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Beyond Secondary Structure

Beyond Secondary Structure. Supersecondary structure (motifs) : small, discrete, commonly observed aggregates of secondary structures b sheet helix-loop-helix bab Domains : independent units of structure b barrel four-helix bundle *Domains and motifs sometimes interchanged*.

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Beyond Secondary Structure

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  1. Beyond Secondary Structure • Supersecondary structure (motifs): small, discrete, commonly observed aggregates of secondary structures • b sheet • helix-loop-helix • bab • Domains: independent units of structure • b barrel • four-helix bundle • *Domains and motifs sometimes interchanged*

  2. Tertiary Structure • Definition: Overall 3D form of a molecule • Folding up secondary structures/motifs/domains • Optimization of interactions between residues • A specific structure is formed • *All proteins have multiple secondary structures, almost always multiple motifs, and in some cases multiple domains*

  3. Tertiary Structure • Specific structures result from long-range interactions • Electrostatic (charged) interactions • Hydrogen bonds (OH, N H, S  H) • Hydrophobic interactions • Soluble proteins have an inside (core) and outside • Folding driven by water- hydrophilic/phobic • Side chain properties specify core/exterior • Some interactions inside, others outside

  4. Tertiary Structure • I. Ionic Interactions (exterior) • Forms between 2 charged side chains: • 1 Negative – Glu,Asp, 1 Positive – Lys,Arg,His   • Also called “salt bridges”. • Ionic interactions are pH-dependent (pKa). • Occurs at the exterior • NOTE: pKs for in the interior of a protein may be very different from free amino acid.

  5. Tertiary Structure • II. Hydrogen bonds • Forms between side chains/backbone/water: • Charged side chains: Glu,Asp,His,Lys,Arg • Polar chains: Ser,Thr,Cys,Asn,Gln,[Tyr,Trp]  • Not a specific covalent bond – lower energy. • Occurs inside, at the exterior, and with water.

  6. Tertiary Structure • III. Hydrophobic Interactions • Forms between side chains of non-polar residues: • Aliphatic (Ala,Val,Leu,Ile,Pro,Met) • Aromatic (Phe,Trp,[Tyr]) • Clusters of side chains- but no requirement for a specific orientation like an H-bond • In the protein interior, away from water • Not pH dependent

  7. Tertiary Structure • IV. Disulfide Bonds • Forms between Cys residues: • Cys-SH + HS-Cys  Cys-S-S-Cys • Catalyzed by specific enzymes • Restricts flexibility of the protein • Usually within a protein, not for linking proteins

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