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BIOMD0000000464 - Koo2013 - Shear stress induced calcium influx and eNOS activation - Model 1

 

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Reference Publication
Publication ID: 23708369
Koo A, Nordsletten D, Umeton R, Yankama B, Ayyadurai S, García-Cardeña G, Dewey CF Jr.
In silico modeling of shear-stress-induced nitric oxide production in endothelial cells through systems biology.
Biophys. J. 2013 May; 104(10): 2295-2306
Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.  [more]
Model
Original Model: Wiesner, T. F., B. C. Berk...
Submitter: Andrew Koo
Submission ID: MODEL1302180003
Submission Date: 18 Feb 2013 20:19:30 UTC
Last Modification Date: 07 Apr 2014 02:58:33 UTC
Creation Date: 19 Aug 2013 13:33:57 UTC
Encoders:  Nick Juty
   Vijayalakshmi Chelliah
   Andrew Koo
set #1
bqbiol:isVersionOf Gene Ontology nitric oxide biosynthetic process
Gene Ontology nitric oxide production involved in inflammatory response
set #2
bqbiol:hasPart Reactome REACT_12443.3
set #3
bqbiol:hasPart Gene Ontology calcium ion import
set #4
bqbiol:hasTaxon Taxonomy Homo sapiens
Notes
Model
Publication ID: 23708369 Submission Date: 18 Feb 2013 20:19:30 UTC Last Modification Date: 07 Apr 2014 02:58:33 UTC Creation Date: 19 Aug 2013 13:33:57 UTC
Mathematical expressions
Reactions
re1 re4 re5 re6
re7 re8 re9 re10
re11 re12    
Physical entities
Compartments Species
default Ca_ex s5 TimeT
s13 Shear Stress  
Cell Ca_c Ca_B IP3
s7 s8 s9
s10 s11  
ER Ca_s    
Global parameters
R_T k1 k2 k3
k4 k5 k6 k7
K1 K2 K3 K4
K5 K_hi k_CICR K_CICR
k_CCE B_T dot_Vp dot_Vex
dot_Vhi dot_q_inpass Cao tau_I
tau_II half fracK  
Reactions (10)
 
 re1 [Ca_B] → [Ca_c];   {Ca_c} , {Ca_B} , {Ca_c} , {Ca_B}
 
 re4 [s5] → [Ca_s];   {Ca_ex} , {Ca_s} , {Ca_ex} , {Ca_s} , {Ca_ex}
 
 re5 [s7] → [IP3];   {Ca_c} , {TimeT} , {Shear Stress} , {TimeT} , {Ca_c} , {TimeT} , {Ca_c}
 
 re6 [IP3] → [s8];   {IP3} , {IP3}
 
 re7 [Ca_s] → [Ca_c];   {IP3} , {Ca_c} , {IP3} , {Ca_s} , {Ca_c} , {IP3} , {Ca_s}
 
 re8 [Ca_c] → [s9];   {Ca_c} , {Ca_c}
 
 re9 [Ca_c] → [s10];   {Ca_c} , {Ca_c}
 
 re10 [s11] → [Ca_c];  
 
 re11 [s13] → [TimeT];  
 
 re12 [Ca_c] → [s9];   {Ca_c} , {Ca_c}
 
  Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 Ca_ex
Compartment: default
Initial amount: 1500000.0  (Units: substance)
 
 s5
Compartment: default
Initial amount: 0.0  (Units: substance)
 
 TimeT
Compartment: default
Initial amount: 0.0  (Units: substance)
 
 s13
Compartment: default
Initial amount: 0.0  (Units: substance)
 
 Shear Stress
Compartment: default
Initial amount: 0.0  (Units: substance)
 
 Cell Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 Ca_c
Compartment: Cell
Initial amount: 117.2  (Units: substance)
 
 Ca_B
Compartment: Cell
Initial amount: 3870.0  (Units: substance)
 
 IP3
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 s7
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 s8
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 s9
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 s10
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 s11
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 ER Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 Ca_s
Compartment: ER
Initial amount: 2830000.0  (Units: substance)
 
Global Parameters (27)
 
   R_T
Value: 44000.0   (Units: dimensionless)
Constant
 
   k1
Value: 6.0E-4   (Units: sub_sec)
Constant
 
   k2
Value: 1.0   (Units: inv_sec)
Constant
 
   k3
Value: 3.32   (Units: inv_sec)
Constant
 
   k4
Value: 2500.0   (Units: sub_sec)
Constant
 
   k5
Value: 5.0E-11   (Units: inv_sec_sub)
Constant
 
   k6
Value: 0.05   (Units: inv_sec_sub)
Constant
 
   k7
Value: 150.0   (Units: inv_sec)
Constant
 
   K1
Constant
 
   K2
Value: 200.0   (Units: substance)
Constant
 
   K3
Value: 150.0   (Units: substance)
Constant
 
   K4
Value: 80.0   (Units: substance)
Constant
 
   K5
Value: 321.0   (Units: substance)
Constant
 
   K_hi
Value: 380.0   (Units: substance)
Constant
 
   k_CICR
Value: 1.0   (Units: dimensionless)
Constant
 
   K_CICR
Constant
 
   k_CCE
Constant
 
   B_T
Value: 120000.0   (Units: substance)
Constant
 
   dot_Vp
Value: 815.0   (Units: sub_sec)
Constant
 
   dot_Vex
Value: 9165.0   (Units: sub_sec)
Constant
 
   dot_Vhi
Value: 2380.0   (Units: sub_sec)
Constant
 
   dot_q_inpass
Value: 3000.0   (Units: sub_sec)
Constant
 
   Cao
Value: 100.0   (Units: substance)
Constant
 
   tau_I
Value: 66.0   (Units: substance)
Constant
 
   tau_II
Value: 0.01   (Units: substance)
Constant
 
   half
Value: 0.5   (Units: dimensionless)
Constant
 
   fracK
Value: 7071067.81   (Units: substance)
Constant
 
re11 (1)
 
   unisec
Value: 1.0   (Units: sub_sec)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000464

Curator's comment: (updated: 19 Aug 2013 13:55:30 BST)

The paper describes four sub-models and an integrated version of the four sub-models. This model corresponds to Model 1 - Shear stress induced calcium influx and eNOS activation. Figure 3A of the paper is reproduced here using Copasi 4.10 (Build 55).

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