Self-Organizing Bio-structures

1. Self-Organizing Bio-structures NB2-2009 L.Duroux

2. Lecture 2 Macromolecular Sequences

3. 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?

4. What is the easiest way to get a functional bio-catalyst? Lysozyme

5. Examples of the ”necessity” for growing larger peptides Protein domains

6. A common case of ”chain-growth”: Protein structural domains Active site (combination of ancestral active site residues) Chymotrypsin Putative ancestral b-barrel structure ‘Modern’ 2-b-barrel structure Activity 1000-10,000 times enhanced

7. 3D structure of Chymotrypsin

8. 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

9. Co-polymerization A step towards macromolecules

10. Famous natural copolymers

11. Model for a copolymer growth rA = kAA / kAB and rB = kBB / kBA

12. Copolymer composition as function of rA and rB • Modelized by Mayo-Lewis equation • 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: • Maleic anhydride (rA = 0.03) • trans-stilbene (rB = 0.03)

13. Monomer Addition by Radical propagation • The polymer chain grows by addition of monomer units: • radical attacks double bond of monomer • new radical forms that is one monomer unit longer • chain reaction • chain has propagated • called free radical polymerisation

14. Rubber : a natural case of addition (co)polymerization

15. 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 • persulfate ion is: [O3S–O–O–SO3]2– • O–O bond breaks readily at 60oC to initiate reaction

16. Some Common Polymers • polyethylene (also called polythene) Glad Wrap • polystyrene bean bags, packing • poly(vinyl acetate) (PVAc) glues, paints • poly(vinyl alcohol) (PVA) glues

17. Polypeptides, polynucleotides: more difficult! • Chaincompositiondifficult to predict: • Severalco-monomers (20 aa, 5nt) • Monomer concentrationsmightvary • Complexinterplaybetweenmanykinetic parameters • Condensationpolymerization (≠ addition) • Thermodynamics not favorable • Needsactivation (energy)

18. Prebiotic activation of monomers

19. Formation of homo-polypeptides • H2O a problem ! • Condensationpossibleonclay • AMP not a pre-bioticmolecule!

20. Other routes to condensation of amino-acids • From amino-acids: • Possible in vesicleswithoutactivation + heat • Heat 180˚C + excessGlu/Aspor Lys • Metal ions + Drying + Heat • Condensation • HCN + addition of side chains • N-carboxyanhydrides (seeChap. 3) • Carbonylsulfide: COS (prebioticvolcanic gas) • Questions: • Whataboutchains longer than 10 amino-acids? • Whataboutchainsequencespecificity?

21. The case of polynucleotides • Activated nucleotide: • Phosphorimidazolide (b) • stereospecificity 3’-5’ (c) • Clay: • water activity reduced • UV-resistance

22. Template-directed oligomerization Still : No explanation for NMPs No explanation for the retention of particular sequences of nucleotides

23. The problem of peptide chains ”selection” & never-born proteins...

24. Aetiology of the current protein set • Consider a chain of 100aa : 20100 possibilities! • Total number of natural proteins: 1015 • Now: 1015 / 20100 ≈ rH / runiverse • What about the ”never-born” or ”obliterated” proteins? • Only one reasonable assumption to limit the set: contingency + thermodynamics!

25. The ”never-born” or ”obliterated” proteins: do they fold? • Is there anything special about the proteins we know (energy, folding...)? • Experimental test: • Screening random-generated peptide library (50aa) • Do they fold?

26. Never-Born proteins: experimental set-up Only folded peptides resist to thrombin cleavage 80 clones tested: 20% resistant

27. The problem of formation (and ”selection”) of macromolecular sequences

28. In which conditions? • Oligopeptides formed (up to 10aa) in various libraries, in prebiotic conditions • Condensation of oligopeptides possible: • Catalytic dipeptides (seryl-histidine, histidyl-histidine) • Reverse reaction favoured in H2O-free medium • Clay support or phase-separation (product insoluble)

29. Peptide-fragments condensation * Catalytic residue = peptidase activity specific to terminal amino acid As a result of contingency: pH, salinity, temperature...

30. A double, independent origin of macromolecules? And life could begin...?

31. Homochirality in chains& chain growth

32. Synthetic Homochirality The case of vinyl polymers : polypropylene (G. Natta) Confers helical conformations to polymer in crystals

33. Theoretical model for chain chirality • Enantiomeric excess: • (D-L)/(D+L) = 0.2 • => 60% D + 40% L • Dn/Ln grows exponentially with n power (binomial distribution) • Enantiomeric excess = 1 when n=20! Homo-poly-Leu

34. Relative abundance of homochiral chains of homo-polypeptides (Trp) White: random distribution Grey: observed composition Over-representation of homochiral peptides

35. Conclusions Prebioticchemistrycouldexplain formation of short peptidechains / oligonucleotides Still problems withactivationchemistry CopolymerizationRulesexplainchaincomposition Never-born proteins universe is huge: some NBP can fold Homochirality in chains is naturallyselected, canbeexplainedstatistically.