An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data

scientific article published on February 24, 2011

An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1016/J.YMBEN.2011.02.005
P953full work available at URLhttps://api.elsevier.com/content/article/PII:S1096717611000176?httpAccept=text/plain
https://api.elsevier.com/content/article/PII:S1096717611000176?httpAccept=text/xml
P698PubMed publication ID21354323
P5875ResearchGate publication ID50214096

P2093author name stringCor Ras
Walter M. van Gulik
Angela ten Pierick
André B. Canelas
Joseph J. Heijnen
P2860cites workUniversally sloppy parameter sensitivities in systems biology modelsQ21145658
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MSQ24680943
Relationship between thermodynamic driving force and one-way fluxes in reversible processesQ28469105
Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome dataQ28766251
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coliQ29615316
A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kineticsQ31087514
Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptidesQ33221531
Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networksQ33286434
Metabolome dynamic responses of Saccharomyces cerevisiae to simultaneous rapid perturbations in external electron acceptor and electron donorQ51063408
In vivo kinetics with rapid perturbation experiments in Saccharomyces cerevisiae using a second-generation BioScopeQ51224857
Thermodynamic constraints for biochemical networksQ51676908
Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equationsQ51714258
Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kineticsQ51870870
Quantitative studies of enzyme-substrate compartmentation, functional coupling and metabolic channelling in muscle cells.Q52235772
In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical modelQ52257228
A model of the pentose phosphate pathway in rat liver cells.Q52352976
Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry.Q54463861
Stoichiometry and compartmentation of NADH metabolism inSaccharomyces cerevisiaeQ56267572
The kinetics of enzyme-catalyzed reactions with two or more substrates or productsQ56610698
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistryQ57232711
How reliable are thermodynamic feasibility statements of biochemical pathways?Q58325224
Trehalose-6-phosphate synthase/phosphatase complex from bakers’ yeast: purification of a proteolytically activated formQ67915303
Characterization of trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase of Saccharomyces cerevisiaeQ69353099
Different signals control the activation of glycolysis in the yeast Saccharomyces cerevisiaeQ72916805
Regulation of fermentative capacity and levels of glycolytic enzymes in chemostat cultures of Saccharomyces cerevisiaeQ73914835
Improved rapid sampling for in vivo kinetics of intracellular metabolites in Saccharomyces cerevisiaeQ74826050
Glucose uptake kinetics and transcription of HXT genes in chemostat cultures of Saccharomyces cerevisiaeQ77772122
Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solutionQ81564298
In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae : I. Experimental observationsQ81660481
Leakage-free rapid quenching technique for yeast metabolomicsQ114870860
Analysis of glycolytic intermediates in Saccharomyces cerevisiae using anion exchange chromatography and electrospray ionization with tandem mass spectrometric detectionQ114871781
Data-based identifiability analysis of non-linear dynamical modelsQ33292131
Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coliQ33574191
Metabolic engineering: techniques for analysis of targets for genetic manipulationsQ33587052
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomicsQ33674206
Energy balance for analysis of complex metabolic networksQ34178210
Thermodynamics of enzyme-catalyzed reactions--a database for quantitative biochemistryQ34321033
Fluxomics: mass spectrometry versus quantitative imagingQ34353897
How can biochemical reactions within cells differ from those in test tubes?Q34545385
The state of magnesium in cells as estimated from the adenylate kinase equilibriumQ34655600
Virtual quantification of metabolites by capillary electrophoresis-electrospray ionization-mass spectrometry: predicting ionization efficiency without chemical standardsQ34960275
Metabolic networks in motion: 13C-based flux analysisQ35194034
Approximative kinetic formats used in metabolic network modelingQ36186685
Thermodynamics of microbial growth and metabolism: an analysis of the current situationQ36268582
Group contribution method for thermodynamic analysis of complex metabolic networksQ36783787
Metabolic flux analysis in eukaryotesQ37694051
Trehalose-6-phosphate, a new regulator of yeast glycolysis that inhibits hexokinases.Q38316854
When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation.Q39346136
Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction ratesQ41847582
Dynamics of glycolytic regulation during adaptation of Saccharomyces cerevisiae to fermentative metabolismQ41893946
Formulating genome-scale kinetic models in the post-genome era.Q42030401
Genome-scale thermodynamic analysis of Escherichia coli metabolismQ42155867
The thermodynamic meaning of metabolic exchange fluxesQ42406509
Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolitesQ43078354
Quantitative evaluation of intracellular metabolite extraction techniques for yeast metabolomicsQ43298868
A comprehensive method for the quantification of the non-oxidative pentose phosphate pathway intermediates in Saccharomyces cerevisiae by GC-IDMS.Q43300874
From fluxes and isotope labeling patterns towards in silico cellsQ43421305
Signal transduction dynamics of the protein kinase-A/phosphofructokinase-2 system in Saccharomyces cerevisiaeQ43566756
Triosephosphate isomerase catalysis is diffusion controlled. Appendix: Analysis of triose phosphate equilibria in aqueous solution by 31P NMR.Q43918535
Development and application of a differential method for reliable metabolome analysis in Escherichia coli.Q44027136
An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strainsQ44436758
Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study.Q44664104
MIRACLE: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolitesQ44766134
Analysis of in vivo kinetics of glycolysis in aerobic Saccharomyces cerevisiae by application of glucose and ethanol pulsesQ45078833
Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standardsQ45203084
Changes in the metabolome of Saccharomyces cerevisiae associated with evolution in aerobic glucose-limited chemostatsQ45251243
Simultaneous quantification of free nucleotides in complex biological samples using ion pair reversed phase liquid chromatography isotope dilution tandem mass spectrometryQ46105157
Kinetic hybrid models composed of mechanistic and simplified enzymatic rate laws--a promising method for speeding up the kinetic modelling of complex metabolic networksQ46167096
Prolonged selection in aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae causes a partial loss of glycolytic capacityQ46471506
Quantitative estimation of channeling from early glycolytic intermediates to CO in intact Escherichia coliQ46566117
Determination of the cytosolic free NAD/NADH ratio in Saccharomyces cerevisiae under steady-state and highly dynamic conditionsQ46668901
Quantitative physiological study of the fast dynamics in the intracellular pH of Saccharomyces cerevisiae in response to glucose and ethanol pulsesQ46869987
A metabolic network stoichiometry analysis of microbial growth and product formationQ47864492
Dynamic modeling of the central carbon metabolism of Escherichia coliQ50970929
P433issue3
P407language of work or nameEnglishQ1860
P921main subjectmodelling biological systemsQ4299308
P304page(s)294-306
P577publication date2011-02-24
P1433published inMetabolic EngineeringQ6822334
P1476titleAn in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data
P478volume13

