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Modelling Biochemical Pathways in PEPA. Muffy Calder Department of Computing Science University of Glasgow Joint work with Jane Hillston and Stephen Gilmore October 2004. Are you in the right room?. Yes, this is computing science! Question - PowerPoint PPT Presentation
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1
Modelling Biochemical Pathways in PEPA
Muffy CalderDepartment of Computing Science
University of Glasgow
Joint work with Jane Hillston and Stephen Gilmore
October 2004
2
Are you in the right room?
Yes, this is computing science!
Question
Can we apply computing science theory and tools to biochemical pathways?
If so,
What analysis do these new models offer?How do these models relate to traditional ones?What are the implications for life scientists?What are the implications for computing science?
3
Cell Signalling or Signal Transduction*
• fundamental cell processes (growth, division, differentiation, apoptosis) determined by signalling
• most signalling via membrane receptors
signalling molecule
receptor
gene effects
* movement of signal from outside cell to inside
4
Abbreviations and notes•7-TMR: seven trans-membrane receptor•small G-proteins: Rap1, Ras, Rac; active when GTP bound•cAMP-GEF: cAMPactivated GTP-Exchange-Factor•AdCyc: Adenylate cyclase•PDE: Phhosphodiesterase•PKA: cAMP activated protein kinase•adaptor proteins: shc, grb2•SOS: Son-of-Sevenless, a GEF for Ras•PI-3 K: Phosphatidylinositol-3 kinase•Akt: a kinase activated by PI-3 K via PI-3 and another kinase, PDK•PAK: a kinased activated by binding to Rac•MKP: MAPK phosphatase, dephosphorylates MAPKs
activation inhibition phosphorylationactivation inhibition phosphorylation
cell membraneReceptor
e.g. 7-TMRcell membrane
Receptore.g. 7-TMR
Receptore.g. 7-TMR
αβγ
heterotrimericG-protein
cytosol
αβγ
heterotrimericG-protein
αβγααβγββγγ
heterotrimericG-protein
cytosol
tyrosinekinaseβ
γtyrosinekinaseββ
γγSOSshc
grb2SOSSOSshcshc
grb2grb2
RasRas
Raf-1Raf-1Raf-1
MEKERK1,2
MEKMEKERK1,2ERK1,2
PI-3 K
Ras
PI-3 K
PI-3 K
RasRasAktAktAkt
PAK
Rac
PAKPAK
RacRac
PKAcAMP
PKAcAMP
PKAPKAcAMPcAMP
αAdCyc
cAMPATP
ααAdCycAdCyc
cAMPATP cAMPcAMPATP
PKAcAMP
PKAPKAcAMPcAMP
cAMPGEF
cAMP
cAMPGEFcAMPGEF
cAMPcAMPRap1Rap1
MEK1,2
ERK1,2
B-Raf
MEK1,2
ERK1,2
MEK1,2MEK1,2
ERK1,2ERK1,2
B-RafB-RafB-Raf
PDE
cAMP AMP
PDE
cAMP AMP
PDEPDE
cAMP AMPcAMPcAMP AMP
nucleus
transcriptionfactors
nucleusnucleus
transcriptionfactors
transcriptionfactors
transcriptionfactors
MKPMKPMKP
A little more complex.. pathways/networks
5
6
RKIP Inhibited ERK Pathwaym1
Raf-1*
m2
k1
m3 Raf-1*/RKIP
m12
MEK
K12/k13
m7
MEK-PP
k6/k7
m5
ERK
m8MEK-PP/ERK-P
k8
m9
ERK-PP
k3
m4
k5
m6
RKIP-P
m10
RP
k9/k10
m11
RKIP-P/RP
k11
m2
k1
m3
k3
Raf-1*/RKIP/ERK-PP
m2
RKIP
k1/k2
m3
k3
k15
m13
k14
From paper by Cho, Shim, Kim, Wolkenhauer, McFerran, Kolch, 2003.
7
RKIP Inhibited ERK Pathwaym1
Raf-1*
m2
k1
m3 Raf-1*/RKIP
m12
MEK
k12/k13
m7
MEK-PP
k6/k7
m5
ERK
m8MEK-PP/ERK-P
k8
m9
ERK-PP
k3
m4
k5
m6
RKIP-P
m10
RP
k9/k10
m11
RKIP-P/RP
k11
m2
k1
m3
k3
Raf-1*/RKIP/ERK-PP
m2
RKIP
k1/k2
m3
k3
k15
m13
k14
From paper by Cho, Shim, Kim, Wolkenhauer, McFerran, Kolch, 2003.
