BIOMD0000000187
type: SBMLModel
area units: metaid_0000005
species: metaid_0000015
substance units: metaid_0000053
time units: metaid_0000054
is version of: GO:0007094
reaction: metaid_0000024
parameter: metaid_0000004
parameter: metaid_0000512
reaction: metaid_0000225
volume units: metaid_0000004
species: metaid_0000021
reaction: metaid_0000023
modified:
  W3 CDTF: Wed Jun 05 17:39:33 BST 2013
species: metaid_0000324
reaction: metaid_0000028
parameter: metaid_0000712
parameter: metaid_0000008
species: metaid_0000022
species: metaid_0000017
units def: metaid_0000042
parameter: metaid_0000612
length unit: length
creator:
  ORG:
    orgname: Fritz Lipmann Institute, Jena, Germany
  n:
    given: Stephan
    family: Diekmann
parameter: metaid_0000045
name: Ibrahim2008 - Mitotic Spindle Assembly Checkpoint - Convey variant
parameter: metaid_0000012
reaction: metaid_0000223
reaction: metaid_0000224
is version of: REACT 2137.2
reaction: metaid_0000027
parameter: metaid_0000007
parameter: metaid_0000812
occurs in: http://identifiers.org/taxonomy/9606
species: metaid_0000322
is described by: http://identifiers.org/pubmed/18253502
creator:
  ORG:
    orgname: Fritz Lipmann Institute, Jena, Germany
  n:
    given: Eberhard
    family: Schmitt
created:
  W3 CDTF: Mon Sep 01 15:18:13 BST 2008
parameter: metaid_1000007
is: MODEL6655578762
event: metaid_0000031
creator:
  ORG:
    orgname: Friedrich-Schiller-University Jena, Germany
  n:
    given: Peter
    family: Dittrich
species: metaid_0000018
parameter: metaid_0000044
reaction: metaid_0000025
reaction: metaid_0000026
parameter: metaid_0000005
parameter: metaid_0000006
compartment: metaid_0000014
species: metaid_0000019
curated: true
species: metaid_0000020
parameter: metaid_0000003
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
notes: Ibrahim2008 - Mitotic Spindle Assembly Checkpoint - Convey variant The Mitotic Spindle Assembly Checkpoint ((M)SAC) is an evolutionary conserved mechanism. This model incorporates the perspectives of three central control pathways, namely Mad1/Mad2 induced Cdc20 sequestering based on the Template Model, MCC formation, and APC inhibition. MCC:APC dissociation is described by two alternatives models, namely the "Dissociation" and the "Convey" model variants. Both these model are available in BioModels Database. This model corresponds to the "Convey" variant. This model is described in the article: In-silico modeling of the mitotic spindle assembly checkpoint. Ibrahim B, Diekmann S, Schmitt E, Dittrich P PLoS One. 2008 Feb 6;3(2):e1555. Abstract: BACKGROUND: The Mitotic Spindle Assembly Checkpoint ((M)SAC) is an evolutionary conserved mechanism that ensures the correct segregation of chromosomes by restraining cell cycle progression from entering anaphase until all chromosomes have made proper bipolar attachments to the mitotic spindle. Its malfunction can lead to cancer. PRINCIPLE FINDINGS: We have constructed and validated for the human (M)SAC mechanism an in silico dynamical model, integrating 11 proteins and complexes. The model incorporates the perspectives of three central control pathways, namely Mad1/Mad2 induced Cdc20 sequestering based on the Template Model, MCC formation, and APC inhibition. Originating from the biochemical reactions for the underlying molecular processes, non-linear ordinary differential equations for the concentrations of 11 proteins and complexes of the (M)SAC are derived. Most of the kinetic constants are taken from literature, the remaining four unknown parameters are derived by an evolutionary optimization procedure for an objective function describing the dynamics of the APC:Cdc20 complex. MCC:APC dissociation is described by two alternatives, namely the "Dissociation" and the "Convey" model variants. The attachment of the kinetochore…
species: metaid_0000323
creator:
  ORG:
    orgname: German Cancer Research Center, Heidelberg
  n:
    given: Bashar
    family: Ibrahim
parameter: metaid_0000010
parameter: metaid_0000011
is part of: hsa04110
species: metaid_0000016
parameter: metaid_0000009
units def: metaid_0000043

