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BIOMD0000000056 - Chen2004 - Cell Cycle Regulation

 

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Reference Publication
Publication ID: 15169868
Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ.
Integrative analysis of cell cycle control in budding yeast.
Mol. Biol. Cell 2004 Aug; 15(8): 3841-3862
Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0406, USA. kchen@vt.edu  [more]
Model
Original Model: BIOMD0000000056.xml.origin
Submitter: Nicolas Le Novère
Submission ID: MODEL6624073334
Submission Date: 10 May 2006 12:47:09 UTC
Last Modification Date: 07 Jun 2013 10:59:38 UTC
Creation Date: 08 May 2006 11:05:34 UTC
Encoders:  Harish Dharuri
   Katherine C Chen
   Lukas Endler
set #1
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
bqbiol:isHomologTo Reactome REACT_152
bqbiol:isVersionOf Gene Ontology mitotic cell cycle
bqbiol:is KEGG Pathway sce04111
Notes
Chen2004 - Cell Cycle Regulation

This is a hypothetical model of cell cycle that describes the molecular mechanism for regulating DNA synthesis, bud emergence, mitosis, and cell division in budding yeast.

This model is described in the article:

Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ
Mol. Biol. Cell. [2004 Aug; Volume: 15 (Issue: 8 )] Page info: 3841-62

Abstract:

The adaptive responses of a living cell to internal and external signals are controlled by networks of proteins whose interactions are so complex that the functional integration of the network cannot be comprehended by intuitive reasoning alone. Mathematical modeling, based on biochemical rate equations, provides a rigorous and reliable tool for unraveling the complexities of molecular regulatory networks. The budding yeast cell cycle is a challenging test case for this approach, because the control system is known in exquisite detail and its function is constrained by the phenotypic properties of >100 genetically engineered strains. We show that a mathematical model built on a consensus picture of this control system is largely successful in explaining the phenotypes of mutants described so far. A few inconsistencies between the model and experiments indicate aspects of the mechanism that require revision. In addition, the model allows one to frame and critique hypotheses about how the division cycle is regulated in wild-type and mutant cells, to predict the phenotypes of new mutant combinations, and to estimate the effective values of biochemical rate constants that are difficult to measure directly in vivo.

The model reproduces the time profiles of the different species in Figure 2 of the paper. The figure depicts the cycle of a daughter cell. Since the Mass Doubling Time (MDT) is 90 minutes, time t=90 from the model simulation will correspond to time t=0 in the paper. The model was successfully tested using MathSBML and SBML odeSolver.

To create a valid SBML file, a local parameter k=1 was added in the reaction 'Inactivation_274_CDC20'. Also, in order to annotate the protein and to have the interaction in the reaction graph to match figure 1 of the article, the reaction rate constants k_{mad2}, k_{bub2} and k_{lte1} are considered as species and renamed as MAD2, BUB2 and LTE1 in the model.

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.

