Glucose metabolism in Plasmodium falciparum trophozoites
DownloadThe investigation entails the construction and validation of a detailed mathematical model for glycolysis of the malaria parasite Plasmodium falciparum in the blood stage trophozoite form.
DOI: 10.15490/seek.1.investigation.56
Zenodo URL: None
Created at: 9th Mar 2017 at 13:13
Model construction
This study includes all the experimental data, SOPs and modelling files for the individual reactions used for the model construction.
HK
Kinetic characterisation en mathematical modelling of HK.
HK Kinetic model
Mathematical model for HK kinetics, GLC and ATP saturation, and inhibition with G6P and ADP.
- HK-SEEK.nb
- HK image.jpg
PGI
Kinetic characterisation en mathematical modelling of PGI.
PGI Kinetic data
Experimental data set for the kinetic characterisation of PGI
- PGI_Kinetics-SEEK.xls
PGI Kinetic model
Mathematica notebook for the parameterisation of the PGI rate equation based on SEEK linked experimental data.
- PGI-SEEK.nb
- PGI image.jpg
PFK
Kinetic characterisation en mathematical modelling of PFK.
PFK Kinetic data
Experimental data set for the kinetic characterisation of PFK
- PFK_kinetics-SEEK.xls
PFK Kinetic model
Mathematica notebook for the parameterisation of the PFK rate equation based on SEEK linked experimental data.
- PFK-SEEK.nb
- PFK image.jpg
ALD
Kinetic characterisation en mathematical modelling of ALD.
ALD Kinetic data
Experimental data set for the kinetic characterisation of ALD
- ALD_Kinetics-SEEK.xls
ALD Kinetic model
Mathematica notebook for the parameterisation of the ALD rate equation based on SEEK linked experimental data.
- ALD-SEEK.nb
- ALD image.jpg
TPI
Kinetic characterisation en mathematical modelling of TPI.
TPI Kinetic data
Experimental data set for the kinetic characterisation of TPI
- TPI_Kinetics-SEEK.xls
TPI Kinetic model
Mathematica notebook for the parameterisation of the TPI rate equation based on SEEK linked experimental data.
- TPI-SEEK.nb
- TPI image.jpg
G3PDH
Kinetic characterisation en mathematical modelling of G3PDH.
G3PDH Kinetic data
Experimental data set for the kinetic characterisation of G3PDH
- G3PDH_kinetics-SEEK.xls
G3PDH Kinetic model
Mathematica notebook for the parameterisation of the G3PDH rate equation based on SEEK linked experimental data.
- G3PDH-SEEK.nb
- G3PDH image.jpg
GAPDH
Kinetic characterisation en mathematical modelling of GAPDH.
GAPDH Kinetic data
Experimental data set for the kinetic characterisation of GAPDH
- GAPDH_Kinetics-SEEK.xls
GAPDH Kinetic model
Mathematica notebook for the parameterisation of the GAPDH rate equation based on SEEK linked experimental data.
- GAPDH-SEEK.nb
- GAPDH image.jpg
PGK
Kinetic characterisation en mathematical modelling of PGK.
PGK Kinetic data
Experimental data set for the kinetic characterisation of PGK
- PGK_Kinetics-SEEK.xls
PGK Kinetic model
Mathematica notebook for the parameterisation of the PGK rate equation based on SEEK linked experimental data.
- PGK-SEEK.nb
- PGK image.jpg
PGM
Kinetic characterisation en mathematical modelling of PGM.
PGM Kinetic data
Experimental data for the phosphoglycerate mutase (EC 5.4.2.12) activity.
- PGM_Kinetics-SEEK.xls
PGM Kinetic model
Mathematica notebook for the parameterisation of the PGM rate equation based on SEEK linked experimental data.
- PGM-SEEK.nb
- PGM image.jpg
ENO
Kinetic characterisation en mathematical modelling of ENO.
ENO Kinetic data
Experimental data set for the kinetic characterisation of ENO
- ENO_Kinetics-SEEK.xls
ENO Kinetic model
Mathematica notebook for the parameterisation of the ENO rate equation based on SEEK linked experimental data.
- ENO-SEEK.nb
- ENO image.jpg
PK
Kinetic characterisation en mathematical modelling of PK.
PK Kinetic model
Mathematica notebook for the parameterisation of the PK rate equation based on the experimental SEEK data set
- PK-SEEK.nb
- PK image.jpg
LDH
Kinetic characterisation and mathematical modelling of LDH.
LDH Kinetic data
Experimental data set for the kinetic characterisation of LDH
- LDH_Kinetics-SEEK.xls
LDH Kinetic model
Mathematica notebook for the parameterisation of the LDH rate equation based on SEEK linked experimental data.
- LDH-SEEK.nb
- LDH image.jpg
GLCtr
No description specified
GLCtr Kinetic data
Experimental data set for the kinetic characterisation of the glucose transport reaction
- GLCtr_Kinetics-SEEK.xls
GLCtr Kinetic model
Mathematica notebook for the parameterisation of the glucose transport rate equation based on SEEK linked experimental data.
- GlcTr-SEEK.nb
- GLCtr image.jpg
GLYtr
No description specified
PYRtr
No description specified
LACtr
No description specified
ATPASE
No description specified
Culturing and synchronisation of P. falciparum
No description specified
Trophozoite Isolation and Lysate Preparation
Assay for the isolation of intact Plasmodium falciparum trophozoites from infected red blood cells and the preparation of a cell free extract that can be used for kinetic analyses.
Model validation
This study includes the experimental data for model validation and the model predictions of that data set.
GLC incubation
SED-ML simulation: https://jjj.bio.vu.nl/models/experiments/penkler2aa_experiment-user/simulate
5mM GLC runout data.
Timecourses of GLC (starting at 5 mM) and LAC, PYR, GLY in the closed system.
- Validation-5mMGLCrunout-penkler2.xlsx
Kinetic model for incubation (penkler2)
Glycolytic model for Plasmodium falciparum; closed system
- penkler2.xml
- penkler2.nb
- penkler2.dat
Validation experiments
SOP for the determination of external metabolites (Glc, Pyr, Gly, Lac) in intact trophozoite incubations, and for the determination of intracellular metabolite concentrations.
- Validation SOP.docx
Steady state
No description specified
Kinetic model for steady state (penkler1)
Glycolytic model for Plasmodium falciparum; open system
- penkler1.xml
- penkler1.nb
- penkler1.dat
Validation experiments
SOP for the determination of external metabolites (Glc, Pyr, Gly, Lac) in intact trophozoite incubations, and for the determination of intracellular metabolite concentrations.
- Validation SOP.docx
Model analysis
No description specified
Inhibition of glucose transport
No description specified
Inhibition of lactate flux
Inhibition of lactate flux due to glucose transport inhibitor
Kinetic model for steady state (penkler1)
Glycolytic model for Plasmodium falciparum; open system
- penkler1.xml
- penkler1.nb
- penkler1.dat
Kinetic model incorporating glucose transport inhibition (vanniekerk1)
No description specified
- vanniekerk1.xml
Validation of lactate flux inhibition by glucose transport inhibitor
No description specified
- LACfluxValidation_Inhibition-SEEK.nb
Supply-demand analysis
No description specified
Kinetic model for steady state (penkler1)
Glycolytic model for Plasmodium falciparum; open system
- penkler1.xml
- penkler1.nb
- penkler1.dat
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Views: 1793 Downloads: 22
Created: 9th Mar 2017 at 13:13
Last updated: 9th Mar 2017 at 13:43
(Since September 2018)
