Eyes everywhere…boulderschool.yale.edu/sites/default/files/files/... · GTP GDP Gα GTP Trp* Na+,...
Transcript of Eyes everywhere…boulderschool.yale.edu/sites/default/files/files/... · GTP GDP Gα GTP Trp* Na+,...
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Copepod's 2 lens telescope
Trilobite fossil 500 million years
Black antHouse Fly
Scallop
Octopus
Cuttlefish
Eyes everywhere…
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Modeling fly phototransduction:
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Limits of modeling?
• vertebrate phototransduction (rods, cones)
• insect phototransduction
• olfaction, taste, etc…
Comparative systems biology?
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Fly photo-transduction
• About the phenomenon
• Molecular mechanism
• Phenomenological Model
• Predictions and comparisons with experiment.
Outline:
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Compound eyeof the fly
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Fly photoreceptor cell
hv
50nm
1.5 μm
Na+, Ca2+
Microvillus
Rhodopsin
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Single photon response in Drosophila: a Quantum Bump
Lowlight
Dimflash
“All-or-none”response
Henderson and Hardie, J.Physiol. (2000) 524, 179
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Comparison of a fly with a toad.
From Hardie and Raghu, Nature 413, (2001)
Single photon response:
Notedifferent scales directions of current!!
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Linearity of macroscopic response
hv
Linearsummationover microvillae
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Average QB wave-form
A miracle fit:
Henderson and Hardie, J.Physiol. (2000) 524, 179
QB aligned at tmax
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QB variability
Peak current Jmax (pA)#
even
ts
rms Jmean J
( )( )
.4max
max
≈ 0
# of
eve
nts
Latency (ms)
Latency distribution
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Multi-photon response
QB waveform
Convolutionwith latencydistribution
Macroscopic response= average QB
Latency distributiondetermines the averagemacroscopic response
!!! Fluctuations control the mean !!!
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Advantages of Drosophila photo-transduction as a model
signaling system:
• Input: Photons• Output: Changes in membrane potential• Single receptor cell preps• Drosophila genetics
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Molecular mechanism offly phototransduction
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Response initiation
IP3 + DAGPIP2
PKCGαβγGDP PLCβ
Trp
Low [Na+], [Ca++]
High [Na+], [Ca++]
Ca pump
*GTPGDP
Gα
GTP Trp*
Na+, Ca++
DAG
Cast: Rh = Rhodopsin; Gαβγ = G-proteinPIP2 = phosphatidyl inositol-bi-phosphateDAG = diacyl glycerolPLCβ = Phospholipase C -beta ; TRP = Transient Receptor Potential Channel
DAG Kinase
Rh
hv
*Rh*
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Positive Feedback
PKC
Na+, Ca++
PLCβ
PIP2 IP3 + DAG
hv
*GαβγGDP GTP
GDP
Gα
GTP Trp
Rh
High [Ca++]
Intermediate [Ca++]
DAG
Trp***
Intermediate [Ca] facilitates opening of Trp channelsand accelerates Ca influx.
Ca pump
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Negative feedback and inactivation
PKC
Na+, Ca++
PLCβ
PIP2 IP3 + DAG
*GαβγGDP GTP
GDP
Gα
GTP
Rh* **
Cast: Ca++ acting directly and indirectly e.g. via PKC = Protein Kinase Cand Cam = CalmodulinArr = Arrestin (inactivates Rh* )
High [Ca++]
High [Ca++]
**Cam ??
Arr
Ca pump
Trp*
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Comparison of early steps
From Hardie and Raghu, Nature 413, (2001)
Vertebrate Drosophila
2nd messengers
cGMPDAG
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…and another cartoonc.
d
a.
b.
From Hardie and Raghu, Nature 413, (2001)
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InaD signaling complex
InaDPDZ domainscaffold
From Hardie and Raghu, Nature 413, (2001)
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Speed and space: the issue of localization and confinement.
Order of magnitude estimate of activation rates:
G* ~ PLC* ~ k [G] ~ 10μm2/s 100 / .3 μm2 > 1 ms-1
Diffusion limit onreaction rate
Protein (areal) density
! FastEnough !
~ 1μm2/s 10 / .3 μm2 =.03ms-1 << 1 ms-1
Possible role for InaD scaffold !
However if:! TooSlow !
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How “complex” should the model
of a complex network be?
