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DARPA BioComp PI Meeting, 2001DARPA BioComp PI Meeting, 2001
““The Eukaryotic Cell Cycle as a Test CaseThe Eukaryotic Cell Cycle as a Test Casefor Modeling Cellular Regulation in a for Modeling Cellular Regulation in a
Collaborative Problem Solving Environment”Collaborative Problem Solving Environment”
PI: John J. Tyson (Biology, Virginia Tech)PI: John J. Tyson (Biology, Virginia Tech)CoPIs: Cliff Shaffer & Layne Watson (CS, Virginia Tech)CoPIs: Cliff Shaffer & Layne Watson (CS, Virginia Tech)
With collaborators atWith collaborators atRockefeller UniversityRockefeller University
University of Kentucky Medical SchoolUniversity of Kentucky Medical SchoolBudapest University of Technology and EconomicsBudapest University of Technology and Economics
Cdc2
Cdc13
START
S
cell d
ivision
G2
FIN
ISH
G1
DNAreplication
Metaphase
Anaphase
cyclin-dependentkinase
cyclin
Three ObjectivesThree Objectives
•ModelingModeling•Experimental ValidationExperimental Validation•Software ToolsSoftware Tools
DoD RelevanceDoD Relevance
The cell cycle is central to all processes of The cell cycle is central to all processes of biological growth, development and biological growth, development and
reproduction.reproduction. • Wound healingWound healing• Nerve regenerationNerve regeneration• Radiation damageRadiation damage• Eukaryotic pathogensEukaryotic pathogens• Tissue cultureTissue culture• CancerCancer
Clb5MBF
P Sic1SCF
Sic1Swi5
Clb2Mcm1
Unaligned chromosomes
Cln2Clb2
Clb5
Cdc20 Cdc20
Cdh1
Cdh1
Cdc20
APC
PPX
Mcm1
SBF
Esp1Esp1 Pds1
Pds1
Cdc20
Net1
Net1P
Cdc14
RENT
Cdc14
Cdc14
Cdc15
Tem1
Bub2
CDKs
Esp1
Mcm1 Mad2
Esp1
Unaligned chromosomes
Cdc15
Lte1
Budding
Cln2SBF
?
Cln3
Bck2
and
growth
Sister chromatid separation
DNA synthesis
Table 6. Properties of clb, sic1, and hct1 mutants
mass at birth
mass at
SBF 50%
mass at
DNA repl.
mass at bud ini.
mass at division
TG1
(min)
changed
parameter
Comments
1 wild type
(daughter) 0.71 1.07
(71’) 1.15 (84’)
1.15 (84’)
1.64 (146’)
84 CT 146 min (time of occurrence of event)
2 clb1 clb2
0.71 1.07 1.16 1.16 No mit k's,b2 = 0
k"s,b2 = 0 Surana 1991 Table 1, G2 arrest.
3 clb1 clb2
1X GAL-CLB2 0.65 1.10 1.19 1.19 1.50 105 k's,b2 = 0.1
k"s,b2 = 0 Surana 1993 Fig 4, 1X GAL-CLB2 is OK, 4X GAL-CLB2 (or 1X GAL-CLB2db) causes telophase arrest.
4 clb5 clb6 0.73 1.07
(65’) 1.30 (99’)
1.17 (80’)
1.70 (146’)
99 k's,b5 = 0 k"s,b5 = 0
Schwob 1993 Fig 4, DNA repl begins 30 min after SBF activation.
5 clb5 clb6
GAL-CLB5 0.61 0.93 0.92 0.96 1.41 73 k's,b5 = 0.1
k"s,b5 = 0 Schwob 1993 Fig 6, DNA repl concurrent with SBF activation in both GAL-CLB5 and GAL-CLB5db.
6 sic1 0.66 1.00
(73’) 0.82 (37’)
1.06 (83’)
1.52 (146’)
38 k's,c1 = 0 k"s,c1 = 0
Schneider 1996 Fig 4, sic1 uncouples S phase from budding.
