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BIOMD0000000087 - Proctor2006_telomere

 

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Reference Publication
Publication ID: 17015293
Proctor CJ, Lydall DA, Boys RJ, Gillespie CS, Shanley DP, Wilkinson DJ, Kirkwood TB.
Modelling the checkpoint response to telomere uncapping in budding yeast.
J R Soc Interface 2007 Feb; 4(12): 73-90
Institute for Ageing and Health, and School of Clinical Medical Sciences-Gerontology, Centre for Integrated Systems Biology of Ageing and Nutrition, Newcastle University, Newcastle upon Tyne NE4 6BE, UK. c.j.proctor@ncl.ac.uk  [more]
Model
Original Model: BIOMD0000000087.xml.origin
Submitter: Carole Proctor
Submission ID: MODEL8679489165
Submission Date: 11 Dec 2006 16:52:02 UTC
Last Modification Date: 05 Jul 2012 14:40:05 UTC
Creation Date: 16 Oct 2006 10:54:06 UTC
Encoders:  Carole Proctor
set #1
bqbiol:isVersionOf Gene Ontology cell cycle checkpoint
bqbiol:isPartOf KEGG Pathway sce04111
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
Notes

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: 17015293 Submission Date: 11 Dec 2006 16:52:02 UTC Last Modification Date: 05 Jul 2012 14:40:05 UTC Creation Date: 16 Oct 2006 10:54:06 UTC
Mathematical expressions
Reactions
Capping Uncapping Rad17binding ExoXactivation
ExoXactivity Rad24independentExo1Activation Rad24dependentExo1Activation Rad17independentExo1Activity
Rad17dependentExo1Activity RPAbinding-stage1 RPAbinding-stage2 RPAbinding-completed
Mec1binding Rad9activation ExoXinhibition ExoXinhibition2
Rad53activation Chk1Activation Exo1inhibition Dun1activation
Chk1cellArrest Dun1cellArrest SDNArepair1 G2DNArepair1
SDNArepair2 G2DNArepair2 Recovery G1cyclinSynthesis
ScyclinSynthesis G2cyclinSynthesis McyclinSynthesis G1toSGenesOn
StoG2GenesOn G2toMGenesOn MtoG1GenesOn G1cyclinDegradation
ScyclinDegradation G2cyclinDegradation McyclinDegradation G1toSProgession
StoG2Progession G2toMProgession MtoG1Progession  
Events
Rad9KinaseActivation ssDNAremoval G2MRecoveryCompleted SphaseRecoveryCompleted
G1CdkActivation SCdkActivation G2CdkActivation MCdkActivation
CellDeath      
Physical entities
Compartments Species
cellMembrane budscar    
nucleus Ctelo Utelo Cdc13
Rad17Utelo Rad17 Rad24
RPA Mec1 ssDNA
RPAssDNA RPAssDNA1 RPAssDNA2
Mec1RPAssDNA ExoXI ExoXA
Exo1I Exo1A Rad9I
Rad9A Rad53I Rad53A
Chk1I Chk1A Dun1I
Dun1A ATP ADP
Rad9Kin recovery G1
S G2 M
G1cyclin Scyclin G2cyclin
Mcyclin G1CdkI G1CdkA
SCdkI SCdkA G2CdkI
G2CdkA MCdkI MCdkA
G1Soff G1Son SG2off
SG2on G2Moff G2Mon
MG1off MG1on sink
     
Global parameters
kalive      
Reactions (43)
 
 Capping [Cdc13] + [Utelo] → [Ctelo];  
 
 Uncapping [Ctelo] → [Cdc13] + [Utelo];  
 
 Rad17binding [Utelo] + [Rad17] + [Rad24] + [ATP] → [Rad17Utelo] + [Rad24] + [ADP];  
 
 ExoXactivation [ExoXI] + [Rad17Utelo] → [ExoXA] + [Rad17Utelo];  
 
 ExoXactivity [ExoXA] + [Rad17Utelo] → [ExoXA] + [Rad17Utelo] + [ssDNA];  
 
 Rad24independentExo1Activation [Exo1I] → [Exo1A];  
 
 Rad24dependentExo1Activation [Exo1I] + [Rad24] → [Exo1A] + [Rad24];  
 
 Rad17independentExo1Activity [Utelo] + [Exo1A] → [Utelo] + [Exo1A] + [ssDNA];  
 
