Self-Organizing Self-Organizing Bio-structures Bio-structures NB2-2009 NB2-2009 L.Duroux L.Duroux
Jan 14, 2016
Self-Organizing Self-Organizing Bio-structuresBio-structures
NB2-2009NB2-2009
L.DurouxL.Duroux
Lecture 2Lecture 2
Macromolecular SequencesMacromolecular Sequences
Introduction-questions:Introduction-questions:
How do we move along from How do we move along from prebiotic small molecules to prebiotic small molecules to oligomers and polymers (DNA & oligomers and polymers (DNA & proteins)?proteins)?
Why the need for long polymeric Why the need for long polymeric chains chains vsvs cooperation of small ones? cooperation of small ones? Why are proteins long polypeptides?Why are proteins long polypeptides?
What is the easiest way to What is the easiest way to get a functional bio-get a functional bio-
catalyst?catalyst?
Lysozyme
Examples of the Examples of the ”necessity” for growing ”necessity” for growing
larger peptideslarger peptidesProtein domainsProtein domains
A common case of ”chain-A common case of ”chain-growth”:growth”:
Protein structural domainsProtein structural domainsChymotrypsin
‘Modern’ 2--barrel structure Putative ancestral -barrel structure
Active site (combination of ancestral active site residues)
Activity 1000-10,000 times enhanced
3D structure of Chymotrypsin3D structure of Chymotrypsin
barrel regulatory domain
barrel catalytic substrate binding domain
nucleotide binding domain
1 continuous + 2 discontinuous domains
A multiple-domain protein: pyruvate kinase
Co-polymerizationCo-polymerization
A step towards A step towards macromoleculesmacromolecules
Famous natural Famous natural copolymerscopolymers
Model for a copolymer Model for a copolymer growthgrowth
rA = kAA / kAB and rB = kBB / kBA
Copolymer composition as Copolymer composition as function function
of rof rAA and r and rBB
Modelized by Mayo-Lewis equationModelized by Mayo-Lewis equation
rrAA = r = rBB >> 1 : homopolymers (AAAA or BBBB) >> 1 : homopolymers (AAAA or BBBB)
rrAA = r = rBB > 1 : block-copolymer (AAAAABBBBBB) > 1 : block-copolymer (AAAAABBBBBB)
rrAA = r = rBB ≈ 1 : random copolymer ≈ 1 : random copolymer (AABAAABBABBB)(AABAAABBABBB)
rrAA = r = rBB ≈ 0 : alternate copolymer ≈ 0 : alternate copolymer (ABABABABABA)(ABABABABABA)
Example:Example: Maleic anhydride (Maleic anhydride (rrAA = 0.03) = 0.03)
trans-stilbene (trans-stilbene (rrBB = 0.03) = 0.03)
Monomer Addition by Monomer Addition by Radical propagationRadical propagation
radical attacks double bond of monomerradical attacks double bond of monomer
H
C C
H H
H
new radical forms that is one monomer unit new radical forms that is one monomer unit longerlonger chain reactionchain reaction
The polymer chain grows by addition of The polymer chain grows by addition of monomer units:monomer units:
chain has chain has propagated propagated called called free radical polymerisationfree radical polymerisation
Rubber : a natural case of Rubber : a natural case of addition (co)polymerizationaddition (co)polymerization
Radical InitiationRadical InitiationQ:Q:From where does the first unpaired electron come?From where does the first unpaired electron come?
A:A: Generated by an Generated by an initiatorinitiator
e.g. hydrogen peroxide (He.g. hydrogen peroxide (H22OO22))has O–O bond (easy to break)has O–O bond (easy to break)generates 2 OHgenerates 2 OH•• radicals radicals
usually don’t use Husually don’t use H22OO22 but other peroxides, but other peroxides, e.g.:e.g.:
potassium persulfate potassium persulfate persulfate ion is: [Opersulfate ion is: [O33S–O–O–SOS–O–O–SO33]]2–2–
O–O bond breaks readily at 60O–O bond breaks readily at 60ooC to initiate reactionC to initiate reaction
Some Common PolymersSome Common Polymers
polyethylene (also called polythene)polyethylene (also called polythene)Glad WrapGlad Wrap
* C C *
H
H
H
H n
* C C *
HH
Hn
* C C *
H
OH
H
H n
* C C *
H
O
H
H n
CCH3
O
poly(vinyl acetate) (poly(vinyl acetate) (PVAcPVAc))glues, paintsglues, paints
poly(vinyl alcohol) (poly(vinyl alcohol) (PVAPVA))gluesglues
polystyrenepolystyrenebean bags, packingbean bags, packing
Polypeptides, Polypeptides, polynucleotides: more polynucleotides: more
difficult!difficult! Chain composition difficult to predict:Chain composition difficult to predict:
Several co-monomers (20 aa, 5nt)Several co-monomers (20 aa, 5nt) Monomer concentrations might varyMonomer concentrations might vary Complex interplay between many kinetic Complex interplay between many kinetic
parametersparameters
Condensation polymerization (≠ Condensation polymerization (≠ addition)addition) Thermodynamics not favorableThermodynamics not favorable Needs activation (energy)Needs activation (energy)
Prebiotic activation of Prebiotic activation of monomersmonomers
Formation of homo-polypeptidesFormation of homo-polypeptides
H2O a problem !H2O a problem !
