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BIOMD0000000107 - Novak1993_M_phase_control

 

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Reference Publication
Publication ID: 8126097
Novak B, Tyson JJ.
Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos.
J. Cell. Sci. 1993 Dec; 106 ( Pt 4): 1153-1168
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg 24060-0406.  [more]
Model
Original Model: BIOMD0000000107.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL5876465734
Submission Date: 10 Apr 2007 03:29:15 UTC
Last Modification Date: 05 Jul 2012 22:43:50 UTC
Creation Date: 05 Apr 2007 16:42:03 UTC
Encoders:  Nicolas Le Novère
   Harish Dharuri
set #1
bqbiol:isHomologTo Reactome REACT_152
bqbiol:isVersionOf Gene Ontology mitotic cell cycle
bqbiol:occursIn Taxonomy Amphibia
Notes

The model reproduces the time profile of active MPF at cyclin concentration of 100nM as depicted in Fig 4A of the paper. Please note that active MPF and cyclin concentrations in the paper are given relative to total cdc2 concentration (100nM). Active MPF (dimer_p) is the cyclin-cdc2 complex that is phosphorylated at Thr161. The model was successfully tested on MathSBML and Jarnac.


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: 8126097 Submission Date: 10 Apr 2007 03:29:15 UTC Last Modification Date: 05 Jul 2012 22:43:50 UTC Creation Date: 05 Apr 2007 16:42:03 UTC
Mathematical expressions
Reactions
cyclin synthesis cyclin degradation cyclin-cdc2 dimer formation Thr161 dephosphorylation
Tyr15 phosphorylation Thr161 phosphorylation cyclin degradation Tyr15 dephosphorylation
Thr161 phosphorylation cyclin degradation Thr161 dephosphorylation Tyr15 phosphorylation
Tyr15 dephosphorylation cyclin degradation cyclin degradation cdc25 activation
cdc25 deactivation wee1 deactivation wee1 activation intermediary enzyme activation
intermediary enzyme deactivation ubiquitin conjugating enzyme activation ubiquitin conjugating enzyme deactivation  
Rules
Assignment Rule (variable: cdc2) Assignment Rule (variable: cdc25) Assignment Rule (variable: wee1) Assignment Rule (variable: intermediary enzyme)
Assignment Rule (variable: ubiquitin conjugating enzyme) Assignment Rule (variable: k25) Assignment Rule (variable: kwee) Assignment Rule (variable: k2)
Assignment Rule (variable: total_cyclin) Assignment Rule (variable: Y15P)    
Physical entities
Compartments Species
cytoplasm cyclin cyclin-cdc2 dimer Thr161 phosphorylated dimer(active MPF)
Tyr15 phosphorylated dimer Thr161-Tyr15 phosphorylated dimer phosphorylated cdc25
phosphorylated wee1 phosphorylated intermediary enzyme ubiquitin conjugating enzyme
cdc2 cdc25 wee1
intermediary enzyme ubiquitin conjugating enzyme  
Global parameters
total_cdc2 total_cdc25 total_wee1 total_IE
total_UbE k25 V25_prime V25_double_prime
kwee Vwee_prime Vwee_double_prime k2
V2_prime V2_double_prime k1AA k3
kinh kcak ka K_a
kbPPase K_b ke K_e
kfPPase K_f kg K_g
khPPAse K_h kc K_c
kd_anti_IE K_d total_cyclin Y15P
Reactions (23)
 
 cyclin synthesis  → [cyclin];  
 
 cyclin degradation [cyclin] → ;  
 
 cyclin-cdc2 dimer formation [cyclin] → [cyclin-cdc2 dimer];   {cdc2}
 
 Thr161 dephosphorylation [Thr161 phosphorylated dimer(active MPF)] → [cyclin-cdc2 dimer];  
 
 Tyr15 phosphorylation [cyclin-cdc2 dimer] → [Tyr15 phosphorylated dimer];  
 
 Thr161 phosphorylation [cyclin-cdc2 dimer] → [Thr161 phosphorylated dimer(active MPF)];  
 
 cyclin degradation [cyclin-cdc2 dimer] → ;  
 
 Tyr15 dephosphorylation [Tyr15 phosphorylated dimer] → [cyclin-cdc2 dimer];  
 
 Thr161 phosphorylation [Tyr15 phosphorylated dimer] → [Thr161-Tyr15 phosphorylated dimer];  
 
 cyclin degradation [Tyr15 phosphorylated dimer] → ;  
 
 Thr161 dephosphorylation [Thr161-Tyr15 phosphorylated dimer] → [Tyr15 phosphorylated dimer];  
 
 Tyr15 phosphorylation [Thr161 phosphorylated dimer(active MPF)] → [Thr161-Tyr15 phosphorylated dimer];  
 