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A naïve model
“Input” TRP channel Ca2+
( G*, PLCβ*, DAG)
low
high
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Kinetic equations:Activation stage ( G-protein; PLCβ; DAG ):
ddt
A A IA= − +−τ 1
QB “generator” stage ( Trp, Ca++ ):
ddt
Trp A F Ca Trp F Ca Trp
ddt
Ca Trp Ca Ca Ca Ca
nTrp
ex Ca
* ( ) ( ) *
[ ] *([ ] [ ]) ([ ] [ ])
*= −
= − − −
+−
−
−
τ
σ τ
1
10
# open channels Positive and negative feedback
Ca++ influx via Trp* Ca++ outflow/pump
Input (Rh activity)
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Feedback Parameterization
F Ca g Ca KCa K
Dm
Dmα α
α
α
α
α( ) ([ ] / )
([ ] / )= +
+1
1
Parameterized by the “strength” gα (~ ratio at high/low [Ca])
Characteristic concentration KDα
and Hill constant mα
Note: this has assumed that feedback in instantaneous…
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Null-clines and fixed points
0 100 200 300 400 5000
0.1
0.2
0.3
0.4
0.5
0.6
0.7
A=.2
.05.03
A=.02
[Ca]/[Ca0]
Trp*
/Trp
[Ca]=0
[TRP*]=0null-cline
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Problems with the simple model
Model Experiment
• In response to a step of Rh* activity (e.g. in Arr mutant ) QB current relaxes to zero
• Ca dynamics is fast rather than slow no “overshoot”
• Long latency is observed
“High”
fixed point
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Order of magnitude estimate of Ca fluxes
[Ca]dark ~ .2μM
[Ca]peak ~ 200μM
1 Ca ion / microvillus
1000 Ca ion / microvillus
30% of 10pA Influx 104 Ca2+ / ms
Hence, Ca is being pumped out very fast ~ 10 ms-1
[Ca] is in a quasi-equilibrium
Note: μ−villus volume ~ 5*10-12 μl
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Microvillus as a Ca compartment
Compare 10 ms-1 with diffusion rate across the microvillus:
τ -1 ~ Dca / d2 ~ 1 μm2/ms / .0025 μm2 = 400 ms -1
But diffusion along the microvillus:
τ -1 ~ 1 μm2/ms / 1 μm2 = 1 ms -1 is too slowcompared to 10ms-1
50nm
1-2 um
Hence it is decoupled from the cell.
Note: microvillae could not be > .3μm in diameter,i.e it is possible the diameter is set by diffusion limit
Ca++
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Slow negative feedback
Assume negative feedback is mediated by a Ca-binding protein (e.g. Calmodulin??)
ddt
B k Ca B Bx x* *[ ]= − −τ 1
F B g B KB K
Dm
Dm− −
−
−
= ++
−
−( *) ([ *] / )
([ *] / )1
1
Slow relaxation
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A more ‘biochemically correct’ model:ddt
G* ...=
ddt
PLC* ...=
ddt
DAG[ ] ...=
ddt
Trp* ...=
ddt
Ca[ ] ...=
ddt
B[ *] ...= DelayedCa negative feedback
F+
F-
Feedback
Cascadeddt
Rh* ...=
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Stochastic effects
Gillespie, 1976, J. Comp. Phys. 22, 403-434see also Bort,Kalos and Lebowitz, 1975, J. Comp. Phys. 17, 10-18
Numbers of active molecules are small !e.g. 1 Rh*, 1-10 G* & PLC*, 10-20 Trp*
Chemical kinetics
Master equation
Numerical simulation
Reaction “shot” noise.
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Stochastic simulationEvent driven Monte-Carlo simulationa.k.a. Gillespie algorithm
Gillespie, 1976, J. Comp. Phys. 22, 403-434see also Bort,Kalos and Lebowitz, 1975, J. Comp. Phys. 17, 10-18
Numbers of molecules (of each flavor) #Xa(t) are updated
#Xa(t) #Xa(t) +/- 1 at times ta,i
distributed according to independent Poisson processes with transition rates Γa,+/− . Simulation picks the next “event” among all possible reactions.
Note: simulation becomes very slow if some of the Reactions are much faster then others. Use a “hybrid” method.
