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BIOMD0000000150 - Morris2002_CellCycle_CDK2Cyclin

 

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Reference Publication
Publication ID: 11959850
Morris MC, Gondeau C, Tainer JA, Divita G.
Kinetic mechanism of activation of the Cdk2/cyclin A complex. Key role of the C-lobe of the Cdk.
J. Biol. Chem. 2002 Jun; 277(26): 23847-23853
The Scripps Research Institute, Molecular Biology, La Jolla, California 92037, USA.  [more]
Model
Original Model: DOQCS logo
Submitter: Sharat Vayttaden
Submission ID: MODEL4821491663
Submission Date: 12 Sep 2007 20:36:08 UTC
Last Modification Date: 01 Dec 2010 22:10:11 UTC
Creation Date: 12 Sep 2007 20:36:08 UTC
Encoders:  Nicolas Le Novère
   Sharat Vayttaden
set #1
bqbiol:isHomologTo Reactome REACT_152
set #2
bqbiol:isVersionOf KEGG Pathway Cell cycle
Gene Ontology mitotic cell cycle
set #3
bqbiol:hasTaxon Taxonomy Saccharomyces cerevisiae
Notes

Notes from the original DOCQS curator:
In this version of the CDK2/Cyclin A complex activation there is discrepancy in the first curve which plots the binding reaction of CDK2 and Cyclin A expressed in E. coli. With the published rate constants the simulation does not match the published graph (Fig.1B) in Morris MC. et al. J Biol Chem. 277(26):23847-53 .

Notes from BioModels DB curator:
Although the parameters are those reported in the table I for CDK2/Cyclin A, the total fluorescence follows exactly the curve reported in the paper for CDK2/Cyclin H in figure 1B. Either the plot legend or the table is wrong.

Model
Publication ID: 11959850 Submission Date: 12 Sep 2007 20:36:08 UTC Last Modification Date: 01 Dec 2010 22:10:11 UTC Creation Date: 12 Sep 2007 20:36:08 UTC
Mathematical expressions
Reactions
Binding Activation    
Rules
Assignment Rule (variable: total_fluorescence)      
Physical entities
Compartments Species
geometry CDK2cycA CyclinA Cdk2
CDK2cycA_star_    
Global parameters
basal_fluorescence total_fluorescence    
Reactions (2)
 
 Binding [Cdk2] + [CyclinA] ↔ [CDK2cycA];  
 
 Activation [CDK2cycA] ↔ [CDK2cycA_star_];  
 
Rules (1)
 
 Assignment Rule (name: total_fluorescence) total_fluorescence = CDK2cycA*599990*1E6/43200+CDK2cycA_star_*599990*1E6/43200+basal_fluorescence
 
   Spatial dimensions: 3.0  Compartment size: 1.0E-12
 
 CDK2cycA
Compartment: geometry
Initial concentration: 0.0
 
 CyclinA
Compartment: geometry
Initial concentration: 4.0E-7
 
 Cdk2
Compartment: geometry
Initial concentration: 1.0E-7
 
 CDK2cycA_star_
Compartment: geometry
Initial concentration: 0.0
 
Global Parameters (2)
 
   basal_fluorescence
Value: 1.21210648148148
 
   total_fluorescence
Value: 0.138886574074074
 
Binding (2)
 
   kf
Value: 1.9E7
Constant
 
   kb
Value: 25.0
Constant
 
Activation (2)
 
   kf
Value: 0.813
Constant
 
   kb
Value: 0.557
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000150

Curator's comment: (updated: 21 Jan 2010 12:22:28 GMT)

The model reproduces figure 1B (plot in blue - the kinetics of Cdk2 with cyclin H) of the original publication. The model was integrated and simulated using Copasi v4.5 (build 30).

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