 Tyr15 dephosphorylation [Thr161-Tyr15 phosphorylated dimer] → [Thr161 phosphorylated dimer(active MPF)];  
 
 cyclin degradation [Thr161-Tyr15 phosphorylated dimer] → ;  
 
 cyclin degradation [Thr161 phosphorylated dimer(active MPF)] → ;  
 
 cdc25 activation  → [phosphorylated cdc25];   {Thr161 phosphorylated dimer(active MPF)}
 
 cdc25 deactivation [phosphorylated cdc25] → ;  
 
 wee1 deactivation  → [phosphorylated wee1];   {Thr161 phosphorylated dimer(active MPF)}
 
 wee1 activation [phosphorylated wee1] → ;  
 
 intermediary enzyme activation  → [phosphorylated intermediary enzyme];   {Thr161 phosphorylated dimer(active MPF)}
 
 intermediary enzyme deactivation [phosphorylated intermediary enzyme] → ;  
 
 ubiquitin conjugating enzyme activation  → [ubiquitin conjugating enzyme];   {phosphorylated intermediary enzyme}
 
 ubiquitin conjugating enzyme deactivation [ubiquitin conjugating enzyme] → ;  
 
Rules (10)
 
 Assignment Rule (name: cdc2) cdc2 = total_cdc2-(dimer+p_dimer+p_dimer_p+dimer_p)
 
 Assignment Rule (name: cdc25) cdc25 = total_cdc25-cdc25_p
 
 Assignment Rule (name: wee1) wee1 = total_wee1-wee1_p
 
 Assignment Rule (name: IE) intermediary enzyme = total_IE-IE_p
 
 Assignment Rule (name: UbE) ubiquitin conjugating enzyme = total_UbE-UbE_star
 
 Assignment Rule (name: k25) k25 = V25_prime*(total_cdc25-cdc25_p)+V25_double_prime*cdc25_p
 
 Assignment Rule (name: kwee) kwee = Vwee_prime*wee1_p+Vwee_double_prime*(total_wee1-wee1_p)
 
 Assignment Rule (name: k2) k2 = V2_prime*(total_UbE-UbE_star)+V2_double_prime*UbE_star
 
 Assignment Rule (name: total_cyclin) total_cyclin = cyclin+dimer+dimer_p+p_dimer+p_dimer_p
 
 Assignment Rule (name: Y15P) Y15P = p_dimer+p_dimer_p
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 cyclin
Compartment: cytoplasm
Initial concentration: 100.0
 
 cyclin-cdc2 dimer
Compartment: cytoplasm
Initial concentration: 0.0
 
 Thr161 phosphorylated dimer(active MPF)
Compartment: cytoplasm
Initial concentration: 0.0
 
 Tyr15 phosphorylated dimer
Compartment: cytoplasm
Initial concentration: 0.0
 
 Thr161-Tyr15 phosphorylated dimer
Compartment: cytoplasm
Initial concentration: 0.0
 
 phosphorylated cdc25
Compartment: cytoplasm
Initial concentration: 0.0
 
 phosphorylated wee1
Compartment: cytoplasm
Initial concentration: 0.0
 
   phosphorylated intermediary enzyme
Compartment: cytoplasm
Initial concentration: 0.0
 
 ubiquitin conjugating enzyme
Compartment: cytoplasm
Initial concentration: 0.0
 
  cdc2
Compartment: cytoplasm
Initial concentration: 0.0
 
  cdc25
Compartment: cytoplasm
Initial concentration: 0.0
 
  wee1
Compartment: cytoplasm
Initial concentration: 0.0
 
   intermediary enzyme
Compartment: cytoplasm
Initial concentration: 0.0
 
  ubiquitin conjugating enzyme
Compartment: cytoplasm
Initial concentration: 0.0
 
Global Parameters (36)
 
   total_cdc2
Value: 100.0
Constant
 
   total_cdc25
Value: 1.0
Constant
 
   total_wee1
Value: 1.0
Constant
 
   total_IE
Value: 1.0
Constant
 
   total_UbE
Value: 1.0
Constant
 
   k25  
 
   V25_prime
Value: 0.1
Constant
 
   V25_double_prime
Value: 2.0
Constant
 
   kwee  
 
   Vwee_prime
Value: 0.1
Constant
 
   Vwee_double_prime
Value: 1.0
Constant
 
   k2  
 
   V2_prime
Value: 0.015
Constant
 
   V2_double_prime
Value: 1.0
Constant
 
   k1AA
Value: 1.0
Constant
 
   k3
Value: 0.01
Constant
 
   kinh
Value: 0.025
Constant
 
   kcak
Value: 0.25
Constant
 
   ka
Value: 0.01
Constant
 
   K_a
Value: 0.1
Constant
 
   kbPPase
Value: 0.125
Constant
 
   K_b
Value: 0.1
Constant
 
   ke
Value: 0.0133
Constant
 
   K_e
Value: 0.3
Constant
 
   kfPPase
Value: 0.1
Constant
 
   K_f
Value: 0.3
Constant
 
   kg
Value: 0.0065
Constant
 
   K_g
Value: 0.01
Constant
 
   khPPAse
Value: 0.087
Constant
 
   K_h
Value: 0.01
Constant
 
   kc
Value: 0.1
Constant
 
   K_c
Value: 0.01
Constant
 
   kd_anti_IE
Value: 0.095
Constant
 
   K_d
Value: 0.01
Constant
 
   total_cyclin  
 
   Y15P  
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000107

Curator's comment: (updated: 07 Mar 2008 14:52:19 PST)

Figure 9 reproduced with COPASI build 24

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