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Systems Biology
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Lecture
What is Systems Biology?
Dynamical systems theory
Metabolic control analysis
-integrative bioinformatics
-(network) modelling
Systems Theory
The behaviour of a system depends on:
THUS:
You cannot understand a system via pure
reductionism (studying the components in
isolation)
Systems behaviour: oscillations
700 8.5
650 7.5
NAD(P)H fluorescenc
concentration (mM)
600 6.5
500 4.5
4 mM KCN
450 3.5
20 mM glucose
Fru-
400 1,6bP 2.5
8 8.5 9 9.5
0 10 20
time (min)
Mixing systems:
Dynamical systems theory, bifurcation theory, chaos theory
2D 3D
1.8
1.6
Isolated enzyme:
1.4
S 1 P
enzyme activity
1.2
v_isolated
1
v_system
0.8
0.6
Enzyme in system:
0.4
S 1 P 2 X 0.2
0
0 2 4 6 8 10 12
[E1]
Metabolic control analysis: a useful theory for formalizing
control and regulation
Enzyme in system:
S 1 P 2 X 2
1.8
1.6
1.4
enzyme activity
Control: 1.2
v_isolated
1
v_system
0.8
Ce1 = %change in e1
0.4
0.2
0
0 2 4 6 8 10 12
[E1]
ei Cei =
J
1
Metabolic control analysis: a useful theory for formalizing
control and regulation
S 1 P 2 X
-integrative bioinformatics
-engineering
-statistics
-modeling/systems theory
-biology
Lecture
What is Systems Biology?
Dynamical systems theory
Metabolic control analysis
-Clustering
-Correlation analysis
-Network reconstruction
-visualisation
Clustering: need a measure of
similarity/distance
ribose
Mice on a high fat diet for 20 weeks
WT VLDLR-/-
e
rat
rat
fib
fib
il
il
ho
ho
LIVER CYTOPLASM
no
no
A
A
A
A
Fis
Fis
CL
Fe
CL
Fe
TV
TV
glucose Galactokinase Senescence marker protein 30 oxidation
metabolism Ketohexokinase Selenium binding protein 56kDa and aging
Fructose biphosphatase 1 Selenium binding protein 56kDa
Malate dehydrogenase T-complex protein 1, beta subunitt
Alpha enolase Peroxyredoxin 6
Alpha enolase Glutathione S-transferase Mu 2
Thriosephophate isomerase Gluthatione S-transferase Mu 1
Phosphoglycerate mutase Heat shock protein 74 kDa
Isocitrate dehydrogenase Epoxide hydrolase
Adenosine kinase Catalase
Adenosine kinase Aldehyde dehydrogenase
lipid Long chain acetyl-CoA dehydrogenase Aldehyde dehydrogenase
metabolism Long chain acyl-CoA thioester hydrolase Aldehyde dehydrogenase
Long chain acyl-CoA thioester hydrolase L-gulonolactone oxidase
Mitochondrial long-chain acyl-CoA thioester Thioether S-methyltransferase homocysteine
Acyl-CoA thioester hydrolase Adenosylhomocysteinase metabolism
Acyl-CoA thioesterase Glycine-N-methyltransferase
Apolipoprotein E Sepiapterin reductase BH4
Apolipoprotein A1 precursor Phenylanaline-4-hydroxylase metabolism
Adipophilin Delta-aminoevulinate dehydratase haem
2-hydroxyphytanoyl-Coa lyase Hydroxymethylbiliane biosynthesis
CTP:phosphocholine cytidyltransferase b2 Pyrophosphatase energy
Isovaleryl CoA dehydrogenase Nicotinate-nucleotide pyrophosphorylase metabolism
Phosphatidylethanolamine-binding protein N-sulfotransferase enzymes
Hypothetical GDSL-like Lipase/ acylhydrolase Proteasome beta subunit
Annexin A5 Nucleoside diphosphate kinase B
protein Formimimo cyclodeaminase Guanidinoacetate N-methyltransferase
metabolism Ornithine aminotransferase Purine nucleoside phosphorylase
Glutamine synthetase Ubiquitin / ribosomal protein CEP52
Glutamine synthetase Tetranectin carcinogenesis marker
Histidine ammonia-lyase Tubulin alpha-2 chain structural proteins
Arginase-1liver
3-hydroxyanthranilate 3,4-dioxygenase
Cysteine sulfinic acid decarboxylase >200% >150% >125% >100% <100% <75% <50% <10%
Multivariate analysis: Principle
component analysis
Fenofibrate
0.6 0.2 Fish oil
PC 2 (20.94%)
CLA
0.4 0.0
PC 2 (30.72%)
Fenofibrate
0.2 -0.2
CLA
0.0 -0.4 Control
m samples
n components
n components
l signals
= .
