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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): 1367-1380
Department of Zoology, University of Cambridge, United Kingdom.  [more]
Model
Original Model: BIOMD0000000200.origin
Submitter: Vijayalakshmi Chelliah
Submission ID: MODEL6409760567
Submission Date: 11 Nov 2008 13:31:30 UTC
Last Modification Date: 03 Jun 2014 14:51:30 UTC
Creation Date: 07 Nov 2008 10:55:33 UTC
Encoders:  Lukas Endler
   Vijayalakshmi Chelliah
   Dennis Bray
set #1
bqmodel:isDerivedFrom BioModels Database Bray1993_chemotaxis
set #2
bqbiol:isVersionOf Gene Ontology chemotaxis
bqbiol:isDescribedBy KEGG Pathway Bacterial chemotaxis - Escherichia coli K-12 MG1655
bqbiol:hasTaxon Taxonomy Escherichia coli
Notes

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.
For more information see the terms of use.
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 8573792 Submission Date: 11 Nov 2008 13:31:30 UTC Last Modification Date: 03 Jun 2014 14:51:30 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 (name: Bias) Bias = 1-Yp^Hill/(2.333*SetYp^Hill+Yp^Hill)
 
 cell Spatial dimensions: 3.0  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
Value: NaN   (Units: dimensionless)
 
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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