Model
Publication ID: 15169868 Submission Date: 10 May 2006 12:47:09 UTC Last Modification Date: 07 Jun 2013 10:59:38 UTC Creation Date: 08 May 2006 11:05:34 UTC
Mathematical expressions
Reactions
Growth Synthesis of CLN2 Degradation of CLN2 Synthesis of CLB2
Degradation of CLB2 Synthesis of CLB5 Degradation of CLB5 Synthesis of SIC1
Phosphorylation of SIC1 Dephosphorylation of SIC1 Fast Degradation of SIC1P Assoc. of CLB2 and SIC1
Dissoc. of CLB2/SIC1 complex Assoc. of CLB5 and SIC1 Dissoc. of CLB5/SIC1 Phosphorylation of C2
Dephosphorylation of C2P Phosphorylation of C5 Dephosphorylation of C5P Degradation of CLB2 in C2
Degradation of CLB5 in C5 Degradation of SIC1 in C2P Degradation of SIC1P in C5P Degradation of CLB2 in C2P
Degradation of CLB5 in C5P CDC6 synthesis Phosphorylation of CDC6 Dephosphorylation of CDC6
Degradation of CDC6P CLB2/CDC6 complex formation CLB2/CDC6 dissociation CLB5/CDC6 complex formation
CLB5/CDC6 dissociation F2 phosphorylation F2P dephosphorylation F5 phosphorylation
F5P dephosphorylation CLB2 degradation in F2 CLB5 degradation in F5 CDC6 degradation in F2P
CDC6 degradation in F5P CLB2 degradation in F2P CLB5 degradation in F5P Synthesis of SWI5
Degradation of SWI5 Degradation of SWI5P Activation of SWI5 Inactivation of SWI5
Activation of IEP Inactivation Synthesis of inactive CDC20 Degradation of inactiveCDC20
Degradation of active CDC20 Activation of CDC20 Inactivation CDH1 synthesis
CDH1 degradation CDH1i degradation CDH1i activation Inactivation
CDC14 synthesis CDC14 degradation Assoc. with NET1 to form RENT Dissoc. from RENT
Assoc with NET1P to form RENTP Dissoc. from RENP Net1 synthesis Net1 degradation
Net1P degradation NET1 phosphorylation dephosphorylation RENT phosphorylation
dephosphorylation Degradation of NET1 in RENT Degradation of NET1P in RENTP Degradation of CDC14 in RENT
Degradation of CDC14 in RENTP TEM1 activation inactivation CDC15 activation
inactivation PPX synthesis degradation PDS1 synthesis
degradation Degradation of PDS1 in PE Assoc. with ESP1 to form PE Disso. from PE
DNA synthesis Negative regulation of DNA synthesis Budding Negative regulation of Cell budding
Spindle formation Spindle disassembly    
Rules
Assignment Rule (variable: BCK2) Assignment Rule (variable: Visbf) Assignment Rule (variable: CLN3) Assignment Rule (variable: Vppc1)
Assignment Rule (variable: Vppf6) Assignment Rule (variable: Vaiep) Assignment Rule (variable: Vacdh) Assignment Rule (variable: Vicdh)
Assignment Rule (variable: Vkpnet) Assignment Rule (variable: Vppnet) Assignment Rule (variable: Vasbf) Assignment Rule (variable: SBF)
Assignment Rule (variable: MCM1) Assignment Rule (variable: mu) Assignment Rule (variable: D) Assignment Rule (variable: F)
Assignment Rule (variable: Vd2c1) Assignment Rule (variable: Vd2f6) Assignment Rule (variable: Vkpc1) Assignment Rule (variable: Vkpf6)
Assignment Rule (variable: Vdb2) Assignment Rule (variable: Vdb5) Assignment Rule (variable: Vdpds) Assignment Rule (variable: Vdppx)
Assignment Rule (variable: CLB2T) Assignment Rule (variable: CLB5T) Assignment Rule (variable: CDC14T) Assignment Rule (variable: NET1T)
Assignment Rule (variable: SIC1T) Assignment Rule (variable: CDC6T) Assignment Rule (variable: CKIT) Assignment Rule (variable: CDC15i)
Assignment Rule (variable: IE) Assignment Rule (variable: PE) Assignment Rule (variable: TEM1GDP)  
Events
reset ORI start DNA synthesis spindle checkpoint cell division
Physical entities
Compartments Species
cell BCK2 BUB2 BUD
C2 C2P C5
C5P CDC14 CDC14T
CDC15 CDC15i CDC20
CDC20i CDC6 CDC6P
CDC6T CDH1 CDH1i
CKIT CLB2 CLB2T
CLB5 CLB5T CLN2
CLN3 ESP1 F2
F2P F5 F5P
IE IEP LTE1
MAD2 MASS MCM1
NET1 NET1P NET1T
ORI PDS1 PE
PPX RENT RENTP
SBF SIC1 SIC1P
SIC1T SPN SWI5
SWI5P TEM1GDP TEM1GTP
Global parameters
b0 bub2h bub2l C0
CDC15T Dn3 ebudb5 ebudn2
ebudn3 ec1b2 ec1b5 ec1k2
ec1n2 ec1n3 ef6b2 ef6b5
ef6k2 ef6n2 ef6n3 eicdhb2
eicdhb5 eicdhn2 eicdhn3 eorib2
eorib5 esbfb5 esbfn2 esbfn3
ESP1T IET J20ppx Jacdh
Jaiep Jamcm Jasbf Jatem
Jd2c1 Jd2f6 Jicdh Jiiep
Jimcm Jisbf Jitem Jn3
Jpds Jspn ka15' ka15''
ka15p ka20' ka20'' kacdh'
kacdh'' kaiep kamcm kasb2
kasb5 kasbf kasesp kasf2
kasf5 kasrent kasrentp kaswi
kd14 kd1c1 kd1f6 kd1pds'
kd20 kd2c1 kd2f6 kd2pds''
kd3c1 kd3f6 kd3pds'' kdb2'
kdb2'' kdb2p kdb5' kdb5''
kdbud kdcdh kdib2 kdib5
kdiesp kdif2 kdif5 kdirent
kdirentp kdn2 kdnet kdori
kdppx' kdppx'' kdspn kdswi
KEZ KEZ2 ki15 kicdh'
kicdh'' kiiep kimcm kisbf'
kisbf'' kiswi kkpnet' kkpnet''
kppc1 kppf6 kppnet' kppnet''
ks14 ks1pds'' ks20' ks20''
ks2pds'' ksb2' ksb2'' ksb5'
ksb5'' ksbud ksc1' ksc1''
kscdh ksf6' ksf6'' ksf6'''
ksn2' ksn2'' ksnet ksori
kspds' ksppx ksspn ksswi'
ksswi'' lte1h lte1l mad2h
mad2l mdt TEM1T D
mu Vdb5 Vdb2 Vasbf
Visbf Vkpc1 Vkpf6 Vacdh
Vicdh Vppnet Vkpnet Vdppx
Vdpds Vaiep Vd2c1 Vd2f6
Vppc1 Vppf6 F  
Reactions (94)
 
