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BIOMD0000000353 - Nag2011_ChloroplasticStarchDegradation

 

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Reference Publication
Publication ID: 21682905
Nag A, Lunacek M, Graf PA, Chang CH.
Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation.
BMC Syst Biol 2011; 5: 94
Computational Sciences Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, MS 1608, Golden, CO 80401, USA.  [more]
Model
Original Model: BIOMD0000000353.origin
Submitter: Ambarish Nag
Submission ID: MODEL1106030000
Submission Date: 03 Jun 2011 18:18:53 UTC
Last Modification Date: 01 Apr 2014 13:29:14 UTC
Creation Date: 01 Nov 2010 00:00:00 UTC
Encoders:  Vijayalakshmi Chelliah
   Ambarish Nag
set #1
bqbiol:isVersionOf Gene Ontology starch catabolic process
set #2
bqbiol:hasTaxon Taxonomy Arabidopsis
set #3
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #4
bqmodel:isDerivedFrom PubMed 18581371
Notes

This model is from the article:
Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation.
Nag A, Lunacek M, Graf PA, Chang CH. BMC Syst Biol.2011 Jun 18;5:94. 21682905,
Abstract:
BACKGROUND: Higher plants and algae are able to fix atmospheric carbon dioxide through photosynthesis and store this fixed carbon in large quantities as starch, which can be hydrolyzed into sugars serving as feedstock for fermentation to biofuels and precursors. Rational engineering of carbon flow in plant cells requires a greater understanding of how starch breakdown fluxes respond to variations in enzyme concentrations, kinetic parameters, and metabolite concentrations. We have therefore developed and simulated a detailed kinetic ordinary differential equation model of the degradation pathways for starch synthesized in plants and green algae, which to our knowledge is the most complete such model reported to date. RESULTS: Simulation with 9 internal metabolites and 8 external metabolites, the concentrations of the latter fixed at reasonable biochemical values, leads to a single reference solution showing β-amylase activity to be the rate-limiting step in carbon flow from starch degradation. Additionally, the response coefficients for stromal glucose to the glucose transporter kcat and KM are substantial, whereas those for cytosolic glucose are not, consistent with a kinetic bottleneck due to transport. Response coefficient norms show stromal maltopentaose and cytosolic glucosylated arabinogalactan to be the most and least globally sensitive metabolites, respectively, and β-amylase kcat and KM for starch to be the kinetic parameters with the largest aggregate effect on metabolite concentrations as a whole. The latter kinetic parameters, together with those for glucose transport, have the greatest effect on stromal glucose, which is a precursor for biofuel synthetic pathways. Exploration of the steady-state solution space with respect to concentrations of 6 external metabolites and 8 dynamic metabolite concentrations show that stromal metabolism is strongly coupled to starch levels, and that transport between compartments serves to lower coupling between metabolic subsystems in different compartments. CONCLUSIONS: We find that in the reference steady state, starch cleavage is the most significant determinant of carbon flux, with turnover of oligosaccharides playing a secondary role. Independence of stationary point with respect to initial dynamic variable values confirms a unique stationary point in the phase space of dynamically varying concentrations of the model network. Stromal maltooligosaccharide metabolism was highly coupled to the available starch concentration. From the most highly converged trajectories, distances between unique fixed points of phase spaces show that cytosolic maltose levels depend on the total concentrations of arabinogalactan and glucose present in the cytosol. In addition, cellular compartmentalization serves to dampen much, but not all, of the effects of one subnetwork on another, such that kinetic modeling of single compartments would likely capture most dynamics that are fast on the timescale of the transport reactions.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 21682905 Submission Date: 03 Jun 2011 18:18:53 UTC Last Modification Date: 01 Apr 2014 13:29:14 UTC Creation Date: 01 Nov 2010 00:00:00 UTC
