Basics of protein structure¶

Proteins are linear polypeptides with distinct structural details and four different levels, termed the primary, secondary, tertiary and quanternary structure. The key points are:

• 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:

  • packing of helices, sheets, hairpins, loops
  • coiled-coil

• quaternary structure

  • assemblies of multiple proteins (identical copies: homomers, different protein molecules: heteromers)
  • proteins and co-factors (e.g., heme group)