 Growth  → [MASS];  
 
 Synthesis of CLN2  → [CLN2];   {SBF} , {MASS}
 
 Degradation of CLN2 [CLN2] → ;  
 
 Synthesis of CLB2  → [CLB2];   {MCM1} , {MASS}
 
 Degradation of CLB2 [CLB2] → ;  
 
 Synthesis of CLB5  → [CLB5];   {SBF} , {MASS}
 
 Degradation of CLB5 [CLB5] → ;  
 
 Synthesis of SIC1  → [SIC1];   {SWI5}
 
 Phosphorylation of SIC1 [SIC1] → [SIC1P];  
 
 Dephosphorylation of SIC1 [SIC1P] → [SIC1];  
 
 Fast Degradation of SIC1P [SIC1P] → ;  
 
 Assoc. of CLB2 and SIC1 [CLB2] + [SIC1] → [C2];  
 
 Dissoc. of CLB2/SIC1 complex [C2] → [CLB2] + [SIC1];  
 
 Assoc. of CLB5 and SIC1 [CLB5] + [SIC1] → [C5];  
 
 Dissoc. of CLB5/SIC1 [C5] → [CLB5] + [SIC1];  
 
 Phosphorylation of C2 [C2] → [C2P];  
 
 Dephosphorylation of C2P [C2P] → [C2];  
 
 Phosphorylation of C5 [C5] → [C5P];  
 
 Dephosphorylation of C5P [C5P] → [C5];  
 
 Degradation of CLB2 in C2 [C2] → [SIC1];  
 
 Degradation of CLB5 in C5 [C5] → [SIC1];  
 
 Degradation of SIC1 in C2P [C2P] → [CLB2];  
 
 Degradation of SIC1P in C5P [C5P] → [CLB5];  
 
 Degradation of CLB2 in C2P [C2P] → [SIC1P];  
 
 Degradation of CLB5 in C5P [C5P] → [SIC1P];  
 
 CDC6 synthesis  → [CDC6];   {SWI5} , {SBF}
 
 Phosphorylation of CDC6 [CDC6] → [CDC6P];  
 
 Dephosphorylation of CDC6 [CDC6P] → [CDC6];  
 
 Degradation of CDC6P [CDC6P] → ;  
 
 CLB2/CDC6 complex formation [CLB2] + [CDC6] → [F2];  
 
 CLB2/CDC6 dissociation [F2] → [CLB2] + [CDC6];  
 
 CLB5/CDC6 complex formation [CLB5] + [CDC6] → [F5];  
 
 CLB5/CDC6 dissociation [F5] → [CLB5] + [CDC6];  
 
