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achcar12

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AKc

{2.0}ADPc = AMPc + ATPc

AKg

{44.5116}ADPg = {22.2558}AMPg + {22.2558}ATPg

ALDc

Fru16BPc = DHAPc + GA3Pc

ALDg

{22.2558}Fru16BPg = {22.2558}DHAPg + {22.2558}GA3Pg

ATPuc

ATPc = ADPc

BPGA13tg

{22.2558}BPGA13g = BPGA13c

DHAPtg

DHAPc = {22.2558}DHAPg

ENOc

PGA2c = PEPc

F16BPtg

{22.2558}Fru16BPg = Fru16BPc

F6Ptg

{22.2558}Fru6Pg = Fru6Pc

G3PDHc

DHAPc + NADHc = Gly3Pc + NADc

G3PDHg

{22.2558}DHAPg + {22.2558}NADHg = {22.2558}Gly3Pg + {22.2558}NADg

G6PPc

Glc6Pc = Glcc

G6Ptg

{22.2558}Glc6Pg = Glc6Pc

GA3Ptg

{22.2558}GA3Pg = GA3Pc

GAPDHc

GA3Pc + NADc + Pic = BPGA13c + NADHc

GAPDHg

Pig + {22.2558}GA3Pg + {22.2558}NADg = {22.2558}BPGA13g + {22.2558}NADHg

GKc

ADPc + Gly3Pc = ATPc + Glyc

GKg

{22.2558}ADPg + {22.2558}Gly3Pg = {22.2558}ATPg + {22.2558}Glyg

GPOc

Gly3Pc = DHAPc

GlcTc

Glce = Glcc

GlcTg

Glcc = {22.2558}Glcg

Gly3Ptg

{22.2558}Gly3Pg = Gly3Pc

GlyTc

Glyc = Glye

Glytg

{22.2558}Glyg = Glyc

HXKc

ATPc + Glcc = ADPc + Glc6Pc

HXKg

{22.2558}ATPg + {22.2558}Glcg = {22.2558}ADPg + {22.2558}Glc6Pg

PFKc

ATPc + Fru6Pc = ADPc + Fru16BPc

PFKg

{22.2558}ATPg + {22.2558}Fru6Pg = {22.2558}ADPg + {22.2558}Fru16BPg

PGA3Tg

{22.2558}PGA3g = PGA3c

PGAMc

PGA3c = PGA2c

PGIc

Glc6Pc = Fru6Pc

PGIg

{22.2558}Glc6Pg = {22.2558}Fru6Pg

PGKc

BPGA13c + ADPc = PGA3c + ATPc

PGKg

{22.2558}BPGA13g + {22.2558}ADPg = {22.2558}PGA3g + {22.2558}ATPg

PYKc

ADPc + PEPc = ATPc + Pyrc

PyrTc

Pyrc = Pyre

TPIc

DHAPc = GA3Pc

TPIg

{22.2558}DHAPg = {22.2558}GA3Pg

Parameters

Global parameters

AKcAKck1*

AKcAKck2*

AKgAKgk1*

AKgAKgk2*

ALDcALDcVmax*

ALDcALDgKeq*

ALDcALDgKiADP*

ALDcALDgKiAMP*

ALDcALDgKiATP*

ALDcALDgKiGA3P*

ALDcALDgKmDHAP*

ALDcALDgKmFru16BP*

ALDcALDgKmGA3P*

ALDgALDgKeq*

ALDgALDgKiADP*

ALDgALDgKiAMP*

ALDgALDgKiATP*

ALDgALDgKiGA3P*

ALDgALDgKmDHAP*

ALDgALDgKmFru16BP*

ALDgALDgKmGA3P*

ALDgALDgVmax*

ATPucATPuck*

BPGA13tgBPGA13tgk*

DHAPtgDHAPtgk*

ENOcENOcKeq*

ENOcENOcKmPEP*

ENOcENOcKmPGA2*

ENOcENOcVmax*

EXTERNAL*

F16BPtgF16BPtgk*

F6PtgF6Ptgk*

G3PDHcG3PDHcVmax*

G3PDHcG3PDHgKeq*

G3PDHcG3PDHgKmDHAP*

G3PDHcG3PDHgKmGly3P*

G3PDHcG3PDHgKmNAD*

G3PDHcG3PDHgKmNADH*

G3PDHgG3PDHgKeq*

G3PDHgG3PDHgKmDHAP*

G3PDHgG3PDHgKmGly3P*

G3PDHgG3PDHgKmNAD*

G3PDHgG3PDHgKmNADH*

G3PDHgG3PDHgVmax*

G6PPcG6PPcKeq*

G6PPcG6PPcKmGlc*

