BIOMD0000000400
type: SBMLModel
rule: 118877
rule: 118858
rule: 118876
parameter: 118935
parameter: 118952
rule: 118872
parameter: 118968
parameter: 118929
parameter: 118922
parameter: 118955
rule: 118868
rule: 118866
rule: 118886
volume units: metaid_0000323
parameter: 118942
rule: 118833
rule: 118865
parameter: 118958
rule: 118861
rule: 118883
substance units: metaid_0000321
parameter: 118945
parameter: 118973
parameter: 118960
parameter: 118948
parameter: 118976
rule: 118893
species: 118901
parameter: 118930
parameter: 118963
rule: 118892
parameter: 118933
parameter: 118950
rule: 118889
parameter: 118966
parameter: 118897
parameter: 118927
rule: 118857
rule: 118855
species: 118915
parameter: 118920
rule: 118875
compartment: 118828
species: 118912
parameter: 118936
parameter: 118953
rule: 118856
parameter: 118969
species: 118906
parameter: 118923
species: 118907
parameter: 118940
length unit: length
parameter: 118917
parameter: 118956
parameter: 118926
parameter: 118943
rule: 118864
parameter: 118971
rule: 118860
rule: 118882
parameter: 118946
parameter: 118974
parameter: 118900
rule: 118881
is: MODEL0913194523
parameter: 118961
species: 118916
is version of: FMA:83108
parameter: 118977
rule: 118878
parameter: 118931
curated: true
rule: 118874
parameter: 118964
notes: This a model from the article: Modeling hypertrophic IP3 transients in the cardiac myocyte. Cooling M, Hunter P, Crampin EJ. Biophys J 2007 Nov 15;93(10):3421-33 17693463 , Abstract: Cardiac hypertrophy is a known risk factor for heart disease, and at the cellular level is caused by a complex interaction of signal transduction pathways. The IP3-calcineurin pathway plays an important role in stimulating the transcription factor NFAT which binds to DNA cooperatively with other hypertrophic transcription factors. Using available kinetic data, we construct a mathematical model of the IP3 signal production system after stimulation by a hypertrophic alpha-adrenergic agonist (endothelin-1) in the mouse atrial cardiac myocyte. We use a global sensitivity analysis to identify key controlling parameters with respect to the resultant IP3 transient, including the phosphorylation of cell-membrane receptors, the ligand strength and binding kinetics to precoupled (with G(alpha)GDP) receptor, and the kinetics associated with precoupling the receptors. We show that the kinetics associated with the receptor system contribute to the behavior of the system to a great extent, with precoupled receptors driving the response to extracellular ligand. Finally, by reparameterizing for a second hypertrophic alpha-adrenergic agonist, angiotensin-II, we show that differences in key receptor kinetic and membrane density parameters are sufficient to explain different observed IP3 transients in essentially the same pathway. This model was taken from the CellML repository and automatically converted to SBML. The original model was: Cooling M, Hunter P, Crampin EJ. (2007) - version02 The original CellML model was created by: Cooling, Mike, m.cooling@aukland.ac.nz The University of Auckland The Bioengineering Institute 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…
time units: metaid_0000322
rule: 118871
species: 118913

118935
type: Parameter
constant: false
value: NaN
name: J5

118952
type: Parameter
is: SBO:0000156
constant: true
value: 1.0
name: kr10

118968
type: Parameter
is: SBO:0000153
constant: true
value: 3.8
name: kf15

118929
type: Parameter
is: SBO:0000156
constant: true
value: 0.001
name: kr3

118922
type: Parameter
constant: false
value: NaN
name: J2

118955
type: Parameter
is: SBO:0000153
constant: true
value: 0.0334
name: kf11

118942
type: Parameter
constant: false
value: NaN
name: J8

118958
type: Parameter
constant: false
value: NaN
name: J12

118945
type: Parameter
is: SBO:0000156
constant: true
value: 0.0167
name: kr8

118973
type: Parameter
constant: false
value: NaN
name: Cpc

118960
type: Parameter
is: SBO:0000153
constant: true
value: 6.0
name: kf12

118948
type: Parameter
is: SBO:0000156
constant: true
value: 1.0
name: kr9

118976
type: Parameter
constant: false
value: NaN
name: Cp

118901
type: Species
initial concentration: 10000.0
initial amount: NaN
constant: false
has part: CHEBI:17552
is: SBO:0000296
in compartment: 118828
boundary condition: false
name: Gd
has only substance units: false
has part: P27600

118828
type: Compartment
is: GO:0005623
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0

118930
type: Parameter
constant: false
value: NaN
name: J4

118963
type: Parameter
constant: false
value: NaN
name: J14

118933
type: Parameter
is: SBO:0000156
constant: false
value: NaN
name: kr4

118950
type: Parameter
constant: false
value: NaN
name: J10

118966
type: Parameter
is: SBO:0000027
constant: true
value: 19.8
name: Km14

118897
type: Parameter
constant: false
value: NaN
name: L

118927
type: Parameter
constant: false
value: NaN
name: J3

118915
type: Species
has only substance units: false
is version of: Q9Z1B3
initial amount: NaN
constant: false
is: SBO:0000252
boundary condition: false
in compartment: 118828
initial concentration: 90.9
name: P

118920
type: Parameter
is: SBO:0000156
constant: false
value: NaN
name: kr1

118912
type: Species
has part: CHEBI:29108
initial amount: NaN
constant: false
has part: Q9Z1B3
in compartment: 118828
boundary condition: false
initial concentration: 9.09
is: SBO:0000296
name: Pc
has only substance units: false