 F2 phosphorylation [F2] → [F2P];  
 
 F2P dephosphorylation [F2P] → [F2];  
 
 F5 phosphorylation [F5] → [F5P];  
 
 F5P dephosphorylation [F5P] → [F5];  
 
 CLB2 degradation in F2 [F2] → [CDC6];  
 
 CLB5 degradation in F5 [F5] → [CDC6];  
 
 CDC6 degradation in F2P [F2P] → [CLB2];  
 
 CDC6 degradation in F5P [F5P] → [CLB5];  
 
 CLB2 degradation in F2P [F2P] → [CDC6P];  
 
 CLB5 degradation in F5P [F5P] → [CDC6P];  
 
 Synthesis of SWI5  → [SWI5];   {MCM1}
 
 Degradation of SWI5 [SWI5] → ;  
 
 Degradation of SWI5P [SWI5P] → ;  
 
 Activation of SWI5 [SWI5P] → [SWI5];   {CDC14}
 
 Inactivation of SWI5 [SWI5] → [SWI5P];   {CLB2}
 
 Activation of IEP [IE] → [IEP];  
 
 Inactivation [IEP] → [IE];  
 
 Synthesis of inactive CDC20  → [CDC20i];   {MCM1}
 
 Degradation of inactiveCDC20 [CDC20i] → ;  
 
 Degradation of active CDC20 [CDC20] → ;  
 
 Activation of CDC20 [CDC20i] → [CDC20];   {IEP}
 
 Inactivation [CDC20] → [CDC20i];   {MAD2}
 
 CDH1 synthesis  → [CDH1];  
 
 CDH1 degradation [CDH1] → ;  
 
 CDH1i degradation [CDH1i] → ;  
 
 CDH1i activation [CDH1i] → [CDH1];  
 
 Inactivation [CDH1] → [CDH1i];  
 
 CDC14 synthesis  → [CDC14];  
 
 CDC14 degradation [CDC14] → ;  
 
 Assoc. with NET1 to form RENT [CDC14] + [NET1] → [RENT];  
 
 Dissoc. from RENT [RENT] → [NET1] + [CDC14];  
 
 Assoc with NET1P to form RENTP [CDC14] + [NET1P] → [RENTP];  
 
 Dissoc. from RENP [RENTP] → [CDC14] + [NET1P];  
 
 Net1 synthesis  → [NET1];  
 
 Net1 degradation [NET1] → ;  
 
 Net1P degradation [NET1P] → ;  
 
 NET1 phosphorylation [NET1] → [NET1P];  
 
 dephosphorylation [NET1P] → [NET1];  
 
 RENT phosphorylation [RENT] → [RENTP];  
 
 dephosphorylation [RENTP] → [RENT];  
 
 Degradation of NET1 in RENT [RENT] → [CDC14];  
 
 Degradation of NET1P in RENTP [RENTP] → [CDC14];  
 
 Degradation of CDC14 in RENT [RENT] → [NET1];  
 
 Degradation of CDC14 in RENTP [RENTP] → [NET1P];  
 
 TEM1 activation [TEM1GDP] → [TEM1GTP];   {LTE1}
 
 inactivation [TEM1GTP] → [TEM1GDP];   {BUB2}
 
 CDC15 activation [CDC15i] → [CDC15];   {TEM1GDP} , {TEM1GTP} , {CDC14}
 
 inactivation [CDC15] → [CDC15i];  
 
 PPX synthesis  → [PPX];  
 
 degradation [PPX] → ;  
 
 PDS1 synthesis  → [PDS1];   {SBF} , {MCM1}
 
 degradation [PDS1] → ;  
 
 Degradation of PDS1 in PE [PE] → [ESP1];  
 
 Assoc. with ESP1 to form PE [PDS1] + [ESP1] → [PE];  
 
 Disso. from PE [PE] → [PDS1] + [ESP1];  
 
 DNA synthesis  → [ORI];   {CLB5} , {CLB2}
 
 Negative regulation of DNA synthesis [ORI] → ;  
 
 Budding  → [BUD];   {CLN2} , {CLN3} , {CLB5}
 
 Negative regulation of Cell budding [BUD] → ;  
 
 Spindle formation  → [SPN];   {CLB2}
 
 Spindle disassembly [SPN] → ;  
 
