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BIOMD0000000502 - Messiha2013 - Pentose phosphate pathway model

 

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Reference Publication
Publication ID: 10.7287/peerj.prepri...
Messiha HL, Kent E, Malys N, Carroll KM, Mendes P, Smallbone K.
Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast
PeerJ PrePrints
School of Life Sciences, The University of Manchester, Manchester, United Kingdom 2 Manchester Center for Integrative Systems Biology, The University of Manchester, Manchester, United Kingdom  [more]
Model
Original Model: BIOMD0000000502.xml.origin
Submitter: Kieran Smallbone
Submission ID: MODEL1311290000
Submission Date: 29 Nov 2013 10:48:14 UTC
Last Modification Date: 28 Feb 2014 16:07:43 UTC
Creation Date: 09 Nov 2011 12:00:00 UTC
Encoders:  Vijayalakshmi Chelliah
   Kieran Smallbone
   Kent Ed
set #1
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #2
bqbiol:hasTaxon Taxonomy Saccharomyces cerevisiae
bqbiol:encodes KEGG Pathway rn00030
Gene Ontology pentose-phosphate shunt
Notes
Messiha2013 - Pentose phosphate pathway model

This model describes the dynamic behaviour of the pentose phosphate pathway with the inclusion of various enzymes involved in the pathway. The model's predictions are compared with experimental observations of transient metabolite concentrations following a glucose pulse.

This model is described in the article:

Hanan L. Messiha, Edward Kent, Naglis Malys, Kathleen M. Carroll, Pedro Mendes, Kieran Smallbone
PeerJ PrePrints 1:e146v2

Abstract:

We present the quantification and kinetic characterisation of the enzymes of the pentose phosphate pathway in Saccharomyces cerevisiae. The data are combined into a mathematical model that describes the dynamics of this system and allows for the predicting changes in metabolite concentrations and fluxes in response to perturbations. We use the model to study the response of yeast to a glucose pulse. We then combine the model with an existing glycolysis one to study the effect of oxidative stress on carbohydrate metabolism. The combination of these two models was made possible by the standardized enzyme kinetic experiments carried out in both studies. This work demonstrates the feasibility of constructing larger network models by merging smaller pathway models.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Model
Publication ID: 10.7287/peerj.prepri... Submission Date: 29 Nov 2013 10:48:14 UTC Last Modification Date: 28 Feb 2014 16:07:43 UTC Creation Date: 09 Nov 2011 12:00:00 UTC
Mathematical expressions
Reactions
GND RKI RPE SOL
TAL TKL (E4P:F6P) TKL (R5P:S7P) ZWF
NADPH oxidase E4P sink R5P sink  
Rules
Assignment Rule (variable: G6P) Assignment Rule (variable: NADP)    
Physical entities
Compartments Species
cell E4P G6L NADPH
P6G R5P Ru5P
S7P X5P NADP
G6P F6P GAP
GND1 GND2 NQM1
RKI1 RPE1 SOL3
TAL1 TKL1 ZWF1
Global parameters
sum_NADP Kx5p_TAL Ke4p_TAL Kr5p_TAL
Kgap_TAL Kf6p_TAL Ks7p_TAL  
Reactions (11)
 
 GND [P6G] + [NADP] → [Ru5P] + [NADPH];   {GND1} , {GND2} , {GND1} , {P6G} , {NADP} , {Ru5P} , {NADPH} , {GND2}
 
 RKI [Ru5P] ↔ [R5P];   {RKI1} , {RKI1} , {Ru5P} , {R5P}
 
 RPE [Ru5P] ↔ [X5P];   {RPE1} , {RPE1} , {Ru5P} , {X5P}
 
 SOL [G6L] → [P6G];   {SOL3} , {SOL3} , {G6L} , {P6G}
 
 TAL [GAP] + [S7P] ↔ [F6P] + [E4P];   {TAL1} , {NQM1} , {TAL1} , {GAP} , {S7P} , {F6P} , {E4P} , {NQM1}
 
 TKL (E4P:F6P) [X5P] + [E4P] ↔ [GAP] + [F6P];   {TKL1} , {R5P} , {S7P} , {TKL1} , {X5P} , {E4P} , {GAP} , {F6P} , {R5P} , {S7P}
 
