In this part of the practical, you will build a series of peptides with repeating backbone torsion angles and look at their characteristics.
Secondary structures consist of stretches of polypeptide having repeating backbone torsion angles.
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.
To start the peptide builder, click here
Here 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 structure and enter your own combinations of backbone torsion angles.
When you build a peptide, you will start a small Java applet which
will allow you to view and rotate the structure. You can also download
the coordinates to view with RasMol. In RasMol, you can give the
command:
hbonds on
to view the hydrogen bonds as dashed lines.
Look at each of the structures and note which ones contain internal hydrogen bonds.
When looking at alpha-helices and beta-strands, experiment with the randomization of the torsion angles and observe how the more realistic structures differ from idealized structures.
IMPORTANT! Generate an alpha-helix and a beta-strand using randomization of the torsion angles and make sure that you download and save the peptides. You will need them later.
Experiment with entering your own combinations of phi and psi angles. Make them as different as you can from the combinations seen in real secondary strustures. Why do you think these structures do not occur?