Alpha Helix
Proline does appear to be capable of assuming
the requisite Ramachandran angles for the alpha helix, so that isn't the source
of the incompatibility between Pro and the helix. The source of its role as a helix breaker
comes rather from side chain constraints and sterics: the proline side chain is
basically jammed into
the space that should be occupied by the backbone of the alpha helix --
a methylene group is in the space that would normally be occupied by a
hydrogen-bonding amide proton, thus disrupting the H-bond network and sterics
of the
helix. Furthermore, the images and linked pdb
files below suggest that the proline side chain interferes with
the backbone helical packing of residues N-terminal to the proline as
well as with the side chains of neighboring residues.
The proline is constrained and thus unable to project out and back like the side chains of
other amino acids. Alpha helices generated in Insight 95.0, images in
Rasmol 2.6.
| Short alpha helix with Pro residue | Short alpha helix with Gln residue instead of Pro. |
|---|---|
|
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| Script for generating images | |