 TKL (R5P:S7P) [X5P] + [R5P] ↔ [GAP] + [S7P];   {TKL1} , {E4P} , {F6P} , {TKL1} , {X5P} , {R5P} , {GAP} , {S7P} , {E4P} , {F6P}
 
 ZWF [G6P] + [NADP] → [G6L] + [NADPH];   {ZWF1} , {ZWF1} , {G6P} , {NADP} , {G6L} , {NADPH}
 
 NADPH oxidase [NADPH] → [NADP];   {NADPH}
 
 E4P sink [E4P] → ;   {E4P}
 
 R5P sink [R5P] → ;   {R5P}
 
Rules (2)
 
 Assignment Rule (name: G6P) G6P = 0.9+piecewise(44.1*t/(48+t+0.45*t^2), t >= 0, 0)
 
 Assignment Rule (name: NADP) NADP = sum_NADP-NADPH
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 E4P
Compartment: cell
Initial concentration: 0.029
 
 G6L
Compartment: cell
Initial concentration: 0.1
 
 NADPH
Compartment: cell
Initial concentration: 0.16
 
 P6G
Compartment: cell
Initial concentration: 0.25
 
 R5P
Compartment: cell
Initial concentration: 0.118
 
 Ru5P
Compartment: cell
Initial concentration: 0.033
 
 S7P
Compartment: cell
Initial concentration: 0.082
 
 X5P
Compartment: cell
Initial concentration: 0.041
 
  NADP
Compartment: cell
Initial concentration: 0.17
 
  G6P
Compartment: cell
Initial concentration: 0.9
 
 F6P
Compartment: cell
Initial concentration: 0.325
Constant
 
 GAP
Compartment: cell
Initial concentration: 0.067
Constant
 
 GND1
Compartment: cell
Initial concentration: 0.013
Constant
 
 GND2
Compartment: cell
Initial concentration: 0.0030
Constant
 
 NQM1
Compartment: cell
Initial concentration: 0.02
Constant
 
 RKI1
Compartment: cell
Initial concentration: 0.05
Constant
 
 RPE1
Compartment: cell
Initial concentration: 0.03
Constant
 
 SOL3
Compartment: cell
Initial concentration: 0.0296
Constant
 
 TAL1
Compartment: cell
Initial concentration: 0.144
Constant
 
 TKL1
Compartment: cell
Initial concentration: 0.455
Constant
 
 ZWF1
Compartment: cell
Initial concentration: 0.02
Constant
 
Global Parameters (7)
 
   sum_NADP
Value: 0.33   (Units: mM)
Constant
 
   Kx5p_TAL
Value: 0.67   (Units: mM)
Constant
 
   Ke4p_TAL
Value: 0.946   (Units: mM)
Constant
 
   Kr5p_TAL
Value: 0.235   (Units: mM)
Constant
 
   Kgap_TAL
Value: 0.1   (Units: mM)
Constant
 
   Kf6p_TAL
Value: 1.1   (Units: mM)
Constant
 
   Ks7p_TAL
Value: 0.15   (Units: mM)
Constant
 
GND (10)
 
   kcat_GND1
Value: 28.0   (Units: per s)
Constant
 
   Kp6g_GND1
Value: 0.062   (Units: mM)
Constant
 
   Knadp_GND1
Value: 0.094   (Units: mM)
Constant
 
   Kru5p_GND1
Value: 0.1   (Units: mM)
Constant
 
   Knadph_GND1
Value: 0.055   (Units: mM)
Constant
 
   kcat_GND2
Value: 27.3   (Units: per s)
Constant
 
   Kp6g_GND2
Value: 0.115   (Units: mM)
Constant
 
   Knadp_GND2
Value: 0.094   (Units: mM)
Constant
 
   Kru5p_GND2
Value: 0.1   (Units: mM)
Constant
 
   Knadph_GND2
Value: 0.055   (Units: mM)
Constant
 
RKI (5)
 
