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BIOMD0000000196 - Srividhya2006_CellCycle

 

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Reference Publication
Publication ID: 16473373
Srividhya J, Gopinathan MS.
A simple time delay model for eukaryotic cell cycle.
J. Theor. Biol. 2006 Aug; 241(3): 617-627
Indiana University School of Informatics, Indiana University, Bloomington, IN 47406, USA. srividhya@iitm.ac.in  [more]
Model
Original Model: BIOMD0000000196.origin
Submitter: Harish Dharuri
Submission ID: MODEL1502077979
Submission Date: 21 Oct 2008 13:01:03 UTC
Last Modification Date: 08 Apr 2016 15:47:20 UTC
Creation Date: 13 Oct 2008 12:53:24 UTC
Encoders:  Harish Dharuri
   Lukas Endler
   Vijayalakshmi Chelliah
   Srividhya Jeyaram
set #1
bqmodel:isDerivedFrom PubMed 11371173
set #2
bqbiol:isVersionOf Reactome REACT_152
bqbiol:hasTaxon Taxonomy Eukaryota
set #3
bqbiol:isVersionOf Gene Ontology cell cycle process
Notes

In this model the values of "free CDK" (Id: x2), "cdc25_P" (x4) "Wee1_P" (Id: y5) and "APC" (Id: y6) are assigned using the parameters describing the total concentrations totcdk (Id: c)), totcdc5, totwee1 and totAPC. So if you want to change the levels of these proteins, you need to change the values ofthese parameters.

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 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: 16473373 Submission Date: 21 Oct 2008 13:01:03 UTC Last Modification Date: 08 Apr 2016 15:47:20 UTC Creation Date: 13 Oct 2008 12:53:24 UTC
Mathematical expressions
Reactions
cyclin synthesis cyclin/cdk complex formation cyclin degradation MPF cyclin subunit degradation
Pre-MPF -> MPF transition MPF -> Pre-MPF transition cdc25 phosphorylation cdc25 dephosphorylation
wee1 dephosphorylation wee1 phosphorylation APC phosphorylation APC dephosphorylation
cell growth      
Rules
Assignment Rule (variable: cdc25_P) Assignment Rule (variable: Wee1_P) Assignment Rule (variable: APC) Assignment Rule (variable: free CDK)
Events
cell_division      
Physical entities
Compartments Species
cell cyclin free CDK MPF
cdc25_P Wee1 APC_P
cell_mass cdc25 Wee1_P
APC Pre_MPF  
Global parameters
vf kf kc Bc
kd B2 vM1 a1
Ka j1 B1 v'M1
j'1 vM2 a2 j2
v'M2 j'3 j'2 vM3
j3 v'M3 B3 vM4
a4 tau j4 v'M4
j'4 mu a totcdc25
totwee1 totAPC totcdk  
Reactions (13)
 
 cyclin synthesis  → [cyclin];  
 
 cyclin/cdk complex formation [cyclin] + [free CDK] → [Pre_MPF];  
 
 cyclin degradation [cyclin] → ;   {APC_P}
 
 MPF cyclin subunit degradation [MPF] → [free CDK];   {APC_P}
 
 Pre-MPF -> MPF transition [Pre_MPF] → [MPF];   {cdc25_P}
 
 MPF -> Pre-MPF transition [MPF] → [Pre_MPF];   {Wee1}
 
 cdc25 phosphorylation [cdc25] → [cdc25_P];   {cell_mass} , {MPF}
 
 cdc25 dephosphorylation [cdc25_P] → [cdc25];  
 
 wee1 dephosphorylation [Wee1_P] → [Wee1];  
 
 wee1 phosphorylation [Wee1] → [Wee1_P];   {MPF} , {cell_mass}
 
 APC phosphorylation [APC] → [APC_P];   {cell_mass} , {MPF}
 
 APC dephosphorylation [APC_P] → [APC];  
 
 cell growth  → [cell_mass];  
 
Rules (4)
 
 Assignment Rule (name: x4) cdc25_P = totcdc25-y4
 
 Assignment Rule (name: y5) Wee1_P = totwee1-x5
 
 Assignment Rule (name: y6) APC = totAPC-x6
 
 Assignment Rule (name: x2) free CDK = (c-Pre_MPF)-x3
 
Events (1)
 
 cell_division
cell_mass = m/2
 
Functions (3)
 
 Mass_Action_0 lambda(k1, k1)
 
 Mass_Action_2 lambda(k1, S1, S2, k1*S1*S2)
 
 Mass_Action_1 lambda(k1, S1, k1*S1)
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 cyclin
Compartment: cell
Initial amount: 0.01
 
  free CDK
Compartment: cell
 
 MPF
Compartment: cell
Initial amount: 0.1
 
  cdc25_P
Compartment: cell
 
 Wee1
Compartment: cell
Initial amount: 0.1
 
 APC_P
Compartment: cell
Initial amount: 0.1
 
 cell_mass
Compartment: cell
Initial amount: 0.473
 
 cdc25
Compartment: cell
Initial amount: 0.9
 
  Wee1_P
Compartment: cell
 
  APC
Compartment: cell
 
 Pre_MPF
Compartment: cell
Initial amount: 0.2
 
Global Parameters (35)
 
   vf
Value: 0.215
Constant
 
   kf
Value: 1.0
Constant
 
   kc
Value: 0.05
Constant
 
   Bc
Value: 3.5
Constant
 
   kd
Value: 0.2
Constant
 
   B2
Value: 3.3
Constant
 
   vM1
Value: 0.7
Constant
 
   a1
Value: 1.2
Constant
 
   Ka
Value: 0.5
Constant
 
   j1
Value: 0.01
Constant
 
   B1
Value: 5.0
Constant
 
   v'M1
Value: 0.55
Constant
 
   j'1
Value: 0.01
Constant
 
   vM2
Value: 0.41
Constant
 
   a2
Value: 1.0
Constant
 
   j2
Value: 0.01
Constant
 
   v'M2
Value: 1.0
Constant
 
   j'3
Value: 0.01
Constant
 
   j'2
Value: 0.01
Constant
 
   vM3
Value: 1.0
Constant
 
   j3
Value: 0.01
Constant
 
   v'M3
Value: 1.0
Constant
 
   B3
Value: 1.0
Constant
 
   vM4
Value: 0.7
Constant
 
   a4
Value: 2.0
Constant
 
   tau
Value: 5.0
Constant
 
   j4
Value: 0.01
Constant
 
   v'M4
Value: 1.0
Constant
 
   j'4
Value: 0.01
Constant
 
   mu
Value: 0.01
Constant
 
   a
Value: 10.0
Constant
 
   totcdc25
Value: 1.0
Constant
 
   totwee1
Value: 1.0
Constant
 
   totAPC
Value: 1.0
Constant
 
   totcdk
Value: 1.1
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000196

Curator's comment: (updated: 18 Jan 2010 16:25:47 GMT)

The figure corresponds to the Figures 2a & 2b of the paper. The model does not reproduce the figures exactly as in paper, but the author suggested that the results of the simulations are correct. The model was simulated using XPPAUT.

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