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BIOMD0000000467 - Koo2013 - Shear stress induced NO production - Model 4

 

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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: MODEL1302180006
Submission Date: 18 Feb 2013 20:30:04 UTC
Last Modification Date: 07 Apr 2014 03:05:10 UTC
Creation Date: 19 Aug 2013 13:37:06 UTC
Encoders:  Nick Juty
   Vijayalakshmi Chelliah
   Andrew Koo
set #1
bqbiol:isVersionOf Gene Ontology nitric oxide production involved in inflammatory response
Gene Ontology nitric oxide biosynthetic process
set #2
bqbiol:isVersionOf Reactome REACT_12443.3
set #3
bqbiol:hasTaxon Taxonomy Homo sapiens
Notes
Model
Publication ID: 23708369 Submission Date: 18 Feb 2013 20:30:04 UTC Last Modification Date: 07 Apr 2014 03:05:10 UTC Creation Date: 19 Aug 2013 13:37:06 UTC
Mathematical expressions
Reactions
re37 re38 re41 re42
re50 re51 re52 re53
re54 re55 re56 re69
re70 re71 re72 re131
re132 re133 re134 re135
re136 re137 re138 re139
Physical entities
Compartments Species
default      
Cell Ca_c pp-AKT:PI3P eNOS-CaM-Ca4
CaM-Ca4 CaM-Ca2 eNOS-CaM-Ca2
eNOS-Cav-1 Calmodulin Hsp90
Hsp90-eNOS-CaM-Ca4 Hsp90-p-eNOS-CaM-Ca4 Hsp90-eNOS-CaM-Ca2
Hsp90-p-eNOS-CaM-Ca2 L-Arg NO
Hsp90-p-eNOS Hsp90-eNOS sa49_degraded
s117 s118  
Global parameters
k1 k1r k2 k2r
k4 k3 k3r k10
Km10 Km10r V10r k6
k7 kD k5  
Reactions (24)
 
 re37 [eNOS-Cav-1] + [CaM-Ca4] → [eNOS-CaM-Ca4];   {CaM-Ca4} , {eNOS-Cav-1}
 
 re38 [CaM-Ca2] + [eNOS-Cav-1] ↔ [eNOS-CaM-Ca2];   {eNOS-Cav-1} , {CaM-Ca2} , {eNOS-CaM-Ca2}
 
 re41 [Calmodulin] ↔ [CaM-Ca2];   {Ca_c} , {Ca_c} , {Calmodulin} , {CaM-Ca2}
 
 re42 [CaM-Ca2] → [CaM-Ca4];   {Ca_c} , {Ca_c} , {CaM-Ca2} , {CaM-Ca4}
 
 re50 [eNOS-CaM-Ca4] ↔ [eNOS-CaM-Ca2];   {Ca_c} , {eNOS-CaM-Ca4} , {Ca_c} , {eNOS-CaM-Ca2}
 
 re51 [eNOS-CaM-Ca4] + [Hsp90] → [Hsp90-eNOS-CaM-Ca4];   {eNOS-CaM-Ca4} , {Hsp90}
 
 re52 [Hsp90-eNOS-CaM-Ca4] ↔ [Hsp90-eNOS-CaM-Ca2];   {Ca_c} , {Hsp90-eNOS-CaM-Ca4} , {Ca_c} , {Hsp90-eNOS-CaM-Ca2}
 
 re53 [Hsp90-eNOS-CaM-Ca2] → [eNOS-CaM-Ca2] + [Hsp90];   {Hsp90-eNOS-CaM-Ca2}
 
 re54 [Hsp90-p-eNOS-CaM-Ca4] ↔ [Hsp90-p-eNOS-CaM-Ca2];   {Ca_c} , {Hsp90-p-eNOS-CaM-Ca4} , {Ca_c} , {Hsp90-p-eNOS-CaM-Ca2}
 
 re55 [Hsp90-eNOS-CaM-Ca4] ↔ [Hsp90-p-eNOS-CaM-Ca4];   {pp-AKT:PI3P} , {Hsp90-eNOS-CaM-Ca4} , {pp-AKT:PI3P} , {Hsp90-p-eNOS-CaM-Ca4}
 
 re56 [Hsp90-eNOS-CaM-Ca2] ↔ [Hsp90-p-eNOS-CaM-Ca2];   {pp-AKT:PI3P} , {Hsp90-eNOS-CaM-Ca2} , {pp-AKT:PI3P} , {Hsp90-p-eNOS-CaM-Ca2}
 
 re69 [L-Arg] → [NO];   {eNOS-CaM-Ca4} , {eNOS-CaM-Ca2} , {Hsp90-eNOS-CaM-Ca2} , {Hsp90-p-eNOS-CaM-Ca2} , {Hsp90-eNOS-CaM-Ca4} , {Hsp90-p-eNOS-CaM-Ca4} , {Hsp90-p-eNOS} , {eNOS-CaM-Ca4} , {Hsp90-eNOS-CaM-Ca4} , {Hsp90-p-eNOS-CaM-Ca2} , {Hsp90-p-eNOS} , {Hsp90-p-eNOS-CaM-Ca4}
 
