Peptide chains alone cannot possibly make the detailed globular structures you saw in the Protein Overview. So how can a linear polypeptide assume the correct shape to become a protein?

Peptide chains do not remain stretched out in the cell. They tend to fold into regular repetetive structures if they can. In these, the C=O and the N-H groups of the peptide bonds are Hydrogen Bonded to each other. These regular forms of protein structure are called secondary (2^o) structures.

a-Helices

If you click on the buttons below you will see an image in the upper frame to the left which can be manipulated to accompany the description.

The a-helix is a rod like structure. It is one peptide chain which has coiled so that adjacent residues are 1.5A apart. There are H-bonds (shown in white) between the N-H and the C=O groups of the backbone. These link the peptide bonds between every fourth amino acid.

If you rotate the helix so you look down the axis of the backbone, and alter the display to "SPACEFILL-VAN DER WAAL'S RADII" you will notice there is almost no space within the a-helix. The sidechains all extend outwards from the helix.

Here is a list of the features of the a-helix.

Right Handed a-helix (coils clockwise) 3.6 residues per turn All C=O and N-H groups are H-bonded H-bonds form between -N-H and C=O of every fourth amino acid in the chain Sidechains point outward 1.5A between adjacent residues

Although the helix itself is quite a rigid structure, it can be curved or kinked, which lends some flexibility to the protein structure.

Two or more polypeptides can entwine to form very long, very stable, structures called a-helical coiled coils. These are often found in keratin (hair), myosin (muscle), epidermin (skin), and fibrin (blood clots). The coiled coils serve a mechanical role for the proteins mentioned above, which are all fibrous proteins.

In this image of a triple strand helical coiled coil, you will need to look very closely at the sidechains. If you can recall the shapes of some of them, you will notice that inside the coiled coil are valine residues (gren) (aliphatic and hydrophobic) whereas on the outside there are Glu, His, Lys, Gln, and Ser residues (all hydrophillic). You might want to rotate the coiled coil to reassure yourself that there really are three helices.

b-Sheets

This secondary structure differs considerably from the ahelix. However b-sheets are classified with a-helices since they are a regular structural element and are held together by hydrogen bonds between the -N-H and C=O groups of the peptide bond.

A polypeptide in a b-sheet is called a b-strand, and is almost fully extended (not coiled) so there is 3.5A between adjacent residues.

The b-sheet is stabilised by H-bonds between the N-H and the C=O groups of different peptides or different parts of the same peptide. The b-strands in a sheet can either run in the same (parallel) or different (anti-parallel) direction.

Here we see a short piece of anti-parallel b-sheet. The H-bonds (shown in white) are perpendicular to the axis of the backbone. They can be seen running between the light blue (nitrogen) atoms of one backbone strand to the (red) oxygen of the other. Note that the H-bond doesn't start at the nitrogen, but at the hydrogen attached to the nitrogen, which isn't shown so as to keep things simple. If you rotate the image so you look at the sheet from the side, you can see the sidechains are above and below the b-sheet. This may be easier to see if you alter the DISPLAY to CARTOONS. You will also see the direction of each strand this way although you should be getting used to working out the orientation of the peptide backbone by now.

Here is a parallel b-sheet. The H-bonds are not perpendicular to the backbone, but at a slight angle. By tilting the sheets on their side, you can see that the side chains point out from the plane of the sheet. If you alter the DISPLAY to CARTOONS, arrows showing the direction of the chains will become apparent.

Combinations

To fold the polypeptide into a tight structure, it is necessary to have combinations of the secondary structures.

Here are two adjacent a-helices, which are linked by a short piece of peptide which is curved so that the two helices are almost at right angles to each other. Note that once again, Valine (the green sidechain) appears almost completely on one side of both helices. The magenta colour of ribbon is used to denote helical regions in protein structures.

Here is an a-helix sitting above two b-strands. Note that the yellow colour of the backbone ribbon is used to denote b-structure in proteins. Use the Chime pop up menu in the structure frame to turn on rotation. Then change the display to "sticks" and the color to "CPK" Turn rotation "off" before selecting the next button.

Hairpin Turns

The shape of some proteins shape depends on the presence of sharp bends in the direction of the the polypeptide chain. This is often accomplished by the formation of a structural element called a b-turn. In the example, brought up by the button above, the flesh coloured amino acid is proline and there are two of them next to each other. Due to the unique structure of proline, this amino acid is often found in tight bends in the polypeptide chain. Note the hydrogen bond (white) which helps maintain the tight turn in the peptide backbone. These bends are often associated with antiparallel b-sheets, hence the name. They are also known as hairpin bends and reverse turns.

Now you should know what happens to the polypeptide after it is made.

You should remember the 2 main types of secondary structure and several details about each of them
(e.g. the main features of an a-helix are? etc.).

When you feel you know enough, move on and see how the polypeptide (now sort of folded) undergoes further folding to form the protein tertiary structure.

Use the navigation links in the lower frame to the left.