Teaching Resources in Biochemistry: Tools for Molecular Structure

Jason Kahn, University of Maryland

This page demonstrates why proline breaks the alpha helix and beta sheet, from a simple-minded perspective on protein structure (mine).

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.
Script for generating images

Beta Sheet

Here the issue does appear to be the accessible regions of the Ramachandran plot. The beta sheet phi angle is about -120 to -140 degrees, and proline is limited to -60 to +25. For an illustration of this, look at an antiparallel beta sheet pdb from the Ramachandran diagram page and imagine substituting in a proline.