Polyproline helix: Difference between revisions

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In proteins, a left-handed poly-Pro helix is formed when sequential residues all adopt (φ,ψ) backbone dihedral angles of roughly $(-75^{\circ },150^{\circ })$ .

Poly-Pro II helix (trans peptide bonds)

The poly-Pro II helix is defined by (φ,ψ) backbone dihedral angles of roughly $(-75^{\circ },150^{\circ })$ and trans isomers of the peptide bonds. The rotation angle $\Omega$ per residue of any polypeptide helix with trans isomers is given by the equation

3\cos \Omega =1-4\cos ^{2}\left[\left(\phi +\psi \right)/2\right]

Substitution of the poly-Pro II (φ,ψ) dihedral angles into this equation yields almost exactly $\Omega =-120^{\circ }$ , i.e., the poly-Pro II helix is a left-handed helix (since $\Omega$ is negative) with three residues per turn ( $360^{\circ }/120^{\circ }=3$ ). The rise per residue is approximately 3.1 Å.

The poly-Pro helix is relatively open and has no internal hydrogen bonding, contrary to the alpha helix and its relatives (the $3_{10}$ helix and $\pi$ 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.

Perhaps surprisingly, the Ramachandran plot is highly populated in the vicinity of the poly-Pro backbone dihedral angles $(-75^{\circ },150^{\circ })$ , comparably to the beta sheet region around $(-135^{\circ },135^{\circ })$ . The poly-Pro backbone dihedral angles are a kind of chimera of an α-helical φ angle and a β-strand ψ angle, and are often observed in turns, most commonly in the first residue of a type II β-turn.

The "mirror image" poly-Pro II helix with backbone dihedral angles $(75^{\circ },-150^{\circ })$ is rarely seen, except in polymers of the achiral amino acid, glycine. This helix is not a true mirror image, since the $\mathrm {C^{\alpha }}$ atoms retain their left-handed chirality. The analog of the poly-Pro helix in poly-glycine is called the poly-Gly II helix.

Poly-Pro I helix (cis peptide bonds)

The poly-Pro I helix is much denser than the poly-Pro II helix owing to the cis isomers of its peptide bonds. Its typical dihedral angles are $(-75^{\circ },160^{\circ })$ are close, but not identical to, those of the poly-Pro II helix. However, the poly-Pro helix is a right-handed helix and more tightly wound, with roughly 3.3 residues per turn (rather than 3). The rise per residue 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

The poly-Pro helices are stuff despite their lack of internal hydrogen bonding, and have been used as a "molecular ruler" in biophysical experiments, e.g., to calibrate distances measured by FRET.

References

Adzhubei AA and Sternberg MJE. (1993) "Left-handed Polyproline II Helices Commonly Occur in Globular Proteins", J. Mol. Biol., 229, 472-493.

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 {{clean up}}
-In [[protein]]s, a left-handed '''poly-Pro helix''' is formed when sequential residues all adopt (φ,ψ) backbone [[dihedral angle]]s of roughly <math>(-75^{\circ}, 145^{\circ})</math>.
+In [[protein]]s, a left-handed '''poly-Pro helix''' is formed when sequential residues all adopt (φ,ψ) backbone [[dihedral angle]]s of roughly <math>(-75^{\circ}, 150^{\circ})</math>.
 ==Poly-Pro II helix (''trans'' peptide bonds)==
+[[Image:poly_Pro_II_topview.png|left|thumb|200px|Top view of a twenty-residue poly-Pro II helix, showing the three-fold symmetry.]]
-Add Figure
+The poly-Pro II helix is defined by (φ,ψ) backbone [[dihedral angle]]s of roughly <math>(-75^{\circ}, 150^{\circ})</math> and ''trans'' isomers of the [[peptide]] bonds.  The rotation angle <math>\Omega</math> per residue of any polypeptide helix with ''trans'' isomers is given by the equation
-Helical pitch, 3 residues per turn
+:<math>
-Surprisingly highly populated region of [[Ramachandran plot]]
+\cos \Omega = 1 - 4 \cos^{2} \left[ \left(\phi + \psi \right)/2 \right]
+</math>
+Substitution of the poly-Pro II (φ,ψ) dihedral angles into this equation yields almost exactly <math>\Omega = -120^{\circ}</math>, i.e., the poly-Pro II helix is a left-handed helix (since <math>\Omega</math> is negative) with three residues per turn (<math>360^{\circ}/120^{\circ} = 3</math>).  The rise per residue is approximately 3.1 Å.
-Discuss mirror image helix (seen with glycine).
+The poly-Pro helix is relatively open and has no internal [[hydrogen bond]]ing, contrary to the [[alpha helix]] and its relatives (the <math>3_{10}</math> helix and <math>\pi</math> helix), as well as the [[beta helix|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.
+[[Image:poly_Pro_II_sideview.png|thumb|200px|right|Side view of a poly-Pro II helix, showing its openness and lack of internal hydrogen bonding.]]
+Perhaps surprisingly, the [[Ramachandran plot]] is highly populated in the vicinity of the poly-Pro backbone dihedral angles <math>(-75^{\circ}, 150^{\circ})</math>, comparably to the [[beta sheet]] region around
+<math>(-135^{\circ}, 135^{\circ})</math>.  The poly-Pro backbone dihedral angles are a kind of chimera of an [[alpha helix|α-helical]] φ angle and a [[beta sheet|β-strand]] ψ angle, and are often observed in [[turn (biochemistry)|turns]], most commonly in the first residue of a type II β-turn.
+The "mirror image" poly-Pro II helix with backbone dihedral angles <math>(75^{\circ}, -150^{\circ})</math> is rarely seen, except in polymers of the achiral amino acid, glycine.  This helix is not a true mirror image, since the <math>\mathrm{C^{\alpha}}</math> atoms retain their left-handed chirality.
+The analog of the poly-Pro helix in poly-glycine is called the poly-Gly II helix.
 ==Poly-Pro I helix (''cis'' peptide bonds)==
+[[Image:poly_Pro_I_sideview.png|left|thumb|200px|Side view of the poly-Pro I helix, showing its greater compaction.]]
-Add Figure
+The poly-Pro I helix is much denser than the poly-Pro II helix owing to the cis isomers of its [[peptide bond]]s.  Its typical dihedral angles are <math>(-75^{\circ}, 160^{\circ})</math> are close, but not identical to, those of the poly-Pro II helix.  However, the poly-Pro helix is a ''right-handed'' helix and more tightly wound, with roughly 3.3 residues per turn (rather than 3).  The rise per residue 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.
+[[Image:poly_Pro_I_topview.png|right|thumb|200px|Top view of a twenty-residue poly-Pro I helix, showing its non-integer number of resiudes per turn.]]
-Much more rare.  Seen mainly with proline-rich segments (duh ;)
-==Structural roles==
+==Structural properties==
+The poly-Pro helices are stuff despite their lack of internal hydrogen bonding, and have been used as a "molecular ruler" in biophysical experiments, e.g., to calibrate distances measured by [[fluorescence resonance energy transfer|FRET]].
-Good "molecular ruler"