-1 +2
Feedback loop
genes
enzyme
transcription translation
mRNA
Feedback
Degradation loop
Metabolic Reactions
Biological knowledge-based modeling
Small systems!
Biological knowledge-based modeling:
Yeast glycolysis
Substrate-accelerated death
)
60
50
40
tps1 -
30
20
10 tps1
F ructose 1,6-bisphosphate (mM)
0
0 1 2 3 4 5 10 20 30 40 50
time (mi n)
3
The biological story:
ATP (mM)
2
No brake: all ATP consumed at
1 hexokinase
tps1
0
0 1 2 3 4 5 10 20 30 40 50
time (min)
Turbo design: optimal strategy for ATP production
In silico tps1 phenotype
danger of turbo design:
If
-the activity of enzyme 1 exceeds the capacity of enzyme 2
-enzyme 1 is insensitive to intermediate I
Then
intermediate I will accumulate, despite a link via adenine
nucleotides
ATP 2 ATP
1 I I II I 2
extreme case: v1 = 2 v2
Turbo explanation of the tps1 phenotype
muscle: arterial
blood: glucose
homeostasis
HK inhibited by -
product glucose 6P
Different niches, different purposes, different regulations
Large systems!
Constraint-based modeling
v1 v2
S
v2 v2 v2
v1 v1 vmax v1
Unique solution Solution space Limited solution space
The Model Development Process
Physiology
Genomics
biochemistry
gene
protein
reaction
Stoichiometric models: constraint-
based analysis
An Optimal
Solution EP or EM
Network
Elementary modes:
Allowable
Reconstruction
Genomics, Physiology Solution Space
1
what are all the
possibilities?
and Biochemistry 2
Application of v2 3
Constraints c
b
4
v1
a
v3
Energy and
5
Biomass Constituents
6
1. Linear Optimization (MILP)
2. Elementary Modes/Extreme Pathways
3. Phenotypic Phase Plane Analysis
4. Gene Deletions
5. Finding Objective Functions
6. Full Phase Space Sampling
elementary modes
Network
Biology vs
Allowable
Reconstruction
Genomics, Physiology Solution Space
1
engineering: what is
the objective function?
and Biochemistry 2
Application of v2 3
Constraints c
b
v1
4
a
Evolution &
Energy and
Biomass Constituents
v3
5
microbes: optimal
biomass formation
6
1. Linear Optimization (MILP)
2. Elementary Modes/Extreme Pathways
3. Phenotypic Phase Plane Analysis
4. Gene Deletions
5. Finding Objective Functions
6. Full Phase Space Sampling
Constraint-based modeling:
predictions of microbes in evolution
T = 37 C
T = 30 C
Flux balance analysis:
optimal flux distribution
200
Corr.Coeff.=0.97
WT (FBA)
FBA v ( (Theor.) 150
P-value=10
C 0.4
-11
8
7
predictions, 9
)
following 100
3
10
Edwards and
Fluxes
1413 11
50
2 12 1
Palsson 456
16
1517
PNAS, 2000
0
perturbation adaptation
response: regulation
State I State II
If there is a purpose for the regulatory design, we can predict state II without
knowing the details of the underlying regulation
How to move forward? Integrate data-driven
and knowledge-based modelling
Systems Biology: an iterative process
Data management/
Bioinformatics
Experimental data
Model building acquisition
Experimental data
The Genomics Demand for
Modeling & Simulation
?
Acknowledgements and collaborations
Willem de Vos
Astrid Mars
Douwe Molenaar Magda Faijes
Arno Wegkamp Christof Francke Steven Rothuizen
Marc Stevens Richard Notebaart
Mariela Serrano Frank van Enckevort
Filipe Santos Jos Boekhorst
Jeroen Hugenholtz Robert Kerkhoven
Michiel Kleerebezem Michiel Wels Systems Biology of LAB
Eddy Smid Roland Siezen
Oscar Kuipers
Jan Kok
Hans Westerhoff
Stanley Brul
Timo Breit
Bert Poolman
Mariet vd Werf
Sef Heijnen Age Smilde
Walter van Gulik
Wouter van Winden