metaid_0000015
type: Species
name: Mad1:C-Mad2
is version of: GO:0043234
initial concentration: 5.0E-8
boundary condition: false
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initial amount: NaN
has only substance units: false
substance units: mole
has part: Q13257
constant: false
has part: Q9Y6D9

metaid_0000014
type: Compartment
is: GO:0005737
constant: true
size: 1.0
spatial dimensions: 3.0
name: Cytoplasm

metaid_0000024
type: Reaction
reversible: false
kinetic law: 771745
product: 771721
reactant: 771697
fast: false
is version of: GO:0006461
reactant: 771709
is version of: GO:0032092
product: 771733

771721
type: SpeciesReference
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species: metaid_0000015

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type: SpeciesReference
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metaid_0000017
type: Species
has part: Q9Y6D9
is version of: GO:0043234
constant: false
boundary condition: false
has part: Q13257
initial concentration: 0.0
in compartment: metaid_0000014
name: Mad1:C-Mad2:O-Mad2*
has only substance units: false
initial amount: NaN
substance units: mole

771709
type: SpeciesReference
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species: metaid_0000018

metaid_0000018
type: Species
initial concentration: 2.2E-7
boundary condition: false
name: Cdc20
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constant: false

771733
type: SpeciesReference
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metaid_0000019
type: Species
initial concentration: 0.0
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constant: false
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name: Cdc20:C-Mad2
boundary condition: false
in compartment: metaid_0000014
substance units: mole
initial amount: NaN
has part: Q12834

metaid_0000004
type: Parameter
constant: true
units: metaid_0000043
value: 1000.0

metaid_0000043
type: SBMLUnitsDef
unit: 771637
unit: 771625
unit: 771613
name: liter per mole per second

771637
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exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

771625
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exponent: -1.0
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kind: MOLE

771613
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

metaid_0000512
type: Parameter
constant: true
units: metaid_0000043
value: 1.0E8

metaid_0000225
type: Reaction
is version of: GO:0043623
reactant: 772057
reversible: true
reactant: 772069
kinetic law: 772093
fast: false
product: 772081
is version of: GO:0007092

772057
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000322

metaid_0000322
type: Species
has part: Q9UM13
has part: P30260
has part: Q9UJX3
is version of: GO:0005680
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name: APC
has part: Q9UJX4
initial concentration: 9.0E-8
has only substance units: false
initial amount: NaN
has part: Q9BS18
has part: Q9UJX2
has part: Q9NYG5
boundary condition: false
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in compartment: metaid_0000014
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constant: false
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772069
type: SpeciesReference
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species: metaid_0000018

772081
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000324

metaid_0000324
type: Species
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has part: Q9UJX4
has part: Q12834
in compartment: metaid_0000014
substance units: mole
constant: false
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initial amount: NaN
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has part: Q13042
boundary condition: false
has part: P30260
has part: Q9BS18
initial concentration: 0.0
name: APC:Cdc20
has part: Q9H1A4
has part: Q9UJX5

metaid_0000021
type: Species
has part: O43684
has part: Q60566
substance units: mole
name: MCC
is: GO:0033597
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initial amount: NaN
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constant: false
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initial concentration: 0.0
boundary condition: false
in compartment: metaid_0000014

metaid_0000023
type: Reaction
is version of: GO:0043241
is version of: GO:0032092
reactant: 771649
is version of: GO:0006461
product: 771673
reversible: true
fast: false
kinetic law: 771685
reactant: 771661

771649
type: SpeciesReference
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species: metaid_0000015

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type: SpeciesReference
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species: metaid_0000017

771661
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species: metaid_0000016

metaid_0000016
type: Species
constant: false
boundary condition: false
is: Q13257
has only substance units: false
name: O-Mad2
substance units: mole
notes: Open conformation of Mad2
initial concentration: 1.3E-7
initial amount: NaN
in compartment: metaid_0000014

metaid_0000028
type: Reaction
kinetic law: 771937
product: 771925
reactant: 771913
reactant: 771901
is version of: GO:0006461
fast: false
reversible: false

