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BIOMD0000000370 - Vinod2011_MitoticExit

 

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Reference Publication
Publication ID: 21288956
Vinod PK, Freire P, Rattani A, Ciliberto A, Uhlmann F, Novak B.
Computational modelling of mitotic exit in budding yeast: the role of separase and Cdc14 endocycles.
J R Soc Interface 2011 Aug; 8(61): 1128-1141
Department of Biochemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.  [more]
Model
Original Model: BIOMD0000000370.origin
Submitter: Bela Novak
Submission ID: MODEL1111030000
Submission Date: 03 Nov 2011 16:25:35 UTC
Last Modification Date: 08 Mar 2012 12:34:01 UTC
Creation Date: 10 Nov 2011 16:53:58 UTC
Encoders:  Vijayalakshmi Chelliah
   Bela Novak
set #1
bqbiol:isVersionOf Gene Ontology mitotic cell cycle
Cell Cycle Ontology mitotic cell cycle
bqmodel:isDerivedFrom BioModels Database BIOMD0000000409
bqbiol:hasTaxon Taxonomy Saccharomyces cerevisiae
Notes

This model is from the article:
Computational modelling of mitotic exit in budding yeast: the role of separase and Cdc14 endocycles
Vinod PK, Freire P, Rattani A, Ciliberto A, Uhlmann F, Novak B. J R Soc Interface. 2011 Aug 7;8(61):1128-41. Epub 2011 Feb 2. 21288956 ,
Abstract:
The operating principles of complex regulatory networks are best understood with the help of mathematical modelling rather than by intuitive reasoning. Hereby, we study the dynamics of the mitotic exit (ME) control system in budding yeast by further developing the Queralt's model. A comprehensive systems view of the network regulating ME is provided based on classical experiments in the literature. In this picture, Cdc20-APC is a critical node controlling both cyclin (Clb2 and Clb5) and phosphatase (Cdc14) branches of the regulatory network. On the basis of experimental situations ranging from single to quintuple mutants, the kinetic parameters of the network are estimated. Numerical analysis of the model quantifies the dependence of ME control on the proteolytic and non-proteolytic functions of separase. We show that the requirement of the non-proteolytic function of separase for ME depends on cyclin-dependent kinase activity. The model is also used for the systematic analysis of the recently discovered Cdc14 endocycles. The significance of Cdc14 endocycles in eukaryotic cell cycle control is discussed as well.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team.
For more information see the terms of use .
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: 21288956 Submission Date: 03 Nov 2011 16:25:35 UTC Last Modification Date: 08 Mar 2012 12:34:01 UTC Creation Date: 10 Nov 2011 16:53:58 UTC
Mathematical expressions
Rules
Assignment Rule (variable: Clb2) Assignment Rule (variable: Clb5) Assignment Rule (variable: Sic1) Assignment Rule (variable: Pds1)
Assignment Rule (variable: Esp1) Assignment Rule (variable: Net1) Assignment Rule (variable: Cdc14c) Assignment Rule (variable: PP)
Assignment Rule (variable: V2) Assignment Rule (variable: V6) Assignment Rule (variable: Vdsic) Assignment Rule (variable: Vacdh)
Assignment Rule (variable: Vicdh) Assignment Rule (variable: Vaswi) Assignment Rule (variable: Viswi) Assignment Rule (variable: Vd)
Assignment Rule (variable: Vp) Assignment Rule (variable: Vexp) Rate Rule (variable: Clb2T) Rate Rule (variable: Clb5T)
Rate Rule (variable: Cln) Rate Rule (variable: Cdc20) Rate Rule (variable: Cdh1) Rate Rule (variable: Sic1T)
Rate Rule (variable: Trim2) Rate Rule (variable: Trim5) Rate Rule (variable: Swi5) Rate Rule (variable: Mcm)
Rate Rule (variable: MBF) Rate Rule (variable: Pds1T) Rate Rule (variable: Esp1T) Rate Rule (variable: Esp1b)
Rate Rule (variable: PoloT) Rate Rule (variable: Polo) Rate Rule (variable: Net1dep) Rate Rule (variable: Net1pp)
Rate Rule (variable: RENT) Rate Rule (variable: RENTp) Rate Rule (variable: Cdc14n) Rate Rule (variable: Tem1)
Rate Rule (variable: Cdc15) Rate Rule (variable: MEN)    
Physical entities
Compartments Species
cell Clb2T Clb5T Cln
Cdc20 Cdh1 Sic1T
Trim2 Trim5 Swi5
Mcm MBF Pds1T
Esp1T PoloT Polo
Net1dep Net1pp RENT
RENTp Cdc14n Tem1
Cdc15 MEN Clb2
Clb5 Sic1 Pds1
Esp1b Esp1 Net1p
Net1 Cdc14c  
Global parameters
PP PPT kpp ki
V2 kdclb2 kdclb2' kdclb2''
V6 kdclb5 kdclb5' Vdsic
kdsic' kdsic" kdsic kdsic'''
Vacdh kdcdh kdcdh' Vicdh
kpcdh kpcdh' kpcdh'' Vaswi
kaswi kaswi' Viswi kiswi
kiswi' kiswi'' Vd kd'
kd Jnet Net1T Vp
kp'' kp''' Vexp kexp
kexp' ksclb2 ksclb2' ksclb5'
ksclb5 kscln' kscln kdcln
ks20' ks20 kd20 kd20'
Jcdh kssic' kssic kasic2
kdsic2 kasic5 kdsic5 Jswi
ksmcm' ksmcm kdmcm Jmcm
Jmbf kambf kimbf' kimbf
kimbf'' kspds' kspds kdpds
kdpds' ksesp kdesp lapds
ldpds kspolo' kspolo kdpolo
kdpolo' Jpolo kapolo kapolo'
kipolo kp' lanet ldnet
kimp Jtem1 katem katem'
kitem'' kitem' kitem Jcdc15
kac15 kac15' kic15 kic15'
lamen ldmen Cdc14T Clb2nd
Swi5T      
Reactions (0)
Rules (42)
 
