a review of peptide and protein structuretminehan.com/chem564pdfs/peptides and proteins.pdf · a...
TRANSCRIPT
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A Review of Peptide and Protein Structure
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Enantiomers, diasteromers, or consitutional isomers?
What is the chemical relationship between the two peptides?
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At pH=7.2,
What is the net charge on this peptide at pH=7.2?
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In the interior of a protein or at protein-protein interfaces:
(desolvationrequired)
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Cyclosporin A- immunosuppressant
Peptide drugs: plagued by proteolysis in the stomach and poorabsorption properties (intestine) and interaction with abundant proteases in blood; poor membrane permeability. Exception: arginine-rich peptides
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Scheme for polypeptide synthesis.
Boc protection of the amino terminal: TFA deprotection
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Fmoc protection of amino terminal: mild base removal
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Carbodiimide coupling:
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Problems with carbodiimide coupling:
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Azlactone: destruction of α-stereochemistry
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HOBt minimizes side reactions in carbodiimide couplings
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Couplings without carbodiimides: the uroniums HBTU, HATU
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For Boc monomers…..
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For Fmoc monomers…
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Native chemical ligation for unprotected peptides
Thiol-thioester exchange occurs rapidly in aqueous solution;intramolecular S-to-N acyl transfer occurs rapidly
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Hydrogen bonding of amides
���Amide bonds are always planar and favor the trans (Z) configuration!
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The “macrodipole”: all carbonyls in an alpha helix point insame direction
Sulfate (SO42-) binding protein
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Antiparallel beta sheets much more common
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The β-Barrel: curvature
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Alpha helices have polar amino acid side chainsthat are solvent accessible
Beta sheets tend to contain more non-polarAmino acids which tend to aggregate
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Stereoelectronic effects : filled-empty interaction
σC-H àσ*CO
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σC-H àσ*C-OσC-H àσ*C-N
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In Alkanes, sterics predominates
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Barriers to rotation about double bonds
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Allylic 1,3 strain
Allylic 1,2 strain
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Allylic 1,3 strain controls the conformations of peptides
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Glutathione is important for rapid disulfide exchange
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Chemical agents capable of disulfide reduction
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Hydrophobicity tends to minimize thevolume of the protein in waterHydrophobic collapse brings togetherbackbone amides and further facilitates backbone hydrogen bondingHydrophobic collapse is the major driving force of protein folding
SinglePolypeptide:aa sequence
SinglePolypeptide:α helix; β sheet
Singlepolypeptideregion that can foldindependently:100aa
Singleor MultipleDomains“protein”
Multiple foldedPolypeptides
Folded peptide:
MultipleQuaternary structures
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Single Polypeptide: aa sequence
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Single Polypeptide: α helix; β sheet
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Single polypeptide region that can fold independently: 100aa
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Folded peptide: Single or Multiple Domains “protein”
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Multiple folded Polypeptides interacting with each other
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Multiple Quaternary structures interacting with each other
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Zinc finger domains recognize DNA sequences
25 aa: consists of an α helix and a peptide loopZif268: transcription factor in which each zinc finger domainrecognizes three base pairs
C2H2 motif
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β-sheet sandwiches: immunoglobulins
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Muscle protein titin: antiparallel β-sheet sandwich
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Cadherin domains: cell-cell anchoring
Cadherin domains require calcium ions for structural support
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Collagen: a left-handed triple helix consisting of repeating units:Gly, pro, pro (or hydroxyproline)
Hydrogen bonds between the three strands
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The gauche diastereomer stabilizes the collagen triple helix
Hydroxyproline 4R:
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Transmembrane proteins: 7 α helices sit within the cell membrane
Rhodopsin containingRetinal (yellow)
α-helical bundle
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Leucine zipper: dimerization domains of c-Fos and c-JunHave leucine residues every seventh amino acid, allowing the two proteins to associate as a coiled coil
DNA binding domain consists of basic amino acids: Arg, lys
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RNA recognition motif: 4 antiparallel β-strands and 2 α-helices
Aromatic amino acids in the sheet engage in π-stacking interactionsWith the bases
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Recognition of short peptides: SH2 domains consist of antiparallelβ-sheet between two α helices. SH2 domains recognize phosphorylatedtyrosines
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Quaternary structure: complexes of non-covalently bound proteins
Ferritin: 24 independently folded proteins stroing 4500 Fe3+ ions