Polyproline helix

Source: Wikipedia, the free encyclopedia.

A polyproline helix is a type of

secondary structure which occurs in proteins comprising repeating proline residues.[1] A left-handed polyproline II helix (PPII, poly-Pro II, κ-helix[2]) is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly (-75°, 150°) and have trans isomers of their peptide bonds. This PPII conformation is also common in proteins and polypeptides with other amino acids apart from proline. 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

Top view of a twenty-residue poly-Pro II helix, showing the three-fold symmetry.
Side view of a poly-Pro II helix, showing its openness and lack of internal hydrogen bonding.

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°, i.e., 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

protein-protein interactions
and even for interactions between the domains of a single protein.

The PPII helix is relatively open and has no internal

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 is 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

lipid membranes in natural conditions. In 2018, a group of researcher from Germany constructed and experimentally observed the first transmembrane PPII helix formed by specifically designed artificial peptides.[7][8]

Polyproline I helix

Top view of a twenty-residue poly-Pro I helix, showing its non-integer number of residues per turn.
Side view of the poly-Pro I helix, showing its greater compaction.

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 is 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

Traditionally, PPII has been considered to be relatively rigid and used as a "molecular ruler" in structural biology, e.g., to calibrate

ion-mobility spectrometry revealed existence of a defined set of intermediates along this process.[12]

References

  1. PMID 23507311
    .
  2. ^ "DSSP". pdb-redo.eu (in Dutch). Retrieved 2023-07-24.
  3. PMID 8429558
    .
  4. PMID 16239469
    .
  5. PMID 18598029
    .
  6. PMID 30430829
    .
  7. PMID 29638132
    .
  8. PMID 31577299
    .
  9. ^ S. Doose, H. Neuweiler, H. Barsch, and M. Sauer, Proc. Natl. Acad. Sci. USA. 104, 17400 (2007)
  10. ^ M. Moradi, V. Babin, C. Roland, T. A. Darden, and C. Sagui, Proc. Natl. Acad. Sci. USA. 106, 20746 (2009)
  11. ^ M. T. Ruggiero, J. Sibik, J. A. Zeitler, and T. M. Korter, Agnew. Chemie. Int. Ed. 55, 6877 (2016)
  12. PMID 30069641
    .
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