Part 1: Protein Structure - Secondary Structures

Secondary structures such as alpha helices and beta strands result from repeating (approximately) the same combination of phi and psi angles as we go along the protein sequence.

Secondary structure is stabilized by hydrogen bonds. In the case of beta-strands, these occur between elements of secondary structure to form beta sheets. In most other forms of secondary structure, hydrogen bonds occur within the structural element. Where hydrogen bonding is non-ideal the structures are less stable.

You will now try building some peptides using different combinations of phi/psi angles.

Using the peptide builder, you can build the most common forms of secondary structure by clicking the appropriate button (e.g. 'alpha helix') and then clicking the 'Build me a peptide!' button.

You can also randomize the phi/psi angles by +/-5 degrees to give a more realistic (rather than a 'perfect') structure and enter your own combinations of backbone torsion angles.

When you build a peptide, you will start a small JavaScript application which will allow you to view and rotate the structure. You can also download the coordinates to view with PyMol, by clicking a link. Don't forget, you must right click the link and choose 'Save Target As...' from the menu.

Once you have downloaded the PDB file of the peptide, open it in PyMol. Then:

The hydrogen bonds will now be displayed as yellow dashed lines.

Note that if you have downloaded an 'imperfect' helix (where the angles were randomized), you may find some hydrogen bonds are indicated in addition to the standard ones that run parallel to the helix).