Condensation Condensation possible on claypossible on clay
AMP not a pre-AMP not a pre-biotic molecule!biotic molecule!
Other routes to condensation of Other routes to condensation of amino-acidsamino-acids
From amino-acids:From amino-acids: Possible in vesicles without activation + heatPossible in vesicles without activation + heat Heat 180˚C + excess Glu/Asp or LysHeat 180˚C + excess Glu/Asp or Lys Metal ions + Drying + HeatMetal ions + Drying + Heat
CondensationCondensation HCN + addition of side chainsHCN + addition of side chains N-carboxyanhydrides (see Chap. 3)N-carboxyanhydrides (see Chap. 3) Carbonyl sulfide: COS (prebiotic volcanic gas)Carbonyl sulfide: COS (prebiotic volcanic gas)
Questions:Questions: What about chains longer than 10 amino-What about chains longer than 10 amino-
acids?acids? What about chain sequence specificity?What about chain sequence specificity?
The case of The case of polynucleotidespolynucleotides
• Activated nucleotide: Phosphorimidazolide (b) stereospecificity 3’-5’ (c)
• Clay:•water activity reduced•UV-resistance
Template-directed Template-directed oligomerizationoligomerization
Still :
No explanation for NMPs
No explanation for the retention of particular sequences of nucleotides
The problem of peptide The problem of peptide chains ”selection”chains ”selection”
& never-born proteins...& never-born proteins...
Aetiology of the current Aetiology of the current protein setprotein set
Consider a chain of 100aa : 20Consider a chain of 100aa : 20100100 possibilities!possibilities!
Total number of natural proteins: 10Total number of natural proteins: 101515 Now: 10Now: 101515 / 20 / 20100100 ≈ r ≈ rHH / r / runiverseuniverse
What about the ”never-born” or What about the ”never-born” or ”obliterated” proteins?”obliterated” proteins?
Only one reasonable assumption to limit Only one reasonable assumption to limit the set: contingency + thermodynamics!the set: contingency + thermodynamics!
The ”never-born” or The ”never-born” or ”obliterated” proteins: do ”obliterated” proteins: do
they fold?they fold? Is there anything special about the Is there anything special about the
proteins we know (energy, folding...)?proteins we know (energy, folding...)?
Experimental test:Experimental test:
Screening random-generated peptide Screening random-generated peptide library (50aa)library (50aa)
Do they fold?Do they fold?
Never-Born proteins: Never-Born proteins: experimental set-upexperimental set-up
Only folded peptides resist to thrombin cleavage
80 clones tested: 20% resistant
The problem of formation The problem of formation (and ”selection”) of (and ”selection”) of
macromolecular macromolecular sequencessequences
In which conditions?In which conditions?
Oligopeptides formed (up to 10aa) in Oligopeptides formed (up to 10aa) in various libraries, in prebiotic conditionsvarious libraries, in prebiotic conditions
Condensation of oligopeptides possible:Condensation of oligopeptides possible: Catalytic dipeptides (seryl-histidine, Catalytic dipeptides (seryl-histidine,
histidyl-histidine)histidyl-histidine) Reverse reaction favoured in H2O-free Reverse reaction favoured in H2O-free
mediummedium Clay support or phase-separation (product Clay support or phase-separation (product
insoluble)insoluble)
Peptide-fragments Peptide-fragments condensationcondensation
As a result of contingency:
pH, salinity, temperature...
* Catalytic residue= peptidase activity specific to terminal amino acid
A double, independent A double, independent origin of macromolecules?origin of macromolecules?
And life could begin...?
Homochirality in chainsHomochirality in chains& chain growth& chain growth
Synthetic HomochiralitySynthetic Homochirality
The case of vinyl polymers : polypropylene (G. Natta)
Confers helical conformations to polymer in crystals
Theoretical model for chain Theoretical model for chain chiralitychirality
Enantiomeric excess:Enantiomeric excess: (D-L)/(D+L) = 0.2(D-L)/(D+L) = 0.2 => 60% D + 40% L=> 60% D + 40% L
DDnn/L/Lnn grows grows exponentially with exponentially with nn power (binomial power (binomial distribution)distribution)
Enantiomeric excess = Enantiomeric excess = 1 when n=20!1 when n=20!
Homo-poly-Leu
Relative abundance of Relative abundance of homochiral chains of homo-homochiral chains of homo-
polypeptides (Trp)polypeptides (Trp)
White: random distributionGrey: observed composition
Over-representation of homochiral peptides
ConclusionsConclusions Prebiotic chemistry could explain formation of Prebiotic chemistry could explain formation of
short peptide chains / oligonucleotidesshort peptide chains / oligonucleotides Still problems with activation chemistryStill problems with activation chemistry
Copolymerization Rules explain chain Copolymerization Rules explain chain compositioncomposition
Never-born proteins universe is huge: some Never-born proteins universe is huge: some NBP can foldNBP can fold
Homochirality in chains is naturally selected, Homochirality in chains is naturally selected, can be explained statistically.can be explained statistically.