 Rad17dependentExo1Activity [Rad17Utelo] + [Exo1A] → [Rad17Utelo] + [Exo1A] + [ssDNA];  
 
 RPAbinding-stage1 [ssDNA] + [RPA] → [RPAssDNA1];  
 
 RPAbinding-stage2 [ssDNA] + [RPAssDNA1] → [RPAssDNA2];  
 
 RPAbinding-completed [ssDNA] + [RPAssDNA2] → [RPAssDNA];  
 
 Mec1binding [RPAssDNA] + [Mec1] → [Mec1RPAssDNA];  
 
 Rad9activation [Rad9Kin] + [Rad9I] → [Rad9Kin] + [Rad9A];  
 
 ExoXinhibition [ExoXA] + [Rad9A] → [ExoXI] + [Rad9A];  
 
 ExoXinhibition2 [ExoXA] + [Rad9I] → [ExoXI] + [Rad9I];  
 
 Rad53activation [Rad53I] + [Rad9A] → [Rad53A] + [Rad9A];  
 
 Chk1Activation [Chk1I] + [Rad9A] → [Chk1A] + [Rad9A];  
 
 Exo1inhibition [Exo1A] + [Rad53A] → [Exo1I] + [Rad53A];  
 
 Dun1activation [Dun1I] + [Rad53A] → [Dun1A] + [Rad53A];  
 
 Chk1cellArrest [Chk1A] + [G2Mon] → [Chk1A] + [G2Moff];  
 
 Dun1cellArrest [Dun1A] + [G2Mon] → [Dun1A] + [G2Moff];  
 
 SDNArepair1 [Mec1RPAssDNA] + [S] → [Mec1] + [RPA] + [S] + 3.0 × [ssDNA];  
 
 G2DNArepair1 [G2] + [G2Moff] + [Mec1RPAssDNA] → [G2] + [G2Moff] + [Mec1] + [RPA] + 3.0 × [ssDNA];  
 
 SDNArepair2 [S] + [ssDNA] → [S];  
 
 G2DNArepair2 [G2] + [G2Moff] + [ssDNA] → [G2] + [G2Moff];  
 
 Recovery [Cdc13] + [Rad17Utelo] + [recovery] → [Ctelo] + [Rad17] + [recovery];  
 
 G1cyclinSynthesis [G1] → [G1cyclin] + [G1];  
 
 ScyclinSynthesis [S] → [Scyclin] + [S];  
 
 G2cyclinSynthesis [G2] → [G2cyclin] + [G2];  
 
 McyclinSynthesis [M] → [Mcyclin] + [M];  
 
 G1toSGenesOn [G1Soff] + [G1] + [G1CdkA] → [G1Son] + [G1] + [G1CdkA];  
 
 StoG2GenesOn [SG2off] + [S] + [SCdkA] → [SG2on] + [S] + [SCdkA];  
 
 G2toMGenesOn [G2Moff] + [G2] + [G2CdkA] → [G2Mon] + [G2] + [G2CdkA];  
 
 MtoG1GenesOn [MG1off] + [M] + [MCdkA] → [MG1on] + [M] + [MCdkA];  
 
 G1cyclinDegradation [G1cyclin] → [sink];  
 
 ScyclinDegradation [Scyclin] → [sink];  
 
 G2cyclinDegradation [G2cyclin] → [sink];  
 
 McyclinDegradation [Mcyclin] → [sink];  
 
 G1toSProgession [G1] + [G1CdkA] + [G1Son] → [G1CdkI] + [G1Soff] + [S];  
 
 StoG2Progession [S] + [SCdkA] + [SG2on] → [G2] + [SCdkI] + [SG2off];  
 
 G2toMProgession [G2] + [G2CdkA] + [G2Mon] → [G2CdkI] + [G2Moff] + [M];  
 
 MtoG1Progession [M] + [MCdkA] + [MG1on] → [budscar] + [G1] + [MCdkI] + [MG1off];  
 
Events (9)
 
 Rad9KinaseActivation
Rad9Kin = 1
 
 ssDNAremoval
recovery = 1
Mec1RPAssDNA = 0
RPAssDNA = 0
ssDNA = 0
 
 G2MRecoveryCompleted
G2Mon = 1
G2Moff = 0
recovery = 0
Rad9A = 0
Rad9I = 20
Chk1A = 0
Chk1I = 60
Dun1A = 0
Dun1I = 3000
Exo1A = 0
Exo1I = 670
ExoXA = 0
ExoXI = 70
Rad53I = 6900
Rad53A = 0
 
