BIOMD0000000405
parameter: COPASI11
curated: true
reaction: COPASI13
is: MODEL1111150000
name: Constant flux (irreversible)
created:
  W3 CDTF: Thu Nov 03 08:34:08 GMT 2011
units def: 408966
units def: 408990
occurs in: http://identifiers.org/taxonomy/131567
reaction: COPASI18
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
reaction: COPASI15
parameter: COPASI10
parameter: COPASI9
reaction: COPASI12
is described by: http://identifiers.org/pubmed/22186735
function def: 506709
is version of: GO:0019899
species: COPASI5
species: COPASI4
compartment: 506473
is version of: CCO:Y0000030
volume units: 408966
modified:
  W3 CDTF: Fri Apr 20 20:27:19 BST 2012
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 Biology 2011; 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. F…
length unit: length
reaction: COPASI17
reaction: COPASI14
species: COPASI2
parameter: COPASI8
species: COPASI6
name: Cookson2011_EnzymaticQueueingCoupling
substance units: 408990
time units: metaid_0000322
creator:
  ORG:
    orgname: Hasty Lab, UCSD Biology
  n:
    given: William
    family: Mather
reaction: COPASI19
parameter: COPASI7
area units: 498119
species: COPASI3
type: SBMLModel
reaction: COPASI16
species: 506561

COPASI13
kinetic law: 409099
product: 409087
reactant: 409075
reactant: 409063
is: SBO:0000344
fast: false
reversible: false
name: binding2
type: Reaction

409015
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI2
is version of: CHEBI:36080
in compartment: 506473
constant: false
has only substance units: false
type: Species
is: SBO:0000252
name: x1
initial concentration: 0.0
initial amount: NaN
boundary condition: false

COPASI17
kinetic law: 409219
product: 409207
reactant: 409195
is: SBO:0000179
fast: false
reversible: false
name: degradation2
type: Reaction

409111
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

409087
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

409195
stoichiometry: 1.0
species: COPASI5
type: SpeciesReference

409039
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI8
is: SBO:0000009
constant: true
value: 500.0
name: lambda2
type: Parameter

COPASI6
is: SBO:0000014
constant: false
boundary condition: false
has only substance units: false
initial concentration: 100.0
initial amount: NaN
in compartment: 506473
name: E
type: Species

COPASI18
kinetic law: 409243
reactant: 409231
is: SBO:0000179
fast: false
reversible: false
name: dilution1
type: Reaction

COPASI14
kinetic law: 409123
product: 409111
is: SBO:0000393
fast: false
reversible: false
name: production1
type: Reaction

409171
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

409255
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

COPASI3
initial concentration: 0.0
type: Species
name: x2
boundary condition: false
initial amount: NaN
has only substance units: false
is: SBO:0000252
in compartment: 506473
is version of: CHEBI:36080
constant: false

408978
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS
type: SBMLUnit

COPASI7
is: SBO:0000009
constant: true
value: 500.0
name: lambda1
type: Parameter

COPASI10
is: SBO:0000009
constant: true
value: 1000.0
name: Kp
type: Parameter

COPASI9
is: SBO:0000009
constant: true
value: 10.0
name: mu
type: Parameter

409231
stoichiometry: 1.0
species: COPASI2
type: SpeciesReference

COPASI15
kinetic law: 409147
product: 409135
is: SBO:0000393
fast: false
reversible: false
name: production2
type: Reaction

506473
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

COPASI19
kinetic law: 409267
reactant: 409255
is: SBO:0000179
fast: false
reversible: false
name: dilution2
type: Reaction

506561
type: Species
constant: false
has only substance units: false
name: E+x1
in compartment: 506473
initial concentration: 1.0
is: SBO:0000296
initial amount: NaN
boundary condition: false
is version of: GO:0043234

409027
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI4
is: SBO:0000014
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 506473
name: E1
type: Species

409075
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

COPASI11
is: SBO:0000009
constant: true
value: 0.03465735902799
name: g
type: Parameter

408990
unit: 409002
name: substance
type: SBMLUnitsDef

409002
exponent: 1.0
scale: 0
multipler: 1.0
kind: ITEM
type: SBMLUnit

409207
stoichiometry: 1.0
species: COPASI6
type: SpeciesReference

408966
unit: 408978
name: volume
type: SBMLUnitsDef

COPASI16
kinetic law: 409183
product: 409171
reactant: 409159
is: SBO:0000179
fast: false
reversible: false
name: degradation1
type: Reaction

409135
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

COPASI5
is: SBO:0000014
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 506473
name: E2
type: Species

409063
stoichiometry: 1.0
species: COPASI3
type: SpeciesReference

409159
stoichiometry: 1.0
species: COPASI4
type: SpeciesReference

COPASI12
kinetic law: 409051
product: 409039
reactant: 409027
reactant: 409015
is: SBO:0000344
fast: false
reversible: false
name: binding1
type: Reaction