Rules (35)
 
 Assignment Rule (name: BCK2) BCK2 = b0*MASS
 
 Assignment Rule (name: Visbf) Visbf = kisbf_p+kisbf_p_p*CLB2
 
 Assignment Rule (name: CLN3) CLN3 = C0*Dn3*MASS/(Jn3+Dn3*MASS)
 
 Assignment Rule (name: Vppc1) Vppc1 = kppc1*CDC14
 
 Assignment Rule (name: Vppf6) Vppf6 = kppf6*CDC14
 
 Assignment Rule (name: Vaiep) Vaiep = kaiep*CLB2
 
 Assignment Rule (name: Vacdh) Vacdh = kacdh_p+kacdh_p_p*CDC14
 
 Assignment Rule (name: Vicdh) Vicdh = kicdh_p+kicdh_p_p*(eicdhn3*CLN3+eicdhn2*CLN2+eicdhb5*CLB5+eicdhb2*CLB2)
 
 Assignment Rule (name: Vkpnet) Vkpnet = (kkpnet_p+kkpnet_p_p*CDC15)*MASS
 
 Assignment Rule (name: Vppnet) Vppnet = kppnet_p+kppnet_p_p*PPX
 
 Assignment Rule (name: Vasbf) Vasbf = kasbf*(esbfn2*CLN2+esbfn3*(CLN3+BCK2)+esbfb5*CLB5)
 
 Assignment Rule (name: SBF) SBF = GK_219(Vasbf, Visbf, Jasbf, Jisbf)
 
 Assignment Rule (name: MCM1) MCM1 = GK_219(kamcm*CLB2, kimcm, Jamcm, Jimcm)
 
 Assignment Rule (name: mu) mu = log(2)/mdt
 
 Assignment Rule (name: D) D = 1.026/mu-32
 
 Assignment Rule (name: F) F = exp((-mu)*D)
 
 Assignment Rule (name: Vd2c1) Vd2c1 = kd2c1*(ec1n3*CLN3+ec1k2*BCK2+ec1n2*CLN2+ec1b5*CLB5+ec1b2*CLB2)
 
 Assignment Rule (name: Vd2f6) Vd2f6 = kd2f6*(ef6n3*CLN3+ef6k2*BCK2+ef6n2*CLN2+ef6b5*CLB5+ef6b2*CLB2)
 
 Assignment Rule (name: Vkpc1) Vkpc1 = kd1c1+Vd2c1/(Jd2c1+SIC1+C2+C5+SIC1P+C2P+C5P)
 
 Assignment Rule (name: Vkpf6) Vkpf6 = kd1f6+Vd2f6/(Jd2f6+CDC6+F2+F5+CDC6P+F2P+F5P)
 
 Assignment Rule (name: Vdb2) Vdb2 = kdb2_p+kdb2_p_p*CDH1+kdb2p*CDC20
 
 Assignment Rule (name: Vdb5) Vdb5 = kdb5_p+kdb5_p_p*CDC20
 
 Assignment Rule (name: Vdpds) Vdpds = kd1pds_p+kd2pds_p_p*CDC20+kd3pds_p_p*CDH1
 
 Assignment Rule (name: Vdppx) Vdppx = kdppx_p+kdppx_p_p*(J20ppx+CDC20)*Jpds/(Jpds+PDS1)
 
 Assignment Rule (name: CLB2T) CLB2T = CLB2+C2+C2P+F2+F2P
 
 Assignment Rule (name: CLB5T) CLB5T = CLB5+C5+C5P+F5+F5P
 
 Assignment Rule (name: CDC14T) CDC14T = CDC14+RENT+RENTP
 
 Assignment Rule (name: NET1T) NET1T = NET1+NET1P+RENT+RENTP
 
 Assignment Rule (name: SIC1T) SIC1T = SIC1+C2+C5+SIC1P+C2P+C5P
 
 Assignment Rule (name: CDC6T) CDC6T = CDC6+F2+F5+CDC6P+F2P+F5P
 
 Assignment Rule (name: CKIT) CKIT = SIC1T+CDC6T
 
 Assignment Rule (name: CDC15i) CDC15i = CDC15T-CDC15
 
 Assignment Rule (name: IE) IE = IET-IEP
 
 Assignment Rule (name: PE) PE = ESP1T-ESP1
 
 Assignment Rule (name: TEM1GDP) TEM1GDP = TEM1T-TEM1GTP
 
Events (4)
 
 reset ORI
ORI = 0
 
 start DNA synthesis
MAD2 = mad2h
BUB2 = bub2h
 
 spindle checkpoint
MAD2 = mad2l
LTE1 = lte1h
BUB2 = bub2l
 
 cell division
MASS = F*MASS
LTE1 = lte1l
BUD = 0
SPN = 0
 
Functions (5)
 
