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General Information info

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 Downloadarticle Smallbone_2013.pdf
Project name not specified

Experiment Description info

Organism Saccharomyces cerevisiae
Strain Y23925
Data type enzyme/protein concentrations
Data units molecules/cell
Execution date not specified

Experimental Details info

Temperature (0C) 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].
---------------------------------References----------------------------------
[1] K.M. Carroll , D.M. Simpson , C.E. Eyers , C.G. Knight , P. Brownridge , W.B. Dunn , C.L. Winder , K. Lanthaler , P. Pir , N. Malys , D.B. Kell , S.G. Oliver , S.J. Gaskell , R.J. Beynon. Mol. Cell. Proteomics, 10, (2011), M111.007633. http://doi.org/dzvw3h
[2] WN. Swainston , D. Jameson , K. Carroll. Proteomics, 11, (2011), 329– 333. http://doi.org/bqc27q

Data file
Downloadproteomic KIMODATAID97_v4.xlsx
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Related Data: AccessID 61 | AccessID 62 | AccessID 69 | AccessID 70 | AccessID 93 | AccessID 98 | AccessID 99 | AccessID 100 | AccessID 111 | AccessID 115 | AccessID 117 | AccessID 120 | AccessID 121 | AccessID 122 | AccessID 123 | AccessID 124


Submission and curation info

Entered by 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 2018-07-16 21:42:33 UTC

Version 4

Status (reviewed) 2018-07-15 21:24:40 UTC




Associated Models


Here we can find relevant models associated with Data EntryID 97:

Model
EntryID
Model name Category Model Type Data used for Access Json
39
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 Visto4 {"affiliation":"Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, UK","article_file_name":null,"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, P\u0131nar Pir, Evangelos Simeonidis, Irena Spasi\u0107, Jill Wishart, Dieter Weichart, Neil W.","biomodels_id":"smallbone18","category":"Metabolism","combine_archive_content_type":null,"combine_archive_file_name":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"comments":"Original model source: in JWS online database.","control":null,"dilution_rate":"","id":39,"journal":"FEBS Letters","keywords":"Glycolysis, Systems biology, Enzyme kinetic, Isoenzyme, Modelling","main_organism":"Saccharomyces cerevisiae","manuscript_title":"A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.","model_name":"smallbone18","model_type":"ordinary differential equations","organism_id":null,"project_name":"","pubmed_id":"23831062","review_journal_id":null,"sbml_file_name":"Smallbone_2013.pdf","software":"Copasi (www.copasi.org)","used_for":"---\n- Model validation\n","year":2013} Administrator KiMoSys



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