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BIOMD0000000405 - Cookson2011_EnzymaticQueueingCoupling

 

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Reference Publication
Publication ID: 22186735
Cookson NA, Mather WH, Danino T, Mondragón-Palomino O, Williams RJ, Tsimring LS, Hasty J.
Queueing up for enzymatic processing: correlated signaling through coupled degradation.
Mol. Syst. Biol. 2011; 7: 561
Molecular Biology Section, Division of Biological Science, University of California, San Diego, CA, USA.  [more]
Model
Original Model: BIOMD0000000405.xml.origin
Submitter: William Mather
Submission ID: MODEL1111150000
Submission Date: 15 Nov 2011 00:23:19 UTC
Last Modification Date: 06 Apr 2014 20:48:51 UTC
Creation Date: 03 Nov 2011 08:34:08 UTC
Encoders:  Vijayalakshmi Chelliah
   William Mather
set #1
bqbiol:hasTaxon Taxonomy cellular organisms
set #2
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #3
bqbiol:isVersionOf Gene Ontology regulation of catalytic activity
Notes

This model is from the article:
Queueing up for enzymatic processing: correlated signaling through coupled degradation.
Natalie A Cookson, William H Mather, Tal Danino, Octavio Mondragón-Palomino, Ruth J Williams, Lev S Tsimring, & Jeff Hasty Molecular Systems Biology2011; 7:561; DOI:10.1038/msb.2011.94
Abstract:
High-throughput technologies have led to the generation of complex wiring diagrams as a post-sequencing paradigm for depicting the interactions between vast and diverse cellular species. While these diagrams are useful for analyzing biological systems on a large scale, a detailed understanding of the molecular mechanisms that underlie the observed network connections is critical for the further development of systems and synthetic biology. Here, we use queueing theory to investigate how ‘waiting lines’ can lead to correlations between protein ‘customers’ that are coupled solely through a downstream set of enzymatic ‘servers’. Using the E. coli ClpXP degradation machine as a model processing system, we observe significant cross-talk between two networks that are indirectly coupled through a common set of processors. We further illustrate the implications of enzymatic queueing using a synthetic biology application, in which two independent synthetic networks demonstrate synchronized behavior when common ClpXP machinery is overburdened. Our results demonstrate that such post-translational processes can lead to dynamic connections in cellular networks and may provide a mechanistic understanding of existing but currently inexplicable links.

Note:
Individual stochastic trajectories for a queueing system in three different conditions, 1) Underloaded, 2) Balanced and 3) Overloaded, demonstrate correlation resonance. The parameter values in this model correspond to the Balanced Condition.

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: 22186735 Submission Date: 15 Nov 2011 00:23:19 UTC Last Modification Date: 06 Apr 2014 20:48:51 UTC Creation Date: 03 Nov 2011 08:34:08 UTC
Mathematical expressions
Reactions
binding1 binding2 production1 production2
degradation1 degradation2 dilution1 dilution2
Physical entities
Compartments Species
compartment x1 x2 E1
E2 E E+x1
Global parameters
lambda1 lambda2 mu Kp
g      
Reactions (8)
 
 binding1 [x1] + [E] → [E1];  
 
 binding2 [x2] + [E] → [E2];  
 
 production1  → [x1];  
 
 production2  → [x2];  
 
 degradation1 [E1] → [E];  
 
 degradation2 [E2] → [E];  
 
 dilution1 [x1] → ;  
 
 dilution2 [x2] → ;  
 
Functions (1)
 
 Constant flux (irreversible) lambda(v, v)
 
   compartment Spatial dimensions: 3.0  Compartment size: 1.0
 
 x1
Compartment: compartment
Initial concentration: 0.0
 
 x2
Compartment: compartment
Initial concentration: 0.0
 
 E1
Compartment: compartment
Initial concentration: 0.0
 
 E2
Compartment: compartment
Initial concentration: 0.0
 
 E
Compartment: compartment
Initial concentration: 100.0
 
 E+x1
Compartment: compartment
Initial concentration: 1.0
 
Global Parameters (5)
 
 lambda1
Value: 500.0
Constant
 
 lambda2
Value: 500.0
Constant
 
 mu
Value: 10.0
Constant
 
 Kp
Value: 1000.0
Constant
 
 g
Value: 0.03465735902799
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000405

Curator's comment: (updated: 12 Jan 2012 11:28:36 GMT)

Figure 1b, that correspond to the "Balanced Condition" is being reproduced here using Copasi v4.7 (Build 34).

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