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BIOMD0000000404 - Bray1993_chemotaxis

 

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Reference Publication
Publication ID: 8334303
Bray D, Bourret RB, Simon MI.
Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis.
Mol. Biol. Cell 1993 May; 4(5): 469-482
Department of Zoology, University of Cambridge, United Kingdom.  [more]
Model
Original Model: BIOMD0000000404.origin
Submitter: Vijayalakshmi Chelliah
Submission ID: MODEL6929313478
Submission Date: 20 Nov 2008 13:17:02 UTC
Last Modification Date: 08 Mar 2012 11:12:55 UTC
Creation Date: 03 Nov 2008 11:29:04 UTC
Encoders:  Nicolas Le Novère
   Lukas Endler
   Vijayalakshmi Chelliah
   Dennis Bray
set #1
bqbiol:isVersionOf KEGG Pathway Bacterial chemotaxis
Gene Ontology chemotaxis
bqbiol:occursIn Taxonomy Escherichia coli
Notes

This version of the model is very close to the version described in the paper with one exception: the binding of aspartate to the various receptor complexes, as well as the formation of the different complexes are modeled using chemical kinetics (mass action law), rather than instant equilibrium. The qualitative behaviour of the model is unchanged. Note that in order to quantitatively replicate the figure 8b, and in particular to have a basal bias of 0.7, we have to change the rate constant of the aspartate-triggered dephosphorylation of CheY from 59000 to 70000. The peaks have then slightly different values.

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: 8334303 Submission Date: 20 Nov 2008 13:17:02 UTC Last Modification Date: 08 Mar 2012 11:12:55 UTC Creation Date: 03 Nov 2008 11:29:04 UTC
Mathematical expressions
Reactions
A->Ap TWA+A->TWA+Ap Tni_WA+A->Tni_WA+Ap Tasp_WA+Yp->Tasp_WA+Y
Ap+Y->A+Yp Y ->Yp Yp->Y Yp+Z->Y+Z
Ap+B->A+Bp Bp->B T+asp<->Tasp T+ni<->Tni
T+W<->TW T+A<->TA W+A<->WA TW+A<->TWA
TA+W<->TWA T+WA<->TWA Tasp+W<->Tasp_W Tasp+A<->Tasp_A
Tasp_W+A<->Tasp_WA Tasp_A+W<->Tasp_WA Tasp+WA<->Tasp_WA Tni+W<->Tni_W
Tni+A<->Tni_A Tni_W+A<->Tni_WA Tni_A+W<->Tni_WA Tni+WA<->Tni_WA
M+Yp<->MYp MYp+Yp<->MYpYp MYpYp+Yp<->MYpYpYp MYpYpYp+Yp<->MYpYpYpYp
TA + asp <-> Tasp_A TW+asp <-> Tasp_W TWA+asp <-> Tasp_WA  
Rules
Assignment Rule (variable: Bias) Assignment Rule (variable: autoPhospho)    
Events
Add ASP Remove ASP    
Physical entities
Compartments Species
cell asp ni T
Tasp Tni W
TW Tasp_W Tni_W
TA Tasp_A Tni_A
WA TWA Tasp_WA
Tni_WA A Ap
B Bp Z
Y Yp M
MYp MYpYp MYpYpYp
MYpYpYpYp ATP  
Global parameters
alpha kappa ka Bias
asp_pulse autoPhospho KmATP  
Reactions (35)
 
 A->Ap [A] → [Ap];  
 
 TWA+A->TWA+Ap [A] → [Ap];   {TWA}
 
 Tni_WA+A->Tni_WA+Ap [A] → [Ap];   {Tni_WA}
 
 Tasp_WA+Yp->Tasp_WA+Y [Tasp_WA] + [Yp] → [Tasp_WA] + [Y];  
 
 Ap+Y->A+Yp [Ap] + [Y] → [A] + [Yp];  
 
 Y ->Yp [Y] → [Yp];  
 
 Yp->Y [Yp] → [Y];  
 
 Yp+Z->Y+Z [Yp] + [Z] → [Y] + [Z];  
 
 Ap+B->A+Bp [Ap] + [B] → [A] + [Bp];  
 
 Bp->B [Bp] → [B];  
 
 T+asp<->Tasp [T] + [asp] ↔ [Tasp];  
 
 T+ni<->Tni [T] + [ni] ↔ [Tni];  
 
 T+W<->TW [T] + [W] ↔ [TW];  
 
 T+A<->TA [T] + [A] ↔ [TA];  
 
 W+A<->WA [W] + [A] ↔ [WA];  
 
 TW+A<->TWA [TW] + [A] ↔ [TWA];  
 
 TA+W<->TWA [TA] + [W] ↔ [TWA];  
 
 T+WA<->TWA [T] + [WA] ↔ [TWA];  
 
 Tasp+W<->Tasp_W [Tasp] + [W] ↔ [Tasp_W];  
 
