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BIOMD0000000468 - Koo2013 - Integrated shear stress induced NO production model

 

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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: BIOMD0000000468.origin
Submitter: Vijayalakshmi Chelliah
Submission ID: MODEL1308190000
Submission Date: 19 Aug 2013 12:44:22 UTC
Last Modification Date: 22 May 2014 18:39:16 UTC
Creation Date: 19 Aug 2013 14:38:04 UTC
Encoders:  Nick Juty
   Vijayalakshmi Chelliah
   Andrew Koo
set #1
bqmodel:isDerivedFrom BioModels Database Koo2013 - Shear stress induced NO production - Model 4
BioModels Database Koo2013 - Shear stress induced eNOS expression - Model 3
BioModels Database Koo2013 - Shear stress induced AKT and eNOS phosphorylation - Model 2
BioModels Database Koo2013 - Shear stress induced calcium influx and eNOS activation - Model 1
set #2
bqbiol:isVersionOf Gene Ontology nitric oxide production involved in inflammatory response
Gene Ontology nitric oxide biosynthetic process
set #3
bqbiol:hasTaxon Taxonomy Homo sapiens
Notes
Model
Publication ID: 23708369 Submission Date: 19 Aug 2013 12:44:22 UTC Last Modification Date: 22 May 2014 18:39:16 UTC Creation Date: 19 Aug 2013 14:38:04 UTC
Mathematical expressions
Reactions
re1 re4 re5 re6
re7 re8 re9 re10
re11 re12 re37 re38
re41 re42 re50 re51
re52 re53 re54 re55
re56 re57 re58 re59
re60 re61 re62 re63
re64 re65 re66 re67
re68 re69 re70 re71
re72 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 re131 re132 re133
re134 re135 re136 re137
re138 re139    
Physical entities
Compartments Species
default Ca_ex s5 Shear Stress
Cell Ca_c Ca_B IP3
s7 s8 s9
s10 s11 TimeT
s13 PDK1 PP2A
AKT PI3P PTEN
PIP2 p-PI3K s3
PI3K Time PDK2
PDK1_cyto p-AKT:PI3P pp-AKT:PI3P
AKT:PI3P s35 s37
pre_time Time pp-JNKK
pp-JNK eNOS-CaM-Ca4 CaM-Ca4
CaM-Ca2 KLF2 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 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 sa49_degraded
s117 s118  
ER Ca_s    
nucleus AP-1 aAP-1 eNOS
eNOS    
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 Vc_Vs dot_Vp
dot_Vex dot_Vhi dot_q_inpass dot_q_instim
Cao tau_I tau_II half
fracK alp gam k8
k11 k12 k13 k14
k15 k16 k17 k18
kp Kmp Kmdp Vdp
k90 kr90 kDD  
Reactions (74)
 
 re1 [Ca_B] → [Ca_c];   {Ca_c} , {Ca_B}
 
 re4 [s5] → [Ca_s];   {Ca_ex} , {Ca_s} , {Ca_ex}
 
 re5 [s7] → [IP3];   {Ca_c} , {TimeT} , {Shear Stress} , {TimeT} , {Ca_c}
 
 re6 [IP3] → [s8];   {IP3}
 
 re7 [Ca_s] → [Ca_c];   {IP3} , {Ca_c} , {IP3} , {Ca_s}
 
 re8 [Ca_c] → [s9];   {Ca_c}
 
 re9 [Ca_c] → [s10];   {Ca_c}
 
 re10 [s11] → [Ca_c];  
 
 re11 [s13] → [TimeT];  
 
 re12 [Ca_c] → [s9];   {Ca_c}
 
 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}
 
 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];  
 
 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}
 
 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}
 
 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)
 
 Ca_ex
Compartment: default
Initial amount: 1500000.0  (Units: substance)
 
 s5
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)
 
 TimeT
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 s13
Compartment: Cell
Initial amount: 0.0  (Units: substance)
 
 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)
 
 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)
 
 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)
 
 KLF2
Compartment: Cell
Initial amount: 10.0  (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)
 
 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)
 
 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)
 
 ER Spatial dimensions: 3.0  Compartment size: 1.0  (Units: volume)
 
 Ca_s
Compartment: ER
Initial amount: 2830000.0  (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)
 
Global Parameters (47)
 