118936
type: Parameter
is: SBO:0000153
constant: true
value: 4.0E-4
name: kf5

118953
type: Parameter
constant: false
value: NaN
name: J11

118969
type: Parameter
is: SBO:0000027
constant: true
value: 5.0
name: Km15

118906
type: Species
in compartment: 118828
has part: CHEBI:17552
has only substance units: false
initial concentration: 5.06
has part: P27600
has part: P35412
is: SBO:0000296
boundary condition: false
initial amount: NaN
constant: false
name: Rg

118923
type: Parameter
is: SBO:0000153
constant: true
value: 2.75E-4
name: kf2

118907
type: Species
constant: false
has part: CHEBI:17552
has part: P35412
has part: CCO:F0001633
boundary condition: false
initial concentration: 0.0
name: Rlg
in compartment: 118828
is: SBO:0000296
has part: P27600
has only substance units: false
initial amount: NaN

118940
type: Parameter
constant: false
value: NaN
name: J7

118917
type: Parameter
constant: false
value: NaN
name: J1

118956
type: Parameter
is: SBO:0000156
constant: false
value: NaN
name: kr11

118926
type: Parameter
is: SBO:0000356
constant: true
value: 27500.0
name: Kd2

118943
type: Parameter
is: SBO:0000153
constant: true
value: 0.0167
name: kf8

118971
type: Parameter
constant: false
value: NaN
name: J16

118946
type: Parameter
constant: false
value: NaN
name: J9

118974
type: Parameter
constant: false
value: NaN
name: Cc

118900
type: Parameter
is: SBO:0000009
constant: true
value: 30.0
name: ts

118961
type: Parameter
constant: false
value: NaN
name: J13

118916
type: Species
has part: Q9Z1B3
is: SBO:0000296
name: Pg
initial amount: NaN
has part: P27600
constant: false
in compartment: 118828
has only substance units: false
has part: CHEBI:15996
initial concentration: 0.0
boundary condition: false

118977
type: Parameter
is: SBO:0000468
constant: true
value: 2550.0
name: Vc

118931
type: Parameter
is: SBO:0000153
constant: true
value: 0.3
name: kf4

118964
type: Parameter
is: SBO:0000153
constant: true
value: 0.444
name: kf14

118913
type: Species
name: Pcg
initial amount: NaN
constant: false
has part: Q9Z1B3
is: SBO:0000296
has part: CHEBI:29108
initial concentration: 0.0
in compartment: 118828
has part: P27600
boundary condition: false
has part: CHEBI:15996
has only substance units: false

118904
type: Species
boundary condition: false
in compartment: 118828
has only substance units: false
is: SBO:0000244
initial concentration: 13.9
initial amount: NaN
constant: false
is version of: P35412
name: R

118910
type: Species
is version of: Q8R071
boundary condition: false
has only substance units: false
initial amount: NaN
name: IP3
in compartment: 118828
is: SBO:0000252
initial concentration: 0.015
constant: false

118934
type: Parameter
is: SBO:0000356
constant: true
value: 3.0E-5
name: Kd4

118951
type: Parameter
is: SBO:0000153
constant: true
value: 0.042
name: kf10

118967
type: Parameter
constant: false
value: NaN
name: J15

118898
type: Parameter
is: SBO:0000515
constant: true
value: 0.1
name: Ls

118928
type: Parameter
is: SBO:0000153
constant: true
value: 1.0
name: kf3

118896
type: Species
is version of: CHEBI:29108
boundary condition: false
is: SBO:0000247
initial concentration: 0.1
has only substance units: false
in compartment: 118828
constant: false
name: Ca
initial amount: NaN

118905
type: Species
initial amount: NaN
has part: P35412
has part: CCO:F0001633
constant: false
boundary condition: false
initial concentration: 0.0
in compartment: 118828
has only substance units: false
name: Rl
is: SBO:0000297

118921
type: Parameter
is: SBO:0000356
constant: true
value: 3.0E-5
name: Kd1

118937
type: Parameter
constant: false
value: NaN
name: J6

118924
type: Parameter
is: SBO:0000156
constant: false
value: NaN
name: kr2

118941
type: Parameter
is: SBO:0000153
constant: true
value: 0.15
name: kf7

118957
type: Parameter
is: SBO:0000356
constant: true
value: 0.1
name: Kd11

118918
type: Parameter
is: SBO:0000153
constant: true
value: 3.0E-4
name: kf1

118911
type: Parameter
is: SBO:0000196
constant: true
value: 4000.0
name: PIP2

118972
type: Parameter
is: SBO:0000153
constant: true
value: 1.25
name: kf16

118947
type: Parameter
is: SBO:0000153
constant: true
value: 0.0042
name: kf9

118909
type: Species
is version of: MOD:00696
initial amount: NaN
has part: CHEBI:17552
has only substance units: false
has part: P27600
name: Rlgp
has part: CCO:F0001633
initial concentration: 0.0
boundary condition: false
has part: P35412
constant: false
is: SBO:0000296
in compartment: 118828

118962
type: Parameter
is: SBO:0000153
constant: true
value: 6.0
name: kf13

118978
type: Parameter
is: SBO:0000468
constant: true
value: 4.61
name: Rpc

118939
type: Parameter
is: SBO:0000153
constant: true
value: 1.0
name: kf6

118902
type: Species
constant: false
initial concentration: 0.0
has part: CHEBI:15996
is: SBO:0000296
in compartment: 118828
has only substance units: false
has part: P27600
name: Gt
boundary condition: false
initial amount: NaN

W3 CDTF: Mon Jul 16 12:57:19 BST 2012

W3 CDTF: Tue Apr 28 12:55:20 BST 2009

ORG:
  orgname: The Bioengineering Institute, The University of Auckland.
n:
  given: Mike
  family: Cooling