Glucose metabolism in Plasmodium falciparum trophozoites (snapshot 1)

The 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

Created at: 9th Mar 2017 at 14:13

Contents

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 data

Experimental data set for the kinetic characterisation of HK

  • HK_Kinetics-SEEK.xls

HK Kinetic model

Mathematical model for HK kinetics, GLC and ATP saturation, and inhibition with G6P and ADP.

  • HK-SEEK.nb
  • HK image.jpg

HK Kinetic characterisation

SOP for measurement of HK activity in extracts.

  • HK SOP.docx

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

PGI Kinetic characterisation

SOP for measurement of PGI activity in extracts.

  • PGI SOP.docx

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

PFK Kinetic characterisation

SOP for measurement of PFK activity in extracts.

  • PFK SOP.docx

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

ALD Kinetic characterisation

SOP for measurement of ALD activity in extracts.

  • ALD SOP.docx

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

TPI Kinetic characterisation

SOP for measurement of TPI activity in extracts.

  • TPI SOP.docx

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

G3PDH Kinetic characterisation

SOP for measurement of G3PDH activity in extracts.

  • G3PDH SOP.docx

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

GAPDH Kinetic characterisation

SOP for measurement of GAPDH activity in extracts.

  • GAPDH SOP.docx

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

PGK Kinetic characterisation

SOP for measurement of PGK activity in extracts.

  • PGK SOP.docx

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

PGM Kinetic characterisation

SOP for measurement of PGM activity in extracts.

  • PGM SOP.docx

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

ENO Kinetic characterisation

SOP for measurement of ENO activity in extracts.

  • ENO SOP.docx

PK

Kinetic characterisation en mathematical modelling of PK.

PK Kinetic data

Experimental data set for the kinetic characterisation of PK

  • PK_Kinetics-SEEK.xls

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

PK Kinetic characterisation

SOP for measurement of PK activity in extracts.

  • PK SOP.docx

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

LDH Kinetic characterisation

SOP for measurement of LDH activity in extracts.

  • LDH SOP.docx

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

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

GLCtr inhibition kinetic data

No description specified

  • GLCtr_Inhibition-SEEK.xls

GLCtr kinetic model incorporating inhibition

No description specified

  • GLCtr_Inhibition-SEEK.nb

Inhibition of lactate flux

Inhibition of lactate flux due to glucose transport inhibitor

Lactate flux inhibition data

No description specified

  • Validation-LacFluxInhibition-vanniekerk1.xlsx

Kinetic model for steady state (penkler1)

Glycolytic model for Plasmodium falciparum; open system

  • penkler1.xml
  • penkler1.nb
  • penkler1.dat

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

Supply demand analysis on penkler1 model

No description specified

  • penkler1_SupplyDemand_SEEK.nb
Fingerprints

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MD5: 67fbe0ecc87159a2a62210576dcd1c19

SHA1: c34e986d22e30dc46fb9412577bc18c6a953b5af

Citation
G. Penkler, F. Du Toit, W. Adams, M. Rautenbach, D. C. Palm, D. D. Van Niekerk, & J. L. Snoep. (2014). Glucose metabolism in Plasmodium falciparum trophozoites. FAIRDOMHub. http://doi.org/10.15490/seek.1.investigation.56
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Snapshot 1 (9th Mar 2017) DOI
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