Transcript Self-Organizing Bio-structures

Self-Organizing Biostructures
NB2-2009
L.Duroux
Lecture 3
Self-Organization and Emergence
Introduction and
definitions
Life as the result of Self-Organization
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Life appeared as result of gradual increase in
molecular complexity (Chap. 3 & 4)
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Happened with NO enzymatic ”intelligence” &
NO DNA/RNA ”memory”
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The dynamics of a system can tend by
themselves to increase the inherent order of a
system -Organization vs Entropy-?
René Descartes
(1596-1650)
S-O in Chemistry
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self-assembly of molecules = supermolecules
reaction-diffusion systems and oscillating
chemical reactions (out-of-equilibrium)
autocatalytic networks (biological evolution)
liquid crystals
See K. Nagayama’s lecture online on selfassembly (1997) at:
http://www.vega.org.uk/video/programme/70
S-O in Biology
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SIZE
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spontaneous folding of proteins and other biomacromolecules
formation of lipid bilayer membranes
homeostasis (the self-maintaining nature of systems from the
cell to the whole organism)
morphogenesis, or how the living organism develops and
grows (embryology)
the coordination of human movement
the creation of structures by social animals, such as social
insects (bees, ants, termites), and many mammals
flocking behaviour (such as the formation of flocks by birds,
schools of fish, etc.)
the origin of life itself from self-organizing chemical systems,
in the theories of hyper cycles and autocatalytic networks
the organization of Earth's biosphere in a way that is broadly
conducive to life (Gaia hypothesis)
The Ingredients of SO
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SO is governed by Thermodynamics ie negative change
in Free Energy (micelle formation) OR by Kinetics
(virus envelope)
Always dictated by internal rules to the system
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Regulated by Feedback (positive OR negative)
Involves multiple interactions
Is a balance between exploitation and exploration
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In general leads to Emergence (new properties)
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What is NOT SO!
(whatever the scale)
Simple molecular
systems
Aggregation of Surfactant molecules: a
case of entropy-driven SO
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In this system (depends on
initial set of conditions):
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Increase of local order
(micelle)
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Increase in global entropy
(freeing of H2O molecules)
Detergents & Aggregates in water
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Another type of order
increase:
compartmentation &
segregation of guest
molecules
SO of a lipidic vesicle
SO of wedge-shaped molecules
Protein folding: a case of
thermodynamic control
Anfinsen experiment with RNaseA, 1970
S-O of complex polymeric proteins
A: Core of pyruvate
dehydrogenase:
homopolymer 24
chains
B: Aspartate
Transcarbamoylase
(ATCase), 2C3 + 3R2
C: F-actin
homopolymer,
13chains/turn
S-O and autocatalysis
Increasing SO rate with time
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In auto-catalytic SO processes, the rate of self-assembly
increases with time
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Examples: DNA duplexes, protein folding...
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Further molecular interactions favored with proximity
Duplex formation in DNA
Duplex formation in t-RNA
Is polymerization a SO
process?
Polymerization vs Self-Assembly
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Polymerization is SO if
spontaneous (nylon,
acrylamide...)
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Polymerization results in
decrease in Entropy
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Step-wise polymerisation
in general not SO
process
Di-Block Copolymers: tools for
design in nanosciences
SO processes under
kinetic control
Activation Energy (in enzymatic processes)
E+S
ES
E+P
The folding of insulin: a case of
thermodynamic and kinetic control
spontaneous
enzymatic
SO and symmetry
breaking
Symmetry breaking in porphyrin aggregates
J-aggregate
•Formation of homochiral helices in a chiral hydrodynamic flow
•Role of vortices in spontaneous symmetry breaking
Template-induced chiral SO: chiral memory
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Less favourable product
trapped kinetically
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Interplay between
thermodynamics and
kinetics factors
Complex biological
systems
Muscle fibers
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Complex assembly of filamentous protein multimers
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Thin filament + Thick filament made of protein
multimers
A thin filament of muscle fiber: Actin
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SO thermodynamically
controlled
A thick filament of muscle fiber: Myosin
myosin
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Thick filament: multimer of myosin heavy chain dimer
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SO thermodynamically controlled: hydrophobic
interactions (coiled-coil) + electrostatics (inter-mers)
Thermodyn. ctrl
Bacteriophage T4
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Combination of
thermodynamics and
kinetics
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63 gene products
The axoneme of a bacterial flagellum
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Result of highly regulated, sequential organization of
protein substructures
Complex interplay between Thermodyn. & Kinetics
Model for SO of
bacterium
flagella
(K. Namba)
SO in Macroscopic systems
Anthill
Migratory bird pattern
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SO : patterns with no ordering center
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Internal forces : complex genetic and social factors
Out-of-Equilibrium SO
Bénard cells & convection
Apparent conflict: SO obtained far from equilibrium!