 Tasp+A<->Tasp_A [Tasp] + [A] ↔ [Tasp_A];  
 
 Tasp_W+A<->Tasp_WA [Tasp_W] + [A] ↔ [Tasp_WA];  
 
 Tasp_A+W<->Tasp_WA [Tasp_A] + [W] ↔ [Tasp_WA];  
 
 Tasp+WA<->Tasp_WA [Tasp] + [WA] ↔ [Tasp_WA];  
 
 Tni+W<->Tni_W [Tni] + [W] ↔ [Tni_W];  
 
 Tni+A<->Tni_A [Tni] + [A] ↔ [Tni_A];  
 
 Tni_W+A<->Tni_WA [Tni_W] + [A] ↔ [Tni_WA];  
 
 Tni_A+W<->Tni_WA [Tni_A] + [W] ↔ [Tni_WA];  
 
 Tni+WA<->Tni_WA [Tni] + [WA] ↔ [Tni_WA];  
 
 M+Yp<->MYp [M] + [Yp] ↔ [MYp];  
 
 MYp+Yp<->MYpYp [MYp] + [Yp] ↔ [MYpYp];  
 
 MYpYp+Yp<->MYpYpYp [MYpYp] + [Yp] ↔ [MYpYpYp];  
 
 MYpYpYp+Yp<->MYpYpYpYp [MYpYpYp] + [Yp] ↔ [MYpYpYpYp];  
 
 TA + asp <-> Tasp_A [TA] + [asp] ↔ [Tasp_A];  
 
 TW+asp <-> Tasp_W [TW] + [asp] ↔ [Tasp_W];  
 
 TWA+asp <-> Tasp_WA [TWA] + [asp] ↔ [Tasp_WA];  
 
Rules (2)
 
 Assignment Rule (name: Bias) Bias = (M+MYp)/(M+MYp+MYpYp+MYpYpYp+MYpYpYpYp)
 
 Assignment Rule (name: parameter_2) autoPhospho = species_1/(species_1+parameter_3)
 
Events (2)
 
 Add ASP
asp = parameter_1
 
 Remove ASP
asp = 0
 
Functions (6)
 
 function_4_motor_r1 lambda(M, MYp, Yp, cell, ka, kappa, ka*(M*Yp-kappa/4*MYp)/cell)
 
 function_4_motor_r2 lambda(MYp, MYpYp, Yp, alpha, cell, ka, kappa, ka*(MYp*Yp-2*alpha*kappa/3*MYpYp)/cell)
 
 function_4_motor_r3 lambda(MYpYp, MYpYpYp, Yp, alpha, cell, ka, kappa, ka*(MYpYp*Yp-3*alpha*alpha*kappa/2*MYpYpYp)/cell)
 
 function_4_motor_r4 lambda(MYpYpYp, MYpYpYpYp, Yp, alpha, cell, ka, kappa, ka*(MYpYpYp*Yp-4*alpha*alpha*alpha*kappa*MYpYpYpYp)/cell)
 
 Autophosphorylation lambda(kcat, correction, E, kcat*correction*E)
 
 ModAutophosphorylation lambda(M, S, kcat, correction, M*S*kcat*correction)
 
 cell Spatial dimensions: 3.0  Compartment size: 1.41E-15
 
 asp
Compartment: cell
Initial concentration: 0.0
 
 ni
Compartment: cell
Initial concentration: 0.0
Constant
 
 T
Compartment: cell
Initial concentration: 3.12E-6
 
 Tasp
Compartment: cell
Initial concentration: 0.0
 
 Tni
Compartment: cell
Initial concentration: 0.0
 
 W
Compartment: cell
Initial concentration: 2.89E-6
 
 TW
Compartment: cell
Initial concentration: 5.91E-7
 
 Tasp_W
Compartment: cell
Initial concentration: 0.0
 
 Tni_W
Compartment: cell
Initial concentration: 0.0
 
 TA
Compartment: cell
Initial concentration: 4.44E-7
 
 Tasp_A
Compartment: cell
Initial concentration: 0.0
 
 Tni_A
Compartment: cell
Initial concentration: 0.0
 
 WA
Compartment: cell
Initial concentration: 6.78E-7
 
 TWA
Compartment: cell
Initial concentration: 8.47E-7
 
 Tasp_WA
Compartment: cell
Initial concentration: 0.0
 
 Tni_WA
Compartment: cell
Initial concentration: 0.0
 
 A
Compartment: cell
Initial concentration: 3.0E-6
 
 Ap
Compartment: cell
Initial concentration: 3.48E-8
 
 B
Compartment: cell
Initial concentration: 1.93E-6
 
 Bp
Compartment: cell
Initial concentration: 6.87E-8
 
 Z
Compartment: cell
Initial concentration: 2.0E-5
 
 Y
Compartment: cell
Initial concentration: 9.9E-6
 
 Yp
Compartment: cell
Initial concentration: 7.0E-9
 
 M
Compartment: cell
Initial concentration: 6.24E-9
 
 MYp
Compartment: cell
Initial concentration: 7.77E-10
 
 MYpYp
Compartment: cell
Initial concentration: 2.99E-10
 
 MYpYpYp
Compartment: cell
Initial concentration: 3.78E-10
 
 MYpYpYpYp
Compartment: cell
Initial concentration: 2.31E-9
 
 ATP
Compartment: cell
Initial concentration: 0.1
Constant
 
Global Parameters (7)
 