 Assignment Rule (name: Clb2_2) Clb2 = (Clb2T_1+Clb2nd_1)-Trim2_1
 
 Assignment Rule (name: Clb5_1) Clb5 = Clb5T_1-Trim5_1
 
 Assignment Rule (name: Sic1_1) Sic1 = (Sic1T_1-Trim2_1)-Trim5_1
 
 Assignment Rule (name: Pds1_1) Pds1 = Pds1T_1-Esp1b_1
 
 Assignment Rule (name: Esp1_1) Esp1 = Esp1T_1-Esp1b_1
 
 Assignment Rule (name: Net1_2) Net1 = ((Net1T_1-Net1p_1)-RENT_1)-Net1pp_1
 
 Assignment Rule (name: Cdc14c_1) Cdc14c = (Cdc14T_1-Cdc14n_1)-RENT_1
 
 Assignment Rule (name: PP_1) PP = PPT_1*(1+kpp_1*ki_1*Esp1_1)/(1+ki_1+Esp1_1)
 
 Assignment Rule (name: V2_1) V2 = kdclb2_1+kdclb2_2*Cdc20_1+kdclb2_3*Cdh1_1
 
 Assignment Rule (name: V6_1) V6 = kdclb5_1+kdclb5_2*Cdc20_1
 
 Assignment Rule (name: Vdsic_1) Vdsic = kdsic_3+kdsic_1*Clb5_1+kdsic_2*Clb2_2+kdsic_4*Cln_1
 
 Assignment Rule (name: Vacdh_1) Vacdh = kdcdh_1*Cdc14n_1+kdcdh_2*Cdc14c_1
 
 Assignment Rule (name: Vicdh_1) Vicdh = kpcdh_1+kpcdh_2*Clb2_2+kpcdh_3*Clb5_1
 
 Assignment Rule (name: Vaswi_1) Vaswi = kaswi_1*Cdc14n_1+kaswi_2*Cdc14c_1
 
 Assignment Rule (name: Viswi_1) Viswi = kiswi_1+kiswi_2*Clb2_2+kiswi_3*Clb5_1
 
 Assignment Rule (name: Vd_1) Vd = (kd_2*PP_1+kd_1*Cdc14n_1)/((Jnet_1+Net1T_1)-Net1dep_1)
 
 Assignment Rule (name: Vp_1) Vp = (kp_3*Clb2_2+kp_4*MEN_1)/(Jnet_1+Net1dep_1)
 
 Assignment Rule (name: Vexp_1) Vexp = kexp_1+kexp_2*MEN_1
 
 Rate Rule (name: Clb2T_1) d [ Clb2T] / d t= (ksclb2_1+ksclb2_2*Mcm_1)-V2_1*Clb2T_1
 
