Alpha Domain Structures

Coiled-coil α helices

2 alpha helices packed twisted together.

A revolution is done in 3.5 instead of 3.6 turns.

Found in fibrous proteins e.g. muscles.

Also found in transcription factors (DNA binding).

Repeated heptad (every 7 amino acid) sequence pattern. ABCDEFG

Hydrophobic 'd' residue like Ile or Leu. Known as leucine zippers

a and d hydrophobic

Draw clockwise and anticlockwise cross section.

e and g ionic (acid + base) e.g. Asp Glu + Lys Arg

Draw knob in holes

Draw -18 degree angle.

Four helix bundle

cross section - hydrophobic core, 3 residues contributed from each helix.

anti-parallel UDUD - cytochrome b562

parallel UUDD - human growth hormone

Rop dimer. 2 x coiled-coil. Coiled-coil is a subunit.

muramidase

27 alpha helix donut

globin fold

part of myoglobin, hemoglobin and light-capturing algae.

8 alpha helices A-H, heme group. GH anti-parallel, rest are at different angles.

Draw pp40. A E F F' heme.

hydrophobic core conserved between helix-helix and helix-heme.

hemoglobin cooperation

tetramer of 2 x (α-globin + β-globin). 4 heme pockets.

When oxygen is bound to the heme, it causes a conformation change due to histidine, this pulls a alpha helix, which pulls the other monomers, making oxygen binding easier.

hemoglobin sickle cell

molecular disease of hemoglobin.

Glu 6 (acid) of β-globin changed to Val (hydrophobic)

Now the valine fits into another deoxygenated hemoglobin. (ok in lungs here O exists), but after delivering O other parts, it sticks together (polymerizes) and forms sickle shapes.

Packing angles

pineapple face.

+25 degrees to helical axis, or -45 degrees.

h1 = 25, h2 = 25, flip(h2) = -25, rotate +50 to match up with 25.

h1 = 25, h2 = -45, flip(h2) = 45, rotate -20 to match with 25.