BIOMD0000000405
type: SBMLModel
parameter: COPASI11
curated: true
reaction: COPASI13
is: MODEL1111150000
name: Constant flux (irreversible)
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
creator:
  ORG:
    orgname: Hasty Lab, UCSD Biology
  n:
    given: William
    family: Mather
function def: 506709
is version of: GO:0019899
species: COPASI5
species: COPASI4
compartment: 506473
is version of: CCO:Y0000030
volume units: 408966
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
created:
  W3 CDTF: Thu Nov 03 08:34:08 GMT 2011
species: COPASI2
parameter: COPASI8
species: COPASI6
name: Cookson2011_EnzymaticQueueingCoupling
modified:
  W3 CDTF: Fri Apr 20 20:27:19 BST 2012
substance units: 408990
time units: metaid_0000322
reaction: COPASI19
parameter: COPASI7
area units: 498119
species: COPASI3
reaction: COPASI16
species: 506561

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

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

409087
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

COPASI5
type: Species
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

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

409075
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

COPASI6
type: Species
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

409063
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

COPASI3
type: Species
initial concentration: 0.0
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

408966
type: SBMLUnitsDef
unit: 408978
name: volume

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

408990
type: SBMLUnitsDef
unit: 409002
name: substance

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

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

409231
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

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

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

409135
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

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

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

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

409039
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

COPASI4
type: Species
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

409027
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

409015
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

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

409207
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

409195
type: SpeciesReference
stoichiometry: 1.0
species: COPASI5

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

409111
type: SpeciesReference
stoichiometry: 1.0
species: COPASI2

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

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

409255
type: SpeciesReference
stoichiometry: 1.0
species: COPASI3

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

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

409171
type: SpeciesReference
stoichiometry: 1.0
species: COPASI6

409159
type: SpeciesReference
stoichiometry: 1.0
species: COPASI4

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