   kcat
Value: 335.0   (Units: per s)
Constant
 
   Kru5p
Value: 2.47   (Units: mM)
Constant
 
   Kr5p
Value: 5.7   (Units: mM)
Constant
 
   Kiru5p
Value: 9.88   (Units: mM)
Constant
 
   Keq
Value: 4.0   (Units: dimensionless)
Constant
 
RPE (4)
 
   kcat
Value: 4020.0   (Units: per s)
Constant
 
   Kru5p
Value: 5.97   (Units: mM)
Constant
 
   Kx5p
Value: 7.7   (Units: mM)
Constant
 
   Keq
Value: 1.4   (Units: dimensionless)
Constant
 
SOL (3)
 
   kcat
Value: 4.3   (Units: per s)
Constant
 
   Kg6l
Value: 0.8   (Units: mM)
Constant
 
   Kp6g
Value: 0.5   (Units: mM)
Constant
 
TAL (11)
 
   kcat_TAL1
Value: 0.694   (Units: per s)
Constant
 
   Kgap_TAL1
Value: 0.272   (Units: mM)
Constant
 
   Ks7p_TAL1
Value: 0.786   (Units: mM)
Constant
 
   Kf6p_TAL1
Value: 1.44   (Units: mM)
Constant
 
   Ke4p_TAL1
Value: 0.362   (Units: mM)
Constant
 
   kcat_NQM1
Value: 0.694   (Units: per s)
Constant
 
   Kgap_NQM1
Value: 0.272   (Units: mM)
Constant
 
   Ks7p_NQM1
Value: 0.786   (Units: mM)
Constant
 
   Kf6p_NQM1
Value: 1.04   (Units: mM)
Constant
 
   Ke4p_NQM1
Value: 0.305   (Units: mM)
Constant
 
   Keq
Value: 1.05   (Units: dimensionless)
Constant
 
TKL (E4P:F6P) (2)
 
   kcat
Value: 47.1   (Units: per s)
Constant
 
   Keq
Value: 10.0   (Units: dimensionless)
Constant
 
TKL (R5P:S7P) (2)
 
   kcat
Value: 40.5   (Units: per s)
Constant
 
   Keq
Value: 1.2   (Units: dimensionless)
Constant
 
ZWF (5)
 
   kcat
Value: 189.0   (Units: per s)
Constant
 
   Kg6p
Value: 0.042   (Units: mM)
Constant
 
   Knadp
Value: 0.045   (Units: mM)
Constant
 
   Kg6l
Value: 0.01   (Units: mM)
Constant
 
   Knadph
Value: 0.017   (Units: mM)
Constant
 
NADPH oxidase (1)
 
   k
Value: 1.0   (Units: per s)
Constant
 
E4P sink (1)
 
   k
Value: 1.0   (Units: per s)
Constant
 
R5P sink (1)
 
   k
Value: 1.0   (Units: per s)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000502

Curator's comment: (updated: 10 Jan 2014 15:53:08 GMT)

Figure 2 of the reference publication has been reproduced here. Green plots are obtained with the initial conditions used in the model. However, in the paper the plots are obtained starting from the steady state conditions. In the paper, this is done as follows using Copasi.
First set the model initial time as -3600s (=1h), then suppress output before -30s, and run the simulation for 3720s (=3600+120).

SBMLsimulator 1.0 was used to run the simulation starting from initial condition (reference) and steady state condition. To obtain the plots from steady state conditions, the species' steady state values were set as initial condition. The plot data was obtained from SBMLsimulator and the plots were generated using gnuplot.

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