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BIOMD0000000466 - Koo2013 - Shear stress induced eNOS expression - Model 3

 

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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: N/A
Submitter: Andrew Koo
Submission ID: MODEL1302180005
Submission Date: 18 Feb 2013 20:27:51 UTC
Last Modification Date: 07 Apr 2014 03:00:36 UTC
Creation Date: 19 Aug 2013 13:36:07 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:isVersionOf Gene Ontology response to fluid shear stress
set #3
bqbiol:isVersionOf Reactome REACT_12443.3
set #4
bqbiol:hasTaxon Taxonomy Homo sapiens
Notes
Model
Publication ID: 23708369 Submission Date: 18 Feb 2013 20:27:51 UTC Last Modification Date: 07 Apr 2014 03:00:36 UTC Creation Date: 19 Aug 2013 13:36:07 UTC
Mathematical expressions
Reactions
re102 re103 re104 re105
re106 re107 re108 re109
re110 re111 re112 re113
re114 re115 re116 re117
re118 re119 re120 re121
re122 re123 re124 re125
re126 re127 re128 re129
Physical entities
Compartments Species
default Shear Stress    
Cell s35 s37 pre_time
Time pp-JNKK pp-JNK
KLF2 eNOS-Cav-1 Shc
p-Src p-FAK Src
FAK JNKK MEKK1
p-Shc JNK p-JNKK
p-MEKK1 Ras:GTP Ras:GDP
p-JNK KLF2 eNOS
p-FAK:Shc Grb2:Sos p-FAK:p-Shc
p-FAK:p-Shc:Grb2:Sos p-Shc:Grb2:Sos  
nucleus AP-1 aAP-1 eNOS
eNOS    
Reactions (28)
 
 re102 [FAK] ↔ [p-FAK];   {Time} , {Shear Stress} , {Time}
 
 re103 [Src] ↔ [p-Src];   {Time} , {Shear Stress} , {Time}
 
 re104 [Shc] + [p-FAK] ↔ [p-FAK:Shc];   {Shc} , {p-FAK} , {p-FAK:Shc}
 
 re105 [p-FAK:Shc] ↔ [p-FAK:p-Shc];   {p-Src} , {p-FAK:Shc} , {p-Src} , {p-FAK:p-Shc}
 
 re106 [p-FAK:p-Shc] + [Grb2:Sos] ↔ [p-FAK:p-Shc:Grb2:Sos];   {Grb2:Sos} , {p-FAK:p-Shc} , {p-FAK:p-Shc:Grb2:Sos}
 
 re107 [p-FAK:p-Shc:Grb2:Sos] ↔ [p-Shc:Grb2:Sos] + [p-FAK];   {p-FAK:p-Shc:Grb2:Sos} , {p-FAK} , {p-Shc:Grb2:Sos}
 
 re108 [p-Shc] → [Shc];   {p-Shc}
 
 re109 [p-Shc:Grb2:Sos] → [p-Shc] + [Grb2:Sos];   {p-Shc:Grb2:Sos}
 
 re110 [eNOS] → [eNOS];   {eNOS}
 
 re111 [eNOS] → [eNOS];   {aAP-1} , {KLF2} , {aAP-1} , {KLF2}
 
 re112 [Ras:GDP] → [Ras:GTP];   {p-Shc:Grb2:Sos} , {p-Shc:Grb2:Sos} , {Ras:GDP}
 
 re113 [Ras:GTP] → [Ras:GDP];   {Ras:GTP}
 
 re114 [MEKK1] → [p-MEKK1];   {Ras:GTP} , {Ras:GTP} , {MEKK1}
 
 re115 [p-MEKK1] → [MEKK1];   {p-MEKK1}
 
 re116 [JNKK] → [p-JNKK];   {p-MEKK1} , {p-MEKK1} , {JNKK}
 
 re117 [p-JNKK] → [JNKK];   {p-JNKK}
 
 re118 [JNK] → [p-JNK];   {pp-JNKK} , {JNK} , {pp-JNKK}
 
 re119 [p-JNK] → [JNK];   {p-JNK}
 
 re120 [eNOS] → [s35];   {eNOS}
 
 re121 [s37] → [eNOS-Cav-1];   {eNOS} , {eNOS}
 
 re122 [pre_time] → [Time];  
 
