Left-handed Polyproline II Helices Commonly Occur in Globular Proteins

The main-chain conformations of 80 proteins were analyzed to identify helical structures that commonly occur but do not fall into the known classes of α-helix, 310-helix and β-sheet. The analysis yielded 96 occurrences of four or more sequential residues forming the threefold left-handed poly-l-proline II (PPII) helix. This contradicts the previously held opinion that left-handed helices are rare in globular proteins. The main-chain dihedral angles of these helices form a cluster in φ-ψ space that has a maximum at -75°,145°, corresponding to conformations with the number of residues per turn (n) = -3·0. We show that 51% of PPII-helices lie within the range of n = - 3·0 (±0·2). It is shown that the PPII segments are distinct from the conformation typical of β-pleated sheets. Although proline residues commonly occurred in PPII-hilices, this side-chain is not obligatory, as 28 of these helices did not contain proline. In addition, we found 120 segments with three Cα atoms forming a PPII-helix. PPII-helices tend to occur on the surface of the protein and, having few main-chain hydrogen bonds with the rest of the protein, tend to be the more mobile segments of the molecule. The geometry of PPII helix allows the polypeptide chain to progress immediately from this conformation to right-handed α-helix and 310 helix, as well as to β-sheet or reverse turn. We conclude that PPII-helices should be considered as a regular conformation and should be added to β-sheets, α-helices, and 310-helices in databases of protein structures, in secondary structure prediction and in tertiary model-building.