 BB lambda(A1, A2, A3, A4, A2-A1+A3*A2+A4*A1)
 
 GK 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)))
 
 Michaelis-Menten lambda(M1, J1, k1, S1, k1*S1*M1/(J1+S1))
 
 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
 
  BCK2
Compartment: cell
 
 BUB2
Compartment: cell
Initial amount: 0.2
 
 BUD
Compartment: cell
Initial amount: 0.008473
 
 C2
Compartment: cell
Initial amount: 0.238404
 
 C2P
Compartment: cell
Initial amount: 0.024034
 
 C5
Compartment: cell
Initial amount: 0.070081
 
 C5P
Compartment: cell
Initial amount: 0.006878
 
 CDC14
Compartment: cell
Initial amount: 0.468344
 
  CDC14T
Compartment: cell
Initial amount: 2.0
 
 CDC15
Compartment: cell
Initial amount: 0.656533
 
  CDC15i
Compartment: cell
 
 CDC20
Compartment: cell
Initial amount: 0.444296
 
 CDC20i
Compartment: cell
Initial amount: 1.472044
 
 CDC6
Compartment: cell
Initial amount: 0.10758
 
 CDC6P
Compartment: cell
Initial amount: 0.015486
 
  CDC6T
Compartment: cell
 
 CDH1
Compartment: cell
Initial amount: 0.930499
 
 CDH1i
Compartment: cell
Initial amount: 0.0695
 
  CKIT
Compartment: cell
 
 CLB2
Compartment: cell
Initial amount: 0.1469227
 
  CLB2T
Compartment: cell
Initial amount: 0.17
 
 CLB5
Compartment: cell
Initial amount: 0.0518014
 
  CLB5T
Compartment: cell
Initial amount: 0.12
 
 CLN2
Compartment: cell
Initial amount: 0.0652511
 
  CLN3
Compartment: cell
 
 ESP1
Compartment: cell
Initial amount: 0.301313
 
 F2
Compartment: cell
Initial amount: 0.236058
 
 F2P
Compartment: cell
Initial amount: 0.0273938
 
 F5
Compartment: cell
Initial amount: 7.24E-5
 
 F5P
Compartment: cell
Initial amount: 7.91E-5
 
  IE
Compartment: cell
 
 IEP
Compartment: cell
Initial amount: 0.1015
 
 LTE1
Compartment: cell
Initial amount: 0.1
 
 MAD2
Compartment: cell
Initial amount: 0.01
 
 MASS
Compartment: cell
Initial amount: 1.206019
 
  MCM1
Compartment: cell
 
 NET1
Compartment: cell
Initial amount: 0.018645
 
 NET1P
Compartment: cell
Initial amount: 0.970271
 
  NET1T
Compartment: cell
Initial amount: 2.8
 
   ORI
Compartment: cell
Initial amount: 9.09E-4
 
 PDS1
Compartment: cell
Initial amount: 0.025612
 
  PE
Compartment: cell
 
 PPX
Compartment: cell
Initial amount: 0.123179
 
 RENT
Compartment: cell
Initial amount: 1.04954
 
 RENTP
Compartment: cell
Initial amount: 0.6
 
  SBF
Compartment: cell
 
 SIC1
Compartment: cell
Initial amount: 0.0228776
 
 SIC1P
Compartment: cell
Initial amount: 0.00641
 
  SIC1T
Compartment: cell
 
 SPN
Compartment: cell
Initial amount: 0.03
 
 SWI5
Compartment: cell
Initial amount: 0.95
 
 SWI5P
Compartment: cell
Initial amount: 0.02
 
  TEM1GDP
Compartment: cell
 
 TEM1GTP
Compartment: cell
Initial amount: 0.9
 
Global Parameters (163)
 