 re123 [pp-JNKK] → [p-JNKK];   {pp-JNKK}
 
 re124 [p-JNKK] → [pp-JNKK];   {p-MEKK1} , {p-JNKK} , {p-MEKK1}
 
 re125 [pp-JNK] → [p-JNK];   {pp-JNK}
 
 re126 [p-JNK] → [pp-JNK];   {pp-JNKK} , {p-JNK} , {pp-JNKK}
 
 re127 [AP-1] → [aAP-1];   {pp-JNK} , {pp-JNK} , {AP-1}
 
 re128 [aAP-1] → [AP-1];   {aAP-1}
 
 re129 [KLF2] → [KLF2];   {Time} , {Time}
 
   Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 Shear Stress
Compartment: default
Initial amount: 0.0  (Units: substance)
 
 Cell Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 s35
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 s37
Compartment: Cell
Initial amount: 10000.0  (Units: substance)
 
 pre_time
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 Time
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 pp-JNKK
Compartment: Cell
Initial amount: 0.006  (Units: substance)
 
 pp-JNK
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 KLF2
Compartment: Cell
Initial amount: 10.0  (Units: substance)
 
 eNOS-Cav-1
Compartment: Cell
Initial amount: 34.98  (Units: substance)
 
 Shc
Compartment: Cell
Initial amount: 819.25  (Units: substance)
 
 p-Src
Compartment: Cell
Initial amount: 18.0  (Units: substance)
 
 p-FAK
Compartment: Cell
Initial amount: 0.605  (Units: substance)
 
 Src
Compartment: Cell
Initial amount: 72.0  (Units: substance)
 
 FAK
Compartment: Cell
Initial amount: 57.0  (Units: substance)
 
 JNKK
Compartment: Cell
Initial amount: 299.706  (Units: substance)
 
 MEKK1
Compartment: Cell
Initial amount: 98.514  (Units: substance)
 
 p-Shc
Compartment: Cell
Initial amount: 157.162  (Units: substance)
 
 JNK
Compartment: Cell
Initial amount: 299.997  (Units: substance)
 
 p-JNKK
Compartment: Cell
Initial amount: 0.288  (Units: substance)
 
 p-MEKK1
Compartment: Cell
Initial amount: 1.486  (Units: substance)
 
 Ras:GTP
Compartment: Cell
Initial amount: 0.616  (Units: substance)
 
 Ras:GDP
Compartment: Cell
Initial amount: 119.384  (Units: substance)
 
 p-JNK
Compartment: Cell
Initial amount: 0.003  (Units: substance)
 
 KLF2
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 eNOS
Compartment: Cell
Initial amount: 3.214  (Units: substance)
 
 p-FAK:Shc
Compartment: Cell
Initial amount: 0.857  (Units: substance)
 
 Grb2:Sos
Compartment: Cell
Initial amount: 3.23  (Units: substance)
 
 p-FAK:p-Shc
Compartment: Cell
Initial amount: 15.962  (Units: substance)
 
 p-FAK:p-Shc:Grb2:Sos
Compartment: Cell
Initial amount: 5.577  (Units: substance)
 
 p-Shc:Grb2:Sos
Compartment: Cell
Initial amount: 1.193  (Units: substance)
 
 nucleus Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 AP-1
Compartment: nucleus
Initial amount: 50.0  (Units: substance)
 
 aAP-1
Compartment: nucleus
Initial amount: 0.0  (Units: substance)
 
 eNOS
Compartment: nucleus
Initial amount: 0.0  (Units: substance)
 
 eNOS
Compartment: nucleus
Initial amount: 0.09  (Units: substance)
 
re102 (5)
 
   normal
Value: 4.0   (Units: nM_inv_s)
Constant
 
   tf
Value: 60.0   (Units: substance)
Constant
 
   unity
Value: 1.0   (Units: dimensionless)
Constant
 
   unimol
Value: 1.0   (Units: substance)
Constant
 
   tiny_num
Value: 1.0E-6   (Units: substance)
Constant
 
re103 (4)
 
   normal
Value: 0.026   (Units: nM_inv_s)
Constant
 
   tf
Value: 540.0   (Units: substance)
Constant
 
   unity
Value: 1.0   (Units: dimensionless)
Constant
 
   unimol
Value: 1.0   (Units: substance)
Constant
 
re104 (2)
 
   k3
Value: 0.1   (Units: inv_nM_s)
Constant
 
   kr3
Value: 1.0   (Units: inv_sec)
Constant
 
re105 (2)
 
   k4
Value: 8.33   (Units: inv_nM_s)
Constant
 
   kr4
Value: 5.0   (Units: inv_sec)
Constant
 
re106 (2)
 
   k5
Value: 60.0   (Units: inv_nM_s)
Constant
 
   kr5
Value: 546.0   (Units: inv_sec)
Constant
 
re107 (2)
 
   k6
Value: 2040.0   (Units: inv_sec)
Constant
 
   kr6
Value: 15700.0   (Units: inv_nM_s)
Constant
 
re108 (2)
 
