This page contains all the figures used in the notes on tertiary alpha helix structures. You may want to keep this page open, or print this page when going through the notes.
Please also note that this page contains pdb structure files and you need Jmol to view, and manipulate, these structures.
Small proteins usually have only one domain involving the whole of the polypeptide chain. Larger proteins can have combinations of different domains, which can be found in other proteins. The figure shows that EGF has one domain (with about 53 amino acids), Chymotrypsin contains two domains (totalling 245 amino acids), Urokinase contains four different domains, Factor IX has five domains (but comprising four different types), and Plasminogen has seven domains (but only three different types). The Kringle domain is a polypeptide of about 85 amino acids with a pattern of three internal disulphide bridges. The calcium binding domain you have seen before in the helix-loop-helix supersecondary structure.
Figure adapted from Brandon and Tooze (1991)
Figure 7.1 Single helix structure
Helix highlighted from coordinates of glucagon (1gcn.pdb). You may like to try these commands:
Three helix bundle highlighted from coordinates of one subunit in 'chain c' (original file contains DNA and the protein dimer) in engrailed homeodomain DNA binding protein (1hdd.pdb). You may like to try these commands:
Four helix bundle highlighted from coordinates of myohemerythrin (2mhr.pdb). Try your own commands to view this structure.
Figure 7.4 Loop Direction in 'up-down' four helix bundles
The loops connecting helices in an antiparallel, or 'up-down', four helix bundle can either turn left (left diagram) or right (right diagram) at the top of the first helix. The right turn is the most common. ROP protein (which you have seen previously) is an example of a 'left handed' loop direction.
Adapted from Richardson JS and Richardson DC (1989)
Figure 7.5 Crossover of four helix bundles
The loops connecting the helices crossover one of the helices in the structure. The crossover on the left is seen in porcine growth hormone and the crossover on the right is seen in apoferritin.
Adapted from Richardson JS and Richardson DC (1989)
Figure 7.6 Interaction of helices in a four helix bundle
The four helix bundle (left diagram) shown in 'top view' (right diagram) where hydrophobic residues (blue) are located in the core of the bundle and the hydrophillic residues (red) are located towards the environment.