G6PPcG6PPcKmGlc6P*

G6PPcG6PPcVmax*

G6PtgG6Ptgk*

GA3PtgGA3Ptgk*

GAPDHcGAPDHcKeq*

GAPDHcGAPDHcKmBPGA13*

GAPDHcGAPDHcKmGA3P*

GAPDHcGAPDHcKmNAD*

GAPDHcGAPDHcKmNADH*

GAPDHcGAPDHcVmax*

GAPDHgGAPDHgKeq*

GAPDHgGAPDHgKmBPGA13*

GAPDHgGAPDHgKmGA3P*

GAPDHgGAPDHgKmNAD*

GAPDHgGAPDHgKmNADH*

GAPDHgGAPDHgVmax*

GKcGKcVmax*

GKcGKgKeq*

GKcGKgKmADP*

GKcGKgKmATP*

GKcGKgKmGly*

GKcGKgKmGly3P*

GKgGKgKeq*

GKgGKgKmADP*

GKgGKgKmATP*

GKgGKgKmGly*

GKgGKgKmGly3P*

GKgGKgVmax*

GPOcGPOcKiSHAM*

GPOcGPOcKmGly3P*

GPOcGPOcVmax*

GlcTcGlcTcKmGlc*

GlcTcGlcTcVmax*

GlcTcGlcTcalpha*

GlcTgGlcTgk*

Gly3PtgGly3Ptgk*

GlyTcGlyTcKmGlye*

GlyTcGlyTcVrmax*

GlyTcGlyTck*

GlyTcGlyTcx*

GlyTcGlyTcy*

GlytgGlytgk*

HXKcHXKcVmax*

HXKcHXKgKeq*

HXKcHXKgKmADP*

HXKcHXKgKmATP*

HXKcHXKgKmGlc*

HXKcHXKgKmGlc6P*

HXKgHXKgKeq*

HXKgHXKgKmADP*

HXKgHXKgKmATP*

HXKgHXKgKmGlc*

HXKgHXKgKmGlc6P*

HXKgHXKgVmax*

O2c*

PFKcPFKcVmax*

PFKcPFKgKeq*

PFKcPFKgKi1*

PFKcPFKgKi2*

PFKcPFKgKmADP*

PFKcPFKgKmATP*

PFKcPFKgKmFru6P*

PFKcPFKgKsATP*

PFKgPFKgKeq*

PFKgPFKgKi1*

PFKgPFKgKi2*

PFKgPFKgKmADP*

PFKgPFKgKmATP*

PFKgPFKgKmFru6P*

PFKgPFKgKsATP*

PFKgPFKgVmax*

PGA3TgPGA3Tgk*

PGAMcPGAMcKeq*

PGAMcPGAMcKmPGA2*

PGAMcPGAMcKmPGA3*

PGAMcPGAMcVmax*

PGIcPGIcVmax*

PGIcPGIgKeq*

PGIcPGIgKmFru6P*

PGIcPGIgKmGlc6P*

PGIgPGIgKeq*

PGIgPGIgKmFru6P*

PGIgPGIgKmGlc6P*

PGIgPGIgVmax*

PGKcPGKcVmax*

PGKcPGKgKeq*

PGKcPGKgKmADP*

PGKcPGKgKmATP*

PGKcPGKgKmBPGA13*

PGKcPGKgKmPGA3*

PGKgPGKgKeq*

PGKgPGKgKmADP*

PGKgPGKgKmATP*

PGKgPGKgKmBPGA13*

PGKgPGKgKmPGA3*

PGKgPGKgVmax*

PYKcPYKcKeq*

PYKcPYKcKiADP*

PYKcPYKcKiATP*

PYKcPYKcKmADP*

PYKcPYKcKmATP*

PYKcPYKcKmPEP*

PYKcPYKcKmPyr*

PYKcPYKcVmax*

PYKcPYKcn*

PyrTcPyrTcKmPyr*

PyrTcPyrTcVmax*

SHAM*

TPIcTPIcVmax*

TPIcTPIgKeq*

TPIcTPIgKmDHAP*

TPIcTPIgKmGA3P*

TPIgTPIgKeq*

TPIgTPIgKmDHAP*

TPIgTPIgKmGA3P*

TPIgTPIgVmax*

cytosol*

default*

glycosome*

default_compartment*

Initial values

ADPc*

ADPg*

AMPc*

AMPg*

ATPc*

ATPg*

BPGA13c*

BPGA13g*

DHAPc*

DHAPg*

Fru16BPc*

Fru16BPg*

Fru6Pc*

Fru6Pg*

GA3Pc*

GA3Pg*

Glc6Pc*

Glc6Pg*

Glcc*

Glcg*

Gly3Pc*

Gly3Pg*

Glyc*

Glyg*

NADHg*

NADg*

PEPc*

PGA2c*

PGA3c*

PGA3g*

Pyrc*

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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Gravity*

Repulsion*

Pool threshold*

Species:

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Model schema*

Start time*

