology, Vol. 181, Issue 21 https://doi.org/10.1128/JB.181.21.6679-6688.1999	journal	November 1999
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Varma, A.; Palsson, B. O. Applied and Environmental Microbiology, Vol. 60, Issue 10 https://doi.org/10.1128/aem.60.10.3724-3731.1994	journal	January 1994
Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism Beard, Daniel A.; Qian, Hong American Journal of Physiology-Endocrinology and Metabolism, Vol. 288, Issue 3 https://doi.org/10.1152/ajpendo.00239.2004	journal	March 2005
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) Reed, Jennifer L.; Vo, Thuy D.; Schilling, Christophe H. Genome Biology, Vol. 4, Issue 9, p. R54 https://doi.org/10.1186/gb-2003-4-9-r54	journal	August 2003
Metabolic Control Analysis under Uncertainty: Framework Development and Case Studies Wang, Liqing; Birol, Inanç; Hatzimanikatis, Vassily Biophysical Journal, Vol. 87, Issue 6 https://doi.org/10.1529/biophysj.104.048090	journal	December 2004

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