Transcript Self-Organizing Bio-structures

Self-Organizing Biostructures
NB2-2009
L.Duroux
Lecture 2
Macromolecular Sequences
Introduction-questions:

How do we move along from prebiotic small
molecules to oligomers and polymers (DNA &
proteins)?

Why the need for long polymeric chains vs
cooperation of small ones?

Why are proteins long polypeptides?
What is the easiest way to get a
functional bio-catalyst?
Lysozyme
Examples of the ”necessity” for
growing larger peptides
Protein domains
A common case of ”chain-growth”:
Protein structural domains
Chymotrypsin
Putative ancestral
b-barrel structure
Active site
(combination
of ancestral
active site
residues)
‘Modern’ 2-b-barrel structure
Activity 1000-10,000 times enhanced
3D structure of Chymotrypsin
A multiple-domain protein: pyruvate kinase
b barrel regulatory domain
a/b barrel catalytic substrate binding
domain
a/b nucleotide binding domain
1 continuous + 2 discontinuous domains
Co-polymerization
A step towards macromolecules
Famous natural copolymers
Model for a copolymer growth
rA = kAA / kAB and rB = kBB / kBA
Copolymer composition as function
of rA and rB

Modelized by Mayo-Lewis equation
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rA = rB >> 1 : homopolymers (AAAA or BBBB)
rA = rB > 1 : block-copolymer (AAAAABBBBBB)
rA = rB ≈ 1 : random copolymer (AABAAABBABBB)
rA = rB ≈ 0 : alternate copolymer (ABABABABABA)
Example:
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Maleic anhydride (rA = 0.03)
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trans-stilbene (rB = 0.03)
Monomer Addition by Radical
propagation
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The polymer chain grows by addition of monomer
units:
H
H
H
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H
H
H
H H H
radical attacks double bond of monomer
new radical forms that is one monomer unit longer
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chain reaction
chain has propagated
 called free radical polymerisation
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H H H
H
C C C C
C C
C C
H
H
H
Rubber : a natural case of addition
(co)polymerization
Radical Initiation
Q:From
where does the first unpaired electron come?
A: Generated

by an initiator
e.g. hydrogen peroxide (H2O2)
 has
O–O bond (easy to break)
 generates 2 OH• radicals

usually don’t use H2O2 but other peroxides, e.g.:
 potassium
persulfate
ion is: [O3S–O–O–SO3]2–
O–O bond breaks readily at 60oC to initiate reaction
persulfate
Some Common Polymers
H H
 polyethylene
(also called polythene)*
Glad Wrap
 polystyrene
H H
H H
C C
*
glues
n
*
n
H H
acetate) (PVAc)
C C
*
H O n
O C
CH3
glues, paints
 poly(vinyl
*
H
bean bags, packing
 poly(vinyl
C C
alcohol) (PVA)
H H
*
C C
H OH
*
n
*
Polypeptides, polynucleotides: more
difficult!

Chain composition difficult to predict:
Several co-monomers (20 aa, 5nt)
 Monomer concentrations might vary
 Complex interplay between many kinetic parameters

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Condensation polymerization (≠ addition)
Thermodynamics not favorable
 Needs activation (energy)
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Prebiotic activation of monomers
Formation of homo-polypeptides
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H2O a problem !
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Condensation possible
on clay
AMP not a pre-biotic
molecule!
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Other routes to condensation of amino-acids
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From amino-acids:
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Condensation
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Possible in vesicles without activation + heat
Heat 180˚C + excess Glu/Asp or Lys
Metal ions + Drying + Heat
HCN + addition of side chains
N-carboxyanhydrides (see Chap. 3)
Carbonyl sulfide: COS (prebiotic volcanic gas)
Questions:
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What about chains longer than 10 amino-acids?
What about chain sequence specificity?
The case of polynucleotides
• Activated nucleotide:
Phosphorimidazolide (b)
stereospecificity 3’-5’ (c)
• Clay:
•water activity reduced
•UV-resistance
Template-directed oligomerization
Still :
No explanation for NMPs
No explanation for the
retention of particular
sequences of nucleotides
The problem of peptide chains
”selection”
& never-born proteins...
Aetiology of the current protein set
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Consider a chain of 100aa : 20100 possibilities!
Total number of natural proteins: 1015
Now: 1015 / 20100 ≈ rH / runiverse
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What about the ”never-born” or ”obliterated”
proteins?
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Only one reasonable assumption to limit the set:
contingency + thermodynamics!
The ”never-born” or ”obliterated”
proteins: do they fold?
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Is there anything special about the proteins we
know (energy, folding...)?
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Experimental test:
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Screening random-generated peptide library (50aa)
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Do they fold?
Never-Born proteins: experimental set-up
Only folded peptides resist
to thrombin cleavage
80 clones tested: 20%
resistant
The problem of formation (and
”selection”) of macromolecular
sequences
In which conditions?
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Oligopeptides formed (up to 10aa) in various
libraries, in prebiotic conditions
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Condensation of oligopeptides possible:
Catalytic dipeptides (seryl-histidine, histidyl-histidine)
 Reverse reaction favoured in H2O-free medium
 Clay support or phase-separation (product insoluble)
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Peptide-fragments condensation
* Catalytic residue
= peptidase activity
specific to terminal
amino acid
As a result of
contingency:
pH, salinity,
temperature...
A double, independent origin of
macromolecules?
And life could begin...?
Homochirality in chains
& chain growth
Synthetic Homochirality
The case of vinyl polymers : polypropylene (G. Natta)
Confers helical conformations to polymer in crystals
Theoretical model for chain chirality
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Enantiomeric excess:
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Homo-poly-Leu
(D-L)/(D+L) = 0.2
=> 60% D + 40% L
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Dn/Ln grows exponentially
with n power (binomial
distribution)
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Enantiomeric excess = 1
when n=20!
Relative abundance of homochiral
chains of homo-polypeptides (Trp)
White: random distribution
Grey: observed composition
Over-representation of
homochiral peptides
Conclusions
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Prebiotic chemistry could explain formation of short
peptide chains / oligonucleotides
Still problems with activation chemistry
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Copolymerization Rules explain chain composition
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Never-born proteins universe is huge: some NBP can
fold
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Homochirality in chains is naturally selected, can be
explained statistically.
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