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BIOMD0000000380 - Smallbone2011_TrehaloseBiosynthesis

 

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Reference Publication
Publication ID: 21943906
Smallbone K, Malys N, Messiha HL, Wishart JA, Simeonidis E.
Building a kinetic model of trehalose biosynthesis in Saccharomyces cerevisiae.
Meth. Enzymol. 2011; 500: 355-370
Manchester Centre for Integrative Systems Biology, The University of Manchester, Manchester, United Kingdom.  [more]
Model
Original Model: BIOMD0000000380.xml.origin
Submitter: Kieran Smallbone
Submission ID: MODEL1010010000
Submission Date: 01 Oct 2010 11:01:07 UTC
Last Modification Date: 16 May 2012 14:48:51 UTC
Creation Date: 12 Jul 2010 00:00:00 UTC
Encoders:  Vijayalakshmi Chelliah
   Kieran Smallbone
set #1
bqbiol:isVersionOf Gene Ontology trehalose biosynthetic process
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
Notes

This model is from the article:
Building a Kinetic Model of Trehalose Biosynthesis in Saccharomyces cerevisiae.
Smallbone K, Malys N, Messiha HL, Wishart JA, Simeonidis E. Methods Enzymol. 2011;500:355-70. 21943906 ,
Abstract:
In this chapter, we describe the steps needed to create a kinetic model of a metabolic pathway based on kinetic data from experimental measurements and literature review. Our methodology is presented by utilizing the example of trehalose metabolism in yeast. The biology of the trehalose cycle is briefly reviewed and discussed.

This SBML model is made available under the Creative Commons Attribution-Share Alike 3.0 Unported Licence (see www.creativecommons.org ).

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 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: 21943906 Submission Date: 01 Oct 2010 11:01:07 UTC Last Modification Date: 16 May 2012 14:48:51 UTC Creation Date: 12 Jul 2010 00:00:00 UTC
Mathematical expressions
Reactions
G6P isomerase glucose transport hexokinase phosphoglucomutase
T6P phosphatase T6P synthase trehalase UDP glucose phosphorylase
Rules
Assignment Rule (variable: log10 change in glucose) Assignment Rule (variable: log10 change in glucose 1-phosphate) Assignment Rule (variable: log10 change in glucose 6-phosphate) Assignment Rule (variable: log10 change in trehalose)
Assignment Rule (variable: log10 change in trehalose 6-phosphate) Assignment Rule (variable: log10 change in UDP glucose)    
Physical entities
Compartments Species
cell glucose glucose 1-phosphate glucose 6-phosphate
trehalose trehalose 6-phosphate UDP glucose
ADP ATP diphosphate
fructose 6-phosphate H+ phosphate
UDP UTP water
     
medium glucose    
Global parameters
heat glc_0 log10 change in glucose g1p_0
log10 change in glucose 1-phosphate g6p_0 log10 change in glucose 6-phosphate trh_0
log10 change in trehalose t6p_0 log10 change in trehalose 6-phosphate udg_0
log10 change in UDP glucose      
Reactions (8)
 
 G6P isomerase [glucose 6-phosphate] ↔ [fructose 6-phosphate];  
 
 glucose transport [glucose] ↔ [glucose];  
 
 hexokinase [glucose] + [ATP] → [glucose 6-phosphate] + [ADP] + [H+];   {trehalose 6-phosphate}
 
 phosphoglucomutase [glucose 6-phosphate] ↔ [glucose 1-phosphate];  
 
 T6P phosphatase [trehalose 6-phosphate] + [water] → [trehalose] + [phosphate];  
 
 T6P synthase [glucose 6-phosphate] + [UDP glucose] → [trehalose 6-phosphate] + [UDP] + [H+];  
 
 trehalase [trehalose] + [water] → 2.0 × [glucose];  
 
 UDP glucose phosphorylase [glucose 1-phosphate] + [UTP] + [H+] → [UDP glucose] + [diphosphate];  
 
Rules (6)
 
 Assignment Rule (name: glc_change) log10 change in glucose = log(10, glc/glc_0)
 
 Assignment Rule (name: g1p_change) log10 change in glucose 1-phosphate = log(10, g1p/g1p_0)
 
 Assignment Rule (name: g6p_change) log10 change in glucose 6-phosphate = log(10, g6p/g6p_0)
 
 Assignment Rule (name: trh_change) log10 change in trehalose = log(10, trh/trh_0)
 
 Assignment Rule (name: t6p_change) log10 change in trehalose 6-phosphate = log(10, t6p/t6p_0)
 
