network dynamics and cell physiology · john j. tyson department of biological sciences &...
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![Page 1: Network Dynamics and Cell Physiology · John J. Tyson Department of Biological Sciences & Virginia Bioinformatics Institute. Outline 1. Cell Signaling: Physiology 2. Cell Signaling:](https://reader036.vdocuments.mx/reader036/viewer/2022071216/6047f4583d1efe3153305e4f/html5/thumbnails/1.jpg)
Network Dynamics andNetwork Dynamics andCell PhysiologyCell Physiology
John J. Tyson John J. Tyson Department of Biological Sciences Department of Biological Sciences & Virginia Bioinformatics Institute& Virginia Bioinformatics Institute
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Outline
1. Cell Signaling: Physiology2. Cell Signaling: Molecular Biology3. Chemical Kinetics4. Sniffers, Buzzers & Toggles5. Bistability & Oscillations in Frog Eggs6. Dynamical Perspective7. Example: Fission Yeast Cell Cycle
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nutrients
repellants
damage
hormones
heat shock
growth & division
movement
geneexpression
death
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BacteriaGlucose
Lactose
lactosemetabolizing
enzymes
1
0 0
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Fission Yeast
14 mm
7 mm
Wild type Mutant(wee1D)
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Fibroblast
Growth Factor
PROLIFERATION
Extracellular Matrix
Cell-Cell Contact
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Fibroblast
ProgrammedCell Death
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http://www.youtube.com/watch?v=I_xh-bkiv_c&NR=1
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Suprachiasmatic Nucleus12hL:12hD
ActivityBody temp
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Outline
1. Cell Signaling: Physiology2. Cell Signaling: Molecular Biology3. Chemical Kinetics4. Sniffers, Buzzers & Toggles5. Bistability & Oscillations in Frog Eggs6. Dynamical Perspective7. Example: Fission Yeast Cell Cycle
![Page 11: Network Dynamics and Cell Physiology · John J. Tyson Department of Biological Sciences & Virginia Bioinformatics Institute. Outline 1. Cell Signaling: Physiology 2. Cell Signaling:](https://reader036.vdocuments.mx/reader036/viewer/2022071216/6047f4583d1efe3153305e4f/html5/thumbnails/11.jpg)
Hanahan & Weinberg (2000)
Signal Transduction Network
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Cdk
C K
I C d k
Cyclin
C K
I
C d k
Cycl in
Cdk
Cycl in
P
Cyclin
Cdk
Each icon represents a chemical species. Each arrow represents a chemical reaction that occurs at a certain rate.
CyclinMPF =
M-phase Promoting Factor
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X(t) = [cyclin]
1 0
0 1
, (0)
( )
dXk X X
dtX t X k t
= =
= +
T i m e ( m i n )
Cycl in(nM )
20
40
402 0 60
In te rphase arres tedFel ix e t a l . (1990)Nature 346 :379 , F ig . 1
Metaphase r e l easedTang e t a l . (1993)E M B O J 1 2 : 3 4 2 7 , F i g . 2
1. Synthesis
Estimate k1 from the “red” data:
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2
2 1 / 2
2 1 / 2
2 1 / 2
2 0
0
1 / 2 0 0 0
1 / 22 2
, ( 0 )
( )
1 1( )
2
ln 2 0.72 , or
k t
k tk t
k t
d Xk X X X
d t
X t X e
X t X X e Xe
e tk k
−
−
= − =
=
= = =
= = ≅
2. Degradation
Estimate k2 from the “blue” and “green” data above.How can it be that cyclin has different half-lives in different phases of the cell cycle?
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3 3 0 0
0 03 0 0
0 0
( ) ( ) ( )( ), (0) 0
(1 )( ) , where ( )
t
t
dMk C t X t k C M X M M
dt
C X eM t k C X
C X e
α
α α−
−
= = − − =
−= = −
−
3. Dimerization
X(t) = [cyclin], C(t) = [Cdc2], M(t) = [dimer],
Estimate k3 from the data below, given that C0 = 100 nM.
