JWS Online

teusink

Detail

Download

Reactions

v_1

hexokinase

Prb + GLCi = G6P

v_10

2-Phospho-D-glycerate 2,3-phosphomutase

P2G = PEP

v_11

2-phospho-D-glycerate hydro-lyase (phosphoenolpyruvate-forming)

PEP = PYR + Prb

v_12

ATP:pyruvate 2-O-phosphotransferase

PYR = CO2 + ACE

v_13

pyruvate carboxy-lyase (acetaldehyde-forming)

{2.0}ACE + {3.0}NAD = SUCC + {3.0}NADH

v_14

glucose transport

GLCo = GLCi

v_15

ethanol:NAD+ oxidoreductase

ACE + NADH = NAD + ETOH

v_16

gpdh

NADH + TRIO = GLY + NAD

v_17

ATP catabolic process

Prb = X

v_2

ATP:D-glucose 6-phosphotransferase

G6P = F6P

v_3

G6P + Prb = Glyc

v_4

{2.0}G6P + Prb = Trh

v_5

alpha-D-Glucose 6-phosphate ketol-isomerase

F6P + Prb = F16P

v_6

ATP:D-fructose-6-phosphate 1-phosphotransferase

F16P = {2.0}TRIO

v_7

D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase(glycerone-phosphate-forming)

TRIO + NAD = BPG + NADH

v_8

D-glyceraldehyde-3-phosphate:NAD+ oxidoreductase (phosphorylating)

BPG = P3G + Prb

v_9

ATP:3-phospho-D-glycerate 1-phosphotransferase

P3G = P2G

Parameters

Global parameters

CPFKAMP*

CPFKATP*

CPFKF16BP*

CPFKF26BP*

CPFKF6P*

CiPFKATP*

F26BP*

KATPASE*

KGLYCOGEN*

KPFKAMP*

KPFKF16BP*

KPFKF26BP*

KSUCC*

KTREHALOSE*

KeqADH*

KeqAK*

KeqALD*

KeqENO*

KeqG3PDH*

KeqGLK*

KeqGLT*

KeqPGI*

KeqPGK*

KeqPGM*

KeqPYK*

KeqTPI*

KiADHACE*

KiADHETOH*

KiADHNAD*

KiADHNADH*

KiPFKATP*

KmADHACE*

KmADHETOH*

KmADHNAD*

KmADHNADH*

KmALDDHAP*

KmALDF16P*

KmALDGAP*

KmALDGAPi*

KmENOP2G*

KmENOPEP*

KmG3PDHDHAP*

KmG3PDHGLY*

KmG3PDHNAD*

KmG3PDHNADH*

KmGAPDHBPG*

KmGAPDHGAP*

KmGAPDHNAD*

KmGAPDHNADH*

KmGLKADP*

KmGLKATP*

KmGLKG6P*

KmGLKGLCi*

KmGLTGLCi*

KmGLTGLCo*

KmPDCPYR*

KmPFKATP*

KmPFKF6P*

KmPGIF6P*

KmPGIG6P*

KmPGKADP*

KmPGKATP*

KmPGKBPG*

KmPGKP3G*

KmPGMP2G*

KmPGMP3G*

KmPYKADP*

KmPYKATP*

KmPYKPEP*

KmPYKPYR*

L0*

SUMAXP*

VmADH*

VmALD*

VmENO*

VmG3PDH*

VmGAPDHf*

VmGAPDHr*

VmGLK*

VmGLT*

VmPDC*

VmPFK*

VmPGI*

VmPGK*

VmPGM*

VmPYK*

gR*

nPDC*

default_compartment*

Constraints

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

Snap to grid*

Show wireframe*

Show modifiers*

Show compartments*

Gravity*

Repulsion*

Pool threshold*

Species:

Reactions:

Middle-click: pin/unpin nodes
Shift-click: pool/unpool species
Right-click: context menu

Apply alternate model layout to overlapping elements in current model:

Model schema*

Start time*

End time*

log scales

y-axis min/max

x-axis min/max

Species

Rates

Assignment rules

Parameter*

Start*

End*

Steps*

Species

Rates

Assignment rules

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.

Bas Teusink
J Passarge
CA Reijenga
E Esgalhado
CC van der Weijden
M Schepper
MC Walsh
Barbara M Bakker
K van Dam
Hans V Westerhoff
Jacky L Snoep

Eur. J. Biochem. 2000; 267 (17): 5313-5329

PubMed: 10951190
ISSN: 0014-2956
URL: http://ncbi.nlm.nih.gov/pubmed/10951190

Abstract

This paper examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes. In nongrowing, anaerobic, compressed Saccharomyces cerevisiae the values of the kinetic parameters of most glycolytic enzymes were determined. For the other enzymes appropriate literature values were collected. By inserting these values into a kinetic model for glycolysis, fluxes and metabolites were calculated. Under the same conditions fluxes and metabolite levels were measured. In our first model, branch reactions were ignored. This model failed to reach the stable steady state that was observed in the experimental flux measurements. Introduction of branches towards trehalose, glycogen, glycerol and succinate did allow such a steady state. The predictions of this branched model were compared with the empirical behavior. Half of the enzymes matched their predicted flux in vivo within a factor of 2. For the other enzymes it was calculated what deviation between in vivo and in vitro kinetic characteristics could explain the discrepancy between in vitro rate and in vivo flux.

No additional notes are available for this model.

JWS Online documentation