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BIOMD0000000193 - Ibrahim2008_MCC_assembly_model_KDM

 

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Reference Publication
Publication ID: 18675311
Ibrahim B, Schmitt E, Dittrich P, Diekmann S.
In silico study of kinetochore control, amplification, and inhibition effects in MCC assembly.
BioSystems 2009 Jan; 95(1): 35-50
Bio Systems Analysis Group, Institute of Computer Science, Friedrich-Schiller-University Jena, Germany. ibrahim@minet.uni-jena.de  [more]
Model
Original Model: BIOMD0000000193.origin
Submitter: Bashar Ibrahim
Submission ID: MODEL1667758030
Submission Date: 19 Sep 2008 11:59:46 UTC
Last Modification Date: 23 Sep 2009 17:12:59 UTC
Creation Date: 27 Nov 2008 10:56:41 UTC
Encoders:  Lukas Endler
   Eberhard Schmitt
   Peter Dittrich
   Stephan Diekmann
   Bashar Ibrahim
set #1
bqbiol:isPartOf KEGG Pathway Cell cycle - Homo sapiens (human)
bqbiol:isVersionOf Reactome REACT_2137.2
Gene Ontology mitotic spindle assembly checkpoint
set #2
bqbiol:occursIn Taxonomy Homo sapiens
Notes
BioSystems (2007), doi:10.1016/j.biosystems.2008.06.007

In-silico study of kinetochore control, amplification, and inhibition effects in MCC assembly


Bashar Ibrahim, Eberhard Schmitt, Peter Dittrich, Stephan Diekmann
This is the kinetochore dependent MCC model (KDM) from the article. For the kinetochore independent MCC model (KIM) replace u*k4f in R4 by k4f and u*k5f in R5 by k5f .

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.
For more information see the terms of use .
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 18675311 Submission Date: 19 Sep 2008 11:59:46 UTC Last Modification Date: 23 Sep 2009 17:12:59 UTC Creation Date: 27 Nov 2008 10:56:41 UTC
Mathematical expressions
Reactions
R1 R2 R3 R4
R5 R6    
Events
Microtubule attachment      
Physical entities
Compartments Species
Cytoplasm Mad1:C-Mad2 O-Mad2 Mad1:C-Mad2:O-Mad2*
Cdc20 Cdc20:C-Mad2 Bub3:BubR1
MCC Bub3:BubR1:Cdc20  
Global parameters
k3f kf6 k5f k5r
k2f k1f k1r k4f
k4r u const_val_0 const_val_1
Reactions (6)
 
 R1 [Mad1:C-Mad2] + [O-Mad2] ↔ [Mad1:C-Mad2:O-Mad2*];  
 
 R2 [Mad1:C-Mad2:O-Mad2*] + [Cdc20] → [Mad1:C-Mad2] + [Cdc20:C-Mad2];  
 
 R3 [Cdc20:C-Mad2] → [Cdc20] + [O-Mad2];  
 
 R4 [Cdc20:C-Mad2] + [Bub3:BubR1] ↔ [MCC];  
 
 R5 [Bub3:BubR1] + [Cdc20] ↔ [Bub3:BubR1:Cdc20];  
 
 R6 [O-Mad2] + [Cdc20] → [Cdc20:C-Mad2];  
 
Events (1)
 
 Microtubule attachment
u = const_val_0
 
 Cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 Mad1:C-Mad2
Compartment: Cytoplasm
Initial concentration: 5.0E-8  (Units: mole)
 
 O-Mad2
Compartment: Cytoplasm
Initial concentration: 1.3E-7  (Units: mole)
 
 Mad1:C-Mad2:O-Mad2*
Compartment: Cytoplasm
Initial concentration: 0.0  (Units: mole)
 
 Cdc20
Compartment: Cytoplasm
Initial concentration: 2.2E-7  (Units: mole)
 
 Cdc20:C-Mad2
Compartment: Cytoplasm
Initial concentration: 0.0  (Units: mole)
 
 Bub3:BubR1
Compartment: Cytoplasm
Initial concentration: 1.3E-7  (Units: mole)
 
 MCC
Compartment: Cytoplasm
Initial concentration: 0.0  (Units: mole)
 
 Bub3:BubR1:Cdc20
Compartment: Cytoplasm
Initial concentration: 0.0  (Units: mole)
 
Global Parameters (12)
 
 k3f
Value: 0.01   (Units: per second)
Constant
 
 kf6
Value: 1000.0   (Units: liter per mole per second)
Constant
 
 k5f
Value: 10000.0   (Units: liter per mole per second)
Constant
 
 k5r
Value: 0.2   (Units: per second)
Constant
 
 k2f
Value: 1.0E7   (Units: liter per mole per second)
Constant
 
 k1f
Value: 200000.0   (Units: liter per mole per second)
Constant
 
 k1r
Value: 0.2   (Units: per second)
Constant
 
 k4f
Value: 1.0E7   (Units: liter per mole per second)
Constant
 
 k4r
Value: 0.02   (Units: per second)
Constant
 
 u
Value: 1.0   (Units: dimensionless)
 
   const_val_0
Constant
 
   const_val_1
Value: 1.0   (Units: dimensionless)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000193

Curator's comment: (updated: 19 Sep 2008 12:59:19 BST)

reproduction of fig. 2 b1,2 using SBML ODESolver 05072008 with options -n,-z,--error 1e-14 and --printstep 1e4

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