T i m e ( m i n )
D i m e r s(n M )
20
40
1 05 1 5
K u m a g a i & D u n p h y ( 1 9 9 5 )M o l B i o l Cel l 6 :199, F ig . 3B
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( )2
1 2
1
2
1
2
, (0) 0 ,
( ) 1
Note: as , ( ) (stable steady state)
k t
dXk k X X
dt
kX t e
k
kt X t
k
−
= − =
= −
→ ∞ →
From your previous estimates of k1 and k2, estimate the steady stateconcentrations of cyclin in interphase and late anaphase (end of mitosis).
4. Synthesis and Degradation
Phase k1 k2 Xss
Interphase
Anaphase
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This case is unusual in that one can write down an “exact” solution of the differential equation in terms of elementary functions. When an exact solution is not available, one canalways take other approaches…
Numerical1 2
1 2
( ) ( )( )
( ) ( ) ( ( ))
X t t X tk k X t
tX t t X t k k X t t
+ ∆ −≅ −
∆+ ∆ ≅ + − ⋅ ∆
This always works, but doesn’t provide much insight.
Graphical
+
dX/dt
X
k1
k1/ k2
dX/dt = 0 at X = k1/k2, called a “steady state” solutionX(t) approaches k1/k2 for t large (“stable” steady state)
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Outline
1. Cell Signaling: Physiology2. Cell Signaling: Molecular Biology3. Chemical Kinetics4. Sniffers, Buzzers & Toggles5. Bistability & Oscillations in Frog Eggs6. Dynamical Perspective7. Example: Fission Yeast Cell Cycle
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R
S
0
0.5
0 1 2 3
resp
on
se (R
)
signal (S)
linear
0
5
0 0.5 1
S=1
R
rate
(dR
/dt)
rate of degradation
rate of synthesis
S=2
S=3
Gene Expression
Signal-ResponseCurve1 2
d,
dR
k S k Rt
= − 1ss
2
k SR
k=
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R
Kinase
RP
ATP ADP
H2OPi
Protein Phosphorylation
0
1
2
0 0.5 1RP
rate
(dR
P/d
t)
0.25
0.5
1
1.5
2
Phosphatase 0
0.5
1
0 1 2 3
resp
on
se (R
P)
Signal (Kinase)
1 R 0
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R
S
EP E0
0.1
0.2
0.3
0.4
0.5
0.6
0 0.5R
rate
(dR
/dt) S=0
S=8
S=16
0
0.5
0 10
resp
on
se (R
)
signal (S)
Protein Synthesis:Positive Feedback
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Example: Fuse
0
0.5
0 10
resp
onse
(R)
signal (S)
dying
Apoptosis(Programmed Cell Death)
living
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Outline
1. Cell Signaling: Physiology2. Cell Signaling: Molecular Biology3. Chemical Kinetics4. Sniffers, Buzzers & Toggles5. Bistability & Oscillations in Frog Eggs6. Dynamical Perspective7. Example: Fission Yeast Cell Cycle
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0
0.5
1
0 1 2
resp
on
se (M
PF
)
signal (cyclin)
MPF
Cdc25-PCdc25
MPF-P
Wee1
(inactive)
0
0.5
1
0 0.5 1 1.5MPF
Cd
c25-
P
0
0.5
1
0 1 2 3
Cd
c25-
P
MPF
S = Total Cyclin
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centrifuge
Solomon’s protocol for cyclin-induced activation of MPF
cytoplasmic extract
pellet
Ca2+ M
Cyclin
Cyclo-heximide
Cyclin
Cdk1
Cell 63:1013 (1990)
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Threshold
0
20
40
60
80
100
120
0 10 20 30
Cyclin (nM)
CD
K a
ctiv
ity
Solomon et al. (1990)Cell 63:1013.
Novak & Tyson (1993) J. Cell Sci. 106:1153
Pomerening et al., Nature Cell Biology 5:346-351 (2003)
Sha et al., PNAS 100:975-980 (2003)
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Testing activation threshold for Mitosis I
Interphase
Mitosis I
∆90Cyclin B1 and 100 µg/ml CHX
Testing Thresholds in Cycling Extracts
Testing inactivation threshold for Mitosis I
Interphase Interphase
Mitosis I
∆90Cyclin B1
100 µg/ml CHX
MPFactivity
time
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16 24 32 400∆90 cyclin B (nM) :
90 min
0 min
60 min
140 min
0∆90 cyclin B (nM) : 16 3224 40
M
M M M
The activation threshold for Mitosis I is between 32 and 40 nM.