 SphaseRecoveryCompleted
recovery = 0
 
 G1CdkActivation
G1CdkA = 1
G1CdkI = 0
 
 SCdkActivation
SCdkA = 1
SCdkI = 0
 
 G2CdkActivation
G2CdkA = 1
G2CdkI = 0
 
 MCdkActivation
MCdkA = 1
MCdkI = 0
 
 CellDeath
kalive = 0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 budscar
Compartment: cellMembrane
Initial amount: 0.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ctelo
Compartment: nucleus
Initial amount: 64.0
 
 Utelo
Compartment: nucleus
Initial amount: 0.0
 
 Cdc13
Compartment: nucleus
Initial amount: 300.0
 
 Rad17Utelo
Compartment: nucleus
Initial amount: 0.0
 
 Rad17
Compartment: nucleus
Initial amount: 70.0
 
 Rad24
Compartment: nucleus
Initial amount: 70.0
 
 RPA
Compartment: nucleus
Initial amount: 4000.0
 
 Mec1
Compartment: nucleus
Initial amount: 4000.0
 
 ssDNA
Compartment: nucleus
Initial amount: 0.0
 
 RPAssDNA
Compartment: nucleus
Initial amount: 0.0
 
 RPAssDNA1
Compartment: nucleus
Initial amount: 0.0
 
 RPAssDNA2
Compartment: nucleus
Initial amount: 0.0
 
 Mec1RPAssDNA
Compartment: nucleus
Initial amount: 0.0
 
 ExoXI
Compartment: nucleus
Initial amount: 70.0
 
 ExoXA
Compartment: nucleus
Initial amount: 0.0
 
 Exo1I
Compartment: nucleus
Initial amount: 670.0
 
 Exo1A
Compartment: nucleus
Initial amount: 0.0
 
 Rad9I
Compartment: nucleus
Initial amount: 20.0
 
 Rad9A
Compartment: nucleus
Initial amount: 0.0
 
 Rad53I
Compartment: nucleus
Initial amount: 6900.0
 
 Rad53A
Compartment: nucleus
Initial amount: 0.0
 
 Chk1I
Compartment: nucleus
Initial amount: 60.0
 
 Chk1A
Compartment: nucleus
Initial amount: 0.0
 
 Dun1I
Compartment: nucleus
Initial amount: 3000.0
 
 Dun1A
Compartment: nucleus
Initial amount: 0.0
 
 ATP
Compartment: nucleus
Initial amount: 10000.0
 
 ADP
Compartment: nucleus
Initial amount: 1000.0
 
   Rad9Kin
Compartment: nucleus
Initial amount: 0.0
 
   recovery
Compartment: nucleus
Initial amount: 0.0
 
 G1
Compartment: nucleus
Initial amount: 1.0
 
 S
Compartment: nucleus
Initial amount: 0.0
 
 G2
Compartment: nucleus
Initial amount: 0.0
 
 M
Compartment: nucleus
Initial amount: 0.0
 
 G1cyclin
Compartment: nucleus
Initial amount: 0.0
 
 Scyclin
Compartment: nucleus
Initial amount: 0.0
 
 G2cyclin
Compartment: nucleus
Initial amount: 0.0
 
 Mcyclin
Compartment: nucleus
Initial amount: 0.0
 
 G1CdkI
Compartment: nucleus
Initial amount: 1.0
 
 G1CdkA
Compartment: nucleus
Initial amount: 0.0
 
 SCdkI
Compartment: nucleus
Initial amount: 1.0
 
 SCdkA
Compartment: nucleus
Initial amount: 0.0
 
 G2CdkI
Compartment: nucleus
Initial amount: 1.0
 
 G2CdkA
Compartment: nucleus
Initial amount: 0.0
 
 MCdkI
Compartment: nucleus
Initial amount: 1.0
 
 MCdkA
Compartment: nucleus
Initial amount: 0.0
 
 G1Soff
Compartment: nucleus
Initial amount: 1.0
 
 G1Son
Compartment: nucleus
Initial amount: 0.0
 
 SG2off
Compartment: nucleus
Initial amount: 1.0
 
 SG2on
Compartment: nucleus
Initial amount: 0.0
 
 G2Moff
Compartment: nucleus
Initial amount: 1.0
 
 G2Mon
Compartment: nucleus
Initial amount: 0.0
 
   MG1off
Compartment: nucleus
Initial amount: 1.0
 
 MG1on
Compartment: nucleus
Initial amount: 0.0
 
   sink
Compartment: nucleus
Initial amount: 0.0
 
Global Parameters (1)
 