   R_T
Value: 44000.0   (Units: dimensionless)
Constant
 
   k1
Value: 0.0012   (Units: sub_sec)
Constant
 
   k2
Value: 2.0   (Units: inv_sec)
Constant
 
   k3
Value: 6.64   (Units: inv_sec)
Constant
 
   k4
Value: 5000.0   (Units: sub_sec)
Constant
 
   k5
Value: 1.0E-10   (Units: inv_sec_sub)
Constant
 
   k6
Value: 0.1   (Units: inv_sec_sub)
Constant
 
   k7
Value: 300.0   (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
 
   Vc_Vs
Value: 3.5   (Units: dimensionless)
Constant
 
   dot_Vp
Value: 1630.0   (Units: sub_sec)
Constant
 
   dot_Vex
Value: 18330.0   (Units: sub_sec)
Constant
 
   dot_Vhi
Value: 4760.0   (Units: sub_sec)
Constant
 
   dot_q_inpass
Value: 6000.0   (Units: sub_sec)
Constant
 
   dot_q_instim
Value: 2500.0   (Units: sub_sec)
Constant
 
   Cao
Value: 100.0   (Units: substance)
Constant
 
   tau_I
Value: 33.0   (Units: substance)
Constant
 
   tau_II
Value: 0.005   (Units: substance)
Constant
 
   half
Value: 0.5   (Units: dimensionless)
Constant
 
   fracK
Value: 7071067.81   (Units: substance)
Constant
 
   alp
Value: 10.0   (Units: time)
Constant
 
   gam
Value: 0.1   (Units: time)
Constant
 
   k8
Value: 7.5E-5   (Units: time)
Constant
 
   k11
Value: 0.004   (Units: inv_sec_sub)
Constant
 
   k12
Value: 10.3   (Units: inv_sec)
Constant
 
   k13
Value: 0.08   (Units: inv_sec_sub)
Constant
 
   k14
Value: 1152.0   (Units: inv_sec)
Constant
 
   k15
Value: 0.015   (Units: inv_sec_sub)
Constant
 
   k16
Constant
 
   k17
Value: 1.5E-4   (Units: inv_sec_sub)
Constant
 
   k18
Value: 1.5   (Units: inv_sec)
Constant
 
   kp
Value: 0.1   (Units: inv_sec)
Constant
 
   Kmp
Value: 5.0   (Units: substance)
Constant
 
   Kmdp
Value: 20.0   (Units: substance)
Constant
 
   Vdp
Value: 4.0   (Units: sub_sec)
Constant
 
   k90
Value: 0.002   (Units: inv_sec_sub)
Constant
 
   kr90
Value: 1.5   (Units: inv_sec)
Constant
 
   kDD
Value: 9.45E-5   (Units: inv_sec)
Constant
 
re11 (1)
 
   unisec
Value: 1.0   (Units: sub_sec)
Constant
 
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)
 
   k58
Value: 0.2   (Units: inv_sec)
Constant
 
   Km58
Value: 6170.0   (Units: substance)
Constant
 
re59 (2)
 
   k59
Value: 7.5   (Units: inv_sec)
Constant
 
   Km59
Value: 80.9   (Units: substance)
Constant
 
re60 (2)
 
   k60
Value: 0.045   (Units: inv_sec_sub)
Constant
 
   kr60
Value: 0.089   (Units: inv_sec)
Constant
 
re61 (2)
 
   k61
Value: 20.0   (Units: inv_sec)
Constant
 
   Km61
Value: 80000.0   (Units: substance)
Constant
 
re62 (2)
 
   k62
Value: 20.0   (Units: inv_sec)
Constant
 
   Km62
Value: 80000.0   (Units: substance)
Constant
 
re63 (2)
 
   k63
Value: 0.037   (Units: inv_sec)
Constant
 
   Km63
Value: 8800.0   (Units: substance)
Constant
 
re64 (2)
 
   k64
Value: 0.04   (Units: inv_sec)
Constant
 
   Km64
Value: 48000.0   (Units: substance)
Constant
 
re65 (2)
 
   k65
Value: 0.163   (Units: inv_sec)
Constant
 
   Km65
Value: 48000.0   (Units: substance)
Constant
 
re66 (1)
 
   k66
Value: 7.0E-4   (Units: inv_sec_sub)
Constant
 
re67 (1)
 
   k67
Value: 0.98   (Units: inv_sec)
Constant
 
re68 (1)
 
   unitime
Value: 1.0   (Units: sub_sec)
Constant
 
re69 (3)
 