End time*

log scales

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Species

Rates

Assignment rules

Parameter*

Start*

End*

Steps*

Species

Rates

Assignment rules

Explicit consideration of topological and parameter uncertainty gives new insights into a well-established model of glycolysis.

Fiona Achcar
Michael P Barrett
Rainer Breitling

FEBS J. 2013; 280 (18): 4640-4651

PubMed: 23865459
PubMed Central: PMC4768353
DOI: 10.1111/febs.12436
ISSN: 1742-4658
URL: http://ncbi.nlm.nih.gov/pubmed/23865459

Abstract

Previous models of glycolysis in the sleeping sickness parasite Trypanosoma brucei assumed that the core part of glycolysis in this unicellular parasite is tightly compartimentalized within an organelle, the glycosome, which had previously been shown to contain most of the glycolytic enzymes. The glycosomes were assumed to be largely impermeable, and exchange of metabolites between the cytosol and the glycosome was assumed to be regulated by specific transporters in the glycosomal membrane. This tight compartmentalization was considered to be essential for parasite viability. Recently, size-specific metabolite pores were discovered in the membrane of glycosomes. These channels are proposed to allow smaller metabolites to diffuse across the membrane but not larger ones. In light of this new finding, we re-analyzed the model taking into account uncertainty about the topology of the metabolic system in T. brucei, as well as uncertainty about the values of all parameters of individual enzymatic reactions. Our analysis shows that these newly-discovered nonspecific pores are not necessarily incompatible with our current knowledge of the glycosomal metabolic system, provided that the known cytosolic activities of the glycosomal enzymes play an important role in the regulation of glycolytic fluxes and the concentration of metabolic intermediates of the pathway.

No additional notes are available for this model.

JWS Online documentation

ADPc
ADPg
AMPc
AMPg
ATPc
ATPg
BPGA13c
BPGA13g
DHAPc
DHAPg
Fru16BPc
Fru16BPg
Fru6Pc
Fru6Pg
GA3Pc
GA3Pg
Glc6Pc
Glc6Pg
Glcc
Glcg
Gly3Pc
Gly3Pg
Glyc
Glyg
NADHg
NADg
PEPc
PGA2c
PGA3c
PGA3g
Pyrc

AKc
AKg
ALDc (ALDc)
ALDg (ALDg)
ATPuc
BPGA13tg
DHAPtg
ENOc
F16BPtg
F6Ptg
G3PDHc
G3PDHg
G6PPc
G6Ptg
GA3Ptg
GAPDHc
GAPDHg
GKc
GKg
GPOc
GlcTc
GlcTg
Gly3Ptg
GlyTc
Glytg
HXKc
HXKg
PFKc
PFKg
PGA3Tg
PGAMc
PGIc
PGIg
PGKc
PGKg
PYKc
PyrTc
TPIc
TPIg