   kalive
Value: 1.0
 
Capping (1)
 
   k1
Value: 5.0E-4
Constant
 
Uncapping (1)
 
   k2
Value: 3.85E-4
Constant
 
Rad17binding (1)
 
   k3
Value: 1.5E-8
Constant
 
ExoXactivation (1)
 
   k4
Value: 0.01
Constant
 
ExoXactivity (1)
 
   k5
Value: 3.0E-4
Constant
 
Rad24independentExo1Activation (1)
 
   k6a
Value: 5.0E-5
Constant
 
Rad24dependentExo1Activation (1)
 
   k6b
Value: 5.0E-4
Constant
 
Rad17independentExo1Activity (1)
 
   k7a
Value: 3.0E-5
Constant
 
Rad17dependentExo1Activity (1)
 
   k7b
Value: 3.0E-5
Constant
 
RPAbinding-stage1 (1)
 
   k8a
Value: 0.0010
Constant
 
RPAbinding-stage2 (1)
 
   k8b
Value: 100.0
Constant
 
RPAbinding-completed (1)
 
   k8c
Value: 100.0
Constant
 
Mec1binding (1)
 
   k8d
Value: 0.0040
Constant
 
Rad9activation (1)
 
   k9
Value: 100.0
Constant
 
ExoXinhibition (1)
 
   k10a
Value: 0.05
Constant
 
ExoXinhibition2 (1)
 
   k10b
Value: 0.05
Constant
 
Rad53activation (1)
 
   k11
Value: 1.0E-5
Constant
 
Chk1Activation (1)
 
   k12
Value: 1.7E-4
Constant
 
Exo1inhibition (1)
 
   k13
Value: 1.0
Constant
 
Dun1activation (1)
 
   k14
Value: 3.3E-6
Constant
 
Chk1cellArrest (1)
 
   k15
Value: 0.2
Constant
 
Dun1cellArrest (1)
 
   k16
Value: 0.1
Constant
 
SDNArepair1 (1)
 
   k17a
Value: 0.05
Constant
 
G2DNArepair1 (1)
 
   k17b
Value: 0.05
Constant
 
SDNArepair2 (1)
 
   k18a
Value: 0.0010
Constant
 
G2DNArepair2 (1)
 
   k18b
Value: 1.0E-5
Constant
 
Recovery (1)
 
   k19
Value: 0.0010
Constant
 
G1cyclinSynthesis (1)
 
   kc1
Value: 0.16
Constant
 
ScyclinSynthesis (1)
 
   kc1
Value: 0.16
Constant
 
G2cyclinSynthesis (1)
 
   kc1
Value: 0.16
Constant
 
McyclinSynthesis (1)
 
   kc1
Value: 0.16
Constant
 
G1toSGenesOn (1)
 
   kc2
Value: 0.01
Constant
 
StoG2GenesOn (1)
 
   kc2
Value: 0.01
Constant
 
G2toMGenesOn (1)
 
   kc2
Value: 0.01
Constant
 
MtoG1GenesOn (1)
 
   kc2
Value: 0.01
Constant
 
G1cyclinDegradation (1)
 
   kc3
Value: 0.0012
Constant
 
ScyclinDegradation (1)
 
   kc3
Value: 0.0012
Constant
 
G2cyclinDegradation (1)
 
   kc3
Value: 0.0012
Constant
 
McyclinDegradation (1)
 
   kc3
Value: 0.0012
Constant
 
G1toSProgession (1)
 
   kc4
Value: 0.01
Constant
 
StoG2Progession (1)
 
   kc4
Value: 0.01
Constant
 
G2toMProgession (1)
 
   kc4
Value: 0.01
Constant
 
MtoG1Progession (1)
 
   kc4
Value: 0.01
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000087

Curator's comment: (updated: 11 Dec 2006 16:53:19 GMT)

Reproduction of Figure 5 of the paper with Gillespie 2.0 and Gnuplot.

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