Try the new BioModels platform (beta)
BioModels Database logo

BioModels Database

spacer

BIOMD0000000169 - Aguda1999_CellCycle

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 10619492
Aguda BD, Tang Y.
The kinetic origins of the restriction point in the mammalian cell cycle.
Cell Prolif. 1999 Oct; 32(5): 321-335
Department of Chemistry & Biochemistry, Laurentian University, Sudbury, Ontario, Canada. daguda@nickel.laurentian.ca  [more]
Model
Original Model: http://www.itb.cnr.it/cell...
Submitter: Nicolas Le Novère
Submission ID: MODEL3897395081
Submission Date: 08 May 2008 11:56:49 UTC
Last Modification Date: 13 Apr 2015 13:56:03 UTC
Creation Date: 03 Apr 2008 13:23:34 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #2
bqbiol:hasTaxon Taxonomy Mammalia
bqbiol:isVersionOf Gene Ontology mitotic cell cycle G1/S transition checkpoint
bqbiol:isPartOf Reactome REACT_1538.1
Notes

The model reproduces the time profiles of p27, E2F and aE/cdk2 as depicted in Figure 5 c of the paper. Model was simulated on MathSBML.


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 10619492 Submission Date: 08 May 2008 11:56:49 UTC Last Modification Date: 13 Apr 2015 13:56:03 UTC Creation Date: 03 Apr 2008 13:23:34 UTC
Mathematical expressions
Reactions
pRB/E2F complex deassociation pRB/E2F complex formation cycE/CDK2 activation cycE/CDK2 deactivation
icycE/CDK2 synthesis E2F synthesis E2F degradation icycE/CDK2 degradation
cycD/CDK4 synthesis cycD/CDK4 degradation p27 synthesis p27 degradation via cycE/CDK2
cycE/CDK2/p27 complex formation cycE/CDK2/p27 deassociation cycD/CDK4/p16 complex formation E2F auto stimulation
cycD/CDK4/p27 complex formation cycD/CDK4/p27 complex deassociation acycE/CDK2 degradation p27 degradation
p16 synthesis p16 degradation p16 synthesis inhibited by pRB pRB synthesis inhibited by p16
pRB synthesis pRB degradation pRB-p dephosphorylation  
Physical entities
Compartments Species
cell pRB_E2F E2F pRB_P
i_cyclinE_CDK2 a_cyclinE_CDK2 pRB
CycD_CDK4 p27 cycE_CDK2_p27
p16 cycD_CDK4_p27  
Global parameters
k1p k1pp k1 k2
kminus2 k3 k3p k4
kminus4 kminus1 k5 k6
kminus6 k7 k8 k9
K10 k17 k18 k19
k20 k21 k22 k23
k24 k25 k25p k26
k26p k27 k28 k29
Reactions (27)
 
 pRB/E2F complex deassociation [pRB_E2F] → [E2F] + [pRB_P];   {pRB_E2F} , {a_cyclinE_CDK2} , {CycD_CDK4} , {cycD_CDK4_p27}
 
 pRB/E2F complex formation [pRB] + [E2F] → [pRB_E2F];  
 
 cycE/CDK2 activation [i_cyclinE_CDK2] → [a_cyclinE_CDK2];  
 
 cycE/CDK2 deactivation [a_cyclinE_CDK2] → [i_cyclinE_CDK2];  
 
 icycE/CDK2 synthesis  → [i_cyclinE_CDK2];   {E2F}
 
 E2F synthesis  → [E2F];  
 
 E2F degradation [E2F] → ;  
 
 icycE/CDK2 degradation [i_cyclinE_CDK2] → ;  
 
 cycD/CDK4 synthesis  → [CycD_CDK4];  
 
 cycD/CDK4 degradation [CycD_CDK4] → ;  
 
 p27 synthesis  → [p27];  
 
 p27 degradation via cycE/CDK2 [p27] → ;   {a_cyclinE_CDK2}
 
 cycE/CDK2/p27 complex formation [a_cyclinE_CDK2] + [p27] → [cycE_CDK2_p27];  
 
 cycE/CDK2/p27 deassociation [cycE_CDK2_p27] → [a_cyclinE_CDK2] + [p27];  
 
 cycD/CDK4/p16 complex formation [CycD_CDK4] + [p16] → ;  
 
