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.