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BIOMD0000000366 - Orfao2008_ThrombinGeneration_AmidolyticActivity

 

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Reference Publication
Publication ID: 10.1016/j.jmaa.2008....
Cunha Orfaoa S, Jank G, Mottaghy K, Walcher S, Zerz E.
Qualitative properties and stabilizability of a model for blood thrombin formation
Journal of Mathematical Analysis and Applications 2008; 346(1): 218–226
Lehrstuhl II für Mathematik, RWTH Aachen, 52056 Aachen, Germany; Universitätsklinikum der RWTH Aachen, Pauwelsstr. 30, 52057 Aachen, Germany; Lehrstuhl A für Mathematik, RWTH Aachen, 52056 Aachen, Germany; Lehrstuhl D für Mathematik, RWTH Aachen, 52056 Aachen, Germany  [more]
Model
Original Model: BIOMD0000000366.xml.origin
Submitter: Michael Schubert
Submission ID: MODEL1108260000
Submission Date: 26 Aug 2011 16:10:29 UTC
Last Modification Date: 28 May 2014 16:48:16 UTC
Creation Date: 26 Aug 2011 16:38:20 UTC
Encoders:  Michael Schubert
set #1
bqmodel:isDerivedFrom BioModels Database Stortelder1997 - Thrombin Generation Amidolytic Activity
set #2
bqbiol:hasTaxon Taxonomy Eukaryota
set #3
bqbiol:isVersionOf Gene Ontology blood coagulation
Notes
Model
Publication ID: 10.1016/j.jmaa.2008.... Submission Date: 26 Aug 2011 16:10:29 UTC Last Modification Date: 28 May 2014 16:48:16 UTC Creation Date: 26 Aug 2011 16:38:20 UTC
Mathematical expressions
Reactions
R1 R2 R3 R4
R5 R6 R7 R8
Rules
Assignment Rule (variable: AmAct)      
Physical entities
Compartments Species
compartment_1 X Xa Xa_ATIII
PL PT Va
IIa V II
IIa_alpha2M IIa_ATIII RVV
Global parameters
kcat_X km_X ki_Xa k_PT
k_PL kcat_V km_V kcat_II
km_II kcat_2 km_2 ki_IIaAlpha2M
ki_IIaATIII AmAct    
Reactions (8)
 
 R1 [X] → [Xa];   {RVV}
 
 R2 [Xa] → [Xa_ATIII];  
 
 R3 [Va] + [Xa] + [PL] ↔ [PT];  
 
 R4 [V] → [Va];   {IIa}
 
 R5 [II] → [IIa];   {PT}
 
 R6 [II] → [IIa];   {Xa}
 
 R7 [IIa] → [IIa_alpha2M];  
 
 R8 [IIa] → [IIa_ATIII];  
 
Rules (1)
 
 Assignment Rule (name: AmAct) AmAct = IIa+0.556*IIa_alpha2M
 
Functions (1)
 
 Henri-Michaelis-Menten (irreversible) kcat lambda(kcat, enzyme, substrate, Km, kcat*enzyme*substrate/(Km+substrate))
 
   compartment_1 Spatial dimensions: 3.0  Compartment size: 1.0
 
 X
Compartment: compartment_1
Initial concentration: 0.1999999
 
 Xa
Compartment: compartment_1
Initial concentration: 0.0
 
 Xa_ATIII
Compartment: compartment_1
Initial concentration: 0.0
 
   PL
Compartment: compartment_1
Initial concentration: 0.04999999
 
   PT
Compartment: compartment_1
Initial concentration: 0.0
 
 Va
Compartment: compartment_1
Initial concentration: 0.0
 
 IIa
Compartment: compartment_1
Initial concentration: 0.0
 
 V
Compartment: compartment_1
Initial concentration: 0.02999999
 
 II
Compartment: compartment_1
Initial concentration: 1.4
 
 IIa_alpha2M
Compartment: compartment_1
Initial concentration: 0.0
 
 IIa_ATIII
Compartment: compartment_1
Initial concentration: 0.0
 
   RVV
Compartment: compartment_1
Initial concentration: 0.03
 
Global Parameters (14)
 
 kcat_X
Value: 239.1
Constant
 
 km_X
Value: 23.65
Constant
 
 ki_Xa
Value: 4.531
Constant
 
 k_PT
Value: 122.9
Constant
 
 k_PL
Value: 801.4
Constant
 
 kcat_V
Value: 7.844
Constant
 
 km_V
Value: 149.7
Constant
 
 kcat_II
Value: 43.87
Constant
 
 km_II
Value: 62.25
Constant
 
 kcat_2
Value: 12.4
Constant
 
 km_2
Value: 0.06148
Constant
 
 ki_IIaAlpha2M
Value: 0.1762
Constant
 
 ki_IIaATIII
Value: 0.7859
Constant
 
   AmAct  
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000366

Curator's comment: (updated: 26 Aug 2011 17:34:13 BST)

Reproduction of figure 2 of the article.

Model integrated using PySCeS and plotted with Matplotlib.

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