Question

Which structural properties allow Glycine and Proline to be "alpha-helix breakers". In which type of seconday structure elements do you expect to fine them?

Answer 1

Properties of glycine and proline that make it as a alpha helix breaker is due to its side constraints as-

1. There is no hydrogen H present in Nitrogen N atom of Pro residue to participate in hydrogen bonding with other residues
2. In these structures, Nitrogen atom is fixed with a rigid structure side chain thus rotation about alpha bond (N---C) is not possible.

Thus it forms a destabilizing link in an alpha helix and have least tendency to form alpha helix

Those secondary structures which disturb regular helical properties and have unusual rotational properties generally behave as alpha helix structures.