Detail View - Data AccessID 97
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General Information
| Manuscript title | A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. |
| PubMed ID | 23831062 |
| Journal | FEBS Letters |
| Year | 2013 |
| 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
|
| Project name | not specified |
Experiment Description
| Organism | Saccharomyces cerevisiae |
| Strain | Y23925 |
| Data type | enzyme/protein concentrations |
| Data units | molecules/cell |
| Execution date | not specified |
Experimental Details
| Temperature (°C) | not specified |
| pH | not specified |
| Carbon source | glucose |
| Culture mode | chemostat |
| Process condition | aerobic |
| Dilution rate (h⁻¹) | µmax |
| Working volume (L) | not specified |
| Biomass concentration (g/L) | monitored by measuring the electrical capacitance of the culture. |
| Medium composition | not specified |
| General protocol information |
Measurement method:
LC-MS/MS |
| Methods description - Notes | S. cerevisiae cells from 50 ml cultures were harvested by centrifugation for 5 min at 4000 g, and the cells mechanically disrupted using a mini bead‐beater (Biospec Products Inc., Bartlesville, USA; http://www.biospec.com/) yielding the cellular cytoplasmic soluble fraction for analysis. The latter was combined with known amounts of the recombinant labelled QconCAT protein (containing diagnostic peptides for the glycolytic enzymes [1]), and co‐digested to completion with trypsin. The resulting peptides were diluted and resolved over a linear incrementing solvent gradient by LC‐MS using a nanoACQUITY chromatograph (Waters MS Technologies) coupled to an LTQ‐Orbitrap XL (ThermoFisher Scientific). Automated data analysis and subsequent calculations were carried out using the QconCAT PrideWizard [2].
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| Data file |
 KIMODATAID97_v4.xlsx
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Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Homepage: http://kdbio.inesc-id.pt/kimosys
Interests: mathematical modeling, accessible data, use of data
Created: 2018-07-15 21:24:27 UTC
Updated: 2020-04-24 16:10:35 UTC
Version: 4
Status: (reviewed) 2018-07-15 21:24:40 UTC
Views: 401
Downloads: 99
Associated Models
Here we can find relevant models associated with Data EntryID 97:
| Model EntryID |
Model name | Category | Model Type | Data used for | Access |
|---|---|---|---|---|---|
| 39 | smallbone18 | Metabolism | ordinary differential equations | Model validation |  |
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