Transcript Can we predict the direction of cell motion - uni

Biophysics of Systems
Dieter Braun
Systems Biophysics
Lecture + Seminar
Di 10.15-13.30 Uhr
Website of Lecture:
http://www.physik.unimuenchen.de/lehre/vorlesungen/sose_10/
Biophysics_of_Systems/index.html
Master Program Biophysics:
bio.physik.lmu.de
Macrophage hunts down Bacterium
A physical view of the (eukaryotic) cell
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www.people.virginia.edu/~rjh9u/cell1.html
Macromolecules
– 5 Billion Proteins
• 5,000 to 10,000
different species
– 1 meter of DNA with
Several Billion bases
– 60 Million tRNAs
– 700,000 mRNAs
Organelles
– 4 Million Ribosomes
– 30,000 Proteasomes
– Dozens of Mitochondria
Chemical Pathways
– Vast numbers
– Tightly coupled
How is a useful
approach possible?
Biosystems: Feedback Loops
Biosystems: Feedback Loops
Promotors,
Protein-Interactions
Inhibitors
Regulation
RNA Interference Compartments
Epigenetics
Reaction Networks
Amplification
Organelles
Cell-Cell Communication
Noise
Diffusion
What is a „Bio-System“ ?
Input
Networks
* Komponents (Molecules, Proteins, RNA...)
* Network-like Connections (kinetic Rates)
* Substructures (Knots, Module)
* Functional Input-Output-Relations
Goal
* Finding building principles (reverse engineering)
(also: tracking how evolution has build it)
• Quantitative Models to describe the system
• Test the model with experimental data
• Prediction of the System behavior
Output
Systems Biology Definition
• Systems Biology integrates experimental and
modeling approaches to study the structure and
dynamical properties of biological systems
• It aims at quantitative experimental results and
building predictive models and simulations of
these systems.
• Current primary focus is the cell and its
subsystems , but the „systems perspective“ will be
extended to tissues, organs, organisms,
populations, ecosystems,..
Signal Pathway in dictyostelium discoideum
cAMP
+
b
g
Ga
b
g
PIP3
PIP2
PI3K*
PTEN
RAS
Cell
polarization
pleckstrin
homology
domain
PH
Rac/Cdc42
CRAC
AcetylcholinAktivierung
Actin
polymerization
Levels of discription of the Signal Transduction
Biochemical
Rate Equations
+ Definition of
Reaction Compartments
+ Diffusion Processes
(Reakt.-Diff-Eq.)
+ Stochastic
Description
Signal-Networks are „complex“
Connection Maps: Signal Transduction Knowledge Environment www.stke.org
How to Approach Complexity
Classical Approach: System Analysis
- Quantitative Data Recording
- Mathematical Modeling
- Simulation
- Comparison with Experiment
Useful analogy:
Signaltransduktion and Elektronic Circuits
Biological Signalnetworks are Combinatorical
Modular view of the chemoattractant-induced
signaling pathway in Dictyostelium
Peter N. Devreotes et al.
Annu. Rev. Cell Dev. Biol. 2004. 20:22
Hierarchical Structure of biologic Organisms
(Z. Oltvai, A.-L. Barabasi, Science 10/25/02)
Modular Biology
as advocated in the
influential paper (Nature 402,
Dec 1999)
Stochastic Genes
From Concentrations to Probabilities
Stochastic Genes
From Concentrations to Probabilities
Inventory of an E-coli: do counting molecules matter?
Number of mRNA/cell
Number of rRNA/cell
Number of tRNA/cell
Number of all RNA/cell
Number of polysaccharides/cell
Number of lipopolysaccharide/cell
Number of lipids/cell
Number of outer membrane proteins
Number of porins (subset of OM)
Number of lipoproteins (OM)
Number of nuclear proteins
Number of ribosomal proteins
Number of all proteins in cell
Number of external proteins (flag/pili)
Number of all proteins
4000
18,000
200,000
222,000
39,000
600,000
25,000,000
300,000
60,000
240,000
100,000
900,000
2,600,000
1,000,000
3,600,000
Note the low number of mRNA !
Repetition: Gen-Expression
With the Genes fixed: how can a bacteria adapt to the
environment?
Answer: Regulation of Gen-Expression
Repressors & Inducers
active
repressor
inactive
repressor
RNAP
inducer
no transcription
transcription
RNAP
promoter
operator
gene
promoter
operator
gene
• Inducers that inactivate repressors:
– IPTG (Isopropylthio-ß-galactoside)  Lac repressor
– aTc (Anhydrotetracycline)  Tet repressor
• Use as a logical Implies gate:
Repressor
Inducer
Output
(NOT R) OR I
Repressor
0
0
1
1
Inducer
0
1
0
1
Output
1
1
0
1
The Effect of
Small Numbers
e.g. by reducing the
transkription rate
or the cell volume
=> Protein levels are constant,
but the fluktuations increase
Stochastic Gen-Expression
Extrinsic Noise
Intrinsic Noise
Search for differences between intrinsic
noise from biochemical processes of e.g.
Gen-Expression) and extrinsic noise from
fluctuations of other cell compartments, e.g.
the conzentration of RNA Polymerase.
Idea of Experiment:
Gene for CFP (cyan fluorescence protein)
und YFP (yellow fluorescence protein) are
controlled by the same, equal promotor, i.e.
the average concentration of CFP und YFP
are the same in a cell: differences are then
attributed to intrinsic noise.
Intrinsic Noise
A: no intrinsic noise => noise is correlated red+green=yellow
B: intrinsic noise => Noise is uncorrelated, differenz colors
Elowitz, M. et al, Science 2002
Stochastic Gen-Expression
Unrepressed LacI
Extrinsic Noise
Repressed LacI
Intrinsic Noise
+Induced by IPTG
Extrinsic Noise
Elowitz, M. et al, Science 2002
Science, 307:1965 (2005)