메뉴 건너뛰기




Volumn 1191, Issue , 2014, Pages 49-63

Constraining the flux space using thermodynamics and integration of metabolomics data

Author keywords

Constraint based analysis; Flux balance analysis; Fluxomics; Metabolic networks; Metabolomics; Thermodynamics based flux balance analysis

Indexed keywords

ARTICLE; GIBBS FREE ENERGY; GLUCOSE TRANSPORT; IONIC STRENGTH; MEMBRANE POTENTIAL; METABOLIC REGULATION; METABOLOMICS; MOLECULAR MECHANICS; NONHUMAN; PENTOSE PHOSPHATE CYCLE; PH; PRIORITY JOURNAL; QUANTUM MECHANICS; STEADY STATE; THERMODYNAMICS; UNCERTAINTY; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; METABOLIC FLUX ANALYSIS; METABOLISM; PHYSIOLOGY; PROCEDURES; SPECIES DIFFERENCE;

EID: 84921865747     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1170-7_3     Document Type: Article
Times cited : (44)

References (39)
  • 1
    • 0033580813 scopus 로고    scopus 로고
    • Systems properties of the Haemophilus influenzae Rd metabolic genotype
    • Edwards JS, Palsson BO (1999) Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem 274(25): 17410–17416
    • (1999) J Biol Chem , vol.274 , Issue.25 , pp. 17410-17416
    • Edwards, J.S.1    Palsson, B.O.2
  • 3
    • 84885911432 scopus 로고    scopus 로고
    • Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance
    • Heavner BD, Smallbone K, Price ND, Walker LP (2013) Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. Database bat059
    • (2013) Database bat059
    • Heavner, B.D.1    Smallbone, K.2    Price, N.D.3    Walker, L.P.4
  • 4
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I, Palsson BO (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5(1):93–121
    • (2010) Nat Protoc , vol.5 , Issue.1 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 5
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
    • Mahadevan R, Schilling CH (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metabolic Engineering. p. 264–276
    • (2003) Metabolic Engineering , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 6
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: Evaluating the consequences of constraints
    • Price N, Reed J, Palsson B (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2(11):886–897
    • (2004) Nat Rev Microbiol , vol.2 , Issue.11 , pp. 886-897
    • Price, N.1    Reed, J.2    Palsson, B.3
  • 7
    • 84857052437 scopus 로고    scopus 로고
    • From network models to network responses: Integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks
    • Soh KC, Miskovic L, Hatzimanikatis V, Nielsen J (2011) From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks. FEMS Yeast Res 12(2):129–143
    • (2011) FEMS Yeast Res , vol.12 , Issue.2 , pp. 129-143
    • Soh, K.C.1    Miskovic, L.2    Hatzimanikatis, V.3    Nielsen, J.4
  • 8
    • 77952952952 scopus 로고    scopus 로고
    • Network thermodynamics in the post-genomic era
    • Soh KC, Hatzimanikatis V (2010) Network thermodynamics in the post-genomic era. Curr Opin Microbiol 13(3):350–357
    • (2010) Curr Opin Microbiol , vol.13 , Issue.3 , pp. 350-357
    • Soh, K.C.1    Hatzimanikatis, V.2
  • 9
    • 33847797256 scopus 로고    scopus 로고
    • Thermodynamics-based metabolic flux analysis
    • Henry C, Broadbelt LJ, Hatzimanikatis V (2007) Thermodynamics-based metabolic flux analysis. Biophys J 92(5):1792–1805
    • (2007) Biophys J , vol.92 , Issue.5 , pp. 1792-1805
    • Henry, C.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 11
    • 8844259501 scopus 로고    scopus 로고
    • Thermodynamics of enzyme-catalyzed reactions– a database for quantitative biochemistry
    • Goldberg RN, Tewari YB, Bhat TN (2004) Thermodynamics of enzyme-catalyzed reactions– a database for quantitative biochemistry. Bioinformatics 20(16):2874–2877
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2874-2877
    • Goldberg, R.N.1    Tewari, Y.B.2    Bhat, T.N.3
  • 12
    • 0024612050 scopus 로고
    • A database and retrieval-system for the Nbs tables of chemical thermodynamic properties
    • Wang PM, Neumann DB (1989) A database and retrieval-system for the Nbs tables of chemical thermodynamic properties. J Chem Inf Comput Sci 29(1):31–38
    • (1989) J Chem Inf Comput Sci , vol.29 , Issue.1 , pp. 31-38
    • Wang, P.M.1    Neumann, D.B.2
  • 13
    • 51049107514 scopus 로고    scopus 로고
    • Group contribution method for thermodynamic analysis of complex metabolic networks