 Rate Rule (name: Clb5T_1) d [ Clb5T] / d t= (ksclb5_2+ksclb5_1*MBF_1)-V6_1*Clb5T_1
 
 Rate Rule (name: Cln_1) d [ Cln] / d t= (kscln_2+kscln_1*MBF_1)-kdcln_1*Cln_1
 
 Rate Rule (name: Cdc20_1) d [ Cdc20] / d t= (ks20_2+ks20_1*Mcm_1)-(kd20_1+kd20_2*Cdh1_1)*Cdc20_1
 
 Rate Rule (name: Cdh1_1) d [ Cdh1] / d t= Vacdh_1*(1-Cdh1_1)/((Jcdh_1+1)-Cdh1_1)-Vicdh_1*Cdh1_1/(Jcdh_1+Cdh1_1)
 
 Rate Rule (name: Sic1T_1) d [ Sic1T] / d t= (kssic_2+kssic_1*Swi5_1)-Vdsic_1*Sic1T_1
 
 Rate Rule (name: Trim2_1) d [ Trim2] / d t= kasic2_1*Clb2_2*Sic1_1-(kdsic2_1+V2_1+Vdsic_1)*Trim2_1
 
 Rate Rule (name: Trim5_1) d [ Trim5] / d t= kasic5_1*Clb5_1*Sic1_1-(kdsic5_1+V6_1+Vdsic_1)*Trim5_1
 
 Rate Rule (name: Swi5_1) d [ Swi5] / d t= Vaswi_1*(Swi5T_1-Swi5_1)/((Jswi_1+Swi5T_1)-Swi5_1)-Viswi_1*Swi5_1/(Jswi_1+Swi5_1)
 
 Rate Rule (name: Mcm_1) d [ Mcm] / d t= (ksmcm_3+ksmcm_1*Clb2_2)*(1-Mcm_1)/((Jmcm_1+1)-Mcm_1)-kdmcm_1*Mcm_1/(Jmcm_1+Mcm_1)
 
 Rate Rule (name: MBF_1) d [ MBF] / d t= kambf_1*(1-MBF_1)/((Jmbf_1+1)-MBF_1)-(kimbf_1*Clb2_2+kimbf_3*Clb5_1)*MBF_1/(Jmbf_1+MBF_1)
 
 Rate Rule (name: Pds1T_1) d [ Pds1T] / d t= (kspds_2+kspds_1*MBF_1)-(kdpds_1+kdpds_2*Cdc20_1)*Pds1T_1
 
 Rate Rule (name: Esp1T_1) d [ Esp1T] / d t= ksesp_1-kdesp_1*Esp1T_1
 
 Rate Rule (name: Esp1b_1) d [ Esp1b] / d t= lapds_1*Pds1_1*Esp1_1-(ldpds_1+kdesp_1+kdpds_1+kdpds_2*Cdc20_1)*Esp1b_1
 
 Rate Rule (name: PoloT_1) d [ PoloT] / d t= (kspolo_2+kspolo_1*Mcm_1)-(kdpolo_1+kdpolo_2*Cdh1_1)*PoloT_1
 
 Rate Rule (name: Polo_1) d [ Polo] / d t= ((kapolo_1+kapolo_2*Clb2_2)*(PoloT_1-Polo_1)/((Jpolo_1+PoloT_1)-Polo_1)-kipolo_1*Polo_1/(Jpolo_1+Polo_1))-(kdpolo_1+kdpolo_2*Cdh1_1)*Polo_1
 
 Rate Rule (name: Net1dep_1) d [ Net1dep] / d t= Vd_1*(Net1T_1-Net1dep_1)-Vp_1*Net1dep_1
 
 Rate Rule (name: Net1pp_1) d [ Net1pp] / d t= kp_1*Polo_1*((Net1T_1-Net1dep_1)-Net1pp_1)-Vd_1*Net1pp_1
 
 Rate Rule (name: RENT_1) d [ RENT] / d t= (lanet_1*((Net1T_1-Net1pp_1)-RENT_1)*Cdc14n_1-ldnet_1*RENT_1)-kp_1*Polo_1*RENTp_1
 
 Rate Rule (name: RENTp_1) d [ RENTp] / d t= (((Vp_1*(RENT_1-RENTp_1)-Vd_1*RENTp_1)+lanet_1*(((Net1T_1-Net1dep_1)-Net1pp_1)-RENTp_1)*Cdc14n_1)-ldnet_1*RENTp_1)-kp_1*Polo_1*RENTp_1
 