   K_cam_no
Value: 17.0   (Units: inv_sec)
Constant
 
   K_p_no
Value: 5.0   (Units: inv_sec)
Constant
 
   K_pcam_no
Value: 17.0   (Units: inv_sec)
Constant
 
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)
 
   k105
Value: 0.1   (Units: inv_nM_s)
Constant
 
   k_105
Value: 1.0   (Units: inv_sec)
Constant
 
re105 (2)
 
   kcat_src
Value: 8.33   (Units: inv_nM_s)
Constant
 
   k_6
Value: 5.0   (Units: inv_sec)
Constant
 
re106 (2)
 
   k107
Value: 60.0   (Units: inv_nM_s)
Constant
 
   k_107
Value: 546.0   (Units: inv_sec)
Constant
 
re107 (2)
 
   k108
Value: 2040.0   (Units: inv_sec)
Constant
 
   k_108
Value: 15700.0   (Units: inv_nM_s)
Constant
 
re108 (2)
 
   V10
Value: 154.0   (Units: nM_inv_s)
Constant
 
   K10
Value: 340.0   (Units: substance)
Constant
 
re109 (1)
 
   k9
Value: 40.8   (Units: inv_sec)
Constant
 
re110 (1)
 
   kT
Value: 0.001   (Units: inv_sec)
Constant
 
re111 (3)
 
   ktr1
Value: 1.2E-4   (Units: nM_inv_s)
Constant
 
   ktr1k2
Value: 9.0E-6   (Units: nM_inv_s)
Constant
 
   tr2
Value: 3.0E-6   (Units: nM_inv_s)
Constant
 
re112 (2)
 
   k111
Value: 0.222   (Units: inv_sec)
Constant
 
   K111
Value: 0.181   (Units: substance)
Constant
 
re113 (2)
 
   V12
Value: 0.289   (Units: nM_inv_s)
Constant
 
   K12
Value: 0.0571   (Units: substance)
Constant
 
re114 (2)
 
   k113
Value: 0.035   (Units: inv_sec)
Constant
 
   K113
Value: 10.0   (Units: substance)
Constant
 
re115 (2)
 
   K18
Value: 8.0   (Units: substance)
Constant
 
   V18
Value: 0.125   (Units: nM_inv_s)
Constant
 
re116 (2)
 
   k19
Value: 0.005   (Units: inv_sec)
Constant
 
   K19
Value: 15.0   (Units: substance)
Constant
 
re117 (2)
 
   K20
Value: 15.0   (Units: substance)
Constant
 
   V20
Value: 0.375   (Units: nM_inv_s)
Constant
 
re118 (2)
 
   k21
Value: 0.002   (Units: inv_sec)
Constant
 
   K21
Value: 30.0   (Units: substance)
Constant
 
re119 (2)
 
   K22
Value: 15.0   (Units: substance)
Constant
 
   V22
Value: 0.05   (Units: nM_inv_s)
Constant
 
re120 (1)
 
   kD
Value: 2.8E-5   (Units: inv_sec)
Constant
 
re121 (2)
 
   kP
Value: 0.02824   (Units: nM_inv_s)
Constant
 
   K30
Value: 16.0   (Units: substance)
Constant
 
re122 (1)
 
   unitime
Value: 1.0   (Units: nM_inv_s)
Constant
 
re123 (2)
 
   V37
Value: 0.375   (Units: nM_inv_s)
Constant
 
   K37
Value: 15.0   (Units: substance)
Constant
 
re124 (2)
 
   k38
Value: 0.005   (Units: inv_sec)
Constant
 
   K38
Value: 15.0   (Units: substance)
Constant
 
re125 (2)
 
   V39
Value: 0.05   (Units: nM_inv_s)
Constant
 
   K39
Value: 15.0   (Units: substance)
Constant
 
re126 (2)
 
   k40
Value: 0.002   (Units: inv_sec)
Constant
 
   K40
Value: 30.0   (Units: substance)
Constant
 
re127 (2)
 
   K43
Value: 25.0   (Units: substance)
Constant
 
   k43
Value: 4.0E-5   (Units: inv_sec)
Constant
 
re128 (2)
 
   K44
Value: 5.0   (Units: substance)
Constant
 
   V44
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 BIOMD0000000468

Curator's comment: (updated: 19 Aug 2013 14:33:04 GMT)

The model is the integration of the all the sub-models (MODEL1302180003-6) described in the paper. Figure 6 of the paper is reproduced here. The model as such reproduces the plot that corresponds to NO production under shear-stress condition (red). To obtain the plot for NO production under no-shear-stress condition (green), shear activating reactions (re5, re57, re102 and re103) should be removed. The corresponding Copasi files can be downloaded below.

Additional file(s)
  • Integrated model - NO production (no-shear-stress):
    Copasi file for the plot that corresponds to NO production without shear stress condition (green). Without shear stress implies that the shear activating reactions (re5, re57, re102 and re103) are removed from the model.
  • Integrated model - NO production (Shear-stress):
    Copasi file for the plot that corresponds to NO production under shear stress condition (red).
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