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penkler1

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vPFvALD

f16bpPF = gapPF + dhapPF

vPFvATPASE

atpPF = adpPF

vPFvENO

p2gPF = pepPF

vPFvG3PDH

dhapPF + nadhPF = nadPF + g3pPF

vPFvGAPDH

nadPF + gapPF = b13pgPF + nadhPF

vPFvGLCtr

glcEX = glcPF

vPFvGLYtr

g3pPF = glyEX

vPFvHK

glcPF + atpPF = g6pPF + adpPF

vPFvLACtr

lacPF = lacEX

vPFvLDH

pyrPF + nadhPF = nadPF + lacPF

vPFvPFK

f6pPF + atpPF = f16bpPF + adpPF

vPFvPGI

g6pPF = f6pPF

vPFvPGK

b13pgPF + adpPF = p3gPF + atpPF

vPFvPGM

p3gPF = p2gPF

vPFvPK

pepPF + adpPF = pyrPF + atpPF

vPFvPYRtr

pyrPF = pyrEX

vPFvTPI

dhapPF = gapPF

Parameters

Global parameters

ConcAdpPF*

ConcAtpPF*

ConcB13pgPF*

ConcDhapPF*

ConcF16bpPF*

ConcF6pPF*

ConcG6pPF*

ConcGapPF*

ConcGlcEX*

ConcGlcPF*

ConcGly3pPF*

ConcGlyEX*

ConcLacEX*

ConcLacPF*

ConcNadPF*

ConcNadhPF*

ConcP2gPF*

ConcP3gPF*

ConcPepPF*

ConcPyrEX*

ConcPyrPF*

KadpPFvHK*

KadpPFvPFK*

KadpPFvPGK*

KadpPFvPK*

KatpPFvHK*

KatpPFvPFK*

KatpPFvPGK*

Kb13pgPFvGAPDH*

Kb13pgPFvPGK*

KdPFvLACtr*

KdPFvPYRtr*

KdhapPFvALD*

KdhapPFvG3PDH*

KdhapPFvTPI*

KeqPFvALD*

KeqPFvENO*

KeqPFvG3PDH*

KeqPFvHK*

KeqPFvPGI*

KeqPFvPGK*

KeqPFvPGM*

KeqPFvTPI*

Kf16bpPFvALD*

Kf16bpPFvPFK*

Kf6pPFvPFK*

Kf6pPFvPGI*

Kg3pPFvG3PDH*

Kg6pPFvHK*

Kg6pPFvPGI*

KgapPFvALD*

KgapPFvGAPDH*

KgapPFvTPI*

KglcPFvHK*

KiadpPFvPK*

KiatpPFvHK*

KiatpPFvPK*

KilacPFvPYRtr*

KipepPFvPK*

KipepPFvTPI*

KipyrPFvLACtr*

KipyrPFvPK*

KlacPFvLACtr*

KlacPFvLDH*

KmPFvATPASE*

KmPFvGLCtr*

KnadPFvG3PDH*

KnadPFvGAPDH*

KnadPFvLDH*

KnadhPFvG3PDH*

KnadhPFvGAPDH*

KnadhPFvLDH*

Kp2gPFvENO*

Kp2gPFvPGM*

Kp3gPFvPGK*

Kp3gPFvPGM*

KpepPFvENO*

KpepPFvPK*

KpyrPFvLDH*

KpyrPFvPYRtr*

LPFvPK*

VPFvALD*

VPFvATPASE*

VPFvENO*

VPFvGAPDH*

VPFvGLCtr*

VPFvHK*

VPFvLACtr*

VPFvPFK*

VPFvPGI*

VPFvPGM*

VPFvPK*

VPFvPYRtr*

VPFvTPI*

VfPFvG3PDH*

VfPFvLDH*

VrPFvGAPDH*

VrPFvLDH*

VrPFvPGK*

alphaPFvGLCtr*

kPFvGLYtr*

pHConversionFactor*

phEX*

phPF*

Vex*

Vpf*

Functions and Rules

Assignment rules

hPF = pHConversionFactor / pow(10, phPF)

hEX = pHConversionFactor / pow(10, phEX)

Function definitions

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.

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End time*

log scales

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Species

Rates

Assignment rules

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Species

Rates

Assignment rules

Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum.

Gerald Penkler
Francois du Toit
Waldo Adams
Marina Rautenbach
Daniel C Palm
David D van Niekerk
Jacky L Snoep

FEBS J. 2015; 282 (8): 1481-1511

PubMed: 25693925
DOI: 10.1111/febs.13237
ISSN: 1742-4658
URL: http://ncbi.nlm.nih.gov/pubmed/25693925

Abstract

UNLABELLED: The enzymes in the Embden-Meyerhof-Parnas pathway of Plasmodium falciparum trophozoites were kinetically characterized and their integrated activities analyzed in a mathematical model. For validation of the model, we compared model predictions for steady-state fluxes and metabolite concentrations of the hexose phosphates with experimental values for intact parasites. The model, which is completely based on kinetic parameters that were measured for the individual enzymes, gives an accurate prediction of the steady-state fluxes and intermediate concentrations. This is the first detailed kinetic model for glucose metabolism in P. falciparum, one of the most prolific malaria-causing protozoa, and the high predictive power of the model makes it a strong tool for future drug target identification studies. The modelling workflow is transparent and reproducible, and completely documented in the SEEK platform, where all experimental data and model files are available for download.
DATABASE: The mathematical models described in the present study have been submitted to the JWS Online Cellular Systems Modelling Database (http://jjj.bio.vu.nl/database/penkler). The investigation and complete experimental data set is available on SEEK (10.15490/seek.1.
INVESTIGATION: 56).

No additional notes are available for this model.

JWS Online documentation

penkler1

Reactions

vPFvALD

vPFvATPASE

vPFvENO

vPFvG3PDH

vPFvGAPDH

vPFvGLCtr

vPFvGLYtr

vPFvHK

vPFvLACtr

vPFvLDH

vPFvPFK

vPFvPGI

vPFvPGK

vPFvPGM

vPFvPK

vPFvPYRtr

vPFvTPI

Parameters

Fixed species

Initial values

Functions and Rules

Assignment rules

Function definitions

Events

Constraints

Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum.

Abstract