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BIOMD0000000200 - Bray1995_chemotaxis_receptorlinkedcomplex

  
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Reference Publication
Publication ID: 8573792
Bray D, Bourret RB.
Computer analysis of the binding reactions leading to a transmembrane receptor-linked multiprotein complex involved in bacterial chemotaxis.
Mol Biol Cell 1995 Oct;6(10):1367-80.
Department of Zoology, University of Cambridge, United Kingdom.  [more]
Model
Original Model: BIOMD0000000200.xml.origin
Submitter: Vijayalakshmi Chelliah
Submission ID: MODEL6409760567
Submission Date: 11 Nov 2008 13:31:30 UTC
Last Modification Date: 05 Oct 2009 13:32:42 UTC
Creation Date: 07 Nov 2008 10:55:33 UTC
Encoders:  Lukas Endler
   Vijayalakshmi Chelliah
   Dennis Bray
set #1
bqbiol:isVersionOf Gene Ontology chemotaxis
bqbiol:isDescribedBy KEGG Pathway eco02030
bqbiol:occursIn Taxonomy Escherichia coli
Notes

This model originates from BioModels Database: A Database of Annotated Published Models. 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: 8573792 Submission Date: 11 Nov 2008 13:31:30 UTC Last Modification Date: 05 Oct 2009 13:32:42 UTC Creation Date: 07 Nov 2008 10:55:33 UTC
Mathematical expressions
Reactions
complex_r1 complex_r2 complex_r3 complex_r4
complex_r5 complex_r6 complex_r7 complex_r8
complex_r9 complex_r10 complex_r11 complex_r12
phosphorylation_r1 phosphorylation_r2 phosphorylation_r3 phosphorylation_r4
phosphorylation_r5 phosphorylation_r6 phosphorylation_r7 phosphorylation_r8
phosphorylation_r9 phosphorylation_r10 phosphotransfer_r1 phosphotransfer_r2
phosphotransfer_r3 phosphotransfer_r4 phosphotransfer_r5 phosphotransfer_r6
phosphotransfer_r7 phosphotransfer_r8 phosphotransfer_r9 phosphotransfer_r10
phosphotransfer_r11 phosphotransfer_r12    
Rules
Assignment Rule (variable: Bias)      
Physical entities
Compartments Species
cell AA AAp W
WAA WAAp WWAA
WWAAp TT TTW
TTWW TTWAA TTWAAp
TTAA TTAAp TTWWAA
TTWWAAp Y Yp
Z B Bp
setYp    
Global parameters
Hill Bias    
Reactions (34)
 
 complex_r1 [TTW] ↔ [TT] + [W];  
 
 complex_r2 [WAA] ↔ [W] + [AA];  
 
 complex_r3 [TTWAA] ↔ [TT] + [WAA];  
 
 complex_r4 [TTWWAA] ↔ [TTW] + [WAA];  
 
 complex_r5 [TTWWAA] ↔ [TTWW] + [AA];  
 
 complex_r6 [TTWWAA] ↔ [TT] + [WWAA];  
 
 complex_r7 [TTAA] ↔ [TT] + [AA];  
 
 complex_r8 [TTWAA] ↔ [TTW] + [AA];  
 
 complex_r9 [TTWWAA] ↔ [TTWAA] + [W];  
 
 complex_r10 [TTWW] ↔ [TTW] + [W];  
 
 complex_r11 [WWAA] ↔ [W] + [WAA];  
 
 complex_r12 [TTWAA] ↔ [TTAA] + [W];  
 
 phosphorylation_r1 [TTWWAA] → [TTWWAAp];  
 
 phosphorylation_r2 [AA] → [AAp];  
 
 phosphorylation_r3 [WAA] → [WAAp];  
 
 phosphorylation_r4 [WWAA] → [WWAAp];  
 
 phosphorylation_r5 [TTAA] → [TTAAp];  
 
 phosphorylation_r6 [TTWAA] → [TTWAAp];  
 
 phosphorylation_r7 [Y] → [Yp];  
 
 phosphorylation_r8 [Yp] → [Y];  
 
 phosphorylation_r9 [Yp] + [Z] → [Y] + [Z];  
 
 phosphorylation_r10 [Bp] → [B];  
 
 phosphotransfer_r1 [B] + [AAp] → [Bp] + [AA];  
 
 phosphotransfer_r2 [B] + [WAAp] → [Bp] + [WAA];  
 
 phosphotransfer_r3 [B] + [WWAAp] → [Bp] + [WWAA];  
 
 phosphotransfer_r4 [B] + [TTAAp] → [Bp] + [TTAA];  
 
 phosphotransfer_r5 [B] + [TTWAAp] → [Bp] + [TTWAA];  
 
 phosphotransfer_r6 [B] + [TTWWAAp] → [Bp] + [TTWWAA];  
 
 phosphotransfer_r7 [Y] + [AAp] → [Yp] + [AA];  
 
 phosphotransfer_r8 [Y] + [WAAp] → [Yp] + [WAA];  
 
 phosphotransfer_r9 [Y] + [WWAAp] → [Yp] + [WWAA];  
 
 phosphotransfer_r10 [Y] + [TTAAp] → [Yp] + [TTAA];  
 
 phosphotransfer_r11 [Y] + [TTWAAp] → [Yp] + [TTWAA];  
 
 phosphotransfer_r12 [Y] + [TTWWAAp] → [Yp] + [TTWWAA];  
 
Rules (1)
 
