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BIOMD0000000195 - Tyson2001_Cell_Cycle_Regulation

 

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Reference Publication
Publication ID: 11371178
Tyson JJ, Novak B.
Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions.
J. Theor. Biol. 2001 May; 210(2): 249-263
Department of Biology, Virginian Polytechnic Institute and State University, Blacksburg, VA 24061, USA. tyson@vt.edu  [more]
Model
Original Model: http://www.itb.cnr.it/cell...
Submitter: Nicolas Le Novère
Submission ID: MODEL3897475441
Submission Date: 23 Sep 2008 11:19:12 UTC
Last Modification Date: 05 Jul 2012 14:50:51 UTC
Creation Date: 26 Feb 2009 10:08:01 UTC
Encoders:  Lukas Endler
set #1
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
bqbiol:isVersionOf KEGG Pathway map04111
Reactome REACT_152.2
Gene Ontology regulation of cell cycle
Notes

This model describes the budding yeast cell cycle model used in fig 8 a in
Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions.
Tyson JJ and Novak B., J Theor Biol 2001 May;210(2):249-63.
It consitsts of the equations (2)-(8), with mu=0.005 min -1 . It was taken from Cell Cycle DB ( file ) and only slightly altered.


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: 11371178 Submission Date: 23 Sep 2008 11:19:12 UTC Last Modification Date: 05 Jul 2012 14:50:51 UTC Creation Date: 26 Feb 2009 10:08:01 UTC
Mathematical expressions
Reactions
CycBt synthesis CycBt degradation CycBt degradation via Cdh1 CycBt degradation via Cdc20a
Cdh1 synthesis Cdh1 degradation Cdc20t synthesis Cdc20t degradation
Cdc20 activation Cdc20a inhibition Cdc20a degradation IEP synthesis
IEP degradation growth CKIt synthesis CKIt degradation
CKIt phosphorilation via SK CKIt Trimer sequestred SK synthesis SK degradation
Rules
Assignment Rule (variable: CycB) Assignment Rule (variable: Trimer) Assignment Rule (variable: TF) Assignment Rule (variable: Mad)
Events
Cell division      
Physical entities
Compartments Species
cell CycBt CycB Cdc20a
Trimer Cdh1 m
Cdc20t IEP Mad
CKIt SK  
Global parameters
k1 k2p k2pp k2ppp
k3p k3pp J3 k4
k5p k5pp J5 k6
n k7 J7 k8
J8 k9 k10 mu
k11 k12p k12pp mmax
k12ppp Keq k13 k14
k15p k15pp k16p k16pp
J15 J16 k4p J4
TF      
Reactions (20)
 
 CycBt synthesis  → [CycBt];  
 
 CycBt degradation [CycBt] → ;  
 
 CycBt degradation via Cdh1 [CycBt] → ;   {Cdh1}
 
 CycBt degradation via Cdc20a [CycBt] → ;   {Cdc20a}
 
 Cdh1 synthesis  → [Cdh1];   {Cdc20a}
 
 Cdh1 degradation [Cdh1] → ;   {SK} , {m} , {CycB}
 
 Cdc20t synthesis  → [Cdc20t];   {CycB} , {m}
 
 Cdc20t degradation [Cdc20t] → ;  
 
 Cdc20 activation  → [Cdc20a];   {Cdc20t} , {IEP}
 
 Cdc20a inhibition [Cdc20a] → ;   {Mad}
 
 Cdc20a degradation [Cdc20a] → ;  
 
 IEP synthesis  → [IEP];   {m} , {CycB}
 
 IEP degradation [IEP] → ;  
 
 growth  → [m];  
 
 CKIt synthesis  → [CKIt];  
 
 CKIt degradation [CKIt] → ;  
 
 CKIt phosphorilation via SK [CKIt] → ;   {SK}
 
 CKIt Trimer sequestred [CKIt] → ;   {m} , {CycB}
 
 SK synthesis  → [SK];  
 
 SK degradation [SK] → ;  
 
Rules (4)
 
 Assignment Rule (name: CycB) CycB = CycBt-2*CycBt*CKIt/(CycBt+CKIt+1/Keq+((CycBt+CKIt+1/Keq)^2-4*CycBt*CKIt)^(1/2))
 
 Assignment Rule (name: Trimer) Trimer = 2*CycBt*CKIt/(CycBt+CKIt+1/Keq+((CycBt+CKIt+1/Keq)^2-4*CycBt*CKIt)^(1/2))
 
 Assignment Rule (name: TF) TF = GK(k15p*m+k15pp*SK, k16p+k16pp*m*CycB, J15, J16)
 
 Assignment Rule (name: Mad) Mad = 1
 
Events (1)
 
 Cell division
m = m/2
 
Functions (1)
 
 Goldbeter Koshland Function lambda(A1, A2, A3, A4, 2*A4*A1/(A2-A1+A3*A2+A4*A1+((A2-A1+A3*A2+A4*A1)^2-4*(A2-A1)*A4*A1)^(0.5)))
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 CycBt
Compartment: cell
Initial amount: 0.0010
 
  CycB
Compartment: cell
 
 Cdc20a
Compartment: cell
Initial amount: 0.0010
 
  Trimer
Compartment: cell
 
 Cdh1
Compartment: cell
Initial amount: 0.0010
 
 m
Compartment: cell
Initial amount: 0.5
 
 Cdc20t
Compartment: cell
Initial amount: 0.0010
 
   IEP
Compartment: cell
Initial amount: 0.0010
 
  Mad
Compartment: cell
 
 CKIt
Compartment: cell
Initial amount: 0.0010
 
 SK
Compartment: cell
Initial amount: 0.0010
 
Global Parameters (37)
 
   k1
Value: 0.04
Constant
 
   k2p
Value: 0.04
Constant
 
   k2pp
Value: 1.0
Constant
 
   k2ppp
Value: 1.0
Constant
 
   k3p
Value: 1.0
Constant
 
   k3pp
Value: 10.0
Constant
 
   J3
Value: 0.04
Constant
 
   k4
Value: 35.0
Constant
 
   k5p
Value: 0.0050
Constant
 
   k5pp
Value: 0.2
Constant
 
   J5
Value: 0.3
Constant
 
   k6
Value: 0.1
Constant
 
   n
Value: 4.0
Constant
 
   k7
Value: 1.0
Constant
 
   J7
Value: 0.0010
Constant
 
   k8
Value: 0.5
Constant
 
   J8
Value: 0.0010
Constant
 
   k9
Value: 0.1
Constant
 
   k10
Value: 0.02
Constant
 
   mu
Value: 0.0050
Constant
 
   k11
Value: 1.0
Constant
 
   k12p
Value: 0.2
Constant
 
   k12pp
Value: 50.0
Constant
 
   mmax
Value: 10.0
Constant
 
   k12ppp
Value: 100.0
Constant
 
   Keq
Value: 1000.0
Constant
 
   k13
Value: 1.0
Constant
 
   k14
Value: 1.0
Constant
 
   k15p
Value: 1.5
Constant
 
   k15pp
Value: 0.05
Constant
 
   k16p
Value: 1.0
Constant
 
   k16pp
Value: 3.0
Constant
 
   J15
Value: 0.01
Constant
 
   J16
Value: 0.01
Constant
 
   k4p
Value: 2.0
Constant
 
   J4
Value: 0.04
Constant
 
   TF
Value: NaN
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000195

Curator's comment: (updated: 23 Sep 2008 12:18:01 BST)

Integrated using XPP under JigCell 6.2.1

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