Mathematical expressions
Reactions
Maltose formation from Starch Maltotriose formation from Starch Maltopentaose degradation Maltose exporter
Plastidic Glucose transporter Hexokinase Cytosolic glucan phosphorylase DPE2
DPE1      
Rules
Assignment Rule (variable: Hexokinase kcat,reverse) Assignment Rule (variable: Starch) Rate Rule (variable: Starch exposed to Beta Amylase due to action of Isoamylase (Starch DB))  
Physical entities
Compartments Species
Cell      
Cytosol H+ Maltose (D)-Glucose
Arabinogalactan (AG) Glucosyl Arabinogalactan (GlcAG) ATP pool
ADP pool Orthophosphate(HPi) pool Glutathione (reduced)
(D)-Glucose-1,6-bisphosphate pool 2,3-Bisphosphoglycerate pool G1P pool
G6P pool Disproportionating enzyme 2(DPE2) Cytosolic Glucan phosphorylase
Hexokinase    
Chloroplast      
Chloroplast Outer Membrane      
Chloroplast Intermembrane Space Maltose exporter (MEX) Glucose transporter (pGlcT)  
Chloroplast Inner Membrane      
Chloroplast Stroma Starch Starch Glucosyl unit Starch exposed to Beta Amylase due to action of Isoamylase (Starch DB)
Maltose Maltotriose Maltopentaose
(D)-Glucose Beta amylase Isoamylase
Disproportionating enzyme 1(DPE1)    
Global parameters
Starch Mol. Wt. Number of Glucosyl units in a Starch molecule Fraction of Starch amenable to degradation by Beta Amylase only Fraction of starch degraded to Maltose
Fraction of starch degraded to Maltotriose Unit conversion factor to meet SBML standards Beta amylase molecular weight Maltopentaose Mol. Wt.
Maltotriose Mol. Wt. Maltose Mol. Wt. DPE1 kcat DPE1 Keq
DPE1 G3 KM DPE1 Glc KM DPE1 G5 KM DPE1 G3 Ki
DPE1 Glc Ki DPE1 G5 Ki DPE2 kcat DPE2 Keq
DPE2 Glc KM DPE2 Maltose KM DPE2 AG KM DPE2 GlcAG KM
DPE2 Glc Ki DPE2 Maltose Ki DPE2 AG Ki DPE2 GlcAG Ki
Cytosolic glucan phosphorylase kcat Cytosolic glucan phosphorylase Glucosyl Arabinogalactan KM Cytosolic glucan phosphorylase Glucosyl Arabinogalactan Ki Cytosolic glucan phosphorylase Arabinogalactan KM
Cytosolic glucan phosphorylase Pi KM Cytosolic glucan phosphorylase G1P KM Cytosolic glucan phosphorylase G1P Ki Cytosolic glucan phosphorylase Keq
Maltose exporter (MEX) kcat Maltose exporter (MEX) KM Glucose transporter (pGlcT) kcat Glucose transporter (pGlcT) KM
Beta Amylase KM for Starch Beta Amylase KM for Maltopentaose Beta Amylase KM for Maltose condensation Keq for Maltotetraose degradation
kcat_betaamylase_Starch kcat_betaamylase_Maltopentaose Isoamylase kcat Hexokinase kcat,forward
Hexokinase kcat,reverse Hexokinase Keq Hexokinase KM(MgATP) Hexokinase Ki(MgATP)
Hexokinase KM(glucose) Hexokinase Ki(glucose) Hexokinase KM(G6P) Hexokinase Ki(G6P)
Hexokinase KM(MgADP) Hexokinase Ki(MgADP) Hexokinase Ki(G6P),2 Hexokinase Ki(2,3-bisphosphoglycerate)
Hexokinase Ki(glucose 1,6-bisphosphate Hexokinase Ki(glutathione)    
Reactions (9)
 
 Maltose formation from Starch 12345.7 × [Starch Glucosyl unit] ↔ 2923.98 × [Maltose];   {Beta amylase} , {Starch} , {Starch exposed to Beta Amylase due to action of Isoamylase (Starch DB)}
 
 Maltotriose formation from Starch 18518.5 × [Starch Glucosyl unit] → 1984.13 × [Maltotriose];   {Beta amylase} , {Starch} , {Starch exposed to Beta Amylase due to action of Isoamylase (Starch DB)}
 
 Maltopentaose degradation 1207.73 × [Maltopentaose] → 2923.98 × [Maltose] + 1984.13 × [Maltotriose];   {Beta amylase}
 
 Maltose exporter [Maltose] → [Maltose];   {Maltose exporter (MEX)}
 
 Plastidic Glucose transporter [(D)-Glucose] → [(D)-Glucose];   {Glucose transporter (pGlcT)}
 