7 sic1 GAL-SIC1 0.80 1.07 1.38 1.17 1.86 94 k's,c1 = 0.1 k"s,c1 = 0
Verma 1997 Fig3B, Nugroho & Mendenhall 1994 Fig 2, most cells are viable.
8 hct1 0.73 1.08 1.17 1.18 1.69 82 k"d,b2 = 0.01 Schwab 1997 Fig 2, viable, size like WT, Clb2 level high
throughout the cycle. 9 sic1 hct1
0.71 No SBF 0.72 No bud No mit k's,c1 = 0
k"d,b2 = 0.01 Visintin 1997, telophase arrest.
10 sic1 GAL-CLB5
first cycle second cycle
0.71 0.52
0.74
0.73
No repl
0.76
1.20
k's,b5 = 0.1 k"s,b5 = 0 k's,c1 = 0
Schwob 1994 Fig 7C, inviable. First cycle OK, DNA repl advanced; but pre-repl complexes cannot form and cell dies after the first cycle.
d CDK dt = k1 - (v2’ + v2” . Cdh1 ) . CDK
d Cdh1dt =
(k3’ + k3” . Cdc20A) (1 - Cdh1) J3 + 1 - Cdh1 -
(k4’ + k4” . CDK . M) Cdh1 J4 + Cdh1
d IEPdt = k9
. CDK . M . (1 – IEP ) – k10 . IEP
d Cdc20T
dt = k5’ + k5” (CDK . M)4
J54 + (CDK . M)4 - k6
. Cdc20T
d Cdc20A
dt = k7
. IEP (Cdc20T - Cdc20A) J7 + Cdc20T - Cdc20A
- k8
. MAD Cdc20A
J8 + Cdc20A - k6
. Cdc20T
Differential equations Parameter values
k1 = 0.0013, v2’ = 0.001, v2” = 0.17,
k3’ = 0.02, k3” = 0.85, k4’ = 0.01, k4” = 0.9,
J3 = 0.01, J4 = 0.01, k9 = 0.38, k10 = 0.2,
k5’ = 0.005, k5” = 2.4, J5 = 0.5, k6 = 0.33,
k7 = 2.2, J7 = 0.05, k8 = 0.2, J8 = 0.05,
…
Predictions: Budding YeastPredictions: Budding Yeast
1. Rate constants1. Rate constants
2. Hysteresis2. Hysteresis
Mendenhall (U Kentucky)Mendenhall (U Kentucky)
Cross (Rockefeller U)Cross (Rockefeller U)
3. Mutants3. Mutants Cross & MendenhallCross & Mendenhall
Predictions: Frog EggsPredictions: Frog Eggs
1. Rate constants (1993)1. Rate constants (1993)
2. Hysteresis (1993)2. Hysteresis (1993)
3. Bifurcation diagram (1998)3. Bifurcation diagram (1998)
ConfirmedConfirmed Kumagai & Dunphy (1995)Kumagai & Dunphy (1995)
ConfirmedConfirmed Moore (unpubl)Moore (unpubl)
Sible & Sha (VA Tech)Sible & Sha (VA Tech)
Under testUnder test Sible & Sha (VA Tech)Sible & Sha (VA Tech)
4. Cdk2/Cyclin E (in ppn)4. Cdk2/Cyclin E (in ppn)Under testUnder test
Sible (VA Tech)Sible (VA Tech)
Software RequirementsSoftware Requirements
Experimental DatabaseExperimental Database
Wiring DiagramWiring Diagram
Differential EquationsDifferential Equations Parameter ValuesParameter Values
AnalysisAnalysis SimulationSimulation
Visualization-TranslationVisualization-Translation
Experimental DatabaseExperimental Database
0 1 20.0
0.5
1.0
G1
M
cell mass
Bifurcation diagram
Cdc20
Cdk1
Clb2,5
Cln2
Sic1Cdh1
Cd
k1 a
ctiv
ity
Parameter EstimationParameter Estimation
DatabaseDatabaseSimulationSimulation
Prop 1Prop 1Prop 1Prop 1
Prop 2Prop 2Prop 2Prop 2
............