 E2F auto stimulation  → [E2F];  
 
 cycD/CDK4/p27 complex formation [p27] + [CycD_CDK4] → [cycD_CDK4_p27];  
 
 cycD/CDK4/p27 complex deassociation [cycD_CDK4_p27] → [p27] + [CycD_CDK4];  
 
 acycE/CDK2 degradation [a_cyclinE_CDK2] → ;  
 
 p27 degradation [p27] → ;  
 
 p16 synthesis  → [p16];  
 
 p16 degradation [p16] → ;  
 
 p16 synthesis inhibited by pRB  → [p16];   {pRB}
 
 pRB synthesis inhibited by p16  → [pRB];   {p16}
 
 pRB synthesis  → [pRB];  
 
 pRB degradation [pRB] → ;  
 
 pRB-p dephosphorylation [pRB_P] → [pRB];  
 
Functions (3)
 
 Mass_Action_1 lambda(k1, S1, k1*S1)
 
 Mass_Action_2 lambda(k1, S1, S2, k1*S1*S2)
 
 Mass_Action_0 lambda(k1, k1)
 
   cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 pRB_E2F
Compartment: cell
Initial amount: 1.95
 
 E2F
Compartment: cell
Initial amount: 0.0
 
 pRB_P
Compartment: cell
Initial amount: 0.01
 
 i_cyclinE_CDK2
Compartment: cell
Initial amount: 0.01
 
 a_cyclinE_CDK2
Compartment: cell
Initial amount: 0.0
 
 pRB
Compartment: cell
Initial amount: 0.05
 
 CycD_CDK4
Compartment: cell
Initial amount: 0.0
 
 p27
Compartment: cell
Initial amount: 15.0
 
 cycE_CDK2_p27
Compartment: cell
Initial amount: 1.0
 
 p16
Compartment: cell
Initial amount: 5.0
 
 cycD_CDK4_p27
Compartment: cell
Initial amount: 0.0
 
Global Parameters (32)
 
   k1p
Value: 0.5
Constant
 
   k1pp
Value: 0.5
Constant
 
   k1
Value: 0.1
Constant
 
   k2
Value: 0.1
Constant
 
   kminus2
Value: 1.0
Constant
 
   k3
Value: 1.42
Constant
 
   k3p
Constant
 
   k4
Value: 1.0E-6
Constant
 
   kminus4
Value: 0.016
Constant
 
   kminus1
Value: 0.001
Constant
 
   k5
Value: 0.02
Constant
 
   k6
Value: 0.018
Constant
 
   kminus6
Value: 5.0
Constant
 
   k7
Value: 1.0E-5
Constant
 
   k8
Value: 2.0
Constant
 
   k9
Value: 2.0
Constant
 
   K10
Value: 0.035
Constant
 
   k17
Value: 3.5
Constant
 
   k18
Value: 1.0E-5
Constant
 
   k19
Value: 0.05
Constant
 
   k20
Value: 0.01
Constant
 
   k21
Value: 0.1
Constant
 
   k22
Value: 0.001
Constant
 
   k23
Value: 0.2
Constant
 
   k24
Value: 0.1
Constant
 
   k25
Value: 0.01
Constant
 
   k25p
Value: 0.02
Constant
 
   k26
Value: 0.01
Constant
 
   k26p
Value: 0.1
Constant
 
   k27
Value: 0.01
Constant
 
   k28
Value: 0.01
Constant
 
   k29
Value: 0.001
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000169

Curator's comment: (updated: 02 May 2008 00:54:04 BST)

The plots correspond to the time profiles of p27, E2F and cycE/CDK2 as depicted in Fig 5c of the paper. MathSBML was used to obtain simulation results.

spacer
spacer