8
RKIP protein expression is reduced in breast cancers
9
RKIP Inhibited ERK Pathway
proteins/complexes
forward /backward
reactions (associations/disassociations)
products
(disassociations)
m1, m2 .. concentrations of
proteins
k1,k2 ..: rate (performance)
coefficients
m1
Raf-1*
m2
k1
m3 Raf-1*/RKIP
m12
MEK
k12/k13
m7
MEK-PP
k6/k7
m5
ERK
m8MEK-PP/ERK-P
k8
m9
ERK-PP
k3
m4
k5
m6
RKIP-P
m10
RP
k9/k10
m11
RKIP-P/RP
k11
m2
k1
m3
k3
Raf-1*/RKIP/ERK-PP
m2
RKIP
k1/k2
m3
k3
k15
m13
k14
10
RKIP Inhibited ERK Pathway
This network seems to be very similar
to producer/consumer networks.
Why not to try usingprocess algebras for
modelling?
m1
Raf-1*
m2
k1
m3 Raf-1*/RKIP
m12
MEK
k12/k13
m7
MEK-PP
k6/k7
m5
ERK
m8MEK-PP/ERK-P
k8
m9
ERK-PP
k3
m4
k5
m6
RKIP-P
m10
RP
k9/k10
m11
RKIP-P/RP
k11
m2
k1
m3
k3
Raf-1*/RKIP/ERK-PP
m2
RKIP
k1/k2
m3
k3
k15
m13
k14
11
Why process algebras for pathways?
• Process algebras are high level formalisms that make interactions and constraints explicit. Structure becomes apparent.
• Reasoning about livelocks and deadlocks.
• Reasoning with (temporal) logics.
• Equivalence relations between high level descriptions.
• Stochastic process algebras allow performance analysis.
12
Process algebra(for dummies)
High level descriptions of interaction, communication and synchronisation
Event α (simple), α!34 (data offer), α?x (data receipt)
Prefix α.S
Choice S + S
Synchronisation P |l| P α l independent concurrent (interleaved) actions
α l synchronised action
Constant A = S assign names to components
Laws P1 + P2 P2 + P1
Relations (bisimulation) a
b c
aaaaa
c bbbc
13
PEPA Process algebra with performance, invented by
Jane Hillston
Prefix (α,r).S
Choice S + S competition between components (race)
Cooperation/ P |l| P a l independent concurrent (interleaved) actions
Synchronisation a l shared action, at rate of slowest
Constant A = S assign names to components
P ::= S | P |l| P
S ::= (α,r).S | S+S | A
14
Performance of Action
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
00.55 1.1 1.65 2.2 2.75 3.3 3.85 4.4 4.95 5.5 6.05 6.6 7.15 7.7 8.25 8.8 9.35 9.9
10.4511
11.55 12.112.6513.213.75 14.314.8515.415.95
t
P(t)
Rates is a rate, from which a probability is derived
tetP −−=1)(
15
Modelling the ERK Pathway in PEPA
• Each reaction is modelled by an event, which has a performance coefficient.
• Each protein is modelled by a process which synchronises others involved in a reaction.
(reagent-centric view)
• Each sub-pathway is modelled by a process which synchronises with other sub-pathways.
(pathway-centric view)
16
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
K6/k7
m6
P6
m4
P5/P6
Reaction Producer(s) Consumer(s)
k1react {P2,P1} {P1/P2}
k2react {P1/P2} {P2,P1}
k3product {P1/P2} {P5}
…
k1react will be a 3-way synchronisation,
k2react will be a 3-way synchronisation,
k3product will be a 2-way synchronisation.
k4
m3
k3
P1/P2
17
Modelling Signalling Dynamics
• There is an important difference between computing science networks and biochemical networks
• We have to distinguish between the individual and the population.
• Previous approaches have modelled at molecular level (individual)– Simulation– State space explosion– Relation to population (what can be inferred?)
18
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
k6/k7
m6
P6
m4
P5/P6
Reagent view: model whether or not a reagent can participate in a reaction (observable/unobservable).
k4
m3
k3
P1/P2
19
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
k6/k7
m6
P6
m4
P5/P6
Reagent view: model whether or not a reagent can participate in a reaction (observable/unobservable).
: each reagent gives rise to a pair of definitions.