    • Jankowski MD, Henry CS, Broadbelt LJ, Hatzimanikatis V (2008) Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J 95(3): 1487–1499
    • (2008) Biophys J , vol.95 , Issue.3 , pp. 1487-1499
    • Jankowski, M.D.1    Henry, C.S.2    Broadbelt, L.J.3    Hatzimanikatis, V.4
  • 14
    • 0025701406 scopus 로고
    • Group contributions for estimating standard Gibbs energies of formation of biochemical compounds in aqueous solution
    • Mavrovouniotis ML (1990) Group contributions for estimating standard Gibbs energies of formation of biochemical compounds in aqueous solution. Biotechnol Bioeng 36(10): 1070–1082
    • (1990) Biotechnol Bioeng , vol.36 , Issue.10 , pp. 1070-1082
    • Mavrovouniotis, M.L.1
  • 15
    • 0026353854 scopus 로고
    • Estimation of standard Gibbs energy changes of biotransformations
    • Mavrovouniotis ML (1991) Estimation of standard Gibbs energy changes of biotransformations. J Biol Chem 266(22):14440–14445
    • (1991) J Biol Chem , vol.266 , Issue.22 , pp. 14440-14445
    • Mavrovouniotis, M.L.1
  • 16
    • 84865136870 scopus 로고    scopus 로고
    • An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
    • Noor E, Bar-Even A, Flamholz A, Lubling Y, Davidi D, Milo R (2012) An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. Bioinformatics 28(15):2037–2044
    • (2012) Bioinformatics , vol.28 , Issue.15 , pp. 2037-2044
    • Noor, E.1    Bar-even, A.2    Flamholz, A.3    Lubling, Y.4    Davidi, D.5    Milo, R.6
  • 17
    • 0009590921 scopus 로고
    • Free-energy calculations— a breakthrough for modeling organic-chemistry in solution
    • Jorgensen WL (1989) Free-energy calculations— a breakthrough for modeling organic-chemistry in solution. Acc Chem Res 22(5): 184–189
    • (1989) Acc Chem Res , vol.22 , Issue.5 , pp. 184-189
    • Jorgensen, W.L.1
  • 18
    • 43949083733 scopus 로고    scopus 로고
    • Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
    • Hu H, Yang WT (2008) Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Annu Rev Phys Chem 59:573–601
    • (2008) Annu Rev Phys Chem , vol.59 , pp. 573-601
    • Hu, H.1    Yang, W.T.2
  • 19
    • 33750899801 scopus 로고    scopus 로고
    • Estimation of absolute free energies of hydration using continuum methods: Accuracy of partial, charge models and optimization of nonpolar contributions
    • Rizzo RC, Aynechi T, Case DA, Kuntz ID (2006) Estimation of absolute free energies of hydration using continuum methods: accuracy of partial, charge models and optimization of nonpolar contributions. J Chem Theory Comput 2(1):128–139
    • (2006) J Chem Theory Comput , vol.2 , Issue.1 , pp. 128-139
    • Rizzo, R.C.1    Aynechi, T.2    Case, D.A.3    Kuntz, I.D.4
  • 20
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    • Feist A, Henry C, Reed J, Krummenacker M, Joyce A, Karp P, Broadbelt L, Hatzimanikatis V, Palsson B (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:121
    • (2007) Mol Syst Biol , vol.3 , pp. 121
    • Feist, A.1    Henry, C.2    Reed, J.3    Krummenacker, M.4    Joyce, A.5    Karp, P.6    Broadbelt, L.7    Hatzimanikatis, V.8
  • 21
    • 78649281194 scopus 로고    scopus 로고
    • Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks
    • Jol SJ, Kummel A, Hatzimanikatis V, Beard DA, Heinemann M (2010) Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks. Biophys J 99(10):3139–3144
    • (2010) Biophys J , vol.99 , Issue.10 , pp. 3139-3144
    • Jol, S.J.1    Kummel, A.2    Hatzimanikatis, V.3    Beard, D.A.4    Heinemann, M.5
  • 25
    • 0001096585 scopus 로고
    • PH homeostasis in Escherichia coli: Measurement by 31P nuclear magnetic resonance of methylphosphonate and phosphate
    • Slonczewski JL, Rosen BP, Alger JR, Macnab RM (1981) PH homeostasis in Escherichia coli: measurement by 31P nuclear magnetic resonance of methylphosphonate and phosphate. Proc Natl Acad Sci U S A 78(10): 6271–6275
    • (1981) Proc Natl Acad Sci U S A , vol.78 , Issue.10 , pp. 6271-6275
    • Slonczewski, J.L.1    Rosen, B.P.2    Alger, J.R.3    Macnab, R.M.4
  • 26
    • 0031596006 scopus 로고    scopus 로고
    • ATP synthesis by the F1Fo ATP synthase of Escherichia coli is obligatorily dependent on the electric potential
    • Kaim G, Dimroth P (1998) ATP synthesis by the F1Fo ATP synthase of Escherichia coli is obligatorily dependent on the electric potential. FEBS Lett 434(1–2):57–60
    • (1998) FEBS Lett , vol.434 , Issue.1-2 , pp. 57-60
    • Kaim, G.1    Dimroth, P.2
  • 27
    • 84865735753 scopus 로고    scopus 로고
    • Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data
    • Toya Y, Nakahigashi K, Tomita M, Shimizu K (2012) Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data. Mol BioSyst 8(10):2593–2604
    • (2012) Mol BioSyst , vol.8 , Issue.10 , pp. 2593-2604
    • Toya, Y.1    Nakahigashi, K.2    Tomita, M.3    Shimizu, K.4
  • 28
    • 70349745413 scopus 로고    scopus 로고
    • Novel biological insights through metabolomics and 13C-flux analysis
    • Zamboni N, Sauer U (2009) Novel biological insights through metabolomics and 13C-flux analysis. Curr Opin Microbiol 12(5):553–558
    • (2009) Curr Opin Microbiol , vol.12 , Issue.5 , pp. 553-558
    • Zamboni, N.1    Sauer, U.2
  • 29
    • 33846061120 scopus 로고    scopus 로고
    • Metabolic networks in motion: 13C-based flux analysis
    • Sauer U (2006) Metabolic networks in motion: 13C-based flux analysis. Mol Syst Biol 2:62
    • (2006) Mol Syst Biol , vol.2 , pp. 62
    • Sauer, U.1
  • 30
    • 0029146299 scopus 로고
    • Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism
    • Szyperski T (1995) Biosynthetically directed fractional 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. Eur J Biochem 232(2):433–448
    • (1995) Eur J Biochem , vol.232 , Issue.2 , pp. 433-448
    • Szyperski, T.1
  • 31
    • 33645752331 scopus 로고    scopus 로고
    • Genome-scale thermodynamic analysis of Escherichia coli metabolism
    • Henry C, Jankowski MD, Broadbelt LJ, Hatzimanikatis V (2006) Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophys J 90(4):1453–1461
    • (2006) Biophys J , vol.90 , Issue.4 , pp. 1453-1461
    • Henry, C.1    Jankowski, M.D.2    Broadbelt, L.J.3    Hatzimanikatis, V.4
  • 32
    • 65549092780 scopus 로고    scopus 로고
    • Use of randomized sampling for analysis of metabolic networks
    • Schellenberger J, Palsson BO (2009) Use of randomized sampling for analysis of metabolic networks. J Biol Chem 284(9):5457–5461
    • (2009) J Biol Chem , vol.284 , Issue.9 , pp. 5457-5461
    • Schellenberger, J.1    Palsson, B.O.2
  • 33
    • 0031679770 scopus 로고    scopus 로고
    • Direction choice for accelerated convergence in hit-and-run sampling
    • Kaufman DE, Smith RL (1998) Direction choice for accelerated convergence in hit-and-run sampling. Oper Res 46(1):84–95
    • (1998) Oper Res , vol.46 , Issue.1 , pp. 84-95
    • Kaufman, D.E.1    Smith, R.L.2
  • 35
    • 78650218972 scopus 로고    scopus 로고
    • Modeling of uncertainties in biochemical reactions
    • Miskovic L, Hatzimanikatis V (2011) Modeling of uncertainties in biochemical reactions. Biotechnol Bioeng 108(2):413–423
    • (2011) Biotechnol Bioeng , vol.108 , Issue.2 , pp. 413-423
    • Miskovic, L.1    Hatzimanikatis, V.2
  • 36
    • 77955058605 scopus 로고    scopus 로고
    • Production of biofuels and biochemicals: In need of an ORACLE
    • Miskovic L, Hatzimanikatis V (2010) Production of biofuels and biochemicals: in need of an ORACLE. Trends Biotechnol 28(8):391–397
    • (2010) Trends Biotechnol , vol.28 , Issue.8 , pp. 391-397
    • Miskovic, L.1    Hatzimanikatis, V.2
  • 37
    • 3843128481 scopus 로고    scopus 로고
    • Reconstruction and Validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
    • Duarte NC, Herrgard MJ, Palsson BO (2004) Reconstruction and Validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14(7):1298–1309
    • (2004) Genome Res , vol.14 , Issue.7 , pp. 1298-1309
    • Duarte, N.C.1    Herrgard, M.J.2    Palsson, B.O.3
  • 38
    • 33750196846 scopus 로고    scopus 로고
    • Influence of gluconeogenic phosphoenol pyruvate carboxykinase (PCK) expression on succinic acid fermentation in Escherichia coli under high bicarbonate condition
    • Kwon YD, Lee SY, Kim P (2006) Influence of gluconeogenic phosphoenol pyruvate carboxykinase (PCK) expression on succinic acid fermentation in Escherichia coli under high bicarbonate condition. J Microbiol Biotechnol 16:1448–1452
    • (2006) J Microbiol Biotechnol , vol.16 , pp. 1448-1452
    • Kwon, Y.D.1    Lee, S.Y.2    Kim, P.3
  • 39
    • 78650595035 scopus 로고    scopus 로고
    • Manipulating redox and ATP balancing for improved production of succinate in
    • Singh A, Soh KC, Hatzimanikatis V, Gill RT (2011) Manipulating redox and ATP balancing for improved production of succinate in E. coli. Metab Eng 13:76–81
    • (2011) E. Coli. Metab Eng , vol.13 , pp. 76-81
    • Singh, A.1    Soh, K.C.2    Hatzimanikatis, V.3    Gill, R.T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.