Oscillating system: patterns/no patterns
At bifurcation point: formation of patterns (diverse shapes)
The Zabotinski-Belousov reaction: Out-of-Eq
reaction with periodic oscillations
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Family of reactions including KBr and sulfuric acid, CeriumIV
(and Ferroin)
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CeIV + FeIII
CeIII + FeII
Excitable: stimulus (mechanical, optical...) induces SO (patterns)
from quiescent state
Bifurcation point & Dissipative system
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The Brusselator (Prigonine,
Nobel Chemistry 1977)
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A (open) system pulled from Eq.
reaches a point of instability
(minimal entropy production)
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At this point (lc) and beyond:
SO occurs
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Dissipative system: exchanges
Energy & Matter with environ.
Genesis of Out-of-Eq. theory
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Alan Turing (1952): system homogenous close to Equilibrium 
unstable far from Eq. (fluctuations)
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Prigonine & Lefever (1968): theoritical model to describe
ingredients necessary for spatial SO in a system
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Belousov & Zabotinsky (1950’s): complex reaction mixture to
”mimic” Krebs cycle, observation of oscillations in colour
(CeriumIV / CeriumIII) and shapes
Characteristics of Out-of-Eq reactions
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Time-dependency of system’s themodynamics
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Irreversible reaction
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Dynamic & non-linear
The notion of
Emergence
SO and Emergence go together
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Emergence can be defined as:
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”The onset of novel properties that arise when a
higher level of complexity is formed from
components of lower complexity, where these
properties are not present”
Assumption (epistemic view):
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The objects forming a complex SO system AND its
levels of structures can be considered as separated
A simple chemical: benzene
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Aromatic character of benzene not present in its atoms
A more complex example: Myoglobin &
Hemoglobin
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Myoglobin transports O2
thanks to heme group
 Shows Michaelis-Menten
behaviour
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Hemoglobin is tetramer
(chains homologous to
myoglobin)
 Shows Sigmoidal
behaviour
Emergence in Geometry
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New properties arise at
each level of hierarchy,
not present at the
previous level
Main characteristics of Emergence in SO
systems
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Deducibility: The emergent property of the whole
cannot be deduced from the properties of its parts
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Downward causation: The properties of higher
hierarchic levels affect properties of lower components
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Non-linearity: SO in dissipative open-systems, far from
equilibria: emergence can occur at points of instability
(bifurcation points)
Life as Emergent property
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”Quorum sensing” in bacteria: cell densitydependent signalling mechanism in bacteria
(biofilm formation, colonization, luminescence)
Vibrio fischeri (LUX gene)
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Complex SO patterns without localized
organization centers (social insects)
Conclusions
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SO systems under Thermodyn. Control: crystallization, micelle formation,
protein folding, DNA hybrid ...
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SO systems under Kinetic Control: protein biosynthesis, virus assembly,
swarm intelligence
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SO under Out-of-Eq. Systems: oscillating reactions, order-out-of-chaos,
convection (tornadoes)
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All living systems are open, far-from-Eq, dynamic, non-linearand dissipative
structures
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Irreversibility in evolution (Arrow of time)
Literature for analysis
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Bucknall & Anderson, 2003
Zeng et al, 2004
Purello, 2003