 Rate Rule (name: Cdc14n_1) d [ Cdc14n] / d t= (((kp_1*Polo_1*RENTp_1-lanet_1*((Net1T_1-Net1pp_1)-RENT_1)*Cdc14n_1)+ldnet_1*RENT_1)-Vexp_1*Cdc14n_1)+kimp_1*Cdc14c_1
 
 Rate Rule (name: Tem1_1) d [ Tem1] / d t= (katem_1+katem_2*Polo_1)*(1-Tem1_1)/((Jtem1_1+1)-Tem1_1)-(kitem_3+kitem_2/(1+kitem_1*Esp1_1))/(Jtem1_1+Tem1_1)*Tem1_1
 
 Rate Rule (name: Cdc15_1) d [ Cdc15] / d t= (kac15_1+kac15_2*Cdc14c_1)*(1-Cdc15_1)/((Jcdc15_1+1)-Cdc15_1)-(kic15_1+kic15_2*Clb2_2)*Cdc15_1/(Jcdc15_1+Cdc15_1)
 
 Rate Rule (name: MEN_1) d [ MEN] / d t= ((lamen_1*(Tem1_1-MEN_1)*(Cdc15_1-MEN_1)-ldmen_1*MEN_1)-(kitem_3+kitem_2/(1+kitem_3*Esp1_1))/(Jtem1_1+Tem1_1)*MEN_1)-(kic15_1+kic15_2*Clb2_2)/(Jcdc15_1+Cdc15_1)*MEN_1
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 Clb2T
Compartment: cell
Initial concentration: 0.999107
 
 Clb5T
Compartment: cell
Initial concentration: 0.201977
 
 Cln
Compartment: cell
Initial concentration: 0.04079
 
 Cdc20
Compartment: cell
Initial concentration: 0.0
 
 Cdh1
Compartment: cell
Initial concentration: 0.0
 
 Sic1T
Compartment: cell
Initial concentration: 0.001683
 
 Trim2
Compartment: cell
Initial concentration: 0.00145
 
 Trim5
Compartment: cell
Initial concentration: 0.0
 
 Swi5
Compartment: cell
Initial concentration: 0.0
 
 Mcm
Compartment: cell
Initial concentration: 0.996743
 
 MBF
Compartment: cell
Initial concentration: 0.001977
 
 Pds1T
Compartment: cell
Initial concentration: 0.601977
 
 Esp1T
Compartment: cell
Initial concentration: 0.25
 
 PoloT
Compartment: cell
Initial concentration: 1.0
 
 Polo
Compartment: cell
Initial concentration: 1.0
 
 Net1dep
Compartment: cell
Initial concentration: 0.0119
 
 Net1pp
Compartment: cell
Initial concentration: 0.0119
 
 RENT
Compartment: cell
Initial concentration: 0.483
 
 RENTp
Compartment: cell
Initial concentration: 0.014
 
 Cdc14n
Compartment: cell
Initial concentration: 0.00214
 
 Tem1
Compartment: cell
Initial concentration: 1.0
 
 Cdc15
Compartment: cell
Initial concentration: 0.933
 
 MEN
Compartment: cell
Initial concentration: 0.0
 
  Clb2
Compartment: cell
 
  Clb5
Compartment: cell
 
  Sic1
Compartment: cell
 
  Pds1
Compartment: cell
 
 Esp1b
Compartment: cell
Initial concentration: 0.24857
 
  Esp1
Compartment: cell
 
 Net1p
Compartment: cell
Initial concentration: 0.013
 
  Net1
Compartment: cell
 
  Cdc14c
Compartment: cell
 
Global Parameters (105)
 
