Basics of protein structureΒΆ

See also illustrations in slides and [BrandenTooze].

Introduction to protein structure

  • polypeptides, amino acids
    • chemical structure of the 20 aa
    • natural aa: L-form (note: look down H-Ca and read CORN == L, otherwise D)
    • peptide bond
    • repeating unit: residue, same backbone, differing sidechain R
    • sequence, primary structure
  • hydrogen bonds: donor-H...acceptor

  • secondary structure
    • alpha-helix (n..n+4 H-bonds of main chain, ~3.6 res per turn)
      • peptide units: phi, psi angles: flexible, omega (peptide bond) fixed (cis/trans)
      • must be right handed (otherwise clashes; only very short helices are left-handed)
    • beta sheet (extended), parallel/anti-parallel

    • (coiled coil)

    • 3-10 helix (n..n+3, 10 atoms between donor and acceptor, 3 res per turn)

    • pi helix (n..n+5)

  • tertiary structure: - helices - sheets - hairpins, loops - coiled-coil

  • quaternary structure

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Analyzing protein structure and topology

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