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BIOMD0000000364 - Lee2010_ThrombinActivation_OneForm

 

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Reference Publication
Publication ID: 20435402
Lee CJ, Wu S, Eun C, Pedersen LG.
A revisit to the one form kinetic model of prothrombinase.
Biophys. Chem. 2010 Jun; 149(1-2): 28-33
Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.  [more]
Model
Original Model: BIOMD0000000364.xml.origin
Submitter: Michael Schubert
Submission ID: MODEL1108260002
Submission Date: 26 Aug 2011 16:13:26 UTC
Last Modification Date: 28 May 2014 16:38:11 UTC
Creation Date: 26 Aug 2011 16:37:45 UTC
Encoders:  Michael Schubert
set #1
bqmodel:isDerivedFrom PubMed 17726029
set #2
bqbiol:hasTaxon Taxonomy Eukaryota
set #3
bqbiol:isVersionOf Gene Ontology blood coagulation
Notes
Model
Publication ID: 20435402 Submission Date: 26 Aug 2011 16:13:26 UTC Last Modification Date: 28 May 2014 16:38:11 UTC Creation Date: 26 Aug 2011 16:37:45 UTC
Mathematical expressions
Reactions
r1 r2 r3 r4
r5 r6 r7 r8
r9 r10 r11 r12
r13 r14 r15 r16
Physical entities
Compartments Species
compartment E E_P_1 P
M M1 E_M1
E_M T E_P_2
P2 P21 E_P21
E_P2 E_P1  
Global parameters
k1 k2 k9 k3
k3a k4 k4a k5
k6 k10 k7 k7a
k8 k8a kC1 kC2
j1 j3 j3a j5
j7 j7a    
Reactions (16)
 
 r1 [E] + [P] ↔ [E_P_1];  
 
 r2 [E_P_1] → [E] + [M];  
 
 r3 [M] → [M1];  
 
 r4 [E] + [M1] ↔ [E_M1];  
 
 r5 [E] + [M] ↔ [E_M];  
 
 r6 [E_M1] → [E] + [T];  
 
 r7 [E_M] → [E] + [T];  
 
 r8 [E] + [P] ↔ [E_P_2];  
 
 r9 [E_P_2] → [E] + [P2];  
 
 r10 [P2] → [P21];  
 
 r11 [E] + [P21] ↔ [E_P21];  
 
 r12 [E] + [P2] ↔ [E_P2];  
 
 r13 [E_P21] → [E] + [T];  
 
 r14 [E_P2] → [E] + [T];  
 
 r15 [E_P_1] → [T];  
 
 r16 [E_P_2] → [T];  
 
   compartment Spatial dimensions: 3.0  Compartment size: 1.0
 
   E
Compartment: compartment
Initial concentration: 1.5E-4
 
   E_P_1
Compartment: compartment
Initial concentration: 0.0
 
   P
Compartment: compartment
Initial concentration: 1.0
 
   M
Compartment: compartment
Initial concentration: 0.0
 
   M1
Compartment: compartment
Initial concentration: 0.0
 
   E_M1
Compartment: compartment
Initial concentration: 0.0
 
   E_M
Compartment: compartment
Initial concentration: 0.0
 
   T
Compartment: compartment
Initial concentration: 0.0
 
   E_P_2
Compartment: compartment
Initial concentration: 0.0
 
   P2
Compartment: compartment
Initial concentration: 0.0
 
   P21
Compartment: compartment
Initial concentration: 0.0
 
   E_P21
Compartment: compartment
Initial concentration: 0.0
 
   E_P2
Compartment: compartment
Initial concentration: 0.0
 
   E_P1
Compartment: compartment
Initial concentration: 0.0
 
Global Parameters (22)
 
 k1
Value: 91.8
Constant
 
 k2
Value: 82.4
Constant
 
 k9
Value: 3.12E-8
Constant
 
 k3
Value: 38.1
Constant
 
 k3a
Value: 151.5
Constant
 
 k4
Value: 38.1
Constant
 
 k4a
Value: 209.9
Constant
 
 k5
Value: 5.16
Constant
 
 k6
Value: 32.3
Constant
 
 k10
Value: 7.23E-10
Constant
 
 k7
Value: 6.76E-8
Constant
 
 k7a
Value: 4.7
Constant
 
 k8
Value: 0.00599
Constant
 
 k8a
Value: 42.6
Constant
 
 kC1
Value: 2.39E-6
Constant
 
 kC2
Value: 0.031
Constant
 
 j1
Value: 33.4
Constant
 
 j3
Value: 1.58E-6
Constant
 
 j3a
Value: 0.185
Constant
 
 j5
Value: 21.8
Constant
 
 j7
Value: 4.46E-9
Constant
 
 j7a
Value: 2.66E-5
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000364

Curator's comment: (updated: 26 Aug 2011 17:28:50 BST)

Reproduction of figure 3 of the article.

Model integrated using PySCeS and plotted with Matplotlib.

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