   b0
Value: 0.054
Constant
 
   bub2h
Value: 1.0
Constant
 
   bub2l
Value: 0.2
 
   C0
Value: 0.4
Constant
 
   CDC15T
Value: 1.0
 
   Dn3
Value: 1.0
Constant
 
   ebudb5
Value: 1.0
Constant
 
   ebudn2
Value: 0.25
Constant
 
   ebudn3
Value: 0.05
Constant
 
   ec1b2
Value: 0.45
Constant
 
   ec1b5
Value: 0.1
Constant
 
   ec1k2
Value: 0.03
Constant
 
   ec1n2
Value: 0.06
Constant
 
   ec1n3
Value: 0.3
Constant
 
   ef6b2
Value: 0.55
Constant
 
   ef6b5
Value: 0.1
Constant
 
   ef6k2
Value: 0.03
Constant
 
   ef6n2
Value: 0.06
Constant
 
   ef6n3
Value: 0.3
Constant
 
   eicdhb2
Value: 1.2
Constant
 
   eicdhb5
Value: 8.0
Constant
 
   eicdhn2
Value: 0.4
Constant
 
   eicdhn3
Value: 0.25
Constant
 
   eorib2
Value: 0.45
Constant
 
   eorib5
Value: 0.9
Constant
 
   esbfb5
Value: 2.0
Constant
 
   esbfn2
Value: 2.0
Constant
 
   esbfn3
Value: 10.0
Constant
 
   ESP1T
Value: 1.0
 
   IET
Value: 1.0
 
   J20ppx
Value: 0.15
Constant
 
   Jacdh
Value: 0.03
Constant
 
   Jaiep
Value: 0.1
Constant
 
   Jamcm
Value: 0.1
Constant
 
   Jasbf
Value: 0.01
Constant
 
   Jatem
Value: 0.1
Constant
 
   Jd2c1
Value: 0.05
Constant
 
   Jd2f6
Value: 0.05
Constant
 
   Jicdh
Value: 0.03
Constant
 
   Jiiep
Value: 0.1
Constant
 
   Jimcm
Value: 0.1
Constant
 
   Jisbf
Value: 0.01
Constant
 
   Jitem
Value: 0.1
Constant
 
   Jn3
Value: 6.0
Constant
 
   Jpds
Value: 0.04
Constant
 
   Jspn
Value: 0.14
Constant
 
   ka15'
Value: 0.0020
Constant
 
   ka15''
Value: 1.0
Constant
 
   ka15p
Value: 0.0010
Constant
 
   ka20'
Value: 0.05
Constant
 
   ka20''
Value: 0.2
Constant
 
   kacdh'
Value: 0.01
Constant
 
   kacdh''
Value: 0.8
Constant
 
   kaiep
Value: 0.1
Constant
 
   kamcm
Value: 1.0
Constant
 
   kasb2
Value: 50.0
Constant
 
   kasb5
Value: 50.0
Constant
 
   kasbf
Value: 0.38
Constant
 
   kasesp
Value: 50.0
Constant
 
   kasf2
Value: 15.0
Constant
 
   kasf5
Value: 0.01
Constant
 
   kasrent
Value: 200.0
Constant
 
   kasrentp
Value: 1.0
Constant
 
   kaswi
Value: 2.0
Constant
 
   kd14
Value: 0.1
Constant
 
   kd1c1
Value: 0.01
Constant
 
   kd1f6
Value: 0.01
Constant
 
   kd1pds'
Value: 0.01
Constant
 
   kd20
Value: 0.3
Constant
 
   kd2c1
Value: 1.0
Constant
 
   kd2f6
Value: 1.0
Constant
 
   kd2pds''
Value: 0.2
Constant
 
   kd3c1
Value: 1.0
Constant
 
   kd3f6
Value: 1.0
Constant
 
   kd3pds''
Value: 0.04
Constant
 
   kdb2'
Value: 0.0030
Constant
 
   kdb2''
Value: 0.4
Constant
 
   kdb2p
Value: 0.15
Constant
 
   kdb5'
Value: 0.01
Constant
 
   kdb5''
Value: 0.16
Constant
 
   kdbud
Value: 0.06
Constant
 
   kdcdh
Value: 0.01
Constant
 
   kdib2
Value: 0.05
Constant
 
   kdib5