P1H = (k1react,k1). P1L
P1L = (k2react,k1). P2H
P2H = (k1react,k1). P2L
P2L = (k2react,k2). P2H + (k4react). P2H
P1/P2H = (k2react,k2). P1/P2L + (k3react, k3). P1/P2L
P1/P2L = (k1react,k1). P1/P2H
P5H = (k6react,k6). P5L + (k4react,k4). P5L
P5L = (k3react,k3). P5H +(k7react,k7). P5H
P6H = (k6react,k6). P6L
P6L = (k7react,k7). P6H
P5/P6H = (k7react,k7). P5/P6L
P5/P6L = (k6react,k6) . P5/P6H
k4
m3
k3
P1/P2
20
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
K6/k7
m6
P6
m4
P5/P6
Reagent view: model configuration
P1H |k1react,k2react|
P2H | k1react,k2react,k4react |
P1/P2L |k1react,k2react,k3react|
P5L |k3react,k6react,k4react|
P6H |k6react,k7react|
P5/P6L
Assuming initial concentrations of m1,m2,m6.
k4
m3
k3
P1/P2
21
Reagent view:
Raf-1*H = (k1react,k1). Raf-1*L + (k12react,k12). Raf-1*L
Raf-1*L = (k5product,k5). Raf-1*H +(k2react,k2). Raf-1*H + (k13react,k13). Raf-1*H + (k14product,k14). Raf-1*H
…
(26 equations)
m1
Raf-1*
m2
k1
m3 Raf-1*/RKIP
m12
MEK
k12/k13
m7
MEK-PP
k6/k7
m5
ERK
m8MEK-PP/ERK-P
k8
m9
ERK-PP
k3
m4
k5
m6
RKIP-P
m10
RP
k9/k10
m11
RKIP-P/RP
k11
m2
k1
m3
k3
Raf-1*/RKIP/ERK-PP
m2
RKIP
k1/k2
m3
k3
k15
m13
k14
22
Signalling DynamicsReagent view: model configuration
Raf-1*H |k1react,k12react,k13react,k5product,k14product|
RKIPH | k1react,k2react,k11product |
Raf-1*H/RKIPL |k3react,k4react|
Raf-1*/RKIP/ERK-PPL |k3react,k4react,k5product|
ERK-PL |k5product,k6react,k7react|
RKIP-PL |k9react,k10react|
RKIP-PL|k9react,k10react|
RKIP-P/RPL|k9react,k10react,k11product|
RPH||
MEKL|k12react,k13react,k15product|
MEK/Raf-1*L|k14product|
MEK-PPH |k8product,k6react,k7react|
MEK-PP/ERKL|k8product|
MEK-PPH|k8product|
ERK-PPH
23
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
K6/k7
m6
P6
m4
P5/P6
Pathway view: model chains of behaviour flow
k4
m3
k3
P1/P2
24
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
K6/k7
m6
P6
m4
P5/P6
Pathway view: model chains of behaviour flow.
Two pathways, corresponding to initial concentrations:
Path10 = (k1react,k1). Path11
Path11 = (k2react).Path10 + (k3product,k3).Path12
Path12 = (k4product,k4).Path10 + (k6react,k6).Path13
Path13 = (k7react,k7).Path12
Path20 = (k6react,k6). Path21
Path21 = (k7react,k6).Path20
Pathway view: model configuration
Path10 | k6react,k7react | Path20
(much simpler!)
k4
m3
k3
P1/P2
25
Pathway view:
Pathway10 = (k9react,k9). Pathway11
Pathway11 = (k11product,k11). Pathway10 + (k10react,k10). Pathway10
…
(5 pathways)
m1
Raf-1*
m2
k1
m3 Raf-1*/RKIP
m12
MEK
k12/k13
m7
MEK-PP
k6/k7
m5
ERK
m8MEK-PP/ERK-P
k8
m9
ERK-PP
k3
m4
k5
m6
RKIP-P
m10
RP
k9/k10
m11
RKIP-P/RP
k11
m2
k1
m3
k3
Raf-1*/RKIP/ERK-PP
m2
RKIP
k1/k2
m3
k3
k15
m13
k14
26
Pathway view: model configuration
Pathway10 |k12react,k13react,k14product| Pathway40
|k3react,k4react,k5product,k6react,k7react,k8product| Pathway30
|k1react,k2react,k3react,k4react,k5product| Pathway20
|k9react,k10react,k11product| Pathway10
27
What is the difference?
• reagent-centric view is a fine grained view
• pathway-centric view is a coarse grained view
– reagent-centric is easier to derive from data– pathway-centric allows one to build up networks from already
known components
Formal proof shows that those two models are equivalent!
This equivalence proof, based on bisimulation, unites two views of the same biochemical pathway.
28
state reagent-view s1 Raf-1*H, RKIPH,Raf-1*/RKIPL,Raf-1*/RKIPERK-PPL, ERKL,RKIP-PL, RKIP-P/RPL, RPH, MEKL,MEK/Raf-1*L,MEK-PPH,MEK-PP/ERKL/ERK-PPH
pathway view Pathway50,Pathway40,Pathway20,Pathway10
s2 …
.
.
.
s28
(28 states)
State space of reagent and pathway model
29
State space of reagent and pathway model
30
Quantitative Analysis
Generate steady-state probability distribution (using linear algebra).
