Tertiary structure

The tertiary structure of a protein is the folding of the linear peptide chain and packing of secondary structures into a 3-dimensional structure.

Practical work

View this structure (delta endotoxin, 1cby) using PyMOL.

• From the PyMOL menus, choose Show->Cartoons and then Hide->Lines.
  You will see the protein rendered using ribbon-arrows for beta-strands and curled ribbons for the alpha helices.
• To make this clearer, choose Colour->by ss from the menus.
  Beta-strands, alpha-helices and coil are now coloured differently.

Observe the structure of the protein with the beta-sheet packed between alpha-helices.

• Now choose Colour->spectrum.
  The structure is now coloured with the N-terminus in blue, running through light-blue, cyan, green, yellow, orange to red at the C-terminus.

Examine the structure to see how parts of the protein distant in sequence come close to one another in the 3-dimensional structure. Follow the chain, tracing it through the protein.

Packing

You will note some individual spheres around the structure. These represent water molecules. They can be removed from the display by using Hide->waters.

The cartoon image does not give a sense of how the atoms of a protein are closely packed.

• To get a better impression of this, choose Show->spheres.
  You will now see that the structure (with the exception of the long N-terminus) is well packed with few gaps between the atoms.