ComparatorComparator
Good fitGood fit
Bad fitBad fit
......
Error Function (parameters)Error Function (parameters)
Parameter EstimationParameter Estimation
trust region Levenburg Marquardt
Jones’ direct search global optimizer
MilestonesMilestones
Year OneYear One Year TwoYear Two Year ThreeYear Three
ModelingModeling Full model of bud Full model of bud yeastyeast
Sensitivity analysisSensitivity analysis
Cdk2/cyclin E in frogCdk2/cyclin E in frog
Morpho checkpointMorpho checkpoint
-factor signalling-factor signalling
Revisions Revisions
Comprehensive Comprehensive model of budding model of budding yeastyeast
Comprehensive Comprehensive model of frog eggmodel of frog egg
ExperimenExperimentt
Absolute prot concen Absolute prot concen in budd yeastin budd yeast
Hysteresis in frog extr Hysteresis in frog extr and in budd yeastand in budd yeast
Kinetic & thermody Kinetic & thermody propertiesproperties
Hopf & SNIPER Hopf & SNIPER bifns in frog extrbifns in frog extr
MutantsMutants
Complex bifns in Complex bifns in budd yeast & frogbudd yeast & frog
Checkpoint signalsCheckpoint signals
SoftwareSoftware Model builderModel builder
Steady-state finderSteady-state finder
ComparatorComparator
Param optimization in Param optimization in frog egg modelfrog egg model
Numer bifn analysisNumer bifn analysis
Run managementRun management
Simul analysisSimul analysis
Param optimization Param optimization in yeast cell modelin yeast cell model
Working PSE for Working PSE for cell cycle modelingcell cycle modeling
DeliverablesDeliverables
Year OneYear One Year TwoYear Two Year ThreeYear Three
ModelingModeling 2 publications2 publications
budding yeastbudding yeast
frog egg developfrog egg develop
1 publication1 publication
morpho checkptmorpho checkpt
2 tech reports2 tech reports
3 publications3 publications
-factor -factor signallingsignalling
compreh yeastcompreh yeast
compreh frogcompreh frog
ExperimenExperimentt
2 publications2 publications
yeast (Cross)yeast (Cross)
frog (Sible)frog (Sible)
1 tech report 1 tech report (Menden)(Menden)
Some combination Some combination of publications and of publications and technical reports on technical reports on experimentsexperiments
3 publications3 publications
irrev trans in irrev trans in yeastyeast
kinet & thermo kinet & thermo parpar
bifns in frog extrbifns in frog extr
SoftwareSoftware 3 software tools3 software tools
model buildermodel builder
steady-state findersteady-state finder
param optimizerparam optimizer
Publications Publications
Software tools forSoftware tools for
run run managementmanagement
bifn analysisbifn analysis
comparisonscomparisons
deter global deter global searchsearch
PublicationsPublications
Suites of integrated Suites of integrated software tools for a software tools for a complete cell-cycle complete cell-cycle problem-solving-problem-solving-environmentenvironment
PersonnelPersonnel
VT FacultyVT Faculty VT StudentsVT Students CollaboratorsCollaborators
ModelingModeling Tyson (25%)Tyson (25%)
Chen (25%)Chen (25%)Ciliberto Ciliberto (25%)(25%)
Yi (25%)Yi (25%)
Novak (20%)Novak (20%)
Pataki (100%)Pataki (100%)
ExperimentExperiment Sible (15%)Sible (15%) Sha (50%)Sha (50%) Cross (25%)Cross (25%)
Liu (100%)Liu (100%)
Menden. Menden. (25%)(25%)
GRA (100%)GRA (100%)
SoftwareSoftware Shaffer Shaffer (15%)(15%)
Watson Watson (15%)(15%)
Ramak. Ramak. (10%)(10%)
Zwolak Zwolak (100%)(100%)
Vass (100%)Vass (100%)
Allen (100%)Allen (100%)