771925
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

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type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

771901
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000712
type: Parameter
constant: true
units: metaid_0000043
value: 5000000.0

metaid_0000008
type: Parameter
constant: true
units: metaid_0000043
value: 1.0E8

metaid_0000022
type: Species
has part: Q12834
has only substance units: false
constant: false
boundary condition: false
initial amount: NaN
substance units: mole
has part: Q60566
name: Bub3:BubR1:Cdc20
initial concentration: 0.0
has part: O43684
in compartment: metaid_0000014

metaid_0000042
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unit: 771591
name: per second

771591
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exponent: -1.0
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kind: SECOND

metaid_0000612
type: Parameter
constant: true
units: metaid_0000042
value: 0.08

metaid_0000045
type: Parameter
constant: true
units: dimensionless
value: 1.0

metaid_0000012
type: Parameter
constant: true
units: metaid_0000042
value: 0.02

metaid_0000223
type: Reaction
reactant: 771949
fast: false
product: 771973
is version of: GO:0051436
is version of: GO:0043623
kinetic law: 771985
reversible: false
reactant: 771961

771949
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

771973
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000323

metaid_0000323
type: Species
has part: Q9BS18
has part: GO:0033597
has part: Q9UJX2
has part: Q9UJX5
name: MCC:APC
boundary condition: false
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substance units: mole
constant: false
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has part: Q9UM13
has part: GO:0005680
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771961
type: SpeciesReference
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species: metaid_0000322

metaid_0000224
type: Reaction
reactant: 771997
is version of: GO:0007092
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is version of: GO:0043624
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kinetic law: 772045
reversible: false

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species: metaid_0000020

metaid_0000020
type: Species
name: Bub3:BubR1
has part: Q60566
substance units: mole
initial concentration: 1.27E-7
has only substance units: false
initial amount: NaN
boundary condition: false
in compartment: metaid_0000014
constant: false
has part: O43684

772033
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000324

metaid_0000027
type: Reaction
is version of: GO:0006461
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reversible: true
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is version of: GO:0043241

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species: metaid_0000022

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type: SpeciesReference
stoichiometry: 1.0
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771865
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

metaid_0000007
type: Parameter
notes: u = 1 : kinetochore unattached u = 0 : kinetochore attached
constant: false
units: dimensionless
value: 1.0

metaid_0000812
type: Parameter
constant: true
units: metaid_0000042
value: 0.08

metaid_1000007
type: Parameter
notes: u = 0 : kinetochore unattached u = 1 : kinetochore attached
constant: false
units: dimensionless
value: 0.0

metaid_0000031
type: Event
event assignment: 772129
event assignment: 772117
trigger: 772105
use values from trigger time: true
name: Microtubule attachment

772105
type: Trigger
persistant: true
initial value: true

metaid_0000044
type: Parameter
constant: true
units: dimensionless
value: 0.0

metaid_0000025
type: Reaction
kinetic law: 771793
product: 771781
product: 771769
reactant: 771757
is version of: GO:0043241
fast: false
reversible: false

771781
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

771769
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

771757
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

metaid_0000026
type: Reaction
reactant: 771817
is version of: GO:0043241
reactant: 771805
kinetic law: 771841
product: 771829
is version of: GO:0006461
reversible: true
is version of: REACT 36.2
fast: false

771817
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

771805
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

771829
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

metaid_0000005
type: Parameter
constant: true
units: metaid_0000043
value: 10000.0

metaid_0000006
type: Parameter
constant: true
units: metaid_0000042
value: 0.2

metaid_0000003
type: Parameter
constant: true
units: metaid_0000042
value: 0.01

metaid_0000010
type: Parameter
constant: true
units: metaid_0000042
value: 0.2

metaid_0000011
type: Parameter
constant: true
units: metaid_0000043
value: 1.0E7

metaid_0000009
type: Parameter
constant: true
units: metaid_0000043
value: 200000.0