 Hexokinase [ATP pool] + [(D)-Glucose] ↔ [G6P pool] + [ADP pool] + [H+];   {Hexokinase} , {Glutathione (reduced)} , {(D)-Glucose-1,6-bisphosphate pool} , {2,3-Bisphosphoglycerate pool}
 
 Cytosolic glucan phosphorylase [Glucosyl Arabinogalactan (GlcAG)] + [Orthophosphate(HPi) pool] ↔ [G1P pool] + [Arabinogalactan (AG)];   {Cytosolic Glucan phosphorylase}
 
 DPE2 [Maltose] + [Arabinogalactan (AG)] ↔ [(D)-Glucose] + [Glucosyl Arabinogalactan (GlcAG)];   {Disproportionating enzyme 2(DPE2)}
 
 DPE1 2.0 × [Maltotriose] ↔ [(D)-Glucose] + [Maltopentaose];   {Disproportionating enzyme 1(DPE1)}
 
Rules (3)
 
 Assignment Rule (name: R00299CY_krev) Hexokinase kcat,reverse = R00299CY_kfor*R00299CY_MgADP_Ki*R00299CY_G6P_KM/(R00299CY_Keq*R00299CY_Glc_Ki*R00299CY_MgATP_KM)
 
 Assignment Rule (name: cpd_C00369_CS) Starch = cpd_C00369Glc_CS*C00369_MW/N_Glc_Starch
 
 Rate Rule (name: cpd_C00369db_CS) d [ Starch exposed to Beta Amylase due to action of Isoamylase (Starch DB)] / d t= ec_3_2_1_68_CS*ec_3_2_1_68_CS_kcat*(1-1/(1+exp(-100*(cpd_C00369db_CS/(cpd_C00369_CS*(1-f_bamylase))-0.3)))+1/(1+exp(-100*(cpd_C00369db_CS/(cpd_C00369_CS*(1-f_bamylase))-0.3)))*(1-1.429*(cpd_C00369db_CS/(cpd_C00369_CS*(1-f_bamylase))-0.3)))
 
 Cell Spatial dimensions: 3.0  Compartment size: 3.534E-12  (Units: volume)
 Cytosol Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 H+
Compartment: Cytosol
Initial concentration: 0.1  (Units: umole)
 
 Maltose
Compartment: Cytosol
Initial concentration: 10.0  (Units: umole)
 
 (D)-Glucose
Compartment: Cytosol
Initial concentration: 10.0  (Units: umole)
 
 Arabinogalactan (AG)
Compartment: Cytosol
Initial concentration: 10000.0  (Units: umole)
 
 Glucosyl Arabinogalactan (GlcAG)
Compartment: Cytosol
Initial concentration: 10000.0  (Units: umole)
 
 ATP pool
Compartment: Cytosol
Initial concentration: 10000.0  (Units: umole)
 
 ADP pool
Compartment: Cytosol
Initial concentration: 10000.0  (Units: umole)
 
 Orthophosphate(HPi) pool
Compartment: Cytosol
Initial concentration: 10000.0  (Units: umole)
 
 Glutathione (reduced)
Compartment: Cytosol
Initial concentration: 1000.0  (Units: umole)
 
 (D)-Glucose-1,6-bisphosphate pool
Compartment: Cytosol
Initial concentration: 10000.0  (Units: umole)
 
 2,3-Bisphosphoglycerate pool
Compartment: Cytosol
Initial concentration: 10000.0  (Units: umole)
 
 G1P pool
Compartment: Cytosol
Initial concentration: 10000.0  (Units: umole)
 
 G6P pool
Compartment: Cytosol
Initial concentration: 10000.0  (Units: umole)
 
 Disproportionating enzyme 2(DPE2)
Compartment: Cytosol
Initial concentration: 2.0  (Units: umole)
 
 Cytosolic Glucan phosphorylase
Compartment: Cytosol
Initial concentration: 2.0  (Units: umole)
 
 Hexokinase
Compartment: Cytosol
Initial concentration: 10.0  (Units: umole)
 
