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| A '''Polyproline Helix''' is a type of [[protein]] [[secondary structure]], which occurs in proteins comprising repeating [[proline]] residues. A left-handed '''polyproline II helix''' ('''PPII''', '''poly-Pro II''') is formed when sequential residues all adopt (φ,ψ) backbone [[dihedral angle]]s of roughly (-75°, 150°) and have ''[[Cis–trans isomerism|trans]]'' isomers of their [[peptide bond]]s. Similarly, a more compact right-handed '''polyproline I helix''' ('''PPI''', '''poly-Pro I''') is formed when sequential residues all adopt (φ,ψ) backbone [[dihedral angle]]s of roughly (-75°, 160°) and have ''[[Cis–trans isomerism|cis]]'' isomers of their [[peptide bond]]s. Of the twenty common naturally occurring [[amino acid]]s, 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 bond]]s that replace [[proline]] with another ''N''-substituted amino acid (such as [[sarcosine]]) are also likely to adopt the ''cis'' isomer.
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| ==Polyproline II helix==
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| [[Image:poly Pro II topview.png|left|thumb|200px|Top view of a twenty-residue poly-Pro II helix, showing the three-fold symmetry.]]
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| The PPII helix is defined by (φ,ψ) backbone [[dihedral angle]]s 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
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| :<math> | |
| 3 \cos \Omega = 1 - 4 \cos^{2} \left[ \left(\phi + \psi \right)/2 \right]
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| </math>
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| 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 [[collagen]], which is composed mainly of proline, [[hydroxyproline]], and [[glycine]]. PPII helices are specifically bound by [[SH3 domain]]s; this binding is important for many [[protein-protein interaction]]s and even for interactions between the domains of a single protein.
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| [[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.]]
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| The PPII helix is relatively open and has no internal [[hydrogen bond]]ing, as opposed to the more common helical [[secondary structure]]s, the [[alpha helix]] and its relatives the [[3 10 helix|3<sub>10</sub> helix]] and the [[pi 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 due to the cyclic side chain.
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| 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 [[turn (biochemistry)|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 [[Chirality (chemistry)|achiral]] amino acid [[glycine]]. The analog of the poly-Pro II helix in poly-glycine is called the '''poly-Gly II helix'''.
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| ==Polyproline I helix==
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| [[Image:poly Pro I sideview.png|left|thumb|200px|Side view of the poly-Pro I helix, showing its greater compaction.]]
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| The poly-Pro I helix is much denser than the PPII helix due to the ''cis'' isomers of its [[peptide bond]]s. 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.
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| [[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 residues per turn.]]
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| ==Structural properties==
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| Traditionally, the relative rigid structure of PPII has been used as a "molecular ruler" in structural biology,
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| e.g., to calibrate [[fluorescence resonance energy transfer|FRET]] efficiency measurements. However recent experimental and theoretical studies have called into question this picture of polyproline peptide as a "rigid rod".<ref>S. Doose, H. Neuweiler, H. Barsch, and M. Sauer, Proc. Natl. Acad. Sci. USA. 104, 17400 (2007)</ref><ref>M. Moradi, V. Babin, C. Roland, T. A. Darden, and C. Sagui, Proc. Natl. Acad. Sci. USA. 106, 20746 (2009)</ref> 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 (''E''<sub>a</sub> ≈ 20 kcal/mol); however, this interconversion may be catalyzed by specific isomerases known as [[prolyl isomerase]]s or PPIases.
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| == References ==
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| {{reflist}}
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| * 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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| {{Protein secondary structure}}
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| [[Category:Protein structural motifs]]
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| [[Category:Helices]]
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