Left-handed polyproline II helices (PPII) are contiguous
elements of protein secondary structure in which the φ
and ψ angles of constituent residues are restricted
to around −75° and 145°, respectively. They
are important in structural proteins, in unfolded states
and as ligands for signaling proteins. Here, we present
a survey of 274 nonhomologous polypeptide chains from proteins
of known structure for regions that form these structures.
Such regions are rare, but the majority of proteins contain
at least one PPII helix. Most PPII helices are shorter
than five residues, although the longest found contained
12 amino acids. Proline predominates in PPII, but Gln and
positively charged residues are also favored. The basis
of Gln's prevalence is its ability to form an i,
i + 1 side-chain to main-chain hydrogen bond with
the backbone carbonyl oxygen of the proceeding residue;
this helps to fix the ψ angle of the Gln and the φ
and ψ of the proceeding residue in PPII conformations
and explains why Gln is favored at the first position in
a PPII helix. PPII helices are highly solvent exposed,
which explains why apolar amino acids are disfavored despite
preferring this region of φ/ψ space when in isolation.
PPII helices have perfect threefold rotational symmetry
and within these structures we find significant correlation
between the hydrophobicity of residues at i and
i + 3; thus, PPII helices in globular proteins
can be considered to be amphipathic.