 re70 [Hsp90-p-eNOS] → [Hsp90-eNOS];   {Hsp90-p-eNOS}
 
 re71 [Hsp90-eNOS] → [eNOS-Cav-1] + [Hsp90];   {Hsp90-eNOS}
 
 re72 [Hsp90-p-eNOS-CaM-Ca2] ↔ [Hsp90-p-eNOS] + [CaM-Ca2];   {Hsp90-p-eNOS-CaM-Ca2} , {Hsp90-p-eNOS} , {CaM-Ca2}
 
 re131 [eNOS-Cav-1] → [sa49_degraded];   {eNOS-Cav-1}
 
 re132 [eNOS-CaM-Ca4] → [s117] + [CaM-Ca4];   {eNOS-CaM-Ca4}
 
 re133 [eNOS-CaM-Ca2] → [s117] + [CaM-Ca2];   {eNOS-CaM-Ca2}
 
 re134 [Hsp90-eNOS] → [Hsp90] + [s118];   {Hsp90-eNOS}
 
 re135 [Hsp90-p-eNOS] → [s118] + [Hsp90];   {Hsp90-p-eNOS}
 
 re136 [Hsp90-eNOS-CaM-Ca2] → [Hsp90] + [CaM-Ca2];   {Hsp90-eNOS-CaM-Ca2}
 
 re137 [Hsp90-p-eNOS-CaM-Ca2] → [Hsp90] + [CaM-Ca2];   {Hsp90-p-eNOS-CaM-Ca2}
 
 re138 [Hsp90-eNOS-CaM-Ca4] → [Hsp90] + [CaM-Ca4];   {Hsp90-eNOS-CaM-Ca4}
 
 re139 [Hsp90-p-eNOS-CaM-Ca4] → [Hsp90] + [CaM-Ca4];   {Hsp90-p-eNOS-CaM-Ca4}
 
   Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 Cell Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 Ca_c
Compartment: Cell
Initial amount: 117.2  (Units: substance)
Constant
 
 pp-AKT:PI3P
Compartment: Cell
Initial amount: 1.723  (Units: substance)
 
 eNOS-CaM-Ca4
Compartment: Cell
Initial amount: 0.0415  (Units: substance)
 
 CaM-Ca4
Compartment: Cell
Initial amount: 2.827  (Units: substance)
 
 CaM-Ca2
Compartment: Cell
Initial amount: 347.52  (Units: substance)
 
 eNOS-CaM-Ca2
Compartment: Cell
Initial amount: 2.12  (Units: substance)
 
 eNOS-Cav-1
Compartment: Cell
Initial amount: 34.98  (Units: substance)
 
 Calmodulin
Compartment: Cell
Initial amount: 7635.36  (Units: substance)
 
 Hsp90
Compartment: Cell
Initial amount: 199987.0  (Units: substance)
 
 Hsp90-eNOS-CaM-Ca4
Compartment: Cell
Initial amount: 1.037  (Units: substance)
 
 Hsp90-p-eNOS-CaM-Ca4
Compartment: Cell
Initial amount: 0.0089  (Units: substance)
 
 Hsp90-eNOS-CaM-Ca2
Compartment: Cell
Initial amount: 10.98  (Units: substance)
 
 Hsp90-p-eNOS-CaM-Ca2
Compartment: Cell
Initial amount: 0.106  (Units: substance)
 
 L-Arg
Compartment: Cell
Initial amount: 500000.0  (Units: substance)
 
 NO
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 Hsp90-p-eNOS
Compartment: Cell
Initial amount: 0.643  (Units: substance)
 
 Hsp90-eNOS
Compartment: Cell
Initial amount: 0.083  (Units: substance)
 
 sa49_degraded
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 s117
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 s118
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
Global Parameters (15)
 
   k1
Value: 0.004   (Units: inv_sec_sub)
Constant
 
   k1r
Value: 10.3   (Units: inv_sec)
Constant
 
   k2
Value: 0.08   (Units: inv_sec_sub)
Constant
 
   k2r
Value: 1152.0   (Units: inv_sec)
Constant
 
   k4
Value: 0.015   (Units: inv_sec_sub)
Constant
 
   k3
Value: 1.5E-4   (Units: inv_sec_sub)
Constant
 
   k3r
Value: 1.5   (Units: inv_sec)
Constant
 
   k10
Value: 0.1   (Units: inv_sec)
Constant
 
   Km10
Value: 5.0   (Units: substance)
Constant
 
   Km10r
Value: 20.0   (Units: substance)
Constant
 
   V10r
Value: 4.0   (Units: sub_sec)
Constant
 
   k6
Value: 0.002   (Units: inv_sec_sub)
Constant
 
   k7
Value: 1.5   (Units: inv_sec)
Constant
 
   kD
Value: 9.45E-5   (Units: inv_sec)
Constant
 
   k5
Value: 115.2   (Units: inv_sec)
Constant
 
re69 (3)
 
   kCaM
Value: 17.0   (Units: inv_sec)
Constant
 
   kp
Value: 5.0   (Units: inv_sec)
Constant
 
   kpCaM
Value: 17.0   (Units: inv_sec)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000467

Curator's comment: (updated: 19 Aug 2013 14:10:20 BST)

The paper describes four sub-models and an integrated version of the four sub-models. This model corresponds to Model 4 - Shear stress induced NO production. There is no Figure corresponding to this sub-model in the paper. Refer to the integrated model (MODEL1308190000).

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