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