General Information info
|Manuscript title||A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.|
|Authors||Kieran Smallbone, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, Neil Swainston, Joseph O. Dada, Farid Khan, Pınar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil W. Hayes, Daniel Jameson, David S. Broomhead, Stephen G. Oliver, Simon J. Gaskell, John E.G. McCarthy, Norman W. Paton, Hans V. Westerhoff, Douglas B. Kell, Pedro Mendes|
|Affiliations||Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK|
|Keywords||Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling|
|Full text article||Smallbone_2013.pdf|
Experiment Description info
|Data type||metabolites at steady-state|
|Execution date||not specified|
Experimental Details info
|Temperature (0C)||not specified|
|Dilution rate (h-1)||µmax|
|Working volume (L)||not specified|
|Biomass concentration (g/L)||monitored by measuring the electrical capacitance of the culture.|
|General protocol information||
10 ml of culture.
Quenching procedure: 10 ml of culture solution into 40 ml of a 60:40 methanol/water solution  stored at a temperature of −47 °C . Immediate separation of cells was performed by applying centrifugation (4000 g for 5 min) followed by removal of the quenching solution.
Extraction technique: freezing-thawing in methanol, methanol-water
Sample analyzing method: GC-MS, LC-MS
|Methods description - Notes||
Samples were analysed using two analytical platforms. Fructose‐1,6‐bisphosphate was quantified applying ultra-performance liquid chromatography mass spectrometry (UPLC‐MS) (Waters Acquity UPLC coupled to a ThermoFisher hybrid electrospray LTQ‐Orbitrap mass spectrometer (ThermoFisher Scientific, http://www.thermofisher.com/)) and the standard addition method for accurate quantification. Other metabolites were quantified applying GC–MS (Agilent 6890 Gas Chromatograph coupled to a Leco Pegasus III electron impact‐time‐of‐flight mass spectrometer (Leco, http://www.leco.com/)) and the external calibration method for accurate quantification. The concentrations determined in the extracted samples were reported as the number of molecules per cell. The gas chromatographic separation of 2‐phosphoglycerate and 3‐phosphoglycerate is technically demanding and was not achieved during this study. Therefore, the combined concentration of both metabolites was reported rather than separate concentrations for each metabolite. Concentrations were calculated relative to an effective cytoplasmic volume of 5 fl.
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Here we can find relevant models associated with Data EntryID 99:
|Model name||Category||Model Type||Data used for||Access|
Authors: Kieran Smallbone, Hanan L. Messiha, Kathleen M. Carroll, Catherine L. Winder, Naglis Malys, Warwick B. Dunn, Ettore Murabito, Neil Swainston, Joseph O. Dada, Farid Khan, Pınar Pir, Evangelos Simeonidis, Irena Spasić, Jill Wishart, Dieter Weichart, Neil W.
Original paper: A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.
|smallbone18||Metabolism||ordinary differential equations||Model validation|