BSCI 1510L Literature and Stats Guide: Protein secondary structures

Fig. 19 Bond rotations in a polypeptide  Image by Alejandro Proto CC BY-SA 3.0  from Wikimedia Commons modified by cropping

A generic polypeptide chain constructed using the pushfit model can be transformed into a secondary structure by rotating the planar peptide units around the bonds they form with the chiral (alpha) carbon (labeled as psi and phi in Fig. 19).  If the planar units are rotated so that all of the oxygen atoms are pointing in the same direction, the polypeptide can be formed into an alpha helix. 

Fig. 20. Alpha helix (same orientation as Fig. 21)

Fig. 21 An alpha helix constructed from pushfit model pieces

Because the oxygen and hydrogen atoms in the planar units are pointing in opposite directions, an oxygen atom in one turn of the helix can hydrogen bond with a hydrogen atom from the next turn.  By forming the helix into a tighter or looser spiral, it is possible to form hydrogen bonds between different oxygen and hydrogen atoms.  The correct "twist" on the helix is one that produces 3.6 residues per turn.  The video below shows how to rotate the pushfit polypeptide into an alpha helix.

Click on the following link to open a new tab or window to examine the the structure of an alpha helix.  (This requires Java and appropriate permissions to view the simulation.)

http://www.biochem.umd.edu/biochem/kahn/teach_res/Secstruc_jmol/jmol-alphahelix.html

You can click and drag to rotate the molecule and look at it from different angles.  Clicking on the buttons at the bottom of the screen will allow you to explore features of the molecule.

Note: if this site or the site linked in the following section are down, here is a somewhat less user-friendly alternative website that can be used to answer the questions:

http://higheredbcs.wiley.com/legacy/college/boyer/0471661791/structure/jmol_intro/sec_str.htm

Click on the following link to open a new tab or window to examine the the structure of an antiparallel beta sheet.  (This requires Java and appropriate permissions to view the simulation.)

http://www.biochem.umd.edu/biochem/kahn/teach_res/Secstruc_jmol/jmol-betasheet.html

You can click and drag to rotate the molecule and look at it from different angles.  Clicking on the buttons at the bottom of the screen will allow you to explore features of the molecule.