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smallbone14

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ADHADH1

AcAld + NADH = NAD + EtOH

ADHADH5

AcAld + NADH = NAD + EtOH

AK

{2.0}ADP = AMP + ATP

ATPase

ATP = ADP

ENOENO1

P2G = PEP

ENOENO2

P2G = PEP

FBA

F16bP = DHAP + GAP

GPD

NADH + DHAP = NAD + G3P

GPM

P3G = P2G

GPP

G3P = GLY

HXKGLK1

ATP + GLC = ADP + G6P

HXKHXK2

ATP + GLC = ADP + G6P

HXT

GLCx = GLC

PDCPDC1

PYR = AcAld

PDCPDC5

PYR = AcAld

PDCPDC6

PYR = AcAld

PFK

ATP + F6P = ADP + F16bP

PGI

G6P = F6P

PGK

ADP + BPG = ATP + P3G

PGM

G6P = G1P

PYK

ADP + PEP = ATP + PYR

TDHTDH1

GAP + NAD = BPG + NADH

TDHTDH2

GAP + NAD = BPG + NADH

TDHTDH3

GAP + NAD = BPG + NADH

TPI

DHAP = GAP

TPP

T6P = TRH

TPS

G6P + UDG = T6P + UDP

UGP

G1P + UTP = UDG

acetatebranch

AcAld + NAD = NADH + ACE

succinatebranch

PYR + {3.0}NAD = {0.75}SUC + {3.0}NADH

udptoutp

ATP + UDP = ADP + UTP

Parameters

Global parameters

ADH1*

ADH5*

ADHADH1Kacald*

ADHADH1Ketoh*

ADHADH1Kiacald*

ADHADH1Kietoh*

ADHADH1Kinad*

ADHADH1Kinadh*

ADHADH1Knad*

ADHADH1Knadh*

ADHADH1kcat*

ADHADH5Kacald*

ADHADH5Ketoh*

ADHADH5Kiacald*

ADHADH5Kietoh*

ADHADH5Kinad*

ADHADH5Kinadh*

ADHADH5Knad*

ADHADH5Knadh*

ADHADH5kcat*

AKKeq*

AKk*

ATPaseKatp*

ATPaseVmax*

CDC19*

ENO1*

ENO2*

ENOENO1Kp2g*

ENOENO1Kpep*

ENOENO1kcat*

ENOENO2Kp2g*

ENOENO2Kpep*

ENOENO2kcat*

EXTERNAL*

F26bP*

FBA1*

FBAKdhap*

FBAKeq*

FBAKf16bp*

FBAKgap*

FBAKigap*

FBAkcat*

GLK1*

GPD1*

GPD2*

GPDKadp*

GPDKatp*

GPDKdhap*

GPDKeq*

GPDKfbp*

GPDKg3p*

GPDKnad*

GPDKnadh*

GPDVmax*

GPM1*

GPMKeq*

GPMKp2g*

GPMKp3g*

GPMVmax*

GPPKg3p*

GPPVmax*

HOR2*

HXK1*

HXK2*

HXKGLK1Kadp*

HXKGLK1Katp*

HXKGLK1Kg6p*

HXKGLK1Kglc*

HXKGLK1kcat*

HXKHXK1Kadp*

HXKHXK1Katp*

HXKHXK1Kg6p*

HXKHXK1Kglc*

HXKHXK1Kit6p*

HXKHXK1kcat*

HXKHXK2Kadp*

HXKHXK2Katp*

HXKHXK2Kg6p*

HXKHXK2Kglc*

HXKHXK2Kit6p*

HXKHXK2kcat*

HXTKglc*

HXTKi*

HXTVmax*

KeqADH*

KeqENO*

KeqHXK*

KeqTDH*

NA*

PDC1*

PDC5*

PDC6*

PDCPDC1Kpyr*

PDCPDC1kcat*

PDCPDC5Kpyr*

PDCPDC5kcat*

PDCPDC6Kpyr*

PDCPDC6kcat*

PFK1*

PFK2*

PFKCamp*

PFKCatp*

PFKCf16*

PFKCf26*

PFKCiatp*

PFKKadp*

PFKKamp*

PFKKatp*

PFKKeq*

PFKKf16*

PFKKf26*

PFKKf6p*

PFKKiatp*

PFKL0*

PFKgR*

PFKkcat*

PGI1*

PGIKeq*

PGIKf6p*

PGIKg6p*

PGIkcat*

PGK1*

PGKKadp*

PGKKatp*

PGKKbpg*

PGKKeq*

PGKKp3g*

PGKkcat*

PGKnHadp*

PGM1*

PGM2*

PGMKeq*

PGMKg1p*

PGMKg6p*

PGMVmax*

PYK2*

PYKKadp*

PYKKatp*

PYKKeq*

PYKKpep*

PYKKpyr*

PYKVmax*

RHR2*

TDH1*

TDH2*

TDH3*

TDHTDH1Kbpg*

TDHTDH1Kgap*

TDHTDH1Knad*

TDHTDH1Knadh*

TDHTDH1kcat*

TDHTDH2Kbpg*

TDHTDH2Kgap*

TDHTDH2Knad*

TDHTDH2Knadh*

TDHTDH2kcat*

TDHTDH3Kbpg*

TDHTDH3Kgap*

TDHTDH3Knad*

TDHTDH3Knadh*