1. Use state finder (in reagent model) to aggregate probabilities.
Example increase k1 from 1 to 100 and the probability of being in a state with ERK-PPH
drops from .257 to .005
2. Perform throughput analysis (in pathway model)
31
Quantitative Analysis
Effect of increasing the rate of k1 on k8product throughput (rate x probability)i.e. effect of binding of RKIP to Raf-1* on ERK-PP
32
Quantitative Analysis
Effect of increasing the rate of k1 on k14product throughput (rate x probability)i.e. effect of binding of RKIP to Raf-1* on MEK-PP
33
Quantitative Analysis - Conclusion
Increasing the rate of binding of RKIP to Raf-1* dampens down the k14product and k8product reactions,
In other words,
it dampens down the ERK pathway.
34
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
K6/k7
m6
P6
m4
P5/P6
Activity matrix
k1 k2 k3 k4 k5 k6 k7
P1 -1 +1 0 0 0 0 0
P2 -1 +1 0 +1 0 0 0
P1/P2 +1 -1 0 0 0 0 0
P5 0 0 +1 -1 0 -1 +1
P6 0 0 0 0 0 -1 +1
P5/P6 0 0 0 0 0 +1 -1
Column: corresponds to a single reaction.
Row: correspond to a reagent; entries indicate whether the concentration is +/- for that reaction.
k4
m3
k3
P1/P2
35
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
K6/k7
m6
P6
m4
P5/P6
Activity matrix
k1 k2 k3 k4 k5 k6 k7
P1 -1 +1 0 0 0 0 0
P2 -1 +1 0 +1 0 0 0
P1/P2 +1 -1 0 0 0 0 0
P5 0 0 +1 -1 0 -1 +1
P6 0 0 0 0 0 -1 +1
P5/P6 0 0 0 0 0 +1 -1
Differential equations
Each row is labelled by a protein concentration. One equation per row.
For row r,
dr = column c A[r,c]) * row x f(A[x,c])
dt
where f(A[x,c]) = if (A[x,c]== -) then x else 1
a rate is a product of the rate constant and current concentration of substrates consumed.
k4
m3
k3
P1/P2
36
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
K6/k7
m6
P6
m4
P5/P6
Activity matrix
k1 k2 k3 k4 k5 k6 k7
P1 -1 +1 0 0 0 0 0
P2 -1 +1 0 +1 0 0 0
P1/P2 +1 -1 0 0 0 0 0
P5 0 0 +1 -1 0 -1 +1
P6 0 0 0 0 0 -1 +1
P5/P6 0 0 0 0 0 +1 -1
Differential equations (mass action)
dm1 = - k1 + k2 (two terms)
dt
k4
m3
k3
P1/P2
37
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
K6/k7
m6
P6
m4
P5/P6
Activity matrix
k1 k2 k3 k4 k5 k6 k7
P1 -1 +1 0 0 0 0 0
P2 -1 +1 0 +1 0 0 0
P1/P2 +1 -1 0 0 0 0 0
P5 0 0 +1 -1 0 -1 +1
P6 0 0 0 0 0 -1 +1
P5/P6 0 0 0 0 0 +1 -1
Differential equations (mass action)
dm1 = - k1*m1*m2 + k2
dt
k4
m3
k3
P1/P2
38
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
K6/k7
m6
P6
m4
P5/P6
Activity matrix
k1 k2 k3 k4 k5 k6 k7
P1 -1 +1 0 0 0 0 0
P2 -1 +1 0 +1 0 0 0
P1/P2 +1 -1 0 0 0 0 0
P5 0 0 +1 -1 0 -1 +1
P6 0 0 0 0 0 -1 +1
P5/P6 0 0 0 0 0 +1 -1
Differential equations (mass action)
dm1 = - k1*m1*m2 + k2*m3 (nonlinear)
dt
k4
m3
k3
P1/P2
39
Signalling Dynamics
m1
P1
m2
P2
k1/k2
m5
P5
K6/k7
m6
P6
m4
P5/P6
Differential equations (mass action)
For RKIP inhibited ERK pathway, change in Raf-1* is:
k4
m3
k3
P1/P2dm1 = - k1*m1*m2 + k2*m3 + k5*m4 – k12*m1*m12 dt +k13*m13 + k14*m13
(catalysis, inhibition, etc. )
40
Discussion & Conclusions• Regent-centric view
– probabilities of states (H/L)– differential equations– fit with data
• Pathway-centric view– simpler model – building blocks, modularity approach
– no further information is gained from having multiple levels.
• Life science – (some) see potential of an interaction approach
• Computing science– individual/population view– continuous, traditional mathematics
41
Further Challenges
• Derivation of the reagent-centric model from experimental data.
• Derivation of pathway-centric models from reagent-centric models and vice-versa.
• Quantification of abstraction over networks – “chop” off bits of network
• Model spatial dynamics (vesicles).
42
The End
Thank you.