Everything about Polyproline Helix totally explained
In
proteins, a left-handed
polyproline II helix (
PPII,
poly-Pro II) is formed when sequential residues all adopt (φ,ψ) backbone
dihedral angles of roughly (-75°, 150°) and have
trans isomers of their
peptide bonds. Similarly, a more compact right-handed
polyproline I helix (
PPI,
poly-Pro I) is formed when sequential residues all adopt (φ,ψ) backbone
dihedral angles of roughly (-75°, 160°) and have
cis isomers of their
peptide bonds. Of the twenty common naturally occurring
amino acids, only
proline is likely to adopt the
cis isomer of the
peptide bond, specifically the X-Pro peptide bond; steric and electronic factors heavily favor the
trans isomer in most other peptide bonds. However,
peptide bonds that replace
proline with another
N-substituted amino acid (such as
sarcosine) are also likely to adopt the
cis isomer.
Polyproline II helix
The PPII helix is defined by (φ,ψ) backbone
dihedral angles of roughly (-75°, 150°) and
trans isomers of the
peptide bonds. The rotation angle Ω per residue of any polypeptide helix with
trans isomers is given by the equation
»
Substitution of the poly-Pro II (φ,ψ) dihedral angles into this equation yields almost exactly Ω = -120°, for example, the PPII helix is a left-handed helix (since Ω is negative) with three residues per turn (360°/120° = 3). The rise per residue is approximately 3.1 Å. This structure is somewhat similar to that adopted in the fibrous protein
collagen, which is composed mainly of proline,
hydroxyproline, and
glycine. PPII helices are specifically bound by
SH3 domains; this binding is important for many
protein-protein interactions and even for interactions between the domains of a single protein.
The PPII helix is relatively open and has no internal
hydrogen bonding, as opposed to the more common helical
secondary structures, the
alpha helix and its relatives the
310 helix and the
pi helix, as well as the
β-helix. The amide nitrogen and oxygen atoms are too far apart (approximately 3.8 Å) and oriented incorrectly for hydrogen bonding. Moreover, these atoms are both H-bond
acceptors in proline; there's no H-bond donor due to the cyclic side chain.
The PPII backbone dihedral angles (-75°, 150°) are observed frequently in proteins, even for amino acids other than
proline. The
Ramachandran plot is highly populated in the PPII region, comparably to the
beta sheet region around (-135°, 135°). For example, the PPII backbone dihedral angles are often observed in
turns, most commonly in the first residue of a type II β-turn. The "mirror image" PPII backbone dihedral angles (75°, -150°) are rarely seen, except in polymers of the
achiral amino acid
glycine. The analog of the poly-Pro II helix in poly-glycine is called the
poly-Gly II helix.
Polyproline I helix
The poly-Pro I helix is much denser than the PPII helix due to the
cis isomers of its
peptide bonds. It is also rarer than the PPII conformation because the
cis isomer is higher in energy than the
trans. Its typical dihedral angles (-75°, 160°) are close, but not identical to, those of the PPII helix. However, the PPI helix is a
right-handed helix and more tightly wound, with roughly 3.3 residues per turn (rather than 3). The rise per residue in the PPI helix is also much smaller, roughly 1.9 Å. Again, there's no internal hydrogen bonding in the poly-Pro I helix, both because an H-bond donor atom is lacking and because the amide nitrogen and oxygen atoms are too distant (roughly 3.8 Å again) and oriented incorrectly.
Structural properties
The poly-Pro helices are stable and stiff despite their lack of internal hydrogen bonding, and have been used as a "molecular ruler" in biophysical experiments, for example, to calibrate distances measured by
FRET. Interconversions between the PPII and PPI helix forms of poly-proline are slow, due to the high activation energy of X-Pro
cis-trans isomerization (
Ea ≈ 20 kcal/mol); however, this interconversion may be catalyzed by specific isomerases known as
prolyl isomerases or PPIases.
Further Information
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