The inactivation threshold for Mitosis I is between 16 and 24 nM.
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0
0.5
1
0 1 2
MP
F
cyclin
MPF
Cdc25-PCdc25
MPF-P(inactive)
cyclin synthesis
cyclin degradationAPC
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If knock-out positive feedback loop, then oscillations become faster and smaller amplitude…
Figure 4. Pomerening, Kim and Ferrell
With + feedback Without + feedback
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• Tyson, Chen & Novak, “Network dynamics and cell physiology,” Nature Rev. Molec. Cell Biol. 2:908 (2001).
• Tyson, Csikasz-Nagy & Novak, “The dynamics of cell cycle regulation,” BioEssays 24:1095 (2002).
• Tyson, Chen & Novak, “Sniffers, buzzers, toggles and blinkers,” Curr. Opin. Cell Biol.15:221 (2003).
• Csikasz-Nagy et al., “Analysis of a generic model of eukaryotic cell-cycle regulation,” Biophys. J. 90:4361 (2006).
References
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Outline
1. Cell Signaling: Physiology2. Cell Signaling: Molecular Biology3. Chemical Kinetics4. Sniffers, Buzzers & Toggles5. Bistability & Oscillations in Frog Eggs6. Dynamical Perspective7. Example: Fission Yeast Cell Cycle
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Cdk
C K
I C d k
Cyclin
C K
I
C d k
Cycl in
Cdk
Cycl in
P
Cyclin
Cdk
Wee1Cdc25
= k1 - (kwee + k2) * MPF + k25 (cyclin - MPF)
= k1 - k2 * cyclin
d MPFdt
d cyclindt
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MPF
Cyclin
Phase Plane dx/dt=f(x,y)dy/dt=g(x,y)
(xo,yo)
∆x=f(xo,yo) ∆t
∆y=g(xo,yo) ∆t
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One-parameter bifurcation diagram
parameter
variable
stable steady stateunstable steady state
saddle-nodesaddle-node
Signal Responset t
p x
OFF
ON
(signal)
(response)
x
y
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One-parameter bifurcation diagram
parameter
variable
stable steady stateunstable steady state
saddle-nodesaddle-node Hopf
(signal)
(response)
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MPF
Cyclin
Phase Plane dx/dt=f(x,y)dy/dt=g(x,y)
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MPF
Cyclin
Phase Plane dx/dt=f(x,y)dy/dt=g(x,y)
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MPF
Cyclin
Phase Plane dx/dt=f(x,y)dy/dt=g(x,y)
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Hopf BifurcationHopf Bifurcation
x2
p1
stable limit cycle
sssuss
slc max
min
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Hopf BifurcationHopf Bifurcation
x2
p1
sssuss
slc
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parameter(signal)
variable(response)
Hopf
Second Parameter
subcritical
Second Parameter
CF
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parameter(signal)
variable(response)
SNIC
Second Parameter
SL
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SNIC BifurcationSNIC Bifurcation
Invariant Circle
Limit Cycle
x2
p1
node
saddle
Saddle-Node on anInvariant Circle
max
min
maxSNIC
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Signal-Response Curve = One-parameter Bifurcation Diagram
•Saddle-Node•Supercritical Hopf•Subcritical Hopf•Cyclic Fold•Saddle-Node Invariant Circle
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Outline
1. Cell Signaling: Physiology2. Cell Signaling: Molecular Biology3. Chemical Kinetics4. Sniffers, Buzzers & Toggles5. Bistability & Oscillations in Frog Eggs6. Dynamical Perspective7. Example: Fission Yeast Cell Cycle
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S
G1
DNAreplication
G2Mmitosis
cell division
1) Alternation ofS phase and M phase.
2) Balanced growth anddivision.