 Chloroplast Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 Chloroplast Outer Membrane Spatial dimensions: 2.0  Compartment size: 1000.0  (Units: area)
 Chloroplast Intermembrane Space Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 Maltose exporter (MEX)
Compartment: Chloroplast Intermembrane Space
Initial concentration: 2.0  (Units: umole)
 
 Glucose transporter (pGlcT)
Compartment: Chloroplast Intermembrane Space
Initial concentration: 20.0  (Units: umole)
 
 Chloroplast Inner Membrane Spatial dimensions: 2.0  Compartment size: 1000.0  (Units: area)
 Chloroplast Stroma Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
  Starch
Compartment: Chloroplast Stroma
  (Units: gram)
 
 Starch Glucosyl unit
Compartment: Chloroplast Stroma
Initial concentration: 1000.0  (Units: umole)
 
 Starch exposed to Beta Amylase due to action of Isoamylase (Starch DB)
Compartment: Chloroplast Stroma
Initial concentration: 0.0  (Units: gram)
 
 Maltose
Compartment: Chloroplast Stroma
Initial concentration: 10.0  (Units: umole)
 
 Maltotriose
Compartment: Chloroplast Stroma
Initial concentration: 100.0  (Units: umole)
 
 Maltopentaose
Compartment: Chloroplast Stroma
Initial concentration: 1000.0  (Units: umole)
 
 (D)-Glucose
Compartment: Chloroplast Stroma
Initial concentration: 10.0  (Units: umole)
 
 Beta amylase
Compartment: Chloroplast Stroma
Initial concentration: 0.00783  (Units: gram)
 
 Isoamylase
Compartment: Chloroplast Stroma
Initial concentration: 0.0118  (Units: gram)
 
 Disproportionating enzyme 1(DPE1)
Compartment: Chloroplast Stroma
Initial concentration: 2.0  (Units: umole)
 
Global Parameters (62)
 
 Starch Mol. Wt.
Value: 0.27   (Units: gm_per_umole)
Constant
 
 Number of Glucosyl units in a Starch molecule
Value: 1667.0   (Units: dimensionless)
Constant
 
 Fraction of Starch amenable to degradation by Beta Amylase only
Value: 0.582   (Units: dimensionless)
Constant
 
 Fraction of starch degraded to Maltose
Value: 0.87   (Units: dimensionless)
Constant
 
 Fraction of starch degraded to Maltotriose
Value: 0.13   (Units: dimensionless)
Constant
 
 Unit conversion factor to meet SBML standards
Value: 1.0   (Units: gm_per_umole)
Constant
 
 Beta amylase molecular weight
Value: 0.206   (Units: gm_per_umole)
Constant
 
 Maltopentaose Mol. Wt.
Value: 8.28E-4   (Units: gm_per_umole)
Constant
 
 Maltotriose Mol. Wt.
Value: 5.04E-4   (Units: gm_per_umole)
Constant
 
 Maltose Mol. Wt.
Value: 3.42E-4   (Units: gm_per_umole)
Constant
 
 DPE1 kcat
Value: 50.0   (Units: per_s)
Constant
 
 DPE1 Keq
Value: 1.0   (Units: dimensionless)
Constant
 
 DPE1 G3 KM
Value: 3300.0   (Units: uM)
Constant
 
 DPE1 Glc KM
Value: 11700.0   (Units: uM)
Constant
 
 DPE1 G5 KM
Value: 210.0   (Units: uM)
Constant
 
 DPE1 G3 Ki
Value: 746.42   (Units: uM)
Constant
 
 DPE1 Glc Ki
Value: 5571.429   (Units: uM)
Constant
 
 DPE1 G5 Ki
Value: 100.0   (Units: uM)
Constant
 
 DPE2 kcat
Value: 50.0   (Units: per_s)
Constant
 
 DPE2 Keq
Value: 1.0   (Units: dimensionless)
Constant
 
 DPE2 Glc KM
Value: 11700.0   (Units: uM)
Constant
 
 DPE2 Maltose KM
Value: 4600.0   (Units: uM)
Constant
 
 DPE2 AG KM
Value: 1100.0   (Units: uM)
Constant
 
 DPE2 GlcAG KM
Value: 1100.0   (Units: uM)
Constant
 
 DPE2 Glc Ki
Value: 5571.429   (Units: uM)
Constant
 
 DPE2 Maltose Ki
Value: 2190.476   (Units: uM)
Constant
 
 DPE2 AG Ki
Value: 1000.0   (Units: uM)
Constant
 
 DPE2 GlcAG Ki
Value: 1000.0   (Units: uM)
Constant
 
 Cytosolic glucan phosphorylase kcat
Value: 50.0   (Units: per_s)
Constant
 
 Cytosolic glucan phosphorylase Glucosyl Arabinogalactan KM
Value: 2100.0   (Units: uM)
Constant
 