Value: 0.06
Constant
 
   kdiesp
Value: 0.5
Constant
 
   kdif2
Value: 0.5
Constant
 
   kdif5
Value: 0.01
Constant
 
   kdirent
Value: 1.0
Constant
 
   kdirentp
Value: 2.0
Constant
 
   kdn2
Value: 0.12
Constant
 
   kdnet
Value: 0.03
Constant
 
   kdori
Value: 0.06
Constant
 
   kdppx'
Value: 0.17
Constant
 
   kdppx''
Value: 2.0
Constant
 
   kdspn
Value: 0.06
Constant
 
   kdswi
Value: 0.08
Constant
 
   KEZ
Value: 0.3
 
   KEZ2
Value: 0.2
 
   ki15
Value: 0.5
Constant
 
   kicdh'
Value: 0.0010
Constant
 
   kicdh''
Value: 0.08
Constant
 
   kiiep
Value: 0.15
Constant
 
   kimcm
Value: 0.15
Constant
 
   kisbf'
Value: 0.6
Constant
 
   kisbf''
Value: 8.0
Constant
 
   kiswi
Value: 0.05
Constant
 
   kkpnet'
Value: 0.01
Constant
 
   kkpnet''
Value: 0.6
Constant
 
   kppc1
Value: 4.0
Constant
 
   kppf6
Value: 4.0
Constant
 
   kppnet'
Value: 0.05
Constant
 
   kppnet''
Value: 3.0
Constant
 
   ks14
Value: 0.2
Constant
 
   ks1pds''
Value: 0.03
Constant
 
   ks20'
Value: 0.0060
Constant
 
   ks20''
Value: 0.6
Constant
 
   ks2pds''
Value: 0.055
Constant
 
   ksb2'
Value: 0.0010
Constant
 
   ksb2''
Value: 0.04
Constant
 
   ksb5'
Value: 8.0E-4
Constant
 
   ksb5''
Value: 0.0050
Constant
 
   ksbud
Value: 0.2
Constant
 
   ksc1'
Value: 0.012
Constant
 
   ksc1''
Value: 0.12
Constant
 
   kscdh
Value: 0.01
Constant
 
   ksf6'
Value: 0.024
Constant
 
   ksf6''
Value: 0.12
Constant
 
   ksf6'''
Value: 0.0040
Constant
 
   ksn2'
Constant
 
   ksn2''
Value: 0.15
Constant
 
   ksnet
Value: 0.084
Constant
 
   ksori
Value: 2.0
Constant
 
   kspds'
Constant
 
   ksppx
Value: 0.1
Constant
 
   ksspn
Value: 0.1
Constant
 
   ksswi'
Value: 0.0050
Constant
 
   ksswi''
Value: 0.08
Constant
 
   lte1h
Value: 1.0
 
   lte1l
Value: 0.1
 
   mad2h
Value: 8.0
Constant
 
   mad2l
Value: 0.01
 
   mdt
Value: 90.0
Constant
 
   TEM1T
Value: 1.0
 
   D
Value: NaN
 
   mu
Value: NaN
 
   Vdb5
Value: NaN
 
   Vdb2
Value: NaN
 
   Vasbf
Value: NaN
 
   Visbf
Value: NaN
 
   Vkpc1
Value: NaN
 
   Vkpf6
Value: NaN
 
   Vacdh
Value: NaN
 
   Vicdh
Value: NaN
 
   Vppnet
Value: NaN
 
   Vkpnet
Value: NaN
 
   Vdppx
Value: NaN
 
   Vdpds
Value: NaN
 
   Vaiep
Value: NaN
 
   Vd2c1
Value: NaN
 
   Vd2f6
Value: NaN
 
   Vppc1
Value: NaN
 
   Vppf6
Value: NaN
 
   F
Value: NaN
 
Inactivation (1)
 
   k
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000056

Curator's comment: (updated: 30 Jan 2009 13:39:26 GMT)

Reproduction of some of the time-courses from fig 2 using SBML odeSolver (cvs 10/2008) with the options: -n -j --time 200 --printstep 1e4

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