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BIOMD0000000465 - Koo2013 - Shear stress induced AKT and eNOS phosphorylation - Model 2

 

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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: Koh, G., H. F. C. Teong, M...
Submitter: Andrew Koo
Submission ID: MODEL1302180004
Submission Date: 18 Feb 2013 20:26:10 UTC
Last Modification Date: 07 Apr 2014 02:59:25 UTC
Creation Date: 19 Aug 2013 13:35:11 UTC
Encoders:  Nick Juty
   Vijayalakshmi Chelliah
   Andrew Koo
set #1
bqbiol:isVersionOf Gene Ontology response to fluid shear stress
set #2
bqbiol:isVersionOf Reactome REACT_12443.3
set #3
bqbiol:hasTaxon Taxonomy Homo sapiens
set #4
bqbiol:isVersionOf Gene Ontology nitric oxide biosynthetic process
Gene Ontology nitric oxide production involved in inflammatory response
Notes
Model
Publication ID: 23708369 Submission Date: 18 Feb 2013 20:26:10 UTC Last Modification Date: 07 Apr 2014 02:59:25 UTC Creation Date: 19 Aug 2013 13:35:11 UTC
Mathematical expressions
Reactions
re57 re58 re59 re60
re61 re62 re63 re64
re65 re66 re67 re68
Physical entities
Compartments Species
default Shear Stress    
Cell PDK1 PP2A AKT
PI3P PTEN PIP2
p-PI3K s3 PI3K
Time PDK2 PDK1_cyto
p-AKT:PI3P pp-AKT:PI3P AKT:PI3P
     
Reactions (12)
 
 re57 [PI3K] ↔ [p-PI3K];   {Time} , {Shear Stress} , {Time}
 
 re58 [PIP2] → [PI3P];   {p-PI3K} , {PIP2} , {p-PI3K}
 
 re59 [PI3P] → [PIP2];   {PTEN} , {PI3P} , {PTEN}
 
 re60 [PI3P] + [AKT] ↔ [AKT:PI3P];   {PI3P} , {AKT} , {AKT:PI3P}
 
 re61 [AKT:PI3P] → [p-AKT:PI3P];   {PDK1} , {AKT:PI3P} , {PDK1}
 
 re62 [p-AKT:PI3P] → [pp-AKT:PI3P];   {PDK2} , {p-AKT:PI3P} , {PDK2}
 
 re63 [p-AKT:PI3P] → [AKT:PI3P];   {PP2A} , {p-AKT:PI3P} , {PP2A}
 
 re64 [pp-AKT:PI3P] → [p-AKT:PI3P];   {PP2A} , {pp-AKT:PI3P} , {PP2A}
 
 re65 [pp-AKT:PI3P] → [PI3P] + [AKT];   {PP2A} , {pp-AKT:PI3P} , {PP2A}
 
 re66 [PDK1_cyto] → [PDK1];   {PI3P} , {PI3P} , {PDK1_cyto}
 
 re67 [PDK1] → [PDK1_cyto];   {PDK1}
 
 re68 [s3] → [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)
 
 PDK1
Compartment: Cell
Initial amount: 0.246  (Units: substance)
 
 PP2A
Compartment: Cell
Initial amount: 150.0  (Units: substance)
 
 AKT
Compartment: Cell
Initial amount: 167.616  (Units: substance)
 
 PI3P
Compartment: Cell
Initial amount: 0.345  (Units: substance)
 
 PTEN
Compartment: Cell
Initial amount: 0.1  (Units: substance)
 
 PIP2
Compartment: Cell
Initial amount: 6967.271  (Units: substance)
 
 p-PI3K
Compartment: Cell
Initial amount: 0.03  (Units: substance)
 
 s3
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 PI3K
Compartment: Cell
Initial amount: 99.97  (Units: substance)
 
 Time
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 PDK2
Compartment: Cell
Initial amount: 3.0  (Units: substance)
 
 PDK1_cyto
Compartment: Cell
Initial amount: 999.754  (Units: substance)
 
 p-AKT:PI3P
Compartment: Cell
Initial amount: 1.457  (Units: substance)
 
 pp-AKT:PI3P
Compartment: Cell
Initial amount: 1.723  (Units: substance)
 
 AKT:PI3P
Compartment: Cell
Initial amount: 29.203  (Units: substance)
 
re57 (4)
 
   normal
Value: 0.907   (Units: sub_sec)
Constant
 
   unity
Value: 1.0   (Units: dimensionless)
Constant
 
   unimol
Value: 1.0   (Units: substance)
Constant
 
   tf
Value: 15.0   (Units: substance)
Constant
 
re58 (2)
 
   k2
Value: 0.2   (Units: inv_sec)
Constant
 
   Km2
Value: 6170.0   (Units: substance)
Constant
 
re59 (2)
 
   k3
Value: 7.5   (Units: inv_sec)
Constant
 
   Km3
Value: 80.9   (Units: substance)
Constant
 
re60 (2)
 
   k4
Value: 0.045   (Units: inv_sec_sub)
Constant
 
   kr4
Value: 0.089   (Units: inv_sec)
Constant
 
re61 (2)
 
   k8
Value: 20.0   (Units: inv_sec)
Constant
 
   Km8
Value: 80000.0   (Units: substance)
Constant
 
re62 (2)
 
   k10
Value: 20.0   (Units: inv_sec)
Constant
 
   Km10
Value: 80000.0   (Units: substance)
Constant
 
re63 (2)
 
   k7
Value: 0.037   (Units: inv_sec)
Constant
 
   Km7
Value: 8800.0   (Units: substance)
Constant
 
re64 (2)
 
   k9
Value: 0.04   (Units: inv_sec)
Constant
 
   Km9
Value: 48000.0   (Units: substance)
Constant
 
re65 (2)
 
   k11
Value: 0.163   (Units: inv_sec)
Constant
 
   Km11
Value: 48000.0   (Units: substance)
Constant
 
re66 (1)
 
   k5
Value: 7.0E-4   (Units: inv_sec_sub)
Constant
 
re67 (1)
 
   k6
Value: 0.98   (Units: inv_sec)
Constant
 
re68 (1)
 
   unitime
Value: 1.0   (Units: sub_sec)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000465

Curator's comment: (updated: 19 Aug 2013 13:58:36 BST)

The paper describes four sub-models and an integrated version of the four sub-models. This model corresponds to Model 2 - Shear stress induced AKT and eNOS phosphorylation. Figure 3B of the paper is reproduced here using Copasi 4.10 (Build 55).

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