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Report
The Eukaryotic Cell Cycle :
Molecules, Mechanisms, and
Mathematical Models
John J. Tyson
Virginia Tech
Bela Novak
Tech Univ Budapest
Computational Molecular Biology
DNA
…TACCCGATGGCGAAATGC...
mRNA
…AUGGGCUACCGCUUUACG...
Protein
…Met -Gly -Tyr -Arg -Phe -Thr...
-P
Enzyme
ATP
Reaction Network
Cell Physiology
E1
ADP
X
E2
Y
E3
Z
E4
G1
S
M
(telophase)
G2
M
(anaphase)
M
(metaphase)
G1
G1 Checkpoint
Sic1
M
S
Cln2
(telophase)
Cdh1
Clb5
Cdk1
Cdc20
Clb2
G2
M
(anaphase)
Metaphase Checkpoint
M
(metaphase)
G2 Checkpoint
Sister chromatid
separation
Budding
SBF
Cln2
Unaligned
Xsomes
Cln3
and
Cdh1
Clb2
Mitosis
Sic1 Clb2
Bck2
Clb5
Clb2
Cdc20
Cdc20
Mcm1
Cdh1
Clb2
Cdc20
Swi5
P
Sic1
Cln2
Sic1 Clb5
Cdc20
MBF
Clb?
Clb5
DNA synthesis
Sic1
SCF
d[Cln2]
 k1  k1' [SBF]  k2 [Cln2]
dt
synthesis

degradation

d[Clb2]
 k3  k3' [Mcm1]  k4  k4' [Cdh1] [Clb2]  k5 [Sic1][Clb2]
dt
synthesis
d[Cdh1]  k

dt
binding
degradation

'

k
6
6 [Cdc20] [Cdh1]T  [Cdh1] 
J 6  [Cdh1]T  [Cdh1]
activation
k



'

k
7
7 [Clb5] [Cdh1]
J 7  [Cdh1]
inactivation
Simulation of the budding yeast cell cycle
2
mass
1
1
.
0
Sic1
Cln2
0
.
5
0
.
0
G1
1
.
5
Cdh1
1
.
0
0
.
5
S/M
Clb2
0
.
5
Cdc20
0
.
0
0
.
0
0
5
0
1
0
0
Time (min)
1
5
0
CKI
CKI = Sic1
Cdk
Cln
Cdk
CycB
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)
84
changed
parameter
Comments
1
wild type
(daughter)
0.71
1.07
(71’)
1.15
(84’)
1.15
(84’)
1.64
(146’)
CT 146 min
(time of occurrence of event)
2
clb1 clb2
0.71
1.07
1.16
1.16
No mit
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
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
9
sic1 hct1
0.71
No SBF
0.72
No bud
No mit
10
sic1 GAL-CLB5
first cycle
second cycle
0.71
0.52
0.74
0.73
No repl
0.76
1.20
k's,b2 = 0
k"s,b2 = 0
Surana 1991 Table 1, G2 arrest.
Schwob 1993 Fig 6, DNA repl concurrent with SBF
activation in both GAL-CLB5 and GAL-CLB5db.
k"d,b2 = 0.01 Schwab 1997 Fig 2, viable, size like WT, Clb2 level high
throughout the cycle.
k's,c1 = 0
Visintin 1997, telophase arrest.
k"d,b2 = 0.01
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.
Why do these calculations?
Is the model “yeast shaped”?
Bioinformatics role: the model organizes lots
of experimental information.
New science: prediction, insight
Cdk1 activity
1
.
0
1
5
0
1
0
0
Cdk1
Clb2,5
0
.
5
M
5
0
period
0
.
0
0
G1
1
mass
Sic1
Cdh1
0
2
Cln2
Bifurcation diagram
Cdk1 activity
1
.
0
Cdk1
Clb2,5
0
.
5
M
Sic1
Cdh1
0
.
0
0
G1
1
cell mass
2
Cln2
How can CS help?
Experimental Database
Wiring Diagram
Differential Equations
Analysis
Parameter Values
Simulation
Visualization-Translation
Experimental Database
Problem-Solving Environment
Cliff Shaffer
Naren Ramakrishnan
Marc Vass
Layne Watson
Jason Zwolak
Parameter Estimation
Simulation
Translation
Database
Prop 1
Good fit
Prop 1
Prop 2
Bad fit
Prop 2
...
...
...
Error Function (parameters)
Parameter Estimation
Kurt Kohn (1999) Mol Biol Cell

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