   V8
Value: 154.0   (Units: nM_inv_s)
Constant
 
   Km8
Value: 340.0   (Units: substance)
Constant
 
re109 (1)
 
   k7
Value: 40.8   (Units: inv_sec)
Constant
 
re110 (1)
 
   k25
Value: 0.001   (Units: inv_sec)
Constant
 
re111 (2)
 
   k24t1
Value: 1.2E-4   (Units: nM_inv_s)
Constant
 
   k24t2
Value: 9.0E-6   (Units: nM_inv_s)
Constant
 
re112 (2)
 
   k9
Value: 0.222   (Units: inv_sec)
Constant
 
   Km9
Value: 0.181   (Units: substance)
Constant
 
re113 (2)
 
   V10
Value: 0.289   (Units: nM_inv_s)
Constant
 
   Km10
Value: 0.0571   (Units: substance)
Constant
 
re114 (2)
 
   k11
Value: 0.035   (Units: inv_sec)
Constant
 
   Km11
Value: 10.0   (Units: substance)
Constant
 
re115 (2)
 
   Km12
Value: 8.0   (Units: substance)
Constant
 
   V12
Value: 0.125   (Units: nM_inv_s)
Constant
 
re116 (2)
 
   k13
Value: 0.005   (Units: inv_sec)
Constant
 
   Km13
Value: 15.0   (Units: substance)
Constant
 
re117 (2)
 
   Km14
Value: 15.0   (Units: substance)
Constant
 
   V14
Value: 0.375   (Units: nM_inv_s)
Constant
 
re118 (2)
 
   k17
Value: 0.002   (Units: inv_sec)
Constant
 
   Km17
Value: 30.0   (Units: substance)
Constant
 
re119 (2)
 
   Km18
Value: 15.0   (Units: substance)
Constant
 
   V18
Value: 0.05   (Units: nM_inv_s)
Constant
 
re120 (1)
 
   k26
Value: 2.8E-5   (Units: inv_sec)
Constant
 
re121 (2)
 
   V27
Value: 0.02824   (Units: nM_inv_s)
Constant
 
   Km27
Value: 16.0   (Units: substance)
Constant
 
re122 (1)
 
   unitime
Value: 1.0   (Units: nM_inv_s)
Constant
 
re123 (2)
 
   V16
Value: 0.375   (Units: nM_inv_s)
Constant
 
   Km16
Value: 15.0   (Units: substance)
Constant
 
re124 (2)
 
   k15
Value: 0.005   (Units: inv_sec)
Constant
 
   Km15
Value: 15.0   (Units: substance)
Constant
 
re125 (2)
 
   V20
Value: 0.05   (Units: nM_inv_s)
Constant
 
   Km20
Value: 15.0   (Units: substance)
Constant
 
re126 (2)
 
   k19
Value: 0.002   (Units: inv_sec)
Constant
 
   Km19
Value: 30.0   (Units: substance)
Constant
 
re127 (2)
 
   Km21
Value: 25.0   (Units: substance)
Constant
 
   k21
Value: 4.0E-5   (Units: inv_sec)
Constant
 
re128 (2)
 
   Km22
Value: 5.0   (Units: substance)
Constant
 
   V22
Value: 0.002   (Units: nM_inv_s)
Constant
 
re129 (5)
 
   tau
Value: 0.55   (Units: dimensionless)
Constant
 
   tc
Value: 3600.0   (Units: substance)
Constant
 
   uc
Value: 3600.0   (Units: dimensionless)
Constant
 
   delay
Value: 5.0   (Units: dimensionless)
Constant
 
   unity
Value: 20.0   (Units: nM_inv_s)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000466

Curator's comment: (updated: 19 Aug 2013 13:57:38 BST)

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

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