 Cytosolic glucan phosphorylase Glucosyl Arabinogalactan Ki
Value: 3800.0   (Units: uM)
Constant
 
 Cytosolic glucan phosphorylase Arabinogalactan KM
Value: 3800.0   (Units: uM)
Constant
 
 Cytosolic glucan phosphorylase Pi KM
Value: 5900.0   (Units: uM)
Constant
 
 Cytosolic glucan phosphorylase G1P KM
Value: 2000.0   (Units: uM)
Constant
 
 Cytosolic glucan phosphorylase G1P Ki
Value: 3100.0   (Units: uM)
Constant
 
 Cytosolic glucan phosphorylase Keq
Value: 6.15E-4   (Units: dimensionless)
Constant
 
 Maltose exporter (MEX) kcat
Value: 5.963   (Units: per_s)
Constant
 
 Maltose exporter (MEX) KM
Value: 4000.0   (Units: uM)
Constant
 
 Glucose transporter (pGlcT) kcat
Value: 240.278   (Units: per_s)
Constant
 
 Glucose transporter (pGlcT) KM
Value: 19300.0   (Units: uM)
Constant
 
 Beta Amylase KM for Starch
Value: 0.5   (Units: gm_per_L)
Constant
 
 Beta Amylase KM for Maltopentaose
Value: 1.46   (Units: gm_per_L)
Constant
 
 Beta Amylase KM for Maltose condensation
Value: 4.19   (Units: gm_per_L_2)
Constant
 
 Keq for Maltotetraose degradation
Value: 18800.0   (Units: gm_per_L)
Constant
 
 kcat_betaamylase_Starch
Value: 0.073   (Units: per_s)
Constant
 
 kcat_betaamylase_Maltopentaose
Value: 0.0913   (Units: per_s)
Constant
 
 Isoamylase kcat
Value: 0.0198   (Units: per_s)
Constant
 
 Hexokinase kcat,forward
Value: 180.0   (Units: per_s)
Constant
 
  Hexokinase kcat,reverse
Value: NaN   (Units: per_s)
 
 Hexokinase Keq
Value: 155.0   (Units: dimensionless)
Constant
 
 Hexokinase KM(MgATP)
Value: 1000.0   (Units: uM)
Constant
 
 Hexokinase Ki(MgATP)
Value: 1000.0   (Units: uM)
Constant
 
 Hexokinase KM(glucose)
Value: 47.0   (Units: uM)
Constant
 
 Hexokinase Ki(glucose)
Value: 47.0   (Units: uM)
Constant
 
 Hexokinase KM(G6P)
Value: 47.0   (Units: uM)
Constant
 
 Hexokinase Ki(G6P)
Value: 47.0   (Units: uM)
Constant
 
 Hexokinase KM(MgADP)
Value: 1000.0   (Units: uM)
Constant
 
 Hexokinase Ki(MgADP)
Value: 1000.0   (Units: uM)
Constant
 
 Hexokinase Ki(G6P),2
Value: 10.0   (Units: uM)
Constant
 
 Hexokinase Ki(2,3-bisphosphoglycerate)
Value: 4000.0   (Units: uM)
Constant
 
 Hexokinase Ki(glucose 1,6-bisphosphate
Value: 30.0   (Units: uM)
Constant
 
 Hexokinase Ki(glutathione)
Value: 3000.0   (Units: uM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000353

Curator's comment: (updated: 15 Aug 2011 15:13:24 BST)

Figure 7 and Figure 11 of the reference article has been reproduced here. The concentrations of Beta-amylase and Isoamylase are in gram/L in the model. So, the units for x-axis (Beta-amylase) is in gram/L in the reproduced figure whereas in the article, it is in microM.
The model was integrated and simulated using Copasi v4.7 (Build 34).

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