TDHTDH3kcat*

TPI1*

TPIKeq*

TPIk*

TPPKt6p*

TPPVmax*

TPS1*

TPS2*

TPSKg6p*

TPSKudg*

TPSVmax*

UGP1*

UGPKg1p*

UGPKiudg*

UGPKiutp*

UGPKutp*

UGPVmax*

acetatebranchk*

cell*

extracellular*

rescaleTRH*

succinatebranchk*

sumAXP*

sumNAD*

sumUXP*

udptoutpk*

volume*

default_compartment*

Functions and Rules

Assignment rules

energycharge = (ADP/2 + ATP)/sumAXP

sumPXG = P2G + P3G

fitconc = Sqrt((1 - (NA*sumPXG*volume)/1618640)^2 + (1 - (NA*volume*DHAP)/3496987)^2 + (1 - (NA*volume*F16bP)/13800392)^2 + (1 - (NA*volume*F6P)/708930)^2 + (1 - (NA*volume*G6P)/2326001)^2 + (1 - (NA*volume*GAP)/951170)^2 + (1 - (NA*volume*GLC)/18909525)^2 + (1 - (NA*volume*PEP)/1836769)^2 + (1 - (NA*volume*PYR)/6348755)^2)/3

Function definitions

Events

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

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.

Kieran Smallbone
Hanan L Messiha
Kathleen M Carroll
Catherine L Winder
Naglis Malys
Warwick B Dunn
Ettore Murabito
Neil Swainston
Joseph O Dada
Farid Khan
Pınar Pir
Evangelos Simeonidis
Irena Spasić
Jill Wishart
Dieter Weichart
Neil W Hayes
Daniel Jameson
David S Broomhead
Stephen G Oliver
Simon J Gaskell
John E G McCarthy
Norman W Paton
Hans V Westerhoff
Douglas B Kell
Pedro Mendes

FEBS Lett. 2013; 587 (17): 2832-2841

PubMed: 23831062
PubMed Central: PMC3764422
DOI: 10.1016/j.febslet.2013.06.043
ISSN: 1873-3468
URL: http://ncbi.nlm.nih.gov/pubmed/23831062

Abstract

We present an experimental and computational pipeline for the generation of kinetic models of metabolism, and demonstrate its application to glycolysis in Saccharomyces cerevisiae. Starting from an approximate mathematical model, we employ a "cycle of knowledge" strategy, identifying the steps with most control over flux. Kinetic parameters of the individual isoenzymes within these steps are measured experimentally under a standardised set of conditions. Experimental strategies are applied to establish a set of in vivo concentrations for isoenzymes and metabolites. The data are integrated into a mathematical model that is used to predict a new set of metabolite concentrations and reevaluate the control properties of the system. This bottom-up modelling study reveals that control over the metabolic network most directly involved in yeast glycolysis is more widely distributed than previously thought.

No additional notes are available for this model.

JWS Online documentation

ADP
AMP
ATP
AcAld
BPG
DHAP
F16bP
F6P
G1P
G3P
G6P
GAP
GLC
NAD
NADH
P2G
P3G
PEP
PYR
T6P
UDG
UDP
UTP

ADHADH1
ADHADH5
AK
ATPase
ENOENO1
ENOENO2
FBA
GPD (GPD)
GPM
GPP
HXKGLK1
HXKHXK2 (HXKHXK2)
HXT
PDCPDC1
PDCPDC5
PDCPDC6
PFK (PFK)
PGI
PGK
PGM
PYK
TDHTDH1
TDHTDH2
TDHTDH3
TPI
TPP
TPS
UGP
acetatebranch
succinatebranch
udptoutp