 Assignment Rule (name: udg_change) log10 change in UDP glucose = log(10, udg/udg_0)
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 glucose
Compartment: cell
Initial concentration: 0.09675
 
 glucose 1-phosphate
Compartment: cell
Initial concentration: 0.1
 
 glucose 6-phosphate
Compartment: cell
Initial concentration: 2.675
 
 trehalose
Compartment: cell
Initial concentration: 0.05
 
 trehalose 6-phosphate
Compartment: cell
Initial concentration: 0.02
 
 UDP glucose
Compartment: cell
Initial concentration: 0.7
 
 ADP
Compartment: cell
Initial concentration: 1.282
 
 ATP
Compartment: cell
Initial concentration: 2.525
 
 diphosphate
Compartment: cell
 
 fructose 6-phosphate
Compartment: cell
Initial concentration: 0.625
 
 H+
Compartment: cell
 
 phosphate
Compartment: cell
 
 UDP
Compartment: cell
Initial concentration: 0.2815
 
 UTP
Compartment: cell
Initial concentration: 0.6491
 
 water
Compartment: cell
 
 medium Spatial dimensions: 3.0  Compartment size: 1.0
 
 glucose
Compartment: medium
Initial concentration: 100.0
 
Global Parameters (13)
 
   heat
Constant
 
   glc_0
Value: 0.09765   (Units: mM)
Constant
 
   log10 change in glucose
Value: NaN   (Units: dimensionless)
 
   g1p_0
Value: 0.1   (Units: mM)
Constant
 
   log10 change in glucose 1-phosphate
Value: NaN   (Units: dimensionless)
 
   g6p_0
Value: 2.675   (Units: mM)
Constant
 
   log10 change in glucose 6-phosphate
Value: NaN   (Units: dimensionless)
 
   trh_0
Value: 0.05   (Units: mM)
Constant
 
   log10 change in trehalose
Value: NaN   (Units: dimensionless)
 
   t6p_0
Value: 0.02   (Units: mM)
Constant
 
   log10 change in trehalose 6-phosphate
Value: NaN   (Units: dimensionless)
 
   udg_0
Value: 0.7   (Units: mM)
Constant
 
   log10 change in UDP glucose
Value: NaN   (Units: dimensionless)
 
G6P isomerase (5)
 
   Vmax
Value: 1071.0   (Units: mM per min)
Constant
 
   Kg6p
Value: 1.4   (Units: mM)
Constant
 
   Kf6p
Value: 0.29   (Units: mM)
Constant
 
   Keq
Value: 0.3   (Units: dimensionless)
Constant
 
   shock
Value: 1.0   (Units: dimensionless)
Constant
 
glucose transport (4)
 
   Vmax
Value: 97.24   (Units: mM per min)
Constant
 
   Kglc
Value: 1.1918   (Units: mM)
Constant
 
   Ki
Value: 0.91   (Units: dimensionless)
Constant
 
   shock
Value: 8.0   (Units: dimensionless)
Constant
 
hexokinase (8)
 
   Vmax
Value: 289.6   (Units: mM per min)
Constant
 
   Kglc
Value: 0.08   (Units: mM)
Constant
 
   Katp
Value: 0.15   (Units: mM)
Constant
 
   Kg6p
Value: 30.0   (Units: mM)
Constant
 
   Kadp
Value: 0.23   (Units: mM)
Constant
 
   Keq
Value: 2000.0   (Units: dimensionless)
Constant
 
   Kit6p
Value: 0.04   (Units: mM)
Constant
 
   shock
Value: 8.0   (Units: dimensionless)
Constant
 
phosphoglucomutase (5)
 
   Vmax
Value: 0.3545   (Units: mM per min)
Constant
 
   Kg6p
Value: 0.05   (Units: mM)
Constant
 
   Kg1p
Value: 0.023   (Units: mM)
Constant
 
   Keq
Value: 0.1667   (Units: dimensionless)
Constant
 
   shock
Value: 16.0   (Units: dimensionless)
Constant
 
T6P phosphatase (3)
 
   Vmax
Value: 6.5   (Units: mM per min)
Constant
 
   Kt6p
Value: 0.5   (Units: mM)
Constant
 
   shock
Value: 18.0   (Units: dimensionless)
Constant
 
T6P synthase (5)
 
   Vmax
Value: 1.371   (Units: mM per min)
Constant
 
   Kg6p
Value: 3.8   (Units: mM)
Constant
 
   Kudg
Value: 0.886   (Units: mM)
Constant
 
   shock
Value: 12.0   (Units: dimensionless)
Constant
 
   activity
Value: 1.0   (Units: dimensionless)
Constant
 
trehalase (3)
 
   Vmax
Value: 15.2   (Units: mM per min)
Constant
 
   Ktrh
Value: 2.99   (Units: mM)
Constant
 
   shock
Value: 6.0   (Units: dimensionless)
Constant
 
UDP glucose phosphorylase (6)
 
   Vmax
Value: 36.82   (Units: mM per min)
Constant
 
   Kutp
Value: 0.11   (Units: mM)
Constant
 
   Kiutp
Value: 0.11   (Units: mM)
Constant
 
   Kg1p
Value: 0.32   (Units: mM)
Constant
 
   Kiudg
Value: 0.0035   (Units: mM)
Constant
 
   shock
Value: 16.0   (Units: dimensionless)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000380

Curator's comment: (updated: 05 Oct 2011 14:26:46 BST)

The steady state concentration in Figure 18.4 of the reference publication has been reproduced here.
The steady state concentration of the metabolites for 1) heat shock can be obtained by setting “heat=1” and 2) TPS1 mutant can be obtained by setting “heat=0” and by setting “activity=0.01” in the reaction T6P synthase.
The model was simulated using Copasi v4.7 (Build 34).

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