 Assignment Rule Bias = 1 - pow(Yp, Hill) / (2.333 * pow(SetYp, Hill) + pow(Yp, Hill))
 
 cell Spatial dimensions: 3  Compartment size: 1.41
 
 AA
Compartment: cell
Initial concentration: 2.5E-6
 
 AAp
Compartment: cell
Initial concentration: 0.0
 
 W
Compartment: cell
Initial concentration: 5.0E-6
 
 WAA
Compartment: cell
Initial concentration: 0.0
 
 WAAp
Compartment: cell
Initial concentration: 0.0
 
 WWAA
Compartment: cell
Initial concentration: 0.0
 
 WWAAp
Compartment: cell
Initial concentration: 0.0
 
 TT
Compartment: cell
Initial concentration: 2.5E-6
 
 TTW
Compartment: cell
Initial concentration: 0.0
 
 TTWW
Compartment: cell
Initial concentration: 0.0
 
 TTWAA
Compartment: cell
Initial concentration: 0.0
 
 TTWAAp
Compartment: cell
Initial concentration: 0.0
 
 TTAA
Compartment: cell
Initial concentration: 0.0
 
 TTAAp
Compartment: cell
Initial concentration: 0.0
 
 TTWWAA
Compartment: cell
Initial concentration: 0.0
 
 TTWWAAp
Compartment: cell
Initial concentration: 0.0
 
 Y
Compartment: cell
Initial concentration: 1.0E-5
 
 Yp
Compartment: cell
Initial concentration: 0.0
 
 Z
Compartment: cell
Initial concentration: 2.0E-5
 
 B
Compartment: cell
Initial concentration: 2.0E-6
 
 Bp
Compartment: cell
Initial concentration: 0.0
 
 setYp
Compartment: cell
Initial concentration: 1.63E-6
 
Global Parameters (2)
 
   Hill
Value: 4.0
Constant
 
   Bias  
 
complex_r1 (2)
 
   k1
Value: 0.00365   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
complex_r2 (2)
 
   k1
Value: 0.00894   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
complex_r3 (2)
 
   k1
Value: 297.0   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
complex_r4 (2)
 
   k1
Value: 0.64   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
complex_r5 (2)
 
   k1
Value: 0.112   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
complex_r6 (2)
 
   k1
Value: 0.0229   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
complex_r7 (2)
 
   k1
Value: 39.3   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
complex_r8 (2)
 
   k1
Value: 727.0   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
complex_r9 (2)
 
   k1
Value: 7.87E-6   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
complex_r10 (2)
 
   k1
Value: 0.0511   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
complex_r11 (2)
 
   k1
Value: 0.102   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
complex_r12 (2)
 
   k1
Value: 0.0676   (Units: persec)
Constant
 
   k2
Value: 1000000.0   (Units: perMpersec)
Constant
 
phosphorylation_r1 (1)
 
   k1
Value: 15.5   (Units: persec)
Constant
 
phosphorylation_r2 (1)
 
   k1
Value: 0.0227   (Units: persec)
Constant
 
phosphorylation_r3 (1)
 
   k1
Value: 0.0227   (Units: persec)
Constant
 
phosphorylation_r4 (1)
 
   k1
Value: 0.0227   (Units: persec)
Constant
 
phosphorylation_r5 (1)
 
   k1
Value: 0.0227   (Units: persec)
Constant
 
phosphorylation_r6 (1)
 
   k1
Value: 0.0227   (Units: persec)
Constant
 
phosphorylation_r7 (1)
 
   k1
Value: 0.00124   (Units: persec)
Constant
 
phosphorylation_r8 (1)
 
   k1
Value: 0.037   (Units: persec)
Constant
 
phosphorylation_r9 (1)
 
   k1
Value: 500000.0   (Units: perMpersec)
Constant
 
phosphorylation_r10 (1)
 
   k1
Value: 0.35   (Units: persec)
Constant
 
phosphotransfer_r1 (1)
 
   k1
Value: 6000000.0   (Units: perMpersec)
Constant
 
phosphotransfer_r2 (1)
 
   k1
Value: 6000000.0   (Units: perMpersec)
Constant
 
phosphotransfer_r3 (1)
 
   k1
Value: 6000000.0   (Units: perMpersec)
Constant
 
phosphotransfer_r4 (1)
 
   k1
Value: 6000000.0   (Units: perMpersec)
Constant
 
phosphotransfer_r5 (1)
 
   k1
Value: 6000000.0   (Units: perMpersec)
Constant
 
phosphotransfer_r6 (1)
 
   k1
Value: 6000000.0   (Units: perMpersec)
Constant
 
phosphotransfer_r7 (1)
 
   k1
Value: 3.0E7   (Units: perMpersec)
Constant
 
phosphotransfer_r8 (1)
 
   k1
Value: 3.0E7   (Units: perMpersec)
Constant
 
phosphotransfer_r9 (1)
 
   k1
Value: 3.0E7   (Units: perMpersec)
Constant
 
phosphotransfer_r10 (1)
 
   k1
Value: 3.0E7   (Units: perMpersec)
Constant
 
phosphotransfer_r11 (1)
 
   k1
Value: 3.0E7   (Units: perMpersec)
Constant
 
phosphotransfer_r12 (1)
 
   k1
Value: 3.0E7   (Units: perMpersec)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000200

Curator's comment: (updated: 11 Nov 2008 13:30:52 GMT)

Figure 4 of the original paper is reproduced for receptor-Tar, CheW) and CheA against Bias. The plot denotes the 12-reaction network model.
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