Reverse relations

cites work (P2860)
Q37962993A flux-sensing mechanism could regulate the switch between respiration and fermentation.
Q37970441A systems-level approach for metabolic engineering of yeast cell factories.
Q97643842An upper limit on Gibbs energy dissipation governs cellular metabolism
Q43806620Changes in substrate availability in Escherichia coli lead to rapid metabolite, flux and growth rate responses
Q49108088Comparative fluxome and metabolome analysis for overproduction of succinate in Escherichia coli
Q34575433Concepts, challenges, and successes in modeling thermodynamics of metabolism
Q38072750Control limits for accumulation of plant metabolites: brute force is no substitute for understanding.
Q41848378Determination of the Cytosolic NADPH/NADP Ratio in Saccharomyces cerevisiae using Shikimate Dehydrogenase as Sensor Reaction.
Q54266728Determination of the in vivo NAD:NADH ratio in Saccharomyces cerevisiae under anaerobic conditions, using alcohol dehydrogenase as sensor reaction.
Q41883859Development of quantitative metabolomics for Pichia pastoris.
Q28829909Differential RNA-seq, Multi-Network Analysis and Metabolic Regulation Analysis of Kluyveromyces marxianus Reveals a Compartmentalised Response to Xylose
Q37992194Energy coupling in Saccharomyces cerevisiae: selected opportunities for metabolic engineering
Q92576510Energy metabolism controls phenotypes by protein efficiency and allocation
Q47681036Engineering Microbial Metabolite Dynamics and Heterogeneity
Q54364642Escherichia coli responds with a rapid and large change in growth rate upon a shift from glucose-limited to glucose-excess conditions
Q28828785Evaluation of rate law approximations in bottom-up kinetic models of metabolism
Q41790231Fast "Feast/Famine" Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae
Q39856357Glucose-methanol co-utilization in Pichia pastoris studied by metabolomics and instationary ¹³C flux analysis.
Q42371059In vivo analysis of NH4+ transport and central N-metabolism of Saccharomyces cerevisiae under aerobic N-limited conditions.
Q42013266In vivo analysis of Saccharomyces cerevisiae plasma membrane ATPase Pma1p isoforms with increased in vitro H+/ATP stoichiometry.
Q53239744Increasing free-energy (ATP) conservation in maltose-grown Saccharomyces cerevisiae by expression of a heterologous maltose phosphorylase
Q50233836Interaction of storage carbohydrates and other cyclic fluxes with central metabolism: A quantitative approach by non-stationary 13C metabolic flux analysis
Q42247962Intracellular product recycling in high succinic acid producing yeast at low pH.
Q83394208Lipase-catalyzed remote kinetic resolution of citalopram intermediate by asymmetric alcoholysis and thermodynamic analysis
Q57232693Lost in Transition: Start-Up of Glycolysis Yields Subpopulations of Nongrowing Cells
Q43704553MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis
Q42227095Metabolic adjustment upon repetitive substrate perturbations using dynamic 13C-tracing in yeast
Q35136555Metabolic modelling in the development of cell factories by synthetic biology
Q37961354Metabolic network reconstruction: advances in in silico interpretation of analytical information
Q93001714Metabolic switches from quiescence to growth in synchronized Saccharomyces cerevisiae
Q38263318Multi-tasking of biosynthetic and energetic functions of glycolysis explained by supply and demand logic
Q38118241Parameter identification of in vivo kinetic models: Limitations and challenges
Q38847267Robust identification of metabolic control for microbial l-methionine production following an easy-to-use puristic approach
Q35005596Steady-state metabolite concentrations reflect a balance between maximizing enzyme efficiency and minimizing total metabolite load
Q38222622Systematic applications of metabolomics in metabolic engineering
Q48364480Topological and kinetic determinants of the modal matrices of dynamic models of metabolism
Q46370193Transport and metabolism of fumaric acid in Saccharomyces cerevisiae in aerobic glucose-limited chemostat culture
Q47787124Water content, adenylate kinase, and mitochondria drive adenylate balance in dehydrating and imbibing seeds

Search more.