3) Checkpoints
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P
Cdc25
Wee1
Wee1P
Cdc25
CycB
P
Cdc20
CK
I
CycB
CycBCK
I
CK
I
CycA
CycA
APC-PAPCTFBI
TFBA
CycE
CycD
TFEA
TFEI
Cyc E,A,B
CycE
TFIA
TFII
CK
I
CycE
Cdc14
Cdc14
Cdc14
CycA
CycA
CycB
CycD
Cdh1CycD
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0 50 100 150 200 250 300
0
1
2
3
4
5
mass/nucleus
P Cdk1CycB
Cdk1CycB
CKI
Cdh1
Cdc20
Wee1
Cdc25
Time (min)
S G2 MG1 S G2 MG1 S
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Gene Viable? Traitcdc2 − No block in G2cdc13 − No block in G2rum1 − Yes sterileste9 − Yes sterileslp1 − Yeswee1 − Yes smallcdc25 − No block in G2
cdc2 OP Yes wtcdc13 OP Yes wtrum1 OP No endoreplic.ste9 OP Yes wtwee1 OP Yes largecdc25 OP Yes small
wee1 − rum1∆ No extremely smallwee1 − cdc25∆ Yes quantized cycleswee1 − cdc25 OP No cutwee1 OP cdc25 − No block in G2
Mutants in Fission YeastMutants in Fission Yeast
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P
Cdc25
Wee1
Wee1P
Cdc25
CycB
P
Cdc20
CK
I
CycB
CycBCK
I
CK
I
CycA
CycA
APC-PAPCTFBI
TFBA
CycE
CycD
TFEA
TFEI
Cyc E,A,B
CycE
TFIA
TFII
CK
I
CycE
Cdc14
Cdc14
Cdc14
CycA
CycA
CycB
CycD
Cdh1CycD
mass/DNA
0.0 0.5 1.0 1.5
Cdc2
/Cdc
13
10-5
10-4
10-3
10-2
10-1
100
G1
Mmass/DNA
0 1 2
Cdc2
/Cdc
13
10-3
10-2
10-1
100
S/G2
M
mass/nucleus
mass/DNA
0.0 0.5 1.0 1.5 2.0
Cdc2
/Cdc
13
0.1
1
M
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0 1 2 3 4 5
0
0.4
0.8
3.0
mass/nucleus
Cdk1
:Cyc
B
G1S/G2
M
SNICHopf SN1SN2SN3
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P
Cdc25
Wee1
Wee1P
Cdc25
CycB
P
Cdc20
CK
I
CycB
CycBCK
I
CK
I
CycA
CycA
APC-PAPCTFBI
TFBA
CycE
CycD
TFEA
TFEI
Cyc E,A,B
CycE
TFIA
TFII
CK
I
CycE
Cdc14
Cdc14
Cdc14
CycA
CycA
CycB
CycD
Cdh1CycD
mass/nucleus
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wee1∆
mass/nucleus
Cdk1
:Cyc
B
0 1 2 3 4 5
0
0.4
0.8
1.2
G1
S/G2
M
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P
Cdc25
Wee1
Wee1P
CycB
P
Cdc20
CK
I
CycB
CycBCK
I
CK
I
CycA
CycA
APC-PAPCTFBI
TFBA
CycE
CycD
TFEA
TFEI
Cyc E,A,B
CycE
TFIA
TFII
CK
I
CycE
Cdc14
Cdc14
Cdc14
CycA
CycA
CycB
CycD
Cdh1CycD
Cdc25
mass/nucleus
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mass/nucleus
Cdk1
:Cyc
B
G1 S/G2
M
0 1 2 3 4 5
0
0.4
0.8
3.0 cki∆
The Start module is not required during mitotic cyclesThe Start module is not required during mitotic cycles
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P
Cdc25
Wee1
Wee1P
Cdc25
CycB
P
Cdc20
CK
I
CycBCK
I
CK
I
CycA
CycA
APC-PAPCTFBI
TFBA
CycE
CycD
TFEA
TFEI
Cyc E,A,B
CycE
TFIA
TFII
CK
I
CycE
Cdc14
Cdc14
Cdc14
CycA
CycA
CycB
CycD
Cdh1CycD
CycB
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0
0.4
0.8
2.0
0 1 2 3 4 5
G1
S/G2
M
cki∆ wee1ts
mass/nucleus
Cdk1
:Cyc
B
Unbalanced Growthand Division …
is Lethal !