 alpha
Value: 0.14
Constant
 
 kappa
Value: 2.25E-7
Constant
 
 ka
Value: 0.1
Constant
 
  Bias
Value: 0.701419432227109
 
 asp_pulse
Value: 1.0E-7
Constant
 
  autoPhospho
Value: 0.997008973080758
 
 KmATP
Value: 3.0E-4
Constant
 
A->Ap (1)
 
   kcat
Value: 0.0010
Constant
 
TWA+A->TWA+Ap (1)
 
   kcat
Value: 75000.0
Constant
 
Tni_WA+A->Tni_WA+Ap (1)
 
   kcat
Value: 200000.0
Constant
 
Tasp_WA+Yp->Tasp_WA+Y (1)
 
   k1
Value: 1.0E8
Constant
 
Ap+Y->A+Yp (1)
 
   k1
Value: 200000.0
Constant
 
Y ->Yp (1)
 
   kcat
Constant
 
Yp->Y (1)
 
   k1
Value: 0.037
Constant
 
Yp+Z->Y+Z (1)
 
   k1
Value: 500000.0
Constant
 
Ap+B->A+Bp (1)
 
   k1
Value: 1000000.0
Constant
 
Bp->B (1)
 
   k1
Value: 1.0
Constant
 
T+asp<->Tasp (2)
 
   k1
Value: 1000000.0
Constant
 
   k2
Value: 1.0
Constant
 
T+ni<->Tni (2)
 
   k1
Value: 1000.0
Constant
 
   k2
Value: 1.0
Constant
 
T+W<->TW (2)
 
   k1
Value: 100000.0
Constant
 
   k2
Value: 1.0
Constant
 
T+A<->TA (2)
 
   k1
Value: 10000.0
Constant
 
   k2
Value: 1.0
Constant
 
W+A<->WA (2)
 
   k1
Value: 100000.0
Constant
 
   k2
Value: 1.0
Constant
 
TW+A<->TWA (2)
 
   k1
Value: 400000.0
Constant
 
   k2
Value: 1.0
Constant
 
TA+W<->TWA (2)
 
   k1
Value: 400000.0
Constant
 
   k2
Value: 1.0
Constant
 
T+WA<->TWA (2)
 
   k1
Value: 400000.0
Constant
 
   k2
Value: 1.0
Constant
 
Tasp+W<->Tasp_W (2)
 
   k1
Value: 100000.0
Constant
 
   k2
Value: 1.0
Constant
 
Tasp+A<->Tasp_A (2)
 
   k1
Value: 10000.0
Constant
 
   k2
Value: 1.0
Constant
 
Tasp_W+A<->Tasp_WA (2)
 
   k1
Value: 400000.0
Constant
 
   k2
Value: 1.0
Constant
 
Tasp_A+W<->Tasp_WA (2)
 
   k1
Value: 400000.0
Constant
 
   k2
Value: 1.0
Constant
 
Tasp+WA<->Tasp_WA (2)
 
   k1
Value: 400000.0
Constant
 
   k2
Value: 1.0
Constant
 
Tni+W<->Tni_W (2)
 
   k1
Value: 0.1
Constant
 
   k2
Value: 1.0
Constant
 
Tni+A<->Tni_A (2)
 
   k1
Value: 0.01
Constant
 
   k2
Value: 1.0
Constant
 
Tni_W+A<->Tni_WA (2)
 
   k1
Value: 0.4
Constant
 
   k2
Value: 1.0
Constant
 
Tni_A+W<->Tni_WA (2)
 
   k1
Value: 0.4
Constant
 
   k2
Value: 1.0
Constant
 
Tni+WA<->Tni_WA (2)
 
   k1
Value: 0.4
Constant
 
   k2
Value: 1.0
Constant
 
TA + asp <-> Tasp_A (2)
 
   k1
Value: 1000000.0
Constant
 
   k2
Value: 1.0
Constant
 
TW+asp <-> Tasp_W (2)
 
   k1
Value: 1000000.0
Constant
 
   k2
Value: 1.0
Constant
 
TWA+asp <-> Tasp_WA (2)
 
   k1
Value: 1000000.0
Constant
 
   k2
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000404

Curator's comment: (updated: 30 Dec 2011 14:03:09 GMT)

Figure 8b of the reference publication has been reproduced here using COPASI 4.8 (build 35).

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