   PP
Value: NaN
 
   PPT
Value: 1.0
Constant
 
   kpp
Value: 0.1
Constant
 
   ki
Value: 40.0
Constant
 
   V2
Value: NaN
 
   kdclb2
Value: 0.02
Constant
 
   kdclb2'
Value: 0.1
Constant
 
   kdclb2''
Value: 0.4
Constant
 
   V6
Value: NaN
 
   kdclb5
Value: 0.01
Constant
 
   kdclb5'
Value: 1.0
Constant
 
   Vdsic
Value: NaN
 
   kdsic'
Value: 2.0
Constant
 
   kdsic"
Value: 2.0
Constant
 
   kdsic
Value: 0.04
Constant
 
   kdsic'''
Value: 1.5
Constant
 
   Vacdh
Value: NaN
 
   kdcdh
Value: 0.03
Constant
 
   kdcdh'
Value: 0.3
Constant
 
   Vicdh
Value: NaN
 
   kpcdh
Value: 0.001
Constant
 
   kpcdh'
Value: 0.04
Constant
 
   kpcdh''
Value: 0.75
Constant
 
   Vaswi
Value: NaN
 
   kaswi
Value: 0.2
Constant
 
   kaswi'
Value: 1.0
Constant
 
   Viswi
Value: NaN
 
   kiswi
Value: 0.01
Constant
 
   kiswi'
Value: 0.5
Constant
 
   kiswi''
Value: 0.75
Constant
 
   Vd
Value: NaN
 
   kd'
Value: 0.1
Constant
 
   kd
Value: 0.45
Constant
 
   Jnet
Value: 0.05
Constant
 
   Net1T
Value: 1.0
Constant
 
   Vp
Value: NaN
 
   kp''
Value: 0.2
Constant
 
   kp'''
Value: 3.0
Constant
 
   Vexp
Value: NaN
 
   kexp
Value: 0.01
Constant
 
   kexp'
Value: 20.0
Constant
 
   ksclb2
Value: 0.015
Constant
 
   ksclb2'
Value: 0.005
Constant
 
   ksclb5'
Value: 0.01
Constant
 
   ksclb5
Value: 0.002
Constant
 
   kscln'
Value: 0.1
Constant
 
   kscln
Value: 0.01
Constant
 
   kdcln
Value: 0.25
Constant
 
   ks20'
Value: 0.05
Constant
 
   ks20
Value: 0.001
Constant
 
   kd20
Value: 0.1
Constant
 
   kd20'
Value: 1.0
Constant
 
   Jcdh
Value: 0.01
Constant
 
   kssic'
Value: 0.2
Constant
 
   kssic
Value: 0.004
Constant
 
   kasic2
Value: 40.0
Constant
 
   kdsic2
Value: 0.1
Constant
 
   kasic5
Value: 10.0
Constant
 
   kdsic5
Value: 0.1
Constant
 
   Jswi
Value: 0.1
Constant
 
   ksmcm'
Value: 1.0
Constant
 
   ksmcm
Value: 0.01
Constant
 
   kdmcm
Value: 0.25
Constant
 
   Jmcm
Value: 0.01
Constant
 
   Jmbf
Value: 0.01
Constant
 
   kambf
Value: 0.1
Constant
 
   kimbf'
Value: 0.5
Constant
 
   kimbf
Constant
 
   kimbf''
Value: 0.5
Constant
 
   kspds'
Value: 0.01
Constant
 
   kspds
Value: 0.006
Constant
 
   kdpds
Value: 0.01
Constant
 
   kdpds'
Value: 2.0
Constant
 
   ksesp
Value: 0.001
Constant
 
   kdesp
Value: 0.004
Constant
 
   lapds
Value: 500.0
Constant
 
   ldpds
Value: 1.0
Constant
 
   kspolo'
Value: 0.05
Constant
 
   kspolo
Value: 0.001
Constant
 
   kdpolo
Value: 0.05
Constant
 
   kdpolo'
Value: 0.5
Constant
 
   Jpolo
Value: 0.1
Constant
 
   kapolo
Constant
 
   kapolo'
Value: 1.0
Constant
 
   kipolo
Value: 0.1
Constant
 
   kp'
Value: 2.0
Constant
 
   lanet
Value: 500.0
Constant
 
   ldnet
Value: 1.0
Constant
 
   kimp
Value: 1.0
Constant
 
   Jtem1
Value: 0.005
Constant
 
   katem
Constant
 
   katem'
Value: 0.6
Constant
 
   kitem''
Value: 20.0
Constant
 
   kitem'
Value: 1.0
Constant
 
   kitem
Value: 0.1
Constant
 
   Jcdc15
Value: 1.0
Constant
 
   kac15
Value: 0.03
Constant
 
   kac15'
Value: 0.5
Constant
 
   kic15
Value: 0.03
Constant
 
   kic15'
Value: 0.2
Constant
 
   lamen
Value: 100.0
 
   ldmen
Value: 0.1
Constant
 
   Cdc14T
Value: 0.5
Constant
 
   Clb2nd
Constant
 
   Swi5T
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000370

Curator's comment: (updated: 10 Nov 2011 16:53:46 GMT)

Figure 2 of the reference publication has been reproduced here. The model was simulated using Copasi v4.7 (Build 34)

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