* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Self-Organizing Bio-structures
Biochemical cascade wikipedia , lookup
Deoxyribozyme wikipedia , lookup
Paracrine signalling wikipedia , lookup
Evolution of metal ions in biological systems wikipedia , lookup
Magnesium transporter wikipedia , lookup
Peptide synthesis wikipedia , lookup
Ancestral sequence reconstruction wikipedia , lookup
Metalloprotein wikipedia , lookup
G protein–coupled receptor wikipedia , lookup
Biochemistry wikipedia , lookup
Interactome wikipedia , lookup
Signal transduction wikipedia , lookup
Ribosomally synthesized and post-translationally modified peptides wikipedia , lookup
Protein purification wikipedia , lookup
Nuclear magnetic resonance spectroscopy of proteins wikipedia , lookup
Western blot wikipedia , lookup
Protein structure prediction wikipedia , lookup
Protein–protein interaction wikipedia , lookup
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 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) Monomer Addition by Radical propagation The polymer chain grows by addition of monomer units: H H H C C H H H H new radical forms that is one monomer unit longer chain reaction chain has propagated called free radical polymerisation H H H radical attacks double bond of monomer H C C C C C C H H 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 Condensation polymerization (≠ addition) Thermodynamics not favorable Needs activation (energy) Prebiotic activation of monomers Formation of homo-polypeptides H2O a problem ! Condensation possible on clay AMP not a pre-biotic molecule! Other routes to condensation of amino-acids From amino-acids: Condensation 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: 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 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! 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? 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? 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) 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 Enantiomeric excess: Homo-poly-Leu (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! Relative abundance of homochiral chains of homo-polypeptides (Trp) White: random distribution Grey: observed composition Over-representation of homochiral peptides Conclusions Prebiotic chemistry could explain formation of short peptide chains / oligonucleotides Still problems with activation chemistry Copolymerization Rules explain chain composition Never-born proteins universe is huge: some NBP can fold Homochirality in chains is naturally selected, can be explained statistically.