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The model is phenomenological…
Many (most?) details are unknown:
e.g. Trp activation may not be directly by DAG,but via its breakdown products;Molecular details of Ca-dependent feedback(s)are not known;etc, etc
there’s much to be explained on a qualitative andquantitative level…
BUT
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Identifying “submodules”ddt
G* ...=
ddt
PLC* ...=
ddt
DAG[ ] ...=
ddt
Trp* ...=
ddt
Ca[ ] ...=
ddt
B[ *] ...= DelayedCa negative feedback
F+
F-
Feedback
Cascadeddt
Rh* ...=
Keydynamicalvariablesdefine“Submodules”
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Rephrased in a “Modular” form: the “ABC model”
“Input” Channel
B
( Rh*, G*)
Activator(PLCβ∗, Dag)
(TRP)
(Ca-dependent inhibition)
Ca++
Ca++
Activator – Buffer – Ca-channel
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Quantum Bump generation
0 200 400 600 800 10000
5
10
15
20
25
20
60
100
140
180
0 600200 400
TRP*
B*/10PLC*
A
Threshold for QB generation
A
High probabilityof TRP channelopening
“INTEGRATE & FIRE”process
B*
(A,B) - “phase” plane
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What about null-cline analysis?Problems:
• 3 variables A,B,C• Stochasticity
• DiscretenessC
B1 2 3 40
“Ghost”fixed point
dXdt
x x x x= → → + = → −0 1 1 Prob ( Prob () )
Generalized “Stochastic Null-cline”
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Can one calculate anything?E.g. estimate the threshold for QB generation:
A-1 A A+1PLC*
C = 0 1 2
PLC*
Am Am f([Ca])Positive feedbackkicks in once channels open
Threshold A = AT such that
Prob (AT -> AT +1) = Prob (C=0 -> C=1)
NOTE: Better still to formulate as a “first passage” problem
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Condition for QB generation
PLC*
[Ca]
12
3
4
0
[Ca]
A
Prob (C=1 C=2) > Prob (C=1 C=0)
Amax~ PLC*
*AT
AT > AQB ([Ca])
AQB ([Ca])
Bistable region/Bimodal response
Reliable QBgeneration
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Quantum Bump theory versus reality
Model ExperimentLatencyhistogram
Average QBprofile
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Fitting the data: QB wave-formTr
p*/T
rpto
t
Time (arbs)
There is a manifoldof parameter valuesproviding good fitfor < QB > shape !!
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So what ???“With 4 parameters I canfit an elephant and with 5 it will wiggle its trunk.”
E. Wigner
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Non-trivial “architectural” constraints
Despite multiplicity of fits, certain constraints emerge:
• Trp activation must be cooperative• Activator intermediate must be relatively stable:
“integrate and fire” regime.• Negative feedback must be delayed• Multiple feedback loops are needed
Etc, …Furthermore:Fitting certain relation between parameters:
“phenotypic manifold”- the manifold in parameter space corresponding to the same quantitative phenotype.
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Many more features to explain quantitatively!
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Constraining the parameter regime…
Help from the data on G-protein hypomorph flies:
• # of G-proteins reduced by ~100• QB “yield” down by factor of 103
• Increased latency (5-fold)• Fully non-linear QB with amplitude
reduced about two-fold
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G-protein hypomorphModel: Experiment:
• Single G* and PLC* can evoke a QB !!• Reduced yield explained by PLC* deactivating
before A reaches the QB threshold• Relation between yield reduction and
increased latency. # PLC* ~ 5 for WT
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What happens in response to continuous activation ?e.g. if Rh* fails to deactivate
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Persistent Rh* activityRelaxation Oscillator
20
60
100
140
180
100 500200 300 400
Trp*
B*
A
Unstable Fixed Point
(A,B*) phase plane
A
B*
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QB trains: theory versus experiment
Qualitative but not quantitative agreement so far…
Model:Arrestin mutant (deficient in Rh* inactivation):
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Predicted [Caex] dependence
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Observed external [Ca2+] dependence
[Caext] mM
Coe
ffof
var
iatio
n
Peak current
Henderson and Hardie, J.Physiol. (2000) 524.1, 179
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What does one learn from the model?
e.g. Mechanisms/parameters controlling:Threshold for QB generation.QB amplitude fluctuations.Latency.Yield (or response failure rate)Latency distribution.
Functional dependences:e.g. dependence of everything on [Ca++ ]ext
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Modeling methodology questions
• Need an intelligent method of searching the parameter spaceand of characterizing the parameter manifold ??? How doesEvolution search the parameter space?
• Characterizing the “space of models”??
• “Convergence proof”?? Given a model that fits N measurements can we expect that it will fit N+1 (even with additional parameters)?
• How accurate should a prediction be for us to believe that the model is correct ?? Unique??
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Summary and ConclusionA phenomenological model can explain observations and make numerous falsifiable predictions (especially for the functional dependence on parameters).
Insight into HOW the system works from understandingthe most relevant parameters and processes.
?????Can one get any insight into WHY the system is constructed the way it is (e.g. vertebrate versus insect)
?????
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AcknowledgementsAlain Pumir, (Inst Non-Lineare Nice, France)
Rama Ranganathan(U. Texas,SW Medical School)
Anirvan Sengupta, (Rutgers)
Peter Detwiler (U. Washington)
Sharad Ramanathan (Harvard)